From 0acf550299d081329e98a848bd321e8cc08ac807 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 7 Jul 2025 11:28:27 -0400 Subject: [PATCH 001/468] Remove duplicate codecov configuration (#3211) * Remove duplicate codecov configuration * Lint * Use auto target --- .github/codecov.yml | 15 --------------- codecov.yml | 15 +++++++++++---- 2 files changed, 11 insertions(+), 19 deletions(-) delete mode 100644 .github/codecov.yml diff --git a/.github/codecov.yml b/.github/codecov.yml deleted file mode 100644 index e9b99c8214..0000000000 --- a/.github/codecov.yml +++ /dev/null @@ -1,15 +0,0 @@ -coverage: - status: - project: - default: - target: 100 - threshold: 0.1 - patch: - default: - target: 100 -comment: - layout: "diff, files" - behavior: default - require_changes: true # if true: only post the comment if coverage changes - branches: # branch names that can post comment - - "main" diff --git a/codecov.yml b/codecov.yml index 9ab6e0fc1b..3e30f82a31 100644 --- a/codecov.yml +++ b/codecov.yml @@ -3,12 +3,19 @@ coverage: patch: default: target: auto - after_n_builds: 10 # Wait for all 10 reports before updating the status project: default: target: auto threshold: 0.1 - after_n_builds: 2 # Wait for all 10 reports before updating the status -comment: false +codecov: + notify: + after_n_builds: 10 # Wait for all 10 reports before updating the status + wait_for_ci: yes +comment: + layout: "diff, files" + behavior: default + require_changes: true # if true: only post the comment if coverage changes + branches: # branch names that can post comment + - "main" github_checks: - annotations: false + annotations: false From e77c70188f395796f157abcb8b148b15f3fe3a5c Mon Sep 17 00:00:00 2001 From: Julia Signell Date: Mon, 7 Jul 2025 17:44:36 +0200 Subject: [PATCH 002/468] Add human readable size for No. bytes stored to `info_complete` (#3190) * Add human readable size for No. bytes stored in info_complete * Fix docs for `info_complete` change * Update changelog --------- Co-authored-by: Davis Bennett --- changes/3190.bugfix.rst | 1 + docs/user-guide/arrays.rst | 9 ++++++--- docs/user-guide/groups.rst | 2 +- docs/user-guide/performance.rst | 4 ++-- src/zarr/core/_info.py | 2 +- tests/test_info.py | 4 ++-- 6 files changed, 13 insertions(+), 9 deletions(-) create mode 100644 changes/3190.bugfix.rst diff --git a/changes/3190.bugfix.rst b/changes/3190.bugfix.rst new file mode 100644 index 0000000000..4e948188e3 --- /dev/null +++ b/changes/3190.bugfix.rst @@ -0,0 +1 @@ +Add human readable size for No. bytes stored to `info_complete` \ No newline at end of file diff --git a/docs/user-guide/arrays.rst b/docs/user-guide/arrays.rst index baaf544e44..f45dfbebe8 100644 --- a/docs/user-guide/arrays.rst +++ b/docs/user-guide/arrays.rst @@ -212,7 +212,7 @@ prints additional diagnostics, e.g.:: Serializer : BytesCodec(endian=) Compressors : (BloscCodec(typesize=4, cname=, clevel=3, shuffle=, blocksize=0),) No. bytes : 400000000 (381.5M) - No. bytes stored : 3558573 + No. bytes stored : 3558573 (3.4M) Storage ratio : 112.4 Chunks Initialized : 100 @@ -286,7 +286,7 @@ Here is an example using a delta filter with the Blosc compressor:: >>> compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=1, shuffle=zarr.codecs.BloscShuffle.shuffle) >>> data = np.arange(100000000, dtype='int32').reshape(10000, 10000) >>> z = zarr.create_array(store='data/example-9.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), filters=filters, compressors=compressors) - >>> z.info + >>> z.info_complete() Type : Array Zarr format : 3 Data type : Int32(endianness='little') @@ -300,6 +300,9 @@ Here is an example using a delta filter with the Blosc compressor:: Serializer : BytesCodec(endian=) Compressors : (BloscCodec(typesize=4, cname=, clevel=1, shuffle=, blocksize=0),) No. bytes : 400000000 (381.5M) + No. bytes stored : 826 + Storage ratio : 484261.5 + Chunks Initialized : 0 For more information about available filter codecs, see the `Numcodecs `_ documentation. @@ -616,7 +619,7 @@ Sharded arrays can be created by providing the ``shards`` parameter to :func:`za Serializer : BytesCodec(endian=None) Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 100000000 (95.4M) - No. bytes stored : 3981473 + No. bytes stored : 3981473 (3.8M) Storage ratio : 25.1 Shards Initialized : 100 diff --git a/docs/user-guide/groups.rst b/docs/user-guide/groups.rst index 4237a9df50..a343c3617e 100644 --- a/docs/user-guide/groups.rst +++ b/docs/user-guide/groups.rst @@ -139,7 +139,7 @@ property. E.g.:: Serializer : BytesCodec(endian=) Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 8000000 (7.6M) - No. bytes stored : 1614 + No. bytes stored : 1614 (1.6K) Storage ratio : 4956.6 Chunks Initialized : 10 >>> baz.info diff --git a/docs/user-guide/performance.rst b/docs/user-guide/performance.rst index 7d24c87373..0f31e5d7be 100644 --- a/docs/user-guide/performance.rst +++ b/docs/user-guide/performance.rst @@ -133,7 +133,7 @@ ratios, depending on the correlation structure within the data. E.g.:: Serializer : BytesCodec(endian=) Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 400000000 (381.5M) - No. bytes stored : 342588911 + No. bytes stored : 342588911 (326.7M) Storage ratio : 1.2 Chunks Initialized : 100 >>> with zarr.config.set({'array.order': 'F'}): @@ -153,7 +153,7 @@ ratios, depending on the correlation structure within the data. E.g.:: Serializer : BytesCodec(endian=) Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 400000000 (381.5M) - No. bytes stored : 342588911 + No. bytes stored : 342588911 (326.7M) Storage ratio : 1.2 Chunks Initialized : 100 diff --git a/src/zarr/core/_info.py b/src/zarr/core/_info.py index d57d17f934..a5b14d573a 100644 --- a/src/zarr/core/_info.py +++ b/src/zarr/core/_info.py @@ -133,7 +133,7 @@ def __repr__(self) -> str: if self._count_bytes_stored is not None: template += "\nNo. bytes stored : {_count_bytes_stored}" - kwargs["_count_stored"] = byte_info(self._count_bytes_stored) + kwargs["_count_bytes_stored"] = byte_info(self._count_bytes_stored) if ( self._count_bytes is not None diff --git a/tests/test_info.py b/tests/test_info.py index 0abaff9ae7..28c8803c83 100644 --- a/tests/test_info.py +++ b/tests/test_info.py @@ -79,7 +79,7 @@ def test_array_info(zarr_format: ZarrFormat) -> None: @pytest.mark.parametrize("zarr_format", ZARR_FORMATS) -@pytest.mark.parametrize("bytes_things", [(1_000_000, "976.6K", 500_000, "500000", "2.0", 5)]) +@pytest.mark.parametrize("bytes_things", [(1_000_000, "976.6K", 500_000, "488.3K", "2.0", 5)]) def test_array_info_complete( zarr_format: ZarrFormat, bytes_things: tuple[int, str, int, str, str, int] ) -> None: @@ -120,7 +120,7 @@ def test_array_info_complete( Serializer : BytesCodec(endian=) Compressors : () No. bytes : {count_bytes} ({count_bytes_formatted}) - No. bytes stored : {count_bytes_stored_formatted} + No. bytes stored : {count_bytes_stored} ({count_bytes_stored_formatted}) Storage ratio : {storage_ratio_formatted} Chunks Initialized : 5""") From d9b5c8c5537a75da1c86fd870ddc4af21eb0d9cf Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Mon, 7 Jul 2025 22:44:32 +0200 Subject: [PATCH 003/468] Bump ruff and update pre-commit legacy alias (#3214) --- .pre-commit-config.yaml | 4 ++-- pyproject.toml | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f016000984..563c87aee0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,9 +6,9 @@ ci: default_stages: [pre-commit, pre-push] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.9 + rev: v0.12.2 hooks: - - id: ruff + - id: ruff-check args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/codespell-project/codespell diff --git a/pyproject.toml b/pyproject.toml index 53b37d6c6d..a48a5eea25 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -324,6 +324,8 @@ ignore = [ "ANN401", "PT011", # TODO: apply this rule "PT012", # TODO: apply this rule + "PT030", # TODO: apply this rule + "PT031", # TODO: apply this rule "RET505", "RET506", "RUF005", From 111d76560152017d6f5c018f5b0f7897ed5d488d Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 7 Jul 2025 17:01:04 -0400 Subject: [PATCH 004/468] Add a release checklist issue template (#3210) * Add a release checklist issue template * Fix typo * Fix indentation * Update release-checklist.md Co-authored-by: Joe Hamman * Tag downstream maintainers in checklist --------- Co-authored-by: Davis Bennett Co-authored-by: Joe Hamman --- .github/ISSUE_TEMPLATE/release-checklist.md | 56 +++++++++++++++++++++ docs/developers/contributing.rst | 36 ++----------- 2 files changed, 59 insertions(+), 33 deletions(-) create mode 100644 .github/ISSUE_TEMPLATE/release-checklist.md diff --git a/.github/ISSUE_TEMPLATE/release-checklist.md b/.github/ISSUE_TEMPLATE/release-checklist.md new file mode 100644 index 0000000000..cfd153b69f --- /dev/null +++ b/.github/ISSUE_TEMPLATE/release-checklist.md @@ -0,0 +1,56 @@ +--- +name: Zarr-Python release checklist +about: Checklist for a new Zarr-Python release. [For project maintainers only!] +title: Release Zarr-Python vX.Y.Z +labels: release-checklist +assignees: '' + +--- + +**Release**: [v0.x.x](https://github.com/zarr-developers/zarr-python/milestones/?) +**Scheduled Date**: 20YY/MM/DD + +**Priority PRs/issues to complete prior to release** + +- [ ] Priority pull request #X + +**Before release**: + +- [ ] Make sure that all pull requests which will be included in the release have been properly documented as changelog files in the [`changes/` directory](https://github.com/zarr-developers/zarr-python/tree/main/changes). +- [ ] Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result to the main branch. +- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/#support-window) to see if the minimum supported version of Python or NumPy needs bumping. +- [ ] Check to ensure that: + - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.py` to find all potential TODOs. + - [ ] All tests pass in the ["Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/test.yml). + - [ ] All tests pass in the ["GPU Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml). + - [ ] All tests pass in the ["Hypothesis" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml). + - [ ] Check that downstream libraries work well (maintainers can make executive decisions about whether all checks are required for this release). + - [ ] Xarray (@jhamman @dcherian @TomNicholas) + - Zarr's upstream compatibility is tested via the [Upstream Dev CI worklow](https://github.com/pydata/xarray/actions/workflows/upstream-dev-ci.yaml). + - Click on the most recent workflow and check that the `upstream-dev` job has run and passed. `upstream-dev` is not run on all all workflow runs. + - Check that the expected version of Zarr-Python was tested using the `Version Info` step of the `upstream-dev` job. + - If testing on a branch other than `main` is needed, open a PR modifying https://github.com/pydata/xarray/blob/90ee30943aedba66a37856b2332a41264e288c20/ci/install-upstream-wheels.sh#L56 and add the `run-upstream` label. + - [ ] Titiler.Xarray (@maxrjones) + - [Modify dependencies](https://github.com/developmentseed/titiler/blob/main/src/titiler/xarray/pyproject.toml) for titiler.xarray. + - Modify triggers for running [the test workflow](https://github.com/developmentseed/titiler/blob/61549f2de07b20cca8fb991cfcdc89b23e18ad05/.github/workflows/ci.yml#L5-L7). + - Push the branch to the repository and check for the actions for any failures. + +**Release**: + +- [ ] Go to https://github.com/zarr-developers/zarr-python/releases. + - [ ] Click "Draft a new release". + - [ ] Choose a version number prefixed with a `v` (e.g. `v0.0.0`). For pre-releases, include the appropriate suffix (e.g. `v0.0.0a1` or `v0.0.0rc2`). + - [ ] Set the description of the release to: `See release notes https://zarr.readthedocs.io/en/stable/release-notes.html#release-0-0-0`, replacing the correct version numbers. For pre-release versions, the URL should omit the pre-release suffix, e.g. "a1" or "rc1". + - [ ] Click on "Generate release notes" to auto-fill the description. + - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too. +- [ ] Verify that release workflows succeeded. + - [ ] The latest version is correct on [PyPI](https://pypi.org/project/zarr/). + - [ ] The stable version is correct on [ReadTheDocs](https://zarr.readthedocs.io/en/stable/). + +**After release**: + +- [ ] Review and merge the pull request on the conda-forge [zarr-feedstock](https://github.com/conda-forge/zarr-feedstock) that will be automatically generated. + +--- + +- [ ] Party :tada: diff --git a/docs/developers/contributing.rst b/docs/developers/contributing.rst index 03388e1544..a5dd814878 100644 --- a/docs/developers/contributing.rst +++ b/docs/developers/contributing.rst @@ -339,36 +339,6 @@ breaking changes may be more frequent than usual. Release procedure ----------------- -Pre-release -~~~~~~~~~~~ -1. Make sure that all pull requests which will be included in the release - have been properly documented as changelog files in the :file:`changes/` directory. -2. Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result - to the main branch. - -Releasing -~~~~~~~~~ -1. Go to https://github.com/zarr-developers/zarr-python/releases -2. Click "Draft a new release". -3. Choose a version number prefixed with a `v` (e.g. `v0.0.0`). - For pre-releases, include the appropriate suffix (e.g. `v0.0.0a1` or `v0.0.0rc2`). -4. Set the description of the release to:: - - See release notes https://zarr.readthedocs.io/en/stable/release-notes.html#release-0-0-0 - - replacing the correct version numbers. For pre-release versions, - the URL should omit the pre-release suffix, e.g. "a1" or "rc1". -5. Click on "Generate release notes" to auto-fill the description. - -After creating the release, the documentation will be built on -https://readthedocs.io. Full releases will be available under -`/stable `_ while -pre-releases will be available under -`/latest `_. - -Post-release -~~~~~~~~~~~~ - -- Review and merge the pull request on the - `conda-forge feedstock `_ that will be - automatically generated. +Open an issue on GitHub announcing the release using the release checklist template: +`https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md `_. +The release checklist includes all steps necessary for the release. From 378d5afa7e1cb2ffbed39610a8ec1420d98343d9 Mon Sep 17 00:00:00 2001 From: bevilacqc Date: Tue, 8 Jul 2025 12:06:35 +0200 Subject: [PATCH 005/468] Update documentation of remote store (#3212) * Add doc about custom remote storage * Add doc about store type to `FsspecStore.from_url` * Add changes * Fix example code * Run pre-commit * Fix typo --------- Co-authored-by: Davis Bennett --- changes/3212.doc.rst | 4 ++++ docs/user-guide/storage.rst | 10 ++++++++++ src/zarr/storage/_fsspec.py | 2 +- 3 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 changes/3212.doc.rst diff --git a/changes/3212.doc.rst b/changes/3212.doc.rst new file mode 100644 index 0000000000..1754d18c92 --- /dev/null +++ b/changes/3212.doc.rst @@ -0,0 +1,4 @@ +- Add a description on how to create a RemoteStore of a specific filesystem to the `Remote Store` section in `docs\user-guide\storage.rst`. +- State in the docstring of `FsspecStore.from_url` that the filesystem type is inferred from the URL scheme. + +It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. \ No newline at end of file diff --git a/docs/user-guide/storage.rst b/docs/user-guide/storage.rst index 4215cbaf20..e5a333872e 100644 --- a/docs/user-guide/storage.rst +++ b/docs/user-guide/storage.rst @@ -87,6 +87,16 @@ API. ``storage_options`` can be used to configure the fsspec backend.: >>> zarr.open_group(store=store, mode='r') > +The type of filesystem (e.g. S3, https, etc..) is inferred from the scheme of the url (e.g. s3 for "**s3**://noaa-nwm-retro-v2-zarr-pds"). +In case a specific filesystem is needed, one can explicitly create it. For example to create a S3 filesystem: + + >>> import fsspec + >>> fs = fsspec.filesystem( + ... 's3', anon=True, asynchronous=True, + ... client_kwargs={'endpoint_url': "https://noaa-nwm-retro-v2-zarr-pds.s3.amazonaws.com"} + ... ) + >>> store = zarr.storage.FsspecStore(fs) + Memory Store ~~~~~~~~~~~~ diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index a1b05a7630..e169eededc 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -216,7 +216,7 @@ def from_url( allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS, ) -> FsspecStore: """ - Create a FsspecStore from a URL. + Create a FsspecStore from a URL. The type of store is determined from the URL scheme. Parameters ---------- From 9bc52fc1f373acd023f44cb2364abd80377f756e Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 9 Jul 2025 17:50:51 +0200 Subject: [PATCH 006/468] Make `create_array` signatures consistent (#2819) * add signature tests for async / sync api, and fix mismatched signatures * test for consistent signatures, and make array default fill value consistently 0 * test for async group / group methods * release notes * default fill value is None * expand changelog * Update asynchronous.py * fix diverged signatures * use fill_value = 0 in metadata consolidation test * make signature tests more verbose * make signatures consistent --- changes/2819.chore.rst | 4 +++ src/zarr/api/asynchronous.py | 5 ++-- src/zarr/core/group.py | 51 +++++++++++++++++++++++--------- tests/test_api.py | 40 ++++++++++++++++++++++++++ tests/test_array.py | 56 ++++++++++++++++++++++++++++++++++++ tests/test_group.py | 18 +++++++++++- 6 files changed, 157 insertions(+), 17 deletions(-) create mode 100644 changes/2819.chore.rst diff --git a/changes/2819.chore.rst b/changes/2819.chore.rst new file mode 100644 index 0000000000..f9a3358309 --- /dev/null +++ b/changes/2819.chore.rst @@ -0,0 +1,4 @@ +Ensure that invocations of ``create_array`` use consistent keyword arguments, with consistent defaults. +Specifically, ``zarr.api.synchronous.create_array`` now takes a ``write_data`` keyword argument; The +``create_array`` method on ``zarr.Group`` takes ``data`` and ``write_data`` keyword arguments. The ``fill_value`` +keyword argument of the various invocations of ``create_array`` has been consistently set to ``None``, where previously it was either ``None`` or ``0``. \ No newline at end of file diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 3b53095636..6b573fd033 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -11,6 +11,7 @@ from zarr.abc.store import Store from zarr.core.array import ( + DEFAULT_FILL_VALUE, Array, AsyncArray, CompressorLike, @@ -860,10 +861,10 @@ async def open_group( async def create( shape: ChunkCoords | int, *, # Note: this is a change from v2 - chunks: ChunkCoords | int | None = None, # TODO: v2 allowed chunks=True + chunks: ChunkCoords | int | bool | None = None, dtype: ZDTypeLike | None = None, compressor: CompressorLike = "auto", - fill_value: Any | None = 0, # TODO: need type + fill_value: Any | None = DEFAULT_FILL_VALUE, order: MemoryOrder | None = None, store: str | StoreLike | None = None, synchronizer: Any | None = None, diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index bad710ed43..0f57495e61 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -20,6 +20,7 @@ from zarr.abc.store import Store, set_or_delete from zarr.core._info import GroupInfo from zarr.core.array import ( + DEFAULT_FILL_VALUE, Array, AsyncArray, CompressorLike, @@ -71,6 +72,7 @@ from zarr.core.buffer import Buffer, BufferPrototype from zarr.core.chunk_key_encodings import ChunkKeyEncodingLike from zarr.core.common import MemoryOrder + from zarr.core.dtype import ZDTypeLike logger = logging.getLogger("zarr.group") @@ -999,22 +1001,24 @@ async def create_array( self, name: str, *, - shape: ShapeLike, - dtype: npt.DTypeLike, + shape: ShapeLike | None = None, + dtype: ZDTypeLike | None = None, + data: np.ndarray[Any, np.dtype[Any]] | None = None, chunks: ChunkCoords | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", compressor: CompressorLike = "auto", serializer: SerializerLike = "auto", - fill_value: Any | None = 0, + fill_value: Any | None = DEFAULT_FILL_VALUE, order: MemoryOrder | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, dimension_names: DimensionNames = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, - config: ArrayConfig | ArrayConfigLike | None = None, + config: ArrayConfigLike | None = None, + write_data: bool = True, ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array within this group. @@ -1102,6 +1106,11 @@ async def create_array( Whether to overwrite an array with the same name in the store, if one exists. config : ArrayConfig or ArrayConfigLike, optional Runtime configuration for the array. + write_data : bool + If a pre-existing array-like object was provided to this function via the ``data`` parameter + then ``write_data`` determines whether the values in that array-like object should be + written to the Zarr array created by this function. If ``write_data`` is ``False``, then the + array will be left empty. Returns ------- @@ -1116,6 +1125,7 @@ async def create_array( name=name, shape=shape, dtype=dtype, + data=data, chunks=chunks, shards=shards, filters=filters, @@ -1130,6 +1140,7 @@ async def create_array( storage_options=storage_options, overwrite=overwrite, config=config, + write_data=write_data, ) @deprecated("Use AsyncGroup.create_array instead.") @@ -2411,22 +2422,24 @@ def create_array( self, name: str, *, - shape: ShapeLike, - dtype: npt.DTypeLike, + shape: ShapeLike | None = None, + dtype: ZDTypeLike | None = None, + data: np.ndarray[Any, np.dtype[Any]] | None = None, chunks: ChunkCoords | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", compressor: CompressorLike = "auto", serializer: SerializerLike = "auto", - fill_value: Any | None = 0, - order: MemoryOrder | None = "C", + fill_value: Any | None = DEFAULT_FILL_VALUE, + order: MemoryOrder | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, dimension_names: DimensionNames = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, - config: ArrayConfig | ArrayConfigLike | None = None, + config: ArrayConfigLike | None = None, + write_data: bool = True, ) -> Array: """Create an array within this group. @@ -2437,10 +2450,13 @@ def create_array( name : str The name of the array relative to the group. If ``path`` is ``None``, the array will be located at the root of the store. - shape : ChunkCoords - Shape of the array. - dtype : npt.DTypeLike - Data type of the array. + shape : ChunkCoords, optional + Shape of the array. Can be ``None`` if ``data`` is provided. + dtype : npt.DTypeLike | None + Data type of the array. Can be ``None`` if ``data`` is provided. + data : Array-like data to use for initializing the array. If this parameter is provided, the + ``shape`` and ``dtype`` parameters must be identical to ``data.shape`` and ``data.dtype``, + or ``None``. chunks : ChunkCoords, optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. @@ -2514,6 +2530,11 @@ def create_array( Whether to overwrite an array with the same name in the store, if one exists. config : ArrayConfig or ArrayConfigLike, optional Runtime configuration for the array. + write_data : bool + If a pre-existing array-like object was provided to this function via the ``data`` parameter + then ``write_data`` determines whether the values in that array-like object should be + written to the Zarr array created by this function. If ``write_data`` is ``False``, then the + array will be left empty. Returns ------- @@ -2528,6 +2549,7 @@ def create_array( name=name, shape=shape, dtype=dtype, + data=data, chunks=chunks, shards=shards, fill_value=fill_value, @@ -2541,6 +2563,7 @@ def create_array( overwrite=overwrite, storage_options=storage_options, config=config, + write_data=write_data, ) ) ) @@ -2813,7 +2836,7 @@ def array( compressors: CompressorsLike = "auto", compressor: CompressorLike = None, serializer: SerializerLike = "auto", - fill_value: Any | None = 0, + fill_value: Any | None = DEFAULT_FILL_VALUE, order: MemoryOrder | None = "C", attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, diff --git a/tests/test_api.py b/tests/test_api.py index e6cb612a82..da61f97847 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1,5 +1,7 @@ from __future__ import annotations +import inspect +import pathlib import re from typing import TYPE_CHECKING @@ -8,6 +10,7 @@ if TYPE_CHECKING: import pathlib + from collections.abc import Callable from zarr.abc.store import Store from zarr.core.common import JSON, MemoryOrder, ZarrFormat @@ -1216,6 +1219,43 @@ def test_open_array_with_mode_r_plus(store: Store, zarr_format: ZarrFormat) -> N z2[:] = 3 +@pytest.mark.parametrize( + ("a_func", "b_func"), + [ + (zarr.api.asynchronous.create_array, zarr.api.synchronous.create_array), + (zarr.api.asynchronous.save, zarr.api.synchronous.save), + (zarr.api.asynchronous.save_array, zarr.api.synchronous.save_array), + (zarr.api.asynchronous.save_group, zarr.api.synchronous.save_group), + (zarr.api.asynchronous.open_group, zarr.api.synchronous.open_group), + (zarr.api.asynchronous.create, zarr.api.synchronous.create), + ], +) +def test_consistent_signatures( + a_func: Callable[[object], object], b_func: Callable[[object], object] +) -> None: + """ + Ensure that pairs of functions have the same signature + """ + base_sig = inspect.signature(a_func) + test_sig = inspect.signature(b_func) + wrong: dict[str, list[object]] = { + "missing_from_test": [], + "missing_from_base": [], + "wrong_type": [], + } + for key, value in base_sig.parameters.items(): + if key not in test_sig.parameters: + wrong["missing_from_test"].append((key, value)) + for key, value in test_sig.parameters.items(): + if key not in base_sig.parameters: + wrong["missing_from_base"].append((key, value)) + if base_sig.parameters[key] != value: + wrong["wrong_type"].append({key: {"test": value, "base": base_sig.parameters[key]}}) + assert wrong["missing_from_base"] == [] + assert wrong["missing_from_test"] == [] + assert wrong["wrong_type"] == [] + + def test_api_exports() -> None: """ Test that the sync API and the async API export the same objects diff --git a/tests/test_array.py b/tests/test_array.py index fe23bc1284..0bca860e84 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -970,6 +970,43 @@ def test_auto_partition_auto_shards( assert auto_shards == expected_shards +def test_chunks_and_shards() -> None: + store = StorePath(MemoryStore()) + shape = (100, 100) + chunks = (5, 5) + shards = (10, 10) + + arr_v3 = zarr.create_array(store=store / "v3", shape=shape, chunks=chunks, dtype="i4") + assert arr_v3.chunks == chunks + assert arr_v3.shards is None + + arr_v3_sharding = zarr.create_array( + store=store / "v3_sharding", + shape=shape, + chunks=chunks, + shards=shards, + dtype="i4", + ) + assert arr_v3_sharding.chunks == chunks + assert arr_v3_sharding.shards == shards + + arr_v2 = zarr.create_array( + store=store / "v2", shape=shape, chunks=chunks, zarr_format=2, dtype="i4" + ) + assert arr_v2.chunks == chunks + assert arr_v2.shards is None + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") +@pytest.mark.parametrize( + ("dtype", "fill_value_expected"), [(" None: + a = zarr.create_array(store, shape=(5,), chunks=(5,), dtype=dtype) + assert a.fill_value == fill_value_expected + + @pytest.mark.parametrize("store", ["memory"], indirect=True) class TestCreateArray: @staticmethod @@ -1769,6 +1806,25 @@ def test_multiprocessing(store: Store, method: Literal["fork", "spawn", "forkser assert all(np.array_equal(r, data) for r in results) +def test_create_array_method_signature() -> None: + """ + Test that the signature of the ``AsyncGroup.create_array`` function has nearly the same signature + as the ``create_array`` function. ``AsyncGroup.create_array`` should take all of the same keyword + arguments as ``create_array`` except ``store``. + """ + + base_sig = inspect.signature(create_array) + meth_sig = inspect.signature(AsyncGroup.create_array) + # ignore keyword arguments that are either missing or have different semantics when + # create_array is invoked as a group method + ignore_kwargs = {"zarr_format", "store", "name"} + # TODO: make this test stronger. right now, it only checks that all the parameters in the + # function signature are used in the method signature. we can be more strict and check that + # the method signature uses no extra parameters. + base_params = dict(filter(lambda kv: kv[0] not in ignore_kwargs, base_sig.parameters.items())) + assert (set(base_params.items()) - set(meth_sig.parameters.items())) == set() + + async def test_sharding_coordinate_selection() -> None: store = MemoryStore() g = zarr.open_group(store, mode="w") diff --git a/tests/test_group.py b/tests/test_group.py index 60a1fcb9bf..ee2317ade4 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -1531,6 +1531,7 @@ def test_create_nodes_concurrency_limit(store: MemoryStore) -> None: @pytest.mark.parametrize( ("a_func", "b_func"), [ + (zarr.core.group.AsyncGroup.create_array, zarr.core.group.Group.create_array), (zarr.core.group.AsyncGroup.create_hierarchy, zarr.core.group.Group.create_hierarchy), (zarr.core.group.create_hierarchy, zarr.core.sync_group.create_hierarchy), (zarr.core.group.create_nodes, zarr.core.sync_group.create_nodes), @@ -1546,7 +1547,22 @@ def test_consistent_signatures( """ base_sig = inspect.signature(a_func) test_sig = inspect.signature(b_func) - assert test_sig.parameters == base_sig.parameters + wrong: dict[str, list[object]] = { + "missing_from_test": [], + "missing_from_base": [], + "wrong_type": [], + } + for key, value in base_sig.parameters.items(): + if key not in test_sig.parameters: + wrong["missing_from_test"].append((key, value)) + for key, value in test_sig.parameters.items(): + if key not in base_sig.parameters: + wrong["missing_from_base"].append((key, value)) + if base_sig.parameters[key] != value: + wrong["wrong_type"].append({key: {"test": value, "base": base_sig.parameters[key]}}) + assert wrong["missing_from_base"] == [] + assert wrong["missing_from_test"] == [] + assert wrong["wrong_type"] == [] @pytest.mark.parametrize("store", ["memory"], indirect=True) From 23edb8009e2488335e1715dd84563b4fb180e572 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Wed, 9 Jul 2025 20:12:57 +0100 Subject: [PATCH 007/468] Merge 3.0.9 & 3.0.10 into main (#3220) * Enable tests on 3.0.x branch (#3135) * Changelog for 3.0.9 * Backport PR #3149: Add GroupNotFound error to API docs (#3179) Co-authored-by: David Stansby * Backport PR #3140: Suppress FileNotFoundError when deleting keys in the obstore adapter (#3180) Co-authored-by: Lukas Bindreiter * Backport PR #3138: Add with_read_only() convenience method to store (#3181) Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Create read only copy if needed when opening a store path (#3156) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py Co-authored-by: Davis Bennett * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py Co-authored-by: David Stansby * Update src/zarr/storage/_common.py Co-authored-by: David Stansby * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760fba89e77a3ec5ad9649ada3a99799feeb6. * Add test * Remove warning * Apply suggestion for try; except shortening Co-authored-by: Tom Nicholas * Improve code coverage --------- Co-authored-by: Davis Bennett Co-authored-by: David Stansby Co-authored-by: Tom Nicholas (cherry picked from commit 5731c6c88ef0c5a3cb7f9701a7fbcee2814febf3) * Create read only copy if needed when opening a store path (#3156) (#3182) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py * Update src/zarr/storage/_common.py * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760fba89e77a3ec5ad9649ada3a99799feeb6. * Add test * Remove warning * Apply suggestion for try; except shortening * Improve code coverage --------- (cherry picked from commit 5731c6c88ef0c5a3cb7f9701a7fbcee2814febf3) Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: David Stansby Co-authored-by: Tom Nicholas * Remove breaking check about `auto_mkdir` for FSSpecStore (#3193) * Remove breaking check from _make_async * Update expected error * Change import structure to protect against AttributeError * changelog * add test to ensure that we can create a read-only copy of the store with auto_mkdir=False * only test if the async wrapper is available --------- Co-authored-by: Davis Bennett (cherry picked from commit 5a24487f09d499c91ce25f24af910c2ede055b5a) * Remove breaking check about `auto_mkdir` for FSSpecStore (#3193) (#3203) * Remove breaking check from _make_async * Update expected error * Change import structure to protect against AttributeError * changelog * add test to ensure that we can create a read-only copy of the store with auto_mkdir=False * only test if the async wrapper is available --------- (cherry picked from commit 5a24487f09d499c91ce25f24af910c2ede055b5a) Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Add missing import for AsyncFileSystemWrapper for `_make_async` in `_fsspec.py` (#3195) * Add missing import for AsyncFileSystemWrapper in `_fsspec.py` * Add missing changelog entry for AsyncFileSystemWrapper import fix * Move AsyncFileSystemWrapper import past the version check in `_fsspec.py` * Add newline after AsyncFileSystemWrapper import in `_fsspec.py` * Simplify import statement for AsyncFileSystemWrapper in `_fsspec.py` --------- Co-authored-by: Altay Sansal (cherry picked from commit 97aa42f551c2e970f66ee629cb31ce426e659b7b) * Auto backport of pr 3195 on 3.0.10 (#3204) * Remove breaking check about `auto_mkdir` for FSSpecStore (#3193) * Remove breaking check from _make_async * Update expected error * Change import structure to protect against AttributeError * changelog * add test to ensure that we can create a read-only copy of the store with auto_mkdir=False * only test if the async wrapper is available --------- Co-authored-by: Davis Bennett (cherry picked from commit 5a24487f09d499c91ce25f24af910c2ede055b5a) * Add missing import for AsyncFileSystemWrapper for `_make_async` in `_fsspec.py` (#3195) * Add missing import for AsyncFileSystemWrapper in `_fsspec.py` * Add missing changelog entry for AsyncFileSystemWrapper import fix * Move AsyncFileSystemWrapper import past the version check in `_fsspec.py` * Add newline after AsyncFileSystemWrapper import in `_fsspec.py` * Simplify import statement for AsyncFileSystemWrapper in `_fsspec.py` --------- Co-authored-by: Altay Sansal (cherry picked from commit 97aa42f551c2e970f66ee629cb31ce426e659b7b) --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: Altay Sansal Co-authored-by: Altay Sansal * 3.0.9 release notes (#3183) * Create read only copy if needed when opening a store path (#3156) * Create read only copy if needed when opening a store path * Add ValueError to Raises section * Update expected warning * Update src/zarr/storage/_common.py Co-authored-by: Davis Bennett * Use ANY_ACCESS_MODE * Update src/zarr/storage/_common.py Co-authored-by: David Stansby * Update src/zarr/storage/_common.py Co-authored-by: David Stansby * Update changes * Try using get_args on definition * Revert "Try using get_args on definition" This reverts commit 7ad760fba89e77a3ec5ad9649ada3a99799feeb6. * Add test * Remove warning * Apply suggestion for try; except shortening Co-authored-by: Tom Nicholas * Improve code coverage --------- Co-authored-by: Davis Bennett Co-authored-by: David Stansby Co-authored-by: Tom Nicholas (cherry picked from commit 5731c6c88ef0c5a3cb7f9701a7fbcee2814febf3) * release notes --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: David Stansby Co-authored-by: Tom Nicholas * release notes --------- Co-authored-by: Lumberbot (aka Jack) <39504233+meeseeksmachine@users.noreply.github.com> Co-authored-by: Lukas Bindreiter Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: Davis Bennett Co-authored-by: Tom Nicholas Co-authored-by: Altay Sansal Co-authored-by: Altay Sansal --- .github/workflows/hypothesis.yaml | 6 ++-- .github/workflows/test.yml | 4 +-- changes/2774.feature.rst | 1 - changes/2921.bugfix.rst | 1 - changes/3021.feature.rst | 1 - changes/3066.feature.rst | 1 - changes/3081.feature.rst | 1 - changes/3082.feature.rst | 1 - changes/3100.bugfix.rst | 3 -- changes/3103.bugfix.rst | 7 ---- changes/3127.bugfix.rst | 2 -- changes/3128.bugfix.rst | 1 - changes/3130.feature.rst | 1 - docs/release-notes.rst | 54 +++++++++++++++++++++++++++++++ 14 files changed, 58 insertions(+), 26 deletions(-) delete mode 100644 changes/2774.feature.rst delete mode 100644 changes/2921.bugfix.rst delete mode 100644 changes/3021.feature.rst delete mode 100644 changes/3066.feature.rst delete mode 100644 changes/3081.feature.rst delete mode 100644 changes/3082.feature.rst delete mode 100644 changes/3100.bugfix.rst delete mode 100644 changes/3103.bugfix.rst delete mode 100644 changes/3127.bugfix.rst delete mode 100644 changes/3128.bugfix.rst delete mode 100644 changes/3130.feature.rst diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 776f859d6e..96eaccbc6b 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -1,11 +1,9 @@ name: Slow Hypothesis CI on: push: - branches: - - "main" + branches: [main, 3.0.x] pull_request: - branches: - - "main" + branches: [main, 3.0.x] types: [opened, reopened, synchronize, labeled] schedule: - cron: "0 0 * * *" # Daily “At 00:00” UTC diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 7cfce41312..909196c8c0 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -5,9 +5,9 @@ name: Test on: push: - branches: [ main ] + branches: [ main, 3.0.x ] pull_request: - branches: [ main ] + branches: [ main, 3.0.x ] workflow_dispatch: concurrency: diff --git a/changes/2774.feature.rst b/changes/2774.feature.rst deleted file mode 100644 index 4df83f54ec..0000000000 --- a/changes/2774.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Add `zarr.storage.FsspecStore.from_mapper()` so that `zarr.open()` supports stores of type `fsspec.mapping.FSMap`. \ No newline at end of file diff --git a/changes/2921.bugfix.rst b/changes/2921.bugfix.rst deleted file mode 100644 index 65db48654f..0000000000 --- a/changes/2921.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Ignore stale child metadata when reconsolidating metadata. diff --git a/changes/3021.feature.rst b/changes/3021.feature.rst deleted file mode 100644 index 8805797ce3..0000000000 --- a/changes/3021.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Implemented ``move`` for ``LocalStore`` and ``ZipStore``. This allows users to move the store to a different root path. \ No newline at end of file diff --git a/changes/3066.feature.rst b/changes/3066.feature.rst deleted file mode 100644 index 89d5ddb1c6..0000000000 --- a/changes/3066.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Added `~zarr.errors.GroupNotFoundError`, which is raised when attempting to open a group that does not exist. diff --git a/changes/3081.feature.rst b/changes/3081.feature.rst deleted file mode 100644 index 8cf83ea7c2..0000000000 --- a/changes/3081.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Adds ``fill_value`` to the list of attributes displayed in the output of the ``AsyncArray.info()`` method. \ No newline at end of file diff --git a/changes/3082.feature.rst b/changes/3082.feature.rst deleted file mode 100644 index e990d1f3a0..0000000000 --- a/changes/3082.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Use :py:func:`numpy.zeros` instead of :py:func:`np.full` for a performance speedup when creating a `zarr.core.buffer.NDBuffer` with `fill_value=0`. \ No newline at end of file diff --git a/changes/3100.bugfix.rst b/changes/3100.bugfix.rst deleted file mode 100644 index 11f06628c0..0000000000 --- a/changes/3100.bugfix.rst +++ /dev/null @@ -1,3 +0,0 @@ -For Zarr format 2, allow fixed-length string arrays to be created without automatically inserting a -``Vlen-UT8`` codec in the array of filters. Fixed-length string arrays do not need this codec. This -change fixes a regression where fixed-length string arrays created with Zarr Python 3 could not be read with Zarr Python 2.18. \ No newline at end of file diff --git a/changes/3103.bugfix.rst b/changes/3103.bugfix.rst deleted file mode 100644 index 93aecce908..0000000000 --- a/changes/3103.bugfix.rst +++ /dev/null @@ -1,7 +0,0 @@ -When creating arrays without explicitly specifying a chunk size using `zarr.create` and other -array creation routines, the chunk size will now set automatically instead of defaulting to the data shape. -For large arrays this will result in smaller default chunk sizes. -To retain previous behaviour, explicitly set the chunk shape to the data shape. - -This fix matches the existing chunking behaviour of -`zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. diff --git a/changes/3127.bugfix.rst b/changes/3127.bugfix.rst deleted file mode 100644 index 35d7f5d329..0000000000 --- a/changes/3127.bugfix.rst +++ /dev/null @@ -1,2 +0,0 @@ -When `zarr.save` has an argument `path=some/path/` and multiple arrays in `args`, the path resulted in `some/path/some/path` due to using the `path` -argument twice while building the array path. This is now fixed. \ No newline at end of file diff --git a/changes/3128.bugfix.rst b/changes/3128.bugfix.rst deleted file mode 100644 index b93416070e..0000000000 --- a/changes/3128.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix `zarr.open` default for argument `mode` when `store` is `read_only` \ No newline at end of file diff --git a/changes/3130.feature.rst b/changes/3130.feature.rst deleted file mode 100644 index 7a64582f06..0000000000 --- a/changes/3130.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Port more stateful testing actions from `Icechunk `_. diff --git a/docs/release-notes.rst b/docs/release-notes.rst index a89046dd6d..8c51250fed 100644 --- a/docs/release-notes.rst +++ b/docs/release-notes.rst @@ -3,6 +3,60 @@ Release notes .. towncrier release notes start +3.0.10 (2025-07-03) +------------------- + +Bugfixes +~~~~~~~~ + +- Removed an unnecessary check from ``_fsspec._make_async`` that would raise an exception when + creating a read-only store backed by a local file system with ``auto_mkdir`` set to ``False``. (:issue:`3193`) +- Add missing import for AsyncFileSystemWrapper for _make_async in _fsspec.py (:issue:`3195`) + + +3.0.9 (2025-06-30) +------------------ + +Features +~~~~~~~~ + +- Add `zarr.storage.FsspecStore.from_mapper()` so that `zarr.open()` supports stores of type `fsspec.mapping.FSMap`. (:issue:`2774`) +- Implemented ``move`` for ``LocalStore`` and ``ZipStore``. This allows users to move the store to a different root path. (:issue:`3021`) +- Added `~zarr.errors.GroupNotFoundError`, which is raised when attempting to open a group that does not exist. (:issue:`3066`) +- Adds ``fill_value`` to the list of attributes displayed in the output of the ``AsyncArray.info()`` method. (:issue:`3081`) +- Use :py:func:`numpy.zeros` instead of :py:func:`np.full` for a performance speedup when creating a `zarr.core.buffer.NDBuffer` with `fill_value=0`. (:issue:`3082`) +- Port more stateful testing actions from `Icechunk `_. (:issue:`3130`) +- Adds a `with_read_only` convenience method to the `Store` abstract base class (raises `NotImplementedError`) and implementations to the `MemoryStore`, `ObjectStore`, `LocalStore`, and `FsspecStore` classes. (:issue:`3138`) + + +Bugfixes +~~~~~~~~ + +- Ignore stale child metadata when reconsolidating metadata. (:issue:`2921`) +- For Zarr format 2, allow fixed-length string arrays to be created without automatically inserting a + ``Vlen-UT8`` codec in the array of filters. Fixed-length string arrays do not need this codec. This + change fixes a regression where fixed-length string arrays created with Zarr Python 3 could not be read with Zarr Python 2.18. (:issue:`3100`) +- When creating arrays without explicitly specifying a chunk size using `zarr.create` and other + array creation routines, the chunk size will now set automatically instead of defaulting to the data shape. + For large arrays this will result in smaller default chunk sizes. + To retain previous behaviour, explicitly set the chunk shape to the data shape. + + This fix matches the existing chunking behaviour of + `zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. (:issue:`3103`) +- When `zarr.save` has an argument `path=some/path/` and multiple arrays in `args`, the path resulted in `some/path/some/path` due to using the `path` + argument twice while building the array path. This is now fixed. (:issue:`3127`) +- Fix `zarr.open` default for argument `mode` when `store` is `read_only` (:issue:`3128`) +- Suppress `FileNotFoundError` when deleting non-existent keys in the `obstore` adapter. + + When writing empty chunks (i.e. chunks where all values are equal to the array's fill value) to a zarr array, zarr + will delete those chunks from the underlying store. For zarr arrays backed by the `obstore` adapter, this will potentially + raise a `FileNotFoundError` if the chunk doesn't already exist. + Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store, + suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect + from the store. (:issue:`3140`) +- Trying to open a StorePath/Array with ``mode='r'`` when the store is not read-only creates a read-only copy of the store. (:issue:`3156`) + + 3.0.8 (2025-05-19) ------------------ From 9d97b24d9bc23565fcc7f1221f9feb52a561ae32 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Wed, 9 Jul 2025 21:33:10 +0100 Subject: [PATCH 008/468] Cleanups to implementation of `create()` (#3111) * Remove duplicate compressor handling * Push filter parsing down the stack * Put not implemented warnings together * Test unimplemented kwargs warn * pre-commit fixes * Fix syncrhonous create() signature --- src/zarr/api/asynchronous.py | 22 ++++++++-------------- src/zarr/api/synchronous.py | 3 ++- src/zarr/core/array.py | 8 ++++++-- tests/test_api.py | 7 +++++++ 4 files changed, 23 insertions(+), 17 deletions(-) diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 6b573fd033..8f244f4b25 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -15,7 +15,6 @@ Array, AsyncArray, CompressorLike, - _get_default_chunk_encoding_v2, create_array, from_array, get_array_metadata, @@ -33,7 +32,7 @@ _warn_order_kwarg, _warn_write_empty_chunks_kwarg, ) -from zarr.core.dtype import ZDTypeLike, get_data_type_from_native_dtype, parse_data_type +from zarr.core.dtype import ZDTypeLike, get_data_type_from_native_dtype from zarr.core.group import ( AsyncGroup, ConsolidatedMetadata, @@ -48,6 +47,8 @@ if TYPE_CHECKING: from collections.abc import Iterable + import numcodecs.abc + from zarr.abc.codec import Codec from zarr.core.buffer import NDArrayLikeOrScalar from zarr.core.chunk_key_encodings import ChunkKeyEncoding @@ -871,7 +872,7 @@ async def create( overwrite: bool = False, path: PathLike | None = None, chunk_store: StoreLike | None = None, - filters: list[dict[str, JSON]] | None = None, # TODO: type has changed + filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, cache_metadata: bool | None = None, cache_attrs: bool | None = None, read_only: bool | None = None, @@ -1009,13 +1010,6 @@ async def create( _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) or _default_zarr_format() ) - zdtype = parse_data_type(dtype, zarr_format=zarr_format) - if zarr_format == 2: - default_filters, default_compressor = _get_default_chunk_encoding_v2(zdtype) - if not filters: - filters = default_filters # type: ignore[assignment] - if compressor == "auto": - compressor = default_compressor if synchronizer is not None: warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2) @@ -1029,14 +1023,14 @@ async def create( warnings.warn("object_codec is not yet implemented", RuntimeWarning, stacklevel=2) if read_only is not None: warnings.warn("read_only is not yet implemented", RuntimeWarning, stacklevel=2) + if meta_array is not None: + warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2) + if order is not None: _warn_order_kwarg() if write_empty_chunks is not None: _warn_write_empty_chunks_kwarg() - if meta_array is not None: - warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2) - mode = kwargs.pop("mode", None) if mode is None: mode = "a" @@ -1067,7 +1061,7 @@ async def create( store_path, shape=shape, chunks=chunks, - dtype=zdtype, + dtype=dtype, compressor=compressor, fill_value=fill_value, overwrite=overwrite, diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index b60f69a673..92b80b1ac8 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -15,6 +15,7 @@ if TYPE_CHECKING: from collections.abc import Iterable + import numcodecs.abc import numpy as np import numpy.typing as npt @@ -613,7 +614,7 @@ def create( overwrite: bool = False, path: PathLike | None = None, chunk_store: StoreLike | None = None, - filters: list[dict[str, JSON]] | None = None, # TODO: type has changed + filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, cache_metadata: bool | None = None, cache_attrs: bool | None = None, read_only: bool | None = None, diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index a44a4b55d1..312dc0bc4d 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -591,7 +591,7 @@ async def _create( chunks: ShapeLike | None = None, dimension_separator: Literal[".", "/"] | None = None, order: MemoryOrder | None = None, - filters: list[dict[str, JSON]] | None = None, + filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, compressor: CompressorLike = "auto", # runtime overwrite: bool = False, @@ -850,9 +850,10 @@ async def _create_v2( else: await ensure_no_existing_node(store_path, zarr_format=2) + default_filters, default_compressor = _get_default_chunk_encoding_v2(dtype) compressor_parsed: CompressorLikev2 if compressor == "auto": - _, compressor_parsed = _get_default_chunk_encoding_v2(dtype) + compressor_parsed = default_compressor elif isinstance(compressor, BytesBytesCodec): raise ValueError( "Cannot use a BytesBytesCodec as a compressor for zarr v2 arrays. " @@ -861,6 +862,9 @@ async def _create_v2( else: compressor_parsed = compressor + if filters is None: + filters = default_filters + metadata = cls._create_metadata_v2( shape=shape, dtype=dtype, diff --git a/tests/test_api.py b/tests/test_api.py index da61f97847..b4f25a375e 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1412,3 +1412,10 @@ def test_auto_chunks(f: Callable[..., Array]) -> None: a = f(**kwargs) assert a.chunks == (500, 500) + + +@pytest.mark.parametrize("kwarg_name", ["synchronizer", "chunk_store", "cache_attrs", "meta_array"]) +def test_unimplemented_kwarg_warnings(kwarg_name: str) -> None: + kwargs = {kwarg_name: 1} + with pytest.warns(RuntimeWarning, match=".* is not yet implemented"): + zarr.create(shape=(1,), **kwargs) # type: ignore[arg-type] From dc75ab5a1fa8949727356657f4612b56eea62fe3 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 10 Jul 2025 18:59:04 +0100 Subject: [PATCH 009/468] Remove redundant release note (#3223) --- changes/3151.bugfix.rst | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 changes/3151.bugfix.rst diff --git a/changes/3151.bugfix.rst b/changes/3151.bugfix.rst deleted file mode 100644 index 15c92dbbb5..0000000000 --- a/changes/3151.bugfix.rst +++ /dev/null @@ -1,2 +0,0 @@ -Fixed an issue preventing correct parsing of NumPy ``int32`` dtypes when constructed via -``np.dtype('i')``. \ No newline at end of file From ded59d90766196259d3a20c395bd2fefc97cb274 Mon Sep 17 00:00:00 2001 From: Mustafa Al Ibrahim Date: Fri, 11 Jul 2025 16:31:52 +0300 Subject: [PATCH 010/468] add missing quote symbol in the dictionary syntax (#3231) Co-authored-by: mosgeo --- src/zarr/core/common.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index a5ef7aeb7a..e86347d808 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -195,7 +195,7 @@ def _warn_write_empty_chunks_kwarg() -> None: msg = ( "The `write_empty_chunks` keyword argument is deprecated and will be removed in future versions. " "To control whether empty chunks are written to storage, either use the `config` keyword " - "argument, as in `config={'write_empty_chunks: True}`," + "argument, as in `config={'write_empty_chunks': True}`," "or change the global 'array.write_empty_chunks' configuration variable." ) warnings.warn(msg, RuntimeWarning, stacklevel=2) @@ -206,7 +206,7 @@ def _warn_order_kwarg() -> None: msg = ( "The `order` keyword argument has no effect for Zarr format 3 arrays. " "To control the memory layout of the array, either use the `config` keyword " - "argument, as in `config={'order: 'C'}`," + "argument, as in `config={'order': 'C'}`," "or change the global 'array.order' configuration variable." ) warnings.warn(msg, RuntimeWarning, stacklevel=2) From c0e39afa25322f8fa05c58bf9befdcc52b554e01 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 11 Jul 2025 17:45:52 +0200 Subject: [PATCH 011/468] remove chunk encoding from config (#3228) * refactor default chunk encoding to skip config. add tests for deprecated config keys * remove chunk encoding configuration from docs * don't create invalid string dtype arrays in test * add v2-style error when creating a vlen dtype without the right codec * test for v2-style error when creating an object array without an object codec * lint * changelog * Update 3228.removal.rst * test coverage --- changes/3228.removal.rst | 16 ++++ docs/user-guide/arrays.rst | 10 --- docs/user-guide/config.rst | 20 +---- src/zarr/core/array.py | 150 +++++++++++++++++++++++++++++-------- src/zarr/core/config.py | 41 +++++----- tests/test_array.py | 87 ++++++++++++++++++--- tests/test_config.py | 80 +++++++------------- tests/test_v2.py | 57 +++++++------- 8 files changed, 286 insertions(+), 175 deletions(-) create mode 100644 changes/3228.removal.rst diff --git a/changes/3228.removal.rst b/changes/3228.removal.rst new file mode 100644 index 0000000000..0463897755 --- /dev/null +++ b/changes/3228.removal.rst @@ -0,0 +1,16 @@ +Removes default chunk encoding settings (filters, serializer, compressors) from the global +configuration object. + +This removal is justified on the basis that storing chunk encoding settings in the config required +a brittle, confusing, and inaccurate categorization of array data types, which was particularly +unsuitable after the recent addition of new data types that didn't fit naturally into the +pre-existing categories. + +The default chunk encoding is the same (Zstandard compression, and the required object codecs for +variable length data types), but the chunk encoding is now generated by functions that cannot be +reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should +instead specify the desired chunk encoding explicitly when creating an array. + +This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that +arrays with a ``VariableLengthUTF8`` or ``VariableLengthBytes`` data type cannot be created without the +correct "object codec". diff --git a/docs/user-guide/arrays.rst b/docs/user-guide/arrays.rst index f45dfbebe8..67b134d442 100644 --- a/docs/user-guide/arrays.rst +++ b/docs/user-guide/arrays.rst @@ -246,16 +246,6 @@ built-in delta filter:: >>> z.compressors (LZMA(codec_name='numcodecs.lzma', codec_config={'filters': [{'id': 3, 'dist': 4}, {'id': 33, 'preset': 1}]}),) -The default compressor can be changed by setting the value of the using Zarr's -:ref:`user-guide-config`, e.g.:: - - >>> with zarr.config.set({'array.v2_default_compressor.default': {'id': 'blosc'}}): - ... z = zarr.create_array(store={}, shape=(100000000,), chunks=(1000000,), dtype='int32', zarr_format=2) - >>> z.filters - () - >>> z.compressors - (Blosc(cname='lz4', clevel=5, shuffle=SHUFFLE, blocksize=0),) - To disable compression, set ``compressors=None`` when creating an array, e.g.:: >>> z = zarr.create_array(store='data/example-8.zarr', shape=(100000000,), chunks=(1000000,), dtype='int32', compressors=None) diff --git a/docs/user-guide/config.rst b/docs/user-guide/config.rst index 5a9d26f2b9..0ae8017ca9 100644 --- a/docs/user-guide/config.rst +++ b/docs/user-guide/config.rst @@ -43,25 +43,7 @@ This is the current default configuration:: >>> zarr.config.pprint() {'array': {'order': 'C', - 'v2_default_compressor': {'default': {'checksum': False, - 'id': 'zstd', - 'level': 0}, - 'variable-length-string': {'checksum': False, - 'id': 'zstd', - 'level': 0}}, - 'v2_default_filters': {'default': None, - 'variable-length-string': [{'id': 'vlen-utf8'}]}, - 'v3_default_compressors': {'default': [{'configuration': {'checksum': False, - 'level': 0}, - 'name': 'zstd'}], - 'variable-length-string': [{'configuration': {'checksum': False, - 'level': 0}, - 'name': 'zstd'}]}, - 'v3_default_filters': {'default': [], 'variable-length-string': []}, - 'v3_default_serializer': {'default': {'configuration': {'endian': 'little'}, - 'name': 'bytes'}, - 'variable-length-string': {'name': 'vlen-utf8'}}, - 'write_empty_chunks': False}, + 'write_empty_chunks': False}, 'async': {'concurrency': 10, 'timeout': None}, 'buffer': 'zarr.buffer.cpu.Buffer', 'codec_pipeline': {'batch_size': 1, diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 312dc0bc4d..a4f7fc086a 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -30,6 +30,8 @@ from zarr.abc.store import Store, set_or_delete from zarr.codecs._v2 import V2Codec from zarr.codecs.bytes import BytesCodec +from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec +from zarr.codecs.zstd import ZstdCodec from zarr.core._info import ArrayInfo from zarr.core.array_spec import ArrayConfig, ArrayConfigLike, parse_array_config from zarr.core.attributes import Attributes @@ -68,11 +70,13 @@ from zarr.core.config import categorize_data_type from zarr.core.config import config as zarr_config from zarr.core.dtype import ( + VariableLengthBytes, + VariableLengthUTF8, ZDType, ZDTypeLike, parse_data_type, ) -from zarr.core.dtype.common import HasEndianness, HasItemSize +from zarr.core.dtype.common import HasEndianness, HasItemSize, HasObjectCodec from zarr.core.indexing import ( BasicIndexer, BasicSelection, @@ -109,6 +113,7 @@ ) from zarr.core.metadata.v2 import ( CompressorLikev2, + get_object_codec_id, parse_compressor, parse_filters, ) @@ -710,7 +715,10 @@ def _create_metadata_v3( shape = parse_shapelike(shape) if codecs is None: - filters, serializer, compressors = _get_default_chunk_encoding_v3(dtype) + filters = default_filters_v3(dtype) + serializer = default_serializer_v3(dtype) + compressors = default_compressors_v3(dtype) + codecs_parsed = (*filters, serializer, *compressors) else: codecs_parsed = tuple(codecs) @@ -850,10 +858,9 @@ async def _create_v2( else: await ensure_no_existing_node(store_path, zarr_format=2) - default_filters, default_compressor = _get_default_chunk_encoding_v2(dtype) compressor_parsed: CompressorLikev2 if compressor == "auto": - compressor_parsed = default_compressor + compressor_parsed = default_compressor_v2(dtype) elif isinstance(compressor, BytesBytesCodec): raise ValueError( "Cannot use a BytesBytesCodec as a compressor for zarr v2 arrays. " @@ -863,7 +870,7 @@ async def _create_v2( compressor_parsed = compressor if filters is None: - filters = default_filters + filters = default_filters_v2(dtype) metadata = cls._create_metadata_v2( shape=shape, @@ -4654,19 +4661,80 @@ def _get_default_chunk_encoding_v3( ) -def _get_default_chunk_encoding_v2( - dtype: ZDType[TBaseDType, TBaseScalar], -) -> tuple[tuple[numcodecs.abc.Codec, ...] | None, numcodecs.abc.Codec | None]: +def default_filters_v3(dtype: ZDType[Any, Any]) -> tuple[ArrayArrayCodec, ...]: """ - Get the default chunk encoding for Zarr format 2 arrays, given a dtype + Given a data type, return the default filters for that data type. + + This is an empty tuple. No data types have default filters. """ - dtype_category = categorize_data_type(dtype) - filters = zarr_config.get("array.v2_default_filters").get(dtype_category) - compressor = zarr_config.get("array.v2_default_compressor").get(dtype_category) - if filters is not None: - filters = tuple(numcodecs.get_codec(f) for f in filters) + return () + + +def default_compressors_v3(dtype: ZDType[Any, Any]) -> tuple[BytesBytesCodec, ...]: + """ + Given a data type, return the default compressors for that data type. + + This is just a tuple containing ``ZstdCodec`` + """ + return (ZstdCodec(),) + + +def default_serializer_v3(dtype: ZDType[Any, Any]) -> ArrayBytesCodec: + """ + Given a data type, return the default serializer for that data type. + + The default serializer for most data types is the ``BytesCodec``, which may or may not be + parameterized with an endianness, depending on whether the data type has endianness. Variable + length strings and variable length bytes have hard-coded serializers -- ``VLenUTF8Codec`` and + ``VLenBytesCodec``, respectively. + + """ + serializer: ArrayBytesCodec = BytesCodec(endian=None) + + if isinstance(dtype, HasEndianness): + serializer = BytesCodec(endian="little") + elif isinstance(dtype, HasObjectCodec): + if dtype.object_codec_id == "vlen-bytes": + serializer = VLenBytesCodec() + elif dtype.object_codec_id == "vlen-utf8": + serializer = VLenUTF8Codec() + else: + msg = f"Data type {dtype} requires an unknown object codec: {dtype.object_codec_id!r}." + raise ValueError(msg) + return serializer + + +def default_filters_v2(dtype: ZDType[Any, Any]) -> tuple[numcodecs.abc.Codec] | None: + """ + Given a data type, return the default filters for that data type. + + For data types that require an object codec, namely variable length data types, + this is a tuple containing the object codec. Otherwise it's ``None``. + """ + if isinstance(dtype, HasObjectCodec): + if dtype.object_codec_id == "vlen-bytes": + from numcodecs import VLenBytes - return filters, numcodecs.get_codec(compressor) + return (VLenBytes(),) + elif dtype.object_codec_id == "vlen-utf8": + from numcodecs import VLenUTF8 + + return (VLenUTF8(),) + else: + msg = f"Data type {dtype} requires an unknown object codec: {dtype.object_codec_id!r}." + raise ValueError(msg) + return None + + +def default_compressor_v2(dtype: ZDType[Any, Any]) -> numcodecs.abc.Codec: + """ + Given a data type, return the default compressors for that data type. + + This is just the numcodecs ``Zstd`` codec. + """ + from numcodecs import Zstd + + return Zstd(level=0, checksum=False) def _parse_chunk_encoding_v2( @@ -4678,14 +4746,13 @@ def _parse_chunk_encoding_v2( """ Generate chunk encoding classes for Zarr format 2 arrays with optional defaults. """ - default_filters, default_compressor = _get_default_chunk_encoding_v2(dtype) _filters: tuple[numcodecs.abc.Codec, ...] | None _compressor: numcodecs.abc.Codec | None if compressor is None or compressor == (): _compressor = None elif compressor == "auto": - _compressor = default_compressor + _compressor = default_compressor_v2(dtype) elif isinstance(compressor, tuple | list) and len(compressor) == 1: _compressor = parse_compressor(compressor[0]) else: @@ -4697,7 +4764,7 @@ def _parse_chunk_encoding_v2( if filters is None: _filters = None elif filters == "auto": - _filters = default_filters + _filters = default_filters_v2(dtype) else: if isinstance(filters, Iterable): for idx, f in enumerate(filters): @@ -4708,7 +4775,33 @@ def _parse_chunk_encoding_v2( ) raise TypeError(msg) _filters = parse_filters(filters) - + if isinstance(dtype, HasObjectCodec): + # check the filters and the compressor for the object codec required for this data type + if _filters is None: + if _compressor is None: + object_codec_id = None + else: + object_codec_id = get_object_codec_id((_compressor.get_config(),)) + else: + object_codec_id = get_object_codec_id( + ( + *[f.get_config() for f in _filters], + _compressor.get_config() if _compressor is not None else None, + ) + ) + if object_codec_id is None: + if isinstance(dtype, VariableLengthUTF8): # type: ignore[unreachable] + codec_name = "the numcodecs.VLenUTF8 codec" # type: ignore[unreachable] + elif isinstance(dtype, VariableLengthBytes): # type: ignore[unreachable] + codec_name = "the numcodecs.VLenBytes codec" # type: ignore[unreachable] + else: + codec_name = f"an unknown object codec with id {dtype.object_codec_id!r}" + msg = ( + f"Data type {dtype} requires {codec_name}, " + "but no such codec was specified in the filters or compressor parameters for " + "this array. " + ) + raise ValueError(msg) return _filters, _compressor @@ -4722,14 +4815,11 @@ def _parse_chunk_encoding_v3( """ Generate chunk encoding classes for v3 arrays with optional defaults. """ - default_array_array, default_array_bytes, default_bytes_bytes = _get_default_chunk_encoding_v3( - dtype - ) if filters is None: out_array_array: tuple[ArrayArrayCodec, ...] = () elif filters == "auto": - out_array_array = default_array_array + out_array_array = default_filters_v3(dtype) else: maybe_array_array: Iterable[Codec | dict[str, JSON]] if isinstance(filters, dict | Codec): @@ -4739,7 +4829,7 @@ def _parse_chunk_encoding_v3( out_array_array = tuple(_parse_array_array_codec(c) for c in maybe_array_array) if serializer == "auto": - out_array_bytes = default_array_bytes + out_array_bytes = default_serializer_v3(dtype) else: # TODO: ensure that the serializer is compatible with the ndarray produced by the # array-array codecs. For example, if a sequence of array-array codecs produces an @@ -4749,7 +4839,7 @@ def _parse_chunk_encoding_v3( if compressors is None: out_bytes_bytes: tuple[BytesBytesCodec, ...] = () elif compressors == "auto": - out_bytes_bytes = default_bytes_bytes + out_bytes_bytes = default_compressors_v3(dtype) else: maybe_bytes_bytes: Iterable[Codec | dict[str, JSON]] if isinstance(compressors, dict | Codec): @@ -4759,17 +4849,11 @@ def _parse_chunk_encoding_v3( out_bytes_bytes = tuple(_parse_bytes_bytes_codec(c) for c in maybe_bytes_bytes) - # specialize codecs as needed given the dtype - - # TODO: refactor so that the config only contains the name of the codec, and we use the dtype - # to create the codec instance, instead of storing a dict representation of a full codec. - # TODO: ensure that the serializer is compatible with the ndarray produced by the # array-array codecs. For example, if a sequence of array-array codecs produces an # array with a single-byte data type, then the serializer should not specify endiannesss. - if isinstance(out_array_bytes, BytesCodec) and not isinstance(dtype, HasEndianness): - # The default endianness in the bytescodec might not be None, so we need to replace it - out_array_bytes = replace(out_array_bytes, endian=None) + + # TODO: add checks to ensure that the right serializer is used for vlen data types return out_array_array, out_array_bytes, out_bytes_bytes diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 05d048ef74..cc3c33cd17 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -78,6 +78,25 @@ def enable_gpu(self) -> ConfigSet: ) +# these keys were removed from the config as part of the 3.1.0 release. +# these deprecations should be removed in 3.1.1 or thereabouts. +deprecations = { + "array.v2_default_compressor.numeric": None, + "array.v2_default_compressor.string": None, + "array.v2_default_compressor.bytes": None, + "array.v2_default_filters.string": None, + "array.v2_default_filters.bytes": None, + "array.v3_default_filters.numeric": None, + "array.v3_default_filters.raw": None, + "array.v3_default_filters.bytes": None, + "array.v3_default_serializer.numeric": None, + "array.v3_default_serializer.string": None, + "array.v3_default_serializer.bytes": None, + "array.v3_default_compressors.string": None, + "array.v3_default_compressors.bytes": None, + "array.v3_default_compressors": None, +} + # The default configuration for zarr config = Config( "zarr", @@ -87,27 +106,6 @@ def enable_gpu(self) -> ConfigSet: "array": { "order": "C", "write_empty_chunks": False, - "v2_default_compressor": { - "default": {"id": "zstd", "level": 0, "checksum": False}, - "variable-length-string": {"id": "zstd", "level": 0, "checksum": False}, - }, - "v2_default_filters": { - "default": None, - "variable-length-string": [{"id": "vlen-utf8"}], - }, - "v3_default_filters": {"default": [], "variable-length-string": []}, - "v3_default_serializer": { - "default": {"name": "bytes", "configuration": {"endian": "little"}}, - "variable-length-string": {"name": "vlen-utf8"}, - }, - "v3_default_compressors": { - "default": [ - {"name": "zstd", "configuration": {"level": 0, "checksum": False}}, - ], - "variable-length-string": [ - {"name": "zstd", "configuration": {"level": 0, "checksum": False}} - ], - }, }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, @@ -132,6 +130,7 @@ def enable_gpu(self) -> ConfigSet: "ndbuffer": "zarr.buffer.cpu.NDBuffer", } ], + deprecations=deprecations, ) diff --git a/tests/test_array.py b/tests/test_array.py index 0bca860e84..4783bca05c 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -35,23 +35,30 @@ _parse_chunk_encoding_v3, chunks_initialized, create_array, + default_filters_v2, + default_serializer_v3, ) from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, default_buffer_prototype from zarr.core.buffer.cpu import NDBuffer from zarr.core.chunk_grids import _auto_partition from zarr.core.chunk_key_encodings import ChunkKeyEncodingParams from zarr.core.common import JSON, MemoryOrder, ZarrFormat -from zarr.core.dtype import parse_data_type -from zarr.core.dtype.common import ENDIANNESS_STR, EndiannessStr -from zarr.core.dtype.npy.common import NUMPY_ENDIANNESS_STR, endianness_from_numpy_str -from zarr.core.dtype.npy.float import Float32, Float64 -from zarr.core.dtype.npy.int import Int16, UInt8 -from zarr.core.dtype.npy.string import VariableLengthUTF8 -from zarr.core.dtype.npy.structured import ( +from zarr.core.dtype import ( + DateTime64, + Float32, + Float64, + Int16, Structured, + TimeDelta64, + UInt8, + VariableLengthBytes, + VariableLengthUTF8, + ZDType, + parse_data_type, ) -from zarr.core.dtype.npy.time import DateTime64, TimeDelta64 -from zarr.core.dtype.wrapper import ZDType +from zarr.core.dtype.common import ENDIANNESS_STR, EndiannessStr +from zarr.core.dtype.npy.common import NUMPY_ENDIANNESS_STR, endianness_from_numpy_str +from zarr.core.dtype.npy.string import UTF8Base from zarr.core.group import AsyncGroup from zarr.core.indexing import BasicIndexer, ceildiv from zarr.core.metadata.v2 import ArrayV2Metadata @@ -1335,6 +1342,8 @@ async def test_invalid_v3_arguments( async def test_v2_chunk_encoding( store: MemoryStore, compressors: CompressorsLike, filters: FiltersLike, dtype: str ) -> None: + if dtype == "str" and filters != "auto": + pytest.skip("Only the auto filters are compatible with str dtype in this test.") arr = await create_array( store=store, dtype=dtype, @@ -1848,3 +1857,63 @@ def test_array_repr(store: Store) -> None: dtype = "uint8" arr = zarr.create_array(store, shape=shape, dtype=dtype) assert str(arr) == f"" + + +class UnknownObjectDtype(UTF8Base[np.dtypes.ObjectDType]): + object_codec_id = "unknown" # type: ignore[assignment] + + def to_native_dtype(self) -> np.dtypes.ObjectDType: + """ + Create a NumPy object dtype from this VariableLengthUTF8 ZDType. + + Returns + ------- + np.dtypes.ObjectDType + The NumPy object dtype. + """ + return np.dtype("o") # type: ignore[return-value] + + +@pytest.mark.parametrize( + "dtype", [VariableLengthUTF8(), VariableLengthBytes(), UnknownObjectDtype()] +) +def test_chunk_encoding_no_object_codec_errors(dtype: ZDType[Any, Any]) -> None: + """ + Test that a valuerror is raised when checking the chunk encoding for a v2 array with a + data type that requires an object codec, but where no object codec is specified + """ + if isinstance(dtype, VariableLengthUTF8): + codec_name = "the numcodecs.VLenUTF8 codec" + elif isinstance(dtype, VariableLengthBytes): + codec_name = "the numcodecs.VLenBytes codec" + else: + codec_name = f"an unknown object codec with id {dtype.object_codec_id!r}" # type: ignore[attr-defined] + msg = ( + f"Data type {dtype} requires {codec_name}, " + "but no such codec was specified in the filters or compressor parameters for " + "this array. " + ) + with pytest.raises(ValueError, match=re.escape(msg)): + _parse_chunk_encoding_v2(filters=None, compressor=None, dtype=dtype) + + +def test_unknown_object_codec_default_serializer_v3() -> None: + """ + Test that we get a valueerrror when trying to create the default serializer for a data type + that requires an unknown object codec + """ + dtype = UnknownObjectDtype() + msg = f"Data type {dtype} requires an unknown object codec: {dtype.object_codec_id!r}." + with pytest.raises(ValueError, match=re.escape(msg)): + default_serializer_v3(dtype) + + +def test_unknown_object_codec_default_filters_v2() -> None: + """ + Test that we get a valueerrror when trying to create the default serializer for a data type + that requires an unknown object codec + """ + dtype = UnknownObjectDtype() + msg = f"Data type {dtype} requires an unknown object codec: {dtype.object_codec_id!r}." + with pytest.raises(ValueError, match=re.escape(msg)): + default_filters_v2(dtype) diff --git a/tests/test_config.py b/tests/test_config.py index e267601272..c59e721c49 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -1,6 +1,6 @@ import os from collections.abc import Iterable -from typing import TYPE_CHECKING, Any +from typing import Any from unittest import mock from unittest.mock import Mock @@ -16,16 +16,13 @@ BloscCodec, BytesCodec, Crc32cCodec, - GzipCodec, ShardingCodec, ) -from zarr.core.array import create_array from zarr.core.array_spec import ArraySpec from zarr.core.buffer import NDBuffer from zarr.core.buffer.core import Buffer from zarr.core.codec_pipeline import BatchedCodecPipeline from zarr.core.config import BadConfigError, config -from zarr.core.dtype import Int8, VariableLengthUTF8 from zarr.core.indexing import SelectorTuple from zarr.registry import ( fully_qualified_name, @@ -38,7 +35,6 @@ register_ndbuffer, register_pipeline, ) -from zarr.storage import MemoryStore from zarr.testing.buffer import ( NDBufferUsingTestNDArrayLike, StoreExpectingTestBuffer, @@ -46,9 +42,6 @@ TestNDArrayLike, ) -if TYPE_CHECKING: - from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType - def test_config_defaults_set() -> None: # regression test for available defaults @@ -60,27 +53,6 @@ def test_config_defaults_set() -> None: "array": { "order": "C", "write_empty_chunks": False, - "v2_default_compressor": { - "default": {"id": "zstd", "level": 0, "checksum": False}, - "variable-length-string": {"id": "zstd", "level": 0, "checksum": False}, - }, - "v2_default_filters": { - "default": None, - "variable-length-string": [{"id": "vlen-utf8"}], - }, - "v3_default_filters": {"default": [], "variable-length-string": []}, - "v3_default_serializer": { - "default": {"name": "bytes", "configuration": {"endian": "little"}}, - "variable-length-string": {"name": "vlen-utf8"}, - }, - "v3_default_compressors": { - "default": [ - {"name": "zstd", "configuration": {"level": 0, "checksum": False}}, - ], - "variable-length-string": [ - {"name": "zstd", "configuration": {"level": 0, "checksum": False}} - ], - }, }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, @@ -323,29 +295,31 @@ class NewCodec2(BytesCodec): get_codec_class("new_codec") -@pytest.mark.parametrize("dtype_category", ["variable-length-string", "default"]) -@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") -async def test_default_codecs(dtype_category: str) -> None: +@pytest.mark.parametrize( + "key", + [ + "array.v2_default_compressor.numeric", + "array.v2_default_compressor.string", + "array.v2_default_compressor.bytes", + "array.v2_default_filters.string", + "array.v2_default_filters.bytes", + "array.v3_default_filters.numeric", + "array.v3_default_filters.raw", + "array.v3_default_filters.bytes", + "array.v3_default_serializer.numeric", + "array.v3_default_serializer.string", + "array.v3_default_serializer.bytes", + "array.v3_default_compressors.string", + "array.v3_default_compressors.bytes", + "array.v3_default_compressors", + ], +) +def test_deprecated_config(key: str) -> None: """ - Test that the default compressors are sensitive to the current setting of the config. + Test that a valuerror is raised when setting the default chunk encoding for a given + data type category """ - zdtype: ZDType[TBaseDType, TBaseScalar] - if dtype_category == "variable-length-string": - zdtype = VariableLengthUTF8() # type: ignore[assignment] - else: - zdtype = Int8() - expected_compressors = (GzipCodec(),) - new_conf = { - f"array.v3_default_compressors.{dtype_category}": [ - c.to_dict() for c in expected_compressors - ] - } - with config.set(new_conf): - arr = await create_array( - shape=(100,), - chunks=(100,), - dtype=zdtype, - zarr_format=3, - store=MemoryStore(), - ) - assert arr.compressors == expected_compressors + + with pytest.raises(ValueError): + with zarr.config.set({key: "foo"}): + pass diff --git a/tests/test_v2.py b/tests/test_v2.py index 29f031663f..4d17305995 100644 --- a/tests/test_v2.py +++ b/tests/test_v2.py @@ -73,37 +73,34 @@ def test_codec_pipeline() -> None: async def test_v2_encode_decode( dtype: str, expected_dtype: str, fill_value: bytes, fill_value_json: str ) -> None: - with config.set( - { - "array.v2_default_filters.bytes": [{"id": "vlen-bytes"}], - "array.v2_default_compressor.bytes": None, - } - ): - store = zarr.storage.MemoryStore() - g = zarr.group(store=store, zarr_format=2) - g.create_array( - name="foo", shape=(3,), chunks=(3,), dtype=dtype, fill_value=fill_value, compressor=None - ) + store = zarr.storage.MemoryStore() + g = zarr.group(store=store, zarr_format=2) + g.create_array( + name="foo", shape=(3,), chunks=(3,), dtype=dtype, fill_value=fill_value, compressor=None + ) - result = await store.get("foo/.zarray", zarr.core.buffer.default_buffer_prototype()) - assert result is not None - - serialized = json.loads(result.to_bytes()) - expected = { - "chunks": [3], - "compressor": None, - "dtype": expected_dtype, - "fill_value": fill_value_json, - "filters": None, - "order": "C", - "shape": [3], - "zarr_format": 2, - "dimension_separator": ".", - } - assert serialized == expected - - data = zarr.open_array(store=store, path="foo")[:] - np.testing.assert_equal(data, np.full((3,), b"X", dtype=dtype)) + result = await store.get("foo/.zarray", zarr.core.buffer.default_buffer_prototype()) + assert result is not None + + serialized = json.loads(result.to_bytes()) + expected = { + "chunks": [3], + "compressor": None, + "dtype": expected_dtype, + "fill_value": fill_value_json, + "filters": None, + "order": "C", + "shape": [3], + "zarr_format": 2, + "dimension_separator": ".", + } + assert serialized == expected + + data = zarr.open_array(store=store, path="foo")[:] + np.testing.assert_equal(data, np.full((3,), b"X", dtype=dtype)) + + data = zarr.open_array(store=store, path="foo")[:] + np.testing.assert_equal(data, np.full((3,), b"X", dtype=dtype)) @pytest.mark.parametrize( From 7154f98fd44d5d55ec91a1849a82d9319330c8c6 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 11 Jul 2025 17:13:54 +0100 Subject: [PATCH 012/468] Bump min numpy version (#3226) * Bump min numpy version * Update src/zarr/testing/strategies.py Co-authored-by: Deepak Cherian --------- Co-authored-by: Davis Bennett Co-authored-by: Deepak Cherian --- .github/workflows/test.yml | 6 +++--- changes/xxxx.feature.rst | 1 + docs/user-guide/installation.rst | 2 +- pyproject.toml | 8 ++++---- src/zarr/testing/strategies.py | 2 +- 5 files changed, 10 insertions(+), 9 deletions(-) create mode 100644 changes/xxxx.feature.rst diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 909196c8c0..4dbe115525 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -21,12 +21,12 @@ jobs: strategy: matrix: python-version: ['3.11', '3.12', '3.13'] - numpy-version: ['1.25', '2.2'] + numpy-version: ['1.26', '2.2'] dependency-set: ["minimal", "optional"] os: ["ubuntu-latest"] include: - python-version: '3.11' - numpy-version: '1.25' + numpy-version: '1.26' dependency-set: 'optional' os: 'macos-latest' - python-version: '3.13' @@ -34,7 +34,7 @@ jobs: dependency-set: 'optional' os: 'macos-latest' - python-version: '3.11' - numpy-version: '1.25' + numpy-version: '1.26' dependency-set: 'optional' os: 'windows-latest' - python-version: '3.13' diff --git a/changes/xxxx.feature.rst b/changes/xxxx.feature.rst new file mode 100644 index 0000000000..1219900cb7 --- /dev/null +++ b/changes/xxxx.feature.rst @@ -0,0 +1 @@ +The minimum version of NumPy has increased to 1.26. diff --git a/docs/user-guide/installation.rst b/docs/user-guide/installation.rst index a79f0763cb..fbd30dedea 100644 --- a/docs/user-guide/installation.rst +++ b/docs/user-guide/installation.rst @@ -8,7 +8,7 @@ Required dependencies include: - `Python `_ (3.11 or later) - `packaging `_ (22.0 or later) -- `numpy `_ (1.25 or later) +- `numpy `_ (1.26 or later) - `numcodecs[crc32c] `_ (0.14 or later) - `typing_extensions `_ (4.9 or later) - `donfig `_ (0.8 or later) diff --git a/pyproject.toml b/pyproject.toml index a48a5eea25..85517d8d0a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ requires-python = ">=3.11" # If you add a new dependency here, please also add it to .pre-commit-config.yml dependencies = [ 'packaging>=22.0', - 'numpy>=1.25', + 'numpy>=1.26', 'numcodecs[crc32c]>=0.14', 'typing_extensions>=4.9', 'donfig>=0.8', @@ -154,7 +154,7 @@ features = ["test"] [[tool.hatch.envs.test.matrix]] python = ["3.11", "3.12", "3.13"] -numpy = ["1.25", "2.2"] +numpy = ["1.26", "2.2"] deps = ["minimal", "optional"] [tool.hatch.envs.test.overrides] @@ -190,7 +190,7 @@ features = ["test", "gpu"] [[tool.hatch.envs.gputest.matrix]] python = ["3.11", "3.12", "3.13"] -numpy = ["1.25", "2.2"] +numpy = ["1.26", "2.2"] version = ["minimal"] [tool.hatch.envs.gputest.scripts] @@ -246,7 +246,7 @@ python = "3.11" dependencies = [ 'zarr[remote]', 'packaging==22.*', - 'numpy==1.25.*', + 'numpy==1.26.*', 'numcodecs==0.14.*', # 0.14 needed for zarr3 codecs 'fsspec==2023.10.0', 's3fs==2023.10.0', diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 5e070b5387..2acf7b944c 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -405,7 +405,7 @@ def orthogonal_indices( newshape[axis] = idxr.size npindexer.append(idxr.reshape(newshape)) - # casting the output of broadcast_arrays is needed for numpy 1.25 + # casting the output of broadcast_arrays is needed for numpy < 2 return tuple(zindexer), tuple(np.broadcast_arrays(*npindexer)) From dfd672bac5bd4789aaddeb271a5c54d847f3c456 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 11 Jul 2025 19:11:21 +0100 Subject: [PATCH 013/468] Fix type of v2 compressors (#3232) * Fix type of v2 compressors * Add bugfix entry --------- Co-authored-by: Davis Bennett --- changes/3232.bugfix.rst | 3 +++ src/zarr/core/metadata/v2.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 changes/3232.bugfix.rst diff --git a/changes/3232.bugfix.rst b/changes/3232.bugfix.rst new file mode 100644 index 0000000000..e777103c83 --- /dev/null +++ b/changes/3232.bugfix.rst @@ -0,0 +1,3 @@ +Fix the type of ``ArrayV2Metadata.codec`` to constrain it to ``numcodecs.abc.Codec | None``. +Previously the type was more permissive, allowing objects that can be parsed into Codecs (e.g., the codec name). +The constructor of ``ArrayV2Metadata`` still allows the permissive input when creating new objects. diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 3ac75e0418..7bdad204b8 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -68,7 +68,7 @@ class ArrayV2Metadata(Metadata): order: MemoryOrder = "C" filters: tuple[numcodecs.abc.Codec, ...] | None = None dimension_separator: Literal[".", "/"] = "." - compressor: CompressorLikev2 + compressor: numcodecs.abc.Codec | None attributes: dict[str, JSON] = field(default_factory=dict) zarr_format: Literal[2] = field(init=False, default=2) From c1ce2fd9bce80687e382aa382c8c6ee53908ad09 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 11 Jul 2025 19:23:33 +0100 Subject: [PATCH 014/468] Remove duplicate release note entries (#3224) --- changes/3138.feature.rst | 1 - changes/3140.bugfix.rst | 8 -------- changes/3156.bugfix.rst | 1 - changes/3193.bugfix.rst | 2 -- changes/3195.bugfix.rst | 1 - 5 files changed, 13 deletions(-) delete mode 100644 changes/3138.feature.rst delete mode 100644 changes/3140.bugfix.rst delete mode 100644 changes/3156.bugfix.rst delete mode 100644 changes/3193.bugfix.rst delete mode 100644 changes/3195.bugfix.rst diff --git a/changes/3138.feature.rst b/changes/3138.feature.rst deleted file mode 100644 index ecd339bf9c..0000000000 --- a/changes/3138.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Adds a `with_read_only` convenience method to the `Store` abstract base class (raises `NotImplementedError`) and implementations to the `MemoryStore`, `ObjectStore`, `LocalStore`, and `FsspecStore` classes. \ No newline at end of file diff --git a/changes/3140.bugfix.rst b/changes/3140.bugfix.rst deleted file mode 100644 index 6ef83c90a5..0000000000 --- a/changes/3140.bugfix.rst +++ /dev/null @@ -1,8 +0,0 @@ -Suppress `FileNotFoundError` when deleting non-existent keys in the `obstore` adapter. - -When writing empty chunks (i.e. chunks where all values are equal to the array's fill value) to a zarr array, zarr -will delete those chunks from the underlying store. For zarr arrays backed by the `obstore` adapter, this will potentially -raise a `FileNotFoundError` if the chunk doesn't already exist. -Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store, -suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect -from the store. diff --git a/changes/3156.bugfix.rst b/changes/3156.bugfix.rst deleted file mode 100644 index 64218b6707..0000000000 --- a/changes/3156.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Trying to open a StorePath/Array with ``mode='r'`` when the store is not read-only creates a read-only copy of the store. diff --git a/changes/3193.bugfix.rst b/changes/3193.bugfix.rst deleted file mode 100644 index a6e387c10c..0000000000 --- a/changes/3193.bugfix.rst +++ /dev/null @@ -1,2 +0,0 @@ -Removed an unnecessary check from ``_fsspec._make_async`` that would raise an exception when -creating a read-only store backed by a local file system with ``auto_mkdir`` set to ``False``. \ No newline at end of file diff --git a/changes/3195.bugfix.rst b/changes/3195.bugfix.rst deleted file mode 100644 index 44a7ce9105..0000000000 --- a/changes/3195.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Add missing import for AsyncFileSystemWrapper for _make_async in _fsspec.py \ No newline at end of file From 0f0563bc59d516d913fc54e943a90559d048e6c9 Mon Sep 17 00:00:00 2001 From: Deepak Cherian Date: Fri, 11 Jul 2025 11:36:43 -0700 Subject: [PATCH 015/468] Update stateful/property tests. (#3161) * Update stateful/property tests. Add actions to 1. overwrite data with oindex 2. read and compare a full array * Reduce freqquency of clear --------- Co-authored-by: Davis Bennett --- src/zarr/testing/stateful.py | 67 +++++++++++++++++++++++++++++---- src/zarr/testing/strategies.py | 68 ++++++++++++++++++---------------- tests/test_properties.py | 8 ++-- 3 files changed, 101 insertions(+), 42 deletions(-) diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index f83d942549..6faf5dc6d3 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -1,5 +1,7 @@ import builtins -from typing import Any +import functools +from collections.abc import Callable +from typing import Any, TypeVar, cast import hypothesis.extra.numpy as npst import hypothesis.strategies as st @@ -24,15 +26,43 @@ from zarr.testing.strategies import ( basic_indices, chunk_paths, + dimension_names, key_ranges, node_names, np_array_and_chunks, - numpy_arrays, + orthogonal_indices, ) from zarr.testing.strategies import keys as zarr_keys MAX_BINARY_SIZE = 100 +F = TypeVar("F", bound=Callable[..., Any]) + + +def with_frequency(frequency: float) -> Callable[[F], F]: + """This needs to be deterministic for hypothesis replaying""" + + def decorator(func: F) -> F: + counter_attr = f"__{func.__name__}_counter" + + @functools.wraps(func) + def wrapper(*args: Any, **kwargs: Any) -> Any: + return func(*args, **kwargs) + + @precondition + def frequency_check(f: Any) -> Any: + if not hasattr(f, counter_attr): + setattr(f, counter_attr, 0) + + current_count = getattr(f, counter_attr) + 1 + setattr(f, counter_attr, current_count) + + return (current_count * frequency) % 1.0 >= (1.0 - frequency) + + return cast(F, frequency_check(wrapper)) + + return decorator + def split_prefix_name(path: str) -> tuple[str, str]: split = path.rsplit("/", maxsplit=1) @@ -90,11 +120,7 @@ def add_group(self, name: str, data: DataObject) -> None: zarr.group(store=self.store, path=path) zarr.group(store=self.model, path=path) - @rule( - data=st.data(), - name=node_names, - array_and_chunks=np_array_and_chunks(arrays=numpy_arrays(zarr_formats=st.just(3))), - ) + @rule(data=st.data(), name=node_names, array_and_chunks=np_array_and_chunks()) def add_array( self, data: DataObject, @@ -122,12 +148,17 @@ def add_array( path=path, store=store, fill_value=fill_value, + zarr_format=3, + dimension_names=data.draw( + dimension_names(ndim=array.ndim), label="dimension names" + ), # Chose bytes codec to avoid wasting time compressing the data being written codecs=[BytesCodec()], ) self.all_arrays.add(path) @rule() + @with_frequency(0.25) def clear(self) -> None: note("clearing") import zarr @@ -192,6 +223,14 @@ def delete_chunk(self, data: DataObject) -> None: self._sync(self.model.delete(path)) self._sync(self.store.delete(path)) + @precondition(lambda self: bool(self.all_arrays)) + @rule(data=st.data()) + def check_array(self, data: DataObject) -> None: + path = data.draw(st.sampled_from(sorted(self.all_arrays))) + actual = zarr.open_array(self.store, path=path)[:] + expected = zarr.open_array(self.model, path=path)[:] + np.testing.assert_equal(actual, expected) + @precondition(lambda self: bool(self.all_arrays)) @rule(data=st.data()) def overwrite_array_basic_indexing(self, data: DataObject) -> None: @@ -206,6 +245,20 @@ def overwrite_array_basic_indexing(self, data: DataObject) -> None: model_array[slicer] = new_data store_array[slicer] = new_data + @precondition(lambda self: bool(self.all_arrays)) + @rule(data=st.data()) + def overwrite_array_orthogonal_indexing(self, data: DataObject) -> None: + array = data.draw(st.sampled_from(sorted(self.all_arrays))) + model_array = zarr.open_array(path=array, store=self.model) + store_array = zarr.open_array(path=array, store=self.store) + indexer, _ = data.draw(orthogonal_indices(shape=model_array.shape)) + note(f"overwriting array orthogonal {indexer=}") + new_data = data.draw( + npst.arrays(shape=model_array.oindex[indexer].shape, dtype=model_array.dtype) # type: ignore[union-attr] + ) + model_array.oindex[indexer] = new_data + store_array.oindex[indexer] = new_data + @precondition(lambda self: bool(self.all_arrays)) @rule(data=st.data()) def resize_array(self, data: DataObject) -> None: diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 2acf7b944c..27f648826d 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -43,7 +43,7 @@ def paths(draw: st.DrawFn, *, max_num_nodes: int | None = None) -> str: return draw(st.just("/") | keys(max_num_nodes=max_num_nodes)) -def v3_dtypes() -> st.SearchStrategy[np.dtype[Any]]: +def dtypes() -> st.SearchStrategy[np.dtype[Any]]: return ( npst.boolean_dtypes() | npst.integer_dtypes(endianness="=") @@ -57,18 +57,12 @@ def v3_dtypes() -> st.SearchStrategy[np.dtype[Any]]: ) +def v3_dtypes() -> st.SearchStrategy[np.dtype[Any]]: + return dtypes() + + def v2_dtypes() -> st.SearchStrategy[np.dtype[Any]]: - return ( - npst.boolean_dtypes() - | npst.integer_dtypes(endianness="=") - | npst.unsigned_integer_dtypes(endianness="=") - | npst.floating_dtypes(endianness="=") - | npst.complex_number_dtypes(endianness="=") - | npst.byte_string_dtypes(endianness="=") - | npst.unicode_string_dtypes(endianness="=") - | npst.datetime64_dtypes(endianness="=") - | npst.timedelta64_dtypes(endianness="=") - ) + return dtypes() def safe_unicode_for_dtype(dtype: np.dtype[np.str_]) -> st.SearchStrategy[str]: @@ -144,7 +138,7 @@ def array_metadata( shape = draw(array_shapes()) ndim = len(shape) chunk_shape = draw(array_shapes(min_dims=ndim, max_dims=ndim)) - np_dtype = draw(v3_dtypes()) + np_dtype = draw(dtypes()) dtype = get_data_type_from_native_dtype(np_dtype) fill_value = draw(npst.from_dtype(np_dtype)) if zarr_format == 2: @@ -179,14 +173,12 @@ def numpy_arrays( *, shapes: st.SearchStrategy[tuple[int, ...]] = array_shapes, dtype: np.dtype[Any] | None = None, - zarr_formats: st.SearchStrategy[ZarrFormat] = zarr_formats, ) -> npt.NDArray[Any]: """ Generate numpy arrays that can be saved in the provided Zarr format. """ - zarr_format = draw(zarr_formats) if dtype is None: - dtype = draw(v3_dtypes() if zarr_format == 3 else v2_dtypes()) + dtype = draw(dtypes()) if np.issubdtype(dtype, np.str_): safe_unicode_strings = safe_unicode_for_dtype(dtype) return draw(npst.arrays(dtype=dtype, shape=shapes, elements=safe_unicode_strings)) @@ -255,17 +247,24 @@ def arrays( attrs: st.SearchStrategy = attrs, zarr_formats: st.SearchStrategy = zarr_formats, ) -> Array: - store = draw(stores) - path = draw(paths) - name = draw(array_names) - attributes = draw(attrs) - zarr_format = draw(zarr_formats) + store = draw(stores, label="store") + path = draw(paths, label="array parent") + name = draw(array_names, label="array name") + attributes = draw(attrs, label="attributes") + zarr_format = draw(zarr_formats, label="zarr format") if arrays is None: - arrays = numpy_arrays(shapes=shapes, zarr_formats=st.just(zarr_format)) - nparray = draw(arrays) - chunk_shape = draw(chunk_shapes(shape=nparray.shape)) + arrays = numpy_arrays(shapes=shapes) + nparray = draw(arrays, label="array data") + chunk_shape = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") + extra_kwargs = {} if zarr_format == 3 and all(c > 0 for c in chunk_shape): - shard_shape = draw(st.none() | shard_shapes(shape=nparray.shape, chunk_shape=chunk_shape)) + shard_shape = draw( + st.none() | shard_shapes(shape=nparray.shape, chunk_shape=chunk_shape), + label="shard shape", + ) + extra_kwargs["dimension_names"] = draw( + dimension_names(ndim=nparray.ndim), label="dimension names" + ) else: shard_shape = None # test that None works too. @@ -286,6 +285,7 @@ def arrays( attributes=attributes, # compressor=compressor, # FIXME fill_value=fill_value, + **extra_kwargs, ) assert isinstance(a, Array) @@ -385,13 +385,19 @@ def orthogonal_indices( npindexer = [] ndim = len(shape) for axis, size in enumerate(shape): - val = draw( - npst.integer_array_indices( + if size != 0: + strategy = npst.integer_array_indices( shape=(size,), result_shape=npst.array_shapes(min_side=1, max_side=size, max_dims=1) - ) - | basic_indices(min_dims=1, shape=(size,), allow_ellipsis=False) - .map(lambda x: (x,) if not isinstance(x, tuple) else x) # bare ints, slices - .filter(bool) # skip empty tuple + ) | basic_indices(min_dims=1, shape=(size,), allow_ellipsis=False) + else: + strategy = basic_indices(min_dims=1, shape=(size,), allow_ellipsis=False) + + val = draw( + strategy + # bare ints, slices + .map(lambda x: (x,) if not isinstance(x, tuple) else x) + # skip empty tuple + .filter(bool) ) (idxr,) = val if isinstance(idxr, int): diff --git a/tests/test_properties.py b/tests/test_properties.py index b8d50ef0b1..27f847fa69 100644 --- a/tests/test_properties.py +++ b/tests/test_properties.py @@ -76,10 +76,10 @@ def deep_equal(a: Any, b: Any) -> bool: @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") -@given(data=st.data(), zarr_format=zarr_formats) -def test_array_roundtrip(data: st.DataObject, zarr_format: int) -> None: - nparray = data.draw(numpy_arrays(zarr_formats=st.just(zarr_format))) - zarray = data.draw(arrays(arrays=st.just(nparray), zarr_formats=st.just(zarr_format))) +@given(data=st.data()) +def test_array_roundtrip(data: st.DataObject) -> None: + nparray = data.draw(numpy_arrays()) + zarray = data.draw(arrays(arrays=st.just(nparray))) assert_array_equal(nparray, zarray[:]) From ea4d7e96c0738526bbf08bb99ed0ea23a6081836 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 11 Jul 2025 21:04:20 +0000 Subject: [PATCH 016/468] chore: update pre-commit hooks (#3213) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.9 → v0.12.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.9...v0.12.2) - [github.com/numpy/numpydoc: v1.8.0 → v1.9.0](https://github.com/numpy/numpydoc/compare/v1.8.0...v1.9.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 563c87aee0..97aefca6dd 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -49,7 +49,7 @@ repos: - id: rst-directive-colons - id: rst-inline-touching-normal - repo: https://github.com/numpy/numpydoc - rev: v1.8.0 + rev: v1.9.0 hooks: - id: numpydoc-validation - repo: https://github.com/twisted/towncrier From 455b4f962a1e4c5b395119409e0d065c5a9642f5 Mon Sep 17 00:00:00 2001 From: Lachlan Deakin Date: Sun, 13 Jul 2025 04:14:03 +1000 Subject: [PATCH 017/468] feat: add `from_array_metadata_and_store` to `CodecPipeline` (#3233) * feat: add `from_array_metadata_and_store` to `CodecPipeline` This enables fancy `CodecPipeline` implementations like `zarrs-python` to support a broader range of Zarr arrays and to construct store wrappers on initialisation. * make `store` keyword-only Co-authored-by: Davis Bennett * changelog --------- Co-authored-by: Davis Bennett --- changes/3233.feature.rst | 1 + src/zarr/abc/codec.py | 22 +++++++++++++++++++++- src/zarr/core/array.py | 16 ++++++++++++++-- 3 files changed, 36 insertions(+), 3 deletions(-) create mode 100644 changes/3233.feature.rst diff --git a/changes/3233.feature.rst b/changes/3233.feature.rst new file mode 100644 index 0000000000..bd20576689 --- /dev/null +++ b/changes/3233.feature.rst @@ -0,0 +1 @@ +Add an alternate `from_array_metadata_and_store` constructor to `CodecPipeline`. diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index d9e3520d42..f8a5447a70 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -12,11 +12,12 @@ from collections.abc import Awaitable, Callable, Iterable from typing import Self - from zarr.abc.store import ByteGetter, ByteSetter + from zarr.abc.store import ByteGetter, ByteSetter, Store from zarr.core.array_spec import ArraySpec from zarr.core.chunk_grids import ChunkGrid from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType from zarr.core.indexing import SelectorTuple + from zarr.core.metadata import ArrayMetadata __all__ = [ "ArrayArrayCodec", @@ -281,6 +282,25 @@ def from_codecs(cls, codecs: Iterable[Codec]) -> Self: """ ... + @classmethod + def from_array_metadata_and_store(cls, array_metadata: ArrayMetadata, store: Store) -> Self: + """Creates a codec pipeline from array metadata and a store path. + + Raises NotImplementedError by default, indicating the CodecPipeline must be created with from_codecs instead. + + Parameters + ---------- + array_metadata : ArrayMetadata + store : Store + + Returns + ------- + Self + """ + raise NotImplementedError( + f"'{type(cls).__name__}' does not implement CodecPipeline.from_array_metadata_and_store." + ) + @property @abstractmethod def supports_partial_decode(self) -> bool: ... diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index a4f7fc086a..42eba1ae9d 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -192,7 +192,15 @@ def parse_array_metadata(data: Any) -> ArrayMetadata: raise TypeError # pragma: no cover -def create_codec_pipeline(metadata: ArrayMetadata) -> CodecPipeline: +def create_codec_pipeline(metadata: ArrayMetadata, *, store: Store | None = None) -> CodecPipeline: + if store is not None: + try: + return get_pipeline_class().from_array_metadata_and_store( + array_metadata=metadata, store=store + ) + except NotImplementedError: + pass + if isinstance(metadata, ArrayV3Metadata): return get_pipeline_class().from_codecs(metadata.codecs) elif isinstance(metadata, ArrayV2Metadata): @@ -311,7 +319,11 @@ def __init__( object.__setattr__(self, "metadata", metadata_parsed) object.__setattr__(self, "store_path", store_path) object.__setattr__(self, "_config", config_parsed) - object.__setattr__(self, "codec_pipeline", create_codec_pipeline(metadata=metadata_parsed)) + object.__setattr__( + self, + "codec_pipeline", + create_codec_pipeline(metadata=metadata_parsed, store=store_path.store), + ) # this overload defines the function signature when zarr_format is 2 @overload From af76fba7b7bdbf8521091cc2aebfd810fb943841 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Brigitta=20Sip=C5=91cz?= Date: Mon, 14 Jul 2025 00:38:05 -0700 Subject: [PATCH 018/468] CI: update actions location (#3237) --- .github/workflows/hypothesis.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 96eaccbc6b..c3c8c946c0 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -87,7 +87,7 @@ jobs: && steps.status.outcome == 'failure' && github.event_name == 'schedule' && github.repository_owner == 'zarr-developers' - uses: xarray-contrib/issue-from-pytest-log@v1 + uses: scientific-python/issue-from-pytest-log-action@v1 with: log-path: output-${{ matrix.python-version }}-log.jsonl issue-title: "Nightly Hypothesis tests failed" From 2c871ae7b88919c16e2bf01787d471c065834747 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 14 Jul 2025 17:34:14 +0200 Subject: [PATCH 019/468] update release note (#3230) --- changes/2819.chore.rst | 20 +++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/changes/2819.chore.rst b/changes/2819.chore.rst index f9a3358309..7fa68f86ef 100644 --- a/changes/2819.chore.rst +++ b/changes/2819.chore.rst @@ -1,4 +1,18 @@ Ensure that invocations of ``create_array`` use consistent keyword arguments, with consistent defaults. -Specifically, ``zarr.api.synchronous.create_array`` now takes a ``write_data`` keyword argument; The -``create_array`` method on ``zarr.Group`` takes ``data`` and ``write_data`` keyword arguments. The ``fill_value`` -keyword argument of the various invocations of ``create_array`` has been consistently set to ``None``, where previously it was either ``None`` or ``0``. \ No newline at end of file + +- ``zarr.api.synchronous.create_array`` now takes a ``write_data`` keyword argument +- The ``Group.create_array`` method takes ``data`` and ``write_data`` keyword arguments. +- The functions ``api.asynchronous.create``, ``api.asynchronous.create_array`` + and the methods ``Group.create_array``, ``Group.array``, had the default + ``fill_value`` changed from ``0`` to the ``DEFAULT_FILL_VALUE`` value, which instructs Zarr to + use the default scalar value associated with the array's data type as the fill value. These are + all functions or methods for array creation that mirror, wrap or are wrapped by, another function + that already has a default ``fill_value`` set to ``DEFAULT_FILL_VALUE``. This change is necessary + to make these functions consistent across the entire codebase, but as this changes default values, + new data might have a different fill value than expected after this change. + + For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this + change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode + strings, the default fill value might be different after this change. Users who were relying on how + Zarr interpreted ``0`` as a non-numeric scalar value should set their desired fill value explicitly + after this change. From 2f64d670098b6f06f6c752c40dee481858bbfb62 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 14 Jul 2025 17:49:20 +0200 Subject: [PATCH 020/468] update release note for dtype refactor (#3229) * update release note for dtype refactor * public API for getting the zarr v3 name * clarify that to_json(zarr_format=3) might return a string --- changes/2874.feature.rst | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/changes/2874.feature.rst b/changes/2874.feature.rst index 4c50532ae0..093f566f74 100644 --- a/changes/2874.feature.rst +++ b/changes/2874.feature.rst @@ -1,9 +1,20 @@ -Adds zarr-specific data type classes. This replaces the internal use of numpy data types for zarr -v2 and a fixed set of string enums for zarr v3. This change is largely internal, but it does -change the type of the ``dtype`` and ``data_type`` fields on the ``ArrayV2Metadata`` and -``ArrayV3Metadata`` classes. It also changes the JSON metadata representation of the -variable-length string data type, but the old metadata representation can still be -used when reading arrays. The logic for automatically choosing the chunk encoding for a given data -type has also changed, and this necessitated changes to the ``config`` API. +Adds zarr-specific data type classes. + +This change adds a ``ZDType`` base class for Zarr V2 and Zarr V3 data types. Child classes are +defined for each NumPy data type. Each child class defines routines for ``JSON`` serialization. +New data types can be created and registered dynamically. + +Prior to this change, Zarr Python had two streams for handling data types. For Zarr V2 arrays, +we used NumPy data type identifiers. For Zarr V3 arrays, we used a fixed set of string enums. Both +of these systems proved hard to extend. + +This change is largely internal, but it does change the type of the ``dtype`` and ``data_type`` +fields on the ``ArrayV2Metadata`` and ``ArrayV3Metadata`` classes. Previously, ``ArrayV2Metadata.dtype`` +was a NumPy ``dtype`` object, and ``ArrayV3Metadata.data_type`` was an internally-defined ``enum``. +After this change, both ``ArrayV2Metadata.dtype`` and ``ArrayV3Metadata.data_type`` are instances of +``ZDType``. A NumPy data type can be generated from a ``ZDType`` via the ``ZDType.to_native_dtype()`` +method. The internally-defined Zarr V3 ``enum`` class is gone entirely, but the ``ZDType.to_json(zarr_format=3)`` +method can be used to generate either a string, or dictionary that has a string ``name`` field, that +represents the string value previously associated with that ``enum``. For more on this new feature, see the `documentation `_ \ No newline at end of file From b267ff66f76f8344fcb29f92972604a947869f75 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 14 Jul 2025 18:08:14 +0200 Subject: [PATCH 021/468] remove usage of the _deprecate_positional_args decorator, and tests for its behavior (#3225) --- src/zarr/api/synchronous.py | 5 ----- src/zarr/core/array.py | 13 ----------- src/zarr/core/group.py | 11 --------- tests/test_api.py | 41 +++------------------------------ tests/test_array.py | 45 ------------------------------------- tests/test_group.py | 20 ----------------- tests/test_sync.py | 7 ------ 7 files changed, 3 insertions(+), 139 deletions(-) diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 92b80b1ac8..4ce02e7b6d 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -6,7 +6,6 @@ import zarr.api.asynchronous as async_api import zarr.core.array -from zarr._compat import _deprecate_positional_args from zarr.core.array import DEFAULT_FILL_VALUE, Array, AsyncArray, CompressorLike from zarr.core.group import Group from zarr.core.sync import sync @@ -160,7 +159,6 @@ def load( ) -@_deprecate_positional_args def open( store: StoreLike | None = None, *, @@ -255,7 +253,6 @@ def save( ) -@_deprecate_positional_args def save_array( store: StoreLike, arr: NDArrayLike, @@ -387,7 +384,6 @@ def array(data: npt.ArrayLike | Array, **kwargs: Any) -> Array: return Array(sync(async_api.array(data=data, **kwargs))) -@_deprecate_positional_args def group( store: StoreLike | None = None, *, @@ -455,7 +451,6 @@ def group( ) -@_deprecate_positional_args def open_group( store: StoreLike | None = None, *, diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 42eba1ae9d..a0b8e9e7dd 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -25,7 +25,6 @@ from typing_extensions import deprecated import zarr -from zarr._compat import _deprecate_positional_args from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec from zarr.abc.store import Store, set_or_delete from zarr.codecs._v2 import V2Codec @@ -442,7 +441,6 @@ async def create( @classmethod @deprecated("Use zarr.api.asynchronous.create_array instead.") - @_deprecate_positional_args async def create( cls, store: StoreLike, @@ -1794,7 +1792,6 @@ class Array: @classmethod @deprecated("Use zarr.create_array instead.") - @_deprecate_positional_args def create( cls, store: StoreLike, @@ -2607,7 +2604,6 @@ def __setitem__(self, selection: Selection, value: npt.ArrayLike) -> None: else: self.set_basic_selection(cast("BasicSelection", pure_selection), value, fields=fields) - @_deprecate_positional_args def get_basic_selection( self, selection: BasicSelection = Ellipsis, @@ -2731,7 +2727,6 @@ def get_basic_selection( ) ) - @_deprecate_positional_args def set_basic_selection( self, selection: BasicSelection, @@ -2827,7 +2822,6 @@ def set_basic_selection( indexer = BasicIndexer(selection, self.shape, self.metadata.chunk_grid) sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) - @_deprecate_positional_args def get_orthogonal_selection( self, selection: OrthogonalSelection, @@ -2952,7 +2946,6 @@ def get_orthogonal_selection( ) ) - @_deprecate_positional_args def set_orthogonal_selection( self, selection: OrthogonalSelection, @@ -3063,7 +3056,6 @@ def set_orthogonal_selection( self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype) ) - @_deprecate_positional_args def get_mask_selection( self, mask: MaskSelection, @@ -3146,7 +3138,6 @@ def get_mask_selection( ) ) - @_deprecate_positional_args def set_mask_selection( self, mask: MaskSelection, @@ -3225,7 +3216,6 @@ def set_mask_selection( indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid) sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) - @_deprecate_positional_args def get_coordinate_selection( self, selection: CoordinateSelection, @@ -3315,7 +3305,6 @@ def get_coordinate_selection( out_array = np.array(out_array).reshape(indexer.sel_shape) return out_array - @_deprecate_positional_args def set_coordinate_selection( self, selection: CoordinateSelection, @@ -3413,7 +3402,6 @@ def set_coordinate_selection( sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) - @_deprecate_positional_args def get_block_selection( self, selection: BasicSelection, @@ -3512,7 +3500,6 @@ def get_block_selection( ) ) - @_deprecate_positional_args def set_block_selection( self, selection: BasicSelection, diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 0f57495e61..e02d09694f 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -15,7 +15,6 @@ from typing_extensions import deprecated import zarr.api.asynchronous as async_api -from zarr._compat import _deprecate_positional_args from zarr.abc.metadata import Metadata from zarr.abc.store import Store, set_or_delete from zarr.core._info import GroupInfo @@ -2417,7 +2416,6 @@ def create(self, *args: Any, **kwargs: Any) -> Array: # Backwards compatibility for 2.x return self.create_array(*args, **kwargs) - @_deprecate_positional_args def create_array( self, name: str, @@ -2635,7 +2633,6 @@ def require_array(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs))) - @_deprecate_positional_args def empty(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """Create an empty array with the specified shape in this Group. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -2657,7 +2654,6 @@ def empty(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.empty(name=name, shape=shape, **kwargs))) - @_deprecate_positional_args def zeros(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """Create an array, with zero being used as the default value for uninitialized portions of the array. @@ -2677,7 +2673,6 @@ def zeros(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.zeros(name=name, shape=shape, **kwargs))) - @_deprecate_positional_args def ones(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """Create an array, with one being used as the default value for uninitialized portions of the array. @@ -2697,7 +2692,6 @@ def ones(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.ones(name=name, shape=shape, **kwargs))) - @_deprecate_positional_args def full( self, *, name: str, shape: ChunkCoords, fill_value: Any | None, **kwargs: Any ) -> Array: @@ -2725,7 +2719,6 @@ def full( ) ) - @_deprecate_positional_args def empty_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: """Create an empty sub-array like `data`. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -2752,7 +2745,6 @@ def empty_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> """ return Array(self._sync(self._async_group.empty_like(name=name, data=data, **kwargs))) - @_deprecate_positional_args def zeros_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: """Create a sub-array of zeros like `data`. @@ -2773,7 +2765,6 @@ def zeros_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> return Array(self._sync(self._async_group.zeros_like(name=name, data=data, **kwargs))) - @_deprecate_positional_args def ones_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: """Create a sub-array of ones like `data`. @@ -2793,7 +2784,6 @@ def ones_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> A """ return Array(self._sync(self._async_group.ones_like(name=name, data=data, **kwargs))) - @_deprecate_positional_args def full_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: """Create a sub-array like `data` filled with the `fill_value` of `data` . @@ -2823,7 +2813,6 @@ def move(self, source: str, dest: str) -> None: return self._sync(self._async_group.move(source, dest)) @deprecated("Use Group.create_array instead.") - @_deprecate_positional_args def array( self, name: str, diff --git a/tests/test_api.py b/tests/test_api.py index b4f25a375e..ea0f62efa2 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -16,7 +16,6 @@ from zarr.core.common import JSON, MemoryOrder, ZarrFormat import contextlib -import warnings from typing import Literal import numpy as np @@ -263,7 +262,7 @@ def test_save_errors() -> None: save_group("data/group.zarr") with pytest.raises(TypeError): # no array provided - save_array("data/group.zarr") + save_array("data/group.zarr") # type: ignore[call-arg] with pytest.raises(ValueError): # no arrays provided save("data/group.zarr") @@ -1116,40 +1115,6 @@ def test_tree() -> None: # copy(source["foo"], dest, dry_run=True, log=True) -def test_open_positional_args_deprecated() -> None: - store = MemoryStore() - with pytest.warns(FutureWarning, match="pass"): - zarr.api.synchronous.open(store, "w", shape=(1,)) - - -def test_save_array_positional_args_deprecated() -> None: - store = MemoryStore() - with warnings.catch_warnings(): - warnings.filterwarnings( - "ignore", message="zarr_version is deprecated", category=DeprecationWarning - ) - with pytest.warns(FutureWarning, match="pass"): - save_array( - store, - np.ones( - 1, - ), - 3, - ) - - -def test_group_positional_args_deprecated() -> None: - store = MemoryStore() - with pytest.warns(FutureWarning, match="pass"): - group(store, True) - - -def test_open_group_positional_args_deprecated() -> None: - store = MemoryStore() - with pytest.warns(FutureWarning, match="pass"): - open_group(store, "w") - - def test_open_falls_back_to_open_group() -> None: # https://github.com/zarr-developers/zarr-python/issues/2309 store = MemoryStore() @@ -1180,9 +1145,9 @@ def test_open_modes_creates_group(tmp_path: pathlib.Path, mode: str) -> None: if mode in ["r", "r+"]: # Expect FileNotFoundError to be raised if 'r' or 'r+' mode with pytest.raises(FileNotFoundError): - zarr.open(store=zarr_dir, mode=mode) + zarr.open(store=zarr_dir, mode=mode) # type: ignore[arg-type] else: - group = zarr.open(store=zarr_dir, mode=mode) + group = zarr.open(store=zarr_dir, mode=mode) # type: ignore[arg-type] assert isinstance(group, Group) diff --git a/tests/test_array.py b/tests/test_array.py index 4783bca05c..c4201b4548 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -39,7 +39,6 @@ default_serializer_v3, ) from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, default_buffer_prototype -from zarr.core.buffer.cpu import NDBuffer from zarr.core.chunk_grids import _auto_partition from zarr.core.chunk_key_encodings import ChunkKeyEncodingParams from zarr.core.common import JSON, MemoryOrder, ZarrFormat @@ -257,50 +256,6 @@ def test_array_v3_fill_value(store: MemoryStore, fill_value: int, dtype_str: str assert arr.fill_value.dtype == arr.dtype -async def test_create_deprecated() -> None: - with pytest.warns(DeprecationWarning): - with pytest.warns(FutureWarning, match=re.escape("Pass shape=(2, 2) as keyword args")): - await zarr.AsyncArray.create(MemoryStore(), (2, 2), dtype="f8") # type: ignore[call-overload] - with pytest.warns(DeprecationWarning): - with pytest.warns(FutureWarning, match=re.escape("Pass shape=(2, 2) as keyword args")): - zarr.Array.create(MemoryStore(), (2, 2), dtype="f8") - - -def test_selection_positional_args_deprecated() -> None: - store = MemoryStore() - arr = zarr.create_array(store, shape=(2, 2), dtype="f8") - - with pytest.warns(FutureWarning, match="Pass out"): - arr.get_basic_selection(..., NDBuffer(array=np.empty((2, 2)))) - - with pytest.warns(FutureWarning, match="Pass fields"): - arr.set_basic_selection(..., 1, None) - - with pytest.warns(FutureWarning, match="Pass out"): - arr.get_orthogonal_selection(..., NDBuffer(array=np.empty((2, 2)))) - - with pytest.warns(FutureWarning, match="Pass"): - arr.set_orthogonal_selection(..., 1, None) - - with pytest.warns(FutureWarning, match="Pass"): - arr.get_mask_selection(np.zeros((2, 2), dtype=bool), NDBuffer(array=np.empty((0,)))) - - with pytest.warns(FutureWarning, match="Pass"): - arr.set_mask_selection(np.zeros((2, 2), dtype=bool), 1, None) - - with pytest.warns(FutureWarning, match="Pass"): - arr.get_coordinate_selection(([0, 1], [0, 1]), NDBuffer(array=np.empty((2,)))) - - with pytest.warns(FutureWarning, match="Pass"): - arr.set_coordinate_selection(([0, 1], [0, 1]), 1, None) - - with pytest.warns(FutureWarning, match="Pass"): - arr.get_block_selection((0, slice(None)), NDBuffer(array=np.empty((2, 2)))) - - with pytest.warns(FutureWarning, match="Pass"): - arr.set_block_selection((0, slice(None)), 1, None) - - @pytest.mark.parametrize("store", ["memory"], indirect=True) async def test_array_v3_nan_fill_value(store: MemoryStore) -> None: shape = (10,) diff --git a/tests/test_group.py b/tests/test_group.py index ee2317ade4..56590f7b6f 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -1446,26 +1446,6 @@ def test_update_attrs() -> None: assert root.attrs["foo"] == "bar" -@pytest.mark.parametrize("method", ["empty", "zeros", "ones", "full"]) -def test_group_deprecated_positional_args(method: str) -> None: - if method == "full": - kwargs = {"fill_value": 0} - else: - kwargs = {} - - root = zarr.group() - with pytest.warns(FutureWarning, match=r"Pass name=.* as keyword args."): - arr = getattr(root, method)("foo", shape=1, **kwargs) - assert arr.shape == (1,) - - method += "_like" - data = np.ones(1) - - with pytest.warns(FutureWarning, match=r"Pass name=.*, data=.* as keyword args."): - arr = getattr(root, method)("foo_like", data, **kwargs) - assert arr.shape == data.shape - - @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) def test_delitem_removes_children(store: Store, zarr_format: ZarrFormat) -> None: # https://github.com/zarr-developers/zarr-python/issues/2191 diff --git a/tests/test_sync.py b/tests/test_sync.py index 13b475f8da..c5eadb0f4f 100644 --- a/tests/test_sync.py +++ b/tests/test_sync.py @@ -15,7 +15,6 @@ loop, sync, ) -from zarr.storage import MemoryStore @pytest.fixture(params=[True, False]) @@ -143,12 +142,6 @@ def bar(self) -> list[int]: assert foo.bar() == list(range(10)) -def test_open_positional_args_deprecate(): - store = MemoryStore() - with pytest.warns(FutureWarning, match="pass"): - zarr.open(store, "w", shape=(1,)) - - @pytest.mark.parametrize("workers", [None, 1, 2]) def test_threadpool_executor(clean_state, workers: int | None) -> None: with zarr.config.set({"threading.max_workers": workers}): From 2331b991aed521dbe137eff191561d0bfa5c5feb Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 14 Jul 2025 20:05:08 +0200 Subject: [PATCH 022/468] fix type hints for hypothesis test (#3240) --- src/zarr/testing/strategies.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 27f648826d..d0726c3dd9 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -256,15 +256,13 @@ def arrays( arrays = numpy_arrays(shapes=shapes) nparray = draw(arrays, label="array data") chunk_shape = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") - extra_kwargs = {} + dim_names: None | list[str | None] = None if zarr_format == 3 and all(c > 0 for c in chunk_shape): shard_shape = draw( st.none() | shard_shapes(shape=nparray.shape, chunk_shape=chunk_shape), label="shard shape", ) - extra_kwargs["dimension_names"] = draw( - dimension_names(ndim=nparray.ndim), label="dimension names" - ) + dim_names = draw(dimension_names(ndim=nparray.ndim), label="dimension names") else: shard_shape = None # test that None works too. @@ -285,7 +283,7 @@ def arrays( attributes=attributes, # compressor=compressor, # FIXME fill_value=fill_value, - **extra_kwargs, + dimension_names=dim_names, ) assert isinstance(a, Array) From cea611b921882fc03203ab6e0c56c108c347d324 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 14 Jul 2025 21:26:46 +0200 Subject: [PATCH 023/468] fix obstore type hints (#3242) * liberally add type:ignores to appease mypy * ok remove the type:ignore statements --- src/zarr/storage/_obstore.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index 1b822a919e..cbe037d86b 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -16,7 +16,7 @@ from zarr.core.config import config if TYPE_CHECKING: - from collections.abc import AsyncGenerator, Coroutine, Iterable + from collections.abc import AsyncGenerator, Coroutine, Iterable, Sequence from typing import Any from obstore import ListResult, ListStream, ObjectMeta, OffsetRange, SuffixRange @@ -216,14 +216,14 @@ def list(self) -> AsyncGenerator[str, None]: # docstring inherited import obstore as obs - objects: ListStream[list[ObjectMeta]] = obs.list(self.store) + objects: ListStream[Sequence[ObjectMeta]] = obs.list(self.store) return _transform_list(objects) def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]: # docstring inherited import obstore as obs - objects: ListStream[list[ObjectMeta]] = obs.list(self.store, prefix=prefix) + objects: ListStream[Sequence[ObjectMeta]] = obs.list(self.store, prefix=prefix) return _transform_list(objects) def list_dir(self, prefix: str) -> AsyncGenerator[str, None]: @@ -235,7 +235,7 @@ def list_dir(self, prefix: str) -> AsyncGenerator[str, None]: async def _transform_list( - list_stream: ListStream[list[ObjectMeta]], + list_stream: ListStream[Sequence[ObjectMeta]], ) -> AsyncGenerator[str, None]: """ Transform the result of list into an async generator of paths. @@ -246,7 +246,8 @@ async def _transform_list( async def _transform_list_dir( - list_result_coroutine: Coroutine[Any, Any, ListResult[list[ObjectMeta]]], prefix: str + list_result_coroutine: Coroutine[Any, Any, ListResult[Sequence[ObjectMeta]]], + prefix: str, ) -> AsyncGenerator[str, None]: """ Transform the result of list_with_delimiter into an async generator of paths. From 23010da88ce847753685a9c2620d4a7d49deeb78 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 14 Jul 2025 22:33:59 +0200 Subject: [PATCH 024/468] don't test self-deletion in stateful tests (#3243) * don't test self-deletion * don't alias * add explanatory comment --- src/zarr/testing/stateful.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index 6faf5dc6d3..8f946159a6 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -343,9 +343,10 @@ def delete_array_using_del(self, data: DataObject) -> None: @precondition(lambda self: len(self.all_groups) >= 2) # fixme don't delete root @rule(data=st.data()) def delete_group_using_del(self, data: DataObject) -> None: - group_path = data.draw( - st.sampled_from(sorted(self.all_groups)), label="Group deletion target" - ) + # ensure that we don't include the root group in the list of member names that we try + # to delete + member_names = tuple(filter(lambda v: "/" in v, sorted(self.all_groups))) + group_path = data.draw(st.sampled_from(member_names), label="Group deletion target") prefix, group_name = split_prefix_name(group_path) note(f"Deleting group '{group_path=!r}', {prefix=!r}, {group_name=!r} using delete") members = zarr.open_group(store=self.model, path=group_path).members(max_depth=None) From 2420f9e2f00687af9f6cd406b6734d7b261349ed Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 15 Jul 2025 09:33:23 +0200 Subject: [PATCH 025/468] 3.1.0 release notes (#3241) * complete partial release note * build release notes * add release note for #3225 * clarify keyword only changes --- changes/2871.feature.rst | 8 ---- changes/2874.feature.rst | 20 -------- changes/3157.doc.rst | 2 - changes/3170.bugfix.rst | 6 --- changes/3190.bugfix.rst | 1 - changes/3191.feature.rst | 1 - changes/3198.bugfix.rst | 4 -- changes/3212.doc.rst | 4 -- changes/3228.removal.rst | 16 ------- changes/3232.bugfix.rst | 3 -- changes/3233.feature.rst | 1 - changes/xxxx.feature.rst | 1 - docs/release-notes.rst | 98 ++++++++++++++++++++++++++++++++++++++++ 13 files changed, 98 insertions(+), 67 deletions(-) delete mode 100644 changes/2871.feature.rst delete mode 100644 changes/2874.feature.rst delete mode 100644 changes/3157.doc.rst delete mode 100644 changes/3170.bugfix.rst delete mode 100644 changes/3190.bugfix.rst delete mode 100644 changes/3191.feature.rst delete mode 100644 changes/3198.bugfix.rst delete mode 100644 changes/3212.doc.rst delete mode 100644 changes/3228.removal.rst delete mode 100644 changes/3232.bugfix.rst delete mode 100644 changes/3233.feature.rst delete mode 100644 changes/xxxx.feature.rst diff --git a/changes/2871.feature.rst b/changes/2871.feature.rst deleted file mode 100644 index a39f30c558..0000000000 --- a/changes/2871.feature.rst +++ /dev/null @@ -1,8 +0,0 @@ -Added public API for Buffer ABCs and implementations. - -Use :mod:`zarr.buffer` to access buffer implementations, and -:mod:`zarr.abc.buffer` for the interface to implement new buffer types. - -Users previously importing buffer from ``zarr.core.buffer`` should update their -imports to use :mod:`zarr.buffer`. As a reminder, all of ``zarr.core`` is -considered a private API that's not covered by zarr-python's versioning policy. \ No newline at end of file diff --git a/changes/2874.feature.rst b/changes/2874.feature.rst deleted file mode 100644 index 093f566f74..0000000000 --- a/changes/2874.feature.rst +++ /dev/null @@ -1,20 +0,0 @@ -Adds zarr-specific data type classes. - -This change adds a ``ZDType`` base class for Zarr V2 and Zarr V3 data types. Child classes are -defined for each NumPy data type. Each child class defines routines for ``JSON`` serialization. -New data types can be created and registered dynamically. - -Prior to this change, Zarr Python had two streams for handling data types. For Zarr V2 arrays, -we used NumPy data type identifiers. For Zarr V3 arrays, we used a fixed set of string enums. Both -of these systems proved hard to extend. - -This change is largely internal, but it does change the type of the ``dtype`` and ``data_type`` -fields on the ``ArrayV2Metadata`` and ``ArrayV3Metadata`` classes. Previously, ``ArrayV2Metadata.dtype`` -was a NumPy ``dtype`` object, and ``ArrayV3Metadata.data_type`` was an internally-defined ``enum``. -After this change, both ``ArrayV2Metadata.dtype`` and ``ArrayV3Metadata.data_type`` are instances of -``ZDType``. A NumPy data type can be generated from a ``ZDType`` via the ``ZDType.to_native_dtype()`` -method. The internally-defined Zarr V3 ``enum`` class is gone entirely, but the ``ZDType.to_json(zarr_format=3)`` -method can be used to generate either a string, or dictionary that has a string ``name`` field, that -represents the string value previously associated with that ``enum``. - -For more on this new feature, see the `documentation `_ \ No newline at end of file diff --git a/changes/3157.doc.rst b/changes/3157.doc.rst deleted file mode 100644 index 6132b195ec..0000000000 --- a/changes/3157.doc.rst +++ /dev/null @@ -1,2 +0,0 @@ -Add a self-contained example of data type extension to the ``examples`` directory, and expanded -the documentation for data types. \ No newline at end of file diff --git a/changes/3170.bugfix.rst b/changes/3170.bugfix.rst deleted file mode 100644 index 856e8356bb..0000000000 --- a/changes/3170.bugfix.rst +++ /dev/null @@ -1,6 +0,0 @@ -Fixes a variety of issues related to string data types. - -- Brings the ``VariableLengthUTF8`` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8 -- Disallows creation of 0-length fixed-length data types -- Adds a regression test for the ``VariableLengthUTF8`` data type that checks against version 3.0.8 -- Allows users to request the ``VariableLengthUTF8`` data type with ``str``, ``"str"``, or ``"string"``. diff --git a/changes/3190.bugfix.rst b/changes/3190.bugfix.rst deleted file mode 100644 index 4e948188e3..0000000000 --- a/changes/3190.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Add human readable size for No. bytes stored to `info_complete` \ No newline at end of file diff --git a/changes/3191.feature.rst b/changes/3191.feature.rst deleted file mode 100644 index 7542eab4f0..0000000000 --- a/changes/3191.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Added `NDBuffer.empty` method for faster ndbuffer initialization. diff --git a/changes/3198.bugfix.rst b/changes/3198.bugfix.rst deleted file mode 100644 index 840996641c..0000000000 --- a/changes/3198.bugfix.rst +++ /dev/null @@ -1,4 +0,0 @@ -Restores the ability to create a Zarr V2 array with a ``null`` fill value by introducing a new -class ``DefaultFillValue``, and setting the default value of the ``fill_value`` parameter in array -creation routines to an instance of ``DefaultFillValue``. For Zarr V3 arrays, ``None`` will act as an -alias for a ``DefaultFillValue`` instance, thus preserving compatibility with existing code. \ No newline at end of file diff --git a/changes/3212.doc.rst b/changes/3212.doc.rst deleted file mode 100644 index 1754d18c92..0000000000 --- a/changes/3212.doc.rst +++ /dev/null @@ -1,4 +0,0 @@ -- Add a description on how to create a RemoteStore of a specific filesystem to the `Remote Store` section in `docs\user-guide\storage.rst`. -- State in the docstring of `FsspecStore.from_url` that the filesystem type is inferred from the URL scheme. - -It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. \ No newline at end of file diff --git a/changes/3228.removal.rst b/changes/3228.removal.rst deleted file mode 100644 index 0463897755..0000000000 --- a/changes/3228.removal.rst +++ /dev/null @@ -1,16 +0,0 @@ -Removes default chunk encoding settings (filters, serializer, compressors) from the global -configuration object. - -This removal is justified on the basis that storing chunk encoding settings in the config required -a brittle, confusing, and inaccurate categorization of array data types, which was particularly -unsuitable after the recent addition of new data types that didn't fit naturally into the -pre-existing categories. - -The default chunk encoding is the same (Zstandard compression, and the required object codecs for -variable length data types), but the chunk encoding is now generated by functions that cannot be -reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should -instead specify the desired chunk encoding explicitly when creating an array. - -This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that -arrays with a ``VariableLengthUTF8`` or ``VariableLengthBytes`` data type cannot be created without the -correct "object codec". diff --git a/changes/3232.bugfix.rst b/changes/3232.bugfix.rst deleted file mode 100644 index e777103c83..0000000000 --- a/changes/3232.bugfix.rst +++ /dev/null @@ -1,3 +0,0 @@ -Fix the type of ``ArrayV2Metadata.codec`` to constrain it to ``numcodecs.abc.Codec | None``. -Previously the type was more permissive, allowing objects that can be parsed into Codecs (e.g., the codec name). -The constructor of ``ArrayV2Metadata`` still allows the permissive input when creating new objects. diff --git a/changes/3233.feature.rst b/changes/3233.feature.rst deleted file mode 100644 index bd20576689..0000000000 --- a/changes/3233.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Add an alternate `from_array_metadata_and_store` constructor to `CodecPipeline`. diff --git a/changes/xxxx.feature.rst b/changes/xxxx.feature.rst deleted file mode 100644 index 1219900cb7..0000000000 --- a/changes/xxxx.feature.rst +++ /dev/null @@ -1 +0,0 @@ -The minimum version of NumPy has increased to 1.26. diff --git a/docs/release-notes.rst b/docs/release-notes.rst index 8c51250fed..700be6b578 100644 --- a/docs/release-notes.rst +++ b/docs/release-notes.rst @@ -3,6 +3,104 @@ Release notes .. towncrier release notes start +3.1.0 (2025-07-14) +------------------ + +Features +~~~~~~~~ + +- Added public API for Buffer ABCs and implementations. + + Use :mod:`zarr.buffer` to access buffer implementations, and + :mod:`zarr.abc.buffer` for the interface to implement new buffer types. + + Users previously importing buffer from ``zarr.core.buffer`` should update their + imports to use :mod:`zarr.buffer`. As a reminder, all of ``zarr.core`` is + considered a private API that's not covered by zarr-python's versioning policy. (:issue:`2871`) +- Adds zarr-specific data type classes. + + This change adds a ``ZDType`` base class for Zarr V2 and Zarr V3 data types. Child classes are + defined for each NumPy data type. Each child class defines routines for ``JSON`` serialization. + New data types can be created and registered dynamically. + + Prior to this change, Zarr Python had two streams for handling data types. For Zarr V2 arrays, + we used NumPy data type identifiers. For Zarr V3 arrays, we used a fixed set of string enums. Both + of these systems proved hard to extend. + + This change is largely internal, but it does change the type of the ``dtype`` and ``data_type`` + fields on the ``ArrayV2Metadata`` and ``ArrayV3Metadata`` classes. Previously, ``ArrayV2Metadata.dtype`` + was a NumPy ``dtype`` object, and ``ArrayV3Metadata.data_type`` was an internally-defined ``enum``. + After this change, both ``ArrayV2Metadata.dtype`` and ``ArrayV3Metadata.data_type`` are instances of + ``ZDType``. A NumPy data type can be generated from a ``ZDType`` via the ``ZDType.to_native_dtype()`` + method. The internally-defined Zarr V3 ``enum`` class is gone entirely, but the ``ZDType.to_json(zarr_format=3)`` + method can be used to generate either a string, or dictionary that has a string ``name`` field, that + represents the string value previously associated with that ``enum``. + + For more on this new feature, see the `documentation `_ (:issue:`2874`) +- Added `NDBuffer.empty` method for faster ndbuffer initialization. (:issue:`3191`) +- The minimum version of NumPy has increased to 1.26. (:issue:`3226`) +- Add an alternate `from_array_metadata_and_store` constructor to `CodecPipeline`. (:issue:`3233`) + + +Bugfixes +~~~~~~~~ + +- Fixes a variety of issues related to string data types. + + - Brings the ``VariableLengthUTF8`` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8 + - Disallows creation of 0-length fixed-length data types + - Adds a regression test for the ``VariableLengthUTF8`` data type that checks against version 3.0.8 + - Allows users to request the ``VariableLengthUTF8`` data type with ``str``, ``"str"``, or ``"string"``. (:issue:`3170`) +- Add human readable size for No. bytes stored to `info_complete` (:issue:`3190`) +- Restores the ability to create a Zarr V2 array with a ``null`` fill value by introducing a new + class ``DefaultFillValue``, and setting the default value of the ``fill_value`` parameter in array + creation routines to an instance of ``DefaultFillValue``. For Zarr V3 arrays, ``None`` will act as an + alias for a ``DefaultFillValue`` instance, thus preserving compatibility with existing code. (:issue:`3198`) +- Fix the type of ``ArrayV2Metadata.codec`` to constrain it to ``numcodecs.abc.Codec | None``. + Previously the type was more permissive, allowing objects that can be parsed into Codecs (e.g., the codec name). + The constructor of ``ArrayV2Metadata`` still allows the permissive input when creating new objects. (:issue:`3232`) + + +Improved Documentation +~~~~~~~~~~~~~~~~~~~~~~ + +- Add a self-contained example of data type extension to the ``examples`` directory, and expanded + the documentation for data types. (:issue:`3157`) +- - Add a description on how to create a RemoteStore of a specific filesystem to the `Remote Store` section in `docs\user-guide\storage.rst`. + - State in the docstring of `FsspecStore.from_url` that the filesystem type is inferred from the URL scheme. + + It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. (:issue:`3212`) + + +Deprecations and Removals +~~~~~~~~~~~~~~~~~~~~~~~~~ + +- Removes default chunk encoding settings (filters, serializer, compressors) from the global + configuration object. + + This removal is justified on the basis that storing chunk encoding settings in the config required + a brittle, confusing, and inaccurate categorization of array data types, which was particularly + unsuitable after the recent addition of new data types that didn't fit naturally into the + pre-existing categories. + + The default chunk encoding is the same (Zstandard compression, and the required object codecs for + variable length data types), but the chunk encoding is now generated by functions that cannot be + reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should + instead specify the desired chunk encoding explicitly when creating an array. + + This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that + arrays with a ``VariableLengthUTF8`` or ``VariableLengthBytes`` data type cannot be created without the + correct "object codec". (:issue:`3228`) +- Removes support for passing keyword-only arguments positionally to the following functions and methods: + ``save_array``, ``open``, ``group``, ``open_group``, ``create``, ``get_basic_selection``, ``set_basic_selection``, + ``get_orthogonal_selection``, ``set_orthogonal_selection``, ``get_mask_selection``, ``set_mask_selection``, + ``get_coordinate_selection``, ``set_coordinate_selection``, ``get_block_selection``, ``set_block_selection``, + ``Group.create_array``, ``Group.empty``, ``Group.zeroes``, ``Group.ones``, ``Group.empty_like``, ``Group.full``, + ``Group.zeros_like``, ``Group.ones_like``, ``Group.full_like``, ``Group.array``. Prior to this change, + passing a keyword-only argument positionally to one of these functions or methods would raise a + deprecation warning. That warning is now gone. Passing keyword-only arguments to these functions + and methods positionally is now an error. + 3.0.10 (2025-07-03) ------------------- From be0963f4a10f69a744ae6ace9e73c00d71b588bc Mon Sep 17 00:00:00 2001 From: ARYAN RAJ Date: Wed, 16 Jul 2025 13:07:15 +0530 Subject: [PATCH 026/468] Remove outdated v3 release announcement bullet from release notes (#3235) * Remove outdated v3 release announcement bullet from release notes * docs: remove outdated release announcement from docs * Restore changelog entry as requested --------- Co-authored-by: Davis Bennett --- docs/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 61d83ef819..05d89a1dcc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -178,7 +178,6 @@ def skip_submodules( ], "collapse_navigation": True, "navigation_with_keys": False, - "announcement": "Zarr-Python 3 is here! Check out the release announcement here.", } # Add any paths that contain custom themes here, relative to this directory. From 8bf006108aad490716854a639e863c5983907684 Mon Sep 17 00:00:00 2001 From: "Christine P. Chai" Date: Wed, 16 Jul 2025 01:41:56 -0700 Subject: [PATCH 027/468] DOC: Remove Twitter icon in Zarr-Python (#3245) * DOC: Remove Twitter icon in Zarr-Python * Added Bluesky and Mastodon icon links --------- Co-authored-by: Davis Bennett --- docs/conf.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 05d89a1dcc..803d2c4255 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -167,8 +167,17 @@ def skip_submodules( # documentation. html_theme_options = { "github_url": "https://github.com/zarr-developers/zarr-python", - "twitter_url": "https://twitter.com/zarr_dev", "icon_links": [ + { + "name": "Bluesky", + "url": "https://bsky.app/profile/zarr.dev", + "icon": "fa-brands fa-bluesky", + }, + { + "name": "Mastodon", + "url": "https://fosstodon.org/@zarr", + "icon": "fa-brands fa-mastodon", + }, { "name": "Zarr Dev", "url": "https://zarr.dev/", From 5e8b02a721921ea950b00fb0cb82ccf58b081f16 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 16 Jul 2025 10:54:50 +0200 Subject: [PATCH 028/468] Multiple imports for an import name (#3234) Co-authored-by: Davis Bennett --- tests/package_with_entrypoint/__init__.py | 4 ++-- tests/test_api.py | 27 +++++++++-------------- 2 files changed, 12 insertions(+), 19 deletions(-) diff --git a/tests/package_with_entrypoint/__init__.py b/tests/package_with_entrypoint/__init__.py index e0d8a52c4d..ae86378cb5 100644 --- a/tests/package_with_entrypoint/__init__.py +++ b/tests/package_with_entrypoint/__init__.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Any, Literal, Self +from typing import TYPE_CHECKING import numpy as np import numpy.typing as npt @@ -14,7 +14,7 @@ if TYPE_CHECKING: from collections.abc import Iterable - from typing import ClassVar, Literal + from typing import Any, ClassVar, Literal, Self from zarr.core.array_spec import ArraySpec from zarr.core.common import ZarrFormat diff --git a/tests/test_api.py b/tests/test_api.py index ea0f62efa2..0f71bfa94f 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1,7 +1,6 @@ from __future__ import annotations import inspect -import pathlib import re from typing import TYPE_CHECKING @@ -9,8 +8,8 @@ import zarr.storage if TYPE_CHECKING: - import pathlib from collections.abc import Callable + from pathlib import Path from zarr.abc.store import Store from zarr.core.common import JSON, MemoryOrder, ZarrFormat @@ -45,10 +44,6 @@ from zarr.storage._utils import normalize_path from zarr.testing.utils import gpu_test -if TYPE_CHECKING: - from collections.abc import Callable - from pathlib import Path - def test_create(memory_store: Store) -> None: store = memory_store @@ -209,9 +204,7 @@ async def test_open_group(memory_store: MemoryStore) -> None: @pytest.mark.parametrize("zarr_format", [None, 2, 3]) -async def test_open_group_unspecified_version( - tmpdir: pathlib.Path, zarr_format: ZarrFormat -) -> None: +async def test_open_group_unspecified_version(tmpdir: Path, zarr_format: ZarrFormat) -> None: """Regression test for https://github.com/zarr-developers/zarr-python/issues/2175""" # create a group with specified zarr format (could be 2, 3, or None) @@ -272,7 +265,7 @@ def test_save_errors() -> None: zarr.save("data/example.zarr", a, mode="w") -def test_open_with_mode_r(tmp_path: pathlib.Path) -> None: +def test_open_with_mode_r(tmp_path: Path) -> None: # 'r' means read only (must exist) with pytest.raises(FileNotFoundError): zarr.open(store=tmp_path, mode="r") @@ -288,7 +281,7 @@ def test_open_with_mode_r(tmp_path: pathlib.Path) -> None: z2[:] = 3 -def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None: +def test_open_with_mode_r_plus(tmp_path: Path) -> None: # 'r+' means read/write (must exist) with pytest.raises(FileNotFoundError): zarr.open(store=tmp_path, mode="r+") @@ -301,7 +294,7 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None: z2[:] = 3 -async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None: +async def test_open_with_mode_a(tmp_path: Path) -> None: # Open without shape argument should default to group g = zarr.open(store=tmp_path, mode="a") assert isinstance(g, Group) @@ -319,7 +312,7 @@ async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None: z2[:] = 3 -def test_open_with_mode_w(tmp_path: pathlib.Path) -> None: +def test_open_with_mode_w(tmp_path: Path) -> None: # 'w' means create (overwrite if exists); arr = zarr.open(store=tmp_path, mode="w", shape=(3, 3)) assert isinstance(arr, Array) @@ -333,7 +326,7 @@ def test_open_with_mode_w(tmp_path: pathlib.Path) -> None: z2[:] = 3 -def test_open_with_mode_w_minus(tmp_path: pathlib.Path) -> None: +def test_open_with_mode_w_minus(tmp_path: Path) -> None: # 'w-' means create (fail if exists) arr = zarr.open(store=tmp_path, mode="w-", shape=(3, 3)) assert isinstance(arr, Array) @@ -405,7 +398,7 @@ def test_load_array(sync_store: Store) -> None: @pytest.mark.parametrize("path", ["data", None]) @pytest.mark.parametrize("load_read_only", [True, False, None]) -def test_load_zip(tmp_path: pathlib.Path, path: str | None, load_read_only: bool | None) -> None: +def test_load_zip(tmp_path: Path, path: str | None, load_read_only: bool | None) -> None: file = tmp_path / "test.zip" data = np.arange(100).reshape(10, 10) @@ -423,7 +416,7 @@ def test_load_zip(tmp_path: pathlib.Path, path: str | None, load_read_only: bool @pytest.mark.parametrize("path", ["data", None]) @pytest.mark.parametrize("load_read_only", [True, False]) -def test_load_local(tmp_path: pathlib.Path, path: str | None, load_read_only: bool) -> None: +def test_load_local(tmp_path: Path, path: str | None, load_read_only: bool) -> None: file = tmp_path / "test.zip" data = np.arange(100).reshape(10, 10) @@ -1139,7 +1132,7 @@ async def test_open_falls_back_to_open_group_async(zarr_format: ZarrFormat) -> N @pytest.mark.parametrize("mode", ["r", "r+", "w", "a"]) -def test_open_modes_creates_group(tmp_path: pathlib.Path, mode: str) -> None: +def test_open_modes_creates_group(tmp_path: Path, mode: str) -> None: # https://github.com/zarr-developers/zarr-python/issues/2490 zarr_dir = tmp_path / f"mode-{mode}-test.zarr" if mode in ["r", "r+"]: From 8405073c727a3dcf1e6eb4f2cbbc6338918f1534 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 16 Jul 2025 14:32:41 +0200 Subject: [PATCH 029/468] add unmerged changelog entry to release notes (#3248) --- changes/2819.chore.rst | 18 ------------------ docs/release-notes.rst | 19 ++++++++++++++++++- 2 files changed, 18 insertions(+), 19 deletions(-) delete mode 100644 changes/2819.chore.rst diff --git a/changes/2819.chore.rst b/changes/2819.chore.rst deleted file mode 100644 index 7fa68f86ef..0000000000 --- a/changes/2819.chore.rst +++ /dev/null @@ -1,18 +0,0 @@ -Ensure that invocations of ``create_array`` use consistent keyword arguments, with consistent defaults. - -- ``zarr.api.synchronous.create_array`` now takes a ``write_data`` keyword argument -- The ``Group.create_array`` method takes ``data`` and ``write_data`` keyword arguments. -- The functions ``api.asynchronous.create``, ``api.asynchronous.create_array`` - and the methods ``Group.create_array``, ``Group.array``, had the default - ``fill_value`` changed from ``0`` to the ``DEFAULT_FILL_VALUE`` value, which instructs Zarr to - use the default scalar value associated with the array's data type as the fill value. These are - all functions or methods for array creation that mirror, wrap or are wrapped by, another function - that already has a default ``fill_value`` set to ``DEFAULT_FILL_VALUE``. This change is necessary - to make these functions consistent across the entire codebase, but as this changes default values, - new data might have a different fill value than expected after this change. - - For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this - change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode - strings, the default fill value might be different after this change. Users who were relying on how - Zarr interpreted ``0`` as a non-numeric scalar value should set their desired fill value explicitly - after this change. diff --git a/docs/release-notes.rst b/docs/release-notes.rst index 700be6b578..e70715eb15 100644 --- a/docs/release-notes.rst +++ b/docs/release-notes.rst @@ -8,7 +8,24 @@ Release notes Features ~~~~~~~~ - +- Ensure that invocations of ``create_array`` use consistent keyword arguments, with consistent defaults. + + ``zarr.api.synchronous.create_array`` now takes a ``write_data`` keyword argument + The ``Group.create_array`` method takes ``data`` and ``write_data`` keyword arguments. + The functions ``api.asynchronous.create``, ``api.asynchronous.create_array`` + and the methods ``Group.create_array``, ``Group.array``, had the default + ``fill_value`` changed from ``0`` to the ``DEFAULT_FILL_VALUE`` value, which instructs Zarr to + use the default scalar value associated with the array's data type as the fill value. These are + all functions or methods for array creation that mirror, wrap or are wrapped by, another function + that already has a default ``fill_value`` set to ``DEFAULT_FILL_VALUE``. This change is necessary + to make these functions consistent across the entire codebase, but as this changes default values, + new data might have a different fill value than expected after this change. + + For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this + change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode + strings, the default fill value might be different after this change. Users who were relying on how + Zarr interpreted ``0`` as a non-numeric scalar value should set their desired fill value explicitly + after this change. - Added public API for Buffer ABCs and implementations. Use :mod:`zarr.buffer` to access buffer implementations, and From 18f41d4cf57382468f9a8f85a52ab772c1e65940 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 16 Jul 2025 15:31:28 +0200 Subject: [PATCH 030/468] add a section showing the parse_data_type function (#3249) --- changes/3249.doc.rst | 2 ++ docs/user-guide/data_types.rst | 45 ++++++++++++++++++++++++++++++++- src/zarr/core/dtype/__init__.py | 26 +++++++++++++++++++ 3 files changed, 72 insertions(+), 1 deletion(-) create mode 100644 changes/3249.doc.rst diff --git a/changes/3249.doc.rst b/changes/3249.doc.rst new file mode 100644 index 0000000000..d46f775d9c --- /dev/null +++ b/changes/3249.doc.rst @@ -0,0 +1,2 @@ +Expand the data type docs to include a demonstration of the ``parse_data_type`` function. +Expand the docstring for the ``parse_data_type`` function. \ No newline at end of file diff --git a/docs/user-guide/data_types.rst b/docs/user-guide/data_types.rst index dc29874b3b..d4b49ca43f 100644 --- a/docs/user-guide/data_types.rst +++ b/docs/user-guide/data_types.rst @@ -409,4 +409,47 @@ We want to avoid a situation where the same native data type matches multiple Za a NumPy data type should *uniquely* specify a single Zarr data type. But data type resolution is dynamic, so it's not possible to statically guarantee this uniqueness constraint. Therefore, we attempt data type resolution against *every* data type class, and if, for some reason, a native data -type matches multiple Zarr data types, we treat this as an error and raise an exception. \ No newline at end of file +type matches multiple Zarr data types, we treat this as an error and raise an exception. + +If you have a NumPy data type and you want to get the corresponding ``ZDType`` instance, you can use +the ``parse_data_type`` function, which will use the dynamic resolution described above. ``parse_data_type`` +handles a range of input types: + +- NumPy data types: + + .. code-block:: python + + >>> import numpy as np + >>> from zarr.dtype import parse_data_type + >>> my_dtype = np.dtype('>M8[10s]') + >>> parse_data_type(my_dtype, zarr_format=2) + DateTime64(endianness='big', scale_factor=10, unit='s') + + +- NumPy data type-compatible strings: + + .. code-block:: python + + >>> dtype_str = '>M8[10s]' + >>> parse_data_type(dtype_str, zarr_format=2) + DateTime64(endianness='big', scale_factor=10, unit='s') + +- ``ZDType`` instances: + + .. code-block:: python + + >>> from zarr.dtype import DateTime64 + >>> zdt = DateTime64(endianness='big', scale_factor=10, unit='s') + >>> parse_data_type(zdt, zarr_format=2) # Use a ZDType (this is a no-op) + DateTime64(endianness='big', scale_factor=10, unit='s') + +- Python dictionaries (requires ``zarr_format=3``). These dictionaries must be consistent with the + ``JSON`` form of the data type: + + .. code-block:: python + + >>> dt_dict = {"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}} + >>> parse_data_type(dt_dict, zarr_format=3) + DateTime64(endianness='little', scale_factor=10, unit='s') + >>> parse_data_type(dt_dict, zarr_format=3).to_json(zarr_format=3) + {'name': 'numpy.datetime64', 'configuration': {'unit': 's', 'scale_factor': 10}} diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index 1d36689ec8..aadf127c9b 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -189,6 +189,32 @@ def parse_data_type( ) -> ZDType[TBaseDType, TBaseScalar]: """ Interpret the input as a ZDType instance. + + Parameters + ---------- + dtype_spec : ZDTypeLike + The input to be interpreted as a ZDType instance. This could be a native data type + (e.g., a NumPy data type), a Python object that can be converted into a native data type, + a ZDType instance (in which case the input is returned unchanged), or a JSON object + representation of a data type. + zarr_format : ZarrFormat + The zarr format version. + + Returns + ------- + ZDType[TBaseDType, TBaseScalar] + The ZDType instance corresponding to the input. + + Examples + -------- + >>> from zarr.dtype import parse_data_type + >>> import numpy as np + >>> parse_data_type("int32", zarr_format=2) + Int32(endianness='little') + >>> parse_data_type(np.dtype('S10'), zarr_format=2) + NullTerminatedBytes(length=10) + >>> parse_data_type({"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, zarr_format=3) + DateTime64(endianness='little', scale_factor=10, unit='s') """ if isinstance(dtype_spec, ZDType): return dtype_spec From 9969a5d5aaf9bb62fdf5757a749535ec411461df Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 16 Jul 2025 18:20:12 +0200 Subject: [PATCH 031/468] make zdtype abstract methods raise notimplementederror (#3251) * make zdtype abstract methods raise notimplementederror * changelog * exclude notimplementederrors from coverage * cover missing methods --- changes/3251.fix.rst | 1 + src/zarr/core/dtype/wrapper.py | 24 ++++++++++++------------ 2 files changed, 13 insertions(+), 12 deletions(-) create mode 100644 changes/3251.fix.rst diff --git a/changes/3251.fix.rst b/changes/3251.fix.rst new file mode 100644 index 0000000000..92f19ae326 --- /dev/null +++ b/changes/3251.fix.rst @@ -0,0 +1 @@ +Ensure that all abstract methods of ``ZDType`` raise a ``NotImplementedError`` when invoked. \ No newline at end of file diff --git a/src/zarr/core/dtype/wrapper.py b/src/zarr/core/dtype/wrapper.py index b53018c137..776aea81d8 100644 --- a/src/zarr/core/dtype/wrapper.py +++ b/src/zarr/core/dtype/wrapper.py @@ -102,9 +102,6 @@ def from_native_dtype(cls: type[Self], dtype: TBaseDType) -> Self: """ Create a ZDType instance from a native data type. - The base implementation first performs a type check via ``cls._check_native_dtype``. - If that type check succeeds, the ZDType class instance is created. - This method is used when taking a user-provided native data type, like a NumPy data type, and creating the corresponding ZDType instance from them. @@ -123,7 +120,7 @@ def from_native_dtype(cls: type[Self], dtype: TBaseDType) -> Self: TypeError If the native data type is not consistent with the wrapped data type. """ - ... + raise NotImplementedError # pragma: no cover @abstractmethod def to_native_dtype(self: Self) -> TDType_co: @@ -135,15 +132,17 @@ def to_native_dtype(self: Self) -> TDType_co: TDType The native data type wrapped by this ZDType. """ - ... + raise NotImplementedError # pragma: no cover @classmethod @abstractmethod - def _from_json_v2(cls: type[Self], data: DTypeJSON) -> Self: ... + def _from_json_v2(cls: type[Self], data: DTypeJSON) -> Self: + raise NotImplementedError # pragma: no cover @classmethod @abstractmethod - def _from_json_v3(cls: type[Self], data: DTypeJSON) -> Self: ... + def _from_json_v3(cls: type[Self], data: DTypeJSON) -> Self: + raise NotImplementedError # pragma: no cover @classmethod def from_json(cls: type[Self], data: DTypeJSON, *, zarr_format: ZarrFormat) -> Self: @@ -190,7 +189,7 @@ def to_json(self, zarr_format: ZarrFormat) -> DTypeSpec_V2 | DTypeSpec_V3: DTypeJSON_V2 | DTypeJSON_V3 The JSON-serializable representation of the wrapped data type """ - ... + raise NotImplementedError # pragma: no cover @abstractmethod def _check_scalar(self, data: object) -> bool: @@ -207,7 +206,7 @@ def _check_scalar(self, data: object) -> bool: Bool True if the object is valid, False otherwise. """ - ... + raise NotImplementedError # pragma: no cover @abstractmethod def cast_scalar(self, data: object) -> TScalar_co: @@ -227,6 +226,7 @@ def cast_scalar(self, data: object) -> TScalar_co: TScalar The cast value. """ + raise NotImplementedError # pragma: no cover @abstractmethod def default_scalar(self) -> TScalar_co: @@ -242,7 +242,7 @@ def default_scalar(self) -> TScalar_co: TScalar The default value for this data type. """ - ... + raise NotImplementedError # pragma: no cover @abstractmethod def from_json_scalar(self: Self, data: JSON, *, zarr_format: ZarrFormat) -> TScalar_co: @@ -262,7 +262,7 @@ def from_json_scalar(self: Self, data: JSON, *, zarr_format: ZarrFormat) -> TSca TScalar The deserialized scalar value. """ - ... + raise NotImplementedError # pragma: no cover @abstractmethod def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> JSON: @@ -285,7 +285,7 @@ def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> JSON: JSON The JSON-serialized scalar. """ - ... + raise NotImplementedError # pragma: no cover def scalar_failed_type_check_msg( From 9ae874c5305436f5e76b97b0a54bece3e5d9ea84 Mon Sep 17 00:00:00 2001 From: Tom Augspurger Date: Wed, 16 Jul 2025 14:48:22 -0500 Subject: [PATCH 032/468] Provide pytest-plugin that registers a 'gpu' marker. (#3258) https://github.com/zarr-developers/zarr-python/pull/3191/files#diff-a801b931f5dd8cd7df666e3f9936ff520669296303d3a3e469514443211885bdR43 changed `zarr.testing.utils` to use a top-level `pytest.mark.gpu`. Many projects, including zarr, run with `--strict-markers` which causes pytest to raise an error if the test you're running uses an unregistered marker. This didn't cause any issues for zarr, since we already registered the `gpu` marker. However, downstream projects are intended to run the `StoreTests`, which exposes them to this marker. To ensure they get it when installing zarr, we'll include an entrypoint with pytest, so that pytest calls our code to register this marker when these tests run. --- changes/+c563f4d4.bugfix.rst | 1 + pyproject.toml | 4 ++++ src/zarr/testing/conftest.py | 9 +++++++++ 3 files changed, 14 insertions(+) create mode 100644 changes/+c563f4d4.bugfix.rst create mode 100644 src/zarr/testing/conftest.py diff --git a/changes/+c563f4d4.bugfix.rst b/changes/+c563f4d4.bugfix.rst new file mode 100644 index 0000000000..6f9fedaa46 --- /dev/null +++ b/changes/+c563f4d4.bugfix.rst @@ -0,0 +1 @@ +Register 'gpu' marker with pytest for downstream StoreTests. diff --git a/pyproject.toml b/pyproject.toml index 85517d8d0a..102ee76df6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -138,6 +138,7 @@ exclude_lines = [ [tool.coverage.run] omit = [ "bench/compress_normal.py", + "src/zarr/testing/conftest.py", # only for downstream projects ] [tool.hatch] @@ -455,3 +456,6 @@ issue_format = ":issue:`{issue}`" [tool.codespell] ignore-words-list = "astroid" + +[project.entry-points.pytest11] +zarr = "zarr.testing" diff --git a/src/zarr/testing/conftest.py b/src/zarr/testing/conftest.py new file mode 100644 index 0000000000..59c148e0ec --- /dev/null +++ b/src/zarr/testing/conftest.py @@ -0,0 +1,9 @@ +import pytest + + +def pytest_configure(config: pytest.Config) -> None: + # The tests in zarr.testing are intended to be run by downstream projects. + # To allow those downstream projects to run with `--strict-markers`, we need + # to register an entry point with pytest11 and register our "plugin" with it, + # which just registers the markers used in zarr.testing + config.addinivalue_line("markers", "gpu: mark a test as requiring CuPy and GPU") From 798b57b5fed1c6ceb2d8444d702b9a1be59e5d53 Mon Sep 17 00:00:00 2001 From: "Christine P. Chai" Date: Thu, 17 Jul 2025 03:05:00 -0700 Subject: [PATCH 033/468] Update the link to CGGH non-profit organization (#3260) --- docs/about.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/about.rst b/docs/about.rst index 7a0af998c0..d2844dc864 100644 --- a/docs/about.rst +++ b/docs/about.rst @@ -18,7 +18,7 @@ Funding ------- The project is fiscally sponsored by `NumFOCUS `_, a US 501(c)(3) public charity, and development is supported by the -`MRC Centre for Genomics and Global Health `_ +`MRC Centre for Genomics and Global Health `_ and the `Chan Zuckerberg Initiative `_. .. _NumCodecs: https://numcodecs.readthedocs.io/ From 001973353f71dae4b625fe6fdc1c5b59242fb8dc Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 17 Jul 2025 16:30:16 +0100 Subject: [PATCH 034/468] Add numcodecs to downstream projects to check before release (#3262) * Add numcodecs to downstream projects to check before release * style: pre-commit fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .github/ISSUE_TEMPLATE/release-checklist.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/ISSUE_TEMPLATE/release-checklist.md b/.github/ISSUE_TEMPLATE/release-checklist.md index cfd153b69f..e754cab54c 100644 --- a/.github/ISSUE_TEMPLATE/release-checklist.md +++ b/.github/ISSUE_TEMPLATE/release-checklist.md @@ -25,6 +25,7 @@ assignees: '' - [ ] All tests pass in the ["GPU Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml). - [ ] All tests pass in the ["Hypothesis" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml). - [ ] Check that downstream libraries work well (maintainers can make executive decisions about whether all checks are required for this release). + - [ ] numcodecs - [ ] Xarray (@jhamman @dcherian @TomNicholas) - Zarr's upstream compatibility is tested via the [Upstream Dev CI worklow](https://github.com/pydata/xarray/actions/workflows/upstream-dev-ci.yaml). - Click on the most recent workflow and check that the `upstream-dev` job has run and passed. `upstream-dev` is not run on all all workflow runs. From 9cbc7b0efffb6f3495b42296014202bfdefd8213 Mon Sep 17 00:00:00 2001 From: Kenneth Li Date: Thu, 17 Jul 2025 17:14:23 -0400 Subject: [PATCH 035/468] obstore implementations for .getsize and .getsize_prefix (#3227) * obstore implementations for .getsize and .getsize_prefix * rm comment * rm typehint --------- Co-authored-by: Davis Bennett --- changes/3227.feature.rst | 1 + src/zarr/storage/_obstore.py | 40 +++++++++++++++++---------------- tests/test_store/test_object.py | 15 +++++++++++++ 3 files changed, 37 insertions(+), 19 deletions(-) create mode 100644 changes/3227.feature.rst diff --git a/changes/3227.feature.rst b/changes/3227.feature.rst new file mode 100644 index 0000000000..ddbedd0a30 --- /dev/null +++ b/changes/3227.feature.rst @@ -0,0 +1 @@ +Add lightweight implementations of .getsize() and .getsize_prefix() for ObjectStore. diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index cbe037d86b..e1469a991e 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -212,19 +212,21 @@ def supports_listing(self) -> bool: # docstring inherited return True - def list(self) -> AsyncGenerator[str, None]: - # docstring inherited + async def _list(self, prefix: str | None = None) -> AsyncGenerator[ObjectMeta, None]: import obstore as obs - objects: ListStream[Sequence[ObjectMeta]] = obs.list(self.store) - return _transform_list(objects) + objects: ListStream[Sequence[ObjectMeta]] = obs.list(self.store, prefix=prefix) + async for batch in objects: + for item in batch: + yield item - def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]: + def list(self) -> AsyncGenerator[str, None]: # docstring inherited - import obstore as obs + return (obj["path"] async for obj in self._list()) - objects: ListStream[Sequence[ObjectMeta]] = obs.list(self.store, prefix=prefix) - return _transform_list(objects) + def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]: + # docstring inherited + return (obj["path"] async for obj in self._list(prefix)) def list_dir(self, prefix: str) -> AsyncGenerator[str, None]: # docstring inherited @@ -233,21 +235,21 @@ def list_dir(self, prefix: str) -> AsyncGenerator[str, None]: coroutine = obs.list_with_delimiter_async(self.store, prefix=prefix) return _transform_list_dir(coroutine, prefix) + async def getsize(self, key: str) -> int: + # docstring inherited + import obstore as obs -async def _transform_list( - list_stream: ListStream[Sequence[ObjectMeta]], -) -> AsyncGenerator[str, None]: - """ - Transform the result of list into an async generator of paths. - """ - async for batch in list_stream: - for item in batch: - yield item["path"] + resp = await obs.head_async(self.store, key) + return resp["size"] + + async def getsize_prefix(self, prefix: str) -> int: + # docstring inherited + sizes = [obj["size"] async for obj in self._list(prefix=prefix)] + return sum(sizes) async def _transform_list_dir( - list_result_coroutine: Coroutine[Any, Any, ListResult[Sequence[ObjectMeta]]], - prefix: str, + list_result_coroutine: Coroutine[Any, Any, ListResult[Sequence[ObjectMeta]]], prefix: str ) -> AsyncGenerator[str, None]: """ Transform the result of list_with_delimiter into an async generator of paths. diff --git a/tests/test_store/test_object.py b/tests/test_store/test_object.py index 4d9e8fcc1f..d8b89e56b7 100644 --- a/tests/test_store/test_object.py +++ b/tests/test_store/test_object.py @@ -75,6 +75,21 @@ def test_store_init_raises(self) -> None: with pytest.raises(TypeError): ObjectStore("path/to/store") + async def test_store_getsize(self, store: ObjectStore) -> None: + buf = cpu.Buffer.from_bytes(b"\x01\x02\x03\x04") + await self.set(store, "key", buf) + size = await store.getsize("key") + assert size == len(buf) + + async def test_store_getsize_prefix(self, store: ObjectStore) -> None: + buf = cpu.Buffer.from_bytes(b"\x01\x02\x03\x04") + await self.set(store, "c/key1/0", buf) + await self.set(store, "c/key2/0", buf) + size = await store.getsize_prefix("c/key1") + assert size == len(buf) + total_size = await store.getsize_prefix("c") + assert total_size == len(buf) * 2 + @pytest.mark.slow_hypothesis def test_zarr_hierarchy(): From 7c6160e520d0fe8d4242c9803560a3505e6e1682 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 17 Jul 2025 23:26:39 +0200 Subject: [PATCH 036/468] remove warnings about vlen-utf8 and vlen-bytes codecs (#3268) * remove warning about vlen-utf8 codec now that a spec is published * remove vlen-bytes warning * changelog * miscify it --- changes/3268.misc.rst | 2 ++ src/zarr/codecs/vlen_utf8.py | 19 ------------------- 2 files changed, 2 insertions(+), 19 deletions(-) create mode 100644 changes/3268.misc.rst diff --git a/changes/3268.misc.rst b/changes/3268.misc.rst new file mode 100644 index 0000000000..cd8f611639 --- /dev/null +++ b/changes/3268.misc.rst @@ -0,0 +1,2 @@ +Removed warnings that were emitted when using the ``vlen-utf8`` and ``vlen-bytes`` codecs. Those +warnings are no longer needed now that both of these codecs are backed by specification documents. \ No newline at end of file diff --git a/src/zarr/codecs/vlen_utf8.py b/src/zarr/codecs/vlen_utf8.py index b7c0418b2e..bad51f33ce 100644 --- a/src/zarr/codecs/vlen_utf8.py +++ b/src/zarr/codecs/vlen_utf8.py @@ -2,7 +2,6 @@ from dataclasses import dataclass from typing import TYPE_CHECKING -from warnings import warn import numpy as np from numcodecs.vlen import VLenBytes, VLenUTF8 @@ -25,15 +24,6 @@ @dataclass(frozen=True) class VLenUTF8Codec(ArrayBytesCodec): - def __init__(self) -> None: - warn( - "The codec `vlen-utf8` is currently not part in the Zarr format 3 specification. It " - "may not be supported by other zarr implementations and may change in the future.", - category=UserWarning, - stacklevel=2, - ) - super().__init__() - @classmethod def from_dict(cls, data: dict[str, JSON]) -> Self: _, configuration_parsed = parse_named_configuration( @@ -80,15 +70,6 @@ def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) - @dataclass(frozen=True) class VLenBytesCodec(ArrayBytesCodec): - def __init__(self) -> None: - warn( - "The codec `vlen-bytes` is currently not part in the Zarr format 3 specification. It " - "may not be supported by other zarr implementations and may change in the future.", - category=UserWarning, - stacklevel=2, - ) - super().__init__() - @classmethod def from_dict(cls, data: dict[str, JSON]) -> Self: _, configuration_parsed = parse_named_configuration( From 7a162bf29158ccde6ffc8f4f8d43cc2c1eb86616 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Thu, 17 Jul 2025 23:39:04 +0200 Subject: [PATCH 037/468] Apply ruff/flake8-pytest-style rule PT012 (#3267) PT012 `pytest.raises()` block should contain a single simple statement --- pyproject.toml | 1 - tests/test_api.py | 2 +- tests/test_config.py | 2 +- tests/test_group.py | 7 ++++--- tests/test_indexing.py | 20 ++++++++++---------- 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 102ee76df6..a4f15e268c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -324,7 +324,6 @@ extend-select = [ ignore = [ "ANN401", "PT011", # TODO: apply this rule - "PT012", # TODO: apply this rule "PT030", # TODO: apply this rule "PT031", # TODO: apply this rule "RET505", diff --git a/tests/test_api.py b/tests/test_api.py index 0f71bfa94f..d9827c7e44 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -259,9 +259,9 @@ def test_save_errors() -> None: with pytest.raises(ValueError): # no arrays provided save("data/group.zarr") + a = np.arange(10) with pytest.raises(TypeError): # mode is no valid argument and would get handled as an array - a = np.arange(10) zarr.save("data/example.zarr", a, mode="w") diff --git a/tests/test_config.py b/tests/test_config.py index c59e721c49..08d67f66bd 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -141,8 +141,8 @@ async def write( _mock.call.assert_called() + config.set({"codec_pipeline.path": "wrong_name"}) with pytest.raises(BadConfigError): - config.set({"codec_pipeline.path": "wrong_name"}) get_pipeline_class() class MockEnvCodecPipeline(CodecPipeline): diff --git a/tests/test_group.py b/tests/test_group.py index 56590f7b6f..9965a039fb 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -655,12 +655,13 @@ def test_group_create_array( if not overwrite: if method == "create_array": - with pytest.raises(ContainsArrayError): + with pytest.raises(ContainsArrayError): # noqa: PT012 a = group.create_array(name=name, shape=shape, dtype=dtype) a[:] = data elif method == "array": - with pytest.raises(ContainsArrayError), pytest.warns(DeprecationWarning): - a = group.array(name=name, shape=shape, dtype=dtype) + with pytest.raises(ContainsArrayError): # noqa: PT012 + with pytest.warns(DeprecationWarning): + a = group.array(name=name, shape=shape, dtype=dtype) a[:] = data assert array.path == normalize_path(name) diff --git a/tests/test_indexing.py b/tests/test_indexing.py index b1707c88a3..fd4bb13bb1 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -1093,17 +1093,17 @@ def test_get_coordinate_selection_2d(store: StorePath) -> None: ix1 = np.array([[1, 3, 2], [1, 0, 0]]) _test_get_coordinate_selection(a, z, (ix0, ix1)) + selection = slice(5, 15), [1, 2, 3] with pytest.raises(IndexError): - selection = slice(5, 15), [1, 2, 3] z.get_coordinate_selection(selection) # type:ignore[arg-type] + selection = [1, 2, 3], slice(5, 15) with pytest.raises(IndexError): - selection = [1, 2, 3], slice(5, 15) z.get_coordinate_selection(selection) # type:ignore[arg-type] + selection = Ellipsis, [1, 2, 3] with pytest.raises(IndexError): - selection = Ellipsis, [1, 2, 3] z.get_coordinate_selection(selection) # type:ignore[arg-type] + selection = Ellipsis with pytest.raises(IndexError): - selection = Ellipsis z.get_coordinate_selection(selection) # type:ignore[arg-type] @@ -1299,14 +1299,14 @@ def test_get_block_selection_2d(store: StorePath) -> None: ): _test_get_block_selection(a, z, selection, expected_idx) + selection = slice(5, 15), [1, 2, 3] with pytest.raises(IndexError): - selection = slice(5, 15), [1, 2, 3] z.get_block_selection(selection) + selection = Ellipsis, [1, 2, 3] with pytest.raises(IndexError): - selection = Ellipsis, [1, 2, 3] z.get_block_selection(selection) + selection = slice(15, 20), slice(None) with pytest.raises(IndexError): # out of bounds - selection = slice(15, 20), slice(None) z.get_block_selection(selection) @@ -1360,14 +1360,14 @@ def test_set_block_selection_2d(store: StorePath) -> None: ): _test_set_block_selection(v, a, z, selection, expected_idx) + selection = slice(5, 15), [1, 2, 3] with pytest.raises(IndexError): - selection = slice(5, 15), [1, 2, 3] z.set_block_selection(selection, 42) + selection = Ellipsis, [1, 2, 3] with pytest.raises(IndexError): - selection = Ellipsis, [1, 2, 3] z.set_block_selection(selection, 42) + selection = slice(15, 20), slice(None) with pytest.raises(IndexError): # out of bounds - selection = slice(15, 20), slice(None) z.set_block_selection(selection, 42) From df40f4f0e9c8c008e7db2ce23993fe1b5f1af62a Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 17 Jul 2025 22:59:46 +0100 Subject: [PATCH 038/468] Fix order handling (#3112) * Fix order handling Fix imports * Update changes/xxx1.bugfix.rst * Rename bugfix entries * Add test for order warning in from_array * Add test for config warning in init_array * Remove spurious test file * Improve order warning --------- Co-authored-by: Davis Bennett --- changes/3112.bugfix.1.rst | 1 + changes/3112.bugfix.2.rst | 1 + changes/3112.bugfix.3.rst | 2 ++ changes/3112.bugfix.4.rst | 1 + changes/3112.bugfix.rst | 1 + src/zarr/api/asynchronous.py | 24 +++---------- src/zarr/core/array.py | 23 +++++++----- src/zarr/core/group.py | 2 +- tests/test_api.py | 70 ++++++++++++++++++++++++++---------- tests/test_array.py | 59 ++++++------------------------ 10 files changed, 90 insertions(+), 94 deletions(-) create mode 100644 changes/3112.bugfix.1.rst create mode 100644 changes/3112.bugfix.2.rst create mode 100644 changes/3112.bugfix.3.rst create mode 100644 changes/3112.bugfix.4.rst create mode 100644 changes/3112.bugfix.rst diff --git a/changes/3112.bugfix.1.rst b/changes/3112.bugfix.1.rst new file mode 100644 index 0000000000..5d7856859c --- /dev/null +++ b/changes/3112.bugfix.1.rst @@ -0,0 +1 @@ +Creating a Zarr format 2 array with the ``order`` keyword argument no longer raises a warning. diff --git a/changes/3112.bugfix.2.rst b/changes/3112.bugfix.2.rst new file mode 100644 index 0000000000..e2c341c99a --- /dev/null +++ b/changes/3112.bugfix.2.rst @@ -0,0 +1 @@ +Creating a Zarr format 3 array with the ``order`` argument now conistently ignores this argument and raises a warning. diff --git a/changes/3112.bugfix.3.rst b/changes/3112.bugfix.3.rst new file mode 100644 index 0000000000..4c934b491b --- /dev/null +++ b/changes/3112.bugfix.3.rst @@ -0,0 +1,2 @@ +When using ``from_array`` to copy a Zarr format 2 array to a Zarr format 3 array, if the memory order of the input array is ``"F"`` a warning is raised and the order ignored. +This is because Zarr format 3 arrays are always stored in "C" order. diff --git a/changes/3112.bugfix.4.rst b/changes/3112.bugfix.4.rst new file mode 100644 index 0000000000..417814943b --- /dev/null +++ b/changes/3112.bugfix.4.rst @@ -0,0 +1 @@ +The ``config`` argument to `zarr.create` (and functions that create arrays) is now used - previously it had no effect. diff --git a/changes/3112.bugfix.rst b/changes/3112.bugfix.rst new file mode 100644 index 0000000000..24069aae3a --- /dev/null +++ b/changes/3112.bugfix.rst @@ -0,0 +1 @@ +Fixed the error message when passing both ``config`` and ``write_empty_chunks`` arguments to reflect the current behaviour (``write_empty_chunks`` takes precedence). diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 8f244f4b25..9a380082b0 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -19,7 +19,7 @@ from_array, get_array_metadata, ) -from zarr.core.array_spec import ArrayConfig, ArrayConfigLike, ArrayConfigParams +from zarr.core.array_spec import ArrayConfigLike, parse_array_config from zarr.core.buffer import NDArrayLike from zarr.core.common import ( JSON, @@ -29,7 +29,6 @@ MemoryOrder, ZarrFormat, _default_zarr_format, - _warn_order_kwarg, _warn_write_empty_chunks_kwarg, ) from zarr.core.dtype import ZDTypeLike, get_data_type_from_native_dtype @@ -1026,8 +1025,6 @@ async def create( if meta_array is not None: warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2) - if order is not None: - _warn_order_kwarg() if write_empty_chunks is not None: _warn_write_empty_chunks_kwarg() @@ -1036,26 +1033,17 @@ async def create( mode = "a" store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options) - config_dict: ArrayConfigParams = {} + config_parsed = parse_array_config(config) if write_empty_chunks is not None: if config is not None: msg = ( "Both write_empty_chunks and config keyword arguments are set. " - "This is redundant. When both are set, write_empty_chunks will be ignored and " - "config will be used." + "This is redundant. When both are set, write_empty_chunks will be used instead " + "of the value in config." ) warnings.warn(UserWarning(msg), stacklevel=1) - config_dict["write_empty_chunks"] = write_empty_chunks - if order is not None and config is not None: - msg = ( - "Both order and config keyword arguments are set. " - "This is redundant. When both are set, order will be ignored and " - "config will be used." - ) - warnings.warn(UserWarning(msg), stacklevel=1) - - config_parsed = ArrayConfig.from_dict(config_dict) + config_parsed = dataclasses.replace(config_parsed, write_empty_chunks=write_empty_chunks) return await AsyncArray._create( store_path, @@ -1258,8 +1246,6 @@ async def open_array( zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) - if "order" in kwargs: - _warn_order_kwarg() if "write_empty_chunks" in kwargs: _warn_write_empty_chunks_kwarg() diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index a0b8e9e7dd..b85c5aba4b 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -62,7 +62,6 @@ _default_zarr_format, _warn_order_kwarg, concurrent_map, - parse_order, parse_shapelike, product, ) @@ -651,7 +650,6 @@ async def _create( if order is not None: _warn_order_kwarg() - config_parsed = replace(config_parsed, order=order) result = await cls._create_v3( store_path, @@ -679,9 +677,10 @@ async def _create( raise ValueError("dimension_names cannot be used for arrays with zarr_format 2.") if order is None: - order_parsed = parse_order(zarr_config.get("array.order")) + order_parsed = config_parsed.order else: order_parsed = order + config_parsed = replace(config_parsed, order=order) result = await cls._create_v2( store_path, @@ -4326,10 +4325,8 @@ async def init_array( chunks_out = chunk_shape_parsed codecs_out = sub_codecs - if config is None: - config = {} - if order is not None and isinstance(config, dict): - config["order"] = config.get("order", order) + if order is not None: + _warn_order_kwarg() meta = AsyncArray._create_metadata_v3( shape=shape_parsed, @@ -4580,8 +4577,18 @@ def _parse_keep_array_attr( serializer = "auto" if fill_value is None: fill_value = data.fill_value - if order is None: + + if data.metadata.zarr_format == 2 and zarr_format == 3 and data.order == "F": + # Can't set order="F" for v3 arrays + warnings.warn( + "The 'order' attribute of a Zarr format 2 array does not have a direct analogue in Zarr format 3. " + "The existing order='F' of the source Zarr format 2 array will be ignored.", + UserWarning, + stacklevel=2, + ) + elif order is None and zarr_format == 2: order = data.order + if chunk_key_encoding is None and zarr_format == data.metadata.zarr_format: if isinstance(data.metadata, ArrayV2Metadata): chunk_key_encoding = {"name": "v2", "separator": data.metadata.dimension_separator} diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index e02d09694f..45ebba34ff 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -2826,7 +2826,7 @@ def array( compressor: CompressorLike = None, serializer: SerializerLike = "auto", fill_value: Any | None = DEFAULT_FILL_VALUE, - order: MemoryOrder | None = "C", + order: MemoryOrder | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, dimension_names: DimensionNames = None, diff --git a/tests/test_api.py b/tests/test_api.py index d9827c7e44..9baca3791b 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -6,6 +6,8 @@ import zarr.codecs import zarr.storage +from zarr.core.array import init_array +from zarr.storage._common import StorePath if TYPE_CHECKING: from collections.abc import Callable @@ -335,34 +337,66 @@ def test_open_with_mode_w_minus(tmp_path: Path) -> None: zarr.open(store=tmp_path, mode="w-") -def test_array_order(zarr_format: ZarrFormat) -> None: - arr = zarr.ones(shape=(2, 2), order=None, zarr_format=zarr_format) - expected = zarr.config.get("array.order") - assert arr.order == expected +@pytest.mark.parametrize("order", ["C", "F", None]) +@pytest.mark.parametrize("config", [{"order": "C"}, {"order": "F"}, {}], ids=["C", "F", "None"]) +def test_array_order( + order: MemoryOrder | None, config: dict[str, MemoryOrder | None], zarr_format: ZarrFormat +) -> None: + """ + Check that: + - For v2, memory order is taken from the `order` keyword argument. + - For v3, memory order is taken from `config`, and when order is passed a warning is raised + - The numpy array returned has the expected order + - For v2, the order metadata is set correctly + """ + default_order = zarr.config.get("array.order") + ctx: contextlib.AbstractContextManager # type: ignore[type-arg] - vals = np.asarray(arr) - if expected == "C": - assert vals.flags.c_contiguous - elif expected == "F": - assert vals.flags.f_contiguous - else: - raise AssertionError + if zarr_format == 3: + if order is None: + ctx = contextlib.nullcontext() + else: + ctx = pytest.warns( + RuntimeWarning, + match="The `order` keyword argument has no effect for Zarr format 3 arrays", + ) + expected_order = config.get("order", default_order) -@pytest.mark.parametrize("order", ["C", "F"]) -def test_array_order_warns(order: MemoryOrder | None, zarr_format: ZarrFormat) -> None: - with pytest.warns(RuntimeWarning, match="The `order` keyword argument .*"): - arr = zarr.ones(shape=(2, 2), order=order, zarr_format=zarr_format) - assert arr.order == order + if zarr_format == 2: + ctx = contextlib.nullcontext() + expected_order = order or config.get("order", default_order) + + with ctx: + arr = zarr.ones(shape=(2, 2), order=order, zarr_format=zarr_format, config=config) + assert arr.order == expected_order vals = np.asarray(arr) - if order == "C": + if expected_order == "C": assert vals.flags.c_contiguous - elif order == "F": + elif expected_order == "F": assert vals.flags.f_contiguous else: raise AssertionError + if zarr_format == 2: + assert arr.metadata.zarr_format == 2 + assert arr.metadata.order == expected_order + + +async def test_init_order_warns() -> None: + with pytest.warns( + RuntimeWarning, match="The `order` keyword argument has no effect for Zarr format 3 arrays" + ): + await init_array( + store_path=StorePath(store=MemoryStore()), + shape=(1,), + dtype="uint8", + config=None, + zarr_format=3, + order="F", + ) + # def test_lazy_loader(): # foo = np.arange(100) diff --git a/tests/test_array.py b/tests/test_array.py index c4201b4548..3f8e61a2e3 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -41,7 +41,7 @@ from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, default_buffer_prototype from zarr.core.chunk_grids import _auto_partition from zarr.core.chunk_key_encodings import ChunkKeyEncodingParams -from zarr.core.common import JSON, MemoryOrder, ZarrFormat +from zarr.core.common import JSON, ZarrFormat from zarr.core.dtype import ( DateTime64, Float32, @@ -61,6 +61,7 @@ from zarr.core.group import AsyncGroup from zarr.core.indexing import BasicIndexer, ceildiv from zarr.core.metadata.v2 import ArrayV2Metadata +from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import sync from zarr.errors import ContainsArrayError, ContainsGroupError from zarr.storage import LocalStore, MemoryStore, StorePath @@ -68,7 +69,6 @@ from .test_dtype.conftest import zdtype_examples if TYPE_CHECKING: - from zarr.core.array_spec import ArrayConfigLike from zarr.core.metadata.v3 import ArrayV3Metadata @@ -1447,52 +1447,6 @@ async def test_data_ignored_params(store: Store) -> None: ): await create_array(store, data=data, shape=None, dtype=data.dtype, overwrite=True) - @staticmethod - @pytest.mark.parametrize("order", ["C", "F", None]) - @pytest.mark.parametrize("with_config", [True, False]) - def test_order( - order: MemoryOrder | None, - with_config: bool, - zarr_format: ZarrFormat, - store: MemoryStore, - ) -> None: - """ - Test that the arrays generated by array indexing have a memory order defined by the config order - value, and that for zarr v2 arrays, the ``order`` field in the array metadata is set correctly. - """ - config: ArrayConfigLike | None = {} - if order is None: - config = {} - expected = zarr.config.get("array.order") - else: - config = {"order": order} - expected = order - - if not with_config: - # Test without passing config parameter - config = None - - arr = zarr.create_array( - store=store, - shape=(2, 2), - zarr_format=zarr_format, - dtype="i4", - order=order, - config=config, - ) - assert arr.order == expected - if zarr_format == 2: - assert arr.metadata.zarr_format == 2 - assert arr.metadata.order == expected - - vals = np.asarray(arr) - if expected == "C": - assert vals.flags.c_contiguous - elif expected == "F": - assert vals.flags.f_contiguous - else: - raise AssertionError - @staticmethod @pytest.mark.parametrize("write_empty_chunks", [True, False]) async def test_write_empty_chunks_config(write_empty_chunks: bool, store: Store) -> None: @@ -1674,6 +1628,15 @@ async def test_from_array_arraylike( np.testing.assert_array_equal(result[...], np.full_like(src, fill_value)) +def test_from_array_F_order() -> None: + arr = zarr.create_array(store={}, data=np.array([1]), order="F", zarr_format=2) + with pytest.warns( + UserWarning, + match="The existing order='F' of the source Zarr format 2 array will be ignored.", + ): + zarr.from_array(store={}, data=arr, zarr_format=3) + + async def test_orthogonal_set_total_slice() -> None: """Ensure that a whole chunk overwrite does not read chunks""" store = MemoryStore() From bc5ca27075e9f706b40e106bddb067b7aab23658 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Fri, 18 Jul 2025 00:23:34 +0200 Subject: [PATCH 039/468] Use `in` and `or` instead of multiple `if`'s (#3266) --- src/zarr/core/dtype/npy/common.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index 264561f25c..67644449a0 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -384,9 +384,7 @@ def check_json_float_v2(data: JSON) -> TypeGuard[JSONFloatV2]: Bool True if the data is a float, False otherwise. """ - if data == "NaN" or data == "Infinity" or data == "-Infinity": - return True - return isinstance(data, float | int) + return data in ("NaN", "Infinity", "-Infinity") or isinstance(data, float | int) def check_json_float_v3(data: JSON) -> TypeGuard[JSONFloatV3]: From 80d4f366d35d972bbca27e91bcf807ac92ee081d Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Fri, 18 Jul 2025 09:02:49 +0200 Subject: [PATCH 040/468] Apply ruff/flake8-pytest-style rule PT031 (#3269) PT031 `pytest.warns()` block should contain a single simple statement Co-authored-by: Davis Bennett --- pyproject.toml | 1 - tests/test_api.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a4f15e268c..aca36eb9db 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -325,7 +325,6 @@ ignore = [ "ANN401", "PT011", # TODO: apply this rule "PT030", # TODO: apply this rule - "PT031", # TODO: apply this rule "RET505", "RET506", "RUF005", diff --git a/tests/test_api.py b/tests/test_api.py index 9baca3791b..7a7650002f 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -470,7 +470,7 @@ def test_tree() -> None: g3.create_group("baz") g5 = g3.create_group("qux") g5.create_array("baz", shape=(100,), chunks=(10,), dtype="float64") - with pytest.warns(DeprecationWarning): + with pytest.warns(DeprecationWarning): # noqa: PT031 assert repr(zarr.tree(g1)) == repr(g1.tree()) assert str(zarr.tree(g1)) == str(g1.tree()) From abbdbf2be70a24e7d662b5ed449c68f6718977f9 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Fri, 18 Jul 2025 21:58:50 +0200 Subject: [PATCH 041/468] Apply ruff/flake8-pytest-style rule PT030 (#3270) PT030 `pytest.warns(UserWarning)` is too broad, set the `match` parameter or use a more specific warning --- pyproject.toml | 1 - tests/test_api.py | 2 +- tests/test_codecs/test_codecs.py | 10 ++++++++-- tests/test_config.py | 2 +- tests/test_group.py | 18 ++++++++++++------ 5 files changed, 22 insertions(+), 11 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index aca36eb9db..0b7cb9f856 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -324,7 +324,6 @@ extend-select = [ ignore = [ "ANN401", "PT011", # TODO: apply this rule - "PT030", # TODO: apply this rule "RET505", "RET506", "RUF005", diff --git a/tests/test_api.py b/tests/test_api.py index 7a7650002f..01fb40f050 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -470,7 +470,7 @@ def test_tree() -> None: g3.create_group("baz") g5 = g3.create_group("qux") g5.create_array("baz", shape=(100,), chunks=(10,), dtype="float64") - with pytest.warns(DeprecationWarning): # noqa: PT031 + with pytest.warns(DeprecationWarning, match=r"Group\.tree instead\."): # noqa: PT031 assert repr(zarr.tree(g1)) == repr(g1.tree()) assert str(zarr.tree(g1)) == str(g1.tree()) diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index 468f395254..d52a9e1c44 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -355,7 +355,10 @@ def test_invalid_metadata(store: Store) -> None: ], ) spath7 = StorePath(store, "warning_inefficient_codecs") - with pytest.warns(UserWarning): + with pytest.warns( + UserWarning, + match="Combining a `sharding_indexed` codec disables partial reads and writes, which may lead to inefficient performance", + ): Array.create( spath7, shape=(16, 16), @@ -372,7 +375,10 @@ def test_invalid_metadata(store: Store) -> None: @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) def test_invalid_metadata_create_array(store: Store) -> None: spath = StorePath(store, "warning_inefficient_codecs") - with pytest.warns(UserWarning): + with pytest.warns( + UserWarning, + match="codec disables partial reads and writes, which may lead to inefficient performance", + ): zarr.create_array( spath, shape=(16, 16), diff --git a/tests/test_config.py b/tests/test_config.py index 08d67f66bd..da5b2cc488 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -287,7 +287,7 @@ class NewCodec2(BytesCodec): # warning because multiple implementations are available but none is selected in the config register_codec("new_codec", NewCodec2) - with pytest.warns(UserWarning): + with pytest.warns(UserWarning, match="not configured in config. Selecting any implementation"): get_codec_class("new_codec") # no warning if multiple implementations are available and one is selected in the config diff --git a/tests/test_group.py b/tests/test_group.py index 9965a039fb..ac1afb539b 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -648,7 +648,7 @@ def test_group_create_array( array = group.create_array(name=name, shape=shape, dtype=dtype) array[:] = data elif method == "array": - with pytest.warns(DeprecationWarning): + with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): array = group.array(name=name, data=data, shape=shape, dtype=dtype) else: raise AssertionError @@ -660,7 +660,7 @@ def test_group_create_array( a[:] = data elif method == "array": with pytest.raises(ContainsArrayError): # noqa: PT012 - with pytest.warns(DeprecationWarning): + with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): a = group.array(name=name, shape=shape, dtype=dtype) a[:] = data @@ -1184,22 +1184,28 @@ def test_create_dataset_with_data(store: Store, zarr_format: ZarrFormat) -> None """ root = Group.from_store(store=store, zarr_format=zarr_format) arr = np.random.random((5, 5)) - with pytest.warns(DeprecationWarning): + with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): data = root.create_dataset("random", data=arr, shape=arr.shape) np.testing.assert_array_equal(np.asarray(data), arr) async def test_create_dataset(store: Store, zarr_format: ZarrFormat) -> None: root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format) - with pytest.warns(DeprecationWarning): + with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): foo = await root.create_dataset("foo", shape=(10,), dtype="uint8") assert foo.shape == (10,) - with pytest.raises(ContainsArrayError), pytest.warns(DeprecationWarning): + with ( + pytest.raises(ContainsArrayError), + pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."), + ): await root.create_dataset("foo", shape=(100,), dtype="int8") _ = await root.create_group("bar") - with pytest.raises(ContainsGroupError), pytest.warns(DeprecationWarning): + with ( + pytest.raises(ContainsGroupError), + pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."), + ): await root.create_dataset("bar", shape=(100,), dtype="int8") From fd5425b954ad5da8b02ae30e4c742fbae1393503 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Tue, 22 Jul 2025 11:56:18 +0100 Subject: [PATCH 042/468] Improve migration guide for codecs (#3273) --- changes/3273.doc.rst | 1 + docs/user-guide/v3_migration.rst | 14 +++++++++++++- 2 files changed, 14 insertions(+), 1 deletion(-) create mode 100644 changes/3273.doc.rst diff --git a/changes/3273.doc.rst b/changes/3273.doc.rst new file mode 100644 index 0000000000..b63b9c3fa3 --- /dev/null +++ b/changes/3273.doc.rst @@ -0,0 +1 @@ +Add a section on codecs to the migration guide. diff --git a/docs/user-guide/v3_migration.rst b/docs/user-guide/v3_migration.rst index a6258534e4..2b53e39b83 100644 --- a/docs/user-guide/v3_migration.rst +++ b/docs/user-guide/v3_migration.rst @@ -58,7 +58,7 @@ the following actions in order: vendor the parts of the specific modules that you need. * ``zarr.attrs`` has gone, with no replacement - * ``zarr.codecs`` has gone, use ``numcodecs`` instead + * ``zarr.codecs`` has changed, see "Codecs" section below for more information * ``zarr.context`` has gone, with no replacement * ``zarr.core`` remains but should be considered private API * ``zarr.hierarchy`` has gone, with no replacement (use ``zarr.Group`` inplace of ``zarr.hierarchy.Group``) @@ -178,6 +178,18 @@ If you are interested in developing a custom store that targets these backends, :ref:`developing custom stores ` or open an `issue `_ to discuss your use case. + +Codecs +~~~~~~ +Codecs defined in ``numcodecs`` (and also imported into the ``zarr.codecs`` namespace in Zarr-Python 2) +should still be used when creating Zarr format 2 arrays. + +Codecs for creating Zarr format 3 arrays are available in two locations: + +- `zarr.codecs` contains Zarr format 3 codecs that are defined in the `codecs section of the Zarr format 3 specification `_. +- `numcodecs.zarr3` contains codecs from ``numcodecs`` that can be used to create Zarr format 3 arrays, but are not necessarily part of the Zarr format 3 specification. + + Dependencies ~~~~~~~~~~~~ From a27d4d6e2641b8ffdeb845a0b12a32c74a2c5810 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 22 Jul 2025 14:15:53 +0200 Subject: [PATCH 043/468] improvements to `parse_dtype` (#3264) * add parse_dtype as ergonomic replacement for parse_data_type, handle more JSON-like inputs, and test for round-trips * update docs * changelog * remove type: ignore * add test to check that parse_dtype is parse_data_type * Update src/zarr/dtype.py Co-authored-by: David Stansby * fix docstring * support the output of to_json(zarr_format=2) as input to parse_dtype * lint * remove infinite recursion * Update src/zarr/core/dtype/__init__.py Co-authored-by: David Stansby * Update src/zarr/core/dtype/__init__.py Co-authored-by: David Stansby * Update src/zarr/core/dtype/__init__.py Co-authored-by: David Stansby * Update src/zarr/core/dtype/__init__.py Co-authored-by: David Stansby * Update src/zarr/core/dtype/__init__.py Co-authored-by: David Stansby * Update src/zarr/core/dtype/__init__.py Co-authored-by: David Stansby --------- Co-authored-by: David Stansby --- changes/3264.fix.rst | 4 ++ docs/user-guide/data_types.rst | 14 ++--- src/zarr/core/array.py | 6 +- src/zarr/core/dtype/__init__.py | 70 ++++++++++++++++++---- src/zarr/dtype.py | 4 +- tests/test_array.py | 4 +- tests/test_dtype_registry.py | 74 ++++++++++++++++-------- tests/test_metadata/test_consolidated.py | 4 +- 8 files changed, 129 insertions(+), 51 deletions(-) create mode 100644 changes/3264.fix.rst diff --git a/changes/3264.fix.rst b/changes/3264.fix.rst new file mode 100644 index 0000000000..efcbab514e --- /dev/null +++ b/changes/3264.fix.rst @@ -0,0 +1,4 @@ +- Expand the range of types accepted by ``parse_data_type`` to include strings and Sequences. +- Move the functionality of ``parse_data_type`` to a new function called ``parse_dtype``. This change + ensures that nomenclature is consistent across the codebase. ``parse_data_type`` remains, so this + change is not breaking. \ No newline at end of file diff --git a/docs/user-guide/data_types.rst b/docs/user-guide/data_types.rst index d4b49ca43f..a968cc4c86 100644 --- a/docs/user-guide/data_types.rst +++ b/docs/user-guide/data_types.rst @@ -412,7 +412,7 @@ attempt data type resolution against *every* data type class, and if, for some r type matches multiple Zarr data types, we treat this as an error and raise an exception. If you have a NumPy data type and you want to get the corresponding ``ZDType`` instance, you can use -the ``parse_data_type`` function, which will use the dynamic resolution described above. ``parse_data_type`` +the ``parse_dtype`` function, which will use the dynamic resolution described above. ``parse_dtype`` handles a range of input types: - NumPy data types: @@ -420,9 +420,9 @@ handles a range of input types: .. code-block:: python >>> import numpy as np - >>> from zarr.dtype import parse_data_type + >>> from zarr.dtype import parse_dtype >>> my_dtype = np.dtype('>M8[10s]') - >>> parse_data_type(my_dtype, zarr_format=2) + >>> parse_dtype(my_dtype, zarr_format=2) DateTime64(endianness='big', scale_factor=10, unit='s') @@ -431,7 +431,7 @@ handles a range of input types: .. code-block:: python >>> dtype_str = '>M8[10s]' - >>> parse_data_type(dtype_str, zarr_format=2) + >>> parse_dtype(dtype_str, zarr_format=2) DateTime64(endianness='big', scale_factor=10, unit='s') - ``ZDType`` instances: @@ -440,7 +440,7 @@ handles a range of input types: >>> from zarr.dtype import DateTime64 >>> zdt = DateTime64(endianness='big', scale_factor=10, unit='s') - >>> parse_data_type(zdt, zarr_format=2) # Use a ZDType (this is a no-op) + >>> parse_dtype(zdt, zarr_format=2) # Use a ZDType (this is a no-op) DateTime64(endianness='big', scale_factor=10, unit='s') - Python dictionaries (requires ``zarr_format=3``). These dictionaries must be consistent with the @@ -449,7 +449,7 @@ handles a range of input types: .. code-block:: python >>> dt_dict = {"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}} - >>> parse_data_type(dt_dict, zarr_format=3) + >>> parse_dtype(dt_dict, zarr_format=3) DateTime64(endianness='little', scale_factor=10, unit='s') - >>> parse_data_type(dt_dict, zarr_format=3).to_json(zarr_format=3) + >>> parse_dtype(dt_dict, zarr_format=3).to_json(zarr_format=3) {'name': 'numpy.datetime64', 'configuration': {'unit': 's', 'scale_factor': 10}} diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index b85c5aba4b..78dddf3669 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -72,7 +72,7 @@ VariableLengthUTF8, ZDType, ZDTypeLike, - parse_data_type, + parse_dtype, ) from zarr.core.dtype.common import HasEndianness, HasItemSize, HasObjectCodec from zarr.core.indexing import ( @@ -617,7 +617,7 @@ async def _create( Deprecated in favor of :func:`zarr.api.asynchronous.create_array`. """ - dtype_parsed = parse_data_type(dtype, zarr_format=zarr_format) + dtype_parsed = parse_dtype(dtype, zarr_format=zarr_format) store_path = await make_store_path(store) shape = parse_shapelike(shape) @@ -4238,7 +4238,7 @@ async def init_array( from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation - zdtype = parse_data_type(dtype, zarr_format=zarr_format) + zdtype = parse_dtype(dtype, zarr_format=zarr_format) shape_parsed = parse_shapelike(shape) chunk_key_encoding_parsed = _parse_chunk_key_encoding( chunk_key_encoding, zarr_format=zarr_format diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index aadf127c9b..bf09a7501e 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -1,5 +1,6 @@ from __future__ import annotations +from collections.abc import Sequence from typing import TYPE_CHECKING, Final, TypeAlias from zarr.core.dtype.common import ( @@ -94,6 +95,7 @@ "ZDType", "data_type_registry", "parse_data_type", + "parse_dtype", ] data_type_registry = DataTypeRegistry() @@ -188,22 +190,26 @@ def parse_data_type( zarr_format: ZarrFormat, ) -> ZDType[TBaseDType, TBaseScalar]: """ - Interpret the input as a ZDType instance. + Interpret the input as a ZDType. + + This function wraps ``parse_dtype``. The only difference is the function name. This function may + be deprecated in a future version of Zarr Python in favor of ``parse_dtype``. Parameters ---------- dtype_spec : ZDTypeLike - The input to be interpreted as a ZDType instance. This could be a native data type - (e.g., a NumPy data type), a Python object that can be converted into a native data type, - a ZDType instance (in which case the input is returned unchanged), or a JSON object - representation of a data type. + The input to be interpreted as a ZDType. This could be a ZDType, which will be returned + directly, or a JSON representation of a ZDType, or a native dtype, or a python object that + can be converted into a native dtype. zarr_format : ZarrFormat - The zarr format version. + The Zarr format version. This parameter is required because this function will attempt to + parse the JSON representation of a data type, and the JSON representation of data types + varies between Zarr 2 and Zarr 3. Returns ------- ZDType[TBaseDType, TBaseScalar] - The ZDType instance corresponding to the input. + The ZDType corresponding to the input. Examples -------- @@ -216,15 +222,57 @@ def parse_data_type( >>> parse_data_type({"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, zarr_format=3) DateTime64(endianness='little', scale_factor=10, unit='s') """ + return parse_dtype(dtype_spec, zarr_format=zarr_format) + + +def parse_dtype( + dtype_spec: ZDTypeLike, + *, + zarr_format: ZarrFormat, +) -> ZDType[TBaseDType, TBaseScalar]: + """ + Convert the input as a ZDType. + + Parameters + ---------- + dtype_spec : ZDTypeLike + The input to be converted to a ZDType. This could be a ZDType, which will be returned + directly, or a JSON representation of a ZDType, or a numpy dtype, or a python object that + can be converted into a native dtype. + zarr_format : ZarrFormat + The Zarr format version. This parameter is required because this function will attempt to + parse the JSON representation of a data type, and the JSON representation of data types + varies between Zarr 2 and Zarr 3. + + Returns + ------- + ZDType[TBaseDType, TBaseScalar] + The ZDType corresponding to the input. + + Examples + -------- + >>> from zarr.dtype import parse_dtype + >>> import numpy as np + >>> parse_dtype("int32", zarr_format=2) + Int32(endianness='little') + >>> parse_dtype(np.dtype('S10'), zarr_format=2) + NullTerminatedBytes(length=10) + >>> parse_dtype({"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, zarr_format=3) + DateTime64(endianness='little', scale_factor=10, unit='s') + """ if isinstance(dtype_spec, ZDType): return dtype_spec - # dict and zarr_format 3 means that we have a JSON object representation of the dtype - if zarr_format == 3 and isinstance(dtype_spec, Mapping): - return get_data_type_from_json(dtype_spec, zarr_format=3) + # First attempt to interpret the input as JSON + if isinstance(dtype_spec, Mapping | str | Sequence): + try: + return get_data_type_from_json(dtype_spec, zarr_format=zarr_format) # type: ignore[arg-type] + except ValueError: + # no data type matched this JSON-like input + pass if dtype_spec in VLEN_UTF8_ALIAS: # If the dtype request is one of the aliases for variable-length UTF-8 strings, # return that dtype. return VariableLengthUTF8() # type: ignore[return-value] # otherwise, we have either a numpy dtype string, or a zarr v3 dtype string, and in either case - # we can create a numpy dtype from it, and do the dtype inference from that + # we can create a native dtype from it, and do the dtype inference from that return get_data_type_from_native_dtype(dtype_spec) # type: ignore[arg-type] diff --git a/src/zarr/dtype.py b/src/zarr/dtype.py index 79f3aa3a0f..80505ba2f7 100644 --- a/src/zarr/dtype.py +++ b/src/zarr/dtype.py @@ -38,7 +38,7 @@ VariableLengthUTF8JSON_V2, ZDType, data_type_registry, - parse_data_type, + parse_dtype, ) __all__ = [ @@ -83,5 +83,5 @@ "ZDType", "data_type_registry", "data_type_registry", - "parse_data_type", + "parse_dtype", ] diff --git a/tests/test_array.py b/tests/test_array.py index 3f8e61a2e3..42f4a1cbdd 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -53,7 +53,7 @@ VariableLengthBytes, VariableLengthUTF8, ZDType, - parse_data_type, + parse_dtype, ) from zarr.core.dtype.common import ENDIANNESS_STR, EndiannessStr from zarr.core.dtype.npy.common import NUMPY_ENDIANNESS_STR, endianness_from_numpy_str @@ -1308,7 +1308,7 @@ async def test_v2_chunk_encoding( filters=filters, ) filters_expected, compressor_expected = _parse_chunk_encoding_v2( - filters=filters, compressor=compressors, dtype=parse_data_type(dtype, zarr_format=2) + filters=filters, compressor=compressors, dtype=parse_dtype(dtype, zarr_format=2) ) assert arr.metadata.zarr_format == 2 # guard for mypy assert arr.metadata.compressor == compressor_expected diff --git a/tests/test_dtype_registry.py b/tests/test_dtype_registry.py index 95ede9e1d7..2716665ff0 100644 --- a/tests/test_dtype_registry.py +++ b/tests/test_dtype_registry.py @@ -3,7 +3,7 @@ import re import sys from pathlib import Path -from typing import TYPE_CHECKING, Any, get_args +from typing import TYPE_CHECKING, Any, Literal, get_args import numpy as np import pytest @@ -15,18 +15,16 @@ AnyDType, Bool, DataTypeRegistry, - DateTime64, FixedLengthUTF32, - Int8, - Int16, TBaseDType, TBaseScalar, - VariableLengthUTF8, ZDType, data_type_registry, get_data_type_from_json, parse_data_type, + parse_dtype, ) +from zarr.core.dtype.common import unpack_dtype_json if TYPE_CHECKING: from collections.abc import Generator @@ -174,28 +172,56 @@ def test_entrypoint_dtype(zarr_format: ZarrFormat) -> None: data_type_registry.unregister(TestDataType._zarr_v3_name) +@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") +@pytest.mark.parametrize("data_type", zdtype_examples, ids=str) +@pytest.mark.parametrize("json_style", [(2, "internal"), (2, "metadata"), (3, None)], ids=str) @pytest.mark.parametrize( - ("dtype_params", "expected", "zarr_format"), - [ - ("str", VariableLengthUTF8(), 2), - ("str", VariableLengthUTF8(), 3), - ("int8", Int8(), 3), - (Int8(), Int8(), 3), - (">i2", Int16(endianness="big"), 2), - ("datetime64[10s]", DateTime64(unit="s", scale_factor=10), 2), - ( - {"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, - DateTime64(unit="s", scale_factor=10), - 3, - ), - ], + "dtype_parser_func", [parse_dtype, parse_data_type], ids=["parse_dtype", "parse_data_type"] ) def test_parse_data_type( - dtype_params: Any, expected: ZDType[Any, Any], zarr_format: ZarrFormat + data_type: ZDType[Any, Any], + json_style: tuple[ZarrFormat, None | Literal["internal", "metadata"]], + dtype_parser_func: Any, ) -> None: """ - Test that parse_data_type accepts alternative representations of ZDType instances, and resolves - those inputs to the expected ZDType instance. + Test the parsing of data types into ZDType instances. + + This function tests the ability of `dtype_parser_func` to correctly + interpret and parse data type specifications into `ZDType` instances + according to the specified Zarr format and JSON style. + + Parameters + ---------- + data_type : ZDType[Any, Any] + The data type to be tested for parsing. + json_style : tuple[ZarrFormat, None or Literal["internal", "metadata"]] + A tuple specifying the Zarr format version and the JSON style + for Zarr V2 2. For Zarr V2 there are 2 JSON styles: "internal", and + "metadata". The internal style takes the form {"name": , "object_codec_id": }, + while the metadata style is just . + dtype_parser_func : Any + The function to be tested for parsing the data type. This is necessary for compatibility + reasons, as we support multiple functions that perform the same data type parsing operation. """ - observed = parse_data_type(dtype_params, zarr_format=zarr_format) - assert observed == expected + zarr_format, style = json_style + dtype_spec: Any + + if zarr_format == 2: + dtype_spec = data_type.to_json(zarr_format=zarr_format) + if style == "internal": + pass + elif style == "metadata": + dtype_spec = unpack_dtype_json(dtype_spec) + else: + raise ValueError(f"Invalid zarr v2 json style: {style}") + else: + dtype_spec = data_type.to_json(zarr_format=zarr_format) + + if dtype_spec == "|O": + # The object data type on its own is ambiguous and should fail to resolve. + msg = "Zarr data type resolution from object failed." + with pytest.raises(ValueError, match=msg): + dtype_parser_func(dtype_spec, zarr_format=zarr_format) + else: + observed = dtype_parser_func(dtype_spec, zarr_format=zarr_format) + assert observed == data_type diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index 395e036db2..ea2f834bb6 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -18,7 +18,7 @@ open_consolidated, ) from zarr.core.buffer import cpu, default_buffer_prototype -from zarr.core.dtype import parse_data_type +from zarr.core.dtype import parse_dtype from zarr.core.group import ConsolidatedMetadata, GroupMetadata from zarr.core.metadata import ArrayV3Metadata from zarr.core.metadata.v2 import ArrayV2Metadata @@ -504,7 +504,7 @@ async def test_consolidated_metadata_backwards_compatibility( async def test_consolidated_metadata_v2(self): store = zarr.storage.MemoryStore() g = await AsyncGroup.from_store(store, attributes={"key": "root"}, zarr_format=2) - dtype = parse_data_type("uint8", zarr_format=2) + dtype = parse_dtype("uint8", zarr_format=2) await g.create_array(name="a", shape=(1,), attributes={"key": "a"}, dtype=dtype) g1 = await g.create_group(name="g1", attributes={"key": "g1"}) await g1.create_group(name="g2", attributes={"key": "g2"}) From 702f7b37fdce447cf371ad492093cba5e4b7d586 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 22 Jul 2025 15:22:00 +0200 Subject: [PATCH 044/468] convert inf, -inf, nan to JSON (#3280) * convert numpy inf, -inf, nan to JSON * changelog --- changes/3280.fix.rst | 2 ++ src/zarr/core/group.py | 6 +++--- src/zarr/core/metadata/v2.py | 4 ++-- src/zarr/core/metadata/v3.py | 2 +- tests/conftest.py | 20 ++++++++++++++++++++ tests/test_attributes.py | 22 +++++++++++++++------- tests/test_dtype/test_npy/test_common.py | 12 +----------- 7 files changed, 44 insertions(+), 24 deletions(-) create mode 100644 changes/3280.fix.rst diff --git a/changes/3280.fix.rst b/changes/3280.fix.rst new file mode 100644 index 0000000000..510c4d2674 --- /dev/null +++ b/changes/3280.fix.rst @@ -0,0 +1,2 @@ +Fix a regression introduced in 3.1.0 that prevented ``inf``, ``-inf``, and ``nan`` values +from being stored in ``attributes``. \ No newline at end of file diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 45ebba34ff..a868ee31fa 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -336,7 +336,7 @@ def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: if self.zarr_format == 3: return { ZARR_JSON: prototype.buffer.from_bytes( - json.dumps(self.to_dict(), indent=json_indent, allow_nan=False).encode() + json.dumps(self.to_dict(), indent=json_indent, allow_nan=True).encode() ) } else: @@ -345,7 +345,7 @@ def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: json.dumps({"zarr_format": self.zarr_format}, indent=json_indent).encode() ), ZATTRS_JSON: prototype.buffer.from_bytes( - json.dumps(self.attributes, indent=json_indent, allow_nan=False).encode() + json.dumps(self.attributes, indent=json_indent, allow_nan=True).encode() ), } if self.consolidated_metadata: @@ -373,7 +373,7 @@ def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: items[ZMETADATA_V2_JSON] = prototype.buffer.from_bytes( json.dumps( - {"metadata": d, "zarr_consolidated_format": 1}, allow_nan=False + {"metadata": d, "zarr_consolidated_format": 1}, allow_nan=True ).encode() ) diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 7bdad204b8..17af3538a9 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -132,10 +132,10 @@ def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: json_indent = config.get("json_indent") return { ZARRAY_JSON: prototype.buffer.from_bytes( - json.dumps(zarray_dict, indent=json_indent, allow_nan=False).encode() + json.dumps(zarray_dict, indent=json_indent, allow_nan=True).encode() ), ZATTRS_JSON: prototype.buffer.from_bytes( - json.dumps(zattrs_dict, indent=json_indent, allow_nan=False).encode() + json.dumps(zattrs_dict, indent=json_indent, allow_nan=True).encode() ), } diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 84872d3dbd..6f79fb4b09 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -288,7 +288,7 @@ def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: d = self.to_dict() return { ZARR_JSON: prototype.buffer.from_bytes( - json.dumps(d, allow_nan=False, indent=json_indent).encode() + json.dumps(d, allow_nan=True, indent=json_indent).encode() ) } diff --git a/tests/conftest.py b/tests/conftest.py index 4d300a1fd4..a1bf423c06 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,7 +1,9 @@ from __future__ import annotations +import math import os import pathlib +from collections.abc import Mapping, Sequence from dataclasses import dataclass, field from typing import TYPE_CHECKING @@ -442,3 +444,21 @@ def skip_object_dtype(dtype: ZDType[Any, Any]) -> None: "type resolution" ) pytest.skip(msg) + + +def nan_equal(a: object, b: object) -> bool: + """ + Convenience function for equality comparison between two values ``a`` and ``b``, that might both + be NaN. Returns True if both ``a`` and ``b`` are NaN, otherwise returns a == b + """ + if math.isnan(a) and math.isnan(b): # type: ignore[arg-type] + return True + return a == b + + +def deep_nan_equal(a: object, b: object) -> bool: + if isinstance(a, Mapping) and isinstance(b, Mapping): + return all(deep_nan_equal(a[k], b[k]) for k in a) + if isinstance(a, Sequence) and isinstance(b, Sequence): + return all(deep_nan_equal(a[i], b[i]) for i in range(len(a))) + return nan_equal(a, b) diff --git a/tests/test_attributes.py b/tests/test_attributes.py index 127b2dbc36..4ce40e2cb0 100644 --- a/tests/test_attributes.py +++ b/tests/test_attributes.py @@ -1,18 +1,26 @@ +import json +from typing import Any + +import numpy as np import pytest import zarr.core import zarr.core.attributes import zarr.storage +from tests.conftest import deep_nan_equal +from zarr.core.common import ZarrFormat -def test_put() -> None: +@pytest.mark.parametrize("zarr_format", [2, 3]) +@pytest.mark.parametrize( + "data", [{"inf": np.inf, "-inf": -np.inf, "nan": np.nan}, {"a": 3, "c": 4}] +) +def test_put(data: dict[str, Any], zarr_format: ZarrFormat) -> None: store = zarr.storage.MemoryStore() - attrs = zarr.core.attributes.Attributes( - zarr.Group.from_store(store, attributes={"a": 1, "b": 2}) - ) - attrs.put({"a": 3, "c": 4}) - expected = {"a": 3, "c": 4} - assert dict(attrs) == expected + attrs = zarr.core.attributes.Attributes(zarr.Group.from_store(store, zarr_format=zarr_format)) + attrs.put(data) + expected = json.loads(json.dumps(data, allow_nan=True)) + assert deep_nan_equal(dict(attrs), expected) def test_asdict() -> None: diff --git a/tests/test_dtype/test_npy/test_common.py b/tests/test_dtype/test_npy/test_common.py index d39d308112..bd77866fc0 100644 --- a/tests/test_dtype/test_npy/test_common.py +++ b/tests/test_dtype/test_npy/test_common.py @@ -1,7 +1,6 @@ from __future__ import annotations import base64 -import math import re import sys from typing import TYPE_CHECKING, Any, get_args @@ -9,6 +8,7 @@ import numpy as np import pytest +from tests.conftest import nan_equal from zarr.core.dtype.common import ENDIANNESS_STR, JSONFloatV2, SpecialFloatStrings from zarr.core.dtype.npy.common import ( NumpyEndiannessStr, @@ -35,16 +35,6 @@ from zarr.core.common import JSON, ZarrFormat -def nan_equal(a: object, b: object) -> bool: - """ - Convenience function for equality comparison between two values ``a`` and ``b``, that might both - be NaN. Returns True if both ``a`` and ``b`` are NaN, otherwise returns a == b - """ - if math.isnan(a) and math.isnan(b): # type: ignore[arg-type] - return True - return a == b - - json_float_v2_roundtrip_cases: tuple[tuple[JSONFloatV2, float | np.floating[Any]], ...] = ( ("Infinity", float("inf")), ("Infinity", np.inf), From 5390e1dcae119af54ed6ec015dce7fa5fdff67d9 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Tue, 22 Jul 2025 14:41:45 +0100 Subject: [PATCH 045/468] Give codecs docstrings (#3274) Co-authored-by: Davis Bennett --- pyproject.toml | 1 - src/zarr/codecs/blosc.py | 2 ++ src/zarr/codecs/bytes.py | 2 ++ src/zarr/codecs/crc32c_.py | 2 ++ src/zarr/codecs/gzip.py | 2 ++ src/zarr/codecs/sharding.py | 2 ++ src/zarr/codecs/transpose.py | 2 ++ src/zarr/codecs/vlen_utf8.py | 2 ++ src/zarr/codecs/zstd.py | 2 ++ 9 files changed, 16 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0b7cb9f856..738330739b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -437,7 +437,6 @@ checks = [ # Currently broken; see https://github.com/numpy/numpydoc/issues/573 # "GL09", "GL10", - "SS02", "SS04", "PR02", "PR03", diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 1c5e52e9a4..f89f127852 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -87,6 +87,8 @@ def parse_blocksize(data: JSON) -> int: @dataclass(frozen=True) class BloscCodec(BytesBytesCodec): + """blosc codec""" + is_fixed_size = False typesize: int | None diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index d663a3b2cc..7576119c82 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -33,6 +33,8 @@ class Endian(Enum): @dataclass(frozen=True) class BytesCodec(ArrayBytesCodec): + """bytes codec""" + is_fixed_size = True endian: Endian | None diff --git a/src/zarr/codecs/crc32c_.py b/src/zarr/codecs/crc32c_.py index 6da673ceac..c2e30f689a 100644 --- a/src/zarr/codecs/crc32c_.py +++ b/src/zarr/codecs/crc32c_.py @@ -20,6 +20,8 @@ @dataclass(frozen=True) class Crc32cCodec(BytesBytesCodec): + """crc32c codec""" + is_fixed_size = True @classmethod diff --git a/src/zarr/codecs/gzip.py b/src/zarr/codecs/gzip.py index b6e693148e..9e6515a4d1 100644 --- a/src/zarr/codecs/gzip.py +++ b/src/zarr/codecs/gzip.py @@ -30,6 +30,8 @@ def parse_gzip_level(data: JSON) -> int: @dataclass(frozen=True) class GzipCodec(BytesBytesCodec): + """gzip codec""" + is_fixed_size = False level: int = 5 diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index cd8676b4d1..888d258649 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -333,6 +333,8 @@ async def finalize( class ShardingCodec( ArrayBytesCodec, ArrayBytesCodecPartialDecodeMixin, ArrayBytesCodecPartialEncodeMixin ): + """Sharding codec""" + chunk_shape: ChunkCoords codecs: tuple[Codec, ...] index_codecs: tuple[Codec, ...] diff --git a/src/zarr/codecs/transpose.py b/src/zarr/codecs/transpose.py index be89690441..c87804685c 100644 --- a/src/zarr/codecs/transpose.py +++ b/src/zarr/codecs/transpose.py @@ -29,6 +29,8 @@ def parse_transpose_order(data: JSON | Iterable[int]) -> tuple[int, ...]: @dataclass(frozen=True) class TransposeCodec(ArrayArrayCodec): + """Transpose codec""" + is_fixed_size = True order: tuple[int, ...] diff --git a/src/zarr/codecs/vlen_utf8.py b/src/zarr/codecs/vlen_utf8.py index bad51f33ce..28c64be1c0 100644 --- a/src/zarr/codecs/vlen_utf8.py +++ b/src/zarr/codecs/vlen_utf8.py @@ -24,6 +24,8 @@ @dataclass(frozen=True) class VLenUTF8Codec(ArrayBytesCodec): + """Variable-length UTF8 codec""" + @classmethod def from_dict(cls, data: dict[str, JSON]) -> Self: _, configuration_parsed = parse_named_configuration( diff --git a/src/zarr/codecs/zstd.py b/src/zarr/codecs/zstd.py index b4a4a13c29..ead41e7b5f 100644 --- a/src/zarr/codecs/zstd.py +++ b/src/zarr/codecs/zstd.py @@ -37,6 +37,8 @@ def parse_checksum(data: JSON) -> bool: @dataclass(frozen=True) class ZstdCodec(BytesBytesCodec): + """zstd codec""" + is_fixed_size = True level: int = 0 From b877f89fa2959e15d3d49bf027792fb23ce97b84 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 23 Jul 2025 10:42:03 +0200 Subject: [PATCH 046/468] PEP 639 compliance (#3283) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Declare licenses using only these two fields, as per PEP 639: * license: SPDX license expression consisting of one or more license identifiers * license-files: list of license file glob patterns Supported by hatchling ≥ 1.27.0: https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license-and-license-files --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 738330739b..6d5a567ae7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["hatchling", "hatch-vcs"] +requires = ["hatchling>=1.27.0", "hatch-vcs"] build-backend = "hatchling.build" [tool.hatch.build.targets.sdist] @@ -47,7 +47,6 @@ classifiers = [ 'Intended Audience :: Developers', 'Intended Audience :: Information Technology', 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: MIT License', 'Programming Language :: Python', 'Topic :: Software Development :: Libraries :: Python Modules', 'Operating System :: Unix', @@ -56,7 +55,8 @@ classifiers = [ 'Programming Language :: Python :: 3.12', 'Programming Language :: Python :: 3.13', ] -license = {text = "MIT License"} +license = "MIT" +license-files = ["LICENSE.txt"] keywords = ["Python", "compressed", "ndimensional-arrays", "zarr"] [project.optional-dependencies] From 9dc744db5ca33cfeb2774619f39ea580811596b7 Mon Sep 17 00:00:00 2001 From: Seth P Date: Wed, 23 Jul 2025 15:12:27 -0400 Subject: [PATCH 047/468] Fix incorrect Group.nmembers for consolidated metadata (#3287) --- changes/3287.bugfix.rst | 1 + src/zarr/core/group.py | 13 ++++++++++++- tests/test_group.py | 10 ++++++++++ 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 changes/3287.bugfix.rst diff --git a/changes/3287.bugfix.rst b/changes/3287.bugfix.rst new file mode 100644 index 0000000000..a4eaa35312 --- /dev/null +++ b/changes/3287.bugfix.rst @@ -0,0 +1 @@ +Fixes Group.nmembers() ignoring depth when using consolidated metadata. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index a868ee31fa..a398aa01aa 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -1307,7 +1307,18 @@ async def nmembers( # check if we can use consolidated metadata, which requires that we have non-None # consolidated metadata at all points in the hierarchy. if self.metadata.consolidated_metadata is not None: - return len(self.metadata.consolidated_metadata.flattened_metadata) + if max_depth is not None and max_depth < 0: + raise ValueError(f"max_depth must be None or >= 0. Got '{max_depth}' instead") + if max_depth is None: + return len(self.metadata.consolidated_metadata.flattened_metadata) + else: + return len( + [ + x + for x in self.metadata.consolidated_metadata.flattened_metadata + if x.count("/") <= max_depth + ] + ) # TODO: consider using aioitertools.builtins.sum for this # return await aioitertools.builtins.sum((1 async for _ in self.members()), start=0) n = 0 diff --git a/tests/test_group.py b/tests/test_group.py index ac1afb539b..7705fa205a 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -1118,12 +1118,22 @@ async def test_group_members_async(store: Store, consolidated_metadata: bool) -> "consolidated_metadata", None, ) + # test depth=0 + nmembers = await group.nmembers(max_depth=0) + assert nmembers == 2 + # test depth=1 + nmembers = await group.nmembers(max_depth=1) + assert nmembers == 4 + # test depth=None all_children = sorted( [x async for x in group.members(max_depth=None)], key=operator.itemgetter(0) ) assert len(all_children) == 4 nmembers = await group.nmembers(max_depth=None) assert nmembers == 4 + # test depth<0 + with pytest.raises(ValueError, match="max_depth"): + await group.nmembers(max_depth=-1) async def test_require_group(store: LocalStore | MemoryStore, zarr_format: ZarrFormat) -> None: From a4e966065bb39ac74e529b599c09d051c148263a Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Thu, 24 Jul 2025 14:35:54 +0200 Subject: [PATCH 048/468] Bump copyright year in LICENSE file (#3286) --- LICENSE.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE.txt b/LICENSE.txt index a4de1c39d3..1e8da4d242 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,6 +1,6 @@ The MIT License (MIT) -Copyright (c) 2015-2024 Zarr Developers +Copyright (c) 2015-2025 Zarr Developers Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal From 3d07ec5aea7aab7e10b4b20a456e85310c8d17e9 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 25 Jul 2025 09:13:59 +0100 Subject: [PATCH 049/468] Put back parse_data_type import (#3292) --- src/zarr/dtype.py | 3 +++ tests/test_dtype_registry.py | 10 ++++++---- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/src/zarr/dtype.py b/src/zarr/dtype.py index 80505ba2f7..616d1c1ce2 100644 --- a/src/zarr/dtype.py +++ b/src/zarr/dtype.py @@ -38,6 +38,9 @@ VariableLengthUTF8JSON_V2, ZDType, data_type_registry, + # Import for backwards compatibility, but not included in __all__ + # so it doesn't show up in the docs + parse_data_type, # noqa: F401 parse_dtype, ) diff --git a/tests/test_dtype_registry.py b/tests/test_dtype_registry.py index 2716665ff0..aedda5272c 100644 --- a/tests/test_dtype_registry.py +++ b/tests/test_dtype_registry.py @@ -13,18 +13,20 @@ from zarr.core.config import config from zarr.core.dtype import ( AnyDType, - Bool, DataTypeRegistry, - FixedLengthUTF32, TBaseDType, TBaseScalar, + get_data_type_from_json, +) +from zarr.core.dtype.common import unpack_dtype_json +from zarr.dtype import ( # type: ignore[attr-defined] + Bool, + FixedLengthUTF32, ZDType, data_type_registry, - get_data_type_from_json, parse_data_type, parse_dtype, ) -from zarr.core.dtype.common import unpack_dtype_json if TYPE_CHECKING: from collections.abc import Generator From 01751d6ce1a01780ae0e120fc2cdd88431382d31 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 25 Jul 2025 11:00:17 +0100 Subject: [PATCH 050/468] Add script to check changelog entries (#3290) * Add script to check changelog entries Fix formatting * Fix changelog entries --------- Co-authored-by: Davis Bennett --- .github/workflows/check_changelogs.yml | 18 +++++++ changes/{3251.fix.rst => 3251.bugfix.rst} | 0 .../{+c563f4d4.bugfix.rst => 3258.bugfix.rst} | 0 changes/{3264.fix.rst => 3264.bugfix.rst} | 0 changes/{3280.fix.rst => 3280.bugfix.rst} | 0 ci/check_changelog_entries.py | 51 +++++++++++++++++++ 6 files changed, 69 insertions(+) create mode 100644 .github/workflows/check_changelogs.yml rename changes/{3251.fix.rst => 3251.bugfix.rst} (100%) rename changes/{+c563f4d4.bugfix.rst => 3258.bugfix.rst} (100%) rename changes/{3264.fix.rst => 3264.bugfix.rst} (100%) rename changes/{3280.fix.rst => 3280.bugfix.rst} (100%) create mode 100644 ci/check_changelog_entries.py diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml new file mode 100644 index 0000000000..8069fc1319 --- /dev/null +++ b/.github/workflows/check_changelogs.yml @@ -0,0 +1,18 @@ +name: Check changelog entries + +on: + pull_request: + +jobs: + check-changelogs: + name: Check changelog entries + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + + - name: Install uv + uses: astral-sh/setup-uv@e92bafb6253dcd438e0484186d7669ea7a8ca1cc # v6.4.3 + + - name: Check changelog entries + run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/changes/3251.fix.rst b/changes/3251.bugfix.rst similarity index 100% rename from changes/3251.fix.rst rename to changes/3251.bugfix.rst diff --git a/changes/+c563f4d4.bugfix.rst b/changes/3258.bugfix.rst similarity index 100% rename from changes/+c563f4d4.bugfix.rst rename to changes/3258.bugfix.rst diff --git a/changes/3264.fix.rst b/changes/3264.bugfix.rst similarity index 100% rename from changes/3264.fix.rst rename to changes/3264.bugfix.rst diff --git a/changes/3280.fix.rst b/changes/3280.bugfix.rst similarity index 100% rename from changes/3280.fix.rst rename to changes/3280.bugfix.rst diff --git a/ci/check_changelog_entries.py b/ci/check_changelog_entries.py new file mode 100644 index 0000000000..9f883f0be4 --- /dev/null +++ b/ci/check_changelog_entries.py @@ -0,0 +1,51 @@ +""" +Check changelog entries have the correct filename structure. +""" + +import sys +from pathlib import Path + +VALID_CHANGELOG_TYPES = ["feature", "bugfix", "doc", "removal", "misc"] +CHANGELOG_DIRECTORY = (Path(__file__).parent.parent / "changes").resolve() + + +def is_int(s: str) -> bool: + try: + int(s) + except ValueError: + return False + else: + return True + + +if __name__ == "__main__": + print(f"Looking for changelog entries in {CHANGELOG_DIRECTORY}") + entries = CHANGELOG_DIRECTORY.glob("*") + entries = [e for e in entries if e.name not in [".gitignore", "README.md"]] + print(f"Found {len(entries)} entries") + print() + + bad_suffix = [e for e in entries if e.suffix != ".rst"] + bad_issue_no = [e for e in entries if not is_int(e.name.split(".")[0])] + bad_type = [e for e in entries if e.name.split(".")[1] not in VALID_CHANGELOG_TYPES] + + if len(bad_suffix) or len(bad_issue_no) or len(bad_type): + if len(bad_suffix): + print("Changelog entries without .rst suffix") + print("-------------------------------------") + print("\n".join([p.name for p in bad_suffix])) + print() + if len(bad_issue_no): + print("Changelog entries without integer issue number") + print("----------------------------------------------") + print("\n".join([p.name for p in bad_issue_no])) + print() + if len(bad_type): + print("Changelog entries without valid type") + print("------------------------------------") + print("\n".join([p.name for p in bad_type])) + print(f"Valid types are: {VALID_CHANGELOG_TYPES}") + print() + sys.exit(1) + + sys.exit(0) From a0c56fbbba12ca4402de3d83043e5f840406d670 Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:07:44 +0100 Subject: [PATCH 051/468] prevent matching ... in longer lines (#3298) --- pyproject.toml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6d5a567ae7..0b09171446 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,7 +70,7 @@ gpu = [ ] # Development extras test = [ - "coverage", + "coverage>=7.10", # Pin possibly due to https://github.com/pytest-dev/pytest-cov/issues/693 "pytest<8.4", "pytest-asyncio", @@ -128,11 +128,8 @@ dev = [ ] [tool.coverage.report] -exclude_lines = [ - "pragma: no cover", - "if TYPE_CHECKING:", - "pragma: ${PY_MAJOR_VERSION} no cover", - '.*\.\.\.' # Ignore "..." lines +exclude_also = [ + 'if TYPE_CHECKING:', ] [tool.coverage.run] From 108ec58dc9f44457a22fa4a95d03633d401a881a Mon Sep 17 00:00:00 2001 From: Tom Nicholas Date: Wed, 30 Jul 2025 09:55:56 -0700 Subject: [PATCH 052/468] Add async oindex and vindex methods to AsyncArray (#3083) Co-authored-by: Davis Bennett --- changes/3083.feature.rst | 1 + src/zarr/core/array.py | 67 +++++++++++++++++++++- src/zarr/core/chunk_grids.py | 2 +- src/zarr/core/common.py | 7 +++ src/zarr/core/indexing.py | 58 ++++++++++++++++--- tests/test_array.py | 4 +- tests/test_indexing.py | 107 +++++++++++++++++++++++++++++++++++ tests/test_properties.py | 41 ++++++++++++-- 8 files changed, 270 insertions(+), 17 deletions(-) create mode 100644 changes/3083.feature.rst diff --git a/changes/3083.feature.rst b/changes/3083.feature.rst new file mode 100644 index 0000000000..4403224df1 --- /dev/null +++ b/changes/3083.feature.rst @@ -0,0 +1 @@ +Added support for async vectorized and orthogonal indexing. \ No newline at end of file diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 78dddf3669..260e94bc88 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -61,6 +61,7 @@ ZarrFormat, _default_zarr_format, _warn_order_kwarg, + ceildiv, concurrent_map, parse_shapelike, product, @@ -76,6 +77,8 @@ ) from zarr.core.dtype.common import HasEndianness, HasItemSize, HasObjectCodec from zarr.core.indexing import ( + AsyncOIndex, + AsyncVIndex, BasicIndexer, BasicSelection, BlockIndex, @@ -92,7 +95,6 @@ Selection, VIndex, _iter_grid, - ceildiv, check_fields, check_no_multi_fields, is_pure_fancy_indexing, @@ -1425,6 +1427,56 @@ async def getitem( ) return await self._get_selection(indexer, prototype=prototype) + async def get_orthogonal_selection( + self, + selection: OrthogonalSelection, + *, + out: NDBuffer | None = None, + fields: Fields | None = None, + prototype: BufferPrototype | None = None, + ) -> NDArrayLikeOrScalar: + if prototype is None: + prototype = default_buffer_prototype() + indexer = OrthogonalIndexer(selection, self.shape, self.metadata.chunk_grid) + return await self._get_selection( + indexer=indexer, out=out, fields=fields, prototype=prototype + ) + + async def get_mask_selection( + self, + mask: MaskSelection, + *, + out: NDBuffer | None = None, + fields: Fields | None = None, + prototype: BufferPrototype | None = None, + ) -> NDArrayLikeOrScalar: + if prototype is None: + prototype = default_buffer_prototype() + indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid) + return await self._get_selection( + indexer=indexer, out=out, fields=fields, prototype=prototype + ) + + async def get_coordinate_selection( + self, + selection: CoordinateSelection, + *, + out: NDBuffer | None = None, + fields: Fields | None = None, + prototype: BufferPrototype | None = None, + ) -> NDArrayLikeOrScalar: + if prototype is None: + prototype = default_buffer_prototype() + indexer = CoordinateIndexer(selection, self.shape, self.metadata.chunk_grid) + out_array = await self._get_selection( + indexer=indexer, out=out, fields=fields, prototype=prototype + ) + + if hasattr(out_array, "shape"): + # restore shape + out_array = np.array(out_array).reshape(indexer.sel_shape) + return out_array + async def _save_metadata(self, metadata: ArrayMetadata, ensure_parents: bool = False) -> None: """ Asynchronously save the array metadata. @@ -1556,6 +1608,19 @@ async def setitem( ) return await self._set_selection(indexer, value, prototype=prototype) + @property + def oindex(self) -> AsyncOIndex[T_ArrayMetadata]: + """Shortcut for orthogonal (outer) indexing, see :func:`get_orthogonal_selection` and + :func:`set_orthogonal_selection` for documentation and examples.""" + return AsyncOIndex(self) + + @property + def vindex(self) -> AsyncVIndex[T_ArrayMetadata]: + """Shortcut for vectorized (inner) indexing, see :func:`get_coordinate_selection`, + :func:`set_coordinate_selection`, :func:`get_mask_selection` and + :func:`set_mask_selection` for documentation and examples.""" + return AsyncVIndex(self) + async def resize(self, new_shape: ShapeLike, delete_outside_chunks: bool = True) -> None: """ Asynchronously resize the array to a new shape. diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 4bf03c89de..6a3d6816a6 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -18,10 +18,10 @@ ChunkCoords, ChunkCoordsLike, ShapeLike, + ceildiv, parse_named_configuration, parse_shapelike, ) -from zarr.core.indexing import ceildiv if TYPE_CHECKING: from collections.abc import Iterator diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index e86347d808..33590c83a5 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -2,6 +2,7 @@ import asyncio import functools +import math import operator import warnings from collections.abc import Iterable, Mapping, Sequence @@ -69,6 +70,12 @@ def product(tup: ChunkCoords) -> int: return functools.reduce(operator.mul, tup, 1) +def ceildiv(a: float, b: float) -> int: + if a == 0: + return 0 + return math.ceil(a / b) + + T = TypeVar("T", bound=tuple[Any, ...]) V = TypeVar("V") diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index c11889f7f4..15cf6f0f1a 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -12,6 +12,7 @@ from typing import ( TYPE_CHECKING, Any, + Generic, Literal, NamedTuple, Protocol, @@ -25,14 +26,16 @@ import numpy as np import numpy.typing as npt -from zarr.core.common import product +from zarr.core.common import ceildiv, product +from zarr.core.metadata import T_ArrayMetadata if TYPE_CHECKING: - from zarr.core.array import Array + from zarr.core.array import Array, AsyncArray from zarr.core.buffer import NDArrayLikeOrScalar from zarr.core.chunk_grids import ChunkGrid from zarr.core.common import ChunkCoords + IntSequence = list[int] | npt.NDArray[np.intp] ArrayOfIntOrBool = npt.NDArray[np.intp] | npt.NDArray[np.bool_] BasicSelector = int | slice | EllipsisType @@ -93,12 +96,6 @@ class Indexer(Protocol): def __iter__(self) -> Iterator[ChunkProjection]: ... -def ceildiv(a: float, b: float) -> int: - if a == 0: - return 0 - return math.ceil(a / b) - - _ArrayIndexingOrder: TypeAlias = Literal["lexicographic"] @@ -960,6 +957,25 @@ def __setitem__(self, selection: OrthogonalSelection, value: npt.ArrayLike) -> N ) +@dataclass(frozen=True) +class AsyncOIndex(Generic[T_ArrayMetadata]): + array: AsyncArray[T_ArrayMetadata] + + async def getitem(self, selection: OrthogonalSelection | Array) -> NDArrayLikeOrScalar: + from zarr.core.array import Array + + # if input is a Zarr array, we materialize it now. + if isinstance(selection, Array): + selection = _zarr_array_to_int_or_bool_array(selection) + + fields, new_selection = pop_fields(selection) + new_selection = ensure_tuple(new_selection) + new_selection = replace_lists(new_selection) + return await self.array.get_orthogonal_selection( + cast(OrthogonalSelection, new_selection), fields=fields + ) + + @dataclass(frozen=True) class BlockIndexer(Indexer): dim_indexers: list[SliceDimIndexer] @@ -1268,6 +1284,32 @@ def __setitem__( raise VindexInvalidSelectionError(new_selection) +@dataclass(frozen=True) +class AsyncVIndex(Generic[T_ArrayMetadata]): + array: AsyncArray[T_ArrayMetadata] + + # TODO: develop Array generic and move zarr.Array[np.intp] | zarr.Array[np.bool_] to ArrayOfIntOrBool + async def getitem( + self, selection: CoordinateSelection | MaskSelection | Array + ) -> NDArrayLikeOrScalar: + # TODO deduplicate these internals with the sync version of getitem + # TODO requires solving this circular sync issue: https://github.com/zarr-developers/zarr-python/pull/3083#discussion_r2230737448 + from zarr.core.array import Array + + # if input is a Zarr array, we materialize it now. + if isinstance(selection, Array): + selection = _zarr_array_to_int_or_bool_array(selection) + fields, new_selection = pop_fields(selection) + new_selection = ensure_tuple(new_selection) + new_selection = replace_lists(new_selection) + if is_coordinate_selection(new_selection, self.array.shape): + return await self.array.get_coordinate_selection(new_selection, fields=fields) + elif is_mask_selection(new_selection, self.array.shape): + return await self.array.get_mask_selection(new_selection, fields=fields) + else: + raise VindexInvalidSelectionError(new_selection) + + def check_fields(fields: Fields | None, dtype: np.dtype[Any]) -> np.dtype[Any]: # early out if fields is None: diff --git a/tests/test_array.py b/tests/test_array.py index 42f4a1cbdd..f672006f9a 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -41,7 +41,7 @@ from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, default_buffer_prototype from zarr.core.chunk_grids import _auto_partition from zarr.core.chunk_key_encodings import ChunkKeyEncodingParams -from zarr.core.common import JSON, ZarrFormat +from zarr.core.common import JSON, ZarrFormat, ceildiv from zarr.core.dtype import ( DateTime64, Float32, @@ -59,7 +59,7 @@ from zarr.core.dtype.npy.common import NUMPY_ENDIANNESS_STR, endianness_from_numpy_str from zarr.core.dtype.npy.string import UTF8Base from zarr.core.group import AsyncGroup -from zarr.core.indexing import BasicIndexer, ceildiv +from zarr.core.indexing import BasicIndexer from zarr.core.metadata.v2 import ArrayV2Metadata from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import sync diff --git a/tests/test_indexing.py b/tests/test_indexing.py index fd4bb13bb1..24b4b65505 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -1994,3 +1994,110 @@ def test_iter_chunk_regions(): assert_array_equal(a[region], np.ones_like(a[region])) a[region] = 0 assert_array_equal(a[region], np.zeros_like(a[region])) + + +class TestAsync: + @pytest.mark.parametrize( + ("indexer", "expected"), + [ + # int + ((0,), np.array([1, 2])), + ((1,), np.array([3, 4])), + ((0, 1), np.array(2)), + # slice + ((slice(None),), np.array([[1, 2], [3, 4]])), + ((slice(0, 1),), np.array([[1, 2]])), + ((slice(1, 2),), np.array([[3, 4]])), + ((slice(0, 2),), np.array([[1, 2], [3, 4]])), + ((slice(0, 0),), np.empty(shape=(0, 2), dtype="i8")), + # ellipsis + ((...,), np.array([[1, 2], [3, 4]])), + ((0, ...), np.array([1, 2])), + ((..., 0), np.array([1, 3])), + ((0, 1, ...), np.array(2)), + # combined + ((0, slice(None)), np.array([1, 2])), + ((slice(None), 0), np.array([1, 3])), + ((slice(None), slice(None)), np.array([[1, 2], [3, 4]])), + # array of ints + (([0]), np.array([[1, 2]])), + (([1]), np.array([[3, 4]])), + (([0], [1]), np.array(2)), + (([0, 1], [0]), np.array([[1], [3]])), + (([0, 1], [0, 1]), np.array([[1, 2], [3, 4]])), + # boolean array + (np.array([True, True]), np.array([[1, 2], [3, 4]])), + (np.array([True, False]), np.array([[1, 2]])), + (np.array([False, True]), np.array([[3, 4]])), + (np.array([False, False]), np.empty(shape=(0, 2), dtype="i8")), + ], + ) + @pytest.mark.asyncio + async def test_async_oindex(self, store, indexer, expected): + z = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") + z[...] = np.array([[1, 2], [3, 4]]) + async_zarr = z._async_array + + result = await async_zarr.oindex.getitem(indexer) + assert_array_equal(result, expected) + + @pytest.mark.asyncio + async def test_async_oindex_with_zarr_array(self, store): + z1 = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") + z1[...] = np.array([[1, 2], [3, 4]]) + async_zarr = z1._async_array + + # create boolean zarr array to index with + z2 = zarr.create_array( + store=store, name="z2", shape=(2,), chunks=(1,), zarr_format=3, dtype="?" + ) + z2[...] = np.array([True, False]) + + result = await async_zarr.oindex.getitem(z2) + expected = np.array([[1, 2]]) + assert_array_equal(result, expected) + + @pytest.mark.parametrize( + ("indexer", "expected"), + [ + (([0], [0]), np.array(1)), + (([0, 1], [0, 1]), np.array([1, 4])), + (np.array([[False, True], [False, True]]), np.array([2, 4])), + ], + ) + @pytest.mark.asyncio + async def test_async_vindex(self, store, indexer, expected): + z = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") + z[...] = np.array([[1, 2], [3, 4]]) + async_zarr = z._async_array + + result = await async_zarr.vindex.getitem(indexer) + assert_array_equal(result, expected) + + @pytest.mark.asyncio + async def test_async_vindex_with_zarr_array(self, store): + z1 = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") + z1[...] = np.array([[1, 2], [3, 4]]) + async_zarr = z1._async_array + + # create boolean zarr array to index with + z2 = zarr.create_array( + store=store, name="z2", shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="?" + ) + z2[...] = np.array([[False, True], [False, True]]) + + result = await async_zarr.vindex.getitem(z2) + expected = np.array([2, 4]) + assert_array_equal(result, expected) + + @pytest.mark.asyncio + async def test_async_invalid_indexer(self, store): + z = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") + z[...] = np.array([[1, 2], [3, 4]]) + async_zarr = z._async_array + + with pytest.raises(IndexError): + await async_zarr.vindex.getitem("invalid_indexer") + + with pytest.raises(IndexError): + await async_zarr.oindex.getitem("invalid_indexer") diff --git a/tests/test_properties.py b/tests/test_properties.py index 27f847fa69..705cfd1b59 100644 --- a/tests/test_properties.py +++ b/tests/test_properties.py @@ -105,33 +105,52 @@ def test_array_creates_implicit_groups(array): # this decorator removes timeout; not ideal but it should avoid intermittent CI failures +@pytest.mark.asyncio @settings(deadline=None) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") @given(data=st.data()) -def test_basic_indexing(data: st.DataObject) -> None: +async def test_basic_indexing(data: st.DataObject) -> None: zarray = data.draw(simple_arrays()) nparray = zarray[:] indexer = data.draw(basic_indices(shape=nparray.shape)) + + # sync get actual = zarray[indexer] assert_array_equal(nparray[indexer], actual) + # async get + async_zarray = zarray._async_array + actual = await async_zarray.getitem(indexer) + assert_array_equal(nparray[indexer], actual) + + # sync set new_data = data.draw(numpy_arrays(shapes=st.just(actual.shape), dtype=nparray.dtype)) zarray[indexer] = new_data nparray[indexer] = new_data assert_array_equal(nparray, zarray[:]) + # TODO test async setitem? + +@pytest.mark.asyncio @given(data=st.data()) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") -def test_oindex(data: st.DataObject) -> None: +async def test_oindex(data: st.DataObject) -> None: # integer_array_indices can't handle 0-size dimensions. zarray = data.draw(simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1))) nparray = zarray[:] - zindexer, npindexer = data.draw(orthogonal_indices(shape=nparray.shape)) + + # sync get actual = zarray.oindex[zindexer] assert_array_equal(nparray[npindexer], actual) + # async get + async_zarray = zarray._async_array + actual = await async_zarray.oindex.getitem(zindexer) + assert_array_equal(nparray[npindexer], actual) + + # sync get assume(zarray.shards is None) # GH2834 for idxr in npindexer: if isinstance(idxr, np.ndarray) and idxr.size != np.unique(idxr).size: @@ -142,22 +161,32 @@ def test_oindex(data: st.DataObject) -> None: zarray.oindex[zindexer] = new_data assert_array_equal(nparray, zarray[:]) + # note: async oindex setitem not yet implemented + +@pytest.mark.asyncio @given(data=st.data()) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") -def test_vindex(data: st.DataObject) -> None: +async def test_vindex(data: st.DataObject) -> None: # integer_array_indices can't handle 0-size dimensions. zarray = data.draw(simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1))) nparray = zarray[:] - indexer = data.draw( npst.integer_array_indices( shape=nparray.shape, result_shape=npst.array_shapes(min_side=1, max_dims=None) ) ) + + # sync get actual = zarray.vindex[indexer] assert_array_equal(nparray[indexer], actual) + # async get + async_zarray = zarray._async_array + actual = await async_zarray.vindex.getitem(indexer) + assert_array_equal(nparray[indexer], actual) + + # sync set # FIXME! # when the indexer is such that a value gets overwritten multiple times, # I think the output depends on chunking. @@ -166,6 +195,8 @@ def test_vindex(data: st.DataObject) -> None: # zarray.vindex[indexer] = new_data # assert_array_equal(nparray, zarray[:]) + # note: async vindex setitem not yet implemented + @given(store=stores, meta=array_metadata()) # type: ignore[misc] @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") From 4eda04eb39bef4bfd309fc85a5c3b10a472cdf16 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 31 Jul 2025 12:45:24 +0100 Subject: [PATCH 053/468] Update CI & release checklist for release branch (#3312) * Run CI on 3.1.x branch * Clarify releasing on a branch --- .github/ISSUE_TEMPLATE/release-checklist.md | 6 ++++-- .github/workflows/gpu_test.yml | 4 ++-- .github/workflows/hypothesis.yaml | 4 ++-- .github/workflows/test.yml | 4 ++-- docs/developers/contributing.rst | 5 ++++- 5 files changed, 14 insertions(+), 9 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/release-checklist.md b/.github/ISSUE_TEMPLATE/release-checklist.md index e754cab54c..ca973c8c38 100644 --- a/.github/ISSUE_TEMPLATE/release-checklist.md +++ b/.github/ISSUE_TEMPLATE/release-checklist.md @@ -7,7 +7,7 @@ assignees: '' --- -**Release**: [v0.x.x](https://github.com/zarr-developers/zarr-python/milestones/?) +**Release**: [v3.x.x](https://github.com/zarr-developers/zarr-python/milestones/?) **Scheduled Date**: 20YY/MM/DD **Priority PRs/issues to complete prior to release** @@ -16,8 +16,9 @@ assignees: '' **Before release**: +- [ ] Make sure the release branch (e.g., `3.1.x`) is up to date with any backports. - [ ] Make sure that all pull requests which will be included in the release have been properly documented as changelog files in the [`changes/` directory](https://github.com/zarr-developers/zarr-python/tree/main/changes). -- [ ] Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result to the main branch. +- [ ] Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result to the release branch. - [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/#support-window) to see if the minimum supported version of Python or NumPy needs bumping. - [ ] Check to ensure that: - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.py` to find all potential TODOs. @@ -41,6 +42,7 @@ assignees: '' - [ ] Go to https://github.com/zarr-developers/zarr-python/releases. - [ ] Click "Draft a new release". - [ ] Choose a version number prefixed with a `v` (e.g. `v0.0.0`). For pre-releases, include the appropriate suffix (e.g. `v0.0.0a1` or `v0.0.0rc2`). + - [ ] Set the target branch to the release branch (e.g., `3.1.x`) - [ ] Set the description of the release to: `See release notes https://zarr.readthedocs.io/en/stable/release-notes.html#release-0-0-0`, replacing the correct version numbers. For pre-release versions, the URL should omit the pre-release suffix, e.g. "a1" or "rc1". - [ ] Click on "Generate release notes" to auto-fill the description. - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too. diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 752440719b..dd1d05db3d 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -5,9 +5,9 @@ name: GPU Test on: push: - branches: [ main ] + branches: [ main, 3.1.x ] pull_request: - branches: [ main ] + branches: [ main, 3.1.x ] workflow_dispatch: env: diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index c3c8c946c0..d47abed208 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -1,9 +1,9 @@ name: Slow Hypothesis CI on: push: - branches: [main, 3.0.x] + branches: [main, 3.1.x] pull_request: - branches: [main, 3.0.x] + branches: [main, 3.1.x] types: [opened, reopened, synchronize, labeled] schedule: - cron: "0 0 * * *" # Daily “At 00:00” UTC diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 4dbe115525..d1921a8306 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -5,9 +5,9 @@ name: Test on: push: - branches: [ main, 3.0.x ] + branches: [ main, 3.1.x ] pull_request: - branches: [ main, 3.0.x ] + branches: [ main, 3.1.x ] workflow_dispatch: concurrency: diff --git a/docs/developers/contributing.rst b/docs/developers/contributing.rst index a5dd814878..a4c5723556 100644 --- a/docs/developers/contributing.rst +++ b/docs/developers/contributing.rst @@ -261,9 +261,12 @@ Pull requests submitted by an external contributor should be reviewed and approv one core developer before being merged. Ideally, pull requests submitted by a core developer should be reviewed and approved by at least one other core developer before being merged. -Pull requests should not be merged until all CI checks have passed (GitHub Actions +Pull requests should not be merged until all CI checks have passed (GitHub Actions, Codecov) against code that has had the latest main merged in. +Before merging the milestone must be set either to decide whether a PR will be in the next +patch, minor, or major release. The next section explains which types of changes go in each release. + Compatibility and versioning policies ------------------------------------- From e4101730fe267ffa422f4fda8cffc0bdd40f7a26 Mon Sep 17 00:00:00 2001 From: Lukas Kluft Date: Fri, 1 Aug 2025 15:04:35 +0200 Subject: [PATCH 054/468] Ensure deterministic ordering of consolidated metadata (#3288) * Sort dictionary keys before returning consolidated metadata * Normalize metadata key before sorting * Casefold metadata key before sorting * Add test to verify order of consolidated metadata * Explain order of consolidated metadata keys in user guide * Remove (now) unnecessary sort in user guide example * Document change --- changes/3288.misc.rst | 1 + docs/user-guide/consolidated_metadata.rst | 10 +++++++- src/zarr/core/group.py | 12 +++++++++- tests/test_metadata/test_consolidated.py | 29 +++++++++++++++++++++++ 4 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 changes/3288.misc.rst diff --git a/changes/3288.misc.rst b/changes/3288.misc.rst new file mode 100644 index 0000000000..af7119487f --- /dev/null +++ b/changes/3288.misc.rst @@ -0,0 +1 @@ +Sort dictionary keys before returning consolidated metadata to ensure deterministic output. diff --git a/docs/user-guide/consolidated_metadata.rst b/docs/user-guide/consolidated_metadata.rst index 4cd72dbc74..05a3aa7fb4 100644 --- a/docs/user-guide/consolidated_metadata.rst +++ b/docs/user-guide/consolidated_metadata.rst @@ -45,7 +45,7 @@ that can be used.: >>> consolidated = zarr.open_group(store=store) >>> consolidated_metadata = consolidated.metadata.consolidated_metadata.metadata >>> from pprint import pprint - >>> pprint(dict(sorted(consolidated_metadata.items()))) + >>> pprint(dict(consolidated_metadata.items())) {'a': ArrayV3Metadata(shape=(1,), data_type=Float64(endianness='little'), chunk_grid=RegularChunkGrid(chunk_shape=(1,)), @@ -100,6 +100,14 @@ With nested groups, the consolidated metadata is available on the children, recu >>> consolidated['child'].metadata.consolidated_metadata ConsolidatedMetadata(metadata={'child': GroupMetadata(attributes={'kind': 'grandchild'}, zarr_format=3, consolidated_metadata=ConsolidatedMetadata(metadata={}, kind='inline', must_understand=False), node_type='group')}, kind='inline', must_understand=False) +.. versionadded:: 3.1.1 + + The keys in the consolidated metadata are sorted prior to writing. Keys are + sorted in ascending order by path depth, where a path is defined as a sequence + of strings joined by ``"/"``. For keys with the same path length, lexicographic + order is used to break the tie. This behaviour ensures deterministic metadata + output for a given group. + Synchronization and Concurrency ------------------------------- diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index a398aa01aa..f18c723a76 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -4,6 +4,7 @@ import itertools import json import logging +import unicodedata import warnings from collections import defaultdict from dataclasses import asdict, dataclass, field, fields, replace @@ -141,7 +142,16 @@ def to_dict(self) -> dict[str, JSON]: return { "kind": self.kind, "must_understand": self.must_understand, - "metadata": {k: v.to_dict() for k, v in self.flattened_metadata.items()}, + "metadata": { + k: v.to_dict() + for k, v in sorted( + self.flattened_metadata.items(), + key=lambda item: ( + item[0].count("/"), + unicodedata.normalize("NFKC", item[0]).casefold(), + ), + ) + }, } @classmethod diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index ea2f834bb6..19eba4fb86 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -467,6 +467,35 @@ def test_to_dict_empty(self): } assert result == expected + @pytest.mark.parametrize("zarr_format", [2, 3]) + async def test_to_dict_order( + self, memory_store: zarr.storage.MemoryStore, zarr_format: ZarrFormat + ) -> None: + with zarr.config.set(default_zarr_format=zarr_format): + g = await group(store=memory_store) + + # Create groups in non-lexicographix order + dtype = "float32" + await g.create_array(name="b", shape=(1,), dtype=dtype) + child = await g.create_group("c", attributes={"key": "child"}) + await g.create_array(name="a", shape=(1,), dtype=dtype) + + await child.create_array("e", shape=(1,), dtype=dtype) + await child.create_array("d", shape=(1,), dtype=dtype) + + # Consolidate metadata and re-open store + await zarr.api.asynchronous.consolidate_metadata(memory_store) + g2 = await zarr.api.asynchronous.open_group(store=memory_store) + + assert list(g2.metadata.consolidated_metadata.metadata) == ["a", "b", "c"] + assert list(g2.metadata.consolidated_metadata.flattened_metadata) == [ + "a", + "b", + "c", + "c/d", + "c/e", + ] + @pytest.mark.parametrize("zarr_format", [2, 3]) async def test_open_consolidated_raises_async(self, zarr_format: ZarrFormat): store = zarr.storage.MemoryStore() From 6547b7fd53bd49b903a8690c5f6ea89e1f0e7124 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Mon, 4 Aug 2025 11:12:26 +0100 Subject: [PATCH 055/468] Refactor make_store_path for clarity (#3308) --- src/zarr/storage/_common.py | 99 ++++++++++++++++++--------------- tests/test_store/test_fsspec.py | 4 +- 2 files changed, 57 insertions(+), 46 deletions(-) diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index e25fa28424..3a63b30e9b 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -323,54 +323,65 @@ async def make_store_path( """ from zarr.storage._fsspec import FsspecStore # circular import - used_storage_options = False path_normalized = normalize_path(path) - if isinstance(store_like, StorePath): - result = store_like / path_normalized - else: - assert mode in (None, "r", "r+", "a", "w", "w-") - # if mode 'r' was provided, we'll open any new stores as read-only - _read_only = mode == "r" - if isinstance(store_like, Store): - store = store_like - elif store_like is None: - store = await MemoryStore.open(read_only=_read_only) - elif isinstance(store_like, Path): - store = await LocalStore.open(root=store_like, read_only=_read_only) - elif isinstance(store_like, str): - storage_options = storage_options or {} - - if _is_fsspec_uri(store_like): - used_storage_options = True - store = FsspecStore.from_url( - store_like, storage_options=storage_options, read_only=_read_only - ) - else: - store = await LocalStore.open(root=Path(store_like), read_only=_read_only) - elif isinstance(store_like, dict): - # We deliberate only consider dict[str, Buffer] here, and not arbitrary mutable mappings. - # By only allowing dictionaries, which are in-memory, we know that MemoryStore appropriate. - store = await MemoryStore.open(store_dict=store_like, read_only=_read_only) - elif _has_fsspec and isinstance(store_like, FSMap): - if path: - raise ValueError( - "'path' was provided but is not used for FSMap store_like objects. Specify the path when creating the FSMap instance instead." - ) - if storage_options: - raise ValueError( - "'storage_options was provided but is not used for FSMap store_like objects. Specify the storage options when creating the FSMap instance instead." - ) - store = FsspecStore.from_mapper(store_like, read_only=_read_only) - else: - raise TypeError(f"Unsupported type for store_like: '{type(store_like).__name__}'") - result = await StorePath.open(store, path=path_normalized, mode=mode) + if ( + not (isinstance(store_like, str) and _is_fsspec_uri(store_like)) + and storage_options is not None + ): + raise TypeError( + "'storage_options' was provided but unused. " + "'storage_options' is only used when the store is passed as a FSSpec URI string.", + ) - if storage_options and not used_storage_options: - msg = "'storage_options' was provided but unused. 'storage_options' is only used for fsspec filesystem stores." - raise TypeError(msg) + assert mode in (None, "r", "r+", "a", "w", "w-") + _read_only = mode == "r" - return result + if isinstance(store_like, StorePath): + # Already a StorePath + return store_like / path_normalized + + elif isinstance(store_like, Store): + # Already a Store + store = store_like + + elif isinstance(store_like, dict): + # Already a dictionary that can be a MemoryStore + # + # We deliberate only consider dict[str, Buffer] here, and not arbitrary mutable mappings. + # By only allowing dictionaries, which are in-memory, we know that MemoryStore appropriate. + store = await MemoryStore.open(store_dict=store_like, read_only=_read_only) + + elif store_like is None: + # Create a new in-memory store + return await make_store_path({}, path=path, mode=mode, storage_options=storage_options) + + elif isinstance(store_like, Path): + # Create a new LocalStore + store = await LocalStore.open(root=store_like, read_only=_read_only) + + elif isinstance(store_like, str): + # Either a FSSpec URI or a local filesystem path + if _is_fsspec_uri(store_like): + store = FsspecStore.from_url( + store_like, storage_options=storage_options, read_only=_read_only + ) + else: + # Assume a filesystem path + return await make_store_path( + Path(store_like), path=path, mode=mode, storage_options=storage_options + ) + + elif _has_fsspec and isinstance(store_like, FSMap): + if path: + raise ValueError( + "'path' was provided but is not used for FSMap store_like objects. Specify the path when creating the FSMap instance instead." + ) + store = FsspecStore.from_mapper(store_like, read_only=_read_only) + else: + raise TypeError(f"Unsupported type for store_like: '{type(store_like).__name__}'") + + return await StorePath.open(store, path=path_normalized, mode=mode) def _is_fsspec_uri(uri: str) -> bool: diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 026b25f8fc..abee298a8c 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -388,8 +388,8 @@ def test_open_s3map_raises() -> None: ): zarr.open(store=mapper, path="bar", mode="w", shape=(3, 3)) with pytest.raises( - ValueError, - match="'storage_options was provided but is not used for FSMap store_like objects", + TypeError, + match="'storage_options' is only used when the store is passed as a FSSpec URI string.", ): zarr.open(store=mapper, storage_options={"anon": True}, mode="w", shape=(3, 3)) From e77f803e1a813a496d59c3d091a263602c308bf1 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 4 Aug 2025 13:03:54 +0200 Subject: [PATCH 056/468] pin setuptools-scm to !=9.0.0 (#3329) * pin setuptools-scm to <9.0.0 * narrower version bounds --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0b09171446..e36d636b0c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["hatchling>=1.27.0", "hatch-vcs"] +requires = ["hatchling>=1.27.0", "hatch-vcs", "setuptools-scm!=9.0.0"] build-backend = "hatchling.build" [tool.hatch.build.targets.sdist] From 1858af1a8a91a1d9dd775ee87c663757e8a3b858 Mon Sep 17 00:00:00 2001 From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com> Date: Mon, 4 Aug 2025 15:42:14 +0200 Subject: [PATCH 057/468] update numpy versions in test case examples (#3331) --- docs/developers/contributing.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/developers/contributing.rst b/docs/developers/contributing.rst index a4c5723556..50bf52730b 100644 --- a/docs/developers/contributing.rst +++ b/docs/developers/contributing.rst @@ -98,7 +98,7 @@ you can do something like the following:: To verify that your development environment is working, you can run the unit tests for one of the test environments, e.g.:: - $ hatch env run --env test.py3.12-2.1-optional run-pytest + $ hatch env run --env test.py3.12-2.2-optional run-pytest Creating a branch ~~~~~~~~~~~~~~~~~ @@ -140,7 +140,7 @@ Zarr includes a suite of unit tests. The simplest way to run the unit tests is to activate your development environment (see `creating a development environment`_ above) and invoke:: - $ hatch env run --env test.py3.12-2.1-optional run-pytest + $ hatch env run --env test.py3.12-2.2-optional run-pytest All tests are automatically run via GitHub Actions for every pull request and must pass before code can be accepted. Test coverage is @@ -188,14 +188,14 @@ Test coverage Zarr strives to maintain 100% test coverage under the latest Python stable release Both unit tests and docstring doctests are included when computing coverage. Running:: - $ hatch env run --env test.py3.12-2.1-optional run-coverage + $ hatch env run --env test.py3.12-2.2-optional run-coverage will automatically run the test suite with coverage and produce a XML coverage report. This should be 100% before code can be accepted into the main code base. You can also generate an HTML coverage report by running:: - $ hatch env run --env test.py3.12-2.1-optional run-coverage-html + $ hatch env run --env test.py3.12-2.2-optional run-coverage-html When submitting a pull request, coverage will also be collected across all supported Python versions via the Codecov service, and will be reported back within the pull From 22b177cc8fa8b385805a40f069b083b85bc214d2 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Mon, 4 Aug 2025 17:12:15 +0100 Subject: [PATCH 058/468] Fix test coverage (#3334) * Fix test coverage * Run GPU tests in GPU CI --- .github/workflows/gpu_test.yml | 2 +- pyproject.toml | 68 ++++++++++++++-------------------- 2 files changed, 28 insertions(+), 42 deletions(-) diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index dd1d05db3d..133265f348 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -63,7 +63,7 @@ jobs: hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env - name: Run Tests run: | - hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage + hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage-gpu - name: Upload coverage uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3 # v5.3.1 diff --git a/pyproject.toml b/pyproject.toml index e36d636b0c..7bbf6cc2a0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -150,6 +150,12 @@ dependencies = [ ] features = ["test"] +[tool.hatch.envs.test.env-vars] +# Required to test with a pytest plugin; see https://pytest-cov.readthedocs.io/en/latest/plugins.html +COV_CORE_SOURCE = "src" +COV_CORE_CONFIG = ".coveragerc" +COV_CORE_DATAFILE = ".coverage.eager" + [[tool.hatch.envs.test.matrix]] python = ["3.11", "3.12", "3.13"] numpy = ["1.26", "2.2"] @@ -161,8 +167,9 @@ matrix.deps.dependencies = [ ] [tool.hatch.envs.test.scripts] -run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" -run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src" +run-coverage = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy" +run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report html" +run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy" run = "run-coverage --no-cov" run-pytest = "run" run-verbose = "run-coverage --verbose" @@ -170,16 +177,8 @@ run-mypy = "mypy src" run-hypothesis = "run-coverage -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*" list-env = "pip list" -[tool.hatch.envs.doctest] -features = ["test", "optional", "remote", "remote_tests"] -description = "Test environment for doctests" - -[tool.hatch.envs.doctest.scripts] -run = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst'" -fix = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst' --accept" -list-env = "pip list" - [tool.hatch.envs.gputest] +template = "test" dependencies = [ "numpy~={matrix:numpy}", "universal_pathlib", @@ -191,22 +190,8 @@ python = ["3.11", "3.12", "3.13"] numpy = ["1.26", "2.2"] version = ["minimal"] -[tool.hatch.envs.gputest.scripts] -run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" -run = "run-coverage --no-cov" -run-verbose = "run-coverage --verbose" -run-mypy = "mypy src" -run-hypothesis = "run-coverage --hypothesis-profile ci --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*" -list-env = "pip list" - -[tool.hatch.envs.docs] -features = ['docs'] - -[tool.hatch.envs.docs.scripts] -build = "cd docs && make html" -serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0" - [tool.hatch.envs.upstream] +template = 'test' python = "3.13" dependencies = [ 'packaging @ git+https://github.com/pypa/packaging', @@ -226,20 +211,12 @@ PIP_INDEX_URL = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simp PIP_EXTRA_INDEX_URL = "https://pypi.org/simple/" PIP_PRE = "1" -[tool.hatch.envs.upstream.scripts] -run = "pytest --verbose" -run-mypy = "mypy src" -run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*" -run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" -run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" -run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src" -list-env = "pip list" - [tool.hatch.envs.min_deps] description = """Test environment for minimum supported dependencies See Spec 0000 for details and drop schedule: https://scientific-python.org/specs/spec-0000/ """ +template = "test" python = "3.11" dependencies = [ 'zarr[remote]', @@ -257,13 +234,22 @@ dependencies = [ 'zarr[remote_tests]', ] -[tool.hatch.envs.min_deps.scripts] -run = "pytest --verbose" -run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*" + +[tool.hatch.envs.doctest] +features = ["test", "optional", "remote", "remote_tests"] +description = "Test environment for doctests" + +[tool.hatch.envs.doctest.scripts] +run = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst'" +fix = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst' --accept" list-env = "pip list" -run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" -run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" -run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src" + +[tool.hatch.envs.docs] +features = ['docs'] + +[tool.hatch.envs.docs.scripts] +build = "cd docs && make html" +serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0" [tool.ruff] line-length = 100 From e985f1d0e61e8a6cfde9427f91b5ebd0c674119d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 5 Aug 2025 12:57:42 +0100 Subject: [PATCH 059/468] chore: update pre-commit hooks (#3337) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore: update pre-commit hooks updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.2 → v0.12.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.2...v0.12.7) - [github.com/pre-commit/mirrors-mypy: v1.16.1 → v1.17.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.16.1...v1.17.1) * Remove unused ignore comment --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: David Stansby --- .pre-commit-config.yaml | 4 ++-- src/zarr/api/asynchronous.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 97aefca6dd..9f91c709c7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ ci: default_stages: [pre-commit, pre-push] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.2 + rev: v0.12.7 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -22,7 +22,7 @@ repos: - id: check-yaml - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.16.1 + rev: v1.17.1 hooks: - id: mypy files: src|tests diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 9a380082b0..dee96ffdee 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -141,7 +141,7 @@ def _like_args(a: ArrayLike, kwargs: dict[str, Any]) -> dict[str, Any]: else: # TODO: Remove type: ignore statement when type inference improves. # mypy cannot correctly infer the type of a.metadata here for some reason. - new["codecs"] = a.metadata.codecs # type: ignore[unreachable] + new["codecs"] = a.metadata.codecs else: # TODO: set default values compressor/codecs From 71cc0c2e38ccd4ea1cfc2bd5f49dd66d4557484e Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 5 Aug 2025 19:06:04 +0200 Subject: [PATCH 060/468] refactor warnings (#3098) * define zarr-specific FutureWarning and DeprecationWarning * make unstablespecificationwarning an instance of zarrfuturewarning * use pytest.warns instead of pytest.raises * changelog * ensure that all deprecations are ZarrDeprecations * add docstrings and export warnings * fix imports * handle warnings in tests explicitly; make userwarnings ZarrUserWarning * fix doctests by making them more realistic * lint and fix typo * move unstable spec warning to errors * handle warnings in gpu tests * handle more warnings * handle another warning * Fix exports * Update src/zarr/errors.py Co-authored-by: David Stansby * Update changes/3098.misc.rst Co-authored-by: David Stansby * Update src/zarr/errors.py Co-authored-by: David Stansby * add test to ensure that ambiguous group.open warns * update changelog --------- Co-authored-by: David Stansby --- changes/3098.misc.rst | 3 + docs/user-guide/arrays.rst | 2 + docs/user-guide/consolidated_metadata.rst | 2 + pyproject.toml | 10 - src/zarr/_compat.py | 4 +- src/zarr/api/asynchronous.py | 46 +++-- src/zarr/api/synchronous.py | 3 +- src/zarr/codecs/transpose.py | 4 +- src/zarr/convenience.py | 3 +- src/zarr/core/array.py | 16 +- src/zarr/core/buffer/gpu.py | 2 + src/zarr/core/chunk_grids.py | 3 +- src/zarr/core/codec_pipeline.py | 2 + src/zarr/core/common.py | 5 +- src/zarr/core/dtype/common.py | 4 +- src/zarr/core/group.py | 22 ++- src/zarr/core/metadata/v2.py | 3 +- src/zarr/creation.py | 3 +- src/zarr/errors.py | 36 +++- src/zarr/registry.py | 2 + src/zarr/storage/__init__.py | 3 +- src/zarr/storage/_fsspec.py | 4 +- src/zarr/testing/__init__.py | 6 +- tests/test_api.py | 11 +- tests/test_array.py | 50 +++-- tests/test_buffer.py | 39 ++-- tests/test_codecs/test_codecs.py | 109 +++-------- tests/test_codecs/test_sharding.py | 31 ++-- tests/test_config.py | 5 +- tests/test_dtype/test_npy/test_bytes.py | 4 +- tests/test_dtype/test_npy/test_string.py | 4 +- tests/test_group.py | 216 +++++++++++++++++++--- tests/test_metadata/test_consolidated.py | 63 ++++++- tests/test_metadata/test_v2.py | 3 +- tests/test_store/test_fsspec.py | 3 +- tests/test_store/test_memory.py | 5 +- tests/test_v2.py | 3 +- 37 files changed, 487 insertions(+), 247 deletions(-) create mode 100644 changes/3098.misc.rst diff --git a/changes/3098.misc.rst b/changes/3098.misc.rst new file mode 100644 index 0000000000..5ec1057365 --- /dev/null +++ b/changes/3098.misc.rst @@ -0,0 +1,3 @@ +Define Zarr-specific warning classes that subclass the Python built-in warnings. +These classes makes it easier to control the visibility of warnings emitted by Zarr Python. +See `zarr.errors` for these warning classes. \ No newline at end of file diff --git a/docs/user-guide/arrays.rst b/docs/user-guide/arrays.rst index 67b134d442..257fac450c 100644 --- a/docs/user-guide/arrays.rst +++ b/docs/user-guide/arrays.rst @@ -238,6 +238,8 @@ built-in delta filter:: >>> import lzma >>> from numcodecs.zarr3 import LZMA + >>> import warnings + >>> warnings.filterwarnings("ignore", category=UserWarning) >>> >>> lzma_filters = [dict(id=lzma.FILTER_DELTA, dist=4), dict(id=lzma.FILTER_LZMA2, preset=1)] >>> compressors = LZMA(filters=lzma_filters) diff --git a/docs/user-guide/consolidated_metadata.rst b/docs/user-guide/consolidated_metadata.rst index 05a3aa7fb4..9d05231f4a 100644 --- a/docs/user-guide/consolidated_metadata.rst +++ b/docs/user-guide/consolidated_metadata.rst @@ -27,6 +27,8 @@ In Python, the consolidated metadata is available on the ``.consolidated_metadat attribute of the ``GroupMetadata`` object. >>> import zarr + >>> import warnings + >>> warnings.filterwarnings("ignore", category=UserWarning) >>> >>> store = zarr.storage.MemoryStore() >>> group = zarr.create_group(store=store) diff --git a/pyproject.toml b/pyproject.toml index 7bbf6cc2a0..95528c4558 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -389,16 +389,6 @@ addopts = [ ] filterwarnings = [ "error", - # TODO: explicitly filter or catch the warnings below where we expect them to be emitted in the tests - "ignore:Consolidated metadata is currently not part in the Zarr format 3 specification.*:UserWarning", - "ignore:Creating a zarr.buffer.gpu.Buffer with an array that does not support the __cuda_array_interface__.*:UserWarning", - "ignore:Automatic shard shape inference is experimental and may change without notice.*:UserWarning", - "ignore:The codec .* is currently not part in the Zarr format 3 specification.*:UserWarning", - "ignore:The dtype .* is currently not part in the Zarr format 3 specification.*:UserWarning", - "ignore:Use zarr.create_array instead.:DeprecationWarning", - "ignore:Duplicate name.*:UserWarning", - "ignore:The `compressor` argument is deprecated. Use `compressors` instead.:UserWarning", - "ignore:Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations.:UserWarning", "ignore:Unclosed client session T: f"{version} passing these as positional arguments " "will result in an error" ), - FutureWarning, + ZarrFutureWarning, stacklevel=2, ) kwargs.update(zip(sig.parameters, args, strict=False)) diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index dee96ffdee..78b68caf73 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -39,7 +39,13 @@ create_hierarchy, ) from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata, ArrayV3Metadata -from zarr.errors import GroupNotFoundError, NodeTypeValidationError +from zarr.errors import ( + GroupNotFoundError, + NodeTypeValidationError, + ZarrDeprecationWarning, + ZarrRuntimeWarning, + ZarrUserWarning, +) from zarr.storage import StorePath from zarr.storage._common import make_store_path @@ -162,7 +168,7 @@ def _handle_zarr_version_or_format( ) if zarr_version is not None: warnings.warn( - "zarr_version is deprecated, use zarr_format", DeprecationWarning, stacklevel=2 + "zarr_version is deprecated, use zarr_format", ZarrDeprecationWarning, stacklevel=2 ) return zarr_version return zarr_format @@ -228,7 +234,7 @@ async def consolidate_metadata( warnings.warn( "Consolidated metadata is currently not part in the Zarr format 3 specification. It " "may not be supported by other zarr implementations and may change in the future.", - category=UserWarning, + category=ZarrUserWarning, stacklevel=1, ) @@ -536,7 +542,7 @@ async def save_group( await asyncio.gather(*aws) -@deprecated("Use AsyncGroup.tree instead.") +@deprecated("Use AsyncGroup.tree instead.", category=ZarrDeprecationWarning) async def tree(grp: AsyncGroup, expand: bool | None = None, level: int | None = None) -> Any: """Provide a rich display of the hierarchy. @@ -674,13 +680,13 @@ async def group( store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options) if chunk_store is not None: - warnings.warn("chunk_store is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if cache_attrs is not None: - warnings.warn("cache_attrs is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if synchronizer is not None: - warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if meta_array is not None: - warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if attributes is None: attributes = {} @@ -827,13 +833,13 @@ async def open_group( zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) if cache_attrs is not None: - warnings.warn("cache_attrs is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if synchronizer is not None: - warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if meta_array is not None: - warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if chunk_store is not None: - warnings.warn("chunk_store is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2) store_path = await make_store_path(store, mode=mode, storage_options=storage_options, path=path) if attributes is None: @@ -1011,19 +1017,19 @@ async def create( ) if synchronizer is not None: - warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if chunk_store is not None: - warnings.warn("chunk_store is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if cache_metadata is not None: - warnings.warn("cache_metadata is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("cache_metadata is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if cache_attrs is not None: - warnings.warn("cache_attrs is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if object_codec is not None: - warnings.warn("object_codec is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("object_codec is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if read_only is not None: - warnings.warn("read_only is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("read_only is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if meta_array is not None: - warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2) + warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if write_empty_chunks is not None: _warn_write_empty_chunks_kwarg() @@ -1042,7 +1048,7 @@ async def create( "This is redundant. When both are set, write_empty_chunks will be used instead " "of the value in config." ) - warnings.warn(UserWarning(msg), stacklevel=1) + warnings.warn(ZarrUserWarning(msg), stacklevel=1) config_parsed = dataclasses.replace(config_parsed, write_empty_chunks=write_empty_chunks) return await AsyncArray._create( diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 4ce02e7b6d..ed1ae2cf2a 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -10,6 +10,7 @@ from zarr.core.group import Group from zarr.core.sync import sync from zarr.core.sync_group import create_hierarchy +from zarr.errors import ZarrDeprecationWarning if TYPE_CHECKING: from collections.abc import Iterable @@ -339,7 +340,7 @@ def save_group( ) -@deprecated("Use Group.tree instead.") +@deprecated("Use Group.tree instead.", category=ZarrDeprecationWarning) def tree(grp: Group, expand: bool | None = None, level: int | None = None) -> Any: """Provide a rich display of the hierarchy. diff --git a/src/zarr/codecs/transpose.py b/src/zarr/codecs/transpose.py index c87804685c..d6310d38a4 100644 --- a/src/zarr/codecs/transpose.py +++ b/src/zarr/codecs/transpose.py @@ -56,7 +56,7 @@ def validate( ) -> None: if len(self.order) != len(shape): raise ValueError( - f"The `order` tuple needs have as many entries as there are dimensions in the array. Got {self.order}." + f"The `order` tuple must have as many entries as there are dimensions in the array. Got {self.order}." ) if len(self.order) != len(set(self.order)): raise ValueError( @@ -71,7 +71,7 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: ndim = array_spec.ndim if len(self.order) != ndim: raise ValueError( - f"The `order` tuple needs have as many entries as there are dimensions in the array. Got {self.order}." + f"The `order` tuple must have as many entries as there are dimensions in the array. Got {self.order}." ) if len(self.order) != len(set(self.order)): raise ValueError( diff --git a/src/zarr/convenience.py b/src/zarr/convenience.py index 88f10663b7..3ca4ffcb4b 100644 --- a/src/zarr/convenience.py +++ b/src/zarr/convenience.py @@ -22,6 +22,7 @@ save_group, tree, ) +from zarr.errors import ZarrDeprecationWarning __all__ = [ "consolidate_metadata", @@ -40,6 +41,6 @@ warnings.warn( "zarr.convenience is deprecated. " "Import these functions from the top level zarr. namespace instead.", - DeprecationWarning, + ZarrDeprecationWarning, stacklevel=2, ) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 260e94bc88..ca8bc414cc 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -119,7 +119,7 @@ ) from zarr.core.metadata.v3 import parse_node_type_array from zarr.core.sync import sync -from zarr.errors import MetadataValidationError +from zarr.errors import MetadataValidationError, ZarrDeprecationWarning, ZarrUserWarning from zarr.registry import ( _parse_array_array_codec, _parse_array_bytes_codec, @@ -232,7 +232,7 @@ async def get_array_metadata( if zarr_json_bytes is not None and zarray_bytes is not None: # warn and favor v3 msg = f"Both zarr.json (Zarr format 3) and .zarray (Zarr format 2) metadata objects exist at {store_path}. Zarr v3 will be used." - warnings.warn(msg, stacklevel=1) + warnings.warn(msg, category=ZarrUserWarning, stacklevel=1) if zarr_json_bytes is None and zarray_bytes is None: raise FileNotFoundError(store_path) # set zarr_format based on which keys were found @@ -441,7 +441,7 @@ async def create( ) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: ... @classmethod - @deprecated("Use zarr.api.asynchronous.create_array instead.") + @deprecated("Use zarr.api.asynchronous.create_array instead.", category=ZarrDeprecationWarning) async def create( cls, store: StoreLike, @@ -1061,7 +1061,7 @@ def serializer(self) -> ArrayBytesCodec | None: ) @property - @deprecated("Use AsyncArray.compressors instead.") + @deprecated("Use AsyncArray.compressors instead.", category=ZarrDeprecationWarning) def compressor(self) -> numcodecs.abc.Codec | None: """ Compressor that is applied to each chunk of the array. @@ -1855,7 +1855,7 @@ class Array: _async_array: AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] @classmethod - @deprecated("Use zarr.create_array instead.") + @deprecated("Use zarr.create_array instead.", category=ZarrDeprecationWarning) def create( cls, store: StoreLike, @@ -2242,7 +2242,7 @@ def serializer(self) -> None | ArrayBytesCodec: return self._async_array.serializer @property - @deprecated("Use Array.compressors instead.") + @deprecated("Use Array.compressors instead.", category=ZarrDeprecationWarning) def compressor(self) -> numcodecs.abc.Codec | None: """ Compressor that is applied to each chunk of the array. @@ -4648,7 +4648,7 @@ def _parse_keep_array_attr( warnings.warn( "The 'order' attribute of a Zarr format 2 array does not have a direct analogue in Zarr format 3. " "The existing order='F' of the source Zarr format 2 array will be ignored.", - UserWarning, + ZarrUserWarning, stacklevel=2, ) elif order is None and zarr_format == 2: @@ -4937,7 +4937,7 @@ def _parse_deprecated_compressor( if zarr_format == 3: warn( "The `compressor` argument is deprecated. Use `compressors` instead.", - category=UserWarning, + category=ZarrUserWarning, stacklevel=2, ) if compressor is None: diff --git a/src/zarr/core/buffer/gpu.py b/src/zarr/core/buffer/gpu.py index d46ee6c8e5..4eca197222 100644 --- a/src/zarr/core/buffer/gpu.py +++ b/src/zarr/core/buffer/gpu.py @@ -13,6 +13,7 @@ from zarr.core.buffer import core from zarr.core.buffer.core import ArrayLike, BufferPrototype, NDArrayLike +from zarr.errors import ZarrUserWarning from zarr.registry import ( register_buffer, register_ndbuffer, @@ -72,6 +73,7 @@ def __init__(self, array_like: ArrayLike) -> None: ) warnings.warn( msg, + category=ZarrUserWarning, stacklevel=2, ) self._data = cp.asarray(array_like) diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 6a3d6816a6..7fa1fc7e38 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -22,6 +22,7 @@ parse_named_configuration, parse_shapelike, ) +from zarr.errors import ZarrUserWarning if TYPE_CHECKING: from collections.abc import Iterator @@ -233,7 +234,7 @@ def _auto_partition( if shard_shape == "auto": warnings.warn( "Automatic shard shape inference is experimental and may change without notice.", - UserWarning, + ZarrUserWarning, stacklevel=2, ) _shards_out = () diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 23c27e40c6..3bc3c1cfc7 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -17,6 +17,7 @@ from zarr.core.common import ChunkCoords, concurrent_map from zarr.core.config import config from zarr.core.indexing import SelectorTuple, is_scalar +from zarr.errors import ZarrUserWarning from zarr.registry import register_pipeline if TYPE_CHECKING: @@ -501,6 +502,7 @@ def codecs_from_list( warn( "Combining a `sharding_indexed` codec disables partial reads and " "writes, which may lead to inefficient performance.", + category=ZarrUserWarning, stacklevel=3, ) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 33590c83a5..4c0247426e 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -23,6 +23,7 @@ from typing_extensions import ReadOnly from zarr.core.config import config as zarr_config +from zarr.errors import ZarrRuntimeWarning if TYPE_CHECKING: from collections.abc import Awaitable, Callable, Iterator @@ -205,7 +206,7 @@ def _warn_write_empty_chunks_kwarg() -> None: "argument, as in `config={'write_empty_chunks': True}`," "or change the global 'array.write_empty_chunks' configuration variable." ) - warnings.warn(msg, RuntimeWarning, stacklevel=2) + warnings.warn(msg, ZarrRuntimeWarning, stacklevel=2) def _warn_order_kwarg() -> None: @@ -216,7 +217,7 @@ def _warn_order_kwarg() -> None: "argument, as in `config={'order': 'C'}`," "or change the global 'array.order' configuration variable." ) - warnings.warn(msg, RuntimeWarning, stacklevel=2) + warnings.warn(msg, ZarrRuntimeWarning, stacklevel=2) def _default_zarr_format() -> ZarrFormat: diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index 3cc31df9e3..652b5fdbe3 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -16,6 +16,7 @@ from typing_extensions import ReadOnly from zarr.core.common import NamedConfig +from zarr.errors import UnstableSpecificationWarning EndiannessStr = Literal["little", "big"] ENDIANNESS_STR: Final = "little", "big" @@ -216,9 +217,6 @@ class HasObjectCodec: object_codec_id: ClassVar[str] -class UnstableSpecificationWarning(FutureWarning): ... - - def v3_unstable_dtype_warning(dtype: object) -> None: """ Emit this warning when a data type does not have a stable zarr v3 spec diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index f18c723a76..4bdc7b549f 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -51,7 +51,13 @@ from zarr.core.config import config from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata from zarr.core.sync import SyncMixin, sync -from zarr.errors import ContainsArrayError, ContainsGroupError, MetadataValidationError +from zarr.errors import ( + ContainsArrayError, + ContainsGroupError, + MetadataValidationError, + ZarrDeprecationWarning, + ZarrUserWarning, +) from zarr.storage import StoreLike, StorePath from zarr.storage._common import ensure_no_existing_node, make_store_path from zarr.storage._utils import _join_paths, _normalize_path_keys, normalize_path @@ -558,7 +564,7 @@ async def open( if zarr_json_bytes is not None and zgroup_bytes is not None: # warn and favor v3 msg = f"Both zarr.json (Zarr format 3) and .zgroup (Zarr format 2) metadata objects exist at {store_path}. Zarr format 3 will be used." - warnings.warn(msg, stacklevel=1) + warnings.warn(msg, category=ZarrUserWarning, stacklevel=1) if zarr_json_bytes is None and zgroup_bytes is None: raise FileNotFoundError( f"could not find zarr.json or .zgroup objects in {store_path}" @@ -1152,7 +1158,7 @@ async def create_array( write_data=write_data, ) - @deprecated("Use AsyncGroup.create_array instead.") + @deprecated("Use AsyncGroup.create_array instead.", category=ZarrDeprecationWarning) async def create_dataset( self, name: str, *, shape: ShapeLike, **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: @@ -1186,7 +1192,7 @@ async def create_dataset( await array.setitem(slice(None), data) return array - @deprecated("Use AsyncGroup.require_array instead.") + @deprecated("Use AsyncGroup.require_array instead.", category=ZarrDeprecationWarning) async def require_dataset( self, name: str, @@ -2587,7 +2593,7 @@ def create_array( ) ) - @deprecated("Use Group.create_array instead.") + @deprecated("Use Group.create_array instead.", category=ZarrDeprecationWarning) def create_dataset(self, name: str, **kwargs: Any) -> Array: """Create an array. @@ -2611,7 +2617,7 @@ def create_dataset(self, name: str, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.create_dataset(name, **kwargs))) - @deprecated("Use Group.require_array instead.") + @deprecated("Use Group.require_array instead.", category=ZarrDeprecationWarning) def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: """Obtain an array, creating if it doesn't exist. @@ -2833,7 +2839,7 @@ def move(self, source: str, dest: str) -> None: """ return self._sync(self._async_group.move(source, dest)) - @deprecated("Use Group.create_array instead.") + @deprecated("Use Group.create_array instead.", category=ZarrDeprecationWarning) def array( self, name: str, @@ -3385,7 +3391,7 @@ async def _iter_members( # in which case `key` cannot be the name of a sub-array or sub-group. warnings.warn( f"Object at {e.args[0]} is not recognized as a component of a Zarr hierarchy.", - UserWarning, + ZarrUserWarning, stacklevel=1, ) continue diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 17af3538a9..9ad6b3bc42 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -11,6 +11,7 @@ from zarr.core.chunk_grids import RegularChunkGrid from zarr.core.dtype import get_data_type_from_json from zarr.core.dtype.common import OBJECT_CODEC_IDS, DTypeSpec_V2 +from zarr.errors import ZarrUserWarning if TYPE_CHECKING: from typing import Literal, Self @@ -188,7 +189,7 @@ def from_dict(cls, data: dict[str, Any]) -> ArrayV2Metadata: "This is contrary to the Zarr V2 specification, and will cause an error in the future. " "Use None (or Null in a JSON document) instead of an empty list of filters." ) - warnings.warn(msg, UserWarning, stacklevel=1) + warnings.warn(msg, ZarrUserWarning, stacklevel=1) _data["filters"] = None _data = {k: v for k, v in _data.items() if k in expected} diff --git a/src/zarr/creation.py b/src/zarr/creation.py index 8197c4950c..622406ed75 100644 --- a/src/zarr/creation.py +++ b/src/zarr/creation.py @@ -23,6 +23,7 @@ zeros, zeros_like, ) +from zarr.errors import ZarrDeprecationWarning __all__ = [ "array", @@ -42,6 +43,6 @@ warnings.warn( "zarr.creation is deprecated. " "Import these functions from the top level zarr. namespace instead.", - DeprecationWarning, + ZarrDeprecationWarning, stacklevel=2, ) diff --git a/src/zarr/errors.py b/src/zarr/errors.py index 4f972a6703..0055ea3c6c 100644 --- a/src/zarr/errors.py +++ b/src/zarr/errors.py @@ -8,6 +8,10 @@ "GroupNotFoundError", "MetadataValidationError", "NodeTypeValidationError", + "UnstableSpecificationWarning", + "ZarrDeprecationWarning", + "ZarrFutureWarning", + "ZarrRuntimeWarning", ] @@ -61,8 +65,38 @@ class MetadataValidationError(BaseZarrError): class NodeTypeValidationError(MetadataValidationError): """ - Specialized exception when the node_type of the metadata document is incorrect.. + Specialized exception when the node_type of the metadata document is incorrect. This can be raised when the value is invalid or unexpected given the context, for example an 'array' node when we expected a 'group'. """ + + +class ZarrFutureWarning(FutureWarning): + """ + A warning intended for end users raised to indicate deprecated features. + """ + + +class UnstableSpecificationWarning(ZarrFutureWarning): + """ + A warning raised to indicate that a feature is outside the Zarr specification. + """ + + +class ZarrDeprecationWarning(DeprecationWarning): + """ + A warning raised to indicate that a feature will be removed in a future release. + """ + + +class ZarrUserWarning(UserWarning): + """ + A warning raised to report problems with user code. + """ + + +class ZarrRuntimeWarning(RuntimeWarning): + """ + A warning for dubious runtime behavior. + """ diff --git a/src/zarr/registry.py b/src/zarr/registry.py index 189d42abed..fc3ffd7f7c 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -7,6 +7,7 @@ from zarr.core.config import BadConfigError, config from zarr.core.dtype import data_type_registry +from zarr.errors import ZarrUserWarning if TYPE_CHECKING: from importlib.metadata import EntryPoint @@ -160,6 +161,7 @@ def get_codec_class(key: str, reload_config: bool = False) -> type[Codec]: warnings.warn( f"Codec '{key}' not configured in config. Selecting any implementation.", stacklevel=2, + category=ZarrUserWarning, ) return list(codec_classes.values())[-1] selected_codec_cls = codec_classes[config_entry] diff --git a/src/zarr/storage/__init__.py b/src/zarr/storage/__init__.py index 6721139375..00df50214f 100644 --- a/src/zarr/storage/__init__.py +++ b/src/zarr/storage/__init__.py @@ -3,6 +3,7 @@ from types import ModuleType from typing import Any +from zarr.errors import ZarrDeprecationWarning from zarr.storage._common import StoreLike, StorePath from zarr.storage._fsspec import FsspecStore from zarr.storage._local import LocalStore @@ -33,7 +34,7 @@ def __setattr__(self, attr: str, value: Any) -> None: "setting zarr.storage.default_compressor is deprecated, use " "zarr.config to configure array.v2_default_compressor " "e.g. config.set({'codecs.zstd':'numcodecs.Zstd', 'array.v2_default_compressor.numeric': 'zstd'})", - DeprecationWarning, + ZarrDeprecationWarning, stacklevel=1, ) else: diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index e169eededc..bbb934cc7d 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -15,6 +15,7 @@ SuffixByteRequest, ) from zarr.core.buffer import Buffer +from zarr.errors import ZarrUserWarning from zarr.storage._common import _dereference_path if TYPE_CHECKING: @@ -101,7 +102,7 @@ class FsspecStore(Store): Warns ----- - UserWarning + ZarrUserWarning If the file system (fs) was not created with `asynchronous=True`. See Also @@ -137,6 +138,7 @@ def __init__( if not self.fs.asynchronous: warnings.warn( f"fs ({fs}) was not created with `asynchronous=True`, this may lead to surprising behavior", + category=ZarrUserWarning, stacklevel=2, ) if "://" in path and not path.startswith("http"): diff --git a/src/zarr/testing/__init__.py b/src/zarr/testing/__init__.py index 0b4d8cf417..21a3572846 100644 --- a/src/zarr/testing/__init__.py +++ b/src/zarr/testing/__init__.py @@ -1,10 +1,14 @@ import importlib.util import warnings +from zarr.errors import ZarrUserWarning + if importlib.util.find_spec("pytest") is not None: from zarr.testing.store import StoreTests else: - warnings.warn("pytest not installed, skipping test suite", stacklevel=2) + warnings.warn( + "pytest not installed, skipping test suite", category=ZarrUserWarning, stacklevel=2 + ) from zarr.testing.utils import assert_bytes_equal diff --git a/tests/test_api.py b/tests/test_api.py index 01fb40f050..12acf80589 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -7,6 +7,7 @@ import zarr.codecs import zarr.storage from zarr.core.array import init_array +from zarr.storage import LocalStore, ZipStore from zarr.storage._common import StorePath if TYPE_CHECKING: @@ -41,8 +42,8 @@ save_group, ) from zarr.core.buffer import NDArrayLike -from zarr.errors import MetadataValidationError -from zarr.storage import LocalStore, MemoryStore, ZipStore +from zarr.errors import MetadataValidationError, ZarrDeprecationWarning, ZarrUserWarning +from zarr.storage import MemoryStore from zarr.storage._utils import normalize_path from zarr.testing.utils import gpu_test @@ -169,7 +170,7 @@ def test_v2_and_v3_exist_at_same_path(store: Store) -> None: zarr.create_array(store, shape=(10,), dtype="uint8", zarr_format=3) zarr.create_array(store, shape=(10,), dtype="uint8", zarr_format=2) msg = f"Both zarr.json (Zarr format 3) and .zarray (Zarr format 2) metadata objects exist at {store}. Zarr v3 will be used." - with pytest.warns(UserWarning, match=re.escape(msg)): + with pytest.warns(ZarrUserWarning, match=re.escape(msg)): zarr.open(store=store) @@ -470,7 +471,7 @@ def test_tree() -> None: g3.create_group("baz") g5 = g3.create_group("qux") g5.create_array("baz", shape=(100,), chunks=(10,), dtype="float64") - with pytest.warns(DeprecationWarning, match=r"Group\.tree instead\."): # noqa: PT031 + with pytest.warns(ZarrDeprecationWarning, match=r"Group\.tree instead\."): # noqa: PT031 assert repr(zarr.tree(g1)) == repr(g1.tree()) assert str(zarr.tree(g1)) == str(g1.tree()) @@ -1350,7 +1351,7 @@ def test_no_overwrite_open(tmp_path: Path, open_func: Callable, mode: str) -> No existing_fpath = add_empty_file(tmp_path) assert existing_fpath.exists() - with contextlib.suppress(FileExistsError, FileNotFoundError, UserWarning): + with contextlib.suppress(FileExistsError, FileNotFoundError, ZarrUserWarning): open_func(store=store, mode=mode) if mode == "w": assert not existing_fpath.exists() diff --git a/tests/test_array.py b/tests/test_array.py index f672006f9a..46b78de7bf 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -63,7 +63,11 @@ from zarr.core.metadata.v2 import ArrayV2Metadata from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import sync -from zarr.errors import ContainsArrayError, ContainsGroupError +from zarr.errors import ( + ContainsArrayError, + ContainsGroupError, + ZarrUserWarning, +) from zarr.storage import LocalStore, MemoryStore, StorePath from .test_dtype.conftest import zdtype_examples @@ -922,13 +926,16 @@ def test_auto_partition_auto_shards( expected_shards += (2 * cs,) else: expected_shards += (cs,) - - auto_shards, _ = _auto_partition( - array_shape=array_shape, - chunk_shape=chunk_shape, - shard_shape="auto", - item_size=dtype.itemsize, - ) + with pytest.warns( + ZarrUserWarning, + match="Automatic shard shape inference is experimental and may change without notice.", + ): + auto_shards, _ = _auto_partition( + array_shape=array_shape, + chunk_shape=chunk_shape, + shard_shape="auto", + item_size=dtype.itemsize, + ) assert auto_shards == expected_shards @@ -1631,7 +1638,7 @@ async def test_from_array_arraylike( def test_from_array_F_order() -> None: arr = zarr.create_array(store={}, data=np.array([1]), order="F", zarr_format=2) with pytest.warns( - UserWarning, + ZarrUserWarning, match="The existing order='F' of the source Zarr format 2 array will be ignored.", ): zarr.from_array(store={}, data=arr, zarr_format=3) @@ -1679,21 +1686,24 @@ def test_roundtrip_numcodecs() -> None: # Create the array with the correct codecs root = zarr.group(store) - root.create_array( - "test", - shape=(720, 1440), - chunks=(720, 1440), - dtype="float64", - compressors=compressors, - filters=filters, - fill_value=-9.99, - dimension_names=["lat", "lon"], - ) + warn_msg = "Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations." + with pytest.warns(UserWarning, match=warn_msg): + root.create_array( + "test", + shape=(720, 1440), + chunks=(720, 1440), + dtype="float64", + compressors=compressors, + filters=filters, + fill_value=-9.99, + dimension_names=["lat", "lon"], + ) BYTES_CODEC = {"name": "bytes", "configuration": {"endian": "little"}} # Read in the array again and check compressor config root = zarr.open_group(store) - metadata = root["test"].metadata.to_dict() + with pytest.warns(UserWarning, match=warn_msg): + metadata = root["test"].metadata.to_dict() expected = (*filters, BYTES_CODEC, *compressors) assert metadata["codecs"] == expected diff --git a/tests/test_buffer.py b/tests/test_buffer.py index bbfa25d138..b50e5abb67 100644 --- a/tests/test_buffer.py +++ b/tests/test_buffer.py @@ -13,6 +13,7 @@ from zarr.codecs.gzip import GzipCodec from zarr.codecs.transpose import TransposeCodec from zarr.codecs.zstd import ZstdCodec +from zarr.errors import ZarrUserWarning from zarr.storage import MemoryStore, StorePath from zarr.testing.buffer import ( NDBufferUsingTestNDArrayLike, @@ -138,13 +139,17 @@ async def test_codecs_use_of_gpu_prototype() -> None: filters=[TransposeCodec(order=(1, 0))], ) expect[:] = cp.arange(100).reshape(10, 10) - - await a.setitem( - selection=(slice(0, 10), slice(0, 10)), - value=expect[:], - prototype=gpu.buffer_prototype, - ) - got = await a.getitem(selection=(slice(0, 10), slice(0, 10)), prototype=gpu.buffer_prototype) + msg = "Creating a zarr.buffer.gpu.Buffer with an array that does not support the __cuda_array_interface__ for zero-copy transfers, falling back to slow copy based path" + with pytest.warns(ZarrUserWarning, match=msg): + await a.setitem( + selection=(slice(0, 10), slice(0, 10)), + value=expect[:], + prototype=gpu.buffer_prototype, + ) + with pytest.warns(ZarrUserWarning, match=msg): + got = await a.getitem( + selection=(slice(0, 10), slice(0, 10)), prototype=gpu.buffer_prototype + ) assert isinstance(got, cp.ndarray) assert cp.array_equal(expect, got) @@ -164,15 +169,17 @@ async def test_sharding_use_of_gpu_prototype() -> None: fill_value=0, ) expect[:] = cp.arange(100).reshape(10, 10) - - await a.setitem( - selection=(slice(0, 10), slice(0, 10)), - value=expect[:], - prototype=gpu.buffer_prototype, - ) - got = await a.getitem( - selection=(slice(0, 10), slice(0, 10)), prototype=gpu.buffer_prototype - ) + msg = "Creating a zarr.buffer.gpu.Buffer with an array that does not support the __cuda_array_interface__ for zero-copy transfers, falling back to slow copy based path" + with pytest.warns(ZarrUserWarning, match=msg): + await a.setitem( + selection=(slice(0, 10), slice(0, 10)), + value=expect[:], + prototype=gpu.buffer_prototype, + ) + with pytest.warns(ZarrUserWarning, match=msg): + got = await a.getitem( + selection=(slice(0, 10), slice(0, 10)), prototype=gpu.buffer_prototype + ) assert isinstance(got, cp.ndarray) assert cp.array_equal(expect, got) diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index d52a9e1c44..a2dad41a1b 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -20,9 +20,12 @@ from zarr.core.buffer import default_buffer_prototype from zarr.core.indexing import BasicSelection, morton_order_iter from zarr.core.metadata.v3 import ArrayV3Metadata +from zarr.dtype import UInt8 +from zarr.errors import ZarrUserWarning from zarr.storage import StorePath if TYPE_CHECKING: + from zarr.abc.codec import Codec from zarr.abc.store import Store from zarr.core.buffer.core import NDArrayLikeOrScalar from zarr.core.common import ChunkCoords, MemoryOrder @@ -290,97 +293,37 @@ async def test_dimension_names(store: Store) -> None: assert "dimension_names" not in json.loads(zarr_json_buffer.to_bytes()) -@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -def test_invalid_metadata(store: Store) -> None: - spath2 = StorePath(store, "invalid_codec_order") - with pytest.raises(TypeError): - Array.create( - spath2, - shape=(16, 16), - chunk_shape=(16, 16), - dtype=np.dtype("uint8"), - fill_value=0, - codecs=[ - BytesCodec(), - TransposeCodec(order=order_from_dim("F", 2)), - ], - ) - spath3 = StorePath(store, "invalid_order") - with pytest.raises(TypeError): - Array.create( - spath3, - shape=(16, 16), - chunk_shape=(16, 16), - dtype=np.dtype("uint8"), - fill_value=0, - codecs=[ - TransposeCodec(order="F"), # type: ignore[arg-type] - BytesCodec(), - ], - ) - spath4 = StorePath(store, "invalid_missing_bytes_codec") - with pytest.raises(ValueError): - Array.create( - spath4, - shape=(16, 16), - chunk_shape=(16, 16), - dtype=np.dtype("uint8"), - fill_value=0, - codecs=[ - TransposeCodec(order=order_from_dim("F", 2)), - ], - ) - spath5 = StorePath(store, "invalid_inner_chunk_shape") - with pytest.raises(ValueError): - Array.create( - spath5, - shape=(16, 16), - chunk_shape=(16, 16), - dtype=np.dtype("uint8"), - fill_value=0, - codecs=[ - ShardingCodec(chunk_shape=(8,)), - ], - ) - spath6 = StorePath(store, "invalid_inner_chunk_shape") - with pytest.raises(ValueError): - Array.create( - spath6, - shape=(16, 16), - chunk_shape=(16, 16), - dtype=np.dtype("uint8"), - fill_value=0, - codecs=[ - ShardingCodec(chunk_shape=(8, 7)), - ], - ) - spath7 = StorePath(store, "warning_inefficient_codecs") - with pytest.warns( - UserWarning, - match="Combining a `sharding_indexed` codec disables partial reads and writes, which may lead to inefficient performance", - ): - Array.create( - spath7, - shape=(16, 16), - chunk_shape=(16, 16), - dtype=np.dtype("uint8"), +@pytest.mark.parametrize( + "codecs", + [ + (BytesCodec(), TransposeCodec(order=order_from_dim("F", 2))), + (TransposeCodec(order=order_from_dim("F", 2)),), + ], +) +def test_invalid_metadata(codecs: tuple[Codec, ...]) -> None: + shape = (16,) + chunks = (16,) + data_type = UInt8() + with pytest.raises(ValueError, match="The `order` tuple must have as many entries"): + ArrayV3Metadata( + shape=shape, + chunk_grid={"name": "regular", "configuration": {"chunk_shape": chunks}}, + chunk_key_encoding={"name": "default", "configuration": {"separator": "/"}}, # type: ignore[arg-type] fill_value=0, - codecs=[ - ShardingCodec(chunk_shape=(8, 8)), - GzipCodec(), - ], + data_type=data_type, + codecs=codecs, + attributes={}, + dimension_names=None, ) -@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -def test_invalid_metadata_create_array(store: Store) -> None: - spath = StorePath(store, "warning_inefficient_codecs") +def test_invalid_metadata_create_array() -> None: with pytest.warns( - UserWarning, + ZarrUserWarning, match="codec disables partial reads and writes, which may lead to inefficient performance", ): zarr.create_array( - spath, + {}, shape=(16, 16), chunks=(16, 16), dtype=np.dtype("uint8"), diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 403fd80e81..eb80545ff3 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -17,7 +17,8 @@ TransposeCodec, ) from zarr.core.buffer import NDArrayLike, default_buffer_prototype -from zarr.storage import StorePath +from zarr.errors import ZarrUserWarning +from zarr.storage import StorePath, ZipStore from ..conftest import ArrayRequest from .test_codecs import _AsyncArrayProxy, order_from_dim @@ -228,7 +229,11 @@ def test_sharding_partial_overwrite( assert np.array_equal(data, read_data) data += 10 - a[:10, :10, :10] = data + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + a[:10, :10, :10] = data + else: + a[:10, :10, :10] = data read_data = a[0:10, 0:10, 0:10] assert np.array_equal(data, read_data) @@ -257,22 +262,22 @@ def test_nested_sharding( ) -> None: data = array_fixture spath = StorePath(store) - a = Array.create( - spath, - shape=data.shape, - chunk_shape=(64, 64, 64), - dtype=data.dtype, - fill_value=0, - codecs=[ - ShardingCodec( + msg = "Combining a `sharding_indexed` codec disables partial reads and writes, which may lead to inefficient performance." + with pytest.warns(ZarrUserWarning, match=msg): + a = zarr.create_array( + spath, + shape=data.shape, + chunks=(64, 64, 64), + dtype=data.dtype, + fill_value=0, + serializer=ShardingCodec( chunk_shape=(32, 32, 32), codecs=[ ShardingCodec(chunk_shape=(16, 16, 16), index_location=inner_index_location) ], index_location=outer_index_location, - ) - ], - ) + ), + ) a[:, :, :] = data diff --git a/tests/test_config.py b/tests/test_config.py index da5b2cc488..0c029dda3a 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -24,6 +24,7 @@ from zarr.core.codec_pipeline import BatchedCodecPipeline from zarr.core.config import BadConfigError, config from zarr.core.indexing import SelectorTuple +from zarr.errors import ZarrUserWarning from zarr.registry import ( fully_qualified_name, get_buffer_class, @@ -287,7 +288,9 @@ class NewCodec2(BytesCodec): # warning because multiple implementations are available but none is selected in the config register_codec("new_codec", NewCodec2) - with pytest.warns(UserWarning, match="not configured in config. Selecting any implementation"): + with pytest.warns( + ZarrUserWarning, match="not configured in config. Selecting any implementation" + ): get_codec_class("new_codec") # no warning if multiple implementations are available and one is selected in the config diff --git a/tests/test_dtype/test_npy/test_bytes.py b/tests/test_dtype/test_npy/test_bytes.py index 78980f7809..39b5416635 100644 --- a/tests/test_dtype/test_npy/test_bytes.py +++ b/tests/test_dtype/test_npy/test_bytes.py @@ -2,8 +2,8 @@ import pytest from tests.test_dtype.test_wrapper import BaseTestZDType -from zarr.core.dtype.common import UnstableSpecificationWarning from zarr.core.dtype.npy.bytes import NullTerminatedBytes, RawBytes, VariableLengthBytes +from zarr.errors import UnstableSpecificationWarning class TestNullTerminatedBytes(BaseTestZDType): @@ -150,7 +150,7 @@ def test_unstable_dtype_warning( Test that we get a warning when serializing a dtype without a zarr v3 spec to json when zarr_format is 3 """ - with pytest.raises(UnstableSpecificationWarning): + with pytest.warns(UnstableSpecificationWarning): zdtype.to_json(zarr_format=3) diff --git a/tests/test_dtype/test_npy/test_string.py b/tests/test_dtype/test_npy/test_string.py index 2cde6a1ac1..19d202d164 100644 --- a/tests/test_dtype/test_npy/test_string.py +++ b/tests/test_dtype/test_npy/test_string.py @@ -5,8 +5,8 @@ from tests.test_dtype.test_wrapper import BaseTestZDType from zarr.core.dtype import FixedLengthUTF32 -from zarr.core.dtype.common import UnstableSpecificationWarning from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING, VariableLengthUTF8 +from zarr.errors import UnstableSpecificationWarning if _NUMPY_SUPPORTS_VLEN_STRING: @@ -136,7 +136,7 @@ def test_unstable_dtype_warning(zdtype: FixedLengthUTF32 | VariableLengthUTF8) - Test that we get a warning when serializing a dtype without a zarr v3 spec to json when zarr_format is 3 """ - with pytest.raises(UnstableSpecificationWarning): + with pytest.warns(UnstableSpecificationWarning): zdtype.to_json(zarr_format=3) diff --git a/tests/test_group.py b/tests/test_group.py index 7705fa205a..e5cfe82daa 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -2,6 +2,7 @@ import contextlib import inspect +import json import operator import pickle import re @@ -39,7 +40,13 @@ ) from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import _collect_aiterator, sync -from zarr.errors import ContainsArrayError, ContainsGroupError, MetadataValidationError +from zarr.errors import ( + ContainsArrayError, + ContainsGroupError, + MetadataValidationError, + ZarrDeprecationWarning, + ZarrUserWarning, +) from zarr.storage import LocalStore, MemoryStore, StorePath, ZipStore from zarr.storage._common import make_store_path from zarr.storage._utils import _join_paths, normalize_path @@ -52,6 +59,7 @@ from _pytest.compat import LEGACY_PATH + from zarr.core.buffer.core import Buffer from zarr.core.common import JSON, ZarrFormat @@ -203,11 +211,17 @@ def test_group_members(store: Store, zarr_format: ZarrFormat, consolidated_metad # this warning shows up when extra objects show up in the hierarchy warn_context = pytest.warns( - UserWarning, match=r"Object at .* is not recognized as a component of a Zarr hierarchy." + ZarrUserWarning, + match=r"(?:Object at .* is not recognized as a component of a Zarr hierarchy.)|(?:Consolidated metadata is currently not part in the Zarr format 3 specification.)", ) if consolidated_metadata: - with warn_context: - zarr.consolidate_metadata(store=store, zarr_format=zarr_format) + if isinstance(store, ZipStore): + with warn_context: + with pytest.warns(UserWarning, match="Duplicate name: "): + zarr.consolidate_metadata(store=store, zarr_format=zarr_format) + else: + with warn_context: + zarr.consolidate_metadata(store=store, zarr_format=zarr_format) # now that we've consolidated the store, we shouldn't get the warnings from the unrecognized objects anymore # we use a nullcontext to handle these cases warn_context = contextlib.nullcontext() @@ -267,7 +281,11 @@ def test_group(store: Store, zarr_format: ZarrFormat) -> None: assert dict(bar2.attrs) == {"baz": "qux"} # update a group's attributes - bar2.attrs.update({"name": "bar"}) + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + bar2.attrs.update({"name": "bar"}) + else: + bar2.attrs.update({"name": "bar"}) # bar.attrs was modified in-place assert dict(bar2.attrs) == {"baz": "qux", "name": "bar"} @@ -340,7 +358,30 @@ def test_group_getitem(store: Store, zarr_format: ZarrFormat, consolidated: bool subsubarray = subgroup.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="uint8") if consolidated: - group = zarr.api.synchronous.consolidate_metadata(store=store, zarr_format=zarr_format) + if zarr_format == 3: + with pytest.warns( # noqa: PT031 + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + group = zarr.api.synchronous.consolidate_metadata( + store=store, zarr_format=zarr_format + ) + else: + group = zarr.api.synchronous.consolidate_metadata( + store=store, zarr_format=zarr_format + ) + else: + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + group = zarr.api.synchronous.consolidate_metadata( + store=store, zarr_format=zarr_format + ) + else: + group = zarr.api.synchronous.consolidate_metadata( + store=store, zarr_format=zarr_format + ) # we're going to assume that `group.metadata` is correct, and reuse that to focus # on indexing in this test. Other tests verify the correctness of group.metadata object.__setattr__( @@ -398,8 +439,11 @@ def test_group_get_with_default(store: Store, zarr_format: ZarrFormat) -> None: # now with a group subgroup = group.require_group("subgroup") - subgroup.attrs["foo"] = "bar" - + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + subgroup.attrs["foo"] = "bar" + else: + subgroup.attrs["foo"] = "bar" result = group.get("subgroup", 8) assert result.attrs["foo"] == "bar" @@ -417,7 +461,22 @@ def test_group_delitem(store: Store, zarr_format: ZarrFormat, consolidated: bool subarray = group.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="uint8") if consolidated: - group = zarr.api.synchronous.consolidate_metadata(store=store, zarr_format=zarr_format) + if zarr_format == 3: + with pytest.warns( # noqa: PT031 + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + group = zarr.api.synchronous.consolidate_metadata( + store=store, zarr_format=zarr_format + ) + else: + group = zarr.api.synchronous.consolidate_metadata( + store=store, zarr_format=zarr_format + ) + else: + group = zarr.api.synchronous.consolidate_metadata(store=store, zarr_format=zarr_format) object.__setattr__( subgroup.metadata, "consolidated_metadata", ConsolidatedMetadata(metadata={}) ) @@ -512,7 +571,22 @@ def test_group_child_iterators(store: Store, zarr_format: ZarrFormat, consolidat expected_arrays = list(zip(expected_array_keys, expected_array_values, strict=False)) if consolidate: - group = zarr.consolidate_metadata(store) + if zarr_format == 3: + with pytest.warns( # noqa: PT031 + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + group = zarr.consolidate_metadata(store) + else: + group = zarr.consolidate_metadata(store) + else: + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + group = zarr.consolidate_metadata(store) + else: + group = zarr.consolidate_metadata(store) if zarr_format == 2: metadata = { "subarray": { @@ -608,7 +682,11 @@ def test_group_update_attributes(store: Store, zarr_format: ZarrFormat) -> None: group = Group.from_store(store, zarr_format=zarr_format, attributes=attrs) assert group.attrs == attrs new_attrs = {"bar": 100} - new_group = group.update_attributes(new_attrs) + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + new_group = group.update_attributes(new_attrs) + else: + new_group = group.update_attributes(new_attrs) updated_attrs = attrs.copy() updated_attrs.update(new_attrs) @@ -623,7 +701,11 @@ async def test_group_update_attributes_async(store: Store, zarr_format: ZarrForm group = Group.from_store(store, zarr_format=zarr_format, attributes=attrs) assert group.attrs == attrs new_attrs = {"bar": 100} - new_group = await group.update_attributes_async(new_attrs) + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name: "): + new_group = await group.update_attributes_async(new_attrs) + else: + new_group = await group.update_attributes_async(new_attrs) assert new_group.attrs == new_attrs @@ -648,8 +730,12 @@ def test_group_create_array( array = group.create_array(name=name, shape=shape, dtype=dtype) array[:] = data elif method == "array": - with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): - array = group.array(name=name, data=data, shape=shape, dtype=dtype) + with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): + with pytest.warns( + ZarrUserWarning, + match="The `compressor` argument is deprecated. Use `compressors` instead.", + ): + array = group.array(name=name, data=data, shape=shape, dtype=dtype) else: raise AssertionError @@ -660,8 +746,12 @@ def test_group_create_array( a[:] = data elif method == "array": with pytest.raises(ContainsArrayError): # noqa: PT012 - with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): - a = group.array(name=name, shape=shape, dtype=dtype) + with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): + with pytest.warns( + ZarrUserWarning, + match="The `compressor` argument is deprecated. Use `compressors` instead.", + ): + a = group.array(name=name, shape=shape, dtype=dtype) a[:] = data assert array.path == normalize_path(name) @@ -1024,7 +1114,11 @@ async def test_asyncgroup_update_attributes(store: Store, zarr_format: ZarrForma store=store, zarr_format=zarr_format, attributes=attributes_old ) - agroup_new_attributes = await agroup.update_attributes(attributes_new) + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name"): + agroup_new_attributes = await agroup.update_attributes(attributes_new) + else: + agroup_new_attributes = await agroup.update_attributes(attributes_new) attributes_updated = attributes_old.copy() attributes_updated.update(attributes_new) assert agroup_new_attributes.attrs == attributes_updated @@ -1099,8 +1193,16 @@ async def test_group_members_async(store: Store, consolidated_metadata: bool) -> assert all_children == expected if consolidated_metadata: - await zarr.api.asynchronous.consolidate_metadata(store=store) - group = await zarr.api.asynchronous.open_group(store=store) + with pytest.warns( # noqa: PT031 + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name"): + await zarr.api.asynchronous.consolidate_metadata(store=store) + else: + await zarr.api.asynchronous.consolidate_metadata(store=store) + group = await zarr.api.asynchronous.open_group(store=store) nmembers = await group.nmembers(max_depth=None) assert nmembers == 6 @@ -1194,27 +1296,27 @@ def test_create_dataset_with_data(store: Store, zarr_format: ZarrFormat) -> None """ root = Group.from_store(store=store, zarr_format=zarr_format) arr = np.random.random((5, 5)) - with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): + with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): data = root.create_dataset("random", data=arr, shape=arr.shape) np.testing.assert_array_equal(np.asarray(data), arr) async def test_create_dataset(store: Store, zarr_format: ZarrFormat) -> None: root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format) - with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."): + with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): foo = await root.create_dataset("foo", shape=(10,), dtype="uint8") assert foo.shape == (10,) with ( pytest.raises(ContainsArrayError), - pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."), + pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."), ): await root.create_dataset("foo", shape=(100,), dtype="int8") _ = await root.create_group("bar") with ( pytest.raises(ContainsGroupError), - pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."), + pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."), ): await root.create_dataset("bar", shape=(100,), dtype="int8") @@ -1253,8 +1355,25 @@ async def test_members_name(store: Store, consolidate: bool, zarr_format: ZarrFo b.create_array("array", shape=(1,), dtype="uint8") if consolidate: - group = zarr.api.synchronous.consolidate_metadata(store) - + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name"): # noqa: PT031 + if zarr_format == 3: + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + group = zarr.api.synchronous.consolidate_metadata(store) + else: + group = zarr.api.synchronous.consolidate_metadata(store) + else: + if zarr_format == 3: + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + group = zarr.api.synchronous.consolidate_metadata(store) + else: + group = zarr.api.synchronous.consolidate_metadata(store) result = group["a"]["b"] assert result.name == "/a/b" @@ -1283,6 +1402,21 @@ def test_open_mutable_mapping_sync(): assert isinstance(group.store_path.store, MemoryStore) +async def test_open_ambiguous_node(): + zarr_json_bytes = default_buffer_prototype().buffer.from_bytes( + json.dumps({"zarr_format": 3, "node_type": "group"}).encode("utf-8") + ) + zgroup_bytes = default_buffer_prototype().buffer.from_bytes( + json.dumps({"zarr_format": 2}).encode("utf-8") + ) + store: dict[str, Buffer] = {"zarr.json": zarr_json_bytes, ".zgroup": zgroup_bytes} + with pytest.warns( + ZarrUserWarning, + match=r"Both zarr\.json \(Zarr format 3\) and \.zgroup \(Zarr format 2\) metadata objects exist at", + ): + await AsyncGroup.open(store, zarr_format=None) + + class TestConsolidated: async def test_group_getitem_consolidated(self, store: Store) -> None: root = await AsyncGroup.from_store(store=store) @@ -1303,7 +1437,15 @@ async def test_group_getitem_consolidated(self, store: Store) -> None: x1 = await x0.create_group("x1") await x1.create_group("x2") - await zarr.api.asynchronous.consolidate_metadata(store) + with pytest.warns( # noqa: PT031 + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name"): + await zarr.api.asynchronous.consolidate_metadata(store) + else: + await zarr.api.asynchronous.consolidate_metadata(store) # On disk, we've consolidated all the metadata in the root zarr.json group = await zarr.api.asynchronous.open(store=store) @@ -1360,7 +1502,15 @@ async def test_group_delitem_consolidated(self, store: Store) -> None: x2 = await x1.create_group("x2") await x2.create_array("data", shape=(1,), dtype="uint8") - await zarr.api.asynchronous.consolidate_metadata(store) + with pytest.warns( # noqa: PT031 + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + if isinstance(store, ZipStore): + with pytest.warns(UserWarning, match="Duplicate name"): + await zarr.api.asynchronous.consolidate_metadata(store) + else: + await zarr.api.asynchronous.consolidate_metadata(store) group = await zarr.api.asynchronous.open_consolidated(store=store) assert len(group.metadata.consolidated_metadata.metadata) == 2 @@ -1384,7 +1534,11 @@ def test_open_consolidated_raises(self, store: Store) -> None: # Now create consolidated metadata... root.create_group("g0") - zarr.consolidate_metadata(store) + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + zarr.consolidate_metadata(store) # and explicitly ignore it. group = zarr.open_group(store=store, use_consolidated=False) @@ -1404,7 +1558,11 @@ async def test_open_consolidated_raises_async(self, store: Store) -> None: # Now create consolidated metadata... await root.create_group("g0") - await zarr.api.asynchronous.consolidate_metadata(store) + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await zarr.api.asynchronous.consolidate_metadata(store) # and explicitly ignore it. group = await zarr.api.asynchronous.open_group(store=store, use_consolidated=False) diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index 19eba4fb86..e23444cf93 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -22,6 +22,7 @@ from zarr.core.group import ConsolidatedMetadata, GroupMetadata from zarr.core.metadata import ArrayV3Metadata from zarr.core.metadata.v2 import ArrayV2Metadata +from zarr.errors import ZarrUserWarning from zarr.storage import StorePath if TYPE_CHECKING: @@ -67,7 +68,11 @@ async def test_consolidated(self, memory_store_with_hierarchy: Store) -> None: # arrays under arrays # single array # etc. - await consolidate_metadata(memory_store_with_hierarchy) + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await consolidate_metadata(memory_store_with_hierarchy) group2 = await AsyncGroup.open(memory_store_with_hierarchy) array_metadata = { @@ -215,7 +220,11 @@ def test_consolidated_sync(self, memory_store): g.create_array(name="lon", shape=(2,), dtype=dtype) g.create_array(name="time", shape=(3,), dtype=dtype) - zarr.api.synchronous.consolidate_metadata(memory_store) + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + zarr.api.synchronous.consolidate_metadata(memory_store) group2 = zarr.api.synchronous.Group.open(memory_store) array_metadata = { @@ -298,7 +307,11 @@ async def test_not_writable_raises(self, memory_store: zarr.storage.MemoryStore) await consolidate_metadata(read_store) async def test_non_root_node(self, memory_store_with_hierarchy: Store) -> None: - await consolidate_metadata(memory_store_with_hierarchy, path="child") + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await consolidate_metadata(memory_store_with_hierarchy, path="child") root = await AsyncGroup.open(memory_store_with_hierarchy) child = await AsyncGroup.open(StorePath(memory_store_with_hierarchy) / "child") @@ -484,7 +497,14 @@ async def test_to_dict_order( await child.create_array("d", shape=(1,), dtype=dtype) # Consolidate metadata and re-open store - await zarr.api.asynchronous.consolidate_metadata(memory_store) + if zarr_format == 3: + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await zarr.api.asynchronous.consolidate_metadata(memory_store) + else: + await zarr.api.asynchronous.consolidate_metadata(memory_store) g2 = await zarr.api.asynchronous.open_group(store=memory_store) assert list(g2.metadata.consolidated_metadata.metadata) == ["a", "b", "c"] @@ -582,7 +602,14 @@ async def test_use_consolidated_false( await g.create_group(name="a") # test a stale read - await zarr.api.asynchronous.consolidate_metadata(memory_store) + if zarr_format == 3: + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await zarr.api.asynchronous.consolidate_metadata(memory_store) + else: + await zarr.api.asynchronous.consolidate_metadata(memory_store) await g.create_group(name="b") stale = await zarr.api.asynchronous.open_group(store=memory_store) @@ -597,7 +624,14 @@ async def test_use_consolidated_false( assert len([x async for x in good.members()]) == 2 # reconsolidate - await zarr.api.asynchronous.consolidate_metadata(memory_store) + if zarr_format == 3: + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await zarr.api.asynchronous.consolidate_metadata(memory_store) + else: + await zarr.api.asynchronous.consolidate_metadata(memory_store) good = await zarr.api.asynchronous.open_group(store=memory_store) assert len([x async for x in good.members()]) == 2 @@ -613,7 +647,11 @@ async def test_stale_child_metadata_ignored(self, memory_store: zarr.storage.Mem await zarr.api.asynchronous.consolidate_metadata(memory_store, path="foo") await root.create_group("foo/bar/spam") - await zarr.api.asynchronous.consolidate_metadata(memory_store) + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await zarr.api.asynchronous.consolidate_metadata(memory_store) reopened = await zarr.api.asynchronous.open_consolidated(store=memory_store, zarr_format=3) result = [x[0] async for x in reopened.members(max_depth=None)] @@ -637,7 +675,7 @@ async def test_use_consolidated_for_children_members( # Now according to the consolidated metadata, "a" has children ["b"] # but according to the unconsolidated metadata, "a" has children ["b", "c"] group = await zarr.api.asynchronous.open_group(store=memory_store, path="a") - with pytest.warns(UserWarning, match="Object at 'c' not found"): + with pytest.warns(ZarrUserWarning, match="Object at 'c' not found"): result = sorted([x[0] async for x in group.members(max_depth=None)]) expected = ["b"] assert result == expected @@ -655,7 +693,14 @@ async def test_consolidated_metadata_encodes_special_chars( ): root = await group(store=memory_store, zarr_format=zarr_format) _time = await root.create_array("time", shape=(12,), dtype=np.float64, fill_value=fill_value) - await zarr.api.asynchronous.consolidate_metadata(memory_store) + if zarr_format == 3: + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await zarr.api.asynchronous.consolidate_metadata(memory_store) + else: + await zarr.api.asynchronous.consolidate_metadata(memory_store) root = await group(store=memory_store, zarr_format=zarr_format) root_buffer = root.metadata.to_buffer_dict(default_buffer_prototype()) diff --git a/tests/test_metadata/test_v2.py b/tests/test_metadata/test_v2.py index a2894529aa..e18841f1f3 100644 --- a/tests/test_metadata/test_v2.py +++ b/tests/test_metadata/test_v2.py @@ -15,6 +15,7 @@ from zarr.core.group import ConsolidatedMetadata, GroupMetadata from zarr.core.metadata import ArrayV2Metadata from zarr.core.metadata.v2 import parse_zarr_format +from zarr.errors import ZarrUserWarning if TYPE_CHECKING: from typing import Any @@ -93,7 +94,7 @@ def test_filters_empty_tuple_warns() -> None: "fill_value": 0, } with pytest.warns( - UserWarning, match="Found an empty list of filters in the array metadata document." + ZarrUserWarning, match="Found an empty list of filters in the array metadata document." ): meta = ArrayV2Metadata.from_dict(metadata_dict) assert meta.filters is None diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index abee298a8c..82a96b5d1e 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -14,6 +14,7 @@ from zarr.abc.store import OffsetByteRequest from zarr.core.buffer import Buffer, cpu, default_buffer_prototype from zarr.core.sync import _collect_aiterator, sync +from zarr.errors import ZarrUserWarning from zarr.storage import FsspecStore from zarr.storage._fsspec import _make_async from zarr.testing.store import StoreTests @@ -258,7 +259,7 @@ def test_init_warns_if_fs_asynchronous_is_false(self) -> None: f"s3://{test_bucket_name}", endpoint_url=endpoint_url, anon=False, asynchronous=False ) store_kwargs = {"fs": fs, "path": path} - with pytest.warns(UserWarning, match=r".* was not created with `asynchronous=True`.*"): + with pytest.warns(ZarrUserWarning, match=r".* was not created with `asynchronous=True`.*"): self.store_cls(**store_kwargs) async def test_empty_nonexistent_path(self, store_kwargs: dict[str, Any]) -> None: diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 4fc3f6e698..0b6bae757d 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -9,6 +9,7 @@ import zarr from zarr.core.buffer import Buffer, cpu, gpu +from zarr.errors import ZarrUserWarning from zarr.storage import GpuMemoryStore, MemoryStore from zarr.testing.store import StoreTests from zarr.testing.utils import gpu_test @@ -130,6 +131,8 @@ def test_from_dict(self) -> None: "a": gpu.Buffer.from_bytes(b"aaaa"), "b": cpu.Buffer.from_bytes(b"bbbb"), } - result = GpuMemoryStore.from_dict(d) + msg = "Creating a zarr.buffer.gpu.Buffer with an array that does not support the __cuda_array_interface__ for zero-copy transfers, falling back to slow copy based path" + with pytest.warns(ZarrUserWarning, match=msg): + result = GpuMemoryStore.from_dict(d) for v in result._store_dict.values(): assert type(v) is gpu.Buffer diff --git a/tests/test_v2.py b/tests/test_v2.py index 4d17305995..70e8f2923f 100644 --- a/tests/test_v2.py +++ b/tests/test_v2.py @@ -21,6 +21,7 @@ from zarr.core.dtype.wrapper import ZDType from zarr.core.group import Group from zarr.core.sync import sync +from zarr.errors import ZarrDeprecationWarning from zarr.storage import MemoryStore, StorePath @@ -226,7 +227,7 @@ def test_v2_non_contiguous(numpy_order: Literal["C", "F"], zarr_order: Literal[" def test_default_compressor_deprecation_warning() -> None: - with pytest.warns(DeprecationWarning, match="default_compressor is deprecated"): + with pytest.warns(ZarrDeprecationWarning, match="default_compressor is deprecated"): zarr.storage.default_compressor = "zarr.codecs.zstd.ZstdCodec()" # type: ignore[attr-defined] From f087c56f748f3f8d0ff4d7850ef3a16b701d4e23 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 6 Aug 2025 10:07:34 +0200 Subject: [PATCH 061/468] Fix typos (#3346) --- src/zarr/core/array.py | 2 +- src/zarr/testing/stateful.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index ca8bc414cc..311a0eb986 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -699,7 +699,7 @@ async def _create( overwrite=overwrite, ) else: - raise ValueError(f"Insupported zarr_format. Got: {zarr_format}") + raise ValueError(f"Unsupported zarr_format. Got: {zarr_format}") if data is not None: # insert user-provided data diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index 8f946159a6..8ada53a55a 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -301,7 +301,7 @@ def delete_dir(self, data: DataObject) -> None: # array_path = data.draw(st.sampled_from(self.all_arrays), label="Array move source") # to_group = data.draw(st.sampled_from(self.all_groups), label="Array move destination") - # # fixme renaiming to self? + # # fixme renaming to self? # array_name = os.path.basename(array_path) # assume(self.model.can_add(to_group, array_name)) # new_path = f"{to_group}/{array_name}".lstrip("/") @@ -318,7 +318,7 @@ def delete_dir(self, data: DataObject) -> None: # from_group_name = os.path.basename(from_group) # assume(self.model.can_add(to_group, from_group_name)) - # # fixme renaiming to self? + # # fixme renaming to self? # new_path = f"{to_group}/{from_group_name}".lstrip("/") # note(f"moving group '{from_group}' -> '{new_path}'") # self.model.rename(from_group, new_path) From 1264a4d190a0f22a3612e302d41f4413f06edf35 Mon Sep 17 00:00:00 2001 From: Bojidar Marinov Date: Wed, 6 Aug 2025 12:54:08 +0300 Subject: [PATCH 062/468] Write chunks with negative zero values and a zero fill value (#3216) * Write chunks with negative zero values and a zero fill value Fixes #3144 * Update changes/3144.bugfix.rst * Use bit patterns for comparing zeroes instead of signbit Co-authored-by: Davis Bennett * fixup: Make sure fill value is a float before checking if it's == 0 * fixup: Make sure we don't copy arrays as we check for zeroes * Attempt using structured void dtypes for CuPy --------- Co-authored-by: Davis Bennett --- changes/3144.bugfix.rst | 1 + src/zarr/core/buffer/core.py | 9 +++++++++ tests/test_array.py | 24 ++++++++++++++++++++++++ 3 files changed, 34 insertions(+) create mode 100644 changes/3144.bugfix.rst diff --git a/changes/3144.bugfix.rst b/changes/3144.bugfix.rst new file mode 100644 index 0000000000..8dde317bb8 --- /dev/null +++ b/changes/3144.bugfix.rst @@ -0,0 +1 @@ +Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value.``` diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index 19125b838f..07bdb8c26e 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -523,6 +523,15 @@ def all_equal(self, other: Any, equal_nan: bool = True) -> bool: if other is None: # Handle None fill_value for Zarr V2 return False + # Handle positive and negative zero by comparing bit patterns: + if ( + np.asarray(other).dtype.kind == "f" + and other == 0.0 + and self._data.dtype.kind not in ("U", "S", "T", "O", "V") + ): + _data, other = np.broadcast_arrays(self._data, np.asarray(other, self._data.dtype)) + void_dtype = "V" + str(_data.dtype.itemsize) + return np.array_equal(_data.view(void_dtype), other.view(void_dtype)) # use array_equal to obtain equal_nan=True functionality # Since fill-value is a scalar, isn't there a faster path than allocating a new array for fill value # every single time we have to write data? diff --git a/tests/test_array.py b/tests/test_array.py index 46b78de7bf..74201a4017 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -870,6 +870,30 @@ def test_write_empty_chunks_behavior( assert arr.nchunks_initialized == arr.nchunks +@pytest.mark.parametrize("store", ["memory"], indirect=True) +@pytest.mark.parametrize("fill_value", [0.0, -0.0]) +@pytest.mark.parametrize("dtype", ["f4", "f2"]) +def test_write_empty_chunks_negative_zero( + zarr_format: ZarrFormat, store: MemoryStore, fill_value: float, dtype: str +) -> None: + # regression test for https://github.com/zarr-developers/zarr-python/issues/3144 + + arr = zarr.create_array( + store=store, + shape=(2,), + zarr_format=zarr_format, + dtype=dtype, + fill_value=fill_value, + chunks=(1,), + config={"write_empty_chunks": False}, + ) + assert arr.nchunks_initialized == 0 + + # initialize the with the negated fill value (-0.0 for +0.0, +0.0 for -0.0) + arr[:] = -fill_value + assert arr.nchunks_initialized == arr.nchunks + + @pytest.mark.parametrize( ("fill_value", "expected"), [ From 926a52fa11845a142f65b10f13c1d9a92c754e6b Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 6 Aug 2025 15:40:54 +0200 Subject: [PATCH 063/468] The important metric is project coverage (#3351) Make patch coverage informational, so that fixing a typo in a line that raises an exception (typically not covered by a test) passes CI. Co-authored-by: Davis Bennett --- codecov.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/codecov.yml b/codecov.yml index 3e30f82a31..ef535fd8fe 100644 --- a/codecov.yml +++ b/codecov.yml @@ -3,6 +3,7 @@ coverage: patch: default: target: auto + informational: true project: default: target: auto From a26926cf4ec51a12ca28ff31c13ef2c8a32d51f9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 11 Aug 2025 10:21:59 +0100 Subject: [PATCH 064/468] Bump actions/download-artifact from 4 to 5 in the actions group (#3363) Bumps the actions group with 1 update: [actions/download-artifact](https://github.com/actions/download-artifact). Updates `actions/download-artifact` from 4 to 5 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/releases.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index c8903aa779..f35cc0c3f5 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -36,7 +36,7 @@ jobs: needs: [build_artifacts] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@v4 + - uses: actions/download-artifact@v5 with: name: releases path: dist @@ -51,7 +51,7 @@ jobs: runs-on: ubuntu-latest if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') steps: - - uses: actions/download-artifact@v4 + - uses: actions/download-artifact@v5 with: name: releases path: dist From 18419f012642f563a0be0556e0b7a3e8611316de Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 13 Aug 2025 17:26:17 +0200 Subject: [PATCH 065/468] use local imports in store ABC to avoid circular import issues (#3372) * use local imports in store ABC to avoid circular import issues * changelog --- changes/3372.misc.rst | 2 ++ src/zarr/abc/store.py | 12 ++++++++---- 2 files changed, 10 insertions(+), 4 deletions(-) create mode 100644 changes/3372.misc.rst diff --git a/changes/3372.misc.rst b/changes/3372.misc.rst new file mode 100644 index 0000000000..fe7da0d265 --- /dev/null +++ b/changes/3372.misc.rst @@ -0,0 +1,2 @@ +Make certain imports in ``zarr.abc.store`` local to method definitions. This minimizes the risk of +circular imports when adding new classes to ``zarr.abc.store``. \ No newline at end of file diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 1fbdb3146c..53e981c3bd 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -6,10 +6,6 @@ from itertools import starmap from typing import TYPE_CHECKING, Protocol, runtime_checkable -from zarr.core.buffer.core import default_buffer_prototype -from zarr.core.common import concurrent_map -from zarr.core.config import config - if TYPE_CHECKING: from collections.abc import AsyncGenerator, AsyncIterator, Iterable from types import TracebackType @@ -438,6 +434,9 @@ async def getsize(self, key: str) -> int: # Note to implementers: this default implementation is very inefficient since # it requires reading the entire object. Many systems will have ways to get the # size of an object without reading it. + # avoid circular import + from zarr.core.buffer.core import default_buffer_prototype + value = await self.get(key, prototype=default_buffer_prototype()) if value is None: raise FileNotFoundError(key) @@ -476,6 +475,11 @@ async def getsize_prefix(self, prefix: str) -> int: # on to getting sizes. Ideally we would overlap those two, which should # improve tail latency and might reduce memory pressure (since not all keys # would be in memory at once). + + # avoid circular import + from zarr.core.common import concurrent_map + from zarr.core.config import config + keys = [(x,) async for x in self.list_prefix(prefix)] limit = config.get("async.concurrency") sizes = await concurrent_map(keys, self.getsize, limit=limit) From 90fb2bdea72f6d4aa92ed62420e11667bc1fe21f Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 13 Aug 2025 17:40:32 +0200 Subject: [PATCH 066/468] add numcodec protocol (#3318) * add numcodec protocol * add tests for numcodecs compatibility * changelog * ignore unknown key * remove re-implementation of get_codec * avoid circular imports by importing lower-level routines exactly where needed * push numcodec prototol into abcs; remove all numcodecs.abc.Codec type annotations * add tests for codecjson typeguard * avoid using zarr's buffer / ndbuffer for numcodec encode / decode * use Any to model input / output types of numcodec protocol * add numcodec protocol * add tests for numcodecs compatibility * changelog * ignore unknown key * remove re-implementation of get_codec * avoid circular imports by importing lower-level routines exactly where needed * push numcodec prototol into abcs; remove all numcodecs.abc.Codec type annotations * add tests for codecjson typeguard * avoid using zarr's buffer / ndbuffer for numcodec encode / decode * use Any to model input / output types of numcodec protocol * Update src/zarr/abc/numcodec.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update src/zarr/abc/numcodec.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update src/zarr/abc/numcodec.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update src/zarr/abc/numcodec.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update src/zarr/abc/numcodec.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * fix docstrings * revert changes to store imports * remove whitespace * fix docstring --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3318.misc.rst | 2 + src/zarr/abc/codec.py | 28 ++++- src/zarr/abc/numcodec.py | 101 ++++++++++++++++++ src/zarr/api/asynchronous.py | 5 +- src/zarr/api/synchronous.py | 4 +- src/zarr/codecs/_v2.py | 10 +- src/zarr/core/_info.py | 7 +- src/zarr/core/array.py | 49 ++++----- src/zarr/core/metadata/v2.py | 33 +++--- src/zarr/registry.py | 30 ++++++ tests/test_abc/__init__.py | 0 tests/test_abc/test_codec.py | 12 +++ tests/test_api.py | 2 +- tests/test_array.py | 20 ++-- tests/test_codecs/test_numcodecs.py | 24 +++++ tests/test_codecs/test_vlen.py | 2 +- .../test_v2_dtype_regression.py | 8 +- 17 files changed, 261 insertions(+), 76 deletions(-) create mode 100644 changes/3318.misc.rst create mode 100644 src/zarr/abc/numcodec.py create mode 100644 tests/test_abc/__init__.py create mode 100644 tests/test_abc/test_codec.py create mode 100644 tests/test_codecs/test_numcodecs.py diff --git a/changes/3318.misc.rst b/changes/3318.misc.rst new file mode 100644 index 0000000000..f8308e6b97 --- /dev/null +++ b/changes/3318.misc.rst @@ -0,0 +1,2 @@ +Define a ``Protocol`` to model the ``numcodecs.abc.Codec`` interface. This is groundwork toward +making ``numcodecs`` an optional dependency for ``zarr-python``. \ No newline at end of file diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index f8a5447a70..d5c995d2ca 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -1,11 +1,14 @@ from __future__ import annotations from abc import abstractmethod -from typing import TYPE_CHECKING, Generic, TypeVar +from collections.abc import Mapping +from typing import TYPE_CHECKING, Generic, TypeGuard, TypeVar + +from typing_extensions import ReadOnly, TypedDict from zarr.abc.metadata import Metadata from zarr.core.buffer import Buffer, NDBuffer -from zarr.core.common import ChunkCoords, concurrent_map +from zarr.core.common import ChunkCoords, NamedConfig, concurrent_map from zarr.core.config import config if TYPE_CHECKING: @@ -34,6 +37,27 @@ CodecInput = TypeVar("CodecInput", bound=NDBuffer | Buffer) CodecOutput = TypeVar("CodecOutput", bound=NDBuffer | Buffer) +TName = TypeVar("TName", bound=str, covariant=True) + + +class CodecJSON_V2(TypedDict, Generic[TName]): + """The JSON representation of a codec for Zarr V2""" + + id: ReadOnly[TName] + + +def _check_codecjson_v2(data: object) -> TypeGuard[CodecJSON_V2[str]]: + return isinstance(data, Mapping) and "id" in data and isinstance(data["id"], str) + + +CodecJSON_V3 = str | NamedConfig[str, Mapping[str, object]] +"""The JSON representation of a codec for Zarr V3.""" + +# The widest type we will *accept* for a codec JSON +# This covers v2 and v3 +CodecJSON = str | Mapping[str, object] +"""The widest type of JSON-like input that could specify a codec.""" + class BaseCodec(Metadata, Generic[CodecInput, CodecOutput]): """Generic base class for codecs. diff --git a/src/zarr/abc/numcodec.py b/src/zarr/abc/numcodec.py new file mode 100644 index 0000000000..76eac1d898 --- /dev/null +++ b/src/zarr/abc/numcodec.py @@ -0,0 +1,101 @@ +from typing import Any, Self, TypeGuard + +from typing_extensions import Protocol + + +class Numcodec(Protocol): + """ + A protocol that models the ``numcodecs.abc.Codec`` interface. + + This protocol should be considered experimental. Expect the type annotations for ``buf`` and + ``out`` to narrow in the future. + """ + + codec_id: str + + def encode(self, buf: Any) -> Any: + """Encode data from ``buf``. + + Parameters + ---------- + buf : Any + Data to be encoded. + + Returns + ------- + enc: Any + Encoded data. + """ + ... + + def decode(self, buf: Any, out: Any | None = None) -> Any: + """ + Decode data in ``buf``. + + Parameters + ---------- + buf : Any + Encoded data. + out : Any + Writeable buffer to store decoded data. If provided, this buffer must + be exactly the right size to store the decoded data. + + Returns + ------- + dec : Any + Decoded data. + """ + ... + + def get_config(self) -> Any: + """ + Return a JSON-serializable configuration dictionary for this + codec. Must include an ``'id'`` field with the codec identifier. + """ + ... + + @classmethod + def from_config(cls, config: Any) -> Self: + """ + Instantiate a codec from a configuration dictionary. + + Parameters + ---------- + config : Any + A configuration dictionary for this codec. + """ + ... + + +def _is_numcodec_cls(obj: object) -> TypeGuard[type[Numcodec]]: + """ + Check if the given object is a class implements the Numcodec protocol. + + The @runtime_checkable decorator does not allow issubclass checks for protocols with non-method + members (i.e., attributes), so we use this function to manually check for the presence of the + required attributes and methods on a given object. + """ + return ( + isinstance(obj, type) + and hasattr(obj, "codec_id") + and isinstance(obj.codec_id, str) + and hasattr(obj, "encode") + and callable(obj.encode) + and hasattr(obj, "decode") + and callable(obj.decode) + and hasattr(obj, "get_config") + and callable(obj.get_config) + and hasattr(obj, "from_config") + and callable(obj.from_config) + ) + + +def _is_numcodec(obj: object) -> TypeGuard[Numcodec]: + """ + Check if the given object implements the Numcodec protocol. + + The @runtime_checkable decorator does not allow issubclass checks for protocols with non-method + members (i.e., attributes), so we use this function to manually check for the presence of the + required attributes and methods on a given object. + """ + return _is_numcodec_cls(type(obj)) diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 78b68caf73..a044ba8594 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -52,9 +52,8 @@ if TYPE_CHECKING: from collections.abc import Iterable - import numcodecs.abc - from zarr.abc.codec import Codec + from zarr.abc.numcodec import Numcodec from zarr.core.buffer import NDArrayLikeOrScalar from zarr.core.chunk_key_encodings import ChunkKeyEncoding from zarr.storage import StoreLike @@ -877,7 +876,7 @@ async def create( overwrite: bool = False, path: PathLike | None = None, chunk_store: StoreLike | None = None, - filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, + filters: Iterable[dict[str, JSON] | Numcodec] | None = None, cache_metadata: bool | None = None, cache_attrs: bool | None = None, read_only: bool | None = None, diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index ed1ae2cf2a..50a1c0fa20 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -15,11 +15,11 @@ if TYPE_CHECKING: from collections.abc import Iterable - import numcodecs.abc import numpy as np import numpy.typing as npt from zarr.abc.codec import Codec + from zarr.abc.numcodec import Numcodec from zarr.api.asynchronous import ArrayLike, PathLike from zarr.core.array import ( CompressorsLike, @@ -610,7 +610,7 @@ def create( overwrite: bool = False, path: PathLike | None = None, chunk_store: StoreLike | None = None, - filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, + filters: Iterable[dict[str, JSON] | Numcodec] | None = None, cache_metadata: bool | None = None, cache_attrs: bool | None = None, read_only: bool | None = None, diff --git a/src/zarr/codecs/_v2.py b/src/zarr/codecs/_v2.py index 08853f27f1..3c6c99c21c 100644 --- a/src/zarr/codecs/_v2.py +++ b/src/zarr/codecs/_v2.py @@ -4,7 +4,6 @@ from dataclasses import dataclass from typing import TYPE_CHECKING -import numcodecs import numpy as np from numcodecs.compat import ensure_bytes, ensure_ndarray_like @@ -12,16 +11,15 @@ from zarr.registry import get_ndbuffer_class if TYPE_CHECKING: - import numcodecs.abc - + from zarr.abc.numcodec import Numcodec from zarr.core.array_spec import ArraySpec from zarr.core.buffer import Buffer, NDBuffer @dataclass(frozen=True) class V2Codec(ArrayBytesCodec): - filters: tuple[numcodecs.abc.Codec, ...] | None - compressor: numcodecs.abc.Codec | None + filters: tuple[Numcodec, ...] | None + compressor: Numcodec | None is_fixed_size = False @@ -86,7 +84,6 @@ async def _encode_single( if self.filters: for f in self.filters: chunk = await asyncio.to_thread(f.encode, chunk) - # check object encoding if ensure_ndarray_like(chunk).dtype == object: raise RuntimeError("cannot write object array without object codec") @@ -96,7 +93,6 @@ async def _encode_single( cdata = await asyncio.to_thread(self.compressor.encode, chunk) else: cdata = chunk - cdata = ensure_bytes(cdata) return chunk_spec.prototype.buffer.from_bytes(cdata) diff --git a/src/zarr/core/_info.py b/src/zarr/core/_info.py index a5b14d573a..fef424346a 100644 --- a/src/zarr/core/_info.py +++ b/src/zarr/core/_info.py @@ -5,9 +5,8 @@ from typing import TYPE_CHECKING, Literal if TYPE_CHECKING: - import numcodecs.abc - from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec + from zarr.abc.numcodec import Numcodec from zarr.core.common import ZarrFormat from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType @@ -88,9 +87,9 @@ class ArrayInfo: _order: Literal["C", "F"] _read_only: bool _store_type: str - _filters: tuple[numcodecs.abc.Codec, ...] | tuple[ArrayArrayCodec, ...] = () + _filters: tuple[Numcodec, ...] | tuple[ArrayArrayCodec, ...] = () _serializer: ArrayBytesCodec | None = None - _compressors: tuple[numcodecs.abc.Codec, ...] | tuple[BytesBytesCodec, ...] = () + _compressors: tuple[Numcodec, ...] | tuple[BytesBytesCodec, ...] = () _count_bytes: int | None = None _count_bytes_stored: int | None = None _count_chunks_initialized: int | None = None diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 311a0eb986..2ce33df7ba 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -19,13 +19,12 @@ ) from warnings import warn -import numcodecs -import numcodecs.abc import numpy as np from typing_extensions import deprecated import zarr from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec +from zarr.abc.numcodec import Numcodec, _is_numcodec from zarr.abc.store import Store, set_or_delete from zarr.codecs._v2 import V2Codec from zarr.codecs.bytes import BytesCodec @@ -607,7 +606,7 @@ async def _create( chunks: ShapeLike | None = None, dimension_separator: Literal[".", "/"] | None = None, order: MemoryOrder | None = None, - filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, + filters: Iterable[dict[str, JSON] | Numcodec] | None = None, compressor: CompressorLike = "auto", # runtime overwrite: bool = False, @@ -818,7 +817,7 @@ def _create_metadata_v2( order: MemoryOrder, dimension_separator: Literal[".", "/"] | None = None, fill_value: Any | None = DEFAULT_FILL_VALUE, - filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, + filters: Iterable[dict[str, JSON] | Numcodec] | None = None, compressor: CompressorLikev2 = None, attributes: dict[str, JSON] | None = None, ) -> ArrayV2Metadata: @@ -856,7 +855,7 @@ async def _create_v2( config: ArrayConfig, dimension_separator: Literal[".", "/"] | None = None, fill_value: Any | None = DEFAULT_FILL_VALUE, - filters: Iterable[dict[str, JSON] | numcodecs.abc.Codec] | None = None, + filters: Iterable[dict[str, JSON] | Numcodec] | None = None, compressor: CompressorLike = "auto", attributes: dict[str, JSON] | None = None, overwrite: bool = False, @@ -1033,7 +1032,7 @@ def size(self) -> int: return np.prod(self.metadata.shape).item() @property - def filters(self) -> tuple[numcodecs.abc.Codec, ...] | tuple[ArrayArrayCodec, ...]: + def filters(self) -> tuple[Numcodec, ...] | tuple[ArrayArrayCodec, ...]: """ Filters that are applied to each chunk of the array, in order, before serializing that chunk to bytes. @@ -1062,7 +1061,7 @@ def serializer(self) -> ArrayBytesCodec | None: @property @deprecated("Use AsyncArray.compressors instead.", category=ZarrDeprecationWarning) - def compressor(self) -> numcodecs.abc.Codec | None: + def compressor(self) -> Numcodec | None: """ Compressor that is applied to each chunk of the array. @@ -1075,7 +1074,7 @@ def compressor(self) -> numcodecs.abc.Codec | None: raise TypeError("`compressor` is not available for Zarr format 3 arrays.") @property - def compressors(self) -> tuple[numcodecs.abc.Codec, ...] | tuple[BytesBytesCodec, ...]: + def compressors(self) -> tuple[Numcodec, ...] | tuple[BytesBytesCodec, ...]: """ Compressors that are applied to each chunk of the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -2227,7 +2226,7 @@ def fill_value(self) -> Any: return self.metadata.fill_value @property - def filters(self) -> tuple[numcodecs.abc.Codec, ...] | tuple[ArrayArrayCodec, ...]: + def filters(self) -> tuple[Numcodec, ...] | tuple[ArrayArrayCodec, ...]: """ Filters that are applied to each chunk of the array, in order, before serializing that chunk to bytes. @@ -2243,7 +2242,7 @@ def serializer(self) -> None | ArrayBytesCodec: @property @deprecated("Use Array.compressors instead.", category=ZarrDeprecationWarning) - def compressor(self) -> numcodecs.abc.Codec | None: + def compressor(self) -> Numcodec | None: """ Compressor that is applied to each chunk of the array. @@ -2254,7 +2253,7 @@ def compressor(self) -> numcodecs.abc.Codec | None: return self._async_array.compressor @property - def compressors(self) -> tuple[numcodecs.abc.Codec, ...] | tuple[BytesBytesCodec, ...]: + def compressors(self) -> tuple[Numcodec, ...] | tuple[BytesBytesCodec, ...]: """ Compressors that are applied to each chunk of the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -3898,23 +3897,21 @@ def _build_parents( FiltersLike: TypeAlias = ( - Iterable[dict[str, JSON] | ArrayArrayCodec | numcodecs.abc.Codec] + Iterable[dict[str, JSON] | ArrayArrayCodec | Numcodec] | ArrayArrayCodec - | Iterable[numcodecs.abc.Codec] - | numcodecs.abc.Codec + | Iterable[Numcodec] + | Numcodec | Literal["auto"] | None ) # Union of acceptable types for users to pass in for both v2 and v3 compressors -CompressorLike: TypeAlias = ( - dict[str, JSON] | BytesBytesCodec | numcodecs.abc.Codec | Literal["auto"] | None -) +CompressorLike: TypeAlias = dict[str, JSON] | BytesBytesCodec | Numcodec | Literal["auto"] | None CompressorsLike: TypeAlias = ( - Iterable[dict[str, JSON] | BytesBytesCodec | numcodecs.abc.Codec] + Iterable[dict[str, JSON] | BytesBytesCodec | Numcodec] | dict[str, JSON] | BytesBytesCodec - | numcodecs.abc.Codec + | Numcodec | Literal["auto"] | None ) @@ -4775,7 +4772,7 @@ def default_serializer_v3(dtype: ZDType[Any, Any]) -> ArrayBytesCodec: return serializer -def default_filters_v2(dtype: ZDType[Any, Any]) -> tuple[numcodecs.abc.Codec] | None: +def default_filters_v2(dtype: ZDType[Any, Any]) -> tuple[Numcodec] | None: """ Given a data type, return the default filters for that data type. @@ -4797,7 +4794,7 @@ def default_filters_v2(dtype: ZDType[Any, Any]) -> tuple[numcodecs.abc.Codec] | return None -def default_compressor_v2(dtype: ZDType[Any, Any]) -> numcodecs.abc.Codec: +def default_compressor_v2(dtype: ZDType[Any, Any]) -> Numcodec: """ Given a data type, return the default compressors for that data type. @@ -4805,7 +4802,7 @@ def default_compressor_v2(dtype: ZDType[Any, Any]) -> numcodecs.abc.Codec: """ from numcodecs import Zstd - return Zstd(level=0, checksum=False) + return Zstd(level=0, checksum=False) # type: ignore[no-any-return] def _parse_chunk_encoding_v2( @@ -4813,12 +4810,12 @@ def _parse_chunk_encoding_v2( compressor: CompressorsLike, filters: FiltersLike, dtype: ZDType[TBaseDType, TBaseScalar], -) -> tuple[tuple[numcodecs.abc.Codec, ...] | None, numcodecs.abc.Codec | None]: +) -> tuple[tuple[Numcodec, ...] | None, Numcodec | None]: """ Generate chunk encoding classes for Zarr format 2 arrays with optional defaults. """ - _filters: tuple[numcodecs.abc.Codec, ...] | None - _compressor: numcodecs.abc.Codec | None + _filters: tuple[Numcodec, ...] | None + _compressor: Numcodec | None if compressor is None or compressor == (): _compressor = None @@ -4839,7 +4836,7 @@ def _parse_chunk_encoding_v2( else: if isinstance(filters, Iterable): for idx, f in enumerate(filters): - if not isinstance(f, numcodecs.abc.Codec): + if not _is_numcodec(f): msg = ( "For Zarr format 2 arrays, all elements of `filters` must be numcodecs codecs. " f"Element at index {idx} has type {type(f)}, which is not a numcodecs codec." diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 9ad6b3bc42..efc6bd7949 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -5,13 +5,13 @@ from functools import cached_property from typing import TYPE_CHECKING, Any, TypeAlias, TypedDict, cast -import numcodecs.abc - from zarr.abc.metadata import Metadata +from zarr.abc.numcodec import Numcodec, _is_numcodec from zarr.core.chunk_grids import RegularChunkGrid from zarr.core.dtype import get_data_type_from_json from zarr.core.dtype.common import OBJECT_CODEC_IDS, DTypeSpec_V2 from zarr.errors import ZarrUserWarning +from zarr.registry import get_numcodec if TYPE_CHECKING: from typing import Literal, Self @@ -31,7 +31,6 @@ import json from dataclasses import dataclass, field, fields, replace -import numcodecs import numpy as np from zarr.core.array_spec import ArrayConfig, ArraySpec @@ -57,7 +56,7 @@ class ArrayV2MetadataDict(TypedDict): # Union of acceptable types for v2 compressors -CompressorLikev2: TypeAlias = dict[str, JSON] | numcodecs.abc.Codec | None +CompressorLikev2: TypeAlias = dict[str, JSON] | Numcodec | None @dataclass(frozen=True, kw_only=True) @@ -67,9 +66,9 @@ class ArrayV2Metadata(Metadata): dtype: ZDType[TBaseDType, TBaseScalar] fill_value: int | float | str | bytes | None = None order: MemoryOrder = "C" - filters: tuple[numcodecs.abc.Codec, ...] | None = None + filters: tuple[Numcodec, ...] | None = None dimension_separator: Literal[".", "/"] = "." - compressor: numcodecs.abc.Codec | None + compressor: Numcodec | None attributes: dict[str, JSON] = field(default_factory=dict) zarr_format: Literal[2] = field(init=False, default=2) @@ -83,7 +82,7 @@ def __init__( order: MemoryOrder, dimension_separator: Literal[".", "/"] = ".", compressor: CompressorLikev2 = None, - filters: Iterable[numcodecs.abc.Codec | dict[str, JSON]] | None = None, + filters: Iterable[Numcodec | dict[str, JSON]] | None = None, attributes: dict[str, JSON] | None = None, ) -> None: """ @@ -198,7 +197,7 @@ def from_dict(cls, data: dict[str, Any]) -> ArrayV2Metadata: def to_dict(self) -> dict[str, JSON]: zarray_dict = super().to_dict() - if isinstance(zarray_dict["compressor"], numcodecs.abc.Codec): + if _is_numcodec(zarray_dict["compressor"]): codec_config = zarray_dict["compressor"].get_config() # Hotfix for https://github.com/zarr-developers/zarr-python/issues/2647 if codec_config["id"] == "zstd" and not codec_config.get("checksum", False): @@ -213,7 +212,7 @@ def to_dict(self) -> dict[str, JSON]: raise TypeError("Invalid type for filters. Expected a list or tuple.") new_filters = [] for f in raw_filters: - if isinstance(f, numcodecs.abc.Codec): + if _is_numcodec(f): new_filters.append(f.get_config()) else: new_filters.append(f) @@ -263,20 +262,20 @@ def parse_zarr_format(data: object) -> Literal[2]: raise ValueError(f"Invalid value. Expected 2. Got {data}.") -def parse_filters(data: object) -> tuple[numcodecs.abc.Codec, ...] | None: +def parse_filters(data: object) -> tuple[Numcodec, ...] | None: """ Parse a potential tuple of filters """ - out: list[numcodecs.abc.Codec] = [] + out: list[Numcodec] = [] if data is None: return data if isinstance(data, Iterable): for idx, val in enumerate(data): - if isinstance(val, numcodecs.abc.Codec): + if _is_numcodec(val): out.append(val) elif isinstance(val, dict): - out.append(numcodecs.get_codec(val)) + out.append(get_numcodec(val)) # type: ignore[arg-type] else: msg = f"Invalid filter at index {idx}. Expected a numcodecs.abc.Codec or a dict representation of numcodecs.abc.Codec. Got {type(val)} instead." raise TypeError(msg) @@ -286,20 +285,20 @@ def parse_filters(data: object) -> tuple[numcodecs.abc.Codec, ...] | None: else: return tuple(out) # take a single codec instance and wrap it in a tuple - if isinstance(data, numcodecs.abc.Codec): + if _is_numcodec(data): return (data,) msg = f"Invalid filters. Expected None, an iterable of numcodecs.abc.Codec or dict representations of numcodecs.abc.Codec. Got {type(data)} instead." raise TypeError(msg) -def parse_compressor(data: object) -> numcodecs.abc.Codec | None: +def parse_compressor(data: object) -> Numcodec | None: """ Parse a potential compressor. """ - if data is None or isinstance(data, numcodecs.abc.Codec): + if data is None or _is_numcodec(data): return data if isinstance(data, dict): - return numcodecs.get_codec(data) + return get_numcodec(data) # type: ignore[arg-type] msg = f"Invalid compressor. Expected None, a numcodecs.abc.Codec, or a dict representation of a numcodecs.abc.Codec. Got {type(data)} instead." raise ValueError(msg) diff --git a/src/zarr/registry.py b/src/zarr/registry.py index fc3ffd7f7c..46216205f7 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -17,8 +17,10 @@ ArrayBytesCodec, BytesBytesCodec, Codec, + CodecJSON_V2, CodecPipeline, ) + from zarr.abc.numcodec import Numcodec from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import JSON @@ -280,3 +282,31 @@ def get_ndbuffer_class(reload_config: bool = False) -> type[NDBuffer]: _collect_entrypoints() + + +def get_numcodec(data: CodecJSON_V2[str]) -> Numcodec: + """ + Resolve a numcodec codec from the numcodecs registry. + + This requires the Numcodecs package to be installed. + + Parameters + ---------- + data : CodecJSON_V2 + The JSON metadata for the codec. + + Returns + ------- + codec : Numcodec + + Examples + -------- + + >>> codec = get_codec({'id': 'zlib', 'level': 1}) + >>> codec + Zlib(level=1) + """ + + from numcodecs.registry import get_codec + + return get_codec(data) # type: ignore[no-any-return] diff --git a/tests/test_abc/__init__.py b/tests/test_abc/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/test_abc/test_codec.py b/tests/test_abc/test_codec.py new file mode 100644 index 0000000000..e0f9ddb7bb --- /dev/null +++ b/tests/test_abc/test_codec.py @@ -0,0 +1,12 @@ +from __future__ import annotations + +from zarr.abc.codec import _check_codecjson_v2 + + +def test_check_codecjson_v2_valid() -> None: + """ + Test that the _check_codecjson_v2 function works + """ + assert _check_codecjson_v2({"id": "gzip"}) + assert not _check_codecjson_v2({"id": 10}) + assert not _check_codecjson_v2([10, 11]) diff --git a/tests/test_api.py b/tests/test_api.py index 12acf80589..69fc9b5b16 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1283,7 +1283,7 @@ def test_gpu_basic(store: Store, zarr_format: ZarrFormat | None) -> None: dtype=src.dtype, overwrite=True, zarr_format=zarr_format, - compressors=compressors, + compressors=compressors, # type: ignore[arg-type] ) z[:10, :10] = src[:10, :10] diff --git a/tests/test_array.py b/tests/test_array.py index 74201a4017..a316ee127f 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -73,6 +73,7 @@ from .test_dtype.conftest import zdtype_examples if TYPE_CHECKING: + from zarr.abc.codec import CodecJSON_V3 from zarr.core.metadata.v3 import ArrayV3Metadata @@ -1346,11 +1347,11 @@ async def test_v2_chunk_encoding( assert arr.metadata.filters == filters_expected # Normalize for property getters - compressor_expected = () if compressor_expected is None else (compressor_expected,) - filters_expected = () if filters_expected is None else filters_expected + arr_compressors_expected = () if compressor_expected is None else (compressor_expected,) + arr_filters_expected = () if filters_expected is None else filters_expected - assert arr.compressors == compressor_expected - assert arr.filters == filters_expected + assert arr.compressors == arr_compressors_expected + assert arr.filters == arr_filters_expected @staticmethod @pytest.mark.parametrize("dtype", [UInt8(), Float32(), VariableLengthUTF8()]) @@ -1388,11 +1389,12 @@ async def test_default_filters_compressors( if default_filters is None: expected_filters = () else: - expected_filters = default_filters + expected_filters = default_filters # type: ignore[assignment] + if default_compressors is None: expected_compressors = () else: - expected_compressors = (default_compressors,) + expected_compressors = (default_compressors,) # type: ignore[assignment] expected_serializer = None else: raise ValueError(f"Invalid zarr_format: {zarr_format}") @@ -1696,7 +1698,7 @@ def test_roundtrip_numcodecs() -> None: {"name": "numcodecs.shuffle", "configuration": {"elementsize": 2}}, {"name": "numcodecs.zlib", "configuration": {"level": 4}}, ] - filters = [ + filters: list[CodecJSON_V3] = [ { "name": "numcodecs.fixedscaleoffset", "configuration": { @@ -1717,8 +1719,8 @@ def test_roundtrip_numcodecs() -> None: shape=(720, 1440), chunks=(720, 1440), dtype="float64", - compressors=compressors, - filters=filters, + compressors=compressors, # type: ignore[arg-type] + filters=filters, # type: ignore[arg-type] fill_value=-9.99, dimension_names=["lat", "lon"], ) diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py new file mode 100644 index 0000000000..1c4d550587 --- /dev/null +++ b/tests/test_codecs/test_numcodecs.py @@ -0,0 +1,24 @@ +from __future__ import annotations + +from numcodecs import GZip + +from zarr.abc.numcodec import _is_numcodec, _is_numcodec_cls +from zarr.registry import get_numcodec + + +def test_get_numcodec() -> None: + assert get_numcodec({"id": "gzip", "level": 2}) == GZip(level=2) # type: ignore[typeddict-unknown-key] + + +def test_is_numcodec() -> None: + """ + Test the _is_numcodec function + """ + assert _is_numcodec(GZip()) + + +def test_is_numcodec_cls() -> None: + """ + Test the _is_numcodec_cls function + """ + assert _is_numcodec_cls(GZip) diff --git a/tests/test_codecs/test_vlen.py b/tests/test_codecs/test_vlen.py index 6fe1863464..cf0905daca 100644 --- a/tests/test_codecs/test_vlen.py +++ b/tests/test_codecs/test_vlen.py @@ -40,7 +40,7 @@ def test_vlen_string( chunks=data.shape, dtype=data.dtype, fill_value="", - compressors=compressor, + compressors=compressor, # type: ignore[arg-type] ) assert isinstance(a.metadata, ArrayV3Metadata) # needed for mypy diff --git a/tests/test_regression/test_v2_dtype_regression.py b/tests/test_regression/test_v2_dtype_regression.py index 9702ca7d23..ffe273490d 100644 --- a/tests/test_regression/test_v2_dtype_regression.py +++ b/tests/test_regression/test_v2_dtype_regression.py @@ -4,7 +4,6 @@ from pathlib import Path from typing import TYPE_CHECKING, Literal -import numcodecs import numpy as np import pytest from numcodecs import LZ4, LZMA, Blosc, GZip, VLenBytes, VLenUTF8, Zstd @@ -13,6 +12,7 @@ import zarr.abc import zarr.abc.codec import zarr.codecs as zarrcodecs +from zarr.abc.numcodec import Numcodec from zarr.core.array import Array from zarr.core.chunk_key_encodings import V2ChunkKeyEncoding from zarr.core.dtype.npy.bytes import VariableLengthBytes @@ -40,12 +40,12 @@ def runner_installed() -> bool: class ArrayParams: values: np.ndarray[tuple[int], np.dtype[np.generic]] fill_value: np.generic | str | int | bytes - filters: tuple[numcodecs.abc.Codec, ...] = () + filters: tuple[Numcodec, ...] = () serializer: str | None = None - compressor: numcodecs.abc.Codec + compressor: Numcodec -basic_codecs = GZip(), Blosc(), LZ4(), LZMA(), Zstd() +basic_codecs: tuple[Numcodec, ...] = GZip(), Blosc(), LZ4(), LZMA(), Zstd() basic_dtypes = "|b", ">i2", ">i4", ">f4", ">f8", "c8", "c16", "M8[10us]", "m8[4ps]" string_dtypes = "U4" From c21d1f92f7f2648a4c55b164510c524a951ac11d Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 13 Aug 2025 17:56:12 +0200 Subject: [PATCH 067/468] ensure that we test examples with a fresh env (#3371) * ensure that we test examples with a fresh env * changelog --- changes/3371.misc.rst | 1 + tests/test_examples.py | 4 +++- 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 changes/3371.misc.rst diff --git a/changes/3371.misc.rst b/changes/3371.misc.rst new file mode 100644 index 0000000000..06655ee402 --- /dev/null +++ b/changes/3371.misc.rst @@ -0,0 +1 @@ +Ensure that tests for executable examples are run in a fresh python environment. \ No newline at end of file diff --git a/tests/test_examples.py b/tests/test_examples.py index c97766364b..54af4119e3 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -72,7 +72,9 @@ def test_scripts_can_run(script_path: Path, tmp_path: Path) -> None: # and then test its behavior. # This allows the example to be useful to users who don't have Zarr installed, but also testable. resave_script(script_path, dest_path) - result = subprocess.run(["uv", "run", str(dest_path)], capture_output=True, text=True) + result = subprocess.run( + ["uv", "run", "--refresh", str(dest_path)], capture_output=True, text=True + ) assert result.returncode == 0, ( f"Script at {script_path} failed to run. Output: {result.stdout} Error: {result.stderr}" ) From 2271067bf59a6158b93faf60b3a10c13d8691621 Mon Sep 17 00:00:00 2001 From: Lucy H <55033656+lhao03@users.noreply.github.com> Date: Thu, 14 Aug 2025 00:54:15 -0700 Subject: [PATCH 068/468] Update docs for user-facing `create_array` api on on `Group`. (#3375) * new doc message for creating arrays with data * also change create_array data docs in api --- src/zarr/api/synchronous.py | 7 +++---- src/zarr/core/group.py | 7 +++---- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 50a1c0fa20..db113f76d0 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -783,13 +783,12 @@ def create_array( The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. shape : ChunkCoords, optional - Shape of the array. Can be ``None`` if ``data`` is provided. + Shape of the array. Must be ``None`` if ``data`` is provided. dtype : ZDTypeLike, optional - Data type of the array. Can be ``None`` if ``data`` is provided. + Data type of the array. Must be ``None`` if ``data`` is provided. data : np.ndarray, optional Array-like data to use for initializing the array. If this parameter is provided, the - ``shape`` and ``dtype`` parameters must be identical to ``data.shape`` and ``data.dtype``, - or ``None``. + ``shape`` and ``dtype`` parameters must be ``None``. chunks : ChunkCoords, optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 4bdc7b549f..9ef8481b9a 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -2476,12 +2476,11 @@ def create_array( The name of the array relative to the group. If ``path`` is ``None``, the array will be located at the root of the store. shape : ChunkCoords, optional - Shape of the array. Can be ``None`` if ``data`` is provided. + Shape of the array. Must be ``None`` if ``data`` is provided. dtype : npt.DTypeLike | None - Data type of the array. Can be ``None`` if ``data`` is provided. + Data type of the array. Must be ``None`` if ``data`` is provided. data : Array-like data to use for initializing the array. If this parameter is provided, the - ``shape`` and ``dtype`` parameters must be identical to ``data.shape`` and ``data.dtype``, - or ``None``. + ``shape`` and ``dtype`` parameters must be ``None``. chunks : ChunkCoords, optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. From 1a4aa5be20479903e58008e606f5acc1396ce1c9 Mon Sep 17 00:00:00 2001 From: Ian Hunt-Isaak Date: Mon, 18 Aug 2025 11:33:53 -0400 Subject: [PATCH 069/468] Fix: respect write_empty_chunks when opening an existing array (#3378) * Fix: respect write_empty_chunks when opening an existing array * doc: add release notes --- changes/3378.bugfix.rst | 3 +++ src/zarr/api/asynchronous.py | 4 +++- tests/test_api.py | 24 ++++++++++++++++++++++++ 3 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 changes/3378.bugfix.rst diff --git a/changes/3378.bugfix.rst b/changes/3378.bugfix.rst new file mode 100644 index 0000000000..1107f76488 --- /dev/null +++ b/changes/3378.bugfix.rst @@ -0,0 +1,3 @@ +Ensure passing `config` is handled properly when `open`ing an existing +array. + diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index a044ba8594..6caff8588b 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -358,7 +358,9 @@ async def open( zarr_format = _metadata_dict["zarr_format"] is_v3_array = zarr_format == 3 and _metadata_dict.get("node_type") == "array" if is_v3_array or zarr_format == 2: - return AsyncArray(store_path=store_path, metadata=_metadata_dict) + return AsyncArray( + store_path=store_path, metadata=_metadata_dict, config=kwargs.get("config") + ) except (AssertionError, FileNotFoundError, NodeTypeValidationError): pass return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs) diff --git a/tests/test_api.py b/tests/test_api.py index 69fc9b5b16..5447a0aa39 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -123,6 +123,30 @@ def test_write_empty_chunks_warns(write_empty_chunks: bool, zarr_format: ZarrFor ) +@pytest.mark.parametrize("zarr_format", [2, 3]) +def test_open_array_respects_write_empty_chunks_config(zarr_format: ZarrFormat) -> None: + """Test that zarr.open() respects write_empty_chunks config.""" + store = MemoryStore() + + _ = zarr.create( + store=store, + path="test_array", + shape=(10,), + chunks=(5,), + dtype="f8", + fill_value=0.0, + zarr_format=zarr_format, + ) + + arr2 = zarr.open(store=store, path="test_array", config={"write_empty_chunks": True}) + assert isinstance(arr2, zarr.Array) + + assert arr2._async_array._config.write_empty_chunks is True + + arr2[0:5] = np.zeros(5) + assert arr2.nchunks_initialized == 1 + + @pytest.mark.parametrize("path", ["foo", "/", "/foo", "///foo/bar"]) @pytest.mark.parametrize("node_type", ["array", "group"]) def test_open_normalized_path( From 7783dc29ace173ec86801d569d9579d0ab742b8b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 18 Aug 2025 18:02:34 +0200 Subject: [PATCH 070/468] chore/remove chunk coords (#3374) * remove ChunkCoords type * add comment * changelog * missing import --- changes/3374.misc.rst | 1 + src/zarr/abc/codec.py | 14 ++-- src/zarr/api/asynchronous.py | 17 ++--- src/zarr/api/synchronous.py | 33 ++++---- src/zarr/codecs/sharding.py | 71 +++++++++-------- src/zarr/codecs/transpose.py | 4 +- src/zarr/core/array.py | 109 ++++++++++++++------------- src/zarr/core/array_spec.py | 5 +- src/zarr/core/buffer/core.py | 10 +-- src/zarr/core/buffer/cpu.py | 4 +- src/zarr/core/buffer/gpu.py | 4 +- src/zarr/core/chunk_grids.py | 22 +++--- src/zarr/core/chunk_key_encodings.py | 13 ++-- src/zarr/core/codec_pipeline.py | 8 +- src/zarr/core/common.py | 10 +-- src/zarr/core/group.py | 45 ++++++----- src/zarr/core/indexing.py | 67 ++++++++-------- src/zarr/core/metadata/v2.py | 17 ++--- src/zarr/core/metadata/v3.py | 15 ++-- src/zarr/testing/buffer.py | 4 +- tests/conftest.py | 29 ++++--- tests/test_codecs/test_codecs.py | 4 +- tests/test_indexing.py | 3 +- 23 files changed, 258 insertions(+), 251 deletions(-) create mode 100644 changes/3374.misc.rst diff --git a/changes/3374.misc.rst b/changes/3374.misc.rst new file mode 100644 index 0000000000..19cefd8d60 --- /dev/null +++ b/changes/3374.misc.rst @@ -0,0 +1 @@ +Replaces usage of the ``zarr.core.common.ChunkCoords`` typealias with ``tuple[int, ...]``. \ No newline at end of file diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index d5c995d2ca..50c3a55eab 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -8,7 +8,7 @@ from zarr.abc.metadata import Metadata from zarr.core.buffer import Buffer, NDBuffer -from zarr.core.common import ChunkCoords, NamedConfig, concurrent_map +from zarr.core.common import NamedConfig, concurrent_map from zarr.core.config import config if TYPE_CHECKING: @@ -120,7 +120,7 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: def validate( self, *, - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], chunk_grid: ChunkGrid, ) -> None: @@ -129,7 +129,7 @@ def validate( Parameters ---------- - shape : ChunkCoords + shape : tuple[int, ...] The array shape dtype : np.dtype[Any] The array data type @@ -335,14 +335,18 @@ def supports_partial_encode(self) -> bool: ... @abstractmethod def validate( - self, *, shape: ChunkCoords, dtype: ZDType[TBaseDType, TBaseScalar], chunk_grid: ChunkGrid + self, + *, + shape: tuple[int, ...], + dtype: ZDType[TBaseDType, TBaseScalar], + chunk_grid: ChunkGrid, ) -> None: """Validates that all codec configurations are compatible with the array metadata. Raises errors when a codec configuration is not compatible. Parameters ---------- - shape : ChunkCoords + shape : tuple[int, ...] The array shape dtype : np.dtype[Any] The array data type diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 6caff8588b..d3613f7c05 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -24,7 +24,6 @@ from zarr.core.common import ( JSON, AccessModeLiteral, - ChunkCoords, DimensionNames, MemoryOrder, ZarrFormat, @@ -106,7 +105,7 @@ def _infer_overwrite(mode: AccessModeLiteral) -> bool: return mode in _OVERWRITE_MODES -def _get_shape_chunks(a: ArrayLike | Any) -> tuple[ChunkCoords | None, ChunkCoords | None]: +def _get_shape_chunks(a: ArrayLike | Any) -> tuple[tuple[int, ...] | None, tuple[int, ...] | None]: """Helper function to get the shape and chunks from an array-like object""" shape = None chunks = None @@ -866,9 +865,9 @@ async def open_group( async def create( - shape: ChunkCoords | int, + shape: tuple[int, ...] | int, *, # Note: this is a change from v2 - chunks: ChunkCoords | int | bool | None = None, + chunks: tuple[int, ...] | int | bool | None = None, dtype: ZDTypeLike | None = None, compressor: CompressorLike = "auto", fill_value: Any | None = DEFAULT_FILL_VALUE, @@ -890,7 +889,7 @@ async def create( meta_array: Any | None = None, # TODO: need type attributes: dict[str, JSON] | None = None, # v3 only - chunk_shape: ChunkCoords | int | None = None, + chunk_shape: tuple[int, ...] | int | None = None, chunk_key_encoding: ( ChunkKeyEncoding | tuple[Literal["default"], Literal[".", "/"]] @@ -1075,7 +1074,7 @@ async def create( async def empty( - shape: ChunkCoords, **kwargs: Any + shape: tuple[int, ...], **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an empty array with the specified shape. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1127,7 +1126,7 @@ async def empty_like( # TODO: add type annotations for fill_value and kwargs async def full( - shape: ChunkCoords, fill_value: Any, **kwargs: Any + shape: tuple[int, ...], fill_value: Any, **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array, with `fill_value` being used as the default value for uninitialized portions of the array. @@ -1174,7 +1173,7 @@ async def full_like( async def ones( - shape: ChunkCoords, **kwargs: Any + shape: tuple[int, ...], **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array, with one being used as the default value for uninitialized portions of the array. @@ -1297,7 +1296,7 @@ async def open_like( async def zeros( - shape: ChunkCoords, **kwargs: Any + shape: tuple[int, ...], **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array, with zero being used as the default value for uninitialized portions of the array. diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index db113f76d0..1146a6876f 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -33,7 +33,6 @@ from zarr.core.common import ( JSON, AccessModeLiteral, - ChunkCoords, DimensionNames, MemoryOrder, ShapeLike, @@ -598,9 +597,9 @@ def create_group( # TODO: add type annotations for kwargs def create( - shape: ChunkCoords | int, + shape: tuple[int, ...] | int, *, # Note: this is a change from v2 - chunks: ChunkCoords | int | bool | None = None, + chunks: tuple[int, ...] | int | bool | None = None, dtype: ZDTypeLike | None = None, compressor: CompressorLike = "auto", fill_value: Any | None = DEFAULT_FILL_VALUE, # TODO: need type @@ -622,7 +621,7 @@ def create( meta_array: Any | None = None, # TODO: need type attributes: dict[str, JSON] | None = None, # v3 only - chunk_shape: ChunkCoords | int | None = None, + chunk_shape: tuple[int, ...] | int | None = None, chunk_key_encoding: ( ChunkKeyEncoding | tuple[Literal["default"], Literal[".", "/"]] @@ -755,7 +754,7 @@ def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: ChunkCoords | Literal["auto"] = "auto", + chunks: tuple[int, ...] | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -782,17 +781,17 @@ def create_array( name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. - shape : ChunkCoords, optional + shape : ShapeLike, optional Shape of the array. Must be ``None`` if ``data`` is provided. dtype : ZDTypeLike, optional Data type of the array. Must be ``None`` if ``data`` is provided. data : np.ndarray, optional Array-like data to use for initializing the array. If this parameter is provided, the ``shape`` and ``dtype`` parameters must be ``None``. - chunks : ChunkCoords, optional + chunks : tuple[int, ...], optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that @@ -920,7 +919,7 @@ def from_array( data: Array | npt.ArrayLike, write_data: bool = True, name: str | None = None, - chunks: Literal["auto", "keep"] | ChunkCoords = "keep", + chunks: Literal["auto", "keep"] | tuple[int, ...] = "keep", shards: ShardsLike | None | Literal["keep"] = "keep", filters: FiltersLike | Literal["keep"] = "keep", compressors: CompressorsLike | Literal["keep"] = "keep", @@ -950,22 +949,22 @@ def from_array( name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. - chunks : ChunkCoords or "auto" or "keep", optional + chunks : tuple[int, ...] or "auto" or "keep", optional Chunk shape of the array. Following values are supported: - "auto": Automatically determine the chunk shape based on the array's shape and dtype. - "keep": Retain the chunk shape of the data array if it is a zarr Array. - - ChunkCoords: A tuple of integers representing the chunk shape. + - tuple[int, ...]: A tuple of integers representing the chunk shape. If not specified, defaults to "keep" if data is a zarr Array, otherwise "auto". - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. Following values are supported: - "auto": Automatically determine the shard shape based on the array's shape and chunk shape. - "keep": Retain the shard shape of the data array if it is a zarr Array. - - ChunkCoords: A tuple of integers representing the shard shape. + - tuple[int, ...]: A tuple of integers representing the shard shape. - None: No sharding. If not specified, defaults to "keep" if data is a zarr Array, otherwise None. @@ -1128,7 +1127,7 @@ def from_array( # TODO: add type annotations for kwargs -def empty(shape: ChunkCoords, **kwargs: Any) -> Array: +def empty(shape: tuple[int, ...], **kwargs: Any) -> Array: """Create an empty array with the specified shape. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1181,7 +1180,7 @@ def empty_like(a: ArrayLike, **kwargs: Any) -> Array: # TODO: add type annotations for kwargs and fill_value -def full(shape: ChunkCoords, fill_value: Any, **kwargs: Any) -> Array: +def full(shape: tuple[int, ...], fill_value: Any, **kwargs: Any) -> Array: """Create an array with a default fill value. Parameters @@ -1222,7 +1221,7 @@ def full_like(a: ArrayLike, **kwargs: Any) -> Array: # TODO: add type annotations for kwargs -def ones(shape: ChunkCoords, **kwargs: Any) -> Array: +def ones(shape: tuple[int, ...], **kwargs: Any) -> Array: """Create an array with a fill value of one. Parameters @@ -1324,7 +1323,7 @@ def open_like(a: ArrayLike, path: str, **kwargs: Any) -> Array: # TODO: add type annotations for kwargs -def zeros(shape: ChunkCoords, **kwargs: Any) -> Array: +def zeros(shape: tuple[int, ...], **kwargs: Any) -> Array: """Create an array with a fill value of zero. Parameters diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 888d258649..2b9b2259d8 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -36,8 +36,7 @@ ) from zarr.core.chunk_grids import ChunkGrid, RegularChunkGrid from zarr.core.common import ( - ChunkCoords, - ChunkCoordsLike, + ShapeLike, parse_enum, parse_named_configuration, parse_shapelike, @@ -62,8 +61,8 @@ from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType MAX_UINT_64 = 2**64 - 1 -ShardMapping = Mapping[ChunkCoords, Buffer] -ShardMutableMapping = MutableMapping[ChunkCoords, Buffer] +ShardMapping = Mapping[tuple[int, ...], Buffer] +ShardMutableMapping = MutableMapping[tuple[int, ...], Buffer] class ShardingCodecIndexLocation(Enum): @@ -82,7 +81,7 @@ def parse_index_location(data: object) -> ShardingCodecIndexLocation: @dataclass(frozen=True) class _ShardingByteGetter(ByteGetter): shard_dict: ShardMapping - chunk_coords: ChunkCoords + chunk_coords: tuple[int, ...] async def get( self, prototype: BufferPrototype, byte_range: ByteRequest | None = None @@ -114,12 +113,12 @@ class _ShardIndex(NamedTuple): offsets_and_lengths: npt.NDArray[np.uint64] @property - def chunks_per_shard(self) -> ChunkCoords: + def chunks_per_shard(self) -> tuple[int, ...]: result = tuple(self.offsets_and_lengths.shape[0:-1]) # The cast is required until https://github.com/numpy/numpy/pull/27211 is merged - return cast("ChunkCoords", result) + return cast("tuple[int, ...]", result) - def _localize_chunk(self, chunk_coords: ChunkCoords) -> ChunkCoords: + def _localize_chunk(self, chunk_coords: tuple[int, ...]) -> tuple[int, ...]: return tuple( chunk_i % shard_i for chunk_i, shard_i in zip(chunk_coords, self.offsets_and_lengths.shape, strict=False) @@ -131,7 +130,7 @@ def is_all_empty(self) -> bool: def get_full_chunk_map(self) -> npt.NDArray[np.bool_]: return np.not_equal(self.offsets_and_lengths[..., 0], MAX_UINT_64) - def get_chunk_slice(self, chunk_coords: ChunkCoords) -> tuple[int, int] | None: + def get_chunk_slice(self, chunk_coords: tuple[int, ...]) -> tuple[int, int] | None: localized_chunk = self._localize_chunk(chunk_coords) chunk_start, chunk_len = self.offsets_and_lengths[localized_chunk] if (chunk_start, chunk_len) == (MAX_UINT_64, MAX_UINT_64): @@ -139,7 +138,7 @@ def get_chunk_slice(self, chunk_coords: ChunkCoords) -> tuple[int, int] | None: else: return (int(chunk_start), int(chunk_start + chunk_len)) - def set_chunk_slice(self, chunk_coords: ChunkCoords, chunk_slice: slice | None) -> None: + def set_chunk_slice(self, chunk_coords: tuple[int, ...], chunk_slice: slice | None) -> None: localized_chunk = self._localize_chunk(chunk_coords) if chunk_slice is None: self.offsets_and_lengths[localized_chunk] = (MAX_UINT_64, MAX_UINT_64) @@ -171,7 +170,7 @@ def is_dense(self, chunk_byte_length: int) -> bool: ) @classmethod - def create_empty(cls, chunks_per_shard: ChunkCoords) -> _ShardIndex: + def create_empty(cls, chunks_per_shard: tuple[int, ...]) -> _ShardIndex: offsets_and_lengths = np.zeros(chunks_per_shard + (2,), dtype=" _ShardReader: shard_index_size = codec._shard_index_size(chunks_per_shard) obj = cls() @@ -198,7 +197,7 @@ async def from_bytes( @classmethod def create_empty( - cls, chunks_per_shard: ChunkCoords, buffer_prototype: BufferPrototype | None = None + cls, chunks_per_shard: tuple[int, ...], buffer_prototype: BufferPrototype | None = None ) -> _ShardReader: if buffer_prototype is None: buffer_prototype = default_buffer_prototype() @@ -208,7 +207,7 @@ def create_empty( obj.index = index return obj - def __getitem__(self, chunk_coords: ChunkCoords) -> Buffer: + def __getitem__(self, chunk_coords: tuple[int, ...]) -> Buffer: chunk_byte_slice = self.index.get_chunk_slice(chunk_coords) if chunk_byte_slice: return self.buf[chunk_byte_slice[0] : chunk_byte_slice[1]] @@ -217,7 +216,7 @@ def __getitem__(self, chunk_coords: ChunkCoords) -> Buffer: def __len__(self) -> int: return int(self.index.offsets_and_lengths.size / 2) - def __iter__(self) -> Iterator[ChunkCoords]: + def __iter__(self) -> Iterator[tuple[int, ...]]: return c_order_iter(self.index.offsets_and_lengths.shape[:-1]) def is_empty(self) -> bool: @@ -231,8 +230,8 @@ class _ShardBuilder(_ShardReader, ShardMutableMapping): @classmethod def merge_with_morton_order( cls, - chunks_per_shard: ChunkCoords, - tombstones: set[ChunkCoords], + chunks_per_shard: tuple[int, ...], + tombstones: set[tuple[int, ...]], *shard_dicts: ShardMapping, ) -> _ShardBuilder: obj = cls.create_empty(chunks_per_shard) @@ -248,7 +247,7 @@ def merge_with_morton_order( @classmethod def create_empty( - cls, chunks_per_shard: ChunkCoords, buffer_prototype: BufferPrototype | None = None + cls, chunks_per_shard: tuple[int, ...], buffer_prototype: BufferPrototype | None = None ) -> _ShardBuilder: if buffer_prototype is None: buffer_prototype = default_buffer_prototype() @@ -257,13 +256,13 @@ def create_empty( obj.index = _ShardIndex.create_empty(chunks_per_shard) return obj - def __setitem__(self, chunk_coords: ChunkCoords, value: Buffer) -> None: + def __setitem__(self, chunk_coords: tuple[int, ...], value: Buffer) -> None: chunk_start = len(self.buf) chunk_length = len(value) self.buf += value self.index.set_chunk_slice(chunk_coords, slice(chunk_start, chunk_start + chunk_length)) - def __delitem__(self, chunk_coords: ChunkCoords) -> None: + def __delitem__(self, chunk_coords: tuple[int, ...]) -> None: raise NotImplementedError async def finalize( @@ -286,24 +285,24 @@ async def finalize( class _MergingShardBuilder(ShardMutableMapping): old_dict: _ShardReader new_dict: _ShardBuilder - tombstones: set[ChunkCoords] = field(default_factory=set) + tombstones: set[tuple[int, ...]] = field(default_factory=set) - def __getitem__(self, chunk_coords: ChunkCoords) -> Buffer: + def __getitem__(self, chunk_coords: tuple[int, ...]) -> Buffer: chunk_bytes_maybe = self.new_dict.get(chunk_coords) if chunk_bytes_maybe is not None: return chunk_bytes_maybe return self.old_dict[chunk_coords] - def __setitem__(self, chunk_coords: ChunkCoords, value: Buffer) -> None: + def __setitem__(self, chunk_coords: tuple[int, ...], value: Buffer) -> None: self.new_dict[chunk_coords] = value - def __delitem__(self, chunk_coords: ChunkCoords) -> None: + def __delitem__(self, chunk_coords: tuple[int, ...]) -> None: self.tombstones.add(chunk_coords) def __len__(self) -> int: return self.old_dict.__len__() - def __iter__(self) -> Iterator[ChunkCoords]: + def __iter__(self) -> Iterator[tuple[int, ...]]: return self.old_dict.__iter__() def is_empty(self) -> bool: @@ -335,7 +334,7 @@ class ShardingCodec( ): """Sharding codec""" - chunk_shape: ChunkCoords + chunk_shape: tuple[int, ...] codecs: tuple[Codec, ...] index_codecs: tuple[Codec, ...] index_location: ShardingCodecIndexLocation = ShardingCodecIndexLocation.end @@ -343,7 +342,7 @@ class ShardingCodec( def __init__( self, *, - chunk_shape: ChunkCoordsLike, + chunk_shape: ShapeLike, codecs: Iterable[Codec | dict[str, JSON]] = (BytesCodec(),), index_codecs: Iterable[Codec | dict[str, JSON]] = (BytesCodec(), Crc32cCodec()), index_location: ShardingCodecIndexLocation | str = ShardingCodecIndexLocation.end, @@ -413,7 +412,7 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: def validate( self, *, - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], chunk_grid: ChunkGrid, ) -> None: @@ -646,14 +645,14 @@ async def _encode_partial_single( ) def _is_total_shard( - self, all_chunk_coords: set[ChunkCoords], chunks_per_shard: ChunkCoords + self, all_chunk_coords: set[tuple[int, ...]], chunks_per_shard: tuple[int, ...] ) -> bool: return len(all_chunk_coords) == product(chunks_per_shard) and all( chunk_coords in all_chunk_coords for chunk_coords in c_order_iter(chunks_per_shard) ) async def _decode_shard_index( - self, index_bytes: Buffer, chunks_per_shard: ChunkCoords + self, index_bytes: Buffer, chunks_per_shard: tuple[int, ...] ) -> _ShardIndex: index_array = next( iter( @@ -686,7 +685,7 @@ async def _encode_shard_index(self, index: _ShardIndex) -> Buffer: assert isinstance(index_bytes, Buffer) return index_bytes - def _shard_index_size(self, chunks_per_shard: ChunkCoords) -> int: + def _shard_index_size(self, chunks_per_shard: tuple[int, ...]) -> int: return ( get_pipeline_class() .from_codecs(self.index_codecs) @@ -695,7 +694,7 @@ def _shard_index_size(self, chunks_per_shard: ChunkCoords) -> int: ) ) - def _get_index_chunk_spec(self, chunks_per_shard: ChunkCoords) -> ArraySpec: + def _get_index_chunk_spec(self, chunks_per_shard: tuple[int, ...]) -> ArraySpec: return ArraySpec( shape=chunks_per_shard + (2,), dtype=UInt64(endianness="little"), @@ -715,7 +714,7 @@ def _get_chunk_spec(self, shard_spec: ArraySpec) -> ArraySpec: prototype=shard_spec.prototype, ) - def _get_chunks_per_shard(self, shard_spec: ArraySpec) -> ChunkCoords: + def _get_chunks_per_shard(self, shard_spec: ArraySpec) -> tuple[int, ...]: return tuple( s // c for s, c in zip( @@ -726,7 +725,7 @@ def _get_chunks_per_shard(self, shard_spec: ArraySpec) -> ChunkCoords: ) async def _load_shard_index_maybe( - self, byte_getter: ByteGetter, chunks_per_shard: ChunkCoords + self, byte_getter: ByteGetter, chunks_per_shard: tuple[int, ...] ) -> _ShardIndex | None: shard_index_size = self._shard_index_size(chunks_per_shard) if self.index_location == ShardingCodecIndexLocation.start: @@ -743,14 +742,14 @@ async def _load_shard_index_maybe( return None async def _load_shard_index( - self, byte_getter: ByteGetter, chunks_per_shard: ChunkCoords + self, byte_getter: ByteGetter, chunks_per_shard: tuple[int, ...] ) -> _ShardIndex: return ( await self._load_shard_index_maybe(byte_getter, chunks_per_shard) ) or _ShardIndex.create_empty(chunks_per_shard) async def _load_full_shard_maybe( - self, byte_getter: ByteGetter, prototype: BufferPrototype, chunks_per_shard: ChunkCoords + self, byte_getter: ByteGetter, prototype: BufferPrototype, chunks_per_shard: tuple[int, ...] ) -> _ShardReader | None: shard_bytes = await byte_getter.get(prototype=prototype) diff --git a/src/zarr/codecs/transpose.py b/src/zarr/codecs/transpose.py index d6310d38a4..92e7da81e1 100644 --- a/src/zarr/codecs/transpose.py +++ b/src/zarr/codecs/transpose.py @@ -8,7 +8,7 @@ from zarr.abc.codec import ArrayArrayCodec from zarr.core.array_spec import ArraySpec -from zarr.core.common import JSON, ChunkCoordsLike, parse_named_configuration +from zarr.core.common import JSON, parse_named_configuration from zarr.registry import register_codec if TYPE_CHECKING: @@ -35,7 +35,7 @@ class TransposeCodec(ArrayArrayCodec): order: tuple[int, ...] - def __init__(self, *, order: ChunkCoordsLike) -> None: + def __init__(self, *, order: Iterable[int]) -> None: order_parsed = parse_transpose_order(order) object.__setattr__(self, "order", order_parsed) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 2ce33df7ba..819379e12f 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -53,7 +53,6 @@ ZARR_JSON, ZARRAY_JSON, ZATTRS_JSON, - ChunkCoords, DimensionNames, MemoryOrder, ShapeLike, @@ -491,7 +490,7 @@ async def create( The fill value of the array (default is None). attributes : dict[str, JSON], optional The attributes of the array (default is None). - chunk_shape : ChunkCoords, optional + chunk_shape : tuple[int, ...], optional The shape of the array's chunks Zarr format 3 only. Zarr format 2 arrays should use `chunks` instead. If not specified, default are guessed based on the shape and dtype. @@ -710,7 +709,7 @@ async def _create( def _create_metadata_v3( shape: ShapeLike, dtype: ZDType[TBaseDType, TBaseScalar], - chunk_shape: ChunkCoords, + chunk_shape: tuple[int, ...], fill_value: Any | None = DEFAULT_FILL_VALUE, chunk_key_encoding: ChunkKeyEncodingLike | None = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, @@ -765,7 +764,7 @@ async def _create_v3( *, shape: ShapeLike, dtype: ZDType[TBaseDType, TBaseScalar], - chunk_shape: ChunkCoords, + chunk_shape: tuple[int, ...], config: ArrayConfig, fill_value: Any | None = DEFAULT_FILL_VALUE, chunk_key_encoding: ( @@ -811,9 +810,9 @@ async def _create_v3( @staticmethod def _create_metadata_v2( - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], - chunks: ChunkCoords, + chunks: tuple[int, ...], order: MemoryOrder, dimension_separator: Literal[".", "/"] | None = None, fill_value: Any | None = DEFAULT_FILL_VALUE, @@ -848,9 +847,9 @@ async def _create_v2( cls, store_path: StorePath, *, - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], - chunks: ChunkCoords, + chunks: tuple[int, ...], order: MemoryOrder, config: ArrayConfig, dimension_separator: Literal[".", "/"] | None = None, @@ -980,7 +979,7 @@ def ndim(self) -> int: return len(self.metadata.shape) @property - def shape(self) -> ChunkCoords: + def shape(self) -> tuple[int, ...]: """Returns the shape of the Array. Returns @@ -991,7 +990,7 @@ def shape(self) -> ChunkCoords: return self.metadata.shape @property - def chunks(self) -> ChunkCoords: + def chunks(self) -> tuple[int, ...]: """Returns the chunk shape of the Array. If sharding is used the inner chunk shape is returned. @@ -1000,13 +999,13 @@ def chunks(self) -> ChunkCoords: Returns ------- - ChunkCoords: + tuple[int, ...]: The chunk shape of the Array. """ return self.metadata.chunks @property - def shards(self) -> ChunkCoords | None: + def shards(self) -> tuple[int, ...] | None: """Returns the shard shape of the Array. Returns None if sharding is not used. @@ -1015,7 +1014,7 @@ def shards(self) -> ChunkCoords | None: Returns ------- - ChunkCoords: + tuple[int, ...]: The shard shape of the Array. """ return self.metadata.shards @@ -1184,7 +1183,7 @@ def basename(self) -> str: return self.name.split("/")[-1] @property - def cdata_shape(self) -> ChunkCoords: + def cdata_shape(self) -> tuple[int, ...]: """ The shape of the chunk grid for this array. @@ -1238,7 +1237,7 @@ async def nbytes_stored(self) -> int: def _iter_chunk_coords( self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None - ) -> Iterator[ChunkCoords]: + ) -> Iterator[tuple[int, ...]]: """ Create an iterator over the coordinates of chunks in chunk grid space. If the `origin` keyword is used, iteration will start at the chunk index specified by `origin`. @@ -1256,7 +1255,7 @@ def _iter_chunk_coords( Yields ------ - chunk_coords: ChunkCoords + chunk_coords: tuple[int, ...] The coordinates of each chunk in the selection. """ return _iter_grid(self.cdata_shape, origin=origin, selection_shape=selection_shape) @@ -1626,7 +1625,7 @@ async def resize(self, new_shape: ShapeLike, delete_outside_chunks: bool = True) Parameters ---------- - new_shape : ChunkCoords + new_shape : tuple[int, ...] The desired new shape of the array. delete_outside_chunks : bool, optional @@ -1674,7 +1673,7 @@ async def _delete_key(key: str) -> None: # Update metadata (in place) object.__setattr__(self, "metadata", new_metadata) - async def append(self, data: npt.ArrayLike, axis: int = 0) -> ChunkCoords: + async def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: """Append `data` to `axis`. Parameters @@ -1860,13 +1859,13 @@ def create( store: StoreLike, *, # v2 and v3 - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDTypeLike, zarr_format: ZarrFormat = 3, fill_value: Any | None = DEFAULT_FILL_VALUE, attributes: dict[str, JSON] | None = None, # v3 only - chunk_shape: ChunkCoords | None = None, + chunk_shape: tuple[int, ...] | None = None, chunk_key_encoding: ( ChunkKeyEncoding | tuple[Literal["default"], Literal[".", "/"]] @@ -1876,7 +1875,7 @@ def create( codecs: Iterable[Codec | dict[str, JSON]] | None = None, dimension_names: DimensionNames = None, # v2 only - chunks: ChunkCoords | None = None, + chunks: tuple[int, ...] | None = None, dimension_separator: Literal[".", "/"] | None = None, order: MemoryOrder | None = None, filters: list[dict[str, JSON]] | None = None, @@ -1894,11 +1893,11 @@ def create( ---------- store : StoreLike The array store that has already been initialized. - shape : ChunkCoords + shape : tuple[int, ...] The shape of the array. dtype : ZDTypeLike The data type of the array. - chunk_shape : ChunkCoords, optional + chunk_shape : tuple[int, ...], optional The shape of the Array's chunks. Zarr format 3 only. Zarr format 2 arrays should use `chunks` instead. If not specified, default are guessed based on the shape and dtype. @@ -1922,7 +1921,7 @@ def create( dimension_names : Iterable[str | None], optional The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. - chunks : ChunkCoords, optional + chunks : tuple[int, ...], optional The shape of the array's chunks. Zarr format 2 only. Zarr format 3 arrays should use ``chunk_shape`` instead. If not specified, default are guessed based on the shape and dtype. @@ -1989,13 +1988,13 @@ def _create( store: StoreLike, *, # v2 and v3 - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDTypeLike, zarr_format: ZarrFormat = 3, fill_value: Any | None = DEFAULT_FILL_VALUE, attributes: dict[str, JSON] | None = None, # v3 only - chunk_shape: ChunkCoords | None = None, + chunk_shape: tuple[int, ...] | None = None, chunk_key_encoding: ( ChunkKeyEncoding | tuple[Literal["default"], Literal[".", "/"]] @@ -2005,7 +2004,7 @@ def _create( codecs: Iterable[Codec | dict[str, JSON]] | None = None, dimension_names: DimensionNames = None, # v2 only - chunks: ChunkCoords | None = None, + chunks: tuple[int, ...] | None = None, dimension_separator: Literal[".", "/"] | None = None, order: MemoryOrder | None = None, filters: list[dict[str, JSON]] | None = None, @@ -2108,23 +2107,23 @@ def ndim(self) -> int: return self._async_array.ndim @property - def shape(self) -> ChunkCoords: + def shape(self) -> tuple[int, ...]: """Returns the shape of the array. Returns ------- - ChunkCoords + tuple[int, ...] The shape of the array. """ return self._async_array.shape @shape.setter - def shape(self, value: ChunkCoords) -> None: + def shape(self, value: tuple[int, ...]) -> None: """Sets the shape of the array by calling resize.""" self.resize(value) @property - def chunks(self) -> ChunkCoords: + def chunks(self) -> tuple[int, ...]: """Returns a tuple of integers describing the length of each dimension of a chunk of the array. If sharding is used the inner chunk shape is returned. @@ -2139,7 +2138,7 @@ def chunks(self) -> ChunkCoords: return self._async_array.chunks @property - def shards(self) -> ChunkCoords | None: + def shards(self) -> tuple[int, ...] | None: """Returns a tuple of integers describing the length of each dimension of a shard of the array. Returns None if sharding is not used. @@ -2261,7 +2260,7 @@ def compressors(self) -> tuple[Numcodec, ...] | tuple[BytesBytesCodec, ...]: return self._async_array.compressors @property - def cdata_shape(self) -> ChunkCoords: + def cdata_shape(self) -> tuple[int, ...]: """ The shape of the chunk grid for this array. """ @@ -2276,7 +2275,7 @@ def nchunks(self) -> int: def _iter_chunk_coords( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None - ) -> Iterator[ChunkCoords]: + ) -> Iterator[tuple[int, ...]]: """ Create an iterator over the coordinates of chunks in chunk grid space. If the `origin` keyword is used, iteration will start at the chunk index specified by `origin`. @@ -2294,7 +2293,7 @@ def _iter_chunk_coords( Yields ------ - chunk_coords: ChunkCoords + chunk_coords: tuple[int, ...] The coordinates of each chunk in the selection. """ yield from self._async_array._iter_chunk_coords( @@ -3709,7 +3708,7 @@ def resize(self, new_shape: ShapeLike) -> None: """ sync(self._async_array.resize(new_shape)) - def append(self, data: npt.ArrayLike, axis: int = 0) -> ChunkCoords: + def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: """Append `data` to `axis`. Parameters @@ -3919,11 +3918,11 @@ def _build_parents( class ShardsConfigParam(TypedDict): - shape: ChunkCoords + shape: tuple[int, ...] index_location: ShardingCodecIndexLocation | None -ShardsLike: TypeAlias = ChunkCoords | ShardsConfigParam | Literal["auto"] +ShardsLike: TypeAlias = tuple[int, ...] | ShardsConfigParam | Literal["auto"] async def from_array( @@ -3932,7 +3931,7 @@ async def from_array( data: Array | npt.ArrayLike, write_data: bool = True, name: str | None = None, - chunks: Literal["auto", "keep"] | ChunkCoords = "keep", + chunks: Literal["auto", "keep"] | tuple[int, ...] = "keep", shards: ShardsLike | None | Literal["keep"] = "keep", filters: FiltersLike | Literal["keep"] = "keep", compressors: CompressorsLike | Literal["keep"] = "keep", @@ -3962,22 +3961,22 @@ async def from_array( name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. - chunks : ChunkCoords or "auto" or "keep", optional + chunks : tuple[int, ...] or "auto" or "keep", optional Chunk shape of the array. Following values are supported: - "auto": Automatically determine the chunk shape based on the array's shape and dtype. - "keep": Retain the chunk shape of the data array if it is a zarr Array. - - ChunkCoords: A tuple of integers representing the chunk shape. + - tuple[int, ...]: A tuple of integers representing the chunk shape. If not specified, defaults to "keep" if data is a zarr Array, otherwise "auto". - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. Following values are supported: - "auto": Automatically determine the shard shape based on the array's shape and chunk shape. - "keep": Retain the shard shape of the data array if it is a zarr Array. - - ChunkCoords: A tuple of integers representing the shard shape. + - tuple[int, ...]: A tuple of integers representing the shard shape. - None: No sharding. If not specified, defaults to "keep" if data is a zarr Array, otherwise None. @@ -4165,7 +4164,9 @@ async def from_array( if write_data: if isinstance(data, Array): - async def _copy_array_region(chunk_coords: ChunkCoords | slice, _data: Array) -> None: + async def _copy_array_region( + chunk_coords: tuple[int, ...] | slice, _data: Array + ) -> None: arr = await _data._async_array.getitem(chunk_coords) await result.setitem(chunk_coords, arr) @@ -4194,7 +4195,7 @@ async def init_array( store_path: StorePath, shape: ShapeLike, dtype: ZDTypeLike, - chunks: ChunkCoords | Literal["auto"] = "auto", + chunks: tuple[int, ...] | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -4214,14 +4215,14 @@ async def init_array( ---------- store_path : StorePath StorePath instance. The path attribute is the name of the array to initialize. - shape : ChunkCoords + shape : tuple[int, ...] Shape of the array. dtype : ZDTypeLike Data type of the array. - chunks : ChunkCoords, optional + chunks : tuple[int, ...], optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that @@ -4413,7 +4414,7 @@ async def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: ChunkCoords | Literal["auto"] = "auto", + chunks: tuple[int, ...] | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -4438,17 +4439,17 @@ async def create_array( name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. - shape : ChunkCoords, optional + shape : tuple[int, ...], optional Shape of the array. Can be ``None`` if ``data`` is provided. dtype : ZDTypeLike | None Data type of the array. Can be ``None`` if ``data`` is provided. data : Array-like data to use for initializing the array. If this parameter is provided, the ``shape`` and ``dtype`` parameters must be identical to ``data.shape`` and ``data.dtype``, or ``None``. - chunks : ChunkCoords, optional + chunks : tuple[int, ...], optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that @@ -4593,7 +4594,7 @@ async def create_array( def _parse_keep_array_attr( data: Array | npt.ArrayLike, - chunks: Literal["auto", "keep"] | ChunkCoords, + chunks: Literal["auto", "keep"] | tuple[int, ...], shards: ShardsLike | None | Literal["keep"], filters: FiltersLike | Literal["keep"], compressors: CompressorsLike | Literal["keep"], @@ -4604,7 +4605,7 @@ def _parse_keep_array_attr( chunk_key_encoding: ChunkKeyEncodingLike | None, dimension_names: DimensionNames, ) -> tuple[ - ChunkCoords | Literal["auto"], + tuple[int, ...] | Literal["auto"], ShardsLike | None, FiltersLike, CompressorsLike, diff --git a/src/zarr/core/array_spec.py b/src/zarr/core/array_spec.py index 279bf6edf0..c4dedaefea 100644 --- a/src/zarr/core/array_spec.py +++ b/src/zarr/core/array_spec.py @@ -16,7 +16,6 @@ from typing import NotRequired from zarr.core.buffer import BufferPrototype - from zarr.core.common import ChunkCoords from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType @@ -88,7 +87,7 @@ def parse_array_config(data: ArrayConfigLike | None) -> ArrayConfig: @dataclass(frozen=True) class ArraySpec: - shape: ChunkCoords + shape: tuple[int, ...] dtype: ZDType[TBaseDType, TBaseScalar] fill_value: Any config: ArrayConfig @@ -96,7 +95,7 @@ class ArraySpec: def __init__( self, - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], fill_value: Any, config: ArrayConfig, diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index 07bdb8c26e..d519b87d45 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -21,7 +21,7 @@ from typing import Self from zarr.codecs.bytes import Endian - from zarr.core.common import BytesLike, ChunkCoords + from zarr.core.common import BytesLike # Everything here is imported into ``zarr.core.buffer`` namespace. __all__: list[str] = [] @@ -59,7 +59,7 @@ def ndim(self) -> int: ... def size(self) -> int: ... @property - def shape(self) -> ChunkCoords: ... + def shape(self) -> tuple[int, ...]: ... def __len__(self) -> int: ... @@ -70,7 +70,7 @@ def __setitem__(self, key: slice, value: Any) -> None: ... def __array__(self) -> npt.NDArray[Any]: ... def reshape( - self, shape: ChunkCoords | Literal[-1], *, order: Literal["A", "C", "F"] = ... + self, shape: tuple[int, ...] | Literal[-1], *, order: Literal["A", "C", "F"] = ... ) -> Self: ... def view(self, dtype: npt.DTypeLike) -> Self: ... @@ -376,7 +376,7 @@ def create( @classmethod def empty( - cls, shape: ChunkCoords, dtype: npt.DTypeLike, order: Literal["C", "F"] = "C" + cls, shape: tuple[int, ...], dtype: npt.DTypeLike, order: Literal["C", "F"] = "C" ) -> Self: """ Create an empty buffer with the given shape, dtype, and order. @@ -496,7 +496,7 @@ def byteorder(self) -> Endian: else: return Endian(sys.byteorder) - def reshape(self, newshape: ChunkCoords | Literal[-1]) -> Self: + def reshape(self, newshape: tuple[int, ...] | Literal[-1]) -> Self: return self.__class__(self._data.reshape(newshape)) def squeeze(self, axis: tuple[int, ...]) -> Self: diff --git a/src/zarr/core/buffer/cpu.py b/src/zarr/core/buffer/cpu.py index 9da0059d0b..34f92ece4a 100644 --- a/src/zarr/core/buffer/cpu.py +++ b/src/zarr/core/buffer/cpu.py @@ -20,7 +20,7 @@ from typing import Self from zarr.core.buffer.core import ArrayLike, NDArrayLike - from zarr.core.common import BytesLike, ChunkCoords + from zarr.core.common import BytesLike class Buffer(core.Buffer): @@ -162,7 +162,7 @@ def create( @classmethod def empty( - cls, shape: ChunkCoords, dtype: npt.DTypeLike, order: Literal["C", "F"] = "C" + cls, shape: tuple[int, ...], dtype: npt.DTypeLike, order: Literal["C", "F"] = "C" ) -> Self: return cls(np.empty(shape=shape, dtype=dtype, order=order)) diff --git a/src/zarr/core/buffer/gpu.py b/src/zarr/core/buffer/gpu.py index 4eca197222..bfe977c50f 100644 --- a/src/zarr/core/buffer/gpu.py +++ b/src/zarr/core/buffer/gpu.py @@ -23,7 +23,7 @@ from collections.abc import Iterable from typing import Self - from zarr.core.common import BytesLike, ChunkCoords + from zarr.core.common import BytesLike try: import cupy as cp @@ -182,7 +182,7 @@ def create( @classmethod def empty( - cls, shape: ChunkCoords, dtype: npt.DTypeLike, order: Literal["C", "F"] = "C" + cls, shape: tuple[int, ...], dtype: npt.DTypeLike, order: Literal["C", "F"] = "C" ) -> Self: return cls(cp.empty(shape=shape, dtype=dtype, order=order)) diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 7fa1fc7e38..94c2e27674 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -15,8 +15,6 @@ from zarr.abc.metadata import Metadata from zarr.core.common import ( JSON, - ChunkCoords, - ChunkCoordsLike, ShapeLike, ceildiv, parse_named_configuration, @@ -32,13 +30,13 @@ def _guess_chunks( - shape: ShapeLike, + shape: tuple[int, ...] | int, typesize: int, *, increment_bytes: int = 256 * 1024, min_bytes: int = 128 * 1024, max_bytes: int = 64 * 1024 * 1024, -) -> ChunkCoords: +) -> tuple[int, ...]: """ Iteratively guess an appropriate chunk layout for an array, given its shape and the size of each element in bytes, and size constraints expressed in bytes. This logic is @@ -46,7 +44,7 @@ def _guess_chunks( Parameters ---------- - shape : ChunkCoords + shape : tuple[int, ...] The chunk shape. typesize : int The size, in bytes, of each element of the chunk. @@ -59,7 +57,7 @@ def _guess_chunks( Returns ------- - ChunkCoords + tuple[int, ...] """ if isinstance(shape, int): @@ -164,19 +162,19 @@ def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid: raise ValueError(f"Unknown chunk grid. Got {name_parsed}.") @abstractmethod - def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]: + def all_chunk_coords(self, array_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: pass @abstractmethod - def get_nchunks(self, array_shape: ChunkCoords) -> int: + def get_nchunks(self, array_shape: tuple[int, ...]) -> int: pass @dataclass(frozen=True) class RegularChunkGrid(ChunkGrid): - chunk_shape: ChunkCoords + chunk_shape: tuple[int, ...] - def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None: + def __init__(self, *, chunk_shape: ShapeLike) -> None: chunk_shape_parsed = parse_shapelike(chunk_shape) object.__setattr__(self, "chunk_shape", chunk_shape_parsed) @@ -190,12 +188,12 @@ def _from_dict(cls, data: dict[str, JSON]) -> Self: def to_dict(self) -> dict[str, JSON]: return {"name": "regular", "configuration": {"chunk_shape": tuple(self.chunk_shape)}} - def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]: + def all_chunk_coords(self, array_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: return itertools.product( *(range(ceildiv(s, c)) for s, c in zip(array_shape, self.chunk_shape, strict=False)) ) - def get_nchunks(self, array_shape: ChunkCoords) -> int: + def get_nchunks(self, array_shape: tuple[int, ...]) -> int: return reduce( operator.mul, itertools.starmap(ceildiv, zip(array_shape, self.chunk_shape, strict=True)), diff --git a/src/zarr/core/chunk_key_encodings.py b/src/zarr/core/chunk_key_encodings.py index 91dfc90365..89a34e6052 100644 --- a/src/zarr/core/chunk_key_encodings.py +++ b/src/zarr/core/chunk_key_encodings.py @@ -10,7 +10,6 @@ from zarr.abc.metadata import Metadata from zarr.core.common import ( JSON, - ChunkCoords, parse_named_configuration, ) @@ -69,11 +68,11 @@ def to_dict(self) -> dict[str, JSON]: return {"name": self.name, "configuration": {"separator": self.separator}} @abstractmethod - def decode_chunk_key(self, chunk_key: str) -> ChunkCoords: + def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: pass @abstractmethod - def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str: + def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: pass @@ -84,12 +83,12 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str: class DefaultChunkKeyEncoding(ChunkKeyEncoding): name: Literal["default"] = "default" - def decode_chunk_key(self, chunk_key: str) -> ChunkCoords: + def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: if chunk_key == "c": return () return tuple(map(int, chunk_key[1:].split(self.separator))) - def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str: + def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: return self.separator.join(map(str, ("c",) + chunk_coords)) @@ -97,9 +96,9 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str: class V2ChunkKeyEncoding(ChunkKeyEncoding): name: Literal["v2"] = "v2" - def decode_chunk_key(self, chunk_key: str) -> ChunkCoords: + def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: return tuple(map(int, chunk_key.split(self.separator))) - def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str: + def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: chunk_identifier = self.separator.join(map(str, chunk_coords)) return "0" if chunk_identifier == "" else chunk_identifier diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 3bc3c1cfc7..63fcda7065 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -14,7 +14,7 @@ Codec, CodecPipeline, ) -from zarr.core.common import ChunkCoords, concurrent_map +from zarr.core.common import concurrent_map from zarr.core.config import config from zarr.core.indexing import SelectorTuple, is_scalar from zarr.errors import ZarrUserWarning @@ -134,7 +134,11 @@ def __iter__(self) -> Iterator[Codec]: yield from self.bytes_bytes_codecs def validate( - self, *, shape: ChunkCoords, dtype: ZDType[TBaseDType, TBaseScalar], chunk_grid: ChunkGrid + self, + *, + shape: tuple[int, ...], + dtype: ZDType[TBaseDType, TBaseScalar], + chunk_grid: ChunkGrid, ) -> None: for codec in self: codec.validate(shape=shape, dtype=dtype, chunk_grid=chunk_grid) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 4c0247426e..ed28fd2da4 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -36,9 +36,9 @@ ZMETADATA_V2_JSON = ".zmetadata" BytesLike = bytes | bytearray | memoryview -ShapeLike = tuple[int, ...] | int -ChunkCoords = tuple[int, ...] -ChunkCoordsLike = Iterable[int] +ShapeLike = Iterable[int] | int +# For backwards compatibility +ChunkCoords: tuple[int, ...] ZarrFormat = Literal[2, 3] NodeType = Literal["array", "group"] JSON = str | int | float | Mapping[str, "JSON"] | Sequence["JSON"] | None @@ -67,7 +67,7 @@ class NamedConfig(TypedDict, Generic[TName, TConfig]): """The configuration of the object.""" -def product(tup: ChunkCoords) -> int: +def product(tup: tuple[int, ...]) -> int: return functools.reduce(operator.mul, tup, 1) @@ -161,7 +161,7 @@ def parse_named_configuration( return name_parsed, configuration_parsed -def parse_shapelike(data: int | Iterable[int]) -> tuple[int, ...]: +def parse_shapelike(data: ShapeLike) -> tuple[int, ...]: if isinstance(data, int): if data < 0: raise ValueError(f"Expected a non-negative integer. Got {data} instead") diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 9ef8481b9a..4c14fb357c 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -41,7 +41,6 @@ ZATTRS_JSON, ZGROUP_JSON, ZMETADATA_V2_JSON, - ChunkCoords, DimensionNames, NodeType, ShapeLike, @@ -1019,7 +1018,7 @@ async def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: ChunkCoords | Literal["auto"] = "auto", + chunks: tuple[int, ...] | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -1044,14 +1043,14 @@ async def create_array( name : str The name of the array relative to the group. If ``path`` is ``None``, the array will be located at the root of the store. - shape : ChunkCoords + shape : tuple[int, ...] Shape of the array. dtype : npt.DTypeLike Data type of the array. - chunks : ChunkCoords, optional + chunks : tuple[int, ...], optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that @@ -1197,7 +1196,7 @@ async def require_dataset( self, name: str, *, - shape: ChunkCoords, + shape: tuple[int, ...], dtype: npt.DTypeLike = None, exact: bool = False, **kwargs: Any, @@ -1616,7 +1615,7 @@ async def tree(self, expand: bool | None = None, level: int | None = None) -> An return await group_tree_async(self, max_depth=level) async def empty( - self, *, name: str, shape: ChunkCoords, **kwargs: Any + self, *, name: str, shape: tuple[int, ...], **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an empty array with the specified shape in this Group. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1639,7 +1638,7 @@ async def empty( return await async_api.empty(shape=shape, store=self.store_path, path=name, **kwargs) async def zeros( - self, *, name: str, shape: ChunkCoords, **kwargs: Any + self, *, name: str, shape: tuple[int, ...], **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array, with zero being used as the default value for uninitialized portions of the array. @@ -1660,7 +1659,7 @@ async def zeros( return await async_api.zeros(shape=shape, store=self.store_path, path=name, **kwargs) async def ones( - self, *, name: str, shape: ChunkCoords, **kwargs: Any + self, *, name: str, shape: tuple[int, ...], **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array, with one being used as the default value for uninitialized portions of the array. @@ -1681,7 +1680,7 @@ async def ones( return await async_api.ones(shape=shape, store=self.store_path, path=name, **kwargs) async def full( - self, *, name: str, shape: ChunkCoords, fill_value: Any | None, **kwargs: Any + self, *, name: str, shape: tuple[int, ...], fill_value: Any | None, **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array, with "fill_value" being used as the default value for uninitialized portions of the array. @@ -2450,7 +2449,7 @@ def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: ChunkCoords | Literal["auto"] = "auto", + chunks: tuple[int, ...] | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -2475,16 +2474,16 @@ def create_array( name : str The name of the array relative to the group. If ``path`` is ``None``, the array will be located at the root of the store. - shape : ChunkCoords, optional + shape : ShapeLike, optional Shape of the array. Must be ``None`` if ``data`` is provided. dtype : npt.DTypeLike | None Data type of the array. Must be ``None`` if ``data`` is provided. data : Array-like data to use for initializing the array. If this parameter is provided, the ``shape`` and ``dtype`` parameters must be ``None``. - chunks : ChunkCoords, optional + chunks : tuple[int, ...], optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that @@ -2659,7 +2658,7 @@ def require_array(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs))) - def empty(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: + def empty(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: """Create an empty array with the specified shape in this Group. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -2680,7 +2679,7 @@ def empty(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.empty(name=name, shape=shape, **kwargs))) - def zeros(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: + def zeros(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: """Create an array, with zero being used as the default value for uninitialized portions of the array. Parameters @@ -2699,7 +2698,7 @@ def zeros(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.zeros(name=name, shape=shape, **kwargs))) - def ones(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: + def ones(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: """Create an array, with one being used as the default value for uninitialized portions of the array. Parameters @@ -2719,7 +2718,7 @@ def ones(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array: return Array(self._sync(self._async_group.ones(name=name, shape=shape, **kwargs))) def full( - self, *, name: str, shape: ChunkCoords, fill_value: Any | None, **kwargs: Any + self, *, name: str, shape: tuple[int, ...], fill_value: Any | None, **kwargs: Any ) -> Array: """Create an array, with "fill_value" being used as the default value for uninitialized portions of the array. @@ -2845,8 +2844,8 @@ def array( *, shape: ShapeLike, dtype: npt.DTypeLike, - chunks: ChunkCoords | Literal["auto"] = "auto", - shards: ChunkCoords | Literal["auto"] | None = None, + chunks: tuple[int, ...] | Literal["auto"] = "auto", + shards: tuple[int, ...] | Literal["auto"] | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", compressor: CompressorLike = None, @@ -2873,14 +2872,14 @@ def array( name : str The name of the array relative to the group. If ``path`` is ``None``, the array will be located at the root of the store. - shape : ChunkCoords + shape : tuple[int, ...] Shape of the array. dtype : npt.DTypeLike Data type of the array. - chunks : ChunkCoords, optional + chunks : tuple[int, ...], optional Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. - shards : ChunkCoords, optional + shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 15cf6f0f1a..16cb271601 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -33,7 +33,6 @@ from zarr.core.array import Array, AsyncArray from zarr.core.buffer import NDArrayLikeOrScalar from zarr.core.chunk_grids import ChunkGrid - from zarr.core.common import ChunkCoords IntSequence = list[int] | npt.NDArray[np.intp] @@ -75,7 +74,7 @@ class VindexInvalidSelectionError(IndexError): ) -def err_too_many_indices(selection: Any, shape: ChunkCoords) -> None: +def err_too_many_indices(selection: Any, shape: tuple[int, ...]) -> None: raise IndexError(f"too many indices for array; expected {len(shape)}, got {len(selection)}") @@ -90,8 +89,8 @@ def _zarr_array_to_int_or_bool_array(arr: Array) -> npt.NDArray[np.intp] | npt.N @runtime_checkable class Indexer(Protocol): - shape: ChunkCoords - drop_axes: ChunkCoords + shape: tuple[int, ...] + drop_axes: tuple[int, ...] def __iter__(self) -> Iterator[ChunkProjection]: ... @@ -105,7 +104,7 @@ def _iter_grid( origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None, order: _ArrayIndexingOrder = "lexicographic", -) -> Iterator[ChunkCoords]: +) -> Iterator[tuple[int, ...]]: """ Iterate over the elements of grid of integers, with the option to restrict the domain of iteration to a contiguous subregion of that grid. @@ -283,7 +282,7 @@ def is_pure_orthogonal_indexing(selection: Selection, ndim: int) -> TypeGuard[Or ) -def get_chunk_shape(chunk_grid: ChunkGrid) -> ChunkCoords: +def get_chunk_shape(chunk_grid: ChunkGrid) -> tuple[int, ...]: from zarr.core.chunk_grids import RegularChunkGrid assert isinstance(chunk_grid, RegularChunkGrid), ( @@ -424,12 +423,12 @@ def __iter__(self) -> Iterator[ChunkDimProjection]: yield ChunkDimProjection(dim_chunk_ix, dim_chunk_sel, dim_out_sel, is_complete_chunk) -def check_selection_length(selection: SelectionNormalized, shape: ChunkCoords) -> None: +def check_selection_length(selection: SelectionNormalized, shape: tuple[int, ...]) -> None: if len(selection) > len(shape): err_too_many_indices(selection, shape) -def replace_ellipsis(selection: Any, shape: ChunkCoords) -> SelectionNormalized: +def replace_ellipsis(selection: Any, shape: tuple[int, ...]) -> SelectionNormalized: selection = ensure_tuple(selection) # count number of ellipsis present @@ -498,7 +497,7 @@ class ChunkProjection(NamedTuple): True if a complete chunk is indexed """ - chunk_coords: ChunkCoords + chunk_coords: tuple[int, ...] chunk_selection: tuple[Selector, ...] | npt.NDArray[np.intp] out_selection: tuple[Selector, ...] | npt.NDArray[np.intp] | slice is_complete_chunk: bool @@ -529,13 +528,13 @@ def is_basic_selection(selection: Any) -> TypeGuard[BasicSelection]: @dataclass(frozen=True) class BasicIndexer(Indexer): dim_indexers: list[IntDimIndexer | SliceDimIndexer] - shape: ChunkCoords - drop_axes: ChunkCoords + shape: tuple[int, ...] + drop_axes: tuple[int, ...] def __init__( self, selection: BasicSelection, - shape: ChunkCoords, + shape: tuple[int, ...], chunk_grid: ChunkGrid, ) -> None: chunk_shape = get_chunk_shape(chunk_grid) @@ -795,7 +794,7 @@ def slice_to_range(s: slice, length: int) -> range: return range(*s.indices(length)) -def ix_(selection: Any, shape: ChunkCoords) -> npt.NDArray[np.intp]: +def ix_(selection: Any, shape: tuple[int, ...]) -> npt.NDArray[np.intp]: """Convert an orthogonal selection to a numpy advanced (fancy) selection, like ``numpy.ix_`` but with support for slices and single ints.""" @@ -845,12 +844,12 @@ def oindex_set(a: npt.NDArray[Any], selection: Selection, value: Any) -> None: @dataclass(frozen=True) class OrthogonalIndexer(Indexer): dim_indexers: list[IntDimIndexer | SliceDimIndexer | IntArrayDimIndexer | BoolArrayDimIndexer] - shape: ChunkCoords - chunk_shape: ChunkCoords + shape: tuple[int, ...] + chunk_shape: tuple[int, ...] is_advanced: bool drop_axes: tuple[int, ...] - def __init__(self, selection: Selection, shape: ChunkCoords, chunk_grid: ChunkGrid) -> None: + def __init__(self, selection: Selection, shape: tuple[int, ...], chunk_grid: ChunkGrid) -> None: chunk_shape = get_chunk_shape(chunk_grid) # handle ellipsis @@ -979,11 +978,11 @@ async def getitem(self, selection: OrthogonalSelection | Array) -> NDArrayLikeOr @dataclass(frozen=True) class BlockIndexer(Indexer): dim_indexers: list[SliceDimIndexer] - shape: ChunkCoords - drop_axes: ChunkCoords + shape: tuple[int, ...] + drop_axes: tuple[int, ...] def __init__( - self, selection: BasicSelection, shape: ChunkCoords, chunk_grid: ChunkGrid + self, selection: BasicSelection, shape: tuple[int, ...], chunk_grid: ChunkGrid ) -> None: chunk_shape = get_chunk_shape(chunk_grid) @@ -1078,7 +1077,7 @@ def __setitem__(self, selection: BasicSelection, value: npt.ArrayLike) -> None: def is_coordinate_selection( - selection: SelectionNormalized, shape: ChunkCoords + selection: SelectionNormalized, shape: tuple[int, ...] ) -> TypeGuard[CoordinateSelectionNormalized]: return ( isinstance(selection, tuple) @@ -1087,7 +1086,7 @@ def is_coordinate_selection( ) -def is_mask_selection(selection: Selection, shape: ChunkCoords) -> TypeGuard[MaskSelection]: +def is_mask_selection(selection: Selection, shape: tuple[int, ...]) -> TypeGuard[MaskSelection]: return ( isinstance(selection, tuple) and len(selection) == 1 @@ -1098,22 +1097,22 @@ def is_mask_selection(selection: Selection, shape: ChunkCoords) -> TypeGuard[Mas @dataclass(frozen=True) class CoordinateIndexer(Indexer): - sel_shape: ChunkCoords + sel_shape: tuple[int, ...] selection: CoordinateSelectionNormalized sel_sort: npt.NDArray[np.intp] | None chunk_nitems_cumsum: npt.NDArray[np.intp] chunk_rixs: npt.NDArray[np.intp] chunk_mixs: tuple[npt.NDArray[np.intp], ...] - shape: ChunkCoords - chunk_shape: ChunkCoords - drop_axes: ChunkCoords + shape: tuple[int, ...] + chunk_shape: tuple[int, ...] + drop_axes: tuple[int, ...] def __init__( - self, selection: CoordinateSelection, shape: ChunkCoords, chunk_grid: ChunkGrid + self, selection: CoordinateSelection, shape: tuple[int, ...], chunk_grid: ChunkGrid ) -> None: chunk_shape = get_chunk_shape(chunk_grid) - cdata_shape: ChunkCoords + cdata_shape: tuple[int, ...] if shape == (): cdata_shape = (1,) else: @@ -1228,7 +1227,9 @@ def __iter__(self) -> Iterator[ChunkProjection]: @dataclass(frozen=True) class MaskIndexer(CoordinateIndexer): - def __init__(self, selection: MaskSelection, shape: ChunkCoords, chunk_grid: ChunkGrid) -> None: + def __init__( + self, selection: MaskSelection, shape: tuple[int, ...], chunk_grid: ChunkGrid + ) -> None: # some initial normalization selection_normalized = cast("tuple[MaskSelection]", ensure_tuple(selection)) selection_normalized = cast("tuple[MaskSelection]", replace_lists(selection_normalized)) @@ -1380,7 +1381,7 @@ def make_slice_selection(selection: Any) -> list[slice]: return ls -def decode_morton(z: int, chunk_shape: ChunkCoords) -> ChunkCoords: +def decode_morton(z: int, chunk_shape: tuple[int, ...]) -> tuple[int, ...]: # Inspired by compressed morton code as implemented in Neuroglancer # https://github.com/google/neuroglancer/blob/master/src/neuroglancer/datasource/precomputed/volume.md#compressed-morton-code bits = tuple(math.ceil(math.log2(c)) for c in chunk_shape) @@ -1398,9 +1399,9 @@ def decode_morton(z: int, chunk_shape: ChunkCoords) -> ChunkCoords: return tuple(out) -def morton_order_iter(chunk_shape: ChunkCoords) -> Iterator[ChunkCoords]: +def morton_order_iter(chunk_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: i = 0 - order: list[ChunkCoords] = [] + order: list[tuple[int, ...]] = [] while len(order) < product(chunk_shape): m = decode_morton(i, chunk_shape) if m not in order and all(x < y for x, y in zip(m, chunk_shape, strict=False)): @@ -1410,12 +1411,12 @@ def morton_order_iter(chunk_shape: ChunkCoords) -> Iterator[ChunkCoords]: yield order[j] -def c_order_iter(chunks_per_shard: ChunkCoords) -> Iterator[ChunkCoords]: +def c_order_iter(chunks_per_shard: tuple[int, ...]) -> Iterator[tuple[int, ...]]: return itertools.product(*(range(x) for x in chunks_per_shard)) def get_indexer( - selection: SelectionWithFields, shape: ChunkCoords, chunk_grid: ChunkGrid + selection: SelectionWithFields, shape: tuple[int, ...], chunk_grid: ChunkGrid ) -> Indexer: _, pure_selection = pop_fields(selection) if is_pure_fancy_indexing(pure_selection, len(shape)): diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index efc6bd7949..3204543426 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -19,7 +19,6 @@ import numpy.typing as npt from zarr.core.buffer import Buffer, BufferPrototype - from zarr.core.common import ChunkCoords from zarr.core.dtype.wrapper import ( TBaseDType, TBaseScalar, @@ -61,8 +60,8 @@ class ArrayV2MetadataDict(TypedDict): @dataclass(frozen=True, kw_only=True) class ArrayV2Metadata(Metadata): - shape: ChunkCoords - chunks: ChunkCoords + shape: tuple[int, ...] + chunks: tuple[int, ...] dtype: ZDType[TBaseDType, TBaseScalar] fill_value: int | float | str | bytes | None = None order: MemoryOrder = "C" @@ -75,9 +74,9 @@ class ArrayV2Metadata(Metadata): def __init__( self, *, - shape: ChunkCoords, + shape: tuple[int, ...], dtype: ZDType[TDType_co, TScalar_co], - chunks: ChunkCoords, + chunks: tuple[int, ...], fill_value: Any, order: MemoryOrder, dimension_separator: Literal[".", "/"] = ".", @@ -123,7 +122,7 @@ def chunk_grid(self) -> RegularChunkGrid: return RegularChunkGrid(chunk_shape=self.chunks) @property - def shards(self) -> ChunkCoords | None: + def shards(self) -> tuple[int, ...] | None: return None def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: @@ -229,7 +228,7 @@ def to_dict(self) -> dict[str, JSON]: return zarray_dict def get_chunk_spec( - self, _chunk_coords: ChunkCoords, array_config: ArrayConfig, prototype: BufferPrototype + self, _chunk_coords: tuple[int, ...], array_config: ArrayConfig, prototype: BufferPrototype ) -> ArraySpec: return ArraySpec( shape=self.chunks, @@ -239,11 +238,11 @@ def get_chunk_spec( prototype=prototype, ) - def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str: + def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: chunk_identifier = self.dimension_separator.join(map(str, chunk_coords)) return "0" if chunk_identifier == "" else chunk_identifier - def update_shape(self, shape: ChunkCoords) -> Self: + def update_shape(self, shape: tuple[int, ...]) -> Self: return replace(self, shape=shape) def update_attributes(self, attributes: dict[str, JSON]) -> Self: diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 6f79fb4b09..e17edb999c 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -12,7 +12,7 @@ from zarr.core.buffer import Buffer, BufferPrototype from zarr.core.chunk_grids import ChunkGrid - from zarr.core.common import JSON, ChunkCoords + from zarr.core.common import JSON from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar @@ -28,7 +28,6 @@ from zarr.core.common import ( JSON, ZARR_JSON, - ChunkCoords, DimensionNames, parse_named_configuration, parse_shapelike, @@ -138,7 +137,7 @@ class ArrayV3MetadataDict(TypedDict): @dataclass(frozen=True, kw_only=True) class ArrayV3Metadata(Metadata): - shape: ChunkCoords + shape: tuple[int, ...] data_type: ZDType[TBaseDType, TBaseScalar] chunk_grid: ChunkGrid chunk_key_encoding: ChunkKeyEncoding @@ -224,7 +223,7 @@ def dtype(self) -> ZDType[TBaseDType, TBaseScalar]: return self.data_type @property - def chunks(self) -> ChunkCoords: + def chunks(self) -> tuple[int, ...]: if isinstance(self.chunk_grid, RegularChunkGrid): from zarr.codecs.sharding import ShardingCodec @@ -242,7 +241,7 @@ def chunks(self) -> ChunkCoords: raise NotImplementedError(msg) @property - def shards(self) -> ChunkCoords | None: + def shards(self) -> tuple[int, ...] | None: if isinstance(self.chunk_grid, RegularChunkGrid): from zarr.codecs.sharding import ShardingCodec @@ -267,7 +266,7 @@ def inner_codecs(self) -> tuple[Codec, ...]: return self.codecs def get_chunk_spec( - self, _chunk_coords: ChunkCoords, array_config: ArrayConfig, prototype: BufferPrototype + self, _chunk_coords: tuple[int, ...], array_config: ArrayConfig, prototype: BufferPrototype ) -> ArraySpec: assert isinstance(self.chunk_grid, RegularChunkGrid), ( "Currently, only regular chunk grid is supported" @@ -280,7 +279,7 @@ def get_chunk_spec( prototype=prototype, ) - def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str: + def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: return self.chunk_key_encoding.encode_chunk_key(chunk_coords) def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: @@ -345,7 +344,7 @@ def to_dict(self) -> dict[str, JSON]: return out_dict - def update_shape(self, shape: ChunkCoords) -> Self: + def update_shape(self, shape: tuple[int, ...]) -> Self: return replace(self, shape=shape) def update_attributes(self, attributes: dict[str, JSON]) -> Self: diff --git a/src/zarr/testing/buffer.py b/src/zarr/testing/buffer.py index 8cbfb2414a..1e167b2156 100644 --- a/src/zarr/testing/buffer.py +++ b/src/zarr/testing/buffer.py @@ -13,8 +13,6 @@ from collections.abc import Iterable from typing import Self - from zarr.core.common import ChunkCoords - __all__ = [ "NDBufferUsingTestNDArrayLike", @@ -56,7 +54,7 @@ def create( @classmethod def empty( cls, - shape: ChunkCoords, + shape: tuple[int, ...], dtype: npt.DTypeLike, order: Literal["C", "F"] = "C", ) -> Self: diff --git a/tests/conftest.py b/tests/conftest.py index a1bf423c06..839be34e01 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -21,7 +21,14 @@ _parse_chunk_key_encoding, ) from zarr.core.chunk_grids import RegularChunkGrid, _auto_partition -from zarr.core.common import JSON, DimensionNames, parse_shapelike +from zarr.core.common import ( + JSON, + DimensionNames, + MemoryOrder, + ShapeLike, + ZarrFormat, + parse_shapelike, +) from zarr.core.config import config as zarr_config from zarr.core.dtype import ( get_data_type_from_native_dtype, @@ -40,8 +47,10 @@ from zarr.abc.codec import Codec from zarr.core.array import CompressorsLike, FiltersLike, SerializerLike, ShardsLike - from zarr.core.chunk_key_encodings import ChunkKeyEncoding, ChunkKeyEncodingLike - from zarr.core.common import ChunkCoords, MemoryOrder, ShapeLike, ZarrFormat + from zarr.core.chunk_key_encodings import ( + ChunkKeyEncoding, + ChunkKeyEncodingLike, + ) from zarr.core.dtype.wrapper import ZDType @@ -152,7 +161,7 @@ def reset_config() -> Generator[None, None, None]: @dataclass class ArrayRequest: - shape: ChunkCoords + shape: tuple[int, ...] dtype: str order: MemoryOrder @@ -229,7 +238,7 @@ def create_array_metadata( *, shape: ShapeLike, dtype: npt.DTypeLike, - chunks: ChunkCoords | Literal["auto"], + chunks: tuple[int, ...] | Literal["auto"], shards: None, filters: FiltersLike, compressors: CompressorsLike, @@ -248,7 +257,7 @@ def create_array_metadata( *, shape: ShapeLike, dtype: npt.DTypeLike, - chunks: ChunkCoords | Literal["auto"], + chunks: tuple[int, ...] | Literal["auto"], shards: ShardsLike | None, filters: FiltersLike, compressors: CompressorsLike, @@ -267,7 +276,7 @@ def create_array_metadata( *, shape: ShapeLike, dtype: npt.DTypeLike, - chunks: ChunkCoords | Literal["auto"] = "auto", + chunks: tuple[int, ...] | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -369,7 +378,7 @@ def create_array_metadata( @overload def meta_from_array( array: np.ndarray[Any, Any], - chunks: ChunkCoords | Literal["auto"], + chunks: tuple[int, ...] | Literal["auto"], shards: None, filters: FiltersLike, compressors: CompressorsLike, @@ -386,7 +395,7 @@ def meta_from_array( @overload def meta_from_array( array: np.ndarray[Any, Any], - chunks: ChunkCoords | Literal["auto"], + chunks: tuple[int, ...] | Literal["auto"], shards: ShardsLike | None, filters: FiltersLike, compressors: CompressorsLike, @@ -405,7 +414,7 @@ def meta_from_array( def meta_from_array( array: np.ndarray[Any, Any], *, - chunks: ChunkCoords | Literal["auto"] = "auto", + chunks: tuple[int, ...] | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index a2dad41a1b..dfedbb83de 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -28,7 +28,7 @@ from zarr.abc.codec import Codec from zarr.abc.store import Store from zarr.core.buffer.core import NDArrayLikeOrScalar - from zarr.core.common import ChunkCoords, MemoryOrder + from zarr.core.common import MemoryOrder @dataclass(frozen=True) @@ -215,7 +215,7 @@ def test_morton() -> None: [3, 2, 1, 6, 4, 5, 2], ], ) -def test_morton2(shape: ChunkCoords) -> None: +def test_morton2(shape: tuple[int, ...]) -> None: order = list(morton_order_iter(shape)) for i, x in enumerate(order): assert x not in order[:i] # no duplicates diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 24b4b65505..a78fe3c706 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -33,7 +33,6 @@ from zarr.core.buffer import BufferPrototype from zarr.core.buffer.core import Buffer - from zarr.core.common import ChunkCoords @pytest.fixture @@ -44,7 +43,7 @@ async def store() -> AsyncGenerator[StorePath]: def zarr_array_from_numpy_array( store: StorePath, a: npt.NDArray[Any], - chunk_shape: ChunkCoords | None = None, + chunk_shape: tuple[int, ...] | None = None, ) -> zarr.Array: z = zarr.create_array( store=store / str(uuid4()), From cc2fa37d0e76e3615b9237e58466a993bb4f1cc1 Mon Sep 17 00:00:00 2001 From: "Christine P. Chai" Date: Mon, 18 Aug 2025 12:28:17 -0700 Subject: [PATCH 071/468] docs: Update the link to sharding in the Zarr roadmap (#3380) Co-authored-by: Davis Bennett --- docs/developers/roadmap.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developers/roadmap.rst b/docs/developers/roadmap.rst index d9fc32b775..716599bab0 100644 --- a/docs/developers/roadmap.rst +++ b/docs/developers/roadmap.rst @@ -56,7 +56,7 @@ Goals - Provide a complete implementation of Zarr V3 through the Zarr-Python API - Clear the way for exciting extensions / ZEPs - (i.e. `sharding `__, + (i.e. `sharding `__, `variable chunking `__, etc.) - Provide a developer API that can be used to implement and register V3 From c2c4e21bedf017f73c22f48acd6956034eb84748 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Tue, 19 Aug 2025 13:41:32 +0300 Subject: [PATCH 072/468] Relax obsolete constraints on setuptools-scm (#3385) This reverts e77f803e1a813a496d59c3d091a263602c308bf1. No need to explicitly avoid a yanked release. Release 9.0.0 has been yanked on PyPI. Actually all 9.*.* releases so far have been yanked, except for the current 9.2.0: https://pypi.org/project/setuptools-scm/#history --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 95528c4558..5a1d60485d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["hatchling>=1.27.0", "hatch-vcs", "setuptools-scm!=9.0.0"] +requires = ["hatchling>=1.27.0", "hatch-vcs"] build-backend = "hatchling.build" [tool.hatch.build.targets.sdist] From 4b26501a6e6a2463aed99ec28130277c7293aff6 Mon Sep 17 00:00:00 2001 From: Tom Augspurger Date: Tue, 19 Aug 2025 06:31:51 -0500 Subject: [PATCH 073/468] Optimize getitem with empty chunks (#3379) Co-authored-by: Davis Bennett --- changes/3368.misc.rst | 2 ++ src/zarr/abc/codec.py | 5 +++++ src/zarr/codecs/sharding.py | 6 ++---- src/zarr/core/array.py | 3 +-- 4 files changed, 10 insertions(+), 6 deletions(-) create mode 100644 changes/3368.misc.rst diff --git a/changes/3368.misc.rst b/changes/3368.misc.rst new file mode 100644 index 0000000000..92c90cff33 --- /dev/null +++ b/changes/3368.misc.rst @@ -0,0 +1,2 @@ +Improved performance of reading arrays by not unnecessarily using +the fill value. diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index 50c3a55eab..fd2773ca0a 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -427,6 +427,11 @@ async def read( The second slice selection determines where in the output array the chunk data will be written. The ByteGetter is used to fetch the necessary bytes. The chunk spec contains information about the construction of an array from the bytes. + + If the Store returns ``None`` for a chunk, then the chunk was not + written and the implementation must set the values of that chunk (or + ``out``) to the fill value for the array. + out : NDBuffer """ ... diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 2b9b2259d8..58d34f62e7 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -451,11 +451,10 @@ async def _decode_single( ) # setup output array - out = chunk_spec.prototype.nd_buffer.create( + out = chunk_spec.prototype.nd_buffer.empty( shape=shard_shape, dtype=shard_spec.dtype.to_native_dtype(), order=shard_spec.order, - fill_value=0, ) shard_dict = await _ShardReader.from_bytes(shard_bytes, self, chunks_per_shard) @@ -498,11 +497,10 @@ async def _decode_partial_single( ) # setup output array - out = shard_spec.prototype.nd_buffer.create( + out = shard_spec.prototype.nd_buffer.empty( shape=indexer.shape, dtype=shard_spec.dtype.to_native_dtype(), order=shard_spec.order, - fill_value=0, ) indexed_chunks = list(indexer) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 819379e12f..51e638edd8 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1349,11 +1349,10 @@ async def _get_selection( f"shape of out argument doesn't match. Expected {indexer.shape}, got {out.shape}" ) else: - out_buffer = prototype.nd_buffer.create( + out_buffer = prototype.nd_buffer.empty( shape=indexer.shape, dtype=out_dtype, order=self.order, - fill_value=self.metadata.fill_value, ) if product(indexer.shape) > 0: # need to use the order from the metadata for v2 From 6a546d639e263fe9a5e11740f667cc5db0115da6 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 19 Aug 2025 21:08:48 +0200 Subject: [PATCH 074/468] chore/add missing tests (#3353) * exclude notimplementederrors from test coverage * add tests for untested features of api.asynchronous * add tests for untested features of api.asynchronous * remove whitespace removal * fix import of arraylike * be more explicit about the data type * Update tests/test_api/test_asynchronous.py Co-authored-by: Tom Augspurger --------- Co-authored-by: Tom Augspurger --- src/zarr/abc/codec.py | 6 +- tests/test_api/test_asynchronous.py | 105 ++++++++++++++++++++++++++++ 2 files changed, 108 insertions(+), 3 deletions(-) create mode 100644 tests/test_api/test_asynchronous.py diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index fd2773ca0a..d41c457b4e 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -138,7 +138,7 @@ def validate( """ async def _decode_single(self, chunk_data: CodecOutput, chunk_spec: ArraySpec) -> CodecInput: - raise NotImplementedError + raise NotImplementedError # pragma: no cover async def decode( self, @@ -161,7 +161,7 @@ async def decode( async def _encode_single( self, chunk_data: CodecInput, chunk_spec: ArraySpec ) -> CodecOutput | None: - raise NotImplementedError + raise NotImplementedError # pragma: no cover async def encode( self, @@ -242,7 +242,7 @@ async def _encode_partial_single( selection: SelectorTuple, chunk_spec: ArraySpec, ) -> None: - raise NotImplementedError + raise NotImplementedError # pragma: no cover async def encode_partial( self, diff --git a/tests/test_api/test_asynchronous.py b/tests/test_api/test_asynchronous.py new file mode 100644 index 0000000000..910fd2883c --- /dev/null +++ b/tests/test_api/test_asynchronous.py @@ -0,0 +1,105 @@ +from __future__ import annotations + +import json +from dataclasses import dataclass +from typing import TYPE_CHECKING + +import numpy as np +import pytest + +from zarr import create_array +from zarr.api.asynchronous import _get_shape_chunks, _like_args, open +from zarr.core.buffer.core import default_buffer_prototype + +if TYPE_CHECKING: + from typing import Any + + import numpy.typing as npt + + from zarr.core.array import Array, AsyncArray + from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata + + +@dataclass +class WithShape: + shape: tuple[int, ...] + + +@dataclass +class WithChunks(WithShape): + chunks: tuple[int, ...] + + +@dataclass +class WithChunkLen(WithShape): + chunklen: int + + +@pytest.mark.parametrize( + ("observed", "expected"), + [ + ({}, (None, None)), + (WithShape(shape=(1, 2)), ((1, 2), None)), + (WithChunks(shape=(1, 2), chunks=(1, 2)), ((1, 2), (1, 2))), + (WithChunkLen(shape=(10, 10), chunklen=1), ((10, 10), (1, 10))), + ], +) +def test_get_shape_chunks( + observed: object, expected: tuple[tuple[int, ...] | None, tuple[int, ...] | None] +) -> None: + """ + Test the _get_shape_chunks function + """ + assert _get_shape_chunks(observed) == expected + + +@pytest.mark.parametrize( + ("observed", "expected"), + [ + (np.arange(10, dtype=np.dtype("int64")), {"shape": (10,), "dtype": np.dtype("int64")}), + (WithChunks(shape=(1, 2), chunks=(1, 2)), {"chunks": (1, 2), "shape": (1, 2)}), + ( + create_array( + {}, + chunks=(10,), + shape=(100,), + dtype="f8", + compressors=None, + filters=None, + zarr_format=2, + )._async_array, + { + "chunks": (10,), + "shape": (100,), + "dtype": np.dtype("f8"), + "compressor": None, + "filters": None, + "order": "C", + }, + ), + ], +) +def test_like_args( + observed: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | Array | npt.NDArray[Any], + expected: object, +) -> None: + """ + Test the like_args function + """ + assert _like_args(observed, {}) == expected + + +async def test_open_no_array() -> None: + """ + Test that zarr.api.asynchronous.open attempts to open a group when no array is found, but shape was specified in kwargs. + This behavior makes no sense but we should still test it. + """ + store = { + "zarr.json": default_buffer_prototype().buffer.from_bytes( + json.dumps({"zarr_format": 3, "node_type": "group"}).encode("utf-8") + ) + } + with pytest.raises( + TypeError, match=r"open_group\(\) got an unexpected keyword argument 'shape'" + ): + await open(store=store, shape=(1,)) From cb389260f95e79edd04a0fa89991e84a46a305da Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 21 Aug 2025 08:36:18 +0100 Subject: [PATCH 075/468] Fix typing in metadata tests (#3393) --- pyproject.toml | 2 +- src/zarr/core/array.py | 4 +- tests/test_metadata/test_consolidated.py | 82 +++++++++++++----------- tests/test_metadata/test_v2.py | 34 ++++++---- tests/test_metadata/test_v3.py | 12 ++-- 5 files changed, 73 insertions(+), 61 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 5a1d60485d..dffca78808 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -352,6 +352,7 @@ module = [ "tests.test_store.test_fsspec", "tests.test_store.test_memory", "tests.test_codecs.test_codecs", + "tests.test_metadata.*", ] strict = false @@ -359,7 +360,6 @@ strict = false # and fix the errors [[tool.mypy.overrides]] module = [ - "tests.test_metadata.*", "tests.test_store.test_core", "tests.test_store.test_logging", "tests.test_store.test_object", diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 51e638edd8..4fcddaa8b5 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -3,7 +3,7 @@ import json import warnings from asyncio import gather -from collections.abc import Iterable +from collections.abc import Iterable, Mapping from dataclasses import dataclass, field, replace from itertools import starmap from logging import getLogger @@ -3907,7 +3907,7 @@ def _build_parents( CompressorsLike: TypeAlias = ( Iterable[dict[str, JSON] | BytesBytesCodec | Numcodec] - | dict[str, JSON] + | Mapping[str, JSON] | BytesBytesCodec | Numcodec | Literal["auto"] diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index e23444cf93..0995be3c6d 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -1,7 +1,7 @@ from __future__ import annotations import json -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Any import numpy as np import pytest @@ -10,8 +10,8 @@ import zarr.api.asynchronous import zarr.api.synchronous import zarr.storage +from zarr import AsyncGroup from zarr.api.asynchronous import ( - AsyncGroup, consolidate_metadata, group, open, @@ -27,11 +27,11 @@ if TYPE_CHECKING: from zarr.abc.store import Store - from zarr.core.common import ZarrFormat + from zarr.core.common import JSON, ZarrFormat @pytest.fixture -async def memory_store_with_hierarchy(memory_store: Store) -> None: +async def memory_store_with_hierarchy(memory_store: Store) -> Store: g = await group(store=memory_store, attributes={"foo": "bar"}) dtype = "uint8" await g.create_array(name="air", shape=(1, 2, 3), dtype=dtype) @@ -51,15 +51,15 @@ async def memory_store_with_hierarchy(memory_store: Store) -> None: class TestConsolidated: - async def test_open_consolidated_false_raises(self): + async def test_open_consolidated_false_raises(self) -> None: store = zarr.storage.MemoryStore() with pytest.raises(TypeError, match="use_consolidated"): - await zarr.api.asynchronous.open_consolidated(store, use_consolidated=False) + await zarr.api.asynchronous.open_consolidated(store, use_consolidated=False) # type: ignore[arg-type] - def test_open_consolidated_false_raises_sync(self): + def test_open_consolidated_false_raises_sync(self) -> None: store = zarr.storage.MemoryStore() with pytest.raises(TypeError, match="use_consolidated"): - zarr.open_consolidated(store, use_consolidated=False) + zarr.open_consolidated(store, use_consolidated=False) # type: ignore[arg-type] async def test_consolidated(self, memory_store_with_hierarchy: Store) -> None: # TODO: Figure out desired keys in @@ -75,7 +75,7 @@ async def test_consolidated(self, memory_store_with_hierarchy: Store) -> None: await consolidate_metadata(memory_store_with_hierarchy) group2 = await AsyncGroup.open(memory_store_with_hierarchy) - array_metadata = { + array_metadata: dict[str, JSON] = { "attributes": {}, "chunk_key_encoding": { "configuration": {"separator": "/"}, @@ -192,13 +192,12 @@ async def test_consolidated(self, memory_store_with_hierarchy: Store) -> None: group4 = await open_consolidated(store=memory_store_with_hierarchy) assert group4.metadata == expected - result_raw = json.loads( - ( - await memory_store_with_hierarchy.get( - "zarr.json", prototype=default_buffer_prototype() - ) - ).to_bytes() - )["consolidated_metadata"] + buf = await memory_store_with_hierarchy.get( + "zarr.json", prototype=default_buffer_prototype() + ) + assert buf is not None + + result_raw = json.loads(buf.to_bytes())["consolidated_metadata"] assert result_raw["kind"] == "inline" assert sorted(result_raw["metadata"]) == [ "air", @@ -212,7 +211,7 @@ async def test_consolidated(self, memory_store_with_hierarchy: Store) -> None: "time", ] - def test_consolidated_sync(self, memory_store): + def test_consolidated_sync(self, memory_store: Store) -> None: g = zarr.api.synchronous.group(store=memory_store, attributes={"foo": "bar"}) dtype = "uint8" g.create_array(name="air", shape=(1, 2, 3), dtype=dtype) @@ -225,9 +224,9 @@ def test_consolidated_sync(self, memory_store): match="Consolidated metadata is currently not part in the Zarr format 3 specification.", ): zarr.api.synchronous.consolidate_metadata(memory_store) - group2 = zarr.api.synchronous.Group.open(memory_store) + group2 = zarr.Group.open(memory_store) - array_metadata = { + array_metadata: dict[str, JSON] = { "attributes": {}, "chunk_key_encoding": { "configuration": {"separator": "/"}, @@ -320,8 +319,8 @@ async def test_non_root_node(self, memory_store_with_hierarchy: Store) -> None: assert "air" not in child.metadata.consolidated_metadata.metadata assert "grandchild" in child.metadata.consolidated_metadata.metadata - def test_consolidated_metadata_from_dict(self): - data = {"must_understand": False} + def test_consolidated_metadata_from_dict(self) -> None: + data: dict[str, JSON] = {"must_understand": False} # missing kind with pytest.raises(ValueError, match="kind='None'"): @@ -343,8 +342,8 @@ def test_consolidated_metadata_from_dict(self): data["metadata"] = {} ConsolidatedMetadata.from_dict(data) - def test_flatten(self): - array_metadata = { + def test_flatten(self) -> None: + array_metadata: dict[str, Any] = { "attributes": {}, "chunk_key_encoding": { "configuration": {"separator": "/"}, @@ -421,27 +420,28 @@ def test_flatten(self): }, ) result = metadata.flattened_metadata + expected = { "air": metadata.metadata["air"], "lat": metadata.metadata["lat"], "child": GroupMetadata( attributes={"key": "child"}, consolidated_metadata=ConsolidatedMetadata(metadata={}) ), - "child/array": metadata.metadata["child"].consolidated_metadata.metadata["array"], + "child/array": metadata.metadata["child"].consolidated_metadata.metadata["array"], # type: ignore[union-attr] "child/grandchild": GroupMetadata( attributes={"key": "grandchild"}, consolidated_metadata=ConsolidatedMetadata(metadata={}), ), "child/grandchild/array": ( metadata.metadata["child"] - .consolidated_metadata.metadata["grandchild"] + .consolidated_metadata.metadata["grandchild"] # type: ignore[union-attr] .consolidated_metadata.metadata["array"] ), } assert result == expected - def test_invalid_metadata_raises(self): - payload = { + def test_invalid_metadata_raises(self) -> None: + payload: dict[str, JSON] = { "kind": "inline", "must_understand": False, "metadata": { @@ -452,7 +452,7 @@ def test_invalid_metadata_raises(self): with pytest.raises(TypeError, match="key='foo', type='list'"): ConsolidatedMetadata.from_dict(payload) - def test_to_dict_empty(self): + def test_to_dict_empty(self) -> None: meta = ConsolidatedMetadata( metadata={ "empty": GroupMetadata( @@ -507,6 +507,7 @@ async def test_to_dict_order( await zarr.api.asynchronous.consolidate_metadata(memory_store) g2 = await zarr.api.asynchronous.open_group(store=memory_store) + assert g2.metadata.consolidated_metadata is not None assert list(g2.metadata.consolidated_metadata.metadata) == ["a", "b", "c"] assert list(g2.metadata.consolidated_metadata.flattened_metadata) == [ "a", @@ -517,7 +518,7 @@ async def test_to_dict_order( ] @pytest.mark.parametrize("zarr_format", [2, 3]) - async def test_open_consolidated_raises_async(self, zarr_format: ZarrFormat): + async def test_open_consolidated_raises_async(self, zarr_format: ZarrFormat) -> None: store = zarr.storage.MemoryStore() await AsyncGroup.from_store(store, zarr_format=zarr_format) with pytest.raises(ValueError): @@ -535,12 +536,15 @@ async def v2_consolidated_metadata_empty_dataset( b'{"metadata":{".zgroup":{"zarr_format":2}},"zarr_consolidated_format":1}' ) return AsyncGroup._from_bytes_v2( - None, zgroup_bytes, zattrs_bytes=None, consolidated_metadata_bytes=zmetadata_bytes + StorePath(memory_store, path=""), + zgroup_bytes, + zattrs_bytes=None, + consolidated_metadata_bytes=zmetadata_bytes, ) async def test_consolidated_metadata_backwards_compatibility( - self, v2_consolidated_metadata_empty_dataset - ): + self, v2_consolidated_metadata_empty_dataset: AsyncGroup + ) -> None: """ Test that consolidated metadata handles a missing .zattrs key. This is necessary for backwards compatibility with zarr-python 2.x. See https://github.com/zarr-developers/zarr-python/issues/2694 """ @@ -550,7 +554,7 @@ async def test_consolidated_metadata_backwards_compatibility( result = await zarr.api.asynchronous.open_consolidated(store, zarr_format=2) assert result.metadata == v2_consolidated_metadata_empty_dataset.metadata - async def test_consolidated_metadata_v2(self): + async def test_consolidated_metadata_v2(self) -> None: store = zarr.storage.MemoryStore() g = await AsyncGroup.from_store(store, attributes={"key": "root"}, zarr_format=2) dtype = parse_dtype("uint8", zarr_format=2) @@ -638,7 +642,9 @@ async def test_use_consolidated_false( assert good.metadata.consolidated_metadata assert sorted(good.metadata.consolidated_metadata.metadata) == ["a", "b"] - async def test_stale_child_metadata_ignored(self, memory_store: zarr.storage.MemoryStore): + async def test_stale_child_metadata_ignored( + self, memory_store: zarr.storage.MemoryStore + ) -> None: # https://github.com/zarr-developers/zarr-python/issues/2921 # When consolidating metadata, we should ignore any (possibly stale) metadata # from previous consolidations, *including at child nodes*. @@ -660,7 +666,7 @@ async def test_stale_child_metadata_ignored(self, memory_store: zarr.storage.Mem async def test_use_consolidated_for_children_members( self, memory_store: zarr.storage.MemoryStore - ): + ) -> None: # A test that has *unconsolidated* metadata at the root group, but discovers # a child group with consolidated metadata. @@ -690,7 +696,7 @@ async def test_use_consolidated_for_children_members( @pytest.mark.parametrize("fill_value", [np.nan, np.inf, -np.inf]) async def test_consolidated_metadata_encodes_special_chars( memory_store: Store, zarr_format: ZarrFormat, fill_value: float -): +) -> None: root = await group(store=memory_store, zarr_format=zarr_format) _time = await root.create_array("time", shape=(12,), dtype=np.float64, fill_value=fill_value) if zarr_format == 3: @@ -728,7 +734,7 @@ def supports_consolidated_metadata(self) -> bool: return False -async def test_consolidate_metadata_raises_for_self_consolidating_stores(): +async def test_consolidate_metadata_raises_for_self_consolidating_stores() -> None: """Verify calling consolidate_metadata on a non supporting stores raises an error.""" memory_store = NonConsolidatedStore() @@ -739,7 +745,7 @@ async def test_consolidate_metadata_raises_for_self_consolidating_stores(): await zarr.api.asynchronous.consolidate_metadata(memory_store) -async def test_open_group_in_non_consolidating_stores(): +async def test_open_group_in_non_consolidating_stores() -> None: memory_store = NonConsolidatedStore() root = await zarr.api.asynchronous.create_group(store=memory_store) await root.create_group("a/b") diff --git a/tests/test_metadata/test_v2.py b/tests/test_metadata/test_v2.py index e18841f1f3..424b2881d6 100644 --- a/tests/test_metadata/test_v2.py +++ b/tests/test_metadata/test_v2.py @@ -18,9 +18,11 @@ from zarr.errors import ZarrUserWarning if TYPE_CHECKING: + from pathlib import Path from typing import Any from zarr.abc.codec import Codec + from zarr.core.common import JSON def test_parse_zarr_format_valid() -> None: @@ -105,7 +107,7 @@ class TestConsolidated: async def v2_consolidated_metadata( self, memory_store: zarr.storage.MemoryStore ) -> zarr.storage.MemoryStore: - zmetadata = { + zmetadata: dict[str, JSON] = { "metadata": { ".zattrs": { "Conventions": "COARDS", @@ -160,8 +162,7 @@ async def v2_consolidated_metadata( }, "zarr_consolidated_format": 1, } - store_dict = {} - store = zarr.storage.MemoryStore(store_dict=store_dict) + store = zarr.storage.MemoryStore() await store.set( ".zattrs", cpu.Buffer.from_bytes(json.dumps({"Conventions": "COARDS"}).encode()) ) @@ -169,19 +170,19 @@ async def v2_consolidated_metadata( await store.set(".zmetadata", cpu.Buffer.from_bytes(json.dumps(zmetadata).encode())) await store.set( "air/.zarray", - cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["air/.zarray"]).encode()), + cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["air/.zarray"]).encode()), # type: ignore[index, call-overload] ) await store.set( "air/.zattrs", - cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["air/.zattrs"]).encode()), + cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["air/.zattrs"]).encode()), # type: ignore[index, call-overload] ) await store.set( "time/.zarray", - cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["time/.zarray"]).encode()), + cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["time/.zarray"]).encode()), # type: ignore[index, call-overload] ) await store.set( "time/.zattrs", - cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["time/.zattrs"]).encode()), + cpu.Buffer.from_bytes(json.dumps(zmetadata["metadata"]["time/.zattrs"]).encode()), # type: ignore[index, call-overload] ) # and a nested group for fun @@ -194,13 +195,13 @@ async def v2_consolidated_metadata( await store.set( "nested/array/.zarray", cpu.Buffer.from_bytes( - json.dumps(zmetadata["metadata"]["nested/array/.zarray"]).encode() + json.dumps(zmetadata["metadata"]["nested/array/.zarray"]).encode() # type: ignore[index, call-overload] ), ) await store.set( "nested/array/.zattrs", cpu.Buffer.from_bytes( - json.dumps(zmetadata["metadata"]["nested/array/.zattrs"]).encode() + json.dumps(zmetadata["metadata"]["nested/array/.zattrs"]).encode() # type: ignore[index, call-overload] ), ) @@ -208,7 +209,7 @@ async def v2_consolidated_metadata( async def test_read_consolidated_metadata( self, v2_consolidated_metadata: zarr.storage.MemoryStore - ): + ) -> None: # .zgroup, .zattrs, .metadata store = v2_consolidated_metadata group = zarr.open_consolidated(store=store, zarr_format=2) @@ -271,10 +272,13 @@ async def test_read_consolidated_metadata( result = group.metadata.consolidated_metadata assert result == expected - async def test_getitem_consolidated(self, v2_consolidated_metadata): + async def test_getitem_consolidated( + self, v2_consolidated_metadata: zarr.storage.MemoryStore + ) -> None: store = v2_consolidated_metadata group = await zarr.api.asynchronous.open_consolidated(store=store, zarr_format=2) air = await group.getitem("air") + assert isinstance(air, zarr.AsyncArray) assert air.metadata.shape == (730,) @@ -320,8 +324,10 @@ def test_zstd_checksum() -> None: @pytest.mark.parametrize("fill_value", [np.void((0, 0), np.dtype([("foo", "i4"), ("bar", "i4")]))]) -def test_structured_dtype_fill_value_serialization(tmp_path, fill_value): - zarr_format = 2 +def test_structured_dtype_fill_value_serialization( + tmp_path: Path, fill_value: np.void | np.dtype[Any] +) -> None: + zarr_format: Literal[2] = 2 group_path = tmp_path / "test.zarr" root_group = zarr.open_group(group_path, mode="w", zarr_format=zarr_format) dtype = np.dtype([("foo", "i4"), ("bar", "i4")]) @@ -335,5 +341,5 @@ def test_structured_dtype_fill_value_serialization(tmp_path, fill_value): zarr.consolidate_metadata(root_group.store, zarr_format=zarr_format) root_group = zarr.open_group(group_path, mode="r") - observed = root_group.metadata.consolidated_metadata.metadata["structured_dtype"].fill_value + observed = root_group.metadata.consolidated_metadata.metadata["structured_dtype"].fill_value # type: ignore[union-attr] assert observed == fill_value diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 4f385afa6d..2093696454 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -128,7 +128,7 @@ def test_jsonify_fill_value_complex(fill_value: Any, dtype_str: str) -> None: Test that parse_fill_value(fill_value, dtype) correctly handles complex values represented as length-2 sequences """ - zarr_format = 3 + zarr_format: Literal[3] = 3 dtype = get_data_type_from_native_dtype(dtype_str) expected = dtype.to_native_dtype().type(complex(*fill_value)) observed = dtype.from_json_scalar(fill_value, zarr_format=zarr_format) @@ -249,7 +249,7 @@ def test_metadata_to_dict( @pytest.mark.parametrize("indent", [2, 4, None]) -def test_json_indent(indent: int): +def test_json_indent(indent: int) -> None: with config.set({"json_indent": indent}): m = GroupMetadata() d = m.to_buffer_dict(default_buffer_prototype())["zarr.json"].to_bytes() @@ -258,9 +258,9 @@ def test_json_indent(indent: int): @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897]) @pytest.mark.parametrize("precision", ["ns", "D"]) -async def test_datetime_metadata(fill_value: int, precision: str) -> None: +async def test_datetime_metadata(fill_value: int, precision: Literal["ns", "D"]) -> None: dtype = DateTime64(unit=precision) - metadata_dict = { + metadata_dict: dict[str, Any] = { "zarr_format": 3, "node_type": "array", "shape": (1,), @@ -284,7 +284,7 @@ async def test_datetime_metadata(fill_value: int, precision: str) -> None: ("data_type", "fill_value"), [("uint8", {}), ("int32", [0, 1]), ("float32", "foo")] ) async def test_invalid_fill_value_raises(data_type: str, fill_value: float) -> None: - metadata_dict = { + metadata_dict: dict[str, Any] = { "zarr_format": 3, "node_type": "array", "shape": (1,), @@ -301,7 +301,7 @@ async def test_invalid_fill_value_raises(data_type: str, fill_value: float) -> N @pytest.mark.parametrize("fill_value", [("NaN"), "Infinity", "-Infinity"]) async def test_special_float_fill_values(fill_value: str) -> None: - metadata_dict = { + metadata_dict: dict[str, Any] = { "zarr_format": 3, "node_type": "array", "shape": (1,), From 0864ee56c3b5f5fa966e1ce71484a541f927e5e6 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Thu, 21 Aug 2025 10:52:11 +0300 Subject: [PATCH 076/468] Use PyPA well-known labels under `project.urls` (#3386) https://packaging.python.org/en/latest/specifications/well-known-project-urls/#well-known-labels Co-authored-by: Davis Bennett --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index dffca78808..52b032f771 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -115,11 +115,11 @@ docs = [ [project.urls] -"Bug Tracker" = "https://github.com/zarr-developers/zarr-python/issues" -Changelog = "https://zarr.readthedocs.io/en/stable/release-notes.html" +issues = "https://github.com/zarr-developers/zarr-python/issues" +changelog = "https://zarr.readthedocs.io/en/stable/release-notes.html" Discussions = "https://github.com/zarr-developers/zarr-python/discussions" -Documentation = "https://zarr.readthedocs.io/" -Homepage = "https://github.com/zarr-developers/zarr-python" +documentation = "https://zarr.readthedocs.io/" +homepage = "https://github.com/zarr-developers/zarr-python" [dependency-groups] dev = [ From c019a5f267fcfee757e5f764a3e3f088a22509da Mon Sep 17 00:00:00 2001 From: ruaridhg <32329546+ruaridhg@users.noreply.github.com> Date: Thu, 21 Aug 2025 09:13:22 +0100 Subject: [PATCH 077/468] Added ArrayNotFoundError (#3367) * Added ArrayNotFoundError * Add changes file * Add ArrayNotFoundError to test_api.py * Fix linting issue * Address PR comments and add tests to cover new cases * Fix linting errors * Add type: ignore comments back in * Change inheritance of errors so Group and Array inherit from Node * Fix missing import * Update changes/3367.bugfix.rst --------- Co-authored-by: ruaridhg Co-authored-by: Davis Bennett --- changes/3367.bugfix.rst | 1 + src/zarr/api/asynchronous.py | 5 +++-- src/zarr/core/array.py | 25 +++++++++++++++++---- src/zarr/errors.py | 42 ++++++++++++++++++++++++++++++++++-- tests/test_api.py | 41 +++++++++++++++++++++++++++-------- 5 files changed, 97 insertions(+), 17 deletions(-) create mode 100644 changes/3367.bugfix.rst diff --git a/changes/3367.bugfix.rst b/changes/3367.bugfix.rst new file mode 100644 index 0000000000..9edef00ca6 --- /dev/null +++ b/changes/3367.bugfix.rst @@ -0,0 +1 @@ +Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected. \ No newline at end of file diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index d3613f7c05..fdbd3b34bd 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -39,6 +39,7 @@ ) from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata, ArrayV3Metadata from zarr.errors import ( + ArrayNotFoundError, GroupNotFoundError, NodeTypeValidationError, ZarrDeprecationWarning, @@ -1257,7 +1258,7 @@ async def open_array( try: return await AsyncArray.open(store_path, zarr_format=zarr_format) - except FileNotFoundError: + except FileNotFoundError as err: if not store_path.read_only and mode in _CREATE_MODES: overwrite = _infer_overwrite(mode) _zarr_format = zarr_format or _default_zarr_format() @@ -1267,7 +1268,7 @@ async def open_array( overwrite=overwrite, **kwargs, ) - raise + raise ArrayNotFoundError(store_path.store, store_path.path) from err async def open_like( diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 4fcddaa8b5..7b3f11d8cd 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -117,7 +117,12 @@ ) from zarr.core.metadata.v3 import parse_node_type_array from zarr.core.sync import sync -from zarr.errors import MetadataValidationError, ZarrDeprecationWarning, ZarrUserWarning +from zarr.errors import ( + ArrayNotFoundError, + MetadataValidationError, + ZarrDeprecationWarning, + ZarrUserWarning, +) from zarr.registry import ( _parse_array_array_codec, _parse_array_bytes_codec, @@ -216,11 +221,19 @@ async def get_array_metadata( (store_path / ZATTRS_JSON).get(prototype=cpu_buffer_prototype), ) if zarray_bytes is None: - raise FileNotFoundError(store_path) + msg = ( + "A Zarr V2 array metadata document was not found in store " + f"{store_path.store!r} at path {store_path.path!r}." + ) + raise ArrayNotFoundError(msg) elif zarr_format == 3: zarr_json_bytes = await (store_path / ZARR_JSON).get(prototype=cpu_buffer_prototype) if zarr_json_bytes is None: - raise FileNotFoundError(store_path) + msg = ( + "A Zarr V3 array metadata document was not found in store " + f"{store_path.store!r} at path {store_path.path!r}." + ) + raise ArrayNotFoundError(msg) elif zarr_format is None: zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather( (store_path / ZARR_JSON).get(prototype=cpu_buffer_prototype), @@ -232,7 +245,11 @@ async def get_array_metadata( msg = f"Both zarr.json (Zarr format 3) and .zarray (Zarr format 2) metadata objects exist at {store_path}. Zarr v3 will be used." warnings.warn(msg, category=ZarrUserWarning, stacklevel=1) if zarr_json_bytes is None and zarray_bytes is None: - raise FileNotFoundError(store_path) + msg = ( + f"Neither Zarr V3 nor Zarr V2 array metadata documents " + f"were found in store {store_path.store!r} at path {store_path.path!r}." + ) + raise ArrayNotFoundError(msg) # set zarr_format based on which keys were found if zarr_json_bytes is not None: zarr_format = 3 diff --git a/src/zarr/errors.py b/src/zarr/errors.py index 0055ea3c6c..867e801e18 100644 --- a/src/zarr/errors.py +++ b/src/zarr/errors.py @@ -1,6 +1,7 @@ from typing import Any __all__ = [ + "ArrayNotFoundError", "BaseZarrError", "ContainsArrayAndGroupError", "ContainsArrayError", @@ -26,12 +27,49 @@ def __init__(self, *args: Any) -> None: super().__init__(self._msg.format(*args)) -class GroupNotFoundError(BaseZarrError, FileNotFoundError): +class NodeNotFoundError(BaseZarrError, FileNotFoundError): + """ + Raised when a node (array or group) is not found at a certain path. + """ + + def __init__(self, *args: Any) -> None: + if len(args) == 1: + # Pre-formatted message + super(BaseZarrError, self).__init__(args[0]) + else: + # Store and path arguments - format them + _msg = "No node found in store {!r} at path {!r}" + super(BaseZarrError, self).__init__(_msg.format(*args)) + + +class ArrayNotFoundError(NodeNotFoundError): + """ + Raised when an array isn't found at a certain path. + """ + + def __init__(self, *args: Any) -> None: + if len(args) == 1: + # Pre-formatted message + super(BaseZarrError, self).__init__(args[0]) + else: + # Store and path arguments - format them + _msg = "No array found in store {!r} at path {!r}" + super(BaseZarrError, self).__init__(_msg.format(*args)) + + +class GroupNotFoundError(NodeNotFoundError): """ Raised when a group isn't found at a certain path. """ - _msg = "No group found in store {!r} at path {!r}" + def __init__(self, *args: Any) -> None: + if len(args) == 1: + # Pre-formatted message + super(BaseZarrError, self).__init__(args[0]) + else: + # Store and path arguments - format them + _msg = "No group found in store {!r} at path {!r}" + super(BaseZarrError, self).__init__(_msg.format(*args)) class ContainsGroupError(BaseZarrError): diff --git a/tests/test_api.py b/tests/test_api.py index 5447a0aa39..3668ef306a 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -6,7 +6,7 @@ import zarr.codecs import zarr.storage -from zarr.core.array import init_array +from zarr.core.array import AsyncArray, init_array from zarr.storage import LocalStore, ZipStore from zarr.storage._common import StorePath @@ -42,7 +42,13 @@ save_group, ) from zarr.core.buffer import NDArrayLike -from zarr.errors import MetadataValidationError, ZarrDeprecationWarning, ZarrUserWarning +from zarr.errors import ( + ArrayNotFoundError, + MetadataValidationError, + NodeNotFoundError, + ZarrDeprecationWarning, + ZarrUserWarning, +) from zarr.storage import MemoryStore from zarr.storage._utils import normalize_path from zarr.testing.utils import gpu_test @@ -70,11 +76,11 @@ def test_create(memory_store: Store) -> None: # create array with float shape with pytest.raises(TypeError): - z = create(shape=(400.5, 100), store=store, overwrite=True) # type: ignore [arg-type] + z = create(shape=(400.5, 100), store=store, overwrite=True) # type: ignore[arg-type] # create array with float chunk shape with pytest.raises(TypeError): - z = create(shape=(400, 100), chunks=(16, 16.5), store=store, overwrite=True) # type: ignore [arg-type] + z = create(shape=(400, 100), chunks=(16, 16.5), store=store, overwrite=True) # type: ignore[arg-type] # TODO: parametrize over everything this function takes @@ -185,10 +191,27 @@ async def test_open_array(memory_store: MemoryStore, zarr_format: ZarrFormat) -> assert z.read_only # path not found - with pytest.raises(FileNotFoundError): + with pytest.raises(NodeNotFoundError): zarr.api.synchronous.open(store="doesnotexist", mode="r", zarr_format=zarr_format) +@pytest.mark.asyncio +async def test_async_array_open_array_not_found() -> None: + """Test that AsyncArray.open raises ArrayNotFoundError when array doesn't exist""" + store = MemoryStore() + # Try to open an array that does not exist + with pytest.raises(ArrayNotFoundError): + await AsyncArray.open(store, zarr_format=2) + + +def test_array_open_array_not_found_sync() -> None: + """Test that Array.open raises ArrayNotFoundError when array doesn't exist""" + store = MemoryStore() + # Try to open an array that does not exist + with pytest.raises(ArrayNotFoundError): + Array.open(store) + + @pytest.mark.parametrize("store", ["memory", "local", "zip"], indirect=True) def test_v2_and_v3_exist_at_same_path(store: Store) -> None: zarr.create_array(store, shape=(10,), dtype="uint8", zarr_format=3) @@ -266,7 +289,7 @@ def test_save(store: Store, n_args: int, n_kwargs: int, path: None | str) -> Non assert isinstance(array, Array) assert_array_equal(array[:], data) else: - save(store, *args, path=path, **kwargs) # type: ignore [arg-type] + save(store, *args, path=path, **kwargs) # type: ignore[arg-type] group = zarr.api.synchronous.open(store, path=path) assert isinstance(group, Group) for array in group.array_values(): @@ -1208,13 +1231,13 @@ async def test_metadata_validation_error() -> None: MetadataValidationError, match="Invalid value for 'zarr_format'. Expected '2, 3, or None'. Got '3.0'.", ): - await zarr.api.asynchronous.open_group(zarr_format="3.0") # type: ignore [arg-type] + await zarr.api.asynchronous.open_group(zarr_format="3.0") # type: ignore[arg-type] with pytest.raises( MetadataValidationError, match="Invalid value for 'zarr_format'. Expected '2, 3, or None'. Got '3.0'.", ): - await zarr.api.asynchronous.open_array(shape=(1,), zarr_format="3.0") # type: ignore [arg-type] + await zarr.api.asynchronous.open_array(shape=(1,), zarr_format="3.0") # type: ignore[arg-type] @pytest.mark.parametrize( @@ -1224,7 +1247,7 @@ async def test_metadata_validation_error() -> None: ) def test_open_array_with_mode_r_plus(store: Store, zarr_format: ZarrFormat) -> None: # 'r+' means read/write (must exist) - with pytest.raises(FileNotFoundError): + with pytest.raises(ArrayNotFoundError): zarr.open_array(store=store, mode="r+", zarr_format=zarr_format) zarr.ones(store=store, shape=(3, 3), zarr_format=zarr_format) z2 = zarr.open_array(store=store, mode="r+") From 94983362f06f9bb4be3f04562b179549e36a87c4 Mon Sep 17 00:00:00 2001 From: Justus Magin Date: Thu, 21 Aug 2025 15:37:43 +0200 Subject: [PATCH 078/468] reraise the `KeyError` for unknown codecs with a more specific error class (#3395) * create a error class for unknown codecs * reraise as a unknown codec error * check that `parse_codecs` raises (v3 only) * monkeypatch to always work with a empty registry * immediatly format the error * changelog --- changes/3395.bugfix.rst | 1 + src/zarr/core/metadata/v3.py | 8 ++++++-- src/zarr/errors.py | 8 ++++++++ tests/test_metadata/test_v3.py | 17 ++++++++++++++++- 4 files changed, 31 insertions(+), 3 deletions(-) create mode 100644 changes/3395.bugfix.rst diff --git a/changes/3395.bugfix.rst b/changes/3395.bugfix.rst new file mode 100644 index 0000000000..73627c174d --- /dev/null +++ b/changes/3395.bugfix.rst @@ -0,0 +1 @@ +Raise a Zarr-specific error class when a codec can't be found by name when deserializing the given codecs. This avoids hiding this error behind a "not part of a zarr hierarchy" warning. diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index e17edb999c..d1420b1ddd 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -34,7 +34,7 @@ ) from zarr.core.config import config from zarr.core.metadata.common import parse_attributes -from zarr.errors import MetadataValidationError, NodeTypeValidationError +from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError from zarr.registry import get_codec_class @@ -63,7 +63,11 @@ def parse_codecs(data: object) -> tuple[Codec, ...]: out += (c,) else: name_parsed, _ = parse_named_configuration(c, require_configuration=False) - out += (get_codec_class(name_parsed).from_dict(c),) + + try: + out += (get_codec_class(name_parsed).from_dict(c),) + except KeyError as e: + raise UnknownCodecError(f"Unknown codec: {e.args[0]!r}") from e return out diff --git a/src/zarr/errors.py b/src/zarr/errors.py index 867e801e18..472199ff1b 100644 --- a/src/zarr/errors.py +++ b/src/zarr/errors.py @@ -101,6 +101,14 @@ class MetadataValidationError(BaseZarrError): _msg = "Invalid value for '{}'. Expected '{}'. Got '{}'." +class UnknownCodecError(BaseZarrError): + """ + Raised when a unknown codec was used. + """ + + _msg = "{}" + + class NodeTypeValidationError(MetadataValidationError): """ Specialized exception when the node_type of the metadata document is incorrect. diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 2093696454..4fdcce7b6b 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -17,10 +17,11 @@ from zarr.core.group import GroupMetadata, parse_node_type from zarr.core.metadata.v3 import ( ArrayV3Metadata, + parse_codecs, parse_dimension_names, parse_zarr_format, ) -from zarr.errors import MetadataValidationError, NodeTypeValidationError +from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError if TYPE_CHECKING: from collections.abc import Sequence @@ -323,3 +324,17 @@ async def test_special_float_fill_values(fill_value: str) -> None: elif fill_value == "-Infinity": assert np.isneginf(m.fill_value) assert d["fill_value"] == "-Infinity" + + +def test_parse_codecs_unknown_codec_raises(monkeypatch: pytest.MonkeyPatch) -> None: + from collections import defaultdict + + import zarr.registry + from zarr.registry import Registry + + # to make sure the codec is always unknown (not sure if that's necessary) + monkeypatch.setattr(zarr.registry, "__codec_registries", defaultdict(Registry)) + + codecs = [{"name": "unknown"}] + with pytest.raises(UnknownCodecError): + parse_codecs(codecs) From c9eefe663b34b019e9673bcaa37a88aae6158280 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 22 Aug 2025 17:20:54 +0200 Subject: [PATCH 079/468] fix chunk/shard iteration (#3299) * factor array element iteration routines into stand-alone functions, and add a failing test * add shard_grid_shape, chunk_grid_shape Co-authored-by: Bojidar Marinov * docstrings * handle null shards * use shard_grid_shape instead of cdata_shape in nchunks * add improved set of low-level iteration routines for arrays * correct deprecation message * check for deprecation warnings around iter_chunk_keys * plug tiny coverage holes * lint * rename chunks_initialized to shards_initialized * add nshards, nshards_initialized * fix doctests * remove iter_chunk_keys * make nchunks_initialized report the product of the number of shards and the number of chunks per shard * changelog * correct name of changelog entry * add test for unsharded data * add test for cdata_shape, shard_grid_shape, chunk_grid_shape * add nshards * expand nchunks_initialized test conditions * restore memorystore * expand test parametrization * unbreak tests * include asyncarray cdata_shape in test * make new API private * docstrings * remove references to private API * Update src/zarr/core/array.py Co-authored-by: Deepak Cherian * Update src/zarr/core/indexing.py Co-authored-by: Deepak Cherian * fix docstring --------- Co-authored-by: Bojidar Marinov Co-authored-by: Deepak Cherian --- changes/3299.bugfix.rst | 4 + src/zarr/core/array.py | 534 ++++++++++++++++++++++++++++++++------ src/zarr/core/indexing.py | 78 +++++- tests/test_array.py | 288 ++++++++++++++++++-- tests/test_indexing.py | 68 +++++ 5 files changed, 865 insertions(+), 107 deletions(-) create mode 100644 changes/3299.bugfix.rst diff --git a/changes/3299.bugfix.rst b/changes/3299.bugfix.rst new file mode 100644 index 0000000000..771fb846b4 --- /dev/null +++ b/changes/3299.bugfix.rst @@ -0,0 +1,4 @@ +Fix a bug in ``create_array`` caused by iterating over chunk-aligned regions instead of +shard-aligned regions when writing data. Additionally, the behavior of ``nchunks_initialized`` +has been adjusted. This function consistently reports the number of chunks present in stored objects, +even when the array uses the sharding codec. \ No newline at end of file diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 7b3f11d8cd..4b34c31de1 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -93,6 +93,7 @@ Selection, VIndex, _iter_grid, + _iter_regions, check_fields, check_no_multi_fields, is_pure_fancy_indexing, @@ -714,7 +715,7 @@ async def _create( overwrite=overwrite, ) else: - raise ValueError(f"Unsupported zarr_format. Got: {zarr_format}") + raise ValueError(f"zarr_format must be 2 or 3, got {zarr_format}") # pragma: no cover if data is not None: # insert user-provided data @@ -1206,27 +1207,74 @@ def cdata_shape(self) -> tuple[int, ...]: Returns ------- - Tuple[int] + tuple[int, ...] The shape of the chunk grid for this array. """ - return tuple(starmap(ceildiv, zip(self.shape, self.chunks, strict=False))) + return self._chunk_grid_shape + + @property + def _chunk_grid_shape(self) -> tuple[int, ...]: + """ + The shape of the chunk grid for this array. + + Returns + ------- + tuple[int, ...] + The shape of the chunk grid for this array. + """ + return tuple(starmap(ceildiv, zip(self.shape, self.chunks, strict=True))) + + @property + def _shard_grid_shape(self) -> tuple[int, ...]: + """ + The shape of the shard grid for this array. + + Returns + ------- + tuple[int, ...] + The shape of the shard grid for this array. + """ + if self.shards is None: + shard_shape = self.chunks + else: + shard_shape = self.shards + return tuple(starmap(ceildiv, zip(self.shape, shard_shape, strict=True))) @property def nchunks(self) -> int: """ - The number of chunks in the stored representation of this array. + The number of chunks in this array. + + Note that if a sharding codec is used, then the number of chunks may exceed the number of + stored objects supporting this array. Returns ------- int The total number of chunks in the array. """ - return product(self.cdata_shape) + return product(self._chunk_grid_shape) + + @property + def _nshards(self) -> int: + """ + The number of shards in this array. + + Returns + ------- + int + The total number of shards in the array. + """ + return product(self._shard_grid_shape) async def nchunks_initialized(self) -> int: """ - Calculate the number of chunks that have been initialized, i.e. the number of chunks that have - been persisted to the storage backend. + Calculate the number of chunks that have been initialized in storage. + + This value is calculated as the product of the number of initialized shards and the number + of chunks per shard. For arrays that do not use sharding, the number of chunks per shard is + effectively 1, and in that case the number of chunks initialized is the same as the number + of stored objects associated with an array. Returns ------- @@ -1240,14 +1288,47 @@ async def nchunks_initialized(self) -> int: Examples -------- - >>> arr = await zarr.api.asynchronous.create(shape=(10,), chunks=(2,)) + >>> arr = await zarr.api.asynchronous.create(shape=(10,), chunks=(1,), shards=(2,)) >>> await arr.nchunks_initialized() 0 >>> await arr.setitem(slice(5), 1) >>> await arr.nchunks_initialized() + 6 + """ + if self.shards is None: + chunks_per_shard = 1 + else: + chunks_per_shard = product( + tuple(a // b for a, b in zip(self.shards, self.chunks, strict=True)) + ) + return (await self._nshards_initialized()) * chunks_per_shard + + async def _nshards_initialized(self) -> int: + """ + Calculate the number of shards that have been initialized in storage. + + This is the number of shards that have been persisted to the storage backend. + + Returns + ------- + nshards_initialized : int + The number of shards that have been initialized. + + Notes + ----- + On :class:`AsyncArray` this is an asynchronous method, unlike the (synchronous) + property :attr:`Array._nshards_initialized`. + + Examples + -------- + >>> arr = await zarr.api.asynchronous.create(shape=(10,), chunks=(2,)) + >>> await arr._nshards_initialized() + 0 + >>> await arr.setitem(slice(5), 1) + >>> await arr._nshards_initialized() 3 """ - return len(await chunks_initialized(self)) + return len(await _shards_initialized(self)) async def nbytes_stored(self) -> int: return await self.store_path.store.getsize_prefix(self.store_path.path) @@ -1256,8 +1337,9 @@ def _iter_chunk_coords( self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None ) -> Iterator[tuple[int, ...]]: """ - Create an iterator over the coordinates of chunks in chunk grid space. If the `origin` - keyword is used, iteration will start at the chunk index specified by `origin`. + Create an iterator over the coordinates of chunks in chunk grid space. + + If the `origin` keyword is used, iteration will start at the chunk index specified by `origin`. The default behavior is to start at the origin of the grid coordinate space. If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region ranging from `[origin, origin selection_shape]`, where the upper bound is exclusive as @@ -1275,21 +1357,56 @@ def _iter_chunk_coords( chunk_coords: tuple[int, ...] The coordinates of each chunk in the selection. """ - return _iter_grid(self.cdata_shape, origin=origin, selection_shape=selection_shape) + return _iter_chunk_coords( + array=self, + origin=origin, + selection_shape=selection_shape, + ) + + def _iter_shard_coords( + self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None + ) -> Iterator[tuple[int, ...]]: + """ + Create an iterator over the coordinates of shards in shard grid space. + + Note that + + If the `origin` keyword is used, iteration will start at the shard index specified by `origin`. + The default behavior is to start at the origin of the grid coordinate space. + If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region + ranging from `[origin, origin selection_shape]`, where the upper bound is exclusive as + per python indexing conventions. + + Parameters + ---------- + origin : Sequence[int] | None, default=None + The origin of the selection relative to the array's shard grid. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in shard grid coordinates. + + Yields + ------ + chunk_coords: tuple[int, ...] + The coordinates of each shard in the selection. + """ + return _iter_shard_coords( + array=self, + origin=origin, + selection_shape=selection_shape, + ) - def _iter_chunk_keys( + def _iter_shard_keys( self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None ) -> Iterator[str]: """ - Iterate over the storage keys of each chunk, relative to an optional origin, and optionally - limited to a contiguous region in chunk grid coordinates. + Iterate over the keys of the stored objects supporting this array. Parameters ---------- origin : Sequence[int] | None, default=None The origin of the selection relative to the array's chunk grid. selection_shape : Sequence[int] | None, default=None - The shape of the selection in chunk grid coordinates. + The shape of the selection in shard grid coordinates. Yields ------ @@ -1297,9 +1414,11 @@ def _iter_chunk_keys( The storage key of each chunk in the selection. """ # Iterate over the coordinates of chunks in chunk grid space. - for k in self._iter_chunk_coords(origin=origin, selection_shape=selection_shape): - # Encode the chunk key from the chunk coordinates. - yield self.metadata.encode_chunk_key(k) + return _iter_shard_keys( + array=self, + origin=origin, + selection_shape=selection_shape, + ) def _iter_chunk_regions( self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -1319,15 +1438,31 @@ def _iter_chunk_regions( region: tuple[slice, ...] A tuple of slice objects representing the region spanned by each chunk in the selection. """ - for cgrid_position in self._iter_chunk_coords( - origin=origin, selection_shape=selection_shape - ): - out: tuple[slice, ...] = () - for c_pos, c_shape in zip(cgrid_position, self.chunks, strict=False): - start = c_pos * c_shape - stop = start + c_shape - out += (slice(start, stop, 1),) - yield out + return _iter_chunk_regions( + array=self, + origin=origin, + selection_shape=selection_shape, + ) + + def _iter_shard_regions( + self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None + ) -> Iterator[tuple[slice, ...]]: + """ + Iterate over the regions spanned by each shard. + + Parameters + ---------- + origin : Sequence[int] | None, default=None + The origin of the selection relative to the array's shard grid. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in shard grid coordinates. + + Yields + ------ + region: tuple[slice, ...] + A tuple of slice objects representing the region spanned by each shard in the selection. + """ + return _iter_shard_regions(array=self, origin=origin, selection_shape=selection_shape) @property def nbytes(self) -> int: @@ -1833,7 +1968,7 @@ async def info_complete(self) -> Any: A property giving just the statically known information about an array. """ return self._info( - await self.nchunks_initialized(), + await self._nshards_initialized(), await self.store_path.store.getsize_prefix(self.store_path.path), ) @@ -2280,41 +2415,38 @@ def cdata_shape(self) -> tuple[int, ...]: """ The shape of the chunk grid for this array. """ - return tuple(starmap(ceildiv, zip(self.shape, self.chunks, strict=False))) + return self._async_array._chunk_grid_shape @property - def nchunks(self) -> int: + def _chunk_grid_shape(self) -> tuple[int, ...]: """ - The number of chunks in the stored representation of this array. + The shape of the chunk grid for this array. """ - return self._async_array.nchunks + return self._async_array._chunk_grid_shape - def _iter_chunk_coords( - self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None - ) -> Iterator[tuple[int, ...]]: + @property + def _shard_grid_shape(self) -> tuple[int, ...]: """ - Create an iterator over the coordinates of chunks in chunk grid space. If the `origin` - keyword is used, iteration will start at the chunk index specified by `origin`. - The default behavior is to start at the origin of the grid coordinate space. - If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region - ranging from `[origin, origin + selection_shape]`, where the upper bound is exclusive as - per python indexing conventions. + The shape of the shard grid for this array. + """ + return self._async_array._shard_grid_shape - Parameters - ---------- - origin : Sequence[int] | None, default=None - The origin of the selection relative to the array's chunk grid. - selection_shape : Sequence[int] | None, default=None - The shape of the selection in chunk grid coordinates. + @property + def nchunks(self) -> int: + """ + The number of chunks in this array. - Yields - ------ - chunk_coords: tuple[int, ...] - The coordinates of each chunk in the selection. + Note that if a sharding codec is used, then the number of chunks may exceed the number of + stored objects supporting this array. """ - yield from self._async_array._iter_chunk_coords( - origin=origin, selection_shape=selection_shape - ) + return self._async_array.nchunks + + @property + def _nshards(self) -> int: + """ + The number of shards in the stored representation of this array. + """ + return self._async_array._nshards @property def nbytes(self) -> int: @@ -2334,30 +2466,51 @@ def nbytes(self) -> int: @property def nchunks_initialized(self) -> int: """ - Calculate the number of chunks that have been initialized, i.e. the number of chunks that have - been persisted to the storage backend. + Calculate the number of chunks that have been initialized in storage. + + This value is calculated as the product of the number of initialized shards and the number of + chunks per shard. For arrays that do not use sharding, the number of chunks per shard is effectively 1, + and in that case the number of chunks initialized is the same as the number of stored objects associated with an + array. For a direct count of the number of initialized stored objects, see ``nshards_initialized``. Returns ------- nchunks_initialized : int The number of chunks that have been initialized. - Notes - ----- - On :class:`Array` this is a (synchronous) property, unlike asynchronous function - :meth:`AsyncArray.nchunks_initialized`. - Examples -------- - >>> arr = await zarr.create(shape=(10,), chunks=(2,)) + >>> arr = zarr.create_array(store={}, shape=(10,), chunks=(1,), shards=(2,)) >>> arr.nchunks_initialized 0 >>> arr[:5] = 1 >>> arr.nchunks_initialized - 3 + 6 """ return sync(self._async_array.nchunks_initialized()) + @property + def _nshards_initialized(self) -> int: + """ + Calculate the number of shards that have been initialized, i.e. the number of shards that have + been persisted to the storage backend. + + Returns + ------- + nshards_initialized : int + The number of shards that have been initialized. + + Examples + -------- + >>> arr = await zarr.create(shape=(10,), chunks=(2,)) + >>> arr._nshards_initialized + 0 + >>> arr[:5] = 1 + >>> arr._nshard_initialized + 3 + """ + return sync(self._async_array._nshards_initialized()) + def nbytes_stored(self) -> int: """ Determine the size, in bytes, of the array actually written to the store. @@ -2368,13 +2521,39 @@ def nbytes_stored(self) -> int: """ return sync(self._async_array.nbytes_stored()) - def _iter_chunk_keys( + def _iter_shard_keys( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None ) -> Iterator[str]: """ - Iterate over the storage keys of each chunk, relative to an optional origin, and optionally + Iterate over the storage keys of each shard, relative to an optional origin, and optionally limited to a contiguous region in chunk grid coordinates. + Parameters + ---------- + origin : Sequence[int] | None, default=None + The origin of the selection relative to the array's shard grid. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in shard grid coordinates. + + Yields + ------ + str + The storage key of each shard in the selection. + """ + return self._async_array._iter_shard_keys(origin=origin, selection_shape=selection_shape) + + def _iter_chunk_coords( + self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None + ) -> Iterator[tuple[int, ...]]: + """ + Create an iterator over the coordinates of chunks in chunk grid space. + + If the `origin` keyword is used, iteration will start at the chunk index specified by `origin`. + The default behavior is to start at the origin of the grid coordinate space. + If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region + ranging from `[origin, origin + selection_shape]`, where the upper bound is exclusive as + per python indexing conventions. + Parameters ---------- origin : Sequence[int] | None, default=None @@ -2384,12 +2563,36 @@ def _iter_chunk_keys( Yields ------ - key: str - The storage key of each chunk in the selection. + tuple[int, ...] + The coordinates of each chunk in the selection. """ - yield from self._async_array._iter_chunk_keys( - origin=origin, selection_shape=selection_shape - ) + return self._async_array._iter_chunk_coords(origin=origin, selection_shape=selection_shape) + + def _iter_shard_coords( + self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None + ) -> Iterator[tuple[int, ...]]: + """ + Create an iterator over the coordinates of shards in shard grid space. + + If the `origin` keyword is used, iteration will start at the shard index specified by `origin`. + The default behavior is to start at the origin of the grid coordinate space. + If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region + ranging from `[origin, origin selection_shape]`, where the upper bound is exclusive as + per python indexing conventions. + + Parameters + ---------- + origin : Sequence[int] | None, default=None + The origin of the selection relative to the array's shard grid. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in shard grid coordinates. + + Yields + ------ + tuple[int, ...] + The coordinates of each shard in the selection. + """ + return self._async_array._iter_shard_coords(origin=origin, selection_shape=selection_shape) def _iter_chunk_regions( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -2406,12 +2609,30 @@ def _iter_chunk_regions( Yields ------ - region: tuple[slice, ...] + tuple[slice, ...] A tuple of slice objects representing the region spanned by each chunk in the selection. """ - yield from self._async_array._iter_chunk_regions( - origin=origin, selection_shape=selection_shape - ) + return self._async_array._iter_chunk_regions(origin=origin, selection_shape=selection_shape) + + def _iter_shard_regions( + self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None + ) -> Iterator[tuple[slice, ...]]: + """ + Iterate over the regions spanned by each shard. + + Parameters + ---------- + origin : Sequence[int] | None, default=None + The origin of the selection relative to the array's chunk grid. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in chunk grid coordinates. + + Yields + ------ + tuple[slice, ...] + A tuple of slice objects representing the region spanned by each chunk in the selection. + """ + return self._async_array._iter_shard_regions(origin=origin, selection_shape=selection_shape) def __array__( self, dtype: npt.DTypeLike | None = None, copy: bool | None = None @@ -3848,7 +4069,7 @@ def info_complete(self) -> Any: return sync(self._async_array.info_complete()) -async def chunks_initialized( +async def _shards_initialized( array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], ) -> tuple[str, ...]: """ @@ -3876,7 +4097,7 @@ async def chunks_initialized( _relativize_path(path=key, prefix=array.store_path.path) for key in store_contents ] return tuple( - chunk_key for chunk_key in array._iter_chunk_keys() if chunk_key in store_contents_relative + chunk_key for chunk_key in array._iter_shard_keys() if chunk_key in store_contents_relative ) @@ -4188,7 +4409,7 @@ async def _copy_array_region( # Stream data from the source array to the new array await concurrent_map( - [(region, data) for region in result._iter_chunk_regions()], + [(region, data) for region in result._iter_shard_regions()], _copy_array_region, zarr.core.config.config.get("async.concurrency"), ) @@ -5007,3 +5228,160 @@ def _parse_data_params( raise ValueError(msg) dtype_out = data.dtype return data, shape_out, dtype_out + + +def _iter_chunk_coords( + array: Array | AsyncArray[Any], + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, +) -> Iterator[tuple[int, ...]]: + """ + Create an iterator over the coordinates of chunks in chunk grid space. If the `origin` + keyword is used, iteration will start at the chunk index specified by `origin`. + The default behavior is to start at the origin of the grid coordinate space. + If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region + ranging from `[origin, origin selection_shape]`, where the upper bound is exclusive as + per python indexing conventions. + + Parameters + ---------- + array : Array | AsyncArray + The array to iterate over. + origin : Sequence[int] | None, default=None + The origin of the selection in grid coordinates. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in grid coordinates. + + Yields + ------ + chunk_coords: tuple[int, ...] + The coordinates of each chunk in the selection. + """ + return _iter_grid(array._chunk_grid_shape, origin=origin, selection_shape=selection_shape) + + +def _iter_shard_coords( + array: Array | AsyncArray[Any], + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, +) -> Iterator[tuple[int, ...]]: + """ + Create an iterator over the coordinates of shards in shard grid space. If the `origin` + keyword is used, iteration will start at the shard index specified by `origin`. + The default behavior is to start at the origin of the grid coordinate space. + If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region + ranging from `[origin, origin selection_shape]`, where the upper bound is exclusive as + per python indexing conventions. + + Parameters + ---------- + array : Array | AsyncArray + The array to iterate over. + origin : Sequence[int] | None, default=None + The origin of the selection in grid coordinates. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in grid coordinates. + + Yields + ------ + chunk_coords: tuple[int, ...] + The coordinates of each shard in the selection. + """ + return _iter_grid(array._shard_grid_shape, origin=origin, selection_shape=selection_shape) + + +def _iter_shard_keys( + array: Array | AsyncArray[Any], + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, +) -> Iterator[str]: + """ + Iterate over the storage keys of each shard, relative to an optional origin, and optionally + limited to a contiguous region in shard grid coordinates. + + Parameters + ---------- + array : Array | AsyncArray + The array to iterate over. + origin : Sequence[int] | None, default=None + The origin of the selection in grid coordinates. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in grid coordinates. + + Yields + ------ + key: str + The storage key of each chunk in the selection. + """ + # Iterate over the coordinates of chunks in chunk grid space. + _iter = _iter_grid(array._shard_grid_shape, origin=origin, selection_shape=selection_shape) + return (array.metadata.encode_chunk_key(k) for k in _iter) + + +def _iter_shard_regions( + array: Array | AsyncArray[Any], + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, +) -> Iterator[tuple[slice, ...]]: + """ + Iterate over the regions spanned by each shard. + + These are the smallest regions of the array that are safe to write concurrently. + + Parameters + ---------- + array : Array | AsyncArray + The array to iterate over. + origin : Sequence[int] | None, default=None + The origin of the selection relative to the array's shard grid. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in shard grid coordinates. + + Yields + ------ + region: tuple[slice, ...] + A tuple of slice objects representing the region spanned by each shard in the selection. + """ + if array.shards is None: + shard_shape = array.chunks + else: + shard_shape = array.shards + + return _iter_regions( + array.shape, shard_shape, origin=origin, selection_shape=selection_shape, trim_excess=True + ) + + +def _iter_chunk_regions( + array: Array | AsyncArray[Any], + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, +) -> Iterator[tuple[slice, ...]]: + """ + Iterate over the regions spanned by each shard. + + These are the smallest regions of the array that are efficient to read concurrently. + + Parameters + ---------- + array : Array | AsyncArray + The array to iterate over. + origin : Sequence[int] | None, default=None + The origin of the selection in grid coordinates. + selection_shape : Sequence[int] | None, default=None + The shape of the selection in grid coordinates. + + Returns + ------- + region: tuple[slice, ...] + A tuple of slice objects representing the region spanned by each shard in the selection. + """ + + return _iter_regions( + array.shape, array.chunks, origin=origin, selection_shape=selection_shape, trim_excess=True + ) diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 16cb271601..2736915f46 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -123,7 +123,7 @@ def _iter_grid( Returns ------- - itertools.product object + Iterator[tuple[int, ...]] An iterator over tuples of integers Examples @@ -134,11 +134,11 @@ def _iter_grid( >>> tuple(iter_grid((2,3))) ((0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2)) - >>> tuple(iter_grid((2,3)), origin=(1,1)) - ((1, 1), (1, 2), (1, 3), (2, 1), (2, 2), (2, 3)) + >>> tuple(iter_grid((2,3), origin=(1,1))) + ((1, 1), (1, 2)) - >>> tuple(iter_grid((2,3)), origin=(1,1), selection_shape=(2,2)) - ((1, 1), (1, 2), (1, 3), (2, 1)) + >>> tuple(iter_grid((2,3), origin=(0,0), selection_shape=(2,2))) + ((0, 0), (0, 1), (1, 0), (1, 1)) """ if origin is None: origin_parsed = (0,) * len(grid_shape) @@ -163,14 +163,74 @@ def _iter_grid( ): if o + ss > gs: raise IndexError( - f"Invalid selection shape ({selection_shape}) for origin ({origin}) and grid shape ({grid_shape}) at axis {idx}." + f"Invalid selection shape ({ss}) for origin ({o}) and grid shape ({gs}) at axis {idx}." ) dimensions += (range(o, o + ss),) - yield from itertools.product(*(dimensions)) + return itertools.product(*(dimensions)) else: - msg = f"Indexing order {order} is not supported at this time." # type: ignore[unreachable] - raise NotImplementedError(msg) + msg = f"Indexing order {order} is not supported at this time." # type: ignore[unreachable] # pragma: no cover + raise NotImplementedError(msg) # pragma: no cover + + +def _iter_regions( + domain_shape: Sequence[int], + region_shape: Sequence[int], + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, + order: _ArrayIndexingOrder = "lexicographic", + trim_excess: bool = True, +) -> Iterator[tuple[slice, ...]]: + """ + Iterate over contiguous regions on a grid of integers, with the option to restrict the + domain of iteration to a contiguous subregion of that grid. + + Parameters + ---------- + domain_shape : Sequence[int] + The size of the domain to iterate over. + region_shape : Sequence[int] + The shape of the region to iterate over. + origin : Sequence[int] | None, default=None + The location, in grid coordinates, of the first region to return. + selection_shape : Sequence[int] | None, default=None + The shape of the selection, in grid coordinates. + order : Literal["lexicographic"], default="lexicographic" + The linear indexing order to use. + + Yields + ------- + + Iterator[tuple[slice, ...]] + An iterator over tuples of slices, where each slice spans a separate contiguous region + + Examples + -------- + >>> tuple(iter_regions((1,), (1,))) + ((slice(0, 1, 1),),) + + >>> tuple(iter_regions((2, 3), (1, 2))) + ((slice(0, 1, 1), slice(0, 2, 1)), (slice(1, 2, 1), slice(0, 2, 1))) + + >>> tuple(iter_regions((2,3), (1,2)), origin=(1,1)) + ((slice(1, 2, 1), slice(1, 3, 1)), (slice(2, 3, 1), slice(1, 3, 1))) + + >>> tuple(iter_regions((2,3), (1,2)), origin=(1,1), selection_shape=(2,2)) + ((slice(1, 2, 1), slice(1, 3, 1)), (slice(2, 3, 1), slice(1, 3, 1))) + """ + grid_shape = tuple(ceildiv(d, s) for d, s in zip(domain_shape, region_shape, strict=True)) + for grid_position in _iter_grid( + grid_shape=grid_shape, origin=origin, selection_shape=selection_shape, order=order + ): + out: list[slice] = [] + for g_pos, r_shape, d_shape in zip(grid_position, region_shape, domain_shape, strict=True): + start = g_pos * r_shape + stop = start + r_shape + if trim_excess: + stop = min(stop, d_shape) + out.append(slice(start, stop, 1)) + yield tuple(out) def is_integer(x: Any) -> TypeGuard[int]: diff --git a/tests/test_array.py b/tests/test_array.py index a316ee127f..97aef9319b 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -31,9 +31,14 @@ from zarr.core.array import ( CompressorsLike, FiltersLike, + _iter_chunk_coords, + _iter_chunk_regions, + _iter_shard_coords, + _iter_shard_keys, + _iter_shard_regions, _parse_chunk_encoding_v2, _parse_chunk_encoding_v3, - chunks_initialized, + _shards_initialized, create_array, default_filters_v2, default_serializer_v3, @@ -59,7 +64,7 @@ from zarr.core.dtype.npy.common import NUMPY_ENDIANNESS_STR, endianness_from_numpy_str from zarr.core.dtype.npy.string import UTF8Base from zarr.core.group import AsyncGroup -from zarr.core.indexing import BasicIndexer +from zarr.core.indexing import BasicIndexer, _iter_grid, _iter_regions from zarr.core.metadata.v2 import ArrayV2Metadata from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import sync @@ -375,48 +380,74 @@ def test_nchunks(test_cls: type[Array] | type[AsyncArray[Any]], nchunks: int) -> @pytest.mark.parametrize("test_cls", [Array, AsyncArray[Any]]) -async def test_nchunks_initialized(test_cls: type[Array] | type[AsyncArray[Any]]) -> None: +@pytest.mark.parametrize( + ("shape", "shard_shape", "chunk_shape"), + [((10,), None, (1,)), ((10,), (1,), (1,)), ((40,), (20,), (5,))], +) +async def test_nchunks_initialized( + test_cls: type[Array] | type[AsyncArray[Any]], + shape: tuple[int, ...], + shard_shape: tuple[int, ...] | None, + chunk_shape: tuple[int, ...], +) -> None: """ - Test that nchunks_initialized accurately returns the number of stored chunks. + Test that nchunks_initialized accurately returns the number of stored partitions. """ store = MemoryStore() - arr = zarr.create_array(store, shape=(100,), chunks=(10,), dtype="i4") + if shard_shape is None: + chunks_per_shard = 1 + else: + chunks_per_shard = np.prod(np.array(shard_shape) // np.array(chunk_shape)) + + arr = zarr.create_array(store, shape=shape, shards=shard_shape, chunks=chunk_shape, dtype="i1") # write chunks one at a time - for idx, region in enumerate(arr._iter_chunk_regions()): + for idx, region in enumerate(arr._iter_shard_regions()): arr[region] = 1 expected = idx + 1 if test_cls == Array: - observed = arr.nchunks_initialized + observed = arr._nshards_initialized + assert observed == arr.nchunks_initialized // chunks_per_shard else: - observed = await arr._async_array.nchunks_initialized() + observed = await arr._async_array._nshards_initialized() + assert observed == await arr._async_array.nchunks_initialized() // chunks_per_shard assert observed == expected # delete chunks - for idx, key in enumerate(arr._iter_chunk_keys()): + for idx, key in enumerate(arr._iter_shard_keys()): sync(arr.store_path.store.delete(key)) if test_cls == Array: - observed = arr.nchunks_initialized + observed = arr._nshards_initialized + assert observed == arr.nchunks_initialized // chunks_per_shard else: - observed = await arr._async_array.nchunks_initialized() - expected = arr.nchunks - idx - 1 + observed = await arr._async_array._nshards_initialized() + assert observed == await arr._async_array.nchunks_initialized() // chunks_per_shard + expected = arr._nshards - idx - 1 assert observed == expected @pytest.mark.parametrize("path", ["", "foo"]) -async def test_chunks_initialized(path: str) -> None: +@pytest.mark.parametrize( + ("shape", "shard_shape", "chunk_shape"), + [((10,), None, (1,)), ((10,), (1,), (1,)), ((40,), (20,), (5,))], +) +async def test_chunks_initialized( + path: str, shape: tuple[int, ...], shard_shape: tuple[int, ...], chunk_shape: tuple[int, ...] +) -> None: """ Test that chunks_initialized accurately returns the keys of stored chunks. """ store = MemoryStore() - arr = zarr.create_array(store, name=path, shape=(100,), chunks=(10,), dtype="i4") + arr = zarr.create_array( + store, name=path, shape=shape, shards=shard_shape, chunks=chunk_shape, dtype="i1" + ) chunks_accumulated = tuple( - accumulate(tuple(tuple(v.split(" ")) for v in arr._iter_chunk_keys())) + accumulate(tuple(tuple(v.split(" ")) for v in arr._iter_shard_keys())) ) - for keys, region in zip(chunks_accumulated, arr._iter_chunk_regions(), strict=False): + for keys, region in zip(chunks_accumulated, arr._iter_shard_regions(), strict=False): arr[region] = 1 - observed = sorted(await chunks_initialized(arr._async_array)) + observed = sorted(await _shards_initialized(arr._async_array)) expected = sorted(keys) assert observed == expected @@ -861,14 +892,14 @@ def test_write_empty_chunks_behavior( # initialize the store with some non-fill value chunks arr[:] = fill_value + 1 - assert arr.nchunks_initialized == arr.nchunks + assert arr._nshards_initialized == arr._nshards arr[:] = fill_value if not write_empty_chunks: - assert arr.nchunks_initialized == 0 + assert arr._nshards_initialized == 0 else: - assert arr.nchunks_initialized == arr.nchunks + assert arr._nshards_initialized == arr._nshards @pytest.mark.parametrize("store", ["memory"], indirect=True) @@ -1871,3 +1902,220 @@ def test_unknown_object_codec_default_filters_v2() -> None: msg = f"Data type {dtype} requires an unknown object codec: {dtype.object_codec_id!r}." with pytest.raises(ValueError, match=re.escape(msg)): default_filters_v2(dtype) + + +@pytest.mark.parametrize( + ("array_shape", "shard_shape", "chunk_shape"), + [ + ((10,), None, (1,)), + ((10,), (1,), (1,)), + ((30, 10), None, (2, 5)), + ((30, 10), (4, 10), (2, 5)), + ], +) +def test_chunk_grid_shape( + array_shape: tuple[int, ...], + shard_shape: tuple[int, ...] | None, + chunk_shape: tuple[int, ...], + zarr_format: ZarrFormat, +) -> None: + """ + Test that the shape of the chunk grid and the shard grid are correctly indicated + """ + if zarr_format == 2 and shard_shape is not None: + with pytest.raises( + ValueError, + match="Zarr format 2 arrays can only be created with `shard_shape` set to `None`.", + ): + arr = zarr.create_array( + {}, + dtype="uint8", + shape=array_shape, + chunks=chunk_shape, + shards=shard_shape, + zarr_format=zarr_format, + ) + pytest.skip("Zarr format 2 arrays can only be created with `shard_shape` set to `None`.") + else: + arr = zarr.create_array( + {}, + dtype="uint8", + shape=array_shape, + chunks=chunk_shape, + shards=shard_shape, + zarr_format=zarr_format, + ) + + chunk_grid_shape = tuple(ceildiv(a, b) for a, b in zip(array_shape, chunk_shape, strict=True)) + if shard_shape is None: + _shard_shape = chunk_shape + else: + _shard_shape = shard_shape + shard_grid_shape = tuple(ceildiv(a, b) for a, b in zip(array_shape, _shard_shape, strict=True)) + assert arr._chunk_grid_shape == chunk_grid_shape + assert arr.cdata_shape == chunk_grid_shape + assert arr._async_array.cdata_shape == chunk_grid_shape + assert arr._shard_grid_shape == shard_grid_shape + assert arr._nshards == np.prod(shard_grid_shape) + + +@pytest.mark.parametrize( + ("array_shape", "shard_shape", "chunk_shape"), [((10,), None, (1,)), ((30, 10), None, (2, 5))] +) +def test_iter_chunk_coords( + array_shape: tuple[int, ...], + shard_shape: tuple[int, ...] | None, + chunk_shape: tuple[int, ...], + zarr_format: ZarrFormat, +) -> None: + """ + Test that we can use the various invocations of iter_chunk_coords to iterate over the coordinates + of the origin of each chunk. + """ + + arr = zarr.create_array( + {}, + dtype="uint8", + shape=array_shape, + chunks=chunk_shape, + shards=shard_shape, + zarr_format=zarr_format, + ) + expected = tuple(_iter_grid(arr._shard_grid_shape)) + observed = tuple(_iter_chunk_coords(arr)) + assert observed == expected + assert observed == tuple(arr._iter_chunk_coords()) + assert observed == tuple(arr._async_array._iter_chunk_coords()) + + +@pytest.mark.parametrize( + ("array_shape", "shard_shape", "chunk_shape"), + [((10,), (1,), (1,)), ((10,), None, (1,)), ((30, 10), (10, 5), (2, 5))], +) +def test_iter_shard_coords( + array_shape: tuple[int, ...], + shard_shape: tuple[int, ...] | None, + chunk_shape: tuple[int, ...], + zarr_format: ZarrFormat, +) -> None: + """ + Test that we can use the various invocations of iter_shard_coords to iterate over the coordinates + of the origin of each shard. + """ + + if zarr_format == 2 and shard_shape is not None: + pytest.skip("Zarr format 2 does not support shard shape.") + + arr = zarr.create_array( + {}, + dtype="uint8", + shape=array_shape, + chunks=chunk_shape, + shards=shard_shape, + zarr_format=zarr_format, + ) + expected = tuple(_iter_grid(arr._shard_grid_shape)) + observed = tuple(_iter_shard_coords(arr)) + assert observed == expected + assert observed == tuple(arr._iter_shard_coords()) + assert observed == tuple(arr._async_array._iter_shard_coords()) + + +@pytest.mark.parametrize( + ("array_shape", "shard_shape", "chunk_shape"), + [((10,), (1,), (1,)), ((10,), None, (1,)), ((30, 10), (10, 5), (2, 5))], +) +def test_iter_shard_keys( + array_shape: tuple[int, ...], + shard_shape: tuple[int, ...] | None, + chunk_shape: tuple[int, ...], + zarr_format: ZarrFormat, +) -> None: + """ + Test that we can use the various invocations of iter_shard_keys to iterate over the stored + keys of the shards of an array. + """ + + if zarr_format == 2 and shard_shape is not None: + pytest.skip("Zarr format 2 does not support shard shape.") + + arr = zarr.create_array( + {}, + dtype="uint8", + shape=array_shape, + chunks=chunk_shape, + shards=shard_shape, + zarr_format=zarr_format, + ) + expected = tuple( + arr.metadata.encode_chunk_key(key) for key in _iter_grid(arr._shard_grid_shape) + ) + observed = tuple(_iter_shard_keys(arr)) + assert observed == expected + assert observed == tuple(arr._iter_shard_keys()) + assert observed == tuple(arr._async_array._iter_shard_keys()) + + +@pytest.mark.parametrize( + ("array_shape", "shard_shape", "chunk_shape"), + [((10,), None, (1,)), ((10,), (1,), (1,)), ((30, 10), (10, 5), (2, 5))], +) +def test_iter_shard_regions( + array_shape: tuple[int, ...], + shard_shape: tuple[int, ...] | None, + chunk_shape: tuple[int, ...], + zarr_format: ZarrFormat, +) -> None: + """ + Test that we can use the various invocations of iter_shard_regions to iterate over the regions + spanned by the shards of an array. + """ + if zarr_format == 2 and shard_shape is not None: + pytest.skip("Zarr format 2 does not support shard shape.") + + arr = zarr.create_array( + {}, + dtype="uint8", + shape=array_shape, + chunks=chunk_shape, + shards=shard_shape, + zarr_format=zarr_format, + ) + if shard_shape is None: + _shard_shape = chunk_shape + else: + _shard_shape = shard_shape + expected = tuple(_iter_regions(arr.shape, _shard_shape)) + observed = tuple(_iter_shard_regions(arr)) + assert observed == expected + assert observed == tuple(arr._iter_shard_regions()) + assert observed == tuple(arr._async_array._iter_shard_regions()) + + +@pytest.mark.parametrize( + ("array_shape", "shard_shape", "chunk_shape"), [((10,), None, (1,)), ((30, 10), None, (2, 5))] +) +def test_iter_chunk_regions( + array_shape: tuple[int, ...], + shard_shape: tuple[int, ...] | None, + chunk_shape: tuple[int, ...], + zarr_format: ZarrFormat, +) -> None: + """ + Test that we can use the various invocations of iter_chunk_regions to iterate over the regions + spanned by the chunks of an array. + """ + arr = zarr.create_array( + {}, + dtype="uint8", + shape=array_shape, + chunks=chunk_shape, + shards=shard_shape, + zarr_format=zarr_format, + ) + + expected = tuple(_iter_regions(arr.shape, chunk_shape)) + observed = tuple(_iter_chunk_regions(arr)) + assert observed == expected + assert observed == tuple(arr._iter_chunk_regions()) + assert observed == tuple(arr._async_array._iter_chunk_regions()) diff --git a/tests/test_indexing.py b/tests/test_indexing.py index a78fe3c706..c6a792b0e5 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -18,7 +18,10 @@ CoordinateSelection, OrthogonalSelection, Selection, + _ArrayIndexingOrder, _iter_grid, + _iter_regions, + ceildiv, make_slice_selection, normalize_integer_selection, oindex, @@ -1995,6 +1998,71 @@ def test_iter_chunk_regions(): assert_array_equal(a[region], np.zeros_like(a[region])) +@pytest.mark.parametrize( + ("domain_shape", "region_shape", "origin", "selection_shape"), + [ + ((9,), (1,), None, (9,)), + ((9,), (1,), (0,), (9,)), + ((3,), (2,), (0,), (1,)), + ((9,), (2,), (2,), (2,)), + ((9, 9), (2, 1), None, None), + ((9, 9), (4, 1), None, None), + ], +) +@pytest.mark.parametrize("order", ["lexicographic"]) +@pytest.mark.parametrize("trim_excess", [True, False]) +def test_iter_regions( + domain_shape: tuple[int, ...], + region_shape: tuple[int, ...], + origin: tuple[int, ...] | None, + selection_shape: tuple[int, ...] | None, + order: _ArrayIndexingOrder, + trim_excess: bool, +) -> None: + """ + Test that iter_regions properly iterates over contiguous regions of a gridded domain. + """ + expected_slices_by_dim: list[list[slice]] = [] + origin_parsed: tuple[int, ...] + selection_shape_parsed: tuple[int, ...] + if origin is None: + origin_parsed = (0,) * len(domain_shape) + else: + origin_parsed = origin + if selection_shape is None: + selection_shape_parsed = tuple( + ceildiv(ds, rs) - o + for ds, o, rs in zip(domain_shape, origin_parsed, region_shape, strict=True) + ) + else: + selection_shape_parsed = selection_shape + for d_s, r_s, o, ss in zip( + domain_shape, region_shape, origin_parsed, selection_shape_parsed, strict=True + ): + _expected_slices: list[slice] = [] + start = o * r_s + for incr in range(start, start + ss * r_s, r_s): + if trim_excess: + term = min(incr + r_s, d_s) + else: + term = incr + r_s + _expected_slices.append(slice(incr, term, 1)) + expected_slices_by_dim.append(_expected_slices) + + expected = tuple(itertools.product(*expected_slices_by_dim)) + observed = tuple( + _iter_regions( + domain_shape, + region_shape, + origin=origin, + selection_shape=selection_shape, + order=order, + trim_excess=trim_excess, + ) + ) + assert observed == expected + + class TestAsync: @pytest.mark.parametrize( ("indexer", "expected"), From 7970f4a077b62a837f1613456765b9c77ca99135 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Sun, 24 Aug 2025 12:30:01 +0100 Subject: [PATCH 080/468] Merge release notes from 3.1.1 (#3399) --- changes/3112.bugfix.1.rst | 1 - changes/3112.bugfix.2.rst | 1 - changes/3112.bugfix.3.rst | 2 -- changes/3112.bugfix.4.rst | 1 - changes/3112.bugfix.rst | 1 - changes/3227.feature.rst | 1 - changes/3249.doc.rst | 2 -- changes/3251.bugfix.rst | 1 - changes/3258.bugfix.rst | 1 - changes/3264.bugfix.rst | 4 ---- changes/3268.misc.rst | 2 -- changes/3273.doc.rst | 1 - changes/3280.bugfix.rst | 2 -- changes/3287.bugfix.rst | 1 - docs/release-notes.rst | 43 +++++++++++++++++++++++++++++++++++++++ 15 files changed, 43 insertions(+), 21 deletions(-) delete mode 100644 changes/3112.bugfix.1.rst delete mode 100644 changes/3112.bugfix.2.rst delete mode 100644 changes/3112.bugfix.3.rst delete mode 100644 changes/3112.bugfix.4.rst delete mode 100644 changes/3112.bugfix.rst delete mode 100644 changes/3227.feature.rst delete mode 100644 changes/3249.doc.rst delete mode 100644 changes/3251.bugfix.rst delete mode 100644 changes/3258.bugfix.rst delete mode 100644 changes/3264.bugfix.rst delete mode 100644 changes/3268.misc.rst delete mode 100644 changes/3273.doc.rst delete mode 100644 changes/3280.bugfix.rst delete mode 100644 changes/3287.bugfix.rst diff --git a/changes/3112.bugfix.1.rst b/changes/3112.bugfix.1.rst deleted file mode 100644 index 5d7856859c..0000000000 --- a/changes/3112.bugfix.1.rst +++ /dev/null @@ -1 +0,0 @@ -Creating a Zarr format 2 array with the ``order`` keyword argument no longer raises a warning. diff --git a/changes/3112.bugfix.2.rst b/changes/3112.bugfix.2.rst deleted file mode 100644 index e2c341c99a..0000000000 --- a/changes/3112.bugfix.2.rst +++ /dev/null @@ -1 +0,0 @@ -Creating a Zarr format 3 array with the ``order`` argument now conistently ignores this argument and raises a warning. diff --git a/changes/3112.bugfix.3.rst b/changes/3112.bugfix.3.rst deleted file mode 100644 index 4c934b491b..0000000000 --- a/changes/3112.bugfix.3.rst +++ /dev/null @@ -1,2 +0,0 @@ -When using ``from_array`` to copy a Zarr format 2 array to a Zarr format 3 array, if the memory order of the input array is ``"F"`` a warning is raised and the order ignored. -This is because Zarr format 3 arrays are always stored in "C" order. diff --git a/changes/3112.bugfix.4.rst b/changes/3112.bugfix.4.rst deleted file mode 100644 index 417814943b..0000000000 --- a/changes/3112.bugfix.4.rst +++ /dev/null @@ -1 +0,0 @@ -The ``config`` argument to `zarr.create` (and functions that create arrays) is now used - previously it had no effect. diff --git a/changes/3112.bugfix.rst b/changes/3112.bugfix.rst deleted file mode 100644 index 24069aae3a..0000000000 --- a/changes/3112.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fixed the error message when passing both ``config`` and ``write_empty_chunks`` arguments to reflect the current behaviour (``write_empty_chunks`` takes precedence). diff --git a/changes/3227.feature.rst b/changes/3227.feature.rst deleted file mode 100644 index ddbedd0a30..0000000000 --- a/changes/3227.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Add lightweight implementations of .getsize() and .getsize_prefix() for ObjectStore. diff --git a/changes/3249.doc.rst b/changes/3249.doc.rst deleted file mode 100644 index d46f775d9c..0000000000 --- a/changes/3249.doc.rst +++ /dev/null @@ -1,2 +0,0 @@ -Expand the data type docs to include a demonstration of the ``parse_data_type`` function. -Expand the docstring for the ``parse_data_type`` function. \ No newline at end of file diff --git a/changes/3251.bugfix.rst b/changes/3251.bugfix.rst deleted file mode 100644 index 92f19ae326..0000000000 --- a/changes/3251.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Ensure that all abstract methods of ``ZDType`` raise a ``NotImplementedError`` when invoked. \ No newline at end of file diff --git a/changes/3258.bugfix.rst b/changes/3258.bugfix.rst deleted file mode 100644 index 6f9fedaa46..0000000000 --- a/changes/3258.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Register 'gpu' marker with pytest for downstream StoreTests. diff --git a/changes/3264.bugfix.rst b/changes/3264.bugfix.rst deleted file mode 100644 index efcbab514e..0000000000 --- a/changes/3264.bugfix.rst +++ /dev/null @@ -1,4 +0,0 @@ -- Expand the range of types accepted by ``parse_data_type`` to include strings and Sequences. -- Move the functionality of ``parse_data_type`` to a new function called ``parse_dtype``. This change - ensures that nomenclature is consistent across the codebase. ``parse_data_type`` remains, so this - change is not breaking. \ No newline at end of file diff --git a/changes/3268.misc.rst b/changes/3268.misc.rst deleted file mode 100644 index cd8f611639..0000000000 --- a/changes/3268.misc.rst +++ /dev/null @@ -1,2 +0,0 @@ -Removed warnings that were emitted when using the ``vlen-utf8`` and ``vlen-bytes`` codecs. Those -warnings are no longer needed now that both of these codecs are backed by specification documents. \ No newline at end of file diff --git a/changes/3273.doc.rst b/changes/3273.doc.rst deleted file mode 100644 index b63b9c3fa3..0000000000 --- a/changes/3273.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Add a section on codecs to the migration guide. diff --git a/changes/3280.bugfix.rst b/changes/3280.bugfix.rst deleted file mode 100644 index 510c4d2674..0000000000 --- a/changes/3280.bugfix.rst +++ /dev/null @@ -1,2 +0,0 @@ -Fix a regression introduced in 3.1.0 that prevented ``inf``, ``-inf``, and ``nan`` values -from being stored in ``attributes``. \ No newline at end of file diff --git a/changes/3287.bugfix.rst b/changes/3287.bugfix.rst deleted file mode 100644 index a4eaa35312..0000000000 --- a/changes/3287.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fixes Group.nmembers() ignoring depth when using consolidated metadata. diff --git a/docs/release-notes.rst b/docs/release-notes.rst index e70715eb15..d5308093e5 100644 --- a/docs/release-notes.rst +++ b/docs/release-notes.rst @@ -3,6 +3,49 @@ Release notes .. towncrier release notes start +3.1.1 (2025-07-28) +------------------ + +Features +~~~~~~~~ + +- Add lightweight implementations of .getsize() and .getsize_prefix() for ObjectStore. (:issue:`3227`) + + +Bugfixes +~~~~~~~~ + +- Creating a Zarr format 2 array with the ``order`` keyword argument no longer raises a warning. (:issue:`3112`) +- Fixed the error message when passing both ``config`` and ``write_empty_chunks`` arguments to reflect the current behaviour (``write_empty_chunks`` takes precedence). (:issue:`3112`) +- Creating a Zarr format 3 array with the ``order`` argument now conistently ignores this argument and raises a warning. (:issue:`3112`) +- When using ``from_array`` to copy a Zarr format 2 array to a Zarr format 3 array, if the memory order of the input array is ``"F"`` a warning is raised and the order ignored. + This is because Zarr format 3 arrays are always stored in "C" order. (:issue:`3112`) +- The ``config`` argument to `zarr.create` (and functions that create arrays) is now used - previously it had no effect. (:issue:`3112`) +- Ensure that all abstract methods of ``ZDType`` raise a ``NotImplementedError`` when invoked. (:issue:`3251`) +- Register 'gpu' marker with pytest for downstream StoreTests. (:issue:`3258`) +- Expand the range of types accepted by ``parse_data_type`` to include strings and Sequences. +- Move the functionality of ``parse_data_type`` to a new function called ``parse_dtype``. This change + ensures that nomenclature is consistent across the codebase. ``parse_data_type`` remains, so this + change is not breaking. (:issue:`3264`) +- Fix a regression introduced in 3.1.0 that prevented ``inf``, ``-inf``, and ``nan`` values + from being stored in ``attributes``. (:issue:`3280`) +- Fixes Group.nmembers() ignoring depth when using consolidated metadata. (:issue:`3287`) + + +Improved Documentation +~~~~~~~~~~~~~~~~~~~~~~ + +- Expand the data type docs to include a demonstration of the ``parse_data_type`` function. + Expand the docstring for the ``parse_data_type`` function. (:issue:`3249`) +- Add a section on codecs to the migration guide. (:issue:`3273`) + + +Misc +~~~~ + +- :issue:`3268` + + 3.1.0 (2025-07-14) ------------------ From dc641fe0b696aed55d1a8c888dff6ced0e9b60e7 Mon Sep 17 00:00:00 2001 From: Gabor Kovacs Date: Mon, 25 Aug 2025 06:57:14 -0700 Subject: [PATCH 081/468] Add default value to init_array config param. Update docstring. (#3391) * Make config in init_array optional * Add default value to init_array config param. * Update docstring. * Add changelog entry. * Fix type casting typo. * Update src/zarr/core/array.py * Update src/zarr/core/array.py * reformat docstring --------- Co-authored-by: Davis Bennett --- changes/3391.feature.rst | 1 + src/zarr/core/array.py | 6 ++++-- src/zarr/testing/utils.py | 2 +- tests/test_api.py | 1 - 4 files changed, 6 insertions(+), 4 deletions(-) create mode 100644 changes/3391.feature.rst diff --git a/changes/3391.feature.rst b/changes/3391.feature.rst new file mode 100644 index 0000000000..45a1472a2c --- /dev/null +++ b/changes/3391.feature.rst @@ -0,0 +1 @@ +Make config param optional in init_array diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 4b34c31de1..47d9dc1047 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -4444,7 +4444,7 @@ async def init_array( chunk_key_encoding: ChunkKeyEncodingLike | None = None, dimension_names: DimensionNames = None, overwrite: bool = False, - config: ArrayConfigLike | None, + config: ArrayConfigLike | None = None, ) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: """Create and persist an array metadata document. @@ -4524,8 +4524,10 @@ async def init_array( Zarr format 3 only. Zarr format 2 arrays should not use this parameter. overwrite : bool, default False Whether to overwrite an array with the same name in the store, if one exists. - config : ArrayConfigLike or None, optional + config : ArrayConfigLike or None, default=None Configuration for this array. + If ``None``, the default array runtime configuration will be used. This default + is stored in the global configuration object. Returns ------- diff --git a/src/zarr/testing/utils.py b/src/zarr/testing/utils.py index 3cb7f5cb99..2a4c3e45c5 100644 --- a/src/zarr/testing/utils.py +++ b/src/zarr/testing/utils.py @@ -46,4 +46,4 @@ def has_cupy() -> bool: # Decorator for GPU tests def gpu_test(func: T) -> T: - return cast("T", gpu_mark(skip_if_no_gpu(func))) + return cast(T, gpu_mark(skip_if_no_gpu(func))) diff --git a/tests/test_api.py b/tests/test_api.py index 3668ef306a..68cdab37da 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -440,7 +440,6 @@ async def test_init_order_warns() -> None: store_path=StorePath(store=MemoryStore()), shape=(1,), dtype="uint8", - config=None, zarr_format=3, order="F", ) From 0e28404b9952008a1604e561afd71725f04eeb07 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Mon, 25 Aug 2025 15:13:56 +0100 Subject: [PATCH 082/468] Prevent mode='r+' from creating new directories (#3307) * Prevent mode='r+' from creating new directories * Add test * Open store for mode = r+ * Add changelog * Fix errr raised when opening non-existent path --------- Co-authored-by: Davis Bennett --- changes/3307.bugfix.rst | 1 + src/zarr/storage/_common.py | 2 +- src/zarr/storage/_local.py | 48 +++++++++++++++++++++++++++++++++---- tests/test_api.py | 9 ++++--- 4 files changed, 52 insertions(+), 8 deletions(-) create mode 100644 changes/3307.bugfix.rst diff --git a/changes/3307.bugfix.rst b/changes/3307.bugfix.rst new file mode 100644 index 0000000000..069205fcc6 --- /dev/null +++ b/changes/3307.bugfix.rst @@ -0,0 +1 @@ +Opening an array or group with ``mode="r+"`` will no longer create new arrays or groups. diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 3a63b30e9b..66a53c19df 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -358,7 +358,7 @@ async def make_store_path( elif isinstance(store_like, Path): # Create a new LocalStore - store = await LocalStore.open(root=store_like, read_only=_read_only) + store = await LocalStore.open(root=store_like, mode=mode) elif isinstance(store_like, str): # Either a FSSpec URI or a local filesystem path diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 43e585415d..1229ec316a 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -5,7 +5,7 @@ import os import shutil from pathlib import Path -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Self from zarr.abc.store import ( ByteRequest, @@ -16,7 +16,7 @@ ) from zarr.core.buffer import Buffer from zarr.core.buffer.core import default_buffer_prototype -from zarr.core.common import concurrent_map +from zarr.core.common import AccessModeLiteral, concurrent_map if TYPE_CHECKING: from collections.abc import AsyncIterator, Iterable @@ -102,16 +102,56 @@ def __init__(self, root: Path | str, *, read_only: bool = False) -> None: ) self.root = root - def with_read_only(self, read_only: bool = False) -> LocalStore: + def with_read_only(self, read_only: bool = False) -> Self: # docstring inherited return type(self)( root=self.root, read_only=read_only, ) - async def _open(self) -> None: + @classmethod + async def open( + cls, root: Path | str, *, read_only: bool = False, mode: AccessModeLiteral | None = None + ) -> Self: + """ + Create and open the store. + + Parameters + ---------- + root : str or Path + Directory to use as root of store. + read_only : bool + Whether the store is read-only + mode : + Mode in which to create the store. This only affects opening the store, + and the final read-only state of the store is controlled through the + read_only parameter. + + Returns + ------- + Store + The opened store instance. + """ + # If mode = 'r+', want to open in read only mode (fail if exists), + # but return a writeable store + if mode is not None: + read_only_creation = mode in ["r", "r+"] + else: + read_only_creation = read_only + store = cls(root, read_only=read_only_creation) + await store._open() + + # Set read_only state + store = store.with_read_only(read_only) + await store._open() + return store + + async def _open(self, *, mode: AccessModeLiteral | None = None) -> None: if not self.read_only: self.root.mkdir(parents=True, exist_ok=True) + + if not self.root.exists(): + raise FileNotFoundError(f"{self.root} does not exist") return await super()._open() async def clear(self) -> None: diff --git a/tests/test_api.py b/tests/test_api.py index 68cdab37da..9950d385a3 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -45,7 +45,6 @@ from zarr.errors import ( ArrayNotFoundError, MetadataValidationError, - NodeNotFoundError, ZarrDeprecationWarning, ZarrUserWarning, ) @@ -191,7 +190,7 @@ async def test_open_array(memory_store: MemoryStore, zarr_format: ZarrFormat) -> assert z.read_only # path not found - with pytest.raises(NodeNotFoundError): + with pytest.raises(FileNotFoundError): zarr.api.synchronous.open(store="doesnotexist", mode="r", zarr_format=zarr_format) @@ -333,8 +332,12 @@ def test_open_with_mode_r(tmp_path: Path) -> None: def test_open_with_mode_r_plus(tmp_path: Path) -> None: # 'r+' means read/write (must exist) + new_store_path = tmp_path / "new_store.zarr" + assert not new_store_path.exists(), "Test should operate on non-existent directory" with pytest.raises(FileNotFoundError): - zarr.open(store=tmp_path, mode="r+") + zarr.open(store=new_store_path, mode="r+") + assert not new_store_path.exists(), "mode='r+' should not create directory" + zarr.ones(store=tmp_path, shape=(3, 3)) z2 = zarr.open(store=tmp_path, mode="r+") assert isinstance(z2, Array) From c9509ee4416499e0b9bf735acb0820d989a61ebe Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 25 Aug 2025 17:29:54 +0200 Subject: [PATCH 083/468] generate 3.1.2 release notes (#3404) --- changes/3083.feature.rst | 1 - changes/3098.misc.rst | 3 --- changes/3144.bugfix.rst | 1 - changes/3288.misc.rst | 1 - changes/3299.bugfix.rst | 4 ---- changes/3307.bugfix.rst | 1 - changes/3318.misc.rst | 2 -- changes/3367.bugfix.rst | 1 - changes/3368.misc.rst | 2 -- changes/3371.misc.rst | 1 - changes/3372.misc.rst | 2 -- changes/3374.misc.rst | 1 - changes/3378.bugfix.rst | 3 --- changes/3391.feature.rst | 1 - changes/3395.bugfix.rst | 1 - docs/release-notes.rst | 31 +++++++++++++++++++++++++++++++ 16 files changed, 31 insertions(+), 25 deletions(-) delete mode 100644 changes/3083.feature.rst delete mode 100644 changes/3098.misc.rst delete mode 100644 changes/3144.bugfix.rst delete mode 100644 changes/3288.misc.rst delete mode 100644 changes/3299.bugfix.rst delete mode 100644 changes/3307.bugfix.rst delete mode 100644 changes/3318.misc.rst delete mode 100644 changes/3367.bugfix.rst delete mode 100644 changes/3368.misc.rst delete mode 100644 changes/3371.misc.rst delete mode 100644 changes/3372.misc.rst delete mode 100644 changes/3374.misc.rst delete mode 100644 changes/3378.bugfix.rst delete mode 100644 changes/3391.feature.rst delete mode 100644 changes/3395.bugfix.rst diff --git a/changes/3083.feature.rst b/changes/3083.feature.rst deleted file mode 100644 index 4403224df1..0000000000 --- a/changes/3083.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Added support for async vectorized and orthogonal indexing. \ No newline at end of file diff --git a/changes/3098.misc.rst b/changes/3098.misc.rst deleted file mode 100644 index 5ec1057365..0000000000 --- a/changes/3098.misc.rst +++ /dev/null @@ -1,3 +0,0 @@ -Define Zarr-specific warning classes that subclass the Python built-in warnings. -These classes makes it easier to control the visibility of warnings emitted by Zarr Python. -See `zarr.errors` for these warning classes. \ No newline at end of file diff --git a/changes/3144.bugfix.rst b/changes/3144.bugfix.rst deleted file mode 100644 index 8dde317bb8..0000000000 --- a/changes/3144.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value.``` diff --git a/changes/3288.misc.rst b/changes/3288.misc.rst deleted file mode 100644 index af7119487f..0000000000 --- a/changes/3288.misc.rst +++ /dev/null @@ -1 +0,0 @@ -Sort dictionary keys before returning consolidated metadata to ensure deterministic output. diff --git a/changes/3299.bugfix.rst b/changes/3299.bugfix.rst deleted file mode 100644 index 771fb846b4..0000000000 --- a/changes/3299.bugfix.rst +++ /dev/null @@ -1,4 +0,0 @@ -Fix a bug in ``create_array`` caused by iterating over chunk-aligned regions instead of -shard-aligned regions when writing data. Additionally, the behavior of ``nchunks_initialized`` -has been adjusted. This function consistently reports the number of chunks present in stored objects, -even when the array uses the sharding codec. \ No newline at end of file diff --git a/changes/3307.bugfix.rst b/changes/3307.bugfix.rst deleted file mode 100644 index 069205fcc6..0000000000 --- a/changes/3307.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Opening an array or group with ``mode="r+"`` will no longer create new arrays or groups. diff --git a/changes/3318.misc.rst b/changes/3318.misc.rst deleted file mode 100644 index f8308e6b97..0000000000 --- a/changes/3318.misc.rst +++ /dev/null @@ -1,2 +0,0 @@ -Define a ``Protocol`` to model the ``numcodecs.abc.Codec`` interface. This is groundwork toward -making ``numcodecs`` an optional dependency for ``zarr-python``. \ No newline at end of file diff --git a/changes/3367.bugfix.rst b/changes/3367.bugfix.rst deleted file mode 100644 index 9edef00ca6..0000000000 --- a/changes/3367.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected. \ No newline at end of file diff --git a/changes/3368.misc.rst b/changes/3368.misc.rst deleted file mode 100644 index 92c90cff33..0000000000 --- a/changes/3368.misc.rst +++ /dev/null @@ -1,2 +0,0 @@ -Improved performance of reading arrays by not unnecessarily using -the fill value. diff --git a/changes/3371.misc.rst b/changes/3371.misc.rst deleted file mode 100644 index 06655ee402..0000000000 --- a/changes/3371.misc.rst +++ /dev/null @@ -1 +0,0 @@ -Ensure that tests for executable examples are run in a fresh python environment. \ No newline at end of file diff --git a/changes/3372.misc.rst b/changes/3372.misc.rst deleted file mode 100644 index fe7da0d265..0000000000 --- a/changes/3372.misc.rst +++ /dev/null @@ -1,2 +0,0 @@ -Make certain imports in ``zarr.abc.store`` local to method definitions. This minimizes the risk of -circular imports when adding new classes to ``zarr.abc.store``. \ No newline at end of file diff --git a/changes/3374.misc.rst b/changes/3374.misc.rst deleted file mode 100644 index 19cefd8d60..0000000000 --- a/changes/3374.misc.rst +++ /dev/null @@ -1 +0,0 @@ -Replaces usage of the ``zarr.core.common.ChunkCoords`` typealias with ``tuple[int, ...]``. \ No newline at end of file diff --git a/changes/3378.bugfix.rst b/changes/3378.bugfix.rst deleted file mode 100644 index 1107f76488..0000000000 --- a/changes/3378.bugfix.rst +++ /dev/null @@ -1,3 +0,0 @@ -Ensure passing `config` is handled properly when `open`ing an existing -array. - diff --git a/changes/3391.feature.rst b/changes/3391.feature.rst deleted file mode 100644 index 45a1472a2c..0000000000 --- a/changes/3391.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Make config param optional in init_array diff --git a/changes/3395.bugfix.rst b/changes/3395.bugfix.rst deleted file mode 100644 index 73627c174d..0000000000 --- a/changes/3395.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Raise a Zarr-specific error class when a codec can't be found by name when deserializing the given codecs. This avoids hiding this error behind a "not part of a zarr hierarchy" warning. diff --git a/docs/release-notes.rst b/docs/release-notes.rst index d5308093e5..45401caa2e 100644 --- a/docs/release-notes.rst +++ b/docs/release-notes.rst @@ -3,6 +3,37 @@ Release notes .. towncrier release notes start +3.1.2 (2025-08-25) +------------------ + +Features +~~~~~~~~ + +- Added support for async vectorized and orthogonal indexing. (:issue:`3083`) +- Make config param optional in init_array (:issue:`3391`) + + +Bugfixes +~~~~~~~~ + +- Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value.``` (:issue:`3144`) +- Fix a bug in ``create_array`` caused by iterating over chunk-aligned regions instead of + shard-aligned regions when writing data. Additionally, the behavior of ``nchunks_initialized`` + has been adjusted. This function consistently reports the number of chunks present in stored objects, + even when the array uses the sharding codec. (:issue:`3299`) +- Opening an array or group with ``mode="r+"`` will no longer create new arrays or groups. (:issue:`3307`) +- Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected. (:issue:`3367`) +- Ensure passing `config` is handled properly when `open`ing an existing + array. (:issue:`3378`) +- Raise a Zarr-specific error class when a codec can't be found by name when deserializing the given codecs. This avoids hiding this error behind a "not part of a zarr hierarchy" warning. (:issue:`3395`) + + +Misc +~~~~ + +- :issue:`3098`, :issue:`3288`, :issue:`3318`, :issue:`3368`, :issue:`3371`, :issue:`3372`, :issue:`3374` + + 3.1.1 (2025-07-28) ------------------ From 96a531bf3b60e556504733c306c27fa6892e07ba Mon Sep 17 00:00:00 2001 From: Stephan Hoyer Date: Thu, 28 Aug 2025 10:41:27 -0700 Subject: [PATCH 084/468] Use atomic writes for new files in LocalStore (#3412) * Use atomic writes in LocalStore Fixes #3411 I use the standard strategy of writing to a temporary file in the same directory, and then renaming it to the desired name. This ensure that Zarr writes are either complete or not written at all. * Lint fixes * import sort * actually fix import order * ruff format * Add release note --- changes/3411.bugfix.rst | 1 + src/zarr/storage/_local.py | 53 +++++++++++++++++++++++++++------- tests/test_store/test_local.py | 44 ++++++++++++++++++++++++++++ 3 files changed, 87 insertions(+), 11 deletions(-) create mode 100644 changes/3411.bugfix.rst diff --git a/changes/3411.bugfix.rst b/changes/3411.bugfix.rst new file mode 100644 index 0000000000..b9303b9666 --- /dev/null +++ b/changes/3411.bugfix.rst @@ -0,0 +1 @@ +LocalStore now uses atomic writes, which should prevent some cases of corrupted data. diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 1229ec316a..717ed04144 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -1,11 +1,14 @@ from __future__ import annotations import asyncio +import contextlib import io import os import shutil +import sys +import uuid from pathlib import Path -from typing import TYPE_CHECKING, Self +from typing import TYPE_CHECKING, BinaryIO, Literal, Self from zarr.abc.store import ( ByteRequest, @@ -19,7 +22,7 @@ from zarr.core.common import AccessModeLiteral, concurrent_map if TYPE_CHECKING: - from collections.abc import AsyncIterator, Iterable + from collections.abc import AsyncIterator, Iterable, Iterator from zarr.core.buffer import BufferPrototype @@ -41,6 +44,39 @@ def _get(path: Path, prototype: BufferPrototype, byte_range: ByteRequest | None) return prototype.buffer.from_bytes(f.read()) +if sys.platform == "win32": + # Per the os.rename docs: + # On Windows, if dst exists a FileExistsError is always raised. + _safe_move = os.rename +else: + # On Unix, os.rename silently replace files, so instead we use os.link like + # atomicwrites: + # https://github.com/untitaker/python-atomicwrites/blob/1.4.1/atomicwrites/__init__.py#L59-L60 + # This also raises FileExistsError if dst exists. + def _safe_move(src: Path, dst: Path) -> None: + os.link(src, dst) + os.unlink(src) + + +@contextlib.contextmanager +def _atomic_write( + path: Path, + mode: Literal["r+b", "wb"], + exclusive: bool = False, +) -> Iterator[BinaryIO]: + tmp_path = path.with_suffix(f".{uuid.uuid4().hex}.partial") + try: + with tmp_path.open(mode) as f: + yield f + if exclusive: + _safe_move(tmp_path, path) + else: + tmp_path.replace(path) + except Exception: + tmp_path.unlink(missing_ok=True) + raise + + def _put( path: Path, value: Buffer, @@ -48,20 +84,15 @@ def _put( exclusive: bool = False, ) -> int | None: path.parent.mkdir(parents=True, exist_ok=True) + # write takes any object supporting the buffer protocol + view = value.as_buffer_like() if start is not None: with path.open("r+b") as f: f.seek(start) - # write takes any object supporting the buffer protocol - f.write(value.as_buffer_like()) + f.write(view) return None else: - view = value.as_buffer_like() - if exclusive: - mode = "xb" - else: - mode = "wb" - with path.open(mode=mode) as f: - # write takes any object supporting the buffer protocol + with _atomic_write(path, "wb", exclusive=exclusive) as f: return f.write(view) diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index 7974d0d633..970bb7d374 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -10,6 +10,7 @@ from zarr import create_array from zarr.core.buffer import Buffer, cpu from zarr.storage import LocalStore +from zarr.storage._local import _atomic_write from zarr.testing.store import StoreTests from zarr.testing.utils import assert_bytes_equal @@ -109,3 +110,46 @@ async def test_move( FileExistsError, match=re.escape(f"Destination root {destination} already exists") ): await store2.move(destination) + + +@pytest.mark.parametrize("exclusive", [True, False]) +def test_atomic_write_successful(tmp_path: pathlib.Path, exclusive: bool) -> None: + path = pathlib.Path(tmp_path) / "data" + with _atomic_write(path, "wb", exclusive=exclusive) as f: + f.write(b"abc") + assert path.read_bytes() == b"abc" + assert list(path.parent.iterdir()) == [path] # no temp files + + +@pytest.mark.parametrize("exclusive", [True, False]) +def test_atomic_write_incomplete(tmp_path: pathlib.Path, exclusive: bool) -> None: + path = pathlib.Path(tmp_path) / "data" + with pytest.raises(RuntimeError): # noqa: PT012 + with _atomic_write(path, "wb", exclusive=exclusive) as f: + f.write(b"a") + raise RuntimeError + assert not path.exists() + assert list(path.parent.iterdir()) == [] # no temp files + + +def test_atomic_write_non_exclusive_preexisting(tmp_path: pathlib.Path) -> None: + path = pathlib.Path(tmp_path) / "data" + with path.open("wb") as f: + f.write(b"xyz") + assert path.read_bytes() == b"xyz" + with _atomic_write(path, "wb", exclusive=False) as f: + f.write(b"abc") + assert path.read_bytes() == b"abc" + assert list(path.parent.iterdir()) == [path] # no temp files + + +def test_atomic_write_exclusive_preexisting(tmp_path: pathlib.Path) -> None: + path = pathlib.Path(tmp_path) / "data" + with path.open("wb") as f: + f.write(b"xyz") + assert path.read_bytes() == b"xyz" + with pytest.raises(FileExistsError): + with _atomic_write(path, "wb", exclusive=True) as f: + f.write(b"abc") + assert path.read_bytes() == b"xyz" + assert list(path.parent.iterdir()) == [path] # no temp files From 710f5dfbc61606ea7119f3c785bae7ba4f3572c9 Mon Sep 17 00:00:00 2001 From: Stephan Hoyer Date: Thu, 28 Aug 2025 11:43:01 -0700 Subject: [PATCH 085/468] Simplify local store tests (#3414) --- tests/test_store/test_local.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index 970bb7d374..79e8f740d4 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -114,7 +114,7 @@ async def test_move( @pytest.mark.parametrize("exclusive", [True, False]) def test_atomic_write_successful(tmp_path: pathlib.Path, exclusive: bool) -> None: - path = pathlib.Path(tmp_path) / "data" + path = tmp_path / "data" with _atomic_write(path, "wb", exclusive=exclusive) as f: f.write(b"abc") assert path.read_bytes() == b"abc" @@ -123,7 +123,7 @@ def test_atomic_write_successful(tmp_path: pathlib.Path, exclusive: bool) -> Non @pytest.mark.parametrize("exclusive", [True, False]) def test_atomic_write_incomplete(tmp_path: pathlib.Path, exclusive: bool) -> None: - path = pathlib.Path(tmp_path) / "data" + path = tmp_path / "data" with pytest.raises(RuntimeError): # noqa: PT012 with _atomic_write(path, "wb", exclusive=exclusive) as f: f.write(b"a") @@ -133,7 +133,7 @@ def test_atomic_write_incomplete(tmp_path: pathlib.Path, exclusive: bool) -> Non def test_atomic_write_non_exclusive_preexisting(tmp_path: pathlib.Path) -> None: - path = pathlib.Path(tmp_path) / "data" + path = tmp_path / "data" with path.open("wb") as f: f.write(b"xyz") assert path.read_bytes() == b"xyz" @@ -144,7 +144,7 @@ def test_atomic_write_non_exclusive_preexisting(tmp_path: pathlib.Path) -> None: def test_atomic_write_exclusive_preexisting(tmp_path: pathlib.Path) -> None: - path = pathlib.Path(tmp_path) / "data" + path = tmp_path / "data" with path.open("wb") as f: f.write(b"xyz") assert path.read_bytes() == b"xyz" From 6d4b5e77e30fa56eb1e03bf34016be5b18f4ddb5 Mon Sep 17 00:00:00 2001 From: Stephan Hoyer Date: Fri, 29 Aug 2025 11:31:56 -0700 Subject: [PATCH 086/468] Remove Store.set_partial_writes (#3413) * Remove Store.set_partial_writes This feature was unused by the rest of Zarr-Python, and was only implemented for LocalStore and stores that wrap other stores. The Zarr v3 spec still mentions partial writes, so it should probably also be updated. * ruff fix * include fsspec --------- Co-authored-by: Davis Bennett --- changes/2859.removal.rst | 2 ++ src/zarr/abc/store.py | 26 ++++++------------------- src/zarr/storage/_common.py | 11 +---------- src/zarr/storage/_fsspec.py | 9 --------- src/zarr/storage/_local.py | 33 ++++---------------------------- src/zarr/storage/_logging.py | 13 ------------- src/zarr/storage/_memory.py | 8 -------- src/zarr/storage/_obstore.py | 12 ------------ src/zarr/storage/_wrapper.py | 10 ---------- src/zarr/storage/_zip.py | 7 ------- src/zarr/testing/stateful.py | 7 ------- src/zarr/testing/store.py | 4 ++-- tests/test_store/test_fsspec.py | 3 --- tests/test_store/test_local.py | 3 --- tests/test_store/test_logging.py | 3 --- tests/test_store/test_memory.py | 6 ------ tests/test_store/test_object.py | 5 ----- tests/test_store/test_wrapper.py | 3 --- tests/test_store/test_zip.py | 3 --- 19 files changed, 15 insertions(+), 153 deletions(-) create mode 100644 changes/2859.removal.rst diff --git a/changes/2859.removal.rst b/changes/2859.removal.rst new file mode 100644 index 0000000000..bd417855f3 --- /dev/null +++ b/changes/2859.removal.rst @@ -0,0 +1,2 @@ +The ``Store.set_partial_writes`` method, which was not used by Zarr-Python, has been removed. +``store.supports_partial_writes`` is now always ``False``. diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 53e981c3bd..e8d1329b17 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -4,7 +4,7 @@ from asyncio import gather from dataclasses import dataclass from itertools import starmap -from typing import TYPE_CHECKING, Protocol, runtime_checkable +from typing import TYPE_CHECKING, Literal, Protocol, runtime_checkable if TYPE_CHECKING: from collections.abc import AsyncGenerator, AsyncIterator, Iterable @@ -12,7 +12,6 @@ from typing import Any, Self, TypeAlias from zarr.core.buffer import Buffer, BufferPrototype - from zarr.core.common import BytesLike __all__ = ["ByteGetter", "ByteSetter", "Store", "set_or_delete"] @@ -310,25 +309,12 @@ async def delete(self, key: str) -> None: ... @property - @abstractmethod - def supports_partial_writes(self) -> bool: - """Does the store support partial writes?""" - ... - - @abstractmethod - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, BytesLike]] - ) -> None: - """Store values at a given key, starting at byte range_start. + def supports_partial_writes(self) -> Literal[False]: + """Does the store support partial writes? - Parameters - ---------- - key_start_values : list[tuple[str, int, BytesLike]] - set of key, range_start, values triples, a key may occur multiple times with different - range_starts, range_starts (considering the length of the respective values) must not - specify overlapping ranges for the same key + Partial writes are no longer used by Zarr, so this is always false. """ - ... + return False @property @abstractmethod @@ -499,7 +485,7 @@ async def get( self, prototype: BufferPrototype, byte_range: ByteRequest | None = None ) -> Buffer | None: ... - async def set(self, value: Buffer, byte_range: ByteRequest | None = None) -> None: ... + async def set(self, value: Buffer) -> None: ... async def delete(self) -> None: ... diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 66a53c19df..ff757f9a99 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -163,7 +163,7 @@ async def get( prototype = default_buffer_prototype() return await self.store.get(self.path, prototype=prototype, byte_range=byte_range) - async def set(self, value: Buffer, byte_range: ByteRequest | None = None) -> None: + async def set(self, value: Buffer) -> None: """ Write bytes to the store. @@ -171,16 +171,7 @@ async def set(self, value: Buffer, byte_range: ByteRequest | None = None) -> Non ---------- value : Buffer The buffer to write. - byte_range : ByteRequest, optional - The range of bytes to write. If None, the entire buffer is written. - - Raises - ------ - NotImplementedError - If `byte_range` is not None, because Store.set does not support partial writes yet. """ - if byte_range is not None: - raise NotImplementedError("Store.set does not have partial writes yet") await self.store.set(self.path, value) async def delete(self) -> None: diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index bbb934cc7d..c5afed521c 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -26,7 +26,6 @@ from fsspec.mapping import FSMap from zarr.core.buffer import BufferPrototype - from zarr.core.common import BytesLike ALLOWED_EXCEPTIONS: tuple[type[Exception], ...] = ( @@ -90,7 +89,6 @@ class FsspecStore(Store): allowed_exceptions supports_writes supports_deletes - supports_partial_writes supports_listing Raises @@ -114,7 +112,6 @@ class FsspecStore(Store): # based on FSSpec supports_writes: bool = True supports_deletes: bool = True - supports_partial_writes: bool = False supports_listing: bool = True fs: AsyncFileSystem @@ -418,12 +415,6 @@ async def get_partial_values( return [None if isinstance(r, Exception) else prototype.buffer.from_bytes(r) for r in res] - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, BytesLike]] - ) -> None: - # docstring inherited - raise NotImplementedError - async def list(self) -> AsyncIterator[str]: # docstring inherited allfiles = await self.fs._find(self.path, detail=False, withdirs=False) diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 717ed04144..f64da71bb4 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -77,23 +77,12 @@ def _atomic_write( raise -def _put( - path: Path, - value: Buffer, - start: int | None = None, - exclusive: bool = False, -) -> int | None: +def _put(path: Path, value: Buffer, exclusive: bool = False) -> int: path.parent.mkdir(parents=True, exist_ok=True) # write takes any object supporting the buffer protocol view = value.as_buffer_like() - if start is not None: - with path.open("r+b") as f: - f.seek(start) - f.write(view) - return None - else: - with _atomic_write(path, "wb", exclusive=exclusive) as f: - return f.write(view) + with _atomic_write(path, "wb", exclusive=exclusive) as f: + return f.write(view) class LocalStore(Store): @@ -111,14 +100,12 @@ class LocalStore(Store): ---------- supports_writes supports_deletes - supports_partial_writes supports_listing root """ supports_writes: bool = True supports_deletes: bool = True - supports_partial_writes: bool = True supports_listing: bool = True root: Path @@ -253,19 +240,7 @@ async def _set(self, key: str, value: Buffer, exclusive: bool = False) -> None: f"LocalStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead." ) path = self.root / key - await asyncio.to_thread(_put, path, value, start=None, exclusive=exclusive) - - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, bytes | bytearray | memoryview]] - ) -> None: - # docstring inherited - self._check_writable() - args = [] - for key, start, value in key_start_values: - assert isinstance(key, str) - path = self.root / key - args.append((_put, path, value, start)) - await concurrent_map(args, asyncio.to_thread, limit=None) # TODO: fix limit + await asyncio.to_thread(_put, path, value, exclusive=exclusive) async def delete(self, key: str) -> None: """ diff --git a/src/zarr/storage/_logging.py b/src/zarr/storage/_logging.py index a2164a418f..dd20d49ae5 100644 --- a/src/zarr/storage/_logging.py +++ b/src/zarr/storage/_logging.py @@ -115,11 +115,6 @@ def supports_deletes(self) -> bool: with self.log(): return self._store.supports_deletes - @property - def supports_partial_writes(self) -> bool: - with self.log(): - return self._store.supports_partial_writes - @property def supports_listing(self) -> bool: with self.log(): @@ -207,14 +202,6 @@ async def delete(self, key: str) -> None: with self.log(key): return await self._store.delete(key=key) - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, bytes | bytearray | memoryview]] - ) -> None: - # docstring inherited - keys = ",".join([k[0] for k in key_start_values]) - with self.log(keys): - return await self._store.set_partial_values(key_start_values=key_start_values) - async def list(self) -> AsyncGenerator[str, None]: # docstring inherited with self.log(): diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index 5c12563136..e6076d9669 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -32,13 +32,11 @@ class MemoryStore(Store): ---------- supports_writes supports_deletes - supports_partial_writes supports_listing """ supports_writes: bool = True supports_deletes: bool = True - supports_partial_writes: bool = True supports_listing: bool = True _store_dict: MutableMapping[str, Buffer] @@ -143,12 +141,6 @@ async def delete(self, key: str) -> None: except KeyError: logger.debug("Key %s does not exist.", key) - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, bytes | bytearray | memoryview[int]]] - ) -> None: - # docstring inherited - raise NotImplementedError - async def list(self) -> AsyncIterator[str]: # docstring inherited for key in self._store_dict: diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index e1469a991e..9bf1df8d8c 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -23,7 +23,6 @@ from obstore.store import ObjectStore as _UpstreamObjectStore from zarr.core.buffer import Buffer, BufferPrototype - from zarr.core.common import BytesLike __all__ = ["ObjectStore"] @@ -196,17 +195,6 @@ async def delete(self, key: str) -> None: with contextlib.suppress(FileNotFoundError): await obs.delete_async(self.store, key) - @property - def supports_partial_writes(self) -> bool: - # docstring inherited - return False - - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, BytesLike]] - ) -> None: - # docstring inherited - raise NotImplementedError - @property def supports_listing(self) -> bool: # docstring inherited diff --git a/src/zarr/storage/_wrapper.py b/src/zarr/storage/_wrapper.py index f21d378191..ba300a4085 100644 --- a/src/zarr/storage/_wrapper.py +++ b/src/zarr/storage/_wrapper.py @@ -9,7 +9,6 @@ from zarr.abc.store import ByteRequest from zarr.core.buffer import Buffer, BufferPrototype - from zarr.core.common import BytesLike from zarr.abc.store import Store @@ -119,15 +118,6 @@ def supports_deletes(self) -> bool: async def delete(self, key: str) -> None: await self._store.delete(key) - @property - def supports_partial_writes(self) -> bool: - return self._store.supports_partial_writes - - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, BytesLike]] - ) -> None: - return await self._store.set_partial_values(key_start_values) - @property def supports_listing(self) -> bool: return self._store.supports_listing diff --git a/src/zarr/storage/_zip.py b/src/zarr/storage/_zip.py index e52f160860..72bf9e335a 100644 --- a/src/zarr/storage/_zip.py +++ b/src/zarr/storage/_zip.py @@ -48,7 +48,6 @@ class ZipStore(Store): allowed_exceptions supports_writes supports_deletes - supports_partial_writes supports_listing path compression @@ -57,7 +56,6 @@ class ZipStore(Store): supports_writes: bool = True supports_deletes: bool = False - supports_partial_writes: bool = False supports_listing: bool = True path: Path @@ -222,11 +220,6 @@ async def set(self, key: str, value: Buffer) -> None: with self._lock: self._set(key, value) - async def set_partial_values( - self, key_start_values: Iterable[tuple[str, int, bytes | bytearray | memoryview[int]]] - ) -> None: - raise NotImplementedError - async def set_if_not_exists(self, key: str, value: Buffer) -> None: self._check_writable() with self._lock: diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index 8ada53a55a..c363c13983 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -467,17 +467,10 @@ def list_dir(self, prefix: str) -> None: def list_prefix(self, prefix: str) -> None: raise NotImplementedError - def set_partial_values(self, key_start_values: Any) -> None: - raise NotImplementedError - @property def supports_listing(self) -> bool: return self.store.supports_listing - @property - def supports_partial_writes(self) -> bool: - return self.supports_partial_writes - @property def supports_writes(self) -> bool: return self.store.supports_writes diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index d2946705f0..ad3b80da41 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -68,8 +68,8 @@ def test_store_repr(self, store: S) -> None: ... @abstractmethod def test_store_supports_writes(self, store: S) -> None: ... - @abstractmethod - def test_store_supports_partial_writes(self, store: S) -> None: ... + def test_store_supports_partial_writes(self, store: S) -> None: + assert not store.supports_partial_writes @abstractmethod def test_store_supports_listing(self, store: S) -> None: ... diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 82a96b5d1e..e970c674d4 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -169,9 +169,6 @@ def test_store_repr(self, store: FsspecStore) -> None: def test_store_supports_writes(self, store: FsspecStore) -> None: assert store.supports_writes - def test_store_supports_partial_writes(self, store: FsspecStore) -> None: - assert not store.supports_partial_writes - def test_store_supports_listing(self, store: FsspecStore) -> None: assert store.supports_listing diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index 79e8f740d4..6756bc83d9 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -38,9 +38,6 @@ def test_store_repr(self, store: LocalStore) -> None: def test_store_supports_writes(self, store: LocalStore) -> None: assert store.supports_writes - def test_store_supports_partial_writes(self, store: LocalStore) -> None: - assert store.supports_partial_writes - def test_store_supports_listing(self, store: LocalStore) -> None: assert store.supports_listing diff --git a/tests/test_store/test_logging.py b/tests/test_store/test_logging.py index 1a89dca874..d99ac5dc4f 100644 --- a/tests/test_store/test_logging.py +++ b/tests/test_store/test_logging.py @@ -44,9 +44,6 @@ def store(self, store_kwargs: str | dict[str, Buffer] | None) -> LoggingStore: def test_store_supports_writes(self, store: LoggingStore) -> None: assert store.supports_writes - def test_store_supports_partial_writes(self, store: LoggingStore) -> None: - assert store.supports_partial_writes - def test_store_supports_listing(self, store: LoggingStore) -> None: assert store.supports_listing diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 0b6bae757d..29fa9b2964 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -54,9 +54,6 @@ def test_store_supports_writes(self, store: MemoryStore) -> None: def test_store_supports_listing(self, store: MemoryStore) -> None: assert store.supports_listing - def test_store_supports_partial_writes(self, store: MemoryStore) -> None: - assert store.supports_partial_writes - async def test_list_prefix(self, store: MemoryStore) -> None: assert True @@ -115,9 +112,6 @@ def test_store_supports_writes(self, store: GpuMemoryStore) -> None: def test_store_supports_listing(self, store: GpuMemoryStore) -> None: assert store.supports_listing - def test_store_supports_partial_writes(self, store: GpuMemoryStore) -> None: - assert store.supports_partial_writes - async def test_list_prefix(self, store: GpuMemoryStore) -> None: assert True diff --git a/tests/test_store/test_object.py b/tests/test_store/test_object.py index d8b89e56b7..3217069c2d 100644 --- a/tests/test_store/test_object.py +++ b/tests/test_store/test_object.py @@ -48,11 +48,6 @@ def test_store_repr(self, store: ObjectStore) -> None: def test_store_supports_writes(self, store: ObjectStore) -> None: assert store.supports_writes - async def test_store_supports_partial_writes(self, store: ObjectStore) -> None: - assert not store.supports_partial_writes - with pytest.raises(NotImplementedError): - await store.set_partial_values([("foo", 0, b"\x01\x02\x03\x04")]) - def test_store_supports_listing(self, store: ObjectStore) -> None: assert store.supports_listing diff --git a/tests/test_store/test_wrapper.py b/tests/test_store/test_wrapper.py index c6edd4f4dd..4478e1468f 100644 --- a/tests/test_store/test_wrapper.py +++ b/tests/test_store/test_wrapper.py @@ -43,9 +43,6 @@ def open_kwargs(self, tmpdir) -> dict[str, str]: def test_store_supports_writes(self, store: WrapperStore) -> None: assert store.supports_writes - def test_store_supports_partial_writes(self, store: WrapperStore) -> None: - assert store.supports_partial_writes - def test_store_supports_listing(self, store: WrapperStore) -> None: assert store.supports_listing diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py index 24b25ed315..744ee82945 100644 --- a/tests/test_store/test_zip.py +++ b/tests/test_store/test_zip.py @@ -72,9 +72,6 @@ def test_store_repr(self, store: ZipStore) -> None: def test_store_supports_writes(self, store: ZipStore) -> None: assert store.supports_writes - def test_store_supports_partial_writes(self, store: ZipStore) -> None: - assert store.supports_partial_writes is False - def test_store_supports_listing(self, store: ZipStore) -> None: assert store.supports_listing From b8dbf564d5f585e2fcecbfe124273e0dc04a80f4 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 29 Aug 2025 21:00:40 +0200 Subject: [PATCH 087/468] chore/unformatted exceptions (#3403) * refactor errors * make metadatavalidationerrors take a single argument * create all errors with a single argument * move indexing-specific errors into the main errors module * ensure tests pass * remove redundant template from array indexing exception * add tests for single-argument templated exceptions * changelog * put the f on the f string * Update src/zarr/core/group.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * fix test for specific error message --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3403.misc.rst | 6 +++ src/zarr/api/asynchronous.py | 6 ++- src/zarr/core/array.py | 3 +- src/zarr/core/group.py | 15 ++++--- src/zarr/core/indexing.py | 68 +++++++++++++++-------------- src/zarr/core/metadata/v3.py | 6 ++- src/zarr/errors.py | 62 +++++++++++++-------------- src/zarr/storage/_common.py | 14 ++++-- tests/test_api.py | 4 +- tests/test_errors.py | 78 ++++++++++++++++++++++++++++++++++ tests/test_group.py | 4 +- tests/test_metadata/test_v3.py | 2 +- 12 files changed, 187 insertions(+), 81 deletions(-) create mode 100644 changes/3403.misc.rst create mode 100644 tests/test_errors.py diff --git a/changes/3403.misc.rst b/changes/3403.misc.rst new file mode 100644 index 0000000000..2ad4821d73 --- /dev/null +++ b/changes/3403.misc.rst @@ -0,0 +1,6 @@ +Moves some indexing-specific exceptions to ``zarr.errors``, and ensures that all Zarr-specific +exception classes accept a pre-formatted string as a single argument. This is a breaking change to +the following exceptions classes: :class:`zarr.errors.BoundsCheckError`, :class:`zarr.errors.NegativeStepError` +:class:`zarr.errors.VindexInvalidSelectionError`. These classes previously generated internally +formatted error messages when given a single argument. After this change, formatting of the error +message is up to the routine invoking the error. \ No newline at end of file diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index fdbd3b34bd..f206d48377 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -862,7 +862,8 @@ async def open_group( overwrite=overwrite, attributes=attributes, ) - raise GroupNotFoundError(store, store_path.path) + msg = f"No group found in store {store!r} at path {store_path.path!r}" + raise GroupNotFoundError(msg) async def create( @@ -1268,7 +1269,8 @@ async def open_array( overwrite=overwrite, **kwargs, ) - raise ArrayNotFoundError(store_path.store, store_path.path) from err + msg = f"No array found in store {store_path.store} at path {store_path.path}" + raise ArrayNotFoundError(msg) from err async def open_like( diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 47d9dc1047..ce19f99ba0 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -257,7 +257,8 @@ async def get_array_metadata( else: zarr_format = 2 else: - raise MetadataValidationError("zarr_format", "2, 3, or None", zarr_format) + msg = f"Invalid value for 'zarr_format'. Expected 2, 3, or None. Got '{zarr_format}'." # type: ignore[unreachable] + raise MetadataValidationError(msg) metadata_dict: dict[str, JSON] if zarr_format == 2: diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 4c14fb357c..7b2e506a14 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -96,7 +96,8 @@ def parse_node_type(data: Any) -> NodeType: """Parse the node_type field from metadata.""" if data in ("array", "group"): return cast("Literal['array', 'group']", data) - raise MetadataValidationError("node_type", "array or group", data) + msg = f"Invalid value for 'node_type'. Expected 'array' or 'group'. Got '{data}'." + raise MetadataValidationError(msg) # todo: convert None to empty dict @@ -574,7 +575,8 @@ async def open( else: zarr_format = 2 else: - raise MetadataValidationError("zarr_format", "2, 3, or None", zarr_format) + msg = f"Invalid value for 'zarr_format'. Expected 2, 3, or None. Got '{zarr_format}'." # type: ignore[unreachable] + raise MetadataValidationError(msg) if zarr_format == 2: # this is checked above, asserting here for mypy @@ -3129,10 +3131,12 @@ async def create_hierarchy( else: # we have proposed an explicit group, which is an error, given that a # group already exists. - raise ContainsGroupError(store, key) + msg = f"A group exists in store {store!r} at path {key!r}." + raise ContainsGroupError(msg) elif isinstance(extant_node, ArrayV2Metadata | ArrayV3Metadata): # we are trying to overwrite an existing array. this is an error. - raise ContainsArrayError(store, key) + msg = f"An array exists in store {store!r} at path {key!r}." + raise ContainsArrayError(msg) nodes_explicit: dict[str, GroupMetadata | ArrayV2Metadata | ArrayV3Metadata] = {} @@ -3549,7 +3553,8 @@ def _build_metadata_v3(zarr_json: dict[str, JSON]) -> ArrayV3Metadata | GroupMet Convert a dict representation of Zarr V3 metadata into the corresponding metadata class. """ if "node_type" not in zarr_json: - raise MetadataValidationError("node_type", "array or group", "nothing (the key is missing)") + msg = "Required key 'node_type' is missing from the provided metadata document." + raise MetadataValidationError(msg) match zarr_json: case {"node_type": "array"}: return ArrayV3Metadata.from_dict(zarr_json) diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 2736915f46..be60f4208f 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -28,6 +28,12 @@ from zarr.core.common import ceildiv, product from zarr.core.metadata import T_ArrayMetadata +from zarr.errors import ( + ArrayIndexError, + BoundsCheckError, + NegativeStepError, + VindexInvalidSelectionError, +) if TYPE_CHECKING: from zarr.core.array import Array, AsyncArray @@ -51,29 +57,6 @@ Fields = str | list[str] | tuple[str, ...] -class ArrayIndexError(IndexError): - pass - - -class BoundsCheckError(IndexError): - _msg = "" - - def __init__(self, dim_len: int) -> None: - self._msg = f"index out of bounds for dimension with length {dim_len}" - - -class NegativeStepError(IndexError): - _msg = "only slices with step >= 1 are supported" - - -class VindexInvalidSelectionError(IndexError): - _msg = ( - "unsupported selection type for vectorized indexing; only " - "coordinate selection (tuple of integer arrays) and mask selection " - "(single Boolean array) are supported; got {!r}" - ) - - def err_too_many_indices(selection: Any, shape: tuple[int, ...]) -> None: raise IndexError(f"too many indices for array; expected {len(shape)}, got {len(selection)}") @@ -361,7 +344,8 @@ def normalize_integer_selection(dim_sel: int, dim_len: int) -> int: # handle out of bounds if dim_sel >= dim_len or dim_sel < 0: - raise BoundsCheckError(dim_len) + msg = f"index out of bounds for dimension with length {dim_len}" + raise BoundsCheckError(msg) return dim_sel @@ -421,7 +405,7 @@ def __init__(self, dim_sel: slice, dim_len: int, dim_chunk_len: int) -> None: # normalize start, stop, step = dim_sel.indices(dim_len) if step < 1: - raise NegativeStepError + raise NegativeStepError("only slices with step >= 1 are supported.") object.__setattr__(self, "start", start) object.__setattr__(self, "stop", stop) @@ -744,7 +728,8 @@ def wraparound_indices(x: npt.NDArray[Any], dim_len: int) -> None: def boundscheck_indices(x: npt.NDArray[Any], dim_len: int) -> None: if np.any(x < 0) or np.any(x >= dim_len): - raise BoundsCheckError(dim_len) + msg = f"index out of bounds for dimension with length {dim_len}" + raise BoundsCheckError(msg) @dataclass(frozen=True) @@ -1098,7 +1083,8 @@ def __init__( dim_indexers.append(dim_indexer) if start >= dim_len or start < 0: - raise BoundsCheckError(dim_len) + msg = f"index out of bounds for dimension with length {dim_len}" + raise BoundsCheckError(msg) shape = tuple(s.nitems for s in dim_indexers) @@ -1329,7 +1315,12 @@ def __getitem__( elif is_mask_selection(new_selection, self.array.shape): return self.array.get_mask_selection(new_selection, fields=fields) else: - raise VindexInvalidSelectionError(new_selection) + msg = ( + "unsupported selection type for vectorized indexing; only " + "coordinate selection (tuple of integer arrays) and mask selection " + f"(single Boolean array) are supported; got {new_selection!r}" + ) + raise VindexInvalidSelectionError(msg) def __setitem__( self, selection: CoordinateSelection | MaskSelection, value: npt.ArrayLike @@ -1342,7 +1333,12 @@ def __setitem__( elif is_mask_selection(new_selection, self.array.shape): self.array.set_mask_selection(new_selection, value, fields=fields) else: - raise VindexInvalidSelectionError(new_selection) + msg = ( + "unsupported selection type for vectorized indexing; only " + "coordinate selection (tuple of integer arrays) and mask selection " + f"(single Boolean array) are supported; got {new_selection!r}" + ) + raise VindexInvalidSelectionError(msg) @dataclass(frozen=True) @@ -1368,7 +1364,12 @@ async def getitem( elif is_mask_selection(new_selection, self.array.shape): return await self.array.get_mask_selection(new_selection, fields=fields) else: - raise VindexInvalidSelectionError(new_selection) + msg = ( + "unsupported selection type for vectorized indexing; only " + "coordinate selection (tuple of integer arrays) and mask selection " + f"(single Boolean array) are supported; got {new_selection!r}" + ) + raise VindexInvalidSelectionError(msg) def check_fields(fields: Fields | None, dtype: np.dtype[Any]) -> np.dtype[Any]: @@ -1487,7 +1488,12 @@ def get_indexer( elif is_mask_selection(new_selection, shape): return MaskIndexer(cast("MaskSelection", selection), shape, chunk_grid) else: - raise VindexInvalidSelectionError(new_selection) + msg = ( + "unsupported selection type for vectorized indexing; only " + "coordinate selection (tuple of integer arrays) and mask selection " + f"(single Boolean array) are supported; got {new_selection!r}" + ) + raise VindexInvalidSelectionError(msg) elif is_pure_orthogonal_indexing(pure_selection, len(shape)): return OrthogonalIndexer(cast("OrthogonalSelection", selection), shape, chunk_grid) else: diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index d1420b1ddd..649a490409 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -41,13 +41,15 @@ def parse_zarr_format(data: object) -> Literal[3]: if data == 3: return 3 - raise MetadataValidationError("zarr_format", 3, data) + msg = f"Invalid value for 'zarr_format'. Expected '3'. Got '{data}'." + raise MetadataValidationError(msg) def parse_node_type_array(data: object) -> Literal["array"]: if data == "array": return "array" - raise NodeTypeValidationError("node_type", "array", data) + msg = f"Invalid value for 'node_type'. Expected 'array'. Got '{data}'." + raise NodeTypeValidationError(msg) def parse_codecs(data: object) -> tuple[Codec, ...]: diff --git a/src/zarr/errors.py b/src/zarr/errors.py index 472199ff1b..331ae52f9e 100644 --- a/src/zarr/errors.py +++ b/src/zarr/errors.py @@ -1,15 +1,17 @@ -from typing import Any - __all__ = [ + "ArrayIndexError", "ArrayNotFoundError", "BaseZarrError", + "BoundsCheckError", "ContainsArrayAndGroupError", "ContainsArrayError", "ContainsGroupError", "GroupNotFoundError", "MetadataValidationError", + "NegativeStepError", "NodeTypeValidationError", "UnstableSpecificationWarning", + "VindexInvalidSelectionError", "ZarrDeprecationWarning", "ZarrFutureWarning", "ZarrRuntimeWarning", @@ -21,10 +23,19 @@ class BaseZarrError(ValueError): Base error which all zarr errors are sub-classed from. """ - _msg = "" + _msg: str = "{}" - def __init__(self, *args: Any) -> None: - super().__init__(self._msg.format(*args)) + def __init__(self, *args: object) -> None: + """ + If a single argument is passed, treat it as a pre-formatted message. + + If multiple arguments are passed, they are used as arguments for a template string class + variable. This behavior is deprecated. + """ + if len(args) == 1: + super().__init__(args[0]) + else: + super().__init__(self._msg.format(*args)) class NodeNotFoundError(BaseZarrError, FileNotFoundError): @@ -32,29 +43,13 @@ class NodeNotFoundError(BaseZarrError, FileNotFoundError): Raised when a node (array or group) is not found at a certain path. """ - def __init__(self, *args: Any) -> None: - if len(args) == 1: - # Pre-formatted message - super(BaseZarrError, self).__init__(args[0]) - else: - # Store and path arguments - format them - _msg = "No node found in store {!r} at path {!r}" - super(BaseZarrError, self).__init__(_msg.format(*args)) - class ArrayNotFoundError(NodeNotFoundError): """ Raised when an array isn't found at a certain path. """ - def __init__(self, *args: Any) -> None: - if len(args) == 1: - # Pre-formatted message - super(BaseZarrError, self).__init__(args[0]) - else: - # Store and path arguments - format them - _msg = "No array found in store {!r} at path {!r}" - super(BaseZarrError, self).__init__(_msg.format(*args)) + _msg = "No array found in store {!r} at path {!r}" class GroupNotFoundError(NodeNotFoundError): @@ -62,14 +57,7 @@ class GroupNotFoundError(NodeNotFoundError): Raised when a group isn't found at a certain path. """ - def __init__(self, *args: Any) -> None: - if len(args) == 1: - # Pre-formatted message - super(BaseZarrError, self).__init__(args[0]) - else: - # Store and path arguments - format them - _msg = "No group found in store {!r} at path {!r}" - super(BaseZarrError, self).__init__(_msg.format(*args)) + _msg = "No group found in store {!r} at path {!r}" class ContainsGroupError(BaseZarrError): @@ -106,8 +94,6 @@ class UnknownCodecError(BaseZarrError): Raised when a unknown codec was used. """ - _msg = "{}" - class NodeTypeValidationError(MetadataValidationError): """ @@ -146,3 +132,15 @@ class ZarrRuntimeWarning(RuntimeWarning): """ A warning for dubious runtime behavior. """ + + +class VindexInvalidSelectionError(IndexError): ... + + +class NegativeStepError(IndexError): ... + + +class BoundsCheckError(IndexError): ... + + +class ArrayIndexError(IndexError): ... diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index ff757f9a99..817bda7892 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -413,9 +413,11 @@ async def ensure_no_existing_node(store_path: StorePath, zarr_format: ZarrFormat extant_node = await _contains_node_v3(store_path) if extant_node == "array": - raise ContainsArrayError(store_path.store, store_path.path) + msg = f"An array exists in store {store_path.store!r} at path {store_path.path!r}." + raise ContainsArrayError(msg) elif extant_node == "group": - raise ContainsGroupError(store_path.store, store_path.path) + msg = f"An array exists in store {store_path.store!r} at path {store_path.path!r}." + raise ContainsGroupError(msg) elif extant_node == "nothing": return msg = f"Invalid value for extant_node: {extant_node}" # type: ignore[unreachable] @@ -476,7 +478,13 @@ async def _contains_node_v2(store_path: StorePath) -> Literal["array", "group", _group = await contains_group(store_path=store_path, zarr_format=2) if _array and _group: - raise ContainsArrayAndGroupError(store_path.store, store_path.path) + msg = ( + "Array and group metadata documents (.zarray and .zgroup) were both found in store " + f"{store_path.store!r} at path {store_path.path!r}. " + "Only one of these files may be present in a given directory / prefix. " + "Remove the .zarray file, or the .zgroup file, or both." + ) + raise ContainsArrayAndGroupError(msg) elif _array: return "array" elif _group: diff --git a/tests/test_api.py b/tests/test_api.py index 9950d385a3..ff969d406f 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1231,13 +1231,13 @@ def test_open_modes_creates_group(tmp_path: Path, mode: str) -> None: async def test_metadata_validation_error() -> None: with pytest.raises( MetadataValidationError, - match="Invalid value for 'zarr_format'. Expected '2, 3, or None'. Got '3.0'.", + match="Invalid value for 'zarr_format'. Expected 2, 3, or None. Got '3.0'.", ): await zarr.api.asynchronous.open_group(zarr_format="3.0") # type: ignore[arg-type] with pytest.raises( MetadataValidationError, - match="Invalid value for 'zarr_format'. Expected '2, 3, or None'. Got '3.0'.", + match="Invalid value for 'zarr_format'. Expected 2, 3, or None. Got '3.0'.", ): await zarr.api.asynchronous.open_array(shape=(1,), zarr_format="3.0") # type: ignore[arg-type] diff --git a/tests/test_errors.py b/tests/test_errors.py new file mode 100644 index 0000000000..ccc9e597bb --- /dev/null +++ b/tests/test_errors.py @@ -0,0 +1,78 @@ +"""Test errors""" + +from zarr.errors import ( + ArrayNotFoundError, + ContainsArrayAndGroupError, + ContainsArrayError, + ContainsGroupError, + GroupNotFoundError, + MetadataValidationError, + NodeTypeValidationError, +) + + +def test_group_not_found_error() -> None: + """ + Test that calling GroupNotFoundError with multiple arguments returns a formatted string. + This is deprecated behavior. + """ + err = GroupNotFoundError("store", "path") + assert str(err) == "No group found in store 'store' at path 'path'" + + +def test_array_not_found_error() -> None: + """ + Test that calling ArrayNotFoundError with multiple arguments returns a formatted string. + This is deprecated behavior. + """ + err = ArrayNotFoundError("store", "path") + assert str(err) == "No array found in store 'store' at path 'path'" + + +def test_metadata_validation_error() -> None: + """ + Test that calling MetadataValidationError with multiple arguments returns a formatted string. + This is deprecated behavior. + """ + err = MetadataValidationError("a", "b", "c") + assert str(err) == "Invalid value for 'a'. Expected 'b'. Got 'c'." + + +def test_contains_group_error() -> None: + """ + Test that calling ContainsGroupError with multiple arguments returns a formatted string. + This is deprecated behavior. + """ + err = ContainsGroupError("store", "path") + assert str(err) == "A group exists in store 'store' at path 'path'." + + +def test_contains_array_error() -> None: + """ + Test that calling ContainsArrayError with multiple arguments returns a formatted string. + This is deprecated behavior. + """ + err = ContainsArrayError("store", "path") + assert str(err) == "An array exists in store 'store' at path 'path'." + + +def test_contains_array_and_group_error() -> None: + """ + Test that calling ContainsArrayAndGroupError with multiple arguments returns a formatted string. + This is deprecated behavior. + """ + err = ContainsArrayAndGroupError("store", "path") + assert str(err) == ( + "Array and group metadata documents (.zarray and .zgroup) were both found in store 'store' " + "at path 'path'. Only one of these files may be present in a given directory / prefix. " + "Remove the .zarray file, or the .zgroup file, or both." + ) + + +def test_node_type_validation_error() -> None: + """ + Test that calling NodeTypeValidationError with multiple arguments returns a formatted string. + This is deprecated behavior. + """ + err = NodeTypeValidationError("a", "b", "c") + assert str(err) == "Invalid value for 'a'. Expected 'b'. Got 'c'." diff --git a/tests/test_group.py b/tests/test_group.py index e5cfe82daa..2d9070bd67 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -2220,8 +2220,8 @@ def test_build_metadata_v3(option: Literal["array", "group", "invalid"]) -> None metadata_dict = GroupMetadata(zarr_format=3).to_dict() metadata_dict.pop("node_type") # TODO: fix the error message - msg = "Invalid value for 'node_type'. Expected 'array or group'. Got 'nothing (the key is missing)'." - with pytest.raises(MetadataValidationError, match=re.escape(msg)): + msg = "Required key 'node_type' is missing from the provided metadata document." + with pytest.raises(MetadataValidationError, match=msg): _build_metadata_v3(metadata_dict) diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 4fdcce7b6b..1405bf533b 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -93,7 +93,7 @@ def test_parse_node_type_valid() -> None: def test_parse_node_type_invalid(node_type: Any) -> None: with pytest.raises( MetadataValidationError, - match=f"Invalid value for 'node_type'. Expected 'array or group'. Got '{node_type}'.", + match=f"Invalid value for 'node_type'. Expected 'array' or 'group'. Got '{node_type}'.", ): parse_node_type(node_type) From 7d43f32121db1bbb51b1871bcbdac9fdd8ed55f2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 1 Sep 2025 22:25:51 +0200 Subject: [PATCH 088/468] chore: update pre-commit hooks (#3423) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.7...v0.12.11) - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0) - [github.com/twisted/towncrier: 24.8.0 → 25.8.0](https://github.com/twisted/towncrier/compare/24.8.0...25.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9f91c709c7..3a75601daa 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ ci: default_stages: [pre-commit, pre-push] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.7 + rev: v0.12.11 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -17,7 +17,7 @@ repos: - id: codespell args: ["-L", "fo,ihs,kake,te", "-S", "fixture"] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 + rev: v6.0.0 hooks: - id: check-yaml - id: trailing-whitespace @@ -53,6 +53,6 @@ repos: hooks: - id: numpydoc-validation - repo: https://github.com/twisted/towncrier - rev: 24.8.0 + rev: 25.8.0 hooks: - id: towncrier-check From 276b9974e97543f5fc49116179c70ad09a2270ba Mon Sep 17 00:00:00 2001 From: "Lachlan (Lachy) Deakin" Date: Tue, 2 Sep 2025 17:40:00 +1000 Subject: [PATCH 089/468] fix: `ChunkCoords` definition (#3425) * fix: `ChunkCoords` definition Broken since #3374 * changelog --- changes/3425.bugfix.rst | 1 + src/zarr/core/common.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 changes/3425.bugfix.rst diff --git a/changes/3425.bugfix.rst b/changes/3425.bugfix.rst new file mode 100644 index 0000000000..71cc147287 --- /dev/null +++ b/changes/3425.bugfix.rst @@ -0,0 +1 @@ +Fix ChunkGrid definition (broken in 3.1.2) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index ed28fd2da4..bebccb65fc 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -38,7 +38,7 @@ BytesLike = bytes | bytearray | memoryview ShapeLike = Iterable[int] | int # For backwards compatibility -ChunkCoords: tuple[int, ...] +ChunkCoords = tuple[int, ...] ZarrFormat = Literal[2, 3] NodeType = Literal["array", "group"] JSON = str | int | float | Mapping[str, "JSON"] | Sequence["JSON"] | None From 6c04c82154724adb1a8768f8aee13fdef73f13c7 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 2 Sep 2025 16:43:51 +0200 Subject: [PATCH 090/468] specify default event loop for async tests (#3424) --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 52b032f771..bea8d77127 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -379,6 +379,7 @@ testpaths = ["tests", "docs/user-guide"] log_cli_level = "INFO" xfail_strict = true asyncio_mode = "auto" +asyncio_default_fixture_loop_scope = "function" doctest_optionflags = [ "NORMALIZE_WHITESPACE", "ELLIPSIS", From 00e781421760ab663679087c9d8484bea752e694 Mon Sep 17 00:00:00 2001 From: Stephan Hoyer Date: Wed, 3 Sep 2025 01:19:05 -0700 Subject: [PATCH 091/468] Ensure absolute paths work with consolidate metadata (#3428) * Ensure absolute paths work with consolidate metadata * bug fix note * ruff format --- changes/3428.bugfix.rst | 1 + src/zarr/core/group.py | 2 +- tests/test_metadata/test_consolidated.py | 15 +++++++++++++++ 3 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 changes/3428.bugfix.rst diff --git a/changes/3428.bugfix.rst b/changes/3428.bugfix.rst new file mode 100644 index 0000000000..d15a3db3ba --- /dev/null +++ b/changes/3428.bugfix.rst @@ -0,0 +1 @@ +Ensure syntax like ``root['/subgroup']`` works equivalently to ``root['subgroup']`` when using consolidated metadata. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 7b2e506a14..15a256fb5d 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -735,7 +735,7 @@ def _getitem_consolidated( assert self.metadata.consolidated_metadata is not None # we support nested getitems like group/subgroup/array - indexers = key.split("/") + indexers = normalize_path(key).split("/") indexers.reverse() metadata: ArrayV2Metadata | ArrayV3Metadata | GroupMetadata = self.metadata diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index 0995be3c6d..9e8b763ef7 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -692,6 +692,21 @@ async def test_use_consolidated_for_children_members( expected = ["b", "b/c"] assert result == expected + async def test_absolute_path_for_subgroup(self, memory_store: zarr.storage.MemoryStore) -> None: + root = await zarr.api.asynchronous.create_group(store=memory_store) + await root.create_group("a/b") + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await zarr.api.asynchronous.consolidate_metadata(memory_store) + + group = await zarr.api.asynchronous.open_group(store=memory_store) + subgroup = await group.getitem("/a") + assert isinstance(subgroup, AsyncGroup) + members = [x async for x in subgroup.keys()] # noqa: SIM118 + assert members == ["b"] + @pytest.mark.parametrize("fill_value", [np.nan, np.inf, -np.inf]) async def test_consolidated_metadata_encodes_special_chars( From b4835432e8805ec65529965cc77a3c3142d6715a Mon Sep 17 00:00:00 2001 From: David Stansby Date: Wed, 3 Sep 2025 20:17:25 +0100 Subject: [PATCH 092/468] Fix creating groups with group() (#3431) * Fix creating groups with group() * Add bugfix entry * Fix import order * Rename 3431.bufix.rst to 3431.bugfix.rst --- changes/3431.bugfix.rst | 2 ++ src/zarr/api/asynchronous.py | 42 ++++++++++------------------- tests/test_api/test_asynchronous.py | 19 ++++++++++++- 3 files changed, 34 insertions(+), 29 deletions(-) create mode 100644 changes/3431.bugfix.rst diff --git a/changes/3431.bugfix.rst b/changes/3431.bugfix.rst new file mode 100644 index 0000000000..cdf166ddd5 --- /dev/null +++ b/changes/3431.bugfix.rst @@ -0,0 +1,2 @@ +Creating a new group with `zarr.group` no longer errors. +This fixes a regression introduced in version 3.1.2. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index f206d48377..409601e474 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -670,38 +670,24 @@ async def group( g : group The new group. """ - - zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) - mode: AccessModeLiteral if overwrite: mode = "w" else: - mode = "r+" - store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options) - - if chunk_store is not None: - warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if cache_attrs is not None: - warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if synchronizer is not None: - warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if meta_array is not None: - warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - - if attributes is None: - attributes = {} - - try: - return await AsyncGroup.open(store=store_path, zarr_format=zarr_format) - except (KeyError, FileNotFoundError): - _zarr_format = zarr_format or _default_zarr_format() - return await AsyncGroup.from_store( - store=store_path, - zarr_format=_zarr_format, - overwrite=overwrite, - attributes=attributes, - ) + mode = "a" + return await open_group( + store=store, + mode=mode, + chunk_store=chunk_store, + cache_attrs=cache_attrs, + synchronizer=synchronizer, + path=path, + zarr_version=zarr_version, + zarr_format=zarr_format, + meta_array=meta_array, + attributes=attributes, + storage_options=storage_options, + ) async def create_group( diff --git a/tests/test_api/test_asynchronous.py b/tests/test_api/test_asynchronous.py index 910fd2883c..0f219fd727 100644 --- a/tests/test_api/test_asynchronous.py +++ b/tests/test_api/test_asynchronous.py @@ -8,10 +8,12 @@ import pytest from zarr import create_array -from zarr.api.asynchronous import _get_shape_chunks, _like_args, open +from zarr.api.asynchronous import _get_shape_chunks, _like_args, group, open from zarr.core.buffer.core import default_buffer_prototype +from zarr.core.group import AsyncGroup if TYPE_CHECKING: + from pathlib import Path from typing import Any import numpy.typing as npt @@ -103,3 +105,18 @@ async def test_open_no_array() -> None: TypeError, match=r"open_group\(\) got an unexpected keyword argument 'shape'" ): await open(store=store, shape=(1,)) + + +async def test_open_group_new_path(tmp_path: Path) -> None: + """ + Test that zarr.api.asynchronous.group properly handles a string representation of a local file + path that does not yet exist. + See https://github.com/zarr-developers/zarr-python/issues/3406 + """ + # tmp_path exists, but tmp_path / "test.zarr" will not, which is important for this test + path = tmp_path / "test.zarr" + grp = await group(store=path, attributes={"a": 1}) + assert isinstance(grp, AsyncGroup) + # Calling group on an existing store should just open that store + grp = await group(store=path) + assert grp.attrs == {"a": 1} From e738e2fb88dbead26a853d9982ff46eab64f313f Mon Sep 17 00:00:00 2001 From: David Stansby Date: Wed, 3 Sep 2025 21:12:17 +0100 Subject: [PATCH 093/468] Raise more helpful errors in _dereference_path (#3392) * Raise more helpful errors in _dereference_path * Add some type ignore comments --------- Co-authored-by: Davis Bennett --- src/zarr/storage/_common.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 817bda7892..177d84cd01 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -31,8 +31,12 @@ def _dereference_path(root: str, path: str) -> str: - assert isinstance(root, str) - assert isinstance(path, str) + if not isinstance(root, str): + msg = f"{root=} is not a string ({type(root)=})" # type: ignore[unreachable] + raise TypeError(msg) + if not isinstance(path, str): + msg = f"{path=} is not a string ({type(path)=})" # type: ignore[unreachable] + raise TypeError(msg) root = root.rstrip("/") path = f"{root}/{path}" if root else path return path.rstrip("/") From ac95b4d9b395749de3c2626909be6dd644c10dd7 Mon Sep 17 00:00:00 2001 From: Stephan Hoyer Date: Thu, 4 Sep 2025 08:51:29 -0700 Subject: [PATCH 094/468] Pass read_only into LocalStore.open() (#3432) Currently, `read_only` is not passed in `open()`, which means the default value of `read_only=False` is confusingly used instead. This mostly just surprisng, but also has minor performance implications because `read_only=False` means Zarr attempts to create directories on this line (which is a no-op because `exist_ok=True`): https://github.com/zarr-developers/zarr-python/blob/e738e2fb88dbead26a853d9982ff46eab64f313f/src/zarr/storage/_local.py#L167-L169 --- src/zarr/storage/_common.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 177d84cd01..90f0b28870 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -353,7 +353,7 @@ async def make_store_path( elif isinstance(store_like, Path): # Create a new LocalStore - store = await LocalStore.open(root=store_like, mode=mode) + store = await LocalStore.open(root=store_like, mode=mode, read_only=_read_only) elif isinstance(store_like, str): # Either a FSSpec URI or a local filesystem path From 3d0e40e171ed91d8315be7e4850c301a2093ca47 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 4 Sep 2025 16:27:26 +0000 Subject: [PATCH 095/468] Bump pypa/gh-action-pypi-publish (#3434) Bumps the github_actions group with 1 update in the /.github/workflows directory: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish). Updates `pypa/gh-action-pypi-publish` from 1.12.4 to 1.13.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.12.4...v1.13.0) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.13.0 dependency-type: direct:production dependency-group: github_actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/releases.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index f35cc0c3f5..ddc9e7b920 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -55,7 +55,7 @@ jobs: with: name: releases path: dist - - uses: pypa/gh-action-pypi-publish@v1.12.4 + - uses: pypa/gh-action-pypi-publish@v1.13.0 with: user: __token__ password: ${{ secrets.pypi_password }} From a8da9209a4a00fcef12e9c05da7046f45d9c3210 Mon Sep 17 00:00:00 2001 From: Kenneth Li Date: Sat, 6 Sep 2025 15:02:41 -0400 Subject: [PATCH 096/468] obstore delete_dir (#3310) * obstore delete_dir * add cl * add a delete test * use obstore list and collect_async * delete test --------- Co-authored-by: Davis Bennett --- changes/3310.feature.rst | 1 + src/zarr/storage/_obstore.py | 13 +++++++++++++ 2 files changed, 14 insertions(+) create mode 100644 changes/3310.feature.rst diff --git a/changes/3310.feature.rst b/changes/3310.feature.rst new file mode 100644 index 0000000000..b21d3219fc --- /dev/null +++ b/changes/3310.feature.rst @@ -0,0 +1 @@ +Add obstore implementation of delete_dir. diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index 9bf1df8d8c..7ef0b40628 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -13,6 +13,7 @@ Store, SuffixByteRequest, ) +from zarr.core.common import concurrent_map from zarr.core.config import config if TYPE_CHECKING: @@ -195,6 +196,18 @@ async def delete(self, key: str) -> None: with contextlib.suppress(FileNotFoundError): await obs.delete_async(self.store, key) + async def delete_dir(self, prefix: str) -> None: + # docstring inherited + import obstore as obs + + self._check_writable() + if prefix != "" and not prefix.endswith("/"): + prefix += "/" + + metas = await obs.list(self.store, prefix).collect_async() + keys = [(m["path"],) for m in metas] + await concurrent_map(keys, self.delete, limit=config.get("async.concurrency")) + @property def supports_listing(self) -> bool: # docstring inherited From ee9c182a17a3851e7b360275dbf13bb323f1d922 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 8 Sep 2025 09:33:23 -0600 Subject: [PATCH 097/468] Bump the actions group across 1 directory with 4 updates (#3439) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 4 ++-- .github/workflows/gpu_test.yml | 4 ++-- .github/workflows/hypothesis.yaml | 4 ++-- .github/workflows/needs_release_notes.yml | 2 +- .github/workflows/releases.yml | 4 ++-- .github/workflows/test.yml | 12 ++++++------ 6 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 8069fc1319..7c18e73f84 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -9,10 +9,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 - name: Install uv - uses: astral-sh/setup-uv@e92bafb6253dcd438e0484186d7669ea7a8ca1cc # v6.4.3 + uses: astral-sh/setup-uv@557e51de59eb14aaaba2ed9621916900a91d50c6 # v6.6.1 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 133265f348..edd52186c5 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -29,7 +29,7 @@ jobs: dependency-set: ["minimal"] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 # - name: cuda-toolkit # uses: Jimver/cuda-toolkit@v0.2.16 # id: cuda-toolkit @@ -49,7 +49,7 @@ jobs: echo $LD_LIBRARY_PATH nvcc -V - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} cache: 'pip' diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index d47abed208..0ca263ae9f 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -28,7 +28,7 @@ jobs: dependency-set: ["optional"] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - name: Set HYPOTHESIS_PROFILE based on trigger run: | if [[ "${{ github.event_name }}" == "schedule" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then @@ -37,7 +37,7 @@ jobs: echo "HYPOTHESIS_PROFILE=ci" >> $GITHUB_ENV fi - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} cache: 'pip' diff --git a/.github/workflows/needs_release_notes.yml b/.github/workflows/needs_release_notes.yml index 7a6c5462b4..d789a926a2 100644 --- a/.github/workflows/needs_release_notes.yml +++ b/.github/workflows/needs_release_notes.yml @@ -11,7 +11,7 @@ jobs: pull-requests: write runs-on: ubuntu-latest steps: - - uses: actions/labeler@8558fd74291d67161a8a78ce36a881fa63b766a9 # v5.0.0 + - uses: actions/labeler@634933edcd8ababfe52f92936142cc22ac488b1b # v6.0.1 with: repo-token: ${{ secrets.GITHUB_TOKEN }} sync-labels: true diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index ddc9e7b920..94522e0874 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -11,12 +11,12 @@ jobs: fail-fast: false steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 with: submodules: true fetch-depth: 0 - - uses: actions/setup-python@v5.2.0 + - uses: actions/setup-python@v6 name: Install Python with: python-version: '3.11' diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d1921a8306..70303060ea 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -44,11 +44,11 @@ jobs: runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 with: fetch-depth: 0 # grab all branches and tags - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -86,11 +86,11 @@ jobs: - python-version: "3.11" dependency-set: upstream steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 with: fetch-depth: 0 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -115,11 +115,11 @@ jobs: name: doctests runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 with: fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: '3.13' cache: 'pip' From 27d689c632a01162a1209c21fc80f7c00485cb98 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 12 Sep 2025 16:32:04 +0200 Subject: [PATCH 098/468] fix/shard iteration redux (#3422) * iterate over shards instead of chunks in second branch * add test * parametrize over array type * changelog * appease mypy --- changes/3422.bugfix.rst | 4 ++++ src/zarr/core/array.py | 2 +- tests/test_array.py | 26 ++++++++++++++++++++++++++ 3 files changed, 31 insertions(+), 1 deletion(-) create mode 100644 changes/3422.bugfix.rst diff --git a/changes/3422.bugfix.rst b/changes/3422.bugfix.rst new file mode 100644 index 0000000000..ed4b8c266d --- /dev/null +++ b/changes/3422.bugfix.rst @@ -0,0 +1,4 @@ +Fix a potential race condition when using :func:`zarr.create_array` with the ``data`` parameter +set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity +that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for +that array. \ No newline at end of file diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index ce19f99ba0..f31b0cc0a4 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -4421,7 +4421,7 @@ async def _copy_arraylike_region(chunk_coords: slice, _data: NDArrayLike) -> Non # Stream data from the source array to the new array await concurrent_map( - [(region, data) for region in result._iter_chunk_regions()], + [(region, data) for region in result._iter_shard_regions()], _copy_arraylike_region, zarr.core.config.config.get("async.concurrency"), ) diff --git a/tests/test_array.py b/tests/test_array.py index 97aef9319b..cf201ce0c7 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -74,6 +74,7 @@ ZarrUserWarning, ) from zarr.storage import LocalStore, MemoryStore, StorePath +from zarr.storage._logging import LoggingStore from .test_dtype.conftest import zdtype_examples @@ -2119,3 +2120,28 @@ def test_iter_chunk_regions( assert observed == expected assert observed == tuple(arr._iter_chunk_regions()) assert observed == tuple(arr._async_array._iter_chunk_regions()) + + +@pytest.mark.parametrize("num_shards", [1, 3]) +@pytest.mark.parametrize("array_type", ["numpy", "zarr"]) +def test_create_array_with_data_num_gets( + num_shards: int, array_type: Literal["numpy", "zarr"] +) -> None: + """ + Test that creating an array with data only invokes a single get request per stored object + """ + store = LoggingStore(store=MemoryStore()) + + chunk_shape = (1,) + shard_shape = (100,) + shape = (shard_shape[0] * num_shards,) + data: Array | npt.NDArray[np.int64] + if array_type == "numpy": + data = np.zeros(shape[0], dtype="int64") + else: + data = zarr.zeros(shape, dtype="int64") + + zarr.create_array(store, data=data, chunks=chunk_shape, shards=shard_shape, fill_value=-1) # type: ignore[arg-type] + # one get for the metadata and one per shard. + # Note: we don't actually need one get per shard, but this is the current behavior + assert store.counter["get"] == 1 + num_shards From af5695689a8add09a4be8afaecbbf59b7a3134da Mon Sep 17 00:00:00 2001 From: Joe Hamman Date: Fri, 12 Sep 2025 08:00:32 -0700 Subject: [PATCH 099/468] feature(ci): updload nightly wheel to scientific python anaconda repo (#3449) * feature(ci): updload nightly wheel to scientific python anaconda repo * add changelog entry * add docs section in "installing" * reformat pip install --- .github/workflows/nightly_wheels.yml | 37 ++++++++++++++++++++++++++++ changes/3449.misc.rst | 1 + docs/user-guide/installation.rst | 13 ++++++++++ 3 files changed, 51 insertions(+) create mode 100644 .github/workflows/nightly_wheels.yml create mode 100644 changes/3449.misc.rst diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml new file mode 100644 index 0000000000..10bc7c5ff1 --- /dev/null +++ b/.github/workflows/nightly_wheels.yml @@ -0,0 +1,37 @@ +name: Nightly Wheels + +on: + schedule: + # Run nightly at 2 AM UTC + - cron: '0 2 * * *' + workflow_dispatch: + +jobs: + build_and_upload_nightly: + name: Build and upload nightly wheels + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v5 + with: + submodules: true + fetch-depth: 0 + + - uses: actions/setup-python@v6 + name: Install Python + with: + python-version: '3.13' + + - name: Install build dependencies + run: | + python -m pip install --upgrade pip + pip install hatch + + - name: Build wheel and sdist + run: hatch build + + - name: Upload nightly wheels + uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd7672769da06 + with: + artifacts_path: dist + anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }} diff --git a/changes/3449.misc.rst b/changes/3449.misc.rst new file mode 100644 index 0000000000..df17bf582e --- /dev/null +++ b/changes/3449.misc.rst @@ -0,0 +1 @@ +Publish nightly wheels to https://anaconda.org/scientific-python-nightly-wheels/. diff --git a/docs/user-guide/installation.rst b/docs/user-guide/installation.rst index fbd30dedea..67705d3be6 100644 --- a/docs/user-guide/installation.rst +++ b/docs/user-guide/installation.rst @@ -42,6 +42,19 @@ Zarr is also published to `conda-forge `_. Install it u Conda does not support optional dependencies, so you will have to manually install any packages needed to enable extra functionality. +Nightly wheels +-------------- + +Development wheels are built nightly and published to the `scientific-python-nightly-wheels `_ index. To install the latest nightly build: + +.. code-block:: console + + $ pip install --pre \ + --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \ + zarr + +Note that nightly wheels may be unstable and are intended for testing purposes. + Dependency support ------------------ Zarr has endorsed `Scientific-Python SPEC 0 `_ and now follows the version support window as outlined below: From d3fa3f5e1ae104ef5f24175b1e94b8e82d899f88 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 12 Sep 2025 16:19:22 +0100 Subject: [PATCH 100/468] Document that copy() functions are not implemented (#3442) --- src/zarr/api/asynchronous.py | 9 +++++++++ src/zarr/api/synchronous.py | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 409601e474..dcfadf6a3f 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -250,14 +250,23 @@ async def consolidate_metadata( async def copy(*args: Any, **kwargs: Any) -> tuple[int, int, int]: + """ + Not implemented. + """ raise NotImplementedError async def copy_all(*args: Any, **kwargs: Any) -> tuple[int, int, int]: + """ + Not implemented. + """ raise NotImplementedError async def copy_store(*args: Any, **kwargs: Any) -> tuple[int, int, int]: + """ + Not implemented. + """ raise NotImplementedError diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 1146a6876f..1e47208dcc 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -112,14 +112,23 @@ def consolidate_metadata( def copy(*args: Any, **kwargs: Any) -> tuple[int, int, int]: + """ + Not implemented. + """ return sync(async_api.copy(*args, **kwargs)) def copy_all(*args: Any, **kwargs: Any) -> tuple[int, int, int]: + """ + Not implemented. + """ return sync(async_api.copy_all(*args, **kwargs)) def copy_store(*args: Any, **kwargs: Any) -> tuple[int, int, int]: + """ + Not implemented. + """ return sync(async_api.copy_store(*args, **kwargs)) From 4011d511dfc95a4e86a12b41d6fb874dcc578630 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 12 Sep 2025 17:31:36 +0200 Subject: [PATCH 101/468] allow int-like floats for int dtype fill values (#3448) * allow int-like floats for int dtype fill values * changelog * add specific test for intish float * correct test * Update tests/test_dtype/test_npy/test_common.py Co-authored-by: Ryan Abernathey --------- Co-authored-by: Ryan Abernathey --- changes/3448.bugfix.rst | 3 +++ src/zarr/core/dtype/npy/common.py | 21 +++++++++++++++++++++ src/zarr/core/dtype/npy/int.py | 3 +++ tests/test_dtype/test_npy/test_common.py | 8 ++++++++ tests/test_dtype/test_npy/test_int.py | 16 ++++++++-------- 5 files changed, 43 insertions(+), 8 deletions(-) create mode 100644 changes/3448.bugfix.rst diff --git a/changes/3448.bugfix.rst b/changes/3448.bugfix.rst new file mode 100644 index 0000000000..6c8b106153 --- /dev/null +++ b/changes/3448.bugfix.rst @@ -0,0 +1,3 @@ +Setting ``fill_value`` to a float like ``0.0`` when the data type of the array is an integer is a common +mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python +will not create such arrays. \ No newline at end of file diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index 67644449a0..ab22b542f0 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -9,6 +9,7 @@ Any, Final, Literal, + NewType, SupportsComplex, SupportsFloat, SupportsIndex, @@ -54,6 +55,9 @@ "generic", ) +IntishFloat = NewType("IntishFloat", float) +"""A type for floats that represent integers, like 1.0 (but not 1.1).""" + NumpyEndiannessStr = Literal[">", "<", "="] NUMPY_ENDIANNESS_STR: Final = ">", "<", "=" @@ -467,6 +471,23 @@ def check_json_int(data: JSON) -> TypeGuard[int]: return bool(isinstance(data, int)) +def check_json_intish_float(data: JSON) -> TypeGuard[IntishFloat]: + """ + Check if a JSON value is an "intish float", i.e. a float that represents an integer, like 0.0. + + Parameters + ---------- + data : JSON + The JSON value to check. + + Returns + ------- + Bool + True if the data is an intish float, False otherwise. + """ + return isinstance(data, float) and data.is_integer() + + def check_json_str(data: JSON) -> TypeGuard[str]: """ Check if a JSON value is a string. diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index 01a79142a3..ac04d4469a 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -25,6 +25,7 @@ ) from zarr.core.dtype.npy.common import ( check_json_int, + check_json_intish_float, endianness_to_numpy_str, get_endianness_from_numpy_dtype, ) @@ -206,6 +207,8 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TIntScalar """ if check_json_int(data): return self._cast_scalar_unchecked(data) + if check_json_intish_float(data): + return self._cast_scalar_unchecked(int(data)) raise TypeError(f"Invalid type: {data}. Expected an integer.") def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> int: diff --git a/tests/test_dtype/test_npy/test_common.py b/tests/test_dtype/test_npy/test_common.py index bd77866fc0..d8912a70ec 100644 --- a/tests/test_dtype/test_npy/test_common.py +++ b/tests/test_dtype/test_npy/test_common.py @@ -20,6 +20,7 @@ check_json_float_v2, check_json_float_v3, check_json_int, + check_json_intish_float, check_json_str, complex_float_to_json_v2, complex_float_to_json_v3, @@ -320,6 +321,13 @@ def test_check_json_int() -> None: assert not check_json_int(1.0) +def test_check_json_intish_float() -> None: + assert check_json_intish_float(0.0) + assert check_json_intish_float(1.0) + assert not check_json_intish_float("0") + assert not check_json_intish_float(1.1) + + def test_check_json_str() -> None: assert check_json_str("0") assert not check_json_str(1.0) diff --git a/tests/test_dtype/test_npy/test_int.py b/tests/test_dtype/test_npy/test_int.py index efc4fae496..0cab3b8e3e 100644 --- a/tests/test_dtype/test_npy/test_int.py +++ b/tests/test_dtype/test_npy/test_int.py @@ -28,7 +28,7 @@ class TestInt8(BaseTestZDType): {"name": "int8", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((Int8(), 1), (Int8(), -1)) + scalar_v2_params = ((Int8(), 1), (Int8(), -1), (Int8(), 1.0)) scalar_v3_params = ((Int8(), 1), (Int8(), -1)) cast_value_params = ( (Int8(), 1, np.int8(1)), @@ -63,7 +63,7 @@ class TestInt16(BaseTestZDType): {"name": "int16", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((Int16(), 1), (Int16(), -1)) + scalar_v2_params = ((Int16(), 1), (Int16(), -1), (Int16(), 1.0)) scalar_v3_params = ((Int16(), 1), (Int16(), -1)) cast_value_params = ( (Int16(), 1, np.int16(1)), @@ -101,7 +101,7 @@ class TestInt32(BaseTestZDType): {"name": "int32", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((Int32(), 1), (Int32(), -1)) + scalar_v2_params = ((Int32(), 1), (Int32(), -1), (Int32(), 1.0)) scalar_v3_params = ((Int32(), 1), (Int32(), -1)) cast_value_params = ( (Int32(), 1, np.int32(1)), @@ -136,7 +136,7 @@ class TestInt64(BaseTestZDType): {"name": "int64", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((Int64(), 1), (Int64(), -1)) + scalar_v2_params = ((Int64(), 1), (Int64(), -1), (Int64(), 1.0)) scalar_v3_params = ((Int64(), 1), (Int64(), -1)) cast_value_params = ( (Int64(), 1, np.int64(1)), @@ -168,7 +168,7 @@ class TestUInt8(BaseTestZDType): {"name": "uint8", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((UInt8(), 1), (UInt8(), 0)) + scalar_v2_params = ((UInt8(), 1), (UInt8(), 0), (UInt8(), 1.0)) scalar_v3_params = ((UInt8(), 1), (UInt8(), 0)) cast_value_params = ( (UInt8(), 1, np.uint8(1)), @@ -203,7 +203,7 @@ class TestUInt16(BaseTestZDType): {"name": "uint16", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((UInt16(), 1), (UInt16(), 0)) + scalar_v2_params = ((UInt16(), 1), (UInt16(), 0), (UInt16(), 1.0)) scalar_v3_params = ((UInt16(), 1), (UInt16(), 0)) cast_value_params = ( (UInt16(), 1, np.uint16(1)), @@ -238,7 +238,7 @@ class TestUInt32(BaseTestZDType): {"name": "uint32", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((UInt32(), 1), (UInt32(), 0)) + scalar_v2_params = ((UInt32(), 1), (UInt32(), 0), (UInt32(), 1.0)) scalar_v3_params = ((UInt32(), 1), (UInt32(), 0)) cast_value_params = ( (UInt32(), 1, np.uint32(1)), @@ -273,7 +273,7 @@ class TestUInt64(BaseTestZDType): {"name": "uint64", "configuration": {"endianness": "little"}}, ) - scalar_v2_params = ((UInt64(), 1), (UInt64(), 0)) + scalar_v2_params = ((UInt64(), 1), (UInt64(), 0), (UInt64(), 1.0)) scalar_v3_params = ((UInt64(), 1), (UInt64(), 0)) cast_value_params = ( (UInt64(), 1, np.uint64(1)), From e76b1e0acd81c5b309c0b3e6acb992740e73101a Mon Sep 17 00:00:00 2001 From: Joe Hamman Date: Fri, 12 Sep 2025 09:37:46 -0700 Subject: [PATCH 102/468] Fix nightly-wheel tag (#3450) --- .github/workflows/nightly_wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 10bc7c5ff1..9052504c0a 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -31,7 +31,7 @@ jobs: run: hatch build - name: Upload nightly wheels - uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd7672769da06 + uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf with: artifacts_path: dist anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }} From bce30dd3cc92a35038b88f80c4c42130670d4100 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sat, 13 Sep 2025 18:58:03 +0200 Subject: [PATCH 103/468] chore/handle numcodecs codecs (#3376) * bring in contents of numcodecs.zarr3 * fix tests * fix docs * fix config test * make zarr.codecs.numcodecs * complete move to zarr.codecs.numcodecs * changelog * register codecs in codecs/__init__.py * remove old registration sites --- changes/3376.misc.rst | 3 + docs/user-guide/config.rst | 42 +++- src/zarr/codecs/__init__.py | 67 ++++++ src/zarr/codecs/blosc.py | 4 - src/zarr/codecs/bytes.py | 7 - src/zarr/codecs/crc32c_.py | 4 - src/zarr/codecs/gzip.py | 4 - src/zarr/codecs/numcodecs/__init__.py | 57 +++++ src/zarr/codecs/numcodecs/_codecs.py | 325 +++++++++++++++++++++++++ src/zarr/codecs/sharding.py | 5 +- src/zarr/codecs/transpose.py | 4 - src/zarr/codecs/vlen_utf8.py | 5 - src/zarr/codecs/zstd.py | 4 - src/zarr/core/config.py | 21 ++ src/zarr/registry.py | 5 +- tests/test_array.py | 4 +- tests/test_codecs/test_numcodecs.py | 333 ++++++++++++++++++++++++++ tests/test_config.py | 21 ++ 18 files changed, 863 insertions(+), 52 deletions(-) create mode 100644 changes/3376.misc.rst create mode 100644 src/zarr/codecs/numcodecs/__init__.py create mode 100644 src/zarr/codecs/numcodecs/_codecs.py diff --git a/changes/3376.misc.rst b/changes/3376.misc.rst new file mode 100644 index 0000000000..68b0d9d855 --- /dev/null +++ b/changes/3376.misc.rst @@ -0,0 +1,3 @@ +Define Zarr V3-specific codecs from numcodecs inside this repo. These codecs can be found in +:mod:`zarr.codecs.numcodecs`. This is necessary to resolve a circular dependency between Zarr +and Numcodecs. \ No newline at end of file diff --git a/docs/user-guide/config.rst b/docs/user-guide/config.rst index 0ae8017ca9..05cfa1e53c 100644 --- a/docs/user-guide/config.rst +++ b/docs/user-guide/config.rst @@ -42,23 +42,43 @@ requires the value of ``codecs.bytes.name`` to be ``'custompackage.NewBytesCodec This is the current default configuration:: >>> zarr.config.pprint() - {'array': {'order': 'C', - 'write_empty_chunks': False}, - 'async': {'concurrency': 10, 'timeout': None}, - 'buffer': 'zarr.buffer.cpu.Buffer', - 'codec_pipeline': {'batch_size': 1, - 'path': 'zarr.core.codec_pipeline.BatchedCodecPipeline'}, - 'codecs': {'blosc': 'zarr.codecs.blosc.BloscCodec', + {'array': {'order': 'C', 'write_empty_chunks': False}, + 'async': {'concurrency': 10, 'timeout': None}, + 'buffer': 'zarr.buffer.cpu.Buffer', + 'codec_pipeline': {'batch_size': 1, + 'path': 'zarr.core.codec_pipeline.BatchedCodecPipeline'}, + 'codecs': {'blosc': 'zarr.codecs.blosc.BloscCodec', 'bytes': 'zarr.codecs.bytes.BytesCodec', 'crc32c': 'zarr.codecs.crc32c_.Crc32cCodec', 'endian': 'zarr.codecs.bytes.BytesCodec', 'gzip': 'zarr.codecs.gzip.GzipCodec', + 'numcodecs.adler32': 'zarr.codecs.numcodecs.Adler32', + 'numcodecs.astype': 'zarr.codecs.numcodecs.AsType', + 'numcodecs.bitround': 'zarr.codecs.numcodecs.BitRound', + 'numcodecs.blosc': 'zarr.codecs.numcodecs.Blosc', + 'numcodecs.bz2': 'zarr.codecs.numcodecs.BZ2', + 'numcodecs.crc32': 'zarr.codecs.numcodecs.CRC32', + 'numcodecs.crc32c': 'zarr.codecs.numcodecs.CRC32C', + 'numcodecs.delta': 'zarr.codecs.numcodecs.Delta', + 'numcodecs.fixedscaleoffset': 'zarr.codecs.numcodecs.FixedScaleOffset', + 'numcodecs.fletcher32': 'zarr.codecs.numcodecs.Fletcher32', + 'numcodecs.gZip': 'zarr.codecs.numcodecs.GZip', + 'numcodecs.jenkins_lookup3': 'zarr.codecs.numcodecs.JenkinsLookup3', + 'numcodecs.lz4': 'zarr.codecs.numcodecs.LZ4', + 'numcodecs.lzma': 'zarr.codecs.numcodecs.LZMA', + 'numcodecs.packbits': 'zarr.codecs.numcodecs.PackBits', + 'numcodecs.pcodec': 'zarr.codecs.numcodecs.PCodec', + 'numcodecs.quantize': 'zarr.codecs.numcodecs.Quantize', + 'numcodecs.shuffle': 'zarr.codecs.numcodecs.Shuffle', + 'numcodecs.zfpy': 'zarr.codecs.numcodecs.ZFPY', + 'numcodecs.zlib': 'zarr.codecs.numcodecs.Zlib', + 'numcodecs.zstd': 'zarr.codecs.numcodecs.Zstd', 'sharding_indexed': 'zarr.codecs.sharding.ShardingCodec', 'transpose': 'zarr.codecs.transpose.TransposeCodec', 'vlen-bytes': 'zarr.codecs.vlen_utf8.VLenBytesCodec', 'vlen-utf8': 'zarr.codecs.vlen_utf8.VLenUTF8Codec', 'zstd': 'zarr.codecs.zstd.ZstdCodec'}, - 'default_zarr_format': 3, - 'json_indent': 2, - 'ndbuffer': 'zarr.buffer.cpu.NDBuffer', - 'threading': {'max_workers': None}} + 'default_zarr_format': 3, + 'json_indent': 2, + 'ndbuffer': 'zarr.buffer.cpu.NDBuffer', + 'threading': {'max_workers': None}} diff --git a/src/zarr/codecs/__init__.py b/src/zarr/codecs/__init__.py index 165dbe476d..7cb4e2a44d 100644 --- a/src/zarr/codecs/__init__.py +++ b/src/zarr/codecs/__init__.py @@ -4,10 +4,34 @@ from zarr.codecs.bytes import BytesCodec, Endian from zarr.codecs.crc32c_ import Crc32cCodec from zarr.codecs.gzip import GzipCodec +from zarr.codecs.numcodecs import ( + BZ2, + CRC32, + CRC32C, + LZ4, + LZMA, + ZFPY, + Adler32, + AsType, + BitRound, + Blosc, + Delta, + FixedScaleOffset, + Fletcher32, + GZip, + JenkinsLookup3, + PackBits, + PCodec, + Quantize, + Shuffle, + Zlib, + Zstd, +) from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation from zarr.codecs.transpose import TransposeCodec from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec from zarr.codecs.zstd import ZstdCodec +from zarr.registry import register_codec __all__ = [ "BloscCname", @@ -24,3 +48,46 @@ "VLenUTF8Codec", "ZstdCodec", ] + +register_codec("blosc", BloscCodec) +register_codec("bytes", BytesCodec) + +# compatibility with earlier versions of ZEP1 +register_codec("endian", BytesCodec) +register_codec("crc32c", Crc32cCodec) +register_codec("gzip", GzipCodec) +register_codec("sharding_indexed", ShardingCodec) +register_codec("zstd", ZstdCodec) +register_codec("vlen-utf8", VLenUTF8Codec) +register_codec("vlen-bytes", VLenBytesCodec) +register_codec("transpose", TransposeCodec) + +# Register all the codecs formerly contained in numcodecs.zarr3 + +register_codec("numcodecs.bz2", BZ2, qualname="zarr.codecs.numcodecs.BZ2") +register_codec("numcodecs.crc32", CRC32, qualname="zarr.codecs.numcodecs.CRC32") +register_codec("numcodecs.crc32c", CRC32C, qualname="zarr.codecs.numcodecs.CRC32C") +register_codec("numcodecs.lz4", LZ4, qualname="zarr.codecs.numcodecs.LZ4") +register_codec("numcodecs.lzma", LZMA, qualname="zarr.codecs.numcodecs.LZMA") +register_codec("numcodecs.zfpy", ZFPY, qualname="zarr.codecs.numcodecs.ZFPY") +register_codec("numcodecs.adler32", Adler32, qualname="zarr.codecs.numcodecs.Adler32") +register_codec("numcodecs.astype", AsType, qualname="zarr.codecs.numcodecs.AsType") +register_codec("numcodecs.bitround", BitRound, qualname="zarr.codecs.numcodecs.BitRound") +register_codec("numcodecs.blosc", Blosc, qualname="zarr.codecs.numcodecs.Blosc") +register_codec("numcodecs.delta", Delta, qualname="zarr.codecs.numcodecs.Delta") +register_codec( + "numcodecs.fixedscaleoffset", + FixedScaleOffset, + qualname="zarr.codecs.numcodecs.FixedScaleOffset", +) +register_codec("numcodecs.fletcher32", Fletcher32, qualname="zarr.codecs.numcodecs.Fletcher32") +register_codec("numcodecs.gzip", GZip, qualname="zarr.codecs.numcodecs.GZip") +register_codec( + "numcodecs.jenkins_lookup3", JenkinsLookup3, qualname="zarr.codecs.numcodecs.JenkinsLookup3" +) +register_codec("numcodecs.pcodec", PCodec, qualname="zarr.codecs.numcodecs.pcodec") +register_codec("numcodecs.packbits", PackBits, qualname="zarr.codecs.numcodecs.PackBits") +register_codec("numcodecs.quantize", Quantize, qualname="zarr.codecs.numcodecs.Quantize") +register_codec("numcodecs.shuffle", Shuffle, qualname="zarr.codecs.numcodecs.Shuffle") +register_codec("numcodecs.zlib", Zlib, qualname="zarr.codecs.numcodecs.Zlib") +register_codec("numcodecs.zstd", Zstd, qualname="zarr.codecs.numcodecs.Zstd") diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index f89f127852..6a482ed6e5 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -14,7 +14,6 @@ from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasItemSize -from zarr.registry import register_codec if TYPE_CHECKING: from typing import Self @@ -199,6 +198,3 @@ async def _encode_single( def compute_encoded_size(self, _input_byte_length: int, _chunk_spec: ArraySpec) -> int: raise NotImplementedError - - -register_codec("blosc", BloscCodec) diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index 7576119c82..39c26bd4a8 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -11,7 +11,6 @@ from zarr.core.buffer import Buffer, NDArrayLike, NDBuffer from zarr.core.common import JSON, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasEndianness -from zarr.registry import register_codec if TYPE_CHECKING: from typing import Self @@ -119,9 +118,3 @@ async def _encode_single( def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: return input_byte_length - - -register_codec("bytes", BytesCodec) - -# compatibility with earlier versions of ZEP1 -register_codec("endian", BytesCodec) diff --git a/src/zarr/codecs/crc32c_.py b/src/zarr/codecs/crc32c_.py index c2e30f689a..b2ea356b0c 100644 --- a/src/zarr/codecs/crc32c_.py +++ b/src/zarr/codecs/crc32c_.py @@ -9,7 +9,6 @@ from zarr.abc.codec import BytesBytesCodec from zarr.core.common import JSON, parse_named_configuration -from zarr.registry import register_codec if TYPE_CHECKING: from typing import Self @@ -65,6 +64,3 @@ async def _encode_single( def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: return input_byte_length + 4 - - -register_codec("crc32c", Crc32cCodec) diff --git a/src/zarr/codecs/gzip.py b/src/zarr/codecs/gzip.py index 9e6515a4d1..610ca9dadd 100644 --- a/src/zarr/codecs/gzip.py +++ b/src/zarr/codecs/gzip.py @@ -9,7 +9,6 @@ from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, parse_named_configuration -from zarr.registry import register_codec if TYPE_CHECKING: from typing import Self @@ -73,6 +72,3 @@ def compute_encoded_size( _chunk_spec: ArraySpec, ) -> int: raise NotImplementedError - - -register_codec("gzip", GzipCodec) diff --git a/src/zarr/codecs/numcodecs/__init__.py b/src/zarr/codecs/numcodecs/__init__.py new file mode 100644 index 0000000000..d68ad3fba6 --- /dev/null +++ b/src/zarr/codecs/numcodecs/__init__.py @@ -0,0 +1,57 @@ +from __future__ import annotations + +from zarr.codecs.numcodecs._codecs import ( + BZ2, + CRC32, + CRC32C, + LZ4, + LZMA, + ZFPY, + Adler32, + AsType, + BitRound, + Blosc, + Delta, + FixedScaleOffset, + Fletcher32, + GZip, + JenkinsLookup3, + PackBits, + PCodec, + Quantize, + Shuffle, + Zlib, + Zstd, + _NumcodecsArrayArrayCodec, + _NumcodecsArrayBytesCodec, + _NumcodecsBytesBytesCodec, + _NumcodecsCodec, +) + +__all__ = [ + "BZ2", + "CRC32", + "CRC32C", + "LZ4", + "LZMA", + "ZFPY", + "Adler32", + "AsType", + "BitRound", + "Blosc", + "Delta", + "FixedScaleOffset", + "Fletcher32", + "GZip", + "JenkinsLookup3", + "PCodec", + "PackBits", + "Quantize", + "Shuffle", + "Zlib", + "Zstd", + "_NumcodecsArrayArrayCodec", + "_NumcodecsArrayBytesCodec", + "_NumcodecsBytesBytesCodec", + "_NumcodecsCodec", +] diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py new file mode 100644 index 0000000000..c7884700c7 --- /dev/null +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -0,0 +1,325 @@ +""" +This module provides compatibility for :py:mod:`numcodecs` in Zarr version 3. + +These codecs were previously defined in :py:mod:`numcodecs`, and have now been moved to `zarr`. + +>>> import zarr +>>> import zarr.codecs.numcodecs as numcodecs +>>> +>>> array = zarr.create_array( +... store="data.zarr", +... shape=(1024, 1024), +... chunks=(64, 64), +... dtype="uint32", +... filters=[numcodecs.zarr3.Delta()], +... compressors=[numcodecs.zarr3.BZ2(level=5)]) +>>> array[:] = np.arange(*array.shape).astype(array.dtype) + +.. note:: + + Please note that the codecs in :py:mod:`zarr.codecs.numcodecs` are not part of the Zarr version + 3 specification. Using these codecs might cause interoperability issues with other Zarr + implementations. +""" + +from __future__ import annotations + +import asyncio +import math +from dataclasses import dataclass, replace +from functools import cached_property +from typing import TYPE_CHECKING, Any, Self +from warnings import warn + +import numpy as np + +from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec +from zarr.abc.metadata import Metadata +from zarr.core.buffer.cpu import as_numpy_array_wrapper +from zarr.core.common import JSON, parse_named_configuration, product +from zarr.dtype import UInt8, ZDType, parse_dtype +from zarr.errors import ZarrUserWarning +from zarr.registry import get_numcodec + +if TYPE_CHECKING: + from zarr.abc.numcodec import Numcodec + from zarr.core.array_spec import ArraySpec + from zarr.core.buffer import Buffer, BufferPrototype, NDBuffer + +CODEC_PREFIX = "numcodecs." + + +def _expect_name_prefix(codec_name: str) -> str: + if not codec_name.startswith(CODEC_PREFIX): + raise ValueError( + f"Expected name to start with '{CODEC_PREFIX}'. Got {codec_name} instead." + ) # pragma: no cover + return codec_name.removeprefix(CODEC_PREFIX) + + +def _parse_codec_configuration(data: dict[str, JSON]) -> dict[str, JSON]: + parsed_name, parsed_configuration = parse_named_configuration(data) + if not parsed_name.startswith(CODEC_PREFIX): + raise ValueError( + f"Expected name to start with '{CODEC_PREFIX}'. Got {parsed_name} instead." + ) # pragma: no cover + id = _expect_name_prefix(parsed_name) + return {"id": id, **parsed_configuration} + + +@dataclass(frozen=True) +class _NumcodecsCodec(Metadata): + codec_name: str + codec_config: dict[str, JSON] + + def __init_subclass__(cls, *, codec_name: str | None = None, **kwargs: Any) -> None: + """To be used only when creating the actual public-facing codec class.""" + super().__init_subclass__(**kwargs) + if codec_name is not None: + namespace = codec_name + + cls_name = f"{CODEC_PREFIX}{namespace}.{cls.__name__}" + cls.codec_name = f"{CODEC_PREFIX}{namespace}" + cls.__doc__ = f""" + See :class:`{cls_name}` for more details and parameters. + """ + + def __init__(self, **codec_config: JSON) -> None: + if not self.codec_name: + raise ValueError( + "The codec name needs to be supplied through the `codec_name` attribute." + ) # pragma: no cover + unprefixed_codec_name = _expect_name_prefix(self.codec_name) + + if "id" not in codec_config: + codec_config = {"id": unprefixed_codec_name, **codec_config} + elif codec_config["id"] != unprefixed_codec_name: + raise ValueError( + f"Codec id does not match {unprefixed_codec_name}. Got: {codec_config['id']}." + ) # pragma: no cover + + object.__setattr__(self, "codec_config", codec_config) + warn( + "Numcodecs codecs are not in the Zarr version 3 specification and " + "may not be supported by other zarr implementations.", + category=ZarrUserWarning, + stacklevel=2, + ) + + @cached_property + def _codec(self) -> Numcodec: + return get_numcodec(self.codec_config) # type: ignore[arg-type] + + @classmethod + def from_dict(cls, data: dict[str, JSON]) -> Self: + codec_config = _parse_codec_configuration(data) + return cls(**codec_config) + + def to_dict(self) -> dict[str, JSON]: + codec_config = self.codec_config.copy() + codec_config.pop("id", None) + return { + "name": self.codec_name, + "configuration": codec_config, + } + + def compute_encoded_size(self, input_byte_length: int, chunk_spec: ArraySpec) -> int: + raise NotImplementedError # pragma: no cover + + # Override __repr__ because dynamically constructed classes don't seem to work otherwise + def __repr__(self) -> str: + codec_config = self.codec_config.copy() + codec_config.pop("id", None) + return f"{self.__class__.__name__}(codec_name={self.codec_name!r}, codec_config={codec_config!r})" + + +class _NumcodecsBytesBytesCodec(_NumcodecsCodec, BytesBytesCodec): + def __init__(self, **codec_config: JSON) -> None: + super().__init__(**codec_config) + + async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> Buffer: + return await asyncio.to_thread( + as_numpy_array_wrapper, + self._codec.decode, + chunk_data, + chunk_spec.prototype, + ) + + def _encode(self, chunk_data: Buffer, prototype: BufferPrototype) -> Buffer: + encoded = self._codec.encode(chunk_data.as_array_like()) + if isinstance(encoded, np.ndarray): # Required for checksum codecs + return prototype.buffer.from_bytes(encoded.tobytes()) + return prototype.buffer.from_bytes(encoded) + + async def _encode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> Buffer: + return await asyncio.to_thread(self._encode, chunk_data, chunk_spec.prototype) + + +class _NumcodecsArrayArrayCodec(_NumcodecsCodec, ArrayArrayCodec): + def __init__(self, **codec_config: JSON) -> None: + super().__init__(**codec_config) + + async def _decode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: + chunk_ndarray = chunk_data.as_ndarray_like() + out = await asyncio.to_thread(self._codec.decode, chunk_ndarray) + return chunk_spec.prototype.nd_buffer.from_ndarray_like(out.reshape(chunk_spec.shape)) + + async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: + chunk_ndarray = chunk_data.as_ndarray_like() + out = await asyncio.to_thread(self._codec.encode, chunk_ndarray) + return chunk_spec.prototype.nd_buffer.from_ndarray_like(out) + + +class _NumcodecsArrayBytesCodec(_NumcodecsCodec, ArrayBytesCodec): + def __init__(self, **codec_config: JSON) -> None: + super().__init__(**codec_config) + + async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + chunk_bytes = chunk_data.to_bytes() + out = await asyncio.to_thread(self._codec.decode, chunk_bytes) + return chunk_spec.prototype.nd_buffer.from_ndarray_like(out.reshape(chunk_spec.shape)) + + async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> Buffer: + chunk_ndarray = chunk_data.as_ndarray_like() + out = await asyncio.to_thread(self._codec.encode, chunk_ndarray) + return chunk_spec.prototype.buffer.from_bytes(out) + + +# bytes-to-bytes codecs +class Blosc(_NumcodecsBytesBytesCodec, codec_name="blosc"): + pass + + +class LZ4(_NumcodecsBytesBytesCodec, codec_name="lz4"): + pass + + +class Zstd(_NumcodecsBytesBytesCodec, codec_name="zstd"): + pass + + +class Zlib(_NumcodecsBytesBytesCodec, codec_name="zlib"): + pass + + +class GZip(_NumcodecsBytesBytesCodec, codec_name="gzip"): + pass + + +class BZ2(_NumcodecsBytesBytesCodec, codec_name="bz2"): + pass + + +class LZMA(_NumcodecsBytesBytesCodec, codec_name="lzma"): + pass + + +class Shuffle(_NumcodecsBytesBytesCodec, codec_name="shuffle"): + def evolve_from_array_spec(self, array_spec: ArraySpec) -> Shuffle: + if self.codec_config.get("elementsize") is None: + dtype = array_spec.dtype.to_native_dtype() + return Shuffle(**{**self.codec_config, "elementsize": dtype.itemsize}) + return self # pragma: no cover + + +# array-to-array codecs ("filters") +class Delta(_NumcodecsArrayArrayCodec, codec_name="delta"): + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + if astype := self.codec_config.get("astype"): + dtype = parse_dtype(np.dtype(astype), zarr_format=3) # type: ignore[call-overload] + return replace(chunk_spec, dtype=dtype) + return chunk_spec + + +class BitRound(_NumcodecsArrayArrayCodec, codec_name="bitround"): + pass + + +class FixedScaleOffset(_NumcodecsArrayArrayCodec, codec_name="fixedscaleoffset"): + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + if astype := self.codec_config.get("astype"): + dtype = parse_dtype(np.dtype(astype), zarr_format=3) # type: ignore[call-overload] + return replace(chunk_spec, dtype=dtype) + return chunk_spec + + def evolve_from_array_spec(self, array_spec: ArraySpec) -> FixedScaleOffset: + if self.codec_config.get("dtype") is None: + dtype = array_spec.dtype.to_native_dtype() + return FixedScaleOffset(**{**self.codec_config, "dtype": str(dtype)}) + return self + + +class Quantize(_NumcodecsArrayArrayCodec, codec_name="quantize"): + def __init__(self, **codec_config: JSON) -> None: + super().__init__(**codec_config) + + def evolve_from_array_spec(self, array_spec: ArraySpec) -> Quantize: + if self.codec_config.get("dtype") is None: + dtype = array_spec.dtype.to_native_dtype() + return Quantize(**{**self.codec_config, "dtype": str(dtype)}) + return self + + +class PackBits(_NumcodecsArrayArrayCodec, codec_name="packbits"): + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + return replace( + chunk_spec, + shape=(1 + math.ceil(product(chunk_spec.shape) / 8),), + dtype=UInt8(), + ) + + # todo: remove this type: ignore when this class can be defined w.r.t. + # a single zarr dtype API + def validate(self, *, dtype: ZDType[Any, Any], **_kwargs: Any) -> None: + # this is bugged and will fail + _dtype = dtype.to_native_dtype() + if _dtype != np.dtype("bool"): + raise ValueError(f"Packbits filter requires bool dtype. Got {dtype}.") + + +class AsType(_NumcodecsArrayArrayCodec, codec_name="astype"): + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + dtype = parse_dtype(np.dtype(self.codec_config["encode_dtype"]), zarr_format=3) # type: ignore[arg-type] + return replace(chunk_spec, dtype=dtype) + + def evolve_from_array_spec(self, array_spec: ArraySpec) -> AsType: + if self.codec_config.get("decode_dtype") is None: + # TODO: remove these coverage exemptions the correct way, i.e. with tests + dtype = array_spec.dtype.to_native_dtype() # pragma: no cover + return AsType(**{**self.codec_config, "decode_dtype": str(dtype)}) # pragma: no cover + return self + + +# bytes-to-bytes checksum codecs +class _NumcodecsChecksumCodec(_NumcodecsBytesBytesCodec): + def compute_encoded_size(self, input_byte_length: int, chunk_spec: ArraySpec) -> int: + return input_byte_length + 4 # pragma: no cover + + +class CRC32(_NumcodecsChecksumCodec, codec_name="crc32"): + pass + + +class CRC32C(_NumcodecsChecksumCodec, codec_name="crc32c"): + pass + + +class Adler32(_NumcodecsChecksumCodec, codec_name="adler32"): + pass + + +class Fletcher32(_NumcodecsChecksumCodec, codec_name="fletcher32"): + pass + + +class JenkinsLookup3(_NumcodecsChecksumCodec, codec_name="jenkins_lookup3"): + pass + + +# array-to-bytes codecs +class PCodec(_NumcodecsArrayBytesCodec, codec_name="pcodec"): + pass + + +class ZFPY(_NumcodecsArrayBytesCodec, codec_name="zfpy"): + pass diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 58d34f62e7..ecbd258ccf 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -51,7 +51,7 @@ morton_order_iter, ) from zarr.core.metadata.v3 import parse_codecs -from zarr.registry import get_ndbuffer_class, get_pipeline_class, register_codec +from zarr.registry import get_ndbuffer_class, get_pipeline_class if TYPE_CHECKING: from collections.abc import Awaitable, Callable, Iterator @@ -760,6 +760,3 @@ async def _load_full_shard_maybe( def compute_encoded_size(self, input_byte_length: int, shard_spec: ArraySpec) -> int: chunks_per_shard = self._get_chunks_per_shard(shard_spec) return input_byte_length + self._shard_index_size(chunks_per_shard) - - -register_codec("sharding_indexed", ShardingCodec) diff --git a/src/zarr/codecs/transpose.py b/src/zarr/codecs/transpose.py index 92e7da81e1..a8570b6e8f 100644 --- a/src/zarr/codecs/transpose.py +++ b/src/zarr/codecs/transpose.py @@ -9,7 +9,6 @@ from zarr.abc.codec import ArrayArrayCodec from zarr.core.array_spec import ArraySpec from zarr.core.common import JSON, parse_named_configuration -from zarr.registry import register_codec if TYPE_CHECKING: from typing import Self @@ -113,6 +112,3 @@ async def _encode_single( def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: return input_byte_length - - -register_codec("transpose", TransposeCodec) diff --git a/src/zarr/codecs/vlen_utf8.py b/src/zarr/codecs/vlen_utf8.py index 28c64be1c0..fa1a229855 100644 --- a/src/zarr/codecs/vlen_utf8.py +++ b/src/zarr/codecs/vlen_utf8.py @@ -9,7 +9,6 @@ from zarr.abc.codec import ArrayBytesCodec from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import JSON, parse_named_configuration -from zarr.registry import register_codec if TYPE_CHECKING: from typing import Self @@ -112,7 +111,3 @@ async def _encode_single( def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: # what is input_byte_length for an object dtype? raise NotImplementedError("compute_encoded_size is not implemented for VLen codecs") - - -register_codec("vlen-utf8", VLenUTF8Codec) -register_codec("vlen-bytes", VLenBytesCodec) diff --git a/src/zarr/codecs/zstd.py b/src/zarr/codecs/zstd.py index ead41e7b5f..27cc9a7777 100644 --- a/src/zarr/codecs/zstd.py +++ b/src/zarr/codecs/zstd.py @@ -12,7 +12,6 @@ from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, parse_named_configuration -from zarr.registry import register_codec if TYPE_CHECKING: from typing import Self @@ -92,6 +91,3 @@ async def _encode_single( def compute_encoded_size(self, _input_byte_length: int, _chunk_spec: ArraySpec) -> int: raise NotImplementedError - - -register_codec("zstd", ZstdCodec) diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index cc3c33cd17..2b7fbbe0c6 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -125,6 +125,27 @@ def enable_gpu(self) -> ConfigSet: "transpose": "zarr.codecs.transpose.TransposeCodec", "vlen-utf8": "zarr.codecs.vlen_utf8.VLenUTF8Codec", "vlen-bytes": "zarr.codecs.vlen_utf8.VLenBytesCodec", + "numcodecs.bz2": "zarr.codecs.numcodecs.BZ2", + "numcodecs.crc32": "zarr.codecs.numcodecs.CRC32", + "numcodecs.crc32c": "zarr.codecs.numcodecs.CRC32C", + "numcodecs.lz4": "zarr.codecs.numcodecs.LZ4", + "numcodecs.lzma": "zarr.codecs.numcodecs.LZMA", + "numcodecs.zfpy": "zarr.codecs.numcodecs.ZFPY", + "numcodecs.adler32": "zarr.codecs.numcodecs.Adler32", + "numcodecs.astype": "zarr.codecs.numcodecs.AsType", + "numcodecs.bitround": "zarr.codecs.numcodecs.BitRound", + "numcodecs.blosc": "zarr.codecs.numcodecs.Blosc", + "numcodecs.delta": "zarr.codecs.numcodecs.Delta", + "numcodecs.fixedscaleoffset": "zarr.codecs.numcodecs.FixedScaleOffset", + "numcodecs.fletcher32": "zarr.codecs.numcodecs.Fletcher32", + "numcodecs.gZip": "zarr.codecs.numcodecs.GZip", + "numcodecs.jenkins_lookup3": "zarr.codecs.numcodecs.JenkinsLookup3", + "numcodecs.pcodec": "zarr.codecs.numcodecs.PCodec", + "numcodecs.packbits": "zarr.codecs.numcodecs.PackBits", + "numcodecs.shuffle": "zarr.codecs.numcodecs.Shuffle", + "numcodecs.quantize": "zarr.codecs.numcodecs.Quantize", + "numcodecs.zlib": "zarr.codecs.numcodecs.Zlib", + "numcodecs.zstd": "zarr.codecs.numcodecs.Zstd", }, "buffer": "zarr.buffer.cpu.Buffer", "ndbuffer": "zarr.buffer.cpu.NDBuffer", diff --git a/src/zarr/registry.py b/src/zarr/registry.py index 46216205f7..5483b65c54 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -126,10 +126,10 @@ def fully_qualified_name(cls: type) -> str: return module + "." + cls.__qualname__ -def register_codec(key: str, codec_cls: type[Codec]) -> None: +def register_codec(key: str, codec_cls: type[Codec], *, qualname: str | None = None) -> None: if key not in __codec_registries: __codec_registries[key] = Registry() - __codec_registries[key].register(codec_cls) + __codec_registries[key].register(codec_cls, qualname=qualname) def register_pipeline(pipe_cls: type[CodecPipeline]) -> None: @@ -155,7 +155,6 @@ def get_codec_class(key: str, reload_config: bool = False) -> type[Codec]: codec_classes = __codec_registries[key] if not codec_classes: raise KeyError(key) - config_entry = config.get("codecs", {}).get(key) if config_entry is None: if len(codec_classes) == 1: diff --git a/tests/test_array.py b/tests/test_array.py index cf201ce0c7..92a5dc77e9 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1745,7 +1745,7 @@ def test_roundtrip_numcodecs() -> None: # Create the array with the correct codecs root = zarr.group(store) warn_msg = "Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations." - with pytest.warns(UserWarning, match=warn_msg): + with pytest.warns(ZarrUserWarning, match=warn_msg): root.create_array( "test", shape=(720, 1440), @@ -1760,7 +1760,7 @@ def test_roundtrip_numcodecs() -> None: BYTES_CODEC = {"name": "bytes", "configuration": {"endian": "little"}} # Read in the array again and check compressor config root = zarr.open_group(store) - with pytest.warns(UserWarning, match=warn_msg): + with pytest.warns(ZarrUserWarning, match=warn_msg): metadata = root["test"].metadata.to_dict() expected = (*filters, BYTES_CODEC, *compressors) assert metadata["codecs"] == expected diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py index 1c4d550587..99c4685a67 100644 --- a/tests/test_codecs/test_numcodecs.py +++ b/tests/test_codecs/test_numcodecs.py @@ -1,10 +1,56 @@ from __future__ import annotations +import contextlib +import pickle +from typing import TYPE_CHECKING, Any + +import numpy as np +import pytest from numcodecs import GZip +from zarr import config, create_array, open_array from zarr.abc.numcodec import _is_numcodec, _is_numcodec_cls +from zarr.codecs import numcodecs as _numcodecs +from zarr.errors import ZarrUserWarning from zarr.registry import get_numcodec +if TYPE_CHECKING: + from collections.abc import Iterator + + +@contextlib.contextmanager +def codec_conf() -> Iterator[Any]: + base_conf = config.get("codecs") + new_conf = { + "numcodecs.bz2": "zarr.codecs.numcodecs.BZ2", + "numcodecs.crc32": "zarr.codecs.numcodecs.CRC32", + "numcodecs.crc32c": "zarr.codecs.numcodecs.CRC32C", + "numcodecs.lz4": "zarr.codecs.numcodecs.LZ4", + "numcodecs.lzma": "zarr.codecs.numcodecs.LZMA", + "numcodecs.zfpy": "zarr.codecs.numcodecs.ZFPY", + "numcodecs.adler32": "zarr.codecs.numcodecs.Adler32", + "numcodecs.astype": "zarr.codecs.numcodecs.AsType", + "numcodecs.bitround": "zarr.codecs.numcodecs.BitRound", + "numcodecs.blosc": "zarr.codecs.numcodecs.Blosc", + "numcodecs.delta": "zarr.codecs.numcodecs.Delta", + "numcodecs.fixedscaleoffset": "zarr.codecs.numcodecs.FixedScaleOffset", + "numcodecs.fletcher32": "zarr.codecs.numcodecs.Fletcher32", + "numcodecs.gZip": "zarr.codecs.numcodecs.GZip", + "numcodecs.jenkinslookup3": "zarr.codecs.numcodecs.JenkinsLookup3", + "numcodecs.pcodec": "zarr.codecs.numcodecs.PCodec", + "numcodecs.packbits": "zarr.codecs.numcodecs.PackBits", + "numcodecs.shuffle": "zarr.codecs.numcodecs.Shuffle", + "numcodecs.quantize": "zarr.codecs.numcodecs.Quantize", + "numcodecs.zlib": "zarr.codecs.numcodecs.Zlib", + "numcodecs.zstd": "zarr.codecs.numcodecs.Zstd", + } + + yield config.set({"codecs": new_conf | base_conf}) + + +if TYPE_CHECKING: + from zarr.core.common import JSON + def test_get_numcodec() -> None: assert get_numcodec({"id": "gzip", "level": 2}) == GZip(level=2) # type: ignore[typeddict-unknown-key] @@ -22,3 +68,290 @@ def test_is_numcodec_cls() -> None: Test the _is_numcodec_cls function """ assert _is_numcodec_cls(GZip) + + +EXPECTED_WARNING_STR = "Numcodecs codecs are not in the Zarr version 3.*" + +ALL_CODECS = tuple( + filter( + lambda v: isinstance(v, _numcodecs._NumcodecsCodec), + tuple(getattr(_numcodecs, cls_name) for cls_name in _numcodecs.__all__), + ) +) + + +@pytest.mark.parametrize("codec_class", ALL_CODECS) +def test_docstring(codec_class: type[_numcodecs._NumcodecsCodec]) -> None: + """ + Test that the docstring for the zarr.numcodecs codecs references the wrapped numcodecs class. + """ + assert "See :class:`numcodecs." in codec_class.__doc__ # type: ignore[operator] + + +@pytest.mark.parametrize( + "codec_class", + [ + _numcodecs.Blosc, + _numcodecs.LZ4, + _numcodecs.Zstd, + _numcodecs.Zlib, + _numcodecs.GZip, + _numcodecs.BZ2, + _numcodecs.LZMA, + _numcodecs.Shuffle, + ], +) +def test_generic_compressor(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec]) -> None: + data = np.arange(0, 256, dtype="uint16").reshape((16, 16)) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + compressors=[codec_class()], + ) + + a[:, :] = data.copy() + np.testing.assert_array_equal(data, a[:, :]) + + +@pytest.mark.parametrize( + ("codec_class", "codec_config"), + [ + (_numcodecs.Delta, {"dtype": "float32"}), + (_numcodecs.FixedScaleOffset, {"offset": 0, "scale": 25.5}), + (_numcodecs.FixedScaleOffset, {"offset": 0, "scale": 51, "astype": "uint16"}), + (_numcodecs.AsType, {"encode_dtype": "float32", "decode_dtype": "float32"}), + ], + ids=[ + "delta", + "fixedscaleoffset", + "fixedscaleoffset2", + "astype", + ], +) +def test_generic_filter( + codec_class: type[_numcodecs._NumcodecsArrayArrayCodec], + codec_config: dict[str, JSON], +) -> None: + data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[ + codec_class(**codec_config), + ], + ) + + a[:, :] = data.copy() + with codec_conf(): + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + b = open_array(a.store, mode="r") + np.testing.assert_array_equal(data, b[:, :]) + + +def test_generic_filter_bitround() -> None: + data = np.linspace(0, 1, 256, dtype="float32").reshape((16, 16)) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[_numcodecs.BitRound(keepbits=3)], + ) + + a[:, :] = data.copy() + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + b = open_array(a.store, mode="r") + assert np.allclose(data, b[:, :], atol=0.1) + + +def test_generic_filter_quantize() -> None: + data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[_numcodecs.Quantize(digits=3)], + ) + + a[:, :] = data.copy() + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + b = open_array(a.store, mode="r") + assert np.allclose(data, b[:, :], atol=0.001) + + +def test_generic_filter_packbits() -> None: + data = np.zeros((16, 16), dtype="bool") + data[0:4, :] = True + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[_numcodecs.PackBits()], + ) + + a[:, :] = data.copy() + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + b = open_array(a.store, mode="r") + np.testing.assert_array_equal(data, b[:, :]) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + with pytest.raises(ValueError, match=".*requires bool dtype.*"): + create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype="uint32", + fill_value=0, + filters=[_numcodecs.PackBits()], + ) + + +@pytest.mark.parametrize( + "codec_class", + [ + _numcodecs.CRC32, + _numcodecs.CRC32C, + _numcodecs.Adler32, + _numcodecs.Fletcher32, + _numcodecs.JenkinsLookup3, + ], +) +def test_generic_checksum(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec]) -> None: + data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + compressors=[codec_class()], + ) + + a[:, :] = data.copy() + with codec_conf(): + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + b = open_array(a.store, mode="r") + np.testing.assert_array_equal(data, b[:, :]) + + +@pytest.mark.parametrize("codec_class", [_numcodecs.PCodec, _numcodecs.ZFPY]) +def test_generic_bytes_codec(codec_class: type[_numcodecs._NumcodecsArrayBytesCodec]) -> None: + try: + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + codec_class()._codec # noqa: B018 + except ValueError as e: # pragma: no cover + if "codec not available" in str(e): + pytest.xfail(f"{codec_class.codec_name} is not available: {e}") + else: + raise + except ImportError as e: # pragma: no cover + pytest.xfail(f"{codec_class.codec_name} is not available: {e}") + + data = np.arange(0, 256, dtype="float32").reshape((16, 16)) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + serializer=codec_class(), + ) + + a[:, :] = data.copy() + np.testing.assert_array_equal(data, a[:, :]) + + +def test_delta_astype() -> None: + data = np.linspace(0, 10, 256, dtype="i8").reshape((16, 16)) + + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[ + _numcodecs.Delta(dtype="i8", astype="i2"), + ], + ) + + a[:, :] = data.copy() + with codec_conf(): + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + b = open_array(a.store, mode="r") + np.testing.assert_array_equal(data, b[:, :]) + + +def test_repr() -> None: + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + codec = _numcodecs.LZ4(level=5) + assert repr(codec) == "LZ4(codec_name='numcodecs.lz4', codec_config={'level': 5})" + + +def test_to_dict() -> None: + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + codec = _numcodecs.LZ4(level=5) + assert codec.to_dict() == {"name": "numcodecs.lz4", "configuration": {"level": 5}} + + +@pytest.mark.parametrize( + "codec_cls", + [ + _numcodecs.Blosc, + _numcodecs.LZ4, + _numcodecs.Zstd, + _numcodecs.Zlib, + _numcodecs.GZip, + _numcodecs.BZ2, + _numcodecs.LZMA, + _numcodecs.Shuffle, + _numcodecs.BitRound, + _numcodecs.Delta, + _numcodecs.FixedScaleOffset, + _numcodecs.Quantize, + _numcodecs.PackBits, + _numcodecs.AsType, + _numcodecs.CRC32, + _numcodecs.CRC32C, + _numcodecs.Adler32, + _numcodecs.Fletcher32, + _numcodecs.JenkinsLookup3, + _numcodecs.PCodec, + _numcodecs.ZFPY, + ], +) +def test_codecs_pickleable(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None: + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + codec = codec_cls() + + expected = codec + + p = pickle.dumps(codec) + actual = pickle.loads(p) + assert actual == expected diff --git a/tests/test_config.py b/tests/test_config.py index 0c029dda3a..60e541efd3 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -73,6 +73,27 @@ def test_config_defaults_set() -> None: "transpose": "zarr.codecs.transpose.TransposeCodec", "vlen-utf8": "zarr.codecs.vlen_utf8.VLenUTF8Codec", "vlen-bytes": "zarr.codecs.vlen_utf8.VLenBytesCodec", + "numcodecs.bz2": "zarr.codecs.numcodecs.BZ2", + "numcodecs.crc32": "zarr.codecs.numcodecs.CRC32", + "numcodecs.crc32c": "zarr.codecs.numcodecs.CRC32C", + "numcodecs.lz4": "zarr.codecs.numcodecs.LZ4", + "numcodecs.lzma": "zarr.codecs.numcodecs.LZMA", + "numcodecs.zfpy": "zarr.codecs.numcodecs.ZFPY", + "numcodecs.adler32": "zarr.codecs.numcodecs.Adler32", + "numcodecs.astype": "zarr.codecs.numcodecs.AsType", + "numcodecs.bitround": "zarr.codecs.numcodecs.BitRound", + "numcodecs.blosc": "zarr.codecs.numcodecs.Blosc", + "numcodecs.delta": "zarr.codecs.numcodecs.Delta", + "numcodecs.fixedscaleoffset": "zarr.codecs.numcodecs.FixedScaleOffset", + "numcodecs.fletcher32": "zarr.codecs.numcodecs.Fletcher32", + "numcodecs.gZip": "zarr.codecs.numcodecs.GZip", + "numcodecs.jenkins_lookup3": "zarr.codecs.numcodecs.JenkinsLookup3", + "numcodecs.pcodec": "zarr.codecs.numcodecs.PCodec", + "numcodecs.packbits": "zarr.codecs.numcodecs.PackBits", + "numcodecs.shuffle": "zarr.codecs.numcodecs.Shuffle", + "numcodecs.quantize": "zarr.codecs.numcodecs.Quantize", + "numcodecs.zlib": "zarr.codecs.numcodecs.Zlib", + "numcodecs.zstd": "zarr.codecs.numcodecs.Zstd", }, "buffer": "zarr.buffer.cpu.Buffer", "ndbuffer": "zarr.buffer.cpu.NDBuffer", From df161b240c48dc247de92b71627c791e65ecf6b2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Sep 2025 12:00:45 +0200 Subject: [PATCH 104/468] Bump astral-sh/setup-uv from 6.6.1 to 6.7.0 in the actions group (#3455) Bumps the actions group with 1 update: [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv). Updates `astral-sh/setup-uv` from 6.6.1 to 6.7.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/557e51de59eb14aaaba2ed9621916900a91d50c6...b75a909f75acd358c2196fb9a5f1299a9a8868a4) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 6.7.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 7c18e73f84..ed7874a504 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -12,7 +12,7 @@ jobs: - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 - name: Install uv - uses: astral-sh/setup-uv@557e51de59eb14aaaba2ed9621916900a91d50c6 # v6.6.1 + uses: astral-sh/setup-uv@b75a909f75acd358c2196fb9a5f1299a9a8868a4 # v6.7.0 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py From a830d020760f80145d1dda196f37da7e215598b9 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Mon, 15 Sep 2025 11:12:53 +0100 Subject: [PATCH 105/468] Raise helpful errors when opening a group with wrong node type. (#3444) * Raise helpful errors when opening a group with wrong node type. * Add changelog * Use custom messages --------- Co-authored-by: Davis Bennett --- changes/3444.feature.rst | 1 + src/zarr/core/group.py | 8 ++++++++ tests/test_group.py | 6 ++++++ 3 files changed, 15 insertions(+) create mode 100644 changes/3444.feature.rst diff --git a/changes/3444.feature.rst b/changes/3444.feature.rst new file mode 100644 index 0000000000..d621c428b6 --- /dev/null +++ b/changes/3444.feature.rst @@ -0,0 +1 @@ +Trying to open a group at a path were a array already exists now raises a helpful error. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 15a256fb5d..85d83713e4 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -53,6 +53,7 @@ from zarr.errors import ( ContainsArrayError, ContainsGroupError, + GroupNotFoundError, MetadataValidationError, ZarrDeprecationWarning, ZarrUserWarning, @@ -673,6 +674,13 @@ def from_dict( store_path: StorePath, data: dict[str, Any], ) -> AsyncGroup: + node_type = data.pop("node_type", None) + if node_type == "array": + msg = f"An array already exists in store {store_path.store} at path {store_path.path}." + raise ContainsArrayError(msg) + elif node_type not in ("group", None): + msg = f"Node type in metadata ({node_type}) is not 'group'" + raise GroupNotFoundError(msg) return cls( metadata=GroupMetadata.from_dict(data), store_path=store_path, diff --git a/tests/test_group.py b/tests/test_group.py index 2d9070bd67..eb4af7336f 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -2234,3 +2234,9 @@ def test_get_roots(roots: tuple[str, ...]): } data = root_nodes | child_nodes assert set(_get_roots(data)) == set(roots) + + +def test_open_array_as_group(): + z = zarr.create_array(shape=(40, 50), chunks=(10, 10), dtype="f8", store={}) + with pytest.raises(ContainsArrayError): + zarr.open_group(z.store) From 62d1a6abc866f28b72dc465317001bb9137f6a5b Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Mon, 15 Sep 2025 20:07:21 +0100 Subject: [PATCH 106/468] Minor fixes for zarr.codecs.numcodecs (#3459) * fix gzip typo * fix failing example at top of zarr-codecs-numcodecs * fix failing tests --- docs/user-guide/config.rst | 2 +- src/zarr/codecs/numcodecs/_codecs.py | 7 ++++--- src/zarr/core/config.py | 2 +- tests/test_codecs/test_numcodecs.py | 2 +- tests/test_config.py | 2 +- 5 files changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/user-guide/config.rst b/docs/user-guide/config.rst index 05cfa1e53c..d55937f2dc 100644 --- a/docs/user-guide/config.rst +++ b/docs/user-guide/config.rst @@ -62,7 +62,7 @@ This is the current default configuration:: 'numcodecs.delta': 'zarr.codecs.numcodecs.Delta', 'numcodecs.fixedscaleoffset': 'zarr.codecs.numcodecs.FixedScaleOffset', 'numcodecs.fletcher32': 'zarr.codecs.numcodecs.Fletcher32', - 'numcodecs.gZip': 'zarr.codecs.numcodecs.GZip', + 'numcodecs.gzip': 'zarr.codecs.numcodecs.GZip', 'numcodecs.jenkins_lookup3': 'zarr.codecs.numcodecs.JenkinsLookup3', 'numcodecs.lz4': 'zarr.codecs.numcodecs.LZ4', 'numcodecs.lzma': 'zarr.codecs.numcodecs.LZMA', diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py index c7884700c7..21bdc4e91b 100644 --- a/src/zarr/codecs/numcodecs/_codecs.py +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -3,6 +3,7 @@ These codecs were previously defined in :py:mod:`numcodecs`, and have now been moved to `zarr`. +>>> import numpy as np >>> import zarr >>> import zarr.codecs.numcodecs as numcodecs >>> @@ -11,9 +12,9 @@ ... shape=(1024, 1024), ... chunks=(64, 64), ... dtype="uint32", -... filters=[numcodecs.zarr3.Delta()], -... compressors=[numcodecs.zarr3.BZ2(level=5)]) ->>> array[:] = np.arange(*array.shape).astype(array.dtype) +... filters=[numcodecs.Delta(dtype="uint32")], +... compressors=[numcodecs.BZ2(level=5)]) +>>> array[:] = np.arange(np.prod(array.shape), dtype=array.dtype).reshape(*array.shape) .. note:: diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 2b7fbbe0c6..a918b789dd 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -138,7 +138,7 @@ def enable_gpu(self) -> ConfigSet: "numcodecs.delta": "zarr.codecs.numcodecs.Delta", "numcodecs.fixedscaleoffset": "zarr.codecs.numcodecs.FixedScaleOffset", "numcodecs.fletcher32": "zarr.codecs.numcodecs.Fletcher32", - "numcodecs.gZip": "zarr.codecs.numcodecs.GZip", + "numcodecs.gzip": "zarr.codecs.numcodecs.GZip", "numcodecs.jenkins_lookup3": "zarr.codecs.numcodecs.JenkinsLookup3", "numcodecs.pcodec": "zarr.codecs.numcodecs.PCodec", "numcodecs.packbits": "zarr.codecs.numcodecs.PackBits", diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py index 99c4685a67..147327ccf3 100644 --- a/tests/test_codecs/test_numcodecs.py +++ b/tests/test_codecs/test_numcodecs.py @@ -35,7 +35,7 @@ def codec_conf() -> Iterator[Any]: "numcodecs.delta": "zarr.codecs.numcodecs.Delta", "numcodecs.fixedscaleoffset": "zarr.codecs.numcodecs.FixedScaleOffset", "numcodecs.fletcher32": "zarr.codecs.numcodecs.Fletcher32", - "numcodecs.gZip": "zarr.codecs.numcodecs.GZip", + "numcodecs.gzip": "zarr.codecs.numcodecs.GZip", "numcodecs.jenkinslookup3": "zarr.codecs.numcodecs.JenkinsLookup3", "numcodecs.pcodec": "zarr.codecs.numcodecs.PCodec", "numcodecs.packbits": "zarr.codecs.numcodecs.PackBits", diff --git a/tests/test_config.py b/tests/test_config.py index 60e541efd3..c7a2eb7394 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -86,7 +86,7 @@ def test_config_defaults_set() -> None: "numcodecs.delta": "zarr.codecs.numcodecs.Delta", "numcodecs.fixedscaleoffset": "zarr.codecs.numcodecs.FixedScaleOffset", "numcodecs.fletcher32": "zarr.codecs.numcodecs.Fletcher32", - "numcodecs.gZip": "zarr.codecs.numcodecs.GZip", + "numcodecs.gzip": "zarr.codecs.numcodecs.GZip", "numcodecs.jenkins_lookup3": "zarr.codecs.numcodecs.JenkinsLookup3", "numcodecs.pcodec": "zarr.codecs.numcodecs.PCodec", "numcodecs.packbits": "zarr.codecs.numcodecs.PackBits", From 9eb2d2800809483b1644fc2828c897ddb0720621 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 16 Sep 2025 23:48:11 +0200 Subject: [PATCH 107/468] docstring cleanup (#3390) * make docs more consistent, and remove outdated references to configuration values that no longer work * add tests for consistent docstrings * add flagrantly failing test for consistent parameter docstrings * add test for consistent docstring usage * add missing docstring and re-parametrize test * fix rst * update docstring for make_store_path * ArrayConfigLike contains ArrayConfig * update chunks docstrings * typo * changelog * Update src/zarr/api/asynchronous.py Co-authored-by: Tom Augspurger * Update src/zarr/core/array.py Co-authored-by: Tom Augspurger * Update src/zarr/api/asynchronous.py Co-authored-by: Tom Augspurger * Update src/zarr/api/synchronous.py Co-authored-by: Tom Augspurger * Update src/zarr/core/array.py Co-authored-by: Tom Augspurger * Update src/zarr/core/array.py Co-authored-by: Tom Augspurger * Update src/zarr/core/array.py Co-authored-by: Tom Augspurger * Update src/zarr/core/group.py Co-authored-by: Tom Augspurger * Update src/zarr/core/group.py Co-authored-by: Tom Augspurger * Update src/zarr/core/group.py Co-authored-by: Tom Augspurger * Update src/zarr/core/array.py Co-authored-by: Tom Augspurger * normalize more docstrings, and make docstring tests easier to interpret --------- Co-authored-by: Tom Augspurger --- changes/3390.misc.rst | 1 + docs/user-guide/config.rst | 1 - pyproject.toml | 1 + src/zarr/api/asynchronous.py | 141 ++++++++++--------- src/zarr/api/synchronous.py | 189 ++++++++++++++++--------- src/zarr/core/array.py | 203 +++++++++++++------------- src/zarr/core/group.py | 219 ++++++++++++++++++++++++----- src/zarr/storage/_common.py | 2 +- tests/test_api/test_synchronous.py | 130 +++++++++++++++++ 9 files changed, 613 insertions(+), 274 deletions(-) create mode 100644 changes/3390.misc.rst create mode 100644 tests/test_api/test_synchronous.py diff --git a/changes/3390.misc.rst b/changes/3390.misc.rst new file mode 100644 index 0000000000..fa229a3ad8 --- /dev/null +++ b/changes/3390.misc.rst @@ -0,0 +1 @@ +Improve documentation consistency across API functions and remove outdated references to deprecated configuration values that no longer work. \ No newline at end of file diff --git a/docs/user-guide/config.rst b/docs/user-guide/config.rst index d55937f2dc..76210da791 100644 --- a/docs/user-guide/config.rst +++ b/docs/user-guide/config.rst @@ -28,7 +28,6 @@ Configuration options include the following: - Default Zarr format ``default_zarr_version`` - Default array order in memory ``array.order`` -- Default filters, serializers and compressors, e.g. ``array.v3_default_filters``, ``array.v3_default_serializer``, ``array.v3_default_compressors``, ``array.v2_default_filters`` and ``array.v2_default_compressor`` - Whether empty chunks are written to storage ``array.write_empty_chunks`` - Async and threading options, e.g. ``async.concurrency`` and ``threading.max_workers`` - Selections of implementations of codecs, codec pipelines and buffers diff --git a/pyproject.toml b/pyproject.toml index bea8d77127..9af39fb85c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -78,6 +78,7 @@ test = [ "pytest-accept", "rich", "mypy", + 'numpydoc', "hypothesis", "pytest-xdist", "packaging", diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index dcfadf6a3f..dd5a162927 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -281,7 +281,7 @@ async def load( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. path : str or None, optional The path within the store from which to load. @@ -325,7 +325,7 @@ async def open( Parameters ---------- - store : Store or str, optional + store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional Persistence mode: 'r' means read only (must exist); 'r+' means @@ -338,8 +338,8 @@ async def open( path : str or None, optional The path within the store to open. storage_options : dict - If the store is backed by an fsspec-based implementation, then this dict will be passed to - the Store constructor for that implementation. Ignored otherwise. + If using an fsspec URL to create the store, these will be passed to + the backend implementation. Ignored otherwise. **kwargs Additional parameters are passed through to :func:`zarr.creation.open_array` or :func:`zarr.hierarchy.open_group`. @@ -409,7 +409,7 @@ async def save( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. *args : ndarray NumPy arrays with data to save. @@ -445,12 +445,13 @@ async def save_array( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. arr : ndarray NumPy array with data to save. zarr_format : {2, 3, None}, optional - The zarr format to use when saving (default is 3 if not specified). + The zarr format to use when saving. The default is ``None``, which will + use the default Zarr format defined in the global configuration object. path : str or None, optional The path within the store where the array will be saved. storage_options : dict @@ -500,7 +501,7 @@ async def save_group( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. *args : ndarray NumPy arrays with data to save. @@ -649,14 +650,13 @@ async def group( Parameters ---------- - store : Store or str, optional - Store or path to directory in file system. + store : StoreLike or None, default=None + Store or path to directory in file system or name of zip file. overwrite : bool, optional If True, delete any pre-existing data in `store` at `path` before creating the group. - chunk_store : Store, optional - Separate storage for chunks. If not provided, `store` will be used - for storage of both chunks and metadata. + chunk_store : StoreLike or None, default=None + Separate storage for chunks. Not implemented. cache_attrs : bool, optional If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior @@ -712,8 +712,8 @@ async def create_group( Parameters ---------- - store : Store or str - Store or path to directory in file system. + store : StoreLike + Store or path to directory in file system or name of zip file. path : str, optional Group path within store. overwrite : bool, optional @@ -768,7 +768,7 @@ async def open_group( Parameters ---------- - store : Store, str, or mapping, optional + store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. Strings are interpreted as paths on the local file system @@ -793,7 +793,7 @@ async def open_group( Array synchronizer. path : str, optional Group path within store. - chunk_store : Store or str, optional + chunk_store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. storage_options : dict If using an fsspec URL to create the store, these will be passed to @@ -869,7 +869,7 @@ async def create( compressor: CompressorLike = "auto", fill_value: Any | None = DEFAULT_FILL_VALUE, order: MemoryOrder | None = None, - store: str | StoreLike | None = None, + store: StoreLike | None = None, synchronizer: Any | None = None, overwrite: bool = False, path: PathLike | None = None, @@ -906,65 +906,58 @@ async def create( shape : int or tuple of ints Array shape. chunks : int or tuple of ints, optional - The shape of the array's chunks. - Zarr format 2 only. Zarr format 3 arrays should use `chunk_shape` instead. - If not specified, default values are guessed based on the shape and dtype. + Chunk shape. If True, will be guessed from ``shape`` and ``dtype``. If + False, will be set to ``shape``, i.e., single chunk for the whole array. + If an int, the chunk size in each dimension will be given by the value + of ``chunks``. Default is True. dtype : str or dtype, optional NumPy dtype. - chunk_shape : int or tuple of ints, optional - The shape of the Array's chunks (default is None). - Zarr format 3 only. Zarr format 2 arrays should use `chunks` instead. - chunk_key_encoding : ChunkKeyEncoding, optional - A specification of how the chunk keys are represented in storage. - Zarr format 3 only. Zarr format 2 arrays should use `dimension_separator` instead. - Default is ``("default", "/")``. - codecs : Sequence of Codecs or dicts, optional - An iterable of Codec or dict serializations of Codecs. The elements of - this collection specify the transformation from array values to stored bytes. - Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. - - If no codecs are provided, default codecs will be used: - - - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``. - - For Unicode strings, the default is ``VLenUTF8Codec`` and ``ZstdCodec``. - - For bytes or objects, the default is ``VLenBytesCodec`` and ``ZstdCodec``. - - These defaults can be changed by modifying the value of ``array.v3_default_filters``, - ``array.v3_default_serializer`` and ``array.v3_default_compressors`` in :mod:`zarr.core.config`. compressor : Codec, optional Primary compressor to compress chunk data. Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. - If neither ``compressor`` nor ``filters`` are provided, a default compressor will be used: - - - For numeric arrays, the default is ``ZstdCodec``. - - For Unicode strings, the default is ``VLenUTF8Codec``. - - For bytes or objects, the default is ``VLenBytesCodec``. + If neither ``compressor`` nor ``filters`` are provided, the default compressor + :class:`zarr.codecs.ZstdCodec` is used. - These defaults can be changed by modifying the value of ``array.v2_default_compressor`` in :mod:`zarr.core.config`. - fill_value : object - Default value to use for uninitialized portions of the array. + If ``compressor`` is set to ``None``, no compression is used. + fill_value : Any, optional + Fill value for the array. order : {'C', 'F'}, optional Deprecated in favor of the ``config`` keyword argument. Pass ``{'order': }`` to ``create`` instead of using this parameter. Memory layout to be used within each chunk. If not specified, the ``array.order`` parameter in the global config will be used. - store : Store or str + store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. synchronizer : object, optional Array synchronizer. overwrite : bool, optional - If True, delete all pre-existing data in `store` at `path` before + If True, delete all pre-existing data in ``store`` at ``path`` before creating the array. path : str, optional Path under which array is stored. - chunk_store : MutableMapping, optional - Separate storage for chunks. If not provided, `store` will be used + chunk_store : StoreLike or None, default=None + Separate storage for chunks. If not provided, ``store`` will be used for storage of both chunks and metadata. - filters : sequence of Codecs, optional - Sequence of filters to use to encode chunk data prior to compression. - Zarr format 2 only. If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` in :mod:`zarr.core.config`. + filters : Iterable[Codec] | Literal["auto"], optional + Iterable of filters to apply to each chunk of the array, in order, before serializing that + chunk to bytes. + + For Zarr format 3, a "filter" is a codec that takes an array and returns an array, + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + + For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the + the order if your filters is consistent with the behavior of each filter. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. cache_metadata : bool, optional If True, array configuration metadata will be cached for the lifetime of the object. If False, array metadata will be reloaded @@ -981,7 +974,6 @@ async def create( dimension_separator : {'.', '/'}, optional Separator placed between the dimensions of a chunk. Zarr format 2 only. Zarr format 3 arrays should use ``chunk_key_encoding`` instead. - Default is ".". write_empty_chunks : bool, optional Deprecated in favor of the ``config`` keyword argument. Pass ``{'write_empty_chunks': }`` to ``create`` instead of using this parameter. @@ -991,15 +983,36 @@ async def create( that chunk is not be stored, and the store entry for that chunk's key is deleted. zarr_format : {2, 3, None}, optional - The zarr format to use when saving. - Default is 3. + The Zarr format to use when creating an array. The default is ``None``, + which instructs Zarr to choose the default Zarr format value defined in the + runtime configuration. meta_array : array-like, optional - An array instance to use for determining arrays to create and return - to users. Use `numpy.empty(())` by default. + Not implemented. + attributes : dict[str, JSON], optional + A dictionary of user attributes to store with the array. + chunk_shape : int or tuple of ints, optional + The shape of the Array's chunks (default is None). + Zarr format 3 only. Zarr format 2 arrays should use `chunks` instead. + chunk_key_encoding : ChunkKeyEncoding, optional + A specification of how the chunk keys are represented in storage. + Zarr format 3 only. Zarr format 2 arrays should use `dimension_separator` instead. + Default is ``("default", "/")``. + codecs : Sequence of Codecs or dicts, optional + An iterable of Codec or dict serializations of Codecs. Zarr V3 only. + + The elements of ``codecs`` specify the transformation from array values to stored bytes. + Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. + + If no codecs are provided, default codecs will be used based on the data type of the array. + For most data types, the default codecs are the tuple ``(BytesCodec(), ZstdCodec())``; + data types that require a special :class:`zarr.abc.codec.ArrayBytesCodec`, like variable-length strings or bytes, + will use the :class:`zarr.abc.codec.ArrayBytesCodec` required for the data type instead of :class:`zarr.codecs.BytesCodec`. + dimension_names : Iterable[str | None] | None = None + An iterable of dimension names. Zarr format 3 only. storage_options : dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. - config : ArrayConfig or ArrayConfigLike, optional + config : ArrayConfigLike, optional Runtime configuration of the array. If provided, will override the default values from `zarr.config.array`. @@ -1224,7 +1237,7 @@ async def open_array( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. zarr_version : {2, 3, None}, optional The zarr format to use when saving. Deprecated in favor of zarr_format. diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 1e47208dcc..d0134a4900 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -142,7 +142,7 @@ def load( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. path : str or None, optional The path within the store from which to load. @@ -182,7 +182,7 @@ def open( Parameters ---------- - store : Store or str, optional + store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional Persistence mode: 'r' means read only (must exist); 'r+' means @@ -198,8 +198,8 @@ def open( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Additional parameters are passed through to :func:`zarr.api.asynchronous.open_array` or - :func:`zarr.api.asynchronous.open_group`. + Additional parameters are passed through to :func:`zarr.creation.open_array` or + :func:`zarr.hierarchy.open_group`. Returns ------- @@ -244,7 +244,7 @@ def save( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. *args : ndarray NumPy arrays with data to save. @@ -278,12 +278,13 @@ def save_array( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. arr : ndarray NumPy array with data to save. zarr_format : {2, 3, None}, optional - The zarr format to use when saving. + The zarr format to use when saving. The default is ``None``, which will + use the default Zarr format defined in the global configuration object. path : str or None, optional The path within the store where the array will be saved. storage_options : dict @@ -320,7 +321,7 @@ def save_group( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. *args : ndarray NumPy arrays with data to save. @@ -411,14 +412,13 @@ def group( Parameters ---------- - store : Store or str, optional - Store or path to directory in file system. + store : StoreLike or None, default=None + Store or path to directory in file system or name of zip file. overwrite : bool, optional If True, delete any pre-existing data in `store` at `path` before creating the group. - chunk_store : Store, optional - Separate storage for chunks. If not provided, `store` will be used - for storage of both chunks and metadata. + chunk_store : StoreLike or None, default=None + Separate storage for chunks. Not implemented. cache_attrs : bool, optional If True (default), user attributes will be cached for attribute read operations. If False, user attributes are reloaded from the store prior @@ -479,7 +479,7 @@ def open_group( Parameters ---------- - store : Store, str, or mapping, optional + store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. Strings are interpreted as paths on the local file system @@ -504,7 +504,7 @@ def open_group( Array synchronizer. path : str, optional Group path within store. - chunk_store : Store or str, optional + chunk_store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. storage_options : dict If using an fsspec URL to create the store, these will be passed to @@ -527,7 +527,7 @@ def open_group( To explicitly *not* use consolidated metadata, set ``use_consolidated=False``, which will fall back to using the regular, non consolidated metadata. - Zarr format 2 allows configuring the key storing the consolidated metadata + Zarr format 2 allowed configuring the key storing the consolidated metadata (``.zmetadata`` by default). Specify the custom key as ``use_consolidated`` to load consolidated metadata from a non-default key. @@ -569,8 +569,8 @@ def create_group( Parameters ---------- - store : Store or str - Store or path to directory in file system. + store : StoreLike + Store or path to directory in file system or name of zip file. path : str, optional Group path within store. overwrite : bool, optional @@ -613,7 +613,7 @@ def create( compressor: CompressorLike = "auto", fill_value: Any | None = DEFAULT_FILL_VALUE, # TODO: need type order: MemoryOrder | None = None, - store: str | StoreLike | None = None, + store: StoreLike | None = None, synchronizer: Any | None = None, overwrite: bool = False, path: PathLike | None = None, @@ -650,35 +650,58 @@ def create( shape : int or tuple of ints Array shape. chunks : int or tuple of ints, optional - Chunk shape. If True, will be guessed from `shape` and `dtype`. If - False, will be set to `shape`, i.e., single chunk for the whole array. + Chunk shape. If True, will be guessed from ``shape`` and ``dtype``. If + False, will be set to ``shape``, i.e., single chunk for the whole array. If an int, the chunk size in each dimension will be given by the value - of `chunks`. Default is True. + of ``chunks``. Default is True. dtype : str or dtype, optional NumPy dtype. compressor : Codec, optional - Primary compressor. - fill_value : object - Default value to use for uninitialized portions of the array. + Primary compressor to compress chunk data. + Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. + + If neither ``compressor`` nor ``filters`` are provided, the default compressor + :class:`zarr.codecs.ZstdCodec` is used. + + If ``compressor`` is set to ``None``, no compression is used. + fill_value : Any, optional + Fill value for the array. order : {'C', 'F'}, optional Deprecated in favor of the ``config`` keyword argument. Pass ``{'order': }`` to ``create`` instead of using this parameter. Memory layout to be used within each chunk. If not specified, the ``array.order`` parameter in the global config will be used. - store : Store or str + store : StoreLike or None, default=None Store or path to directory in file system or name of zip file. synchronizer : object, optional Array synchronizer. overwrite : bool, optional - If True, delete all pre-existing data in `store` at `path` before + If True, delete all pre-existing data in ``store`` at ``path`` before creating the array. path : str, optional Path under which array is stored. - chunk_store : MutableMapping, optional - Separate storage for chunks. If not provided, `store` will be used + chunk_store : StoreLike or None, default=None + Separate storage for chunks. If not provided, ``store`` will be used for storage of both chunks and metadata. - filters : sequence of Codecs, optional - Sequence of filters to use to encode chunk data prior to compression. + filters : Iterable[Codec] | Literal["auto"], optional + Iterable of filters to apply to each chunk of the array, in order, before serializing that + chunk to bytes. + + For Zarr format 3, a "filter" is a codec that takes an array and returns an array, + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + + For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the + the order if your filters is consistent with the behavior of each filter. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. cache_metadata : bool, optional If True, array configuration metadata will be cached for the lifetime of the object. If False, array metadata will be reloaded @@ -694,6 +717,7 @@ def create( A codec to encode object arrays, only needed if dtype=object. dimension_separator : {'.', '/'}, optional Separator placed between the dimensions of a chunk. + Zarr format 2 only. Zarr format 3 arrays should use ``chunk_key_encoding`` instead. write_empty_chunks : bool, optional Deprecated in favor of the ``config`` keyword argument. Pass ``{'write_empty_chunks': }`` to ``create`` instead of using this parameter. @@ -703,10 +727,32 @@ def create( that chunk is not be stored, and the store entry for that chunk's key is deleted. zarr_format : {2, 3, None}, optional - The zarr format to use when saving. + The Zarr format to use when creating an array. The default is ``None``, + which instructs Zarr to choose the default Zarr format value defined in the + runtime configuration. meta_array : array-like, optional - An array instance to use for determining arrays to create and return - to users. Use `numpy.empty(())` by default. + Not implemented. + attributes : dict[str, JSON], optional + A dictionary of user attributes to store with the array. + chunk_shape : int or tuple of ints, optional + The shape of the Array's chunks (default is None). + Zarr format 3 only. Zarr format 2 arrays should use `chunks` instead. + chunk_key_encoding : ChunkKeyEncoding, optional + A specification of how the chunk keys are represented in storage. + Zarr format 3 only. Zarr format 2 arrays should use `dimension_separator` instead. + Default is ``("default", "/")``. + codecs : Sequence of Codecs or dicts, optional + An iterable of Codec or dict serializations of Codecs. Zarr V3 only. + + The elements of ``codecs`` specify the transformation from array values to stored bytes. + Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. + + If no codecs are provided, default codecs will be used based on the data type of the array. + For most data types, the default codecs are the tuple ``(BytesCodec(), ZstdCodec())``; + data types that require a special :class:`zarr.abc.codec.ArrayBytesCodec`, like variable-length strings or bytes, + will use the :class:`zarr.abc.codec.ArrayBytesCodec` required for the data type instead of :class:`zarr.codecs.BytesCodec`. + dimension_names : Iterable[str | None] | None = None + An iterable of dimension names. Zarr format 3 only. storage_options : dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. @@ -757,7 +803,7 @@ def create( def create_array( - store: str | StoreLike, + store: StoreLike, *, name: str | None = None, shape: ShapeLike | None = None, @@ -785,41 +831,42 @@ def create_array( Parameters ---------- - store : str or Store + store : StoreLike Store or path to directory in file system or name of zip file. name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. shape : ShapeLike, optional Shape of the array. Must be ``None`` if ``data`` is provided. - dtype : ZDTypeLike, optional + dtype : ZDTypeLike | None Data type of the array. Must be ``None`` if ``data`` is provided. data : np.ndarray, optional Array-like data to use for initializing the array. If this parameter is provided, the ``shape`` and ``dtype`` parameters must be ``None``. - chunks : tuple[int, ...], optional + chunks : tuple[int, ...] | Literal["auto"], default="auto" Chunk shape of the array. - If not specified, default are guessed based on the shape and dtype. + If chunks is "auto", a chunk shape is guessed based on the shape of the array and the dtype. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. - filters : Iterable[Codec], optional + filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v3_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. compressors : Iterable[Codec], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -856,7 +903,7 @@ def create_array( The zarr format to use when saving. attributes : dict, optional Attributes for the array. - chunk_key_encoding : ChunkKeyEncoding, optional + chunk_key_encoding : ChunkKeyEncodingLike, optional A specification of how the chunk keys are represented in storage. For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. @@ -868,7 +915,7 @@ def create_array( Ignored otherwise. overwrite : bool, default False Whether to overwrite an array with the same name in the store, if one exists. - If `True`, all existing paths in the store will be deleted. + If ``True``, all existing paths in the store will be deleted. config : ArrayConfigLike, optional Runtime configuration for the array. write_data : bool @@ -923,7 +970,7 @@ def create_array( def from_array( - store: str | StoreLike, + store: StoreLike, *, data: Array | npt.ArrayLike, write_data: bool = True, @@ -947,8 +994,8 @@ def from_array( Parameters ---------- - store : str or Store - Store or path to directory in file system or name of zip file for the new array. + store : StoreLike + Store or path to directory in file system or name of zip file. data : Array | array-like The array to copy. write_data : bool, default True @@ -977,24 +1024,27 @@ def from_array( - None: No sharding. If not specified, defaults to "keep" if data is a zarr Array, otherwise None. - filters : Iterable[Codec] or "auto" or "keep", optional + filters : Iterable[Codec] | Literal["auto", "keep"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - Following values are supported: - - - Iterable[Codec]: List of filters to apply to the array. - - "auto": Automatically determine the filters based on the array's dtype. - - "keep": Retain the filters of the data array if it is a zarr Array. + The default value of ``"keep"`` instructs Zarr to infer ``filters`` from ``data``. + If that inference is not possible, Zarr will fall back to the behavior specified by ``"auto"``, + which is to choose default filters based on the data type of the array and the Zarr format specified. + For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple ``()``. + The only cases where default filters are not empty is when the Zarr format is 2, and the + data type is a variable-length data type like :class:`zarr.dtype.VariableLengthUTF8` or + :class:`zarr.dtype.VariableLengthUTF8`. In these cases, the default filters is a tuple with a + single element which is a codec specific to that particular data type. - If no ``filters`` are provided, defaults to "keep" if data is a zarr Array, otherwise "auto". + To create an array with no filters, provide an empty iterable or the value ``None``. compressors : Iterable[Codec] or "auto" or "keep", optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -1046,7 +1096,7 @@ def from_array( For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. If not specified and the data array has the same zarr format as the target array, the chunk key encoding of the data array is used. - dimension_names : Iterable[str], optional + dimension_names : Iterable[str | None] | None The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. If not specified, defaults to the dimension names of the data array. @@ -1272,6 +1322,7 @@ def open_array( store: StoreLike | None = None, *, zarr_version: ZarrFormat | None = None, + zarr_format: ZarrFormat | None = None, path: PathLike = "", storage_options: dict[str, Any] | None = None, **kwargs: Any, @@ -1280,9 +1331,11 @@ def open_array( Parameters ---------- - store : Store or str + store : StoreLike Store or path to directory in file system or name of zip file. zarr_version : {2, 3, None}, optional + The zarr format to use when saving. Deprecated in favor of zarr_format. + zarr_format : {2, 3, None}, optional The zarr format to use when saving. path : str, optional Path in store to array. @@ -1290,7 +1343,8 @@ def open_array( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Any keyword arguments to pass to ``create``. + Any keyword arguments to pass to :func:`create`. + Returns ------- @@ -1302,6 +1356,7 @@ def open_array( async_api.open_array( store=store, zarr_version=zarr_version, + zarr_format=zarr_format, path=path, storage_options=storage_options, **kwargs, diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index f31b0cc0a4..960b322a25 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -64,7 +64,6 @@ parse_shapelike, product, ) -from zarr.core.config import categorize_data_type from zarr.core.config import config as zarr_config from zarr.core.dtype import ( VariableLengthBytes, @@ -524,12 +523,6 @@ async def create( If no codecs are provided, default codecs will be used: - - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``. - - For Unicode strings, the default is ``VLenUTF8Codec`` and ``ZstdCodec``. - - For bytes or objects, the default is ``VLenBytesCodec`` and ``ZstdCodec``. - - These defaults can be changed by modifying the value of ``array.v3_default_filters``, - ``array.v3_default_serializer`` and ``array.v3_default_compressors`` in :mod:`zarr.core.config`. dimension_names : Iterable[str | None], optional The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. @@ -546,11 +539,25 @@ async def create( If `zarr_format`` is 3, then this parameter is deprecated, because memory order is a runtime parameter for Zarr 3 arrays. The recommended way to specify the memory order for Zarr 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. - filters : list[dict[str, JSON]], optional - Sequence of filters to use to encode chunk data prior to compression. - Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. If no ``filters`` - are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` in :mod:`zarr.core.config`. + filters : Iterable[Codec] | Literal["auto"], optional + Iterable of filters to apply to each chunk of the array, in order, before serializing that + chunk to bytes. + + For Zarr format 3, a "filter" is a codec that takes an array and returns an array, + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + + For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the + the order if your filters is consistent with the behavior of each filter. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. compressor : dict[str, JSON], optional The compressor used to compress the data (default is None). Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. @@ -2067,9 +2074,6 @@ def create( - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``. - For Unicode strings, the default is ``VLenUTF8Codec`` and ``ZstdCodec``. - For bytes or objects, the default is ``VLenBytesCodec`` and ``ZstdCodec``. - - These defaults can be changed by modifying the value of ``array.v3_default_filters``, - ``array.v3_default_serializer`` and ``array.v3_default_compressors`` in :mod:`zarr.core.config`. dimension_names : Iterable[str | None], optional The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. @@ -2086,11 +2090,25 @@ def create( If `zarr_format`` is 3, then this parameter is deprecated, because memory order is a runtime parameter for Zarr 3 arrays. The recommended way to specify the memory order for Zarr 3 arrays is via the ``config`` parameter, e.g. ``{'order': 'C'}``. - filters : list[dict[str, JSON]], optional - Sequence of filters to use to encode chunk data prior to compression. - Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. If no ``filters`` - are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` in :mod:`zarr.core.config`. + filters : Iterable[Codec] | Literal["auto"], optional + Iterable of filters to apply to each chunk of the array, in order, before serializing that + chunk to bytes. + + For Zarr format 3, a "filter" is a codec that takes an array and returns an array, + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + + For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the + the order if your filters is consistent with the behavior of each filter. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. compressor : dict[str, JSON], optional Primary compressor to compress chunk data. Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. @@ -2232,7 +2250,7 @@ def open( Parameters ---------- - store : Store + store : StoreLike Store containing the Array. Returns @@ -4164,7 +4182,7 @@ class ShardsConfigParam(TypedDict): async def from_array( - store: str | StoreLike, + store: StoreLike, *, data: Array | npt.ArrayLike, write_data: bool = True, @@ -4182,14 +4200,14 @@ async def from_array( dimension_names: DimensionNames = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, - config: ArrayConfig | ArrayConfigLike | None = None, + config: ArrayConfigLike | None = None, ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array from an existing array or array-like. Parameters ---------- - store : str or Store - Store or path to directory in file system or name of zip file for the new array. + store : StoreLike + Store or path to directory in file system or name of zip file. data : Array | array-like The array to copy. write_data : bool, default True @@ -4218,24 +4236,27 @@ async def from_array( - None: No sharding. If not specified, defaults to "keep" if data is a zarr Array, otherwise None. - filters : Iterable[Codec] or "auto" or "keep", optional + filters : Iterable[Codec] | Literal["auto", "keep"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - Following values are supported: - - - Iterable[Codec]: List of filters to apply to the array. - - "auto": Automatically determine the filters based on the array's dtype. - - "keep": Retain the filters of the data array if it is a zarr Array. + The default value of ``"keep"`` instructs Zarr to infer ``filters`` from ``data``. + If that inference is not possible, Zarr will fall back to the behavior specified by ``"auto"``, + which is to choose default filters based on the data type of the array and the Zarr format specified. + For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple ``()``. + The only cases where default filters are not empty is when the Zarr format is 2, and the + data type is a variable-length data type like :class:`zarr.dtype.VariableLengthUTF8` or + :class:`zarr.dtype.VariableLengthUTF8`. In these cases, the default filters is a tuple with a + single element which is a codec specific to that particular data type. - If no ``filters`` are provided, defaults to "keep" if data is a zarr Array, otherwise "auto". + To create an array with no filters, provide an empty iterable or the value ``None``. compressors : Iterable[Codec] or "auto" or "keep", optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -4287,7 +4308,7 @@ async def from_array( For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. If not specified and the data array has the same zarr format as the target array, the chunk key encoding of the data array is used. - dimension_names : Iterable[str | None], optional + dimension_names : Iterable[str | None] | None The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. If not specified, defaults to the dimension names of the data array. @@ -4462,46 +4483,40 @@ async def init_array( If not specified, default are guessed based on the shape and dtype. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. - filters : Iterable[Codec], optional + filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v3_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. - compressors : Iterable[Codec], optional + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. + compressors : Iterable[Codec] | Literal["auto"], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. - For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. - If no ``compressors`` are provided, a default set of compressors will be used. - These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default compressors. + The default value of ``"auto"`` instructs Zarr to use a default of :class:`zarr.codecs.ZstdCodec`. - For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may - be provided for Zarr format 2. - If no ``compressor`` is provided, a default compressor will be used. - in :mod:`zarr.core.config`. - Use ``None`` to omit the default compressor. - serializer : dict[str, JSON] | ArrayBytesCodec, optional + To create an array with no compressors, provide an empty iterable or the value ``None``. + serializer : dict[str, JSON] | ArrayBytesCodec | Literal["auto"], optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. - If no ``serializer`` is provided, a default serializer will be used. - These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in :mod:`zarr.core.config`. + + The default value of ``"auto"`` instructs Zarr to use a default codec based on the data type of the array. + For most data types this default codec is :class:`zarr.codecs.BytesCodec`. + For :class:`zarr.dtype.VariableLengthUTF8`, the default codec is :class:`zarr.codecs.VlenUTF8Codec`. + For :class:`zarr.dtype.VariableLengthBytes`, the default codec is :class:`zarr.codecs.VlenBytesCodec`. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -4648,7 +4663,7 @@ async def init_array( async def create_array( - store: str | StoreLike, + store: StoreLike, *, name: str | None = None, shape: ShapeLike | None = None, @@ -4674,41 +4689,42 @@ async def create_array( Parameters ---------- - store : str or Store + store : StoreLike Store or path to directory in file system or name of zip file. name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. - shape : tuple[int, ...], optional - Shape of the array. Can be ``None`` if ``data`` is provided. + shape : ShapeLike, optional + Shape of the array. Must be ``None`` if ``data`` is provided. dtype : ZDTypeLike | None - Data type of the array. Can be ``None`` if ``data`` is provided. - data : Array-like data to use for initializing the array. If this parameter is provided, the - ``shape`` and ``dtype`` parameters must be identical to ``data.shape`` and ``data.dtype``, - or ``None``. - chunks : tuple[int, ...], optional + Data type of the array. Must be ``None`` if ``data`` is provided. + data : np.ndarray, optional + Array-like data to use for initializing the array. If this parameter is provided, the + ``shape`` and ``dtype`` parameters must be ``None``. + chunks : tuple[int, ...] | Literal["auto"], default="auto" Chunk shape of the array. - If not specified, default are guessed based on the shape and dtype. + If chunks is "auto", a chunk shape is guessed based on the shape of the array and the dtype. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. - filters : Iterable[Codec], optional + filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v3_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. compressors : Iterable[Codec], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -4757,6 +4773,7 @@ async def create_array( Ignored otherwise. overwrite : bool, default False Whether to overwrite an array with the same name in the store, if one exists. + If ``True``, all existing paths in the store will be deleted. config : ArrayConfigLike, optional Runtime configuration for the array. write_data : bool @@ -4950,26 +4967,6 @@ def _parse_chunk_key_encoding( return result -def _get_default_chunk_encoding_v3( - dtype: ZDType[TBaseDType, TBaseScalar], -) -> tuple[tuple[ArrayArrayCodec, ...], ArrayBytesCodec, tuple[BytesBytesCodec, ...]]: - """ - Get the default ArrayArrayCodecs, ArrayBytesCodec, and BytesBytesCodec for a given dtype. - """ - - dtype_category = categorize_data_type(dtype) - - filters = zarr_config.get("array.v3_default_filters").get(dtype_category) - compressors = zarr_config.get("array.v3_default_compressors").get(dtype_category) - serializer = zarr_config.get("array.v3_default_serializer").get(dtype_category) - - return ( - tuple(_parse_array_array_codec(f) for f in filters), - _parse_array_bytes_codec(serializer), - tuple(_parse_bytes_bytes_codec(c) for c in compressors), - ) - - def default_filters_v3(dtype: ZDType[Any, Any]) -> tuple[ArrayArrayCodec, ...]: """ Given a data type, return the default filters for that data type. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 85d83713e4..f5bb14c48e 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -74,7 +74,7 @@ ) from typing import Any - from zarr.core.array_spec import ArrayConfig, ArrayConfigLike + from zarr.core.array_spec import ArrayConfigLike from zarr.core.buffer import Buffer, BufferPrototype from zarr.core.chunk_key_encodings import ChunkKeyEncodingLike from zarr.core.common import MemoryOrder @@ -1062,24 +1062,25 @@ async def create_array( If not specified, default are guessed based on the shape and dtype. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. - filters : Iterable[Codec], optional + filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v3_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. compressors : Iterable[Codec], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -2448,9 +2449,149 @@ def require_groups(self, *names: str) -> tuple[Group, ...]: """ return tuple(map(Group, self._sync(self._async_group.require_groups(*names)))) - def create(self, *args: Any, **kwargs: Any) -> Array: - # Backwards compatibility for 2.x - return self.create_array(*args, **kwargs) + def create( + self, + name: str, + *, + shape: ShapeLike | None = None, + dtype: ZDTypeLike | None = None, + data: np.ndarray[Any, np.dtype[Any]] | None = None, + chunks: tuple[int, ...] | Literal["auto"] = "auto", + shards: ShardsLike | None = None, + filters: FiltersLike = "auto", + compressors: CompressorsLike = "auto", + compressor: CompressorLike = "auto", + serializer: SerializerLike = "auto", + fill_value: Any | None = DEFAULT_FILL_VALUE, + order: MemoryOrder | None = None, + attributes: dict[str, JSON] | None = None, + chunk_key_encoding: ChunkKeyEncodingLike | None = None, + dimension_names: DimensionNames = None, + storage_options: dict[str, Any] | None = None, + overwrite: bool = False, + config: ArrayConfigLike | None = None, + write_data: bool = True, + ) -> Array: + """Create an array within this group. + + This method lightly wraps :func:`zarr.core.array.create_array`. + + Parameters + ---------- + name : str + The name of the array relative to the group. If ``path`` is ``None``, the array will be located + at the root of the store. + shape : ShapeLike, optional + Shape of the array. Must be ``None`` if ``data`` is provided. + dtype : npt.DTypeLike | None + Data type of the array. Must be ``None`` if ``data`` is provided. + data : Array-like data to use for initializing the array. If this parameter is provided, the + ``shape`` and ``dtype`` parameters must be ``None``. + chunks : tuple[int, ...], optional + Chunk shape of the array. + If not specified, default are guessed based on the shape and dtype. + shards : tuple[int, ...], optional + Shard shape of the array. The default value of ``None`` results in no sharding at all. + filters : Iterable[Codec] | Literal["auto"], optional + Iterable of filters to apply to each chunk of the array, in order, before serializing that + chunk to bytes. + + For Zarr format 3, a "filter" is a codec that takes an array and returns an array, + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + + For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the + the order if your filters is consistent with the behavior of each filter. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. + compressors : Iterable[Codec], optional + List of compressors to apply to the array. Compressors are applied in order, and after any + filters are applied (if any are specified) and the data is serialized into bytes. + + For Zarr format 3, a "compressor" is a codec that takes a bytestream, and + returns another bytestream. Multiple compressors my be provided for Zarr format 3. + If no ``compressors`` are provided, a default set of compressors will be used. + These defaults can be changed by modifying the value of ``array.v3_default_compressors`` + in :mod:`zarr.core.config`. + Use ``None`` to omit default compressors. + + For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may + be provided for Zarr format 2. + If no ``compressor`` is provided, a default compressor will be used. + in :mod:`zarr.core.config`. + Use ``None`` to omit the default compressor. + compressor : Codec, optional + Deprecated in favor of ``compressors``. + serializer : dict[str, JSON] | ArrayBytesCodec, optional + Array-to-bytes codec to use for encoding the array data. + Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. + If no ``serializer`` is provided, a default serializer will be used. + These defaults can be changed by modifying the value of ``array.v3_default_serializer`` + in :mod:`zarr.core.config`. + fill_value : Any, optional + Fill value for the array. + order : {"C", "F"}, optional + The memory of the array (default is "C"). + For Zarr format 2, this parameter sets the memory order of the array. + For Zarr format 3, this parameter is deprecated, because memory order + is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory + order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. + If no ``order`` is provided, a default order will be used. + This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + attributes : dict, optional + Attributes for the array. + chunk_key_encoding : ChunkKeyEncoding, optional + A specification of how the chunk keys are represented in storage. + For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. + For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. + dimension_names : Iterable[str], optional + The names of the dimensions (default is None). + Zarr format 3 only. Zarr format 2 arrays should not use this parameter. + storage_options : dict, optional + If using an fsspec URL to create the store, these will be passed to the backend implementation. + Ignored otherwise. + overwrite : bool, default False + Whether to overwrite an array with the same name in the store, if one exists. + config : ArrayConfig or ArrayConfigLike, optional + Runtime configuration for the array. + write_data : bool + If a pre-existing array-like object was provided to this function via the ``data`` parameter + then ``write_data`` determines whether the values in that array-like object should be + written to the Zarr array created by this function. If ``write_data`` is ``False``, then the + array will be left empty. + + Returns + ------- + AsyncArray + """ + return self.create_array( + name, + shape=shape, + dtype=dtype, + data=data, + chunks=chunks, + shards=shards, + filters=filters, + compressors=compressors, + compressor=compressor, + serializer=serializer, + fill_value=fill_value, + order=order, + attributes=attributes, + chunk_key_encoding=chunk_key_encoding, + dimension_names=dimension_names, + storage_options=storage_options, + overwrite=overwrite, + config=config, + write_data=write_data, + ) def create_array( self, @@ -2495,24 +2636,25 @@ def create_array( If not specified, default are guessed based on the shape and dtype. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. - filters : Iterable[Codec], optional + filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v3_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. compressors : Iterable[Codec], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -2867,7 +3009,7 @@ def array( dimension_names: DimensionNames = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, - config: ArrayConfig | ArrayConfigLike | None = None, + config: ArrayConfigLike | None = None, data: npt.ArrayLike | None = None, ) -> Array: """Create an array within this group. @@ -2891,24 +3033,25 @@ def array( If not specified, default are guessed based on the shape and dtype. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. - filters : Iterable[Codec], optional + filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of ``ArrayArrayCodec``, or dict representations - of ``ArrayArrayCodec``. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v3_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a + dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. - If no ``filters`` are provided, a default set of filters will be used. - These defaults can be changed by modifying the value of ``array.v2_default_filters`` - in :mod:`zarr.core.config`. - Use ``None`` to omit default filters. + + The default value of ``"auto"`` instructs Zarr to use a default used based on the data + type of the array and the Zarr format specified. For all data types in Zarr V3, and most + data types in Zarr V2, the default filters are empty. The only cases where default filters + are not empty is when the Zarr format is 2, and the data type is a variable-length data type like + :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + the default filters contains a single element which is a codec specific to that particular data type. + + To create an array with no filters, provide an empty iterable or the value ``None``. compressors : Iterable[Codec], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 90f0b28870..5df2c11c5c 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -294,7 +294,7 @@ async def make_store_path( Parameters ---------- - store_like : StoreLike | None + store_like : StoreLike or None, default=None The object to convert to a `StorePath` object. path : str | None, optional The path to use when creating the `StorePath` object. If None, the diff --git a/tests/test_api/test_synchronous.py b/tests/test_api/test_synchronous.py new file mode 100644 index 0000000000..d6ae61f1ca --- /dev/null +++ b/tests/test_api/test_synchronous.py @@ -0,0 +1,130 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING, Any, Final + +import pytest +from numpydoc.docscrape import NumpyDocString + +import zarr +from zarr.api import asynchronous, synchronous + +if TYPE_CHECKING: + from collections.abc import Callable + +MATCHED_EXPORT_NAMES: Final[tuple[str, ...]] = tuple( + sorted(set(synchronous.__all__) | set(asynchronous.__all__)) +) +"""A sorted tuple of names that are exported by both the sync and async APIs.""" + +MATCHED_CALLABLE_NAMES: Final[tuple[str, ...]] = tuple( + x for x in MATCHED_EXPORT_NAMES if callable(getattr(synchronous, x)) +) +"""A sorted tuple of callable names that are exported by both the sync and async APIs.""" + + +@pytest.mark.parametrize("callable_name", MATCHED_CALLABLE_NAMES) +def test_docstrings_match(callable_name: str) -> None: + """ + Tests that the docstrings for the sync and async define identical parameters. + """ + callable_a = getattr(synchronous, callable_name) + callable_b = getattr(asynchronous, callable_name) + if callable_a.__doc__ is None: + assert callable_b.__doc__ is None + else: + params_a = NumpyDocString(callable_a.__doc__)["Parameters"] + params_b = NumpyDocString(callable_b.__doc__)["Parameters"] + mismatch = [] + for idx, (a, b) in enumerate(zip(params_a, params_b, strict=False)): + if a != b: + mismatch.append((idx, (a, b))) + assert mismatch == [] + + +@pytest.mark.parametrize( + ("parameter_name", "array_creation_routines"), + [ + ( + ("store", "path"), + ( + asynchronous.create_array, + synchronous.create_array, + asynchronous.create_group, + synchronous.create_group, + zarr.AsyncGroup.create_array, + zarr.Group.create_array, + ), + ), + ( + ( + "store", + "path", + ), + ( + asynchronous.create, + synchronous.create, + zarr.Group.create, + zarr.AsyncArray.create, + zarr.Array.create, + ), + ), + ( + ( + ( + "filters", + "codecs", + "compressors", + "compressor", + "chunks", + "shape", + "dtype", + "shardsfill_value", + ) + ), + ( + asynchronous.create, + synchronous.create, + asynchronous.create_array, + synchronous.create_array, + zarr.AsyncGroup.create_array, + zarr.Group.create_array, + zarr.AsyncGroup.create_dataset, + zarr.Group.create_dataset, + ), + ), + ], + ids=str, +) +def test_docstring_consistent_parameters( + parameter_name: str, array_creation_routines: tuple[Callable[[Any], Any], ...] +) -> None: + """ + Tests that array and group creation routines document the same parameters consistently. + This test inspects the docstrings of sets of callables and generates two dicts: + + - a dict where the keys are parameter descriptions and the values are the names of the routines with those + descriptions + - a dict where the keys are parameter types and the values are the names of the routines with those types + + If each dict has just 1 value, then the parameter description and type in the docstring must be + identical across different routines. But if these dicts have multiple values, then there must be + routines that use the same parameter but document it differently, which will trigger a test failure. + """ + descs: dict[tuple[str, ...], tuple[str, ...]] = {} + types: dict[str, tuple[str, ...]] = {} + for routine in array_creation_routines: + key = f"{routine.__module__}.{routine.__qualname__}" + docstring = NumpyDocString(routine.__doc__) + param_dict = {d.name: d for d in docstring["Parameters"]} + if parameter_name in param_dict: + val = param_dict[parameter_name] + if tuple(val.desc) in descs: + descs[tuple(val.desc)] = descs[tuple(val.desc)] + (key,) + else: + descs[tuple(val.desc)] = (key,) + if val.type in types: + types[val.type] = types[val.type] + (key,) + else: + types[val.type] = (key,) + assert len(descs) <= 1 + assert len(types) <= 1 From 3c883a3c578b6e9fdb4d5fd7a160ce992aaec1b3 Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Wed, 17 Sep 2025 09:26:41 +0100 Subject: [PATCH 108/468] Add CLI for converting v2 metadata to v3 (#3257) * add rough cli converter structure * allow zstd, gzip and numcodecs zarr 3 compression * convert filters to v3 * create BytesCodec with correct endian * handle C vs F order in v2 metadata * save group and array metadata to file * create overall conversion functions for store, array or group * add minimal typer cli * add initial tests for converter * add tests for conversion of groups and nested groups and arrays * add tests for conversion of compressors and filters * test conversion of order and endianness * add tests for edge cases of incorrect codecs * add tests for / separator * draft of metadata remover and add test for internal paths * add clear command to cli with tests * add test for metadata removal with path# * add verbose logging option * add dry run option to cli * add test for dry-run * add zarr-converter script and enable cli dep in tests * use v2 chunk key encoding type * update endianness of test data type * check converted arrays can be accessed * remove uses of pathlib walk, as it didn't exist in python 3.11 * include tags in checkout for gpu test, to avoid numcodecs.zarr3 requesting a zarr version greater than 3 * rename cli commands from review comments * remove path option * allow metadata to be written to a separate store location * add overwrite and remove-v2-metadata options * add force option * use v2, v3 format for CLI * split into convert_group and convert_array functions * update command names in converter tests * update test filename to reflect command name change * fix tests for sub-groups * add tests for --force * add test for migrating to separate output location * add test for remove-v2-metadata option * update test names to match command name * add test for --remove-v2-metadata with separate output location * separate cli fixtures from the tests * add test for overwrite option in separate location * fix failing test * small fixes to tests * fix pre-commit errors * update docstrings with review comments * pass filters and compressors to processing functions, rather than full metadata * use Store as input rather than StoreLike * move conversion functions into public api * fail on discovery of consolidated metadata * minor changes from review * use same logger throughout zarr-python * add release notes and docs for the cli * tidy up formatting of zarr.metadata api docs * fix failing tests * add a section about --verbose to the docs * update docstrings to reference zarr.codecs.numcodecs --------- Co-authored-by: Davis Bennett --- .github/workflows/gpu_test.yml | 2 + changes/1798.feature.rst | 2 + docs/user-guide/cli.rst | 127 ++++++ docs/user-guide/index.rst | 1 + pyproject.toml | 6 +- src/zarr/__init__.py | 58 +++ src/zarr/_cli/__init__.py | 0 src/zarr/_cli/cli.py | 186 +++++++++ src/zarr/metadata/__init__.py | 0 src/zarr/metadata/migrate_v3.py | 294 +++++++++++++ src/zarr/storage/_common.py | 138 ++++--- tests/conftest.py | 23 ++ tests/test_cli/conftest.py | 146 +++++++ tests/test_cli/test_migrate_v3.py | 666 ++++++++++++++++++++++++++++++ tests/test_codec_entrypoints.py | 18 - tests/test_dtype_registry.py | 22 - 16 files changed, 1599 insertions(+), 90 deletions(-) create mode 100644 changes/1798.feature.rst create mode 100644 docs/user-guide/cli.rst create mode 100644 src/zarr/_cli/__init__.py create mode 100644 src/zarr/_cli/cli.py create mode 100644 src/zarr/metadata/__init__.py create mode 100644 src/zarr/metadata/migrate_v3.py create mode 100644 tests/test_cli/conftest.py create mode 100644 tests/test_cli/test_migrate_v3.py diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index edd52186c5..7782114764 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -30,6 +30,8 @@ jobs: steps: - uses: actions/checkout@v5 + with: + fetch-depth: 0 # grab all branches and tags # - name: cuda-toolkit # uses: Jimver/cuda-toolkit@v0.2.16 # id: cuda-toolkit diff --git a/changes/1798.feature.rst b/changes/1798.feature.rst new file mode 100644 index 0000000000..64d4efdf08 --- /dev/null +++ b/changes/1798.feature.rst @@ -0,0 +1,2 @@ +Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also +provided under zarr.metadata. diff --git a/docs/user-guide/cli.rst b/docs/user-guide/cli.rst new file mode 100644 index 0000000000..822b60d389 --- /dev/null +++ b/docs/user-guide/cli.rst @@ -0,0 +1,127 @@ +.. _user-guide-cli: + +Command-line interface +======================== + +Zarr-Python provides a command-line interface that enables: + +- migration of Zarr v2 metadata to v3 +- removal of v2 or v3 metadata + +To see available commands run the following in a terminal: + +.. code-block:: bash + + $ zarr --help + +or to get help on individual commands: + +.. code-block:: bash + + $ zarr migrate --help + + $ zarr remove-metadata --help + + +Migrate metadata from v2 to v3 +------------------------------ + +Migrate to a separate location +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +To migrate a Zarr array/group's metadata from v2 to v3 run: + +.. code-block:: bash + + $ zarr migrate v3 path/to/input.zarr path/to/output.zarr + +This will write new ``zarr.json`` files to ``output.zarr``, leaving ``input.zarr`` un-touched. +Note - this will migrate the entire Zarr hierarchy, so if ``input.zarr`` contains multiple groups/arrays, +new ``zarr.json`` will be made for all of them. + +Migrate in-place +~~~~~~~~~~~~~~~~ + +If you'd prefer to migrate the metadata in-place run: + +.. code-block:: bash + + $ zarr migrate v3 path/to/input.zarr + +This will write new ``zarr.json`` files to ``input.zarr``, leaving the existing v2 metadata un-touched. + +To open the array/group using the new metadata use: + +.. code-block:: python + + >>> import zarr + >>> zarr_with_v3_metadata = zarr.open('path/to/input.zarr', zarr_format=3) + +Once you are happy with the conversion, you can run the following to remove the old v2 metadata: + +.. code-block:: bash + + $ zarr remove-metadata v2 path/to/input.zarr + +Note there is also a shortcut to migrate and remove v2 metadata in one step: + +.. code-block:: bash + + $ zarr migrate v3 path/to/input.zarr --remove-v2-metadata + + +Remove metadata +---------------- + +Remove v2 metadata using: + +.. code-block:: bash + + $ zarr remove-metadata v2 path/to/input.zarr + +or v3 with: + +.. code-block:: bash + + $ zarr remove-metadata v3 path/to/input.zarr + +By default, this will only allow removal of metadata if a valid alternative exists. For example, you can't +remove v2 metadata unless v3 metadata exists at that location. + +To override this behaviour use ``--force``: + +.. code-block:: bash + + $ zarr remove-metadata v3 path/to/input.zarr --force + + +Dry run +-------- +All commands provide a ``--dry-run`` option that will log changes that would be made on a real run, without creating +or modifying any files. + +.. code-block:: bash + + $ zarr migrate v3 path/to/input.zarr --dry-run + + Dry run enabled - no new files will be created or changed. Log of files that would be created on a real run: + Saving metadata to path/to/input.zarr/zarr.json + + +Verbose +-------- +You can also add ``--verbose`` **before** any command, to see a full log of its actions: + +.. code-block:: bash + + $ zarr --verbose migrate v3 path/to/input.zarr + + $ zarr --verbose remove-metadata v2 path/to/input.zarr + + +Equivalent functions +-------------------- +All features of the command-line interface are also available via functions under +:mod:`zarr.metadata`. + + diff --git a/docs/user-guide/index.rst b/docs/user-guide/index.rst index f92c576f32..a83a30172b 100644 --- a/docs/user-guide/index.rst +++ b/docs/user-guide/index.rst @@ -13,6 +13,7 @@ User guide storage config v3_migration + cli Advanced Topics --------------- diff --git a/pyproject.toml b/pyproject.toml index 9af39fb85c..11d91944d5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,6 +68,7 @@ remote = [ gpu = [ "cupy-cuda12x", ] +cli = ["typer"] # Development extras test = [ "coverage>=7.10", @@ -114,6 +115,9 @@ docs = [ 'pytest' ] +[project.scripts] +zarr = "zarr._cli.cli:app" + [project.urls] issues = "https://github.com/zarr-developers/zarr-python/issues" @@ -164,7 +168,7 @@ deps = ["minimal", "optional"] [tool.hatch.envs.test.overrides] matrix.deps.dependencies = [ - {value = "zarr[remote, remote_tests, test, optional]", if = ["optional"]} + {value = "zarr[remote, remote_tests, test, optional, cli]", if = ["optional"]} ] [tool.hatch.envs.test.scripts] diff --git a/src/zarr/__init__.py b/src/zarr/__init__.py index 0d58ecf8e8..3c6195c28f 100644 --- a/src/zarr/__init__.py +++ b/src/zarr/__init__.py @@ -1,3 +1,7 @@ +import functools +import logging +from typing import Literal + from zarr._version import version as __version__ from zarr.api.synchronous import ( array, @@ -37,6 +41,8 @@ # in case setuptools scm screw up and find version to be 0.0.0 assert not __version__.startswith("0.0.0") +_logger = logging.getLogger(__name__) + def print_debug_info() -> None: """ @@ -85,6 +91,58 @@ def print_packages(packages: list[str]) -> None: print_packages(optional) +# The decorator ensures this always returns the same handler (and it is only +# attached once). +@functools.cache +def _ensure_handler() -> logging.Handler: + """ + The first time this function is called, attach a `StreamHandler` using the + same format as `logging.basicConfig` to the Zarr-Python root logger. + + Return this handler every time this function is called. + """ + handler = logging.StreamHandler() + handler.setFormatter(logging.Formatter(logging.BASIC_FORMAT)) + _logger.addHandler(handler) + return handler + + +def set_log_level( + level: Literal["NOTSET", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], +) -> None: + """Set the logging level for Zarr-Python. + + Zarr-Python uses the standard library `logging` framework under the root + logger 'zarr'. This is a helper function to: + + - set Zarr-Python's root logger level + - set the root logger handler's level, creating the handler + if it does not exist yet + + Parameters + ---------- + level : str + The logging level to set. + """ + _logger.setLevel(level) + _ensure_handler().setLevel(level) + + +def set_format(log_format: str) -> None: + """Set the format of logging messages from Zarr-Python. + + Zarr-Python uses the standard library `logging` framework under the root + logger 'zarr'. This sets the format of log messages from the root logger's StreamHandler. + + Parameters + ---------- + log_format : str + A string determining the log format (as defined in the standard library's `logging` module + for logging.Formatter) + """ + _ensure_handler().setFormatter(logging.Formatter(fmt=log_format)) + + __all__ = [ "Array", "AsyncArray", diff --git a/src/zarr/_cli/__init__.py b/src/zarr/_cli/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/src/zarr/_cli/cli.py b/src/zarr/_cli/cli.py new file mode 100644 index 0000000000..785efe505b --- /dev/null +++ b/src/zarr/_cli/cli.py @@ -0,0 +1,186 @@ +import logging +from enum import Enum +from typing import Annotated, Literal, cast + +import typer + +import zarr +import zarr.metadata.migrate_v3 as migrate_metadata +from zarr.core.sync import sync +from zarr.storage._common import make_store + +app = typer.Typer() + +logger = logging.getLogger(__name__) + + +def _set_logging_level(*, verbose: bool) -> None: + if verbose: + lvl = "INFO" + else: + lvl = "WARNING" + zarr.set_log_level(cast(Literal["INFO", "WARNING"], lvl)) + zarr.set_format("%(message)s") + + +class ZarrFormat(str, Enum): + v2 = "v2" + v3 = "v3" + + +class ZarrFormatV3(str, Enum): + """Limit CLI choice to only v3""" + + v3 = "v3" + + +@app.command() # type: ignore[misc] +def migrate( + zarr_format: Annotated[ + ZarrFormatV3, + typer.Argument( + help="Zarr format to migrate to. Currently only 'v3' is supported.", + ), + ], + input_store: Annotated[ + str, + typer.Argument( + help=( + "Input Zarr to migrate - should be a store, path to directory in file system or name of zip file " + "e.g. 'data/example-1.zarr', 's3://example-bucket/example'..." + ) + ), + ], + output_store: Annotated[ + str | None, + typer.Argument( + help=( + "Output location to write generated metadata (no array data will be copied). If not provided, " + "metadata will be written to input_store. Should be a store, path to directory in file system " + "or name of zip file e.g. 'data/example-1.zarr', 's3://example-bucket/example'..." + ) + ), + ] = None, + dry_run: Annotated[ + bool, + typer.Option( + help="Enable a dry-run: files that would be converted are logged, but no new files are created or changed." + ), + ] = False, + overwrite: Annotated[ + bool, + typer.Option( + help="Remove any existing v3 metadata at the output location, before migration starts." + ), + ] = False, + force: Annotated[ + bool, + typer.Option( + help=( + "Only used when --overwrite is given. Allows v3 metadata to be removed when no valid " + "v2 metadata exists at the output location." + ) + ), + ] = False, + remove_v2_metadata: Annotated[ + bool, + typer.Option( + help="Remove v2 metadata (if any) from the output location, after migration is complete." + ), + ] = False, +) -> None: + """Migrate all v2 metadata in a zarr hierarchy to v3. This will create a zarr.json file for each level + (every group / array). v2 files (.zarray, .zattrs etc.) will be left as-is. + """ + if dry_run: + _set_logging_level(verbose=True) + logger.info( + "Dry run enabled - no new files will be created or changed. Log of files that would be created on a real run:" + ) + + input_zarr_store = sync(make_store(input_store, mode="r+")) + + if output_store is not None: + output_zarr_store = sync(make_store(output_store, mode="w-")) + write_store = output_zarr_store + else: + output_zarr_store = None + write_store = input_zarr_store + + if overwrite: + sync(migrate_metadata.remove_metadata(write_store, 3, force=force, dry_run=dry_run)) + + migrate_metadata.migrate_v2_to_v3( + input_store=input_zarr_store, output_store=output_zarr_store, dry_run=dry_run + ) + + if remove_v2_metadata: + # There should always be valid v3 metadata at the output location after migration, so force=False + sync(migrate_metadata.remove_metadata(write_store, 2, force=False, dry_run=dry_run)) + + +@app.command() # type: ignore[misc] +def remove_metadata( + zarr_format: Annotated[ + ZarrFormat, + typer.Argument(help="Which format's metadata to remove - v2 or v3."), + ], + store: Annotated[ + str, + typer.Argument( + help="Store or path to directory in file system or name of zip file e.g. 'data/example-1.zarr', 's3://example-bucket/example'..." + ), + ], + force: Annotated[ + bool, + typer.Option( + help=( + "Allow metadata to be deleted when no valid alternative exists e.g. allow deletion of v2 metadata, " + "when no v3 metadata is present." + ) + ), + ] = False, + dry_run: Annotated[ + bool, + typer.Option( + help="Enable a dry-run: files that would be deleted are logged, but no files are removed or changed." + ), + ] = False, +) -> None: + """Remove all v2 (.zarray, .zattrs, .zgroup, .zmetadata) or v3 (zarr.json) metadata files from the given Zarr. + Note - this will remove metadata files at all levels of the hierarchy (every group and array). + """ + if dry_run: + _set_logging_level(verbose=True) + logger.info( + "Dry run enabled - no files will be deleted or changed. Log of files that would be deleted on a real run:" + ) + input_zarr_store = sync(make_store(store, mode="r+")) + + sync( + migrate_metadata.remove_metadata( + store=input_zarr_store, + zarr_format=cast(Literal[2, 3], int(zarr_format[1:])), + force=force, + dry_run=dry_run, + ) + ) + + +@app.callback() # type: ignore[misc] +def main( + verbose: Annotated[ + bool, + typer.Option( + help="enable verbose logging - will print info about metadata files being deleted / saved." + ), + ] = False, +) -> None: + """ + See available commands below - access help for individual commands with zarr COMMAND --help. + """ + _set_logging_level(verbose=verbose) + + +if __name__ == "__main__": + app() diff --git a/src/zarr/metadata/__init__.py b/src/zarr/metadata/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/src/zarr/metadata/migrate_v3.py b/src/zarr/metadata/migrate_v3.py new file mode 100644 index 0000000000..5fc5fe0df5 --- /dev/null +++ b/src/zarr/metadata/migrate_v3.py @@ -0,0 +1,294 @@ +import asyncio +import logging +from typing import Literal, cast + +import numcodecs.abc + +import zarr +from zarr import Array, Group +from zarr.abc.codec import ArrayArrayCodec, BytesBytesCodec, Codec +from zarr.abc.store import Store +from zarr.codecs.blosc import BloscCodec, BloscShuffle +from zarr.codecs.bytes import BytesCodec +from zarr.codecs.gzip import GzipCodec +from zarr.codecs.transpose import TransposeCodec +from zarr.codecs.zstd import ZstdCodec +from zarr.core.buffer.core import default_buffer_prototype +from zarr.core.chunk_key_encodings import V2ChunkKeyEncoding +from zarr.core.common import ( + ZARR_JSON, + ZARRAY_JSON, + ZATTRS_JSON, + ZGROUP_JSON, + ZMETADATA_V2_JSON, + ZarrFormat, +) +from zarr.core.dtype.common import HasEndianness +from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType +from zarr.core.group import GroupMetadata +from zarr.core.metadata.v2 import ArrayV2Metadata +from zarr.core.metadata.v3 import ArrayV3Metadata +from zarr.core.sync import sync +from zarr.registry import get_codec_class +from zarr.storage import StorePath + +_logger = logging.getLogger(__name__) + + +def migrate_v2_to_v3( + *, + input_store: Store, + output_store: Store | None = None, + dry_run: bool = False, +) -> None: + """Migrate all v2 metadata in a Zarr store to v3. + + This will create a zarr.json file at each level of a Zarr hierarchy (for every group / array). + v2 files (.zarray, .zattrs etc.) will be left as-is. + + Parameters + ---------- + input_store : Store + Input Zarr to migrate. + output_store : Store, optional + Output location to write v3 metadata (no array data will be copied). If not provided, v3 metadata will be + written to input_store. + dry_run : bool, optional + Enable a 'dry run' - files that would be created are logged, but no files are created or changed. + """ + + zarr_v2 = zarr.open(store=input_store, mode="r+") + + if output_store is not None: + # w- access to not allow overwrite of existing data + output_path = sync(StorePath.open(output_store, path="", mode="w-")) + else: + output_path = zarr_v2.store_path + + migrate_to_v3(zarr_v2, output_path, dry_run=dry_run) + + +def migrate_to_v3(zarr_v2: Array | Group, output_path: StorePath, dry_run: bool = False) -> None: + """Migrate all v2 metadata in a Zarr array/group to v3. + + Note - if a group is provided, then all arrays / groups within this group will also be converted. + A zarr.json file will be created for each level and written to output_path, with any v2 files + (.zarray, .zattrs etc.) left as-is. + + Parameters + ---------- + zarr_v2 : Array | Group + An array or group with zarr_format = 2 + output_path : StorePath + The store path to write generated v3 metadata to. + dry_run : bool, optional + Enable a 'dry run' - files that would be created are logged, but no files are created or changed. + """ + if not zarr_v2.metadata.zarr_format == 2: + raise TypeError("Only arrays / groups with zarr v2 metadata can be converted") + + if isinstance(zarr_v2.metadata, GroupMetadata): + _convert_group(zarr_v2, output_path, dry_run) + else: + _convert_array(zarr_v2, output_path, dry_run) + + +async def remove_metadata( + store: Store, + zarr_format: ZarrFormat, + force: bool = False, + dry_run: bool = False, +) -> None: + """Remove all v2 (.zarray, .zattrs, .zgroup, .zmetadata) or v3 (zarr.json) metadata files from the given Zarr. + + Note - this will remove metadata files at all levels of the hierarchy (every group and array). + + Parameters + ---------- + store : Store + Zarr to remove metadata from. + zarr_format : ZarrFormat + Which format's metadata to remove - 2 or 3. + force : bool, optional + When False, metadata can only be removed if a valid alternative exists e.g. deletion of v2 metadata will + only be allowed when v3 metadata is also present. When True, metadata can be removed when there is no + alternative. + dry_run : bool, optional + Enable a 'dry run' - files that would be deleted are logged, but no files are removed or changed. + """ + + if not store.supports_deletes: + raise ValueError("Store must support deletes to remove metadata") + store_path = await StorePath.open(store, path="", mode="r+") + + metadata_files_all = { + 2: [ZARRAY_JSON, ZATTRS_JSON, ZGROUP_JSON, ZMETADATA_V2_JSON], + 3: [ZARR_JSON], + } + + if zarr_format == 2: + alternative_metadata = 3 + else: + alternative_metadata = 2 + + awaitables = [] + async for file_path in store.list(): + parent_path, _, file_name = file_path.rpartition("/") + + if file_name not in metadata_files_all[zarr_format]: + continue + + if force or await _metadata_exists( + cast(Literal[2, 3], alternative_metadata), store_path / parent_path + ): + _logger.info("Deleting metadata at %s", store_path / file_path) + if not dry_run: + awaitables.append((store_path / file_path).delete()) + else: + raise ValueError( + f"Cannot remove v{zarr_format} metadata at {store_path / file_path} - no v{alternative_metadata} " + "metadata exists. To delete anyway, use the 'force' option." + ) + + await asyncio.gather(*awaitables) + + +def _convert_group(zarr_v2: Group, output_path: StorePath, dry_run: bool) -> None: + if zarr_v2.metadata.consolidated_metadata is not None: + raise NotImplementedError("Migration of consolidated metadata isn't supported.") + + # process members of the group + for key in zarr_v2: + migrate_to_v3(zarr_v2[key], output_path=output_path / key, dry_run=dry_run) + + # write group's converted metadata + group_metadata_v3 = GroupMetadata( + attributes=zarr_v2.metadata.attributes, zarr_format=3, consolidated_metadata=None + ) + sync(_save_v3_metadata(group_metadata_v3, output_path, dry_run=dry_run)) + + +def _convert_array(zarr_v2: Array, output_path: StorePath, dry_run: bool) -> None: + array_metadata_v3 = _convert_array_metadata(cast(ArrayV2Metadata, zarr_v2.metadata)) + sync(_save_v3_metadata(array_metadata_v3, output_path, dry_run=dry_run)) + + +async def _metadata_exists(zarr_format: ZarrFormat, store_path: StorePath) -> bool: + metadata_files_required = {2: [ZARRAY_JSON, ZGROUP_JSON], 3: [ZARR_JSON]} + + for metadata_file in metadata_files_required[zarr_format]: + if await (store_path / metadata_file).exists(): + return True + + return False + + +def _convert_array_metadata(metadata_v2: ArrayV2Metadata) -> ArrayV3Metadata: + chunk_key_encoding = V2ChunkKeyEncoding(separator=metadata_v2.dimension_separator) + + codecs: list[Codec] = [] + + # array-array codecs + if metadata_v2.order == "F": + # F is equivalent to order: n-1, ... 1, 0 + codecs.append(TransposeCodec(order=list(range(len(metadata_v2.shape) - 1, -1, -1)))) + + if metadata_v2.filters is not None: + codecs.extend(_convert_filters(metadata_v2.filters)) + + # array-bytes codecs + if not isinstance(metadata_v2.dtype, HasEndianness): + codecs.append(BytesCodec(endian=None)) + else: + codecs.append(BytesCodec(endian=metadata_v2.dtype.endianness)) + + # bytes-bytes codecs + if metadata_v2.compressor is not None: + bytes_bytes_codec = _convert_compressor(metadata_v2.compressor, metadata_v2.dtype) + codecs.append(bytes_bytes_codec) + + return ArrayV3Metadata( + shape=metadata_v2.shape, + data_type=metadata_v2.dtype, + chunk_grid=metadata_v2.chunk_grid, + chunk_key_encoding=chunk_key_encoding, + fill_value=metadata_v2.fill_value, + codecs=codecs, + attributes=metadata_v2.attributes, + dimension_names=None, + storage_transformers=None, + ) + + +def _convert_filters(filters: tuple[numcodecs.abc.Codec, ...]) -> list[ArrayArrayCodec]: + filters_codecs = [_find_numcodecs_zarr3(filter) for filter in filters] + for codec in filters_codecs: + if not isinstance(codec, ArrayArrayCodec): + raise TypeError(f"Filter {type(codec)} is not an ArrayArrayCodec") + + return cast(list[ArrayArrayCodec], filters_codecs) + + +def _convert_compressor( + compressor: numcodecs.abc.Codec, dtype: ZDType[TBaseDType, TBaseScalar] +) -> BytesBytesCodec: + match compressor.codec_id: + case "blosc": + return BloscCodec( + typesize=dtype.to_native_dtype().itemsize, + cname=compressor.cname, + clevel=compressor.clevel, + shuffle=BloscShuffle.from_int(compressor.shuffle), + blocksize=compressor.blocksize, + ) + + case "zstd": + return ZstdCodec( + level=compressor.level, + checksum=compressor.checksum, + ) + + case "gzip": + return GzipCodec(level=compressor.level) + + case _: + # If possible, find matching zarr.codecs.numcodecs codec + compressor_codec = _find_numcodecs_zarr3(compressor) + + if not isinstance(compressor_codec, BytesBytesCodec): + raise TypeError(f"Compressor {type(compressor_codec)} is not a BytesBytesCodec") + + return compressor_codec + + +def _find_numcodecs_zarr3(numcodecs_codec: numcodecs.abc.Codec) -> Codec: + """Find matching zarr.codecs.numcodecs codec (if it exists)""" + + numcodec_name = f"numcodecs.{numcodecs_codec.codec_id}" + numcodec_dict = { + "name": numcodec_name, + "configuration": numcodecs_codec.get_config(), + } + + try: + codec_v3 = get_codec_class(numcodec_name) + except KeyError as exc: + raise ValueError( + f"Couldn't find corresponding zarr.codecs.numcodecs codec for {numcodecs_codec.codec_id}" + ) from exc + + return codec_v3.from_dict(numcodec_dict) + + +async def _save_v3_metadata( + metadata_v3: ArrayV3Metadata | GroupMetadata, output_path: StorePath, dry_run: bool = False +) -> None: + zarr_json_path = output_path / ZARR_JSON + if await zarr_json_path.exists(): + raise ValueError(f"{ZARR_JSON} already exists at {zarr_json_path}") + + _logger.info("Saving metadata to %s", zarr_json_path) + to_save = metadata_v3.to_buffer_dict(default_buffer_prototype()) + + if not dry_run: + await zarr_json_path.set_if_not_exists(to_save[ZARR_JSON]) diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 5df2c11c5c..6febb08281 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -262,45 +262,30 @@ def __eq__(self, other: object) -> bool: StoreLike: TypeAlias = Store | StorePath | FSMap | Path | str | dict[str, Buffer] -async def make_store_path( +async def make_store( store_like: StoreLike | None, *, - path: str | None = "", mode: AccessModeLiteral | None = None, storage_options: dict[str, Any] | None = None, -) -> StorePath: +) -> Store: """ - Convert a `StoreLike` object into a StorePath object. - - This function takes a `StoreLike` object and returns a `StorePath` object. The - `StoreLike` object can be a `Store`, `StorePath`, `Path`, `str`, or `dict[str, Buffer]`. - If the `StoreLike` object is a Store or `StorePath`, it is converted to a - `StorePath` object. If the `StoreLike` object is a Path or str, it is converted - to a LocalStore object and then to a `StorePath` object. If the `StoreLike` - object is a dict[str, Buffer], it is converted to a `MemoryStore` object and - then to a `StorePath` object. + Convert a `StoreLike` object into a Store object. - If the `StoreLike` object is None, a `MemoryStore` object is created and - converted to a `StorePath` object. + `StoreLike` objects are converted to `Store` as follows: - If the `StoreLike` object is a str and starts with a protocol, it is - converted to a RemoteStore object and then to a `StorePath` object. - - If the `StoreLike` object is a dict[str, Buffer] and the mode is not None, - the `MemoryStore` object is created with the given mode. - - If the `StoreLike` object is a str and starts with a protocol, the - RemoteStore object is created with the given mode and storage options. + - `Store` or `StorePath` = `Store` object. + - `Path` or `str` = `LocalStore` object. + - `str` that starts with a protocol = `FsspecStore` object. + - `dict[str, Buffer]` = `MemoryStore` object. + - `None` = `MemoryStore` object. + - `FSMap` = `FsspecStore` object. Parameters ---------- - store_like : StoreLike or None, default=None - The object to convert to a `StorePath` object. - path : str | None, optional - The path to use when creating the `StorePath` object. If None, the - default path is the empty string. + store_like : StoreLike | None + The object to convert to a `Store` object. mode : StoreAccessMode | None, optional - The mode to use when creating the `StorePath` object. If None, the + The mode to use when creating the `Store` object. If None, the default mode is 'r'. storage_options : dict[str, Any] | None, optional The storage options to use when creating the `RemoteStore` object. If @@ -308,18 +293,16 @@ async def make_store_path( Returns ------- - StorePath - The converted StorePath object. + Store + The converted Store object. Raises ------ TypeError - If the StoreLike object is not one of the supported types. + If the StoreLike object is not one of the supported types, or if storage_options is provided but not used. """ from zarr.storage._fsspec import FsspecStore # circular import - path_normalized = normalize_path(path) - if ( not (isinstance(store_like, str) and _is_fsspec_uri(store_like)) and storage_options is not None @@ -333,50 +316,107 @@ async def make_store_path( _read_only = mode == "r" if isinstance(store_like, StorePath): - # Already a StorePath - return store_like / path_normalized + # Get underlying store + return store_like.store elif isinstance(store_like, Store): # Already a Store - store = store_like + return store_like elif isinstance(store_like, dict): # Already a dictionary that can be a MemoryStore # # We deliberate only consider dict[str, Buffer] here, and not arbitrary mutable mappings. # By only allowing dictionaries, which are in-memory, we know that MemoryStore appropriate. - store = await MemoryStore.open(store_dict=store_like, read_only=_read_only) + return await MemoryStore.open(store_dict=store_like, read_only=_read_only) elif store_like is None: # Create a new in-memory store - return await make_store_path({}, path=path, mode=mode, storage_options=storage_options) + return await make_store({}, mode=mode, storage_options=storage_options) elif isinstance(store_like, Path): # Create a new LocalStore - store = await LocalStore.open(root=store_like, mode=mode, read_only=_read_only) + return await LocalStore.open(root=store_like, mode=mode, read_only=_read_only) elif isinstance(store_like, str): # Either a FSSpec URI or a local filesystem path if _is_fsspec_uri(store_like): - store = FsspecStore.from_url( + return FsspecStore.from_url( store_like, storage_options=storage_options, read_only=_read_only ) else: # Assume a filesystem path - return await make_store_path( - Path(store_like), path=path, mode=mode, storage_options=storage_options - ) + return await make_store(Path(store_like), mode=mode, storage_options=storage_options) elif _has_fsspec and isinstance(store_like, FSMap): - if path: - raise ValueError( - "'path' was provided but is not used for FSMap store_like objects. Specify the path when creating the FSMap instance instead." - ) - store = FsspecStore.from_mapper(store_like, read_only=_read_only) + return FsspecStore.from_mapper(store_like, read_only=_read_only) + else: raise TypeError(f"Unsupported type for store_like: '{type(store_like).__name__}'") - return await StorePath.open(store, path=path_normalized, mode=mode) + +async def make_store_path( + store_like: StoreLike | None, + *, + path: str | None = "", + mode: AccessModeLiteral | None = None, + storage_options: dict[str, Any] | None = None, +) -> StorePath: + """ + Convert a `StoreLike` object into a StorePath object. + + This function takes a `StoreLike` object and returns a `StorePath` object. See `make_store` for details + of which `Store` is used for each type of `store_like` object. + + Parameters + ---------- + store_like : StoreLike or None, default=None + The object to convert to a `StorePath` object. + path : str | None, optional + The path to use when creating the `StorePath` object. If None, the + default path is the empty string. + mode : StoreAccessMode | None, optional + The mode to use when creating the `StorePath` object. If None, the + default mode is 'r'. + storage_options : dict[str, Any] | None, optional + The storage options to use when creating the `RemoteStore` object. If + None, the default storage options are used. + + Returns + ------- + StorePath + The converted StorePath object. + + Raises + ------ + TypeError + If the StoreLike object is not one of the supported types, or if storage_options is provided but not used. + ValueError + If path is provided for a store that does not support it. + + See Also + -------- + make_store + """ + path_normalized = normalize_path(path) + + if isinstance(store_like, StorePath): + # Already a StorePath + if storage_options: + raise TypeError( + "'storage_options' was provided but unused. " + "'storage_options' is only used when the store is passed as a FSSpec URI string.", + ) + return store_like / path_normalized + + elif _has_fsspec and isinstance(store_like, FSMap) and path: + raise ValueError( + "'path' was provided but is not used for FSMap store_like objects. Specify the path when creating the FSMap instance instead." + ) + + else: + store = await make_store(store_like, mode=mode, storage_options=storage_options) + return await StorePath.open(store, path=path_normalized, mode=mode) def _is_fsspec_uri(uri: str) -> bool: diff --git a/tests/conftest.py b/tests/conftest.py index 839be34e01..91975408aa 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -3,6 +3,7 @@ import math import os import pathlib +import sys from collections.abc import Mapping, Sequence from dataclasses import dataclass, field from typing import TYPE_CHECKING @@ -12,6 +13,7 @@ import pytest from hypothesis import HealthCheck, Verbosity, settings +import zarr.registry from zarr import AsyncGroup, config from zarr.abc.store import Store from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation @@ -186,6 +188,27 @@ def zarr_format(request: pytest.FixtureRequest) -> ZarrFormat: raise ValueError(msg) +def _clear_registries() -> None: + registries = zarr.registry._collect_entrypoints() + for registry in registries: + registry.lazy_load_list.clear() + + +@pytest.fixture +def set_path() -> Generator[None, None, None]: + tests_dir = str(pathlib.Path(__file__).parent.absolute()) + sys.path.append(tests_dir) + _clear_registries() + zarr.registry._collect_entrypoints() + + yield + + sys.path.remove(tests_dir) + _clear_registries() + zarr.registry._collect_entrypoints() + config.reset() + + def pytest_addoption(parser: Any) -> None: parser.addoption( "--run-slow-hypothesis", diff --git a/tests/test_cli/conftest.py b/tests/test_cli/conftest.py new file mode 100644 index 0000000000..4f95f47b5e --- /dev/null +++ b/tests/test_cli/conftest.py @@ -0,0 +1,146 @@ +from pathlib import Path +from typing import Any, Literal + +import pytest + +import zarr +from zarr.abc.store import Store +from zarr.core.common import ZarrFormat + + +def create_nested_zarr( + store: Store, + attributes: dict[str, Any] | None = None, + separator: Literal[".", "/"] = ".", + zarr_format: ZarrFormat = 2, +) -> list[str]: + """Create a zarr with nested groups / arrays for testing, returning the paths to all.""" + + if attributes is None: + attributes = {"baz": 42, "qux": [1, 4, 7, 12]} + + # 3 levels of nested groups + group_0 = zarr.create_group(store=store, zarr_format=zarr_format, attributes=attributes) + group_1 = group_0.create_group(name="group_1", attributes=attributes) + group_2 = group_1.create_group(name="group_2", attributes=attributes) + paths = [group_0.path, group_1.path, group_2.path] + + # 1 array per group + for i, group in enumerate([group_0, group_1, group_2]): + array = group.create_array( + name=f"array_{i}", + shape=(10, 10), + chunks=(5, 5), + dtype="uint16", + attributes=attributes, + chunk_key_encoding={"name": "v2", "separator": separator}, + ) + array[:] = 1 + paths.append(array.path) + + return paths + + +@pytest.fixture +def expected_paths() -> list[Path]: + """Expected paths for create_nested_zarr, with no metadata files or chunks""" + return [ + Path("array_0"), + Path("group_1"), + Path("group_1/array_1"), + Path("group_1/group_2"), + Path("group_1/group_2/array_2"), + ] + + +@pytest.fixture +def expected_chunks() -> list[Path]: + """Expected chunks for create_nested_zarr""" + return [ + Path("array_0/0.0"), + Path("array_0/0.1"), + Path("array_0/1.0"), + Path("array_0/1.1"), + Path("group_1/array_1/0.0"), + Path("group_1/array_1/0.1"), + Path("group_1/array_1/1.0"), + Path("group_1/array_1/1.1"), + Path("group_1/group_2/array_2/0.0"), + Path("group_1/group_2/array_2/0.1"), + Path("group_1/group_2/array_2/1.0"), + Path("group_1/group_2/array_2/1.1"), + ] + + +@pytest.fixture +def expected_v3_metadata() -> list[Path]: + """Expected v3 metadata for create_nested_zarr""" + return sorted( + [ + Path("zarr.json"), + Path("array_0/zarr.json"), + Path("group_1/zarr.json"), + Path("group_1/array_1/zarr.json"), + Path("group_1/group_2/zarr.json"), + Path("group_1/group_2/array_2/zarr.json"), + ] + ) + + +@pytest.fixture +def expected_v2_metadata() -> list[Path]: + """Expected v2 metadata for create_nested_zarr""" + return sorted( + [ + Path(".zgroup"), + Path(".zattrs"), + Path("array_0/.zarray"), + Path("array_0/.zattrs"), + Path("group_1/.zgroup"), + Path("group_1/.zattrs"), + Path("group_1/array_1/.zarray"), + Path("group_1/array_1/.zattrs"), + Path("group_1/group_2/.zgroup"), + Path("group_1/group_2/.zattrs"), + Path("group_1/group_2/array_2/.zarray"), + Path("group_1/group_2/array_2/.zattrs"), + ] + ) + + +@pytest.fixture +def expected_paths_no_metadata( + expected_paths: list[Path], expected_chunks: list[Path] +) -> list[Path]: + return sorted(expected_paths + expected_chunks) + + +@pytest.fixture +def expected_paths_v3_metadata( + expected_paths: list[Path], expected_chunks: list[Path], expected_v3_metadata: list[Path] +) -> list[Path]: + return sorted(expected_paths + expected_chunks + expected_v3_metadata) + + +@pytest.fixture +def expected_paths_v3_metadata_no_chunks( + expected_paths: list[Path], expected_v3_metadata: list[Path] +) -> list[Path]: + return sorted(expected_paths + expected_v3_metadata) + + +@pytest.fixture +def expected_paths_v2_metadata( + expected_paths: list[Path], expected_chunks: list[Path], expected_v2_metadata: list[Path] +) -> list[Path]: + return sorted(expected_paths + expected_chunks + expected_v2_metadata) + + +@pytest.fixture +def expected_paths_v2_v3_metadata( + expected_paths: list[Path], + expected_chunks: list[Path], + expected_v2_metadata: list[Path], + expected_v3_metadata: list[Path], +) -> list[Path]: + return sorted(expected_paths + expected_chunks + expected_v2_metadata + expected_v3_metadata) diff --git a/tests/test_cli/test_migrate_v3.py b/tests/test_cli/test_migrate_v3.py new file mode 100644 index 0000000000..b96c98019b --- /dev/null +++ b/tests/test_cli/test_migrate_v3.py @@ -0,0 +1,666 @@ +import lzma +from pathlib import Path +from typing import Literal, cast + +import numcodecs +import numcodecs.abc +import numpy as np +import pytest + +import zarr +from tests.test_cli.conftest import create_nested_zarr +from zarr.abc.codec import Codec +from zarr.codecs.blosc import BloscCodec +from zarr.codecs.bytes import BytesCodec +from zarr.codecs.gzip import GzipCodec +from zarr.codecs.numcodecs import LZMA, Delta +from zarr.codecs.transpose import TransposeCodec +from zarr.codecs.zstd import ZstdCodec +from zarr.core.array import Array +from zarr.core.chunk_grids import RegularChunkGrid +from zarr.core.chunk_key_encodings import V2ChunkKeyEncoding +from zarr.core.common import JSON, ZarrFormat +from zarr.core.dtype.npy.int import UInt8, UInt16 +from zarr.core.group import Group, GroupMetadata +from zarr.core.metadata.v3 import ArrayV3Metadata +from zarr.storage._local import LocalStore + +typer_testing = pytest.importorskip( + "typer.testing", reason="optional cli dependencies aren't installed" +) +cli = pytest.importorskip("zarr._cli.cli", reason="optional cli dependencies aren't installed") + +runner = typer_testing.CliRunner() + +NUMCODECS_USER_WARNING = "Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations." + + +def test_migrate_array(local_store: LocalStore) -> None: + shape = (10, 10) + chunks = (10, 10) + dtype = "uint16" + compressors = numcodecs.Blosc(cname="zstd", clevel=3, shuffle=1) + fill_value = 2 + attributes = cast(dict[str, JSON], {"baz": 42, "qux": [1, 4, 7, 12]}) + + zarr.create_array( + store=local_store, + shape=shape, + chunks=chunks, + dtype=dtype, + compressors=compressors, + zarr_format=2, + fill_value=fill_value, + attributes=attributes, + ) + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + assert (local_store.root / "zarr.json").exists() + + zarr_array = zarr.open(local_store.root, zarr_format=3) + + expected_metadata = ArrayV3Metadata( + shape=shape, + data_type=UInt16(endianness="little"), + chunk_grid=RegularChunkGrid(chunk_shape=chunks), + chunk_key_encoding=V2ChunkKeyEncoding(separator="."), + fill_value=fill_value, + codecs=( + BytesCodec(endian="little"), + BloscCodec(typesize=2, cname="zstd", clevel=3, shuffle="shuffle", blocksize=0), + ), + attributes=attributes, + dimension_names=None, + storage_transformers=None, + ) + assert zarr_array.metadata == expected_metadata + + +def test_migrate_group(local_store: LocalStore) -> None: + attributes = {"baz": 42, "qux": [1, 4, 7, 12]} + zarr.create_group(store=local_store, zarr_format=2, attributes=attributes) + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + assert (local_store.root / "zarr.json").exists() + + zarr_array = zarr.open(local_store.root, zarr_format=3) + expected_metadata = GroupMetadata( + attributes=attributes, zarr_format=3, consolidated_metadata=None + ) + assert zarr_array.metadata == expected_metadata + + +@pytest.mark.parametrize("separator", [".", "/"]) +def test_migrate_nested_groups_and_arrays_in_place( + local_store: LocalStore, separator: str, expected_v3_metadata: list[Path] +) -> None: + """Test that zarr.json are made at the correct points in a hierarchy of groups and arrays + (including when there are additional dirs due to using a / separator)""" + + attributes = {"baz": 42, "qux": [1, 4, 7, 12]} + paths = create_nested_zarr(local_store, attributes=attributes, separator=separator) + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + + zarr_json_paths = sorted(local_store.root.rglob("zarr.json")) + expected_zarr_json_paths = [local_store.root / p for p in expected_v3_metadata] + assert zarr_json_paths == expected_zarr_json_paths + + # Check converted zarr can be opened + metadata accessed at all levels + zarr_array = zarr.open(local_store.root, zarr_format=3) + for path in paths: + zarr_v3 = cast(Array | Group, zarr_array[path]) + metadata = zarr_v3.metadata + assert metadata.zarr_format == 3 + assert metadata.attributes == attributes + + +@pytest.mark.parametrize("separator", [".", "/"]) +async def test_migrate_nested_groups_and_arrays_separate_location( + tmp_path: Path, + separator: str, + expected_v2_metadata: list[Path], + expected_v3_metadata: list[Path], +) -> None: + """Test that zarr.json are made at the correct paths, when saving to a separate output location.""" + + input_zarr_path = tmp_path / "input.zarr" + output_zarr_path = tmp_path / "output.zarr" + + local_store = await LocalStore.open(str(input_zarr_path)) + create_nested_zarr(local_store, separator=separator) + + result = runner.invoke(cli.app, ["migrate", "v3", str(input_zarr_path), str(output_zarr_path)]) + assert result.exit_code == 0 + + # Files in input zarr should be unchanged i.e. still v2 only + zarr_json_paths = sorted(input_zarr_path.rglob("zarr.json")) + assert len(zarr_json_paths) == 0 + + paths = [ + path + for path in input_zarr_path.rglob("*") + if path.stem in [".zarray", ".zgroup", ".zattrs"] + ] + expected_paths = [input_zarr_path / p for p in expected_v2_metadata] + assert sorted(paths) == expected_paths + + # Files in output zarr should only contain v3 metadata + zarr_json_paths = sorted(output_zarr_path.rglob("zarr.json")) + expected_zarr_json_paths = [output_zarr_path / p for p in expected_v3_metadata] + assert zarr_json_paths == expected_zarr_json_paths + + +def test_remove_v2_metadata_option_in_place( + local_store: LocalStore, expected_paths_v3_metadata: list[Path] +) -> None: + create_nested_zarr(local_store) + + # convert v2 metadata to v3, then remove v2 metadata + result = runner.invoke( + cli.app, ["migrate", "v3", str(local_store.root), "--remove-v2-metadata"] + ) + assert result.exit_code == 0 + + paths = sorted(local_store.root.rglob("*")) + expected_paths = [local_store.root / p for p in expected_paths_v3_metadata] + assert paths == expected_paths + + +async def test_remove_v2_metadata_option_separate_location( + tmp_path: Path, + expected_paths_v2_metadata: list[Path], + expected_paths_v3_metadata_no_chunks: list[Path], +) -> None: + """Check that when using --remove-v2-metadata with a separate output location, no v2 metadata is removed from + the input location.""" + + input_zarr_path = tmp_path / "input.zarr" + output_zarr_path = tmp_path / "output.zarr" + + local_store = await LocalStore.open(str(input_zarr_path)) + create_nested_zarr(local_store) + + result = runner.invoke( + cli.app, + ["migrate", "v3", str(input_zarr_path), str(output_zarr_path), "--remove-v2-metadata"], + ) + assert result.exit_code == 0 + + # input image should be unchanged + paths = sorted(input_zarr_path.rglob("*")) + expected_paths = [input_zarr_path / p for p in expected_paths_v2_metadata] + assert paths == expected_paths + + # output image should be only v3 metadata + paths = sorted(output_zarr_path.rglob("*")) + expected_paths = [output_zarr_path / p for p in expected_paths_v3_metadata_no_chunks] + assert paths == expected_paths + + +def test_overwrite_option_in_place( + local_store: LocalStore, expected_paths_v2_v3_metadata: list[Path] +) -> None: + create_nested_zarr(local_store) + + # add v3 metadata in place + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + + # check that v3 metadata can be overwritten with --overwrite + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root), "--overwrite"]) + assert result.exit_code == 0 + + paths = sorted(local_store.root.rglob("*")) + expected_paths = [local_store.root / p for p in expected_paths_v2_v3_metadata] + assert paths == expected_paths + + +async def test_overwrite_option_separate_location( + tmp_path: Path, + expected_paths_v2_metadata: list[Path], + expected_paths_v3_metadata_no_chunks: list[Path], +) -> None: + input_zarr_path = tmp_path / "input.zarr" + output_zarr_path = tmp_path / "output.zarr" + + local_store = await LocalStore.open(str(input_zarr_path)) + create_nested_zarr(local_store) + + # create v3 metadata at output_zarr_path + result = runner.invoke( + cli.app, + ["migrate", "v3", str(input_zarr_path), str(output_zarr_path)], + ) + assert result.exit_code == 0 + + # re-run with --overwrite option + result = runner.invoke( + cli.app, + ["migrate", "v3", str(input_zarr_path), str(output_zarr_path), "--overwrite", "--force"], + ) + assert result.exit_code == 0 + + # original image should be un-changed + paths = sorted(input_zarr_path.rglob("*")) + expected_paths = [input_zarr_path / p for p in expected_paths_v2_metadata] + assert paths == expected_paths + + # output image is only v3 metadata + paths = sorted(output_zarr_path.rglob("*")) + expected_paths = [output_zarr_path / p for p in expected_paths_v3_metadata_no_chunks] + assert paths == expected_paths + + +@pytest.mark.parametrize("separator", [".", "/"]) +def test_migrate_sub_group( + local_store: LocalStore, separator: str, expected_v3_metadata: list[Path] +) -> None: + """Test that only arrays/groups within group_1 are converted (+ no other files in store)""" + + create_nested_zarr(local_store, separator=separator) + group_path = local_store.root / "group_1" + + result = runner.invoke(cli.app, ["migrate", "v3", str(group_path)]) + assert result.exit_code == 0 + + zarr_json_paths = sorted(local_store.root.rglob("zarr.json")) + expected_zarr_json_paths = [ + local_store.root / p + for p in expected_v3_metadata + if group_path in (local_store.root / p).parents + ] + assert zarr_json_paths == expected_zarr_json_paths + + +@pytest.mark.parametrize( + ("compressor_v2", "compressor_v3"), + [ + ( + numcodecs.Blosc(cname="zstd", clevel=3, shuffle=1), + BloscCodec(typesize=2, cname="zstd", clevel=3, shuffle="shuffle", blocksize=0), + ), + (numcodecs.Zstd(level=3), ZstdCodec(level=3)), + (numcodecs.GZip(level=3), GzipCodec(level=3)), + ], + ids=["blosc", "zstd", "gzip"], +) +def test_migrate_compressor( + local_store: LocalStore, compressor_v2: numcodecs.abc.Codec, compressor_v3: Codec +) -> None: + zarr_array = zarr.create_array( + store=local_store, + shape=(10, 10), + chunks=(10, 10), + dtype="uint16", + compressors=compressor_v2, + zarr_format=2, + fill_value=0, + ) + zarr_array[:] = 1 + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + assert (local_store.root / "zarr.json").exists() + + zarr_array = zarr.open_array(local_store.root, zarr_format=3) + metadata = zarr_array.metadata + assert metadata.zarr_format == 3 + assert metadata.codecs == ( + BytesCodec(endian="little"), + compressor_v3, + ) + assert np.all(zarr_array[:] == 1) + + +@pytest.mark.filterwarnings(f"ignore:{NUMCODECS_USER_WARNING}:UserWarning") +def test_migrate_numcodecs_compressor(local_store: LocalStore) -> None: + """Test migration of a numcodecs compressor without a zarr.codecs equivalent.""" + + lzma_settings = { + "format": lzma.FORMAT_RAW, + "check": -1, + "preset": None, + "filters": [ + {"id": lzma.FILTER_DELTA, "dist": 4}, + {"id": lzma.FILTER_LZMA2, "preset": 1}, + ], + } + + zarr_array = zarr.create_array( + store=local_store, + shape=(10, 10), + chunks=(10, 10), + dtype="uint16", + compressors=numcodecs.LZMA.from_config(lzma_settings), + zarr_format=2, + fill_value=0, + ) + zarr_array[:] = 1 + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + assert (local_store.root / "zarr.json").exists() + + zarr_array = zarr.open_array(local_store.root, zarr_format=3) + metadata = zarr_array.metadata + assert metadata.zarr_format == 3 + assert metadata.codecs == ( + BytesCodec(endian="little"), + LZMA( + format=lzma_settings["format"], + check=lzma_settings["check"], + preset=lzma_settings["preset"], + filters=lzma_settings["filters"], + ), + ) + assert np.all(zarr_array[:] == 1) + + +@pytest.mark.filterwarnings(f"ignore:{NUMCODECS_USER_WARNING}:UserWarning") +def test_migrate_filter(local_store: LocalStore) -> None: + filter_v2 = numcodecs.Delta(dtype=" None: + zarr_array = zarr.create_array( + store=local_store, + shape=(10, 10), + chunks=(10, 10), + dtype="uint16", + compressors=None, + zarr_format=2, + fill_value=0, + order=order, + ) + zarr_array[:] = 1 + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + assert (local_store.root / "zarr.json").exists() + + zarr_array = zarr.open_array(local_store.root, zarr_format=3) + metadata = zarr_array.metadata + assert metadata.zarr_format == 3 + assert metadata.codecs == expected_codecs + assert np.all(zarr_array[:] == 1) + + +@pytest.mark.parametrize( + ("dtype", "expected_data_type", "expected_codecs"), + [ + ("uint8", UInt8(), (BytesCodec(endian=None),)), + ("uint16", UInt16(), (BytesCodec(endian="little"),)), + ], + ids=["single_byte", "multi_byte"], +) +def test_migrate_endian( + local_store: LocalStore, + dtype: str, + expected_data_type: UInt8 | UInt16, + expected_codecs: tuple[Codec], +) -> None: + zarr_array = zarr.create_array( + store=local_store, + shape=(10, 10), + chunks=(10, 10), + dtype=dtype, + compressors=None, + zarr_format=2, + fill_value=0, + ) + zarr_array[:] = 1 + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + assert (local_store.root / "zarr.json").exists() + + zarr_array = zarr.open_array(local_store.root, zarr_format=3) + metadata = zarr_array.metadata + assert metadata.zarr_format == 3 + assert metadata.data_type == expected_data_type + assert metadata.codecs == expected_codecs + assert np.all(zarr_array[:] == 1) + + +@pytest.mark.parametrize("node_type", ["array", "group"]) +def test_migrate_v3(local_store: LocalStore, node_type: str) -> None: + """Attempting to convert a v3 array/group should always fail""" + + if node_type == "array": + zarr.create_array( + store=local_store, shape=(10, 10), chunks=(10, 10), zarr_format=3, dtype="uint16" + ) + else: + zarr.create_group(store=local_store, zarr_format=3) + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 1 + assert isinstance(result.exception, TypeError) + assert str(result.exception) == "Only arrays / groups with zarr v2 metadata can be converted" + + +def test_migrate_consolidated_metadata(local_store: LocalStore) -> None: + """Attempting to convert a group with consolidated metadata should always fail""" + + group = zarr.create_group(store=local_store, zarr_format=2) + group.create_array(shape=(1,), name="a", dtype="uint8") + zarr.consolidate_metadata(local_store) + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 1 + assert isinstance(result.exception, NotImplementedError) + assert str(result.exception) == "Migration of consolidated metadata isn't supported." + + +def test_migrate_unknown_codec(local_store: LocalStore) -> None: + """Attempting to convert a codec without a v3 equivalent should always fail""" + + zarr.create_array( + store=local_store, + shape=(10, 10), + chunks=(10, 10), + dtype="uint16", + filters=[numcodecs.Categorize(labels=["a", "b"], dtype=object)], + zarr_format=2, + fill_value=0, + ) + + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 1 + assert isinstance(result.exception, ValueError) + assert ( + str(result.exception) + == "Couldn't find corresponding zarr.codecs.numcodecs codec for categorize" + ) + + +def test_migrate_incorrect_filter(local_store: LocalStore) -> None: + """Attempting to convert a filter (which is the wrong type of codec) should always fail""" + + zarr.create_array( + store=local_store, + shape=(10, 10), + chunks=(10, 10), + dtype="uint16", + filters=[numcodecs.Zstd(level=3)], + zarr_format=2, + fill_value=0, + ) + + with pytest.warns(UserWarning, match=NUMCODECS_USER_WARNING): + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + + assert result.exit_code == 1 + assert isinstance(result.exception, TypeError) + assert ( + str(result.exception) + == "Filter is not an ArrayArrayCodec" + ) + + +def test_migrate_incorrect_compressor(local_store: LocalStore) -> None: + """Attempting to convert a compressor (which is the wrong type of codec) should always fail""" + + zarr.create_array( + store=local_store, + shape=(10, 10), + chunks=(10, 10), + dtype="uint16", + compressors=numcodecs.Delta(dtype=" is not a BytesBytesCodec" + ) + + +@pytest.mark.parametrize("zarr_format", [2, 3]) +def test_remove_metadata_fails_without_force( + local_store: LocalStore, zarr_format: ZarrFormat +) -> None: + """Test removing metadata (when no alternate metadata is present) fails without --force.""" + + create_nested_zarr(local_store, zarr_format=zarr_format) + + result = runner.invoke(cli.app, ["remove-metadata", f"v{zarr_format}", str(local_store.root)]) + assert result.exit_code == 1 + assert isinstance(result.exception, ValueError) + assert str(result.exception).startswith(f"Cannot remove v{zarr_format} metadata at file") + + +@pytest.mark.parametrize("zarr_format", [2, 3]) +def test_remove_metadata_succeeds_with_force( + local_store: LocalStore, zarr_format: ZarrFormat, expected_paths_no_metadata: list[Path] +) -> None: + """Test removing metadata (when no alternate metadata is present) succeeds with --force.""" + + create_nested_zarr(local_store, zarr_format=zarr_format) + + result = runner.invoke( + cli.app, ["remove-metadata", f"v{zarr_format}", str(local_store.root), "--force"] + ) + assert result.exit_code == 0 + + paths = sorted(local_store.root.rglob("*")) + expected_paths = [local_store.root / p for p in expected_paths_no_metadata] + assert paths == expected_paths + + +def test_remove_metadata_sub_group( + local_store: LocalStore, expected_paths_no_metadata: list[Path] +) -> None: + """Test only v2 metadata within group_1 is removed and rest remains un-changed.""" + + create_nested_zarr(local_store) + + result = runner.invoke( + cli.app, ["remove-metadata", "v2", str(local_store.root / "group_1"), "--force"] + ) + assert result.exit_code == 0 + + # check all metadata files inside group_1 are removed (.zattrs / .zgroup / .zarray should remain only inside the top + # group) + paths = sorted(local_store.root.rglob("*")) + + expected_paths = [local_store.root / p for p in expected_paths_no_metadata] + expected_paths.append(local_store.root / ".zattrs") + expected_paths.append(local_store.root / ".zgroup") + expected_paths.append(local_store.root / "array_0" / ".zarray") + expected_paths.append(local_store.root / "array_0" / ".zattrs") + assert paths == sorted(expected_paths) + + +@pytest.mark.parametrize( + ("zarr_format", "expected_output_paths"), + [("v2", "expected_paths_v3_metadata"), ("v3", "expected_paths_v2_metadata")], +) +def test_remove_metadata_after_conversion( + local_store: LocalStore, + request: pytest.FixtureRequest, + zarr_format: str, + expected_output_paths: str, +) -> None: + """Test all v2/v3 metadata can be removed after metadata conversion (all groups / arrays / + metadata of other versions should remain as-is)""" + + create_nested_zarr(local_store) + + # convert v2 metadata to v3 (so now both v2 and v3 metadata present!), then remove either the v2 or v3 metadata + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + assert result.exit_code == 0 + result = runner.invoke(cli.app, ["remove-metadata", zarr_format, str(local_store.root)]) + assert result.exit_code == 0 + + paths = sorted(local_store.root.rglob("*")) + expected_paths = request.getfixturevalue(expected_output_paths) + expected_paths = [local_store.root / p for p in expected_paths] + assert paths == expected_paths + + +@pytest.mark.parametrize("cli_command", ["migrate", "remove-metadata"]) +def test_dry_run( + local_store: LocalStore, cli_command: str, expected_paths_v2_metadata: list[Path] +) -> None: + """Test that all files are un-changed after a dry run""" + + create_nested_zarr(local_store) + + if cli_command == "migrate": + result = runner.invoke( + cli.app, ["migrate", "v3", str(local_store.root), "--overwrite", "--force", "--dry-run"] + ) + else: + result = runner.invoke( + cli.app, ["remove-metadata", "v2", str(local_store.root), "--force", "--dry-run"] + ) + + assert result.exit_code == 0 + + paths = sorted(local_store.root.rglob("*")) + expected_paths = [local_store.root / p for p in expected_paths_v2_metadata] + assert paths == expected_paths diff --git a/tests/test_codec_entrypoints.py b/tests/test_codec_entrypoints.py index e1ef027dd4..fc7b79fe54 100644 --- a/tests/test_codec_entrypoints.py +++ b/tests/test_codec_entrypoints.py @@ -1,26 +1,8 @@ -import os.path -import sys -from collections.abc import Generator - import pytest import zarr.registry from zarr import config -here = os.path.abspath(os.path.dirname(__file__)) - - -@pytest.fixture -def set_path() -> Generator[None, None, None]: - sys.path.append(here) - zarr.registry._collect_entrypoints() - yield - sys.path.remove(here) - registries = zarr.registry._collect_entrypoints() - for registry in registries: - registry.lazy_load_list.clear() - config.reset() - @pytest.mark.usefixtures("set_path") @pytest.mark.parametrize("codec_name", ["TestEntrypointCodec", "TestEntrypointGroup.Codec"]) diff --git a/tests/test_dtype_registry.py b/tests/test_dtype_registry.py index aedda5272c..58b14fe07a 100644 --- a/tests/test_dtype_registry.py +++ b/tests/test_dtype_registry.py @@ -1,16 +1,12 @@ from __future__ import annotations import re -import sys -from pathlib import Path from typing import TYPE_CHECKING, Any, Literal, get_args import numpy as np import pytest -import zarr from tests.conftest import skip_object_dtype -from zarr.core.config import config from zarr.core.dtype import ( AnyDType, DataTypeRegistry, @@ -29,8 +25,6 @@ ) if TYPE_CHECKING: - from collections.abc import Generator - from zarr.core.common import ZarrFormat from .test_dtype.conftest import zdtype_examples @@ -147,22 +141,6 @@ def test_match_dtype_unique( data_type_registry_fixture.match_json(instance_dict, zarr_format=zarr_format) -# this is copied from the registry tests -- we should deduplicate -here = str(Path(__file__).parent.absolute()) - - -@pytest.fixture -def set_path() -> Generator[None, None, None]: - sys.path.append(here) - zarr.registry._collect_entrypoints() - yield - sys.path.remove(here) - registries = zarr.registry._collect_entrypoints() - for registry in registries: - registry.lazy_load_list.clear() - config.reset() - - @pytest.mark.usefixtures("set_path") def test_entrypoint_dtype(zarr_format: ZarrFormat) -> None: from package_with_entrypoint import TestDataType From 680533265f46dac06dc3f19ad23c70732f9da99a Mon Sep 17 00:00:00 2001 From: Remco Leijenaar <55834815+RFLeijenaar@users.noreply.github.com> Date: Wed, 17 Sep 2025 23:02:55 +0200 Subject: [PATCH 109/468] Add registry for chunk key encodings for extensibility (#3436) * Add registry for chunk key encodings. * Fix error message for unknown chunk key encoding in create_array test * Removed unneccsary type ignore * Use entrypoint.name as the key for registering chunk key encodings. - Change register_chunk_key_encoding function to take key as first arg similar to codec. * Move parsing of init args in CKE to __post_init__. This enables users to add additional fields to a custom ChunkKeyEncoding without having to override __init__ and taking care of immutability of the attrs. * Clarify ChunkKeyEncoding base class - Enforce encode_chunk_key to be implemented (abstractmethod in ABC) - Make decode_chunk_key optional (raise NotImplementedError by default) Note, the latter is never raised by the current zarr implementation. * Make `name` a ClassVar in ChunkKeyEncoding. This automatically removes it as an init argument. * Remove `separator` from ChunkKeyEncoding base. * Fix typing errors. * Update docs output to match code changes. * Add release notes --------- Co-authored-by: Davis Bennett --- changes/3436.feature.rst | 2 + docs/user-guide/consolidated_metadata.rst | 73 ++++++++------- src/zarr/core/array.py | 12 +-- src/zarr/core/chunk_key_encodings.py | 104 +++++++++++++--------- src/zarr/core/metadata/v3.py | 8 +- src/zarr/registry.py | 31 ++++++- tests/conftest.py | 4 +- tests/test_array.py | 4 +- tests/test_codecs/test_codecs.py | 2 +- 9 files changed, 146 insertions(+), 94 deletions(-) create mode 100644 changes/3436.feature.rst diff --git a/changes/3436.feature.rst b/changes/3436.feature.rst new file mode 100644 index 0000000000..85e28bb8b1 --- /dev/null +++ b/changes/3436.feature.rst @@ -0,0 +1,2 @@ +Adds a registry for chunk key encodings for extensibility. +This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. diff --git a/docs/user-guide/consolidated_metadata.rst b/docs/user-guide/consolidated_metadata.rst index 9d05231f4a..ae50c602ca 100644 --- a/docs/user-guide/consolidated_metadata.rst +++ b/docs/user-guide/consolidated_metadata.rst @@ -49,44 +49,41 @@ that can be used.: >>> from pprint import pprint >>> pprint(dict(consolidated_metadata.items())) {'a': ArrayV3Metadata(shape=(1,), - data_type=Float64(endianness='little'), - chunk_grid=RegularChunkGrid(chunk_shape=(1,)), - chunk_key_encoding=DefaultChunkKeyEncoding(name='default', - separator='/'), - fill_value=np.float64(0.0), - codecs=(BytesCodec(endian=), - ZstdCodec(level=0, checksum=False)), - attributes={}, - dimension_names=None, - zarr_format=3, - node_type='array', - storage_transformers=()), - 'b': ArrayV3Metadata(shape=(2, 2), - data_type=Float64(endianness='little'), - chunk_grid=RegularChunkGrid(chunk_shape=(2, 2)), - chunk_key_encoding=DefaultChunkKeyEncoding(name='default', - separator='/'), - fill_value=np.float64(0.0), - codecs=(BytesCodec(endian=), - ZstdCodec(level=0, checksum=False)), - attributes={}, - dimension_names=None, - zarr_format=3, - node_type='array', - storage_transformers=()), - 'c': ArrayV3Metadata(shape=(3, 3, 3), - data_type=Float64(endianness='little'), - chunk_grid=RegularChunkGrid(chunk_shape=(3, 3, 3)), - chunk_key_encoding=DefaultChunkKeyEncoding(name='default', - separator='/'), - fill_value=np.float64(0.0), - codecs=(BytesCodec(endian=), - ZstdCodec(level=0, checksum=False)), - attributes={}, - dimension_names=None, - zarr_format=3, - node_type='array', - storage_transformers=())} + data_type=Float64(endianness='little'), + chunk_grid=RegularChunkGrid(chunk_shape=(1,)), + chunk_key_encoding=DefaultChunkKeyEncoding(separator='/'), + fill_value=np.float64(0.0), + codecs=(BytesCodec(endian=), + ZstdCodec(level=0, checksum=False)), + attributes={}, + dimension_names=None, + zarr_format=3, + node_type='array', + storage_transformers=()), + 'b': ArrayV3Metadata(shape=(2, 2), + data_type=Float64(endianness='little'), + chunk_grid=RegularChunkGrid(chunk_shape=(2, 2)), + chunk_key_encoding=DefaultChunkKeyEncoding(separator='/'), + fill_value=np.float64(0.0), + codecs=(BytesCodec(endian=), + ZstdCodec(level=0, checksum=False)), + attributes={}, + dimension_names=None, + zarr_format=3, + node_type='array', + storage_transformers=()), + 'c': ArrayV3Metadata(shape=(3, 3, 3), + data_type=Float64(endianness='little'), + chunk_grid=RegularChunkGrid(chunk_shape=(3, 3, 3)), + chunk_key_encoding=DefaultChunkKeyEncoding(separator='/'), + fill_value=np.float64(0.0), + codecs=(BytesCodec(endian=), + ZstdCodec(level=0, checksum=False)), + attributes={}, + dimension_names=None, + zarr_format=3, + node_type='array', + storage_transformers=())} Operations on the group to get children automatically use the consolidated metadata.: diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 960b322a25..e5fa451914 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -47,6 +47,7 @@ ChunkKeyEncodingLike, DefaultChunkKeyEncoding, V2ChunkKeyEncoding, + parse_chunk_key_encoding, ) from zarr.core.common import ( JSON, @@ -4602,6 +4603,7 @@ async def init_array( order_parsed = zarr_config.get("array.order") else: order_parsed = order + chunk_key_encoding_parsed = cast("V2ChunkKeyEncoding", chunk_key_encoding_parsed) meta = AsyncArray._create_metadata_v2( shape=shape_parsed, @@ -4951,13 +4953,11 @@ def _parse_chunk_key_encoding( """ if data is None: if zarr_format == 2: - result = ChunkKeyEncoding.from_dict({"name": "v2", "separator": "."}) + data = {"name": "v2", "configuration": {"separator": "."}} else: - result = ChunkKeyEncoding.from_dict({"name": "default", "separator": "/"}) - elif isinstance(data, ChunkKeyEncoding): - result = data - else: - result = ChunkKeyEncoding.from_dict(data) + data = {"name": "default", "configuration": {"separator": "/"}} + result = parse_chunk_key_encoding(data) + if zarr_format == 2 and result.name != "v2": msg = ( "Invalid chunk key encoding. For Zarr format 2 arrays, the `name` field of the " diff --git a/src/zarr/core/chunk_key_encodings.py b/src/zarr/core/chunk_key_encodings.py index 89a34e6052..42d7615c61 100644 --- a/src/zarr/core/chunk_key_encodings.py +++ b/src/zarr/core/chunk_key_encodings.py @@ -1,17 +1,18 @@ from __future__ import annotations -from abc import abstractmethod +from abc import ABC, abstractmethod from dataclasses import dataclass -from typing import TYPE_CHECKING, Literal, TypeAlias, TypedDict, cast +from typing import TYPE_CHECKING, ClassVar, Literal, TypeAlias, TypedDict, cast if TYPE_CHECKING: - from typing import NotRequired + from typing import NotRequired, Self from zarr.abc.metadata import Metadata from zarr.core.common import ( JSON, parse_named_configuration, ) +from zarr.registry import get_chunk_key_encoding_class, register_chunk_key_encoding SeparatorLiteral = Literal[".", "/"] @@ -28,60 +29,49 @@ class ChunkKeyEncodingParams(TypedDict): @dataclass(frozen=True) -class ChunkKeyEncoding(Metadata): - name: str - separator: SeparatorLiteral = "." +class ChunkKeyEncoding(ABC, Metadata): + """ + Defines how chunk coordinates are mapped to store keys. - def __init__(self, *, separator: SeparatorLiteral) -> None: - separator_parsed = parse_separator(separator) + Subclasses must define a class variable `name` and implement `encode_chunk_key`. + """ - object.__setattr__(self, "separator", separator_parsed) + name: ClassVar[str] @classmethod - def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncodingLike) -> ChunkKeyEncoding: - if isinstance(data, ChunkKeyEncoding): - return data - - # handle ChunkKeyEncodingParams - if "name" in data and "separator" in data: - data = {"name": data["name"], "configuration": {"separator": data["separator"]}} - - # TODO: remove this cast when we are statically typing the JSON metadata completely. - data = cast("dict[str, JSON]", data) - - # configuration is optional for chunk key encodings - name_parsed, config_parsed = parse_named_configuration(data, require_configuration=False) - if name_parsed == "default": - if config_parsed is None: - # for default, normalize missing configuration to use the "/" separator. - config_parsed = {"separator": "/"} - return DefaultChunkKeyEncoding(**config_parsed) # type: ignore[arg-type] - if name_parsed == "v2": - if config_parsed is None: - # for v2, normalize missing configuration to use the "." separator. - config_parsed = {"separator": "."} - return V2ChunkKeyEncoding(**config_parsed) # type: ignore[arg-type] - msg = f"Unknown chunk key encoding. Got {name_parsed}, expected one of ('v2', 'default')." - raise ValueError(msg) + def from_dict(cls, data: dict[str, JSON]) -> Self: + _, config_parsed = parse_named_configuration(data, require_configuration=False) + return cls(**config_parsed if config_parsed else {}) def to_dict(self) -> dict[str, JSON]: - return {"name": self.name, "configuration": {"separator": self.separator}} + return {"name": self.name, "configuration": super().to_dict()} - @abstractmethod def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: - pass + """ + Optional: decode a chunk key string into chunk coordinates. + Not required for normal operation; override if needed for testing or debugging. + """ + raise NotImplementedError(f"{self.__class__.__name__} does not implement decode_chunk_key.") @abstractmethod def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: - pass + """ + Encode chunk coordinates into a chunk key string. + Must be implemented by subclasses. + """ -ChunkKeyEncodingLike: TypeAlias = ChunkKeyEncodingParams | ChunkKeyEncoding +ChunkKeyEncodingLike: TypeAlias = dict[str, JSON] | ChunkKeyEncodingParams | ChunkKeyEncoding @dataclass(frozen=True) class DefaultChunkKeyEncoding(ChunkKeyEncoding): - name: Literal["default"] = "default" + name: ClassVar[Literal["default"]] = "default" + separator: SeparatorLiteral = "/" + + def __post_init__(self) -> None: + separator_parsed = parse_separator(self.separator) + object.__setattr__(self, "separator", separator_parsed) def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: if chunk_key == "c": @@ -94,7 +84,12 @@ def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: @dataclass(frozen=True) class V2ChunkKeyEncoding(ChunkKeyEncoding): - name: Literal["v2"] = "v2" + name: ClassVar[Literal["v2"]] = "v2" + separator: SeparatorLiteral = "." + + def __post_init__(self) -> None: + separator_parsed = parse_separator(self.separator) + object.__setattr__(self, "separator", separator_parsed) def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: return tuple(map(int, chunk_key.split(self.separator))) @@ -102,3 +97,30 @@ def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: chunk_identifier = self.separator.join(map(str, chunk_coords)) return "0" if chunk_identifier == "" else chunk_identifier + + +def parse_chunk_key_encoding(data: ChunkKeyEncodingLike) -> ChunkKeyEncoding: + """ + Take an implicit specification of a chunk key encoding and parse it into a ChunkKeyEncoding object. + """ + if isinstance(data, ChunkKeyEncoding): + return data + + # handle ChunkKeyEncodingParams + if "name" in data and "separator" in data: + data = {"name": data["name"], "configuration": {"separator": data["separator"]}} + + # Now must be a named config + data = cast("dict[str, JSON]", data) + + name_parsed, _ = parse_named_configuration(data, require_configuration=False) + try: + chunk_key_encoding = get_chunk_key_encoding_class(name_parsed).from_dict(data) + except KeyError as e: + raise ValueError(f"Unknown chunk key encoding: {e.args[0]!r}") from e + + return chunk_key_encoding + + +register_chunk_key_encoding("default", DefaultChunkKeyEncoding) +register_chunk_key_encoding("v2", V2ChunkKeyEncoding) diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 649a490409..cafcb99281 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -24,7 +24,11 @@ from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.chunk_grids import ChunkGrid, RegularChunkGrid -from zarr.core.chunk_key_encodings import ChunkKeyEncoding, ChunkKeyEncodingLike +from zarr.core.chunk_key_encodings import ( + ChunkKeyEncoding, + ChunkKeyEncodingLike, + parse_chunk_key_encoding, +) from zarr.core.common import ( JSON, ZARR_JSON, @@ -174,7 +178,7 @@ def __init__( shape_parsed = parse_shapelike(shape) chunk_grid_parsed = ChunkGrid.from_dict(chunk_grid) - chunk_key_encoding_parsed = ChunkKeyEncoding.from_dict(chunk_key_encoding) + chunk_key_encoding_parsed = parse_chunk_key_encoding(chunk_key_encoding) dimension_names_parsed = parse_dimension_names(dimension_names) # Note: relying on a type method is numpy-specific fill_value_parsed = data_type.cast_scalar(fill_value) diff --git a/src/zarr/registry.py b/src/zarr/registry.py index 5483b65c54..092b4cafc0 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -22,15 +22,18 @@ ) from zarr.abc.numcodec import Numcodec from zarr.core.buffer import Buffer, NDBuffer + from zarr.core.chunk_key_encodings import ChunkKeyEncoding from zarr.core.common import JSON __all__ = [ "Registry", "get_buffer_class", + "get_chunk_key_encoding_class", "get_codec_class", "get_ndbuffer_class", "get_pipeline_class", "register_buffer", + "register_chunk_key_encoding", "register_codec", "register_ndbuffer", "register_pipeline", @@ -44,9 +47,9 @@ def __init__(self) -> None: super().__init__() self.lazy_load_list: list[EntryPoint] = [] - def lazy_load(self) -> None: + def lazy_load(self, use_entrypoint_name: bool = False) -> None: for e in self.lazy_load_list: - self.register(e.load()) + self.register(e.load(), qualname=e.name if use_entrypoint_name else None) self.lazy_load_list.clear() @@ -60,10 +63,11 @@ def register(self, cls: type[T], qualname: str | None = None) -> None: __pipeline_registry: Registry[CodecPipeline] = Registry() __buffer_registry: Registry[Buffer] = Registry() __ndbuffer_registry: Registry[NDBuffer] = Registry() +__chunk_key_encoding_registry: Registry[ChunkKeyEncoding] = Registry() """ The registry module is responsible for managing implementations of codecs, -pipelines, buffers and ndbuffers and collecting them from entrypoints. +pipelines, buffers, ndbuffers, and chunk key encodings and collecting them from entrypoints. The implementation used is determined by the config. The registry module is also responsible for managing dtypes. @@ -99,6 +103,13 @@ def _collect_entrypoints() -> list[Registry[Any]]: data_type_registry._lazy_load_list.extend(entry_points.select(group="zarr.data_type")) data_type_registry._lazy_load_list.extend(entry_points.select(group="zarr", name="data_type")) + __chunk_key_encoding_registry.lazy_load_list.extend( + entry_points.select(group="zarr.chunk_key_encoding") + ) + __chunk_key_encoding_registry.lazy_load_list.extend( + entry_points.select(group="zarr", name="chunk_key_encoding") + ) + __pipeline_registry.lazy_load_list.extend(entry_points.select(group="zarr.codec_pipeline")) __pipeline_registry.lazy_load_list.extend( entry_points.select(group="zarr", name="codec_pipeline") @@ -114,6 +125,7 @@ def _collect_entrypoints() -> list[Registry[Any]]: __pipeline_registry, __buffer_registry, __ndbuffer_registry, + __chunk_key_encoding_registry, ] @@ -144,6 +156,10 @@ def register_buffer(cls: type[Buffer], qualname: str | None = None) -> None: __buffer_registry.register(cls, qualname) +def register_chunk_key_encoding(key: str, cls: type) -> None: + __chunk_key_encoding_registry.register(cls, key) + + def get_codec_class(key: str, reload_config: bool = False) -> type[Codec]: if reload_config: _reload_config() @@ -280,6 +296,15 @@ def get_ndbuffer_class(reload_config: bool = False) -> type[NDBuffer]: ) +def get_chunk_key_encoding_class(key: str) -> type[ChunkKeyEncoding]: + __chunk_key_encoding_registry.lazy_load(use_entrypoint_name=True) + if key not in __chunk_key_encoding_registry: + raise KeyError( + f"Chunk key encoding '{key}' not found in registered chunk key encodings: {list(__chunk_key_encoding_registry)}." + ) + return __chunk_key_encoding_registry[key] + + _collect_entrypoints() diff --git a/tests/conftest.py b/tests/conftest.py index 91975408aa..63c8950cff 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -6,7 +6,7 @@ import sys from collections.abc import Mapping, Sequence from dataclasses import dataclass, field -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, cast import numpy as np import numpy.typing as npt @@ -52,6 +52,7 @@ from zarr.core.chunk_key_encodings import ( ChunkKeyEncoding, ChunkKeyEncodingLike, + V2ChunkKeyEncoding, ) from zarr.core.dtype.wrapper import ZDType @@ -339,6 +340,7 @@ def create_array_metadata( filters_parsed, compressor_parsed = _parse_chunk_encoding_v2( compressor=compressors, filters=filters, dtype=dtype_parsed ) + chunk_key_encoding_parsed = cast("V2ChunkKeyEncoding", chunk_key_encoding_parsed) return ArrayV2Metadata( shape=shape_parsed, dtype=dtype_parsed, diff --git a/tests/test_array.py b/tests/test_array.py index 92a5dc77e9..5e3c10dce4 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1247,11 +1247,11 @@ async def test_chunk_key_encoding( chunk_key_encoding = ChunkKeyEncodingParams(name=name, separator=separator) # type: ignore[typeddict-item] error_msg = "" if name == "invalid": - error_msg = "Unknown chunk key encoding." + error_msg = r'Unknown chunk key encoding: "Chunk key encoding \'invalid\' not found in registered chunk key encodings: \[.*\]."' if zarr_format == 2 and name == "default": error_msg = "Invalid chunk key encoding. For Zarr format 2 arrays, the `name` field of the chunk key encoding must be 'v2'." if error_msg: - with pytest.raises(ValueError, match=re.escape(error_msg)): + with pytest.raises(ValueError, match=error_msg): arr = await create_array( store=store, dtype="uint8", diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index dfedbb83de..1884d501a5 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -308,7 +308,7 @@ def test_invalid_metadata(codecs: tuple[Codec, ...]) -> None: ArrayV3Metadata( shape=shape, chunk_grid={"name": "regular", "configuration": {"chunk_shape": chunks}}, - chunk_key_encoding={"name": "default", "configuration": {"separator": "/"}}, # type: ignore[arg-type] + chunk_key_encoding={"name": "default", "configuration": {"separator": "/"}}, fill_value=0, data_type=data_type, codecs=codecs, From 62551c706b9d6d2cefbb9b0145deb98a49702e2a Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 17 Sep 2025 23:57:42 +0200 Subject: [PATCH 110/468] fix:*-like creation routines take kwargs (#2992) * ensure that user-provided array creation kwargs can pass through array-like creation routines * test for kwarg propagation through array-like routines * propagate fill value if unspecified * changelog * Update 2992.fix.rst * add test for open_like * Update 2992.fix.rst * lint * add likeargs typeddict * explicitly iterate over functions in test * add test cases for fill_value in test_array_like_creation * use correct type: ignore statement * remove test that made no sense after allowing dtype inference in full_like --- changes/2992.bugfix.rst | 3 + src/zarr/api/asynchronous.py | 52 ++++++++++------- tests/test_api.py | 87 ++++++++++++++++++++++++++++- tests/test_api/test_asynchronous.py | 2 +- tests/test_group.py | 62 +++++++++++++++++++- 5 files changed, 183 insertions(+), 23 deletions(-) create mode 100644 changes/2992.bugfix.rst diff --git a/changes/2992.bugfix.rst b/changes/2992.bugfix.rst new file mode 100644 index 0000000000..7e4211cdde --- /dev/null +++ b/changes/2992.bugfix.rst @@ -0,0 +1,3 @@ +Fix a bug preventing ``ones_like``, ``full_like``, ``empty_like``, ``zeros_like`` and ``open_like`` functions from accepting +an explicit specification of array attributes like shape, dtype, chunks etc. The functions ``full_like``, +``empty_like``, and ``open_like`` now also more consistently infer a ``fill_value`` parameter from the provided array. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index dd5a162927..b79c41801e 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -3,7 +3,7 @@ import asyncio import dataclasses import warnings -from typing import TYPE_CHECKING, Any, Literal, cast +from typing import TYPE_CHECKING, Any, Literal, NotRequired, TypedDict, cast import numpy as np import numpy.typing as npt @@ -56,6 +56,7 @@ from zarr.abc.numcodec import Numcodec from zarr.core.buffer import NDArrayLikeOrScalar from zarr.core.chunk_key_encodings import ChunkKeyEncoding + from zarr.core.metadata.v2 import CompressorLikev2 from zarr.storage import StoreLike # TODO: this type could use some more thought @@ -124,10 +125,20 @@ def _get_shape_chunks(a: ArrayLike | Any) -> tuple[tuple[int, ...] | None, tuple return shape, chunks -def _like_args(a: ArrayLike, kwargs: dict[str, Any]) -> dict[str, Any]: +class _LikeArgs(TypedDict): + shape: NotRequired[tuple[int, ...]] + chunks: NotRequired[tuple[int, ...]] + dtype: NotRequired[np.dtype[np.generic]] + order: NotRequired[Literal["C", "F"]] + filters: NotRequired[tuple[Numcodec, ...] | None] + compressor: NotRequired[CompressorLikev2] + codecs: NotRequired[tuple[Codec, ...]] + + +def _like_args(a: ArrayLike) -> _LikeArgs: """Set default values for shape and chunks if they are not present in the array-like object""" - new = kwargs.copy() + new: _LikeArgs = {} shape, chunks = _get_shape_chunks(a) if shape is not None: @@ -138,9 +149,9 @@ def _like_args(a: ArrayLike, kwargs: dict[str, Any]) -> dict[str, Any]: if hasattr(a, "dtype"): new["dtype"] = a.dtype - if isinstance(a, AsyncArray): - new["order"] = a.order + if isinstance(a, AsyncArray | Array): if isinstance(a.metadata, ArrayV2Metadata): + new["order"] = a.order new["compressor"] = a.metadata.compressor new["filters"] = a.metadata.filters else: @@ -1087,7 +1098,7 @@ async def empty( shape: tuple[int, ...], **kwargs: Any ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an empty array with the specified shape. The contents will be filled with the - array's fill value or zeros if no fill value is provided. + specified fill value or zeros if no fill value is provided. Parameters ---------- @@ -1102,8 +1113,7 @@ async def empty( retrieve data from an empty Zarr array, any values may be returned, and these are not guaranteed to be stable from one access to the next. """ - - return await create(shape=shape, fill_value=None, **kwargs) + return await create(shape=shape, **kwargs) async def empty_like( @@ -1130,8 +1140,10 @@ async def empty_like( retrieve data from an empty Zarr array, any values may be returned, and these are not guaranteed to be stable from one access to the next. """ - like_kwargs = _like_args(a, kwargs) - return await empty(**like_kwargs) + like_kwargs = _like_args(a) | kwargs + if isinstance(a, (AsyncArray | Array)): + like_kwargs.setdefault("fill_value", a.metadata.fill_value) + return await empty(**like_kwargs) # type: ignore[arg-type] # TODO: add type annotations for fill_value and kwargs @@ -1176,10 +1188,10 @@ async def full_like( Array The new array. """ - like_kwargs = _like_args(a, kwargs) - if isinstance(a, AsyncArray): + like_kwargs = _like_args(a) | kwargs + if isinstance(a, (AsyncArray | Array)): like_kwargs.setdefault("fill_value", a.metadata.fill_value) - return await full(**like_kwargs) + return await full(**like_kwargs) # type: ignore[arg-type] async def ones( @@ -1220,8 +1232,8 @@ async def ones_like( Array The new array. """ - like_kwargs = _like_args(a, kwargs) - return await ones(**like_kwargs) + like_kwargs = _like_args(a) | kwargs + return await ones(**like_kwargs) # type: ignore[arg-type] async def open_array( @@ -1300,10 +1312,10 @@ async def open_like( AsyncArray The opened array. """ - like_kwargs = _like_args(a, kwargs) + like_kwargs = _like_args(a) | kwargs if isinstance(a, (AsyncArray | Array)): - kwargs.setdefault("fill_value", a.metadata.fill_value) - return await open_array(path=path, **like_kwargs) + like_kwargs.setdefault("fill_value", a.metadata.fill_value) + return await open_array(path=path, **like_kwargs) # type: ignore[arg-type] async def zeros( @@ -1344,5 +1356,5 @@ async def zeros_like( Array The new array. """ - like_kwargs = _like_args(a, kwargs) - return await zeros(**like_kwargs) + like_kwargs = _like_args(a) | kwargs + return await zeros(**like_kwargs) # type: ignore[arg-type] diff --git a/tests/test_api.py b/tests/test_api.py index ff969d406f..30f648a815 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -2,7 +2,7 @@ import inspect import re -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Any import zarr.codecs import zarr.storage @@ -82,6 +82,91 @@ def test_create(memory_store: Store) -> None: z = create(shape=(400, 100), chunks=(16, 16.5), store=store, overwrite=True) # type: ignore[arg-type] +@pytest.mark.parametrize( + "func", + [ + zarr.api.asynchronous.zeros_like, + zarr.api.asynchronous.ones_like, + zarr.api.asynchronous.empty_like, + zarr.api.asynchronous.full_like, + zarr.api.asynchronous.open_like, + ], +) +@pytest.mark.parametrize("out_shape", ["keep", (10, 10)]) +@pytest.mark.parametrize("out_chunks", ["keep", (10, 10)]) +@pytest.mark.parametrize("out_dtype", ["keep", "int8"]) +@pytest.mark.parametrize("out_fill", ["keep", 4]) +async def test_array_like_creation( + zarr_format: ZarrFormat, + func: Callable[[Any], Any], + out_shape: Literal["keep"] | tuple[int, ...], + out_chunks: Literal["keep"] | tuple[int, ...], + out_dtype: str, + out_fill: Literal["keep"] | int, +) -> None: + """ + Test zeros_like, ones_like, empty_like, full_like, ensuring that we can override the + shape, chunks, dtype and fill_value of the array-like object provided to these functions with + appropriate keyword arguments + """ + ref_fill = 100 + ref_arr = zarr.create_array( + store={}, + shape=(11, 12), + dtype="uint8", + chunks=(11, 12), + zarr_format=zarr_format, + fill_value=ref_fill, + ) + kwargs: dict[str, object] = {} + if func is zarr.api.asynchronous.full_like: + if out_fill == "keep": + expect_fill = ref_fill + else: + expect_fill = out_fill + kwargs["fill_value"] = expect_fill + elif func is zarr.api.asynchronous.zeros_like: + expect_fill = 0 + elif func is zarr.api.asynchronous.ones_like: + expect_fill = 1 + elif func is zarr.api.asynchronous.empty_like: + if out_fill == "keep": + expect_fill = ref_fill + else: + kwargs["fill_value"] = out_fill + expect_fill = out_fill + elif func is zarr.api.asynchronous.open_like: # type: ignore[comparison-overlap] + if out_fill == "keep": + expect_fill = ref_fill + else: + kwargs["fill_value"] = out_fill + expect_fill = out_fill + kwargs["mode"] = "w" + else: + raise AssertionError + if out_shape != "keep": + kwargs["shape"] = out_shape + expect_shape = out_shape + else: + expect_shape = ref_arr.shape + if out_chunks != "keep": + kwargs["chunks"] = out_chunks + expect_chunks = out_chunks + else: + expect_chunks = ref_arr.chunks + if out_dtype != "keep": + kwargs["dtype"] = out_dtype + expect_dtype = out_dtype + else: + expect_dtype = ref_arr.dtype # type: ignore[assignment] + + new_arr = await func(ref_arr, path="foo", zarr_format=zarr_format, **kwargs) # type: ignore[call-arg] + assert new_arr.shape == expect_shape + assert new_arr.chunks == expect_chunks + assert new_arr.dtype == expect_dtype + assert np.all(Array(new_arr)[:] == expect_fill) + + # TODO: parametrize over everything this function takes @pytest.mark.parametrize("store", ["memory"], indirect=True) def test_create_array(store: Store, zarr_format: ZarrFormat) -> None: diff --git a/tests/test_api/test_asynchronous.py b/tests/test_api/test_asynchronous.py index 0f219fd727..8757127985 100644 --- a/tests/test_api/test_asynchronous.py +++ b/tests/test_api/test_asynchronous.py @@ -88,7 +88,7 @@ def test_like_args( """ Test the like_args function """ - assert _like_args(observed, {}) == expected + assert _like_args(observed) == expected async def test_open_no_array() -> None: diff --git a/tests/test_group.py b/tests/test_group.py index eb4af7336f..e7ce2bad16 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -8,7 +8,7 @@ import re import time import warnings -from typing import TYPE_CHECKING, Any, Literal +from typing import TYPE_CHECKING, Any, Literal, get_args import numpy as np import pytest @@ -761,6 +761,66 @@ def test_group_create_array( assert np.array_equal(array[:], data) +LikeMethodName = Literal["zeros_like", "ones_like", "empty_like", "full_like"] + + +@pytest.mark.parametrize("method_name", get_args(LikeMethodName)) +@pytest.mark.parametrize("out_shape", ["keep", (10, 10)]) +@pytest.mark.parametrize("out_chunks", ["keep", (10, 10)]) +@pytest.mark.parametrize("out_dtype", ["keep", "int8"]) +def test_group_array_like_creation( + zarr_format: ZarrFormat, + method_name: LikeMethodName, + out_shape: Literal["keep"] | tuple[int, ...], + out_chunks: Literal["keep"] | tuple[int, ...], + out_dtype: str, +) -> None: + """ + Test Group.{zeros_like, ones_like, empty_like, full_like}, ensuring that we can override the + shape, chunks, and dtype of the array-like object provided to these functions with + appropriate keyword arguments + """ + ref_arr = zarr.ones(store={}, shape=(11, 12), dtype="uint8", chunks=(11, 12)) + group = Group.from_store({}, zarr_format=zarr_format) + kwargs = {} + if method_name == "full_like": + expect_fill = 4 + kwargs["fill_value"] = expect_fill + meth = group.full_like + elif method_name == "zeros_like": + expect_fill = 0 + meth = group.zeros_like + elif method_name == "ones_like": + expect_fill = 1 + meth = group.ones_like + elif method_name == "empty_like": + expect_fill = ref_arr.fill_value + meth = group.empty_like + else: + raise AssertionError + if out_shape != "keep": + kwargs["shape"] = out_shape + expect_shape = out_shape + else: + expect_shape = ref_arr.shape + if out_chunks != "keep": + kwargs["chunks"] = out_chunks + expect_chunks = out_chunks + else: + expect_chunks = ref_arr.chunks + if out_dtype != "keep": + kwargs["dtype"] = out_dtype + expect_dtype = out_dtype + else: + expect_dtype = ref_arr.dtype + + new_arr = meth(name="foo", data=ref_arr, **kwargs) + assert new_arr.shape == expect_shape + assert new_arr.chunks == expect_chunks + assert new_arr.dtype == expect_dtype + assert np.all(new_arr[:] == expect_fill) + + def test_group_array_creation( store: Store, zarr_format: ZarrFormat, From de947648e6ab6e7079ddb4f33b6b56070c3e6657 Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Thu, 18 Sep 2025 19:20:56 +0100 Subject: [PATCH 111/468] Prevent creation of arrays/groups under a parent array (#3407) * restrict arrays as parents of other arrays * use common save_metadata function for groups and arrays * add test for creation under a parent array * fix failing tests * fix failing doctest * remove dependency on AsyncGroup * document changes --------- Co-authored-by: Davis Bennett --- changes/2582.bugfix.rst | 2 + docs/user-guide/arrays.rst | 3 +- src/zarr/core/array.py | 54 ++------------------- src/zarr/core/group.py | 19 +------- src/zarr/core/metadata/io.py | 92 ++++++++++++++++++++++++++++++++++++ src/zarr/storage/_common.py | 35 +++++++++----- tests/test_group.py | 18 +++++++ tests/test_indexing.py | 16 +++---- 8 files changed, 151 insertions(+), 88 deletions(-) create mode 100644 changes/2582.bugfix.rst create mode 100644 src/zarr/core/metadata/io.py diff --git a/changes/2582.bugfix.rst b/changes/2582.bugfix.rst new file mode 100644 index 0000000000..1c8c7fab5c --- /dev/null +++ b/changes/2582.bugfix.rst @@ -0,0 +1,2 @@ +Prevents creation of groups (.create_group) or arrays (.create_array) as children +of an existing array. diff --git a/docs/user-guide/arrays.rst b/docs/user-guide/arrays.rst index 257fac450c..a498cb44a3 100644 --- a/docs/user-guide/arrays.rst +++ b/docs/user-guide/arrays.rst @@ -567,11 +567,12 @@ Any combination of integer and slice can be used for block indexing:: >>> >>> root = zarr.create_group('data/example-19.zarr') >>> foo = root.create_array(name='foo', shape=(1000, 100), chunks=(10, 10), dtype='float32') - >>> bar = root.create_array(name='foo/bar', shape=(100,), dtype='int32') + >>> bar = root.create_array(name='bar', shape=(100,), dtype='int32') >>> foo[:, :] = np.random.random((1000, 100)) >>> bar[:] = np.arange(100) >>> root.tree() / + ├── bar (100,) int32 └── foo (1000, 100) float32 diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index e5fa451914..793d1a034b 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -25,7 +25,6 @@ import zarr from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec from zarr.abc.numcodec import Numcodec, _is_numcodec -from zarr.abc.store import Store, set_or_delete from zarr.codecs._v2 import V2Codec from zarr.codecs.bytes import BytesCodec from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec @@ -110,6 +109,7 @@ ArrayV3MetadataDict, T_ArrayMetadata, ) +from zarr.core.metadata.io import save_metadata from zarr.core.metadata.v2 import ( CompressorLikev2, get_object_codec_id, @@ -140,9 +140,9 @@ import numpy.typing as npt from zarr.abc.codec import CodecPipeline + from zarr.abc.store import Store from zarr.codecs.sharding import ShardingCodecIndexLocation from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar - from zarr.core.group import AsyncGroup from zarr.storage import StoreLike @@ -1639,24 +1639,7 @@ async def _save_metadata(self, metadata: ArrayMetadata, ensure_parents: bool = F """ Asynchronously save the array metadata. """ - to_save = metadata.to_buffer_dict(cpu_buffer_prototype) - awaitables = [set_or_delete(self.store_path / key, value) for key, value in to_save.items()] - - if ensure_parents: - # To enable zarr.create(store, path="a/b/c"), we need to create all the intermediate groups. - parents = _build_parents(self) - - for parent in parents: - awaitables.extend( - [ - (parent.store_path / key).set_if_not_exists(value) - for key, value in parent.metadata.to_buffer_dict( - cpu_buffer_prototype - ).items() - ] - ) - - await gather(*awaitables) + await save_metadata(self.store_path, metadata, ensure_parents=ensure_parents) async def _set_selection( self, @@ -4121,37 +4104,6 @@ async def _shards_initialized( ) -def _build_parents( - node: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup, -) -> list[AsyncGroup]: - from zarr.core.group import AsyncGroup, GroupMetadata - - store = node.store_path.store - path = node.store_path.path - if not path: - return [] - - required_parts = path.split("/")[:-1] - parents = [ - # the root group - AsyncGroup( - metadata=GroupMetadata(zarr_format=node.metadata.zarr_format), - store_path=StorePath(store=store, path=""), - ) - ] - - for i, part in enumerate(required_parts): - p = "/".join(required_parts[:i] + [part]) - parents.append( - AsyncGroup( - metadata=GroupMetadata(zarr_format=node.metadata.zarr_format), - store_path=StorePath(store=store, path=p), - ) - ) - - return parents - - FiltersLike: TypeAlias = ( Iterable[dict[str, JSON] | ArrayArrayCodec | Numcodec] | ArrayArrayCodec diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index f5bb14c48e..1c41a8a4a8 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -28,7 +28,6 @@ FiltersLike, SerializerLike, ShardsLike, - _build_parents, _parse_deprecated_compressor, create_array, ) @@ -49,6 +48,7 @@ ) from zarr.core.config import config from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata +from zarr.core.metadata.io import save_metadata from zarr.core.sync import SyncMixin, sync from zarr.errors import ( ContainsArrayError, @@ -818,22 +818,7 @@ async def get( return default async def _save_metadata(self, ensure_parents: bool = False) -> None: - to_save = self.metadata.to_buffer_dict(default_buffer_prototype()) - awaitables = [set_or_delete(self.store_path / key, value) for key, value in to_save.items()] - - if ensure_parents: - parents = _build_parents(self) - for parent in parents: - awaitables.extend( - [ - (parent.store_path / key).set_if_not_exists(value) - for key, value in parent.metadata.to_buffer_dict( - default_buffer_prototype() - ).items() - ] - ) - - await asyncio.gather(*awaitables) + await save_metadata(self.store_path, self.metadata, ensure_parents=ensure_parents) @property def path(self) -> str: diff --git a/src/zarr/core/metadata/io.py b/src/zarr/core/metadata/io.py new file mode 100644 index 0000000000..7b63f5493b --- /dev/null +++ b/src/zarr/core/metadata/io.py @@ -0,0 +1,92 @@ +from __future__ import annotations + +import asyncio +from typing import TYPE_CHECKING + +from zarr.abc.store import set_or_delete +from zarr.core.buffer.core import default_buffer_prototype +from zarr.errors import ContainsArrayError +from zarr.storage._common import StorePath, ensure_no_existing_node + +if TYPE_CHECKING: + from zarr.core.common import ZarrFormat + from zarr.core.group import GroupMetadata + from zarr.core.metadata import ArrayMetadata + + +def _build_parents(store_path: StorePath, zarr_format: ZarrFormat) -> dict[str, GroupMetadata]: + from zarr.core.group import GroupMetadata + + path = store_path.path + if not path: + return {} + + required_parts = path.split("/")[:-1] + + # the root group + parents = {"": GroupMetadata(zarr_format=zarr_format)} + + for i, part in enumerate(required_parts): + parent_path = "/".join(required_parts[:i] + [part]) + parents[parent_path] = GroupMetadata(zarr_format=zarr_format) + + return parents + + +async def save_metadata( + store_path: StorePath, metadata: ArrayMetadata | GroupMetadata, ensure_parents: bool = False +) -> None: + """Asynchronously save the array or group metadata. + + Parameters + ---------- + store_path : StorePath + Location to save metadata. + metadata : ArrayMetadata | GroupMetadata + Metadata to save. + ensure_parents : bool, optional + Create any missing parent groups, and check no existing parents are arrays. + + Raises + ------ + ValueError + """ + to_save = metadata.to_buffer_dict(default_buffer_prototype()) + set_awaitables = [set_or_delete(store_path / key, value) for key, value in to_save.items()] + + if ensure_parents: + # To enable zarr.create(store, path="a/b/c"), we need to create all the intermediate groups. + parents = _build_parents(store_path, metadata.zarr_format) + ensure_array_awaitables = [] + + for parent_path, parent_metadata in parents.items(): + parent_store_path = StorePath(store_path.store, parent_path) + + # Error if an array already exists at any parent location. Only groups can have child nodes. + ensure_array_awaitables.append( + ensure_no_existing_node( + parent_store_path, parent_metadata.zarr_format, node_type="array" + ) + ) + set_awaitables.extend( + [ + (parent_store_path / key).set_if_not_exists(value) + for key, value in parent_metadata.to_buffer_dict( + default_buffer_prototype() + ).items() + ] + ) + + # Checks for parent arrays must happen first, before any metadata is modified + try: + await asyncio.gather(*ensure_array_awaitables) + except ContainsArrayError as e: + # clear awaitables to avoid RuntimeWarning: coroutine was never awaited + for awaitable in set_awaitables: + awaitable.close() + + raise ValueError( + f"A parent of {store_path} is an array - only groups may have child nodes." + ) from e + + await asyncio.gather(*set_awaitables) diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 6febb08281..4b1f5e4ae3 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -435,7 +435,11 @@ def _is_fsspec_uri(uri: str) -> bool: return "://" in uri or ("::" in uri and "local://" not in uri) -async def ensure_no_existing_node(store_path: StorePath, zarr_format: ZarrFormat) -> None: +async def ensure_no_existing_node( + store_path: StorePath, + zarr_format: ZarrFormat, + node_type: Literal["array", "group"] | None = None, +) -> None: """ Check if a store_path is safe for array / group creation. Returns `None` or raises an exception. @@ -446,6 +450,8 @@ async def ensure_no_existing_node(store_path: StorePath, zarr_format: ZarrFormat The storage location to check. zarr_format : ZarrFormat The Zarr format to check. + node_type : str | None, optional + Raise an error if an "array", or "group" exists. By default (when None), raises an error for either. Raises ------ @@ -456,16 +462,23 @@ async def ensure_no_existing_node(store_path: StorePath, zarr_format: ZarrFormat elif zarr_format == 3: extant_node = await _contains_node_v3(store_path) - if extant_node == "array": - msg = f"An array exists in store {store_path.store!r} at path {store_path.path!r}." - raise ContainsArrayError(msg) - elif extant_node == "group": - msg = f"An array exists in store {store_path.store!r} at path {store_path.path!r}." - raise ContainsGroupError(msg) - elif extant_node == "nothing": - return - msg = f"Invalid value for extant_node: {extant_node}" # type: ignore[unreachable] - raise ValueError(msg) + match extant_node: + case "array": + if node_type != "group": + msg = f"An array exists in store {store_path.store!r} at path {store_path.path!r}." + raise ContainsArrayError(msg) + + case "group": + if node_type != "array": + msg = f"A group exists in store {store_path.store!r} at path {store_path.path!r}." + raise ContainsGroupError(msg) + + case "nothing": + return + + case _: + msg = f"Invalid value for extant_node: {extant_node}" # type: ignore[unreachable] + raise ValueError(msg) async def _contains_node_v3(store_path: StorePath) -> Literal["array", "group", "nothing"]: diff --git a/tests/test_group.py b/tests/test_group.py index e7ce2bad16..6f1f4e68fa 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -761,6 +761,24 @@ def test_group_create_array( assert np.array_equal(array[:], data) +@pytest.mark.parametrize("method", ["create_array", "create_group"]) +def test_create_with_parent_array(store: Store, zarr_format: ZarrFormat, method: str): + """Test that groups/arrays cannot be created under a parent array.""" + + # create a group with a child array + group = Group.from_store(store, zarr_format=zarr_format) + group.create_array(name="arr_1", shape=(10, 10), dtype="uint8") + + error_msg = r"A parent of .* is an array - only groups may have child nodes." + if method == "create_array": + with pytest.raises(ValueError, match=error_msg): + group.create_array("arr_1/group_1/group_2/arr_2", shape=(10, 10), dtype="uint8") + + else: + with pytest.raises(ValueError, match=error_msg): + group.create_group("arr_1/group_1/group_2/group_3") + + LikeMethodName = Literal["zeros_like", "ones_like", "empty_like", "full_like"] diff --git a/tests/test_indexing.py b/tests/test_indexing.py index c6a792b0e5..609db6cdce 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -2110,14 +2110,14 @@ async def test_async_oindex(self, store, indexer, expected): @pytest.mark.asyncio async def test_async_oindex_with_zarr_array(self, store): - z1 = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") + group = zarr.create_group(store=store, zarr_format=3) + + z1 = group.create_array(name="z1", shape=(2, 2), chunks=(1, 1), dtype="i8") z1[...] = np.array([[1, 2], [3, 4]]) async_zarr = z1._async_array # create boolean zarr array to index with - z2 = zarr.create_array( - store=store, name="z2", shape=(2,), chunks=(1,), zarr_format=3, dtype="?" - ) + z2 = group.create_array(name="z2", shape=(2,), chunks=(1,), dtype="?") z2[...] = np.array([True, False]) result = await async_zarr.oindex.getitem(z2) @@ -2143,14 +2143,14 @@ async def test_async_vindex(self, store, indexer, expected): @pytest.mark.asyncio async def test_async_vindex_with_zarr_array(self, store): - z1 = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") + group = zarr.create_group(store=store, zarr_format=3) + + z1 = group.create_array(name="z1", shape=(2, 2), chunks=(1, 1), dtype="i8") z1[...] = np.array([[1, 2], [3, 4]]) async_zarr = z1._async_array # create boolean zarr array to index with - z2 = zarr.create_array( - store=store, name="z2", shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="?" - ) + z2 = group.create_array(name="z2", shape=(2, 2), chunks=(1, 1), dtype="?") z2[...] = np.array([[False, True], [False, True]]) result = await async_zarr.vindex.getitem(z2) From b5e0793ad32d6b6e0992a11ae92f36c6bf0c4592 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 18 Sep 2025 21:45:04 +0200 Subject: [PATCH 112/468] 3.1.3 release notes (#3472) (#3474) --- changes/1798.feature.rst | 2 -- changes/2582.bugfix.rst | 2 -- changes/2859.removal.rst | 2 -- changes/2992.bugfix.rst | 3 --- changes/3310.feature.rst | 1 - changes/3376.misc.rst | 3 --- changes/3390.misc.rst | 1 - changes/3403.misc.rst | 6 ----- changes/3411.bugfix.rst | 1 - changes/3422.bugfix.rst | 4 ---- changes/3425.bugfix.rst | 1 - changes/3428.bugfix.rst | 1 - changes/3431.bugfix.rst | 2 -- changes/3436.feature.rst | 2 -- changes/3444.feature.rst | 1 - changes/3448.bugfix.rst | 3 --- changes/3449.misc.rst | 1 - docs/release-notes.rst | 49 ++++++++++++++++++++++++++++++++++++++++ 18 files changed, 49 insertions(+), 36 deletions(-) delete mode 100644 changes/1798.feature.rst delete mode 100644 changes/2582.bugfix.rst delete mode 100644 changes/2859.removal.rst delete mode 100644 changes/2992.bugfix.rst delete mode 100644 changes/3310.feature.rst delete mode 100644 changes/3376.misc.rst delete mode 100644 changes/3390.misc.rst delete mode 100644 changes/3403.misc.rst delete mode 100644 changes/3411.bugfix.rst delete mode 100644 changes/3422.bugfix.rst delete mode 100644 changes/3425.bugfix.rst delete mode 100644 changes/3428.bugfix.rst delete mode 100644 changes/3431.bugfix.rst delete mode 100644 changes/3436.feature.rst delete mode 100644 changes/3444.feature.rst delete mode 100644 changes/3448.bugfix.rst delete mode 100644 changes/3449.misc.rst diff --git a/changes/1798.feature.rst b/changes/1798.feature.rst deleted file mode 100644 index 64d4efdf08..0000000000 --- a/changes/1798.feature.rst +++ /dev/null @@ -1,2 +0,0 @@ -Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also -provided under zarr.metadata. diff --git a/changes/2582.bugfix.rst b/changes/2582.bugfix.rst deleted file mode 100644 index 1c8c7fab5c..0000000000 --- a/changes/2582.bugfix.rst +++ /dev/null @@ -1,2 +0,0 @@ -Prevents creation of groups (.create_group) or arrays (.create_array) as children -of an existing array. diff --git a/changes/2859.removal.rst b/changes/2859.removal.rst deleted file mode 100644 index bd417855f3..0000000000 --- a/changes/2859.removal.rst +++ /dev/null @@ -1,2 +0,0 @@ -The ``Store.set_partial_writes`` method, which was not used by Zarr-Python, has been removed. -``store.supports_partial_writes`` is now always ``False``. diff --git a/changes/2992.bugfix.rst b/changes/2992.bugfix.rst deleted file mode 100644 index 7e4211cdde..0000000000 --- a/changes/2992.bugfix.rst +++ /dev/null @@ -1,3 +0,0 @@ -Fix a bug preventing ``ones_like``, ``full_like``, ``empty_like``, ``zeros_like`` and ``open_like`` functions from accepting -an explicit specification of array attributes like shape, dtype, chunks etc. The functions ``full_like``, -``empty_like``, and ``open_like`` now also more consistently infer a ``fill_value`` parameter from the provided array. diff --git a/changes/3310.feature.rst b/changes/3310.feature.rst deleted file mode 100644 index b21d3219fc..0000000000 --- a/changes/3310.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Add obstore implementation of delete_dir. diff --git a/changes/3376.misc.rst b/changes/3376.misc.rst deleted file mode 100644 index 68b0d9d855..0000000000 --- a/changes/3376.misc.rst +++ /dev/null @@ -1,3 +0,0 @@ -Define Zarr V3-specific codecs from numcodecs inside this repo. These codecs can be found in -:mod:`zarr.codecs.numcodecs`. This is necessary to resolve a circular dependency between Zarr -and Numcodecs. \ No newline at end of file diff --git a/changes/3390.misc.rst b/changes/3390.misc.rst deleted file mode 100644 index fa229a3ad8..0000000000 --- a/changes/3390.misc.rst +++ /dev/null @@ -1 +0,0 @@ -Improve documentation consistency across API functions and remove outdated references to deprecated configuration values that no longer work. \ No newline at end of file diff --git a/changes/3403.misc.rst b/changes/3403.misc.rst deleted file mode 100644 index 2ad4821d73..0000000000 --- a/changes/3403.misc.rst +++ /dev/null @@ -1,6 +0,0 @@ -Moves some indexing-specific exceptions to ``zarr.errors``, and ensures that all Zarr-specific -exception classes accept a pre-formatted string as a single argument. This is a breaking change to -the following exceptions classes: :class:`zarr.errors.BoundsCheckError`, :class:`zarr.errors.NegativeStepError` -:class:`zarr.errors.VindexInvalidSelectionError`. These classes previously generated internally -formatted error messages when given a single argument. After this change, formatting of the error -message is up to the routine invoking the error. \ No newline at end of file diff --git a/changes/3411.bugfix.rst b/changes/3411.bugfix.rst deleted file mode 100644 index b9303b9666..0000000000 --- a/changes/3411.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -LocalStore now uses atomic writes, which should prevent some cases of corrupted data. diff --git a/changes/3422.bugfix.rst b/changes/3422.bugfix.rst deleted file mode 100644 index ed4b8c266d..0000000000 --- a/changes/3422.bugfix.rst +++ /dev/null @@ -1,4 +0,0 @@ -Fix a potential race condition when using :func:`zarr.create_array` with the ``data`` parameter -set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity -that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for -that array. \ No newline at end of file diff --git a/changes/3425.bugfix.rst b/changes/3425.bugfix.rst deleted file mode 100644 index 71cc147287..0000000000 --- a/changes/3425.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix ChunkGrid definition (broken in 3.1.2) diff --git a/changes/3428.bugfix.rst b/changes/3428.bugfix.rst deleted file mode 100644 index d15a3db3ba..0000000000 --- a/changes/3428.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Ensure syntax like ``root['/subgroup']`` works equivalently to ``root['subgroup']`` when using consolidated metadata. diff --git a/changes/3431.bugfix.rst b/changes/3431.bugfix.rst deleted file mode 100644 index cdf166ddd5..0000000000 --- a/changes/3431.bugfix.rst +++ /dev/null @@ -1,2 +0,0 @@ -Creating a new group with `zarr.group` no longer errors. -This fixes a regression introduced in version 3.1.2. diff --git a/changes/3436.feature.rst b/changes/3436.feature.rst deleted file mode 100644 index 85e28bb8b1..0000000000 --- a/changes/3436.feature.rst +++ /dev/null @@ -1,2 +0,0 @@ -Adds a registry for chunk key encodings for extensibility. -This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. diff --git a/changes/3444.feature.rst b/changes/3444.feature.rst deleted file mode 100644 index d621c428b6..0000000000 --- a/changes/3444.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Trying to open a group at a path were a array already exists now raises a helpful error. diff --git a/changes/3448.bugfix.rst b/changes/3448.bugfix.rst deleted file mode 100644 index 6c8b106153..0000000000 --- a/changes/3448.bugfix.rst +++ /dev/null @@ -1,3 +0,0 @@ -Setting ``fill_value`` to a float like ``0.0`` when the data type of the array is an integer is a common -mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python -will not create such arrays. \ No newline at end of file diff --git a/changes/3449.misc.rst b/changes/3449.misc.rst deleted file mode 100644 index df17bf582e..0000000000 --- a/changes/3449.misc.rst +++ /dev/null @@ -1 +0,0 @@ -Publish nightly wheels to https://anaconda.org/scientific-python-nightly-wheels/. diff --git a/docs/release-notes.rst b/docs/release-notes.rst index 45401caa2e..8a6061b40e 100644 --- a/docs/release-notes.rst +++ b/docs/release-notes.rst @@ -3,6 +3,55 @@ Release notes .. towncrier release notes start +zarr 3.1.3 (2025-09-18) +----------------------- + +Features +~~~~~~~~ + +- Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also + provided under zarr.metadata. (:issue:`1798`) +- Add obstore implementation of delete_dir. (:issue:`3310`) +- Adds a registry for chunk key encodings for extensibility. + This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. (:issue:`3436`) +- Trying to open a group at a path were a array already exists now raises a helpful error. (:issue:`3444`) + + +Bugfixes +~~~~~~~~ + +- Prevents creation of groups (.create_group) or arrays (.create_array) as children + of an existing array. (:issue:`2582`) +- Fix a bug preventing ``ones_like``, ``full_like``, ``empty_like``, ``zeros_like`` and ``open_like`` functions from accepting + an explicit specification of array attributes like shape, dtype, chunks etc. The functions ``full_like``, + ``empty_like``, and ``open_like`` now also more consistently infer a ``fill_value`` parameter from the provided array. (:issue:`2992`) +- LocalStore now uses atomic writes, which should prevent some cases of corrupted data. (:issue:`3411`) +- Fix a potential race condition when using :func:`zarr.create_array` with the ``data`` parameter + set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity + that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for + that array. (:issue:`3422`) +- Fix ChunkGrid definition (broken in 3.1.2) (:issue:`3425`) +- Ensure syntax like ``root['/subgroup']`` works equivalently to ``root['subgroup']`` when using consolidated metadata. (:issue:`3428`) +- Creating a new group with `zarr.group` no longer errors. + This fixes a regression introduced in version 3.1.2. (:issue:`3431`) +- Setting ``fill_value`` to a float like ``0.0`` when the data type of the array is an integer is a common + mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python + will not create such arrays. (:issue:`3448`) + + +Deprecations and Removals +~~~~~~~~~~~~~~~~~~~~~~~~~ + +- The ``Store.set_partial_writes`` method, which was not used by Zarr-Python, has been removed. + ``store.supports_partial_writes`` is now always ``False``. (:issue:`2859`) + + +Misc +~~~~ + +- :issue:`3376`, :issue:`3390`, :issue:`3403`, :issue:`3449` + + 3.1.2 (2025-08-25) ------------------ From ef136e9d58eeaa1c1922d56ea9f0d92f3fcc4db6 Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Fri, 19 Sep 2025 07:27:35 -0700 Subject: [PATCH 113/468] Add sharding to multiprocessing test (#3475) * add sharding to multiprocessing test * Update tests/test_array.py --------- Co-authored-by: Davis Bennett --- tests/test_array.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/tests/test_array.py b/tests/test_array.py index 5e3c10dce4..5219616739 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1789,12 +1789,20 @@ def _index_array(arr: Array, index: Any) -> Any: ], ) @pytest.mark.parametrize("store", ["local"], indirect=True) -def test_multiprocessing(store: Store, method: Literal["fork", "spawn", "forkserver"]) -> None: +@pytest.mark.parametrize("shards", [None, (20,)]) +def test_multiprocessing( + store: Store, method: Literal["fork", "spawn", "forkserver"], shards: tuple[int, ...] | None +) -> None: """ Test that arrays can be pickled and indexed in child processes """ data = np.arange(100) - arr = zarr.create_array(store=store, data=data) + chunks: Literal["auto"] | tuple[int, ...] + if shards is None: + chunks = "auto" + else: + chunks = (1,) + arr = zarr.create_array(store=store, data=data, shards=shards, chunks=chunks) ctx = mp.get_context(method) with ctx.Pool() as pool: results = pool.starmap(_index_array, [(arr, slice(len(data)))]) From 8b35cf4faef122cdb897c46b2311e70b5f3eb6ad Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Fri, 19 Sep 2025 13:54:20 -0400 Subject: [PATCH 114/468] Use mkdocs-material for Zarr-Python documentation (#3118) * Use mkdocs-material for Zarr-Python documentation * Update towncrier instructions * Update readthedocs config * Remove conda section * Install hatch for rtd * Move build step * Start a shell with hatch * Use commands * Don't use hatch * Figure out redirects later * Format docstrings with ruff * git ignore docs output * Specify towncrier start * Add redirects * Don't use version extra * Convert changes to markdown * Use cards on homepage for now * Execute examples in quickstart * Execute examples in array user guide * Auto-doc for some modules * Cleanup quickstart * Filter warnings in quickstart * Add links to quickstart * Add index pages * Remove $ from console * Update code block formatting for arrays * Add cross-references to arrays * Executable blocks and cross-references in groups user guide * Fix links * Executable code blocks in attrs user-guide * Add external inventories * Add cross-references to storage * Executable storage guide * Executable config code blocks * Update V3 migration links * Executable code blocks in data types * Executable code blocks in performance * Use mkdocs build --strict rather than doctest * Executable code blocks in consolidated metadata * Better pprint * Add buffer protocol to API * Cross-references in extending * References in gpu guide * References in gpu guide * Fix indentation * Formatting * Add new release notes * Inherit docstrings * Add buffer API page * Fix some links * Update changelog check * Update dependency * Update cross-references * Add cross-reference * Convert references and admonitions * Improve numpy dtype cross-references * Show source * Update changelog entries to markdown * Strict RTD build * Fix numpydoc errors * Allow related section * Update numpydoc validation config * Fix docstring failures * Update config ref --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/labeler.yml | 2 +- .github/workflows/test.yml | 6 +- .gitignore | 4 +- .pre-commit-config.yaml | 1 + .readthedocs.yaml | 12 +- changes/README.md | 2 +- ci/check_changelog_entries.py | 4 +- docs/Makefile | 231 ------ docs/_static/custom.css | 110 --- docs/_static/custom.js | 17 - docs/_static/index_api.svg | 97 --- docs/_static/index_contribute.svg | 76 -- docs/_static/index_getting_started.svg | 66 -- docs/_static/index_user_guide.svg | 67 -- docs/about.rst | 24 - docs/api/abc/buffer.md | 5 + docs/api/abc/codec.md | 5 + docs/api/abc/metadata.md | 5 + docs/api/abc/store.md | 5 + docs/api/api_async.md | 5 + docs/api/api_sync.md | 5 + docs/api/array.md | 2 + docs/api/buffer.md | 3 + docs/api/codecs.md | 5 + docs/api/config.md | 5 + docs/api/convenience.md | 10 + docs/api/create.md | 19 + docs/api/deprecated/convenience.md | 1 + docs/api/deprecated/creation.md | 1 + docs/api/dtype.md | 5 + docs/api/errors.md | 5 + docs/api/group.md | 2 + docs/api/index.md | 64 ++ docs/api/load.md | 5 + docs/api/open.md | 9 + docs/api/registry.md | 5 + docs/api/save.md | 7 + docs/api/storage.md | 11 + docs/api/testing.md | 23 + docs/conf.py | 387 ---------- docs/contributing.md | 233 ++++++ docs/developers/contributing.rst | 347 --------- docs/developers/index.rst | 9 - docs/developers/roadmap.rst | 696 ------------------ docs/index.md | 88 +++ docs/index.rst | 113 --- docs/overrides/main.html | 9 + docs/overrides/stylesheets/extra.css | 52 ++ docs/quick-start.md | 176 +++++ docs/quickstart.rst | 209 ------ docs/release-notes.md | 465 ++++++++++++ docs/release-notes.rst | 561 -------------- docs/talks/scipy2019/submission.rst | 144 ---- docs/user-guide/arrays.md | 575 +++++++++++++++ docs/user-guide/arrays.rst | 632 ---------------- docs/user-guide/attributes.md | 37 + docs/user-guide/attributes.rst | 30 - docs/user-guide/cli.md | 113 +++ docs/user-guide/cli.rst | 127 ---- docs/user-guide/config.md | 50 ++ docs/user-guide/config.rst | 83 --- docs/user-guide/consolidated_metadata.md | 123 ++++ docs/user-guide/consolidated_metadata.rst | 143 ---- docs/user-guide/data_types.md | 427 +++++++++++ docs/user-guide/data_types.rst | 455 ------------ .../{extending.rst => extending.md} | 74 +- docs/user-guide/gpu.md | 31 + docs/user-guide/gpu.rst | 37 - docs/user-guide/groups.md | 137 ++++ docs/user-guide/groups.rst | 172 ----- docs/user-guide/index.md | 41 ++ docs/user-guide/index.rst | 32 - docs/user-guide/installation.md | 59 ++ docs/user-guide/installation.rst | 67 -- docs/user-guide/performance.md | 206 ++++++ docs/user-guide/performance.rst | 278 ------- docs/user-guide/storage.md | 149 ++++ docs/user-guide/storage.rst | 158 ---- docs/user-guide/v3_migration.md | 228 ++++++ docs/user-guide/v3_migration.rst | 250 ------- mkdocs.yml | 198 +++++ pyproject.toml | 57 +- src/zarr/abc/store.py | 2 +- src/zarr/api/asynchronous.py | 54 +- src/zarr/api/synchronous.py | 79 +- src/zarr/codecs/numcodecs/_codecs.py | 11 +- src/zarr/convenience.py | 6 +- src/zarr/core/array.py | 434 ++++++----- src/zarr/core/attributes.py | 14 +- src/zarr/core/buffer/core.py | 2 +- src/zarr/core/buffer/cpu.py | 2 +- src/zarr/core/config.py | 18 +- src/zarr/core/dtype/npy/bool.py | 12 +- src/zarr/core/dtype/npy/bytes.py | 89 +-- src/zarr/core/dtype/npy/complex.py | 8 +- src/zarr/core/dtype/npy/float.py | 18 +- src/zarr/core/dtype/npy/int.py | 46 +- src/zarr/core/dtype/npy/string.py | 44 +- src/zarr/core/dtype/npy/structured.py | 42 +- src/zarr/core/dtype/npy/time.py | 98 +-- src/zarr/core/group.py | 167 +++-- src/zarr/core/indexing.py | 2 +- src/zarr/creation.py | 5 +- src/zarr/storage/_memory.py | 4 +- 105 files changed, 4317 insertions(+), 6231 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/_static/custom.css delete mode 100644 docs/_static/custom.js delete mode 100644 docs/_static/index_api.svg delete mode 100644 docs/_static/index_contribute.svg delete mode 100644 docs/_static/index_getting_started.svg delete mode 100644 docs/_static/index_user_guide.svg delete mode 100644 docs/about.rst create mode 100644 docs/api/abc/buffer.md create mode 100644 docs/api/abc/codec.md create mode 100644 docs/api/abc/metadata.md create mode 100644 docs/api/abc/store.md create mode 100644 docs/api/api_async.md create mode 100644 docs/api/api_sync.md create mode 100644 docs/api/array.md create mode 100644 docs/api/buffer.md create mode 100644 docs/api/codecs.md create mode 100644 docs/api/config.md create mode 100644 docs/api/convenience.md create mode 100644 docs/api/create.md create mode 100644 docs/api/deprecated/convenience.md create mode 100644 docs/api/deprecated/creation.md create mode 100644 docs/api/dtype.md create mode 100644 docs/api/errors.md create mode 100644 docs/api/group.md create mode 100644 docs/api/index.md create mode 100644 docs/api/load.md create mode 100644 docs/api/open.md create mode 100644 docs/api/registry.md create mode 100644 docs/api/save.md create mode 100644 docs/api/storage.md create mode 100644 docs/api/testing.md delete mode 100644 docs/conf.py create mode 100644 docs/contributing.md delete mode 100644 docs/developers/contributing.rst delete mode 100644 docs/developers/index.rst delete mode 100644 docs/developers/roadmap.rst create mode 100644 docs/index.md delete mode 100644 docs/index.rst create mode 100644 docs/overrides/main.html create mode 100644 docs/overrides/stylesheets/extra.css create mode 100644 docs/quick-start.md delete mode 100644 docs/quickstart.rst create mode 100644 docs/release-notes.md delete mode 100644 docs/release-notes.rst delete mode 100644 docs/talks/scipy2019/submission.rst create mode 100644 docs/user-guide/arrays.md delete mode 100644 docs/user-guide/arrays.rst create mode 100644 docs/user-guide/attributes.md delete mode 100644 docs/user-guide/attributes.rst create mode 100644 docs/user-guide/cli.md delete mode 100644 docs/user-guide/cli.rst create mode 100644 docs/user-guide/config.md delete mode 100644 docs/user-guide/config.rst create mode 100644 docs/user-guide/consolidated_metadata.md delete mode 100644 docs/user-guide/consolidated_metadata.rst create mode 100644 docs/user-guide/data_types.md delete mode 100644 docs/user-guide/data_types.rst rename docs/user-guide/{extending.rst => extending.md} (50%) create mode 100644 docs/user-guide/gpu.md delete mode 100644 docs/user-guide/gpu.rst create mode 100644 docs/user-guide/groups.md delete mode 100644 docs/user-guide/groups.rst create mode 100644 docs/user-guide/index.md delete mode 100644 docs/user-guide/index.rst create mode 100644 docs/user-guide/installation.md delete mode 100644 docs/user-guide/installation.rst create mode 100644 docs/user-guide/performance.md delete mode 100644 docs/user-guide/performance.rst create mode 100644 docs/user-guide/storage.md delete mode 100644 docs/user-guide/storage.rst create mode 100644 docs/user-guide/v3_migration.md delete mode 100644 docs/user-guide/v3_migration.rst create mode 100644 mkdocs.yml diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 9b64c97d0a..c36428b300 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -3,7 +3,7 @@ TODO: * [ ] Add unit tests and/or doctests in docstrings * [ ] Add docstrings and API docs for any new/modified user-facing classes and functions -* [ ] New/modified features documented in `docs/user-guide/*.rst` +* [ ] New/modified features documented in `docs/user-guide/*.md` * [ ] Changes documented as a new file in `changes/` * [ ] GitHub Actions have all passed * [ ] Test coverage is 100% (Codecov passes) diff --git a/.github/labeler.yml b/.github/labeler.yml index ede89c9d35..7eb74211ea 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -1,4 +1,4 @@ needs release notes: - all: - changed-files: - - all-globs-to-all-files: '!changes/*.rst' + - all-globs-to-all-files: '!changes/*.md' diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 70303060ea..e58c8f9dc9 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -129,11 +129,11 @@ jobs: pip install hatch - name: Set Up Hatch Env run: | - hatch env create doctest - hatch env run -e doctest list-env + hatch env create docs + hatch env run -e docs list-env - name: Run Tests run: | - hatch env run --env doctest run + hatch env run --env docs check test-complete: name: Test complete diff --git a/.gitignore b/.gitignore index 1b2b63e651..f2f41270ca 100644 --- a/.gitignore +++ b/.gitignore @@ -49,9 +49,9 @@ coverage.xml # Django stuff: *.log -# Sphinx documentation +# Documentation +site/ docs/_build/ -docs/api docs/data data data.zip diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3a75601daa..3e2826f10f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,6 +20,7 @@ repos: rev: v6.0.0 hooks: - id: check-yaml + exclude: mkdocs.yml - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.17.1 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 6253a7196f..894778c5a4 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -11,12 +11,11 @@ build: then towncrier build --version Unreleased --yes; fi - -sphinx: - configuration: docs/conf.py - fail_on_warning: true - -formats: all + build: + html: + - mkdocs build --strict --site-dir $READTHEDOCS_OUTPUT/html +mkdocs: + configuration: mkdocs.yml python: install: @@ -24,3 +23,4 @@ python: path: . extra_requirements: - docs + - remote diff --git a/changes/README.md b/changes/README.md index 74ed9f94a9..889a52baa4 100644 --- a/changes/README.md +++ b/changes/README.md @@ -1,7 +1,7 @@ Writing a changelog entry ------------------------- -Please put a new file in this directory named `xxxx..rst`, where +Please put a new file in this directory named `xxxx..md`, where - `xxxx` is the pull request number associated with this entry - `` is one of: diff --git a/ci/check_changelog_entries.py b/ci/check_changelog_entries.py index 9f883f0be4..da2700e32a 100644 --- a/ci/check_changelog_entries.py +++ b/ci/check_changelog_entries.py @@ -25,13 +25,13 @@ def is_int(s: str) -> bool: print(f"Found {len(entries)} entries") print() - bad_suffix = [e for e in entries if e.suffix != ".rst"] + bad_suffix = [e for e in entries if e.suffix != ".md"] bad_issue_no = [e for e in entries if not is_int(e.name.split(".")[0])] bad_type = [e for e in entries if e.name.split(".")[1] not in VALID_CHANGELOG_TYPES] if len(bad_suffix) or len(bad_issue_no) or len(bad_type): if len(bad_suffix): - print("Changelog entries without .rst suffix") + print("Changelog entries without .md suffix") print("-------------------------------------") print("\n".join([p.name for p in bad_suffix])) print() diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index f42ee840e9..0000000000 --- a/docs/Makefile +++ /dev/null @@ -1,231 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -W --keep-going -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) - $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from https://www.sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " applehelp to make an Apple Help Book" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " epub3 to make an epub3" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - @echo " coverage to run coverage check of the documentation (if enabled)" - @echo " dummy to check syntax errors of document sources" - -.PHONY: clean -clean: - rm -rf $(BUILDDIR)/* - rm -rf $(BUILDDIR)/../api - -.PHONY: html -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -.PHONY: dirhtml -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -.PHONY: singlehtml -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -.PHONY: pickle -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -.PHONY: json -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -.PHONY: htmlhelp -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -.PHONY: qthelp -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/zarr.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/zarr.qhc" - -.PHONY: applehelp -applehelp: - $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp - @echo - @echo "Build finished. The help book is in $(BUILDDIR)/applehelp." - @echo "N.B. You won't be able to view it unless you put it in" \ - "~/Library/Documentation/Help or install it in your application" \ - "bundle." - -.PHONY: devhelp -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/zarr" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/zarr" - @echo "# devhelp" - -.PHONY: epub -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -.PHONY: epub3 -epub3: - $(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3 - @echo - @echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3." - -.PHONY: latex -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -.PHONY: latexpdf -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -.PHONY: latexpdfja -latexpdfja: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through platex and dvipdfmx..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -.PHONY: text -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -.PHONY: man -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -.PHONY: texinfo -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -.PHONY: info -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -.PHONY: gettext -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." - -.PHONY: changes -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -.PHONY: linkcheck -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -.PHONY: doctest -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." - -.PHONY: coverage -coverage: - $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage - @echo "Testing of coverage in the sources finished, look at the " \ - "results in $(BUILDDIR)/coverage/python.txt." - -.PHONY: xml -xml: - $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml - @echo - @echo "Build finished. The XML files are in $(BUILDDIR)/xml." - -.PHONY: pseudoxml -pseudoxml: - $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml - @echo - @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." - -.PHONY: dummy -dummy: - $(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy - @echo - @echo "Build finished. Dummy builder generates no files." diff --git a/docs/_static/custom.css b/docs/_static/custom.css deleted file mode 100644 index 1d32606f9a..0000000000 --- a/docs/_static/custom.css +++ /dev/null @@ -1,110 +0,0 @@ -@import url('https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;0,900;1,400;1,700;1,900&family=Open+Sans:ital,wght@0,400;0,600;1,400;1,600&display=swap'); - -body { - font-family: 'Open Sans', sans-serif; -} - -pre, code { - font-size: 100%; - line-height: 155%; -} - -/* Style the active version button. - -- dev: orange -- stable: green -- old, PR: red - -Colors from: - -Wong, B. Points of view: Color blindness. -Nat Methods 8, 441 (2011). https://doi.org/10.1038/nmeth.1618 -*/ - -/* If the active version has the name "dev", style it orange */ -#version_switcher_button[data-active-version-name*="dev"] { - background-color: #E69F00; - border-color: #E69F00; - color:#000000; -} - -/* green for `stable` */ -#version_switcher_button[data-active-version-name*="stable"] { - background-color: #009E73; - border-color: #009E73; -} - -/* red for `old` */ -#version_switcher_button:not([data-active-version-name*="stable"], [data-active-version-name*="dev"], [data-active-version-name=""]) { - background-color: #980F0F; - border-color: #980F0F; -} - -/* Main page overview cards */ - -.sd-card { - background: #fff; - border-radius: 0; - padding: 30px 10px 20px 10px; - margin: 10px 0px; -} - -.sd-card .sd-card-header { - text-align: center; -} - -.sd-card .sd-card-header .sd-card-text { - margin: 0px; -} - -.sd-card .sd-card-img-top { - height: 52px; - width: 52px; - margin-left: auto; - margin-right: auto; -} - -.sd-card .sd-card-header { - border: none; - background-color: white; - font-size: var(--pst-font-size-h5); - font-weight: bold; - padding: 2.5rem 0rem 0.5rem 0rem; -} - -.sd-card .sd-card-footer { - border: none; - background-color: white; -} - -.sd-card .sd-card-footer .sd-card-text { - max-width: 220px; - margin-left: auto; - margin-right: auto; -} - -/* Dark theme tweaking */ -html[data-theme=dark] .sd-card img[src*='.svg'] { - filter: invert(0.82) brightness(0.8) contrast(1.2); -} - -/* Main index page overview cards */ -html[data-theme=dark] .sd-card { - background-color:var(--pst-color-background); -} - -html[data-theme=dark] .sd-shadow-sm { - box-shadow: 0 .1rem 1rem rgba(250, 250, 250, .6) !important -} - -html[data-theme=dark] .sd-card .sd-card-header { - background-color:var(--pst-color-background); -} - -html[data-theme=dark] .sd-card .sd-card-footer { - background-color:var(--pst-color-background); -} - -html[data-theme=dark] h1 { - color: var(--pst-color-primary); -} diff --git a/docs/_static/custom.js b/docs/_static/custom.js deleted file mode 100644 index 52f1cba9e0..0000000000 --- a/docs/_static/custom.js +++ /dev/null @@ -1,17 +0,0 @@ -// handle redirects -(() => { - let anchorMap = { - "installation": "installation.html", - "getting-started": "getting_started.html#getting-started", - "highlights": "getting_started.html#highlights", - "contributing": "contributing.html", - "projects-using-zarr": "getting_started.html#projects-using-zarr", - "contents": "getting_started.html#contents", - "indices-and-tables": "api.html#indices-and-tables" - } - - let hash = window.location.hash.substring(1); - if (hash && hash in anchorMap) { - window.location.replace(anchorMap[hash]); - } -})(); diff --git a/docs/_static/index_api.svg b/docs/_static/index_api.svg deleted file mode 100644 index 69f7ba1d2d..0000000000 --- a/docs/_static/index_api.svg +++ /dev/null @@ -1,97 +0,0 @@ - - - - - - - - - - image/svg+xml - - - - - - - - - - - - - - - - - diff --git a/docs/_static/index_contribute.svg b/docs/_static/index_contribute.svg deleted file mode 100644 index de3d902379..0000000000 --- a/docs/_static/index_contribute.svg +++ /dev/null @@ -1,76 +0,0 @@ - - - - - - - - - - image/svg+xml - - - - - - - - - - - - diff --git a/docs/_static/index_getting_started.svg b/docs/_static/index_getting_started.svg deleted file mode 100644 index 2d36622cb7..0000000000 --- a/docs/_static/index_getting_started.svg +++ /dev/null @@ -1,66 +0,0 @@ - - - - - - - - - - image/svg+xml - - - - - - - - - diff --git a/docs/_static/index_user_guide.svg b/docs/_static/index_user_guide.svg deleted file mode 100644 index bd17053517..0000000000 --- a/docs/_static/index_user_guide.svg +++ /dev/null @@ -1,67 +0,0 @@ - - - - - - - - - - image/svg+xml - - - - - - - - - diff --git a/docs/about.rst b/docs/about.rst deleted file mode 100644 index d2844dc864..0000000000 --- a/docs/about.rst +++ /dev/null @@ -1,24 +0,0 @@ -About -===== - -Zarr is a format for the storage of chunked, compressed, N-dimensional arrays -inspired by `HDF5 `_, `h5py -`_ and `bcolz `_. - -These documents describe the Zarr-Python implementation. More information -about the Zarr format can be found on the `main website `_. - -Projects using Zarr -------------------- - -If you are using Zarr-Python, we would `love to hear about it -`_. - -Funding -------- -The project is fiscally sponsored by `NumFOCUS `_, a US -501(c)(3) public charity, and development is supported by the -`MRC Centre for Genomics and Global Health `_ -and the `Chan Zuckerberg Initiative `_. - -.. _NumCodecs: https://numcodecs.readthedocs.io/ diff --git a/docs/api/abc/buffer.md b/docs/api/abc/buffer.md new file mode 100644 index 0000000000..ac814d20b6 --- /dev/null +++ b/docs/api/abc/buffer.md @@ -0,0 +1,5 @@ +--- +title: buffer +--- + +::: zarr.abc.buffer diff --git a/docs/api/abc/codec.md b/docs/api/abc/codec.md new file mode 100644 index 0000000000..d4eaecabe9 --- /dev/null +++ b/docs/api/abc/codec.md @@ -0,0 +1,5 @@ +--- +title: codec +--- + +::: zarr.abc.codec diff --git a/docs/api/abc/metadata.md b/docs/api/abc/metadata.md new file mode 100644 index 0000000000..7cc1e00662 --- /dev/null +++ b/docs/api/abc/metadata.md @@ -0,0 +1,5 @@ +--- +title: metadata +--- + +::: zarr.abc.metadata diff --git a/docs/api/abc/store.md b/docs/api/abc/store.md new file mode 100644 index 0000000000..f711448541 --- /dev/null +++ b/docs/api/abc/store.md @@ -0,0 +1,5 @@ +--- +title: store +--- + +::: zarr.abc.store diff --git a/docs/api/api_async.md b/docs/api/api_async.md new file mode 100644 index 0000000000..f5df894134 --- /dev/null +++ b/docs/api/api_async.md @@ -0,0 +1,5 @@ +--- +title: asynchronous +--- + +::: zarr.api.asynchronous \ No newline at end of file diff --git a/docs/api/api_sync.md b/docs/api/api_sync.md new file mode 100644 index 0000000000..83ff118db5 --- /dev/null +++ b/docs/api/api_sync.md @@ -0,0 +1,5 @@ +--- +title: synchronous +--- + +::: zarr.api.synchronous \ No newline at end of file diff --git a/docs/api/array.md b/docs/api/array.md new file mode 100644 index 0000000000..ff61cb1fe2 --- /dev/null +++ b/docs/api/array.md @@ -0,0 +1,2 @@ +::: zarr.Array +::: zarr.AsyncArray diff --git a/docs/api/buffer.md b/docs/api/buffer.md new file mode 100644 index 0000000000..aa089957cf --- /dev/null +++ b/docs/api/buffer.md @@ -0,0 +1,3 @@ +::: zarr.buffer +::: zarr.buffer.cpu +::: zarr.buffer.gpu diff --git a/docs/api/codecs.md b/docs/api/codecs.md new file mode 100644 index 0000000000..5cf66b304e --- /dev/null +++ b/docs/api/codecs.md @@ -0,0 +1,5 @@ +--- +title: codecs +--- + +::: zarr.codecs \ No newline at end of file diff --git a/docs/api/config.md b/docs/api/config.md new file mode 100644 index 0000000000..30803918f5 --- /dev/null +++ b/docs/api/config.md @@ -0,0 +1,5 @@ +--- +title: config +--- + +::: zarr.config diff --git a/docs/api/convenience.md b/docs/api/convenience.md new file mode 100644 index 0000000000..f2614e3724 --- /dev/null +++ b/docs/api/convenience.md @@ -0,0 +1,10 @@ +--- +title: convenience +--- + +::: zarr.consolidate_metadata +::: zarr.copy +::: zarr.copy_all +::: zarr.copy_store +::: zarr.print_debug_info +::: zarr.tree diff --git a/docs/api/create.md b/docs/api/create.md new file mode 100644 index 0000000000..971e9c293c --- /dev/null +++ b/docs/api/create.md @@ -0,0 +1,19 @@ +--- +title: create +--- + +::: zarr.array +::: zarr.create +::: zarr.create_array +::: zarr.create_group +::: zarr.create_hierarchy +::: zarr.empty +::: zarr.empty_like +::: zarr.full +::: zarr.full_like +::: zarr.from_array +::: zarr.group +::: zarr.ones +::: zarr.ones_like +::: zarr.zeros +::: zarr.zeros_like diff --git a/docs/api/deprecated/convenience.md b/docs/api/deprecated/convenience.md new file mode 100644 index 0000000000..91bcb15f71 --- /dev/null +++ b/docs/api/deprecated/convenience.md @@ -0,0 +1 @@ +::: zarr.convenience \ No newline at end of file diff --git a/docs/api/deprecated/creation.md b/docs/api/deprecated/creation.md new file mode 100644 index 0000000000..5d18a06a4a --- /dev/null +++ b/docs/api/deprecated/creation.md @@ -0,0 +1 @@ +::: zarr.creation diff --git a/docs/api/dtype.md b/docs/api/dtype.md new file mode 100644 index 0000000000..c08910b97f --- /dev/null +++ b/docs/api/dtype.md @@ -0,0 +1,5 @@ +--- +title: dtype +--- + +::: zarr.dtype diff --git a/docs/api/errors.md b/docs/api/errors.md new file mode 100644 index 0000000000..2ba2213071 --- /dev/null +++ b/docs/api/errors.md @@ -0,0 +1,5 @@ +--- +title: errors +--- + +::: zarr.errors \ No newline at end of file diff --git a/docs/api/group.md b/docs/api/group.md new file mode 100644 index 0000000000..0cf9372de2 --- /dev/null +++ b/docs/api/group.md @@ -0,0 +1,2 @@ +::: zarr.Group +::: zarr.AsyncGroup diff --git a/docs/api/index.md b/docs/api/index.md new file mode 100644 index 0000000000..8e6be1058e --- /dev/null +++ b/docs/api/index.md @@ -0,0 +1,64 @@ +# API Reference + +Complete reference documentation for the Zarr-Python API. + +## Core API + +### Essential Classes and Functions + +- **[Array](array.md)** - The main Zarr array class for N-dimensional data +- **[Group](group.md)** - Hierarchical organization of arrays and subgroups +- **[Create](create.md)** - Functions for creating new arrays and groups +- **[Open](open.md)** - Opening existing Zarr stores and arrays + +### Data Operations + +- **[Load](load.md)** - Loading data from Zarr stores +- **[Save](save.md)** - Saving data to Zarr format +- **[Convenience](convenience.md)** - High-level convenience functions + +### Data Types and Configuration + +- **[Data Types](dtype.md)** - Supported NumPy data types and type handling +- **[Configuration](config.md)** - Runtime configuration and settings + +## Storage and Compression + +- **[Codecs](codecs.md)** - Compression and filtering codecs +- **[Storage](storage.md)** - Storage backend implementations and interfaces +- **[Registry](registry.md)** - Codec and storage backend registry + +## API Variants + +Zarr-Python provides both synchronous and asynchronous APIs: + +- **[Async API](api_async.md)** - Asynchronous operations for concurrent access +- **[Sync API](api_sync.md)** - Synchronous operations for simple usage + +## Abstract Base Classes + +The ABC module defines interfaces for extending Zarr: + +- **[Codec ABC](abc/codec.md)** - Interface for custom compression codecs +- **[Metadata ABC](abc/metadata.md)** - Interface for metadata handling +- **[Store ABC](abc/store.md)** - Interface for custom storage backends + +## Utilities + +- **[Errors](errors.md)** - Exception classes and error handling +- **[Testing](testing.md)** - Utilities for testing Zarr-based code + + +## Migration and Compatibility + +- **[Deprecated Functions](deprecated/convenience.md)** - Legacy convenience functions +- **[Deprecated Creation](deprecated/creation.md)** - Legacy array creation functions + +These deprecated modules are maintained for backward compatibility but should be avoided in new code. + +## Getting Help + +- Check the [User Guide](../user-guide/index.md) for tutorials and examples +- Browse function signatures and docstrings in the API reference +- Report issues on [GitHub](https://github.com/zarr-developers/zarr-python) +- Join discussions on the [Zarr community forum](https://github.com/zarr-developers/community) diff --git a/docs/api/load.md b/docs/api/load.md new file mode 100644 index 0000000000..d6463ca976 --- /dev/null +++ b/docs/api/load.md @@ -0,0 +1,5 @@ +--- +title: load +--- + +::: zarr.load diff --git a/docs/api/open.md b/docs/api/open.md new file mode 100644 index 0000000000..c59f896129 --- /dev/null +++ b/docs/api/open.md @@ -0,0 +1,9 @@ +--- +title: open +--- + +::: zarr.open +::: zarr.open_array +::: zarr.open_consolidated +::: zarr.open_group +::: zarr.open_like diff --git a/docs/api/registry.md b/docs/api/registry.md new file mode 100644 index 0000000000..d2c3769596 --- /dev/null +++ b/docs/api/registry.md @@ -0,0 +1,5 @@ +--- +title: registry +--- + +::: zarr.registry \ No newline at end of file diff --git a/docs/api/save.md b/docs/api/save.md new file mode 100644 index 0000000000..c611d10a4c --- /dev/null +++ b/docs/api/save.md @@ -0,0 +1,7 @@ +--- +title: save +--- + +::: zarr.save +::: zarr.save_array +::: zarr.save_group diff --git a/docs/api/storage.md b/docs/api/storage.md new file mode 100644 index 0000000000..33580d1d8a --- /dev/null +++ b/docs/api/storage.md @@ -0,0 +1,11 @@ +--- +title: storage +--- + +## Attributes + +::: zarr.storage.StoreLike + +## Classes + +::: zarr.storage diff --git a/docs/api/testing.md b/docs/api/testing.md new file mode 100644 index 0000000000..1412950ee3 --- /dev/null +++ b/docs/api/testing.md @@ -0,0 +1,23 @@ +--- +title: testing +--- + +## Buffer + +::: zarr.testing.buffer + +## Stateful + +::: zarr.testing.stateful + +## Store + +::: zarr.testing.store + +## Strategies + +::: zarr.testing.strategies + +## Utils + +::: zarr.testing.utils diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 803d2c4255..0000000000 --- a/docs/conf.py +++ /dev/null @@ -1,387 +0,0 @@ -#!/usr/bin/env python3 -# -# zarr documentation build configuration file, created by -# sphinx-quickstart on Mon May 2 21:40:09 2016. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - - -import os -import sys -from importlib.metadata import version as get_version -from typing import Any - -import sphinx -import sphinx.application - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -sys.path.append(os.path.abspath("..")) - - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.autosummary", - "sphinx.ext.intersphinx", - 'autoapi.extension', - "numpydoc", - "sphinx_issues", - "sphinx_copybutton", - "sphinx_design", - 'sphinx_reredirects', - "sphinx.ext.viewcode", -] - -issues_github_path = "zarr-developers/zarr-python" - -autoapi_dirs = ['../src/zarr'] -autoapi_add_toctree_entry = False -autoapi_generate_api_docs = True -autoapi_member_order = "groupwise" -autoapi_root = "api" -autoapi_keep_files = True -autoapi_options = [ 'members', 'undoc-members', 'show-inheritance', 'show-module-summary', 'imported-members', 'inherited-members'] - -def skip_submodules( - app: sphinx.application.Sphinx, - what: str, - name: str, - obj: object, - skip: bool, - options: dict[str, Any] - ) -> bool: - # Skip documenting zarr.codecs submodules - # codecs are documented in the main zarr.codecs namespace - if what == "module" and name.startswith("zarr.codecs.") or name.startswith("zarr.core"): - skip = True - return skip - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# source_suffix = ['.rst', '.md'] -source_suffix = ".rst" - -# The encoding of source files. -# source_encoding = 'utf-8-sig' - -# The main toctree document. -main_doc = "index" - -# General information about the project. -project = "zarr" -copyright = "2025, Zarr Developers" -author = "Zarr Developers" - -version = get_version("zarr") -release = get_version("zarr") - -redirects = { - "spec": "https://zarr-specs.readthedocs.io", - "spec/v1": 'https://zarr-specs.readthedocs.io/en/latest/v1/v1.0.html', - "spec/v2": "https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html", - "spec/v3": "https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html", - "license": "https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt", - "tutorial": "user-guide", - "getting-started": "quickstart", - "roadmap": "developers/roadmap.html", - "installation": "user-guide/installation.html", - "api": "api/zarr/index", - "release": "release-notes.html", -} - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = "en" - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "talks"] - -# The reST default role (used for this markup: `text`) to use for all -# documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# A list of ignored prefixes for module index sorting. -# modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -# keep_warnings = False - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = "pydata_sphinx_theme" - -html_favicon = "_static/logo1.png" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -html_theme_options = { - "github_url": "https://github.com/zarr-developers/zarr-python", - "icon_links": [ - { - "name": "Bluesky", - "url": "https://bsky.app/profile/zarr.dev", - "icon": "fa-brands fa-bluesky", - }, - { - "name": "Mastodon", - "url": "https://fosstodon.org/@zarr", - "icon": "fa-brands fa-mastodon", - }, - { - "name": "Zarr Dev", - "url": "https://zarr.dev/", - "icon": "_static/logo1.png", - "type": "local", - }, - ], - "collapse_navigation": True, - "navigation_with_keys": False, -} - -# Add any paths that contain custom themes here, relative to this directory. -# html_theme_path = [] - -# The name for this set of Sphinx documents. -# " v documentation" by default. -# html_title = 'zarr v@@' - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -html_logo = "_static/logo_horizontal.svg" - - -def setup(app: sphinx.application.Sphinx) -> None: - app.add_css_file("custom.css") - app.connect("autoapi-skip-member", skip_submodules) - - -# The name of an image file (relative to this directory) to use as a favicon of -# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] -html_js_files = [ - "custom.js", -] - -# Add any extra paths that contain custom files (such as robots.txt or -# .htaccess) here, relative to this directory. These files are copied -# directly to the root of the documentation. -# html_extra_path = [] - -# If not None, a 'Last updated on:' timestamp is inserted at every page -# bottom, using the given strftime format. -# The empty string is equivalent to '%b %d, %Y'. -# html_last_updated_fmt = None - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -html_sidebars = {"tutorial": []} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -# html_additional_pages = {} - -# If false, no module index is generated. -# html_domain_indices = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, links to the reST sources are added to the pages. -# html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -# html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -# html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = None - -# Language to be used for generating the HTML full-text search index. -# Sphinx supports the following languages: -# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' -# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh' -# html_search_language = 'en' - -# A dictionary with options for the search language support, empty by default. -# 'ja' uses this config value. -# 'zh' user can custom change `jieba` dictionary path. -# html_search_options = {'type': 'default'} - -# The name of a javascript file (relative to the configuration directory) that -# implements a search results scorer. If empty, the default will be used. -# html_search_scorer = 'scorer.js' - -# Output file base name for HTML help builder. -htmlhelp_basename = "zarrdoc" - -maximum_signature_line_length = 80 - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - #'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). - #'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. - #'preamble': '', - # Latex figure (float) alignment - #'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (main_doc, "zarr.tex", "Zarr-Python", author, "manual"), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False - -# If true, show page references after internal links. -# latex_show_pagerefs = False - -# If true, show URL addresses after external links. -# latex_show_urls = False - -# Documents to append as an appendix to all manuals. -# latex_appendices = [] - -# If false, no module index is generated. -# latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [(main_doc, "zarr", "Zarr-Python", [author], 1)] - -# If true, show URL addresses after external links. -# man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ( - main_doc, - "zarr", - "Zarr-Python", - author, - "zarr", - "One line description of project.", - "Miscellaneous", - ), -] - -# Documents to append as an appendix to all manuals. -# texinfo_appendices = [] - -# If false, no module index is generated. -# texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -# texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -# texinfo_no_detailmenu = False - - -# Example configuration for intersphinx: refer to the Python standard library. -# use in refs e.g: -# :ref:`comparison manual ` -intersphinx_mapping = { - "python": ("https://docs.python.org/3/", None), - "numpy": ("https://numpy.org/doc/stable/", None), - "numcodecs": ("https://numcodecs.readthedocs.io/en/stable/", None), - "obstore": ("https://developmentseed.org/obstore/latest/", None), -} - - -# sphinx-copybutton configuration -copybutton_prompt_text = r">>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: " -copybutton_line_continuation_character = "\\" -copybutton_prompt_is_regexp = True diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 0000000000..7bfa6f6a18 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,233 @@ +# Contributing + +Zarr is a community maintained project. We welcome contributions in the form of bug reports, bug fixes, documentation, enhancement proposals and more. This page provides information on how best to contribute. + +## Asking for help + +If you have a question about how to use Zarr, please post your question on StackOverflow using the ["zarr" tag](https://stackoverflow.com/questions/tagged/zarr). If you don't get a response within a day or two, feel free to raise a [GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new) including a link to your StackOverflow question. We will try to respond to questions as quickly as possible, but please bear in mind that there may be periods where we have limited time to answer questions due to other commitments. + +## Bug reports + +If you find a bug, please raise a [GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new). Please include the following items in a bug report: + +1. A minimal, self-contained snippet of Python code reproducing the problem. You can format the code nicely using markdown, e.g.: + +```python +import zarr +g = zarr.group() +# etc. +``` + +2. An explanation of why the current behaviour is wrong/not desired, and what you expect instead. + +3. Information about the version of Zarr, along with versions of dependencies and the Python interpreter, and installation information. The version of Zarr can be obtained from the `zarr.__version__` property. Please also state how Zarr was installed, e.g., "installed via pip into a virtual environment", or "installed using conda". Information about other packages installed can be obtained by executing `pip freeze` (if using pip to install packages) or `conda env export` (if using conda to install packages) from the operating system command prompt. The version of the Python interpreter can be obtained by running a Python interactive session, e.g.: + +```console +python +``` + +```ansi +Python 3.12.7 | packaged by conda-forge | (main, Oct 4 2024, 15:57:01) [Clang 17.0.6 ] on darwin +``` + +## Enhancement proposals + +If you have an idea about a new feature or some other improvement to Zarr, please raise a [GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new) first to discuss. + +We very much welcome ideas and suggestions for how to improve Zarr, but please bear in mind that we are likely to be conservative in accepting proposals for new features. The reasons for this are that we would like to keep the Zarr code base lean and focused on a core set of functionalities, and available time for development, review and maintenance of new features is limited. But if you have a great idea, please don't let that stop you from posting it on GitHub, just please don't be offended if we respond cautiously. + +## Contributing code and/or documentation + +### Forking the repository + +The Zarr source code is hosted on GitHub at the following location: + +* [https://github.com/zarr-developers/zarr-python](https://github.com/zarr-developers/zarr-python) + +You will need your own fork to work on the code. Go to the link above and hit the ["Fork"](https://github.com/zarr-developers/zarr-python/fork) button. Then clone your fork to your local machine: + +```bash +git clone git@github.com:your-user-name/zarr-python.git +cd zarr-python +git remote add upstream git@github.com:zarr-developers/zarr-python.git +``` + +### Creating a development environment + +To work with the Zarr source code, it is recommended to use [hatch](https://hatch.pypa.io/latest/index.html) to create and manage development environments. Hatch will automatically install all Zarr dependencies using the same versions as are used by the core developers and continuous integration services. Assuming you have a Python 3 interpreter already installed, and you have cloned the Zarr source code and your current working directory is the root of the repository, you can do something like the following: + +```bash +pip install hatch +hatch env show # list all available environments +``` + +To verify that your development environment is working, you can run the unit tests for one of the test environments, e.g.: + +```bash +hatch env run --env test.py3.12-2.2-optional run-pytest +``` + +### Creating a branch + +Before you do any new work or submit a pull request, please open an issue on GitHub to report the bug or propose the feature you'd like to add. + +It's best to synchronize your fork with the upstream repository, then create a new, separate branch for each piece of work you want to do. E.g.: + +```bash +git checkout main +git fetch upstream +git checkout -b shiny-new-feature upstream/main +git push -u origin shiny-new-feature +``` + +This changes your working directory to the 'shiny-new-feature' branch. Keep any changes in this branch specific to one bug or feature so it is clear what the branch brings to Zarr. + +To update this branch with latest code from Zarr, you can retrieve the changes from the main branch and perform a rebase: + +```bash +git fetch upstream +git rebase upstream/main +``` + +This will replay your commits on top of the latest Zarr git main. If this leads to merge conflicts, these need to be resolved before submitting a pull request. Alternatively, you can merge the changes in from upstream/main instead of rebasing, which can be simpler: + +```bash +git pull upstream main +``` + +Again, any conflicts need to be resolved before submitting a pull request. + +### Running the test suite + +Zarr includes a suite of unit tests. The simplest way to run the unit tests is to activate your development environment (see [creating a development environment](#creating-a-development-environment) above) and invoke: + +```bash +hatch env run --env test.py3.12-2.2-optional run-pytest +``` + +All tests are automatically run via GitHub Actions for every pull request and must pass before code can be accepted. Test coverage is also collected automatically via the Codecov service. + +> **Note:** Previous versions of Zarr-Python made extensive use of doctests. These tests were not maintained during the 3.0 refactor but may be brought back in the future. See issue #2614 for more details. + +### Code standards - using pre-commit + +All code must conform to the PEP8 standard. Regarding line length, lines up to 100 characters are allowed, although please try to keep under 90 wherever possible. + +`Zarr` uses a set of `pre-commit` hooks and the `pre-commit` bot to format, type-check, and prettify the codebase. `pre-commit` can be installed locally by running: + +```bash +python -m pip install pre-commit +``` + +The hooks can be installed locally by running: + +```bash +pre-commit install +``` + +This would run the checks every time a commit is created locally. These checks will also run on every commit pushed to an open PR, resulting in some automatic styling fixes by the `pre-commit` bot. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running: + +```bash +pre-commit run --all-files +``` + +If you would like to skip the failing checks and push the code for further discussion, use the `--no-verify` option with `git commit`. + +### Test coverage + +> **Note:** Test coverage for Zarr-Python 3 is currently not at 100%. This is a known issue and help is welcome to bring test coverage back to 100%. See issue #2613 for more details. + +Zarr strives to maintain 100% test coverage under the latest Python stable release. Both unit tests and docstring doctests are included when computing coverage. Running: + +```bash +hatch env run --env test.py3.12-2.2-optional run-coverage +``` + +will automatically run the test suite with coverage and produce a XML coverage report. This should be 100% before code can be accepted into the main code base. + +You can also generate an HTML coverage report by running: + +```bash +hatch env run --env test.py3.12-2.2-optional run-coverage-html +``` + +When submitting a pull request, coverage will also be collected across all supported Python versions via the Codecov service, and will be reported back within the pull request. Codecov coverage must also be 100% before code can be accepted. + +### Documentation + +Docstrings for user-facing classes and functions should follow the [numpydoc](https://numpydoc.readthedocs.io/en/stable/format.html#docstring-standard) standard, including sections for Parameters and Examples. All examples should run and pass as doctests under Python 3.11. + +Zarr uses mkdocs for documentation, hosted on readthedocs.org. Documentation is written in the Markdown markup language (.md files) in the `docs` folder. The documentation consists both of prose and API documentation. All user-facing classes and functions are included in the API documentation, under the `docs/api` folder using the [mkdocstrings](https://mkdocstrings.github.io/) extension. Add any new public functions or classes to the relevant markdown file in `docs/api/*.md`. Any new features or important usage information should be included in the user-guide (`docs/user-guide`). Any changes should also be included as a new file in the `changes` directory. + +The documentation can be built locally by running: + +```bash +hatch --env docs run build +``` + +The resulting built documentation will be available in the `docs/_build/html` folder. + +Hatch can also be used to serve continuously updating version of the documentation during development at [http://0.0.0.0:8000/](http://0.0.0.0:8000/). This can be done by running: + +```bash +hatch --env docs run serve +``` + +### Changelog + +zarr-python uses [towncrier](https://towncrier.readthedocs.io/en/stable/tutorial.html) to manage release notes. Most pull requests should include at least one news fragment describing the changes. To add a release note, you'll need the GitHub issue or pull request number and the type of your change (`feature`, `bugfix`, `doc`, `removal`, `misc`). With that, run `towncrier create` with your development environment, which will prompt you for the issue number, change type, and the news text: + +```bash +towncrier create +``` + +Alternatively, you can manually create the files in the `changes` directory using the naming convention `{issue-number}.{change-type}.md`. + +See the [towncrier](https://towncrier.readthedocs.io/en/stable/tutorial.html) docs for more. + +## Merging pull requests + +Pull requests submitted by an external contributor should be reviewed and approved by at least one core developer before being merged. Ideally, pull requests submitted by a core developer should be reviewed and approved by at least one other core developer before being merged. + +Pull requests should not be merged until all CI checks have passed (GitHub Actions, Codecov) against code that has had the latest main merged in. + +Before merging the milestone must be set either to decide whether a PR will be in the next patch, minor, or major release. The next section explains which types of changes go in each release. + +## Compatibility and versioning policies + +### Versioning + +Versions of this library are identified by a triplet of integers with the form `..`, for example `3.0.4`. A release of `zarr-python` is associated with a new version identifier. That new identifier is generated by incrementing exactly one of the components of the previous version identifier by 1. When incrementing the `major` component of the version identifier, the `minor` and `patch` components is reset to 0. When incrementing the minor component, the patch component is reset to 0. + +Releases are classified by the library changes contained in that release. This classification determines which component of the version identifier is incremented on release. + +* **major** releases (for example, `2.18.0` -> `3.0.0`) are for changes that will require extensive adaptation efforts from many users and downstream projects. For example, breaking changes to widely-used user-facing APIs should only be applied in a major release. + + Users and downstream projects should carefully consider the impact of a major release before adopting it. In advance of a major release, developers should communicate the scope of the upcoming changes, and help users prepare for them. + +* **minor** releases (for example, `3.0.0` -> `3.1.0`) are for changes that do not require significant effort from most users or downstream downstream projects to respond to. API changes are possible in minor releases if the burden on users imposed by those changes is sufficiently small. + + For example, a recently released API may need fixes or refinements that are breaking, but low impact due to the recency of the feature. Such API changes are permitted in a minor release. + + Minor releases are safe for most users and downstream projects to adopt. + +* **patch** releases (for example, `3.1.0` -> `3.1.1`) are for changes that contain no breaking or behaviour changes for downstream projects or users. Examples of changes suitable for a patch release are bugfixes and documentation improvements. + + Users should always feel safe upgrading to a the latest patch release. + +Note that this versioning scheme is not consistent with [Semantic Versioning](https://semver.org/). Contrary to SemVer, the Zarr library may release breaking changes in `minor` releases, or even `patch` releases under exceptional circumstances. But we should strive to avoid doing so. + +A better model for our versioning scheme is [Intended Effort Versioning](https://jacobtomlinson.dev/effver/), or "EffVer". The guiding principle off EffVer is to categorize releases based on the *expected effort required to upgrade to that release*. + +Zarr developers should make changes as smooth as possible for users. This means making backwards-compatible changes wherever possible. When a backwards-incompatible change is necessary, users should be notified well in advance, e.g. via informative deprecation warnings. + +### Data format compatibility + +The Zarr library is an implementation of a file format standard defined externally -- see the [Zarr specifications website](https://zarr-specs.readthedocs.io) for the list of Zarr file format specifications. + +If an existing Zarr format version changes, or a new version of the Zarr format is released, then the Zarr library will generally require changes. It is very likely that a new Zarr format will require extensive breaking changes to the Zarr library, and so support for a new Zarr format in the Zarr library will almost certainly come in new `major` release. When the Zarr library adds support for a new Zarr format, there may be a period of accelerated changes as developers refine newly added APIs and deprecate old APIs. In such a transitional phase breaking changes may be more frequent than usual. + +## Release procedure + +Open an issue on GitHub announcing the release using the release checklist template: +[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md>). The release checklist includes all steps necessary for the release. \ No newline at end of file diff --git a/docs/developers/contributing.rst b/docs/developers/contributing.rst deleted file mode 100644 index 50bf52730b..0000000000 --- a/docs/developers/contributing.rst +++ /dev/null @@ -1,347 +0,0 @@ -.. _dev-guide-contributing: - -Contributing to Zarr -==================== - -Zarr is a community maintained project. We welcome contributions in the form of bug -reports, bug fixes, documentation, enhancement proposals and more. This page provides -information on how best to contribute. - -Asking for help ---------------- - -If you have a question about how to use Zarr, please post your question on -StackOverflow using the `"zarr" tag `_. -If you don't get a response within a day or two, feel free to raise a `GitHub issue -`_ including a link to your StackOverflow -question. We will try to respond to questions as quickly as possible, but please bear -in mind that there may be periods where we have limited time to answer questions -due to other commitments. - -Bug reports ------------ - -If you find a bug, please raise a `GitHub issue -`_. Please include the following items in -a bug report: - -1. A minimal, self-contained snippet of Python code reproducing the problem. You can - format the code nicely using markdown, e.g.:: - - - ```python - import zarr - g = zarr.group() - # etc. - ``` - -2. An explanation of why the current behaviour is wrong/not desired, and what you - expect instead. - -3. Information about the version of Zarr, along with versions of dependencies and the - Python interpreter, and installation information. The version of Zarr can be obtained - from the ``zarr.__version__`` property. Please also state how Zarr was installed, - e.g., "installed via pip into a virtual environment", or "installed using conda". - Information about other packages installed can be obtained by executing ``pip freeze`` - (if using pip to install packages) or ``conda env export`` (if using conda to install - packages) from the operating system command prompt. The version of the Python - interpreter can be obtained by running a Python interactive session, e.g.:: - - $ python - Python 3.12.7 | packaged by conda-forge | (main, Oct 4 2024, 15:57:01) [Clang 17.0.6 ] on darwin - -Enhancement proposals ---------------------- - -If you have an idea about a new feature or some other improvement to Zarr, please raise a -`GitHub issue `_ first to discuss. - -We very much welcome ideas and suggestions for how to improve Zarr, but please bear in -mind that we are likely to be conservative in accepting proposals for new features. The -reasons for this are that we would like to keep the Zarr code base lean and focused on -a core set of functionalities, and available time for development, review and maintenance -of new features is limited. But if you have a great idea, please don't let that stop -you from posting it on GitHub, just please don't be offended if we respond cautiously. - -Contributing code and/or documentation --------------------------------------- - -Forking the repository -~~~~~~~~~~~~~~~~~~~~~~ - -The Zarr source code is hosted on GitHub at the following location: - -* `https://github.com/zarr-developers/zarr-python `_ - -You will need your own fork to work on the code. Go to the link above and hit -the `"Fork" `_ button. -Then clone your fork to your local machine:: - - $ git clone git@github.com:your-user-name/zarr-python.git - $ cd zarr-python - $ git remote add upstream git@github.com:zarr-developers/zarr-python.git - -Creating a development environment -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -To work with the Zarr source code, it is recommended to use -`hatch `_ to create and manage development -environments. Hatch will automatically install all Zarr dependencies using the same -versions as are used by the core developers and continuous integration services. -Assuming you have a Python 3 interpreter already installed, and you have cloned the -Zarr source code and your current working directory is the root of the repository, -you can do something like the following:: - - $ pip install hatch - $ hatch env show # list all available environments - -To verify that your development environment is working, you can run the unit tests -for one of the test environments, e.g.:: - - $ hatch env run --env test.py3.12-2.2-optional run-pytest - -Creating a branch -~~~~~~~~~~~~~~~~~ - -Before you do any new work or submit a pull request, please open an issue on GitHub to -report the bug or propose the feature you'd like to add. - -It's best to synchronize your fork with the upstream repository, then create a -new, separate branch for each piece of work you want to do. E.g.:: - - git checkout main - git fetch upstream - git checkout -b shiny-new-feature upstream/main - git push -u origin shiny-new-feature - -This changes your working directory to the 'shiny-new-feature' branch. Keep any changes in -this branch specific to one bug or feature so it is clear what the branch brings to -Zarr. - -To update this branch with latest code from Zarr, you can retrieve the changes from -the main branch and perform a rebase:: - - git fetch upstream - git rebase upstream/main - -This will replay your commits on top of the latest Zarr git main. If this leads to -merge conflicts, these need to be resolved before submitting a pull request. -Alternatively, you can merge the changes in from upstream/main instead of rebasing, -which can be simpler:: - - git pull upstream main - -Again, any conflicts need to be resolved before submitting a pull request. - -Running the test suite -~~~~~~~~~~~~~~~~~~~~~~ - -Zarr includes a suite of unit tests. The simplest way to run the unit tests -is to activate your development environment -(see `creating a development environment`_ above) and invoke:: - - $ hatch env run --env test.py3.12-2.2-optional run-pytest - -All tests are automatically run via GitHub Actions for every pull -request and must pass before code can be accepted. Test coverage is -also collected automatically via the Codecov service. - -.. note:: - Previous versions of Zarr-Python made extensive use of doctests. These tests were - not maintained during the 3.0 refactor but may be brought back in the future. - See :issue:`2614` for more details. - -Code standards - using pre-commit -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -All code must conform to the PEP8 standard. Regarding line length, lines up to 100 -characters are allowed, although please try to keep under 90 wherever possible. - -``Zarr`` uses a set of ``pre-commit`` hooks and the ``pre-commit`` bot to format, -type-check, and prettify the codebase. ``pre-commit`` can be installed locally by -running:: - - $ python -m pip install pre-commit - -The hooks can be installed locally by running:: - - $ pre-commit install - -This would run the checks every time a commit is created locally. These checks will also run -on every commit pushed to an open PR, resulting in some automatic styling fixes by the -``pre-commit`` bot. The checks will by default only run on the files modified by a commit, -but the checks can be triggered for all the files by running:: - - $ pre-commit run --all-files - -If you would like to skip the failing checks and push the code for further discussion, use -the ``--no-verify`` option with ``git commit``. - - -Test coverage -~~~~~~~~~~~~~ - -.. note:: - Test coverage for Zarr-Python 3 is currently not at 100%. This is a known issue and help - is welcome to bring test coverage back to 100%. See :issue:`2613` for more details. - -Zarr strives to maintain 100% test coverage under the latest Python stable release -Both unit tests and docstring doctests are included when computing coverage. Running:: - - $ hatch env run --env test.py3.12-2.2-optional run-coverage - -will automatically run the test suite with coverage and produce a XML coverage report. -This should be 100% before code can be accepted into the main code base. - -You can also generate an HTML coverage report by running:: - - $ hatch env run --env test.py3.12-2.2-optional run-coverage-html - -When submitting a pull request, coverage will also be collected across all supported -Python versions via the Codecov service, and will be reported back within the pull -request. Codecov coverage must also be 100% before code can be accepted. - -Documentation -~~~~~~~~~~~~~ - -Docstrings for user-facing classes and functions should follow the -`numpydoc -`_ -standard, including sections for Parameters and Examples. All examples -should run and pass as doctests under Python 3.11. - -Zarr uses Sphinx for documentation, hosted on readthedocs.org. Documentation is -written in the RestructuredText markup language (.rst files) in the ``docs`` folder. -The documentation consists both of prose and API documentation. All user-facing classes -and functions are included in the API documentation, under the ``docs/api`` folder -using the `autodoc `_ -extension to sphinx. Any new features or important usage information should be included in the -user-guide (``docs/user-guide``). Any changes should also be included as a new file in the -:file:`changes` directory. - -The documentation can be built locally by running:: - - $ hatch --env docs run build - -The resulting built documentation will be available in the ``docs/_build/html`` folder. - -Hatch can also be used to serve continuously updating version of the documentation -during development at `http://0.0.0.0:8000/ `_. This can be done by running:: - - $ hatch --env docs run serve - -.. _changelog: - -Changelog -~~~~~~~~~ - -zarr-python uses `towncrier`_ to manage release notes. Most pull requests should -include at least one news fragment describing the changes. To add a release -note, you'll need the GitHub issue or pull request number and the type of your -change (``feature``, ``bugfix``, ``doc``, ``removal``, ``misc``). With that, run -```towncrier create``` with your development environment, which will prompt you -for the issue number, change type, and the news text:: - - towncrier create - -Alternatively, you can manually create the files in the ``changes`` directory -using the naming convention ``{issue-number}.{change-type}.rst``. - -See the `towncrier`_ docs for more. - -.. _towncrier: https://towncrier.readthedocs.io/en/stable/tutorial.html - -The following information is mainly for core developers, but may also be of interest to -contributors. - -Merging pull requests ---------------------- - -Pull requests submitted by an external contributor should be reviewed and approved by at least -one core developer before being merged. Ideally, pull requests submitted by a core developer -should be reviewed and approved by at least one other core developer before being merged. - -Pull requests should not be merged until all CI checks have passed (GitHub Actions, -Codecov) against code that has had the latest main merged in. - -Before merging the milestone must be set either to decide whether a PR will be in the next -patch, minor, or major release. The next section explains which types of changes go in each release. - -Compatibility and versioning policies -------------------------------------- - -Versioning -~~~~~~~~~~ -Versions of this library are identified by a triplet of integers with the form -``..``, for example ``3.0.4``. A release of ``zarr-python`` is associated with a new -version identifier. That new identifier is generated by incrementing exactly one of the components of -the previous version identifier by 1. When incrementing the ``major`` component of the version identifier, -the ``minor`` and ``patch`` components is reset to 0. When incrementing the minor component, -the patch component is reset to 0. - -Releases are classified by the library changes contained in that release. This classification -determines which component of the version identifier is incremented on release. - -* ``major`` releases (for example, ``2.18.0`` -> ``3.0.0``) are for changes that will - require extensive adaptation efforts from many users and downstream projects. - For example, breaking changes to widely-used user-facing APIs should only be applied in a major release. - - - Users and downstream projects should carefully consider the impact of a major release before - adopting it. - In advance of a major release, developers should communicate the scope of the upcoming changes, - and help users prepare for them. - -* ``minor`` releases (or example, ``3.0.0`` -> ``3.1.0``) are for changes that do not require - significant effort from most users or downstream downstream projects to respond to. API changes - are possible in minor releases if the burden on users imposed by those changes is sufficiently small. - - For example, a recently released API may need fixes or refinements that are breaking, but low impact - due to the recency of the feature. Such API changes are permitted in a minor release. - - - Minor releases are safe for most users and downstream projects to adopt. - - -* ``patch`` releases (for example, ``3.1.0`` -> ``3.1.1``) are for changes that contain no breaking - or behaviour changes for downstream projects or users. Examples of changes suitable for a patch release are - bugfixes and documentation improvements. - - - Users should always feel safe upgrading to a the latest patch release. - -Note that this versioning scheme is not consistent with `Semantic Versioning `_. -Contrary to SemVer, the Zarr library may release breaking changes in ``minor`` releases, or even -``patch`` releases under exceptional circumstances. But we should strive to avoid doing so. - -A better model for our versioning scheme is `Intended Effort Versioning `_, -or "EffVer". The guiding principle off EffVer is to categorize releases based on the *expected effort -required to upgrade to that release*. - -Zarr developers should make changes as smooth as possible for users. This means making -backwards-compatible changes wherever possible. When a backwards-incompatible change is necessary, -users should be notified well in advance, e.g. via informative deprecation warnings. - -Data format compatibility -""""""""""""""""""""""""" - -The Zarr library is an implementation of a file format standard defined externally -- -see the `Zarr specifications website `_ for the list of -Zarr file format specifications. - - -If an existing Zarr format version changes, or a new version of the Zarr format is released, then -the Zarr library will generally require changes. It is very likely that a new Zarr format will -require extensive breaking changes to the Zarr library, and so support for a new Zarr format in the -Zarr library will almost certainly come in new ``major`` release. -When the Zarr library adds support for a new Zarr format, there may be a period of accelerated -changes as developers refine newly added APIs and deprecate old APIs. In such a transitional phase -breaking changes may be more frequent than usual. - - -Release procedure ------------------ - -Open an issue on GitHub announcing the release using the release checklist template: -`https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md `_. -The release checklist includes all steps necessary for the release. diff --git a/docs/developers/index.rst b/docs/developers/index.rst deleted file mode 100644 index 4bccb3a469..0000000000 --- a/docs/developers/index.rst +++ /dev/null @@ -1,9 +0,0 @@ - -Developer's Guide ------------------ - -.. toctree:: - :maxdepth: 1 - - contributing - roadmap diff --git a/docs/developers/roadmap.rst b/docs/developers/roadmap.rst deleted file mode 100644 index 716599bab0..0000000000 --- a/docs/developers/roadmap.rst +++ /dev/null @@ -1,696 +0,0 @@ -Roadmap -======= - -- Status: active -- Author: Joe Hamman -- Created On: October 31, 2023 -- Input from: - - - Davis Bennett / @d-v-b - - Norman Rzepka / @normanrz - - Deepak Cherian @dcherian - - Brian Davis / @monodeldiablo - - Oliver McCormack / @olimcc - - Ryan Abernathey / @rabernat - - Jack Kelly / @JackKelly - - Martin Durrant / @martindurant - -.. note:: - - This document was written in the early stages of the 3.0 refactor. Some - aspects of the design have changed since this was originally written. - Questions and discussion about the contents of this document should be directed to - `this GitHub Discussion `__. - -Introduction ------------- - -This document lays out a design proposal for version 3.0 of the -`Zarr-Python `__ package. A -specific focus of the design is to bring Zarr-Python’s API up to date -with the `Zarr V3 -specification `__, -with the hope of enabling the development of the many features and -extensions that motivated the V3 Spec. The ideas presented here are -expected to result in a major release of Zarr-Python (version 3.0) -including significant a number of breaking API changes. For clarity, -“V3” will be used to describe the version of the Zarr specification and -“3.0” will be used to describe the release tag of the Zarr-Python -project. - -Current status of V3 in Zarr-Python -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -During the development of the V3 Specification, a `prototype -implementation `__ -was added to the Zarr-Python library. Since that implementation, the V3 -spec evolved in significant ways and as a result, the Zarr-Python -library is now out of sync with the approved spec. Downstream libraries -(e.g. `Xarray `__) have added support -for this implementation and will need to migrate to the accepted spec -when its available in Zarr-Python. - -Goals ------ - -- Provide a complete implementation of Zarr V3 through the Zarr-Python - API -- Clear the way for exciting extensions / ZEPs - (i.e. `sharding `__, - `variable chunking `__, - etc.) -- Provide a developer API that can be used to implement and register V3 - extensions -- Improve the performance of Zarr-Python by streamlining the interface - between the Store layer and higher level APIs (e.g. Groups and - Arrays) -- Clean up the internal and user facing APIs -- Improve code quality and robustness (e.g. achieve 100% type hint - coverage) -- Align the Zarr-Python array API with the `array API - Standard `__ - -Examples of what 3.0 will enable? ---------------------------------- - -1. Reading and writing V3 spec-compliant groups and arrays -2. V3 extensions including sharding and variable chunking. -3. Improved performance by leveraging concurrency when - creating/reading/writing to stores (imagine a - ``create_hierarchy(zarr_objects)`` function). -4. User-developed extensions (e.g. storage-transformers) can be - registered with Zarr-Python at runtime - -Non-goals (of this document) ----------------------------- - -- Implementation of any unaccepted Zarr V3 extensions -- Major revisions to the Zarr V3 spec - -Requirements ------------- - -1. Read and write spec compliant V2 and V3 data -2. Limit unnecessary traffic to/from the store -3. Cleanly define the Array/Group/Store abstractions -4. Cleanly define how V2 will be supported going forward -5. Provide a clear roadmap to help users upgrade to 3.0 -6. Developer tools / hooks for registering extensions - -Design ------- - -Async API -~~~~~~~~~ - -Zarr-Python is an IO library. As such, supporting concurrent action -against the storage layer is critical to achieving acceptable -performance. The Zarr-Python 2 was not designed with asynchronous -computation in mind and as a result has struggled to effectively -leverage the benefits of concurrency. At one point, ``getitems`` and -``setitems`` support was added to the Zarr store model but that is only -used for operating on a set of chunks in a single variable. - -With Zarr-Python 3.0, we have the opportunity to revisit this design. -The proposal here is as follows: - -1. The ``Store`` interface will be entirely async. -2. On top of the async ``Store`` interface, we will provide an - ``AsyncArray`` and ``AsyncGroup`` interface. -3. Finally, the primary user facing API will be synchronous ``Array`` - and ``Group`` classes that wrap the async equivalents. - -**Examples** - -- **Store** - - .. code:: python - - class Store: - ... - async def get(self, key: str) -> bytes: - ... - async def get_partial_values(self, key_ranges: List[Tuple[str, Tuple[int, Optional[int]]]]) -> bytes: - ... - # (no sync interface here) - -- **Array** - - .. code:: python - - class AsyncArray: - ... - - async def getitem(self, selection: Selection) -> np.ndarray: - # the core logic for getitem goes here - - class Array: - _async_array: AsyncArray - - def __getitem__(self, selection: Selection) -> np.ndarray: - return sync(self._async_array.getitem(selection)) - -- **Group** - - .. code:: python - - class AsyncGroup: - ... - - async def create_group(self, path: str, **kwargs) -> AsyncGroup: - # the core logic for create_group goes here - - class Group: - _async_group: AsyncGroup - - def create_group(self, path: str, **kwargs) -> Group: - return sync(self._async_group.create_group(path, **kwargs)) - - **Internal Synchronization API** - -With the ``Store`` and core ``AsyncArray``/ ``AsyncGroup`` classes being -predominantly async, Zarr-Python will need an internal API to provide a -synchronous API. The proposal here is to use the approach in -`fsspec `__ -to provide a high-level ``sync`` function that takes an ``awaitable`` -and runs it in its managed IO Loop / thread. - -| **FAQ** 1. Why two levels of Arrays/groups? a. First, this is an - intentional decision and departure from the current Zarrita - implementation b. The idea is that users rarely want to mix - interfaces. Either they are working within an async context (currently - quite rare) or they are in a typical synchronous context. c. Splitting - the two will allow us to clearly define behavior on the ``AsyncObj`` - and simply wrap it in the ``SyncObj``. 2. What if a store is only has - a synchronous backend? a. First off, this is expected to be a fairly - rare occurrence. Most storage backends have async interfaces. b. But - in the event a storage backend doesn’t have a async interface, there - is nothing wrong with putting synchronous code in ``async`` methods. - There are approaches to enabling concurrent action through wrappers - like AsyncIO’s ``loop.run_in_executor`` (`ref - 1 `__, - `ref 2 `__, `ref - 3 `__, - `ref - 4 `__. -| 3. Will Zarr help manage the async contexts encouraged by some - libraries - (e.g. `AioBotoCore `__)? - a. Many async IO libraries require entering an async context before - interacting with the API. We expect some experimentation to be needed - here but the initial design will follow something close to what fsspec - does (`example in - s3fs `__). - 4. Why not provide a synchronous Store interface? a. We could but this - design is simpler. It would mean supporting it in the ``AsyncGroup`` - and ``AsyncArray`` classes which, may be more trouble than its worth. - Storage backends that do not have an async API will be encouraged to - wrap blocking calls in an async wrapper - (e.g. ``loop.run_in_executor``). - -Store API -~~~~~~~~~ - -The ``Store`` API is specified directly in the V3 specification. All V3 -stores should implement this abstract API, omitting Write and List -support as needed. As described above, all stores will be expected to -expose the required methods as async methods. - -**Example** - -.. code:: python - - class ReadWriteStore: - ... - async def get(self, key: str) -> bytes: - ... - - async def get_partial_values(self, key_ranges: List[Tuple[str, int, int]) -> bytes: - ... - - async def set(self, key: str, value: Union[bytes, bytearray, memoryview]) -> None: - ... # required for writable stores - - async def set_partial_values(self, key_start_values: List[Tuple[str, int, Union[bytes, bytearray, memoryview]]]) -> None: - ... # required for writable stores - - async def list(self) -> List[str]: - ... # required for listable stores - - async def list_prefix(self, prefix: str) -> List[str]: - ... # required for listable stores - - async def list_dir(self, prefix: str) -> List[str]: - ... # required for listable stores - - # additional (optional methods) - async def getsize(self, prefix: str) -> int: - ... - - async def rename(self, src: str, dest: str) -> None - ... - - -Recognizing that there are many Zarr applications today that rely on the -``MutableMapping`` interface supported by Zarr-Python 2, a wrapper store -will be developed to allow existing stores to plug directly into this -API. - -Array API -~~~~~~~~~ - -The user facing array interface will implement a subset of the `Array -API Standard `__. Most of the -computational parts of the Array API Standard don’t fit into Zarr right -now. That’s okay. What matters most is that we ensure we can give -downstream applications a compliant API. - -*Note, Zarr already does most of this so this is more about formalizing -the relationship than a substantial change in API.* - -+------------------------+------------------------+-------------------------+-------------------------+ -| | Included | Not Included | Unknown / Maybe Possible| -+========================+========================+=========================+=========================+ -| **Attributes** | ``dtype`` | ``mT`` | ``device`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``ndim`` | ``T`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``shape`` | | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``size`` | | | -+------------------------+------------------------+-------------------------+-------------------------+ -| **Methods** | ``__getitem__`` | ``__array_namespace__`` | ``to_device`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``__setitem__`` | ``__abs__`` | ``__bool__`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``__eq__`` | ``__add__`` | ``__complex__`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``__bool__`` | ``__and__`` | ``__dlpack__`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__floordiv__`` | ``__dlpack_device__`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__ge__`` | ``__float__`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__gt__`` | ``__index__`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__invert__`` | ``__int__`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__le__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__lshift__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__lt__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__matmul__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__mod__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__mul__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__ne__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__neg__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__or__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__pos__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__pow__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__rshift__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__sub__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__truediv__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | | ``__xor__`` | | -+------------------------+------------------------+-------------------------+-------------------------+ -| **Creation functions** | ``zeros`` | | ``arange`` | -| (``zarr.creation``) | | | | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``zeros_like`` | | ``asarray`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``ones`` | | ``eye`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``ones_like`` | | ``from_dlpack`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``full`` | | ``linspace`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``full_like`` | | ``meshgrid`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``empty`` | | ``tril`` | -+------------------------+------------------------+-------------------------+-------------------------+ -| | ``empty_like`` | | ``triu`` | -+------------------------+------------------------+-------------------------+-------------------------+ - -In addition to the core array API defined above, the Array class should -have the following Zarr specific properties: - -- ``.metadata`` (see Metadata Interface below) -- ``.attrs`` - (pulled from metadata object) -- ``.info`` - (repolicated from existing property †) - -*† In Zarr-Python 2, the info property listed the store to identify -initialized chunks. By default this will be turned off in 3.0 but will -be configurable.* - -**Indexing** - -Zarr-Python currently supports ``__getitem__`` style indexing and the -special ``oindex`` and ``vindex`` indexers. These are not part of the -current Array API standard (see -`data-apis/array-api#669 `__) -but they have been `proposed as a -NEP `__. -Zarr-Python will maintain these in 3.0. - -We are also exploring a new high-level indexing API that will enabled -optimized batch/concurrent loading of many chunks. We expect this to be -important to enable performant loading of data in the context of -sharding. See `this -discussion `__ -for more detail. - -Concurrent indexing across multiple arrays will be possible using the -AsyncArray API. - -**Async and Sync Array APIs** - -Most the logic to support Zarr Arrays will live in the ``AsyncArray`` -class. There are a few notable differences that should be called out. - -=============== ============ -Sync Method Async Method -=============== ============ -``__getitem__`` ``getitem`` -``__setitem__`` ``setitem`` -``__eq__`` ``equals`` -=============== ============ - -**Metadata interface** - -Zarr-Python 2.\* closely mirrors the V2 spec metadata schema in the -Array and Group classes. In 3.0, we plan to move the underlying metadata -representation to a separate interface (e.g. ``Array.metadata``). This -interface will return either a ``V2ArrayMetadata`` or -``V3ArrayMetadata`` object (both will inherit from a parent -``ArrayMetadataABC`` class. The ``V2ArrayMetadata`` and -``V3ArrayMetadata`` classes will be responsible for producing valid JSON -representations of their metadata, and yielding a consistent view to the -``Array`` or ``Group`` class. - -Group API -~~~~~~~~~ - -The main question is how closely we should follow the existing -Zarr-Python implementation / ``MutableMapping`` interface. The table -below shows the primary ``Group`` methods in Zarr-Python 2 and attempts -to identify if and how they would be implemented in 3.0. - -+---------------------+------------------+------------------+-----------------------+ -| V2 Group Methods | ``AsyncGroup`` | ``Group`` | ``h5py_compat.Group`` | -+=====================+==================+==================+=======================+ -| ``__len__`` | ``length`` | ``__len__`` | ``__len__`` | -+---------------------+------------------+------------------+-----------------------+ -| ``__iter__`` | ``__aiter__`` | ``__iter__`` | ``__iter__`` | -+---------------------+------------------+------------------+-----------------------+ -| ``__contains__`` | ``contains`` | ``__contains__`` | ``__contains__`` | -+---------------------+------------------+------------------+-----------------------+ -| ``__getitem__`` | ``getitem`` | ``__getitem__`` | ``__getitem__`` | -+---------------------+------------------+------------------+-----------------------+ -| ``__enter__`` | N/A | N/A | ``__enter__`` | -+---------------------+------------------+------------------+-----------------------+ -| ``__exit__`` | N/A | N/A | ``__exit__`` | -+---------------------+------------------+------------------+-----------------------+ -| ``group_keys`` | ``group_keys`` | ``group_keys`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``groups`` | ``groups`` | ``groups`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``array_keys`` | ``array_key`` | ``array_keys`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``arrays`` | ``arrays`` | ``arrays`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``visit`` | ? | ? | ``visit`` | -+---------------------+------------------+------------------+-----------------------+ -| ``visitkeys`` | ? | ? | ? | -+---------------------+------------------+------------------+-----------------------+ -| ``visitvalues`` | ? | ? | ? | -+---------------------+------------------+------------------+-----------------------+ -| ``visititems`` | ? | ? | ``visititems`` | -+---------------------+------------------+------------------+-----------------------+ -| ``tree`` | ``tree`` | ``tree`` | ``Both`` | -+---------------------+------------------+------------------+-----------------------+ -| ``create_group`` | ``create_group`` | ``create_group`` | ``create_group`` | -+---------------------+------------------+------------------+-----------------------+ -| ``require_group`` | N/A | N/A | ``require_group`` | -+---------------------+------------------+------------------+-----------------------+ -| ``create_groups`` | ? | ? | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``require_groups`` | ? | ? | ? | -+---------------------+------------------+------------------+-----------------------+ -| ``create_dataset`` | N/A | N/A | ``create_dataset`` | -+---------------------+------------------+------------------+-----------------------+ -| ``require_dataset`` | N/A | N/A | ``require_dataset`` | -+---------------------+------------------+------------------+-----------------------+ -| ``create`` | ``create_array`` | ``create_array`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``empty`` | ``empty`` | ``empty`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``zeros`` | ``zeros`` | ``zeros`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``ones`` | ``ones`` | ``ones`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``full`` | ``full`` | ``full`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``array`` | ``create_array`` | ``create_array`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``empty_like`` | ``empty_like`` | ``empty_like`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``zeros_like`` | ``zeros_like`` | ``zeros_like`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``ones_like`` | ``ones_like`` | ``ones_like`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``full_like`` | ``full_like`` | ``full_like`` | N/A | -+---------------------+------------------+------------------+-----------------------+ -| ``move`` | ``move`` | ``move`` | ``move`` | -+---------------------+------------------+------------------+-----------------------+ - -**``zarr.h5compat.Group``** --- -Zarr-Python 2.\* made an attempt to align its API with that of -`h5py `__. With 3.0, we will -relax this alignment in favor of providing an explicit compatibility -module (``zarr.h5py_compat``). This module will expose the ``Group`` and -``Dataset`` APIs that map to Zarr-Python’s ``Group`` and ``Array`` -objects. - -Creation API -~~~~~~~~~~~~ - -Zarr-Python 2.\* bundles together the creation and serialization of Zarr -objects. Zarr-Python 3.\* will make it possible to create objects in -memory separate from serializing them. This will specifically enable -writing hierarchies of Zarr objects in a single batch step. For example: - -.. code:: python - - - arr1 = Array(shape=(10, 10), path="foo/bar", dtype="i4", store=store) - arr2 = Array(shape=(10, 10), path="foo/spam", dtype="f8", store=store) - - arr1.save() - arr2.save() - - # or equivalently - - zarr.save_many([arr1 ,arr2]) - -*Note: this batch creation API likely needs additional design effort -prior to implementation.* - -Plugin API -~~~~~~~~~~ - -Zarr V3 was designed to be extensible at multiple layers. Zarr-Python -will support these extensions through a combination of `Abstract Base -Classes `__ (ABCs) and -`Entrypoints `__. - -**ABCs** - -Zarr V3 will expose Abstract base classes for the following objects: - -- ``Store``, ``ReadStore``, ``ReadWriteStore``, ``ReadListStore``, and - ``ReadWriteListStore`` -- ``BaseArray``, ``SynchronousArray``, and ``AsynchronousArray`` -- ``BaseGroup``, ``SynchronousGroup``, and ``AsynchronousGroup`` -- ``Codec``, ``ArrayArrayCodec``, ``ArrayBytesCodec``, - ``BytesBytesCodec`` - -**Entrypoints** - -Lots more thinking here but the idea here is to provide entrypoints for -``data type``, ``chunk grid``, ``chunk key encoding``, ``codecs``, -``storage_transformers`` and ``stores``. These might look something -like: - -:: - - entry_points=""" - [zarr.codecs] - blosc_codec=codec_plugin:make_blosc_codec - zlib_codec=codec_plugin:make_zlib_codec - """ - -Python type hints and static analysis -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Target 100% Mypy coverage in 3.0 source. - -Observability -~~~~~~~~~~~~~ - -A persistent problem in Zarr-Python is diagnosing problems that span -many parts of the stack. To address this in 3.0, we will add a basic -logging framework that can be used to debug behavior at various levels -of the stack. We propose to add the separate loggers for the following -namespaces: - -- ``array`` -- ``group`` -- ``store`` -- ``codec`` - -These should be documented such that users know how to activate them and -developers know how to use them when developing extensions. - -Dependencies -~~~~~~~~~~~~ - -Today, Zarr-Python has the following required dependencies: - -.. code:: python - - dependencies = [ - 'asciitree', - 'numpy>=1.20,!=1.21.0', - 'fasteners', - 'numcodecs>=0.10.0', - ] - -What other dependencies should be considered? - -1. Attrs - Zarrita makes extensive use of the Attrs library -2. Fsspec - Zarrita has a hard dependency on Fsspec. This could be - easily relaxed though. - -Breaking changes relative to Zarr-Python 2.\* ---------------------------------------------- - -1. H5py compat moved to a stand alone module? -2. ``Group.__getitem__`` support moved to ``Group.members.__getitem__``? -3. Others? - -Open questions --------------- - -1. How to treat V2 - - a. Note: Zarrita currently implements a separate ``V2Array`` and - ``V3Array`` classes. This feels less than ideal. - b. We could easily convert metadata from v2 to the V3 Array, but what - about writing? - c. Ideally, we don’t have completely separate code paths. But if its - too complicated to support both within one interface, its probably - better. - -2. How and when to remove the current implementation of V3. - - a. It’s hidden behind a hard-to-use feature flag so we probably don’t - need to do anything. - -3. How to model runtime configuration? -4. Which extensions belong in Zarr-Python and which belong in separate - packages? - - a. We don’t need to take a strong position on this here. It’s likely - that someone will want to put Sharding in. That will be useful to - develop in parallel because it will give us a good test case for - the plugin interface. - -Testing -------- - -Zarr-python 3.0 adds a major new dimension to Zarr: Async support. This -also comes with a compatibility risk, we will need to thoroughly test -support in key execution environments. Testing plan: - Reuse the -existing test suite for testing the ``v3`` API. - ``xfail`` tests that -expose breaking changes with ``3.0 - breaking change`` description. This -will help identify additional and/or unintentional breaking changes - -Rework tests that were only testing internal APIs. - Add a set of -functional / integration tests targeting real-world workflows in various -contexts (e.g. w/ Dask) - -Development process -------------------- - -Zarr-Python 3.0 will introduce a number of new APIs and breaking changes -to existing APIs. In order to facilitate ongoing support for Zarr-Python -2.*, we will take on the following development process: - -- Create a ``v3`` branch that can be use for developing the core - functionality apart from the ``main`` branch. This will allow us to - support ongoing work and bug fixes on the ``main`` branch. -- Put the ``3.0`` APIs inside a ``zarr.v3`` module. Imports from this - namespace will all be new APIs that users can develop and test - against once the ``v3`` branch is merged to ``main``. -- Kickstart the process by pulling in the current state of ``zarrita`` - - which has many of the features described in this design. -- Release a series of 2.\* releases with the ``v3`` namespace -- When ``v3`` is complete, move contents of ``v3`` to the package root - -**Milestones** - -Below are a set of specific milestones leading toward the completion of -this process. As work begins, we expect this list to grow in -specificity. - -1. Port current version of Zarrita to Zarr-Python -2. Formalize Async interface by splitting ``Array`` and ``Group`` - objects into Sync and Async versions -3. Implement “fancy” indexing operations on the ``AsyncArray`` -4. Implement an abstract base class for the ``Store`` interface and a - wrapper ``Store`` to make use of existing ``MutableMapping`` stores. -5. Rework the existing unit test suite to use the ``v3`` namespace. -6. Develop a plugin interface for extensions -7. Develop a set of functional and integration tests -8. Work with downstream libraries (Xarray, Dask, etc.) to test new APIs - -TODOs ------ - -The following subjects are not covered in detail above but perhaps -should be. Including them here so they are not forgotten. - -1. [Store] Should Zarr provide an API for caching objects after first - read/list/etc. Read only stores? -2. [Array] buffer protocol support -3. [Array] ``meta_array`` support -4. [Extensions] Define how Zarr-Python will consume the various plugin - types -5. [Misc] H5py compatibility requires a bit more work and a champion to - drive it forward. -6. [Misc] Define ``chunk_store`` API in 3.0 -7. [Misc] Define ``synchronizer`` API in 3.0 - -References ----------- - -1. `Zarr-Python - repository `__ -2. `Zarr core specification (version 3.0) — Zarr specs - documentation `__ -3. `Zarrita repository `__ -4. `Async-Zarr `__ -5. `Zarr-Python Discussion - Topic `__ diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000000..8508d8e0cf --- /dev/null +++ b/docs/index.md @@ -0,0 +1,88 @@ +# Zarr-Python + +**Useful links**: +[Source Repository](https://github.com/zarr-developers/zarr-python) | +[Issue Tracker](https://github.com/zarr-developers/zarr-python/issues) | +[Developer Chat](https://ossci.zulipchat.com/) | +[Zarr specifications](https://zarr-specs.readthedocs.io) + + +Zarr is a powerful library for storage of n-dimensional arrays, supporting chunking, +compression, and various backends, making it a versatile choice for scientific and +large-scale data. + +Zarr-Python is a Python library for reading and writing Zarr groups and arrays. Highlights include: + +* Specification support for both Zarr format 2 and 3. +* Create and read from N-dimensional arrays using NumPy-like semantics. +* Flexible storage enables reading and writing from local, cloud and in-memory stores. +* High performance: Enables fast I/O with support for asynchronous I/O and multi-threading. +* Extensible: Customizable with user-defined codecs and stores. + +## Installation + +Zarr requires Python 3.11 or higher. You can install it via `pip`: + +```bash +pip install zarr +``` + +or `conda`: + +```bash +conda install --channel conda-forge zarr +``` + +## Navigating the documentation + +
+ +- [:material-clock-fast:{ .lg .middle } __Quick start__](quick-start.md) + + --- + + New to Zarr? Check out the quick start guide. It contains a brief + introduction to Zarr's main concepts and links to additional tutorials. + + +- [:material-book-open:{ .lg .middle } __User guide__](user-guide/installation.md) + + --- + + A detailed guide for how to use Zarr-Python. + + +- [:material-api:{ .lg .middle } __API Reference__](api/open.md) + + --- + + The reference guide contains a detailed description of the functions, modules, + and objects included in Zarr. The reference describes how the methods work and + which parameters can be used. It assumes that you have an understanding of the + key concepts. + + +- [:material-account-group:{ .lg .middle } __Contributor's Guide__](contributing.md) + + --- + + Want to contribute to Zarr? We welcome contributions in the form of bug reports, + bug fixes, documentation, enhancement proposals and more. The contributing guidelines + will guide you through the process of improving Zarr. + +
+ + +## Project Status + +More information about the Zarr format can be found on the [main website](https://zarr.dev). + +If you are using Zarr-Python, we would [love to hear about it](https://github.com/zarr-developers/community/issues/19). + +### Funding and Support +The project is fiscally sponsored by [NumFOCUS](https://numfocus.org/), a US +501(c)(3) public charity, and development has been supported by the +[MRC Centre for Genomics and Global Health](https://github.com/cggh/) +and the [Chan Zuckerberg Initiative](https://chanzuckerberg.com/). + +[Donate to Zarr](https://numfocus.org/donate-to-zarr) to support the project! diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 83d427e290..0000000000 --- a/docs/index.rst +++ /dev/null @@ -1,113 +0,0 @@ -.. _zarr_docs_mainpage: - -*********** -Zarr-Python -*********** - -.. toctree:: - :maxdepth: 1 - :hidden: - - quickstart - user-guide/index - API reference - release-notes - developers/index - about - -**Version**: |version| - -**Useful links**: -`Source Repository `_ | -`Issue Tracker `_ | -`Developer Chat `_ | -`Zarr specifications `_ - -Zarr-Python is a Python library for reading and writing Zarr groups and arrays. Highlights include: - -* Specification support for both Zarr format 2 and 3. -* Create and read from N-dimensional arrays using NumPy-like semantics. -* Flexible storage enables reading and writing from local, cloud and in-memory stores. -* High performance: Enables fast I/O with support for asynchronous I/O and multi-threading. -* Extensible: Customizable with user-defined codecs and stores. - -.. grid:: 2 - - .. grid-item-card:: - :img-top: _static/index_getting_started.svg - - Quick Start - ^^^^^^^^^^^ - - New to Zarr? Check out the quick start guide. It contains a brief - introduction to Zarr's main concepts and links to additional tutorials. - - +++ - - .. button-ref:: quickstart - :expand: - :color: dark - :click-parent: - - To the Quick Start - - .. grid-item-card:: - :img-top: _static/index_user_guide.svg - - Guide - ^^^^^ - - A detailed guide for how to use Zarr-Python. - - +++ - - .. button-ref:: user-guide/index - :expand: - :color: dark - :click-parent: - - To the user guide - - .. grid-item-card:: - :img-top: _static/index_api.svg - - API Reference - ^^^^^^^^^^^^^ - - The reference guide contains a detailed description of the functions, - modules, and objects included in Zarr. The reference describes how the - methods work and which parameters can be used. It assumes that you have an - understanding of the key concepts. - - +++ - - .. button-ref:: api/zarr/index - :expand: - :color: dark - :click-parent: - - To the API reference - - .. grid-item-card:: - :img-top: _static/index_contribute.svg - - Contributor's Guide - ^^^^^^^^^^^^^^^^^^^ - - Want to contribute to Zarr? We welcome contributions in the form of bug reports, - bug fixes, documentation, enhancement proposals and more. The contributing guidelines - will guide you through the process of improving Zarr. - - +++ - - .. button-ref:: developers/contributing - :expand: - :color: dark - :click-parent: - - To the contributor's guide - - -**Download documentation**: `PDF/Zipped HTML `_ - -.. _NumCodecs: https://numcodecs.readthedocs.io diff --git a/docs/overrides/main.html b/docs/overrides/main.html new file mode 100644 index 0000000000..d61a1f54dc --- /dev/null +++ b/docs/overrides/main.html @@ -0,0 +1,9 @@ + +{% extends "base.html" %} + +{% block outdated %} + You're not viewing the latest version. + + Click here to go to latest. + +{% endblock %} diff --git a/docs/overrides/stylesheets/extra.css b/docs/overrides/stylesheets/extra.css new file mode 100644 index 0000000000..3e2ef3d330 --- /dev/null +++ b/docs/overrides/stylesheets/extra.css @@ -0,0 +1,52 @@ +:root, +[data-md-color-scheme="default"] { + /* --md-primary-fg-color: #cf3f02; + --md-default-fg-color: #443f3f; */ + --boxShadowD: 0px 12px 24px 0px rgba(68, 63, 63, 0.08), + 0px 0px 4px 0px rgba(68, 63, 63, 0.08); +} +body { + margin: 0; + padding: 0; + /* font-size: 16px; */ +} +h1, +h2, +h3, +h4, +h5, +h6 { + font-family: var(--md-heading-font); + font-weight: bold; +} +.md-typeset h1, +.md-typeset h2 { + font-weight: normal; + color: var(--md-default-fg-color); +} +.md-typeset h3, +.md-typeset h4 { + font-weight: bold; + color: var(--md-default-fg-color); +} +.md-button, +.md-typeset .md-button { + font-family: var(--md-heading-font); +} +.md-content .supheading { + font-family: var(--md-heading-font); + text-transform: uppercase; + color: var(--md-primary-fg-color); + font-size: 0.75rem; + font-weight: bold; +} + +.md-header__button.md-logo img, +.md-header__button.md-logo svg { + height: 2rem; + width: auto; +} + +.md-header { + padding: 0.2rem 0; +} diff --git a/docs/quick-start.md b/docs/quick-start.md new file mode 100644 index 0000000000..42ac95d169 --- /dev/null +++ b/docs/quick-start.md @@ -0,0 +1,176 @@ +This section will help you get up and running with +the Zarr library in Python to efficiently manage and analyze multi-dimensional arrays. + +### Creating an Array + +To get started, you can create a simple Zarr array: + +```python exec="true" session="quickstart" +import shutil +shutil.rmtree('data', ignore_errors=True) +import numpy as np +from pprint import pprint +import io +import warnings + +warnings.filterwarnings( + "ignore", + message="Numcodecs codecs are not in the Zarr version 3 specification*", + category=UserWarning +) +np.random.seed(0) +``` + +```python exec="true" session="quickstart" source="above" result="ansi" +import zarr +import numpy as np + +# Create a 2D Zarr array +z = zarr.create_array( + store="data/example-1.zarr", + shape=(100, 100), + chunks=(10, 10), + dtype="f4" +) + +# Assign data to the array +z[:, :] = np.random.random((100, 100)) +print(z.info) +``` + +Here, we created a 2D array of shape `(100, 100)`, chunked into blocks of +`(10, 10)`, and filled it with random floating-point data. This array was +written to a `LocalStore` in the `data/example-1.zarr` directory. + +#### Compression and Filters + +Zarr supports data compression and filters. For example, to use Blosc compression: + + +```python exec="true" session="quickstart" source="above" result="code" + +# Create a 2D Zarr array with Blosc compression +z = zarr.create_array( + store="data/example-2.zarr", + shape=(100, 100), + chunks=(10, 10), + dtype="f4", + compressors=zarr.codecs.BloscCodec( + cname="zstd", + clevel=3, + shuffle=zarr.codecs.BloscShuffle.shuffle + ) +) + +# Assign data to the array +z[:, :] = np.random.random((100, 100)) +print(z.info) +``` + +This compresses the data using the Blosc codec with shuffle enabled for better compression. + + +### Hierarchical Groups + +Zarr allows you to create hierarchical groups, similar to directories: + +```python exec="true" session="quickstart" source="above" result="ansi" + +# Create nested groups and add arrays +root = zarr.group("data/example-3.zarr") +foo = root.create_group(name="foo") +bar = root.create_array( + name="bar", shape=(100, 10), chunks=(10, 10), dtype="f4" +) +spam = foo.create_array(name="spam", shape=(10,), dtype="i4") + +# Assign values +bar[:, :] = np.random.random((100, 10)) +spam[:] = np.arange(10) + +# print the hierarchy +print(root.tree()) +``` + +This creates a group with two datasets: `foo` and `bar`. + +#### Batch Hierarchy Creation + +Zarr provides tools for creating a collection of arrays and groups with a single function call. +Suppose we want to copy existing groups and arrays into a new storage backend: + +```python exec="true" session="quickstart" source="above" result="html" + +# Create nested groups and add arrays +root = zarr.group("data/example-4.zarr", attributes={'name': 'root'}) +foo = root.create_group(name="foo") +bar = root.create_array( + name="bar", shape=(100, 10), chunks=(10, 10), dtype="f4" +) +nodes = {'': root.metadata} | {k: v.metadata for k,v in root.members()} +# Report nodes +output = io.StringIO() +pprint(nodes, stream=output, width=60, depth=3) +result = output.getvalue() +print(result) +# Create new hierarchy from nodes +new_nodes = dict(zarr.create_hierarchy(store=zarr.storage.MemoryStore(), nodes=nodes)) +new_root = new_nodes[''] +assert new_root.attrs == root.attrs +``` + +Note that [`zarr.create_hierarchy`][] will only initialize arrays and groups -- copying array data must +be done in a separate step. + +### Persistent Storage + +Zarr supports persistent storage to disk or cloud-compatible backends. While examples above +utilized a [`zarr.storage.LocalStore`][], a number of other storage options are available. + +Zarr integrates seamlessly with cloud object storage such as Amazon S3 and Google Cloud Storage +using external libraries like [s3fs](https://s3fs.readthedocs.io) or +[gcsfs](https://gcsfs.readthedocs.io): + +```python + +import s3fs + +z = zarr.create_array("s3://example-bucket/foo", mode="w", shape=(100, 100), chunks=(10, 10), dtype="f4") +z[:, :] = np.random.random((100, 100)) +``` + +A single-file store can also be created using the [`zarr.storage.ZipStore`][]: + +```python exec="true" session="quickstart" source="above" + +# Store the array in a ZIP file +store = zarr.storage.ZipStore("data/example-5.zip", mode="w") + +z = zarr.create_array( + store=store, + shape=(100, 100), + chunks=(10, 10), + dtype="f4" +) + +# write to the array +z[:, :] = np.random.random((100, 100)) + +# the ZipStore must be explicitly closed +store.close() +``` + +To open an existing array from a ZIP file: + +```python exec="true" session="quickstart" source="above" result="code" + +# Open the ZipStore in read-only mode +store = zarr.storage.ZipStore("data/example-5.zip", read_only=True) + +z = zarr.open_array(store, mode='r') + +# read the data as a NumPy Array +print(z[:]) +``` + +Read more about Zarr's storage options in the [User Guide](user-guide/index.md). diff --git a/docs/quickstart.rst b/docs/quickstart.rst deleted file mode 100644 index 66bdae2a2e..0000000000 --- a/docs/quickstart.rst +++ /dev/null @@ -1,209 +0,0 @@ -.. only:: doctest - - >>> import shutil - >>> shutil.rmtree('data', ignore_errors=True) - >>> - >>> import numpy as np - >>> np.random.seed(0) - -Quickstart -========== - -Welcome to the Zarr-Python Quickstart guide! This page will help you get up and running with -the Zarr library in Python to efficiently manage and analyze multi-dimensional arrays. - -Zarr is a powerful library for storage of n-dimensional arrays, supporting chunking, -compression, and various backends, making it a versatile choice for scientific and -large-scale data. - -Installation ------------- - -Zarr requires Python 3.11 or higher. You can install it via `pip`: - -.. code-block:: bash - - pip install zarr - -or `conda`: - -.. code-block:: bash - - conda install --channel conda-forge zarr - -Creating an Array ------------------ - -To get started, you can create a simple Zarr array:: - - >>> import zarr - >>> import numpy as np - >>> - >>> # Create a 2D Zarr array - >>> z = zarr.create_array( - ... store="data/example-1.zarr", - ... shape=(100, 100), - ... chunks=(10, 10), - ... dtype="f4" - ... ) - >>> - >>> # Assign data to the array - >>> z[:, :] = np.random.random((100, 100)) - >>> z.info - Type : Array - Zarr format : 3 - Data type : DataType.float32 - Shape : (100, 100) - Chunk shape : (10, 10) - Order : C - Read-only : False - Store type : LocalStore - Codecs : [{'endian': }, {'level': 0, 'checksum': False}] - No. bytes : 40000 (39.1K) - -Here, we created a 2D array of shape ``(100, 100)``, chunked into blocks of -``(10, 10)``, and filled it with random floating-point data. This array was -written to a ``LocalStore`` in the ``data/example-1.zarr`` directory. - -Compression and Filters -~~~~~~~~~~~~~~~~~~~~~~~ - -Zarr supports data compression and filters. For example, to use Blosc compression:: - - >>> z = zarr.create_array( - ... "data/example-3.zarr", - ... mode="w", shape=(100, 100), - ... chunks=(10, 10), dtype="f4", - ... compressors=zarr.codecs.BloscCodec(cname="zstd", clevel=3, shuffle=zarr.codecs.BloscShuffle.shuffle) - ... ) - >>> z[:, :] = np.random.random((100, 100)) - >>> - >>> z.info - Type : Array - Zarr format : 3 - Data type : DataType.float32 - Shape : (100, 100) - Chunk shape : (10, 10) - Order : C - Read-only : False - Store type : LocalStore - Codecs : [{'endian': }, {'level': 0, 'checksum': False}] - No. bytes : 40000 (39.1K) - -This compresses the data using the Zstandard codec with shuffle enabled for better compression. - -Hierarchical Groups -------------------- - -Zarr allows you to create hierarchical groups, similar to directories:: - - >>> # Create nested groups and add arrays - >>> root = zarr.group("data/example-2.zarr") - >>> foo = root.create_group(name="foo") - >>> bar = root.create_array( - ... name="bar", shape=(100, 10), chunks=(10, 10), dtype="f4" - ... ) - >>> spam = foo.create_array(name="spam", shape=(10,), dtype="i4") - >>> - >>> # Assign values - >>> bar[:, :] = np.random.random((100, 10)) - >>> spam[:] = np.arange(10) - >>> - >>> # print the hierarchy - >>> root.tree() - / - ├── bar (100, 10) float32 - └── foo - └── spam (10,) int32 - - -This creates a group with two datasets: ``foo`` and ``bar``. - -Batch Hierarchy Creation -~~~~~~~~~~~~~~~~~~~~~~~~ - -Zarr provides tools for creating a collection of arrays and groups with a single function call. -Suppose we want to copy existing groups and arrays into a new storage backend: - - >>> # Create nested groups and add arrays - >>> root = zarr.group("data/example-3.zarr", attributes={'name': 'root'}) - >>> foo = root.create_group(name="foo") - >>> bar = root.create_array( - ... name="bar", shape=(100, 10), chunks=(10, 10), dtype="f4" - ... ) - >>> nodes = {'': root.metadata} | {k: v.metadata for k,v in root.members()} - >>> print(nodes) - >>> from zarr.storage import MemoryStore - >>> new_nodes = dict(zarr.create_hierarchy(store=MemoryStore(), nodes=nodes)) - >>> new_root = new_nodes[''] - >>> assert new_root.attrs == root.attrs - -Note that :func:`zarr.create_hierarchy` will only initialize arrays and groups -- copying array data must -be done in a separate step. - -Persistent Storage ------------------- - -Zarr supports persistent storage to disk or cloud-compatible backends. While examples above -utilized a :class:`zarr.storage.LocalStore`, a number of other storage options are available. - -Zarr integrates seamlessly with cloud object storage such as Amazon S3 and Google Cloud Storage -using external libraries like `s3fs `_ or -`gcsfs `_:: - - >>> import s3fs # doctest: +SKIP - >>> - >>> z = zarr.create_array("s3://example-bucket/foo", mode="w", shape=(100, 100), chunks=(10, 10), dtype="f4") # doctest: +SKIP - >>> z[:, :] = np.random.random((100, 100)) # doctest: +SKIP - -A single-file store can also be created using the the :class:`zarr.storage.ZipStore`:: - - >>> # Store the array in a ZIP file - >>> store = zarr.storage.ZipStore("data/example-3.zip", mode='w') - >>> - >>> z = zarr.create_array( - ... store=store, - ... mode="w", - ... shape=(100, 100), - ... chunks=(10, 10), - ... dtype="f4" - ... ) - >>> - >>> # write to the array - >>> z[:, :] = np.random.random((100, 100)) - >>> - >>> # the ZipStore must be explicitly closed - >>> store.close() - -To open an existing array from a ZIP file:: - - >>> # Open the ZipStore in read-only mode - >>> store = zarr.storage.ZipStore("data/example-3.zip", read_only=True) - >>> - >>> z = zarr.open_array(store, mode='r') - >>> - >>> # read the data as a NumPy Array - >>> z[:] - array([[0.66734236, 0.15667458, 0.98720884, ..., 0.36229587, 0.67443246, - 0.34315267], - [0.65787303, 0.9544212 , 0.4830079 , ..., 0.33097172, 0.60423803, - 0.45621237], - [0.27632037, 0.9947008 , 0.42434934, ..., 0.94860053, 0.6226942 , - 0.6386924 ], - ..., - [0.12854576, 0.934397 , 0.19524333, ..., 0.11838563, 0.4967675 , - 0.43074256], - [0.82029045, 0.4671437 , 0.8090906 , ..., 0.7814118 , 0.42650765, - 0.95929915], - [0.4335856 , 0.7565437 , 0.7828931 , ..., 0.48119593, 0.66220033, - 0.6652362 ]], shape=(100, 100), dtype=float32) - -Read more about Zarr's storage options in the :ref:`User Guide `. - -Next Steps ----------- - -Now that you're familiar with the basics, explore the following resources: - -- `User Guide `_ -- `API Reference `_ diff --git a/docs/release-notes.md b/docs/release-notes.md new file mode 100644 index 0000000000..2fa947d5eb --- /dev/null +++ b/docs/release-notes.md @@ -0,0 +1,465 @@ +# Release notes + + + +# zarr 3.1.3 (2025-09-18) + +## Features + +- Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also provided under zarr.metadata. ([#1798](https://github.com/zarr-developers/zarr-python/issues/1798)) +- Add obstore implementation of delete_dir. ([#3310](https://github.com/zarr-developers/zarr-python/issues/3310)) +- Adds a registry for chunk key encodings for extensibility. This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. ([#3436](https://github.com/zarr-developers/zarr-python/issues/3436)) +- Trying to open a group at a path were a array already exists now raises a helpful error. ([#3444](https://github.com/zarr-developers/zarr-python/issues/3444)) + +## Bugfixes + +- Prevents creation of groups (.create_group) or arrays (.create_array) as children of an existing array. ([#2582](https://github.com/zarr-developers/zarr-python/issues/2582)) +- Fix a bug preventing `ones_like`, `full_like`, `empty_like`, `zeros_like` and `open_like` functions from accepting an explicit specification of array attributes like shape, dtype, chunks etc. The functions `full_like`, `empty_like`, and `open_like` now also more consistently infer a `fill_value` parameter from the provided array. ([#2992](https://github.com/zarr-developers/zarr-python/issues/2992)) +- LocalStore now uses atomic writes, which should prevent some cases of corrupted data. ([#3411](https://github.com/zarr-developers/zarr-python/issues/3411)) +- Fix a potential race condition when using `zarr.create_array` with the `data` parameter set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for that array. ([#3422](https://github.com/zarr-developers/zarr-python/issues/3422)) +- Fix ChunkGrid definition (broken in 3.1.2) ([#3425](https://github.com/zarr-developers/zarr-python/issues/3425)) +- Ensure syntax like `root['/subgroup']` works equivalently to `root['subgroup']` when using consolidated metadata. ([#3428](https://github.com/zarr-developers/zarr-python/issues/3428)) +- Creating a new group with `zarr.group` no longer errors. This fixes a regression introduced in version 3.1.2. ([#3431](https://github.com/zarr-developers/zarr-python/issues/3431)) +- Setting `fill_value` to a float like `0.0` when the data type of the array is an integer is a common mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python will not create such arrays. ([#3448](https://github.com/zarr-developers/zarr-python/issues/3448)) + +## Deprecations and Removals + +- The `Store.set_partial_writes` method, which was not used by Zarr-Python, has been removed. `store.supports_partial_writes` is now always `False`. ([#2859](https://github.com/zarr-developers/zarr-python/issues/2859)) + +## Misc + +- [#3376](https://github.com/zarr-developers/zarr-python/issues/3376), [#3390](https://github.com/zarr-developers/zarr-python/issues/3390), [#3403](https://github.com/zarr-developers/zarr-python/issues/3403), [#3449](https://github.com/zarr-developers/zarr-python/issues/3449) + +## 3.1.2 (2025-08-25) + +### Features + +- Added support for async vectorized and orthogonal indexing. ([#3083](https://github.com/zarr-developers/zarr-python/issues/3083)) +- Make config param optional in init_array ([#3391](https://github.com/zarr-developers/zarr-python/issues/3391)) + +### Bugfixes + +- Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value. ([#3144](https://github.com/zarr-developers/zarr-python/issues/3144)) +- Fix a bug in `create_array` caused by iterating over chunk-aligned regions instead of shard-aligned regions when writing data. Additionally, the behavior of `nchunks_initialized` has been adjusted. This function consistently reports the number of chunks present in stored objects, even when the array uses the sharding codec. ([#3299](https://github.com/zarr-developers/zarr-python/issues/3299)) +- Opening an array or group with `mode="r+"` will no longer create new arrays or groups. ([#3307](https://github.com/zarr-developers/zarr-python/issues/3307)) +- Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected. ([#3367](https://github.com/zarr-developers/zarr-python/issues/3367)) +- Ensure passing `config` is handled properly when `open`ing an existing array. ([#3378](https://github.com/zarr-developers/zarr-python/issues/3378)) +- Raise a Zarr-specific error class when a codec can't be found by name when deserializing the given codecs. This avoids hiding this error behind a "not part of a zarr hierarchy" warning. ([#3395](https://github.com/zarr-developers/zarr-python/issues/3395)) + +### Misc + +- [#3098](https://github.com/zarr-developers/zarr-python/issues/3098), [#3288](https://github.com/zarr-developers/zarr-python/issues/3288), [#3318](https://github.com/zarr-developers/zarr-python/issues/3318), [#3368](https://github.com/zarr-developers/zarr-python/issues/3368), [#3371](https://github.com/zarr-developers/zarr-python/issues/3371), [#3372](https://github.com/zarr-developers/zarr-python/issues/3372), [#3374](https://github.com/zarr-developers/zarr-python/issues/3374) + +## 3.1.1 (2025-07-28) + +### Features + +- Add lightweight implementations of `.getsize()` and `.getsize_prefix()` for ObjectStore. ([#3227](https://github.com/zarr-developers/zarr-python/issues/3227)) + +### Bugfixes + +- Creating a Zarr format 2 array with the `order` keyword argument no longer raises a warning. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) +- Fixed the error message when passing both `config` and `write_empty_chunks` arguments to reflect the current behaviour (`write_empty_chunks` takes precedence). ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) +- Creating a Zarr format 3 array with the `order` argument now consistently ignores this argument and raises a warning. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) +- When using [`from_array`][zarr.api.asynchronous.from_array] to copy a Zarr format 2 array to a Zarr format 3 array, if the memory order of the input array is `"F"` a warning is raised and the order ignored. This is because Zarr format 3 arrays are always stored in "C" order. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) +- The `config` argument to [`zarr.create`][zarr.create] (and functions that create arrays) is now used - previously it had no effect. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) +- Ensure that all abstract methods of [`ZDType`][zarr.core.dtype.ZDType] raise a `NotImplementedError` when invoked. ([#3251](https://github.com/zarr-developers/zarr-python/issues/3251)) +- Register 'gpu' marker with pytest for downstream StoreTests. ([#3258](https://github.com/zarr-developers/zarr-python/issues/3258)) +- Expand the range of types accepted by `parse_data_type` to include strings and Sequences. +- Move the functionality of `zarr.core.dtype.parse_data_type` to a new function called `zarr.dtype.parse_dtype`. This change ensures that nomenclature is consistent across the codebase. `zarr.core.dtype.parse_data_type` remains, so this change is not breaking. ([#3264](https://github.com/zarr-developers/zarr-python/issues/3264)) +- Fix a regression introduced in 3.1.0 that prevented `inf`, `-inf`, and `nan` values from being stored in `attributes`. ([#3280](https://github.com/zarr-developers/zarr-python/issues/3280)) +- Fixes [`Group.nmembers()`][zarr.Group.nmembers] ignoring depth when using consolidated metadata. ([#3287](https://github.com/zarr-developers/zarr-python/issues/3287)) + +### Improved Documentation + +- Expand the data type docs to include a demonstration of the `parse_data_type` function. Expand the docstring for the `parse_data_type` function. ([#3249](https://github.com/zarr-developers/zarr-python/issues/3249)) +- Add a section on codecs to the migration guide. ([#3273](https://github.com/zarr-developers/zarr-python/issues/3273)) + +### Misc + +- Remove warnings about vlen-utf8 and vlen-bytes codecs ([#3268](https://github.com/zarr-developers/zarr-python/issues/3268)) + +## 3.1.0 (2025-07-14) + +### Features + +- Ensure that invocations of `create_array` use consistent keyword arguments, with consistent defaults. + + [`zarr.api.synchronous.create_array`][] now takes a `write_data` keyword argument + The `Group.create_array` method takes `data` and `write_data` keyword arguments. + The functions [`zarr.api.asynchronous.create`][], [`zarr.api.asynchronous.create_array`] + and the methods `Group.create_array`, `Group.array`, had the default + `fill_value` changed from `0` to the `DEFAULT_FILL_VALUE` value, which instructs Zarr to + use the default scalar value associated with the array's data type as the fill value. These are + all functions or methods for array creation that mirror, wrap or are wrapped by, another function + that already has a default `fill_value` set to `DEFAULT_FILL_VALUE`. This change is necessary + to make these functions consistent across the entire codebase, but as this changes default values, + new data might have a different fill value than expected after this change. + + For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this + change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode + strings, the default fill value might be different after this change. Users who were relying on how + Zarr interpreted `0` as a non-numeric scalar value should set their desired fill value explicitly + after this change. + +- Added public API for Buffer ABCs and implementations. + + Use `zarr.buffer` to access buffer implementations, and + `zarr.abc.buffer` for the interface to implement new buffer types. + + Users previously importing buffer from `zarr.core.buffer` should update their + imports to use `zarr.buffer`. As a reminder, all of `zarr.core` is + considered a private API that's not covered by zarr-python's versioning policy. ([#2871](https://github.com/zarr-developers/zarr-python/issues/2871)) + +- Adds zarr-specific data type classes. + + This change adds a `ZDType` base class for Zarr V2 and Zarr V3 data types. Child classes are + defined for each NumPy data type. Each child class defines routines for `JSON` serialization. + New data types can be created and registered dynamically. + + Prior to this change, Zarr Python had two streams for handling data types. For Zarr V2 arrays, + we used NumPy data type identifiers. For Zarr V3 arrays, we used a fixed set of string enums. Both + of these systems proved hard to extend. + + This change is largely internal, but it does change the type of the `dtype` and `data_type` + fields on the `ArrayV2Metadata` and `ArrayV3Metadata` classes. Previously, `ArrayV2Metadata.dtype` + was a NumPy `dtype` object, and `ArrayV3Metadata.data_type` was an internally-defined `enum`. + After this change, both `ArrayV2Metadata.dtype` and `ArrayV3Metadata.data_type` are instances of + `ZDType`. A NumPy data type can be generated from a `ZDType` via the `ZDType.to_native_dtype()` + method. The internally-defined Zarr V3 `enum` class is gone entirely, but the `ZDType.to_json(zarr_format=3)` + method can be used to generate either a string, or dictionary that has a string `name` field, that + represents the string value previously associated with that `enum`. + + For more on this new feature, see the [documentation](user-guide/data_types.md) ([#2874](https://github.com/zarr-developers/zarr-python/issues/2874)) + +- Added `NDBuffer.empty` method for faster ndbuffer initialization. ([#3191](https://github.com/zarr-developers/zarr-python/issues/3191)) + +- The minimum version of NumPy has increased to 1.26. ([#3226](https://github.com/zarr-developers/zarr-python/issues/3226)) + +- Add an alternate `from_array_metadata_and_store` constructor to `CodecPipeline`. ([#3233](https://github.com/zarr-developers/zarr-python/issues/3233)) + +### Bugfixes + +- Fixes a variety of issues related to string data types. + + - Brings the `VariableLengthUTF8` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8 + - Disallows creation of 0-length fixed-length data types + - Adds a regression test for the `VariableLengthUTF8` data type that checks against version 3.0.8 + - Allows users to request the `VariableLengthUTF8` data type with `str`, `"str"`, or `"string"`. ([#3170](https://github.com/zarr-developers/zarr-python/issues/3170)) + +- Add human readable size for No. bytes stored to `info_complete` ([#3190](https://github.com/zarr-developers/zarr-python/issues/3190)) + +- Restores the ability to create a Zarr V2 array with a `null` fill value by introducing a new + class `DefaultFillValue`, and setting the default value of the `fill_value` parameter in array + creation routines to an instance of `DefaultFillValue`. For Zarr V3 arrays, `None` will act as an + alias for a `DefaultFillValue` instance, thus preserving compatibility with existing code. ([#3198](https://github.com/zarr-developers/zarr-python/issues/3198)) + +- Fix the type of `ArrayV2Metadata.codec` to constrain it to `numcodecs.abc.Codec | None`. + Previously the type was more permissive, allowing objects that can be parsed into Codecs (e.g., the codec name). + The constructor of `ArrayV2Metadata` still allows the permissive input when creating new objects. ([#3232](https://github.com/zarr-developers/zarr-python/issues/3232)) + +### Improved Documentation + +- Add a self-contained example of data type extension to the `examples` directory, and expanded + the documentation for data types. ([#3157](https://github.com/zarr-developers/zarr-python/issues/3157)) + +- Add a description on how to create a RemoteStore of a specific filesystem to the `Remote Store` section in `docs/user-guide/storage.md`. + State in the docstring of `FsspecStore.from_url` that the filesystem type is inferred from the URL scheme. + + It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. ([#3212](https://github.com/zarr-developers/zarr-python/issues/3212)) + +### Deprecations and Removals + +- Removes default chunk encoding settings (filters, serializer, compressors) from the global + configuration object. + + This removal is justified on the basis that storing chunk encoding settings in the config required + a brittle, confusing, and inaccurate categorization of array data types, which was particularly + unsuitable after the recent addition of new data types that didn't fit naturally into the + pre-existing categories. + + The default chunk encoding is the same (Zstandard compression, and the required object codecs for + variable length data types), but the chunk encoding is now generated by functions that cannot be + reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should + instead specify the desired chunk encoding explicitly when creating an array. + + This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that + arrays with a `VariableLengthUTF8` or `VariableLengthBytes` data type cannot be created without the + correct "object codec". ([#3228](https://github.com/zarr-developers/zarr-python/issues/3228)) + +- Removes support for passing keyword-only arguments positionally to the following functions and methods: + `save_array`, `open`, `group`, `open_group`, `create`, `get_basic_selection`, `set_basic_selection`, + `get_orthogonal_selection`, `set_orthogonal_selection`, `get_mask_selection`, `set_mask_selection`, + `get_coordinate_selection`, `set_coordinate_selection`, `get_block_selection`, `set_block_selection`, + `Group.create_array`, `Group.empty`, `Group.zeroes`, `Group.ones`, `Group.empty_like`, `Group.full`, + `Group.zeros_like`, `Group.ones_like`, `Group.full_like`, `Group.array`. Prior to this change, + passing a keyword-only argument positionally to one of these functions or methods would raise a + deprecation warning. That warning is now gone. Passing keyword-only arguments to these functions + and methods positionally is now an error. + +## 3.0.10 (2025-07-03) + +### Bugfixes + +- Removed an unnecessary check from `_fsspec._make_async` that would raise an exception when + creating a read-only store backed by a local file system with `auto_mkdir` set to `False`. ([#3193](https://github.com/zarr-developers/zarr-python/issues/3193)) + +- Add missing import for AsyncFileSystemWrapper for _make_async in _fsspec.py ([#3195](https://github.com/zarr-developers/zarr-python/issues/3195)) + +## 3.0.9 (2025-06-30) + +### Features + +- Add `zarr.storage.FsspecStore.from_mapper()` so that `zarr.open()` supports stores of type `fsspec.mapping.FSMap`. ([#2774](https://github.com/zarr-developers/zarr-python/issues/2774)) + +- Implemented `move` for `LocalStore` and `ZipStore`. This allows users to move the store to a different root path. ([#3021](https://github.com/zarr-developers/zarr-python/issues/3021)) + +- Added `zarr.errors.GroupNotFoundError`, which is raised when attempting to open a group that does not exist. ([#3066](https://github.com/zarr-developers/zarr-python/issues/3066)) + +- Adds `fill_value` to the list of attributes displayed in the output of the `AsyncArray.info()` method. ([#3081](https://github.com/zarr-developers/zarr-python/issues/3081)) + +- Use `numpy.zeros` instead of `np.full` for a performance speedup when creating a `zarr.core.buffer.NDBuffer` with `fill_value=0`. ([#3082](https://github.com/zarr-developers/zarr-python/issues/3082)) + +- Port more stateful testing actions from [Icechunk](https://icechunk.io). ([#3130](https://github.com/zarr-developers/zarr-python/issues/3130)) + +- Adds a `with_read_only` convenience method to the `Store` abstract base class (raises `NotImplementedError`) and implementations to the `MemoryStore`, `ObjectStore`, `LocalStore`, and `FsspecStore` classes. ([#3138](https://github.com/zarr-developers/zarr-python/issues/3138)) + +### Bugfixes + +- Ignore stale child metadata when reconsolidating metadata. ([#2921](https://github.com/zarr-developers/zarr-python/issues/2921)) + +- For Zarr format 2, allow fixed-length string arrays to be created without automatically inserting a + `Vlen-UT8` codec in the array of filters. Fixed-length string arrays do not need this codec. This + change fixes a regression where fixed-length string arrays created with Zarr Python 3 could not be read with Zarr Python 2.18. ([#3100](https://github.com/zarr-developers/zarr-python/issues/3100)) + +- When creating arrays without explicitly specifying a chunk size using `zarr.create` and other + array creation routines, the chunk size will now set automatically instead of defaulting to the data shape. + For large arrays this will result in smaller default chunk sizes. + To retain previous behaviour, explicitly set the chunk shape to the data shape. + + This fix matches the existing chunking behaviour of + `zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. ([#3103](https://github.com/zarr-developers/zarr-python/issues/3103)) + +- When `zarr.save` has an argument `path=some/path/` and multiple arrays in `args`, the path resulted in `some/path/some/path` due to using the `path` + argument twice while building the array path. This is now fixed. ([#3127](https://github.com/zarr-developers/zarr-python/issues/3127)) + +- Fix `zarr.open` default for argument `mode` when `store` is `read_only` ([#3128](https://github.com/zarr-developers/zarr-python/issues/3128)) + +- Suppress `FileNotFoundError` when deleting non-existent keys in the `obstore` adapter. + + When writing empty chunks (i.e. chunks where all values are equal to the array's fill value) to a zarr array, zarr + will delete those chunks from the underlying store. For zarr arrays backed by the `obstore` adapter, this will potentially + raise a `FileNotFoundError` if the chunk doesn't already exist. + Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store, + suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect + from the store. ([#3140](https://github.com/zarr-developers/zarr-python/issues/3140)) + +- Trying to open a StorePath/Array with `mode='r'` when the store is not read-only creates a read-only copy of the store. ([#3156](https://github.com/zarr-developers/zarr-python/issues/3156)) + +## 3.0.8 (2025-05-19) + +!!! warning + + In versions 3.0.0 to 3.0.7 opening arrays or groups with `mode='a'` (the default for many builtin functions) would cause any existing paths in the store to be deleted. This is fixed in 3.0.8, and we recommend all users upgrade to avoid this bug that could cause unintentional data loss. + +### Features + +- Added a `print_debug_info` function for bug reports. ([#2913](https://github.com/zarr-developers/zarr-python/issues/2913)) + +### Bugfixes + +- Fix a bug that prevented the number of initialized chunks being counted properly. ([#2862](https://github.com/zarr-developers/zarr-python/issues/2862)) +- Fixed sharding with GPU buffers. ([#2978](https://github.com/zarr-developers/zarr-python/issues/2978)) +- Fix structured `dtype` fill value serialization for consolidated metadata ([#2998](https://github.com/zarr-developers/zarr-python/issues/2998)) +- It is now possible to specify no compressor when creating a zarr format 2 array. + This can be done by passing `compressor=None` to the various array creation routines. + + The default behaviour of automatically choosing a suitable default compressor remains if the compressor argument is not given. + To reproduce the behaviour in previous zarr-python versions when `compressor=None` was passed, pass `compressor='auto'` instead. ([#3039](https://github.com/zarr-developers/zarr-python/issues/3039)) +- Fixed the typing of `dimension_names` arguments throughout so that it now accepts iterables that contain `None` alongside `str`. ([#3045](https://github.com/zarr-developers/zarr-python/issues/3045)) +- Using various functions to open data with `mode='a'` no longer deletes existing data in the store. ([#3062](https://github.com/zarr-developers/zarr-python/issues/3062)) +- Internally use `typesize` constructor parameter for `numcodecs.blosc.Blosc` to improve compression ratios back to the v2-package levels. ([#2962](https://github.com/zarr-developers/zarr-python/issues/2962)) +- Specifying the memory order of Zarr format 2 arrays using the `order` keyword argument has been fixed. ([#2950](https://github.com/zarr-developers/zarr-python/issues/2950)) + +### Misc + +- [#2972](https://github.com/zarr-developers/zarr-python/issues/2972), [#3027](https://github.com/zarr-developers/zarr-python/issues/3027), [#3049](https://github.com/zarr-developers/zarr-python/issues/3049) + +## 3.0.7 (2025-04-22) + +### Features + +- Add experimental ObjectStore storage class based on obstore. ([#1661](https://github.com/zarr-developers/zarr-python/issues/1661)) +- Add `zarr.from_array` using concurrent streaming of source data ([#2622](https://github.com/zarr-developers/zarr-python/issues/2622)) + +### Bugfixes + +- 0-dimensional arrays are now returning a scalar. Therefore, the return type of `__getitem__` changed + to NDArrayLikeOrScalar. This change is to make the behavior of 0-dimensional arrays consistent with + `numpy` scalars. ([#2718](https://github.com/zarr-developers/zarr-python/issues/2718)) +- Fix `fill_value` serialization for `NaN` in `ArrayV2Metadata` and add property-based testing of round-trip serialization ([#2802](https://github.com/zarr-developers/zarr-python/issues/2802)) +- Fixes `ConsolidatedMetadata` serialization of `nan`, `inf`, and `-inf` to be + consistent with the behavior of `ArrayMetadata`. ([#2996](https://github.com/zarr-developers/zarr-python/issues/2996)) + +### Improved Documentation + +- Updated the 3.0 migration guide to include the removal of "." syntax for getting group members. ([#2991](https://github.com/zarr-developers/zarr-python/issues/2991), [#2997](https://github.com/zarr-developers/zarr-python/issues/2997)) + +### Misc + +- Define a new versioning policy based on Effective Effort Versioning. This replaces the old Semantic + Versioning-based policy. ([#2924](https://github.com/zarr-developers/zarr-python/issues/2924), [#2910](https://github.com/zarr-developers/zarr-python/issues/2910)) +- Make warning filters in the tests more specific, so warnings emitted by tests added in the future + are more likely to be caught instead of ignored. ([#2714](https://github.com/zarr-developers/zarr-python/issues/2714)) +- Avoid an unnecessary memory copy when writing Zarr to a local file ([#2944](https://github.com/zarr-developers/zarr-python/issues/2944)) + +## 3.0.6 (2025-03-20) + +### Bugfixes + +- Restore functionality of `del z.attrs['key']` to actually delete the key. ([#2908](https://github.com/zarr-developers/zarr-python/issues/2908)) + +## 3.0.5 (2025-03-07) + +### Bugfixes + +- Fixed a bug where `StorePath` creation would not apply standard path normalization to the `path` parameter, + which led to the creation of arrays and groups with invalid keys. ([#2850](https://github.com/zarr-developers/zarr-python/issues/2850)) +- Prevent update_attributes calls from deleting old attributes ([#2870](https://github.com/zarr-developers/zarr-python/issues/2870)) + +### Misc + +- [#2796](https://github.com/zarr-developers/zarr-python/issues/2796) + +## 3.0.4 (2025-02-23) + +### Features + +- Adds functions for concurrently creating multiple arrays and groups. ([#2665](https://github.com/zarr-developers/zarr-python/issues/2665)) + +### Bugfixes + +- Fixed a bug where `ArrayV2Metadata` could save `filters` as an empty array. ([#2847](https://github.com/zarr-developers/zarr-python/issues/2847)) +- Fix a bug when setting values of a smaller last chunk. ([#2851](https://github.com/zarr-developers/zarr-python/issues/2851)) + +### Misc + +- [#2828](https://github.com/zarr-developers/zarr-python/issues/2828) + +## 3.0.3 (2025-02-14) + +### Features + +- Improves performance of FsspecStore.delete_dir for remote filesystems supporting concurrent/batched deletes, e.g., s3fs. ([#2661](https://github.com/zarr-developers/zarr-python/issues/2661)) +- Added `zarr.config.enable_gpu` to update Zarr's configuration to use GPUs. ([#2751](https://github.com/zarr-developers/zarr-python/issues/2751)) +- Avoid reading chunks during writes where possible. [#757](https://github.com/zarr-developers/zarr-python/issues/757) ([#2784](https://github.com/zarr-developers/zarr-python/issues/2784)) +- `LocalStore` learned to `delete_dir`. This makes array and group deletes more efficient. ([#2804](https://github.com/zarr-developers/zarr-python/issues/2804)) +- Add `zarr.testing.strategies.array_metadata` to generate ArrayV2Metadata and ArrayV3Metadata instances. ([#2813](https://github.com/zarr-developers/zarr-python/issues/2813)) +- Add arbitrary `shards` to Hypothesis strategy for generating arrays. ([#2822](https://github.com/zarr-developers/zarr-python/issues/2822)) + +### Bugfixes + +- Fixed bug with Zarr using device memory, instead of host memory, for storing metadata when using GPUs. ([#2751](https://github.com/zarr-developers/zarr-python/issues/2751)) +- The array returned by `zarr.empty` and an empty `zarr.core.buffer.cpu.NDBuffer` will now be filled with the + specified fill value, or with zeros if no fill value is provided. + This fixes a bug where Zarr format 2 data with no fill value was written with un-predictable chunk sizes. ([#2755](https://github.com/zarr-developers/zarr-python/issues/2755)) +- Fix zip-store path checking for stores with directories listed as files. ([#2758](https://github.com/zarr-developers/zarr-python/issues/2758)) +- Use removeprefix rather than replace when removing filename prefixes in `FsspecStore.list` ([#2778](https://github.com/zarr-developers/zarr-python/issues/2778)) +- Enable automatic removal of `needs release notes` with labeler action ([#2781](https://github.com/zarr-developers/zarr-python/issues/2781)) +- Use the proper label config ([#2785](https://github.com/zarr-developers/zarr-python/issues/2785)) +- Alters the behavior of `create_array` to ensure that any groups implied by the array's name are created if they do not already exist. Also simplifies the type signature for any function that takes an ArrayConfig-like object. ([#2795](https://github.com/zarr-developers/zarr-python/issues/2795)) +- Enitialise empty chunks to the default fill value during writing and add default fill values for datetime, timedelta, structured, and other (void* fixed size) data types ([#2799](https://github.com/zarr-developers/zarr-python/issues/2799)) +- Ensure utf8 compliant strings are used to construct numpy arrays in property-based tests ([#2801](https://github.com/zarr-developers/zarr-python/issues/2801)) +- Fix pickling for ZipStore ([#2807](https://github.com/zarr-developers/zarr-python/issues/2807)) +- Update numcodecs to not overwrite codec configuration ever. Closes [#2800](https://github.com/zarr-developers/zarr-python/issues/2800). ([#2811](https://github.com/zarr-developers/zarr-python/issues/2811)) +- Fix fancy indexing (e.g. arr[5, [0, 1]]) with the sharding codec ([#2817](https://github.com/zarr-developers/zarr-python/issues/2817)) + +### Improved Documentation + +- Added new user guide on GPU. ([#2751](https://github.com/zarr-developers/zarr-python/issues/2751)) + +## 3.0.2 (2025-01-31) + +### Features + +- Test `getsize()` and `getsize_prefix()` in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Test that a `ValueError` is raised for invalid byte range syntax in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Separate instantiating and opening a store in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Add a test for using Stores as a context managers in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Implemented `LogingStore.open()`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- `LoggingStore` is now a generic class. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Change StoreTest's `test_store_repr`, `test_store_supports_writes`, + `test_store_supports_partial_writes`, and `test_store_supports_listing` + to to be implemented using `@abstractmethod`, rather raising `NotImplementedError`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Test the error raised for invalid buffer arguments in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Test that data can be written to a store that's not yet open using the store.set method in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Adds a new function `init_array` for initializing an array in storage, and refactors `create_array` + to use `init_array`. `create_array` takes two new parameters: `data`, an optional array-like object, and `write_data`, a bool which defaults to `True`. + If `data` is given to `create_array`, then the `dtype` and `shape` attributes of `data` are used to define the + corresponding attributes of the resulting Zarr array. Additionally, if `data` given and `write_data` is `True`, + then the values in `data` will be written to the newly created array. ([#2761](https://github.com/zarr-developers/zarr-python/issues/2761)) + +### Bugfixes + +- Wrap sync fsspec filesystems with `AsyncFileSystemWrapper`. ([#2533](https://github.com/zarr-developers/zarr-python/issues/2533)) +- Added backwards compatibility for Zarr format 2 structured arrays. ([#2681](https://github.com/zarr-developers/zarr-python/issues/2681)) +- Update equality for `LoggingStore` and `WrapperStore` such that 'other' must also be a `LoggingStore` or `WrapperStore` respectively, rather than only checking the types of the stores they wrap. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Ensure that `ZipStore` is open before getting or setting any values. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Use stdout rather than stderr as the default stream for `LoggingStore`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Match the errors raised by read only stores in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Fixed `ZipStore` to make sure the correct attributes are saved when instances are pickled. + This fixes a previous bug that prevent using `ZipStore` with a `ProcessPoolExecutor`. ([#2762](https://github.com/zarr-developers/zarr-python/issues/2762)) +- Updated the optional test dependencies to include `botocore` and `fsspec`. ([#2768](https://github.com/zarr-developers/zarr-python/issues/2768)) +- Fixed the fsspec tests to skip if `botocore` is not installed. + Previously they would have failed with an import error. ([#2768](https://github.com/zarr-developers/zarr-python/issues/2768)) +- Optimize full chunk writes. ([#2782](https://github.com/zarr-developers/zarr-python/issues/2782)) + +### Improved Documentation + +- Changed the machinery for creating changelog entries. + Now individual entries should be added as files to the `changes` directory in the `zarr-python` repository, instead of directly to the changelog file. ([#2736](https://github.com/zarr-developers/zarr-python/issues/2736)) + +### Other + +- Created a type alias `ChunkKeyEncodingLike` to model the union of `ChunkKeyEncoding` instances and the dict form of the + parameters of those instances. `ChunkKeyEncodingLike` should be used by high-level functions to provide a convenient + way for creating `ChunkKeyEncoding` objects. ([#2763](https://github.com/zarr-developers/zarr-python/issues/2763)) + +## 3.0.1 (Jan. 17, 2025) + +* Implement `zarr.from_array` using concurrent streaming ([#2622](https://github.com/zarr-developers/zarr-python/issues/2622)). + +### Bug fixes + +* Fixes `order` argument for Zarr format 2 arrays ([#2679](https://github.com/zarr-developers/zarr-python/issues/2679)). +* Fixes a bug that prevented reading Zarr format 2 data with consolidated + metadata written using `zarr-python` version 2 ([#2694](https://github.com/zarr-developers/zarr-python/issues/2694)). +* Ensure that compressor=None results in no compression when writing Zarr + format 2 data ([#2708](https://github.com/zarr-developers/zarr-python/issues/2708)). +* Fix for empty consolidated metadata dataset: backwards compatibility with + Zarr-Python 2 ([#2695](https://github.com/zarr-developers/zarr-python/issues/2695)). + +### Documentation + +* Add v3.0.0 release announcement banner ([#2677](https://github.com/zarr-developers/zarr-python/issues/2677)). +* Quickstart guide alignment with V3 API ([#2697](https://github.com/zarr-developers/zarr-python/issues/2697)). +* Fix doctest failures related to numcodecs 0.15 ([#2727](https://github.com/zarr-developers/zarr-python/issues/2727)). + +### Other + +* Removed some unnecessary files from the source distribution + to reduce its size. ([#2686](https://github.com/zarr-developers/zarr-python/issues/2686)). +* Enable codecov in GitHub actions ([#2682](https://github.com/zarr-developers/zarr-python/issues/2682)). +* Speed up hypothesis tests ([#2650](https://github.com/zarr-developers/zarr-python/issues/2650)). +* Remove multiple imports for an import name ([#2723](https://github.com/zarr-developers/zarr-python/issues/2723)). + +## 3.0.0 (Jan. 9, 2025) + +3.0.0 is a new major release of Zarr-Python, with many breaking changes. +See the [v3 migration guide](user-guide/v3_migration.md) for a listing of what's changed. + +Normal release note service will resume with further releases in the 3.0.0 +series. + +Release notes for the zarr-python 2.x and 1.x releases can be found here: +https://zarr.readthedocs.io/en/support-v2/release.html diff --git a/docs/release-notes.rst b/docs/release-notes.rst deleted file mode 100644 index 8a6061b40e..0000000000 --- a/docs/release-notes.rst +++ /dev/null @@ -1,561 +0,0 @@ -Release notes -============= - -.. towncrier release notes start - -zarr 3.1.3 (2025-09-18) ------------------------ - -Features -~~~~~~~~ - -- Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also - provided under zarr.metadata. (:issue:`1798`) -- Add obstore implementation of delete_dir. (:issue:`3310`) -- Adds a registry for chunk key encodings for extensibility. - This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. (:issue:`3436`) -- Trying to open a group at a path were a array already exists now raises a helpful error. (:issue:`3444`) - - -Bugfixes -~~~~~~~~ - -- Prevents creation of groups (.create_group) or arrays (.create_array) as children - of an existing array. (:issue:`2582`) -- Fix a bug preventing ``ones_like``, ``full_like``, ``empty_like``, ``zeros_like`` and ``open_like`` functions from accepting - an explicit specification of array attributes like shape, dtype, chunks etc. The functions ``full_like``, - ``empty_like``, and ``open_like`` now also more consistently infer a ``fill_value`` parameter from the provided array. (:issue:`2992`) -- LocalStore now uses atomic writes, which should prevent some cases of corrupted data. (:issue:`3411`) -- Fix a potential race condition when using :func:`zarr.create_array` with the ``data`` parameter - set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity - that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for - that array. (:issue:`3422`) -- Fix ChunkGrid definition (broken in 3.1.2) (:issue:`3425`) -- Ensure syntax like ``root['/subgroup']`` works equivalently to ``root['subgroup']`` when using consolidated metadata. (:issue:`3428`) -- Creating a new group with `zarr.group` no longer errors. - This fixes a regression introduced in version 3.1.2. (:issue:`3431`) -- Setting ``fill_value`` to a float like ``0.0`` when the data type of the array is an integer is a common - mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python - will not create such arrays. (:issue:`3448`) - - -Deprecations and Removals -~~~~~~~~~~~~~~~~~~~~~~~~~ - -- The ``Store.set_partial_writes`` method, which was not used by Zarr-Python, has been removed. - ``store.supports_partial_writes`` is now always ``False``. (:issue:`2859`) - - -Misc -~~~~ - -- :issue:`3376`, :issue:`3390`, :issue:`3403`, :issue:`3449` - - -3.1.2 (2025-08-25) ------------------- - -Features -~~~~~~~~ - -- Added support for async vectorized and orthogonal indexing. (:issue:`3083`) -- Make config param optional in init_array (:issue:`3391`) - - -Bugfixes -~~~~~~~~ - -- Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value.``` (:issue:`3144`) -- Fix a bug in ``create_array`` caused by iterating over chunk-aligned regions instead of - shard-aligned regions when writing data. Additionally, the behavior of ``nchunks_initialized`` - has been adjusted. This function consistently reports the number of chunks present in stored objects, - even when the array uses the sharding codec. (:issue:`3299`) -- Opening an array or group with ``mode="r+"`` will no longer create new arrays or groups. (:issue:`3307`) -- Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected. (:issue:`3367`) -- Ensure passing `config` is handled properly when `open`ing an existing - array. (:issue:`3378`) -- Raise a Zarr-specific error class when a codec can't be found by name when deserializing the given codecs. This avoids hiding this error behind a "not part of a zarr hierarchy" warning. (:issue:`3395`) - - -Misc -~~~~ - -- :issue:`3098`, :issue:`3288`, :issue:`3318`, :issue:`3368`, :issue:`3371`, :issue:`3372`, :issue:`3374` - - -3.1.1 (2025-07-28) ------------------- - -Features -~~~~~~~~ - -- Add lightweight implementations of .getsize() and .getsize_prefix() for ObjectStore. (:issue:`3227`) - - -Bugfixes -~~~~~~~~ - -- Creating a Zarr format 2 array with the ``order`` keyword argument no longer raises a warning. (:issue:`3112`) -- Fixed the error message when passing both ``config`` and ``write_empty_chunks`` arguments to reflect the current behaviour (``write_empty_chunks`` takes precedence). (:issue:`3112`) -- Creating a Zarr format 3 array with the ``order`` argument now conistently ignores this argument and raises a warning. (:issue:`3112`) -- When using ``from_array`` to copy a Zarr format 2 array to a Zarr format 3 array, if the memory order of the input array is ``"F"`` a warning is raised and the order ignored. - This is because Zarr format 3 arrays are always stored in "C" order. (:issue:`3112`) -- The ``config`` argument to `zarr.create` (and functions that create arrays) is now used - previously it had no effect. (:issue:`3112`) -- Ensure that all abstract methods of ``ZDType`` raise a ``NotImplementedError`` when invoked. (:issue:`3251`) -- Register 'gpu' marker with pytest for downstream StoreTests. (:issue:`3258`) -- Expand the range of types accepted by ``parse_data_type`` to include strings and Sequences. -- Move the functionality of ``parse_data_type`` to a new function called ``parse_dtype``. This change - ensures that nomenclature is consistent across the codebase. ``parse_data_type`` remains, so this - change is not breaking. (:issue:`3264`) -- Fix a regression introduced in 3.1.0 that prevented ``inf``, ``-inf``, and ``nan`` values - from being stored in ``attributes``. (:issue:`3280`) -- Fixes Group.nmembers() ignoring depth when using consolidated metadata. (:issue:`3287`) - - -Improved Documentation -~~~~~~~~~~~~~~~~~~~~~~ - -- Expand the data type docs to include a demonstration of the ``parse_data_type`` function. - Expand the docstring for the ``parse_data_type`` function. (:issue:`3249`) -- Add a section on codecs to the migration guide. (:issue:`3273`) - - -Misc -~~~~ - -- :issue:`3268` - - -3.1.0 (2025-07-14) ------------------- - -Features -~~~~~~~~ -- Ensure that invocations of ``create_array`` use consistent keyword arguments, with consistent defaults. - - ``zarr.api.synchronous.create_array`` now takes a ``write_data`` keyword argument - The ``Group.create_array`` method takes ``data`` and ``write_data`` keyword arguments. - The functions ``api.asynchronous.create``, ``api.asynchronous.create_array`` - and the methods ``Group.create_array``, ``Group.array``, had the default - ``fill_value`` changed from ``0`` to the ``DEFAULT_FILL_VALUE`` value, which instructs Zarr to - use the default scalar value associated with the array's data type as the fill value. These are - all functions or methods for array creation that mirror, wrap or are wrapped by, another function - that already has a default ``fill_value`` set to ``DEFAULT_FILL_VALUE``. This change is necessary - to make these functions consistent across the entire codebase, but as this changes default values, - new data might have a different fill value than expected after this change. - - For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this - change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode - strings, the default fill value might be different after this change. Users who were relying on how - Zarr interpreted ``0`` as a non-numeric scalar value should set their desired fill value explicitly - after this change. -- Added public API for Buffer ABCs and implementations. - - Use :mod:`zarr.buffer` to access buffer implementations, and - :mod:`zarr.abc.buffer` for the interface to implement new buffer types. - - Users previously importing buffer from ``zarr.core.buffer`` should update their - imports to use :mod:`zarr.buffer`. As a reminder, all of ``zarr.core`` is - considered a private API that's not covered by zarr-python's versioning policy. (:issue:`2871`) -- Adds zarr-specific data type classes. - - This change adds a ``ZDType`` base class for Zarr V2 and Zarr V3 data types. Child classes are - defined for each NumPy data type. Each child class defines routines for ``JSON`` serialization. - New data types can be created and registered dynamically. - - Prior to this change, Zarr Python had two streams for handling data types. For Zarr V2 arrays, - we used NumPy data type identifiers. For Zarr V3 arrays, we used a fixed set of string enums. Both - of these systems proved hard to extend. - - This change is largely internal, but it does change the type of the ``dtype`` and ``data_type`` - fields on the ``ArrayV2Metadata`` and ``ArrayV3Metadata`` classes. Previously, ``ArrayV2Metadata.dtype`` - was a NumPy ``dtype`` object, and ``ArrayV3Metadata.data_type`` was an internally-defined ``enum``. - After this change, both ``ArrayV2Metadata.dtype`` and ``ArrayV3Metadata.data_type`` are instances of - ``ZDType``. A NumPy data type can be generated from a ``ZDType`` via the ``ZDType.to_native_dtype()`` - method. The internally-defined Zarr V3 ``enum`` class is gone entirely, but the ``ZDType.to_json(zarr_format=3)`` - method can be used to generate either a string, or dictionary that has a string ``name`` field, that - represents the string value previously associated with that ``enum``. - - For more on this new feature, see the `documentation `_ (:issue:`2874`) -- Added `NDBuffer.empty` method for faster ndbuffer initialization. (:issue:`3191`) -- The minimum version of NumPy has increased to 1.26. (:issue:`3226`) -- Add an alternate `from_array_metadata_and_store` constructor to `CodecPipeline`. (:issue:`3233`) - - -Bugfixes -~~~~~~~~ - -- Fixes a variety of issues related to string data types. - - - Brings the ``VariableLengthUTF8`` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8 - - Disallows creation of 0-length fixed-length data types - - Adds a regression test for the ``VariableLengthUTF8`` data type that checks against version 3.0.8 - - Allows users to request the ``VariableLengthUTF8`` data type with ``str``, ``"str"``, or ``"string"``. (:issue:`3170`) -- Add human readable size for No. bytes stored to `info_complete` (:issue:`3190`) -- Restores the ability to create a Zarr V2 array with a ``null`` fill value by introducing a new - class ``DefaultFillValue``, and setting the default value of the ``fill_value`` parameter in array - creation routines to an instance of ``DefaultFillValue``. For Zarr V3 arrays, ``None`` will act as an - alias for a ``DefaultFillValue`` instance, thus preserving compatibility with existing code. (:issue:`3198`) -- Fix the type of ``ArrayV2Metadata.codec`` to constrain it to ``numcodecs.abc.Codec | None``. - Previously the type was more permissive, allowing objects that can be parsed into Codecs (e.g., the codec name). - The constructor of ``ArrayV2Metadata`` still allows the permissive input when creating new objects. (:issue:`3232`) - - -Improved Documentation -~~~~~~~~~~~~~~~~~~~~~~ - -- Add a self-contained example of data type extension to the ``examples`` directory, and expanded - the documentation for data types. (:issue:`3157`) -- - Add a description on how to create a RemoteStore of a specific filesystem to the `Remote Store` section in `docs\user-guide\storage.rst`. - - State in the docstring of `FsspecStore.from_url` that the filesystem type is inferred from the URL scheme. - - It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. (:issue:`3212`) - - -Deprecations and Removals -~~~~~~~~~~~~~~~~~~~~~~~~~ - -- Removes default chunk encoding settings (filters, serializer, compressors) from the global - configuration object. - - This removal is justified on the basis that storing chunk encoding settings in the config required - a brittle, confusing, and inaccurate categorization of array data types, which was particularly - unsuitable after the recent addition of new data types that didn't fit naturally into the - pre-existing categories. - - The default chunk encoding is the same (Zstandard compression, and the required object codecs for - variable length data types), but the chunk encoding is now generated by functions that cannot be - reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should - instead specify the desired chunk encoding explicitly when creating an array. - - This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that - arrays with a ``VariableLengthUTF8`` or ``VariableLengthBytes`` data type cannot be created without the - correct "object codec". (:issue:`3228`) -- Removes support for passing keyword-only arguments positionally to the following functions and methods: - ``save_array``, ``open``, ``group``, ``open_group``, ``create``, ``get_basic_selection``, ``set_basic_selection``, - ``get_orthogonal_selection``, ``set_orthogonal_selection``, ``get_mask_selection``, ``set_mask_selection``, - ``get_coordinate_selection``, ``set_coordinate_selection``, ``get_block_selection``, ``set_block_selection``, - ``Group.create_array``, ``Group.empty``, ``Group.zeroes``, ``Group.ones``, ``Group.empty_like``, ``Group.full``, - ``Group.zeros_like``, ``Group.ones_like``, ``Group.full_like``, ``Group.array``. Prior to this change, - passing a keyword-only argument positionally to one of these functions or methods would raise a - deprecation warning. That warning is now gone. Passing keyword-only arguments to these functions - and methods positionally is now an error. - -3.0.10 (2025-07-03) -------------------- - -Bugfixes -~~~~~~~~ - -- Removed an unnecessary check from ``_fsspec._make_async`` that would raise an exception when - creating a read-only store backed by a local file system with ``auto_mkdir`` set to ``False``. (:issue:`3193`) -- Add missing import for AsyncFileSystemWrapper for _make_async in _fsspec.py (:issue:`3195`) - - -3.0.9 (2025-06-30) ------------------- - -Features -~~~~~~~~ - -- Add `zarr.storage.FsspecStore.from_mapper()` so that `zarr.open()` supports stores of type `fsspec.mapping.FSMap`. (:issue:`2774`) -- Implemented ``move`` for ``LocalStore`` and ``ZipStore``. This allows users to move the store to a different root path. (:issue:`3021`) -- Added `~zarr.errors.GroupNotFoundError`, which is raised when attempting to open a group that does not exist. (:issue:`3066`) -- Adds ``fill_value`` to the list of attributes displayed in the output of the ``AsyncArray.info()`` method. (:issue:`3081`) -- Use :py:func:`numpy.zeros` instead of :py:func:`np.full` for a performance speedup when creating a `zarr.core.buffer.NDBuffer` with `fill_value=0`. (:issue:`3082`) -- Port more stateful testing actions from `Icechunk `_. (:issue:`3130`) -- Adds a `with_read_only` convenience method to the `Store` abstract base class (raises `NotImplementedError`) and implementations to the `MemoryStore`, `ObjectStore`, `LocalStore`, and `FsspecStore` classes. (:issue:`3138`) - - -Bugfixes -~~~~~~~~ - -- Ignore stale child metadata when reconsolidating metadata. (:issue:`2921`) -- For Zarr format 2, allow fixed-length string arrays to be created without automatically inserting a - ``Vlen-UT8`` codec in the array of filters. Fixed-length string arrays do not need this codec. This - change fixes a regression where fixed-length string arrays created with Zarr Python 3 could not be read with Zarr Python 2.18. (:issue:`3100`) -- When creating arrays without explicitly specifying a chunk size using `zarr.create` and other - array creation routines, the chunk size will now set automatically instead of defaulting to the data shape. - For large arrays this will result in smaller default chunk sizes. - To retain previous behaviour, explicitly set the chunk shape to the data shape. - - This fix matches the existing chunking behaviour of - `zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. (:issue:`3103`) -- When `zarr.save` has an argument `path=some/path/` and multiple arrays in `args`, the path resulted in `some/path/some/path` due to using the `path` - argument twice while building the array path. This is now fixed. (:issue:`3127`) -- Fix `zarr.open` default for argument `mode` when `store` is `read_only` (:issue:`3128`) -- Suppress `FileNotFoundError` when deleting non-existent keys in the `obstore` adapter. - - When writing empty chunks (i.e. chunks where all values are equal to the array's fill value) to a zarr array, zarr - will delete those chunks from the underlying store. For zarr arrays backed by the `obstore` adapter, this will potentially - raise a `FileNotFoundError` if the chunk doesn't already exist. - Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store, - suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect - from the store. (:issue:`3140`) -- Trying to open a StorePath/Array with ``mode='r'`` when the store is not read-only creates a read-only copy of the store. (:issue:`3156`) - - -3.0.8 (2025-05-19) ------------------- - -.. warning:: - - In versions 3.0.0 to 3.0.7 opening arrays or groups with ``mode='a'`` (the default for many builtin functions) - would cause any existing paths in the store to be deleted. This is fixed in 3.0.8, and - we recommend all users upgrade to avoid this bug that could cause unintentional data loss. - -Features -~~~~~~~~ - -- Added a `print_debug_info` function for bug reports. (:issue:`2913`) - - -Bugfixes -~~~~~~~~ - -- Fix a bug that prevented the number of initialized chunks being counted properly. (:issue:`2862`) -- Fixed sharding with GPU buffers. (:issue:`2978`) -- Fix structured `dtype` fill value serialization for consolidated metadata (:issue:`2998`) -- It is now possible to specify no compressor when creating a zarr format 2 array. - This can be done by passing ``compressor=None`` to the various array creation routines. - - The default behaviour of automatically choosing a suitable default compressor remains if the compressor argument is not given. - To reproduce the behaviour in previous zarr-python versions when ``compressor=None`` was passed, pass ``compressor='auto'`` instead. (:issue:`3039`) -- Fixed the typing of ``dimension_names`` arguments throughout so that it now accepts iterables that contain `None` alongside `str`. (:issue:`3045`) -- Using various functions to open data with ``mode='a'`` no longer deletes existing data in the store. (:issue:`3062`) -- Internally use `typesize` constructor parameter for :class:`numcodecs.blosc.Blosc` to improve compression ratios back to the v2-package levels. (:issue:`2962`) -- Specifying the memory order of Zarr format 2 arrays using the ``order`` keyword argument has been fixed. (:issue:`2950`) - - -Misc -~~~~ - -- :issue:`2972`, :issue:`3027`, :issue:`3049` - - -3.0.7 (2025-04-22) ------------------- - -Features -~~~~~~~~ - -- Add experimental ObjectStore storage class based on obstore. (:issue:`1661`) -- Add ``zarr.from_array`` using concurrent streaming of source data (:issue:`2622`) - - -Bugfixes -~~~~~~~~ - -- 0-dimensional arrays are now returning a scalar. Therefore, the return type of ``__getitem__`` changed - to NDArrayLikeOrScalar. This change is to make the behavior of 0-dimensional arrays consistent with - ``numpy`` scalars. (:issue:`2718`) -- Fix `fill_value` serialization for `NaN` in `ArrayV2Metadata` and add property-based testing of round-trip serialization (:issue:`2802`) -- Fixes `ConsolidatedMetadata` serialization of `nan`, `inf`, and `-inf` to be - consistent with the behavior of `ArrayMetadata`. (:issue:`2996`) - - -Improved Documentation -~~~~~~~~~~~~~~~~~~~~~~ - -- Updated the 3.0 migration guide to include the removal of "." syntax for getting group members. (:issue:`2991`, :issue:`2997`) - - -Misc -~~~~ -- Define a new versioning policy based on Effective Effort Versioning. This replaces the old Semantic - Versioning-based policy. (:issue:`2924`, :issue:`2910`) -- Make warning filters in the tests more specific, so warnings emitted by tests added in the future - are more likely to be caught instead of ignored. (:issue:`2714`) -- Avoid an unnecessary memory copy when writing Zarr to a local file (:issue:`2944`) - - -3.0.6 (2025-03-20) ------------------- - -Bugfixes -~~~~~~~~ - -- Restore functionality of `del z.attrs['key']` to actually delete the key. (:issue:`2908`) - - -3.0.5 (2025-03-07) ------------------- - -Bugfixes -~~~~~~~~ - -- Fixed a bug where ``StorePath`` creation would not apply standard path normalization to the ``path`` parameter, - which led to the creation of arrays and groups with invalid keys. (:issue:`2850`) -- Prevent update_attributes calls from deleting old attributes (:issue:`2870`) - - -Misc -~~~~ - -- :issue:`2796` - -3.0.4 (2025-02-23) ------------------- - -Features -~~~~~~~~ - -- Adds functions for concurrently creating multiple arrays and groups. (:issue:`2665`) - -Bugfixes -~~~~~~~~ - -- Fixed a bug where ``ArrayV2Metadata`` could save ``filters`` as an empty array. (:issue:`2847`) -- Fix a bug when setting values of a smaller last chunk. (:issue:`2851`) - -Misc -~~~~ - -- :issue:`2828` - - -3.0.3 (2025-02-14) ------------------- - -Features -~~~~~~~~ - -- Improves performance of FsspecStore.delete_dir for remote filesystems supporting concurrent/batched deletes, e.g., s3fs. (:issue:`2661`) -- Added :meth:`zarr.config.enable_gpu` to update Zarr's configuration to use GPUs. (:issue:`2751`) -- Avoid reading chunks during writes where possible. :issue:`757` (:issue:`2784`) -- :py:class:`LocalStore` learned to ``delete_dir``. This makes array and group deletes more efficient. (:issue:`2804`) -- Add `zarr.testing.strategies.array_metadata` to generate ArrayV2Metadata and ArrayV3Metadata instances. (:issue:`2813`) -- Add arbitrary `shards` to Hypothesis strategy for generating arrays. (:issue:`2822`) - - -Bugfixes -~~~~~~~~ - -- Fixed bug with Zarr using device memory, instead of host memory, for storing metadata when using GPUs. (:issue:`2751`) -- The array returned by ``zarr.empty`` and an empty ``zarr.core.buffer.cpu.NDBuffer`` will now be filled with the - specified fill value, or with zeros if no fill value is provided. - This fixes a bug where Zarr format 2 data with no fill value was written with un-predictable chunk sizes. (:issue:`2755`) -- Fix zip-store path checking for stores with directories listed as files. (:issue:`2758`) -- Use removeprefix rather than replace when removing filename prefixes in `FsspecStore.list` (:issue:`2778`) -- Enable automatic removal of `needs release notes` with labeler action (:issue:`2781`) -- Use the proper label config (:issue:`2785`) -- Alters the behavior of ``create_array`` to ensure that any groups implied by the array's name are created if they do not already exist. Also simplifies the type signature for any function that takes an ArrayConfig-like object. (:issue:`2795`) -- Enitialise empty chunks to the default fill value during writing and add default fill values for datetime, timedelta, structured, and other (void* fixed size) data types (:issue:`2799`) -- Ensure utf8 compliant strings are used to construct numpy arrays in property-based tests (:issue:`2801`) -- Fix pickling for ZipStore (:issue:`2807`) -- Update numcodecs to not overwrite codec configuration ever. Closes :issue:`2800`. (:issue:`2811`) -- Fix fancy indexing (e.g. arr[5, [0, 1]]) with the sharding codec (:issue:`2817`) - - -Improved Documentation -~~~~~~~~~~~~~~~~~~~~~~ - -- Added new user guide on :ref:`user-guide-gpu`. (:issue:`2751`) - - -3.0.2 (2025-01-31) ------------------- - -Features -~~~~~~~~ - -- Test ``getsize()`` and ``getsize_prefix()`` in ``StoreTests``. (:issue:`2693`) -- Test that a ``ValueError`` is raised for invalid byte range syntax in ``StoreTests``. (:issue:`2693`) -- Separate instantiating and opening a store in ``StoreTests``. (:issue:`2693`) -- Add a test for using Stores as a context managers in ``StoreTests``. (:issue:`2693`) -- Implemented ``LogingStore.open()``. (:issue:`2693`) -- ``LoggingStore`` is now a generic class. (:issue:`2693`) -- Change StoreTest's ``test_store_repr``, ``test_store_supports_writes``, - ``test_store_supports_partial_writes``, and ``test_store_supports_listing`` - to to be implemented using ``@abstractmethod``, rather raising ``NotImplementedError``. (:issue:`2693`) -- Test the error raised for invalid buffer arguments in ``StoreTests``. (:issue:`2693`) -- Test that data can be written to a store that's not yet open using the store.set method in ``StoreTests``. (:issue:`2693`) -- Adds a new function ``init_array`` for initializing an array in storage, and refactors ``create_array`` - to use ``init_array``. ``create_array`` takes two new parameters: ``data``, an optional array-like object, and ``write_data``, a bool which defaults to ``True``. - If ``data`` is given to ``create_array``, then the ``dtype`` and ``shape`` attributes of ``data`` are used to define the - corresponding attributes of the resulting Zarr array. Additionally, if ``data`` given and ``write_data`` is ``True``, - then the values in ``data`` will be written to the newly created array. (:issue:`2761`) - - -Bugfixes -~~~~~~~~ - -- Wrap sync fsspec filesystems with ``AsyncFileSystemWrapper``. (:issue:`2533`) -- Added backwards compatibility for Zarr format 2 structured arrays. (:issue:`2681`) -- Update equality for ``LoggingStore`` and ``WrapperStore`` such that 'other' must also be a ``LoggingStore`` or ``WrapperStore`` respectively, rather than only checking the types of the stores they wrap. (:issue:`2693`) -- Ensure that ``ZipStore`` is open before getting or setting any values. (:issue:`2693`) -- Use stdout rather than stderr as the default stream for ``LoggingStore``. (:issue:`2693`) -- Match the errors raised by read only stores in ``StoreTests``. (:issue:`2693`) -- Fixed ``ZipStore`` to make sure the correct attributes are saved when instances are pickled. - This fixes a previous bug that prevent using ``ZipStore`` with a ``ProcessPoolExecutor``. (:issue:`2762`) -- Updated the optional test dependencies to include ``botocore`` and ``fsspec``. (:issue:`2768`) -- Fixed the fsspec tests to skip if ``botocore`` is not installed. - Previously they would have failed with an import error. (:issue:`2768`) -- Optimize full chunk writes. (:issue:`2782`) - - -Improved Documentation -~~~~~~~~~~~~~~~~~~~~~~ - -- Changed the machinery for creating changelog entries. - Now individual entries should be added as files to the `changes` directory in the `zarr-python` repository, instead of directly to the changelog file. (:issue:`2736`) - -Other -~~~~~ - -- Created a type alias ``ChunkKeyEncodingLike`` to model the union of ``ChunkKeyEncoding`` instances and the dict form of the - parameters of those instances. ``ChunkKeyEncodingLike`` should be used by high-level functions to provide a convenient - way for creating ``ChunkKeyEncoding`` objects. (:issue:`2763`) - - -3.0.1 (Jan. 17, 2025) ---------------------- - -* Implement ``zarr.from_array`` using concurrent streaming (:issue:`2622`). - -Bug fixes -~~~~~~~~~ -* Fixes ``order`` argument for Zarr format 2 arrays (:issue:`2679`). - -* Fixes a bug that prevented reading Zarr format 2 data with consolidated - metadata written using ``zarr-python`` version 2 (:issue:`2694`). - -* Ensure that compressor=None results in no compression when writing Zarr - format 2 data (:issue:`2708`). - -* Fix for empty consolidated metadata dataset: backwards compatibility with - Zarr-Python 2 (:issue:`2695`). - -Documentation -~~~~~~~~~~~~~ -* Add v3.0.0 release announcement banner (:issue:`2677`). - -* Quickstart guide alignment with V3 API (:issue:`2697`). - -* Fix doctest failures related to numcodecs 0.15 (:issue:`2727`). - -Other -~~~~~ -* Removed some unnecessary files from the source distribution - to reduce its size. (:issue:`2686`). - -* Enable codecov in GitHub actions (:issue:`2682`). - -* Speed up hypothesis tests (:issue:`2650`). - -* Remove multiple imports for an import name (:issue:`2723`). - - -.. _release_3.0.0: - -3.0.0 (Jan. 9, 2025) --------------------- - -3.0.0 is a new major release of Zarr-Python, with many breaking changes. -See the :ref:`v3 migration guide` for a listing of what's changed. - -Normal release note service will resume with further releases in the 3.0.0 -series. - -Release notes for the zarr-python 2.x and 1.x releases can be found here: -https://zarr.readthedocs.io/en/support-v2/release.html diff --git a/docs/talks/scipy2019/submission.rst b/docs/talks/scipy2019/submission.rst deleted file mode 100644 index 57fd925b1f..0000000000 --- a/docs/talks/scipy2019/submission.rst +++ /dev/null @@ -1,144 +0,0 @@ -Zarr - scalable storage of tensor data for use in parallel and distributed computing -==================================================================================== - -SciPy 2019 submission. - - -Short summary -------------- - -Many scientific problems involve computing over large N-dimensional -typed arrays of data, and reading or writing data is often the major -bottleneck limiting speed or scalability. The Zarr project is -developing a simple, scalable approach to storage of such data in a -way that is compatible with a range of approaches to distributed and -parallel computing. We describe the Zarr protocol and data storage -format, and the current state of implementations for various -programming languages including Python. We also describe current uses -of Zarr in malaria genomics, the Human Cell Atlas, and the Pangeo -project. - - -Abstract --------- - -Background -~~~~~~~~~~ - -Across a broad range of scientific disciplines, data are naturally -represented and stored as N-dimensional typed arrays, also known as -tensors. The volume of data being generated is outstripping our -ability to analyse it, and scientific communities are looking for ways -to leverage modern multi-core CPUs and distributed computing -platforms, including cloud computing. Retrieval and storage of data is -often the major bottleneck, and new approaches to data storage are -needed to accelerate distributed computations and enable them to scale -on a variety of platforms. - -Methods -~~~~~~~ - -We have designed a new storage format and protocol for tensor data -[1_], and have released an open source Python implementation [2_, -3_]. Our approach builds on data storage concepts from HDF5 [4_], -particularly chunking and compression, and hierarchical organisation -of datasets. Key design goals include: a simple protocol and format -that can be implemented in other programming languages; support for -multiple concurrent readers or writers; support for a variety of -parallel computing environments, from multi-threaded execution on a -single CPU to multi-process execution across a multi-node cluster; -pluggable storage subsystem with support for file systems, key-value -databases and cloud object stores; pluggable encoding subsystem with -support for a variety of modern compressors. - -Results -~~~~~~~ - -We illustrate the use of Zarr with examples from several scientific -domains. Zarr is being used within the Pangeo project [5_], which is -building a community platform for big data geoscience. The Pangeo -community have converted a number of existing climate modelling and -satellite observation datasets to Zarr [6_], and have demonstrated -their use in computations using HPC and cloud computing -environments. Within the MalariaGEN project [7_], Zarr is used to -store genome variation data from next-generation sequencing of natural -populations of malaria parasites and mosquitoes [8_] and these data -are used as input to analyses of the evolution of these organisms in -response to selective pressure from anti-malarial drugs and -insecticides. Zarr is being used within the Human Cell Atlas (HCA) -project [9_], which is building a reference atlas of healthy human -cell types. This project hopes to leverage this information to better -understand the dysregulation of cellular states that underly human -disease. The Human Cell Atlas uses Zarr as the output data format -because it enables the project to easily generate matrices containing -user-selected subsets of cells. - -Conclusions -~~~~~~~~~~~ - -Zarr is generating interest across a range of scientific domains, and -work is ongoing to establish a community process to support further -development of the specifications and implementations in other -programming languages [10_, 11_, 12_] and building interoperability -with a similar project called N5 [13_]. Other packages within the -PyData ecosystem, notably Dask [14_], Xarray [15_] and Intake [16_], -have added capability to read and write Zarr, and together these -packages provide a compelling solution for large scale data science -using Python [17_]. Zarr has recently been presented in several -venues, including a webinar for the ESIP Federation tech dive series -[18_], and a talk at the AGU Fall Meeting 2018 [19_]. - - -References -~~~~~~~~~~ - -.. _1: https://zarr.readthedocs.io/en/stable/spec/v2.html -.. _2: https://github.com/zarr-developers/zarr-python -.. _3: https://github.com/zarr-developers/numcodecs -.. _4: https://www.hdfgroup.org/solutions/hdf5/ -.. _5: https://pangeo.io/ -.. _6: https://pangeo.io/catalog.html -.. _7: https://www.malariagen.net/ -.. _8: http://alimanfoo.github.io/2016/09/21/genotype-compression-benchmark.html -.. _9: https://www.humancellatlas.org/ -.. _10: https://github.com/constantinpape/z5 -.. _11: https://github.com/lasersonlab/ndarray.scala -.. _12: https://github.com/meggart/ZarrNative.jl -.. _13: https://github.com/saalfeldlab/n5 -.. _14: http://docs.dask.org/en/latest/array-creation.html -.. _15: http://xarray.pydata.org/en/stable/io.html -.. _16: https://github.com/ContinuumIO/intake-xarray -.. _17: http://matthewrocklin.com/blog/work/2018/01/22/pangeo-2 -.. _18: http://wiki.esipfed.org/index.php/Interoperability_and_Technology/Tech_Dive_Webinar_Series#8_March.2C_2018:_.22Zarr:_A_simple.2C_open.2C_scalable_solution_for_big_NetCDF.2FHDF_data_on_the_Cloud.22:_Alistair_Miles.2C_University_of_Oxford. -.. _19: https://agu.confex.com/agu/fm18/meetingapp.cgi/Paper/390015 - - -Authors -------- - -Project contributors are listed in alphabetical order by surname. - -* `Ryan Abernathey `_, Columbia University -* `Stephan Balmer `_, Meteotest -* `Ambrose Carr `_, Chan Zuckerberg Initiative -* `Tim Crone `_, Columbia University -* `Martin Durant `_, Anaconda, inc. -* `Jan Funke `_, HHMI Janelia -* `Darren Gallagher `_, Satavia -* `Fabian Gans `_, Max Planck Institute for Biogeochemistry -* `Shikhar Goenka `_, Satavia -* `Joe Hamman `_, NCAR -* `Stephan Hoyer `_, Google -* `Jerome Kelleher `_, University of Oxford -* `John Kirkham `_, HHMI Janelia -* `Alistair Miles `_, University of Oxford -* `Josh Moore `_, University of Dundee -* `Charles Noyes `_, University of Southern California -* `Tarik Onalan `_ -* `Constantin Pape `_, University of Heidelberg -* `Zain Patel `_, University of Cambridge -* `Matthew Rocklin `_, NVIDIA -* `Stephan Saafeld `_, HHMI Janelia -* `Vincent Schut `_, Satelligence -* `Justin Swaney `_, MIT -* `Ryan Williams `_, Chan Zuckerberg Initiative diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md new file mode 100644 index 0000000000..25a1347fe3 --- /dev/null +++ b/docs/user-guide/arrays.md @@ -0,0 +1,575 @@ +# Working with arrays + +## Creating an array + +Zarr has several functions for creating arrays. For example: + +```python exec="true" session="arrays" +import shutil +shutil.rmtree('data', ignore_errors=True) +import numpy as np + +np.random.seed(0) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +import zarr +store = zarr.storage.MemoryStore() +z = zarr.create_array(store=store, shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') +print(z) +``` + +The code above creates a 2-dimensional array of 32-bit integers with 10000 rows +and 10000 columns, divided into chunks where each chunk has 1000 rows and 1000 +columns (and so there will be 100 chunks in total). The data is written to a +[`zarr.storage.MemoryStore`][] (e.g. an in-memory dict). See +[Persistent arrays](#persistent-arrays) for details on storing arrays in other stores, +and see [Data types](data_types.md) for an in-depth look at the data types supported +by Zarr. + +See the [creation API documentation](../api/create.md) for more detailed information about +creating arrays. + +## Reading and writing data + +Zarr arrays support a similar interface to [NumPy](https://numpy.org/doc/stable/) +arrays for reading and writing data. For example, the entire array can be filled +with a scalar value: + +```python exec="true" session="arrays" source="above" +z[:] = 42 +``` + +Regions of the array can also be written to, e.g.: + +```python exec="true" session="arrays" source="above" +import numpy as np + +z[0, :] = np.arange(10000) +z[:, 0] = np.arange(10000) +``` + +The contents of the array can be retrieved by slicing, which will load the +requested region into memory as a NumPy array, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[0, 0]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[-1, -1]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[0, :]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[:, 0]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[:]) +``` + +Read more about NumPy-style indexing can be found in the +[NumPy documentation](https://numpy.org/doc/stable/user/basics.indexing.html). + +## Persistent arrays + +In the examples above, compressed data for each chunk of the array was stored in +main memory. Zarr arrays can also be stored on a file system, enabling +persistence of data between sessions. To do this, we can change the store +argument to point to a filesystem path: + +```python exec="true" session="arrays" source="above" +z1 = zarr.create_array(store='data/example-1.zarr', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') +``` + +The array above will store its configuration metadata and all compressed chunk +data in a directory called `'data/example-1.zarr'` relative to the current working +directory. The [`zarr.create_array`][] function provides a convenient way +to create a new persistent array or continue working with an existing +array. Note, there is no need to close an array: data are automatically +flushed to disk, and files are automatically closed whenever an array is modified. + +Persistent arrays support the same interface for reading and writing data, +e.g.: + +```python exec="true" session="arrays" source="above" +z1[:] = 42 +z1[0, :] = np.arange(10000) +z1[:, 0] = np.arange(10000) +``` + +Check that the data have been written and can be read again: + +```python exec="true" session="arrays" source="above" result="ansi" +z2 = zarr.open_array('data/example-1.zarr', mode='r') +print(np.all(z1[:] == z2[:])) +``` + +If you are just looking for a fast and convenient way to save NumPy arrays to +disk then load back into memory later, the functions +[`zarr.save`][] and [`zarr.load`][] may be +useful. E.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +a = np.arange(10) +zarr.save('data/example-2.zarr', a) +print(zarr.load('data/example-2.zarr')) +``` + +Please note that there are a number of other options for persistent array +storage, see the [Storage Guide](storage.md) for more details. + +## Resizing and appending + +A Zarr array can be resized, which means that any of its dimensions can be +increased or decreased in length. For example: + +```python exec="true" session="arrays" source="above" result="ansi" +z = zarr.create_array(store='data/example-3.zarr', shape=(10000, 10000), dtype='int32',chunks=(1000, 1000)) +z[:] = 42 +print(f"Original shape: {z.shape}") +z.resize((20000, 10000)) +print(f"New shape: {z.shape}") +``` + +Note that when an array is resized, the underlying data are not rearranged in +any way. If one or more dimensions are shrunk, any chunks falling outside the +new array shape will be deleted from the underlying store. + +[`zarr.Array.append`][] is provided as a convenience function, which can be +used to append data to any axis. E.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +a = np.arange(10000000, dtype='int32').reshape(10000, 1000) +z = zarr.create_array(store='data/example-4.zarr', shape=a.shape, dtype=a.dtype, chunks=(1000, 100)) +z[:] = a +print(f"Original shape: {z.shape}") +z.append(a) +print(f"Shape after first append: {z.shape}") +z.append(np.vstack([a, a]), axis=1) +print(f"Shape after second append: {z.shape}") +``` + +## Compressors + +A number of different compressors can be used with Zarr. Zarr includes Blosc, +Zstandard and Gzip compressors. Additional compressors are available through +a separate package called [NumCodecs](https://numcodecs.readthedocs.io/) which provides various +compressor libraries including LZ4, Zlib, BZ2 and LZMA. +Different compressors can be provided via the `compressors` keyword +argument accepted by all array creation functions. For example: + +```python exec="true" session="arrays" source="above" result="ansi" +compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=3, shuffle=zarr.codecs.BloscShuffle.bitshuffle) +data = np.arange(100000000, dtype='int32').reshape(10000, 10000) +z = zarr.create_array(store='data/example-5.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=compressors) +z[:] = data +print(z.compressors) +``` + +This array above will use Blosc as the primary compressor, using the Zstandard +algorithm (compression level 3) internally within Blosc, and with the +bit-shuffle filter applied. + +When using a compressor, it can be useful to get some diagnostics on the +compression ratio. Zarr arrays provide the [`zarr.Array.info`][] property +which can be used to print useful diagnostics, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.info) +``` + +The [`zarr.Array.info_complete`][] method inspects the underlying store and +prints additional diagnostics, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.info_complete()) +``` + +!!! note + [`zarr.Array.info_complete`][] will inspect the underlying store and may + be slow for large arrays. Use [`zarr.Array.info`][] if detailed storage + statistics are not needed. + +If you don't specify a compressor, by default Zarr uses the Zstandard +compressor. + +In addition to Blosc and Zstandard, other compression libraries can also be used. For example, +here is an array using Gzip compression, level 1: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(100000000, dtype='int32').reshape(10000, 10000) +z = zarr.create_array(store='data/example-6.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=zarr.codecs.GzipCodec(level=1)) +z[:] = data +print(f"Compressors: {z.compressors}") +``` + +Here is an example using LZMA from [NumCodecs](https://numcodecs.readthedocs.io/) with a custom filter pipeline including LZMA's +built-in delta filter: + +```python exec="true" session="arrays" source="above" result="ansi" +import lzma +from numcodecs.zarr3 import LZMA + +lzma_filters = [dict(id=lzma.FILTER_DELTA, dist=4), dict(id=lzma.FILTER_LZMA2, preset=1)] +compressors = LZMA(filters=lzma_filters) +data = np.arange(100000000, dtype='int32').reshape(10000, 10000) +z = zarr.create_array(store='data/example-7.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=compressors) +print(f"Compressors: {z.compressors}") +``` + +To disable compression, set `compressors=None` when creating an array, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +z = zarr.create_array( + store='data/example-8.zarr', + shape=(100000000,), + chunks=(1000000,), + dtype='int32', + compressors=None +) +print(f"Compressors: {z.compressors}") +``` + +## Filters + +In some cases, compression can be improved by transforming the data in some +way. For example, if nearby values tend to be correlated, then shuffling the +bytes within each numerical value or storing the difference between adjacent +values may increase compression ratio. Some compressors provide built-in filters +that apply transformations to the data prior to compression. For example, the +Blosc compressor has built-in implementations of byte- and bit-shuffle filters, +and the LZMA compressor has a built-in implementation of a delta +filter. However, to provide additional flexibility for implementing and using +filters in combination with different compressors, Zarr also provides a +mechanism for configuring filters outside of the primary compressor. + +Here is an example using a delta filter with the Blosc compressor: + +```python exec="true" session="arrays" source="above" result="ansi" +from numcodecs.zarr3 import Delta + +filters = [Delta(dtype='int32')] +compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=1, shuffle=zarr.codecs.BloscShuffle.shuffle) +data = np.arange(100000000, dtype='int32').reshape(10000, 10000) +z = zarr.create_array(store='data/example-9.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), filters=filters, compressors=compressors) +print(z.info_complete()) +``` + +For more information about available filter codecs, see the [Numcodecs](https://numcodecs.readthedocs.io/) documentation. + +## Advanced indexing + +Zarr arrays support several methods for advanced or "fancy" +indexing, which enable a subset of data items to be extracted or updated in an +array without loading the entire array into memory. + +Note that although this functionality is similar to some of the advanced +indexing capabilities available on NumPy arrays and on h5py datasets, **the Zarr +API for advanced indexing is different from both NumPy and h5py**, so please +read this section carefully. For a complete description of the indexing API, +see the documentation for the [`zarr.Array`][] class. + +### Indexing with coordinate arrays + +Items from a Zarr array can be extracted by providing an integer array of +coordinates. E.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(10) ** 2 +z = zarr.create_array(store='data/example-10.zarr', shape=data.shape, dtype=data.dtype) +z[:] = data +print(z[:]) +print(z.get_coordinate_selection([2, 5])) +``` + +Coordinate arrays can also be used to update data, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +z.set_coordinate_selection([2, 5], [-1, -2]) +print(z[:]) +``` + +For multidimensional arrays, coordinates must be provided for each dimension, +e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(15).reshape(3, 5) +z = zarr.create_array(store='data/example-11.zarr', shape=data.shape, dtype=data.dtype) +z[:] = data +print(z[:]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.get_coordinate_selection(([0, 2], [1, 3]))) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +z.set_coordinate_selection(([0, 2], [1, 3]), [-1, -2]) +print(z[:]) +``` + +For convenience, coordinate indexing is also available via the `vindex` +property, as well as the square bracket operator, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.vindex[[0, 2], [1, 3]]) +z.vindex[[0, 2], [1, 3]] = [-3, -4] +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[:]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[[0, 2], [1, 3]]) +``` + +When the indexing arrays have different shapes, they are broadcast together. +That is, the following two calls are equivalent: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[1, [1, 3]]) +print(z[[1, 1], [1, 3]]) +``` + +### Indexing with a mask array + +Items can also be extracted by providing a Boolean mask. E.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(10) ** 2 +z = zarr.create_array(store='data/example-12.zarr', shape=data.shape, dtype=data.dtype) +z[:] = data +print(z[:]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +sel = np.zeros_like(z, dtype=bool) +sel[2] = True +sel[5] = True +print(z.get_mask_selection(sel)) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +z.set_mask_selection(sel, [-1, -2]) +print(z[:]) +``` + +Here's a multidimensional example: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(15).reshape(3, 5) +z = zarr.create_array(store='data/example-13.zarr', shape=data.shape, dtype=data.dtype) +z[:] = data +print(z[:]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +sel = np.zeros_like(z, dtype=bool) +sel[0, 1] = True +sel[2, 3] = True +print(z.get_mask_selection(sel)) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +z.set_mask_selection(sel, [-1, -2]) +print(z[:]) +``` + +For convenience, mask indexing is also available via the `vindex` property, +e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.vindex[sel]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" + +z.vindex[sel] = [-3, -4] +print(z[:]) +``` + +Mask indexing is conceptually the same as coordinate indexing, and is +implemented internally via the same machinery. Both styles of indexing allow +selecting arbitrary items from an array, also known as point selection. + +### Orthogonal indexing + +Zarr arrays also support methods for orthogonal indexing, which allows +selections to be made along each dimension of an array independently. For +example, this allows selecting a subset of rows and/or columns from a +2-dimensional array. E.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(15).reshape(3, 5) +z = zarr.create_array(store='data/example-14.zarr', shape=data.shape, dtype=data.dtype) +z[:] = data +print(z[:]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.get_orthogonal_selection(([0, 2], slice(None)))) # select first and third rows +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.get_orthogonal_selection((slice(None), [1, 3]))) # select second and fourth columns) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.get_orthogonal_selection(([0, 2], [1, 3]))) # select rows [0, 2] and columns [1, 4] +``` + +Data can also be modified, e.g.: + +```python exec="true" session="arrays" source="above" +z.set_orthogonal_selection(([0, 2], [1, 3]), [[-1, -2], [-3, -4]]) +``` + +For convenience, the orthogonal indexing functionality is also available via the +`oindex` property, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(15).reshape(3, 5) +z = zarr.create_array(store='data/example-15.zarr', shape=data.shape, dtype=data.dtype) +z[:] = data +print(z.oindex[[0, 2], :]) # select first and third rows +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.oindex[:, [1, 3]]) # select second and fourth columns +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.oindex[[0, 2], [1, 3]]) # select rows [0, 2] and columns [1, 4] +``` + +```python exec="true" session="arrays" source="above" result="ansi" +z.oindex[[0, 2], [1, 3]] = [[-1, -2], [-3, -4]] +print(z[:]) +``` + +Any combination of integer, slice, 1D integer array and/or 1D Boolean array can +be used for orthogonal indexing. + +If the index contains at most one iterable, and otherwise contains only slices and integers, +orthogonal indexing is also available directly on the array: + +```python exec="true" session="arrays" source="above" result="ansi" +data = np.arange(15).reshape(3, 5) +z = zarr.create_array(store='data/example-16.zarr', shape=data.shape, dtype=data.dtype) +z[:] = data +print(np.all(z.oindex[[0, 2], :] == z[[0, 2], :])) +``` + +### Block Indexing + +Zarr also support block indexing, which allows selections of whole chunks based on their +logical indices along each dimension of an array. For example, this allows selecting +a subset of chunk aligned rows and/or columns from a 2-dimensional array. E.g.: + +```python exec="true" session="arrays" source="above" +data = np.arange(100).reshape(10, 10) +z = zarr.create_array(store='data/example-17.zarr', shape=data.shape, dtype=data.dtype, chunks=(3, 3)) +z[:] = data +``` + +Retrieve items by specifying their block coordinates: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.get_block_selection(1)) +``` + +Equivalent slicing: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z[3:6]) +``` + +For convenience, the block selection functionality is also available via the +`blocks` property, e.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.blocks[1]) +``` + +Block index arrays may be multidimensional to index multidimensional arrays. +For example: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.blocks[0, 1:3]) +``` + +Data can also be modified. Let's start by a simple 2D array: + +```python exec="true" session="arrays" source="above" +z = zarr.create_array(store='data/example-18.zarr', shape=(6, 6), dtype=int, chunks=(2, 2)) +``` + +Set data for a selection of items: + +```python exec="true" session="arrays" source="above" result="ansi" +z.set_block_selection((1, 0), 1) +print(z[...]) +``` + +For convenience, this functionality is also available via the `blocks` property. +E.g.: + +```python exec="true" session="arrays" source="above" result="ansi" +z.blocks[:, 2] = 7 +print(z[...]) +``` + +Any combination of integer and slice can be used for block indexing: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.blocks[2, 1:3]) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +root = zarr.create_group('data/example-19.zarr') +foo = root.create_array(name='foo', shape=(1000, 100), chunks=(10, 10), dtype='float32') +bar = root.create_array(name='bar', shape=(100,), dtype='int32') +foo[:, :] = np.random.random((1000, 100)) +bar[:] = np.arange(100) +print(root.tree()) +``` + +## Sharding + +Using small chunk shapes in very large arrays can lead to a very large number of chunks. +This can become a performance issue for file systems and object storage. +With Zarr format 3, a new sharding feature has been added to address this issue. + +With sharding, multiple chunks can be stored in a single storage object (e.g. a file). +Within a shard, chunks are compressed and serialized separately. +This allows individual chunks to be read independently. +However, when writing data, a full shard must be written in one go for optimal +performance and to avoid concurrency issues. +That means that shards are the units of writing and chunks are the units of reading. +Users need to configure the chunk and shard shapes accordingly. + +Sharded arrays can be created by providing the `shards` parameter to [`zarr.create_array`][]. + +```python exec="true" session="arrays" source="above" result="ansi" +a = zarr.create_array('data/example-20.zarr', shape=(10000, 10000), shards=(1000, 1000), chunks=(100, 100), dtype='uint8') +a[:] = (np.arange(10000 * 10000) % 256).astype('uint8').reshape(10000, 10000) +print(a.info_complete()) +``` + +In this example a shard shape of (1000, 1000) and a chunk shape of (100, 100) is used. +This means that `10*10` chunks are stored in each shard, and there are `10*10` shards in total. +Without the `shards` argument, there would be 10,000 chunks stored as individual files. + +## Missing features in 3.0 + +The following features have not been ported to 3.0 yet. + +### Copying and migrating data + +See the Zarr-Python 2 documentation on [Copying and migrating data](https://zarr.readthedocs.io/en/support-v2/tutorial.html#copying-migrating-data) for more details. diff --git a/docs/user-guide/arrays.rst b/docs/user-guide/arrays.rst deleted file mode 100644 index a498cb44a3..0000000000 --- a/docs/user-guide/arrays.rst +++ /dev/null @@ -1,632 +0,0 @@ -.. only:: doctest - - >>> import shutil - >>> shutil.rmtree('data', ignore_errors=True) - -.. _user-guide-arrays: - -Working with arrays -=================== - -Creating an array ------------------ - -Zarr has several functions for creating arrays. For example:: - - >>> import zarr - >>> store = zarr.storage.MemoryStore() - >>> z = zarr.create_array(store=store, shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') - >>> z - - -The code above creates a 2-dimensional array of 32-bit integers with 10000 rows -and 10000 columns, divided into chunks where each chunk has 1000 rows and 1000 -columns (and so there will be 100 chunks in total). The data is written to a -:class:`zarr.storage.MemoryStore` (e.g. an in-memory dict). See -:ref:`user-guide-persist` for details on storing arrays in other stores, and see -:ref:`user-guide-data-types` for an in-depth look at the data types supported by Zarr. - -For a complete list of array creation routines see the :mod:`zarr` -module documentation. - -.. _user-guide-array: - -Reading and writing data ------------------------- - -Zarr arrays support a similar interface to `NumPy `_ -arrays for reading and writing data. For example, the entire array can be filled -with a scalar value:: - - >>> z[:] = 42 - -Regions of the array can also be written to, e.g.:: - - >>> import numpy as np - >>> - >>> z[0, :] = np.arange(10000) - >>> z[:, 0] = np.arange(10000) - -The contents of the array can be retrieved by slicing, which will load the -requested region into memory as a NumPy array, e.g.:: - - >>> z[0, 0] - array(0, dtype=int32) - >>> z[-1, -1] - array(42, dtype=int32) - >>> z[0, :] - array([ 0, 1, 2, ..., 9997, 9998, 9999], - shape=(10000,), dtype=int32) - >>> z[:, 0] - array([ 0, 1, 2, ..., 9997, 9998, 9999], - shape=(10000,), dtype=int32) - >>> z[:] - array([[ 0, 1, 2, ..., 9997, 9998, 9999], - [ 1, 42, 42, ..., 42, 42, 42], - [ 2, 42, 42, ..., 42, 42, 42], - ..., - [9997, 42, 42, ..., 42, 42, 42], - [9998, 42, 42, ..., 42, 42, 42], - [9999, 42, 42, ..., 42, 42, 42]], - shape=(10000, 10000), dtype=int32) - -Read more about NumPy-style indexing can be found in the -`NumPy documentation `_. - -.. _user-guide-persist: - -Persistent arrays ------------------ - -In the examples above, compressed data for each chunk of the array was stored in -main memory. Zarr arrays can also be stored on a file system, enabling -persistence of data between sessions. To do this, we can change the store -argument to point to a filesystem path:: - - >>> z1 = zarr.create_array(store='data/example-1.zarr', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') - -The array above will store its configuration metadata and all compressed chunk -data in a directory called ``'data/example-1.zarr'`` relative to the current working -directory. The :func:`zarr.create_array` function provides a convenient way -to create a new persistent array or continue working with an existing -array. Note, there is no need to close an array: data are automatically -flushed to disk, and files are automatically closed whenever an array is modified. - -Persistent arrays support the same interface for reading and writing data, -e.g.:: - - >>> z1[:] = 42 - >>> z1[0, :] = np.arange(10000) - >>> z1[:, 0] = np.arange(10000) - -Check that the data have been written and can be read again:: - - >>> z2 = zarr.open_array('data/example-1.zarr', mode='r') - >>> np.all(z1[:] == z2[:]) - np.True_ - -If you are just looking for a fast and convenient way to save NumPy arrays to -disk then load back into memory later, the functions -:func:`zarr.save` and :func:`zarr.load` may be -useful. E.g.:: - - >>> a = np.arange(10) - >>> zarr.save('data/example-2.zarr', a) - >>> zarr.load('data/example-2.zarr') - array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]) - -Please note that there are a number of other options for persistent array -storage, see the :ref:`Storage Guide ` guide for more details. - -.. _user-guide-resize: - -Resizing and appending ----------------------- - -A Zarr array can be resized, which means that any of its dimensions can be -increased or decreased in length. For example:: - - >>> z = zarr.create_array(store='data/example-3.zarr', shape=(10000, 10000), dtype='int32',chunks=(1000, 1000)) - >>> z[:] = 42 - >>> z.shape - (10000, 10000) - >>> z.resize((20000, 10000)) - >>> z.shape - (20000, 10000) - -Note that when an array is resized, the underlying data are not rearranged in -any way. If one or more dimensions are shrunk, any chunks falling outside the -new array shape will be deleted from the underlying store. - -:func:`zarr.Array.append` is provided as a convenience function, which can be -used to append data to any axis. E.g.:: - - >>> a = np.arange(10000000, dtype='int32').reshape(10000, 1000) - >>> z = zarr.create_array(store='data/example-4.zarr', shape=a.shape, dtype=a.dtype, chunks=(1000, 100)) - >>> z[:] = a - >>> z.shape - (10000, 1000) - >>> z.append(a) - (20000, 1000) - >>> z.append(np.vstack([a, a]), axis=1) - (20000, 2000) - >>> z.shape - (20000, 2000) - -.. _user-guide-compress: - -Compressors ------------ - -A number of different compressors can be used with Zarr. Zarr includes Blosc, -Zstandard and Gzip compressors. Additional compressors are available through -a separate package called NumCodecs_ which provides various -compressor libraries including LZ4, Zlib, BZ2 and LZMA. -Different compressors can be provided via the ``compressors`` keyword -argument accepted by all array creation functions. For example:: - - >>> compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=3, shuffle=zarr.codecs.BloscShuffle.bitshuffle) - >>> data = np.arange(100000000, dtype='int32').reshape(10000, 10000) - >>> z = zarr.create_array(store='data/example-5.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=compressors) - >>> z[:] = data - >>> z.compressors - (BloscCodec(typesize=4, cname=, clevel=3, shuffle=, blocksize=0),) - -This array above will use Blosc as the primary compressor, using the Zstandard -algorithm (compression level 3) internally within Blosc, and with the -bit-shuffle filter applied. - -When using a compressor, it can be useful to get some diagnostics on the -compression ratio. Zarr arrays provide the :attr:`zarr.Array.info` property -which can be used to print useful diagnostics, e.g.:: - - >>> z.info - Type : Array - Zarr format : 3 - Data type : Int32(endianness='little') - Fill value : 0 - Shape : (10000, 10000) - Chunk shape : (1000, 1000) - Order : C - Read-only : False - Store type : LocalStore - Filters : () - Serializer : BytesCodec(endian=) - Compressors : (BloscCodec(typesize=4, cname=, clevel=3, shuffle=, blocksize=0),) - No. bytes : 400000000 (381.5M) - -The :func:`zarr.Array.info_complete` method inspects the underlying store and -prints additional diagnostics, e.g.:: - - >>> z.info_complete() - Type : Array - Zarr format : 3 - Data type : Int32(endianness='little') - Fill value : 0 - Shape : (10000, 10000) - Chunk shape : (1000, 1000) - Order : C - Read-only : False - Store type : LocalStore - Filters : () - Serializer : BytesCodec(endian=) - Compressors : (BloscCodec(typesize=4, cname=, clevel=3, shuffle=, blocksize=0),) - No. bytes : 400000000 (381.5M) - No. bytes stored : 3558573 (3.4M) - Storage ratio : 112.4 - Chunks Initialized : 100 - -.. note:: - :func:`zarr.Array.info_complete` will inspect the underlying store and may - be slow for large arrays. Use :attr:`zarr.Array.info` if detailed storage - statistics are not needed. - -If you don't specify a compressor, by default Zarr uses the Zstandard -compressor. - -In addition to Blosc and Zstandard, other compression libraries can also be used. For example, -here is an array using Gzip compression, level 1:: - - >>> data = np.arange(100000000, dtype='int32').reshape(10000, 10000) - >>> z = zarr.create_array(store='data/example-6.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=zarr.codecs.GzipCodec(level=1)) - >>> z[:] = data - >>> z.compressors - (GzipCodec(level=1),) - -Here is an example using LZMA from NumCodecs_ with a custom filter pipeline including LZMA's -built-in delta filter:: - - >>> import lzma - >>> from numcodecs.zarr3 import LZMA - >>> import warnings - >>> warnings.filterwarnings("ignore", category=UserWarning) - >>> - >>> lzma_filters = [dict(id=lzma.FILTER_DELTA, dist=4), dict(id=lzma.FILTER_LZMA2, preset=1)] - >>> compressors = LZMA(filters=lzma_filters) - >>> data = np.arange(100000000, dtype='int32').reshape(10000, 10000) - >>> z = zarr.create_array(store='data/example-7.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=compressors) - >>> z.compressors - (LZMA(codec_name='numcodecs.lzma', codec_config={'filters': [{'id': 3, 'dist': 4}, {'id': 33, 'preset': 1}]}),) - -To disable compression, set ``compressors=None`` when creating an array, e.g.:: - - >>> z = zarr.create_array(store='data/example-8.zarr', shape=(100000000,), chunks=(1000000,), dtype='int32', compressors=None) - >>> z.compressors - () - -.. _user-guide-filters: - -Filters -------- - -In some cases, compression can be improved by transforming the data in some -way. For example, if nearby values tend to be correlated, then shuffling the -bytes within each numerical value or storing the difference between adjacent -values may increase compression ratio. Some compressors provide built-in filters -that apply transformations to the data prior to compression. For example, the -Blosc compressor has built-in implementations of byte- and bit-shuffle filters, -and the LZMA compressor has a built-in implementation of a delta -filter. However, to provide additional flexibility for implementing and using -filters in combination with different compressors, Zarr also provides a -mechanism for configuring filters outside of the primary compressor. - -Here is an example using a delta filter with the Blosc compressor:: - - >>> from numcodecs.zarr3 import Delta - >>> - >>> filters = [Delta(dtype='int32')] - >>> compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=1, shuffle=zarr.codecs.BloscShuffle.shuffle) - >>> data = np.arange(100000000, dtype='int32').reshape(10000, 10000) - >>> z = zarr.create_array(store='data/example-9.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), filters=filters, compressors=compressors) - >>> z.info_complete() - Type : Array - Zarr format : 3 - Data type : Int32(endianness='little') - Fill value : 0 - Shape : (10000, 10000) - Chunk shape : (1000, 1000) - Order : C - Read-only : False - Store type : LocalStore - Filters : (Delta(codec_name='numcodecs.delta', codec_config={'dtype': 'int32'}),) - Serializer : BytesCodec(endian=) - Compressors : (BloscCodec(typesize=4, cname=, clevel=1, shuffle=, blocksize=0),) - No. bytes : 400000000 (381.5M) - No. bytes stored : 826 - Storage ratio : 484261.5 - Chunks Initialized : 0 - -For more information about available filter codecs, see the `Numcodecs -`_ documentation. - -.. _user-guide-indexing: - -Advanced indexing ------------------ - -Zarr arrays support several methods for advanced or "fancy" -indexing, which enable a subset of data items to be extracted or updated in an -array without loading the entire array into memory. - -Note that although this functionality is similar to some of the advanced -indexing capabilities available on NumPy arrays and on h5py datasets, **the Zarr -API for advanced indexing is different from both NumPy and h5py**, so please -read this section carefully. For a complete description of the indexing API, -see the documentation for the :class:`zarr.Array` class. - -Indexing with coordinate arrays -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Items from a Zarr array can be extracted by providing an integer array of -coordinates. E.g.:: - - >>> data = np.arange(10) ** 2 - >>> z = zarr.create_array(store='data/example-10.zarr', shape=data.shape, dtype=data.dtype) - >>> z[:] = data - >>> z[:] - array([ 0, 1, 4, 9, 16, 25, 36, 49, 64, 81]) - >>> z.get_coordinate_selection([2, 5]) - array([ 4, 25]) - -Coordinate arrays can also be used to update data, e.g.:: - - >>> z.set_coordinate_selection([2, 5], [-1, -2]) - >>> z[:] - array([ 0, 1, -1, 9, 16, -2, 36, 49, 64, 81]) - -For multidimensional arrays, coordinates must be provided for each dimension, -e.g.:: - - >>> data = np.arange(15).reshape(3, 5) - >>> z = zarr.create_array(store='data/example-11.zarr', shape=data.shape, dtype=data.dtype) - >>> z[:] = data - >>> z[:] - array([[ 0, 1, 2, 3, 4], - [ 5, 6, 7, 8, 9], - [10, 11, 12, 13, 14]]) - >>> z.get_coordinate_selection(([0, 2], [1, 3])) - array([ 1, 13]) - >>> z.set_coordinate_selection(([0, 2], [1, 3]), [-1, -2]) - >>> z[:] - array([[ 0, -1, 2, 3, 4], - [ 5, 6, 7, 8, 9], - [10, 11, 12, -2, 14]]) - -For convenience, coordinate indexing is also available via the ``vindex`` -property, as well as the square bracket operator, e.g.:: - - >>> z.vindex[[0, 2], [1, 3]] - array([-1, -2]) - >>> z.vindex[[0, 2], [1, 3]] = [-3, -4] - >>> z[:] - array([[ 0, -3, 2, 3, 4], - [ 5, 6, 7, 8, 9], - [10, 11, 12, -4, 14]]) - >>> z[[0, 2], [1, 3]] - array([-3, -4]) - -When the indexing arrays have different shapes, they are broadcast together. -That is, the following two calls are equivalent:: - - >>> z[1, [1, 3]] - array([6, 8]) - >>> z[[1, 1], [1, 3]] - array([6, 8]) - -Indexing with a mask array -~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Items can also be extracted by providing a Boolean mask. E.g.:: - - >>> data = np.arange(10) ** 2 - >>> z = zarr.create_array(store='data/example-12.zarr', shape=data.shape, dtype=data.dtype) - >>> z[:] = data - >>> z[:] - array([ 0, 1, 4, 9, 16, 25, 36, 49, 64, 81]) - >>> sel = np.zeros_like(z, dtype=bool) - >>> sel[2] = True - >>> sel[5] = True - >>> z.get_mask_selection(sel) - array([ 4, 25]) - >>> z.set_mask_selection(sel, [-1, -2]) - >>> z[:] - array([ 0, 1, -1, 9, 16, -2, 36, 49, 64, 81]) - -Here's a multidimensional example:: - - >>> data = np.arange(15).reshape(3, 5) - >>> z = zarr.create_array(store='data/example-13.zarr', shape=data.shape, dtype=data.dtype) - >>> z[:] = data - >>> z[:] - array([[ 0, 1, 2, 3, 4], - [ 5, 6, 7, 8, 9], - [10, 11, 12, 13, 14]]) - >>> sel = np.zeros_like(z, dtype=bool) - >>> sel[0, 1] = True - >>> sel[2, 3] = True - >>> z.get_mask_selection(sel) - array([ 1, 13]) - >>> z.set_mask_selection(sel, [-1, -2]) - >>> z[:] - array([[ 0, -1, 2, 3, 4], - [ 5, 6, 7, 8, 9], - [10, 11, 12, -2, 14]]) - -For convenience, mask indexing is also available via the ``vindex`` property, -e.g.:: - - >>> z.vindex[sel] - array([-1, -2]) - >>> z.vindex[sel] = [-3, -4] - >>> z[:] - array([[ 0, -3, 2, 3, 4], - [ 5, 6, 7, 8, 9], - [10, 11, 12, -4, 14]]) - -Mask indexing is conceptually the same as coordinate indexing, and is -implemented internally via the same machinery. Both styles of indexing allow -selecting arbitrary items from an array, also known as point selection. - -Orthogonal indexing -~~~~~~~~~~~~~~~~~~~ - -Zarr arrays also support methods for orthogonal indexing, which allows -selections to be made along each dimension of an array independently. For -example, this allows selecting a subset of rows and/or columns from a -2-dimensional array. E.g.:: - - >>> data = np.arange(15).reshape(3, 5) - >>> z = zarr.create_array(store='data/example-14.zarr', shape=data.shape, dtype=data.dtype) - >>> z[:] = data - >>> z[:] - array([[ 0, 1, 2, 3, 4], - [ 5, 6, 7, 8, 9], - [10, 11, 12, 13, 14]]) - >>> z.get_orthogonal_selection(([0, 2], slice(None))) # select first and third rows - array([[ 0, 1, 2, 3, 4], - [10, 11, 12, 13, 14]]) - >>> z.get_orthogonal_selection((slice(None), [1, 3])) # select second and fourth columns - array([[ 1, 3], - [ 6, 8], - [11, 13]]) - >>> z.get_orthogonal_selection(([0, 2], [1, 3])) # select rows [0, 2] and columns [1, 4] - array([[ 1, 3], - [11, 13]]) - -Data can also be modified, e.g.:: - - >>> z.set_orthogonal_selection(([0, 2], [1, 3]), [[-1, -2], [-3, -4]]) - -For convenience, the orthogonal indexing functionality is also available via the -``oindex`` property, e.g.:: - - >>> data = np.arange(15).reshape(3, 5) - >>> z = zarr.create_array(store='data/example-15.zarr', shape=data.shape, dtype=data.dtype) - >>> z[:] = data - >>> z.oindex[[0, 2], :] # select first and third rows - array([[ 0, 1, 2, 3, 4], - [10, 11, 12, 13, 14]]) - >>> z.oindex[:, [1, 3]] # select second and fourth columns - array([[ 1, 3], - [ 6, 8], - [11, 13]]) - >>> z.oindex[[0, 2], [1, 3]] # select rows [0, 2] and columns [1, 4] - array([[ 1, 3], - [11, 13]]) - >>> z.oindex[[0, 2], [1, 3]] = [[-1, -2], [-3, -4]] - >>> z[:] - array([[ 0, -1, 2, -2, 4], - [ 5, 6, 7, 8, 9], - [10, -3, 12, -4, 14]]) - -Any combination of integer, slice, 1D integer array and/or 1D Boolean array can -be used for orthogonal indexing. - -If the index contains at most one iterable, and otherwise contains only slices and integers, -orthogonal indexing is also available directly on the array:: - - >>> data = np.arange(15).reshape(3, 5) - >>> z = zarr.create_array(store='data/example-16.zarr', shape=data.shape, dtype=data.dtype) - >>> z[:] = data - >>> np.all(z.oindex[[0, 2], :] == z[[0, 2], :]) - np.True_ - -Block Indexing -~~~~~~~~~~~~~~ - -Zarr also support block indexing, which allows selections of whole chunks based on their -logical indices along each dimension of an array. For example, this allows selecting -a subset of chunk aligned rows and/or columns from a 2-dimensional array. E.g.:: - - >>> data = np.arange(100).reshape(10, 10) - >>> z = zarr.create_array(store='data/example-17.zarr', shape=data.shape, dtype=data.dtype, chunks=(3, 3)) - >>> z[:] = data - -Retrieve items by specifying their block coordinates:: - - >>> z.get_block_selection(1) - array([[30, 31, 32, 33, 34, 35, 36, 37, 38, 39], - [40, 41, 42, 43, 44, 45, 46, 47, 48, 49], - [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]]) - -Equivalent slicing:: - - >>> z[3:6] - array([[30, 31, 32, 33, 34, 35, 36, 37, 38, 39], - [40, 41, 42, 43, 44, 45, 46, 47, 48, 49], - [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]]) - -For convenience, the block selection functionality is also available via the -`blocks` property, e.g.:: - - >>> z.blocks[1] - array([[30, 31, 32, 33, 34, 35, 36, 37, 38, 39], - [40, 41, 42, 43, 44, 45, 46, 47, 48, 49], - [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]]) - -Block index arrays may be multidimensional to index multidimensional arrays. -For example:: - - >>> z.blocks[0, 1:3] - array([[ 3, 4, 5, 6, 7, 8], - [13, 14, 15, 16, 17, 18], - [23, 24, 25, 26, 27, 28]]) - -Data can also be modified. Let's start by a simple 2D array:: - - >>> z = zarr.create_array(store='data/example-18.zarr', shape=(6, 6), dtype=int, chunks=(2, 2)) - -Set data for a selection of items:: - - >>> z.set_block_selection((1, 0), 1) - >>> z[...] - array([[0, 0, 0, 0, 0, 0], - [0, 0, 0, 0, 0, 0], - [1, 1, 0, 0, 0, 0], - [1, 1, 0, 0, 0, 0], - [0, 0, 0, 0, 0, 0], - [0, 0, 0, 0, 0, 0]]) - -For convenience, this functionality is also available via the ``blocks`` property. -E.g.:: - - >>> z.blocks[:, 2] = 7 - >>> z[...] - array([[0, 0, 0, 0, 7, 7], - [0, 0, 0, 0, 7, 7], - [1, 1, 0, 0, 7, 7], - [1, 1, 0, 0, 7, 7], - [0, 0, 0, 0, 7, 7], - [0, 0, 0, 0, 7, 7]]) - -Any combination of integer and slice can be used for block indexing:: - - >>> z.blocks[2, 1:3] - array([[0, 0, 7, 7], - [0, 0, 7, 7]]) - >>> - >>> root = zarr.create_group('data/example-19.zarr') - >>> foo = root.create_array(name='foo', shape=(1000, 100), chunks=(10, 10), dtype='float32') - >>> bar = root.create_array(name='bar', shape=(100,), dtype='int32') - >>> foo[:, :] = np.random.random((1000, 100)) - >>> bar[:] = np.arange(100) - >>> root.tree() - / - ├── bar (100,) int32 - └── foo (1000, 100) float32 - - -.. _user-guide-sharding: - -Sharding --------- - -Using small chunk shapes in very large arrays can lead to a very large number of chunks. -This can become a performance issue for file systems and object storage. -With Zarr format 3, a new sharding feature has been added to address this issue. - -With sharding, multiple chunks can be stored in a single storage object (e.g. a file). -Within a shard, chunks are compressed and serialized separately. -This allows individual chunks to be read independently. -However, when writing data, a full shard must be written in one go for optimal -performance and to avoid concurrency issues. -That means that shards are the units of writing and chunks are the units of reading. -Users need to configure the chunk and shard shapes accordingly. - -Sharded arrays can be created by providing the ``shards`` parameter to :func:`zarr.create_array`. - - >>> a = zarr.create_array('data/example-20.zarr', shape=(10000, 10000), shards=(1000, 1000), chunks=(100, 100), dtype='uint8') - >>> a[:] = (np.arange(10000 * 10000) % 256).astype('uint8').reshape(10000, 10000) - >>> a.info_complete() - Type : Array - Zarr format : 3 - Data type : UInt8() - Fill value : 0 - Shape : (10000, 10000) - Shard shape : (1000, 1000) - Chunk shape : (100, 100) - Order : C - Read-only : False - Store type : LocalStore - Filters : () - Serializer : BytesCodec(endian=None) - Compressors : (ZstdCodec(level=0, checksum=False),) - No. bytes : 100000000 (95.4M) - No. bytes stored : 3981473 (3.8M) - Storage ratio : 25.1 - Shards Initialized : 100 - -In this example a shard shape of (1000, 1000) and a chunk shape of (100, 100) is used. -This means that 10*10 chunks are stored in each shard, and there are 10*10 shards in total. -Without the ``shards`` argument, there would be 10,000 chunks stored as individual files. - -Missing features in 3.0 ------------------------ - - -The following features have not been ported to 3.0 yet. - -Copying and migrating data -~~~~~~~~~~~~~~~~~~~~~~~~~~ - -See the Zarr-Python 2 documentation on `Copying and migrating data `_ for more details. diff --git a/docs/user-guide/attributes.md b/docs/user-guide/attributes.md new file mode 100644 index 0000000000..44d2f9fa87 --- /dev/null +++ b/docs/user-guide/attributes.md @@ -0,0 +1,37 @@ +# Working with attributes + +Zarr arrays and groups support custom key/value attributes, which can be useful for +storing application-specific metadata. For example: + +```python exec="true" session="arrays" source="above" result="ansi" +import zarr +store = zarr.storage.MemoryStore() +root = zarr.create_group(store=store) +root.attrs['foo'] = 'bar' +z = root.create_array(name='zzz', shape=(10000, 10000), dtype='int32') +z.attrs['baz'] = 42 +z.attrs['qux'] = [1, 4, 7, 12] +print(sorted(root.attrs)) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print('foo' in root.attrs) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(root.attrs['foo']) +``` +```python exec="true" session="arrays" source="above" result="ansi" +print(sorted(z.attrs)) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.attrs['baz']) +``` + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.attrs['qux']) +``` + +Internally Zarr uses JSON to store array attributes, so attribute values must be +JSON serializable. diff --git a/docs/user-guide/attributes.rst b/docs/user-guide/attributes.rst deleted file mode 100644 index ed48623e29..0000000000 --- a/docs/user-guide/attributes.rst +++ /dev/null @@ -1,30 +0,0 @@ -.. _user-guide-attrs: - -Working with attributes -======================= - -Zarr arrays and groups support custom key/value attributes, which can be useful for -storing application-specific metadata. For example:: - - >>> import zarr - >>> store = zarr.storage.MemoryStore() - >>> root = zarr.create_group(store=store) - >>> root.attrs['foo'] = 'bar' - >>> z = root.create_array(name='zzz', shape=(10000, 10000), dtype='int32') - >>> z.attrs['baz'] = 42 - >>> z.attrs['qux'] = [1, 4, 7, 12] - >>> sorted(root.attrs) - ['foo'] - >>> 'foo' in root.attrs - True - >>> root.attrs['foo'] - 'bar' - >>> sorted(z.attrs) - ['baz', 'qux'] - >>> z.attrs['baz'] - 42 - >>> z.attrs['qux'] - [1, 4, 7, 12] - -Internally Zarr uses JSON to store array attributes, so attribute values must be -JSON serializable. diff --git a/docs/user-guide/cli.md b/docs/user-guide/cli.md new file mode 100644 index 0000000000..fc812c1a20 --- /dev/null +++ b/docs/user-guide/cli.md @@ -0,0 +1,113 @@ +# Command-line interface + +Zarr-Python provides a command-line interface that enables: + +- migration of Zarr v2 metadata to v3 +- removal of v2 or v3 metadata + +To see available commands run the following in a terminal: + +```bash +zarr --help +``` + +or to get help on individual commands: + +```bash +zarr migrate --help + +zarr remove-metadata --help +``` + +## Migrate metadata from v2 to v3 + +### Migrate to a separate location + +To migrate a Zarr array/group's metadata from v2 to v3 run: + +```bash +zarr migrate v3 path/to/input.zarr path/to/output.zarr +``` + +This will write new `zarr.json` files to `output.zarr`, leaving `input.zarr` un-touched. +Note - this will migrate the entire Zarr hierarchy, so if `input.zarr` contains multiple groups/arrays, +new `zarr.json` will be made for all of them. + +### Migrate in-place + +If you'd prefer to migrate the metadata in-place run: + +```bash +zarr migrate v3 path/to/input.zarr +``` + +This will write new `zarr.json` files to `input.zarr`, leaving the existing v2 metadata un-touched. + +To open the array/group using the new metadata use: + +```python +import zarr +zarr_with_v3_metadata = zarr.open('path/to/input.zarr', zarr_format=3) +``` + +Once you are happy with the conversion, you can run the following to remove the old v2 metadata: + +```bash +zarr remove-metadata v2 path/to/input.zarr +``` + +Note there is also a shortcut to migrate and remove v2 metadata in one step: + +```bash +zarr migrate v3 path/to/input.zarr --remove-v2-metadata +``` + +## Remove metadata + +Remove v2 metadata using: + +```bash +zarr remove-metadata v2 path/to/input.zarr +``` + +or v3 with: + +```bash +zarr remove-metadata v3 path/to/input.zarr +``` + +By default, this will only allow removal of metadata if a valid alternative exists. For example, you can't +remove v2 metadata unless v3 metadata exists at that location. + +To override this behaviour use `--force`: + +```bash +zarr remove-metadata v3 path/to/input.zarr --force +``` + +## Dry run + +All commands provide a `--dry-run` option that will log changes that would be made on a real run, without creating +or modifying any files. + +```bash +zarr migrate v3 path/to/input.zarr --dry-run + +Dry run enabled - no new files will be created or changed. Log of files that would be created on a real run: +Saving metadata to path/to/input.zarr/zarr.json +``` + +## Verbose + +You can also add `--verbose` **before** any command, to see a full log of its actions: + +```bash +zarr --verbose migrate v3 path/to/input.zarr + +zarr --verbose remove-metadata v2 path/to/input.zarr +``` + +## Equivalent functions + +All features of the command-line interface are also available via functions under +`zarr.metadata`. \ No newline at end of file diff --git a/docs/user-guide/cli.rst b/docs/user-guide/cli.rst deleted file mode 100644 index 822b60d389..0000000000 --- a/docs/user-guide/cli.rst +++ /dev/null @@ -1,127 +0,0 @@ -.. _user-guide-cli: - -Command-line interface -======================== - -Zarr-Python provides a command-line interface that enables: - -- migration of Zarr v2 metadata to v3 -- removal of v2 or v3 metadata - -To see available commands run the following in a terminal: - -.. code-block:: bash - - $ zarr --help - -or to get help on individual commands: - -.. code-block:: bash - - $ zarr migrate --help - - $ zarr remove-metadata --help - - -Migrate metadata from v2 to v3 ------------------------------- - -Migrate to a separate location -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -To migrate a Zarr array/group's metadata from v2 to v3 run: - -.. code-block:: bash - - $ zarr migrate v3 path/to/input.zarr path/to/output.zarr - -This will write new ``zarr.json`` files to ``output.zarr``, leaving ``input.zarr`` un-touched. -Note - this will migrate the entire Zarr hierarchy, so if ``input.zarr`` contains multiple groups/arrays, -new ``zarr.json`` will be made for all of them. - -Migrate in-place -~~~~~~~~~~~~~~~~ - -If you'd prefer to migrate the metadata in-place run: - -.. code-block:: bash - - $ zarr migrate v3 path/to/input.zarr - -This will write new ``zarr.json`` files to ``input.zarr``, leaving the existing v2 metadata un-touched. - -To open the array/group using the new metadata use: - -.. code-block:: python - - >>> import zarr - >>> zarr_with_v3_metadata = zarr.open('path/to/input.zarr', zarr_format=3) - -Once you are happy with the conversion, you can run the following to remove the old v2 metadata: - -.. code-block:: bash - - $ zarr remove-metadata v2 path/to/input.zarr - -Note there is also a shortcut to migrate and remove v2 metadata in one step: - -.. code-block:: bash - - $ zarr migrate v3 path/to/input.zarr --remove-v2-metadata - - -Remove metadata ----------------- - -Remove v2 metadata using: - -.. code-block:: bash - - $ zarr remove-metadata v2 path/to/input.zarr - -or v3 with: - -.. code-block:: bash - - $ zarr remove-metadata v3 path/to/input.zarr - -By default, this will only allow removal of metadata if a valid alternative exists. For example, you can't -remove v2 metadata unless v3 metadata exists at that location. - -To override this behaviour use ``--force``: - -.. code-block:: bash - - $ zarr remove-metadata v3 path/to/input.zarr --force - - -Dry run --------- -All commands provide a ``--dry-run`` option that will log changes that would be made on a real run, without creating -or modifying any files. - -.. code-block:: bash - - $ zarr migrate v3 path/to/input.zarr --dry-run - - Dry run enabled - no new files will be created or changed. Log of files that would be created on a real run: - Saving metadata to path/to/input.zarr/zarr.json - - -Verbose --------- -You can also add ``--verbose`` **before** any command, to see a full log of its actions: - -.. code-block:: bash - - $ zarr --verbose migrate v3 path/to/input.zarr - - $ zarr --verbose remove-metadata v2 path/to/input.zarr - - -Equivalent functions --------------------- -All features of the command-line interface are also available via functions under -:mod:`zarr.metadata`. - - diff --git a/docs/user-guide/config.md b/docs/user-guide/config.md new file mode 100644 index 0000000000..21fe9b5def --- /dev/null +++ b/docs/user-guide/config.md @@ -0,0 +1,50 @@ +# Runtime configuration + +[`zarr.config`][] is responsible for managing the configuration of zarr and +is based on the [donfig](https://github.com/pytroll/donfig) Python library. + +Configuration values can be set using code like the following: + +```python exec="true" session="config" source="above" result="ansi" + +import zarr + +print(zarr.config.get('array.order')) +``` + +```python exec="true" session="config" source="above" result="ansi" +zarr.config.set({'array.order': 'F'}) + +print(zarr.config.get('array.order')) +``` + +Alternatively, configuration values can be set using environment variables, e.g. +`ZARR_ARRAY__ORDER=F`. + +The configuration can also be read from a YAML file in standard locations. +For more information, see the +[donfig documentation](https://donfig.readthedocs.io/en/latest/). + +Configuration options include the following: + +- Default Zarr format `default_zarr_version` +- Default array order in memory `array.order` +- Whether empty chunks are written to storage `array.write_empty_chunks` +- Async and threading options, e.g. `async.concurrency` and `threading.max_workers` +- Selections of implementations of codecs, codec pipelines and buffers +- Enabling GPU support with `zarr.config.enable_gpu()`. See GPU support for more. + +For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, +first register the implementations in the registry and then select them in the config. +For example, an implementation of the bytes codec in a class `'custompackage.NewBytesCodec'`, +requires the value of `codecs.bytes.name` to be `'custompackage.NewBytesCodec'`. + +This is the current default configuration: + +```python exec="true" session="config" source="above" result="ansi" +from pprint import pprint +import io +output = io.StringIO() +zarr.config.pprint(stream=output, width=60) +print(output.getvalue()) +``` diff --git a/docs/user-guide/config.rst b/docs/user-guide/config.rst deleted file mode 100644 index 76210da791..0000000000 --- a/docs/user-guide/config.rst +++ /dev/null @@ -1,83 +0,0 @@ -.. _user-guide-config: - -Runtime configuration -===================== - -``zarr.config`` is responsible for managing the configuration of zarr and -is based on the `donfig `_ Python library. - -Configuration values can be set using code like the following:: - - >>> import zarr - >>> - >>> zarr.config.set({'array.order': 'F'}) - - >>> - >>> # revert this change so it doesn't impact the rest of the docs - >>> zarr.config.set({'array.order': 'C'}) - - -Alternatively, configuration values can be set using environment variables, e.g. -``ZARR_ARRAY__ORDER=F``. - -The configuration can also be read from a YAML file in standard locations. -For more information, see the -`donfig documentation `_. - -Configuration options include the following: - -- Default Zarr format ``default_zarr_version`` -- Default array order in memory ``array.order`` -- Whether empty chunks are written to storage ``array.write_empty_chunks`` -- Async and threading options, e.g. ``async.concurrency`` and ``threading.max_workers`` -- Selections of implementations of codecs, codec pipelines and buffers -- Enabling GPU support with ``zarr.config.enable_gpu()``. See :ref:`user-guide-gpu` for more. - -For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, -first register the implementations in the registry and then select them in the config. -For example, an implementation of the bytes codec in a class ``'custompackage.NewBytesCodec'``, -requires the value of ``codecs.bytes.name`` to be ``'custompackage.NewBytesCodec'``. - -This is the current default configuration:: - - >>> zarr.config.pprint() - {'array': {'order': 'C', 'write_empty_chunks': False}, - 'async': {'concurrency': 10, 'timeout': None}, - 'buffer': 'zarr.buffer.cpu.Buffer', - 'codec_pipeline': {'batch_size': 1, - 'path': 'zarr.core.codec_pipeline.BatchedCodecPipeline'}, - 'codecs': {'blosc': 'zarr.codecs.blosc.BloscCodec', - 'bytes': 'zarr.codecs.bytes.BytesCodec', - 'crc32c': 'zarr.codecs.crc32c_.Crc32cCodec', - 'endian': 'zarr.codecs.bytes.BytesCodec', - 'gzip': 'zarr.codecs.gzip.GzipCodec', - 'numcodecs.adler32': 'zarr.codecs.numcodecs.Adler32', - 'numcodecs.astype': 'zarr.codecs.numcodecs.AsType', - 'numcodecs.bitround': 'zarr.codecs.numcodecs.BitRound', - 'numcodecs.blosc': 'zarr.codecs.numcodecs.Blosc', - 'numcodecs.bz2': 'zarr.codecs.numcodecs.BZ2', - 'numcodecs.crc32': 'zarr.codecs.numcodecs.CRC32', - 'numcodecs.crc32c': 'zarr.codecs.numcodecs.CRC32C', - 'numcodecs.delta': 'zarr.codecs.numcodecs.Delta', - 'numcodecs.fixedscaleoffset': 'zarr.codecs.numcodecs.FixedScaleOffset', - 'numcodecs.fletcher32': 'zarr.codecs.numcodecs.Fletcher32', - 'numcodecs.gzip': 'zarr.codecs.numcodecs.GZip', - 'numcodecs.jenkins_lookup3': 'zarr.codecs.numcodecs.JenkinsLookup3', - 'numcodecs.lz4': 'zarr.codecs.numcodecs.LZ4', - 'numcodecs.lzma': 'zarr.codecs.numcodecs.LZMA', - 'numcodecs.packbits': 'zarr.codecs.numcodecs.PackBits', - 'numcodecs.pcodec': 'zarr.codecs.numcodecs.PCodec', - 'numcodecs.quantize': 'zarr.codecs.numcodecs.Quantize', - 'numcodecs.shuffle': 'zarr.codecs.numcodecs.Shuffle', - 'numcodecs.zfpy': 'zarr.codecs.numcodecs.ZFPY', - 'numcodecs.zlib': 'zarr.codecs.numcodecs.Zlib', - 'numcodecs.zstd': 'zarr.codecs.numcodecs.Zstd', - 'sharding_indexed': 'zarr.codecs.sharding.ShardingCodec', - 'transpose': 'zarr.codecs.transpose.TransposeCodec', - 'vlen-bytes': 'zarr.codecs.vlen_utf8.VLenBytesCodec', - 'vlen-utf8': 'zarr.codecs.vlen_utf8.VLenUTF8Codec', - 'zstd': 'zarr.codecs.zstd.ZstdCodec'}, - 'default_zarr_format': 3, - 'json_indent': 2, - 'ndbuffer': 'zarr.buffer.cpu.NDBuffer', - 'threading': {'max_workers': None}} diff --git a/docs/user-guide/consolidated_metadata.md b/docs/user-guide/consolidated_metadata.md new file mode 100644 index 0000000000..d4fc9d6bab --- /dev/null +++ b/docs/user-guide/consolidated_metadata.md @@ -0,0 +1,123 @@ +# Consolidated metadata + +!!! warning + The Consolidated Metadata feature in Zarr-Python is considered experimental for v3 + stores. [zarr-specs#309](https://github.com/zarr-developers/zarr-specs/pull/309) + has proposed a formal extension to the v3 specification to support consolidated metadata. + +Zarr-Python implements the [Consolidated Metadata](https://github.com/zarr-developers/zarr-specs/pull/309) for v2 and v3 stores. +Consolidated metadata can reduce the time needed to load the metadata for an +entire hierarchy, especially when the metadata is being served over a network. +Consolidated metadata essentially stores all the metadata for a hierarchy in the +metadata of the root Group. + +## Usage + +If consolidated metadata is present in a Zarr Group's metadata then it is used +by default. The initial read to open the group will need to communicate with +the store (reading from a file for a [`zarr.storage.LocalStore`][], making a +network request for a [`zarr.storage.FsspecStore`][]). After that, any subsequent +metadata reads get child Group or Array nodes will *not* require reads from the store. + +In Python, the consolidated metadata is available on the `.consolidated_metadata` +attribute of the `GroupMetadata` object. + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +import zarr +import warnings + +warnings.filterwarnings("ignore", category=UserWarning) +store = zarr.storage.MemoryStore() +group = zarr.create_group(store=store) +print(group) +array = group.create_array(shape=(1,), name='a', dtype='float64') +print(array) +``` + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +array = group.create_array(shape=(2, 2), name='b', dtype='float64') +print(array) +``` + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +array = group.create_array(shape=(3, 3, 3), name='c', dtype='float64') +print(array) +``` + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +result = zarr.consolidate_metadata(store) +print(result) +``` + +If we open that group, the Group's metadata has a `zarr.core.group.ConsolidatedMetadata` +that can be used.: + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +from pprint import pprint +import io + +consolidated = zarr.open_group(store=store) +consolidated_metadata = consolidated.metadata.consolidated_metadata.metadata + +# Note: pprint can be users without capturing the output regularly +output = io.StringIO() +pprint(dict(sorted(consolidated_metadata.items())), stream=output, width=60) +print(output.getvalue()) +``` + +Operations on the group to get children automatically use the consolidated metadata.: + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +print(consolidated['a']) # no read / HTTP request to the Store is required +``` + +With nested groups, the consolidated metadata is available on the children, recursively.: + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +child = group.create_group('child', attributes={'kind': 'child'}) +grandchild = child.create_group('child', attributes={'kind': 'grandchild'}) +consolidated = zarr.consolidate_metadata(store) + +output = io.StringIO() +pprint(consolidated['child'].metadata.consolidated_metadata, stream=output, width=60) +print(output.getvalue()) +``` + +!!! info "Added in version 3.1.1" + The keys in the consolidated metadata are sorted prior to writing. Keys are + sorted in ascending order by path depth, where a path is defined as a sequence + of strings joined by `"/"`. For keys with the same path length, lexicographic + order is used to break the tie. This behaviour ensures deterministic metadata + output for a given group. + +## Synchronization and Concurrency + +Consolidated metadata is intended for read-heavy use cases on slowly changing +hierarchies. For hierarchies where new nodes are constantly being added, +removed, or modified, consolidated metadata may not be desirable. + +1. It will add some overhead to each update operation, since the metadata + would need to be re-consolidated to keep it in sync with the store. +2. Readers using consolidated metadata will regularly see a "past" version + of the metadata, at the time they read the root node with its consolidated + metadata. + + +## Stores Without Support for Consolidated Metadata + +Some stores may want to opt out of the consolidated metadata mechanism. This +may be for several reasons like: + +* They want to maintain read-write consistency, which is challenging with + consolidated metadata. +* They have their own consolidated metadata mechanism. +* They offer good enough performance without need for consolidation. + +This type of store can declare it doesn't want consolidation by implementing +`Store.supports_consolidated_metadata` and returning `False`. For stores that don't support +consolidation, Zarr will: + +* Raise an error on `consolidate_metadata` calls, maintaining the store in + its unconsolidated state. +* Raise an error in `AsyncGroup.open(..., use_consolidated=True)` +* Not use consolidated metadata in `AsyncGroup.open(..., use_consolidated=None)` diff --git a/docs/user-guide/consolidated_metadata.rst b/docs/user-guide/consolidated_metadata.rst deleted file mode 100644 index ae50c602ca..0000000000 --- a/docs/user-guide/consolidated_metadata.rst +++ /dev/null @@ -1,143 +0,0 @@ -.. _user-guide-consolidated-metadata: - -Consolidated metadata -===================== - -.. warning:: - The Consolidated Metadata feature in Zarr-Python is considered experimental for v3 - stores. `zarr-specs#309 `_ - has proposed a formal extension to the v3 specification to support consolidated metadata. - -Zarr-Python implements the `Consolidated Metadata`_ for v2 and v3 stores. -Consolidated metadata can reduce the time needed to load the metadata for an -entire hierarchy, especially when the metadata is being served over a network. -Consolidated metadata essentially stores all the metadata for a hierarchy in the -metadata of the root Group. - -Usage ------ - -If consolidated metadata is present in a Zarr Group's metadata then it is used -by default. The initial read to open the group will need to communicate with -the store (reading from a file for a :class:`zarr.storage.LocalStore`, making a -network request for a :class:`zarr.storage.FsspecStore`). After that, any subsequent -metadata reads get child Group or Array nodes will *not* require reads from the store. - -In Python, the consolidated metadata is available on the ``.consolidated_metadata`` -attribute of the ``GroupMetadata`` object. - - >>> import zarr - >>> import warnings - >>> warnings.filterwarnings("ignore", category=UserWarning) - >>> - >>> store = zarr.storage.MemoryStore() - >>> group = zarr.create_group(store=store) - >>> group.create_array(shape=(1,), name='a', dtype='float64') - - >>> group.create_array(shape=(2, 2), name='b', dtype='float64') - - >>> group.create_array(shape=(3, 3, 3), name='c', dtype='float64') - - >>> zarr.consolidate_metadata(store) - - -If we open that group, the Group's metadata has a :class:`zarr.core.group.ConsolidatedMetadata` -that can be used.: - - >>> consolidated = zarr.open_group(store=store) - >>> consolidated_metadata = consolidated.metadata.consolidated_metadata.metadata - >>> from pprint import pprint - >>> pprint(dict(consolidated_metadata.items())) - {'a': ArrayV3Metadata(shape=(1,), - data_type=Float64(endianness='little'), - chunk_grid=RegularChunkGrid(chunk_shape=(1,)), - chunk_key_encoding=DefaultChunkKeyEncoding(separator='/'), - fill_value=np.float64(0.0), - codecs=(BytesCodec(endian=), - ZstdCodec(level=0, checksum=False)), - attributes={}, - dimension_names=None, - zarr_format=3, - node_type='array', - storage_transformers=()), - 'b': ArrayV3Metadata(shape=(2, 2), - data_type=Float64(endianness='little'), - chunk_grid=RegularChunkGrid(chunk_shape=(2, 2)), - chunk_key_encoding=DefaultChunkKeyEncoding(separator='/'), - fill_value=np.float64(0.0), - codecs=(BytesCodec(endian=), - ZstdCodec(level=0, checksum=False)), - attributes={}, - dimension_names=None, - zarr_format=3, - node_type='array', - storage_transformers=()), - 'c': ArrayV3Metadata(shape=(3, 3, 3), - data_type=Float64(endianness='little'), - chunk_grid=RegularChunkGrid(chunk_shape=(3, 3, 3)), - chunk_key_encoding=DefaultChunkKeyEncoding(separator='/'), - fill_value=np.float64(0.0), - codecs=(BytesCodec(endian=), - ZstdCodec(level=0, checksum=False)), - attributes={}, - dimension_names=None, - zarr_format=3, - node_type='array', - storage_transformers=())} - -Operations on the group to get children automatically use the consolidated metadata.: - - >>> consolidated['a'] # no read / HTTP request to the Store is required - - -With nested groups, the consolidated metadata is available on the children, recursively.: - - >>> child = group.create_group('child', attributes={'kind': 'child'}) - >>> grandchild = child.create_group('child', attributes={'kind': 'grandchild'}) - >>> consolidated = zarr.consolidate_metadata(store) - >>> - >>> consolidated['child'].metadata.consolidated_metadata - ConsolidatedMetadata(metadata={'child': GroupMetadata(attributes={'kind': 'grandchild'}, zarr_format=3, consolidated_metadata=ConsolidatedMetadata(metadata={}, kind='inline', must_understand=False), node_type='group')}, kind='inline', must_understand=False) - -.. versionadded:: 3.1.1 - - The keys in the consolidated metadata are sorted prior to writing. Keys are - sorted in ascending order by path depth, where a path is defined as a sequence - of strings joined by ``"/"``. For keys with the same path length, lexicographic - order is used to break the tie. This behaviour ensures deterministic metadata - output for a given group. - -Synchronization and Concurrency -------------------------------- - -Consolidated metadata is intended for read-heavy use cases on slowly changing -hierarchies. For hierarchies where new nodes are constantly being added, -removed, or modified, consolidated metadata may not be desirable. - -1. It will add some overhead to each update operation, since the metadata - would need to be re-consolidated to keep it in sync with the store. -2. Readers using consolidated metadata will regularly see a "past" version - of the metadata, at the time they read the root node with its consolidated - metadata. - -.. _Consolidated Metadata: https://github.com/zarr-developers/zarr-specs/pull/309 - -Stores Without Support for Consolidated Metadata ------------------------------------------------- - -Some stores may want to opt out of the consolidated metadata mechanism. This -may be for several reasons like: - -* They want to maintain read-write consistency, which is challenging with - consolidated metadata. -* They have their own consolidated metadata mechanism. -* They offer good enough performance without need for consolidation. - -This type of store can declare it doesn't want consolidation by implementing -`Store.supports_consolidated_metadata` and returning `False`. For stores that don't support -consolidation, Zarr will: - -* Raise an error on `consolidate_metadata` calls, maintaining the store in - its unconsolidated state. -* Raise an error in `AsyncGroup.open(..., use_consolidated=True)` -* Not use consolidated metadata in `AsyncGroup.open(..., use_consolidated=None)` diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md new file mode 100644 index 0000000000..82b7c89809 --- /dev/null +++ b/docs/user-guide/data_types.md @@ -0,0 +1,427 @@ +# Array data types + +## Zarr's Data Type Model + +Zarr is designed for interoperability with NumPy, so if you are familiar with NumPy or any other +N-dimensional array library, Zarr's model for array data types should seem familiar. However, Zarr +data types have some unique features that are described in this document. + +Zarr arrays operate under an essential design constraint: unlike NumPy arrays, Zarr arrays +are designed to be stored and accessed by other Zarr implementations. This means that, among other things, +Zarr data types must be serializable to metadata documents in accordance with the Zarr specifications, +which adds some unique aspects to the Zarr data type model. + +The following sections explain Zarr's data type model in greater detail and demonstrate the +Zarr Python APIs for working with Zarr data types. + +### Array Data Types + +Every Zarr array has a data type, which defines the meaning of the array's elements. An array's data +type is encoded in the JSON metadata for the array. This means that the data type of an array must be +JSON-serializable. + +In Zarr V2, the data type of an array is stored in the `dtype` field in array metadata. +Zarr V3 changed the name of this field to `data_type` and also defined new rules for the values +that can be assigned to the `data_type` field. + +For example, in Zarr V2, the boolean array data type was represented in array metadata as the +string `"|b1"`. In Zarr V3, the same type is represented as the string `"bool"`. + +### Scalars + +Zarr also specifies how array elements, i.e., scalars, are encoded in array metadata. This is necessary +because Zarr uses a field in array metadata to define a default value for chunks that are not stored. +This field, called `fill_value` in both Zarr V2 and Zarr V3 metadata documents, contains a +JSON value that can be decoded to a scalar value compatible with the array's data type. + +For the boolean data type, the scalar encoding is simple—booleans are natively supported by +JSON, so Zarr saves booleans as JSON booleans. Other scalars, like floats or raw bytes, have +more elaborate encoding schemes, and in some cases, this scheme depends on the Zarr format version. + +## Data Types in Zarr Version 2 + +Version 2 of the Zarr format defined its data types relative to +[NumPy's data types](https://numpy.org/doc/2.1/reference/arrays.dtypes.html#data-type-objects-dtype), +and added a few non-NumPy data types as well. With one exception ([structured data types](#structured-data-type)), the Zarr +V2 JSON identifier for a data type is just the NumPy `str` attribute of that data type: + +```python exec="true" session="data_types" source="above" result="ansi" +import zarr +import numpy as np +import json + +store = {} +np_dtype = np.dtype('int64') +print(np_dtype.str) +``` + +```python exec="true" session="data_types" source="above" result="ansi" +z = zarr.create_array(store=store, shape=(1,), dtype=np_dtype, zarr_format=2) +dtype_meta = json.loads(store['.zarray'].to_bytes())["dtype"] +print(dtype_meta) +``` + +!!! note + + The `<` character in the data type metadata encodes the + [endianness](https://numpy.org/doc/2.2/reference/generated/numpy.dtype.byteorder.html), + or "byte order," of the data type. As per the NumPy model, + in Zarr version 2 each data type has an endianness where applicable. + However, Zarr version 3 data types do not store endianness information. + +There are two special cases to consider: ["structured" data types](#structured-data-type), and +["object"](#object-data-type) data types. + +### Structured Data Type + +NumPy allows the construction of a so-called "structured" data types comprised of ordered collections +of named fields, where each field is itself a distinct NumPy data type. See the NumPy documentation +[here](https://numpy.org/doc/stable/user/basics.rec.html). + +Crucially, NumPy does not use a special data type for structured data types—instead, NumPy +implements structured data types as an optional feature of the so-called "Void" data type, which models +arbitrary fixed-size byte strings. The `str` attribute of a regular NumPy void +data type is the same as the `str` of a NumPy structured data type. This means that the `str` +attribute does not convey information about the fields contained in a structured data type. +For these reasons, Zarr V2 uses a special data type encoding for structured data types. +They are stored in JSON as lists of pairs, where the first element is a string, and the second +element is a Zarr V2 data type specification. This representation supports recursion. + +For example: + +```python exec="true" session="data_types" source="above" result="ansi" +store = {} +np_dtype = np.dtype([('field_a', '>i2'), ('field_b', [('subfield_c', '>f4'), ('subfield_d', 'i2')])]) +print(np_dtype.str) +``` + +```python exec="true" session="data_types" source="above" result="ansi" +z = zarr.create_array(store=store, shape=(1,), dtype=np_dtype, zarr_format=2) +dtype_meta = json.loads(store['.zarray'].to_bytes())["dtype"] +print(dtype_meta) +``` + +### Object Data Type + +The NumPy "object" type is essentially an array of references to arbitrary Python objects. +It can model arrays of variable-length UTF-8 strings, arrays of variable-length byte strings, or +even arrays of variable-length arrays, each with a distinct data type. This makes the "object" data +type expressive, but also complicated to store. + +Zarr Python cannot persistently store references to arbitrary Python objects. But if each of those Python +objects has a consistent type, then we can use a special encoding procedure to store the array. This +is how Zarr Python stores variable-length UTF-8 strings, or variable-length byte strings. + +Although these are separate data types in this library, they are both "object" arrays in NumPy, which means +they have the *same* Zarr V2 string representation: `"|O"`. + +So for Zarr V2 we have to disambiguate different "object" data type arrays on the basis of their +encoding procedure, i.e., the codecs declared in the `filters` and `compressor` attributes of array +metadata. + +If an array with data type "object" used the `"vlen-utf8"` codec, then it was interpreted as an +array of variable-length strings. If an array with data type "object" used the `"vlen-bytes"` +codec, then it was interpreted as an array of variable-length byte strings. + +This all means that the `dtype` field alone does not fully specify a data type in Zarr V2. +The name of the object codec used, if one was used, is also required. +Although this fact can be ignored for many simple numeric data types, any comprehensive approach to +Zarr V2 data types must either reject the "object" data types or include the "object codec" +identifier in the JSON form of the basic data type model. + +## Data Types in Zarr Version 3 + +The NumPy-based Zarr V2 data type representation was effective for simple data types but struggled +with more complex data types, like "object" and "structured" data types. To address these limitations, +Zarr V3 introduced several key changes to how data types are represented: + +- Instead of copying NumPy character codecs, Zarr V3 defines an identifier for each data type. + The basic data types are identified by strings like `"int8"`, `"int16"`, etc., and data types + that require a configuration can be identified by a JSON object. + + For example, this JSON object declares a datetime data type: + + ```json + { + "name": "numpy.datetime64", + "configuration": { + "unit": "s", + "scale_factor": 10 + } + } + ``` + +- Zarr V3 data types do not have endianness. This is a departure from Zarr V2, where multi-byte + data types are defined with endianness information. Instead, Zarr V3 requires that the endianness + of encoded array chunks is specified in the `codecs` attribute of array metadata. The Zarr + V3 specification leaves the in-memory endianness of decoded array chunks as an implementation detail. + +For more about data types in Zarr V3, see the +[V3 specification](https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html). + +## Data Types in Zarr Python + +The two Zarr formats that Zarr Python supports specify data types in different ways: data types in +Zarr version 2 are encoded as NumPy-compatible strings (or lists, in the case of structured data +types), while data types in Zarr V3 are encoded as either strings or JSON objects. Zarr V3 data +types do not have any associated endianness information, unlike Zarr V2 data types. + +Zarr Python needs to support both Zarr V2 and V3, which means we need to abstract over these differences. +We do this with an abstract Zarr data type class: [ZDType][zarr.dtype.ZDType] +which provides Zarr V2 and Zarr V3 compatibility routines for "native" data types. + +In this context, a "native" data type is a Python class, typically defined in another library, that +models an array's data type. For example, [`numpy.dtypes.UInt8DType`][] is a native data type defined in NumPy. +Zarr Python wraps the NumPy `uint8` with a [ZDType][zarr.dtype.ZDType] instance called +[UInt8][zarr.dtype.UInt8]. + +As of this writing, the only native data types Zarr Python supports are NumPy data types. We could +avoid the "native data type" jargon and just say "NumPy data type," but we do not want to rule out the +possibility of using non-NumPy array backends in the future. + +Each data type supported by Zarr Python is modeled by a [ZDType][zarr.dtype.ZDType] subclass, which provides an +API for the following operations: + +- Encoding and decoding a native data type +- Encoding and decoding a data type to and from Zarr V2 and Zarr V3 array metadata +- Encoding and decoding a scalar value to and from Zarr V2 and Zarr V3 array metadata +- Casting a Python object to a scalar value consistent with the data type + +### List of data types + +The following section lists the data types built in to Zarr Python. With a few exceptions, Zarr +Python supports nearly all of the data types in NumPy. If you need a data type that is not listed +here, it's possible to create it yourself: see [Adding New Data Types](#adding-new-data-types). + +#### Boolean +- [Boolean][zarr.dtype.Bool] + +#### Integral +- [Signed 8-bit integer][zarr.dtype.Int8] +- [Signed 16-bit integer][zarr.dtype.Int16] +- [Signed 32-bit integer][zarr.dtype.Int32] +- [Signed 64-bit integer][zarr.dtype.Int64] +- [Unsigned 8-bit integer][zarr.dtype.UInt8] +- [Unsigned 16-bit integer][zarr.dtype.UInt16] +- [Unsigned 32-bit integer][zarr.dtype.UInt32] +- [Unsigned 64-bit integer][zarr.dtype.UInt64] + +#### Floating-point +- [16-bit floating-point][zarr.dtype.Float16] +- [32-bit floating-point][zarr.dtype.Float32] +- [64-bit floating-point][zarr.dtype.Float64] +- [64-bit complex floating-point][zarr.dtype.Complex64] +- [128-bit complex floating-point][zarr.dtype.Complex128] + +#### String +- [Fixed-length UTF-32 string][zarr.dtype.FixedLengthUTF32] +- [Variable-length UTF-8 string][zarr.dtype.VariableLengthUTF8] + +#### Bytes +- [Fixed-length null-terminated bytes][zarr.dtype.NullTerminatedBytes] +- [Fixed-length raw bytes][zarr.dtype.RawBytes] +- [Variable-length bytes][zarr.dtype.VariableLengthBytes] + +#### Temporal +- [DateTime64][zarr.dtype.DateTime64] +- [TimeDelta64][zarr.dtype.TimeDelta64] + +#### Struct-like +- [Structured][zarr.dtype.Structured] + +### Example Usage + +This section will demonstrates the basic usage of Zarr data types. + +Create a `ZDType` from a native data type: + +```python exec="true" session="data_types" source="above" +from zarr.core.dtype import Int8 +import numpy as np +int8 = Int8.from_native_dtype(np.dtype('int8')) +``` + +Convert back to a native data type: + +```python exec="true" session="data_types" source="above" +native_dtype = int8.to_native_dtype() +assert native_dtype == np.dtype('int8') +``` + +Get the default scalar value for the data type: + +```python exec="true" session="data_types" source="above" +default_value = int8.default_scalar() +assert default_value == np.int8(0) +``` + +Serialize to JSON for Zarr V2: + +```python exec="true" session="data_types" source="above" result="ansi" +json_v2 = int8.to_json(zarr_format=2) +print(json_v2) +{'name': '|i1', 'object_codec_id': None} +``` + +!!! note + + The representation returned by `to_json(zarr_format=2)` is more abstract than the literal contents + of Zarr V2 array metadata, because the JSON representation used by the `ZDType` classes must be + distinct across different data types. As noted [earlier](#object-data-type), Zarr V2 identifies + multiple distinct data types with the "object" data type identifier `"|O"`. Extra information + is needed to disambiguate these data types from one another. That's the reason for the + `object_codec_id` field you see here. + +And for V3: + +```python exec="true" session="data_types" source="above" result="ansi" +json_v3 = int8.to_json(zarr_format=3) +print(json_v3) +``` + +Serialize a scalar value to JSON: + +```python exec="true" session="data_types" source="above" result="ansi" +json_value = int8.to_json_scalar(42, zarr_format=3) +print(json_value) +``` + +Deserialize a scalar value from JSON: + +```python exec="true" session="data_types" source="above" +scalar_value = int8.from_json_scalar(42, zarr_format=3) +assert scalar_value == np.int8(42) +``` + +### Adding New Data Types + +Each Zarr data type is a separate Python class that inherits from +[ZDType][zarr.dtype.ZDType]. You can define a custom data type by +writing your own subclass of [ZDType][zarr.dtype.ZDType] and adding +your data type to the data type registry. A complete example of this process is included below. + +The source code for this example can be found in the `examples/custom_dtype.py` file in the Zarr +Python project directory. + +```python +--8<-- "examples/custom_dtype.py" +``` + +### Data Type Resolution + +Although Zarr Python uses a different data type model from NumPy, you can still define a Zarr array +with a NumPy data type object: + +```python exec="true" session="data_types" source="above" result="ansi" +from zarr import create_array +import numpy as np +a = create_array({}, shape=(10,), dtype=np.dtype('int')) +print(a) +``` + +Or a string representation of a NumPy data type: + +```python exec="true" session="data_types" source="above" result="ansi" +a = create_array({}, shape=(10,), dtype=' +``` + +This example illustrates a general problem Zarr Python has to solve: how can we allow users to +specify a data type as a string or a NumPy `dtype` object, and produce the right Zarr data type +from that input? We call this process "data type resolution." Zarr Python also performs data type +resolution when reading stored arrays, although in this case the input is a JSON value instead +of a NumPy data type. + +For simple data types like `int`, the solution could be extremely simple: just +maintain a lookup table that maps a NumPy data type to the Zarr data type equivalent. But not all +data types are so simple. Consider this case: + +```python exec="true" session="data_types" source="above" +from zarr import create_array +import warnings +import numpy as np +warnings.simplefilter("ignore", category=FutureWarning) +a = create_array({}, shape=(10,), dtype=[('a', 'f8'), ('b', 'i8')]) +print(a.dtype) # this is the NumPy data type +``` + +```python exec="true" session="data_types" source="above" +print(a.metadata.data_type) # this is the Zarr data type +``` + +In this example, we created a +[NumPy structured data type](https://numpy.org/doc/stable/user/basics.rec.html#structured-datatypes). +This data type is a container that can hold any NumPy data type, which makes it recursive. It is +not possible to make a lookup table that relates all NumPy structured data types to their Zarr +equivalents, as there is a nearly unbounded number of different structured data types. So instead of +a static lookup table, Zarr Python relies on a dynamic approach to data type resolution. + +Zarr Python defines a collection of Zarr data types. This collection, called a "data type registry," +is essentially a dictionary where the keys are strings (a canonical name for each data type), and the +values are the data type classes themselves. Dynamic data type resolution entails iterating over +these data type classes, invoking that class' [from_native_dtype][zarr.dtype.ZDType.from_native_dtype] +method, and returning a concrete data type instance if and only if exactly one of those constructor +invocations is successful. + +In plain language, we take some user input, like a NumPy data type, offer it to all the +known data type classes, and return an instance of the one data type class that can accept that user input. + +We want to avoid a situation where the same native data type matches multiple Zarr data types; that is, +a NumPy data type should *uniquely* specify a single Zarr data type. But data type resolution is +dynamic, so it's not possible to statically guarantee this uniqueness constraint. Therefore, we +attempt data type resolution against *every* data type class, and if, for some reason, a native data +type matches multiple Zarr data types, we treat this as an error and raise an exception. + +If you have a NumPy data type and you want to get the corresponding `ZDType` instance, you can use +the `parse_dtype` function, which will use the dynamic resolution described above. `parse_dtype` +handles a range of input types: + +- NumPy data types: + + ```python exec="true" session="data_types" source="above" result="ansi" + import numpy as np + from zarr.dtype import parse_dtype + my_dtype = np.dtype('>M8[10s]') + print(parse_dtype(my_dtype, zarr_format=2)) + ``` + +- NumPy data type-compatible strings: + + ```python exec="true" session="data_types" source="above" result="ansi" + dtype_str = '>M8[10s]' + print(parse_dtype(dtype_str, zarr_format=2)) + ``` + +- `ZDType` instances: + + ```python exec="true" session="data_types" source="above" result="ansi" + from zarr.dtype import DateTime64 + zdt = DateTime64(endianness='big', scale_factor=10, unit='s') + print(parse_dtype(zdt, zarr_format=2)) # Use a ZDType (this is a no-op) + ``` + +- Python dictionaries (requires `zarr_format=3`). These dictionaries must be consistent with the + `JSON` form of the data type: + + ```python exec="true" session="data_types" source="above" result="ansi" + dt_dict = {"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}} + print(parse_dtype(dt_dict, zarr_format=3)) + ``` + + ```python exec="true" session="data_types" source="above" result="ansi" + print(parse_dtype(dt_dict, zarr_format=3).to_json(zarr_format=3)) + ``` diff --git a/docs/user-guide/data_types.rst b/docs/user-guide/data_types.rst deleted file mode 100644 index a968cc4c86..0000000000 --- a/docs/user-guide/data_types.rst +++ /dev/null @@ -1,455 +0,0 @@ -.. _user-guide-data-types: - -Array data types -================ - -Zarr's Data Type Model ----------------------- - -Zarr is designed for interoperability with NumPy, so if you are familiar with NumPy or any other -N-dimensional array library, Zarr's model for array data types should seem familiar. However, Zarr -data types have some unique features that are described in this document. - -Zarr arrays operate under an essential design constraint: unlike NumPy arrays, Zarr arrays -are designed to be stored and accessed by other Zarr implementations. This means that, among other things, -Zarr data types must be serializable to metadata documents in accordance with the Zarr specifications, -which adds some unique aspects to the Zarr data type model. - -The following sections explain Zarr's data type model in greater detail and demonstrate the -Zarr Python APIs for working with Zarr data types. - -Array Data Types -^^^^^^^^^^^^^^^^ - -Every Zarr array has a data type, which defines the meaning of the array's elements. An array's data -type is encoded in the JSON metadata for the array. This means that the data type of an array must be -JSON-serializable. - -In Zarr V2, the data type of an array is stored in the ``dtype`` field in array metadata. -Zarr V3 changed the name of this field to ``data_type`` and also defined new rules for the values -that can be assigned to the ``data_type`` field. - -For example, in Zarr V2, the boolean array data type was represented in array metadata as the -string ``"|b1"``. In Zarr V3, the same type is represented as the string ``"bool"``. - -Scalars -^^^^^^^ - -Zarr also specifies how array elements, i.e., scalars, are encoded in array metadata. This is necessary -because Zarr uses a field in array metadata to define a default value for chunks that are not stored. -This field, called ``fill_value`` in both Zarr V2 and Zarr V3 metadata documents, contains a -JSON value that can be decoded to a scalar value compatible with the array's data type. - -For the boolean data type, the scalar encoding is simple—booleans are natively supported by -JSON, so Zarr saves booleans as JSON booleans. Other scalars, like floats or raw bytes, have -more elaborate encoding schemes, and in some cases, this scheme depends on the Zarr format version. - -Data Types in Zarr Version 2 ----------------------------- - -Version 2 of the Zarr format defined its data types relative to -`NumPy's data types `_, -and added a few non-NumPy data types as well. With one exception (`structured data types <#structured-data-type>`_), the Zarr -V2 JSON identifier for a data type is just the NumPy ``str`` attribute of that data type: - -.. code-block:: python - - >>> import zarr - >>> import numpy as np - >>> import json - >>> - >>> store = {} - >>> np_dtype = np.dtype('int64') - >>> np_dtype.str - '>> z = zarr.create_array(store=store, shape=(1,), dtype=np_dtype, zarr_format=2) - >>> dtype_meta = json.loads(store['.zarray'].to_bytes())["dtype"] - >>> dtype_meta - '`_, - or "byte order," of the data type. As per the NumPy model, - in Zarr version 2 each data type has an endianness where applicable. - However, Zarr version 3 data types do not store endianness information. - -There are two special cases to consider: `"structured" data types <#structured-data-type>`_, and -`"object" <#object-data-type>`_ data types. - -Structured Data Type -^^^^^^^^^^^^^^^^^^^^ - -NumPy allows the construction of a so-called "structured" data types comprised of ordered collections -of named fields, where each field is itself a distinct NumPy data type. See the NumPy documentation -`here `_. - -Crucially, NumPy does not use a special data type for structured data types—instead, NumPy -implements structured data types as an optional feature of the so-called "Void" data type, which models -arbitrary fixed-size byte strings. The ``str`` attribute of a regular NumPy void -data type is the same as the ``str`` of a NumPy structured data type. This means that the ``str`` -attribute does not convey information about the fields contained in a structured data type. -For these reasons, Zarr V2 uses a special data type encoding for structured data types. -They are stored in JSON as lists of pairs, where the first element is a string, and the second -element is a Zarr V2 data type specification. This representation supports recursion. - -For example: - -.. code-block:: python - - >>> store = {} - >>> np_dtype = np.dtype([('field_a', '>i2'), ('field_b', [('subfield_c', '>f4'), ('subfield_d', 'i2')])]) - >>> np_dtype.str - '|V8' - >>> z = zarr.create_array(store=store, shape=(1,), dtype=np_dtype, zarr_format=2) - >>> dtype_meta = json.loads(store['.zarray'].to_bytes())["dtype"] - >>> dtype_meta - [['field_a', '>i2'], ['field_b', [['subfield_c', '>f4'], ['subfield_d', '`_. - -Data Types in Zarr Python -------------------------- - -The two Zarr formats that Zarr Python supports specify data types in different ways: data types in -Zarr version 2 are encoded as NumPy-compatible strings (or lists, in the case of structured data -types), while data types in Zarr V3 are encoded as either strings or JSON objects. Zarr V3 data -types do not have any associated endianness information, unlike Zarr V2 data types. - -Zarr Python needs to support both Zarr V2 and V3, which means we need to abstract over these differences. -We do this with an abstract Zarr data type class: `ZDType <../api/zarr/dtype/index.html#zarr.dtype.ZDType>`_, -which provides Zarr V2 and Zarr V3 compatibility routines for "native" data types. - -In this context, a "native" data type is a Python class, typically defined in another library, that -models an array's data type. For example, ``np.dtypes.UInt8DType`` is a native data type defined in NumPy. -Zarr Python wraps the NumPy ``uint8`` with a ``ZDType`` instance called -`UInt8 <../api/zarr/dtype/index.html#zarr.dtype.ZDType>`_. - -As of this writing, the only native data types Zarr Python supports are NumPy data types. We could -avoid the "native data type" jargon and just say "NumPy data type," but we do not want to rule out the -possibility of using non-NumPy array backends in the future. - -Each data type supported by Zarr Python is modeled by a ``ZDType`` subclass, which provides an -API for the following operations: - -- Encoding and decoding a native data type -- Encoding and decoding a data type to and from Zarr V2 and Zarr V3 array metadata -- Encoding and decoding a scalar value to and from Zarr V2 and Zarr V3 array metadata -- Casting a Python object to a scalar value consistent with the data type - -List of data types -^^^^^^^^^^^^^^^^^^ - -The following section lists the data types built in to Zarr Python. With a few exceptions, Zarr -Python supports nearly all of the data types in NumPy. If you need a data type that is not listed -here, it's possible to create it yourself: see :ref:`adding-new-data-types`. - -Boolean -""""""" -- `Boolean <../api/zarr/dtype/index.html#zarr.dtype.Bool>`_ - -Integral -"""""""" -- `Signed 8-bit integer <../api/zarr/dtype/index.html#zarr.dtype.Int8>`_ -- `Signed 16-bit integer <../api/zarr/dtype/index.html#zarr.dtype.Int16>`_ -- `Signed 32-bit integer <../api/zarr/dtype/index.html#zarr.dtype.Int32>`_ -- `Signed 64-bit integer <../api/zarr/dtype/index.html#zarr.dtype.Int64>`_ -- `Unsigned 8-bit integer <../api/zarr/dtype/index.html#zarr.dtype.UInt8>`_ -- `Unsigned 16-bit integer <../api/zarr/dtype/index.html#zarr.dtype.UInt16>`_ -- `Unsigned 32-bit integer <../api/zarr/dtype/index.html#zarr.dtype.UInt32>`_ -- `Unsigned 64-bit integer <../api/zarr/dtype/index.html#zarr.dtype.UInt64>`_ - -Floating-point -"""""""""""""" -- `16-bit floating-point <../api/zarr/dtype/index.html#zarr.dtype.Float16>`_ -- `32-bit floating-point <../api/zarr/dtype/index.html#zarr.dtype.Float32>`_ -- `64-bit floating-point <../api/zarr/dtype/index.html#zarr.dtype.Float64>`_ -- `64-bit complex floating-point <../api/zarr/dtype/index.html#zarr.dtype.Complex64>`_ -- `128-bit complex floating-point <../api/zarr/dtype/index.html#zarr.dtype.Complex128>`_ - -String -"""""" -- `Fixed-length UTF-32 string <../api/zarr/dtype/index.html#zarr.dtype.FixedLengthUTF32>`_ -- `Variable-length UTF-8 string <../api/zarr/dtype/index.html#zarr.dtype.VariableLengthUTF8>`_ - -Bytes -""""" -- `Fixed-length null-terminated bytes <../api/zarr/dtype/index.html#zarr.dtype.NullTerminatedBytes>`_ -- `Fixed-length raw bytes <../api/zarr/dtype/index.html#zarr.dtype.RawBytes>`_ -- `Variable-length bytes <../api/zarr/dtype/index.html#zarr.dtype.VariableLengthBytes>`_ - -Temporal -"""""""" -- `DateTime64 <../api/zarr/dtype/index.html#zarr.dtype.DateTime64>`_ -- `TimeDelta64 <../api/zarr/dtype/index.html#zarr.dtype.TimeDelta64>`_ - -Struct-like -""""""""""" -- `Structured <../api/zarr/dtype/index.html#zarr.dtype.Structured>`_ - -Example Usage -^^^^^^^^^^^^^ - -This section will demonstrates the basic usage of Zarr data types. - -Create a ``ZDType`` from a native data type: - -.. code-block:: python - - >>> from zarr.core.dtype import Int8 - >>> import numpy as np - >>> int8 = Int8.from_native_dtype(np.dtype('int8')) - -Convert back to a native data type: - -.. code-block:: python - - >>> native_dtype = int8.to_native_dtype() - >>> assert native_dtype == np.dtype('int8') - -Get the default scalar value for the data type: - -.. code-block:: python - - >>> default_value = int8.default_scalar() - >>> assert default_value == np.int8(0) - -Serialize to JSON for Zarr V2: - -.. code-block:: python - - >>> json_v2 = int8.to_json(zarr_format=2) - >>> json_v2 - {'name': '|i1', 'object_codec_id': None} - -.. note:: - - The representation returned by ``to_json(zarr_format=2)`` is more abstract than the literal contents - of Zarr V2 array metadata, because the JSON representation used by the ``ZDType`` classes must be - distinct across different data types. As noted `earlier <#object-data-type>`_, Zarr V2 identifies - multiple distinct data types with the "object" data type identifier ``"|O"``. Extra information - is needed to disambiguate these data types from one another. That's the reason for the - ``object_codec_id`` field you see here. - -And for V3: - -.. code-block:: python - - >>> json_v3 = int8.to_json(zarr_format=3) - >>> json_v3 - 'int8' - -Serialize a scalar value to JSON: - -.. code-block:: python - - >>> json_value = int8.to_json_scalar(42, zarr_format=3) - >>> json_value - 42 - -Deserialize a scalar value from JSON: - -.. code-block:: python - - >>> scalar_value = int8.from_json_scalar(42, zarr_format=3) - >>> assert scalar_value == np.int8(42) - -.. _adding-new-data-types: - -Adding New Data Types -^^^^^^^^^^^^^^^^^^^^^ - -Each Zarr data type is a separate Python class that inherits from -`ZDType <../api/zarr/dtype/index.html#zarr.dtype.ZDType>`_. You can define a custom data type by -writing your own subclass of `ZDType <../api/zarr/dtype/index.html#zarr.dtype.ZDType>`_ and adding -your data type to the data type registry. A complete example of this process is included below. - -The source code for this example can be found in the ``examples/custom_dtype.py`` file in the Zarr -Python project directory. - -.. literalinclude:: ../../examples/custom_dtype.py - :language: python - -Data Type Resolution -^^^^^^^^^^^^^^^^^^^^ - -Although Zarr Python uses a different data type model from NumPy, you can still define a Zarr array -with a NumPy data type object: - -.. code-block:: python - - >>> from zarr import create_array - >>> import numpy as np - >>> a = create_array({}, shape=(10,), dtype=np.dtype('int')) - >>> a - - -Or a string representation of a NumPy data type: - -.. code-block:: python - - >>> a = create_array({}, shape=(10,), dtype='>> a - - -The ``Array`` object presents itself like a NumPy array, including exposing a NumPy -data type as its ``dtype`` attribute: - -.. code-block:: python - - >>> type(a.dtype) - - -But if we inspect the metadata for the array, we can see the Zarr data type object: - -.. code-block:: python - - >>> type(a.metadata.data_type) - - -This example illustrates a general problem Zarr Python has to solve: how can we allow users to -specify a data type as a string or a NumPy ``dtype`` object, and produce the right Zarr data type -from that input? We call this process "data type resolution." Zarr Python also performs data type -resolution when reading stored arrays, although in this case the input is a JSON value instead -of a NumPy data type. - -For simple data types like ``int``, the solution could be extremely simple: just -maintain a lookup table that maps a NumPy data type to the Zarr data type equivalent. But not all -data types are so simple. Consider this case: - -.. code-block:: python - - >>> from zarr import create_array - >>> import warnings - >>> import numpy as np - >>> warnings.simplefilter("ignore", category=FutureWarning) - >>> a = create_array({}, shape=(10,), dtype=[('a', 'f8'), ('b', 'i8')]) - >>> a.dtype # this is the NumPy data type - dtype([('a', '>> a.metadata.data_type # this is the Zarr data type - Structured(fields=(('a', Float64(endianness='little')), ('b', Int64(endianness='little')))) - -In this example, we created a -`NumPy structured data type `_. -This data type is a container that can hold any NumPy data type, which makes it recursive. It is -not possible to make a lookup table that relates all NumPy structured data types to their Zarr -equivalents, as there is a nearly unbounded number of different structured data types. So instead of -a static lookup table, Zarr Python relies on a dynamic approach to data type resolution. - -Zarr Python defines a collection of Zarr data types. This collection, called a "data type registry," -is essentially a dictionary where the keys are strings (a canonical name for each data type), and the -values are the data type classes themselves. Dynamic data type resolution entails iterating over -these data type classes, invoking that class' `from_native_dtype <#api/dtype/ZDType.from_native_dtype>`_ -method, and returning a concrete data type instance if and only if exactly one of those constructor -invocations is successful. - -In plain language, we take some user input, like a NumPy data type, offer it to all the -known data type classes, and return an instance of the one data type class that can accept that user input. - -We want to avoid a situation where the same native data type matches multiple Zarr data types; that is, -a NumPy data type should *uniquely* specify a single Zarr data type. But data type resolution is -dynamic, so it's not possible to statically guarantee this uniqueness constraint. Therefore, we -attempt data type resolution against *every* data type class, and if, for some reason, a native data -type matches multiple Zarr data types, we treat this as an error and raise an exception. - -If you have a NumPy data type and you want to get the corresponding ``ZDType`` instance, you can use -the ``parse_dtype`` function, which will use the dynamic resolution described above. ``parse_dtype`` -handles a range of input types: - -- NumPy data types: - - .. code-block:: python - - >>> import numpy as np - >>> from zarr.dtype import parse_dtype - >>> my_dtype = np.dtype('>M8[10s]') - >>> parse_dtype(my_dtype, zarr_format=2) - DateTime64(endianness='big', scale_factor=10, unit='s') - - -- NumPy data type-compatible strings: - - .. code-block:: python - - >>> dtype_str = '>M8[10s]' - >>> parse_dtype(dtype_str, zarr_format=2) - DateTime64(endianness='big', scale_factor=10, unit='s') - -- ``ZDType`` instances: - - .. code-block:: python - - >>> from zarr.dtype import DateTime64 - >>> zdt = DateTime64(endianness='big', scale_factor=10, unit='s') - >>> parse_dtype(zdt, zarr_format=2) # Use a ZDType (this is a no-op) - DateTime64(endianness='big', scale_factor=10, unit='s') - -- Python dictionaries (requires ``zarr_format=3``). These dictionaries must be consistent with the - ``JSON`` form of the data type: - - .. code-block:: python - - >>> dt_dict = {"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}} - >>> parse_dtype(dt_dict, zarr_format=3) - DateTime64(endianness='little', scale_factor=10, unit='s') - >>> parse_dtype(dt_dict, zarr_format=3).to_json(zarr_format=3) - {'name': 'numpy.datetime64', 'configuration': {'unit': 's', 'scale_factor': 10}} diff --git a/docs/user-guide/extending.rst b/docs/user-guide/extending.md similarity index 50% rename from docs/user-guide/extending.rst rename to docs/user-guide/extending.md index 4487e07ddf..d857fa3356 100644 --- a/docs/user-guide/extending.rst +++ b/docs/user-guide/extending.md @@ -1,20 +1,17 @@ - -Extending Zarr -============== +# Extending Zarr Zarr-Python 3 was designed to be extensible. This means that you can extend the library by writing custom classes and plugins. Currently, Zarr can be extended in the following ways: -Custom codecs -------------- +## Custom codecs -.. note:: +!!! note This section explains how custom codecs can be created for Zarr format 3 arrays. For Zarr format 2, codecs should subclass the - `numcodecs.abc.Codec `_ + [numcodecs.abc.Codec](https://numcodecs.readthedocs.io/en/stable/abc.html#numcodecs.abc.Codec) base class and register through - `numcodecs.registry.register_codec `_. + [numcodecs.registry.register_codec](https://numcodecs.readthedocs.io/en/stable/registry.html#numcodecs.registry.register_codec). There are three types of codecs in Zarr: - array-to-array @@ -24,71 +21,68 @@ There are three types of codecs in Zarr: Array-to-array codecs are used to transform the array data before serializing to bytes. Examples include delta encoding or scaling codecs. Array-to-bytes codecs are used for serializing the array data to bytes. In Zarr, the main codec to use for numeric arrays -is the :class:`zarr.codecs.BytesCodec`. Bytes-to-bytes codecs transform the serialized bytestreams +is the [`zarr.codecs.BytesCodec`][]. Bytes-to-bytes codecs transform the serialized bytestreams of the array data. Examples include compression codecs, such as -:class:`zarr.codecs.GzipCodec`, :class:`zarr.codecs.BloscCodec` or -:class:`zarr.codecs.ZstdCodec`, and codecs that add a checksum to the bytestream, such as -:class:`zarr.codecs.Crc32cCodec`. +[`zarr.codecs.GzipCodec`][], [`zarr.codecs.BloscCodec`][] or +[`zarr.codecs.ZstdCodec`][], and codecs that add a checksum to the bytestream, such as +[`zarr.codecs.Crc32cCodec`][]. Custom codecs for Zarr are implemented by subclassing the relevant base class, see -:class:`zarr.abc.codec.ArrayArrayCodec`, :class:`zarr.abc.codec.ArrayBytesCodec` and -:class:`zarr.abc.codec.BytesBytesCodec`. Most custom codecs should implemented the -``_encode_single`` and ``_decode_single`` methods. These methods operate on single chunks -of the array data. Alternatively, custom codecs can implement the ``encode`` and ``decode`` +[`zarr.abc.codec.ArrayArrayCodec`][], [`zarr.abc.codec.ArrayBytesCodec`][] and +[`zarr.abc.codec.BytesBytesCodec`][]. Most custom codecs should implemented the +`_encode_single` and `_decode_single` methods. These methods operate on single chunks +of the array data. Alternatively, custom codecs can implement the `encode` and `decode` methods, which operate on batches of chunks, in case the codec is intended to implement its own batch processing. Custom codecs should also implement the following methods: -- ``compute_encoded_size``, which returns the byte size of the encoded data given the byte - size of the original data. It should raise ``NotImplementedError`` for codecs with +- `compute_encoded_size`, which returns the byte size of the encoded data given the byte + size of the original data. It should raise `NotImplementedError` for codecs with variable-sized outputs, such as compression codecs. -- ``validate`` (optional), which can be used to check that the codec metadata is compatible with the +- `validate` (optional), which can be used to check that the codec metadata is compatible with the array metadata. It should raise errors if not. -- ``resolve_metadata`` (optional), which is important for codecs that change the shape, +- `resolve_metadata` (optional), which is important for codecs that change the shape, dtype or fill value of a chunk. -- ``evolve_from_array_spec`` (optional), which can be useful for automatically filling in +- `evolve_from_array_spec` (optional), which can be useful for automatically filling in codec configuration metadata from the array metadata. To use custom codecs in Zarr, they need to be registered using the -`entrypoint mechanism `_. -Commonly, entrypoints are declared in the ``pyproject.toml`` of your package under the -``[project.entry-points."zarr.codecs"]`` section. Zarr will automatically discover and +[entrypoint mechanism](https://packaging.python.org/en/latest/specifications/entry-points/). +Commonly, entrypoints are declared in the `pyproject.toml` of your package under the +`[project.entry-points."zarr.codecs"]` section. Zarr will automatically discover and load all codecs registered with the entrypoint mechanism from imported modules. -.. code-block:: toml - - [project.entry-points."zarr.codecs"] - "custompackage.fancy_codec" = "custompackage:FancyCodec" +```toml +[project.entry-points."zarr.codecs"] +"custompackage.fancy_codec" = "custompackage:FancyCodec" +``` New codecs need to have their own unique identifier. To avoid naming collisions, it is strongly recommended to prefix the codec identifier with a unique name. For example, -the codecs from ``numcodecs`` are prefixed with ``numcodecs.``, e.g. ``numcodecs.delta``. +the codecs from `numcodecs` are prefixed with `numcodecs.`, e.g. `numcodecs.delta`. -.. note:: +!!! note Note that the extension mechanism for the Zarr format 3 is still under development. Requirements for custom codecs including the choice of codec identifiers might change in the future. It is also possible to register codecs as replacements for existing codecs. This might be useful for providing specialized implementations, such as GPU-based codecs. In case of -multiple codecs, the :mod:`zarr.core.config` mechanism can be used to select the preferred +multiple codecs, the [`zarr.config`][] mechanism can be used to select the preferred implementation. -Custom stores -------------- +## Custom stores Coming soon. -Custom array buffers --------------------- +## Custom array buffers Zarr-python provides control over where and how arrays stored in memory through -:mod:`zarr.buffer`. Currently both CPU (the default) and GPU implementations are -provided (see :ref:`user-guide-gpu` for more). You can implement your own buffer -classes by implementing the interface defined in :mod:`zarr.abc.buffer`. +[`zarr.abc.buffer.Buffer`][]. Currently both CPU (the default) and GPU implementations are +provided (see [Using GPUs with Zarr](gpu.md) for more information). You can implement your own buffer +classes by implementing the interface defined in [`zarr.abc.buffer.BufferPrototype`][]. -Other extensions ----------------- +## Other extensions In the future, Zarr will support writing custom custom data types and chunk grids. diff --git a/docs/user-guide/gpu.md b/docs/user-guide/gpu.md new file mode 100644 index 0000000000..3317bdf065 --- /dev/null +++ b/docs/user-guide/gpu.md @@ -0,0 +1,31 @@ +# Using GPUs with Zarr + +Zarr can use GPUs to accelerate your workload by running `zarr.Config.enable_gpu`. + +!!! note + `zarr-python` currently supports reading the ndarray data into device (GPU) + memory as the final stage of the codec pipeline. Data will still be read into + or copied to host (CPU) memory for encoding and decoding. + + In the future, codecs will be available compressing and decompressing data on + the GPU, avoiding the need to move data between the host and device for + compression and decompression. + +## Reading data into device memory + +[`zarr.config`][] configures Zarr to use GPU memory for the data +buffers used internally by Zarr via `enable_gpu()`. + +```python +import zarr +import cupy as cp +zarr.config.enable_gpu() +store = zarr.storage.MemoryStore() +z = zarr.create_array( + store=store, shape=(100, 100), chunks=(10, 10), dtype="float32", +) +type(z[:10, :10]) +# cupy.ndarray +``` + +Note that the output type is a `cupy.ndarray` rather than a NumPy array. diff --git a/docs/user-guide/gpu.rst b/docs/user-guide/gpu.rst deleted file mode 100644 index 4d3492f8bd..0000000000 --- a/docs/user-guide/gpu.rst +++ /dev/null @@ -1,37 +0,0 @@ -.. _user-guide-gpu: - -Using GPUs with Zarr -==================== - -Zarr can use GPUs to accelerate your workload by running -:meth:`zarr.config.enable_gpu`. - -.. note:: - - `zarr-python` currently supports reading the ndarray data into device (GPU) - memory as the final stage of the codec pipeline. Data will still be read into - or copied to host (CPU) memory for encoding and decoding. - - In the future, codecs will be available compressing and decompressing data on - the GPU, avoiding the need to move data between the host and device for - compression and decompression. - -Reading data into device memory -------------------------------- - -:meth:`zarr.config.enable_gpu` configures Zarr to use GPU memory for the data -buffers used internally by Zarr. - -.. code-block:: python - - >>> import zarr - >>> import cupy as cp # doctest: +SKIP - >>> zarr.config.enable_gpu() # doctest: +SKIP - >>> store = zarr.storage.MemoryStore() # doctest: +SKIP - >>> z = zarr.create_array( # doctest: +SKIP - ... store=store, shape=(100, 100), chunks=(10, 10), dtype="float32", - ... ) - >>> type(z[:10, :10]) # doctest: +SKIP - cupy.ndarray - -Note that the output type is a ``cupy.ndarray`` rather than a NumPy array. diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md new file mode 100644 index 0000000000..8a3f9ff7bf --- /dev/null +++ b/docs/user-guide/groups.md @@ -0,0 +1,137 @@ +# Working with groups + +Zarr supports hierarchical organization of arrays via groups. As with arrays, +groups can be stored in memory, on disk, or via other storage systems that +support a similar interface. + +To create a group, use the [`zarr.group`][] function: + +```python exec="true" session="groups" source="above" result="ansi" +import zarr +store = zarr.storage.MemoryStore() +root = zarr.create_group(store=store) +print(root) +``` + +Groups have a similar API to the Group class from [h5py](https://www.h5py.org/). For example, groups can contain other groups: + +```python exec="true" session="groups" source="above" +foo = root.create_group('foo') +bar = foo.create_group('bar') +``` + +Groups can also contain arrays, e.g.: + +```python exec="true" session="groups" source="above" result="ansi" +z1 = bar.create_array(name='baz', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') +print(z1) +``` + +Members of a group can be accessed via the suffix notation, e.g.: + +```python exec="true" session="groups" source="above" result="ansi" +print(root['foo']) +``` + +The '/' character can be used to access multiple levels of the hierarchy in one +call, e.g.: + +```python exec="true" session="groups" source="above" result="ansi" +print(root['foo/bar']) +``` + +```python exec="true" session="groups" source="above" result="ansi" +print(root['foo/bar/baz']) +``` + +The [`zarr.Group.tree`][] method can be used to print a tree +representation of the hierarchy, e.g.: + +```python exec="true" session="groups" source="above" result="ansi" +print(root.tree()) +``` + +The [`zarr.open_group`][] function provides a convenient way to create or +re-open a group stored in a directory on the file-system, with sub-groups stored in +sub-directories, e.g.: + +```python exec="true" session="groups" source="above" result="ansi" +root = zarr.open_group('data/group.zarr', mode='w') +print(root) +``` + +```python exec="true" session="groups" source="above" result="ansi" +z = root.create_array(name='foo/bar/baz', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') +print(z) +``` + +For more information on groups see the [`zarr.Group` API docs](../api/group.md). + +## Batch Group Creation + +You can also create multiple groups concurrently with a single function call. [`zarr.create_hierarchy`][] takes +a [`zarr Storage instance`](../api/storage.md) instance and a dict of `key : metadata` pairs, parses that dict, and +writes metadata documents to storage: + +```python exec="true" session="groups" source="above" result="ansi" +from zarr import create_hierarchy +from zarr.core.group import GroupMetadata +from zarr.storage import LocalStore + +from pprint import pprint +import io + +node_spec = {'a/b/c': GroupMetadata()} +nodes_created = dict(create_hierarchy(store=LocalStore(root='data'), nodes=node_spec)) +# Report nodes (pprint is used for cleaner rendering in the docs) +output = io.StringIO() +pprint(nodes_created, stream=output, width=60) +print(output.getvalue()) +``` + +Note that we only specified a single group named `a/b/c`, but 4 groups were created. These additional groups +were created to ensure that the desired node `a/b/c` is connected to the root group `''` by a sequence +of intermediate groups. [`zarr.create_hierarchy`][] normalizes the `nodes` keyword argument to +ensure that the resulting hierarchy is complete, i.e. all groups or arrays are connected to the root +of the hierarchy via intermediate groups. + +Because [`zarr.create_hierarchy`][] concurrently creates metadata documents, it's more efficient +than repeated calls to [`create_group`][zarr.create_group] or [`create_array`][zarr.create_array], provided you can statically define +the metadata for the groups and arrays you want to create. + +## Array and group diagnostics + +Diagnostic information about arrays and groups is available via the `info` +property. E.g.: + +```python exec="true" session="groups" source="above" result="ansi" +store = zarr.storage.MemoryStore() +root = zarr.group(store=store) +foo = root.create_group('foo') +bar = foo.create_array(name='bar', shape=1000000, chunks=100000, dtype='int64') +bar[:] = 42 +baz = foo.create_array(name='baz', shape=(1000, 1000), chunks=(100, 100), dtype='float32') +baz[:] = 4.2 +print(root.info) +``` + +```python exec="true" session="groups" source="above" result="ansi" +print(foo.info) +``` + +```python exec="true" session="groups" source="above" result="ansi" +print(bar.info_complete()) +``` + +```python exec="true" session="groups" source="above" result="ansi" +print(baz.info) +``` + +Groups also have the [`zarr.Group.tree`][] method, e.g.: + +```python exec="true" session="groups" source="above" result="ansi" +print(root.tree()) +``` + +!!! note + [`zarr.Group.tree`][] requires the optional [rich](https://rich.readthedocs.io/en/stable/) dependency. It can be installed with the `[tree]` extra. \ No newline at end of file diff --git a/docs/user-guide/groups.rst b/docs/user-guide/groups.rst deleted file mode 100644 index a343c3617e..0000000000 --- a/docs/user-guide/groups.rst +++ /dev/null @@ -1,172 +0,0 @@ -.. only:: doctest - - >>> import shutil - >>> shutil.rmtree('data', ignore_errors=True) - -.. _user-guide-groups: - -Working with groups -=================== - -Zarr supports hierarchical organization of arrays via groups. As with arrays, -groups can be stored in memory, on disk, or via other storage systems that -support a similar interface. - -To create a group, use the :func:`zarr.group` function:: - - >>> import zarr - >>> store = zarr.storage.MemoryStore() - >>> root = zarr.create_group(store=store) - >>> root - - -Groups have a similar API to the Group class from `h5py -`_. For example, groups can contain other groups:: - - >>> foo = root.create_group('foo') - >>> bar = foo.create_group('bar') - -Groups can also contain arrays, e.g.:: - - >>> z1 = bar.create_array(name='baz', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') - >>> z1 - - -Members of a group can be accessed via the suffix notation, e.g.:: - - >>> root['foo'] - - -The '/' character can be used to access multiple levels of the hierarchy in one -call, e.g.:: - - >>> root['foo/bar'] - - >>> root['foo/bar/baz'] - - -The :func:`zarr.Group.tree` method can be used to print a tree -representation of the hierarchy, e.g.:: - - >>> root.tree() - / - └── foo - └── bar - └── baz (10000, 10000) int32 - - -The :func:`zarr.open_group` function provides a convenient way to create or -re-open a group stored in a directory on the file-system, with sub-groups stored in -sub-directories, e.g.:: - - >>> root = zarr.open_group('data/group.zarr', mode='w') - >>> root - - >>> - >>> z = root.create_array(name='foo/bar/baz', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') - >>> z - - -.. TODO: uncomment after __enter__ and __exit__ are implemented -.. Groups can be used as context managers (in a ``with`` statement). -.. If the underlying store has a ``close`` method, it will be called on exit. - -For more information on groups see the :class:`zarr.Group` API docs. - -.. _user-guide-diagnostics: - -Batch Group Creation --------------------- - -You can also create multiple groups concurrently with a single function call. :func:`zarr.create_hierarchy` takes -a :class:`zarr.storage.Store` instance and a dict of ``key : metadata`` pairs, parses that dict, and -writes metadata documents to storage: - - >>> from zarr import create_hierarchy - >>> from zarr.core.group import GroupMetadata - >>> from zarr.storage import LocalStore - >>> node_spec = {'a/b/c': GroupMetadata()} - >>> nodes_created = dict(create_hierarchy(store=LocalStore(root='data'), nodes=node_spec)) - >>> print(sorted(nodes_created.items(), key=lambda kv: len(kv[0]))) - [('', ), ('a', ), ('a/b', ), ('a/b/c', )] - -Note that we only specified a single group named ``a/b/c``, but 4 groups were created. These additional groups -were created to ensure that the desired node ``a/b/c`` is connected to the root group ``''`` by a sequence -of intermediate groups. :func:`zarr.create_hierarchy` normalizes the ``nodes`` keyword argument to -ensure that the resulting hierarchy is complete, i.e. all groups or arrays are connected to the root -of the hierarchy via intermediate groups. - -Because :func:`zarr.create_hierarchy` concurrently creates metadata documents, it's more efficient -than repeated calls to :func:`create_group` or :func:`create_array`, provided you can statically define -the metadata for the groups and arrays you want to create. - -Array and group diagnostics ---------------------------- - -Diagnostic information about arrays and groups is available via the ``info`` -property. E.g.:: - - >>> store = zarr.storage.MemoryStore() - >>> root = zarr.group(store=store) - >>> foo = root.create_group('foo') - >>> bar = foo.create_array(name='bar', shape=1000000, chunks=100000, dtype='int64') - >>> bar[:] = 42 - >>> baz = foo.create_array(name='baz', shape=(1000, 1000), chunks=(100, 100), dtype='float32') - >>> baz[:] = 4.2 - >>> root.info - Name : - Type : Group - Zarr format : 3 - Read-only : False - Store type : MemoryStore - >>> foo.info - Name : foo - Type : Group - Zarr format : 3 - Read-only : False - Store type : MemoryStore - >>> bar.info_complete() - Type : Array - Zarr format : 3 - Data type : Int64(endianness='little') - Fill value : 0 - Shape : (1000000,) - Chunk shape : (100000,) - Order : C - Read-only : False - Store type : MemoryStore - Filters : () - Serializer : BytesCodec(endian=) - Compressors : (ZstdCodec(level=0, checksum=False),) - No. bytes : 8000000 (7.6M) - No. bytes stored : 1614 (1.6K) - Storage ratio : 4956.6 - Chunks Initialized : 10 - >>> baz.info - Type : Array - Zarr format : 3 - Data type : Float32(endianness='little') - Fill value : 0.0 - Shape : (1000, 1000) - Chunk shape : (100, 100) - Order : C - Read-only : False - Store type : MemoryStore - Filters : () - Serializer : BytesCodec(endian=) - Compressors : (ZstdCodec(level=0, checksum=False),) - No. bytes : 4000000 (3.8M) - -Groups also have the :func:`zarr.Group.tree` method, e.g.:: - - >>> root.tree() - / - └── foo - ├── bar (1000000,) int64 - └── baz (1000, 1000) float32 - - -.. note:: - - :func:`zarr.Group.tree` requires the optional `rich `_ - dependency. It can be installed with the ``[tree]`` extra. diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md new file mode 100644 index 0000000000..14808457bd --- /dev/null +++ b/docs/user-guide/index.md @@ -0,0 +1,41 @@ +# User Guide + +Welcome to the user guide, where you can learn more about using Zarr-Python! + +## Getting Started + +New to Zarr-Python? Start here: + +- **[Installation](installation.md)** - Install Zarr-Python +- **[Quick-start](../quick-start.md)** - Quick overview of core functionality + +## Core Concepts + +Learn the essential building blocks: + +- **[Arrays](arrays.md)** - Learn the fundamentals of working with arrays +- **[Groups](groups.md)** - Organize your data with groups +- **[Attributes](attributes.md)** - Configure metadata to your data structures +- **[Storage](storage.md)** - Learn how data is stored and accessed + +## Configuration & Setup + +Customize your experience: + +- **[Runtime Configuration](config.md)** - Configure Zarr-Python for your needs +- **[V3 Migration](v3_migration.md)** - Upgrading from version 2 to version 3 + +## Advanced Topics + +Take your skills to the next level: + +- **[Data Types](data_types.md)** - Learn about supported and extensible data types +- **[Performance](performance.md)** - Optimize for speed and efficiency +- **[GPU](gpu.md)** - Leverage GPU acceleration +- **[Extending](extending.md)** - Extend functionality with custom code +- **[Consolidated Metadata](consolidated_metadata.md)** - Advanced metadata management + +## Need Help? + +- Browse the [API Reference](../api/index.md) for detailed function documentation +- Report issues on [GitHub](https://github.com/zarr-developers/zarr-python/issues?q=sort%3Aupdated-desc+is%3Aissue+is%3Aopen) diff --git a/docs/user-guide/index.rst b/docs/user-guide/index.rst deleted file mode 100644 index a83a30172b..0000000000 --- a/docs/user-guide/index.rst +++ /dev/null @@ -1,32 +0,0 @@ -.. _user-guide: - -User guide -========== - -.. toctree:: - :maxdepth: 1 - - installation - arrays - groups - attributes - storage - config - v3_migration - cli - -Advanced Topics ---------------- - -.. toctree:: - :maxdepth: 1 - - data_types - performance - consolidated_metadata - extending - gpu - - -.. Coming soon - async diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md new file mode 100644 index 0000000000..f672a348cd --- /dev/null +++ b/docs/user-guide/installation.md @@ -0,0 +1,59 @@ +# Installation + +## Required dependencies + +Required dependencies include: + +- [Python](https://docs.python.org/3/) (3.11 or later) +- [packaging](https://packaging.pypa.io) (22.0 or later) +- [numpy](https://numpy.org) (1.26 or later) +- [numcodecs[crc32c]](https://numcodecs.readthedocs.io) (0.14 or later) +- [typing_extensions](https://typing-extensions.readthedocs.io) (4.9 or later) +- [donfig](https://donfig.readthedocs.io) (0.8 or later) + +## pip + +Zarr is available on [PyPI](https://pypi.org/project/zarr/). Install it using `pip`: + +```console +pip install zarr +``` + +There are a number of optional dependency groups you can install for extra functionality. +These can be installed using `pip install "zarr[]"`, e.g. `pip install "zarr[gpu]"` + +- `gpu`: support for GPUs +- `remote`: support for reading/writing to remote data stores + +Additional optional dependencies include `rich`, `universal_pathlib`. These must be installed separately. + +## conda + +Zarr is also published to [conda-forge](https://conda-forge.org). Install it using `conda`: + +```console +conda install -c conda-forge zarr +``` + +Conda does not support optional dependencies, so you will have to manually install any packages +needed to enable extra functionality. + +# Nightly wheels + +Development wheels are built nightly and published to the [scientific-python-nightly-wheels](https://anaconda.org/scientific-python-nightly-wheels) index. To install the latest nightly build: + +```console +pip install --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple zarr +``` + +Note that nightly wheels may be unstable and are intended for testing purposes. +## Dependency support + +Zarr has endorsed [Scientific-Python SPEC 0](https://scientific-python.org/specs/spec-0000/) and now follows the version support window as outlined below: + +- Python: 36 months after initial release +- Core package dependencies (e.g. NumPy): 24 months after initial release + +## Development + +To install the latest development version of Zarr, see the contributing guide. diff --git a/docs/user-guide/installation.rst b/docs/user-guide/installation.rst deleted file mode 100644 index 67705d3be6..0000000000 --- a/docs/user-guide/installation.rst +++ /dev/null @@ -1,67 +0,0 @@ -Installation -============ - -Required dependencies ---------------------- - -Required dependencies include: - -- `Python `_ (3.11 or later) -- `packaging `_ (22.0 or later) -- `numpy `_ (1.26 or later) -- `numcodecs[crc32c] `_ (0.14 or later) -- `typing_extensions `_ (4.9 or later) -- `donfig `_ (0.8 or later) - -pip ---- - -Zarr is available on `PyPI `_. Install it using ``pip``: - -.. code-block:: console - - $ pip install zarr - -There are a number of optional dependency groups you can install for extra functionality. -These can be installed using ``pip install "zarr[]"``, e.g. ``pip install "zarr[gpu]"`` - -- ``gpu``: support for GPUs -- ``remote``: support for reading/writing to remote data stores - -Additional optional dependencies include ``rich``, ``universal_pathlib``. These must be installed separately. - -conda ------ - -Zarr is also published to `conda-forge `_. Install it using ``conda``: - -.. code-block:: console - - $ conda install -c conda-forge zarr - -Conda does not support optional dependencies, so you will have to manually install any packages -needed to enable extra functionality. - -Nightly wheels --------------- - -Development wheels are built nightly and published to the `scientific-python-nightly-wheels `_ index. To install the latest nightly build: - -.. code-block:: console - - $ pip install --pre \ - --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \ - zarr - -Note that nightly wheels may be unstable and are intended for testing purposes. - -Dependency support ------------------- -Zarr has endorsed `Scientific-Python SPEC 0 `_ and now follows the version support window as outlined below: - -- Python: 36 months after initial release -- Core package dependencies (e.g. NumPy): 24 months after initial release - -Development ------------ -To install the latest development version of Zarr, see the :ref:`contributing guide `. diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md new file mode 100644 index 0000000000..ad101319f1 --- /dev/null +++ b/docs/user-guide/performance.md @@ -0,0 +1,206 @@ +# Optimizing performance + +## Chunk optimizations + +### Chunk size and shape + +In general, chunks of at least 1 megabyte (1M) uncompressed size seem to provide +better performance, at least when using the Blosc compression library. + +The optimal chunk shape will depend on how you want to access the data. E.g., +for a 2-dimensional array, if you only ever take slices along the first +dimension, then chunk across the second dimension. If you know you want to chunk +across an entire dimension you can use the full size of that dimension within the +`chunks` argument, e.g.: + +```python exec="true" session="performance" source="above" result="ansi" +import zarr +z1 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(100, 10000), dtype='int32') +print(z1.chunks) +``` + +Alternatively, if you only ever take slices along the second dimension, then +chunk across the first dimension, e.g.: + +```python exec="true" session="performance" source="above" result="ansi" +z2 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(10000, 100), dtype='int32') +print(z2.chunks) +``` + +If you require reasonable performance for both access patterns then you need to +find a compromise, e.g.: + +```python exec="true" session="performance" source="above" result="ansi" +z3 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') +print(z3.chunks) +``` + +If you are feeling lazy, you can let Zarr guess a chunk shape for your data by +providing `chunks='auto'`, although please note that the algorithm for guessing +a chunk shape is based on simple heuristics and may be far from optimal. E.g.: + +```python exec="true" session="performance" source="above" result="ansi" +z4 = zarr.create_array(store={}, shape=(10000, 10000), chunks='auto', dtype='int32') +print(z4.chunks) +``` + +If you know you are always going to be loading the entire array into memory, you +can turn off chunks by providing `chunks` equal to `shape`, in which case there +will be one single chunk for the array: + +```python exec="true" session="performance" source="above" result="ansi" +z5 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(10000, 10000), dtype='int32') +print(z5.chunks) +``` + +### Sharding + +If you have large arrays but need small chunks to efficiently access the data, you can +use sharding. Sharding provides a mechanism to store multiple chunks in a single +storage object or file. This can be useful because traditional file systems and object +storage systems may have performance issues storing and accessing many files. +Additionally, small files can be inefficient to store if they are smaller than the +block size of the file system. + +Picking a good combination of chunk shape and shard shape is important for performance. +The chunk shape determines what unit of your data can be read independently, while the +shard shape determines what unit of your data can be written efficiently. + +For an example, consider you have a 100 GB array and need to read small chunks of 1 MB. +Without sharding, each chunk would be one file resulting in 100,000 files. That can +already cause performance issues on some file systems. +With sharding, you could use a shard size of 1 GB. This would result in 1000 chunks per +file and 100 files in total, which seems manageable for most storage systems. +You would still be able to read each 1 MB chunk independently, but you would need to +write your data in 1 GB increments. + +To use sharding, you need to specify the `shards` parameter when creating the array. + +```python exec="true" session="performance" source="above" result="ansi" +z6 = zarr.create_array(store={}, shape=(10000, 10000, 1000), shards=(1000, 1000, 1000), chunks=(100, 100, 100), dtype='uint8') +print(z6.info) +``` + +### Chunk memory layout + +The order of bytes **within each chunk** of an array can be changed via the +`order` config option, to use either C or Fortran layout. For +multi-dimensional arrays, these two layouts may provide different compression +ratios, depending on the correlation structure within the data. E.g.: + +```python exec="true" session="performance" source="above" result="ansi" +import numpy as np + +a = np.arange(100000000, dtype='int32').reshape(10000, 10000).T +c = zarr.create_array(store={}, shape=a.shape, chunks=(1000, 1000), dtype=a.dtype, config={'order': 'C'}) +c[:] = a +print(c.info_complete()) +``` + +```python exec="true" session="performance" source="above" result="ansi" +with zarr.config.set({'array.order': 'F'}): + f = zarr.create_array(store={}, shape=a.shape, chunks=(1000, 1000), dtype=a.dtype) + f[:] = a +print(f.info_complete()) + +``` + +In the above example, Fortran order gives a better compression ratio. This is an +artificial example but illustrates the general point that changing the order of +bytes within chunks of an array may improve the compression ratio, depending on +the structure of the data, the compression algorithm used, and which compression +filters (e.g., byte-shuffle) have been applied. + +### Empty chunks + +It is possible to configure how Zarr handles the storage of chunks that are "empty" +(i.e., every element in the chunk is equal to the array's fill value). When creating +an array with `write_empty_chunks=False`, Zarr will check whether a chunk is empty before compression and storage. If a chunk is empty, +then Zarr does not store it, and instead deletes the chunk from storage +if the chunk had been previously stored. + +This optimization prevents storing redundant objects and can speed up reads, but the cost is +added computation during array writes, since the contents of +each chunk must be compared to the fill value, and these advantages are contingent on the content of the array. +If you know that your data will form chunks that are almost always non-empty, then there is no advantage to the optimization described above. +In this case, creating an array with `write_empty_chunks=True` (the default) will instruct Zarr to write every chunk without checking for emptiness. + +The following example illustrates the effect of the `write_empty_chunks` flag on +the time required to write an array with different values.: + +```python exec="true" session="performance" source="above" result="ansi" +import zarr +import numpy as np +import time + +def timed_write(write_empty_chunks): + """ + Measure the time required and number of objects created when writing + to a Zarr array with random ints or fill value. + """ + chunks = (8192,) + shape = (chunks[0] * 1024,) + data = np.random.randint(0, 255, shape) + dtype = 'uint8' + arr = zarr.create_array( + f'data/example-{write_empty_chunks}.zarr', + shape=shape, + chunks=chunks, + dtype=dtype, + fill_value=0, + config={'write_empty_chunks': write_empty_chunks} + ) + # initialize all chunks + arr[:] = 100 + result = [] + for value in (data, arr.fill_value): + start = time.time() + arr[:] = value + elapsed = time.time() - start + result.append((elapsed, arr.nchunks_initialized)) + return result + +# log results +for write_empty_chunks in (True, False): + full, empty = timed_write(write_empty_chunks) + print(f'\nwrite_empty_chunks={write_empty_chunks}:\n\tRandom Data: {full[0]:.4f}s, {full[1]} objects stored\n\t Empty Data: {empty[0]:.4f}s, {empty[1]} objects stored\n') +``` + +In this example, writing random data is slightly slower with `write_empty_chunks=True`, +but writing empty data is substantially faster and generates far fewer objects in storage. + +### Changing chunk shapes (rechunking) + +Coming soon. + +## Parallel computing and synchronization + +Coming soon. + +## Pickle support + +Zarr arrays and groups can be pickled, as long as the underlying store object can be +pickled. With the exception of the `zarr.storage.MemoryStore`, any of the +storage classes provided in the `zarr.storage` module can be pickled. + +If an array or group is backed by a persistent store such as the a `zarr.storage.LocalStore`, +`zarr.storage.ZipStore` or `zarr.storage.FsspecStore` then the store data +**are not** pickled. The only thing that is pickled is the necessary parameters to allow the store +to re-open any underlying files or databases upon being unpickled. + +E.g., pickle/unpickle an local store array: + +```python exec="true" session="performance" source="above" result="ansi" +import pickle +data = np.arange(100000) +z1 = zarr.create_array(store='data/perf-example-2.zarr', shape=data.shape, chunks=data.shape, dtype=data.dtype) +z1[:] = data +s = pickle.dumps(z1) +z2 = pickle.loads(s) +assert z1 == z2 +print(np.all(z1[:] == z2[:])) +``` + +## Configuring Blosc + +Coming soon. diff --git a/docs/user-guide/performance.rst b/docs/user-guide/performance.rst deleted file mode 100644 index 0f31e5d7be..0000000000 --- a/docs/user-guide/performance.rst +++ /dev/null @@ -1,278 +0,0 @@ -.. only:: doctest - - >>> import shutil - >>> shutil.rmtree('data', ignore_errors=True) - -.. _user-guide-performance: - -Optimizing performance -====================== - -.. _user-guide-chunks: - -Chunk optimizations -------------------- - -.. _user-guide-chunks-shape: - -Chunk size and shape -~~~~~~~~~~~~~~~~~~~~ - -In general, chunks of at least 1 megabyte (1M) uncompressed size seem to provide -better performance, at least when using the Blosc compression library. - -The optimal chunk shape will depend on how you want to access the data. E.g., -for a 2-dimensional array, if you only ever take slices along the first -dimension, then chunk across the second dimension. If you know you want to chunk -across an entire dimension you can use the full size of that dimension within the -``chunks`` argument, e.g.:: - - >>> import zarr - >>> z1 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(100, 10000), dtype='int32') - >>> z1.chunks - (100, 10000) - -Alternatively, if you only ever take slices along the second dimension, then -chunk across the first dimension, e.g.:: - - >>> z2 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(10000, 100), dtype='int32') - >>> z2.chunks - (10000, 100) - -If you require reasonable performance for both access patterns then you need to -find a compromise, e.g.:: - - >>> z3 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') - >>> z3.chunks - (1000, 1000) - -If you are feeling lazy, you can let Zarr guess a chunk shape for your data by -providing ``chunks='auto'``, although please note that the algorithm for guessing -a chunk shape is based on simple heuristics and may be far from optimal. E.g.:: - - >>> z4 = zarr.create_array(store={}, shape=(10000, 10000), chunks='auto', dtype='int32') - >>> z4.chunks - (625, 625) - -If you know you are always going to be loading the entire array into memory, you -can turn off chunks by providing ``chunks`` equal to ``shape``, in which case there -will be one single chunk for the array:: - - >>> z5 = zarr.create_array(store={}, shape=(10000, 10000), chunks=(10000, 10000), dtype='int32') - >>> z5.chunks - (10000, 10000) - - -Sharding -~~~~~~~~ - -If you have large arrays but need small chunks to efficiently access the data, you can -use sharding. Sharding provides a mechanism to store multiple chunks in a single -storage object or file. This can be useful because traditional file systems and object -storage systems may have performance issues storing and accessing many files. -Additionally, small files can be inefficient to store if they are smaller than the -block size of the file system. - -Picking a good combination of chunk shape and shard shape is important for performance. -The chunk shape determines what unit of your data can be read independently, while the -shard shape determines what unit of your data can be written efficiently. - -For an example, consider you have a 100 GB array and need to read small chunks of 1 MB. -Without sharding, each chunk would be one file resulting in 100,000 files. That can -already cause performance issues on some file systems. -With sharding, you could use a shard size of 1 GB. This would result in 1000 chunks per -file and 100 files in total, which seems manageable for most storage systems. -You would still be able to read each 1 MB chunk independently, but you would need to -write your data in 1 GB increments. - -To use sharding, you need to specify the ``shards`` parameter when creating the array. - - >>> z6 = zarr.create_array(store={}, shape=(10000, 10000, 1000), shards=(1000, 1000, 1000), chunks=(100, 100, 100), dtype='uint8') - >>> z6.info - Type : Array - Zarr format : 3 - Data type : UInt8() - Fill value : 0 - Shape : (10000, 10000, 1000) - Shard shape : (1000, 1000, 1000) - Chunk shape : (100, 100, 100) - Order : C - Read-only : False - Store type : MemoryStore - Filters : () - Serializer : BytesCodec(endian=None) - Compressors : (ZstdCodec(level=0, checksum=False),) - No. bytes : 100000000000 (93.1G) - -.. _user-guide-chunks-order: - -Chunk memory layout -~~~~~~~~~~~~~~~~~~~ - -The order of bytes **within each chunk** of an array can be changed via the -``order`` config option, to use either C or Fortran layout. For -multi-dimensional arrays, these two layouts may provide different compression -ratios, depending on the correlation structure within the data. E.g.:: - - >>> import numpy as np - >>> - >>> a = np.arange(100000000, dtype='int32').reshape(10000, 10000).T - >>> c = zarr.create_array(store={}, shape=a.shape, chunks=(1000, 1000), dtype=a.dtype, config={'order': 'C'}) - >>> c[:] = a - >>> c.info_complete() - Type : Array - Zarr format : 3 - Data type : Int32(endianness='little') - Fill value : 0 - Shape : (10000, 10000) - Chunk shape : (1000, 1000) - Order : C - Read-only : False - Store type : MemoryStore - Filters : () - Serializer : BytesCodec(endian=) - Compressors : (ZstdCodec(level=0, checksum=False),) - No. bytes : 400000000 (381.5M) - No. bytes stored : 342588911 (326.7M) - Storage ratio : 1.2 - Chunks Initialized : 100 - >>> with zarr.config.set({'array.order': 'F'}): - ... f = zarr.create_array(store={}, shape=a.shape, chunks=(1000, 1000), dtype=a.dtype) - ... f[:] = a - >>> f.info_complete() - Type : Array - Zarr format : 3 - Data type : Int32(endianness='little') - Fill value : 0 - Shape : (10000, 10000) - Chunk shape : (1000, 1000) - Order : F - Read-only : False - Store type : MemoryStore - Filters : () - Serializer : BytesCodec(endian=) - Compressors : (ZstdCodec(level=0, checksum=False),) - No. bytes : 400000000 (381.5M) - No. bytes stored : 342588911 (326.7M) - Storage ratio : 1.2 - Chunks Initialized : 100 - -In the above example, Fortran order gives a better compression ratio. This is an -artificial example but illustrates the general point that changing the order of -bytes within chunks of an array may improve the compression ratio, depending on -the structure of the data, the compression algorithm used, and which compression -filters (e.g., byte-shuffle) have been applied. - -.. _user-guide-chunks-empty-chunks: - -Empty chunks -~~~~~~~~~~~~ - -It is possible to configure how Zarr handles the storage of chunks that are "empty" -(i.e., every element in the chunk is equal to the array's fill value). When creating -an array with ``write_empty_chunks=False``, Zarr will check whether a chunk is empty before compression and storage. If a chunk is empty, -then Zarr does not store it, and instead deletes the chunk from storage -if the chunk had been previously stored. - -This optimization prevents storing redundant objects and can speed up reads, but the cost is -added computation during array writes, since the contents of -each chunk must be compared to the fill value, and these advantages are contingent on the content of the array. -If you know that your data will form chunks that are almost always non-empty, then there is no advantage to the optimization described above. -In this case, creating an array with ``write_empty_chunks=True`` (the default) will instruct Zarr to write every chunk without checking for emptiness. - -The following example illustrates the effect of the ``write_empty_chunks`` flag on -the time required to write an array with different values.:: - - >>> import zarr - >>> import numpy as np - >>> import time - >>> - >>> def timed_write(write_empty_chunks): - ... """ - ... Measure the time required and number of objects created when writing - ... to a Zarr array with random ints or fill value. - ... """ - ... chunks = (8192,) - ... shape = (chunks[0] * 1024,) - ... data = np.random.randint(0, 255, shape) - ... dtype = 'uint8' - ... arr = zarr.create_array( - ... f'data/example-{write_empty_chunks}.zarr', - ... shape=shape, - ... chunks=chunks, - ... dtype=dtype, - ... fill_value=0, - ... config={'write_empty_chunks': write_empty_chunks} - ... ) - ... # initialize all chunks - ... arr[:] = 100 - ... result = [] - ... for value in (data, arr.fill_value): - ... start = time.time() - ... arr[:] = value - ... elapsed = time.time() - start - ... result.append((elapsed, arr.nchunks_initialized)) - ... return result - ... # log results - >>> for write_empty_chunks in (True, False): - ... full, empty = timed_write(write_empty_chunks) - ... print(f'\nwrite_empty_chunks={write_empty_chunks}:\n\tRandom Data: {full[0]:.4f}s, {full[1]} objects stored\n\t Empty Data: {empty[0]:.4f}s, {empty[1]} objects stored\n') - write_empty_chunks=True: - Random Data: ..., 1024 objects stored - Empty Data: ...s, 1024 objects stored - - write_empty_chunks=False: - Random Data: ...s, 1024 objects stored - Empty Data: ...s, 0 objects stored - - -In this example, writing random data is slightly slower with ``write_empty_chunks=True``, -but writing empty data is substantially faster and generates far fewer objects in storage. - -.. _user-guide-rechunking: - -Changing chunk shapes (rechunking) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Coming soon. - -.. _user-guide-sync: - -Parallel computing and synchronization --------------------------------------- - -Coming soon. - -.. _user-guide-pickle: - -Pickle support --------------- - -Zarr arrays and groups can be pickled, as long as the underlying store object can be -pickled. With the exception of the :class:`zarr.storage.MemoryStore`, any of the -storage classes provided in the :mod:`zarr.storage` module can be pickled. - -If an array or group is backed by a persistent store such as the a :class:`zarr.storage.LocalStore`, -:class:`zarr.storage.ZipStore` or :class:`zarr.storage.FsspecStore` then the store data -**are not** pickled. The only thing that is pickled is the necessary parameters to allow the store -to re-open any underlying files or databases upon being unpickled. - -E.g., pickle/unpickle an local store array:: - - >>> import pickle - >>> data = np.arange(100000) - >>> z1 = zarr.create_array(store='data/example-2.zarr', shape=data.shape, chunks=data.shape, dtype=data.dtype) - >>> z1[:] = data - >>> s = pickle.dumps(z1) - >>> z2 = pickle.loads(s) - >>> z1 == z2 - True - >>> np.all(z1[:] == z2[:]) - np.True_ - -.. _user-guide-tips-blosc: - -Configuring Blosc ------------------ - -Coming soon. diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md new file mode 100644 index 0000000000..86dac188a5 --- /dev/null +++ b/docs/user-guide/storage.md @@ -0,0 +1,149 @@ +# Storage guide + +Zarr-Python supports multiple storage backends, including: local file systems, +Zip files, remote stores via [fsspec](https://filesystem-spec.readthedocs.io) (S3, HTTP, etc.), and in-memory stores. In +Zarr-Python 3, stores must implement the abstract store API from +[`zarr.abc.store.Store`][]. + +!!! note + Unlike Zarr-Python 2 where the store interface was built around a generic `MutableMapping` + API, Zarr-Python 3 utilizes a custom store API that utilizes Python's AsyncIO library. + +## Implicit Store Creation + +In most cases, it is not required to create a `Store` object explicitly. Passing a string +to Zarr's top level API will result in the store being created automatically: + +```python exec="true" session="storage" source="above" result="ansi" +import zarr + +# Implicitly create a writable LocalStore +group = zarr.create_group(store='data/foo/bar') +print(group) +``` + +```python exec="true" session="storage" source="above" result="ansi" +# Implicitly create a read-only FsspecStore +group = zarr.open_group( + store='s3://noaa-nwm-retro-v2-zarr-pds', + mode='r', + storage_options={'anon': True} +) +print(group) +``` + +```python exec="true" session="storage" source="above" result="ansi" +# Implicitly creates a MemoryStore +data = {} +group = zarr.create_group(store=data) +print(group) +``` + +## Explicit Store Creation + +In some cases, it may be helpful to create a store instance directly. Zarr-Python offers four +built-in store: [`zarr.storage.LocalStore`][], [`zarr.storage.FsspecStore`][], +[`zarr.storage.ZipStore`][], [`zarr.storage.MemoryStore`][], and [`zarr.storage.ObjectStore`][]. + +### Local Store + +The [`zarr.storage.LocalStore`][] stores data in a nested set of directories on a local +filesystem: + +```python exec="true" session="storage" source="above" result="ansi" +store = zarr.storage.LocalStore('data/foo/bar', read_only=True) +group = zarr.open_group(store=store, mode='r') +print(group) +``` + +### Zip Store + +The [`zarr.storage.ZipStore`][] stores the contents of a Zarr hierarchy in a single +Zip file. The [Zip Store specification](https://github.com/zarr-developers/zarr-specs/pull/311) is currently in draft form: + +```python exec="true" session="storage" source="above" result="ansi" +store = zarr.storage.ZipStore('data.zip', mode='w') +array = zarr.create_array(store=store, shape=(2,), dtype='float64') +print(array) +``` + +### Remote Store + +The [`zarr.storage.FsspecStore`][] stores the contents of a Zarr hierarchy in following the same +logical layout as the [`LocalStore`][zarr.storage.LocalStore], except the store is assumed to be on a remote storage system +such as cloud object storage (e.g. AWS S3, Google Cloud Storage, Azure Blob Store). The +[`zarr.storage.FsspecStore`][] is backed by [fsspec](https://filesystem-spec.readthedocs.io) and can support any backend +that implements the [AbstractFileSystem](https://filesystem-spec.readthedocs.io/en/stable/api.html#fsspec.spec.AbstractFileSystem) +API. `storage_options` can be used to configure the fsspec backend: + +```python exec="true" session="storage" source="above" result="ansi" +store = zarr.storage.FsspecStore.from_url( + 's3://noaa-nwm-retro-v2-zarr-pds', + read_only=True, + storage_options={'anon': True} +) +group = zarr.open_group(store=store, mode='r') +print(group) +``` + +The type of filesystem (e.g. S3, https, etc..) is inferred from the scheme of the url (e.g. s3 for "**s3**://noaa-nwm-retro-v2-zarr-pds"). +In case a specific filesystem is needed, one can explicitly create it. For example to create a S3 filesystem: + +```python exec="true" session="storage" source="above" result="ansi" +import fsspec +fs = fsspec.filesystem( + 's3', anon=True, asynchronous=True, + client_kwargs={'endpoint_url': "https://noaa-nwm-retro-v2-zarr-pds.s3.amazonaws.com"} +) +store = zarr.storage.FsspecStore(fs) +print(store) +``` + + +### Memory Store + +The [`zarr.storage.MemoryStore`][] a in-memory store that allows for serialization of +Zarr data (metadata and chunks) to a dictionary: + +```python exec="true" session="storage" source="above" result="ansi" +data = {} +store = zarr.storage.MemoryStore(data) +array = zarr.create_array(store=store, shape=(2,), dtype='float64') +print(array) +``` + +### Object Store + +[`zarr.storage.ObjectStore`][] stores the contents of the Zarr hierarchy using any ObjectStore +[storage implementation](https://developmentseed.org/obstore/latest/api/store/), including AWS S3 ([`obstore.store.S3Store`][]), Google Cloud Storage ([`obstore.store.GCSStore`][]), and Azure Blob Storage ([`obstore.store.AzureStore`][]). This store is backed by [obstore](https://developmentseed.org/obstore/latest/), which +builds on the production quality Rust library [object_store](https://docs.rs/object_store/latest/object_store/). + +```python exec="true" session="storage" source="above" result="ansi" +from zarr.storage import ObjectStore +from obstore.store import MemoryStore + +store = ObjectStore(MemoryStore()) +array = zarr.create_array(store=store, shape=(2,), dtype='float64') +print(array) +``` + +Here's an example of using ObjectStore for accessing remote data: + +```python exec="true" session="storage" source="above" result="ansi" +from zarr.storage import ObjectStore +from obstore.store import S3Store + +s3_store = S3Store('noaa-nwm-retro-v2-zarr-pds', skip_signature=True, region="us-west-2") +store = zarr.storage.ObjectStore(store=s3_store, read_only=True) +group = zarr.open_group(store=store, mode='r') +print(group.info) +``` + +!!! warning + The [`zarr.storage.ObjectStore`][] class is experimental. + +## Developing custom stores + +Zarr-Python [`zarr.abc.store.Store`][] API is meant to be extended. The Store Abstract Base +Class includes all of the methods needed to be a fully operational store in Zarr Python. +Zarr also provides a test harness for custom stores: [`zarr.testing.store.StoreTests`][]. diff --git a/docs/user-guide/storage.rst b/docs/user-guide/storage.rst deleted file mode 100644 index e5a333872e..0000000000 --- a/docs/user-guide/storage.rst +++ /dev/null @@ -1,158 +0,0 @@ -.. only:: doctest - - >>> import shutil - >>> shutil.rmtree('data', ignore_errors=True) - -.. _user-guide-storage: - -Storage guide -============= - -Zarr-Python supports multiple storage backends, including: local file systems, -Zip files, remote stores via fsspec_ (S3, HTTP, etc.), and in-memory stores. In -Zarr-Python 3, stores must implement the abstract store API from -:class:`zarr.abc.store.Store`. - -.. note:: - Unlike Zarr-Python 2 where the store interface was built around a generic ``MutableMapping`` - API, Zarr-Python 3 utilizes a custom store API that utilizes Python's AsyncIO library. - -Implicit Store Creation ------------------------ - -In most cases, it is not required to create a ``Store`` object explicitly. Passing a string -to Zarr's top level API will result in the store being created automatically.: - - >>> import zarr - >>> - >>> # Implicitly create a writable LocalStore - >>> zarr.create_group(store='data/foo/bar') - - >>> - >>> # Implicitly create a read-only FsspecStore - >>> zarr.open_group( - ... store='s3://noaa-nwm-retro-v2-zarr-pds', - ... mode='r', - ... storage_options={'anon': True} - ... ) - > - >>> - >>> # Implicitly creates a MemoryStore - >>> data = {} - >>> zarr.create_group(store=data) - - -Explicit Store Creation ------------------------ - -In some cases, it may be helpful to create a store instance directly. Zarr-Python offers four -built-in store: :class:`zarr.storage.LocalStore`, :class:`zarr.storage.FsspecStore`, -:class:`zarr.storage.ZipStore`, :class:`zarr.storage.MemoryStore`, and :class:`zarr.storage.ObjectStore`. - -Local Store -~~~~~~~~~~~ - -The :class:`zarr.storage.LocalStore` stores data in a nested set of directories on a local -filesystem.: - - >>> store = zarr.storage.LocalStore('data/foo/bar', read_only=True) - >>> zarr.open_group(store=store, mode='r') - - -Zip Store -~~~~~~~~~ - -The :class:`zarr.storage.ZipStore` stores the contents of a Zarr hierarchy in a single -Zip file. The `Zip Store specification`_ is currently in draft form.: - - >>> store = zarr.storage.ZipStore('data.zip', mode='w') - >>> zarr.create_array(store=store, shape=(2,), dtype='float64') - - -Remote Store -~~~~~~~~~~~~ - -The :class:`zarr.storage.FsspecStore` stores the contents of a Zarr hierarchy in following the same -logical layout as the ``LocalStore``, except the store is assumed to be on a remote storage system -such as cloud object storage (e.g. AWS S3, Google Cloud Storage, Azure Blob Store). The -:class:`zarr.storage.FsspecStore` is backed by `fsspec`_ and can support any backend -that implements the `AbstractFileSystem `_ -API. ``storage_options`` can be used to configure the fsspec backend.: - - >>> store = zarr.storage.FsspecStore.from_url( - ... 's3://noaa-nwm-retro-v2-zarr-pds', - ... read_only=True, - ... storage_options={'anon': True} - ... ) - >>> zarr.open_group(store=store, mode='r') - > - -The type of filesystem (e.g. S3, https, etc..) is inferred from the scheme of the url (e.g. s3 for "**s3**://noaa-nwm-retro-v2-zarr-pds"). -In case a specific filesystem is needed, one can explicitly create it. For example to create a S3 filesystem: - - >>> import fsspec - >>> fs = fsspec.filesystem( - ... 's3', anon=True, asynchronous=True, - ... client_kwargs={'endpoint_url': "https://noaa-nwm-retro-v2-zarr-pds.s3.amazonaws.com"} - ... ) - >>> store = zarr.storage.FsspecStore(fs) - -Memory Store -~~~~~~~~~~~~ - -The :class:`zarr.storage.MemoryStore` a in-memory store that allows for serialization of -Zarr data (metadata and chunks) to a dictionary.: - - >>> data = {} - >>> store = zarr.storage.MemoryStore(data) - >>> # TODO: replace with create_array after #2463 - >>> zarr.create_array(store=store, shape=(2,), dtype='float64') - - -Object Store -~~~~~~~~~~~~ - -:class:`zarr.storage.ObjectStore` stores the contents of the Zarr hierarchy using any ObjectStore -`storage implementation `_, including AWS S3 (:class:`obstore.store.S3Store`), Google Cloud Storage (:class:`obstore.store.GCSStore`), and Azure Blob Storage (:class:`obstore.store.AzureStore`). This store is backed by `obstore `_, which -builds on the production quality Rust library `object_store `_. - - - >>> from zarr.storage import ObjectStore - >>> from obstore.store import MemoryStore - >>> - >>> store = ObjectStore(MemoryStore()) - >>> zarr.create_array(store=store, shape=(2,), dtype='float64') - - -Here's an example of using ObjectStore for accessing remote data: - - >>> from zarr.storage import ObjectStore - >>> from obstore.store import S3Store - >>> - >>> s3_store = S3Store('noaa-nwm-retro-v2-zarr-pds', skip_signature=True, region="us-west-2") - >>> store = zarr.storage.ObjectStore(store=s3_store, read_only=True) - >>> group = zarr.open_group(store=store, mode='r') - >>> group.info - Name : - Type : Group - Zarr format : 2 - Read-only : True - Store type : ObjectStore - No. members : 12 - No. arrays : 12 - No. groups : 0 - -.. warning:: - The :class:`zarr.storage.ObjectStore` class is experimental. - -.. _user-guide-custom-stores: - -Developing custom stores ------------------------- - -Zarr-Python :class:`zarr.abc.store.Store` API is meant to be extended. The Store Abstract Base -Class includes all of the methods needed to be a fully operational store in Zarr Python. -Zarr also provides a test harness for custom stores: :class:`zarr.testing.store.StoreTests`. - -.. _Zip Store Specification: https://github.com/zarr-developers/zarr-specs/pull/311 -.. _fsspec: https://filesystem-spec.readthedocs.io diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md new file mode 100644 index 0000000000..c3a7ddbafe --- /dev/null +++ b/docs/user-guide/v3_migration.md @@ -0,0 +1,228 @@ +# 3.0 Migration Guide + +Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the +goals motivating this refactor included: + +* adding support for the Zarr format 3 specification (along with the Zarr format 2 specification) +* cleaning up internal and user facing APIs +* improving performance (particularly in high latency storage environments like + cloud object stores) + +To accommodate this, Zarr-Python 3 introduces a number of changes to the API, including a number +of significant breaking changes and deprecations. + +This page provides a guide explaining breaking changes and deprecations to help you +migrate your code from version 2 to version 3. If we have missed anything, please +open a [GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new) +so we can improve this guide. + +## Compatibility target + +The goals described above necessitated some breaking changes to the API (hence the +major version update), but where possible we have maintained backwards compatibility +in the most widely used parts of the API. This in the [`zarr.Array`][] and +[`zarr.Group`][] classes and the "top-level API" (e.g. [`zarr.open_array`][] and +[`zarr.open_group`][]). + +## Getting ready for 3.0 + +Before migrating to Zarr-Python 3, we suggest projects that depend on Zarr-Python take +the following actions in order: + +1. Pin the supported Zarr-Python version to `zarr>=2,<3`. This is a best practice + and will protect your users from any incompatibilities that may arise during the + release of Zarr-Python 3. This pin can be removed after migrating to Zarr-Python 3. +2. Limit your imports from the Zarr-Python package. Most of the primary API `zarr.*` + will be compatible in Zarr-Python 3. However, the following breaking API changes are + planned: + + - `numcodecs.*` will no longer be available in `zarr.*`. To migrate, import codecs + directly from `numcodecs`: + + ```python + from numcodecs import Blosc + # instead of: + # from zarr import Blosc + ``` + + - The `zarr.v3_api_available` feature flag is being removed. In Zarr-Python 3 + the v3 API is always available, so you shouldn't need to use this flag. + - The following internal modules are being removed or significantly changed. If + your application relies on imports from any of the below modules, you will need + to either a) modify your application to no longer rely on these imports or b) + vendor the parts of the specific modules that you need. + + * `zarr.attrs` has gone, with no replacement + * `zarr.codecs` has changed, see "Codecs" section below for more information + * `zarr.context` has gone, with no replacement + * `zarr.core` remains but should be considered private API + * `zarr.hierarchy` has gone, with no replacement (use `zarr.Group` inplace of `zarr.hierarchy.Group`) + * `zarr.indexing` has gone, with no replacement + * `zarr.meta` has gone, with no replacement + * `zarr.meta_v1` has gone, with no replacement + * `zarr.sync` has gone, with no replacement + * `zarr.types` has gone, with no replacement + * `zarr.util` has gone, with no replacement + * `zarr.n5` has gone, see below for an alternative N5 options + +3. Test that your package works with version 3. +4. Update the pin to include `zarr>=3,<4`. + +## Zarr-Python 2 support window + +Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for +its performance improvements and new features. Security and bug fixes will be made to +the 2.x series for at least six months following the first Zarr-Python 3 release. +If you need to use the latest Zarr-Python 2 release, you can install it with: + +```console +$ pip install "zarr==2.*" +``` + +!!! note + Development and maintenance of the 2.x release series has moved to the + [support/v2](https://github.com/zarr-developers/zarr-python/tree/support/v2) branch. + Issues and pull requests related to this branch are tagged with the + [V2](https://github.com/zarr-developers/zarr-python/labels/V2) label. + +## Migrating to Zarr-Python 3 + +The following sections provide details on breaking changes in Zarr-Python 3. + +### The Array class + +1. Disallow direct construction - the signature for initializing the `Array` class has changed + significantly. Please use [`zarr.create_array`][] or [`zarr.open_array`][] instead of + directly constructing the [`zarr.Array`][] class. + +2. Defaulting to `zarr_format=3` - newly created arrays will use the version 3 of the + Zarr specification. To continue using version 2, set `zarr_format=2` when creating arrays + or set `default_zarr_version=2` in Zarr's runtime configuration. + +### The Group class + +1. Disallow direct construction - use [`zarr.open_group`][] or [`zarr.create_group`][] + instead of directly constructing the `zarr.Group` class. +2. Most of the h5py compatibility methods are deprecated and will issue warnings if used. + The following functions are drop in replacements that have the same signature and functionality: + + - Use [`zarr.Group.create_array`][] in place of `zarr.Group.create_dataset` + - Use [`zarr.Group.require_array`][] in place of `zarr.Group.require_dataset` +3. Disallow "." syntax for getting group members. To get a member of a group named `foo`, + use `group["foo"]` in place of `group.foo`. + +### The Store class + +The Store API has changed significant in Zarr-Python 3. The most notable changes to the +Store API are: + +#### Store Import Paths + +Several store implementations have moved from the top-level module to `zarr.storage`: + +```diff title="Store import changes from v2 to v3" +# Before (v2) +- from zarr import MemoryStore, DirectoryStore ++ from zarr.storage import MemoryStore, LocalStore # LocalStore replaces DirectoryStore +``` + +Common replacements: + +| v2 Import | v3 Import | +|-------------------------|------------------------------------| +| `zarr.MemoryStore` | [`zarr.storage.MemoryStore`][] | +| `zarr.DirectoryStore` | [`zarr.storage.LocalStore`][] | +| `zarr.TempStore` | Use [`tempfile.TemporaryDirectory`][] with [`LocalStore`][zarr.storage.LocalStore] | + +1. Replaced the `MutableMapping` base class in favor of a custom abstract base class + ([`zarr.abc.store.Store`][]). +2. Switched to an asynchronous interface for all store methods that result in IO. This + change ensures that all store methods are non-blocking and are as performant as + possible. + +Beyond the changes store interface, a number of deprecated stores were also removed in +Zarr-Python 3. See issue #1274 for more details on the removal of these stores. + +- `N5Store` - see https://github.com/zarr-developers/n5py for an alternative interface to + N5 formatted data. +- `ABSStore` - use the [`zarr.storage.FsspecStore`][] instead along with fsspec's + [adlfs backend](https://github.com/fsspec/adlfs). + +The following stores have been removed altogether. Users who need these stores will have to +implement their own version in zarr-python v3. + +- `DBMStore` +- `LMDBStore` +- `SQLiteStore` +- `MongoDBStore` +- `RedisStore` + +At present, the latter five stores in this list do not have an equivalent in Zarr-Python 3. +If you are interested in developing a custom store that targets these backends, see +[developing custom stores](storage.md/#developing-custom-stores) or open an +[issue](https://github.com/zarr-developers/zarr-python/issues) to discuss your use case. + +### Codecs + +Codecs defined in ``numcodecs`` (and also imported into the ``zarr.codecs`` namespace in Zarr-Python 2) +should still be used when creating Zarr format 2 arrays. + +Codecs for creating Zarr format 3 arrays are available in two locations: + +- `zarr.codecs` contains Zarr format 3 codecs that are defined in the [codecs section of the Zarr format 3 specification](https://zarr-specs.readthedocs.io/en/latest/v3/codecs/index.html). +- `numcodecs.zarr3` contains codecs from `numcodecs` that can be used to create Zarr format 3 arrays, but are not necessarily part of the Zarr format 3 specification. + +### Dependencies + +When installing using `pip`: + +- The new `remote` dependency group can be used to install a supported version of + `fsspec`, required for remote data access. +- The new `gpu` dependency group can be used to install a supported version of + `cuda`, required for GPU functionality. +- The `jupyter` optional dependency group has been removed, since v3 contains no + jupyter specific functionality. + +### Miscellaneous + +- The keyword argument `zarr_version` available in most creation functions in `zarr` + (e.g. [`zarr.create`][], [`zarr.open`][], [`zarr.group`][], [`zarr.array`][]) has + been deprecated in favor of `zarr_format`. + +## 🚧 Work in Progress 🚧 + +Zarr-Python 3 is still under active development, and is not yet fully complete. +The following list summarizes areas of the codebase that we expect to build out +after the 3.0.0 release. If features listed below are important to your use case +of Zarr-Python, please open (or comment on) a +[GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new). + +- The following functions / methods have not been ported to Zarr-Python 3 yet: + + * `zarr.copy` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) + * `zarr.copy_all` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) + * `zarr.copy_store` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) + * `zarr.Group.move` ([issue #2108](https://github.com/zarr-developers/zarr-python/issues/2108)) + +- The following features (corresponding to function arguments to functions in + `zarr`) have not been ported to Zarr-Python 3 yet. Using these features + will raise a warning or a `NotImplementedError`: + + * `cache_attrs` + * `cache_metadata` + * `chunk_store` ([issue #2495](https://github.com/zarr-developers/zarr-python/issues/2495)) + * `meta_array` + * `object_codec` ([issue #2617](https://github.com/zarr-developers/zarr-python/issues/2617)) + * `synchronizer` ([issue #1596](https://github.com/zarr-developers/zarr-python/issues/1596)) + * `dimension_separator` + +- The following features that were supported by Zarr-Python 2 have not been ported + to Zarr-Python 3 yet: + + * Structured arrays / dtypes ([issue #2134](https://github.com/zarr-developers/zarr-python/issues/2134)) + * Fixed-length string dtypes ([issue #2347](https://github.com/zarr-developers/zarr-python/issues/2347)) + * Datetime and timedelta dtypes ([issue #2616](https://github.com/zarr-developers/zarr-python/issues/2616)) + * Object dtypes ([issue #2616](https://github.com/zarr-developers/zarr-python/issues/2616)) + * Ragged arrays ([issue #2618](https://github.com/zarr-developers/zarr-python/issues/2618)) + * Groups and Arrays do not implement `__enter__` and `__exit__` protocols ([issue #2619](https://github.com/zarr-developers/zarr-python/issues/2619)) + * Default filters for object dtypes for Zarr format 2 arrays ([issue #2627](https://github.com/zarr-developers/zarr-python/issues/2627)) diff --git a/docs/user-guide/v3_migration.rst b/docs/user-guide/v3_migration.rst deleted file mode 100644 index 2b53e39b83..0000000000 --- a/docs/user-guide/v3_migration.rst +++ /dev/null @@ -1,250 +0,0 @@ -.. _v3 migration guide: - -3.0 Migration Guide -=================== - -Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the -goals motivating this refactor included: - -* adding support for the Zarr format 3 specification (along with the Zarr format 2 specification) -* cleaning up internal and user facing APIs -* improving performance (particularly in high latency storage environments like - cloud object stores) - -To accommodate this, Zarr-Python 3 introduces a number of changes to the API, including a number -of significant breaking changes and deprecations. - -This page provides a guide explaining breaking changes and deprecations to help you -migrate your code from version 2 to version 3. If we have missed anything, please -open a `GitHub issue `_ -so we can improve this guide. - -Compatibility target --------------------- - -The goals described above necessitated some breaking changes to the API (hence the -major version update), but where possible we have maintained backwards compatibility -in the most widely used parts of the API. This in the :class:`zarr.Array` and -:class:`zarr.Group` classes and the "top-level API" (e.g. :func:`zarr.open_array` and -:func:`zarr.open_group`). - -Getting ready for 3.0 ---------------------- - -Before migrating to Zarr-Python 3, we suggest projects that depend on Zarr-Python take -the following actions in order: - -1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice - and will protect your users from any incompatibilities that may arise during the - release of Zarr-Python 3. This pin can be removed after migrating to Zarr-Python 3. -2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` - will be compatible in Zarr-Python 3. However, the following breaking API changes are - planned: - - - ``numcodecs.*`` will no longer be available in ``zarr.*``. To migrate, import codecs - directly from ``numcodecs``: - - .. code-block:: python - - from numcodecs import Blosc - # instead of: - # from zarr import Blosc - - - The ``zarr.v3_api_available`` feature flag is being removed. In Zarr-Python 3 - the v3 API is always available, so you shouldn't need to use this flag. - - The following internal modules are being removed or significantly changed. If - your application relies on imports from any of the below modules, you will need - to either a) modify your application to no longer rely on these imports or b) - vendor the parts of the specific modules that you need. - - * ``zarr.attrs`` has gone, with no replacement - * ``zarr.codecs`` has changed, see "Codecs" section below for more information - * ``zarr.context`` has gone, with no replacement - * ``zarr.core`` remains but should be considered private API - * ``zarr.hierarchy`` has gone, with no replacement (use ``zarr.Group`` inplace of ``zarr.hierarchy.Group``) - * ``zarr.indexing`` has gone, with no replacement - * ``zarr.meta`` has gone, with no replacement - * ``zarr.meta_v1`` has gone, with no replacement - * ``zarr.sync`` has gone, with no replacement - * ``zarr.types`` has gone, with no replacement - * ``zarr.util`` has gone, with no replacement - * ``zarr.n5`` has gone, see below for an alternative N5 options - -3. Test that your package works with version 3. -4. Update the pin to include ``zarr>=3,<4``. - -Zarr-Python 2 support window ----------------------------- - -Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for -its performance improvements and new features. Security and bug fixes will be made to -the 2.x series for at least six months following the first Zarr-Python 3 release. -If you need to use the latest Zarr-Python 2 release, you can install it with: - -.. code-block:: console - - $ pip install "zarr==2.*" - -.. note:: - Development and maintenance of the 2.x release series has moved to the - `support/v2 `_ branch. - Issues and pull requests related to this branch are tagged with the - `V2 `_ label. - -Migrating to Zarr-Python 3 --------------------------- - -The following sections provide details on breaking changes in Zarr-Python 3. - -The Array class -~~~~~~~~~~~~~~~ - -1. Disallow direct construction - the signature for initializing the ``Array`` class has changed - significantly. Please use :func:`zarr.create_array` or :func:`zarr.open_array` instead of - directly constructing the :class:`zarr.Array` class. - -2. Defaulting to ``zarr_format=3`` - newly created arrays will use the version 3 of the - Zarr specification. To continue using version 2, set ``zarr_format=2`` when creating arrays - or set ``default_zarr_version=2`` in Zarr's :ref:`runtime configuration `. - -The Group class -~~~~~~~~~~~~~~~ - -1. Disallow direct construction - use :func:`zarr.open_group` or :func:`zarr.create_group` - instead of directly constructing the :class:`zarr.Group` class. -2. Most of the h5py compatibility methods are deprecated and will issue warnings if used. - The following functions are drop in replacements that have the same signature and functionality: - - - Use :func:`zarr.Group.create_array` in place of :func:`zarr.Group.create_dataset` - - Use :func:`zarr.Group.require_array` in place of :func:`zarr.Group.require_dataset` -3. Disallow "." syntax for getting group members. To get a member of a group named ``foo``, - use ``group["foo"]`` in place of ``group.foo``. - -The Store class -~~~~~~~~~~~~~~~ - -The Store API has changed significant in Zarr-Python 3. The most notable changes to the -Store API are: - -Store Import Paths -^^^^^^^^^^^^^^^^^^ -Several store implementations have moved from the top-level module to ``zarr.storage``: - -.. code-block:: diff - :caption: Store import changes from v2 to v3 - - # Before (v2) - - from zarr import MemoryStore, DirectoryStore - + from zarr.storage import MemoryStore, LocalStore # LocalStore replaces DirectoryStore - -Common replacements: - -+-------------------------+------------------------------------+ -| v2 Import | v3 Import | -+=========================+====================================+ -| ``zarr.MemoryStore`` | ``zarr.storage.MemoryStore`` | -+-------------------------+------------------------------------+ -| ``zarr.DirectoryStore`` | ``zarr.storage.LocalStore`` | -+-------------------------+------------------------------------+ -| ``zarr.TempStore`` | Use ``tempfile.TemporaryDirectory``| -| | with ``LocalStore`` | -+-------------------------+------------------------------------+ - -1. Replaced the ``MutableMapping`` base class in favor of a custom abstract base class - (:class:`zarr.abc.store.Store`). -2. Switched to an asynchronous interface for all store methods that result in IO. This - change ensures that all store methods are non-blocking and are as performant as - possible. - -Beyond the changes store interface, a number of deprecated stores were also removed in -Zarr-Python 3. See :issue:`1274` for more details on the removal of these stores. - -- ``N5Store`` - see https://github.com/zarr-developers/n5py for an alternative interface to - N5 formatted data. -- ``ABSStore`` - use the :class:`zarr.storage.FsspecStore` instead along with fsspec's - `adlfs backend `_. - -The following stores have been removed altogether. Users who need these stores will have to -implement their own version in zarr-python v3. - -- ``DBMStore`` -- ``LMDBStore`` -- ``SQLiteStore`` -- ``MongoDBStore`` -- ``RedisStore`` - -At present, the latter five stores in this list do not have an equivalent in Zarr-Python 3. -If you are interested in developing a custom store that targets these backends, see -:ref:`developing custom stores ` or open an -`issue `_ to discuss your use case. - - -Codecs -~~~~~~ -Codecs defined in ``numcodecs`` (and also imported into the ``zarr.codecs`` namespace in Zarr-Python 2) -should still be used when creating Zarr format 2 arrays. - -Codecs for creating Zarr format 3 arrays are available in two locations: - -- `zarr.codecs` contains Zarr format 3 codecs that are defined in the `codecs section of the Zarr format 3 specification `_. -- `numcodecs.zarr3` contains codecs from ``numcodecs`` that can be used to create Zarr format 3 arrays, but are not necessarily part of the Zarr format 3 specification. - - -Dependencies -~~~~~~~~~~~~ - -When installing using ``pip``: - -- The new ``remote`` dependency group can be used to install a supported version of - ``fsspec``, required for remote data access. -- The new ``gpu`` dependency group can be used to install a supported version of - ``cuda``, required for GPU functionality. -- The ``jupyter`` optional dependency group has been removed, since v3 contains no - jupyter specific functionality. - -Miscellaneous -~~~~~~~~~~~~~ - -- The keyword argument ``zarr_version`` available in most creation functions in :mod:`zarr` - (e.g. :func:`zarr.create`, :func:`zarr.open`, :func:`zarr.group`, :func:`zarr.array`) has - been deprecated in favor of ``zarr_format``. - -🚧 Work in Progress 🚧 ----------------------- - -Zarr-Python 3 is still under active development, and is not yet fully complete. -The following list summarizes areas of the codebase that we expect to build out -after the 3.0.0 release. If features listed below are important to your use case -of Zarr-Python, please open (or comment on) a -`GitHub issue `_. - -- The following functions / methods have not been ported to Zarr-Python 3 yet: - - * :func:`zarr.copy` (:issue:`2407`) - * :func:`zarr.copy_all` (:issue:`2407`) - * :func:`zarr.copy_store` (:issue:`2407`) - * :func:`zarr.Group.move` (:issue:`2108`) - -- The following features (corresponding to function arguments to functions in - :mod:`zarr`) have not been ported to Zarr-Python 3 yet. Using these features - will raise a warning or a ``NotImplementedError``: - - * ``cache_attrs`` - * ``cache_metadata`` - * ``chunk_store`` (:issue:`2495`) - * ``meta_array`` - * ``object_codec`` (:issue:`2617`) - * ``synchronizer`` (:issue:`1596`) - * ``dimension_separator`` - -- The following features that were supported by Zarr-Python 2 have not been ported - to Zarr-Python 3 yet: - - * Structured arrays / dtypes (:issue:`2134`) - * Fixed-length string dtypes (:issue:`2347`) - * Datetime and timedelta dtypes (:issue:`2616`) - * Object dtypes (:issue:`2617`) - * Ragged arrays (:issue:`2618`) - * Groups and Arrays do not implement ``__enter__`` and ``__exit__`` protocols (:issue:`2619`) - * Big Endian dtypes (:issue:`2324`) - * Default filters for object dtypes for Zarr format 2 arrays (:issue:`2627`) diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000000..c938ec36a8 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,198 @@ +# Based on https://github.com/developmentseed/obspec/blob/main/mkdocs.yml +site_name: zarr-python +repo_name: zarr-developers/zarr-python +repo_url: https://github.com/zarr-developers/zarr-python +site_description: An implementation of chunked, compressed, N-dimensional arrays for Python. +site_author: Alistair Miles +site_url: https://zarr.readthedocs.io/ +docs_dir: docs + +nav: + - "index.md" + - "quick-start.md" + - User Guide: + - user-guide/index.md + - user-guide/installation.md + - user-guide/arrays.md + - user-guide/groups.md + - user-guide/attributes.md + - user-guide/storage.md + - user-guide/config.md + - user-guide/cli.md + - user-guide/v3_migration.md + - user-guide/data_types.md + - user-guide/performance.md + - user-guide/extending.md + - user-guide/gpu.md + - user-guide/consolidated_metadata.md + - API Reference: + - api/index.md + - api/array.md + - api/group.md + - api/create.md + - api/dtype.md + - api/open.md + - api/load.md + - api/save.md + - api/buffer.md + - api/convenience.md + - api/config.md + - api/codecs.md + - api/errors.md + - api/registry.md + - api/storage.md + - api/testing.md + - Async API: api/api_async.md + - Sync API: api/api_sync.md + - ABC: + - api/abc/buffer.md + - api/abc/codec.md + - api/abc/metadata.md + - api/abc/store.md + - deprecated: + - Convenience sub-module: api/deprecated/convenience.md + - Creation sub-module: api/deprecated/creation.md + - release-notes.md + - contributing.md +watch: + - src/zarr + - docs + +theme: + language: en + name: material + custom_dir: docs/overrides + logo: _static/logo_horizontal.svg + palette: + # Palette toggle for automatic mode + - media: "(prefers-color-scheme)" + toggle: + icon: material/brightness-auto + name: Switch to light mode + + # Palette toggle for light mode + - media: "(prefers-color-scheme: light)" + primary: blue grey + accent: pink + toggle: + icon: material/brightness-7 + name: Switch to dark mode + + # Palette toggle for dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: grey + accent: pink + toggle: + icon: material/brightness-4 + name: Switch to system preference + + font: + text: Roboto + code: Roboto Mono + + features: + - content.code.annotate + - content.code.copy + - navigation.indexes + - navigation.instant + - navigation.tracking + - search.suggest + - search.share + +extra: + social: + - icon: fontawesome/brands/mastodon + link: https://fosstodon.org/@zarr + - icon: fontawesome/brands/bluesky + link: https://bsky.app/profile/zarr.dev + +extra_css: + - overrides/stylesheets/extra.css + +plugins: + - search + - markdown-exec + - mkdocstrings: + enable_inventory: true + handlers: + python: + paths: [src/zarr] + options: + allow_inspection: true + docstring_section_style: list + docstring_style: numpy + inherited_members: true + line_length: 60 + separate_signature: true + show_root_heading: true + show_signature_annotations: true + show_source: true + show_symbol_type_toc: true + signature_crossrefs: true + extensions: + - griffe_inherited_docstrings + + inventories: + - https://docs.python.org/3/objects.inv + - https://docs.xarray.dev/en/stable/objects.inv + - https://numpy.org/doc/stable/objects.inv + - https://numcodecs.readthedocs.io/en/stable/objects.inv + - https://developmentseed.org/obstore/latest/objects.inv + - https://filesystem-spec.readthedocs.io/en/latest/objects.inv + - https://requests.readthedocs.io/en/latest/objects.inv + - https://docs.aiohttp.org/en/stable/objects.inv + - https://s3fs.readthedocs.io/en/latest/objects.inv + - https://docs.h5py.org/en/stable/objects.inv + - https://icechunk.io/en/stable/objects.inv + - https://lithops-cloud.github.io/docs/objects.inv + - https://docs.dask.org/en/stable/objects.inv + - redirects: + redirect_maps: + 'spec/index.md': 'https://zarr-specs.readthedocs.io' + 'spec/v1.md': 'https://zarr-specs.readthedocs.io/en/latest/v1/v1.0.html' + 'spec/v2.md': 'https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html' + 'spec/v3.md': 'https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html' + 'license.md': 'https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt' + 'tutorial.md': 'user-guide/installation.md' + 'getting-started.md': 'quick-start.md' + 'roadmap.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' + 'installation.md': 'user-guide/installation.md' + 'release.md': 'release-notes.md' + +# https://github.com/developmentseed/titiler/blob/50934c929cca2fa8d3c408d239015f8da429c6a8/docs/mkdocs.yml#L115-L140 +markdown_extensions: + - admonition + - attr_list + - codehilite: + guess_lang: false + - def_list + - footnotes + - md_in_html + - pymdownx.arithmatex + - pymdownx.betterem + - pymdownx.caret: + insert: false + - pymdownx.details + - pymdownx.escapeall: + hardbreak: true + nbsp: true + - pymdownx.magiclink: + hide_protocol: true + repo_url_shortener: true + - pymdownx.smartsymbols + - pymdownx.superfences + - pymdownx.tasklist: + custom_checkbox: true + - pymdownx.tilde + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg + - toc: + permalink: true + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite + - pymdownx.snippets diff --git a/pyproject.toml b/pyproject.toml index 11d91944d5..f6293a6df1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -96,15 +96,15 @@ remote_tests = [ optional = ["rich", "universal-pathlib"] docs = [ # Doc building - 'sphinx==8.1.3', - 'sphinx-autobuild>=2021.3.14', - 'sphinx-autoapi==3.4.0', - 'sphinx_design', - 'sphinx-issues', - 'sphinx-copybutton', - 'sphinx-reredirects', - 'pydata-sphinx-theme', - 'numpydoc', + "mkdocs-material[imaging]>=9.6.14", + "mkdocs>=1.6.1", + "mkdocstrings>=0.29.1", + "mkdocstrings-python>=1.16.10", + "mike>=2.1.3", + "mkdocs-redirects>=1.2.0", + "markdown-exec[ansi]", + "griffe-inherited-docstrings", + "ruff", # Changelog generation 'towncrier', # Optional dependencies to run examples @@ -195,6 +195,14 @@ python = ["3.11", "3.12", "3.13"] numpy = ["1.26", "2.2"] version = ["minimal"] +[tool.hatch.envs.gputest.scripts] +run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" +run = "run-coverage --no-cov" +run-verbose = "run-coverage --verbose" +run-mypy = "mypy src" +run-hypothesis = "run-coverage --hypothesis-profile ci --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*" +list-env = "pip list" + [tool.hatch.envs.upstream] template = 'test' python = "3.13" @@ -239,22 +247,15 @@ dependencies = [ 'zarr[remote_tests]', ] - -[tool.hatch.envs.doctest] -features = ["test", "optional", "remote", "remote_tests"] -description = "Test environment for doctests" - -[tool.hatch.envs.doctest.scripts] -run = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst'" -fix = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst' --accept" -list-env = "pip list" - [tool.hatch.envs.docs] -features = ['docs'] +features = ['docs', 'remote'] [tool.hatch.envs.docs.scripts] -build = "cd docs && make html" -serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0" +serve = "mkdocs serve" +build = "mkdocs build" +check = "mkdocs build --strict" +readthedocs = "rm -rf $READTHEDOCS_OUTPUT/html && cp -r site $READTHEDOCS_OUTPUT/html" +list-env = "pip list" [tool.ruff] line-length = 100 @@ -411,8 +412,9 @@ ignore = [ [tool.numpydoc_validation] # See https://numpydoc.readthedocs.io/en/latest/validation.html#built-in-validation-checks for list of checks checks = [ - "GL06", - "GL07", + # Requires third-party support; see https://github.com/numpy/numpydoc/issues/463 + # "GL06", + # "GL07", # Currently broken; see https://github.com/numpy/numpydoc/issues/573 # "GL09", "GL10", @@ -425,9 +427,10 @@ checks = [ [tool.towncrier] directory = 'changes' -filename = "docs/release-notes.rst" -underlines = ["-", "~", "^"] -issue_format = ":issue:`{issue}`" +filename = "docs/release-notes.md" +underlines = ["", "", ""] +issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues{issue})" +start_string = "\n" [tool.codespell] ignore-words-list = "astroid" diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index e8d1329b17..4b3edf78d1 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -450,7 +450,7 @@ async def getsize_prefix(self, prefix: str) -> int: Notes ----- ``getsize_prefix`` is just provided as a potentially faster alternative to - listing all the keys under a prefix calling :meth:`Store.getsize` on each. + listing all the keys under a prefix calling [`Store.getsize`][zarr.abc.store.Store.getsize] on each. In general, ``prefix`` should be the path of an Array or Group in the Store. Implementations may differ on the behavior when some other ``prefix`` diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index b79c41801e..881341ace2 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -306,7 +306,7 @@ async def load( See Also -------- - save, savez + save Notes ----- @@ -352,8 +352,8 @@ async def open( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Additional parameters are passed through to :func:`zarr.creation.open_array` or - :func:`zarr.hierarchy.open_group`. + Additional parameters are passed through to [`zarr.creation.open_array`][] or + [`open_group`][zarr.api.asynchronous.open_group]. Returns ------- @@ -398,7 +398,7 @@ async def open_consolidated( *args: Any, use_consolidated: Literal[True] = True, **kwargs: Any ) -> AsyncGroup: """ - Alias for :func:`open_group` with ``use_consolidated=True``. + Alias for [`open_group`][zarr.api.asynchronous.open_group] with ``use_consolidated=True``. """ if use_consolidated is not True: raise TypeError( @@ -469,7 +469,7 @@ async def save_array( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Passed through to :func:`create`, e.g., compressor. + Passed through to [`create`][zarr.api.asynchronous.create], e.g., compressor. """ zarr_format = ( _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) @@ -568,8 +568,8 @@ async def save_group( async def tree(grp: AsyncGroup, expand: bool | None = None, level: int | None = None) -> Any: """Provide a rich display of the hierarchy. - .. deprecated:: 3.0.0 - `zarr.tree()` is deprecated and will be removed in a future release. + !!! warning "Deprecated" + `zarr.tree()` is deprecated since v3.0.0 and will be removed in a future release. Use `group.tree()` instead. Parameters @@ -599,7 +599,7 @@ async def array( data : array_like The data to fill the array with. **kwargs - Passed through to :func:`create`. + Passed through to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -734,7 +734,7 @@ async def create_group( The zarr format to use when saving. If no ``zarr_format`` is provided, the default format will be used. This default can be changed by modifying the value of ``default_zarr_format`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. storage_options : dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. @@ -783,12 +783,12 @@ async def open_group( Store or path to directory in file system or name of zip file. Strings are interpreted as paths on the local file system - and used as the ``root`` argument to :class:`zarr.storage.LocalStore`. + and used as the ``root`` argument to [zarr.storage.LocalStore][]. Dictionaries are used as the ``store_dict`` argument in - :class:`zarr.storage.MemoryStore``. + [zarr.storage.MemoryStore][]. - By default (``store=None``) a new :class:`zarr.storage.MemoryStore` + By default (``store=None``) a new [zarr.storage.MemoryStore][] is created. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional @@ -928,7 +928,7 @@ async def create( Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. If neither ``compressor`` nor ``filters`` are provided, the default compressor - :class:`zarr.codecs.ZstdCodec` is used. + [`zarr.codecs.ZstdCodec`][] is used. If ``compressor`` is set to ``None``, no compression is used. fill_value : Any, optional @@ -955,8 +955,8 @@ async def create( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -965,7 +965,7 @@ async def create( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -1016,8 +1016,8 @@ async def create( If no codecs are provided, default codecs will be used based on the data type of the array. For most data types, the default codecs are the tuple ``(BytesCodec(), ZstdCodec())``; - data types that require a special :class:`zarr.abc.codec.ArrayBytesCodec`, like variable-length strings or bytes, - will use the :class:`zarr.abc.codec.ArrayBytesCodec` required for the data type instead of :class:`zarr.codecs.BytesCodec`. + data types that require a special [`zarr.abc.codec.ArrayBytesCodec`][], like variable-length strings or bytes, + will use the [`zarr.abc.codec.ArrayBytesCodec`][] required for the data type instead of [`zarr.codecs.BytesCodec`][]. dimension_names : Iterable[str | None] | None = None An iterable of dimension names. Zarr format 3 only. storage_options : dict @@ -1105,7 +1105,7 @@ async def empty( shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Notes ----- @@ -1127,7 +1127,7 @@ async def empty_like( a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -1160,7 +1160,7 @@ async def full( fill_value : scalar Fill value. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -1181,7 +1181,7 @@ async def full_like( a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1205,7 +1205,7 @@ async def ones( shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1225,7 +1225,7 @@ async def ones_like( a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1261,7 +1261,7 @@ async def open_array( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Any keyword arguments to pass to :func:`create`. + Any keyword arguments to pass to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -1329,7 +1329,7 @@ async def zeros( shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1349,7 +1349,7 @@ async def zeros_like( a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Returns ------- diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index d0134a4900..728822a326 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -198,8 +198,8 @@ def open( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Additional parameters are passed through to :func:`zarr.creation.open_array` or - :func:`zarr.hierarchy.open_group`. + Additional parameters are passed through to [`zarr.creation.open_array`][] or + [`open_group`][zarr.api.asynchronous.open_group]. Returns ------- @@ -225,7 +225,7 @@ def open( def open_consolidated(*args: Any, use_consolidated: Literal[True] = True, **kwargs: Any) -> Group: """ - Alias for :func:`open_group` with ``use_consolidated=True``. + Alias for [`open_group`][zarr.api.synchronous.open_group] with ``use_consolidated=True``. """ return Group( sync(async_api.open_consolidated(*args, use_consolidated=use_consolidated, **kwargs)) @@ -291,7 +291,7 @@ def save_array( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Passed through to :func:`create`, e.g., compressor. + Passed through to [`create`][zarr.api.asynchronous.create], e.g., compressor. """ return sync( async_api.save_array( @@ -353,8 +353,8 @@ def save_group( def tree(grp: Group, expand: bool | None = None, level: int | None = None) -> Any: """Provide a rich display of the hierarchy. - .. deprecated:: 3.0.0 - `zarr.tree()` is deprecated and will be removed in a future release. + !!! warning "Deprecated" + `zarr.tree()` is deprecated since v3.0.0 and will be removed in a future release. Use `group.tree()` instead. Parameters @@ -383,7 +383,7 @@ def array(data: npt.ArrayLike | Array, **kwargs: Any) -> Array: data : array_like The data to fill the array with. **kwargs - Passed through to :func:`create`. + Passed through to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -483,12 +483,12 @@ def open_group( Store or path to directory in file system or name of zip file. Strings are interpreted as paths on the local file system - and used as the ``root`` argument to :class:`zarr.storage.LocalStore`. + and used as the ``root`` argument to [zarr.storage.LocalStore][]. Dictionaries are used as the ``store_dict`` argument in - :class:`zarr.storage.MemoryStore``. + [zarr.storage.MemoryStore][]. - By default (``store=None``) a new :class:`zarr.storage.MemoryStore` + By default (``store=None``) a new [zarr.storage.MemoryStore][] is created. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional @@ -580,7 +580,7 @@ def create_group( The zarr format to use when saving. If no ``zarr_format`` is provided, the default format will be used. This default can be changed by modifying the value of ``default_zarr_format`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. storage_options : dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. @@ -661,7 +661,7 @@ def create( Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. If neither ``compressor`` nor ``filters`` are provided, the default compressor - :class:`zarr.codecs.ZstdCodec` is used. + [`zarr.codecs.ZstdCodec`][] is used. If ``compressor`` is set to ``None``, no compression is used. fill_value : Any, optional @@ -688,8 +688,8 @@ def create( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -698,7 +698,7 @@ def create( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -749,8 +749,8 @@ def create( If no codecs are provided, default codecs will be used based on the data type of the array. For most data types, the default codecs are the tuple ``(BytesCodec(), ZstdCodec())``; - data types that require a special :class:`zarr.abc.codec.ArrayBytesCodec`, like variable-length strings or bytes, - will use the :class:`zarr.abc.codec.ArrayBytesCodec` required for the data type instead of :class:`zarr.codecs.BytesCodec`. + data types that require a special [`zarr.abc.codec.ArrayBytesCodec`][], like variable-length strings or bytes, + will use the [`zarr.abc.codec.ArrayBytesCodec`][] required for the data type instead of [`zarr.codecs.BytesCodec`][]. dimension_names : Iterable[str | None] | None = None An iterable of dimension names. Zarr format 3 only. storage_options : dict @@ -827,7 +827,7 @@ def create_array( ) -> Array: """Create an array. - This function wraps :func:`zarr.core.array.create_array`. + This function wraps [zarr.core.array.create_array][]. Parameters ---------- @@ -853,8 +853,9 @@ def create_array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -863,7 +864,7 @@ def create_array( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -875,20 +876,20 @@ def create_array( returns another bytestream. Multiple compressors my be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. If no ``compressor`` is provided, a default compressor will be used. - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit the default compressor. serializer : dict[str, JSON] | ArrayBytesCodec, optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. If no ``serializer`` is provided, a default serializer will be used. These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -898,7 +899,7 @@ def create_array( is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. zarr_format : {2, 3}, optional The zarr format to use when saving. attributes : dict, optional @@ -1029,8 +1030,8 @@ def from_array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -1040,8 +1041,8 @@ def from_array( which is to choose default filters based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple ``()``. The only cases where default filters are not empty is when the Zarr format is 2, and the - data type is a variable-length data type like :class:`zarr.dtype.VariableLengthUTF8` or - :class:`zarr.dtype.VariableLengthUTF8`. In these cases, the default filters is a tuple with a + data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or + [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters is a tuple with a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -1071,7 +1072,7 @@ def from_array( - dict[str, JSON]: A dict representation of an ``ArrayBytesCodec``. - ArrayBytesCodec: An instance of ``ArrayBytesCodec``. - "auto": a default serializer will be used. These defaults can be changed by modifying the value of - ``array.v3_default_serializer`` in :mod:`zarr.core.config`. + ``array.v3_default_serializer`` in [`zarr.config`][zarr.config]. - "keep": Retain the serializer of the input array if it is a zarr Array. fill_value : Any, optional @@ -1195,7 +1196,7 @@ def empty(shape: tuple[int, ...], **kwargs: Any) -> Array: shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -1222,7 +1223,7 @@ def empty_like(a: ArrayLike, **kwargs: Any) -> Array: a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -1249,7 +1250,7 @@ def full(shape: tuple[int, ...], fill_value: Any, **kwargs: Any) -> Array: fill_value : scalar Fill value. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Returns ------- @@ -1269,7 +1270,7 @@ def full_like(a: ArrayLike, **kwargs: Any) -> Array: a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1288,7 +1289,7 @@ def ones(shape: tuple[int, ...], **kwargs: Any) -> Array: shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1307,7 +1308,7 @@ def ones_like(a: ArrayLike, **kwargs: Any) -> Array: a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1343,7 +1344,7 @@ def open_array( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Any keyword arguments to pass to :func:`create`. + Any keyword arguments to pass to [`create`][zarr.api.asynchronous.create]. Returns @@ -1395,7 +1396,7 @@ def zeros(shape: tuple[int, ...], **kwargs: Any) -> Array: shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`zarr.api.asynchronous.create`][]. Returns ------- @@ -1414,7 +1415,7 @@ def zeros_like(a: ArrayLike, **kwargs: Any) -> Array: a : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [`create`][zarr.api.asynchronous.create]. Returns ------- diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py index 21bdc4e91b..651682d317 100644 --- a/src/zarr/codecs/numcodecs/_codecs.py +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -1,7 +1,7 @@ """ -This module provides compatibility for :py:mod:`numcodecs` in Zarr version 3. +This module provides compatibility for [numcodecs][] in Zarr version 3. -These codecs were previously defined in :py:mod:`numcodecs`, and have now been moved to `zarr`. +These codecs were previously defined in [numcodecs][], and have now been moved to `zarr`. >>> import numpy as np >>> import zarr @@ -16,9 +16,8 @@ ... compressors=[numcodecs.BZ2(level=5)]) >>> array[:] = np.arange(np.prod(array.shape), dtype=array.dtype).reshape(*array.shape) -.. note:: - - Please note that the codecs in :py:mod:`zarr.codecs.numcodecs` are not part of the Zarr version +!!! note + Please note that the codecs in [zarr.codecs.numcodecs][] are not part of the Zarr version 3 specification. Using these codecs might cause interoperability issues with other Zarr implementations. """ @@ -82,7 +81,7 @@ def __init_subclass__(cls, *, codec_name: str | None = None, **kwargs: Any) -> N cls_name = f"{CODEC_PREFIX}{namespace}.{cls.__name__}" cls.codec_name = f"{CODEC_PREFIX}{namespace}" cls.__doc__ = f""" - See :class:`{cls_name}` for more details and parameters. + See [{cls_name}][] for more details and parameters. """ def __init__(self, **codec_config: JSON) -> None: diff --git a/src/zarr/convenience.py b/src/zarr/convenience.py index 3ca4ffcb4b..391ffc5186 100644 --- a/src/zarr/convenience.py +++ b/src/zarr/convenience.py @@ -1,10 +1,8 @@ """ Convenience helpers. -.. warning:: - - This sub-module is deprecated. All functions here are defined - in the top level zarr namespace instead. +!!! warning "Deprecated" + This sub-module is deprecated. All functions here are defined in the top level zarr namespace instead. """ import warnings diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 793d1a034b..6aefc38031 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -492,8 +492,9 @@ async def create( ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Method to create a new asynchronous array instance. - .. deprecated:: 3.0.0 - Deprecated in favor of :func:`zarr.api.asynchronous.create_array`. + !!! warning "Deprecated" + `AsyncArray.create()` is deprecated since v3.0.0 and will be removed in a future release. + Use [`zarr.api.asynchronous.create_array`][] instead. Parameters ---------- @@ -523,7 +524,6 @@ async def create( Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. If no codecs are provided, default codecs will be used: - dimension_names : Iterable[str | None], optional The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. @@ -537,7 +537,7 @@ async def create( order : Literal["C", "F"], optional The memory of the array (default is "C"). If ``zarr_format`` is 2, this parameter sets the memory order of the array. - If `zarr_format`` is 3, then this parameter is deprecated, because memory order + If ``zarr_format`` is 3, then this parameter is deprecated, because memory order is a runtime parameter for Zarr 3 arrays. The recommended way to specify the memory order for Zarr 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. filters : Iterable[Codec] | Literal["auto"], optional @@ -545,8 +545,8 @@ async def create( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -555,7 +555,7 @@ async def create( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -569,7 +569,7 @@ async def create( - For Unicode strings, the default is ``VLenUTF8Codec``. - For bytes or objects, the default is ``VLenBytesCodec``. - These defaults can be changed by modifying the value of ``array.v2_default_compressor`` in :mod:`zarr.core.config`. + These defaults can be changed by modifying the value of ``array.v2_default_compressor`` in [`zarr.config`][zarr.config]. overwrite : bool, optional Whether to raise an error if the store already exists (default is False). data : npt.ArrayLike, optional @@ -640,8 +640,7 @@ async def _create( config: ArrayConfigLike | None = None, ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Method to create a new asynchronous array instance. - See :func:`AsyncArray.create` for more details. - Deprecated in favor of :func:`zarr.api.asynchronous.create_array`. + Deprecated in favor of [`zarr.api.asynchronous.create_array`][]. """ dtype_parsed = parse_dtype(dtype, zarr_format=zarr_format) @@ -1091,9 +1090,9 @@ def compressor(self) -> Numcodec | None: """ Compressor that is applied to each chunk of the array. - .. deprecated:: 3.0.0 - `array.compressor` is deprecated and will be removed in a future release. - Use `array.compressors` instead. + !!! warning "Deprecated" + `Array.compressor` is deprecated since v3.0.0 and will be removed in a future release. + Use [`Array.compressors`][zarr.AsyncArray.compressors] instead. """ if self.metadata.zarr_format == 2: return self.metadata.compressor @@ -1292,8 +1291,8 @@ async def nchunks_initialized(self) -> int: Notes ----- - On :class:`AsyncArray` this is an asynchronous method, unlike the (synchronous) - property :attr:`Array.nchunks_initialized`. + On [`AsyncArray`][zarr.AsyncArray] this is an asynchronous method, unlike the (synchronous) + property [`Array.nchunks_initialized`][zarr.Array.nchunks_initialized]. Examples -------- @@ -1325,8 +1324,8 @@ async def _nshards_initialized(self) -> int: Notes ----- - On :class:`AsyncArray` this is an asynchronous method, unlike the (synchronous) - property :attr:`Array._nshards_initialized`. + On [`AsyncArray`][zarr.AsyncArray] this is an asynchronous method, unlike the (synchronous) + property [`Array._nshards_initialized`][zarr.Array._nshards_initialized]. Examples -------- @@ -1751,15 +1750,15 @@ async def setitem( @property def oindex(self) -> AsyncOIndex[T_ArrayMetadata]: - """Shortcut for orthogonal (outer) indexing, see :func:`get_orthogonal_selection` and - :func:`set_orthogonal_selection` for documentation and examples.""" + """Shortcut for orthogonal (outer) indexing, see [get_orthogonal_selection][zarr.Array.get_orthogonal_selection] and + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection] for documentation and examples.""" return AsyncOIndex(self) @property def vindex(self) -> AsyncVIndex[T_ArrayMetadata]: - """Shortcut for vectorized (inner) indexing, see :func:`get_coordinate_selection`, - :func:`set_coordinate_selection`, :func:`get_mask_selection` and - :func:`set_mask_selection` for documentation and examples.""" + """Shortcut for vectorized (inner) indexing, see [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], [get_mask_selection][zarr.Array.get_mask_selection] and + [set_mask_selection][zarr.Array.set_mask_selection] for documentation and examples.""" return AsyncVIndex(self) async def resize(self, new_shape: ShapeLike, delete_outside_chunks: bool = True) -> None: @@ -1915,10 +1914,9 @@ def info(self) -> Any: ------- ArrayInfo - See Also - -------- - AsyncArray.info_complete - All information about a group, including dynamic information + Related + ------- + [zarr.AsyncArray.info_complete][] - All information about a group, including dynamic information like the number of bytes and chunks written. Examples @@ -1954,10 +1952,9 @@ async def info_complete(self) -> Any: ------- ArrayInfo - See Also - -------- - AsyncArray.info - A property giving just the statically known information about an array. + Related + ------- + [zarr.AsyncArray.info][] - A property giving just the statically known information about an array. """ return self._info( await self._nshards_initialized(), @@ -2029,8 +2026,9 @@ def create( ) -> Array: """Creates a new Array instance from an initialized store. - .. deprecated:: 3.0.0 - Deprecated in favor of :func:`zarr.create_array`. + !!! warning "Deprecated" + `Array.create()` is deprecated since v3.0.0 and will be removed in a future release. + Use [`zarr.create_array`][] instead. Parameters ---------- @@ -2071,16 +2069,17 @@ def create( order : Literal["C", "F"], optional The memory of the array (default is "C"). If ``zarr_format`` is 2, this parameter sets the memory order of the array. - If `zarr_format`` is 3, then this parameter is deprecated, because memory order + If ``zarr_format`` is 3, then this parameter is deprecated, because memory order is a runtime parameter for Zarr 3 arrays. The recommended way to specify the memory order for Zarr 3 arrays is via the ``config`` parameter, e.g. ``{'order': 'C'}``. + filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -2089,7 +2088,7 @@ def create( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -2103,7 +2102,7 @@ def create( - For Unicode strings, the default is ``VLenUTF8Codec``. - For bytes or objects, the default is ``VLenBytesCodec``. - These defaults can be changed by modifying the value of ``array.v2_default_compressor`` in :mod:`zarr.core.config`. + These defaults can be changed by modifying the value of ``array.v2_default_compressor`` in [`zarr.config`][zarr.config]. overwrite : bool, optional Whether to raise an error if the store already exists (default is False). @@ -2168,8 +2167,7 @@ def _create( config: ArrayConfigLike | None = None, ) -> Array: """Creates a new Array instance from an initialized store. - See :func:`Array.create` for more details. - Deprecated in favor of :func:`zarr.create_array`. + Deprecated in favor of [`zarr.create_array`][]. """ async_array = sync( AsyncArray._create( @@ -2330,12 +2328,12 @@ def dtype(self) -> np.dtype[Any]: @property def attrs(self) -> Attributes: - """Returns a MutableMapping containing user-defined attributes. + """Returns a [MutableMapping][collections.abc.MutableMapping] containing user-defined attributes. Returns ------- - attrs : MutableMapping - A MutableMapping object containing user-defined attributes. + attrs + A [MutableMapping][collections.abc.MutableMapping] object containing user-defined attributes. Notes ----- @@ -2399,9 +2397,9 @@ def compressor(self) -> Numcodec | None: """ Compressor that is applied to each chunk of the array. - .. deprecated:: 3.0.0 - `array.compressor` is deprecated and will be removed in a future release. - Use `array.compressors` instead. + !!! warning "Deprecated" + `array.compressor` is deprecated since v3.0.0 and will be removed in a future release. + Use [`array.compressors`][zarr.Array.compressors] instead. """ return self._async_array.compressor @@ -2776,9 +2774,9 @@ def __getitem__(self, selection: Selection) -> NDArrayLikeOrScalar: fields Currently the implementation for __getitem__ is provided by - :func:`vindex` if the indexing is pure fancy indexing (ie a + [`vindex`][zarr.Array.vindex] if the indexing is pure fancy indexing (ie a broadcast-compatible tuple of integer array indices), or by - :func:`set_basic_selection` otherwise. + [`set_basic_selection`][zarr.Array.set_basic_selection] otherwise. Effectively, this means that the following indexing modes are supported: @@ -2789,14 +2787,16 @@ def __getitem__(self, selection: Selection) -> NDArrayLikeOrScalar: - fancy indexing (vectorized list of integers) For specific indexing options including outer indexing, see the - methods listed under See Also. + methods listed under Related. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_coordinate_selection, set_coordinate_selection, get_orthogonal_selection, - set_orthogonal_selection, get_block_selection, set_block_selection, - vindex, oindex, blocks, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], [set_basic_selection][zarr.Array.set_basic_selection] + [get_mask_selection][zarr.Array.get_mask_selection], [set_mask_selection][zarr.Array.set_mask_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_block_selection][zarr.Array.get_block_selection], [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], [blocks][zarr.Array.blocks], [__setitem__][zarr.Array.__setitem__] """ fields, pure_selection = pop_fields(selection) @@ -2875,27 +2875,35 @@ def __setitem__(self, selection: Selection, value: npt.ArrayLike) -> None: fields Currently the implementation for __setitem__ is provided by - :func:`vindex` if the indexing is pure fancy indexing (ie a + [`vindex`][zarr.Array.vindex] if the indexing is pure fancy indexing (ie a broadcast-compatible tuple of integer array indices), or by - :func:`set_basic_selection` otherwise. + [`set_basic_selection`][zarr.Array.set_basic_selection] otherwise. Effectively, this means that the following indexing modes are supported: - - integer indexing - - slice indexing - - mixed slice and integer indexing - - boolean indexing - - fancy indexing (vectorized list of integers) + - integer indexing + - slice indexing + - mixed slice and integer indexing + - boolean indexing + - fancy indexing (vectorized list of integers) For specific indexing options including outer indexing, see the - methods listed under See Also. + methods listed under Related. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_coordinate_selection, set_coordinate_selection, get_orthogonal_selection, - set_orthogonal_selection, get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__] """ fields, pure_selection = pop_fields(selection) @@ -3006,15 +3014,23 @@ def get_basic_selection( the `fields` parameter. This method provides the implementation for accessing data via the - square bracket notation (__getitem__). See :func:`__getitem__` for examples + square bracket notation (__getitem__). See [`__getitem__`][zarr.Array.__getitem__] for examples using the alternative notation. - See Also - -------- - set_basic_selection, get_mask_selection, set_mask_selection, - get_coordinate_selection, set_coordinate_selection, get_orthogonal_selection, - set_orthogonal_selection, get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ @@ -3108,15 +3124,23 @@ def set_basic_selection( the `fields` parameter. This method provides the underlying implementation for modifying data via square - bracket notation, see :func:`__setitem__` for equivalent examples using the + bracket notation, see [`__setitem__`][zarr.Array.__setitem__] for equivalent examples using the alternative notation. - See Also - -------- - get_basic_selection, get_mask_selection, set_mask_selection, - get_coordinate_selection, set_coordinate_selection, get_orthogonal_selection, - set_orthogonal_selection, get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: @@ -3231,12 +3255,20 @@ def get_orthogonal_selection( Slices with step > 1 are supported, but slices with negative step are not. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_coordinate_selection, set_coordinate_selection, set_orthogonal_selection, - get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: @@ -3343,13 +3375,20 @@ def set_orthogonal_selection( Slices with step > 1 are supported, but slices with negative step are not. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_coordinate_selection, set_coordinate_selection, get_orthogonal_selection, - get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ - + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: prototype = default_buffer_prototype() @@ -3423,12 +3462,20 @@ def get_mask_selection( coordinate indexing. Internally the mask array is converted to coordinate arrays by calling `np.nonzero`. - See Also - -------- - get_basic_selection, set_basic_selection, set_mask_selection, - get_orthogonal_selection, set_orthogonal_selection, get_coordinate_selection, - set_coordinate_selection, get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: @@ -3505,12 +3552,20 @@ def set_mask_selection( coordinate indexing. Internally the mask array is converted to coordinate arrays by calling `np.nonzero`. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, - get_orthogonal_selection, set_orthogonal_selection, get_coordinate_selection, - set_coordinate_selection, get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: @@ -3585,12 +3640,20 @@ def get_coordinate_selection( before being applied. The shape of the output will be the same as the shape of each coordinate array after broadcasting. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_orthogonal_selection, set_orthogonal_selection, set_coordinate_selection, - get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: @@ -3669,12 +3732,20 @@ def set_coordinate_selection( Slices are not supported. Coordinate arrays must be provided for all dimensions of the array. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_orthogonal_selection, set_orthogonal_selection, get_coordinate_selection, - get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: @@ -3785,13 +3856,20 @@ def get_block_selection( [13, 14, 15, 16, 17, 18], [23, 24, 25, 26, 27, 28]]) - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_orthogonal_selection, set_orthogonal_selection, get_coordinate_selection, - set_coordinate_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ - + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: prototype = default_buffer_prototype() @@ -3878,12 +3956,20 @@ def set_block_selection( Slices are supported. However, only with a step size of one. - See Also - -------- - get_basic_selection, set_basic_selection, get_mask_selection, set_mask_selection, - get_orthogonal_selection, set_orthogonal_selection, get_coordinate_selection, - get_block_selection, set_block_selection, - vindex, oindex, blocks, __getitem__, __setitem__ + Related + ------- + [get_basic_selection][zarr.Array.get_basic_selection], + [set_basic_selection][zarr.Array.set_basic_selection], + [get_mask_selection][zarr.Array.get_mask_selection], + [set_mask_selection][zarr.Array.set_mask_selection], + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [get_block_selection][zarr.Array.get_block_selection], + [set_block_selection][zarr.Array.set_block_selection], + [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], + [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__], + [__setitem__][zarr.Array.__setitem__] """ if prototype is None: @@ -3893,21 +3979,28 @@ def set_block_selection( @property def vindex(self) -> VIndex: - """Shortcut for vectorized (inner) indexing, see :func:`get_coordinate_selection`, - :func:`set_coordinate_selection`, :func:`get_mask_selection` and - :func:`set_mask_selection` for documentation and examples.""" + """Shortcut for vectorized (inner) indexing, see + [get_coordinate_selection][zarr.Array.get_coordinate_selection], + [set_coordinate_selection][zarr.Array.set_coordinate_selection], + [get_mask_selection][zarr.Array.get_mask_selection] and + [set_mask_selection][zarr.Array.set_mask_selection] for documentation and + examples.""" return VIndex(self) @property def oindex(self) -> OIndex: - """Shortcut for orthogonal (outer) indexing, see :func:`get_orthogonal_selection` and - :func:`set_orthogonal_selection` for documentation and examples.""" + """Shortcut for orthogonal (outer) indexing, see + [get_orthogonal_selection][zarr.Array.get_orthogonal_selection] and + [set_orthogonal_selection][zarr.Array.set_orthogonal_selection] for + documentation and examples.""" return OIndex(self) @property def blocks(self) -> BlockIndex: - """Shortcut for blocked chunked indexing, see :func:`get_block_selection` and - :func:`set_block_selection` for documentation and examples.""" + """Shortcut for blocked chunked indexing, see + [get_block_selection][zarr.Array.get_block_selection] and + [set_block_selection][zarr.Array.set_block_selection] for documentation and + examples.""" return BlockIndex(self) def resize(self, new_shape: ShapeLike) -> None: @@ -4027,11 +4120,10 @@ def info(self) -> Any: ------- ArrayInfo - See Also - -------- - Array.info_complete - All information about a group, including dynamic information - like the number of bytes and chunks written. + Related + ------- + [zarr.Array.info_complete][] - All information about a group, + including dynamic information like the number of bytes and chunks written. Examples -------- @@ -4064,10 +4156,9 @@ def info_complete(self) -> Any: ------- ArrayInfo - See Also - -------- - Array.info - The statically known subset of metadata about an array. + Related + ------- + [zarr.Array.info][] - The statically known subset of metadata about an array. """ return sync(self._async_array.info_complete()) @@ -4088,9 +4179,9 @@ async def _shards_initialized( chunks_initialized : tuple[str, ...] The keys of the chunks that have been initialized. - See Also - -------- - nchunks_initialized + Related + ------- + [nchunks_initialized][zarr.Array.nchunks_initialized] """ store_contents = [ @@ -4194,8 +4285,8 @@ async def from_array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -4205,8 +4296,8 @@ async def from_array( which is to choose default filters based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple ``()``. The only cases where default filters are not empty is when the Zarr format is 2, and the - data type is a variable-length data type like :class:`zarr.dtype.VariableLengthUTF8` or - :class:`zarr.dtype.VariableLengthUTF8`. In these cases, the default filters is a tuple with a + data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or + [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters is a tuple with a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -4236,7 +4327,7 @@ async def from_array( - dict[str, JSON]: A dict representation of an ``ArrayBytesCodec``. - ArrayBytesCodec: An instance of ``ArrayBytesCodec``. - "auto": a default serializer will be used. These defaults can be changed by modifying the value of - ``array.v3_default_serializer`` in :mod:`zarr.core.config`. + ``array.v3_default_serializer`` in [`zarr.config`][zarr.config]. - "keep": Retain the serializer of the input array if it is a zarr Array. fill_value : Any, optional @@ -4441,8 +4532,8 @@ async def init_array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -4451,7 +4542,7 @@ async def init_array( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -4459,7 +4550,7 @@ async def init_array( List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. - The default value of ``"auto"`` instructs Zarr to use a default of :class:`zarr.codecs.ZstdCodec`. + The default value of ``"auto"`` instructs Zarr to use a default of [`zarr.codecs.ZstdCodec`][]. To create an array with no compressors, provide an empty iterable or the value ``None``. serializer : dict[str, JSON] | ArrayBytesCodec | Literal["auto"], optional @@ -4467,9 +4558,9 @@ async def init_array( Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. The default value of ``"auto"`` instructs Zarr to use a default codec based on the data type of the array. - For most data types this default codec is :class:`zarr.codecs.BytesCodec`. - For :class:`zarr.dtype.VariableLengthUTF8`, the default codec is :class:`zarr.codecs.VlenUTF8Codec`. - For :class:`zarr.dtype.VariableLengthBytes`, the default codec is :class:`zarr.codecs.VlenBytesCodec`. + For most data types this default codec is [`zarr.codecs.BytesCodec`][]. + For [`zarr.dtype.VariableLengthUTF8`][], the default codec is [`zarr.codecs.VlenUTF8Codec`][]. + For [`zarr.dtype.VariableLengthBytes`][], the default codec is [`zarr.codecs.VlenBytesCodec`][]. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -4479,7 +4570,7 @@ async def init_array( is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. zarr_format : {2, 3}, optional The zarr format to use when saving. attributes : dict, optional @@ -4665,8 +4756,9 @@ async def create_array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -4675,7 +4767,7 @@ async def create_array( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -4687,20 +4779,20 @@ async def create_array( returns another bytestream. Multiple compressors my be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. If no ``compressor`` is provided, a default compressor will be used. - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit the default compressor. serializer : dict[str, JSON] | ArrayBytesCodec, optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. If no ``serializer`` is provided, a default serializer will be used. These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -4710,7 +4802,7 @@ async def create_array( is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. zarr_format : {2, 3}, optional The zarr format to use when saving. attributes : dict, optional diff --git a/src/zarr/core/attributes.py b/src/zarr/core/attributes.py index e699c4f66d..e000839436 100644 --- a/src/zarr/core/attributes.py +++ b/src/zarr/core/attributes.py @@ -42,13 +42,13 @@ def put(self, d: dict[str, JSON]) -> None: Equivalent to the following pseudo-code, but performed atomically. - .. code-block:: python - - >>> attrs = {"a": 1, "b": 2} - >>> attrs.clear() - >>> attrs.update({"a": 3", "c": 4}) - >>> attrs - {'a': 3, 'c': 4} + ```python + >>> attrs = {"a": 1, "b": 2} + >>> attrs.clear() + >>> attrs.update({"a": 3", "c": 4}) + >>> attrs + {'a': 3, 'c': 4} + ``` """ self._obj.metadata.attributes.clear() self._obj = self._obj.update_attributes(d) diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index d519b87d45..189916dc91 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -218,7 +218,7 @@ def from_bytes(cls, bytes_like: BytesLike) -> Self: Parameters ---------- bytes_like - bytes-like object + bytes-like object Returns ------- diff --git a/src/zarr/core/buffer/cpu.py b/src/zarr/core/buffer/cpu.py index 34f92ece4a..415b9d928c 100644 --- a/src/zarr/core/buffer/cpu.py +++ b/src/zarr/core/buffer/cpu.py @@ -86,7 +86,7 @@ def from_bytes(cls, bytes_like: BytesLike) -> Self: Parameters ---------- bytes_like - bytes-like object + bytes-like object Returns ------- diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index a918b789dd..5d463ec79c 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -8,21 +8,21 @@ to be ``your.module.NewBytesCodec``. Donfig can be configured programmatically, by environment variables, or from YAML files in standard locations. - .. code-block:: python + ```python + from your.module import NewBytesCodec + from zarr.core.config import register_codec, config - from your.module import NewBytesCodec - from zarr.core.config import register_codec, config - - register_codec("bytes", NewBytesCodec) - config.set({"codecs.bytes": "your.module.NewBytesCodec"}) + register_codec("bytes", NewBytesCodec) + config.set({"codecs.bytes": "your.module.NewBytesCodec"}) + ``` Instead of setting the value programmatically with ``config.set``, you can also set the value with an environment variable. The environment variable ``ZARR_CODECS__BYTES`` can be set to ``your.module.NewBytesCodec``. The double underscore ``__`` is used to indicate nested access. - .. code-block:: bash - - export ZARR_CODECS__BYTES="your.module.NewBytesCodec" + ```bash + export ZARR_CODECS__BYTES="your.module.NewBytesCodec" + ``` For more information, see the Donfig documentation at https://github.com/pytroll/donfig. """ diff --git a/src/zarr/core/dtype/npy/bool.py b/src/zarr/core/dtype/npy/bool.py index 37371cd0cd..3e7f5b72f0 100644 --- a/src/zarr/core/dtype/npy/bool.py +++ b/src/zarr/core/dtype/npy/bool.py @@ -23,8 +23,8 @@ class Bool(ZDType[np.dtypes.BoolDType, np.bool_], HasItemSize): """ A Zarr data type for arrays containing booleans. - Wraps the ``np.dtypes.BoolDType`` data type. Scalars for this data type are instances of - ``np.bool_``. + Wraps the [`np.dtypes.BoolDType`][numpy.dtypes.BoolDType] data type. Scalars for this data type are instances of + [`np.bool_`][numpy.bool_]. Attributes ---------- @@ -41,7 +41,7 @@ class Bool(ZDType[np.dtypes.BoolDType, np.bool_], HasItemSize): ---------- This class implements the boolean data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding)and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ _zarr_v3_name: ClassVar[Literal["bool"]] = "bool" @@ -236,7 +236,7 @@ def cast_scalar(self, data: object) -> np.bool_: Returns ------- - ``np.bool_`` + bool : np.bool_ The numpy boolean scalar. Raises @@ -258,7 +258,7 @@ def default_scalar(self) -> np.bool_: Returns ------- - ``np.bool_`` + bool : np.bool_ The default value. """ return np.False_ @@ -294,7 +294,7 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.bool_: Returns ------- - ``np.bool_`` + bool : np.bool_ The numpy boolean scalar. Raises diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index b7c764dcd9..16c3326f63 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -36,11 +36,11 @@ class FixedLengthBytesConfig(TypedDict): Examples -------- - .. code-block:: python - - { - "length_bytes": 12 - } + ```python + { + "length_bytes": 12 + } + ``` """ length_bytes: int @@ -56,17 +56,17 @@ class NullterminatedBytesJSON_V2(DTypeConfig_V2[str, None]): References ---------- The structure of the ``name`` field is defined in the Zarr V2 - `specification document `__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python - - { - "name": "|S10", - "object_codec_id": None - } + ```python + { + "name": "|S10", + "object_codec_id": None + } + ``` """ @@ -83,14 +83,14 @@ class NullTerminatedBytesJSON_V3( Examples -------- - .. code-block:: python - - { - "name": "null_terminated_bytes", - "configuration": { - "length_bytes": 12 - } + ```python + { + "name": "null_terminated_bytes", + "configuration": { + "length_bytes": 12 } + } + ``` """ @@ -105,17 +105,18 @@ class RawBytesJSON_V2(DTypeConfig_V2[str, None]): References ---------- The structure of the ``name`` field is defined in the Zarr V2 - `specification document `__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python + ```python { "name": "|V10", "object_codec_id": None } + ``` """ @@ -130,12 +131,14 @@ class RawBytesJSON_V3(NamedConfig[Literal["raw_bytes"], FixedLengthBytesConfig]) Examples -------- - .. code-block:: python - - { - "name": "raw_bytes", - "configuration": { - "length_bytes": 12 + ```python + { + "name": "raw_bytes", + "configuration": { + "length_bytes": 12 + } + } + ``` """ @@ -149,16 +152,16 @@ class VariableLengthBytesJSON_V2(DTypeConfig_V2[Literal["|O"], Literal["vlen-byt References ---------- The structure of the ``name`` field is defined in the Zarr V2 - `specification document `__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python - - { - "name": "|O", - "object_codec_id": "vlen-bytes" - } + ```python + { + "name": "|O", + "object_codec_id": "vlen-bytes" + } + ``` """ @@ -167,8 +170,8 @@ class NullTerminatedBytes(ZDType[np.dtypes.BytesDType[int], np.bytes_], HasLengt """ A Zarr data type for arrays containing fixed-length null-terminated byte sequences. - Wraps the ``np.dtypes.BytesDType`` data type. Scalars for this data type are instances of - ``np.bytes_``. + Wraps the [`np.dtypes.BytesDType`][numpy.dtypes.BytesDType] data type. Scalars for this data type are instances of + [`np.bytes_`][numpy.bytes_]. This data type is parametrized by an integral length which specifies size in bytes of each scalar. Because this data type uses null-terminated semantics, indexing into @@ -410,7 +413,7 @@ def _check_scalar(self, data: object) -> TypeGuard[BytesLike]: def _cast_scalar_unchecked(self, data: BytesLike) -> np.bytes_: """ - Cast the provided scalar data to ``np.bytes_``, truncating if necessary. + Cast the provided scalar data to [`np.bytes_`][numpy.bytes_], truncating if necessary. Parameters ---------- @@ -419,7 +422,7 @@ def _cast_scalar_unchecked(self, data: BytesLike) -> np.bytes_: Returns ------- - np.bytes_ + bytes : [`np.bytes_`][numpy.bytes_] The casted data as a NumPy bytes scalar. Notes @@ -447,7 +450,7 @@ def cast_scalar(self, data: object) -> np.bytes_: Returns ------- - ``np.bytes_`` + bytes : [`np.bytes_`][numpy.bytes_] The data cast as a NumPy bytes scalar. Raises @@ -470,7 +473,7 @@ def default_scalar(self) -> np.bytes_: Returns ------- - ``np.bytes_`` + bytes : [`np.bytes_`][numpy.bytes_] The default scalar value. """ return np.bytes_(b"") @@ -499,7 +502,7 @@ def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> str: def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.bytes_: """ - Read a JSON-serializable value as ``np.bytes_``. + Read a JSON-serializable value as [`np.bytes_`][numpy.bytes_]. Parameters ---------- @@ -510,7 +513,7 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.bytes_: Returns ------- - ``np.bytes_`` + bytes : [`np.bytes_`][numpy.bytes_] The NumPy bytes scalar obtained from decoding the base64 string. Raises @@ -543,7 +546,7 @@ class RawBytes(ZDType[np.dtypes.VoidDType[int], np.void], HasLength, HasItemSize """ A Zarr data type for arrays containing fixed-length sequences of raw bytes. - Wraps the NumPy ``void`` data type. Scalars for this data type are instances of ``np.void``. + Wraps the NumPy ``void`` data type. Scalars for this data type are instances of [`np.void`][numpy.void]. This data type is parametrized by an integral length which specifies size in bytes of each scalar belonging to this data type. diff --git a/src/zarr/core/dtype/npy/complex.py b/src/zarr/core/dtype/npy/complex.py index 2f432a9e0a..99abee5e24 100644 --- a/src/zarr/core/dtype/npy/complex.py +++ b/src/zarr/core/dtype/npy/complex.py @@ -353,8 +353,8 @@ class Complex64(BaseComplex[np.dtypes.Complex64DType, np.complex64]): """ A Zarr data type for arrays containing 64 bit complex floats. - Wraps the ``np.dtypes.Complex64DType`` data type. Scalars for this data type - are instances of ``np.complex64``. + Wraps the [`np.dtypes.Complex64DType`][numpy.dtypes.Complex64DType] data type. Scalars for this data type + are instances of [`np.complex64`][numpy.complex64]. Attributes ---------- @@ -388,8 +388,8 @@ class Complex128(BaseComplex[np.dtypes.Complex128DType, np.complex128], HasEndia """ A Zarr data type for arrays containing 64 bit complex floats. - Wraps the ``np.dtypes.Complex128DType`` data type. Scalars for this data type - are instances of ``np.complex128``. + Wraps the [`np.dtypes.Complex128DType`][numpy.dtypes.Complex128DType] data type. Scalars for this data type + are instances of [`np.complex128`][numpy.complex128]. Attributes ---------- diff --git a/src/zarr/core/dtype/npy/float.py b/src/zarr/core/dtype/npy/float.py index 3113bc5b61..bedb44b52d 100644 --- a/src/zarr/core/dtype/npy/float.py +++ b/src/zarr/core/dtype/npy/float.py @@ -314,8 +314,8 @@ class Float16(BaseFloat[np.dtypes.Float16DType, np.float16]): """ A Zarr data type for arrays containing 16-bit floating point numbers. - Wraps the ``np.dtypes.Float16DType`` data type. Scalars for this data type are instances - of ``np.float16``. + Wraps the [`np.dtypes.Float16DType`][numpy.dtypes.Float16DType] data type. Scalars for this data type are instances + of [`np.float16`][numpy.float16]. Attributes ---------- @@ -326,7 +326,7 @@ class Float16(BaseFloat[np.dtypes.Float16DType, np.float16]): ---------- This class implements the float16 data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.Float16DType @@ -351,8 +351,8 @@ class Float32(BaseFloat[np.dtypes.Float32DType, np.float32]): """ A Zarr data type for arrays containing 32-bit floating point numbers. - Wraps the ``np.dtypes.Float32DType`` data type. Scalars for this data type are instances - of ``np.float32``. + Wraps the [`np.dtypes.Float32DType`][numpy.dtypes.Float32DType] data type. Scalars for this data type are instances + of [`np.float32`][numpy.float32]. Attributes ---------- @@ -363,7 +363,7 @@ class Float32(BaseFloat[np.dtypes.Float32DType, np.float32]): ---------- This class implements the float32 data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.Float32DType @@ -388,8 +388,8 @@ class Float64(BaseFloat[np.dtypes.Float64DType, np.float64]): """ A Zarr data type for arrays containing 64-bit floating point numbers. - Wraps the ``np.dtypes.Float64DType`` data type. Scalars for this data type are instances - of ``np.float64``. + Wraps the [`np.dtypes.Float64DType`][numpy.dtypes.Float64DType] data type. Scalars for this data type are instances + of [`np.float64`][numpy.float64]. Attributes ---------- @@ -400,7 +400,7 @@ class Float64(BaseFloat[np.dtypes.Float64DType, np.float64]): ---------- This class implements the float64 data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.Float64DType diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index ac04d4469a..6f7ebc2f55 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -236,8 +236,8 @@ class Int8(BaseInt[np.dtypes.Int8DType, np.int8]): """ A Zarr data type for arrays containing 8-bit signed integers. - Wraps the ``np.dtypes.Int8DType`` data type. Scalars for this data type are - instances of ``np.int8``. + Wraps the [`np.dtypes.Int8DType`][numpy.dtypes.Int8DType] data type. Scalars for this data type are + instances of [`np.int8`][numpy.int8]. Attributes ---------- @@ -248,7 +248,7 @@ class Int8(BaseInt[np.dtypes.Int8DType, np.int8]): ---------- This class implements the 8-bit signed integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.Int8DType @@ -393,7 +393,7 @@ class UInt8(BaseInt[np.dtypes.UInt8DType, np.uint8]): """ A Zarr data type for arrays containing 8-bit unsigned integers. - Wraps the ``np.dtypes.UInt8DType`` data type. Scalars for this data type are instances of ``np.uint8``. + Wraps the [`np.dtypes.UInt8DType`][numpy.dtypes.UInt8DType] data type. Scalars for this data type are instances of [`np.uint8`][numpy.uint8]. Attributes ---------- @@ -404,7 +404,7 @@ class UInt8(BaseInt[np.dtypes.UInt8DType, np.uint8]): ---------- This class implements the 8-bit unsigned integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.UInt8DType @@ -539,8 +539,8 @@ class Int16(BaseInt[np.dtypes.Int16DType, np.int16], HasEndianness): """ A Zarr data type for arrays containing 16-bit signed integers. - Wraps the ``np.dtypes.Int16DType`` data type. Scalars for this data type are instances of - ``np.int16``. + Wraps the [`np.dtypes.Int16DType`][numpy.dtypes.Int16DType] data type. Scalars for this data type are instances of + [`np.int16`][numpy.int16]. Attributes ---------- @@ -551,7 +551,7 @@ class Int16(BaseInt[np.dtypes.Int16DType, np.int16], HasEndianness): ---------- This class implements the 16-bit signed integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.Int16DType @@ -701,8 +701,8 @@ class UInt16(BaseInt[np.dtypes.UInt16DType, np.uint16], HasEndianness): """ A Zarr data type for arrays containing 16-bit unsigned integers. - Wraps the ``np.dtypes.UInt16DType`` data type. Scalars for this data type are instances of - ``np.uint16``. + Wraps the [`np.dtypes.UInt16DType`][numpy.dtypes.UInt16DType] data type. Scalars for this data type are instances of + [`np.uint16`][numpy.uint16]. Attributes ---------- @@ -713,7 +713,7 @@ class UInt16(BaseInt[np.dtypes.UInt16DType, np.uint16], HasEndianness): ---------- This class implements the unsigned 16-bit unsigned integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.UInt16DType @@ -863,8 +863,8 @@ class Int32(BaseInt[np.dtypes.Int32DType, np.int32], HasEndianness): """ A Zarr data type for arrays containing 32-bit signed integers. - Wraps the ``np.dtypes.Int32DType`` data type. Scalars for this data type are instances of - ``np.int32``. + Wraps the [`np.dtypes.Int32DType`][numpy.dtypes.Int32DType] data type. Scalars for this data type are instances of + [`np.int32`][numpy.int32]. Attributes ---------- @@ -875,7 +875,7 @@ class Int32(BaseInt[np.dtypes.Int32DType, np.int32], HasEndianness): ---------- This class implements the 32-bit signed integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.Int32DType @@ -1046,8 +1046,8 @@ class UInt32(BaseInt[np.dtypes.UInt32DType, np.uint32], HasEndianness): """ A Zarr data type for arrays containing 32-bit unsigned integers. - Wraps the ``np.dtypes.UInt32DType`` data type. Scalars for this data type are instances of - ``np.uint32``. + Wraps the [`np.dtypes.UInt32DType`][numpy.dtypes.UInt32DType] data type. Scalars for this data type are instances of + [`np.uint32`][numpy.uint32]. Attributes ---------- @@ -1058,7 +1058,7 @@ class UInt32(BaseInt[np.dtypes.UInt32DType, np.uint32], HasEndianness): ---------- This class implements the 32-bit unsigned integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.UInt32DType @@ -1204,8 +1204,8 @@ class Int64(BaseInt[np.dtypes.Int64DType, np.int64], HasEndianness): """ A Zarr data type for arrays containing 64-bit signed integers. - Wraps the ``np.dtypes.Int64DType`` data type. Scalars for this data type are instances of - ``np.int64``. + Wraps the [`np.dtypes.Int64DType`][numpy.dtypes.Int64DType] data type. Scalars for this data type are instances of + [`np.int64`][numpy.int64]. Attributes ---------- @@ -1216,7 +1216,7 @@ class Int64(BaseInt[np.dtypes.Int64DType, np.int64], HasEndianness): ---------- This class implements the 64-bit signed integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.Int64DType @@ -1362,8 +1362,8 @@ class UInt64(BaseInt[np.dtypes.UInt64DType, np.uint64], HasEndianness): """ A Zarr data type for arrays containing 64-bit unsigned integers. - Wraps the ``np.dtypes.UInt64DType`` data type. Scalars for this data type - are instances of ``np.uint64``. + Wraps the [`np.dtypes.UInt64DType`][numpy.dtypes.UInt64DType] data type. Scalars for this data type + are instances of [`np.uint64`][numpy.uint64]. Attributes ---------- @@ -1374,7 +1374,7 @@ class UInt64(BaseInt[np.dtypes.UInt64DType, np.uint64], HasEndianness): ---------- This class implements the unsigned 64-bit integer data type defined in Zarr V2 and V3. - See the `Zarr V2 `__ and `Zarr V3 `__ specification documents for details. + See the [Zarr V2](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding) and [Zarr V3](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/data-types/index.rst) specification documents for details. """ dtype_cls = np.dtypes.UInt64DType diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index 32375a1c71..ee8cc71aaf 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -70,17 +70,17 @@ class FixedLengthUTF32JSON_V2(DTypeConfig_V2[str, None]): References ---------- The structure of the ``name`` field is defined in the Zarr V2 - `specification document `__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python - - { - "name": "`__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python - - { - "name": "|O", - "object_codec_id": "vlen-utf8" - } + ```python + { + "name": "|O", + "object_codec_id": "vlen-utf8" + } + ``` """ @@ -467,7 +467,7 @@ class UTF8Base(ZDType[TDType_co, str], HasObjectCodec): ---------- This data type does not have a Zarr V3 specification. - The Zarr V2 data type specification can be found `here `__. + The Zarr V2 data type specification can be found [here](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). """ _zarr_v3_name: ClassVar[Literal["string"]] = "string" diff --git a/src/zarr/core/dtype/npy/structured.py b/src/zarr/core/dtype/npy/structured.py index a0e3b0fbd4..7aa546ea9c 100644 --- a/src/zarr/core/dtype/npy/structured.py +++ b/src/zarr/core/dtype/npy/structured.py @@ -41,19 +41,19 @@ class StructuredJSON_V2(DTypeConfig_V2[StructuredName_V2, None]): References ---------- The structure of the ``name`` field is defined in the Zarr V2 - `specification document `__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python - - { - "name": [ - ["f0", "`__. + The Zarr V2 data type specification can be found [here](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). """ _zarr_v3_name: ClassVar[Literal["structured"]] = "structured" diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index d523e16940..402a140321 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -113,9 +113,9 @@ class TimeConfig(TypedDict): Examples -------- - .. code-block:: python - - {"unit": "ms", "scale_factor": 1} + ```python + {"unit": "ms", "scale_factor": 1} + ``` """ unit: ReadOnly[DateTimeUnit] @@ -129,19 +129,19 @@ class DateTime64JSON_V3(NamedConfig[Literal["numpy.datetime64"], TimeConfig]): References ---------- This representation is defined in the ``numpy.datetime64`` - `specification document `__. + [specification document](https://zarr-specs.readthedocs.io/en/latest/spec/v3/datatypes.html#numpy-datetime64). Examples -------- - .. code-block:: python - - { - "name": "numpy.datetime64", - "configuration": { - "unit": "ms", - "scale_factor": 1 - } - } + ```python + { + "name": "numpy.datetime64", + "configuration": { + "unit": "ms", + "scale_factor": 1 + } + } + ``` """ @@ -152,19 +152,19 @@ class TimeDelta64JSON_V3(NamedConfig[Literal["numpy.timedelta64"], TimeConfig]): References ---------- This representation is defined in the numpy.timedelta64 - `specification document `__. + [specification document](https://zarr-specs.readthedocs.io/en/latest/spec/v3/datatypes.html#numpy-timedelta64). Examples -------- - .. code-block:: python - - { - "name": "numpy.timedelta64", - "configuration": { - "unit": "ms", - "scale_factor": 1 - } - } + ```python + { + "name": "numpy.timedelta64", + "configuration": { + "unit": "ms", + "scale_factor": 1 + } + } + ``` """ @@ -178,17 +178,17 @@ class TimeDelta64JSON_V2(DTypeConfig_V2[str, None]): References ---------- The structure of the ``name`` field is defined in the Zarr V2 - `specification document `__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python - - { - "name": "`__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). Examples -------- - .. code-block:: python - - { - "name": "`__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). The Zarr V3 representation of this data type is defined in the ``numpy.timedelta64`` - `specification document `__ + [specification document](https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.timedelta64) """ # mypy infers the type of np.dtypes.TimeDelta64DType to be @@ -452,15 +452,15 @@ def _from_json_v3(cls, data: DTypeJSON) -> Self: For example: - .. code-block:: json - - { - "name": "numpy.timedelta64", - "configuration": { - "unit": "generic", - "scale_factor": 1 - } + ```json + { + "name": "numpy.timedelta64", + "configuration": { + "unit": "generic", + "scale_factor": 1 } + } + ``` """ if cls._check_json_v3(data): @@ -615,10 +615,10 @@ class DateTime64(TimeDTypeBase[np.dtypes.DateTime64DType, np.datetime64], HasEnd References ---------- The Zarr V2 representation of this data type is defined in the Zarr V2 - `specification document `__. + [specification document](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). The Zarr V3 representation of this data type is defined in the ``numpy.datetime64`` - `specification document `__ + [specification document](https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.datetime64) """ dtype_cls = np.dtypes.DateTime64DType # type: ignore[assignment] diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 1c41a8a4a8..e71c55c10f 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -857,9 +857,9 @@ def info(self) -> Any: ------- GroupInfo - See Also - -------- - AsyncGroup.info_complete + Related + ------- + [zarr.AsyncGroup.info_complete][] All information about a group, including dynamic information """ @@ -881,9 +881,9 @@ async def info_complete(self) -> Any: ------- GroupInfo - See Also - -------- - AsyncGroup.info + Related + ------- + [zarr.AsyncGroup.info][] """ members = [x[1].metadata async for x in self.members(max_depth=None)] return self._info(members=members) @@ -1031,7 +1031,7 @@ async def create_array( ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array within this group. - This method lightly wraps :func:`zarr.core.array.create_array`. + This method lightly wraps [zarr.core.array.create_array][]. Parameters ---------- @@ -1052,8 +1052,8 @@ async def create_array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -1062,7 +1062,7 @@ async def create_array( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -1074,13 +1074,13 @@ async def create_array( returns another bytestream. Multiple compressors my be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. If no ``compressor`` is provided, a default compressor will be used. - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit the default compressor. compressor : Codec, optional Deprecated in favor of ``compressors``. @@ -1089,7 +1089,7 @@ async def create_array( Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. If no ``serializer`` is provided, a default serializer will be used. These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -1099,7 +1099,7 @@ async def create_array( is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. attributes : dict, optional Attributes for the array. chunk_key_encoding : ChunkKeyEncoding, optional @@ -1159,18 +1159,19 @@ async def create_dataset( ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Create an array. - .. deprecated:: 3.0.0 - The h5py compatibility methods will be removed in 3.1.0. Use `AsyncGroup.create_array` instead. + !!! warning "Deprecated" + `AsyncGroup.create_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. + Use `AsyncGroup.create_array` instead. Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the :func:`zarr.AsyncGroup.require_dataset` method. + with h5py, Zarr groups also implement the [zarr.AsyncGroup.require_dataset][] method. Parameters ---------- name : str Array name. **kwargs : dict - Additional arguments passed to :func:`zarr.AsyncGroup.create_array`. + Additional arguments passed to [zarr.AsyncGroup.create_array][]. Returns ------- @@ -1199,13 +1200,14 @@ async def require_dataset( ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Obtain an array, creating if it doesn't exist. - .. deprecated:: 3.0.0 - The h5py compatibility methods will be removed in 3.1.0. Use `AsyncGroup.require_dataset` instead. + !!! warning "Deprecated" + `AsyncGroup.require_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. + Use `AsyncGroup.require_dataset` instead. Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the :func:`zarr.AsyncGroup.create_dataset` method. + with h5py, Zarr groups also implement the [zarr.AsyncGroup.create_dataset][] method. - Other `kwargs` are as per :func:`zarr.AsyncGroup.create_dataset`. + Other `kwargs` are as per [zarr.AsyncGroup.create_dataset][]. Parameters ---------- @@ -1236,7 +1238,7 @@ async def require_array( ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: """Obtain an array, creating if it doesn't exist. - Other `kwargs` are as per :func:`zarr.AsyncGroup.create_dataset`. + Other `kwargs` are as per [zarr.AsyncGroup.create_dataset][]. Parameters ---------- @@ -1623,7 +1625,7 @@ async def empty( shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Notes ----- @@ -1645,7 +1647,7 @@ async def zeros( shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -1666,7 +1668,7 @@ async def ones( shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -1689,7 +1691,7 @@ async def full( fill_value : scalar Value to fill the array with. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -1717,7 +1719,7 @@ async def empty_like( data : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -1738,7 +1740,7 @@ async def zeros_like( data : array-like The array to create the new array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -1759,7 +1761,7 @@ async def ones_like( data : array-like The array to create the new array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -1780,7 +1782,7 @@ async def full_like( data : array-like The array to create the new array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2067,9 +2069,9 @@ def info(self) -> Any: ------- GroupInfo - See Also - -------- - Group.info_complete + Related + ------- + [zarr.Group.info_complete][] All information about a group, including dynamic information like the children members. """ @@ -2086,9 +2088,9 @@ def info_complete(self) -> Any: ------- GroupInfo - See Also - -------- - Group.info + Related + ------- + [zarr.Group.info][] """ return self._sync(self._async_group.info_complete()) @@ -2459,7 +2461,7 @@ def create( ) -> Array: """Create an array within this group. - This method lightly wraps :func:`zarr.core.array.create_array`. + This method lightly wraps [`zarr.core.array.create_array`][]. Parameters ---------- @@ -2482,8 +2484,8 @@ def create( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -2492,7 +2494,7 @@ def create( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -2504,13 +2506,13 @@ def create( returns another bytestream. Multiple compressors my be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in :mod:`zarr.core.config`. + in [`zarr.config`][]. Use ``None`` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. If no ``compressor`` is provided, a default compressor will be used. - in :mod:`zarr.core.config`. + in [`zarr.config`][]. Use ``None`` to omit the default compressor. compressor : Codec, optional Deprecated in favor of ``compressors``. @@ -2519,7 +2521,7 @@ def create( Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. If no ``serializer`` is provided, a default serializer will be used. These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in :mod:`zarr.core.config`. + in [`zarr.config`][]. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -2529,7 +2531,7 @@ def create( is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][]. attributes : dict, optional Attributes for the array. chunk_key_encoding : ChunkKeyEncoding, optional @@ -2603,7 +2605,7 @@ def create_array( ) -> Array: """Create an array within this group. - This method lightly wraps :func:`zarr.core.array.create_array`. + This method lightly wraps [zarr.core.array.create_array][]. Parameters ---------- @@ -2626,8 +2628,8 @@ def create_array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -2636,7 +2638,7 @@ def create_array( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -2648,13 +2650,13 @@ def create_array( returns another bytestream. Multiple compressors my be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. If no ``compressor`` is provided, a default compressor will be used. - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit the default compressor. compressor : Codec, optional Deprecated in favor of ``compressors``. @@ -2663,7 +2665,7 @@ def create_array( Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. If no ``serializer`` is provided, a default serializer will be used. These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -2673,7 +2675,7 @@ def create_array( is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. attributes : dict, optional Attributes for the array. chunk_key_encoding : ChunkKeyEncoding, optional @@ -2732,19 +2734,20 @@ def create_array( def create_dataset(self, name: str, **kwargs: Any) -> Array: """Create an array. - .. deprecated:: 3.0.0 - The h5py compatibility methods will be removed in 3.1.0. Use `Group.create_array` instead. + !!! warning "Deprecated" + `Group.create_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. + Use `Group.create_array` instead. Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the :func:`zarr.Group.require_dataset` method. + with h5py, Zarr groups also implement the [zarr.Group.require_dataset][] method. Parameters ---------- name : str Array name. **kwargs : dict - Additional arguments passed to :func:`zarr.Group.create_array` + Additional arguments passed to [zarr.Group.create_array][] Returns ------- @@ -2756,20 +2759,21 @@ def create_dataset(self, name: str, **kwargs: Any) -> Array: def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: """Obtain an array, creating if it doesn't exist. - .. deprecated:: 3.0.0 - The h5py compatibility methods will be removed in 3.1.0. Use `Group.require_array` instead. + !!! warning "Deprecated" + `Group.require_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. + Use `Group.require_array` instead. Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the :func:`zarr.Group.create_dataset` method. + with h5py, Zarr groups also implement the [zarr.Group.create_dataset][] method. - Other `kwargs` are as per :func:`zarr.Group.create_dataset`. + Other `kwargs` are as per [zarr.Group.create_dataset][]. Parameters ---------- name : str Array name. **kwargs : - See :func:`zarr.Group.create_dataset`. + See [zarr.Group.create_dataset][]. Returns ------- @@ -2780,14 +2784,14 @@ def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Arra def require_array(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: """Obtain an array, creating if it doesn't exist. - Other `kwargs` are as per :func:`zarr.Group.create_array`. + Other `kwargs` are as per [zarr.Group.create_array][]. Parameters ---------- name : str Array name. **kwargs : - See :func:`zarr.Group.create_array`. + See [zarr.Group.create_array][]. Returns ------- @@ -2806,7 +2810,7 @@ def empty(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Notes ----- @@ -2826,7 +2830,7 @@ def zeros(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2845,7 +2849,7 @@ def ones(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: shape : int or tuple of int Shape of the empty array. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2868,7 +2872,7 @@ def full( fill_value : scalar Value to fill the array with. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2892,7 +2896,7 @@ def empty_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> data : array-like The array to create an empty array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2917,7 +2921,7 @@ def zeros_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> data : array-like The array to create the new array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2937,7 +2941,7 @@ def ones_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> A data : array-like The array to create the new array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2956,7 +2960,7 @@ def full_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> A data : array-like The array to create the new array like. **kwargs - Keyword arguments passed to :func:`zarr.api.asynchronous.create`. + Keyword arguments passed to [zarr.api.asynchronous.create][]. Returns ------- @@ -2999,10 +3003,11 @@ def array( ) -> Array: """Create an array within this group. - .. deprecated:: 3.0.0 + !!! warning "Deprecated" + `Group.array()` is deprecated since v3.0.0 and will be removed in a future release. Use `Group.create_array` instead. - This method lightly wraps :func:`zarr.core.array.create_array`. + This method lightly wraps [zarr.core.array.create_array][]. Parameters ---------- @@ -3023,8 +3028,8 @@ def array( chunk to bytes. For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of :class:`zarr.abc.codec.ArrayArrayCodec`, or a - dict representations of :class:`zarr.abc.codec.ArrayArrayCodec`. + and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a + dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the the order if your filters is consistent with the behavior of each filter. @@ -3033,7 +3038,7 @@ def array( type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - :class:`zarr.dtype.VariableLengthUTF8` or :class:`zarr.dtype.VariableLengthUTF8`. In these cases, + [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. To create an array with no filters, provide an empty iterable or the value ``None``. @@ -3045,13 +3050,13 @@ def array( returns another bytestream. Multiple compressors my be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. If no ``compressor`` is provided, a default compressor will be used. - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. Use ``None`` to omit the default compressor. compressor : Codec, optional Deprecated in favor of ``compressors``. @@ -3060,7 +3065,7 @@ def array( Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. If no ``serializer`` is provided, a default serializer will be used. These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in :mod:`zarr.core.config`. + in [`zarr.config`][zarr.config]. fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional @@ -3070,7 +3075,7 @@ def array( is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in :mod:`zarr.core.config`. + This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. attributes : dict, optional Attributes for the array. chunk_key_encoding : ChunkKeyEncoding, optional diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index be60f4208f..243096b029 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -183,7 +183,7 @@ def _iter_regions( The linear indexing order to use. Yields - ------- + ------ Iterator[tuple[slice, ...]] An iterator over tuples of slices, where each slice spans a separate contiguous region diff --git a/src/zarr/creation.py b/src/zarr/creation.py index 622406ed75..605b5af5de 100644 --- a/src/zarr/creation.py +++ b/src/zarr/creation.py @@ -1,10 +1,9 @@ """ Helpers for creating arrays. -.. warning:: +!!! warning "Deprecated" + This sub-module is deprecated. All functions here are defined in the top level zarr namespace instead. - This sub-module is deprecated. All functions here are defined - in the top level zarr namespace instead. """ import warnings diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index e6076d9669..a3fd058680 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -188,7 +188,7 @@ class GpuMemoryStore(MemoryStore): Parameters ---------- store_dict : MutableMapping, optional - A mutable mapping with string keys and :class:`zarr.core.buffer.gpu.Buffer` + A mutable mapping with string keys and [zarr.core.buffer.gpu.Buffer][] values. read_only : bool Whether to open the store in read-only mode. @@ -222,7 +222,7 @@ def from_dict(cls, store_dict: MutableMapping[str, Buffer]) -> Self: ---------- store_dict : mapping A mapping of strings keys to arbitrary Buffers. The buffer data - will be moved into a :class:`gpu.Buffer`. + will be moved into a [`gpu.Buffer`][zarr.core.buffer.gpu.Buffer]. Returns ------- From 24385abcac414f6fe7a619204189676a760bb0ba Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Fri, 19 Sep 2025 14:48:38 -0400 Subject: [PATCH 115/468] Changelog entry for docs change (#3476) --- changes/3118.doc.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 changes/3118.doc.md diff --git a/changes/3118.doc.md b/changes/3118.doc.md new file mode 100644 index 0000000000..58adb1db76 --- /dev/null +++ b/changes/3118.doc.md @@ -0,0 +1 @@ +Use mkdocs-material for Zarr-Python documentation \ No newline at end of file From 64c2bdc5eeb8f12a3e098e964c90fc16a3d74a54 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Mon, 22 Sep 2025 23:53:24 +0200 Subject: [PATCH 116/468] chore: update pre-commit hooks (#3481) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - github.com/astral-sh/ruff-pre-commit: v0.12.11 → v0.13.1 - github.com/pre-commit/mirrors-mypy: v1.17.1 → v1.18.2 --- .pre-commit-config.yaml | 4 ++-- pyproject.toml | 2 +- src/zarr/core/dtype/wrapper.py | 5 +---- 3 files changed, 4 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3e2826f10f..da3e2be9b2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ ci: default_stages: [pre-commit, pre-push] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.11 + rev: v0.13.1 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -23,7 +23,7 @@ repos: exclude: mkdocs.yml - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.17.1 + rev: v1.18.2 hooks: - id: mypy files: src|tests diff --git a/pyproject.toml b/pyproject.toml index f6293a6df1..8b251fdd55 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -316,9 +316,9 @@ ignore = [ "RET505", "RET506", "RUF005", + "RUF043", "SIM108", "TRY003", - "UP038", # https://github.com/astral-sh/ruff/issues/7871 # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules "W191", "E111", diff --git a/src/zarr/core/dtype/wrapper.py b/src/zarr/core/dtype/wrapper.py index 776aea81d8..e44449585b 100644 --- a/src/zarr/core/dtype/wrapper.py +++ b/src/zarr/core/dtype/wrapper.py @@ -71,10 +71,7 @@ class variable, and it should generally be unique across different data types. """ # this class will create a native data type - # mypy currently disallows class variables to contain type parameters - # but it seems OK for us to use it here: - # https://github.com/python/typing/discussions/1424#discussioncomment-7989934 - dtype_cls: ClassVar[type[TDType_co]] # type: ignore[misc] + dtype_cls: ClassVar[type[TDType_co]] _zarr_v3_name: ClassVar[str] @classmethod From 2d3d7907e21875b6942b453aab58ce8aefc4191a Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 22 Sep 2025 18:05:40 -0400 Subject: [PATCH 117/468] Customize color theme for docs (#3477) Co-authored-by: Davis Bennett --- docs/_static/logo_bw.png | Bin 0 -> 45208 bytes docs/overrides/stylesheets/extra.css | 250 ++++++++++++++++++++++----- mkdocs.yml | 24 ++- 3 files changed, 216 insertions(+), 58 deletions(-) create mode 100644 docs/_static/logo_bw.png diff --git a/docs/_static/logo_bw.png b/docs/_static/logo_bw.png new file mode 100644 index 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z^Ee1Y+ceifEyAgYmkaX>G}m$`D7&wddPsHvZ3c^Rjor4*FKl{Ttzg|2HHk .admonition-title { + background-color: rgba(227, 75, 117, 0.1); + border-color: var(--md-primary-fg-color); +} + +.md-typeset .admonition.tip { + border-color: var(--gradient-mid-1); +} + +.md-typeset .admonition.tip > .admonition-title { + background-color: rgba(229, 122, 119, 0.1); + border-color: var(--gradient-mid-1); +} + +.md-typeset .admonition.warning { + border-color: var(--gradient-end); +} + +.md-typeset .admonition.warning > .admonition-title { + background-color: rgba(187, 16, 133, 0.1); + border-color: var(--gradient-end); +} + +/* Links */ +.md-content a { + color: var(--md-accent-fg-color); +} + +.md-content a:hover { + color: var(--gradient-end); +} + +/* Table of contents */ +.md-nav--secondary .md-nav__link--active { + color: var(--md-accent-fg-color); + border-left: 2px solid var(--md-accent-fg-color); + padding-left: calc(1rem - 2px); +} + +/* Footer */ +.md-footer { + background-color: var(--gradient-end); +} + +/* Buttons and interactive elements */ +.md-button { + background: linear-gradient(135deg, var(--md-primary-fg-color), var(--md-accent-fg-color)); + border: none; + color: white; + transition: all 0.3s ease; +} + +.md-button:hover { + transform: translateY(-2px); + box-shadow: 0 4px 12px rgba(187, 16, 133, 0.3); +} + +/* Scrollbar styling */ +::-webkit-scrollbar { + width: 8px; +} + +::-webkit-scrollbar-track { + background: rgba(187, 16, 133, 0.1); +} + +::-webkit-scrollbar-thumb { + background: linear-gradient( + 180deg, + var(--md-primary-fg-color), + var(--md-accent-fg-color) + ); + border-radius: 4px; +} + +::-webkit-scrollbar-thumb:hover { + background: linear-gradient( + 180deg, + var(--md-accent-fg-color), + var(--gradient-end) + ); +} + +/* Search results highlighting */ +.md-search-result__title { color: var(--md-primary-fg-color); - font-size: 0.75rem; - font-weight: bold; +} + +.md-search-result__teaser mark { + background-color: rgba(224, 16, 115, 0.2); + color: var(--gradient-end); } .md-header__button.md-logo img, .md-header__button.md-logo svg { - height: 2rem; - width: auto; + height: 42px !important; /* Increase from default ~24px */ + width: auto !important; + max-height: none !important; + padding: 0 0 0 16px !important; /* Keep left padding, remove others */ + margin: 0 !important; /* Remove any margin */ } -.md-header { - padding: 0.2rem 0; +/* Also remove padding from the logo button container except left */ +.md-header__button.md-logo { + padding: 0 0 0 8px !important; /* Keep some left padding on container */ + margin: 0 !important; + min-width: auto !important; } diff --git a/mkdocs.yml b/mkdocs.yml index c938ec36a8..009f6a52ee 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -62,30 +62,26 @@ theme: language: en name: material custom_dir: docs/overrides - logo: _static/logo_horizontal.svg - palette: - # Palette toggle for automatic mode - - media: "(prefers-color-scheme)" - toggle: - icon: material/brightness-auto - name: Switch to light mode + logo: _static/logo_bw.png - # Palette toggle for light mode + palette: + # Light mode - media: "(prefers-color-scheme: light)" - primary: blue grey - accent: pink + scheme: default + primary: custom + accent: custom toggle: icon: material/brightness-7 name: Switch to dark mode - # Palette toggle for dark mode + # Dark mode - media: "(prefers-color-scheme: dark)" scheme: slate - primary: grey - accent: pink + primary: custom + accent: custom toggle: icon: material/brightness-4 - name: Switch to system preference + name: Switch to light mode font: text: Roboto From 45756b0ca8cd9031fba76b72df65be93ecec45af Mon Sep 17 00:00:00 2001 From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Date: Mon, 22 Sep 2025 23:30:59 +0100 Subject: [PATCH 118/468] Document StoreLike values in user guide (#3480) * document valid values for StoreLike in user guide * fix doctests for storelike examples * make links mkdocs style * fix user guide links for mkdocs * link all StoreLike refs to the user guide * add changes note * remove old storage rst file --------- Co-authored-by: Davis Bennett --- changes/3303.doc.md | 1 + docs/user-guide/storage.md | 50 ++++++++++++++++++++++++++- mkdocs.yml | 1 + src/zarr/api/asynchronous.py | 58 +++++++++++++++++++------------ src/zarr/api/synchronous.py | 66 +++++++++++++++++++++++------------- src/zarr/core/array.py | 24 +++++++++---- src/zarr/core/group.py | 8 +++-- src/zarr/storage/_common.py | 8 +++-- 8 files changed, 159 insertions(+), 57 deletions(-) create mode 100644 changes/3303.doc.md diff --git a/changes/3303.doc.md b/changes/3303.doc.md new file mode 100644 index 0000000000..ebae05f7e4 --- /dev/null +++ b/changes/3303.doc.md @@ -0,0 +1 @@ +Document different values of StoreLike with examples in the user guide. \ No newline at end of file diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index 86dac188a5..ea48f8f622 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -12,7 +12,8 @@ Zarr-Python 3, stores must implement the abstract store API from ## Implicit Store Creation In most cases, it is not required to create a `Store` object explicitly. Passing a string -to Zarr's top level API will result in the store being created automatically: +(or other [StoreLike value](#storelike)) to Zarr's top level API will result in the store +being created automatically: ```python exec="true" session="storage" source="above" result="ansi" import zarr @@ -39,6 +40,53 @@ group = zarr.create_group(store=data) print(group) ``` +[](){#user-guide-store-like} +### StoreLike + +`StoreLike` values can be: + +- a `Path` or string indicating a location on the local file system. + This will create a [local store](#local-store): + ```python exec="true" session="storage" source="above" result="ansi" + group = zarr.open_group(store='data/foo/bar') + print(group) + ``` + ```python exec="true" session="storage" source="above" result="ansi" + from pathlib import Path + group = zarr.open_group(store=Path('data/foo/bar')) + print(group) + ``` + +- an FSSpec URI string, indicating a [remote store](#remote-store) location: + ```python exec="true" session="storage" source="above" result="ansi" + group = zarr.open_group( + store='s3://noaa-nwm-retro-v2-zarr-pds', + mode='r', + storage_options={'anon': True} + ) + print(group) + ``` + +- an empty dictionary or None, which will create a new [memory store](#memory-store): + ```python exec="true" session="storage" source="above" result="ansi" + group = zarr.create_group(store={}) + print(group) + ``` + ```python exec="true" session="storage" source="above" result="ansi" + group = zarr.create_group(store=None) + print(group) + ``` + +- a dictionary of string to [`Buffer`][zarr.abc.buffer.Buffer] mappings. This will + create a [memory store](#memory-store), using this dictionary as the + [`store_dict` argument][zarr.storage.MemoryStore]. + +- an FSSpec [FSMap object](https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.FSMap), + which will create an [FsspecStore](#remote-store). + +- a [`Store`][zarr.abc.store.Store] or [`StorePath`][zarr.storage.StorePath] - + see explicit store creation below. + ## Explicit Store Creation In some cases, it may be helpful to create a store instance directly. Zarr-Python offers four diff --git a/mkdocs.yml b/mkdocs.yml index 009f6a52ee..53b8eef7d4 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -107,6 +107,7 @@ extra_css: - overrides/stylesheets/extra.css plugins: + - autorefs - search - markdown-exec - mkdocstrings: diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 881341ace2..179f1ddb4a 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -199,7 +199,9 @@ async def consolidate_metadata( Parameters ---------- store : StoreLike - The store-like object whose metadata you wish to consolidate. + The store-like object whose metadata you wish to consolidate. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. path : str, optional A path to a group in the store to consolidate at. Only children below that group will be consolidated. @@ -293,7 +295,9 @@ async def load( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. path : str or None, optional The path within the store from which to load. @@ -337,7 +341,9 @@ async def open( Parameters ---------- store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional Persistence mode: 'r' means read only (must exist); 'r+' means read/write (must exist); 'a' means read/write (create if doesn't @@ -421,7 +427,9 @@ async def save( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. *args : ndarray NumPy arrays with data to save. zarr_format : {2, 3, None}, optional @@ -457,7 +465,9 @@ async def save_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. arr : ndarray NumPy array with data to save. zarr_format : {2, 3, None}, optional @@ -513,7 +523,9 @@ async def save_group( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. *args : ndarray NumPy arrays with data to save. zarr_format : {2, 3, None}, optional @@ -662,7 +674,9 @@ async def group( Parameters ---------- store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. overwrite : bool, optional If True, delete any pre-existing data in `store` at `path` before creating the group. @@ -724,7 +738,9 @@ async def create_group( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. path : str, optional Group path within store. overwrite : bool, optional @@ -780,17 +796,9 @@ async def open_group( Parameters ---------- store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. - - Strings are interpreted as paths on the local file system - and used as the ``root`` argument to [zarr.storage.LocalStore][]. - - Dictionaries are used as the ``store_dict`` argument in - [zarr.storage.MemoryStore][]. - - By default (``store=None``) a new [zarr.storage.MemoryStore][] - is created. - + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional Persistence mode: 'r' means read only (must exist); 'r+' means read/write (must exist); 'a' means read/write (create if doesn't @@ -805,7 +813,9 @@ async def open_group( path : str, optional Group path within store. chunk_store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + Separate storage for chunks. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. storage_options : dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. @@ -939,7 +949,9 @@ async def create( Memory layout to be used within each chunk. If not specified, the ``array.order`` parameter in the global config will be used. store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. synchronizer : object, optional Array synchronizer. overwrite : bool, optional @@ -1250,7 +1262,9 @@ async def open_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. zarr_version : {2, 3, None}, optional The zarr format to use when saving. Deprecated in favor of zarr_format. zarr_format : {2, 3, None}, optional diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 728822a326..8713f55daf 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -88,7 +88,9 @@ def consolidate_metadata( Parameters ---------- store : StoreLike - The store-like object whose metadata you wish to consolidate. + The store-like object whose metadata you wish to consolidate. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. path : str, optional A path to a group in the store to consolidate at. Only children below that group will be consolidated. @@ -143,7 +145,9 @@ def load( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. path : str or None, optional The path within the store from which to load. @@ -183,7 +187,9 @@ def open( Parameters ---------- store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional Persistence mode: 'r' means read only (must exist); 'r+' means read/write (must exist); 'a' means read/write (create if doesn't @@ -245,7 +251,9 @@ def save( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. *args : ndarray NumPy arrays with data to save. zarr_format : {2, 3, None}, optional @@ -279,7 +287,9 @@ def save_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. arr : ndarray NumPy array with data to save. zarr_format : {2, 3, None}, optional @@ -322,7 +332,9 @@ def save_group( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. *args : ndarray NumPy arrays with data to save. zarr_format : {2, 3, None}, optional @@ -413,7 +425,9 @@ def group( Parameters ---------- store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. overwrite : bool, optional If True, delete any pre-existing data in `store` at `path` before creating the group. @@ -480,17 +494,9 @@ def open_group( Parameters ---------- store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. - - Strings are interpreted as paths on the local file system - and used as the ``root`` argument to [zarr.storage.LocalStore][]. - - Dictionaries are used as the ``store_dict`` argument in - [zarr.storage.MemoryStore][]. - - By default (``store=None``) a new [zarr.storage.MemoryStore][] - is created. - + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. mode : {'r', 'r+', 'a', 'w', 'w-'}, optional Persistence mode: 'r' means read only (must exist); 'r+' means read/write (must exist); 'a' means read/write (create if doesn't @@ -505,7 +511,9 @@ def open_group( path : str, optional Group path within store. chunk_store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + Separate storage for chunks. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. storage_options : dict If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. @@ -570,7 +578,9 @@ def create_group( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. path : str, optional Group path within store. overwrite : bool, optional @@ -672,7 +682,9 @@ def create( Memory layout to be used within each chunk. If not specified, the ``array.order`` parameter in the global config will be used. store : StoreLike or None, default=None - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. synchronizer : object, optional Array synchronizer. overwrite : bool, optional @@ -832,7 +844,9 @@ def create_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. @@ -996,7 +1010,9 @@ def from_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. data : Array | array-like The array to copy. write_data : bool, default True @@ -1333,7 +1349,9 @@ def open_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. zarr_version : {2, 3, None}, optional The zarr format to use when saving. Deprecated in favor of zarr_format. zarr_format : {2, 3, None}, optional diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 6aefc38031..59ca8f5929 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -499,7 +499,9 @@ async def create( Parameters ---------- store : StoreLike - The store where the array will be created. + The store where the array will be created. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. shape : ShapeLike The shape of the array. dtype : ZDTypeLike @@ -967,7 +969,9 @@ async def open( Parameters ---------- store : StoreLike - The store containing the Zarr array. + The store containing the Zarr array. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. zarr_format : ZarrFormat | None, optional The Zarr format version (default is 3). @@ -2033,7 +2037,9 @@ def create( Parameters ---------- store : StoreLike - The array store that has already been initialized. + The array store that has already been initialized. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. shape : tuple[int, ...] The shape of the array. dtype : ZDTypeLike @@ -2233,7 +2239,9 @@ def open( Parameters ---------- store : StoreLike - Store containing the Array. + Store containing the Array. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. Returns ------- @@ -4251,7 +4259,9 @@ async def from_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. data : Array | array-like The array to copy. write_data : bool, default True @@ -4735,7 +4745,9 @@ async def create_array( Parameters ---------- store : StoreLike - Store or path to directory in file system or name of zip file. + StoreLike object to open. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index e71c55c10f..71d2b52194 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -1823,7 +1823,9 @@ def from_store( Parameters ---------- store : StoreLike - StoreLike containing the Group. + StoreLike containing the Group. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. attributes : dict, optional A dictionary of JSON-serializable values with user-defined attributes. zarr_format : {2, 3}, optional @@ -1863,7 +1865,9 @@ def open( Parameters ---------- store : StoreLike - Store containing the Group. + Store containing the Group. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. zarr_format : {2, 3, None}, optional Zarr storage format version. diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 4b1f5e4ae3..9ecfe4c201 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -283,7 +283,9 @@ async def make_store( Parameters ---------- store_like : StoreLike | None - The object to convert to a `Store` object. + The `StoreLike` object to convert to a `Store` object. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. mode : StoreAccessMode | None, optional The mode to use when creating the `Store` object. If None, the default mode is 'r'. @@ -371,7 +373,9 @@ async def make_store_path( Parameters ---------- store_like : StoreLike or None, default=None - The object to convert to a `StorePath` object. + The `StoreLike` object to convert to a `StorePath` object. See the + [storage documentation in the user guide][user-guide-store-like] + for a description of all valid StoreLike values. path : str | None, optional The path to use when creating the `StorePath` object. If None, the default path is the empty string. From 027849481c09a79a357367aab5602b26f4808079 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Tue, 23 Sep 2025 10:24:05 +0100 Subject: [PATCH 119/468] Include shard/chunk shapes in size mismatch error (#3485) --- src/zarr/codecs/sharding.py | 3 ++- tests/test_codecs/test_sharding.py | 18 ++++++++++++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index ecbd258ccf..b0fd75cef7 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -431,7 +431,8 @@ def validate( ) ): raise ValueError( - "The array's `chunk_shape` needs to be divisible by the shard's inner `chunk_shape`." + f"The array's `chunk_shape` (got {chunk_grid.chunk_shape}) " + f"needs to be divisible by the shard's inner `chunk_shape` (got {self.chunk_shape})." ) async def _decode_single( diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index eb80545ff3..7eb4deccbf 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -1,4 +1,5 @@ import pickle +import re from typing import Any import numpy as np @@ -486,3 +487,20 @@ def test_invalid_metadata(store: Store) -> None: dtype=np.dtype("uint8"), fill_value=0, ) + + +def test_invalid_shard_shape() -> None: + with pytest.raises( + ValueError, + match=re.escape( + "The array's `chunk_shape` (got (16, 16)) needs to be divisible by the shard's inner `chunk_shape` (got (9,))." + ), + ): + zarr.create_array( + {}, + shape=(16, 16), + shards=(16, 16), + chunks=(9,), + dtype=np.dtype("uint8"), + fill_value=0, + ) From 48e7f4dc60922332970a000eab2e6ba83566fbac Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 23 Sep 2025 14:36:04 +0200 Subject: [PATCH 120/468] fix pcodec resolution failure (#3483) * fix pcodec registration typo, add zfpy and pcodec to test dependencies, fix numcodec tests * changelog * remove zfpy test dep --- changes/3483.bugfix.md | 1 + pyproject.toml | 2 +- src/zarr/codecs/__init__.py | 2 +- tests/test_codecs/test_numcodecs.py | 11 ++++++++--- 4 files changed, 11 insertions(+), 5 deletions(-) create mode 100644 changes/3483.bugfix.md diff --git a/changes/3483.bugfix.md b/changes/3483.bugfix.md new file mode 100644 index 0000000000..b6672d348a --- /dev/null +++ b/changes/3483.bugfix.md @@ -0,0 +1 @@ +Fix a bug that prevented `PCodec` from being properly resolved when loading arrays using that compressor. \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 8b251fdd55..6164f69382 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,7 +84,7 @@ test = [ "pytest-xdist", "packaging", "tomlkit", - "uv" + "uv", ] remote_tests = [ 'zarr[remote]', diff --git a/src/zarr/codecs/__init__.py b/src/zarr/codecs/__init__.py index 7cb4e2a44d..4c621290e7 100644 --- a/src/zarr/codecs/__init__.py +++ b/src/zarr/codecs/__init__.py @@ -85,7 +85,7 @@ register_codec( "numcodecs.jenkins_lookup3", JenkinsLookup3, qualname="zarr.codecs.numcodecs.JenkinsLookup3" ) -register_codec("numcodecs.pcodec", PCodec, qualname="zarr.codecs.numcodecs.pcodec") +register_codec("numcodecs.pcodec", PCodec, qualname="zarr.codecs.numcodecs.PCodec") register_codec("numcodecs.packbits", PackBits, qualname="zarr.codecs.numcodecs.PackBits") register_codec("numcodecs.quantize", Quantize, qualname="zarr.codecs.numcodecs.Quantize") register_codec("numcodecs.shuffle", Shuffle, qualname="zarr.codecs.numcodecs.Shuffle") diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py index 147327ccf3..68f4e0cf7b 100644 --- a/tests/test_codecs/test_numcodecs.py +++ b/tests/test_codecs/test_numcodecs.py @@ -12,7 +12,7 @@ from zarr.abc.numcodec import _is_numcodec, _is_numcodec_cls from zarr.codecs import numcodecs as _numcodecs from zarr.errors import ZarrUserWarning -from zarr.registry import get_numcodec +from zarr.registry import get_codec_class, get_numcodec if TYPE_CHECKING: from collections.abc import Iterator @@ -74,18 +74,23 @@ def test_is_numcodec_cls() -> None: ALL_CODECS = tuple( filter( - lambda v: isinstance(v, _numcodecs._NumcodecsCodec), + lambda v: issubclass(v, _numcodecs._NumcodecsCodec) and hasattr(v, "codec_name"), tuple(getattr(_numcodecs, cls_name) for cls_name in _numcodecs.__all__), ) ) +@pytest.mark.parametrize("codec_cls", ALL_CODECS) +def test_get_codec_class(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None: + assert get_codec_class(codec_cls.codec_name) == codec_cls # type: ignore[comparison-overlap] + + @pytest.mark.parametrize("codec_class", ALL_CODECS) def test_docstring(codec_class: type[_numcodecs._NumcodecsCodec]) -> None: """ Test that the docstring for the zarr.numcodecs codecs references the wrapped numcodecs class. """ - assert "See :class:`numcodecs." in codec_class.__doc__ # type: ignore[operator] + assert "See [numcodecs." in codec_class.__doc__ # type: ignore[operator] @pytest.mark.parametrize( From e1990c0f065c8575c1ee345bb31c986775e0e635 Mon Sep 17 00:00:00 2001 From: Ian Hunt-Isaak Date: Thu, 25 Sep 2025 08:19:35 -0400 Subject: [PATCH 121/468] Fix string integer parsing (#3489) * fix: allow for intlike strings in json parsing * floatish strings * tests * float tests --- src/zarr/core/dtype/npy/common.py | 59 +++++++++++++++++++++++++ src/zarr/core/dtype/npy/float.py | 5 +++ src/zarr/core/dtype/npy/int.py | 5 +++ tests/test_dtype/test_npy/test_float.py | 44 ++++++++++++++++++ tests/test_dtype/test_npy/test_int.py | 39 ++++++++++++++++ 5 files changed, 152 insertions(+) diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index ab22b542f0..107b3bd12d 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -58,6 +58,12 @@ IntishFloat = NewType("IntishFloat", float) """A type for floats that represent integers, like 1.0 (but not 1.1).""" +IntishStr = NewType("IntishStr", str) +"""A type for strings that represent integers, like "0" or "42".""" + +FloatishStr = NewType("FloatishStr", str) +"""A type for strings that represent floats, like "3.14" or "-2.5".""" + NumpyEndiannessStr = Literal[">", "<", "="] NUMPY_ENDIANNESS_STR: Final = ">", "<", "=" @@ -488,6 +494,59 @@ def check_json_intish_float(data: JSON) -> TypeGuard[IntishFloat]: return isinstance(data, float) and data.is_integer() +def check_json_intish_str(data: JSON) -> TypeGuard[IntishStr]: + """ + Check if a JSON value is a string that represents an integer, like "0", "42", or "-5". + + Parameters + ---------- + data : JSON + The JSON value to check. + + Returns + ------- + bool + True if the data is a string representing an integer, False otherwise. + """ + if not isinstance(data, str): + return False + + try: + int(data) + except ValueError: + return False + else: + return True + + +def check_json_floatish_str(data: JSON) -> TypeGuard[FloatishStr]: + """ + Check if a JSON value is a string that represents a float, like "3.14", "-2.5", or "0.0". + + Note: This function is intended to be used AFTER check_json_float_v2/v3, so it only + handles regular string representations that those functions don't cover. + + Parameters + ---------- + data : JSON + The JSON value to check. + + Returns + ------- + bool + True if the data is a string representing a regular float, False otherwise. + """ + if not isinstance(data, str): + return False + + try: + float(data) + except ValueError: + return False + else: + return True + + def check_json_str(data: JSON) -> TypeGuard[str]: """ Check if a JSON value is a string. diff --git a/src/zarr/core/dtype/npy/float.py b/src/zarr/core/dtype/npy/float.py index bedb44b52d..0be2cbca9b 100644 --- a/src/zarr/core/dtype/npy/float.py +++ b/src/zarr/core/dtype/npy/float.py @@ -19,6 +19,7 @@ TFloatScalar_co, check_json_float_v2, check_json_float_v3, + check_json_floatish_str, endianness_to_numpy_str, float_from_json_v2, float_from_json_v3, @@ -270,6 +271,8 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TFloatScal if zarr_format == 2: if check_json_float_v2(data): return self._cast_scalar_unchecked(float_from_json_v2(data)) + elif check_json_floatish_str(data): + return self._cast_scalar_unchecked(float(data)) else: raise TypeError( f"Invalid type: {data}. Expected a float or a special string encoding of a float." @@ -277,6 +280,8 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TFloatScal elif zarr_format == 3: if check_json_float_v3(data): return self._cast_scalar_unchecked(float_from_json_v3(data)) + elif check_json_floatish_str(data): + return self._cast_scalar_unchecked(float(data)) else: raise TypeError( f"Invalid type: {data}. Expected a float or a special string encoding of a float." diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index 6f7ebc2f55..580776a865 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -26,6 +26,7 @@ from zarr.core.dtype.npy.common import ( check_json_int, check_json_intish_float, + check_json_intish_str, endianness_to_numpy_str, get_endianness_from_numpy_dtype, ) @@ -209,6 +210,10 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TIntScalar return self._cast_scalar_unchecked(data) if check_json_intish_float(data): return self._cast_scalar_unchecked(int(data)) + + if check_json_intish_str(data): + return self._cast_scalar_unchecked(int(data)) + raise TypeError(f"Invalid type: {data}. Expected an integer.") def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> int: diff --git a/tests/test_dtype/test_npy/test_float.py b/tests/test_dtype/test_npy/test_float.py index 90fa27c9cf..1bbcbbc81f 100644 --- a/tests/test_dtype/test_npy/test_float.py +++ b/tests/test_dtype/test_npy/test_float.py @@ -167,3 +167,47 @@ class TestFloat64(_BaseTestFloat): ("0x3ff0000000000000", 1.0), ) item_size_params = (Float64(),) + + +def test_check_json_floatish_str() -> None: + """Test the check_json_floatish_str function.""" + from zarr.core.dtype.npy.common import check_json_floatish_str + + # Test valid string floats + assert check_json_floatish_str("3.14") + assert check_json_floatish_str("0.0") + assert check_json_floatish_str("-2.5") + assert check_json_floatish_str("1.0") + + # Test invalid cases + assert not check_json_floatish_str("not_a_number") + assert not check_json_floatish_str("") + assert not check_json_floatish_str(3.14) # actual float, not string + assert not check_json_floatish_str(42) # int + assert not check_json_floatish_str(None) + + # Test that special cases still work via float() conversion + # (these will be handled by existing functions first in practice) + assert check_json_floatish_str("NaN") + assert check_json_floatish_str("Infinity") + assert check_json_floatish_str("-Infinity") + + +def test_string_float_from_json_scalar() -> None: + """Test that string representations of floats can be parsed by from_json_scalar.""" + # Test with Float32 + dtype_instance = Float32() + result = dtype_instance.from_json_scalar("3.14", zarr_format=3) + assert abs(result - np.float32(3.14)) < 1e-6 + assert isinstance(result, np.float32) + + # Test other cases + result = dtype_instance.from_json_scalar("0.0", zarr_format=3) + assert result == np.float32(0.0) + + result = dtype_instance.from_json_scalar("-2.5", zarr_format=3) + assert result == np.float32(-2.5) + + # Test that it works for v2 format too + result = dtype_instance.from_json_scalar("1.5", zarr_format=2) + assert result == np.float32(1.5) diff --git a/tests/test_dtype/test_npy/test_int.py b/tests/test_dtype/test_npy/test_int.py index 0cab3b8e3e..f53ec7f5ae 100644 --- a/tests/test_dtype/test_npy/test_int.py +++ b/tests/test_dtype/test_npy/test_int.py @@ -281,3 +281,42 @@ class TestUInt64(BaseTestZDType): ) invalid_scalar_params = ((UInt64(), {"set!"}), (UInt64(), ("tuple",))) item_size_params = (UInt64(),) + + +def test_check_json_intish_str() -> None: + """Test the check_json_intish_str function.""" + from zarr.core.dtype.npy.common import check_json_intish_str + + # Test valid string integers + assert check_json_intish_str("0") + assert check_json_intish_str("42") + assert check_json_intish_str("-5") + assert check_json_intish_str("123") + + # Test invalid cases + assert not check_json_intish_str("3.14") + assert not check_json_intish_str("not_a_number") + assert not check_json_intish_str("") + assert not check_json_intish_str(42) # actual int, not string + assert not check_json_intish_str(3.14) # float + assert not check_json_intish_str(None) + + +def test_string_integer_from_json_scalar() -> None: + """Test that string representations of integers can be parsed by from_json_scalar.""" + # Test the specific reproducer case + dtype_instance = Int32() + result = dtype_instance.from_json_scalar("0", zarr_format=3) + assert result == np.int32(0) + assert isinstance(result, np.int32) + + # Test other cases + result = dtype_instance.from_json_scalar("42", zarr_format=3) + assert result == np.int32(42) + + result = dtype_instance.from_json_scalar("-5", zarr_format=3) + assert result == np.int32(-5) + + # Test that it works for v2 format too + result = dtype_instance.from_json_scalar("123", zarr_format=2) + assert result == np.int32(123) From 1cd4f7e0ef6a2193e2f4084640cff693f2bad0b4 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 30 Sep 2025 22:22:42 +0200 Subject: [PATCH 122/468] add experimental module (#3490) * add experimental module * changelog --- changes/3490.feature.md | 1 + src/zarr/experimental/__init__.py | 1 + 2 files changed, 2 insertions(+) create mode 100644 changes/3490.feature.md create mode 100644 src/zarr/experimental/__init__.py diff --git a/changes/3490.feature.md b/changes/3490.feature.md new file mode 100644 index 0000000000..899cdcf75d --- /dev/null +++ b/changes/3490.feature.md @@ -0,0 +1 @@ +Adds a `zarr.experimental` module for unstable user-facing features. \ No newline at end of file diff --git a/src/zarr/experimental/__init__.py b/src/zarr/experimental/__init__.py new file mode 100644 index 0000000000..3863510c65 --- /dev/null +++ b/src/zarr/experimental/__init__.py @@ -0,0 +1 @@ +"""The experimental module is a site for exporting new or experimental Zarr features.""" From 2eb89e1f213879c51f048c35bbfd6674c1abe285 Mon Sep 17 00:00:00 2001 From: ruaridhg <32329546+ruaridhg@users.noreply.github.com> Date: Thu, 2 Oct 2025 09:54:07 +0100 Subject: [PATCH 123/468] CacheStore containing source store and cache store (#3366) * Add _cache.py first attempt * test.py ran without error, creating test.zarr/ * Added testing for cache.py LRUStoreCache for v3 * Fix ruff errors * Add working example comparing LocalStore to LRUStoreCache * Delete test.py to clean-up * Added lrustorecache to changes and user-guide docs * Fix linting issues * Implement dual store cache * Fixed failing tests * Fix linting errors * Add logger info * Delete unnecessary extra functionality * Rename to caching_store * Add test_storage.py * Fix logic in _caching_store.py * Update tests to match caching_store implemtation * Delete LRUStoreCache files * Update __init__ * Add functionality for max_size * Add tests for cache_info and clear_cache * Delete test.py * Fix linting errors * Update feature description * Fix errors * Fix cachingstore.rst errors * Fix cachingstore.rst errors * Fixed eviction key logic with proper size tracking * Increase code coverage to 98% * Fix linting errors * move cache store to experimental, fix bugs * update changelog * remove logging config override, remove dead code, adjust evict_key logic, and avoid calling exists unnecessarily * add docs * add tests for relaxed cache coherency * adjust code examples (but we don't know if they work, because we don't have doctests working) * apply changes based on AI code review, and move tests into tests/test_experimental * update changelog * fix exception log --------- Co-authored-by: ruaridhg Co-authored-by: Davis Bennett --- changes/3366.feature.md | 1 + docs/user-guide/experimental.md | 272 ++++++ mkdocs.yml | 1 + pyproject.toml | 1 + src/zarr/experimental/cache_store.py | 383 +++++++++ tests/test_experimental/test_cache_store.py | 864 ++++++++++++++++++++ 6 files changed, 1522 insertions(+) create mode 100644 changes/3366.feature.md create mode 100644 docs/user-guide/experimental.md create mode 100644 src/zarr/experimental/cache_store.py create mode 100644 tests/test_experimental/test_cache_store.py diff --git a/changes/3366.feature.md b/changes/3366.feature.md new file mode 100644 index 0000000000..550c9f4436 --- /dev/null +++ b/changes/3366.feature.md @@ -0,0 +1 @@ +Adds `zarr.experimental.cache_store.CacheStore`, a `Store` that implements caching by combining two other `Store` instances. See the [docs page](https://zarr.readthedocs.io/en/latest/user-guide/experimental#cachestore) for more information about this feature. \ No newline at end of file diff --git a/docs/user-guide/experimental.md b/docs/user-guide/experimental.md new file mode 100644 index 0000000000..aead2dedab --- /dev/null +++ b/docs/user-guide/experimental.md @@ -0,0 +1,272 @@ +# Experimental features + +This section contains documentation for experimental Zarr Python features. The features described here are exciting and potentially useful, but also volatile -- we might change them at any time. Take this into account if you consider depending on these features. + +## `CacheStore` + +Zarr Python 3.1.4 adds `zarr.experimental.cache_store.CacheStore` provides a dual-store caching implementation +that can be wrapped around any Zarr store to improve performance for repeated data access. +This is particularly useful when working with remote stores (e.g., S3, HTTP) where network +latency can significantly impact data access speed. + +The CacheStore implements a cache that uses a separate Store instance as the cache backend, +providing persistent caching capabilities with time-based expiration, size-based eviction, +and flexible cache storage options. It automatically evicts the least recently used items +when the cache reaches its maximum size. + +Because the `CacheStore` uses an ordinary Zarr `Store` object as the caching layer, you can reuse the data stored in the cache later. + +> **Note:** The CacheStore is a wrapper store that maintains compatibility with the full +> `zarr.abc.store.Store` API while adding transparent caching functionality. + +## Basic Usage + +Creating a CacheStore requires both a source store and a cache store. The cache store +can be any Store implementation, providing flexibility in cache persistence: + +```python exec="true" session="experimental" source="above" result="ansi" +import zarr +from zarr.storage import LocalStore +import numpy as np +from tempfile import mkdtemp +from zarr.experimental.cache_store import CacheStore + +# Create a local store and a separate cache store +local_store_path = mkdtemp(suffix='.zarr') +source_store = LocalStore(local_store_path) +cache_store = zarr.storage.MemoryStore() # In-memory cache +cached_store = CacheStore( + store=source_store, + cache_store=cache_store, + max_size=256*1024*1024 # 256MB cache +) + +# Create an array using the cached store +zarr_array = zarr.zeros((100, 100), chunks=(10, 10), dtype='f8', store=cached_store, mode='w') + +# Write some data to force chunk creation +zarr_array[:] = np.random.random((100, 100)) +``` + +The dual-store architecture allows you to use different store types for source and cache, +such as a remote store for source data and a local store for persistent caching. + +## Performance Benefits + +The CacheStore provides significant performance improvements for repeated data access: + +```python exec="true" session="experimental" source="above" result="ansi" +import time + +# Benchmark reading with cache +start = time.time() +for _ in range(100): + _ = zarr_array[:] +elapsed_cache = time.time() - start + +# Compare with direct store access (without cache) +zarr_array_nocache = zarr.open(local_store_path, mode='r') +start = time.time() +for _ in range(100): + _ = zarr_array_nocache[:] +elapsed_nocache = time.time() - start + +# Cache provides speedup for repeated access +speedup = elapsed_nocache / elapsed_cache +``` + +Cache effectiveness is particularly pronounced with repeated access to the same data chunks. + + +## Cache Configuration + +The CacheStore can be configured with several parameters: + +**max_size**: Controls the maximum size of cached data in bytes + +```python exec="true" session="experimental" source="above" result="ansi" +# 256MB cache with size limit +cache = CacheStore( + store=source_store, + cache_store=cache_store, + max_size=256*1024*1024 +) + +# Unlimited cache size (use with caution) +cache = CacheStore( + store=source_store, + cache_store=cache_store, + max_size=None +) +``` + +**max_age_seconds**: Controls time-based cache expiration + +```python exec="true" session="experimental" source="above" result="ansi" +# Cache expires after 1 hour +cache = CacheStore( + store=source_store, + cache_store=cache_store, + max_age_seconds=3600 +) + +# Cache never expires +cache = CacheStore( + store=source_store, + cache_store=cache_store, + max_age_seconds="infinity" +) +``` + +**cache_set_data**: Controls whether written data is cached + +```python exec="true" session="experimental" source="above" result="ansi" +# Cache data when writing (default) +cache = CacheStore( + store=source_store, + cache_store=cache_store, + cache_set_data=True +) + +# Don't cache written data (read-only cache) +cache = CacheStore( + store=source_store, + cache_store=cache_store, + cache_set_data=False +) +``` + +## Cache Statistics + +The CacheStore provides statistics to monitor cache performance and state: + +```python exec="true" session="experimental" source="above" result="ansi" +# Access some data to generate cache activity +data = zarr_array[0:50, 0:50] # First access - cache miss +data = zarr_array[0:50, 0:50] # Second access - cache hit + +# Get comprehensive cache information +info = cached_store.cache_info() +print(info['cache_store_type']) # e.g., 'MemoryStore' +print(info['max_age_seconds']) +print(info['max_size']) +print(info['current_size']) +print(info['tracked_keys']) +print(info['cached_keys']) +print(info['cache_set_data']) +``` + +The `cache_info()` method returns a dictionary with detailed information about the cache state. + +## Cache Management + +The CacheStore provides methods for manual cache management: + +```python exec="true" session="experimental" source="above" result="ansi" +# Clear all cached data and tracking information +import asyncio +asyncio.run(cached_store.clear_cache()) + +# Check cache info after clearing +info = cached_store.cache_info() +assert info['tracked_keys'] == 0 +assert info['current_size'] == 0 +``` + +The `clear_cache()` method is an async method that clears both the cache store +(if it supports the `clear` method) and all internal tracking data. + +## Best Practices + +1. **Choose appropriate cache store**: Use MemoryStore for fast temporary caching or LocalStore for persistent caching +2. **Size the cache appropriately**: Set `max_size` based on available storage and expected data access patterns +3. **Use with remote stores**: The cache provides the most benefit when wrapping slow remote stores +4. **Monitor cache statistics**: Use `cache_info()` to tune cache size and access patterns +5. **Consider data locality**: Group related data accesses together to improve cache efficiency +6. **Set appropriate expiration**: Use `max_age_seconds` for time-sensitive data or "infinity" for static data + +## Working with Different Store Types + +The CacheStore can wrap any store that implements the `zarr.abc.store.Store` interface +and use any store type for the cache backend: + +### Local Store with Memory Cache + +```python exec="true" session="experimental-memory-cache" source="above" result="ansi" +from zarr.storage import LocalStore, MemoryStore +from zarr.experimental.cache_store import CacheStore +from tempfile import mkdtemp + +local_store_path = mkdtemp(suffix='.zarr') +source_store = LocalStore(local_store_path) +cache_store = MemoryStore() +cached_store = CacheStore( + store=source_store, + cache_store=cache_store, + max_size=128*1024*1024 +) +``` + +### Memory Store with Persistent Cache + +```python exec="true" session="experimental-local-cache" source="above" result="ansi" +from tempfile import mkdtemp +from zarr.storage import MemoryStore, LocalStore +from zarr.experimental.cache_store import CacheStore + +memory_store = MemoryStore() +local_store_path = mkdtemp(suffix='.zarr') +persistent_cache = LocalStore(local_store_path) +cached_store = CacheStore( + store=memory_store, + cache_store=persistent_cache, + max_size=256*1024*1024 +) +``` + +The dual-store architecture provides flexibility in choosing the best combination +of source and cache stores for your specific use case. + +## Examples from Real Usage + +Here's a complete example demonstrating cache effectiveness: + +```python exec="true" session="experimental-final" source="above" result="ansi" +import numpy as np +import time +from tempfile import mkdtemp +import zarr +import zarr.storage +from zarr.experimental.cache_store import CacheStore + +# Create test data with dual-store cache +local_store_path = mkdtemp(suffix='.zarr') +source_store = zarr.storage.LocalStore(local_store_path) +cache_store = zarr.storage.MemoryStore() +cached_store = CacheStore( + store=source_store, + cache_store=cache_store, + max_size=256*1024*1024 +) +zarr_array = zarr.zeros((100, 100), chunks=(10, 10), dtype='f8', store=cached_store, mode='w') +zarr_array[:] = np.random.random((100, 100)) + +# Demonstrate cache effectiveness with repeated access +start = time.time() +data = zarr_array[20:30, 20:30] # First access (cache miss) +first_access = time.time() - start + +start = time.time() +data = zarr_array[20:30, 20:30] # Second access (cache hit) +second_access = time.time() - start + +# Check cache statistics +info = cached_store.cache_info() +assert info['cached_keys'] > 0 # Should have cached keys +assert info['current_size'] > 0 # Should have cached data +print(f"Cache contains {info['cached_keys']} keys with {info['current_size']} bytes") +``` + +This example shows how the CacheStore can significantly reduce access times for repeated +data reads, particularly important when working with remote data sources. The dual-store +architecture allows for flexible cache persistence and management. diff --git a/mkdocs.yml b/mkdocs.yml index 53b8eef7d4..4c7a1a4df2 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -25,6 +25,7 @@ nav: - user-guide/extending.md - user-guide/gpu.md - user-guide/consolidated_metadata.md + - user-guide/experimental.md - API Reference: - api/index.md - api/array.md diff --git a/pyproject.toml b/pyproject.toml index 6164f69382..d72eef9dbc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -399,6 +399,7 @@ filterwarnings = [ "ignore:Unclosed client session >> import zarr + >>> from zarr.storage import MemoryStore + >>> from zarr.experimental.cache_store import CacheStore + >>> + >>> # Create a cached store + >>> source_store = MemoryStore() + >>> cache_store = MemoryStore() + >>> cached_store = CacheStore( + ... store=source_store, + ... cache_store=cache_store, + ... max_age_seconds=60, + ... max_size=1024*1024 + ... ) + >>> + >>> # Use it like any other store + >>> array = zarr.create(shape=(100,), store=cached_store) + >>> array[:] = 42 + + """ + + _cache: Store + max_age_seconds: int | Literal["infinity"] + max_size: int | None + key_insert_times: dict[str, float] + cache_set_data: bool + _cache_order: OrderedDict[str, None] # Track access order for LRU + _current_size: int # Track current cache size + _key_sizes: dict[str, int] # Track size of each cached key + _lock: asyncio.Lock + _hits: int # Cache hit counter + _misses: int # Cache miss counter + _evictions: int # Cache eviction counter + + def __init__( + self, + store: Store, + *, + cache_store: Store, + max_age_seconds: int | str = "infinity", + max_size: int | None = None, + key_insert_times: dict[str, float] | None = None, + cache_set_data: bool = True, + ) -> None: + super().__init__(store) + + if not cache_store.supports_deletes: + msg = ( + f"The provided cache store {cache_store} does not support deletes. " + "The cache_store must support deletes for CacheStore to function properly." + ) + raise ValueError(msg) + + self._cache = cache_store + # Validate and set max_age_seconds + if isinstance(max_age_seconds, str): + if max_age_seconds != "infinity": + raise ValueError("max_age_seconds string value must be 'infinity'") + self.max_age_seconds = "infinity" + else: + self.max_age_seconds = max_age_seconds + self.max_size = max_size + if key_insert_times is None: + self.key_insert_times = {} + else: + self.key_insert_times = key_insert_times + + self.cache_set_data = cache_set_data + self._cache_order = OrderedDict() + self._current_size = 0 + self._key_sizes = {} + self._lock = asyncio.Lock() + self._hits = 0 + self._misses = 0 + self._evictions = 0 + + def _is_key_fresh(self, key: str) -> bool: + """Check if a cached key is still fresh based on max_age_seconds. + + Uses monotonic time for accurate elapsed time measurement. + """ + if self.max_age_seconds == "infinity": + return True + now = time.monotonic() + elapsed = now - self.key_insert_times.get(key, 0) + return elapsed < self.max_age_seconds + + async def _accommodate_value(self, value_size: int) -> None: + """Ensure there is enough space in the cache for a new value. + + Must be called while holding self._lock. + """ + if self.max_size is None: + return + + # Remove least recently used items until we have enough space + while self._current_size + value_size > self.max_size and self._cache_order: + # Get the least recently used key (first in OrderedDict) + lru_key = next(iter(self._cache_order)) + await self._evict_key(lru_key) + + async def _evict_key(self, key: str) -> None: + """Evict a key from the cache. + + Must be called while holding self._lock. + Updates size tracking atomically with deletion. + """ + try: + key_size = self._key_sizes.get(key, 0) + + # Delete from cache store + await self._cache.delete(key) + + # Update tracking after successful deletion + self._remove_from_tracking(key) + self._current_size = max(0, self._current_size - key_size) + self._evictions += 1 + + logger.debug("_evict_key: evicted key %s, freed %d bytes", key, key_size) + except Exception: + logger.exception("_evict_key: failed to evict key %s", key) + raise # Re-raise to signal eviction failure + + async def _cache_value(self, key: str, value: Buffer) -> None: + """Cache a value with size tracking. + + This method holds the lock for the entire operation to ensure atomicity. + """ + value_size = len(value) + + # Check if value exceeds max size + if self.max_size is not None and value_size > self.max_size: + logger.warning( + "_cache_value: value size %d exceeds max_size %d, skipping cache", + value_size, + self.max_size, + ) + return + + async with self._lock: + # If key already exists, subtract old size first + if key in self._key_sizes: + old_size = self._key_sizes[key] + self._current_size -= old_size + logger.debug("_cache_value: updating existing key %s, old size %d", key, old_size) + + # Make room for the new value (this calls _evict_key_locked internally) + await self._accommodate_value(value_size) + + # Update tracking atomically + self._cache_order[key] = None # OrderedDict to track access order + self._current_size += value_size + self._key_sizes[key] = value_size + self.key_insert_times[key] = time.monotonic() + + logger.debug("_cache_value: cached key %s with size %d bytes", key, value_size) + + async def _update_access_order(self, key: str) -> None: + """Update the access order for LRU tracking.""" + if key in self._cache_order: + async with self._lock: + # Move to end (most recently used) + self._cache_order.move_to_end(key) + + def _remove_from_tracking(self, key: str) -> None: + """Remove a key from all tracking structures. + + Must be called while holding self._lock. + """ + self._cache_order.pop(key, None) + self.key_insert_times.pop(key, None) + self._key_sizes.pop(key, None) + + async def _get_try_cache( + self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Buffer | None: + """Try to get data from cache first, falling back to source store.""" + maybe_cached_result = await self._cache.get(key, prototype, byte_range) + if maybe_cached_result is not None: + logger.debug("_get_try_cache: key %s found in cache (HIT)", key) + self._hits += 1 + # Update access order for LRU + await self._update_access_order(key) + return maybe_cached_result + else: + logger.debug( + "_get_try_cache: key %s not found in cache (MISS), fetching from store", key + ) + self._misses += 1 + maybe_fresh_result = await super().get(key, prototype, byte_range) + if maybe_fresh_result is None: + # Key doesn't exist in source store + await self._cache.delete(key) + async with self._lock: + self._remove_from_tracking(key) + else: + # Cache the newly fetched value + await self._cache.set(key, maybe_fresh_result) + await self._cache_value(key, maybe_fresh_result) + return maybe_fresh_result + + async def _get_no_cache( + self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Buffer | None: + """Get data directly from source store and update cache.""" + self._misses += 1 + maybe_fresh_result = await super().get(key, prototype, byte_range) + if maybe_fresh_result is None: + # Key doesn't exist in source, remove from cache and tracking + await self._cache.delete(key) + async with self._lock: + self._remove_from_tracking(key) + else: + logger.debug("_get_no_cache: key %s found in store, setting in cache", key) + await self._cache.set(key, maybe_fresh_result) + await self._cache_value(key, maybe_fresh_result) + return maybe_fresh_result + + async def get( + self, + key: str, + prototype: BufferPrototype, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + """ + Retrieve data from the store, using cache when appropriate. + + Parameters + ---------- + key : str + The key to retrieve + prototype : BufferPrototype + Buffer prototype for creating the result buffer + byte_range : ByteRequest, optional + Byte range to retrieve + + Returns + ------- + Buffer | None + The retrieved data, or None if not found + """ + if not self._is_key_fresh(key): + logger.debug("get: key %s is not fresh, fetching from store", key) + return await self._get_no_cache(key, prototype, byte_range) + else: + logger.debug("get: key %s is fresh, trying cache", key) + return await self._get_try_cache(key, prototype, byte_range) + + async def set(self, key: str, value: Buffer) -> None: + """ + Store data in the underlying store and optionally in cache. + + Parameters + ---------- + key : str + The key to store under + value : Buffer + The data to store + """ + logger.debug("set: setting key %s in store", key) + await super().set(key, value) + if self.cache_set_data: + logger.debug("set: setting key %s in cache", key) + await self._cache.set(key, value) + await self._cache_value(key, value) + else: + logger.debug("set: deleting key %s from cache", key) + await self._cache.delete(key) + async with self._lock: + self._remove_from_tracking(key) + + async def delete(self, key: str) -> None: + """ + Delete data from both the underlying store and cache. + + Parameters + ---------- + key : str + The key to delete + """ + logger.debug("delete: deleting key %s from store", key) + await super().delete(key) + logger.debug("delete: deleting key %s from cache", key) + await self._cache.delete(key) + async with self._lock: + self._remove_from_tracking(key) + + def cache_info(self) -> dict[str, Any]: + """Return information about the cache state.""" + return { + "cache_store_type": type(self._cache).__name__, + "max_age_seconds": "infinity" + if self.max_age_seconds == "infinity" + else self.max_age_seconds, + "max_size": self.max_size, + "current_size": self._current_size, + "cache_set_data": self.cache_set_data, + "tracked_keys": len(self.key_insert_times), + "cached_keys": len(self._cache_order), + } + + def cache_stats(self) -> dict[str, Any]: + """Return cache performance statistics.""" + total_requests = self._hits + self._misses + hit_rate = self._hits / total_requests if total_requests > 0 else 0.0 + return { + "hits": self._hits, + "misses": self._misses, + "evictions": self._evictions, + "total_requests": total_requests, + "hit_rate": hit_rate, + } + + async def clear_cache(self) -> None: + """Clear all cached data and tracking information.""" + # Clear the cache store if it supports clear + if hasattr(self._cache, "clear"): + await self._cache.clear() + + # Reset tracking + async with self._lock: + self.key_insert_times.clear() + self._cache_order.clear() + self._key_sizes.clear() + self._current_size = 0 + logger.debug("clear_cache: cleared all cache data") + + def __repr__(self) -> str: + """Return string representation of the cache store.""" + return ( + f"{self.__class__.__name__}(" + f"store={self._store!r}, " + f"cache_store={self._cache!r}, " + f"max_age_seconds={self.max_age_seconds}, " + f"max_size={self.max_size}, " + f"current_size={self._current_size}, " + f"cached_keys={len(self._cache_order)})" + ) diff --git a/tests/test_experimental/test_cache_store.py b/tests/test_experimental/test_cache_store.py new file mode 100644 index 0000000000..d4a45f78f1 --- /dev/null +++ b/tests/test_experimental/test_cache_store.py @@ -0,0 +1,864 @@ +""" +Tests for the dual-store cache implementation. +""" + +import asyncio +import time + +import pytest + +from zarr.abc.store import Store +from zarr.core.buffer.core import default_buffer_prototype +from zarr.core.buffer.cpu import Buffer as CPUBuffer +from zarr.experimental.cache_store import CacheStore +from zarr.storage import MemoryStore + + +class TestCacheStore: + """Test the dual-store cache implementation.""" + + @pytest.fixture + def source_store(self) -> MemoryStore: + """Create a source store with some test data.""" + return MemoryStore() + + @pytest.fixture + def cache_store(self) -> MemoryStore: + """Create an empty cache store.""" + return MemoryStore() + + @pytest.fixture + def cached_store(self, source_store: Store, cache_store: Store) -> CacheStore: + """Create a cached store instance.""" + return CacheStore(source_store, cache_store=cache_store, key_insert_times={}) + + async def test_basic_caching(self, cached_store: CacheStore, source_store: Store) -> None: + """Test basic cache functionality.""" + # Store some data + test_data = CPUBuffer.from_bytes(b"test data") + await cached_store.set("test_key", test_data) + + # Verify it's in both stores + assert await source_store.exists("test_key") + assert await cached_store._cache.exists("test_key") + + # Retrieve and verify caching works + result = await cached_store.get("test_key", default_buffer_prototype()) + assert result is not None + assert result.to_bytes() == b"test data" + + async def test_cache_miss_and_population( + self, cached_store: CacheStore, source_store: Store + ) -> None: + """Test cache miss and subsequent population.""" + # Put data directly in source store (bypassing cache) + test_data = CPUBuffer.from_bytes(b"source data") + await source_store.set("source_key", test_data) + + # First access should miss cache but populate it + result = await cached_store.get("source_key", default_buffer_prototype()) + assert result is not None + assert result.to_bytes() == b"source data" + + # Verify data is now in cache + assert await cached_store._cache.exists("source_key") + + async def test_cache_expiration(self) -> None: + """Test cache expiration based on max_age_seconds.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_age_seconds=1, # 1 second expiration + key_insert_times={}, + ) + + # Store data + test_data = CPUBuffer.from_bytes(b"expiring data") + await cached_store.set("expire_key", test_data) + + # Should be fresh initially (if _is_key_fresh method exists) + if hasattr(cached_store, "_is_key_fresh"): + assert cached_store._is_key_fresh("expire_key") + + # Wait for expiration + await asyncio.sleep(1.1) + + # Should now be stale + assert not cached_store._is_key_fresh("expire_key") + else: + # Skip freshness check if method doesn't exist + await asyncio.sleep(1.1) + # Just verify the data is still accessible + result = await cached_store.get("expire_key", default_buffer_prototype()) + assert result is not None + + async def test_cache_set_data_false(self, source_store: Store, cache_store: Store) -> None: + """Test behavior when cache_set_data=False.""" + cached_store = CacheStore( + source_store, cache_store=cache_store, cache_set_data=False, key_insert_times={} + ) + + test_data = CPUBuffer.from_bytes(b"no cache data") + await cached_store.set("no_cache_key", test_data) + + # Data should be in source but not cache + assert await source_store.exists("no_cache_key") + assert not await cache_store.exists("no_cache_key") + + async def test_delete_removes_from_both_stores(self, cached_store: CacheStore) -> None: + """Test that delete removes from both source and cache.""" + test_data = CPUBuffer.from_bytes(b"delete me") + await cached_store.set("delete_key", test_data) + + # Verify in both stores + assert await cached_store._store.exists("delete_key") + assert await cached_store._cache.exists("delete_key") + + # Delete + await cached_store.delete("delete_key") + + # Verify removed from both + assert not await cached_store._store.exists("delete_key") + assert not await cached_store._cache.exists("delete_key") + + async def test_exists_checks_source_store( + self, cached_store: CacheStore, source_store: Store + ) -> None: + """Test that exists() checks the source store (source of truth).""" + # Put data directly in source + test_data = CPUBuffer.from_bytes(b"exists test") + await source_store.set("exists_key", test_data) + + # Should exist even though not in cache + assert await cached_store.exists("exists_key") + + async def test_list_operations(self, cached_store: CacheStore, source_store: Store) -> None: + """Test listing operations delegate to source store.""" + # Add some test data + test_data = CPUBuffer.from_bytes(b"list test") + await cached_store.set("list/item1", test_data) + await cached_store.set("list/item2", test_data) + await cached_store.set("other/item3", test_data) + + # Test list_dir + list_items = [key async for key in cached_store.list_dir("list/")] + assert len(list_items) >= 2 # Should include our items + + # Test list_prefix + prefix_items = [key async for key in cached_store.list_prefix("list/")] + assert len(prefix_items) >= 2 + + async def test_stale_cache_refresh(self) -> None: + """Test that stale cache entries are refreshed from source.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, cache_store=cache_store, max_age_seconds=1, key_insert_times={} + ) + + # Store initial data + old_data = CPUBuffer.from_bytes(b"old data") + await cached_store.set("refresh_key", old_data) + + # Wait for expiration + await asyncio.sleep(1.1) + + # Update source store directly (simulating external update) + new_data = CPUBuffer.from_bytes(b"new data") + await source_store.set("refresh_key", new_data) + + # Access should refresh from source when cache is stale + result = await cached_store.get("refresh_key", default_buffer_prototype()) + assert result is not None + assert result.to_bytes() == b"new data" + + async def test_infinity_max_age(self, cached_store: CacheStore) -> None: + """Test that 'infinity' max_age means cache never expires.""" + # Skip test if _is_key_fresh method doesn't exist + if not hasattr(cached_store, "_is_key_fresh"): + pytest.skip("_is_key_fresh method not implemented") + + test_data = CPUBuffer.from_bytes(b"eternal data") + await cached_store.set("eternal_key", test_data) + + # Should always be fresh + assert cached_store._is_key_fresh("eternal_key") + + # Even after time passes + await asyncio.sleep(0.1) + assert cached_store._is_key_fresh("eternal_key") + + async def test_cache_returns_cached_data_for_performance( + self, cached_store: CacheStore, source_store: Store + ) -> None: + """Test that cache returns cached data for performance, even if not in source.""" + # Skip test if key_insert_times attribute doesn't exist + if not hasattr(cached_store, "key_insert_times"): + pytest.skip("key_insert_times attribute not implemented") + + # Put data in cache but not source (simulates orphaned cache entry) + test_data = CPUBuffer.from_bytes(b"orphaned data") + await cached_store._cache.set("orphan_key", test_data) + cached_store.key_insert_times["orphan_key"] = time.monotonic() + + # Cache should return data for performance (no source verification) + result = await cached_store.get("orphan_key", default_buffer_prototype()) + assert result is not None + assert result.to_bytes() == b"orphaned data" + + # Cache entry should remain (performance optimization) + assert await cached_store._cache.exists("orphan_key") + assert "orphan_key" in cached_store.key_insert_times + + async def test_cache_coherency_through_expiration(self) -> None: + """Test that cache coherency is managed through cache expiration, not source verification.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_age_seconds=1, # Short expiration for coherency + ) + + # Add data to both stores + test_data = CPUBuffer.from_bytes(b"original data") + await cached_store.set("coherency_key", test_data) + + # Remove from source (simulating external deletion) + await source_store.delete("coherency_key") + + # Cache should still return cached data (performance optimization) + result = await cached_store.get("coherency_key", default_buffer_prototype()) + assert result is not None + assert result.to_bytes() == b"original data" + + # Wait for cache expiration + await asyncio.sleep(1.1) + + # Now stale cache should be refreshed from source + result = await cached_store.get("coherency_key", default_buffer_prototype()) + assert result is None # Key no longer exists in source + + async def test_cache_info(self, cached_store: CacheStore) -> None: + """Test cache_info method returns correct information.""" + # Test initial state + info = cached_store.cache_info() + + # Check all expected keys are present + expected_keys = { + "cache_store_type", + "max_age_seconds", + "max_size", + "current_size", + "cache_set_data", + "tracked_keys", + "cached_keys", + } + assert set(info.keys()) == expected_keys + + # Check initial values + assert info["cache_store_type"] == "MemoryStore" + assert info["max_age_seconds"] == "infinity" + assert info["max_size"] is None # Default unlimited + assert info["current_size"] == 0 + assert info["cache_set_data"] is True + assert info["tracked_keys"] == 0 + assert info["cached_keys"] == 0 + + # Add some data and verify tracking + test_data = CPUBuffer.from_bytes(b"test data for cache info") + await cached_store.set("info_test_key", test_data) + + # Check updated info + updated_info = cached_store.cache_info() + assert updated_info["tracked_keys"] == 1 + assert updated_info["cached_keys"] == 1 + assert updated_info["current_size"] > 0 # Should have some size now + + async def test_cache_info_with_max_size(self) -> None: + """Test cache_info with max_size configuration.""" + source_store = MemoryStore() + cache_store = MemoryStore() + + # Create cache with specific max_size and max_age + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_size=1024, + max_age_seconds=300, + key_insert_times={}, + ) + + info = cached_store.cache_info() + assert info["max_size"] == 1024 + assert info["max_age_seconds"] == 300 + assert info["current_size"] == 0 + + async def test_clear_cache(self, cached_store: CacheStore) -> None: + """Test clear_cache method clears all cache data and tracking.""" + # Add some test data + test_data1 = CPUBuffer.from_bytes(b"test data 1") + test_data2 = CPUBuffer.from_bytes(b"test data 2") + + await cached_store.set("clear_test_1", test_data1) + await cached_store.set("clear_test_2", test_data2) + + # Verify data is cached + info_before = cached_store.cache_info() + assert info_before["tracked_keys"] == 2 + assert info_before["cached_keys"] == 2 + assert info_before["current_size"] > 0 + + # Verify data exists in cache + assert await cached_store._cache.exists("clear_test_1") + assert await cached_store._cache.exists("clear_test_2") + + # Clear the cache + await cached_store.clear_cache() + + # Verify cache is cleared + info_after = cached_store.cache_info() + assert info_after["tracked_keys"] == 0 + assert info_after["cached_keys"] == 0 + assert info_after["current_size"] == 0 + + # Verify data is removed from cache store (if it supports clear) + if hasattr(cached_store._cache, "clear"): + # If cache store supports clear, all data should be gone + assert not await cached_store._cache.exists("clear_test_1") + assert not await cached_store._cache.exists("clear_test_2") + + # Verify data still exists in source store + assert await cached_store._store.exists("clear_test_1") + assert await cached_store._store.exists("clear_test_2") + + async def test_max_age_infinity(self) -> None: + """Test cache with infinite max age.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_age_seconds="infinity") + + # Add data and verify it never expires + test_data = CPUBuffer.from_bytes(b"test data") + await cached_store.set("test_key", test_data) + + # Even after time passes, key should be fresh + assert cached_store._is_key_fresh("test_key") + + async def test_max_age_numeric(self) -> None: + """Test cache with numeric max age.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_age_seconds=1, # 1 second + ) + + # Add data + test_data = CPUBuffer.from_bytes(b"test data") + await cached_store.set("test_key", test_data) + + # Key should be fresh initially + assert cached_store._is_key_fresh("test_key") + + # Manually set old timestamp to test expiration + cached_store.key_insert_times["test_key"] = time.monotonic() - 2 # 2 seconds ago + + # Key should now be stale + assert not cached_store._is_key_fresh("test_key") + + async def test_cache_set_data_disabled(self) -> None: + """Test cache behavior when cache_set_data is False.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, cache_set_data=False) + + # Set data + test_data = CPUBuffer.from_bytes(b"test data") + await cached_store.set("test_key", test_data) + + # Data should be in source but not in cache + assert await source_store.exists("test_key") + assert not await cache_store.exists("test_key") + + # Cache info should show no cached data + info = cached_store.cache_info() + assert info["cache_set_data"] is False + assert info["cached_keys"] == 0 + + async def test_eviction_with_max_size(self) -> None: + """Test LRU eviction when max_size is exceeded.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_size=100, # Small cache size + ) + + # Add data that exceeds cache size + small_data = CPUBuffer.from_bytes(b"a" * 40) # 40 bytes + medium_data = CPUBuffer.from_bytes(b"b" * 40) # 40 bytes + large_data = CPUBuffer.from_bytes(b"c" * 40) # 40 bytes (would exceed 100 byte limit) + + # Set first two items + await cached_store.set("key1", small_data) + await cached_store.set("key2", medium_data) + + # Cache should have 2 items + info = cached_store.cache_info() + assert info["cached_keys"] == 2 + assert info["current_size"] == 80 + + # Add third item - should trigger eviction of first item + await cached_store.set("key3", large_data) + + # Cache should still have items but first one may be evicted + info = cached_store.cache_info() + assert info["current_size"] <= 100 + + async def test_value_exceeds_max_size(self) -> None: + """Test behavior when a single value exceeds max_size.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_size=50, # Small cache size + ) + + # Try to cache data larger than max_size + large_data = CPUBuffer.from_bytes(b"x" * 100) # 100 bytes > 50 byte limit + await cached_store.set("large_key", large_data) + + # Data should be in source but not cached + assert await source_store.exists("large_key") + info = cached_store.cache_info() + assert info["cached_keys"] == 0 + assert info["current_size"] == 0 + + async def test_get_nonexistent_key(self) -> None: + """Test getting a key that doesn't exist in either store.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store) + + # Try to get nonexistent key + result = await cached_store.get("nonexistent", default_buffer_prototype()) + assert result is None + + # Should not create any cache entries + info = cached_store.cache_info() + assert info["cached_keys"] == 0 + + async def test_delete_both_stores(self) -> None: + """Test that delete removes from both source and cache stores.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store) + + # Add data + test_data = CPUBuffer.from_bytes(b"test data") + await cached_store.set("test_key", test_data) + + # Verify it's in both stores + assert await source_store.exists("test_key") + assert await cache_store.exists("test_key") + + # Delete + await cached_store.delete("test_key") + + # Verify it's removed from both + assert not await source_store.exists("test_key") + assert not await cache_store.exists("test_key") + + # Verify tracking is updated + info = cached_store.cache_info() + assert info["cached_keys"] == 0 + + async def test_invalid_max_age_seconds(self) -> None: + """Test that invalid max_age_seconds values raise ValueError.""" + source_store = MemoryStore() + cache_store = MemoryStore() + + with pytest.raises(ValueError, match="max_age_seconds string value must be 'infinity'"): + CacheStore(source_store, cache_store=cache_store, max_age_seconds="invalid") + + async def test_unlimited_cache_size(self) -> None: + """Test behavior when max_size is None (unlimited).""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_size=None, # Unlimited cache + ) + + # Add large amounts of data + for i in range(10): + large_data = CPUBuffer.from_bytes(b"x" * 1000) # 1KB each + await cached_store.set(f"large_key_{i}", large_data) + + # All should be cached since there's no size limit + info = cached_store.cache_info() + assert info["cached_keys"] == 10 + assert info["current_size"] == 10000 # 10 * 1000 bytes + + async def test_evict_key_exception_handling(self) -> None: + """Test exception handling in _evict_key method.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=100) + + # Add some data + test_data = CPUBuffer.from_bytes(b"test data") + await cached_store.set("test_key", test_data) + + # Manually corrupt the tracking to trigger exception + # Remove from one structure but not others to create inconsistency + del cached_store._cache_order["test_key"] + + # Try to evict - should handle the KeyError gracefully + await cached_store._evict_key("test_key") + + # Should still work and not crash + info = cached_store.cache_info() + assert isinstance(info, dict) + + async def test_get_no_cache_delete_tracking(self) -> None: + """Test _get_no_cache when key doesn't exist and needs cleanup.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store) + + # First, add key to cache tracking but not to source + test_data = CPUBuffer.from_bytes(b"test data") + await cache_store.set("phantom_key", test_data) + await cached_store._cache_value("phantom_key", test_data) + + # Verify it's in tracking + assert "phantom_key" in cached_store._cache_order + assert "phantom_key" in cached_store.key_insert_times + + # Now try to get it - since it's not in source, should clean up tracking + result = await cached_store._get_no_cache("phantom_key", default_buffer_prototype()) + assert result is None + + # Should have cleaned up tracking + assert "phantom_key" not in cached_store._cache_order + assert "phantom_key" not in cached_store.key_insert_times + + async def test_accommodate_value_no_max_size(self) -> None: + """Test _accommodate_value early return when max_size is None.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + source_store, + cache_store=cache_store, + max_size=None, # No size limit + ) + + # This should return early without doing anything + await cached_store._accommodate_value(1000000) # Large value + + # Should not affect anything since max_size is None + info = cached_store.cache_info() + assert info["current_size"] == 0 + + async def test_concurrent_set_operations(self) -> None: + """Test that concurrent set operations don't corrupt cache size tracking.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=1000) + + # Create 10 concurrent set operations + async def set_data(key: str) -> None: + data = CPUBuffer.from_bytes(b"x" * 50) + await cached_store.set(key, data) + + # Run concurrently + await asyncio.gather(*[set_data(f"key_{i}") for i in range(10)]) + + info = cached_store.cache_info() + # Expected: 10 keys * 50 bytes = 500 bytes + assert info["cached_keys"] == 10 + assert info["current_size"] == 500 # WOULD FAIL due to race condition + + async def test_concurrent_eviction_race(self) -> None: + """Test concurrent evictions don't corrupt size tracking.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=200) + + # Fill cache to near capacity + data = CPUBuffer.from_bytes(b"x" * 80) + await cached_store.set("key1", data) + await cached_store.set("key2", data) + + # Now trigger two concurrent sets that both need to evict + async def set_large(key: str) -> None: + large_data = CPUBuffer.from_bytes(b"y" * 100) + await cached_store.set(key, large_data) + + await asyncio.gather(set_large("key3"), set_large("key4")) + + info = cached_store.cache_info() + # Size should be consistent with tracked keys + assert info["current_size"] <= 200 # Might pass + # But verify actual cache store size matches tracking + total_size = sum(cached_store._key_sizes.get(k, 0) for k in cached_store._cache_order) + assert total_size == info["current_size"] # WOULD FAIL + + async def test_concurrent_get_and_evict(self) -> None: + """Test get operations during eviction don't cause corruption.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=100) + + # Setup + data = CPUBuffer.from_bytes(b"x" * 40) + await cached_store.set("key1", data) + await cached_store.set("key2", data) + + # Concurrent: read key1 while adding key3 (triggers eviction) + async def read_key() -> None: + for _ in range(100): + await cached_store.get("key1", default_buffer_prototype()) + + async def write_key() -> None: + for i in range(10): + new_data = CPUBuffer.from_bytes(b"y" * 40) + await cached_store.set(f"new_{i}", new_data) + + await asyncio.gather(read_key(), write_key()) + + # Verify consistency + info = cached_store.cache_info() + assert info["current_size"] <= 100 + assert len(cached_store._cache_order) == len(cached_store._key_sizes) + + async def test_eviction_actually_deletes_from_cache_store(self) -> None: + """Test that eviction removes keys from cache_store, not just tracking.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=100) + + # Add data that will be evicted + data1 = CPUBuffer.from_bytes(b"x" * 60) + data2 = CPUBuffer.from_bytes(b"y" * 60) + + await cached_store.set("key1", data1) + + # Verify key1 is in cache_store + assert await cache_store.exists("key1") + + # Add key2, which should evict key1 + await cached_store.set("key2", data2) + + # Check tracking - key1 should be removed + assert "key1" not in cached_store._cache_order + assert "key1" not in cached_store._key_sizes + + # CRITICAL: key1 should also be removed from cache_store + assert not await cache_store.exists("key1"), ( + "Evicted key still exists in cache_store! _evict_key doesn't actually delete." + ) + + # But key1 should still exist in source store + assert await source_store.exists("key1") + + async def test_eviction_no_orphaned_keys(self) -> None: + """Test that eviction doesn't leave orphaned keys in cache_store.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=150) + + # Add multiple keys that will cause evictions + for i in range(10): + data = CPUBuffer.from_bytes(b"x" * 60) + await cached_store.set(f"key_{i}", data) + + # Check tracking + info = cached_store.cache_info() + tracked_keys = info["cached_keys"] + + # Count actual keys in cache_store + actual_keys = 0 + async for _ in cache_store.list(): + actual_keys += 1 + + # Cache store should have same number of keys as tracking + assert actual_keys == tracked_keys, ( + f"Cache store has {actual_keys} keys but tracking shows {tracked_keys}. " + f"Eviction doesn't delete from cache_store!" + ) + + async def test_size_accounting_with_key_updates(self) -> None: + """Test that updating the same key replaces size instead of accumulating.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=500) + + # Set initial value + data1 = CPUBuffer.from_bytes(b"x" * 100) + await cached_store.set("same_key", data1) + + info1 = cached_store.cache_info() + assert info1["current_size"] == 100 + + # Update with different size + data2 = CPUBuffer.from_bytes(b"y" * 200) + await cached_store.set("same_key", data2) + + info2 = cached_store.cache_info() + + # Should be 200, not 300 (update replaces, doesn't accumulate) + assert info2["current_size"] == 200, ( + f"Expected size 200 but got {info2['current_size']}. " + "Updating same key should replace, not accumulate." + ) + + async def test_all_tracked_keys_exist_in_cache_store(self) -> None: + """Test invariant: all keys in tracking should exist in cache_store.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(source_store, cache_store=cache_store, max_size=500) + + # Add some data + for i in range(5): + data = CPUBuffer.from_bytes(b"x" * 50) + await cached_store.set(f"key_{i}", data) + + # Every key in tracking should exist in cache_store + for key in cached_store._cache_order: + assert await cache_store.exists(key), ( + f"Key '{key}' is tracked but doesn't exist in cache_store" + ) + + # Every key in _key_sizes should exist in cache_store + for key in cached_store._key_sizes: + assert await cache_store.exists(key), ( + f"Key '{key}' has size tracked but doesn't exist in cache_store" + ) + + # Additional coverage tests for 100% coverage + + async def test_cache_store_requires_delete_support(self) -> None: + """Test that CacheStore validates cache_store supports deletes.""" + from unittest.mock import MagicMock + + # Create a mock store that doesn't support deletes + source_store = MemoryStore() + cache_store = MagicMock() + cache_store.supports_deletes = False + + with pytest.raises(ValueError, match="does not support deletes"): + CacheStore(store=source_store, cache_store=cache_store) + + async def test_evict_key_exception_handling_with_real_error( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """Test _evict_key exception handling when deletion fails.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store, max_size=100) + + # Set up a key in tracking + buffer = CPUBuffer.from_bytes(b"test data") + await cached_store.set("test_key", buffer) + + # Mock the cache delete to raise an exception + async def failing_delete(key: str) -> None: + raise RuntimeError("Simulated cache deletion failure") + + monkeypatch.setattr(cache_store, "delete", failing_delete) + + # Attempt to evict should raise the exception + with pytest.raises(RuntimeError, match="Simulated cache deletion failure"): + async with cached_store._lock: + await cached_store._evict_key("test_key") + + async def test_cache_stats_method(self) -> None: + """Test cache_stats method returns correct statistics.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store, max_size=1000) + + # Initially, stats should be zero + stats = cached_store.cache_stats() + assert stats["hits"] == 0 + assert stats["misses"] == 0 + assert stats["evictions"] == 0 + assert stats["total_requests"] == 0 + assert stats["hit_rate"] == 0.0 + + # Perform some operations + buffer = CPUBuffer.from_bytes(b"x" * 100) + + # Write to source store directly to avoid affecting stats + await source_store.set("key1", buffer) + + # First get is a miss (not in cache yet) + result1 = await cached_store.get("key1", default_buffer_prototype()) + assert result1 is not None + + # Second get is a hit (now in cache) + result2 = await cached_store.get("key1", default_buffer_prototype()) + assert result2 is not None + + stats = cached_store.cache_stats() + assert stats["hits"] == 1 + assert stats["misses"] == 1 + assert stats["total_requests"] == 2 + assert stats["hit_rate"] == 0.5 + + async def test_cache_stats_with_evictions(self) -> None: + """Test cache_stats tracks evictions correctly.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + store=source_store, + cache_store=cache_store, + max_size=150, # Small size to force eviction + ) + + # Add items that will trigger eviction + buffer1 = CPUBuffer.from_bytes(b"x" * 100) + buffer2 = CPUBuffer.from_bytes(b"y" * 100) + + await cached_store.set("key1", buffer1) + await cached_store.set("key2", buffer2) # Should evict key1 + + stats = cached_store.cache_stats() + assert stats["evictions"] == 1 + + def test_repr_method(self) -> None: + """Test __repr__ returns useful string representation.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + store=source_store, cache_store=cache_store, max_age_seconds=60, max_size=1024 + ) + + repr_str = repr(cached_store) + + # Check that repr contains key information + assert "CacheStore" in repr_str + assert "max_age_seconds=60" in repr_str + assert "max_size=1024" in repr_str + assert "current_size=0" in repr_str + assert "cached_keys=0" in repr_str + + async def test_cache_stats_zero_division_protection(self) -> None: + """Test cache_stats handles zero requests correctly.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store) + + # With no requests, hit_rate should be 0.0 (not NaN or error) + stats = cached_store.cache_stats() + assert stats["hit_rate"] == 0.0 + assert stats["total_requests"] == 0 From be519b006f3073c3c0d56801cd2daa597538fd59 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 2 Oct 2025 13:12:13 +0100 Subject: [PATCH 124/468] Make ObjectStore a generic class (#3486) Co-authored-by: Davis Bennett --- src/zarr/storage/_obstore.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index 7ef0b40628..5c2197ecf6 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -4,7 +4,7 @@ import contextlib import pickle from collections import defaultdict -from typing import TYPE_CHECKING, TypedDict +from typing import TYPE_CHECKING, Generic, Self, TypedDict, TypeVar from zarr.abc.store import ( ByteRequest, @@ -34,7 +34,10 @@ ) -class ObjectStore(Store): +T_Store = TypeVar("T_Store", bound="_UpstreamObjectStore") + + +class ObjectStore(Store, Generic[T_Store]): """ Store that uses obstore for fast read/write from AWS, GCP, Azure. @@ -51,7 +54,7 @@ class ObjectStore(Store): raise an issue with any comments/concerns about the store. """ - store: _UpstreamObjectStore + store: T_Store """The underlying obstore instance.""" def __eq__(self, value: object) -> bool: @@ -61,15 +64,15 @@ def __eq__(self, value: object) -> bool: if not self.read_only == value.read_only: return False - return self.store == value.store + return self.store == value.store # type: ignore[no-any-return] - def __init__(self, store: _UpstreamObjectStore, *, read_only: bool = False) -> None: + def __init__(self, store: T_Store, *, read_only: bool = False) -> None: if not store.__class__.__module__.startswith("obstore"): raise TypeError(f"expected ObjectStore class, got {store!r}") super().__init__(read_only=read_only) self.store = store - def with_read_only(self, read_only: bool = False) -> ObjectStore: + def with_read_only(self, read_only: bool = False) -> Self: # docstring inherited return type(self)( store=self.store, From e0751ab9ca84efebb4a769b3bbbbc61eb2f330f6 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 2 Oct 2025 17:24:44 +0100 Subject: [PATCH 125/468] Fix typing in store tests (#3394) * Fix typing in test_core * Fix typing in test_logging * Fix typing in test_object * Fix typing in test_stateful * Fix typing in test_wrapper * Fix wrapper store tests * Fix store in test * Fix merge conflicts * Adapt ObjectStore tests for new generic class * Fix generic assignment in tests --------- Co-authored-by: Davis Bennett --- pyproject.toml | 10 ++--- src/zarr/storage/_wrapper.py | 3 +- tests/test_store/test_core.py | 52 ++++++++++++++++--------- tests/test_store/test_logging.py | 48 +++++++++++++---------- tests/test_store/test_object.py | 45 +++++++++++++-------- tests/test_store/test_stateful.py | 8 ++-- tests/test_store/test_wrapper.py | 65 ++++++++++++++++++------------- 7 files changed, 139 insertions(+), 92 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d72eef9dbc..5733f42950 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -359,6 +359,11 @@ module = [ "tests.test_store.test_memory", "tests.test_codecs.test_codecs", "tests.test_metadata.*", + "tests.test_store.test_core", + "tests.test_store.test_logging", + "tests.test_store.test_object", + "tests.test_store.test_stateful", + "tests.test_store.test_wrapper", ] strict = false @@ -366,11 +371,6 @@ strict = false # and fix the errors [[tool.mypy.overrides]] module = [ - "tests.test_store.test_core", - "tests.test_store.test_logging", - "tests.test_store.test_object", - "tests.test_store.test_stateful", - "tests.test_store.test_wrapper", "tests.test_group", "tests.test_indexing", "tests.test_properties", diff --git a/src/zarr/storage/_wrapper.py b/src/zarr/storage/_wrapper.py index ba300a4085..64a5b2d83c 100644 --- a/src/zarr/storage/_wrapper.py +++ b/src/zarr/storage/_wrapper.py @@ -7,8 +7,9 @@ from types import TracebackType from typing import Any, Self + from zarr.abc.buffer import Buffer from zarr.abc.store import ByteRequest - from zarr.core.buffer import Buffer, BufferPrototype + from zarr.core.buffer import BufferPrototype from zarr.abc.store import Store diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index a3850de90f..6589c68e09 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -1,5 +1,7 @@ import tempfile +from collections.abc import Callable, Generator from pathlib import Path +from typing import Any, Literal import pytest from _pytest.compat import LEGACY_PATH @@ -21,7 +23,9 @@ @pytest.fixture( params=["none", "temp_dir_str", "temp_dir_path", "store_path", "memory_store", "dict"] ) -def store_like(request): +def store_like( + request: pytest.FixtureRequest, +) -> Generator[None | str | Path | StorePath | MemoryStore | dict[Any, Any], None, None]: if request.param == "none": yield None elif request.param == "temp_dir_str": @@ -42,7 +46,7 @@ def store_like(request): @pytest.mark.parametrize("write_group", [True, False]) @pytest.mark.parametrize("zarr_format", [2, 3]) async def test_contains_group( - local_store, path: str, write_group: bool, zarr_format: ZarrFormat + local_store: LocalStore, path: str, write_group: bool, zarr_format: ZarrFormat ) -> None: """ Test that the contains_group method correctly reports the existence of a group. @@ -58,7 +62,7 @@ async def test_contains_group( @pytest.mark.parametrize("write_array", [True, False]) @pytest.mark.parametrize("zarr_format", [2, 3]) async def test_contains_array( - local_store, path: str, write_array: bool, zarr_format: ZarrFormat + local_store: LocalStore, path: str, write_array: bool, zarr_format: ZarrFormat ) -> None: """ Test that the contains array method correctly reports the existence of an array. @@ -71,13 +75,15 @@ async def test_contains_array( @pytest.mark.parametrize("func", [contains_array, contains_group]) -async def test_contains_invalid_format_raises(local_store, func: callable) -> None: +async def test_contains_invalid_format_raises( + local_store: LocalStore, func: Callable[[Any], Any] +) -> None: """ Test contains_group and contains_array raise errors for invalid zarr_formats """ store_path = StorePath(local_store) with pytest.raises(ValueError): - assert await func(store_path, zarr_format="3.0") + assert await func(store_path, zarr_format="3.0") # type: ignore[call-arg] @pytest.mark.parametrize("path", [None, "", "bar"]) @@ -113,29 +119,37 @@ async def test_make_store_path_local( @pytest.mark.parametrize("path", [None, "", "bar"]) @pytest.mark.parametrize("mode", ["r", "w"]) async def test_make_store_path_store_path( - tmpdir: LEGACY_PATH, path: str, mode: AccessModeLiteral + tmp_path: Path, path: str, mode: AccessModeLiteral ) -> None: """ Test invoking make_store_path when the input is another store_path. In particular we want to ensure that a new path is handled correctly. """ ro = mode == "r" - store_like = await StorePath.open(LocalStore(str(tmpdir), read_only=ro), path="root", mode=mode) + store_like = await StorePath.open( + LocalStore(str(tmp_path), read_only=ro), path="root", mode=mode + ) store_path = await make_store_path(store_like, path=path, mode=mode) assert isinstance(store_path.store, LocalStore) - assert Path(store_path.store.root) == Path(tmpdir) + assert Path(store_path.store.root) == tmp_path path_normalized = normalize_path(path) assert store_path.path == (store_like / path_normalized).path assert store_path.read_only == ro @pytest.mark.parametrize("modes", [(True, "w"), (False, "x")]) -async def test_store_path_invalid_mode_raises(tmpdir: LEGACY_PATH, modes: tuple) -> None: +async def test_store_path_invalid_mode_raises( + tmp_path: Path, modes: tuple[bool, Literal["w", "x"]] +) -> None: """ Test that ValueErrors are raise for invalid mode. """ with pytest.raises(ValueError): - await StorePath.open(LocalStore(str(tmpdir), read_only=modes[0]), path=None, mode=modes[1]) + await StorePath.open( + LocalStore(str(tmp_path), read_only=modes[0]), + path="", + mode=modes[1], # type:ignore[arg-type] + ) async def test_make_store_path_invalid() -> None: @@ -143,10 +157,10 @@ async def test_make_store_path_invalid() -> None: Test that invalid types raise TypeError """ with pytest.raises(TypeError): - await make_store_path(1) # type: ignore[arg-type] + await make_store_path(1) -async def test_make_store_path_fsspec(monkeypatch) -> None: +async def test_make_store_path_fsspec() -> None: pytest.importorskip("fsspec") pytest.importorskip("requests") pytest.importorskip("aiohttp") @@ -161,7 +175,7 @@ async def test_make_store_path_storage_options_raises(store_like: StoreLike) -> async def test_unsupported() -> None: with pytest.raises(TypeError, match="Unsupported type for store_like: 'int'"): - await make_store_path(1) # type: ignore[arg-type] + await make_store_path(1) @pytest.mark.parametrize( @@ -184,12 +198,12 @@ def test_normalize_path_upath() -> None: assert normalize_path(upath.UPath("foo/bar")) == "foo/bar" -def test_normalize_path_none(): +def test_normalize_path_none() -> None: assert normalize_path(None) == "" @pytest.mark.parametrize("path", [".", ".."]) -def test_normalize_path_invalid(path: str): +def test_normalize_path_invalid(path: str) -> None: with pytest.raises(ValueError): normalize_path(path) @@ -230,7 +244,7 @@ def test_invalid(paths: tuple[str, str]) -> None: _normalize_paths(paths) -def test_normalize_path_keys(): +def test_normalize_path_keys() -> None: """ Test that ``_normalize_path_keys`` just applies the normalize_path function to each key of its input @@ -272,10 +286,10 @@ def test_different_open_mode(tmp_path: LEGACY_PATH) -> None: # Test with a store that doesn't implement .with_read_only() zarr_path = tmp_path / "foo.zarr" - store = ZipStore(zarr_path, mode="w") - zarr.create((100,), store=store, zarr_format=2, path="a") + zip_store = ZipStore(zarr_path, mode="w") + zarr.create((100,), store=zip_store, zarr_format=2, path="a") with pytest.raises( ValueError, match="Store is not read-only but mode is 'r'. Unable to create a read-only copy of the store. Please use a read-only store or a storage class that implements .with_read_only().", ): - zarr.open_array(store=store, path="a", zarr_format=2, mode="r") + zarr.open_array(store=zip_store, path="a", zarr_format=2, mode="r") diff --git a/tests/test_store/test_logging.py b/tests/test_store/test_logging.py index d99ac5dc4f..e4a0f64b48 100644 --- a/tests/test_store/test_logging.py +++ b/tests/test_store/test_logging.py @@ -1,7 +1,7 @@ from __future__ import annotations import logging -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, TypedDict import pytest @@ -11,49 +11,57 @@ from zarr.testing.store import StoreTests if TYPE_CHECKING: - from _pytest.compat import LEGACY_PATH + from pathlib import Path from zarr.abc.store import Store -class TestLoggingStore(StoreTests[LoggingStore, cpu.Buffer]): - store_cls = LoggingStore +class StoreKwargs(TypedDict): + store: LocalStore + log_level: str + + +class TestLoggingStore(StoreTests[LoggingStore[LocalStore], cpu.Buffer]): + # store_cls is needed to do an isintsance check, so can't be a subscripted generic + store_cls = LoggingStore # type: ignore[assignment] buffer_cls = cpu.Buffer - async def get(self, store: LoggingStore, key: str) -> Buffer: + async def get(self, store: LoggingStore[LocalStore], key: str) -> Buffer: return self.buffer_cls.from_bytes((store._store.root / key).read_bytes()) - async def set(self, store: LoggingStore, key: str, value: Buffer) -> None: + async def set(self, store: LoggingStore[LocalStore], key: str, value: Buffer) -> None: parent = (store._store.root / key).parent if not parent.exists(): parent.mkdir(parents=True) (store._store.root / key).write_bytes(value.to_bytes()) @pytest.fixture - def store_kwargs(self, tmpdir: LEGACY_PATH) -> dict[str, str]: - return {"store": LocalStore(str(tmpdir)), "log_level": "DEBUG"} + def store_kwargs(self, tmp_path: Path) -> StoreKwargs: + return {"store": LocalStore(str(tmp_path)), "log_level": "DEBUG"} @pytest.fixture - def open_kwargs(self, tmpdir) -> dict[str, str]: - return {"store_cls": LocalStore, "root": str(tmpdir), "log_level": "DEBUG"} + def open_kwargs(self, tmp_path: Path) -> dict[str, type[LocalStore] | str]: + return {"store_cls": LocalStore, "root": str(tmp_path), "log_level": "DEBUG"} @pytest.fixture - def store(self, store_kwargs: str | dict[str, Buffer] | None) -> LoggingStore: + def store(self, store_kwargs: StoreKwargs) -> LoggingStore[LocalStore]: return self.store_cls(**store_kwargs) - def test_store_supports_writes(self, store: LoggingStore) -> None: + def test_store_supports_writes(self, store: LoggingStore[LocalStore]) -> None: assert store.supports_writes - def test_store_supports_listing(self, store: LoggingStore) -> None: + def test_store_supports_listing(self, store: LoggingStore[LocalStore]) -> None: assert store.supports_listing - def test_store_repr(self, store: LoggingStore) -> None: + def test_store_repr(self, store: LoggingStore[LocalStore]) -> None: assert f"{store!r}" == f"LoggingStore(LocalStore, 'file://{store._store.root.as_posix()}')" - def test_store_str(self, store: LoggingStore) -> None: + def test_store_str(self, store: LoggingStore[LocalStore]) -> None: assert str(store) == f"logging-file://{store._store.root.as_posix()}" - async def test_default_handler(self, local_store, capsys) -> None: + async def test_default_handler( + self, local_store: LocalStore, capsys: pytest.CaptureFixture[str] + ) -> None: # Store and then remove existing handlers to enter default handler code path handlers = logging.getLogger().handlers[:] for h in handlers: @@ -61,7 +69,7 @@ async def test_default_handler(self, local_store, capsys) -> None: # Test logs are sent to stdout wrapped = LoggingStore(store=local_store) buffer = default_buffer_prototype().buffer - res = await wrapped.set("foo/bar/c/0", buffer.from_bytes(b"\x01\x02\x03\x04")) + res = await wrapped.set("foo/bar/c/0", buffer.from_bytes(b"\x01\x02\x03\x04")) # type: ignore[func-returns-value] assert res is None captured = capsys.readouterr() assert len(captured) == 2 @@ -71,7 +79,7 @@ async def test_default_handler(self, local_store, capsys) -> None: for h in handlers: logging.getLogger().addHandler(h) - def test_is_open_setter_raises(self, store: LoggingStore) -> None: + def test_is_open_setter_raises(self, store: LoggingStore[LocalStore]) -> None: "Test that a user cannot change `_is_open` without opening the underlying store." with pytest.raises( NotImplementedError, match="LoggingStore must be opened via the `_open` method" @@ -80,12 +88,12 @@ def test_is_open_setter_raises(self, store: LoggingStore) -> None: @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) -async def test_logging_store(store: Store, caplog) -> None: +async def test_logging_store(store: Store, caplog: pytest.LogCaptureFixture) -> None: wrapped = LoggingStore(store=store, log_level="DEBUG") buffer = default_buffer_prototype().buffer caplog.clear() - res = await wrapped.set("foo/bar/c/0", buffer.from_bytes(b"\x01\x02\x03\x04")) + res = await wrapped.set("foo/bar/c/0", buffer.from_bytes(b"\x01\x02\x03\x04")) # type: ignore[func-returns-value] assert res is None assert len(caplog.record_tuples) == 2 for tup in caplog.record_tuples: diff --git a/tests/test_store/test_object.py b/tests/test_store/test_object.py index 3217069c2d..cc0b44f540 100644 --- a/tests/test_store/test_object.py +++ b/tests/test_store/test_object.py @@ -1,5 +1,6 @@ # ruff: noqa: E402 -from typing import Any +from pathlib import Path +from typing import TypedDict import pytest @@ -16,42 +17,51 @@ from zarr.testing.store import StoreTests -class TestObjectStore(StoreTests[ObjectStore, cpu.Buffer]): - store_cls = ObjectStore +class StoreKwargs(TypedDict): + store: LocalStore + read_only: bool + + +class TestObjectStore(StoreTests[ObjectStore[LocalStore], cpu.Buffer]): + # store_cls is needed to do an isintsance check, so can't be a subscripted generic + store_cls = ObjectStore # type: ignore[assignment] buffer_cls = cpu.Buffer @pytest.fixture - def store_kwargs(self, tmpdir) -> dict[str, Any]: - store = LocalStore(prefix=tmpdir) + def store_kwargs(self, tmp_path: Path) -> StoreKwargs: + store = LocalStore(prefix=tmp_path) return {"store": store, "read_only": False} @pytest.fixture - def store(self, store_kwargs: dict[str, str | bool]) -> ObjectStore: + def store(self, store_kwargs: StoreKwargs) -> ObjectStore[LocalStore]: return self.store_cls(**store_kwargs) - async def get(self, store: ObjectStore, key: str) -> Buffer: + async def get(self, store: ObjectStore[LocalStore], key: str) -> Buffer: assert isinstance(store.store, LocalStore) new_local_store = LocalStore(prefix=store.store.prefix) return self.buffer_cls.from_bytes(obstore.get(new_local_store, key).bytes()) - async def set(self, store: ObjectStore, key: str, value: Buffer) -> None: + async def set(self, store: ObjectStore[LocalStore], key: str, value: Buffer) -> None: assert isinstance(store.store, LocalStore) new_local_store = LocalStore(prefix=store.store.prefix) obstore.put(new_local_store, key, value.to_bytes()) - def test_store_repr(self, store: ObjectStore) -> None: + def test_store_repr(self, store: ObjectStore[LocalStore]) -> None: from fnmatch import fnmatch pattern = "ObjectStore(object_store://LocalStore(*))" assert fnmatch(f"{store!r}", pattern) - def test_store_supports_writes(self, store: ObjectStore) -> None: + def test_store_supports_writes(self, store: ObjectStore[LocalStore]) -> None: assert store.supports_writes - def test_store_supports_listing(self, store: ObjectStore) -> None: + def test_store_supports_partial_writes(self, store: ObjectStore[LocalStore]) -> None: + assert not store.supports_partial_writes + + def test_store_supports_listing(self, store: ObjectStore[LocalStore]) -> None: assert store.supports_listing - def test_store_equal(self, store: ObjectStore) -> None: + def test_store_equal(self, store: ObjectStore[LocalStore]) -> None: """Test store equality""" # Test equality against a different instance type assert store != 0 @@ -59,6 +69,7 @@ def test_store_equal(self, store: ObjectStore) -> None: new_memory_store = ObjectStore(MemoryStore()) assert store != new_memory_store # Test equality against a read only store + assert isinstance(store.store, LocalStore) new_local_store = ObjectStore(LocalStore(prefix=store.store.prefix), read_only=True) assert store != new_local_store # Test two memory stores cannot be equal @@ -68,15 +79,15 @@ def test_store_equal(self, store: ObjectStore) -> None: def test_store_init_raises(self) -> None: """Test __init__ raises appropriate error for improper store type""" with pytest.raises(TypeError): - ObjectStore("path/to/store") + ObjectStore("path/to/store") # type: ignore[type-var] - async def test_store_getsize(self, store: ObjectStore) -> None: + async def test_store_getsize(self, store: ObjectStore[LocalStore]) -> None: buf = cpu.Buffer.from_bytes(b"\x01\x02\x03\x04") await self.set(store, "key", buf) size = await store.getsize("key") assert size == len(buf) - async def test_store_getsize_prefix(self, store: ObjectStore) -> None: + async def test_store_getsize_prefix(self, store: ObjectStore[LocalStore]) -> None: buf = cpu.Buffer.from_bytes(b"\x01\x02\x03\x04") await self.set(store, "c/key1/0", buf) await self.set(store, "c/key2/0", buf) @@ -87,10 +98,10 @@ async def test_store_getsize_prefix(self, store: ObjectStore) -> None: @pytest.mark.slow_hypothesis -def test_zarr_hierarchy(): +def test_zarr_hierarchy() -> None: sync_store = ObjectStore(MemoryStore()) def mk_test_instance_sync() -> ZarrHierarchyStateMachine: return ZarrHierarchyStateMachine(sync_store) - run_state_machine_as_test(mk_test_instance_sync) + run_state_machine_as_test(mk_test_instance_sync) # type: ignore[no-untyped-call] diff --git a/tests/test_store/test_stateful.py b/tests/test_store/test_stateful.py index c0997c3df3..6ea89d91d6 100644 --- a/tests/test_store/test_stateful.py +++ b/tests/test_store/test_stateful.py @@ -16,18 +16,18 @@ @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") -def test_zarr_hierarchy(sync_store: Store): +def test_zarr_hierarchy(sync_store: Store) -> None: def mk_test_instance_sync() -> ZarrHierarchyStateMachine: return ZarrHierarchyStateMachine(sync_store) if isinstance(sync_store, ZipStore): pytest.skip(reason="ZipStore does not support delete") - run_state_machine_as_test(mk_test_instance_sync) + run_state_machine_as_test(mk_test_instance_sync) # type: ignore[no-untyped-call] def test_zarr_store(sync_store: Store) -> None: - def mk_test_instance_sync() -> None: + def mk_test_instance_sync() -> ZarrStoreStateMachine: return ZarrStoreStateMachine(sync_store) if isinstance(sync_store, ZipStore): @@ -38,4 +38,4 @@ def mk_test_instance_sync() -> None: # It assumes that `set` and `delete` are the only two operations that modify state. # But LocalStore, directories can hang around even after a key is delete-d. pytest.skip(reason="Test isn't suitable for LocalStore.") - run_state_machine_as_test(mk_test_instance_sync) + run_state_machine_as_test(mk_test_instance_sync) # type: ignore[no-untyped-call] diff --git a/tests/test_store/test_wrapper.py b/tests/test_store/test_wrapper.py index 4478e1468f..b34a63d5d0 100644 --- a/tests/test_store/test_wrapper.py +++ b/tests/test_store/test_wrapper.py @@ -1,69 +1,80 @@ from __future__ import annotations -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Any, TypedDict import pytest -from zarr.core.buffer.cpu import Buffer, buffer_prototype +from zarr.abc.store import ByteRequest, Store +from zarr.core.buffer import Buffer +from zarr.core.buffer.cpu import Buffer as CPUBuffer +from zarr.core.buffer.cpu import buffer_prototype from zarr.storage import LocalStore, WrapperStore from zarr.testing.store import StoreTests if TYPE_CHECKING: - from _pytest.compat import LEGACY_PATH + from pathlib import Path - from zarr.abc.store import Store from zarr.core.buffer.core import BufferPrototype +class StoreKwargs(TypedDict): + store: LocalStore + + +class OpenKwargs(TypedDict): + store_cls: type[LocalStore] + root: str + + # TODO: fix this warning @pytest.mark.filterwarnings( "ignore:coroutine 'ClientCreatorContext.__aexit__' was never awaited:RuntimeWarning" ) -class TestWrapperStore(StoreTests[WrapperStore, Buffer]): +class TestWrapperStore(StoreTests[WrapperStore[Any], Buffer]): store_cls = WrapperStore - buffer_cls = Buffer + buffer_cls = CPUBuffer - async def get(self, store: WrapperStore, key: str) -> Buffer: + async def get(self, store: WrapperStore[LocalStore], key: str) -> Buffer: return self.buffer_cls.from_bytes((store._store.root / key).read_bytes()) - async def set(self, store: WrapperStore, key: str, value: Buffer) -> None: + async def set(self, store: WrapperStore[LocalStore], key: str, value: Buffer) -> None: parent = (store._store.root / key).parent if not parent.exists(): parent.mkdir(parents=True) (store._store.root / key).write_bytes(value.to_bytes()) @pytest.fixture - def store_kwargs(self, tmpdir: LEGACY_PATH) -> dict[str, str]: - return {"store": LocalStore(str(tmpdir))} + def store_kwargs(self, tmp_path: Path) -> StoreKwargs: + return {"store": LocalStore(str(tmp_path))} @pytest.fixture - def open_kwargs(self, tmpdir) -> dict[str, str]: - return {"store_cls": LocalStore, "root": str(tmpdir)} + def open_kwargs(self, tmp_path: Path) -> OpenKwargs: + return {"store_cls": LocalStore, "root": str(tmp_path)} - def test_store_supports_writes(self, store: WrapperStore) -> None: + def test_store_supports_writes(self, store: WrapperStore[LocalStore]) -> None: assert store.supports_writes - def test_store_supports_listing(self, store: WrapperStore) -> None: + def test_store_supports_listing(self, store: WrapperStore[LocalStore]) -> None: assert store.supports_listing - def test_store_repr(self, store: WrapperStore) -> None: + def test_store_repr(self, store: WrapperStore[LocalStore]) -> None: assert f"{store!r}" == f"WrapperStore(LocalStore, 'file://{store._store.root.as_posix()}')" - def test_store_str(self, store: WrapperStore) -> None: + def test_store_str(self, store: WrapperStore[LocalStore]) -> None: assert str(store) == f"wrapping-file://{store._store.root.as_posix()}" - def test_check_writeable(self, store: WrapperStore) -> None: + def test_check_writeable(self, store: WrapperStore[LocalStore]) -> None: """ Test _check_writeable() runs without errors. """ store._check_writable() - def test_close(self, store: WrapperStore) -> None: + def test_close(self, store: WrapperStore[LocalStore]) -> None: "Test store can be closed" store.close() assert not store._is_open - def test_is_open_setter_raises(self, store: WrapperStore) -> None: + def test_is_open_setter_raises(self, store: WrapperStore[LocalStore]) -> None: """ Test that a user cannot change `_is_open` without opening the underlying store. """ @@ -80,13 +91,13 @@ def test_is_open_setter_raises(self, store: WrapperStore) -> None: @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=True) async def test_wrapped_set(store: Store, capsys: pytest.CaptureFixture[str]) -> None: # define a class that prints when it sets - class NoisySetter(WrapperStore): + class NoisySetter(WrapperStore[Store]): async def set(self, key: str, value: Buffer) -> None: print(f"setting {key}") await super().set(key, value) key = "foo" - value = Buffer.from_bytes(b"bar") + value = CPUBuffer.from_bytes(b"bar") store_wrapped = NoisySetter(store) await store_wrapped.set(key, value) captured = capsys.readouterr() @@ -98,15 +109,17 @@ async def set(self, key: str, value: Buffer) -> None: @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=True) async def test_wrapped_get(store: Store, capsys: pytest.CaptureFixture[str]) -> None: # define a class that prints when it sets - class NoisyGetter(WrapperStore): - def get(self, key: str, prototype: BufferPrototype) -> None: + class NoisyGetter(WrapperStore[Any]): + async def get( + self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> None: print(f"getting {key}") - return super().get(key, prototype=prototype) + await super().get(key, prototype=prototype, byte_range=byte_range) key = "foo" - value = Buffer.from_bytes(b"bar") + value = CPUBuffer.from_bytes(b"bar") store_wrapped = NoisyGetter(store) await store_wrapped.set(key, value) - assert await store_wrapped.get(key, buffer_prototype) == value + await store_wrapped.get(key, buffer_prototype) captured = capsys.readouterr() assert f"getting {key}" in captured.out From 49db79ab7f39fc5c8ce8dce3de783527e81c684d Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 3 Oct 2025 17:27:00 +0200 Subject: [PATCH 126/468] chore/doctests (#3500) * Add _cache.py first attempt * test.py ran without error, creating test.zarr/ * Added testing for cache.py LRUStoreCache for v3 * Fix ruff errors * Add working example comparing LocalStore to LRUStoreCache * Delete test.py to clean-up * Added lrustorecache to changes and user-guide docs * Fix linting issues * Implement dual store cache * Fixed failing tests * Fix linting errors * Add logger info * Delete unnecessary extra functionality * Rename to caching_store * Add test_storage.py * Fix logic in _caching_store.py * Update tests to match caching_store implemtation * Delete LRUStoreCache files * Update __init__ * Add functionality for max_size * Add tests for cache_info and clear_cache * Delete test.py * Fix linting errors * Update feature description * Fix errors * Fix cachingstore.rst errors * Fix cachingstore.rst errors * Fixed eviction key logic with proper size tracking * Increase code coverage to 98% * Fix linting errors * move cache store to experimental, fix bugs * update changelog * remove logging config override, remove dead code, adjust evict_key logic, and avoid calling exists unnecessarily * add docs * add tests for relaxed cache coherency * adjust code examples (but we don't know if they work, because we don't have doctests working) * update ci; don't save temporary files for cachestore; add doctest env * add doctests * remove test_cache_store * update ci * update ci * update ci, finally * remove unnecessary doctest script * restore s3 tests * add s3fs dep * test code examples in src * fix broken code examples * remove ectopic changelog * make docstring code examples executible, and fix errors * update async docstrings --------- Co-authored-by: ruaridhg Co-authored-by: ruaridhg <32329546+ruaridhg@users.noreply.github.com> --- .github/workflows/test.yml | 5 +- docs/user-guide/storage.md | 4 + pyproject.toml | 15 ++- src/zarr/api/synchronous.py | 121 +++++++++++++----------- src/zarr/codecs/numcodecs/_codecs.py | 27 +++--- src/zarr/core/array.py | 129 +++++++++++++++++--------- src/zarr/core/attributes.py | 10 +- src/zarr/core/dtype/__init__.py | 36 +++---- src/zarr/core/dtype/npy/string.py | 1 + src/zarr/core/dtype/npy/structured.py | 2 +- src/zarr/core/group.py | 78 +++++++++------- src/zarr/core/indexing.py | 38 ++++---- src/zarr/core/sync.py | 4 - src/zarr/core/sync_group.py | 18 ++-- src/zarr/experimental/cache_store.py | 37 ++++---- src/zarr/registry.py | 10 +- src/zarr/storage/_common.py | 15 +-- src/zarr/storage/_utils.py | 22 +++-- tests/test_docs.py | 120 ++++++++++++++++++++++++ 19 files changed, 461 insertions(+), 231 deletions(-) create mode 100644 tests/test_docs.py diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e58c8f9dc9..971fc415af 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -129,11 +129,10 @@ jobs: pip install hatch - name: Set Up Hatch Env run: | - hatch env create docs - hatch env run -e docs list-env + hatch run doctest:pip list - name: Run Tests run: | - hatch env run --env docs check + hatch run doctest:test test-complete: name: Test complete diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index ea48f8f622..0fea19a3f5 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -25,6 +25,7 @@ print(group) ```python exec="true" session="storage" source="above" result="ansi" # Implicitly create a read-only FsspecStore +# Note: requires s3fs to be installed group = zarr.open_group( store='s3://noaa-nwm-retro-v2-zarr-pds', mode='r', @@ -59,6 +60,7 @@ print(group) - an FSSpec URI string, indicating a [remote store](#remote-store) location: ```python exec="true" session="storage" source="above" result="ansi" + # Note: requires s3fs to be installed group = zarr.open_group( store='s3://noaa-nwm-retro-v2-zarr-pds', mode='r', @@ -125,6 +127,7 @@ that implements the [AbstractFileSystem](https://filesystem-spec.readthedocs.io/ API. `storage_options` can be used to configure the fsspec backend: ```python exec="true" session="storage" source="above" result="ansi" +# Note: requires s3fs to be installed store = zarr.storage.FsspecStore.from_url( 's3://noaa-nwm-retro-v2-zarr-pds', read_only=True, @@ -138,6 +141,7 @@ The type of filesystem (e.g. S3, https, etc..) is inferred from the scheme of th In case a specific filesystem is needed, one can explicitly create it. For example to create a S3 filesystem: ```python exec="true" session="storage" source="above" result="ansi" +# Note: requires s3fs to be installed import fsspec fs = fsspec.filesystem( 's3', anon=True, asynchronous=True, diff --git a/pyproject.toml b/pyproject.toml index 5733f42950..8095f87188 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -255,6 +255,18 @@ serve = "mkdocs serve" build = "mkdocs build" check = "mkdocs build --strict" readthedocs = "rm -rf $READTHEDOCS_OUTPUT/html && cp -r site $READTHEDOCS_OUTPUT/html" + +[tool.hatch.envs.doctest] +description = "Test environment for validating executable code blocks in documentation" +features = ['test', 'remote'] # Include remote dependencies for s3fs +dependencies = [ + "s3fs>=2023.10.0", + "pytest", + "pytest-examples", +] + +[tool.hatch.envs.doctest.scripts] +test = "pytest tests/test_docs.py -v" list-env = "pip list" [tool.ruff] @@ -396,7 +408,8 @@ addopts = [ ] filterwarnings = [ "error", - "ignore:Unclosed client session >> import zarr - >>> store = zarr.storage.MemoryStore() - >>> arr = await zarr.create_array( - >>> store=store, - >>> shape=(100,100), - >>> chunks=(10,10), - >>> dtype='i4', - >>> fill_value=0) - + ```python + import zarr + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, + shape=(100,100), + chunks=(10,10), + dtype='i4', + fill_value=0) + # + ``` """ return Array( sync( @@ -1132,49 +1134,64 @@ def from_array( Examples -------- - Create an array from an existing Array:: - - >>> import zarr - >>> store = zarr.storage.MemoryStore() - >>> store2 = zarr.storage.LocalStore('example.zarr') - >>> arr = zarr.create_array( - >>> store=store, - >>> shape=(100,100), - >>> chunks=(10,10), - >>> dtype='int32', - >>> fill_value=0) - >>> arr2 = zarr.from_array(store2, data=arr) - - - Create an array from an existing NumPy array:: - - >>> import numpy as np - >>> arr3 = zarr.from_array( - zarr.storage.MemoryStore(), - >>> data=np.arange(10000, dtype='i4').reshape(100, 100), - >>> ) - - - Create an array from any array-like object:: - - >>> arr4 = zarr.from_array( - >>> zarr.storage.MemoryStore(), - >>> data=[[1, 2], [3, 4]], - >>> ) - - >>> arr4[...] - array([[1, 2],[3, 4]]) - - Create an array from an existing Array without copying the data:: - - >>> arr5 = zarr.from_array( - >>> zarr.storage.MemoryStore(), - >>> data=arr4, - >>> write_data=False, - >>> ) - - >>> arr5[...] - array([[0, 0],[0, 0]]) + Create an array from an existing Array: + + ```python + import zarr + store = zarr.storage.MemoryStore() + store2 = zarr.storage.LocalStore('example_from_array.zarr') + arr = zarr.create_array( + store=store, + shape=(100,100), + chunks=(10,10), + dtype='int32', + fill_value=0) + arr2 = zarr.from_array(store2, data=arr, overwrite=True) + # + ``` + + Create an array from an existing NumPy array: + + ```python + import zarr + import numpy as np + arr3 = zarr.from_array( + zarr.storage.MemoryStore(), + data=np.arange(10000, dtype='i4').reshape(100, 100), + ) + # + ``` + + Create an array from any array-like object: + + ```python + import zarr + arr4 = zarr.from_array( + zarr.storage.MemoryStore(), + data=[[1, 2], [3, 4]], + ) + # + arr4[...] + # array([[1, 2],[3, 4]]) + ``` + + Create an array from an existing Array without copying the data: + + ```python + import zarr + arr4 = zarr.from_array( + zarr.storage.MemoryStore(), + data=[[1, 2], [3, 4]], + ) + arr5 = zarr.from_array( + zarr.storage.MemoryStore(), + data=arr4, + write_data=False, + ) + # + arr5[...] + # array([[0, 0],[0, 0]]) + ``` """ return Array( sync( diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py index 651682d317..4a3d88a84f 100644 --- a/src/zarr/codecs/numcodecs/_codecs.py +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -3,18 +3,21 @@ These codecs were previously defined in [numcodecs][], and have now been moved to `zarr`. ->>> import numpy as np ->>> import zarr ->>> import zarr.codecs.numcodecs as numcodecs ->>> ->>> array = zarr.create_array( -... store="data.zarr", -... shape=(1024, 1024), -... chunks=(64, 64), -... dtype="uint32", -... filters=[numcodecs.Delta(dtype="uint32")], -... compressors=[numcodecs.BZ2(level=5)]) ->>> array[:] = np.arange(np.prod(array.shape), dtype=array.dtype).reshape(*array.shape) +```python +import numpy as np +import zarr +import zarr.codecs.numcodecs as numcodecs + +array = zarr.create_array( + store="data_numcodecs.zarr", + shape=(1024, 1024), + chunks=(64, 64), + dtype="uint32", + filters=[numcodecs.Delta(dtype="uint32")], + compressors=[numcodecs.BZ2(level=5)], + overwrite=True) +array[:] = np.arange(np.prod(array.shape), dtype=array.dtype).reshape(*array.shape) +``` !!! note Please note that the codecs in [zarr.codecs.numcodecs][] are not part of the Zarr version diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 59ca8f5929..42d6201ba9 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -982,10 +982,24 @@ async def open( Examples -------- - >>> import zarr - >>> store = zarr.storage.MemoryStore() - >>> async_arr = await AsyncArray.open(store) # doctest: +ELLIPSIS - + ```python + import asyncio + import zarr + from zarr.core.array import AsyncArray + + async def example(): + store = zarr.storage.MemoryStore() + # First create an array to open + await zarr.api.asynchronous.create_array( + store=store, shape=(100, 100), dtype="int32" + ) + # Now open it + async_arr = await AsyncArray.open(store) + return async_arr + + async_arr = asyncio.run(example()) + # + ``` """ store_path = await make_store_path(store) metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format) @@ -1300,12 +1314,23 @@ async def nchunks_initialized(self) -> int: Examples -------- - >>> arr = await zarr.api.asynchronous.create(shape=(10,), chunks=(1,), shards=(2,)) - >>> await arr.nchunks_initialized() - 0 - >>> await arr.setitem(slice(5), 1) - >>> await arr.nchunks_initialized() - 6 + ```python + import asyncio + import zarr.api.asynchronous + + async def example(): + arr = await zarr.api.asynchronous.create(shape=(10,), chunks=(1,)) + count = await arr.nchunks_initialized() + print(f"Initial: {count}") + #> Initial: 0 + await arr.setitem(slice(5), 1) + count = await arr.nchunks_initialized() + print(f"After write: {count}") + #> After write: 5 + return count + + result = asyncio.run(example()) + ``` """ if self.shards is None: chunks_per_shard = 1 @@ -1333,12 +1358,23 @@ async def _nshards_initialized(self) -> int: Examples -------- - >>> arr = await zarr.api.asynchronous.create(shape=(10,), chunks=(2,)) - >>> await arr._nshards_initialized() - 0 - >>> await arr.setitem(slice(5), 1) - >>> await arr._nshards_initialized() - 3 + ```python + import asyncio + import zarr.api.asynchronous + + async def example(): + arr = await zarr.api.asynchronous.create(shape=(10,), chunks=(2,)) + count = await arr._nshards_initialized() + print(f"Initial: {count}") + #> Initial: 0 + await arr.setitem(slice(5), 1) + count = await arr._nshards_initialized() + print(f"After write: {count}") + #> After write: 3 + return count + + result = asyncio.run(example()) + ``` """ return len(await _shards_initialized(self)) @@ -1566,18 +1602,25 @@ async def getitem( Examples -------- - >>> import zarr - >>> store = zarr.storage.MemoryStore() - >>> async_arr = await zarr.api.asynchronous.create_array( - ... store=store, - ... shape=(100,100), - ... chunks=(10,10), - ... dtype='i4', - ... fill_value=0) - - >>> await async_arr.getitem((0,1)) # doctest: +ELLIPSIS - array(0, dtype=int32) - + ```python + import asyncio + import zarr.api.asynchronous + + async def example(): + store = zarr.storage.MemoryStore() + async_arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(100,100), + chunks=(10,10), + dtype='i4', + fill_value=0) + result = await async_arr.getitem((0,1)) + print(result) + #> 0 + return result + + value = asyncio.run(example()) + ``` """ if prototype is None: prototype = default_buffer_prototype() @@ -4014,7 +4057,7 @@ def blocks(self) -> BlockIndex: def resize(self, new_shape: ShapeLike) -> None: """ Change the shape of the array by growing or shrinking one or more - dimensions. + dimensions. This is an in-place operation that modifies the array. Parameters ---------- @@ -4032,20 +4075,20 @@ def resize(self, new_shape: ShapeLike) -> None: Examples -------- - >>> import zarr - >>> z = zarr.zeros(shape=(10000, 10000), - >>> chunk_shape=(1000, 1000), - >>> dtype="i4",) - >>> z.shape - (10000, 10000) - >>> z = z.resize(20000, 1000) - >>> z.shape - (20000, 1000) - >>> z2 = z.resize(50, 50) - >>> z.shape - (20000, 1000) - >>> z2.shape - (50, 50) + ```python + import zarr + z = zarr.zeros(shape=(10000, 10000), + chunk_shape=(1000, 1000), + dtype="int32",) + z.shape + #> (10000, 10000) + z.resize((20000, 1000)) + z.shape + #> (20000, 1000) + z.resize((50, 50)) + z.shape + #>(50, 50) + ``` """ sync(self._async_array.resize(new_shape)) diff --git a/src/zarr/core/attributes.py b/src/zarr/core/attributes.py index e000839436..7097385081 100644 --- a/src/zarr/core/attributes.py +++ b/src/zarr/core/attributes.py @@ -43,11 +43,11 @@ def put(self, d: dict[str, JSON]) -> None: Equivalent to the following pseudo-code, but performed atomically. ```python - >>> attrs = {"a": 1, "b": 2} - >>> attrs.clear() - >>> attrs.update({"a": 3", "c": 4}) - >>> attrs - {'a': 3, 'c': 4} + attrs = {"a": 1, "b": 2} + attrs.clear() + attrs.update({"a": "3", "c": 4}) + print(attrs) + #> {'a': '3', 'c': 4} ``` """ self._obj.metadata.attributes.clear() diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index bf09a7501e..f3077c32e5 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -213,14 +213,16 @@ def parse_data_type( Examples -------- - >>> from zarr.dtype import parse_data_type - >>> import numpy as np - >>> parse_data_type("int32", zarr_format=2) - Int32(endianness='little') - >>> parse_data_type(np.dtype('S10'), zarr_format=2) - NullTerminatedBytes(length=10) - >>> parse_data_type({"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, zarr_format=3) - DateTime64(endianness='little', scale_factor=10, unit='s') + ```python + from zarr.dtype import parse_data_type + import numpy as np + parse_data_type("int32", zarr_format=2) + # Int32(endianness='little') + parse_data_type(np.dtype('S10'), zarr_format=2) + # NullTerminatedBytes(length=10) + parse_data_type({"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, zarr_format=3) + # DateTime64(endianness='little', scale_factor=10, unit='s') + ``` """ return parse_dtype(dtype_spec, zarr_format=zarr_format) @@ -251,14 +253,16 @@ def parse_dtype( Examples -------- - >>> from zarr.dtype import parse_dtype - >>> import numpy as np - >>> parse_dtype("int32", zarr_format=2) - Int32(endianness='little') - >>> parse_dtype(np.dtype('S10'), zarr_format=2) - NullTerminatedBytes(length=10) - >>> parse_dtype({"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, zarr_format=3) - DateTime64(endianness='little', scale_factor=10, unit='s') + ```python + from zarr.dtype import parse_dtype + import numpy as np + parse_dtype("int32", zarr_format=2) + # Int32(endianness='little') + parse_dtype(np.dtype('S10'), zarr_format=2) + # NullTerminatedBytes(length=10) + parse_dtype({"name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 10}}, zarr_format=3) + # DateTime64(endianness='little', scale_factor=10, unit='s') + ``` """ if isinstance(dtype_spec, ZDType): return dtype_spec diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index ee8cc71aaf..41d3a60078 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -99,6 +99,7 @@ class FixedLengthUTF32JSON_V3(NamedConfig[Literal["fixed_length_utf32"], LengthB "name": "fixed_length_utf32", "configuration": { "length_bytes": 12 + } } ``` """ diff --git a/src/zarr/core/dtype/npy/structured.py b/src/zarr/core/dtype/npy/structured.py index 7aa546ea9c..8bedee07ef 100644 --- a/src/zarr/core/dtype/npy/structured.py +++ b/src/zarr/core/dtype/npy/structured.py @@ -74,7 +74,7 @@ class StructuredJSON_V3( "name": "structured", "configuration": { "fields": [ - ["f0", "int32], + ["f0", "int32"], ["f1", "float64"], ] } diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 71d2b52194..492211d097 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -292,21 +292,24 @@ def flattened_metadata(self) -> dict[str, ArrayV2Metadata | ArrayV3Metadata | Gr Examples -------- - >>> cm = ConsolidatedMetadata( - ... metadata={ - ... "group-0": GroupMetadata( - ... consolidated_metadata=ConsolidatedMetadata( - ... { - ... "group-0-0": GroupMetadata(), - ... } - ... ) - ... ), - ... "group-1": GroupMetadata(), - ... } - ... ) - {'group-0': GroupMetadata(attributes={}, zarr_format=3, consolidated_metadata=None, node_type='group'), - 'group-0/group-0-0': GroupMetadata(attributes={}, zarr_format=3, consolidated_metadata=None, node_type='group'), - 'group-1': GroupMetadata(attributes={}, zarr_format=3, consolidated_metadata=None, node_type='group')} + ```python + from zarr.core.group import ConsolidatedMetadata, GroupMetadata + cm = ConsolidatedMetadata( + metadata={ + "group-0": GroupMetadata( + consolidated_metadata=ConsolidatedMetadata( + { + "group-0-0": GroupMetadata(), + } + ) + ), + "group-1": GroupMetadata(), + } + ) + # {'group-0': GroupMetadata(attributes={}, zarr_format=3, consolidated_metadata=None, node_type='group'), + # 'group-0/group-0-0': GroupMetadata(attributes={}, zarr_format=3, consolidated_metadata=None, node_type='group'), + # 'group-1': GroupMetadata(attributes={}, zarr_format=3, consolidated_metadata=None, node_type='group')} + ``` """ metadata = {} @@ -1894,16 +1897,19 @@ def __getitem__(self, path: str) -> Array | Group: Examples -------- - >>> import zarr - >>> group = Group.from_store(zarr.storage.MemoryStore() - >>> group.create_array(name="subarray", shape=(10,), chunks=(10,)) - >>> group.create_group(name="subgroup").create_array(name="subarray", shape=(10,), chunks=(10,)) - >>> group["subarray"] - - >>> group["subgroup"] - - >>> group["subgroup"]["subarray"] - + ```python + import zarr + from zarr.core.group import Group + group = Group.from_store(zarr.storage.MemoryStore()) + group.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="float64") + group.create_group(name="subgroup").create_array(name="subarray", shape=(10,), chunks=(10,), dtype="float64") + group["subarray"] + # + group["subgroup"] + # + group["subgroup"]["subarray"] + # + ``` """ obj = self._sync(self._async_group.getitem(path)) @@ -1929,15 +1935,19 @@ def get(self, path: str, default: DefaultT | None = None) -> Array | Group | Def Examples -------- - >>> import zarr - >>> group = Group.from_store(zarr.storage.MemoryStore() - >>> group.create_array(name="subarray", shape=(10,), chunks=(10,)) - >>> group.create_group(name="subgroup") - >>> group.get("subarray") - - >>> group.get("subgroup") - - >>> group.get("nonexistent", None) + ```python + import zarr + from zarr.core.group import Group + group = Group.from_store(zarr.storage.MemoryStore()) + group.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="float64") + group.create_group(name="subgroup") + group.get("subarray") + # + group.get("subgroup") + # + group.get("nonexistent", None) + # None + ``` """ try: diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 243096b029..c357ca7ccc 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -111,17 +111,20 @@ def _iter_grid( Examples -------- - >>> tuple(iter_grid((1,))) - ((0,),) + ```python + from zarr.core.indexing import _iter_grid + tuple(_iter_grid((1,))) + # ((0,),) - >>> tuple(iter_grid((2,3))) - ((0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2)) + tuple(_iter_grid((2,3))) + # ((0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2)) - >>> tuple(iter_grid((2,3), origin=(1,1))) - ((1, 1), (1, 2)) + tuple(_iter_grid((2,3), origin=(1,1))) + # ((1, 1), (1, 2)) - >>> tuple(iter_grid((2,3), origin=(0,0), selection_shape=(2,2))) - ((0, 0), (0, 1), (1, 0), (1, 1)) + tuple(_iter_grid((2,3), origin=(0,0), selection_shape=(2,2))) + # ((0, 0), (0, 1), (1, 0), (1, 1)) + ``` """ if origin is None: origin_parsed = (0,) * len(grid_shape) @@ -190,17 +193,20 @@ def _iter_regions( Examples -------- - >>> tuple(iter_regions((1,), (1,))) - ((slice(0, 1, 1),),) + ```python + from zarr.core.indexing import _iter_regions + tuple(_iter_regions((1,), (1,))) + # ((slice(0, 1, 1),),) - >>> tuple(iter_regions((2, 3), (1, 2))) - ((slice(0, 1, 1), slice(0, 2, 1)), (slice(1, 2, 1), slice(0, 2, 1))) + tuple(_iter_regions((2, 3), (1, 2))) + # ((slice(0, 1, 1), slice(0, 2, 1)), (slice(1, 2, 1), slice(0, 2, 1))) - >>> tuple(iter_regions((2,3), (1,2)), origin=(1,1)) - ((slice(1, 2, 1), slice(1, 3, 1)), (slice(2, 3, 1), slice(1, 3, 1))) + tuple(_iter_regions((2,3), (1,2), origin=(1,1))) + # ((slice(1, 2, 1), slice(1, 3, 1)), (slice(2, 3, 1), slice(1, 3, 1))) - >>> tuple(iter_regions((2,3), (1,2)), origin=(1,1), selection_shape=(2,2)) - ((slice(1, 2, 1), slice(1, 3, 1)), (slice(2, 3, 1), slice(1, 3, 1))) + tuple(_iter_regions((2,3), (1,2), origin=(0,0), selection_shape=(2,2))) + # ((slice(0, 1, 1), slice(0, 2, 1)), (slice(1, 2, 1), slice(0, 2, 1))) + ``` """ grid_shape = tuple(ceildiv(d, s) for d, s in zip(domain_shape, region_shape, strict=True)) for grid_position in _iter_grid( diff --git a/src/zarr/core/sync.py b/src/zarr/core/sync.py index ffb04e764d..fe435cc2b8 100644 --- a/src/zarr/core/sync.py +++ b/src/zarr/core/sync.py @@ -128,10 +128,6 @@ def sync( ) -> T: """ Make loop run coroutine until it returns. Runs in other thread - - Examples - -------- - >>> sync(async_function(), existing_loop) """ if loop is None: # NB: if the loop is not running *yet*, it is OK to submit work diff --git a/src/zarr/core/sync_group.py b/src/zarr/core/sync_group.py index 39d8a17992..2a416f555f 100644 --- a/src/zarr/core/sync_group.py +++ b/src/zarr/core/sync_group.py @@ -94,15 +94,17 @@ def create_hierarchy( Examples -------- - >>> from zarr import create_hierarchy - >>> from zarr.storage import MemoryStore - >>> from zarr.core.group import GroupMetadata - - >>> store = MemoryStore() - >>> nodes = {'a': GroupMetadata(attributes={'name': 'leaf'})} - >>> nodes_created = dict(create_hierarchy(store=store, nodes=nodes)) - >>> print(nodes) + ```python + from zarr import create_hierarchy + from zarr.storage import MemoryStore + from zarr.core.group import GroupMetadata + + store = MemoryStore() + nodes = {'a': GroupMetadata(attributes={'name': 'leaf'})} + nodes_created = dict(create_hierarchy(store=store, nodes=nodes)) + print(nodes) # {'a': GroupMetadata(attributes={'name': 'leaf'}, zarr_format=3, consolidated_metadata=None, node_type='group')} + ``` """ coro = create_hierarchy_async(store=store, nodes=nodes, overwrite=overwrite) diff --git a/src/zarr/experimental/cache_store.py b/src/zarr/experimental/cache_store.py index d228cc6a12..3456c94320 100644 --- a/src/zarr/experimental/cache_store.py +++ b/src/zarr/experimental/cache_store.py @@ -44,23 +44,25 @@ class CacheStore(WrapperStore[Store]): Examples -------- - >>> import zarr - >>> from zarr.storage import MemoryStore - >>> from zarr.experimental.cache_store import CacheStore - >>> - >>> # Create a cached store - >>> source_store = MemoryStore() - >>> cache_store = MemoryStore() - >>> cached_store = CacheStore( - ... store=source_store, - ... cache_store=cache_store, - ... max_age_seconds=60, - ... max_size=1024*1024 - ... ) - >>> - >>> # Use it like any other store - >>> array = zarr.create(shape=(100,), store=cached_store) - >>> array[:] = 42 + ```python + import zarr + from zarr.storage import MemoryStore + from zarr.experimental.cache_store import CacheStore + + # Create a cached store + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore( + store=source_store, + cache_store=cache_store, + max_age_seconds=60, + max_size=1024*1024 + ) + + # Use it like any other store + array = zarr.create(shape=(100,), store=cached_store) + array[:] = 42 + ``` """ @@ -109,7 +111,6 @@ def __init__( self.key_insert_times = {} else: self.key_insert_times = key_insert_times - self.cache_set_data = cache_set_data self._cache_order = OrderedDict() self._current_size = 0 diff --git a/src/zarr/registry.py b/src/zarr/registry.py index 092b4cafc0..a8dd2a1c6c 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -325,10 +325,12 @@ def get_numcodec(data: CodecJSON_V2[str]) -> Numcodec: Examples -------- - - >>> codec = get_codec({'id': 'zlib', 'level': 1}) - >>> codec - Zlib(level=1) + ```python + from zarr.registry import get_numcodec + codec = get_numcodec({'id': 'zlib', 'level': 1}) + codec + # Zlib(level=1) + ``` """ from numcodecs.registry import get_codec diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 9ecfe4c201..d762097cc3 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -429,12 +429,15 @@ def _is_fsspec_uri(uri: str) -> bool: Examples -------- - >>> _is_fsspec_uri("s3://bucket") - True - >>> _is_fsspec_uri("my-directory") - False - >>> _is_fsspec_uri("local://my-directory") - False + ```python + from zarr.storage._common import _is_fsspec_uri + _is_fsspec_uri("s3://bucket") + # True + _is_fsspec_uri("my-directory") + # False + _is_fsspec_uri("local://my-directory") + # False + ``` """ return "://" in uri or ("::" in uri and "local://" not in uri) diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index 145790278c..39c28d44c3 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -84,10 +84,13 @@ def _join_paths(paths: Iterable[str]) -> str: Examples -------- - >>> _join_paths(["", "a", "b"]) - 'a/b' - >>> _join_paths(["a", "b", "c"]) - 'a/b/c' + ```python + from zarr.storage._utils import _join_paths + _join_paths(["", "a", "b"]) + # 'a/b' + _join_paths(["a", "b", "c"]) + # 'a/b/c' + ``` """ return "/".join(filter(lambda v: v != "", paths)) @@ -116,10 +119,13 @@ def _relativize_path(*, path: str, prefix: str) -> str: Examples -------- - >>> _relativize_path(path="", prefix="a/b") - 'a/b' - >>> _relativize_path(path="a/b", prefix="a/b/c") - 'c' + ```python + from zarr.storage._utils import _relativize_path + _relativize_path(path="a/b", prefix="") + # 'a/b' + _relativize_path(path="a/b/c", prefix="a/b") + # 'c' + ``` """ if prefix == "": return path diff --git a/tests/test_docs.py b/tests/test_docs.py new file mode 100644 index 0000000000..d467e478e8 --- /dev/null +++ b/tests/test_docs.py @@ -0,0 +1,120 @@ +""" +Tests for executable code blocks in markdown documentation. + +This module uses pytest-examples to validate that all Python code examples +with exec="true" in the documentation execute successfully. +""" + +from __future__ import annotations + +from collections import defaultdict +from pathlib import Path + +import pytest + +pytest.importorskip("pytest_examples") +from pytest_examples import CodeExample, EvalExample, find_examples + +# Find all markdown files with executable code blocks +DOCS_ROOT = Path(__file__).parent.parent / "docs" +SOURCES_ROOT = Path(__file__).parent.parent / "src" / "zarr" + + +def find_markdown_files_with_exec() -> list[Path]: + """Find all markdown files containing exec="true" code blocks.""" + markdown_files = [] + + for md_file in DOCS_ROOT.rglob("*.md"): + try: + content = md_file.read_text(encoding="utf-8") + if 'exec="true"' in content: + markdown_files.append(md_file) + except Exception: + # Skip files that can't be read + continue + + return sorted(markdown_files) + + +def group_examples_by_session() -> list[tuple[str, str]]: + """ + Group examples by their session and file, maintaining order. + + Returns a list of session_key tuples where session_key is + (file_path, session_name). + """ + all_examples = list(find_examples(DOCS_ROOT)) + + # Group by file and session + sessions = defaultdict(list) + + for example in all_examples: + settings = example.prefix_settings() + if settings.get("exec") != "true": + continue + + # Use file path and session name as key + file_path = example.path + session_name = settings.get("session", "_default") + session_key = (str(file_path), session_name) + + sessions[session_key].append(example) + + # Return sorted list of session keys for consistent test ordering + return sorted(sessions.keys(), key=lambda x: (x[0], x[1])) + + +def name_example(path: str, session: str) -> str: + """Generate a readable name for a test case from file path and session.""" + return f"{Path(path).relative_to(DOCS_ROOT)}:{session}" + + +# Get all example sessions +@pytest.mark.parametrize( + "session_key", group_examples_by_session(), ids=lambda v: name_example(v[0], v[1]) +) +def test_documentation_examples( + session_key: tuple[str, str], + eval_example: EvalExample, +) -> None: + """ + Test that all exec="true" code examples in documentation execute successfully. + + This test groups examples by session (file + session name) and runs them + sequentially in the same execution context, allowing code to build on + previous examples. + + This test uses pytest-examples to: + - Find all code examples with exec="true" in markdown files + - Group them by session + - Execute them in order within the same context + - Verify no exceptions are raised + """ + file_path, session_name = session_key + + # Get examples for this session + all_examples = list(find_examples(DOCS_ROOT)) + examples = [] + for example in all_examples: + settings = example.prefix_settings() + if settings.get("exec") != "true": + continue + if str(example.path) == file_path and settings.get("session", "_default") == session_name: + examples.append(example) + + # Run all examples in this session sequentially, preserving state + module_globals: dict[str, object] = {} + for example in examples: + # TODO: uncomment this line when we are ready to fix output checks + # result = eval_example.run_print_check(example, module_globals=module_globals) + result = eval_example.run(example, module_globals=module_globals) + # Update globals with the results from this execution + module_globals.update(result) + + +@pytest.mark.parametrize("example", find_examples(str(SOURCES_ROOT)), ids=str) +def test_docstrings(example: CodeExample, eval_example: EvalExample) -> None: + """Test our docstring examples.""" + if example.path.name == "config.py" and "your.module" in example.source: + pytest.skip("Skip testing docstring example that assumes nonexistent module.") + eval_example.run_print_check(example) From dc5334e5b3392d0ee5b1e19d6f6ab5261ec3425c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 3 Oct 2025 17:44:39 +0200 Subject: [PATCH 127/468] docs/examples (#3502) * add documentation for examples * update docs deployment * fix broken link * update main examples documentation * changelog * Update mkdocs.yml Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3502.doc.md | 1 + docs/user-guide/data_types.md | 10 +---- docs/user-guide/examples/custom_dtype.md | 7 ++++ examples/README.md | 44 +++++++++++++++++++++ examples/custom_dtype/README.md | 22 +++++++++++ examples/{ => custom_dtype}/custom_dtype.py | 0 mkdocs.yml | 2 + pyproject.toml | 2 +- 8 files changed, 79 insertions(+), 9 deletions(-) create mode 100644 changes/3502.doc.md create mode 100644 docs/user-guide/examples/custom_dtype.md create mode 100644 examples/README.md create mode 100644 examples/custom_dtype/README.md rename examples/{ => custom_dtype}/custom_dtype.py (100%) diff --git a/changes/3502.doc.md b/changes/3502.doc.md new file mode 100644 index 0000000000..031c046bf4 --- /dev/null +++ b/changes/3502.doc.md @@ -0,0 +1 @@ +Reorganize the top-level `examples` directory to give each example its own sub-directory. Adds content to the docs for each example. \ No newline at end of file diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md index 82b7c89809..aa19baf891 100644 --- a/docs/user-guide/data_types.md +++ b/docs/user-guide/data_types.md @@ -298,14 +298,8 @@ assert scalar_value == np.int8(42) Each Zarr data type is a separate Python class that inherits from [ZDType][zarr.dtype.ZDType]. You can define a custom data type by writing your own subclass of [ZDType][zarr.dtype.ZDType] and adding -your data type to the data type registry. A complete example of this process is included below. - -The source code for this example can be found in the `examples/custom_dtype.py` file in the Zarr -Python project directory. - -```python ---8<-- "examples/custom_dtype.py" -``` +your data type to the data type registry. To see an executable demonstration +of this process, see the [`custom_dtype` example](../user-guide/examples/custom_dtype.md). ### Data Type Resolution diff --git a/docs/user-guide/examples/custom_dtype.md b/docs/user-guide/examples/custom_dtype.md new file mode 100644 index 0000000000..d6736e25dd --- /dev/null +++ b/docs/user-guide/examples/custom_dtype.md @@ -0,0 +1,7 @@ +--8<-- "examples/custom_dtype/README.md" + +## Source Code + +```python +--8<-- "examples/custom_dtype/custom_dtype.py" +``` diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 0000000000..a6b5fa2179 --- /dev/null +++ b/examples/README.md @@ -0,0 +1,44 @@ +# Zarr Python Examples + +This directory contains complete, runnable examples demonstrating various features and use cases of Zarr Python. + +## Directory Structure + +Each example is organized in its own subdirectory with the following structure: + +``` +examples/ +├── example_name/ +│ ├── README.md # Documentation for the example +│ └── example_name.py # Python source code +└── ... +``` + +## Adding New Examples + +To add a new example: + +1. Create a new subdirectory: `examples/my_example/` +2. Add your Python code: `examples/my_example/my_example.py` +3. Create documentation: `examples/my_example/README.md` +4. Create a documentation page at `docs/user-guide/examples/my_example.md`. The documentation page should simply link to the `README.md` and the source code, e.g.: + + ```` + # docs/user-guide/examples/my_example.md + --8<-- "examples/my_example/README.md" + + ## Source Code + + ```python + --8<-- "examples/my_example/my_example.py" + ``` + ```` +5. Update `mkdocs.yml` to include the new example in the navigation. + +### Example README.md Format + +Your README.md should include: + +- A title (`# Example Name`) +- Description of what the example demonstrates +- Instructions for running the example diff --git a/examples/custom_dtype/README.md b/examples/custom_dtype/README.md new file mode 100644 index 0000000000..c0722d0661 --- /dev/null +++ b/examples/custom_dtype/README.md @@ -0,0 +1,22 @@ +# Custom Data Type Example + +This example demonstrates how to extend Zarr Python by defining a new data type. + +The example shows how to: + +- Define a custom `ZDType` class for the `int2` data type from [`ml_dtypes`](https://pypi.org/project/ml-dtypes/) +- Implement all required methods for serialization and deserialization +- Register the custom data type with Zarr's registry +- Create and use arrays with the custom data type in both Zarr v2 and v3 formats + +## Running the Example + +```bash +python examples/custom_dtype/custom_dtype.py +``` + +Or run with uv: + +```bash +uv run examples/custom_dtype/custom_dtype.py +``` diff --git a/examples/custom_dtype.py b/examples/custom_dtype/custom_dtype.py similarity index 100% rename from examples/custom_dtype.py rename to examples/custom_dtype/custom_dtype.py diff --git a/mkdocs.yml b/mkdocs.yml index 4c7a1a4df2..c9edf338af 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -26,6 +26,8 @@ nav: - user-guide/gpu.md - user-guide/consolidated_metadata.md - user-guide/experimental.md + - Examples: + - user-guide/examples/custom_dtype.md - API Reference: - api/index.md - api/array.md diff --git a/pyproject.toml b/pyproject.toml index 8095f87188..56ba14fa7e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -251,7 +251,7 @@ dependencies = [ features = ['docs', 'remote'] [tool.hatch.envs.docs.scripts] -serve = "mkdocs serve" +serve = "mkdocs serve --watch src" build = "mkdocs build" check = "mkdocs build --strict" readthedocs = "rm -rf $READTHEDOCS_OUTPUT/html && cp -r site $READTHEDOCS_OUTPUT/html" From 6811c9483a86a0e5c835b4f3c3a2dd09254c38e5 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Tue, 7 Oct 2025 12:41:44 +0300 Subject: [PATCH 128/468] Imported name is not used anywhere in the module (#3300) --- tests/test_config.py | 1 - tests/test_v2.py | 6 ++---- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/tests/test_config.py b/tests/test_config.py index c7a2eb7394..103cbddbef 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -8,7 +8,6 @@ import pytest import zarr -import zarr.api from zarr import zeros from zarr.abc.codec import CodecPipeline from zarr.abc.store import ByteSetter, Store diff --git a/tests/test_v2.py b/tests/test_v2.py index 70e8f2923f..b223e022c6 100644 --- a/tests/test_v2.py +++ b/tests/test_v2.py @@ -2,11 +2,9 @@ from pathlib import Path from typing import Any, Literal -import numcodecs.abc -import numcodecs.vlen import numpy as np import pytest -from numcodecs import Delta +from numcodecs import Delta, Zlib from numcodecs.blosc import Blosc from numcodecs.zstd import Zstd @@ -124,7 +122,7 @@ def test_v2_encode_decode_with_data(dtype: ZDType[Any, Any], value: str) -> None np.testing.assert_equal(data, expected) -@pytest.mark.parametrize("filters", [[], [numcodecs.Delta(dtype=" None: array_fixture = [42] From 9f69611d3957c99653509c7cca7db96b2c395f37 Mon Sep 17 00:00:00 2001 From: Joe Hamman Date: Mon, 13 Oct 2025 15:09:40 +0200 Subject: [PATCH 129/468] chore(crc32c): replace crc32c with google-crc32c dependency (#3515) * chore(crc32c): replace crc32c with google-crc32c dependency * handle missing numcodecs crc32c * handle missing UnknownCodecError * changelog * update docs --- .gitignore | 1 + .pre-commit-config.yaml | 3 ++- changes/3515.misc.md | 1 + docs/user-guide/installation.md | 3 ++- pyproject.toml | 3 ++- src/zarr/codecs/crc32c_.py | 8 +++++--- tests/test_codecs/test_numcodecs.py | 21 +++++++++++++++++++-- 7 files changed, 32 insertions(+), 8 deletions(-) create mode 100644 changes/3515.misc.md diff --git a/.gitignore b/.gitignore index f2f41270ca..b79ce264c8 100644 --- a/.gitignore +++ b/.gitignore @@ -90,3 +90,4 @@ tests/.hypothesis .hypothesis/ zarr/version.py +zarr.egg-info/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index da3e2be9b2..8488e38d4d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -31,7 +31,8 @@ repos: # Package dependencies - packaging - donfig - - numcodecs[crc32c] + - numcodecs + - google-crc32c>=1.5 - numpy==2.1 # until https://github.com/numpy/numpy/issues/28034 is resolved - typing_extensions - universal-pathlib diff --git a/changes/3515.misc.md b/changes/3515.misc.md new file mode 100644 index 0000000000..06a94c98a0 --- /dev/null +++ b/changes/3515.misc.md @@ -0,0 +1 @@ +Replace `crc32c` dependency with `google-crc32c` to resolve licensing concerns. The `crc32c` library uses LGPL license, while `google-crc32c` uses the more permissive Apache 2.0 license. This change maintains full backward compatibility with existing CRC32C-encoded data. diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md index f672a348cd..89c78804b2 100644 --- a/docs/user-guide/installation.md +++ b/docs/user-guide/installation.md @@ -7,7 +7,8 @@ Required dependencies include: - [Python](https://docs.python.org/3/) (3.11 or later) - [packaging](https://packaging.pypa.io) (22.0 or later) - [numpy](https://numpy.org) (1.26 or later) -- [numcodecs[crc32c]](https://numcodecs.readthedocs.io) (0.14 or later) +- [numcodecs](https://numcodecs.readthedocs.io) (0.14 or later) +- [google-crc32c](https://github.com/googleapis/python-crc32c) (1.5 or later) - [typing_extensions](https://typing-extensions.readthedocs.io) (4.9 or later) - [donfig](https://donfig.readthedocs.io) (0.8 or later) diff --git a/pyproject.toml b/pyproject.toml index 56ba14fa7e..7f14971396 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,8 @@ requires-python = ">=3.11" dependencies = [ 'packaging>=22.0', 'numpy>=1.26', - 'numcodecs[crc32c]>=0.14', + 'numcodecs>=0.14', + 'google-crc32c>=1.5', 'typing_extensions>=4.9', 'donfig>=0.8', ] diff --git a/src/zarr/codecs/crc32c_.py b/src/zarr/codecs/crc32c_.py index b2ea356b0c..9536d0d558 100644 --- a/src/zarr/codecs/crc32c_.py +++ b/src/zarr/codecs/crc32c_.py @@ -3,9 +3,9 @@ from dataclasses import dataclass from typing import TYPE_CHECKING, cast +import google_crc32c import numpy as np import typing_extensions -from crc32c import crc32c from zarr.abc.codec import BytesBytesCodec from zarr.core.common import JSON, parse_named_configuration @@ -42,7 +42,7 @@ async def _decode_single( # Need to do a manual cast until https://github.com/numpy/numpy/issues/26783 is resolved computed_checksum = np.uint32( - crc32c(cast("typing_extensions.Buffer", inner_bytes)) + google_crc32c.value(cast("typing_extensions.Buffer", inner_bytes)) ).tobytes() stored_checksum = bytes(crc32_bytes) if computed_checksum != stored_checksum: @@ -58,7 +58,9 @@ async def _encode_single( ) -> Buffer | None: data = chunk_bytes.as_numpy_array() # Calculate the checksum and "cast" it to a numpy array - checksum = np.array([crc32c(cast("typing_extensions.Buffer", data))], dtype=np.uint32) + checksum = np.array( + [google_crc32c.value(cast("typing_extensions.Buffer", data))], dtype=np.uint32 + ) # Append the checksum (as bytes) to the data return chunk_spec.prototype.buffer.from_array_like(np.append(data, checksum.view("B"))) diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py index 68f4e0cf7b..ddfca71294 100644 --- a/tests/test_codecs/test_numcodecs.py +++ b/tests/test_codecs/test_numcodecs.py @@ -8,6 +8,12 @@ import pytest from numcodecs import GZip +try: + from numcodecs.errors import UnknownCodecError +except ImportError: + # Older versions of numcodecs don't have a separate errors module + UnknownCodecError = ValueError + from zarr import config, create_array, open_array from zarr.abc.numcodec import _is_numcodec, _is_numcodec_cls from zarr.codecs import numcodecs as _numcodecs @@ -243,6 +249,13 @@ def test_generic_filter_packbits() -> None: ], ) def test_generic_checksum(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec]) -> None: + # Check if the codec is available in numcodecs + try: + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + codec_class()._codec # noqa: B018 + except UnknownCodecError as e: # pragma: no cover + pytest.skip(f"{codec_class.codec_name} is not available in numcodecs: {e}") + data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): @@ -352,8 +365,12 @@ def test_to_dict() -> None: ], ) def test_codecs_pickleable(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None: - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - codec = codec_cls() + # Check if the codec is available in numcodecs + try: + with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): + codec = codec_cls() + except UnknownCodecError as e: # pragma: no cover + pytest.skip(f"{codec_cls.codec_name} is not available in numcodecs: {e}") expected = codec From 14b372cee1a2f0200d1e18b3ea61d1c7644f56da Mon Sep 17 00:00:00 2001 From: Joe Hamman Date: Wed, 15 Oct 2025 12:19:40 +0200 Subject: [PATCH 130/468] feature: update default config setting for async.concurrency from 10->64 (#3526) --- src/zarr/core/config.py | 2 +- tests/test_config.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 5d463ec79c..fe61ae7955 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -107,7 +107,7 @@ def enable_gpu(self) -> ConfigSet: "order": "C", "write_empty_chunks": False, }, - "async": {"concurrency": 10, "timeout": None}, + "async": {"concurrency": 64, "timeout": None}, "threading": {"max_workers": None}, "json_indent": 2, "codec_pipeline": { diff --git a/tests/test_config.py b/tests/test_config.py index 103cbddbef..150aca7c96 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -54,7 +54,7 @@ def test_config_defaults_set() -> None: "order": "C", "write_empty_chunks": False, }, - "async": {"concurrency": 10, "timeout": None}, + "async": {"concurrency": 64, "timeout": None}, "threading": {"max_workers": None}, "json_indent": 2, "codec_pipeline": { @@ -100,7 +100,7 @@ def test_config_defaults_set() -> None: ] ) assert config.get("array.order") == "C" - assert config.get("async.concurrency") == 10 + assert config.get("async.concurrency") == 64 assert config.get("async.timeout") is None assert config.get("codec_pipeline.batch_size") == 1 assert config.get("json_indent") == 2 @@ -108,7 +108,7 @@ def test_config_defaults_set() -> None: @pytest.mark.parametrize( ("key", "old_val", "new_val"), - [("array.order", "C", "F"), ("async.concurrency", 10, 20), ("json_indent", 2, 0)], + [("array.order", "C", "F"), ("async.concurrency", 64, 128), ("json_indent", 2, 0)], ) def test_config_defaults_can_be_overridden(key: str, old_val: Any, new_val: Any) -> None: assert config.get(key) == old_val From 6b7ce9c2358b357b0f5692b6f17cf333aa82da11 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 20 Oct 2025 10:29:05 +0000 Subject: [PATCH 131/468] chore: update pre-commit hooks (#3509) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.13.1 → v0.13.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.1...v0.13.3) - [github.com/scientific-python/cookie: 2025.05.02 → 2025.10.01](https://github.com/scientific-python/cookie/compare/2025.05.02...2025.10.01) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8488e38d4d..a213d9c427 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ ci: default_stages: [pre-commit, pre-push] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.13.1 + rev: v0.13.3 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -42,7 +42,7 @@ repos: - hypothesis - s3fs - repo: https://github.com/scientific-python/cookie - rev: 2025.05.02 + rev: 2025.10.01 hooks: - id: sp-repo-review - repo: https://github.com/pre-commit/pygrep-hooks From 2adacb8480ef4f7c74bfedb6f66b9f248a93371b Mon Sep 17 00:00:00 2001 From: Joe Hamman Date: Mon, 20 Oct 2025 12:46:51 +0200 Subject: [PATCH 132/468] Document changes to async.concurrency defaults and performance considerations. (#3528) * feature: update default config setting for async.concurrency from 10->64 * doc: write docs on concurrency/dask/threading/performance --------- Co-authored-by: Davis Bennett --- changes/3526.feature.md | 1 + docs/user-guide/performance.md | 79 +++++++++++++++++++++++++++++++++- 2 files changed, 79 insertions(+), 1 deletion(-) create mode 100644 changes/3526.feature.md diff --git a/changes/3526.feature.md b/changes/3526.feature.md new file mode 100644 index 0000000000..7746611855 --- /dev/null +++ b/changes/3526.feature.md @@ -0,0 +1 @@ +Increased the default value of `async.concurrency` from 10 to 64 to improve parallelism and throughput for concurrent I/O operations. This change enables better performance out-of-the-box for most workloads. Users with specific resource constraints or when using many Dask threads may want to lower this value via the `ZARR_ASYNC_CONCURRENCY` environment variable or by setting `zarr.config.set({'async.concurrency': N})`. diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index ad101319f1..88d8e69936 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -175,7 +175,84 @@ Coming soon. ## Parallel computing and synchronization -Coming soon. +Zarr is designed to support parallel computing and enables concurrent reads and writes to arrays. This section covers how to optimize Zarr's concurrency settings for different parallel computing scenarios. + +### Concurrent I/O operations + +Zarr uses asynchronous I/O internally to enable concurrent reads and writes across multiple chunks. The level of concurrency is controlled by the `async.concurrency` configuration setting, which determines the maximum number of concurrent I/O operations. + +The default value is 64, which provides good performance for most workloads. You can adjust this value based on your specific needs: + +```python +import zarr + +# Set concurrency for the current session +zarr.config.set({'async.concurrency': 128}) + +# Or use environment variable +# export ZARR_ASYNC_CONCURRENCY=128 +``` + +Higher concurrency values can improve throughput when: +- Working with remote storage (e.g., S3, GCS) where network latency is high +- Reading/writing many small chunks in parallel +- The storage backend can handle many concurrent requests + +Lower concurrency values may be beneficial when: +- Working with local storage with limited I/O bandwidth +- Memory is constrained (each concurrent operation requires buffer space) +- Using Zarr within a parallel computing framework (see below) + +### Using Zarr with Dask + +[Dask](https://www.dask.org/) is a popular parallel computing library that works well with Zarr for processing large arrays. When using Zarr with Dask, it's important to consider the interaction between Dask's thread pool and Zarr's concurrency settings. + +**Important**: When using many Dask threads, you may need to reduce both Zarr's `async.concurrency` and `threading.max_workers` settings to avoid creating too many concurrent operations. The total number of concurrent I/O operations can be roughly estimated as: + +``` +total_concurrency ≈ dask_threads × zarr_async_concurrency +``` + +For example, if you're running Dask with 10 threads and Zarr's default concurrency of 64, you could potentially have up to 640 concurrent operations, which may overwhelm your storage system or cause memory issues. + +**Recommendation**: When using Dask with many threads, configure Zarr's concurrency settings: + +```python +import zarr +import dask.array as da + +# If using Dask with many threads (e.g., 8-16), reduce Zarr's concurrency settings +zarr.config.set({ + 'async.concurrency': 4, # Limit concurrent async operations + 'threading.max_workers': 4, # Limit Zarr's internal thread pool +}) + +# Open Zarr array +z = zarr.open_array('data/large_array.zarr', mode='r') + +# Create Dask array from Zarr array +arr = da.from_array(z, chunks=z.chunks) + +# Process with Dask +result = arr.mean(axis=0).compute() +``` + +**Configuration guidelines for Dask workloads**: + +- `async.concurrency`: Controls the maximum number of concurrent async I/O operations. Start with a lower value (e.g., 4-8) when using many Dask threads. +- `threading.max_workers`: Controls Zarr's internal thread pool size for blocking operations (defaults to CPU count). Reduce this to avoid thread contention with Dask's scheduler. + +You may need to experiment with different values to find the optimal balance for your workload. Monitor your system's resource usage and adjust these settings based on whether your storage system or CPU is the bottleneck. + +### Thread safety and process safety + +Zarr arrays are designed to be thread-safe for concurrent reads and writes from multiple threads within the same process. However, proper synchronization is required when writing to overlapping regions from multiple threads. + +For multi-process parallelism, Zarr provides safe concurrent writes as long as: +- Different processes write to different chunks +- The storage backend supports atomic writes (most do) + +When writing to the same chunks from multiple processes, you should use external synchronization mechanisms or ensure that writes are coordinated to avoid race conditions. ## Pickle support From 950066bf126ffc67acaa6b49156a8912ec4179f9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 Oct 2025 15:28:28 +0200 Subject: [PATCH 133/468] Bump the actions group with 2 updates (#3507) Bumps the actions group with 2 updates: [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) and [peter-evans/create-issue-from-file](https://github.com/peter-evans/create-issue-from-file). Updates `astral-sh/setup-uv` from 6.7.0 to 6.8.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/b75a909f75acd358c2196fb9a5f1299a9a8868a4...d0cc045d04ccac9d8b7881df0226f9e82c39688e) Updates `peter-evans/create-issue-from-file` from 5 to 6 - [Release notes](https://github.com/peter-evans/create-issue-from-file/releases) - [Commits](https://github.com/peter-evans/create-issue-from-file/compare/v5...v6) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 6.8.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: peter-evans/create-issue-from-file dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/check_changelogs.yml | 2 +- .github/workflows/issue-metrics.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index ed7874a504..b9ffaa6c7f 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -12,7 +12,7 @@ jobs: - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 - name: Install uv - uses: astral-sh/setup-uv@b75a909f75acd358c2196fb9a5f1299a9a8868a4 # v6.7.0 + uses: astral-sh/setup-uv@2ddd2b9cb38ad8efd50337e8ab201519a34c9f24 # v7.1.1 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 34bda59ff6..5f3a098611 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -35,7 +35,7 @@ jobs: SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' - name: Create issue - uses: peter-evans/create-issue-from-file@v5 + uses: peter-evans/create-issue-from-file@v6 with: title: Monthly issue metrics report token: ${{ secrets.GITHUB_TOKEN }} From bc86a613db89d47ae2951448bfca0252f1465c12 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 21 Oct 2025 20:39:49 +0200 Subject: [PATCH 134/468] don't serialize consolidated metadata if it's `None` (#3535) * don't serialize consolidated metadata if it's unset (for zarr v3 groups) * changelog --- changes/3535.bugfix.md | 2 ++ src/zarr/core/group.py | 5 ++- tests/test_metadata/test_v3.py | 57 +++++++++++++++++++++++++++++++++- 3 files changed, 62 insertions(+), 2 deletions(-) create mode 100644 changes/3535.bugfix.md diff --git a/changes/3535.bugfix.md b/changes/3535.bugfix.md new file mode 100644 index 0000000000..7e1ce8f834 --- /dev/null +++ b/changes/3535.bugfix.md @@ -0,0 +1,2 @@ +Fixed a bug where the `"consolidated_metadata"` key was written to metadata documents even when +consolidated metadata was not used, resulting in invalid metadata documents. \ No newline at end of file diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 492211d097..26aed4fd60 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -432,8 +432,11 @@ def from_dict(cls, data: dict[str, Any]) -> GroupMetadata: def to_dict(self) -> dict[str, Any]: result = asdict(replace(self, consolidated_metadata=None)) - if self.consolidated_metadata: + if self.consolidated_metadata is not None: result["consolidated_metadata"] = self.consolidated_metadata.to_dict() + else: + # Leave consolidated metadata unset if it's None + result.pop("consolidated_metadata") return result diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 1405bf533b..f2c672a14e 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -7,6 +7,7 @@ import numpy as np import pytest +from zarr import consolidate_metadata, create_group from zarr.codecs.bytes import BytesCodec from zarr.core.buffer import default_buffer_prototype from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding, V2ChunkKeyEncoding @@ -21,7 +22,12 @@ parse_dimension_names, parse_zarr_format, ) -from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError +from zarr.errors import ( + MetadataValidationError, + NodeTypeValidationError, + UnknownCodecError, + ZarrUserWarning, +) if TYPE_CHECKING: from collections.abc import Sequence @@ -338,3 +344,52 @@ def test_parse_codecs_unknown_codec_raises(monkeypatch: pytest.MonkeyPatch) -> N codecs = [{"name": "unknown"}] with pytest.raises(UnknownCodecError): parse_codecs(codecs) + + +@pytest.mark.parametrize("use_consolidated", [True, False]) +@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}]) +def test_group_to_dict(use_consolidated: bool, attributes: None | dict[str, Any]) -> None: + """ + Test that the output of GroupMetadata.to_dict() is what we expect + """ + store: dict[str, object] = {} + if attributes is None: + expect_attributes = {} + else: + expect_attributes = attributes + + group = create_group(store, attributes=attributes, zarr_format=3) + group.create_group("foo") + if use_consolidated: + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + group = consolidate_metadata(store) + meta = group.metadata + expect = { + "node_type": "group", + "zarr_format": 3, + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": { + "foo": { + "attributes": {}, + "zarr_format": 3, + "node_type": "group", + "consolidated_metadata": { + "kind": "inline", + "metadata": {}, + "must_understand": False, + }, + } + }, + }, + "attributes": expect_attributes, + } + else: + meta = group.metadata + expect = {"node_type": "group", "zarr_format": 3, "attributes": expect_attributes} + + assert meta.to_dict() == expect From 7fe95b5f8cb840f3818c0f16fdc6e93e01cb420e Mon Sep 17 00:00:00 2001 From: "Christine P. Chai" Date: Tue, 21 Oct 2025 15:59:47 -0700 Subject: [PATCH 135/468] DOC: a array -> an array (#3537) * DOC: a array -> an array * Apply suggestion from @joshmoore --------- Co-authored-by: Josh Moore --- docs/release-notes.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/release-notes.md b/docs/release-notes.md index 2fa947d5eb..9e809f194e 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -9,7 +9,7 @@ - Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also provided under zarr.metadata. ([#1798](https://github.com/zarr-developers/zarr-python/issues/1798)) - Add obstore implementation of delete_dir. ([#3310](https://github.com/zarr-developers/zarr-python/issues/3310)) - Adds a registry for chunk key encodings for extensibility. This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. ([#3436](https://github.com/zarr-developers/zarr-python/issues/3436)) -- Trying to open a group at a path were a array already exists now raises a helpful error. ([#3444](https://github.com/zarr-developers/zarr-python/issues/3444)) +- Trying to open a group at a path where an array already exists now raises a helpful error. ([#3444](https://github.com/zarr-developers/zarr-python/issues/3444)) ## Bugfixes From e3ee5912ed0c40a05aca8236de7ad71f02963707 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 22 Oct 2025 14:32:16 +0200 Subject: [PATCH 136/468] Fix: allow "bytes" as an alias for "variable_length_bytes" (#3532) * add bytes alias for VariableLengthBytes * make alias test stand-alone * changelog --- changes/3532.misc.md | 2 ++ src/zarr/core/dtype/npy/bytes.py | 2 +- tests/test_dtype/test_npy/test_bytes.py | 7 +++++++ 3 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 changes/3532.misc.md diff --git a/changes/3532.misc.md b/changes/3532.misc.md new file mode 100644 index 0000000000..0249aa899c --- /dev/null +++ b/changes/3532.misc.md @@ -0,0 +1,2 @@ +Accept `"bytes"` as an alias for `"variable_length_bytes"` when parsing `JSON`-encoded Zarr V3 +data types. \ No newline at end of file diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index 16c3326f63..cb7d86e957 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -1046,7 +1046,7 @@ def _check_json_v3(cls, data: DTypeJSON) -> TypeGuard[Literal["variable_length_b True if the input is a valid representation of this class in Zarr V3, False otherwise. """ - return data == cls._zarr_v3_name + return data in (cls._zarr_v3_name, "bytes") @classmethod def _from_json_v2(cls, data: DTypeJSON) -> Self: diff --git a/tests/test_dtype/test_npy/test_bytes.py b/tests/test_dtype/test_npy/test_bytes.py index 39b5416635..6a4bcc4691 100644 --- a/tests/test_dtype/test_npy/test_bytes.py +++ b/tests/test_dtype/test_npy/test_bytes.py @@ -140,6 +140,13 @@ class TestVariableLengthBytes(BaseTestZDType): item_size_params = (VariableLengthBytes(),) +def test_vlen_bytes_alias() -> None: + """Test that "bytes" is an accepted alias for "variable_length_bytes" in JSON metadata""" + a = VariableLengthBytes.from_json("bytes", zarr_format=3) + b = VariableLengthBytes.from_json("variable_length_bytes", zarr_format=3) + assert a == b + + @pytest.mark.parametrize( "zdtype", [NullTerminatedBytes(length=10), RawBytes(length=10), VariableLengthBytes()] ) From 61ca06bc42564fa4c7ead262fd466772942572df Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 22 Oct 2025 20:56:46 +0200 Subject: [PATCH 137/468] fix: accept extra fields in array metadata (#3530) * add support for reading and preserving unknown, permitted fields in array metadata. * sort in error message * sort keys in the right place * changelog * rename changelog --- changes/3530.bugfix.md | 2 + src/zarr/core/array.py | 6 +- src/zarr/core/chunk_grids.py | 5 +- src/zarr/core/chunk_key_encodings.py | 9 ++- src/zarr/core/common.py | 17 +++-- src/zarr/core/metadata/__init__.py | 6 +- src/zarr/core/metadata/v3.py | 109 +++++++++++++++++++++++---- tests/test_metadata/test_v3.py | 72 +++++++++++++++++- 8 files changed, 194 insertions(+), 32 deletions(-) create mode 100644 changes/3530.bugfix.md diff --git a/changes/3530.bugfix.md b/changes/3530.bugfix.md new file mode 100644 index 0000000000..36a1787a3a --- /dev/null +++ b/changes/3530.bugfix.md @@ -0,0 +1,2 @@ +Fixed a bug that prevented Zarr Python from opening Zarr V3 array metadata documents that contained + extra keys with permissible values (dicts with a `"must_understand"` key set to `"false"`). \ No newline at end of file diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 42d6201ba9..8bd8be40b2 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -103,10 +103,10 @@ from zarr.core.metadata import ( ArrayMetadata, ArrayMetadataDict, + ArrayMetadataJSON_V3, ArrayV2Metadata, ArrayV2MetadataDict, ArrayV3Metadata, - ArrayV3MetadataDict, T_ArrayMetadata, ) from zarr.core.metadata.io import save_metadata @@ -319,7 +319,7 @@ def __init__( @overload def __init__( self: AsyncArray[ArrayV3Metadata], - metadata: ArrayV3Metadata | ArrayV3MetadataDict, + metadata: ArrayV3Metadata | ArrayMetadataJSON_V3, store_path: StorePath, config: ArrayConfigLike | None = None, ) -> None: ... @@ -1004,7 +1004,7 @@ async def example(): store_path = await make_store_path(store) metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format) # TODO: remove this cast when we have better type hints - _metadata_dict = cast("ArrayV3MetadataDict", metadata_dict) + _metadata_dict = cast("ArrayMetadataJSON_V3", metadata_dict) return cls(store_path=store_path, metadata=_metadata_dict) @property diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 94c2e27674..cf5bd8cdbe 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -15,6 +15,7 @@ from zarr.abc.metadata import Metadata from zarr.core.common import ( JSON, + NamedConfig, ShapeLike, ceildiv, parse_named_configuration, @@ -152,7 +153,7 @@ def normalize_chunks(chunks: Any, shape: tuple[int, ...], typesize: int) -> tupl @dataclass(frozen=True) class ChunkGrid(Metadata): @classmethod - def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid: + def from_dict(cls, data: dict[str, JSON] | ChunkGrid | NamedConfig[str, Any]) -> ChunkGrid: if isinstance(data, ChunkGrid): return data @@ -180,7 +181,7 @@ def __init__(self, *, chunk_shape: ShapeLike) -> None: object.__setattr__(self, "chunk_shape", chunk_shape_parsed) @classmethod - def _from_dict(cls, data: dict[str, JSON]) -> Self: + def _from_dict(cls, data: dict[str, JSON] | NamedConfig[str, Any]) -> Self: _, configuration_parsed = parse_named_configuration(data, "regular") return cls(**configuration_parsed) # type: ignore[arg-type] diff --git a/src/zarr/core/chunk_key_encodings.py b/src/zarr/core/chunk_key_encodings.py index 42d7615c61..5c9f77118a 100644 --- a/src/zarr/core/chunk_key_encodings.py +++ b/src/zarr/core/chunk_key_encodings.py @@ -2,7 +2,7 @@ from abc import ABC, abstractmethod from dataclasses import dataclass -from typing import TYPE_CHECKING, ClassVar, Literal, TypeAlias, TypedDict, cast +from typing import TYPE_CHECKING, Any, ClassVar, Literal, TypeAlias, TypedDict, cast if TYPE_CHECKING: from typing import NotRequired, Self @@ -10,6 +10,7 @@ from zarr.abc.metadata import Metadata from zarr.core.common import ( JSON, + NamedConfig, parse_named_configuration, ) from zarr.registry import get_chunk_key_encoding_class, register_chunk_key_encoding @@ -61,7 +62,9 @@ def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: """ -ChunkKeyEncodingLike: TypeAlias = dict[str, JSON] | ChunkKeyEncodingParams | ChunkKeyEncoding +ChunkKeyEncodingLike: TypeAlias = ( + dict[str, JSON] | ChunkKeyEncodingParams | ChunkKeyEncoding | NamedConfig[str, Any] +) @dataclass(frozen=True) @@ -108,7 +111,7 @@ def parse_chunk_key_encoding(data: ChunkKeyEncodingLike) -> ChunkKeyEncoding: # handle ChunkKeyEncodingParams if "name" in data and "separator" in data: - data = {"name": data["name"], "configuration": {"separator": data["separator"]}} + data = {"name": data["name"], "configuration": {"separator": data["separator"]}} # type: ignore[typeddict-item] # Now must be a named config data = cast("dict[str, JSON]", data) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index bebccb65fc..651ebd72f3 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -14,6 +14,7 @@ Final, Generic, Literal, + NotRequired, TypedDict, TypeVar, cast, @@ -63,8 +64,8 @@ class NamedConfig(TypedDict, Generic[TName, TConfig]): name: ReadOnly[TName] """The name of the object.""" - configuration: ReadOnly[TConfig] - """The configuration of the object.""" + configuration: NotRequired[ReadOnly[TConfig]] + """The configuration of the object. Not required.""" def product(tup: tuple[int, ...]) -> int: @@ -134,18 +135,24 @@ def parse_configuration(data: JSON) -> JSON: @overload def parse_named_configuration( - data: JSON, expected_name: str | None = None + data: JSON | NamedConfig[str, Any], expected_name: str | None = None ) -> tuple[str, dict[str, JSON]]: ... @overload def parse_named_configuration( - data: JSON, expected_name: str | None = None, *, require_configuration: bool = True + data: JSON | NamedConfig[str, Any], + expected_name: str | None = None, + *, + require_configuration: bool = True, ) -> tuple[str, dict[str, JSON] | None]: ... def parse_named_configuration( - data: JSON, expected_name: str | None = None, *, require_configuration: bool = True + data: JSON | NamedConfig[str, Any], + expected_name: str | None = None, + *, + require_configuration: bool = True, ) -> tuple[str, JSON | None]: if not isinstance(data, dict): raise TypeError(f"Expected dict, got {type(data)}") diff --git a/src/zarr/core/metadata/__init__.py b/src/zarr/core/metadata/__init__.py index 43b5ec98fe..691399c0f9 100644 --- a/src/zarr/core/metadata/__init__.py +++ b/src/zarr/core/metadata/__init__.py @@ -1,17 +1,17 @@ from typing import TypeAlias, TypeVar from .v2 import ArrayV2Metadata, ArrayV2MetadataDict -from .v3 import ArrayV3Metadata, ArrayV3MetadataDict +from .v3 import ArrayMetadataJSON_V3, ArrayV3Metadata ArrayMetadata: TypeAlias = ArrayV2Metadata | ArrayV3Metadata -ArrayMetadataDict: TypeAlias = ArrayV2MetadataDict | ArrayV3MetadataDict +ArrayMetadataDict: TypeAlias = ArrayV2MetadataDict | ArrayMetadataJSON_V3 T_ArrayMetadata = TypeVar("T_ArrayMetadata", ArrayV2Metadata, ArrayV3Metadata) __all__ = [ "ArrayMetadata", "ArrayMetadataDict", + "ArrayMetadataJSON_V3", "ArrayV2Metadata", "ArrayV2MetadataDict", "ArrayV3Metadata", - "ArrayV3MetadataDict", ] diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index cafcb99281..a14373c340 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -1,6 +1,7 @@ from __future__ import annotations -from typing import TYPE_CHECKING, TypedDict +from collections.abc import Mapping +from typing import TYPE_CHECKING, NotRequired, TypedDict, TypeGuard, cast from zarr.abc.metadata import Metadata from zarr.core.buffer.core import default_buffer_prototype @@ -33,6 +34,7 @@ JSON, ZARR_JSON, DimensionNames, + NamedConfig, parse_named_configuration, parse_shapelike, ) @@ -136,13 +138,61 @@ def parse_storage_transformers(data: object) -> tuple[dict[str, JSON], ...]: ) -class ArrayV3MetadataDict(TypedDict): +class AllowedExtraField(TypedDict): + """ + This class models allowed extra fields in array metadata. + They are ignored by Zarr Python. + """ + + must_understand: Literal[False] + + +def check_allowed_extra_field(data: object) -> TypeGuard[AllowedExtraField]: + """ + Check if the extra field is allowed according to the Zarr v3 spec. The object + must be a mapping with a "must_understand" key set to `False`. + """ + return isinstance(data, Mapping) and data.get("must_understand") is False + + +def parse_extra_fields( + data: Mapping[str, AllowedExtraField] | None, +) -> dict[str, AllowedExtraField]: + if data is None: + return {} + else: + conflict_keys = ARRAY_METADATA_KEYS & set(data.keys()) + if len(conflict_keys) > 0: + msg = ( + "Invalid extra fields. " + "The following keys: " + f"{sorted(conflict_keys)} " + "are invalid because they collide with keys reserved for use by the " + "array metadata document." + ) + raise ValueError(msg) + return dict(data) + + +class ArrayMetadataJSON_V3(TypedDict): """ A typed dictionary model for zarr v3 metadata. """ zarr_format: Literal[3] - attributes: dict[str, JSON] + node_type: Literal["array"] + data_type: str | NamedConfig[str, Mapping[str, object]] + shape: tuple[int, ...] + chunk_grid: NamedConfig[str, Mapping[str, object]] + chunk_key_encoding: NamedConfig[str, Mapping[str, object]] + fill_value: object + codecs: tuple[str | NamedConfig[str, Mapping[str, object]], ...] + attributes: NotRequired[Mapping[str, JSON]] + storage_transformers: NotRequired[tuple[NamedConfig[str, Mapping[str, object]], ...]] + dimension_names: NotRequired[tuple[str | None]] + + +ARRAY_METADATA_KEYS = set(ArrayMetadataJSON_V3.__annotations__.keys()) @dataclass(frozen=True, kw_only=True) @@ -158,19 +208,21 @@ class ArrayV3Metadata(Metadata): zarr_format: Literal[3] = field(default=3, init=False) node_type: Literal["array"] = field(default="array", init=False) storage_transformers: tuple[dict[str, JSON], ...] + extra_fields: dict[str, AllowedExtraField] def __init__( self, *, shape: Iterable[int], data_type: ZDType[TBaseDType, TBaseScalar], - chunk_grid: dict[str, JSON] | ChunkGrid, + chunk_grid: dict[str, JSON] | ChunkGrid | NamedConfig[str, Any], chunk_key_encoding: ChunkKeyEncodingLike, fill_value: object, - codecs: Iterable[Codec | dict[str, JSON]], + codecs: Iterable[Codec | dict[str, JSON] | NamedConfig[str, Any] | str], attributes: dict[str, JSON] | None, dimension_names: DimensionNames, storage_transformers: Iterable[dict[str, JSON]] | None = None, + extra_fields: Mapping[str, AllowedExtraField] | None = None, ) -> None: """ Because the class is a frozen dataclass, we set attributes using object.__setattr__ @@ -185,7 +237,7 @@ def __init__( attributes_parsed = parse_attributes(attributes) codecs_parsed_partial = parse_codecs(codecs) storage_transformers_parsed = parse_storage_transformers(storage_transformers) - + extra_fields_parsed = parse_extra_fields(extra_fields) array_spec = ArraySpec( shape=shape_parsed, dtype=data_type, @@ -205,6 +257,7 @@ def __init__( object.__setattr__(self, "fill_value", fill_value_parsed) object.__setattr__(self, "attributes", attributes_parsed) object.__setattr__(self, "storage_transformers", storage_transformers_parsed) + object.__setattr__(self, "extra_fields", extra_fields_parsed) self._validate_metadata() @@ -323,16 +376,45 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: except ValueError as e: raise TypeError(f"Invalid fill_value: {fill!r}") from e - # dimension_names key is optional, normalize missing to `None` - _data["dimension_names"] = _data.pop("dimension_names", None) - - # attributes key is optional, normalize missing to `None` - _data["attributes"] = _data.pop("attributes", None) - - return cls(**_data, fill_value=fill_value_parsed, data_type=data_type) # type: ignore[arg-type] + # check if there are extra keys + extra_keys = set(_data.keys()) - ARRAY_METADATA_KEYS + allowed_extra_fields: dict[str, AllowedExtraField] = {} + invalid_extra_fields = {} + for key in extra_keys: + val = _data[key] + if check_allowed_extra_field(val): + allowed_extra_fields[key] = val + else: + invalid_extra_fields[key] = val + if len(invalid_extra_fields) > 0: + msg = ( + "Got a Zarr V3 metadata document with the following disallowed extra fields:" + f"{sorted(invalid_extra_fields.keys())}." + 'Extra fields are not allowed unless they are a dict with a "must_understand" key' + "which is assigned the value `False`." + ) + raise MetadataValidationError(msg) + # TODO: replace this with a real type check! + _data_typed = cast(ArrayMetadataJSON_V3, _data) + + return cls( + shape=_data_typed["shape"], + chunk_grid=_data_typed["chunk_grid"], + chunk_key_encoding=_data_typed["chunk_key_encoding"], + codecs=_data_typed["codecs"], + attributes=_data_typed.get("attributes", {}), # type: ignore[arg-type] + dimension_names=_data_typed.get("dimension_names", None), + fill_value=fill_value_parsed, + data_type=data_type, + extra_fields=allowed_extra_fields, + storage_transformers=_data_typed.get("storage_transformers", ()), # type: ignore[arg-type] + ) def to_dict(self) -> dict[str, JSON]: out_dict = super().to_dict() + extra_fields = out_dict.pop("extra_fields") + out_dict = out_dict | extra_fields # type: ignore[operator] + out_dict["fill_value"] = self.data_type.to_json_scalar( self.fill_value, zarr_format=self.zarr_format ) @@ -351,7 +433,6 @@ def to_dict(self) -> dict[str, JSON]: dtype_meta = out_dict["data_type"] if isinstance(dtype_meta, ZDType): out_dict["data_type"] = dtype_meta.to_json(zarr_format=3) # type: ignore[unreachable] - return out_dict def update_shape(self, shape: tuple[int, ...]) -> Self: diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index f2c672a14e..01ed921053 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -12,11 +12,12 @@ from zarr.core.buffer import default_buffer_prototype from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding, V2ChunkKeyEncoding from zarr.core.config import config -from zarr.core.dtype import get_data_type_from_native_dtype +from zarr.core.dtype import UInt8, get_data_type_from_native_dtype from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING from zarr.core.dtype.npy.time import DateTime64 from zarr.core.group import GroupMetadata, parse_node_type from zarr.core.metadata.v3 import ( + ArrayMetadataJSON_V3, ArrayV3Metadata, parse_codecs, parse_dimension_names, @@ -33,8 +34,9 @@ from collections.abc import Sequence from typing import Any + from zarr.core.types import JSON + from zarr.abc.codec import Codec - from zarr.core.common import JSON from zarr.core.metadata.v3 import ( @@ -346,6 +348,72 @@ def test_parse_codecs_unknown_codec_raises(monkeypatch: pytest.MonkeyPatch) -> N parse_codecs(codecs) +@pytest.mark.parametrize( + "extra_value", + [ + {"must_understand": False, "param": 10}, + {"must_understand": True}, + 10, + ], +) +def test_from_dict_extra_fields(extra_value: dict[str, object] | int) -> None: + """ + Test that from_dict accepts extra fields if they have are a JSON object with + "must_understand": false, and raises an exception otherwise. + """ + metadata_dict: ArrayMetadataJSON_V3 = { # type: ignore[typeddict-unknown-key] + "zarr_format": 3, + "node_type": "array", + "shape": (1,), + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}}, + "data_type": "uint8", + "chunk_key_encoding": {"name": "default", "configuration": {"separator": "."}}, + "codecs": ({"name": "bytes"},), + "fill_value": 0, + "storage_transformers": (), + "attributes": {}, + "foo": extra_value, + } + + if isinstance(extra_value, dict) and extra_value.get("must_understand") is False: + # should be accepted + metadata = ArrayV3Metadata.from_dict(metadata_dict) # type: ignore[arg-type] + assert isinstance(metadata, ArrayV3Metadata) + assert metadata.to_dict() == metadata_dict + else: + # should raise an exception + with pytest.raises(MetadataValidationError, match="Got a Zarr V3 metadata document"): + metadata = ArrayV3Metadata.from_dict(metadata_dict) # type: ignore[arg-type] + + +def test_init_invalid_extra_fields() -> None: + """ + Test that initializing ArrayV3Metadata with extra fields fails when those fields + shadow the array metadata fields. + """ + extra_fields: dict[str, object] = {"shape": (10,), "data_type": "uint8"} + conflict_keys = set(extra_fields.keys()) + msg = ( + "Invalid extra fields. " + "The following keys: " + f"{sorted(conflict_keys)} " + "are invalid because they collide with keys reserved for use by the " + "array metadata document." + ) + with pytest.raises(ValueError, match=re.escape(msg)): + ArrayV3Metadata( + shape=(10,), + data_type=UInt8(), + chunk_grid={"name": "regular", "configuration": {"chunk_shape": (10,)}}, + chunk_key_encoding={"name": "default", "configuration": {"separator": "/"}}, + fill_value=0, + codecs=({"name": "bytes", "configuration": {"endian": "little"}},), + attributes={}, + dimension_names=None, + extra_fields=extra_fields, # type: ignore[arg-type] + ) + + @pytest.mark.parametrize("use_consolidated", [True, False]) @pytest.mark.parametrize("attributes", [None, {"foo": "bar"}]) def test_group_to_dict(use_consolidated: bool, attributes: None | dict[str, Any]) -> None: From d6d921e1a99a5574fb05efac63821fec8d55625c Mon Sep 17 00:00:00 2001 From: Fredrik Jansson Date: Wed, 22 Oct 2025 21:18:18 +0200 Subject: [PATCH 138/468] fsspec path handling (#3343) * fsspec path handling Proposed as fix for #3201. Some filesystems need the scheme as part of the path, while others don't. FsspecStore.from_url() throws an exception if the scheme is left in the path, for any filesystem except http and https. However, the swift fs also needs the scheme in the path. This commit removes the exception, rather than adding more special cases. * fsspec path handling: remove test for scheme in path --------- Co-authored-by: Davis Bennett --- src/zarr/storage/_fsspec.py | 10 ---------- tests/test_store/test_fsspec.py | 8 -------- 2 files changed, 18 deletions(-) diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index c5afed521c..7945fba467 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -138,10 +138,6 @@ def __init__( category=ZarrUserWarning, stacklevel=2, ) - if "://" in path and not path.startswith("http"): - # `not path.startswith("http")` is a special case for the http filesystem (¯\_(ツ)_/¯) - scheme, _ = path.split("://", maxsplit=1) - raise ValueError(f"path argument to FsspecStore must not include scheme ({scheme}://)") @classmethod def from_upath( @@ -246,12 +242,6 @@ def from_url( if not fs.async_impl: fs = _make_async(fs) - # fsspec is not consistent about removing the scheme from the path, so check and strip it here - # https://github.com/fsspec/filesystem_spec/issues/1722 - if "://" in path and not path.startswith("http"): - # `not path.startswith("http")` is a special case for the http filesystem (¯\_(ツ)_/¯) - path = fs._strip_protocol(path) - return cls(fs=fs, path=path, read_only=read_only, allowed_exceptions=allowed_exceptions) def with_read_only(self, read_only: bool = False) -> FsspecStore: diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index e970c674d4..1e3ed26568 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -238,14 +238,6 @@ def test_from_upath(self) -> None: assert result.fs.asynchronous assert result.path == f"{test_bucket_name}/foo/bar" - def test_init_raises_if_path_has_scheme(self, store_kwargs: dict[str, Any]) -> None: - # regression test for https://github.com/zarr-developers/zarr-python/issues/2342 - store_kwargs["path"] = "s3://" + store_kwargs["path"] - with pytest.raises( - ValueError, match="path argument to FsspecStore must not include scheme .*" - ): - self.store_cls(**store_kwargs) - def test_init_warns_if_fs_asynchronous_is_false(self) -> None: try: from fsspec import url_to_fs From 82147c132cb807a0c572ae08b6b62f726dbb4eca Mon Sep 17 00:00:00 2001 From: Christine Smit Date: Wed, 22 Oct 2025 15:30:39 -0400 Subject: [PATCH 139/468] Doc update (#3539) * Added resize() function signature change to V3 Migration documentation * Added towncrier note --------- Co-authored-by: Davis Bennett --- changes/3536.doc.md | 1 + docs/user-guide/v3_migration.md | 4 ++++ 2 files changed, 5 insertions(+) create mode 100644 changes/3536.doc.md diff --git a/changes/3536.doc.md b/changes/3536.doc.md new file mode 100644 index 0000000000..742a0cc3db --- /dev/null +++ b/changes/3536.doc.md @@ -0,0 +1 @@ +Updated 3.0 Migration Guide to include function signature change to zarr.Array.resize function. diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index c3a7ddbafe..291c348710 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -99,6 +99,10 @@ The following sections provide details on breaking changes in Zarr-Python 3. Zarr specification. To continue using version 2, set `zarr_format=2` when creating arrays or set `default_zarr_version=2` in Zarr's runtime configuration. +3. Function signature change to [`zarr.Array.resize`][] - the `resize` function now takes a + `zarr.core.common.ShapeLike` input rather than separate arguments for each dimension. + Use `resize((10,10))` in place of `resize(10,10)`. + ### The Group class 1. Disallow direct construction - use [`zarr.open_group`][] or [`zarr.create_group`][] From fc8e8ad1a143b1f39a2e08b470857a5e48a38bca Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 23 Oct 2025 13:16:38 -0400 Subject: [PATCH 140/468] Fix 404 page (#3543) --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index c9edf338af..151ecbbaa0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -4,7 +4,7 @@ repo_name: zarr-developers/zarr-python repo_url: https://github.com/zarr-developers/zarr-python site_description: An implementation of chunked, compressed, N-dimensional arrays for Python. site_author: Alistair Miles -site_url: https://zarr.readthedocs.io/ +site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://zarr.readthedocs.io/'] docs_dir: docs nav: From fe42655ae265e045f850e12f30726aa8668d6dde Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 24 Oct 2025 17:32:17 +0200 Subject: [PATCH 141/468] fix invalid blosc defaults (#3545) * re-arrange blosc codec to avoid invalid default values * changelog --- changes/3545.misc.md | 1 + src/zarr/codecs/blosc.py | 242 ++++++++++++++++++++++++++++---- src/zarr/core/common.py | 18 ++- tests/test_codecs/test_blosc.py | 48 ++++++- 4 files changed, 278 insertions(+), 31 deletions(-) create mode 100644 changes/3545.misc.md diff --git a/changes/3545.misc.md b/changes/3545.misc.md new file mode 100644 index 0000000000..9ab63462b1 --- /dev/null +++ b/changes/3545.misc.md @@ -0,0 +1 @@ +Changes the internal logic of the `BloscCodec` class to ensure that the `typesize` end `shuffle` parameters are not nullable. \ No newline at end of file diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 6a482ed6e5..ba89c59bf4 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -1,10 +1,11 @@ from __future__ import annotations import asyncio +import warnings from dataclasses import dataclass, replace from enum import Enum from functools import cached_property -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Final, Literal, NotRequired, TypedDict import numcodecs from numcodecs.blosc import Blosc @@ -12,8 +13,9 @@ from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper -from zarr.core.common import JSON, parse_enum, parse_named_configuration +from zarr.core.common import JSON, NamedRequiredConfig, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasItemSize +from zarr.errors import ZarrDeprecationWarning if TYPE_CHECKING: from typing import Self @@ -21,6 +23,40 @@ from zarr.core.array_spec import ArraySpec from zarr.core.buffer import Buffer +Shuffle = Literal["noshuffle", "shuffle", "bitshuffle"] +"""The shuffle values permitted for the blosc codec""" + +SHUFFLE: Final = ("noshuffle", "shuffle", "bitshuffle") + +CName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] +"""The codec identifiers used in the blosc codec """ + + +class BloscConfigV2(TypedDict): + """Configuration for the V2 Blosc codec""" + + cname: CName + clevel: int + shuffle: int + blocksize: int + typesize: NotRequired[int] + + +class BloscConfigV3(TypedDict): + """Configuration for the V3 Blosc codec""" + + cname: CName + clevel: int + shuffle: Shuffle + blocksize: int + typesize: int + + +class BloscJSON_V3(NamedRequiredConfig[Literal["blosc"], BloscConfigV3]): + """ + The JSON form of the Blosc codec in Zarr V3. + """ + class BloscShuffle(Enum): """ @@ -86,29 +122,186 @@ def parse_blocksize(data: JSON) -> int: @dataclass(frozen=True) class BloscCodec(BytesBytesCodec): - """blosc codec""" + """ + Blosc compression codec for zarr. + + Blosc is a high-performance compressor optimized for binary data. It uses a + combination of blocking, shuffling, and fast compression algorithms to achieve + excellent compression ratios and speed. + + Attributes + ---------- + tunable_attrs : set of {'typesize', 'shuffle'} + Attributes that will be automatically tuned when `evolve_from_array_spec()` + is called. By default, contains {'typesize', 'shuffle'}. When either + `typesize` or `shuffle` is explicitly set to None during initialization, + the corresponding attribute is added to this set (if not already present), + allowing it to be overridden based on the array's dtype. + is_fixed_size : bool + Always False for Blosc codec, as compression produces variable-sized output. + typesize : int + The data type size in bytes used for shuffle filtering. + cname : BloscCname + The compression algorithm being used (lz4, lz4hc, blosclz, snappy, zlib, or zstd). + clevel : int + The compression level (0-9). + shuffle : BloscShuffle + The shuffle filter mode (noshuffle, shuffle, or bitshuffle). + blocksize : int + The size of compressed blocks in bytes (0 for automatic). + + Parameters + ---------- + typesize : int, optional + The data type size in bytes. This affects how the shuffle filter processes + the data. If None (deprecated), defaults to 1 and the attribute is marked + as tunable. Default: 1. + cname : BloscCname or {'lz4', 'lz4hc', 'blosclz', 'snappy', 'zlib', 'zstd'}, optional + The compression algorithm to use. Default: 'zstd'. + clevel : int, optional + The compression level, from 0 (no compression) to 9 (maximum compression). + Higher values provide better compression at the cost of speed. Default: 5. + shuffle : BloscShuffle or {'noshuffle', 'shuffle', 'bitshuffle'}, optional + The shuffle filter to apply before compression: + + - 'noshuffle': No shuffling + - 'shuffle': Byte shuffling (better for typesize > 1) + - 'bitshuffle': Bit shuffling (better for typesize == 1) + + If None (deprecated), defaults to 'bitshuffle' and the attribute is marked + as tunable. Default: 'bitshuffle'. + blocksize : int, optional + The requested size of compressed blocks in bytes. A value of 0 means + automatic block size selection. Default: 0. + tunable_attrs : set of {'typesize', 'shuffle'}, optional + Names of attributes that can be automatically adjusted by + `evolve_from_array_spec()`. This allows the codec to adapt its parameters + based on the array's data type when the array is created. If None, defaults + to {'typesize', 'shuffle'}. + + Notes + ----- + **Tunable Attributes Logic**: + + The `tunable_attrs` mechanism allows codec parameters to be automatically + adjusted based on the array's data type: + + 1. **Initialization**: During `__init__`, if `tunable_attrs` is None, it + defaults to {'typesize', 'shuffle'}. This means both attributes can be + tuned by default. + + 2. **Deprecated None Values**: If `typesize` or `shuffle` is explicitly set + to None: + + - A deprecation warning is issued + - The parameter is set to a default value (1 for typesize, 'bitshuffle' + for shuffle) + - The attribute name is added to `tunable_attrs` + + 3. **Evolution**: When `evolve_from_array_spec()` is called (typically during + array creation), it creates a new codec instance with updated parameters: + + - If 'typesize' is in `tunable_attrs`, it's set to the array dtype's + item size + - If 'shuffle' is in `tunable_attrs`, it's set to 'bitshuffle' if + item_size == 1, otherwise 'shuffle' + + 4. **Explicit Values**: If you explicitly set `typesize=4` or + `shuffle='noshuffle'`, these values are NOT in `tunable_attrs` by default + and will not be changed by `evolve_from_array_spec()`. + + **Thread Safety**: This codec sets `numcodecs.blosc.use_threads = False` at + module import time to avoid threading issues in asyncio contexts. + + Examples + -------- + Create a Blosc codec with default settings: + + >>> codec = BloscCodec() + >>> codec.typesize + 1 + >>> codec.shuffle + + + Create a codec with specific compression settings: + + >>> codec = BloscCodec(cname='zstd', clevel=9, shuffle='shuffle') + >>> codec.cname + + + Use deprecated None values (will be tuned automatically): + + >>> codec = BloscCodec(typesize=None, shuffle=None) # doctest: +SKIP + DeprecationWarning: The typesize parameter was set to None... + >>> 'typesize' in codec.tunable_attrs + True + >>> 'shuffle' in codec.tunable_attrs + True + + Prevent automatic tuning: + + >>> codec = BloscCodec(typesize=4, shuffle='noshuffle', tunable_attrs=set()) + >>> codec.tunable_attrs + set() + + See Also + -------- + BloscShuffle : Enum for shuffle filter options + BloscCname : Enum for compression algorithm options + """ + tunable_attrs: set[Literal["typesize", "shuffle"]] is_fixed_size = False - typesize: int | None - cname: BloscCname = BloscCname.zstd - clevel: int = 5 - shuffle: BloscShuffle | None = BloscShuffle.noshuffle - blocksize: int = 0 + typesize: int + cname: BloscCname + clevel: int + shuffle: BloscShuffle + blocksize: int def __init__( self, *, - typesize: int | None = None, - cname: BloscCname | str = BloscCname.zstd, + typesize: int | None = 1, + cname: BloscCname | CName = BloscCname.zstd, clevel: int = 5, - shuffle: BloscShuffle | str | None = None, + shuffle: BloscShuffle | Shuffle | None = "bitshuffle", blocksize: int = 0, + tunable_attrs: set[Literal["typesize", "shuffle"]] | None = None, ) -> None: - typesize_parsed = parse_typesize(typesize) if typesize is not None else None + # set default value of tunable_attrs + if tunable_attrs is None: + object.__setattr__(self, "tunable_attrs", {"typesize", "shuffle"}) + else: + object.__setattr__(self, "tunable_attrs", tunable_attrs) + + # If typesize was set to None: warn, replace it with a valid typesize + # and flag the typesize attribute as safe to replace later + if typesize is None: + msg = ( + "The typesize parameter was set to None. This is deprecated. " + "Provide a positive int for the typesize parameter instead. " + ) + warnings.warn(msg, ZarrDeprecationWarning, stacklevel=2) + typesize = 1 + self.tunable_attrs.update({"typesize"}) + + # If shuffle was set to None: warn, replace it with a valid typesize + # and flag the shuffle attribute as safe to replace later + if shuffle is None: + msg = ( + "The shuffle parameter was set to None. This is deprecated. " + "Provide a valid shuffle literal string -- " + f"one of {SHUFFLE!r} -- instead." + ) + warnings.warn(msg, ZarrDeprecationWarning, stacklevel=2) + shuffle = BloscShuffle.bitshuffle + self.tunable_attrs.update({"shuffle"}) + + typesize_parsed = parse_typesize(typesize) cname_parsed = parse_enum(cname, BloscCname) clevel_parsed = parse_clevel(clevel) - shuffle_parsed = parse_enum(shuffle, BloscShuffle) if shuffle is not None else None + shuffle_parsed = parse_enum(shuffle, BloscShuffle) blocksize_parsed = parse_blocksize(blocksize) object.__setattr__(self, "typesize", typesize_parsed) @@ -123,11 +316,7 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: return cls(**configuration_parsed) # type: ignore[arg-type] def to_dict(self) -> dict[str, JSON]: - if self.typesize is None: - raise ValueError("`typesize` needs to be set for serialization.") - if self.shuffle is None: - raise ValueError("`shuffle` needs to be set for serialization.") - return { + result: BloscJSON_V3 = { "name": "blosc", "configuration": { "typesize": self.typesize, @@ -137,15 +326,22 @@ def to_dict(self) -> dict[str, JSON]: "blocksize": self.blocksize, }, } + return result # type: ignore[return-value] def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: + """ + Create a new codec with typesize and shuffle parameters adjusted + according to the size of each element in the data type + associated with array_spec. Parameters are only updated if they were set to + None when self.__init__ was called. + """ item_size = 1 if isinstance(array_spec.dtype, HasItemSize): item_size = array_spec.dtype.item_size new_codec = self - if new_codec.typesize is None: + if "typesize" in self.tunable_attrs: new_codec = replace(new_codec, typesize=item_size) - if new_codec.shuffle is None: + if "shuffle" in self.tunable_attrs: new_codec = replace( new_codec, shuffle=(BloscShuffle.bitshuffle if item_size == 1 else BloscShuffle.shuffle), @@ -155,15 +351,13 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: @cached_property def _blosc_codec(self) -> Blosc: - if self.shuffle is None: - raise ValueError("`shuffle` needs to be set for decoding and encoding.") map_shuffle_str_to_int = { BloscShuffle.noshuffle: 0, BloscShuffle.shuffle: 1, BloscShuffle.bitshuffle: 2, } - config_dict = { - "cname": self.cname.name, + config_dict: BloscConfigV2 = { + "cname": self.cname.name, # type: ignore[typeddict-item] "clevel": self.clevel, "shuffle": map_shuffle_str_to_int[self.shuffle], "blocksize": self.blocksize, diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 651ebd72f3..9b3d297298 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -55,7 +55,7 @@ class NamedConfig(TypedDict, Generic[TName, TConfig]): """ A typed dictionary representing an object with a name and configuration, where the configuration - is a mapping of string keys to values, e.g. another typed dictionary or a JSON object. + is an optional mapping of string keys to values, e.g. another typed dictionary or a JSON object. This class is generic with two type parameters: the type of the name (``TName``) and the type of the configuration (``TConfig``). @@ -68,6 +68,22 @@ class NamedConfig(TypedDict, Generic[TName, TConfig]): """The configuration of the object. Not required.""" +class NamedRequiredConfig(TypedDict, Generic[TName, TConfig]): + """ + A typed dictionary representing an object with a name and configuration, where the configuration + is a mapping of string keys to values, e.g. another typed dictionary or a JSON object. + + This class is generic with two type parameters: the type of the name (``TName``) and the type of + the configuration (``TConfig``). + """ + + name: ReadOnly[TName] + """The name of the object.""" + + configuration: ReadOnly[TConfig] + """The configuration of the object.""" + + def product(tup: tuple[int, ...]) -> int: return functools.reduce(operator.mul, tup, 1) diff --git a/tests/test_codecs/test_blosc.py b/tests/test_codecs/test_blosc.py index 6e6e9df383..e557dbe1f3 100644 --- a/tests/test_codecs/test_blosc.py +++ b/tests/test_codecs/test_blosc.py @@ -1,4 +1,5 @@ import json +from typing import Literal import numcodecs import numpy as np @@ -6,19 +7,22 @@ from packaging.version import Version import zarr -from zarr.abc.store import Store from zarr.codecs import BloscCodec +from zarr.codecs.blosc import BloscShuffle +from zarr.core.array_spec import ArraySpec from zarr.core.buffer import default_buffer_prototype -from zarr.storage import StorePath +from zarr.core.dtype import UInt16 +from zarr.errors import ZarrDeprecationWarning +from zarr.storage import MemoryStore, StorePath -@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) @pytest.mark.parametrize("dtype", ["uint8", "uint16"]) -async def test_blosc_evolve(store: Store, dtype: str) -> None: +async def test_blosc_evolve(dtype: str) -> None: typesize = np.dtype(dtype).itemsize path = "blosc_evolve" + store = MemoryStore() spath = StorePath(store, path) - await zarr.api.asynchronous.create_array( + zarr.create_array( spath, shape=(16, 16), chunks=(16, 16), @@ -38,7 +42,7 @@ async def test_blosc_evolve(store: Store, dtype: str) -> None: path2 = "blosc_evolve_sharding" spath2 = StorePath(store, path2) - await zarr.api.asynchronous.create_array( + zarr.create_array( spath2, shape=(16, 16), chunks=(16, 16), @@ -58,6 +62,38 @@ async def test_blosc_evolve(store: Store, dtype: str) -> None: assert blosc_configuration_json["shuffle"] == "shuffle" +@pytest.mark.parametrize("tunable_attrs", [{"typesize"}, {"shuffle"}, {"typesize", "shuffle"}]) +def test_tunable_attrs(tunable_attrs: set[Literal["typesize", "shuffle"]]) -> None: + """ + Test that the tunable_attrs parameter is respected when calling evolve_from_array_spec + """ + codec = BloscCodec(tunable_attrs=tunable_attrs) + new_dtype = UInt16() + array_spec = ArraySpec( + shape=(1,), + dtype=new_dtype, + fill_value=1, + prototype=default_buffer_prototype(), + config={}, # type: ignore[arg-type] + ) + + evolved_codec = codec.evolve_from_array_spec(array_spec=array_spec) + if "typesize" in tunable_attrs: + assert evolved_codec.typesize == new_dtype.item_size + else: + assert evolved_codec.typesize == codec.typesize + if "shuffle" in tunable_attrs: + assert evolved_codec.shuffle == BloscShuffle.shuffle + else: + assert evolved_codec.shuffle == codec.shuffle + + +@pytest.mark.parametrize("kwargs", [{"typesize": None}, {"shuffle": None}]) +def test_invalid_parameters_warns(kwargs: dict[str, object]) -> None: + with pytest.warns(ZarrDeprecationWarning, match="The .* parameter was set to None."): + BloscCodec(**kwargs) # type: ignore[arg-type] + + async def test_typesize() -> None: a = np.arange(1000000, dtype=np.uint64) codecs = [zarr.codecs.BytesCodec(), zarr.codecs.BloscCodec()] From b75aeb195f7cbd1babac5ea034b224b843a7a258 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 27 Oct 2025 09:27:11 +0100 Subject: [PATCH 142/468] Bump the actions group with 3 updates (#3549) --- .github/workflows/check_changelogs.yml | 2 +- .github/workflows/releases.yml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index b9ffaa6c7f..d331ae1e6a 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -12,7 +12,7 @@ jobs: - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 - name: Install uv - uses: astral-sh/setup-uv@2ddd2b9cb38ad8efd50337e8ab201519a34c9f24 # v7.1.1 + uses: astral-sh/setup-uv@85856786d1ce8acfbcc2f13a5f3fbd6b938f9f41 # v7.1.2 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 94522e0874..32732689a9 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -27,7 +27,7 @@ jobs: pip install hatch - name: Build wheel and sdist run: hatch build - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@v5 with: name: releases path: dist @@ -36,7 +36,7 @@ jobs: needs: [build_artifacts] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@v5 + - uses: actions/download-artifact@v6 with: name: releases path: dist @@ -51,7 +51,7 @@ jobs: runs-on: ubuntu-latest if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') steps: - - uses: actions/download-artifact@v5 + - uses: actions/download-artifact@v6 with: name: releases path: dist From b0e5c6997300ef3eb0f11be390ff6abfcb0e0428 Mon Sep 17 00:00:00 2001 From: Terraputix Date: Mon, 27 Oct 2025 13:04:20 +0100 Subject: [PATCH 143/468] fix for failing numcodecs.zarr3 codecs (#3326) * add array copy for array view * fix broken codecs without copying --------- Co-authored-by: Davis Bennett --- src/zarr/core/codec_pipeline.py | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 63fcda7065..fd557ac43e 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -301,6 +301,22 @@ def _merge_chunk_array( is_complete_chunk: bool, drop_axes: tuple[int, ...], ) -> NDBuffer: + if ( + is_complete_chunk + and value.shape == chunk_spec.shape + # Guard that this is not a partial chunk at the end with is_complete_chunk=True + and value[out_selection].shape == chunk_spec.shape + ): + return value + if existing_chunk_array is None: + chunk_array = chunk_spec.prototype.nd_buffer.create( + shape=chunk_spec.shape, + dtype=chunk_spec.dtype.to_native_dtype(), + order=chunk_spec.order, + fill_value=fill_value_or_default(chunk_spec), + ) + else: + chunk_array = existing_chunk_array.copy() # make a writable copy if chunk_selection == () or is_scalar( value.as_ndarray_like(), chunk_spec.dtype.to_native_dtype() ): @@ -316,20 +332,6 @@ def _merge_chunk_array( for idx in range(chunk_spec.ndim) ) chunk_value = chunk_value[item] - if is_complete_chunk and chunk_value.shape == chunk_spec.shape: - # TODO: For the last chunk, we could have is_complete_chunk=True - # that is smaller than the chunk_spec.shape but this throws - # an error in the _decode_single - return chunk_value - if existing_chunk_array is None: - chunk_array = chunk_spec.prototype.nd_buffer.create( - shape=chunk_spec.shape, - dtype=chunk_spec.dtype.to_native_dtype(), - order=chunk_spec.order, - fill_value=fill_value_or_default(chunk_spec), - ) - else: - chunk_array = existing_chunk_array.copy() # make a writable copy chunk_array[chunk_selection] = chunk_value return chunk_array From 591b895a81d9289255efc77479563fcb0cc8b8c5 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 27 Oct 2025 13:44:37 +0100 Subject: [PATCH 144/468] fix/simpler blosc tuning (#3553) * only autotune when the default parameters were chosen, or they were set to None * better refactoring of blosc codec * changelog --- changes/3545.misc.md | 1 - changes/3553.misc.md | 1 + src/zarr/codecs/blosc.py | 104 ++++++-------------------------- tests/test_codecs/test_blosc.py | 31 +++++----- 4 files changed, 35 insertions(+), 102 deletions(-) delete mode 100644 changes/3545.misc.md create mode 100644 changes/3553.misc.md diff --git a/changes/3545.misc.md b/changes/3545.misc.md deleted file mode 100644 index 9ab63462b1..0000000000 --- a/changes/3545.misc.md +++ /dev/null @@ -1 +0,0 @@ -Changes the internal logic of the `BloscCodec` class to ensure that the `typesize` end `shuffle` parameters are not nullable. \ No newline at end of file diff --git a/changes/3553.misc.md b/changes/3553.misc.md new file mode 100644 index 0000000000..1354b2da56 --- /dev/null +++ b/changes/3553.misc.md @@ -0,0 +1 @@ +Changes the internal logic of the `BloscCodec` class to ensure that the `typesize` and `shuffle` parameters are not set to `None` when creating a new instance of `BloscCodec`. \ No newline at end of file diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index ba89c59bf4..5b91cfa005 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -1,8 +1,7 @@ from __future__ import annotations import asyncio -import warnings -from dataclasses import dataclass, replace +from dataclasses import dataclass, field, replace from enum import Enum from functools import cached_property from typing import TYPE_CHECKING, Final, Literal, NotRequired, TypedDict @@ -15,7 +14,6 @@ from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, NamedRequiredConfig, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasItemSize -from zarr.errors import ZarrDeprecationWarning if TYPE_CHECKING: from typing import Self @@ -131,12 +129,6 @@ class BloscCodec(BytesBytesCodec): Attributes ---------- - tunable_attrs : set of {'typesize', 'shuffle'} - Attributes that will be automatically tuned when `evolve_from_array_spec()` - is called. By default, contains {'typesize', 'shuffle'}. When either - `typesize` or `shuffle` is explicitly set to None during initialization, - the corresponding attribute is added to this set (if not already present), - allowing it to be overridden based on the array's dtype. is_fixed_size : bool Always False for Blosc codec, as compression produces variable-sized output. typesize : int @@ -154,8 +146,8 @@ class BloscCodec(BytesBytesCodec): ---------- typesize : int, optional The data type size in bytes. This affects how the shuffle filter processes - the data. If None (deprecated), defaults to 1 and the attribute is marked - as tunable. Default: 1. + the data. If None, defaults to 1 and the attribute is marked as tunable. + Default: 1. cname : BloscCname or {'lz4', 'lz4hc', 'blosclz', 'snappy', 'zlib', 'zstd'}, optional The compression algorithm to use. Default: 'zstd'. clevel : int, optional @@ -168,47 +160,17 @@ class BloscCodec(BytesBytesCodec): - 'shuffle': Byte shuffling (better for typesize > 1) - 'bitshuffle': Bit shuffling (better for typesize == 1) - If None (deprecated), defaults to 'bitshuffle' and the attribute is marked + If None, defaults to 'bitshuffle' and the attribute is marked as tunable. Default: 'bitshuffle'. blocksize : int, optional The requested size of compressed blocks in bytes. A value of 0 means automatic block size selection. Default: 0. - tunable_attrs : set of {'typesize', 'shuffle'}, optional - Names of attributes that can be automatically adjusted by - `evolve_from_array_spec()`. This allows the codec to adapt its parameters - based on the array's data type when the array is created. If None, defaults - to {'typesize', 'shuffle'}. Notes ----- - **Tunable Attributes Logic**: - - The `tunable_attrs` mechanism allows codec parameters to be automatically - adjusted based on the array's data type: - - 1. **Initialization**: During `__init__`, if `tunable_attrs` is None, it - defaults to {'typesize', 'shuffle'}. This means both attributes can be - tuned by default. - - 2. **Deprecated None Values**: If `typesize` or `shuffle` is explicitly set - to None: - - - A deprecation warning is issued - - The parameter is set to a default value (1 for typesize, 'bitshuffle' - for shuffle) - - The attribute name is added to `tunable_attrs` - - 3. **Evolution**: When `evolve_from_array_spec()` is called (typically during - array creation), it creates a new codec instance with updated parameters: - - - If 'typesize' is in `tunable_attrs`, it's set to the array dtype's - item size - - If 'shuffle' is in `tunable_attrs`, it's set to 'bitshuffle' if - item_size == 1, otherwise 'shuffle' - - 4. **Explicit Values**: If you explicitly set `typesize=4` or - `shuffle='noshuffle'`, these values are NOT in `tunable_attrs` by default - and will not be changed by `evolve_from_array_spec()`. + **Tunable attributes**: If `typesize` or `shuffle` are set to None during + initialization, they are marked as tunable attributes. This means they can be + adjusted later based on the data type of the array being compressed. **Thread Safety**: This codec sets `numcodecs.blosc.use_threads = False` at module import time to avoid threading issues in asyncio contexts. @@ -229,28 +191,14 @@ class BloscCodec(BytesBytesCodec): >>> codec.cname - Use deprecated None values (will be tuned automatically): - - >>> codec = BloscCodec(typesize=None, shuffle=None) # doctest: +SKIP - DeprecationWarning: The typesize parameter was set to None... - >>> 'typesize' in codec.tunable_attrs - True - >>> 'shuffle' in codec.tunable_attrs - True - - Prevent automatic tuning: - - >>> codec = BloscCodec(typesize=4, shuffle='noshuffle', tunable_attrs=set()) - >>> codec.tunable_attrs - set() - See Also -------- BloscShuffle : Enum for shuffle filter options BloscCname : Enum for compression algorithm options """ - tunable_attrs: set[Literal["typesize", "shuffle"]] + # This attribute tracks parameters were set to None at init time, and thus tunable + _tunable_attrs: set[Literal["typesize", "shuffle"]] = field(init=False) is_fixed_size = False typesize: int @@ -262,41 +210,25 @@ class BloscCodec(BytesBytesCodec): def __init__( self, *, - typesize: int | None = 1, + typesize: int | None = None, cname: BloscCname | CName = BloscCname.zstd, clevel: int = 5, - shuffle: BloscShuffle | Shuffle | None = "bitshuffle", + shuffle: BloscShuffle | Shuffle | None = None, blocksize: int = 0, - tunable_attrs: set[Literal["typesize", "shuffle"]] | None = None, ) -> None: - # set default value of tunable_attrs - if tunable_attrs is None: - object.__setattr__(self, "tunable_attrs", {"typesize", "shuffle"}) - else: - object.__setattr__(self, "tunable_attrs", tunable_attrs) + object.__setattr__(self, "_tunable_attrs", set()) - # If typesize was set to None: warn, replace it with a valid typesize + # If typesize was set to None, replace it with a valid typesize # and flag the typesize attribute as safe to replace later if typesize is None: - msg = ( - "The typesize parameter was set to None. This is deprecated. " - "Provide a positive int for the typesize parameter instead. " - ) - warnings.warn(msg, ZarrDeprecationWarning, stacklevel=2) typesize = 1 - self.tunable_attrs.update({"typesize"}) + self._tunable_attrs.update({"typesize"}) - # If shuffle was set to None: warn, replace it with a valid typesize + # If shuffle was set to None, replace it with a valid shuffle # and flag the shuffle attribute as safe to replace later if shuffle is None: - msg = ( - "The shuffle parameter was set to None. This is deprecated. " - "Provide a valid shuffle literal string -- " - f"one of {SHUFFLE!r} -- instead." - ) - warnings.warn(msg, ZarrDeprecationWarning, stacklevel=2) shuffle = BloscShuffle.bitshuffle - self.tunable_attrs.update({"shuffle"}) + self._tunable_attrs.update({"shuffle"}) typesize_parsed = parse_typesize(typesize) cname_parsed = parse_enum(cname, BloscCname) @@ -339,9 +271,9 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: if isinstance(array_spec.dtype, HasItemSize): item_size = array_spec.dtype.item_size new_codec = self - if "typesize" in self.tunable_attrs: + if "typesize" in self._tunable_attrs: new_codec = replace(new_codec, typesize=item_size) - if "shuffle" in self.tunable_attrs: + if "shuffle" in self._tunable_attrs: new_codec = replace( new_codec, shuffle=(BloscShuffle.bitshuffle if item_size == 1 else BloscShuffle.shuffle), diff --git a/tests/test_codecs/test_blosc.py b/tests/test_codecs/test_blosc.py index e557dbe1f3..6f4821f8b1 100644 --- a/tests/test_codecs/test_blosc.py +++ b/tests/test_codecs/test_blosc.py @@ -1,5 +1,4 @@ import json -from typing import Literal import numcodecs import numpy as np @@ -8,11 +7,10 @@ import zarr from zarr.codecs import BloscCodec -from zarr.codecs.blosc import BloscShuffle +from zarr.codecs.blosc import BloscShuffle, Shuffle from zarr.core.array_spec import ArraySpec from zarr.core.buffer import default_buffer_prototype from zarr.core.dtype import UInt16 -from zarr.errors import ZarrDeprecationWarning from zarr.storage import MemoryStore, StorePath @@ -62,12 +60,21 @@ async def test_blosc_evolve(dtype: str) -> None: assert blosc_configuration_json["shuffle"] == "shuffle" -@pytest.mark.parametrize("tunable_attrs", [{"typesize"}, {"shuffle"}, {"typesize", "shuffle"}]) -def test_tunable_attrs(tunable_attrs: set[Literal["typesize", "shuffle"]]) -> None: +@pytest.mark.parametrize("shuffle", [None, "bitshuffle", BloscShuffle.shuffle]) +@pytest.mark.parametrize("typesize", [None, 1, 2]) +def test_tunable_attrs_param(shuffle: None | Shuffle | BloscShuffle, typesize: None | int) -> None: """ - Test that the tunable_attrs parameter is respected when calling evolve_from_array_spec + Test that the tunable_attrs parameter is set as expected when creating a BloscCodec, """ - codec = BloscCodec(tunable_attrs=tunable_attrs) + codec = BloscCodec(typesize=typesize, shuffle=shuffle) + + if shuffle is None: + assert codec.shuffle == BloscShuffle.bitshuffle # default shuffle + assert "shuffle" in codec._tunable_attrs + if typesize is None: + assert codec.typesize == 1 # default typesize + assert "typesize" in codec._tunable_attrs + new_dtype = UInt16() array_spec = ArraySpec( shape=(1,), @@ -78,22 +85,16 @@ def test_tunable_attrs(tunable_attrs: set[Literal["typesize", "shuffle"]]) -> No ) evolved_codec = codec.evolve_from_array_spec(array_spec=array_spec) - if "typesize" in tunable_attrs: + if typesize is None: assert evolved_codec.typesize == new_dtype.item_size else: assert evolved_codec.typesize == codec.typesize - if "shuffle" in tunable_attrs: + if shuffle is None: assert evolved_codec.shuffle == BloscShuffle.shuffle else: assert evolved_codec.shuffle == codec.shuffle -@pytest.mark.parametrize("kwargs", [{"typesize": None}, {"shuffle": None}]) -def test_invalid_parameters_warns(kwargs: dict[str, object]) -> None: - with pytest.warns(ZarrDeprecationWarning, match="The .* parameter was set to None."): - BloscCodec(**kwargs) # type: ignore[arg-type] - - async def test_typesize() -> None: a = np.arange(1000000, dtype=np.uint64) codecs = [zarr.codecs.BytesCodec(), zarr.codecs.BloscCodec()] From b3e9aed305092236c5db70deee0b26dad648d3b0 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 27 Oct 2025 18:36:34 +0100 Subject: [PATCH 145/468] remove dead code (#3555) --- src/zarr/core/config.py | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index fe61ae7955..5acf242ef7 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -36,21 +36,11 @@ if TYPE_CHECKING: from donfig.config_obj import ConfigSet - from zarr.core.dtype.wrapper import ZDType - class BadConfigError(ValueError): _msg = "bad Config: %r" -# These values are used for rough categorization of data types -# we use this for choosing a default encoding scheme based on the data type. Specifically, -# these categories are keys in a configuration dictionary. -# it is not a part of the ZDType class because these categories are more of an implementation detail -# of our config system rather than a useful attribute of any particular data type. -DTypeCategory = Literal["variable-length-string", "default"] - - class Config(DConfig): # type: ignore[misc] """The Config will collect configuration from config files and environment variables @@ -160,17 +150,3 @@ def parse_indexing_order(data: Any) -> Literal["C", "F"]: return cast("Literal['C', 'F']", data) msg = f"Expected one of ('C', 'F'), got {data} instead." raise ValueError(msg) - - -def categorize_data_type(dtype: ZDType[Any, Any]) -> DTypeCategory: - """ - Classify a ZDType. The return value is a string which belongs to the type ``DTypeCategory``. - - This is used by the config system to determine how to encode arrays with the associated data type - when the user has not specified a particular serialization scheme. - """ - from zarr.core.dtype import VariableLengthUTF8 - - if isinstance(dtype, VariableLengthUTF8): - return "variable-length-string" - return "default" From e6ef2b132dcbb0f1475a9a9ca0e9a89824891adc Mon Sep 17 00:00:00 2001 From: "Noah D. Brenowitz" Date: Fri, 31 Oct 2025 14:18:07 -0700 Subject: [PATCH 146/468] optimize shard writing (#3561) * optimize shard writing Writing to sharded arrays was up to 10x slower for largish chunk sizes because the _ShardBuilder object has many calls to np.concatenate. This commit coalesces these into a single concatenate call, and improves write performance by a factor of 10 on the benchmarking script in #3560. Added a new core.Buffer.combine API Resolves #3560 Signed-off-by: Noah D. Brenowitz * remove redundant method Signed-off-by: Noah D. Brenowitz * remove redundant np.asayarray Signed-off-by: Noah D. Brenowitz * clarify ShardBuilder API remove inheritance, hide the index attribute and remove some indirection Signed-off-by: Noah D. Brenowitz * Remove shard builder objects just use dicts Signed-off-by: Noah D. Brenowitz * fix missing chunk case Signed-off-by: Noah D. Brenowitz * add release note --------- Signed-off-by: Noah D. Brenowitz --- changes/3560.bugfix.md | 1 + src/zarr/codecs/sharding.py | 193 ++++++++++++----------------------- src/zarr/core/buffer/core.py | 7 +- src/zarr/core/buffer/cpu.py | 15 ++- src/zarr/core/buffer/gpu.py | 17 +-- 5 files changed, 87 insertions(+), 146 deletions(-) create mode 100644 changes/3560.bugfix.md diff --git a/changes/3560.bugfix.md b/changes/3560.bugfix.md new file mode 100644 index 0000000000..c3306cb6ac --- /dev/null +++ b/changes/3560.bugfix.md @@ -0,0 +1 @@ +Improve write performance to large shards by up to 10x. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index b0fd75cef7..8124ea44ea 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -1,7 +1,7 @@ from __future__ import annotations from collections.abc import Iterable, Mapping, MutableMapping -from dataclasses import dataclass, field, replace +from dataclasses import dataclass, replace from enum import Enum from functools import lru_cache from operator import itemgetter @@ -54,15 +54,15 @@ from zarr.registry import get_ndbuffer_class, get_pipeline_class if TYPE_CHECKING: - from collections.abc import Awaitable, Callable, Iterator + from collections.abc import Iterator from typing import Self from zarr.core.common import JSON from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType MAX_UINT_64 = 2**64 - 1 -ShardMapping = Mapping[tuple[int, ...], Buffer] -ShardMutableMapping = MutableMapping[tuple[int, ...], Buffer] +ShardMapping = Mapping[tuple[int, ...], Buffer | None] +ShardMutableMapping = MutableMapping[tuple[int, ...], Buffer | None] class ShardingCodecIndexLocation(Enum): @@ -219,114 +219,6 @@ def __len__(self) -> int: def __iter__(self) -> Iterator[tuple[int, ...]]: return c_order_iter(self.index.offsets_and_lengths.shape[:-1]) - def is_empty(self) -> bool: - return self.index.is_all_empty() - - -class _ShardBuilder(_ShardReader, ShardMutableMapping): - buf: Buffer - index: _ShardIndex - - @classmethod - def merge_with_morton_order( - cls, - chunks_per_shard: tuple[int, ...], - tombstones: set[tuple[int, ...]], - *shard_dicts: ShardMapping, - ) -> _ShardBuilder: - obj = cls.create_empty(chunks_per_shard) - for chunk_coords in morton_order_iter(chunks_per_shard): - if chunk_coords in tombstones: - continue - for shard_dict in shard_dicts: - maybe_value = shard_dict.get(chunk_coords, None) - if maybe_value is not None: - obj[chunk_coords] = maybe_value - break - return obj - - @classmethod - def create_empty( - cls, chunks_per_shard: tuple[int, ...], buffer_prototype: BufferPrototype | None = None - ) -> _ShardBuilder: - if buffer_prototype is None: - buffer_prototype = default_buffer_prototype() - obj = cls() - obj.buf = buffer_prototype.buffer.create_zero_length() - obj.index = _ShardIndex.create_empty(chunks_per_shard) - return obj - - def __setitem__(self, chunk_coords: tuple[int, ...], value: Buffer) -> None: - chunk_start = len(self.buf) - chunk_length = len(value) - self.buf += value - self.index.set_chunk_slice(chunk_coords, slice(chunk_start, chunk_start + chunk_length)) - - def __delitem__(self, chunk_coords: tuple[int, ...]) -> None: - raise NotImplementedError - - async def finalize( - self, - index_location: ShardingCodecIndexLocation, - index_encoder: Callable[[_ShardIndex], Awaitable[Buffer]], - ) -> Buffer: - index_bytes = await index_encoder(self.index) - if index_location == ShardingCodecIndexLocation.start: - empty_chunks_mask = self.index.offsets_and_lengths[..., 0] == MAX_UINT_64 - self.index.offsets_and_lengths[~empty_chunks_mask, 0] += len(index_bytes) - index_bytes = await index_encoder(self.index) # encode again with corrected offsets - out_buf = index_bytes + self.buf - else: - out_buf = self.buf + index_bytes - return out_buf - - -@dataclass(frozen=True) -class _MergingShardBuilder(ShardMutableMapping): - old_dict: _ShardReader - new_dict: _ShardBuilder - tombstones: set[tuple[int, ...]] = field(default_factory=set) - - def __getitem__(self, chunk_coords: tuple[int, ...]) -> Buffer: - chunk_bytes_maybe = self.new_dict.get(chunk_coords) - if chunk_bytes_maybe is not None: - return chunk_bytes_maybe - return self.old_dict[chunk_coords] - - def __setitem__(self, chunk_coords: tuple[int, ...], value: Buffer) -> None: - self.new_dict[chunk_coords] = value - - def __delitem__(self, chunk_coords: tuple[int, ...]) -> None: - self.tombstones.add(chunk_coords) - - def __len__(self) -> int: - return self.old_dict.__len__() - - def __iter__(self) -> Iterator[tuple[int, ...]]: - return self.old_dict.__iter__() - - def is_empty(self) -> bool: - full_chunk_coords_map = self.old_dict.index.get_full_chunk_map() - full_chunk_coords_map = np.logical_or( - full_chunk_coords_map, self.new_dict.index.get_full_chunk_map() - ) - for tombstone in self.tombstones: - full_chunk_coords_map[tombstone] = False - return bool(np.array_equiv(full_chunk_coords_map, False)) - - async def finalize( - self, - index_location: ShardingCodecIndexLocation, - index_encoder: Callable[[_ShardIndex], Awaitable[Buffer]], - ) -> Buffer: - shard_builder = _ShardBuilder.merge_with_morton_order( - self.new_dict.index.chunks_per_shard, - self.tombstones, - self.new_dict, - self.old_dict, - ) - return await shard_builder.finalize(index_location, index_encoder) - @dataclass(frozen=True) class ShardingCodec( @@ -573,7 +465,7 @@ async def _encode_single( ) ) - shard_builder = _ShardBuilder.create_empty(chunks_per_shard) + shard_builder = dict.fromkeys(morton_order_iter(chunks_per_shard)) await self.codec_pipeline.write( [ @@ -589,7 +481,11 @@ async def _encode_single( shard_array, ) - return await shard_builder.finalize(self.index_location, self._encode_shard_index) + return await self._encode_shard_dict( + shard_builder, + chunks_per_shard=chunks_per_shard, + buffer_prototype=default_buffer_prototype(), + ) async def _encode_partial_single( self, @@ -603,15 +499,13 @@ async def _encode_partial_single( chunks_per_shard = self._get_chunks_per_shard(shard_spec) chunk_spec = self._get_chunk_spec(shard_spec) - shard_dict = _MergingShardBuilder( - await self._load_full_shard_maybe( - byte_getter=byte_setter, - prototype=chunk_spec.prototype, - chunks_per_shard=chunks_per_shard, - ) - or _ShardReader.create_empty(chunks_per_shard), - _ShardBuilder.create_empty(chunks_per_shard), + shard_reader = await self._load_full_shard_maybe( + byte_getter=byte_setter, + prototype=chunk_spec.prototype, + chunks_per_shard=chunks_per_shard, ) + shard_reader = shard_reader or _ShardReader.create_empty(chunks_per_shard) + shard_dict = {k: shard_reader.get(k) for k in morton_order_iter(chunks_per_shard)} indexer = list( get_indexer( @@ -632,16 +526,57 @@ async def _encode_partial_single( ], shard_array, ) + buf = await self._encode_shard_dict( + shard_dict, + chunks_per_shard=chunks_per_shard, + buffer_prototype=default_buffer_prototype(), + ) - if shard_dict.is_empty(): + if buf is None: await byte_setter.delete() else: - await byte_setter.set( - await shard_dict.finalize( - self.index_location, - self._encode_shard_index, - ) - ) + await byte_setter.set(buf) + + async def _encode_shard_dict( + self, + map: ShardMapping, + chunks_per_shard: tuple[int, ...], + buffer_prototype: BufferPrototype, + ) -> Buffer | None: + index = _ShardIndex.create_empty(chunks_per_shard) + + buffers = [] + + template = buffer_prototype.buffer.create_zero_length() + chunk_start = 0 + for chunk_coords in morton_order_iter(chunks_per_shard): + value = map.get(chunk_coords) + if value is None: + continue + + if len(value) == 0: + continue + + chunk_length = len(value) + buffers.append(value) + index.set_chunk_slice(chunk_coords, slice(chunk_start, chunk_start + chunk_length)) + chunk_start += chunk_length + + if len(buffers) == 0: + return None + + index_bytes = await self._encode_shard_index(index) + if self.index_location == ShardingCodecIndexLocation.start: + empty_chunks_mask = index.offsets_and_lengths[..., 0] == MAX_UINT_64 + index.offsets_and_lengths[~empty_chunks_mask, 0] += len(index_bytes) + index_bytes = await self._encode_shard_index( + index + ) # encode again with corrected offsets + buffers.insert(0, index_bytes) + else: + buffers.append(index_bytes) + + return template.combine(buffers) def _is_total_shard( self, all_chunk_coords: set[tuple[int, ...]], chunks_per_shard: tuple[int, ...] diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index 189916dc91..ddd3073af2 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -2,6 +2,7 @@ import sys from abc import ABC, abstractmethod +from collections.abc import Iterable from typing import ( TYPE_CHECKING, Any, @@ -294,9 +295,13 @@ def __len__(self) -> int: return self._data.size @abstractmethod + def combine(self, others: Iterable[Buffer]) -> Self: + """Concatenate many buffers""" + ... + def __add__(self, other: Buffer) -> Self: """Concatenate two buffers""" - ... + return self.combine([other]) def __eq__(self, other: object) -> bool: # Another Buffer class can override this to choose a more efficient path diff --git a/src/zarr/core/buffer/cpu.py b/src/zarr/core/buffer/cpu.py index 415b9d928c..58275d2843 100644 --- a/src/zarr/core/buffer/cpu.py +++ b/src/zarr/core/buffer/cpu.py @@ -107,14 +107,13 @@ def as_numpy_array(self) -> npt.NDArray[Any]: """ return np.asanyarray(self._data) - def __add__(self, other: core.Buffer) -> Self: - """Concatenate two buffers""" - - other_array = other.as_array_like() - assert other_array.dtype == np.dtype("B") - return self.__class__( - np.concatenate((np.asanyarray(self._data), np.asanyarray(other_array))) - ) + def combine(self, others: Iterable[core.Buffer]) -> Self: + data = [np.asanyarray(self._data)] + for buf in others: + other_array = buf.as_array_like() + assert other_array.dtype == np.dtype("B") + data.append(np.asanyarray(other_array)) + return self.__class__(np.concatenate(data)) class NDBuffer(core.NDBuffer): diff --git a/src/zarr/core/buffer/gpu.py b/src/zarr/core/buffer/gpu.py index bfe977c50f..2a591884ae 100644 --- a/src/zarr/core/buffer/gpu.py +++ b/src/zarr/core/buffer/gpu.py @@ -107,14 +107,15 @@ def from_bytes(cls, bytes_like: BytesLike) -> Self: def as_numpy_array(self) -> npt.NDArray[Any]: return cast("npt.NDArray[Any]", cp.asnumpy(self._data)) - def __add__(self, other: core.Buffer) -> Self: - other_array = other.as_array_like() - assert other_array.dtype == np.dtype("B") - gpu_other = Buffer(other_array) - gpu_other_array = gpu_other.as_array_like() - return self.__class__( - cp.concatenate((cp.asanyarray(self._data), cp.asanyarray(gpu_other_array))) - ) + def combine(self, others: Iterable[core.Buffer]) -> Self: + data = [cp.asanyarray(self._data)] + for other in others: + other_array = other.as_array_like() + assert other_array.dtype == np.dtype("B") + gpu_other = Buffer(other_array) + gpu_other_array = gpu_other.as_array_like() + data.append(cp.asanyarray(gpu_other_array)) + return self.__class__(cp.concatenate(data)) class NDBuffer(core.NDBuffer): From 6df448f1d665f34e6875da9f6689aa720ffa2ee2 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 3 Nov 2025 10:43:22 +0100 Subject: [PATCH 147/468] chore: make tests faster (#3533) * trim down test configuration to reduce runtime * adjust comments and squeeze arrays to a smaller size * changelog * revert to 300 max_examples --- changes/3533.misc.md | 1 + tests/test_indexing.py | 128 ++++++++++++++++------------------------- 2 files changed, 50 insertions(+), 79 deletions(-) create mode 100644 changes/3533.misc.md diff --git a/changes/3533.misc.md b/changes/3533.misc.md new file mode 100644 index 0000000000..237efc9b5b --- /dev/null +++ b/changes/3533.misc.md @@ -0,0 +1 @@ +Reduced the runtime of the test suite by simplifying test cases. \ No newline at end of file diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 609db6cdce..c0bf7dd270 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -601,21 +601,16 @@ def test_get_orthogonal_selection_1d_bool(store: StorePath) -> None: # noinspection PyStatementEffect def test_get_orthogonal_selection_1d_int(store: StorePath) -> None: # setup - a = np.arange(1050, dtype=int) + a = np.arange(550, dtype=int) z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) np.random.seed(42) # test with different degrees of sparseness - for p in 2, 0.5, 0.1, 0.01: - # unordered + for p in 0.5, 0.01: + # sorted integer arrays ix = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - _test_get_orthogonal_selection(a, z, ix) - # increasing ix.sort() _test_get_orthogonal_selection(a, z, ix) - # decreasing - ix = ix[::-1] - _test_get_orthogonal_selection(a, z, ix) selections = basic_selections_1d + [ # test wraparound @@ -660,12 +655,12 @@ def _test_get_orthogonal_selection_2d( # noinspection PyStatementEffect def test_get_orthogonal_selection_2d(store: StorePath) -> None: # setup - a = np.arange(10000, dtype=int).reshape(1000, 10) + a = np.arange(5400, dtype=int).reshape(600, 9) z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) np.random.seed(42) # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: + for p in 0.5, 0.01: # boolean arrays ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) @@ -679,16 +674,12 @@ def test_get_orthogonal_selection_2d(store: StorePath) -> None: for selection in selections: _test_get_orthogonal_selection(a, z, selection) - # integer arrays + # sorted integer arrays ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) - _test_get_orthogonal_selection_2d(a, z, ix0, ix1) ix0.sort() ix1.sort() _test_get_orthogonal_selection_2d(a, z, ix0, ix1) - ix0 = ix0[::-1] - ix1 = ix1[::-1] - _test_get_orthogonal_selection_2d(a, z, ix0, ix1) for selection_2d in basic_selections_2d: _test_get_orthogonal_selection(a, z, selection_2d) @@ -709,33 +700,33 @@ def _test_get_orthogonal_selection_3d( ) -> None: selections = [ # single value - (84, 42, 4), + (60, 15, 4), (-1, -1, -1), # index all axes with array (ix0, ix1, ix2), # mixed indexing with single array / slices - (ix0, slice(15, 25), slice(1, 5)), - (slice(50, 70), ix1, slice(1, 5)), - (slice(50, 70), slice(15, 25), ix2), - (ix0, slice(15, 25, 5), slice(1, 5, 2)), - (slice(50, 70, 3), ix1, slice(1, 5, 2)), - (slice(50, 70, 3), slice(15, 25, 5), ix2), + (ix0, slice(10, 20), slice(1, 5)), + (slice(30, 50), ix1, slice(1, 5)), + (slice(30, 50), slice(10, 20), ix2), + (ix0, slice(10, 20, 5), slice(1, 5, 2)), + (slice(30, 50, 3), ix1, slice(1, 5, 2)), + (slice(30, 50, 3), slice(10, 20, 5), ix2), # mixed indexing with single array / ints - (ix0, 42, 4), - (84, ix1, 4), - (84, 42, ix2), + (ix0, 15, 4), + (60, ix1, 4), + (60, 15, ix2), # mixed indexing with single array / slice / int - (ix0, slice(15, 25), 4), - (42, ix1, slice(1, 5)), - (slice(50, 70), 42, ix2), + (ix0, slice(10, 20), 4), + (15, ix1, slice(1, 5)), + (slice(30, 50), 15, ix2), # mixed indexing with two array / slice (ix0, ix1, slice(1, 5)), - (slice(50, 70), ix1, ix2), - (ix0, slice(15, 25), ix2), + (slice(30, 50), ix1, ix2), + (ix0, slice(10, 20), ix2), # mixed indexing with two array / integer (ix0, ix1, 4), - (42, ix1, ix2), - (ix0, 42, ix2), + (15, ix1, ix2), + (ix0, 15, ix2), ] for selection in selections: _test_get_orthogonal_selection(a, z, selection) @@ -743,31 +734,26 @@ def _test_get_orthogonal_selection_3d( def test_get_orthogonal_selection_3d(store: StorePath) -> None: # setup - a = np.arange(100000, dtype=int).reshape(200, 50, 10) + a = np.arange(32400, dtype=int).reshape(120, 30, 9) z = zarr_array_from_numpy_array(store, a, chunk_shape=(60, 20, 3)) np.random.seed(42) # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: + for p in 0.5, 0.01: # boolean arrays ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) ix2 = np.random.binomial(1, 0.5, size=a.shape[2]).astype(bool) _test_get_orthogonal_selection_3d(a, z, ix0, ix1, ix2) - # integer arrays + # sorted integer arrays ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) ix2 = np.random.choice(a.shape[2], size=int(a.shape[2] * 0.5), replace=True) - _test_get_orthogonal_selection_3d(a, z, ix0, ix1, ix2) ix0.sort() ix1.sort() ix2.sort() _test_get_orthogonal_selection_3d(a, z, ix0, ix1, ix2) - ix0 = ix0[::-1] - ix1 = ix1[::-1] - ix2 = ix2[::-1] - _test_get_orthogonal_selection_3d(a, z, ix0, ix1, ix2) def test_orthogonal_indexing_edge_cases(store: StorePath) -> None: @@ -805,24 +791,21 @@ def _test_set_orthogonal_selection( def test_set_orthogonal_selection_1d(store: StorePath) -> None: # setup - v = np.arange(1050, dtype=int) + v = np.arange(550, dtype=int) a = np.empty(v.shape, dtype=int) z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) # test with different degrees of sparseness np.random.seed(42) - for p in 0.5, 0.1, 0.01: + for p in 0.5, 0.01: # boolean arrays ix = np.random.binomial(1, p, size=a.shape[0]).astype(bool) _test_set_orthogonal_selection(v, a, z, ix) - # integer arrays + # sorted integer arrays ix = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - _test_set_orthogonal_selection(v, a, z, ix) ix.sort() _test_set_orthogonal_selection(v, a, z, ix) - ix = ix[::-1] - _test_set_orthogonal_selection(v, a, z, ix) # basic selections for selection in basic_selections_1d: @@ -870,28 +853,24 @@ def _test_set_orthogonal_selection_2d( def test_set_orthogonal_selection_2d(store: StorePath) -> None: # setup - v = np.arange(10000, dtype=int).reshape(1000, 10) + v = np.arange(5400, dtype=int).reshape(600, 9) a = np.empty_like(v) z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) np.random.seed(42) # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: + for p in 0.5, 0.01: # boolean arrays ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) _test_set_orthogonal_selection_2d(v, a, z, ix0, ix1) - # integer arrays + # sorted integer arrays ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) - _test_set_orthogonal_selection_2d(v, a, z, ix0, ix1) ix0.sort() ix1.sort() _test_set_orthogonal_selection_2d(v, a, z, ix0, ix1) - ix0 = ix0[::-1] - ix1 = ix1[::-1] - _test_set_orthogonal_selection_2d(v, a, z, ix0, ix1) for selection in basic_selections_2d: _test_set_orthogonal_selection(v, a, z, selection) @@ -907,20 +886,20 @@ def _test_set_orthogonal_selection_3d( ) -> None: selections = ( # single value - (84, 42, 4), + (60, 15, 4), (-1, -1, -1), # index all axes with bool array (ix0, ix1, ix2), # mixed indexing with single bool array / slice or int - (ix0, slice(15, 25), slice(1, 5)), - (slice(50, 70), ix1, slice(1, 5)), - (slice(50, 70), slice(15, 25), ix2), - (ix0, 42, 4), - (84, ix1, 4), - (84, 42, ix2), - (ix0, slice(15, 25), 4), - (slice(50, 70), ix1, 4), - (slice(50, 70), 42, ix2), + (ix0, slice(10, 20), slice(1, 5)), + (slice(30, 50), ix1, slice(1, 5)), + (slice(30, 50), slice(10, 20), ix2), + (ix0, 15, 4), + (60, ix1, 4), + (60, 15, ix2), + (ix0, slice(10, 20), 4), + (slice(30, 50), ix1, 4), + (slice(30, 50), 15, ix2), # indexing with two arrays / slice (ix0, ix1, slice(1, 5)), # indexing with two arrays / integer @@ -932,37 +911,28 @@ def _test_set_orthogonal_selection_3d( def test_set_orthogonal_selection_3d(store: StorePath) -> None: # setup - v = np.arange(100000, dtype=int).reshape(200, 50, 10) + v = np.arange(32400, dtype=int).reshape(120, 30, 9) a = np.empty_like(v) z = zarr_array_from_numpy_array(store, a, chunk_shape=(60, 20, 3)) np.random.seed(42) # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: + for p in 0.5, 0.01: # boolean arrays ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) ix2 = np.random.binomial(1, 0.5, size=a.shape[2]).astype(bool) _test_set_orthogonal_selection_3d(v, a, z, ix0, ix1, ix2) - # integer arrays + # sorted integer arrays ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) ix2 = np.random.choice(a.shape[2], size=int(a.shape[2] * 0.5), replace=True) - _test_set_orthogonal_selection_3d(v, a, z, ix0, ix1, ix2) - - # sorted increasing ix0.sort() ix1.sort() ix2.sort() _test_set_orthogonal_selection_3d(v, a, z, ix0, ix1, ix2) - # sorted decreasing - ix0 = ix0[::-1] - ix1 = ix1[::-1] - ix2 = ix2[::-1] - _test_set_orthogonal_selection_3d(v, a, z, ix0, ix1, ix2) - def test_orthogonal_indexing_fallback_on_get_setitem(store: StorePath) -> None: z = zarr_array_from_numpy_array(store, np.zeros((20, 20))) @@ -1128,13 +1098,13 @@ def _test_set_coordinate_selection( def test_set_coordinate_selection_1d(store: StorePath) -> None: # setup - v = np.arange(1050, dtype=int) + v = np.arange(550, dtype=int) a = np.empty(v.shape, dtype=v.dtype) z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) np.random.seed(42) # test with different degrees of sparseness - for p in 2, 0.5, 0.1, 0.01: + for p in 0.5, 0.01: n = int(a.size * p) ix = np.random.choice(a.shape[0], size=n, replace=True) _test_set_coordinate_selection(v, a, z, ix) @@ -1152,13 +1122,13 @@ def test_set_coordinate_selection_1d(store: StorePath) -> None: def test_set_coordinate_selection_2d(store: StorePath) -> None: # setup - v = np.arange(10000, dtype=int).reshape(1000, 10) + v = np.arange(5400, dtype=int).reshape(600, 9) a = np.empty_like(v) z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) np.random.seed(42) # test with different degrees of sparseness - for p in 2, 0.5, 0.1, 0.01: + for p in 0.5, 0.01: n = int(a.size * p) ix0 = np.random.choice(a.shape[0], size=n, replace=True) ix1 = np.random.choice(a.shape[1], size=n, replace=True) From eb1b6e869115925f7b653e60bd542abd410a9a4e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 3 Nov 2025 19:33:39 +0000 Subject: [PATCH 148/468] chore: update pre-commit hooks (#3566) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.3...v0.14.3) - [github.com/scientific-python/cookie: 2025.10.01 → 2025.10.20](https://github.com/scientific-python/cookie/compare/2025.10.01...2025.10.20) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a213d9c427..cb1b75d90b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ ci: default_stages: [pre-commit, pre-push] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.13.3 + rev: v0.14.3 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -42,7 +42,7 @@ repos: - hypothesis - s3fs - repo: https://github.com/scientific-python/cookie - rev: 2025.10.01 + rev: 2025.10.20 hooks: - id: sp-repo-review - repo: https://github.com/pre-commit/pygrep-hooks From c8d8e6430b67264eb4457dc337746856a46965cc Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Tue, 4 Nov 2025 16:32:46 -0500 Subject: [PATCH 149/468] Improve compatibility between old sphinx and new mkdocs setup (#3544) * Add more redirects for sphinx->mkdocs migration * Add entry point for top-level API * Explicit setting * Add missing pages * Add redirects --------- Co-authored-by: Davis Bennett --- docs/api/abc/buffer.md | 7 +++++ docs/api/abc/codec.md | 1 + docs/api/api_sync.md | 6 ++++ docs/api/codecs.md | 4 ++- docs/api/index.md | 6 ++++ docs/api/metadata.md | 6 ++++ docs/api/testing.md | 10 ++++++ mkdocs.yml | 69 ++++++++++++++++++++++++++++++++++++++++++ 8 files changed, 108 insertions(+), 1 deletion(-) create mode 100644 docs/api/metadata.md diff --git a/docs/api/abc/buffer.md b/docs/api/abc/buffer.md index ac814d20b6..d1ace2c899 100644 --- a/docs/api/abc/buffer.md +++ b/docs/api/abc/buffer.md @@ -2,4 +2,11 @@ title: buffer --- +::: zarr.abc + options: + show_root_heading: true + show_root_toc_entry: true + members: false + + ::: zarr.abc.buffer diff --git a/docs/api/abc/codec.md b/docs/api/abc/codec.md index d4eaecabe9..7d808fbb54 100644 --- a/docs/api/abc/codec.md +++ b/docs/api/abc/codec.md @@ -3,3 +3,4 @@ title: codec --- ::: zarr.abc.codec +::: zarr.abc.numcodec diff --git a/docs/api/api_sync.md b/docs/api/api_sync.md index 83ff118db5..63a4aec537 100644 --- a/docs/api/api_sync.md +++ b/docs/api/api_sync.md @@ -2,4 +2,10 @@ title: synchronous --- +::: zarr.api + options: + show_root_heading: true + show_root_toc_entry: true + members: false + ::: zarr.api.synchronous \ No newline at end of file diff --git a/docs/api/codecs.md b/docs/api/codecs.md index 5cf66b304e..151efeac32 100644 --- a/docs/api/codecs.md +++ b/docs/api/codecs.md @@ -2,4 +2,6 @@ title: codecs --- -::: zarr.codecs \ No newline at end of file +::: zarr.codecs + +::: zarr.codecs.numcodecs diff --git a/docs/api/index.md b/docs/api/index.md index 8e6be1058e..6160230ac0 100644 --- a/docs/api/index.md +++ b/docs/api/index.md @@ -2,6 +2,12 @@ Complete reference documentation for the Zarr-Python API. +::: zarr + options: + show_root_heading: true + show_root_toc_entry: true + members: false + ## Core API ### Essential Classes and Functions diff --git a/docs/api/metadata.md b/docs/api/metadata.md new file mode 100644 index 0000000000..12eb909086 --- /dev/null +++ b/docs/api/metadata.md @@ -0,0 +1,6 @@ +--- +title: metadata +--- + +::: zarr.metadata +::: zarr.metadata.migrate_v3 diff --git a/docs/api/testing.md b/docs/api/testing.md index 1412950ee3..eef48614b5 100644 --- a/docs/api/testing.md +++ b/docs/api/testing.md @@ -2,6 +2,12 @@ title: testing --- +::: zarr.testing + options: + show_root_heading: true + show_root_toc_entry: true + members: false + ## Buffer ::: zarr.testing.buffer @@ -21,3 +27,7 @@ title: testing ## Utils ::: zarr.testing.utils + +## Conftest + +::: zarr.testing.conftest diff --git a/mkdocs.yml b/mkdocs.yml index 151ecbbaa0..647f211240 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -6,6 +6,7 @@ site_description: An implementation of chunked, compressed, N-dimensional arrays site_author: Alistair Miles site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://zarr.readthedocs.io/'] docs_dir: docs +use_directory_urls: true nav: - "index.md" @@ -42,6 +43,7 @@ nav: - api/config.md - api/codecs.md - api/errors.md + - api/metadata.md - api/registry.md - api/storage.md - api/testing.md @@ -130,6 +132,7 @@ plugins: show_source: true show_symbol_type_toc: true signature_crossrefs: true + show_if_no_docstring: true extensions: - griffe_inherited_docstrings @@ -154,11 +157,77 @@ plugins: 'spec/v2.md': 'https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html' 'spec/v3.md': 'https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html' 'license.md': 'https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt' + 'genindex.html.md': 'index.md' + 'py-modindex.html.md': 'index.md' + 'search.html.md': 'index.md' 'tutorial.md': 'user-guide/installation.md' 'getting-started.md': 'quick-start.md' 'roadmap.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' 'installation.md': 'user-guide/installation.md' 'release.md': 'release-notes.md' + 'about.html.md': 'index.md' + 'arrays.html.md': 'user-guide/arrays.md' + 'attributes.html.md': 'user-guide/attributes.md' + 'cli.html.md': 'user-guide/cli.md' + 'config.html.md': 'user-guide/config.md' + 'consolidated_metadata.html.md': 'user-guide/consolidated_metadata.md' + 'data_types.html.md': 'user-guide/data_types.md' + 'extending.html.md': 'user-guide/extending.md' + 'gpu.html.md': 'user-guide/gpu.md' + 'groups.html.md': 'user-guide/groups.md' + 'installation.html.md': 'user-guide/installation.md' + 'performance.html.md': 'user-guide/performance.md' + 'quickstart.html.md': 'quick-start.md' + 'release-notes.html.md': 'release-notes.md' + 'storage.html.md': 'user-guide/storage.md' + 'v3_migration.html.md': 'user-guide/v3_migration.md' + 'user-guide/arrays.html.md': 'user-guide/arrays.md' + 'user-guide/attributes.html.md': 'user-guide/attributes.md' + 'user-guide/cli.html.md': 'user-guide/cli.md' + 'user-guide/config.html.md': 'user-guide/config.md' + 'user-guide/consolidated_metadata.html.md': 'user-guide/consolidated_metadata.md' + 'user-guide/data_types.html.md': 'user-guide/data_types.md' + 'user-guide/extending.html.md': 'user-guide/extending.md' + 'user-guide/gpu.html.md': 'user-guide/gpu.md' + 'user-guide/groups.html.md': 'user-guide/groups.md' + 'user-guide/installation.html.md': 'user-guide/installation.md' + 'user-guide/performance.html.md': 'user-guide/performance.md' + 'user-guide/storage.html.md': 'user-guide/storage.md' + 'user-guide/v3_migration.html.md': 'user-guide/v3_migration.md' + 'developers/contributing.html.md': 'contributing.md' + 'developers/index.html.md': 'contributing.md' + 'developers/roadmap.html.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' + 'api/zarr/index.html.md': 'api/index.md' + 'api/zarr/abc/index.html.md': 'api/abc/buffer.md' + 'api/zarr/abc/buffer/index.html.md': 'api/abc/buffer.md' + 'api/zarr/abc/codec/index.html.md': 'api/abc/codec.md' + 'api/zarr/abc/metadata/index.html.md': 'api/abc/metadata.md' + 'api/zarr/abc/numcodec/index.html.md': 'api/abc/codec.md' + 'api/zarr/abc/store/index.html.md': 'api/abc/store.md' + 'api/zarr/api/index.html.md': 'api/index.md' + 'api/zarr/api/asynchronous/index.html.md': 'api/api_async.md' + 'api/zarr/api/synchronous/index.html.md': 'api/api_sync.md' + 'api/zarr/buffer/index.html.md': 'api/buffer.md' + 'api/zarr/buffer/cpu/index.html.md': 'api/buffer.md' + 'api/zarr/buffer/gpu/index.html.md': 'api/buffer.md' + 'api/zarr/codecs/index.html.md': 'api/codecs.md' + 'api/zarr/codecs/numcodecs/index.html.md': 'api/codecs.md' + 'api/zarr/convenience/index.html.md': 'api/convenience.md' + 'api/zarr/creation/index.html.md': 'api/deprecated/creation.md' + 'api/zarr/dtype/index.html.md': 'api/dtype.md' + 'api/zarr/errors/index.html.md': 'api/errors.md' + 'api/zarr/metadata/index.html.md': 'api/metadata.md' + 'api/zarr/metadata/migrate_v3/index.html.md': 'api/metadata.md' + 'api/zarr/registry/index.html.md': 'api/registry.md' + 'api/zarr/storage/index.html.md': 'api/storage.md' + 'api/zarr/testing/index.html.md': 'api/testing.md' + 'api/zarr/testing/buffer/index.html.md': 'api/testing.md' + 'api/zarr/testing/conftest/index.html.md': 'api/testing.md' + 'api/zarr/testing/stateful/index.html.md': 'api/testing.md' + 'api/zarr/testing/store/index.html.md': 'api/testing.md' + 'api/zarr/testing/strategies/index.html.md': 'api/testing.md' + 'api/zarr/testing/utils/index.html.md': 'api/testing.md' + # https://github.com/developmentseed/titiler/blob/50934c929cca2fa8d3c408d239015f8da429c6a8/docs/mkdocs.yml#L115-L140 markdown_extensions: From d0c3b7faf93e69fbddb17d43ba972e1ddbe3a169 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 6 Nov 2025 15:25:27 +0100 Subject: [PATCH 150/468] Add an issue template for feature requests (#3572) --- .github/ISSUE_TEMPLATE/config.yml | 4 ++-- .github/ISSUE_TEMPLATE/feature_request.yml | 11 +++++++++++ 2 files changed, 13 insertions(+), 2 deletions(-) create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 27239f5861..d219a73737 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,8 +1,8 @@ blank_issues_enabled: true contact_links: - - name: Propose a new major feature + - name: Propose a new Zarr specification feature url: https://github.com/zarr-developers/zarr-specs - about: A new major feature should be discussed in the Zarr specifications repository. + about: A new feature for the Zarr storage specification should be opened on the zarr-specs repository. - name: Discuss something on ZulipChat url: https://ossci.zulipchat.com/ about: For questions like "How do I do X with Zarr?", consider posting your question to our developer chat. diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml new file mode 100644 index 0000000000..f067655f22 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,11 @@ +name: Feature Request +description: Request a new feature for zarr-python +# labels: [] +body: +- type: textarea + attributes: + label: Describe the new feature you'd like + description: > + Please provide a description of what new feature or functionality you'd like to see in zarr-python. + validations: + required: true From 7d0b62da45f6d8e5f5d93953d71fe9ef76f79e1c Mon Sep 17 00:00:00 2001 From: "Christine P. Chai" Date: Tue, 11 Nov 2025 00:45:09 -0800 Subject: [PATCH 151/468] DOC: Correct typos in zarr-python documentation (#3579) --- docs/user-guide/performance.md | 2 +- src/zarr/core/buffer/core.py | 4 ++-- src/zarr/core/buffer/gpu.py | 6 +++--- src/zarr/core/dtype/common.py | 2 +- src/zarr/errors.py | 2 +- src/zarr/registry.py | 8 ++++---- src/zarr/testing/buffer.py | 2 +- src/zarr/testing/strategies.py | 2 +- 8 files changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 88d8e69936..6760cf055c 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -265,7 +265,7 @@ If an array or group is backed by a persistent store such as the a `zarr.storage **are not** pickled. The only thing that is pickled is the necessary parameters to allow the store to re-open any underlying files or databases upon being unpickled. -E.g., pickle/unpickle an local store array: +E.g., pickle/unpickle a local store array: ```python exec="true" session="performance" source="above" result="ansi" import pickle diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index ddd3073af2..f0d01566c3 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -125,7 +125,7 @@ class Buffer(ABC): We use Buffer throughout Zarr to represent a contiguous block of memory. - A Buffer is backed by a underlying array-like instance that represents + A Buffer is backed by an underlying array-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the array-like instance can be copied/converted to a regular Numpy array @@ -315,7 +315,7 @@ class NDBuffer: We use NDBuffer throughout Zarr to represent a n-dimensional memory block. - A NDBuffer is backed by a underlying ndarray-like instance that represents + A NDBuffer is backed by an underlying ndarray-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the ndarray-like instance can be copied/converted to a regular Numpy array diff --git a/src/zarr/core/buffer/gpu.py b/src/zarr/core/buffer/gpu.py index 2a591884ae..d99c1d2818 100644 --- a/src/zarr/core/buffer/gpu.py +++ b/src/zarr/core/buffer/gpu.py @@ -36,7 +36,7 @@ class Buffer(core.Buffer): We use Buffer throughout Zarr to represent a contiguous block of memory. - A Buffer is backed by a underlying array-like instance that represents + A Buffer is backed by an underlying array-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the array-like instance can be copied/converted to a regular Numpy array @@ -90,7 +90,7 @@ def create_zero_length(cls) -> Self: @classmethod def from_buffer(cls, buffer: core.Buffer) -> Self: - """Create an GPU Buffer given an arbitrary Buffer + """Create a GPU Buffer given an arbitrary Buffer This will try to be zero-copy if `buffer` is already on the GPU and will trigger a copy if not. @@ -123,7 +123,7 @@ class NDBuffer(core.NDBuffer): We use NDBuffer throughout Zarr to represent a n-dimensional memory block. - A NDBuffer is backed by a underlying ndarray-like instance that represents + A NDBuffer is backed by an underlying ndarray-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the ndarray-like instance can be copied/converted to a regular Numpy array diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index 652b5fdbe3..6b70f595ba 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -98,7 +98,7 @@ def check_structured_dtype_name_v2(data: Sequence[object]) -> TypeGuard[Structur def check_dtype_name_v2(data: object) -> TypeGuard[DTypeName_V2]: """ - Type guard for narrowing the type of a python object to an valid zarr v2 dtype name. + Type guard for narrowing the type of a python object to a valid zarr v2 dtype name. """ if isinstance(data, str): return True diff --git a/src/zarr/errors.py b/src/zarr/errors.py index 331ae52f9e..bcd6a08deb 100644 --- a/src/zarr/errors.py +++ b/src/zarr/errors.py @@ -91,7 +91,7 @@ class MetadataValidationError(BaseZarrError): class UnknownCodecError(BaseZarrError): """ - Raised when a unknown codec was used. + Raised when an unknown codec was used. """ diff --git a/src/zarr/registry.py b/src/zarr/registry.py index a8dd2a1c6c..d0850a1387 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -227,11 +227,11 @@ def _parse_array_bytes_codec(data: dict[str, JSON] | Codec) -> ArrayBytesCodec: if isinstance(data, dict): result = _resolve_codec(data) if not isinstance(result, ArrayBytesCodec): - msg = f"Expected a dict representation of a ArrayBytesCodec; got a dict representation of a {type(result)} instead." + msg = f"Expected a dict representation of an ArrayBytesCodec; got a dict representation of a {type(result)} instead." raise TypeError(msg) else: if not isinstance(data, ArrayBytesCodec): - raise TypeError(f"Expected a ArrayBytesCodec. Got {type(data)} instead.") + raise TypeError(f"Expected an ArrayBytesCodec. Got {type(data)} instead.") result = data return result @@ -247,11 +247,11 @@ def _parse_array_array_codec(data: dict[str, JSON] | Codec) -> ArrayArrayCodec: if isinstance(data, dict): result = _resolve_codec(data) if not isinstance(result, ArrayArrayCodec): - msg = f"Expected a dict representation of a ArrayArrayCodec; got a dict representation of a {type(result)} instead." + msg = f"Expected a dict representation of an ArrayArrayCodec; got a dict representation of a {type(result)} instead." raise TypeError(msg) else: if not isinstance(data, ArrayArrayCodec): - raise TypeError(f"Expected a ArrayArrayCodec. Got {type(data)} instead.") + raise TypeError(f"Expected an ArrayArrayCodec. Got {type(data)} instead.") result = data return result diff --git a/src/zarr/testing/buffer.py b/src/zarr/testing/buffer.py index 1e167b2156..4b652bc93d 100644 --- a/src/zarr/testing/buffer.py +++ b/src/zarr/testing/buffer.py @@ -45,7 +45,7 @@ def create( order: Literal["C", "F"] = "C", fill_value: Any | None = None, ) -> Self: - """Overwrite `NDBuffer.create` to create an TestNDArrayLike instance""" + """Overwrite `NDBuffer.create` to create a TestNDArrayLike instance""" ret = cls(TestNDArrayLike(shape=shape, dtype=dtype, order=order)) if fill_value is not None: ret.fill(fill_value) diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index d0726c3dd9..d6c863e086 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -377,7 +377,7 @@ def orthogonal_indices( """ Strategy that returns (1) a tuple of integer arrays used for orthogonal indexing of Zarr arrays. - (2) an tuple of integer arrays that can be used for equivalent indexing of numpy arrays + (2) a tuple of integer arrays that can be used for equivalent indexing of numpy arrays """ zindexer = [] npindexer = [] From 4bc70bd25b579e0fb98610c5285b591e634e9bab Mon Sep 17 00:00:00 2001 From: Mark Keller <7525285+keller-mark@users.noreply.github.com> Date: Thu, 13 Nov 2025 03:31:41 -0500 Subject: [PATCH 152/468] Update get method to use default buffer prototype (#3581) Set default value for prototype parameter in get method. --- src/zarr/storage/_memory.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index a3fd058680..904be922d7 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -5,6 +5,7 @@ from zarr.abc.store import ByteRequest, Store from zarr.core.buffer import Buffer, gpu +from zarr.core.buffer.core import default_buffer_prototype from zarr.core.common import concurrent_map from zarr.storage._utils import _normalize_byte_range_index @@ -79,10 +80,12 @@ def __eq__(self, other: object) -> bool: async def get( self, key: str, - prototype: BufferPrototype, + prototype: BufferPrototype | None = None, byte_range: ByteRequest | None = None, ) -> Buffer | None: # docstring inherited + if prototype is None: + prototype = default_buffer_prototype() if not self._is_open: await self._open() assert isinstance(key, str) From 182504c0244d508d43e6c1f4b2c33807c08d0009 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 13 Nov 2025 17:15:29 +0100 Subject: [PATCH 153/468] concurrency limit 64 -> 10 (#3578) * concurrency limit 64 -> 10 * update reference to concurrency limit in docs * update tests * remove release note --- changes/3526.feature.md | 1 - docs/user-guide/performance.md | 11 ++++++++--- src/zarr/core/config.py | 2 +- tests/test_config.py | 6 +++--- 4 files changed, 12 insertions(+), 8 deletions(-) delete mode 100644 changes/3526.feature.md diff --git a/changes/3526.feature.md b/changes/3526.feature.md deleted file mode 100644 index 7746611855..0000000000 --- a/changes/3526.feature.md +++ /dev/null @@ -1 +0,0 @@ -Increased the default value of `async.concurrency` from 10 to 64 to improve parallelism and throughput for concurrent I/O operations. This change enables better performance out-of-the-box for most workloads. Users with specific resource constraints or when using many Dask threads may want to lower this value via the `ZARR_ASYNC_CONCURRENCY` environment variable or by setting `zarr.config.set({'async.concurrency': N})`. diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 6760cf055c..c39ca7d25d 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -175,13 +175,18 @@ Coming soon. ## Parallel computing and synchronization -Zarr is designed to support parallel computing and enables concurrent reads and writes to arrays. This section covers how to optimize Zarr's concurrency settings for different parallel computing scenarios. +Zarr is designed to support parallel computing and enables concurrent reads and writes to arrays. +This section covers how to optimize Zarr's concurrency settings for different parallel computing +scenarios. ### Concurrent I/O operations -Zarr uses asynchronous I/O internally to enable concurrent reads and writes across multiple chunks. The level of concurrency is controlled by the `async.concurrency` configuration setting, which determines the maximum number of concurrent I/O operations. +Zarr uses asynchronous I/O internally to enable concurrent reads and writes across multiple chunks. +The level of concurrency is controlled by the `async.concurrency` configuration setting, which +determines the maximum number of concurrent I/O operations. -The default value is 64, which provides good performance for most workloads. You can adjust this value based on your specific needs: +The default value is 10, which is a conservative value. You may get improved performance by tuning +the concurrency limit. You can adjust this value based on your specific needs: ```python import zarr diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 5acf242ef7..908922a5f2 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -97,7 +97,7 @@ def enable_gpu(self) -> ConfigSet: "order": "C", "write_empty_chunks": False, }, - "async": {"concurrency": 64, "timeout": None}, + "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, "json_indent": 2, "codec_pipeline": { diff --git a/tests/test_config.py b/tests/test_config.py index 150aca7c96..ec72967b98 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -54,7 +54,7 @@ def test_config_defaults_set() -> None: "order": "C", "write_empty_chunks": False, }, - "async": {"concurrency": 64, "timeout": None}, + "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, "json_indent": 2, "codec_pipeline": { @@ -100,7 +100,7 @@ def test_config_defaults_set() -> None: ] ) assert config.get("array.order") == "C" - assert config.get("async.concurrency") == 64 + assert config.get("async.concurrency") == 10 assert config.get("async.timeout") is None assert config.get("codec_pipeline.batch_size") == 1 assert config.get("json_indent") == 2 @@ -108,7 +108,7 @@ def test_config_defaults_set() -> None: @pytest.mark.parametrize( ("key", "old_val", "new_val"), - [("array.order", "C", "F"), ("async.concurrency", 64, 128), ("json_indent", 2, 0)], + [("array.order", "C", "F"), ("async.concurrency", 10, 128), ("json_indent", 2, 0)], ) def test_config_defaults_can_be_overridden(key: str, old_val: Any, new_val: Any) -> None: assert config.get(key) == old_val From 95585eec7b4d308929c678a508ce14d1a6f34140 Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Mon, 17 Nov 2025 11:14:27 -0800 Subject: [PATCH 154/468] feat: bounded size `auto` sharding via `zarr.config` (#3574) * feat: bounded size `auto` sharding via `zarr.config` * chore: add docs + `config` * fix: config test * chore: relnote * fix: coverage * refactor: variable declaration order * fix: docstring + argu --------- Co-authored-by: Davis Bennett --- changes/3547.feature.md | 1 + docs/user-guide/performance.md | 2 ++ src/zarr/core/chunk_grids.py | 58 +++++++++++++++++++++++++++++++--- src/zarr/core/config.py | 1 + tests/test_array.py | 53 ++++++++++++++++++++++--------- tests/test_config.py | 1 + 6 files changed, 96 insertions(+), 20 deletions(-) create mode 100644 changes/3547.feature.md diff --git a/changes/3547.feature.md b/changes/3547.feature.md new file mode 100644 index 0000000000..280f577804 --- /dev/null +++ b/changes/3547.feature.md @@ -0,0 +1 @@ +Add a `array.target_shard_size_bytes` to [`zarr.config`][] to allow users to set a maximum number of bytes per-shard when `shards="auto"` in, for example, [`zarr.create_array`][]. \ No newline at end of file diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index c39ca7d25d..cebec7815a 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -81,6 +81,8 @@ z6 = zarr.create_array(store={}, shape=(10000, 10000, 1000), shards=(1000, 1000, print(z6.info) ``` +`shards` can be `"auto"` as well, in which case the `array.target_shard_size_bytes` setting can be used to control the size of shards (i.e., the size of the shard will be as close to without being bigger than `target_shard_size_bytes`); otherwise, a default is used. + ### Chunk memory layout The order of bytes **within each chunk** of an array can be changed via the diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index cf5bd8cdbe..7ebd68b5b4 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -12,6 +12,7 @@ import numpy as np +import zarr from zarr.abc.metadata import Metadata from zarr.core.common import ( JSON, @@ -202,6 +203,43 @@ def get_nchunks(self, array_shape: tuple[int, ...]) -> int: ) +def _guess_num_chunks_per_axis_shard( + chunk_shape: tuple[int, ...], item_size: int, max_bytes: int, array_shape: tuple[int, ...] +) -> int: + """Generate the number of chunks per axis to hit a target max byte size for a shard. + + For example, for a (2,2,2) chunk size and item size 4, maximum bytes of 256 would return 2. + In other words the shard would be a (2,2,2) grid of (2,2,2) chunks + i.e., prod(chunk_shape) * (returned_val * len(chunk_shape)) * item_size = 256 bytes. + + Parameters + ---------- + chunk_shape + The shape of the (inner) chunks. + item_size + The item size of the data i.e., 2 for uint16. + max_bytes + The maximum number of bytes per shard to allow. + array_shape + The shape of the underlying array. + + Returns + ------- + The number of chunks per axis. + """ + bytes_per_chunk = np.prod(chunk_shape) * item_size + if max_bytes < bytes_per_chunk: + return 1 + num_axes = len(chunk_shape) + chunks_per_shard = 1 + # First check for byte size, second check to make sure we don't go bigger than the array shape + while (bytes_per_chunk * ((chunks_per_shard + 1) ** num_axes)) <= max_bytes and all( + c * (chunks_per_shard + 1) <= a for c, a in zip(chunk_shape, array_shape, strict=True) + ): + chunks_per_shard += 1 + return chunks_per_shard + + def _auto_partition( *, array_shape: tuple[int, ...], @@ -237,12 +275,22 @@ def _auto_partition( stacklevel=2, ) _shards_out = () + target_shard_size_bytes = zarr.config.get("array.target_shard_size_bytes", None) + num_chunks_per_shard_axis = ( + _guess_num_chunks_per_axis_shard( + chunk_shape=_chunks_out, + item_size=item_size, + max_bytes=target_shard_size_bytes, + array_shape=array_shape, + ) + if (has_auto_shard := (target_shard_size_bytes is not None)) + else 2 + ) for a_shape, c_shape in zip(array_shape, _chunks_out, strict=True): - # TODO: make a better heuristic than this. - # for each axis, if there are more than 8 chunks along that axis, then put - # 2 chunks in each shard for that axis. - if a_shape // c_shape > 8: - _shards_out += (c_shape * 2,) + # The previous heuristic was `a_shape // c_shape > 8` and now, with target_shard_size_bytes, we only check that the shard size is less than the array size. + can_shard_axis = a_shape // c_shape > 8 if not has_auto_shard else True + if can_shard_axis: + _shards_out += (c_shape * num_chunks_per_shard_axis,) else: _shards_out += (c_shape,) elif isinstance(shard_shape, dict): diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 908922a5f2..f8f8ea4f5f 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -96,6 +96,7 @@ def enable_gpu(self) -> ConfigSet: "array": { "order": "C", "write_empty_chunks": False, + "target_shard_size_bytes": None, }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, diff --git a/tests/test_array.py b/tests/test_array.py index 5219616739..cece223138 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -966,33 +966,56 @@ async def test_nbytes( @pytest.mark.parametrize( - ("array_shape", "chunk_shape"), - [((256,), (2,))], + ("array_shape", "chunk_shape", "target_shard_size_bytes", "expected_shards"), + [ + pytest.param( + (256, 256), + (32, 32), + 129 * 129, + (128, 128), + id="2d_chunking_max_byes_does_not_evenly_divide", + ), + pytest.param( + (256, 256), (32, 32), 64 * 64, (64, 64), id="2d_chunking_max_byes_evenly_divides" + ), + pytest.param( + (256, 256), + (64, 32), + 128 * 128, + (128, 64), + id="2d_non_square_chunking_max_byes_evenly_divides", + ), + pytest.param((256,), (2,), 255, (254,), id="max_bytes_just_below_array_shape"), + pytest.param((256,), (2,), 256, (256,), id="max_bytes_equal_to_array_shape"), + pytest.param((256,), (2,), 16, (16,), id="max_bytes_normal_val"), + pytest.param((256,), (2,), 2, (2,), id="max_bytes_same_as_chunk"), + pytest.param((256,), (2,), 1, (2,), id="max_bytes_less_than_chunk"), + pytest.param((256,), (2,), None, (4,), id="use_default_auto_setting"), + pytest.param((4,), (2,), None, (2,), id="small_array_shape_does_not_shard"), + ], ) def test_auto_partition_auto_shards( - array_shape: tuple[int, ...], chunk_shape: tuple[int, ...] + array_shape: tuple[int, ...], + chunk_shape: tuple[int, ...], + target_shard_size_bytes: int | None, + expected_shards: tuple[int, ...], ) -> None: """ Test that automatically picking a shard size returns a tuple of 2 * the chunk shape for any axis where there are 8 or more chunks. """ dtype = np.dtype("uint8") - expected_shards: tuple[int, ...] = () - for cs, a_len in zip(chunk_shape, array_shape, strict=False): - if a_len // cs >= 8: - expected_shards += (2 * cs,) - else: - expected_shards += (cs,) with pytest.warns( ZarrUserWarning, match="Automatic shard shape inference is experimental and may change without notice.", ): - auto_shards, _ = _auto_partition( - array_shape=array_shape, - chunk_shape=chunk_shape, - shard_shape="auto", - item_size=dtype.itemsize, - ) + with zarr.config.set({"array.target_shard_size_bytes": target_shard_size_bytes}): + auto_shards, _ = _auto_partition( + array_shape=array_shape, + chunk_shape=chunk_shape, + shard_shape="auto", + item_size=dtype.itemsize, + ) assert auto_shards == expected_shards diff --git a/tests/test_config.py b/tests/test_config.py index ec72967b98..c3102e8efe 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -53,6 +53,7 @@ def test_config_defaults_set() -> None: "array": { "order": "C", "write_empty_chunks": False, + "target_shard_size_bytes": None, }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, From d0ff496ecb70b01b3b1553b246d750002496c292 Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Mon, 17 Nov 2025 11:24:13 -0800 Subject: [PATCH 155/468] feat: make `async_array` public (#3556) * feat: make `async_array` public * chore: relnote * fix: clarify docstring --------- Co-authored-by: Davis Bennett --- changes/3556.feature.md | 1 + src/zarr/core/array.py | 106 ++++++++++++++++++++++------------------ tests/test_api.py | 2 +- tests/test_array.py | 34 ++++++------- tests/test_v2.py | 6 +-- 5 files changed, 80 insertions(+), 69 deletions(-) create mode 100644 changes/3556.feature.md diff --git a/changes/3556.feature.md b/changes/3556.feature.md new file mode 100644 index 0000000000..3b51c2c99e --- /dev/null +++ b/changes/3556.feature.md @@ -0,0 +1 @@ +Make `async_array` on the [`zarr.Array`][] class public (`_async_array` will remain untouched, but its stability is not guaranteed). diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 8bd8be40b2..1139ee0ade 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -2039,6 +2039,16 @@ class Array: _async_array: AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] + @property + def async_array(self) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: + """An asynchronous version of the current array. Useful for batching requests. + + Returns + ------- + An asynchronous array whose metadata + store matches that of this synchronous array. + """ + return self._async_array + @classmethod @deprecated("Use zarr.create_array instead.", category=ZarrDeprecationWarning) def create( @@ -2296,7 +2306,7 @@ def open( @property def store(self) -> Store: - return self._async_array.store + return self.async_array.store @property def ndim(self) -> int: @@ -2307,7 +2317,7 @@ def ndim(self) -> int: int The number of dimensions in the array. """ - return self._async_array.ndim + return self.async_array.ndim @property def shape(self) -> tuple[int, ...]: @@ -2318,7 +2328,7 @@ def shape(self) -> tuple[int, ...]: tuple[int, ...] The shape of the array. """ - return self._async_array.shape + return self.async_array.shape @shape.setter def shape(self, value: tuple[int, ...]) -> None: @@ -2338,7 +2348,7 @@ def chunks(self) -> tuple[int, ...]: tuple A tuple of integers representing the length of each dimension of a chunk. """ - return self._async_array.chunks + return self.async_array.chunks @property def shards(self) -> tuple[int, ...] | None: @@ -2353,7 +2363,7 @@ def shards(self) -> tuple[int, ...] | None: tuple | None A tuple of integers representing the length of each dimension of a shard or None if sharding is not used. """ - return self._async_array.shards + return self.async_array.shards @property def size(self) -> int: @@ -2364,7 +2374,7 @@ def size(self) -> int: int Total number of elements in the array. """ - return self._async_array.size + return self.async_array.size @property def dtype(self) -> np.dtype[Any]: @@ -2375,7 +2385,7 @@ def dtype(self) -> np.dtype[Any]: np.dtype The NumPy data type. """ - return self._async_array.dtype + return self.async_array.dtype @property def attrs(self) -> Attributes: @@ -2395,33 +2405,33 @@ def attrs(self) -> Attributes: @property def path(self) -> str: """Storage path.""" - return self._async_array.path + return self.async_array.path @property def name(self) -> str: """Array name following h5py convention.""" - return self._async_array.name + return self.async_array.name @property def basename(self) -> str: """Final component of name.""" - return self._async_array.basename + return self.async_array.basename @property def metadata(self) -> ArrayMetadata: - return self._async_array.metadata + return self.async_array.metadata @property def store_path(self) -> StorePath: - return self._async_array.store_path + return self.async_array.store_path @property def order(self) -> MemoryOrder: - return self._async_array.order + return self.async_array.order @property def read_only(self) -> bool: - return self._async_array.read_only + return self.async_array.read_only @property def fill_value(self) -> Any: @@ -2433,14 +2443,14 @@ def filters(self) -> tuple[Numcodec, ...] | tuple[ArrayArrayCodec, ...]: Filters that are applied to each chunk of the array, in order, before serializing that chunk to bytes. """ - return self._async_array.filters + return self.async_array.filters @property def serializer(self) -> None | ArrayBytesCodec: """ Array-to-bytes codec to use for serializing the chunks into bytes. """ - return self._async_array.serializer + return self.async_array.serializer @property @deprecated("Use Array.compressors instead.", category=ZarrDeprecationWarning) @@ -2452,7 +2462,7 @@ def compressor(self) -> Numcodec | None: `array.compressor` is deprecated since v3.0.0 and will be removed in a future release. Use [`array.compressors`][zarr.Array.compressors] instead. """ - return self._async_array.compressor + return self.async_array.compressor @property def compressors(self) -> tuple[Numcodec, ...] | tuple[BytesBytesCodec, ...]: @@ -2460,28 +2470,28 @@ def compressors(self) -> tuple[Numcodec, ...] | tuple[BytesBytesCodec, ...]: Compressors that are applied to each chunk of the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. """ - return self._async_array.compressors + return self.async_array.compressors @property def cdata_shape(self) -> tuple[int, ...]: """ The shape of the chunk grid for this array. """ - return self._async_array._chunk_grid_shape + return self.async_array._chunk_grid_shape @property def _chunk_grid_shape(self) -> tuple[int, ...]: """ The shape of the chunk grid for this array. """ - return self._async_array._chunk_grid_shape + return self.async_array._chunk_grid_shape @property def _shard_grid_shape(self) -> tuple[int, ...]: """ The shape of the shard grid for this array. """ - return self._async_array._shard_grid_shape + return self.async_array._shard_grid_shape @property def nchunks(self) -> int: @@ -2491,14 +2501,14 @@ def nchunks(self) -> int: Note that if a sharding codec is used, then the number of chunks may exceed the number of stored objects supporting this array. """ - return self._async_array.nchunks + return self.async_array.nchunks @property def _nshards(self) -> int: """ The number of shards in the stored representation of this array. """ - return self._async_array._nshards + return self.async_array._nshards @property def nbytes(self) -> int: @@ -2513,7 +2523,7 @@ def nbytes(self) -> int: dtypes. It is not possible to determine the size of an array with variable-length elements from the shape and dtype alone. """ - return self._async_array.nbytes + return self.async_array.nbytes @property def nchunks_initialized(self) -> int: @@ -2539,7 +2549,7 @@ def nchunks_initialized(self) -> int: >>> arr.nchunks_initialized 6 """ - return sync(self._async_array.nchunks_initialized()) + return sync(self.async_array.nchunks_initialized()) @property def _nshards_initialized(self) -> int: @@ -2561,7 +2571,7 @@ def _nshards_initialized(self) -> int: >>> arr._nshard_initialized 3 """ - return sync(self._async_array._nshards_initialized()) + return sync(self.async_array._nshards_initialized()) def nbytes_stored(self) -> int: """ @@ -2571,7 +2581,7 @@ def nbytes_stored(self) -> int: ------- size : int """ - return sync(self._async_array.nbytes_stored()) + return sync(self.async_array.nbytes_stored()) def _iter_shard_keys( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -2592,7 +2602,7 @@ def _iter_shard_keys( str The storage key of each shard in the selection. """ - return self._async_array._iter_shard_keys(origin=origin, selection_shape=selection_shape) + return self.async_array._iter_shard_keys(origin=origin, selection_shape=selection_shape) def _iter_chunk_coords( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -2618,7 +2628,7 @@ def _iter_chunk_coords( tuple[int, ...] The coordinates of each chunk in the selection. """ - return self._async_array._iter_chunk_coords(origin=origin, selection_shape=selection_shape) + return self.async_array._iter_chunk_coords(origin=origin, selection_shape=selection_shape) def _iter_shard_coords( self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -2644,7 +2654,7 @@ def _iter_shard_coords( tuple[int, ...] The coordinates of each shard in the selection. """ - return self._async_array._iter_shard_coords(origin=origin, selection_shape=selection_shape) + return self.async_array._iter_shard_coords(origin=origin, selection_shape=selection_shape) def _iter_chunk_regions( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -2664,7 +2674,7 @@ def _iter_chunk_regions( tuple[slice, ...] A tuple of slice objects representing the region spanned by each chunk in the selection. """ - return self._async_array._iter_chunk_regions(origin=origin, selection_shape=selection_shape) + return self.async_array._iter_chunk_regions(origin=origin, selection_shape=selection_shape) def _iter_shard_regions( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -2684,7 +2694,7 @@ def _iter_shard_regions( tuple[slice, ...] A tuple of slice objects representing the region spanned by each chunk in the selection. """ - return self._async_array._iter_shard_regions(origin=origin, selection_shape=selection_shape) + return self.async_array._iter_shard_regions(origin=origin, selection_shape=selection_shape) def __array__( self, dtype: npt.DTypeLike | None = None, copy: bool | None = None @@ -3088,7 +3098,7 @@ def get_basic_selection( if prototype is None: prototype = default_buffer_prototype() return sync( - self._async_array._get_selection( + self.async_array._get_selection( BasicIndexer(selection, self.shape, self.metadata.chunk_grid), out=out, fields=fields, @@ -3197,7 +3207,7 @@ def set_basic_selection( if prototype is None: prototype = default_buffer_prototype() indexer = BasicIndexer(selection, self.shape, self.metadata.chunk_grid) - sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) + sync(self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) def get_orthogonal_selection( self, @@ -3326,7 +3336,7 @@ def get_orthogonal_selection( prototype = default_buffer_prototype() indexer = OrthogonalIndexer(selection, self.shape, self.metadata.chunk_grid) return sync( - self._async_array._get_selection( + self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype ) ) @@ -3445,7 +3455,7 @@ def set_orthogonal_selection( prototype = default_buffer_prototype() indexer = OrthogonalIndexer(selection, self.shape, self.metadata.chunk_grid) return sync( - self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype) + self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype) ) def get_mask_selection( @@ -3533,7 +3543,7 @@ def get_mask_selection( prototype = default_buffer_prototype() indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid) return sync( - self._async_array._get_selection( + self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype ) ) @@ -3622,7 +3632,7 @@ def set_mask_selection( if prototype is None: prototype = default_buffer_prototype() indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid) - sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) + sync(self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) def get_coordinate_selection( self, @@ -3711,7 +3721,7 @@ def get_coordinate_selection( prototype = default_buffer_prototype() indexer = CoordinateIndexer(selection, self.shape, self.metadata.chunk_grid) out_array = sync( - self._async_array._get_selection( + self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype ) ) @@ -3824,7 +3834,7 @@ def set_coordinate_selection( f"elements with an array of {value.shape[0]} elements." ) - sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) + sync(self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) def get_block_selection( self, @@ -3926,7 +3936,7 @@ def get_block_selection( prototype = default_buffer_prototype() indexer = BlockIndexer(selection, self.shape, self.metadata.chunk_grid) return sync( - self._async_array._get_selection( + self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype ) ) @@ -4026,7 +4036,7 @@ def set_block_selection( if prototype is None: prototype = default_buffer_prototype() indexer = BlockIndexer(selection, self.shape, self.metadata.chunk_grid) - sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) + sync(self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) @property def vindex(self) -> VIndex: @@ -4090,7 +4100,7 @@ def resize(self, new_shape: ShapeLike) -> None: #>(50, 50) ``` """ - sync(self._async_array.resize(new_shape)) + sync(self.async_array.resize(new_shape)) def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: """Append `data` to `axis`. @@ -4126,7 +4136,7 @@ def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: >>> z.shape (20000, 2000) """ - return sync(self._async_array.append(data, axis=axis)) + return sync(self.async_array.append(data, axis=axis)) def update_attributes(self, new_attributes: dict[str, JSON]) -> Array: """ @@ -4154,7 +4164,7 @@ def update_attributes(self, new_attributes: dict[str, JSON]) -> Array: overwritten by the new values. """ # TODO: remove this cast when type inference improves - new_array = sync(self._async_array.update_attributes(new_attributes)) + new_array = sync(self.async_array.update_attributes(new_attributes)) # TODO: remove this cast when type inference improves _new_array = cast("AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]", new_array) return type(self)(_new_array) @@ -4191,7 +4201,7 @@ def info(self) -> Any: Codecs : [BytesCodec(endian=)] No. bytes : 40 """ - return self._async_array.info + return self.async_array.info def info_complete(self) -> Any: """ @@ -4211,7 +4221,7 @@ def info_complete(self) -> Any: ------- [zarr.Array.info][] - The statically known subset of metadata about an array. """ - return sync(self._async_array.info_complete()) + return sync(self.async_array.info_complete()) async def _shards_initialized( @@ -4523,7 +4533,7 @@ async def from_array( async def _copy_array_region( chunk_coords: tuple[int, ...] | slice, _data: Array ) -> None: - arr = await _data._async_array.getitem(chunk_coords) + arr = await _data.async_array.getitem(chunk_coords) await result.setitem(chunk_coords, arr) # Stream data from the source array to the new array diff --git a/tests/test_api.py b/tests/test_api.py index 30f648a815..816de784ca 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -231,7 +231,7 @@ def test_open_array_respects_write_empty_chunks_config(zarr_format: ZarrFormat) arr2 = zarr.open(store=store, path="test_array", config={"write_empty_chunks": True}) assert isinstance(arr2, zarr.Array) - assert arr2._async_array._config.write_empty_chunks is True + assert arr2.async_array._config.write_empty_chunks is True arr2[0:5] = np.zeros(5) assert arr2.nchunks_initialized == 1 diff --git a/tests/test_array.py b/tests/test_array.py index cece223138..ebffd93b3c 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -376,7 +376,7 @@ def test_nchunks(test_cls: type[Array] | type[AsyncArray[Any]], nchunks: int) -> if test_cls == Array: observed = arr.nchunks else: - observed = arr._async_array.nchunks + observed = arr.async_array.nchunks assert observed == expected @@ -410,8 +410,8 @@ async def test_nchunks_initialized( observed = arr._nshards_initialized assert observed == arr.nchunks_initialized // chunks_per_shard else: - observed = await arr._async_array._nshards_initialized() - assert observed == await arr._async_array.nchunks_initialized() // chunks_per_shard + observed = await arr.async_array._nshards_initialized() + assert observed == await arr.async_array.nchunks_initialized() // chunks_per_shard assert observed == expected # delete chunks @@ -421,8 +421,8 @@ async def test_nchunks_initialized( observed = arr._nshards_initialized assert observed == arr.nchunks_initialized // chunks_per_shard else: - observed = await arr._async_array._nshards_initialized() - assert observed == await arr._async_array.nchunks_initialized() // chunks_per_shard + observed = await arr.async_array._nshards_initialized() + assert observed == await arr.async_array.nchunks_initialized() // chunks_per_shard expected = arr._nshards - idx - 1 assert observed == expected @@ -448,7 +448,7 @@ async def test_chunks_initialized( ) for keys, region in zip(chunks_accumulated, arr._iter_shard_regions(), strict=False): arr[region] = 1 - observed = sorted(await _shards_initialized(arr._async_array)) + observed = sorted(await _shards_initialized(arr.async_array)) expected = sorted(keys) assert observed == expected @@ -500,7 +500,7 @@ def test_info_v2(self, chunks: tuple[int, int], shards: tuple[int, int] | None) result = arr.info expected = ArrayInfo( _zarr_format=2, - _data_type=arr._async_array._zdtype, + _data_type=arr.async_array._zdtype, _fill_value=arr.fill_value, _shape=(8, 8), _chunk_shape=chunks, @@ -518,7 +518,7 @@ def test_info_v3(self, chunks: tuple[int, int], shards: tuple[int, int] | None) result = arr.info expected = ArrayInfo( _zarr_format=3, - _data_type=arr._async_array._zdtype, + _data_type=arr.async_array._zdtype, _fill_value=arr.fill_value, _shape=(8, 8), _chunk_shape=chunks, @@ -544,7 +544,7 @@ def test_info_complete(self, chunks: tuple[int, int], shards: tuple[int, int] | result = arr.info_complete() expected = ArrayInfo( _zarr_format=3, - _data_type=arr._async_array._zdtype, + _data_type=arr.async_array._zdtype, _fill_value=arr.fill_value, _shape=(8, 8), _chunk_shape=chunks, @@ -889,7 +889,7 @@ def test_write_empty_chunks_behavior( config={"write_empty_chunks": write_empty_chunks}, ) - assert arr._async_array._config.write_empty_chunks == write_empty_chunks + assert arr.async_array._config.write_empty_chunks == write_empty_chunks # initialize the store with some non-fill value chunks arr[:] = fill_value + 1 @@ -960,7 +960,7 @@ async def test_nbytes( store = MemoryStore() arr = zarr.create_array(store=store, shape=shape, dtype=dtype, fill_value=0) if array_type == "async": - assert arr._async_array.nbytes == np.prod(arr.shape) * arr.dtype.itemsize + assert arr.async_array.nbytes == np.prod(arr.shape) * arr.dtype.itemsize else: assert arr.nbytes == np.prod(arr.shape) * arr.dtype.itemsize @@ -1986,7 +1986,7 @@ def test_chunk_grid_shape( shard_grid_shape = tuple(ceildiv(a, b) for a, b in zip(array_shape, _shard_shape, strict=True)) assert arr._chunk_grid_shape == chunk_grid_shape assert arr.cdata_shape == chunk_grid_shape - assert arr._async_array.cdata_shape == chunk_grid_shape + assert arr.async_array.cdata_shape == chunk_grid_shape assert arr._shard_grid_shape == shard_grid_shape assert arr._nshards == np.prod(shard_grid_shape) @@ -2017,7 +2017,7 @@ def test_iter_chunk_coords( observed = tuple(_iter_chunk_coords(arr)) assert observed == expected assert observed == tuple(arr._iter_chunk_coords()) - assert observed == tuple(arr._async_array._iter_chunk_coords()) + assert observed == tuple(arr.async_array._iter_chunk_coords()) @pytest.mark.parametrize( @@ -2050,7 +2050,7 @@ def test_iter_shard_coords( observed = tuple(_iter_shard_coords(arr)) assert observed == expected assert observed == tuple(arr._iter_shard_coords()) - assert observed == tuple(arr._async_array._iter_shard_coords()) + assert observed == tuple(arr.async_array._iter_shard_coords()) @pytest.mark.parametrize( @@ -2085,7 +2085,7 @@ def test_iter_shard_keys( observed = tuple(_iter_shard_keys(arr)) assert observed == expected assert observed == tuple(arr._iter_shard_keys()) - assert observed == tuple(arr._async_array._iter_shard_keys()) + assert observed == tuple(arr.async_array._iter_shard_keys()) @pytest.mark.parametrize( @@ -2121,7 +2121,7 @@ def test_iter_shard_regions( observed = tuple(_iter_shard_regions(arr)) assert observed == expected assert observed == tuple(arr._iter_shard_regions()) - assert observed == tuple(arr._async_array._iter_shard_regions()) + assert observed == tuple(arr.async_array._iter_shard_regions()) @pytest.mark.parametrize( @@ -2150,7 +2150,7 @@ def test_iter_chunk_regions( observed = tuple(_iter_chunk_regions(arr)) assert observed == expected assert observed == tuple(arr._iter_chunk_regions()) - assert observed == tuple(arr._async_array._iter_chunk_regions()) + assert observed == tuple(arr.async_array._iter_chunk_regions()) @pytest.mark.parametrize("num_shards", [1, 3]) diff --git a/tests/test_v2.py b/tests/test_v2.py index b223e022c6..cb990f6159 100644 --- a/tests/test_v2.py +++ b/tests/test_v2.py @@ -143,13 +143,13 @@ def test_create_array_defaults(store: Store) -> None: g = zarr.open(store, mode="w", zarr_format=2) assert isinstance(g, Group) arr = g.create_array("one", dtype="i8", shape=(1,), chunks=(1,), compressor=None) - assert arr._async_array.compressor is None + assert arr.async_array.compressor is None assert not (arr.filters) arr = g.create_array("two", dtype="i8", shape=(1,), chunks=(1,)) - assert arr._async_array.compressor is not None + assert arr.async_array.compressor is not None assert not (arr.filters) arr = g.create_array("three", dtype="i8", shape=(1,), chunks=(1,), compressor=Zstd()) - assert arr._async_array.compressor is not None + assert arr.async_array.compressor is not None assert not (arr.filters) with pytest.raises(ValueError): g.create_array( From 54dcedeeee8bb280d5027e24043ba354bc2f381e Mon Sep 17 00:00:00 2001 From: David Stansby Date: Mon, 17 Nov 2025 20:37:39 +0100 Subject: [PATCH 156/468] Improve store section in migration guide (#3552) * Improve store section in migration guide * Update docs/user-guide/v3_migration.md Co-authored-by: Davis Bennett --------- Co-authored-by: Davis Bennett --- docs/user-guide/v3_migration.md | 45 +++++++++++++++------------------ 1 file changed, 21 insertions(+), 24 deletions(-) diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index 291c348710..15425de27a 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -117,51 +117,48 @@ The following sections provide details on breaking changes in Zarr-Python 3. ### The Store class -The Store API has changed significant in Zarr-Python 3. The most notable changes to the -Store API are: +The Store API has changed significant in Zarr-Python 3. -#### Store Import Paths +#### The base store class -Several store implementations have moved from the top-level module to `zarr.storage`: +The `MutableMapping` base class has been replaced in favor of a custom abstract base class ([`zarr.abc.store.Store`][]). +An asynchronous interface is used for all store methods that use I/O. +This change ensures that these store methods are non-blocking and are as performant as possible. + +#### Store implementations + +Store implementations have moved from the top-level module to `zarr.storage`: ```diff title="Store import changes from v2 to v3" # Before (v2) -- from zarr import MemoryStore, DirectoryStore -+ from zarr.storage import MemoryStore, LocalStore # LocalStore replaces DirectoryStore +- from zarr import MemoryStore ++ from zarr.storage import MemoryStore ``` -Common replacements: +The following stores have been renamed or changed: -| v2 Import | v3 Import | -|-------------------------|------------------------------------| -| `zarr.MemoryStore` | [`zarr.storage.MemoryStore`][] | -| `zarr.DirectoryStore` | [`zarr.storage.LocalStore`][] | -| `zarr.TempStore` | Use [`tempfile.TemporaryDirectory`][] with [`LocalStore`][zarr.storage.LocalStore] | +| v2 | v3 | +|------------------------|------------------------------------| +| `DirectoryStore` | [`zarr.storage.LocalStore`][] | +| `FSStore` | [`zarr.storage.FsspecStore`][] | +| `TempStore` | Use [`tempfile.TemporaryDirectory`][] with [`LocalStore`][zarr.storage.LocalStore] | +| `zarr. -1. Replaced the `MutableMapping` base class in favor of a custom abstract base class - ([`zarr.abc.store.Store`][]). -2. Switched to an asynchronous interface for all store methods that result in IO. This - change ensures that all store methods are non-blocking and are as performant as - possible. -Beyond the changes store interface, a number of deprecated stores were also removed in -Zarr-Python 3. See issue #1274 for more details on the removal of these stores. +A number of deprecated stores were also removed. +See issue #1274 for more details on the removal of these stores. - `N5Store` - see https://github.com/zarr-developers/n5py for an alternative interface to N5 formatted data. - `ABSStore` - use the [`zarr.storage.FsspecStore`][] instead along with fsspec's [adlfs backend](https://github.com/fsspec/adlfs). - -The following stores have been removed altogether. Users who need these stores will have to -implement their own version in zarr-python v3. - - `DBMStore` - `LMDBStore` - `SQLiteStore` - `MongoDBStore` - `RedisStore` -At present, the latter five stores in this list do not have an equivalent in Zarr-Python 3. +The latter five stores in this list do not have an equivalent in Zarr-Python 3. If you are interested in developing a custom store that targets these backends, see [developing custom stores](storage.md/#developing-custom-stores) or open an [issue](https://github.com/zarr-developers/zarr-python/issues) to discuss your use case. From edd47db7959fb8a355bd7560878fdafc11277fc2 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Mon, 17 Nov 2025 20:54:49 +0100 Subject: [PATCH 157/468] Parametrize Array with v2/v3 metadata (#3304) * Parametrize Array with v2/v3 metadata * Try fixing docstrings * Add an AnyAsyncArray type * Add async array v2 and v3 types * Add changelog entry * Pass sub-classes through returns. * Chage release note to MarkDown --------- Co-authored-by: Davis Bennett --- changes/3304.feature.md | 2 + src/zarr/api/asynchronous.py | 53 ++---- src/zarr/api/synchronous.py | 33 ++-- src/zarr/core/array.py | 74 ++++----- src/zarr/core/attributes.py | 4 +- src/zarr/core/group.py | 155 ++++++++---------- src/zarr/core/indexing.py | 19 ++- src/zarr/core/metadata/__init__.py | 2 +- src/zarr/core/sync_group.py | 10 +- src/zarr/metadata/migrate_v3.py | 7 +- src/zarr/testing/strategies.py | 3 +- src/zarr/types.py | 23 +++ tests/test_api.py | 5 +- tests/test_api/test_asynchronous.py | 8 +- tests/test_array.py | 24 +-- tests/test_attributes.py | 9 +- tests/test_cli/test_migrate_v3.py | 4 +- tests/test_codecs/test_codecs.py | 5 +- .../test_v2_dtype_regression.py | 10 +- 19 files changed, 221 insertions(+), 229 deletions(-) create mode 100644 changes/3304.feature.md create mode 100644 src/zarr/types.py diff --git a/changes/3304.feature.md b/changes/3304.feature.md new file mode 100644 index 0000000000..45dbd85731 --- /dev/null +++ b/changes/3304.feature.md @@ -0,0 +1,2 @@ +The `Array` class can now also be parametrized in the same manner as the `AsyncArray` class, allowing Zarr format v2 and v3 `Array`s to be distinguished. +New types have been added to `zarr.types` to help with this. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 179f1ddb4a..6164cda957 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -3,7 +3,7 @@ import asyncio import dataclasses import warnings -from typing import TYPE_CHECKING, Any, Literal, NotRequired, TypedDict, cast +from typing import TYPE_CHECKING, Any, Literal, NotRequired, TypeAlias, TypedDict, cast import numpy as np import numpy.typing as npt @@ -37,7 +37,7 @@ GroupMetadata, create_hierarchy, ) -from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata, ArrayV3Metadata +from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata from zarr.errors import ( ArrayNotFoundError, GroupNotFoundError, @@ -58,9 +58,10 @@ from zarr.core.chunk_key_encodings import ChunkKeyEncoding from zarr.core.metadata.v2 import CompressorLikev2 from zarr.storage import StoreLike + from zarr.types import AnyArray, AnyAsyncArray # TODO: this type could use some more thought - ArrayLike = AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | Array | npt.NDArray[Any] + ArrayLike: TypeAlias = AnyAsyncArray | AnyArray | npt.NDArray[Any] PathLike = str __all__ = [ @@ -335,7 +336,7 @@ async def open( path: str | None = None, storage_options: dict[str, Any] | None = None, **kwargs: Any, # TODO: type kwargs as valid args to open_array -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup: +) -> AnyAsyncArray | AsyncGroup: """Convenience function to open a group or array using file-mode-like semantics. Parameters @@ -601,9 +602,7 @@ async def tree(grp: AsyncGroup, expand: bool | None = None, level: int | None = return await grp.tree(expand=expand, level=level) -async def array( - data: npt.ArrayLike | Array, **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def array(data: npt.ArrayLike | AnyArray, **kwargs: Any) -> AnyAsyncArray: """Create an array filled with `data`. Parameters @@ -919,7 +918,7 @@ async def create( storage_options: dict[str, Any] | None = None, config: ArrayConfigLike | None = None, **kwargs: Any, -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +) -> AnyAsyncArray: """Create an array. Parameters @@ -1106,9 +1105,7 @@ async def create( ) -async def empty( - shape: tuple[int, ...], **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def empty(shape: tuple[int, ...], **kwargs: Any) -> AnyAsyncArray: """Create an empty array with the specified shape. The contents will be filled with the specified fill value or zeros if no fill value is provided. @@ -1128,9 +1125,7 @@ async def empty( return await create(shape=shape, **kwargs) -async def empty_like( - a: ArrayLike, **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def empty_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: """Create an empty array like `a`. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1159,9 +1154,7 @@ async def empty_like( # TODO: add type annotations for fill_value and kwargs -async def full( - shape: tuple[int, ...], fill_value: Any, **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def full(shape: tuple[int, ...], fill_value: Any, **kwargs: Any) -> AnyAsyncArray: """Create an array, with `fill_value` being used as the default value for uninitialized portions of the array. @@ -1183,9 +1176,7 @@ async def full( # TODO: add type annotations for kwargs -async def full_like( - a: ArrayLike, **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def full_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: """Create a filled array like `a`. Parameters @@ -1206,9 +1197,7 @@ async def full_like( return await full(**like_kwargs) # type: ignore[arg-type] -async def ones( - shape: tuple[int, ...], **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def ones(shape: tuple[int, ...], **kwargs: Any) -> AnyAsyncArray: """Create an array, with one being used as the default value for uninitialized portions of the array. @@ -1227,9 +1216,7 @@ async def ones( return await create(shape=shape, fill_value=1, **kwargs) -async def ones_like( - a: ArrayLike, **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def ones_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: """Create an array of ones like `a`. Parameters @@ -1256,7 +1243,7 @@ async def open_array( path: PathLike = "", storage_options: dict[str, Any] | None = None, **kwargs: Any, # TODO: type kwargs as valid args to save -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +) -> AnyAsyncArray: """Open an array using file-mode-like semantics. Parameters @@ -1307,9 +1294,7 @@ async def open_array( raise ArrayNotFoundError(msg) from err -async def open_like( - a: ArrayLike, path: str, **kwargs: Any -) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: +async def open_like(a: ArrayLike, path: str, **kwargs: Any) -> AnyAsyncArray: """Open a persistent array like `a`. Parameters @@ -1332,9 +1317,7 @@ async def open_like( return await open_array(path=path, **like_kwargs) # type: ignore[arg-type] -async def zeros( - shape: tuple[int, ...], **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def zeros(shape: tuple[int, ...], **kwargs: Any) -> AnyAsyncArray: """Create an array, with zero being used as the default value for uninitialized portions of the array. @@ -1353,9 +1336,7 @@ async def zeros( return await create(shape=shape, fill_value=0, **kwargs) -async def zeros_like( - a: ArrayLike, **kwargs: Any -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +async def zeros_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: """Create an array of zeros like `a`. Parameters diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 54bfeaa9fc..1204eba3c9 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -40,6 +40,7 @@ ) from zarr.core.dtype import ZDTypeLike from zarr.storage import StoreLike + from zarr.types import AnyArray __all__ = [ "array", @@ -181,7 +182,7 @@ def open( path: str | None = None, storage_options: dict[str, Any] | None = None, **kwargs: Any, # TODO: type kwargs as valid args to async_api.open -) -> Array | Group: +) -> AnyArray | Group: """Open a group or array using file-mode-like semantics. Parameters @@ -387,7 +388,7 @@ def tree(grp: Group, expand: bool | None = None, level: int | None = None) -> An # TODO: add type annotations for kwargs -def array(data: npt.ArrayLike | Array, **kwargs: Any) -> Array: +def array(data: npt.ArrayLike | AnyArray, **kwargs: Any) -> AnyArray: """Create an array filled with `data`. Parameters @@ -652,7 +653,7 @@ def create( storage_options: dict[str, Any] | None = None, config: ArrayConfigLike | None = None, **kwargs: Any, -) -> Array: +) -> AnyArray: """Create an array. Parameters @@ -836,7 +837,7 @@ def create_array( overwrite: bool = False, config: ArrayConfigLike | None = None, write_data: bool = True, -) -> Array: +) -> AnyArray: """Create an array. This function wraps [zarr.core.array.create_array][]. @@ -989,7 +990,7 @@ def create_array( def from_array( store: StoreLike, *, - data: Array | npt.ArrayLike, + data: AnyArray | npt.ArrayLike, write_data: bool = True, name: str | None = None, chunks: Literal["auto", "keep"] | tuple[int, ...] = "keep", @@ -1006,7 +1007,7 @@ def from_array( storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, -) -> Array: +) -> AnyArray: """Create an array from an existing array or array-like. Parameters @@ -1220,7 +1221,7 @@ def from_array( # TODO: add type annotations for kwargs -def empty(shape: tuple[int, ...], **kwargs: Any) -> Array: +def empty(shape: tuple[int, ...], **kwargs: Any) -> AnyArray: """Create an empty array with the specified shape. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1247,7 +1248,7 @@ def empty(shape: tuple[int, ...], **kwargs: Any) -> Array: # TODO: move ArrayLike to common module # TODO: add type annotations for kwargs -def empty_like(a: ArrayLike, **kwargs: Any) -> Array: +def empty_like(a: ArrayLike, **kwargs: Any) -> AnyArray: """Create an empty array like another array. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1273,7 +1274,7 @@ def empty_like(a: ArrayLike, **kwargs: Any) -> Array: # TODO: add type annotations for kwargs and fill_value -def full(shape: tuple[int, ...], fill_value: Any, **kwargs: Any) -> Array: +def full(shape: tuple[int, ...], fill_value: Any, **kwargs: Any) -> AnyArray: """Create an array with a default fill value. Parameters @@ -1295,7 +1296,7 @@ def full(shape: tuple[int, ...], fill_value: Any, **kwargs: Any) -> Array: # TODO: move ArrayLike to common module # TODO: add type annotations for kwargs -def full_like(a: ArrayLike, **kwargs: Any) -> Array: +def full_like(a: ArrayLike, **kwargs: Any) -> AnyArray: """Create a filled array like another array. Parameters @@ -1314,7 +1315,7 @@ def full_like(a: ArrayLike, **kwargs: Any) -> Array: # TODO: add type annotations for kwargs -def ones(shape: tuple[int, ...], **kwargs: Any) -> Array: +def ones(shape: tuple[int, ...], **kwargs: Any) -> AnyArray: """Create an array with a fill value of one. Parameters @@ -1333,7 +1334,7 @@ def ones(shape: tuple[int, ...], **kwargs: Any) -> Array: # TODO: add type annotations for kwargs -def ones_like(a: ArrayLike, **kwargs: Any) -> Array: +def ones_like(a: ArrayLike, **kwargs: Any) -> AnyArray: """Create an array of ones like another array. Parameters @@ -1360,7 +1361,7 @@ def open_array( path: PathLike = "", storage_options: dict[str, Any] | None = None, **kwargs: Any, -) -> Array: +) -> AnyArray: """Open an array using file-mode-like semantics. Parameters @@ -1402,7 +1403,7 @@ def open_array( # TODO: add type annotations for kwargs -def open_like(a: ArrayLike, path: str, **kwargs: Any) -> Array: +def open_like(a: ArrayLike, path: str, **kwargs: Any) -> AnyArray: """Open a persistent array like another array. Parameters @@ -1423,7 +1424,7 @@ def open_like(a: ArrayLike, path: str, **kwargs: Any) -> Array: # TODO: add type annotations for kwargs -def zeros(shape: tuple[int, ...], **kwargs: Any) -> Array: +def zeros(shape: tuple[int, ...], **kwargs: Any) -> AnyArray: """Create an array with a fill value of zero. Parameters @@ -1442,7 +1443,7 @@ def zeros(shape: tuple[int, ...], **kwargs: Any) -> Array: # TODO: add type annotations for kwargs -def zeros_like(a: ArrayLike, **kwargs: Any) -> Array: +def zeros_like(a: ArrayLike, **kwargs: Any) -> AnyArray: """Create an array of zeros like another array. Parameters diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 1139ee0ade..6b20ee950d 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -144,6 +144,7 @@ from zarr.codecs.sharding import ShardingCodecIndexLocation from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar from zarr.storage import StoreLike + from zarr.types import AnyArray, AnyAsyncArray, AsyncArrayV2, AsyncArrayV3 # Array and AsyncArray are defined in the base ``zarr`` namespace @@ -310,7 +311,7 @@ class AsyncArray(Generic[T_ArrayMetadata]): @overload def __init__( - self: AsyncArray[ArrayV2Metadata], + self: AsyncArrayV2, metadata: ArrayV2Metadata | ArrayV2MetadataDict, store_path: StorePath, config: ArrayConfigLike | None = None, @@ -318,7 +319,7 @@ def __init__( @overload def __init__( - self: AsyncArray[ArrayV3Metadata], + self: AsyncArrayV3, metadata: ArrayV3Metadata | ArrayMetadataJSON_V3, store_path: StorePath, config: ArrayConfigLike | None = None, @@ -364,7 +365,7 @@ async def create( overwrite: bool = False, data: npt.ArrayLike | None = None, config: ArrayConfigLike | None = None, - ) -> AsyncArray[ArrayV2Metadata]: ... + ) -> AsyncArrayV2: ... # this overload defines the function signature when zarr_format is 3 @overload @@ -393,7 +394,7 @@ async def create( overwrite: bool = False, data: npt.ArrayLike | None = None, config: ArrayConfigLike | None = None, - ) -> AsyncArray[ArrayV3Metadata]: ... + ) -> AsyncArrayV3: ... @overload @classmethod @@ -421,7 +422,7 @@ async def create( overwrite: bool = False, data: npt.ArrayLike | None = None, config: ArrayConfigLike | None = None, - ) -> AsyncArray[ArrayV3Metadata]: ... + ) -> AsyncArrayV3: ... @overload @classmethod @@ -455,7 +456,7 @@ async def create( overwrite: bool = False, data: npt.ArrayLike | None = None, config: ArrayConfigLike | None = None, - ) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: ... + ) -> AnyAsyncArray: ... @classmethod @deprecated("Use zarr.api.asynchronous.create_array instead.", category=ZarrDeprecationWarning) @@ -489,7 +490,7 @@ async def create( overwrite: bool = False, data: npt.ArrayLike | None = None, config: ArrayConfigLike | None = None, - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Method to create a new asynchronous array instance. !!! warning "Deprecated" @@ -640,7 +641,7 @@ async def _create( overwrite: bool = False, data: npt.ArrayLike | None = None, config: ArrayConfigLike | None = None, - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Method to create a new asynchronous array instance. Deprecated in favor of [`zarr.api.asynchronous.create_array`][]. """ @@ -661,7 +662,7 @@ async def _create( _chunks = normalize_chunks(chunk_shape, shape, item_size) config_parsed = parse_array_config(config) - result: AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] + result: AnyAsyncArray if zarr_format == 3: if dimension_separator is not None: raise ValueError( @@ -805,7 +806,7 @@ async def _create_v3( dimension_names: DimensionNames = None, attributes: dict[str, JSON] | None = None, overwrite: bool = False, - ) -> AsyncArray[ArrayV3Metadata]: + ) -> AsyncArrayV3: if overwrite: if store_path.store.supports_deletes: await store_path.delete_dir() @@ -886,7 +887,7 @@ async def _create_v2( compressor: CompressorLike = "auto", attributes: dict[str, JSON] | None = None, overwrite: bool = False, - ) -> AsyncArray[ArrayV2Metadata]: + ) -> AsyncArrayV2: if overwrite: if store_path.store.supports_deletes: await store_path.delete_dir() @@ -930,7 +931,7 @@ def from_dict( cls, store_path: StorePath, data: dict[str, JSON], - ) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: + ) -> AnyAsyncArray: """ Create a Zarr array from a dictionary, with support for both Zarr format 2 and 3 metadata. @@ -946,7 +947,7 @@ def from_dict( Returns ------- - AsyncArray[ArrayV3Metadata] or AsyncArray[ArrayV2Metadata] + AsyncArrayV3 or AsyncArrayV2 The created Zarr array, either using Zarr format 2 or 3 metadata based on the provided data. Raises @@ -962,7 +963,7 @@ async def open( cls, store: StoreLike, zarr_format: ZarrFormat | None = 3, - ) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: + ) -> AnyAsyncArray: """ Async method to open an existing Zarr array from a given store. @@ -2032,15 +2033,15 @@ def _info( # TODO: Array can be a frozen data class again once property setters (e.g. shape) are removed @dataclass(frozen=False) -class Array: +class Array(Generic[T_ArrayMetadata]): """ A Zarr array. """ - _async_array: AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] + _async_array: AsyncArray[T_ArrayMetadata] @property - def async_array(self) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: + def async_array(self) -> AsyncArray[T_ArrayMetadata]: """An asynchronous version of the current array. Useful for batching requests. Returns @@ -2080,7 +2081,7 @@ def create( # runtime overwrite: bool = False, config: ArrayConfigLike | None = None, - ) -> Array: + ) -> AnyArray: """Creates a new Array instance from an initialized store. !!! warning "Deprecated" @@ -2224,7 +2225,7 @@ def _create( # runtime overwrite: bool = False, config: ArrayConfigLike | None = None, - ) -> Array: + ) -> Self: """Creates a new Array instance from an initialized store. Deprecated in favor of [`zarr.create_array`][]. """ @@ -2256,7 +2257,7 @@ def from_dict( cls, store_path: StorePath, data: dict[str, JSON], - ) -> Array: + ) -> Self: """ Create a Zarr array from a dictionary. @@ -2286,7 +2287,7 @@ def from_dict( def open( cls, store: StoreLike, - ) -> Array: + ) -> Self: """Opens an existing Array from a store. Parameters @@ -4138,7 +4139,7 @@ def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: """ return sync(self.async_array.append(data, axis=axis)) - def update_attributes(self, new_attributes: dict[str, JSON]) -> Array: + def update_attributes(self, new_attributes: dict[str, JSON]) -> Self: """ Update the array's attributes. @@ -4163,11 +4164,8 @@ def update_attributes(self, new_attributes: dict[str, JSON]) -> Array: - The updated attributes will be merged with existing attributes, and any conflicts will be overwritten by the new values. """ - # TODO: remove this cast when type inference improves new_array = sync(self.async_array.update_attributes(new_attributes)) - # TODO: remove this cast when type inference improves - _new_array = cast("AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]", new_array) - return type(self)(_new_array) + return type(self)(new_array) def __repr__(self) -> str: return f"" @@ -4225,7 +4223,7 @@ def info_complete(self) -> Any: async def _shards_initialized( - array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], + array: AnyAsyncArray, ) -> tuple[str, ...]: """ Return the keys of the chunks that have been persisted to the storage backend. @@ -4289,7 +4287,7 @@ class ShardsConfigParam(TypedDict): async def from_array( store: StoreLike, *, - data: Array | npt.ArrayLike, + data: AnyArray | npt.ArrayLike, write_data: bool = True, name: str | None = None, chunks: Literal["auto", "keep"] | tuple[int, ...] = "keep", @@ -4306,7 +4304,7 @@ async def from_array( storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +) -> AnyAsyncArray: """Create an array from an existing array or array-like. Parameters @@ -4531,7 +4529,7 @@ async def from_array( if isinstance(data, Array): async def _copy_array_region( - chunk_coords: tuple[int, ...] | slice, _data: Array + chunk_coords: tuple[int, ...] | slice, _data: AnyArray ) -> None: arr = await _data.async_array.getitem(chunk_coords) await result.setitem(chunk_coords, arr) @@ -4574,7 +4572,7 @@ async def init_array( dimension_names: DimensionNames = None, overwrite: bool = False, config: ArrayConfigLike | None = None, -) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata]: +) -> AnyAsyncArray: """Create and persist an array metadata document. Parameters @@ -4792,7 +4790,7 @@ async def create_array( overwrite: bool = False, config: ArrayConfigLike | None = None, write_data: bool = True, -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +) -> AnyAsyncArray: """Create an array. Parameters @@ -4961,7 +4959,7 @@ async def create_array( def _parse_keep_array_attr( - data: Array | npt.ArrayLike, + data: AnyArray | npt.ArrayLike, chunks: Literal["auto", "keep"] | tuple[int, ...], shards: ShardsLike | None | Literal["keep"], filters: FiltersLike | Literal["keep"], @@ -5340,7 +5338,7 @@ def _parse_data_params( def _iter_chunk_coords( - array: Array | AsyncArray[Any], + array: AnyArray | AnyAsyncArray, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None, @@ -5371,7 +5369,7 @@ def _iter_chunk_coords( def _iter_shard_coords( - array: Array | AsyncArray[Any], + array: AnyArray | AnyAsyncArray, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None, @@ -5402,7 +5400,7 @@ def _iter_shard_coords( def _iter_shard_keys( - array: Array | AsyncArray[Any], + array: AnyArray | AnyAsyncArray, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None, @@ -5431,7 +5429,7 @@ def _iter_shard_keys( def _iter_shard_regions( - array: Array | AsyncArray[Any], + array: AnyArray | AnyAsyncArray, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None, @@ -5466,7 +5464,7 @@ def _iter_shard_regions( def _iter_chunk_regions( - array: Array | AsyncArray[Any], + array: AnyArray | AnyAsyncArray, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None, diff --git a/src/zarr/core/attributes.py b/src/zarr/core/attributes.py index 7097385081..7f29e44365 100644 --- a/src/zarr/core/attributes.py +++ b/src/zarr/core/attributes.py @@ -8,12 +8,12 @@ if TYPE_CHECKING: from collections.abc import Iterator - from zarr.core.array import Array from zarr.core.group import Group + from zarr.types import AnyArray class Attributes(MutableMapping[str, JSON]): - def __init__(self, obj: Array | Group) -> None: + def __init__(self, obj: AnyArray | Group) -> None: # key=".zattrs", read_only=False, cache=True, synchronizer=None self._obj = obj diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 26aed4fd60..9b5fee275b 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -79,6 +79,7 @@ from zarr.core.chunk_key_encodings import ChunkKeyEncodingLike from zarr.core.common import MemoryOrder from zarr.core.dtype import ZDTypeLike + from zarr.types import AnyArray, AnyAsyncArray, ArrayV2, ArrayV3, AsyncArrayV2, AsyncArrayV3 logger = logging.getLogger("zarr.group") @@ -113,7 +114,11 @@ def parse_attributes(data: Any) -> dict[str, Any]: @overload -def _parse_async_node(node: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]) -> Array: ... +def _parse_async_node(node: AsyncArrayV3) -> ArrayV3: ... + + +@overload +def _parse_async_node(node: AsyncArrayV2) -> ArrayV2: ... @overload @@ -121,8 +126,8 @@ def _parse_async_node(node: AsyncGroup) -> Group: ... def _parse_async_node( - node: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup, -) -> Array | Group: + node: AnyAsyncArray | AsyncGroup, +) -> AnyArray | Group: """Wrap an AsyncArray in an Array, or an AsyncGroup in a Group.""" if isinstance(node, AsyncArray): return Array(node) @@ -712,7 +717,7 @@ async def setitem(self, key: str, value: Any) -> None: async def getitem( self, key: str, - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup: + ) -> AnyAsyncArray | AsyncGroup: """ Get a subarray or subgroup from the group. @@ -740,7 +745,7 @@ async def getitem( def _getitem_consolidated( self, store_path: StorePath, key: str, prefix: str - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup: + ) -> AnyAsyncArray | AsyncGroup: # getitem, in the special case where we have consolidated metadata. # Note that this is a regular def (non async) function. # This shouldn't do any additional I/O. @@ -803,7 +808,7 @@ async def delitem(self, key: str) -> None: async def get( self, key: str, default: DefaultT | None = None - ) -> AsyncArray[Any] | AsyncGroup | DefaultT | None: + ) -> AnyAsyncArray | AsyncGroup | DefaultT | None: """Obtain a group member, returning default if not found. Parameters @@ -983,9 +988,7 @@ async def require_group(self, name: str, overwrite: bool = False) -> AsyncGroup: grp = await self.create_group(name, overwrite=True) else: try: - item: ( - AsyncGroup | AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] - ) = await self.getitem(name) + item: AsyncGroup | AnyAsyncArray = await self.getitem(name) if not isinstance(item, AsyncGroup): raise TypeError( f"Incompatible object ({item.__class__.__name__}) already exists" @@ -1034,7 +1037,7 @@ async def create_array( overwrite: bool = False, config: ArrayConfigLike | None = None, write_data: bool = True, - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Create an array within this group. This method lightly wraps [zarr.core.array.create_array][]. @@ -1160,9 +1163,7 @@ async def create_array( ) @deprecated("Use AsyncGroup.create_array instead.", category=ZarrDeprecationWarning) - async def create_dataset( - self, name: str, *, shape: ShapeLike, **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + async def create_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> AnyAsyncArray: """Create an array. !!! warning "Deprecated" @@ -1203,7 +1204,7 @@ async def require_dataset( dtype: npt.DTypeLike = None, exact: bool = False, **kwargs: Any, - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Obtain an array, creating if it doesn't exist. !!! warning "Deprecated" @@ -1241,7 +1242,7 @@ async def require_array( dtype: npt.DTypeLike = None, exact: bool = False, **kwargs: Any, - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Obtain an array, creating if it doesn't exist. Other `kwargs` are as per [zarr.AsyncGroup.create_dataset][]. @@ -1351,7 +1352,7 @@ async def members( *, use_consolidated_for_children: bool = True, ) -> AsyncGenerator[ - tuple[str, AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup], + tuple[str, AnyAsyncArray | AsyncGroup], None, ]: """ @@ -1390,7 +1391,7 @@ async def members( def _members_consolidated( self, max_depth: int | None, prefix: str = "" ) -> Generator[ - tuple[str, AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup], + tuple[str, AnyAsyncArray | AsyncGroup], None, ]: consolidated_metadata = self.metadata.consolidated_metadata @@ -1415,9 +1416,7 @@ def _members_consolidated( async def _members( self, max_depth: int | None, *, use_consolidated_for_children: bool = True - ) -> AsyncGenerator[ - tuple[str, AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] | AsyncGroup], None - ]: + ) -> AsyncGenerator[tuple[str, AnyAsyncArray | AsyncGroup], None]: skip_keys: tuple[str, ...] if self.metadata.zarr_format == 2: skip_keys = (".zattrs", ".zgroup", ".zarray", ".zmetadata") @@ -1457,9 +1456,7 @@ async def create_hierarchy( nodes: dict[str, ArrayV2Metadata | ArrayV3Metadata | GroupMetadata], *, overwrite: bool = False, - ) -> AsyncIterator[ - tuple[str, AsyncGroup | AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]] - ]: + ) -> AsyncIterator[tuple[str, AsyncGroup | AnyAsyncArray]]: """ Create a hierarchy of arrays or groups rooted at this group. @@ -1573,9 +1570,7 @@ async def group_values(self) -> AsyncGenerator[AsyncGroup, None]: async def arrays( self, - ) -> AsyncGenerator[ - tuple[str, AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]], None - ]: + ) -> AsyncGenerator[tuple[str, AnyAsyncArray], None]: """Iterate over arrays.""" async for key, value in self.members(): if isinstance(value, AsyncArray): @@ -1588,7 +1583,7 @@ async def array_keys(self) -> AsyncGenerator[str, None]: async def array_values( self, - ) -> AsyncGenerator[AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], None]: + ) -> AsyncGenerator[AnyAsyncArray, None]: """Iterate over array values.""" async for _, array in self.arrays(): yield array @@ -1618,9 +1613,7 @@ async def tree(self, expand: bool | None = None, level: int | None = None) -> An raise NotImplementedError("'expand' is not yet implemented.") return await group_tree_async(self, max_depth=level) - async def empty( - self, *, name: str, shape: tuple[int, ...], **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + async def empty(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> AnyAsyncArray: """Create an empty array with the specified shape in this Group. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1641,9 +1634,7 @@ async def empty( """ return await async_api.empty(shape=shape, store=self.store_path, path=name, **kwargs) - async def zeros( - self, *, name: str, shape: tuple[int, ...], **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + async def zeros(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> AnyAsyncArray: """Create an array, with zero being used as the default value for uninitialized portions of the array. Parameters @@ -1662,9 +1653,7 @@ async def zeros( """ return await async_api.zeros(shape=shape, store=self.store_path, path=name, **kwargs) - async def ones( - self, *, name: str, shape: tuple[int, ...], **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + async def ones(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> AnyAsyncArray: """Create an array, with one being used as the default value for uninitialized portions of the array. Parameters @@ -1685,7 +1674,7 @@ async def ones( async def full( self, *, name: str, shape: tuple[int, ...], fill_value: Any | None, **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Create an array, with "fill_value" being used as the default value for uninitialized portions of the array. Parameters @@ -1714,7 +1703,7 @@ async def full( async def empty_like( self, *, name: str, data: async_api.ArrayLike, **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Create an empty sub-array like `data`. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -1736,7 +1725,7 @@ async def empty_like( async def zeros_like( self, *, name: str, data: async_api.ArrayLike, **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Create a sub-array of zeros like `data`. Parameters @@ -1757,7 +1746,7 @@ async def zeros_like( async def ones_like( self, *, name: str, data: async_api.ArrayLike, **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Create a sub-array of ones like `data`. Parameters @@ -1778,7 +1767,7 @@ async def ones_like( async def full_like( self, *, name: str, data: async_api.ArrayLike, **kwargs: Any - ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + ) -> AnyAsyncArray: """Create a sub-array like `data` filled with the `fill_value` of `data` . Parameters @@ -1885,7 +1874,7 @@ def open( obj = sync(AsyncGroup.open(store, zarr_format=zarr_format)) return cls(obj) - def __getitem__(self, path: str) -> Array | Group: + def __getitem__(self, path: str) -> AnyArray | Group: """Obtain a group member. Parameters @@ -1921,7 +1910,7 @@ def __getitem__(self, path: str) -> Array | Group: else: return Group(obj) - def get(self, path: str, default: DefaultT | None = None) -> Array | Group | DefaultT | None: + def get(self, path: str, default: DefaultT | None = None) -> AnyArray | Group | DefaultT | None: """Obtain a group member, returning default if not found. Parameters @@ -2161,7 +2150,7 @@ def nmembers(self, max_depth: int | None = 0) -> int: def members( self, max_depth: int | None = 0, *, use_consolidated_for_children: bool = True - ) -> tuple[tuple[str, Array | Group], ...]: + ) -> tuple[tuple[str, AnyArray | Group], ...]: """ Returns an AsyncGenerator over the arrays and groups contained in this group. This method requires that `store_path.store` supports directory listing. @@ -2197,7 +2186,7 @@ def create_hierarchy( nodes: dict[str, ArrayV2Metadata | ArrayV3Metadata | GroupMetadata], *, overwrite: bool = False, - ) -> Iterator[tuple[str, Group | Array]]: + ) -> Iterator[tuple[str, Group | AnyArray]]: """ Create a hierarchy of arrays or groups rooted at this group. @@ -2336,7 +2325,7 @@ def group_values(self) -> Generator[Group, None]: for _, group in self.groups(): yield group - def arrays(self) -> Generator[tuple[str, Array], None]: + def arrays(self) -> Generator[tuple[str, AnyArray], None]: """Return the sub-arrays of this group as a generator of (name, array) pairs Examples @@ -2367,7 +2356,7 @@ def array_keys(self) -> Generator[str, None]: for name, _ in self.arrays(): yield name - def array_values(self) -> Generator[Array, None]: + def array_values(self) -> Generator[AnyArray, None]: """Return an iterator over group members. Examples @@ -2475,7 +2464,7 @@ def create( overwrite: bool = False, config: ArrayConfigLike | None = None, write_data: bool = True, - ) -> Array: + ) -> AnyArray: """Create an array within this group. This method lightly wraps [`zarr.core.array.create_array`][]. @@ -2619,7 +2608,7 @@ def create_array( overwrite: bool = False, config: ArrayConfigLike | None = None, write_data: bool = True, - ) -> Array: + ) -> AnyArray: """Create an array within this group. This method lightly wraps [zarr.core.array.create_array][]. @@ -2748,7 +2737,7 @@ def create_array( ) @deprecated("Use Group.create_array instead.", category=ZarrDeprecationWarning) - def create_dataset(self, name: str, **kwargs: Any) -> Array: + def create_dataset(self, name: str, **kwargs: Any) -> AnyArray: """Create an array. !!! warning "Deprecated" @@ -2773,7 +2762,7 @@ def create_dataset(self, name: str, **kwargs: Any) -> Array: return Array(self._sync(self._async_group.create_dataset(name, **kwargs))) @deprecated("Use Group.require_array instead.", category=ZarrDeprecationWarning) - def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: + def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> AnyArray: """Obtain an array, creating if it doesn't exist. !!! warning "Deprecated" @@ -2798,7 +2787,7 @@ def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Arra """ return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs))) - def require_array(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: + def require_array(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> AnyArray: """Obtain an array, creating if it doesn't exist. Other `kwargs` are as per [zarr.Group.create_array][]. @@ -2816,7 +2805,7 @@ def require_array(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs))) - def empty(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: + def empty(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> AnyArray: """Create an empty array with the specified shape in this Group. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -2837,7 +2826,7 @@ def empty(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.empty(name=name, shape=shape, **kwargs))) - def zeros(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: + def zeros(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> AnyArray: """Create an array, with zero being used as the default value for uninitialized portions of the array. Parameters @@ -2856,7 +2845,7 @@ def zeros(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: """ return Array(self._sync(self._async_group.zeros(name=name, shape=shape, **kwargs))) - def ones(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: + def ones(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> AnyArray: """Create an array, with one being used as the default value for uninitialized portions of the array. Parameters @@ -2877,7 +2866,7 @@ def ones(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> Array: def full( self, *, name: str, shape: tuple[int, ...], fill_value: Any | None, **kwargs: Any - ) -> Array: + ) -> AnyArray: """Create an array, with "fill_value" being used as the default value for uninitialized portions of the array. Parameters @@ -2902,7 +2891,7 @@ def full( ) ) - def empty_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: + def empty_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> AnyArray: """Create an empty sub-array like `data`. The contents will be filled with the array's fill value or zeros if no fill value is provided. @@ -2928,7 +2917,7 @@ def empty_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> """ return Array(self._sync(self._async_group.empty_like(name=name, data=data, **kwargs))) - def zeros_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: + def zeros_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> AnyArray: """Create a sub-array of zeros like `data`. Parameters @@ -2948,7 +2937,7 @@ def zeros_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> return Array(self._sync(self._async_group.zeros_like(name=name, data=data, **kwargs))) - def ones_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: + def ones_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> AnyArray: """Create a sub-array of ones like `data`. Parameters @@ -2967,7 +2956,7 @@ def ones_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> A """ return Array(self._sync(self._async_group.ones_like(name=name, data=data, **kwargs))) - def full_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> Array: + def full_like(self, *, name: str, data: async_api.ArrayLike, **kwargs: Any) -> AnyArray: """Create a sub-array like `data` filled with the `fill_value` of `data` . Parameters @@ -3017,7 +3006,7 @@ def array( overwrite: bool = False, config: ArrayConfigLike | None = None, data: npt.ArrayLike | None = None, - ) -> Array: + ) -> AnyArray: """Create an array within this group. !!! warning "Deprecated" @@ -3147,9 +3136,7 @@ async def create_hierarchy( store: Store, nodes: dict[str, GroupMetadata | ArrayV2Metadata | ArrayV3Metadata], overwrite: bool = False, -) -> AsyncIterator[ - tuple[str, AsyncGroup | AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]] -]: +) -> AsyncIterator[tuple[str, AsyncGroup | AnyAsyncArray]]: """ Create a complete zarr hierarchy from a collection of metadata objects. @@ -3313,9 +3300,7 @@ async def create_nodes( *, store: Store, nodes: dict[str, GroupMetadata | ArrayV2Metadata | ArrayV3Metadata], -) -> AsyncIterator[ - tuple[str, AsyncGroup | AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]] -]: +) -> AsyncIterator[tuple[str, AsyncGroup | AnyAsyncArray]]: """Create a collection of arrays and / or groups concurrently. Note: no attempt is made to validate that these arrays and / or groups collectively form a @@ -3493,7 +3478,7 @@ def _ensure_consistent_zarr_format( async def _getitem_semaphore( node: AsyncGroup, key: str, semaphore: asyncio.Semaphore | None -) -> AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] | AsyncGroup: +) -> AnyAsyncArray | AsyncGroup: """ Wrap Group.getitem with an optional semaphore. @@ -3513,9 +3498,7 @@ async def _iter_members( node: AsyncGroup, skip_keys: tuple[str, ...], semaphore: asyncio.Semaphore | None, -) -> AsyncGenerator[ - tuple[str, AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] | AsyncGroup], None -]: +) -> AsyncGenerator[tuple[str, AnyAsyncArray | AsyncGroup], None]: """ Iterate over the arrays and groups contained in a group. @@ -3530,7 +3513,7 @@ async def _iter_members( Yields ------ - tuple[str, AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] | AsyncGroup] + tuple[str, AnyAsyncArray | AsyncGroup] """ # retrieve keys from storage @@ -3569,9 +3552,7 @@ async def _iter_members_deep( skip_keys: tuple[str, ...], semaphore: asyncio.Semaphore | None = None, use_consolidated_for_children: bool = True, -) -> AsyncGenerator[ - tuple[str, AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] | AsyncGroup], None -]: +) -> AsyncGenerator[tuple[str, AnyAsyncArray | AsyncGroup], None]: """ Iterate over the arrays and groups contained in a group, and optionally the arrays and groups contained in those groups. @@ -3594,7 +3575,7 @@ async def _iter_members_deep( Yields ------ - tuple[str, AsyncArray[ArrayV3Metadata] | AsyncArray[ArrayV2Metadata] | AsyncGroup] + tuple[str, AnyAsyncArray | AsyncGroup] """ to_recurse = {} @@ -3609,7 +3590,7 @@ async def _iter_members_deep( if ( is_group and not use_consolidated_for_children - and node.metadata.consolidated_metadata is not None # type: ignore [union-attr] + and node.metadata.consolidated_metadata is not None ): node = cast("AsyncGroup", node) # We've decided not to trust consolidated metadata at this point, because we're @@ -3738,15 +3719,11 @@ def _build_metadata_v2( @overload -def _build_node( - *, store: Store, path: str, metadata: ArrayV2Metadata -) -> AsyncArray[ArrayV2Metadata]: ... +def _build_node(*, store: Store, path: str, metadata: ArrayV2Metadata) -> AsyncArrayV2: ... @overload -def _build_node( - *, store: Store, path: str, metadata: ArrayV3Metadata -) -> AsyncArray[ArrayV3Metadata]: ... +def _build_node(*, store: Store, path: str, metadata: ArrayV3Metadata) -> AsyncArrayV3: ... @overload @@ -3755,7 +3732,7 @@ def _build_node(*, store: Store, path: str, metadata: GroupMetadata) -> AsyncGro def _build_node( *, store: Store, path: str, metadata: ArrayV3Metadata | ArrayV2Metadata | GroupMetadata -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup: +) -> AnyAsyncArray | AsyncGroup: """ Take a metadata object and return a node (AsyncArray or AsyncGroup). """ @@ -3769,7 +3746,7 @@ def _build_node( raise ValueError(f"Unexpected metadata type: {type(metadata)}") # pragma: no cover -async def _get_node_v2(store: Store, path: str) -> AsyncArray[ArrayV2Metadata] | AsyncGroup: +async def _get_node_v2(store: Store, path: str) -> AsyncArrayV2 | AsyncGroup: """ Read a Zarr v2 AsyncArray or AsyncGroup from a path in a Store. @@ -3788,7 +3765,7 @@ async def _get_node_v2(store: Store, path: str) -> AsyncArray[ArrayV2Metadata] | return _build_node(store=store, path=path, metadata=metadata) -async def _get_node_v3(store: Store, path: str) -> AsyncArray[ArrayV3Metadata] | AsyncGroup: +async def _get_node_v3(store: Store, path: str) -> AsyncArrayV3 | AsyncGroup: """ Read a Zarr v3 AsyncArray or AsyncGroup from a path in a Store. @@ -3807,9 +3784,7 @@ async def _get_node_v3(store: Store, path: str) -> AsyncArray[ArrayV3Metadata] | return _build_node(store=store, path=path, metadata=metadata) -async def get_node( - store: Store, path: str, zarr_format: ZarrFormat -) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | AsyncGroup: +async def get_node(store: Store, path: str, zarr_format: ZarrFormat) -> AnyAsyncArray | AsyncGroup: """ Get an AsyncArray or AsyncGroup from a path in a Store. @@ -3887,7 +3862,7 @@ async def create_rooted_hierarchy( store: Store, nodes: dict[str, GroupMetadata | ArrayV2Metadata | ArrayV3Metadata], overwrite: bool = False, -) -> AsyncGroup | AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: +) -> AsyncGroup | AnyAsyncArray: """ Create an ``AsyncGroup`` or ``AsyncArray`` from a store and a dict of metadata documents. This function ensures that its input contains a specification of a root node, diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index c357ca7ccc..7f704bf2b7 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -36,9 +36,10 @@ ) if TYPE_CHECKING: - from zarr.core.array import Array, AsyncArray + from zarr.core.array import AsyncArray from zarr.core.buffer import NDArrayLikeOrScalar from zarr.core.chunk_grids import ChunkGrid + from zarr.types import AnyArray IntSequence = list[int] | npt.NDArray[np.intp] @@ -61,7 +62,7 @@ def err_too_many_indices(selection: Any, shape: tuple[int, ...]) -> None: raise IndexError(f"too many indices for array; expected {len(shape)}, got {len(selection)}") -def _zarr_array_to_int_or_bool_array(arr: Array) -> npt.NDArray[np.intp] | npt.NDArray[np.bool_]: +def _zarr_array_to_int_or_bool_array(arr: AnyArray) -> npt.NDArray[np.intp] | npt.NDArray[np.bool_]: if arr.dtype.kind in ("i", "b"): return np.asarray(arr) else: @@ -981,10 +982,10 @@ def __iter__(self) -> Iterator[ChunkProjection]: @dataclass(frozen=True) class OIndex: - array: Array + array: AnyArray # TODO: develop Array generic and move zarr.Array[np.intp] | zarr.Array[np.bool_] to ArrayOfIntOrBool - def __getitem__(self, selection: OrthogonalSelection | Array) -> NDArrayLikeOrScalar: + def __getitem__(self, selection: OrthogonalSelection | AnyArray) -> NDArrayLikeOrScalar: from zarr.core.array import Array # if input is a Zarr array, we materialize it now. @@ -1011,7 +1012,7 @@ def __setitem__(self, selection: OrthogonalSelection, value: npt.ArrayLike) -> N class AsyncOIndex(Generic[T_ArrayMetadata]): array: AsyncArray[T_ArrayMetadata] - async def getitem(self, selection: OrthogonalSelection | Array) -> NDArrayLikeOrScalar: + async def getitem(self, selection: OrthogonalSelection | AnyArray) -> NDArrayLikeOrScalar: from zarr.core.array import Array # if input is a Zarr array, we materialize it now. @@ -1111,7 +1112,7 @@ def __iter__(self) -> Iterator[ChunkProjection]: @dataclass(frozen=True) class BlockIndex: - array: Array + array: AnyArray def __getitem__(self, selection: BasicSelection) -> NDArrayLikeOrScalar: fields, new_selection = pop_fields(selection) @@ -1302,11 +1303,11 @@ def __init__( @dataclass(frozen=True) class VIndex: - array: Array + array: AnyArray # TODO: develop Array generic and move zarr.Array[np.intp] | zarr.Array[np.bool_] to ArrayOfIntOrBool def __getitem__( - self, selection: CoordinateSelection | MaskSelection | Array + self, selection: CoordinateSelection | MaskSelection | AnyArray ) -> NDArrayLikeOrScalar: from zarr.core.array import Array @@ -1353,7 +1354,7 @@ class AsyncVIndex(Generic[T_ArrayMetadata]): # TODO: develop Array generic and move zarr.Array[np.intp] | zarr.Array[np.bool_] to ArrayOfIntOrBool async def getitem( - self, selection: CoordinateSelection | MaskSelection | Array + self, selection: CoordinateSelection | MaskSelection | AnyArray ) -> NDArrayLikeOrScalar: # TODO deduplicate these internals with the sync version of getitem # TODO requires solving this circular sync issue: https://github.com/zarr-developers/zarr-python/pull/3083#discussion_r2230737448 diff --git a/src/zarr/core/metadata/__init__.py b/src/zarr/core/metadata/__init__.py index 691399c0f9..57385386b6 100644 --- a/src/zarr/core/metadata/__init__.py +++ b/src/zarr/core/metadata/__init__.py @@ -5,7 +5,7 @@ ArrayMetadata: TypeAlias = ArrayV2Metadata | ArrayV3Metadata ArrayMetadataDict: TypeAlias = ArrayV2MetadataDict | ArrayMetadataJSON_V3 -T_ArrayMetadata = TypeVar("T_ArrayMetadata", ArrayV2Metadata, ArrayV3Metadata) +T_ArrayMetadata = TypeVar("T_ArrayMetadata", ArrayV2Metadata, ArrayV3Metadata, covariant=True) __all__ = [ "ArrayMetadata", diff --git a/src/zarr/core/sync_group.py b/src/zarr/core/sync_group.py index 2a416f555f..8af514e938 100644 --- a/src/zarr/core/sync_group.py +++ b/src/zarr/core/sync_group.py @@ -13,14 +13,14 @@ from collections.abc import Iterator from zarr.abc.store import Store - from zarr.core.array import Array from zarr.core.common import ZarrFormat from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata + from zarr.types import AnyArray def create_nodes( *, store: Store, nodes: dict[str, GroupMetadata | ArrayV2Metadata | ArrayV3Metadata] -) -> Iterator[tuple[str, Group | Array]]: +) -> Iterator[tuple[str, Group | AnyArray]]: """Create a collection of arrays and / or groups concurrently. Note: no attempt is made to validate that these arrays and / or groups collectively form a @@ -53,7 +53,7 @@ def create_hierarchy( store: Store, nodes: dict[str, GroupMetadata | ArrayV2Metadata | ArrayV3Metadata], overwrite: bool = False, -) -> Iterator[tuple[str, Group | Array]]: +) -> Iterator[tuple[str, Group | AnyArray]]: """ Create a complete zarr hierarchy from a collection of metadata objects. @@ -117,7 +117,7 @@ def create_rooted_hierarchy( store: Store, nodes: dict[str, GroupMetadata | ArrayV2Metadata | ArrayV3Metadata], overwrite: bool = False, -) -> Group | Array: +) -> Group | AnyArray: """ Create a Zarr hierarchy with a root, and return the root node, which could be a ``Group`` or ``Array`` instance. @@ -142,7 +142,7 @@ def create_rooted_hierarchy( return _parse_async_node(async_node) -def get_node(store: Store, path: str, zarr_format: ZarrFormat) -> Array | Group: +def get_node(store: Store, path: str, zarr_format: ZarrFormat) -> AnyArray | Group: """ Get an Array or Group from a path in a Store. diff --git a/src/zarr/metadata/migrate_v3.py b/src/zarr/metadata/migrate_v3.py index 5fc5fe0df5..8f83e01f20 100644 --- a/src/zarr/metadata/migrate_v3.py +++ b/src/zarr/metadata/migrate_v3.py @@ -5,7 +5,7 @@ import numcodecs.abc import zarr -from zarr import Array, Group +from zarr import Group from zarr.abc.codec import ArrayArrayCodec, BytesBytesCodec, Codec from zarr.abc.store import Store from zarr.codecs.blosc import BloscCodec, BloscShuffle @@ -31,6 +31,7 @@ from zarr.core.sync import sync from zarr.registry import get_codec_class from zarr.storage import StorePath +from zarr.types import AnyArray _logger = logging.getLogger(__name__) @@ -68,7 +69,7 @@ def migrate_v2_to_v3( migrate_to_v3(zarr_v2, output_path, dry_run=dry_run) -def migrate_to_v3(zarr_v2: Array | Group, output_path: StorePath, dry_run: bool = False) -> None: +def migrate_to_v3(zarr_v2: AnyArray | Group, output_path: StorePath, dry_run: bool = False) -> None: """Migrate all v2 metadata in a Zarr array/group to v3. Note - if a group is provided, then all arrays / groups within this group will also be converted. @@ -168,7 +169,7 @@ def _convert_group(zarr_v2: Group, output_path: StorePath, dry_run: bool) -> Non sync(_save_v3_metadata(group_metadata_v3, output_path, dry_run=dry_run)) -def _convert_array(zarr_v2: Array, output_path: StorePath, dry_run: bool) -> None: +def _convert_array(zarr_v2: AnyArray, output_path: StorePath, dry_run: bool) -> None: array_metadata_v3 = _convert_array_metadata(cast(ArrayV2Metadata, zarr_v2.metadata)) sync(_save_v3_metadata(array_metadata_v3, output_path, dry_run=dry_run)) diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index d6c863e086..5eb17214fe 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -23,6 +23,7 @@ from zarr.storage import MemoryStore, StoreLike from zarr.storage._common import _dereference_path from zarr.storage._utils import normalize_path +from zarr.types import AnyArray # Copied from Xarray _attr_keys = st.text(st.characters(), min_size=1) @@ -246,7 +247,7 @@ def arrays( arrays: st.SearchStrategy | None = None, attrs: st.SearchStrategy = attrs, zarr_formats: st.SearchStrategy = zarr_formats, -) -> Array: +) -> AnyArray: store = draw(stores, label="store") path = draw(paths, label="array parent") name = draw(array_names, label="array name") diff --git a/src/zarr/types.py b/src/zarr/types.py new file mode 100644 index 0000000000..38990982f9 --- /dev/null +++ b/src/zarr/types.py @@ -0,0 +1,23 @@ +from typing import Any, TypeAlias + +from zarr.core.array import Array, AsyncArray +from zarr.core.metadata.v2 import ArrayV2Metadata +from zarr.core.metadata.v3 import ArrayV3Metadata + +AnyAsyncArray: TypeAlias = AsyncArray[Any] +"""A Zarr format 2 or 3 `AsyncArray`""" + +AsyncArrayV2: TypeAlias = AsyncArray[ArrayV2Metadata] +"""A Zarr format 2 `AsyncArray`""" + +AsyncArrayV3: TypeAlias = AsyncArray[ArrayV3Metadata] +"""A Zarr format 3 `AsyncArray`""" + +AnyArray: TypeAlias = Array[Any] +"""A Zarr format 2 or 3 `Array`""" + +ArrayV2: TypeAlias = Array[ArrayV2Metadata] +"""A Zarr format 2 `Array`""" + +ArrayV3: TypeAlias = Array[ArrayV3Metadata] +"""A Zarr format 3 `Array`""" diff --git a/tests/test_api.py b/tests/test_api.py index 816de784ca..adea150ae1 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -16,6 +16,7 @@ from zarr.abc.store import Store from zarr.core.common import JSON, MemoryOrder, ZarrFormat + from zarr.types import AnyArray import contextlib from typing import Literal @@ -242,7 +243,7 @@ def test_open_array_respects_write_empty_chunks_config(zarr_format: ZarrFormat) def test_open_normalized_path( memory_store: MemoryStore, path: str, node_type: Literal["array", "group"] ) -> None: - node: Group | Array + node: Group | AnyArray if node_type == "group": node = group(store=memory_store, path=path) elif node_type == "array": @@ -1519,7 +1520,7 @@ def test_no_overwrite_load(tmp_path: Path) -> None: zarr.zeros_like, ], ) -def test_auto_chunks(f: Callable[..., Array]) -> None: +def test_auto_chunks(f: Callable[..., AnyArray]) -> None: # Make sure chunks are set automatically across the public API # TODO: test shards with this test too shape = (1000, 1000) diff --git a/tests/test_api/test_asynchronous.py b/tests/test_api/test_asynchronous.py index 8757127985..362195e858 100644 --- a/tests/test_api/test_asynchronous.py +++ b/tests/test_api/test_asynchronous.py @@ -18,8 +18,9 @@ import numpy.typing as npt - from zarr.core.array import Array, AsyncArray + from zarr.core.array import AsyncArray from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata + from zarr.types import AnyArray @dataclass @@ -82,7 +83,10 @@ def test_get_shape_chunks( ], ) def test_like_args( - observed: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | Array | npt.NDArray[Any], + observed: AsyncArray[ArrayV2Metadata] + | AsyncArray[ArrayV3Metadata] + | AnyArray + | npt.NDArray[Any], expected: object, ) -> None: """ diff --git a/tests/test_array.py b/tests/test_array.py index ebffd93b3c..61828be0aa 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -19,7 +19,7 @@ import zarr.api.asynchronous import zarr.api.synchronous as sync_api from tests.conftest import skip_object_dtype -from zarr import Array, AsyncArray, Group +from zarr import Array, Group from zarr.abc.store import Store from zarr.codecs import ( BytesCodec, @@ -29,6 +29,7 @@ ) from zarr.core._info import ArrayInfo from zarr.core.array import ( + AsyncArray, CompressorsLike, FiltersLike, _iter_chunk_coords, @@ -66,7 +67,6 @@ from zarr.core.group import AsyncGroup from zarr.core.indexing import BasicIndexer, _iter_grid, _iter_regions from zarr.core.metadata.v2 import ArrayV2Metadata -from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import sync from zarr.errors import ( ContainsArrayError, @@ -75,12 +75,12 @@ ) from zarr.storage import LocalStore, MemoryStore, StorePath from zarr.storage._logging import LoggingStore +from zarr.types import AnyArray, AnyAsyncArray from .test_dtype.conftest import zdtype_examples if TYPE_CHECKING: from zarr.abc.codec import CodecJSON_V3 - from zarr.core.metadata.v3 import ArrayV3Metadata @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) @@ -363,9 +363,9 @@ def test_storage_transformers(store: MemoryStore, zarr_format: ZarrFormat | str) Array.from_dict(StorePath(store), data=metadata_dict) -@pytest.mark.parametrize("test_cls", [Array, AsyncArray[Any]]) +@pytest.mark.parametrize("test_cls", [AnyArray, AnyAsyncArray]) @pytest.mark.parametrize("nchunks", [2, 5, 10]) -def test_nchunks(test_cls: type[Array] | type[AsyncArray[Any]], nchunks: int) -> None: +def test_nchunks(test_cls: type[AnyArray] | type[AnyAsyncArray], nchunks: int) -> None: """ Test that nchunks returns the number of chunks defined for the array. """ @@ -380,13 +380,13 @@ def test_nchunks(test_cls: type[Array] | type[AsyncArray[Any]], nchunks: int) -> assert observed == expected -@pytest.mark.parametrize("test_cls", [Array, AsyncArray[Any]]) +@pytest.mark.parametrize("test_cls", [Array, AsyncArray]) @pytest.mark.parametrize( ("shape", "shard_shape", "chunk_shape"), [((10,), None, (1,)), ((10,), (1,), (1,)), ((40,), (20,), (5,))], ) async def test_nchunks_initialized( - test_cls: type[Array] | type[AsyncArray[Any]], + test_cls: type[AnyArray] | type[AnyAsyncArray], shape: tuple[int, ...], shard_shape: tuple[int, ...] | None, chunk_shape: tuple[int, ...], @@ -1386,7 +1386,7 @@ async def test_v2_chunk_encoding( ) -> None: if dtype == "str" and filters != "auto": pytest.skip("Only the auto filters are compatible with str dtype in this test.") - arr = await create_array( + arr: AsyncArray[ArrayV2Metadata] = await create_array( store=store, dtype=dtype, shape=(10,), @@ -1483,7 +1483,7 @@ async def test_with_data(impl: Literal["sync", "async"], store: Store) -> None: """ data = np.arange(10) name = "foo" - arr: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata] | Array + arr: AnyAsyncArray | AnyArray if impl == "sync": arr = sync_api.create_array(store, name=name, data=data) stored = arr[:] @@ -1704,7 +1704,7 @@ async def test_from_array_arraylike( store: Store, chunks: Literal["auto", "keep"] | tuple[int, int], write_data: bool, - src: Array | npt.ArrayLike, + src: AnyArray | npt.ArrayLike, ) -> None: fill_value = 42 result = zarr.from_array( @@ -1789,7 +1789,7 @@ def test_roundtrip_numcodecs() -> None: assert metadata["codecs"] == expected -def _index_array(arr: Array, index: Any) -> Any: +def _index_array(arr: AnyArray, index: Any) -> Any: return arr[index] @@ -2166,7 +2166,7 @@ def test_create_array_with_data_num_gets( chunk_shape = (1,) shard_shape = (100,) shape = (shard_shape[0] * num_shards,) - data: Array | npt.NDArray[np.int64] + data: AnyArray | npt.NDArray[np.int64] if array_type == "numpy": data = np.zeros(shape[0], dtype="int64") else: diff --git a/tests/test_attributes.py b/tests/test_attributes.py index 4ce40e2cb0..269704d2a0 100644 --- a/tests/test_attributes.py +++ b/tests/test_attributes.py @@ -1,5 +1,5 @@ import json -from typing import Any +from typing import TYPE_CHECKING, Any import numpy as np import pytest @@ -10,6 +10,9 @@ from tests.conftest import deep_nan_equal from zarr.core.common import ZarrFormat +if TYPE_CHECKING: + from zarr.types import AnyArray + @pytest.mark.parametrize("zarr_format", [2, 3]) @pytest.mark.parametrize( @@ -74,7 +77,7 @@ def test_update_no_changes() -> None: @pytest.mark.parametrize("group", [True, False]) def test_del_works(group: bool) -> None: store = zarr.storage.MemoryStore() - z: zarr.Group | zarr.Array + z: zarr.Group | AnyArray if group: z = zarr.create_group(store) else: @@ -84,7 +87,7 @@ def test_del_works(group: bool) -> None: del z.attrs["a"] assert dict(z.attrs) == {"c": 4} - z2: zarr.Group | zarr.Array + z2: zarr.Group | AnyArray if group: z2 = zarr.open_group(store) else: diff --git a/tests/test_cli/test_migrate_v3.py b/tests/test_cli/test_migrate_v3.py index b96c98019b..8bda31d208 100644 --- a/tests/test_cli/test_migrate_v3.py +++ b/tests/test_cli/test_migrate_v3.py @@ -16,7 +16,6 @@ from zarr.codecs.numcodecs import LZMA, Delta from zarr.codecs.transpose import TransposeCodec from zarr.codecs.zstd import ZstdCodec -from zarr.core.array import Array from zarr.core.chunk_grids import RegularChunkGrid from zarr.core.chunk_key_encodings import V2ChunkKeyEncoding from zarr.core.common import JSON, ZarrFormat @@ -24,6 +23,7 @@ from zarr.core.group import Group, GroupMetadata from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.storage._local import LocalStore +from zarr.types import AnyArray typer_testing = pytest.importorskip( "typer.testing", reason="optional cli dependencies aren't installed" @@ -112,7 +112,7 @@ def test_migrate_nested_groups_and_arrays_in_place( # Check converted zarr can be opened + metadata accessed at all levels zarr_array = zarr.open(local_store.root, zarr_format=3) for path in paths: - zarr_v3 = cast(Array | Group, zarr_array[path]) + zarr_v3 = cast(AnyArray | Group, zarr_array[path]) metadata = zarr_v3.metadata assert metadata.zarr_format == 3 assert metadata.attributes == attributes diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index 1884d501a5..eae7168d49 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -29,11 +29,12 @@ from zarr.abc.store import Store from zarr.core.buffer.core import NDArrayLikeOrScalar from zarr.core.common import MemoryOrder + from zarr.types import AnyAsyncArray @dataclass(frozen=True) class _AsyncArrayProxy: - array: AsyncArray[Any] + array: AnyAsyncArray def __getitem__(self, selection: BasicSelection) -> _AsyncArraySelectionProxy: return _AsyncArraySelectionProxy(self.array, selection) @@ -41,7 +42,7 @@ def __getitem__(self, selection: BasicSelection) -> _AsyncArraySelectionProxy: @dataclass(frozen=True) class _AsyncArraySelectionProxy: - array: AsyncArray[Any] + array: AnyAsyncArray selection: BasicSelection async def get(self) -> NDArrayLikeOrScalar: diff --git a/tests/test_regression/test_v2_dtype_regression.py b/tests/test_regression/test_v2_dtype_regression.py index ffe273490d..4f3329e88c 100644 --- a/tests/test_regression/test_v2_dtype_regression.py +++ b/tests/test_regression/test_v2_dtype_regression.py @@ -13,11 +13,11 @@ import zarr.abc.codec import zarr.codecs as zarrcodecs from zarr.abc.numcodec import Numcodec -from zarr.core.array import Array from zarr.core.chunk_key_encodings import V2ChunkKeyEncoding from zarr.core.dtype.npy.bytes import VariableLengthBytes from zarr.core.dtype.npy.string import VariableLengthUTF8 from zarr.storage import LocalStore +from zarr.types import ArrayV2, ArrayV3 if TYPE_CHECKING: from zarr.core.dtype import ZDTypeLike @@ -106,7 +106,7 @@ class ArrayParams: @pytest.fixture -def source_array_v2(tmp_path: Path, request: pytest.FixtureRequest) -> Array: +def source_array_v2(tmp_path: Path, request: pytest.FixtureRequest) -> ArrayV2: """ Writes a zarr array to a temporary directory based on the provided ArrayParams. The array is returned. @@ -144,7 +144,7 @@ def source_array_v2(tmp_path: Path, request: pytest.FixtureRequest) -> Array: @pytest.fixture -def source_array_v3(tmp_path: Path, request: pytest.FixtureRequest) -> Array: +def source_array_v3(tmp_path: Path, request: pytest.FixtureRequest) -> ArrayV3: """ Writes a zarr array to a temporary directory based on the provided ArrayParams. The array is returned. @@ -198,7 +198,7 @@ def source_array_v3(tmp_path: Path, request: pytest.FixtureRequest) -> Array: "source_array_v2", array_cases_v2_18, indirect=True, ids=tuple(map(str, array_cases_v2_18)) ) @pytest.mark.parametrize("script_path", script_paths) -def test_roundtrip_v2(source_array_v2: Array, tmp_path: Path, script_path: Path) -> None: +def test_roundtrip_v2(source_array_v2: ArrayV2, tmp_path: Path, script_path: Path) -> None: out_path = tmp_path / "out" copy_op = subprocess.run( [ @@ -222,7 +222,7 @@ def test_roundtrip_v2(source_array_v2: Array, tmp_path: Path, script_path: Path) @pytest.mark.parametrize( "source_array_v3", array_cases_v3_08, indirect=True, ids=tuple(map(str, array_cases_v3_08)) ) -def test_roundtrip_v3(source_array_v3: Array, tmp_path: Path) -> None: +def test_roundtrip_v3(source_array_v3: ArrayV3, tmp_path: Path) -> None: script_path = Path(__file__).resolve().parent / "scripts" / "v3.0.8.py" out_path = tmp_path / "out" copy_op = subprocess.run( From 8eb244f3957f59210d2fb73a26cf9aeac12a7fa8 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 20 Nov 2025 15:07:57 -0500 Subject: [PATCH 158/468] Reduce number of documentation redirects needed (#3584) * Reduce number of documentation redirects needed * Revert other structural changes from 3.1.3 * Fixup --- docs/api/buffer.md | 3 - docs/api/testing.md | 33 ------ docs/api/{ => zarr}/abc/buffer.md | 0 docs/api/{ => zarr}/abc/codec.md | 1 - docs/api/zarr/abc/index.md | 7 ++ docs/api/{ => zarr}/abc/metadata.md | 0 docs/api/zarr/abc/numcodec.md | 5 + docs/api/{ => zarr}/abc/store.md | 0 .../api/asynchronous.md} | 0 docs/api/zarr/api/index.md | 5 + .../{api_sync.md => zarr/api/synchronous.md} | 0 docs/api/{ => zarr}/array.md | 0 docs/api/zarr/buffer/cpu.md | 1 + docs/api/zarr/buffer/gpu.md | 1 + docs/api/zarr/buffer/index.md | 3 + docs/api/{ => zarr}/codecs.md | 2 - docs/api/zarr/codecs/numcodecs.md | 5 + docs/api/{ => zarr}/config.md | 0 docs/api/{ => zarr}/convenience.md | 0 docs/api/{ => zarr}/create.md | 0 docs/api/{ => zarr}/deprecated/convenience.md | 0 docs/api/{ => zarr}/deprecated/creation.md | 0 docs/api/{ => zarr}/dtype.md | 0 docs/api/{ => zarr}/errors.md | 0 docs/api/{ => zarr}/group.md | 0 docs/api/{ => zarr}/index.md | 8 +- docs/api/{ => zarr}/load.md | 0 docs/api/{ => zarr}/metadata.md | 0 docs/api/{ => zarr}/open.md | 0 docs/api/{ => zarr}/registry.md | 0 docs/api/{ => zarr}/save.md | 0 docs/api/{ => zarr}/storage.md | 0 docs/api/zarr/testing/buffer.md | 3 + docs/api/zarr/testing/conftest.md | 3 + docs/api/zarr/testing/index.md | 12 +++ docs/api/zarr/testing/stateful.md | 3 + docs/api/zarr/testing/store.md | 4 + docs/api/zarr/testing/strategies.md | 4 + docs/api/zarr/testing/utils.md | 3 + docs/index.md | 2 +- docs/user-guide/arrays.md | 2 +- docs/user-guide/groups.md | 4 +- docs/user-guide/index.md | 2 +- mkdocs.yml | 102 ++++++++---------- 44 files changed, 113 insertions(+), 105 deletions(-) delete mode 100644 docs/api/buffer.md delete mode 100644 docs/api/testing.md rename docs/api/{ => zarr}/abc/buffer.md (100%) rename docs/api/{ => zarr}/abc/codec.md (65%) create mode 100644 docs/api/zarr/abc/index.md rename docs/api/{ => zarr}/abc/metadata.md (100%) create mode 100644 docs/api/zarr/abc/numcodec.md rename docs/api/{ => zarr}/abc/store.md (100%) rename docs/api/{api_async.md => zarr/api/asynchronous.md} (100%) create mode 100644 docs/api/zarr/api/index.md rename docs/api/{api_sync.md => zarr/api/synchronous.md} (100%) rename docs/api/{ => zarr}/array.md (100%) create mode 100644 docs/api/zarr/buffer/cpu.md create mode 100644 docs/api/zarr/buffer/gpu.md create mode 100644 docs/api/zarr/buffer/index.md rename docs/api/{ => zarr}/codecs.md (59%) create mode 100644 docs/api/zarr/codecs/numcodecs.md rename docs/api/{ => zarr}/config.md (100%) rename docs/api/{ => zarr}/convenience.md (100%) rename docs/api/{ => zarr}/create.md (100%) rename docs/api/{ => zarr}/deprecated/convenience.md (100%) rename docs/api/{ => zarr}/deprecated/creation.md (100%) rename docs/api/{ => zarr}/dtype.md (100%) rename docs/api/{ => zarr}/errors.md (100%) rename docs/api/{ => zarr}/group.md (100%) rename docs/api/{ => zarr}/index.md (86%) rename docs/api/{ => zarr}/load.md (100%) rename docs/api/{ => zarr}/metadata.md (100%) rename docs/api/{ => zarr}/open.md (100%) rename docs/api/{ => zarr}/registry.md (100%) rename docs/api/{ => zarr}/save.md (100%) rename docs/api/{ => zarr}/storage.md (100%) create mode 100644 docs/api/zarr/testing/buffer.md create mode 100644 docs/api/zarr/testing/conftest.md create mode 100644 docs/api/zarr/testing/index.md create mode 100644 docs/api/zarr/testing/stateful.md create mode 100644 docs/api/zarr/testing/store.md create mode 100644 docs/api/zarr/testing/strategies.md create mode 100644 docs/api/zarr/testing/utils.md diff --git a/docs/api/buffer.md b/docs/api/buffer.md deleted file mode 100644 index aa089957cf..0000000000 --- a/docs/api/buffer.md +++ /dev/null @@ -1,3 +0,0 @@ -::: zarr.buffer -::: zarr.buffer.cpu -::: zarr.buffer.gpu diff --git a/docs/api/testing.md b/docs/api/testing.md deleted file mode 100644 index eef48614b5..0000000000 --- a/docs/api/testing.md +++ /dev/null @@ -1,33 +0,0 @@ ---- -title: testing ---- - -::: zarr.testing - options: - show_root_heading: true - show_root_toc_entry: true - members: false - -## Buffer - -::: zarr.testing.buffer - -## Stateful - -::: zarr.testing.stateful - -## Store - -::: zarr.testing.store - -## Strategies - -::: zarr.testing.strategies - -## Utils - -::: zarr.testing.utils - -## Conftest - -::: zarr.testing.conftest diff --git a/docs/api/abc/buffer.md b/docs/api/zarr/abc/buffer.md similarity index 100% rename from docs/api/abc/buffer.md rename to docs/api/zarr/abc/buffer.md diff --git a/docs/api/abc/codec.md b/docs/api/zarr/abc/codec.md similarity index 65% rename from docs/api/abc/codec.md rename to docs/api/zarr/abc/codec.md index 7d808fbb54..d4eaecabe9 100644 --- a/docs/api/abc/codec.md +++ b/docs/api/zarr/abc/codec.md @@ -3,4 +3,3 @@ title: codec --- ::: zarr.abc.codec -::: zarr.abc.numcodec diff --git a/docs/api/zarr/abc/index.md b/docs/api/zarr/abc/index.md new file mode 100644 index 0000000000..7c2fb2ef13 --- /dev/null +++ b/docs/api/zarr/abc/index.md @@ -0,0 +1,7 @@ +## Abstract base classes + +- **[buffer](./buffer.md)** - Providing access to underlying memory via [buffers](https://docs.python.org/3/c-api/buffer.html) +- **[codec](./codec.md)** - Expressing [zarr codecs](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-encoding) +- **[metadata](./metadata.md)** - Creating metadata classes compatible with the Zarr API +- **[numcodec](./numcodec.md)** - Protocols and classes for modeling codec interface used by numcodecs +- **[store](./store.md)** - ABC for implementing Zarr stores and managing getting and setting bytes in a store \ No newline at end of file diff --git a/docs/api/abc/metadata.md b/docs/api/zarr/abc/metadata.md similarity index 100% rename from docs/api/abc/metadata.md rename to docs/api/zarr/abc/metadata.md diff --git a/docs/api/zarr/abc/numcodec.md b/docs/api/zarr/abc/numcodec.md new file mode 100644 index 0000000000..ffbca600cc --- /dev/null +++ b/docs/api/zarr/abc/numcodec.md @@ -0,0 +1,5 @@ +--- +title: numcodec +--- + +::: zarr.abc.numcodec diff --git a/docs/api/abc/store.md b/docs/api/zarr/abc/store.md similarity index 100% rename from docs/api/abc/store.md rename to docs/api/zarr/abc/store.md diff --git a/docs/api/api_async.md b/docs/api/zarr/api/asynchronous.md similarity index 100% rename from docs/api/api_async.md rename to docs/api/zarr/api/asynchronous.md diff --git a/docs/api/zarr/api/index.md b/docs/api/zarr/api/index.md new file mode 100644 index 0000000000..75b4fff62b --- /dev/null +++ b/docs/api/zarr/api/index.md @@ -0,0 +1,5 @@ +--- +title: API +--- + +Zarr provides both an [async](./asynchronous.md) and a [sync](./synchronous.md) API. See those pages for more details. diff --git a/docs/api/api_sync.md b/docs/api/zarr/api/synchronous.md similarity index 100% rename from docs/api/api_sync.md rename to docs/api/zarr/api/synchronous.md diff --git a/docs/api/array.md b/docs/api/zarr/array.md similarity index 100% rename from docs/api/array.md rename to docs/api/zarr/array.md diff --git a/docs/api/zarr/buffer/cpu.md b/docs/api/zarr/buffer/cpu.md new file mode 100644 index 0000000000..9d4726d3ea --- /dev/null +++ b/docs/api/zarr/buffer/cpu.md @@ -0,0 +1 @@ +::: zarr.buffer.cpu diff --git a/docs/api/zarr/buffer/gpu.md b/docs/api/zarr/buffer/gpu.md new file mode 100644 index 0000000000..e2276d8d82 --- /dev/null +++ b/docs/api/zarr/buffer/gpu.md @@ -0,0 +1 @@ +::: zarr.buffer.gpu diff --git a/docs/api/zarr/buffer/index.md b/docs/api/zarr/buffer/index.md new file mode 100644 index 0000000000..0b303781e1 --- /dev/null +++ b/docs/api/zarr/buffer/index.md @@ -0,0 +1,3 @@ +Zarr provides buffer classes for both the [cpu](./cpu.md) and [gpu](./gpu.md). Generic buffer functionality is also detailed below. + +::: zarr.buffer diff --git a/docs/api/codecs.md b/docs/api/zarr/codecs.md similarity index 59% rename from docs/api/codecs.md rename to docs/api/zarr/codecs.md index 151efeac32..c5a0f046ed 100644 --- a/docs/api/codecs.md +++ b/docs/api/zarr/codecs.md @@ -3,5 +3,3 @@ title: codecs --- ::: zarr.codecs - -::: zarr.codecs.numcodecs diff --git a/docs/api/zarr/codecs/numcodecs.md b/docs/api/zarr/codecs/numcodecs.md new file mode 100644 index 0000000000..ce2a7de145 --- /dev/null +++ b/docs/api/zarr/codecs/numcodecs.md @@ -0,0 +1,5 @@ +--- +title: numcodecs +--- + +::: zarr.codecs.numcodecs diff --git a/docs/api/config.md b/docs/api/zarr/config.md similarity index 100% rename from docs/api/config.md rename to docs/api/zarr/config.md diff --git a/docs/api/convenience.md b/docs/api/zarr/convenience.md similarity index 100% rename from docs/api/convenience.md rename to docs/api/zarr/convenience.md diff --git a/docs/api/create.md b/docs/api/zarr/create.md similarity index 100% rename from docs/api/create.md rename to docs/api/zarr/create.md diff --git a/docs/api/deprecated/convenience.md b/docs/api/zarr/deprecated/convenience.md similarity index 100% rename from docs/api/deprecated/convenience.md rename to docs/api/zarr/deprecated/convenience.md diff --git a/docs/api/deprecated/creation.md b/docs/api/zarr/deprecated/creation.md similarity index 100% rename from docs/api/deprecated/creation.md rename to docs/api/zarr/deprecated/creation.md diff --git a/docs/api/dtype.md b/docs/api/zarr/dtype.md similarity index 100% rename from docs/api/dtype.md rename to docs/api/zarr/dtype.md diff --git a/docs/api/errors.md b/docs/api/zarr/errors.md similarity index 100% rename from docs/api/errors.md rename to docs/api/zarr/errors.md diff --git a/docs/api/group.md b/docs/api/zarr/group.md similarity index 100% rename from docs/api/group.md rename to docs/api/zarr/group.md diff --git a/docs/api/index.md b/docs/api/zarr/index.md similarity index 86% rename from docs/api/index.md rename to docs/api/zarr/index.md index 6160230ac0..f6ae2bda83 100644 --- a/docs/api/index.md +++ b/docs/api/zarr/index.md @@ -38,8 +38,8 @@ Complete reference documentation for the Zarr-Python API. Zarr-Python provides both synchronous and asynchronous APIs: -- **[Async API](api_async.md)** - Asynchronous operations for concurrent access -- **[Sync API](api_sync.md)** - Synchronous operations for simple usage +- **[Async API](./api/asynchronous.md)** - Asynchronous operations for concurrent access +- **[Sync API](./api/synchronous.md)** - Synchronous operations for simple usage ## Abstract Base Classes @@ -52,7 +52,7 @@ The ABC module defines interfaces for extending Zarr: ## Utilities - **[Errors](errors.md)** - Exception classes and error handling -- **[Testing](testing.md)** - Utilities for testing Zarr-based code +- **[Testing](testing/index.md)** - Utilities for testing Zarr-based code ## Migration and Compatibility @@ -64,7 +64,7 @@ These deprecated modules are maintained for backward compatibility but should be ## Getting Help -- Check the [User Guide](../user-guide/index.md) for tutorials and examples +- Check the [User Guide](../../user-guide/index.md) for tutorials and examples - Browse function signatures and docstrings in the API reference - Report issues on [GitHub](https://github.com/zarr-developers/zarr-python) - Join discussions on the [Zarr community forum](https://github.com/zarr-developers/community) diff --git a/docs/api/load.md b/docs/api/zarr/load.md similarity index 100% rename from docs/api/load.md rename to docs/api/zarr/load.md diff --git a/docs/api/metadata.md b/docs/api/zarr/metadata.md similarity index 100% rename from docs/api/metadata.md rename to docs/api/zarr/metadata.md diff --git a/docs/api/open.md b/docs/api/zarr/open.md similarity index 100% rename from docs/api/open.md rename to docs/api/zarr/open.md diff --git a/docs/api/registry.md b/docs/api/zarr/registry.md similarity index 100% rename from docs/api/registry.md rename to docs/api/zarr/registry.md diff --git a/docs/api/save.md b/docs/api/zarr/save.md similarity index 100% rename from docs/api/save.md rename to docs/api/zarr/save.md diff --git a/docs/api/storage.md b/docs/api/zarr/storage.md similarity index 100% rename from docs/api/storage.md rename to docs/api/zarr/storage.md diff --git a/docs/api/zarr/testing/buffer.md b/docs/api/zarr/testing/buffer.md new file mode 100644 index 0000000000..e0ae5e5dfd --- /dev/null +++ b/docs/api/zarr/testing/buffer.md @@ -0,0 +1,3 @@ +## Buffer + +::: zarr.testing.buffer diff --git a/docs/api/zarr/testing/conftest.md b/docs/api/zarr/testing/conftest.md new file mode 100644 index 0000000000..67cecfd9b8 --- /dev/null +++ b/docs/api/zarr/testing/conftest.md @@ -0,0 +1,3 @@ +## Conftest + +::: zarr.testing.conftest diff --git a/docs/api/zarr/testing/index.md b/docs/api/zarr/testing/index.md new file mode 100644 index 0000000000..4ef56ec69c --- /dev/null +++ b/docs/api/zarr/testing/index.md @@ -0,0 +1,12 @@ +--- +title: testing +--- + +See the following sub-modules: + +- [buffer](./buffer.md) +- [conftest](./conftest.md) +- [stateful](./stateful.md) +- [store](./store.md) +- [strategies](./strategies.md) +- [utils](./utils.md) diff --git a/docs/api/zarr/testing/stateful.md b/docs/api/zarr/testing/stateful.md new file mode 100644 index 0000000000..53c51b11ec --- /dev/null +++ b/docs/api/zarr/testing/stateful.md @@ -0,0 +1,3 @@ +## Stateful + +::: zarr.testing.stateful diff --git a/docs/api/zarr/testing/store.md b/docs/api/zarr/testing/store.md new file mode 100644 index 0000000000..f190c65f95 --- /dev/null +++ b/docs/api/zarr/testing/store.md @@ -0,0 +1,4 @@ + +## Store + +::: zarr.testing.store diff --git a/docs/api/zarr/testing/strategies.md b/docs/api/zarr/testing/strategies.md new file mode 100644 index 0000000000..dd6d546165 --- /dev/null +++ b/docs/api/zarr/testing/strategies.md @@ -0,0 +1,4 @@ + +## Strategies + +::: zarr.testing.strategies diff --git a/docs/api/zarr/testing/utils.md b/docs/api/zarr/testing/utils.md new file mode 100644 index 0000000000..61202ac4b2 --- /dev/null +++ b/docs/api/zarr/testing/utils.md @@ -0,0 +1,3 @@ +## Utils + +::: zarr.testing.utils diff --git a/docs/index.md b/docs/index.md index 8508d8e0cf..b61646d6a6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -52,7 +52,7 @@ conda install --channel conda-forge zarr A detailed guide for how to use Zarr-Python. -- [:material-api:{ .lg .middle } __API Reference__](api/open.md) +- [:material-api:{ .lg .middle } __API Reference__](api/zarr/open.md) --- diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 25a1347fe3..e03b9c9355 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -27,7 +27,7 @@ columns (and so there will be 100 chunks in total). The data is written to a and see [Data types](data_types.md) for an in-depth look at the data types supported by Zarr. -See the [creation API documentation](../api/create.md) for more detailed information about +See the [creation API documentation](../api/zarr/create.md) for more detailed information about creating arrays. ## Reading and writing data diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index 8a3f9ff7bf..57201216b6 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -65,12 +65,12 @@ z = root.create_array(name='foo/bar/baz', shape=(10000, 10000), chunks=(1000, 10 print(z) ``` -For more information on groups see the [`zarr.Group` API docs](../api/group.md). +For more information on groups see the [`zarr.Group` API docs](../api/zarr/group.md). ## Batch Group Creation You can also create multiple groups concurrently with a single function call. [`zarr.create_hierarchy`][] takes -a [`zarr Storage instance`](../api/storage.md) instance and a dict of `key : metadata` pairs, parses that dict, and +a [`zarr Storage instance`](../api/zarr/storage.md) instance and a dict of `key : metadata` pairs, parses that dict, and writes metadata documents to storage: ```python exec="true" session="groups" source="above" result="ansi" diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md index 14808457bd..fda9bcaa90 100644 --- a/docs/user-guide/index.md +++ b/docs/user-guide/index.md @@ -37,5 +37,5 @@ Take your skills to the next level: ## Need Help? -- Browse the [API Reference](../api/index.md) for detailed function documentation +- Browse the [API Reference](../api/zarr/index.md) for detailed function documentation - Report issues on [GitHub](https://github.com/zarr-developers/zarr-python/issues?q=sort%3Aupdated-desc+is%3Aissue+is%3Aopen) diff --git a/mkdocs.yml b/mkdocs.yml index 647f211240..9bc4957f5d 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -30,33 +30,48 @@ nav: - Examples: - user-guide/examples/custom_dtype.md - API Reference: - - api/index.md - - api/array.md - - api/group.md - - api/create.md - - api/dtype.md - - api/open.md - - api/load.md - - api/save.md - - api/buffer.md - - api/convenience.md - - api/config.md - - api/codecs.md - - api/errors.md - - api/metadata.md - - api/registry.md - - api/storage.md - - api/testing.md - - Async API: api/api_async.md - - Sync API: api/api_sync.md + - api/zarr/index.md + - api/zarr/array.md + - api/zarr/group.md + - api/zarr/create.md + - api/zarr/dtype.md + - api/zarr/load.md + - api/zarr/open.md + - api/zarr/save.md + - api/zarr/codecs.md + - api/zarr/codecs/numcodecs.md + - api/zarr/config.md + - api/zarr/convenience.md + - api/zarr/errors.md + - api/zarr/metadata.md + - api/zarr/registry.md + - api/zarr/storage.md - ABC: - - api/abc/buffer.md - - api/abc/codec.md - - api/abc/metadata.md - - api/abc/store.md + - api/zarr/abc/index.md + - api/zarr/abc/buffer.md + - api/zarr/abc/codec.md + - api/zarr/abc/numcodec.md + - api/zarr/abc/metadata.md + - api/zarr/abc/store.md + - API: + - api/zarr/api/index.md + - api/zarr/api/asynchronous.md + - api/zarr/api/synchronous.md + - Buffer: + - api/zarr/buffer/index.md + - api/zarr/buffer/cpu.md + - api/zarr/buffer/gpu.md + - Testing: + - api/zarr/testing/index.md + - api/zarr/testing/buffer.md + - api/zarr/testing/conftest.md + - api/zarr/testing/stateful.md + - api/zarr/testing/store.md + - api/zarr/testing/strategies.md + - api/zarr/testing/utils.md - deprecated: - - Convenience sub-module: api/deprecated/convenience.md - - Creation sub-module: api/deprecated/creation.md + - Convenience sub-module: api/zarr/deprecated/convenience.md + - Creation sub-module: api/zarr/deprecated/creation.md - release-notes.md - contributing.md watch: @@ -197,39 +212,12 @@ plugins: 'developers/contributing.html.md': 'contributing.md' 'developers/index.html.md': 'contributing.md' 'developers/roadmap.html.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' - 'api/zarr/index.html.md': 'api/index.md' - 'api/zarr/abc/index.html.md': 'api/abc/buffer.md' - 'api/zarr/abc/buffer/index.html.md': 'api/abc/buffer.md' - 'api/zarr/abc/codec/index.html.md': 'api/abc/codec.md' - 'api/zarr/abc/metadata/index.html.md': 'api/abc/metadata.md' - 'api/zarr/abc/numcodec/index.html.md': 'api/abc/codec.md' - 'api/zarr/abc/store/index.html.md': 'api/abc/store.md' - 'api/zarr/api/index.html.md': 'api/index.md' - 'api/zarr/api/asynchronous/index.html.md': 'api/api_async.md' - 'api/zarr/api/synchronous/index.html.md': 'api/api_sync.md' - 'api/zarr/buffer/index.html.md': 'api/buffer.md' - 'api/zarr/buffer/cpu/index.html.md': 'api/buffer.md' - 'api/zarr/buffer/gpu/index.html.md': 'api/buffer.md' - 'api/zarr/codecs/index.html.md': 'api/codecs.md' - 'api/zarr/codecs/numcodecs/index.html.md': 'api/codecs.md' - 'api/zarr/convenience/index.html.md': 'api/convenience.md' - 'api/zarr/creation/index.html.md': 'api/deprecated/creation.md' - 'api/zarr/dtype/index.html.md': 'api/dtype.md' - 'api/zarr/errors/index.html.md': 'api/errors.md' - 'api/zarr/metadata/index.html.md': 'api/metadata.md' - 'api/zarr/metadata/migrate_v3/index.html.md': 'api/metadata.md' - 'api/zarr/registry/index.html.md': 'api/registry.md' - 'api/zarr/storage/index.html.md': 'api/storage.md' - 'api/zarr/testing/index.html.md': 'api/testing.md' - 'api/zarr/testing/buffer/index.html.md': 'api/testing.md' - 'api/zarr/testing/conftest/index.html.md': 'api/testing.md' - 'api/zarr/testing/stateful/index.html.md': 'api/testing.md' - 'api/zarr/testing/store/index.html.md': 'api/testing.md' - 'api/zarr/testing/strategies/index.html.md': 'api/testing.md' - 'api/zarr/testing/utils/index.html.md': 'api/testing.md' + 'api/zarr/creation.md': 'api/zarr/deprecated/creation.md' + 'api/zarr/codecs/numcodecs.md': 'api/zarr/deprecated/creation.md' + 'api.md': 'api/zarr/index.md' + 'api/zarr/metadata/migrate_v3.md': 'api/zarr/metadata.md' - -# https://github.com/developmentseed/titiler/blob/50934c929cca2fa8d3c408d239015f8da429c6a8/docs/mkdocs.yml#L115-L140 +# Based on https://github.com/developmentseed/titiler/blob/50934c929cca2fa8d3c408d239015f8da429c6a8/docs/mkdocs.yml#L115-L140 markdown_extensions: - admonition - attr_list From 8a670219c24f4e0025b31f4070538dc57ac08b6e Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 20 Nov 2025 23:11:22 +0100 Subject: [PATCH 159/468] update imports in docs (#3591) * update imports in docs * fix tests --- docs/user-guide/arrays.md | 4 ++-- tests/test_regression/scripts/v3.0.8.py | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index e03b9c9355..1675c853fa 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -213,7 +213,7 @@ built-in delta filter: ```python exec="true" session="arrays" source="above" result="ansi" import lzma -from numcodecs.zarr3 import LZMA +from zarr.codecs.numcodecs import LZMA lzma_filters = [dict(id=lzma.FILTER_DELTA, dist=4), dict(id=lzma.FILTER_LZMA2, preset=1)] compressors = LZMA(filters=lzma_filters) @@ -251,7 +251,7 @@ mechanism for configuring filters outside of the primary compressor. Here is an example using a delta filter with the Blosc compressor: ```python exec="true" session="arrays" source="above" result="ansi" -from numcodecs.zarr3 import Delta +from zarr.codecs.numcodecs import Delta filters = [Delta(dtype='int32')] compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=1, shuffle=zarr.codecs.BloscShuffle.shuffle) diff --git a/tests/test_regression/scripts/v3.0.8.py b/tests/test_regression/scripts/v3.0.8.py index f93f43fd57..5a055665e8 100644 --- a/tests/test_regression/scripts/v3.0.8.py +++ b/tests/test_regression/scripts/v3.0.8.py @@ -1,7 +1,8 @@ # /// script # requires-python = "==3.12" # dependencies = [ -# "zarr==3.0.8" +# "zarr==3.0.8", +# "numcodecs==0.16.3" # ] # /// From 2530ce0262b7b41ec965e507a4ec7947dec9717f Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 21 Nov 2025 00:49:15 +0100 Subject: [PATCH 160/468] 3.1.4 release notes (#3540) * compile release notes * add latest release notes * prose * typo * build release notes --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3118.doc.md | 1 - changes/3303.doc.md | 1 - changes/3304.feature.md | 2 -- changes/3366.feature.md | 1 - changes/3483.bugfix.md | 1 - changes/3490.feature.md | 1 - changes/3502.doc.md | 1 - changes/3515.misc.md | 1 - changes/3530.bugfix.md | 2 -- changes/3532.misc.md | 2 -- changes/3533.misc.md | 1 - changes/3535.bugfix.md | 2 -- changes/3536.doc.md | 1 - changes/3547.feature.md | 1 - changes/3553.misc.md | 1 - changes/3556.feature.md | 1 - changes/3560.bugfix.md | 1 - docs/release-notes.md | 32 ++++++++++++++++++++++++++++++++ 18 files changed, 32 insertions(+), 21 deletions(-) delete mode 100644 changes/3118.doc.md delete mode 100644 changes/3303.doc.md delete mode 100644 changes/3304.feature.md delete mode 100644 changes/3366.feature.md delete mode 100644 changes/3483.bugfix.md delete mode 100644 changes/3490.feature.md delete mode 100644 changes/3502.doc.md delete mode 100644 changes/3515.misc.md delete mode 100644 changes/3530.bugfix.md delete mode 100644 changes/3532.misc.md delete mode 100644 changes/3533.misc.md delete mode 100644 changes/3535.bugfix.md delete mode 100644 changes/3536.doc.md delete mode 100644 changes/3547.feature.md delete mode 100644 changes/3553.misc.md delete mode 100644 changes/3556.feature.md delete mode 100644 changes/3560.bugfix.md diff --git a/changes/3118.doc.md b/changes/3118.doc.md deleted file mode 100644 index 58adb1db76..0000000000 --- a/changes/3118.doc.md +++ /dev/null @@ -1 +0,0 @@ -Use mkdocs-material for Zarr-Python documentation \ No newline at end of file diff --git a/changes/3303.doc.md b/changes/3303.doc.md deleted file mode 100644 index ebae05f7e4..0000000000 --- a/changes/3303.doc.md +++ /dev/null @@ -1 +0,0 @@ -Document different values of StoreLike with examples in the user guide. \ No newline at end of file diff --git a/changes/3304.feature.md b/changes/3304.feature.md deleted file mode 100644 index 45dbd85731..0000000000 --- a/changes/3304.feature.md +++ /dev/null @@ -1,2 +0,0 @@ -The `Array` class can now also be parametrized in the same manner as the `AsyncArray` class, allowing Zarr format v2 and v3 `Array`s to be distinguished. -New types have been added to `zarr.types` to help with this. diff --git a/changes/3366.feature.md b/changes/3366.feature.md deleted file mode 100644 index 550c9f4436..0000000000 --- a/changes/3366.feature.md +++ /dev/null @@ -1 +0,0 @@ -Adds `zarr.experimental.cache_store.CacheStore`, a `Store` that implements caching by combining two other `Store` instances. See the [docs page](https://zarr.readthedocs.io/en/latest/user-guide/experimental#cachestore) for more information about this feature. \ No newline at end of file diff --git a/changes/3483.bugfix.md b/changes/3483.bugfix.md deleted file mode 100644 index b6672d348a..0000000000 --- a/changes/3483.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix a bug that prevented `PCodec` from being properly resolved when loading arrays using that compressor. \ No newline at end of file diff --git a/changes/3490.feature.md b/changes/3490.feature.md deleted file mode 100644 index 899cdcf75d..0000000000 --- a/changes/3490.feature.md +++ /dev/null @@ -1 +0,0 @@ -Adds a `zarr.experimental` module for unstable user-facing features. \ No newline at end of file diff --git a/changes/3502.doc.md b/changes/3502.doc.md deleted file mode 100644 index 031c046bf4..0000000000 --- a/changes/3502.doc.md +++ /dev/null @@ -1 +0,0 @@ -Reorganize the top-level `examples` directory to give each example its own sub-directory. Adds content to the docs for each example. \ No newline at end of file diff --git a/changes/3515.misc.md b/changes/3515.misc.md deleted file mode 100644 index 06a94c98a0..0000000000 --- a/changes/3515.misc.md +++ /dev/null @@ -1 +0,0 @@ -Replace `crc32c` dependency with `google-crc32c` to resolve licensing concerns. The `crc32c` library uses LGPL license, while `google-crc32c` uses the more permissive Apache 2.0 license. This change maintains full backward compatibility with existing CRC32C-encoded data. diff --git a/changes/3530.bugfix.md b/changes/3530.bugfix.md deleted file mode 100644 index 36a1787a3a..0000000000 --- a/changes/3530.bugfix.md +++ /dev/null @@ -1,2 +0,0 @@ -Fixed a bug that prevented Zarr Python from opening Zarr V3 array metadata documents that contained - extra keys with permissible values (dicts with a `"must_understand"` key set to `"false"`). \ No newline at end of file diff --git a/changes/3532.misc.md b/changes/3532.misc.md deleted file mode 100644 index 0249aa899c..0000000000 --- a/changes/3532.misc.md +++ /dev/null @@ -1,2 +0,0 @@ -Accept `"bytes"` as an alias for `"variable_length_bytes"` when parsing `JSON`-encoded Zarr V3 -data types. \ No newline at end of file diff --git a/changes/3533.misc.md b/changes/3533.misc.md deleted file mode 100644 index 237efc9b5b..0000000000 --- a/changes/3533.misc.md +++ /dev/null @@ -1 +0,0 @@ -Reduced the runtime of the test suite by simplifying test cases. \ No newline at end of file diff --git a/changes/3535.bugfix.md b/changes/3535.bugfix.md deleted file mode 100644 index 7e1ce8f834..0000000000 --- a/changes/3535.bugfix.md +++ /dev/null @@ -1,2 +0,0 @@ -Fixed a bug where the `"consolidated_metadata"` key was written to metadata documents even when -consolidated metadata was not used, resulting in invalid metadata documents. \ No newline at end of file diff --git a/changes/3536.doc.md b/changes/3536.doc.md deleted file mode 100644 index 742a0cc3db..0000000000 --- a/changes/3536.doc.md +++ /dev/null @@ -1 +0,0 @@ -Updated 3.0 Migration Guide to include function signature change to zarr.Array.resize function. diff --git a/changes/3547.feature.md b/changes/3547.feature.md deleted file mode 100644 index 280f577804..0000000000 --- a/changes/3547.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add a `array.target_shard_size_bytes` to [`zarr.config`][] to allow users to set a maximum number of bytes per-shard when `shards="auto"` in, for example, [`zarr.create_array`][]. \ No newline at end of file diff --git a/changes/3553.misc.md b/changes/3553.misc.md deleted file mode 100644 index 1354b2da56..0000000000 --- a/changes/3553.misc.md +++ /dev/null @@ -1 +0,0 @@ -Changes the internal logic of the `BloscCodec` class to ensure that the `typesize` and `shuffle` parameters are not set to `None` when creating a new instance of `BloscCodec`. \ No newline at end of file diff --git a/changes/3556.feature.md b/changes/3556.feature.md deleted file mode 100644 index 3b51c2c99e..0000000000 --- a/changes/3556.feature.md +++ /dev/null @@ -1 +0,0 @@ -Make `async_array` on the [`zarr.Array`][] class public (`_async_array` will remain untouched, but its stability is not guaranteed). diff --git a/changes/3560.bugfix.md b/changes/3560.bugfix.md deleted file mode 100644 index c3306cb6ac..0000000000 --- a/changes/3560.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Improve write performance to large shards by up to 10x. diff --git a/docs/release-notes.md b/docs/release-notes.md index 9e809f194e..6ac2f0100f 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,6 +2,38 @@ +# 3.14 (2025-11-20) + +### Features + +- The `Array` class can now also be parametrized in the same manner as the `AsyncArray` class, allowing Zarr format v2 and v3 `Array`s to be distinguished. + New types have been added to `zarr.types` to help with this. ([#3304](https://github.com/zarr-developers/zarr-python/issues3304)) +- Adds `zarr.experimental.cache_store.CacheStore`, a `Store` that implements caching by combining two other `Store` instances. See the [docs page](https://zarr.readthedocs.io/en/latest/user-guide/experimental#cachestore) for more information about this feature. ([#3366](https://github.com/zarr-developers/zarr-python/issues3366)) +- Adds a `zarr.experimental` module for unstable user-facing features. ([#3490](https://github.com/zarr-developers/zarr-python/issues3490)) +- Add a `array.target_shard_size_bytes` to [`zarr.config`][] to allow users to set a maximum number of bytes per-shard when `shards="auto"` in, for example, [`zarr.create_array`][]. ([#3547](https://github.com/zarr-developers/zarr-python/issues3547)) +- Make `async_array` on the [`zarr.Array`][] class public (`_async_array` will remain untouched, but its stability is not guaranteed). ([#3556](https://github.com/zarr-developers/zarr-python/issues3556)) + +### Bugfixes + +- Fix a bug that prevented `PCodec` from being properly resolved when loading arrays using that compressor. ([#3483](https://github.com/zarr-developers/zarr-python/issues3483)) +- Fixed a bug that prevented Zarr Python from opening Zarr V3 array metadata documents that contained + extra keys with permissible values (dicts with a `"must_understand"` key set to `"false"`). ([#3530](https://github.com/zarr-developers/zarr-python/issues3530)) +- Fixed a bug where the `"consolidated_metadata"` key was written to metadata documents even when + consolidated metadata was not used, resulting in invalid metadata documents. ([#3535](https://github.com/zarr-developers/zarr-python/issues3535)) +- Improve write performance to large shards by up to 10x. ([#3560](https://github.com/zarr-developers/zarr-python/issues3560)) + +### Improved Documentation + +- Use mkdocs-material for Zarr-Python documentation ([#3118](https://github.com/zarr-developers/zarr-python/issues3118)) +- Document different values of StoreLike with examples in the user guide. ([#3303](https://github.com/zarr-developers/zarr-python/issues3303)) +- Reorganize the top-level `examples` directory to give each example its own sub-directory. Adds content to the docs for each example. ([#3502](https://github.com/zarr-developers/zarr-python/issues3502)) +- Updated 3.0 Migration Guide to include function signature change to zarr.Array.resize function. ([#3536](https://github.com/zarr-developers/zarr-python/issues3536)) + +### Misc + +- [#3515](https://github.com/zarr-developers/zarr-python/issues3515), [#3532](https://github.com/zarr-developers/zarr-python/issues3532), [#3533](https://github.com/zarr-developers/zarr-python/issues3533), [#3553](https://github.com/zarr-developers/zarr-python/issues3553) + + # zarr 3.1.3 (2025-09-18) ## Features From 5b8887dd82f1898966844f167f45ea8b5044edcd Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 21 Nov 2025 13:36:37 +0100 Subject: [PATCH 161/468] 3.1.4, not pi (#3594) * 3.1.4, not pi * fix links * fix header structure * release notes * rename change entry --- changes/3594.bugfix.md | 1 + docs/release-notes.md | 40 ++++++++++++++++++++-------------------- 2 files changed, 21 insertions(+), 20 deletions(-) create mode 100644 changes/3594.bugfix.md diff --git a/changes/3594.bugfix.md b/changes/3594.bugfix.md new file mode 100644 index 0000000000..8a43120cb3 --- /dev/null +++ b/changes/3594.bugfix.md @@ -0,0 +1 @@ +Fix formatting errors in the release notes section of the docs. \ No newline at end of file diff --git a/docs/release-notes.md b/docs/release-notes.md index 6ac2f0100f..03da403574 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,48 +2,48 @@ -# 3.14 (2025-11-20) +## 3.1.4 (2025-11-20) ### Features - The `Array` class can now also be parametrized in the same manner as the `AsyncArray` class, allowing Zarr format v2 and v3 `Array`s to be distinguished. - New types have been added to `zarr.types` to help with this. ([#3304](https://github.com/zarr-developers/zarr-python/issues3304)) -- Adds `zarr.experimental.cache_store.CacheStore`, a `Store` that implements caching by combining two other `Store` instances. See the [docs page](https://zarr.readthedocs.io/en/latest/user-guide/experimental#cachestore) for more information about this feature. ([#3366](https://github.com/zarr-developers/zarr-python/issues3366)) -- Adds a `zarr.experimental` module for unstable user-facing features. ([#3490](https://github.com/zarr-developers/zarr-python/issues3490)) -- Add a `array.target_shard_size_bytes` to [`zarr.config`][] to allow users to set a maximum number of bytes per-shard when `shards="auto"` in, for example, [`zarr.create_array`][]. ([#3547](https://github.com/zarr-developers/zarr-python/issues3547)) -- Make `async_array` on the [`zarr.Array`][] class public (`_async_array` will remain untouched, but its stability is not guaranteed). ([#3556](https://github.com/zarr-developers/zarr-python/issues3556)) + New types have been added to `zarr.types` to help with this. ([#3304](https://github.com/zarr-developers/zarr-python/issues/3304)) +- Adds `zarr.experimental.cache_store.CacheStore`, a `Store` that implements caching by combining two other `Store` instances. See the [docs page](https://zarr.readthedocs.io/en/latest/user-guide/experimental#cachestore) for more information about this feature. ([#3366](https://github.com/zarr-developers/zarr-python/issues/3366)) +- Adds a `zarr.experimental` module for unstable user-facing features. ([#3490](https://github.com/zarr-developers/zarr-python/issues/3490)) +- Add a `array.target_shard_size_bytes` to [`zarr.config`][] to allow users to set a maximum number of bytes per-shard when `shards="auto"` in, for example, [`zarr.create_array`][]. ([#3547](https://github.com/zarr-developers/zarr-python/issues/3547)) +- Make `async_array` on the [`zarr.Array`][] class public (`_async_array` will remain untouched, but its stability is not guaranteed). ([#3556](https://github.com/zarr-developers/zarr-python/issues/3556)) ### Bugfixes -- Fix a bug that prevented `PCodec` from being properly resolved when loading arrays using that compressor. ([#3483](https://github.com/zarr-developers/zarr-python/issues3483)) +- Fix a bug that prevented `PCodec` from being properly resolved when loading arrays using that compressor. ([#3483](https://github.com/zarr-developers/zarr-python/issues/3483)) - Fixed a bug that prevented Zarr Python from opening Zarr V3 array metadata documents that contained - extra keys with permissible values (dicts with a `"must_understand"` key set to `"false"`). ([#3530](https://github.com/zarr-developers/zarr-python/issues3530)) + extra keys with permissible values (dicts with a `"must_understand"` key set to `"false"`). ([#3530](https://github.com/zarr-developers/zarr-python/issues/3530)) - Fixed a bug where the `"consolidated_metadata"` key was written to metadata documents even when - consolidated metadata was not used, resulting in invalid metadata documents. ([#3535](https://github.com/zarr-developers/zarr-python/issues3535)) -- Improve write performance to large shards by up to 10x. ([#3560](https://github.com/zarr-developers/zarr-python/issues3560)) + consolidated metadata was not used, resulting in invalid metadata documents. ([#3535](https://github.com/zarr-developers/zarr-python/issues/3535)) +- Improve write performance to large shards by up to 10x. ([#3560](https://github.com/zarr-developers/zarr-python/issues/3560)) ### Improved Documentation -- Use mkdocs-material for Zarr-Python documentation ([#3118](https://github.com/zarr-developers/zarr-python/issues3118)) -- Document different values of StoreLike with examples in the user guide. ([#3303](https://github.com/zarr-developers/zarr-python/issues3303)) -- Reorganize the top-level `examples` directory to give each example its own sub-directory. Adds content to the docs for each example. ([#3502](https://github.com/zarr-developers/zarr-python/issues3502)) -- Updated 3.0 Migration Guide to include function signature change to zarr.Array.resize function. ([#3536](https://github.com/zarr-developers/zarr-python/issues3536)) +- Use mkdocs-material for Zarr-Python documentation ([#3118](https://github.com/zarr-developers/zarr-python/issues/3118)) +- Document different values of StoreLike with examples in the user guide. ([#3303](https://github.com/zarr-developers/zarr-python/issues/3303)) +- Reorganize the top-level `examples` directory to give each example its own sub-directory. Adds content to the docs for each example. ([#3502](https://github.com/zarr-developers/zarr-python/issues/3502)) +- Updated 3.0 Migration Guide to include function signature change to zarr.Array.resize function. ([#3536](https://github.com/zarr-developers/zarr-python/issues/3536)) ### Misc -- [#3515](https://github.com/zarr-developers/zarr-python/issues3515), [#3532](https://github.com/zarr-developers/zarr-python/issues3532), [#3533](https://github.com/zarr-developers/zarr-python/issues3533), [#3553](https://github.com/zarr-developers/zarr-python/issues3553) +- [#3515](https://github.com/zarr-developers/zarr-python/issues/3515), [#3532](https://github.com/zarr-developers/zarr-python/issues/3532), [#3533](https://github.com/zarr-developers/zarr-python/issues/3533), [#3553](https://github.com/zarr-developers/zarr-python/issues/3553) -# zarr 3.1.3 (2025-09-18) +## zarr 3.1.3 (2025-09-18) -## Features +### Features - Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also provided under zarr.metadata. ([#1798](https://github.com/zarr-developers/zarr-python/issues/1798)) - Add obstore implementation of delete_dir. ([#3310](https://github.com/zarr-developers/zarr-python/issues/3310)) - Adds a registry for chunk key encodings for extensibility. This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. ([#3436](https://github.com/zarr-developers/zarr-python/issues/3436)) - Trying to open a group at a path where an array already exists now raises a helpful error. ([#3444](https://github.com/zarr-developers/zarr-python/issues/3444)) -## Bugfixes +### Bugfixes - Prevents creation of groups (.create_group) or arrays (.create_array) as children of an existing array. ([#2582](https://github.com/zarr-developers/zarr-python/issues/2582)) - Fix a bug preventing `ones_like`, `full_like`, `empty_like`, `zeros_like` and `open_like` functions from accepting an explicit specification of array attributes like shape, dtype, chunks etc. The functions `full_like`, `empty_like`, and `open_like` now also more consistently infer a `fill_value` parameter from the provided array. ([#2992](https://github.com/zarr-developers/zarr-python/issues/2992)) @@ -54,11 +54,11 @@ - Creating a new group with `zarr.group` no longer errors. This fixes a regression introduced in version 3.1.2. ([#3431](https://github.com/zarr-developers/zarr-python/issues/3431)) - Setting `fill_value` to a float like `0.0` when the data type of the array is an integer is a common mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python will not create such arrays. ([#3448](https://github.com/zarr-developers/zarr-python/issues/3448)) -## Deprecations and Removals +### Deprecations and Removals - The `Store.set_partial_writes` method, which was not used by Zarr-Python, has been removed. `store.supports_partial_writes` is now always `False`. ([#2859](https://github.com/zarr-developers/zarr-python/issues/2859)) -## Misc +### Misc - [#3376](https://github.com/zarr-developers/zarr-python/issues/3376), [#3390](https://github.com/zarr-developers/zarr-python/issues/3390), [#3403](https://github.com/zarr-developers/zarr-python/issues/3403), [#3449](https://github.com/zarr-developers/zarr-python/issues/3449) From 7d8105fbc494060c4faf8e633cc80e71511582e3 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 21 Nov 2025 15:04:31 +0100 Subject: [PATCH 162/468] update release notes (#3598) --- changes/3594.bugfix.md | 1 - docs/release-notes.md | 7 +++++++ 2 files changed, 7 insertions(+), 1 deletion(-) delete mode 100644 changes/3594.bugfix.md diff --git a/changes/3594.bugfix.md b/changes/3594.bugfix.md deleted file mode 100644 index 8a43120cb3..0000000000 --- a/changes/3594.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix formatting errors in the release notes section of the docs. \ No newline at end of file diff --git a/docs/release-notes.md b/docs/release-notes.md index 03da403574..71c095e19a 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,6 +2,13 @@ +# zarr 3.1.5 (2025-11-21) + +## Bugfixes + +- Fix formatting errors in the release notes section of the docs. ([#3594](https://github.com/zarr-developers/zarr-python/issues/3594)) + + ## 3.1.4 (2025-11-20) ### Features From 3ae34cf5cb758912c005706c141597c498e38ddb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Nov 2025 12:18:22 +0100 Subject: [PATCH 163/468] Bump the actions group with 2 updates (#3600) Bumps the actions group with 2 updates: [actions/checkout](https://github.com/actions/checkout) and [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv). Updates `actions/checkout` from 5 to 6 - [Release notes](https://github.com/actions/checkout/releases) - [Commits](https://github.com/actions/checkout/compare/v5...v6) Updates `astral-sh/setup-uv` from 7.1.2 to 7.1.4 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/85856786d1ce8acfbcc2f13a5f3fbd6b938f9f41...1e862dfacbd1d6d858c55d9b792c756523627244) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 7.1.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 4 ++-- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/nightly_wheels.yml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/test.yml | 6 +++--- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index d331ae1e6a..d0545a2570 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -9,10 +9,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0 + - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0 - name: Install uv - uses: astral-sh/setup-uv@85856786d1ce8acfbcc2f13a5f3fbd6b938f9f41 # v7.1.2 + uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 7782114764..d81cd896b9 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -29,7 +29,7 @@ jobs: dependency-set: ["minimal"] steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 with: fetch-depth: 0 # grab all branches and tags # - name: cuda-toolkit diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 0ca263ae9f..b0c1855713 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -28,7 +28,7 @@ jobs: dependency-set: ["optional"] steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - name: Set HYPOTHESIS_PROFILE based on trigger run: | if [[ "${{ github.event_name }}" == "schedule" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 9052504c0a..9d1a81569d 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 with: submodules: true fetch-depth: 0 diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 32732689a9..0e48f0b526 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -11,7 +11,7 @@ jobs: fail-fast: false steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 with: submodules: true fetch-depth: 0 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 971fc415af..d528907868 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -44,7 +44,7 @@ jobs: runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 with: fetch-depth: 0 # grab all branches and tags - name: Set up Python @@ -86,7 +86,7 @@ jobs: - python-version: "3.11" dependency-set: upstream steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 with: fetch-depth: 0 - name: Set up Python @@ -115,7 +115,7 @@ jobs: name: doctests runs-on: ubuntu-latest steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 with: fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3 - name: Set up Python From 94d543ccff70f6348029027887868e443ae4cfaa Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Mon, 24 Nov 2025 06:29:31 -0500 Subject: [PATCH 164/468] fix: clearer description of `array.target_shard_size` (#3599) Co-authored-by: Davis Bennett --- docs/user-guide/performance.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index cebec7815a..a2e986a1b8 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -81,7 +81,7 @@ z6 = zarr.create_array(store={}, shape=(10000, 10000, 1000), shards=(1000, 1000, print(z6.info) ``` -`shards` can be `"auto"` as well, in which case the `array.target_shard_size_bytes` setting can be used to control the size of shards (i.e., the size of the shard will be as close to without being bigger than `target_shard_size_bytes`); otherwise, a default is used. +`shards` can be `"auto"` as well, in which case the `array.target_shard_size_bytes` setting can be used to control the size of shards (i.e., the size of the chunks cumulatively and uncompressed within the shard will be as close to, without being bigger than, `array.target_shard_size_bytes`); otherwise, a default is used. ### Chunk memory layout From e456b098bbdf4f2db6d285c5648eeda07a272a4b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 27 Nov 2025 16:56:02 +0100 Subject: [PATCH 165/468] chore/pin pytest asyncio (#3606) * bump mininum version of typing_extensions * pin pytest-asyncio * < not <= --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7f14971396..68f3b97811 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -75,7 +75,7 @@ test = [ "coverage>=7.10", # Pin possibly due to https://github.com/pytest-dev/pytest-cov/issues/693 "pytest<8.4", - "pytest-asyncio", + "pytest-asyncio<1.2.0", "pytest-cov", "pytest-accept", "rich", From 20670e61718535ddefe6e60487541af0993fa8d6 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 27 Nov 2025 17:06:12 +0100 Subject: [PATCH 166/468] fix tests for stand-alone example scripts (#3605) * add test that fails when there are no examples detected * use rglob instead of glob to find example scripts * changelog --- changes/3605.misc.md | 1 + tests/test_examples.py | 9 ++++++++- 2 files changed, 9 insertions(+), 1 deletion(-) create mode 100644 changes/3605.misc.md diff --git a/changes/3605.misc.md b/changes/3605.misc.md new file mode 100644 index 0000000000..b8c0757b69 --- /dev/null +++ b/changes/3605.misc.md @@ -0,0 +1 @@ +Fix a bug in the test suite that prevented stand-alone example scripts from being tested. \ No newline at end of file diff --git a/tests/test_examples.py b/tests/test_examples.py index 54af4119e3..152b0a1a88 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -11,7 +11,7 @@ from packaging.requirements import Requirement examples_dir = "examples" -script_paths = Path(examples_dir).glob("*.py") +script_paths = tuple(Path(examples_dir).rglob("*.py")) PEP_723_REGEX: Final = r"(?m)^# /// (?P[a-zA-Z0-9-]+)$\s(?P(^#(| .*)$\s)+)^# ///$" @@ -62,6 +62,13 @@ def resave_script(source_path: Path, dest_path: Path) -> None: dest_path.write_text(dest_text) +def test_script_paths() -> None: + """ + Test that our test fixture is working properly and collecting script paths. + """ + assert len(script_paths) > 0 + + @pytest.mark.skipif( sys.platform in ("win32",), reason="This test fails due for unknown reasons on Windows in CI." ) From ee0e69a74898b9e0467df517fc55a337bbb5fb06 Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Thu, 27 Nov 2025 11:26:12 -0500 Subject: [PATCH 167/468] fix: auto-chunking when auto-sharding 1MiB number (#3603) * fix: 1024 bytes is not 1MiB! * fix: correct number * chore: add test * chore: relnote * fix: name * Apply suggestion from @d-v-b --------- Co-authored-by: Davis Bennett --- changes/3603.bugfix.md | 1 + src/zarr/core/chunk_grids.py | 4 +++- tests/test_array.py | 18 ++++++++++++++++++ 3 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 changes/3603.bugfix.md diff --git a/changes/3603.bugfix.md b/changes/3603.bugfix.md new file mode 100644 index 0000000000..37e1da5cb1 --- /dev/null +++ b/changes/3603.bugfix.md @@ -0,0 +1 @@ +Correct the target bytes number for auto-chunking when auto-sharding. \ No newline at end of file diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 7ebd68b5b4..2c7945fa64 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -62,6 +62,8 @@ def _guess_chunks( tuple[int, ...] """ + if min_bytes >= max_bytes: + raise ValueError(f"Cannot have more min_bytes ({min_bytes}) than max_bytes ({max_bytes})") if isinstance(shape, int): shape = (shape,) @@ -264,7 +266,7 @@ def _auto_partition( else: if chunk_shape == "auto": # aim for a 1MiB chunk - _chunks_out = _guess_chunks(array_shape, item_size, max_bytes=1024) + _chunks_out = _guess_chunks(array_shape, item_size, max_bytes=1048576) else: _chunks_out = chunk_shape diff --git a/tests/test_array.py b/tests/test_array.py index 61828be0aa..67be294827 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1019,6 +1019,24 @@ def test_auto_partition_auto_shards( assert auto_shards == expected_shards +def test_auto_partition_auto_shards_with_auto_chunks_should_be_close_to_1MiB() -> None: + """ + Test that automatically picking a shard size and a chunk size gives roughly 1MiB chunks. + """ + with pytest.warns( + ZarrUserWarning, + match="Automatic shard shape inference is experimental and may change without notice.", + ): + with zarr.config.set({"array.target_shard_size_bytes": 10_000_000}): + _, chunk_shape = _auto_partition( + array_shape=(10_000_000,), + chunk_shape="auto", + shard_shape="auto", + item_size=1, + ) + assert chunk_shape == (625000,) + + def test_chunks_and_shards() -> None: store = StorePath(MemoryStore()) shape = (100, 100) From 65fec71428fb219dfcd30810c76f9cde0569259e Mon Sep 17 00:00:00 2001 From: Xavier Nogueira <58796351+xaviernogueira@users.noreply.github.com> Date: Tue, 16 Dec 2025 11:31:43 -0800 Subject: [PATCH 168/468] Some minor linter \ type-hint fixes for my own sanity (#3623) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * ✏️ using ZarrFormat instead of duplication * ✏️ making linter happy (numpy has Literal[True, False]) * Create 3623.misc.md --- changes/3623.misc.md | 5 +++++ examples/custom_dtype/custom_dtype.py | 2 +- src/zarr/_cli/cli.py | 11 ++++++----- src/zarr/metadata/migrate_v3.py | 4 ++-- src/zarr/testing/strategies.py | 10 ++++++---- tests/package_with_entrypoint/__init__.py | 2 +- 6 files changed, 21 insertions(+), 13 deletions(-) create mode 100644 changes/3623.misc.md diff --git a/changes/3623.misc.md b/changes/3623.misc.md new file mode 100644 index 0000000000..4060e55e5f --- /dev/null +++ b/changes/3623.misc.md @@ -0,0 +1,5 @@ +This PR contains minor, non-function-altering, changes to use `ZarrFormat` across the repo as opposed to duplicating is with `Literal[2,3]`. + +Additionally, it fixes broken linting by using a `Literal[True, False]` type hint for Numpy hypothesis testing, as opposed to `bool`. + +Basically improves the typehints and reduces fat-finger error surface area slightly. diff --git a/examples/custom_dtype/custom_dtype.py b/examples/custom_dtype/custom_dtype.py index a98f3414f6..ec38d782b6 100644 --- a/examples/custom_dtype/custom_dtype.py +++ b/examples/custom_dtype/custom_dtype.py @@ -217,7 +217,7 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> ml_dtypes. # this parametrized function will create arrays in zarr v2 and v3 using our new data type @pytest.mark.parametrize("zarr_format", [2, 3]) -def test_custom_dtype(tmp_path: Path, zarr_format: Literal[2, 3]) -> None: +def test_custom_dtype(tmp_path: Path, zarr_format: ZarrFormat) -> None: # create array and write values z_w = zarr.create_array( store=tmp_path, shape=(4,), dtype="int2", zarr_format=zarr_format, compressors=None diff --git a/src/zarr/_cli/cli.py b/src/zarr/_cli/cli.py index 785efe505b..35521f01ab 100644 --- a/src/zarr/_cli/cli.py +++ b/src/zarr/_cli/cli.py @@ -6,6 +6,7 @@ import zarr import zarr.metadata.migrate_v3 as migrate_metadata +from zarr.core.common import ZarrFormat from zarr.core.sync import sync from zarr.storage._common import make_store @@ -23,12 +24,12 @@ def _set_logging_level(*, verbose: bool) -> None: zarr.set_format("%(message)s") -class ZarrFormat(str, Enum): +class CLIZarrFormat(str, Enum): v2 = "v2" v3 = "v3" -class ZarrFormatV3(str, Enum): +class CLIZarrFormatV3(str, Enum): """Limit CLI choice to only v3""" v3 = "v3" @@ -37,7 +38,7 @@ class ZarrFormatV3(str, Enum): @app.command() # type: ignore[misc] def migrate( zarr_format: Annotated[ - ZarrFormatV3, + CLIZarrFormatV3, typer.Argument( help="Zarr format to migrate to. Currently only 'v3' is supported.", ), @@ -122,7 +123,7 @@ def migrate( @app.command() # type: ignore[misc] def remove_metadata( zarr_format: Annotated[ - ZarrFormat, + CLIZarrFormat, typer.Argument(help="Which format's metadata to remove - v2 or v3."), ], store: Annotated[ @@ -160,7 +161,7 @@ def remove_metadata( sync( migrate_metadata.remove_metadata( store=input_zarr_store, - zarr_format=cast(Literal[2, 3], int(zarr_format[1:])), + zarr_format=cast(ZarrFormat, int(zarr_format[1:])), force=force, dry_run=dry_run, ) diff --git a/src/zarr/metadata/migrate_v3.py b/src/zarr/metadata/migrate_v3.py index 8f83e01f20..a72939100d 100644 --- a/src/zarr/metadata/migrate_v3.py +++ b/src/zarr/metadata/migrate_v3.py @@ -1,6 +1,6 @@ import asyncio import logging -from typing import Literal, cast +from typing import cast import numcodecs.abc @@ -140,7 +140,7 @@ async def remove_metadata( continue if force or await _metadata_exists( - cast(Literal[2, 3], alternative_metadata), store_path / parent_path + cast(ZarrFormat, alternative_metadata), store_path / parent_path ): _logger.info("Deleting metadata at %s", store_path / file_path) if not dry_run: diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 5eb17214fe..330f220b56 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -25,6 +25,8 @@ from zarr.storage._utils import normalize_path from zarr.types import AnyArray +TrueOrFalse = Literal[True, False] + # Copied from Xarray _attr_keys = st.text(st.characters(), min_size=1) _attr_values = st.recursive( @@ -131,7 +133,7 @@ def array_metadata( draw: st.DrawFn, *, array_shapes: Callable[..., st.SearchStrategy[tuple[int, ...]]] = npst.array_shapes, - zarr_formats: st.SearchStrategy[Literal[2, 3]] = zarr_formats, + zarr_formats: st.SearchStrategy[ZarrFormat] = zarr_formats, attributes: SearchStrategy[Mapping[str, JSON] | None] = attrs, ) -> ArrayV2Metadata | ArrayV3Metadata: zarr_format = draw(zarr_formats) @@ -348,8 +350,8 @@ def basic_indices( shape: tuple[int, ...], min_dims: int = 0, max_dims: int | None = None, - allow_newaxis: bool = False, - allow_ellipsis: bool = True, + allow_newaxis: TrueOrFalse = False, + allow_ellipsis: TrueOrFalse = True, ) -> Any: """Basic indices without unsupported negative slices.""" strategy = npst.basic_indices( @@ -362,7 +364,7 @@ def basic_indices( lambda idxr: ( not ( is_negative_slice(idxr) - or (isinstance(idxr, tuple) and any(is_negative_slice(idx) for idx in idxr)) # type: ignore[redundant-expr] + or (isinstance(idxr, tuple) and any(is_negative_slice(idx) for idx in idxr)) ) ) ) diff --git a/tests/package_with_entrypoint/__init__.py b/tests/package_with_entrypoint/__init__.py index ae86378cb5..7b5dfb5a1e 100644 --- a/tests/package_with_entrypoint/__init__.py +++ b/tests/package_with_entrypoint/__init__.py @@ -84,7 +84,7 @@ class TestDataType(Bool): _zarr_v3_name: ClassVar[Literal["test"]] = "test" # type: ignore[assignment] @classmethod - def from_json(cls, data: DTypeJSON, *, zarr_format: Literal[2, 3]) -> Self: + def from_json(cls, data: DTypeJSON, *, zarr_format: ZarrFormat) -> Self: if zarr_format == 2 and data == {"name": cls._zarr_v3_name, "object_codec_id": None}: return cls() if zarr_format == 3 and data == cls._zarr_v3_name: From b8736917c351418dce3fb425ee16f747136da96e Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 17 Dec 2025 14:08:53 +0100 Subject: [PATCH 169/468] remove pytest pin (#3619) * remove pytest pin * remove pytest-asyncio upper bound * update changelog * move type: ignores around to pass pre-commit checks * bump typing-extensions to the minimum required by pytest-asyncio * bump typing_extensions in min deps test * tweak type: ignore declarations * remove type: ignore --- changes/3619.misc.md | 1 + pyproject.toml | 9 ++++----- 2 files changed, 5 insertions(+), 5 deletions(-) create mode 100644 changes/3619.misc.md diff --git a/changes/3619.misc.md b/changes/3619.misc.md new file mode 100644 index 0000000000..8c36e473b5 --- /dev/null +++ b/changes/3619.misc.md @@ -0,0 +1 @@ +Remove upper bounds on `pytest` and `pytest-asyncio` test dependencies. \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 68f3b97811..d1cb55c6cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,7 @@ dependencies = [ 'numpy>=1.26', 'numcodecs>=0.14', 'google-crc32c>=1.5', - 'typing_extensions>=4.9', + 'typing_extensions>=4.12', 'donfig>=0.8', ] @@ -73,9 +73,8 @@ cli = ["typer"] # Development extras test = [ "coverage>=7.10", - # Pin possibly due to https://github.com/pytest-dev/pytest-cov/issues/693 - "pytest<8.4", - "pytest-asyncio<1.2.0", + "pytest", + "pytest-asyncio", "pytest-cov", "pytest-accept", "rich", @@ -240,7 +239,7 @@ dependencies = [ 'fsspec==2023.10.0', 's3fs==2023.10.0', 'universal_pathlib==0.0.22', - 'typing_extensions==4.9.*', + 'typing_extensions==4.12.*', 'donfig==0.8.*', 'obstore==0.5.*', # test deps From 34859c4510d6a08028b50b3b84b2e57c84c7e373 Mon Sep 17 00:00:00 2001 From: Mark Harfouche Date: Sun, 28 Dec 2025 23:44:56 -0500 Subject: [PATCH 170/468] use the result of the broadcasted array to check the contents (#3629) --- src/zarr/core/buffer/core.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index f0d01566c3..c402904049 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -542,7 +542,7 @@ def all_equal(self, other: Any, equal_nan: bool = True) -> bool: # every single time we have to write data? _data, other = np.broadcast_arrays(self._data, other) return np.array_equal( - self._data, + _data, other, equal_nan=equal_nan if self._data.dtype.kind not in ("U", "S", "T", "O", "V") From 8207dd344e9df0e8ed06b024df4b3b3ebfa53f23 Mon Sep 17 00:00:00 2001 From: "Christine P. Chai" Date: Wed, 31 Dec 2025 07:48:03 -0800 Subject: [PATCH 171/468] docs: Correct grammar issues in a/an usage (#3634) * docs: Correct grammar issues in a/an usage * Update src/zarr/storage/_fsspec.py --------- Co-authored-by: Tom Augspurger --- docs/user-guide/storage.md | 2 +- src/zarr/core/array.py | 2 +- src/zarr/core/buffer/core.py | 6 +++--- src/zarr/core/buffer/cpu.py | 4 ++-- src/zarr/core/buffer/gpu.py | 2 +- src/zarr/core/dtype/npy/bytes.py | 2 +- src/zarr/core/dtype/npy/int.py | 22 +++++++++++----------- src/zarr/core/metadata/v3.py | 2 +- src/zarr/storage/_common.py | 6 +++--- src/zarr/storage/_fsspec.py | 6 +++--- src/zarr/storage/_utils.py | 2 +- src/zarr/testing/buffer.py | 2 +- tests/test_store/test_fsspec.py | 2 +- tests/test_store/test_logging.py | 2 +- tests/test_store/test_object.py | 2 +- 15 files changed, 32 insertions(+), 32 deletions(-) diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index 0fea19a3f5..2b200c27b9 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -154,7 +154,7 @@ print(store) ### Memory Store -The [`zarr.storage.MemoryStore`][] a in-memory store that allows for serialization of +The [`zarr.storage.MemoryStore`][] an in-memory store that allows for serialization of Zarr data (metadata and chunks) to a dictionary: ```python exec="true" session="storage" source="above" result="ansi" diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 6b20ee950d..7febc02a2d 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1723,7 +1723,7 @@ async def _set_selection( value = cast("NDArrayLike", value) # We accept any ndarray like object from the user and convert it - # to a NDBuffer (or subclass). From this point onwards, we only pass + # to an NDBuffer (or subclass). From this point onwards, we only pass # Buffer and NDBuffer between components. value_buffer = prototype.nd_buffer.from_ndarray_like(value) diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index c402904049..9602a55258 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -315,7 +315,7 @@ class NDBuffer: We use NDBuffer throughout Zarr to represent a n-dimensional memory block. - A NDBuffer is backed by an underlying ndarray-like instance that represents + An NDBuffer is backed by an underlying ndarray-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the ndarray-like instance can be copied/converted to a regular Numpy array @@ -368,7 +368,7 @@ def create( Notes ----- - A subclass can overwrite this method to create a ndarray-like object + A subclass can overwrite this method to create an ndarray-like object other then the default Numpy array. """ if cls is NDBuffer: @@ -416,7 +416,7 @@ def empty( @classmethod def from_ndarray_like(cls, ndarray_like: NDArrayLike) -> Self: - """Create a new buffer of a ndarray-like object + """Create a new buffer of an ndarray-like object Parameters ---------- diff --git a/src/zarr/core/buffer/cpu.py b/src/zarr/core/buffer/cpu.py index 58275d2843..8994281b58 100644 --- a/src/zarr/core/buffer/cpu.py +++ b/src/zarr/core/buffer/cpu.py @@ -28,7 +28,7 @@ class Buffer(core.Buffer): We use Buffer throughout Zarr to represent a contiguous block of memory. - A Buffer is backed by a underlying array-like instance that represents + A Buffer is backed by an underlying array-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the array-like instance can be copied/converted to a regular Numpy array @@ -121,7 +121,7 @@ class NDBuffer(core.NDBuffer): We use NDBuffer throughout Zarr to represent a n-dimensional memory block. - A NDBuffer is backed by a underlying ndarray-like instance that represents + An NDBuffer is backed by an underlying ndarray-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the ndarray-like instance can be copied/converted to a regular Numpy array diff --git a/src/zarr/core/buffer/gpu.py b/src/zarr/core/buffer/gpu.py index d99c1d2818..8672942364 100644 --- a/src/zarr/core/buffer/gpu.py +++ b/src/zarr/core/buffer/gpu.py @@ -123,7 +123,7 @@ class NDBuffer(core.NDBuffer): We use NDBuffer throughout Zarr to represent a n-dimensional memory block. - A NDBuffer is backed by an underlying ndarray-like instance that represents + An NDBuffer is backed by an underlying ndarray-like instance that represents the memory. The memory type is unspecified; can be regular host memory, CUDA device memory, or something else. The only requirement is that the ndarray-like instance can be copied/converted to a regular Numpy array diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index cb7d86e957..2cf5985d69 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -899,7 +899,7 @@ def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> str: def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.void: """ - Read a JSON-serializable value as a np.void. + Read a JSON-serializable value as an np.void. Parameters ---------- diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index 580776a865..f71f535abb 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -263,7 +263,7 @@ class Int8(BaseInt[np.dtypes.Int8DType, np.int8]): @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ - Create an Int8 from a np.dtype('int8') instance. + Create an Int8 from an np.dtype('int8') instance. Parameters ---------- @@ -288,7 +288,7 @@ def from_native_dtype(cls, dtype: TBaseDType) -> Self: def to_native_dtype(self: Self) -> np.dtypes.Int8DType: """ - Convert the Int8 instance to a np.dtype('int8') instance. + Convert the Int8 instance to an np.dtype('int8') instance. Returns ------- @@ -419,7 +419,7 @@ class UInt8(BaseInt[np.dtypes.UInt8DType, np.uint8]): @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ - Create a UInt8 from a np.dtype('uint8') instance. + Create a UInt8 from an np.dtype('uint8') instance. """ if cls._check_native_dtype(dtype): return cls() @@ -566,7 +566,7 @@ class Int16(BaseInt[np.dtypes.Int16DType, np.int16], HasEndianness): @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ - Create an instance of this data type from a np.dtype('int16') instance. + Create an instance of this data type from an np.dtype('int16') instance. Parameters ---------- @@ -591,7 +591,7 @@ def from_native_dtype(cls, dtype: TBaseDType) -> Self: def to_native_dtype(self) -> np.dtypes.Int16DType: """ - Convert the data type to a np.dtype('int16') instance. + Convert the data type to an np.dtype('int16') instance. Returns ------- @@ -728,7 +728,7 @@ class UInt16(BaseInt[np.dtypes.UInt16DType, np.uint16], HasEndianness): @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ - Create an instance of this data type from a np.dtype('uint16') instance. + Create an instance of this data type from an np.dtype('uint16') instance. Parameters ---------- @@ -753,7 +753,7 @@ def from_native_dtype(cls, dtype: TBaseDType) -> Self: def to_native_dtype(self) -> np.dtypes.UInt16DType: """ - Convert the data type to a np.dtype('uint16') instance. + Convert the data type to an np.dtype('uint16') instance. Returns ------- @@ -911,7 +911,7 @@ def _check_native_dtype(cls: type[Self], dtype: TBaseDType) -> TypeGuard[np.dtyp @classmethod def from_native_dtype(cls: type[Self], dtype: TBaseDType) -> Self: """ - Create an Int32 from a np.dtype('int32') instance. + Create an Int32 from an np.dtype('int32') instance. Parameters ---------- @@ -936,7 +936,7 @@ def from_native_dtype(cls: type[Self], dtype: TBaseDType) -> Self: def to_native_dtype(self: Self) -> np.dtypes.Int32DType: """ - Convert the Int32 instance to a np.dtype('int32') instance. + Convert the Int32 instance to an np.dtype('int32') instance. Returns ------- @@ -1073,7 +1073,7 @@ class UInt32(BaseInt[np.dtypes.UInt32DType, np.uint32], HasEndianness): @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ - Create a UInt32 from a np.dtype('uint32') instance. + Create a UInt32 from an np.dtype('uint32') instance. Parameters ---------- @@ -1231,7 +1231,7 @@ class Int64(BaseInt[np.dtypes.Int64DType, np.int64], HasEndianness): @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ - Create an Int64 from a np.dtype('int64') instance. + Create an Int64 from an np.dtype('int64') instance. Parameters ---------- diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index a14373c340..5ce155bd9a 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -117,7 +117,7 @@ def parse_dimension_names(data: object) -> tuple[str | None, ...] | None: elif isinstance(data, Iterable) and all(isinstance(x, type(None) | str) for x in data): return tuple(data) else: - msg = f"Expected either None or a iterable of str, got {type(data)}" + msg = f"Expected either None or an iterable of str, got {type(data)}" raise TypeError(msg) diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index d762097cc3..4bea04f024 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -311,7 +311,7 @@ async def make_store( ): raise TypeError( "'storage_options' was provided but unused. " - "'storage_options' is only used when the store is passed as a FSSpec URI string.", + "'storage_options' is only used when the store is passed as an FSSpec URI string.", ) assert mode in (None, "r", "r+", "a", "w", "w-") @@ -341,7 +341,7 @@ async def make_store( return await LocalStore.open(root=store_like, mode=mode, read_only=_read_only) elif isinstance(store_like, str): - # Either a FSSpec URI or a local filesystem path + # Either an FSSpec URI or a local filesystem path if _is_fsspec_uri(store_like): return FsspecStore.from_url( store_like, storage_options=storage_options, read_only=_read_only @@ -409,7 +409,7 @@ async def make_store_path( if storage_options: raise TypeError( "'storage_options' was provided but unused. " - "'storage_options' is only used when the store is passed as a FSSpec URI string.", + "'storage_options' is only used when the store is passed as an FSSpec URI string.", ) return store_like / path_normalized diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 7945fba467..f9e4ed375d 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -147,7 +147,7 @@ def from_upath( allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS, ) -> FsspecStore: """ - Create a FsspecStore from an upath object. + Create an FsspecStore from a upath object. Parameters ---------- @@ -178,7 +178,7 @@ def from_mapper( allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS, ) -> FsspecStore: """ - Create a FsspecStore from a FSMap object. + Create an FsspecStore from an FSMap object. Parameters ---------- @@ -211,7 +211,7 @@ def from_url( allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS, ) -> FsspecStore: """ - Create a FsspecStore from a URL. The type of store is determined from the URL scheme. + Create an FsspecStore from a URL. The type of store is determined from the URL scheme. Parameters ---------- diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index 39c28d44c3..10ac395b36 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -51,7 +51,7 @@ def normalize_path(path: str | bytes | Path | None) -> str: def _normalize_byte_range_index(data: Buffer, byte_range: ByteRequest | None) -> tuple[int, int]: """ - Convert an ByteRequest into an explicit start and stop + Convert a ByteRequest into an explicit start and stop """ if byte_range is None: start = 0 diff --git a/src/zarr/testing/buffer.py b/src/zarr/testing/buffer.py index 4b652bc93d..6096ece2f8 100644 --- a/src/zarr/testing/buffer.py +++ b/src/zarr/testing/buffer.py @@ -22,7 +22,7 @@ class TestNDArrayLike(np.ndarray): - """An example of a ndarray-like class""" + """An example of an ndarray-like class""" __test__ = False diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 1e3ed26568..a2c07b7ed1 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -379,7 +379,7 @@ def test_open_s3map_raises() -> None: zarr.open(store=mapper, path="bar", mode="w", shape=(3, 3)) with pytest.raises( TypeError, - match="'storage_options' is only used when the store is passed as a FSSpec URI string.", + match="'storage_options' is only used when the store is passed as an FSSpec URI string.", ): zarr.open(store=mapper, storage_options={"anon": True}, mode="w", shape=(3, 3)) diff --git a/tests/test_store/test_logging.py b/tests/test_store/test_logging.py index e4a0f64b48..fa566e45aa 100644 --- a/tests/test_store/test_logging.py +++ b/tests/test_store/test_logging.py @@ -22,7 +22,7 @@ class StoreKwargs(TypedDict): class TestLoggingStore(StoreTests[LoggingStore[LocalStore], cpu.Buffer]): - # store_cls is needed to do an isintsance check, so can't be a subscripted generic + # store_cls is needed to do an isinstance check, so can't be a subscripted generic store_cls = LoggingStore # type: ignore[assignment] buffer_cls = cpu.Buffer diff --git a/tests/test_store/test_object.py b/tests/test_store/test_object.py index cc0b44f540..6a4b796639 100644 --- a/tests/test_store/test_object.py +++ b/tests/test_store/test_object.py @@ -23,7 +23,7 @@ class StoreKwargs(TypedDict): class TestObjectStore(StoreTests[ObjectStore[LocalStore], cpu.Buffer]): - # store_cls is needed to do an isintsance check, so can't be a subscripted generic + # store_cls is needed to do an isinstance check, so can't be a subscripted generic store_cls = ObjectStore # type: ignore[assignment] buffer_cls = cpu.Buffer From 6cc2b0d13de8341f8e15bb276c93aaab295fbffb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 8 Jan 2026 10:49:58 +0100 Subject: [PATCH 172/468] Bump the actions group across 1 directory with 5 updates (#3630) Bumps the actions group with 5 updates in the / directory: | Package | From | To | | --- | --- | --- | | [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) | `7.1.4` | `7.1.6` | | [actions/cache](https://github.com/actions/cache) | `4` | `5` | | [scientific-python/upload-nightly-action](https://github.com/scientific-python/upload-nightly-action) | `0.6.2` | `0.6.3` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `5` | `6` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `6` | `7` | Updates `astral-sh/setup-uv` from 7.1.4 to 7.1.6 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/1e862dfacbd1d6d858c55d9b792c756523627244...681c641aba71e4a1c380be3ab5e12ad51f415867) Updates `actions/cache` from 4 to 5 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v4...v5) Updates `scientific-python/upload-nightly-action` from 0.6.2 to 0.6.3 - [Release notes](https://github.com/scientific-python/upload-nightly-action/releases) - [Commits](https://github.com/scientific-python/upload-nightly-action/compare/b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf...5748273c71e2d8d3a61f3a11a16421c8954f9ecf) Updates `actions/upload-artifact` from 5 to 6 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v5...v6) Updates `actions/download-artifact` from 6 to 7 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v6...v7) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 7.1.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/cache dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: scientific-python/upload-nightly-action dependency-version: 0.6.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/download-artifact dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 2 +- .github/workflows/hypothesis.yaml | 4 ++-- .github/workflows/nightly_wheels.yml | 2 +- .github/workflows/releases.yml | 6 +++--- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index d0545a2570..297b414967 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -12,7 +12,7 @@ jobs: - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0 - name: Install uv - uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4 + uses: astral-sh/setup-uv@681c641aba71e4a1c380be3ab5e12ad51f415867 # v7.1.6 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index b0c1855713..96dbcaa6f6 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -52,7 +52,7 @@ jobs: # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache - name: Restore cached hypothesis directory id: restore-hypothesis-cache - uses: actions/cache/restore@v4 + uses: actions/cache/restore@v5 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} @@ -70,7 +70,7 @@ jobs: - name: Save cached hypothesis directory id: save-hypothesis-cache if: always() && steps.status.outcome != 'skipped' - uses: actions/cache/save@v4 + uses: actions/cache/save@v5 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 9d1a81569d..dbbc0354e9 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -31,7 +31,7 @@ jobs: run: hatch build - name: Upload nightly wheels - uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf + uses: scientific-python/upload-nightly-action@5748273c71e2d8d3a61f3a11a16421c8954f9ecf with: artifacts_path: dist anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }} diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 0e48f0b526..bca01466bb 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -27,7 +27,7 @@ jobs: pip install hatch - name: Build wheel and sdist run: hatch build - - uses: actions/upload-artifact@v5 + - uses: actions/upload-artifact@v6 with: name: releases path: dist @@ -36,7 +36,7 @@ jobs: needs: [build_artifacts] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@v6 + - uses: actions/download-artifact@v7 with: name: releases path: dist @@ -51,7 +51,7 @@ jobs: runs-on: ubuntu-latest if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') steps: - - uses: actions/download-artifact@v6 + - uses: actions/download-artifact@v7 with: name: releases path: dist From 034cd20c41b536baf3fd2bd1413ae62bc1854b9c Mon Sep 17 00:00:00 2001 From: Raman <69149285+ramanbansal1@users.noreply.github.com> Date: Thu, 8 Jan 2026 17:20:08 +0530 Subject: [PATCH 173/468] ci: align pre-commit Python with tooling config (#3633) Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cb1b75d90b..54474a432d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,6 +4,10 @@ ci: autofix_commit_msg: "style: pre-commit fixes" autofix_prs: false default_stages: [pre-commit, pre-push] + +default_language_version: + python: python3.11 + repos: - repo: https://github.com/astral-sh/ruff-pre-commit rev: v0.14.3 From 79d864ef6c44ddecc3e6a71199d8fd2f74f8d095 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 8 Jan 2026 13:22:13 +0000 Subject: [PATCH 174/468] chore: update pre-commit hooks (#3610) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore: update pre-commit hooks updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.3 → v0.14.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.3...v0.14.10) - [github.com/pre-commit/mirrors-mypy: v1.18.2 → v1.19.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.18.2...v1.19.1) - [github.com/scientific-python/cookie: 2025.10.20 → 2025.11.21](https://github.com/scientific-python/cookie/compare/2025.10.20...2025.11.21) - [github.com/numpy/numpydoc: v1.9.0 → v1.10.0](https://github.com/numpy/numpydoc/compare/v1.9.0...v1.10.0) * update JSON union to include bool * apply fixes to resolve pre-commit violations --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 8 ++++---- pyproject.toml | 1 + src/zarr/_cli/cli.py | 6 +++--- src/zarr/core/common.py | 2 +- tests/test_metadata/test_v2.py | 3 ++- 5 files changed, 11 insertions(+), 9 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 54474a432d..c4132530af 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,7 +10,7 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.3 + rev: v0.14.10 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -27,7 +27,7 @@ repos: exclude: mkdocs.yml - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.18.2 + rev: v1.19.1 hooks: - id: mypy files: src|tests @@ -46,7 +46,7 @@ repos: - hypothesis - s3fs - repo: https://github.com/scientific-python/cookie - rev: 2025.10.20 + rev: 2025.11.21 hooks: - id: sp-repo-review - repo: https://github.com/pre-commit/pygrep-hooks @@ -55,7 +55,7 @@ repos: - id: rst-directive-colons - id: rst-inline-touching-normal - repo: https://github.com/numpy/numpydoc - rev: v1.9.0 + rev: v1.10.0 hooks: - id: numpydoc-validation - repo: https://github.com/twisted/towncrier diff --git a/pyproject.toml b/pyproject.toml index d1cb55c6cf..a39956af5e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -395,6 +395,7 @@ ignore_errors = true minversion = "7" testpaths = ["tests", "docs/user-guide"] log_cli_level = "INFO" +log_level = "INFO" xfail_strict = true asyncio_mode = "auto" asyncio_default_fixture_loop_scope = "function" diff --git a/src/zarr/_cli/cli.py b/src/zarr/_cli/cli.py index 35521f01ab..78f4955d84 100644 --- a/src/zarr/_cli/cli.py +++ b/src/zarr/_cli/cli.py @@ -35,7 +35,7 @@ class CLIZarrFormatV3(str, Enum): v3 = "v3" -@app.command() # type: ignore[misc] +@app.command() # type: ignore[untyped-decorator] def migrate( zarr_format: Annotated[ CLIZarrFormatV3, @@ -120,7 +120,7 @@ def migrate( sync(migrate_metadata.remove_metadata(write_store, 2, force=False, dry_run=dry_run)) -@app.command() # type: ignore[misc] +@app.command() # type: ignore[untyped-decorator] def remove_metadata( zarr_format: Annotated[ CLIZarrFormat, @@ -168,7 +168,7 @@ def remove_metadata( ) -@app.callback() # type: ignore[misc] +@app.callback() # type: ignore[untyped-decorator] def main( verbose: Annotated[ bool, diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 9b3d297298..d38949657e 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -42,7 +42,7 @@ ChunkCoords = tuple[int, ...] ZarrFormat = Literal[2, 3] NodeType = Literal["array", "group"] -JSON = str | int | float | Mapping[str, "JSON"] | Sequence["JSON"] | None +JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None MemoryOrder = Literal["C", "F"] AccessModeLiteral = Literal["r", "r+", "a", "w", "w-"] ANY_ACCESS_MODE: Final = "r", "r+", "a", "w", "w-" diff --git a/tests/test_metadata/test_v2.py b/tests/test_metadata/test_v2.py index 424b2881d6..8c3082e924 100644 --- a/tests/test_metadata/test_v2.py +++ b/tests/test_metadata/test_v2.py @@ -309,12 +309,13 @@ def test_from_dict_extra_fields() -> None: def test_zstd_checksum() -> None: + compressor_config: dict[str, JSON] = {"id": "zstd", "level": 5, "checksum": False} arr = zarr.create_array( {}, shape=(10,), chunks=(10,), dtype="int32", - compressors={"id": "zstd", "level": 5, "checksum": False}, + compressors=compressor_config, zarr_format=2, ) metadata = json.loads( From 884a8c91afcc3efe28b3da952be3b85125c453cb Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Thu, 8 Jan 2026 14:42:49 +0100 Subject: [PATCH 175/468] adjust docstrings (#3615) Co-authored-by: Davis Bennett --- src/zarr/core/array.py | 52 +++++++++++++++++++++++++++++++----------- 1 file changed, 39 insertions(+), 13 deletions(-) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 7febc02a2d..00536a1ec0 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1256,6 +1256,8 @@ def _shard_grid_shape(self) -> tuple[int, ...]: """ The shape of the shard grid for this array. + When no shards are present this will automatically fall back to the chunk grid. + Returns ------- tuple[int, ...] @@ -1287,10 +1289,12 @@ def _nshards(self) -> int: """ The number of shards in this array. + If no shards are present this will fall back to giving the number of chunks + Returns ------- int - The total number of shards in the array. + The total number of shards or if absent, chunks in the array. """ return product(self._shard_grid_shape) @@ -1418,6 +1422,8 @@ def _iter_shard_coords( """ Create an iterator over the coordinates of shards in shard grid space. + This will fall back to chunk grid space in case no shards are present. + Note that If the `origin` keyword is used, iteration will start at the shard index specified by `origin`. @@ -1436,7 +1442,7 @@ def _iter_shard_coords( Yields ------ chunk_coords: tuple[int, ...] - The coordinates of each shard in the selection. + The coordinates of each shard in the selection or chunk in case of no shard being present. """ return _iter_shard_coords( array=self, @@ -1450,6 +1456,9 @@ def _iter_shard_keys( """ Iterate over the keys of the stored objects supporting this array. + Although only stored objects, e.g. shards should have keys, in case no + shards are present this automatically falls back to chunks. + Parameters ---------- origin : Sequence[int] | None, default=None @@ -1460,7 +1469,8 @@ def _iter_shard_keys( Yields ------ key: str - The storage key of each chunk in the selection. + The storage key of each shard in the selection or in case of no shard + present of each chunk although the latter case as technically incorrect. """ # Iterate over the coordinates of chunks in chunk grid space. return _iter_shard_keys( @@ -1499,6 +1509,8 @@ def _iter_shard_regions( """ Iterate over the regions spanned by each shard. + This will automatically fall back to chunks if no shards are present. + Parameters ---------- origin : Sequence[int] | None, default=None @@ -1509,7 +1521,8 @@ def _iter_shard_regions( Yields ------ region: tuple[slice, ...] - A tuple of slice objects representing the region spanned by each shard in the selection. + A tuple of slice objects representing the region spanned by each shard in the selection or chunk in the + absence of shards. """ return _iter_shard_regions(array=self, origin=origin, selection_shape=selection_shape) @@ -2591,6 +2604,9 @@ def _iter_shard_keys( Iterate over the storage keys of each shard, relative to an optional origin, and optionally limited to a contiguous region in chunk grid coordinates. + If no shards are present this falls back to chunks, though in this case these are then actually + not storage keys. + Parameters ---------- origin : Sequence[int] | None, default=None @@ -2601,7 +2617,8 @@ def _iter_shard_keys( Yields ------ str - The storage key of each shard in the selection. + The storage key of each shard in the selection or chunk though chunks technically do not have + storage keys. """ return self.async_array._iter_shard_keys(origin=origin, selection_shape=selection_shape) @@ -2681,7 +2698,7 @@ def _iter_shard_regions( self, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None ) -> Iterator[tuple[slice, ...]]: """ - Iterate over the regions spanned by each shard. + Iterate over the regions spanned by each shard or chunk if no shard is present. Parameters ---------- @@ -2693,7 +2710,8 @@ def _iter_shard_regions( Yields ------ tuple[slice, ...] - A tuple of slice objects representing the region spanned by each chunk in the selection. + A tuple of slice objects representing the region spanned by each shard or if no shard is present, + chunk in the selection. """ return self.async_array._iter_shard_regions(origin=origin, selection_shape=selection_shape) @@ -4226,7 +4244,9 @@ async def _shards_initialized( array: AnyAsyncArray, ) -> tuple[str, ...]: """ - Return the keys of the chunks that have been persisted to the storage backend. + Return the keys of the shards that have been persisted to the storage backend. + + This will fall back to chunks in case no shards are present. Parameters ---------- @@ -4236,7 +4256,7 @@ async def _shards_initialized( Returns ------- chunks_initialized : tuple[str, ...] - The keys of the chunks that have been initialized. + The keys of the shards or if these are not present, chunks that have been initialized. Related ------- @@ -5381,6 +5401,8 @@ def _iter_shard_coords( If the `selection_shape` keyword is used, iteration will be bounded over a contiguous region ranging from `[origin, origin selection_shape]`, where the upper bound is exclusive as per python indexing conventions. + If no shards are present this will iterate over the coordinates of chunks in chunk grid space + instead. Parameters ---------- @@ -5394,7 +5416,7 @@ def _iter_shard_coords( Yields ------ chunk_coords: tuple[int, ...] - The coordinates of each shard in the selection. + The coordinates of each shard in the selection or chunks if no shards are present. """ return _iter_grid(array._shard_grid_shape, origin=origin, selection_shape=selection_shape) @@ -5409,6 +5431,8 @@ def _iter_shard_keys( Iterate over the storage keys of each shard, relative to an optional origin, and optionally limited to a contiguous region in shard grid coordinates. + This automatically falls back to chunks when no shards are present. + Parameters ---------- array : Array | AsyncArray @@ -5421,7 +5445,7 @@ def _iter_shard_keys( Yields ------ key: str - The storage key of each chunk in the selection. + The storage key of each shard in the selection or chunk when no shards are present. """ # Iterate over the coordinates of chunks in chunk grid space. _iter = _iter_grid(array._shard_grid_shape, origin=origin, selection_shape=selection_shape) @@ -5437,7 +5461,8 @@ def _iter_shard_regions( """ Iterate over the regions spanned by each shard. - These are the smallest regions of the array that are safe to write concurrently. + These are the smallest regions of the array that are safe to write concurrently. When + no shards are present this will fall back to chunks. Parameters ---------- @@ -5451,7 +5476,8 @@ def _iter_shard_regions( Yields ------ region: tuple[slice, ...] - A tuple of slice objects representing the region spanned by each shard in the selection. + A tuple of slice objects representing the region spanned by each shard in the selection or chunk + when no shards are present. """ if array.shards is None: shard_shape = array.chunks From 87d2041b2cd52639d7d64d4711b700e921403a63 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 8 Jan 2026 12:56:12 -0500 Subject: [PATCH 176/468] Add experimental section to the API docs (#3642) Co-authored-by: Davis Bennett --- docs/api/zarr/experimental.md | 9 +++++++++ docs/user-guide/experimental.md | 17 ++++++++++------- mkdocs.yml | 1 + 3 files changed, 20 insertions(+), 7 deletions(-) create mode 100644 docs/api/zarr/experimental.md diff --git a/docs/api/zarr/experimental.md b/docs/api/zarr/experimental.md new file mode 100644 index 0000000000..60f1f987b5 --- /dev/null +++ b/docs/api/zarr/experimental.md @@ -0,0 +1,9 @@ +--- +title: experimental +--- + +Experimental functionality is not stable and may change or be removed at any point. + +## Classes + +::: zarr.experimental.cache_store diff --git a/docs/user-guide/experimental.md b/docs/user-guide/experimental.md index aead2dedab..eaa53a4622 100644 --- a/docs/user-guide/experimental.md +++ b/docs/user-guide/experimental.md @@ -4,7 +4,7 @@ This section contains documentation for experimental Zarr Python features. The f ## `CacheStore` -Zarr Python 3.1.4 adds `zarr.experimental.cache_store.CacheStore` provides a dual-store caching implementation +Zarr Python 3.1.4 adds [`zarr.experimental.cache_store.CacheStore`][] provides a dual-store caching implementation that can be wrapped around any Zarr store to improve performance for repeated data access. This is particularly useful when working with remote stores (e.g., S3, HTTP) where network latency can significantly impact data access speed. @@ -24,7 +24,7 @@ Because the `CacheStore` uses an ordinary Zarr `Store` object as the caching lay Creating a CacheStore requires both a source store and a cache store. The cache store can be any Store implementation, providing flexibility in cache persistence: -```python exec="true" session="experimental" source="above" result="ansi" +```python exec="true" session="experimental" source="above" import zarr from zarr.storage import LocalStore import numpy as np @@ -73,6 +73,7 @@ elapsed_nocache = time.time() - start # Cache provides speedup for repeated access speedup = elapsed_nocache / elapsed_cache +print(f"Speedup is {speedup}") ``` Cache effectiveness is particularly pronounced with repeated access to the same data chunks. @@ -84,7 +85,7 @@ The CacheStore can be configured with several parameters: **max_size**: Controls the maximum size of cached data in bytes -```python exec="true" session="experimental" source="above" result="ansi" +```python exec="true" session="experimental" source="above" # 256MB cache with size limit cache = CacheStore( store=source_store, @@ -102,7 +103,7 @@ cache = CacheStore( **max_age_seconds**: Controls time-based cache expiration -```python exec="true" session="experimental" source="above" result="ansi" +```python exec="true" session="experimental" source="above" # Cache expires after 1 hour cache = CacheStore( store=source_store, @@ -162,7 +163,7 @@ The `cache_info()` method returns a dictionary with detailed information about t The CacheStore provides methods for manual cache management: -```python exec="true" session="experimental" source="above" result="ansi" +```python exec="true" session="experimental" source="above" # Clear all cached data and tracking information import asyncio asyncio.run(cached_store.clear_cache()) @@ -192,7 +193,7 @@ and use any store type for the cache backend: ### Local Store with Memory Cache -```python exec="true" session="experimental-memory-cache" source="above" result="ansi" +```python exec="true" session="experimental-memory-cache" source="above" from zarr.storage import LocalStore, MemoryStore from zarr.experimental.cache_store import CacheStore from tempfile import mkdtemp @@ -209,7 +210,7 @@ cached_store = CacheStore( ### Memory Store with Persistent Cache -```python exec="true" session="experimental-local-cache" source="above" result="ansi" +```python exec="true" session="experimental-local-cache" source="above" from tempfile import mkdtemp from zarr.storage import MemoryStore, LocalStore from zarr.experimental.cache_store import CacheStore @@ -255,10 +256,12 @@ zarr_array[:] = np.random.random((100, 100)) start = time.time() data = zarr_array[20:30, 20:30] # First access (cache miss) first_access = time.time() - start +print(f"First access took {first_access}") start = time.time() data = zarr_array[20:30, 20:30] # Second access (cache hit) second_access = time.time() - start +print(f"Second access took {second_access}") # Check cache statistics info = cached_store.cache_info() diff --git a/mkdocs.yml b/mkdocs.yml index 9bc4957f5d..61872b6234 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -46,6 +46,7 @@ nav: - api/zarr/metadata.md - api/zarr/registry.md - api/zarr/storage.md + - api/zarr/experimental.md - ABC: - api/zarr/abc/index.md - api/zarr/abc/buffer.md From acdd892234dbb62833c5d57e59b94d180cd1115d Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 8 Jan 2026 13:07:06 -0500 Subject: [PATCH 177/468] Add instructions to contributing guide about executable docs (#3645) --- docs/contributing.md | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/docs/contributing.md b/docs/contributing.md index 7bfa6f6a18..7869a61276 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -173,6 +173,40 @@ Hatch can also be used to serve continuously updating version of the documentati hatch --env docs run serve ``` +#### Adding executable code blocks in the documentation + +Zarr uses [Markdown Exec](https://pawamoy.github.io/markdown-exec/usage/) to execute code blocks in Markdown files. Add `exec="on"` to a code block header for it to be executed when the docs are built. For example: + +````md +```python exec="on" +print("Hello world") +``` +```` + +Below are other useful options that can be added to the code block. See [Markdown Exec's documentation](https://pawamoy.github.io/markdown-exec/usage/#options-summary) for a full list: + + - `source="above"` makes sure the code within the code block is also rendered in the documentation (rather than just the output). + - `session=""` executes code blocks in a named session reusing previously defined variables. + - `result="ansi"` or `result="html"` to render the output. If the code does not produce output, you should leave off the `result` option to prevent an empty cell from rendering in the docs. + +For example: + +````md +```python exec="true" session="contributing" source="above" result="ansi" +print("Hello world") +``` +```` + +renders as: + +```python exec="true" session="contributing" source="above" result="ansi" +print("Hello world") +``` + +#### Building documentation without executing code blocks + +Sometimes, you may want the documentation to build quicker. You can disable code block execution by commenting out the [markdown-exec](https://github.com/zarr-developers/zarr-python/blob/884a8c91afcc3efe28b3da952be3b85125c453cb/mkdocs.yml#L132 plugin in the mkdocs configuration file). This will make code blocks and cross references render incorrectly (i.e., expect build warnings), but also reduces build time by ~3x. Be sure to undo the commenting out before opening your pull request. + ### Changelog zarr-python uses [towncrier](https://towncrier.readthedocs.io/en/stable/tutorial.html) to manage release notes. Most pull requests should include at least one news fragment describing the changes. To add a release note, you'll need the GitHub issue or pull request number and the type of your change (`feature`, `bugfix`, `doc`, `removal`, `misc`). With that, run `towncrier create` with your development environment, which will prompt you for the issue number, change type, and the news text: From e67935a5a708e60fd9f8a595ff38479bebe50505 Mon Sep 17 00:00:00 2001 From: Mathieu Scheltienne Date: Mon, 12 Jan 2026 12:22:04 +0100 Subject: [PATCH 178/468] Fix deprecation of setting shape on a numpy array in 2.5+ (#3648) * fix deprecation * add changelog entry --- changes/3648.misc.md | 1 + src/zarr/codecs/vlen_utf8.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 changes/3648.misc.md diff --git a/changes/3648.misc.md b/changes/3648.misc.md new file mode 100644 index 0000000000..156f8671de --- /dev/null +++ b/changes/3648.misc.md @@ -0,0 +1 @@ +Fix deprecation of setting a shape on an array directly in ``numpy`` 2.5+. diff --git a/src/zarr/codecs/vlen_utf8.py b/src/zarr/codecs/vlen_utf8.py index fa1a229855..d8e6072333 100644 --- a/src/zarr/codecs/vlen_utf8.py +++ b/src/zarr/codecs/vlen_utf8.py @@ -50,7 +50,7 @@ async def _decode_single( raw_bytes = chunk_bytes.as_array_like() decoded = _vlen_utf8_codec.decode(raw_bytes) assert decoded.dtype == np.object_ - decoded.shape = chunk_spec.shape + decoded = decoded.reshape(chunk_spec.shape) as_string_dtype = decoded.astype(chunk_spec.dtype.to_native_dtype(), copy=False) return chunk_spec.prototype.nd_buffer.from_numpy_array(as_string_dtype) @@ -95,7 +95,7 @@ async def _decode_single( raw_bytes = chunk_bytes.as_array_like() decoded = _vlen_bytes_codec.decode(raw_bytes) assert decoded.dtype == np.object_ - decoded.shape = chunk_spec.shape + decoded = decoded.reshape(chunk_spec.shape) return chunk_spec.prototype.nd_buffer.from_numpy_array(decoded) async def _encode_single( From 7166a8dbdfb2b017f2ff2fe69ee5f2ead24a756a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Jan 2026 13:54:23 +0100 Subject: [PATCH 179/468] Bump astral-sh/setup-uv from 7.1.6 to 7.2.0 in the actions group (#3646) Bumps the actions group with 1 update: [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv). Updates `astral-sh/setup-uv` from 7.1.6 to 7.2.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/681c641aba71e4a1c380be3ab5e12ad51f415867...61cb8a9741eeb8a550a1b8544337180c0fc8476b) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 7.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/check_changelogs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 297b414967..7b05c364da 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -12,7 +12,7 @@ jobs: - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0 - name: Install uv - uses: astral-sh/setup-uv@681c641aba71e4a1c380be3ab5e12ad51f415867 # v7.1.6 + uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py From 1c05c1a10b68ce990374083e8db989357372dff9 Mon Sep 17 00:00:00 2001 From: Mathieu Scheltienne Date: Mon, 12 Jan 2026 17:57:30 +0100 Subject: [PATCH 180/468] Set copy=False in reshape operation (#3649) * set copy=False in reshape operation * add compat reshape with conditional * fix docstring * fix mypy * remove tuple unpacking which makes it more readable --- src/zarr/_compat.py | 42 +++++++++++++++++++++++++++++++++++- src/zarr/codecs/vlen_utf8.py | 5 +++-- 2 files changed, 44 insertions(+), 3 deletions(-) diff --git a/src/zarr/_compat.py b/src/zarr/_compat.py index 87427b486e..ae973d6292 100644 --- a/src/zarr/_compat.py +++ b/src/zarr/_compat.py @@ -2,10 +2,16 @@ from collections.abc import Callable from functools import wraps from inspect import Parameter, signature -from typing import Any, TypeVar +from typing import TYPE_CHECKING, Any, TypeVar + +import numpy as np +from packaging.version import Version from zarr.errors import ZarrFutureWarning +if TYPE_CHECKING: + from numpy.typing import NDArray + T = TypeVar("T") # Based off https://github.com/scikit-learn/scikit-learn/blob/e87b32a81c70abed8f2e97483758eb64df8255e9/sklearn/utils/validation.py#L63 @@ -68,3 +74,37 @@ def inner_f(*args: Any, **kwargs: Any) -> T: return _inner_deprecate_positional_args(func) return _inner_deprecate_positional_args # type: ignore[return-value] + + +def _reshape_view(arr: "NDArray[Any]", shape: tuple[int, ...]) -> "NDArray[Any]": + """Reshape an array without copying data. + + This function provides compatibility across NumPy versions for reshaping arrays + as views. On NumPy >= 2.1, it uses ``reshape(copy=False)`` which explicitly + fails if a view cannot be created. On older versions, it uses direct shape + assignment which has the same behavior but is deprecated in 2.5+. + + Parameters + ---------- + arr : NDArray + The array to reshape. + shape : tuple of int + The new shape. + + Returns + ------- + NDArray + A reshaped view of the array. + + Raises + ------ + AttributeError + If a view cannot be created (the array is not contiguous) on NumPy < 2.1. + ValueError + If a view cannot be created (the array is not contiguous) on NumPy >= 2.1. + """ + if Version(np.__version__) >= Version("2.1"): + return arr.reshape(shape, copy=False) # type: ignore[call-overload, no-any-return] + else: + arr.shape = shape + return arr diff --git a/src/zarr/codecs/vlen_utf8.py b/src/zarr/codecs/vlen_utf8.py index d8e6072333..fb1fb76126 100644 --- a/src/zarr/codecs/vlen_utf8.py +++ b/src/zarr/codecs/vlen_utf8.py @@ -6,6 +6,7 @@ import numpy as np from numcodecs.vlen import VLenBytes, VLenUTF8 +from zarr._compat import _reshape_view from zarr.abc.codec import ArrayBytesCodec from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import JSON, parse_named_configuration @@ -50,7 +51,7 @@ async def _decode_single( raw_bytes = chunk_bytes.as_array_like() decoded = _vlen_utf8_codec.decode(raw_bytes) assert decoded.dtype == np.object_ - decoded = decoded.reshape(chunk_spec.shape) + decoded = _reshape_view(decoded, chunk_spec.shape) as_string_dtype = decoded.astype(chunk_spec.dtype.to_native_dtype(), copy=False) return chunk_spec.prototype.nd_buffer.from_numpy_array(as_string_dtype) @@ -95,7 +96,7 @@ async def _decode_single( raw_bytes = chunk_bytes.as_array_like() decoded = _vlen_bytes_codec.decode(raw_bytes) assert decoded.dtype == np.object_ - decoded = decoded.reshape(chunk_spec.shape) + decoded = _reshape_view(decoded, chunk_spec.shape) return chunk_spec.prototype.nd_buffer.from_numpy_array(decoded) async def _encode_single( From c7b166e06fca4b055c3736e3d6403e4e1abf2dd3 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 15 Jan 2026 10:40:48 +0100 Subject: [PATCH 181/468] Bump mimimum supported version of numpy (#3636) * Bump mimimum supported version of numpy * Update changelog entry filename --------- Co-authored-by: Davis Bennett --- .github/workflows/test.yml | 6 +++--- changes/3636.misc.md | 1 + docs/user-guide/installation.md | 2 +- pyproject.toml | 8 ++++---- 4 files changed, 9 insertions(+), 8 deletions(-) create mode 100644 changes/3636.misc.md diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d528907868..d5cb568288 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -21,12 +21,12 @@ jobs: strategy: matrix: python-version: ['3.11', '3.12', '3.13'] - numpy-version: ['1.26', '2.2'] + numpy-version: ['2.0', '2.2'] dependency-set: ["minimal", "optional"] os: ["ubuntu-latest"] include: - python-version: '3.11' - numpy-version: '1.26' + numpy-version: '2.0' dependency-set: 'optional' os: 'macos-latest' - python-version: '3.13' @@ -34,7 +34,7 @@ jobs: dependency-set: 'optional' os: 'macos-latest' - python-version: '3.11' - numpy-version: '1.26' + numpy-version: '2.0' dependency-set: 'optional' os: 'windows-latest' - python-version: '3.13' diff --git a/changes/3636.misc.md b/changes/3636.misc.md new file mode 100644 index 0000000000..a814160c8b --- /dev/null +++ b/changes/3636.misc.md @@ -0,0 +1 @@ +The minimum required version of NumPy is now 2.0. diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md index 89c78804b2..4d323643f1 100644 --- a/docs/user-guide/installation.md +++ b/docs/user-guide/installation.md @@ -6,7 +6,7 @@ Required dependencies include: - [Python](https://docs.python.org/3/) (3.11 or later) - [packaging](https://packaging.pypa.io) (22.0 or later) -- [numpy](https://numpy.org) (1.26 or later) +- [numpy](https://numpy.org) (2.0 or later) - [numcodecs](https://numcodecs.readthedocs.io) (0.14 or later) - [google-crc32c](https://github.com/googleapis/python-crc32c) (1.5 or later) - [typing_extensions](https://typing-extensions.readthedocs.io) (4.9 or later) diff --git a/pyproject.toml b/pyproject.toml index a39956af5e..6f76259979 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ requires-python = ">=3.11" # If you add a new dependency here, please also add it to .pre-commit-config.yml dependencies = [ 'packaging>=22.0', - 'numpy>=1.26', + 'numpy>=2.0', 'numcodecs>=0.14', 'google-crc32c>=1.5', 'typing_extensions>=4.12', @@ -163,7 +163,7 @@ COV_CORE_DATAFILE = ".coverage.eager" [[tool.hatch.envs.test.matrix]] python = ["3.11", "3.12", "3.13"] -numpy = ["1.26", "2.2"] +numpy = ["2.0", "2.2"] deps = ["minimal", "optional"] [tool.hatch.envs.test.overrides] @@ -192,7 +192,7 @@ features = ["test", "gpu"] [[tool.hatch.envs.gputest.matrix]] python = ["3.11", "3.12", "3.13"] -numpy = ["1.26", "2.2"] +numpy = ["2.0", "2.2"] version = ["minimal"] [tool.hatch.envs.gputest.scripts] @@ -234,7 +234,7 @@ python = "3.11" dependencies = [ 'zarr[remote]', 'packaging==22.*', - 'numpy==1.26.*', + 'numpy==2.0.*', 'numcodecs==0.14.*', # 0.14 needed for zarr3 codecs 'fsspec==2023.10.0', 's3fs==2023.10.0', From 7eba7f16f95470cf6d73ca642ca2ebe7c45b1ca2 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 15 Jan 2026 11:01:16 +0100 Subject: [PATCH 182/468] add benchmarks using pytest-benchmark and codspeed (#3562) * add benchmarks * remove failing zipstore * don't do benchmarking in default pytest runs * changelog * codspeed workflow * lint * remove pedantic mode * only run benchmarks in one environment * use better string id for test params, make test data 1MB, and simplify params * move layout to an external file * get workloads to resemble recent sharding perf tests * test ids * tweak tests * tweak tests * fix typo * add slice indexing benchmarks * remove readme * add docs documentation * simplify pytest benchmark options * use --codspeed flag in benchmark ci * measure walltime in ci * Update .github/workflows/codspeed.yml Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Apply suggestion from @maxrjones Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * add --ignore option to main test and gpu test invocations * add comment * ignore codspeed warnings * update workflow --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- .github/workflows/codspeed.yml | 35 +++++++++++++ changes/3562.misc.md | 1 + docs/contributing.md | 11 ++++- pyproject.toml | 12 +++-- tests/benchmarks/__init__.py | 0 tests/benchmarks/common.py | 8 +++ tests/benchmarks/conftest.py | 15 ++++++ tests/benchmarks/test_e2e.py | 82 +++++++++++++++++++++++++++++++ tests/benchmarks/test_indexing.py | 43 ++++++++++++++++ 9 files changed, 203 insertions(+), 4 deletions(-) create mode 100644 .github/workflows/codspeed.yml create mode 100644 changes/3562.misc.md create mode 100644 tests/benchmarks/__init__.py create mode 100644 tests/benchmarks/common.py create mode 100644 tests/benchmarks/conftest.py create mode 100644 tests/benchmarks/test_e2e.py create mode 100644 tests/benchmarks/test_indexing.py diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml new file mode 100644 index 0000000000..6951d119e4 --- /dev/null +++ b/.github/workflows/codspeed.yml @@ -0,0 +1,35 @@ +name: CodSpeed Benchmarks + +on: + push: + branches: + - "main" + pull_request: + # `workflow_dispatch` allows CodSpeed to trigger backtest + # performance analysis in order to generate initial data. + workflow_dispatch: + +permissions: + contents: read + +jobs: + benchmarks: + name: Run benchmarks + runs-on: codspeed-macro + steps: + - uses: actions/checkout@v5 + with: + fetch-depth: 0 # grab all branches and tags + - name: Set up Python + uses: actions/setup-python@v6 + with: + python-version: "3.11" + - name: Install Hatch + run: | + python -m pip install --upgrade pip + pip install hatch + - name: Run the benchmarks + uses: CodSpeedHQ/action@v4 + with: + mode: walltime + run: hatch run test.py3.11-2.0-minimal:pytest tests/benchmarks --codspeed diff --git a/changes/3562.misc.md b/changes/3562.misc.md new file mode 100644 index 0000000000..e164ab39f8 --- /dev/null +++ b/changes/3562.misc.md @@ -0,0 +1 @@ +Add continuous performance benchmarking infrastructure. \ No newline at end of file diff --git a/docs/contributing.md b/docs/contributing.md index 7869a61276..3bbbcf6ea4 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -264,4 +264,13 @@ If an existing Zarr format version changes, or a new version of the Zarr format ## Release procedure Open an issue on GitHub announcing the release using the release checklist template: -[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md>). The release checklist includes all steps necessary for the release. \ No newline at end of file +[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md>). The release checklist includes all steps necessary for the release. + +## Benchmarks + +Zarr uses [pytest-benchmark](https://pytest-benchmark.readthedocs.io/en/latest/) for running +performance benchmarks as part of our test suite. The benchmarks can be are found in `tests/benchmarks`. +By default pytest is configured to run these benchmarks as plain tests (i.e., no benchmarking). To run +a benchmark with timing measurements, use the `--benchmark-enable` when invoking `pytest`. + +The benchmarks are run as part of the continuous integration suite through [codspeed](https://codspeed.io/zarr-developers/zarr-python). \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 6f76259979..bc0b97d3e0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -82,6 +82,8 @@ test = [ 'numpydoc', "hypothesis", "pytest-xdist", + "pytest-benchmark", + "pytest-codspeed", "packaging", "tomlkit", "uv", @@ -175,11 +177,12 @@ matrix.deps.dependencies = [ run-coverage = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy" run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report html" run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy" -run = "run-coverage --no-cov" +run = "run-coverage --no-cov --ignore tests/benchmarks" run-pytest = "run" run-verbose = "run-coverage --verbose" run-mypy = "mypy src" run-hypothesis = "run-coverage -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*" +run-benchmark = "pytest --benchmark-enable tests/benchmarks" list-env = "pip list" [tool.hatch.envs.gputest] @@ -196,7 +199,7 @@ numpy = ["2.0", "2.2"] version = ["minimal"] [tool.hatch.envs.gputest.scripts] -run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy" +run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks" run = "run-coverage --no-cov" run-verbose = "run-coverage --verbose" run-mypy = "mypy src" @@ -405,7 +408,10 @@ doctest_optionflags = [ "IGNORE_EXCEPTION_DETAIL", ] addopts = [ - "--durations=10", "-ra", "--strict-config", "--strict-markers", + "--benchmark-columns", "min,mean,stddev,outliers,rounds,iterations", + "--benchmark-disable", # benchmark routines run as tests without benchmarking instrumentation + "--durations", "10", + "-ra", "--strict-config", "--strict-markers", ] filterwarnings = [ "error", diff --git a/tests/benchmarks/__init__.py b/tests/benchmarks/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/benchmarks/common.py b/tests/benchmarks/common.py new file mode 100644 index 0000000000..e8809156a6 --- /dev/null +++ b/tests/benchmarks/common.py @@ -0,0 +1,8 @@ +from dataclasses import dataclass + + +@dataclass(kw_only=True, frozen=True) +class Layout: + shape: tuple[int, ...] + chunks: tuple[int, ...] + shards: tuple[int, ...] | None diff --git a/tests/benchmarks/conftest.py b/tests/benchmarks/conftest.py new file mode 100644 index 0000000000..be069d162d --- /dev/null +++ b/tests/benchmarks/conftest.py @@ -0,0 +1,15 @@ +"""Pytest configuration for benchmark tests.""" + +import pytest + +# Filter CodSpeed instrumentation warnings that can occur intermittently +# when registering benchmark results. This is a known issue with the +# CodSpeed walltime instrumentation hooks. +# See: https://github.com/CodSpeedHQ/pytest-codspeed + + +def pytest_configure(config: pytest.Config) -> None: + config.addinivalue_line( + "filterwarnings", + "ignore:Failed to set executed benchmark:RuntimeWarning", + ) diff --git a/tests/benchmarks/test_e2e.py b/tests/benchmarks/test_e2e.py new file mode 100644 index 0000000000..65d0e65ac9 --- /dev/null +++ b/tests/benchmarks/test_e2e.py @@ -0,0 +1,82 @@ +""" +Benchmarks for end-to-end read/write performance of Zarr +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING + +from tests.benchmarks.common import Layout + +if TYPE_CHECKING: + from pytest_benchmark.fixture import BenchmarkFixture + + from zarr.abc.store import Store + from zarr.core.common import NamedConfig +from operator import getitem, setitem +from typing import Any, Literal + +import pytest + +from zarr import create_array + +CompressorName = Literal["gzip"] | None + +compressors: dict[CompressorName, NamedConfig[Any, Any] | None] = { + None: None, + "gzip": {"name": "gzip", "configuration": {"level": 1}}, +} + + +layouts: tuple[Layout, ...] = ( + # No shards, just 1000 chunks + Layout(shape=(1_000_000,), chunks=(1000,), shards=None), + # 1:1 chunk:shard shape, should measure overhead of sharding + Layout(shape=(1_000_000,), chunks=(1000,), shards=(1000,)), + # One shard with all the chunks, should measure overhead of handling inner shard chunks + Layout(shape=(1_000_000,), chunks=(100,), shards=(10000 * 100,)), +) + + +@pytest.mark.parametrize("compression_name", [None, "gzip"]) +@pytest.mark.parametrize("layout", layouts, ids=str) +@pytest.mark.parametrize("store", ["memory", "local"], indirect=["store"]) +def test_write_array( + store: Store, layout: Layout, compression_name: CompressorName, benchmark: BenchmarkFixture +) -> None: + """ + Test the time required to fill an array with a single value + """ + arr = create_array( + store, + dtype="uint8", + shape=layout.shape, + chunks=layout.chunks, + shards=layout.shards, + compressors=compressors[compression_name], # type: ignore[arg-type] + fill_value=0, + ) + + benchmark(setitem, arr, Ellipsis, 1) + + +@pytest.mark.parametrize("compression_name", [None, "gzip"]) +@pytest.mark.parametrize("layout", layouts, ids=str) +@pytest.mark.parametrize("store", ["memory", "local"], indirect=["store"]) +def test_read_array( + store: Store, layout: Layout, compression_name: CompressorName, benchmark: BenchmarkFixture +) -> None: + """ + Test the time required to fill an array with a single value + """ + arr = create_array( + store, + dtype="uint8", + shape=layout.shape, + chunks=layout.chunks, + shards=layout.shards, + compressors=compressors[compression_name], # type: ignore[arg-type] + fill_value=0, + ) + arr[:] = 1 + benchmark(getitem, arr, Ellipsis) diff --git a/tests/benchmarks/test_indexing.py b/tests/benchmarks/test_indexing.py new file mode 100644 index 0000000000..1ad4f4b575 --- /dev/null +++ b/tests/benchmarks/test_indexing.py @@ -0,0 +1,43 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from pytest_benchmark.fixture import BenchmarkFixture + + from zarr.abc.store import Store + +from operator import getitem + +import pytest + +from zarr import create_array + +indexers = ( + (0,) * 3, + (slice(None),) * 3, + (slice(0, None, 4),) * 3, + (slice(10),) * 3, + (slice(10, -10, 4),) * 3, + (slice(None), slice(0, 3, 2), slice(0, 10)), +) + + +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("indexer", indexers, ids=str) +def test_slice_indexing( + store: Store, indexer: tuple[int | slice], benchmark: BenchmarkFixture +) -> None: + data = create_array( + store=store, + shape=(105,) * 3, + dtype="uint8", + chunks=(10,) * 3, + shards=None, + compressors=None, + filters=None, + fill_value=0, + ) + + data[:] = 1 + benchmark(getitem, data, indexer) From 4cddcf5c78137bb37b692e463afd7d4d526d353f Mon Sep 17 00:00:00 2001 From: David Stansby Date: Thu, 15 Jan 2026 19:39:04 +0100 Subject: [PATCH 183/468] Simplify testing of different numpy versions (#3654) --- .github/workflows/codspeed.yml | 2 +- .github/workflows/gpu_test.yml | 9 ++++----- .github/workflows/hypothesis.yaml | 7 +++---- .github/workflows/test.yml | 18 ++++++++---------- pyproject.toml | 6 ------ 5 files changed, 16 insertions(+), 26 deletions(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 6951d119e4..24d453280c 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,4 +32,4 @@ jobs: uses: CodSpeedHQ/action@v4 with: mode: walltime - run: hatch run test.py3.11-2.0-minimal:pytest tests/benchmarks --codspeed + run: hatch run test.py3.11-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index d81cd896b9..6011610681 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -19,13 +19,12 @@ concurrency: jobs: test: - name: py=${{ matrix.python-version }}, np=${{ matrix.numpy-version }}, deps=${{ matrix.dependency-set }} + name: py=${{ matrix.python-version }}, deps=${{ matrix.dependency-set }} runs-on: gpu-runner strategy: matrix: python-version: ['3.11'] - numpy-version: ['2.2'] dependency-set: ["minimal"] steps: @@ -61,11 +60,11 @@ jobs: pip install hatch - name: Set Up Hatch Env run: | - hatch env create gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} - hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env + hatch env create gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} + hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env - name: Run Tests run: | - hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage-gpu + hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-coverage-gpu - name: Upload coverage uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3 # v5.3.1 diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 96dbcaa6f6..abf7c5f4ce 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -24,7 +24,6 @@ jobs: strategy: matrix: python-version: ['3.12'] - numpy-version: ['2.2'] dependency-set: ["optional"] steps: @@ -47,8 +46,8 @@ jobs: pip install hatch - name: Set Up Hatch Env run: | - hatch env create test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} - hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env + hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} + hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache - name: Restore cached hypothesis directory id: restore-hypothesis-cache @@ -64,7 +63,7 @@ jobs: id: status run: | echo "Using Hypothesis profile: $HYPOTHESIS_PROFILE" - hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-hypothesis + hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-hypothesis # explicitly save the cache so it gets updated, also do this even if it fails. - name: Save cached hypothesis directory diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d5cb568288..15fe94d3f9 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -16,29 +16,27 @@ concurrency: jobs: test: - name: os=${{ matrix.os }}, py=${{ matrix.python-version }}, np=${{ matrix.numpy-version }}, deps=${{ matrix.dependency-set }} + name: os=${{ matrix.os }}, py=${{ matrix.python-version }}, deps=${{ matrix.dependency-set }} strategy: matrix: python-version: ['3.11', '3.12', '3.13'] - numpy-version: ['2.0', '2.2'] dependency-set: ["minimal", "optional"] os: ["ubuntu-latest"] include: - python-version: '3.11' - numpy-version: '2.0' dependency-set: 'optional' os: 'macos-latest' + - python-version: '3.13' - numpy-version: '2.2' dependency-set: 'optional' os: 'macos-latest' + - python-version: '3.11' - numpy-version: '2.0' dependency-set: 'optional' os: 'windows-latest' + - python-version: '3.13' - numpy-version: '2.2' dependency-set: 'optional' os: 'windows-latest' runs-on: ${{ matrix.os }} @@ -58,13 +56,13 @@ jobs: pip install hatch - name: Set Up Hatch Env run: | - hatch env create test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} - hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env + hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} + hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env - name: Run Tests env: HYPOTHESIS_PROFILE: ci run: | - hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage + hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-coverage - name: Upload coverage if: ${{ matrix.dependency-set == 'optional' && matrix.os == 'ubuntu-latest' }} uses: codecov/codecov-action@v5 @@ -152,4 +150,4 @@ jobs: contains(needs.*.result, 'cancelled') run: exit 1 - name: Success - run: echo Success! + run: echo Success! \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index bc0b97d3e0..4e9e16730a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -152,9 +152,6 @@ version.source = "vcs" hooks.vcs.version-file = "src/zarr/_version.py" [tool.hatch.envs.test] -dependencies = [ - "numpy~={matrix:numpy}", -] features = ["test"] [tool.hatch.envs.test.env-vars] @@ -165,7 +162,6 @@ COV_CORE_DATAFILE = ".coverage.eager" [[tool.hatch.envs.test.matrix]] python = ["3.11", "3.12", "3.13"] -numpy = ["2.0", "2.2"] deps = ["minimal", "optional"] [tool.hatch.envs.test.overrides] @@ -188,14 +184,12 @@ list-env = "pip list" [tool.hatch.envs.gputest] template = "test" dependencies = [ - "numpy~={matrix:numpy}", "universal_pathlib", ] features = ["test", "gpu"] [[tool.hatch.envs.gputest.matrix]] python = ["3.11", "3.12", "3.13"] -numpy = ["2.0", "2.2"] version = ["minimal"] [tool.hatch.envs.gputest.scripts] From e94504e92b231928ed375f4e740d49269ab23d8e Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 16 Jan 2026 12:10:03 +0100 Subject: [PATCH 184/468] Clean up test extra dependencies (#3656) * Clean up test extra dependencies * Add changelog * Put back uv in test deps Co-authored-by: Davis Bennett --------- Co-authored-by: Davis Bennett --- changes/3656.misc.md | 1 + pyproject.toml | 12 +++++++++--- 2 files changed, 10 insertions(+), 3 deletions(-) create mode 100644 changes/3656.misc.md diff --git a/changes/3656.misc.md b/changes/3656.misc.md new file mode 100644 index 0000000000..159f24d072 --- /dev/null +++ b/changes/3656.misc.md @@ -0,0 +1 @@ +Removed *rich* and *mypy* from the `[test]` dependencies, and added a new `[dev]` dependency group that can be used to install all the development dependencies. diff --git a/pyproject.toml b/pyproject.toml index 4e9e16730a..e09bab4cb9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,15 +70,13 @@ gpu = [ "cupy-cuda12x", ] cli = ["typer"] -# Development extras +# Testing extras test = [ "coverage>=7.10", "pytest", "pytest-asyncio", "pytest-cov", "pytest-accept", - "rich", - "mypy", 'numpydoc', "hypothesis", "pytest-xdist", @@ -116,6 +114,14 @@ docs = [ 'astroid<4', 'pytest' ] +# All development extras +dev = [ + "zarr[optional]", + "zarr[test]", + "zarr[remote_tests]", + "zarr[docs]", + "mypy", +] [project.scripts] zarr = "zarr._cli.cli:app" From c06923d3888b07c37d90c11a665be3ca11dbd949 Mon Sep 17 00:00:00 2001 From: "Christine P. Chai" Date: Mon, 19 Jan 2026 01:23:47 -0800 Subject: [PATCH 185/468] docs: Correct some typos in documentation (#3661) * docs: an python object -> a python object * docs: a XML -> an XML * docs: a S3 -> an S3 --- docs/contributing.md | 4 ++-- docs/user-guide/storage.md | 2 +- src/zarr/core/dtype/wrapper.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/contributing.md b/docs/contributing.md index 3bbbcf6ea4..e42ba0edf1 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -143,7 +143,7 @@ Zarr strives to maintain 100% test coverage under the latest Python stable relea hatch env run --env test.py3.12-2.2-optional run-coverage ``` -will automatically run the test suite with coverage and produce a XML coverage report. This should be 100% before code can be accepted into the main code base. +will automatically run the test suite with coverage and produce an XML coverage report. This should be 100% before code can be accepted into the main code base. You can also generate an HTML coverage report by running: @@ -273,4 +273,4 @@ performance benchmarks as part of our test suite. The benchmarks can be are foun By default pytest is configured to run these benchmarks as plain tests (i.e., no benchmarking). To run a benchmark with timing measurements, use the `--benchmark-enable` when invoking `pytest`. -The benchmarks are run as part of the continuous integration suite through [codspeed](https://codspeed.io/zarr-developers/zarr-python). \ No newline at end of file +The benchmarks are run as part of the continuous integration suite through [codspeed](https://codspeed.io/zarr-developers/zarr-python). diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index 2b200c27b9..82b576b889 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -138,7 +138,7 @@ print(group) ``` The type of filesystem (e.g. S3, https, etc..) is inferred from the scheme of the url (e.g. s3 for "**s3**://noaa-nwm-retro-v2-zarr-pds"). -In case a specific filesystem is needed, one can explicitly create it. For example to create a S3 filesystem: +In case a specific filesystem is needed, one can explicitly create it. For example to create an S3 filesystem: ```python exec="true" session="storage" source="above" result="ansi" # Note: requires s3fs to be installed diff --git a/src/zarr/core/dtype/wrapper.py b/src/zarr/core/dtype/wrapper.py index e44449585b..fdc5f747f0 100644 --- a/src/zarr/core/dtype/wrapper.py +++ b/src/zarr/core/dtype/wrapper.py @@ -191,7 +191,7 @@ def to_json(self, zarr_format: ZarrFormat) -> DTypeSpec_V2 | DTypeSpec_V3: @abstractmethod def _check_scalar(self, data: object) -> bool: """ - Check that an python object is a valid scalar value for the wrapped data type. + Check that a python object is a valid scalar value for the wrapped data type. Parameters ---------- From 68359bc30caa0d549ab18e36f3c92887c707372d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 20 Jan 2026 10:31:13 +0100 Subject: [PATCH 186/468] Bump actions/checkout from 5 to 6 in the actions group (#3659) Bumps the actions group with 1 update: [actions/checkout](https://github.com/actions/checkout). Updates `actions/checkout` from 5 to 6 - [Release notes](https://github.com/actions/checkout/releases) - [Commits](https://github.com/actions/checkout/compare/v5...v6) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/check_changelogs.yml | 2 +- .github/workflows/codspeed.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 7b05c364da..9b39233dd8 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0 + - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1 - name: Install uv uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0 diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 24d453280c..c9c2f7b4c1 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -17,7 +17,7 @@ jobs: name: Run benchmarks runs-on: codspeed-macro steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 with: fetch-depth: 0 # grab all branches and tags - name: Set up Python From 3fa19d237971baa6fadce176bdd93d88eb452e10 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 23 Jan 2026 15:28:14 +0100 Subject: [PATCH 187/468] chore/use prek (#3658) * bring back pre-commit ci * restore needs release notes * restore readme * add prek workflow * changelog * changelog content --- .github/workflows/lint.yml | 25 +++++++++++++++++++++++++ .pre-commit-config.yaml | 3 ++- changes/3658.misc.md | 1 + docs/contributing.md | 36 ++++++++++++++++++++++++++++++------ pyproject.toml | 3 ++- 5 files changed, 60 insertions(+), 8 deletions(-) create mode 100644 .github/workflows/lint.yml create mode 100644 changes/3658.misc.md diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000000..1c28f0b3d7 --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,25 @@ +name: Lint + +on: + push: + branches: [main, 3.1.x] + pull_request: + branches: [main, 3.1.x] + workflow_dispatch: + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + lint: + name: Lint + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + - name: Install uv + uses: astral-sh/setup-uv@v5 + - name: Install prek + run: uv tool install prek + - name: Run prek + run: prek run --all-files diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c4132530af..f85b500784 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,8 +1,9 @@ ci: autoupdate_commit_msg: "chore: update pre-commit hooks" autoupdate_schedule: "monthly" - autofix_commit_msg: "style: pre-commit fixes" autofix_prs: false + skip: [] # pre-commit.ci only checks for updates, prek runs hooks locally + default_stages: [pre-commit, pre-push] default_language_version: diff --git a/changes/3658.misc.md b/changes/3658.misc.md new file mode 100644 index 0000000000..f400d97473 --- /dev/null +++ b/changes/3658.misc.md @@ -0,0 +1 @@ +Switch from `pre-commit` to [`prek`](https://github.com/j178/prek) for pre-commit checks. \ No newline at end of file diff --git a/docs/contributing.md b/docs/contributing.md index e42ba0edf1..c330504536 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -109,26 +109,50 @@ All tests are automatically run via GitHub Actions for every pull request and mu > **Note:** Previous versions of Zarr-Python made extensive use of doctests. These tests were not maintained during the 3.0 refactor but may be brought back in the future. See issue #2614 for more details. -### Code standards - using pre-commit +### Code standards - using prek All code must conform to the PEP8 standard. Regarding line length, lines up to 100 characters are allowed, although please try to keep under 90 wherever possible. -`Zarr` uses a set of `pre-commit` hooks and the `pre-commit` bot to format, type-check, and prettify the codebase. `pre-commit` can be installed locally by running: +`Zarr` uses a set of git hooks managed by [`prek`](https://github.com/j178/prek), a fast, Rust-based pre-commit hook manager that is fully compatible with `.pre-commit-config.yaml` files. `prek` can be installed locally by running: ```bash -python -m pip install pre-commit +uv tool install prek +``` + +or: + +```bash +pip install prek ``` The hooks can be installed locally by running: ```bash -pre-commit install +prek install +``` + +This would run the checks every time a commit is created locally. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running: + +```bash +prek run --all-files +``` + +You can also run hooks only for files in a specific directory: + +```bash +prek run --directory src/zarr +``` + +Or run hooks for files changed in the last commit: + +```bash +prek run --last-commit ``` -This would run the checks every time a commit is created locally. These checks will also run on every commit pushed to an open PR, resulting in some automatic styling fixes by the `pre-commit` bot. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running: +To list all available hooks: ```bash -pre-commit run --all-files +prek list ``` If you would like to skip the failing checks and push the code for further discussion, use the `--no-verify` option with `git commit`. diff --git a/pyproject.toml b/pyproject.toml index e09bab4cb9..068caa1f0d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ maintainers = [ { name = "Deepak Cherian" } ] requires-python = ">=3.11" -# If you add a new dependency here, please also add it to .pre-commit-config.yml +# If you add a new dependency here, please also add it to .pre-commit-config.yaml dependencies = [ 'packaging>=22.0', 'numpy>=2.0', @@ -428,6 +428,7 @@ markers = [ ignore = [ "PC111", # fix Python code in documentation - enable later "PC180", # for JavaScript - not interested + "PC902", # pre-commit.ci custom autofix message - not using autofix ] [tool.numpydoc_validation] From b30ae18c36a24b4ed79da7d40905d205ab70e3ec Mon Sep 17 00:00:00 2001 From: Alden Keefe Sampson Date: Sun, 25 Jan 2026 11:36:51 -0500 Subject: [PATCH 188/468] Add benchmarks for sharded + local store indexing (#3663) * Add benchmarks for sharded + local store indexing Parameterize with shards and no shards. Parameterize with local + memory store to have an example of a store which has some modest latency. * use latencystore with 10ms get latency instead of localstore * use .01s of latency * set get latency to .0001s --------- Co-authored-by: Davis Bennett --- tests/benchmarks/test_indexing.py | 15 ++++++++++++--- tests/conftest.py | 7 +++++-- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/tests/benchmarks/test_indexing.py b/tests/benchmarks/test_indexing.py index 1ad4f4b575..9ca0d8e1af 100644 --- a/tests/benchmarks/test_indexing.py +++ b/tests/benchmarks/test_indexing.py @@ -22,18 +22,27 @@ (slice(None), slice(0, 3, 2), slice(0, 10)), ) +shards = ( + None, + (50,) * 3, +) + -@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("store", ["memory", "memory_get_latency"], indirect=["store"]) @pytest.mark.parametrize("indexer", indexers, ids=str) +@pytest.mark.parametrize("shards", shards, ids=str) def test_slice_indexing( - store: Store, indexer: tuple[int | slice], benchmark: BenchmarkFixture + store: Store, + indexer: tuple[int | slice], + shards: tuple[int, ...] | None, + benchmark: BenchmarkFixture, ) -> None: data = create_array( store=store, shape=(105,) * 3, dtype="uint8", chunks=(10,) * 3, - shards=None, + shards=shards, compressors=None, filters=None, fill_value=0, diff --git a/tests/conftest.py b/tests/conftest.py index 63c8950cff..23a1e87d0a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -40,6 +40,7 @@ from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import sync from zarr.storage import FsspecStore, LocalStore, MemoryStore, StorePath, ZipStore +from zarr.testing.store import LatencyStore if TYPE_CHECKING: from collections.abc import Generator @@ -58,8 +59,8 @@ async def parse_store( - store: Literal["local", "memory", "fsspec", "zip"], path: str -) -> LocalStore | MemoryStore | FsspecStore | ZipStore: + store: Literal["local", "memory", "fsspec", "zip", "memory_get_latency"], path: str +) -> LocalStore | MemoryStore | FsspecStore | ZipStore | LatencyStore: if store == "local": return await LocalStore.open(path) if store == "memory": @@ -68,6 +69,8 @@ async def parse_store( return await FsspecStore.open(url=path) if store == "zip": return await ZipStore.open(path + "/zarr.zip", mode="w") + if store == "memory_get_latency": + return LatencyStore(MemoryStore(), get_latency=0.0001, set_latency=0) raise AssertionError From 0e61449904c42b1f1efcf11c153a39c8c620a3c1 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 26 Jan 2026 09:52:47 +0100 Subject: [PATCH 189/468] Add methods for getting bytes + json to store abc (#3638) * add store routines for getting bytes and json * check for FileNotFoundError when a key is missing * remove storepath methods * changelog * rename methods * continue renaming / test refactoring * refactor new test functions * make new methods private * remove changelog entry for private API --- src/zarr/abc/store.py | 212 ++++++++++++++++++++++++++++- src/zarr/storage/_local.py | 232 +++++++++++++++++++++++++++++++- src/zarr/storage/_memory.py | 232 +++++++++++++++++++++++++++++++- src/zarr/testing/store.py | 43 +++++- tests/test_store/test_local.py | 54 ++++++++ tests/test_store/test_memory.py | 51 +++++++ 6 files changed, 819 insertions(+), 5 deletions(-) diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 4b3edf78d1..87df89a683 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -1,11 +1,14 @@ from __future__ import annotations +import asyncio +import json from abc import ABC, abstractmethod -from asyncio import gather from dataclasses import dataclass from itertools import starmap from typing import TYPE_CHECKING, Literal, Protocol, runtime_checkable +from zarr.core.sync import sync + if TYPE_CHECKING: from collections.abc import AsyncGenerator, AsyncIterator, Iterable from types import TracebackType @@ -206,6 +209,211 @@ async def get( """ ... + async def _get_bytes( + self, key: str, *, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> bytes: + """ + Retrieve raw bytes from the store asynchronously. + + This is a convenience method that wraps ``get()`` and converts the result + to bytes. Use this when you need the raw byte content of a stored value. + + Parameters + ---------- + key : str + The key identifying the data to retrieve. + prototype : BufferPrototype + The buffer prototype to use for reading the data. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. + + Returns + ------- + bytes + The raw bytes stored at the given key. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + + See Also + -------- + get : Lower-level method that returns a Buffer object. + get_bytes : Synchronous version of this method. + get_json : Asynchronous method for retrieving and parsing JSON data. + + Examples + -------- + >>> store = await MemoryStore.open() + >>> await store.set("data", Buffer.from_bytes(b"hello world")) + >>> data = await store.get_bytes("data", prototype=default_buffer_prototype()) + >>> print(data) + b'hello world' + """ + buffer = await self.get(key, prototype, byte_range) + if buffer is None: + raise FileNotFoundError(key) + return buffer.to_bytes() + + def _get_bytes_sync( + self, key: str = "", *, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> bytes: + """ + Retrieve raw bytes from the store synchronously. + + This is a synchronous wrapper around ``get_bytes()``. It should only + be called from non-async code. For async contexts, use ``get_bytes()`` + instead. + + Parameters + ---------- + key : str, optional + The key identifying the data to retrieve. Defaults to an empty string. + prototype : BufferPrototype + The buffer prototype to use for reading the data. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. + + Returns + ------- + bytes + The raw bytes stored at the given key. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + + Warnings + -------- + Do not call this method from async functions. Use ``get_bytes()`` instead + to avoid blocking the event loop. + + See Also + -------- + get_bytes : Asynchronous version of this method. + get_json_sync : Synchronous method for retrieving and parsing JSON data. + + Examples + -------- + >>> store = MemoryStore() + >>> await store.set("data", Buffer.from_bytes(b"hello world")) + >>> data = store.get_bytes_sync("data", prototype=default_buffer_prototype()) + >>> print(data) + b'hello world' + """ + + return sync(self._get_bytes(key, prototype=prototype, byte_range=byte_range)) + + async def _get_json( + self, key: str, *, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Any: + """ + Retrieve and parse JSON data from the store asynchronously. + + This is a convenience method that retrieves bytes from the store and + parses them as JSON. + + Parameters + ---------- + key : str + The key identifying the JSON data to retrieve. + prototype : BufferPrototype + The buffer prototype to use for reading the data. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. + Note: Using byte ranges with JSON may result in invalid JSON. + + Returns + ------- + Any + The parsed JSON data. This follows the behavior of ``json.loads()`` and + can be any JSON-serializable type: dict, list, str, int, float, bool, or None. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + json.JSONDecodeError + If the stored data is not valid JSON. + + See Also + -------- + get_bytes : Method for retrieving raw bytes. + get_json_sync : Synchronous version of this method. + + Examples + -------- + >>> store = await MemoryStore.open() + >>> metadata = {"zarr_format": 3, "node_type": "array"} + >>> await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> data = await store.get_json("zarr.json", prototype=default_buffer_prototype()) + >>> print(data) + {'zarr_format': 3, 'node_type': 'array'} + """ + + return json.loads(await self._get_bytes(key, prototype=prototype, byte_range=byte_range)) + + def _get_json_sync( + self, key: str = "", *, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Any: + """ + Retrieve and parse JSON data from the store synchronously. + + This is a synchronous wrapper around ``get_json()``. It should only + be called from non-async code. For async contexts, use ``get_json()`` + instead. + + Parameters + ---------- + key : str, optional + The key identifying the JSON data to retrieve. Defaults to an empty string. + prototype : BufferPrototype + The buffer prototype to use for reading the data. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. + Note: Using byte ranges with JSON may result in invalid JSON. + + Returns + ------- + Any + The parsed JSON data. This follows the behavior of ``json.loads()`` and + can be any JSON-serializable type: dict, list, str, int, float, bool, or None. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + json.JSONDecodeError + If the stored data is not valid JSON. + + Warnings + -------- + Do not call this method from async functions. Use ``get_json()`` instead + to avoid blocking the event loop. + + See Also + -------- + get_json : Asynchronous version of this method. + get_bytes_sync : Synchronous method for retrieving raw bytes without parsing. + + Examples + -------- + >>> store = MemoryStore() + >>> metadata = {"zarr_format": 3, "node_type": "array"} + >>> store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> data = store.get_json_sync("zarr.json", prototype=default_buffer_prototype()) + >>> print(data) + {'zarr_format': 3, 'node_type': 'array'} + """ + + return sync(self._get_json(key, prototype=prototype, byte_range=byte_range)) + @abstractmethod async def get_partial_values( self, @@ -278,7 +486,7 @@ async def _set_many(self, values: Iterable[tuple[str, Buffer]]) -> None: """ Insert multiple (key, value) pairs into storage. """ - await gather(*starmap(self.set, values)) + await asyncio.gather(*starmap(self.set, values)) @property def supports_consolidated_metadata(self) -> bool: diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index f64da71bb4..80233a112d 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -8,7 +8,7 @@ import sys import uuid from pathlib import Path -from typing import TYPE_CHECKING, BinaryIO, Literal, Self +from typing import TYPE_CHECKING, Any, BinaryIO, Literal, Self from zarr.abc.store import ( ByteRequest, @@ -306,6 +306,236 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: except (FileNotFoundError, NotADirectoryError): pass + async def _get_bytes( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> bytes: + """ + Retrieve raw bytes from the local store asynchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + + Returns + ------- + bytes + The raw bytes stored at the given key. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + + See Also + -------- + Store.get_bytes : Base implementation with full documentation. + get_bytes_sync : Synchronous version of this method. + + Examples + -------- + >>> store = await LocalStore.open("data") + >>> await store.set("data", Buffer.from_bytes(b"hello")) + >>> # No need to specify prototype for LocalStore + >>> data = await store.get_bytes("data") + >>> print(data) + b'hello' + """ + if prototype is None: + prototype = default_buffer_prototype() + return await super()._get_bytes(key, prototype=prototype, byte_range=byte_range) + + def _get_bytes_sync( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> bytes: + """ + Retrieve raw bytes from the local store synchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + + Returns + ------- + bytes + The raw bytes stored at the given key. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + + Warnings + -------- + Do not call this method from async functions. Use ``get_bytes()`` instead. + + See Also + -------- + Store.get_bytes_sync : Base implementation with full documentation. + get_bytes : Asynchronous version of this method. + + Examples + -------- + >>> store = LocalStore("data") + >>> store.set("data", Buffer.from_bytes(b"hello")) + >>> # No need to specify prototype for LocalStore + >>> data = store.get_bytes("data") + >>> print(data) + b'hello' + """ + if prototype is None: + prototype = default_buffer_prototype() + return super()._get_bytes_sync(key, prototype=prototype, byte_range=byte_range) + + async def _get_json( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Any: + """ + Retrieve and parse JSON data from the local store asynchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_json`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the JSON data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Note: Using byte ranges with JSON may result in invalid JSON. + + Returns + ------- + Any + The parsed JSON data. This follows the behavior of ``json.loads()`` and + can be any JSON-serializable type: dict, list, str, int, float, bool, or None. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + json.JSONDecodeError + If the stored data is not valid JSON. + + See Also + -------- + Store.get_json : Base implementation with full documentation. + get_json_sync : Synchronous version of this method. + get_bytes : Method for retrieving raw bytes without parsing. + + Examples + -------- + >>> store = await LocalStore.open("data") + >>> import json + >>> metadata = {"zarr_format": 3, "node_type": "array"} + >>> await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> # No need to specify prototype for LocalStore + >>> data = await store.get_json("zarr.json") + >>> print(data) + {'zarr_format': 3, 'node_type': 'array'} + """ + if prototype is None: + prototype = default_buffer_prototype() + return await super()._get_json(key, prototype=prototype, byte_range=byte_range) + + def _get_json_sync( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Any: + """ + Retrieve and parse JSON data from the local store synchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_json`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the JSON data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Note: Using byte ranges with JSON may result in invalid JSON. + + Returns + ------- + Any + The parsed JSON data. This follows the behavior of ``json.loads()`` and + can be any JSON-serializable type: dict, list, str, int, float, bool, or None. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + json.JSONDecodeError + If the stored data is not valid JSON. + + Warnings + -------- + Do not call this method from async functions. Use ``get_json()`` instead. + + See Also + -------- + Store.get_json_sync : Base implementation with full documentation. + get_json : Asynchronous version of this method. + get_bytes_sync : Method for retrieving raw bytes without parsing. + + Examples + -------- + >>> store = LocalStore("data") + >>> import json + >>> metadata = {"zarr_format": 3, "node_type": "array"} + >>> store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> # No need to specify prototype for LocalStore + >>> data = store.get_json("zarr.json") + >>> print(data) + {'zarr_format': 3, 'node_type': 'array'} + """ + if prototype is None: + prototype = default_buffer_prototype() + return super()._get_json_sync(key, prototype=prototype, byte_range=byte_range) + async def move(self, dest_root: Path | str) -> None: """ Move the store to another path. The old root directory is deleted. diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index 904be922d7..e6f9b7a512 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -1,7 +1,7 @@ from __future__ import annotations from logging import getLogger -from typing import TYPE_CHECKING, Self +from typing import TYPE_CHECKING, Any, Self from zarr.abc.store import ByteRequest, Store from zarr.core.buffer import Buffer, gpu @@ -175,6 +175,236 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: for key in keys_unique: yield key + async def _get_bytes( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> bytes: + """ + Retrieve raw bytes from the memory store asynchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + + Returns + ------- + bytes + The raw bytes stored at the given key. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + + See Also + -------- + Store.get_bytes : Base implementation with full documentation. + get_bytes_sync : Synchronous version of this method. + + Examples + -------- + >>> store = await MemoryStore.open() + >>> await store.set("data", Buffer.from_bytes(b"hello")) + >>> # No need to specify prototype for MemoryStore + >>> data = await store.get_bytes("data") + >>> print(data) + b'hello' + """ + if prototype is None: + prototype = default_buffer_prototype() + return await super()._get_bytes(key, prototype=prototype, byte_range=byte_range) + + def _get_bytes_sync( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> bytes: + """ + Retrieve raw bytes from the memory store synchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + + Returns + ------- + bytes + The raw bytes stored at the given key. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + + Warnings + -------- + Do not call this method from async functions. Use ``get_bytes()`` instead. + + See Also + -------- + Store.get_bytes_sync : Base implementation with full documentation. + get_bytes : Asynchronous version of this method. + + Examples + -------- + >>> store = MemoryStore() + >>> store.set("data", Buffer.from_bytes(b"hello")) + >>> # No need to specify prototype for MemoryStore + >>> data = store.get_bytes("data") + >>> print(data) + b'hello' + """ + if prototype is None: + prototype = default_buffer_prototype() + return super()._get_bytes_sync(key, prototype=prototype, byte_range=byte_range) + + async def _get_json( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Any: + """ + Retrieve and parse JSON data from the memory store asynchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_json`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the JSON data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Note: Using byte ranges with JSON may result in invalid JSON. + + Returns + ------- + Any + The parsed JSON data. This follows the behavior of ``json.loads()`` and + can be any JSON-serializable type: dict, list, str, int, float, bool, or None. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + json.JSONDecodeError + If the stored data is not valid JSON. + + See Also + -------- + Store.get_json : Base implementation with full documentation. + get_json_sync : Synchronous version of this method. + get_bytes : Method for retrieving raw bytes without parsing. + + Examples + -------- + >>> store = await MemoryStore.open() + >>> import json + >>> metadata = {"zarr_format": 3, "node_type": "array"} + >>> await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> # No need to specify prototype for MemoryStore + >>> data = await store.get_json("zarr.json") + >>> print(data) + {'zarr_format': 3, 'node_type': 'array'} + """ + if prototype is None: + prototype = default_buffer_prototype() + return await super()._get_json(key, prototype=prototype, byte_range=byte_range) + + def _get_json_sync( + self, + key: str = "", + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Any: + """ + Retrieve and parse JSON data from the memory store synchronously. + + This is a convenience override that makes the ``prototype`` parameter optional + by defaulting to the standard buffer prototype. See the base ``Store.get_json`` + for full documentation. + + Parameters + ---------- + key : str, optional + The key identifying the JSON data to retrieve. Defaults to an empty string. + prototype : BufferPrototype, optional + The buffer prototype to use for reading the data. If None, uses + ``default_buffer_prototype()``. + byte_range : ByteRequest, optional + If specified, only retrieve a portion of the stored data. + Note: Using byte ranges with JSON may result in invalid JSON. + + Returns + ------- + Any + The parsed JSON data. This follows the behavior of ``json.loads()`` and + can be any JSON-serializable type: dict, list, str, int, float, bool, or None. + + Raises + ------ + FileNotFoundError + If the key does not exist in the store. + json.JSONDecodeError + If the stored data is not valid JSON. + + Warnings + -------- + Do not call this method from async functions. Use ``get_json()`` instead. + + See Also + -------- + Store.get_json_sync : Base implementation with full documentation. + get_json : Asynchronous version of this method. + get_bytes_sync : Method for retrieving raw bytes without parsing. + + Examples + -------- + >>> store = MemoryStore() + >>> import json + >>> metadata = {"zarr_format": 3, "node_type": "array"} + >>> store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> # No need to specify prototype for MemoryStore + >>> data = store.get_json("zarr.json") + >>> print(data) + {'zarr_format': 3, 'node_type': 'array'} + """ + if prototype is None: + prototype = default_buffer_prototype() + return super()._get_json_sync(key, prototype=prototype, byte_range=byte_range) + class GpuMemoryStore(MemoryStore): """ diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index ad3b80da41..5daf8284eb 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -1,6 +1,7 @@ from __future__ import annotations import asyncio +import json import pickle from abc import abstractmethod from typing import TYPE_CHECKING, Generic, TypeVar @@ -23,7 +24,7 @@ SuffixByteRequest, ) from zarr.core.buffer import Buffer, default_buffer_prototype -from zarr.core.sync import _collect_aiterator +from zarr.core.sync import _collect_aiterator, sync from zarr.storage._utils import _normalize_byte_range_index from zarr.testing.utils import assert_bytes_equal @@ -526,6 +527,46 @@ async def test_set_if_not_exists(self, store: S) -> None: result = await store.get("k2", default_buffer_prototype()) assert result == new + async def test_get_bytes(self, store: S) -> None: + """ + Test that the get_bytes method reads bytes. + """ + data = b"hello world" + key = "zarr.json" + await self.set(store, key, self.buffer_cls.from_bytes(data)) + assert await store._get_bytes(key, prototype=default_buffer_prototype()) == data + with pytest.raises(FileNotFoundError): + await store._get_bytes("nonexistent_key", prototype=default_buffer_prototype()) + + def test_get_bytes_sync(self, store: S) -> None: + """ + Test that the get_bytes_sync method reads bytes. + """ + data = b"hello world" + key = "zarr.json" + sync(self.set(store, key, self.buffer_cls.from_bytes(data))) + assert store._get_bytes_sync(key, prototype=default_buffer_prototype()) == data + + async def test_get_json(self, store: S) -> None: + """ + Test that the get_json method reads json. + """ + data = {"foo": "bar"} + data_bytes = json.dumps(data).encode("utf-8") + key = "zarr.json" + await self.set(store, key, self.buffer_cls.from_bytes(data_bytes)) + assert await store._get_json(key, prototype=default_buffer_prototype()) == data + + def test_get_json_sync(self, store: S) -> None: + """ + Test that the get_json method reads json. + """ + data = {"foo": "bar"} + data_bytes = json.dumps(data).encode("utf-8") + key = "zarr.json" + sync(self.set(store, key, self.buffer_cls.from_bytes(data_bytes))) + assert store._get_json_sync(key, prototype=default_buffer_prototype()) == data + class LatencyStore(WrapperStore[Store]): """ diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index 6756bc83d9..bdc9b48121 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -1,7 +1,9 @@ from __future__ import annotations +import json import pathlib import re +from typing import TYPE_CHECKING import numpy as np import pytest @@ -9,11 +11,15 @@ import zarr from zarr import create_array from zarr.core.buffer import Buffer, cpu +from zarr.core.sync import sync from zarr.storage import LocalStore from zarr.storage._local import _atomic_write from zarr.testing.store import StoreTests from zarr.testing.utils import assert_bytes_equal +if TYPE_CHECKING: + from zarr.core.buffer import BufferPrototype + class TestLocalStore(StoreTests[LocalStore, cpu.Buffer]): store_cls = LocalStore @@ -108,6 +114,54 @@ async def test_move( ): await store2.move(destination) + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + async def test_get_bytes_with_prototype_none( + self, store: LocalStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_bytes works with prototype=None.""" + data = b"hello world" + key = "test_key" + await self.set(store, key, self.buffer_cls.from_bytes(data)) + + result = await store._get_bytes(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + def test_get_bytes_sync_with_prototype_none( + self, store: LocalStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_bytes_sync works with prototype=None.""" + data = b"hello world" + key = "test_key" + sync(self.set(store, key, self.buffer_cls.from_bytes(data))) + + result = store._get_bytes_sync(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + async def test_get_json_with_prototype_none( + self, store: LocalStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_json works with prototype=None.""" + data = {"foo": "bar", "number": 42} + key = "test.json" + await self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode())) + + result = await store._get_json(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + def test_get_json_sync_with_prototype_none( + self, store: LocalStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_json_sync works with prototype=None.""" + data = {"foo": "bar", "number": 42} + key = "test.json" + sync(self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode()))) + + result = store._get_json_sync(key, prototype=buffer_cls) + assert result == data + @pytest.mark.parametrize("exclusive", [True, False]) def test_atomic_write_successful(tmp_path: pathlib.Path, exclusive: bool) -> None: diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 29fa9b2964..03c8b24271 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -1,5 +1,6 @@ from __future__ import annotations +import json import re from typing import TYPE_CHECKING, Any @@ -9,12 +10,14 @@ import zarr from zarr.core.buffer import Buffer, cpu, gpu +from zarr.core.sync import sync from zarr.errors import ZarrUserWarning from zarr.storage import GpuMemoryStore, MemoryStore from zarr.testing.store import StoreTests from zarr.testing.utils import gpu_test if TYPE_CHECKING: + from zarr.core.buffer import BufferPrototype from zarr.core.common import ZarrFormat @@ -76,6 +79,54 @@ async def test_deterministic_size( np.testing.assert_array_equal(a[:3], 1) np.testing.assert_array_equal(a[3:], 0) + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + async def test_get_bytes_with_prototype_none( + self, store: MemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_bytes works with prototype=None.""" + data = b"hello world" + key = "test_key" + await self.set(store, key, self.buffer_cls.from_bytes(data)) + + result = await store._get_bytes(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + def test_get_bytes_sync_with_prototype_none( + self, store: MemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_bytes_sync works with prototype=None.""" + data = b"hello world" + key = "test_key" + sync(self.set(store, key, self.buffer_cls.from_bytes(data))) + + result = store._get_bytes_sync(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + async def test_get_json_with_prototype_none( + self, store: MemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_json works with prototype=None.""" + data = {"foo": "bar", "number": 42} + key = "test.json" + await self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode())) + + result = await store._get_json(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + def test_get_json_sync_with_prototype_none( + self, store: MemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_json_sync works with prototype=None.""" + data = {"foo": "bar", "number": 42} + key = "test.json" + sync(self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode()))) + + result = store._get_json_sync(key, prototype=buffer_cls) + assert result == data + # TODO: fix this warning @pytest.mark.filterwarnings("ignore:Unclosed client session:ResourceWarning") From 20d04d241b21e3ecdefd1bc0caac99d8c0391e77 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 26 Jan 2026 13:58:34 +0100 Subject: [PATCH 190/468] Bump astral-sh/setup-uv from 5 to 7 in the actions group (#3669) Bumps the actions group with 1 update: [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv). Updates `astral-sh/setup-uv` from 5 to 7 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/v5...v7) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 1c28f0b3d7..7a7b846bdb 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -18,7 +18,7 @@ jobs: steps: - uses: actions/checkout@v6 - name: Install uv - uses: astral-sh/setup-uv@v5 + uses: astral-sh/setup-uv@v7 - name: Install prek run: uv tool install prek - name: Run prek From d44baf65a54275a0e6675aa76fcf4f46a1b41df6 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 26 Jan 2026 14:28:06 +0100 Subject: [PATCH 191/468] only run codspeed benchmarks on PRs labelled 'benchmark' (#3673) * only run codspeed benchmarks on PRs labelled 'benchmark' * changelog * rename changelog --- .github/workflows/codspeed.yml | 6 ++++++ changes/3673.misc.md | 1 + 2 files changed, 7 insertions(+) create mode 100644 changes/3673.misc.md diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index c9c2f7b4c1..278c8fa877 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -5,6 +5,7 @@ on: branches: - "main" pull_request: + types: [labeled, synchronize] # `workflow_dispatch` allows CodSpeed to trigger backtest # performance analysis in order to generate initial data. workflow_dispatch: @@ -16,6 +17,11 @@ jobs: benchmarks: name: Run benchmarks runs-on: codspeed-macro + # Only run benchmarks for: pushes to main, manual triggers, or PRs with 'benchmark' label + if: | + github.event_name == 'push' || + github.event_name == 'workflow_dispatch' || + (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark')) steps: - uses: actions/checkout@v6 with: diff --git a/changes/3673.misc.md b/changes/3673.misc.md new file mode 100644 index 0000000000..83643f5d3c --- /dev/null +++ b/changes/3673.misc.md @@ -0,0 +1 @@ +Benchmark CI now only runs for PRs with the `benchmark` label, reducing CodSpeed credit usage. From 9c47b6d4410e6b4ef6bf446beb953482b3a0e15b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 30 Jan 2026 18:00:35 +0100 Subject: [PATCH 192/468] Improve the usability of array runtime config (#3668) * - Add .config property to Array - Make .config attribute of AsyncArray public - Add .with_config method to Array and AsyncArray - Use .config attribute in docs * bring back _config as an alias for config; update docstring * release note * add docs for with_config --- changes/3668.feature.md | 4 ++ docs/user-guide/arrays.md | 26 +++++++++++ docs/user-guide/performance.md | 9 +++- src/zarr/core/array.py | 84 +++++++++++++++++++++++++++++++--- src/zarr/core/array_spec.py | 6 +++ tests/test_api.py | 2 +- tests/test_array.py | 42 ++++++++++++++++- 7 files changed, 162 insertions(+), 11 deletions(-) create mode 100644 changes/3668.feature.md diff --git a/changes/3668.feature.md b/changes/3668.feature.md new file mode 100644 index 0000000000..def196ec8a --- /dev/null +++ b/changes/3668.feature.md @@ -0,0 +1,4 @@ +Exposes the array runtime configuration as an attribute called `config` on the `Array` and +`AsyncArray` classes. The previous `AsyncArray._config` attribute is now a deprecated alias for `AsyncArray.config`. + +Adds a method for creating a new `Array` / `AsyncArray` instance with a new runtime configuration, and fixes inaccurate documentation about the `write_empty_chunks` configuration parameter. \ No newline at end of file diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 1675c853fa..f63f5bc6b2 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -154,6 +154,32 @@ z.append(np.vstack([a, a]), axis=1) print(f"Shape after second append: {z.shape}") ``` +## Runtime configuration + +Zarr arrays are parametrized with a configuration that determines certain aspects of array behavior. + +We currently support two configuration options for arrays: `write_empty_chunks` and `order`. + +| field | type | default | description | +| - | - | - | - | +| `write_empty_chunks` | `bool` | `False` | Controls whether empty chunks are written to storage. See [Empty chunks](performance.md#empty-chunks). +| `order` | `Literal["C", "F"]` | `"C"` | The memory layout of arrays returned when reading data from the store. + +You can specify the configuration when you create an array with the `config` keyword argument. +`config` can be passed as either a `dict` or an `ArrayConfig` object. + +```python exec="true" session="arrays" source="above" result="ansi" +arr = zarr.create_array({}, shape=(10,), dtype='int8', config={"write_empty_chunks": True}) +print(arr.config) +``` + +To get an array view with a different config, use the `with_config` method. + +```python exec="true" session="arrays" source="above" result="ansi" +arr_f = arr.with_config({"order": "F"}) +print(arr_f.config) +``` + ## Compressors A number of different compressors can be used with Zarr. Zarr includes Blosc, diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index a2e986a1b8..0e0fa3cd55 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -125,7 +125,14 @@ This optimization prevents storing redundant objects and can speed up reads, but added computation during array writes, since the contents of each chunk must be compared to the fill value, and these advantages are contingent on the content of the array. If you know that your data will form chunks that are almost always non-empty, then there is no advantage to the optimization described above. -In this case, creating an array with `write_empty_chunks=True` (the default) will instruct Zarr to write every chunk without checking for emptiness. +In this case, creating an array with `write_empty_chunks=True` will instruct Zarr to write every chunk without checking for emptiness. + +The default value of `write_empty_chunks` is `False`: + +```python exec="true" session="performance" source="above" result="ansi" +arr = zarr.create_array(store={}, shape=(1,), dtype='uint8') +assert arr.config.write_empty_chunks == False +``` The following example illustrates the effect of the `write_empty_chunks` flag on the time required to write an array with different values.: diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 00536a1ec0..a3a2aff250 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -144,7 +144,7 @@ from zarr.codecs.sharding import ShardingCodecIndexLocation from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar from zarr.storage import StoreLike - from zarr.types import AnyArray, AnyAsyncArray, AsyncArrayV2, AsyncArrayV3 + from zarr.types import AnyArray, AnyAsyncArray, ArrayV2, ArrayV3, AsyncArrayV2, AsyncArrayV3 # Array and AsyncArray are defined in the base ``zarr`` namespace @@ -300,14 +300,14 @@ class AsyncArray(Generic[T_ArrayMetadata]): The path to the Zarr store. codec_pipeline : CodecPipeline The codec pipeline used for encoding and decoding chunks. - _config : ArrayConfig + config : ArrayConfig The runtime configuration of the array. """ metadata: T_ArrayMetadata store_path: StorePath codec_pipeline: CodecPipeline = field(init=False) - _config: ArrayConfig + config: ArrayConfig @overload def __init__( @@ -336,7 +336,7 @@ def __init__( object.__setattr__(self, "metadata", metadata_parsed) object.__setattr__(self, "store_path", store_path) - object.__setattr__(self, "_config", config_parsed) + object.__setattr__(self, "config", config_parsed) object.__setattr__( self, "codec_pipeline", @@ -1012,6 +1012,11 @@ async def example(): def store(self) -> Store: return self.store_path.store + @property + @deprecated("Use AsyncArray.config instead.", category=ZarrDeprecationWarning) + def _config(self) -> ArrayConfig: + return self.config + @property def ndim(self) -> int: """Returns the number of dimensions in the Array. @@ -1165,7 +1170,7 @@ def order(self) -> MemoryOrder: if self.metadata.zarr_format == 2: return self.metadata.order else: - return self._config.order + return self.config.order @property def attrs(self) -> dict[str, JSON]: @@ -1298,6 +1303,35 @@ def _nshards(self) -> int: """ return product(self._shard_grid_shape) + @overload + def with_config(self: AsyncArrayV2, config: ArrayConfigLike) -> AsyncArrayV2: ... + + @overload + def with_config(self: AsyncArrayV3, config: ArrayConfigLike) -> AsyncArrayV3: ... + + def with_config(self, config: ArrayConfigLike) -> Self: + """ + Return a copy of this Array with a new runtime configuration. + + Parameters + ---------- + + config : ArrayConfigLike + The runtime config for the new Array. Any keys not specified will be inherited + from the current array's config. + + Returns + ------- + A new Array + """ + if isinstance(config, ArrayConfig): + new_config = config + else: + # Merge new config with existing config, so missing keys are inherited + # from the current array rather than from global defaults + new_config = ArrayConfig(**{**self.config.to_dict(), **config}) # type: ignore[arg-type] + return type(self)(metadata=self.metadata, store_path=self.store_path, config=new_config) + async def nchunks_initialized(self) -> int: """ Calculate the number of chunks that have been initialized in storage. @@ -1570,7 +1604,7 @@ async def _get_selection( ) if product(indexer.shape) > 0: # need to use the order from the metadata for v2 - _config = self._config + _config = self.config if self.metadata.zarr_format == 2: _config = replace(_config, order=self.order) @@ -1741,7 +1775,7 @@ async def _set_selection( value_buffer = prototype.nd_buffer.from_ndarray_like(value) # need to use the order from the metadata for v2 - _config = self._config + _config = self.config if self.metadata.zarr_format == 2: _config = replace(_config, order=self.metadata.order) @@ -2063,6 +2097,19 @@ def async_array(self) -> AsyncArray[T_ArrayMetadata]: """ return self._async_array + @property + def config(self) -> ArrayConfig: + """ + The runtime configuration for this array. This is a read-only property. To modify the + runtime configuration, use `Array.with_config` to create a new `Array` with the modified + configuration. + + Returns + ------- + An `ArrayConfig` object that defines the runtime configuration for the array. + """ + return self.async_array.config + @classmethod @deprecated("Use zarr.create_array instead.", category=ZarrDeprecationWarning) def create( @@ -2524,6 +2571,29 @@ def _nshards(self) -> int: """ return self.async_array._nshards + @overload + def with_config(self: ArrayV2, config: ArrayConfigLike) -> ArrayV2: ... + + @overload + def with_config(self: ArrayV3, config: ArrayConfigLike) -> ArrayV3: ... + + def with_config(self, config: ArrayConfigLike) -> Self: + """ + Return a copy of this Array with a new runtime configuration. + + Parameters + ---------- + + config : ArrayConfigLike + The runtime config for the new Array. Any keys not specified will be inherited + from the current array's config. + + Returns + ------- + A new Array + """ + return type(self)(self._async_array.with_config(config)) + @property def nbytes(self) -> int: """ diff --git a/src/zarr/core/array_spec.py b/src/zarr/core/array_spec.py index c4dedaefea..421dfbf145 100644 --- a/src/zarr/core/array_spec.py +++ b/src/zarr/core/array_spec.py @@ -69,6 +69,12 @@ def from_dict(cls, data: ArrayConfigParams) -> Self: kwargs_out[field_name] = data[field_name] return cls(**kwargs_out) + def to_dict(self) -> ArrayConfigParams: + """ + Serialize an instance of this class to a dict. + """ + return {"order": self.order, "write_empty_chunks": self.write_empty_chunks} + ArrayConfigLike = ArrayConfig | ArrayConfigParams diff --git a/tests/test_api.py b/tests/test_api.py index adea150ae1..82c75807df 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -232,7 +232,7 @@ def test_open_array_respects_write_empty_chunks_config(zarr_format: ZarrFormat) arr2 = zarr.open(store=store, path="test_array", config={"write_empty_chunks": True}) assert isinstance(arr2, zarr.Array) - assert arr2.async_array._config.write_empty_chunks is True + assert arr2.async_array.config.write_empty_chunks is True arr2[0:5] = np.zeros(5) assert arr2.nchunks_initialized == 1 diff --git a/tests/test_array.py b/tests/test_array.py index 67be294827..b7d7bc723d 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -44,6 +44,7 @@ default_filters_v2, default_serializer_v3, ) +from zarr.core.array_spec import ArrayConfig, ArrayConfigParams from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, default_buffer_prototype from zarr.core.chunk_grids import _auto_partition from zarr.core.chunk_key_encodings import ChunkKeyEncodingParams @@ -889,7 +890,7 @@ def test_write_empty_chunks_behavior( config={"write_empty_chunks": write_empty_chunks}, ) - assert arr.async_array._config.write_empty_chunks == write_empty_chunks + assert arr.async_array.config.write_empty_chunks == write_empty_chunks # initialize the store with some non-fill value chunks arr[:] = fill_value + 1 @@ -1562,7 +1563,7 @@ async def test_write_empty_chunks_config(write_empty_chunks: bool, store: Store) """ with zarr.config.set({"array.write_empty_chunks": write_empty_chunks}): arr = await create_array(store, shape=(2, 2), dtype="i4") - assert arr._config.write_empty_chunks == write_empty_chunks + assert arr.config.write_empty_chunks == write_empty_chunks @staticmethod @pytest.mark.parametrize("path", [None, "", "/", "/foo", "foo", "foo/bar"]) @@ -2194,3 +2195,40 @@ def test_create_array_with_data_num_gets( # one get for the metadata and one per shard. # Note: we don't actually need one get per shard, but this is the current behavior assert store.counter["get"] == 1 + num_shards + + +@pytest.mark.parametrize("config", [{}, {"write_empty_chunks": True}, {"order": "C"}]) +def test_with_config(config: ArrayConfigParams) -> None: + """ + Test that `AsyncArray.with_config` and `Array.with_config` create a copy of the source + array with a new runtime configuration. + """ + # the config we start with + source_config: ArrayConfigParams = {"write_empty_chunks": False, "order": "F"} + source_array = zarr.create_array({}, shape=(1,), dtype="uint8", config=source_config) + + new_async_array_config_dict = source_array._async_array.with_config(config).config.to_dict() + new_array_config_dict = source_array.with_config(config).config.to_dict() + + for key in source_config: + if key in config: + assert new_async_array_config_dict[key] == config[key] # type: ignore[literal-required] + assert new_array_config_dict[key] == config[key] # type: ignore[literal-required] + else: + assert new_async_array_config_dict[key] == source_config[key] # type: ignore[literal-required] + assert new_array_config_dict[key] == source_config[key] # type: ignore[literal-required] + + +def test_with_config_polymorphism() -> None: + """ + Test that `AsyncArray.with_config` and `Array.with_config` accept dicts and full array config + objects. + """ + source_config: ArrayConfig = ArrayConfig.from_dict({"write_empty_chunks": False, "order": "F"}) + source_config_dict = source_config.to_dict() + + arr = zarr.create_array({}, shape=(1,), dtype="uint8") + arr_source_config = arr.with_config(source_config) + arr_source_config_dict = arr.with_config(source_config_dict) + + assert arr_source_config.config == arr_source_config_dict.config From b712f96d60da811e737cf23569e1ccc64281b7a5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 2 Feb 2026 19:14:52 +0000 Subject: [PATCH 193/468] chore: update pre-commit hooks (#3689) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.10 → v0.14.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.10...v0.14.14) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f85b500784..8b6c41901c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.10 + rev: v0.14.14 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] From 22ea09f410e3b3b89069aeb3f1a6e0d8a1040187 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Sun, 8 Feb 2026 11:17:30 +0100 Subject: [PATCH 194/468] Fix HTML syntax errors in README.md table (#3694) Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> --- README.md | 49 +++++++++++++++++++++++++------------------------ 1 file changed, 25 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 97f5617934..3911ba17b8 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,7 @@ + @@ -23,9 +24,9 @@ Package Status - - status - + + status + @@ -47,17 +48,16 @@ Pre-commit Status - + pre-commit status - Coverage - coverage + coverage @@ -70,27 +70,28 @@ - Developer Chat - - - - - + Developer Chat + + + + + - Funding - - - CZI's Essential Open Source Software for Science - - + Funding + + + CZI's Essential Open Source Software for Science + + - Citation - - - DOI - - + + Citation + + + DOI + + From 229a69065fc77a43b0ebc50b31a35b6b5ea0b0df Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 11 Feb 2026 12:30:26 +0100 Subject: [PATCH 195/468] Fix grammar, typos, and clarity issues in documentation (#1) (#3693) Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: Davis Bennett --- docs/contributing.md | 16 ++++++++-------- docs/quick-start.md | 4 ++-- docs/user-guide/arrays.md | 4 ++-- docs/user-guide/extending.md | 2 +- docs/user-guide/groups.md | 2 +- docs/user-guide/storage.md | 4 ++-- docs/user-guide/v3_migration.md | 2 +- 7 files changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/contributing.md b/docs/contributing.md index c330504536..e4f341a8b3 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -131,7 +131,7 @@ The hooks can be installed locally by running: prek install ``` -This would run the checks every time a commit is created locally. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running: +This will run the checks every time a commit is created locally. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running: ```bash prek run --all-files @@ -249,13 +249,13 @@ Pull requests submitted by an external contributor should be reviewed and approv Pull requests should not be merged until all CI checks have passed (GitHub Actions, Codecov) against code that has had the latest main merged in. -Before merging the milestone must be set either to decide whether a PR will be in the next patch, minor, or major release. The next section explains which types of changes go in each release. +Before merging, the milestone must be set to decide whether a PR will be in the next patch, minor, or major release. The next section explains which types of changes go in each release. ## Compatibility and versioning policies ### Versioning -Versions of this library are identified by a triplet of integers with the form `..`, for example `3.0.4`. A release of `zarr-python` is associated with a new version identifier. That new identifier is generated by incrementing exactly one of the components of the previous version identifier by 1. When incrementing the `major` component of the version identifier, the `minor` and `patch` components is reset to 0. When incrementing the minor component, the patch component is reset to 0. +Versions of this library are identified by a triplet of integers with the form `..`, for example `3.0.4`. A release of `zarr-python` is associated with a new version identifier. That new identifier is generated by incrementing exactly one of the components of the previous version identifier by 1. When incrementing the `major` component of the version identifier, the `minor` and `patch` components are reset to 0. When incrementing the minor component, the patch component is reset to 0. Releases are classified by the library changes contained in that release. This classification determines which component of the version identifier is incremented on release. @@ -263,7 +263,7 @@ Releases are classified by the library changes contained in that release. This c Users and downstream projects should carefully consider the impact of a major release before adopting it. In advance of a major release, developers should communicate the scope of the upcoming changes, and help users prepare for them. -* **minor** releases (for example, `3.0.0` -> `3.1.0`) are for changes that do not require significant effort from most users or downstream downstream projects to respond to. API changes are possible in minor releases if the burden on users imposed by those changes is sufficiently small. +* **minor** releases (for example, `3.0.0` -> `3.1.0`) are for changes that do not require significant effort from most users or downstream projects to respond to. API changes are possible in minor releases if the burden on users imposed by those changes is sufficiently small. For example, a recently released API may need fixes or refinements that are breaking, but low impact due to the recency of the feature. Such API changes are permitted in a minor release. @@ -271,11 +271,11 @@ Releases are classified by the library changes contained in that release. This c * **patch** releases (for example, `3.1.0` -> `3.1.1`) are for changes that contain no breaking or behaviour changes for downstream projects or users. Examples of changes suitable for a patch release are bugfixes and documentation improvements. - Users should always feel safe upgrading to a the latest patch release. + Users should always feel safe upgrading to the latest patch release. Note that this versioning scheme is not consistent with [Semantic Versioning](https://semver.org/). Contrary to SemVer, the Zarr library may release breaking changes in `minor` releases, or even `patch` releases under exceptional circumstances. But we should strive to avoid doing so. -A better model for our versioning scheme is [Intended Effort Versioning](https://jacobtomlinson.dev/effver/), or "EffVer". The guiding principle off EffVer is to categorize releases based on the *expected effort required to upgrade to that release*. +A better model for our versioning scheme is [Intended Effort Versioning](https://jacobtomlinson.dev/effver/), or "EffVer". The guiding principle of EffVer is to categorize releases based on the *expected effort required to upgrade to that release*. Zarr developers should make changes as smooth as possible for users. This means making backwards-compatible changes wherever possible. When a backwards-incompatible change is necessary, users should be notified well in advance, e.g. via informative deprecation warnings. @@ -288,12 +288,12 @@ If an existing Zarr format version changes, or a new version of the Zarr format ## Release procedure Open an issue on GitHub announcing the release using the release checklist template: -[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md>). The release checklist includes all steps necessary for the release. +[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md). The release checklist includes all steps necessary for the release. ## Benchmarks Zarr uses [pytest-benchmark](https://pytest-benchmark.readthedocs.io/en/latest/) for running -performance benchmarks as part of our test suite. The benchmarks can be are found in `tests/benchmarks`. +performance benchmarks as part of our test suite. The benchmarks are found in `tests/benchmarks`. By default pytest is configured to run these benchmarks as plain tests (i.e., no benchmarking). To run a benchmark with timing measurements, use the `--benchmark-enable` when invoking `pytest`. diff --git a/docs/quick-start.md b/docs/quick-start.md index 42ac95d169..bb7a556b96 100644 --- a/docs/quick-start.md +++ b/docs/quick-start.md @@ -1,4 +1,4 @@ -This section will help you get up and running with +This section will help you get up and running with the Zarr library in Python to efficiently manage and analyze multi-dimensional arrays. ### Creating an Array @@ -92,7 +92,7 @@ spam[:] = np.arange(10) print(root.tree()) ``` -This creates a group with two datasets: `foo` and `bar`. +This creates a group hierarchy with a group (`foo`) and two arrays (`bar` and `spam`). #### Batch Hierarchy Creation diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index f63f5bc6b2..cd6a93cac9 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -72,7 +72,7 @@ print(z[:, 0]) print(z[:]) ``` -Read more about NumPy-style indexing can be found in the +More information about NumPy-style indexing can be found in the [NumPy documentation](https://numpy.org/doc/stable/user/basics.indexing.html). ## Persistent arrays @@ -297,7 +297,7 @@ array without loading the entire array into memory. Note that although this functionality is similar to some of the advanced indexing capabilities available on NumPy arrays and on h5py datasets, **the Zarr API for advanced indexing is different from both NumPy and h5py**, so please -read this section carefully. For a complete description of the indexing API, +read this section carefully. For a complete description of the indexing API, see the documentation for the [`zarr.Array`][] class. ### Indexing with coordinate arrays diff --git a/docs/user-guide/extending.md b/docs/user-guide/extending.md index d857fa3356..39444135df 100644 --- a/docs/user-guide/extending.md +++ b/docs/user-guide/extending.md @@ -29,7 +29,7 @@ of the array data. Examples include compression codecs, such as Custom codecs for Zarr are implemented by subclassing the relevant base class, see [`zarr.abc.codec.ArrayArrayCodec`][], [`zarr.abc.codec.ArrayBytesCodec`][] and -[`zarr.abc.codec.BytesBytesCodec`][]. Most custom codecs should implemented the +[`zarr.abc.codec.BytesBytesCodec`][]. Most custom codecs should implement the `_encode_single` and `_decode_single` methods. These methods operate on single chunks of the array data. Alternatively, custom codecs can implement the `encode` and `decode` methods, which operate on batches of chunks, in case the codec is intended to implement diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index 57201216b6..e093590dfe 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -13,7 +13,7 @@ root = zarr.create_group(store=store) print(root) ``` -Groups have a similar API to the Group class from [h5py](https://www.h5py.org/). For example, groups can contain other groups: +Groups have a similar API to the Group class from [h5py](https://www.h5py.org/). For example, groups can contain other groups: ```python exec="true" session="groups" source="above" foo = root.create_group('foo') diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index 82b576b889..e75cd21381 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -91,8 +91,8 @@ print(group) ## Explicit Store Creation -In some cases, it may be helpful to create a store instance directly. Zarr-Python offers four -built-in store: [`zarr.storage.LocalStore`][], [`zarr.storage.FsspecStore`][], +In some cases, it may be helpful to create a store instance directly. Zarr-Python offers +built-in stores: [`zarr.storage.LocalStore`][], [`zarr.storage.FsspecStore`][], [`zarr.storage.ZipStore`][], [`zarr.storage.MemoryStore`][], and [`zarr.storage.ObjectStore`][]. ### Local Store diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index 15425de27a..d5a8067a88 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -20,7 +20,7 @@ so we can improve this guide. The goals described above necessitated some breaking changes to the API (hence the major version update), but where possible we have maintained backwards compatibility -in the most widely used parts of the API. This in the [`zarr.Array`][] and +in the most widely used parts of the API. This includes the [`zarr.Array`][] and [`zarr.Group`][] classes and the "top-level API" (e.g. [`zarr.open_array`][] and [`zarr.open_group`][]). From f4d122135fb010127484bcad717606b3c15bcb51 Mon Sep 17 00:00:00 2001 From: "Philipp A." Date: Wed, 11 Feb 2026 13:43:39 +0100 Subject: [PATCH 196/468] fix: raise error when encountering nullable string dtype (#3695) * fix: raise error when encountering nullable string dtype * add change entry * fix typing * move exception on na_object-bearing-string-dtype to inside from_native_dtype --------- Co-authored-by: Davis Vann Bennett --- changes/3695.bugfix.md | 1 + src/zarr/core/dtype/npy/string.py | 37 +++++++++++++++++++++++++++++++ src/zarr/core/dtype/registry.py | 4 ++++ tests/test_dtype_registry.py | 12 ++++++++++ 4 files changed, 54 insertions(+) create mode 100644 changes/3695.bugfix.md diff --git a/changes/3695.bugfix.md b/changes/3695.bugfix.md new file mode 100644 index 0000000000..a7d847e4f1 --- /dev/null +++ b/changes/3695.bugfix.md @@ -0,0 +1 @@ +Raise error when trying to encode :class:`numpy.dtypes.StringDType` with `na_object` set. \ No newline at end of file diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index 41d3a60078..904280a330 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -742,6 +742,43 @@ class VariableLengthUTF8(UTF8Base[np.dtypes.StringDType]): # type: ignore[type- dtype_cls = np.dtypes.StringDType + @classmethod + def from_native_dtype(cls, dtype: TBaseDType) -> Self: + """ + Create an instance of this data type from a compatible NumPy data type. + We reject NumPy StringDType instances that have the `na_object` field set, + because this is not representable by the Zarr `string` data type. + + Parameters + ---------- + dtype : TBaseDType + The native data type. + + Returns + ------- + Self + An instance of this data type. + + Raises + ------ + DataTypeValidationError + If the input is not compatible with this data type. + ValueError + If the input is `numpy.dtypes.StringDType` and has `na_object` set. + """ + if cls._check_native_dtype(dtype): + if hasattr(dtype, "na_object"): + msg = ( + f"Zarr data type resolution from {dtype} failed. " + "Attempted to resolve a zarr data type from a `numpy.dtypes.StringDType` " + "with `na_object` set, which is not supported." + ) + raise ValueError(msg) + return cls() + raise DataTypeValidationError( + f"Invalid data type: {dtype}. Expected an instance of {cls.dtype_cls}" + ) + def to_native_dtype(self) -> np.dtypes.StringDType: """ Create a NumPy string dtype from this VariableLengthUTF8 ZDType. diff --git a/src/zarr/core/dtype/registry.py b/src/zarr/core/dtype/registry.py index cb9ab50044..315945cf4e 100644 --- a/src/zarr/core/dtype/registry.py +++ b/src/zarr/core/dtype/registry.py @@ -161,6 +161,10 @@ def match_dtype(self, dtype: TBaseDType) -> ZDType[TBaseDType, TBaseScalar]: raise ValueError(msg) matched: list[ZDType[TBaseDType, TBaseScalar]] = [] for val in self.contents.values(): + # DataTypeValidationError means "this dtype doesn't match me", which is + # expected and suppressed. Other exceptions (e.g. ValueError for a dtype + # that matches the type but has an invalid configuration) are propagated + # to the caller. with contextlib.suppress(DataTypeValidationError): matched.append(val.from_native_dtype(dtype)) if len(matched) == 1: diff --git a/tests/test_dtype_registry.py b/tests/test_dtype_registry.py index 58b14fe07a..b7ceb502b7 100644 --- a/tests/test_dtype_registry.py +++ b/tests/test_dtype_registry.py @@ -15,9 +15,11 @@ get_data_type_from_json, ) from zarr.core.dtype.common import unpack_dtype_json +from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING from zarr.dtype import ( # type: ignore[attr-defined] Bool, FixedLengthUTF32, + VariableLengthUTF8, ZDType, data_type_registry, parse_data_type, @@ -74,6 +76,16 @@ def test_match_dtype( data_type_registry_fixture.register(wrapper_cls._zarr_v3_name, wrapper_cls) assert isinstance(data_type_registry_fixture.match_dtype(np.dtype(dtype_str)), wrapper_cls) + @pytest.mark.skipif(not _NUMPY_SUPPORTS_VLEN_STRING, reason="requires numpy with T dtype") + @staticmethod + def test_match_dtype_string_na_object_error( + data_type_registry_fixture: DataTypeRegistry, + ) -> None: + data_type_registry_fixture.register(VariableLengthUTF8._zarr_v3_name, VariableLengthUTF8) # type: ignore[arg-type] + dtype: np.dtype[Any] = np.dtypes.StringDType(na_object=None) # type: ignore[call-arg] + with pytest.raises(ValueError, match=r"Zarr data type resolution from StringDType.*failed"): + data_type_registry_fixture.match_dtype(dtype) + @staticmethod def test_unregistered_dtype(data_type_registry_fixture: DataTypeRegistry) -> None: """ From 74a248da387b471ba1c2278467a91d8f836cd69f Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 11 Feb 2026 17:57:02 +0100 Subject: [PATCH 197/468] lift async array methods to stand-alone functions (#3676) * lift array methods to separate functions * don't use deprecated attribute * don't use deprecated attribute --- src/zarr/core/array.py | 951 ++++++++++++++++++++++++++++++++--------- 1 file changed, 748 insertions(+), 203 deletions(-) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index a3a2aff250..7abb0075dc 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1371,13 +1371,7 @@ async def example(): result = asyncio.run(example()) ``` """ - if self.shards is None: - chunks_per_shard = 1 - else: - chunks_per_shard = product( - tuple(a // b for a, b in zip(self.shards, self.chunks, strict=True)) - ) - return (await self._nshards_initialized()) * chunks_per_shard + return await _nchunks_initialized(self) async def _nshards_initialized(self) -> int: """ @@ -1415,10 +1409,10 @@ async def example(): result = asyncio.run(example()) ``` """ - return len(await _shards_initialized(self)) + return await _nshards_initialized(self) async def nbytes_stored(self) -> int: - return await self.store_path.store.getsize_prefix(self.store_path.path) + return await _nbytes_stored(self.store_path) def _iter_chunk_coords( self, *, origin: Sequence[int] | None = None, selection_shape: Sequence[int] | None = None @@ -1583,49 +1577,16 @@ async def _get_selection( out: NDBuffer | None = None, fields: Fields | None = None, ) -> NDArrayLikeOrScalar: - # check fields are sensible - out_dtype = check_fields(fields, self.dtype) - - # setup output buffer - if out is not None: - if isinstance(out, NDBuffer): - out_buffer = out - else: - raise TypeError(f"out argument needs to be an NDBuffer. Got {type(out)!r}") - if out_buffer.shape != indexer.shape: - raise ValueError( - f"shape of out argument doesn't match. Expected {indexer.shape}, got {out.shape}" - ) - else: - out_buffer = prototype.nd_buffer.empty( - shape=indexer.shape, - dtype=out_dtype, - order=self.order, - ) - if product(indexer.shape) > 0: - # need to use the order from the metadata for v2 - _config = self.config - if self.metadata.zarr_format == 2: - _config = replace(_config, order=self.order) - - # reading chunks and decoding them - await self.codec_pipeline.read( - [ - ( - self.store_path / self.metadata.encode_chunk_key(chunk_coords), - self.metadata.get_chunk_spec(chunk_coords, _config, prototype=prototype), - chunk_selection, - out_selection, - is_complete_chunk, - ) - for chunk_coords, chunk_selection, out_selection, is_complete_chunk in indexer - ], - out_buffer, - drop_axes=indexer.drop_axes, - ) - if isinstance(indexer, BasicIndexer) and indexer.shape == (): - return out_buffer.as_scalar() - return out_buffer.as_ndarray_like() + return await _get_selection( + self.store_path, + self.metadata, + self.codec_pipeline, + self.config, + indexer, + prototype=prototype, + out=out, + fields=fields, + ) async def getitem( self, @@ -1670,14 +1631,14 @@ async def example(): value = asyncio.run(example()) ``` """ - if prototype is None: - prototype = default_buffer_prototype() - indexer = BasicIndexer( + return await _getitem( + self.store_path, + self.metadata, + self.codec_pipeline, + self.config, selection, - shape=self.metadata.shape, - chunk_grid=self.metadata.chunk_grid, + prototype=prototype, ) - return await self._get_selection(indexer, prototype=prototype) async def get_orthogonal_selection( self, @@ -1687,11 +1648,15 @@ async def get_orthogonal_selection( fields: Fields | None = None, prototype: BufferPrototype | None = None, ) -> NDArrayLikeOrScalar: - if prototype is None: - prototype = default_buffer_prototype() - indexer = OrthogonalIndexer(selection, self.shape, self.metadata.chunk_grid) - return await self._get_selection( - indexer=indexer, out=out, fields=fields, prototype=prototype + return await _get_orthogonal_selection( + self.store_path, + self.metadata, + self.codec_pipeline, + self.config, + selection, + out=out, + fields=fields, + prototype=prototype, ) async def get_mask_selection( @@ -1702,11 +1667,15 @@ async def get_mask_selection( fields: Fields | None = None, prototype: BufferPrototype | None = None, ) -> NDArrayLikeOrScalar: - if prototype is None: - prototype = default_buffer_prototype() - indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid) - return await self._get_selection( - indexer=indexer, out=out, fields=fields, prototype=prototype + return await _get_mask_selection( + self.store_path, + self.metadata, + self.codec_pipeline, + self.config, + mask, + out=out, + fields=fields, + prototype=prototype, ) async def get_coordinate_selection( @@ -1717,18 +1686,17 @@ async def get_coordinate_selection( fields: Fields | None = None, prototype: BufferPrototype | None = None, ) -> NDArrayLikeOrScalar: - if prototype is None: - prototype = default_buffer_prototype() - indexer = CoordinateIndexer(selection, self.shape, self.metadata.chunk_grid) - out_array = await self._get_selection( - indexer=indexer, out=out, fields=fields, prototype=prototype + return await _get_coordinate_selection( + self.store_path, + self.metadata, + self.codec_pipeline, + self.config, + selection, + out=out, + fields=fields, + prototype=prototype, ) - if hasattr(out_array, "shape"): - # restore shape - out_array = np.array(out_array).reshape(indexer.sel_shape) - return out_array - async def _save_metadata(self, metadata: ArrayMetadata, ensure_parents: bool = False) -> None: """ Asynchronously save the array metadata. @@ -1743,56 +1711,15 @@ async def _set_selection( prototype: BufferPrototype, fields: Fields | None = None, ) -> None: - # check fields are sensible - check_fields(fields, self.dtype) - fields = check_no_multi_fields(fields) - - # check value shape - if np.isscalar(value): - array_like = prototype.buffer.create_zero_length().as_array_like() - if isinstance(array_like, np._typing._SupportsArrayFunc): - # TODO: need to handle array types that don't support __array_function__ - # like PyTorch and JAX - array_like_ = cast("np._typing._SupportsArrayFunc", array_like) - value = np.asanyarray(value, dtype=self.dtype, like=array_like_) - else: - if not hasattr(value, "shape"): - value = np.asarray(value, self.dtype) - # assert ( - # value.shape == indexer.shape - # ), f"shape of value doesn't match indexer shape. Expected {indexer.shape}, got {value.shape}" - if not hasattr(value, "dtype") or value.dtype.name != self.dtype.name: - if hasattr(value, "astype"): - # Handle things that are already NDArrayLike more efficiently - value = value.astype(dtype=self.dtype, order="A") - else: - value = np.array(value, dtype=self.dtype, order="A") - value = cast("NDArrayLike", value) - - # We accept any ndarray like object from the user and convert it - # to an NDBuffer (or subclass). From this point onwards, we only pass - # Buffer and NDBuffer between components. - value_buffer = prototype.nd_buffer.from_ndarray_like(value) - - # need to use the order from the metadata for v2 - _config = self.config - if self.metadata.zarr_format == 2: - _config = replace(_config, order=self.metadata.order) - - # merging with existing data and encoding chunks - await self.codec_pipeline.write( - [ - ( - self.store_path / self.metadata.encode_chunk_key(chunk_coords), - self.metadata.get_chunk_spec(chunk_coords, _config, prototype), - chunk_selection, - out_selection, - is_complete_chunk, - ) - for chunk_coords, chunk_selection, out_selection, is_complete_chunk in indexer - ], - value_buffer, - drop_axes=indexer.drop_axes, + return await _set_selection( + self.store_path, + self.metadata, + self.codec_pipeline, + self.config, + indexer, + value, + prototype=prototype, + fields=fields, ) async def setitem( @@ -1834,14 +1761,15 @@ async def setitem( - This method is asynchronous and should be awaited. - Supports basic indexing, where the selection is contiguous and does not involve advanced indexing. """ - if prototype is None: - prototype = default_buffer_prototype() - indexer = BasicIndexer( + return await _setitem( + self.store_path, + self.metadata, + self.codec_pipeline, + self.config, selection, - shape=self.metadata.shape, - chunk_grid=self.metadata.chunk_grid, + value, + prototype=prototype, ) - return await self._set_selection(indexer, value, prototype=prototype) @property def oindex(self) -> AsyncOIndex[T_ArrayMetadata]: @@ -1883,32 +1811,7 @@ async def resize(self, new_shape: ShapeLike, delete_outside_chunks: bool = True) ----- - This method is asynchronous and should be awaited. """ - new_shape = parse_shapelike(new_shape) - assert len(new_shape) == len(self.metadata.shape) - new_metadata = self.metadata.update_shape(new_shape) - - if delete_outside_chunks: - # Remove all chunks outside of the new shape - old_chunk_coords = set(self.metadata.chunk_grid.all_chunk_coords(self.metadata.shape)) - new_chunk_coords = set(self.metadata.chunk_grid.all_chunk_coords(new_shape)) - - async def _delete_key(key: str) -> None: - await (self.store_path / key).delete() - - await concurrent_map( - [ - (self.metadata.encode_chunk_key(chunk_coords),) - for chunk_coords in old_chunk_coords.difference(new_chunk_coords) - ], - _delete_key, - zarr_config.get("async.concurrency"), - ) - - # Write new metadata - await self._save_metadata(new_metadata) - - # Update metadata (in place) - object.__setattr__(self, "metadata", new_metadata) + return await _resize(self, new_shape, delete_outside_chunks) async def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: """Append `data` to `axis`. @@ -1929,40 +1832,7 @@ async def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: The size of all dimensions other than `axis` must match between this array and `data`. """ - # ensure data is array-like - if not hasattr(data, "shape"): - data = np.asanyarray(data) - - self_shape_preserved = tuple(s for i, s in enumerate(self.shape) if i != axis) - data_shape_preserved = tuple(s for i, s in enumerate(data.shape) if i != axis) - if self_shape_preserved != data_shape_preserved: - raise ValueError( - f"shape of data to append is not compatible with the array. " - f"The shape of the data is ({data_shape_preserved})" - f"and the shape of the array is ({self_shape_preserved})." - "All dimensions must match except for the dimension being " - "appended." - ) - # remember old shape - old_shape = self.shape - - # determine new shape - new_shape = tuple( - self.shape[i] if i != axis else self.shape[i] + data.shape[i] - for i in range(len(self.shape)) - ) - - # resize - await self.resize(new_shape) - - # store data - append_selection = tuple( - slice(None) if i != axis else slice(old_shape[i], new_shape[i]) - for i in range(len(self.shape)) - ) - await self.setitem(append_selection, data) - - return new_shape + return await _append(self, data, axis) async def update_attributes(self, new_attributes: dict[str, JSON]) -> Self: """ @@ -1990,11 +1860,7 @@ async def update_attributes(self, new_attributes: dict[str, JSON]) -> Self: - The updated attributes will be merged with existing attributes, and any conflicts will be overwritten by the new values. """ - self.metadata.attributes.update(new_attributes) - - # Write new metadata - await self._save_metadata(self.metadata) - + await _update_attributes(self, new_attributes) return self def __repr__(self) -> str: @@ -2051,10 +1917,7 @@ async def info_complete(self) -> Any: ------- [zarr.AsyncArray.info][] - A property giving just the statically known information about an array. """ - return self._info( - await self._nshards_initialized(), - await self.store_path.store.getsize_prefix(self.store_path.path), - ) + return await _info_complete(self) def _info( self, count_chunks_initialized: int | None = None, count_bytes_stored: int | None = None @@ -5588,3 +5451,685 @@ def _iter_chunk_regions( return _iter_regions( array.shape, array.chunks, origin=origin, selection_shape=selection_shape, trim_excess=True ) + + +async def _nchunks_initialized( + array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], +) -> int: + """ + Calculate the number of chunks that have been initialized in storage. + + This value is calculated as the product of the number of initialized shards and the number + of chunks per shard. For arrays that do not use sharding, the number of chunks per shard is + effectively 1, and in that case the number of chunks initialized is the same as the number + of stored objects associated with an array. + + Parameters + ---------- + array : AsyncArray + The array to inspect. + + Returns + ------- + nchunks_initialized : int + The number of chunks that have been initialized. + """ + if array.shards is None: + chunks_per_shard = 1 + else: + chunks_per_shard = product( + tuple(a // b for a, b in zip(array.shards, array.chunks, strict=True)) + ) + return (await _nshards_initialized(array)) * chunks_per_shard + + +async def _nshards_initialized( + array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], +) -> int: + """ + Calculate the number of shards that have been initialized in storage. + + This is the number of shards that have been persisted to the storage backend. + + Parameters + ---------- + array : AsyncArray + The array to inspect. + + Returns + ------- + nshards_initialized : int + The number of shards that have been initialized. + """ + return len(await _shards_initialized(array)) + + +async def _nbytes_stored( + store_path: StorePath, +) -> int: + """ + Calculate the number of bytes stored for an array. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + + Returns + ------- + nbytes_stored : int + The number of bytes stored. + """ + return await store_path.store.getsize_prefix(store_path.path) + + +async def _get_selection( + store_path: StorePath, + metadata: ArrayMetadata, + codec_pipeline: CodecPipeline, + config: ArrayConfig, + indexer: Indexer, + *, + prototype: BufferPrototype, + out: NDBuffer | None = None, + fields: Fields | None = None, +) -> NDArrayLikeOrScalar: + """ + Get a selection from an array. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + metadata : ArrayMetadata + The array metadata. + codec_pipeline : CodecPipeline + The codec pipeline for encoding/decoding. + config : ArrayConfig + The array configuration. + indexer : Indexer + The indexer specifying the selection. + prototype : BufferPrototype + A buffer prototype to use for the retrieved data. + out : NDBuffer | None, optional + An output buffer to write the data to. + fields : Fields | None, optional + Fields to select from structured arrays. + + Returns + ------- + NDArrayLikeOrScalar + The selected data. + """ + # Get dtype from metadata + if metadata.zarr_format == 2: + zdtype = metadata.dtype + else: + zdtype = metadata.data_type + dtype = zdtype.to_native_dtype() + + # Determine memory order + if metadata.zarr_format == 2: + order = metadata.order + else: + order = config.order + + # check fields are sensible + out_dtype = check_fields(fields, dtype) + + # setup output buffer + if out is not None: + if isinstance(out, NDBuffer): + out_buffer = out + else: + raise TypeError(f"out argument needs to be an NDBuffer. Got {type(out)!r}") + if out_buffer.shape != indexer.shape: + raise ValueError( + f"shape of out argument doesn't match. Expected {indexer.shape}, got {out.shape}" + ) + else: + out_buffer = prototype.nd_buffer.empty( + shape=indexer.shape, + dtype=out_dtype, + order=order, + ) + if product(indexer.shape) > 0: + # need to use the order from the metadata for v2 + _config = config + if metadata.zarr_format == 2: + _config = replace(_config, order=order) + + # reading chunks and decoding them + await codec_pipeline.read( + [ + ( + store_path / metadata.encode_chunk_key(chunk_coords), + metadata.get_chunk_spec(chunk_coords, _config, prototype=prototype), + chunk_selection, + out_selection, + is_complete_chunk, + ) + for chunk_coords, chunk_selection, out_selection, is_complete_chunk in indexer + ], + out_buffer, + drop_axes=indexer.drop_axes, + ) + if isinstance(indexer, BasicIndexer) and indexer.shape == (): + return out_buffer.as_scalar() + return out_buffer.as_ndarray_like() + + +async def _getitem( + store_path: StorePath, + metadata: ArrayMetadata, + codec_pipeline: CodecPipeline, + config: ArrayConfig, + selection: BasicSelection, + *, + prototype: BufferPrototype | None = None, +) -> NDArrayLikeOrScalar: + """ + Retrieve a subset of the array's data based on the provided selection. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + metadata : ArrayMetadata + The array metadata. + codec_pipeline : CodecPipeline + The codec pipeline for encoding/decoding. + config : ArrayConfig + The array configuration. + selection : BasicSelection + A selection object specifying the subset of data to retrieve. + prototype : BufferPrototype, optional + A buffer prototype to use for the retrieved data (default is None). + + Returns + ------- + NDArrayLikeOrScalar + The retrieved subset of the array's data. + """ + if prototype is None: + prototype = default_buffer_prototype() + indexer = BasicIndexer( + selection, + shape=metadata.shape, + chunk_grid=metadata.chunk_grid, + ) + return await _get_selection( + store_path, metadata, codec_pipeline, config, indexer, prototype=prototype + ) + + +async def _get_orthogonal_selection( + store_path: StorePath, + metadata: ArrayMetadata, + codec_pipeline: CodecPipeline, + config: ArrayConfig, + selection: OrthogonalSelection, + *, + out: NDBuffer | None = None, + fields: Fields | None = None, + prototype: BufferPrototype | None = None, +) -> NDArrayLikeOrScalar: + """ + Get an orthogonal selection from the array. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + metadata : ArrayMetadata + The array metadata. + codec_pipeline : CodecPipeline + The codec pipeline for encoding/decoding. + config : ArrayConfig + The array configuration. + selection : OrthogonalSelection + The orthogonal selection specification. + out : NDBuffer | None, optional + An output buffer to write the data to. + fields : Fields | None, optional + Fields to select from structured arrays. + prototype : BufferPrototype | None, optional + A buffer prototype to use for the retrieved data. + + Returns + ------- + NDArrayLikeOrScalar + The selected data. + """ + if prototype is None: + prototype = default_buffer_prototype() + indexer = OrthogonalIndexer(selection, metadata.shape, metadata.chunk_grid) + return await _get_selection( + store_path, + metadata, + codec_pipeline, + config, + indexer=indexer, + out=out, + fields=fields, + prototype=prototype, + ) + + +async def _get_mask_selection( + store_path: StorePath, + metadata: ArrayMetadata, + codec_pipeline: CodecPipeline, + config: ArrayConfig, + mask: MaskSelection, + *, + out: NDBuffer | None = None, + fields: Fields | None = None, + prototype: BufferPrototype | None = None, +) -> NDArrayLikeOrScalar: + """ + Get a mask selection from the array. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + metadata : ArrayMetadata + The array metadata. + codec_pipeline : CodecPipeline + The codec pipeline for encoding/decoding. + config : ArrayConfig + The array configuration. + mask : MaskSelection + The boolean mask specifying the selection. + out : NDBuffer | None, optional + An output buffer to write the data to. + fields : Fields | None, optional + Fields to select from structured arrays. + prototype : BufferPrototype | None, optional + A buffer prototype to use for the retrieved data. + + Returns + ------- + NDArrayLikeOrScalar + The selected data. + """ + if prototype is None: + prototype = default_buffer_prototype() + indexer = MaskIndexer(mask, metadata.shape, metadata.chunk_grid) + return await _get_selection( + store_path, + metadata, + codec_pipeline, + config, + indexer=indexer, + out=out, + fields=fields, + prototype=prototype, + ) + + +async def _get_coordinate_selection( + store_path: StorePath, + metadata: ArrayMetadata, + codec_pipeline: CodecPipeline, + config: ArrayConfig, + selection: CoordinateSelection, + *, + out: NDBuffer | None = None, + fields: Fields | None = None, + prototype: BufferPrototype | None = None, +) -> NDArrayLikeOrScalar: + """ + Get a coordinate selection from the array. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + metadata : ArrayMetadata + The array metadata. + codec_pipeline : CodecPipeline + The codec pipeline for encoding/decoding. + config : ArrayConfig + The array configuration. + selection : CoordinateSelection + The coordinate selection specification. + out : NDBuffer | None, optional + An output buffer to write the data to. + fields : Fields | None, optional + Fields to select from structured arrays. + prototype : BufferPrototype | None, optional + A buffer prototype to use for the retrieved data. + + Returns + ------- + NDArrayLikeOrScalar + The selected data. + """ + if prototype is None: + prototype = default_buffer_prototype() + indexer = CoordinateIndexer(selection, metadata.shape, metadata.chunk_grid) + out_array = await _get_selection( + store_path, + metadata, + codec_pipeline, + config, + indexer=indexer, + out=out, + fields=fields, + prototype=prototype, + ) + + if hasattr(out_array, "shape"): + # restore shape + out_array = np.array(out_array).reshape(indexer.sel_shape) + return out_array + + +async def _set_selection( + store_path: StorePath, + metadata: ArrayMetadata, + codec_pipeline: CodecPipeline, + config: ArrayConfig, + indexer: Indexer, + value: npt.ArrayLike, + *, + prototype: BufferPrototype, + fields: Fields | None = None, +) -> None: + """ + Set a selection in an array. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + metadata : ArrayMetadata + The array metadata. + codec_pipeline : CodecPipeline + The codec pipeline for encoding/decoding. + config : ArrayConfig + The array configuration. + indexer : Indexer + The indexer specifying the selection. + value : npt.ArrayLike + The values to write. + prototype : BufferPrototype + A buffer prototype to use. + fields : Fields | None, optional + Fields to select from structured arrays. + """ + # Get dtype from metadata + if metadata.zarr_format == 2: + zdtype = metadata.dtype + else: + zdtype = metadata.data_type + dtype = zdtype.to_native_dtype() + + # check fields are sensible + check_fields(fields, dtype) + fields = check_no_multi_fields(fields) + + # check value shape + if np.isscalar(value): + array_like = prototype.buffer.create_zero_length().as_array_like() + if isinstance(array_like, np._typing._SupportsArrayFunc): + # TODO: need to handle array types that don't support __array_function__ + # like PyTorch and JAX + array_like_ = cast("np._typing._SupportsArrayFunc", array_like) + value = np.asanyarray(value, dtype=dtype, like=array_like_) + else: + if not hasattr(value, "shape"): + value = np.asarray(value, dtype) + # assert ( + # value.shape == indexer.shape + # ), f"shape of value doesn't match indexer shape. Expected {indexer.shape}, got {value.shape}" + if not hasattr(value, "dtype") or value.dtype.name != dtype.name: + if hasattr(value, "astype"): + # Handle things that are already NDArrayLike more efficiently + value = value.astype(dtype=dtype, order="A") + else: + value = np.array(value, dtype=dtype, order="A") + value = cast("NDArrayLike", value) + + # We accept any ndarray like object from the user and convert it + # to an NDBuffer (or subclass). From this point onwards, we only pass + # Buffer and NDBuffer between components. + value_buffer = prototype.nd_buffer.from_ndarray_like(value) + + # Determine memory order + if metadata.zarr_format == 2: + order = metadata.order + else: + order = config.order + + # need to use the order from the metadata for v2 + _config = config + if metadata.zarr_format == 2: + _config = replace(_config, order=order) + + # merging with existing data and encoding chunks + await codec_pipeline.write( + [ + ( + store_path / metadata.encode_chunk_key(chunk_coords), + metadata.get_chunk_spec(chunk_coords, _config, prototype), + chunk_selection, + out_selection, + is_complete_chunk, + ) + for chunk_coords, chunk_selection, out_selection, is_complete_chunk in indexer + ], + value_buffer, + drop_axes=indexer.drop_axes, + ) + + +async def _setitem( + store_path: StorePath, + metadata: ArrayMetadata, + codec_pipeline: CodecPipeline, + config: ArrayConfig, + selection: BasicSelection, + value: npt.ArrayLike, + prototype: BufferPrototype | None = None, +) -> None: + """ + Set values in the array using basic indexing. + + Parameters + ---------- + store_path : StorePath + The store path of the array. + metadata : ArrayMetadata + The array metadata. + codec_pipeline : CodecPipeline + The codec pipeline for encoding/decoding. + config : ArrayConfig + The array configuration. + selection : BasicSelection + The selection defining the region of the array to set. + value : npt.ArrayLike + The values to be written into the selected region of the array. + prototype : BufferPrototype or None, optional + A prototype buffer that defines the structure and properties of the array chunks being modified. + If None, the default buffer prototype is used. + """ + if prototype is None: + prototype = default_buffer_prototype() + indexer = BasicIndexer( + selection, + shape=metadata.shape, + chunk_grid=metadata.chunk_grid, + ) + return await _set_selection( + store_path, metadata, codec_pipeline, config, indexer, value, prototype=prototype + ) + + +async def _resize( + array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], + new_shape: ShapeLike, + delete_outside_chunks: bool = True, +) -> None: + """ + Resize an array to a new shape. + + Parameters + ---------- + array : AsyncArray + The array to resize. + new_shape : ShapeLike + The desired new shape of the array. + delete_outside_chunks : bool, optional + If True (default), chunks that fall outside the new shape will be deleted. + If False, the data in those chunks will be preserved. + """ + new_shape = parse_shapelike(new_shape) + assert len(new_shape) == len(array.metadata.shape) + new_metadata = array.metadata.update_shape(new_shape) + + if delete_outside_chunks: + # Remove all chunks outside of the new shape + old_chunk_coords = set(array.metadata.chunk_grid.all_chunk_coords(array.metadata.shape)) + new_chunk_coords = set(array.metadata.chunk_grid.all_chunk_coords(new_shape)) + + async def _delete_key(key: str) -> None: + await (array.store_path / key).delete() + + await concurrent_map( + [ + (array.metadata.encode_chunk_key(chunk_coords),) + for chunk_coords in old_chunk_coords.difference(new_chunk_coords) + ], + _delete_key, + zarr_config.get("async.concurrency"), + ) + + # Write new metadata + await save_metadata(array.store_path, new_metadata) + + # Update metadata (in place) + object.__setattr__(array, "metadata", new_metadata) + + +async def _append( + array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], + data: npt.ArrayLike, + axis: int = 0, +) -> tuple[int, ...]: + """ + Append data to an array along the specified axis. + + Parameters + ---------- + array : AsyncArray + The array to append to. + data : npt.ArrayLike + Data to be appended. + axis : int + Axis along which to append. + + Returns + ------- + new_shape : tuple[int, ...] + The new shape of the array after appending. + + Notes + ----- + The size of all dimensions other than `axis` must match between the + array and `data`. + """ + # ensure data is array-like + if not hasattr(data, "shape"): + data = np.asanyarray(data) + + self_shape_preserved = tuple(s for i, s in enumerate(array.shape) if i != axis) + data_shape_preserved = tuple(s for i, s in enumerate(data.shape) if i != axis) + if self_shape_preserved != data_shape_preserved: + raise ValueError( + f"shape of data to append is not compatible with the array. " + f"The shape of the data is ({data_shape_preserved})" + f"and the shape of the array is ({self_shape_preserved})." + "All dimensions must match except for the dimension being " + "appended." + ) + # remember old shape + old_shape = array.shape + + # determine new shape + new_shape = tuple( + array.shape[i] if i != axis else array.shape[i] + data.shape[i] + for i in range(len(array.shape)) + ) + + # resize + await _resize(array, new_shape) + + # store data + append_selection = tuple( + slice(None) if i != axis else slice(old_shape[i], new_shape[i]) + for i in range(len(array.shape)) + ) + await _setitem( + array.store_path, + array.metadata, + array.codec_pipeline, + array.config, + append_selection, + data, + ) + + return new_shape + + +async def _update_attributes( + array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], + new_attributes: dict[str, JSON], +) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]: + """ + Update the array's attributes. + + Parameters + ---------- + array : AsyncArray + The array whose attributes to update. + new_attributes : dict[str, JSON] + A dictionary of new attributes to update or add to the array. + + Returns + ------- + AsyncArray + The array with the updated attributes. + """ + array.metadata.attributes.update(new_attributes) + + # Write new metadata + await save_metadata(array.store_path, array.metadata) + + return array + + +async def _info_complete( + array: AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata], +) -> Any: + """ + Return all the information for an array, including dynamic information like storage size. + + Parameters + ---------- + array : AsyncArray + The array to get info for. + + Returns + ------- + ArrayInfo + Complete information about the array including: + - The count of chunks initialized + - The sum of the bytes written + """ + return array._info( + await _nshards_initialized(array), + await array.store_path.store.getsize_prefix(array.store_path.path), + ) From 2a032a8d370cf8e16097e3285e697dd70b89d717 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 12 Feb 2026 15:17:52 +0100 Subject: [PATCH 198/468] don't use depdendabot for the support/v2 branch (#3701) --- .github/dependabot.yml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 469b6a4d19..82419a5143 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -10,17 +10,6 @@ updates: actions: patterns: - "*" - - # Updates for support/v2 branch - - package-ecosystem: "pip" - directory: "/" - target-branch: "support/v2" - schedule: - interval: "weekly" - groups: - requirements: - patterns: - - "*" - package-ecosystem: "github-actions" directory: "/" target-branch: "support/v2" From 1ed266d9bab6a95e30f9c8de914104ca5237e21c Mon Sep 17 00:00:00 2001 From: Adam Newgas Date: Thu, 12 Feb 2026 20:28:52 +0000 Subject: [PATCH 199/468] Support with read only in wrappers (#3700) * Support with_read_only in LoggingStore and LatencyStore. Fixes #3699 * Support CacheStore.with_read_only * Add entry to changes/ * use a dataclass for mutable cache state --------- Co-authored-by: Davis Bennett --- changes/3700.bugfix.md | 1 + src/zarr/experimental/cache_store.py | 143 +++++++++++--------- src/zarr/storage/_logging.py | 3 + src/zarr/storage/_wrapper.py | 13 +- src/zarr/testing/store.py | 9 +- tests/test_experimental/test_cache_store.py | 102 ++++++++++---- tests/test_store/test_latency.py | 57 ++++++++ tests/test_store/test_logging.py | 40 ++++++ 8 files changed, 268 insertions(+), 100 deletions(-) create mode 100644 changes/3700.bugfix.md create mode 100644 tests/test_store/test_latency.py diff --git a/changes/3700.bugfix.md b/changes/3700.bugfix.md new file mode 100644 index 0000000000..86acb71d0e --- /dev/null +++ b/changes/3700.bugfix.md @@ -0,0 +1 @@ +CacheStore, LoggingStore and LatencyStore now support with_read_only. \ No newline at end of file diff --git a/src/zarr/experimental/cache_store.py b/src/zarr/experimental/cache_store.py index 3456c94320..87adc90c83 100644 --- a/src/zarr/experimental/cache_store.py +++ b/src/zarr/experimental/cache_store.py @@ -4,7 +4,8 @@ import logging import time from collections import OrderedDict -from typing import TYPE_CHECKING, Any, Literal +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, Any, Literal, Self from zarr.abc.store import ByteRequest, Store from zarr.storage._wrapper import WrapperStore @@ -15,6 +16,18 @@ from zarr.core.buffer.core import Buffer, BufferPrototype +@dataclass(slots=True) +class _CacheState: + cache_order: OrderedDict[str, None] = field(default_factory=OrderedDict) + current_size: int = 0 + key_sizes: dict[str, int] = field(default_factory=dict) + lock: asyncio.Lock = field(default_factory=asyncio.Lock) + hits: int = 0 + misses: int = 0 + evictions: int = 0 + key_insert_times: dict[str, float] = field(default_factory=dict) + + class CacheStore(WrapperStore[Store]): """ A dual-store caching implementation for Zarr stores. @@ -36,9 +49,6 @@ class CacheStore(WrapperStore[Store]): Maximum size of the cache in bytes. When exceeded, least recently used items are evicted. None means unlimited size. Default is None. Note: Individual values larger than max_size will not be cached. - key_insert_times : dict[str, float] | None, optional - Dictionary to track insertion times (using monotonic time). - Primarily for internal use. Default is None (creates new dict). cache_set_data : bool, optional Whether to cache data when it's written to the store. Default is True. @@ -69,15 +79,8 @@ class CacheStore(WrapperStore[Store]): _cache: Store max_age_seconds: int | Literal["infinity"] max_size: int | None - key_insert_times: dict[str, float] cache_set_data: bool - _cache_order: OrderedDict[str, None] # Track access order for LRU - _current_size: int # Track current cache size - _key_sizes: dict[str, int] # Track size of each cached key - _lock: asyncio.Lock - _hits: int # Cache hit counter - _misses: int # Cache miss counter - _evictions: int # Cache eviction counter + _state: _CacheState def __init__( self, @@ -86,7 +89,6 @@ def __init__( cache_store: Store, max_age_seconds: int | str = "infinity", max_size: int | None = None, - key_insert_times: dict[str, float] | None = None, cache_set_data: bool = True, ) -> None: super().__init__(store) @@ -107,18 +109,25 @@ def __init__( else: self.max_age_seconds = max_age_seconds self.max_size = max_size - if key_insert_times is None: - self.key_insert_times = {} - else: - self.key_insert_times = key_insert_times self.cache_set_data = cache_set_data - self._cache_order = OrderedDict() - self._current_size = 0 - self._key_sizes = {} - self._lock = asyncio.Lock() - self._hits = 0 - self._misses = 0 - self._evictions = 0 + self._state = _CacheState() + + def _with_store(self, store: Store) -> Self: + # Cannot support this operation because it would share a cache, but have a new store + # So cache keys would conflict + raise NotImplementedError("CacheStore does not support this operation.") + + def with_read_only(self, read_only: bool = False) -> Self: + # Create a new cache store that shares the same cache and mutable state + store = type(self)( + store=self._store.with_read_only(read_only), + cache_store=self._cache, + max_age_seconds=self.max_age_seconds, + max_size=self.max_size, + cache_set_data=self.cache_set_data, + ) + store._state = self._state + return store def _is_key_fresh(self, key: str) -> bool: """Check if a cached key is still fresh based on max_age_seconds. @@ -128,7 +137,7 @@ def _is_key_fresh(self, key: str) -> bool: if self.max_age_seconds == "infinity": return True now = time.monotonic() - elapsed = now - self.key_insert_times.get(key, 0) + elapsed = now - self._state.key_insert_times.get(key, 0) return elapsed < self.max_age_seconds async def _accommodate_value(self, value_size: int) -> None: @@ -140,9 +149,9 @@ async def _accommodate_value(self, value_size: int) -> None: return # Remove least recently used items until we have enough space - while self._current_size + value_size > self.max_size and self._cache_order: + while self._state.current_size + value_size > self.max_size and self._state.cache_order: # Get the least recently used key (first in OrderedDict) - lru_key = next(iter(self._cache_order)) + lru_key = next(iter(self._state.cache_order)) await self._evict_key(lru_key) async def _evict_key(self, key: str) -> None: @@ -152,15 +161,15 @@ async def _evict_key(self, key: str) -> None: Updates size tracking atomically with deletion. """ try: - key_size = self._key_sizes.get(key, 0) + key_size = self._state.key_sizes.get(key, 0) # Delete from cache store await self._cache.delete(key) # Update tracking after successful deletion self._remove_from_tracking(key) - self._current_size = max(0, self._current_size - key_size) - self._evictions += 1 + self._state.current_size = max(0, self._state.current_size - key_size) + self._state.evictions += 1 logger.debug("_evict_key: evicted key %s, freed %d bytes", key, key_size) except Exception: @@ -183,39 +192,39 @@ async def _cache_value(self, key: str, value: Buffer) -> None: ) return - async with self._lock: + async with self._state.lock: # If key already exists, subtract old size first - if key in self._key_sizes: - old_size = self._key_sizes[key] - self._current_size -= old_size + if key in self._state.key_sizes: + old_size = self._state.key_sizes[key] + self._state.current_size -= old_size logger.debug("_cache_value: updating existing key %s, old size %d", key, old_size) # Make room for the new value (this calls _evict_key_locked internally) await self._accommodate_value(value_size) # Update tracking atomically - self._cache_order[key] = None # OrderedDict to track access order - self._current_size += value_size - self._key_sizes[key] = value_size - self.key_insert_times[key] = time.monotonic() + self._state.cache_order[key] = None # OrderedDict to track access order + self._state.current_size += value_size + self._state.key_sizes[key] = value_size + self._state.key_insert_times[key] = time.monotonic() logger.debug("_cache_value: cached key %s with size %d bytes", key, value_size) async def _update_access_order(self, key: str) -> None: """Update the access order for LRU tracking.""" - if key in self._cache_order: - async with self._lock: + if key in self._state.cache_order: + async with self._state.lock: # Move to end (most recently used) - self._cache_order.move_to_end(key) + self._state.cache_order.move_to_end(key) def _remove_from_tracking(self, key: str) -> None: """Remove a key from all tracking structures. - Must be called while holding self._lock. + Must be called while holding self._state.lock. """ - self._cache_order.pop(key, None) - self.key_insert_times.pop(key, None) - self._key_sizes.pop(key, None) + self._state.cache_order.pop(key, None) + self._state.key_insert_times.pop(key, None) + self._state.key_sizes.pop(key, None) async def _get_try_cache( self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None @@ -224,7 +233,7 @@ async def _get_try_cache( maybe_cached_result = await self._cache.get(key, prototype, byte_range) if maybe_cached_result is not None: logger.debug("_get_try_cache: key %s found in cache (HIT)", key) - self._hits += 1 + self._state.hits += 1 # Update access order for LRU await self._update_access_order(key) return maybe_cached_result @@ -232,12 +241,12 @@ async def _get_try_cache( logger.debug( "_get_try_cache: key %s not found in cache (MISS), fetching from store", key ) - self._misses += 1 + self._state.misses += 1 maybe_fresh_result = await super().get(key, prototype, byte_range) if maybe_fresh_result is None: # Key doesn't exist in source store await self._cache.delete(key) - async with self._lock: + async with self._state.lock: self._remove_from_tracking(key) else: # Cache the newly fetched value @@ -249,12 +258,12 @@ async def _get_no_cache( self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None ) -> Buffer | None: """Get data directly from source store and update cache.""" - self._misses += 1 + self._state.misses += 1 maybe_fresh_result = await super().get(key, prototype, byte_range) if maybe_fresh_result is None: # Key doesn't exist in source, remove from cache and tracking await self._cache.delete(key) - async with self._lock: + async with self._state.lock: self._remove_from_tracking(key) else: logger.debug("_get_no_cache: key %s found in store, setting in cache", key) @@ -312,7 +321,7 @@ async def set(self, key: str, value: Buffer) -> None: else: logger.debug("set: deleting key %s from cache", key) await self._cache.delete(key) - async with self._lock: + async with self._state.lock: self._remove_from_tracking(key) async def delete(self, key: str) -> None: @@ -328,7 +337,7 @@ async def delete(self, key: str) -> None: await super().delete(key) logger.debug("delete: deleting key %s from cache", key) await self._cache.delete(key) - async with self._lock: + async with self._state.lock: self._remove_from_tracking(key) def cache_info(self) -> dict[str, Any]: @@ -339,20 +348,20 @@ def cache_info(self) -> dict[str, Any]: if self.max_age_seconds == "infinity" else self.max_age_seconds, "max_size": self.max_size, - "current_size": self._current_size, + "current_size": self._state.current_size, "cache_set_data": self.cache_set_data, - "tracked_keys": len(self.key_insert_times), - "cached_keys": len(self._cache_order), + "tracked_keys": len(self._state.key_insert_times), + "cached_keys": len(self._state.cache_order), } def cache_stats(self) -> dict[str, Any]: """Return cache performance statistics.""" - total_requests = self._hits + self._misses - hit_rate = self._hits / total_requests if total_requests > 0 else 0.0 + total_requests = self._state.hits + self._state.misses + hit_rate = self._state.hits / total_requests if total_requests > 0 else 0.0 return { - "hits": self._hits, - "misses": self._misses, - "evictions": self._evictions, + "hits": self._state.hits, + "misses": self._state.misses, + "evictions": self._state.evictions, "total_requests": total_requests, "hit_rate": hit_rate, } @@ -364,11 +373,11 @@ async def clear_cache(self) -> None: await self._cache.clear() # Reset tracking - async with self._lock: - self.key_insert_times.clear() - self._cache_order.clear() - self._key_sizes.clear() - self._current_size = 0 + async with self._state.lock: + self._state.key_insert_times.clear() + self._state.cache_order.clear() + self._state.key_sizes.clear() + self._state.current_size = 0 logger.debug("clear_cache: cleared all cache data") def __repr__(self) -> str: @@ -379,6 +388,6 @@ def __repr__(self) -> str: f"cache_store={self._cache!r}, " f"max_age_seconds={self.max_age_seconds}, " f"max_size={self.max_size}, " - f"current_size={self._current_size}, " - f"cached_keys={len(self._cache_order)})" + f"current_size={self._state.current_size}, " + f"cached_keys={len(self._state.cache_order)})" ) diff --git a/src/zarr/storage/_logging.py b/src/zarr/storage/_logging.py index dd20d49ae5..98dca6b23d 100644 --- a/src/zarr/storage/_logging.py +++ b/src/zarr/storage/_logging.py @@ -77,6 +77,9 @@ def _default_handler(self) -> logging.Handler: ) return handler + def _with_store(self, store: T_Store) -> Self: + return type(self)(store=store, log_level=self.log_level, log_handler=self.log_handler) + @contextmanager def log(self, hint: Any = "") -> Generator[None, None, None]: """Context manager to log method calls diff --git a/src/zarr/storage/_wrapper.py b/src/zarr/storage/_wrapper.py index 64a5b2d83c..e8a2859abc 100644 --- a/src/zarr/storage/_wrapper.py +++ b/src/zarr/storage/_wrapper.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Generic, TypeVar +from typing import TYPE_CHECKING, Generic, TypeVar, cast if TYPE_CHECKING: from collections.abc import AsyncGenerator, AsyncIterator, Iterable @@ -31,14 +31,23 @@ class WrapperStore(Store, Generic[T_Store]): def __init__(self, store: T_Store) -> None: self._store = store + def _with_store(self, store: T_Store) -> Self: + """ + Constructs a new instance of the wrapper store with the same details but a new store. + """ + return type(self)(store=store) + @classmethod async def open(cls: type[Self], store_cls: type[T_Store], *args: Any, **kwargs: Any) -> Self: store = store_cls(*args, **kwargs) await store._open() return cls(store=store) + def with_read_only(self, read_only: bool = False) -> Self: + return self._with_store(cast(T_Store, self._store.with_read_only(read_only))) + def __enter__(self) -> Self: - return type(self)(self._store.__enter__()) + return self._with_store(self._store.__enter__()) def __exit__( self, diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index 5daf8284eb..aac730e8cf 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -4,7 +4,7 @@ import json import pickle from abc import abstractmethod -from typing import TYPE_CHECKING, Generic, TypeVar +from typing import TYPE_CHECKING, Generic, Self, TypeVar from zarr.storage import WrapperStore @@ -578,10 +578,13 @@ class LatencyStore(WrapperStore[Store]): get_latency: float set_latency: float - def __init__(self, cls: Store, *, get_latency: float = 0, set_latency: float = 0) -> None: + def __init__(self, store: Store, *, get_latency: float = 0, set_latency: float = 0) -> None: self.get_latency = float(get_latency) self.set_latency = float(set_latency) - self._store = cls + self._store = store + + def _with_store(self, store: Store) -> Self: + return type(self)(store, get_latency=self.get_latency, set_latency=self.set_latency) async def set(self, key: str, value: Buffer) -> None: """ diff --git a/tests/test_experimental/test_cache_store.py b/tests/test_experimental/test_cache_store.py index d4a45f78f1..50d3d9506b 100644 --- a/tests/test_experimental/test_cache_store.py +++ b/tests/test_experimental/test_cache_store.py @@ -30,7 +30,61 @@ def cache_store(self) -> MemoryStore: @pytest.fixture def cached_store(self, source_store: Store, cache_store: Store) -> CacheStore: """Create a cached store instance.""" - return CacheStore(source_store, cache_store=cache_store, key_insert_times={}) + return CacheStore(source_store, cache_store=cache_store) + + async def test_with_read_only_round_trip(self) -> None: + """ + Ensure that CacheStore.with_read_only returns another CacheStore with + the requested read_only state, shares cache state, and does not change + the original store's read_only flag. + """ + source = MemoryStore() + cache = MemoryStore() + + # Start from a read-only underlying store + source_ro = source.with_read_only(read_only=True) + cached_ro = CacheStore(store=source_ro, cache_store=cache) + assert cached_ro.read_only + + buf = CPUBuffer.from_bytes(b"0123") + + # Cannot write through the read-only cache store + with pytest.raises( + ValueError, match="store was opened in read-only mode and does not support writing" + ): + await cached_ro.set("foo", buf) + + # Create a writable cache store from the read-only one + writer = cached_ro.with_read_only(read_only=False) + assert isinstance(writer, CacheStore) + assert not writer.read_only + + # Cache configuration and state are shared + assert writer._cache is cached_ro._cache + assert writer._state is cached_ro._state + assert writer._state.key_insert_times is cached_ro._state.key_insert_times + + # Writes via the writable cache store succeed and are cached + await writer.set("foo", buf) + out = await writer.get("foo", default_buffer_prototype()) + assert out is not None + assert out.to_bytes() == buf.to_bytes() + + # The original cache store remains read-only + assert cached_ro.read_only + with pytest.raises( + ValueError, match="store was opened in read-only mode and does not support writing" + ): + await cached_ro.set("bar", buf) + + # Creating a read-only copy from the writable cache store works and is enforced + reader = writer.with_read_only(read_only=True) + assert isinstance(reader, CacheStore) + assert reader.read_only + with pytest.raises( + ValueError, match="store was opened in read-only mode and does not support writing" + ): + await reader.set("baz", buf) async def test_basic_caching(self, cached_store: CacheStore, source_store: Store) -> None: """Test basic cache functionality.""" @@ -71,7 +125,6 @@ async def test_cache_expiration(self) -> None: source_store, cache_store=cache_store, max_age_seconds=1, # 1 second expiration - key_insert_times={}, ) # Store data @@ -96,9 +149,7 @@ async def test_cache_expiration(self) -> None: async def test_cache_set_data_false(self, source_store: Store, cache_store: Store) -> None: """Test behavior when cache_set_data=False.""" - cached_store = CacheStore( - source_store, cache_store=cache_store, cache_set_data=False, key_insert_times={} - ) + cached_store = CacheStore(source_store, cache_store=cache_store, cache_set_data=False) test_data = CPUBuffer.from_bytes(b"no cache data") await cached_store.set("no_cache_key", test_data) @@ -154,9 +205,7 @@ async def test_stale_cache_refresh(self) -> None: """Test that stale cache entries are refreshed from source.""" source_store = MemoryStore() cache_store = MemoryStore() - cached_store = CacheStore( - source_store, cache_store=cache_store, max_age_seconds=1, key_insert_times={} - ) + cached_store = CacheStore(source_store, cache_store=cache_store, max_age_seconds=1) # Store initial data old_data = CPUBuffer.from_bytes(b"old data") @@ -194,14 +243,10 @@ async def test_cache_returns_cached_data_for_performance( self, cached_store: CacheStore, source_store: Store ) -> None: """Test that cache returns cached data for performance, even if not in source.""" - # Skip test if key_insert_times attribute doesn't exist - if not hasattr(cached_store, "key_insert_times"): - pytest.skip("key_insert_times attribute not implemented") - # Put data in cache but not source (simulates orphaned cache entry) test_data = CPUBuffer.from_bytes(b"orphaned data") await cached_store._cache.set("orphan_key", test_data) - cached_store.key_insert_times["orphan_key"] = time.monotonic() + cached_store._state.key_insert_times["orphan_key"] = time.monotonic() # Cache should return data for performance (no source verification) result = await cached_store.get("orphan_key", default_buffer_prototype()) @@ -210,7 +255,7 @@ async def test_cache_returns_cached_data_for_performance( # Cache entry should remain (performance optimization) assert await cached_store._cache.exists("orphan_key") - assert "orphan_key" in cached_store.key_insert_times + assert "orphan_key" in cached_store._state.key_insert_times async def test_cache_coherency_through_expiration(self) -> None: """Test that cache coherency is managed through cache expiration, not source verification.""" @@ -288,7 +333,6 @@ async def test_cache_info_with_max_size(self) -> None: cache_store=cache_store, max_size=1024, max_age_seconds=300, - key_insert_times={}, ) info = cached_store.cache_info() @@ -365,7 +409,7 @@ async def test_max_age_numeric(self) -> None: assert cached_store._is_key_fresh("test_key") # Manually set old timestamp to test expiration - cached_store.key_insert_times["test_key"] = time.monotonic() - 2 # 2 seconds ago + cached_store._state.key_insert_times["test_key"] = time.monotonic() - 2 # 2 seconds ago # Key should now be stale assert not cached_store._is_key_fresh("test_key") @@ -519,7 +563,7 @@ async def test_evict_key_exception_handling(self) -> None: # Manually corrupt the tracking to trigger exception # Remove from one structure but not others to create inconsistency - del cached_store._cache_order["test_key"] + del cached_store._state.cache_order["test_key"] # Try to evict - should handle the KeyError gracefully await cached_store._evict_key("test_key") @@ -540,16 +584,16 @@ async def test_get_no_cache_delete_tracking(self) -> None: await cached_store._cache_value("phantom_key", test_data) # Verify it's in tracking - assert "phantom_key" in cached_store._cache_order - assert "phantom_key" in cached_store.key_insert_times + assert "phantom_key" in cached_store._state.cache_order + assert "phantom_key" in cached_store._state.key_insert_times # Now try to get it - since it's not in source, should clean up tracking result = await cached_store._get_no_cache("phantom_key", default_buffer_prototype()) assert result is None # Should have cleaned up tracking - assert "phantom_key" not in cached_store._cache_order - assert "phantom_key" not in cached_store.key_insert_times + assert "phantom_key" not in cached_store._state.cache_order + assert "phantom_key" not in cached_store._state.key_insert_times async def test_accommodate_value_no_max_size(self) -> None: """Test _accommodate_value early return when max_size is None.""" @@ -609,7 +653,9 @@ async def set_large(key: str) -> None: # Size should be consistent with tracked keys assert info["current_size"] <= 200 # Might pass # But verify actual cache store size matches tracking - total_size = sum(cached_store._key_sizes.get(k, 0) for k in cached_store._cache_order) + total_size = sum( + cached_store._state.key_sizes.get(k, 0) for k in cached_store._state.cache_order + ) assert total_size == info["current_size"] # WOULD FAIL async def test_concurrent_get_and_evict(self) -> None: @@ -638,7 +684,7 @@ async def write_key() -> None: # Verify consistency info = cached_store.cache_info() assert info["current_size"] <= 100 - assert len(cached_store._cache_order) == len(cached_store._key_sizes) + assert len(cached_store._state.cache_order) == len(cached_store._state.key_sizes) async def test_eviction_actually_deletes_from_cache_store(self) -> None: """Test that eviction removes keys from cache_store, not just tracking.""" @@ -659,8 +705,8 @@ async def test_eviction_actually_deletes_from_cache_store(self) -> None: await cached_store.set("key2", data2) # Check tracking - key1 should be removed - assert "key1" not in cached_store._cache_order - assert "key1" not in cached_store._key_sizes + assert "key1" not in cached_store._state.cache_order + assert "key1" not in cached_store._state.key_sizes # CRITICAL: key1 should also be removed from cache_store assert not await cache_store.exists("key1"), ( @@ -733,13 +779,13 @@ async def test_all_tracked_keys_exist_in_cache_store(self) -> None: await cached_store.set(f"key_{i}", data) # Every key in tracking should exist in cache_store - for key in cached_store._cache_order: + for key in cached_store._state.cache_order: assert await cache_store.exists(key), ( f"Key '{key}' is tracked but doesn't exist in cache_store" ) # Every key in _key_sizes should exist in cache_store - for key in cached_store._key_sizes: + for key in cached_store._state.key_sizes: assert await cache_store.exists(key), ( f"Key '{key}' has size tracked but doesn't exist in cache_store" ) @@ -778,7 +824,7 @@ async def failing_delete(key: str) -> None: # Attempt to evict should raise the exception with pytest.raises(RuntimeError, match="Simulated cache deletion failure"): - async with cached_store._lock: + async with cached_store._state.lock: await cached_store._evict_key("test_key") async def test_cache_stats_method(self) -> None: diff --git a/tests/test_store/test_latency.py b/tests/test_store/test_latency.py new file mode 100644 index 0000000000..38ffb17dd6 --- /dev/null +++ b/tests/test_store/test_latency.py @@ -0,0 +1,57 @@ +from __future__ import annotations + +import pytest + +from zarr.core.buffer import default_buffer_prototype +from zarr.storage import MemoryStore +from zarr.testing.store import LatencyStore + + +async def test_latency_store_with_read_only_round_trip() -> None: + """ + Ensure that LatencyStore.with_read_only returns another LatencyStore with + the requested read_only state, preserves latency configuration, and does + not change the original wrapper. + """ + base = await MemoryStore.open() + # Start from a read-only underlying store + ro_base = base.with_read_only(read_only=True) + latency_ro = LatencyStore(ro_base, get_latency=0.01, set_latency=0.02) + + assert latency_ro.read_only + assert latency_ro.get_latency == pytest.approx(0.01) + assert latency_ro.set_latency == pytest.approx(0.02) + + buf = default_buffer_prototype().buffer.from_bytes(b"abcd") + + # Cannot write through the read-only wrapper + with pytest.raises( + ValueError, match="store was opened in read-only mode and does not support writing" + ): + await latency_ro.set("key", buf) + + # Create a writable wrapper from the read-only one + writer = latency_ro.with_read_only(read_only=False) + assert isinstance(writer, LatencyStore) + assert not writer.read_only + # Latency configuration is preserved + assert writer.get_latency == latency_ro.get_latency + assert writer.set_latency == latency_ro.set_latency + + # Writes via the writable wrapper succeed + await writer.set("key", buf) + out = await writer.get("key", prototype=default_buffer_prototype()) + assert out is not None + assert out.to_bytes() == buf.to_bytes() + + # Creating a read-only copy from the writable wrapper works and is enforced + reader = writer.with_read_only(read_only=True) + assert isinstance(reader, LatencyStore) + assert reader.read_only + with pytest.raises( + ValueError, match="store was opened in read-only mode and does not support writing" + ): + await reader.set("other", buf) + + # The original read-only wrapper remains read-only + assert latency_ro.read_only diff --git a/tests/test_store/test_logging.py b/tests/test_store/test_logging.py index fa566e45aa..96cd184938 100644 --- a/tests/test_store/test_logging.py +++ b/tests/test_store/test_logging.py @@ -86,6 +86,46 @@ def test_is_open_setter_raises(self, store: LoggingStore[LocalStore]) -> None: ): store._is_open = True + async def test_with_read_only_round_trip(self, local_store: LocalStore) -> None: + """ + Ensure that LoggingStore.with_read_only returns another LoggingStore with + the requested read_only state, preserves logging configuration, and does + not change the original store. + """ + # Start from a read-only underlying store + ro_store = local_store.with_read_only(read_only=True) + wrapped_ro = LoggingStore(store=ro_store, log_level="INFO") + assert wrapped_ro.read_only + + buf = default_buffer_prototype().buffer.from_bytes(b"0123") + + # Cannot write through the read-only wrapper + with pytest.raises( + ValueError, match="store was opened in read-only mode and does not support writing" + ): + await wrapped_ro.set("foo", buf) + + # Create a writable wrapper + writer = wrapped_ro.with_read_only(read_only=False) + assert isinstance(writer, LoggingStore) + assert not writer.read_only + # logging configuration is preserved + assert writer.log_level == wrapped_ro.log_level + assert writer.log_handler == wrapped_ro.log_handler + + # Writes via the writable wrapper succeed + await writer.set("foo", buf) + out = await writer.get("foo", prototype=default_buffer_prototype()) + assert out is not None + assert out.to_bytes() == buf.to_bytes() + + # The original wrapper remains read-only + assert wrapped_ro.read_only + with pytest.raises( + ValueError, match="store was opened in read-only mode and does not support writing" + ): + await wrapped_ro.set("bar", buf) + @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) async def test_logging_store(store: Store, caplog: pytest.LogCaptureFixture) -> None: From 3e7d24d888a089a82ea1eaef3a53a3d7fa21d052 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 12 Feb 2026 22:08:44 +0100 Subject: [PATCH 200/468] perf:improve performance of morton order iter (#3705) * improve performance of morton order iter * changelog --- changes/3705.bugfix.md | 1 + src/zarr/core/indexing.py | 19 +++++---- tests/test_codecs/test_codecs.py | 66 +++++++++++++++++++++++++------- 3 files changed, 65 insertions(+), 21 deletions(-) create mode 100644 changes/3705.bugfix.md diff --git a/changes/3705.bugfix.md b/changes/3705.bugfix.md new file mode 100644 index 0000000000..2abcb4ee7c --- /dev/null +++ b/changes/3705.bugfix.md @@ -0,0 +1 @@ +Fix a performance bug in morton curve generation. \ No newline at end of file diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 7f704bf2b7..beffa99cfa 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -7,7 +7,7 @@ from collections.abc import Iterator, Sequence from dataclasses import dataclass from enum import Enum -from functools import reduce +from functools import lru_cache, reduce from types import EllipsisType from typing import ( TYPE_CHECKING, @@ -1467,16 +1467,21 @@ def decode_morton(z: int, chunk_shape: tuple[int, ...]) -> tuple[int, ...]: return tuple(out) -def morton_order_iter(chunk_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: - i = 0 +@lru_cache +def _morton_order(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: + n_total = product(chunk_shape) order: list[tuple[int, ...]] = [] - while len(order) < product(chunk_shape): + i = 0 + while len(order) < n_total: m = decode_morton(i, chunk_shape) - if m not in order and all(x < y for x, y in zip(m, chunk_shape, strict=False)): + if all(x < y for x, y in zip(m, chunk_shape, strict=False)): order.append(m) i += 1 - for j in range(product(chunk_shape)): - yield order[j] + return tuple(order) + + +def morton_order_iter(chunk_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: + return iter(_morton_order(tuple(chunk_shape))) def c_order_iter(chunks_per_shard: tuple[int, ...]) -> Iterator[tuple[int, ...]]: diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index eae7168d49..fa2017876e 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -18,7 +18,7 @@ TransposeCodec, ) from zarr.core.buffer import default_buffer_prototype -from zarr.core.indexing import BasicSelection, morton_order_iter +from zarr.core.indexing import BasicSelection, decode_morton, morton_order_iter from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.dtype import UInt8 from zarr.errors import ZarrUserWarning @@ -171,7 +171,8 @@ def test_open(store: Store) -> None: assert a.metadata == b.metadata -def test_morton() -> None: +def test_morton_exact_order() -> None: + """Test exact morton ordering for power-of-2 shapes.""" assert list(morton_order_iter((2, 2))) == [(0, 0), (1, 0), (0, 1), (1, 1)] assert list(morton_order_iter((2, 2, 2))) == [ (0, 0, 0), @@ -206,21 +207,58 @@ def test_morton() -> None: @pytest.mark.parametrize( "shape", [ - [2, 2, 2], - [5, 2], - [2, 5], - [2, 9, 2], - [3, 2, 12], - [2, 5, 1], - [4, 3, 6, 2, 7], - [3, 2, 1, 6, 4, 5, 2], + (2, 2, 2), + (5, 2), + (2, 5), + (2, 9, 2), + (3, 2, 12), + (2, 5, 1), + (4, 3, 6, 2, 7), + (3, 2, 1, 6, 4, 5, 2), + (1,), + (1, 1), + (5, 1, 3), + (1, 4, 1, 2), ], ) -def test_morton2(shape: tuple[int, ...]) -> None: +def test_morton_is_permutation(shape: tuple[int, ...]) -> None: + """Test that morton_order_iter produces every valid coordinate exactly once.""" + import itertools + + from zarr.core.common import product + + order = list(morton_order_iter(shape)) + expected_len = product(shape) + # completeness: every valid coordinate is present + assert len(order) == expected_len + # no duplicates + assert len(set(order)) == expected_len + # all coordinates are within bounds + assert all(all(c < s for c, s in zip(coord, shape, strict=True)) for coord in order) + # the set of coordinates equals the full cartesian product + assert set(order) == set(itertools.product(*(range(s) for s in shape))) + + +@pytest.mark.parametrize( + "shape", + [ + (2, 2), + (4, 4), + (2, 2, 2), + (4, 4, 4), + (2, 2, 2, 2), + ], +) +def test_morton_ordering(shape: tuple[int, ...]) -> None: + """Test that the iteration order matches consecutive decode_morton outputs. + + For power-of-2 shapes, every decode_morton output is in-bounds, + so the ordering should be exactly decode_morton(0), decode_morton(1), ... + """ + order = list(morton_order_iter(shape)) - for i, x in enumerate(order): - assert x not in order[:i] # no duplicates - assert all(x[j] < shape[j] for j in range(len(shape))) # all indices are within bounds + for i, coord in enumerate(order): + assert coord == decode_morton(i, shape) @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) From a06318ed3ace289d7b53bf55f99df50979e4dc68 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 12 Feb 2026 22:24:05 +0100 Subject: [PATCH 201/468] allow numpy ints in shapelike (#3706) * allow numpy ints in shapelike * changelog * type checker --- changes/3706.misc.md | 1 + src/zarr/core/common.py | 16 +++++++++++----- tests/test_common.py | 14 ++++++++++---- 3 files changed, 22 insertions(+), 9 deletions(-) create mode 100644 changes/3706.misc.md diff --git a/changes/3706.misc.md b/changes/3706.misc.md new file mode 100644 index 0000000000..70a0e44c58 --- /dev/null +++ b/changes/3706.misc.md @@ -0,0 +1 @@ +Allow NumPy ints as input when declaring a shape. \ No newline at end of file diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index d38949657e..275d062eba 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -21,6 +21,7 @@ overload, ) +import numpy as np from typing_extensions import ReadOnly from zarr.core.config import config as zarr_config @@ -37,7 +38,7 @@ ZMETADATA_V2_JSON = ".zmetadata" BytesLike = bytes | bytearray | memoryview -ShapeLike = Iterable[int] | int +ShapeLike = Iterable[int | np.integer[Any]] | int | np.integer[Any] # For backwards compatibility ChunkCoords = tuple[int, ...] ZarrFormat = Literal[2, 3] @@ -185,23 +186,28 @@ def parse_named_configuration( def parse_shapelike(data: ShapeLike) -> tuple[int, ...]: - if isinstance(data, int): + """ + Parse a shape-like input into an explicit shape. + """ + if isinstance(data, int | np.integer): if data < 0: raise ValueError(f"Expected a non-negative integer. Got {data} instead") - return (data,) + return (int(data),) try: data_tuple = tuple(data) except TypeError as e: msg = f"Expected an integer or an iterable of integers. Got {data} instead." raise TypeError(msg) from e - if not all(isinstance(v, int) for v in data_tuple): + if not all(isinstance(v, int | np.integer) for v in data_tuple): msg = f"Expected an iterable of integers. Got {data} instead." raise TypeError(msg) if not all(v > -1 for v in data_tuple): msg = f"Expected all values to be non-negative. Got {data} instead." raise ValueError(msg) - return data_tuple + + # cast NumPy scalars to plain python ints + return tuple(int(x) for x in data_tuple) def parse_fill_value(data: Any) -> Any: diff --git a/tests/test_common.py b/tests/test_common.py index 0944c3375a..0dedde1d6b 100644 --- a/tests/test_common.py +++ b/tests/test_common.py @@ -1,5 +1,6 @@ from __future__ import annotations +from collections.abc import Iterable from typing import TYPE_CHECKING, get_args import numpy as np @@ -15,7 +16,6 @@ from zarr.core.config import parse_indexing_order if TYPE_CHECKING: - from collections.abc import Iterable from typing import Any, Literal @@ -115,9 +115,15 @@ def test_parse_shapelike_invalid_iterable_values(data: Any) -> None: parse_shapelike(data) -@pytest.mark.parametrize("data", [range(10), [0, 1, 2, 3], (3, 4, 5), ()]) -def test_parse_shapelike_valid(data: Iterable[int]) -> None: - assert parse_shapelike(data) == tuple(data) +@pytest.mark.parametrize( + "data", [range(10), [0, 1, 2, np.uint64(3)], (3, 4, 5), (), 1, np.uint8(1)] +) +def test_parse_shapelike_valid(data: Iterable[int] | int) -> None: + if isinstance(data, Iterable): + expected = tuple(data) + else: + expected = (data,) + assert parse_shapelike(data) == expected # todo: more dtypes From e03cfc897ac5e0a20001ee37580dce19ea3f567a Mon Sep 17 00:00:00 2001 From: antoinegaston <104137175+antoinegaston@users.noreply.github.com> Date: Fri, 13 Feb 2026 13:37:10 +0100 Subject: [PATCH 202/468] =?UTF-8?q?=F0=9F=90=9B=20Fix=20obstore=20listdir?= =?UTF-8?q?=20method=20using=20=5Frelativize=5Fpath=20(#3657)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 🐛 Fix obstore listdir method using _relativize_path * 📝 Add changelog entry * its a bugfix --------- Co-authored-by: Davis Bennett --- changes/3657.bugfix.md | 1 + src/zarr/storage/_obstore.py | 12 ++++++++---- src/zarr/testing/store.py | 36 ++++++++++++++++++++++++------------ 3 files changed, 33 insertions(+), 16 deletions(-) create mode 100644 changes/3657.bugfix.md diff --git a/changes/3657.bugfix.md b/changes/3657.bugfix.md new file mode 100644 index 0000000000..1411704674 --- /dev/null +++ b/changes/3657.bugfix.md @@ -0,0 +1 @@ +Fix obstore _transform_list_dir implementation to correctly relativize paths (removing lstrip usage). \ No newline at end of file diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index 5c2197ecf6..6e4011da59 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -4,6 +4,8 @@ import contextlib import pickle from collections import defaultdict +from itertools import chain +from operator import itemgetter from typing import TYPE_CHECKING, Generic, Self, TypedDict, TypeVar from zarr.abc.store import ( @@ -15,6 +17,7 @@ ) from zarr.core.common import concurrent_map from zarr.core.config import config +from zarr.storage._utils import _relativize_path if TYPE_CHECKING: from collections.abc import AsyncGenerator, Coroutine, Iterable, Sequence @@ -263,10 +266,11 @@ async def _transform_list_dir( # We assume that the underlying object-store implementation correctly handles the # prefix, so we don't double-check that the returned results actually start with the # given prefix. - prefixes = [obj.lstrip(prefix).lstrip("/") for obj in list_result["common_prefixes"]] - objects = [obj["path"].removeprefix(prefix).lstrip("/") for obj in list_result["objects"]] - for item in prefixes + objects: - yield item + prefix = prefix.rstrip("/") + for path in chain( + list_result["common_prefixes"], map(itemgetter("path"), list_result["objects"]) + ): + yield _relativize_path(path=path, prefix=prefix) class _BoundedRequest(TypedDict): diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index aac730e8cf..1b8e85ed98 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -492,24 +492,36 @@ async def test_list_empty_path(self, store: S) -> None: assert observed_prefix_sorted == expected_prefix_sorted async def test_list_dir(self, store: S) -> None: - root = "foo" - store_dict = { - root + "/zarr.json": self.buffer_cls.from_bytes(b"bar"), - root + "/c/1": self.buffer_cls.from_bytes(b"\x01"), - } + roots_and_keys: list[tuple[str, dict[str, Buffer]]] = [ + ( + "foo", + { + "foo/zarr.json": self.buffer_cls.from_bytes(b"bar"), + "foo/c/1": self.buffer_cls.from_bytes(b"\x01"), + }, + ), + ( + "foo/bar", + { + "foo/bar/foobar_first_child": self.buffer_cls.from_bytes(b"1"), + "foo/bar/foobar_second_child/zarr.json": self.buffer_cls.from_bytes(b"2"), + }, + ), + ] assert await _collect_aiterator(store.list_dir("")) == () - assert await _collect_aiterator(store.list_dir(root)) == () - await store._set_many(store_dict.items()) + for root, store_dict in roots_and_keys: + assert await _collect_aiterator(store.list_dir(root)) == () - keys_observed = await _collect_aiterator(store.list_dir(root)) - keys_expected = {k.removeprefix(root + "/").split("/")[0] for k in store_dict} + await store._set_many(store_dict.items()) - assert sorted(keys_observed) == sorted(keys_expected) + keys_observed = await _collect_aiterator(store.list_dir(root)) + keys_expected = {k.removeprefix(root + "/").split("/")[0] for k in store_dict} + assert sorted(keys_observed) == sorted(keys_expected) - keys_observed = await _collect_aiterator(store.list_dir(root + "/")) - assert sorted(keys_expected) == sorted(keys_observed) + keys_observed = await _collect_aiterator(store.list_dir(root + "/")) + assert sorted(keys_expected) == sorted(keys_observed) async def test_set_if_not_exists(self, store: S) -> None: key = "k" From 23596c148087d868a07427315a4d9b05112a0015 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 13 Feb 2026 15:19:16 +0100 Subject: [PATCH 203/468] perf:remove isinstance check (#3704) * remove isinstance check inside bytescodec * remove isinstance check inside bytescodec * changelog --- changes/3704.misc.md | 1 + src/zarr/codecs/bytes.py | 11 ++--------- 2 files changed, 3 insertions(+), 9 deletions(-) create mode 100644 changes/3704.misc.md diff --git a/changes/3704.misc.md b/changes/3704.misc.md new file mode 100644 index 0000000000..d15d4924e0 --- /dev/null +++ b/changes/3704.misc.md @@ -0,0 +1 @@ +Remove an expensive `isinstance` check from the bytes codec decoding routine. \ No newline at end of file diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index 39c26bd4a8..1fbdeef497 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -5,10 +5,8 @@ from enum import Enum from typing import TYPE_CHECKING -import numpy as np - from zarr.abc.codec import ArrayBytesCodec -from zarr.core.buffer import Buffer, NDArrayLike, NDBuffer +from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import JSON, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasEndianness @@ -72,7 +70,6 @@ async def _decode_single( chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> NDBuffer: - assert isinstance(chunk_bytes, Buffer) # TODO: remove endianness enum in favor of literal union endian_str = self.endian.value if self.endian is not None else None if isinstance(chunk_spec.dtype, HasEndianness): @@ -80,12 +77,8 @@ async def _decode_single( else: dtype = chunk_spec.dtype.to_native_dtype() as_array_like = chunk_bytes.as_array_like() - if isinstance(as_array_like, NDArrayLike): - as_nd_array_like = as_array_like - else: - as_nd_array_like = np.asanyarray(as_array_like) chunk_array = chunk_spec.prototype.nd_buffer.from_ndarray_like( - as_nd_array_like.view(dtype=dtype) + as_array_like.view(dtype=dtype) # type: ignore[attr-defined] ) # ensure correct chunk shape From 306e480fe27c2e3b50cdf7b00b49a6569e5b8e3c Mon Sep 17 00:00:00 2001 From: jnotjay <88787588+jakenotjay@users.noreply.github.com> Date: Tue, 17 Feb 2026 16:57:57 +0000 Subject: [PATCH 204/468] Skip chunk coordinate enumeration in resize when array is only growing (#3650) (#3702) * Skip chunk coordinate enumeration in resize when array is only growing (#3650) * Add tests for growth, shrink, and mixed resize operations to ensure chunk enumeration skipped correctly * changelog --------- Co-authored-by: Davis Bennett Co-authored-by: Deepak Cherian --- changes/3702.bugfix.md | 1 + src/zarr/core/array.py | 5 +++- tests/test_array.py | 67 ++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 72 insertions(+), 1 deletion(-) create mode 100644 changes/3702.bugfix.md diff --git a/changes/3702.bugfix.md b/changes/3702.bugfix.md new file mode 100644 index 0000000000..94a2902567 --- /dev/null +++ b/changes/3702.bugfix.md @@ -0,0 +1 @@ +Skip chunk coordinate enumeration in resize when the array is only growing, avoiding unbounded memory usage for large arrays. \ No newline at end of file diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 7abb0075dc..564d0e915a 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -5990,7 +5990,10 @@ async def _resize( assert len(new_shape) == len(array.metadata.shape) new_metadata = array.metadata.update_shape(new_shape) - if delete_outside_chunks: + # ensure deletion is only run if array is shrinking as the delete_outside_chunks path is unbounded in memory + only_growing = all(new >= old for new, old in zip(new_shape, array.metadata.shape, strict=True)) + + if delete_outside_chunks and not only_growing: # Remove all chunks outside of the new shape old_chunk_coords = set(array.metadata.chunk_grid.all_chunk_coords(array.metadata.shape)) new_chunk_coords = set(array.metadata.chunk_grid.all_chunk_coords(new_shape)) diff --git a/tests/test_array.py b/tests/test_array.py index b7d7bc723d..01a82e1938 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -781,6 +781,73 @@ def test_resize_2d(store: MemoryStore, zarr_format: ZarrFormat) -> None: assert new_shape == result.shape +@pytest.mark.parametrize("store", ["memory"], indirect=True) +def test_resize_growing_skips_chunk_enumeration( + store: MemoryStore, zarr_format: ZarrFormat +) -> None: + """Growing an array should not enumerate chunk coords for deletion (#3650 mitigation).""" + from zarr.core.chunk_grids import RegularChunkGrid + + z = zarr.create( + shape=(10, 10), + chunks=(5, 5), + dtype="i4", + fill_value=0, + store=store, + zarr_format=zarr_format, + ) + z[:] = np.ones((10, 10), dtype="i4") + + # growth only - ensure no chunk coords are enumerated + with mock.patch.object( + RegularChunkGrid, + "all_chunk_coords", + wraps=z.metadata.chunk_grid.all_chunk_coords, + ) as mock_coords: + z.resize((20, 20)) + mock_coords.assert_not_called() + + assert z.shape == (20, 20) + np.testing.assert_array_equal(np.ones((10, 10), dtype="i4"), z[:10, :10]) + np.testing.assert_array_equal(np.zeros((10, 10), dtype="i4"), z[10:, 10:]) + + # shrink - ensure no regression of behaviour + with mock.patch.object( + RegularChunkGrid, + "all_chunk_coords", + wraps=z.metadata.chunk_grid.all_chunk_coords, + ) as mock_coords: + z.resize((5, 5)) + assert mock_coords.call_count > 0 + + assert z.shape == (5, 5) + np.testing.assert_array_equal(np.ones((5, 5), dtype="i4"), z[:]) + + # mixed: grow dim 0, shrink dim 1 - ensure deletion path runs + z2 = zarr.create( + shape=(10, 10), + chunks=(5, 5), + dtype="i4", + fill_value=0, + store=store, + zarr_format=zarr_format, + overwrite=True, + ) + z2[:] = np.ones((10, 10), dtype="i4") + + with mock.patch.object( + RegularChunkGrid, + "all_chunk_coords", + wraps=z2.metadata.chunk_grid.all_chunk_coords, + ) as mock_coords: + z2.resize((20, 5)) + assert mock_coords.call_count > 0 + + assert z2.shape == (20, 5) + np.testing.assert_array_equal(np.ones((10, 5), dtype="i4"), z2[:10, :]) + np.testing.assert_array_equal(np.zeros((10, 5), dtype="i4"), z2[10:, :]) + + @pytest.mark.parametrize("store", ["memory"], indirect=True) def test_append_1d(store: MemoryStore, zarr_format: ZarrFormat) -> None: a = np.arange(105) From 36caf1fc4dc0f422ea6d3309e838589c3bc99a2d Mon Sep 17 00:00:00 2001 From: Mark Kittisopikul Date: Wed, 18 Feb 2026 03:22:57 -0500 Subject: [PATCH 205/468] perf:Add additional sharding benchmarks (#3712) * test:Add sharding indexing benchmarks * test:Add morton_order_iter benchmark tests * tests:Add single chunk write test for sharding * Document changes --------- Co-authored-by: Davis Bennett --- changes/3712.misc.md | 1 + tests/benchmarks/test_indexing.py | 215 ++++++++++++++++++++++++++++++ 2 files changed, 216 insertions(+) create mode 100644 changes/3712.misc.md diff --git a/changes/3712.misc.md b/changes/3712.misc.md new file mode 100644 index 0000000000..8fa2f2d2f7 --- /dev/null +++ b/changes/3712.misc.md @@ -0,0 +1 @@ +Added benchmarks for Morton order computation in sharded arrays. diff --git a/tests/benchmarks/test_indexing.py b/tests/benchmarks/test_indexing.py index 9ca0d8e1af..dff2269dcb 100644 --- a/tests/benchmarks/test_indexing.py +++ b/tests/benchmarks/test_indexing.py @@ -50,3 +50,218 @@ def test_slice_indexing( data[:] = 1 benchmark(getitem, data, indexer) + + +# Benchmark for Morton order optimization with power-of-2 shards +# Morton order is used internally by sharding codec for chunk iteration +morton_shards = ( + (16,) * 3, # With 2x2x2 chunks: 8x8x8 = 512 chunks per shard + (32,) * 3, # With 2x2x2 chunks: 16x16x16 = 4096 chunks per shard +) + + +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("shards", morton_shards, ids=str) +def test_sharded_morton_indexing( + store: Store, + shards: tuple[int, ...], + benchmark: BenchmarkFixture, +) -> None: + """Benchmark sharded array indexing with power-of-2 chunks per shard. + + This benchmark exercises the Morton order iteration path in the sharding + codec, which benefits from the hypercube and vectorization optimizations. + The Morton order cache is cleared before each iteration to measure the + full computation cost. + """ + from zarr.core.indexing import _morton_order + + # Create array where each shard contains many small chunks + # e.g., shards=(32,32,32) with chunks=(2,2,2) means 16x16x16 = 4096 chunks per shard + shape = tuple(s * 2 for s in shards) # 2 shards per dimension + chunks = (2,) * 3 # Small chunks to maximize chunks per shard + + data = create_array( + store=store, + shape=shape, + dtype="uint8", + chunks=chunks, + shards=shards, + compressors=None, + filters=None, + fill_value=0, + ) + + data[:] = 1 + # Read a sub-shard region to exercise Morton order iteration + indexer = (slice(shards[0]),) * 3 + + def read_with_cache_clear() -> None: + _morton_order.cache_clear() + getitem(data, indexer) + + benchmark(read_with_cache_clear) + + +# Benchmark with larger chunks_per_shard to make Morton order impact more visible +large_morton_shards = ( + (32,) * 3, # With 1x1x1 chunks: 32x32x32 = 32768 chunks per shard +) + + +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("shards", large_morton_shards, ids=str) +def test_sharded_morton_indexing_large( + store: Store, + shards: tuple[int, ...], + benchmark: BenchmarkFixture, +) -> None: + """Benchmark sharded array indexing with large chunks_per_shard. + + Uses 1x1x1 chunks to maximize chunks_per_shard (32^3 = 32768), making + the Morton order computation a more significant portion of total time. + The Morton order cache is cleared before each iteration. + """ + from zarr.core.indexing import _morton_order + + # 1x1x1 chunks means chunks_per_shard equals shard shape + shape = tuple(s * 2 for s in shards) # 2 shards per dimension + chunks = (1,) * 3 # 1x1x1 chunks: chunks_per_shard = shards + + data = create_array( + store=store, + shape=shape, + dtype="uint8", + chunks=chunks, + shards=shards, + compressors=None, + filters=None, + fill_value=0, + ) + + data[:] = 1 + # Read one full shard + indexer = (slice(shards[0]),) * 3 + + def read_with_cache_clear() -> None: + _morton_order.cache_clear() + getitem(data, indexer) + + benchmark(read_with_cache_clear) + + +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("shards", large_morton_shards, ids=str) +def test_sharded_morton_single_chunk( + store: Store, + shards: tuple[int, ...], + benchmark: BenchmarkFixture, +) -> None: + """Benchmark reading a single chunk from a large shard. + + This isolates the Morton order computation overhead by minimizing I/O. + Reading one chunk from a shard with 32^3 = 32768 chunks still requires + computing the full Morton order, making the optimization impact clear. + The Morton order cache is cleared before each iteration. + """ + from zarr.core.indexing import _morton_order + + # 1x1x1 chunks means chunks_per_shard equals shard shape + shape = tuple(s * 2 for s in shards) # 2 shards per dimension + chunks = (1,) * 3 # 1x1x1 chunks: chunks_per_shard = shards + + data = create_array( + store=store, + shape=shape, + dtype="uint8", + chunks=chunks, + shards=shards, + compressors=None, + filters=None, + fill_value=0, + ) + + data[:] = 1 + # Read only a single chunk (1x1x1) from the shard + indexer = (slice(1),) * 3 + + def read_with_cache_clear() -> None: + _morton_order.cache_clear() + getitem(data, indexer) + + benchmark(read_with_cache_clear) + + +# Benchmark for morton_order_iter directly (no I/O) +morton_iter_shapes = ( + (8, 8, 8), # 512 elements + (16, 16, 16), # 4096 elements + (32, 32, 32), # 32768 elements +) + + +@pytest.mark.parametrize("shape", morton_iter_shapes, ids=str) +def test_morton_order_iter( + shape: tuple[int, ...], + benchmark: BenchmarkFixture, +) -> None: + """Benchmark morton_order_iter directly without I/O. + + This isolates the Morton order computation to measure the + optimization impact without array read/write overhead. + The cache is cleared before each iteration. + """ + from zarr.core.indexing import _morton_order, morton_order_iter + + def compute_morton_order() -> None: + _morton_order.cache_clear() + # Consume the iterator to force computation + list(morton_order_iter(shape)) + + benchmark(compute_morton_order) + + +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("shards", large_morton_shards, ids=str) +def test_sharded_morton_write_single_chunk( + store: Store, + shards: tuple[int, ...], + benchmark: BenchmarkFixture, +) -> None: + """Benchmark writing a single chunk to a large shard. + + This is the clearest end-to-end demonstration of Morton order optimization. + Writing a single chunk to a shard with 32^3 = 32768 chunks requires + computing the full Morton order, but minimizes I/O overhead. + + Expected improvement: ~160ms (matching Morton computation speedup of ~178ms). + The Morton order cache is cleared before each iteration. + """ + import numpy as np + + from zarr.core.indexing import _morton_order + + # 1x1x1 chunks means chunks_per_shard equals shard shape + shape = tuple(s * 2 for s in shards) # 2 shards per dimension + chunks = (1,) * 3 # 1x1x1 chunks: chunks_per_shard = shards + + data = create_array( + store=store, + shape=shape, + dtype="uint8", + chunks=chunks, + shards=shards, + compressors=None, + filters=None, + fill_value=0, + ) + + # Write data for a single chunk + write_data = np.ones((1, 1, 1), dtype="uint8") + indexer = (slice(1), slice(1), slice(1)) + + def write_with_cache_clear() -> None: + _morton_order.cache_clear() + data[indexer] = write_data + + benchmark(write_with_cache_clear) From d45f846cf44e139103a6ad91a0ff330230194af2 Mon Sep 17 00:00:00 2001 From: Mark Kittisopikul Date: Thu, 19 Feb 2026 09:28:10 -0500 Subject: [PATCH 206/468] perf: Optimize Morton order with hypercube and vectorization (#3708) * perf: Skip bounds check for initial elements in 2^n hypercube * lint:Use a list comprehension rather than a for loop * pref:Add decode_morton_vectorized * perf:Replace math.log2() with bit_length() * perf:Use magic numbers for 2D and 3D * perf:Add 4D Morton magic numbers * perf:Add Morton magic numbers for 5D * perf:Remove singleton dimensions to reduce ndims * Add changes * fix:Address type annotation and linting issues * perf:Remove magic number functions * test:Add power of 2 sharding indexing tests * test: Add Morton order benchmarks with cache clearing Add benchmarks that clear the _morton_order LRU cache before each iteration to measure the full Morton computation cost: - test_sharded_morton_indexing: 512-4096 chunks per shard - test_sharded_morton_indexing_large: 32768 chunks per shard Co-Authored-By: Claude Opus 4.5 * fix:Bound LRU cache of _morton_order to 16 * test:Add a single chunk test for a large shard * test:Add indexing benchmarks for writing * tests:Add single chunk write test for sharding * Update 3708.misc.md --------- Co-authored-by: Claude Opus 4.5 Co-authored-by: Davis Bennett --- changes/3708.misc.md | 1 + src/zarr/core/indexing.py | 94 +++++++++++++++++++++++++++++++++++++-- 2 files changed, 91 insertions(+), 4 deletions(-) create mode 100644 changes/3708.misc.md diff --git a/changes/3708.misc.md b/changes/3708.misc.md new file mode 100644 index 0000000000..dce7546c97 --- /dev/null +++ b/changes/3708.misc.md @@ -0,0 +1 @@ +Optimize Morton order computation with hypercube optimization, vectorized decoding, and singleton dimension removal, providing 10-45x speedup for typical chunk shapes. diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index beffa99cfa..df79728a85 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -1452,7 +1452,7 @@ def make_slice_selection(selection: Any) -> list[slice]: def decode_morton(z: int, chunk_shape: tuple[int, ...]) -> tuple[int, ...]: # Inspired by compressed morton code as implemented in Neuroglancer # https://github.com/google/neuroglancer/blob/master/src/neuroglancer/datasource/precomputed/volume.md#compressed-morton-code - bits = tuple(math.ceil(math.log2(c)) for c in chunk_shape) + bits = tuple((c - 1).bit_length() for c in chunk_shape) max_coords_bits = max(bits) input_bit = 0 input_value = z @@ -1467,16 +1467,102 @@ def decode_morton(z: int, chunk_shape: tuple[int, ...]) -> tuple[int, ...]: return tuple(out) -@lru_cache +def decode_morton_vectorized( + z: npt.NDArray[np.intp], chunk_shape: tuple[int, ...] +) -> npt.NDArray[np.intp]: + """Vectorized Morton code decoding for multiple z values. + + Parameters + ---------- + z : ndarray + 1D array of Morton codes to decode. + chunk_shape : tuple of int + Shape defining the coordinate space. + + Returns + ------- + ndarray + 2D array of shape (len(z), len(chunk_shape)) containing decoded coordinates. + """ + n_dims = len(chunk_shape) + bits = tuple((c - 1).bit_length() for c in chunk_shape) + + max_coords_bits = max(bits) if bits else 0 + out = np.zeros((len(z), n_dims), dtype=np.intp) + + input_bit = 0 + for coord_bit in range(max_coords_bits): + for dim in range(n_dims): + if coord_bit < bits[dim]: + # Extract bit at position input_bit from all z values + bit_values = (z >> input_bit) & 1 + # Place bit at coord_bit position in dimension dim + out[:, dim] |= bit_values << coord_bit + input_bit += 1 + + return out + + +@lru_cache(maxsize=16) def _morton_order(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: n_total = product(chunk_shape) - order: list[tuple[int, ...]] = [] - i = 0 + if n_total == 0: + return () + + # Optimization: Remove singleton dimensions to enable magic number usage + # for shapes like (1,1,32,32,32). Compute Morton on squeezed shape, then expand. + singleton_dims = tuple(i for i, s in enumerate(chunk_shape) if s == 1) + if singleton_dims: + squeezed_shape = tuple(s for s in chunk_shape if s != 1) + if squeezed_shape: + # Compute Morton order on squeezed shape + squeezed_order = _morton_order(squeezed_shape) + # Expand coordinates to include singleton dimensions (always 0) + expanded: list[tuple[int, ...]] = [] + for coord in squeezed_order: + full_coord: list[int] = [] + squeezed_idx = 0 + for i in range(len(chunk_shape)): + if chunk_shape[i] == 1: + full_coord.append(0) + else: + full_coord.append(coord[squeezed_idx]) + squeezed_idx += 1 + expanded.append(tuple(full_coord)) + return tuple(expanded) + else: + # All dimensions are singletons, just return the single point + return ((0,) * len(chunk_shape),) + + n_dims = len(chunk_shape) + + # Find the largest power-of-2 hypercube that fits within chunk_shape. + # Within this hypercube, Morton codes are guaranteed to be in bounds. + min_dim = min(chunk_shape) + if min_dim >= 1: + power = min_dim.bit_length() - 1 # floor(log2(min_dim)) + hypercube_size = 1 << power # 2^power + n_hypercube = hypercube_size**n_dims + else: + n_hypercube = 0 + + # Within the hypercube, no bounds checking needed - use vectorized decoding + order: list[tuple[int, ...]] + if n_hypercube > 0: + z_values = np.arange(n_hypercube, dtype=np.intp) + hypercube_coords = decode_morton_vectorized(z_values, chunk_shape) + order = [tuple(row) for row in hypercube_coords] + else: + order = [] + + # For remaining elements, bounds checking is needed + i = n_hypercube while len(order) < n_total: m = decode_morton(i, chunk_shape) if all(x < y for x, y in zip(m, chunk_shape, strict=False)): order.append(m) i += 1 + return tuple(order) From f8b3d3840a2ab6004c9504e6c96ab85298ff122f Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 19 Feb 2026 15:51:19 +0100 Subject: [PATCH 207/468] fix/nested shard reads (#3655) * fix partial nested shard reads * changelog --- changes/3655.bugfix.md | 1 + src/zarr/codecs/sharding.py | 13 +++++++-- tests/test_codecs/test_sharding.py | 47 ++++++++++++++---------------- 3 files changed, 33 insertions(+), 28 deletions(-) create mode 100644 changes/3655.bugfix.md diff --git a/changes/3655.bugfix.md b/changes/3655.bugfix.md new file mode 100644 index 0000000000..67d384f00d --- /dev/null +++ b/changes/3655.bugfix.md @@ -0,0 +1 @@ +Fixed a bug in the sharding codec that prevented nested shard reads in certain cases. \ No newline at end of file diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 8124ea44ea..b54b3c2257 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -52,6 +52,7 @@ ) from zarr.core.metadata.v3 import parse_codecs from zarr.registry import get_ndbuffer_class, get_pipeline_class +from zarr.storage._utils import _normalize_byte_range_index if TYPE_CHECKING: from collections.abc import Iterator @@ -86,11 +87,16 @@ class _ShardingByteGetter(ByteGetter): async def get( self, prototype: BufferPrototype, byte_range: ByteRequest | None = None ) -> Buffer | None: - assert byte_range is None, "byte_range is not supported within shards" assert prototype == default_buffer_prototype(), ( f"prototype is not supported within shards currently. diff: {prototype} != {default_buffer_prototype()}" ) - return self.shard_dict.get(self.chunk_coords) + value = self.shard_dict.get(self.chunk_coords) + if value is None: + return None + if byte_range is None: + return value + start, stop = _normalize_byte_range_index(value, byte_range) + return value[start:stop] @dataclass(frozen=True) @@ -597,7 +603,8 @@ async def _decode_shard_index( ) ) ) - assert index_array is not None + # This cannot be None because we have the bytes already + index_array = cast(NDBuffer, index_array) return _ShardIndex(index_array.as_numpy_array()) async def _encode_shard_index(self, index: _ShardIndex) -> Buffer: diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 7eb4deccbf..d0e2d09b7c 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -18,7 +18,6 @@ TransposeCodec, ) from zarr.core.buffer import NDArrayLike, default_buffer_prototype -from zarr.errors import ZarrUserWarning from zarr.storage import StorePath, ZipStore from ..conftest import ArrayRequest @@ -239,12 +238,14 @@ def test_sharding_partial_overwrite( assert np.array_equal(data, read_data) +# Zip storage raises a warning about a duplicate name, which we ignore. +@pytest.mark.filterwarnings("ignore:Duplicate name.*:UserWarning") @pytest.mark.parametrize( "array_fixture", [ - ArrayRequest(shape=(128,) * 3, dtype="uint16", order="F"), + ArrayRequest(shape=(127, 128, 129), dtype="uint16", order="F"), ], - indirect=["array_fixture"], + indirect=True, ) @pytest.mark.parametrize( "outer_index_location", @@ -263,24 +264,23 @@ def test_nested_sharding( ) -> None: data = array_fixture spath = StorePath(store) - msg = "Combining a `sharding_indexed` codec disables partial reads and writes, which may lead to inefficient performance." - with pytest.warns(ZarrUserWarning, match=msg): - a = zarr.create_array( - spath, - shape=data.shape, - chunks=(64, 64, 64), - dtype=data.dtype, - fill_value=0, - serializer=ShardingCodec( - chunk_shape=(32, 32, 32), - codecs=[ - ShardingCodec(chunk_shape=(16, 16, 16), index_location=inner_index_location) - ], - index_location=outer_index_location, - ), - ) + # compressors=None ensures no BytesBytesCodec is added, which keeps + # supports_partial_decode=True and exercises the partial decode path + a = zarr.create_array( + spath, + data=data, + chunks=(64,) * data.ndim, + compressors=None, + serializer=ShardingCodec( + chunk_shape=(32,) * data.ndim, + codecs=[ + ShardingCodec(chunk_shape=(16,) * data.ndim, index_location=inner_index_location) + ], + index_location=outer_index_location, + ), + ) - a[:, :, :] = data + a[:] = data read_data = a[0 : data.shape[0], 0 : data.shape[1], 0 : data.shape[2]] assert isinstance(read_data, NDArrayLike) @@ -326,13 +326,10 @@ def test_nested_sharding_create_array( filters=None, compressors=None, ) - print(a.metadata.to_dict()) - a[:, :, :] = data + a[:] = data - read_data = a[0 : data.shape[0], 0 : data.shape[1], 0 : data.shape[2]] - assert isinstance(read_data, NDArrayLike) - assert data.shape == read_data.shape + read_data = a[:] assert np.array_equal(data, read_data) From 2f9b0b3164075344686f5f46417014d61b209e55 Mon Sep 17 00:00:00 2001 From: Mark Kittisopikul Date: Fri, 20 Feb 2026 15:09:55 -0500 Subject: [PATCH 208/468] perf: Vectorize get_chunk_slice for faster sharded writes (#3713) * perf: Skip bounds check for initial elements in 2^n hypercube * lint:Use a list comprehension rather than a for loop * pref:Add decode_morton_vectorized * perf:Replace math.log2() with bit_length() * perf:Use magic numbers for 2D and 3D * perf:Add 4D Morton magic numbers * perf:Add Morton magic numbers for 5D * perf:Remove singleton dimensions to reduce ndims * Add changes * fix:Address type annotation and linting issues * perf:Remove magic number functions * test:Add power of 2 sharding indexing tests * test: Add Morton order benchmarks with cache clearing Add benchmarks that clear the _morton_order LRU cache before each iteration to measure the full Morton computation cost: - test_sharded_morton_indexing: 512-4096 chunks per shard - test_sharded_morton_indexing_large: 32768 chunks per shard Co-Authored-By: Claude Opus 4.5 * fix:Bound LRU cache of _morton_order to 16 * test:Add a single chunk test for a large shard * test:Add indexing benchmarks for writing * tests:Add single chunk write test for sharding * perf: Vectorize get_chunk_slice for faster sharded writes Add vectorized methods to _ShardIndex and _ShardReader for batch chunk slice lookups, reducing per-chunk function call overhead when writing to shards. Co-Authored-By: Claude Opus 4.5 * refactor: Return ndarray from _morton_order, simplify to_dict_vectorized _morton_order now returns a read-only npt.NDArray[np.intp] (annotated as Iterable[Sequence[int]]) instead of a tuple of tuples, eliminating the intermediate list-of-tuples allocation. morton_order_iter converts rows to tuples on the fly. to_dict_vectorized no longer requires a redundant chunk_coords_tuples argument; tuple conversion happens inline during dict population. get_chunk_slices_vectorized accepts any integer array dtype (npt.NDArray[np.integer[Any]]) and casts to uint64 internally. Co-Authored-By: Claude Sonnet 4.6 * perf: Cache tuple keys separately from ndarray in _morton_order_keys Add _morton_order_keys() as a second lru_cache that converts the ndarray returned by _morton_order into a tuple of tuples. This restores cached access to hashable chunk coordinate keys without reverting to the old dual-argument interface. morton_order_iter now uses _morton_order_keys, and to_dict_vectorized derives its keys from _morton_order_keys internally using the shard index shape, keeping the call site single-argument. Result: test_sharded_morton_write_single_chunk[(32,32,32)] improves from ~33ms to ~7ms (~5x speedup over prior to this PR's changes). Co-Authored-By: Claude Sonnet 4.6 * tests: Clear _morton_order_keys cache alongside _morton_order in benchmarks All benchmark functions that call _morton_order.cache_clear() now also call _morton_order_keys.cache_clear() to ensure both caches are reset before each benchmark iteration. Co-Authored-By: Claude Sonnet 4.6 * refactor: Use npt.NDArray[np.intp] as return type for _morton_order More precise than Iterable[Sequence[int]] and accurately reflects the actual return value. Remove the now-unused Iterable import. Co-Authored-By: Claude Sonnet 4.6 --------- Co-authored-by: Claude Opus 4.5 Co-authored-by: Davis Bennett --- changes/3713.misc.md | 1 + src/zarr/codecs/sharding.py | 72 ++++++++++++++++++++++++++++++- src/zarr/core/indexing.py | 61 +++++++++++++------------- tests/benchmarks/test_indexing.py | 15 ++++--- 4 files changed, 114 insertions(+), 35 deletions(-) create mode 100644 changes/3713.misc.md diff --git a/changes/3713.misc.md b/changes/3713.misc.md new file mode 100644 index 0000000000..9b0680dfc0 --- /dev/null +++ b/changes/3713.misc.md @@ -0,0 +1 @@ +Vectorize get_chunk_slice for faster sharded array writes. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index b54b3c2257..85162c2f74 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -46,6 +46,8 @@ from zarr.core.indexing import ( BasicIndexer, SelectorTuple, + _morton_order, + _morton_order_keys, c_order_iter, get_indexer, morton_order_iter, @@ -144,6 +146,45 @@ def get_chunk_slice(self, chunk_coords: tuple[int, ...]) -> tuple[int, int] | No else: return (int(chunk_start), int(chunk_start + chunk_len)) + def get_chunk_slices_vectorized( + self, chunk_coords_array: npt.NDArray[np.integer[Any]] + ) -> tuple[npt.NDArray[np.uint64], npt.NDArray[np.uint64], npt.NDArray[np.bool_]]: + """Get chunk slices for multiple coordinates at once. + + Parameters + ---------- + chunk_coords_array : ndarray of shape (n_chunks, n_dims) + Array of chunk coordinates to look up. + + Returns + ------- + starts : ndarray of shape (n_chunks,) + Start byte positions for each chunk. + ends : ndarray of shape (n_chunks,) + End byte positions for each chunk. + valid : ndarray of shape (n_chunks,) + Boolean mask indicating which chunks are non-empty. + """ + # Localize coordinates via modulo (vectorized) + shard_shape = np.array(self.offsets_and_lengths.shape[:-1], dtype=np.uint64) + localized = chunk_coords_array.astype(np.uint64) % shard_shape + + # Build index tuple for advanced indexing + index_tuple = tuple(localized[:, i] for i in range(localized.shape[1])) + + # Fetch all offsets and lengths at once + offsets_and_lengths = self.offsets_and_lengths[index_tuple] + starts = offsets_and_lengths[:, 0] + lengths = offsets_and_lengths[:, 1] + + # Check for valid (non-empty) chunks + valid = starts != MAX_UINT_64 + + # Compute end positions + ends = starts + lengths + + return starts, ends, valid + def set_chunk_slice(self, chunk_coords: tuple[int, ...], chunk_slice: slice | None) -> None: localized_chunk = self._localize_chunk(chunk_coords) if chunk_slice is None: @@ -225,6 +266,34 @@ def __len__(self) -> int: def __iter__(self) -> Iterator[tuple[int, ...]]: return c_order_iter(self.index.offsets_and_lengths.shape[:-1]) + def to_dict_vectorized( + self, + chunk_coords_array: npt.NDArray[np.integer[Any]], + ) -> dict[tuple[int, ...], Buffer | None]: + """Build a dict of chunk coordinates to buffers using vectorized lookup. + + Parameters + ---------- + chunk_coords_array : ndarray of shape (n_chunks, n_dims) + Array of chunk coordinates for vectorized index lookup. + + Returns + ------- + dict mapping chunk coordinate tuples to Buffer or None + """ + starts, ends, valid = self.index.get_chunk_slices_vectorized(chunk_coords_array) + chunks_per_shard = tuple(self.index.offsets_and_lengths.shape[:-1]) + chunk_coords_keys = _morton_order_keys(chunks_per_shard) + + result: dict[tuple[int, ...], Buffer | None] = {} + for i, coords in enumerate(chunk_coords_keys): + if valid[i]: + result[coords] = self.buf[int(starts[i]) : int(ends[i])] + else: + result[coords] = None + + return result + @dataclass(frozen=True) class ShardingCodec( @@ -511,7 +580,8 @@ async def _encode_partial_single( chunks_per_shard=chunks_per_shard, ) shard_reader = shard_reader or _ShardReader.create_empty(chunks_per_shard) - shard_dict = {k: shard_reader.get(k) for k in morton_order_iter(chunks_per_shard)} + # Use vectorized lookup for better performance + shard_dict = shard_reader.to_dict_vectorized(np.asarray(_morton_order(chunks_per_shard))) indexer = list( get_indexer( diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index df79728a85..454f7e2290 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -1504,10 +1504,13 @@ def decode_morton_vectorized( @lru_cache(maxsize=16) -def _morton_order(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: +def _morton_order(chunk_shape: tuple[int, ...]) -> npt.NDArray[np.intp]: n_total = product(chunk_shape) + n_dims = len(chunk_shape) if n_total == 0: - return () + out = np.empty((0, n_dims), dtype=np.intp) + out.flags.writeable = False + return out # Optimization: Remove singleton dimensions to enable magic number usage # for shapes like (1,1,32,32,32). Compute Morton on squeezed shape, then expand. @@ -1515,26 +1518,19 @@ def _morton_order(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: if singleton_dims: squeezed_shape = tuple(s for s in chunk_shape if s != 1) if squeezed_shape: - # Compute Morton order on squeezed shape - squeezed_order = _morton_order(squeezed_shape) - # Expand coordinates to include singleton dimensions (always 0) - expanded: list[tuple[int, ...]] = [] - for coord in squeezed_order: - full_coord: list[int] = [] - squeezed_idx = 0 - for i in range(len(chunk_shape)): - if chunk_shape[i] == 1: - full_coord.append(0) - else: - full_coord.append(coord[squeezed_idx]) - squeezed_idx += 1 - expanded.append(tuple(full_coord)) - return tuple(expanded) + # Compute Morton order on squeezed shape, then expand singleton dims (always 0) + squeezed_order = np.asarray(_morton_order(squeezed_shape)) + out = np.zeros((n_total, n_dims), dtype=np.intp) + squeezed_col = 0 + for full_col in range(n_dims): + if chunk_shape[full_col] != 1: + out[:, full_col] = squeezed_order[:, squeezed_col] + squeezed_col += 1 else: # All dimensions are singletons, just return the single point - return ((0,) * len(chunk_shape),) - - n_dims = len(chunk_shape) + out = np.zeros((1, n_dims), dtype=np.intp) + out.flags.writeable = False + return out # Find the largest power-of-2 hypercube that fits within chunk_shape. # Within this hypercube, Morton codes are guaranteed to be in bounds. @@ -1547,27 +1543,34 @@ def _morton_order(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: n_hypercube = 0 # Within the hypercube, no bounds checking needed - use vectorized decoding - order: list[tuple[int, ...]] if n_hypercube > 0: z_values = np.arange(n_hypercube, dtype=np.intp) - hypercube_coords = decode_morton_vectorized(z_values, chunk_shape) - order = [tuple(row) for row in hypercube_coords] + order: npt.NDArray[np.intp] = decode_morton_vectorized(z_values, chunk_shape) else: - order = [] + order = np.empty((0, n_dims), dtype=np.intp) - # For remaining elements, bounds checking is needed + # For remaining elements outside the hypercube, bounds checking is needed + remaining: list[tuple[int, ...]] = [] i = n_hypercube - while len(order) < n_total: + while len(order) + len(remaining) < n_total: m = decode_morton(i, chunk_shape) if all(x < y for x, y in zip(m, chunk_shape, strict=False)): - order.append(m) + remaining.append(m) i += 1 - return tuple(order) + if remaining: + order = np.vstack([order, np.array(remaining, dtype=np.intp)]) + order.flags.writeable = False + return order + + +@lru_cache(maxsize=16) +def _morton_order_keys(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: + return tuple(tuple(int(x) for x in row) for row in _morton_order(chunk_shape)) def morton_order_iter(chunk_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: - return iter(_morton_order(tuple(chunk_shape))) + return iter(_morton_order_keys(tuple(chunk_shape))) def c_order_iter(chunks_per_shard: tuple[int, ...]) -> Iterator[tuple[int, ...]]: diff --git a/tests/benchmarks/test_indexing.py b/tests/benchmarks/test_indexing.py index dff2269dcb..d30d731f0f 100644 --- a/tests/benchmarks/test_indexing.py +++ b/tests/benchmarks/test_indexing.py @@ -74,7 +74,7 @@ def test_sharded_morton_indexing( The Morton order cache is cleared before each iteration to measure the full computation cost. """ - from zarr.core.indexing import _morton_order + from zarr.core.indexing import _morton_order, _morton_order_keys # Create array where each shard contains many small chunks # e.g., shards=(32,32,32) with chunks=(2,2,2) means 16x16x16 = 4096 chunks per shard @@ -98,6 +98,7 @@ def test_sharded_morton_indexing( def read_with_cache_clear() -> None: _morton_order.cache_clear() + _morton_order_keys.cache_clear() getitem(data, indexer) benchmark(read_with_cache_clear) @@ -122,7 +123,7 @@ def test_sharded_morton_indexing_large( the Morton order computation a more significant portion of total time. The Morton order cache is cleared before each iteration. """ - from zarr.core.indexing import _morton_order + from zarr.core.indexing import _morton_order, _morton_order_keys # 1x1x1 chunks means chunks_per_shard equals shard shape shape = tuple(s * 2 for s in shards) # 2 shards per dimension @@ -145,6 +146,7 @@ def test_sharded_morton_indexing_large( def read_with_cache_clear() -> None: _morton_order.cache_clear() + _morton_order_keys.cache_clear() getitem(data, indexer) benchmark(read_with_cache_clear) @@ -164,7 +166,7 @@ def test_sharded_morton_single_chunk( computing the full Morton order, making the optimization impact clear. The Morton order cache is cleared before each iteration. """ - from zarr.core.indexing import _morton_order + from zarr.core.indexing import _morton_order, _morton_order_keys # 1x1x1 chunks means chunks_per_shard equals shard shape shape = tuple(s * 2 for s in shards) # 2 shards per dimension @@ -187,6 +189,7 @@ def test_sharded_morton_single_chunk( def read_with_cache_clear() -> None: _morton_order.cache_clear() + _morton_order_keys.cache_clear() getitem(data, indexer) benchmark(read_with_cache_clear) @@ -211,10 +214,11 @@ def test_morton_order_iter( optimization impact without array read/write overhead. The cache is cleared before each iteration. """ - from zarr.core.indexing import _morton_order, morton_order_iter + from zarr.core.indexing import _morton_order, _morton_order_keys, morton_order_iter def compute_morton_order() -> None: _morton_order.cache_clear() + _morton_order_keys.cache_clear() # Consume the iterator to force computation list(morton_order_iter(shape)) @@ -239,7 +243,7 @@ def test_sharded_morton_write_single_chunk( """ import numpy as np - from zarr.core.indexing import _morton_order + from zarr.core.indexing import _morton_order, _morton_order_keys # 1x1x1 chunks means chunks_per_shard equals shard shape shape = tuple(s * 2 for s in shards) # 2 shards per dimension @@ -262,6 +266,7 @@ def test_sharded_morton_write_single_chunk( def write_with_cache_clear() -> None: _morton_order.cache_clear() + _morton_order_keys.cache_clear() data[indexer] = write_data benchmark(write_with_cache_clear) From efed3a481178a7bb60e5be831f05cf760c63d402 Mon Sep 17 00:00:00 2001 From: Ian Hunt-Isaak Date: Fri, 20 Feb 2026 23:23:03 -0500 Subject: [PATCH 209/468] TEST: fix group selection for delete (#3707) Co-authored-by: Deepak Cherian --- src/zarr/testing/stateful.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index c363c13983..382f1467da 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -340,13 +340,13 @@ def delete_array_using_del(self, data: DataObject) -> None: self.all_arrays.remove(array_path) @precondition(lambda self: self.store.supports_deletes) - @precondition(lambda self: len(self.all_groups) >= 2) # fixme don't delete root + @precondition(lambda self: bool(self.all_groups)) @rule(data=st.data()) def delete_group_using_del(self, data: DataObject) -> None: - # ensure that we don't include the root group in the list of member names that we try - # to delete - member_names = tuple(filter(lambda v: "/" in v, sorted(self.all_groups))) - group_path = data.draw(st.sampled_from(member_names), label="Group deletion target") + group_path = data.draw( + st.sampled_from(sorted(self.all_groups)), + label="Group deletion target", + ) prefix, group_name = split_prefix_name(group_path) note(f"Deleting group '{group_path=!r}', {prefix=!r}, {group_name=!r} using delete") members = zarr.open_group(store=self.model, path=group_path).members(max_depth=None) @@ -359,9 +359,7 @@ def delete_group_using_del(self, data: DataObject) -> None: group = zarr.open_group(store=store, path=prefix) group[group_name] # check that it exists del group[group_name] - if group_path != "/": - # The root group is always present - self.all_groups.remove(group_path) + self.all_groups.remove(group_path) # # --------------- assertions ----------------- # def check_group_arrays(self, group): From 32c7ab98c82611b456754f8ce14694d2fe7fb2fc Mon Sep 17 00:00:00 2001 From: Mark Kittisopikul Date: Tue, 24 Feb 2026 09:04:16 -0500 Subject: [PATCH 210/468] Add non-power-of-2 shapes for Morton coding to benchmarks (#3717) * tests: Add non-power-of-2 shard shapes to benchmarks Add (30,30,30) to large_morton_shards and (10,10,10), (20,20,20), (30,30,30) to morton_iter_shapes to benchmark the scalar fallback path for non-power-of-2 shapes, which are not fully covered by the vectorized hypercube path. Co-Authored-By: Claude Sonnet 4.6 * tests: Add near-miss power-of-2 shape (33,33,33) to benchmarks Documents the performance penalty when a shard shape is just above a power-of-2 boundary, causing n_z to jump from 32,768 to 262,144. Co-Authored-By: Claude Sonnet 4.6 * style: Apply ruff format to benchmark file Co-Authored-By: Claude Sonnet 4.6 * changes: Add changelog entry for PR #3717 Co-Authored-By: Claude Sonnet 4.6 --------- Co-authored-by: Claude Sonnet 4.6 Co-authored-by: Davis Bennett --- changes/3717.misc.md | 1 + tests/benchmarks/test_indexing.py | 15 +++++++++++---- 2 files changed, 12 insertions(+), 4 deletions(-) create mode 100644 changes/3717.misc.md diff --git a/changes/3717.misc.md b/changes/3717.misc.md new file mode 100644 index 0000000000..5fed76b2b7 --- /dev/null +++ b/changes/3717.misc.md @@ -0,0 +1 @@ +Add benchmarks for Morton order computation with non-power-of-2 and near-miss shard shapes, covering both pure computation and end-to-end read/write performance. diff --git a/tests/benchmarks/test_indexing.py b/tests/benchmarks/test_indexing.py index d30d731f0f..385a85b5b5 100644 --- a/tests/benchmarks/test_indexing.py +++ b/tests/benchmarks/test_indexing.py @@ -106,7 +106,10 @@ def read_with_cache_clear() -> None: # Benchmark with larger chunks_per_shard to make Morton order impact more visible large_morton_shards = ( - (32,) * 3, # With 1x1x1 chunks: 32x32x32 = 32768 chunks per shard + (32,) * 3, # With 1x1x1 chunks: 32x32x32 = 32768 chunks per shard (power-of-2) + (30,) * 3, # With 1x1x1 chunks: 30x30x30 = 27000 chunks per shard (non-power-of-2) + (33,) + * 3, # With 1x1x1 chunks: 33x33x33 = 35937 chunks per shard (near-miss: just above power-of-2) ) @@ -197,9 +200,13 @@ def read_with_cache_clear() -> None: # Benchmark for morton_order_iter directly (no I/O) morton_iter_shapes = ( - (8, 8, 8), # 512 elements - (16, 16, 16), # 4096 elements - (32, 32, 32), # 32768 elements + (8, 8, 8), # 512 elements (power-of-2) + (10, 10, 10), # 1000 elements (non-power-of-2) + (16, 16, 16), # 4096 elements (power-of-2) + (20, 20, 20), # 8000 elements (non-power-of-2) + (32, 32, 32), # 32768 elements (power-of-2) + (30, 30, 30), # 27000 elements (non-power-of-2) + (33, 33, 33), # 35937 elements (near-miss: just above power-of-2, n_z=262144) ) From 879e1cec04e5008fc215b8753c37eea0d54aaa4e Mon Sep 17 00:00:00 2001 From: Mark Kittisopikul Date: Wed, 25 Feb 2026 15:34:12 -0500 Subject: [PATCH 211/468] perf: Fix near-miss penalty in _morton_order with hybrid ceiling+argsort strategy (#3718) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * tests: Add non-power-of-2 shard shapes to benchmarks Add (30,30,30) to large_morton_shards and (10,10,10), (20,20,20), (30,30,30) to morton_iter_shapes to benchmark the scalar fallback path for non-power-of-2 shapes, which are not fully covered by the vectorized hypercube path. Co-Authored-By: Claude Sonnet 4.6 * tests: Add near-miss power-of-2 shape (33,33,33) to benchmarks Documents the performance penalty when a shard shape is just above a power-of-2 boundary, causing n_z to jump from 32,768 to 262,144. Co-Authored-By: Claude Sonnet 4.6 * style: Apply ruff format to benchmark file Co-Authored-By: Claude Sonnet 4.6 * changes: Add changelog entry for PR #3717 Co-Authored-By: Claude Sonnet 4.6 * perf: Fix near-miss penalty in _morton_order with hybrid ceiling+argsort strategy For shapes just above a power-of-2 (e.g. (33,33,33)), the ceiling-only approach generates n_z=262,144 Morton codes for only 35,937 valid coordinates (7.3× overgeneration). The floor+scalar approach is even worse since the scalar loop iterates n_z-n_floor times (229,376 for (33,33,33)), not n_total-n_floor. The fix: when n_z > 4*n_total, use an argsort strategy that enumerates all n_total valid coordinates via meshgrid, encodes each to a Morton code using vectorized bit manipulation, then sorts by Morton code. This avoids the large overgeneration while remaining fully vectorized. Result for test_morton_order_iter: (30,30,30): 24ms (ceiling, ratio=1.21) (32,32,32): 28ms (ceiling, ratio=1.00) (33,33,33): 32ms (argsort, ratio=7.3 → fixed from ~820ms with scalar) Co-Authored-By: Claude Sonnet 4.6 * fix: Address pre-commit CI failures in _morton_order - Replace Unicode multiplication sign × with ASCII x in comment (RUF003) - Add explicit type annotation for np.argsort result to satisfy mypy Co-Authored-By: Claude Sonnet 4.6 * fix: Cast argsort result via np.asarray to resolve mypy no-any-return np.stack returns Any in mypy's view, so indexing into it also returns Any. Using np.asarray(..., dtype=np.intp) makes the type explicit and avoids the no-any-return error at the return site. Co-Authored-By: Claude Sonnet 4.6 * fix: Pre-declare order type to resolve mypy no-any-return in _morton_order np.asarray and np.stack return Any with numpy 2.1 type stubs, causing mypy to infer the return type as Any. Pre-declaring order as npt.NDArray[np.intp] before the if/else makes the intended type explicit. Co-Authored-By: Claude Sonnet 4.6 --------- Co-authored-by: Claude Sonnet 4.6 Co-authored-by: Davis Bennett --- src/zarr/core/indexing.py | 86 ++++++++++++++++++--------------------- 1 file changed, 40 insertions(+), 46 deletions(-) diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 454f7e2290..73fd53087d 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -1512,54 +1512,48 @@ def _morton_order(chunk_shape: tuple[int, ...]) -> npt.NDArray[np.intp]: out.flags.writeable = False return out - # Optimization: Remove singleton dimensions to enable magic number usage - # for shapes like (1,1,32,32,32). Compute Morton on squeezed shape, then expand. - singleton_dims = tuple(i for i, s in enumerate(chunk_shape) if s == 1) - if singleton_dims: - squeezed_shape = tuple(s for s in chunk_shape if s != 1) - if squeezed_shape: - # Compute Morton order on squeezed shape, then expand singleton dims (always 0) - squeezed_order = np.asarray(_morton_order(squeezed_shape)) - out = np.zeros((n_total, n_dims), dtype=np.intp) - squeezed_col = 0 - for full_col in range(n_dims): - if chunk_shape[full_col] != 1: - out[:, full_col] = squeezed_order[:, squeezed_col] - squeezed_col += 1 - else: - # All dimensions are singletons, just return the single point - out = np.zeros((1, n_dims), dtype=np.intp) - out.flags.writeable = False - return out - - # Find the largest power-of-2 hypercube that fits within chunk_shape. - # Within this hypercube, Morton codes are guaranteed to be in bounds. - min_dim = min(chunk_shape) - if min_dim >= 1: - power = min_dim.bit_length() - 1 # floor(log2(min_dim)) - hypercube_size = 1 << power # 2^power - n_hypercube = hypercube_size**n_dims + # Ceiling hypercube: smallest power-of-2 hypercube whose Morton codes span + # all valid coordinates in chunk_shape. (c-1).bit_length() gives the number + # of bits needed to index c values (0 for singleton dims). n_z = 2**total_bits + # is the size of this hypercube. + total_bits = sum((c - 1).bit_length() for c in chunk_shape) + n_z = 1 << total_bits if total_bits > 0 else 1 + + # Decode all Morton codes in the ceiling hypercube, then filter to valid coords. + # This is fully vectorized. For shapes with n_z >> n_total (e.g. (33,33,33): + # n_z=262144, n_total=35937), consider the argsort strategy below. + order: npt.NDArray[np.intp] + if n_z <= 4 * n_total: + # Ceiling strategy: decode all n_z codes vectorized, filter in-bounds. + # Works well when the overgeneration ratio n_z/n_total is small (≤4). + z_values = np.arange(n_z, dtype=np.intp) + all_coords = decode_morton_vectorized(z_values, chunk_shape) + shape_arr = np.array(chunk_shape, dtype=np.intp) + valid_mask = np.all(all_coords < shape_arr, axis=1) + order = all_coords[valid_mask] else: - n_hypercube = 0 + # Argsort strategy: enumerate all n_total valid coordinates directly, + # encode each to a Morton code, then sort by code. Avoids the 8x or + # larger overgeneration penalty for near-miss shapes like (33,33,33). + # Cost: O(n_total * bits) encode + O(n_total log n_total) sort, + # vs O(n_z * bits) = O(8 * n_total * bits) for ceiling. + grids = np.meshgrid(*[np.arange(c, dtype=np.intp) for c in chunk_shape], indexing="ij") + all_coords = np.stack([g.ravel() for g in grids], axis=1) + + # Encode all coordinates to Morton codes (vectorized). + bits_per_dim = tuple((c - 1).bit_length() for c in chunk_shape) + max_coord_bits = max(bits_per_dim) + z_codes = np.zeros(n_total, dtype=np.intp) + output_bit = 0 + for coord_bit in range(max_coord_bits): + for dim in range(n_dims): + if coord_bit < bits_per_dim[dim]: + z_codes |= ((all_coords[:, dim] >> coord_bit) & 1) << output_bit + output_bit += 1 + + sort_idx: npt.NDArray[np.intp] = np.argsort(z_codes, kind="stable") + order = np.asarray(all_coords[sort_idx], dtype=np.intp) - # Within the hypercube, no bounds checking needed - use vectorized decoding - if n_hypercube > 0: - z_values = np.arange(n_hypercube, dtype=np.intp) - order: npt.NDArray[np.intp] = decode_morton_vectorized(z_values, chunk_shape) - else: - order = np.empty((0, n_dims), dtype=np.intp) - - # For remaining elements outside the hypercube, bounds checking is needed - remaining: list[tuple[int, ...]] = [] - i = n_hypercube - while len(order) + len(remaining) < n_total: - m = decode_morton(i, chunk_shape) - if all(x < y for x, y in zip(m, chunk_shape, strict=False)): - remaining.append(m) - i += 1 - - if remaining: - order = np.vstack([order, np.array(remaining, dtype=np.intp)]) order.flags.writeable = False return order From 974c06c4d7ce235ec038fa5a979bddcbbe47e761 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 27 Feb 2026 19:37:14 -0500 Subject: [PATCH 212/468] chore/update hatch + use dependency groups (#3728) --- .github/workflows/codspeed.yml | 6 +- .github/workflows/gpu_test.yml | 17 ++-- .github/workflows/hypothesis.yaml | 6 +- .github/workflows/nightly_wheels.yml | 8 +- .github/workflows/releases.yml | 8 +- .github/workflows/test.yml | 18 ++-- .readthedocs.yaml | 11 +-- changes/3728.misc.md | 1 + docs/contributing.md | 8 +- pyproject.toml | 119 +++++++++++++-------------- tests/test_store/test_fsspec.py | 4 + 11 files changed, 100 insertions(+), 106 deletions(-) create mode 100644 changes/3728.misc.md diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 278c8fa877..7192b6d78a 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -31,9 +31,9 @@ jobs: with: python-version: "3.11" - name: Install Hatch - run: | - python -m pip install --upgrade pip - pip install hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Run the benchmarks uses: CodSpeedHQ/action@v4 with: diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 6011610681..337a2d2578 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -19,13 +19,12 @@ concurrency: jobs: test: - name: py=${{ matrix.python-version }}, deps=${{ matrix.dependency-set }} + name: py=${{ matrix.python-version }} runs-on: gpu-runner strategy: matrix: python-version: ['3.11'] - dependency-set: ["minimal"] steps: - uses: actions/checkout@v6 @@ -54,17 +53,17 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: 'pip' - - name: Install Hatch and CuPy - run: | - python -m pip install --upgrade pip - pip install hatch + - name: Install Hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Set Up Hatch Env run: | - hatch env create gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} - hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env + hatch env create gputest.py${{ matrix.python-version }} + hatch env run -e gputest.py${{ matrix.python-version }} list-env - name: Run Tests run: | - hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-coverage-gpu + hatch env run --env gputest.py${{ matrix.python-version }} run-coverage - name: Upload coverage uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3 # v5.3.1 diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index abf7c5f4ce..d8a0acdfd4 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -41,9 +41,9 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install Hatch - run: | - python -m pip install --upgrade pip - pip install hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Set Up Hatch Env run: | hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index dbbc0354e9..82a8676834 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -22,10 +22,10 @@ jobs: with: python-version: '3.13' - - name: Install build dependencies - run: | - python -m pip install --upgrade pip - pip install hatch + - name: Install Hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Build wheel and sdist run: hatch build diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index bca01466bb..054bc00e45 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -21,10 +21,10 @@ jobs: with: python-version: '3.11' - - name: Install PyBuild - run: | - python -m pip install --upgrade pip - pip install hatch + - name: Install Hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Build wheel and sdist run: hatch build - uses: actions/upload-artifact@v6 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 15fe94d3f9..bd6a3a91a7 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -51,9 +51,9 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install Hatch - run: | - python -m pip install --upgrade pip - pip install hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Set Up Hatch Env run: | hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} @@ -93,9 +93,9 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install Hatch - run: | - python -m pip install --upgrade pip - pip install hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Set Up Hatch Env run: | hatch env create ${{ matrix.dependency-set }} @@ -122,9 +122,9 @@ jobs: python-version: '3.13' cache: 'pip' - name: Install Hatch - run: | - python -m pip install --upgrade pip - pip install hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' - name: Set Up Hatch Env run: | hatch run doctest:pip list diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 894778c5a4..1edd099ebd 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,6 +5,9 @@ build: tools: python: "3.12" jobs: + install: + - pip install --upgrade pip + - pip install .[remote] --group docs pre_build: - | if [ "$READTHEDOCS_VERSION_TYPE" != "tag" ]; @@ -16,11 +19,3 @@ build: - mkdocs build --strict --site-dir $READTHEDOCS_OUTPUT/html mkdocs: configuration: mkdocs.yml - -python: - install: - - method: pip - path: . - extra_requirements: - - docs - - remote diff --git a/changes/3728.misc.md b/changes/3728.misc.md new file mode 100644 index 0000000000..a3cbb8d3f0 --- /dev/null +++ b/changes/3728.misc.md @@ -0,0 +1 @@ +Move development dependencies (`test`, `remote_tests`, `docs`, `dev`) from optional dependencies to [dependency groups](https://packaging.python.org/en/latest/specifications/dependency-groups/). This may cause breakage for anyone who used e.g. `pip install zarr[test]` to get access to test dependencies. To install these dependency groups from a local checkout, use `pip install --group ` (pip 25.1+) or `uv run --group `. \ No newline at end of file diff --git a/docs/contributing.md b/docs/contributing.md index e4f341a8b3..a4bbaafbd5 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -64,7 +64,7 @@ hatch env show # list all available environments To verify that your development environment is working, you can run the unit tests for one of the test environments, e.g.: ```bash -hatch env run --env test.py3.12-2.2-optional run-pytest +hatch env run --env test.py3.12-optional run ``` ### Creating a branch @@ -102,7 +102,7 @@ Again, any conflicts need to be resolved before submitting a pull request. Zarr includes a suite of unit tests. The simplest way to run the unit tests is to activate your development environment (see [creating a development environment](#creating-a-development-environment) above) and invoke: ```bash -hatch env run --env test.py3.12-2.2-optional run-pytest +hatch env run --env test.py3.12-optional run ``` All tests are automatically run via GitHub Actions for every pull request and must pass before code can be accepted. Test coverage is also collected automatically via the Codecov service. @@ -164,7 +164,7 @@ If you would like to skip the failing checks and push the code for further discu Zarr strives to maintain 100% test coverage under the latest Python stable release. Both unit tests and docstring doctests are included when computing coverage. Running: ```bash -hatch env run --env test.py3.12-2.2-optional run-coverage +hatch env run --env test.py3.12-optional run-coverage ``` will automatically run the test suite with coverage and produce an XML coverage report. This should be 100% before code can be accepted into the main code base. @@ -172,7 +172,7 @@ will automatically run the test suite with coverage and produce an XML coverage You can also generate an HTML coverage report by running: ```bash -hatch env run --env test.py3.12-2.2-optional run-coverage-html +hatch env run --env test.py3.12-optional run-coverage-html ``` When submitting a pull request, coverage will also be collected across all supported Python versions via the Codecov service, and will be reported back within the pull request. Codecov coverage must also be 100% before code can be accepted. diff --git a/pyproject.toml b/pyproject.toml index 068caa1f0d..02ebdc4176 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["hatchling>=1.27.0", "hatch-vcs"] +requires = ["hatchling>=1.29.0", "hatch-vcs"] build-backend = "hatchling.build" [tool.hatch.build.targets.sdist] @@ -61,7 +61,7 @@ license-files = ["LICENSE.txt"] keywords = ["Python", "compressed", "ndimensional-arrays", "zarr"] [project.optional-dependencies] -# User extras +# User-facing extras (shipped in package metadata) remote = [ "fsspec>=2023.10.0", "obstore>=0.5.1", @@ -70,30 +70,43 @@ gpu = [ "cupy-cuda12x", ] cli = ["typer"] -# Testing extras +optional = ["rich", "universal-pathlib"] + +[project.scripts] +zarr = "zarr._cli.cli:app" + + +[project.urls] +issues = "https://github.com/zarr-developers/zarr-python/issues" +changelog = "https://zarr.readthedocs.io/en/stable/release-notes.html" +Discussions = "https://github.com/zarr-developers/zarr-python/discussions" +documentation = "https://zarr.readthedocs.io/" +homepage = "https://github.com/zarr-developers/zarr-python" + +[dependency-groups] test = [ "coverage>=7.10", "pytest", "pytest-asyncio", "pytest-cov", "pytest-accept", - 'numpydoc', + "numpydoc", "hypothesis", "pytest-xdist", "pytest-benchmark", "pytest-codspeed", - "packaging", "tomlkit", "uv", ] -remote_tests = [ - 'zarr[remote]', +remote-tests = [ + {include-group = "test"}, + "fsspec>=2023.10.0", + "obstore>=0.5.1", "botocore", "s3fs>=2023.10.0", "moto[s3,server]", "requests", ] -optional = ["rich", "universal-pathlib"] docs = [ # Doc building "mkdocs-material[imaging]>=9.6.14", @@ -106,40 +119,23 @@ docs = [ "griffe-inherited-docstrings", "ruff", # Changelog generation - 'towncrier', + "towncrier", # Optional dependencies to run examples - 'numcodecs[msgpack]', - 'rich', - 's3fs>=2023.10.0', - 'astroid<4', - 'pytest' + "numcodecs[msgpack]", + "rich", + "s3fs>=2023.10.0", + "astroid<4", + "pytest", ] -# All development extras dev = [ - "zarr[optional]", - "zarr[test]", - "zarr[remote_tests]", - "zarr[docs]", + {include-group = "test"}, + {include-group = "remote-tests"}, + {include-group = "docs"}, + "rich", + "universal-pathlib", "mypy", ] -[project.scripts] -zarr = "zarr._cli.cli:app" - - -[project.urls] -issues = "https://github.com/zarr-developers/zarr-python/issues" -changelog = "https://zarr.readthedocs.io/en/stable/release-notes.html" -Discussions = "https://github.com/zarr-developers/zarr-python/discussions" -documentation = "https://zarr.readthedocs.io/" -homepage = "https://github.com/zarr-developers/zarr-python" - -[dependency-groups] -dev = [ - "ipykernel>=6.29.5", - "pip>=25.0.1", -] - [tool.coverage.report] exclude_also = [ 'if TYPE_CHECKING:', @@ -158,7 +154,7 @@ version.source = "vcs" hooks.vcs.version-file = "src/zarr/_version.py" [tool.hatch.envs.test] -features = ["test"] +dependency-groups = ["test"] [tool.hatch.envs.test.env-vars] # Required to test with a pytest plugin; see https://pytest-cov.readthedocs.io/en/latest/plugins.html @@ -171,16 +167,19 @@ python = ["3.11", "3.12", "3.13"] deps = ["minimal", "optional"] [tool.hatch.envs.test.overrides] -matrix.deps.dependencies = [ - {value = "zarr[remote, remote_tests, test, optional, cli]", if = ["optional"]} +matrix.deps.features = [ + {value = "remote", if = ["optional"]}, + {value = "optional", if = ["optional"]}, + {value = "cli", if = ["optional"]}, +] +matrix.deps.dependency-groups = [ + {value = "remote-tests", if = ["optional"]}, ] [tool.hatch.envs.test.scripts] run-coverage = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy" run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report html" -run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy" run = "run-coverage --no-cov --ignore tests/benchmarks" -run-pytest = "run" run-verbose = "run-coverage --verbose" run-mypy = "mypy src" run-hypothesis = "run-coverage -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*" @@ -189,27 +188,22 @@ list-env = "pip list" [tool.hatch.envs.gputest] template = "test" -dependencies = [ +extra-dependencies = [ "universal_pathlib", ] -features = ["test", "gpu"] +features = ["gpu"] [[tool.hatch.envs.gputest.matrix]] python = ["3.11", "3.12", "3.13"] -version = ["minimal"] [tool.hatch.envs.gputest.scripts] -run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks" +run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-report xml --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks" run = "run-coverage --no-cov" -run-verbose = "run-coverage --verbose" -run-mypy = "mypy src" -run-hypothesis = "run-coverage --hypothesis-profile ci --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*" -list-env = "pip list" [tool.hatch.envs.upstream] template = 'test' python = "3.13" -dependencies = [ +extra-dependencies = [ 'packaging @ git+https://github.com/pypa/packaging', 'numpy', # from scientific-python-nightly-wheels 'numcodecs @ git+https://github.com/zarr-developers/numcodecs', @@ -218,8 +212,6 @@ dependencies = [ 'typing_extensions @ git+https://github.com/python/typing_extensions', 'donfig @ git+https://github.com/pytroll/donfig', 'obstore @ git+https://github.com/developmentseed/obstore@main#subdirectory=obstore', - # test deps - 'zarr[test]', ] [tool.hatch.envs.upstream.env-vars] @@ -234,8 +226,9 @@ See Spec 0000 for details and drop schedule: https://scientific-python.org/specs """ template = "test" python = "3.11" -dependencies = [ - 'zarr[remote]', +features = ["remote"] +dependency-groups = ["remote-tests"] +extra-dependencies = [ 'packaging==22.*', 'numpy==2.0.*', 'numcodecs==0.14.*', # 0.14 needed for zarr3 codecs @@ -245,13 +238,11 @@ dependencies = [ 'typing_extensions==4.12.*', 'donfig==0.8.*', 'obstore==0.5.*', - # test deps - 'zarr[test]', - 'zarr[remote_tests]', ] [tool.hatch.envs.docs] -features = ['docs', 'remote'] +features = ['remote'] +dependency-groups = ['docs'] [tool.hatch.envs.docs.scripts] serve = "mkdocs serve --watch src" @@ -261,10 +252,10 @@ readthedocs = "rm -rf $READTHEDOCS_OUTPUT/html && cp -r site $READTHEDOCS_OUTPUT [tool.hatch.envs.doctest] description = "Test environment for validating executable code blocks in documentation" -features = ['test', 'remote'] # Include remote dependencies for s3fs -dependencies = [ +features = ['remote'] +dependency-groups = ['test'] +extra-dependencies = [ "s3fs>=2023.10.0", - "pytest", "pytest-examples", ] @@ -416,7 +407,11 @@ addopts = [ filterwarnings = [ "error", "ignore:Unclosed client session Date: Sat, 28 Feb 2026 09:49:31 -0500 Subject: [PATCH 213/468] perf: add sync methods to codecs (#3721) * add sync methods to codecs * Clarify memory conversion in blosc encoding Add comments to clarify memory conversion in encoding. * changelog --- changes/3721.misc.md | 1 + src/zarr/abc/codec.py | 20 ++++++++++++++++++- src/zarr/codecs/blosc.py | 27 +++++++++++++++++--------- src/zarr/codecs/bytes.py | 18 ++++++++++++++++-- src/zarr/codecs/crc32c_.py | 18 ++++++++++++++++-- src/zarr/codecs/gzip.py | 27 ++++++++++++++++++++------ src/zarr/codecs/transpose.py | 20 ++++++++++++++++--- src/zarr/codecs/vlen_utf8.py | 37 +++++++++++++++++++++++++++++++----- src/zarr/codecs/zstd.py | 24 ++++++++++++++++------- 9 files changed, 157 insertions(+), 35 deletions(-) create mode 100644 changes/3721.misc.md diff --git a/changes/3721.misc.md b/changes/3721.misc.md new file mode 100644 index 0000000000..c170712882 --- /dev/null +++ b/changes/3721.misc.md @@ -0,0 +1 @@ +Adds synchronous (non-async) encoding and decoding methods to CPU-bound codecs. This is necessary for performance optimizations based on avoiding `asyncio` overhead. These new methods are described by a new protocol: `SupportsSyncCodec`. \ No newline at end of file diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index d41c457b4e..3ec5ec522b 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -2,7 +2,7 @@ from abc import abstractmethod from collections.abc import Mapping -from typing import TYPE_CHECKING, Generic, TypeGuard, TypeVar +from typing import TYPE_CHECKING, Generic, Protocol, TypeGuard, TypeVar, runtime_checkable from typing_extensions import ReadOnly, TypedDict @@ -32,6 +32,7 @@ "CodecInput", "CodecOutput", "CodecPipeline", + "SupportsSyncCodec", ] CodecInput = TypeVar("CodecInput", bound=NDBuffer | Buffer) @@ -59,6 +60,23 @@ def _check_codecjson_v2(data: object) -> TypeGuard[CodecJSON_V2[str]]: """The widest type of JSON-like input that could specify a codec.""" +@runtime_checkable +class SupportsSyncCodec(Protocol): + """Protocol for codecs that support synchronous encode/decode. + + Codecs implementing this protocol provide ``_decode_sync`` and ``_encode_sync`` + methods that perform encoding/decoding without requiring an async event loop. + """ + + def _decode_sync( + self, chunk_data: NDBuffer | Buffer, chunk_spec: ArraySpec + ) -> NDBuffer | Buffer: ... + + def _encode_sync( + self, chunk_data: NDBuffer | Buffer, chunk_spec: ArraySpec + ) -> NDBuffer | Buffer | None: ... + + class BaseCodec(Metadata, Generic[CodecInput, CodecOutput]): """Generic base class for codecs. diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 5b91cfa005..62ceff7659 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -299,28 +299,37 @@ def _blosc_codec(self) -> Blosc: config_dict["typesize"] = self.typesize return Blosc.from_config(config_dict) + def _decode_sync( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer: + return as_numpy_array_wrapper(self._blosc_codec.decode, chunk_bytes, chunk_spec.prototype) + async def _decode_single( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> Buffer: - return await asyncio.to_thread( - as_numpy_array_wrapper, self._blosc_codec.decode, chunk_bytes, chunk_spec.prototype - ) + return await asyncio.to_thread(self._decode_sync, chunk_bytes, chunk_spec) - async def _encode_single( + def _encode_sync( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> Buffer | None: # Since blosc only support host memory, we convert the input and output of the encoding # between numpy array and buffer - return await asyncio.to_thread( - lambda chunk: chunk_spec.prototype.buffer.from_bytes( - self._blosc_codec.encode(chunk.as_numpy_array()) - ), - chunk_bytes, + return chunk_spec.prototype.buffer.from_bytes( + self._blosc_codec.encode(chunk_bytes.as_numpy_array()) ) + async def _encode_single( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return await asyncio.to_thread(self._encode_sync, chunk_bytes, chunk_spec) + def compute_encoded_size(self, _input_byte_length: int, _chunk_spec: ArraySpec) -> int: raise NotImplementedError diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index 1fbdeef497..86bb354fb5 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -65,7 +65,7 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: ) return self - async def _decode_single( + def _decode_sync( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, @@ -88,7 +88,14 @@ async def _decode_single( ) return chunk_array - async def _encode_single( + async def _decode_single( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + return self._decode_sync(chunk_bytes, chunk_spec) + + def _encode_sync( self, chunk_array: NDBuffer, chunk_spec: ArraySpec, @@ -109,5 +116,12 @@ async def _encode_single( nd_array = nd_array.ravel().view(dtype="B") return chunk_spec.prototype.buffer.from_array_like(nd_array) + async def _encode_single( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return self._encode_sync(chunk_array, chunk_spec) + def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: return input_byte_length diff --git a/src/zarr/codecs/crc32c_.py b/src/zarr/codecs/crc32c_.py index 9536d0d558..ebe2ac8f7a 100644 --- a/src/zarr/codecs/crc32c_.py +++ b/src/zarr/codecs/crc32c_.py @@ -31,7 +31,7 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: def to_dict(self) -> dict[str, JSON]: return {"name": "crc32c"} - async def _decode_single( + def _decode_sync( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, @@ -51,7 +51,14 @@ async def _decode_single( ) return chunk_spec.prototype.buffer.from_array_like(inner_bytes) - async def _encode_single( + async def _decode_single( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer: + return self._decode_sync(chunk_bytes, chunk_spec) + + def _encode_sync( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, @@ -64,5 +71,12 @@ async def _encode_single( # Append the checksum (as bytes) to the data return chunk_spec.prototype.buffer.from_array_like(np.append(data, checksum.view("B"))) + async def _encode_single( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return self._encode_sync(chunk_bytes, chunk_spec) + def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: return input_byte_length + 4 diff --git a/src/zarr/codecs/gzip.py b/src/zarr/codecs/gzip.py index 610ca9dadd..b8591748f7 100644 --- a/src/zarr/codecs/gzip.py +++ b/src/zarr/codecs/gzip.py @@ -2,6 +2,7 @@ import asyncio from dataclasses import dataclass +from functools import cached_property from typing import TYPE_CHECKING from numcodecs.gzip import GZip @@ -48,23 +49,37 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: def to_dict(self) -> dict[str, JSON]: return {"name": "gzip", "configuration": {"level": self.level}} + @cached_property + def _gzip_codec(self) -> GZip: + return GZip(self.level) + + def _decode_sync( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer: + return as_numpy_array_wrapper(self._gzip_codec.decode, chunk_bytes, chunk_spec.prototype) + async def _decode_single( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> Buffer: - return await asyncio.to_thread( - as_numpy_array_wrapper, GZip(self.level).decode, chunk_bytes, chunk_spec.prototype - ) + return await asyncio.to_thread(self._decode_sync, chunk_bytes, chunk_spec) + + def _encode_sync( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return as_numpy_array_wrapper(self._gzip_codec.encode, chunk_bytes, chunk_spec.prototype) async def _encode_single( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> Buffer | None: - return await asyncio.to_thread( - as_numpy_array_wrapper, GZip(self.level).encode, chunk_bytes, chunk_spec.prototype - ) + return await asyncio.to_thread(self._encode_sync, chunk_bytes, chunk_spec) def compute_encoded_size( self, diff --git a/src/zarr/codecs/transpose.py b/src/zarr/codecs/transpose.py index a8570b6e8f..609448a59c 100644 --- a/src/zarr/codecs/transpose.py +++ b/src/zarr/codecs/transpose.py @@ -95,20 +95,34 @@ def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: prototype=chunk_spec.prototype, ) - async def _decode_single( + def _decode_sync( self, chunk_array: NDBuffer, chunk_spec: ArraySpec, ) -> NDBuffer: - inverse_order = np.argsort(self.order) + inverse_order = tuple(int(i) for i in np.argsort(self.order)) return chunk_array.transpose(inverse_order) - async def _encode_single( + async def _decode_single( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + return self._decode_sync(chunk_array, chunk_spec) + + def _encode_sync( self, chunk_array: NDBuffer, _chunk_spec: ArraySpec, ) -> NDBuffer | None: return chunk_array.transpose(self.order) + async def _encode_single( + self, + chunk_array: NDBuffer, + _chunk_spec: ArraySpec, + ) -> NDBuffer | None: + return self._encode_sync(chunk_array, _chunk_spec) + def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: return input_byte_length diff --git a/src/zarr/codecs/vlen_utf8.py b/src/zarr/codecs/vlen_utf8.py index fb1fb76126..a10cb7c335 100644 --- a/src/zarr/codecs/vlen_utf8.py +++ b/src/zarr/codecs/vlen_utf8.py @@ -40,8 +40,7 @@ def to_dict(self) -> dict[str, JSON]: def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: return self - # TODO: expand the tests for this function - async def _decode_single( + def _decode_sync( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, @@ -55,7 +54,14 @@ async def _decode_single( as_string_dtype = decoded.astype(chunk_spec.dtype.to_native_dtype(), copy=False) return chunk_spec.prototype.nd_buffer.from_numpy_array(as_string_dtype) - async def _encode_single( + async def _decode_single( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + return self._decode_sync(chunk_bytes, chunk_spec) + + def _encode_sync( self, chunk_array: NDBuffer, chunk_spec: ArraySpec, @@ -65,6 +71,13 @@ async def _encode_single( _vlen_utf8_codec.encode(chunk_array.as_numpy_array()) ) + async def _encode_single( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return self._encode_sync(chunk_array, chunk_spec) + def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: # what is input_byte_length for an object dtype? raise NotImplementedError("compute_encoded_size is not implemented for VLen codecs") @@ -86,7 +99,7 @@ def to_dict(self) -> dict[str, JSON]: def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: return self - async def _decode_single( + def _decode_sync( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, @@ -99,7 +112,14 @@ async def _decode_single( decoded = _reshape_view(decoded, chunk_spec.shape) return chunk_spec.prototype.nd_buffer.from_numpy_array(decoded) - async def _encode_single( + async def _decode_single( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + return self._decode_sync(chunk_bytes, chunk_spec) + + def _encode_sync( self, chunk_array: NDBuffer, chunk_spec: ArraySpec, @@ -109,6 +129,13 @@ async def _encode_single( _vlen_bytes_codec.encode(chunk_array.as_numpy_array()) ) + async def _encode_single( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return self._encode_sync(chunk_array, chunk_spec) + def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: # what is input_byte_length for an object dtype? raise NotImplementedError("compute_encoded_size is not implemented for VLen codecs") diff --git a/src/zarr/codecs/zstd.py b/src/zarr/codecs/zstd.py index 27cc9a7777..f93c25a3c7 100644 --- a/src/zarr/codecs/zstd.py +++ b/src/zarr/codecs/zstd.py @@ -38,7 +38,7 @@ def parse_checksum(data: JSON) -> bool: class ZstdCodec(BytesBytesCodec): """zstd codec""" - is_fixed_size = True + is_fixed_size = False level: int = 0 checksum: bool = False @@ -71,23 +71,33 @@ def _zstd_codec(self) -> Zstd: config_dict = {"level": self.level, "checksum": self.checksum} return Zstd.from_config(config_dict) + def _decode_sync( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer: + return as_numpy_array_wrapper(self._zstd_codec.decode, chunk_bytes, chunk_spec.prototype) + async def _decode_single( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> Buffer: - return await asyncio.to_thread( - as_numpy_array_wrapper, self._zstd_codec.decode, chunk_bytes, chunk_spec.prototype - ) + return await asyncio.to_thread(self._decode_sync, chunk_bytes, chunk_spec) + + def _encode_sync( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return as_numpy_array_wrapper(self._zstd_codec.encode, chunk_bytes, chunk_spec.prototype) async def _encode_single( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> Buffer | None: - return await asyncio.to_thread( - as_numpy_array_wrapper, self._zstd_codec.encode, chunk_bytes, chunk_spec.prototype - ) + return await asyncio.to_thread(self._encode_sync, chunk_bytes, chunk_spec) def compute_encoded_size(self, _input_byte_length: int, _chunk_spec: ArraySpec) -> int: raise NotImplementedError From b8094d8765e4f6de5121806ed8f209ffac315168 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sun, 1 Mar 2026 11:50:34 -0500 Subject: [PATCH 214/468] fix: implement separate cache for byte-range-requests (#3710) * implement separate cache for byte-range-requests * changelog --- changes/3710.bugfix.md | 1 + src/zarr/abc/store.py | 6 +- src/zarr/experimental/cache_store.py | 245 ++++++++++++-------- tests/test_experimental/test_cache_store.py | 165 +++++++++++-- 4 files changed, 307 insertions(+), 110 deletions(-) create mode 100644 changes/3710.bugfix.md diff --git a/changes/3710.bugfix.md b/changes/3710.bugfix.md new file mode 100644 index 0000000000..a40ddcee23 --- /dev/null +++ b/changes/3710.bugfix.md @@ -0,0 +1 @@ +Add a dedicated in-memory cache for byte-range requests to the experimental `CacheStore`. \ No newline at end of file diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 87df89a683..f677c197dc 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -19,7 +19,7 @@ __all__ = ["ByteGetter", "ByteSetter", "Store", "set_or_delete"] -@dataclass +@dataclass(frozen=True, slots=True) class RangeByteRequest: """Request a specific byte range""" @@ -29,7 +29,7 @@ class RangeByteRequest: """The end of the byte range request (exclusive).""" -@dataclass +@dataclass(frozen=True, slots=True) class OffsetByteRequest: """Request all bytes starting from a given byte offset""" @@ -37,7 +37,7 @@ class OffsetByteRequest: """The byte offset for the offset range request.""" -@dataclass +@dataclass(frozen=True, slots=True) class SuffixByteRequest: """Request up to the last `n` bytes""" diff --git a/src/zarr/experimental/cache_store.py b/src/zarr/experimental/cache_store.py index 87adc90c83..1535b42f67 100644 --- a/src/zarr/experimental/cache_store.py +++ b/src/zarr/experimental/cache_store.py @@ -15,17 +15,23 @@ if TYPE_CHECKING: from zarr.core.buffer.core import Buffer, BufferPrototype +# A cache entry identifier. Plain ``str`` for full-key entries that live in +# the Store-backed cache; ``(str, ByteRequest)`` for byte-range entries that +# live in the in-memory range cache. +_CacheEntryKey = str | tuple[str, ByteRequest] + @dataclass(slots=True) class _CacheState: - cache_order: OrderedDict[str, None] = field(default_factory=OrderedDict) + cache_order: OrderedDict[_CacheEntryKey, None] = field(default_factory=OrderedDict) current_size: int = 0 - key_sizes: dict[str, int] = field(default_factory=dict) + key_sizes: dict[_CacheEntryKey, int] = field(default_factory=dict) lock: asyncio.Lock = field(default_factory=asyncio.Lock) hits: int = 0 misses: int = 0 evictions: int = 0 - key_insert_times: dict[str, float] = field(default_factory=dict) + key_insert_times: dict[_CacheEntryKey, float] = field(default_factory=dict) + range_cache: dict[str, dict[ByteRequest, Buffer]] = field(default_factory=dict) class CacheStore(WrapperStore[Store]): @@ -36,6 +42,11 @@ class CacheStore(WrapperStore[Store]): as the cache backend. This provides persistent caching capabilities with time-based expiration, size-based eviction, and flexible cache storage options. + Full-key reads are cached in the Store-backed cache. Byte-range reads are + cached in a separate in-memory dictionary so that partial reads never + pollute the filesystem (or other persistent backend). Both caches share + the same ``max_size`` budget and LRU eviction policy. + Parameters ---------- store : Store @@ -129,21 +140,21 @@ def with_read_only(self, read_only: bool = False) -> Self: store._state = self._state return store - def _is_key_fresh(self, key: str) -> bool: - """Check if a cached key is still fresh based on max_age_seconds. + def _is_key_fresh(self, entry_key: _CacheEntryKey) -> bool: + """Check if a cached entry is still fresh based on max_age_seconds. Uses monotonic time for accurate elapsed time measurement. """ if self.max_age_seconds == "infinity": return True now = time.monotonic() - elapsed = now - self._state.key_insert_times.get(key, 0) + elapsed = now - self._state.key_insert_times.get(entry_key, 0) return elapsed < self.max_age_seconds async def _accommodate_value(self, value_size: int) -> None: """Ensure there is enough space in the cache for a new value. - Must be called while holding self._lock. + Must be called while holding self._state.lock. """ if self.max_size is None: return @@ -154,30 +165,39 @@ async def _accommodate_value(self, value_size: int) -> None: lru_key = next(iter(self._state.cache_order)) await self._evict_key(lru_key) - async def _evict_key(self, key: str) -> None: - """Evict a key from the cache. - - Must be called while holding self._lock. - Updates size tracking atomically with deletion. - """ - try: - key_size = self._state.key_sizes.get(key, 0) - - # Delete from cache store - await self._cache.delete(key) + async def _evict_key(self, entry_key: _CacheEntryKey) -> None: + """Evict a cache entry. - # Update tracking after successful deletion - self._remove_from_tracking(key) - self._state.current_size = max(0, self._state.current_size - key_size) - self._state.evictions += 1 + Must be called while holding self._state.lock. - logger.debug("_evict_key: evicted key %s, freed %d bytes", key, key_size) - except Exception: - logger.exception("_evict_key: failed to evict key %s", key) - raise # Re-raise to signal eviction failure + For ``str`` keys the entry is deleted from the Store-backed cache. + For ``(str, ByteRequest)`` keys the entry is removed from the + in-memory range cache. + """ + key_size = self._state.key_sizes.get(entry_key, 0) - async def _cache_value(self, key: str, value: Buffer) -> None: - """Cache a value with size tracking. + if isinstance(entry_key, str): + await self._cache.delete(entry_key) + else: + base_key, byte_range = entry_key + per_key = self._state.range_cache.get(base_key) + if per_key is not None: + per_key.pop(byte_range, None) + if not per_key: + del self._state.range_cache[base_key] + + self._state.cache_order.pop(entry_key, None) + self._state.key_insert_times.pop(entry_key, None) + self._state.key_sizes.pop(entry_key, None) + self._state.current_size = max(0, self._state.current_size - key_size) + self._state.evictions += 1 + + async def _track_entry(self, entry_key: _CacheEntryKey, value: Buffer) -> bool: + """Register *entry_key* in the shared size / LRU tracking. + + Returns ``True`` if the entry was tracked, ``False`` if the value + exceeds ``max_size`` and was skipped. Callers should roll back any + data they already stored when this returns ``False``. This method holds the lock for the entire operation to ensure atomicity. """ @@ -185,91 +205,128 @@ async def _cache_value(self, key: str, value: Buffer) -> None: # Check if value exceeds max size if self.max_size is not None and value_size > self.max_size: - logger.warning( - "_cache_value: value size %d exceeds max_size %d, skipping cache", - value_size, - self.max_size, - ) - return + return False async with self._state.lock: # If key already exists, subtract old size first - if key in self._state.key_sizes: - old_size = self._state.key_sizes[key] + if entry_key in self._state.key_sizes: + old_size = self._state.key_sizes[entry_key] self._state.current_size -= old_size - logger.debug("_cache_value: updating existing key %s, old size %d", key, old_size) - # Make room for the new value (this calls _evict_key_locked internally) + # Make room for the new value await self._accommodate_value(value_size) # Update tracking atomically - self._state.cache_order[key] = None # OrderedDict to track access order + self._state.cache_order[entry_key] = None self._state.current_size += value_size - self._state.key_sizes[key] = value_size - self._state.key_insert_times[key] = time.monotonic() + self._state.key_sizes[entry_key] = value_size + self._state.key_insert_times[entry_key] = time.monotonic() - logger.debug("_cache_value: cached key %s with size %d bytes", key, value_size) + return True - async def _update_access_order(self, key: str) -> None: + async def _update_access_order(self, entry_key: _CacheEntryKey) -> None: """Update the access order for LRU tracking.""" - if key in self._state.cache_order: + if entry_key in self._state.cache_order: async with self._state.lock: - # Move to end (most recently used) - self._state.cache_order.move_to_end(key) + self._state.cache_order.move_to_end(entry_key) - def _remove_from_tracking(self, key: str) -> None: - """Remove a key from all tracking structures. + def _remove_from_tracking(self, entry_key: _CacheEntryKey) -> None: + """Remove an entry from all tracking structures. Must be called while holding self._state.lock. """ - self._state.cache_order.pop(key, None) - self._state.key_insert_times.pop(key, None) - self._state.key_sizes.pop(key, None) + self._state.cache_order.pop(entry_key, None) + self._state.key_insert_times.pop(entry_key, None) + self._state.key_sizes.pop(entry_key, None) + + def _invalidate_range_entries(self, key: str) -> None: + """Remove all byte-range entries for *key* from the range cache and tracking. + + Must be called while holding self._state.lock. + """ + per_key = self._state.range_cache.pop(key, None) + if per_key is not None: + for byte_range in per_key: + entry_key: _CacheEntryKey = (key, byte_range) + entry_size = self._state.key_sizes.pop(entry_key, 0) + self._state.cache_order.pop(entry_key, None) + self._state.key_insert_times.pop(entry_key, None) + self._state.current_size = max(0, self._state.current_size - entry_size) + + # ------------------------------------------------------------------ + # get helpers + # ------------------------------------------------------------------ + + async def _cache_miss( + self, key: str, byte_range: ByteRequest | None, result: Buffer | None + ) -> None: + """Handle a cache miss by storing or cleaning up after a source-store fetch.""" + if result is None: + if byte_range is None: + await self._cache.delete(key) + async with self._state.lock: + self._remove_from_tracking(key) + else: + entry_key: _CacheEntryKey = (key, byte_range) + async with self._state.lock: + per_key = self._state.range_cache.get(key) + if per_key is not None: + per_key.pop(byte_range, None) + if not per_key: + del self._state.range_cache[key] + self._remove_from_tracking(entry_key) + else: + if byte_range is None: + await self._cache.set(key, result) + await self._track_entry(key, result) + else: + entry_key = (key, byte_range) + self._state.range_cache.setdefault(key, {})[byte_range] = result + tracked = await self._track_entry(entry_key, result) + if not tracked: + # Value too large for the cache — roll back the insertion + per_key = self._state.range_cache.get(key) + if per_key is not None: + per_key.pop(byte_range, None) + if not per_key: + del self._state.range_cache[key] async def _get_try_cache( self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None ) -> Buffer | None: """Try to get data from cache first, falling back to source store.""" - maybe_cached_result = await self._cache.get(key, prototype, byte_range) - if maybe_cached_result is not None: - logger.debug("_get_try_cache: key %s found in cache (HIT)", key) - self._state.hits += 1 - # Update access order for LRU - await self._update_access_order(key) - return maybe_cached_result + if byte_range is None: + # Full-key read — use Store-backed cache + maybe_cached = await self._cache.get(key, prototype) + if maybe_cached is not None: + self._state.hits += 1 + await self._update_access_order(key) + return maybe_cached else: - logger.debug( - "_get_try_cache: key %s not found in cache (MISS), fetching from store", key - ) - self._state.misses += 1 - maybe_fresh_result = await super().get(key, prototype, byte_range) - if maybe_fresh_result is None: - # Key doesn't exist in source store - await self._cache.delete(key) - async with self._state.lock: - self._remove_from_tracking(key) - else: - # Cache the newly fetched value - await self._cache.set(key, maybe_fresh_result) - await self._cache_value(key, maybe_fresh_result) - return maybe_fresh_result + # Byte-range read — use in-memory range cache + entry_key: _CacheEntryKey = (key, byte_range) + per_key = self._state.range_cache.get(key) + if per_key is not None: + cached_buf = per_key.get(byte_range) + if cached_buf is not None: + self._state.hits += 1 + await self._update_access_order(entry_key) + return cached_buf + + # Cache miss — fetch from source store + self._state.misses += 1 + result = await super().get(key, prototype, byte_range) + await self._cache_miss(key, byte_range, result) + return result async def _get_no_cache( self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None ) -> Buffer | None: """Get data directly from source store and update cache.""" self._state.misses += 1 - maybe_fresh_result = await super().get(key, prototype, byte_range) - if maybe_fresh_result is None: - # Key doesn't exist in source, remove from cache and tracking - await self._cache.delete(key) - async with self._state.lock: - self._remove_from_tracking(key) - else: - logger.debug("_get_no_cache: key %s found in store, setting in cache", key) - await self._cache.set(key, maybe_fresh_result) - await self._cache_value(key, maybe_fresh_result) - return maybe_fresh_result + result = await super().get(key, prototype, byte_range) + await self._cache_miss(key, byte_range, result) + return result async def get( self, @@ -294,11 +351,10 @@ async def get( Buffer | None The retrieved data, or None if not found """ - if not self._is_key_fresh(key): - logger.debug("get: key %s is not fresh, fetching from store", key) + entry_key: _CacheEntryKey = (key, byte_range) if byte_range is not None else key + if not self._is_key_fresh(entry_key): return await self._get_no_cache(key, prototype, byte_range) else: - logger.debug("get: key %s is fresh, trying cache", key) return await self._get_try_cache(key, prototype, byte_range) async def set(self, key: str, value: Buffer) -> None: @@ -312,14 +368,14 @@ async def set(self, key: str, value: Buffer) -> None: value : Buffer The data to store """ - logger.debug("set: setting key %s in store", key) await super().set(key, value) + # Invalidate all cached byte-range entries (source data changed) + async with self._state.lock: + self._invalidate_range_entries(key) if self.cache_set_data: - logger.debug("set: setting key %s in cache", key) await self._cache.set(key, value) - await self._cache_value(key, value) + await self._track_entry(key, value) else: - logger.debug("set: deleting key %s from cache", key) await self._cache.delete(key) async with self._state.lock: self._remove_from_tracking(key) @@ -333,9 +389,10 @@ async def delete(self, key: str) -> None: key : str The key to delete """ - logger.debug("delete: deleting key %s from store", key) await super().delete(key) - logger.debug("delete: deleting key %s from cache", key) + # Invalidate all cached byte-range entries + async with self._state.lock: + self._invalidate_range_entries(key) await self._cache.delete(key) async with self._state.lock: self._remove_from_tracking(key) @@ -377,8 +434,8 @@ async def clear_cache(self) -> None: self._state.key_insert_times.clear() self._state.cache_order.clear() self._state.key_sizes.clear() + self._state.range_cache.clear() self._state.current_size = 0 - logger.debug("clear_cache: cleared all cache data") def __repr__(self) -> str: """Return string representation of the cache store.""" diff --git a/tests/test_experimental/test_cache_store.py b/tests/test_experimental/test_cache_store.py index 50d3d9506b..fc17ccd5e1 100644 --- a/tests/test_experimental/test_cache_store.py +++ b/tests/test_experimental/test_cache_store.py @@ -7,7 +7,7 @@ import pytest -from zarr.abc.store import Store +from zarr.abc.store import RangeByteRequest, Store, SuffixByteRequest from zarr.core.buffer.core import default_buffer_prototype from zarr.core.buffer.cpu import Buffer as CPUBuffer from zarr.experimental.cache_store import CacheStore @@ -581,7 +581,7 @@ async def test_get_no_cache_delete_tracking(self) -> None: # First, add key to cache tracking but not to source test_data = CPUBuffer.from_bytes(b"test data") await cache_store.set("phantom_key", test_data) - await cached_store._cache_value("phantom_key", test_data) + await cached_store._track_entry("phantom_key", test_data) # Verify it's in tracking assert "phantom_key" in cached_store._state.cache_order @@ -778,17 +778,20 @@ async def test_all_tracked_keys_exist_in_cache_store(self) -> None: data = CPUBuffer.from_bytes(b"x" * 50) await cached_store.set(f"key_{i}", data) - # Every key in tracking should exist in cache_store - for key in cached_store._state.cache_order: - assert await cache_store.exists(key), ( - f"Key '{key}' is tracked but doesn't exist in cache_store" - ) - - # Every key in _key_sizes should exist in cache_store - for key in cached_store._state.key_sizes: - assert await cache_store.exists(key), ( - f"Key '{key}' has size tracked but doesn't exist in cache_store" - ) + # Every str key in tracking should exist in cache_store + # (tuple keys are byte-range entries stored in-memory, not in the Store) + for entry_key in cached_store._state.cache_order: + if isinstance(entry_key, str): + assert await cache_store.exists(entry_key), ( + f"Key '{entry_key}' is tracked but doesn't exist in cache_store" + ) + + # Every str key in _key_sizes should exist in cache_store + for entry_key in cached_store._state.key_sizes: + if isinstance(entry_key, str): + assert await cache_store.exists(entry_key), ( + f"Key '{entry_key}' has size tracked but doesn't exist in cache_store" + ) # Additional coverage tests for 100% coverage @@ -908,3 +911,139 @@ async def test_cache_stats_zero_division_protection(self) -> None: stats = cached_store.cache_stats() assert stats["hit_rate"] == 0.0 assert stats["total_requests"] == 0 + + async def test_byte_range_does_not_corrupt_cache(self) -> None: + """Test that fetching a byte range does not store partial data under the full key. + + Reproduces https://github.com/zarr-developers/zarr-python/issues/3690: + when a byte-range read populates the cache, subsequent reads of different + ranges (or the full key) return wrong data. + """ + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store) + + full_data = b"bar baz" + await source_store.set("foo", CPUBuffer.from_bytes(full_data)) + + proto = default_buffer_prototype() + + # First read: byte range [0, 3) -> b"bar" + bar = await cached_store.get("foo", proto, byte_range=RangeByteRequest(0, 3)) + assert bar is not None + assert bar.to_bytes() == b"bar" + + # Second read: different byte range [4, 7) -> b"baz" + baz = await cached_store.get("foo", proto, byte_range=RangeByteRequest(4, 7)) + assert baz is not None + assert baz.to_bytes() == b"baz" + + # Third read: full key -> full data + full = await cached_store.get("foo", proto) + assert full is not None + assert full.to_bytes() == full_data + + async def test_full_read_then_byte_range(self) -> None: + """Test that a cached full read correctly serves subsequent byte-range requests.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store) + + full_data = b"hello world" + await source_store.set("key", CPUBuffer.from_bytes(full_data)) + + proto = default_buffer_prototype() + + # Full read populates cache + full = await cached_store.get("key", proto) + assert full is not None + assert full.to_bytes() == full_data + + # Byte-range reads should return the correct slices + part = await cached_store.get("key", proto, byte_range=RangeByteRequest(0, 5)) + assert part is not None + assert part.to_bytes() == b"hello" + + part2 = await cached_store.get("key", proto, byte_range=RangeByteRequest(6, 11)) + assert part2 is not None + assert part2.to_bytes() == b"world" + + suffix = await cached_store.get("key", proto, byte_range=SuffixByteRequest(5)) + assert suffix is not None + assert suffix.to_bytes() == b"world" + + async def test_byte_range_set_then_read(self) -> None: + """Test that data written via set() can be read back with byte ranges.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store) + + full_data = b"abcdefghij" + await cached_store.set("key", CPUBuffer.from_bytes(full_data)) + + proto = default_buffer_prototype() + + # Byte-range reads from the cached data + mid = await cached_store.get("key", proto, byte_range=RangeByteRequest(3, 7)) + assert mid is not None + assert mid.to_bytes() == b"defg" + + # Full read should still work + full = await cached_store.get("key", proto) + assert full is not None + assert full.to_bytes() == full_data + + async def test_set_invalidates_cached_byte_ranges(self) -> None: + """Test that set() invalidates previously cached byte-range entries.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store) + + proto = default_buffer_prototype() + + # Populate source and cache some byte ranges + await source_store.set("key", CPUBuffer.from_bytes(b"old data!!")) + r1 = await cached_store.get("key", proto, byte_range=RangeByteRequest(0, 3)) + assert r1 is not None + assert r1.to_bytes() == b"old" + + # Byte-range entry should be in range_cache + assert ("key", RangeByteRequest(0, 3)) in cached_store._state.cache_order + + # Overwrite via set() — range entries must be invalidated + await cached_store.set("key", CPUBuffer.from_bytes(b"NEW DATA!!")) + + # The old range entry should be gone from tracking and range_cache + assert ("key", RangeByteRequest(0, 3)) not in cached_store._state.cache_order + assert "key" not in cached_store._state.range_cache + + # A fresh byte-range read should return the new data + r2 = await cached_store.get("key", proto, byte_range=RangeByteRequest(0, 3)) + assert r2 is not None + assert r2.to_bytes() == b"NEW" + + async def test_delete_invalidates_cached_byte_ranges(self) -> None: + """Test that delete() removes previously cached byte-range entries.""" + source_store = MemoryStore() + cache_store = MemoryStore() + cached_store = CacheStore(store=source_store, cache_store=cache_store) + + proto = default_buffer_prototype() + + # Populate and cache a byte range + await source_store.set("key", CPUBuffer.from_bytes(b"hello world")) + r = await cached_store.get("key", proto, byte_range=RangeByteRequest(0, 5)) + assert r is not None + assert r.to_bytes() == b"hello" + + assert ("key", RangeByteRequest(0, 5)) in cached_store._state.cache_order + + # Delete the key — range entries must be cleaned up + await cached_store.delete("key") + + assert ("key", RangeByteRequest(0, 5)) not in cached_store._state.cache_order + assert "key" not in cached_store._state.range_cache + + # Key is gone from source + result = await cached_store.get("key", proto) + assert result is None From faec389608a32ff0a21b4d15577e7513855d7501 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Tue, 3 Mar 2026 10:19:58 +0200 Subject: [PATCH 215/468] chore: update ruff and fix new ruff issues (#3739) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Apply ruff/pyupgrade rule UP042 Class inherits from both `str` and `enum.Enum` * Apply ruff/refurb rule FURB110 Replace ternary `if` expression with `or` operator * Apply ruff/refurb rule FURB171 Membership test against single-item container * Apply ruff preview rule RUF068 `__all__` contains duplicate entries * Apply ruff/refurb preview rule FURB140 Use `itertools.starmap` instead of the generator * Bump ruff: 0.14.14 → 0.15.4 * Update tests/test_examples.py Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> --------- Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 2 +- src/zarr/_cli/cli.py | 6 +++--- src/zarr/core/chunk_key_encodings.py | 2 +- src/zarr/core/dtype/__init__.py | 1 - src/zarr/core/indexing.py | 2 +- src/zarr/dtype.py | 2 -- tests/test_api.py | 2 ++ tests/test_array.py | 6 +++--- tests/test_examples.py | 2 +- tests/test_properties.py | 5 +++-- 10 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8b6c41901c..3eb29e32df 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.14 + rev: v0.15.4 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] diff --git a/src/zarr/_cli/cli.py b/src/zarr/_cli/cli.py index 78f4955d84..de55826582 100644 --- a/src/zarr/_cli/cli.py +++ b/src/zarr/_cli/cli.py @@ -1,5 +1,5 @@ import logging -from enum import Enum +from enum import StrEnum from typing import Annotated, Literal, cast import typer @@ -24,12 +24,12 @@ def _set_logging_level(*, verbose: bool) -> None: zarr.set_format("%(message)s") -class CLIZarrFormat(str, Enum): +class CLIZarrFormat(StrEnum): v2 = "v2" v3 = "v3" -class CLIZarrFormatV3(str, Enum): +class CLIZarrFormatV3(StrEnum): """Limit CLI choice to only v3""" v3 = "v3" diff --git a/src/zarr/core/chunk_key_encodings.py b/src/zarr/core/chunk_key_encodings.py index 5c9f77118a..9eef80656d 100644 --- a/src/zarr/core/chunk_key_encodings.py +++ b/src/zarr/core/chunk_key_encodings.py @@ -42,7 +42,7 @@ class ChunkKeyEncoding(ABC, Metadata): @classmethod def from_dict(cls, data: dict[str, JSON]) -> Self: _, config_parsed = parse_named_configuration(data, require_configuration=False) - return cls(**config_parsed if config_parsed else {}) + return cls(**config_parsed or {}) def to_dict(self) -> dict[str, JSON]: return {"name": self.name, "configuration": super().to_dict()} diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index f3077c32e5..1049a2063f 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -81,7 +81,6 @@ "TBaseDType", "TBaseScalar", "TimeDelta64", - "TimeDelta64", "TimeDelta64JSON_V2", "TimeDelta64JSON_V3", "UInt8", diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 73fd53087d..d226c03675 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -209,7 +209,7 @@ def _iter_regions( # ((slice(0, 1, 1), slice(0, 2, 1)), (slice(1, 2, 1), slice(0, 2, 1))) ``` """ - grid_shape = tuple(ceildiv(d, s) for d, s in zip(domain_shape, region_shape, strict=True)) + grid_shape = tuple(itertools.starmap(ceildiv, zip(domain_shape, region_shape, strict=True))) for grid_position in _iter_grid( grid_shape=grid_shape, origin=origin, selection_shape=selection_shape, order=order ): diff --git a/src/zarr/dtype.py b/src/zarr/dtype.py index 616d1c1ce2..2c7eb651b0 100644 --- a/src/zarr/dtype.py +++ b/src/zarr/dtype.py @@ -72,7 +72,6 @@ "StructuredJSON_V2", "StructuredJSON_V3", "TimeDelta64", - "TimeDelta64", "TimeDelta64JSON_V2", "TimeDelta64JSON_V3", "UInt8", @@ -85,6 +84,5 @@ "VariableLengthUTF8JSON_V2", "ZDType", "data_type_registry", - "data_type_registry", "parse_dtype", ] diff --git a/tests/test_api.py b/tests/test_api.py index 82c75807df..07c3c8590d 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1529,6 +1529,7 @@ def test_auto_chunks(f: Callable[..., AnyArray]) -> None: array = np.zeros(shape, dtype=dtype) store = zarr.storage.MemoryStore() + # ruff: disable[FURB171] if f in [zarr.full, zarr.full_like]: kwargs["fill_value"] = 0 if f in [zarr.array]: @@ -1537,6 +1538,7 @@ def test_auto_chunks(f: Callable[..., AnyArray]) -> None: kwargs["a"] = array if f in [zarr.create_array]: kwargs["store"] = store + # ruff: enable[FURB171] a = f(**kwargs) assert a.chunks == (500, 500) diff --git a/tests/test_array.py b/tests/test_array.py index 01a82e1938..5b85c6ba1d 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -6,7 +6,7 @@ import pickle import re import sys -from itertools import accumulate +from itertools import accumulate, starmap from typing import TYPE_CHECKING, Any, Literal from unittest import mock @@ -2064,12 +2064,12 @@ def test_chunk_grid_shape( zarr_format=zarr_format, ) - chunk_grid_shape = tuple(ceildiv(a, b) for a, b in zip(array_shape, chunk_shape, strict=True)) + chunk_grid_shape = tuple(starmap(ceildiv, zip(array_shape, chunk_shape, strict=True))) if shard_shape is None: _shard_shape = chunk_shape else: _shard_shape = shard_shape - shard_grid_shape = tuple(ceildiv(a, b) for a, b in zip(array_shape, _shard_shape, strict=True)) + shard_grid_shape = tuple(starmap(ceildiv, zip(array_shape, _shard_shape, strict=True))) assert arr._chunk_grid_shape == chunk_grid_shape assert arr.cdata_shape == chunk_grid_shape assert arr.async_array.cdata_shape == chunk_grid_shape diff --git a/tests/test_examples.py b/tests/test_examples.py index 152b0a1a88..9f8085e8c2 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -70,7 +70,7 @@ def test_script_paths() -> None: @pytest.mark.skipif( - sys.platform in ("win32",), reason="This test fails due for unknown reasons on Windows in CI." + sys.platform == "win32", reason="This test fails for unknown reasons on Windows in CI." ) @pytest.mark.parametrize("script_path", script_paths) def test_scripts_can_run(script_path: Path, tmp_path: Path) -> None: diff --git a/tests/test_properties.py b/tests/test_properties.py index 705cfd1b59..bab659c976 100644 --- a/tests/test_properties.py +++ b/tests/test_properties.py @@ -1,3 +1,4 @@ +import itertools import json import numbers from typing import Any @@ -60,7 +61,7 @@ def deep_equal(a: Any, b: Any) -> bool: if isinstance(a, np.ndarray) and isinstance(b, np.ndarray): if a.shape != b.shape: return False - return all(deep_equal(x, y) for x, y in zip(a.flat, b.flat, strict=False)) + return all(itertools.starmap(deep_equal, zip(a.flat, b.flat, strict=False))) if isinstance(a, dict) and isinstance(b, dict): if set(a.keys()) != set(b.keys()): @@ -70,7 +71,7 @@ def deep_equal(a: Any, b: Any) -> bool: if isinstance(a, (list, tuple)) and isinstance(b, (list, tuple)): if len(a) != len(b): return False - return all(deep_equal(x, y) for x, y in zip(a, b, strict=False)) + return all(itertools.starmap(deep_equal, zip(a, b, strict=False))) return a == b From ca53f8e5bc002797ed531a1c49c162189f65f9d5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 3 Mar 2026 21:08:30 +0100 Subject: [PATCH 216/468] chore: update pre-commit hooks (#3738) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore: update pre-commit hooks updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.14 → v0.15.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.14...v0.15.4) - [github.com/scientific-python/cookie: 2025.11.21 → 2026.03.02](https://github.com/scientific-python/cookie/compare/2025.11.21...2026.03.02) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3eb29e32df..8f00ca7173 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -47,7 +47,7 @@ repos: - hypothesis - s3fs - repo: https://github.com/scientific-python/cookie - rev: 2025.11.21 + rev: 2026.03.02 hooks: - id: sp-repo-review - repo: https://github.com/pre-commit/pygrep-hooks From c50668bef3a056e1b00b434b56bd073741e59f0f Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Fri, 6 Mar 2026 21:02:49 +0200 Subject: [PATCH 217/468] Use the prek GitHub Action (#3745) Much simpler... --- .github/workflows/lint.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 7a7b846bdb..cc76093694 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -17,9 +17,4 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v6 - - name: Install uv - uses: astral-sh/setup-uv@v7 - - name: Install prek - run: uv tool install prek - - name: Run prek - run: prek run --all-files + - uses: j178/prek-action@v1 From 266f2bb519f567baee760c80ebe72bb34ce94cf2 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Fri, 6 Mar 2026 22:15:21 +0200 Subject: [PATCH 218/468] Limit privilege escalation and token theft in workflows (#3742) https://lists.openssf-vuln.org/g/siren/message/6 - Added explicit permissions blocks to restrict access (mostly contents: read, id-token: write). - Limited event triggers to only trusted branches - Added workflow_dispatch where missing. Co-authored-by: Davis Bennett --- .github/workflows/check_changelogs.yml | 4 ++++ .github/workflows/gpu_test.yml | 3 +++ .github/workflows/hypothesis.yaml | 3 +++ .github/workflows/lint.yml | 3 +++ .github/workflows/needs_release_notes.yml | 3 ++- .github/workflows/nightly_wheels.yml | 3 +++ .github/workflows/releases.yml | 10 +++++++++- .github/workflows/test.yml | 5 ++++- 8 files changed, 31 insertions(+), 3 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 9b39233dd8..02b57a5e36 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -2,6 +2,10 @@ name: Check changelog entries on: pull_request: + workflow_dispatch: + +permissions: + contents: read jobs: check-changelogs: diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 337a2d2578..c474485dc0 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -13,6 +13,9 @@ on: env: LD_LIBRARY_PATH: /usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/lib64 +permissions: + contents: read + concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index d8a0acdfd4..1ec6b4806d 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -9,6 +9,9 @@ on: - cron: "0 0 * * *" # Daily “At 00:00” UTC workflow_dispatch: # allows you to trigger manually +permissions: + contents: read + env: FORCE_COLOR: 3 diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index cc76093694..0050b2f06a 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -7,6 +7,9 @@ on: branches: [main, 3.1.x] workflow_dispatch: +permissions: + contents: read + concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true diff --git a/.github/workflows/needs_release_notes.yml b/.github/workflows/needs_release_notes.yml index d789a926a2..b7b467d790 100644 --- a/.github/workflows/needs_release_notes.yml +++ b/.github/workflows/needs_release_notes.yml @@ -1,7 +1,8 @@ name: "Pull Request Labeler" on: - - pull_request_target + - pull_request_target: + types: [opened, reopened, synchronize] jobs: labeler: diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 82a8676834..834d563722 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -6,6 +6,9 @@ on: - cron: '0 2 * * *' workflow_dispatch: +permissions: + contents: read + jobs: build_and_upload_nightly: name: Build and upload nightly wheels diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 054bc00e45..e3e3c446fa 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -1,6 +1,14 @@ name: Wheels -on: [push, pull_request] +on: + push: + branches: [main] + pull_request: + branches: [main] + workflow_dispatch: + +permissions: + contents: read jobs: diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index bd6a3a91a7..5af29c960e 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -10,6 +10,9 @@ on: branches: [ main, 3.1.x ] workflow_dispatch: +permissions: + contents: read + concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true @@ -150,4 +153,4 @@ jobs: contains(needs.*.result, 'cancelled') run: exit 1 - name: Success - run: echo Success! \ No newline at end of file + run: echo Success! From b6d3ae2e184bdd5078baa991ab21f270f782fb90 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Fri, 6 Mar 2026 22:39:55 +0200 Subject: [PATCH 219/468] No need to check reST files (#3743) There are no reST files left, everything has been moved to Markdown. --- .pre-commit-config.yaml | 5 ----- pyproject.toml | 1 + 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8f00ca7173..f86fb3d9c1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -50,11 +50,6 @@ repos: rev: 2026.03.02 hooks: - id: sp-repo-review - - repo: https://github.com/pre-commit/pygrep-hooks - rev: v1.10.0 - hooks: - - id: rst-directive-colons - - id: rst-inline-touching-normal - repo: https://github.com/numpy/numpydoc rev: v1.10.0 hooks: diff --git a/pyproject.toml b/pyproject.toml index 02ebdc4176..18bdeda07c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -422,6 +422,7 @@ markers = [ [tool.repo-review] ignore = [ "PC111", # fix Python code in documentation - enable later + "PC170", # use PyGrep hooks - no *.rst files to check "PC180", # for JavaScript - not interested "PC902", # pre-commit.ci custom autofix message - not using autofix ] From 8d018608f1abbbbf3b50e5908c611efe74cbed87 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 9 Mar 2026 22:15:57 -0400 Subject: [PATCH 220/468] chore: Pre-commit hook for multi-character lstrip/rstrip (#3756) --- .pre-commit-config.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f86fb3d9c1..37f41b8222 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -54,6 +54,15 @@ repos: rev: v1.10.0 hooks: - id: numpydoc-validation + - repo: local + hooks: + - id: ban-lstrip-rstrip + name: ban lstrip/rstrip + language: pygrep + # Matches .lstrip() or .rstrip() where the string argument is 2+ characters. + entry: "\\.(lstrip|rstrip)\\([\"'][^\"']{2,}[\"']\\)" + types: [python] + files: ^(src|tests)/ - repo: https://github.com/twisted/towncrier rev: 25.8.0 hooks: From a89b927a27808b4663f1e64e28b7e105c59d37d6 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Wed, 11 Mar 2026 03:47:10 -0400 Subject: [PATCH 221/468] docs: use dark text color on light mode search bar (#3760) --- docs/overrides/stylesheets/extra.css | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/overrides/stylesheets/extra.css b/docs/overrides/stylesheets/extra.css index fab7e4ba13..ff94fc78a2 100644 --- a/docs/overrides/stylesheets/extra.css +++ b/docs/overrides/stylesheets/extra.css @@ -52,14 +52,14 @@ color: white; } -/* Search box styling */ -.md-search__input { +/* Search box styling in the header */ +.md-header .md-search__input { background-color: rgba(255, 255, 255, 0.15); border: 1px solid rgba(255, 255, 255, 0.2); color: white; } -.md-search__input::placeholder { +.md-header .md-search__input::placeholder { color: rgba(255, 255, 255, 0.7); } From 1cb1cce812b7c9ead180df5b2d8e759cb68b7f1c Mon Sep 17 00:00:00 2001 From: Alan Bishop Date: Wed, 11 Mar 2026 01:11:24 -0700 Subject: [PATCH 222/468] docs: add example of creating uncompressed arrays (#3464) (#3752) Add a clear, simple example in the Compression section of the user guide showing how to create an array without compression by setting compressors=None. This addresses user confusion about the default compression behavior and provides an easy-to-copy example for the common use case of disabling compression entirely. Closes #3464 Co-authored-by: Cipher Co-authored-by: Davis Bennett --- changes/3464.doc.md | 1 + docs/user-guide/arrays.md | 7 +++++++ 2 files changed, 8 insertions(+) create mode 100644 changes/3464.doc.md diff --git a/changes/3464.doc.md b/changes/3464.doc.md new file mode 100644 index 0000000000..155a4575f4 --- /dev/null +++ b/changes/3464.doc.md @@ -0,0 +1 @@ +Add documentation example for creating uncompressed arrays in the Compression section of the user guide. diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index cd6a93cac9..a44c096b73 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -224,6 +224,13 @@ print(z.info_complete()) If you don't specify a compressor, by default Zarr uses the Zstandard compressor. +To create an array without any compression, set `compressors=None`: + +```python exec="true" session="arrays" source="above" result="ansi" +z_no_compress = zarr.create_array(store='data/example-uncompressed.zarr', shape=(10000, 10000), chunks=(1000, 1000), dtype='int32', compressors=None) +print(f"Compressors: {z_no_compress.compressors}") +``` + In addition to Blosc and Zstandard, other compression libraries can also be used. For example, here is an array using Gzip compression, level 1: From fa61ed8e9d1f2c92cf1b7b763c35affd5175a429 Mon Sep 17 00:00:00 2001 From: Alan Bishop Date: Wed, 11 Mar 2026 04:03:16 -0700 Subject: [PATCH 223/468] fix: BaseFloat._check_scalar rejects invalid string values (#3586) (#3762) * fix: BaseFloat._check_scalar rejects invalid string values (#3586) BaseFloat._check_scalar returned True for all strings because the FloatLike type union includes str. This allowed invalid strings like 'not valid' to pass the check and then raise a confusing ValueError in _cast_scalar_unchecked instead of the expected TypeError. Fix _check_scalar to validate string inputs by attempting conversion: - Valid float strings (e.g. 'NaN', 'inf', '-inf', '1.5') return True - Invalid strings (e.g. 'not valid') return False, causing cast_scalar to raise TypeError as expected Add test cases for invalid string inputs to invalid_scalar_params. Fixes #3586 * style: fix ruff formatting and TRY300 in _check_scalar --------- Co-authored-by: Cipher --- src/zarr/core/dtype/npy/float.py | 10 ++++++++++ tests/test_dtype/test_npy/test_float.py | 15 ++++++++++++--- 2 files changed, 22 insertions(+), 3 deletions(-) diff --git a/src/zarr/core/dtype/npy/float.py b/src/zarr/core/dtype/npy/float.py index 0be2cbca9b..2a23cb429d 100644 --- a/src/zarr/core/dtype/npy/float.py +++ b/src/zarr/core/dtype/npy/float.py @@ -201,6 +201,16 @@ def _check_scalar(self, data: object) -> TypeGuard[FloatLike]: TypeGuard[FloatLike] True if the input is a valid scalar value, False otherwise. """ + if isinstance(data, str): + # Only accept strings that are valid float representations (e.g. "NaN", "inf"). + # Plain strings that cannot be converted should return False so that cast_scalar + # raises TypeError rather than a confusing ValueError. + try: + self.to_native_dtype().type(data) + except (ValueError, OverflowError): + return False + else: + return True return isinstance(data, FloatLike) def _cast_scalar_unchecked(self, data: FloatLike) -> TFloatScalar_co: diff --git a/tests/test_dtype/test_npy/test_float.py b/tests/test_dtype/test_npy/test_float.py index 1bbcbbc81f..8d8e768263 100644 --- a/tests/test_dtype/test_npy/test_float.py +++ b/tests/test_dtype/test_npy/test_float.py @@ -65,7 +65,10 @@ class TestFloat16(_BaseTestFloat): (Float16(), -1.0, np.float16(-1.0)), (Float16(), "NaN", np.float16("NaN")), ) - invalid_scalar_params = ((Float16(), {"set!"}),) + invalid_scalar_params = ( + (Float16(), {"set!"}), + (Float16(), "not_a_float"), + ) hex_string_params = (("0x7fc0", np.nan), ("0x7fc1", np.nan), ("0x3c00", 1.0)) item_size_params = (Float16(),) @@ -113,7 +116,10 @@ class TestFloat32(_BaseTestFloat): (Float32(), -1.0, np.float32(-1.0)), (Float32(), "NaN", np.float32("NaN")), ) - invalid_scalar_params = ((Float32(), {"set!"}),) + invalid_scalar_params = ( + (Float32(), {"set!"}), + (Float32(), "not_a_float"), + ) hex_string_params = (("0x7fc00000", np.nan), ("0x7fc00001", np.nan), ("0x3f800000", 1.0)) item_size_params = (Float32(),) @@ -160,7 +166,10 @@ class TestFloat64(_BaseTestFloat): (Float64(), -1.0, np.float64(-1.0)), (Float64(), "NaN", np.float64("NaN")), ) - invalid_scalar_params = ((Float64(), {"set!"}),) + invalid_scalar_params = ( + (Float64(), {"set!"}), + (Float64(), "not_a_float"), + ) hex_string_params = ( ("0x7ff8000000000000", np.nan), ("0x7ff8000000000001", np.nan), From a02d9961618f548f8bc398c1124d707e7a9819f7 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 12 Mar 2026 10:18:51 -0400 Subject: [PATCH 224/468] docs: fix docstring for Array.cdata_shape (#3768) --- src/zarr/core/array.py | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 564d0e915a..486216fa32 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1235,24 +1235,28 @@ def basename(self) -> str: @property def cdata_shape(self) -> tuple[int, ...]: """ - The shape of the chunk grid for this array. + The number of chunks along each dimension. + + When sharding is used, this counts inner chunks (not shards) per dimension. Returns ------- tuple[int, ...] - The shape of the chunk grid for this array. + The number of chunks along each dimension. """ return self._chunk_grid_shape @property def _chunk_grid_shape(self) -> tuple[int, ...]: """ - The shape of the chunk grid for this array. + The number of chunks along each dimension. + + When sharding is used, this counts inner chunks (not shards) per dimension. Returns ------- tuple[int, ...] - The shape of the chunk grid for this array. + The number of chunks along each dimension. """ return tuple(starmap(ceildiv, zip(self.shape, self.chunks, strict=True))) @@ -2399,14 +2403,23 @@ def compressors(self) -> tuple[Numcodec, ...] | tuple[BytesBytesCodec, ...]: @property def cdata_shape(self) -> tuple[int, ...]: """ - The shape of the chunk grid for this array. + The number of chunks along each dimension. + + When sharding is used, this counts inner chunks (not shards) per dimension. """ return self.async_array._chunk_grid_shape @property def _chunk_grid_shape(self) -> tuple[int, ...]: """ - The shape of the chunk grid for this array. + The number of chunks along each dimension. + + When sharding is used, this counts inner chunks (not shards) per dimension. + + Returns + ------- + tuple[int, ...] + The number of chunks along each dimension. """ return self.async_array._chunk_grid_shape From 93dbf785a4cb98345b59cc35f7997b6e9256a24b Mon Sep 17 00:00:00 2001 From: Alan Bishop Date: Fri, 13 Mar 2026 09:21:23 -0700 Subject: [PATCH 225/468] fix: apply drop_axes squeeze in partial decode path for sharding (#3691) (#3763) * fix: apply drop_axes squeeze in partial decode path for sharding When reading sharded arrays with mixed integer/list indexing (e.g. arr[0:10, 0, [0, 1]]), the outer OrthogonalIndexer produces chunk selections that have been ix_()-transformed for orthogonal advanced indexing. Integer indices become single-element ranges (size-1 dims) via ix_() to enable NumPy orthogonal indexing. In CodecPipeline.read_batch(), the non-partial path correctly applies drop_axes.squeeze() to remove those size-1 integer dimensions before writing to the output buffer. However, the partial decode path (used by ShardingCodec) was missing this squeeze step. Fixes #3691 Also: Fix line length violation in test error message to comply with 100 character linting limit. * fix(mypy): add type ignore comments for dynamic array indexing in sharding test The test uses complex indexing patterns (mixed integer/list indices) that mypy's zarr.Array stubs don't recognize as valid. Add specific type ignore comments for [index] and [union-attr] errors to suppress false positives. * fix(mypy): correct type-ignore codes for union attribute access in sharding test - Line 542: Fix assert accessing .shape by changing from [index] to [union-attr] - Line 544: Add missing type-ignore[union-attr] for f-string .shape access - Lines 554-555: Remove unused type-ignore[index] comments on assignments The mypy errors were caused by indexing operations returning union types that include scalar types (int, float, etc.), which don't have a .shape attribute. The proper fix uses type-ignore[union-attr] for attribute access, not [index]. --------- Co-authored-by: Cipher Co-authored-by: Davis Bennett --- src/zarr/core/codec_pipeline.py | 6 ++-- tests/test_codecs/test_sharding.py | 56 +++++++++++++++++++++++++++++- 2 files changed, 59 insertions(+), 3 deletions(-) diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index fd557ac43e..eed49556d3 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -263,6 +263,8 @@ async def read_batch( chunk_array_batch, batch_info, strict=False ): if chunk_array is not None: + if drop_axes: + chunk_array = chunk_array.squeeze(axis=drop_axes) out[out_selection] = chunk_array else: out[out_selection] = fill_value_or_default(chunk_spec) @@ -285,7 +287,7 @@ async def read_batch( ): if chunk_array is not None: tmp = chunk_array[chunk_selection] - if drop_axes != (): + if drop_axes: tmp = tmp.squeeze(axis=drop_axes) out[out_selection] = tmp else: @@ -324,7 +326,7 @@ def _merge_chunk_array( else: chunk_value = value[out_selection] # handle missing singleton dimensions - if drop_axes != (): + if drop_axes: item = tuple( None # equivalent to np.newaxis if idx in drop_axes diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index d0e2d09b7c..d7cbeb5bdb 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -490,7 +490,8 @@ def test_invalid_shard_shape() -> None: with pytest.raises( ValueError, match=re.escape( - "The array's `chunk_shape` (got (16, 16)) needs to be divisible by the shard's inner `chunk_shape` (got (9,))." + "The array's `chunk_shape` (got (16, 16)) needs to be divisible " + "by the shard's inner `chunk_shape` (got (9,))." ), ): zarr.create_array( @@ -501,3 +502,56 @@ def test_invalid_shard_shape() -> None: dtype=np.dtype("uint8"), fill_value=0, ) + + +@pytest.mark.parametrize("store", ["local"], indirect=["store"]) +def test_sharding_mixed_integer_list_indexing(store: Store) -> None: + """Regression test for https://github.com/zarr-developers/zarr-python/issues/3691. + + Mixed integer/list indexing on sharded arrays should return the same + shape and data as on equivalent chunked arrays. + """ + import numpy as np + + data = np.arange(200 * 100 * 10, dtype=np.uint8).reshape(200, 100, 10) + + chunked = zarr.create_array( + store, + name="chunked", + shape=(200, 100, 10), + dtype=np.uint8, + chunks=(200, 100, 1), + overwrite=True, + ) + chunked[:, :, :] = data + + sharded = zarr.create_array( + store, + name="sharded", + shape=(200, 100, 10), + dtype=np.uint8, + chunks=(200, 100, 1), + shards=(200, 100, 10), + overwrite=True, + ) + sharded[:, :, :] = data + + # Mixed integer + list indexing + c = chunked[0:10, 0, [0, 1]] # type: ignore[index] + s = sharded[0:10, 0, [0, 1]] # type: ignore[index] + assert c.shape == s.shape == (10, 2), ( # type: ignore[union-attr] + f"Expected (10, 2), got chunked={c.shape}, sharded={s.shape}" # type: ignore[union-attr] + ) + np.testing.assert_array_equal(c, s) + + # Multiple integer axes + c2 = chunked[0, 0, [0, 1, 2]] # type: ignore[index] + s2 = sharded[0, 0, [0, 1, 2]] # type: ignore[index] + assert c2.shape == s2.shape == (3,) # type: ignore[union-attr] + np.testing.assert_array_equal(c2, s2) + + # Slice + integer + slice + c3 = chunked[0:5, 1, 0:3] + s3 = sharded[0:5, 1, 0:3] + assert c3.shape == s3.shape == (5, 3) # type: ignore[union-attr] + np.testing.assert_array_equal(c3, s3) From 1bfa53f6167336fc5c6b353975b2af56cde1eb6b Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Fri, 13 Mar 2026 13:18:44 -0400 Subject: [PATCH 226/468] docs: add favicon (#3775) --- docs/_static/favicon-96x96.png | Bin 0 -> 12714 bytes mkdocs.yml | 1 + 2 files changed, 1 insertion(+) create mode 100644 docs/_static/favicon-96x96.png diff --git a/docs/_static/favicon-96x96.png b/docs/_static/favicon-96x96.png new 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fccf372eb82caed6589566f35a9e6eaaf177251d Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 16 Mar 2026 08:22:04 -0400 Subject: [PATCH 227/468] fix: validate that dask-style chunks have regular shapes (#3779) * fix: validate that dask-style chunks have regular shapes * Apply suggestion from @dcherian Co-authored-by: Deepak Cherian * Fix shortcircuit option --------- Co-authored-by: Deepak Cherian --- src/zarr/core/chunk_grids.py | 13 ++++++++----- tests/test_chunk_grids.py | 9 +++++++++ 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 2c7945fa64..c903eba013 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -126,11 +126,14 @@ def normalize_chunks(chunks: Any, shape: tuple[int, ...], typesize: int) -> tupl chunks = tuple(int(chunks) for _ in shape) # handle dask-style chunks (iterable of iterables) - if all(isinstance(c, (tuple | list)) for c in chunks): - # take first chunk size for each dimension - chunks = tuple( - c[0] for c in chunks - ) # TODO: check/error/warn for irregular chunks (e.g. if c[0] != c[1:-1]) + if all(isinstance(c, (tuple, list)) for c in chunks): + for i, c in enumerate(chunks): + if any(x != y for x, y in itertools.pairwise(c[:-1])) or (len(c) > 1 and c[-1] > c[0]): + raise ValueError( + f"Irregular chunk sizes in dimension {i}: {tuple(c)}. " + "Only uniform chunks (with an optional smaller final chunk) are supported." + ) + chunks = tuple(c[0] for c in chunks) # handle bad dimensionality if len(chunks) > len(shape): diff --git a/tests/test_chunk_grids.py b/tests/test_chunk_grids.py index 4c69c483ae..2920b5d6f3 100644 --- a/tests/test_chunk_grids.py +++ b/tests/test_chunk_grids.py @@ -35,6 +35,10 @@ def test_guess_chunks(shape: tuple[int, ...], itemsize: int) -> None: ((30, None, None), (100, 20, 10), 1, (30, 20, 10)), ((30, 20, None), (100, 20, 10), 1, (30, 20, 10)), ((30, 20, 10), (100, 20, 10), 1, (30, 20, 10)), + # dask-style chunks (uniform with optional smaller final chunk) + (((100, 100, 100), (50, 50)), (300, 100), 1, (100, 50)), + (((100, 100, 50),), (250,), 1, (100,)), + (((100,),), (100,), 1, (100,)), # auto chunking (None, (100,), 1, (100,)), (-1, (100,), 1, (100,)), @@ -52,3 +56,8 @@ def test_normalize_chunks_errors() -> None: normalize_chunks("foo", (100,), 1) with pytest.raises(ValueError): normalize_chunks((100, 10), (100,), 1) + # dask-style irregular chunks should raise + with pytest.raises(ValueError, match="Irregular chunk sizes"): + normalize_chunks(((10, 20, 30),), (60,), 1) + with pytest.raises(ValueError, match="Irregular chunk sizes"): + normalize_chunks(((100, 100), (10, 20)), (200, 30), 1) From 7c78574850527e5acbfbda837ca0e7d9cf44f1f4 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 16 Mar 2026 08:47:19 -0400 Subject: [PATCH 228/468] docs: add glossary (#3767) * docs: add glossary * Add glossary * Update docs/user-guide/glossary.md Co-authored-by: Davis Bennett * Add caveat --------- Co-authored-by: Davis Bennett --- docs/user-guide/glossary.md | 110 ++++++++++++++++++++++++++++++++++++ docs/user-guide/index.md | 4 ++ mkdocs.yml | 1 + 3 files changed, 115 insertions(+) create mode 100644 docs/user-guide/glossary.md diff --git a/docs/user-guide/glossary.md b/docs/user-guide/glossary.md new file mode 100644 index 0000000000..a490b7c341 --- /dev/null +++ b/docs/user-guide/glossary.md @@ -0,0 +1,110 @@ +# Glossary + +This page defines key terms used throughout the zarr-python documentation and API. + +## Array Structure + +### Array + +An N-dimensional typed array stored in a Zarr [store](#store). An array's +[metadata](#metadata) defines its shape, data type, chunk layout, and codecs. + +### Chunk + +The fundamental unit of data in a Zarr array. An array is divided into chunks +along each dimension according to the [chunk grid](#chunk-grid), which is currently +part of Zarr's private API. Each chunk is independently compressed and encoded +through the array's [codec](#codec) pipeline. + +When [sharding](#shard) is used, "chunk" refers to the inner chunks within each +shard, because those are the compressible units. The chunks are the smallest units +that can be read independently. + +!!! warning "Convention specific to zarr-python" + The use of "chunk" to mean the inner sub-chunk within a shard is a convention + adopted by zarr-python's `Array` API. In the Zarr V3 specification and in other + Zarr implementations, "chunk" may refer to the top-level grid cells (which + zarr-python calls "shards" when the sharding codec is used). Be aware of this + distinction when working across libraries. + +**API**: [`Array.chunks`][zarr.Array.chunks] returns the chunk shape. When +sharding is used, this is the inner chunk shape. + +### Chunk Grid + +The partitioning of an array's elements into [chunks](#chunk). In Zarr V3, the +chunk grid is defined in the array [metadata](#metadata) and determines the +boundaries of each storage object. + +When sharding is used, the chunk grid defines the [shard](#shard) boundaries, +not the inner chunk boundaries. The inner chunk shape is defined within the +[sharding codec](#shard). + +**API**: The `chunk_grid` field in array metadata contains the storage-level +grid. + +### Shard + +A storage object that contains one or more [chunks](#chunk). Sharding reduces the +number of objects in a [store](#store) by grouping chunks together, which +improves performance on file systems and object storage. + +Within each shard, chunks are compressed independently and can be read +individually. However, writing requires updating the full shard for consistency, +making shards the unit of writing and chunks the unit of reading. + +Sharding is implemented as a [codec](#codec) (the sharding indexed codec). +When sharding is used: + +- The [chunk grid](#chunk-grid) in metadata defines the shard boundaries +- The sharding codec's `chunk_shape` defines the inner chunk size +- Each shard contains `shard_shape / chunk_shape` chunks per dimension + +**API**: [`Array.shards`][zarr.Array.shards] returns the shard shape, or `None` +if sharding is not used. [`Array.chunks`][zarr.Array.chunks] returns the inner +chunk shape. + +## Storage + +### Store + +A key-value storage backend that holds Zarr data and metadata. Stores implement +the [`zarr.abc.store.Store`][] interface. Examples include local file systems, +cloud object storage (S3, GCS, Azure), zip files, and in-memory dictionaries. + +Each [chunk](#chunk) or [shard](#shard) is stored as a single value (object or +file) in the store, addressed by a key derived from its grid coordinates. + +### Metadata + +The JSON document (`zarr.json`) that describes an [array](#array) or group. For +arrays, metadata includes the shape, data type, [chunk grid](#chunk-grid), fill +value, and [codec](#codec) pipeline. Metadata is stored alongside the data in +the [store](#store). Zarr-Python does not yet expose its internal metadata +representation as part of its public API. + +## Codecs + +### Codec + +A transformation applied to array data during reading and writing. Codecs are +chained into a pipeline and come in three types: + +- **Array-to-array**: Transforms like transpose that rearrange array elements +- **Array-to-bytes**: Serialization that converts an array to a byte sequence + (exactly one required) +- **Bytes-to-bytes**: Compression or checksums applied to the serialized bytes + +The [sharding indexed codec](#shard) is a special array-to-bytes codec that +groups multiple [chunks](#chunk) into a single storage object. + +## API Properties + +The following properties are available on [`zarr.Array`][]: + +| Property | Description | +|----------|-------------| +| `.chunks` | Chunk shape — the inner chunk shape when sharding is used | +| `.shards` | Shard shape, or `None` if no sharding | +| `.nchunks` | Total number of independently compressible units across the array | +| `.cdata_shape` | Number of independently compressible units per dimension | diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md index fda9bcaa90..ff6e354d80 100644 --- a/docs/user-guide/index.md +++ b/docs/user-guide/index.md @@ -35,6 +35,10 @@ Take your skills to the next level: - **[Extending](extending.md)** - Extend functionality with custom code - **[Consolidated Metadata](consolidated_metadata.md)** - Advanced metadata management +## Reference + +- **[Glossary](glossary.md)** - Definitions of key terms (chunks, shards, codecs, etc.) + ## Need Help? - Browse the [API Reference](../api/zarr/index.md) for detailed function documentation diff --git a/mkdocs.yml b/mkdocs.yml index c73b6d0e30..24adb66457 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -27,6 +27,7 @@ nav: - user-guide/gpu.md - user-guide/consolidated_metadata.md - user-guide/experimental.md + - user-guide/glossary.md - Examples: - user-guide/examples/custom_dtype.md - API Reference: From 46654adf21f97de725df35b5eebc93161edb4a63 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 16 Mar 2026 10:23:53 -0400 Subject: [PATCH 229/468] docs: fix search color (#3777) --- docs/overrides/stylesheets/extra.css | 5 ----- 1 file changed, 5 deletions(-) diff --git a/docs/overrides/stylesheets/extra.css b/docs/overrides/stylesheets/extra.css index ff94fc78a2..6cb7c74e8d 100644 --- a/docs/overrides/stylesheets/extra.css +++ b/docs/overrides/stylesheets/extra.css @@ -56,11 +56,6 @@ .md-header .md-search__input { background-color: rgba(255, 255, 255, 0.15); border: 1px solid rgba(255, 255, 255, 0.2); - color: white; -} - -.md-header .md-search__input::placeholder { - color: rgba(255, 255, 255, 0.7); } /* Navigation tabs */ From 03355b87b8a9f015571a808efaa9f5bcee9a9ced Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 16 Mar 2026 21:20:48 +0100 Subject: [PATCH 230/468] perf/store sync (#3725) * add sync methods to codecs * add CodecChain dataclass and sync codec tests Introduces CodecChain, a frozen dataclass that chains array-array, array-bytes, and bytes-bytes codecs with synchronous encode/decode methods. Pure compute only -- no IO, no threading, no batching. Also adds sync roundtrip tests for individual codecs (blosc, gzip, zstd, crc32c, bytes, transpose, vlen) and CodecChain integration tests. Co-Authored-By: Claude Opus 4.6 * refactor codecchain * separate codecs and specs * add synchronous methods to stores * fix merge error * guard storepath methods that rely on underlying sync impl * scrub out set-range logic * remove is-zstd-fixed-size test * remove codecchain * revert delete comment --------- Co-authored-by: Claude Opus 4.6 Co-authored-by: Deepak Cherian --- src/zarr/abc/store.py | 36 ++++++++++++++- src/zarr/storage/_common.py | 39 +++++++++++++++- src/zarr/storage/_local.py | 50 ++++++++++++++++++++ src/zarr/storage/_memory.py | 44 +++++++++++++++++- src/zarr/testing/store.py | 71 ++++++++++++++++++++++++++++- tests/test_codecs/test_blosc.py | 29 +++++++++++- tests/test_codecs/test_crc32c.py | 33 ++++++++++++++ tests/test_codecs/test_endian.py | 29 ++++++++++++ tests/test_codecs/test_gzip.py | 28 ++++++++++++ tests/test_codecs/test_transpose.py | 28 ++++++++++++ tests/test_codecs/test_vlen.py | 11 ++++- tests/test_codecs/test_zstd.py | 28 ++++++++++++ tests/test_indexing.py | 17 +++++++ 13 files changed, 436 insertions(+), 7 deletions(-) create mode 100644 tests/test_codecs/test_crc32c.py diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index f677c197dc..d2ab353d43 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -16,7 +16,16 @@ from zarr.core.buffer import Buffer, BufferPrototype -__all__ = ["ByteGetter", "ByteSetter", "Store", "set_or_delete"] +__all__ = [ + "ByteGetter", + "ByteSetter", + "Store", + "SupportsDeleteSync", + "SupportsGetSync", + "SupportsSetSync", + "SupportsSyncStore", + "set_or_delete", +] @dataclass(frozen=True, slots=True) @@ -700,6 +709,31 @@ async def delete(self) -> None: ... async def set_if_not_exists(self, default: Buffer) -> None: ... +@runtime_checkable +class SupportsGetSync(Protocol): + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: ... + + +@runtime_checkable +class SupportsSetSync(Protocol): + def set_sync(self, key: str, value: Buffer) -> None: ... + + +@runtime_checkable +class SupportsDeleteSync(Protocol): + def delete_sync(self, key: str) -> None: ... + + +@runtime_checkable +class SupportsSyncStore(SupportsGetSync, SupportsSetSync, SupportsDeleteSync, Protocol): ... + + async def set_or_delete(byte_setter: ByteSetter, value: Buffer | None) -> None: """Set or delete a value in a byte setter diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 4bea04f024..08c05864aa 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -5,7 +5,13 @@ from pathlib import Path from typing import TYPE_CHECKING, Any, Literal, Self, TypeAlias -from zarr.abc.store import ByteRequest, Store +from zarr.abc.store import ( + ByteRequest, + Store, + SupportsDeleteSync, + SupportsGetSync, + SupportsSetSync, +) from zarr.core.buffer import Buffer, default_buffer_prototype from zarr.core.common import ( ANY_ACCESS_MODE, @@ -228,6 +234,37 @@ async def is_empty(self) -> bool: """ return await self.store.is_empty(self.path) + # ------------------------------------------------------------------- + # Synchronous IO delegation + # ------------------------------------------------------------------- + + def get_sync( + self, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + """Synchronous read — delegates to ``self.store.get_sync(self.path, ...)``.""" + if not isinstance(self.store, SupportsGetSync): + raise TypeError(f"Store {type(self.store).__name__} does not support synchronous get.") + if prototype is None: + prototype = default_buffer_prototype() + return self.store.get_sync(self.path, prototype=prototype, byte_range=byte_range) + + def set_sync(self, value: Buffer) -> None: + """Synchronous write — delegates to ``self.store.set_sync(self.path, value)``.""" + if not isinstance(self.store, SupportsSetSync): + raise TypeError(f"Store {type(self.store).__name__} does not support synchronous set.") + self.store.set_sync(self.path, value) + + def delete_sync(self) -> None: + """Synchronous delete — delegates to ``self.store.delete_sync(self.path)``.""" + if not isinstance(self.store, SupportsDeleteSync): + raise TypeError( + f"Store {type(self.store).__name__} does not support synchronous delete." + ) + self.store.delete_sync(self.path) + def __truediv__(self, other: str) -> StorePath: """Combine this store path with another path""" return self.__class__(self.store, _dereference_path(self.path, other)) diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 80233a112d..96f1e61746 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -187,6 +187,56 @@ def __repr__(self) -> str: def __eq__(self, other: object) -> bool: return isinstance(other, type(self)) and self.root == other.root + # ------------------------------------------------------------------- + # Synchronous store methods + # ------------------------------------------------------------------- + + def _ensure_open_sync(self) -> None: + if not self._is_open: + if not self.read_only: + self.root.mkdir(parents=True, exist_ok=True) + if not self.root.exists(): + raise FileNotFoundError(f"{self.root} does not exist") + self._is_open = True + + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + if prototype is None: + prototype = default_buffer_prototype() + self._ensure_open_sync() + assert isinstance(key, str) + path = self.root / key + try: + return _get(path, prototype, byte_range) + except (FileNotFoundError, IsADirectoryError, NotADirectoryError): + return None + + def set_sync(self, key: str, value: Buffer) -> None: + self._ensure_open_sync() + self._check_writable() + assert isinstance(key, str) + if not isinstance(value, Buffer): + raise TypeError( + f"LocalStore.set(): `value` must be a Buffer instance. " + f"Got an instance of {type(value)} instead." + ) + path = self.root / key + _put(path, value) + + def delete_sync(self, key: str) -> None: + self._ensure_open_sync() + self._check_writable() + path = self.root / key + if path.is_dir(): + shutil.rmtree(path) + else: + path.unlink(missing_ok=True) + async def get( self, key: str, diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index e6f9b7a512..1194894b9d 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -77,6 +77,49 @@ def __eq__(self, other: object) -> bool: and self.read_only == other.read_only ) + # ------------------------------------------------------------------- + # Synchronous store methods + # ------------------------------------------------------------------- + + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + if prototype is None: + prototype = default_buffer_prototype() + if not self._is_open: + self._is_open = True + assert isinstance(key, str) + try: + value = self._store_dict[key] + start, stop = _normalize_byte_range_index(value, byte_range) + return prototype.buffer.from_buffer(value[start:stop]) + except KeyError: + return None + + def set_sync(self, key: str, value: Buffer) -> None: + self._check_writable() + if not self._is_open: + self._is_open = True + assert isinstance(key, str) + if not isinstance(value, Buffer): + raise TypeError( + f"MemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead." + ) + self._store_dict[key] = value + + def delete_sync(self, key: str) -> None: + self._check_writable() + if not self._is_open: + self._is_open = True + try: + del self._store_dict[key] + except KeyError: + logger.debug("Key %s does not exist.", key) + async def get( self, key: str, @@ -122,7 +165,6 @@ async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None raise TypeError( f"MemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead." ) - if byte_range is not None: buf = self._store_dict[key] buf[byte_range[0] : byte_range[1]] = value diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index 1b8e85ed98..ce83715b86 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -11,7 +11,6 @@ if TYPE_CHECKING: from typing import Any - from zarr.abc.store import ByteRequest from zarr.core.buffer.core import BufferPrototype import pytest @@ -22,6 +21,9 @@ RangeByteRequest, Store, SuffixByteRequest, + SupportsDeleteSync, + SupportsGetSync, + SupportsSetSync, ) from zarr.core.buffer import Buffer, default_buffer_prototype from zarr.core.sync import _collect_aiterator, sync @@ -39,6 +41,27 @@ class StoreTests(Generic[S, B]): store_cls: type[S] buffer_cls: type[B] + @staticmethod + def _require_get_sync(store: S) -> SupportsGetSync: + """Skip unless *store* implements :class:`SupportsGetSync`.""" + if not isinstance(store, SupportsGetSync): + pytest.skip("store does not implement SupportsGetSync") + return store # type: ignore[unreachable] + + @staticmethod + def _require_set_sync(store: S) -> SupportsSetSync: + """Skip unless *store* implements :class:`SupportsSetSync`.""" + if not isinstance(store, SupportsSetSync): + pytest.skip("store does not implement SupportsSetSync") + return store # type: ignore[unreachable] + + @staticmethod + def _require_delete_sync(store: S) -> SupportsDeleteSync: + """Skip unless *store* implements :class:`SupportsDeleteSync`.""" + if not isinstance(store, SupportsDeleteSync): + pytest.skip("store does not implement SupportsDeleteSync") + return store # type: ignore[unreachable] + @abstractmethod async def set(self, store: S, key: str, value: Buffer) -> None: """ @@ -579,6 +602,52 @@ def test_get_json_sync(self, store: S) -> None: sync(self.set(store, key, self.buffer_cls.from_bytes(data_bytes))) assert store._get_json_sync(key, prototype=default_buffer_prototype()) == data + # ------------------------------------------------------------------- + # Synchronous store methods (SupportsSyncStore protocol) + # ------------------------------------------------------------------- + + def test_get_sync(self, store: S) -> None: + getter = self._require_get_sync(store) + data_buf = self.buffer_cls.from_bytes(b"\x01\x02\x03\x04") + key = "sync_get" + sync(self.set(store, key, data_buf)) + result = getter.get_sync(key) + assert result is not None + assert_bytes_equal(result, data_buf) + + def test_get_sync_missing(self, store: S) -> None: + getter = self._require_get_sync(store) + result = getter.get_sync("nonexistent") + assert result is None + + def test_set_sync(self, store: S) -> None: + setter = self._require_set_sync(store) + data_buf = self.buffer_cls.from_bytes(b"\x01\x02\x03\x04") + key = "sync_set" + setter.set_sync(key, data_buf) + result = sync(self.get(store, key)) + assert_bytes_equal(result, data_buf) + + def test_delete_sync(self, store: S) -> None: + setter = self._require_set_sync(store) + deleter = self._require_delete_sync(store) + getter = self._require_get_sync(store) + if not store.supports_deletes: + pytest.skip("store does not support deletes") + data_buf = self.buffer_cls.from_bytes(b"\x01\x02\x03\x04") + key = "sync_delete" + setter.set_sync(key, data_buf) + deleter.delete_sync(key) + result = getter.get_sync(key) + assert result is None + + def test_delete_sync_missing(self, store: S) -> None: + deleter = self._require_delete_sync(store) + if not store.supports_deletes: + pytest.skip("store does not support deletes") + # should not raise + deleter.delete_sync("nonexistent_sync") + class LatencyStore(WrapperStore[Store]): """ diff --git a/tests/test_codecs/test_blosc.py b/tests/test_codecs/test_blosc.py index 6f4821f8b1..0201beb8de 100644 --- a/tests/test_codecs/test_blosc.py +++ b/tests/test_codecs/test_blosc.py @@ -6,11 +6,12 @@ from packaging.version import Version import zarr +from zarr.abc.codec import SupportsSyncCodec from zarr.codecs import BloscCodec from zarr.codecs.blosc import BloscShuffle, Shuffle -from zarr.core.array_spec import ArraySpec +from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.buffer import default_buffer_prototype -from zarr.core.dtype import UInt16 +from zarr.core.dtype import UInt16, get_data_type_from_native_dtype from zarr.storage import MemoryStore, StorePath @@ -110,3 +111,27 @@ async def test_typesize() -> None: else: expected_size = 10216 assert size == expected_size, msg + + +def test_blosc_codec_supports_sync() -> None: + assert isinstance(BloscCodec(), SupportsSyncCodec) + + +def test_blosc_codec_sync_roundtrip() -> None: + codec = BloscCodec(typesize=8) + arr = np.arange(100, dtype="float64") + zdtype = get_data_type_from_native_dtype(arr.dtype) + spec = ArraySpec( + shape=arr.shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + buf = default_buffer_prototype().buffer.from_array_like(arr.view("B")) + + encoded = codec._encode_sync(buf, spec) + assert encoded is not None + decoded = codec._decode_sync(encoded, spec) + result = np.frombuffer(decoded.as_numpy_array(), dtype="float64") + np.testing.assert_array_equal(arr, result) diff --git a/tests/test_codecs/test_crc32c.py b/tests/test_codecs/test_crc32c.py new file mode 100644 index 0000000000..3ab1070f60 --- /dev/null +++ b/tests/test_codecs/test_crc32c.py @@ -0,0 +1,33 @@ +from __future__ import annotations + +import numpy as np + +from zarr.abc.codec import SupportsSyncCodec +from zarr.codecs.crc32c_ import Crc32cCodec +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import default_buffer_prototype +from zarr.core.dtype import get_data_type_from_native_dtype + + +def test_crc32c_codec_supports_sync() -> None: + assert isinstance(Crc32cCodec(), SupportsSyncCodec) + + +def test_crc32c_codec_sync_roundtrip() -> None: + codec = Crc32cCodec() + arr = np.arange(100, dtype="float64") + zdtype = get_data_type_from_native_dtype(arr.dtype) + spec = ArraySpec( + shape=arr.shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + buf = default_buffer_prototype().buffer.from_array_like(arr.view("B")) + + encoded = codec._encode_sync(buf, spec) + assert encoded is not None + decoded = codec._decode_sync(encoded, spec) + result = np.frombuffer(decoded.as_numpy_array(), dtype="float64") + np.testing.assert_array_equal(arr, result) diff --git a/tests/test_codecs/test_endian.py b/tests/test_codecs/test_endian.py index ab64afb1b8..c505cee828 100644 --- a/tests/test_codecs/test_endian.py +++ b/tests/test_codecs/test_endian.py @@ -4,8 +4,12 @@ import pytest import zarr +from zarr.abc.codec import SupportsSyncCodec from zarr.abc.store import Store from zarr.codecs import BytesCodec +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import NDBuffer, default_buffer_prototype +from zarr.core.dtype import get_data_type_from_native_dtype from zarr.storage import StorePath from .test_codecs import _AsyncArrayProxy @@ -33,6 +37,31 @@ async def test_endian(store: Store, endian: Literal["big", "little"]) -> None: assert np.array_equal(data, readback_data) +def test_bytes_codec_supports_sync() -> None: + assert isinstance(BytesCodec(), SupportsSyncCodec) + + +def test_bytes_codec_sync_roundtrip() -> None: + codec = BytesCodec() + arr = np.arange(100, dtype="float64") + zdtype = get_data_type_from_native_dtype(arr.dtype) + spec = ArraySpec( + shape=arr.shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + nd_buf: NDBuffer = default_buffer_prototype().nd_buffer.from_numpy_array(arr) + + codec = codec.evolve_from_array_spec(spec) + + encoded = codec._encode_sync(nd_buf, spec) + assert encoded is not None + decoded = codec._decode_sync(encoded, spec) + np.testing.assert_array_equal(arr, decoded.as_numpy_array()) + + @pytest.mark.filterwarnings("ignore:The endianness of the requested serializer") @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) @pytest.mark.parametrize("dtype_input_endian", [">u2", " None: a[:, :] = data assert np.array_equal(data, a[:, :]) + + +def test_gzip_codec_supports_sync() -> None: + assert isinstance(GzipCodec(), SupportsSyncCodec) + + +def test_gzip_codec_sync_roundtrip() -> None: + codec = GzipCodec(level=1) + arr = np.arange(100, dtype="float64") + zdtype = get_data_type_from_native_dtype(arr.dtype) + spec = ArraySpec( + shape=arr.shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + buf = default_buffer_prototype().buffer.from_array_like(arr.view("B")) + + encoded = codec._encode_sync(buf, spec) + assert encoded is not None + decoded = codec._decode_sync(encoded, spec) + result = np.frombuffer(decoded.as_numpy_array(), dtype="float64") + np.testing.assert_array_equal(arr, result) diff --git a/tests/test_codecs/test_transpose.py b/tests/test_codecs/test_transpose.py index 06ec668ad3..949bb72a62 100644 --- a/tests/test_codecs/test_transpose.py +++ b/tests/test_codecs/test_transpose.py @@ -3,9 +3,13 @@ import zarr from zarr import AsyncArray, config +from zarr.abc.codec import SupportsSyncCodec from zarr.abc.store import Store from zarr.codecs import TransposeCodec +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import NDBuffer, default_buffer_prototype from zarr.core.common import MemoryOrder +from zarr.core.dtype import get_data_type_from_native_dtype from zarr.storage import StorePath from .test_codecs import _AsyncArrayProxy @@ -93,3 +97,27 @@ def test_transpose_invalid( chunk_key_encoding={"name": "v2", "separator": "."}, filters=[TransposeCodec(order=order)], # type: ignore[arg-type] ) + + +def test_transpose_codec_supports_sync() -> None: + assert isinstance(TransposeCodec(order=(0, 1)), SupportsSyncCodec) + + +def test_transpose_codec_sync_roundtrip() -> None: + codec = TransposeCodec(order=(1, 0)) + arr = np.arange(12, dtype="float64").reshape(3, 4) + zdtype = get_data_type_from_native_dtype(arr.dtype) + spec = ArraySpec( + shape=arr.shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + nd_buf: NDBuffer = default_buffer_prototype().nd_buffer.from_numpy_array(arr) + + encoded = codec._encode_sync(nd_buf, spec) + assert encoded is not None + resolved_spec = codec.resolve_metadata(spec) + decoded = codec._decode_sync(encoded, resolved_spec) + np.testing.assert_array_equal(arr, decoded.as_numpy_array()) diff --git a/tests/test_codecs/test_vlen.py b/tests/test_codecs/test_vlen.py index cf0905daca..f3445824b3 100644 --- a/tests/test_codecs/test_vlen.py +++ b/tests/test_codecs/test_vlen.py @@ -5,9 +5,10 @@ import zarr from zarr import Array -from zarr.abc.codec import Codec +from zarr.abc.codec import Codec, SupportsSyncCodec from zarr.abc.store import Store from zarr.codecs import ZstdCodec +from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec from zarr.core.dtype import get_data_type_from_native_dtype from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING from zarr.core.metadata.v3 import ArrayV3Metadata @@ -62,3 +63,11 @@ def test_vlen_string( assert np.array_equal(data, b[:, :]) assert b.metadata.data_type == get_data_type_from_native_dtype(data.dtype) assert a.dtype == data.dtype + + +def test_vlen_utf8_codec_supports_sync() -> None: + assert isinstance(VLenUTF8Codec(), SupportsSyncCodec) + + +def test_vlen_bytes_codec_supports_sync() -> None: + assert isinstance(VLenBytesCodec(), SupportsSyncCodec) diff --git a/tests/test_codecs/test_zstd.py b/tests/test_codecs/test_zstd.py index 6068f53443..3f3f15a41a 100644 --- a/tests/test_codecs/test_zstd.py +++ b/tests/test_codecs/test_zstd.py @@ -2,8 +2,12 @@ import pytest import zarr +from zarr.abc.codec import SupportsSyncCodec from zarr.abc.store import Store from zarr.codecs import ZstdCodec +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import default_buffer_prototype +from zarr.core.dtype import get_data_type_from_native_dtype from zarr.storage import StorePath @@ -23,3 +27,27 @@ def test_zstd(store: Store, checksum: bool) -> None: a[:, :] = data assert np.array_equal(data, a[:, :]) + + +def test_zstd_codec_supports_sync() -> None: + assert isinstance(ZstdCodec(), SupportsSyncCodec) + + +def test_zstd_codec_sync_roundtrip() -> None: + codec = ZstdCodec(level=1) + arr = np.arange(100, dtype="float64") + zdtype = get_data_type_from_native_dtype(arr.dtype) + spec = ArraySpec( + shape=arr.shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + buf = default_buffer_prototype().buffer.from_array_like(arr.view("B")) + + encoded = codec._encode_sync(buf, spec) + assert encoded is not None + decoded = codec._decode_sync(encoded, spec) + result = np.frombuffer(decoded.as_numpy_array(), dtype="float64") + np.testing.assert_array_equal(arr, result) diff --git a/tests/test_indexing.py b/tests/test_indexing.py index c0bf7dd270..9c734fb0c3 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -34,6 +34,7 @@ if TYPE_CHECKING: from collections.abc import AsyncGenerator + from zarr.abc.store import ByteRequest from zarr.core.buffer import BufferPrototype from zarr.core.buffer.core import Buffer @@ -83,6 +84,22 @@ async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None self.counter["__setitem__", key_suffix] += 1 return await super().set(key, value, byte_range) + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + key_suffix = "/".join(key.split("/")[1:]) + self.counter["__getitem__", key_suffix] += 1 + return super().get_sync(key, prototype=prototype, byte_range=byte_range) + + def set_sync(self, key: str, value: Buffer) -> None: + key_suffix = "/".join(key.split("/")[1:]) + self.counter["__setitem__", key_suffix] += 1 + return super().set_sync(key, value) + def test_normalize_integer_selection() -> None: assert 1 == normalize_integer_selection(1, 100) From 65e137583972ccfd88fbc614ef41b3cd3ab4f303 Mon Sep 17 00:00:00 2001 From: Ian Hunt-Isaak Date: Tue, 17 Mar 2026 14:32:32 -0400 Subject: [PATCH 231/468] Remove `rich` as required for `tree()` (#3778) * remove rich dependency for tree * lint + pr number * keyword only * Apply suggestion from @maxrjones Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3778.misc.md | 1 + docs/user-guide/groups.md | 2 - docs/user-guide/installation.md | 2 +- pyproject.toml | 4 +- src/zarr/__init__.py | 1 - src/zarr/core/_tree.py | 131 ++++++++++++++++++++++++-------- src/zarr/core/group.py | 40 ++++++++-- tests/test_api.py | 1 - tests/test_tree.py | 64 +++++++++++++--- 9 files changed, 188 insertions(+), 58 deletions(-) create mode 100644 changes/3778.misc.md diff --git a/changes/3778.misc.md b/changes/3778.misc.md new file mode 100644 index 0000000000..17f26666ed --- /dev/null +++ b/changes/3778.misc.md @@ -0,0 +1 @@ +`Group.tree()` no longer requires the `rich` dependency. Tree rendering now uses built-in ANSI bold for terminals and HTML bold for Jupyter. New parameters: `plain=True` for unstyled output, and `max_nodes` (default 500) to truncate large hierarchies with early bailout. diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index e093590dfe..58a9c1c806 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -133,5 +133,3 @@ Groups also have the [`zarr.Group.tree`][] method, e.g.: print(root.tree()) ``` -!!! note - [`zarr.Group.tree`][] requires the optional [rich](https://rich.readthedocs.io/en/stable/) dependency. It can be installed with the `[tree]` extra. \ No newline at end of file diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md index 4d323643f1..6c1414e81a 100644 --- a/docs/user-guide/installation.md +++ b/docs/user-guide/installation.md @@ -26,7 +26,7 @@ These can be installed using `pip install "zarr[]"`, e.g. `pip install "z - `gpu`: support for GPUs - `remote`: support for reading/writing to remote data stores -Additional optional dependencies include `rich`, `universal_pathlib`. These must be installed separately. +Additional optional dependencies include `universal_pathlib`. These must be installed separately. ## conda diff --git a/pyproject.toml b/pyproject.toml index 18bdeda07c..4853636ef9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,7 +70,7 @@ gpu = [ "cupy-cuda12x", ] cli = ["typer"] -optional = ["rich", "universal-pathlib"] +optional = ["universal-pathlib"] [project.scripts] zarr = "zarr._cli.cli:app" @@ -122,7 +122,6 @@ docs = [ "towncrier", # Optional dependencies to run examples "numcodecs[msgpack]", - "rich", "s3fs>=2023.10.0", "astroid<4", "pytest", @@ -131,7 +130,6 @@ dev = [ {include-group = "test"}, {include-group = "remote-tests"}, {include-group = "docs"}, - "rich", "universal-pathlib", "mypy", ] diff --git a/src/zarr/__init__.py b/src/zarr/__init__.py index 3c6195c28f..cdf3840c3b 100644 --- a/src/zarr/__init__.py +++ b/src/zarr/__init__.py @@ -78,7 +78,6 @@ def print_packages(packages: list[str]) -> None: "s3fs", "gcsfs", "universal-pathlib", - "rich", "obstore", ] diff --git a/src/zarr/core/_tree.py b/src/zarr/core/_tree.py index eed807ec95..a528bf9876 100644 --- a/src/zarr/core/_tree.py +++ b/src/zarr/core/_tree.py @@ -1,17 +1,11 @@ -import io -import os +import sys +from collections import deque from collections.abc import Sequence +from html import escape as html_escape from typing import Any from zarr.core.group import AsyncGroup -try: - import rich - import rich.console - import rich.tree -except ImportError as e: - raise ImportError("'rich' is required for Group.tree") from e - class TreeRepr: """ @@ -21,45 +15,120 @@ class TreeRepr: of Zarr's public API. """ - def __init__(self, tree: rich.tree.Tree) -> None: - self._tree = tree + def __init__(self, text: str, html: str, truncated: str = "") -> None: + self._text = text + self._html = html + self._truncated = truncated def __repr__(self) -> str: - color_system = os.environ.get("OVERRIDE_COLOR_SYSTEM", rich.get_console().color_system) - console = rich.console.Console(file=io.StringIO(), color_system=color_system) - console.print(self._tree) - return str(console.file.getvalue()) + if self._truncated: + return self._truncated + self._text + return self._text def _repr_mimebundle_( self, - include: Sequence[str], - exclude: Sequence[str], + include: Sequence[str] | None = None, + exclude: Sequence[str] | None = None, **kwargs: Any, ) -> dict[str, str]: + text = self._truncated + self._text if self._truncated else self._text # For jupyter support. - # Unsure why mypy infers the return type to by Any - return self._tree._repr_mimebundle_(include=include, exclude=exclude, **kwargs) # type: ignore[no-any-return] + html_body = self._truncated + self._html if self._truncated else self._html + html = ( + '
"
+            f"{html_body}
\n" + ) + return {"text/plain": text, "text/html": html} + +async def group_tree_async( + group: AsyncGroup, + max_depth: int | None = None, + *, + max_nodes: int = 500, + plain: bool = False, +) -> TreeRepr: + members: list[tuple[str, Any]] = [] + truncated = False + async for item in group.members(max_depth=max_depth): + if len(members) == max_nodes: + truncated = True + break + members.append(item) + members.sort(key=lambda key_node: key_node[0]) -async def group_tree_async(group: AsyncGroup, max_depth: int | None = None) -> TreeRepr: - tree = rich.tree.Tree(label=f"[bold]{group.name}[/bold]") - nodes = {"": tree} - members = sorted([x async for x in group.members(max_depth=max_depth)]) + # Set up styling tokens: ANSI bold for terminals, HTML for Jupyter, + # or empty strings when plain=True (useful for LLMs, logging, files). + if plain: + ansi_open = ansi_close = html_open = html_close = "" + else: + # Avoid emitting ANSI escape codes when output is piped or in CI. + use_ansi = sys.stdout.isatty() + ansi_open = "\x1b[1m" if use_ansi else "" + ansi_close = "\x1b[0m" if use_ansi else "" + html_open = "" + html_close = "" + # Group members by parent key so we can render the tree level by level. + nodes: dict[str, list[tuple[str, Any]]] = {} for key, node in members: if key.count("/") == 0: parent_key = "" else: parent_key = key.rsplit("/", 1)[0] - parent = nodes[parent_key] + nodes.setdefault(parent_key, []).append((key, node)) - # We want what the spec calls the node "name", the part excluding all leading - # /'s and path segments. But node.name includes all that, so we build it here. + # Render the tree iteratively (not recursively) to avoid hitting + # Python's recursion limit on deeply nested hierarchies. + # Each stack frame is (prefix_string, remaining_children_at_this_level). + text_lines = [f"{ansi_open}{group.name}{ansi_close}"] + html_lines = [f"{html_open}{html_escape(group.name)}{html_close}"] + stack = [("", deque(nodes.get("", [])))] + while stack: + prefix, remaining = stack[-1] + if not remaining: + stack.pop() + continue + key, node = remaining.popleft() name = key.rsplit("/")[-1] + escaped_name = html_escape(name) + # if we popped the last item then remaining will + # now be empty - that's how we got past the if not remaining + # above, but this can still be true. + is_last = not remaining + connector = "└── " if is_last else "├── " if isinstance(node, AsyncGroup): - label = f"[bold]{name}[/bold]" + text_lines.append(f"{prefix}{connector}{ansi_open}{name}{ansi_close}") + html_lines.append(f"{prefix}{connector}{html_open}{escaped_name}{html_close}") else: - label = f"[bold]{name}[/bold] {node.shape} {node.dtype}" - nodes[key] = parent.add(label) - - return TreeRepr(tree) + text_lines.append( + f"{prefix}{connector}{ansi_open}{name}{ansi_close} {node.shape} {node.dtype}" + ) + html_lines.append( + f"{prefix}{connector}{html_open}{escaped_name}{html_close}" + f" {html_escape(str(node.shape))} {html_escape(str(node.dtype))}" + ) + # Descend into children with an accumulated prefix: + # Example showing how prefix accumulates: + # / + # ├── a prefix = "" + # │ ├── b prefix = "" + "│ " + # │ │ └── x prefix = "" + "│ " + "│ " + # │ └── c prefix = "" + "│ " + # └── d prefix = "" + # └── e prefix = "" + " " + if children := nodes.get(key, []): + if is_last: + child_prefix = prefix + " " + else: + child_prefix = prefix + "│ " + stack.append((child_prefix, deque(children))) + text = "\n".join(text_lines) + "\n" + html = "\n".join(html_lines) + "\n" + note = ( + f"Truncated at max_nodes={max_nodes}, some nodes and their children may be missing\n" + if truncated + else "" + ) + return TreeRepr(text, html, truncated=note) diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 9b5fee275b..080e90ff0f 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -1588,12 +1588,17 @@ async def array_values( async for _, array in self.arrays(): yield array - async def tree(self, expand: bool | None = None, level: int | None = None) -> Any: + async def tree( + self, + expand: bool | None = None, + level: int | None = None, + *, + max_nodes: int = 500, + plain: bool = False, + ) -> Any: """ Return a tree-like representation of a hierarchy. - This requires the optional ``rich`` dependency. - Parameters ---------- expand : bool, optional @@ -1601,6 +1606,12 @@ async def tree(self, expand: bool | None = None, level: int | None = None) -> An it's used. level : int, optional The maximum depth below this Group to display in the tree. + max_nodes : int + Maximum number of nodes to display before truncating. Default is 500. + plain : bool, optional + If True, return a plain-text tree without ANSI styling. This is + useful when the output will be consumed by an LLM or written to a + file. Default is False. Returns ------- @@ -1611,7 +1622,7 @@ async def tree(self, expand: bool | None = None, level: int | None = None) -> An if expand is not None: raise NotImplementedError("'expand' is not yet implemented.") - return await group_tree_async(self, max_depth=level) + return await group_tree_async(self, max_depth=level, max_nodes=max_nodes, plain=plain) async def empty(self, *, name: str, shape: tuple[int, ...], **kwargs: Any) -> AnyAsyncArray: """Create an empty array with the specified shape in this Group. The contents will @@ -2371,12 +2382,17 @@ def array_values(self) -> Generator[AnyArray, None]: for _, array in self.arrays(): yield array - def tree(self, expand: bool | None = None, level: int | None = None) -> Any: + def tree( + self, + expand: bool | None = None, + level: int | None = None, + *, + max_nodes: int = 500, + plain: bool = False, + ) -> Any: """ Return a tree-like representation of a hierarchy. - This requires the optional ``rich`` dependency. - Parameters ---------- expand : bool, optional @@ -2384,13 +2400,21 @@ def tree(self, expand: bool | None = None, level: int | None = None) -> Any: it's used. level : int, optional The maximum depth below this Group to display in the tree. + max_nodes : int + Maximum number of nodes to display before truncating. Default is 500. + plain : bool, optional + If True, return a plain-text tree without ANSI styling. This is + useful when the output will be consumed by an LLM or written to a + file. Default is False. Returns ------- TreeRepr A pretty-printable object displaying the hierarchy. """ - return self._sync(self._async_group.tree(expand=expand, level=level)) + return self._sync( + self._async_group.tree(expand=expand, level=level, max_nodes=max_nodes, plain=plain) + ) def create_group(self, name: str, **kwargs: Any) -> Group: """Create a sub-group. diff --git a/tests/test_api.py b/tests/test_api.py index 07c3c8590d..a306ff3dc3 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -599,7 +599,6 @@ def test_load_local(tmp_path: Path, path: str | None, load_read_only: bool) -> N def test_tree() -> None: - pytest.importorskip("rich") g1 = zarr.group() g1.create_group("foo") g3 = g1.create_group("bar") diff --git a/tests/test_tree.py b/tests/test_tree.py index b4a5106998..78ea121f4d 100644 --- a/tests/test_tree.py +++ b/tests/test_tree.py @@ -1,4 +1,3 @@ -import os import textwrap from typing import Any @@ -6,12 +5,19 @@ import zarr -pytest.importorskip("rich") - @pytest.mark.parametrize("root_name", [None, "root"]) -def test_tree(root_name: Any) -> None: - os.environ["OVERRIDE_COLOR_SYSTEM"] = "truecolor" +@pytest.mark.parametrize("atty", [True, False]) +@pytest.mark.parametrize("plain", [True, False]) +def test_tree(root_name: Any, atty: bool, plain: bool, monkeypatch: pytest.MonkeyPatch) -> None: + monkeypatch.setattr("sys.stdout.isatty", lambda: atty) + + if atty and not plain: + BOPEN = "\x1b[1m" + BCLOSE = "\x1b[0m" + else: + BOPEN = "" + BCLOSE = "" g = zarr.group(path=root_name) A = g.create_group("A") @@ -25,12 +31,9 @@ def test_tree(root_name: Any) -> None: C.create_array(name="x", shape=(0,), dtype="float64") D.create_array(name="x", shape=(0,), dtype="float64") - result = repr(g.tree()) + result = repr(g.tree(plain=plain)) root = root_name or "" - BOPEN = "\x1b[1m" - BCLOSE = "\x1b[0m" - expected = textwrap.dedent(f"""\ {BOPEN}/{root}{BCLOSE} ├── {BOPEN}A{BCLOSE} @@ -46,15 +49,54 @@ def test_tree(root_name: Any) -> None: assert result == expected - result = repr(g.tree(level=0)) + result = repr(g.tree(level=0, plain=plain)) expected = textwrap.dedent(f"""\ {BOPEN}/{root}{BCLOSE} ├── {BOPEN}A{BCLOSE} └── {BOPEN}B{BCLOSE} """) - assert result == expected + if not plain: + tree = g.tree(plain=False) + bundle = tree._repr_mimebundle_() + assert "text/plain" in bundle + assert "text/html" in bundle + assert "A" in bundle["text/html"] + assert "x" in bundle["text/html"] + assert " None: + g = zarr.group() + g.create_group("a") + g.create_group("b") + g.create_group("c") + g.create_group("d") + g.create_group("e") + + result = repr(g.tree(max_nodes=3, plain=True)) + assert "Truncated at max_nodes=3" in result + # Should show exactly 3 nodes (lines with ── connectors). + lines = result.strip().split("\n") + node_lines = [line for line in lines if "──" in line] + assert len(node_lines) == 3 + + # Full tree should not show truncation message. + full = repr(g.tree(max_nodes=500, plain=True)) + assert "truncated" not in full + + +def test_tree_html_escaping() -> None: + g = zarr.group() + g.create_group("") + + tree = g.tree() + bundle = tree._repr_mimebundle_() + assert "<img" in bundle["text/html"] + assert "" in bundle["text/plain"] + def test_expand_not_implemented() -> None: g = zarr.group() From 536ce9dbfb573f9f99a836bc1417a41566cb3426 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Tue, 17 Mar 2026 18:00:06 -0400 Subject: [PATCH 232/468] chore: less frequent codspeed runs (#3784) --- .github/workflows/codspeed.yml | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 7192b6d78a..bc4f1c1d4c 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -1,13 +1,10 @@ name: CodSpeed Benchmarks on: - push: - branches: - - "main" + schedule: + - cron: '0 9 * * 1' # Every Monday at 9am UTC pull_request: - types: [labeled, synchronize] - # `workflow_dispatch` allows CodSpeed to trigger backtest - # performance analysis in order to generate initial data. + types: [labeled] workflow_dispatch: permissions: @@ -17,15 +14,14 @@ jobs: benchmarks: name: Run benchmarks runs-on: codspeed-macro - # Only run benchmarks for: pushes to main, manual triggers, or PRs with 'benchmark' label if: | - github.event_name == 'push' || + github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' || (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark')) steps: - uses: actions/checkout@v6 with: - fetch-depth: 0 # grab all branches and tags + fetch-depth: 0 - name: Set up Python uses: actions/setup-python@v6 with: From 4acebeba7be73e7e3ee1442e89741a3295cea8fc Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 19 Mar 2026 16:05:55 +0100 Subject: [PATCH 233/468] Add missing slash character to towncrier issue format (#3788) --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4853636ef9..b3816f22c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -445,7 +445,7 @@ checks = [ directory = 'changes' filename = "docs/release-notes.md" underlines = ["", "", ""] -issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues{issue})" +issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues/{issue})" start_string = "\n" [tool.codespell] From a323ac71e98081d6c10214ffdd7ef0eaa4e9db7f Mon Sep 17 00:00:00 2001 From: Joe Hamman Date: Thu, 19 Mar 2026 09:26:15 -0700 Subject: [PATCH 234/468] doc: add ai use policy to contributing guide (#3769) * doc: add ai use policy to contributing guide * add changelog entry * Update docs/contributing.md Co-authored-by: Davis Bennett --------- Co-authored-by: Davis Bennett --- changes/3769.doc.md | 1 + docs/contributing.md | 26 ++++++++++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 changes/3769.doc.md diff --git a/changes/3769.doc.md b/changes/3769.doc.md new file mode 100644 index 0000000000..f622ac525f --- /dev/null +++ b/changes/3769.doc.md @@ -0,0 +1 @@ +Add AI-assisted code policy to the contributing guide. diff --git a/docs/contributing.md b/docs/contributing.md index a4bbaafbd5..b2c1ae635c 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -36,6 +36,32 @@ If you have an idea about a new feature or some other improvement to Zarr, pleas We very much welcome ideas and suggestions for how to improve Zarr, but please bear in mind that we are likely to be conservative in accepting proposals for new features. The reasons for this are that we would like to keep the Zarr code base lean and focused on a core set of functionalities, and available time for development, review and maintenance of new features is limited. But if you have a great idea, please don't let that stop you from posting it on GitHub, just please don't be offended if we respond cautiously. +## AI-assisted contributions + +AI coding tools are increasingly common in open source development. These tools are welcome in Zarr-Python, but the same standards apply to all contributions regardless of how they were produced — whether written by hand, with AI assistance, or generated entirely by an AI tool. + +### You are responsible for your changes + +If you submit a pull request, you are responsible for understanding and having fully reviewed the changes. You must be able to explain why each change is correct and how it fits into the project. + +### Communication must be your own + +PR descriptions, issue comments, and review responses must be in your own words. The substance and reasoning must come from you. Using AI to polish grammar or phrasing is fine, but do not paste AI-generated text as comments or review responses. + +### Review every line + +You must have personally reviewed and understood all changes before submitting. If you used AI to generate code, you are expected to have read it critically and tested it. The PR description should explain the approach and reasoning — do not leave it to reviewers to figure out what the code does and why. + +### Keep PRs reviewable + +Generating code with AI is fast; reviewing it is not. A large diff shifts the burden from the contributor to the reviewer. PRs that cannot be reviewed in reasonable time with reasonable effort may be closed, regardless of their potential usefulness or correctness. Use AI tools not only to write code but to prepare better, more reviewable PRs — well-structured commits, clear descriptions, and minimal scope. + +If you are planning a large AI-assisted contribution (e.g., a significant refactor or a new subsystem), **open an issue first** to discuss the scope and approach with maintainers. Maintainers may also request that large changes be broken into smaller, reviewable pieces. + +### Documentation + +The same principles apply to documentation. Zarr has domain-specific semantics (chunked storage, codec pipelines, Zarr v2/v3 format details) that AI tools frequently get wrong. Do not submit documentation that you haven't carefully read and verified. + ## Contributing code and/or documentation ### Forking the repository From 9a71d590b928fa516df4fa389a7c1dcc0bc93101 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 19 Mar 2026 17:52:37 +0100 Subject: [PATCH 235/468] chore/towncrier header (#3789) * have towncrier use h2 header for each release note * remove h1 headers --- docs/release-notes.md | 2 +- pyproject.toml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/release-notes.md b/docs/release-notes.md index 71c095e19a..25ebdb8edf 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,7 +2,7 @@ -# zarr 3.1.5 (2025-11-21) +## zarr 3.1.5 (2025-11-21) ## Bugfixes diff --git a/pyproject.toml b/pyproject.toml index b3816f22c9..b1077e3e5d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -445,6 +445,7 @@ checks = [ directory = 'changes' filename = "docs/release-notes.md" underlines = ["", "", ""] +title_format = "## {version} ({project_date})" issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues/{issue})" start_string = "\n" From 81164542885a3cdd95e8583de12ff678954bf16d Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 19 Mar 2026 15:52:01 -0400 Subject: [PATCH 236/468] chore: Use OIDC for publishing (#3791) * Use OIDC for publishing * Update requires * Attest --- .github/workflows/releases.yml | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index e3e3c446fa..bb9256568c 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -10,6 +10,10 @@ on: permissions: contents: read +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: build_artifacts: @@ -35,7 +39,7 @@ jobs: version: '1.16.5' - name: Build wheel and sdist run: hatch build - - uses: actions/upload-artifact@v6 + - uses: actions/upload-artifact@v7 with: name: releases path: dist @@ -55,16 +59,24 @@ jobs: ls dist upload_pypi: - needs: [build_artifacts] + needs: [build_artifacts, test_dist_pypi] runs-on: ubuntu-latest if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') + environment: + name: releases + url: https://pypi.org/p/zarr + permissions: + id-token: write + attestations: write + artifact-metadata: write steps: - uses: actions/download-artifact@v7 with: name: releases path: dist - - uses: pypa/gh-action-pypi-publish@v1.13.0 + - name: Generate artifact attestation + uses: actions/attest@v4 with: - user: __token__ - password: ${{ secrets.pypi_password }} - # To test: repository_url: https://test.pypi.org/legacy/ + subject-path: dist/* + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@v1.13.0 From 25ee087e8f408a7f883c25709c6bb9013348c64c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 19 Mar 2026 21:17:42 +0100 Subject: [PATCH 237/468] chore/3.1.6 release notes (#3790) * have towncrier use h2 header for each release note * remove h1 headers * release notes * rebuild release notes docs with #3769 * add more release notes * style * Update release-notes.md Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3464.doc.md | 1 - changes/3562.misc.md | 1 - changes/3603.bugfix.md | 1 - changes/3605.misc.md | 1 - changes/3619.misc.md | 1 - changes/3623.misc.md | 5 ----- changes/3636.misc.md | 1 - changes/3648.misc.md | 1 - changes/3655.bugfix.md | 1 - changes/3656.misc.md | 1 - changes/3657.bugfix.md | 1 - changes/3658.misc.md | 1 - changes/3668.feature.md | 4 ---- changes/3673.misc.md | 1 - changes/3695.bugfix.md | 1 - changes/3700.bugfix.md | 1 - changes/3702.bugfix.md | 1 - changes/3704.misc.md | 1 - changes/3705.bugfix.md | 1 - changes/3706.misc.md | 1 - changes/3708.misc.md | 1 - changes/3710.bugfix.md | 1 - changes/3712.misc.md | 1 - changes/3713.misc.md | 1 - changes/3717.misc.md | 1 - changes/3721.misc.md | 1 - changes/3728.misc.md | 1 - changes/3769.doc.md | 1 - changes/3778.misc.md | 1 - docs/release-notes.md | 36 ++++++++++++++++++++++++++++++++++++ 30 files changed, 36 insertions(+), 36 deletions(-) delete mode 100644 changes/3464.doc.md delete mode 100644 changes/3562.misc.md delete mode 100644 changes/3603.bugfix.md delete mode 100644 changes/3605.misc.md delete mode 100644 changes/3619.misc.md delete mode 100644 changes/3623.misc.md delete mode 100644 changes/3636.misc.md delete mode 100644 changes/3648.misc.md delete mode 100644 changes/3655.bugfix.md delete mode 100644 changes/3656.misc.md delete mode 100644 changes/3657.bugfix.md delete mode 100644 changes/3658.misc.md delete mode 100644 changes/3668.feature.md delete mode 100644 changes/3673.misc.md delete mode 100644 changes/3695.bugfix.md delete mode 100644 changes/3700.bugfix.md delete mode 100644 changes/3702.bugfix.md delete mode 100644 changes/3704.misc.md delete mode 100644 changes/3705.bugfix.md delete mode 100644 changes/3706.misc.md delete mode 100644 changes/3708.misc.md delete mode 100644 changes/3710.bugfix.md delete mode 100644 changes/3712.misc.md delete mode 100644 changes/3713.misc.md delete mode 100644 changes/3717.misc.md delete mode 100644 changes/3721.misc.md delete mode 100644 changes/3728.misc.md delete mode 100644 changes/3769.doc.md delete mode 100644 changes/3778.misc.md diff --git a/changes/3464.doc.md b/changes/3464.doc.md deleted file mode 100644 index 155a4575f4..0000000000 --- a/changes/3464.doc.md +++ /dev/null @@ -1 +0,0 @@ -Add documentation example for creating uncompressed arrays in the Compression section of the user guide. diff --git a/changes/3562.misc.md b/changes/3562.misc.md deleted file mode 100644 index e164ab39f8..0000000000 --- a/changes/3562.misc.md +++ /dev/null @@ -1 +0,0 @@ -Add continuous performance benchmarking infrastructure. \ No newline at end of file diff --git a/changes/3603.bugfix.md b/changes/3603.bugfix.md deleted file mode 100644 index 37e1da5cb1..0000000000 --- a/changes/3603.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Correct the target bytes number for auto-chunking when auto-sharding. \ No newline at end of file diff --git a/changes/3605.misc.md b/changes/3605.misc.md deleted file mode 100644 index b8c0757b69..0000000000 --- a/changes/3605.misc.md +++ /dev/null @@ -1 +0,0 @@ -Fix a bug in the test suite that prevented stand-alone example scripts from being tested. \ No newline at end of file diff --git a/changes/3619.misc.md b/changes/3619.misc.md deleted file mode 100644 index 8c36e473b5..0000000000 --- a/changes/3619.misc.md +++ /dev/null @@ -1 +0,0 @@ -Remove upper bounds on `pytest` and `pytest-asyncio` test dependencies. \ No newline at end of file diff --git a/changes/3623.misc.md b/changes/3623.misc.md deleted file mode 100644 index 4060e55e5f..0000000000 --- a/changes/3623.misc.md +++ /dev/null @@ -1,5 +0,0 @@ -This PR contains minor, non-function-altering, changes to use `ZarrFormat` across the repo as opposed to duplicating is with `Literal[2,3]`. - -Additionally, it fixes broken linting by using a `Literal[True, False]` type hint for Numpy hypothesis testing, as opposed to `bool`. - -Basically improves the typehints and reduces fat-finger error surface area slightly. diff --git a/changes/3636.misc.md b/changes/3636.misc.md deleted file mode 100644 index a814160c8b..0000000000 --- a/changes/3636.misc.md +++ /dev/null @@ -1 +0,0 @@ -The minimum required version of NumPy is now 2.0. diff --git a/changes/3648.misc.md b/changes/3648.misc.md deleted file mode 100644 index 156f8671de..0000000000 --- a/changes/3648.misc.md +++ /dev/null @@ -1 +0,0 @@ -Fix deprecation of setting a shape on an array directly in ``numpy`` 2.5+. diff --git a/changes/3655.bugfix.md b/changes/3655.bugfix.md deleted file mode 100644 index 67d384f00d..0000000000 --- a/changes/3655.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed a bug in the sharding codec that prevented nested shard reads in certain cases. \ No newline at end of file diff --git a/changes/3656.misc.md b/changes/3656.misc.md deleted file mode 100644 index 159f24d072..0000000000 --- a/changes/3656.misc.md +++ /dev/null @@ -1 +0,0 @@ -Removed *rich* and *mypy* from the `[test]` dependencies, and added a new `[dev]` dependency group that can be used to install all the development dependencies. diff --git a/changes/3657.bugfix.md b/changes/3657.bugfix.md deleted file mode 100644 index 1411704674..0000000000 --- a/changes/3657.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix obstore _transform_list_dir implementation to correctly relativize paths (removing lstrip usage). \ No newline at end of file diff --git a/changes/3658.misc.md b/changes/3658.misc.md deleted file mode 100644 index f400d97473..0000000000 --- a/changes/3658.misc.md +++ /dev/null @@ -1 +0,0 @@ -Switch from `pre-commit` to [`prek`](https://github.com/j178/prek) for pre-commit checks. \ No newline at end of file diff --git a/changes/3668.feature.md b/changes/3668.feature.md deleted file mode 100644 index def196ec8a..0000000000 --- a/changes/3668.feature.md +++ /dev/null @@ -1,4 +0,0 @@ -Exposes the array runtime configuration as an attribute called `config` on the `Array` and -`AsyncArray` classes. The previous `AsyncArray._config` attribute is now a deprecated alias for `AsyncArray.config`. - -Adds a method for creating a new `Array` / `AsyncArray` instance with a new runtime configuration, and fixes inaccurate documentation about the `write_empty_chunks` configuration parameter. \ No newline at end of file diff --git a/changes/3673.misc.md b/changes/3673.misc.md deleted file mode 100644 index 83643f5d3c..0000000000 --- a/changes/3673.misc.md +++ /dev/null @@ -1 +0,0 @@ -Benchmark CI now only runs for PRs with the `benchmark` label, reducing CodSpeed credit usage. diff --git a/changes/3695.bugfix.md b/changes/3695.bugfix.md deleted file mode 100644 index a7d847e4f1..0000000000 --- a/changes/3695.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Raise error when trying to encode :class:`numpy.dtypes.StringDType` with `na_object` set. \ No newline at end of file diff --git a/changes/3700.bugfix.md b/changes/3700.bugfix.md deleted file mode 100644 index 86acb71d0e..0000000000 --- a/changes/3700.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -CacheStore, LoggingStore and LatencyStore now support with_read_only. \ No newline at end of file diff --git a/changes/3702.bugfix.md b/changes/3702.bugfix.md deleted file mode 100644 index 94a2902567..0000000000 --- a/changes/3702.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Skip chunk coordinate enumeration in resize when the array is only growing, avoiding unbounded memory usage for large arrays. \ No newline at end of file diff --git a/changes/3704.misc.md b/changes/3704.misc.md deleted file mode 100644 index d15d4924e0..0000000000 --- a/changes/3704.misc.md +++ /dev/null @@ -1 +0,0 @@ -Remove an expensive `isinstance` check from the bytes codec decoding routine. \ No newline at end of file diff --git a/changes/3705.bugfix.md b/changes/3705.bugfix.md deleted file mode 100644 index 2abcb4ee7c..0000000000 --- a/changes/3705.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix a performance bug in morton curve generation. \ No newline at end of file diff --git a/changes/3706.misc.md b/changes/3706.misc.md deleted file mode 100644 index 70a0e44c58..0000000000 --- a/changes/3706.misc.md +++ /dev/null @@ -1 +0,0 @@ -Allow NumPy ints as input when declaring a shape. \ No newline at end of file diff --git a/changes/3708.misc.md b/changes/3708.misc.md deleted file mode 100644 index dce7546c97..0000000000 --- a/changes/3708.misc.md +++ /dev/null @@ -1 +0,0 @@ -Optimize Morton order computation with hypercube optimization, vectorized decoding, and singleton dimension removal, providing 10-45x speedup for typical chunk shapes. diff --git a/changes/3710.bugfix.md b/changes/3710.bugfix.md deleted file mode 100644 index a40ddcee23..0000000000 --- a/changes/3710.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Add a dedicated in-memory cache for byte-range requests to the experimental `CacheStore`. \ No newline at end of file diff --git a/changes/3712.misc.md b/changes/3712.misc.md deleted file mode 100644 index 8fa2f2d2f7..0000000000 --- a/changes/3712.misc.md +++ /dev/null @@ -1 +0,0 @@ -Added benchmarks for Morton order computation in sharded arrays. diff --git a/changes/3713.misc.md b/changes/3713.misc.md deleted file mode 100644 index 9b0680dfc0..0000000000 --- a/changes/3713.misc.md +++ /dev/null @@ -1 +0,0 @@ -Vectorize get_chunk_slice for faster sharded array writes. diff --git a/changes/3717.misc.md b/changes/3717.misc.md deleted file mode 100644 index 5fed76b2b7..0000000000 --- a/changes/3717.misc.md +++ /dev/null @@ -1 +0,0 @@ -Add benchmarks for Morton order computation with non-power-of-2 and near-miss shard shapes, covering both pure computation and end-to-end read/write performance. diff --git a/changes/3721.misc.md b/changes/3721.misc.md deleted file mode 100644 index c170712882..0000000000 --- a/changes/3721.misc.md +++ /dev/null @@ -1 +0,0 @@ -Adds synchronous (non-async) encoding and decoding methods to CPU-bound codecs. This is necessary for performance optimizations based on avoiding `asyncio` overhead. These new methods are described by a new protocol: `SupportsSyncCodec`. \ No newline at end of file diff --git a/changes/3728.misc.md b/changes/3728.misc.md deleted file mode 100644 index a3cbb8d3f0..0000000000 --- a/changes/3728.misc.md +++ /dev/null @@ -1 +0,0 @@ -Move development dependencies (`test`, `remote_tests`, `docs`, `dev`) from optional dependencies to [dependency groups](https://packaging.python.org/en/latest/specifications/dependency-groups/). This may cause breakage for anyone who used e.g. `pip install zarr[test]` to get access to test dependencies. To install these dependency groups from a local checkout, use `pip install --group ` (pip 25.1+) or `uv run --group `. \ No newline at end of file diff --git a/changes/3769.doc.md b/changes/3769.doc.md deleted file mode 100644 index f622ac525f..0000000000 --- a/changes/3769.doc.md +++ /dev/null @@ -1 +0,0 @@ -Add AI-assisted code policy to the contributing guide. diff --git a/changes/3778.misc.md b/changes/3778.misc.md deleted file mode 100644 index 17f26666ed..0000000000 --- a/changes/3778.misc.md +++ /dev/null @@ -1 +0,0 @@ -`Group.tree()` no longer requires the `rich` dependency. Tree rendering now uses built-in ANSI bold for terminals and HTML bold for Jupyter. New parameters: `plain=True` for unstyled output, and `max_nodes` (default 500) to truncate large hierarchies with early bailout. diff --git a/docs/release-notes.md b/docs/release-notes.md index 25ebdb8edf..b974ae10c7 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,6 +2,42 @@ +## 3.1.6 (2026-03-19) + +### Features + +- Exposes the array runtime configuration as an attribute called `config` on the `Array` and + `AsyncArray` classes. The previous `AsyncArray._config` attribute is now a deprecated alias for `AsyncArray.config`. ([#3668](https://github.com/zarr-developers/zarr-python/issues/3668)) +- Adds a method for creating a new `Array` / `AsyncArray` instance with a new runtime configuration, and fixes inaccurate documentation about the `write_empty_chunks` configuration parameter. ([#3668](https://github.com/zarr-developers/zarr-python/issues/3668)) +- Adds synchronous methods to stores that do not benefit from an async event loop. The shape of these methods is defined by protocol classes to support structural subtyping. ([#3725](https://github.com/zarr-developers/zarr-python/pull/3725)) +- Fix near-miss penalty in `_morton_order` with hybrid ceiling+argsort strategy. ([#3718](https://github.com/zarr-developers/zarr-python/pull/3718)) + +### Bugfixes + +- Correct the target bytes number for auto-chunking when auto-sharding. ([#3603](https://github.com/zarr-developers/zarr-python/issues/3603)) +- Fixed a bug in the sharding codec that prevented nested shard reads in certain cases. ([#3655](https://github.com/zarr-developers/zarr-python/issues/3655)) +- Fix obstore `_transform_list_dir` implementation to correctly relativize paths (removing `lstrip` usage). ([#3657](https://github.com/zarr-developers/zarr-python/issues/3657)) +- Raise error when trying to encode :class:`numpy.dtypes.StringDType` with `na_object` set. ([#3695](https://github.com/zarr-developers/zarr-python/issues/3695)) +- `CacheStore`, `LoggingStore` and `LatencyStore` now support with_read_only. ([#3700](https://github.com/zarr-developers/zarr-python/issues/3700)) +- Skip chunk coordinate enumeration in resize when the array is only growing, avoiding unbounded memory usage for large arrays. ([#3702](https://github.com/zarr-developers/zarr-python/issues/3702)) +- Fix a performance bug in morton curve generation. ([#3705](https://github.com/zarr-developers/zarr-python/issues/3705)) +- Add a dedicated in-memory cache for byte-range requests to the experimental `CacheStore`. ([#3710](https://github.com/zarr-developers/zarr-python/issues/3710)) +- `BaseFloat._check_scalar` rejects invalid string values. ([#3586](https://github.com/zarr-developers/zarr-python/issues/3586)) +- Apply drop_axes squeeze in partial decode path for sharding. ([#3763](https://github.com/zarr-developers/zarr-python/issues/3763)) +- Set `copy=False` in reshape operation. ([#3649](https://github.com/zarr-developers/zarr-python/issues/3649)) +- Validate that dask-style chunks have regular shapes. ([#3779](https://github.com/zarr-developers/zarr-python/issues/3779)) + +### Improved Documentation + +- Add documentation example for creating uncompressed arrays in the Compression section of the user guide. ([#3464](https://github.com/zarr-developers/zarr-python/issues/3464)) +- Add AI-assisted code policy to the contributing guide. ([#3769](https://github.com/zarr-developers/zarr-python/issues/3769)) +- Added a glossary. ([#3767](https://github.com/zarr-developers/zarr-python/issues/3767)) + +### Misc + +- [#3562](https://github.com/zarr-developers/zarr-python/issues/3562), [#3605](https://github.com/zarr-developers/zarr-python/issues/3605), [#3619](https://github.com/zarr-developers/zarr-python/issues/3619), [#3623](https://github.com/zarr-developers/zarr-python/issues/3623), [#3636](https://github.com/zarr-developers/zarr-python/issues/3636), [#3648](https://github.com/zarr-developers/zarr-python/issues/3648), [#3656](https://github.com/zarr-developers/zarr-python/issues/3656), [#3658](https://github.com/zarr-developers/zarr-python/issues/3658), [#3673](https://github.com/zarr-developers/zarr-python/issues/3673), [#3704](https://github.com/zarr-developers/zarr-python/issues/3704), [#3706](https://github.com/zarr-developers/zarr-python/issues/3706), [#3708](https://github.com/zarr-developers/zarr-python/issues/3708), [#3712](https://github.com/zarr-developers/zarr-python/issues/3712), [#3713](https://github.com/zarr-developers/zarr-python/issues/3713), [#3717](https://github.com/zarr-developers/zarr-python/issues/3717), [#3721](https://github.com/zarr-developers/zarr-python/issues/3721), [#3728](https://github.com/zarr-developers/zarr-python/issues/3728), [#3778](https://github.com/zarr-developers/zarr-python/issues/3778) + + ## zarr 3.1.5 (2025-11-21) ## Bugfixes From 420f11ce5bca6cf05b0bd9bd296c106caf2c9711 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 20 Mar 2026 21:30:54 +0100 Subject: [PATCH 238/468] Rename the `DimensionNames` type to `DimensionNamesLike`. (#3800) The reason for this change is the fact that the `DimensionNames` type is does not model the actual type of the `dimension_names` attribute on the Array V3 Metadata class, but rather a wider input type that is ultimately narrowed to that actual type. For this reason, it should use the same `XLike` name convention as the other wide input types that get narrowed to a more restricted type. --- src/zarr/api/asynchronous.py | 4 ++-- src/zarr/api/synchronous.py | 8 ++++---- src/zarr/core/array.py | 30 +++++++++++++++--------------- src/zarr/core/common.py | 3 ++- src/zarr/core/group.py | 10 +++++----- src/zarr/core/metadata/v3.py | 4 ++-- tests/conftest.py | 6 +++--- 7 files changed, 33 insertions(+), 32 deletions(-) diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 6164cda957..66cf3bad7e 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -24,7 +24,7 @@ from zarr.core.common import ( JSON, AccessModeLiteral, - DimensionNames, + DimensionNamesLike, MemoryOrder, ZarrFormat, _default_zarr_format, @@ -914,7 +914,7 @@ async def create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, config: ArrayConfigLike | None = None, **kwargs: Any, diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 1204eba3c9..4e718a234e 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -33,7 +33,7 @@ from zarr.core.common import ( JSON, AccessModeLiteral, - DimensionNames, + DimensionNamesLike, MemoryOrder, ShapeLike, ZarrFormat, @@ -649,7 +649,7 @@ def create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, config: ArrayConfigLike | None = None, **kwargs: Any, @@ -832,7 +832,7 @@ def create_array( zarr_format: ZarrFormat | None = 3, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, @@ -1003,7 +1003,7 @@ def from_array( zarr_format: ZarrFormat | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 486216fa32..b82c77fa9c 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -53,7 +53,7 @@ ZARR_JSON, ZARRAY_JSON, ZATTRS_JSON, - DimensionNames, + DimensionNamesLike, MemoryOrder, ShapeLike, ZarrFormat, @@ -389,7 +389,7 @@ async def create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, # runtime overwrite: bool = False, data: npt.ArrayLike | None = None, @@ -417,7 +417,7 @@ async def create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, # runtime overwrite: bool = False, data: npt.ArrayLike | None = None, @@ -445,7 +445,7 @@ async def create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, # v2 only chunks: ShapeLike | None = None, dimension_separator: Literal[".", "/"] | None = None, @@ -479,7 +479,7 @@ async def create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, # v2 only chunks: ShapeLike | None = None, dimension_separator: Literal[".", "/"] | None = None, @@ -630,7 +630,7 @@ async def _create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, # v2 only chunks: ShapeLike | None = None, dimension_separator: Literal[".", "/"] | None = None, @@ -742,7 +742,7 @@ def _create_metadata_v3( fill_value: Any | None = DEFAULT_FILL_VALUE, chunk_key_encoding: ChunkKeyEncodingLike | None = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, attributes: dict[str, JSON] | None = None, ) -> ArrayV3Metadata: """ @@ -803,7 +803,7 @@ async def _create_v3( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, attributes: dict[str, JSON] | None = None, overwrite: bool = False, ) -> AsyncArrayV3: @@ -1998,7 +1998,7 @@ def create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, # v2 only chunks: tuple[int, ...] | None = None, dimension_separator: Literal[".", "/"] | None = None, @@ -2142,7 +2142,7 @@ def _create( | None ) = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, # v2 only chunks: tuple[int, ...] | None = None, dimension_separator: Literal[".", "/"] | None = None, @@ -4266,7 +4266,7 @@ async def from_array( zarr_format: ZarrFormat | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, @@ -4535,7 +4535,7 @@ async def init_array( zarr_format: ZarrFormat | None = 3, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, overwrite: bool = False, config: ArrayConfigLike | None = None, ) -> AnyAsyncArray: @@ -4751,7 +4751,7 @@ async def create_array( zarr_format: ZarrFormat | None = 3, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, @@ -4935,7 +4935,7 @@ def _parse_keep_array_attr( order: MemoryOrder | None, zarr_format: ZarrFormat | None, chunk_key_encoding: ChunkKeyEncodingLike | None, - dimension_names: DimensionNames, + dimension_names: DimensionNamesLike, ) -> tuple[ tuple[int, ...] | Literal["auto"], ShardsLike | None, @@ -4946,7 +4946,7 @@ def _parse_keep_array_attr( MemoryOrder | None, ZarrFormat, ChunkKeyEncodingLike | None, - DimensionNames, + DimensionNamesLike, ]: if isinstance(data, Array): if chunks == "keep": diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 275d062eba..a61271a941 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -47,7 +47,8 @@ MemoryOrder = Literal["C", "F"] AccessModeLiteral = Literal["r", "r+", "a", "w", "w-"] ANY_ACCESS_MODE: Final = "r", "r+", "a", "w", "w-" -DimensionNames = Iterable[str | None] | None +DimensionNamesLike = Iterable[str | None] | None +DimensionNames = DimensionNamesLike # for backwards compatibility TName = TypeVar("TName", bound=str) TConfig = TypeVar("TConfig", bound=Mapping[str, object]) diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 080e90ff0f..17b8b541b1 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -40,7 +40,7 @@ ZATTRS_JSON, ZGROUP_JSON, ZMETADATA_V2_JSON, - DimensionNames, + DimensionNamesLike, NodeType, ShapeLike, ZarrFormat, @@ -1032,7 +1032,7 @@ async def create_array( order: MemoryOrder | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, @@ -2483,7 +2483,7 @@ def create( order: MemoryOrder | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, @@ -2627,7 +2627,7 @@ def create_array( order: MemoryOrder | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, @@ -3025,7 +3025,7 @@ def array( order: MemoryOrder | None = None, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, storage_options: dict[str, Any] | None = None, overwrite: bool = False, config: ArrayConfigLike | None = None, diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 5ce155bd9a..2a5da50c7b 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -33,7 +33,7 @@ from zarr.core.common import ( JSON, ZARR_JSON, - DimensionNames, + DimensionNamesLike, NamedConfig, parse_named_configuration, parse_shapelike, @@ -220,7 +220,7 @@ def __init__( fill_value: object, codecs: Iterable[Codec | dict[str, JSON] | NamedConfig[str, Any] | str], attributes: dict[str, JSON] | None, - dimension_names: DimensionNames, + dimension_names: DimensionNamesLike, storage_transformers: Iterable[dict[str, JSON]] | None = None, extra_fields: Mapping[str, AllowedExtraField] | None = None, ) -> None: diff --git a/tests/conftest.py b/tests/conftest.py index 23a1e87d0a..86db02f6bf 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -25,7 +25,7 @@ from zarr.core.chunk_grids import RegularChunkGrid, _auto_partition from zarr.core.common import ( JSON, - DimensionNames, + DimensionNamesLike, MemoryOrder, ShapeLike, ZarrFormat, @@ -313,7 +313,7 @@ def create_array_metadata( zarr_format: ZarrFormat, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncoding | ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, ) -> ArrayV2Metadata | ArrayV3Metadata: """ Create array metadata @@ -452,7 +452,7 @@ def meta_from_array( zarr_format: ZarrFormat = 3, attributes: dict[str, JSON] | None = None, chunk_key_encoding: ChunkKeyEncoding | ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNames = None, + dimension_names: DimensionNamesLike = None, ) -> ArrayV3Metadata | ArrayV2Metadata: """ Create array metadata from an array From 427df3b6a0b56530806df59c3b28de8acbd4cba9 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Sat, 21 Mar 2026 15:11:40 -0400 Subject: [PATCH 239/468] docs: remove incorrect redirect (#3801) --- mkdocs.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 24adb66457..e2c4148e15 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -216,7 +216,6 @@ plugins: 'developers/index.html.md': 'contributing.md' 'developers/roadmap.html.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' 'api/zarr/creation.md': 'api/zarr/deprecated/creation.md' - 'api/zarr/codecs/numcodecs.md': 'api/zarr/deprecated/creation.md' 'api.md': 'api/zarr/index.md' 'api/zarr/metadata/migrate_v3.md': 'api/zarr/metadata.md' From 93dd0e45e31c15b0b3931227718c19db5e61dd20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Randy=20D=C3=B6ring?= <30527984+radoering@users.noreply.github.com> Date: Sat, 21 Mar 2026 20:42:02 +0100 Subject: [PATCH 240/468] fix: handle special uint32 arrays on Windows correctly (#3797) * fix: handle special uint32 arrays on Windows correctly * add changelog entry --------- Co-authored-by: Davis Bennett --- changes/3797.bugfix.md | 2 ++ src/zarr/core/dtype/npy/int.py | 22 ++++++++++++++++++++++ tests/test_dtype/test_npy/test_int.py | 11 ++++++++++- 3 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 changes/3797.bugfix.md diff --git a/changes/3797.bugfix.md b/changes/3797.bugfix.md new file mode 100644 index 0000000000..c683213c5d --- /dev/null +++ b/changes/3797.bugfix.md @@ -0,0 +1,2 @@ +Fix an issue that prevents the correct parsing of special NumPy ``uint32`` dtypes resulting e.g. +from bit wise operations on ``uint32`` arrays on Windows. diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index f71f535abb..e5007b7acb 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -1070,6 +1070,28 @@ class UInt32(BaseInt[np.dtypes.UInt32DType, np.uint32], HasEndianness): _zarr_v3_name: ClassVar[Literal["uint32"]] = "uint32" _zarr_v2_names: ClassVar[tuple[Literal[">u4"], Literal["u4", " TypeGuard[np.dtypes.UInt32DType]: + """ + A type guard that checks if the input is assignable to the type of ``cls.dtype_class`` + + This method is overridden for this particular data type because of a Windows-specific issue + where ``np.array([1], dtype=np.uint32) & 1`` creates an instance of ``np.dtypes.UIntDType``, + rather than an instance of ``np.dtypes.UInt32DType``, even though both represent 32-bit + unsigned integers. (In contrast to ``np.dtype('i')``, ``np.dtype('u')`` raises an error.) + + Parameters + ---------- + dtype : TDType + The dtype to check. + + Returns + ------- + Bool + True if the dtype matches, False otherwise. + """ + return super()._check_native_dtype(dtype) or dtype == np.dtypes.UInt32DType() + @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ diff --git a/tests/test_dtype/test_npy/test_int.py b/tests/test_dtype/test_npy/test_int.py index f53ec7f5ae..9eab053080 100644 --- a/tests/test_dtype/test_npy/test_int.py +++ b/tests/test_dtype/test_npy/test_int.py @@ -216,7 +216,16 @@ class TestUInt16(BaseTestZDType): class TestUInt32(BaseTestZDType): test_cls = UInt32 scalar_type = np.uint32 - valid_dtype = (np.dtype(">u4"), np.dtype("u4"), np.dtype(" Date: Mon, 23 Mar 2026 16:11:13 +0100 Subject: [PATCH 241/468] add release trigger that takes a tag as input (#3821) This change to `release.yml` should allow us to use `workflow-dispatch`, i.e., manual triggering, to invoke the release workflow, with an explicit tag as input. This supports publishing a tagged release outside of the commit that creates that tag. This is useful for situations where we issued a release, but the github actions workflow was broken in some way that prevented us from uploading the release to pypi. --- .github/workflows/releases.yml | 24 ++++++++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index bb9256568c..50d68d45df 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -6,6 +6,16 @@ on: pull_request: branches: [main] workflow_dispatch: + inputs: + tag: + description: 'Git tag to build and publish (e.g. v3.1.6)' + required: true + type: string + test_pypi: + description: 'Publish to Test PyPI instead of PyPI' + required: false + type: boolean + default: true permissions: contents: read @@ -25,6 +35,7 @@ jobs: steps: - uses: actions/checkout@v6 with: + ref: ${{ inputs.tag || github.ref }} submodules: true fetch-depth: 0 @@ -61,10 +72,12 @@ jobs: upload_pypi: needs: [build_artifacts, test_dist_pypi] runs-on: ubuntu-latest - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') + if: >- + (github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')) + || github.event_name == 'workflow_dispatch' environment: name: releases - url: https://pypi.org/p/zarr + url: ${{ (github.event_name == 'workflow_dispatch' && inputs.test_pypi) && 'https://test.pypi.org/p/zarr' || 'https://pypi.org/p/zarr' }} permissions: id-token: write attestations: write @@ -80,3 +93,10 @@ jobs: subject-path: dist/* - name: Publish package to PyPI uses: pypa/gh-action-pypi-publish@v1.13.0 + if: ${{ !(github.event_name == 'workflow_dispatch' && inputs.test_pypi) }} + + - name: Publish package to Test PyPI + uses: pypa/gh-action-pypi-publish@v1.13.0 + if: ${{ github.event_name == 'workflow_dispatch' && inputs.test_pypi }} + with: + repository-url: https://test.pypi.org/legacy/ From 46843bed56aa80b5b4b861823402adf994a47ecb Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 23 Mar 2026 18:22:20 +0100 Subject: [PATCH 242/468] Removes testpypi as a target for the workflow-dispatch-triggered release workflow. (#3822) * Removes testpypi as a target for the workflow-dispatch-triggered release workflow. Zarr Python is not configured for OIDC on TestPyPI, and there was a bug in the previous workflow that prevented command line declaration of the PyPI target (real or test) from being evaluated correctly. To simplify this, TestPyPI is removed, and only RealPyPI can be the target for publishing. * update --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- .github/workflows/releases.yml | 35 ++++++++++++++++++++-------------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 50d68d45df..d0f1fda3be 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -11,11 +11,6 @@ on: description: 'Git tag to build and publish (e.g. v3.1.6)' required: true type: string - test_pypi: - description: 'Publish to Test PyPI instead of PyPI' - required: false - type: boolean - default: true permissions: contents: read @@ -26,7 +21,26 @@ concurrency: jobs: + validate_tag: + if: github.event_name == 'workflow_dispatch' + runs-on: ubuntu-latest + steps: + - name: Validate tag format + run: | + if [[ ! "${{ inputs.tag }}" =~ ^v[0-9]+\.[0-9]+\.[0-9]+([a-z]+[0-9]*)?$ ]]; then + echo "::error::Invalid tag format '${{ inputs.tag }}'. Expected format: v1.2.3, v1.2.3a1, v1.2.3rc1" + exit 1 + fi + - name: Verify tag exists + run: | + git ls-remote --tags "${{ github.server_url }}/${{ github.repository }}" "${{ inputs.tag }}" | grep -q "${{ inputs.tag }}" || { + echo "::error::Tag '${{ inputs.tag }}' does not exist in the repository" + exit 1 + } + build_artifacts: + needs: [validate_tag] + if: always() && (needs.validate_tag.result == 'success' || needs.validate_tag.result == 'skipped') name: Build wheel on ubuntu-latest runs-on: ubuntu-latest strategy: @@ -74,10 +88,10 @@ jobs: runs-on: ubuntu-latest if: >- (github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')) - || github.event_name == 'workflow_dispatch' + || (github.event_name == 'workflow_dispatch' && startsWith(inputs.tag, 'v')) environment: name: releases - url: ${{ (github.event_name == 'workflow_dispatch' && inputs.test_pypi) && 'https://test.pypi.org/p/zarr' || 'https://pypi.org/p/zarr' }} + url: https://pypi.org/p/zarr permissions: id-token: write attestations: write @@ -93,10 +107,3 @@ jobs: subject-path: dist/* - name: Publish package to PyPI uses: pypa/gh-action-pypi-publish@v1.13.0 - if: ${{ !(github.event_name == 'workflow_dispatch' && inputs.test_pypi) }} - - - name: Publish package to Test PyPI - uses: pypa/gh-action-pypi-publish@v1.13.0 - if: ${{ github.event_name == 'workflow_dispatch' && inputs.test_pypi }} - with: - repository-url: https://test.pypi.org/legacy/ From b76e006defeee035c4fa0fd60f871e2a950eb89d Mon Sep 17 00:00:00 2001 From: Sam Levang <39069044+slevang@users.noreply.github.com> Date: Tue, 24 Mar 2026 05:09:48 -0400 Subject: [PATCH 243/468] perf: full shard write fast path (#3793) * ensure no get on full shard writes * clean up test --------- Co-authored-by: Davis Bennett --- src/zarr/codecs/sharding.py | 36 ++++++++++++++++++++++++++---------- tests/test_array.py | 31 ++++++++++++++++++++++++++++--- 2 files changed, 54 insertions(+), 13 deletions(-) diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 85162c2f74..9f26bc57b1 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -1,6 +1,6 @@ from __future__ import annotations -from collections.abc import Iterable, Mapping, MutableMapping +from collections.abc import Iterable, Mapping, MutableMapping, Sequence from dataclasses import dataclass, replace from enum import Enum from functools import lru_cache @@ -45,6 +45,7 @@ from zarr.core.dtype.npy.int import UInt64 from zarr.core.indexing import ( BasicIndexer, + ChunkProjection, SelectorTuple, _morton_order, _morton_order_keys, @@ -574,21 +575,26 @@ async def _encode_partial_single( chunks_per_shard = self._get_chunks_per_shard(shard_spec) chunk_spec = self._get_chunk_spec(shard_spec) - shard_reader = await self._load_full_shard_maybe( - byte_getter=byte_setter, - prototype=chunk_spec.prototype, - chunks_per_shard=chunks_per_shard, - ) - shard_reader = shard_reader or _ShardReader.create_empty(chunks_per_shard) - # Use vectorized lookup for better performance - shard_dict = shard_reader.to_dict_vectorized(np.asarray(_morton_order(chunks_per_shard))) - indexer = list( get_indexer( selection, shape=shard_shape, chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape) ) ) + if self._is_complete_shard_write(indexer, chunks_per_shard): + shard_dict = dict.fromkeys(morton_order_iter(chunks_per_shard)) + else: + shard_reader = await self._load_full_shard_maybe( + byte_getter=byte_setter, + prototype=chunk_spec.prototype, + chunks_per_shard=chunks_per_shard, + ) + shard_reader = shard_reader or _ShardReader.create_empty(chunks_per_shard) + # Use vectorized lookup for better performance + shard_dict = shard_reader.to_dict_vectorized( + np.asarray(_morton_order(chunks_per_shard)) + ) + await self.codec_pipeline.write( [ ( @@ -661,6 +667,16 @@ def _is_total_shard( chunk_coords in all_chunk_coords for chunk_coords in c_order_iter(chunks_per_shard) ) + def _is_complete_shard_write( + self, + indexed_chunks: Sequence[ChunkProjection], + chunks_per_shard: tuple[int, ...], + ) -> bool: + all_chunk_coords = {chunk_coords for chunk_coords, *_ in indexed_chunks} + return self._is_total_shard(all_chunk_coords, chunks_per_shard) and all( + is_complete_chunk for *_, is_complete_chunk in indexed_chunks + ) + async def _decode_shard_index( self, index_bytes: Buffer, chunks_per_shard: tuple[int, ...] ) -> _ShardIndex: diff --git a/tests/test_array.py b/tests/test_array.py index 5b85c6ba1d..8ea79b5f10 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -2259,9 +2259,34 @@ def test_create_array_with_data_num_gets( data = zarr.zeros(shape, dtype="int64") zarr.create_array(store, data=data, chunks=chunk_shape, shards=shard_shape, fill_value=-1) # type: ignore[arg-type] - # one get for the metadata and one per shard. - # Note: we don't actually need one get per shard, but this is the current behavior - assert store.counter["get"] == 1 + num_shards + # One get for the metadata; full-shard writes should not read shard payloads. + assert store.counter["get"] == 1 + + +@pytest.mark.parametrize( + ("selection", "expected_gets"), + [(slice(None), 0), (slice(1, 9), 1)], +) +def test_shard_write_num_gets(selection: slice, expected_gets: int) -> None: + """ + Test that partial-shard writes read the existing data and full-shard writes don't. + """ + store = LoggingStore(store=MemoryStore()) + arr = zarr.create_array( + store, + shape=(10,), + chunks=(1,), + shards=(10,), + dtype="int64", + fill_value=-1, + ) + arr[:] = 0 + + store.counter.clear() + + arr[selection] = 1 + + assert store.counter["get"] == expected_gets @pytest.mark.parametrize("config", [{}, {"write_empty_chunks": True}, {"order": "C"}]) From 79d552ae01919298a75bda064eb9a9735749cf6a Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 24 Mar 2026 16:08:09 +0100 Subject: [PATCH 244/468] Revert the changes applied in #3821 + #3822 (#3825) Reverts our `releases.yml` workflow to the state as of 93dd0e45, i.e. no option to publish a tag declared in workflow dispatch. --- .github/workflows/releases.yml | 29 +---------------------------- 1 file changed, 1 insertion(+), 28 deletions(-) diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index d0f1fda3be..bb9256568c 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -6,11 +6,6 @@ on: pull_request: branches: [main] workflow_dispatch: - inputs: - tag: - description: 'Git tag to build and publish (e.g. v3.1.6)' - required: true - type: string permissions: contents: read @@ -21,26 +16,7 @@ concurrency: jobs: - validate_tag: - if: github.event_name == 'workflow_dispatch' - runs-on: ubuntu-latest - steps: - - name: Validate tag format - run: | - if [[ ! "${{ inputs.tag }}" =~ ^v[0-9]+\.[0-9]+\.[0-9]+([a-z]+[0-9]*)?$ ]]; then - echo "::error::Invalid tag format '${{ inputs.tag }}'. Expected format: v1.2.3, v1.2.3a1, v1.2.3rc1" - exit 1 - fi - - name: Verify tag exists - run: | - git ls-remote --tags "${{ github.server_url }}/${{ github.repository }}" "${{ inputs.tag }}" | grep -q "${{ inputs.tag }}" || { - echo "::error::Tag '${{ inputs.tag }}' does not exist in the repository" - exit 1 - } - build_artifacts: - needs: [validate_tag] - if: always() && (needs.validate_tag.result == 'success' || needs.validate_tag.result == 'skipped') name: Build wheel on ubuntu-latest runs-on: ubuntu-latest strategy: @@ -49,7 +25,6 @@ jobs: steps: - uses: actions/checkout@v6 with: - ref: ${{ inputs.tag || github.ref }} submodules: true fetch-depth: 0 @@ -86,9 +61,7 @@ jobs: upload_pypi: needs: [build_artifacts, test_dist_pypi] runs-on: ubuntu-latest - if: >- - (github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')) - || (github.event_name == 'workflow_dispatch' && startsWith(inputs.tag, 'v')) + if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') environment: name: releases url: https://pypi.org/p/zarr From 690c5bb0c645f94661436b1673eb5771aefe8821 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 24 Mar 2026 16:33:12 +0100 Subject: [PATCH 245/468] Fix needs_release_notes.yml workflow (#3824) Remove a leading "-" character that violated github-actions-flavored yaml syntax. This should prevent email spam from failing workflows, and also prevent the workflow itself from failing. --- .github/workflows/needs_release_notes.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/needs_release_notes.yml b/.github/workflows/needs_release_notes.yml index b7b467d790..e9dd3ce25a 100644 --- a/.github/workflows/needs_release_notes.yml +++ b/.github/workflows/needs_release_notes.yml @@ -1,8 +1,8 @@ name: "Pull Request Labeler" on: - - pull_request_target: - types: [opened, reopened, synchronize] + pull_request_target: + types: [opened, reopened, synchronize] jobs: labeler: From 3a2ce2ff7c1f1938d35d77eef8ed2cec6a026f5f Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 25 Mar 2026 20:20:31 +0100 Subject: [PATCH 246/468] feat: return a useful value from `CodecPipeline.read()` (#3828) * Add a new type `GetResult` to `src/zarr/abc/codec.py`. This type is a typeddict that stores information about a completed attempt to fetch a stored resource, e.g. a chunk. Currently, `GetResult` only stores whether the resource was present or missing. We can add more capacity to this type in the future. * add tests for codec pipeline * Remove whitespace * changelog --- changes/3828.misc.md | 2 + src/zarr/abc/codec.py | 19 +++++++-- src/zarr/core/codec_pipeline.py | 32 +++++++++++---- tests/test_codec_pipeline.py | 71 +++++++++++++++++++++++++++++++++ 4 files changed, 113 insertions(+), 11 deletions(-) create mode 100644 changes/3828.misc.md create mode 100644 tests/test_codec_pipeline.py diff --git a/changes/3828.misc.md b/changes/3828.misc.md new file mode 100644 index 0000000000..8704ecceb6 --- /dev/null +++ b/changes/3828.misc.md @@ -0,0 +1,2 @@ +`CodecPipeline.read` and `CodecPipeline.read_batch` now return a tuple of typeddict objects +that each carry information about the request for a chunk from storage. \ No newline at end of file diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index 3ec5ec522b..86a0e6cabd 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -2,7 +2,7 @@ from abc import abstractmethod from collections.abc import Mapping -from typing import TYPE_CHECKING, Generic, Protocol, TypeGuard, TypeVar, runtime_checkable +from typing import TYPE_CHECKING, Generic, Literal, Protocol, TypeGuard, TypeVar, runtime_checkable from typing_extensions import ReadOnly, TypedDict @@ -32,9 +32,17 @@ "CodecInput", "CodecOutput", "CodecPipeline", + "GetResult", "SupportsSyncCodec", ] + +class GetResult(TypedDict): + """Metadata about a store get operation.""" + + status: Literal["present", "missing"] + + CodecInput = TypeVar("CodecInput", bound=NDBuffer | Buffer) CodecOutput = TypeVar("CodecOutput", bound=NDBuffer | Buffer) @@ -433,13 +441,13 @@ async def read( batch_info: Iterable[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], out: NDBuffer, drop_axes: tuple[int, ...] = (), - ) -> None: + ) -> tuple[GetResult, ...]: """Reads chunk data from the store, decodes it and writes it into an output array. Partial decoding may be utilized if the codecs and stores support it. Parameters ---------- - batch_info : Iterable[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple]] + batch_info : Iterable[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple, bool]] Ordered set of information about the chunks. The first slice selection determines which parts of the chunk will be fetched. The second slice selection determines where in the output array the chunk data will be written. @@ -451,6 +459,11 @@ async def read( ``out``) to the fill value for the array. out : NDBuffer + + Returns + ------- + tuple[GetResult, ...] + One result per chunk in ``batch_info``. """ ... diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index eed49556d3..e25863ae23 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -13,6 +13,7 @@ BytesBytesCodec, Codec, CodecPipeline, + GetResult, ) from zarr.core.common import concurrent_map from zarr.core.config import config @@ -251,26 +252,34 @@ async def read_batch( batch_info: Iterable[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], out: NDBuffer, drop_axes: tuple[int, ...] = (), - ) -> None: + ) -> tuple[GetResult, ...]: + results: list[GetResult] = [] if self.supports_partial_decode: + batch_info_list = list(batch_info) chunk_array_batch = await self.decode_partial_batch( [ (byte_getter, chunk_selection, chunk_spec) - for byte_getter, chunk_spec, chunk_selection, *_ in batch_info + for byte_getter, chunk_spec, chunk_selection, *_ in batch_info_list ] ) for chunk_array, (_, chunk_spec, _, out_selection, _) in zip( - chunk_array_batch, batch_info, strict=False + chunk_array_batch, batch_info_list, strict=False ): if chunk_array is not None: if drop_axes: chunk_array = chunk_array.squeeze(axis=drop_axes) out[out_selection] = chunk_array + results.append(GetResult(status="present")) else: out[out_selection] = fill_value_or_default(chunk_spec) + results.append(GetResult(status="missing")) else: + batch_info_list = list(batch_info) chunk_bytes_batch = await concurrent_map( - [(byte_getter, array_spec.prototype) for byte_getter, array_spec, *_ in batch_info], + [ + (byte_getter, array_spec.prototype) + for byte_getter, array_spec, *_ in batch_info_list + ], lambda byte_getter, prototype: byte_getter.get(prototype), config.get("async.concurrency"), ) @@ -278,20 +287,23 @@ async def read_batch( [ (chunk_bytes, chunk_spec) for chunk_bytes, (_, chunk_spec, *_) in zip( - chunk_bytes_batch, batch_info, strict=False + chunk_bytes_batch, batch_info_list, strict=False ) ], ) for chunk_array, (_, chunk_spec, chunk_selection, out_selection, _) in zip( - chunk_array_batch, batch_info, strict=False + chunk_array_batch, batch_info_list, strict=False ): if chunk_array is not None: tmp = chunk_array[chunk_selection] if drop_axes: tmp = tmp.squeeze(axis=drop_axes) out[out_selection] = tmp + results.append(GetResult(status="present")) else: out[out_selection] = fill_value_or_default(chunk_spec) + results.append(GetResult(status="missing")) + return tuple(results) def _merge_chunk_array( self, @@ -471,8 +483,8 @@ async def read( batch_info: Iterable[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], out: NDBuffer, drop_axes: tuple[int, ...] = (), - ) -> None: - await concurrent_map( + ) -> tuple[GetResult, ...]: + batch_results = await concurrent_map( [ (single_batch_info, out, drop_axes) for single_batch_info in batched(batch_info, self.batch_size) @@ -480,6 +492,10 @@ async def read( self.read_batch, config.get("async.concurrency"), ) + results: list[GetResult] = [] + for batch in batch_results: + results.extend(batch) + return tuple(results) async def write( self, diff --git a/tests/test_codec_pipeline.py b/tests/test_codec_pipeline.py new file mode 100644 index 0000000000..8d044c10d7 --- /dev/null +++ b/tests/test_codec_pipeline.py @@ -0,0 +1,71 @@ +from __future__ import annotations + +import pytest + +import zarr +from zarr.core.buffer.core import default_buffer_prototype +from zarr.core.indexing import BasicIndexer +from zarr.storage import MemoryStore + + +@pytest.mark.parametrize( + ("write_slice", "read_slice", "expected_statuses"), + [ + # Write all chunks, read all — all present + (slice(None), slice(None), ("present", "present", "present")), + # Write first chunk only, read all — first present, rest missing + (slice(0, 2), slice(None), ("present", "missing", "missing")), + # Write nothing, read all — all missing + (None, slice(None), ("missing", "missing", "missing")), + ], +) +async def test_read_returns_get_results( + write_slice: slice | None, + read_slice: slice, + expected_statuses: tuple[str, ...], +) -> None: + """ + Test that CodecPipeline.read returns a tuple of GetResult with correct statuses. + """ + store = MemoryStore() + arr = zarr.open_array(store, mode="w", shape=(6,), chunks=(2,), dtype="int64", fill_value=-1) + + if write_slice is not None: + arr[write_slice] = 0 + + async_arr = arr._async_array + pipeline = async_arr.codec_pipeline + metadata = async_arr.metadata + + prototype = default_buffer_prototype() + config = async_arr.config + indexer = BasicIndexer( + read_slice, + shape=metadata.shape, + chunk_grid=metadata.chunk_grid, + ) + + out_buffer = prototype.nd_buffer.empty( + shape=indexer.shape, + dtype=metadata.dtype.to_native_dtype(), + order=config.order, + ) + + results = await pipeline.read( + [ + ( + async_arr.store_path / metadata.encode_chunk_key(chunk_coords), + metadata.get_chunk_spec(chunk_coords, config, prototype=prototype), + chunk_selection, + out_selection, + is_complete_chunk, + ) + for chunk_coords, chunk_selection, out_selection, is_complete_chunk in indexer + ], + out_buffer, + drop_axes=indexer.drop_axes, + ) + + assert len(results) == len(expected_statuses) + for result, expected_status in zip(results, expected_statuses, strict=True): + assert result["status"] == expected_status From 8ca385ac9c62a9e467dfdf61f635c6738db9b471 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 26 Mar 2026 10:39:39 +0100 Subject: [PATCH 247/468] docs: fix the docstring for `CodecPipeline.write` (#3836) * Fix the docstring for `CodecPipeline.write` The annotation for the `batch_info` parameter in `CodecPipeline.write` omits the final bool from the tuple. This PR corrects the type annotation in the docstring. * docs: changelog * docs: rename changelog file --- changes/3836.doc.md | 2 ++ src/zarr/abc/codec.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 changes/3836.doc.md diff --git a/changes/3836.doc.md b/changes/3836.doc.md new file mode 100644 index 0000000000..a3138a9a45 --- /dev/null +++ b/changes/3836.doc.md @@ -0,0 +1,2 @@ +Corrects the type annotation reported for the `batch_info` parameter in the `CodecPipeline.write` +method docstring. \ No newline at end of file diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index 86a0e6cabd..d0fb42bd95 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -480,7 +480,7 @@ async def write( Parameters ---------- - batch_info : Iterable[tuple[ByteSetter, ArraySpec, SelectorTuple, SelectorTuple]] + batch_info : Iterable[tuple[ByteSetter, ArraySpec, SelectorTuple, SelectorTuple, bool]] Ordered set of information about the chunks. The first slice selection determines which parts of the chunk will be encoded. The second slice selection determines where in the value array the chunk data is located. From 5d92e8539f0211f7ca301f7330b5a59bc2f84637 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 27 Mar 2026 08:23:33 +0100 Subject: [PATCH 248/468] Improve layout of work in progress page (#3841) * Improve layout of work in progress page * Remove out of date entries --- docs/user-guide/v3_migration.md | 39 +++++++++++++++------------------ 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index d5a8067a88..8f835d4440 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -198,32 +198,29 @@ after the 3.0.0 release. If features listed below are important to your use case of Zarr-Python, please open (or comment on) a [GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new). -- The following functions / methods have not been ported to Zarr-Python 3 yet: +The following functions / methods have not been ported to Zarr-Python 3 yet: - * `zarr.copy` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) - * `zarr.copy_all` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) - * `zarr.copy_store` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) - * `zarr.Group.move` ([issue #2108](https://github.com/zarr-developers/zarr-python/issues/2108)) +- `zarr.copy` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) +- `zarr.copy_all` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) +- `zarr.copy_store` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) +- `zarr.Group.move` ([issue #2108](https://github.com/zarr-developers/zarr-python/issues/2108)) -- The following features (corresponding to function arguments to functions in +The following features (corresponding to function arguments to functions in `zarr`) have not been ported to Zarr-Python 3 yet. Using these features will raise a warning or a `NotImplementedError`: - * `cache_attrs` - * `cache_metadata` - * `chunk_store` ([issue #2495](https://github.com/zarr-developers/zarr-python/issues/2495)) - * `meta_array` - * `object_codec` ([issue #2617](https://github.com/zarr-developers/zarr-python/issues/2617)) - * `synchronizer` ([issue #1596](https://github.com/zarr-developers/zarr-python/issues/1596)) - * `dimension_separator` +- `cache_attrs` +- `cache_metadata` +- `chunk_store` ([issue #2495](https://github.com/zarr-developers/zarr-python/issues/2495)) +- `meta_array` +- `object_codec` ([issue #2617](https://github.com/zarr-developers/zarr-python/issues/2617)) +- `synchronizer` ([issue #1596](https://github.com/zarr-developers/zarr-python/issues/1596)) +- `dimension_separator` -- The following features that were supported by Zarr-Python 2 have not been ported +The following features that were supported by Zarr-Python 2 have not been ported to Zarr-Python 3 yet: - * Structured arrays / dtypes ([issue #2134](https://github.com/zarr-developers/zarr-python/issues/2134)) - * Fixed-length string dtypes ([issue #2347](https://github.com/zarr-developers/zarr-python/issues/2347)) - * Datetime and timedelta dtypes ([issue #2616](https://github.com/zarr-developers/zarr-python/issues/2616)) - * Object dtypes ([issue #2616](https://github.com/zarr-developers/zarr-python/issues/2616)) - * Ragged arrays ([issue #2618](https://github.com/zarr-developers/zarr-python/issues/2618)) - * Groups and Arrays do not implement `__enter__` and `__exit__` protocols ([issue #2619](https://github.com/zarr-developers/zarr-python/issues/2619)) - * Default filters for object dtypes for Zarr format 2 arrays ([issue #2627](https://github.com/zarr-developers/zarr-python/issues/2627)) +- Object dtypes ([issue #2616](https://github.com/zarr-developers/zarr-python/issues/2616)) +- Ragged arrays ([issue #2618](https://github.com/zarr-developers/zarr-python/issues/2618)) +- Groups and Arrays do not implement `__enter__` and `__exit__` protocols ([issue #2619](https://github.com/zarr-developers/zarr-python/issues/2619)) +- Default filters for object dtypes for Zarr format 2 arrays ([issue #2627](https://github.com/zarr-developers/zarr-python/issues/2627)) From 03e70f540853553678a75a868a07600e69984c70 Mon Sep 17 00:00:00 2001 From: Sam Levang <39069044+slevang@users.noreply.github.com> Date: Fri, 27 Mar 2026 11:48:09 -0400 Subject: [PATCH 249/468] perf: oindex optimization (#3830) * oindex single dim optimization * changelog * changelog type * Apply suggestions from code review Co-authored-by: Deepak Cherian * lint --------- Co-authored-by: Deepak Cherian --- changes/3830.misc.md | 1 + src/zarr/core/indexing.py | 25 ++++++++++++++++--------- 2 files changed, 17 insertions(+), 9 deletions(-) create mode 100644 changes/3830.misc.md diff --git a/changes/3830.misc.md b/changes/3830.misc.md new file mode 100644 index 0000000000..f622038f7e --- /dev/null +++ b/changes/3830.misc.md @@ -0,0 +1 @@ +Optimize the performance of indexing operations when using an array-like indexer on a single dimension. diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index d226c03675..f0c6c3c256 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -966,15 +966,22 @@ def __iter__(self) -> Iterator[ChunkProjection]: # handle advanced indexing arrays orthogonally if self.is_advanced: - # N.B., numpy doesn't support orthogonal indexing directly as yet, - # so need to work around via np.ix_. Also np.ix_ does not support a - # mixture of arrays and slices or integers, so need to convert slices - # and integers into ranges. - chunk_selection = ix_(chunk_selection, self.chunk_shape) - - # special case for non-monotonic indices - if not is_basic_selection(out_selection): - out_selection = ix_(out_selection, self.shape) + # NumPy can handle a single array-indexed dimension directly, + # which preserves full slices and avoids an + # unnecessary advanced-indexing copy. Integer-indexed + # dimensions still need the ix_ path for downstream squeezing. + # Example: we skip `ix_` for array[:, :, [1, 2, 3]] + n_array_dims = sum(isinstance(sel, np.ndarray) for sel in chunk_selection) + + if n_array_dims > 1 or self.drop_axes: + # N.B., numpy doesn't support orthogonal indexing directly + # for multiple array-indexed dimensions, so we need to + # convert the orthogonal selection into coordinate arrays. + chunk_selection = ix_(chunk_selection, self.chunk_shape) + + # special case for non-monotonic indices + if not is_basic_selection(out_selection): + out_selection = ix_(out_selection, self.shape) is_complete_chunk = all(p.is_complete_chunk for p in dim_projections) yield ChunkProjection(chunk_coords, chunk_selection, out_selection, is_complete_chunk) From ea13af5a3f7fc489e37a62f043c4b45a9ae55027 Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Fri, 27 Mar 2026 18:15:15 +0100 Subject: [PATCH 250/468] chore: spec0 compat (python 3.14 compat, python 3.12 min) (#3564) * chore: spec0 compat (python 3.14 compat, numpy 2 min) * fix: point oh * fix: `universal_pathlib` min bound * fix: new generic syntax (leave `covariant` untouched) * feat: `uv` in `hatch` * fix: try covariance handling * fix: allow covariance in `ZDType` * fix: remove covariance in `common.py` * fix: remove covariance in `codec.py` * fix: remove unused `TypeVar` * fix: bye byte `covariant`! * fix: merge issue * fix: more merge issues * fix: universal_pathlib * fix: pre-commit * fix: no more needed to pin numpy * chore: relnote * `yaml` not `yml` * fix: some `NDArrayLike` fixes * fix: back to old numpy * Revert "fix: some `NDArrayLike` fixes" This reverts commit 73b72b15629d3249c8c056a8bedd15a8aa383d69. * fix: try 3.12 * fix: oops * fix: ok that still produces some wierd output locally? * chore: try printing out full issue * fix: try skipping darwin build * fix: bring back `GetResult` --------- Co-authored-by: Deepak Cherian --- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/gpu_test.yml | 2 +- .github/workflows/nightly_wheels.yml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/test.yml | 16 +++---- .pre-commit-config.yaml | 4 +- changes/3546.misc.md | 1 + docs/contributing.md | 2 +- docs/index.md | 2 +- docs/user-guide/installation.md | 2 +- examples/custom_dtype/custom_dtype.py | 2 +- pyproject.toml | 23 ++++++---- src/zarr/_compat.py | 6 +-- src/zarr/abc/codec.py | 46 +++++++++---------- src/zarr/abc/numcodec.py | 4 +- src/zarr/abc/store.py | 4 +- src/zarr/api/asynchronous.py | 4 +- src/zarr/core/array.py | 17 +++---- src/zarr/core/buffer/core.py | 2 +- src/zarr/core/chunk_key_encodings.py | 4 +- src/zarr/core/codec_pipeline.py | 9 ++-- src/zarr/core/common.py | 22 ++------- src/zarr/core/dtype/__init__.py | 4 +- src/zarr/core/dtype/common.py | 11 ++--- src/zarr/core/dtype/npy/common.py | 15 ------ src/zarr/core/dtype/npy/complex.py | 27 +++++------ src/zarr/core/dtype/npy/float.py | 29 ++++++------ src/zarr/core/dtype/npy/int.py | 25 +++++----- src/zarr/core/dtype/npy/string.py | 6 +-- src/zarr/core/dtype/npy/time.py | 20 +++----- src/zarr/core/dtype/wrapper.py | 26 ++++------- src/zarr/core/group.py | 10 ++-- src/zarr/core/indexing.py | 15 ++---- src/zarr/core/metadata/__init__.py | 7 +-- src/zarr/core/metadata/v2.py | 8 ++-- src/zarr/core/sync.py | 17 ++++--- src/zarr/registry.py | 6 +-- src/zarr/storage/_common.py | 4 +- src/zarr/storage/_logging.py | 6 +-- src/zarr/storage/_obstore.py | 7 +-- src/zarr/storage/_utils.py | 20 +++++--- src/zarr/storage/_wrapper.py | 6 +-- src/zarr/testing/stateful.py | 6 +-- src/zarr/testing/store.py | 8 +--- src/zarr/testing/utils.py | 7 +-- src/zarr/types.py | 14 +++--- tests/test_regression/scripts/v2.18.py | 2 +- .../test_v2_dtype_regression.py | 7 ++- tests/test_store/test_core.py | 8 +--- 49 files changed, 212 insertions(+), 287 deletions(-) create mode 100644 changes/3546.misc.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 84bb89d82a..e765e3136e 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -61,7 +61,7 @@ body: value: | ```python # /// script - # requires-python = ">=3.11" + # requires-python = ">=3.12" # dependencies = [ # "zarr@git+https://github.com/zarr-developers/zarr-python.git@main", # ] diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index c474485dc0..4fdffab057 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -27,7 +27,7 @@ jobs: runs-on: gpu-runner strategy: matrix: - python-version: ['3.11'] + python-version: ['3.12'] steps: - uses: actions/checkout@v6 diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 834d563722..56ffe8f1b4 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -23,7 +23,7 @@ jobs: - uses: actions/setup-python@v6 name: Install Python with: - python-version: '3.13' + python-version: '3.14' - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index bb9256568c..fde8ff9804 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -31,7 +31,7 @@ jobs: - uses: actions/setup-python@v6 name: Install Python with: - python-version: '3.11' + python-version: '3.12' - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5af29c960e..8c55c7e93d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -23,23 +23,23 @@ jobs: strategy: matrix: - python-version: ['3.11', '3.12', '3.13'] + python-version: ['3.12', '3.13', '3.14'] dependency-set: ["minimal", "optional"] os: ["ubuntu-latest"] include: - - python-version: '3.11' + - python-version: '3.12' dependency-set: 'optional' os: 'macos-latest' - - python-version: '3.13' + - python-version: '3.14' dependency-set: 'optional' os: 'macos-latest' - - python-version: '3.11' + - python-version: '3.12' dependency-set: 'optional' os: 'windows-latest' - - python-version: '3.13' + - python-version: '3.14' dependency-set: 'optional' os: 'windows-latest' runs-on: ${{ matrix.os }} @@ -79,12 +79,12 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.11', "3.13"] + python-version: ['3.12', "3.14"] dependency-set: ["upstream", "min_deps"] exclude: - - python-version: "3.13" + - python-version: "3.14" dependency-set: min_deps - - python-version: "3.11" + - python-version: "3.12" dependency-set: upstream steps: - uses: actions/checkout@v6 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 37f41b8222..5d2b5de860 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ ci: default_stages: [pre-commit, pre-push] default_language_version: - python: python3.11 + python: python3.12 repos: - repo: https://github.com/astral-sh/ruff-pre-commit @@ -38,7 +38,7 @@ repos: - donfig - numcodecs - google-crc32c>=1.5 - - numpy==2.1 # until https://github.com/numpy/numpy/issues/28034 is resolved + - numpy==2.1 # https://github.com/zarr-developers/zarr-python/issues/3780 + https://github.com/zarr-developers/zarr-python/issues/3688 - typing_extensions - universal-pathlib - obstore>=0.5.1 diff --git a/changes/3546.misc.md b/changes/3546.misc.md new file mode 100644 index 0000000000..77fa0acb5f --- /dev/null +++ b/changes/3546.misc.md @@ -0,0 +1 @@ +Upgrade to spec0 compat (python 3.14 max, python 3.12 min). \ No newline at end of file diff --git a/docs/contributing.md b/docs/contributing.md index b2c1ae635c..e62ce54c35 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -205,7 +205,7 @@ When submitting a pull request, coverage will also be collected across all suppo ### Documentation -Docstrings for user-facing classes and functions should follow the [numpydoc](https://numpydoc.readthedocs.io/en/stable/format.html#docstring-standard) standard, including sections for Parameters and Examples. All examples should run and pass as doctests under Python 3.11. +Docstrings for user-facing classes and functions should follow the [numpydoc](https://numpydoc.readthedocs.io/en/stable/format.html#docstring-standard) standard, including sections for Parameters and Examples. All examples should run and pass as doctests under Python 3.12. Zarr uses mkdocs for documentation, hosted on readthedocs.org. Documentation is written in the Markdown markup language (.md files) in the `docs` folder. The documentation consists both of prose and API documentation. All user-facing classes and functions are included in the API documentation, under the `docs/api` folder using the [mkdocstrings](https://mkdocstrings.github.io/) extension. Add any new public functions or classes to the relevant markdown file in `docs/api/*.md`. Any new features or important usage information should be included in the user-guide (`docs/user-guide`). Any changes should also be included as a new file in the `changes` directory. diff --git a/docs/index.md b/docs/index.md index b61646d6a6..b8c2b07ee7 100644 --- a/docs/index.md +++ b/docs/index.md @@ -21,7 +21,7 @@ Zarr-Python is a Python library for reading and writing Zarr groups and arrays. ## Installation -Zarr requires Python 3.11 or higher. You can install it via `pip`: +Zarr requires Python 3.12 or higher. You can install it via `pip`: ```bash pip install zarr diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md index 6c1414e81a..c902acf171 100644 --- a/docs/user-guide/installation.md +++ b/docs/user-guide/installation.md @@ -4,7 +4,7 @@ Required dependencies include: -- [Python](https://docs.python.org/3/) (3.11 or later) +- [Python](https://docs.python.org/3/) (3.12 or later) - [packaging](https://packaging.pypa.io) (22.0 or later) - [numpy](https://numpy.org) (2.0 or later) - [numcodecs](https://numcodecs.readthedocs.io) (0.14 or later) diff --git a/examples/custom_dtype/custom_dtype.py b/examples/custom_dtype/custom_dtype.py index ec38d782b6..eee510349b 100644 --- a/examples/custom_dtype/custom_dtype.py +++ b/examples/custom_dtype/custom_dtype.py @@ -1,5 +1,5 @@ # /// script -# requires-python = ">=3.11" +# requires-python = ">=3.12" # dependencies = [ # "zarr @ git+https://github.com/zarr-developers/zarr-python.git@main", # "ml_dtypes==0.5.1", diff --git a/pyproject.toml b/pyproject.toml index b1077e3e5d..8277c3f752 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,11 +29,11 @@ maintainers = [ { name = "Tom Augspurger", email = "tom.w.augspurger@gmail.com" }, { name = "Deepak Cherian" } ] -requires-python = ">=3.11" +requires-python = ">=3.12" # If you add a new dependency here, please also add it to .pre-commit-config.yaml dependencies = [ 'packaging>=22.0', - 'numpy>=2.0', + 'numpy>=2', 'numcodecs>=0.14', 'google-crc32c>=1.5', 'typing_extensions>=4.12', @@ -52,9 +52,9 @@ classifiers = [ 'Topic :: Software Development :: Libraries :: Python Modules', 'Operating System :: Unix', 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.11', 'Programming Language :: Python :: 3.12', 'Programming Language :: Python :: 3.13', + 'Programming Language :: Python :: 3.14', ] license = "MIT" license-files = ["LICENSE.txt"] @@ -161,7 +161,7 @@ COV_CORE_CONFIG = ".coveragerc" COV_CORE_DATAFILE = ".coverage.eager" [[tool.hatch.envs.test.matrix]] -python = ["3.11", "3.12", "3.13"] +python = ["3.12", "3.13", "3.14"] deps = ["minimal", "optional"] [tool.hatch.envs.test.overrides] @@ -192,7 +192,7 @@ extra-dependencies = [ features = ["gpu"] [[tool.hatch.envs.gputest.matrix]] -python = ["3.11", "3.12", "3.13"] +python = ["3.12", "3.13"] [tool.hatch.envs.gputest.scripts] run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-report xml --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks" @@ -200,7 +200,7 @@ run = "run-coverage --no-cov" [tool.hatch.envs.upstream] template = 'test' -python = "3.13" +python = "3.14" extra-dependencies = [ 'packaging @ git+https://github.com/pypa/packaging', 'numpy', # from scientific-python-nightly-wheels @@ -223,7 +223,7 @@ description = """Test environment for minimum supported dependencies See Spec 0000 for details and drop schedule: https://scientific-python.org/specs/spec-0000/ """ template = "test" -python = "3.11" +python = "3.12" features = ["remote"] dependency-groups = ["remote-tests"] extra-dependencies = [ @@ -232,12 +232,15 @@ extra-dependencies = [ 'numcodecs==0.14.*', # 0.14 needed for zarr3 codecs 'fsspec==2023.10.0', 's3fs==2023.10.0', - 'universal_pathlib==0.0.22', + 'universal_pathlib==0.2.0', 'typing_extensions==4.12.*', 'donfig==0.8.*', 'obstore==0.5.*', ] +[tool.hatch.envs.defaults] +installer = "uv" + [tool.hatch.envs.docs] features = ['remote'] dependency-groups = ['docs'] @@ -343,7 +346,7 @@ ignore = [ "tests/**" = ["ANN001", "ANN201", "RUF029", "SIM117", "SIM300"] [tool.mypy] -python_version = "3.11" +python_version = "3.12" ignore_missing_imports = true namespace_packages = false @@ -409,7 +412,7 @@ filterwarnings = [ # s3fs finalizers can fail during session cleanup when aiobotocore sessions are garbage # collected without being entered. This is a known issue in s3fs/aiobotocore, and pytest # per-test filterwarnings markers can't catch it (https://github.com/pytest-dev/pytest/issues/14096). - "ignore:Exception ignored in[\\s\\S]*Session was never entered:pytest.PytestUnraisableExceptionWarning", + "ignore:Exception ignored ((on calling weakref callback)|(in[\\s\\S]*Session was never entered)):pytest.PytestUnraisableExceptionWarning", ] markers = [ "asyncio: mark test as asyncio test", diff --git a/src/zarr/_compat.py b/src/zarr/_compat.py index ae973d6292..061e75dbe4 100644 --- a/src/zarr/_compat.py +++ b/src/zarr/_compat.py @@ -2,7 +2,7 @@ from collections.abc import Callable from functools import wraps from inspect import Parameter, signature -from typing import TYPE_CHECKING, Any, TypeVar +from typing import TYPE_CHECKING, Any import numpy as np from packaging.version import Version @@ -12,12 +12,10 @@ if TYPE_CHECKING: from numpy.typing import NDArray -T = TypeVar("T") - # Based off https://github.com/scikit-learn/scikit-learn/blob/e87b32a81c70abed8f2e97483758eb64df8255e9/sklearn/utils/validation.py#L63 -def _deprecate_positional_args( +def _deprecate_positional_args[T]( func: Callable[..., T] | None = None, *, version: str = "3.1.0" ) -> Callable[..., T]: """Decorator for methods that issues warnings for positional arguments. diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index d0fb42bd95..50472e807a 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -2,7 +2,7 @@ from abc import abstractmethod from collections.abc import Mapping -from typing import TYPE_CHECKING, Generic, Literal, Protocol, TypeGuard, TypeVar, runtime_checkable +from typing import TYPE_CHECKING, Literal, Protocol, TypeGuard, runtime_checkable from typing_extensions import ReadOnly, TypedDict @@ -43,13 +43,11 @@ class GetResult(TypedDict): status: Literal["present", "missing"] -CodecInput = TypeVar("CodecInput", bound=NDBuffer | Buffer) -CodecOutput = TypeVar("CodecOutput", bound=NDBuffer | Buffer) +type CodecInput = NDBuffer | Buffer +type CodecOutput = NDBuffer | Buffer -TName = TypeVar("TName", bound=str, covariant=True) - -class CodecJSON_V2(TypedDict, Generic[TName]): +class CodecJSON_V2[TName: str](TypedDict): """The JSON representation of a codec for Zarr V2""" id: ReadOnly[TName] @@ -85,7 +83,7 @@ def _encode_sync( ) -> NDBuffer | Buffer | None: ... -class BaseCodec(Metadata, Generic[CodecInput, CodecOutput]): +class BaseCodec[CI: CodecInput, CO: CodecOutput](Metadata): """Generic base class for codecs. Codecs can be registered via zarr.codecs.registry. @@ -163,13 +161,13 @@ def validate( The array chunk grid """ - async def _decode_single(self, chunk_data: CodecOutput, chunk_spec: ArraySpec) -> CodecInput: + async def _decode_single(self, chunk_data: CO, chunk_spec: ArraySpec) -> CI: raise NotImplementedError # pragma: no cover async def decode( self, - chunks_and_specs: Iterable[tuple[CodecOutput | None, ArraySpec]], - ) -> Iterable[CodecInput | None]: + chunks_and_specs: Iterable[tuple[CO | None, ArraySpec]], + ) -> Iterable[CI | None]: """Decodes a batch of chunks. Chunks can be None in which case they are ignored by the codec. @@ -180,25 +178,23 @@ async def decode( Returns ------- - Iterable[CodecInput | None] + Iterable[CI | None] """ return await _batching_helper(self._decode_single, chunks_and_specs) - async def _encode_single( - self, chunk_data: CodecInput, chunk_spec: ArraySpec - ) -> CodecOutput | None: + async def _encode_single(self, chunk_data: CI, chunk_spec: ArraySpec) -> CO | None: raise NotImplementedError # pragma: no cover async def encode( self, - chunks_and_specs: Iterable[tuple[CodecInput | None, ArraySpec]], - ) -> Iterable[CodecOutput | None]: + chunks_and_specs: Iterable[tuple[CI | None, ArraySpec]], + ) -> Iterable[CO | None]: """Encodes a batch of chunks. Chunks can be None in which case they are ignored by the codec. Parameters ---------- - chunks_and_specs : Iterable[tuple[CodecInput | None, ArraySpec]] + chunks_and_specs : Iterable[tuple[CI | None, ArraySpec]] Ordered set of to-be-encoded chunks with their accompanying chunk spec. Returns @@ -491,10 +487,10 @@ async def write( ... -async def _batching_helper( - func: Callable[[CodecInput, ArraySpec], Awaitable[CodecOutput | None]], - batch_info: Iterable[tuple[CodecInput | None, ArraySpec]], -) -> list[CodecOutput | None]: +async def _batching_helper[CI: CodecInput, CO: CodecOutput]( + func: Callable[[CI, ArraySpec], Awaitable[CO | None]], + batch_info: Iterable[tuple[CI | None, ArraySpec]], +) -> list[CO | None]: return await concurrent_map( list(batch_info), _noop_for_none(func), @@ -502,10 +498,10 @@ async def _batching_helper( ) -def _noop_for_none( - func: Callable[[CodecInput, ArraySpec], Awaitable[CodecOutput | None]], -) -> Callable[[CodecInput | None, ArraySpec], Awaitable[CodecOutput | None]]: - async def wrap(chunk: CodecInput | None, chunk_spec: ArraySpec) -> CodecOutput | None: +def _noop_for_none[CI: CodecInput, CO: CodecOutput]( + func: Callable[[CI, ArraySpec], Awaitable[CO | None]], +) -> Callable[[CI | None, ArraySpec], Awaitable[CO | None]]: + async def wrap(chunk: CI | None, chunk_spec: ArraySpec) -> CO | None: if chunk is None: return None return await func(chunk, chunk_spec) diff --git a/src/zarr/abc/numcodec.py b/src/zarr/abc/numcodec.py index 76eac1d898..d60422209a 100644 --- a/src/zarr/abc/numcodec.py +++ b/src/zarr/abc/numcodec.py @@ -1,6 +1,4 @@ -from typing import Any, Self, TypeGuard - -from typing_extensions import Protocol +from typing import Any, Protocol, Self, TypeGuard class Numcodec(Protocol): diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index d2ab353d43..600df17ee5 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -12,7 +12,7 @@ if TYPE_CHECKING: from collections.abc import AsyncGenerator, AsyncIterator, Iterable from types import TracebackType - from typing import Any, Self, TypeAlias + from typing import Any, Self from zarr.core.buffer import Buffer, BufferPrototype @@ -54,7 +54,7 @@ class SuffixByteRequest: """The number of bytes from the suffix to request.""" -ByteRequest: TypeAlias = RangeByteRequest | OffsetByteRequest | SuffixByteRequest +type ByteRequest = RangeByteRequest | OffsetByteRequest | SuffixByteRequest class Store(ABC): diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 66cf3bad7e..c776176665 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -3,7 +3,7 @@ import asyncio import dataclasses import warnings -from typing import TYPE_CHECKING, Any, Literal, NotRequired, TypeAlias, TypedDict, cast +from typing import TYPE_CHECKING, Any, Literal, NotRequired, TypedDict, cast import numpy as np import numpy.typing as npt @@ -61,7 +61,7 @@ from zarr.types import AnyArray, AnyAsyncArray # TODO: this type could use some more thought - ArrayLike: TypeAlias = AnyAsyncArray | AnyArray | npt.NDArray[Any] + type ArrayLike = AnyAsyncArray | AnyArray | npt.NDArray[Any] PathLike = str __all__ = [ diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index b82c77fa9c..b5212656f4 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -10,9 +10,7 @@ from typing import ( TYPE_CHECKING, Any, - Generic, Literal, - TypeAlias, TypedDict, cast, overload, @@ -107,7 +105,6 @@ ArrayV2Metadata, ArrayV2MetadataDict, ArrayV3Metadata, - T_ArrayMetadata, ) from zarr.core.metadata.io import save_metadata from zarr.core.metadata.v2 import ( @@ -279,7 +276,7 @@ async def get_array_metadata( @dataclass(frozen=True) -class AsyncArray(Generic[T_ArrayMetadata]): +class AsyncArray[T_ArrayMetadata: (ArrayV2Metadata, ArrayV3Metadata)]: """ An asynchronous array class representing a chunked array stored in a Zarr store. @@ -1947,7 +1944,7 @@ def _info( # TODO: Array can be a frozen data class again once property setters (e.g. shape) are removed @dataclass(frozen=False) -class Array(Generic[T_ArrayMetadata]): +class Array[T_ArrayMetadata: (ArrayV2Metadata, ArrayV3Metadata)]: """ A Zarr array. """ @@ -4220,7 +4217,7 @@ async def _shards_initialized( ) -FiltersLike: TypeAlias = ( +type FiltersLike = ( Iterable[dict[str, JSON] | ArrayArrayCodec | Numcodec] | ArrayArrayCodec | Iterable[Numcodec] @@ -4229,9 +4226,9 @@ async def _shards_initialized( | None ) # Union of acceptable types for users to pass in for both v2 and v3 compressors -CompressorLike: TypeAlias = dict[str, JSON] | BytesBytesCodec | Numcodec | Literal["auto"] | None +type CompressorLike = dict[str, JSON] | BytesBytesCodec | Numcodec | Literal["auto"] | None -CompressorsLike: TypeAlias = ( +type CompressorsLike = ( Iterable[dict[str, JSON] | BytesBytesCodec | Numcodec] | Mapping[str, JSON] | BytesBytesCodec @@ -4239,7 +4236,7 @@ async def _shards_initialized( | Literal["auto"] | None ) -SerializerLike: TypeAlias = dict[str, JSON] | ArrayBytesCodec | Literal["auto"] +type SerializerLike = dict[str, JSON] | ArrayBytesCodec | Literal["auto"] class ShardsConfigParam(TypedDict): @@ -4247,7 +4244,7 @@ class ShardsConfigParam(TypedDict): index_location: ShardingCodecIndexLocation | None -ShardsLike: TypeAlias = tuple[int, ...] | ShardsConfigParam | Literal["auto"] +type ShardsLike = tuple[int, ...] | ShardsConfigParam | Literal["auto"] async def from_array( diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index 9602a55258..ddfb179213 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -267,7 +267,7 @@ def as_buffer_like(self) -> BytesLike: ------- An object that implements the Python buffer protocol """ - return memoryview(self.as_numpy_array()) # type: ignore[arg-type] + return memoryview(self.as_numpy_array()) def to_bytes(self) -> bytes: """Returns the buffer as `bytes` (host memory). diff --git a/src/zarr/core/chunk_key_encodings.py b/src/zarr/core/chunk_key_encodings.py index 9eef80656d..098f2c8981 100644 --- a/src/zarr/core/chunk_key_encodings.py +++ b/src/zarr/core/chunk_key_encodings.py @@ -2,7 +2,7 @@ from abc import ABC, abstractmethod from dataclasses import dataclass -from typing import TYPE_CHECKING, Any, ClassVar, Literal, TypeAlias, TypedDict, cast +from typing import TYPE_CHECKING, Any, ClassVar, Literal, TypedDict, cast if TYPE_CHECKING: from typing import NotRequired, Self @@ -62,7 +62,7 @@ def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: """ -ChunkKeyEncodingLike: TypeAlias = ( +type ChunkKeyEncodingLike = ( dict[str, JSON] | ChunkKeyEncodingParams | ChunkKeyEncoding | NamedConfig[str, Any] ) diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index e25863ae23..d8c4cabdf9 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -2,7 +2,7 @@ from dataclasses import dataclass from itertools import islice, pairwise -from typing import TYPE_CHECKING, Any, TypeVar +from typing import TYPE_CHECKING, Any from warnings import warn from zarr.abc.codec import ( @@ -31,11 +31,8 @@ from zarr.core.chunk_grids import ChunkGrid from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType -T = TypeVar("T") -U = TypeVar("U") - -def _unzip2(iterable: Iterable[tuple[T, U]]) -> tuple[list[T], list[U]]: +def _unzip2[T, U](iterable: Iterable[tuple[T, U]]) -> tuple[list[T], list[U]]: out0: list[T] = [] out1: list[U] = [] for item0, item1 in iterable: @@ -44,7 +41,7 @@ def _unzip2(iterable: Iterable[tuple[T, U]]) -> tuple[list[T], list[U]]: return (out0, out1) -def batched(iterable: Iterable[T], n: int) -> Iterable[tuple[T, ...]]: +def batched[T](iterable: Iterable[T], n: int) -> Iterable[tuple[T, ...]]: if n < 1: raise ValueError("n must be at least one") it = iter(iterable) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index a61271a941..077f459d3b 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -12,11 +12,9 @@ TYPE_CHECKING, Any, Final, - Generic, Literal, NotRequired, TypedDict, - TypeVar, cast, overload, ) @@ -50,11 +48,8 @@ DimensionNamesLike = Iterable[str | None] | None DimensionNames = DimensionNamesLike # for backwards compatibility -TName = TypeVar("TName", bound=str) -TConfig = TypeVar("TConfig", bound=Mapping[str, object]) - -class NamedConfig(TypedDict, Generic[TName, TConfig]): +class NamedConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): """ A typed dictionary representing an object with a name and configuration, where the configuration is an optional mapping of string keys to values, e.g. another typed dictionary or a JSON object. @@ -70,7 +65,7 @@ class NamedConfig(TypedDict, Generic[TName, TConfig]): """The configuration of the object. Not required.""" -class NamedRequiredConfig(TypedDict, Generic[TName, TConfig]): +class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): """ A typed dictionary representing an object with a name and configuration, where the configuration is a mapping of string keys to values, e.g. another typed dictionary or a JSON object. @@ -96,11 +91,7 @@ def ceildiv(a: float, b: float) -> int: return math.ceil(a / b) -T = TypeVar("T", bound=tuple[Any, ...]) -V = TypeVar("V") - - -async def concurrent_map( +async def concurrent_map[T: tuple[Any, ...], V]( items: Iterable[T], func: Callable[..., Awaitable[V]], limit: int | None = None, @@ -118,15 +109,12 @@ async def run(item: tuple[Any]) -> V: return await asyncio.gather(*[asyncio.ensure_future(run(item)) for item in items]) -E = TypeVar("E", bound=Enum) - - -def enum_names(enum: type[E]) -> Iterator[str]: +def enum_names[E: Enum](enum: type[E]) -> Iterator[str]: for item in enum: yield item.name -def parse_enum(data: object, cls: type[E]) -> E: +def parse_enum[E: Enum](data: object, cls: type[E]) -> E: if isinstance(data, cls): return data if not isinstance(data, str): diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index 1049a2063f..7c7b0fc5c6 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -1,7 +1,7 @@ from __future__ import annotations from collections.abc import Sequence -from typing import TYPE_CHECKING, Final, TypeAlias +from typing import TYPE_CHECKING, Final from zarr.core.dtype.common import ( DataTypeValidationError, @@ -149,7 +149,7 @@ VLEN_UTF8_ALIAS: Final = ("str", str, "string") # This type models inputs that can be coerced to a ZDType -ZDTypeLike: TypeAlias = npt.DTypeLike | ZDType[TBaseDType, TBaseScalar] | Mapping[str, JSON] | str +type ZDTypeLike = npt.DTypeLike | ZDType[TBaseDType, TBaseScalar] | Mapping[str, JSON] | str for dtype in ANY_DTYPE: # mypy does not know that all the elements of ANY_DTYPE are subclasses of ZDType diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index 6b70f595ba..87e46b53d2 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -6,11 +6,9 @@ from typing import ( ClassVar, Final, - Generic, Literal, TypedDict, TypeGuard, - TypeVar, ) from typing_extensions import ReadOnly @@ -53,13 +51,10 @@ # This models the type of the name a dtype might have in zarr v2 array metadata DTypeName_V2 = StructuredName_V2 | str -TDTypeNameV2_co = TypeVar("TDTypeNameV2_co", bound=DTypeName_V2, covariant=True) -TObjectCodecID_co = TypeVar("TObjectCodecID_co", bound=None | str, covariant=True) - -class DTypeConfig_V2(TypedDict, Generic[TDTypeNameV2_co, TObjectCodecID_co]): - name: ReadOnly[TDTypeNameV2_co] - object_codec_id: ReadOnly[TObjectCodecID_co] +class DTypeConfig_V2[TDTypeNameV2: DTypeName_V2, TObjectCodecID: None | str](TypedDict): + name: ReadOnly[TDTypeNameV2] + object_codec_id: ReadOnly[TObjectCodecID] DTypeSpec_V2 = DTypeConfig_V2[DTypeName_V2, None | str] diff --git a/src/zarr/core/dtype/npy/common.py b/src/zarr/core/dtype/npy/common.py index 107b3bd12d..f413f5f678 100644 --- a/src/zarr/core/dtype/npy/common.py +++ b/src/zarr/core/dtype/npy/common.py @@ -15,7 +15,6 @@ SupportsIndex, SupportsInt, TypeGuard, - TypeVar, ) import numpy as np @@ -67,20 +66,6 @@ NumpyEndiannessStr = Literal[">", "<", "="] NUMPY_ENDIANNESS_STR: Final = ">", "<", "=" -TFloatDType_co = TypeVar( - "TFloatDType_co", - bound=np.dtypes.Float16DType | np.dtypes.Float32DType | np.dtypes.Float64DType, - covariant=True, -) -TFloatScalar_co = TypeVar( - "TFloatScalar_co", bound=np.float16 | np.float32 | np.float64, covariant=True -) - -TComplexDType_co = TypeVar( - "TComplexDType_co", bound=np.dtypes.Complex64DType | np.dtypes.Complex128DType, covariant=True -) -TComplexScalar_co = TypeVar("TComplexScalar_co", bound=np.complex64 | np.complex128, covariant=True) - def endianness_from_numpy_str(endianness: NumpyEndiannessStr) -> EndiannessStr: """ diff --git a/src/zarr/core/dtype/npy/complex.py b/src/zarr/core/dtype/npy/complex.py index 99abee5e24..76a0f05869 100644 --- a/src/zarr/core/dtype/npy/complex.py +++ b/src/zarr/core/dtype/npy/complex.py @@ -22,8 +22,6 @@ ) from zarr.core.dtype.npy.common import ( ComplexLike, - TComplexDType_co, - TComplexScalar_co, check_json_complex_float_v2, check_json_complex_float_v3, complex_float_from_json_v2, @@ -40,7 +38,10 @@ @dataclass(frozen=True) -class BaseComplex(ZDType[TComplexDType_co, TComplexScalar_co], HasEndianness, HasItemSize): +class BaseComplex[ + DType: np.dtypes.Complex64DType | np.dtypes.Complex128DType, + Scalar: np.complex64 | np.complex128, +](ZDType[DType, Scalar], HasEndianness, HasItemSize): """ A base class for Zarr data types that wrap NumPy complex float data types. """ @@ -74,18 +75,18 @@ def from_native_dtype(cls, dtype: TBaseDType) -> Self: f"Invalid data type: {dtype}. Expected an instance of {cls.dtype_cls}" ) - def to_native_dtype(self) -> TComplexDType_co: + def to_native_dtype(self) -> DType: """ Convert this class to a NumPy complex dtype with the appropriate byte order. Returns ------- - TComplexDType_co + DType A NumPy data type object representing the complex data type with the specified byte order. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[no-any-return,call-overload] @classmethod def _check_json_v2(cls, data: DTypeJSON) -> TypeGuard[DTypeConfig_V2[str, None]]: @@ -235,7 +236,7 @@ def _check_scalar(self, data: object) -> TypeGuard[ComplexLike]: """ return isinstance(data, ComplexLike) - def _cast_scalar_unchecked(self, data: ComplexLike) -> TComplexScalar_co: + def _cast_scalar_unchecked(self, data: ComplexLike) -> Scalar: """ Cast the provided scalar data to the native scalar type of this class. @@ -246,7 +247,7 @@ def _cast_scalar_unchecked(self, data: ComplexLike) -> TComplexScalar_co: Returns ------- - TComplexScalar_co + Scalar The casted data as a numpy complex scalar. Notes @@ -256,7 +257,7 @@ def _cast_scalar_unchecked(self, data: ComplexLike) -> TComplexScalar_co: """ return self.to_native_dtype().type(data) # type: ignore[return-value] - def cast_scalar(self, data: object) -> TComplexScalar_co: + def cast_scalar(self, data: object) -> Scalar: """ Attempt to cast a given object to a numpy complex scalar. @@ -267,7 +268,7 @@ def cast_scalar(self, data: object) -> TComplexScalar_co: Returns ------- - TComplexScalar_co + Scalar The data cast as a numpy complex scalar. Raises @@ -283,7 +284,7 @@ def cast_scalar(self, data: object) -> TComplexScalar_co: ) raise TypeError(msg) - def default_scalar(self) -> TComplexScalar_co: + def default_scalar(self) -> Scalar: """ Get the default value, which is 0 cast to this dtype @@ -294,7 +295,7 @@ def default_scalar(self) -> TComplexScalar_co: """ return self._cast_scalar_unchecked(0) - def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TComplexScalar_co: + def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> Scalar: """ Read a JSON-serializable value as a numpy float. @@ -307,7 +308,7 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TComplexSc Returns ------- - TScalar_co + Scalar The numpy float. """ if zarr_format == 2: diff --git a/src/zarr/core/dtype/npy/float.py b/src/zarr/core/dtype/npy/float.py index 2a23cb429d..668e169d8b 100644 --- a/src/zarr/core/dtype/npy/float.py +++ b/src/zarr/core/dtype/npy/float.py @@ -15,8 +15,6 @@ ) from zarr.core.dtype.npy.common import ( FloatLike, - TFloatDType_co, - TFloatScalar_co, check_json_float_v2, check_json_float_v3, check_json_floatish_str, @@ -34,7 +32,10 @@ @dataclass(frozen=True) -class BaseFloat(ZDType[TFloatDType_co, TFloatScalar_co], HasEndianness, HasItemSize): +class BaseFloat[ + DType: np.dtypes.Float16DType | np.dtypes.Float32DType | np.dtypes.Float64DType, + Scalar: np.float16 | np.float32 | np.float64, +](ZDType[DType, Scalar], HasEndianness, HasItemSize): """ A base class for Zarr data types that wrap NumPy float data types. """ @@ -63,17 +64,17 @@ def from_native_dtype(cls, dtype: TBaseDType) -> Self: f"Invalid data type: {dtype}. Expected an instance of {cls.dtype_cls}" ) - def to_native_dtype(self) -> TFloatDType_co: + def to_native_dtype(self) -> DType: """ Convert the wrapped data type to a NumPy data type. Returns ------- - TFloatDType_co + DType The NumPy data type. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[no-any-return,call-overload] @classmethod def _check_json_v2(cls, data: DTypeJSON) -> TypeGuard[DTypeConfig_V2[str, None]]: @@ -213,7 +214,7 @@ def _check_scalar(self, data: object) -> TypeGuard[FloatLike]: return True return isinstance(data, FloatLike) - def _cast_scalar_unchecked(self, data: FloatLike) -> TFloatScalar_co: + def _cast_scalar_unchecked(self, data: FloatLike) -> Scalar: """ Cast a scalar value to a NumPy float scalar. @@ -224,12 +225,12 @@ def _cast_scalar_unchecked(self, data: FloatLike) -> TFloatScalar_co: Returns ------- - TFloatScalar_co + Scalar The NumPy float scalar. """ return self.to_native_dtype().type(data) # type: ignore[return-value] - def cast_scalar(self, data: object) -> TFloatScalar_co: + def cast_scalar(self, data: object) -> Scalar: """ Cast a scalar value to a NumPy float scalar. @@ -240,7 +241,7 @@ def cast_scalar(self, data: object) -> TFloatScalar_co: Returns ------- - TFloatScalar_co + Scalar The NumPy float scalar. """ if self._check_scalar(data): @@ -251,18 +252,18 @@ def cast_scalar(self, data: object) -> TFloatScalar_co: ) raise TypeError(msg) - def default_scalar(self) -> TFloatScalar_co: + def default_scalar(self) -> Scalar: """ Get the default value, which is 0 cast to this zdtype. Returns ------- - TFloatScalar_co + Scalar The default value. """ return self._cast_scalar_unchecked(0) - def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TFloatScalar_co: + def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> Scalar: """ Read a JSON-serializable value as a NumPy float scalar. @@ -275,7 +276,7 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TFloatScal Returns ------- - TFloatScalar_co + Scalar The NumPy float scalar. """ if zarr_format == 2: diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index e5007b7acb..e5b8fa6aa1 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -9,7 +9,6 @@ SupportsIndex, SupportsInt, TypeGuard, - TypeVar, overload, ) @@ -48,13 +47,15 @@ _NumpyIntScalar = ( np.int8 | np.int16 | np.int32 | np.int64 | np.uint8 | np.uint16 | np.uint32 | np.uint64 ) -TIntDType_co = TypeVar("TIntDType_co", bound=_NumpyIntDType, covariant=True) -TIntScalar_co = TypeVar("TIntScalar_co", bound=_NumpyIntScalar, covariant=True) + IntLike = SupportsInt | SupportsIndex | bytes | str @dataclass(frozen=True) -class BaseInt(ZDType[TIntDType_co, TIntScalar_co], HasItemSize): +class BaseInt[ + DType: _NumpyIntDType, + Scalar: np.int8 | np.int16 | np.int32 | np.int64 | np.uint8 | np.uint16 | np.uint32 | np.uint64, +](ZDType[DType, Scalar], HasItemSize): """ A base class for integer data types in Zarr. @@ -129,7 +130,7 @@ def _check_scalar(self, data: object) -> TypeGuard[IntLike]: return isinstance(data, IntLike) - def _cast_scalar_unchecked(self, data: IntLike) -> TIntScalar_co: + def _cast_scalar_unchecked(self, data: IntLike) -> Scalar: """ Casts a given scalar value to the native integer scalar type without type checking. @@ -140,13 +141,13 @@ def _cast_scalar_unchecked(self, data: IntLike) -> TIntScalar_co: Returns ------- - TIntScalar_co + Scalar The casted integer scalar of the native dtype. """ return self.to_native_dtype().type(data) # type: ignore[return-value] - def cast_scalar(self, data: object) -> TIntScalar_co: + def cast_scalar(self, data: object) -> Scalar: """ Attempt to cast a given object to a NumPy integer scalar. @@ -157,7 +158,7 @@ def cast_scalar(self, data: object) -> TIntScalar_co: Returns ------- - TIntScalar_co + Scalar The data cast as a NumPy integer scalar. Raises @@ -174,18 +175,18 @@ def cast_scalar(self, data: object) -> TIntScalar_co: ) raise TypeError(msg) - def default_scalar(self) -> TIntScalar_co: + def default_scalar(self) -> Scalar: """ Get the default value, which is 0 cast to this dtype. Returns ------- - TIntScalar_co + Scalar The default value. """ return self._cast_scalar_unchecked(0) - def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TIntScalar_co: + def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> Scalar: """ Read a JSON-serializable value as a NumPy int scalar. @@ -198,7 +199,7 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> TIntScalar Returns ------- - TIntScalar_co + Scalar The NumPy int scalar. Raises diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index 904280a330..069d0b128d 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -33,7 +33,7 @@ endianness_to_numpy_str, get_endianness_from_numpy_dtype, ) -from zarr.core.dtype.wrapper import TDType_co, ZDType +from zarr.core.dtype.wrapper import ZDType if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat @@ -453,7 +453,7 @@ class VariableLengthUTF8JSON_V2(DTypeConfig_V2[Literal["|O"], Literal["vlen-utf8 # If NumPy 2 is installed, then VariableLengthUTF8 is defined with the NumPy variable length # string dtype as the native dtype. Otherwise, VariableLengthUTF8 is defined with the NumPy object # dtype as the native dtype. -class UTF8Base(ZDType[TDType_co, str], HasObjectCodec): +class UTF8Base[DType: TBaseDType](ZDType[DType, str], HasObjectCodec): """ A base class for variable-length UTF-8 string data types. @@ -740,7 +740,7 @@ class VariableLengthUTF8(UTF8Base[np.dtypes.StringDType]): # type: ignore[type- The object codec ID for this data type. """ - dtype_cls = np.dtypes.StringDType + dtype_cls = np.dtypes.StringDType # type: ignore[assignment] @classmethod def from_native_dtype(cls, dtype: TBaseDType) -> Self: diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index 402a140321..1a46f77983 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -9,7 +9,6 @@ Self, TypedDict, TypeGuard, - TypeVar, cast, get_args, overload, @@ -90,16 +89,6 @@ def check_json_time(data: JSON) -> TypeGuard[Literal["NaT"] | int]: return check_json_int(data) or data == "NaT" -BaseTimeDType_co = TypeVar( - "BaseTimeDType_co", - bound=np.dtypes.TimeDelta64DType | np.dtypes.DateTime64DType, - covariant=True, -) -BaseTimeScalar_co = TypeVar( - "BaseTimeScalar_co", bound=np.timedelta64 | np.datetime64, covariant=True -) - - class TimeConfig(TypedDict): """ The configuration for the numpy.timedelta64 or numpy.datetime64 data type in Zarr V3. @@ -217,7 +206,10 @@ class DateTime64JSON_V2(DTypeConfig_V2[str, None]): @dataclass(frozen=True, kw_only=True, slots=True) -class TimeDTypeBase(ZDType[BaseTimeDType_co, BaseTimeScalar_co], HasEndianness, HasItemSize): +class TimeDTypeBase[ + DType: np.dtypes.TimeDelta64DType | np.dtypes.DateTime64DType, + Scalar: np.timedelta64 | np.datetime64, +](ZDType[DType, Scalar], HasEndianness, HasItemSize): """ A base class for data types that represent time via the NumPy TimeDelta64 and DateTime64 data types. @@ -275,7 +267,7 @@ def from_native_dtype(cls, dtype: TBaseDType) -> Self: f"Invalid data type: {dtype}. Expected an instance of {cls.dtype_cls}" ) - def to_native_dtype(self) -> BaseTimeDType_co: + def to_native_dtype(self) -> DType: # Numpy does not allow creating datetime64 or timedelta64 via # np.dtypes.{dtype_name}() # so we use np.dtype with a formatted string. @@ -285,7 +277,7 @@ def to_native_dtype(self) -> BaseTimeDType_co: Returns ------- - BaseTimeDType_co + DType A NumPy data type object representing the time data type with the specified unit, scale factor, and byte order. """ diff --git a/src/zarr/core/dtype/wrapper.py b/src/zarr/core/dtype/wrapper.py index fdc5f747f0..42d5d88473 100644 --- a/src/zarr/core/dtype/wrapper.py +++ b/src/zarr/core/dtype/wrapper.py @@ -28,11 +28,9 @@ from typing import ( TYPE_CHECKING, ClassVar, - Generic, Literal, Self, TypeGuard, - TypeVar, overload, ) @@ -44,20 +42,14 @@ # This the upper bound for the scalar types we support. It's numpy scalars + str, # because the new variable-length string dtype in numpy does not have a corresponding scalar type -TBaseScalar = np.generic | str | bytes +type TBaseScalar = np.generic | str | bytes # This is the bound for the dtypes that we support. If we support non-numpy dtypes, # then this bound will need to be widened. -TBaseDType = np.dtype[np.generic] - -# These two type parameters are covariant because we want -# x : ZDType[BaseDType, BaseScalar] = ZDType[SubDType, SubScalar] -# to type check -TScalar_co = TypeVar("TScalar_co", bound=TBaseScalar, covariant=True) -TDType_co = TypeVar("TDType_co", bound=TBaseDType, covariant=True) +type TBaseDType = np.dtype[np.generic] @dataclass(frozen=True, kw_only=True, slots=True) -class ZDType(ABC, Generic[TDType_co, TScalar_co]): +class ZDType[DType: TBaseDType, Scalar: TBaseScalar](ABC): """ Abstract base class for wrapping native array data types, e.g. numpy dtypes @@ -71,11 +63,11 @@ class variable, and it should generally be unique across different data types. """ # this class will create a native data type - dtype_cls: ClassVar[type[TDType_co]] + dtype_cls: ClassVar[type[TBaseDType]] _zarr_v3_name: ClassVar[str] @classmethod - def _check_native_dtype(cls: type[Self], dtype: TBaseDType) -> TypeGuard[TDType_co]: + def _check_native_dtype(cls: type[Self], dtype: TBaseDType) -> TypeGuard[DType]: """ Check that a native data type matches the dtype_cls class attribute. @@ -120,7 +112,7 @@ def from_native_dtype(cls: type[Self], dtype: TBaseDType) -> Self: raise NotImplementedError # pragma: no cover @abstractmethod - def to_native_dtype(self: Self) -> TDType_co: + def to_native_dtype(self: Self) -> DType: """ Return an instance of the wrapped data type. This operation inverts ``from_native_dtype``. @@ -206,7 +198,7 @@ def _check_scalar(self, data: object) -> bool: raise NotImplementedError # pragma: no cover @abstractmethod - def cast_scalar(self, data: object) -> TScalar_co: + def cast_scalar(self, data: object) -> Scalar: """ Cast a python object to the wrapped scalar type. @@ -226,7 +218,7 @@ def cast_scalar(self, data: object) -> TScalar_co: raise NotImplementedError # pragma: no cover @abstractmethod - def default_scalar(self) -> TScalar_co: + def default_scalar(self) -> Scalar: """ Get the default scalar value for the wrapped data type. @@ -242,7 +234,7 @@ def default_scalar(self) -> TScalar_co: raise NotImplementedError # pragma: no cover @abstractmethod - def from_json_scalar(self: Self, data: JSON, *, zarr_format: ZarrFormat) -> TScalar_co: + def from_json_scalar(self: Self, data: JSON, *, zarr_format: ZarrFormat) -> Scalar: """ Read a JSON-serializable value as a scalar. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 17b8b541b1..760f91722c 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -9,7 +9,7 @@ from collections import defaultdict from dataclasses import asdict, dataclass, field, fields, replace from itertools import accumulate -from typing import TYPE_CHECKING, Literal, TypeVar, assert_never, cast, overload +from typing import TYPE_CHECKING, Literal, assert_never, cast, overload import numpy as np import numpy.typing as npt @@ -83,8 +83,6 @@ logger = logging.getLogger("zarr.group") -DefaultT = TypeVar("DefaultT") - def parse_zarr_format(data: Any) -> ZarrFormat: """Parse the zarr_format field from metadata.""" @@ -806,7 +804,7 @@ async def delitem(self, key: str) -> None: self.metadata.consolidated_metadata.metadata.pop(key, None) await self._save_metadata() - async def get( + async def get[DefaultT]( self, key: str, default: DefaultT | None = None ) -> AnyAsyncArray | AsyncGroup | DefaultT | None: """Obtain a group member, returning default if not found. @@ -1921,7 +1919,9 @@ def __getitem__(self, path: str) -> AnyArray | Group: else: return Group(obj) - def get(self, path: str, default: DefaultT | None = None) -> AnyArray | Group | DefaultT | None: + def get[DefaultT]( + self, path: str, default: DefaultT | None = None + ) -> AnyArray | Group | DefaultT | None: """Obtain a group member, returning default if not found. Parameters diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index f0c6c3c256..4461074a64 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -12,13 +12,10 @@ from typing import ( TYPE_CHECKING, Any, - Generic, Literal, NamedTuple, Protocol, - TypeAlias, TypeGuard, - TypeVar, cast, runtime_checkable, ) @@ -27,7 +24,8 @@ import numpy.typing as npt from zarr.core.common import ceildiv, product -from zarr.core.metadata import T_ArrayMetadata +from zarr.core.metadata.v2 import ArrayV2Metadata +from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.errors import ( ArrayIndexError, BoundsCheckError, @@ -79,7 +77,7 @@ class Indexer(Protocol): def __iter__(self) -> Iterator[ChunkProjection]: ... -_ArrayIndexingOrder: TypeAlias = Literal["lexicographic"] +type _ArrayIndexingOrder = Literal["lexicographic"] def _iter_grid( @@ -522,9 +520,6 @@ def replace_lists(selection: SelectionNormalized) -> SelectionNormalized: ) -T = TypeVar("T") - - def ensure_tuple(v: Any) -> SelectionNormalized: if not isinstance(v, tuple): v = (v,) @@ -1016,7 +1011,7 @@ def __setitem__(self, selection: OrthogonalSelection, value: npt.ArrayLike) -> N @dataclass(frozen=True) -class AsyncOIndex(Generic[T_ArrayMetadata]): +class AsyncOIndex[T_ArrayMetadata: (ArrayV2Metadata, ArrayV3Metadata)]: array: AsyncArray[T_ArrayMetadata] async def getitem(self, selection: OrthogonalSelection | AnyArray) -> NDArrayLikeOrScalar: @@ -1356,7 +1351,7 @@ def __setitem__( @dataclass(frozen=True) -class AsyncVIndex(Generic[T_ArrayMetadata]): +class AsyncVIndex[T_ArrayMetadata: (ArrayV2Metadata, ArrayV3Metadata)]: array: AsyncArray[T_ArrayMetadata] # TODO: develop Array generic and move zarr.Array[np.intp] | zarr.Array[np.bool_] to ArrayOfIntOrBool diff --git a/src/zarr/core/metadata/__init__.py b/src/zarr/core/metadata/__init__.py index 57385386b6..cacfc933b5 100644 --- a/src/zarr/core/metadata/__init__.py +++ b/src/zarr/core/metadata/__init__.py @@ -1,11 +1,8 @@ -from typing import TypeAlias, TypeVar - from .v2 import ArrayV2Metadata, ArrayV2MetadataDict from .v3 import ArrayMetadataJSON_V3, ArrayV3Metadata -ArrayMetadata: TypeAlias = ArrayV2Metadata | ArrayV3Metadata -ArrayMetadataDict: TypeAlias = ArrayV2MetadataDict | ArrayMetadataJSON_V3 -T_ArrayMetadata = TypeVar("T_ArrayMetadata", ArrayV2Metadata, ArrayV3Metadata, covariant=True) +ArrayMetadata = ArrayV2Metadata | ArrayV3Metadata +type ArrayMetadataDict = ArrayV2MetadataDict | ArrayMetadataJSON_V3 __all__ = [ "ArrayMetadata", diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 3204543426..f0781e1313 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -3,7 +3,7 @@ import warnings from collections.abc import Iterable, Sequence from functools import cached_property -from typing import TYPE_CHECKING, Any, TypeAlias, TypedDict, cast +from typing import TYPE_CHECKING, Any, TypedDict, cast from zarr.abc.metadata import Metadata from zarr.abc.numcodec import Numcodec, _is_numcodec @@ -22,8 +22,6 @@ from zarr.core.dtype.wrapper import ( TBaseDType, TBaseScalar, - TDType_co, - TScalar_co, ZDType, ) @@ -55,7 +53,7 @@ class ArrayV2MetadataDict(TypedDict): # Union of acceptable types for v2 compressors -CompressorLikev2: TypeAlias = dict[str, JSON] | Numcodec | None +type CompressorLikev2 = dict[str, JSON] | Numcodec | None @dataclass(frozen=True, kw_only=True) @@ -75,7 +73,7 @@ def __init__( self, *, shape: tuple[int, ...], - dtype: ZDType[TDType_co, TScalar_co], + dtype: ZDType[TBaseDType, TBaseScalar], chunks: tuple[int, ...], fill_value: Any, order: MemoryOrder, diff --git a/src/zarr/core/sync.py b/src/zarr/core/sync.py index fe435cc2b8..7bcb0bf034 100644 --- a/src/zarr/core/sync.py +++ b/src/zarr/core/sync.py @@ -6,7 +6,7 @@ import os import threading from concurrent.futures import ThreadPoolExecutor, wait -from typing import TYPE_CHECKING, TypeVar +from typing import TYPE_CHECKING from typing_extensions import ParamSpec @@ -20,7 +20,6 @@ P = ParamSpec("P") -T = TypeVar("T") # From https://github.com/fsspec/filesystem_spec/blob/master/fsspec/asyn.py @@ -110,7 +109,7 @@ def reset_resources_after_fork() -> None: os.register_at_fork(after_in_child=reset_resources_after_fork) -async def _runner(coro: Coroutine[Any, Any, T]) -> T | BaseException: +async def _runner[T](coro: Coroutine[Any, Any, T]) -> T | BaseException: """ Await a coroutine and return the result of running it. If awaiting the coroutine raises an exception, the exception will be returned. @@ -121,7 +120,7 @@ async def _runner(coro: Coroutine[Any, Any, T]) -> T | BaseException: return ex -def sync( +def sync[T]( coro: Coroutine[Any, Any, T], loop: asyncio.AbstractEventLoop | None = None, timeout: float | None = None, @@ -182,7 +181,7 @@ def _get_loop() -> asyncio.AbstractEventLoop: return loop[0] -async def _collect_aiterator(data: AsyncIterator[T]) -> tuple[T, ...]: +async def _collect_aiterator[T](data: AsyncIterator[T]) -> tuple[T, ...]: """ Collect an entire async iterator into a tuple """ @@ -190,7 +189,7 @@ async def _collect_aiterator(data: AsyncIterator[T]) -> tuple[T, ...]: return tuple(result) -def collect_aiterator(data: AsyncIterator[T]) -> tuple[T, ...]: +def collect_aiterator[T](data: AsyncIterator[T]) -> tuple[T, ...]: """ Synchronously collect an entire async iterator into a tuple. """ @@ -198,7 +197,7 @@ def collect_aiterator(data: AsyncIterator[T]) -> tuple[T, ...]: class SyncMixin: - def _sync(self, coroutine: Coroutine[Any, Any, T]) -> T: + def _sync[T](self, coroutine: Coroutine[Any, Any, T]) -> T: # TODO: refactor this to to take *args and **kwargs and pass those to the method # this should allow us to better type the sync wrapper return sync( @@ -206,14 +205,14 @@ def _sync(self, coroutine: Coroutine[Any, Any, T]) -> T: timeout=config.get("async.timeout"), ) - def _sync_iter(self, async_iterator: AsyncIterator[T]) -> list[T]: + def _sync_iter[T](self, async_iterator: AsyncIterator[T]) -> list[T]: async def iter_to_list() -> list[T]: return [item async for item in async_iterator] return self._sync(iter_to_list()) -async def _with_semaphore( +async def _with_semaphore[T]( func: Callable[[], Awaitable[T]], semaphore: asyncio.Semaphore | None = None ) -> T: """ diff --git a/src/zarr/registry.py b/src/zarr/registry.py index d0850a1387..a1938b575c 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -3,7 +3,7 @@ import warnings from collections import defaultdict from importlib.metadata import entry_points as get_entry_points -from typing import TYPE_CHECKING, Any, Generic, TypeVar +from typing import TYPE_CHECKING, Any from zarr.core.config import BadConfigError, config from zarr.core.dtype import data_type_registry @@ -39,10 +39,8 @@ "register_pipeline", ] -T = TypeVar("T") - -class Registry(dict[str, type[T]], Generic[T]): +class Registry[T](dict[str, type[T]]): def __init__(self) -> None: super().__init__() self.lazy_load_list: list[EntryPoint] = [] diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 08c05864aa..7138ad7622 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -3,7 +3,7 @@ import importlib.util import json from pathlib import Path -from typing import TYPE_CHECKING, Any, Literal, Self, TypeAlias +from typing import TYPE_CHECKING, Any, Literal, Self from zarr.abc.store import ( ByteRequest, @@ -296,7 +296,7 @@ def __eq__(self, other: object) -> bool: return False -StoreLike: TypeAlias = Store | StorePath | FSMap | Path | str | dict[str, Buffer] +type StoreLike = Store | StorePath | FSMap | Path | str | dict[str, Buffer] async def make_store( diff --git a/src/zarr/storage/_logging.py b/src/zarr/storage/_logging.py index 98dca6b23d..a4c376c332 100644 --- a/src/zarr/storage/_logging.py +++ b/src/zarr/storage/_logging.py @@ -6,7 +6,7 @@ import time from collections import defaultdict from contextlib import contextmanager -from typing import TYPE_CHECKING, Any, Self, TypeVar +from typing import TYPE_CHECKING, Any, Self from zarr.abc.store import Store from zarr.storage._wrapper import WrapperStore @@ -19,10 +19,8 @@ counter: defaultdict[str, int] -T_Store = TypeVar("T_Store", bound=Store) - -class LoggingStore(WrapperStore[T_Store]): +class LoggingStore[T_Store: Store](WrapperStore[T_Store]): """ Store that logs all calls to another wrapped store. diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index 6e4011da59..ffea523f9f 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -6,7 +6,7 @@ from collections import defaultdict from itertools import chain from operator import itemgetter -from typing import TYPE_CHECKING, Generic, Self, TypedDict, TypeVar +from typing import TYPE_CHECKING, Self, TypedDict from zarr.abc.store import ( ByteRequest, @@ -37,10 +37,7 @@ ) -T_Store = TypeVar("T_Store", bound="_UpstreamObjectStore") - - -class ObjectStore(Store, Generic[T_Store]): +class ObjectStore[T_Store: "_UpstreamObjectStore"](Store): """ Store that uses obstore for fast read/write from AWS, GCP, Azure. diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index 10ac395b36..8939ead30b 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -1,8 +1,18 @@ from __future__ import annotations +import importlib import re from pathlib import Path -from typing import TYPE_CHECKING, TypeVar + +if importlib.util.find_spec("upath"): + from upath.core import UPath +else: + + class UPath: # type: ignore[no-redef] + pass + + +from typing import TYPE_CHECKING from zarr.abc.store import OffsetByteRequest, RangeByteRequest, SuffixByteRequest @@ -20,7 +30,8 @@ def normalize_path(path: str | bytes | Path | None) -> str: result = str(path, "ascii") # handle pathlib.Path - elif isinstance(path, Path): + + elif isinstance(path, Path | UPath): result = str(path) elif isinstance(path, str): @@ -155,10 +166,7 @@ def _normalize_paths(paths: Iterable[str]) -> tuple[str, ...]: return tuple(path_map.keys()) -T = TypeVar("T") - - -def _normalize_path_keys(data: Mapping[str, T]) -> dict[str, T]: +def _normalize_path_keys[T](data: Mapping[str, T]) -> dict[str, T]: """ Normalize the keys of the input dict according to the normalization scheme used for zarr node paths. If any two keys in the input normalize to the same value, raise a ValueError. diff --git a/src/zarr/storage/_wrapper.py b/src/zarr/storage/_wrapper.py index e8a2859abc..50fe5c0e59 100644 --- a/src/zarr/storage/_wrapper.py +++ b/src/zarr/storage/_wrapper.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Generic, TypeVar, cast +from typing import TYPE_CHECKING, cast if TYPE_CHECKING: from collections.abc import AsyncGenerator, AsyncIterator, Iterable @@ -13,10 +13,8 @@ from zarr.abc.store import Store -T_Store = TypeVar("T_Store", bound=Store) - -class WrapperStore(Store, Generic[T_Store]): +class WrapperStore[T_Store: Store](Store): """ Store that wraps an existing Store. diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index 382f1467da..4bdc7db491 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -1,7 +1,7 @@ import builtins import functools from collections.abc import Callable -from typing import Any, TypeVar, cast +from typing import Any, cast import hypothesis.extra.numpy as npst import hypothesis.strategies as st @@ -36,10 +36,8 @@ MAX_BINARY_SIZE = 100 -F = TypeVar("F", bound=Callable[..., Any]) - -def with_frequency(frequency: float) -> Callable[[F], F]: +def with_frequency[F: Callable[..., Any]](frequency: float) -> Callable[[F], F]: """This needs to be deterministic for hypothesis replaying""" def decorator(func: F) -> F: diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index ce83715b86..91c174b589 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -4,7 +4,7 @@ import json import pickle from abc import abstractmethod -from typing import TYPE_CHECKING, Generic, Self, TypeVar +from typing import TYPE_CHECKING, Self from zarr.storage import WrapperStore @@ -33,11 +33,7 @@ __all__ = ["StoreTests"] -S = TypeVar("S", bound=Store) -B = TypeVar("B", bound=Buffer) - - -class StoreTests(Generic[S, B]): +class StoreTests[S: Store, B: Buffer]: store_cls: type[S] buffer_cls: type[B] diff --git a/src/zarr/testing/utils.py b/src/zarr/testing/utils.py index 2a4c3e45c5..94f73f6798 100644 --- a/src/zarr/testing/utils.py +++ b/src/zarr/testing/utils.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import TYPE_CHECKING, TypeVar, cast +from typing import TYPE_CHECKING, cast import pytest @@ -37,13 +37,10 @@ def has_cupy() -> bool: return False -T = TypeVar("T") - - gpu_mark = pytest.mark.gpu skip_if_no_gpu = pytest.mark.skipif(not has_cupy(), reason="CuPy not installed or no GPU available") # Decorator for GPU tests -def gpu_test(func: T) -> T: +def gpu_test[T](func: T) -> T: return cast(T, gpu_mark(skip_if_no_gpu(func))) diff --git a/src/zarr/types.py b/src/zarr/types.py index 38990982f9..c159d5d5f2 100644 --- a/src/zarr/types.py +++ b/src/zarr/types.py @@ -1,23 +1,23 @@ -from typing import Any, TypeAlias +from typing import Any from zarr.core.array import Array, AsyncArray from zarr.core.metadata.v2 import ArrayV2Metadata from zarr.core.metadata.v3 import ArrayV3Metadata -AnyAsyncArray: TypeAlias = AsyncArray[Any] +type AnyAsyncArray = AsyncArray[Any] """A Zarr format 2 or 3 `AsyncArray`""" -AsyncArrayV2: TypeAlias = AsyncArray[ArrayV2Metadata] +type AsyncArrayV2 = AsyncArray[ArrayV2Metadata] """A Zarr format 2 `AsyncArray`""" -AsyncArrayV3: TypeAlias = AsyncArray[ArrayV3Metadata] +type AsyncArrayV3 = AsyncArray[ArrayV3Metadata] """A Zarr format 3 `AsyncArray`""" -AnyArray: TypeAlias = Array[Any] +type AnyArray = Array[Any] """A Zarr format 2 or 3 `Array`""" -ArrayV2: TypeAlias = Array[ArrayV2Metadata] +type ArrayV2 = Array[ArrayV2Metadata] """A Zarr format 2 `Array`""" -ArrayV3: TypeAlias = Array[ArrayV3Metadata] +type ArrayV3 = Array[ArrayV3Metadata] """A Zarr format 3 `Array`""" diff --git a/tests/test_regression/scripts/v2.18.py b/tests/test_regression/scripts/v2.18.py index 39e1c5210c..4c730b9c79 100644 --- a/tests/test_regression/scripts/v2.18.py +++ b/tests/test_regression/scripts/v2.18.py @@ -1,5 +1,5 @@ # /// script -# requires-python = ">=3.11" +# requires-python = ">=3.12" # dependencies = [ # "zarr==2.18", # "numcodecs==0.15" diff --git a/tests/test_regression/test_v2_dtype_regression.py b/tests/test_regression/test_v2_dtype_regression.py index 4f3329e88c..2607f9aa36 100644 --- a/tests/test_regression/test_v2_dtype_regression.py +++ b/tests/test_regression/test_v2_dtype_regression.py @@ -1,4 +1,5 @@ import subprocess +import sys from dataclasses import dataclass from itertools import product from pathlib import Path @@ -193,6 +194,10 @@ def source_array_v3(tmp_path: Path, request: pytest.FixtureRequest) -> ArrayV3: script_paths = [Path(__file__).resolve().parent / "scripts" / "v2.18.py"] +@pytest.mark.skipif( + sys.platform == "darwin" and sys.version_info >= (3, 14), + reason="Numcodecs pinned to 0.15 does not build on newer macos installations with newer python versions: see discussion https://github.com/zarr-developers/zarr-python/pull/3564#issuecomment-4081145034", +) @pytest.mark.skipif(not runner_installed(), reason="no python script runner installed") @pytest.mark.parametrize( "source_array_v2", array_cases_v2_18, indirect=True, ids=tuple(map(str, array_cases_v2_18)) @@ -211,7 +216,7 @@ def test_roundtrip_v2(source_array_v2: ArrayV2, tmp_path: Path, script_path: Pat capture_output=True, text=True, ) - assert copy_op.returncode == 0 + assert copy_op.returncode == 0, "stdout " + copy_op.stdout + "\n stderr" + copy_op.stderr out_array = zarr.open_array(store=out_path, mode="r", zarr_format=2) assert source_array_v2.metadata.to_dict() == out_array.metadata.to_dict() assert np.array_equal(source_array_v2[:], out_array[:]) diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index 6589c68e09..e673bfd40b 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -145,11 +145,7 @@ async def test_store_path_invalid_mode_raises( Test that ValueErrors are raise for invalid mode. """ with pytest.raises(ValueError): - await StorePath.open( - LocalStore(str(tmp_path), read_only=modes[0]), - path="", - mode=modes[1], # type:ignore[arg-type] - ) + await StorePath.open(LocalStore(str(tmp_path), read_only=modes[0]), path="", mode=modes[1]) # type: ignore[arg-type] async def test_make_store_path_invalid() -> None: @@ -195,7 +191,7 @@ def test_normalize_path_valid(path: str | bytes | Path) -> None: def test_normalize_path_upath() -> None: upath = pytest.importorskip("upath") - assert normalize_path(upath.UPath("foo/bar")) == "foo/bar" + assert normalize_path(upath.UPath("foo/bar", protocol="memory")) == "memory:/foo/bar" def test_normalize_path_none() -> None: From 19a383ff200b5dd2cd11bea13b5152a6c3a1ef0e Mon Sep 17 00:00:00 2001 From: Sam Levang <39069044+slevang@users.noreply.github.com> Date: Fri, 27 Mar 2026 15:29:55 -0400 Subject: [PATCH 251/468] fix: remove numcodecs off-spec warning (#3833) * move warning into to_dict * remove warning entirely * changelog * changelog type --------- Co-authored-by: Davis Bennett --- changes/3833.misc.md | 1 + src/zarr/codecs/numcodecs/_codecs.py | 8 -- tests/test_array.py | 25 ++-- tests/test_cli/test_migrate_v3.py | 10 +- tests/test_codecs/test_numcodecs.py | 195 ++++++++++++--------------- 5 files changed, 100 insertions(+), 139 deletions(-) create mode 100644 changes/3833.misc.md diff --git a/changes/3833.misc.md b/changes/3833.misc.md new file mode 100644 index 0000000000..1f3c87b482 --- /dev/null +++ b/changes/3833.misc.md @@ -0,0 +1 @@ +Remove the warning that is emitted when any Numcodecs codec is instantiated. diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py index 4a3d88a84f..06c085ad2a 100644 --- a/src/zarr/codecs/numcodecs/_codecs.py +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -32,7 +32,6 @@ from dataclasses import dataclass, replace from functools import cached_property from typing import TYPE_CHECKING, Any, Self -from warnings import warn import numpy as np @@ -41,7 +40,6 @@ from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, parse_named_configuration, product from zarr.dtype import UInt8, ZDType, parse_dtype -from zarr.errors import ZarrUserWarning from zarr.registry import get_numcodec if TYPE_CHECKING: @@ -102,12 +100,6 @@ def __init__(self, **codec_config: JSON) -> None: ) # pragma: no cover object.__setattr__(self, "codec_config", codec_config) - warn( - "Numcodecs codecs are not in the Zarr version 3 specification and " - "may not be supported by other zarr implementations.", - category=ZarrUserWarning, - stacklevel=2, - ) @cached_property def _codec(self) -> Numcodec: diff --git a/tests/test_array.py b/tests/test_array.py index 8ea79b5f10..bf6f651283 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1853,24 +1853,21 @@ def test_roundtrip_numcodecs() -> None: # Create the array with the correct codecs root = zarr.group(store) - warn_msg = "Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations." - with pytest.warns(ZarrUserWarning, match=warn_msg): - root.create_array( - "test", - shape=(720, 1440), - chunks=(720, 1440), - dtype="float64", - compressors=compressors, # type: ignore[arg-type] - filters=filters, # type: ignore[arg-type] - fill_value=-9.99, - dimension_names=["lat", "lon"], - ) + root.create_array( + "test", + shape=(720, 1440), + chunks=(720, 1440), + dtype="float64", + compressors=compressors, # type: ignore[arg-type] + filters=filters, # type: ignore[arg-type] + fill_value=-9.99, + dimension_names=["lat", "lon"], + ) BYTES_CODEC = {"name": "bytes", "configuration": {"endian": "little"}} # Read in the array again and check compressor config root = zarr.open_group(store) - with pytest.warns(ZarrUserWarning, match=warn_msg): - metadata = root["test"].metadata.to_dict() + metadata = root["test"].metadata.to_dict() expected = (*filters, BYTES_CODEC, *compressors) assert metadata["codecs"] == expected diff --git a/tests/test_cli/test_migrate_v3.py b/tests/test_cli/test_migrate_v3.py index 8bda31d208..6e169e5f48 100644 --- a/tests/test_cli/test_migrate_v3.py +++ b/tests/test_cli/test_migrate_v3.py @@ -32,8 +32,6 @@ runner = typer_testing.CliRunner() -NUMCODECS_USER_WARNING = "Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations." - def test_migrate_array(local_store: LocalStore) -> None: shape = (10, 10) @@ -316,7 +314,6 @@ def test_migrate_compressor( assert np.all(zarr_array[:] == 1) -@pytest.mark.filterwarnings(f"ignore:{NUMCODECS_USER_WARNING}:UserWarning") def test_migrate_numcodecs_compressor(local_store: LocalStore) -> None: """Test migration of a numcodecs compressor without a zarr.codecs equivalent.""" @@ -360,7 +357,6 @@ def test_migrate_numcodecs_compressor(local_store: LocalStore) -> None: assert np.all(zarr_array[:] == 1) -@pytest.mark.filterwarnings(f"ignore:{NUMCODECS_USER_WARNING}:UserWarning") def test_migrate_filter(local_store: LocalStore) -> None: filter_v2 = numcodecs.Delta(dtype=" None: fill_value=0, ) - with pytest.warns(UserWarning, match=NUMCODECS_USER_WARNING): - result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) assert result.exit_code == 1 assert isinstance(result.exception, TypeError) @@ -548,8 +543,7 @@ def test_migrate_incorrect_compressor(local_store: LocalStore) -> None: fill_value=0, ) - with pytest.warns(UserWarning, match=NUMCODECS_USER_WARNING): - result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) + result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)]) assert result.exit_code == 1 assert isinstance(result.exception, TypeError) diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py index ddfca71294..eec0ecacae 100644 --- a/tests/test_codecs/test_numcodecs.py +++ b/tests/test_codecs/test_numcodecs.py @@ -17,7 +17,6 @@ from zarr import config, create_array, open_array from zarr.abc.numcodec import _is_numcodec, _is_numcodec_cls from zarr.codecs import numcodecs as _numcodecs -from zarr.errors import ZarrUserWarning from zarr.registry import get_codec_class, get_numcodec if TYPE_CHECKING: @@ -76,8 +75,6 @@ def test_is_numcodec_cls() -> None: assert _is_numcodec_cls(GZip) -EXPECTED_WARNING_STR = "Numcodecs codecs are not in the Zarr version 3.*" - ALL_CODECS = tuple( filter( lambda v: issubclass(v, _numcodecs._NumcodecsCodec) and hasattr(v, "codec_name"), @@ -115,15 +112,14 @@ def test_docstring(codec_class: type[_numcodecs._NumcodecsCodec]) -> None: def test_generic_compressor(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec]) -> None: data = np.arange(0, 256, dtype="uint16").reshape((16, 16)) - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - compressors=[codec_class()], - ) + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + compressors=[codec_class()], + ) a[:, :] = data.copy() np.testing.assert_array_equal(data, a[:, :]) @@ -150,60 +146,54 @@ def test_generic_filter( ) -> None: data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - filters=[ - codec_class(**codec_config), - ], - ) + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[ + codec_class(**codec_config), + ], + ) a[:, :] = data.copy() with codec_conf(): - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - b = open_array(a.store, mode="r") + b = open_array(a.store, mode="r") np.testing.assert_array_equal(data, b[:, :]) def test_generic_filter_bitround() -> None: data = np.linspace(0, 1, 256, dtype="float32").reshape((16, 16)) - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - filters=[_numcodecs.BitRound(keepbits=3)], - ) + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[_numcodecs.BitRound(keepbits=3)], + ) a[:, :] = data.copy() - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - b = open_array(a.store, mode="r") + b = open_array(a.store, mode="r") assert np.allclose(data, b[:, :], atol=0.1) def test_generic_filter_quantize() -> None: data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - filters=[_numcodecs.Quantize(digits=3)], - ) + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[_numcodecs.Quantize(digits=3)], + ) a[:, :] = data.copy() - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - b = open_array(a.store, mode="r") + b = open_array(a.store, mode="r") assert np.allclose(data, b[:, :], atol=0.001) @@ -211,32 +201,29 @@ def test_generic_filter_packbits() -> None: data = np.zeros((16, 16), dtype="bool") data[0:4, :] = True - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[_numcodecs.PackBits()], + ) + + a[:, :] = data.copy() + b = open_array(a.store, mode="r") + np.testing.assert_array_equal(data, b[:, :]) + + with pytest.raises(ValueError, match=".*requires bool dtype.*"): + create_array( {}, shape=data.shape, chunks=(16, 16), - dtype=data.dtype, + dtype="uint32", fill_value=0, filters=[_numcodecs.PackBits()], ) - a[:, :] = data.copy() - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - b = open_array(a.store, mode="r") - np.testing.assert_array_equal(data, b[:, :]) - - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - with pytest.raises(ValueError, match=".*requires bool dtype.*"): - create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype="uint32", - fill_value=0, - filters=[_numcodecs.PackBits()], - ) - @pytest.mark.parametrize( "codec_class", @@ -251,35 +238,31 @@ def test_generic_filter_packbits() -> None: def test_generic_checksum(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec]) -> None: # Check if the codec is available in numcodecs try: - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - codec_class()._codec # noqa: B018 + codec_class()._codec # noqa: B018 except UnknownCodecError as e: # pragma: no cover pytest.skip(f"{codec_class.codec_name} is not available in numcodecs: {e}") data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - compressors=[codec_class()], - ) + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + compressors=[codec_class()], + ) a[:, :] = data.copy() with codec_conf(): - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - b = open_array(a.store, mode="r") + b = open_array(a.store, mode="r") np.testing.assert_array_equal(data, b[:, :]) @pytest.mark.parametrize("codec_class", [_numcodecs.PCodec, _numcodecs.ZFPY]) def test_generic_bytes_codec(codec_class: type[_numcodecs._NumcodecsArrayBytesCodec]) -> None: try: - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - codec_class()._codec # noqa: B018 + codec_class()._codec # noqa: B018 except ValueError as e: # pragma: no cover if "codec not available" in str(e): pytest.xfail(f"{codec_class.codec_name} is not available: {e}") @@ -290,15 +273,14 @@ def test_generic_bytes_codec(codec_class: type[_numcodecs._NumcodecsArrayBytesCo data = np.arange(0, 256, dtype="float32").reshape((16, 16)) - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - serializer=codec_class(), - ) + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + serializer=codec_class(), + ) a[:, :] = data.copy() np.testing.assert_array_equal(data, a[:, :]) @@ -307,34 +289,30 @@ def test_generic_bytes_codec(codec_class: type[_numcodecs._NumcodecsArrayBytesCo def test_delta_astype() -> None: data = np.linspace(0, 10, 256, dtype="i8").reshape((16, 16)) - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - a = create_array( - {}, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - filters=[ - _numcodecs.Delta(dtype="i8", astype="i2"), - ], - ) + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[ + _numcodecs.Delta(dtype="i8", astype="i2"), + ], + ) a[:, :] = data.copy() with codec_conf(): - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - b = open_array(a.store, mode="r") + b = open_array(a.store, mode="r") np.testing.assert_array_equal(data, b[:, :]) def test_repr() -> None: - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - codec = _numcodecs.LZ4(level=5) + codec = _numcodecs.LZ4(level=5) assert repr(codec) == "LZ4(codec_name='numcodecs.lz4', codec_config={'level': 5})" def test_to_dict() -> None: - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - codec = _numcodecs.LZ4(level=5) + codec = _numcodecs.LZ4(level=5) assert codec.to_dict() == {"name": "numcodecs.lz4", "configuration": {"level": 5}} @@ -367,8 +345,7 @@ def test_to_dict() -> None: def test_codecs_pickleable(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None: # Check if the codec is available in numcodecs try: - with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR): - codec = codec_cls() + codec = codec_cls() except UnknownCodecError as e: # pragma: no cover pytest.skip(f"{codec_cls.codec_name} is not available in numcodecs: {e}") From 2dc4036a3086b67804df1bcd53229c9b85c70633 Mon Sep 17 00:00:00 2001 From: Leo Ji Date: Mon, 30 Mar 2026 11:47:46 -0400 Subject: [PATCH 252/468] DOC: remove result="ansi" causing empty code blocks in user guide (#3845) * DOC: remove result="ansi" causing empty code blocks in user guide Closes #3506. Made-with: Cursor * DOC: add changelog entry for #3845 --------- Co-authored-by: Leo Ji --- changes/3845.doc.md | 1 + docs/user-guide/experimental.md | 8 ++++---- 2 files changed, 5 insertions(+), 4 deletions(-) create mode 100644 changes/3845.doc.md diff --git a/changes/3845.doc.md b/changes/3845.doc.md new file mode 100644 index 0000000000..c478596103 --- /dev/null +++ b/changes/3845.doc.md @@ -0,0 +1 @@ +Remove result="ansi" from code blocks in the user guide that were causing empty output cells in the rendered documentation. diff --git a/docs/user-guide/experimental.md b/docs/user-guide/experimental.md index eaa53a4622..c7f86337a3 100644 --- a/docs/user-guide/experimental.md +++ b/docs/user-guide/experimental.md @@ -55,7 +55,7 @@ such as a remote store for source data and a local store for persistent caching. The CacheStore provides significant performance improvements for repeated data access: -```python exec="true" session="experimental" source="above" result="ansi" +```python exec="true" session="experimental" source="above" import time # Benchmark reading with cache @@ -121,7 +121,7 @@ cache = CacheStore( **cache_set_data**: Controls whether written data is cached -```python exec="true" session="experimental" source="above" result="ansi" +```python exec="true" session="experimental" source="above" # Cache data when writing (default) cache = CacheStore( store=source_store, @@ -141,7 +141,7 @@ cache = CacheStore( The CacheStore provides statistics to monitor cache performance and state: -```python exec="true" session="experimental" source="above" result="ansi" +```python exec="true" session="experimental" source="above" # Access some data to generate cache activity data = zarr_array[0:50, 0:50] # First access - cache miss data = zarr_array[0:50, 0:50] # Second access - cache hit @@ -232,7 +232,7 @@ of source and cache stores for your specific use case. Here's a complete example demonstrating cache effectiveness: -```python exec="true" session="experimental-final" source="above" result="ansi" +```python exec="true" session="experimental-final" source="above" import numpy as np import time from tempfile import mkdtemp From ac8340209442b8597199e00583fe5a49170bd128 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Tue, 31 Mar 2026 02:24:45 -0400 Subject: [PATCH 253/468] chore: use `coverage run` instead of `pytest --cov` (#3847) * chore: improve code coverage reporting * update after_n_builds * fix: use `coverage run` instead of `pytest --cov` for accurate import-time coverage The pytest11 entry point (`zarr = "zarr.testing"`) imports 76 zarr modules during plugin loading, before pytest-cov starts measuring. This caused all module-level code (class definitions, imports, decorators) to appear uncovered, dropping reported coverage well below actual test coverage. `coverage run -m pytest` starts tracing before any imports, resolving the issue. * Revert changes * Revert change --- .github/workflows/gpu_test.yml | 1 + .github/workflows/hypothesis.yaml | 1 + .github/workflows/test.yml | 2 ++ codecov.yml | 14 +++++++++++++- pyproject.toml | 29 +++++++++++++++++++---------- 5 files changed, 36 insertions(+), 11 deletions(-) diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 4fdffab057..d3aa03d2f6 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -72,4 +72,5 @@ jobs: uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3 # v5.3.1 with: token: ${{ secrets.CODECOV_TOKEN }} + flags: gpu verbose: true # optional (default = false) diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 1ec6b4806d..a6a5ebbe6a 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -81,6 +81,7 @@ jobs: uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} + flags: tests verbose: true # optional (default = false) - name: Generate and publish the report diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8c55c7e93d..d0e244f507 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -71,6 +71,7 @@ jobs: uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} + flags: tests verbose: true # optional (default = false) test-upstream-and-min-deps: @@ -110,6 +111,7 @@ jobs: uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} + flags: tests verbose: true # optional (default = false) doctests: diff --git a/codecov.yml b/codecov.yml index ef535fd8fe..a3783cc39a 100644 --- a/codecov.yml +++ b/codecov.yml @@ -8,9 +8,21 @@ coverage: default: target: auto threshold: 0.1 + flags: + - tests +flags: + tests: + paths: + - src/ + carryforward: true + gpu: + paths: + - src/ + carryforward: true codecov: notify: - after_n_builds: 10 # Wait for all 10 reports before updating the status + # 6 = test.yml: 3 (optional+ubuntu) + 2 (upstream + min_deps), hypothesis: 1 + after_n_builds: 6 wait_for_ci: yes comment: layout: "diff, files" diff --git a/pyproject.toml b/pyproject.toml index 8277c3f752..96932a9611 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -155,10 +155,6 @@ hooks.vcs.version-file = "src/zarr/_version.py" dependency-groups = ["test"] [tool.hatch.envs.test.env-vars] -# Required to test with a pytest plugin; see https://pytest-cov.readthedocs.io/en/latest/plugins.html -COV_CORE_SOURCE = "src" -COV_CORE_CONFIG = ".coveragerc" -COV_CORE_DATAFILE = ".coverage.eager" [[tool.hatch.envs.test.matrix]] python = ["3.12", "3.13", "3.14"] @@ -175,13 +171,23 @@ matrix.deps.dependency-groups = [ ] [tool.hatch.envs.test.scripts] -run-coverage = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy" -run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report html" -run = "run-coverage --no-cov --ignore tests/benchmarks" +run-coverage = [ + "coverage run --source=src -m pytest --junitxml=junit.xml -o junit_family=legacy {args:}", + "coverage xml", +] +run-coverage-html = [ + "coverage run --source=src -m pytest {args:}", + "coverage html", +] +run = "pytest --ignore tests/benchmarks" run-verbose = "run-coverage --verbose" run-mypy = "mypy src" -run-hypothesis = "run-coverage -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*" +run-hypothesis = [ + "coverage run --source=src -m pytest -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful* {args:}", + "coverage xml", +] run-benchmark = "pytest --benchmark-enable tests/benchmarks" +serve-coverage-html = "python -m http.server -d htmlcov 8000" list-env = "pip list" [tool.hatch.envs.gputest] @@ -195,8 +201,11 @@ features = ["gpu"] python = ["3.12", "3.13"] [tool.hatch.envs.gputest.scripts] -run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-report xml --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks" -run = "run-coverage --no-cov" +run-coverage = [ + "coverage run --source=src -m pytest -m gpu --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks {args:}", + "coverage xml", +] +run = "pytest -m gpu --ignore tests/benchmarks" [tool.hatch.envs.upstream] template = 'test' From 0081fef667d6e8777b61c5ff331f79c8e7c0bac1 Mon Sep 17 00:00:00 2001 From: Leo Ji Date: Tue, 31 Mar 2026 00:11:26 -0700 Subject: [PATCH 254/468] DOC: document init_group removal in v3 migration guide (#3851) Closes #2720 Made-with: Cursor Co-authored-by: Leo Ji Co-authored-by: Davis Bennett --- changes/2720.doc.md | 1 + docs/user-guide/v3_migration.md | 9 +++++++++ 2 files changed, 10 insertions(+) create mode 100644 changes/2720.doc.md diff --git a/changes/2720.doc.md b/changes/2720.doc.md new file mode 100644 index 0000000000..a48b700ca1 --- /dev/null +++ b/changes/2720.doc.md @@ -0,0 +1 @@ +Document removal of `zarr.storage.init_group` in v3 migration guide, with replacement using `zarr.open_group`/`zarr.create_group`. diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index 8f835d4440..f9974305ed 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -114,6 +114,15 @@ The following sections provide details on breaking changes in Zarr-Python 3. - Use [`zarr.Group.require_array`][] in place of `zarr.Group.require_dataset` 3. Disallow "." syntax for getting group members. To get a member of a group named `foo`, use `group["foo"]` in place of `group.foo`. +4. The `zarr.storage.init_group` low-level helper function has been removed. Use + [`zarr.open_group`][] or [`zarr.create_group`][] instead: + + ```diff + - from zarr.storage import init_group + - init_group(store, overwrite=True, path="my/path") + + import zarr + + zarr.open_group(store, mode="w", path="my/path") + ``` ### The Store class From c9b534af6291e3817273b8232ce0cabd584f40a3 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 31 Mar 2026 15:01:20 +0200 Subject: [PATCH 255/468] perf/chunktransform (#3722) * add sync methods to codecs * add CodecChain dataclass and sync codec tests Introduces CodecChain, a frozen dataclass that chains array-array, array-bytes, and bytes-bytes codecs with synchronous encode/decode methods. Pure compute only -- no IO, no threading, no batching. Also adds sync roundtrip tests for individual codecs (blosc, gzip, zstd, crc32c, bytes, transpose, vlen) and CodecChain integration tests. Co-Authored-By: Claude Opus 4.6 * refactor codecchain * separate codecs and specs * add synchronous methods to stores * chunktransform * remove memorystore changes * chunktransform requires sync codecs * lint * simplify chunktransform by remove layers * rename to encode / decode * docs: improve type: ignore explanations * refactor: SupportsSyncCodec is generic, like BaseCodec * chore: remove shape and dtype attributes * test: update tests * test: clean up tests * chore: remove type: ignores --------- Co-authored-by: Claude Opus 4.6 --- src/zarr/abc/codec.py | 15 ++-- src/zarr/core/codec_pipeline.py | 108 +++++++++++++++++++++- tests/test_sync_codec_pipeline.py | 145 ++++++++++++++++++++++++++++++ 3 files changed, 259 insertions(+), 9 deletions(-) create mode 100644 tests/test_sync_codec_pipeline.py diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index 50472e807a..79c0dcf72e 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -67,20 +67,19 @@ def _check_codecjson_v2(data: object) -> TypeGuard[CodecJSON_V2[str]]: @runtime_checkable -class SupportsSyncCodec(Protocol): +class SupportsSyncCodec[CI: CodecInput, CO: CodecOutput](Protocol): """Protocol for codecs that support synchronous encode/decode. - Codecs implementing this protocol provide ``_decode_sync`` and ``_encode_sync`` + Codecs implementing this protocol provide `_decode_sync` and `_encode_sync` methods that perform encoding/decoding without requiring an async event loop. + + The type parameters mirror `BaseCodec`: `CI` is the decoded type and `CO` is + the encoded type. """ - def _decode_sync( - self, chunk_data: NDBuffer | Buffer, chunk_spec: ArraySpec - ) -> NDBuffer | Buffer: ... + def _decode_sync(self, chunk_data: CO, chunk_spec: ArraySpec) -> CI: ... - def _encode_sync( - self, chunk_data: NDBuffer | Buffer, chunk_spec: ArraySpec - ) -> NDBuffer | Buffer | None: ... + def _encode_sync(self, chunk_data: CI, chunk_spec: ArraySpec) -> CO | None: ... class BaseCodec[CI: CodecInput, CO: CodecOutput](Metadata): diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index d8c4cabdf9..0edc47ff6b 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -1,6 +1,6 @@ from __future__ import annotations -from dataclasses import dataclass +from dataclasses import dataclass, field from itertools import islice, pairwise from typing import TYPE_CHECKING, Any from warnings import warn @@ -14,6 +14,7 @@ Codec, CodecPipeline, GetResult, + SupportsSyncCodec, ) from zarr.core.common import concurrent_map from zarr.core.config import config @@ -66,6 +67,111 @@ def fill_value_or_default(chunk_spec: ArraySpec) -> Any: return fill_value +@dataclass(slots=True, kw_only=True) +class ChunkTransform: + """A synchronous codec chain bound to an ArraySpec. + + Provides `encode` and `decode` for pure-compute codec operations + (no IO, no threading, no batching). + + All codecs must implement `SupportsSyncCodec`. Construction will + raise `TypeError` if any codec does not. + """ + + codecs: tuple[Codec, ...] + array_spec: ArraySpec + + # (sync codec, input_spec) pairs in pipeline order. + _aa_codecs: tuple[tuple[SupportsSyncCodec[NDBuffer, NDBuffer], ArraySpec], ...] = field( + init=False, repr=False, compare=False + ) + _ab_codec: SupportsSyncCodec[NDBuffer, Buffer] = field(init=False, repr=False, compare=False) + _ab_spec: ArraySpec = field(init=False, repr=False, compare=False) + _bb_codecs: tuple[SupportsSyncCodec[Buffer, Buffer], ...] = field( + init=False, repr=False, compare=False + ) + + def __post_init__(self) -> None: + non_sync = [c for c in self.codecs if not isinstance(c, SupportsSyncCodec)] + if non_sync: + names = ", ".join(type(c).__name__ for c in non_sync) + raise TypeError( + f"All codecs must implement SupportsSyncCodec. The following do not: {names}" + ) + + aa, ab, bb = codecs_from_list(list(self.codecs)) + + aa_codecs: list[tuple[SupportsSyncCodec[NDBuffer, NDBuffer], ArraySpec]] = [] + spec = self.array_spec + for aa_codec in aa: + assert isinstance(aa_codec, SupportsSyncCodec) + aa_codecs.append((aa_codec, spec)) + spec = aa_codec.resolve_metadata(spec) + + self._aa_codecs = tuple(aa_codecs) + assert isinstance(ab, SupportsSyncCodec) + self._ab_codec = ab + self._ab_spec = spec + bb_sync: list[SupportsSyncCodec[Buffer, Buffer]] = [] + for bb_codec in bb: + assert isinstance(bb_codec, SupportsSyncCodec) + bb_sync.append(bb_codec) + self._bb_codecs = tuple(bb_sync) + + def decode( + self, + chunk_bytes: Buffer, + ) -> NDBuffer: + """Decode a single chunk through the full codec chain, synchronously. + + Pure compute -- no IO. + """ + data: Buffer = chunk_bytes + for bb_codec in reversed(self._bb_codecs): + data = bb_codec._decode_sync(data, self._ab_spec) + + chunk_array: NDBuffer = self._ab_codec._decode_sync(data, self._ab_spec) + + for aa_codec, spec in reversed(self._aa_codecs): + chunk_array = aa_codec._decode_sync(chunk_array, spec) + + return chunk_array + + def encode( + self, + chunk_array: NDBuffer, + ) -> Buffer | None: + """Encode a single chunk through the full codec chain, synchronously. + + Pure compute -- no IO. + """ + aa_data: NDBuffer = chunk_array + for aa_codec, spec in self._aa_codecs: + aa_result = aa_codec._encode_sync(aa_data, spec) + if aa_result is None: + return None + aa_data = aa_result + + ab_result = self._ab_codec._encode_sync(aa_data, self._ab_spec) + if ab_result is None: + return None + + bb_data: Buffer = ab_result + for bb_codec in self._bb_codecs: + bb_result = bb_codec._encode_sync(bb_data, self._ab_spec) + if bb_result is None: + return None + bb_data = bb_result + + return bb_data + + def compute_encoded_size(self, byte_length: int, array_spec: ArraySpec) -> int: + for codec in self.codecs: + byte_length = codec.compute_encoded_size(byte_length, array_spec) + array_spec = codec.resolve_metadata(array_spec) + return byte_length + + @dataclass(frozen=True) class BatchedCodecPipeline(CodecPipeline): """Default codec pipeline. diff --git a/tests/test_sync_codec_pipeline.py b/tests/test_sync_codec_pipeline.py new file mode 100644 index 0000000000..1bfde7c837 --- /dev/null +++ b/tests/test_sync_codec_pipeline.py @@ -0,0 +1,145 @@ +from __future__ import annotations + +from typing import Any + +import numpy as np +import pytest + +from zarr.abc.codec import ArrayBytesCodec, Codec +from zarr.codecs.bytes import BytesCodec +from zarr.codecs.crc32c_ import Crc32cCodec +from zarr.codecs.gzip import GzipCodec +from zarr.codecs.transpose import TransposeCodec +from zarr.codecs.zstd import ZstdCodec +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import Buffer, NDBuffer, default_buffer_prototype +from zarr.core.codec_pipeline import ChunkTransform +from zarr.core.dtype import get_data_type_from_native_dtype + + +class AsyncOnlyCodec(ArrayBytesCodec): + """A codec that only supports async, for testing rejection of non-sync codecs.""" + + is_fixed_size = True + + async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + raise NotImplementedError # pragma: no cover + + async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> Buffer | None: + raise NotImplementedError # pragma: no cover + + def compute_encoded_size(self, input_byte_length: int, chunk_spec: ArraySpec) -> int: + return input_byte_length # pragma: no cover + + +def _make_array_spec(shape: tuple[int, ...], dtype: np.dtype[np.generic]) -> ArraySpec: + zdtype = get_data_type_from_native_dtype(dtype) + return ArraySpec( + shape=shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + + +def _make_nd_buffer(arr: np.ndarray[Any, np.dtype[Any]]) -> NDBuffer: + return default_buffer_prototype().nd_buffer.from_numpy_array(arr) + + +@pytest.mark.parametrize( + ("shape", "codecs"), + [ + ((100,), (BytesCodec(),)), + ((100,), (BytesCodec(), GzipCodec())), + ((3, 4), (TransposeCodec(order=(1, 0)), BytesCodec(), ZstdCodec())), + ], + ids=["bytes-only", "with-compression", "full-chain"], +) +def test_construction(shape: tuple[int, ...], codecs: tuple[Codec, ...]) -> None: + """Construction succeeds when all codecs implement SupportsSyncCodec.""" + spec = _make_array_spec(shape, np.dtype("float64")) + ChunkTransform(codecs=codecs, array_spec=spec) + + +@pytest.mark.parametrize( + ("shape", "codecs"), + [ + ((100,), (AsyncOnlyCodec(),)), + ((3, 4), (TransposeCodec(order=(1, 0)), AsyncOnlyCodec())), + ], + ids=["async-only", "mixed-sync-and-async"], +) +def test_construction_rejects_non_sync(shape: tuple[int, ...], codecs: tuple[Codec, ...]) -> None: + """Construction raises TypeError when any codec lacks SupportsSyncCodec.""" + spec = _make_array_spec(shape, np.dtype("float64")) + with pytest.raises(TypeError, match="AsyncOnlyCodec"): + ChunkTransform(codecs=codecs, array_spec=spec) + + +@pytest.mark.parametrize( + ("arr", "codecs"), + [ + (np.arange(100, dtype="float64"), (BytesCodec(),)), + (np.arange(100, dtype="float64"), (BytesCodec(), GzipCodec(level=1))), + ( + np.arange(12, dtype="float64").reshape(3, 4), + (TransposeCodec(order=(1, 0)), BytesCodec(), ZstdCodec(level=1)), + ), + (np.arange(100, dtype="float64"), (BytesCodec(), Crc32cCodec())), + (np.arange(50, dtype="int32"), (BytesCodec(), ZstdCodec(level=1))), + ], + ids=["bytes-only", "gzip", "transpose+zstd", "crc32c", "int32"], +) +def test_encode_decode_roundtrip( + arr: np.ndarray[Any, np.dtype[Any]], codecs: tuple[Codec, ...] +) -> None: + """Data survives a full encode/decode cycle.""" + spec = _make_array_spec(arr.shape, arr.dtype) + chain = ChunkTransform(codecs=codecs, array_spec=spec) + nd_buf = _make_nd_buffer(arr) + + encoded = chain.encode(nd_buf) + assert encoded is not None + decoded = chain.decode(encoded) + np.testing.assert_array_equal(arr, decoded.as_numpy_array()) + + +@pytest.mark.parametrize( + ("shape", "codecs", "input_size", "expected_size"), + [ + ((100,), (BytesCodec(),), 800, 800), + ((100,), (BytesCodec(), Crc32cCodec()), 800, 804), + ((3, 4), (TransposeCodec(order=(1, 0)), BytesCodec()), 96, 96), + ], + ids=["bytes-only", "crc32c", "transpose"], +) +def test_compute_encoded_size( + shape: tuple[int, ...], + codecs: tuple[Codec, ...], + input_size: int, + expected_size: int, +) -> None: + """compute_encoded_size returns the correct byte length.""" + spec = _make_array_spec(shape, np.dtype("float64")) + chain = ChunkTransform(codecs=codecs, array_spec=spec) + assert chain.compute_encoded_size(input_size, spec) == expected_size + + +def test_encode_returns_none_propagation() -> None: + """When an AA codec returns None, encode short-circuits and returns None.""" + + class NoneReturningAACodec(TransposeCodec): + """An ArrayArrayCodec that always returns None from encode.""" + + def _encode_sync(self, chunk_array: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer | None: + return None + + spec = _make_array_spec((3, 4), np.dtype("float64")) + chain = ChunkTransform( + codecs=(NoneReturningAACodec(order=(1, 0)), BytesCodec()), + array_spec=spec, + ) + arr = np.arange(12, dtype="float64").reshape(3, 4) + nd_buf = _make_nd_buffer(arr) + assert chain.encode(nd_buf) is None From 1bbc826302bbd7f7d13b1c7dac94ce2036787985 Mon Sep 17 00:00:00 2001 From: William Snell <59493198+williamsnell@users.noreply.github.com> Date: Fri, 3 Apr 2026 09:53:41 +1300 Subject: [PATCH 256/468] Fill missing chunks (#3748) * Add `codec_pipeline.fill_missing_chunks` config * Set default for `fill_missing_chunks` in config.py. Add test replicating example in zarr-python #486. * Add fill_missing_chunks to examples of config options. * Add to /changes * Parameterize tests to make sure we hit both branches of `if self.supports_partial_decode`. * Fix lint errors: remove parentheses, type kwargs. * Move config from codec_pipeline -> array. Update docs, tests. * Delegate missing-shard detection away from _get_chunk_spec. Codify expected behaviour of fill_missing_chunks for both sharding and write_empty_chunks via tests. Use elif to make control flow slightly clearer. * Define ChunkNotFoundError; expose chunk key and chunk index in ChunkNotFoundError * update docs * fix links * cleanup * Pass chunk indexes up * fill_missing_chunks -> read_missing_chunks * Resolve behavioural differences between main and maxrjones@37a40e3. Update docstrings to match current behaviour. Move description of sharding behaviour to test, now that it has no dedicated codepath. --------- Co-authored-by: Tom White Co-authored-by: Davis Bennett Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3748.feature.md | 1 + docs/user-guide/arrays.md | 14 ++++- docs/user-guide/config.md | 1 + src/zarr/core/array.py | 21 +++++++- src/zarr/core/array_spec.py | 21 ++++++-- src/zarr/core/config.py | 1 + src/zarr/errors.py | 7 +++ tests/test_config.py | 105 +++++++++++++++++++++++++++++++++++- 8 files changed, 164 insertions(+), 7 deletions(-) create mode 100644 changes/3748.feature.md diff --git a/changes/3748.feature.md b/changes/3748.feature.md new file mode 100644 index 0000000000..5fd94fe0a3 --- /dev/null +++ b/changes/3748.feature.md @@ -0,0 +1 @@ +Added `array.read_missing_chunks` configuration option. When set to `False`, reading missing chunks raises a `ChunkNotFoundError` instead of filling them with the array's fill value. diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index a44c096b73..5db5c946a3 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -158,13 +158,25 @@ print(f"Shape after second append: {z.shape}") Zarr arrays are parametrized with a configuration that determines certain aspects of array behavior. -We currently support two configuration options for arrays: `write_empty_chunks` and `order`. +We currently support three configuration options for arrays: `write_empty_chunks`, `read_missing_chunks`, and `order`. | field | type | default | description | | - | - | - | - | | `write_empty_chunks` | `bool` | `False` | Controls whether empty chunks are written to storage. See [Empty chunks](performance.md#empty-chunks). +| `read_missing_chunks` | `bool` | `True` | Controls whether missing chunks are filled with the array's fill value on read. If `False`, reading missing chunks raises a [`ChunkNotFoundError`][zarr.errors.ChunkNotFoundError]. | `order` | `Literal["C", "F"]` | `"C"` | The memory layout of arrays returned when reading data from the store. +!!! info + The Zarr V3 spec states that readers should interpret an uninitialized chunk as containing the + array's `fill_value`. By default, Zarr-Python follows this behavior: a missing chunk is treated + as uninitialized and filled with the array's `fill_value`. However, if you know that all chunks + have been written (i.e., are initialized), you may want to treat a missing chunk as an error. Set + `read_missing_chunks=False` to raise a [`ChunkNotFoundError`][zarr.errors.ChunkNotFoundError] instead. + +!!! note + `write_empty_chunks=False` skips writing chunks that are entirely the array's fill value. + If `read_missing_chunks=False`, attempting to read these missing chunks will raise a [`ChunkNotFoundError`][zarr.errors.ChunkNotFoundError]. + You can specify the configuration when you create an array with the `config` keyword argument. `config` can be passed as either a `dict` or an `ArrayConfig` object. diff --git a/docs/user-guide/config.md b/docs/user-guide/config.md index 21fe9b5def..41e03cbf0b 100644 --- a/docs/user-guide/config.md +++ b/docs/user-guide/config.md @@ -30,6 +30,7 @@ Configuration options include the following: - Default Zarr format `default_zarr_version` - Default array order in memory `array.order` - Whether empty chunks are written to storage `array.write_empty_chunks` +- Whether missing chunks are filled with the array's fill value on read `array.read_missing_chunks` (default `True`). Set to `False` to raise a [`ChunkNotFoundError`][zarr.errors.ChunkNotFoundError] instead. - Async and threading options, e.g. `async.concurrency` and `threading.max_workers` - Selections of implementations of codecs, codec pipelines and buffers - Enabling GPU support with `zarr.config.enable_gpu()`. See GPU support for more. diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index b5212656f4..0f0e8c7866 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -117,6 +117,7 @@ from zarr.core.sync import sync from zarr.errors import ( ArrayNotFoundError, + ChunkNotFoundError, MetadataValidationError, ZarrDeprecationWarning, ZarrUserWarning, @@ -5610,7 +5611,8 @@ async def _get_selection( _config = replace(_config, order=order) # reading chunks and decoding them - await codec_pipeline.read( + indexed_chunks = list(indexer) + results = await codec_pipeline.read( [ ( store_path / metadata.encode_chunk_key(chunk_coords), @@ -5619,11 +5621,26 @@ async def _get_selection( out_selection, is_complete_chunk, ) - for chunk_coords, chunk_selection, out_selection, is_complete_chunk in indexer + for chunk_coords, chunk_selection, out_selection, is_complete_chunk in indexed_chunks ], out_buffer, drop_axes=indexer.drop_axes, ) + if _config.read_missing_chunks is False: + missing_info = [] + for i, result in enumerate(results): + if result["status"] == "missing": + coords = indexed_chunks[i][0] + key = metadata.encode_chunk_key(coords) + missing_info.append(f" chunk '{key}' (grid position {coords})") + if missing_info: + chunks_str = "\n".join(missing_info) + raise ChunkNotFoundError( + f"{len(missing_info)} chunk(s) not found in store '{store_path}'.\n" + f"Set the 'array.read_missing_chunks' config to True to fill " + f"missing chunks with the fill value.\n" + f"Missing chunks:\n{chunks_str}" + ) if isinstance(indexer, BasicIndexer) and indexer.shape == (): return out_buffer.as_scalar() return out_buffer.as_ndarray_like() diff --git a/src/zarr/core/array_spec.py b/src/zarr/core/array_spec.py index 421dfbf145..2b5eb0191c 100644 --- a/src/zarr/core/array_spec.py +++ b/src/zarr/core/array_spec.py @@ -28,6 +28,7 @@ class ArrayConfigParams(TypedDict): order: NotRequired[MemoryOrder] write_empty_chunks: NotRequired[bool] + read_missing_chunks: NotRequired[bool] @dataclass(frozen=True) @@ -41,17 +42,25 @@ class ArrayConfig: The memory layout of the arrays returned when reading data from the store. write_empty_chunks : bool If True, empty chunks will be written to the store. + read_missing_chunks : bool + If True, missing chunks will be filled with the array's fill value on read. + If False, reading missing chunks will raise a ``ChunkNotFoundError``. """ order: MemoryOrder write_empty_chunks: bool + read_missing_chunks: bool - def __init__(self, order: MemoryOrder, write_empty_chunks: bool) -> None: + def __init__( + self, order: MemoryOrder, write_empty_chunks: bool, *, read_missing_chunks: bool = True + ) -> None: order_parsed = parse_order(order) write_empty_chunks_parsed = parse_bool(write_empty_chunks) + read_missing_chunks_parsed = parse_bool(read_missing_chunks) object.__setattr__(self, "order", order_parsed) object.__setattr__(self, "write_empty_chunks", write_empty_chunks_parsed) + object.__setattr__(self, "read_missing_chunks", read_missing_chunks_parsed) @classmethod def from_dict(cls, data: ArrayConfigParams) -> Self: @@ -62,7 +71,9 @@ def from_dict(cls, data: ArrayConfigParams) -> Self: """ kwargs_out: ArrayConfigParams = {} for f in fields(ArrayConfig): - field_name = cast("Literal['order', 'write_empty_chunks']", f.name) + field_name = cast( + "Literal['order', 'write_empty_chunks', 'read_missing_chunks']", f.name + ) if field_name not in data: kwargs_out[field_name] = zarr_config.get(f"array.{field_name}") else: @@ -73,7 +84,11 @@ def to_dict(self) -> ArrayConfigParams: """ Serialize an instance of this class to a dict. """ - return {"order": self.order, "write_empty_chunks": self.write_empty_chunks} + return { + "order": self.order, + "write_empty_chunks": self.write_empty_chunks, + "read_missing_chunks": self.read_missing_chunks, + } ArrayConfigLike = ArrayConfig | ArrayConfigParams diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index f8f8ea4f5f..de50475992 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -96,6 +96,7 @@ def enable_gpu(self) -> ConfigSet: "array": { "order": "C", "write_empty_chunks": False, + "read_missing_chunks": True, "target_shard_size_bytes": None, }, "async": {"concurrency": 10, "timeout": None}, diff --git a/src/zarr/errors.py b/src/zarr/errors.py index bcd6a08deb..5a6bb54bef 100644 --- a/src/zarr/errors.py +++ b/src/zarr/errors.py @@ -3,6 +3,7 @@ "ArrayNotFoundError", "BaseZarrError", "BoundsCheckError", + "ChunkNotFoundError", "ContainsArrayAndGroupError", "ContainsArrayError", "ContainsGroupError", @@ -144,3 +145,9 @@ class BoundsCheckError(IndexError): ... class ArrayIndexError(IndexError): ... + + +class ChunkNotFoundError(BaseZarrError): + """ + Raised when a chunk that was expected to exist in storage was not retrieved successfully. + """ diff --git a/tests/test_config.py b/tests/test_config.py index c3102e8efe..a095d99e54 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -23,7 +23,7 @@ from zarr.core.codec_pipeline import BatchedCodecPipeline from zarr.core.config import BadConfigError, config from zarr.core.indexing import SelectorTuple -from zarr.errors import ZarrUserWarning +from zarr.errors import ChunkNotFoundError, ZarrUserWarning from zarr.registry import ( fully_qualified_name, get_buffer_class, @@ -53,6 +53,7 @@ def test_config_defaults_set() -> None: "array": { "order": "C", "write_empty_chunks": False, + "read_missing_chunks": True, "target_shard_size_bytes": None, }, "async": {"concurrency": 10, "timeout": None}, @@ -319,6 +320,108 @@ class NewCodec2(BytesCodec): get_codec_class("new_codec") +@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) +@pytest.mark.parametrize( + "kwargs", + [ + {"shards": (4, 4)}, + {"compressors": None}, + ], + ids=["partial_decode", "full_decode"], +) +def test_config_read_missing_chunks(store: Store, kwargs: dict[str, Any]) -> None: + arr = zarr.create_array( + store=store, + shape=(4, 4), + chunks=(2, 2), + dtype="int32", + fill_value=42, + **kwargs, + ) + + # default behavior: missing chunks are filled with the fill value + result = zarr.open_array(store)[:] + assert np.array_equal(result, np.full((4, 4), 42, dtype="int32")) + + # with read_missing_chunks=False, reading missing chunks raises an error + with config.set({"array.read_missing_chunks": False}): + with pytest.raises(ChunkNotFoundError): + zarr.open_array(store)[:] + + # after writing data, all chunks exist and no error is raised + arr[:] = np.arange(16, dtype="int32").reshape(4, 4) + with config.set({"array.read_missing_chunks": False}): + result = zarr.open_array(store)[:] + assert np.array_equal(result, np.arange(16, dtype="int32").reshape(4, 4)) + + +@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) +def test_config_read_missing_chunks_sharded_inner(store: Store) -> None: + """Because the shard index and inner chunks should be stored + together in a single storage object (read: a file or blob), + we delegate to the shard index the responsibility of determining + what chunks should be present. + + Thus, `read_missing_chunks` raises an error only if the entire *shard* + is missing. Missing inner chunks are filled with the array's fill value + and do not raise an error, even if `read_missing_chunks=False` at the + array level. + """ + arr = zarr.create_array( + store=store, + shape=(8, 4), + chunks=(2, 2), + shards=(4, 4), + dtype="int32", + fill_value=42, + ) + + # write only one inner chunk in the first shard, leaving the second shard empty + arr[0:2, 0:2] = np.ones((2, 2), dtype="int32") + + with config.set({"array.read_missing_chunks": False}): + a = zarr.open_array(store) + + # first shard exists: missing inner chunks are filled, no error + result = a[:4] + expected = np.full((4, 4), 42, dtype="int32") + expected[0:2, 0:2] = 1 + assert np.array_equal(result, expected) + + # second shard is entirely missing: raises an error + with pytest.raises(ChunkNotFoundError): + a[4:] + + +@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) +def test_config_read_missing_chunks_write_empty_chunks(store: Store) -> None: + """write_empty_chunks=False drops chunks equal to fill_value, which then + appear missing to read_missing_chunks=False.""" + arr = zarr.create_array( + store=store, + shape=(4,), + chunks=(2,), + dtype="int32", + fill_value=0, + config={"write_empty_chunks": False, "read_missing_chunks": False}, + ) + + # write non-fill-value data: chunks are stored + arr[:] = [1, 2, 3, 4] + assert np.array_equal(arr[:], [1, 2, 3, 4]) + + # overwrite with fill_value: chunks are dropped by write_empty_chunks=False + arr[:] = 0 + with pytest.raises(ChunkNotFoundError): + arr[:] + + # with write_empty_chunks=True, chunks are kept and no error is raised + with config.set({"array.write_empty_chunks": True}): + arr = zarr.open_array(store) + arr[:] = 0 + assert np.array_equal(arr[:], [0, 0, 0, 0]) + + @pytest.mark.parametrize( "key", [ From 8f14d676fb8f794a78315865b2a0ee0f6fd397df Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Fri, 3 Apr 2026 11:12:41 +0200 Subject: [PATCH 257/468] fix: numpy default NaT handling (#3863) * fix: numpy default NaT handling * fix: timedelta64 handling * fix: use isnat --------- Co-authored-by: Davis Bennett --- src/zarr/core/dtype/npy/time.py | 4 +++- tests/test_dtype/test_npy/test_time.py | 8 +++++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index 1a46f77983..c4495e167c 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -545,6 +545,8 @@ def cast_scalar(self, data: object) -> np.timedelta64: raise a TypeError. """ if self._check_scalar(data): + if isinstance(data, np.timedelta64) and np.isnat(data): + return np.timedelta64("NaT", self.unit) return self._cast_scalar_unchecked(data) msg = ( f"Cannot convert object {data!r} with type {type(data)} to a scalar compatible with the " @@ -559,7 +561,7 @@ def default_scalar(self) -> np.timedelta64: This method provides a default value for the timedelta64 scalar, which is a 'Not-a-Time' (NaT) value. """ - return np.timedelta64("NaT") + return np.timedelta64("NaT", self.unit) def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.timedelta64: """ diff --git a/tests/test_dtype/test_npy/test_time.py b/tests/test_dtype/test_npy/test_time.py index b94b600cbf..1b1f428e40 100644 --- a/tests/test_dtype/test_npy/test_time.py +++ b/tests/test_dtype/test_npy/test_time.py @@ -115,7 +115,7 @@ class TestTimeDelta64(_TestTimeBase): cast_value_params = ( (TimeDelta64(unit="ns", scale_factor=1), "1", np.timedelta64(1, "ns")), - (TimeDelta64(unit="ns", scale_factor=1), "NaT", np.timedelta64("NaT")), + (TimeDelta64(unit="ns", scale_factor=1), "NaT", np.timedelta64("NaT", "ns")), ) invalid_scalar_params = ( (TimeDelta64(unit="Y", scale_factor=1), 1.3), @@ -148,6 +148,12 @@ def test_time_scale_factor_too_low() -> None: TimeDelta64(scale_factor=scale_factor) +def test_default_is_NaT() -> None: + np.testing.assert_equal( + TimeDelta64(unit="ns", scale_factor=1).default_scalar(), np.timedelta64("NaT", "ns") + ) + + def test_time_scale_factor_too_high() -> None: """ Test that an invalid unit raises a ValueError. From 325439a3cf9c4b77d7b7121f5979c097101c0147 Mon Sep 17 00:00:00 2001 From: Leo Ji Date: Sat, 4 Apr 2026 23:00:12 -0700 Subject: [PATCH 258/468] DOC: document threading.max_workers config option (#3852) Closes #3492 Made-with: Cursor Co-authored-by: Leo Ji Co-authored-by: Davis Bennett --- changes/3492.doc.md | 1 + docs/user-guide/performance.md | 22 ++++++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 changes/3492.doc.md diff --git a/changes/3492.doc.md b/changes/3492.doc.md new file mode 100644 index 0000000000..66719c7b50 --- /dev/null +++ b/changes/3492.doc.md @@ -0,0 +1 @@ +Document the `threading.max_workers` configuration option in the performance guide. diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 0e0fa3cd55..6d3ec063d2 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -217,6 +217,28 @@ Lower concurrency values may be beneficial when: - Memory is constrained (each concurrent operation requires buffer space) - Using Zarr within a parallel computing framework (see below) +### Thread pool size (`threading.max_workers`) + +When synchronous Zarr code calls async operations internally, Zarr uses a +`ThreadPoolExecutor` to run those coroutines. The `threading.max_workers` +configuration option controls the maximum number of worker threads in that pool. +By default it is `None`, which lets Python choose the pool size (typically +`min(32, os.cpu_count() + 4)`). + +You can set it explicitly when you want more predictable resource usage: + +```python +import zarr + +zarr.config.set({'threading.max_workers': 8}) +``` + +Reducing this value can help avoid overloading the event loop when Zarr is used +inside a parallel computing framework such as Dask that already manages its own +thread pool (see the Dask section below). Increasing it may improve throughput +in CPU-bound workloads where many synchronous-to-async dispatches happen +concurrently. + ### Using Zarr with Dask [Dask](https://www.dask.org/) is a popular parallel computing library that works well with Zarr for processing large arrays. When using Zarr with Dask, it's important to consider the interaction between Dask's thread pool and Zarr's concurrency settings. From 378ef107b9fc466c459c97ef6be4f00285a07b7b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sun, 5 Apr 2026 08:29:03 +0200 Subject: [PATCH 259/468] chore: add zizmor to repo checks (#3837) * chore: Add zizmor to pre-commit and github actions Zizmor is tool that analyzes github actions and checks for security vulnerabilities. Running it as part of pre-commit, and part of CI, will help ensure that we don't accidentally make changes that lead to a security vulnerability. * docs: changelog * chore: obey zizmor * chore: obey zizmor again * chore: explcitly declare shell * chore: codecov and nightly wheels use environments * chore: revert codecov-upload and nightly wheel environment usage * chore: Restore environments for codecov upload and nightly wheel upload Adds environments back to codecov and nightly wheel uploads, but this time with deployment: false, which ensures that these workflows don't generate a lot of notifications on github. * Update .github/workflows/zizmor.yml Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- .github/dependabot.yml | 4 ++ .github/workflows/check_changelogs.yml | 6 +++ .github/workflows/codspeed.yml | 11 ++++-- .github/workflows/gpu_test.yml | 19 ++++++--- .github/workflows/hypothesis.yaml | 35 ++++++++++++----- .github/workflows/issue-metrics.yml | 12 ++++-- .github/workflows/lint.yml | 6 ++- .github/workflows/needs_release_notes.yml | 17 ++++++-- .github/workflows/nightly_wheels.yml | 12 +++++- .github/workflows/releases.yml | 23 ++++++----- .github/workflows/test.yml | 48 ++++++++++++++++------- .github/workflows/zizmor.yml | 35 +++++++++++++++++ .pre-commit-config.yaml | 4 ++ changes/3837.misc.md | 1 + 14 files changed, 177 insertions(+), 56 deletions(-) create mode 100644 .github/workflows/zizmor.yml create mode 100644 changes/3837.misc.md diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 82419a5143..c6ab07e397 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -10,6 +10,8 @@ updates: actions: patterns: - "*" + cooldown: + default-days: 7 - package-ecosystem: "github-actions" directory: "/" target-branch: "support/v2" @@ -19,3 +21,5 @@ updates: actions: patterns: - "*" + cooldown: + default-days: 7 diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 02b57a5e36..04eb880592 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -7,6 +7,10 @@ on: permissions: contents: read +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: check-changelogs: name: Check changelog entries @@ -14,6 +18,8 @@ jobs: steps: - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1 + with: + persist-credentials: false - name: Install uv uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0 diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index bc4f1c1d4c..91226c19a3 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -10,6 +10,10 @@ on: permissions: contents: read +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: benchmarks: name: Run benchmarks @@ -19,11 +23,12 @@ jobs: github.event_name == 'workflow_dispatch' || (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark')) steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: fetch-depth: 0 + persist-credentials: false - name: Set up Python - uses: actions/setup-python@v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: "3.11" - name: Install Hatch @@ -31,7 +36,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@v4 + uses: CodSpeedHQ/action@1c8ae4843586d3ba879736b7f6b7b0c990757fab # v4.12.1 with: mode: walltime run: hatch run test.py3.11-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index d3aa03d2f6..777a5c3d64 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -23,16 +23,19 @@ concurrency: jobs: test: name: py=${{ matrix.python-version }} - + environment: + name: codecov-upload + deployment: false runs-on: gpu-runner strategy: matrix: python-version: ['3.12'] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: fetch-depth: 0 # grab all branches and tags + persist-credentials: false # - name: cuda-toolkit # uses: Jimver/cuda-toolkit@v0.2.16 # id: cuda-toolkit @@ -52,7 +55,7 @@ jobs: echo $LD_LIBRARY_PATH nvcc -V - name: Set up Python - uses: actions/setup-python@v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -61,12 +64,16 @@ jobs: with: version: '1.16.5' - name: Set Up Hatch Env + env: + HATCH_ENV: gputest.py${{ matrix.python-version }} run: | - hatch env create gputest.py${{ matrix.python-version }} - hatch env run -e gputest.py${{ matrix.python-version }} list-env + hatch env create "$HATCH_ENV" + hatch env run -e "$HATCH_ENV" list-env - name: Run Tests + env: + HATCH_ENV: gputest.py${{ matrix.python-version }} run: | - hatch env run --env gputest.py${{ matrix.python-version }} run-coverage + hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3 # v5.3.1 diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index a6a5ebbe6a..df1ae06c5f 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -12,6 +12,10 @@ on: permissions: contents: read +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + env: FORCE_COLOR: 3 @@ -19,6 +23,9 @@ jobs: hypothesis: name: Slow Hypothesis Tests + environment: + name: codecov-upload + deployment: false runs-on: "ubuntu-latest" defaults: run: @@ -30,16 +37,20 @@ jobs: dependency-set: ["optional"] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false - name: Set HYPOTHESIS_PROFILE based on trigger + env: + EVENT_NAME: ${{ github.event_name }} run: | - if [[ "${{ github.event_name }}" == "schedule" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then + if [[ "$EVENT_NAME" == "schedule" || "$EVENT_NAME" == "workflow_dispatch" ]]; then echo "HYPOTHESIS_PROFILE=nightly" >> $GITHUB_ENV else echo "HYPOTHESIS_PROFILE=ci" >> $GITHUB_ENV fi - name: Set up Python - uses: actions/setup-python@v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -48,13 +59,15 @@ jobs: with: version: '1.16.5' - name: Set Up Hatch Env + env: + HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run: | - hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} - hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env + hatch env create "$HATCH_ENV" + hatch env run -e "$HATCH_ENV" list-env # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache - name: Restore cached hypothesis directory id: restore-hypothesis-cache - uses: actions/cache/restore@v5 + uses: actions/cache/restore@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} @@ -64,21 +77,23 @@ jobs: - name: Run slow Hypothesis tests if: success() id: status + env: + HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run: | echo "Using Hypothesis profile: $HYPOTHESIS_PROFILE" - hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-hypothesis + hatch env run --env "$HATCH_ENV" run-hypothesis # explicitly save the cache so it gets updated, also do this even if it fails. - name: Save cached hypothesis directory id: save-hypothesis-cache if: always() && steps.status.outcome != 'skipped' - uses: actions/cache/save@v5 + uses: actions/cache/save@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} - name: Upload coverage - uses: codecov/codecov-action@v5 + uses: codecov/codecov-action@1af58845a975a7985b0beb0cbe6fbbb71a41dbad # v5.5.3 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests @@ -90,7 +105,7 @@ jobs: && steps.status.outcome == 'failure' && github.event_name == 'schedule' && github.repository_owner == 'zarr-developers' - uses: scientific-python/issue-from-pytest-log-action@v1 + uses: scientific-python/issue-from-pytest-log-action@8e905db353437cda1d6a773de245343fbfc940dd # v1.5.0 with: log-path: output-${{ matrix.python-version }}-log.jsonl issue-title: "Nightly Hypothesis tests failed" diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 5f3a098611..3746be05ac 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -7,13 +7,17 @@ on: permissions: contents: read +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: build: name: issue metrics runs-on: ubuntu-latest permissions: - issues: write - pull-requests: read + issues: write # Required to create the metrics report issue + pull-requests: read # Required to read PR metrics steps: - name: Get dates for last month shell: bash @@ -29,13 +33,13 @@ jobs: echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV" - name: Run issue-metrics tool - uses: github/issue-metrics@v3 + uses: github/issue-metrics@67526e7bd8100b870f10b1c120780a8375777b43 # v3.25.5 env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' - name: Create issue - uses: peter-evans/create-issue-from-file@v6 + uses: peter-evans/create-issue-from-file@fca9117c27cdc29c6c4db3b86c48e4115a786710 # v6.0.0 with: title: Monthly issue metrics report token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 0050b2f06a..ebcf74b3d7 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -19,5 +19,7 @@ jobs: name: Lint runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 - - uses: j178/prek-action@v1 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + - uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1.1.1 diff --git a/.github/workflows/needs_release_notes.yml b/.github/workflows/needs_release_notes.yml index e9dd3ce25a..037d7ffa78 100644 --- a/.github/workflows/needs_release_notes.yml +++ b/.github/workflows/needs_release_notes.yml @@ -1,15 +1,24 @@ name: "Pull Request Labeler" on: - pull_request_target: + # pull_request_target is needed to label PRs from forks. + # This workflow only runs actions/labeler (no code checkout), so it's safe. + pull_request_target: # zizmor: ignore[dangerous-triggers] types: [opened, reopened, synchronize] +permissions: {} + +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number }} + cancel-in-progress: true + jobs: labeler: - if: ${{ github.event.pull_request.user.login != 'dependabot[bot]' }} && ${{ github.event.pull_request.user.login != 'pre-commit-ci[bot]' }} + name: Label pull request + if: ${{ github.event.pull_request.user.login != 'dependabot[bot]' && github.event.pull_request.user.login != 'pre-commit-ci[bot]' }} permissions: - contents: read - pull-requests: write + contents: read # Required to read label configuration + pull-requests: write # Required to add labels to PRs runs-on: ubuntu-latest steps: - uses: actions/labeler@634933edcd8ababfe52f92936142cc22ac488b1b # v6.0.1 diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 56ffe8f1b4..8446d8fbe4 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -9,18 +9,26 @@ on: permissions: contents: read +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: build_and_upload_nightly: name: Build and upload nightly wheels + environment: + name: nightly-wheel-upload + deployment: false runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: submodules: true fetch-depth: 0 + persist-credentials: false - - uses: actions/setup-python@v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 name: Install Python with: python-version: '3.14' diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index fde8ff9804..750c67ac57 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -23,12 +23,13 @@ jobs: fail-fast: false steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: submodules: true fetch-depth: 0 + persist-credentials: false - - uses: actions/setup-python@v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 name: Install Python with: python-version: '3.12' @@ -39,16 +40,17 @@ jobs: version: '1.16.5' - name: Build wheel and sdist run: hatch build - - uses: actions/upload-artifact@v7 + - uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0 with: name: releases path: dist test_dist_pypi: + name: Test distribution artifacts needs: [build_artifacts] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@v7 + - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 with: name: releases path: dist @@ -59,6 +61,7 @@ jobs: ls dist upload_pypi: + name: Upload to PyPI needs: [build_artifacts, test_dist_pypi] runs-on: ubuntu-latest if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') @@ -66,17 +69,17 @@ jobs: name: releases url: https://pypi.org/p/zarr permissions: - id-token: write - attestations: write - artifact-metadata: write + id-token: write # Required for OIDC trusted publishing to PyPI + attestations: write # Required for artifact attestation + artifact-metadata: write # Required for artifact attestation metadata steps: - - uses: actions/download-artifact@v7 + - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 with: name: releases path: dist - name: Generate artifact attestation - uses: actions/attest@v4 + uses: actions/attest@59d89421af93a897026c735860bf21b6eb4f7b26 # v4.1.0 with: subject-path: dist/* - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@v1.13.0 + uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d0e244f507..27727b8bc2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -20,6 +20,12 @@ concurrency: jobs: test: name: os=${{ matrix.os }}, py=${{ matrix.python-version }}, deps=${{ matrix.dependency-set }} + environment: + name: codecov-upload + deployment: false + defaults: + run: + shell: bash strategy: matrix: @@ -45,11 +51,12 @@ jobs: runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: fetch-depth: 0 # grab all branches and tags + persist-credentials: false - name: Set up Python - uses: actions/setup-python@v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -58,17 +65,20 @@ jobs: with: version: '1.16.5' - name: Set Up Hatch Env + env: + HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run: | - hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} - hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env + hatch env create "$HATCH_ENV" + hatch env run -e "$HATCH_ENV" list-env - name: Run Tests env: HYPOTHESIS_PROFILE: ci + HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run: | - hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-coverage + hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage if: ${{ matrix.dependency-set == 'optional' && matrix.os == 'ubuntu-latest' }} - uses: codecov/codecov-action@v5 + uses: codecov/codecov-action@1af58845a975a7985b0beb0cbe6fbbb71a41dbad # v5.5.3 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests @@ -76,7 +86,9 @@ jobs: test-upstream-and-min-deps: name: py=${{ matrix.python-version }}-${{ matrix.dependency-set }} - + environment: + name: codecov-upload + deployment: false runs-on: ubuntu-latest strategy: matrix: @@ -88,11 +100,12 @@ jobs: - python-version: "3.12" dependency-set: upstream steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: fetch-depth: 0 + persist-credentials: false - name: Set up Python - uses: actions/setup-python@v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -101,14 +114,18 @@ jobs: with: version: '1.16.5' - name: Set Up Hatch Env + env: + HATCH_ENV: ${{ matrix.dependency-set }} run: | - hatch env create ${{ matrix.dependency-set }} - hatch env run -e ${{ matrix.dependency-set }} list-env + hatch env create "$HATCH_ENV" + hatch env run -e "$HATCH_ENV" list-env - name: Run Tests + env: + HATCH_ENV: ${{ matrix.dependency-set }} run: | - hatch env run --env ${{ matrix.dependency-set }} run-coverage + hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@v5 + uses: codecov/codecov-action@1af58845a975a7985b0beb0cbe6fbbb71a41dbad # v5.5.3 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests @@ -118,11 +135,12 @@ jobs: name: doctests runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3 + persist-credentials: false - name: Set up Python - uses: actions/setup-python@v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: '3.13' cache: 'pip' diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml new file mode 100644 index 0000000000..19313ab6ec --- /dev/null +++ b/.github/workflows/zizmor.yml @@ -0,0 +1,35 @@ +name: GitHub Actions Security Analysis + +on: + push: + branches: [main] + paths: + - '.github/workflows/**' + - '.github/actions/**' + pull_request: + branches: ["**"] + paths: + - '.github/workflows/**' + - '.github/actions/**' + workflow_dispatch: + +permissions: {} + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + zizmor: + name: Run zizmor + runs-on: ubuntu-latest + permissions: + security-events: write # Required by zizmor-action to upload SARIF files + steps: + - name: Checkout repository + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + + - name: Run zizmor + uses: zizmorcore/zizmor-action@71321a20a9ded102f6e9ce5718a2fcec2c4f70d8 # v0.5.2 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5d2b5de860..d91b35fa4f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -63,6 +63,10 @@ repos: entry: "\\.(lstrip|rstrip)\\([\"'][^\"']{2,}[\"']\\)" types: [python] files: ^(src|tests)/ + - repo: https://github.com/zizmorcore/zizmor-pre-commit + rev: v1.23.1 + hooks: + - id: zizmor - repo: https://github.com/twisted/towncrier rev: 25.8.0 hooks: diff --git a/changes/3837.misc.md b/changes/3837.misc.md new file mode 100644 index 0000000000..1a2c6f0e4f --- /dev/null +++ b/changes/3837.misc.md @@ -0,0 +1 @@ +Add the static github actions tool `zizmor` to our CI and pre-commit checks. \ No newline at end of file From dd86ac74aa225acac27ad66b1a95c787ec41200c Mon Sep 17 00:00:00 2001 From: Leo Ji Date: Sun, 5 Apr 2026 00:21:08 -0700 Subject: [PATCH 260/468] fix: convert zarr Array to numpy before __setitem__ async dispatch (#3857) * fix: convert zarr Array to numpy before __setitem__ async dispatch When the value passed to Array.__setitem__ is itself a zarr Array, the codec pipeline later calls value[...] from inside an already-running async event loop, which raises SyncError. Convert the value to a NumPy array eagerly before entering the async context to avoid this. Closes #3611 Made-with: Cursor * fix: restore skip marker on test_setitem_repeated_index Inserting test_setitem_zarr_array_as_value between the existing @pytest.mark.skip decorator and test_setitem_repeated_index accidentally moved the skip onto the new test, leaving test_setitem_repeated_index unskipped and failing. Restore the skip to its original target. Made-with: Cursor --------- Co-authored-by: Leo Ji --- changes/3611.bugfix.md | 1 + src/zarr/core/array.py | 6 ++++++ tests/test_indexing.py | 18 ++++++++++++++++++ 3 files changed, 25 insertions(+) create mode 100644 changes/3611.bugfix.md diff --git a/changes/3611.bugfix.md b/changes/3611.bugfix.md new file mode 100644 index 0000000000..8b889d79fc --- /dev/null +++ b/changes/3611.bugfix.md @@ -0,0 +1 @@ +Fix `SyncError` raised when assigning a `zarr.Array` as the value in a `__setitem__` call (e.g. `dst[:] = src` where `src` is a zarr array). The source array is now converted to a NumPy array before entering the async codec pipeline. diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 0f0e8c7866..7d1915fd33 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -2930,6 +2930,12 @@ def __setitem__(self, selection: Selection, value: npt.ArrayLike) -> None: [blocks][zarr.Array.blocks], [__getitem__][zarr.Array.__getitem__] """ + # Converting a zarr Array to numpy here avoids a SyncError that occurs when + # value.__getitem__ is called inside the async codec pipeline (which already + # runs within a running event loop). np.asarray triggers Array.__array__, + # which reads the data synchronously before we enter the async context. + if isinstance(value, Array): + value = np.asarray(value) fields, pure_selection = pop_fields(selection) if is_pure_fancy_indexing(pure_selection, self.ndim): self.vindex[cast("CoordinateSelection | MaskSelection", selection)] = value diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 9c734fb0c3..0c0a6182d8 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -443,6 +443,24 @@ def test_orthogonal_indexing_fallback_on_getitem_2d( np.testing.assert_array_equal(z[index], expected_result) +def test_setitem_zarr_array_as_value() -> None: + # Regression test for https://github.com/zarr-developers/zarr-python/issues/3611 + # Assigning a zarr Array as the value used to raise + # SyncError("Calling sync() from within a running loop") because the codec + # pipeline tried to index the zarr array inside an already-running async loop. + src = zarr.array(np.arange(10), chunks=(5,)) + dst = zarr.zeros(10, chunks=(5,), dtype=src.dtype) + + # Full assignment + dst[:] = src + assert_array_equal(dst[:], np.arange(10)) + + # Slice assignment + dst2 = zarr.zeros(10, chunks=(5,), dtype=src.dtype) + dst2[2:7] = src[2:7] + assert_array_equal(dst2[2:7], np.arange(2, 7)) + + @pytest.mark.skip(reason="fails on ubuntu, windows; numpy=2.2; in CI") def test_setitem_repeated_index(): array = zarr.array(data=np.zeros((4,)), chunks=(1,)) From ca9bd3eaf3ccf0e6116d80cf1c1e8d8b7f314128 Mon Sep 17 00:00:00 2001 From: Leo Ji Date: Mon, 6 Apr 2026 04:13:02 -0700 Subject: [PATCH 261/468] fix: auto-open ZipStore in list(), list_dir() and exists() (#3855) ZipStore._get() and ._set() already auto-open the zip file when called without a prior open(). Apply the same pattern to list(), list_dir(), and exists() so that all store methods behave consistently when the store has not been explicitly opened. Closes #3846 Made-with: Cursor Co-authored-by: Leo Ji Co-authored-by: Davis Bennett --- changes/3846.bugfix.md | 1 + src/zarr/storage/_zip.py | 6 ++++++ tests/test_store/test_zip.py | 25 +++++++++++++++++++++++++ 3 files changed, 32 insertions(+) create mode 100644 changes/3846.bugfix.md diff --git a/changes/3846.bugfix.md b/changes/3846.bugfix.md new file mode 100644 index 0000000000..bfda1b1693 --- /dev/null +++ b/changes/3846.bugfix.md @@ -0,0 +1 @@ +Fix `ZipStore.list()`, `list_dir()`, and `exists()` to auto-open the zip file when called before `open()`, consistent with the existing behavior of `get()` and `set()`. diff --git a/src/zarr/storage/_zip.py b/src/zarr/storage/_zip.py index 72bf9e335a..c5c7cbf3e8 100644 --- a/src/zarr/storage/_zip.py +++ b/src/zarr/storage/_zip.py @@ -245,6 +245,8 @@ async def delete(self, key: str) -> None: async def exists(self, key: str) -> bool: # docstring inherited + if not self._is_open: + self._sync_open() with self._lock: try: self._zf.getinfo(key) @@ -255,6 +257,8 @@ async def exists(self, key: str) -> bool: async def list(self) -> AsyncIterator[str]: # docstring inherited + if not self._is_open: + self._sync_open() with self._lock: for key in self._zf.namelist(): yield key @@ -267,6 +271,8 @@ async def list_prefix(self, prefix: str) -> AsyncIterator[str]: async def list_dir(self, prefix: str) -> AsyncIterator[str]: # docstring inherited + if not self._is_open: + self._sync_open() prefix = prefix.rstrip("/") keys = self._zf.namelist() diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py index 744ee82945..5975a6d2a0 100644 --- a/tests/test_store/test_zip.py +++ b/tests/test_store/test_zip.py @@ -139,6 +139,31 @@ def test_externally_zipped_store(self, tmp_path: Path) -> None: assert isinstance(group := zipped["foo"], Group) assert list(group.keys()) == list(group.keys()) + async def test_list_without_explicit_open(self, tmp_path: Path) -> None: + # ZipStore.list(), list_dir(), and exists() should auto-open + # the zip file just like _get() and _set() do. + zip_path = tmp_path / "data.zip" + zarr_path = tmp_path / "foo.zarr" + root = zarr.open_group(store=zarr_path, mode="w") + root["x"] = np.array([1, 2, 3]) + shutil.make_archive(str(zarr_path), "zip", zarr_path) + shutil.move(str(zarr_path) + ".zip", zip_path) + + store = ZipStore(zip_path, mode="r") + assert not store._is_open + + keys = [k async for k in store.list()] + assert len(keys) > 0 + + store2 = ZipStore(zip_path, mode="r") + assert not store2._is_open + assert await store2.exists(keys[0]) + + store3 = ZipStore(zip_path, mode="r") + assert not store3._is_open + dir_keys = [k async for k in store3.list_dir("")] + assert len(dir_keys) > 0 + async def test_move(self, tmp_path: Path) -> None: origin = tmp_path / "origin.zip" destination = tmp_path / "some_folder" / "destination.zip" From d8df81b3b1544e497d368c91568619df798a2199 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 Apr 2026 19:52:10 +0000 Subject: [PATCH 262/468] chore: update pre-commit hooks (#3876) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.4 → v0.15.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.4...v0.15.9) - [github.com/codespell-project/codespell: v2.4.1 → v2.4.2](https://github.com/codespell-project/codespell/compare/v2.4.1...v2.4.2) - [github.com/pre-commit/mirrors-mypy: v1.19.1 → v1.20.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.19.1...v1.20.0) - [github.com/scientific-python/cookie: 2026.03.02 → 2026.04.04](https://github.com/scientific-python/cookie/compare/2026.03.02...2026.04.04) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d91b35fa4f..f5284d8229 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,13 +11,13 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.4 + rev: v0.15.9 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/codespell-project/codespell - rev: v2.4.1 + rev: v2.4.2 hooks: - id: codespell args: ["-L", "fo,ihs,kake,te", "-S", "fixture"] @@ -28,7 +28,7 @@ repos: exclude: mkdocs.yml - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.19.1 + rev: v1.20.0 hooks: - id: mypy files: src|tests @@ -47,7 +47,7 @@ repos: - hypothesis - s3fs - repo: https://github.com/scientific-python/cookie - rev: 2026.03.02 + rev: 2026.04.04 hooks: - id: sp-repo-review - repo: https://github.com/numpy/numpydoc From 4f23e8c55fc397aeebf2b16ef57fb2524e52ca00 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 6 Apr 2026 16:36:35 -0400 Subject: [PATCH 263/468] chore: fix release workflow triggers (#3794) * chore: fix release workflow triggers * Update conditional --- .github/workflows/releases.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 750c67ac57..0920b5be12 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -1,6 +1,9 @@ name: Wheels on: + release: + types: + - published push: branches: [main] pull_request: @@ -64,7 +67,7 @@ jobs: name: Upload to PyPI needs: [build_artifacts, test_dist_pypi] runs-on: ubuntu-latest - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') + if: github.event_name == 'release' environment: name: releases url: https://pypi.org/p/zarr From 57c82b4d778360e8b7b0b188eaa0b7e1ade92cee Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 6 Apr 2026 17:01:38 -0400 Subject: [PATCH 264/468] Revert "chore: update pre-commit hooks" (#3877) This reverts commit d8df81b3b1544e497d368c91568619df798a2199. Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f5284d8229..d91b35fa4f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,13 +11,13 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.9 + rev: v0.15.4 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/codespell-project/codespell - rev: v2.4.2 + rev: v2.4.1 hooks: - id: codespell args: ["-L", "fo,ihs,kake,te", "-S", "fixture"] @@ -28,7 +28,7 @@ repos: exclude: mkdocs.yml - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.20.0 + rev: v1.19.1 hooks: - id: mypy files: src|tests @@ -47,7 +47,7 @@ repos: - hypothesis - s3fs - repo: https://github.com/scientific-python/cookie - rev: 2026.04.04 + rev: 2026.03.02 hooks: - id: sp-repo-review - repo: https://github.com/numpy/numpydoc From 00c1463bddfcf825669e020e6382ceda4df9be3c Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Tue, 7 Apr 2026 00:24:09 +0300 Subject: [PATCH 265/468] chore: fix typos (#3844) --- docs/release-notes.md | 2 +- tests/test_array.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/release-notes.md b/docs/release-notes.md index b974ae10c7..e79d359e3f 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -461,7 +461,7 @@ - Test that a `ValueError` is raised for invalid byte range syntax in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Separate instantiating and opening a store in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Add a test for using Stores as a context managers in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Implemented `LogingStore.open()`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Implemented `LoggingStore.open()`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - `LoggingStore` is now a generic class. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Change StoreTest's `test_store_repr`, `test_store_supports_writes`, `test_store_supports_partial_writes`, and `test_store_supports_listing` diff --git a/tests/test_array.py b/tests/test_array.py index bf6f651283..867bfb6cb2 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -209,19 +209,19 @@ def test_array_name_properties_with_group( @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") @pytest.mark.parametrize("store", ["memory"], indirect=True) -@pytest.mark.parametrize("specifiy_fill_value", [True, False]) +@pytest.mark.parametrize("specify_fill_value", [True, False]) @pytest.mark.parametrize( "zdtype", zdtype_examples, ids=tuple(str(type(v)) for v in zdtype_examples) ) def test_array_fill_value_default( - store: MemoryStore, specifiy_fill_value: bool, zdtype: ZDType[Any, Any] + store: MemoryStore, specify_fill_value: bool, zdtype: ZDType[Any, Any] ) -> None: """ Test that creating an array with the fill_value parameter set to None, or unspecified, results in the expected fill_value attribute of the array, i.e. the default value of the dtype """ shape = (10,) - if specifiy_fill_value: + if specify_fill_value: arr = zarr.create_array( store=store, shape=shape, From a4c440478869da50b2147e00176dffc883ac69ea Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 6 Apr 2026 23:01:59 -0400 Subject: [PATCH 266/468] Update TEAM.md (#3879) --- TEAM.md | 1 + 1 file changed, 1 insertion(+) diff --git a/TEAM.md b/TEAM.md index e6975d7c04..dc22a1ee87 100644 --- a/TEAM.md +++ b/TEAM.md @@ -10,6 +10,7 @@ - @dstansby (David Stansby) - @dcherian (Deepak Cherian) - @TomAugspurger (Tom Augspurger) +- @maxrjones (Max Jones) ## Emeritus core-developers - @alimanfoo (Alistair Miles) From ad99861eb8d7b36620bbf81476c121d989c5379b Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Tue, 7 Apr 2026 11:25:19 -0400 Subject: [PATCH 267/468] chore: separate benchmarks into a distinct CI job (#3873) * chore: separate benchmarks into a separate job * Maintain code coverage --------- Co-authored-by: Davis Bennett --- .github/workflows/test.yml | 24 +++++++++++++++++++++++- pyproject.toml | 4 ++-- tests/test_codecs/test_codecs.py | 1 + 3 files changed, 26 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 27727b8bc2..7ff7a8f6ae 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -155,6 +155,27 @@ jobs: run: | hatch run doctest:test + benchmarks: + name: Benchmark smoke test + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + fetch-depth: 0 + persist-credentials: false + - name: Set up Python + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + with: + python-version: '3.13' + cache: 'pip' + - name: Install Hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' + - name: Run Benchmarks + run: | + hatch env run --env "test.py3.13-minimal" run-benchmark + test-complete: name: Test complete @@ -162,7 +183,8 @@ jobs: [ test, test-upstream-and-min-deps, - doctests + doctests, + benchmarks ] if: always() runs-on: ubuntu-latest diff --git a/pyproject.toml b/pyproject.toml index 96932a9611..8796255b94 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -172,11 +172,11 @@ matrix.deps.dependency-groups = [ [tool.hatch.envs.test.scripts] run-coverage = [ - "coverage run --source=src -m pytest --junitxml=junit.xml -o junit_family=legacy {args:}", + "coverage run --source=src -m pytest --ignore tests/benchmarks --junitxml=junit.xml -o junit_family=legacy {args:}", "coverage xml", ] run-coverage-html = [ - "coverage run --source=src -m pytest {args:}", + "coverage run --source=src -m pytest --ignore tests/benchmarks {args:}", "coverage html", ] run = "pytest --ignore tests/benchmarks" diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index fa2017876e..6e3e3f6d28 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -219,6 +219,7 @@ def test_morton_exact_order() -> None: (1, 1), (5, 1, 3), (1, 4, 1, 2), + (5, 5, 5), # triggers argsort strategy (n_z/n_total > 4) ], ) def test_morton_is_permutation(shape: tuple[int, ...]) -> None: From 373910c63ba7b9bd32aa154c20b6568b5a0d06c1 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Tue, 7 Apr 2026 12:01:38 -0400 Subject: [PATCH 268/468] feat: add experimental support for rectilinear (variable-sized) chunks (#3802) Introduces a unified `ChunkGridMetadata` model that handles both regular and rectilinear chunk layouts through a common `RegularDimension`/`VaryingDimension` abstraction. Rectilinear chunks are gated behind a feature flag (`zarr.config.set({'array.rectilinear_chunks': True})`). Key changes: - New `ChunkGridMetadata` replaces `RegularChunkGrid` as the internal representation, supporting both regular and rectilinear dimensions - Rectilinear chunk grids can be created via nested sequences passed to `chunks` (e.g., `[[10, 20, 30], [50, 50]]`) - Rectilinear sharding: shard boundaries can be rectilinear while inner chunks remain regular - Existing arrays with regular chunk grids are read/written identically Breaking change: - `BaseCodec.validate()` and `CodecPipeline.validate()` now receive `ChunkGridMetadata` instead of `ChunkGrid` for the `chunk_grid` parameter --------- Co-authored-by: Davis Bennett Co-authored-by: David Stansby Co-authored-by: Deepak Cherian Co-authored-by: Ilan Gold Co-authored-by: Sam Levang <39069044+slevang@users.noreply.github.com> --- changes/3802.feature.md | 16 + design/chunk-grid.md | 711 ++++ docs/user-guide/arrays.md | 165 + docs/user-guide/config.md | 1 + .../examples/rectilinear_chunks.ipynb | 428 +++ docs/user-guide/glossary.md | 17 +- mkdocs.yml | 6 + pyproject.toml | 1 + src/zarr/abc/codec.py | 14 +- src/zarr/api/synchronous.py | 21 +- src/zarr/codecs/sharding.py | 49 +- src/zarr/codecs/transpose.py | 4 +- src/zarr/core/_info.py | 2 +- src/zarr/core/array.py | 421 ++- src/zarr/core/chunk_grids.py | 606 +++- src/zarr/core/codec_pipeline.py | 4 +- src/zarr/core/common.py | 87 + src/zarr/core/config.py | 1 + src/zarr/core/group.py | 9 +- src/zarr/core/indexing.py | 179 +- src/zarr/core/metadata/v2.py | 20 +- src/zarr/core/metadata/v3.py | 371 ++- src/zarr/experimental/__init__.py | 4 + src/zarr/metadata/migrate_v3.py | 4 +- src/zarr/testing/stateful.py | 71 +- src/zarr/testing/strategies.py | 258 +- tests/conftest.py | 8 +- tests/test_api.py | 13 + tests/test_array.py | 18 +- tests/test_cli/test_migrate_v3.py | 3 +- tests/test_codec_pipeline.py | 5 +- tests/test_codecs/test_sharding.py | 7 +- tests/test_config.py | 1 + tests/test_group.py | 4 +- tests/test_indexing.py | 10 +- tests/test_properties.py | 37 +- tests/test_store/test_stateful.py | 10 + tests/test_unified_chunk_grid.py | 2855 +++++++++++++++++ 38 files changed, 6014 insertions(+), 427 deletions(-) create mode 100644 changes/3802.feature.md create mode 100644 design/chunk-grid.md create mode 100644 docs/user-guide/examples/rectilinear_chunks.ipynb create mode 100644 tests/test_unified_chunk_grid.py diff --git a/changes/3802.feature.md b/changes/3802.feature.md new file mode 100644 index 0000000000..c57a7a98da --- /dev/null +++ b/changes/3802.feature.md @@ -0,0 +1,16 @@ +Add support for rectilinear (variable-sized) chunk grids. This feature is experimental and +must be explicitly enabled via ``zarr.config.set({'array.rectilinear_chunks': True})``. + +Rectilinear chunks can be used through: + +- **Creating arrays**: Pass nested sequences (e.g., ``[[10, 20, 30], [50, 50]]``) to ``chunks`` + in ``zarr.create_array``, ``zarr.from_array``, ``zarr.zeros``, ``zarr.ones``, ``zarr.full``, + ``zarr.open``, and related functions, or to ``chunk_shape`` in ``zarr.create``. +- **Opening existing arrays**: Arrays stored with the ``rectilinear`` chunk grid are read + transparently via ``zarr.open`` and ``zarr.open_array``. +- **Rectilinear sharding**: Shard boundaries can be rectilinear while inner chunks remain regular. + +**Breaking change**: The ``validate`` method on ``BaseCodec`` and ``CodecPipeline`` now receives +a ``ChunkGridMetadata`` instance instead of a ``ChunkGrid`` instance for the ``chunk_grid`` +parameter. Third-party codecs that override ``validate`` and inspect the chunk grid will need to +update their type annotations. No known downstream packages were using this parameter. diff --git a/design/chunk-grid.md b/design/chunk-grid.md new file mode 100644 index 0000000000..eaa5fffad5 --- /dev/null +++ b/design/chunk-grid.md @@ -0,0 +1,711 @@ +# Unified Chunk Grid + +Version: 6 + +Design document for adding rectilinear (variable) chunk grid support to **zarr-python**, conforming to the [rectilinear chunk grid extension spec](https://github.com/zarr-developers/zarr-extensions/pull/25). + +**Related:** + +- [#3750](https://github.com/zarr-developers/zarr-python/issues/3750) (single ChunkGrid proposal) +- [#3534](https://github.com/zarr-developers/zarr-python/pull/3534) (rectilinear implementation) +- [#3735](https://github.com/zarr-developers/zarr-python/pull/3735) (chunk grid module/registry) +- [ZEP0003](https://github.com/zarr-developers/zeps/blob/main/draft/ZEP0003.md) (variable chunking spec) +- [zarr-specs#370](https://github.com/zarr-developers/zarr-specs/pull/370) (sharding v1.1: non-divisible subchunks) +- [zarr-extensions#25](https://github.com/zarr-developers/zarr-extensions/pull/25) (rectilinear extension) +- [zarr-extensions#34](https://github.com/zarr-developers/zarr-extensions/issues/34) (sharding + rectilinear) + +## Problem + +Chunk grids form a hierarchy — the rectilinear grid is strictly more general than the regular grid. Any regular grid is expressible as a rectilinear grid. There is no known chunk grid that is both (a) more general than rectilinear and (b) retains the axis-aligned tessellation properties Zarr assumes. All known grids are special cases: + +| Grid type | Description | Example | +|---|---|---| +| Regular | Uniform chunk size, boundary chunks padded with fill_value | `[10, 10, 10, 10]` | +| Regular-bounded (zarrs) | Uniform chunk size, boundary chunks trimmed to array extent | `[10, 10, 10, 5]` | +| HPC boundary-padded | Regular interior, larger boundary chunks ([VirtualiZarr#217](https://github.com/zarr-developers/VirtualiZarr/issues/217)) | `[10, 8, 8, 8, 10]` | +| Fully variable | Arbitrary per-chunk sizes | `[5, 12, 3, 20]` | + +Prior iterations on the chunk grid design were based on the Zarr V3 spec's definition of chunk grids as an extension point alongside codecs, dtypes, etc. Therefore, we started designing the chunk grid implementation following a similar registry-based approach. However, in practice chunk grids are fundamentally different than codecs. Codecs are independent; supporting `zstd` tells you nothing about `gzip`. Chunk grids are not: every regular grid is a valid rectilinear grid. A registry-based plugin system makes sense for codecs but adds complexity without clear benefit for chunk grids. Here we start from some basic goals and propose a more fitting design for supporting different chunk grids in zarr-python. + +## Goals + +1. **Follow the zarr extension proposal.** The implementation should conform to the [rectilinear chunk grid spec](https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear), not innovate on the metadata format. +2. **Minimize changes to the public API.** Users creating regular arrays should see no difference. Rectilinear is additive. +3. **Maintain backwards compatibility.** Existing code using `.chunks`, `isinstance` checks, or importing `RegularChunkGrid`/`RectilinearChunkGrid` from `zarr.core.chunk_grids` should continue to work where practical (with deprecation warnings where appropriate). Internal code paths/imports may be broken with justification. +4. **Design for future iteration.** The internal architecture should allow refactoring (e.g., metadata/array separation, new dimension types) without breaking the public API. +5. **Minimize downstream changes.** xarray, VirtualiZarr, Icechunk, Cubed, etc. should need minimal updates. +6. **Minimize time to stable release.** Ship behind a feature flag, stabilize through real-world usage, promote to stable API. +7. **The new API should be useful.** `read_chunk_sizes`/`write_chunk_sizes`, `ChunkGrid.__getitem__`, `is_regular` — these should solve real problems, not just expose internals. +8. **Extensible for other serialization structures.** The per-dimension design should support future encodings (tile, temporal) without changes to indexing or codecs. + +## Design + +### Design choices + +1. **A chunk grid is a concrete arrangement of chunks.** Not an abstract tiling pattern. This means that the chunk grid is bound to specific array dimensions, which enables the chunk grid to answer any question about any chunk (offset, size, count) without external parameters. +2. **One implementation, multiple serialization forms.** A single `ChunkGrid` class handles all chunking logic. The serialization format (`"regular"` vs `"rectilinear"`) is chosen by the metadata layer, not the grid. +3. **No chunk grid registry.** Simple name-based dispatch in the metadata layer's `parse_chunk_grid()`. +4. **Fixed vs Varying per dimension.** `FixedDimension(size, extent)` for uniform chunks; `VaryingDimension(edges, extent)` for per-chunk edge lengths with precomputed prefix sums. Avoids expanding regular dimensions into lists of identical values. +5. **Transparent transitions.** Operations like `resize()` can move an array from regular to rectilinear chunking. + +### Internal representation + +```python +@dataclass(frozen=True) +class FixedDimension: + """Uniform chunk size. Boundary chunks contain less data but are + encoded at full size by the codec pipeline.""" + size: int # chunk edge length (>= 0) + extent: int # array dimension length + + def __post_init__(self) -> None: + # validates size >= 0 and extent >= 0 + + @property + def nchunks(self) -> int: + if self.size == 0: + return 0 + return ceildiv(self.extent, self.size) + + def index_to_chunk(self, idx: int) -> int: + return idx // self.size # raises IndexError if OOB + def chunk_offset(self, chunk_ix: int) -> int: + return chunk_ix * self.size # raises IndexError if OOB + def chunk_size(self, chunk_ix: int) -> int: + return self.size # always uniform; raises IndexError if OOB + def data_size(self, chunk_ix: int) -> int: + return max(0, min(self.size, self.extent - chunk_ix * self.size)) # raises IndexError if OOB + @property + def unique_edge_lengths(self) -> Iterable[int]: + return (self.size,) # O(1) + def indices_to_chunks(self, indices: NDArray) -> NDArray: + return indices // self.size + def with_extent(self, new_extent: int) -> FixedDimension: + return FixedDimension(size=self.size, extent=new_extent) + def resize(self, new_extent: int) -> FixedDimension: + return FixedDimension(size=self.size, extent=new_extent) + +@dataclass(frozen=True) +class VaryingDimension: + """Explicit per-chunk sizes. The last chunk may extend past the array + extent (extent < sum(edges)), in which case data_size clips to the + valid region while chunk_size returns the full edge length for codec + processing. This underflow is allowed to match how regular grids + handle boundary chunks, and to support shrinking an array without + rewriting chunk edges (the spec allows trailing edges beyond the extent).""" + edges: tuple[int, ...] # per-chunk edge lengths (all > 0) + cumulative: tuple[int, ...] # prefix sums for O(log n) lookup + extent: int # array dimension length (may be < sum(edges)) + + def __init__(self, edges: Sequence[int], extent: int) -> None: + # validates edges non-empty, all > 0, extent >= 0, extent <= sum(edges) + # computes cumulative via itertools.accumulate + # uses object.__setattr__ for frozen dataclass + + @property + def nchunks(self) -> int: + # number of chunks that overlap [0, extent) + if extent == 0: + return 0 + return bisect.bisect_left(self.cumulative, extent) + 1 + + @property + def ngridcells(self) -> int: + return len(self.edges) + + def index_to_chunk(self, idx: int) -> int: + return bisect.bisect_right(self.cumulative, idx) # raises IndexError if OOB + def chunk_offset(self, chunk_ix: int) -> int: + return self.cumulative[chunk_ix - 1] if chunk_ix > 0 else 0 # raises IndexError if OOB + def chunk_size(self, chunk_ix: int) -> int: + return self.edges[chunk_ix] # raises IndexError if OOB + def data_size(self, chunk_ix: int) -> int: + offset = self.chunk_offset(chunk_ix) + return max(0, min(self.edges[chunk_ix], self.extent - offset)) # raises IndexError if OOB + @property + def unique_edge_lengths(self) -> Iterable[int]: + # lazy generator: yields unseen values, short-circuits deduplication + def indices_to_chunks(self, indices: NDArray) -> NDArray: + return np.searchsorted(self.cumulative, indices, side='right') + def with_extent(self, new_extent: int) -> VaryingDimension: + # validates cumulative[-1] >= new_extent (O(1)), re-binds extent + return VaryingDimension(self.edges, extent=new_extent) + def resize(self, new_extent: int) -> VaryingDimension: + # grow past edge sum: append chunk of size (new_extent - sum(edges)) + # shrink or grow within edge sum: preserve all edges, re-bind extent +``` + +Both types implement the `DimensionGrid` protocol: `nchunks`, `extent`, `index_to_chunk`, `chunk_offset`, `chunk_size`, `data_size`, `indices_to_chunks`, `unique_edge_lengths`, `with_extent`, `resize`. Memory usage scales with the number of *varying* dimensions, not total chunks. + +All per-chunk methods (`chunk_offset`, `chunk_size`, `data_size`) raise `IndexError` for out-of-bounds chunk indices, providing consistent fail-fast behavior across both dimension types. + +The two size methods serve different consumers: + +| Method | Returns | Consumer | +|---|---|---| +| `chunk_size` | Buffer size for codec processing | Codec pipeline (`ArraySpec.shape`) | +| `data_size` | Valid data region within the buffer | Indexing pipeline (`chunk_selection` slicing) | + +For `FixedDimension`, these differ only at the boundary. For `VaryingDimension`, these differ only when the last chunk extends past the extent (i.e., `extent < sum(edges)`). This matches current zarr-python behavior: `get_chunk_spec` passes the full `chunk_shape` to the codec for all chunks, and the indexer generates a `chunk_selection` that clips the decoded buffer. + +### DimensionGrid Protocol + +```python +@runtime_checkable +class DimensionGrid(Protocol): + """Structural interface shared by FixedDimension and VaryingDimension.""" + + @property + def nchunks(self) -> int: ... + @property + def ngridcells(self) -> int: ... + @property + def extent(self) -> int: ... + def index_to_chunk(self, idx: int) -> int: ... + def chunk_offset(self, chunk_ix: int) -> int: ... # raises IndexError if OOB + def chunk_size(self, chunk_ix: int) -> int: ... # raises IndexError if OOB + def data_size(self, chunk_ix: int) -> int: ... # raises IndexError if OOB + def indices_to_chunks(self, indices: NDArray[np.intp]) -> NDArray[np.intp]: ... + @property + def unique_edge_lengths(self) -> Iterable[int]: ... + def with_extent(self, new_extent: int) -> DimensionGrid: ... + def resize(self, new_extent: int) -> DimensionGrid: ... +``` + +The protocol is `@runtime_checkable`, enabling polymorphic handling of both dimension types without `isinstance` checks. + +`nchunks` and `ngridcells` differ when `extent < sum(edges)`: `nchunks` counts only chunks that overlap `[0, extent)`, while `ngridcells` counts total defined grid cells (i.e., `len(edges)`). For `FixedDimension`, both are equal. For `VaryingDimension`, they differ after a resize that shrinks the extent below the edge sum. + +### ChunkSpec + +```python +@dataclass(frozen=True) +class ChunkSpec: + slices: tuple[slice, ...] # valid data region in array coordinates + codec_shape: tuple[int, ...] # buffer shape for codec processing + + @property + def shape(self) -> tuple[int, ...]: + return tuple(s.stop - s.start for s in self.slices) + + @property + def is_boundary(self) -> bool: + return self.shape != self.codec_shape +``` + +For interior chunks, `shape == codec_shape`. For boundary chunks of a regular grid, `codec_shape` is the full declared chunk size while `shape` is clipped. For rectilinear grids, `shape == codec_shape` unless the last chunk extends past the extent. + +### API + +```python +# Creating arrays +arr = zarr.create_array(shape=(100, 200), chunks=(10, 20)) # regular +arr = zarr.create_array(shape=(60, 100), chunks=[[10, 20, 30], [25, 25, 25, 25]]) # rectilinear + +# ChunkGrid as a collection +grid = arr._chunk_grid # ChunkGrid (bound to array shape) +grid.grid_shape # (10, 10) — number of chunks per dimension +grid.ndim # 2 +grid.is_regular # True if all dimensions are Fixed + +spec = grid[0, 1] # ChunkSpec for chunk at grid position (0, 1) +spec.slices # (slice(0, 10), slice(20, 40)) +spec.shape # (10, 20) — data shape +spec.codec_shape # (10, 20) — same for interior chunks + +boundary = grid[9, 0] # boundary chunk (extent=100, size=10) +boundary.shape # (10, 20) — data shape +boundary.codec_shape # (10, 20) — codec sees full buffer + +grid[99, 99] # None — out of bounds + +for spec in grid: # iterate all chunks + ... + +# .chunks property: retained for regular grids, raises NotImplementedError for rectilinear +arr.chunks # (10, 20) + +# .read_chunk_sizes / .write_chunk_sizes: works for all grids (dask-style) +arr.write_chunk_sizes # ((10, 10, ..., 10), (20, 20, ..., 20)) +``` + +`ChunkGrid.__getitem__` constructs `ChunkSpec` using `chunk_size` for `codec_shape` and `data_size` for `slices`: + +```python +def __getitem__(self, coords: int | tuple[int, ...]) -> ChunkSpec | None: + if isinstance(coords, int): + coords = (coords,) + slices = [] + codec_shape = [] + for dim, ix in zip(self.dimensions, coords): + if ix < 0 or ix >= dim.nchunks: + return None + offset = dim.chunk_offset(ix) + slices.append(slice(offset, offset + dim.data_size(ix))) + codec_shape.append(dim.chunk_size(ix)) + return ChunkSpec(tuple(slices), tuple(codec_shape)) +``` + +#### Construction + +`from_sizes` requires `array_shape`, binding the extent per dimension at construction time. This is a core design choice: a chunk grid is a concrete arrangement for a specific array, not an abstract tiling pattern. + +```python +# Regular grid — all FixedDimension +grid = ChunkGrid.from_sizes(array_shape=(100, 200), chunk_sizes=(10, 20)) + +# Rectilinear grid — extent = sum(edges) when shape matches +grid = ChunkGrid.from_sizes(array_shape=(60, 100), chunk_sizes=[[10, 20, 30], [25, 25, 25, 25]]) + +# Rectilinear grid with boundary clipping — last chunk extends past array extent +# e.g., shape=(55, 90) but edges sum to (60, 100): data_size clips at extent +grid = ChunkGrid.from_sizes(array_shape=(55, 90), chunk_sizes=[[10, 20, 30], [25, 25, 25, 25]]) + +# Direct construction +grid = ChunkGrid(dimensions=(FixedDimension(10, 100), VaryingDimension([10, 20, 30], 55))) +``` + +When `extent < sum(edges)`, the dimension is always stored as `VaryingDimension` (even if all edges are identical) to preserve the explicit edge count. The last chunk's `chunk_size` returns the full declared edge (codec buffer) while `data_size` clips to the extent. This mirrors how `FixedDimension` handles boundary chunks in regular grids. + +#### Serialization + +```python +# Regular grid: +{"name": "regular", "configuration": {"chunk_shape": [10, 20]}} + +# Rectilinear grid (with RLE compression and "kind" field): +{"name": "rectilinear", "configuration": {"kind": "inline", "chunk_shapes": [[10, 20, 30], [[25, 4]]]}} +``` + +Both names deserialize to the same `ChunkGrid` class. The serialized form does not include the array extent — that comes from `shape` in array metadata and is combined with the chunk grid when constructing a `ChunkGrid` via `ChunkGrid.from_metadata()`. + +**The `ChunkGrid` does not serialize itself.** The format choice (`"regular"` vs `"rectilinear"`) belongs to `ArrayV3Metadata`. Serialization and deserialization are handled by the metadata-layer chunk grid classes (`RegularChunkGridMetadata` and `RectilinearChunkGridMetadata` in `metadata/v3.py`), which provide `to_dict()` and `from_dict()` methods. + +For `create_array`, the format is inferred from the `chunks` argument: a flat tuple produces `"regular"`, a nested list produces `"rectilinear"`. The `_is_rectilinear_chunks()` helper detects nested sequences like `[[10, 20], [5, 5]]`. + +##### Rectilinear spec compliance + +The rectilinear format requires `"kind": "inline"` (validated by `validate_rectilinear_kind()`). Per the spec, each element of `chunk_shapes` can be: + +- A bare integer `m`: repeated until `sum >= array_extent` +- A list of bare integers: explicit per-chunk sizes +- A mixed array of bare integers and `[value, count]` RLE pairs + +RLE compression is used when serializing: runs of identical sizes become `[value, count]` pairs, singletons stay as bare integers. + +```python +# compress_rle([10, 10, 10, 5]) -> [[10, 3], 5] +# expand_rle([[10, 3], 5]) -> [10, 10, 10, 5] +``` + +For a single-element `chunk_shapes` tuple like `(10,)`, `RectilinearChunkGridMetadata.to_dict()` serializes it as a bare integer `10`. Per the rectilinear spec, a bare integer is repeated until the sum >= extent, preserving the full codec buffer size for boundary chunks. + +**Zero-extent handling:** Regular grids serialize zero-extent dimensions without issue (the format encodes only `chunk_shape`, no edges). Rectilinear grids cannot represent zero-extent dimensions because the spec requires at least one positive-integer edge length per axis. + +#### read_chunk_sizes / write_chunk_sizes + +The `read_chunk_sizes` and `write_chunk_sizes` properties provide universal access to per-dimension chunk data sizes, matching the dask `Array.chunks` convention. They work for both regular and rectilinear grids: + +- `write_chunk_sizes`: always returns outer (storage) chunk sizes +- `read_chunk_sizes`: returns inner chunk sizes when sharding is used, otherwise same as `write_chunk_sizes` + +```python +>>> arr = zarr.create_array(store, shape=(100, 80), chunks=(30, 40)) +>>> arr.write_chunk_sizes +((30, 30, 30, 10), (40, 40)) + +>>> arr = zarr.create_array(store, shape=(60, 100), chunks=[[10, 20, 30], [50, 50]]) +>>> arr.write_chunk_sizes +((10, 20, 30), (50, 50)) +``` + +The underlying `ChunkGrid.chunk_sizes` property (on the grid, not the array) returns the same as `write_chunk_sizes`. + +#### Resize + +```python +arr.resize((80, 100)) # re-binds extent; FixedDimension stays fixed +arr.resize((200, 100)) # VaryingDimension grows by appending a new chunk +arr.resize((30, 100)) # VaryingDimension shrinks: preserves all edges, re-binds extent +``` + +Resize uses `ChunkGrid.update_shape(new_shape)`, which delegates to each dimension's `.resize()` method: +- `FixedDimension.resize()`: simply re-binds the extent (identical to `with_extent`) +- `VaryingDimension.resize()`: grow past `sum(edges)` appends a chunk covering the gap; shrink or grow within `sum(edges)` preserves all edges and re-binds the extent (the spec allows trailing edges beyond the array extent) + +**Known limitation (deferred):** When growing a `VaryingDimension`, the current implementation always appends a single chunk covering the new region. For example, `[10, 10, 10]` resized from 30 to 45 produces `[10, 10, 10, 15]` instead of the more natural `[10, 10, 10, 10, 10]`. A future improvement should add an optional `chunks` parameter to `resize()` that controls how the new region is partitioned, with a sane default (e.g., repeating the last chunk size). This is safely deferrable because: +- `FixedDimension` already handles resize correctly (regular grids stay regular) +- The single-chunk default produces valid state, just suboptimal chunk layout +- Rectilinear arrays are behind an experimental feature flag +- Adding an optional parameter is backwards-compatible + +Open design questions for the `chunks` parameter: +- Does it describe the new region only, or the entire post-resize array? +- Must the overlapping portion agree with existing chunks (no rechunking)? +- What is the type? Same as `chunks` in `create_array`? + +#### from_array + +The `from_array()` function handles both regular and rectilinear source arrays: + +```python +src = zarr.create_array(store, shape=(60, 100), chunks=[[10, 20, 30], [50, 50]]) +new = zarr.from_array(data=src, store=new_store, chunks="keep") +# Preserves rectilinear structure: new.write_chunk_sizes == ((10, 20, 30), (50, 50)) +``` + +When `chunks="keep"`, the logic checks `data._chunk_grid.is_regular`: +- Regular: extracts `data.chunks` (flat tuple) and preserves shards +- Rectilinear: extracts `data.write_chunk_sizes` (nested tuples) and forces shards to None + +### Indexing + +The indexing pipeline is coupled to regular grid assumptions — every per-dimension indexer takes a scalar `dim_chunk_len: int` and uses `//` and `*`: + +```python +dim_chunk_ix = self.dim_sel // self.dim_chunk_len # IntDimIndexer +dim_offset = dim_chunk_ix * self.dim_chunk_len # SliceDimIndexer +``` + +Replace `dim_chunk_len: int` with the dimension object (`FixedDimension | VaryingDimension`). The shared interface means the indexer code structure stays the same — `dim_sel // dim_chunk_len` becomes `dim_grid.index_to_chunk(dim_sel)`. O(1) for regular, binary search for varying. + +### Codec pipeline + +Today, `get_chunk_spec()` returns the same `ArraySpec(shape=chunk_grid.chunk_shape)` for every chunk. For rectilinear grids, each chunk has a different codec shape: + +```python +def get_chunk_spec(self, chunk_coords, array_config, prototype) -> ArraySpec: + spec = self._chunk_grid[chunk_coords] + return ArraySpec(shape=spec.codec_shape, ...) +``` + +Note `spec.codec_shape`, not `spec.shape`. For regular grids, `codec_shape` is uniform (preserving current behavior). The boundary clipping flow is unchanged: + +``` +Write: user data → pad to codec_shape with fill_value → encode → store +Read: store → decode to codec_shape → slice via chunk_selection → user data +``` + +### Sharding + +The `ShardingCodec` constructs a `ChunkGrid` per shard using the shard shape as extent and the subchunk shape as `FixedDimension`. Each shard is self-contained — it doesn't need to know whether the outer grid is regular or rectilinear. Validation checks that every unique edge length per dimension is divisible by the inner chunk size, using `dim.unique_edge_lengths` for efficient polymorphic iteration (O(1) for fixed dimensions, lazy-deduplicated for varying). + +``` +Level 1 — Outer chunk grid (shard boundaries): regular or rectilinear +Level 2 — Inner subchunk grid (within each shard): always regular +Level 3 — Shard index: ceil(shard_dim / subchunk_dim) entries per dimension +``` + +[zarr-specs#370](https://github.com/zarr-developers/zarr-specs/pull/370) lifts the requirement that subchunk shapes evenly divide the shard shape. With the proposed `ChunkGrid`, this just means removing the `shard_shape % subchunk_shape == 0` validation — `FixedDimension` already handles boundary clipping via `data_size`. + +| Outer grid | Subchunk divisibility | Required change | +|---|---|---| +| Regular | Evenly divides (v1.0) | None | +| Regular | Non-divisible (v1.1) | Remove divisibility validation | +| Rectilinear | Evenly divides | Remove "sharding incompatible" guard | +| Rectilinear | Non-divisible | Both changes | + +### What this replaces + +| Current | Proposed | +|---|---| +| `ChunkGrid` ABC + `RegularChunkGrid` subclass | Single concrete `ChunkGrid` with `is_regular` | +| `RectilinearChunkGrid` (#3534) | Same `ChunkGrid` class | +| Chunk grid registry + entrypoints (#3735) | Direct name dispatch | +| `arr.chunks` | Retained for regular; `arr.read_chunk_sizes`/`arr.write_chunk_sizes` for general use | +| `get_chunk_shape(shape, coord)` | `grid[coord].codec_shape` or `grid[coord].shape` | + +## Design decisions + +### Why store the extent in ChunkGrid? + +The chunk grid is a concrete arrangement, not an abstract tiling pattern. A finite collection naturally has an extent. Storing it enables `__getitem__`, eliminates `dim_len` parameters from every method, and makes the grid self-describing. + +This does *not* mean `ArrayV3Metadata.shape` should delegate to the grid. The array shape remains an independent field in metadata. The extent is passed into the grid at construction time so it can answer boundary questions without external parameters. It is **not** serialized as part of the chunk grid JSON — it comes from the `shape` field in array metadata and is combined with the chunk grid configuration in `ChunkGrid.from_metadata()`. + +### Why distinguish chunk_size from data_size? + +A chunk in a regular grid has two sizes. `chunk_size` is the buffer size the codec processes — always `size` for `FixedDimension`, even at the boundary (padded with `fill_value`). `data_size` is the valid data region — clipped to `extent % size` at the boundary. The indexing layer uses `data_size` to generate `chunk_selection` slices. + +This matches current zarr-python behavior and matters for: +1. **Backward compatibility.** Existing stores have boundary chunks encoded at full `chunk_shape`. +2. **Codec simplicity.** Codecs assume uniform input shapes for regular grids. +3. **Shard index correctness.** The index assumes `subchunk_dim`-sized entries. + +For `VaryingDimension`, `chunk_size == data_size` when `extent == sum(edges)`. When `extent < sum(edges)` (e.g., after a resize that keeps the last chunk oversized), `data_size` clips the last chunk. This is the fundamental difference: `FixedDimension` has a declared size plus an extent that clips data; `VaryingDimension` has explicit sizes that normally *are* the extent but can also extend past it. + +### Why not a chunk grid registry? + +There is no known chunk grid outside the rectilinear family that retains the tessellation properties zarr-python assumes. A `match` on the grid name is sufficient. + +### Why a single ChunkGrid class instead of RegularChunkGrid + RectilinearChunkGrid? + +[Discussed in #3534.](https://github.com/zarr-developers/zarr-python/pull/3534) @d-v-b argued that `RegularChunkGrid` is unnecessary since rectilinear is more general; @dcherian argued that downstream libraries need a fast way to detect regular grids without inspecting potentially millions of chunk edges (see [xarray#9808](https://github.com/pydata/xarray/pull/9808)). + +The resolution: a single `ChunkGrid` class with an `is_regular` property (O(1), cached at construction). This gives downstream code the fast-path detection @dcherian needed without the class hierarchy complexity @d-v-b wanted to avoid. The metadata document's `name` field (`"regular"` vs `"rectilinear"`) is also available for clients who inspect JSON directly. + +A backwards-compatibility shim in `chunk_grids.py` preserves the old `RegularChunkGrid` / `RectilinearChunkGrid` import paths with deprecation warnings — see [Backwards compatibility](#backwards-compatibility). + +### Why is ChunkGrid a concrete class instead of a Protocol/ABC? + +The old design had `ChunkGrid` as an ABC with `RegularChunkGrid` as its only subclass. #3534 added `RectilinearChunkGrid` as a second subclass. This branch makes `ChunkGrid` a single concrete class instead, with separate metadata DTOs (`RegularChunkGridMetadata` and `RectilinearChunkGridMetadata` in `metadata/v3.py`) for serialization. + +All known grids are special cases of rectilinear, so there's no need for a class hierarchy at the grid level. A `ChunkGrid` Protocol/ABC would mean every caller programs against an abstract interface and adding a grid type requires implementing ~15 methods. A single class is simpler. + +Note: the *dimension* types (`FixedDimension`, `VaryingDimension`) do use a `DimensionGrid` Protocol — that's where the polymorphism lives. The grid-level class is concrete; the dimension-level types are polymorphic. If a genuinely novel grid type emerges that can't be expressed as a combination of per-dimension types, a grid-level Protocol can be extracted. + +### Why `.chunks` raises for rectilinear grids + +[Debated in #3534.](https://github.com/zarr-developers/zarr-python/pull/3534) @d-v-b suggested making `.chunks` return `tuple[tuple[int, ...], ...]` (dask-style) for all grids. @dcherian strongly objected: every downstream consumer expects `tuple[int, ...]`, and silently returning a different type would be worse than raising. Materializing O(10M) chunk edges into a Python tuple is also a real performance risk ([xarray#8902](https://github.com/pydata/xarray/issues/8902#issuecomment-2546127373)). + +The resolution: +- `.chunks` is retained for regular grids (returns `tuple[int, ...]` as before) +- `.chunks` raises `NotImplementedError` for rectilinear grids with a message pointing to `.read_chunk_sizes`/`.write_chunk_sizes` +- `.read_chunk_sizes` and `.write_chunk_sizes` return `tuple[tuple[int, ...], ...]` (dask convention) for all grids + +@maxrjones noted in review that deprecating `.chunks` for regular grids was not desirable. The current branch does not deprecate it. + +### User control over grid serialization format + +@d-v-b raised in #3534 that users need a way to say "these chunks are regular, but serialize as rectilinear" (e.g., to allow future append/extend workflows without format changes). @jhamman initially made nested-list input always produce `RectilinearChunkGridMetadata`. + +The current branch resolves this via the metadata-layer chunk grid classes. When metadata is deserialized, the original name (from `{"name": "regular"}` or `{"name": "rectilinear"}`) determines which metadata class is instantiated (`RegularChunkGridMetadata` or `RectilinearChunkGridMetadata`), and that class handles serialization via `to_dict()`. Current inference behavior for `create_array`: +- `chunks=(10, 20)` (flat tuple) → infers `"regular"` +- `chunks=[[10, 20], [5, 5]]` (nested lists with varying sizes) → infers `"rectilinear"` +- `chunks=[[10, 10], [20, 20]]` (nested lists with uniform sizes) → `from_sizes` collapses to `FixedDimension`, so `is_regular=True` and infers `"regular"` + +**Open question:** Should uniform nested lists preserve `"rectilinear"` to support future append workflows without a format change? This could be addressed by checking the input form before collapsing, or by allowing users to pass `chunk_grid_name` explicitly through the `create_array` API. + +### Deferred: Tiled/periodic chunk patterns + +[#3750 discussion](https://github.com/zarr-developers/zarr-python/issues/3750) identified periodic chunk patterns as a use case not efficiently served by RLE alone. RLE compresses runs of identical values (`np.repeat`), but periodic patterns like days-per-month (`[31, 28, 31, 30, ...]` repeated 30 years) need a tile encoding (`np.tile`). Real-world examples include: + +- **Oceanographic models** (ROMS): HPC boundary-padded chunks like `[10, 8, 8, 8, 10]` — handled by RLE +- **Temporal axes**: days-per-month, hours-per-day — need tile encoding for compact metadata +- **Temporal-aware grids**: date/time-aware chunk grids that layer over other axes (raised by @LDeakin) + +A `TiledDimension` prototype was built ([commit 9c0f582](https://github.com/maxrjones/zarr-python/commit/9c0f582f)) demonstrating that the per-dimension design supports this without changes to indexing or the codec pipeline. However, it was intentionally excluded from this release because: + +1. **Metadata format must come first.** Tile encoding requires a new `kind` value in the rectilinear spec (currently only `"inline"` is defined). This should go through [zarr-extensions#25](https://github.com/zarr-developers/zarr-extensions/pull/25), not zarr-python unilaterally. +2. **The per-dimension architecture doesn't preclude it.** A future `TiledDimension` can implement the `DimensionGrid` protocol alongside `FixedDimension` and `VaryingDimension` with no changes to indexing, codecs, or the `ChunkGrid` class. +3. **RLE covers the MVP.** Most real-world variable chunk patterns (HPC boundaries, irregular partitions) are efficiently encoded with RLE. Tile encoding is an optimization for a specific (temporal) subset. + +### Metadata / Array separation (partially implemented) + +An earlier design doc proposed decoupling `ChunkGrid` (runtime) from `ArrayV3Metadata` (serialization), so that metadata would store only a plain dict and the array layer would construct the `ChunkGrid`. + +The current implementation partially realizes this separation: + +- **Metadata DTOs** (`RegularChunkGridMetadata`, `RectilinearChunkGridMetadata` in `metadata/v3.py`): Pure data, frozen dataclasses, no array shape. These live on `ArrayV3Metadata.chunk_grid` and represent only what goes into `zarr.json`. +- **`ChunkGrid`** (`chunk_grids.py`): Shape-bound, supports indexing, iteration, and chunk specs. Lives on `AsyncArray._chunk_grid`, constructed from metadata + `shape` via `ChunkGrid.from_metadata()`. + +This means `ArrayV3Metadata.chunk_grid` is now a `ChunkGridMetadata` (the DTO union type), **not** the runtime `ChunkGrid`. Code that previously accessed runtime methods on `metadata.chunk_grid` (e.g., `all_chunk_coords()`, `__getitem__`) must now use the grid from the array layer instead. + +The name controls serialization format; each metadata DTO class provides its own `to_dict()` method for serialization. The `ChunkGrid` handles all runtime queries. + +## Prior art + +**zarrs (Rust):** Three independent grid types behind a `ChunkGridTraits` trait. Key patterns adopted: Fixed vs Varying per dimension, prefix sums + binary search, `Option` for out-of-bounds, `NonZeroU64` for chunk dimensions, separate subchunk grid per shard, array shape at construction. + +**TensorStore (C++):** Stores only `chunk_shape` — boundary clipping via `valid_data_bounds` at query time. Both `RegularGridRef` and `IrregularGrid` internally. No registry. + +## Migration + +### Public API compatibility + +The user-facing API is fully backward-compatible. Existing code that creates, opens, reads, and writes zarr arrays continues to work without changes: + +- `zarr.create_array`, `zarr.open`, `zarr.open_array`, `zarr.open_group` -- unchanged signatures. The `chunks` parameter type is *widened* (now also accepts nested sequences for rectilinear grids), but all existing call patterns still work. +- `arr.chunks` -- returns `tuple[int, ...]` for regular arrays, same as before. +- `arr.shape`, `arr.dtype`, `arr.ndim`, `arr.shards` -- unchanged. +- Top-level `zarr` exports -- unchanged. +- Rectilinear chunks are gated behind `zarr.config.set({'array.rectilinear_chunks': True})`, so they cannot be created accidentally. + +New additions (purely additive): `arr.read_chunk_sizes`, `arr.write_chunk_sizes`, `zarr.experimental.ChunkGrid`, `zarr.experimental.ChunkSpec`. + +The breaking changes discussed below are confined to **internal modules** (`zarr.core.chunk_grids`, `zarr.core.metadata.v3`, `zarr.core.indexing`) that downstream libraries like cubed and VirtualiZarr access directly. + +### Internal API compatibility trade-off analysis + +This section analyzes the internal breaking changes from the metadata/array separation and evaluates two strategies: (A) add backward-compatibility shims in zarr-python, vs. (B) require downstream packages to update. The baseline is **no shims at all**. + +#### What breaks without any shims + +Three API changes affect downstream code: + +1. **`RegularChunkGrid` class removed from `zarr.core.chunk_grids`.** On `main`, `RegularChunkGrid` is defined in `chunk_grids.py` as a `Metadata` subclass. This branch replaces it with `RegularChunkGridMetadata` in `metadata/v3.py`. Without a shim, `from zarr.core.chunk_grids import RegularChunkGrid` raises `ImportError`. + +2. **`RegularChunkGrid` no longer available from `zarr.core.metadata.v3`.** On `main`, `v3.py` imports `RegularChunkGrid` from `chunk_grids.py` for internal use. VirtualiZarr imports it from this location (`from zarr.core.metadata.v3 import RegularChunkGrid`). Without the internal import, this raises `ImportError`. + +3. **`OrthogonalIndexer` constructor expects `ChunkGrid`, not `RegularChunkGrid`/`RegularChunkGridMetadata`.** Even if the import shims above resolve to `RegularChunkGridMetadata`, the indexer constructors access `chunk_grid._dimensions`, which only exists on the runtime `ChunkGrid` class. Cubed constructs `OrthogonalIndexer(selection, shape, RegularChunkGrid(chunk_shape=chunks))` directly. + +#### Downstream impact without shims + +**VirtualiZarr** (5 line changes across 2 files): + +```python +# manifests/array.py (line 6): import +- from zarr.core.metadata.v3 import ArrayV3Metadata, RegularChunkGrid ++ from zarr.core.metadata.v3 import ArrayV3Metadata, RegularChunkGridMetadata + +# manifests/array.py (line 53): isinstance check +- if not isinstance(_metadata.chunk_grid, RegularChunkGrid): ++ if not isinstance(_metadata.chunk_grid, RegularChunkGridMetadata): + +# parsers/zarr.py (line 16): import +- from zarr.core.chunk_grids import RegularChunkGrid ++ from zarr.core.metadata.v3 import RegularChunkGridMetadata + +# parsers/zarr.py (line 270): isinstance check +- if not isinstance(array_v3_metadata.chunk_grid, RegularChunkGrid): ++ if not isinstance(array_v3_metadata.chunk_grid, RegularChunkGridMetadata): + +# parsers/zarr.py (line 390): cast +- cast(RegularChunkGrid, metadata.chunk_grid).chunk_shape ++ cast(RegularChunkGridMetadata, metadata.chunk_grid).chunk_shape +``` + +The `manifests/array.py` import is from `zarr.core.metadata.v3` (never a documented export; VirtualiZarr relied on a transitive import). The `parsers/zarr.py` import is from `zarr.core.chunk_grids` (the canonical location on `main`). Both are straightforward renames. The `.chunk_shape` attribute is unchanged on the new class. + +If VirtualiZarr needs to support both old and new zarr-python, a version-conditional import adds ~5 more lines. + +**Cubed** (3 line changes in 1 file): + +```python +# core/ops.py (lines 626-631) +def _create_zarr_indexer(selection, shape, chunks): + if zarr.__version__[0] == "3": +- from zarr.core.chunk_grids import RegularChunkGrid ++ from zarr.core.chunk_grids import ChunkGrid + from zarr.core.indexing import OrthogonalIndexer +- return OrthogonalIndexer(selection, shape, RegularChunkGrid(chunk_shape=chunks)) ++ return OrthogonalIndexer(selection, shape, ChunkGrid.from_sizes(shape, chunks)) +``` + +Note that `ChunkGrid` is *not* a renamed class. `RegularChunkGrid(chunk_shape=chunks)` took only chunk sizes; `ChunkGrid.from_sizes(shape, chunks)` also requires the array shape. The `shape` parameter is already available at this call site. + +If cubed needs to support both old and new zarr-python: + +```python +def _create_zarr_indexer(selection, shape, chunks): + if zarr.__version__[0] == "3": + from zarr.core.indexing import OrthogonalIndexer + try: + from zarr.core.chunk_grids import ChunkGrid + return OrthogonalIndexer(selection, shape, ChunkGrid.from_sizes(shape, chunks)) + except ImportError: + from zarr.core.chunk_grids import RegularChunkGrid + return OrthogonalIndexer(selection, shape, RegularChunkGrid(chunk_shape=chunks)) + else: + from zarr.indexing import OrthogonalIndexer + return OrthogonalIndexer(selection, ZarrArrayIndexingAdaptor(shape, chunks)) +``` + +#### What shims can cover + +**Shim 1: `__getattr__` in `chunk_grids.py`** (~15 lines) + +Maps `RegularChunkGrid` to `RegularChunkGridMetadata` with a deprecation warning. Covers: +- The `from zarr.core.chunk_grids import RegularChunkGrid` import pattern (used by cubed and VirtualiZarr's `parsers/zarr.py`) +- `isinstance(x, RegularChunkGrid)` checks (because the name resolves to the actual class) +- `RegularChunkGrid(chunk_shape=(...))` construction (because `RegularChunkGridMetadata` accepts the same arguments) + +Does **not** cover: passing the result to `OrthogonalIndexer`, because `RegularChunkGridMetadata` lacks `._dimensions`. + +**Shim 2: `__getattr__` in `metadata/v3.py`** (~12 lines) + +Same pattern, covers VirtualiZarr's import from `zarr.core.metadata.v3`. Mirrors Shim 1 for a different import path. + +**Shim 3: Auto-coerce `ChunkGridMetadata` in indexer constructors** (~30 lines) + +A helper function + 1-line insertion in each of `BasicIndexer`, `OrthogonalIndexer`, `CoordinateIndexer`, and `MaskIndexer`: + +```python +def _resolve_chunk_grid(chunk_grid, shape): + """Coerce ChunkGridMetadata to runtime ChunkGrid if needed.""" + from zarr.core.chunk_grids import ChunkGrid as _ChunkGrid + from zarr.core.metadata.v3 import ChunkGridMetadata + if isinstance(chunk_grid, _ChunkGrid): + return chunk_grid + if isinstance(chunk_grid, ChunkGridMetadata): + warnings.warn( + "Passing ChunkGridMetadata to indexers is deprecated. " + "Use ChunkGrid.from_sizes() instead.", + DeprecationWarning, stacklevel=2, + ) + if hasattr(chunk_grid, "chunk_shape"): + return _ChunkGrid.from_sizes(shape, tuple(chunk_grid.chunk_shape)) + return _ChunkGrid.from_sizes(shape, chunk_grid.chunk_shapes) + raise TypeError(f"Expected ChunkGrid or ChunkGridMetadata, got {type(chunk_grid)}") +``` + +This covers cubed's `OrthogonalIndexer(selection, shape, RegularChunkGrid(...))` pattern end-to-end (combined with Shim 1). + +#### Comparison + +| | No shims | Shims 1+2 only | Shims 1+2+3 | +|---|---|---|---| +| **zarr-python additions** | 0 lines | ~27 lines | ~57 lines | +| **VirtualiZarr changes** | 5 lines | 0 lines | 0 lines | +| **Cubed changes** | 3 lines | 3 lines | 0 lines | +| **Maintenance burden** | None | Low (deprecation shims are well-understood) | Medium (indexer coercion blurs metadata/runtime boundary) | +| **API clarity** | Clean (metadata DTOs and runtime types are distinct) | Good (old names redirect to new names) | Weaker (indexers implicitly accept two type families) | + +With Shims 1+2 only, VirtualiZarr's `manifests/array.py` import from `zarr.core.metadata.v3` is covered by Shim 2, and the `parsers/zarr.py` import from `zarr.core.chunk_grids` is covered by Shim 1. The `isinstance` checks work because both shims resolve to `RegularChunkGridMetadata`. The `cast` works because `.chunk_shape` is unchanged. So VirtualiZarr needs 0 changes with Shims 1+2. The 3 lines for cubed remain because Shim 1 resolves the import but `OrthogonalIndexer` still needs a runtime `ChunkGrid`. + +### Downstream migration + +Migration from `main` (where only `RegularChunkGrid` and the abstract `ChunkGrid` ABC exist): + +| Old pattern (on `main`) | New pattern | +|---|---| +| `from zarr.core.chunk_grids import RegularChunkGrid` | `from zarr.core.metadata.v3 import RegularChunkGridMetadata` | +| `from zarr.core.chunk_grids import ChunkGrid` (ABC) | `from zarr.core.chunk_grids import ChunkGrid` (concrete class, different API) | +| `isinstance(cg, RegularChunkGrid)` | `isinstance(cg, RegularChunkGridMetadata)` or `grid.is_regular` on the runtime `ChunkGrid` | +| `cg.chunk_shape` on `RegularChunkGrid` | `cg.chunk_shape` on `RegularChunkGridMetadata` (unchanged) | +| `ChunkGrid.from_dict(data)` | `parse_chunk_grid(data)` from `zarr.core.metadata.v3` | +| `chunk_grid.all_chunk_coords(array_shape)` | `chunk_grid.all_chunk_coords()` (shape now stored in grid) | +| `chunk_grid.get_nchunks(array_shape)` | `chunk_grid.get_nchunks()` (shape now stored in grid) | + +During the earlier [#3534](https://github.com/zarr-developers/zarr-python/pull/3534) effort (which used separate `RegularChunkGrid`/`RectilinearChunkGrid` classes), downstream PRs and issues were opened to explore compatibility: + +- xarray ([#10880](https://github.com/pydata/xarray/pull/10880)), VirtualiZarr ([#877](https://github.com/zarr-developers/VirtualiZarr/pull/877)), Icechunk ([#1338](https://github.com/earth-mover/icechunk/issues/1338)), cubed ([#876](https://github.com/cubed-dev/cubed/issues/876)) + +These target #3534's API, not this branch's unified `ChunkGrid` design. New downstream POC branches for this design are linked in [Proofs of concepts](#proofs-of-concepts). + +### Credits + +This implementation builds on prior work: + +- **[#3534](https://github.com/zarr-developers/zarr-python/pull/3534)** (@jhamman) — RLE helpers, validation logic, test cases, and the review discussion that shaped the architecture. +- **[#3737](https://github.com/zarr-developers/zarr-python/pull/3737)** — extent-in-grid idea (adopted per-dimension). +- **[#1483](https://github.com/zarr-developers/zarr-python/pull/1483)** — original variable chunking POC. +- **[#3736](https://github.com/zarr-developers/zarr-python/pull/3736)** — resolved by storing extent per-dimension. + + +## Open questions + +1. **Resize defaults (deferred):** When growing a rectilinear array, should `resize()` accept an optional `chunks` parameter? See the [Resize section](#resize) for details and open design questions. Regular arrays already stay regular on resize. +2. **`ChunkSpec` complexity:** `ChunkSpec` carries both `slices` and `codec_shape`. Should the grid expose separate methods for codec vs data queries instead? +3. **`__getitem__` with slices:** Should `grid[0, :]` or `grid[0:3, :]` return a sub-grid or an iterator of `ChunkSpec`s? +4. **Uniform nested lists:** Should `chunks=[[10, 10], [20, 20]]` serialize as `"rectilinear"` (preserving user intent for future append) or `"regular"` (current behavior, collapses uniform edges)? See [User control over grid serialization format](#user-control-over-grid-serialization-format). +5. **`zarr.open` with rectilinear:** @tomwhite noted in #3534 that `zarr.open(mode="w")` doesn't support rectilinear chunks directly. This could be addressed in a follow-up. + +## Proofs of concepts + +- Zarr-Python: + - branch - https://github.com/maxrjones/zarr-python/tree/poc/unified-chunk-grid + - diff - https://github.com/zarr-developers/zarr-python/compare/main...maxrjones:zarr-python:poc/unified-chunk-grid?expand=1 +- Xarray: + - branch - https://github.com/maxrjones/xarray/tree/poc/unified-zarr-chunk-grid + - diff - https://github.com/pydata/xarray/compare/main...maxrjones:xarray:poc/unified-zarr-chunk-grid?expand=1 +- VirtualiZarr: + - branch - https://github.com/maxrjones/VirtualiZarr/tree/poc/unified-chunk-grid + - diff - https://github.com/zarr-developers/VirtualiZarr/compare/main...maxrjones:VirtualiZarr:poc/unified-chunk-grid?expand=1 +- Virtual TIFF: + - branch - https://github.com/virtual-zarr/virtual-tiff/tree/poc/unified-chunk-grid + - diff - https://github.com/virtual-zarr/virtual-tiff/compare/main...poc/unified-chunk-grid?expand=1 +- Cubed: + - branch - https://github.com/maxrjones/cubed/tree/poc/unified-chunk-grid +- Microbenchmarks: + - https://github.com/maxrjones/zarr-chunk-grid-tests/tree/unified-chunk-grid diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 5db5c946a3..46ff803464 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -611,6 +611,171 @@ In this example a shard shape of (1000, 1000) and a chunk shape of (100, 100) is This means that `10*10` chunks are stored in each shard, and there are `10*10` shards in total. Without the `shards` argument, there would be 10,000 chunks stored as individual files. +## Rectilinear (variable) chunk grids + +!!! warning "Experimental" + Rectilinear chunk grids are an experimental feature and may change in + future releases. This feature is expected to stabilize in Zarr version 3.3. + + Because the feature is still stabilizing, it is disabled by default and + must be explicitly enabled: + + ```python + import zarr + zarr.config.set({"array.rectilinear_chunks": True}) + ``` + + Or via the environment variable `ZARR_ARRAY__RECTILINEAR_CHUNKS=True`. + + The examples below assume this config has been set. + +By default, Zarr arrays use a regular chunk grid where every chunk along a +given dimension has the same size (except possibly the final boundary chunk). +Rectilinear chunk grids allow each chunk along a dimension to have a different +size. This is useful when the natural partitioning of the data is not uniform — +for example, satellite swaths of varying width, time series with irregular +intervals, or spatial tiles of different extents. + +### Creating arrays with rectilinear chunks + +To create an array with rectilinear chunks, pass a nested list to the `chunks` +parameter where each inner list gives the chunk sizes along one dimension: + +```python exec="true" session="arrays" source="above" result="ansi" +zarr.config.set({"array.rectilinear_chunks": True}) +z = zarr.create_array( + store=zarr.storage.MemoryStore(), + shape=(60, 100), + chunks=[[10, 20, 30], [50, 50]], + dtype='int32', +) +print(z.info) +``` + +In this example the first dimension is split into three chunks of sizes 10, 20, +and 30, while the second dimension is split into two equal chunks of size 50. + +### Reading and writing data + +Rectilinear arrays support the same indexing interface as regular arrays. +Reads and writes that cross chunk boundaries of different sizes are handled +automatically: + +```python exec="true" session="arrays" source="above" result="ansi" +import numpy as np +data = np.arange(60 * 100, dtype='int32').reshape(60, 100) +z[:] = data +# Read a slice that spans the first two chunks (sizes 10 and 20) along axis 0 +print(z[5:25, 0:5]) +``` + +### Inspecting chunk sizes + +The `.write_chunk_sizes` property returns the actual data size of each storage +chunk along every dimension. It works for both regular and rectilinear arrays +and returns a tuple of tuples (matching the dask `Array.chunks` convention). +When sharding is used, `.read_chunk_sizes` returns the inner chunk sizes instead: + +```python exec="true" session="arrays" source="above" result="ansi" +print(z.write_chunk_sizes) +``` + +For regular arrays, this includes the boundary chunk: + +```python exec="true" session="arrays" source="above" result="ansi" +z_regular = zarr.create_array( + store=zarr.storage.MemoryStore(), + shape=(100, 80), + chunks=(30, 40), + dtype='int32', +) +print(z_regular.write_chunk_sizes) +``` + +Note that the `.chunks` property is only available for regular chunk grids. For +rectilinear arrays, use `.write_chunk_sizes` (or `.read_chunk_sizes`) instead. + +### Resizing and appending + +Rectilinear arrays can be resized. When growing past the current edge sum, a +new chunk is appended covering the additional extent. When shrinking, the chunk +edges are preserved and the extent is re-bound (chunks beyond the new extent +simply become inactive): + +```python exec="true" session="arrays" source="above" result="ansi" +z = zarr.create_array( + store=zarr.storage.MemoryStore(), + shape=(30,), + chunks=[[10, 20]], + dtype='float64', +) +z[:] = np.arange(30, dtype='float64') +print(f"Before resize: chunk_sizes={z.write_chunk_sizes}") +z.resize((50,)) +print(f"After resize: chunk_sizes={z.write_chunk_sizes}") +``` + +The `append` method also works with rectilinear arrays: + +```python exec="true" session="arrays" source="above" result="ansi" +z.append(np.arange(10, dtype='float64')) +print(f"After append: shape={z.shape}, chunk_sizes={z.write_chunk_sizes}") +``` + +### Compressors and filters + +Rectilinear arrays work with all codecs — compressors, filters, and checksums. +Since each chunk may have a different size, the codec pipeline processes each +chunk independently: + +```python exec="true" session="arrays" source="above" result="ansi" +z = zarr.create_array( + store=zarr.storage.MemoryStore(), + shape=(60, 100), + chunks=[[10, 20, 30], [50, 50]], + dtype='float64', + filters=[zarr.codecs.TransposeCodec(order=(1, 0))], + compressors=[zarr.codecs.BloscCodec(cname='zstd', clevel=3)], +) +z[:] = np.arange(60 * 100, dtype='float64').reshape(60, 100) +np.testing.assert_array_equal(z[:], np.arange(60 * 100, dtype='float64').reshape(60, 100)) +print("Roundtrip OK") +``` + +### Rectilinear shard boundaries + +Rectilinear chunk grids can also be used for shard boundaries when combined +with sharding. In this case, the outer grid (shards) is rectilinear while the +inner chunks remain regular. Each shard dimension must be divisible by the +corresponding inner chunk size: + +```python exec="true" session="arrays" source="above" result="ansi" +z = zarr.create_array( + store=zarr.storage.MemoryStore(), + shape=(120, 100), + chunks=(10, 10), + shards=[[60, 40, 20], [50, 50]], + dtype='int32', +) +z[:] = np.arange(120 * 100, dtype='int32').reshape(120, 100) +print(z[50:70, 40:60]) +``` + +Note that rectilinear inner chunks with sharding are not supported — only the +shard boundaries can be rectilinear. + +### Metadata format + +Rectilinear chunk grid metadata uses run-length encoding (RLE) for compact +serialization. When reading metadata, both bare integers and `[value, count]` +pairs are accepted: + +- `[10, 20, 30]` — three chunks with explicit sizes +- `[[10, 3]]` — three chunks of size 10 (RLE shorthand) +- `[[10, 3], 5]` — three chunks of size 10, then one chunk of size 5 + +When writing, Zarr automatically compresses repeated values into RLE format. + ## Missing features in 3.0 The following features have not been ported to 3.0 yet. diff --git a/docs/user-guide/config.md b/docs/user-guide/config.md index 41e03cbf0b..044f170c02 100644 --- a/docs/user-guide/config.md +++ b/docs/user-guide/config.md @@ -30,6 +30,7 @@ Configuration options include the following: - Default Zarr format `default_zarr_version` - Default array order in memory `array.order` - Whether empty chunks are written to storage `array.write_empty_chunks` +- Enable experimental rectilinear chunks `array.rectilinear_chunks` - Whether missing chunks are filled with the array's fill value on read `array.read_missing_chunks` (default `True`). Set to `False` to raise a [`ChunkNotFoundError`][zarr.errors.ChunkNotFoundError] instead. - Async and threading options, e.g. `async.concurrency` and `threading.max_workers` - Selections of implementations of codecs, codec pipelines and buffers diff --git a/docs/user-guide/examples/rectilinear_chunks.ipynb b/docs/user-guide/examples/rectilinear_chunks.ipynb new file mode 100644 index 0000000000..a2dd636ee8 --- /dev/null +++ b/docs/user-guide/examples/rectilinear_chunks.ipynb @@ -0,0 +1,428 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "da9139cc", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:20.792275Z", + "iopub.status.busy": "2026-03-30T13:18:20.792050Z", + "iopub.status.idle": "2026-03-30T13:18:20.801655Z", + "shell.execute_reply": "2026-03-30T13:18:20.797952Z", + "shell.execute_reply.started": "2026-03-30T13:18:20.792253Z" + } + }, + "outputs": [], + "source": [ + "# /// script\n", + "# requires-python = \">=3.12\"\n", + "# dependencies = [\n", + "# \"dask\",\n", + "# \"healpix-geo\",\n", + "# \"matplotlib\",\n", + "# \"numpy\",\n", + "# \"obstore\",\n", + "# \"xarray\",\n", + "# \"zarr\",\n", + "# ]\n", + "#\n", + "# [tool.uv.sources]\n", + "# zarr = { git = \"https://github.com/zarr-developers/zarr-python\", branch = \"main\" }\n", + "# xarray = { git = \"https://github.com/maxrjones/xarray\", branch = \"poc/unified-zarr-chunk-grid\" }\n", + "# ///" + ] + }, + { + "cell_type": "markdown", + "id": "71gnhfq4pfe", + "metadata": {}, + "source": [ + "# Rectilinear Chunk Grids\n", + "\n", + "This notebook demonstrates the unified chunk grid implementation from [#3802](https://github.com/zarr-developers/zarr-python/pull/3802), which adds support for rectilinear (variable) chunk grids.\n", + "\n", + "Note that it requires installing from a fork of Xarray; this will ideally be incorporated in the codebase and included in a future Xarray release.\n", + "\n", + "Rectilinear grids allow different chunk sizes along each dimension, which is useful for data that doesn't partition evenly. For example, sparse HEALPix cells grouped by parent tile, boundary-padded HPC arrays, or ingesting existing variable-chunked datasets via VirtualiZarr." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "9e9nyjdx06f", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:20.802629Z", + "iopub.status.busy": "2026-03-30T13:18:20.802471Z", + "iopub.status.idle": "2026-03-30T13:18:21.183147Z", + "shell.execute_reply": "2026-03-30T13:18:21.182751Z", + "shell.execute_reply.started": "2026-03-30T13:18:20.802615Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import tempfile\n", + "from pathlib import Path\n", + "import json\n", + "\n", + "import numpy as np\n", + "import xarray as xr\n", + "from healpix_geo import nested\n", + "from obstore.store import HTTPStore\n", + "\n", + "import zarr\n", + "from zarr.storage import ObjectStore\n", + "\n", + "zarr.config.set({'async.concurrency': 128}) # Increase concurrency for better performance with obstore\n", + "zarr.config.set({\"array.rectilinear_chunks\": True}) # Opt-in to rectilinear chunks\n" + ] + }, + { + "cell_type": "markdown", + "id": "kj1o9xik9l", + "metadata": {}, + "source": [ + "## 1. Inspect HEALPix dataset\n", + "\n", + "Load the remote Zarr store to understand the data structure before chunking it." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "v6cot74r1gq", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:21.183653Z", + "iopub.status.busy": "2026-03-30T13:18:21.183505Z", + "iopub.status.idle": "2026-03-30T13:18:22.028419Z", + "shell.execute_reply": "2026-03-30T13:18:22.027356Z", + "shell.execute_reply.started": "2026-03-30T13:18:21.183644Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Members: [('cell_ids', ), ('da', )]\n", + "Attrs: {}\n", + "Write chunk sizes: ((55611, 55611, 55611, 55609),)\n" + ] + } + ], + "source": [ + "ob_store = HTTPStore.from_url(\"https://data-taos.ifremer.fr/GRID4EARTH/no_chunk_healpix.zarr\")\n", + "store = ObjectStore(ob_store)\n", + "g = zarr.open_group(store, mode=\"r\", zarr_format=2, use_consolidated=True)\n", + "arr = g['da']\n", + "\n", + "print(\"Members:\", list(g.members()))\n", + "print(\"Attrs:\", dict(g.attrs))\n", + "print(\"Write chunk sizes:\", arr.write_chunk_sizes)" + ] + }, + { + "cell_type": "markdown", + "id": "wmuqi66d46", + "metadata": {}, + "source": [ + "## 2. HEALPix-style variable chunking\n", + "\n", + "Inspired by [this use case](https://github.com/zarr-developers/zarr-python/pull/3534#issuecomment-3848669859): HEALPix grids where cells are grouped by parent tile at a coarser resolution level, producing variable-sized chunks along the cell dimension when accounting for sparsity." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "90bc91b9", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:22.029842Z", + "iopub.status.busy": "2026-03-30T13:18:22.029258Z", + "iopub.status.idle": "2026-03-30T13:18:23.629597Z", + "shell.execute_reply": "2026-03-30T13:18:23.628896Z", + "shell.execute_reply.started": "2026-03-30T13:18:22.029824Z" + } + }, + "outputs": [], + "source": [ + "da = xr.open_zarr(\n", + " store,\n", + " zarr_format=2,\n", + " consolidated=True,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "0d7785b0-d72f-4ef8-8a57-91d61f07be96", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:23.630244Z", + "iopub.status.busy": "2026-03-30T13:18:23.629978Z", + "iopub.status.idle": "2026-03-30T13:18:23.633850Z", + "shell.execute_reply": "2026-03-30T13:18:23.632930Z", + "shell.execute_reply.started": "2026-03-30T13:18:23.630232Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "10" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "depth = da.cell_ids.attrs['level']\n", + "depth" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "72c80224-dcac-4724-8caf-5717b29a25d5", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:23.634211Z", + "iopub.status.busy": "2026-03-30T13:18:23.634119Z", + "iopub.status.idle": "2026-03-30T13:18:23.642291Z", + "shell.execute_reply": "2026-03-30T13:18:23.641668Z", + "shell.execute_reply.started": "2026-03-30T13:18:23.634203Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "array([ 25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603,\n", + " 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879,\n", + " 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096,\n", + " 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096,\n", + " 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714,\n", + " 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438,\n", + " 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23])" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "new_depth = depth-6\n", + "parents = nested.zoom_to(da.cell_ids, depth=depth, new_depth=new_depth)\n", + "_, chunk_sizes =np.unique(parents, return_counts=True)\n", + "chunk_sizes" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "a79a281b-ca74-49c3-a467-60490a4ad63e", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:23.642721Z", + "iopub.status.busy": "2026-03-30T13:18:23.642622Z", + "iopub.status.idle": "2026-03-30T13:18:23.649165Z", + "shell.execute_reply": "2026-03-30T13:18:23.648723Z", + "shell.execute_reply.started": "2026-03-30T13:18:23.642712Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "Frozen({'cell_ids': (25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096, 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096, 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714, 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23)})" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "da = da.chunk({\"cell_ids\": tuple(chunk_sizes.tolist())})\n", + "da.chunks" + ] + }, + { + "cell_type": "markdown", + "id": "bsp6y7otkzb", + "metadata": {}, + "source": [ + "## 3. Write as rectilinear Zarr V3\n", + "\n", + "Write the variable-chunked dataset to a local Zarr V3 store with rectilinear chunk grids enabled." + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "ribguojdr0s", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:23.649823Z", + "iopub.status.busy": "2026-03-30T13:18:23.649737Z", + "iopub.status.idle": "2026-03-30T13:18:24.089390Z", + "shell.execute_reply": "2026-03-30T13:18:24.088640Z", + "shell.execute_reply.started": "2026-03-30T13:18:23.649815Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Written to: /var/folders/70/hc_nynms54d8lp67z4rsfctc0000gp/T/tmp6dibcrho/healpix_rectilinear.zarr\n" + ] + } + ], + "source": [ + "output_path = Path(tempfile.mkdtemp()) / \"healpix_rectilinear.zarr\"\n", + "\n", + "encoding = {\n", + " \"da\": {\"chunks\": [chunk_sizes.tolist()]},\n", + " \"cell_ids\": {\"chunks\": [chunk_sizes.tolist()]},\n", + "}\n", + "\n", + "da.to_zarr(output_path, zarr_format=3, mode=\"w\", encoding=encoding, consolidated=False)\n", + "\n", + "print(f\"Written to: {output_path}\")" + ] + }, + { + "cell_type": "markdown", + "id": "rbfm1hn63g9", + "metadata": {}, + "source": [ + "## 4. Verify rectilinear metadata\n", + "\n", + "Inspect the output store to confirm the chunk grid is serialized as `\"rectilinear\"` in `zarr.json`,\n", + "following the [rectilinear chunk grid extension spec](https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear).\n", + "\n", + "Key things to look for in `chunk_grid`:\n", + "- **`name`**: `\"rectilinear\"` (the extension identifier)\n", + "- **`configuration.kind`**: `\"inline\"` (edge lengths stored directly in metadata)\n", + "- **`configuration.chunk_shapes`**: one entry per dimension — here a single list for the 1D `cell_ids` axis. Each element is either:\n", + " - a **bare integer** for a unique edge length (e.g., `25`, `645`)\n", + " - a **`[value, count]` array** using [run-length encoding](https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear#run-length-encoding) for consecutive repeated sizes (e.g., `[4096, 4]` means four consecutive chunks of size 4096)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "mpdn5hxp7lp", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:24.090312Z", + "iopub.status.busy": "2026-03-30T13:18:24.090192Z", + "iopub.status.idle": "2026-03-30T13:18:24.093595Z", + "shell.execute_reply": "2026-03-30T13:18:24.092908Z", + "shell.execute_reply.started": "2026-03-30T13:18:24.090303Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'name': 'rectilinear', 'configuration': {'kind': 'inline', 'chunk_shapes': [[25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, [4096, 2], 3327, 4047, [4096, 2], 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, [4096, 4], 3515, 1395, 4096, 3622, [4096, 2], 3875, [4096, 5], 2034, 4096, 358, 3991, [4096, 4], 2714, 1210, [4096, 4], 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23]]}}\n" + ] + } + ], + "source": [ + "\n", + "# Read the zarr.json for the 'da' array\n", + "da_meta_path = output_path / \"da\" / \"zarr.json\"\n", + "meta = json.loads(da_meta_path.read_text())\n", + "print(meta['chunk_grid'])" + ] + }, + { + "cell_type": "markdown", + "id": "inz7s8ugu2c", + "metadata": {}, + "source": [ + "## 5. Round-trip verification\n", + "\n", + "Read the rectilinear store back and confirm the chunk sizes are preserved." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "308gxly6r3j", + "metadata": { + "execution": { + "iopub.execute_input": "2026-03-30T13:18:24.094252Z", + "iopub.status.busy": "2026-03-30T13:18:24.094013Z", + "iopub.status.idle": "2026-03-30T13:18:24.117313Z", + "shell.execute_reply": "2026-03-30T13:18:24.116670Z", + "shell.execute_reply.started": "2026-03-30T13:18:24.094242Z" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Round-trip chunk sizes: Frozen({'cell_ids': (25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096, 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096, 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714, 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23)})\n" + ] + } + ], + "source": [ + "roundtrip = xr.open_zarr(output_path, zarr_format=3, consolidated=False)\n", + "\n", + "print(\"Round-trip chunk sizes:\", roundtrip.chunks)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e8d42341-c242-44f5-ad6a-491370e3ffab", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.0" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/user-guide/glossary.md b/docs/user-guide/glossary.md index a490b7c341..3eb63925cc 100644 --- a/docs/user-guide/glossary.md +++ b/docs/user-guide/glossary.md @@ -36,12 +36,23 @@ The partitioning of an array's elements into [chunks](#chunk). In Zarr V3, the chunk grid is defined in the array [metadata](#metadata) and determines the boundaries of each storage object. +Zarr V3 supports two chunk grid types: + +- **Regular**: All chunks have the same shape (the last chunk along each + dimension may be smaller than the declared size). +- **Rectilinear** *(experimental)*: Each dimension can have different chunk + sizes, specified as a list of edge lengths per dimension. Enable with + `zarr.config.set({'array.rectilinear_chunks': True})`. + When sharding is used, the chunk grid defines the [shard](#shard) boundaries, not the inner chunk boundaries. The inner chunk shape is defined within the [sharding codec](#shard). **API**: The `chunk_grid` field in array metadata contains the storage-level -grid. +grid. [`Array.chunks`][zarr.Array.chunks] returns the chunk shape for regular +grids. For all grid types, `Array.read_chunk_sizes` and `Array.write_chunk_sizes` +return the per-dimension chunk sizes in dask-style `tuple[tuple[int, ...], ...]` +format. ### Shard @@ -104,7 +115,9 @@ The following properties are available on [`zarr.Array`][]: | Property | Description | |----------|-------------| -| `.chunks` | Chunk shape — the inner chunk shape when sharding is used | +| `.chunks` | Chunk shape — the inner chunk shape when sharding is used. Raises for rectilinear grids | | `.shards` | Shard shape, or `None` if no sharding | +| `.read_chunk_sizes` | Per-dimension chunk data sizes (`tuple[tuple[int, ...], ...]`). Works for all grid types | +| `.write_chunk_sizes` | Per-dimension storage chunk sizes (`tuple[tuple[int, ...], ...]`). Works for all grid types | | `.nchunks` | Total number of independently compressible units across the array | | `.cdata_shape` | Number of independently compressible units per dimension | diff --git a/mkdocs.yml b/mkdocs.yml index e2c4148e15..ce39fd0f2e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -30,6 +30,7 @@ nav: - user-guide/glossary.md - Examples: - user-guide/examples/custom_dtype.md + - user-guide/examples/rectilinear_chunks.ipynb - API Reference: - api/zarr/index.md - api/zarr/array.md @@ -132,6 +133,11 @@ extra_css: plugins: - autorefs - search + - mkdocs-jupyter: + include: ["docs/user-guide/examples/*.ipynb"] + execute: false + ignore_h1_titles: true + show_input: true - markdown-exec - mkdocstrings: enable_inventory: true diff --git a/pyproject.toml b/pyproject.toml index 8796255b94..bcab8dd105 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -114,6 +114,7 @@ docs = [ "mkdocstrings>=0.29.1", "mkdocstrings-python>=1.16.10", "mike>=2.1.3", + "mkdocs-jupyter>=0.25.1", "mkdocs-redirects>=1.2.0", "markdown-exec[ansi]", "griffe-inherited-docstrings", diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index 79c0dcf72e..eed2119aff 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -17,10 +17,10 @@ from zarr.abc.store import ByteGetter, ByteSetter, Store from zarr.core.array_spec import ArraySpec - from zarr.core.chunk_grids import ChunkGrid from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType from zarr.core.indexing import SelectorTuple from zarr.core.metadata import ArrayMetadata + from zarr.core.metadata.v3 import ChunkGridMetadata __all__ = [ "ArrayArrayCodec", @@ -145,7 +145,7 @@ def validate( *, shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], - chunk_grid: ChunkGrid, + chunk_grid: ChunkGridMetadata, ) -> None: """Validates that the codec configuration is compatible with the array metadata. Raises errors when the codec configuration is not compatible. @@ -156,8 +156,8 @@ def validate( The array shape dtype : np.dtype[Any] The array data type - chunk_grid : ChunkGrid - The array chunk grid + chunk_grid : ChunkGridMetadata + The array chunk grid metadata """ async def _decode_single(self, chunk_data: CO, chunk_spec: ArraySpec) -> CI: @@ -360,7 +360,7 @@ def validate( *, shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], - chunk_grid: ChunkGrid, + chunk_grid: ChunkGridMetadata, ) -> None: """Validates that all codec configurations are compatible with the array metadata. Raises errors when a codec configuration is not compatible. @@ -371,8 +371,8 @@ def validate( The array shape dtype : np.dtype[Any] The array data type - chunk_grid : ChunkGrid - The array chunk grid + chunk_grid : ChunkGridMetadata + The array chunk grid metadata """ ... diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 4e718a234e..a865f97646 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -33,6 +33,7 @@ from zarr.core.common import ( JSON, AccessModeLiteral, + ChunksLike, DimensionNamesLike, MemoryOrder, ShapeLike, @@ -822,7 +823,7 @@ def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: tuple[int, ...] | Literal["auto"] = "auto", + chunks: ChunksLike | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -858,9 +859,13 @@ def create_array( data : np.ndarray, optional Array-like data to use for initializing the array. If this parameter is provided, the ``shape`` and ``dtype`` parameters must be ``None``. - chunks : tuple[int, ...] | Literal["auto"], default="auto" + chunks : tuple[int, ...] | Sequence[Sequence[int]] | Literal["auto"], default="auto" Chunk shape of the array. If chunks is "auto", a chunk shape is guessed based on the shape of the array and the dtype. + A nested list of per-dimension edge sizes creates a rectilinear grid. + Rectilinear chunk grids are experimental and must be explicitly enabled + with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + feature is stabilizing. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec] | Literal["auto"], optional @@ -993,7 +998,7 @@ def from_array( data: AnyArray | npt.ArrayLike, write_data: bool = True, name: str | None = None, - chunks: Literal["auto", "keep"] | tuple[int, ...] = "keep", + chunks: ChunksLike | Literal["auto", "keep"] = "keep", shards: ShardsLike | None | Literal["keep"] = "keep", filters: FiltersLike | Literal["keep"] = "keep", compressors: CompressorsLike | Literal["keep"] = "keep", @@ -1025,13 +1030,17 @@ def from_array( name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. - chunks : tuple[int, ...] or "auto" or "keep", optional + chunks : tuple[int, ...] or Sequence[Sequence[int]] or "auto" or "keep", optional Chunk shape of the array. Following values are supported: - "auto": Automatically determine the chunk shape based on the array's shape and dtype. - - "keep": Retain the chunk shape of the data array if it is a zarr Array. - - tuple[int, ...]: A tuple of integers representing the chunk shape. + - "keep": Retain the chunk grid of the data array if it is a zarr Array. + - tuple[int, ...]: A tuple of integers representing the chunk shape (regular grid). + - Sequence[Sequence[int]]: Per-dimension chunk edge lists (rectilinear grid). + Rectilinear chunk grids are experimental and must be explicitly enabled + with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + feature is stabilizing. If not specified, defaults to "keep" if data is a zarr Array, otherwise "auto". shards : tuple[int, ...], optional diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 9f26bc57b1..609e32f87d 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -34,7 +34,7 @@ default_buffer_prototype, numpy_buffer_prototype, ) -from zarr.core.chunk_grids import ChunkGrid, RegularChunkGrid +from zarr.core.chunk_grids import ChunkGrid from zarr.core.common import ( ShapeLike, parse_enum, @@ -53,7 +53,12 @@ get_indexer, morton_order_iter, ) -from zarr.core.metadata.v3 import parse_codecs +from zarr.core.metadata.v3 import ( + ChunkGridMetadata, + RectilinearChunkGridMetadata, + RegularChunkGridMetadata, + parse_codecs, +) from zarr.registry import get_ndbuffer_class, get_pipeline_class from zarr.storage._utils import _normalize_byte_range_index @@ -382,26 +387,30 @@ def validate( *, shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], - chunk_grid: ChunkGrid, + chunk_grid: ChunkGridMetadata, ) -> None: if len(self.chunk_shape) != len(shape): raise ValueError( "The shard's `chunk_shape` and array's `shape` need to have the same number of dimensions." ) - if not isinstance(chunk_grid, RegularChunkGrid): - raise TypeError("Sharding is only compatible with regular chunk grids.") - if not all( - s % c == 0 - for s, c in zip( - chunk_grid.chunk_shape, - self.chunk_shape, - strict=False, + if isinstance(chunk_grid, RegularChunkGridMetadata): + edges_per_dim: tuple[tuple[int, ...], ...] = tuple((s,) for s in chunk_grid.chunk_shape) + elif isinstance(chunk_grid, RectilinearChunkGridMetadata): + edges_per_dim = tuple( + (s,) if isinstance(s, int) else s for s in chunk_grid.chunk_shapes ) - ): - raise ValueError( - f"The array's `chunk_shape` (got {chunk_grid.chunk_shape}) " - f"needs to be divisible by the shard's inner `chunk_shape` (got {self.chunk_shape})." + else: + raise TypeError( + f"Sharding is only compatible with regular and rectilinear chunk grids, " + f"got {type(chunk_grid)}" ) + for i, (edges, inner) in enumerate(zip(edges_per_dim, self.chunk_shape, strict=False)): + for edge in set(edges): + if edge % inner != 0: + raise ValueError( + f"Chunk edge length {edge} in dimension {i} is not " + f"divisible by the shard's inner chunk size {inner}." + ) async def _decode_single( self, @@ -416,7 +425,7 @@ async def _decode_single( indexer = BasicIndexer( tuple(slice(0, s) for s in shard_shape), shape=shard_shape, - chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape), + chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), ) # setup output array @@ -462,7 +471,7 @@ async def _decode_partial_single( indexer = get_indexer( selection, shape=shard_shape, - chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape), + chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), ) # setup output array @@ -537,7 +546,7 @@ async def _encode_single( BasicIndexer( tuple(slice(0, s) for s in shard_shape), shape=shard_shape, - chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape), + chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), ) ) @@ -577,7 +586,9 @@ async def _encode_partial_single( indexer = list( get_indexer( - selection, shape=shard_shape, chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape) + selection, + shape=shard_shape, + chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), ) ) diff --git a/src/zarr/codecs/transpose.py b/src/zarr/codecs/transpose.py index 609448a59c..5756fba2b4 100644 --- a/src/zarr/codecs/transpose.py +++ b/src/zarr/codecs/transpose.py @@ -14,8 +14,8 @@ from typing import Self from zarr.core.buffer import NDBuffer - from zarr.core.chunk_grids import ChunkGrid from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType + from zarr.core.metadata.v3 import ChunkGridMetadata def parse_transpose_order(data: JSON | Iterable[int]) -> tuple[int, ...]: @@ -51,7 +51,7 @@ def validate( self, shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], - chunk_grid: ChunkGrid, + chunk_grid: ChunkGridMetadata, ) -> None: if len(self.order) != len(shape): raise ValueError( diff --git a/src/zarr/core/_info.py b/src/zarr/core/_info.py index fef424346a..1503f05b26 100644 --- a/src/zarr/core/_info.py +++ b/src/zarr/core/_info.py @@ -117,7 +117,7 @@ def __repr__(self) -> str: if self._chunk_shape is None: # for non-regular chunk grids - kwargs["chunk_shape"] = "" + kwargs["_chunk_shape"] = "" template += "\nFilters : {_filters}" diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 7d1915fd33..4736805b9d 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -3,7 +3,7 @@ import json import warnings from asyncio import gather -from collections.abc import Iterable, Mapping +from collections.abc import Iterable, Mapping, Sequence from dataclasses import dataclass, field, replace from itertools import starmap from logging import getLogger @@ -28,7 +28,7 @@ from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec from zarr.codecs.zstd import ZstdCodec from zarr.core._info import ArrayInfo -from zarr.core.array_spec import ArrayConfig, ArrayConfigLike, parse_array_config +from zarr.core.array_spec import ArrayConfig, ArrayConfigLike, ArraySpec, parse_array_config from zarr.core.attributes import Attributes from zarr.core.buffer import ( BufferPrototype, @@ -38,7 +38,11 @@ default_buffer_prototype, ) from zarr.core.buffer.cpu import buffer_prototype as cpu_buffer_prototype -from zarr.core.chunk_grids import RegularChunkGrid, _auto_partition, normalize_chunks +from zarr.core.chunk_grids import ( + ChunkGrid, + _auto_partition, + normalize_chunks, +) from zarr.core.chunk_key_encodings import ( ChunkKeyEncoding, ChunkKeyEncodingLike, @@ -51,6 +55,7 @@ ZARR_JSON, ZARRAY_JSON, ZATTRS_JSON, + ChunksLike, DimensionNamesLike, MemoryOrder, ShapeLike, @@ -113,7 +118,13 @@ parse_compressor, parse_filters, ) -from zarr.core.metadata.v3 import parse_node_type_array +from zarr.core.metadata.v3 import ( + ChunkGridMetadata, + RectilinearChunkGridMetadata, + RegularChunkGridMetadata, + parse_node_type_array, + resolve_chunks, +) from zarr.core.sync import sync from zarr.errors import ( ArrayNotFoundError, @@ -132,7 +143,7 @@ from zarr.storage._utils import _relativize_path if TYPE_CHECKING: - from collections.abc import Iterator, Sequence + from collections.abc import Iterator from typing import Self import numpy.typing as npt @@ -174,6 +185,18 @@ class DefaultFillValue: DEFAULT_FILL_VALUE = DefaultFillValue() +def _chunk_sizes_from_shape( + array_shape: tuple[int, ...], chunk_shape: tuple[int, ...] +) -> tuple[tuple[int, ...], ...]: + """Compute dask-style chunk sizes from an array shape and uniform chunk shape.""" + result: list[tuple[int, ...]] = [] + for s, c in zip(array_shape, chunk_shape, strict=True): + nchunks = ceildiv(s, c) + sizes = tuple(min(c, s - i * c) for i in range(nchunks)) + result.append(sizes) + return tuple(result) + + def parse_array_metadata(data: Any) -> ArrayMetadata: if isinstance(data, ArrayMetadata): return data @@ -305,6 +328,7 @@ class AsyncArray[T_ArrayMetadata: (ArrayV2Metadata, ArrayV3Metadata)]: metadata: T_ArrayMetadata store_path: StorePath codec_pipeline: CodecPipeline = field(init=False) + _chunk_grid: ChunkGrid = field(init=False) config: ArrayConfig @overload @@ -335,6 +359,7 @@ def __init__( object.__setattr__(self, "metadata", metadata_parsed) object.__setattr__(self, "store_path", store_path) object.__setattr__(self, "config", config_parsed) + object.__setattr__(self, "_chunk_grid", ChunkGrid.from_metadata(metadata_parsed)) object.__setattr__( self, "codec_pipeline", @@ -651,13 +676,11 @@ async def _create( if chunks is not None and chunk_shape is not None: raise ValueError("Only one of chunk_shape or chunks can be provided.") - item_size = 1 - if isinstance(dtype_parsed, HasItemSize): - item_size = dtype_parsed.item_size - if chunks: - _chunks = normalize_chunks(chunks, shape, item_size) - else: - _chunks = normalize_chunks(chunk_shape, shape, item_size) + + from zarr.core.chunk_grids import _is_rectilinear_chunks + + _raw_chunks = chunks if chunks is not None else chunk_shape + config_parsed = parse_array_config(config) result: AnyAsyncArray @@ -678,11 +701,14 @@ async def _create( if order is not None: _warn_order_kwarg() + item_size = 1 + if isinstance(dtype_parsed, HasItemSize): + item_size = dtype_parsed.item_size + chunk_grid = resolve_chunks(_raw_chunks, shape, item_size) result = await cls._create_v3( store_path, shape=shape, dtype=dtype_parsed, - chunk_shape=_chunks, fill_value=fill_value, chunk_key_encoding=chunk_key_encoding, codecs=codecs, @@ -690,6 +716,7 @@ async def _create( attributes=attributes, overwrite=overwrite, config=config_parsed, + chunk_grid=chunk_grid, ) elif zarr_format == 2: if codecs is not None: @@ -702,6 +729,16 @@ async def _create( ) if dimension_names is not None: raise ValueError("dimension_names cannot be used for arrays with zarr_format 2.") + if _is_rectilinear_chunks(_raw_chunks): + raise ValueError("Zarr format 2 does not support rectilinear chunk grids.") + + item_size = 1 + if isinstance(dtype_parsed, HasItemSize): + item_size = dtype_parsed.item_size + if chunks: + _chunks = normalize_chunks(chunks, shape, item_size) + else: + _chunks = normalize_chunks(chunk_shape, shape, item_size) if order is None: order_parsed = config_parsed.order @@ -736,16 +773,14 @@ async def _create( def _create_metadata_v3( shape: ShapeLike, dtype: ZDType[TBaseDType, TBaseScalar], - chunk_shape: tuple[int, ...], + chunk_grid: ChunkGridMetadata, fill_value: Any | None = DEFAULT_FILL_VALUE, chunk_key_encoding: ChunkKeyEncodingLike | None = None, codecs: Iterable[Codec | dict[str, JSON]] | None = None, dimension_names: DimensionNamesLike = None, attributes: dict[str, JSON] | None = None, ) -> ArrayV3Metadata: - """ - Create an instance of ArrayV3Metadata. - """ + """Create an instance of ArrayV3Metadata.""" filters: tuple[ArrayArrayCodec, ...] compressors: tuple[BytesBytesCodec, ...] @@ -772,11 +807,10 @@ def _create_metadata_v3( else: fill_value_parsed = fill_value - chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape) return ArrayV3Metadata( shape=shape, data_type=dtype, - chunk_grid=chunk_grid_parsed, + chunk_grid=chunk_grid, chunk_key_encoding=chunk_key_encoding_parsed, fill_value=fill_value_parsed, codecs=codecs_parsed, # type: ignore[arg-type] @@ -791,7 +825,7 @@ async def _create_v3( *, shape: ShapeLike, dtype: ZDType[TBaseDType, TBaseScalar], - chunk_shape: tuple[int, ...], + chunk_grid: ChunkGridMetadata, config: ArrayConfig, fill_value: Any | None = DEFAULT_FILL_VALUE, chunk_key_encoding: ( @@ -823,7 +857,7 @@ async def _create_v3( metadata = cls._create_metadata_v3( shape=shape, dtype=dtype, - chunk_shape=chunk_shape, + chunk_grid=chunk_grid, fill_value=fill_value, chunk_key_encoding=chunk_key_encoding, codecs=codecs, @@ -1042,23 +1076,78 @@ def chunks(self) -> tuple[int, ...]: """Returns the chunk shape of the Array. If sharding is used the inner chunk shape is returned. - Only defined for arrays using using `RegularChunkGrid`. - If array doesn't use `RegularChunkGrid`, `NotImplementedError` is raised. + Only defined for arrays using a regular chunk grid. + If array uses a rectilinear chunk grid, `NotImplementedError` is raised. Returns ------- tuple[int, ...]: The chunk shape of the Array. """ + # TODO: move sharding awareness out of metadata return self.metadata.chunks + @property + def read_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: + """Per-dimension data sizes of chunks used for reading, clipped to the array extent. + + Boundary chunks that extend past the array shape are clipped, so + the last size along a dimension may be smaller than the declared + chunk size. This matches the dask ``Array.chunks`` convention. + + When sharding is used, returns the inner chunk sizes. + Otherwise, returns the outer chunk sizes (same as ``write_chunk_sizes``). + + Returns + ------- + tuple[tuple[int, ...], ...] + One inner tuple per dimension containing the data size of each + chunk (not the encoded buffer size). + + Examples + -------- + >>> arr = zarr.create_array(store, shape=(100, 80), chunks=(30, 40)) + >>> arr.read_chunk_sizes + ((30, 30, 30, 10), (40, 40)) + """ + from zarr.codecs.sharding import ShardingCodec + + codecs: tuple[Codec, ...] = getattr(self.metadata, "codecs", ()) + if len(codecs) == 1 and isinstance(codecs[0], ShardingCodec): + inner_chunk_shape = codecs[0].chunk_shape + return _chunk_sizes_from_shape(self.shape, inner_chunk_shape) + return self._chunk_grid.chunk_sizes + + @property + def write_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: + """Per-dimension data sizes of storage chunks, clipped to the array extent. + + Always returns the outer chunk sizes, regardless of sharding. + Boundary chunks that extend past the array shape are clipped, so + the last size along a dimension may be smaller than the declared + chunk size. This matches the dask ``Array.chunks`` convention. + + Returns + ------- + tuple[tuple[int, ...], ...] + One inner tuple per dimension containing the data size of each + chunk (not the encoded buffer size). + + Examples + -------- + >>> arr = zarr.create_array(store, shape=(100, 80), chunks=(30, 40)) + >>> arr.write_chunk_sizes + ((30, 30, 30, 10), (40, 40)) + """ + return self._chunk_grid.chunk_sizes + @property def shards(self) -> tuple[int, ...] | None: """Returns the shard shape of the Array. Returns None if sharding is not used. - Only defined for arrays using using `RegularChunkGrid`. - If array doesn't use `RegularChunkGrid`, `NotImplementedError` is raised. + Only defined for arrays using a regular chunk grid. + If array uses a rectilinear chunk grid, `NotImplementedError` is raised. Returns ------- @@ -1256,7 +1345,16 @@ def _chunk_grid_shape(self) -> tuple[int, ...]: tuple[int, ...] The number of chunks along each dimension. """ - return tuple(starmap(ceildiv, zip(self.shape, self.chunks, strict=True))) + # TODO: refactor — extract a sharding_codec property on ArrayV3Metadata + # to replace the repeated `len == 1 and isinstance` pattern. + from zarr.codecs.sharding import ShardingCodec + + codecs: tuple[Codec, ...] = getattr(self.metadata, "codecs", ()) + if len(codecs) == 1 and isinstance(codecs[0], ShardingCodec): + # When sharding, count inner chunks across the whole array + chunk_shape = codecs[0].chunk_shape + return tuple(starmap(ceildiv, zip(self.shape, chunk_shape, strict=True))) + return self._chunk_grid.grid_shape @property def _shard_grid_shape(self) -> tuple[int, ...]: @@ -1584,6 +1682,7 @@ async def _get_selection( self.metadata, self.codec_pipeline, self.config, + self._chunk_grid, indexer, prototype=prototype, out=out, @@ -1638,6 +1737,7 @@ async def example(): self.metadata, self.codec_pipeline, self.config, + self._chunk_grid, selection, prototype=prototype, ) @@ -1655,6 +1755,7 @@ async def get_orthogonal_selection( self.metadata, self.codec_pipeline, self.config, + self._chunk_grid, selection, out=out, fields=fields, @@ -1674,6 +1775,7 @@ async def get_mask_selection( self.metadata, self.codec_pipeline, self.config, + self._chunk_grid, mask, out=out, fields=fields, @@ -1693,6 +1795,7 @@ async def get_coordinate_selection( self.metadata, self.codec_pipeline, self.config, + self._chunk_grid, selection, out=out, fields=fields, @@ -1718,6 +1821,7 @@ async def _set_selection( self.metadata, self.codec_pipeline, self.config, + self._chunk_grid, indexer, value, prototype=prototype, @@ -1768,6 +1872,7 @@ async def setitem( self.metadata, self.codec_pipeline, self.config, + self._chunk_grid, selection, value, prototype=prototype, @@ -1924,6 +2029,7 @@ async def info_complete(self) -> Any: def _info( self, count_chunks_initialized: int | None = None, count_bytes_stored: int | None = None ) -> Any: + chunk_shape = self.chunks if self._chunk_grid.is_regular else None return ArrayInfo( _zarr_format=self.metadata.zarr_format, _data_type=self._zdtype, @@ -1931,7 +2037,7 @@ def _info( _shape=self.shape, _order=self.order, _shard_shape=self.shards, - _chunk_shape=self.chunks, + _chunk_shape=chunk_shape, _read_only=self.read_only, _compressors=self.compressors, _filters=self.filters, @@ -1975,6 +2081,11 @@ def config(self) -> ArrayConfig: """ return self.async_array.config + @property + def _chunk_grid(self) -> ChunkGrid: + """The chunk grid for this array, bound to the array's shape.""" + return self.async_array._chunk_grid + @classmethod @deprecated("Use zarr.create_array instead.", category=ZarrDeprecationWarning) def create( @@ -2266,8 +2377,8 @@ def chunks(self) -> tuple[int, ...]: """Returns a tuple of integers describing the length of each dimension of a chunk of the array. If sharding is used the inner chunk shape is returned. - Only defined for arrays using using `RegularChunkGrid`. - If array doesn't use `RegularChunkGrid`, `NotImplementedError` is raised. + Only defined for arrays using a regular chunk grid. + If array uses a rectilinear chunk grid, `NotImplementedError` is raised. Returns ------- @@ -2276,13 +2387,61 @@ def chunks(self) -> tuple[int, ...]: """ return self.async_array.chunks + @property + def read_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: + """Per-dimension data sizes of chunks used for reading, clipped to the array extent. + + Boundary chunks that extend past the array shape are clipped, so + the last size along a dimension may be smaller than the declared + chunk size. This matches the dask ``Array.chunks`` convention. + + When sharding is used, returns the inner chunk sizes. + Otherwise, returns the outer chunk sizes (same as ``write_chunk_sizes``). + + Returns + ------- + tuple[tuple[int, ...], ...] + One inner tuple per dimension containing the data size of each + chunk (not the encoded buffer size). + + Examples + -------- + >>> arr = zarr.open_array(store) + >>> arr.read_chunk_sizes + ((30, 30, 30, 10), (40, 40)) + """ + return self.async_array.read_chunk_sizes + + @property + def write_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: + """Per-dimension data sizes of storage chunks, clipped to the array extent. + + Always returns the outer chunk sizes, regardless of sharding. + Boundary chunks that extend past the array shape are clipped, so + the last size along a dimension may be smaller than the declared + chunk size. This matches the dask ``Array.chunks`` convention. + + Returns + ------- + tuple[tuple[int, ...], ...] + One inner tuple per dimension containing the data size of each + chunk (not the encoded buffer size). + + Examples + -------- + >>> arr = zarr.open_array(store) + >>> arr.write_chunk_sizes + ((30, 30, 30, 10), (40, 40)) + """ + return self.async_array.write_chunk_sizes + @property def shards(self) -> tuple[int, ...] | None: """Returns a tuple of integers describing the length of each dimension of a shard of the array. Returns None if sharding is not used. - Only defined for arrays using using `RegularChunkGrid`. - If array doesn't use `RegularChunkGrid`, `NotImplementedError` is raised. + Only defined for arrays using a regular chunk grid. + If array uses a rectilinear chunk grid, `NotImplementedError` is raised. Returns ------- @@ -2671,7 +2830,7 @@ def __array__( raise ValueError(msg) arr = self[...] - arr_np: NDArrayLike = np.array(arr, dtype=dtype) + arr_np = np.array(arr, dtype=dtype) if dtype is not None: arr_np = arr_np.astype(dtype) @@ -3068,7 +3227,7 @@ def get_basic_selection( prototype = default_buffer_prototype() return sync( self.async_array._get_selection( - BasicIndexer(selection, self.shape, self.metadata.chunk_grid), + BasicIndexer(selection, self.shape, self._chunk_grid), out=out, fields=fields, prototype=prototype, @@ -3175,7 +3334,7 @@ def set_basic_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = BasicIndexer(selection, self.shape, self.metadata.chunk_grid) + indexer = BasicIndexer(selection, self.shape, self._chunk_grid) sync(self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) def get_orthogonal_selection( @@ -3303,7 +3462,7 @@ def get_orthogonal_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = OrthogonalIndexer(selection, self.shape, self.metadata.chunk_grid) + indexer = OrthogonalIndexer(selection, self.shape, self._chunk_grid) return sync( self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype @@ -3422,7 +3581,7 @@ def set_orthogonal_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = OrthogonalIndexer(selection, self.shape, self.metadata.chunk_grid) + indexer = OrthogonalIndexer(selection, self.shape, self._chunk_grid) return sync( self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype) ) @@ -3510,7 +3669,7 @@ def get_mask_selection( if prototype is None: prototype = default_buffer_prototype() - indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid) + indexer = MaskIndexer(mask, self.shape, self._chunk_grid) return sync( self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype @@ -3600,7 +3759,7 @@ def set_mask_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid) + indexer = MaskIndexer(mask, self.shape, self._chunk_grid) sync(self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) def get_coordinate_selection( @@ -3688,7 +3847,7 @@ def get_coordinate_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = CoordinateIndexer(selection, self.shape, self.metadata.chunk_grid) + indexer = CoordinateIndexer(selection, self.shape, self._chunk_grid) out_array = sync( self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype @@ -3781,7 +3940,7 @@ def set_coordinate_selection( if prototype is None: prototype = default_buffer_prototype() # setup indexer - indexer = CoordinateIndexer(selection, self.shape, self.metadata.chunk_grid) + indexer = CoordinateIndexer(selection, self.shape, self._chunk_grid) # handle value - need ndarray-like flatten value if not is_scalar(value, self.dtype): @@ -3903,7 +4062,7 @@ def get_block_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = BlockIndexer(selection, self.shape, self.metadata.chunk_grid) + indexer = BlockIndexer(selection, self.shape, self._chunk_grid) return sync( self.async_array._get_selection( indexer=indexer, out=out, fields=fields, prototype=prototype @@ -4004,7 +4163,7 @@ def set_block_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = BlockIndexer(selection, self.shape, self.metadata.chunk_grid) + indexer = BlockIndexer(selection, self.shape, self._chunk_grid) sync(self.async_array._set_selection(indexer, value, fields=fields, prototype=prototype)) @property @@ -4251,7 +4410,7 @@ class ShardsConfigParam(TypedDict): index_location: ShardingCodecIndexLocation | None -type ShardsLike = tuple[int, ...] | ShardsConfigParam | Literal["auto"] +type ShardsLike = tuple[int, ...] | Sequence[Sequence[int]] | ShardsConfigParam | Literal["auto"] async def from_array( @@ -4260,7 +4419,7 @@ async def from_array( data: AnyArray | npt.ArrayLike, write_data: bool = True, name: str | None = None, - chunks: Literal["auto", "keep"] | tuple[int, ...] = "keep", + chunks: ChunksLike | Literal["auto", "keep"] = "keep", shards: ShardsLike | None | Literal["keep"] = "keep", filters: FiltersLike | Literal["keep"] = "keep", compressors: CompressorsLike | Literal["keep"] = "keep", @@ -4292,13 +4451,17 @@ async def from_array( name : str or None, optional The name of the array within the store. If ``name`` is ``None``, the array will be located at the root of the store. - chunks : tuple[int, ...] or "auto" or "keep", optional + chunks : tuple[int, ...] or Sequence[Sequence[int]] or "auto" or "keep", optional Chunk shape of the array. Following values are supported: - "auto": Automatically determine the chunk shape based on the array's shape and dtype. - - "keep": Retain the chunk shape of the data array if it is a zarr Array. - - tuple[int, ...]: A tuple of integers representing the chunk shape. + - "keep": Retain the chunk grid of the data array if it is a zarr Array. + - tuple[int, ...]: A tuple of integers representing the chunk shape (regular grid). + - Sequence[Sequence[int]]: Per-dimension chunk edge lists (rectilinear grid). + Rectilinear chunk grids are experimental and must be explicitly enabled + with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + feature is stabilizing. If not specified, defaults to "keep" if data is a zarr Array, otherwise "auto". shards : tuple[int, ...], optional @@ -4529,7 +4692,7 @@ async def init_array( store_path: StorePath, shape: ShapeLike, dtype: ZDTypeLike, - chunks: tuple[int, ...] | Literal["auto"] = "auto", + chunks: ChunksLike | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -4645,14 +4808,52 @@ async def init_array( else: await ensure_no_existing_node(store_path, zarr_format=zarr_format) + # Detect rectilinear (nested list) chunks or shards, e.g. [[10, 20, 30], [25, 25]] + from zarr.core.chunk_grids import _is_rectilinear_chunks + + rectilinear_meta: RectilinearChunkGridMetadata | None = None + rectilinear_shards = _is_rectilinear_chunks(shards) + + if _is_rectilinear_chunks(chunks): + if zarr_format == 2: + raise ValueError("Zarr format 2 does not support rectilinear chunk grids.") + if shards is not None: + raise ValueError( + "Rectilinear chunks with sharding is not supported. " + "Use rectilinear shards instead: " + "chunks=(inner_size, ...), shards=[[shard_sizes], ...]" + ) + rectilinear_meta = RectilinearChunkGridMetadata( + chunk_shapes=tuple(tuple(dim_edges) for dim_edges in chunks) + ) + # Use first chunk size per dim as placeholder for _auto_partition + chunks_flat: tuple[int, ...] | Literal["auto"] = tuple(dim_edges[0] for dim_edges in chunks) + else: + # Normalize scalar int to per-dimension tuple (e.g. chunks=100000 for a 1D array) + if isinstance(chunks, int): + chunks = tuple(chunks for _ in shape_parsed) + chunks_flat = cast("tuple[int, ...] | Literal['auto']", chunks) + + # Handle rectilinear shards: shards=[[60, 40, 20], [50, 50]] + # means variable-sized shard boundaries with uniform inner chunks + shards_for_partition: ShardsLike | None = shards + if _is_rectilinear_chunks(shards): + if zarr_format == 2: + raise ValueError("Zarr format 2 does not support rectilinear chunk grids.") + rectilinear_meta = RectilinearChunkGridMetadata( + chunk_shapes=tuple(tuple(dim_edges) for dim_edges in shards) + ) + # Use first shard size per dim as placeholder for _auto_partition + shards_for_partition = tuple(dim_edges[0] for dim_edges in shards) + item_size = 1 if isinstance(zdtype, HasItemSize): item_size = zdtype.item_size shard_shape_parsed, chunk_shape_parsed = _auto_partition( array_shape=shape_parsed, - shard_shape=shards, - chunk_shape=chunks, + shard_shape=shards_for_partition, + chunk_shape=chunks_flat, item_size=item_size, ) chunks_out: tuple[int, ...] @@ -4708,10 +4909,15 @@ async def init_array( sharding_codec = ShardingCodec( chunk_shape=chunk_shape_parsed, codecs=sub_codecs, index_location=index_location ) + # Use rectilinear grid for validation when shards are rectilinear + if rectilinear_shards and rectilinear_meta is not None: + validation_grid: ChunkGridMetadata = rectilinear_meta + else: + validation_grid = RegularChunkGridMetadata(chunk_shape=shard_shape_parsed) sharding_codec.validate( shape=chunk_shape_parsed, dtype=zdtype, - chunk_grid=RegularChunkGrid(chunk_shape=shard_shape_parsed), + chunk_grid=validation_grid, ) codecs_out = (sharding_codec,) chunks_out = shard_shape_parsed @@ -4722,11 +4928,16 @@ async def init_array( if order is not None: _warn_order_kwarg() + grid: ChunkGridMetadata + if rectilinear_meta is not None: + grid = rectilinear_meta + else: + grid = RegularChunkGridMetadata(chunk_shape=chunks_out) meta = AsyncArray._create_metadata_v3( shape=shape_parsed, dtype=zdtype, fill_value=fill_value, - chunk_shape=chunks_out, + chunk_grid=grid, chunk_key_encoding=chunk_key_encoding_parsed, codecs=codecs_out, dimension_names=dimension_names, @@ -4745,7 +4956,7 @@ async def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: tuple[int, ...] | Literal["auto"] = "auto", + chunks: ChunksLike | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -4779,9 +4990,13 @@ async def create_array( data : np.ndarray, optional Array-like data to use for initializing the array. If this parameter is provided, the ``shape`` and ``dtype`` parameters must be ``None``. - chunks : tuple[int, ...] | Literal["auto"], default="auto" + chunks : tuple[int, ...] | Sequence[Sequence[int]] | Literal["auto"], default="auto" Chunk shape of the array. If chunks is "auto", a chunk shape is guessed based on the shape of the array and the dtype. + A nested list of per-dimension edge sizes creates a rectilinear grid. + Rectilinear chunk grids are experimental and must be explicitly enabled + with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + feature is stabilizing. shards : tuple[int, ...], optional Shard shape of the array. The default value of ``None`` results in no sharding at all. filters : Iterable[Codec] | Literal["auto"], optional @@ -4930,7 +5145,7 @@ async def create_array( def _parse_keep_array_attr( data: AnyArray | npt.ArrayLike, - chunks: Literal["auto", "keep"] | tuple[int, ...], + chunks: ChunksLike | Literal["auto", "keep"], shards: ShardsLike | None | Literal["keep"], filters: FiltersLike | Literal["keep"], compressors: CompressorsLike | Literal["keep"], @@ -4941,7 +5156,7 @@ def _parse_keep_array_attr( chunk_key_encoding: ChunkKeyEncodingLike | None, dimension_names: DimensionNamesLike, ) -> tuple[ - tuple[int, ...] | Literal["auto"], + ChunksLike | Literal["auto"], ShardsLike | None, FiltersLike, CompressorsLike, @@ -4954,9 +5169,12 @@ def _parse_keep_array_attr( ]: if isinstance(data, Array): if chunks == "keep": - chunks = data.chunks + if data._chunk_grid.is_regular: + chunks = data.chunks + else: + chunks = data.write_chunk_sizes if shards == "keep": - shards = data.shards + shards = data.shards if data._chunk_grid.is_regular else None if zarr_format is None: zarr_format = data.metadata.zarr_format if filters == "keep": @@ -5008,8 +5226,10 @@ def _parse_keep_array_attr( compressors = "auto" if serializer == "keep": serializer = "auto" + # After resolving "keep" above, chunks is never "keep" at this point. + chunks_out: ChunksLike | Literal["auto"] = chunks # type: ignore[assignment] return ( - chunks, + chunks_out, shards, filters, compressors, @@ -5465,9 +5685,7 @@ def _iter_chunk_regions( A tuple of slice objects representing the region spanned by each shard in the selection. """ - return _iter_regions( - array.shape, array.chunks, origin=origin, selection_shape=selection_shape, trim_excess=True - ) + return array._chunk_grid.iter_chunk_regions(origin=origin, selection_shape=selection_shape) async def _nchunks_initialized( @@ -5540,11 +5758,32 @@ async def _nbytes_stored( return await store_path.store.getsize_prefix(store_path.path) +def _get_chunk_spec( + metadata: ArrayMetadata, + chunk_grid: ChunkGrid, + chunk_coords: tuple[int, ...], + array_config: ArrayConfig, + prototype: BufferPrototype, +) -> ArraySpec: + """Build an ArraySpec for a single chunk using the ChunkGrid.""" + spec = chunk_grid[chunk_coords] + if spec is None: + raise IndexError(f"Chunk coordinates {chunk_coords} are out of bounds.") + return ArraySpec( + shape=spec.codec_shape, + dtype=metadata.dtype, + fill_value=metadata.fill_value, + config=array_config, + prototype=prototype, + ) + + async def _get_selection( store_path: StorePath, metadata: ArrayMetadata, codec_pipeline: CodecPipeline, config: ArrayConfig, + chunk_grid: ChunkGrid, indexer: Indexer, *, prototype: BufferPrototype, @@ -5622,7 +5861,7 @@ async def _get_selection( [ ( store_path / metadata.encode_chunk_key(chunk_coords), - metadata.get_chunk_spec(chunk_coords, _config, prototype=prototype), + _get_chunk_spec(metadata, chunk_grid, chunk_coords, _config, prototype), chunk_selection, out_selection, is_complete_chunk, @@ -5657,6 +5896,7 @@ async def _getitem( metadata: ArrayMetadata, codec_pipeline: CodecPipeline, config: ArrayConfig, + chunk_grid: ChunkGrid, selection: BasicSelection, *, prototype: BufferPrototype | None = None, @@ -5674,6 +5914,8 @@ async def _getitem( The codec pipeline for encoding/decoding. config : ArrayConfig The array configuration. + chunk_grid : ChunkGrid + The chunk grid. selection : BasicSelection A selection object specifying the subset of data to retrieve. prototype : BufferPrototype, optional @@ -5689,10 +5931,10 @@ async def _getitem( indexer = BasicIndexer( selection, shape=metadata.shape, - chunk_grid=metadata.chunk_grid, + chunk_grid=chunk_grid, ) return await _get_selection( - store_path, metadata, codec_pipeline, config, indexer, prototype=prototype + store_path, metadata, codec_pipeline, config, chunk_grid, indexer, prototype=prototype ) @@ -5701,6 +5943,7 @@ async def _get_orthogonal_selection( metadata: ArrayMetadata, codec_pipeline: CodecPipeline, config: ArrayConfig, + chunk_grid: ChunkGrid, selection: OrthogonalSelection, *, out: NDBuffer | None = None, @@ -5720,6 +5963,8 @@ async def _get_orthogonal_selection( The codec pipeline for encoding/decoding. config : ArrayConfig The array configuration. + chunk_grid : ChunkGrid + The chunk grid. selection : OrthogonalSelection The orthogonal selection specification. out : NDBuffer | None, optional @@ -5736,12 +5981,13 @@ async def _get_orthogonal_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = OrthogonalIndexer(selection, metadata.shape, metadata.chunk_grid) + indexer = OrthogonalIndexer(selection, metadata.shape, chunk_grid) return await _get_selection( store_path, metadata, codec_pipeline, config, + chunk_grid, indexer=indexer, out=out, fields=fields, @@ -5754,6 +6000,7 @@ async def _get_mask_selection( metadata: ArrayMetadata, codec_pipeline: CodecPipeline, config: ArrayConfig, + chunk_grid: ChunkGrid, mask: MaskSelection, *, out: NDBuffer | None = None, @@ -5773,6 +6020,8 @@ async def _get_mask_selection( The codec pipeline for encoding/decoding. config : ArrayConfig The array configuration. + chunk_grid : ChunkGrid + The chunk grid. mask : MaskSelection The boolean mask specifying the selection. out : NDBuffer | None, optional @@ -5789,12 +6038,13 @@ async def _get_mask_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = MaskIndexer(mask, metadata.shape, metadata.chunk_grid) + indexer = MaskIndexer(mask, metadata.shape, chunk_grid) return await _get_selection( store_path, metadata, codec_pipeline, config, + chunk_grid, indexer=indexer, out=out, fields=fields, @@ -5807,6 +6057,7 @@ async def _get_coordinate_selection( metadata: ArrayMetadata, codec_pipeline: CodecPipeline, config: ArrayConfig, + chunk_grid: ChunkGrid, selection: CoordinateSelection, *, out: NDBuffer | None = None, @@ -5826,6 +6077,8 @@ async def _get_coordinate_selection( The codec pipeline for encoding/decoding. config : ArrayConfig The array configuration. + chunk_grid : ChunkGrid + The chunk grid. selection : CoordinateSelection The coordinate selection specification. out : NDBuffer | None, optional @@ -5842,12 +6095,13 @@ async def _get_coordinate_selection( """ if prototype is None: prototype = default_buffer_prototype() - indexer = CoordinateIndexer(selection, metadata.shape, metadata.chunk_grid) + indexer = CoordinateIndexer(selection, metadata.shape, chunk_grid) out_array = await _get_selection( store_path, metadata, codec_pipeline, config, + chunk_grid, indexer=indexer, out=out, fields=fields, @@ -5856,7 +6110,7 @@ async def _get_coordinate_selection( if hasattr(out_array, "shape"): # restore shape - out_array = np.array(out_array).reshape(indexer.sel_shape) + out_array = cast("NDArrayLikeOrScalar", np.array(out_array).reshape(indexer.sel_shape)) return out_array @@ -5865,6 +6119,7 @@ async def _set_selection( metadata: ArrayMetadata, codec_pipeline: CodecPipeline, config: ArrayConfig, + chunk_grid: ChunkGrid, indexer: Indexer, value: npt.ArrayLike, *, @@ -5884,6 +6139,8 @@ async def _set_selection( The codec pipeline for encoding/decoding. config : ArrayConfig The array configuration. + chunk_grid : ChunkGrid + The chunk grid. indexer : Indexer The indexer specifying the selection. value : npt.ArrayLike @@ -5947,7 +6204,7 @@ async def _set_selection( [ ( store_path / metadata.encode_chunk_key(chunk_coords), - metadata.get_chunk_spec(chunk_coords, _config, prototype), + _get_chunk_spec(metadata, chunk_grid, chunk_coords, _config, prototype), chunk_selection, out_selection, is_complete_chunk, @@ -5964,6 +6221,7 @@ async def _setitem( metadata: ArrayMetadata, codec_pipeline: CodecPipeline, config: ArrayConfig, + chunk_grid: ChunkGrid, selection: BasicSelection, value: npt.ArrayLike, prototype: BufferPrototype | None = None, @@ -5981,6 +6239,8 @@ async def _setitem( The codec pipeline for encoding/decoding. config : ArrayConfig The array configuration. + chunk_grid : ChunkGrid + The chunk grid. selection : BasicSelection The selection defining the region of the array to set. value : npt.ArrayLike @@ -5994,10 +6254,17 @@ async def _setitem( indexer = BasicIndexer( selection, shape=metadata.shape, - chunk_grid=metadata.chunk_grid, + chunk_grid=chunk_grid, ) return await _set_selection( - store_path, metadata, codec_pipeline, config, indexer, value, prototype=prototype + store_path, + metadata, + codec_pipeline, + config, + chunk_grid, + indexer, + value, + prototype=prototype, ) @@ -6021,15 +6288,17 @@ async def _resize( """ new_shape = parse_shapelike(new_shape) assert len(new_shape) == len(array.metadata.shape) + new_metadata = array.metadata.update_shape(new_shape) + new_chunk_grid = ChunkGrid.from_metadata(new_metadata) # ensure deletion is only run if array is shrinking as the delete_outside_chunks path is unbounded in memory only_growing = all(new >= old for new, old in zip(new_shape, array.metadata.shape, strict=True)) if delete_outside_chunks and not only_growing: # Remove all chunks outside of the new shape - old_chunk_coords = set(array.metadata.chunk_grid.all_chunk_coords(array.metadata.shape)) - new_chunk_coords = set(array.metadata.chunk_grid.all_chunk_coords(new_shape)) + old_chunk_coords = set(array._chunk_grid.all_chunk_coords()) + new_chunk_coords = set(new_chunk_grid.all_chunk_coords()) async def _delete_key(key: str) -> None: await (array.store_path / key).delete() @@ -6046,8 +6315,9 @@ async def _delete_key(key: str) -> None: # Write new metadata await save_metadata(array.store_path, new_metadata) - # Update metadata (in place) + # Update metadata and chunk_grid (in place) object.__setattr__(array, "metadata", new_metadata) + object.__setattr__(array, "_chunk_grid", new_chunk_grid) async def _append( @@ -6113,6 +6383,7 @@ async def _append( array.metadata, array.codec_pipeline, array.config, + array._chunk_grid, append_selection, data, ) diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index c903eba013..3d7313cd5d 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -1,34 +1,568 @@ from __future__ import annotations +import bisect import itertools import math import numbers import operator import warnings -from abc import abstractmethod -from dataclasses import dataclass +from dataclasses import dataclass, field from functools import reduce -from typing import TYPE_CHECKING, Any, Literal +from typing import TYPE_CHECKING, Any, Literal, Protocol, TypeGuard, cast, runtime_checkable import numpy as np +import numpy.typing as npt import zarr -from zarr.abc.metadata import Metadata from zarr.core.common import ( - JSON, - NamedConfig, ShapeLike, ceildiv, - parse_named_configuration, parse_shapelike, ) from zarr.errors import ZarrUserWarning if TYPE_CHECKING: - from collections.abc import Iterator - from typing import Self + from collections.abc import Iterable, Iterator, Sequence from zarr.core.array import ShardsLike + from zarr.core.metadata import ArrayMetadata + + +@dataclass(frozen=True) +class FixedDimension: + """Uniform chunk size. Boundary chunks contain less data but are + encoded at full size by the codec pipeline.""" + + size: int # chunk edge length (>= 0) + extent: int # array dimension length + nchunks: int = field(init=False, repr=False) + ngridcells: int = field(init=False, repr=False) + + def __post_init__(self) -> None: + if self.size < 0: + raise ValueError(f"FixedDimension size must be >= 0, got {self.size}") + if self.extent < 0: + raise ValueError(f"FixedDimension extent must be >= 0, got {self.extent}") + if self.size == 0: + n = 0 + else: + n = ceildiv(self.extent, self.size) + object.__setattr__(self, "nchunks", n) + object.__setattr__(self, "ngridcells", n) + + def index_to_chunk(self, idx: int) -> int: + if idx < 0: + raise IndexError(f"Negative index {idx} is not allowed") + if idx >= self.extent: + raise IndexError(f"Index {idx} is out of bounds for extent {self.extent}") + if self.size == 0: + return 0 + return idx // self.size + + def chunk_offset(self, chunk_ix: int) -> int: + """Byte-aligned start position of chunk *chunk_ix* in array coordinates. + + Does not validate *chunk_ix* — callers must ensure it is in + ``[0, nchunks)``. Use ``ChunkGrid.__getitem__`` for safe access. + """ + return chunk_ix * self.size + + def chunk_size(self, chunk_ix: int) -> int: + """Buffer size for codec processing — always uniform. + + Does not validate *chunk_ix* — callers must ensure it is in + ``[0, nchunks)``. Use ``ChunkGrid.__getitem__`` for safe access. + """ + return self.size + + def data_size(self, chunk_ix: int) -> int: + """Valid data region within the buffer — clipped at extent. + + Does not validate *chunk_ix* — callers must ensure it is in + ``[0, nchunks)``. Use ``ChunkGrid.__getitem__`` for safe access. + """ + if self.size == 0: + return 0 + return max(0, min(self.size, self.extent - chunk_ix * self.size)) + + @property + def _unique_edge_lengths(self) -> Iterable[int]: + """Distinct chunk edge lengths for this dimension. + + Used by shard validation to check that every unique edge length + is divisible by the inner chunk size. O(1) for fixed dimensions + since there is only one edge length. + """ + return (self.size,) + + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: + if self.size == 0: + return np.zeros_like(indices) + return indices // self.size + + def with_extent(self, new_extent: int) -> FixedDimension: + """Re-bind to *new_extent* without modifying edges. + + Used when constructing a grid from existing metadata where edges + are already correct. Raises on + ``VaryingDimension`` if edges don't cover the new extent. + """ + return FixedDimension(size=self.size, extent=new_extent) + + def resize(self, new_extent: int) -> FixedDimension: + """Adapt for a user-initiated array resize, growing edges if needed. + + For ``FixedDimension`` this is identical to ``with_extent`` since + regular grids don't store explicit edges. + """ + return FixedDimension(size=self.size, extent=new_extent) + + @property + def _size_repr(self) -> str: + return str(self.size) + + +@dataclass(frozen=True) +class VaryingDimension: + """Explicit per-chunk sizes. The last chunk may extend past the array + extent (``extent < sum(edges)``), in which case ``data_size`` clips to + the valid region while ``chunk_size`` returns the full edge length for + codec processing. This underflow is allowed to match how regular grids + handle boundary chunks, and to support shrinking an array without + rewriting chunk edges (the spec allows trailing edges beyond the extent).""" + + edges: tuple[int, ...] # per-chunk edge lengths (all > 0) + cumulative: tuple[int, ...] # prefix sums for O(log n) lookup + extent: int # array dimension length (may be < sum(edges) after resize) + nchunks: int = field(init=False, repr=False) # cached at construction + ngridcells: int = field(init=False, repr=False) # cached at construction + + # TODO(perf): for long dimensions (O(million chunks)): + # - with_extent/resize recompute cumulative sums and nchunks from scratch; + # add a fast path that reuses the existing cumulative tuple. + # - Consider storing cumulative as ndarray so bisect calls can use + # np.searchsorted. Scalar lookups (chunk_offset, index_to_chunk) + # would need benchmarking to confirm no regression. + def __init__(self, edges: Sequence[int], extent: int) -> None: + edges_tuple = tuple(edges) + if not edges_tuple: + raise ValueError("VaryingDimension edges must not be empty") + if any(e <= 0 for e in edges_tuple): + raise ValueError(f"All edge lengths must be > 0, got {edges_tuple}") + cumulative = tuple(itertools.accumulate(edges_tuple)) + if extent < 0: + raise ValueError(f"VaryingDimension extent must be >= 0, got {extent}") + if extent > cumulative[-1]: + raise ValueError( + f"VaryingDimension extent {extent} exceeds sum of edges {cumulative[-1]}" + ) + object.__setattr__(self, "edges", edges_tuple) + object.__setattr__(self, "cumulative", cumulative) + object.__setattr__(self, "extent", extent) + # Cache nchunks: number of chunks that overlap [0, extent) + if extent == 0: + n = 0 + else: + n = bisect.bisect_left(cumulative, extent) + 1 + object.__setattr__(self, "nchunks", n) + object.__setattr__(self, "ngridcells", len(edges_tuple)) + + def index_to_chunk(self, idx: int) -> int: + if idx < 0 or idx >= self.extent: + raise IndexError(f"Index {idx} out of bounds for dimension with extent {self.extent}") + return bisect.bisect_right(self.cumulative, idx) + + def chunk_offset(self, chunk_ix: int) -> int: + """Start position of chunk *chunk_ix* in array coordinates. + + Does not validate *chunk_ix* — callers must ensure it is in + ``[0, ngridcells)``. Use ``ChunkGrid.__getitem__`` for safe access. + """ + return self.cumulative[chunk_ix - 1] if chunk_ix > 0 else 0 + + def chunk_size(self, chunk_ix: int) -> int: + """Buffer size for codec processing. + + Does not validate *chunk_ix* — callers must ensure it is in + ``[0, ngridcells)``. Use ``ChunkGrid.__getitem__`` for safe access. + """ + return self.edges[chunk_ix] + + def data_size(self, chunk_ix: int) -> int: + """Valid data region within the buffer — clipped at extent. + + Does not validate *chunk_ix* — callers must ensure it is in + ``[0, ngridcells)``. Use ``ChunkGrid.__getitem__`` for safe access. + """ + offset = self.cumulative[chunk_ix - 1] if chunk_ix > 0 else 0 + return max(0, min(self.edges[chunk_ix], self.extent - offset)) + + @property + def _unique_edge_lengths(self) -> Iterable[int]: + """Distinct chunk edge lengths for this dimension (lazily deduplicated). + + Used by shard validation to check that every unique edge length + is divisible by the inner chunk size. Lazy deduplication avoids + materializing all edges for dimensions with many repeated sizes. + """ + seen: set[int] = set() + for e in self.edges: + if e not in seen: + seen.add(e) + yield e + + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: + return np.searchsorted(self.cumulative, indices, side="right") + + def with_extent(self, new_extent: int) -> VaryingDimension: + """Re-bind to *new_extent* without modifying edges. + + Used when constructing a grid from existing metadata where edges + are already correct. Raises if the + existing edges don't cover *new_extent*. + """ + edge_sum = self.cumulative[-1] + if edge_sum < new_extent: + raise ValueError( + f"VaryingDimension edge sum {edge_sum} is less than new extent {new_extent}" + ) + return VaryingDimension(self.edges, extent=new_extent) + + def resize(self, new_extent: int) -> VaryingDimension: + """Adapt for a user-initiated array resize, growing edges if needed. + + Unlike ``with_extent``, this never fails — if *new_extent* exceeds + the current edge sum, a new chunk is appended to cover the gap. + Shrinking preserves all edges (the spec allows trailing edges + beyond the array extent). + """ + if new_extent == self.extent: + return self + elif new_extent > self.cumulative[-1]: + expanded_edges = list(self.edges) + [new_extent - self.cumulative[-1]] + return VaryingDimension(expanded_edges, extent=new_extent) + else: + return VaryingDimension(self.edges, extent=new_extent) + + @property + def _size_repr(self) -> str: + return repr(tuple(self.edges)) + + +@runtime_checkable +class DimensionGrid(Protocol): + """Structural interface shared by FixedDimension and VaryingDimension.""" + + @property + def nchunks(self) -> int: ... + @property + def ngridcells(self) -> int: ... + @property + def extent(self) -> int: ... + def index_to_chunk(self, idx: int) -> int: ... + def chunk_offset(self, chunk_ix: int) -> int: ... + def chunk_size(self, chunk_ix: int) -> int: ... + def data_size(self, chunk_ix: int) -> int: ... + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: ... + @property + def _unique_edge_lengths(self) -> Iterable[int]: ... + def with_extent(self, new_extent: int) -> DimensionGrid: ... + def resize(self, new_extent: int) -> DimensionGrid: ... + @property + def _size_repr(self) -> str: ... + + +@dataclass(frozen=True) +class ChunkSpec: + """Specification of a single chunk's location and size. + + ``slices`` gives the valid data region in array coordinates. + ``codec_shape`` gives the buffer shape for codec processing. + For interior chunks these are equal. For boundary chunks of a regular + grid, ``codec_shape`` is the full declared chunk size while ``shape`` + is clipped. For rectilinear grids, ``shape == codec_shape`` unless the + last chunk extends past the array extent. + """ + + slices: tuple[slice, ...] + codec_shape: tuple[int, ...] + + @property + def shape(self) -> tuple[int, ...]: + return tuple(s.stop - s.start for s in self.slices) + + @property + def is_boundary(self) -> bool: + return self.shape != self.codec_shape + + +# A single dimension's rectilinear chunk spec: bare int (uniform shorthand), +# list of ints (explicit edges), or mixed RLE (e.g. [[10, 3], 5]). + + +def _is_rectilinear_chunks(chunks: Any) -> TypeGuard[Sequence[Sequence[int]]]: + """Check if chunks is a nested sequence (e.g. [[10, 20], [5, 5]]). + + Returns True for inputs like [[10, 20], [5, 5]] or [(10, 20), (5, 5)]. + Returns False for flat sequences like (10, 10) or [10, 10]. + """ + if isinstance(chunks, (str, int, ChunkGrid)): + return False + if not hasattr(chunks, "__iter__"): + return False + try: + first_elem = next(iter(chunks), None) + if first_elem is None: + return False + return hasattr(first_elem, "__iter__") and not isinstance(first_elem, (str, bytes, int)) + except (TypeError, StopIteration): + return False + + +@dataclass(frozen=True) +class ChunkGrid: + """ + Unified chunk grid supporting both regular and rectilinear chunking. + + A chunk grid is a concrete arrangement of chunks for a specific array. + It stores the extent (array dimension length) per dimension, enabling + ``grid[coords]`` to return a ``ChunkSpec`` without external parameters. + + Internally represents each dimension as either FixedDimension (uniform chunks) + or VaryingDimension (per-chunk edge lengths with prefix sums). + """ + + _dimensions: tuple[DimensionGrid, ...] + _is_regular: bool + + def __init__(self, *, dimensions: tuple[DimensionGrid, ...]) -> None: + object.__setattr__(self, "_dimensions", dimensions) + object.__setattr__( + self, "_is_regular", all(isinstance(d, FixedDimension) for d in dimensions) + ) + + def __repr__(self) -> str: + sizes = ", ".join(d._size_repr for d in self._dimensions) + shape = tuple(d.extent for d in self._dimensions) + return f"ChunkGrid(chunk_sizes=({sizes}), array_shape={shape})" + + @classmethod + def from_metadata(cls, metadata: ArrayMetadata) -> ChunkGrid: + """Construct a ChunkGrid from array metadata. + + For v2 metadata, builds from shape and chunks. + For v3 metadata, dispatches on the chunk grid type. + """ + from zarr.core.metadata import ArrayV2Metadata + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata, RegularChunkGridMetadata + + if isinstance(metadata, ArrayV2Metadata): + return cls.from_sizes(metadata.shape, tuple(metadata.chunks)) + chunk_grid_meta = metadata.chunk_grid + if isinstance(chunk_grid_meta, RegularChunkGridMetadata): + return cls.from_sizes(metadata.shape, tuple(chunk_grid_meta.chunk_shape)) + elif isinstance(chunk_grid_meta, RectilinearChunkGridMetadata): + return cls.from_sizes(metadata.shape, chunk_grid_meta.chunk_shapes) + else: + raise TypeError(f"Unknown chunk grid metadata type: {type(chunk_grid_meta)}") + + @classmethod + def from_sizes( + cls, + array_shape: ShapeLike, + chunk_sizes: Sequence[int | Sequence[int]], + ) -> ChunkGrid: + """Create a ChunkGrid from per-dimension chunk size specifications. + + Parameters + ---------- + array_shape + The array shape (one extent per dimension). + chunk_sizes + Per-dimension chunk sizes. Each element is either: + + - An ``int`` — regular (fixed) chunk size for that dimension. + - A ``Sequence[int]`` — explicit per-chunk edge lengths. If all + edges are identical and cover the extent, the dimension is + stored as ``FixedDimension``; otherwise as ``VaryingDimension``. + """ + extents = parse_shapelike(array_shape) + if len(extents) != len(chunk_sizes): + raise ValueError( + f"array_shape has {len(extents)} dimensions but chunk_sizes " + f"has {len(chunk_sizes)} dimensions" + ) + dims: list[DimensionGrid] = [] + for dim_spec, extent in zip(chunk_sizes, extents, strict=True): + if isinstance(dim_spec, int): + dims.append(FixedDimension(size=dim_spec, extent=extent)) + else: + edges_list = list(dim_spec) + if not edges_list: + raise ValueError("Each dimension must have at least one chunk") + edge_sum = sum(edges_list) + if ( + edges_list[0] > 0 + and all(e == edges_list[0] for e in edges_list) + and (extent == edge_sum or len(edges_list) == ceildiv(extent, edges_list[0])) + ): + dims.append(FixedDimension(size=edges_list[0], extent=extent)) + else: + dims.append(VaryingDimension(edges_list, extent=extent)) + return cls(dimensions=tuple(dims)) + + # -- Properties -- + + @property + def ndim(self) -> int: + return len(self._dimensions) + + @property + def is_regular(self) -> bool: + return self._is_regular + + @property + def grid_shape(self) -> tuple[int, ...]: + """Number of chunks per dimension.""" + return tuple(d.nchunks for d in self._dimensions) + + @property + def chunk_shape(self) -> tuple[int, ...]: + """Return the uniform chunk shape. Raises if grid is not regular.""" + if not self.is_regular: + raise ValueError( + "chunk_shape is only available for regular chunk grids. " + "Use grid[coords] for per-chunk sizes." + ) + return tuple(d.size for d in self._dimensions if isinstance(d, FixedDimension)) + + @property + def chunk_sizes(self) -> tuple[tuple[int, ...], ...]: + """Per-dimension chunk sizes, including the final boundary chunk. + + Returns the actual data size of each chunk (clipped at the array + extent), matching the dask ``Array.chunks`` convention. Works for + both regular and rectilinear grids. + + Returns + ------- + tuple[tuple[int, ...], ...] + One inner tuple per dimension, each containing the data size + of every chunk along that dimension. + """ + return tuple(tuple(d.data_size(i) for i in range(d.nchunks)) for d in self._dimensions) + + # -- Collection interface -- + + def __getitem__(self, coords: int | tuple[int, ...]) -> ChunkSpec | None: + """Return the ChunkSpec for a chunk at the given grid position, or None if OOB.""" + if isinstance(coords, int): + coords = (coords,) + if len(coords) != self.ndim: + raise ValueError( + f"Expected {self.ndim} coordinate(s) for a {self.ndim}-d chunk grid, " + f"got {len(coords)}." + ) + slices: list[slice] = [] + codec_shape: list[int] = [] + for dim, ix in zip(self._dimensions, coords, strict=True): + if ix < 0 or ix >= dim.nchunks: + return None + offset = dim.chunk_offset(ix) + slices.append(slice(offset, offset + dim.data_size(ix), 1)) + codec_shape.append(dim.chunk_size(ix)) + return ChunkSpec(tuple(slices), tuple(codec_shape)) + + def __iter__(self) -> Iterator[ChunkSpec]: + """Iterate all chunks, yielding ChunkSpec for each.""" + for coords in itertools.product(*(range(d.nchunks) for d in self._dimensions)): + spec = self[coords] + if spec is not None: + yield spec + + def all_chunk_coords( + self, + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, + ) -> Iterator[tuple[int, ...]]: + """Iterate over chunk coordinates, optionally restricted to a subregion. + + Parameters + ---------- + origin : Sequence[int] | None + The first chunk coordinate to return. Defaults to the grid origin. + selection_shape : Sequence[int] | None + The number of chunks per dimension to iterate. Defaults to the + remaining extent from origin. + """ + if origin is None: + origin_parsed = (0,) * self.ndim + else: + origin_parsed = tuple(origin) + if selection_shape is None: + selection_shape_parsed = tuple( + g - o for o, g in zip(origin_parsed, self.grid_shape, strict=True) + ) + else: + selection_shape_parsed = tuple(selection_shape) + ranges = tuple( + range(o, o + s) for o, s in zip(origin_parsed, selection_shape_parsed, strict=True) + ) + return itertools.product(*ranges) + + def iter_chunk_regions( + self, + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, + ) -> Iterator[tuple[slice, ...]]: + """Iterate over the data regions (slices) spanned by each chunk. + + Parameters + ---------- + origin : Sequence[int] | None + The first chunk coordinate to return. Defaults to the grid origin. + selection_shape : Sequence[int] | None + The number of chunks per dimension to iterate. Defaults to the + remaining extent from origin. + """ + for coords in self.all_chunk_coords(origin=origin, selection_shape=selection_shape): + spec = self[coords] + if spec is not None: + yield spec.slices + + def get_nchunks(self) -> int: + return reduce(operator.mul, (d.nchunks for d in self._dimensions), 1) + + # -- Resize -- + + def update_shape(self, new_shape: tuple[int, ...]) -> ChunkGrid: + """Return a new ChunkGrid adjusted for *new_shape*. + + For regular (FixedDimension) axes the extent is simply re-bound. + For varying (VaryingDimension) axes: + * **grow**: a new chunk whose size equals the growth is appended. + * **shrink**: trailing chunks that lie entirely beyond *new_shape* are + dropped; the last retained chunk is the one whose cumulative offset + first reaches or exceeds the new extent. + * **no change**: the dimension is kept as-is. + + Raises + ------ + ValueError + If *new_shape* has the wrong number of dimensions. + """ + if len(new_shape) != self.ndim: + raise ValueError( + f"new_shape has {len(new_shape)} dimensions but " + f"chunk grid has {self.ndim} dimensions" + ) + dims = tuple( + dim.resize(new_extent) + for dim, new_extent in zip(self._dimensions, new_shape, strict=True) + ) + return ChunkGrid(dimensions=dims) def _guess_chunks( @@ -156,58 +690,6 @@ def normalize_chunks(chunks: Any, shape: tuple[int, ...], typesize: int) -> tupl return tuple(int(c) for c in chunks) -@dataclass(frozen=True) -class ChunkGrid(Metadata): - @classmethod - def from_dict(cls, data: dict[str, JSON] | ChunkGrid | NamedConfig[str, Any]) -> ChunkGrid: - if isinstance(data, ChunkGrid): - return data - - name_parsed, _ = parse_named_configuration(data) - if name_parsed == "regular": - return RegularChunkGrid._from_dict(data) - raise ValueError(f"Unknown chunk grid. Got {name_parsed}.") - - @abstractmethod - def all_chunk_coords(self, array_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: - pass - - @abstractmethod - def get_nchunks(self, array_shape: tuple[int, ...]) -> int: - pass - - -@dataclass(frozen=True) -class RegularChunkGrid(ChunkGrid): - chunk_shape: tuple[int, ...] - - def __init__(self, *, chunk_shape: ShapeLike) -> None: - chunk_shape_parsed = parse_shapelike(chunk_shape) - - object.__setattr__(self, "chunk_shape", chunk_shape_parsed) - - @classmethod - def _from_dict(cls, data: dict[str, JSON] | NamedConfig[str, Any]) -> Self: - _, configuration_parsed = parse_named_configuration(data, "regular") - - return cls(**configuration_parsed) # type: ignore[arg-type] - - def to_dict(self) -> dict[str, JSON]: - return {"name": "regular", "configuration": {"chunk_shape": tuple(self.chunk_shape)}} - - def all_chunk_coords(self, array_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: - return itertools.product( - *(range(ceildiv(s, c)) for s, c in zip(array_shape, self.chunk_shape, strict=False)) - ) - - def get_nchunks(self, array_shape: tuple[int, ...]) -> int: - return reduce( - operator.mul, - itertools.starmap(ceildiv, zip(array_shape, self.chunk_shape, strict=True)), - 1, - ) - - def _guess_num_chunks_per_axis_shard( chunk_shape: tuple[int, ...], item_size: int, max_bytes: int, array_shape: tuple[int, ...] ) -> int: @@ -301,6 +783,6 @@ def _auto_partition( elif isinstance(shard_shape, dict): _shards_out = tuple(shard_shape["shape"]) else: - _shards_out = shard_shape + _shards_out = cast("tuple[int, ...]", shard_shape) return _shards_out, _chunks_out diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 0edc47ff6b..4cecc3a6d1 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -29,8 +29,8 @@ from zarr.abc.store import ByteGetter, ByteSetter from zarr.core.array_spec import ArraySpec from zarr.core.buffer import Buffer, BufferPrototype, NDBuffer - from zarr.core.chunk_grids import ChunkGrid from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType + from zarr.core.metadata.v3 import ChunkGridMetadata def _unzip2[T, U](iterable: Iterable[tuple[T, U]]) -> tuple[list[T], list[U]]: @@ -242,7 +242,7 @@ def validate( *, shape: tuple[int, ...], dtype: ZDType[TBaseDType, TBaseScalar], - chunk_grid: ChunkGrid, + chunk_grid: ChunkGridMetadata, ) -> None: for codec in self: codec.validate(shape=shape, dtype=dtype, chunk_grid=chunk_grid) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 077f459d3b..a16257df7c 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -37,6 +37,7 @@ BytesLike = bytes | bytearray | memoryview ShapeLike = Iterable[int | np.integer[Any]] | int | np.integer[Any] +ChunksLike = ShapeLike | Sequence[Sequence[int]] | None # For backwards compatibility ChunkCoords = tuple[int, ...] ZarrFormat = Literal[2, 3] @@ -241,3 +242,89 @@ def _warn_order_kwarg() -> None: def _default_zarr_format() -> ZarrFormat: """Return the default zarr_version""" return cast("ZarrFormat", int(zarr_config.get("default_zarr_format", 3))) + + +def expand_rle(data: Sequence[int | list[int]]) -> list[int]: + """Expand a mixed array of bare integers and RLE pairs. + + Per the rectilinear chunk grid spec, each element can be: + - a bare integer (an explicit edge length) + - a two-element array ``[value, count]`` (run-length encoded) + """ + result: list[int] = [] + for item in data: + if isinstance(item, (int, float)) and not isinstance(item, bool): + val = int(item) + if val < 1: + raise ValueError(f"Chunk edge length must be >= 1, got {val}") + result.append(val) + elif isinstance(item, list) and len(item) == 2: + size, count = int(item[0]), int(item[1]) + if size < 1: + raise ValueError(f"Chunk edge length must be >= 1, got {size}") + if count < 1: + raise ValueError(f"RLE repeat count must be >= 1, got {count}") + result.extend([size] * count) + else: + raise ValueError(f"RLE entries must be an integer or [size, count], got {item}") + return result + + +def compress_rle(sizes: Sequence[int]) -> list[int | list[int]]: + """Compress chunk sizes to mixed RLE format per the rectilinear spec. + + Runs of length > 1 are emitted as ``[value, count]`` pairs; runs of + length 1 are emitted as bare integers:: + + [10, 10, 10, 5] -> [[10, 3], 5] + """ + if not sizes: + return [] + result: list[int | list[int]] = [] + current = sizes[0] + count = 1 + for s in sizes[1:]: + if s == current: + count += 1 + else: + result.append([current, count] if count > 1 else current) + current = s + count = 1 + result.append([current, count] if count > 1 else current) + return result + + +def validate_rectilinear_kind(kind: str | None) -> None: + """Validate the ``kind`` field of a rectilinear chunk grid configuration. + + The rectilinear spec requires ``kind: "inline"``. + """ + if kind is None: + raise ValueError( + "Rectilinear chunk grid configuration requires a 'kind' field. " + "Only 'inline' is currently supported." + ) + if kind != "inline": + raise ValueError( + f"Unsupported rectilinear chunk grid kind: {kind!r}. " + "Only 'inline' is currently supported." + ) + + +def validate_rectilinear_edges( + chunk_shapes: Sequence[int | Sequence[int]], array_shape: Sequence[int] +) -> None: + """Validate that rectilinear chunk edges cover the array extent per dimension. + + Bare-int dimensions (regular step) always cover any extent, so they are + skipped. Explicit edge lists must sum to at least the array extent. + """ + for i, (dim_spec, extent) in enumerate(zip(chunk_shapes, array_shape, strict=True)): + if isinstance(dim_spec, int): + continue + edge_sum = sum(dim_spec) + if edge_sum < extent: + raise ValueError( + f"Rectilinear chunk edges for dimension {i} sum to {edge_sum} " + f"but array shape extent is {extent} (edge sum must be >= extent)" + ) diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index de50475992..7dcbc78e31 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -98,6 +98,7 @@ def enable_gpu(self) -> ConfigSet: "write_empty_chunks": False, "read_missing_chunks": True, "target_shard_size_bytes": None, + "rectilinear_chunks": False, }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 760f91722c..b810041e7b 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -40,6 +40,7 @@ ZATTRS_JSON, ZGROUP_JSON, ZMETADATA_V2_JSON, + ChunksLike, DimensionNamesLike, NodeType, ShapeLike, @@ -1020,7 +1021,7 @@ async def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: tuple[int, ...] | Literal["auto"] = "auto", + chunks: ChunksLike | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -2473,7 +2474,7 @@ def create( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: tuple[int, ...] | Literal["auto"] = "auto", + chunks: ChunksLike | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -2617,7 +2618,7 @@ def create_array( shape: ShapeLike | None = None, dtype: ZDTypeLike | None = None, data: np.ndarray[Any, np.dtype[Any]] | None = None, - chunks: tuple[int, ...] | Literal["auto"] = "auto", + chunks: ChunksLike | Literal["auto"] = "auto", shards: ShardsLike | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", @@ -3015,7 +3016,7 @@ def array( *, shape: ShapeLike, dtype: npt.DTypeLike, - chunks: tuple[int, ...] | Literal["auto"] = "auto", + chunks: ChunksLike | Literal["auto"] = "auto", shards: tuple[int, ...] | Literal["auto"] | None = None, filters: FiltersLike = "auto", compressors: CompressorsLike = "auto", diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 4461074a64..cb81164209 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -1,7 +1,6 @@ from __future__ import annotations import itertools -import math import numbers import operator from collections.abc import Iterator, Sequence @@ -36,7 +35,7 @@ if TYPE_CHECKING: from zarr.core.array import AsyncArray from zarr.core.buffer import NDArrayLikeOrScalar - from zarr.core.chunk_grids import ChunkGrid + from zarr.core.chunk_grids import ChunkGrid, DimensionGrid from zarr.types import AnyArray @@ -330,15 +329,6 @@ def is_pure_orthogonal_indexing(selection: Selection, ndim: int) -> TypeGuard[Or ) -def get_chunk_shape(chunk_grid: ChunkGrid) -> tuple[int, ...]: - from zarr.core.chunk_grids import RegularChunkGrid - - assert isinstance(chunk_grid, RegularChunkGrid), ( - "Only regular chunk grid is supported, currently." - ) - return chunk_grid.chunk_shape - - def normalize_integer_selection(dim_sel: int, dim_len: int) -> int: # normalize type to int dim_sel = int(dim_sel) @@ -378,35 +368,41 @@ class ChunkDimProjection(NamedTuple): class IntDimIndexer: dim_sel: int dim_len: int - dim_chunk_len: int + dim_grid: DimensionGrid nitems: int = 1 - def __init__(self, dim_sel: int, dim_len: int, dim_chunk_len: int) -> None: + def __init__(self, dim_sel: int, dim_len: int, dim_grid: DimensionGrid) -> None: object.__setattr__(self, "dim_sel", normalize_integer_selection(dim_sel, dim_len)) object.__setattr__(self, "dim_len", dim_len) - object.__setattr__(self, "dim_chunk_len", dim_chunk_len) + object.__setattr__(self, "dim_grid", dim_grid) def __iter__(self) -> Iterator[ChunkDimProjection]: - dim_chunk_ix = self.dim_sel // self.dim_chunk_len - dim_offset = dim_chunk_ix * self.dim_chunk_len + g = self.dim_grid + dim_chunk_ix = g.index_to_chunk(self.dim_sel) + dim_offset = g.chunk_offset(dim_chunk_ix) dim_chunk_sel = self.dim_sel - dim_offset dim_out_sel = None - is_complete_chunk = self.dim_chunk_len == 1 + is_complete_chunk = g.data_size(dim_chunk_ix) == 1 yield ChunkDimProjection(dim_chunk_ix, dim_chunk_sel, dim_out_sel, is_complete_chunk) @dataclass(frozen=True) class SliceDimIndexer: dim_len: int - dim_chunk_len: int nitems: int nchunks: int + dim_grid: DimensionGrid start: int stop: int step: int - def __init__(self, dim_sel: slice, dim_len: int, dim_chunk_len: int) -> None: + def __init__( + self, + dim_sel: slice, + dim_len: int, + dim_grid: DimensionGrid, + ) -> None: # normalize start, stop, step = dim_sel.indices(dim_len) if step < 1: @@ -417,23 +413,25 @@ def __init__(self, dim_sel: slice, dim_len: int, dim_chunk_len: int) -> None: object.__setattr__(self, "step", step) object.__setattr__(self, "dim_len", dim_len) - object.__setattr__(self, "dim_chunk_len", dim_chunk_len) + object.__setattr__(self, "dim_grid", dim_grid) object.__setattr__(self, "nitems", max(0, ceildiv((stop - start), step))) - object.__setattr__(self, "nchunks", ceildiv(dim_len, dim_chunk_len)) + object.__setattr__(self, "nchunks", dim_grid.nchunks) def __iter__(self) -> Iterator[ChunkDimProjection]: # figure out the range of chunks we need to visit - dim_chunk_ix_from = 0 if self.start == 0 else self.start // self.dim_chunk_len - dim_chunk_ix_to = ceildiv(self.stop, self.dim_chunk_len) + if self.start >= self.stop: + return # empty slice + g = self.dim_grid + dim_chunk_ix_from = g.index_to_chunk(self.start) if self.start > 0 else 0 + dim_chunk_ix_to = g.index_to_chunk(self.stop - 1) + 1 if self.stop > 0 else 0 # iterate over chunks in range for dim_chunk_ix in range(dim_chunk_ix_from, dim_chunk_ix_to): # compute offsets for chunk within overall array - dim_offset = dim_chunk_ix * self.dim_chunk_len - dim_limit = min(self.dim_len, (dim_chunk_ix + 1) * self.dim_chunk_len) - + dim_offset = g.chunk_offset(dim_chunk_ix) # determine chunk length, accounting for trailing chunk - dim_chunk_len = dim_limit - dim_offset + dim_chunk_len = g.data_size(dim_chunk_ix) + dim_limit = dim_offset + dim_chunk_len if self.start < dim_offset: # selection starts before current chunk @@ -443,7 +441,6 @@ def __iter__(self) -> Iterator[ChunkDimProjection]: dim_chunk_sel_start += self.step - remainder # compute number of previous items, provides offset into output array dim_out_offset = ceildiv((dim_offset - self.start), self.step) - else: # selection starts within current chunk dim_chunk_sel_start = self.start - dim_offset @@ -452,7 +449,6 @@ def __iter__(self) -> Iterator[ChunkDimProjection]: if self.stop > dim_limit: # selection ends after current chunk dim_chunk_sel_stop = dim_chunk_len - else: # selection ends within current chunk dim_chunk_sel_stop = self.stop - dim_offset @@ -465,7 +461,6 @@ def __iter__(self) -> Iterator[ChunkDimProjection]: continue dim_out_sel = slice(dim_out_offset, dim_out_offset + dim_chunk_nitems) - is_complete_chunk = ( dim_chunk_sel_start == 0 and (self.stop >= dim_limit) and self.step in [1, None] ) @@ -583,21 +578,19 @@ def __init__( shape: tuple[int, ...], chunk_grid: ChunkGrid, ) -> None: - chunk_shape = get_chunk_shape(chunk_grid) + dim_grids = chunk_grid._dimensions # handle ellipsis selection_normalized = replace_ellipsis(selection, shape) # setup per-dimension indexers dim_indexers: list[IntDimIndexer | SliceDimIndexer] = [] - for dim_sel, dim_len, dim_chunk_len in zip( - selection_normalized, shape, chunk_shape, strict=True - ): + for dim_sel, dim_len, dim_grid in zip(selection_normalized, shape, dim_grids, strict=True): dim_indexer: IntDimIndexer | SliceDimIndexer if is_integer(dim_sel): - dim_indexer = IntDimIndexer(dim_sel, dim_len, dim_chunk_len) + dim_indexer = IntDimIndexer(dim_sel, dim_len, dim_grid) elif is_slice(dim_sel): - dim_indexer = SliceDimIndexer(dim_sel, dim_len, dim_chunk_len) + dim_indexer = SliceDimIndexer(dim_sel, dim_len, dim_grid) else: raise IndexError( @@ -630,7 +623,7 @@ def __iter__(self) -> Iterator[ChunkProjection]: class BoolArrayDimIndexer: dim_sel: npt.NDArray[np.bool_] dim_len: int - dim_chunk_len: int + dim_grid: DimensionGrid nchunks: int chunk_nitems: npt.NDArray[Any] @@ -638,7 +631,12 @@ class BoolArrayDimIndexer: nitems: int dim_chunk_ixs: npt.NDArray[np.intp] - def __init__(self, dim_sel: npt.NDArray[np.bool_], dim_len: int, dim_chunk_len: int) -> None: + def __init__( + self, + dim_sel: npt.NDArray[np.bool_], + dim_len: int, + dim_grid: DimensionGrid, + ) -> None: # check number of dimensions if not is_bool_array(dim_sel, 1): raise IndexError("Boolean arrays in an orthogonal selection must be 1-dimensional only") @@ -649,13 +647,16 @@ def __init__(self, dim_sel: npt.NDArray[np.bool_], dim_len: int, dim_chunk_len: f"Boolean array has the wrong length for dimension; expected {dim_len}, got {dim_sel.shape[0]}" ) + g = dim_grid + nchunks = g.nchunks + # precompute number of selected items for each chunk - nchunks = ceildiv(dim_len, dim_chunk_len) chunk_nitems = np.zeros(nchunks, dtype="i8") for dim_chunk_ix in range(nchunks): - dim_offset = dim_chunk_ix * dim_chunk_len + dim_offset = g.chunk_offset(dim_chunk_ix) + chunk_len = g.data_size(dim_chunk_ix) chunk_nitems[dim_chunk_ix] = np.count_nonzero( - dim_sel[dim_offset : dim_offset + dim_chunk_len] + dim_sel[dim_offset : dim_offset + chunk_len] ) chunk_nitems_cumsum = np.cumsum(chunk_nitems) nitems = chunk_nitems_cumsum[-1] @@ -664,7 +665,7 @@ def __init__(self, dim_sel: npt.NDArray[np.bool_], dim_len: int, dim_chunk_len: # store attributes object.__setattr__(self, "dim_sel", dim_sel) object.__setattr__(self, "dim_len", dim_len) - object.__setattr__(self, "dim_chunk_len", dim_chunk_len) + object.__setattr__(self, "dim_grid", dim_grid) object.__setattr__(self, "nchunks", nchunks) object.__setattr__(self, "chunk_nitems", chunk_nitems) object.__setattr__(self, "chunk_nitems_cumsum", chunk_nitems_cumsum) @@ -672,15 +673,19 @@ def __init__(self, dim_sel: npt.NDArray[np.bool_], dim_len: int, dim_chunk_len: object.__setattr__(self, "dim_chunk_ixs", dim_chunk_ixs) def __iter__(self) -> Iterator[ChunkDimProjection]: + g = self.dim_grid + # iterate over chunks with at least one item for dim_chunk_ix in self.dim_chunk_ixs: # find region in chunk - dim_offset = dim_chunk_ix * self.dim_chunk_len - dim_chunk_sel = self.dim_sel[dim_offset : dim_offset + self.dim_chunk_len] - - # pad out if final chunk - if dim_chunk_sel.shape[0] < self.dim_chunk_len: - tmp = np.zeros(self.dim_chunk_len, dtype=bool) + dim_offset = g.chunk_offset(dim_chunk_ix) + chunk_len = g.data_size(dim_chunk_ix) + dim_chunk_sel = self.dim_sel[dim_offset : dim_offset + chunk_len] + + # pad out if boundary chunk (codec buffer may be larger than valid data region) + codec_size = g.chunk_size(dim_chunk_ix) + if dim_chunk_sel.shape[0] < codec_size: + tmp = np.zeros(codec_size, dtype=bool) tmp[: dim_chunk_sel.shape[0]] = dim_chunk_sel dim_chunk_sel = tmp @@ -739,7 +744,7 @@ class IntArrayDimIndexer: """Integer array selection against a single dimension.""" dim_len: int - dim_chunk_len: int + dim_grid: DimensionGrid nchunks: int nitems: int order: Order @@ -753,7 +758,7 @@ def __init__( self, dim_sel: npt.NDArray[np.intp], dim_len: int, - dim_chunk_len: int, + dim_grid: DimensionGrid, wraparound: bool = True, boundscheck: bool = True, order: Order = Order.UNKNOWN, @@ -764,7 +769,8 @@ def __init__( raise IndexError("integer arrays in an orthogonal selection must be 1-dimensional only") nitems = len(dim_sel) - nchunks = ceildiv(dim_len, dim_chunk_len) + g = dim_grid + nchunks = g.nchunks # handle wraparound if wraparound: @@ -777,7 +783,7 @@ def __init__( # determine which chunk is needed for each selection item # note: for dense integer selections, the division operation here is the # bottleneck - dim_sel_chunk = dim_sel // dim_chunk_len + dim_sel_chunk = g.indices_to_chunks(dim_sel) # determine order of indices if order == Order.UNKNOWN: @@ -806,7 +812,7 @@ def __init__( # store attributes object.__setattr__(self, "dim_len", dim_len) - object.__setattr__(self, "dim_chunk_len", dim_chunk_len) + object.__setattr__(self, "dim_grid", dim_grid) object.__setattr__(self, "nchunks", nchunks) object.__setattr__(self, "nitems", nitems) object.__setattr__(self, "order", order) @@ -817,6 +823,8 @@ def __init__( object.__setattr__(self, "chunk_nitems_cumsum", chunk_nitems_cumsum) def __iter__(self) -> Iterator[ChunkDimProjection]: + g = self.dim_grid + for dim_chunk_ix in self.dim_chunk_ixs: dim_out_sel: slice | npt.NDArray[np.intp] # find region in output @@ -831,7 +839,7 @@ def __iter__(self) -> Iterator[ChunkDimProjection]: dim_out_sel = self.dim_out_sel[start:stop] # find region in chunk - dim_offset = dim_chunk_ix * self.dim_chunk_len + dim_offset = g.chunk_offset(dim_chunk_ix) dim_chunk_sel = self.dim_sel[start:stop] - dim_offset is_complete_chunk = False # TODO yield ChunkDimProjection(dim_chunk_ix, dim_chunk_sel, dim_out_sel, is_complete_chunk) @@ -891,13 +899,13 @@ def oindex_set(a: npt.NDArray[Any], selection: Selection, value: Any) -> None: @dataclass(frozen=True) class OrthogonalIndexer(Indexer): dim_indexers: list[IntDimIndexer | SliceDimIndexer | IntArrayDimIndexer | BoolArrayDimIndexer] + dim_grids: tuple[DimensionGrid, ...] shape: tuple[int, ...] - chunk_shape: tuple[int, ...] is_advanced: bool drop_axes: tuple[int, ...] def __init__(self, selection: Selection, shape: tuple[int, ...], chunk_grid: ChunkGrid) -> None: - chunk_shape = get_chunk_shape(chunk_grid) + dim_grids = chunk_grid._dimensions # handle ellipsis selection = replace_ellipsis(selection, shape) @@ -909,19 +917,19 @@ def __init__(self, selection: Selection, shape: tuple[int, ...], chunk_grid: Chu dim_indexers: list[ IntDimIndexer | SliceDimIndexer | IntArrayDimIndexer | BoolArrayDimIndexer ] = [] - for dim_sel, dim_len, dim_chunk_len in zip(selection, shape, chunk_shape, strict=True): + for dim_sel, dim_len, dim_grid in zip(selection, shape, dim_grids, strict=True): dim_indexer: IntDimIndexer | SliceDimIndexer | IntArrayDimIndexer | BoolArrayDimIndexer if is_integer(dim_sel): - dim_indexer = IntDimIndexer(dim_sel, dim_len, dim_chunk_len) + dim_indexer = IntDimIndexer(dim_sel, dim_len, dim_grid) elif isinstance(dim_sel, slice): - dim_indexer = SliceDimIndexer(dim_sel, dim_len, dim_chunk_len) + dim_indexer = SliceDimIndexer(dim_sel, dim_len, dim_grid) elif is_integer_array(dim_sel): - dim_indexer = IntArrayDimIndexer(dim_sel, dim_len, dim_chunk_len) + dim_indexer = IntArrayDimIndexer(dim_sel, dim_len, dim_grid) elif is_bool_array(dim_sel): - dim_indexer = BoolArrayDimIndexer(dim_sel, dim_len, dim_chunk_len) + dim_indexer = BoolArrayDimIndexer(dim_sel, dim_len, dim_grid) else: raise IndexError( @@ -944,8 +952,8 @@ def __init__(self, selection: Selection, shape: tuple[int, ...], chunk_grid: Chu drop_axes = () object.__setattr__(self, "dim_indexers", dim_indexers) + object.__setattr__(self, "dim_grids", dim_grids) object.__setattr__(self, "shape", shape) - object.__setattr__(self, "chunk_shape", chunk_shape) object.__setattr__(self, "is_advanced", is_advanced) object.__setattr__(self, "drop_axes", drop_axes) @@ -972,7 +980,11 @@ def __iter__(self) -> Iterator[ChunkProjection]: # N.B., numpy doesn't support orthogonal indexing directly # for multiple array-indexed dimensions, so we need to # convert the orthogonal selection into coordinate arrays. - chunk_selection = ix_(chunk_selection, self.chunk_shape) + chunk_shape = tuple( + g.chunk_size(p.dim_chunk_ix) + for g, p in zip(self.dim_grids, dim_projections, strict=True) + ) + chunk_selection = ix_(chunk_selection, chunk_shape) # special case for non-monotonic indices if not is_basic_selection(out_selection): @@ -1038,7 +1050,7 @@ class BlockIndexer(Indexer): def __init__( self, selection: BasicSelection, shape: tuple[int, ...], chunk_grid: ChunkGrid ) -> None: - chunk_shape = get_chunk_shape(chunk_grid) + dim_grids = chunk_grid._dimensions # handle ellipsis selection_normalized = replace_ellipsis(selection, shape) @@ -1048,17 +1060,20 @@ def __init__( # setup per-dimension indexers dim_indexers = [] - for dim_sel, dim_len, dim_chunk_size in zip( - selection_normalized, shape, chunk_shape, strict=True - ): - dim_numchunks = int(np.ceil(dim_len / dim_chunk_size)) + for dim_sel, dim_len, dim_grid in zip(selection_normalized, shape, dim_grids, strict=True): + dim_numchunks = dim_grid.nchunks if is_integer(dim_sel): if dim_sel < 0: dim_sel = dim_numchunks + dim_sel - start = dim_sel * dim_chunk_size - stop = start + dim_chunk_size + if dim_sel < 0 or dim_sel >= dim_numchunks: + raise BoundsCheckError( + f"block index out of bounds for dimension with {dim_numchunks} chunk(s)" + ) + + start = dim_grid.chunk_offset(dim_sel) + stop = start + dim_grid.chunk_size(dim_sel) slice_ = slice(start, stop) elif is_slice(dim_sel): @@ -1078,8 +1093,8 @@ def __init__( if stop < 0: stop = dim_numchunks + stop - start *= dim_chunk_size - stop *= dim_chunk_size + start = dim_grid.chunk_offset(start) if start < dim_numchunks else dim_len + stop = dim_grid.chunk_offset(stop) if stop < dim_numchunks else dim_len slice_ = slice(start, stop) else: @@ -1088,10 +1103,10 @@ def __init__( f"expected integer or slice, got {type(dim_sel)!r}" ) - dim_indexer = SliceDimIndexer(slice_, dim_len, dim_chunk_size) + dim_indexer = SliceDimIndexer(slice_, dim_len, dim_grid) dim_indexers.append(dim_indexer) - if start >= dim_len or start < 0: + if slice_.start >= dim_len or slice_.start < 0: msg = f"index out of bounds for dimension with length {dim_len}" raise BoundsCheckError(msg) @@ -1159,19 +1174,19 @@ class CoordinateIndexer(Indexer): chunk_rixs: npt.NDArray[np.intp] chunk_mixs: tuple[npt.NDArray[np.intp], ...] shape: tuple[int, ...] - chunk_shape: tuple[int, ...] + dim_grids: tuple[DimensionGrid, ...] drop_axes: tuple[int, ...] def __init__( self, selection: CoordinateSelection, shape: tuple[int, ...], chunk_grid: ChunkGrid ) -> None: - chunk_shape = get_chunk_shape(chunk_grid) + dim_grids = chunk_grid._dimensions cdata_shape: tuple[int, ...] if shape == (): cdata_shape = (1,) else: - cdata_shape = tuple(math.ceil(s / c) for s, c in zip(shape, chunk_shape, strict=True)) + cdata_shape = tuple(g.nchunks for g in dim_grids) nchunks = reduce(operator.mul, cdata_shape, 1) # some initial normalization @@ -1201,8 +1216,8 @@ def __init__( # compute chunk index for each point in the selection chunks_multi_index = tuple( - dim_sel // dim_chunk_len - for (dim_sel, dim_chunk_len) in zip(selection_normalized, chunk_shape, strict=True) + g.indices_to_chunks(dim_sel) + for (dim_sel, g) in zip(selection_normalized, dim_grids, strict=True) ) # broadcast selection - this will raise error if array dimensions don't match @@ -1248,7 +1263,7 @@ def __init__( object.__setattr__(self, "chunk_nitems_cumsum", chunk_nitems_cumsum) object.__setattr__(self, "chunk_rixs", chunk_rixs) object.__setattr__(self, "chunk_mixs", chunk_mixs) - object.__setattr__(self, "chunk_shape", chunk_shape) + object.__setattr__(self, "dim_grids", dim_grids) object.__setattr__(self, "shape", shape) object.__setattr__(self, "drop_axes", ()) @@ -1268,8 +1283,8 @@ def __iter__(self) -> Iterator[ChunkProjection]: out_selection = self.sel_sort[start:stop] chunk_offsets = tuple( - dim_chunk_ix * dim_chunk_len - for dim_chunk_ix, dim_chunk_len in zip(chunk_coords, self.chunk_shape, strict=True) + g.chunk_offset(dim_chunk_ix) + for dim_chunk_ix, g in zip(chunk_coords, self.dim_grids, strict=True) ) chunk_selection = tuple( dim_sel[start:stop] - dim_chunk_offset diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index f0781e1313..8626d480a7 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -7,7 +7,6 @@ from zarr.abc.metadata import Metadata from zarr.abc.numcodec import Numcodec, _is_numcodec -from zarr.core.chunk_grids import RegularChunkGrid from zarr.core.dtype import get_data_type_from_json from zarr.core.dtype.common import OBJECT_CODEC_IDS, DTypeSpec_V2 from zarr.errors import ZarrUserWarning @@ -19,6 +18,7 @@ import numpy.typing as npt from zarr.core.buffer import Buffer, BufferPrototype + from zarr.core.chunk_grids import ChunkGrid from zarr.core.dtype.wrapper import ( TBaseDType, TBaseScalar, @@ -116,8 +116,22 @@ def ndim(self) -> int: return len(self.shape) @cached_property - def chunk_grid(self) -> RegularChunkGrid: - return RegularChunkGrid(chunk_shape=self.chunks) + def chunk_grid(self) -> ChunkGrid: + """Backwards-compatible chunk grid property. + + .. deprecated:: + Access the chunk grid via the array layer instead. + This property will be removed in a future release. + """ + from zarr.core.chunk_grids import ChunkGrid + + warnings.warn( + "ArrayV2Metadata.chunk_grid is deprecated. " + "Use ChunkGrid.from_metadata(metadata) instead.", + DeprecationWarning, + stacklevel=2, + ) + return ChunkGrid.from_sizes(self.shape, tuple(self.chunks)) @property def shards(self) -> tuple[int, ...] | None: diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 2a5da50c7b..7773e2489d 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -1,30 +1,14 @@ from __future__ import annotations -from collections.abc import Mapping -from typing import TYPE_CHECKING, NotRequired, TypedDict, TypeGuard, cast - -from zarr.abc.metadata import Metadata -from zarr.core.buffer.core import default_buffer_prototype -from zarr.core.dtype import VariableLengthUTF8, ZDType, get_data_type_from_json -from zarr.core.dtype.common import check_dtype_spec_v3 - -if TYPE_CHECKING: - from typing import Self - - from zarr.core.buffer import Buffer, BufferPrototype - from zarr.core.chunk_grids import ChunkGrid - from zarr.core.common import JSON - from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar - - import json -from collections.abc import Iterable +from collections.abc import Iterable, Mapping, Sequence from dataclasses import dataclass, field, replace -from typing import Any, Literal +from typing import TYPE_CHECKING, Any, Literal, NotRequired, TypedDict, TypeGuard, cast from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec +from zarr.abc.metadata import Metadata from zarr.core.array_spec import ArrayConfig, ArraySpec -from zarr.core.chunk_grids import ChunkGrid, RegularChunkGrid +from zarr.core.buffer.core import default_buffer_prototype from zarr.core.chunk_key_encodings import ( ChunkKeyEncoding, ChunkKeyEncodingLike, @@ -33,16 +17,30 @@ from zarr.core.common import ( JSON, ZARR_JSON, + ChunksLike, DimensionNamesLike, NamedConfig, + NamedRequiredConfig, + compress_rle, + expand_rle, parse_named_configuration, parse_shapelike, + validate_rectilinear_edges, + validate_rectilinear_kind, ) from zarr.core.config import config +from zarr.core.dtype import VariableLengthUTF8, ZDType, get_data_type_from_json +from zarr.core.dtype.common import check_dtype_spec_v3 from zarr.core.metadata.common import parse_attributes from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError from zarr.registry import get_codec_class +if TYPE_CHECKING: + from typing import Self + + from zarr.core.buffer import Buffer, BufferPrototype + from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar + def parse_zarr_format(data: object) -> Literal[3]: if data == 3: @@ -174,6 +172,245 @@ def parse_extra_fields( return dict(data) +# JSON type for a single dimension's rectilinear spec: +# bare int (uniform shorthand), or list of ints / [value, count] RLE pairs. +RectilinearDimSpecJSON = int | list[int | list[int]] + + +class RegularChunkGridMetadataConfig(TypedDict): + chunk_shape: Sequence[int] + + +class RectilinearChunkGridMetadataConfig(TypedDict): + kind: Literal["inline"] + chunk_shapes: Sequence[RectilinearDimSpecJSON] + + +RegularChunkGridMetadataJSON = NamedRequiredConfig[ + Literal["regular"], RegularChunkGridMetadataConfig +] +RectilinearChunkGridMetadataJSON = NamedRequiredConfig[ + Literal["rectilinear"], RectilinearChunkGridMetadataConfig +] + + +def _parse_chunk_shape(chunk_shape: Iterable[int]) -> tuple[int, ...]: + """Validate and normalize a regular chunk shape. + + Delegates to ``_validate_chunk_shapes`` — a regular chunk shape is just + a sequence of bare ints (one per dimension), each of which must be >= 1. + """ + result = _validate_chunk_shapes(tuple(chunk_shape)) + # Regular grids only have bare ints — cast is safe after validation + return cast(tuple[int, ...], result) + + +def _validate_chunk_shapes( + chunk_shapes: Sequence[int | Sequence[int]], +) -> tuple[int | tuple[int, ...], ...]: + """Validate per-dimension chunk specifications. + + Each element is either a bare ``int`` (regular step size, must be >= 1) + or a sequence of explicit edge lengths (all must be >= 1, non-empty). + """ + result: list[int | tuple[int, ...]] = [] + for dim_idx, dim_spec in enumerate(chunk_shapes): + if isinstance(dim_spec, int): + if dim_spec < 1: + raise ValueError( + f"Dimension {dim_idx}: integer chunk edge length must be >= 1, got {dim_spec}" + ) + result.append(dim_spec) + else: + edges = tuple(dim_spec) + if not edges: + raise ValueError(f"Dimension {dim_idx} has no chunk edges.") + bad = [i for i, e in enumerate(edges) if e < 1] + if bad: + raise ValueError( + f"Dimension {dim_idx} has invalid edge lengths at indices {bad}: " + f"{[edges[i] for i in bad]}" + ) + result.append(edges) + return tuple(result) + + +@dataclass(frozen=True, kw_only=True) +class RegularChunkGridMetadata(Metadata): + """Metadata-only description of a regular chunk grid. + + Stores just the chunk shape — no array extent, no runtime logic. + This is what lives on ``ArrayV3Metadata.chunk_grid``. + """ + + chunk_shape: tuple[int, ...] + + def __post_init__(self) -> None: + chunk_shape_parsed = _parse_chunk_shape(self.chunk_shape) + object.__setattr__(self, "chunk_shape", chunk_shape_parsed) + + @property + def ndim(self) -> int: + return len(self.chunk_shape) + + def to_dict(self) -> RegularChunkGridMetadataJSON: # type: ignore[override] + return { + "name": "regular", + "configuration": {"chunk_shape": self.chunk_shape}, + } + + @classmethod + def from_dict(cls, data: RegularChunkGridMetadataJSON) -> Self: # type: ignore[override] + parse_named_configuration(data, "regular") # validate name + configuration = data["configuration"] + return cls(chunk_shape=_parse_chunk_shape(configuration["chunk_shape"])) + + +@dataclass(frozen=True, kw_only=True) +class RectilinearChunkGridMetadata(Metadata): + """Metadata-only description of a rectilinear chunk grid. + + Each element of ``chunk_shapes`` is either: + + - A bare ``int`` — a regular step size that repeats to cover the axis + (the spec's single-integer shorthand). + - A ``tuple[int, ...]`` — explicit per-chunk edge lengths (already + expanded from any RLE encoding). + + This distinction matters for faithful round-tripping: a bare int + serializes back as a bare int, while a single-element tuple serializes + as a list. + """ + + chunk_shapes: tuple[int | tuple[int, ...], ...] + + def __post_init__(self) -> None: + from zarr.core.config import config + + if not config.get("array.rectilinear_chunks"): + raise ValueError( + "Rectilinear chunk grids are experimental and disabled by default. " + "Enable them with: zarr.config.set({'array.rectilinear_chunks': True}) " + "or set the environment variable ZARR_ARRAY__RECTILINEAR_CHUNKS=True" + ) + object.__setattr__(self, "chunk_shapes", _validate_chunk_shapes(self.chunk_shapes)) + + @property + def ndim(self) -> int: + return len(self.chunk_shapes) + + def to_dict(self) -> RectilinearChunkGridMetadataJSON: # type: ignore[override] + serialized_dims: list[RectilinearDimSpecJSON] = [] + for dim_spec in self.chunk_shapes: + if isinstance(dim_spec, int): + # Bare int shorthand — serialize as-is + serialized_dims.append(dim_spec) + else: + rle = compress_rle(dim_spec) + # Use RLE only if it's actually shorter + if len(rle) < len(dim_spec): + serialized_dims.append(rle) + else: + serialized_dims.append(list(dim_spec)) + return { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": tuple(serialized_dims), + }, + } + + def update_shape( + self, old_shape: tuple[int, ...], new_shape: tuple[int, ...] + ) -> RectilinearChunkGridMetadata: + """Return a new RectilinearChunkGridMetadata with edges adjusted for *new_shape*. + + - Bare-int dimensions stay as bare ints (they cover any extent). + - Explicit-edge dimensions: if the new extent exceeds the sum of + edges, a new chunk is appended to cover the additional extent. + Otherwise edges are kept as-is (the spec allows trailing edges + beyond the array extent). + """ + new_chunk_shapes: list[int | tuple[int, ...]] = [] + for dim_spec, new_ext in zip(self.chunk_shapes, new_shape, strict=True): + if isinstance(dim_spec, int): + # Bare int covers any extent — no change needed + new_chunk_shapes.append(dim_spec) + else: + edge_sum = sum(dim_spec) + if new_ext > edge_sum: + new_chunk_shapes.append((*dim_spec, new_ext - edge_sum)) + else: + new_chunk_shapes.append(dim_spec) + return RectilinearChunkGridMetadata(chunk_shapes=tuple(new_chunk_shapes)) + + @classmethod + def from_dict(cls, data: RectilinearChunkGridMetadataJSON) -> Self: # type: ignore[override] + parse_named_configuration(data, "rectilinear") # validate name + configuration = data["configuration"] + validate_rectilinear_kind(configuration.get("kind")) + raw_shapes = configuration["chunk_shapes"] + parsed: list[int | tuple[int, ...]] = [] + for dim_spec in raw_shapes: + if isinstance(dim_spec, int): + if dim_spec < 1: + raise ValueError(f"Integer chunk edge length must be >= 1, got {dim_spec}") + parsed.append(dim_spec) + elif isinstance(dim_spec, list): + parsed.append(tuple(expand_rle(dim_spec))) + else: + raise TypeError( + f"Invalid chunk_shapes entry: expected int or list, got {type(dim_spec)}" + ) + return cls(chunk_shapes=tuple(parsed)) + + +ChunkGridMetadata = RegularChunkGridMetadata | RectilinearChunkGridMetadata + + +def resolve_chunks( + chunks: ChunksLike, + shape: tuple[int, ...], + typesize: int, +) -> ChunkGridMetadata: + """Construct a chunk grid from user-facing input (e.g. ``create_array(chunks=...)``). + + Nested sequences like ``[[10, 20], [5, 5]]`` produce a ``RectilinearChunkGridMetadata``. + Flat inputs like ``(10, 10)`` or a scalar ``int`` produce a ``RegularChunkGridMetadata`` + after normalization via :func:`~zarr.core.chunk_grids.normalize_chunks`. + + See Also + -------- + parse_chunk_grid : Deserialize a chunk grid from stored JSON metadata. + """ + from zarr.core.chunk_grids import _is_rectilinear_chunks, normalize_chunks + + if _is_rectilinear_chunks(chunks): + return RectilinearChunkGridMetadata(chunk_shapes=tuple(tuple(c) for c in chunks)) + + return RegularChunkGridMetadata(chunk_shape=normalize_chunks(chunks, shape, typesize)) + + +def parse_chunk_grid( + data: dict[str, JSON] | ChunkGridMetadata | NamedConfig[str, Any], +) -> ChunkGridMetadata: + """Deserialize a chunk grid from stored JSON metadata or pass through an existing instance. + + See Also + -------- + resolve_chunks : Construct a chunk grid from user-facing input. + """ + if isinstance(data, (RegularChunkGridMetadata, RectilinearChunkGridMetadata)): + return data + + name, _ = parse_named_configuration(data) + if name == "regular": + return RegularChunkGridMetadata.from_dict(data) # type: ignore[arg-type] + if name == "rectilinear": + return RectilinearChunkGridMetadata.from_dict(data) # type: ignore[arg-type] + raise ValueError(f"Unknown chunk grid name: {name!r}") + + class ArrayMetadataJSON_V3(TypedDict): """ A typed dictionary model for zarr v3 metadata. @@ -199,7 +436,7 @@ class ArrayMetadataJSON_V3(TypedDict): class ArrayV3Metadata(Metadata): shape: tuple[int, ...] data_type: ZDType[TBaseDType, TBaseScalar] - chunk_grid: ChunkGrid + chunk_grid: ChunkGridMetadata chunk_key_encoding: ChunkKeyEncoding fill_value: Any codecs: tuple[Codec, ...] @@ -215,7 +452,7 @@ def __init__( *, shape: Iterable[int], data_type: ZDType[TBaseDType, TBaseScalar], - chunk_grid: dict[str, JSON] | ChunkGrid | NamedConfig[str, Any], + chunk_grid: dict[str, JSON] | ChunkGridMetadata | NamedConfig[str, Any], chunk_key_encoding: ChunkKeyEncodingLike, fill_value: object, codecs: Iterable[Codec | dict[str, JSON] | NamedConfig[str, Any] | str], @@ -229,7 +466,7 @@ def __init__( """ shape_parsed = parse_shapelike(shape) - chunk_grid_parsed = ChunkGrid.from_dict(chunk_grid) + chunk_grid_parsed = parse_chunk_grid(chunk_grid) chunk_key_encoding_parsed = parse_chunk_key_encoding(chunk_key_encoding) dimension_names_parsed = parse_dimension_names(dimension_names) # Note: relying on a type method is numpy-specific @@ -262,12 +499,10 @@ def __init__( self._validate_metadata() def _validate_metadata(self) -> None: - if isinstance(self.chunk_grid, RegularChunkGrid) and len(self.shape) != len( - self.chunk_grid.chunk_shape - ): - raise ValueError( - "`chunk_shape` and `shape` need to have the same number of dimensions." - ) + if len(self.shape) != self.chunk_grid.ndim: + raise ValueError("`chunk_grid` and `shape` need to have the same number of dimensions.") + if isinstance(self.chunk_grid, RectilinearChunkGridMetadata): + validate_rectilinear_edges(self.chunk_grid.chunk_shapes, self.shape) if self.dimension_names is not None and len(self.shape) != len(self.dimension_names): raise ValueError( "`dimension_names` and `shape` need to have the same number of dimensions." @@ -285,63 +520,46 @@ def ndim(self) -> int: def dtype(self) -> ZDType[TBaseDType, TBaseScalar]: return self.data_type + # TODO: move these properties to the Array class. + # They require knowledge of codecs (ShardingCodec) and don't belong on a metadata DTO. + @property def chunks(self) -> tuple[int, ...]: - if isinstance(self.chunk_grid, RegularChunkGrid): - from zarr.codecs.sharding import ShardingCodec + if not isinstance(self.chunk_grid, RegularChunkGridMetadata): + msg = ( + "The `chunks` attribute is only defined for arrays using regular chunk grids. " + "This array has a rectilinear chunk grid. Use `read_chunk_sizes` for general access." + ) + raise NotImplementedError(msg) - if len(self.codecs) == 1 and isinstance(self.codecs[0], ShardingCodec): - sharding_codec = self.codecs[0] - assert isinstance(sharding_codec, ShardingCodec) # for mypy - return sharding_codec.chunk_shape - else: - return self.chunk_grid.chunk_shape + from zarr.codecs.sharding import ShardingCodec - msg = ( - f"The `chunks` attribute is only defined for arrays using `RegularChunkGrid`." - f"This array has a {self.chunk_grid} instead." - ) - raise NotImplementedError(msg) + if len(self.codecs) == 1 and isinstance(self.codecs[0], ShardingCodec): + return self.codecs[0].chunk_shape + return self.chunk_grid.chunk_shape @property def shards(self) -> tuple[int, ...] | None: - if isinstance(self.chunk_grid, RegularChunkGrid): - from zarr.codecs.sharding import ShardingCodec - - if len(self.codecs) == 1 and isinstance(self.codecs[0], ShardingCodec): - return self.chunk_grid.chunk_shape - else: - return None - - msg = ( - f"The `shards` attribute is only defined for arrays using `RegularChunkGrid`." - f"This array has a {self.chunk_grid} instead." - ) - raise NotImplementedError(msg) + from zarr.codecs.sharding import ShardingCodec + + if len(self.codecs) == 1 and isinstance(self.codecs[0], ShardingCodec): + if not isinstance(self.chunk_grid, RegularChunkGridMetadata): + msg = ( + "The `shards` attribute is only defined for arrays using regular chunk grids. " + "This array has a rectilinear chunk grid. Use `write_chunk_sizes` for general access." + ) + raise NotImplementedError(msg) + return self.chunk_grid.chunk_shape + return None @property def inner_codecs(self) -> tuple[Codec, ...]: - if isinstance(self.chunk_grid, RegularChunkGrid): - from zarr.codecs.sharding import ShardingCodec + from zarr.codecs.sharding import ShardingCodec - if len(self.codecs) == 1 and isinstance(self.codecs[0], ShardingCodec): - return self.codecs[0].codecs + if len(self.codecs) == 1 and isinstance(self.codecs[0], ShardingCodec): + return self.codecs[0].codecs return self.codecs - def get_chunk_spec( - self, _chunk_coords: tuple[int, ...], array_config: ArrayConfig, prototype: BufferPrototype - ) -> ArraySpec: - assert isinstance(self.chunk_grid, RegularChunkGrid), ( - "Currently, only regular chunk grid is supported" - ) - return ArraySpec( - shape=self.chunk_grid.chunk_shape, - dtype=self.dtype, - fill_value=self.fill_value, - config=array_config, - prototype=prototype, - ) - def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: return self.chunk_key_encoding.encode_chunk_key(chunk_coords) @@ -415,6 +633,8 @@ def to_dict(self) -> dict[str, JSON]: extra_fields = out_dict.pop("extra_fields") out_dict = out_dict | extra_fields # type: ignore[operator] + out_dict["chunk_grid"] = self.chunk_grid.to_dict() + out_dict["fill_value"] = self.data_type.to_json_scalar( self.fill_value, zarr_format=self.zarr_format ) @@ -436,7 +656,10 @@ def to_dict(self) -> dict[str, JSON]: return out_dict def update_shape(self, shape: tuple[int, ...]) -> Self: - return replace(self, shape=shape) + chunk_grid = self.chunk_grid + if isinstance(chunk_grid, RectilinearChunkGridMetadata): + chunk_grid = chunk_grid.update_shape(self.shape, shape) + return replace(self, shape=shape, chunk_grid=chunk_grid) def update_attributes(self, attributes: dict[str, JSON]) -> Self: return replace(self, attributes=attributes) diff --git a/src/zarr/experimental/__init__.py b/src/zarr/experimental/__init__.py index 3863510c65..f7caaf96a1 100644 --- a/src/zarr/experimental/__init__.py +++ b/src/zarr/experimental/__init__.py @@ -1 +1,5 @@ """The experimental module is a site for exporting new or experimental Zarr features.""" + +from zarr.core.chunk_grids import ChunkGrid, ChunkSpec + +__all__ = ["ChunkGrid", "ChunkSpec"] diff --git a/src/zarr/metadata/migrate_v3.py b/src/zarr/metadata/migrate_v3.py index a72939100d..370af75a6d 100644 --- a/src/zarr/metadata/migrate_v3.py +++ b/src/zarr/metadata/migrate_v3.py @@ -27,7 +27,7 @@ from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType from zarr.core.group import GroupMetadata from zarr.core.metadata.v2 import ArrayV2Metadata -from zarr.core.metadata.v3 import ArrayV3Metadata +from zarr.core.metadata.v3 import ArrayV3Metadata, RegularChunkGridMetadata from zarr.core.sync import sync from zarr.registry import get_codec_class from zarr.storage import StorePath @@ -211,7 +211,7 @@ def _convert_array_metadata(metadata_v2: ArrayV2Metadata) -> ArrayV3Metadata: return ArrayV3Metadata( shape=metadata_v2.shape, data_type=metadata_v2.dtype, - chunk_grid=metadata_v2.chunk_grid, + chunk_grid=RegularChunkGridMetadata(chunk_shape=metadata_v2.chunks), chunk_key_encoding=chunk_key_encoding, fill_value=metadata_v2.fill_value, codecs=codecs, diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index 4bdc7db491..d6c43f4ecc 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -23,13 +23,14 @@ from zarr.core.buffer import Buffer, BufferPrototype, cpu, default_buffer_prototype from zarr.core.sync import SyncMixin from zarr.storage import LocalStore, MemoryStore +from zarr.testing.strategies import ( + arrays as zarr_arrays, +) from zarr.testing.strategies import ( basic_indices, chunk_paths, - dimension_names, key_ranges, node_names, - np_array_and_chunks, orthogonal_indices, ) from zarr.testing.strategies import keys as zarr_keys @@ -118,18 +119,11 @@ def add_group(self, name: str, data: DataObject) -> None: zarr.group(store=self.store, path=path) zarr.group(store=self.model, path=path) - @rule(data=st.data(), name=node_names, array_and_chunks=np_array_and_chunks()) - def add_array( - self, - data: DataObject, - name: str, - array_and_chunks: tuple[np.ndarray[Any, Any], tuple[int, ...]], - ) -> None: + @rule(data=st.data(), name=node_names) + def add_array(self, data: DataObject, name: str) -> None: # Handle possible case-insensitive file systems (e.g. MacOS) if isinstance(self.store, LocalStore): name = name.lower() - array, chunks = array_and_chunks - fill_value = data.draw(npst.from_dtype(array.dtype)) if self.all_groups: parent = data.draw(st.sampled_from(sorted(self.all_groups)), label="Array parent") else: @@ -138,21 +132,46 @@ def add_array( # TODO: support overwriting potentially by just skipping `self.can_add` path = f"{parent}/{name}".lstrip("/") assume(self.can_add(path)) - note(f"Adding array: path='{path}' shape={array.shape} chunks={chunks}") - for store in [self.store, self.model]: - zarr.array( - array, - chunks=chunks, - path=path, - store=store, - fill_value=fill_value, - zarr_format=3, - dimension_names=data.draw( - dimension_names(ndim=array.ndim), label="dimension names" - ), - # Chose bytes codec to avoid wasting time compressing the data being written - codecs=[BytesCodec()], - ) + + # Generate array on the model store using the arrays strategy + a = data.draw( + zarr_arrays( + stores=st.just(self.model), + paths=st.just(parent), + array_names=st.just(name), + zarr_formats=st.just(3), + compressors=st.just(BytesCodec()), + open_mode="a", + ), + label="generated array", + ) + note(f"Adding array: path='{path}' shape={a.shape} chunks={a.metadata.chunk_grid}") + + # Recreate the same array in the store under test + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata, RegularChunkGridMetadata + + chunk_grid = a.metadata.chunk_grid + chunks_param: tuple[int, ...] | list[list[int]] + if isinstance(chunk_grid, RectilinearChunkGridMetadata): + chunks_param = [ + list(dim) if isinstance(dim, tuple) else [dim] for dim in chunk_grid.chunk_shapes + ] + elif isinstance(chunk_grid, RegularChunkGridMetadata): + chunks_param = chunk_grid.chunk_shape + else: + chunks_param = a.chunks + + root = zarr.open_group(store=self.store, mode="a") + arr = root.create_array( + path, + shape=a.shape, + chunks=chunks_param, + dtype=a.dtype, + fill_value=a.fill_value, + dimension_names=a.metadata.dimension_names, # type: ignore[union-attr] + compressors=None, + ) + arr[:] = a[:] self.all_arrays.add(path) @rule() diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 330f220b56..e382235e0e 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -1,6 +1,7 @@ import math import sys from collections.abc import Callable, Mapping +from contextlib import nullcontext from typing import Any, Literal import hypothesis.extra.numpy as npst @@ -14,11 +15,11 @@ from zarr.abc.store import RangeByteRequest, Store from zarr.codecs.bytes import BytesCodec from zarr.core.array import Array -from zarr.core.chunk_grids import RegularChunkGrid from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding -from zarr.core.common import JSON, ZarrFormat +from zarr.core.common import JSON, AccessModeLiteral, ZarrFormat from zarr.core.dtype import get_data_type_from_native_dtype from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata +from zarr.core.metadata.v3 import RectilinearChunkGridMetadata, RegularChunkGridMetadata from zarr.core.sync import sync from zarr.storage import MemoryStore, StoreLike from zarr.storage._common import _dereference_path @@ -140,11 +141,11 @@ def array_metadata( # separator = draw(st.sampled_from(['/', '\\'])) shape = draw(array_shapes()) ndim = len(shape) - chunk_shape = draw(array_shapes(min_dims=ndim, max_dims=ndim)) np_dtype = draw(dtypes()) dtype = get_data_type_from_native_dtype(np_dtype) fill_value = draw(npst.from_dtype(np_dtype)) if zarr_format == 2: + chunk_shape = draw(array_shapes(min_dims=ndim, max_dims=ndim, min_side=1)) return ArrayV2Metadata( shape=shape, chunks=chunk_shape, @@ -157,10 +158,11 @@ def array_metadata( compressor=None, ) else: + chunk_grid = draw(chunk_grids(shape=shape)) return ArrayV3Metadata( shape=shape, data_type=dtype, - chunk_grid=RegularChunkGrid(chunk_shape=chunk_shape), + chunk_grid=chunk_grid, fill_value=fill_value, attributes=draw(attributes), # type: ignore[arg-type] dimension_names=draw(dimension_names(ndim=ndim)), @@ -194,11 +196,17 @@ def chunk_shapes(draw: st.DrawFn, *, shape: tuple[int, ...]) -> tuple[int, ...]: # We want this strategy to shrink towards arrays with smaller number of chunks # 1. st.integers() shrinks towards smaller values. So we use that to generate number of chunks numchunks = draw( - st.tuples(*[st.integers(min_value=0 if size == 0 else 1, max_value=size) for size in shape]) + st.tuples( + *[ + st.integers(min_value=0 if size == 0 else 1, max_value=max(size, 1)) + for size in shape + ] + ) ) # 2. and now generate the chunks tuple + # Chunk sizes must be >= 1 per spec; for zero-extent dimensions use 1. chunks = tuple( - size // nchunks if nchunks > 0 else 0 + max(1, size // nchunks) if nchunks > 0 else 1 for size, nchunks in zip(shape, numchunks, strict=True) ) @@ -228,7 +236,7 @@ def np_array_and_chunks( draw: st.DrawFn, *, arrays: st.SearchStrategy[npt.NDArray[Any]] = numpy_arrays(), # noqa: B008 -) -> tuple[np.ndarray, tuple[int, ...]]: # type: ignore[type-arg] +) -> tuple[np.ndarray[Any, Any], tuple[int, ...]]: """A hypothesis strategy to generate small sized random arrays. Returns: a tuple of the array and a suitable random chunking for it. @@ -249,6 +257,7 @@ def arrays( arrays: st.SearchStrategy | None = None, attrs: st.SearchStrategy = attrs, zarr_formats: st.SearchStrategy = zarr_formats, + open_mode: AccessModeLiteral = "w", ) -> AnyArray: store = draw(stores, label="store") path = draw(paths, label="array parent") @@ -258,16 +267,22 @@ def arrays( if arrays is None: arrays = numpy_arrays(shapes=shapes) nparray = draw(arrays, label="array data") - chunk_shape = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") dim_names: None | list[str | None] = None - if zarr_format == 3 and all(c > 0 for c in chunk_shape): - shard_shape = draw( - st.none() | shard_shapes(shape=nparray.shape, chunk_shape=chunk_shape), - label="shard shape", - ) + + # For v3 arrays, optionally use RectilinearChunkGridMetadata + chunk_grid_meta: RegularChunkGridMetadata | RectilinearChunkGridMetadata | None = None + shard_shape = None + if zarr_format == 3: + chunk_grid_meta = draw(chunk_grids(shape=nparray.shape), label="chunk grid") + + # Sharding is only supported with regular chunk grids, and has complex + # divisibility constraints that don't play well with hypothesis shrinking. + # Disabled for now — sharding should be tested separately. + dim_names = draw(dimension_names(ndim=nparray.ndim), label="dimension names") else: - shard_shape = None + dim_names = None + # test that None works too. fill_value = draw(st.one_of([st.none(), npst.from_dtype(nparray.dtype)])) # compressor = draw(compressors) @@ -275,19 +290,38 @@ def arrays( expected_attrs = {} if attributes is None else attributes array_path = _dereference_path(path, name) - root = zarr.open_group(store, mode="w", zarr_format=zarr_format) - - a = root.create_array( - array_path, - shape=nparray.shape, - chunks=chunk_shape, - shards=shard_shape, - dtype=nparray.dtype, - attributes=attributes, - # compressor=compressor, # FIXME - fill_value=fill_value, - dimension_names=dim_names, - ) + root = zarr.open_group(store, mode=open_mode, zarr_format=zarr_format) + + # Convert chunk grid metadata to a form create_array accepts: + # - RegularChunkGridMetadata -> flat tuple of ints + # - RectilinearChunkGridMetadata -> nested list of ints (triggers rectilinear path) + # - v2 -> flat tuple of ints + chunks_param: tuple[int, ...] | list[list[int]] + use_rectilinear = False + if zarr_format == 3 and chunk_grid_meta is not None: + if isinstance(chunk_grid_meta, RectilinearChunkGridMetadata): + chunks_param = [ + list(dim) if isinstance(dim, tuple) else [dim] + for dim in chunk_grid_meta.chunk_shapes + ] + use_rectilinear = True + else: + chunks_param = chunk_grid_meta.chunk_shape + else: + chunks_param = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") + + with zarr.config.set({"array.rectilinear_chunks": True}) if use_rectilinear else nullcontext(): + a = root.create_array( + array_path, + shape=nparray.shape, + chunks=chunks_param, + shards=shard_shape, + dtype=nparray.dtype, + attributes=attributes, + # compressor=compressor, # FIXME + fill_value=fill_value, + dimension_names=dim_names, + ) assert isinstance(a, Array) if a.metadata.zarr_format == 3: @@ -297,8 +331,16 @@ def arrays( assert a.name == "/" + a.path assert isinstance(root[array_path], Array) assert nparray.shape == a.shape - assert chunk_shape == a.chunks - assert shard_shape == a.shards + + # Verify chunks — for rectilinear grids, .chunks raises + if zarr_format == 3: + if isinstance(a.metadata.chunk_grid, RectilinearChunkGridMetadata): + assert shard_shape is None + else: + assert isinstance(a.metadata.chunk_grid, RegularChunkGridMetadata) + assert a.metadata.chunk_grid.chunk_shape == a.chunks + assert shard_shape == a.shards + assert a.basename == name, (a.basename, name) assert dict(a.attrs) == expected_attrs @@ -324,6 +366,119 @@ def simple_arrays( ) +@st.composite +def rectilinear_chunks(draw: st.DrawFn, *, shape: tuple[int, ...]) -> list[list[int]]: + """Generate valid rectilinear chunk shapes for a given array shape. + + Uses two modes per dimension: + - "expanded": random divider points create arbitrary chunk sizes + - "rle": uniform chunks with optional remainder, optionally shuffled + + Keeps max chunks per dimension <= 20 to avoid performance issues + in property tests. With higher dimensions, the total chunk count + grows multiplicatively. + """ + chunk_shapes: list[list[int]] = [] + for size in shape: + assert size > 0 + if size > 1: + mode = draw(st.sampled_from(["expanded", "rle"])) + if mode == "expanded": + event("rectilinear expanded") + max_chunks = min(size - 1, 20) + nchunks = draw(st.integers(min_value=1, max_value=max_chunks)) + dividers = sorted( + draw( + st.lists( + st.integers(min_value=1, max_value=size - 1), + min_size=nchunks - 1, + max_size=nchunks - 1, + unique=True, + ) + ) + ) + chunk_shapes.append( + [a - b for a, b in zip(dividers + [size], [0] + dividers, strict=False)] + ) + else: + # RLE mode: uniform chunks with optional remainder + max_chunk_size = min(size, 20) + chunk_size = draw(st.integers(min_value=1, max_value=max_chunk_size)) + n_full = size // chunk_size + remainder = size % chunk_size + chunks_list = [chunk_size] * n_full + if remainder > 0: + chunks_list.append(remainder) + # Optionally shuffle to create non-contiguous duplicate patterns + if draw(st.booleans()): + event("rectilinear rle shuffled") + chunks_list = draw(st.permutations(chunks_list)) + else: + event("rectilinear rle") + chunk_shapes.append(list(chunks_list)) + else: + chunk_shapes.append([1]) + return chunk_shapes + + +@st.composite +def chunk_grids( + draw: st.DrawFn, *, shape: tuple[int, ...] +) -> RegularChunkGridMetadata | RectilinearChunkGridMetadata: + """Generate either a RegularChunkGridMetadata or RectilinearChunkGridMetadata. + + This allows property tests to exercise both chunk grid types. + """ + # RectilinearChunkGridMetadata doesn't support zero-sized dimensions, + # so use RegularChunkGridMetadata if any dimension is 0 + if any(s == 0 for s in shape): + event("using RegularChunkGridMetadata (zero-sized dimensions)") + return RegularChunkGridMetadata(chunk_shape=draw(chunk_shapes(shape=shape))) + + if draw(st.booleans()): + chunks = draw(rectilinear_chunks(shape=shape)) + event("using RectilinearChunkGridMetadata") + with zarr.config.set({"array.rectilinear_chunks": True}): + return RectilinearChunkGridMetadata(chunk_shapes=tuple(tuple(dim) for dim in chunks)) + else: + event("using RegularChunkGridMetadata") + return RegularChunkGridMetadata(chunk_shape=draw(chunk_shapes(shape=shape))) + + +# Rectilinear arrays need min_side >= 1 so every dimension has at least one element +_rectilinear_shapes = npst.array_shapes(max_dims=3, min_side=1, max_side=20) + + +@st.composite +def rectilinear_arrays( + draw: st.DrawFn, + *, + shapes: st.SearchStrategy[tuple[int, ...]] = _rectilinear_shapes, +) -> Any: + """Generate a zarr v3 array with rectilinear (variable) chunk grid.""" + shape = draw(shapes) + chunk_shapes = draw(rectilinear_chunks(shape=shape)) + + np_dtype = draw(dtypes()) + nparray = draw(numpy_arrays(shapes=st.just(shape), dtype=np_dtype)) + fill_value = draw(st.one_of([st.none(), npst.from_dtype(np_dtype)])) + dim_names = draw(dimension_names(ndim=len(shape))) + + store = MemoryStore() + with zarr.config.set({"array.rectilinear_chunks": True}): + a = zarr.create_array( + store=store, + shape=shape, + chunks=chunk_shapes, + dtype=np_dtype, + fill_value=fill_value, + dimension_names=dim_names, + ) + a[:] = nparray + + return a + + def is_negative_slice(idx: Any) -> bool: return isinstance(idx, slice) and idx.step is not None and idx.step < 0 @@ -439,6 +594,51 @@ def make_request(start: int, length: int) -> RangeByteRequest: return st.lists(key_tuple, min_size=1, max_size=10) +@st.composite +def complex_rectilinear_arrays( + draw: st.DrawFn, + *, + stores: st.SearchStrategy[StoreLike] = stores, + paths: st.SearchStrategy[str] = paths(), # noqa: B008 + array_names: st.SearchStrategy = array_names, + attrs: st.SearchStrategy = attrs, +) -> tuple[npt.NDArray[Any], AnyArray]: + """Generate a rectilinear array with many small chunks. + + The shape is derived from the chunk edges (5-10 chunks per dim, + sizes 1-5), exercising higher chunk counts than ``rectilinear_arrays``. + """ + ndim = draw(st.integers(min_value=1, max_value=3)) + nchunks = draw(st.integers(min_value=5, max_value=10)) + dim_chunks = st.lists(st.integers(min_value=1, max_value=5), min_size=nchunks, max_size=nchunks) + chunk_shapes = draw(st.lists(dim_chunks, min_size=ndim, max_size=ndim)) + + shape = tuple(sum(dim) for dim in chunk_shapes) + nparray = draw(numpy_arrays(shapes=st.just(shape))) + dim_names = draw(dimension_names(ndim=ndim)) + fill_value = draw(st.one_of([st.none(), npst.from_dtype(nparray.dtype)])) + attributes = draw(attrs) + + store = draw(stores, label="store") + path = draw(paths, label="array parent") + name = draw(array_names, label="array name") + array_path = _dereference_path(path, name) + + root = zarr.open_group(store, mode="w", zarr_format=3) + with zarr.config.set({"array.rectilinear_chunks": True}): + a = root.create_array( + array_path, + shape=shape, + chunks=chunk_shapes, + dtype=nparray.dtype, + fill_value=fill_value, + dimension_names=dim_names, + attributes=attributes, + ) + a[:] = nparray + return nparray, a + + @st.composite def chunk_paths(draw: st.DrawFn, ndim: int, numblocks: tuple[int, ...], subset: bool = True) -> str: blockidx = draw( diff --git a/tests/conftest.py b/tests/conftest.py index 86db02f6bf..a02006d6a9 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -22,7 +22,7 @@ _parse_chunk_encoding_v3, _parse_chunk_key_encoding, ) -from zarr.core.chunk_grids import RegularChunkGrid, _auto_partition +from zarr.core.chunk_grids import _auto_partition from zarr.core.common import ( JSON, DimensionNamesLike, @@ -37,7 +37,7 @@ ) from zarr.core.dtype.common import HasItemSize from zarr.core.metadata.v2 import ArrayV2Metadata -from zarr.core.metadata.v3 import ArrayV3Metadata +from zarr.core.metadata.v3 import ArrayV3Metadata, RegularChunkGridMetadata from zarr.core.sync import sync from zarr.storage import FsspecStore, LocalStore, MemoryStore, StorePath, ZipStore from zarr.testing.store import LatencyStore @@ -379,7 +379,7 @@ def create_array_metadata( sharding_codec.validate( shape=chunk_shape_parsed, dtype=dtype_parsed, - chunk_grid=RegularChunkGrid(chunk_shape=shard_shape_parsed), + chunk_grid=RegularChunkGridMetadata(chunk_shape=shard_shape_parsed), ) codecs_out = (sharding_codec,) chunks_out = shard_shape_parsed @@ -390,7 +390,7 @@ def create_array_metadata( return ArrayV3Metadata( shape=shape_parsed, data_type=dtype_parsed, - chunk_grid=RegularChunkGrid(chunk_shape=chunks_out), + chunk_grid={"name": "regular", "configuration": {"chunk_shape": chunks_out}}, chunk_key_encoding=chunk_key_encoding_parsed, fill_value=fill_value, codecs=codecs_out, diff --git a/tests/test_api.py b/tests/test_api.py index a306ff3dc3..4198d56c78 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -280,6 +280,19 @@ async def test_open_array(memory_store: MemoryStore, zarr_format: ZarrFormat) -> zarr.api.synchronous.open(store="doesnotexist", mode="r", zarr_format=zarr_format) +def test_open_array_rectilinear_chunks(tmp_path: Path) -> None: + """zarr.open with rectilinear (dask-style) chunks preserves the chunk grid.""" + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata + + chunks = ((3, 3, 4), (5, 5)) + with zarr.config.set({"array.rectilinear_chunks": True}): + z = zarr.open(store=tmp_path, shape=(10, 10), dtype="float64", chunks=chunks, mode="w") + assert isinstance(z, Array) + assert z.shape == (10, 10) + assert isinstance(z.metadata.chunk_grid, RectilinearChunkGridMetadata) + assert z.read_chunk_sizes == ((3, 3, 4), (5, 5)) + + @pytest.mark.asyncio async def test_async_array_open_array_not_found() -> None: """Test that AsyncArray.open raises ArrayNotFoundError when array doesn't exist""" diff --git a/tests/test_array.py b/tests/test_array.py index 867bfb6cb2..f7f564f30e 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -786,8 +786,6 @@ def test_resize_growing_skips_chunk_enumeration( store: MemoryStore, zarr_format: ZarrFormat ) -> None: """Growing an array should not enumerate chunk coords for deletion (#3650 mitigation).""" - from zarr.core.chunk_grids import RegularChunkGrid - z = zarr.create( shape=(10, 10), chunks=(5, 5), @@ -798,11 +796,13 @@ def test_resize_growing_skips_chunk_enumeration( ) z[:] = np.ones((10, 10), dtype="i4") + grid_cls = type(z._chunk_grid) + # growth only - ensure no chunk coords are enumerated with mock.patch.object( - RegularChunkGrid, + grid_cls, "all_chunk_coords", - wraps=z.metadata.chunk_grid.all_chunk_coords, + wraps=z._chunk_grid.all_chunk_coords, ) as mock_coords: z.resize((20, 20)) mock_coords.assert_not_called() @@ -813,9 +813,9 @@ def test_resize_growing_skips_chunk_enumeration( # shrink - ensure no regression of behaviour with mock.patch.object( - RegularChunkGrid, + grid_cls, "all_chunk_coords", - wraps=z.metadata.chunk_grid.all_chunk_coords, + wraps=z._chunk_grid.all_chunk_coords, ) as mock_coords: z.resize((5, 5)) assert mock_coords.call_count > 0 @@ -836,9 +836,9 @@ def test_resize_growing_skips_chunk_enumeration( z2[:] = np.ones((10, 10), dtype="i4") with mock.patch.object( - RegularChunkGrid, + grid_cls, "all_chunk_coords", - wraps=z2.metadata.chunk_grid.all_chunk_coords, + wraps=z2._chunk_grid.all_chunk_coords, ) as mock_coords: z2.resize((20, 5)) assert mock_coords.call_count > 0 @@ -1576,7 +1576,7 @@ async def test_with_data(impl: Literal["sync", "async"], store: Store) -> None: elif impl == "async": arr = await create_array(store, name=name, data=data, zarr_format=3) stored = await arr._get_selection( - BasicIndexer(..., shape=arr.shape, chunk_grid=arr.metadata.chunk_grid), + BasicIndexer(..., shape=arr.shape, chunk_grid=arr._chunk_grid), prototype=default_buffer_prototype(), ) else: diff --git a/tests/test_cli/test_migrate_v3.py b/tests/test_cli/test_migrate_v3.py index 6e169e5f48..7213aada12 100644 --- a/tests/test_cli/test_migrate_v3.py +++ b/tests/test_cli/test_migrate_v3.py @@ -16,7 +16,6 @@ from zarr.codecs.numcodecs import LZMA, Delta from zarr.codecs.transpose import TransposeCodec from zarr.codecs.zstd import ZstdCodec -from zarr.core.chunk_grids import RegularChunkGrid from zarr.core.chunk_key_encodings import V2ChunkKeyEncoding from zarr.core.common import JSON, ZarrFormat from zarr.core.dtype.npy.int import UInt8, UInt16 @@ -61,7 +60,7 @@ def test_migrate_array(local_store: LocalStore) -> None: expected_metadata = ArrayV3Metadata( shape=shape, data_type=UInt16(endianness="little"), - chunk_grid=RegularChunkGrid(chunk_shape=chunks), + chunk_grid={"name": "regular", "configuration": {"chunk_shape": chunks}}, chunk_key_encoding=V2ChunkKeyEncoding(separator="."), fill_value=fill_value, codecs=( diff --git a/tests/test_codec_pipeline.py b/tests/test_codec_pipeline.py index 8d044c10d7..48e15b0643 100644 --- a/tests/test_codec_pipeline.py +++ b/tests/test_codec_pipeline.py @@ -3,6 +3,7 @@ import pytest import zarr +from zarr.core.array import _get_chunk_spec from zarr.core.buffer.core import default_buffer_prototype from zarr.core.indexing import BasicIndexer from zarr.storage import MemoryStore @@ -42,7 +43,7 @@ async def test_read_returns_get_results( indexer = BasicIndexer( read_slice, shape=metadata.shape, - chunk_grid=metadata.chunk_grid, + chunk_grid=async_arr._chunk_grid, ) out_buffer = prototype.nd_buffer.empty( @@ -55,7 +56,7 @@ async def test_read_returns_get_results( [ ( async_arr.store_path / metadata.encode_chunk_key(chunk_coords), - metadata.get_chunk_spec(chunk_coords, config, prototype=prototype), + _get_chunk_spec(metadata, async_arr._chunk_grid, chunk_coords, config, prototype), chunk_selection, out_selection, is_complete_chunk, diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index d7cbeb5bdb..43d03caf11 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -1,5 +1,4 @@ import pickle -import re from typing import Any import numpy as np @@ -489,9 +488,9 @@ def test_invalid_metadata(store: Store) -> None: def test_invalid_shard_shape() -> None: with pytest.raises( ValueError, - match=re.escape( - "The array's `chunk_shape` (got (16, 16)) needs to be divisible " - "by the shard's inner `chunk_shape` (got (9,))." + match=( + f"Chunk edge length {16} in dimension {0} is not " + f"divisible by the shard's inner chunk size {9}\\." ), ): zarr.create_array( diff --git a/tests/test_config.py b/tests/test_config.py index a095d99e54..4e293e968f 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -55,6 +55,7 @@ def test_config_defaults_set() -> None: "write_empty_chunks": False, "read_missing_chunks": True, "target_shard_size_bytes": None, + "rectilinear_chunks": False, }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, diff --git a/tests/test_group.py b/tests/test_group.py index 6f1f4e68fa..e53b0b9ea0 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -1176,9 +1176,7 @@ async def test_asyncgroup_create_array( assert subnode.store_path.store == store assert subnode.shape == shape assert subnode.dtype == dtype - # todo: fix the type annotation of array.metadata.chunk_grid so that we get some autocomplete - # here. - assert subnode.metadata.chunk_grid.chunk_shape == chunk_shape + assert subnode._chunk_grid.chunk_shape == chunk_shape assert subnode.metadata.zarr_format == zarr_format diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 0c0a6182d8..c45942eee7 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -1254,8 +1254,8 @@ def test_get_block_selection_1d(store: StorePath) -> None: _test_get_block_selection(a, z, selection, expected_idx) bad_selections = block_selections_1d_bad + [ - z.metadata.chunk_grid.get_nchunks(z.shape) + 1, # out of bounds - -(z.metadata.chunk_grid.get_nchunks(z.shape) + 1), # out of bounds + z._chunk_grid.get_nchunks() + 1, # out of bounds + -(z._chunk_grid.get_nchunks() + 1), # out of bounds ] for selection_bad in bad_selections: @@ -1968,9 +1968,11 @@ def test_indexing_with_zarr_array(store: StorePath) -> None: @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -@pytest.mark.parametrize("shape", [(0, 2, 3), (0), (3, 0)]) +@pytest.mark.parametrize("shape", [(0, 2, 3), (0,), (3, 0)]) def test_zero_sized_chunks(store: StorePath, shape: list[int]) -> None: - z = zarr.create_array(store=store, shape=shape, chunks=shape, zarr_format=3, dtype="f8") + # Chunk sizes must be >= 1 per spec; use 1 for zero-extent dimensions. + chunks = tuple(max(1, s) for s in shape) + z = zarr.create_array(store=store, shape=shape, chunks=chunks, zarr_format=3, dtype="f8") z[...] = 42 assert_array_equal(z[...], np.zeros(shape, dtype="f8")) diff --git a/tests/test_properties.py b/tests/test_properties.py index bab659c976..0e5dcf77b0 100644 --- a/tests/test_properties.py +++ b/tests/test_properties.py @@ -1,12 +1,14 @@ import itertools import json import numbers +from collections.abc import Generator from typing import Any import numpy as np import pytest from numpy.testing import assert_array_equal +import zarr from zarr.core.buffer import default_buffer_prototype pytest.importorskip("hypothesis") @@ -23,14 +25,23 @@ array_metadata, arrays, basic_indices, + complex_rectilinear_arrays, numpy_arrays, orthogonal_indices, + rectilinear_arrays, simple_arrays, stores, zarr_formats, ) +@pytest.fixture(autouse=True) +def _enable_rectilinear_chunks() -> Generator[None, None, None]: + """Enable rectilinear chunks for all property tests since strategies may generate them.""" + with zarr.config.set({"array.rectilinear_chunks": True}): + yield + + def deep_equal(a: Any, b: Any) -> bool: """Deep equality check with handling of special cases for array metadata classes""" if isinstance(a, (complex, np.complexfloating)) and isinstance( @@ -111,7 +122,7 @@ def test_array_creates_implicit_groups(array): @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") @given(data=st.data()) async def test_basic_indexing(data: st.DataObject) -> None: - zarray = data.draw(simple_arrays()) + zarray = data.draw(st.one_of(simple_arrays(), rectilinear_arrays())) nparray = zarray[:] indexer = data.draw(basic_indices(shape=nparray.shape)) @@ -133,12 +144,27 @@ async def test_basic_indexing(data: st.DataObject) -> None: # TODO test async setitem? +@pytest.mark.asyncio +@settings(deadline=None) +@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") +@given(data=st.data()) +async def test_basic_indexing_complex_rectilinear(data: st.DataObject) -> None: + nparray, zarray = data.draw(complex_rectilinear_arrays()) + indexer = data.draw(basic_indices(shape=nparray.shape)) + assert_array_equal(nparray[indexer], zarray[indexer]) + + @pytest.mark.asyncio @given(data=st.data()) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") async def test_oindex(data: st.DataObject) -> None: # integer_array_indices can't handle 0-size dimensions. - zarray = data.draw(simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1))) + zarray = data.draw( + st.one_of( + simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1)), + rectilinear_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1, max_side=20)), + ) + ) nparray = zarray[:] zindexer, npindexer = data.draw(orthogonal_indices(shape=nparray.shape)) @@ -170,7 +196,12 @@ async def test_oindex(data: st.DataObject) -> None: @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") async def test_vindex(data: st.DataObject) -> None: # integer_array_indices can't handle 0-size dimensions. - zarray = data.draw(simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1))) + zarray = data.draw( + st.one_of( + simple_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1)), + rectilinear_arrays(shapes=npst.array_shapes(max_dims=3, min_side=1, max_side=20)), + ) + ) nparray = zarray[:] indexer = data.draw( npst.integer_array_indices( diff --git a/tests/test_store/test_stateful.py b/tests/test_store/test_stateful.py index 6ea89d91d6..82b482d0ff 100644 --- a/tests/test_store/test_stateful.py +++ b/tests/test_store/test_stateful.py @@ -1,9 +1,12 @@ # Stateful tests for arbitrary Zarr stores. +from collections.abc import Generator + import pytest from hypothesis.stateful import ( run_state_machine_as_test, ) +import zarr from zarr.abc.store import Store from zarr.storage import LocalStore, ZipStore from zarr.testing.stateful import ZarrHierarchyStateMachine, ZarrStoreStateMachine @@ -15,6 +18,13 @@ ] +@pytest.fixture(autouse=True) +def _enable_rectilinear_chunks() -> Generator[None, None, None]: + """Enable rectilinear chunks since strategies may generate them.""" + with zarr.config.set({"array.rectilinear_chunks": True}): + yield + + @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") def test_zarr_hierarchy(sync_store: Store) -> None: def mk_test_instance_sync() -> ZarrHierarchyStateMachine: diff --git a/tests/test_unified_chunk_grid.py b/tests/test_unified_chunk_grid.py new file mode 100644 index 0000000000..0df5a5d9fd --- /dev/null +++ b/tests/test_unified_chunk_grid.py @@ -0,0 +1,2855 @@ +""" +Tests for the unified ChunkGrid design (POC). + +Tests the core ChunkGrid with FixedDimension/VaryingDimension internals, +ChunkSpec, serialization round-trips, indexing with rectilinear grids, +and end-to-end array creation + read/write. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +import numpy as np +import pytest + +import zarr +from zarr.core.chunk_grids import ( + ChunkGrid, + ChunkSpec, + FixedDimension, + VaryingDimension, + _is_rectilinear_chunks, +) +from zarr.core.common import compress_rle, expand_rle +from zarr.core.metadata.v3 import ( + RectilinearChunkGridMetadata, + RectilinearChunkGridMetadataJSON, + RegularChunkGridMetadata, + parse_chunk_grid, +) +from zarr.errors import BoundsCheckError +from zarr.storage import MemoryStore + +if TYPE_CHECKING: + from collections.abc import Generator + from pathlib import Path + + +@pytest.fixture(autouse=True) +def _enable_rectilinear_chunks() -> Generator[None, None, None]: + """Enable rectilinear chunks for all tests in this module.""" + with zarr.config.set({"array.rectilinear_chunks": True}): + yield + + +def _edges(grid: ChunkGrid, dim: int) -> tuple[int, ...]: + """Extract the per-chunk edge lengths for *dim* from a ChunkGrid.""" + d = grid._dimensions[dim] + if isinstance(d, FixedDimension): + return tuple(d.size for _ in range(d.nchunks)) + if isinstance(d, VaryingDimension): + return tuple(d.edges) + raise TypeError(f"Unexpected dimension type: {type(d)}") + + +# --------------------------------------------------------------------------- +# Dimension index_to_chunk bounds tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("dim", "index", "match"), + [ + (VaryingDimension([10, 20, 30], extent=60), 60, "out of bounds"), + (VaryingDimension([10, 20, 30], extent=60), 100, "out of bounds"), + (FixedDimension(size=10, extent=95), 95, "out of bounds"), + (FixedDimension(size=10, extent=95), -1, "Negative"), + ], + ids=[ + "varying-at-extent", + "varying-past-extent", + "fixed-at-extent", + "fixed-negative", + ], +) +def test_dimension_index_to_chunk_bounds( + dim: FixedDimension | VaryingDimension, index: int, match: str +) -> None: + """Out-of-bounds or negative indices raise IndexError for both dimension types""" + with pytest.raises(IndexError, match=match): + dim.index_to_chunk(index) + + +@pytest.mark.parametrize( + ("dim", "index", "expected"), + [ + (VaryingDimension([10, 20, 30], extent=60), 59, 2), + (FixedDimension(size=10, extent=95), 94, 9), + ], + ids=["varying-last-valid", "fixed-last-valid"], +) +def test_dimension_index_to_chunk_last_valid( + dim: FixedDimension | VaryingDimension, index: int, expected: int +) -> None: + """Last valid index maps to the correct chunk for both dimension types""" + assert dim.index_to_chunk(index) == expected + + +# --------------------------------------------------------------------------- +# Rectilinear feature flag tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + "action", + [ + lambda: RectilinearChunkGridMetadata(chunk_shapes=((10, 20), (25, 25))), + lambda: RectilinearChunkGridMetadata.from_dict( + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[10, 20, 30], [50, 50]]}, + } + ), + lambda: zarr.create_array(MemoryStore(), shape=(30,), chunks=[[10, 20]], dtype="int32"), + ], + ids=["constructor", "from_dict", "create_array"], +) +def test_rectilinear_feature_flag_blocked(action: Any) -> None: + """Rectilinear chunk operations raise ValueError when the feature flag is disabled""" + with zarr.config.set({"array.rectilinear_chunks": False}): + with pytest.raises(ValueError, match="experimental and disabled by default"): + action() + + +def test_rectilinear_feature_flag_enabled() -> None: + """Rectilinear chunk grid construction succeeds when the feature flag is enabled""" + with zarr.config.set({"array.rectilinear_chunks": True}): + grid = RectilinearChunkGridMetadata(chunk_shapes=((10, 20), (25, 25))) + assert grid.ndim == 2 + + +# --------------------------------------------------------------------------- +# FixedDimension tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ( + "size", + "extent", + "chunk_ix", + "expected_nchunks", + "expected_chunk_size", + "expected_data_size", + "expected_offset", + ), + [ + (10, 100, 0, 10, 10, 10, 0), + (10, 100, 1, 10, 10, 10, 10), + (10, 100, 9, 10, 10, 10, 90), + (10, 95, 9, 10, 10, 5, 90), # boundary chunk + (0, 0, None, 0, None, None, None), # zero-size + ], + ids=["start", "middle", "end", "boundary", "zero-size"], +) +def test_fixed_dimension( + size: int, + extent: int, + chunk_ix: int | None, + expected_nchunks: int, + expected_chunk_size: int | None, + expected_data_size: int | None, + expected_offset: int | None, +) -> None: + """FixedDimension properties match expected values for various chunk/extent combinations""" + d = FixedDimension(size=size, extent=extent) + assert d.nchunks == expected_nchunks + if chunk_ix is not None: + assert d.chunk_size(chunk_ix) == expected_chunk_size + assert d.data_size(chunk_ix) == expected_data_size + assert d.chunk_offset(chunk_ix) == expected_offset + + +@pytest.mark.parametrize( + ("idx", "expected"), + [(0, 0), (9, 0), (10, 1), (25, 2)], +) +def test_fixed_dimension_index_to_chunk(idx: int, expected: int) -> None: + """FixedDimension.index_to_chunk maps element indices to correct chunk indices""" + d = FixedDimension(size=10, extent=100) + assert d.index_to_chunk(idx) == expected + + +def test_fixed_dimension_indices_to_chunks() -> None: + """FixedDimension.indices_to_chunks vectorizes index-to-chunk mapping over an array""" + d = FixedDimension(size=10, extent=100) + indices = np.array([0, 5, 10, 15, 99]) + np.testing.assert_array_equal(d.indices_to_chunks(indices), [0, 0, 1, 1, 9]) + + +@pytest.mark.parametrize( + ("size", "extent", "match"), + [(-1, 100, "must be >= 0"), (10, -1, "must be >= 0")], + ids=["negative-size", "negative-extent"], +) +def test_fixed_dimension_rejects_negative(size: int, extent: int, match: str) -> None: + """FixedDimension raises ValueError for negative size or extent""" + with pytest.raises(ValueError, match=match): + FixedDimension(size=size, extent=extent) + + +# --------------------------------------------------------------------------- +# VaryingDimension tests +# --------------------------------------------------------------------------- + + +def test_varying_dimension_construction() -> None: + """VaryingDimension stores edges, cumulative sums, nchunks, and extent correctly""" + d = VaryingDimension([10, 20, 30], extent=60) + assert d.edges == (10, 20, 30) + assert d.cumulative == (10, 30, 60) + assert d.nchunks == 3 + assert d.extent == 60 + + +@pytest.mark.parametrize( + ( + "chunk_idx", + "expected_offset", + "expected_size", + "expected_data", + "expected_chunk_for_first_idx", + ), + [ + (0, 0, 10, 10, 0), + (1, 10, 20, 20, 1), + (2, 30, 30, 30, 2), + ], +) +def test_varying_dimension( + chunk_idx: int, + expected_offset: int, + expected_size: int, + expected_data: int, + expected_chunk_for_first_idx: int, +) -> None: + """VaryingDimension chunk_offset, chunk_size, data_size, and index_to_chunk return correct values""" + d = VaryingDimension([10, 20, 30], extent=60) + assert d.chunk_offset(chunk_idx) == expected_offset + assert d.chunk_size(chunk_idx) == expected_size + assert d.data_size(chunk_idx) == expected_data + assert d.index_to_chunk(expected_offset) == expected_chunk_for_first_idx + + +def test_varying_dimension_indices_to_chunks() -> None: + """VaryingDimension.indices_to_chunks vectorizes index-to-chunk mapping over an array""" + d = VaryingDimension([10, 20, 30], extent=60) + indices = np.array([0, 9, 10, 29, 30, 59]) + np.testing.assert_array_equal(d.indices_to_chunks(indices), [0, 0, 1, 1, 2, 2]) + + +@pytest.mark.parametrize( + ("edges", "extent", "match"), + [ + ([], 0, "must not be empty"), + ([10, 0, 5], 15, "must be > 0"), + ], + ids=["empty", "zero-edge"], +) +def test_varying_dimension_rejects_invalid(edges: list[int], extent: int, match: str) -> None: + """VaryingDimension raises ValueError for empty edges or zero-length edges""" + with pytest.raises(ValueError, match=match): + VaryingDimension(edges, extent=extent) + + +# --------------------------------------------------------------------------- +# ChunkSpec tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("slices", "codec_shape", "expected_shape", "expected_boundary"), + [ + ((slice(0, 10), slice(0, 20)), (10, 20), (10, 20), False), + ((slice(90, 95), slice(0, 20)), (10, 20), (5, 20), True), + ((slice(10, 10),), (0,), (0,), False), + ((slice(0, 10), slice(0, 5)), (10, 10), (10, 5), True), + ], + ids=["basic", "boundary", "empty-slices", "multidim-boundary"], +) +def test_chunk_spec( + slices: tuple[slice, ...], + codec_shape: tuple[int, ...], + expected_shape: tuple[int, ...], + expected_boundary: bool, +) -> None: + """ChunkSpec reports correct shape and boundary status from slices and codec_shape""" + spec = ChunkSpec(slices=slices, codec_shape=codec_shape) + assert spec.shape == expected_shape + assert spec.is_boundary == expected_boundary + + +# --------------------------------------------------------------------------- +# ChunkGrid construction tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("array_shape", "chunk_sizes", "expected_regular", "expected_ndim", "expected_chunk_shape"), + [ + ((100, 200), (10, 20), True, 2, (10, 20)), + ((), (), True, 0, ()), + ((60, 100), [[10, 20, 30], [25, 25, 25, 25]], False, 2, None), + ((30, 50), [[10, 10, 10], [25, 25]], True, 2, (10, 25)), # uniform edges → regular + ], + ids=["regular", "zero-dim", "rectilinear", "uniform-becomes-regular"], +) +def test_chunk_grid_construction( + array_shape: tuple[int, ...], + chunk_sizes: Any, + expected_regular: bool, + expected_ndim: int, + expected_chunk_shape: tuple[int, ...] | None, +) -> None: + """ChunkGrid.from_sizes produces grids with correct regularity, ndim, and chunk_shape""" + g = ChunkGrid.from_sizes(array_shape, chunk_sizes) + assert g.is_regular == expected_regular + assert g.ndim == expected_ndim + if expected_chunk_shape is not None: + assert g.chunk_shape == expected_chunk_shape + else: + with pytest.raises(ValueError, match="only available for regular"): + _ = g.chunk_shape + + +def test_chunk_grid_rectilinear_uniform_dim_is_fixed() -> None: + """A rectilinear grid with all-same sizes in one dim stores it as Fixed.""" + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [25, 25, 25, 25]]) + assert isinstance(g._dimensions[0], VaryingDimension) + assert isinstance(g._dimensions[1], FixedDimension) + + +# --------------------------------------------------------------------------- +# ChunkGrid query tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("shape", "chunks", "expected_grid_shape"), + [ + ((100, 200), (10, 20), (10, 10)), + ((95, 200), (10, 20), (10, 10)), + ((60, 100), [[10, 20, 30], [25, 25, 25, 25]], (3, 4)), + ], + ids=["regular", "regular-boundary", "rectilinear"], +) +def test_chunk_grid_shape( + shape: tuple[int, ...], + chunks: Any, + expected_grid_shape: tuple[int, ...], +) -> None: + """ChunkGrid.grid_shape returns the expected number of chunks per dimension""" + g = ChunkGrid.from_sizes(shape, chunks) + assert g.grid_shape == expected_grid_shape + + +@pytest.mark.parametrize( + ( + "array_shape", + "chunk_sizes", + "coords", + "expected_shape", + "expected_codec_shape", + "expected_boundary", + ), + [ + # regular interior + ((100, 200), (10, 20), (0, 0), (10, 20), (10, 20), False), + # regular boundary + ((95, 200), (10, 20), (9, 0), (5, 20), (10, 20), True), + # rectilinear + ((60, 100), [[10, 20, 30], [25, 25, 25, 25]], (0, 0), (10, 25), (10, 25), False), + ((60, 100), [[10, 20, 30], [25, 25, 25, 25]], (1, 0), (20, 25), (20, 25), False), + ((60, 100), [[10, 20, 30], [25, 25, 25, 25]], (2, 3), (30, 25), (30, 25), False), + ], + ids=["regular", "regular-boundary", "rectilinear-0,0", "rectilinear-1,0", "rectilinear-2,3"], +) +def test_chunk_grid_getitem( + array_shape: tuple[int, ...], + chunk_sizes: Any, + coords: tuple[int, ...], + expected_shape: tuple[int, ...], + expected_codec_shape: tuple[int, ...], + expected_boundary: bool, +) -> None: + """ChunkGrid.__getitem__ returns a ChunkSpec with correct shape, codec_shape, and boundary flag""" + g = ChunkGrid.from_sizes(array_shape, chunk_sizes) + spec = g[coords] + assert spec is not None + assert spec.shape == expected_shape + assert spec.codec_shape == expected_codec_shape + assert spec.is_boundary == expected_boundary + + +@pytest.mark.parametrize( + ("array_shape", "chunk_sizes", "coords"), + [ + ((100, 200), (10, 20), (99, 0)), + ((60, 100), [[10, 20, 30], [25, 25, 25, 25]], (3, 0)), + ], + ids=["regular-oob", "rectilinear-oob"], +) +def test_chunk_grid_getitem_oob( + array_shape: tuple[int, ...], chunk_sizes: Any, coords: tuple[int, ...] +) -> None: + """Out-of-bounds chunk coordinates return None""" + g = ChunkGrid.from_sizes(array_shape, chunk_sizes) + assert g[coords] is None + + +def test_chunk_grid_getitem_slices() -> None: + """ChunkSpec.slices reflect the correct start/stop for a rectilinear chunk""" + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [25, 25, 25, 25]]) + spec = g[(1, 2)] + assert spec is not None + assert spec.slices == (slice(10, 30, 1), slice(50, 75, 1)) + + +# -- all_chunk_coords tests -- + + +@pytest.mark.parametrize( + ("array_shape", "chunk_sizes", "origin", "selection_shape", "expected_coords"), + [ + # rectilinear grid + ( + (60, 100), + [[10, 20, 30], [50, 50]], + None, + None, + [(0, 0), (0, 1), (1, 0), (1, 1), (2, 0), (2, 1)], + ), + ((60, 100), [[10, 20, 30], [50, 50]], (1, 0), None, [(1, 0), (1, 1), (2, 0), (2, 1)]), + ((60, 100), [[10, 20, 30], [50, 50]], None, (2, 1), [(0, 0), (1, 0)]), + ((60, 100), [[10, 20, 30], [50, 50]], (1, 1), (2, 1), [(1, 1), (2, 1)]), + # regular grid + ((30, 40), (10, 20), (2, 1), None, [(2, 1)]), + ((30, 40), (10, 20), None, (0, 0), []), + ((60, 80), (20, 20), (0, 2), (3, 1), [(0, 2), (1, 2), (2, 2)]), + ], + ids=[ + "all", + "with-origin", + "with-sel-shape", + "origin+sel", + "last-chunk", + "zero-sel", + "single-dim", + ], +) +def test_all_chunk_coords( + array_shape: tuple[int, ...], + chunk_sizes: Any, + origin: tuple[int, ...] | None, + selection_shape: tuple[int, ...] | None, + expected_coords: list[tuple[int, ...]], +) -> None: + """all_chunk_coords yields the expected coordinates with optional origin and selection_shape""" + g = ChunkGrid.from_sizes(array_shape, chunk_sizes) + kwargs: dict[str, Any] = {} + if origin is not None: + kwargs["origin"] = origin + if selection_shape is not None: + kwargs["selection_shape"] = selection_shape + assert list(g.all_chunk_coords(**kwargs)) == expected_coords + + +def test_chunk_grid_get_nchunks() -> None: + """get_nchunks returns the total number of chunks across all dimensions""" + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + assert g.get_nchunks() == 6 + + +def test_chunk_grid_iter() -> None: + """Iterating a ChunkGrid yields the correct number of ChunkSpec objects""" + g = ChunkGrid.from_sizes((30, 40), (10, 20)) + specs = list(g) + assert len(specs) == 6 + assert all(isinstance(s, ChunkSpec) for s in specs) + + +# --------------------------------------------------------------------------- +# RLE tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("compressed", "expected"), + [ + ([[10, 3]], [10, 10, 10]), + ([[10, 2], [20, 1]], [10, 10, 20]), + ], +) +def test_rle_expand(compressed: list[Any], expected: list[int]) -> None: + """RLE-encoded edges expand correctly""" + assert expand_rle(compressed) == expected + + +@pytest.mark.parametrize( + ("original", "expected"), + [ + ([10, 10, 10], [[10, 3]]), + ([10, 10, 20], [[10, 2], 20]), + ([5], [5]), + ([10, 20, 30], [10, 20, 30]), + ], +) +def test_rle_compress(original: list[int], expected: list[Any]) -> None: + """compress_rle produces the expected RLE encoding for various input sequences""" + assert compress_rle(original) == expected + + +def test_rle_roundtrip() -> None: + """compress_rle followed by expand_rle recovers the original sequence""" + original = [10, 10, 10, 20, 20, 30] + compressed = compress_rle(original) + assert expand_rle(compressed) == original + + +@pytest.mark.parametrize( + ("rle_input", "match"), + [ + ([0], "Chunk edge length must be >= 1"), + ([-5], "Chunk edge length must be >= 1"), + ([[0, 3]], "Chunk edge length must be >= 1"), + ([[-10, 2]], "Chunk edge length must be >= 1"), + ([[5, 0]], "RLE repeat count must be >= 1"), + ([[5, -1]], "RLE repeat count must be >= 1"), + ], + ids=[ + "zero-edge", + "negative-edge", + "zero-rle-size", + "negative-rle-size", + "zero-rle-count", + "negative-rle-count", + ], +) +def test_rle_expand_rejects_invalid(rle_input: list[Any], match: str) -> None: + """expand_rle raises ValueError for zero/negative edge lengths or repeat counts""" + with pytest.raises(ValueError, match=match): + expand_rle(rle_input) + + +# -- expand_rle handles JSON floats -- + + +def test_expand_rle_bare_integer_floats_accepted() -> None: + """JSON parsers may emit 10.0 for the integer 10; expand_rle should handle it.""" + result = expand_rle([10.0, 20.0]) # type: ignore[list-item] + assert result == [10, 20] + + +def test_expand_rle_pair_with_float_count() -> None: + """expand_rle accepts float repeat counts that are integer-valued""" + result = expand_rle([[10, 3.0]]) # type: ignore[list-item] + assert result == [10, 10, 10] + + +# --------------------------------------------------------------------------- +# _is_rectilinear_chunks tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("value", "expected"), + [ + ([[10, 20], [5, 5]], True), + (((10, 20), (5, 5)), True), + ((10, 20), False), + ([10, 20], False), + (10, False), + ("auto", False), + ([], False), + ([[]], True), + (ChunkGrid.from_sizes((10,), (5,)), False), + (None, False), + (3.14, False), + ], + ids=[ + "nested-lists", + "nested-tuples", + "flat-tuple", + "flat-list", + "single-int", + "string", + "empty-list", + "empty-nested-list", + "chunk-grid-instance", + "none", + "float", + ], +) +def test_is_rectilinear_chunks(value: Any, expected: bool) -> None: + """_is_rectilinear_chunks correctly identifies nested sequences as rectilinear""" + assert _is_rectilinear_chunks(value) is expected + + +def test_is_rectilinear_chunks_handles_broken_iterable() -> None: + """_is_rectilinear_chunks returns False for objects that raise on iteration.""" + + class BrokenIter: + def __iter__(self) -> Any: + raise TypeError("cannot iterate") + + assert _is_rectilinear_chunks(BrokenIter()) is False + + +# --------------------------------------------------------------------------- +# Serialization tests +# --------------------------------------------------------------------------- + + +def test_serialization_error_non_regular_chunk_shape() -> None: + """Accessing chunk_shape on a non-regular grid raises ValueError.""" + grid = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [25, 25, 25, 25]]) + with pytest.raises(ValueError, match="only available for regular"): + grid.chunk_shape # noqa: B018 + + +def test_serialization_error_zero_extent_rectilinear() -> None: + """RectilinearChunkGridMetadata rejects empty edge tuples.""" + with pytest.raises(ValueError, match="has no chunk edges"): + RectilinearChunkGridMetadata(chunk_shapes=((),)) + + +def test_serialization_unknown_name_parse() -> None: + """Parsing metadata with an unknown chunk grid name raises ValueError""" + with pytest.raises(ValueError, match="Unknown chunk grid"): + parse_chunk_grid({"name": "hexagonal", "configuration": {}}) + + +def test_from_metadata_unknown_chunk_grid_type() -> None: + """ChunkGrid.from_metadata raises TypeError for unrecognised chunk grid metadata.""" + from unittest.mock import MagicMock + + from zarr.core.metadata.v3 import ArrayV3Metadata + + mock_meta = MagicMock(spec=ArrayV3Metadata) + mock_meta.chunk_grid = MagicMock() # not Regular or Rectilinear + with pytest.raises(TypeError, match="Unknown chunk grid metadata type"): + ChunkGrid.from_metadata(mock_meta) + + +def test_from_sizes_rejects_empty_edge_list() -> None: + """ChunkGrid.from_sizes raises ValueError when a dimension has an empty edge list.""" + with pytest.raises(ValueError, match="at least one chunk"): + ChunkGrid.from_sizes((10,), ([],)) + + +# --------------------------------------------------------------------------- +# Spec compliance tests +# --------------------------------------------------------------------------- + + +def test_spec_kind_inline_required_on_deserialize() -> None: + """Deserialization requires kind: 'inline'.""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"chunk_shapes": [[10, 20], [15, 15]]}, + } + with pytest.raises(ValueError, match="requires a 'kind' field"): + parse_chunk_grid(data) + + +def test_spec_kind_unknown_rejected() -> None: + """Unsupported rectilinear chunk grid kind raises ValueError on parse""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "reference", "chunk_shapes": [[10, 20], [15, 15]]}, + } + with pytest.raises(ValueError, match="Unsupported rectilinear chunk grid kind"): + parse_chunk_grid(data) + + +def test_spec_integer_shorthand_per_dimension() -> None: + """A bare integer in chunk_shapes means repeat until >= extent.""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [4, [1, 2, 3]]}, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + g = ChunkGrid.from_sizes((6, 6), meta.chunk_shapes) + assert _edges(g, 0) == (4, 4) + assert _edges(g, 1) == (1, 2, 3) + + +def test_spec_mixed_rle_and_bare_integers() -> None: + """An array can mix bare integers and [value, count] RLE pairs.""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[[1, 3], 3]]}, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + g = ChunkGrid.from_sizes((6,), meta.chunk_shapes) + assert _edges(g, 0) == (1, 1, 1, 3) + + +def test_spec_overflow_chunks_allowed() -> None: + """Edge sum >= extent is valid (overflow chunks permitted).""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[4, 4, 4]]}, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + g = ChunkGrid.from_sizes((6,), meta.chunk_shapes) + assert _edges(g, 0) == (4, 4, 4) + + +def test_spec_example() -> None: + """The full example from the spec README.""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": [ + 4, + [1, 2, 3], + [[4, 2]], + [[1, 3], 3], + [4, 4, 4], + ], + }, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + g = ChunkGrid.from_sizes((6, 6, 6, 6, 6), meta.chunk_shapes) + assert _edges(g, 0) == (4, 4) + assert _edges(g, 1) == (1, 2, 3) + assert _edges(g, 2) == (4, 4) + assert _edges(g, 3) == (1, 1, 1, 3) + assert _edges(g, 4) == (4, 4, 4) + + +# --------------------------------------------------------------------------- +# parse_chunk_grid validation tests +# --------------------------------------------------------------------------- + + +def test_parse_chunk_grid_varying_extent_mismatch_raises() -> None: + """Reconstructing a ChunkGrid with mismatched extents raises ValueError""" + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + with pytest.raises(ValueError, match="extent"): + ChunkGrid( + dimensions=tuple( + dim.with_extent(ext) for dim, ext in zip(g._dimensions, (100, 100), strict=True) + ) + ) + + +def test_parse_chunk_grid_varying_extent_match_ok() -> None: + """Reconstructing a ChunkGrid with matching extents succeeds""" + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + g2 = ChunkGrid( + dimensions=tuple( + dim.with_extent(ext) for dim, ext in zip(g._dimensions, (60, 100), strict=True) + ) + ) + assert g2._dimensions[0].extent == 60 + + +@pytest.mark.parametrize( + ("chunk_shapes", "array_shape", "match"), + [ + ([[10, 20, 30], [25, 25]], (100, 50), "extent 100 exceeds sum of edges 60"), + ([[50, 50], [10, 20]], (100, 50), "extent 50 exceeds sum of edges 30"), + ], + ids=["first-dim-mismatch", "second-dim-mismatch"], +) +def test_parse_chunk_grid_rectilinear_extent_mismatch_raises( + chunk_shapes: list[list[int]], array_shape: tuple[int, ...], match: str +) -> None: + """Rectilinear grid raises ValueError when array extent exceeds sum of edges""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": chunk_shapes}, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + with pytest.raises(ValueError, match=match): + ChunkGrid.from_sizes(array_shape, meta.chunk_shapes) + + +def test_parse_chunk_grid_rectilinear_extent_match_passes() -> None: + """Rectilinear grid with matching extents parses and builds successfully""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[10, 20, 30], [25, 25]]}, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + g = ChunkGrid.from_sizes((60, 50), meta.chunk_shapes) + assert g.grid_shape == (3, 2) + + +def test_parse_chunk_grid_rectilinear_ndim_mismatch_raises() -> None: + """Mismatched ndim between array shape and chunk_sizes raises ValueError""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[10, 20], [25, 25]]}, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + with pytest.raises(ValueError, match="3 dimensions but chunk_sizes has 2"): + ChunkGrid.from_sizes((30, 50, 100), meta.chunk_shapes) + + +def test_parse_chunk_grid_rectilinear_rle_extent_validated() -> None: + """RLE-encoded edges are expanded before validation.""" + data: dict[str, Any] = { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[[10, 5]], [[25, 2]]]}, + } + meta = parse_chunk_grid(data) + assert isinstance(meta, RectilinearChunkGridMetadata) + g = ChunkGrid.from_sizes((50, 50), meta.chunk_shapes) + assert g.grid_shape == (5, 2) + with pytest.raises(ValueError, match="extent 100 exceeds sum of edges 50"): + ChunkGrid.from_sizes((100, 50), meta.chunk_shapes) + + +def test_parse_chunk_grid_varying_dimension_extent_mismatch_on_chunkgrid_input() -> None: + """ChunkGrid constructor rejects VaryingDimension with extent exceeding sum of edges""" + g = ChunkGrid.from_sizes((60, 50), [[10, 20, 30], [25, 25]]) + with pytest.raises(ValueError, match="less than"): + ChunkGrid( + dimensions=tuple( + dim.with_extent(ext) for dim, ext in zip(g._dimensions, (100, 50), strict=True) + ) + ) + + +# --------------------------------------------------------------------------- +# Rectilinear indexing tests +# --------------------------------------------------------------------------- + + +def test_basic_indexer_rectilinear() -> None: + """BasicIndexer produces correct projections for a full-slice rectilinear selection""" + from zarr.core.indexing import BasicIndexer + + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + indexer = BasicIndexer( + selection=(slice(None), slice(None)), + shape=(60, 100), + chunk_grid=g, + ) + projections = list(indexer) + assert len(projections) == 6 + + p0 = projections[0] + assert p0.chunk_coords == (0, 0) + assert p0.chunk_selection == (slice(0, 10, 1), slice(0, 50, 1)) + + p1 = projections[2] + assert p1.chunk_coords == (1, 0) + assert p1.chunk_selection == (slice(0, 20, 1), slice(0, 50, 1)) + + +def test_basic_indexer_int_selection() -> None: + """BasicIndexer with integer selection maps to the correct chunk and local offset""" + from zarr.core.indexing import BasicIndexer + + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + indexer = BasicIndexer( + selection=(15, slice(None)), + shape=(60, 100), + chunk_grid=g, + ) + projections = list(indexer) + assert len(projections) == 2 + assert projections[0].chunk_coords == (1, 0) + assert projections[0].chunk_selection == (5, slice(0, 50, 1)) + + +def test_basic_indexer_slice_subset() -> None: + """BasicIndexer with partial slices spans the expected chunk dimensions""" + from zarr.core.indexing import BasicIndexer + + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + indexer = BasicIndexer( + selection=(slice(5, 35), slice(0, 50)), + shape=(60, 100), + chunk_grid=g, + ) + projections = list(indexer) + chunk_coords_dim0 = sorted({p.chunk_coords[0] for p in projections}) + assert chunk_coords_dim0 == [0, 1, 2] + + +def test_orthogonal_indexer_rectilinear() -> None: + """OrthogonalIndexer produces the expected number of projections for a rectilinear grid""" + from zarr.core.indexing import OrthogonalIndexer + + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + indexer = OrthogonalIndexer( + selection=(slice(None), slice(None)), + shape=(60, 100), + chunk_grid=g, + ) + projections = list(indexer) + assert len(projections) == 6 + + +def test_oob_block_raises_bounds_check_error() -> None: + """Out-of-bounds block index should raise BoundsCheckError, not IndexError.""" + store = MemoryStore() + a = zarr.create_array(store, shape=(30,), chunks=[[10, 20]], dtype="int32") + with pytest.raises(BoundsCheckError): + a.get_block_selection((2,)) + + +# --------------------------------------------------------------------------- +# End-to-end tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("shape", "chunks", "expected_regular"), + [ + ((100, 200), (10, 20), True), + ((60, 100), [[10, 20, 30], [50, 50]], False), + ], + ids=["regular", "rectilinear"], +) +def test_e2e_create_array( + tmp_path: Path, shape: tuple[int, ...], chunks: Any, expected_regular: bool +) -> None: + """End-to-end array creation sets correct regularity and ndim on chunk_grid""" + arr = zarr.create_array( + store=tmp_path / "arr.zarr", + shape=shape, + chunks=chunks, + dtype="float32", + ) + assert ChunkGrid.from_metadata(arr.metadata).is_regular == expected_regular + assert ChunkGrid.from_metadata(arr.metadata).ndim == len(shape) + + +@pytest.mark.parametrize( + ("shape", "chunks", "grid_type_name", "grid_name"), + [ + ((100, 200), (10, 20), "RegularChunkGridMetadata", "regular"), + ((60, 100), [[10, 20, 30], [50, 50]], "RectilinearChunkGridMetadata", "rectilinear"), + ], + ids=["regular", "rectilinear"], +) +def test_e2e_chunk_grid_serializes( + tmp_path: Path, shape: tuple[int, ...], chunks: Any, grid_type_name: str, grid_name: str +) -> None: + """Array metadata serializes chunk_grid with the correct type and name""" + from zarr.core.metadata.v3 import ( + ArrayV3Metadata, + RectilinearChunkGridMetadata, + RegularChunkGridMetadata, + ) + + grid_type = ( + RegularChunkGridMetadata + if grid_type_name == "RegularChunkGridMetadata" + else RectilinearChunkGridMetadata + ) + arr = zarr.create_array( + store=tmp_path / "arr.zarr", + shape=shape, + chunks=chunks, + dtype="float32", + ) + assert isinstance(arr.metadata, ArrayV3Metadata) + assert isinstance(arr.metadata.chunk_grid, grid_type) + d = arr.metadata.to_dict() + chunk_grid_dict = d["chunk_grid"] + assert isinstance(chunk_grid_dict, dict) + assert chunk_grid_dict["name"] == grid_name + + +def test_e2e_chunk_grid_name_roundtrip_preserves_rectilinear(tmp_path: Path) -> None: + """A rectilinear grid with uniform edges stays 'rectilinear' through to_dict/from_dict.""" + from zarr.core.metadata.v3 import ArrayV3Metadata, RectilinearChunkGridMetadata + + meta_dict: dict[str, Any] = { + "zarr_format": 3, + "node_type": "array", + "shape": [100, 100], + "chunk_grid": { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[[50, 2]], [[25, 4]]]}, + }, + "chunk_key_encoding": {"name": "default"}, + "data_type": "float32", + "fill_value": 0.0, + "codecs": [{"name": "bytes", "configuration": {"endian": "little"}}], + } + meta = ArrayV3Metadata.from_dict(meta_dict) + assert isinstance(meta.chunk_grid, RectilinearChunkGridMetadata) + d = meta.to_dict() + chunk_grid_dict = d["chunk_grid"] + assert isinstance(chunk_grid_dict, dict) + assert chunk_grid_dict["name"] == "rectilinear" + + +def test_e2e_chunk_grid_name_regular_from_dict(tmp_path: Path) -> None: + """A 'regular' chunk grid name is preserved through from_dict.""" + from zarr.core.metadata.v3 import ArrayV3Metadata, RegularChunkGridMetadata + + meta_dict: dict[str, Any] = { + "zarr_format": 3, + "node_type": "array", + "shape": [100, 100], + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [50, 25]}, + }, + "chunk_key_encoding": {"name": "default"}, + "data_type": "float32", + "fill_value": 0.0, + "codecs": [{"name": "bytes", "configuration": {"endian": "little"}}], + } + meta = ArrayV3Metadata.from_dict(meta_dict) + assert isinstance(meta.chunk_grid, RegularChunkGridMetadata) + d = meta.to_dict() + chunk_grid_dict = d["chunk_grid"] + assert isinstance(chunk_grid_dict, dict) + assert chunk_grid_dict["name"] == "regular" + + +# --------------------------------------------------------------------------- +# Sharding compatibility tests +# --------------------------------------------------------------------------- + + +def test_sharding_accepts_rectilinear_outer_grid() -> None: + """ShardingCodec.validate should not reject rectilinear outer grids.""" + from zarr.codecs.sharding import ShardingCodec + from zarr.core.dtype import Float32 + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata + + codec = ShardingCodec(chunk_shape=(5, 5)) + grid_meta = RectilinearChunkGridMetadata(chunk_shapes=((10, 20, 30), (50, 50))) + + codec.validate( + shape=(60, 100), + dtype=Float32(), + chunk_grid=grid_meta, + ) + + +def test_sharding_rejects_non_divisible_rectilinear() -> None: + """Rectilinear shard sizes not divisible by inner chunk_shape should raise.""" + from zarr.codecs.sharding import ShardingCodec + from zarr.core.dtype import Float32 + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata + + codec = ShardingCodec(chunk_shape=(5, 5)) + grid_meta = RectilinearChunkGridMetadata(chunk_shapes=((10, 20, 17), (50, 50))) + + with pytest.raises(ValueError, match="divisible"): + codec.validate( + shape=(47, 100), + dtype=Float32(), + chunk_grid=grid_meta, + ) + + +def test_sharding_accepts_divisible_rectilinear() -> None: + """Rectilinear shard sizes all divisible by inner chunk_shape should pass.""" + from zarr.codecs.sharding import ShardingCodec + from zarr.core.dtype import Float32 + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata + + codec = ShardingCodec(chunk_shape=(5, 5)) + grid_meta = RectilinearChunkGridMetadata(chunk_shapes=((10, 20, 30), (50, 50))) + + codec.validate( + shape=(60, 100), + dtype=Float32(), + chunk_grid=grid_meta, + ) + + +def test_sharding_rejects_non_divisible_among_repeated_edges() -> None: + """Shard validation catches a non-divisible edge even among many repeated valid ones.""" + from zarr.codecs.sharding import ShardingCodec + from zarr.core.dtype import Float32 + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata + + # edges (10, 10, 7) — 7 is not divisible by 5 + codec = ShardingCodec(chunk_shape=(5,)) + grid_meta = RectilinearChunkGridMetadata(chunk_shapes=((10, 10, 7),)) + with pytest.raises(ValueError, match="divisible"): + codec.validate(shape=(27,), dtype=Float32(), chunk_grid=grid_meta) + + +def test_sharding_accepts_all_repeated_divisible_edges() -> None: + """Shard validation passes when all distinct edges are divisible by inner chunk size.""" + from zarr.codecs.sharding import ShardingCodec + from zarr.core.dtype import Float32 + from zarr.core.metadata.v3 import RectilinearChunkGridMetadata + + # edges (10, 10, 20, 10) — unique values {10, 20}, both divisible by 5 + codec = ShardingCodec(chunk_shape=(5,)) + grid_meta = RectilinearChunkGridMetadata(chunk_shapes=((10, 10, 20, 10),)) + codec.validate(shape=(50,), dtype=Float32(), chunk_grid=grid_meta) + + +# --------------------------------------------------------------------------- +# Edge cases +# --------------------------------------------------------------------------- + + +def test_edge_case_chunk_grid_boundary_getitem() -> None: + """ChunkGrid with boundary FixedDimension via direct construction.""" + g = ChunkGrid(dimensions=(FixedDimension(10, 95), FixedDimension(20, 40))) + spec = g[(9, 1)] + assert spec is not None + assert spec.shape == (5, 20) + assert spec.codec_shape == (10, 20) + assert spec.is_boundary + + +def test_edge_case_chunk_grid_boundary_iter() -> None: + """Iterating a boundary grid yields correct boundary ChunkSpecs.""" + g = ChunkGrid(dimensions=(FixedDimension(10, 25),)) + specs = list(g) + assert len(specs) == 3 + assert specs[0].shape == (10,) + assert specs[1].shape == (10,) + assert specs[2].shape == (5,) + assert specs[2].is_boundary + assert not specs[0].is_boundary + + +def test_edge_case_chunk_grid_boundary_shape() -> None: + """shape property with boundary extent.""" + g = ChunkGrid(dimensions=(FixedDimension(10, 95),)) + assert g.grid_shape == (10,) + + +# -- Zero-size and zero-extent -- + + +@pytest.mark.parametrize( + ("size", "extent"), + [(0, 0), (0, 5), (10, 0)], + ids=["zero-size-zero-extent", "zero-size-nonzero-extent", "zero-extent-nonzero-size"], +) +def test_edge_case_zero_size_or_extent(size: int, extent: int) -> None: + """FixedDimension with zero size or extent has zero chunks and getitem returns None""" + d = FixedDimension(size=size, extent=extent) + assert d.nchunks == 0 + g = ChunkGrid(dimensions=(d,)) + assert g[0] is None + + +def test_edge_case_zero_size_data_and_indices() -> None: + """FixedDimension(size=0) handles data_size, index_to_chunk, and indices_to_chunks safely.""" + d = FixedDimension(size=0, extent=0) + # Zero-sized chunks have zero data + assert d.data_size(0) == 0 + # Vectorized lookup maps every index to chunk 0 (avoids division by zero) + indices = np.array([0, 0, 0], dtype=np.intp) + np.testing.assert_array_equal(d.indices_to_chunks(indices), np.zeros(3, dtype=np.intp)) + + +def test_edge_case_zero_size_nonzero_extent_index() -> None: + """FixedDimension(size=0, extent>0) maps valid indices to chunk 0 without dividing by zero.""" + d = FixedDimension(size=0, extent=5) + assert d.nchunks == 0 + # index_to_chunk avoids division by zero and returns 0 + assert d.index_to_chunk(0) == 0 + assert d.index_to_chunk(4) == 0 + + +def test_edge_case_zero_size_data_and_index() -> None: + """FixedDimension(size=0) returns zero for data_size and maps indices to chunk 0.""" + d = FixedDimension(size=0, extent=0) + # data_size returns 0 for a zero-sized chunk + assert d.data_size(0) == 0 + # vectorized indices_to_chunks returns zeros + indices = np.array([0, 0, 0], dtype=np.intp) + np.testing.assert_array_equal(d.indices_to_chunks(indices), np.zeros(3, dtype=np.intp)) + + +# -- 0-d grid -- + + +def test_0d_grid_getitem() -> None: + """0-d grid has exactly one chunk at coords ().""" + g = ChunkGrid.from_sizes((), ()) + spec = g[()] + assert spec is not None + assert spec.shape == () + assert spec.codec_shape == () + assert not spec.is_boundary + + +def test_0d_grid_iter() -> None: + """0-d grid iteration yields a single ChunkSpec.""" + g = ChunkGrid.from_sizes((), ()) + specs = list(g) + assert len(specs) == 1 + + +def test_0d_grid_all_chunk_coords() -> None: + """0-d grid has one chunk coord: the empty tuple.""" + g = ChunkGrid.from_sizes((), ()) + coords = list(g.all_chunk_coords()) + assert coords == [()] + + +def test_0d_grid_nchunks() -> None: + """0-d grid reports exactly one chunk""" + g = ChunkGrid.from_sizes((), ()) + assert g.get_nchunks() == 1 + + +# -- parse_chunk_grid edge cases -- + + +def test_parse_chunk_grid_preserves_varying_extent() -> None: + """parse_chunk_grid does not overwrite VaryingDimension extent.""" + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + assert isinstance(g._dimensions[0], VaryingDimension) + assert g._dimensions[0].extent == 60 + + g2 = ChunkGrid( + dimensions=tuple( + dim.with_extent(ext) for dim, ext in zip(g._dimensions, (60, 100), strict=True) + ) + ) + assert isinstance(g2._dimensions[0], VaryingDimension) + assert g2._dimensions[0].extent == 60 + + +def test_parse_chunk_grid_rebinds_fixed_extent() -> None: + """parse_chunk_grid updates FixedDimension extent from array shape.""" + g = ChunkGrid.from_sizes((100, 200), (10, 20)) + assert g._dimensions[0].extent == 100 + + g2 = ChunkGrid( + dimensions=tuple( + dim.with_extent(ext) for dim, ext in zip(g._dimensions, (50, 100), strict=True) + ) + ) + assert isinstance(g2._dimensions[0], FixedDimension) + assert g2._dimensions[0].extent == 50 + assert g2.grid_shape == (5, 5) + + +# -- ChunkGrid.__getitem__ validation -- + + +def test_getitem_int_1d_regular() -> None: + """Integer indexing works for 1-d regular grids.""" + g = ChunkGrid.from_sizes((100,), (10,)) + spec = g[0] + assert spec is not None + assert spec.shape == (10,) + assert spec.slices == (slice(0, 10, 1),) + spec = g[9] + assert spec is not None + assert spec.shape == (10,) + + +def test_getitem_int_1d_rectilinear() -> None: + """Integer indexing works for 1-d rectilinear grids.""" + g = ChunkGrid.from_sizes((100,), [[20, 30, 50]]) + spec = g[0] + assert spec is not None + assert spec.shape == (20,) + spec = g[1] + assert spec is not None + assert spec.shape == (30,) + spec = g[2] + assert spec is not None + assert spec.shape == (50,) + + +@pytest.mark.parametrize( + ("shape", "chunks", "match"), + [ + ((), (), "Expected 0 coordinate.*got 1"), + ((100, 200), (10, 20), "Expected 2 coordinate.*got 1"), + ], + ids=["0d", "2d"], +) +def test_getitem_int_ndim_mismatch_raises( + shape: tuple[int, ...], chunks: tuple[int, ...], match: str +) -> None: + """Integer indexing on a multi-dim or 0-d grid raises ValueError for ndim mismatch""" + g = ChunkGrid.from_sizes(shape, chunks) + with pytest.raises(ValueError, match=match): + g[0] + + +@pytest.mark.parametrize( + "index", + [(10,), (99,), (-1,)], + ids=["oob-10", "oob-99", "negative"], +) +def test_getitem_oob_returns_none(index: tuple[int, ...]) -> None: + """Out-of-bounds or negative chunk indices return None""" + g = ChunkGrid.from_sizes((100,), (10,)) + assert g[index] is None + + +# -- Rectilinear with zero-nchunks FixedDimension -- + + +def test_zero_nchunks_fixed_dim_in_rectilinear() -> None: + """A rectilinear grid with a 0-extent FixedDimension still has valid size.""" + g = ChunkGrid( + dimensions=( + VaryingDimension([10, 20], extent=30), + FixedDimension(size=10, extent=0), + ) + ) + assert g.grid_shape == (2, 0) + + +# -- VaryingDimension data_size -- + + +def test_varying_dim_data_size_equals_chunk_size() -> None: + """For VaryingDimension, data_size == chunk_size (no padding).""" + d = VaryingDimension([10, 20, 5], extent=35) + for i in range(3): + assert d.data_size(i) == d.chunk_size(i) + + +# --------------------------------------------------------------------------- +# OrthogonalIndexer rectilinear tests +# --------------------------------------------------------------------------- + + +def test_orthogonal_int_array_selection_rectilinear() -> None: + """Integer array selection with rectilinear grid must produce correct + chunk-local selections.""" + from zarr.core.indexing import OrthogonalIndexer + + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + indexer = OrthogonalIndexer( + selection=(np.array([5, 15, 35]), slice(None)), + shape=(60, 100), + chunk_grid=g, + ) + projections = list(indexer) + chunk_coords = [p.chunk_coords for p in projections] + assert chunk_coords == [(0, 0), (0, 1), (1, 0), (1, 1), (2, 0), (2, 1)] + + +def test_orthogonal_bool_array_selection_rectilinear() -> None: + """Boolean array selection with rectilinear grid produces correct chunk projections.""" + from zarr.core.indexing import OrthogonalIndexer + + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + mask = np.zeros(60, dtype=bool) + mask[5] = True + mask[15] = True + mask[35] = True + indexer = OrthogonalIndexer( + selection=(mask, slice(None)), + shape=(60, 100), + chunk_grid=g, + ) + projections = list(indexer) + assert len(projections) == 6 + chunk_coords = [p.chunk_coords for p in projections] + assert (0, 0) in chunk_coords + assert (1, 0) in chunk_coords + assert (2, 0) in chunk_coords + assert (0, 1) in chunk_coords + assert (1, 1) in chunk_coords + assert (2, 1) in chunk_coords + + +def test_orthogonal_advanced_indexing_produces_correct_projections() -> None: + """Verify OrthogonalIndexer produces correct chunk projections + for advanced indexing with VaryingDimension.""" + from zarr.core.indexing import OrthogonalIndexer + + g = ChunkGrid.from_sizes((60, 100), [[10, 20, 30], [50, 50]]) + indexer = OrthogonalIndexer( + selection=(np.array([5, 15]), slice(None)), + shape=(60, 100), + chunk_grid=g, + ) + projections = list(indexer) + assert len(projections) == 4 + coords = [p.chunk_coords for p in projections] + assert (0, 0) in coords + assert (0, 1) in coords + assert (1, 0) in coords + assert (1, 1) in coords + + +# --------------------------------------------------------------------------- +# Full pipeline rectilinear tests (helpers) +# --------------------------------------------------------------------------- + + +def _make_1d(tmp_path: Path) -> tuple[zarr.Array[Any], np.ndarray[Any, Any]]: + a = np.arange(30, dtype="int32") + z = zarr.create_array( + store=tmp_path / "arr1d.zarr", + shape=(30,), + chunks=[[5, 10, 15]], + dtype="int32", + ) + z[:] = a + return z, a + + +def _make_2d(tmp_path: Path) -> tuple[zarr.Array[Any], np.ndarray[Any, Any]]: + a = np.arange(6000, dtype="int32").reshape(60, 100) + z = zarr.create_array( + store=tmp_path / "arr2d.zarr", + shape=(60, 100), + chunks=[[10, 20, 30], [25, 25, 25, 25]], + dtype="int32", + ) + z[:] = a + return z, a + + +# --- Basic selection --- + + +def test_pipeline_basic_selection_1d(tmp_path: Path) -> None: + """1D rectilinear basic selections match numpy for ints, slices, and full-array reads""" + z, a = _make_1d(tmp_path) + sels: list[Any] = [0, 4, 5, 14, 15, 29, -1, slice(None), slice(3, 18), slice(0, 0)] + for sel in sels: + np.testing.assert_array_equal(z[sel], a[sel], err_msg=f"sel={sel}") + + +def test_pipeline_basic_selection_1d_strided(tmp_path: Path) -> None: + """1D rectilinear strided slice selections match numpy""" + z, a = _make_1d(tmp_path) + for sel in [slice(None, None, 2), slice(1, 25, 3), slice(0, 30, 7)]: + np.testing.assert_array_equal(z[sel], a[sel], err_msg=f"sel={sel}") + + +def test_pipeline_basic_selection_2d(tmp_path: Path) -> None: + """2D rectilinear basic selections match numpy across chunk boundaries""" + z, a = _make_2d(tmp_path) + selections: list[Any] = [ + 42, + -1, + (9, 24), + (10, 25), + (30, 50), + (59, 99), + slice(None), + (slice(5, 35), slice(20, 80)), + (slice(0, 10), slice(0, 25)), + (slice(10, 10), slice(None)), + (slice(None, None, 3), slice(None, None, 7)), + ] + for sel in selections: + np.testing.assert_array_equal(z[sel], a[sel], err_msg=f"sel={sel}") + + +# --- Orthogonal selection --- + + +def test_pipeline_orthogonal_selection_1d_bool(tmp_path: Path) -> None: + """1D boolean orthogonal indexing on rectilinear arrays matches numpy""" + z, a = _make_1d(tmp_path) + ix = np.zeros(30, dtype=bool) + ix[[0, 4, 5, 14, 15, 29]] = True + np.testing.assert_array_equal(z.oindex[ix], a[ix]) + + +def test_pipeline_orthogonal_selection_1d_int(tmp_path: Path) -> None: + """1D integer and negative-index orthogonal selection on rectilinear arrays matches numpy""" + z, a = _make_1d(tmp_path) + ix = np.array([0, 4, 5, 14, 15, 29]) + np.testing.assert_array_equal(z.oindex[ix], a[ix]) + ix_neg = np.array([0, -1, -15, -25]) + np.testing.assert_array_equal(z.oindex[ix_neg], a[ix_neg]) + + +def test_pipeline_orthogonal_selection_2d_bool(tmp_path: Path) -> None: + """2D boolean orthogonal selection on rectilinear arrays matches numpy""" + z, a = _make_2d(tmp_path) + ix0 = np.zeros(60, dtype=bool) + ix0[[0, 9, 10, 29, 30, 59]] = True + ix1 = np.zeros(100, dtype=bool) + ix1[[0, 24, 25, 49, 50, 99]] = True + np.testing.assert_array_equal(z.oindex[ix0, ix1], a[np.ix_(ix0, ix1)]) + + +def test_pipeline_orthogonal_selection_2d_int(tmp_path: Path) -> None: + """2D integer orthogonal selection on rectilinear arrays matches numpy""" + z, a = _make_2d(tmp_path) + ix0 = np.array([0, 9, 10, 29, 30, 59]) + ix1 = np.array([0, 24, 25, 49, 50, 99]) + np.testing.assert_array_equal(z.oindex[ix0, ix1], a[np.ix_(ix0, ix1)]) + + +def test_pipeline_orthogonal_selection_2d_mixed(tmp_path: Path) -> None: + """2D mixed int-array and slice orthogonal selection on rectilinear arrays matches numpy""" + z, a = _make_2d(tmp_path) + ix = np.array([0, 9, 10, 29, 30, 59]) + np.testing.assert_array_equal(z.oindex[ix, slice(25, 75)], a[np.ix_(ix, np.arange(25, 75))]) + np.testing.assert_array_equal( + z.oindex[slice(10, 30), ix[:4]], a[np.ix_(np.arange(10, 30), ix[:4])] + ) + + +# --- Coordinate (vindex) selection --- + + +def test_pipeline_coordinate_selection_1d(tmp_path: Path) -> None: + """1D coordinate (vindex) selection on rectilinear arrays matches numpy""" + z, a = _make_1d(tmp_path) + ix = np.array([0, 4, 5, 14, 15, 29]) + np.testing.assert_array_equal(z.vindex[ix], a[ix]) + + +def test_pipeline_coordinate_selection_2d(tmp_path: Path) -> None: + """2D coordinate (vindex) selection on rectilinear arrays matches numpy""" + z, a = _make_2d(tmp_path) + r = np.array([0, 9, 10, 29, 30, 59]) + c = np.array([0, 24, 25, 49, 50, 99]) + np.testing.assert_array_equal(z.vindex[r, c], a[r, c]) + + +def test_pipeline_coordinate_selection_2d_bool_mask(tmp_path: Path) -> None: + """2D boolean mask vindex selection on rectilinear arrays matches numpy""" + z, a = _make_2d(tmp_path) + mask = a > 3000 + np.testing.assert_array_equal(z.vindex[mask], a[mask]) + + +# --- Block selection --- + + +def test_pipeline_block_selection_1d(tmp_path: Path) -> None: + """1D block selection on rectilinear arrays returns correct chunk data""" + z, a = _make_1d(tmp_path) + np.testing.assert_array_equal(z.blocks[0], a[0:5]) + np.testing.assert_array_equal(z.blocks[1], a[5:15]) + np.testing.assert_array_equal(z.blocks[2], a[15:30]) + np.testing.assert_array_equal(z.blocks[-1], a[15:30]) + np.testing.assert_array_equal(z.blocks[0:2], a[0:15]) + np.testing.assert_array_equal(z.blocks[1:3], a[5:30]) + np.testing.assert_array_equal(z.blocks[:], a[:]) + + +def test_pipeline_block_selection_2d(tmp_path: Path) -> None: + """2D block selection on rectilinear arrays returns correct chunk data""" + z, a = _make_2d(tmp_path) + np.testing.assert_array_equal(z.blocks[0, 0], a[0:10, 0:25]) + np.testing.assert_array_equal(z.blocks[1, 2], a[10:30, 50:75]) + np.testing.assert_array_equal(z.blocks[2, 3], a[30:60, 75:100]) + np.testing.assert_array_equal(z.blocks[-1, -1], a[30:60, 75:100]) + np.testing.assert_array_equal(z.blocks[0:2, 1:3], a[0:30, 25:75]) + np.testing.assert_array_equal(z.blocks[:, :], a[:, :]) + + +def test_pipeline_set_block_selection_1d(tmp_path: Path) -> None: + """Writing via 1D block selection on rectilinear arrays persists correctly""" + z, a = _make_1d(tmp_path) + val = np.full(10, -1, dtype="int32") + z.blocks[1] = val + a[5:15] = val + np.testing.assert_array_equal(z[:], a) + + +def test_pipeline_set_block_selection_2d(tmp_path: Path) -> None: + """Writing via 2D block selection on rectilinear arrays persists correctly""" + z, a = _make_2d(tmp_path) + val = np.full((30, 50), -99, dtype="int32") + z.blocks[0:2, 1:3] = val + a[0:30, 25:75] = val + np.testing.assert_array_equal(z[:], a) + + +def test_pipeline_block_selection_slice_stop_at_nchunks(tmp_path: Path) -> None: + """Block slice with stop == nchunks exercises the dim_len fallback.""" + z, a = _make_1d(tmp_path) + np.testing.assert_array_equal(z.blocks[1:3], a[5:30]) + np.testing.assert_array_equal(z.blocks[0:10], a[:]) + + +def test_pipeline_block_selection_slice_stop_at_nchunks_2d(tmp_path: Path) -> None: + """Same fallback test for 2D rectilinear arrays.""" + z, a = _make_2d(tmp_path) + np.testing.assert_array_equal(z.blocks[2:3, 3:4], a[30:60, 75:100]) + np.testing.assert_array_equal(z.blocks[0:99, 0:99], a[:, :]) + + +# --- Set coordinate selection --- + + +def test_pipeline_set_coordinate_selection_1d(tmp_path: Path) -> None: + """Writing via 1D coordinate selection on rectilinear arrays persists correctly""" + z, a = _make_1d(tmp_path) + ix = np.array([0, 4, 5, 14, 15, 29]) + val = np.full(len(ix), -7, dtype="int32") + z.vindex[ix] = val + a[ix] = val + np.testing.assert_array_equal(z[:], a) + + +def test_pipeline_set_coordinate_selection_2d(tmp_path: Path) -> None: + """Writing via 2D coordinate selection on rectilinear arrays persists correctly""" + z, a = _make_2d(tmp_path) + r = np.array([0, 9, 10, 29, 30, 59]) + c = np.array([0, 24, 25, 49, 50, 99]) + val = np.full(len(r), -42, dtype="int32") + z.vindex[r, c] = val + a[r, c] = val + np.testing.assert_array_equal(z[:], a) + + +# --- Set selection --- + + +def test_pipeline_set_basic_selection(tmp_path: Path) -> None: + """Writing via basic slice selection on rectilinear arrays persists correctly""" + z, a = _make_2d(tmp_path) + new_data = np.full((20, 50), -1, dtype="int32") + z[5:25, 10:60] = new_data + a[5:25, 10:60] = new_data + np.testing.assert_array_equal(z[:], a) + + +def test_pipeline_set_orthogonal_selection(tmp_path: Path) -> None: + """Writing via orthogonal selection on rectilinear arrays persists correctly""" + z, a = _make_2d(tmp_path) + rows = np.array([0, 10, 30]) + cols = np.array([0, 25, 50, 75]) + val = np.full((3, 4), -99, dtype="int32") + z.oindex[rows, cols] = val + a[np.ix_(rows, cols)] = val + np.testing.assert_array_equal(z[:], a) + + +# --- Higher dimensions --- + + +def test_pipeline_3d_array(tmp_path: Path) -> None: + """3D rectilinear array write and read-back match numpy""" + shape = (12, 20, 15) + chunk_shapes = [[4, 8], [5, 5, 10], [5, 10]] + a = np.arange(int(np.prod(shape)), dtype="int32").reshape(shape) + z = zarr.create_array( + store=tmp_path / "arr3d.zarr", + shape=shape, + chunks=chunk_shapes, + dtype="int32", + ) + z[:] = a + np.testing.assert_array_equal(z[:], a) + np.testing.assert_array_equal(z[2:10, 3:18, 4:14], a[2:10, 3:18, 4:14]) + + +def test_pipeline_1d_single_chunk(tmp_path: Path) -> None: + """Single-chunk rectilinear array write and read-back match numpy""" + a = np.arange(20, dtype="int32") + z = zarr.create_array( + store=tmp_path / "arr1c.zarr", + shape=(20,), + chunks=[[20]], + dtype="int32", + ) + z[:] = a + np.testing.assert_array_equal(z[:], a) + + +# --- Persistence roundtrip --- + + +def test_pipeline_persistence_roundtrip(tmp_path: Path) -> None: + """Rectilinear array survives close and reopen with correct data""" + _, a = _make_2d(tmp_path) + z2 = zarr.open_array(store=tmp_path / "arr2d.zarr", mode="r") + assert not ChunkGrid.from_metadata(z2.metadata).is_regular + np.testing.assert_array_equal(z2[:], a) + + +# --- Highly irregular chunks --- + + +def test_pipeline_highly_irregular_chunks(tmp_path: Path) -> None: + """Highly irregular chunk sizes produce correct write and partial-read results""" + shape = (100, 100) + chunk_shapes = [[5, 10, 15, 20, 50], [100]] + a = np.arange(10000, dtype="int32").reshape(shape) + z = zarr.create_array( + store=tmp_path / "irreg.zarr", + shape=shape, + chunks=chunk_shapes, + dtype="int32", + ) + z[:] = a + np.testing.assert_array_equal(z[:], a) + np.testing.assert_array_equal(z[3:97, 10:90], a[3:97, 10:90]) + + +# --- API validation --- + + +def test_pipeline_v2_rejects_rectilinear(tmp_path: Path) -> None: + """Creating a rectilinear array with zarr_format=2 raises ValueError""" + with pytest.raises(ValueError, match="Zarr format 2"): + zarr.create_array( + store=tmp_path / "v2.zarr", + shape=(30,), + chunks=[[10, 20]], + dtype="int32", + zarr_format=2, + ) + + +def test_pipeline_sharding_rejects_rectilinear_chunks_with_shards(tmp_path: Path) -> None: + """Rectilinear chunks (inner) with sharding is not supported.""" + with pytest.raises(ValueError, match="Rectilinear chunks with sharding"): + zarr.create_array( + store=tmp_path / "shard.zarr", + shape=(60, 100), + chunks=[[10, 20, 30], [25, 25, 25, 25]], + shards=(30, 50), + dtype="int32", + ) + + +def test_pipeline_rectilinear_shards_roundtrip(tmp_path: Path) -> None: + """Rectilinear shards with uniform inner chunks: full write/read roundtrip.""" + data = np.arange(120 * 100, dtype="int32").reshape(120, 100) + arr = zarr.create_array( + store=tmp_path / "rect_shards.zarr", + shape=(120, 100), + chunks=(10, 10), + shards=[[60, 40, 20], [50, 50]], + dtype="int32", + ) + arr[:] = data + result = arr[:] + np.testing.assert_array_equal(result, data) + + +def test_pipeline_rectilinear_shards_partial_read(tmp_path: Path) -> None: + """Partial reads across rectilinear shard boundaries.""" + data = np.arange(120 * 100, dtype="float64").reshape(120, 100) + arr = zarr.create_array( + store=tmp_path / "rect_shards.zarr", + shape=(120, 100), + chunks=(10, 10), + shards=[[60, 40, 20], [50, 50]], + dtype="float64", + ) + arr[:] = data + result = arr[50:70, 40:60] + np.testing.assert_array_equal(result, data[50:70, 40:60]) + + +def test_pipeline_rectilinear_shards_validates_divisibility(tmp_path: Path) -> None: + """Inner chunk_shape must divide every shard's dimensions.""" + with pytest.raises(ValueError, match="divisible"): + zarr.create_array( + store=tmp_path / "bad.zarr", + shape=(120, 100), + chunks=(10, 10), + shards=[[60, 45, 15], [50, 50]], + dtype="int32", + ) + + +def test_pipeline_nchunks(tmp_path: Path) -> None: + """Rectilinear array reports the correct total number of chunks""" + z, _ = _make_2d(tmp_path) + assert ChunkGrid.from_metadata(z.metadata).get_nchunks() == 12 + + +def test_pipeline_parse_chunk_grid_regular_from_dict() -> None: + """parse_chunk_grid constructs a regular grid from a metadata dict.""" + d: dict[str, Any] = {"name": "regular", "configuration": {"chunk_shape": [10, 20]}} + meta = parse_chunk_grid(d) + assert isinstance(meta, RegularChunkGridMetadata) + g = ChunkGrid.from_sizes((100, 200), tuple(meta.chunk_shape)) + assert g.is_regular + assert g.chunk_shape == (10, 20) + assert g.grid_shape == (10, 10) + assert g.get_nchunks() == 100 + + +# --------------------------------------------------------------------------- +# VaryingDimension boundary tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("edges", "extent", "chunk_idx", "expected_data_size"), + [ + ([10, 20, 30], 50, 0, 10), + ([10, 20, 30], 50, 1, 20), + ([10, 20, 30], 50, 2, 20), + ([10, 20, 30], 60, 2, 30), + ([10, 20, 30], 31, 0, 10), + ([10, 20, 30], 31, 1, 20), + ([10, 20, 30], 31, 2, 1), + ], + ids=[ + "interior-0", + "interior-1", + "boundary-clipped", + "exact-no-clip", + "single-element-boundary-0", + "single-element-boundary-1", + "single-element-boundary-2", + ], +) +def test_varying_dimension_boundary_data_size( + edges: list[int], extent: int, chunk_idx: int, expected_data_size: int +) -> None: + """VaryingDimension.data_size clips correctly at boundary chunks""" + d = VaryingDimension(edges, extent=extent) + assert d.data_size(chunk_idx) == expected_data_size + + +def test_varying_dimension_boundary_extent_parameter() -> None: + """VaryingDimension preserves extent and full chunk_size even when extent < sum of edges""" + d = VaryingDimension([10, 20, 30], extent=50) + assert d.extent == 50 + assert d.chunk_size(2) == 30 + + +def test_varying_dimension_extent_exceeds_sum_rejected() -> None: + """VaryingDimension rejects extent greater than sum of edges""" + with pytest.raises(ValueError, match="exceeds sum of edges"): + VaryingDimension([10, 20], extent=50) + + +def test_varying_dimension_negative_extent_rejected() -> None: + """VaryingDimension rejects negative extent""" + with pytest.raises(ValueError, match="must be >= 0"): + VaryingDimension([10, 20], extent=-1) + + +def test_varying_dimension_zero_extent() -> None: + """VaryingDimension with extent=0 has zero active chunks but retains all grid cells.""" + d = VaryingDimension([10, 20], extent=0) + assert d.nchunks == 0 + assert d.ngridcells == 2 + # No chunks overlap [0, 0), so the grid is structurally non-empty but logically empty + g = ChunkGrid(dimensions=(d,)) + assert g.grid_shape == (0,) + assert list(g) == [] + + +def test_varying_dimension_boundary_chunk_spec() -> None: + """ChunkGrid with a boundary VaryingDimension produces correct ChunkSpec.""" + g = ChunkGrid(dimensions=(VaryingDimension([10, 20, 30], extent=50),)) + spec = g[(2,)] + assert spec is not None + assert spec.codec_shape == (30,) + assert spec.shape == (20,) + assert spec.is_boundary is True + + +def test_varying_dimension_interior_chunk_spec() -> None: + """Interior VaryingDimension chunk has matching codec_shape and shape with no boundary""" + g = ChunkGrid(dimensions=(VaryingDimension([10, 20, 30], extent=50),)) + spec = g[(0,)] + assert spec is not None + assert spec.codec_shape == (10,) + assert spec.shape == (10,) + assert spec.is_boundary is False + + +# --------------------------------------------------------------------------- +# Multiple overflow chunks tests +# --------------------------------------------------------------------------- + + +def test_overflow_multiple_chunks_past_extent() -> None: + """Edges past extent are structural; nchunks counts active only.""" + g = ChunkGrid.from_sizes((50,), [[10, 20, 30, 40]]) + d = g._dimensions[0] + assert d.ngridcells == 4 + assert d.nchunks == 3 + assert d.data_size(0) == 10 + assert d.data_size(1) == 20 + assert d.data_size(2) == 20 + assert d.chunk_size(2) == 30 + + +def test_overflow_chunk_spec_past_extent_is_oob() -> None: + """Chunk entirely past the extent is out of bounds (not active).""" + g = ChunkGrid.from_sizes((50,), [[10, 20, 30, 40]]) + spec = g[(3,)] + assert spec is None + + +def test_overflow_chunk_spec_partial() -> None: + """ChunkSpec for a partially-overflowing chunk clips correctly.""" + g = ChunkGrid.from_sizes((50,), [[10, 20, 30, 40]]) + spec = g[(2,)] + assert spec is not None + assert spec.shape == (20,) + assert spec.codec_shape == (30,) + assert spec.is_boundary is True + assert spec.slices == (slice(30, 50, 1),) + + +def test_overflow_chunk_sizes() -> None: + """chunk_sizes only includes active chunks.""" + g = ChunkGrid.from_sizes((50,), [[10, 20, 30, 40]]) + assert g.chunk_sizes == ((10, 20, 20),) + + +def test_overflow_multidim() -> None: + """Overflow in multiple dimensions simultaneously.""" + g = ChunkGrid.from_sizes((45, 100), [[10, 20, 30], [40, 40, 40]]) + assert g.chunk_sizes == ((10, 20, 15), (40, 40, 20)) + spec = g[(2, 2)] + assert spec is not None + assert spec.shape == (15, 20) + assert spec.codec_shape == (30, 40) + + +def test_overflow_uniform_edges_collapses_to_fixed() -> None: + """Uniform edges where len == ceildiv(extent, edge) collapse to FixedDimension.""" + g = ChunkGrid.from_sizes((35,), [[10, 10, 10, 10]]) + assert isinstance(g._dimensions[0], FixedDimension) + assert g.is_regular + assert g.chunk_sizes == ((10, 10, 10, 5),) + assert g._dimensions[0].nchunks == 4 + + +def test_overflow_index_to_chunk_near_extent() -> None: + """Index lookup near and at the extent boundary.""" + d = VaryingDimension([10, 20, 30, 40], extent=50) + assert d.index_to_chunk(29) == 1 + assert d.index_to_chunk(30) == 2 + assert d.index_to_chunk(49) == 2 + + +# --------------------------------------------------------------------------- +# Boundary indexing tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ( + "dim", + "mask", + "dim_len", + "expected_chunk_ix", + "expected_sel_len", + "expected_first_two", + "expected_third", + ), + [ + ( + FixedDimension(size=5, extent=7), + np.array([False, False, False, False, False, True, True]), + 7, + 1, + 5, + (np.True_, np.True_), + np.False_, + ), + ( + VaryingDimension([5, 10], extent=7), + np.array([False, False, False, False, False, True, True]), + 7, + 1, + 10, + (np.True_, np.True_), + np.False_, + ), + ], + ids=["fixed-boundary", "varying-boundary"], +) +def test_bool_indexer_boundary( + dim: FixedDimension | VaryingDimension, + mask: np.ndarray[Any, Any], + dim_len: int, + expected_chunk_ix: int, + expected_sel_len: int, + expected_first_two: tuple[Any, Any], + expected_third: Any, +) -> None: + """BoolArrayDimIndexer pads to codec size for boundary chunks.""" + from zarr.core.indexing import BoolArrayDimIndexer + + indexer = BoolArrayDimIndexer(mask, dim_len, dim) + projections = list(indexer) + assert len(projections) == 1 + p = projections[0] + assert p.dim_chunk_ix == expected_chunk_ix + sel = p.dim_chunk_sel + assert isinstance(sel, np.ndarray) + assert sel.shape[0] == expected_sel_len + assert sel[0] is expected_first_two[0] + assert sel[1] is expected_first_two[1] + assert sel[2] is expected_third + + +def test_bool_indexer_no_padding_interior() -> None: + """No padding needed for interior chunks.""" + from zarr.core.indexing import BoolArrayDimIndexer + + dim = FixedDimension(size=5, extent=10) + mask = np.array([True, False, False, False, False, False, False, False, False, False]) + indexer = BoolArrayDimIndexer(mask, 10, dim) + projections = list(indexer) + assert len(projections) == 1 + p = projections[0] + assert p.dim_chunk_ix == 0 + sel = p.dim_chunk_sel + assert isinstance(sel, np.ndarray) + assert sel.shape[0] == 5 + + +def test_slice_indexer_varying_boundary() -> None: + """SliceDimIndexer clips to data_size at boundary for VaryingDimension.""" + from zarr.core.indexing import SliceDimIndexer + + dim = VaryingDimension([5, 10], extent=7) + indexer = SliceDimIndexer(slice(None), 7, dim) + projections = list(indexer) + assert len(projections) == 2 + assert projections[0].dim_chunk_sel == slice(0, 5, 1) + assert projections[1].dim_chunk_sel == slice(0, 2, 1) + + +def test_int_array_indexer_varying_boundary() -> None: + """IntArrayDimIndexer handles indices near boundary correctly.""" + from zarr.core.indexing import IntArrayDimIndexer + + dim = VaryingDimension([5, 10], extent=7) + indices = np.array([6]) + indexer = IntArrayDimIndexer(indices, 7, dim) + projections = list(indexer) + assert len(projections) == 1 + assert projections[0].dim_chunk_ix == 1 + sel = projections[0].dim_chunk_sel + assert isinstance(sel, np.ndarray) + np.testing.assert_array_equal(sel, [1]) + + +@pytest.mark.parametrize( + "dim", + [FixedDimension(size=2, extent=10), VaryingDimension([5, 5], extent=10)], + ids=["fixed", "varying"], +) +def test_slice_indexer_empty_slice_at_boundary(dim: FixedDimension | VaryingDimension) -> None: + """SliceDimIndexer yields no projections for an empty slice at the dimension boundary.""" + from zarr.core.indexing import SliceDimIndexer + + indexer = SliceDimIndexer(slice(10, 10), 10, dim) + projections = list(indexer) + assert len(projections) == 0 + + +def test_orthogonal_indexer_varying_boundary_advanced() -> None: + """OrthogonalIndexer with advanced indexing uses per-chunk chunk_size.""" + from zarr.core.indexing import OrthogonalIndexer + + g = ChunkGrid( + dimensions=( + VaryingDimension([5, 10], extent=7), + FixedDimension(size=4, extent=8), + ) + ) + indexer = OrthogonalIndexer( + selection=(np.array([0, 6]), slice(None)), + shape=(7, 8), + chunk_grid=g, + ) + projections = list(indexer) + assert len(projections) == 4 + coords = {p.chunk_coords for p in projections} + assert coords == {(0, 0), (0, 1), (1, 0), (1, 1)} + + +# --------------------------------------------------------------------------- +# update_shape tests +# --------------------------------------------------------------------------- + + +def test_update_shape_no_change() -> None: + """update_shape with the same shape preserves edges unchanged""" + grid = ChunkGrid.from_sizes((60, 50), [[10, 20, 30], [25, 25]]) + new_grid = grid.update_shape((60, 50)) + assert _edges(new_grid, 0) == (10, 20, 30) + assert _edges(new_grid, 1) == (25, 25) + + +def test_update_shape_grow_single_dim() -> None: + """Growing a single dimension appends a new edge chunk""" + grid = ChunkGrid.from_sizes((60, 50), [[10, 20, 30], [25, 25]]) + new_grid = grid.update_shape((80, 50)) + assert _edges(new_grid, 0) == (10, 20, 30, 20) + assert _edges(new_grid, 1) == (25, 25) + + +def test_update_shape_grow_multiple_dims() -> None: + """Growing multiple dimensions appends correctly sized edge chunks""" + grid = ChunkGrid.from_sizes((30, 50), [[10, 20], [20, 30]]) + new_grid = grid.update_shape((45, 65)) + assert _edges(new_grid, 0) == (10, 20, 15) + assert _edges(new_grid, 1) == (20, 30, 15) + + +def test_update_shape_shrink_single_dim() -> None: + """Shrinking a single dimension reduces nchunks while preserving edges""" + grid = ChunkGrid.from_sizes((100, 50), [[10, 20, 30, 40], [25, 25]]) + new_grid = grid.update_shape((35, 50)) + assert _edges(new_grid, 0) == (10, 20, 30, 40) + assert new_grid._dimensions[0].nchunks == 3 + assert _edges(new_grid, 1) == (25, 25) + + +def test_update_shape_shrink_to_single_chunk() -> None: + """Shrinking to fit within the first chunk reduces nchunks to 1""" + grid = ChunkGrid.from_sizes((60, 50), [[10, 20, 30], [25, 25]]) + new_grid = grid.update_shape((5, 50)) + assert _edges(new_grid, 0) == (10, 20, 30) + assert new_grid._dimensions[0].nchunks == 1 + assert _edges(new_grid, 1) == (25, 25) + + +def test_update_shape_shrink_multiple_dims() -> None: + """Shrinking multiple dimensions reduces nchunks in each dimension""" + grid = ChunkGrid.from_sizes((40, 60), [[10, 10, 15, 5], [20, 25, 15]]) + new_grid = grid.update_shape((25, 35)) + assert _edges(new_grid, 0) == (10, 10, 15, 5) + assert new_grid._dimensions[0].nchunks == 3 + assert _edges(new_grid, 1) == (20, 25, 15) + assert new_grid._dimensions[1].nchunks == 2 + + +def test_update_shape_dimension_mismatch_error() -> None: + """update_shape raises ValueError when new shape has different ndim""" + grid = ChunkGrid.from_sizes((30, 70), [[10, 20], [30, 40]]) + with pytest.raises(ValueError, match="dimensions"): + grid.update_shape((30, 70, 100)) + + +def test_update_shape_boundary_cases() -> None: + """update_shape handles grow-one-dim and shrink-both-dims edge cases correctly""" + grid = ChunkGrid.from_sizes((60, 40), [[10, 20, 30], [15, 25]]) + new_grid = grid.update_shape((60, 65)) + assert _edges(new_grid, 0) == (10, 20, 30) + assert _edges(new_grid, 1) == (15, 25, 25) + + grid2 = ChunkGrid.from_sizes((60, 50), [[10, 20, 30], [15, 25, 10]]) + new_grid2 = grid2.update_shape((30, 40)) + assert _edges(new_grid2, 0) == (10, 20, 30) + assert new_grid2._dimensions[0].nchunks == 2 + assert _edges(new_grid2, 1) == (15, 25, 10) + assert new_grid2._dimensions[1].nchunks == 2 + + +def test_update_shape_regular_preserves_extents(tmp_path: Path) -> None: + """Resize a regular array -- chunk_grid extents must match new shape.""" + z = zarr.create_array( + store=tmp_path / "regular.zarr", + shape=(100,), + chunks=(10,), + dtype="int32", + ) + z[:] = np.arange(100, dtype="int32") + z.resize(50) + assert z.shape == (50,) + assert ChunkGrid.from_metadata(z.metadata)._dimensions[0].extent == 50 + + +# --------------------------------------------------------------------------- +# update_shape boundary tests +# --------------------------------------------------------------------------- + + +def test_update_shape_shrink_creates_boundary() -> None: + """Shrinking extent into a chunk creates a boundary with clipped data_size""" + grid = ChunkGrid.from_sizes((60,), [[10, 20, 30]]) + new_grid = grid.update_shape((45,)) + dim = new_grid._dimensions[0] + assert isinstance(dim, VaryingDimension) + assert dim.edges == (10, 20, 30) + assert dim.extent == 45 + assert dim.chunk_size(2) == 30 + assert dim.data_size(2) == 15 + + +def test_update_shape_shrink_to_exact_boundary() -> None: + """Shrinking to an exact chunk boundary reduces nchunks without partial data""" + grid = ChunkGrid.from_sizes((60,), [[10, 20, 30]]) + new_grid = grid.update_shape((30,)) + dim = new_grid._dimensions[0] + assert isinstance(dim, VaryingDimension) + assert dim.edges == (10, 20, 30) + assert dim.nchunks == 2 + assert dim.ngridcells == 3 + assert dim.extent == 30 + assert dim.data_size(1) == 20 + + +def test_update_shape_shrink_chunk_spec() -> None: + """After shrink, ChunkSpec reflects boundary correctly.""" + grid = ChunkGrid.from_sizes((60,), [[10, 20, 30]]) + new_grid = grid.update_shape((45,)) + spec = new_grid[(2,)] + assert spec is not None + assert spec.codec_shape == (30,) + assert spec.shape == (15,) + assert spec.is_boundary is True + + +def test_update_shape_parse_chunk_grid_rebinds_extent() -> None: + """parse_chunk_grid re-binds VaryingDimension extent to array shape.""" + g = ChunkGrid.from_sizes((60,), [[10, 20, 30]]) + g2 = ChunkGrid( + dimensions=tuple( + dim.with_extent(ext) for dim, ext in zip(g._dimensions, (50,), strict=True) + ) + ) + dim = g2._dimensions[0] + assert isinstance(dim, VaryingDimension) + assert dim.extent == 50 + assert dim.data_size(2) == 20 + + +# --------------------------------------------------------------------------- +# Resize rectilinear tests +# --------------------------------------------------------------------------- + + +async def test_async_resize_grow() -> None: + """Async resize grow appends new edge chunks and preserves existing data""" + store = zarr.storage.MemoryStore() + arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(30, 40), + chunks=[[10, 20], [20, 20]], + dtype="i4", + zarr_format=3, + ) + data = np.arange(30 * 40, dtype="i4").reshape(30, 40) + await arr.setitem(slice(None), data) + + await arr.resize((50, 60)) + assert arr.shape == (50, 60) + assert _edges(ChunkGrid.from_metadata(arr.metadata), 0) == (10, 20, 20) + assert _edges(ChunkGrid.from_metadata(arr.metadata), 1) == (20, 20, 20) + result = await arr.getitem((slice(0, 30), slice(0, 40))) + np.testing.assert_array_equal(result, data) + + +async def test_async_resize_shrink() -> None: + """Async resize shrink truncates data to the new shape""" + store = zarr.storage.MemoryStore() + arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(60, 50), + chunks=[[10, 20, 30], [25, 25]], + dtype="f4", + zarr_format=3, + ) + data = np.arange(60 * 50, dtype="f4").reshape(60, 50) + await arr.setitem(slice(None), data) + + await arr.resize((25, 30)) + assert arr.shape == (25, 30) + result = await arr.getitem(slice(None)) + np.testing.assert_array_equal(result, data[:25, :30]) + + +def test_sync_resize_grow() -> None: + """Sync resize grow expands the array and preserves existing data""" + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, + shape=(20, 30), + chunks=[[8, 12], [10, 20]], + dtype="u1", + zarr_format=3, + ) + data = np.arange(20 * 30, dtype="u1").reshape(20, 30) + arr[:] = data + arr.resize((35, 45)) + assert arr.shape == (35, 45) + np.testing.assert_array_equal(arr[:20, :30], data) + + +def test_sync_resize_shrink() -> None: + """Sync resize shrink truncates the array and returns correct data""" + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, + shape=(40, 50), + chunks=[[10, 15, 15], [20, 30]], + dtype="i2", + zarr_format=3, + ) + data = np.arange(40 * 50, dtype="i2").reshape(40, 50) + arr[:] = data + arr.resize((15, 30)) + assert arr.shape == (15, 30) + np.testing.assert_array_equal(arr[:], data[:15, :30]) + + +# --------------------------------------------------------------------------- +# Append rectilinear tests +# --------------------------------------------------------------------------- + + +async def test_append_first_axis() -> None: + """Appending along axis 0 grows the array and concatenates data correctly""" + store = zarr.storage.MemoryStore() + arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(30, 20), + chunks=[[10, 20], [10, 10]], + dtype="i4", + zarr_format=3, + ) + initial = np.arange(30 * 20, dtype="i4").reshape(30, 20) + await arr.setitem(slice(None), initial) + + append_data = np.arange(30 * 20, 45 * 20, dtype="i4").reshape(15, 20) + await arr.append(append_data, axis=0) + assert arr.shape == (45, 20) + + result = await arr.getitem(slice(None)) + np.testing.assert_array_equal(result, np.vstack([initial, append_data])) + + +async def test_append_second_axis() -> None: + """Appending along axis 1 grows the array and concatenates data correctly""" + store = zarr.storage.MemoryStore() + arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(20, 30), + chunks=[[10, 10], [10, 20]], + dtype="f4", + zarr_format=3, + ) + initial = np.arange(20 * 30, dtype="f4").reshape(20, 30) + await arr.setitem(slice(None), initial) + + append_data = np.arange(20 * 30, 20 * 45, dtype="f4").reshape(20, 15) + await arr.append(append_data, axis=1) + assert arr.shape == (20, 45) + + result = await arr.getitem(slice(None)) + np.testing.assert_array_equal(result, np.hstack([initial, append_data])) + + +def test_sync_append() -> None: + """Sync append grows the array and preserves both initial and appended data""" + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, + shape=(20, 20), + chunks=[[8, 12], [7, 13]], + dtype="u2", + zarr_format=3, + ) + initial = np.arange(20 * 20, dtype="u2").reshape(20, 20) + arr[:] = initial + + append_data = np.arange(20 * 20, 25 * 20, dtype="u2").reshape(5, 20) + arr.append(append_data, axis=0) + assert arr.shape == (25, 20) + np.testing.assert_array_equal(arr[:20, :], initial) + np.testing.assert_array_equal(arr[20:, :], append_data) + + +async def test_multiple_appends() -> None: + """Multiple sequential appends accumulate data correctly""" + store = zarr.storage.MemoryStore() + arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(10, 10), + chunks=[[3, 7], [4, 6]], + dtype="i4", + zarr_format=3, + ) + initial = np.arange(10 * 10, dtype="i4").reshape(10, 10) + await arr.setitem(slice(None), initial) + + all_data = [initial] + for i in range(3): + chunk = np.full((5, 10), i + 100, dtype="i4") + await arr.append(chunk, axis=0) + all_data.append(chunk) + + assert arr.shape == (25, 10) + result = await arr.getitem(slice(None)) + np.testing.assert_array_equal(result, np.vstack(all_data)) + + +async def test_append_with_partial_edge_chunks() -> None: + """Appending data that creates partial edge chunks preserves all data""" + store = zarr.storage.MemoryStore() + arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(25, 30), + chunks=[[10, 15], [12, 18]], + dtype="f8", + zarr_format=3, + ) + initial = np.random.default_rng(42).random((25, 30)) + await arr.setitem(slice(None), initial) + + append_data = np.random.default_rng(43).random((10, 30)) + await arr.append(append_data, axis=0) + assert arr.shape == (35, 30) + + result = np.asarray(await arr.getitem(slice(None))) + np.testing.assert_array_almost_equal(result, np.vstack([initial, append_data])) + + +async def test_append_small_data() -> None: + """Appending a small amount of data smaller than a chunk works correctly""" + store = zarr.storage.MemoryStore() + arr = await zarr.api.asynchronous.create_array( + store=store, + shape=(20, 20), + chunks=[[8, 12], [7, 13]], + dtype="i4", + zarr_format=3, + ) + data = np.arange(20 * 20, dtype="i4").reshape(20, 20) + await arr.setitem(slice(None), data) + + small = np.full((3, 20), 999, dtype="i4") + await arr.append(small, axis=0) + assert arr.shape == (23, 20) + result = await arr.getitem((slice(20, 23), slice(None))) + np.testing.assert_array_equal(result, small) + + +# --------------------------------------------------------------------------- +# V2 regression tests +# --------------------------------------------------------------------------- + + +def test_v2_create_and_readback(tmp_path: Path) -> None: + """Basic V2 array: create, write, read back.""" + data = np.arange(60, dtype="float64").reshape(6, 10) + a = zarr.create_array( + store=tmp_path / "v2.zarr", + shape=data.shape, + chunks=(3, 5), + dtype=data.dtype, + zarr_format=2, + ) + a[:] = data + np.testing.assert_array_equal(a[:], data) + + +def test_v2_chunk_grid_is_regular(tmp_path: Path) -> None: + """V2 chunk_grid produces a regular ChunkGrid with FixedDimensions.""" + a = zarr.create_array( + store=tmp_path / "v2.zarr", + shape=(20, 30), + chunks=(10, 15), + dtype="int32", + zarr_format=2, + ) + grid = ChunkGrid.from_metadata(a.metadata) + assert grid.is_regular + assert grid.chunk_shape == (10, 15) + assert grid.grid_shape == (2, 2) + assert all(isinstance(d, FixedDimension) for d in grid._dimensions) + + +def test_v2_boundary_chunks(tmp_path: Path) -> None: + """V2 boundary chunks: codec buffer size stays full, data is clipped.""" + a = zarr.create_array( + store=tmp_path / "v2.zarr", + shape=(25,), + chunks=(10,), + dtype="int32", + zarr_format=2, + ) + grid = ChunkGrid.from_metadata(a.metadata) + assert grid._dimensions[0].nchunks == 3 + assert grid._dimensions[0].chunk_size(2) == 10 + assert grid._dimensions[0].data_size(2) == 5 + + +def test_v2_slicing_with_boundary(tmp_path: Path) -> None: + """V2 array slicing across boundary chunks returns correct data.""" + data = np.arange(25, dtype="int32") + a = zarr.create_array( + store=tmp_path / "v2.zarr", + shape=(25,), + chunks=(10,), + dtype="int32", + zarr_format=2, + ) + a[:] = data + np.testing.assert_array_equal(a[18:25], data[18:25]) + np.testing.assert_array_equal(a[:], data) + + +def test_v2_metadata_roundtrip(tmp_path: Path) -> None: + """V2 metadata survives store close and reopen.""" + store_path = tmp_path / "v2.zarr" + data = np.arange(12, dtype="float32").reshape(3, 4) + a = zarr.create_array( + store=store_path, + shape=data.shape, + chunks=(2, 2), + dtype=data.dtype, + zarr_format=2, + ) + a[:] = data + + b = zarr.open_array(store=store_path, mode="r") + assert b.metadata.zarr_format == 2 + assert b.chunks == (2, 2) + assert ChunkGrid.from_metadata(b.metadata).chunk_shape == (2, 2) + np.testing.assert_array_equal(b[:], data) + + +def test_v2_chunk_spec_via_grid(tmp_path: Path) -> None: + """ChunkSpec from V2 grid has correct slices and codec_shape.""" + a = zarr.create_array( + store=tmp_path / "v2.zarr", + shape=(15, 20), + chunks=(10, 10), + dtype="int32", + zarr_format=2, + ) + grid = ChunkGrid.from_metadata(a.metadata) + spec = grid[(0, 0)] + assert spec is not None + assert spec.shape == (10, 10) + assert spec.codec_shape == (10, 10) + spec = grid[(1, 1)] + assert spec is not None + assert spec.shape == (5, 10) + assert spec.codec_shape == (10, 10) + + +# --------------------------------------------------------------------------- +# ChunkSizes tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("shape", "chunks", "expected"), + [ + ((100, 80), (30, 40), ((30, 30, 30, 10), (40, 40))), + ((90, 80), (30, 40), ((30, 30, 30), (40, 40))), + ((60, 100), [[10, 20, 30], [50, 50]], ((10, 20, 30), (50, 50))), + ((10,), (10,), ((10,),)), + ], + ids=["regular", "regular-exact", "rectilinear", "single-chunk"], +) +def test_chunk_sizes( + shape: tuple[int, ...], chunks: Any, expected: tuple[tuple[int, ...], ...] +) -> None: + """chunk_sizes returns the per-dimension tuple of actual data sizes""" + grid = ChunkGrid.from_sizes(shape, chunks) + assert grid.chunk_sizes == expected + + +def test_array_read_chunk_sizes_regular() -> None: + """Regular array exposes correct read_chunk_sizes and write_chunk_sizes""" + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, shape=(100, 80), chunks=(30, 40), dtype="i4", zarr_format=3 + ) + assert arr.read_chunk_sizes == ((30, 30, 30, 10), (40, 40)) + assert arr.write_chunk_sizes == ((30, 30, 30, 10), (40, 40)) + + +def test_array_read_chunk_sizes_rectilinear() -> None: + """Rectilinear array exposes correct read_chunk_sizes and write_chunk_sizes""" + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, shape=(60, 100), chunks=[[10, 20, 30], [50, 50]], dtype="i4", zarr_format=3 + ) + assert arr.read_chunk_sizes == ((10, 20, 30), (50, 50)) + assert arr.write_chunk_sizes == ((10, 20, 30), (50, 50)) + + +def test_array_sharded_chunk_sizes() -> None: + """Sharded array read_chunk_sizes reflects inner chunks and write_chunk_sizes reflects shards""" + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, + shape=(120, 80), + chunks=(60, 40), + shards=(120, 80), + dtype="i4", + zarr_format=3, + ) + assert arr.read_chunk_sizes == ((60, 60), (40, 40)) + assert arr.write_chunk_sizes == ((120,), (80,)) + + +# --------------------------------------------------------------------------- +# Info display test +# --------------------------------------------------------------------------- + + +def test_chunk_grid_repr_regular() -> None: + """ChunkGrid repr shows uniform chunk sizes and array shape for regular grids.""" + grid = ChunkGrid.from_sizes((100, 200), (10, 20)) + r = repr(grid) + assert r == "ChunkGrid(chunk_sizes=(10, 20), array_shape=(100, 200))" + + +def test_chunk_grid_repr_rectilinear() -> None: + """ChunkGrid repr shows per-chunk edge tuples for rectilinear dimensions.""" + grid = ChunkGrid.from_sizes((30,), ([10, 20],)) + r = repr(grid) + assert "(10, 20)" in r + assert "(30,)" in r + + +def test_info_display_rectilinear() -> None: + """Array.info should not crash for rectilinear grids.""" + store = zarr.storage.MemoryStore() + arr = zarr.create_array( + store=store, + shape=(30,), + chunks=[[10, 20]], + dtype="i4", + zarr_format=3, + ) + info = arr.info + text = repr(info) + assert "" in text + assert "Array" in text + + +# --------------------------------------------------------------------------- +# nchunks tests +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("shape", "chunks", "expected"), + [ + ((30,), [[10, 20]], 2), + ((30, 40), [[10, 20], [15, 25]], 4), + ], + ids=["1d", "2d"], +) +def test_nchunks_rectilinear( + shape: tuple[int, ...], chunks: list[list[int]], expected: int +) -> None: + """Array.nchunks reports correct total chunk count for rectilinear arrays""" + store = MemoryStore() + a = zarr.create_array(store, shape=shape, chunks=chunks, dtype="int32") + assert a.nchunks == expected + + +# --------------------------------------------------------------------------- +# iter_chunk_regions test +# --------------------------------------------------------------------------- + + +def test_iter_chunk_regions_rectilinear() -> None: + """_iter_chunk_regions should work for rectilinear arrays.""" + from zarr.core.array import _iter_chunk_regions + + store = MemoryStore() + a = zarr.create_array(store, shape=(30,), chunks=[[10, 20]], dtype="int32") + regions = list(_iter_chunk_regions(a)) + assert len(regions) == 2 + assert regions[0] == (slice(0, 10, 1),) + assert regions[1] == (slice(10, 30, 1),) + + +# --------------------------------------------------------------------------- +# RectilinearChunkGridMetadata metadata object tests (already parametrized) +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("json_input", "expected_chunk_shapes"), + [ + ( + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [4, 8]}, + }, + (4, 8), + ), + ( + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[1, 2, 3], [10, 20]]}, + }, + ((1, 2, 3), (10, 20)), + ), + ( + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[[4, 3]], [10, 20]]}, + }, + ((4, 4, 4), (10, 20)), + ), + ( + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[[1, 3], 3], [5]]}, + }, + ((1, 1, 1, 3), (5,)), + ), + ( + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [4, [10, 20]]}, + }, + (4, (10, 20)), + ), + ], +) +def test_rectilinear_from_dict( + json_input: RectilinearChunkGridMetadataJSON, + expected_chunk_shapes: tuple[int | tuple[int, ...], ...], +) -> None: + """RectilinearChunkGridMetadata.from_dict correctly parses all spec forms.""" + grid = RectilinearChunkGridMetadata.from_dict(json_input) + assert grid.chunk_shapes == expected_chunk_shapes + + +@pytest.mark.parametrize( + ("chunk_shapes", "expected_json_shapes"), + [ + ((4, 8), [4, 8]), + (((4,), (8,)), [[4], [8]]), + (((10, 20), (5, 5)), [[10, 20], [[5, 2]]]), + (((4, 4, 4), (10, 20)), [[[4, 3]], [10, 20]]), + ((4, (10, 20)), [4, [10, 20]]), + ], +) +def test_rectilinear_to_dict( + chunk_shapes: tuple[int | tuple[int, ...], ...], + expected_json_shapes: list[Any], +) -> None: + """RectilinearChunkGridMetadata.to_dict serializes back to spec-compliant JSON.""" + grid = RectilinearChunkGridMetadata(chunk_shapes=chunk_shapes) + result = grid.to_dict() + assert result["name"] == "rectilinear" + assert result["configuration"]["kind"] == "inline" + assert list(result["configuration"]["chunk_shapes"]) == expected_json_shapes + + +@pytest.mark.parametrize( + "json_input", + [ + {"name": "rectilinear", "configuration": {"kind": "inline", "chunk_shapes": [4, 8]}}, + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[1, 2, 3], [10, 20]]}, + }, + { + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[[4, 3]], [[5, 2]]]}, + }, + ], +) +def test_rectilinear_roundtrip(json_input: RectilinearChunkGridMetadataJSON) -> None: + """from_dict -> to_dict -> from_dict produces the same grid.""" + grid1 = RectilinearChunkGridMetadata.from_dict(json_input) + grid2 = RectilinearChunkGridMetadata.from_dict(grid1.to_dict()) + assert grid1.chunk_shapes == grid2.chunk_shapes + + +# --------------------------------------------------------------------------- +# Hypothesis property tests +# --------------------------------------------------------------------------- + + +pytest.importorskip("hypothesis") + +import hypothesis.strategies as st # noqa: E402 +from hypothesis import event, given, settings # noqa: E402 + + +@st.composite +def rectilinear_chunks_st(draw: st.DrawFn, *, shape: tuple[int, ...]) -> list[list[int]]: + """Generate valid rectilinear chunk shapes for a given array shape.""" + chunk_shapes: list[list[int]] = [] + for size in shape: + assert size > 0 + max_chunks = min(size, 10) + nchunks = draw(st.integers(min_value=1, max_value=max_chunks)) + if nchunks == 1: + chunk_shapes.append([size]) + else: + dividers = sorted( + draw( + st.lists( + st.integers(min_value=1, max_value=size - 1), + min_size=nchunks - 1, + max_size=nchunks - 1, + unique=True, + ) + ) + ) + chunk_shapes.append( + [a - b for a, b in zip(dividers + [size], [0] + dividers, strict=False)] + ) + return chunk_shapes + + +@st.composite +def rectilinear_arrays_st(draw: st.DrawFn) -> tuple[zarr.Array[Any], np.ndarray[Any, Any]]: + """Generate a rectilinear zarr array with random data, shape, and chunks.""" + from zarr.storage import MemoryStore + + ndim = draw(st.integers(min_value=1, max_value=3)) + shape = draw(st.tuples(*[st.integers(min_value=2, max_value=20) for _ in range(ndim)])) + chunk_shapes = draw(rectilinear_chunks_st(shape=shape)) + event(f"ndim={ndim}, shape={shape}") + + a = np.arange(int(np.prod(shape)), dtype="int32").reshape(shape) + store = MemoryStore() + z = zarr.create_array(store=store, shape=shape, chunks=chunk_shapes, dtype="int32") + z[:] = a + return z, a + + +@settings(deadline=None, max_examples=50) +@given(data=st.data()) +def test_property_block_indexing_rectilinear(data: st.DataObject) -> None: + """Property test: block indexing on rectilinear arrays matches numpy.""" + z, a = data.draw(rectilinear_arrays_st()) + grid = ChunkGrid.from_metadata(z.metadata) + + for dim in range(a.ndim): + dim_grid = grid._dimensions[dim] + block_ix = data.draw(st.integers(min_value=0, max_value=dim_grid.nchunks - 1)) + sel = [slice(None)] * a.ndim + start = dim_grid.chunk_offset(block_ix) + stop = start + dim_grid.data_size(block_ix) + sel[dim] = slice(start, stop) + block_sel: list[slice | int] = [slice(None)] * a.ndim + block_sel[dim] = block_ix + np.testing.assert_array_equal( + z.blocks[tuple(block_sel)], + a[tuple(sel)], + err_msg=f"dim={dim}, block={block_ix}", + ) From c966cfacbc647522ab5630e2965d880b380e946a Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Tue, 7 Apr 2026 13:44:19 -0400 Subject: [PATCH 269/468] Pin mkdocs<2 (#3881) --- pyproject.toml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index bcab8dd105..93ef8c5e4b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -110,7 +110,7 @@ remote-tests = [ docs = [ # Doc building "mkdocs-material[imaging]>=9.6.14", - "mkdocs>=1.6.1", + "mkdocs>=1.6.1,<2", "mkdocstrings>=0.29.1", "mkdocstrings-python>=1.16.10", "mike>=2.1.3", @@ -255,6 +255,10 @@ installer = "uv" features = ['remote'] dependency-groups = ['docs'] +[tool.hatch.envs.docs.env-vars] +DISABLE_MKDOCS_2_WARNING = "true" +NO_MKDOCS_2_WARNING = "true" + [tool.hatch.envs.docs.scripts] serve = "mkdocs serve --watch src" build = "mkdocs build" From bd23984c9ff9df536127493cbbce4f0c32b90440 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Wed, 8 Apr 2026 12:33:10 -0400 Subject: [PATCH 270/468] chore: add a CI workflow that identifies unlinked types (#3882) Co-authored-by: Davis Bennett --- .github/workflows/docs.yml | 31 ++++++++++++++ ci/check_unlinked_types.py | 88 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 119 insertions(+) create mode 100644 .github/workflows/docs.yml create mode 100644 ci/check_unlinked_types.py diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000000..6d380e1304 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,31 @@ +name: Docs + +on: + push: + branches: [main] + pull_request: + branches: [main] + workflow_dispatch: + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + docs: + name: Check docs + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + - uses: astral-sh/setup-uv@f0ec1fc3b38f5e7cd731bb6ce540c5af426746bb # v6.1.0 + - run: uv sync --group docs + - run: uv run mkdocs build + env: + DISABLE_MKDOCS_2_WARNING: "true" + NO_MKDOCS_2_WARNING: "true" + - run: uv run python ci/check_unlinked_types.py diff --git a/ci/check_unlinked_types.py b/ci/check_unlinked_types.py new file mode 100644 index 0000000000..3ccfaab397 --- /dev/null +++ b/ci/check_unlinked_types.py @@ -0,0 +1,88 @@ +"""Check for unlinked type annotations in built documentation. + +mkdocstrings renders resolved types as links and unresolved +types as Name without an anchor. +This script finds all such unlinked types in the built HTML and reports them. + +Usage: + python ci/check_unlinked_types.py [site_dir] + +Raises ValueError if unlinked types are found. +""" + +from __future__ import annotations + +import re +import sys +from pathlib import Path + +# Matches the griffe/mkdocstrings pattern for unlinked cross-references: +# Name +UNLINKED_PATTERN = re.compile( + r'(?P[^<]+)' +) + +# Patterns to exclude from the report +EXCLUDE_PATTERNS = [ + # TypeVars and type parameters (single brackets like Foo[T]) + re.compile(r"\[.+\]$"), + # Dataclass field / namedtuple field references (contain parens) + re.compile(r"\("), + # Private names + re.compile(r"\._"), + # Dunder attributes + re.compile(r"\.__\w+__$"), + # Testing utilities + re.compile(r"^zarr\.testing\."), + # Third-party types (hypothesis, pytest, etc.) + re.compile(r"^(hypothesis|pytest|typing_extensions|builtins|dataclasses)\."), +] + + +def should_exclude(qualname: str) -> bool: + return any(p.search(qualname) for p in EXCLUDE_PATTERNS) + + +def find_unlinked_types(site_dir: Path) -> dict[str, set[str]]: + """Find all unlinked types in built HTML files. + + Returns a dict mapping qualified type names to the set of pages where they appear. + """ + api_dir = site_dir / "api" + if not api_dir.exists(): + raise FileNotFoundError(f"{api_dir} does not exist. Run 'mkdocs build' first.") + + unlinked: dict[str, set[str]] = {} + for html_file in api_dir.rglob("*.html"): + content = html_file.read_text(errors="replace") + rel_path = str(html_file.relative_to(site_dir)) + for match in UNLINKED_PATTERN.finditer(content): + qualname = match.group("qualname") + if not should_exclude(qualname): + unlinked.setdefault(qualname, set()).add(rel_path) + + return unlinked + + +def main() -> None: + site_dir = Path(sys.argv[1]) if len(sys.argv) > 1 else Path("site") + unlinked = find_unlinked_types(site_dir) + + if not unlinked: + print("No unlinked types found.") + return + + lines = [f"Found {len(unlinked)} unlinked types:\n"] + for qualname in sorted(unlinked): + pages = sorted(unlinked[qualname]) + lines.append(f" {qualname}") + lines.extend(f" - {page}" for page in pages) + + all_pages = {p for ps in unlinked.values() for p in ps} + lines.append(f"\nTotal: {len(unlinked)} unlinked types across {len(all_pages)} pages") + report = "\n".join(lines) + raise ValueError(report) + + +if __name__ == "__main__": + main() From 85dfbcb2adb7c7bd157b908ceb23e772c9604b45 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 9 Apr 2026 14:44:59 +0200 Subject: [PATCH 271/468] chore: prefix registry variable names with a single underscore (#3894) * chore: prefix registry variable names with a single underscore * fix: fix test --- src/zarr/registry.py | 86 +++++++++++++++++----------------- tests/test_metadata/test_v3.py | 2 +- 2 files changed, 44 insertions(+), 44 deletions(-) diff --git a/src/zarr/registry.py b/src/zarr/registry.py index a1938b575c..8f3879a2a3 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -57,11 +57,11 @@ def register(self, cls: type[T], qualname: str | None = None) -> None: self[qualname] = cls -__codec_registries: dict[str, Registry[Codec]] = defaultdict(Registry) -__pipeline_registry: Registry[CodecPipeline] = Registry() -__buffer_registry: Registry[Buffer] = Registry() -__ndbuffer_registry: Registry[NDBuffer] = Registry() -__chunk_key_encoding_registry: Registry[ChunkKeyEncoding] = Registry() +_codec_registries: dict[str, Registry[Codec]] = defaultdict(Registry) +_pipeline_registry: Registry[CodecPipeline] = Registry() +_buffer_registry: Registry[Buffer] = Registry() +_ndbuffer_registry: Registry[NDBuffer] = Registry() +_chunk_key_encoding_registry: Registry[ChunkKeyEncoding] = Registry() """ The registry module is responsible for managing implementations of codecs, @@ -93,37 +93,37 @@ def _collect_entrypoints() -> list[Registry[Any]]: """ entry_points = get_entry_points() - __buffer_registry.lazy_load_list.extend(entry_points.select(group="zarr.buffer")) - __buffer_registry.lazy_load_list.extend(entry_points.select(group="zarr", name="buffer")) - __ndbuffer_registry.lazy_load_list.extend(entry_points.select(group="zarr.ndbuffer")) - __ndbuffer_registry.lazy_load_list.extend(entry_points.select(group="zarr", name="ndbuffer")) + _buffer_registry.lazy_load_list.extend(entry_points.select(group="zarr.buffer")) + _buffer_registry.lazy_load_list.extend(entry_points.select(group="zarr", name="buffer")) + _ndbuffer_registry.lazy_load_list.extend(entry_points.select(group="zarr.ndbuffer")) + _ndbuffer_registry.lazy_load_list.extend(entry_points.select(group="zarr", name="ndbuffer")) data_type_registry._lazy_load_list.extend(entry_points.select(group="zarr.data_type")) data_type_registry._lazy_load_list.extend(entry_points.select(group="zarr", name="data_type")) - __chunk_key_encoding_registry.lazy_load_list.extend( + _chunk_key_encoding_registry.lazy_load_list.extend( entry_points.select(group="zarr.chunk_key_encoding") ) - __chunk_key_encoding_registry.lazy_load_list.extend( + _chunk_key_encoding_registry.lazy_load_list.extend( entry_points.select(group="zarr", name="chunk_key_encoding") ) - __pipeline_registry.lazy_load_list.extend(entry_points.select(group="zarr.codec_pipeline")) - __pipeline_registry.lazy_load_list.extend( + _pipeline_registry.lazy_load_list.extend(entry_points.select(group="zarr.codec_pipeline")) + _pipeline_registry.lazy_load_list.extend( entry_points.select(group="zarr", name="codec_pipeline") ) for e in entry_points.select(group="zarr.codecs"): - __codec_registries[e.name].lazy_load_list.append(e) + _codec_registries[e.name].lazy_load_list.append(e) for group in entry_points.groups: if group.startswith("zarr.codecs."): codec_name = group.split(".")[2] - __codec_registries[codec_name].lazy_load_list.extend(entry_points.select(group=group)) + _codec_registries[codec_name].lazy_load_list.extend(entry_points.select(group=group)) return [ - *__codec_registries.values(), - __pipeline_registry, - __buffer_registry, - __ndbuffer_registry, - __chunk_key_encoding_registry, + *_codec_registries.values(), + _pipeline_registry, + _buffer_registry, + _ndbuffer_registry, + _chunk_key_encoding_registry, ] @@ -137,36 +137,36 @@ def fully_qualified_name(cls: type) -> str: def register_codec(key: str, codec_cls: type[Codec], *, qualname: str | None = None) -> None: - if key not in __codec_registries: - __codec_registries[key] = Registry() - __codec_registries[key].register(codec_cls, qualname=qualname) + if key not in _codec_registries: + _codec_registries[key] = Registry() + _codec_registries[key].register(codec_cls, qualname=qualname) def register_pipeline(pipe_cls: type[CodecPipeline]) -> None: - __pipeline_registry.register(pipe_cls) + _pipeline_registry.register(pipe_cls) def register_ndbuffer(cls: type[NDBuffer], qualname: str | None = None) -> None: - __ndbuffer_registry.register(cls, qualname) + _ndbuffer_registry.register(cls, qualname) def register_buffer(cls: type[Buffer], qualname: str | None = None) -> None: - __buffer_registry.register(cls, qualname) + _buffer_registry.register(cls, qualname) def register_chunk_key_encoding(key: str, cls: type) -> None: - __chunk_key_encoding_registry.register(cls, key) + _chunk_key_encoding_registry.register(cls, key) def get_codec_class(key: str, reload_config: bool = False) -> type[Codec]: if reload_config: _reload_config() - if key in __codec_registries: + if key in _codec_registries: # logger.debug("Auto loading codec '%s' from entrypoint", codec_id) - __codec_registries[key].lazy_load() + _codec_registries[key].lazy_load() - codec_classes = __codec_registries[key] + codec_classes = _codec_registries[key] if not codec_classes: raise KeyError(key) config_entry = config.get("codecs", {}).get(key) @@ -257,50 +257,50 @@ def _parse_array_array_codec(data: dict[str, JSON] | Codec) -> ArrayArrayCodec: def get_pipeline_class(reload_config: bool = False) -> type[CodecPipeline]: if reload_config: _reload_config() - __pipeline_registry.lazy_load() + _pipeline_registry.lazy_load() path = config.get("codec_pipeline.path") - pipeline_class = __pipeline_registry.get(path) + pipeline_class = _pipeline_registry.get(path) if pipeline_class: return pipeline_class raise BadConfigError( - f"Pipeline class '{path}' not found in registered pipelines: {list(__pipeline_registry)}." + f"Pipeline class '{path}' not found in registered pipelines: {list(_pipeline_registry)}." ) def get_buffer_class(reload_config: bool = False) -> type[Buffer]: if reload_config: _reload_config() - __buffer_registry.lazy_load() + _buffer_registry.lazy_load() path = config.get("buffer") - buffer_class = __buffer_registry.get(path) + buffer_class = _buffer_registry.get(path) if buffer_class: return buffer_class raise BadConfigError( - f"Buffer class '{path}' not found in registered buffers: {list(__buffer_registry)}." + f"Buffer class '{path}' not found in registered buffers: {list(_buffer_registry)}." ) def get_ndbuffer_class(reload_config: bool = False) -> type[NDBuffer]: if reload_config: _reload_config() - __ndbuffer_registry.lazy_load() + _ndbuffer_registry.lazy_load() path = config.get("ndbuffer") - ndbuffer_class = __ndbuffer_registry.get(path) + ndbuffer_class = _ndbuffer_registry.get(path) if ndbuffer_class: return ndbuffer_class raise BadConfigError( - f"NDBuffer class '{path}' not found in registered buffers: {list(__ndbuffer_registry)}." + f"NDBuffer class '{path}' not found in registered buffers: {list(_ndbuffer_registry)}." ) def get_chunk_key_encoding_class(key: str) -> type[ChunkKeyEncoding]: - __chunk_key_encoding_registry.lazy_load(use_entrypoint_name=True) - if key not in __chunk_key_encoding_registry: + _chunk_key_encoding_registry.lazy_load(use_entrypoint_name=True) + if key not in _chunk_key_encoding_registry: raise KeyError( - f"Chunk key encoding '{key}' not found in registered chunk key encodings: {list(__chunk_key_encoding_registry)}." + f"Chunk key encoding '{key}' not found in registered chunk key encodings: {list(_chunk_key_encoding_registry)}." ) - return __chunk_key_encoding_registry[key] + return _chunk_key_encoding_registry[key] _collect_entrypoints() diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 01ed921053..8658b7b393 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -341,7 +341,7 @@ def test_parse_codecs_unknown_codec_raises(monkeypatch: pytest.MonkeyPatch) -> N from zarr.registry import Registry # to make sure the codec is always unknown (not sure if that's necessary) - monkeypatch.setattr(zarr.registry, "__codec_registries", defaultdict(Registry)) + monkeypatch.setattr(zarr.registry, "_codec_registries", defaultdict(Registry)) codecs = [{"name": "unknown"}] with pytest.raises(UnknownCodecError): From 9681cf998a006f4a5f50f90a4ff288b1e3bba606 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 9 Apr 2026 09:39:18 -0400 Subject: [PATCH 272/468] chore: update failure conditions for docs workflow (#3887) Co-authored-by: Davis Bennett --- .github/workflows/docs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6d380e1304..005dfa2af8 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -29,3 +29,4 @@ jobs: DISABLE_MKDOCS_2_WARNING: "true" NO_MKDOCS_2_WARNING: "true" - run: uv run python ci/check_unlinked_types.py + continue-on-error: true From e6207b77835d3cbaff0c4f7d26873ce5b50b95e5 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 13 Apr 2026 18:39:14 +0200 Subject: [PATCH 273/468] fix: simplify and fix codspeed workflow (#3895) --- .github/workflows/codspeed.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 91226c19a3..8d67cf18d9 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -27,10 +27,6 @@ jobs: with: fetch-depth: 0 persist-credentials: false - - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 - with: - python-version: "3.11" - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: @@ -39,4 +35,4 @@ jobs: uses: CodSpeedHQ/action@1c8ae4843586d3ba879736b7f6b7b0c990757fab # v4.12.1 with: mode: walltime - run: hatch run test.py3.11-minimal:pytest tests/benchmarks --codspeed + run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed From 9391f43412a86fa4f0ab1ee1c5c9fa4f4bea118c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 13 Apr 2026 21:43:47 +0200 Subject: [PATCH 274/468] chore: remove deprecated convenience and creation modules (#3900) * chore: remove deprecated convenience and creation modules * docs: remove references to deprecated modules from docs * docs: changelog * docs: remove redirect to absent page --- changes/3900.misc.md | 1 + docs/api/zarr/convenience.md | 10 ------ docs/api/zarr/deprecated/convenience.md | 1 - docs/api/zarr/deprecated/creation.md | 1 - docs/api/zarr/index.md | 8 ----- mkdocs.yml | 5 --- src/zarr/api/asynchronous.py | 4 +-- src/zarr/api/synchronous.py | 4 +-- src/zarr/convenience.py | 44 ----------------------- src/zarr/creation.py | 47 ------------------------- 10 files changed, 5 insertions(+), 120 deletions(-) create mode 100644 changes/3900.misc.md delete mode 100644 docs/api/zarr/convenience.md delete mode 100644 docs/api/zarr/deprecated/convenience.md delete mode 100644 docs/api/zarr/deprecated/creation.md delete mode 100644 src/zarr/convenience.py delete mode 100644 src/zarr/creation.py diff --git a/changes/3900.misc.md b/changes/3900.misc.md new file mode 100644 index 0000000000..d38de0ce2e --- /dev/null +++ b/changes/3900.misc.md @@ -0,0 +1 @@ +Remove deprecated `zarr.convenience` and `zarr.creation` modules. \ No newline at end of file diff --git a/docs/api/zarr/convenience.md b/docs/api/zarr/convenience.md deleted file mode 100644 index f2614e3724..0000000000 --- a/docs/api/zarr/convenience.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -title: convenience ---- - -::: zarr.consolidate_metadata -::: zarr.copy -::: zarr.copy_all -::: zarr.copy_store -::: zarr.print_debug_info -::: zarr.tree diff --git a/docs/api/zarr/deprecated/convenience.md b/docs/api/zarr/deprecated/convenience.md deleted file mode 100644 index 91bcb15f71..0000000000 --- a/docs/api/zarr/deprecated/convenience.md +++ /dev/null @@ -1 +0,0 @@ -::: zarr.convenience \ No newline at end of file diff --git a/docs/api/zarr/deprecated/creation.md b/docs/api/zarr/deprecated/creation.md deleted file mode 100644 index 5d18a06a4a..0000000000 --- a/docs/api/zarr/deprecated/creation.md +++ /dev/null @@ -1 +0,0 @@ -::: zarr.creation diff --git a/docs/api/zarr/index.md b/docs/api/zarr/index.md index f6ae2bda83..194edb7913 100644 --- a/docs/api/zarr/index.md +++ b/docs/api/zarr/index.md @@ -21,7 +21,6 @@ Complete reference documentation for the Zarr-Python API. - **[Load](load.md)** - Loading data from Zarr stores - **[Save](save.md)** - Saving data to Zarr format -- **[Convenience](convenience.md)** - High-level convenience functions ### Data Types and Configuration @@ -55,13 +54,6 @@ The ABC module defines interfaces for extending Zarr: - **[Testing](testing/index.md)** - Utilities for testing Zarr-based code -## Migration and Compatibility - -- **[Deprecated Functions](deprecated/convenience.md)** - Legacy convenience functions -- **[Deprecated Creation](deprecated/creation.md)** - Legacy array creation functions - -These deprecated modules are maintained for backward compatibility but should be avoided in new code. - ## Getting Help - Check the [User Guide](../../user-guide/index.md) for tutorials and examples diff --git a/mkdocs.yml b/mkdocs.yml index ce39fd0f2e..7a4bfa35ef 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -43,7 +43,6 @@ nav: - api/zarr/codecs.md - api/zarr/codecs/numcodecs.md - api/zarr/config.md - - api/zarr/convenience.md - api/zarr/errors.md - api/zarr/metadata.md - api/zarr/registry.md @@ -72,9 +71,6 @@ nav: - api/zarr/testing/store.md - api/zarr/testing/strategies.md - api/zarr/testing/utils.md - - deprecated: - - Convenience sub-module: api/zarr/deprecated/convenience.md - - Creation sub-module: api/zarr/deprecated/creation.md - release-notes.md - contributing.md watch: @@ -221,7 +217,6 @@ plugins: 'developers/contributing.html.md': 'contributing.md' 'developers/index.html.md': 'contributing.md' 'developers/roadmap.html.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' - 'api/zarr/creation.md': 'api/zarr/deprecated/creation.md' 'api.md': 'api/zarr/index.md' 'api/zarr/metadata/migrate_v3.md': 'api/zarr/metadata.md' diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index c776176665..60c0e6c97a 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -359,8 +359,8 @@ async def open( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Additional parameters are passed through to [`zarr.creation.open_array`][] or - [`open_group`][zarr.api.asynchronous.open_group]. + Additional parameters are passed through to `zarr.open_array` or + `zarr.open_group`. Returns ------- diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index a865f97646..688f2a110d 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -206,8 +206,8 @@ def open( If using an fsspec URL to create the store, these will be passed to the backend implementation. Ignored otherwise. **kwargs - Additional parameters are passed through to [`zarr.creation.open_array`][] or - [`open_group`][zarr.api.asynchronous.open_group]. + Additional parameters are passed through to `zarr.open_array` or + `zarr.open_group`. Returns ------- diff --git a/src/zarr/convenience.py b/src/zarr/convenience.py deleted file mode 100644 index 391ffc5186..0000000000 --- a/src/zarr/convenience.py +++ /dev/null @@ -1,44 +0,0 @@ -""" -Convenience helpers. - -!!! warning "Deprecated" - This sub-module is deprecated. All functions here are defined in the top level zarr namespace instead. -""" - -import warnings - -from zarr.api.synchronous import ( - consolidate_metadata, - copy, - copy_all, - copy_store, - load, - open, - open_consolidated, - save, - save_array, - save_group, - tree, -) -from zarr.errors import ZarrDeprecationWarning - -__all__ = [ - "consolidate_metadata", - "copy", - "copy_all", - "copy_store", - "load", - "open", - "open_consolidated", - "save", - "save_array", - "save_group", - "tree", -] - -warnings.warn( - "zarr.convenience is deprecated. " - "Import these functions from the top level zarr. namespace instead.", - ZarrDeprecationWarning, - stacklevel=2, -) diff --git a/src/zarr/creation.py b/src/zarr/creation.py deleted file mode 100644 index 605b5af5de..0000000000 --- a/src/zarr/creation.py +++ /dev/null @@ -1,47 +0,0 @@ -""" -Helpers for creating arrays. - -!!! warning "Deprecated" - This sub-module is deprecated. All functions here are defined in the top level zarr namespace instead. - -""" - -import warnings - -from zarr.api.synchronous import ( - array, - create, - empty, - empty_like, - full, - full_like, - ones, - ones_like, - open_array, - open_like, - zeros, - zeros_like, -) -from zarr.errors import ZarrDeprecationWarning - -__all__ = [ - "array", - "create", - "empty", - "empty_like", - "full", - "full_like", - "ones", - "ones_like", - "open_array", - "open_like", - "zeros", - "zeros_like", -] - -warnings.warn( - "zarr.creation is deprecated. " - "Import these functions from the top level zarr. namespace instead.", - ZarrDeprecationWarning, - stacklevel=2, -) From 0ea15fd7a2d898ffa445aeacbba9ad64707c9117 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 14 Apr 2026 07:31:10 +0200 Subject: [PATCH 275/468] chore: remove .create methods from arrays (#3903) --- changes/3903.misc.md | 1 + src/zarr/core/array.py | 412 ----------------------------- tests/test_api/test_synchronous.py | 2 - 3 files changed, 1 insertion(+), 414 deletions(-) create mode 100644 changes/3903.misc.md diff --git a/changes/3903.misc.md b/changes/3903.misc.md new file mode 100644 index 0000000000..7dc0a83177 --- /dev/null +++ b/changes/3903.misc.md @@ -0,0 +1 @@ +Remove deprecated `AsyncArray.create` and `Array.create` methods. \ No newline at end of file diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 4736805b9d..f0cd5dd734 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -366,273 +366,6 @@ def __init__( create_codec_pipeline(metadata=metadata_parsed, store=store_path.store), ) - # this overload defines the function signature when zarr_format is 2 - @overload - @classmethod - async def create( - cls, - store: StoreLike, - *, - # v2 and v3 - shape: ShapeLike, - dtype: ZDTypeLike, - zarr_format: Literal[2], - fill_value: Any | None = DEFAULT_FILL_VALUE, - attributes: dict[str, JSON] | None = None, - chunks: ShapeLike | None = None, - dimension_separator: Literal[".", "/"] | None = None, - order: MemoryOrder | None = None, - filters: list[dict[str, JSON]] | None = None, - compressor: CompressorLikev2 | Literal["auto"] = "auto", - # runtime - overwrite: bool = False, - data: npt.ArrayLike | None = None, - config: ArrayConfigLike | None = None, - ) -> AsyncArrayV2: ... - - # this overload defines the function signature when zarr_format is 3 - @overload - @classmethod - async def create( - cls, - store: StoreLike, - *, - # v2 and v3 - shape: ShapeLike, - dtype: ZDTypeLike, - zarr_format: Literal[3], - fill_value: Any | None = DEFAULT_FILL_VALUE, - attributes: dict[str, JSON] | None = None, - # v3 only - chunk_shape: ShapeLike | None = None, - chunk_key_encoding: ( - ChunkKeyEncoding - | tuple[Literal["default"], Literal[".", "/"]] - | tuple[Literal["v2"], Literal[".", "/"]] - | None - ) = None, - codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNamesLike = None, - # runtime - overwrite: bool = False, - data: npt.ArrayLike | None = None, - config: ArrayConfigLike | None = None, - ) -> AsyncArrayV3: ... - - @overload - @classmethod - async def create( - cls, - store: StoreLike, - *, - # v2 and v3 - shape: ShapeLike, - dtype: ZDTypeLike, - zarr_format: Literal[3] = 3, - fill_value: Any | None = DEFAULT_FILL_VALUE, - attributes: dict[str, JSON] | None = None, - # v3 only - chunk_shape: ShapeLike | None = None, - chunk_key_encoding: ( - ChunkKeyEncoding - | tuple[Literal["default"], Literal[".", "/"]] - | tuple[Literal["v2"], Literal[".", "/"]] - | None - ) = None, - codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNamesLike = None, - # runtime - overwrite: bool = False, - data: npt.ArrayLike | None = None, - config: ArrayConfigLike | None = None, - ) -> AsyncArrayV3: ... - - @overload - @classmethod - async def create( - cls, - store: StoreLike, - *, - # v2 and v3 - shape: ShapeLike, - dtype: ZDTypeLike, - zarr_format: ZarrFormat, - fill_value: Any | None = DEFAULT_FILL_VALUE, - attributes: dict[str, JSON] | None = None, - # v3 only - chunk_shape: ShapeLike | None = None, - chunk_key_encoding: ( - ChunkKeyEncoding - | tuple[Literal["default"], Literal[".", "/"]] - | tuple[Literal["v2"], Literal[".", "/"]] - | None - ) = None, - codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNamesLike = None, - # v2 only - chunks: ShapeLike | None = None, - dimension_separator: Literal[".", "/"] | None = None, - order: MemoryOrder | None = None, - filters: list[dict[str, JSON]] | None = None, - compressor: CompressorLike = "auto", - # runtime - overwrite: bool = False, - data: npt.ArrayLike | None = None, - config: ArrayConfigLike | None = None, - ) -> AnyAsyncArray: ... - - @classmethod - @deprecated("Use zarr.api.asynchronous.create_array instead.", category=ZarrDeprecationWarning) - async def create( - cls, - store: StoreLike, - *, - # v2 and v3 - shape: ShapeLike, - dtype: ZDTypeLike, - zarr_format: ZarrFormat = 3, - fill_value: Any | None = DEFAULT_FILL_VALUE, - attributes: dict[str, JSON] | None = None, - # v3 only - chunk_shape: ShapeLike | None = None, - chunk_key_encoding: ( - ChunkKeyEncodingLike - | tuple[Literal["default"], Literal[".", "/"]] - | tuple[Literal["v2"], Literal[".", "/"]] - | None - ) = None, - codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNamesLike = None, - # v2 only - chunks: ShapeLike | None = None, - dimension_separator: Literal[".", "/"] | None = None, - order: MemoryOrder | None = None, - filters: list[dict[str, JSON]] | None = None, - compressor: CompressorLike = "auto", - # runtime - overwrite: bool = False, - data: npt.ArrayLike | None = None, - config: ArrayConfigLike | None = None, - ) -> AnyAsyncArray: - """Method to create a new asynchronous array instance. - - !!! warning "Deprecated" - `AsyncArray.create()` is deprecated since v3.0.0 and will be removed in a future release. - Use [`zarr.api.asynchronous.create_array`][] instead. - - Parameters - ---------- - store : StoreLike - The store where the array will be created. See the - [storage documentation in the user guide][user-guide-store-like] - for a description of all valid StoreLike values. - shape : ShapeLike - The shape of the array. - dtype : ZDTypeLike - The data type of the array. - zarr_format : ZarrFormat, optional - The Zarr format version (default is 3). - fill_value : Any, optional - The fill value of the array (default is None). - attributes : dict[str, JSON], optional - The attributes of the array (default is None). - chunk_shape : tuple[int, ...], optional - The shape of the array's chunks - Zarr format 3 only. Zarr format 2 arrays should use `chunks` instead. - If not specified, default are guessed based on the shape and dtype. - chunk_key_encoding : ChunkKeyEncodingLike, optional - A specification of how the chunk keys are represented in storage. - Zarr format 3 only. Zarr format 2 arrays should use `dimension_separator` instead. - Default is ``("default", "/")``. - codecs : Sequence of Codecs or dicts, optional - An iterable of Codec or dict serializations of Codecs. The elements of - this collection specify the transformation from array values to stored bytes. - Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. - - If no codecs are provided, default codecs will be used: - dimension_names : Iterable[str | None], optional - The names of the dimensions (default is None). - Zarr format 3 only. Zarr format 2 arrays should not use this parameter. - chunks : ShapeLike, optional - The shape of the array's chunks. - Zarr format 2 only. Zarr format 3 arrays should use ``chunk_shape`` instead. - If not specified, default are guessed based on the shape and dtype. - dimension_separator : Literal[".", "/"], optional - The dimension separator (default is "."). - Zarr format 2 only. Zarr format 3 arrays should use ``chunk_key_encoding`` instead. - order : Literal["C", "F"], optional - The memory of the array (default is "C"). - If ``zarr_format`` is 2, this parameter sets the memory order of the array. - If ``zarr_format`` is 3, then this parameter is deprecated, because memory order - is a runtime parameter for Zarr 3 arrays. The recommended way to specify the memory - order for Zarr 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. - filters : Iterable[Codec] | Literal["auto"], optional - Iterable of filters to apply to each chunk of the array, in order, before serializing that - chunk to bytes. - - For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a - dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. - - For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. - - The default value of ``"auto"`` instructs Zarr to use a default used based on the data - type of the array and the Zarr format specified. For all data types in Zarr V3, and most - data types in Zarr V2, the default filters are empty. The only cases where default filters - are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, - the default filters contains a single element which is a codec specific to that particular data type. - - To create an array with no filters, provide an empty iterable or the value ``None``. - compressor : dict[str, JSON], optional - The compressor used to compress the data (default is None). - Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. - - If no ``compressor`` is provided, a default compressor will be used: - - - For numeric arrays, the default is ``ZstdCodec``. - - For Unicode strings, the default is ``VLenUTF8Codec``. - - For bytes or objects, the default is ``VLenBytesCodec``. - - These defaults can be changed by modifying the value of ``array.v2_default_compressor`` in [`zarr.config`][zarr.config]. - overwrite : bool, optional - Whether to raise an error if the store already exists (default is False). - data : npt.ArrayLike, optional - The data to be inserted into the array (default is None). - config : ArrayConfigLike, optional - Runtime configuration for the array. - - Returns - ------- - AsyncArray - The created asynchronous array instance. - """ - return await cls._create( - store, - # v2 and v3 - shape=shape, - dtype=dtype, - zarr_format=zarr_format, - fill_value=fill_value, - attributes=attributes, - # v3 only - chunk_shape=chunk_shape, - chunk_key_encoding=chunk_key_encoding, - codecs=codecs, - dimension_names=dimension_names, - # v2 only - chunks=chunks, - dimension_separator=dimension_separator, - order=order, - filters=filters, - compressor=compressor, - # runtime - overwrite=overwrite, - data=data, - config=config, - ) - @classmethod async def _create( cls, @@ -2086,151 +1819,6 @@ def _chunk_grid(self) -> ChunkGrid: """The chunk grid for this array, bound to the array's shape.""" return self.async_array._chunk_grid - @classmethod - @deprecated("Use zarr.create_array instead.", category=ZarrDeprecationWarning) - def create( - cls, - store: StoreLike, - *, - # v2 and v3 - shape: tuple[int, ...], - dtype: ZDTypeLike, - zarr_format: ZarrFormat = 3, - fill_value: Any | None = DEFAULT_FILL_VALUE, - attributes: dict[str, JSON] | None = None, - # v3 only - chunk_shape: tuple[int, ...] | None = None, - chunk_key_encoding: ( - ChunkKeyEncoding - | tuple[Literal["default"], Literal[".", "/"]] - | tuple[Literal["v2"], Literal[".", "/"]] - | None - ) = None, - codecs: Iterable[Codec | dict[str, JSON]] | None = None, - dimension_names: DimensionNamesLike = None, - # v2 only - chunks: tuple[int, ...] | None = None, - dimension_separator: Literal[".", "/"] | None = None, - order: MemoryOrder | None = None, - filters: list[dict[str, JSON]] | None = None, - compressor: CompressorLike = "auto", - # runtime - overwrite: bool = False, - config: ArrayConfigLike | None = None, - ) -> AnyArray: - """Creates a new Array instance from an initialized store. - - !!! warning "Deprecated" - `Array.create()` is deprecated since v3.0.0 and will be removed in a future release. - Use [`zarr.create_array`][] instead. - - Parameters - ---------- - store : StoreLike - The array store that has already been initialized. See the - [storage documentation in the user guide][user-guide-store-like] - for a description of all valid StoreLike values. - shape : tuple[int, ...] - The shape of the array. - dtype : ZDTypeLike - The data type of the array. - chunk_shape : tuple[int, ...], optional - The shape of the Array's chunks. - Zarr format 3 only. Zarr format 2 arrays should use `chunks` instead. - If not specified, default are guessed based on the shape and dtype. - chunk_key_encoding : ChunkKeyEncodingLike, optional - A specification of how the chunk keys are represented in storage. - Zarr format 3 only. Zarr format 2 arrays should use `dimension_separator` instead. - Default is ``("default", "/")``. - codecs : Sequence of Codecs or dicts, optional - An iterable of Codec or dict serializations of Codecs. The elements of - this collection specify the transformation from array values to stored bytes. - Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. - - If no codecs are provided, default codecs will be used: - - - For numeric arrays, the default is ``BytesCodec`` and ``ZstdCodec``. - - For Unicode strings, the default is ``VLenUTF8Codec`` and ``ZstdCodec``. - - For bytes or objects, the default is ``VLenBytesCodec`` and ``ZstdCodec``. - dimension_names : Iterable[str | None], optional - The names of the dimensions (default is None). - Zarr format 3 only. Zarr format 2 arrays should not use this parameter. - chunks : tuple[int, ...], optional - The shape of the array's chunks. - Zarr format 2 only. Zarr format 3 arrays should use ``chunk_shape`` instead. - If not specified, default are guessed based on the shape and dtype. - dimension_separator : Literal[".", "/"], optional - The dimension separator (default is "."). - Zarr format 2 only. Zarr format 3 arrays should use ``chunk_key_encoding`` instead. - order : Literal["C", "F"], optional - The memory of the array (default is "C"). - If ``zarr_format`` is 2, this parameter sets the memory order of the array. - If ``zarr_format`` is 3, then this parameter is deprecated, because memory order - is a runtime parameter for Zarr 3 arrays. The recommended way to specify the memory - order for Zarr 3 arrays is via the ``config`` parameter, e.g. ``{'order': 'C'}``. - - filters : Iterable[Codec] | Literal["auto"], optional - Iterable of filters to apply to each chunk of the array, in order, before serializing that - chunk to bytes. - - For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a - dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. - - For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. - - The default value of ``"auto"`` instructs Zarr to use a default used based on the data - type of the array and the Zarr format specified. For all data types in Zarr V3, and most - data types in Zarr V2, the default filters are empty. The only cases where default filters - are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, - the default filters contains a single element which is a codec specific to that particular data type. - - To create an array with no filters, provide an empty iterable or the value ``None``. - compressor : dict[str, JSON], optional - Primary compressor to compress chunk data. - Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. - - If no ``compressor`` is provided, a default compressor will be used: - - - For numeric arrays, the default is ``ZstdCodec``. - - For Unicode strings, the default is ``VLenUTF8Codec``. - - For bytes or objects, the default is ``VLenBytesCodec``. - - These defaults can be changed by modifying the value of ``array.v2_default_compressor`` in [`zarr.config`][zarr.config]. - overwrite : bool, optional - Whether to raise an error if the store already exists (default is False). - - Returns - ------- - Array - Array created from the store. - """ - return cls._create( - store, - # v2 and v3 - shape=shape, - dtype=dtype, - zarr_format=zarr_format, - attributes=attributes, - fill_value=fill_value, - # v3 only - chunk_shape=chunk_shape, - chunk_key_encoding=chunk_key_encoding, - codecs=codecs, - dimension_names=dimension_names, - # v2 only - chunks=chunks, - dimension_separator=dimension_separator, - order=order, - filters=filters, - compressor=compressor, - # runtime - overwrite=overwrite, - config=config, - ) - @classmethod def _create( cls, diff --git a/tests/test_api/test_synchronous.py b/tests/test_api/test_synchronous.py index d6ae61f1ca..55d89d73de 100644 --- a/tests/test_api/test_synchronous.py +++ b/tests/test_api/test_synchronous.py @@ -64,8 +64,6 @@ def test_docstrings_match(callable_name: str) -> None: asynchronous.create, synchronous.create, zarr.Group.create, - zarr.AsyncArray.create, - zarr.Array.create, ), ), ( From 2fbd30aa0eb7b57a73d698b935cbd1e88c25faab Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 15 Apr 2026 09:16:48 +0200 Subject: [PATCH 276/468] chore: clean up metadata tests (#3897) * chore: make types more accurate * test: add test helpers and simplify metadata tests * chore: lint * changelog * chore: bump typing-extensions * Update src/zarr/core/metadata/v3.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * test: add tests for ARRAY_METADATA_KEYS --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3897.misc.md | 2 + pyproject.toml | 4 +- src/zarr/core/metadata/v3.py | 55 ++- tests/conftest.py | 19 + tests/test_metadata/conftest.py | 41 +++ tests/test_metadata/test_v3.py | 613 +++++++++++++------------------- 6 files changed, 350 insertions(+), 384 deletions(-) create mode 100644 changes/3897.misc.md create mode 100644 tests/test_metadata/conftest.py diff --git a/changes/3897.misc.md b/changes/3897.misc.md new file mode 100644 index 0000000000..53b2bd9b52 --- /dev/null +++ b/changes/3897.misc.md @@ -0,0 +1,2 @@ +Bump the minimum version of `typing-extensions` to 4.13 to support the `extra_items` +keyword argument on `TypedDict` (PEP 728). \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 93ef8c5e4b..b4783b5be3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,7 @@ dependencies = [ 'numpy>=2', 'numcodecs>=0.14', 'google-crc32c>=1.5', - 'typing_extensions>=4.12', + 'typing_extensions>=4.13', 'donfig>=0.8', ] @@ -243,7 +243,7 @@ extra-dependencies = [ 'fsspec==2023.10.0', 's3fs==2023.10.0', 'universal_pathlib==0.2.0', - 'typing_extensions==4.12.*', + 'typing_extensions==4.13.*', 'donfig==0.8.*', 'obstore==0.5.*', ] diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 7773e2489d..a8f2b05518 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -3,7 +3,9 @@ import json from collections.abc import Iterable, Mapping, Sequence from dataclasses import dataclass, field, replace -from typing import TYPE_CHECKING, Any, Literal, NotRequired, TypedDict, TypeGuard, cast +from typing import TYPE_CHECKING, Any, Final, Literal, NotRequired, TypeGuard, cast + +from typing_extensions import TypedDict from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec from zarr.abc.metadata import Metadata @@ -136,10 +138,11 @@ def parse_storage_transformers(data: object) -> tuple[dict[str, JSON], ...]: ) -class AllowedExtraField(TypedDict): +class AllowedExtraField(TypedDict, extra_items=JSON): # type: ignore[call-arg] """ This class models allowed extra fields in array metadata. - They are ignored by Zarr Python. + They must have ``must_understand`` set to ``False``, and may contain + arbitrary additional JSON data. """ must_understand: Literal[False] @@ -411,25 +414,43 @@ def parse_chunk_grid( raise ValueError(f"Unknown chunk grid name: {name!r}") -class ArrayMetadataJSON_V3(TypedDict): +class ArrayMetadataJSON_V3(TypedDict, extra_items=AllowedExtraField): # type: ignore[call-arg] """ - A typed dictionary model for zarr v3 metadata. + A typed dictionary model for zarr v3 array metadata. + + Extra keys are permitted if they conform to ``AllowedExtraField`` + (i.e. they are mappings with ``must_understand: false``). """ zarr_format: Literal[3] node_type: Literal["array"] - data_type: str | NamedConfig[str, Mapping[str, object]] + data_type: str | NamedConfig[str, Mapping[str, JSON]] shape: tuple[int, ...] - chunk_grid: NamedConfig[str, Mapping[str, object]] - chunk_key_encoding: NamedConfig[str, Mapping[str, object]] - fill_value: object - codecs: tuple[str | NamedConfig[str, Mapping[str, object]], ...] + chunk_grid: str | NamedConfig[str, Mapping[str, JSON]] + chunk_key_encoding: str | NamedConfig[str, Mapping[str, JSON]] + fill_value: JSON + codecs: tuple[str | NamedConfig[str, Mapping[str, JSON]], ...] attributes: NotRequired[Mapping[str, JSON]] - storage_transformers: NotRequired[tuple[NamedConfig[str, Mapping[str, object]], ...]] - dimension_names: NotRequired[tuple[str | None]] - - -ARRAY_METADATA_KEYS = set(ArrayMetadataJSON_V3.__annotations__.keys()) + storage_transformers: NotRequired[tuple[str | NamedConfig[str, Mapping[str, JSON]], ...]] + dimension_names: NotRequired[tuple[str | None, ...]] + + +""" +The names of the fields of the array metadata document defined in the zarr V3 spec. +""" +ARRAY_METADATA_KEYS: Final[set[str]] = { + "zarr_format", + "node_type", + "data_type", + "shape", + "chunk_grid", + "chunk_key_encoding", + "fill_value", + "codecs", + "attributes", + "storage_transformers", + "dimension_names", +} @dataclass(frozen=True, kw_only=True) @@ -617,8 +638,8 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: return cls( shape=_data_typed["shape"], - chunk_grid=_data_typed["chunk_grid"], - chunk_key_encoding=_data_typed["chunk_key_encoding"], + chunk_grid=_data_typed["chunk_grid"], # type: ignore[arg-type] + chunk_key_encoding=_data_typed["chunk_key_encoding"], # type: ignore[arg-type] codecs=_data_typed["codecs"], attributes=_data_typed.get("attributes", {}), # type: ignore[arg-type] dimension_names=_data_typed.get("dimension_names", None), diff --git a/tests/conftest.py b/tests/conftest.py index a02006d6a9..bc9b8c35aa 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -58,6 +58,25 @@ from zarr.core.dtype.wrapper import ZDType +@dataclass +class Expect[TIn, TOut]: + """A test case with explicit input, expected output, and a human-readable id.""" + + input: TIn + output: TOut + id: str + + +@dataclass +class ExpectFail[TIn]: + """A test case that should raise an exception.""" + + input: TIn + exception: type[Exception] + id: str + msg: str | None = None + + async def parse_store( store: Literal["local", "memory", "fsspec", "zip", "memory_get_latency"], path: str ) -> LocalStore | MemoryStore | FsspecStore | ZipStore | LatencyStore: diff --git a/tests/test_metadata/conftest.py b/tests/test_metadata/conftest.py new file mode 100644 index 0000000000..24f2417fce --- /dev/null +++ b/tests/test_metadata/conftest.py @@ -0,0 +1,41 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +from zarr.codecs.bytes import BytesCodec + +if TYPE_CHECKING: + from zarr.core.metadata.v3 import ArrayMetadataJSON_V3 + + +def minimal_metadata_dict_v3( + extra_fields: dict[str, Any] | None = None, **overrides: Any +) -> ArrayMetadataJSON_V3: + """Build a minimal valid V3 array metadata JSON dict. + + The output matches the shape of ``ArrayV3Metadata.to_dict()`` — all + fields that ``to_dict`` always emits are included. + + Parameters + ---------- + extra_fields : dict, optional + Extra keys to inject into the dict (e.g. extension fields). + **overrides + Override any of the standard metadata fields. + """ + d: ArrayMetadataJSON_V3 = { + "zarr_format": 3, + "node_type": "array", + "shape": (4, 4), + "data_type": "uint8", + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (4, 4)}}, + "chunk_key_encoding": {"name": "default", "configuration": {"separator": "/"}}, + "fill_value": 0, + "codecs": (BytesCodec().to_dict(),), # type: ignore[typeddict-item] + "attributes": {}, + "storage_transformers": (), + } + d.update(overrides) # type: ignore[typeddict-item] + if extra_fields is not None: + d.update(extra_fields) # type: ignore[typeddict-item] + return d diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 8658b7b393..bb106e2474 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -1,406 +1,270 @@ +"""Tests for zarr v3 metadata classes and parsing helpers.""" + from __future__ import annotations import json -import re -from typing import TYPE_CHECKING, Literal +from typing import TYPE_CHECKING -import numpy as np import pytest -from zarr import consolidate_metadata, create_group -from zarr.codecs.bytes import BytesCodec +from tests.conftest import Expect, ExpectFail +from tests.test_metadata.conftest import minimal_metadata_dict_v3 from zarr.core.buffer import default_buffer_prototype -from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding, V2ChunkKeyEncoding from zarr.core.config import config -from zarr.core.dtype import UInt8, get_data_type_from_native_dtype -from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING -from zarr.core.dtype.npy.time import DateTime64 +from zarr.core.dtype import UInt8 from zarr.core.group import GroupMetadata, parse_node_type from zarr.core.metadata.v3 import ( + ARRAY_METADATA_KEYS, ArrayMetadataJSON_V3, ArrayV3Metadata, parse_codecs, parse_dimension_names, + parse_node_type_array, parse_zarr_format, ) from zarr.errors import ( MetadataValidationError, NodeTypeValidationError, UnknownCodecError, - ZarrUserWarning, ) if TYPE_CHECKING: - from collections.abc import Sequence from typing import Any - from zarr.core.types import JSON - - from zarr.abc.codec import Codec - - -from zarr.core.metadata.v3 import ( - parse_node_type_array, -) -bool_dtypes = ("bool",) - -int_dtypes = ( - "int8", - "int16", - "int32", - "int64", - "uint8", - "uint16", - "uint32", - "uint64", -) +# --------------------------------------------------------------------------- +# Parsing helpers +# --------------------------------------------------------------------------- -float_dtypes = ( - "float16", - "float32", - "float64", -) -complex_dtypes = ("complex64", "complex128") -flexible_dtypes = ("str", "bytes", "void") -if _NUMPY_SUPPORTS_VLEN_STRING: - vlen_string_dtypes = ("T",) -else: - vlen_string_dtypes = ("O",) - -dtypes = ( - *bool_dtypes, - *int_dtypes, - *float_dtypes, - *complex_dtypes, - *flexible_dtypes, - *vlen_string_dtypes, -) +def test_parse_zarr_format_valid() -> None: + """The integer 3 is the only valid zarr_format for v3.""" + assert parse_zarr_format(3) == 3 @pytest.mark.parametrize("data", [None, 1, 2, 4, 5, "3"]) def test_parse_zarr_format_invalid(data: Any) -> None: - with pytest.raises( - MetadataValidationError, - match=f"Invalid value for 'zarr_format'. Expected '3'. Got '{data}'.", - ): + """Non-3 values are rejected.""" + with pytest.raises(MetadataValidationError): parse_zarr_format(data) -def test_parse_zarr_format_valid() -> None: - assert parse_zarr_format(3) == 3 - - def test_parse_node_type_valid() -> None: + """'array' and 'group' are the only valid node types.""" assert parse_node_type("array") == "array" assert parse_node_type("group") == "group" -@pytest.mark.parametrize("node_type", [None, 2, "other"]) -def test_parse_node_type_invalid(node_type: Any) -> None: - with pytest.raises( - MetadataValidationError, - match=f"Invalid value for 'node_type'. Expected 'array' or 'group'. Got '{node_type}'.", - ): - parse_node_type(node_type) +@pytest.mark.parametrize("data", [None, 2, "other"]) +def test_parse_node_type_invalid(data: Any) -> None: + """Non-string and unrecognized values are rejected.""" + with pytest.raises(MetadataValidationError): + parse_node_type(data) + + +def test_parse_node_type_array_valid() -> None: + """parse_node_type_array accepts only 'array'.""" + assert parse_node_type_array("array") == "array" @pytest.mark.parametrize("data", [None, "group"]) def test_parse_node_type_array_invalid(data: Any) -> None: - with pytest.raises( - NodeTypeValidationError, - match=f"Invalid value for 'node_type'. Expected 'array'. Got '{data}'.", - ): + """parse_node_type_array rejects 'group' and non-string values.""" + with pytest.raises(NodeTypeValidationError): parse_node_type_array(data) -def test_parse_node_typev_array_alid() -> None: - assert parse_node_type_array("array") == "array" +@pytest.mark.parametrize("data", [None, ("a", "b", "c"), ["a", "a", "a"], ()]) +def test_parse_dimension_names_valid(data: Any) -> None: + """None, tuples of strings, lists of strings, and empty tuples are accepted.""" + result = parse_dimension_names(data) + if data is None: + assert result is None + else: + assert result == tuple(data) -@pytest.mark.parametrize("data", [(), [1, 2, "a"], {"foo": 10}]) -def parse_dimension_names_invalid(data: Any) -> None: - with pytest.raises(TypeError, match="Expected either None or iterable of str,"): +@pytest.mark.parametrize("data", [[1, 2, "a"], [None, 3]]) +def test_parse_dimension_names_invalid(data: Any) -> None: + """Iterables containing non-string elements are rejected.""" + with pytest.raises(TypeError, match="Expected either None or"): parse_dimension_names(data) -@pytest.mark.parametrize("data", [None, ("a", "b", "c"), ["a", "a", "a"]]) -def parse_dimension_names_valid(data: Sequence[str] | None) -> None: - assert parse_dimension_names(data) == data +def test_parse_codecs_unknown_raises(monkeypatch: pytest.MonkeyPatch) -> None: + """An unregistered codec name raises UnknownCodecError.""" + from collections import defaultdict + import zarr.registry + from zarr.registry import Registry -@pytest.mark.parametrize("fill_value", [[1.0, 0.0], [0, 1]]) -@pytest.mark.parametrize("dtype_str", [*complex_dtypes]) -def test_jsonify_fill_value_complex(fill_value: Any, dtype_str: str) -> None: - """ - Test that parse_fill_value(fill_value, dtype) correctly handles complex values represented - as length-2 sequences - """ - zarr_format: Literal[3] = 3 - dtype = get_data_type_from_native_dtype(dtype_str) - expected = dtype.to_native_dtype().type(complex(*fill_value)) - observed = dtype.from_json_scalar(fill_value, zarr_format=zarr_format) - assert observed == expected - assert dtype.to_json_scalar(observed, zarr_format=zarr_format) == tuple(fill_value) + monkeypatch.setattr(zarr.registry, "_codec_registries", defaultdict(Registry)) + with pytest.raises(UnknownCodecError): + parse_codecs([{"name": "unknown"}]) -@pytest.mark.parametrize("fill_value", [{"foo": 10}]) -@pytest.mark.parametrize("dtype_str", [*int_dtypes, *float_dtypes, *complex_dtypes]) -def test_parse_fill_value_invalid_type(fill_value: Any, dtype_str: str) -> None: - """ - Test that parse_fill_value(fill_value, dtype) raises TypeError for invalid non-sequential types. - This test excludes bool because the bool constructor takes anything. - """ - dtype_instance = get_data_type_from_native_dtype(dtype_str) - with pytest.raises(TypeError, match=f"Invalid type: {fill_value}"): - dtype_instance.from_json_scalar(fill_value, zarr_format=3) +# --------------------------------------------------------------------------- +# Types +# --------------------------------------------------------------------------- -@pytest.mark.parametrize( - "fill_value", - [ - [ - 1, - ], - (1, 23, 4), - ], -) -@pytest.mark.parametrize("dtype_str", [*int_dtypes, *float_dtypes]) -def test_parse_fill_value_invalid_type_sequence(fill_value: Any, dtype_str: str) -> None: +def test_array_metadata_keys_matches_typeddict() -> None: """ - Test that parse_fill_value(fill_value, dtype) raises TypeError for invalid sequential types. - This test excludes bool because the bool constructor takes anything, and complex because - complex values can be created from length-2 sequences. + Test that the variable modelling the set of keys for array v3 metadata matches + the keys of the typeddict model for the metadata. """ - dtype_instance = get_data_type_from_native_dtype(dtype_str) - with pytest.raises(TypeError, match=re.escape(f"Invalid type: {fill_value}")): - dtype_instance.from_json_scalar(fill_value, zarr_format=3) - - -@pytest.mark.parametrize("chunk_grid", ["regular"]) -@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}]) -@pytest.mark.parametrize("codecs", [[BytesCodec(endian=None)]]) -@pytest.mark.parametrize("fill_value", [0, 1]) -@pytest.mark.parametrize("chunk_key_encoding", ["v2", "default"]) -@pytest.mark.parametrize("dimension_separator", [".", "/", None]) -@pytest.mark.parametrize("dimension_names", ["nones", "strings", "missing"]) -@pytest.mark.parametrize("storage_transformers", [None, ()]) -def test_metadata_to_dict( - chunk_grid: str, - codecs: list[Codec], - fill_value: Any, - chunk_key_encoding: Literal["v2", "default"], - dimension_separator: Literal[".", "/"] | None, - dimension_names: Literal["nones", "strings", "missing"], - attributes: dict[str, Any] | None, - storage_transformers: tuple[dict[str, JSON]] | None, -) -> None: - shape = (1, 2, 3) - data_type_str = "uint8" - if chunk_grid == "regular": - cgrid = {"name": "regular", "configuration": {"chunk_shape": (1, 1, 1)}} - - cke: dict[str, Any] - cke_name_dict = {"name": chunk_key_encoding} - if dimension_separator is not None: - cke = cke_name_dict | {"configuration": {"separator": dimension_separator}} - else: - cke = cke_name_dict - dnames: tuple[str | None, ...] | None - - if dimension_names == "strings": - dnames = tuple(map(str, range(len(shape)))) - elif dimension_names == "missing": - dnames = None - elif dimension_names == "nones": - dnames = (None,) * len(shape) - - metadata_dict = { - "zarr_format": 3, - "node_type": "array", - "shape": shape, - "chunk_grid": cgrid, - "data_type": data_type_str, - "chunk_key_encoding": cke, - "codecs": tuple(c.to_dict() for c in codecs), - "fill_value": fill_value, - "storage_transformers": storage_transformers, - } - - if attributes is not None: - metadata_dict["attributes"] = attributes - if dnames is not None: - metadata_dict["dimension_names"] = dnames - - metadata = ArrayV3Metadata.from_dict(metadata_dict) - observed = metadata.to_dict() - expected = metadata_dict.copy() + assert ARRAY_METADATA_KEYS == set(ArrayMetadataJSON_V3.__annotations__.keys()) - # if unset or None or (), storage_transformers gets normalized to () - assert observed["storage_transformers"] == () - observed.pop("storage_transformers") - expected.pop("storage_transformers") - if attributes is None: - assert observed["attributes"] == {} - observed.pop("attributes") +# --------------------------------------------------------------------------- +# ArrayV3Metadata: round-trip +# --------------------------------------------------------------------------- - if dimension_separator is None: - if chunk_key_encoding == "default": - expected_cke_dict = DefaultChunkKeyEncoding(separator="/").to_dict() - else: - expected_cke_dict = V2ChunkKeyEncoding(separator=".").to_dict() - assert observed["chunk_key_encoding"] == expected_cke_dict - observed.pop("chunk_key_encoding") - expected.pop("chunk_key_encoding") - assert observed == expected - - -@pytest.mark.parametrize("indent", [2, 4, None]) -def test_json_indent(indent: int) -> None: - with config.set({"json_indent": indent}): - m = GroupMetadata() - d = m.to_buffer_dict(default_buffer_prototype())["zarr.json"].to_bytes() - assert d == json.dumps(json.loads(d), indent=indent).encode() - - -@pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897]) -@pytest.mark.parametrize("precision", ["ns", "D"]) -async def test_datetime_metadata(fill_value: int, precision: Literal["ns", "D"]) -> None: - dtype = DateTime64(unit=precision) - metadata_dict: dict[str, Any] = { - "zarr_format": 3, - "node_type": "array", - "shape": (1,), - "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}}, - "data_type": dtype.to_json(zarr_format=3), - "chunk_key_encoding": {"name": "default", "separator": "."}, - "codecs": (BytesCodec(),), - "fill_value": dtype.to_json_scalar( - dtype.to_native_dtype().type(fill_value, dtype.unit), zarr_format=3 - ), - } - metadata = ArrayV3Metadata.from_dict(metadata_dict) - # ensure there isn't a TypeError here. - d = metadata.to_buffer_dict(default_buffer_prototype()) - - result = json.loads(d["zarr.json"].to_bytes()) - assert result["fill_value"] == fill_value +# Codecs after evolution for single-byte (uint8) and multi-byte (float64) types. +_UINT8_CODECS = ({"name": "bytes"},) +_FLOAT64_CODECS = ({"name": "bytes", "configuration": {"endian": "little"}},) @pytest.mark.parametrize( - ("data_type", "fill_value"), [("uint8", {}), ("int32", [0, 1]), ("float32", "foo")] + "case", + [ + Expect( + input={}, + output=minimal_metadata_dict_v3(codecs=_UINT8_CODECS), + id="minimal", + ), + Expect( + input={"attributes": {"key": "value"}}, + output=minimal_metadata_dict_v3(attributes={"key": "value"}, codecs=_UINT8_CODECS), + id="with_attributes", + ), + Expect( + input={"dimension_names": ("x", "y")}, + output=minimal_metadata_dict_v3(dimension_names=("x", "y"), codecs=_UINT8_CODECS), + id="with_dimension_names", + ), + Expect( + input={"storage_transformers": ()}, + output=minimal_metadata_dict_v3(storage_transformers=(), codecs=_UINT8_CODECS), + id="with_storage_transformers", + ), + Expect( + input={"data_type": "float64", "fill_value": 0.0}, + output=minimal_metadata_dict_v3( + data_type="float64", fill_value=0.0, codecs=_FLOAT64_CODECS + ), + id="float64", + ), + Expect( + input={"chunk_key_encoding": {"name": "v2", "configuration": {"separator": "."}}}, + output=minimal_metadata_dict_v3( + chunk_key_encoding={"name": "v2", "configuration": {"separator": "."}}, + codecs=_UINT8_CODECS, + ), + id="v2_chunk_key_encoding", + ), + Expect( + input={"data_type": "float64", "fill_value": "NaN"}, + output=minimal_metadata_dict_v3( + data_type="float64", fill_value="NaN", codecs=_FLOAT64_CODECS + ), + id="nan_fill_value", + ), + Expect( + input={"data_type": "float64", "fill_value": "Infinity"}, + output=minimal_metadata_dict_v3( + data_type="float64", fill_value="Infinity", codecs=_FLOAT64_CODECS + ), + id="inf_fill_value", + ), + Expect( + input={"data_type": "float64", "fill_value": "-Infinity"}, + output=minimal_metadata_dict_v3( + data_type="float64", fill_value="-Infinity", codecs=_FLOAT64_CODECS + ), + id="neg_inf_fill_value", + ), + Expect( + input={ + "attributes": {}, + "storage_transformers": (), + "extra_fields": {"my_ext": {"must_understand": False, "data": [1, 2, 3]}}, + }, + output=minimal_metadata_dict_v3( + attributes={}, + storage_transformers=(), + codecs=_UINT8_CODECS, + extra_fields={"my_ext": {"must_understand": False, "data": [1, 2, 3]}}, + ), + id="extra_fields", + ), + ], + ids=lambda case: case.id, ) -async def test_invalid_fill_value_raises(data_type: str, fill_value: float) -> None: - metadata_dict: dict[str, Any] = { - "zarr_format": 3, - "node_type": "array", - "shape": (1,), - "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}}, - "data_type": data_type, - "chunk_key_encoding": {"name": "default", "separator": "."}, - "codecs": ({"name": "bytes"},), - "fill_value": fill_value, # this is not a valid fill value for uint8 - } - # multiple things can go wrong here, so we don't match on the error message. - with pytest.raises(TypeError): - ArrayV3Metadata.from_dict(metadata_dict) +def test_array_metadata_roundtrip(case: Expect[dict[str, Any], dict[str, Any]]) -> None: + """from_dict(d).to_dict() produces the expected output, including codec evolution.""" + d = minimal_metadata_dict_v3(**case.input) + m = ArrayV3Metadata.from_dict(d) # type: ignore[arg-type] + assert m.to_dict() == case.output -@pytest.mark.parametrize("fill_value", [("NaN"), "Infinity", "-Infinity"]) -async def test_special_float_fill_values(fill_value: str) -> None: - metadata_dict: dict[str, Any] = { - "zarr_format": 3, - "node_type": "array", - "shape": (1,), - "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}}, - "data_type": "float64", - "chunk_key_encoding": {"name": "default", "separator": "."}, - "codecs": [{"name": "bytes"}], - "fill_value": fill_value, # this is not a valid fill value for uint8 - } - m = ArrayV3Metadata.from_dict(metadata_dict) - d = json.loads(m.to_buffer_dict(default_buffer_prototype())["zarr.json"].to_bytes()) - assert m.fill_value is not None - if fill_value == "NaN": - assert np.isnan(m.fill_value) - assert d["fill_value"] == "NaN" - elif fill_value == "Infinity": - assert np.isposinf(m.fill_value) - assert d["fill_value"] == "Infinity" - elif fill_value == "-Infinity": - assert np.isneginf(m.fill_value) - assert d["fill_value"] == "-Infinity" - - -def test_parse_codecs_unknown_codec_raises(monkeypatch: pytest.MonkeyPatch) -> None: - from collections import defaultdict - - import zarr.registry - from zarr.registry import Registry +# --------------------------------------------------------------------------- +# ArrayV3Metadata: failure modes +# --------------------------------------------------------------------------- - # to make sure the codec is always unknown (not sure if that's necessary) - monkeypatch.setattr(zarr.registry, "_codec_registries", defaultdict(Registry)) - codecs = [{"name": "unknown"}] - with pytest.raises(UnknownCodecError): - parse_codecs(codecs) +@pytest.mark.parametrize( + "case", + [ + ExpectFail( + input={"dimension_names": ("x", "y", "z")}, + exception=ValueError, + msg="dimension_names.*shape", + id="dimension_names_length_mismatch", + ), + ExpectFail( + input={"data_type": "uint8", "fill_value": {}}, + exception=TypeError, + id="invalid_fill_value_type", + ), + ], + ids=lambda case: case.id, +) +def test_array_metadata_from_dict_fails(case: ExpectFail[dict[str, Any]]) -> None: + """from_dict rejects invalid metadata documents.""" + d = minimal_metadata_dict_v3(**case.input) + with pytest.raises(case.exception, match=case.msg): + ArrayV3Metadata.from_dict(d) # type: ignore[arg-type] @pytest.mark.parametrize( - "extra_value", + "case", [ - {"must_understand": False, "param": 10}, - {"must_understand": True}, - 10, + ExpectFail( + input=minimal_metadata_dict_v3(extra_fields={"my_ext": {"must_understand": True}}), + exception=MetadataValidationError, + msg="disallowed extra fields", + id="must_understand_true", + ), + ExpectFail( + input=minimal_metadata_dict_v3(extra_fields={"my_ext": 42}), + exception=MetadataValidationError, + msg="disallowed extra fields", + id="non_dict_extra_field", + ), ], + ids=lambda case: case.id, ) -def test_from_dict_extra_fields(extra_value: dict[str, object] | int) -> None: - """ - Test that from_dict accepts extra fields if they have are a JSON object with - "must_understand": false, and raises an exception otherwise. - """ - metadata_dict: ArrayMetadataJSON_V3 = { # type: ignore[typeddict-unknown-key] - "zarr_format": 3, - "node_type": "array", - "shape": (1,), - "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (1,)}}, - "data_type": "uint8", - "chunk_key_encoding": {"name": "default", "configuration": {"separator": "."}}, - "codecs": ({"name": "bytes"},), - "fill_value": 0, - "storage_transformers": (), - "attributes": {}, - "foo": extra_value, - } - - if isinstance(extra_value, dict) and extra_value.get("must_understand") is False: - # should be accepted - metadata = ArrayV3Metadata.from_dict(metadata_dict) # type: ignore[arg-type] - assert isinstance(metadata, ArrayV3Metadata) - assert metadata.to_dict() == metadata_dict - else: - # should raise an exception - with pytest.raises(MetadataValidationError, match="Got a Zarr V3 metadata document"): - metadata = ArrayV3Metadata.from_dict(metadata_dict) # type: ignore[arg-type] +def test_array_metadata_extra_fields_rejected(case: ExpectFail[dict[str, Any]]) -> None: + """from_dict rejects extra fields that don't conform to the spec.""" + with pytest.raises(case.exception, match=case.msg): + ArrayV3Metadata.from_dict(case.input) -def test_init_invalid_extra_fields() -> None: - """ - Test that initializing ArrayV3Metadata with extra fields fails when those fields - shadow the array metadata fields. - """ +def test_init_extra_fields_collision() -> None: + """Extra field keys that collide with reserved metadata field names are rejected.""" extra_fields: dict[str, object] = {"shape": (10,), "data_type": "uint8"} - conflict_keys = set(extra_fields.keys()) - msg = ( - "Invalid extra fields. " - "The following keys: " - f"{sorted(conflict_keys)} " - "are invalid because they collide with keys reserved for use by the " - "array metadata document." - ) - with pytest.raises(ValueError, match=re.escape(msg)): + with pytest.raises(ValueError, match="collide with keys reserved"): ArrayV3Metadata( shape=(10,), data_type=UInt8(), @@ -414,50 +278,69 @@ def test_init_invalid_extra_fields() -> None: ) -@pytest.mark.parametrize("use_consolidated", [True, False]) +# --------------------------------------------------------------------------- +# JSON indent +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize("indent", [2, 4, None]) +def test_json_indent(indent: int | None) -> None: + """The json_indent config setting controls indentation in to_buffer_dict output.""" + with config.set({"json_indent": indent}): + m = GroupMetadata() + d = m.to_buffer_dict(default_buffer_prototype())["zarr.json"].to_bytes() + assert d == json.dumps(json.loads(d), indent=indent).encode() + + +# --------------------------------------------------------------------------- +# GroupMetadata.to_dict +# --------------------------------------------------------------------------- + + @pytest.mark.parametrize("attributes", [None, {"foo": "bar"}]) -def test_group_to_dict(use_consolidated: bool, attributes: None | dict[str, Any]) -> None: - """ - Test that the output of GroupMetadata.to_dict() is what we expect - """ - store: dict[str, object] = {} - if attributes is None: - expect_attributes = {} - else: - expect_attributes = attributes +def test_group_metadata_to_dict(attributes: dict[str, Any] | None) -> None: + """GroupMetadata.to_dict produces the expected v3 JSON structure.""" + meta = GroupMetadata(attributes=attributes) + assert meta.to_dict() == { + "zarr_format": 3, + "node_type": "group", + "attributes": attributes or {}, + } + + +@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}]) +def test_group_metadata_to_dict_consolidated(attributes: dict[str, Any] | None) -> None: + """GroupMetadata.to_dict includes consolidated_metadata when present.""" + from zarr import consolidate_metadata, create_group + from zarr.errors import ZarrUserWarning + store: dict[str, object] = {} group = create_group(store, attributes=attributes, zarr_format=3) group.create_group("foo") - if use_consolidated: - with pytest.warns( - ZarrUserWarning, - match="Consolidated metadata is currently not part in the Zarr format 3 specification.", - ): - group = consolidate_metadata(store) - meta = group.metadata - expect = { - "node_type": "group", - "zarr_format": 3, - "consolidated_metadata": { - "kind": "inline", - "must_understand": False, - "metadata": { - "foo": { - "attributes": {}, - "zarr_format": 3, - "node_type": "group", - "consolidated_metadata": { - "kind": "inline", - "metadata": {}, - "must_understand": False, - }, - } - }, - }, - "attributes": expect_attributes, - } - else: - meta = group.metadata - expect = {"node_type": "group", "zarr_format": 3, "attributes": expect_attributes} + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + group = consolidate_metadata(store) - assert meta.to_dict() == expect + assert group.metadata.to_dict() == { + "zarr_format": 3, + "node_type": "group", + "attributes": attributes or {}, + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": { + "foo": { + "attributes": {}, + "zarr_format": 3, + "node_type": "group", + "consolidated_metadata": { + "kind": "inline", + "metadata": {}, + "must_understand": False, + }, + } + }, + }, + } From 520344adc7843f3b56eba51269d265ddeed3c44b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 16 Apr 2026 08:37:48 +0200 Subject: [PATCH 277/468] chore: expunge deprecated `zarr_version` parameter (#3901) * chore: expunge deprecated `zarr_version` parameter - remove `zarr_version` from functions - remove special function for handling `zarr_format` and `zarr_version` parameters - correct references in the docs to `zarr_version` - correct references in the docs to configuration for the default zarr format * docs: changelog --- changes/3901.misc.md | 1 + docs/user-guide/config.md | 2 +- docs/user-guide/v3_migration.md | 6 ++-- src/zarr/api/asynchronous.py | 57 ++++----------------------------- src/zarr/api/synchronous.py | 28 ++-------------- src/zarr/core/common.py | 2 +- 6 files changed, 15 insertions(+), 81 deletions(-) create mode 100644 changes/3901.misc.md diff --git a/changes/3901.misc.md b/changes/3901.misc.md new file mode 100644 index 0000000000..d1f08d80eb --- /dev/null +++ b/changes/3901.misc.md @@ -0,0 +1 @@ +Remove the deprecated `zarr_version` parameter from several functions and methods. That parameter is replaced with `zarr_format`. \ No newline at end of file diff --git a/docs/user-guide/config.md b/docs/user-guide/config.md index 044f170c02..8a8fa94c3d 100644 --- a/docs/user-guide/config.md +++ b/docs/user-guide/config.md @@ -27,7 +27,7 @@ For more information, see the Configuration options include the following: -- Default Zarr format `default_zarr_version` +- Default Zarr format `default_zarr_format` - Default array order in memory `array.order` - Whether empty chunks are written to storage `array.write_empty_chunks` - Enable experimental rectilinear chunks `array.rectilinear_chunks` diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index f9974305ed..c6b3de1c6c 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -97,7 +97,7 @@ The following sections provide details on breaking changes in Zarr-Python 3. 2. Defaulting to `zarr_format=3` - newly created arrays will use the version 3 of the Zarr specification. To continue using version 2, set `zarr_format=2` when creating arrays - or set `default_zarr_version=2` in Zarr's runtime configuration. + or set `default_zarr_format=2` in Zarr's runtime configuration. 3. Function signature change to [`zarr.Array.resize`][] - the `resize` function now takes a `zarr.core.common.ShapeLike` input rather than separate arguments for each dimension. @@ -195,9 +195,9 @@ When installing using `pip`: ### Miscellaneous -- The keyword argument `zarr_version` available in most creation functions in `zarr` +- The keyword argument `zarr_version` in most creation functions in `zarr` (e.g. [`zarr.create`][], [`zarr.open`][], [`zarr.group`][], [`zarr.array`][]) has - been deprecated in favor of `zarr_format`. + been removed. Use `zarr_format` instead. ## 🚧 Work in Progress 🚧 diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 60c0e6c97a..19b3c0c3fa 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -169,22 +169,6 @@ def _like_args(a: ArrayLike) -> _LikeArgs: return new -def _handle_zarr_version_or_format( - *, zarr_version: ZarrFormat | None, zarr_format: ZarrFormat | None -) -> ZarrFormat | None: - """Handle the deprecated zarr_version kwarg and return zarr_format""" - if zarr_format is not None and zarr_version is not None and zarr_format != zarr_version: - raise ValueError( - f"zarr_format {zarr_format} does not match zarr_version {zarr_version}, please only set one" - ) - if zarr_version is not None: - warnings.warn( - "zarr_version is deprecated, use zarr_format", ZarrDeprecationWarning, stacklevel=2 - ) - return zarr_version - return zarr_format - - async def consolidate_metadata( store: StoreLike, path: str | None = None, @@ -289,7 +273,6 @@ async def load( store: StoreLike, path: str | None = None, zarr_format: ZarrFormat | None = None, - zarr_version: ZarrFormat | None = None, ) -> NDArrayLikeOrScalar | dict[str, NDArrayLikeOrScalar]: """Load data from an array or group into memory. @@ -318,7 +301,6 @@ async def load( If loading data from a group of arrays, data will not be immediately loaded into memory. Rather, arrays will be loaded into memory as they are requested. """ - zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) obj = await open(store=store, path=path, zarr_format=zarr_format) if isinstance(obj, AsyncArray): @@ -331,7 +313,6 @@ async def open( *, store: StoreLike | None = None, mode: AccessModeLiteral | None = None, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, storage_options: dict[str, Any] | None = None, @@ -367,7 +348,7 @@ async def open( z : array or group Return type depends on what exists in the given store. """ - zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) + if mode is None: if isinstance(store, (Store, StorePath)) and store.read_only: mode = "r" @@ -418,7 +399,6 @@ async def open_consolidated( async def save( store: StoreLike, *args: NDArrayLike, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, **kwargs: Any, # TODO: type kwargs as valid args to save @@ -440,7 +420,6 @@ async def save( **kwargs NumPy arrays with data to save. """ - zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) if len(args) == 0 and len(kwargs) == 0: raise ValueError("at least one array must be provided") @@ -454,7 +433,6 @@ async def save_array( store: StoreLike, arr: NDArrayLike, *, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, storage_options: dict[str, Any] | None = None, @@ -482,10 +460,8 @@ async def save_array( **kwargs Passed through to [`create`][zarr.api.asynchronous.create], e.g., compressor. """ - zarr_format = ( - _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) - or _default_zarr_format() - ) + if zarr_format is None: + zarr_format = _default_zarr_format() if not isinstance(arr, NDArrayLike): raise TypeError("arr argument must be numpy or other NDArrayLike array") @@ -512,7 +488,6 @@ async def save_array( async def save_group( store: StoreLike, *args: NDArrayLike, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, storage_options: dict[str, Any] | None = None, @@ -542,13 +517,8 @@ async def save_group( store_path = await make_store_path(store, path=path, mode="w", storage_options=storage_options) - zarr_format = ( - _handle_zarr_version_or_format( - zarr_version=zarr_version, - zarr_format=zarr_format, - ) - or _default_zarr_format() - ) + if zarr_format is None: + zarr_format = _default_zarr_format() for arg in args: if not isinstance(arg, NDArrayLike): @@ -662,7 +632,6 @@ async def group( cache_attrs: bool | None = None, # not used, default changed synchronizer: Any | None = None, # not used path: str | None = None, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, meta_array: Any | None = None, # not used attributes: dict[str, JSON] | None = None, @@ -715,7 +684,6 @@ async def group( cache_attrs=cache_attrs, synchronizer=synchronizer, path=path, - zarr_version=zarr_version, zarr_format=zarr_format, meta_array=meta_array, attributes=attributes, @@ -784,7 +752,6 @@ async def open_group( path: str | None = None, chunk_store: StoreLike | None = None, # not used storage_options: dict[str, Any] | None = None, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, meta_array: Any | None = None, # not used attributes: dict[str, JSON] | None = None, @@ -846,8 +813,6 @@ async def open_group( The new group. """ - zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) - if cache_attrs is not None: warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2) if synchronizer is not None: @@ -901,7 +866,6 @@ async def create( object_codec: Codec | None = None, # TODO: type has changed dimension_separator: Literal[".", "/"] | None = None, write_empty_chunks: bool | None = None, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, meta_array: Any | None = None, # TODO: need type attributes: dict[str, JSON] | None = None, @@ -1043,10 +1007,8 @@ async def create( z : array The array. """ - zarr_format = ( - _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) - or _default_zarr_format() - ) + if zarr_format is None: + zarr_format = _default_zarr_format() if synchronizer is not None: warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2) @@ -1238,7 +1200,6 @@ async def ones_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: async def open_array( *, # note: this is a change from v2 store: StoreLike | None = None, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: PathLike = "", storage_options: dict[str, Any] | None = None, @@ -1252,8 +1213,6 @@ async def open_array( StoreLike object to open. See the [storage documentation in the user guide][user-guide-store-like] for a description of all valid StoreLike values. - zarr_version : {2, 3, None}, optional - The zarr format to use when saving. Deprecated in favor of zarr_format. zarr_format : {2, 3, None}, optional The zarr format to use when saving. path : str, optional @@ -1273,8 +1232,6 @@ async def open_array( mode = kwargs.pop("mode", None) store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options) - zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format) - if "write_empty_chunks" in kwargs: _warn_write_empty_chunks_kwarg() diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 688f2a110d..09397e3d41 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -140,7 +140,6 @@ def load( store: StoreLike, path: str | None = None, zarr_format: ZarrFormat | None = None, - zarr_version: ZarrFormat | None = None, ) -> NDArrayLikeOrScalar | dict[str, NDArrayLikeOrScalar]: """Load data from an array or group into memory. @@ -169,16 +168,13 @@ def load( If loading data from a group of arrays, data will not be immediately loaded into memory. Rather, arrays will be loaded into memory as they are requested. """ - return sync( - async_api.load(store=store, zarr_version=zarr_version, zarr_format=zarr_format, path=path) - ) + return sync(async_api.load(store=store, zarr_format=zarr_format, path=path)) def open( store: StoreLike | None = None, *, mode: AccessModeLiteral | None = None, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, storage_options: dict[str, Any] | None = None, @@ -218,7 +214,6 @@ def open( async_api.open( store=store, mode=mode, - zarr_version=zarr_version, zarr_format=zarr_format, path=path, storage_options=storage_options, @@ -243,7 +238,6 @@ def open_consolidated(*args: Any, use_consolidated: Literal[True] = True, **kwar def save( store: StoreLike, *args: NDArrayLike, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, **kwargs: Any, # TODO: type kwargs as valid args to async_api.save @@ -265,18 +259,13 @@ def save( **kwargs NumPy arrays with data to save. """ - return sync( - async_api.save( - store, *args, zarr_version=zarr_version, zarr_format=zarr_format, path=path, **kwargs - ) - ) + return sync(async_api.save(store, *args, zarr_format=zarr_format, path=path, **kwargs)) def save_array( store: StoreLike, arr: NDArrayLike, *, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, storage_options: dict[str, Any] | None = None, @@ -309,7 +298,6 @@ def save_array( async_api.save_array( store=store, arr=arr, - zarr_version=zarr_version, zarr_format=zarr_format, path=path, storage_options=storage_options, @@ -321,7 +309,6 @@ def save_array( def save_group( store: StoreLike, *args: NDArrayLike, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, path: str | None = None, storage_options: dict[str, Any] | None = None, @@ -354,7 +341,6 @@ def save_group( async_api.save_group( store, *args, - zarr_version=zarr_version, zarr_format=zarr_format, path=path, storage_options=storage_options, @@ -416,7 +402,6 @@ def group( cache_attrs: bool | None = None, # not used, default changed synchronizer: Any | None = None, # not used path: str | None = None, - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, meta_array: Any | None = None, # not used attributes: dict[str, JSON] | None = None, @@ -466,7 +451,6 @@ def group( cache_attrs=cache_attrs, synchronizer=synchronizer, path=path, - zarr_version=zarr_version, zarr_format=zarr_format, meta_array=meta_array, attributes=attributes, @@ -485,7 +469,6 @@ def open_group( path: str | None = None, chunk_store: StoreLike | None = None, # not used in async api storage_options: dict[str, Any] | None = None, # not used in async api - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, meta_array: Any | None = None, # not used in async api attributes: dict[str, JSON] | None = None, @@ -556,7 +539,6 @@ def open_group( path=path, chunk_store=chunk_store, storage_options=storage_options, - zarr_version=zarr_version, zarr_format=zarr_format, meta_array=meta_array, attributes=attributes, @@ -637,7 +619,6 @@ def create( object_codec: Codec | None = None, # TODO: type has changed dimension_separator: Literal[".", "/"] | None = None, write_empty_chunks: bool | None = None, # TODO: default has changed - zarr_version: ZarrFormat | None = None, # deprecated zarr_format: ZarrFormat | None = None, meta_array: Any | None = None, # TODO: need type attributes: dict[str, JSON] | None = None, @@ -800,7 +781,6 @@ def create( object_codec=object_codec, dimension_separator=dimension_separator, write_empty_chunks=write_empty_chunks, - zarr_version=zarr_version, zarr_format=zarr_format, meta_array=meta_array, attributes=attributes, @@ -1365,7 +1345,6 @@ def ones_like(a: ArrayLike, **kwargs: Any) -> AnyArray: def open_array( store: StoreLike | None = None, *, - zarr_version: ZarrFormat | None = None, zarr_format: ZarrFormat | None = None, path: PathLike = "", storage_options: dict[str, Any] | None = None, @@ -1379,8 +1358,6 @@ def open_array( StoreLike object to open. See the [storage documentation in the user guide][user-guide-store-like] for a description of all valid StoreLike values. - zarr_version : {2, 3, None}, optional - The zarr format to use when saving. Deprecated in favor of zarr_format. zarr_format : {2, 3, None}, optional The zarr format to use when saving. path : str, optional @@ -1401,7 +1378,6 @@ def open_array( sync( async_api.open_array( store=store, - zarr_version=zarr_version, zarr_format=zarr_format, path=path, storage_options=storage_options, diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index a16257df7c..2279820d7a 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -240,7 +240,7 @@ def _warn_order_kwarg() -> None: def _default_zarr_format() -> ZarrFormat: - """Return the default zarr_version""" + """Return the default zarr_format.""" return cast("ZarrFormat", int(zarr_config.get("default_zarr_format", 3))) From ab883638dc75680df89d774ac6b61394ed4c12df Mon Sep 17 00:00:00 2001 From: Ian Hunt-Isaak Date: Thu, 16 Apr 2026 15:05:40 -0400 Subject: [PATCH 278/468] test: don't force rectilinear config true in the test (#3909) --- src/zarr/testing/strategies.py | 35 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index e382235e0e..6832ded5fb 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -1,7 +1,6 @@ import math import sys from collections.abc import Callable, Mapping -from contextlib import nullcontext from typing import Any, Literal import hypothesis.extra.numpy as npst @@ -297,31 +296,28 @@ def arrays( # - RectilinearChunkGridMetadata -> nested list of ints (triggers rectilinear path) # - v2 -> flat tuple of ints chunks_param: tuple[int, ...] | list[list[int]] - use_rectilinear = False if zarr_format == 3 and chunk_grid_meta is not None: if isinstance(chunk_grid_meta, RectilinearChunkGridMetadata): chunks_param = [ list(dim) if isinstance(dim, tuple) else [dim] for dim in chunk_grid_meta.chunk_shapes ] - use_rectilinear = True else: chunks_param = chunk_grid_meta.chunk_shape else: chunks_param = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") - with zarr.config.set({"array.rectilinear_chunks": True}) if use_rectilinear else nullcontext(): - a = root.create_array( - array_path, - shape=nparray.shape, - chunks=chunks_param, - shards=shard_shape, - dtype=nparray.dtype, - attributes=attributes, - # compressor=compressor, # FIXME - fill_value=fill_value, - dimension_names=dim_names, - ) + a = root.create_array( + array_path, + shape=nparray.shape, + chunks=chunks_param, + shards=shard_shape, + dtype=nparray.dtype, + attributes=attributes, + # compressor=compressor, # FIXME + fill_value=fill_value, + dimension_names=dim_names, + ) assert isinstance(a, Array) if a.metadata.zarr_format == 3: @@ -427,6 +423,10 @@ def chunk_grids( ) -> RegularChunkGridMetadata | RectilinearChunkGridMetadata: """Generate either a RegularChunkGridMetadata or RectilinearChunkGridMetadata. + This strategy depends on the global state of the config having rectilinear chunk grids enabled or not. + This means that it may be a possible source of a hypothesis FlakyStrategy error due dependence + on global state. However, in practice this seems unlikely to happen. + This allows property tests to exercise both chunk grid types. """ # RectilinearChunkGridMetadata doesn't support zero-sized dimensions, @@ -435,11 +435,10 @@ def chunk_grids( event("using RegularChunkGridMetadata (zero-sized dimensions)") return RegularChunkGridMetadata(chunk_shape=draw(chunk_shapes(shape=shape))) - if draw(st.booleans()): + if zarr.config.get("array.rectilinear_chunks") and draw(st.booleans()): chunks = draw(rectilinear_chunks(shape=shape)) event("using RectilinearChunkGridMetadata") - with zarr.config.set({"array.rectilinear_chunks": True}): - return RectilinearChunkGridMetadata(chunk_shapes=tuple(tuple(dim) for dim in chunks)) + return RectilinearChunkGridMetadata(chunk_shapes=tuple(tuple(dim) for dim in chunks)) else: event("using RegularChunkGridMetadata") return RegularChunkGridMetadata(chunk_shape=draw(chunk_shapes(shape=shape))) From dd5a32196ab909807cb8595909da8ec095b84b88 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 16 Apr 2026 22:00:46 +0200 Subject: [PATCH 279/468] chore: remove deprecated group methods (#3902) * chore: remove group.array * chore: *_dataset methods from group * docs: changelog --- changes/3902.misc.md | 1 + docs/user-guide/v3_migration.md | 8 +- src/zarr/core/group.py | 273 +---------------------------- tests/test_api/test_synchronous.py | 2 - tests/test_group.py | 65 +------ 5 files changed, 11 insertions(+), 338 deletions(-) create mode 100644 changes/3902.misc.md diff --git a/changes/3902.misc.md b/changes/3902.misc.md new file mode 100644 index 0000000000..ddfc9813e2 --- /dev/null +++ b/changes/3902.misc.md @@ -0,0 +1 @@ +Remove deprecated `Group` methods `array`, `require_dataset`, and `create_dataset`. \ No newline at end of file diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index c6b3de1c6c..b700bf7a25 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -107,11 +107,11 @@ The following sections provide details on breaking changes in Zarr-Python 3. 1. Disallow direct construction - use [`zarr.open_group`][] or [`zarr.create_group`][] instead of directly constructing the `zarr.Group` class. -2. Most of the h5py compatibility methods are deprecated and will issue warnings if used. - The following functions are drop in replacements that have the same signature and functionality: +2. The h5py compatibility methods `create_dataset` and `require_dataset` have been removed. + Use the following replacements: - - Use [`zarr.Group.create_array`][] in place of `zarr.Group.create_dataset` - - Use [`zarr.Group.require_array`][] in place of `zarr.Group.require_dataset` + - [`zarr.Group.create_array`][] in place of `Group.create_dataset` + - [`zarr.Group.require_array`][] in place of `Group.require_dataset` 3. Disallow "." syntax for getting group members. To get a member of a group named `foo`, use `group["foo"]` in place of `group.foo`. 4. The `zarr.storage.init_group` low-level helper function has been removed. Use diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index b810041e7b..97f75c12bd 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -13,7 +13,6 @@ import numpy as np import numpy.typing as npt -from typing_extensions import deprecated import zarr.api.asynchronous as async_api from zarr.abc.metadata import Metadata @@ -56,7 +55,6 @@ ContainsGroupError, GroupNotFoundError, MetadataValidationError, - ZarrDeprecationWarning, ZarrUserWarning, ) from zarr.storage import StoreLike, StorePath @@ -1161,78 +1159,6 @@ async def create_array( write_data=write_data, ) - @deprecated("Use AsyncGroup.create_array instead.", category=ZarrDeprecationWarning) - async def create_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> AnyAsyncArray: - """Create an array. - - !!! warning "Deprecated" - `AsyncGroup.create_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. - Use `AsyncGroup.create_array` instead. - - Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the [zarr.AsyncGroup.require_dataset][] method. - - Parameters - ---------- - name : str - Array name. - **kwargs : dict - Additional arguments passed to [zarr.AsyncGroup.create_array][]. - - Returns - ------- - a : AsyncArray - """ - data = kwargs.pop("data", None) - # create_dataset in zarr 2.x requires shape but not dtype if data is - # provided. Allow this configuration by inferring dtype from data if - # necessary and passing it to create_array - if "dtype" not in kwargs and data is not None: - kwargs["dtype"] = data.dtype - array = await self.create_array(name, shape=shape, **kwargs) - if data is not None: - await array.setitem(slice(None), data) - return array - - @deprecated("Use AsyncGroup.require_array instead.", category=ZarrDeprecationWarning) - async def require_dataset( - self, - name: str, - *, - shape: tuple[int, ...], - dtype: npt.DTypeLike = None, - exact: bool = False, - **kwargs: Any, - ) -> AnyAsyncArray: - """Obtain an array, creating if it doesn't exist. - - !!! warning "Deprecated" - `AsyncGroup.require_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. - Use `AsyncGroup.require_dataset` instead. - - Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the [zarr.AsyncGroup.create_dataset][] method. - - Other `kwargs` are as per [zarr.AsyncGroup.create_dataset][]. - - Parameters - ---------- - name : str - Array name. - shape : int or tuple of ints - Array shape. - dtype : str or dtype, optional - NumPy dtype. - exact : bool, optional - If True, require `dtype` to match exactly. If false, require - `dtype` can be cast from array dtype. - - Returns - ------- - a : AsyncArray - """ - return await self.require_array(name, shape=shape, dtype=dtype, exact=exact, **kwargs) - async def require_array( self, name: str, @@ -1244,7 +1170,7 @@ async def require_array( ) -> AnyAsyncArray: """Obtain an array, creating if it doesn't exist. - Other `kwargs` are as per [zarr.AsyncGroup.create_dataset][]. + Other `kwargs` are as per [zarr.AsyncGroup.create_array][]. Parameters ---------- @@ -2761,57 +2687,6 @@ def create_array( ) ) - @deprecated("Use Group.create_array instead.", category=ZarrDeprecationWarning) - def create_dataset(self, name: str, **kwargs: Any) -> AnyArray: - """Create an array. - - !!! warning "Deprecated" - `Group.create_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. - Use `Group.create_array` instead. - - - Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the [zarr.Group.require_dataset][] method. - - Parameters - ---------- - name : str - Array name. - **kwargs : dict - Additional arguments passed to [zarr.Group.create_array][] - - Returns - ------- - a : Array - """ - return Array(self._sync(self._async_group.create_dataset(name, **kwargs))) - - @deprecated("Use Group.require_array instead.", category=ZarrDeprecationWarning) - def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> AnyArray: - """Obtain an array, creating if it doesn't exist. - - !!! warning "Deprecated" - `Group.require_dataset()` is deprecated since v3.0.0 and will be removed in v3.1.0. - Use `Group.require_array` instead. - - Arrays are known as "datasets" in HDF5 terminology. For compatibility - with h5py, Zarr groups also implement the [zarr.Group.create_dataset][] method. - - Other `kwargs` are as per [zarr.Group.create_dataset][]. - - Parameters - ---------- - name : str - Array name. - **kwargs : - See [zarr.Group.create_dataset][]. - - Returns - ------- - a : Array - """ - return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs))) - def require_array(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> AnyArray: """Obtain an array, creating if it doesn't exist. @@ -3009,152 +2884,6 @@ def move(self, source: str, dest: str) -> None: """ return self._sync(self._async_group.move(source, dest)) - @deprecated("Use Group.create_array instead.", category=ZarrDeprecationWarning) - def array( - self, - name: str, - *, - shape: ShapeLike, - dtype: npt.DTypeLike, - chunks: ChunksLike | Literal["auto"] = "auto", - shards: tuple[int, ...] | Literal["auto"] | None = None, - filters: FiltersLike = "auto", - compressors: CompressorsLike = "auto", - compressor: CompressorLike = None, - serializer: SerializerLike = "auto", - fill_value: Any | None = DEFAULT_FILL_VALUE, - order: MemoryOrder | None = None, - attributes: dict[str, JSON] | None = None, - chunk_key_encoding: ChunkKeyEncodingLike | None = None, - dimension_names: DimensionNamesLike = None, - storage_options: dict[str, Any] | None = None, - overwrite: bool = False, - config: ArrayConfigLike | None = None, - data: npt.ArrayLike | None = None, - ) -> AnyArray: - """Create an array within this group. - - !!! warning "Deprecated" - `Group.array()` is deprecated since v3.0.0 and will be removed in a future release. - Use `Group.create_array` instead. - - This method lightly wraps [zarr.core.array.create_array][]. - - Parameters - ---------- - name : str - The name of the array relative to the group. If ``path`` is ``None``, the array will be located - at the root of the store. - shape : tuple[int, ...] - Shape of the array. - dtype : npt.DTypeLike - Data type of the array. - chunks : tuple[int, ...], optional - Chunk shape of the array. - If not specified, default are guessed based on the shape and dtype. - shards : tuple[int, ...], optional - Shard shape of the array. The default value of ``None`` results in no sharding at all. - filters : Iterable[Codec] | Literal["auto"], optional - Iterable of filters to apply to each chunk of the array, in order, before serializing that - chunk to bytes. - - For Zarr format 3, a "filter" is a codec that takes an array and returns an array, - and these values must be instances of [`zarr.abc.codec.ArrayArrayCodec`][], or a - dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. - - For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. - - The default value of ``"auto"`` instructs Zarr to use a default used based on the data - type of the array and the Zarr format specified. For all data types in Zarr V3, and most - data types in Zarr V2, the default filters are empty. The only cases where default filters - are not empty is when the Zarr format is 2, and the data type is a variable-length data type like - [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, - the default filters contains a single element which is a codec specific to that particular data type. - - To create an array with no filters, provide an empty iterable or the value ``None``. - compressors : Iterable[Codec], optional - List of compressors to apply to the array. Compressors are applied in order, and after any - filters are applied (if any are specified) and the data is serialized into bytes. - - For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. - If no ``compressors`` are provided, a default set of compressors will be used. - These defaults can be changed by modifying the value of ``array.v3_default_compressors`` - in [`zarr.config`][zarr.config]. - Use ``None`` to omit default compressors. - - For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may - be provided for Zarr format 2. - If no ``compressor`` is provided, a default compressor will be used. - in [`zarr.config`][zarr.config]. - Use ``None`` to omit the default compressor. - compressor : Codec, optional - Deprecated in favor of ``compressors``. - serializer : dict[str, JSON] | ArrayBytesCodec, optional - Array-to-bytes codec to use for encoding the array data. - Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. - If no ``serializer`` is provided, a default serializer will be used. - These defaults can be changed by modifying the value of ``array.v3_default_serializer`` - in [`zarr.config`][zarr.config]. - fill_value : Any, optional - Fill value for the array. - order : {"C", "F"}, optional - The memory of the array (default is "C"). - For Zarr format 2, this parameter sets the memory order of the array. - For Zarr format 3, this parameter is deprecated, because memory order - is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory - order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. - If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. - attributes : dict, optional - Attributes for the array. - chunk_key_encoding : ChunkKeyEncoding, optional - A specification of how the chunk keys are represented in storage. - For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. - For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. - dimension_names : Iterable[str], optional - The names of the dimensions (default is None). - Zarr format 3 only. Zarr format 2 arrays should not use this parameter. - storage_options : dict, optional - If using an fsspec URL to create the store, these will be passed to the backend implementation. - Ignored otherwise. - overwrite : bool, default False - Whether to overwrite an array with the same name in the store, if one exists. - config : ArrayConfig or ArrayConfigLike, optional - Runtime configuration for the array. - data : array_like - The data to fill the array with. - - Returns - ------- - AsyncArray - """ - compressors = _parse_deprecated_compressor(compressor, compressors) - return Array( - self._sync( - self._async_group.create_dataset( - name=name, - shape=shape, - dtype=dtype, - chunks=chunks, - shards=shards, - fill_value=fill_value, - attributes=attributes, - chunk_key_encoding=chunk_key_encoding, - compressors=compressors, - serializer=serializer, - dimension_names=dimension_names, - order=order, - filters=filters, - overwrite=overwrite, - storage_options=storage_options, - config=config, - data=data, - ) - ) - ) - async def create_hierarchy( *, diff --git a/tests/test_api/test_synchronous.py b/tests/test_api/test_synchronous.py index 55d89d73de..9e4aab438d 100644 --- a/tests/test_api/test_synchronous.py +++ b/tests/test_api/test_synchronous.py @@ -86,8 +86,6 @@ def test_docstrings_match(callable_name: str) -> None: synchronous.create_array, zarr.AsyncGroup.create_array, zarr.Group.create_array, - zarr.AsyncGroup.create_dataset, - zarr.Group.create_dataset, ), ), ], diff --git a/tests/test_group.py b/tests/test_group.py index e53b0b9ea0..f9b3a208a8 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -44,7 +44,6 @@ ContainsArrayError, ContainsGroupError, MetadataValidationError, - ZarrDeprecationWarning, ZarrUserWarning, ) from zarr.storage import LocalStore, MemoryStore, StorePath, ZipStore @@ -709,13 +708,11 @@ async def test_group_update_attributes_async(store: Store, zarr_format: ZarrForm assert new_group.attrs == new_attrs -@pytest.mark.parametrize("method", ["create_array", "array"]) @pytest.mark.parametrize("name", ["a", "/a"]) def test_group_create_array( store: Store, zarr_format: ZarrFormat, overwrite: bool, - method: Literal["create_array", "array"], name: str, ) -> None: """ @@ -726,33 +723,13 @@ def test_group_create_array( dtype = "uint8" data = np.arange(np.prod(shape)).reshape(shape).astype(dtype) - if method == "create_array": - array = group.create_array(name=name, shape=shape, dtype=dtype) - array[:] = data - elif method == "array": - with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): - with pytest.warns( - ZarrUserWarning, - match="The `compressor` argument is deprecated. Use `compressors` instead.", - ): - array = group.array(name=name, data=data, shape=shape, dtype=dtype) - else: - raise AssertionError + array = group.create_array(name=name, shape=shape, dtype=dtype) + array[:] = data if not overwrite: - if method == "create_array": - with pytest.raises(ContainsArrayError): # noqa: PT012 - a = group.create_array(name=name, shape=shape, dtype=dtype) - a[:] = data - elif method == "array": - with pytest.raises(ContainsArrayError): # noqa: PT012 - with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): - with pytest.warns( - ZarrUserWarning, - match="The `compressor` argument is deprecated. Use `compressors` instead.", - ): - a = group.array(name=name, shape=shape, dtype=dtype) - a[:] = data + with pytest.raises(ContainsArrayError): # noqa: PT012 + a = group.create_array(name=name, shape=shape, dtype=dtype) + a[:] = data assert array.path == normalize_path(name) assert array.name == "/" + array.path @@ -1365,38 +1342,6 @@ async def test_require_groups(store: LocalStore | MemoryStore, zarr_format: Zarr assert no_group == () -def test_create_dataset_with_data(store: Store, zarr_format: ZarrFormat) -> None: - """Check that deprecated create_dataset method allows input data. - - See https://github.com/zarr-developers/zarr-python/issues/2631. - """ - root = Group.from_store(store=store, zarr_format=zarr_format) - arr = np.random.random((5, 5)) - with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): - data = root.create_dataset("random", data=arr, shape=arr.shape) - np.testing.assert_array_equal(np.asarray(data), arr) - - -async def test_create_dataset(store: Store, zarr_format: ZarrFormat) -> None: - root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format) - with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."): - foo = await root.create_dataset("foo", shape=(10,), dtype="uint8") - assert foo.shape == (10,) - - with ( - pytest.raises(ContainsArrayError), - pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."), - ): - await root.create_dataset("foo", shape=(100,), dtype="int8") - - _ = await root.create_group("bar") - with ( - pytest.raises(ContainsGroupError), - pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."), - ): - await root.create_dataset("bar", shape=(100,), dtype="int8") - - async def test_require_array(store: Store, zarr_format: ZarrFormat) -> None: root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format) foo1 = await root.require_array("foo", shape=(10,), dtype="i8", attributes={"foo": 101}) From be0a7b8296c84d9d60ead631cd8dcf9f03cee999 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 21 Apr 2026 21:24:26 +0200 Subject: [PATCH 280/468] feat/memory store registry (#3679) * memory store registry * Add a `ManagedMemoryStore` class that uses an internal registry of dictionaries to manage memory-based zarr storage. Instances of `ManagedMemoryStore` have a URL representation based on the `id` of the backing dict, e.g. `memory:///`. This means the same memory-backed store can be accessed without passing an explicit store reference. * Allow a user-specified name for `ManagedMemoryStore` instances. Ensure that `ManagedMemoryStore` names do not contain the separator character "/" Ensure that `ManagedMemoryStore` instances are tied the PID of the creating process * Update docs to use `memory://` urls instead of explicitly creating a store * changelog * lint * refactor URL parsing logic * simplify PID check * update store docs * fix windows filepath parsing bug, and add tests for parse_store_url * test: Add missing tests for _dereference_path Also, change the `ExpectFail` helper class to require the `msg` parameter be set. Allowing a default value of `None` will make all `pytest.raises(case.exception, match=case.msg)` checks pass, which is not the intended behavior. * refactor: remove _dereference_path in favor of _join_paths --- changes/3679.feature.md | 3 + docs/user-guide/arrays.md | 7 +- docs/user-guide/attributes.md | 15 +- docs/user-guide/consolidated_metadata.md | 9 +- docs/user-guide/gpu.md | 3 +- docs/user-guide/groups.md | 6 +- src/zarr/storage/__init__.py | 3 +- src/zarr/storage/_common.py | 73 ++--- src/zarr/storage/_fsspec.py | 16 +- src/zarr/storage/_memory.py | 376 ++++++++++++++++++++++- src/zarr/storage/_utils.py | 83 ++++- src/zarr/testing/strategies.py | 7 +- tests/conftest.py | 2 +- tests/test_metadata/test_v3.py | 1 + tests/test_store/test_memory.py | 330 +++++++++++++++++++- tests/test_store/test_utils.py | 97 ++++++ 16 files changed, 941 insertions(+), 90 deletions(-) create mode 100644 changes/3679.feature.md create mode 100644 tests/test_store/test_utils.py diff --git a/changes/3679.feature.md b/changes/3679.feature.md new file mode 100644 index 0000000000..cdf35382e4 --- /dev/null +++ b/changes/3679.feature.md @@ -0,0 +1,3 @@ +Adds a new in-memory storage backend called `ManagedMemoryStore`. Instances of `ManagedMemoryStore` +function similarly to `MemoryStore`, but instances of `ManagedMemoryStore` can be constructed from +a URL like `memory://store`. \ No newline at end of file diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 46ff803464..6a0ecfda92 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -14,15 +14,14 @@ np.random.seed(0) ```python exec="true" session="arrays" source="above" result="ansi" import zarr -store = zarr.storage.MemoryStore() -z = zarr.create_array(store=store, shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') +z = zarr.create_array(store="memory://arrays-demo", shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') print(z) ``` The code above creates a 2-dimensional array of 32-bit integers with 10000 rows and 10000 columns, divided into chunks where each chunk has 1000 rows and 1000 -columns (and so there will be 100 chunks in total). The data is written to a -[`zarr.storage.MemoryStore`][] (e.g. an in-memory dict). See +columns (and so there will be 100 chunks in total). The data is written to an +in-memory store (see [`zarr.storage.MemoryStore`][] for more details). See [Persistent arrays](#persistent-arrays) for details on storing arrays in other stores, and see [Data types](data_types.md) for an in-depth look at the data types supported by Zarr. diff --git a/docs/user-guide/attributes.md b/docs/user-guide/attributes.md index 44d2f9fa87..d5961ed38a 100644 --- a/docs/user-guide/attributes.md +++ b/docs/user-guide/attributes.md @@ -3,10 +3,9 @@ Zarr arrays and groups support custom key/value attributes, which can be useful for storing application-specific metadata. For example: -```python exec="true" session="arrays" source="above" result="ansi" +```python exec="true" session="attributes" source="above" result="ansi" import zarr -store = zarr.storage.MemoryStore() -root = zarr.create_group(store=store) +root = zarr.create_group(store="memory://attributes-demo") root.attrs['foo'] = 'bar' z = root.create_array(name='zzz', shape=(10000, 10000), dtype='int32') z.attrs['baz'] = 42 @@ -14,22 +13,22 @@ z.attrs['qux'] = [1, 4, 7, 12] print(sorted(root.attrs)) ``` -```python exec="true" session="arrays" source="above" result="ansi" +```python exec="true" session="attributes" source="above" result="ansi" print('foo' in root.attrs) ``` -```python exec="true" session="arrays" source="above" result="ansi" +```python exec="true" session="attributes" source="above" result="ansi" print(root.attrs['foo']) ``` -```python exec="true" session="arrays" source="above" result="ansi" +```python exec="true" session="attributes" source="above" result="ansi" print(sorted(z.attrs)) ``` -```python exec="true" session="arrays" source="above" result="ansi" +```python exec="true" session="attributes" source="above" result="ansi" print(z.attrs['baz']) ``` -```python exec="true" session="arrays" source="above" result="ansi" +```python exec="true" session="attributes" source="above" result="ansi" print(z.attrs['qux']) ``` diff --git a/docs/user-guide/consolidated_metadata.md b/docs/user-guide/consolidated_metadata.md index d4fc9d6bab..c5cd31e5fc 100644 --- a/docs/user-guide/consolidated_metadata.md +++ b/docs/user-guide/consolidated_metadata.md @@ -27,8 +27,7 @@ import zarr import warnings warnings.filterwarnings("ignore", category=UserWarning) -store = zarr.storage.MemoryStore() -group = zarr.create_group(store=store) +group = zarr.create_group(store="memory://consolidated-metadata-demo") print(group) array = group.create_array(shape=(1,), name='a', dtype='float64') print(array) @@ -45,7 +44,7 @@ print(array) ``` ```python exec="true" session="consolidated_metadata" source="above" result="ansi" -result = zarr.consolidate_metadata(store) +result = zarr.consolidate_metadata("memory://consolidated-metadata-demo") print(result) ``` @@ -56,7 +55,7 @@ that can be used.: from pprint import pprint import io -consolidated = zarr.open_group(store=store) +consolidated = zarr.open_group(store="memory://consolidated-metadata-demo") consolidated_metadata = consolidated.metadata.consolidated_metadata.metadata # Note: pprint can be users without capturing the output regularly @@ -76,7 +75,7 @@ With nested groups, the consolidated metadata is available on the children, recu ```python exec="true" session="consolidated_metadata" source="above" result="ansi" child = group.create_group('child', attributes={'kind': 'child'}) grandchild = child.create_group('child', attributes={'kind': 'grandchild'}) -consolidated = zarr.consolidate_metadata(store) +consolidated = zarr.consolidate_metadata("memory://consolidated-metadata-demo") output = io.StringIO() pprint(consolidated['child'].metadata.consolidated_metadata, stream=output, width=60) diff --git a/docs/user-guide/gpu.md b/docs/user-guide/gpu.md index 3317bdf065..ff86263cf0 100644 --- a/docs/user-guide/gpu.md +++ b/docs/user-guide/gpu.md @@ -20,9 +20,8 @@ buffers used internally by Zarr via `enable_gpu()`. import zarr import cupy as cp zarr.config.enable_gpu() -store = zarr.storage.MemoryStore() z = zarr.create_array( - store=store, shape=(100, 100), chunks=(10, 10), dtype="float32", + store="memory://gpu-demo", shape=(100, 100), chunks=(10, 10), dtype="float32", ) type(z[:10, :10]) # cupy.ndarray diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index 58a9c1c806..7664e4c1dc 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -8,8 +8,7 @@ To create a group, use the [`zarr.group`][] function: ```python exec="true" session="groups" source="above" result="ansi" import zarr -store = zarr.storage.MemoryStore() -root = zarr.create_group(store=store) +root = zarr.create_group(store="memory://groups-demo") print(root) ``` @@ -105,8 +104,7 @@ Diagnostic information about arrays and groups is available via the `info` property. E.g.: ```python exec="true" session="groups" source="above" result="ansi" -store = zarr.storage.MemoryStore() -root = zarr.group(store=store) +root = zarr.group(store="memory://diagnostics-demo") foo = root.create_group('foo') bar = foo.create_array(name='bar', shape=1000000, chunks=100000, dtype='int64') bar[:] = 42 diff --git a/src/zarr/storage/__init__.py b/src/zarr/storage/__init__.py index 00df50214f..f1bd1724af 100644 --- a/src/zarr/storage/__init__.py +++ b/src/zarr/storage/__init__.py @@ -8,7 +8,7 @@ from zarr.storage._fsspec import FsspecStore from zarr.storage._local import LocalStore from zarr.storage._logging import LoggingStore -from zarr.storage._memory import GpuMemoryStore, MemoryStore +from zarr.storage._memory import GpuMemoryStore, ManagedMemoryStore, MemoryStore from zarr.storage._obstore import ObjectStore from zarr.storage._wrapper import WrapperStore from zarr.storage._zip import ZipStore @@ -18,6 +18,7 @@ "GpuMemoryStore", "LocalStore", "LoggingStore", + "ManagedMemoryStore", "MemoryStore", "ObjectStore", "StoreLike", diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 7138ad7622..1aff894119 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -23,8 +23,8 @@ ) from zarr.errors import ContainsArrayAndGroupError, ContainsArrayError, ContainsGroupError from zarr.storage._local import LocalStore -from zarr.storage._memory import MemoryStore -from zarr.storage._utils import normalize_path +from zarr.storage._memory import ManagedMemoryStore, MemoryStore +from zarr.storage._utils import _join_paths, normalize_path, parse_store_url _has_fsspec = importlib.util.find_spec("fsspec") if _has_fsspec: @@ -36,18 +36,6 @@ from zarr.core.buffer import BufferPrototype -def _dereference_path(root: str, path: str) -> str: - if not isinstance(root, str): - msg = f"{root=} is not a string ({type(root)=})" # type: ignore[unreachable] - raise TypeError(msg) - if not isinstance(path, str): - msg = f"{path=} is not a string ({type(path)=})" # type: ignore[unreachable] - raise TypeError(msg) - root = root.rstrip("/") - path = f"{root}/{path}" if root else path - return path.rstrip("/") - - class StorePath: """ Path-like interface for a Store. @@ -267,10 +255,10 @@ def delete_sync(self) -> None: def __truediv__(self, other: str) -> StorePath: """Combine this store path with another path""" - return self.__class__(self.store, _dereference_path(self.path, other)) + return self.__class__(self.store, _join_paths([self.path, other])) def __str__(self) -> str: - return _dereference_path(str(self.store), self.path) + return _join_paths([str(self.store), self.path]) def __repr__(self) -> str: return f"StorePath({self.store.__class__.__name__}, '{self}')" @@ -342,14 +330,17 @@ async def make_store( """ from zarr.storage._fsspec import FsspecStore # circular import - if ( - not (isinstance(store_like, str) and _is_fsspec_uri(store_like)) - and storage_options is not None - ): - raise TypeError( - "'storage_options' was provided but unused. " - "'storage_options' is only used when the store is passed as an FSSpec URI string.", - ) + # Parse URL early so we can reuse the result for both validation and routing + parsed = parse_store_url(store_like) if isinstance(store_like, str) else None + + # Check if storage_options is valid for this store_like + if storage_options is not None: + is_fsspec_uri = parsed is not None and parsed.scheme not in ("", "memory", "file") + if not is_fsspec_uri: + raise TypeError( + "'storage_options' was provided but unused. " + "'storage_options' is only used when the store is passed as an FSSpec URI string.", + ) assert mode in (None, "r", "r+", "a", "w", "w-") _read_only = mode == "r" @@ -377,15 +368,18 @@ async def make_store( # Create a new LocalStore return await LocalStore.open(root=store_like, mode=mode, read_only=_read_only) - elif isinstance(store_like, str): - # Either an FSSpec URI or a local filesystem path - if _is_fsspec_uri(store_like): + elif isinstance(store_like, str) and parsed is not None: + if parsed.scheme == "memory": + # Create or get a ManagedMemoryStore + return ManagedMemoryStore(name=parsed.name, path=parsed.path, read_only=_read_only) + elif parsed.scheme == "file" or not parsed.scheme: + # Local filesystem path — use parsed.path to strip the file:// scheme + return await make_store(Path(parsed.path), mode=mode, storage_options=storage_options) + else: + # Assume fsspec can handle it (s3://, gs://, http://, etc.) return FsspecStore.from_url( store_like, storage_options=storage_options, read_only=_read_only ) - else: - # Assume a filesystem path - return await make_store(Path(store_like), mode=mode, storage_options=storage_options) elif _has_fsspec and isinstance(store_like, FSMap): return FsspecStore.from_mapper(store_like, read_only=_read_only) @@ -460,25 +454,6 @@ async def make_store_path( return await StorePath.open(store, path=path_normalized, mode=mode) -def _is_fsspec_uri(uri: str) -> bool: - """ - Check if a URI looks like a non-local fsspec URI. - - Examples - -------- - ```python - from zarr.storage._common import _is_fsspec_uri - _is_fsspec_uri("s3://bucket") - # True - _is_fsspec_uri("my-directory") - # False - _is_fsspec_uri("local://my-directory") - # False - ``` - """ - return "://" in uri or ("::" in uri and "local://" not in uri) - - async def ensure_no_existing_node( store_path: StorePath, zarr_format: ZarrFormat, diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index f9e4ed375d..ac50a0527f 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -16,7 +16,7 @@ ) from zarr.core.buffer import Buffer from zarr.errors import ZarrUserWarning -from zarr.storage._common import _dereference_path +from zarr.storage._utils import _join_paths if TYPE_CHECKING: from collections.abc import AsyncIterator, Iterable @@ -282,7 +282,7 @@ async def get( # docstring inherited if not self._is_open: await self._open() - path = _dereference_path(self.path, key) + path = _join_paths([self.path, key]) try: if byte_range is None: @@ -329,7 +329,7 @@ async def set( raise TypeError( f"FsspecStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead." ) - path = _dereference_path(self.path, key) + path = _join_paths([self.path, key]) # write data if byte_range: raise NotImplementedError @@ -338,7 +338,7 @@ async def set( async def delete(self, key: str) -> None: # docstring inherited self._check_writable() - path = _dereference_path(self.path, key) + path = _join_paths([self.path, key]) try: await self.fs._rm(path) except FileNotFoundError: @@ -354,14 +354,14 @@ async def delete_dir(self, prefix: str) -> None: ) self._check_writable() - path_to_delete = _dereference_path(self.path, prefix) + path_to_delete = _join_paths([self.path, prefix]) with suppress(*self.allowed_exceptions): await self.fs._rm(path_to_delete, recursive=True) async def exists(self, key: str) -> bool: # docstring inherited - path = _dereference_path(self.path, key) + path = _join_paths([self.path, key]) exists: bool = await self.fs._exists(path) return exists @@ -378,7 +378,7 @@ async def get_partial_values( starts: list[int | None] = [] stops: list[int | None] = [] for key, byte_range in key_ranges: - paths.append(_dereference_path(self.path, key)) + paths.append(_join_paths([self.path, key])) if byte_range is None: starts.append(None) stops.append(None) @@ -429,7 +429,7 @@ async def list_prefix(self, prefix: str) -> AsyncIterator[str]: yield onefile.removeprefix(f"{self.path}/") async def getsize(self, key: str) -> int: - path = _dereference_path(self.path, key) + path = _join_paths([self.path, key]) info = await self.fs._info(path) size = info.get("size") diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index 1194894b9d..53d3cfbfde 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -1,5 +1,8 @@ from __future__ import annotations +import os +import threading +import weakref from logging import getLogger from typing import TYPE_CHECKING, Any, Self @@ -7,7 +10,12 @@ from zarr.core.buffer import Buffer, gpu from zarr.core.buffer.core import default_buffer_prototype from zarr.core.common import concurrent_map -from zarr.storage._utils import _normalize_byte_range_index +from zarr.storage._utils import ( + _join_paths, + _normalize_byte_range_index, + normalize_path, + parse_store_url, +) if TYPE_CHECKING: from collections.abc import AsyncIterator, Iterable, MutableMapping @@ -517,3 +525,369 @@ async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None # Convert to gpu.Buffer gpu_value = value if isinstance(value, gpu.Buffer) else gpu.Buffer.from_buffer(value) await super().set(key, gpu_value, byte_range=byte_range) + + +# ----------------------------------------------------------------------------- +# ManagedMemoryStore and its registry +# ----------------------------------------------------------------------------- +# ManagedMemoryStore owns the lifecycle of its backing dict, enabling proper +# weakref-based tracking. This allows memory:// URLs to be resolved back to +# the store's dict within the same process. + + +class _ManagedStoreDict(dict[str, Buffer]): + """ + A dict subclass that supports weak references. + + Regular dicts don't support weakrefs, but we need to track managed store dicts + in a WeakValueDictionary so they can be garbage collected when no longer + referenced. This subclass adds the necessary __weakref__ slot. + """ + + __slots__ = ("__weakref__",) + + +class _ManagedStoreDictRegistry: + """ + Registry for managed store dicts. + + This registry is the source of truth for managed store dicts. It creates + new dicts, tracks them via weak references, and looks them up by name. + """ + + def __init__(self) -> None: + self._registry: weakref.WeakValueDictionary[str, _ManagedStoreDict] = ( + weakref.WeakValueDictionary() + ) + self._counter = 0 + self._lock = threading.Lock() + + def _generate_name(self) -> str: + """Generate a unique name for a store. + + Must be called while holding `self._lock`. + """ + name = str(self._counter) + self._counter += 1 + return name + + def get_or_create(self, name: str | None = None) -> tuple[_ManagedStoreDict, str]: + """ + Get an existing managed dict by name, or create a new one. + + Thread-safe: uses a lock to prevent TOCTOU races between + checking for an existing entry and inserting a new one. + + Parameters + ---------- + name : str | None + The name for the store. If None, a unique name is auto-generated. + If a store with this name already exists, returns the existing store. + Names cannot contain '/' characters. + + Returns + ------- + tuple[_ManagedStoreDict, str] + The store dict and its name. + + Raises + ------ + ValueError + If the name contains '/' characters. + """ + with self._lock: + if name is None: + name = self._generate_name() + elif "/" in name: + raise ValueError( + f"Store name cannot contain '/': {name!r}. " + "Use the 'path' parameter to specify a path within the store." + ) + + existing = self._registry.get(name) + if existing is not None: + return existing, name + + store_dict = _ManagedStoreDict() + self._registry[name] = store_dict + return store_dict, name + + def get(self, name: str) -> _ManagedStoreDict | None: + """ + Look up a managed store dict by name. + + Parameters + ---------- + name : str + The name of the store. + + Returns + ------- + _ManagedStoreDict | None + The store dict if found, None otherwise. + """ + return self._registry.get(name) + + +_managed_store_dict_registry = _ManagedStoreDictRegistry() + + +class ManagedMemoryStore(MemoryStore): + """ + A memory store that owns and manages the lifecycle of its backing dict. + + Unlike ``MemoryStore`` which accepts any ``MutableMapping``, this store + creates and owns its backing dict internally. This enables proper lifecycle + management and allows the store to be looked up by its ``memory://`` URL + within the same process. + + Parameters + ---------- + name : str | None + The name for this store, used in the ``memory://`` URL. If None, a unique + name is auto-generated. If a store with this name already exists, the + new store will share the same backing dict. + path : str + The root path for this store. All keys will be prefixed with this path. + read_only : bool + Whether the store is read-only. + + Attributes + ---------- + name : str + The name of this store. + path : str + The root path of this store. + + Notes + ----- + The backing dict is tracked via weak references and will be garbage collected + when no ``ManagedMemoryStore`` instances reference it. URLs pointing to a + garbage-collected store will fail to resolve. + + See Also + -------- + MemoryStore : A memory store that accepts any MutableMapping. + + Examples + -------- + >>> store = ManagedMemoryStore(name="my-data") + >>> str(store) + 'memory://my-data' + >>> # Later, resolve the URL back to the store's dict + >>> store2 = ManagedMemoryStore.from_url("memory://my-data") + >>> store2._store_dict is store._store_dict + True + >>> # Create a store with a path prefix + >>> store3 = ManagedMemoryStore.from_url("memory://my-data/subdir") + >>> store3.path + 'subdir' + """ + + _store_dict: _ManagedStoreDict + _name: str + path: str + + def __init__(self, name: str | None = None, *, path: str = "", read_only: bool = False) -> None: + # Skip MemoryStore.__init__ and call Store.__init__ directly + # because we manage _store_dict via the registry, not via a user-supplied + # MutableMapping. If MemoryStore.__init__ ever adds logic beyond setting + # _store_dict, that logic must be replicated here. + Store.__init__(self, read_only=read_only) + + # Get or create a managed dict from the registry + self._store_dict, self._name = _managed_store_dict_registry.get_or_create(name) + self.path = normalize_path(path) + + def __str__(self) -> str: + return _join_paths([f"memory://{self._name}", self.path]) + + def __repr__(self) -> str: + return f"ManagedMemoryStore('{self}')" + + def __eq__(self, other: object) -> bool: + return ( + isinstance(other, type(self)) + and self._store_dict is other._store_dict + and self.path == other.path + and self.read_only == other.read_only + ) + + @property + def name(self) -> str: + """The name of this store, used in the memory:// URL.""" + return self._name + + @classmethod + def _from_managed_dict( + cls, + managed_dict: _ManagedStoreDict, + name: str, + *, + path: str = "", + read_only: bool = False, + ) -> ManagedMemoryStore: + """Internal: create a store from an existing managed dict.""" + store = object.__new__(cls) + Store.__init__(store, read_only=read_only) + store._store_dict = managed_dict + store._name = name + store.path = normalize_path(path) + return store + + def with_read_only(self, read_only: bool = False) -> ManagedMemoryStore: + # docstring inherited + return type(self)._from_managed_dict( + self._store_dict, self._name, path=self.path, read_only=read_only + ) + + @classmethod + def from_url(cls, url: str, *, read_only: bool = False) -> ManagedMemoryStore: + """ + Create a ManagedMemoryStore from a memory:// URL. + + This looks up the backing dict in the process-wide registry and creates + a new store instance that shares the same dict. + + Parameters + ---------- + url : str + A URL like "memory://my-store" or "memory://my-store/path/to/data" + identifying the store and optional path prefix. + read_only : bool + Whether the new store should be read-only. + + Returns + ------- + ManagedMemoryStore + A store sharing the same backing dict as the original. + + Raises + ------ + ValueError + If the URL is not a valid memory:// URL or the store has been + garbage collected. + """ + parsed = parse_store_url(url) + if parsed.scheme != "memory": + raise ValueError( + f"Expected a 'memory://' URL, got scheme {parsed.scheme!r} in '{url}'." + ) + name = parsed.name or "" + managed_dict = _managed_store_dict_registry.get(name) + if managed_dict is None: + raise ValueError( + f"Memory store not found for URL '{url}'. " + "The store may have been garbage collected." + ) + return cls._from_managed_dict(managed_dict, name, path=parsed.path, read_only=read_only) + + # Override MemoryStore methods to use path prefix and check process + + async def get( + self, + key: str, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + # docstring inherited + return await super().get( + _join_paths([self.path, key]), prototype=prototype, byte_range=byte_range + ) + + async def get_partial_values( + self, + prototype: BufferPrototype, + key_ranges: Iterable[tuple[str, ByteRequest | None]], + ) -> list[Buffer | None]: + # docstring inherited + key_ranges = [(_join_paths([self.path, key]), byte_range) for key, byte_range in key_ranges] + return await super().get_partial_values(prototype, key_ranges) + + async def exists(self, key: str) -> bool: + # docstring inherited + return await super().exists(_join_paths([self.path, key])) + + async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None = None) -> None: + # docstring inherited + return await super().set(_join_paths([self.path, key]), value, byte_range=byte_range) + + async def set_if_not_exists(self, key: str, value: Buffer) -> None: + # docstring inherited + return await super().set_if_not_exists(_join_paths([self.path, key]), value) + + async def delete(self, key: str) -> None: + # docstring inherited + return await super().delete(_join_paths([self.path, key])) + + async def list(self) -> AsyncIterator[str]: + # docstring inherited + prefix = self.path + "/" if self.path else "" + async for key in super().list(): + if key.startswith(prefix): + yield key.removeprefix(prefix) + + async def list_prefix(self, prefix: str) -> AsyncIterator[str]: + # docstring inherited + # Manual concatenation instead of _join_paths because we need "path/" + # as the prefix when prefix is empty (to list all keys under self.path) + full_prefix = f"{self.path}/{prefix}" if self.path else prefix + path_prefix = self.path + "/" if self.path else "" + async for key in super().list_prefix(full_prefix): + yield key.removeprefix(path_prefix) + + async def list_dir(self, prefix: str) -> AsyncIterator[str]: + # docstring inherited + full_prefix = _join_paths([self.path, prefix]) + async for key in super().list_dir(full_prefix): + yield key + + def __reduce__( + self, + ) -> tuple[type[ManagedMemoryStore], tuple[str | None], dict[str, Any]]: + """ + Support pickling of ManagedMemoryStore. + + On unpickle, the store will reconnect to an existing store with the same + name if one exists in the registry, or create a new empty store otherwise. + + Note that the backing dict data is NOT serialized - only the store's + identity (name, path, read_only) is preserved. If the original store has + been garbage collected, the unpickled store will have an empty dict. + + The current process ID is preserved so that cross-process unpickling can be + detected and will raise an error at unpickle time. + """ + return ( + self.__class__, + (self._name,), + { + "path": self.path, + "read_only": self.read_only, + "created_pid": os.getpid(), + }, + ) + + def __setstate__(self, state: dict[str, Any]) -> None: + """Restore state after unpickling. + + The pickle protocol calls ``cls(name)`` (via ``__reduce__``'s args) + then ``__setstate__(state)``. ``__init__`` already set up + ``_store_dict`` and ``_name`` from the registry — we just restore + path and read_only here. + """ + # Check for cross-process usage first, before mutating state + created_pid = state.get("created_pid") + if created_pid is not None and created_pid != os.getpid(): + raise RuntimeError( + f"ManagedMemoryStore '{self._name}' was created in process {created_pid} " + f"but is being unpickled in process {os.getpid()}. " + "ManagedMemoryStore instances cannot be shared across processes because " + "their backing dict is not serialized. Use a persistent store (e.g., " + "LocalStore, ZipStore) for cross-process data sharing." + ) + + self.path = normalize_path(state.get("path", "")) + # Use the Store-level _read_only attribute directly because + # Store.__init__ was already called by __init__ during unpickling + self._read_only = state.get("read_only", False) diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index 8939ead30b..722a2d3568 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -2,7 +2,8 @@ import importlib import re -from pathlib import Path +from pathlib import Path, PureWindowsPath +from urllib.parse import urlparse if importlib.util.find_spec("upath"): from upath.core import UPath @@ -12,7 +13,8 @@ class UPath: # type: ignore[no-redef] pass -from typing import TYPE_CHECKING +import sys +from typing import TYPE_CHECKING, NamedTuple from zarr.abc.store import OffsetByteRequest, RangeByteRequest, SuffixByteRequest @@ -23,6 +25,83 @@ class UPath: # type: ignore[no-redef] from zarr.core.buffer import Buffer +class ParsedStoreUrl(NamedTuple): + """ + Parsed components of a store URL. + + Attributes + ---------- + scheme : str + The URL scheme (e.g., "memory", "file", "s3"). Empty string for local paths. + name : str | None + The store name/host component. For memory:// URLs this is the store name. + None if empty. + path : str + The path component within the store. + raw : str + The original URL string. + """ + + scheme: str + name: str | None + path: str + raw: str + + +def parse_store_url(url: str) -> ParsedStoreUrl: + """ + Parse a store URL into its components. + + Parameters + ---------- + url : str + A URL like "memory://store-name/path" or "s3://bucket/key" or a local path. + + Returns + ------- + ParsedStoreUrl + Named tuple with scheme, name, path, and raw URL. + + Examples + -------- + >>> parse_store_url("memory://mystore") + ParsedStoreUrl(scheme='memory', name='mystore', path='', raw='memory://mystore') + + >>> parse_store_url("memory://mystore/path/to/data") + ParsedStoreUrl(scheme='memory', name='mystore', path='path/to/data', raw='memory://mystore/path/to/data') + + >>> parse_store_url("s3://bucket/key") + ParsedStoreUrl(scheme='s3', name='bucket', path='key', raw='s3://bucket/key') + + >>> parse_store_url("/local/path") + ParsedStoreUrl(scheme='', name=None, path='/local/path', raw='/local/path') + + Note that ``memory://name/path`` and ``memory:///path`` are different: + the first has ``name="name"`` and ``path="path"``, while the second has + ``name=None`` and ``path="/path"`` (no host component between ``//`` and ``/``). + """ + # On Windows, bare paths like "C:\foo" or "C:/foo" cause urlparse to + # misinterpret the drive letter as a URL scheme. Detect this early and + # return a local-path result without going through urlparse. + if sys.platform == "win32" and PureWindowsPath(url).drive: + return ParsedStoreUrl(scheme="", name=None, path=url, raw=url) + + parsed = urlparse(url) + + # netloc is the "host" part (store name for memory://, bucket for s3://, etc.) + name = parsed.netloc or None + + # For URLs with a scheme and netloc (like memory://store/path or s3://bucket/key), + # strip the leading slash from the path component. + # For local paths (no scheme), preserve the path as-is. + if parsed.scheme and parsed.netloc: + path = parsed.path.lstrip("/") + else: + path = parsed.path + + return ParsedStoreUrl(scheme=parsed.scheme, name=name, path=path, raw=url) + + def normalize_path(path: str | bytes | Path | None) -> str: if path is None: result = "" diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 6832ded5fb..3bb059b3a8 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -21,8 +21,7 @@ from zarr.core.metadata.v3 import RectilinearChunkGridMetadata, RegularChunkGridMetadata from zarr.core.sync import sync from zarr.storage import MemoryStore, StoreLike -from zarr.storage._common import _dereference_path -from zarr.storage._utils import normalize_path +from zarr.storage._utils import _join_paths, normalize_path from zarr.types import AnyArray TrueOrFalse = Literal[True, False] @@ -288,7 +287,7 @@ def arrays( expected_attrs = {} if attributes is None else attributes - array_path = _dereference_path(path, name) + array_path = _join_paths([path, name]) root = zarr.open_group(store, mode=open_mode, zarr_format=zarr_format) # Convert chunk grid metadata to a form create_array accepts: @@ -621,7 +620,7 @@ def complex_rectilinear_arrays( store = draw(stores, label="store") path = draw(paths, label="array parent") name = draw(array_names, label="array name") - array_path = _dereference_path(path, name) + array_path = _join_paths([path, name]) root = zarr.open_group(store, mode="w", zarr_format=3) with zarr.config.set({"array.rectilinear_chunks": True}): diff --git a/tests/conftest.py b/tests/conftest.py index bc9b8c35aa..de1730fff9 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -74,7 +74,7 @@ class ExpectFail[TIn]: input: TIn exception: type[Exception] id: str - msg: str | None = None + msg: str async def parse_store( diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index bb106e2474..2bd8488702 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -225,6 +225,7 @@ def test_array_metadata_roundtrip(case: Expect[dict[str, Any], dict[str, Any]]) ExpectFail( input={"data_type": "uint8", "fill_value": {}}, exception=TypeError, + msg=".*", id="invalid_fill_value_type", ), ], diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 03c8b24271..4ffc15a87b 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -12,7 +12,7 @@ from zarr.core.buffer import Buffer, cpu, gpu from zarr.core.sync import sync from zarr.errors import ZarrUserWarning -from zarr.storage import GpuMemoryStore, MemoryStore +from zarr.storage import GpuMemoryStore, ManagedMemoryStore, MemoryStore from zarr.testing.store import StoreTests from zarr.testing.utils import gpu_test @@ -181,3 +181,331 @@ def test_from_dict(self) -> None: result = GpuMemoryStore.from_dict(d) for v in result._store_dict.values(): assert type(v) is gpu.Buffer + + +class TestManagedMemoryStore(StoreTests[ManagedMemoryStore, cpu.Buffer]): + store_cls = ManagedMemoryStore + buffer_cls = cpu.Buffer + + async def set(self, store: ManagedMemoryStore, key: str, value: Buffer) -> None: + store._store_dict[key] = value + + async def get(self, store: ManagedMemoryStore, key: str) -> Buffer: + return store._store_dict[key] + + @pytest.fixture + def store_kwargs(self, request: pytest.FixtureRequest) -> dict[str, Any]: + # Use a unique name per test to avoid sharing state between tests + # but ensure the name is deterministic for equality tests + # Replace '/' with '-' since store names cannot contain '/' + sanitized_name = request.node.name.replace("/", "-") + return {"name": f"test-{sanitized_name}"} + + @pytest.fixture + async def store(self, store_kwargs: dict[str, Any]) -> ManagedMemoryStore: + return self.store_cls(**store_kwargs) + + def test_store_repr(self, store: ManagedMemoryStore) -> None: + assert str(store) == f"memory://{store.name}" + + async def test_serializable_store(self, store: ManagedMemoryStore) -> None: + """ + Test pickling semantics for ManagedMemoryStore. + + When pickled and unpickled within the same process (where the original + store still exists in the registry), the unpickled store reconnects to + the same backing dict. + """ + import pickle + + # Add some data to the store + await store.set("test-key", self.buffer_cls.from_bytes(b"test-value")) + + # Pickle and unpickle the store + pickled = pickle.dumps(store) + store2 = pickle.loads(pickled) + + # The unpickled store should reconnect to the same backing dict + assert store2._store_dict is store._store_dict + assert store2.name == store.name + assert store2.path == store.path + assert store2.read_only == store.read_only + + # The data should be accessible + result = await store2.get("test-key") + assert result is not None + assert result.to_bytes() == b"test-value" + + async def test_pickle_with_path(self) -> None: + """Test that path is preserved through pickle round-trip.""" + import pickle + + store = ManagedMemoryStore(name="pickle-path-test", path="some/path") + await store.set("key", self.buffer_cls.from_bytes(b"value")) + + pickled = pickle.dumps(store) + store2 = pickle.loads(pickled) + + assert store2.path == "some/path" + assert store2._store_dict is store._store_dict + + # Check that operations use the path correctly + result = await store2.get("key") + assert result is not None + assert result.to_bytes() == b"value" + + def test_pickle_after_gc(self) -> None: + """ + Test that unpickling after the original store is garbage collected + creates a new empty store with the same name (in the same process). + """ + import gc + import pickle + + # Create a store with a unique name and pickle it + store = ManagedMemoryStore(name="gc-pickle-test") + store._store_dict["key"] = self.buffer_cls.from_bytes(b"value") + pickled = pickle.dumps(store) + + # Delete the store and garbage collect + del store + gc.collect() + + # Unpickling should create a new store with an empty dict + store2 = pickle.loads(pickled) + assert store2.name == "gc-pickle-test" + # The dict is empty because the original was garbage collected + assert len(store2._store_dict) == 0 + + async def test_cross_process_detection(self) -> None: + """ + Test that unpickling a ManagedMemoryStore in a different process raises an error. + + This prevents silent data loss when a store is pickled and unpickled + in a different process (e.g., with multiprocessing). + """ + import os + + store = ManagedMemoryStore(name="cross-process-test") + await store.set("key", self.buffer_cls.from_bytes(b"value")) + + # Get the reduce tuple and modify the state to simulate a different process + cls, args, state = store.__reduce__() + state["created_pid"] = os.getpid() + 1 # Fake a different process ID + + # Manually reconstruct what pickle.loads would do + # This simulates unpickling data that was pickled in a different process + reconstructed = cls(*args) + with pytest.raises(RuntimeError, match="was created in process"): + reconstructed.__setstate__(state) + + def test_store_supports_writes(self, store: ManagedMemoryStore) -> None: + assert store.supports_writes + + def test_store_supports_listing(self, store: ManagedMemoryStore) -> None: + assert store.supports_listing + + @pytest.mark.parametrize("dtype", ["uint8", "float32", "int64"]) + @pytest.mark.parametrize("zarr_format", [2, 3]) + async def test_deterministic_size( + self, store: MemoryStore, dtype: npt.DTypeLike, zarr_format: ZarrFormat + ) -> None: + a = zarr.empty( + store=store, + shape=(3,), + chunks=(1000,), + dtype=dtype, + zarr_format=zarr_format, + overwrite=True, + ) + a[...] = 1 + a.resize((1000,)) + + np.testing.assert_array_equal(a[:3], 1) + np.testing.assert_array_equal(a[3:], 0) + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + async def test_get_bytes_with_prototype_none( + self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_bytes works with prototype=None.""" + data = b"hello world" + key = "test_key" + await self.set(store, key, self.buffer_cls.from_bytes(data)) + + result = await store._get_bytes(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + def test_get_bytes_sync_with_prototype_none( + self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_bytes_sync works with prototype=None.""" + data = b"hello world" + key = "test_key" + sync(self.set(store, key, self.buffer_cls.from_bytes(data))) + + result = store._get_bytes_sync(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + async def test_get_json_with_prototype_none( + self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_json works with prototype=None.""" + data = {"foo": "bar", "number": 42} + key = "test.json" + await self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode())) + + result = await store._get_json(key, prototype=buffer_cls) + assert result == data + + @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) + def test_get_json_sync_with_prototype_none( + self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype + ) -> None: + """Test that get_json_sync works with prototype=None.""" + data = {"foo": "bar", "number": 42} + key = "test.json" + sync(self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode()))) + + result = store._get_json_sync(key, prototype=buffer_cls) + assert result == data + + def test_from_url(self, store: ManagedMemoryStore) -> None: + """Test that from_url creates a store sharing the same dict.""" + url = str(store) + store2 = ManagedMemoryStore.from_url(url) + assert store2._store_dict is store._store_dict + + def test_from_url_with_path(self, store: ManagedMemoryStore) -> None: + """Test that from_url extracts path component from URL.""" + url = str(store) + "/some/path" + store2 = ManagedMemoryStore.from_url(url) + assert store2._store_dict is store._store_dict + assert store2.path == "some/path" + assert str(store2) == url + + def test_from_url_invalid(self) -> None: + """Test that from_url raises ValueError for non-existent store.""" + with pytest.raises(ValueError, match="Memory store not found"): + ManagedMemoryStore.from_url("memory://nonexistent-store") + + def test_from_url_not_memory_scheme(self) -> None: + """Test that from_url raises ValueError for non-memory URLs.""" + with pytest.raises(ValueError, match="Expected a 'memory://' URL"): + ManagedMemoryStore.from_url("file:///tmp/test") + + def test_named_store(self) -> None: + """Test that stores can be created with explicit names.""" + store = ManagedMemoryStore(name="my-test-store") + assert store.name == "my-test-store" + assert str(store) == "memory://my-test-store" + + def test_named_store_shares_dict(self) -> None: + """Test that creating a store with the same name shares the dict.""" + store1 = ManagedMemoryStore(name="shared-store") + store2 = ManagedMemoryStore(name="shared-store") + assert store1._store_dict is store2._store_dict + assert store1.name == store2.name + + def test_auto_generated_name(self) -> None: + """Test that stores get auto-generated names when none provided.""" + store = ManagedMemoryStore() + assert store.name is not None + assert str(store) == f"memory://{store.name}" + + def test_with_read_only_shares_dict(self, store: ManagedMemoryStore) -> None: + """Test that with_read_only creates a store sharing the same dict.""" + store2 = store.with_read_only(True) + assert store2._store_dict is store._store_dict + assert store2.read_only is True + assert store.read_only is False + + def test_with_read_only_preserves_path(self) -> None: + """Test that with_read_only preserves the path.""" + store = ManagedMemoryStore(name="path-test", path="some/path") + store2 = store.with_read_only(True) + assert store2.path == "some/path" + assert store2._store_dict is store._store_dict + + async def test_path_prefix_operations(self) -> None: + """Test that store operations use the path prefix correctly.""" + store = ManagedMemoryStore(name="prefix-test") + store_with_path = ManagedMemoryStore.from_url("memory://prefix-test/subdir") + + # Write via store_with_path + await store_with_path.set("key", self.buffer_cls.from_bytes(b"value")) + + # The key should be stored with the prefix in the underlying dict + assert "subdir/key" in store._store_dict + assert "key" not in store._store_dict + + # Read via store_with_path should work + result = await store_with_path.get("key") + assert result is not None + assert result.to_bytes() == b"value" + + # Read via store without path should use full key + result2 = await store.get("subdir/key") + assert result2 is not None + assert result2.to_bytes() == b"value" + + async def test_path_list_operations(self) -> None: + """Test that list operations filter by path prefix.""" + store = ManagedMemoryStore(name="list-test") + + # Set up some keys at different paths + await store.set("a/key1", self.buffer_cls.from_bytes(b"v1")) + await store.set("a/key2", self.buffer_cls.from_bytes(b"v2")) + await store.set("b/key3", self.buffer_cls.from_bytes(b"v3")) + + # Create a store with path "a" + store_a = ManagedMemoryStore.from_url("memory://list-test/a") + + # list() should only return keys under "a", without the "a/" prefix + keys = [k async for k in store_a.list()] + assert sorted(keys) == ["key1", "key2"] + + async def test_path_exists(self) -> None: + """Test that exists() uses the path prefix.""" + store = ManagedMemoryStore(name="exists-test") + await store.set("prefix/key", self.buffer_cls.from_bytes(b"value")) + + store_with_path = ManagedMemoryStore.from_url("memory://exists-test/prefix") + assert await store_with_path.exists("key") + assert not await store_with_path.exists("prefix/key") + + def test_path_normalization(self) -> None: + """Test that paths are normalized.""" + store1 = ManagedMemoryStore(name="norm-test", path="a/b/") + store2 = ManagedMemoryStore(name="norm-test", path="/a/b") + store3 = ManagedMemoryStore(name="norm-test", path="a//b") + assert store1.path == "a/b" + assert store2.path == "a/b" + assert store3.path == "a/b" + + def test_name_cannot_contain_slash(self) -> None: + """Test that store names cannot contain '/'.""" + with pytest.raises(ValueError, match="cannot contain '/'"): + ManagedMemoryStore(name="foo/bar") + + def test_garbage_collection(self) -> None: + """Test that the dict is garbage collected when no stores reference it.""" + import gc + + store = ManagedMemoryStore() + url = str(store) + + # URL should resolve while store exists + store2 = ManagedMemoryStore.from_url(url) + assert store2._store_dict is store._store_dict + + # Delete both stores + del store + del store2 + gc.collect() + + # URL should no longer resolve + with pytest.raises(ValueError, match="garbage collected"): + ManagedMemoryStore.from_url(url) diff --git a/tests/test_store/test_utils.py b/tests/test_store/test_utils.py new file mode 100644 index 0000000000..b1934e7eae --- /dev/null +++ b/tests/test_store/test_utils.py @@ -0,0 +1,97 @@ +from __future__ import annotations + +import sys +from unittest.mock import patch + +import pytest + +from zarr.storage._utils import ParsedStoreUrl, parse_store_url + + +class TestParseStoreUrl: + """Tests for parse_store_url.""" + + def test_memory_url(self) -> None: + result = parse_store_url("memory://mystore") + assert result == ParsedStoreUrl( + scheme="memory", name="mystore", path="", raw="memory://mystore" + ) + + def test_memory_url_with_path(self) -> None: + result = parse_store_url("memory://mystore/path/to/data") + assert result == ParsedStoreUrl( + scheme="memory", + name="mystore", + path="path/to/data", + raw="memory://mystore/path/to/data", + ) + + def test_memory_url_no_name(self) -> None: + result = parse_store_url("memory://") + assert result.scheme == "memory" + assert result.name is None + + def test_s3_url(self) -> None: + result = parse_store_url("s3://bucket/key") + assert result == ParsedStoreUrl( + scheme="s3", name="bucket", path="key", raw="s3://bucket/key" + ) + + def test_file_url(self) -> None: + result = parse_store_url("file:///tmp/test") + assert result.scheme == "file" + + def test_local_absolute_path(self) -> None: + result = parse_store_url("/local/path") + assert result == ParsedStoreUrl(scheme="", name=None, path="/local/path", raw="/local/path") + + def test_local_relative_path(self) -> None: + result = parse_store_url("relative/path") + assert result == ParsedStoreUrl( + scheme="", name=None, path="relative/path", raw="relative/path" + ) + + @pytest.mark.parametrize( + "url", + [ + "C:\\Users\\foo", + "C:/Users/foo", + "D:/data/zarr", + "c:/test", + ], + ) + def test_windows_drive_letter(self, url: str) -> None: + """On Windows, bare drive-letter paths must be treated as local paths.""" + with patch.object(sys, "platform", "win32"): + result = parse_store_url(url) + assert result.scheme == "" + assert result.name is None + assert result.path == url + assert result.raw == url + + @pytest.mark.parametrize( + "url", + [ + "file:///C:/Users/foo", + "file://C:/Users/foo", + ], + ) + def test_file_url_with_drive_letter_on_windows(self, url: str) -> None: + """file:// URLs with drive letters are not treated as bare paths.""" + with patch.object(sys, "platform", "win32"): + result = parse_store_url(url) + assert result.scheme == "file" + + @pytest.mark.parametrize( + "url", + [ + "C:\\Users\\foo", + "C:/Users/foo", + ], + ) + def test_drive_letter_not_special_on_non_windows(self, url: str) -> None: + """On non-Windows platforms, drive-letter paths go through urlparse.""" + with patch.object(sys, "platform", "linux"): + result = parse_store_url(url) + # urlparse interprets the drive letter as a scheme + assert result.scheme == "c" From 82170464470197bcd816993aa059ee00dafee214 Mon Sep 17 00:00:00 2001 From: Brian Michell Date: Tue, 21 Apr 2026 14:50:29 -0500 Subject: [PATCH 281/468] Implement support for `structured` and `struct` zarr-extension defined dtypes (#3781) * Implement official support for `structured` and `struct` dtypes according to new extension. * Update docs and add changelog * Implement `struct` subclass instead of modifying `structured` * Remove Structured from AnyDType to fix test_match_dtype_unique * Revert removal of linting ignore flag * Fix dtype support * Fix import sort order -- Linting * Resolve https://github.com/zarr-developers/zarr-python/pull/3781#discussion_r3058558246 Only register `Struct` and allow it to appropriately pick up `structured` dtype * Linting --------- Co-authored-by: Davis Vann Bennett --- changes/3781.feature.md | 1 + docs/user-guide/data_types.md | 31 +++ src/zarr/codecs/bytes.py | 17 +- src/zarr/core/array.py | 6 +- src/zarr/core/dtype/__init__.py | 14 +- src/zarr/core/dtype/npy/structured.py | 213 +++++++++++++++++-- src/zarr/dtype.py | 4 + tests/test_dtype/conftest.py | 5 +- tests/test_dtype/test_npy/test_structured.py | 196 ++++++++++++++--- tests/test_v2.py | 5 +- 10 files changed, 441 insertions(+), 51 deletions(-) create mode 100644 changes/3781.feature.md diff --git a/changes/3781.feature.md b/changes/3781.feature.md new file mode 100644 index 0000000000..191ca5ed4a --- /dev/null +++ b/changes/3781.feature.md @@ -0,0 +1 @@ +Added `Struct` class (subclass of `Structured`) implementing the zarr-extensions `struct` dtype spec. Uses object-style field format and dict fill values. Legacy `Structured` remains available for backward compatibility. diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md index aa19baf891..3cdafb5f28 100644 --- a/docs/user-guide/data_types.md +++ b/docs/user-guide/data_types.md @@ -229,6 +229,37 @@ here, it's possible to create it yourself: see [Adding New Data Types](#adding-n #### Struct-like - [Structured][zarr.dtype.Structured] +!!! note "Zarr V3 Structured Data Types" + + In Zarr V3, structured data types are specified using the `struct` extension defined in the + [zarr-extensions repository](https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/struct). + The JSON representation uses an object format for fields: + + ```json + { + "name": "struct", + "configuration": { + "fields": [ + {"name": "x", "data_type": "float32"}, + {"name": "y", "data_type": "int64"} + ] + } + } + ``` + + For backward compatibility, Zarr Python also accepts the legacy `structured` name with + tuple-format fields when reading existing data. + + Fill values for structured types are represented as JSON objects mapping field names to values: + + ```json + {"x": 1.5, "y": 42} + ``` + + When using structured types with multi-byte fields, the `bytes` codec must specify an + explicit `endian` parameter. If omitted, Zarr Python assumes little-endian for legacy + compatibility but emits a warning. + ### Example Usage This section will demonstrates the basic usage of Zarr data types. diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index 86bb354fb5..48f8b57c49 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -1,6 +1,7 @@ from __future__ import annotations import sys +import warnings from dataclasses import dataclass, replace from enum import Enum from typing import TYPE_CHECKING @@ -9,6 +10,7 @@ from zarr.core.buffer import Buffer, NDBuffer from zarr.core.common import JSON, parse_enum, parse_named_configuration from zarr.core.dtype.common import HasEndianness +from zarr.core.dtype.npy.structured import Struct if TYPE_CHECKING: from typing import Self @@ -56,7 +58,20 @@ def to_dict(self) -> dict[str, JSON]: return {"name": "bytes", "configuration": {"endian": self.endian.value}} def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: - if not isinstance(array_spec.dtype, HasEndianness): + if isinstance(array_spec.dtype, Struct): + if array_spec.dtype.has_multi_byte_fields(): + if self.endian is None: + warnings.warn( + "Missing 'endian' for structured dtype with multi-byte fields. " + "Assuming little-endian for legacy compatibility.", + UserWarning, + stacklevel=2, + ) + return replace(self, endian=Endian.little) + else: + if self.endian is not None: + return replace(self, endian=None) + elif not isinstance(array_spec.dtype, HasEndianness): if self.endian is not None: return replace(self, endian=None) elif self.endian is None: diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index f0cd5dd734..8183a63beb 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -69,6 +69,7 @@ ) from zarr.core.config import config as zarr_config from zarr.core.dtype import ( + Structured, VariableLengthBytes, VariableLengthUTF8, ZDType, @@ -4879,10 +4880,13 @@ def default_serializer_v3(dtype: ZDType[Any, Any]) -> ArrayBytesCodec: length strings and variable length bytes have hard-coded serializers -- ``VLenUTF8Codec`` and ``VLenBytesCodec``, respectively. + Structured data types with multi-byte fields use ``BytesCodec`` with little-endian encoding. """ serializer: ArrayBytesCodec = BytesCodec(endian=None) - if isinstance(dtype, HasEndianness): + if isinstance(dtype, HasEndianness) or ( + isinstance(dtype, Structured) and dtype.has_multi_byte_fields() + ): serializer = BytesCodec(endian="little") elif isinstance(dtype, HasObjectCodec): if dtype.object_codec_id == "vlen-bytes": diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index 7c7b0fc5c6..95af6f8389 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -21,7 +21,13 @@ from zarr.core.dtype.npy.complex import Complex64, Complex128 from zarr.core.dtype.npy.float import Float16, Float32, Float64 from zarr.core.dtype.npy.int import Int8, Int16, Int32, Int64, UInt8, UInt16, UInt32, UInt64 -from zarr.core.dtype.npy.structured import Structured, StructuredJSON_V2, StructuredJSON_V3 +from zarr.core.dtype.npy.structured import ( + Struct, + StructJSON_V3, + Structured, + StructuredJSON_V2, + StructuredJSON_V3, +) from zarr.core.dtype.npy.time import ( DateTime64, DateTime64JSON_V2, @@ -75,6 +81,8 @@ "RawBytes", "RawBytesJSON_V2", "RawBytesJSON_V3", + "Struct", + "StructJSON_V3", "Structured", "StructuredJSON_V2", "StructuredJSON_V3", @@ -124,7 +132,7 @@ | ComplexFloatDType | StringDType | BytesDType - | Structured + | Struct | TimeDType | VariableLengthBytes ) @@ -137,7 +145,7 @@ *COMPLEX_FLOAT_DTYPE, *STRING_DTYPE, *BYTES_DTYPE, - Structured, + Struct, *TIME_DTYPE, VariableLengthBytes, ) diff --git a/src/zarr/core/dtype/npy/structured.py b/src/zarr/core/dtype/npy/structured.py index 8bedee07ef..d111924e6c 100644 --- a/src/zarr/core/dtype/npy/structured.py +++ b/src/zarr/core/dtype/npy/structured.py @@ -61,11 +61,10 @@ class StructuredJSON_V3( NamedConfig[Literal["structured"], dict[str, Sequence[Sequence[str | DTypeJSON]]]] ): """ - A JSON representation of a structured data type in Zarr V3. + A JSON representation of a structured data type in Zarr V3 (legacy format). - References - ---------- - This representation is not currently defined in an external specification. + This is the legacy format using tuple-style field definitions. + For the canonical format, see ``StructJSON_V3``. Examples -------- @@ -83,14 +82,44 @@ class StructuredJSON_V3( """ +class StructJSON_V3( + NamedConfig[Literal["struct"], dict[str, Sequence[dict[str, str | DTypeJSON]]]] +): + """ + A JSON representation of a structured data type in Zarr V3 (canonical format). + + References + ---------- + The Zarr V3 specification for this data type is defined in the zarr-extensions repository: + https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/struct + + Examples + -------- + ```python + { + "name": "struct", + "configuration": { + "fields": [ + {"name": "f0", "data_type": "int32"}, + {"name": "f1", "data_type": "float64"}, + ] + } + } + ``` + """ + + @dataclass(frozen=True, kw_only=True) class Structured(ZDType[np.dtypes.VoidDType[int], np.void], HasItemSize): """ - A Zarr data type for arrays containing structured scalars, AKA "record arrays". + A Zarr data type for arrays containing structured scalars, AKA "record arrays" (legacy format). Wraps the NumPy `np.dtypes.VoidDType` if the data type has fields. Scalars for this data type are instances of `np.void`, with a ``fields`` attribute. + This class handles the legacy "structured" format with tuple-style field definitions. + For the canonical "struct" format, see ``Struct``. + Attributes ---------- fields : Sequence[tuple[str, ZDType]] @@ -98,8 +127,6 @@ class Structured(ZDType[np.dtypes.VoidDType[int], np.void], HasItemSize): References ---------- - This data type does not have a Zarr V3 specification. - The Zarr V2 data type specification can be found [here](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). """ @@ -234,7 +261,6 @@ def _check_json_v3(cls, data: DTypeJSON) -> TypeGuard[StructuredJSON_V3]: True if the input is a valid JSON representation of a structured data type for Zarr V3, False otherwise. """ - return ( isinstance(data, dict) and set(data.keys()) == {"name", "configuration"} @@ -268,7 +294,6 @@ def _from_json_v2(cls, data: DTypeJSON) -> Self: @classmethod def _from_json_v3(cls, data: DTypeJSON) -> Self: - # avoid circular import from zarr.core.dtype import get_data_type_from_json if cls._check_json_v3(data): @@ -445,7 +470,7 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.void: return cast("np.void", np.array([as_bytes]).view(dtype)[0]) raise TypeError(f"Invalid type: {data}. Expected a string.") - def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> str: + def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> str | dict[str, JSON]: """ Convert a scalar to a JSON-serializable string representation. @@ -458,9 +483,10 @@ def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> str: Returns ------- - str + str | dict[str, JSON] A string representation of the scalar, which is a base64-encoded - string of the bytes that make up the scalar. + string of the bytes that make up the scalar. Subclasses may return + a dict for V3 format. """ return bytes_to_json(self.cast_scalar(data).tobytes(), zarr_format) @@ -475,3 +501,166 @@ def item_size(self) -> int: The size of a single scalar in bytes. """ return self.to_native_dtype().itemsize + + def has_multi_byte_fields(self) -> bool: + """ + Check if this structured dtype has any fields with item_size > 1. + + Returns + ------- + bool + True if any field has item_size > 1, False otherwise. + """ + return any( + isinstance(field_dtype, HasItemSize) and field_dtype.item_size > 1 + for _, field_dtype in self.fields + ) + + +@dataclass(frozen=True, kw_only=True) +class Struct(Structured): + """ + A Zarr data type for arrays containing structured scalars, AKA "record arrays". + + Wraps the NumPy `np.dtypes.VoidDType` if the data type has fields. Scalars for this data + type are instances of `np.void`, with a ``fields`` attribute. + + This is the canonical data type registered for structured arrays. It reads both + the canonical ``"struct"`` format (object-style fields) and the legacy ``"structured"`` + format (tuple-style fields), but always writes the canonical ``"struct"`` format. + + Attributes + ---------- + fields : Sequence[tuple[str, ZDType]] + The fields of the structured dtype. + + References + ---------- + The Zarr V3 specification for this data type is defined in the zarr-extensions repository: + https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/struct + + The Zarr V2 data type specification can be found [here](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). + """ + + _zarr_v3_name: ClassVar[Literal["struct"]] = "struct" # type: ignore[assignment] + + @classmethod + def _check_json_v3(cls, data: DTypeJSON) -> TypeGuard[StructJSON_V3]: # type: ignore[override] + return ( + isinstance(data, dict) + and set(data.keys()) == {"name", "configuration"} + and data["name"] in ("struct", "structured") + and isinstance(data["configuration"], dict) + and set(data["configuration"].keys()) == {"fields"} + ) + + @classmethod + def _from_json_v3(cls, data: DTypeJSON) -> Self: + from zarr.core.dtype import get_data_type_from_json + + if cls._check_json_v3(data): + config = data["configuration"] + meta_fields = config["fields"] + parsed_fields: list[tuple[str, ZDType[TBaseDType, TBaseScalar]]] = [] + for field in meta_fields: + if isinstance(field, dict): + f_name = field["name"] + f_dtype = field["data_type"] + else: + # Legacy tuple-style field format from "structured" dtype + f_name, f_dtype = field # type: ignore[unreachable] + parsed_fields.append((f_name, get_data_type_from_json(f_dtype, zarr_format=3))) # type: ignore[arg-type] + return cls(fields=tuple(parsed_fields)) + msg = f"Invalid JSON representation of {cls.__name__}. Got {data!r}, expected a JSON object with the key {cls._zarr_v3_name!r}" + raise DataTypeValidationError(msg) + + @overload # type: ignore[override] + def to_json(self, zarr_format: Literal[2]) -> StructuredJSON_V2: ... + + @overload + def to_json(self, zarr_format: Literal[3]) -> StructJSON_V3: ... + + def to_json(self, zarr_format: ZarrFormat) -> StructuredJSON_V2 | StructJSON_V3: + if zarr_format == 2: + fields_v2 = [ + [f_name, f_dtype.to_json(zarr_format=zarr_format)["name"]] + for f_name, f_dtype in self.fields + ] + return {"name": fields_v2, "object_codec_id": None} + elif zarr_format == 3: + v3_unstable_dtype_warning(self) + fields_v3 = [ + {"name": f_name, "data_type": f_dtype.to_json(zarr_format=zarr_format)} + for f_name, f_dtype in self.fields + ] + return cast( + "StructJSON_V3", + {"name": self._zarr_v3_name, "configuration": {"fields": fields_v3}}, + ) + raise ValueError(f"zarr_format must be 2 or 3, got {zarr_format}") # pragma: no cover + + def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.void: + """ + Read a JSON-serializable value as a NumPy structured scalar. + + Parameters + ---------- + data : JSON + The JSON-serializable value. Can be either: + - A dict mapping field names to values (primary format for V3) + - A base64-encoded string (legacy format, for backward compatibility) + zarr_format : ZarrFormat + The zarr format version. + + Returns + ------- + np.void + The NumPy structured scalar. + + Raises + ------ + TypeError + If the input is not a dict or base64-encoded string. + """ + if isinstance(data, dict): + field_values = [] + for field_name, field_dtype in self.fields: + if field_name in data: + field_values.append( + field_dtype.from_json_scalar(data[field_name], zarr_format=zarr_format) + ) + else: + field_values.append(field_dtype.default_scalar()) + return self._cast_scalar_unchecked(tuple(field_values)) + elif check_json_str(data): + as_bytes = bytes_from_json(data, zarr_format=zarr_format) + dtype = self.to_native_dtype() + return cast("np.void", np.array([as_bytes]).view(dtype)[0]) + raise TypeError(f"Invalid type: {data}. Expected a dict or base64-encoded string.") + + def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> str | dict[str, JSON]: + """ + Convert a scalar to a JSON-serializable representation. + + Parameters + ---------- + data : object + The scalar to convert. + zarr_format : ZarrFormat + The zarr format version. + + Returns + ------- + str | dict[str, JSON] + For V2: A base64-encoded string of the bytes that make up the scalar. + For V3: A dict mapping field names to their JSON-serialized values. + """ + scalar = self.cast_scalar(data) + if zarr_format == 2: + return bytes_to_json(scalar.tobytes(), zarr_format) + result: dict[str, JSON] = {} + for field_name, field_dtype in self.fields: + result[field_name] = field_dtype.to_json_scalar( + scalar[field_name], zarr_format=zarr_format + ) + return result diff --git a/src/zarr/dtype.py b/src/zarr/dtype.py index 2c7eb651b0..f75219aab8 100644 --- a/src/zarr/dtype.py +++ b/src/zarr/dtype.py @@ -22,6 +22,8 @@ RawBytes, RawBytesJSON_V2, RawBytesJSON_V3, + Struct, + StructJSON_V3, Structured, StructuredJSON_V2, StructuredJSON_V3, @@ -68,6 +70,8 @@ "RawBytes", "RawBytesJSON_V2", "RawBytesJSON_V3", + "Struct", + "StructJSON_V3", "Structured", "StructuredJSON_V2", "StructuredJSON_V3", diff --git a/tests/test_dtype/conftest.py b/tests/test_dtype/conftest.py index 0650d143c6..4c585bfdf6 100644 --- a/tests/test_dtype/conftest.py +++ b/tests/test_dtype/conftest.py @@ -6,14 +6,13 @@ from zarr.core.dtype import data_type_registry from zarr.core.dtype.common import HasLength -from zarr.core.dtype.npy.structured import Structured +from zarr.core.dtype.npy.structured import Struct from zarr.core.dtype.npy.time import DateTime64, TimeDelta64 from zarr.core.dtype.wrapper import ZDType zdtype_examples: tuple[ZDType[Any, Any], ...] = () for wrapper_cls in data_type_registry.contents.values(): - # The Structured dtype has to be constructed with some actual fields - if wrapper_cls is Structured: + if wrapper_cls is Struct: with warnings.catch_warnings(): warnings.simplefilter("ignore") zdtype_examples += ( diff --git a/tests/test_dtype/test_npy/test_structured.py b/tests/test_dtype/test_npy/test_structured.py index e2cd2a6dfe..554c3b4e41 100644 --- a/tests/test_dtype/test_npy/test_structured.py +++ b/tests/test_dtype/test_npy/test_structured.py @@ -11,12 +11,16 @@ Float64, Int32, Int64, + Struct, Structured, + UInt8, ) -class TestStructured(BaseTestZDType): - test_cls = Structured +class TestStruct(BaseTestZDType): + """Test the canonical 'struct' dtype format.""" + + test_cls = Struct valid_dtype = ( np.dtype([("field1", np.int32), ("field2", np.float64)]), np.dtype([("field1", np.int64), ("field2", np.int32)]), @@ -32,29 +36,32 @@ class TestStructured(BaseTestZDType): ) valid_json_v3 = ( { - "name": "structured", + "name": "struct", "configuration": { "fields": [ - ["field1", "int32"], - ["field2", "float64"], + {"name": "field1", "data_type": "int32"}, + {"name": "field2", "data_type": "float64"}, ] }, }, { - "name": "structured", + "name": "struct", "configuration": { "fields": [ - [ - "field1", - { + { + "name": "field1", + "data_type": { "name": "numpy.datetime64", "configuration": {"unit": "s", "scale_factor": 1}, }, - ], - [ - "field2", - {"name": "fixed_length_utf32", "configuration": {"length_bytes": 32}}, - ], + }, + { + "name": "field2", + "data_type": { + "name": "fixed_length_utf32", + "configuration": {"length_bytes": 32}, + }, + }, ] }, }, @@ -65,7 +72,7 @@ class TestStructured(BaseTestZDType): ) invalid_json_v3 = ( { - "name": "structured", + "name": "struct", "configuration": { "fields": [ ("field1", {"name": "int32", "configuration": {"endianness": "invalid"}}), @@ -77,35 +84,38 @@ class TestStructured(BaseTestZDType): ) scalar_v2_params = ( - (Structured(fields=(("field1", Int32()), ("field2", Float64()))), "AQAAAAAAAAAAAPA/"), - (Structured(fields=(("field1", Float16()), ("field2", Int32()))), "AQAAAAAA"), + (Struct(fields=(("field1", Int32()), ("field2", Float64()))), "AQAAAAAAAAAAAPA/"), + (Struct(fields=(("field1", Float16()), ("field2", Int32()))), "AQAAAAAA"), ) scalar_v3_params = ( - (Structured(fields=(("field1", Int32()), ("field2", Float64()))), "AQAAAAAAAAAAAPA/"), - (Structured(fields=(("field1", Int64()), ("field2", Int32()))), "AQAAAAAAAAAAAPA/"), + ( + Struct(fields=(("field1", Int32()), ("field2", Float64()))), + {"field1": 1, "field2": 1.0}, + ), + (Struct(fields=(("field1", Int64()), ("field2", Int32()))), {"field1": 1, "field2": 1}), ) cast_value_params = ( ( - Structured(fields=(("field1", Int32()), ("field2", Float64()))), + Struct(fields=(("field1", Int32()), ("field2", Float64()))), (1, 2.0), np.array((1, 2.0), dtype=[("field1", np.int32), ("field2", np.float64)]), ), ( - Structured(fields=(("field1", Int64()), ("field2", Int32()))), + Struct(fields=(("field1", Int64()), ("field2", Int32()))), (3, 4.5), np.array((3, 4.5), dtype=[("field1", np.int64), ("field2", np.int32)]), ), ) item_size_params = ( - Structured(fields=(("field1", Int32()), ("field2", Float64()))), - Structured(fields=(("field1", Int64()), ("field2", Int32()))), + Struct(fields=(("field1", Int32()), ("field2", Float64()))), + Struct(fields=(("field1", Int64()), ("field2", Int32()))), ) invalid_scalar_params = ( - (Structured(fields=(("field1", Int32()), ("field2", Float64()))), "i am a string"), - (Structured(fields=(("field1", Int32()), ("field2", Float64()))), {"type": "dict"}), + (Struct(fields=(("field1", Int32()), ("field2", Float64()))), "i am a string"), + (Struct(fields=(("field1", Int32()), ("field2", Float64()))), {"type": "dict"}), ) def scalar_equals(self, scalar1: Any, scalar2: Any) -> bool: @@ -114,11 +124,139 @@ def scalar_equals(self, scalar1: Any, scalar2: Any) -> bool: return super().scalar_equals(scalar1, scalar2) +class TestStructured: + """Test the legacy 'structured' dtype format.""" + + def test_invalid_size(self) -> None: + """Test that it's impossible to create a data type that has no fields.""" + fields = () + msg = f"must have at least one field. Got {fields!r}" + with pytest.raises(ValueError, match=msg): + Structured(fields=fields) + + def test_structured_legacy_name_with_tuple_format(self) -> None: + """Test that the legacy 'structured' name with tuple field format is accepted.""" + json_v3 = { + "name": "structured", + "configuration": { + "fields": [ + ["field1", "int32"], + ["field2", "float64"], + ] + }, + } + dtype = Structured.from_json(json_v3, zarr_format=3) + assert dtype.fields[0][0] == "field1" + assert dtype.fields[1][0] == "field2" + + @pytest.mark.filterwarnings("ignore::zarr.errors.UnstableSpecificationWarning") + def test_structured_writes_tuple_format(self) -> None: + """Test that 'structured' writes the tuple field format.""" + dtype = Structured(fields=(("field1", Int32()), ("field2", Float64()))) + json_v3 = dtype.to_json(zarr_format=3) + assert json_v3["name"] == "structured" + assert json_v3["configuration"]["fields"][0] == ["field1", "int32"] + + def test_invalid_size() -> None: - """ - Test that it's impossible to create a data type that has no fields - """ + """Test that it's impossible to create a data type that has no fields.""" fields = () msg = f"must have at least one field. Got {fields!r}" with pytest.raises(ValueError, match=msg): - Structured(fields=fields) + Struct(fields=fields) + + +@pytest.mark.filterwarnings("ignore::zarr.errors.UnstableSpecificationWarning") +def test_struct_name_is_primary() -> None: + """Test that 'struct' is the primary name written to JSON.""" + dtype = Struct(fields=(("field1", Int32()), ("field2", Float64()))) + json_v3 = dtype.to_json(zarr_format=3) + assert json_v3["name"] == "struct" + + +def test_struct_reads_legacy_tuple_format() -> None: + """Test that 'struct' dtype reads the legacy tuple field format.""" + json_v3 = { + "name": "struct", + "configuration": { + "fields": [ + ["field1", "int32"], + ["field2", "float64"], + ] + }, + } + dtype = Struct.from_json(json_v3, zarr_format=3) + assert isinstance(dtype, Struct) + assert dtype.fields[0][0] == "field1" + assert dtype.fields[1][0] == "field2" + + +def test_struct_reads_canonical_object_format() -> None: + """Test that 'struct' dtype reads the new object field format.""" + json_v3 = { + "name": "struct", + "configuration": { + "fields": [ + {"name": "field1", "data_type": "int32"}, + {"name": "field2", "data_type": "float64"}, + ] + }, + } + dtype = Struct.from_json(json_v3, zarr_format=3) + assert isinstance(dtype, Struct) + assert dtype.fields[0][0] == "field1" + assert dtype.fields[1][0] == "field2" + + +def test_fill_value_dict_form() -> None: + """Test that dict form fill values are properly parsed.""" + dtype = Struct(fields=(("x", Int32()), ("y", Float64()))) + fill_value = dtype.from_json_scalar({"x": 42, "y": 3.14}, zarr_format=3) + assert fill_value["x"] == 42 + assert fill_value["y"] == 3.14 + + +def test_fill_value_dict_form_missing_fields() -> None: + """Test that missing fields in dict form fill values use defaults.""" + dtype = Struct(fields=(("x", Int32()), ("y", Float64()))) + fill_value = dtype.from_json_scalar({"x": 42}, zarr_format=3) + assert fill_value["x"] == 42 + assert fill_value["y"] == 0.0 + + +def test_fill_value_legacy_base64() -> None: + """Test that legacy base64-encoded fill values are still readable.""" + dtype = Struct(fields=(("field1", Int32()), ("field2", Float64()))) + fill_value = dtype.from_json_scalar("AQAAAAAAAAAAAPA/", zarr_format=3) + assert fill_value["field1"] == 1 + assert fill_value["field2"] == 1.0 + + +def test_fill_value_to_json_dict_form() -> None: + """Test that fill values are serialized as dict form.""" + dtype = Struct(fields=(("x", Int32()), ("y", Float64()))) + scalar = np.array((42, 3.14), dtype=[("x", np.int32), ("y", np.float64)])[()] + json_val = dtype.to_json_scalar(scalar, zarr_format=3) + assert isinstance(json_val, dict) + assert json_val["x"] == 42 + assert json_val["y"] == 3.14 + + +def test_has_multi_byte_fields_true() -> None: + """Test that has_multi_byte_fields returns True for dtypes with multi-byte fields.""" + dtype = Struct(fields=(("field1", Int32()), ("field2", Float64()))) + assert dtype.has_multi_byte_fields() is True + + +def test_has_multi_byte_fields_false() -> None: + """Test that has_multi_byte_fields returns False for dtypes with only single-byte fields.""" + dtype = Struct(fields=(("field1", UInt8()), ("field2", UInt8()))) + assert dtype.has_multi_byte_fields() is False + + +def test_struct_from_native_dtype() -> None: + """Test that Struct can be created from native numpy dtype.""" + dtype = np.dtype([("field1", np.int32), ("field2", np.float64)]) + struct = Struct.from_native_dtype(dtype) + assert struct.fields[0][0] == "field1" + assert struct.fields[1][0] == "field2" diff --git a/tests/test_v2.py b/tests/test_v2.py index cb990f6159..3a063ac509 100644 --- a/tests/test_v2.py +++ b/tests/test_v2.py @@ -14,8 +14,9 @@ from zarr import config from zarr.abc.store import Store from zarr.core.buffer.core import default_buffer_prototype -from zarr.core.dtype import FixedLengthUTF32, Structured, VariableLengthUTF8 +from zarr.core.dtype import FixedLengthUTF32, VariableLengthUTF8 from zarr.core.dtype.npy.bytes import NullTerminatedBytes +from zarr.core.dtype.npy.structured import Struct from zarr.core.dtype.wrapper import ZDType from zarr.core.group import Group from zarr.core.sync import sync @@ -283,7 +284,7 @@ def test_structured_dtype_roundtrip(fill_value: float | bytes, tmp_path: Path) - def test_parse_structured_fill_value_valid( fill_value: Any, dtype: np.dtype[Any], expected_result: Any ) -> None: - zdtype = Structured.from_native_dtype(dtype) + zdtype = Struct.from_native_dtype(dtype) result = zdtype.cast_scalar(fill_value) assert result.dtype == expected_result.dtype assert result == expected_result From 866aa8d67b5be975c23da3a9d1a4dafe0b83cb0d Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 22 Apr 2026 15:21:56 +0200 Subject: [PATCH 282/468] fix: make upstream tests pass (#3920) * fix: declare a unit when creating NaT datetime * fix: use latest version of ml_dtypes in example script * docs: changelog --- changes/3920.bugfix.md | 1 + examples/custom_dtype/custom_dtype.py | 2 +- src/zarr/core/dtype/npy/time.py | 2 +- tests/test_dtype/test_npy/test_time.py | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) create mode 100644 changes/3920.bugfix.md diff --git a/changes/3920.bugfix.md b/changes/3920.bugfix.md new file mode 100644 index 0000000000..289d12970c --- /dev/null +++ b/changes/3920.bugfix.md @@ -0,0 +1 @@ +Use the unit associated with the `Datetime64` data type when creating the default `Nat` scalar value. \ No newline at end of file diff --git a/examples/custom_dtype/custom_dtype.py b/examples/custom_dtype/custom_dtype.py index eee510349b..a13283a681 100644 --- a/examples/custom_dtype/custom_dtype.py +++ b/examples/custom_dtype/custom_dtype.py @@ -2,7 +2,7 @@ # requires-python = ">=3.12" # dependencies = [ # "zarr @ git+https://github.com/zarr-developers/zarr-python.git@main", -# "ml_dtypes==0.5.1", +# "ml_dtypes==0.5.4", # "pytest==8.4.1" # ] # /// diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index c4495e167c..6a864dc889 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -851,7 +851,7 @@ def default_scalar(self) -> np.datetime64: The default scalar value, which is a 'Not-a-Time' (NaT) value """ - return np.datetime64("NaT") + return np.datetime64("NaT", self.unit) def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.datetime64: """ diff --git a/tests/test_dtype/test_npy/test_time.py b/tests/test_dtype/test_npy/test_time.py index 1b1f428e40..67ba3bd130 100644 --- a/tests/test_dtype/test_npy/test_time.py +++ b/tests/test_dtype/test_npy/test_time.py @@ -66,7 +66,7 @@ class TestDateTime64(_TestTimeBase): cast_value_params = ( (DateTime64(unit="Y", scale_factor=1), "1", np.datetime64("1", "Y")), (DateTime64(unit="s", scale_factor=1), "2005-02-25", np.datetime64("2005-02-25", "s")), - (DateTime64(unit="ns", scale_factor=1), "NaT", np.datetime64("NaT")), + (DateTime64(unit="ns", scale_factor=1), "NaT", np.datetime64("NaT", "ns")), ) invalid_scalar_params = ( (DateTime64(unit="Y", scale_factor=1), 1.3), From 0733a99b9aeeea505f4a2985950a8c4891d94089 Mon Sep 17 00:00:00 2001 From: Leo Ji Date: Thu, 23 Apr 2026 09:18:38 -0700 Subject: [PATCH 283/468] docs: add experimental API policy to contributing guide (#3853) Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- docs/contributing.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/docs/contributing.md b/docs/contributing.md index e62ce54c35..a1a75d0010 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -311,6 +311,29 @@ The Zarr library is an implementation of a file format standard defined external If an existing Zarr format version changes, or a new version of the Zarr format is released, then the Zarr library will generally require changes. It is very likely that a new Zarr format will require extensive breaking changes to the Zarr library, and so support for a new Zarr format in the Zarr library will almost certainly come in new `major` release. When the Zarr library adds support for a new Zarr format, there may be a period of accelerated changes as developers refine newly added APIs and deprecate old APIs. In such a transitional phase breaking changes may be more frequent than usual. + +## Experimental API policy + +The `zarr.experimental` namespace contains features that are under active development and may change without notice. When contributing to or depending on experimental features, please keep the following in mind: + +### For contributors + +When adding a new feature to `zarr.experimental`: + +1. Place the feature under `src/zarr/experimental/` and export it from `src/zarr/experimental/__init__.py`. +2. Document the feature in `docs/user-guide/experimental.md` and note clearly that it is experimental. +3. Add a changelog entry categorized as `feature`. + +We aim to either **promote** or **remove** experimental features within **6 months** of their addition. To promote a feature to stable: + +1. Move it from `zarr.experimental` to the appropriate stable module. +2. Keep a deprecated re-export in `zarr.experimental` for one minor release. +3. Update the documentation to reflect the stable location. + +### For users + +Features in `zarr.experimental` carry no stability guarantees. They may be changed or removed in any release, including patch releases. If you depend on an experimental feature, pin your `zarr-python` version accordingly. + ## Release procedure Open an issue on GitHub announcing the release using the release checklist template: From 029c376000c0cf3b9c311966ce8a1f4387112797 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 24 Apr 2026 09:46:12 +0200 Subject: [PATCH 284/468] fix: apply path normalization to fsspec store (#3924) * fix: apply path normalization to fsspec store * docs: changelog * Update 3924.bugfix.md --- changes/3924.bugfix.md | 1 + src/zarr/storage/_fsspec.py | 4 ++-- tests/test_store/test_fsspec.py | 22 ++++++++++++++++++++++ 3 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 changes/3924.bugfix.md diff --git a/changes/3924.bugfix.md b/changes/3924.bugfix.md new file mode 100644 index 0000000000..54382d775e --- /dev/null +++ b/changes/3924.bugfix.md @@ -0,0 +1 @@ +Apply path normalization to the `path` attribute of `FsspecStore`, ensuring that leading and trailing "/" symbols are removed. diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index ac50a0527f..74e5869a66 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -16,7 +16,7 @@ ) from zarr.core.buffer import Buffer from zarr.errors import ZarrUserWarning -from zarr.storage._utils import _join_paths +from zarr.storage._utils import _join_paths, normalize_path if TYPE_CHECKING: from collections.abc import AsyncIterator, Iterable @@ -127,7 +127,7 @@ def __init__( ) -> None: super().__init__(read_only=read_only) self.fs = fs - self.path = path + self.path = normalize_path(path) self.allowed_exceptions = allowed_exceptions if not self.fs.async_impl: diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 5e9e33f0e4..00b989a5de 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -17,6 +17,7 @@ from zarr.errors import ZarrUserWarning from zarr.storage import FsspecStore from zarr.storage._fsspec import _make_async +from zarr.storage._utils import normalize_path from zarr.testing.store import StoreTests if TYPE_CHECKING: @@ -286,6 +287,27 @@ def array_roundtrip(store: FsspecStore) -> None: np.testing.assert_array_equal(arr[:], data) +@pytest.mark.skipif( + parse_version(fsspec.__version__) < parse_version("2024.12.0"), + reason="No AsyncFileSystemWrapper", +) +@pytest.mark.parametrize("path", ["", "/", "//", "foo", "foo/", "/foo", "/foo/", "//foo//"]) +def test_fsspec_store_path_normalization(path: str) -> None: + """`FsspecStore.path` is normalized to the canonical form, matching + `normalize_path`, regardless of the surface representation the caller + supplies. + + Regression test for https://github.com/zarr-developers/zarr-python/issues/3922 + -- when a caller passed `path="/"` the leading slash flowed through + unmodified to subsequent `_join_paths([self.path, key])` calls, producing + `"//key"` and missing the underlying object. + """ + sync_fs = fsspec.filesystem("memory") + fs = _make_async(sync_fs) + store = FsspecStore(fs=fs, path=path) + assert store.path == normalize_path(path) + + @pytest.mark.skipif( parse_version(fsspec.__version__) < parse_version("2024.12.0"), reason="No AsyncFileSystemWrapper", From c4730be82182808554a0f17731757370293bf737 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 29 Apr 2026 15:41:40 +0300 Subject: [PATCH 285/468] Use f-strings (#3928) --- src/zarr/core/buffer/core.py | 2 +- src/zarr/core/group.py | 2 +- src/zarr/registry.py | 2 +- src/zarr/storage/_fsspec.py | 4 +-- src/zarr/storage/_memory.py | 8 ++--- src/zarr/storage/_utils.py | 4 +-- src/zarr/storage/_zip.py | 4 +-- src/zarr/testing/store.py | 8 ++--- src/zarr/testing/strategies.py | 2 +- tests/conftest.py | 4 +-- tests/test_api.py | 34 +++++++++---------- tests/test_array.py | 2 +- tests/test_codec_entrypoints.py | 4 +-- tests/test_group.py | 22 ++++++------ .../test_v2_dtype_regression.py | 2 +- tests/test_store/test_memory.py | 2 +- tests/test_store/test_zip.py | 2 +- 17 files changed, 54 insertions(+), 54 deletions(-) diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index ddfb179213..58a59975b7 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -535,7 +535,7 @@ def all_equal(self, other: Any, equal_nan: bool = True) -> bool: and self._data.dtype.kind not in ("U", "S", "T", "O", "V") ): _data, other = np.broadcast_arrays(self._data, np.asarray(other, self._data.dtype)) - void_dtype = "V" + str(_data.dtype.itemsize) + void_dtype = f"V{_data.dtype.itemsize}" return np.array_equal(_data.view(void_dtype), other.view(void_dtype)) # use array_equal to obtain equal_nan=True functionality # Since fill-value is a scalar, isn't there a faster path than allocating a new array for fill value diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 97f75c12bd..83a9cc6000 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -840,7 +840,7 @@ def name(self) -> str: # follow h5py convention: add leading slash name = self.path if name[0] != "/": - name = "/" + name + name = f"/{name}" return name return "/" diff --git a/src/zarr/registry.py b/src/zarr/registry.py index 8f3879a2a3..48f60fabd7 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -133,7 +133,7 @@ def _reload_config() -> None: def fully_qualified_name(cls: type) -> str: module = cls.__module__ - return module + "." + cls.__qualname__ + return f"{module}.{cls.__qualname__}" def register_codec(key: str, codec_cls: type[Codec], *, qualname: str | None = None) -> None: diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 74e5869a66..1ca44a4e26 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -408,7 +408,7 @@ async def get_partial_values( async def list(self) -> AsyncIterator[str]: # docstring inherited allfiles = await self.fs._find(self.path, detail=False, withdirs=False) - for onefile in (a.removeprefix(self.path + "/") for a in allfiles): + for onefile in (a.removeprefix(f"{self.path}/") for a in allfiles): yield onefile async def list_dir(self, prefix: str) -> AsyncIterator[str]: @@ -418,7 +418,7 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: allfiles = await self.fs._ls(prefix, detail=False) except FileNotFoundError: return - for onefile in (a.replace(prefix + "/", "") for a in allfiles): + for onefile in (a.replace(f"{prefix}/", "") for a in allfiles): yield onefile.removeprefix(self.path).removeprefix("/") async def list_prefix(self, prefix: str) -> AsyncIterator[str]: diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index 53d3cfbfde..bd91029732 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -217,9 +217,9 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: # a pseudo directory when there's a nested item and we're listing an # intermediate level. keys_unique = { - key.removeprefix(prefix + "/").split("/")[0] + key.removeprefix(f"{prefix}/").split("/")[0] for key in self._store_dict - if key.startswith(prefix + "/") and key != prefix + if key.startswith(f"{prefix}/") and key != prefix } for key in keys_unique: @@ -822,7 +822,7 @@ async def delete(self, key: str) -> None: async def list(self) -> AsyncIterator[str]: # docstring inherited - prefix = self.path + "/" if self.path else "" + prefix = f"{self.path}/" if self.path else "" async for key in super().list(): if key.startswith(prefix): yield key.removeprefix(prefix) @@ -832,7 +832,7 @@ async def list_prefix(self, prefix: str) -> AsyncIterator[str]: # Manual concatenation instead of _join_paths because we need "path/" # as the prefix when prefix is empty (to list all keys under self.path) full_prefix = f"{self.path}/{prefix}" if self.path else prefix - path_prefix = self.path + "/" if self.path else "" + path_prefix = f"{self.path}/" if self.path else "" async for key in super().list_prefix(full_prefix): yield key.removeprefix(path_prefix) diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index 722a2d3568..2ff9baa5ab 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -220,10 +220,10 @@ def _relativize_path(*, path: str, prefix: str) -> str: if prefix == "": return path else: - _prefix = prefix + "/" + _prefix = f"{prefix}/" if not path.startswith(_prefix): raise ValueError(f"The first component of {path} does not start with {prefix}.") - return path.removeprefix(f"{prefix}/") + return path.removeprefix(_prefix) def _normalize_paths(paths: Iterable[str]) -> tuple[str, ...]: diff --git a/src/zarr/storage/_zip.py b/src/zarr/storage/_zip.py index c5c7cbf3e8..897797e999 100644 --- a/src/zarr/storage/_zip.py +++ b/src/zarr/storage/_zip.py @@ -285,8 +285,8 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: yield key else: for key in keys: - if key.startswith(prefix + "/") and key.strip("/") != prefix: - k = key.removeprefix(prefix + "/").split("/")[0] + if key.startswith(f"{prefix}/") and key.strip("/") != prefix: + k = key.removeprefix(f"{prefix}/").split("/")[0] if k not in seen: seen.add(k) yield k diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index 91c174b589..a0bbe6b4b2 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -449,8 +449,8 @@ async def test_list(self, store: S) -> None: prefix = "foo" data = self.buffer_cls.from_bytes(b"") store_dict = { - prefix + "/zarr.json": data, - **{prefix + f"/c/{idx}": data for idx in range(10)}, + f"{prefix}/zarr.json": data, + **{f"{prefix}/c/{idx}": data for idx in range(10)}, } await store._set_many(store_dict.items()) expected_sorted = sorted(store_dict.keys()) @@ -536,10 +536,10 @@ async def test_list_dir(self, store: S) -> None: await store._set_many(store_dict.items()) keys_observed = await _collect_aiterator(store.list_dir(root)) - keys_expected = {k.removeprefix(root + "/").split("/")[0] for k in store_dict} + keys_expected = {k.removeprefix(f"{root}/").split("/")[0] for k in store_dict} assert sorted(keys_observed) == sorted(keys_expected) - keys_observed = await _collect_aiterator(store.list_dir(root + "/")) + keys_observed = await _collect_aiterator(store.list_dir(f"{root}/")) assert sorted(keys_expected) == sorted(keys_observed) async def test_set_if_not_exists(self, store: S) -> None: diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 3bb059b3a8..1b0ede1148 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -323,7 +323,7 @@ def arrays( assert a.fill_value is not None assert a.name is not None assert a.path == normalize_path(array_path) - assert a.name == "/" + a.path + assert a.name == f"/{a.path}" assert isinstance(root[array_path], Array) assert nparray.shape == a.shape diff --git a/tests/conftest.py b/tests/conftest.py index de1730fff9..6577f8afa0 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -87,7 +87,7 @@ async def parse_store( if store == "fsspec": return await FsspecStore.open(url=path) if store == "zip": - return await ZipStore.open(path + "/zarr.zip", mode="w") + return await ZipStore.open(f"{path}/zarr.zip", mode="w") if store == "memory_get_latency": return LatencyStore(MemoryStore(), get_latency=0.0001, set_latency=0) raise AssertionError @@ -143,7 +143,7 @@ async def store2(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> Store: def sync_store(request: pytest.FixtureRequest, tmp_path: LEGACY_PATH) -> Store: result = sync(parse_store(request.param, str(tmp_path))) if not isinstance(result, Store): - raise TypeError("Wrong store class returned by test fixture! got " + result + " instead") + raise TypeError(f"Wrong store class returned by test fixture! got {result} instead") return result diff --git a/tests/test_api.py b/tests/test_api.py index 4198d56c78..d8c4d20f4a 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -822,9 +822,9 @@ def test_tree() -> None: # assert len(source) == len(dest) # for key in source: # if self._version == 3: -# dest_key = key[:10] + "new/" + key[10:] +# dest_key = f"{key[:10]}new/{key[10:]}" # else: -# dest_key = "new/" + key +# dest_key = f"new/{key}" # assert source[key] == dest[dest_key] # def test_source_dest_path(self): @@ -841,7 +841,7 @@ def test_tree() -> None: # assert source[key] == dest[dest_key] # else: # assert key not in dest -# assert ("new/" + key) not in dest +# assert (f"new/{key}") not in dest # def test_excludes_includes(self): # source = self.source @@ -853,16 +853,16 @@ def test_tree() -> None: # assert len(dest) == 2 # root = "" -# assert root + "foo" not in dest +# assert "f{root}foo" not in dest # # multiple excludes # dest = self._get_dest_store() # excludes = "b.z", ".*x" # copy_store(source, dest, excludes=excludes) # assert len(dest) == 1 -# assert root + "foo" in dest -# assert root + "bar/baz" not in dest -# assert root + "bar/qux" not in dest +# assert f"{root}foo" in dest +# assert f"{root}bar/baz" not in dest +# assert f"{root}bar/qux" not in dest # # excludes and includes # dest = self._get_dest_store() @@ -870,9 +870,9 @@ def test_tree() -> None: # includes = ".*x" # copy_store(source, dest, excludes=excludes, includes=includes) # assert len(dest) == 2 -# assert root + "foo" in dest -# assert root + "bar/baz" not in dest -# assert root + "bar/qux" in dest +# assert f"{root}foo" in dest +# assert f"{root}bar/baz" not in dest +# assert f"{root}bar/qux" in dest # def test_dry_run(self): # source = self.source @@ -884,7 +884,7 @@ def test_tree() -> None: # source = self.source # dest = self._get_dest_store() # root = "" -# dest[root + "bar/baz"] = b"mmm" +# dest[f"{root}bar/baz"] = b"mmm" # # default ('raise') # with pytest.raises(CopyError): @@ -897,16 +897,16 @@ def test_tree() -> None: # # skip # copy_store(source, dest, if_exists="skip") # assert 3 == len(dest) -# assert dest[root + "foo"] == b"xxx" -# assert dest[root + "bar/baz"] == b"mmm" -# assert dest[root + "bar/qux"] == b"zzz" +# assert dest[f"{root}foo"] == b"xxx" +# assert dest[f"{root}bar/baz"] == b"mmm" +# assert dest[f"{root}bar/qux"] == b"zzz" # # replace # copy_store(source, dest, if_exists="replace") # assert 3 == len(dest) -# assert dest[root + "foo"] == b"xxx" -# assert dest[root + "bar/baz"] == b"yyy" -# assert dest[root + "bar/qux"] == b"zzz" +# assert dest[f"{root}foo"] == b"xxx" +# assert dest[f"{root}bar/baz"] == b"yyy" +# assert dest[f"{root}bar/qux"] == b"zzz" # # invalid option # with pytest.raises(ValueError): diff --git a/tests/test_array.py b/tests/test_array.py index f7f564f30e..132c4c26c3 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1645,7 +1645,7 @@ async def test_name(store: Store, zarr_format: ZarrFormat, path: str | None) -> else: expected_path = path assert arr.path == expected_path - assert arr.name == "/" + expected_path + assert arr.name == f"/{expected_path}" # test that implicit groups were created path_parts = expected_path.split("/") diff --git a/tests/test_codec_entrypoints.py b/tests/test_codec_entrypoints.py index fc7b79fe54..69cd0a1577 100644 --- a/tests/test_codec_entrypoints.py +++ b/tests/test_codec_entrypoints.py @@ -7,7 +7,7 @@ @pytest.mark.usefixtures("set_path") @pytest.mark.parametrize("codec_name", ["TestEntrypointCodec", "TestEntrypointGroup.Codec"]) def test_entrypoint_codec(codec_name: str) -> None: - config.set({"codecs.test": "package_with_entrypoint." + codec_name}) + config.set({"codecs.test": f"package_with_entrypoint.{codec_name}"}) cls_test = zarr.registry.get_codec_class("test") assert cls_test.__qualname__ == codec_name @@ -24,7 +24,7 @@ def test_entrypoint_pipeline() -> None: def test_entrypoint_buffer(buffer_name: str) -> None: config.set( { - "buffer": "package_with_entrypoint." + buffer_name, + "buffer": f"package_with_entrypoint.{buffer_name}", "ndbuffer": "package_with_entrypoint.TestEntrypointNDBuffer", } ) diff --git a/tests/test_group.py b/tests/test_group.py index f9b3a208a8..e05df0dfcb 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -66,7 +66,7 @@ async def store(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> Store: result = await parse_store(request.param, str(tmpdir)) if not isinstance(result, Store): - raise TypeError("Wrong store class returned by test fixture! got " + result + " instead") + raise TypeError(f"Wrong store class returned by test fixture! got {result} instead") return result @@ -150,7 +150,7 @@ def test_group_name_properties( """ root = Group.from_store(store=StorePath(store=store, path=root_name), zarr_format=zarr_format) assert root.path == normalize_path(root_name) - assert root.name == "/" + root.path + assert root.name == f"/{root.path}" assert root.basename == root.path branch = root.create_group(branch_name) @@ -158,7 +158,7 @@ def test_group_name_properties( assert branch.path == normalize_path(branch_name) else: assert branch.path == "/".join([root.path, normalize_path(branch_name)]) - assert branch.name == "/" + branch.path + assert branch.name == f"/{branch.path}" assert branch.basename == branch_name.split("/")[-1] @@ -732,7 +732,7 @@ def test_group_create_array( a[:] = data assert array.path == normalize_path(name) - assert array.name == "/" + array.path + assert array.name == f"/{array.path}" assert array.shape == shape assert array.dtype == np.dtype(dtype) assert np.array_equal(array[:], data) @@ -1082,10 +1082,10 @@ async def test_asyncgroup_delitem(store: Store, zarr_format: ZarrFormat) -> None # todo: clean up the code duplication here if zarr_format == 2: - assert not await agroup.store_path.store.exists(array_name + "/" + ".zarray") - assert not await agroup.store_path.store.exists(array_name + "/" + ".zattrs") + assert not await agroup.store_path.store.exists(f"{array_name}/.zarray") + assert not await agroup.store_path.store.exists(f"{array_name}/.zattrs") elif zarr_format == 3: - assert not await agroup.store_path.store.exists(array_name + "/" + "zarr.json") + assert not await agroup.store_path.store.exists(f"{array_name}/zarr.json") else: raise AssertionError @@ -1093,10 +1093,10 @@ async def test_asyncgroup_delitem(store: Store, zarr_format: ZarrFormat) -> None _ = await agroup.create_group(sub_group_path, attributes={"foo": 100}) await agroup.delitem(sub_group_path) if zarr_format == 2: - assert not await agroup.store_path.store.exists(array_name + "/" + ".zgroup") - assert not await agroup.store_path.store.exists(array_name + "/" + ".zattrs") + assert not await agroup.store_path.store.exists(f"{array_name}/.zgroup") + assert not await agroup.store_path.store.exists(f"{array_name}/.zattrs") elif zarr_format == 3: - assert not await agroup.store_path.store.exists(array_name + "/" + "zarr.json") + assert not await agroup.store_path.store.exists(f"{array_name}/zarr.json") else: raise AssertionError @@ -1113,7 +1113,7 @@ async def test_asyncgroup_create_group( assert isinstance(subgroup, AsyncGroup) assert subgroup.path == normalize_path(name) - assert subgroup.name == "/" + subgroup.path + assert subgroup.name == f"/{subgroup.path}" assert subgroup.attrs == attributes assert subgroup.store_path.path == subgroup.path assert subgroup.store_path.store == store diff --git a/tests/test_regression/test_v2_dtype_regression.py b/tests/test_regression/test_v2_dtype_regression.py index 2607f9aa36..c7b4a53a52 100644 --- a/tests/test_regression/test_v2_dtype_regression.py +++ b/tests/test_regression/test_v2_dtype_regression.py @@ -216,7 +216,7 @@ def test_roundtrip_v2(source_array_v2: ArrayV2, tmp_path: Path, script_path: Pat capture_output=True, text=True, ) - assert copy_op.returncode == 0, "stdout " + copy_op.stdout + "\n stderr" + copy_op.stderr + assert copy_op.returncode == 0, f"stdout {copy_op.stdout}\n stderr{copy_op.stderr}" out_array = zarr.open_array(store=out_path, mode="r", zarr_format=2) assert source_array_v2.metadata.to_dict() == out_array.metadata.to_dict() assert np.array_equal(source_array_v2[:], out_array[:]) diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 4ffc15a87b..92e292bef1 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -380,7 +380,7 @@ def test_from_url(self, store: ManagedMemoryStore) -> None: def test_from_url_with_path(self, store: ManagedMemoryStore) -> None: """Test that from_url extracts path component from URL.""" - url = str(store) + "/some/path" + url = f"{store}/some/path" store2 = ManagedMemoryStore.from_url(url) assert store2._store_dict is store._store_dict assert store2.path == "some/path" diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py index 5975a6d2a0..be51bcedcb 100644 --- a/tests/test_store/test_zip.py +++ b/tests/test_store/test_zip.py @@ -147,7 +147,7 @@ async def test_list_without_explicit_open(self, tmp_path: Path) -> None: root = zarr.open_group(store=zarr_path, mode="w") root["x"] = np.array([1, 2, 3]) shutil.make_archive(str(zarr_path), "zip", zarr_path) - shutil.move(str(zarr_path) + ".zip", zip_path) + shutil.move(f"{zarr_path}.zip", zip_path) store = ZipStore(zip_path, mode="r") assert not store._is_open From 279d400a19d510df6384bb1e93c4817dc867072b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 29 Apr 2026 14:13:11 -0400 Subject: [PATCH 286/468] fix(storage): preserve leading slashes in FsspecStore.path (#3926) * fix(storage): preserve leading slashes in FsspecStore.path #3924 ran the constructor's `path` argument through `normalize_path`, which is intended for zarr logical keys and strips leading slashes. Applied to a filesystem-side root, this turned absolute paths like /home/foo/data.zarr into the relative home/foo/data.zarr, breaking LocalFileSystem-backed FsspecStore for any caller that passed an absolute path. Downstream impact: titiler-xarray's test-upstream job fails on every dataset_3d.zarr fixture access. The original #3922 issue (path="/" producing "//key" via _join_paths) is still resolved: rstrip("/") collapses "/" to "", so the join filter drops it. Trailing slashes are also still stripped. Updates the existing test_fsspec_store_path_normalization parametrization with the new (correct) expectations and adds two absolute-path cases. Co-Authored-By: Claude Opus 4.7 (1M context) * docs: changelog name * docs: remove redundant changelog entries * fix: restore old path normalization logic, and add regression tests --------- Co-authored-by: Claude Opus 4.7 (1M context) --- changes/3924.bugfix.md | 1 - src/zarr/storage/_fsspec.py | 18 ++--- src/zarr/storage/_utils.py | 47 ++++++++++++ tests/test_store/test_fsspec.py | 124 +++++++++++++++++++++++++++----- 4 files changed, 162 insertions(+), 28 deletions(-) delete mode 100644 changes/3924.bugfix.md diff --git a/changes/3924.bugfix.md b/changes/3924.bugfix.md deleted file mode 100644 index 54382d775e..0000000000 --- a/changes/3924.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Apply path normalization to the `path` attribute of `FsspecStore`, ensuring that leading and trailing "/" symbols are removed. diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 1ca44a4e26..14386d1aac 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -16,7 +16,7 @@ ) from zarr.core.buffer import Buffer from zarr.errors import ZarrUserWarning -from zarr.storage._utils import _join_paths, normalize_path +from zarr.storage._utils import _dereference_path if TYPE_CHECKING: from collections.abc import AsyncIterator, Iterable @@ -127,7 +127,7 @@ def __init__( ) -> None: super().__init__(read_only=read_only) self.fs = fs - self.path = normalize_path(path) + self.path = path self.allowed_exceptions = allowed_exceptions if not self.fs.async_impl: @@ -282,7 +282,7 @@ async def get( # docstring inherited if not self._is_open: await self._open() - path = _join_paths([self.path, key]) + path = _dereference_path(self.path, key) try: if byte_range is None: @@ -329,7 +329,7 @@ async def set( raise TypeError( f"FsspecStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead." ) - path = _join_paths([self.path, key]) + path = _dereference_path(self.path, key) # write data if byte_range: raise NotImplementedError @@ -338,7 +338,7 @@ async def set( async def delete(self, key: str) -> None: # docstring inherited self._check_writable() - path = _join_paths([self.path, key]) + path = _dereference_path(self.path, key) try: await self.fs._rm(path) except FileNotFoundError: @@ -354,14 +354,14 @@ async def delete_dir(self, prefix: str) -> None: ) self._check_writable() - path_to_delete = _join_paths([self.path, prefix]) + path_to_delete = _dereference_path(self.path, prefix) with suppress(*self.allowed_exceptions): await self.fs._rm(path_to_delete, recursive=True) async def exists(self, key: str) -> bool: # docstring inherited - path = _join_paths([self.path, key]) + path = _dereference_path(self.path, key) exists: bool = await self.fs._exists(path) return exists @@ -378,7 +378,7 @@ async def get_partial_values( starts: list[int | None] = [] stops: list[int | None] = [] for key, byte_range in key_ranges: - paths.append(_join_paths([self.path, key])) + paths.append(_dereference_path(self.path, key)) if byte_range is None: starts.append(None) stops.append(None) @@ -429,7 +429,7 @@ async def list_prefix(self, prefix: str) -> AsyncIterator[str]: yield onefile.removeprefix(f"{self.path}/") async def getsize(self, key: str) -> int: - path = _join_paths([self.path, key]) + path = _dereference_path(self.path, key) info = await self.fs._info(path) size = info.get("size") diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index 2ff9baa5ab..1f8e9b0a29 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -185,6 +185,53 @@ def _join_paths(paths: Iterable[str]) -> str: return "/".join(filter(lambda v: v != "", paths)) +def _dereference_path(root: str, path: str) -> str: + """ + Combine a store-side root with a key into a single fully-qualified path. + + Unlike `_join_paths`, this is purpose-built for the case where `root` is + an opaque backend-side prefix that may use `"/"` as a sentinel for "root + of the filesystem" (notably for fsspec's `ReferenceFileSystem`). A + trailing `"/"` is stripped from `root` before joining; if `root` is then + empty, the bare `path` is returned so that joining `"/"` with `"key"` + yields `"key"` rather than `"//key"`. A trailing `"/"` on the result is + also stripped. + + Leading slashes on `root` are preserved -- a backend-side path like + `"/home/foo/data.zarr"` is an absolute filesystem path for + `LocalFileSystem` and must not lose its leading separator. + + Parameters + ---------- + root : str + The backend-side root of a store. May be `""`, `"/"`, an absolute + filesystem path, or a backend-specific prefix. + path : str + The key within the store, typically a zarr key like `"zarr.json"` + or `"a/b/c/zarr.json"`. + + Returns + ------- + str + `root` and `path` joined by a single `"/"`, with the `"/"` sentinel + collapsed and trailing slashes removed. + + Examples + -------- + ```python + from zarr.storage._utils import _dereference_path + _dereference_path("/", "zarr.json") # 'zarr.json' + _dereference_path("", "zarr.json") # 'zarr.json' + _dereference_path("/home/foo", "zarr.json") # '/home/foo/zarr.json' + _dereference_path("/home/foo/", "zarr.json") # '/home/foo/zarr.json' + _dereference_path("bucket/p", "zarr.json") # 'bucket/p/zarr.json' + ``` + """ + root = root.rstrip("/") + path = f"{root}/{path}" if root else path + return path.rstrip("/") + + def _relativize_path(*, path: str, prefix: str) -> str: """ Make a "/"-delimited path relative to some prefix. If the prefix is '', then the path is diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 00b989a5de..9ef2c0afcd 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -17,7 +17,6 @@ from zarr.errors import ZarrUserWarning from zarr.storage import FsspecStore from zarr.storage._fsspec import _make_async -from zarr.storage._utils import normalize_path from zarr.testing.store import StoreTests if TYPE_CHECKING: @@ -287,25 +286,114 @@ def array_roundtrip(store: FsspecStore) -> None: np.testing.assert_array_equal(arr[:], data) -@pytest.mark.skipif( - parse_version(fsspec.__version__) < parse_version("2024.12.0"), - reason="No AsyncFileSystemWrapper", +@pytest.mark.parametrize( + ("root", "key", "expected"), + [ + # `"/"` as root collapses so that bare-key backends (notably + # ReferenceFileSystem) get the right key. Regression test for + # https://github.com/zarr-developers/zarr-python/issues/3922 . + ("/", "zarr.json", "zarr.json"), + ("", "zarr.json", "zarr.json"), + # Trailing slashes on the root are stripped before joining. + ("foo/", "zarr.json", "foo/zarr.json"), + ("foo", "zarr.json", "foo/zarr.json"), + # Leading slashes on the root are preserved -- absolute filesystem + # paths must stay absolute. Regression test for the titiler-xarray + # breakage that #3924 introduced when `normalize_path` was applied to + # `FsspecStore.path`. + ("/home/runner/data.zarr", "zarr.json", "/home/runner/data.zarr/zarr.json"), + ("/home/runner/data.zarr/", "zarr.json", "/home/runner/data.zarr/zarr.json"), + # Multi-segment keys. + ("/home/foo", "a/b/zarr.json", "/home/foo/a/b/zarr.json"), + ("", "a/b/zarr.json", "a/b/zarr.json"), + # Trailing slash on the result is stripped (relevant when key is ""). + ("/home/foo", "", "/home/foo"), + ], ) -@pytest.mark.parametrize("path", ["", "/", "//", "foo", "foo/", "/foo", "/foo/", "//foo//"]) -def test_fsspec_store_path_normalization(path: str) -> None: - """`FsspecStore.path` is normalized to the canonical form, matching - `normalize_path`, regardless of the surface representation the caller - supplies. - - Regression test for https://github.com/zarr-developers/zarr-python/issues/3922 - -- when a caller passed `path="/"` the leading slash flowed through - unmodified to subsequent `_join_paths([self.path, key])` calls, producing - `"//key"` and missing the underlying object. +def test_dereference_path(root: str, key: str, expected: str) -> None: + """Verify the contract `_dereference_path` provides for `FsspecStore`. + + `FsspecStore.path` is stored verbatim; the join with a key must collapse a + sentinel `"/"` root, strip trailing slashes, and preserve leading + slashes on absolute paths. + """ + from zarr.storage._utils import _dereference_path + + assert _dereference_path(root, key) == expected + + +async def test_fsspec_store_open_group_via_reference_filesystem() -> None: + """End-to-end regression test for + https://github.com/zarr-developers/zarr-python/issues/3922 . + + ``ReferenceFileSystem`` keys its refs by bare strings like ``"zarr.json"``. + The bug was that ``FsspecStore(fs=ref_fs, path="/")`` produced + ``"//zarr.json"`` at the join site and failed to find the entry, raising + ``GroupNotFoundError``. This test pins ``path="/"`` explicitly to keep + coverage even if the default value changes later. + """ + import json + + from fsspec.implementations.reference import ReferenceFileSystem + + group_json = json.dumps({"zarr_format": 3, "node_type": "group", "attributes": {}}) + fs = ReferenceFileSystem( + fo={"version": 1, "refs": {"zarr.json": group_json}}, + asynchronous=True, + ) + store = FsspecStore(fs=fs, path="/", read_only=True) + group = await zarr.api.asynchronous.open_group(store, mode="r") + assert group.metadata.zarr_format == 3 + + +async def test_fsspec_store_read_array_chunk_via_reference_filesystem() -> None: + """End-to-end regression test that exercises the byte-range read path + against ``ReferenceFileSystem``. + + Beyond opening a group (covered by + ``test_fsspec_store_open_group_via_reference_filesystem``), this test + constructs a small zarr v3 array whose chunk lives in the refs dict and + reads it through the store. Path-handling bugs on the byte-range + fetch path (used by kerchunk-style virtualization) would surface here + rather than at metadata-open time. """ - sync_fs = fsspec.filesystem("memory") - fs = _make_async(sync_fs) - store = FsspecStore(fs=fs, path=path) - assert store.path == normalize_path(path) + import json + + import numpy as np + from fsspec.implementations.reference import ReferenceFileSystem + + # Construct a minimal v3 zarr: a single 1-D uint8 array of length 4 with + # one chunk of size 4. The chunk bytes are little-endian uint8s 1..4. + array_meta = json.dumps( + { + "zarr_format": 3, + "node_type": "array", + "shape": [4], + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [4]}}, + "data_type": "uint8", + "chunk_key_encoding": {"name": "default", "configuration": {"separator": "/"}}, + "fill_value": 0, + "codecs": [{"name": "bytes", "configuration": {"endian": "little"}}], + "attributes": {}, + } + ) + chunk_bytes = bytes([1, 2, 3, 4]) + + refs: dict[str, str] = { + "zarr.json": array_meta, + # ReferenceFileSystem accepts raw bytes via base64 encoding or + # latin-1-decoded strings; latin-1 round-trips bytes 1:1. + "c/0": chunk_bytes.decode("latin-1"), + } + + fs = ReferenceFileSystem( + fo={"version": 1, "refs": refs}, + asynchronous=True, + ) + store = FsspecStore(fs=fs, path="/", read_only=True) + array = await zarr.api.asynchronous.open_array(store=store, mode="r") + data = await array.getitem(slice(None)) + np.testing.assert_array_equal(data, np.array([1, 2, 3, 4], dtype="uint8")) @pytest.mark.skipif( From 23e96350b83079b7ef8c31fe5430024ef4a66d50 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 30 Apr 2026 16:40:11 -0400 Subject: [PATCH 287/468] feat: add cast_value and scale_offset codecs (#3874) * feat: add cast_value and scale_offset codecs Defines two new codecs that together provide a v3-native replacement for the existing `numcodecs.fixedscaleoffset` codec. The `cast_value` codec requires an optional dependency on the `cast-value-rs` package. * docs: changelog * chore: simplify scalar map handling * chore: coverage * chore: preserve JSON encoding of scale and offset parameters * chore: internal cleanup * fix: use explicit list of data type names * docs: add comment * fix: make encode / decode stricter about dtypes * test: don't use async incorrectly * test: patch holes in test coverage * chore: lint * chore: remove cast-value-rs group, and add cast-value-rs to optional deps * improve docstrings --- changes/3874.feature.md | 1 + pyproject.toml | 2 + src/zarr/codecs/__init__.py | 6 + src/zarr/codecs/cast_value.py | 386 +++++++++++++++++++++ src/zarr/codecs/scale_offset.py | 415 ++++++++++++++++++++++ tests/test_codecs/conftest.py | 20 ++ tests/test_codecs/test_cast_value.py | 445 ++++++++++++++++++++++++ tests/test_codecs/test_scale_offset.py | 457 +++++++++++++++++++++++++ 8 files changed, 1732 insertions(+) create mode 100644 changes/3874.feature.md create mode 100644 src/zarr/codecs/cast_value.py create mode 100644 src/zarr/codecs/scale_offset.py create mode 100644 tests/test_codecs/conftest.py create mode 100644 tests/test_codecs/test_cast_value.py create mode 100644 tests/test_codecs/test_scale_offset.py diff --git a/changes/3874.feature.md b/changes/3874.feature.md new file mode 100644 index 0000000000..592c5b330d --- /dev/null +++ b/changes/3874.feature.md @@ -0,0 +1 @@ +Add `cast_value` and `scale_offset` codecs. \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index b4783b5be3..4e3fc109e4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -69,6 +69,7 @@ remote = [ gpu = [ "cupy-cuda12x", ] +cast-value-rs = ["cast-value-rs"] cli = ["typer"] optional = ["universal-pathlib"] @@ -166,6 +167,7 @@ matrix.deps.features = [ {value = "remote", if = ["optional"]}, {value = "optional", if = ["optional"]}, {value = "cli", if = ["optional"]}, + {value = "cast-value-rs", if = ["optional"]}, ] matrix.deps.dependency-groups = [ {value = "remote-tests", if = ["optional"]}, diff --git a/src/zarr/codecs/__init__.py b/src/zarr/codecs/__init__.py index 4c621290e7..756bd97ed2 100644 --- a/src/zarr/codecs/__init__.py +++ b/src/zarr/codecs/__init__.py @@ -2,6 +2,7 @@ from zarr.codecs.blosc import BloscCname, BloscCodec, BloscShuffle from zarr.codecs.bytes import BytesCodec, Endian +from zarr.codecs.cast_value import CastValue from zarr.codecs.crc32c_ import Crc32cCodec from zarr.codecs.gzip import GzipCodec from zarr.codecs.numcodecs import ( @@ -27,6 +28,7 @@ Zlib, Zstd, ) +from zarr.codecs.scale_offset import ScaleOffset from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation from zarr.codecs.transpose import TransposeCodec from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec @@ -38,9 +40,11 @@ "BloscCodec", "BloscShuffle", "BytesCodec", + "CastValue", "Crc32cCodec", "Endian", "GzipCodec", + "ScaleOffset", "ShardingCodec", "ShardingCodecIndexLocation", "TransposeCodec", @@ -50,12 +54,14 @@ ] register_codec("blosc", BloscCodec) +register_codec("cast_value", CastValue) register_codec("bytes", BytesCodec) # compatibility with earlier versions of ZEP1 register_codec("endian", BytesCodec) register_codec("crc32c", Crc32cCodec) register_codec("gzip", GzipCodec) +register_codec("scale_offset", ScaleOffset) register_codec("sharding_indexed", ShardingCodec) register_codec("zstd", ZstdCodec) register_codec("vlen-utf8", VLenUTF8Codec) diff --git a/src/zarr/codecs/cast_value.py b/src/zarr/codecs/cast_value.py new file mode 100644 index 0000000000..d8c503464e --- /dev/null +++ b/src/zarr/codecs/cast_value.py @@ -0,0 +1,386 @@ +"""Cast-value array-to-array codec. + +Value-converts array elements to a new data type during encoding, +and back to the original data type during decoding, with configurable +rounding, out-of-range handling, and explicit scalar mappings. + +Requires the optional ``cast-value-rs`` package for the actual casting +logic. Install it with: ``pip install cast-value-rs``. +""" + +from __future__ import annotations + +from collections.abc import Mapping +from dataclasses import dataclass, replace +from typing import TYPE_CHECKING, Final, Literal, TypedDict, cast + +import numpy as np + +from zarr.abc.codec import ArrayArrayCodec +from zarr.core.common import JSON, parse_named_configuration +from zarr.core.dtype import get_data_type_from_json + +if TYPE_CHECKING: + from typing import NotRequired, Self + + from zarr.core.array_spec import ArraySpec + from zarr.core.buffer import NDBuffer + from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType + from zarr.core.metadata.v3 import ChunkGridMetadata + + class ScalarMapJSON(TypedDict): + encode: NotRequired[list[tuple[object, object]]] + decode: NotRequired[list[tuple[object, object]]] + + +RoundingMode = Literal[ + "nearest-even", + "towards-zero", + "towards-positive", + "towards-negative", + "nearest-away", +] + +OutOfRangeMode = Literal["clamp", "wrap"] + + +class ScalarMap(TypedDict, total=False): + """ + The normalized, in-memory form of a scalar map. + """ + + encode: Mapping[str | float | int, str | float | int] + decode: Mapping[str | float | int, str | float | int] + + +# see https://github.com/zarr-developers/zarr-extensions/tree/main/codecs/cast_value +PERMITTED_DATA_TYPE_NAMES: Final[set[str]] = { + "int2", + "int4", + "int8", + "int16", + "int32", + "int64", + "int64uint2", + "uint4", + "uint8", + "uint16", + "uint32", + "uint64", + "uint64float4_e2m1fn", + "float6_e2m3fn", + "float6_e3m2fn", + "float8_e3m4", + "float8_e4m3", + "float8_e4m3b11fnuz", + "float8_e4m3fnuz", + "float8_e5m2", + "float8_e5m2fnuz", + "float8_e8m0fnu", + "bfloat16", + "float16", + "float32", + "float64", +} + + +def parse_scalar_map(obj: ScalarMapJSON | ScalarMap) -> ScalarMap: + """ + Parse a scalar map into its normalized dict-of-dicts form. + + Accepts either the JSON form (lists of tuples) or an already-normalized form + (dicts). For example, ``{"encode": [("NaN", 0)]}`` becomes + ``{"encode": {"NaN": 0}}``. + """ + result: ScalarMap = {} + for direction in ("encode", "decode"): + if direction in obj: + entries = obj[direction] + if entries is not None: + if isinstance(entries, Mapping): + result[direction] = entries + else: + result[direction] = dict(entries) # type: ignore[arg-type] + return result + + +# --------------------------------------------------------------------------- +# Backend: cast-value-rs +# --------------------------------------------------------------------------- + +try: + from cast_value_rs import cast_array as cast_array_rs + + _HAS_RUST_BACKEND = True +except ModuleNotFoundError: + _HAS_RUST_BACKEND = False + + +def _check_representable( + value: JSON, + zdtype: ZDType[TBaseDType, TBaseScalar], + label: str, +) -> None: + """Raise ``ValueError`` if *value* cannot be parsed by *zdtype*.""" + try: + zdtype.from_json_scalar(value, zarr_format=3) + except (TypeError, ValueError, OverflowError) as e: + raise ValueError( + f"{label} {value!r} is not representable in dtype {zdtype.to_native_dtype()}." + ) from e + + +# --------------------------------------------------------------------------- +# Codec +# --------------------------------------------------------------------------- + + +@dataclass(frozen=True) +class CastValue(ArrayArrayCodec): + """Cast-value array-to-array codec. + + Value-converts array elements to a new data type during encoding, + and back to the original data type during decoding. + + Requires the `cast-value-rs` package for the actual casting logic. + + Parameters + ---------- + data_type : str or ZDType + Target zarr v3 data type. Strings are looked up by spec name + (e.g. "uint8", "float32"); a `ZDType` instance is used as-is. + rounding : RoundingMode + How to round when exact representation is impossible. Default is + "nearest-even". + out_of_range : OutOfRangeMode or None + What to do when a value is outside the target's range. `None` means + error; "clamp" clips to range; "wrap" uses modular arithmetic + (only valid for integer types). Default is `None`. + scalar_map : ScalarMap, ScalarMapJSON, or None + Explicit mapping from input scalars to output scalars. Default is + `None`. + + Attributes + ---------- + dtype : ZDType + Resolved target data type (a `ZDType` instance, regardless of + whether the constructor received a string or a `ZDType`). + rounding : RoundingMode + The rounding mode, as supplied to the constructor. + out_of_range : OutOfRangeMode or None + The out-of-range behaviour, as supplied to the constructor. + scalar_map : ScalarMap or None + Parsed scalar map (always normalized to `ScalarMap` form). + + References + ---------- + + - The `cast_value` codec spec: https://github.com/zarr-developers/zarr-extensions/tree/main/codecs/cast_value + """ + + is_fixed_size = True + + dtype: ZDType[TBaseDType, TBaseScalar] + rounding: RoundingMode + out_of_range: OutOfRangeMode | None + scalar_map: ScalarMap | None + + def __init__( + self, + *, + data_type: str | ZDType[TBaseDType, TBaseScalar], + rounding: RoundingMode = "nearest-even", + out_of_range: OutOfRangeMode | None = None, + scalar_map: ScalarMapJSON | ScalarMap | None = None, + ) -> None: + if isinstance(data_type, str): + zdtype = get_data_type_from_json(data_type, zarr_format=3) + else: + zdtype = data_type + if zdtype.to_json(zarr_format=3) not in PERMITTED_DATA_TYPE_NAMES: + raise ValueError( + f"Invalid target data type {data_type!r}. " + f"cast_value codec only supports integer and floating-point data types. " + f"Got {zdtype}." + ) + object.__setattr__(self, "dtype", zdtype) + object.__setattr__(self, "rounding", rounding) + object.__setattr__(self, "out_of_range", out_of_range) + if scalar_map is not None: + parsed = parse_scalar_map(scalar_map) + else: + parsed = None + object.__setattr__(self, "scalar_map", parsed) + + @classmethod + def from_dict(cls, data: dict[str, JSON]) -> Self: + _, configuration_parsed = parse_named_configuration( + data, "cast_value", require_configuration=True + ) + return cls(**configuration_parsed) # type: ignore[arg-type] + + def to_dict(self) -> dict[str, JSON]: + config: dict[str, JSON] = {"data_type": cast("JSON", self.dtype.to_json(zarr_format=3))} + if self.rounding != "nearest-even": + config["rounding"] = self.rounding + if self.out_of_range is not None: + config["out_of_range"] = self.out_of_range + if self.scalar_map is not None: + json_map: dict[str, list[tuple[object, object]]] = {} + for direction in ("encode", "decode"): + if direction in self.scalar_map: + json_map[direction] = [(k, v) for k, v in self.scalar_map[direction].items()] + config["scalar_map"] = cast("JSON", json_map) + return {"name": "cast_value", "configuration": config} + + def validate( + self, + *, + shape: tuple[int, ...], + dtype: ZDType[TBaseDType, TBaseScalar], + chunk_grid: ChunkGridMetadata, + ) -> None: + target_name = dtype.to_json(zarr_format=3) + if target_name not in PERMITTED_DATA_TYPE_NAMES: + raise ValueError( + f"The cast_value codec only supports integer and floating-point data types. " + f"Got dtype {target_name}." + ) + target_native = dtype.to_native_dtype() + if self.out_of_range == "wrap" and not np.issubdtype(target_native, np.integer): + raise ValueError("out_of_range='wrap' is only valid for integer target types.") + + if self.scalar_map is not None: + self._validate_scalar_map(dtype, self.dtype) + + def _validate_scalar_map( + self, + source_zdtype: ZDType[TBaseDType, TBaseScalar], + target_zdtype: ZDType[TBaseDType, TBaseScalar], + ) -> None: + """Validate that scalar map entries are compatible with source/target dtypes.""" + assert self.scalar_map is not None + # For encode: keys are source values, values are target values. + # For decode: keys are target values, values are source values. + direction_dtypes: dict[ + str, tuple[ZDType[TBaseDType, TBaseScalar], ZDType[TBaseDType, TBaseScalar]] + ] = { + "encode": (source_zdtype, target_zdtype), + "decode": (target_zdtype, source_zdtype), + } + for direction, (key_zdtype, val_zdtype) in direction_dtypes.items(): + if direction not in self.scalar_map: + continue + sub_map = self.scalar_map[direction] # type: ignore[literal-required] + for k, v in sub_map.items(): + _check_representable(k, key_zdtype, f"scalar_map {direction} key") + _check_representable(v, val_zdtype, f"scalar_map {direction} value") + + def _do_cast( + self, + arr: np.ndarray, # type: ignore[type-arg] + *, + target_dtype: np.dtype, # type: ignore[type-arg] + scalar_map: Mapping[str | float | int, str | float | int] | None, + ) -> np.ndarray: # type: ignore[type-arg] + if not _HAS_RUST_BACKEND: + raise ImportError( + "The cast_value codec requires the 'cast-value-rs' package. " + "Install it with: pip install cast-value-rs" + ) + scalar_map_entries: dict[float | int, float | int] | None = None + if scalar_map is not None: + src_dtype = arr.dtype + to_src = int if np.issubdtype(src_dtype, np.integer) else float + to_tgt = int if np.issubdtype(target_dtype, np.integer) else float + scalar_map_entries = {to_src(k): to_tgt(v) for k, v in scalar_map.items()} + return cast_array_rs( # type: ignore[no-any-return] + arr, + target_dtype=target_dtype, + rounding_mode=self.rounding, + out_of_range_mode=self.out_of_range, + scalar_map_entries=scalar_map_entries, + ) + + def _get_scalar_map( + self, direction: str + ) -> Mapping[str | float | int, str | float | int] | None: + """Extract the encode or decode mapping from scalar_map, or None.""" + if self.scalar_map is None: + return None + return self.scalar_map.get(direction) # type: ignore[return-value] + + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + """ + Update the fill value of the output spec by applying casting procedure. + """ + target_zdtype = self.dtype + target_native = target_zdtype.to_native_dtype() + source_native = chunk_spec.dtype.to_native_dtype() + + fill = chunk_spec.fill_value + fill_arr = np.array([fill], dtype=source_native) + + new_fill_arr = self._do_cast( + fill_arr, target_dtype=target_native, scalar_map=self._get_scalar_map("encode") + ) + new_fill = target_native.type(new_fill_arr[0]) + + return replace(chunk_spec, dtype=target_zdtype, fill_value=new_fill) + + def _encode_sync( + self, + chunk_array: NDBuffer, + _chunk_spec: ArraySpec, + ) -> NDBuffer | None: + arr = chunk_array.as_ndarray_like() + target_native = self.dtype.to_native_dtype() + + result = self._do_cast( + np.asarray(arr), target_dtype=target_native, scalar_map=self._get_scalar_map("encode") + ) + return chunk_array.__class__.from_ndarray_like(result) + + async def _encode_single( + self, + chunk_data: NDBuffer, + chunk_spec: ArraySpec, + ) -> NDBuffer | None: + return self._encode_sync(chunk_data, chunk_spec) + + def _decode_sync( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + arr = chunk_array.as_ndarray_like() + target_native = chunk_spec.dtype.to_native_dtype() + + result = self._do_cast( + np.asarray(arr), target_dtype=target_native, scalar_map=self._get_scalar_map("decode") + ) + return chunk_array.__class__.from_ndarray_like(result) + + async def _decode_single( + self, + chunk_data: NDBuffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + return self._decode_sync(chunk_data, chunk_spec) + + def compute_encoded_size(self, input_byte_length: int, chunk_spec: ArraySpec) -> int: + dtype_name = chunk_spec.dtype.to_json(zarr_format=3) + if dtype_name not in PERMITTED_DATA_TYPE_NAMES: + raise ValueError( + "cast_value codec only supports fixed-size integer and floating-point data types. " + f"Got source dtype: {chunk_spec.dtype}." + ) + source_itemsize = chunk_spec.dtype.to_native_dtype().itemsize + target_itemsize = self.dtype.to_native_dtype().itemsize + if source_itemsize == 0 or target_itemsize == 0: + raise ValueError( + "cast_value codec requires fixed-size data types. " + f"Got source itemsize={source_itemsize}, target itemsize={target_itemsize}." + ) + num_elements = input_byte_length // source_itemsize + return num_elements * target_itemsize diff --git a/src/zarr/codecs/scale_offset.py b/src/zarr/codecs/scale_offset.py new file mode 100644 index 0000000000..c96e177c6b --- /dev/null +++ b/src/zarr/codecs/scale_offset.py @@ -0,0 +1,415 @@ +from __future__ import annotations + +from dataclasses import dataclass, replace +from typing import TYPE_CHECKING, Any, cast + +import numpy as np +import numpy.typing as npt + +from zarr.abc.codec import ArrayArrayCodec +from zarr.core.common import JSON, parse_named_configuration + +if TYPE_CHECKING: + from typing import Self + + from zarr.core.array_spec import ArraySpec + from zarr.core.buffer import NDBuffer + from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType + from zarr.core.metadata.v3 import ChunkGridMetadata + + +_WIDE_INT = np.dtype(np.int64) + + +def _encode_fits_natively(dtype: np.dtype[Any], offset: int, scale: int) -> bool: + """Static range proof: is ``(x - offset) * scale`` always in range for every ``x`` in dtype? + + Uses Python ints (unbounded) to avoid overflow in the proof itself. + """ + info = np.iinfo(dtype) + d_lo = int(info.min) - offset + d_hi = int(info.max) - offset + # Taking min/max of both products handles negative scale without a sign branch. + products = (d_lo * scale, d_hi * scale) + lo, hi = min(products), max(products) + return info.min <= lo and hi <= info.max + + +def _decode_fits_natively(dtype: np.dtype[Any], offset: int, scale: int) -> bool: + """Static range proof for decode: is ``x // scale + offset`` always in range?""" + info = np.iinfo(dtype) + # x // scale is bounded by the extremes of x / scale (integer division stays within that range) + if scale > 0: + q_lo, q_hi = int(info.min) // scale, int(info.max) // scale + else: + q_lo, q_hi = int(info.max) // scale, int(info.min) // scale + lo, hi = q_lo + offset, q_hi + offset + return info.min <= lo and hi <= info.max + + +def _check_int_range( + values: npt.NDArray[np.integer[Any]], target: np.dtype[np.integer[Any]] +) -> None: + """Raise if any value is outside the representable range of ``target``. + + Uses a single min/max pass instead of two ``np.any`` passes. + """ + info = np.iinfo(target) + lo, hi = values.min(), values.max() + if lo < info.min or hi > info.max: + raise ValueError( + f"scale_offset produced a value outside the range of dtype {target} " + f"[{info.min}, {info.max}]." + ) + + +def _check_exact_division( + arr: npt.NDArray[np.integer[Any]], scale: np.integer[Any], scale_repr: object +) -> None: + """Raise ValueError if ``arr`` has any element not exactly divisible by ``scale``.""" + if np.any(arr % scale): + raise ValueError( + f"scale_offset decode produced a non-zero remainder when dividing by " + f"scale={scale_repr!r}; result is not exactly representable in dtype {arr.dtype}." + ) + + +def _encode_int_native( + arr: npt.NDArray[np.integer[Any]], offset: np.integer[Any], scale: np.integer[Any] +) -> npt.NDArray[np.integer[Any]]: + """Compute ``(arr - offset) * scale`` directly in ``arr.dtype``. + + This is the fast path; it exists only as a separate function to make the contract with + ``_encode_fits_natively`` explicit: the caller must have already proved that no ``x`` in + ``arr.dtype``'s range can overflow, so we can skip widening and range-checking entirely. + Using it without that proof would silently wrap on overflow. + """ + return cast("npt.NDArray[np.integer[Any]]", (arr - offset) * scale) + + +def _encode_int_widened( + arr: npt.NDArray[np.integer[Any]], offset: np.integer[Any], scale: np.integer[Any] +) -> npt.NDArray[np.integer[Any]]: + """Overflow-checked integer encode for int8..int64 and uint8..uint32. + + Exists because numpy integer arithmetic silently wraps on overflow, which the spec + forbids. We widen to int64, perform the arithmetic there (int64 holds the product of any + two values from these dtypes), range-check against the target dtype, then cast back. + uint64 cannot use this path because its range exceeds int64 — see ``_encode_uint64``. + """ + wide_arr = arr.astype(_WIDE_INT, copy=False) + result = (wide_arr - _WIDE_INT.type(offset)) * _WIDE_INT.type(scale) + _check_int_range(result, arr.dtype) + return result.astype(arr.dtype, copy=False) + + +def _encode_float( + arr: npt.NDArray[np.floating[Any]], offset: np.floating[Any], scale: np.floating[Any] +) -> npt.NDArray[np.floating[Any]]: + """Encode float arrays in-dtype, guarding only against silent promotion. + + Float arithmetic doesn't need widening — float64 is already the widest supported dtype, + and ``inf``/``nan`` from overflow are representable IEEE 754 values, so no range check is + required by the spec. The one thing that can still go wrong is numpy promoting the + result to a wider float dtype (e.g. float32 * float64 scalar -> float64), which would + violate the spec's "arithmetic semantics of the input array's data type" clause. + """ + result = cast("npt.NDArray[np.floating[Any]]", (arr - offset) * scale) + if result.dtype != arr.dtype: + raise ValueError( + f"scale_offset changed dtype from {arr.dtype} to {result.dtype}. " + f"Arithmetic must preserve the data type." + ) + return result + + +def _check_py_int_range( + result: np.ndarray[tuple[Any, ...], np.dtype[Any]], + target: np.dtype[np.unsignedinteger[Any]], +) -> None: + """Range-check an ``object``-dtype ndarray holding Python ints against ``target``'s iinfo. + + Exists as a uint64-specific counterpart to ``_check_int_range``. That one compares numpy + integers against ``iinfo``; here the values are unbounded Python ints produced by + ``_encode_uint64`` / ``_decode_uint64``, so we rely on Python's arbitrary-precision + comparison to detect values outside the target dtype's range. + """ + info = np.iinfo(target) + # np.min/np.max on an object array returns a Python int (which compares correctly with iinfo). + # Works uniformly for 0-d arrays where .flat iteration is awkward. + lo = np.min(result) + hi = np.max(result) + if lo < int(info.min) or hi > int(info.max): + raise ValueError( + f"scale_offset produced a value outside the range of dtype {target} " + f"[{info.min}, {info.max}]." + ) + + +def _encode_uint64( + arr: npt.NDArray[np.unsignedinteger[Any]], offset: int, scale: int +) -> npt.NDArray[np.unsignedinteger[Any]]: + """Encode uint64 via Python-int arithmetic in an ``object``-dtype array. + + Exists because uint64's range [0, 2**64) exceeds int64, so the int64 widening used by + ``_encode_int_widened`` would itself overflow. Python ints are unbounded, so computing + via ``object`` dtype is correct by construction. The trade-off is speed: object-dtype + arithmetic is interpreted per element and is roughly 10x slower than ufunc paths. + """ + obj = arr.astype(object, copy=False) + # np.asarray restores ndarray-ness in the 0-d/scalar edge case. + result = np.asarray((obj - offset) * scale, dtype=object) + _check_py_int_range(result, arr.dtype) + return cast("npt.NDArray[np.unsignedinteger[Any]]", result.astype(arr.dtype, copy=False)) + + +def _decode_uint64( + arr: npt.NDArray[np.unsignedinteger[Any]], offset: int, scale: int +) -> npt.NDArray[np.unsignedinteger[Any]]: + """Decode uint64 via Python-int arithmetic. See ``_encode_uint64`` for why.""" + obj = arr.astype(object, copy=False) + result = np.asarray((obj // scale) + offset, dtype=object) + _check_py_int_range(result, arr.dtype) + return cast("npt.NDArray[np.unsignedinteger[Any]]", result.astype(arr.dtype, copy=False)) + + +def _decode_int_native( + arr: npt.NDArray[np.integer[Any]], offset: np.integer[Any], scale: np.integer[Any] +) -> npt.NDArray[np.integer[Any]]: + """Compute ``arr // scale + offset`` directly in ``arr.dtype``. + + Fast-path counterpart to ``_encode_int_native``; same contract. Caller must have proved + via ``_decode_fits_natively`` that the result can't overflow. Divisibility is checked + upstream in ``_decode`` before this is called, so ``//`` is exact here. + """ + return cast("npt.NDArray[np.integer[Any]]", (arr // scale) + offset) + + +def _decode_int_widened( + arr: npt.NDArray[np.integer[Any]], offset: np.integer[Any], scale: np.integer[Any] +) -> npt.NDArray[np.integer[Any]]: + """Overflow-checked integer decode for int8..int64 and uint8..uint32. + + Counterpart to ``_encode_int_widened``. Widens to int64 so the addition of ``offset`` + after division can't silently wrap, then range-checks against the target dtype. + """ + wide_arr = arr.astype(_WIDE_INT, copy=False) + result = (wide_arr // _WIDE_INT.type(scale)) + _WIDE_INT.type(offset) + _check_int_range(result, arr.dtype) + return result.astype(arr.dtype, copy=False) + + +def _decode_float( + arr: npt.NDArray[np.floating[Any]], offset: np.floating[Any], scale: np.floating[Any] +) -> npt.NDArray[np.floating[Any]]: + """Decode float arrays in-dtype, guarding only against silent promotion. + + Counterpart to ``_encode_float``; same reasoning. ``arr / scale`` is true division and + always well-defined for floats (including ``0/0 = nan`` and ``x/0 = ±inf``), so no range + or exactness check is needed. + """ + result = cast("npt.NDArray[np.floating[Any]]", (arr / scale) + offset) + if result.dtype != arr.dtype: + raise ValueError( + f"scale_offset changed dtype from {arr.dtype} to {result.dtype}. " + f"Arithmetic must preserve the data type." + ) + return result + + +def _encode( + arr: np.ndarray[tuple[Any, ...], np.dtype[Any]], + offset: np.generic, + scale: np.generic, +) -> np.ndarray[tuple[Any, ...], np.dtype[Any]]: + """Compute ``(arr - offset) * scale`` without silent overflow, returning ``arr.dtype``.""" + # uint64 is split out first because its full range (up to 2**64-1) doesn't fit in int64, + # so the widening strategy used for every other integer dtype would itself overflow. + if arr.dtype == np.uint64: + u_arr = cast("npt.NDArray[np.unsignedinteger[Any]]", arr) + return _encode_uint64(u_arr, int(offset), int(scale)) + if np.issubdtype(arr.dtype, np.integer): + i_arr = cast("npt.NDArray[np.integer[Any]]", arr) + i_offset = cast("np.integer[Any]", offset) + i_scale = cast("np.integer[Any]", scale) + # Fast path: if a static proof shows no ``x`` in the dtype's range can overflow, + # skip the int64 widening and run the arithmetic directly in the input dtype. + if _encode_fits_natively(arr.dtype, int(offset), int(scale)): + return _encode_int_native(i_arr, i_offset, i_scale) + return _encode_int_widened(i_arr, i_offset, i_scale) + # Float path: arithmetic stays in-dtype (no widening); only guard against numpy + # silently promoting a narrower float to a wider one via scalar type mismatch. + f_arr = cast("npt.NDArray[np.floating[Any]]", arr) + f_offset = cast("np.floating[Any]", offset) + f_scale = cast("np.floating[Any]", scale) + return _encode_float(f_arr, f_offset, f_scale) + + +def _decode( + arr: np.ndarray[tuple[Any, ...], np.dtype[Any]], + offset: np.generic, + scale: np.generic, + *, + scale_repr: object, +) -> np.ndarray[tuple[Any, ...], np.dtype[Any]]: + """Compute ``arr / scale + offset`` without silent overflow, returning ``arr.dtype``.""" + # uint64: same reasoning as _encode — its range exceeds int64, so the Python-int path is the + # only correct option. Exactness check runs first so non-divisible inputs fail before the + # slower object-dtype arithmetic. + if arr.dtype == np.uint64: + u_arr = cast("npt.NDArray[np.unsignedinteger[Any]]", arr) + _check_exact_division(u_arr, cast("np.integer[Any]", scale), scale_repr) + return _decode_uint64(u_arr, int(offset), int(scale)) + if np.issubdtype(arr.dtype, np.integer): + i_arr = cast("npt.NDArray[np.integer[Any]]", arr) + i_offset = cast("np.integer[Any]", offset) + i_scale = cast("np.integer[Any]", scale) + # The spec requires decode to use true division and error if the result isn't + # representable. For integers that means the remainder must be zero; if any element + # isn't exactly divisible we fail here rather than silently truncating via //. + _check_exact_division(i_arr, i_scale, scale_repr) + # Fast path mirrors _encode: static proof that ``x // scale + offset`` stays in dtype. + if _decode_fits_natively(arr.dtype, int(offset), int(scale)): + return _decode_int_native(i_arr, i_offset, i_scale) + return _decode_int_widened(i_arr, i_offset, i_scale) + # Float path: division is well-defined; only guard against dtype promotion. + f_arr = cast("npt.NDArray[np.floating[Any]]", arr) + f_offset = cast("np.floating[Any]", offset) + f_scale = cast("np.floating[Any]", scale) + return _decode_float(f_arr, f_offset, f_scale) + + +@dataclass(frozen=True) +class ScaleOffset(ArrayArrayCodec): + """Scale-offset array-to-array codec. + + Encodes values with `out = (in - offset) * scale` and decodes with + `out = (in / scale) + offset`, using the input array's data type semantics. + Intermediate or final values that are not representable in that dtype are reported + as errors (integer overflow, unsigned underflow, non-exact integer division). + + Parameters + ---------- + offset : int, float, or str + Value subtracted during encoding. Strings preserve the exact JSON + representation when round-tripping metadata. Default is 0. + scale : int, float, or str + Value multiplied during encoding (after offset subtraction). Strings + preserve the exact JSON representation when round-tripping metadata. + Default is 1. + + Attributes + ---------- + offset : int, float, or str + The offset value, as supplied to the constructor. + scale : int, float, or str + The scale value, as supplied to the constructor. + + References + ---------- + + - The `scale_offset` codec spec: https://github.com/zarr-developers/zarr-extensions/tree/main/codecs/scale_offset + """ + + is_fixed_size = True + + offset: int | float | str + scale: int | float | str + + def __init__(self, *, offset: object = 0, scale: object = 1) -> None: + if not isinstance(offset, int | float | str): + raise TypeError(f"offset must be a number or string, got {type(offset).__name__}") + if not isinstance(scale, int | float | str): + raise TypeError(f"scale must be a number or string, got {type(scale).__name__}") + object.__setattr__(self, "offset", offset) + object.__setattr__(self, "scale", scale) + + @classmethod + def from_dict(cls, data: dict[str, JSON]) -> Self: + _, configuration_parsed = parse_named_configuration( + data, "scale_offset", require_configuration=False + ) + configuration_parsed = configuration_parsed or {} + return cls(**configuration_parsed) + + def to_dict(self) -> dict[str, JSON]: + if self.offset == 0 and self.scale == 1: + return {"name": "scale_offset"} + config: dict[str, JSON] = {} + if self.offset != 0: + config["offset"] = self.offset + if self.scale != 1: + config["scale"] = self.scale + return {"name": "scale_offset", "configuration": config} + + def validate( + self, + *, + shape: tuple[int, ...], + dtype: ZDType[TBaseDType, TBaseScalar], + chunk_grid: ChunkGridMetadata, + ) -> None: + native = dtype.to_native_dtype() + if not np.issubdtype(native, np.integer) and not np.issubdtype(native, np.floating): + raise ValueError( + f"scale_offset codec only supports integer and floating-point data types. " + f"Got {dtype}." + ) + if self.scale == 0: + raise ValueError("scale_offset scale must be non-zero.") + for name, value in [("offset", self.offset), ("scale", self.scale)]: + try: + dtype.from_json_scalar(value, zarr_format=3) + except (TypeError, ValueError, OverflowError) as e: + raise ValueError( + f"scale_offset {name} value {value!r} is not representable in dtype {native}." + ) from e + + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + zdtype = chunk_spec.dtype + fill = np.asarray(zdtype.cast_scalar(chunk_spec.fill_value)) + offset = cast("np.generic", zdtype.from_json_scalar(self.offset, zarr_format=3)) + scale = cast("np.generic", zdtype.from_json_scalar(self.scale, zarr_format=3)) + new_fill = _encode(fill, offset, scale) + return replace(chunk_spec, fill_value=new_fill.reshape(()).item()) + + def _decode_sync( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + arr = cast("np.ndarray[tuple[Any, ...], np.dtype[Any]]", chunk_array.as_ndarray_like()) + zdtype = chunk_spec.dtype + offset = cast("np.generic", zdtype.from_json_scalar(self.offset, zarr_format=3)) + scale = cast("np.generic", zdtype.from_json_scalar(self.scale, zarr_format=3)) + result = _decode(arr, offset, scale, scale_repr=self.scale) + return chunk_spec.prototype.nd_buffer.from_ndarray_like(result) + + async def _decode_single( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + return self._decode_sync(chunk_array, chunk_spec) + + def _encode_sync( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> NDBuffer | None: + arr = cast("np.ndarray[tuple[Any, ...], np.dtype[Any]]", chunk_array.as_ndarray_like()) + zdtype = chunk_spec.dtype + offset = cast("np.generic", zdtype.from_json_scalar(self.offset, zarr_format=3)) + scale = cast("np.generic", zdtype.from_json_scalar(self.scale, zarr_format=3)) + result = _encode(arr, offset, scale) + return chunk_spec.prototype.nd_buffer.from_ndarray_like(result) + + async def _encode_single( + self, + chunk_array: NDBuffer, + _chunk_spec: ArraySpec, + ) -> NDBuffer | None: + return self._encode_sync(chunk_array, _chunk_spec) + + def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -> int: + return input_byte_length diff --git a/tests/test_codecs/conftest.py b/tests/test_codecs/conftest.py new file mode 100644 index 0000000000..b654ab1ec0 --- /dev/null +++ b/tests/test_codecs/conftest.py @@ -0,0 +1,20 @@ +from __future__ import annotations + +from dataclasses import dataclass + + +@dataclass(frozen=True) +class Expect[TIn, TOut]: + """Model an input and an expected output value for a test case.""" + + input: TIn + expected: TOut + + +@dataclass(frozen=True) +class ExpectErr[TIn]: + """Model an input and an expected error message for a test case.""" + + input: TIn + msg: str + exception_cls: type[Exception] diff --git a/tests/test_codecs/test_cast_value.py b/tests/test_codecs/test_cast_value.py new file mode 100644 index 0000000000..cb456c0584 --- /dev/null +++ b/tests/test_codecs/test_cast_value.py @@ -0,0 +1,445 @@ +from __future__ import annotations + +from typing import Any + +import numpy as np +import pytest + +import zarr +from tests.test_codecs.conftest import Expect, ExpectErr +from zarr.codecs.cast_value import CastValue + +try: + import cast_value_rs # noqa: F401 + + _HAS_CAST_VALUE_RS = True +except ModuleNotFoundError: + _HAS_CAST_VALUE_RS = False + +requires_cast_value_rs = pytest.mark.skipif( + not _HAS_CAST_VALUE_RS, reason="cast-value-rs not installed" +) + + +# --------------------------------------------------------------------------- +# Serialization +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + "case", + [ + Expect( + input=CastValue(data_type="uint8"), + expected={"name": "cast_value", "configuration": {"data_type": "uint8"}}, + ), + Expect( + input=CastValue( + data_type="uint8", + rounding="towards-zero", + out_of_range="clamp", + scalar_map={"encode": [("NaN", 0)]}, + ), + expected={ + "name": "cast_value", + "configuration": { + "data_type": "uint8", + "rounding": "towards-zero", + "out_of_range": "clamp", + "scalar_map": {"encode": [("NaN", 0)]}, + }, + }, + ), + ], + ids=["minimal", "full"], +) +def test_to_dict(case: Expect[CastValue, dict[str, Any]]) -> None: + """to_dict produces the expected JSON structure.""" + assert case.input.to_dict() == case.expected + + +@pytest.mark.parametrize( + "case", + [ + Expect( + input={"name": "cast_value", "configuration": {"data_type": "float32"}}, + expected=("float32", "nearest-even", None), + ), + Expect( + input={ + "name": "cast_value", + "configuration": { + "data_type": "int16", + "rounding": "towards-zero", + "out_of_range": "clamp", + }, + }, + expected=("int16", "towards-zero", "clamp"), + ), + ], + ids=["defaults", "explicit"], +) +def test_from_dict(case: Expect[dict[str, Any], tuple[str, str, str | None]]) -> None: + """from_dict deserializes configuration with correct values and defaults.""" + codec = CastValue.from_dict(case.input) + dtype_name, rounding, out_of_range = case.expected + assert codec.dtype.to_native_dtype() == np.dtype(dtype_name) + assert codec.rounding == rounding + assert codec.out_of_range == out_of_range + + +@pytest.mark.parametrize( + "codec", + [ + CastValue(data_type="int16", rounding="towards-zero", out_of_range="clamp"), + CastValue( + data_type="uint8", + out_of_range="clamp", + scalar_map={"encode": [("NaN", 0)], "decode": [(0, "NaN")]}, + ), + ], + ids=["no-scalar-map", "with-scalar-map"], +) +def test_serialization_roundtrip(codec: CastValue) -> None: + """to_dict followed by from_dict produces an equal codec.""" + restored = CastValue.from_dict(codec.to_dict()) + assert codec == restored + + +# --------------------------------------------------------------------------- +# Construction +# --------------------------------------------------------------------------- + + +def test_construction_accepts_zdtype_object() -> None: + """data_type can be a ZDType instance, not just a JSON string.""" + from zarr.core.dtype import UInt8 + + codec = CastValue(data_type=UInt8()) + assert codec.dtype.to_native_dtype() == np.dtype("uint8") + + +def test_construction_rejects_invalid_target_dtype() -> None: + """Construction rejects target dtypes not in PERMITTED_DATA_TYPE_NAMES.""" + with pytest.raises(ValueError, match="Invalid target data type"): + CastValue(data_type="complex64") + + +# --------------------------------------------------------------------------- +# Validation +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + "case", + [ + ExpectErr( + input={"dtype": "complex128", "target": "float64"}, + msg="only supports integer and floating-point", + exception_cls=ValueError, + ), + ExpectErr( + input={"dtype": "float32", "target": "int32", "out_of_range": "wrap"}, + msg="only valid for integer", + exception_cls=ValueError, + ), + ], + ids=["complex-source", "wrap-float-target"], +) +def test_validation_rejects_invalid(case: ExpectErr[dict[str, Any]]) -> None: + """Invalid dtype or out_of_range combinations are rejected at array creation.""" + with pytest.raises(case.exception_cls, match=case.msg): + zarr.create_array( + store={}, + shape=(10,), + dtype=case.input["dtype"], + chunks=(10,), + filters=[ + CastValue( + data_type=case.input["target"], + out_of_range=case.input.get("out_of_range"), + ) + ], + compressors=None, + fill_value=0, + ) + + +def test_zero_itemsize_raises() -> None: + """Variable-length dtypes (itemsize=0) are rejected by compute_encoded_size.""" + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.dtype.npy.string import VariableLengthUTF8 + + codec = CastValue(data_type="uint8") + spec = ArraySpec( + shape=(10,), + dtype=VariableLengthUTF8(), # type: ignore[arg-type] + fill_value="", + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + with pytest.raises(ValueError, match="fixed-size integer and floating-point data types"): + codec.compute_encoded_size(100, spec) + + +# --------------------------------------------------------------------------- +# Encode / decode +# --------------------------------------------------------------------------- + + +@requires_cast_value_rs +@pytest.mark.parametrize( + "case", + [ + Expect(input=("float64", "float32"), expected=np.arange(50, dtype="float64")), + Expect(input=("float32", "float64"), expected=np.arange(50, dtype="float32")), + Expect(input=("int32", "int64"), expected=np.arange(50, dtype="int32")), + Expect(input=("int64", "int16"), expected=np.arange(50, dtype="int64")), + Expect(input=("float64", "int32"), expected=np.arange(50, dtype="float64")), + Expect(input=("int32", "float64"), expected=np.arange(50, dtype="int32")), + ], + ids=["f64→f32", "f32→f64", "i32→i64", "i64→i16", "f64→i32", "i32→f64"], +) +def test_encode_decode_roundtrip( + case: Expect[tuple[str, str], np.ndarray[Any, np.dtype[Any]]], +) -> None: + """Small integer data survives encode → decode for each dtype pair.""" + import zarr + + source_dtype, target_dtype = case.input + arr = zarr.create_array( + store={}, + shape=(50,), + dtype=source_dtype, + chunks=(50,), + filters=[CastValue(data_type=target_dtype)], + compressors=None, + fill_value=0, + ) + arr[:] = case.expected + np.testing.assert_array_equal(arr[:], case.expected) + + +@requires_cast_value_rs +@pytest.mark.parametrize( + "case", + [ + Expect( + input=np.array([1.7, -1.7, 2.5, -2.5], dtype="float64"), + expected=np.array([1, -1, 2, -2], dtype="float64"), + ), + ], + ids=["towards-zero"], +) +def test_float_to_int_rounding( + case: Expect[np.ndarray[Any, np.dtype[Any]], np.ndarray[Any, np.dtype[Any]]], +) -> None: + """Fractional float values are truncated towards zero when cast to int32.""" + import zarr + + arr = zarr.create_array( + store={}, + shape=case.input.shape, + dtype=case.input.dtype, + chunks=case.input.shape, + filters=[CastValue(data_type="int32", rounding="towards-zero", out_of_range="clamp")], + compressors=None, + fill_value=0, + ) + arr[:] = case.input + np.testing.assert_array_equal(arr[:], case.expected) + + +@requires_cast_value_rs +@pytest.mark.parametrize( + "case", + [ + Expect( + input=np.array([0, 200, -200], dtype="int32"), + expected=np.array([0, 127, -128], dtype="int32"), + ), + ], + ids=["int32→int8"], +) +def test_out_of_range_clamp( + case: Expect[np.ndarray[Any, np.dtype[Any]], np.ndarray[Any, np.dtype[Any]]], +) -> None: + """Values outside the int8 range are clamped to [-128, 127].""" + import zarr + + arr = zarr.create_array( + store={}, + shape=case.input.shape, + dtype=case.input.dtype, + chunks=case.input.shape, + filters=[CastValue(data_type="int8", out_of_range="clamp")], + compressors=None, + fill_value=0, + ) + arr[:] = case.input + np.testing.assert_array_equal(arr[:], case.expected) + + +def test_compute_encoded_size() -> None: + """compute_encoded_size correctly scales byte length by itemsize ratio.""" + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.dtype import get_data_type_from_json + + codec = CastValue(data_type="int16") + spec = ArraySpec( + shape=(10,), + dtype=get_data_type_from_json("float64", zarr_format=3), + fill_value=0, + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + # 10 float64 elements = 80 bytes -> 10 int16 elements = 20 bytes + assert codec.compute_encoded_size(80, spec) == 20 + + +@requires_cast_value_rs +def test_scalar_map_encode_decode_roundtrip() -> None: + """Scalar map entries are applied during encode and decode.""" + import zarr + + data = np.array([1.0, float("nan"), 3.0], dtype="float64") + arr = zarr.create_array( + store={}, + shape=data.shape, + dtype="float64", + chunks=data.shape, + filters=[ + CastValue( + data_type="int32", + rounding="nearest-even", + out_of_range="clamp", + scalar_map={"encode": [("NaN", -999)], "decode": [(-999, "NaN")]}, + ), + ], + compressors=None, + fill_value=1, + ) + arr[:] = data + result = np.asarray(arr[:]) + np.testing.assert_equal(result[0], 1.0) + np.testing.assert_equal(result[2], 3.0) + assert np.isnan(result[1]) + + +@pytest.mark.parametrize( + "case", + [ + ExpectErr( + input={ + "dtype": "int32", + "target": "int8", + "scalar_map": {"encode": [("NaN", 0)]}, + }, + msg="not representable in dtype int32", + exception_cls=ValueError, + ), + ExpectErr( + input={ + "dtype": "int32", + "target": "float64", + "scalar_map": {"decode": [(0, "NaN")]}, + }, + msg="not representable in dtype int32", + exception_cls=ValueError, + ), + ExpectErr( + input={ + "dtype": "float64", + "target": "int8", + "scalar_map": {"encode": [("NaN", 999)]}, + }, + msg="not representable in dtype int8", + exception_cls=ValueError, + ), + ExpectErr( + input={ + "dtype": "float64", + "target": "int8", + "scalar_map": {"encode": [("NaN", 1.5)]}, + }, + msg="not representable in dtype int8", + exception_cls=ValueError, + ), + ], + ids=[ + "nan-key-for-int-source", + "nan-value-for-int-decode-target", + "encode-value-out-of-range", + "encode-value-not-integer", + ], +) +def test_scalar_map_validation_rejects_invalid(case: ExpectErr[dict[str, Any]]) -> None: + """Invalid scalar_map entries are rejected at array creation.""" + import zarr + + with pytest.raises(case.exception_cls, match=case.msg): + zarr.create_array( + store={}, + shape=(10,), + dtype=case.input["dtype"], + chunks=(10,), + filters=[ + CastValue( + data_type=case.input["target"], + out_of_range="clamp", + scalar_map=case.input["scalar_map"], + ) + ], + compressors=None, + fill_value=0, + ) + + +@requires_cast_value_rs +def test_combined_with_scale_offset() -> None: + """scale_offset followed by cast_value compresses float64 into int16 and round-trips.""" + import zarr + from zarr.codecs.scale_offset import ScaleOffset + + arr = zarr.create_array( + store={}, + shape=(100,), + dtype="float64", + chunks=(100,), + filters=[ + ScaleOffset(offset=0, scale=10), + CastValue(data_type="int16", rounding="nearest-even", out_of_range="clamp"), + ], + compressors=None, + fill_value=0, + ) + data = np.arange(100, dtype="float64") * 0.1 + arr[:] = data + result = arr[:] + np.testing.assert_array_almost_equal(result, data, decimal=1) # type: ignore[arg-type] + + +@pytest.mark.parametrize( + "case", + [ + Expect( + input={"encode": [("NaN", 0)]}, + expected={"encode": {"NaN": 0}}, + ), + Expect( + input={"encode": [("NaN", 0)], "decode": [(0, "NaN")]}, + expected={"encode": {"NaN": 0}, "decode": {0: "NaN"}}, + ), + Expect( + input={"encode": {"NaN": 0}}, + expected={"encode": {"NaN": 0}}, + ), + ], + ids=["encode-only", "both-directions", "already-normalized"], +) +def test_parse_scalar_map(case: Expect[Any, Any]) -> None: + from zarr.codecs.cast_value import parse_scalar_map + + assert parse_scalar_map(case.input) == case.expected diff --git a/tests/test_codecs/test_scale_offset.py b/tests/test_codecs/test_scale_offset.py new file mode 100644 index 0000000000..99a5e3b99d --- /dev/null +++ b/tests/test_codecs/test_scale_offset.py @@ -0,0 +1,457 @@ +from __future__ import annotations + +from typing import Any + +import numpy as np +import pytest + +import zarr +from tests.test_codecs.conftest import Expect, ExpectErr +from zarr.codecs.scale_offset import ( + ScaleOffset, + _decode, + _decode_fits_natively, + _encode, +) +from zarr.core.buffer.core import default_buffer_prototype +from zarr.storage._memory import MemoryStore + +# --------------------------------------------------------------------------- +# Serialization +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + "case", + [ + Expect(input=ScaleOffset(), expected={"name": "scale_offset"}), + Expect( + input=ScaleOffset(offset=5), + expected={"name": "scale_offset", "configuration": {"offset": 5}}, + ), + Expect( + input=ScaleOffset(scale=0.1), + expected={"name": "scale_offset", "configuration": {"scale": 0.1}}, + ), + Expect( + input=ScaleOffset(offset=5, scale=0.1), + expected={"name": "scale_offset", "configuration": {"offset": 5, "scale": 0.1}}, + ), + ], + ids=["default", "offset-only", "scale-only", "both"], +) +def test_to_dict(case: Expect[ScaleOffset, dict[str, Any]]) -> None: + """to_dict produces the expected JSON structure.""" + assert case.input.to_dict() == case.expected + + +@pytest.mark.parametrize( + "case", + [ + Expect(input={"name": "scale_offset"}, expected=(0, 1)), + Expect( + input={"name": "scale_offset", "configuration": {"offset": 3, "scale": 2}}, + expected=(3, 2), + ), + ], + ids=["no-config", "with-config"], +) +def test_from_dict(case: Expect[dict[str, Any], tuple[int | float, int | float]]) -> None: + """from_dict deserializes configuration with correct values and defaults.""" + codec = ScaleOffset.from_dict(case.input) + expected_offset, expected_scale = case.expected + assert codec.offset == expected_offset + assert codec.scale == expected_scale + + +def test_serialization_roundtrip() -> None: + """to_dict followed by from_dict produces an equal codec.""" + original = ScaleOffset(offset=7, scale=0.5) + restored = ScaleOffset.from_dict(original.to_dict()) + assert original == restored + + +# --------------------------------------------------------------------------- +# Construction +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + "case", + [ + ExpectErr( + input={"offset": [1, 2]}, + msg="offset must be a number or string", + exception_cls=TypeError, + ), + ExpectErr( + input={"scale": [1, 2]}, msg="scale must be a number or string", exception_cls=TypeError + ), + ], + ids=["list-offset", "list-scale"], +) +def test_construction_rejects_non_numeric(case: ExpectErr[dict[str, Any]]) -> None: + """Non-numeric offset or scale is rejected at construction time.""" + with pytest.raises(case.exception_cls, match=case.msg): + ScaleOffset(**case.input) + + +@pytest.mark.parametrize( + "case", + [ + Expect(input={"offset": 5, "scale": 2}, expected=(5, 2)), + Expect(input={"offset": 0.5, "scale": 0.1}, expected=(0.5, 0.1)), + ], + ids=["int", "float"], +) +def test_construction_accepts_numeric( + case: Expect[dict[str, Any], tuple[int | float, int | float]], +) -> None: + """Integer and float values are accepted for both parameters.""" + codec = ScaleOffset(**case.input) + assert codec.offset == case.expected[0] + assert codec.scale == case.expected[1] + + +# --------------------------------------------------------------------------- +# Encode / decode +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("dtype", "offset", "scale"), + [ + ("float64", 10.0, 0.1), + ("float32", 5.0, 2.0), + ("int32", 0, 1), + ], + ids=["float64", "float32", "int32-identity"], +) +def test_encode_decode_roundtrip(dtype: str, offset: float, scale: float) -> None: + """Data survives encode → decode.""" + + arr = zarr.create_array( + store={}, + shape=(100,), + dtype=dtype, + chunks=(100,), + filters=[ScaleOffset(offset=offset, scale=scale)], + compressors=None, + fill_value=0, + ) + data = np.arange(100, dtype=dtype) + arr[:] = data + np.testing.assert_array_almost_equal(arr[:], data) # type: ignore[arg-type] + + +def test_fill_value_transformed() -> None: + """Fill value is transformed through the encode formula and read back correctly.""" + arr = zarr.create_array( + store={}, + shape=(10,), + dtype="float64", + chunks=(10,), + filters=[ScaleOffset(offset=5, scale=2)], + compressors=None, + fill_value=10.0, + ) + # fill_value=10.0, encode: (10 - 5) * 2 = 10.0 stored + # Reading back without writing should return the original fill value + np.testing.assert_array_equal(arr[:], np.full(10, 10.0)) + + +def test_identity_is_noop() -> None: + """Default codec (offset=0, scale=1) is a no-op.""" + import zarr + + arr = zarr.create_array( + store={}, + shape=(50,), + dtype="float64", + chunks=(50,), + filters=[ScaleOffset()], + compressors=None, + fill_value=0, + ) + data = np.arange(50, dtype="float64") + arr[:] = data + np.testing.assert_array_equal(arr[:], data) + + +def test_rejects_complex_dtype() -> None: + """Complex dtypes are rejected at array creation time.""" + + with pytest.raises(ValueError, match="only supports integer and floating-point"): + zarr.create_array( + store={}, + shape=(10,), + dtype="complex128", + chunks=(10,), + filters=[ScaleOffset(offset=1, scale=2)], + compressors=None, + fill_value=0, + ) + + +def test_uint64_large_value_roundtrip() -> None: + """uint64 values above 2**63 must survive encode+decode (spec requires uint64 support).""" + + arr = zarr.create_array( + store={}, + shape=(3,), + dtype="uint64", + chunks=(3,), + filters=[ScaleOffset(offset=0, scale=1)], + compressors=None, + fill_value=0, + ) + # Value above int64.max (2**63 - 1) — would wrap if we used int64 as wide dtype. + data = np.array([0, 2**63, 2**64 - 1], dtype="uint64") + arr[:] = data + np.testing.assert_array_equal(arr[:], data) + + +def test_float_nan_inf_preserved() -> None: + """NaN and Inf are representable in float dtypes per IEEE 754 and must pass through.""" + + arr = np.array([1.0, np.nan, np.inf, -np.inf], dtype="float64") + encoded = _encode(arr, np.float64(0.0), np.float64(2.0)) + np.testing.assert_array_equal(encoded[[0]], np.array([2.0])) + assert np.isnan(encoded[1]) + assert encoded[2] == np.inf + assert encoded[3] == -np.inf + decoded = _decode(encoded, np.float64(0.0), np.float64(2.0), scale_repr=2.0) + np.testing.assert_array_equal(decoded[[0]], np.array([1.0])) + assert np.isnan(decoded[1]) + + +def test_uint64_encode_rejects_underflow() -> None: + """uint64 underflow during encode raises rather than silently wrapping.""" + + arr = zarr.create_array( + store={}, + shape=(3,), + dtype="uint64", + chunks=(3,), + filters=[ScaleOffset(offset=100, scale=1)], + compressors=None, + fill_value=100, + ) + with pytest.raises(ValueError, match="outside the range of dtype uint64"): + arr[:] = np.array([100, 50, 200], dtype="uint64") + + +def test_rejects_zero_scale() -> None: + """scale=0 is rejected (destroys data and breaks decode division).""" + + with pytest.raises(ValueError, match="scale must be non-zero"): + zarr.create_array( + store={}, + shape=(10,), + dtype="int32", + chunks=(10,), + filters=[ScaleOffset(offset=0, scale=0)], + compressors=None, + fill_value=0, + ) + + +@pytest.mark.parametrize( + "case", + [ + ExpectErr( + input={"dtype": "int32", "offset": 1.5, "scale": 1}, + msg="offset value 1.5 is not representable", + exception_cls=ValueError, + ), + ExpectErr( + input={"dtype": "int32", "offset": 0, "scale": 0.5}, + msg="scale value 0.5 is not representable", + exception_cls=ValueError, + ), + ExpectErr( + input={"dtype": "int16", "offset": "NaN", "scale": 1}, + msg="offset value 'NaN' is not representable", + exception_cls=ValueError, + ), + ], + ids=["float-offset-for-int", "float-scale-for-int", "nan-offset-for-int"], +) +def test_rejects_unrepresentable_scale_offset(case: ExpectErr[dict[str, Any]]) -> None: + """Scale/offset values that can't be represented in the array dtype are rejected.""" + + with pytest.raises(case.exception_cls, match=case.msg): + zarr.create_array( + store={}, + shape=(10,), + dtype=case.input["dtype"], + chunks=(10,), + filters=[ScaleOffset(offset=case.input["offset"], scale=case.input["scale"])], + compressors=None, + fill_value=0, + ) + + +def test_dtype_preservation() -> None: + """Integer scale/offset arithmetic preserves the array dtype when division is exact.""" + + arr = zarr.create_array( + store={}, + shape=(10,), + dtype="int8", + chunks=(10,), + filters=[ScaleOffset(offset=1, scale=2)], + compressors=None, + fill_value=0, + ) + data = np.arange(10, dtype="int8") + arr[:] = data + # encode=(x-1)*2 is always divisible by scale=2, so decode is exact + np.testing.assert_array_equal(arr[:], data) + + +async def test_integer_decode_rejects_non_exact_division() -> None: + """Decoding an integer array raises when the stored value isn't divisible by scale.""" + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(3,), + dtype="int8", + chunks=(3,), + filters=[ScaleOffset(offset=0, scale=2)], + compressors=None, + fill_value=0, + ) + # Write raw encoded bytes directly so we can inject a value that isn't divisible by scale. + # Array layout: int8 [2, 3, 4]; 3 % 2 != 0, so decode must fail. + + buf = default_buffer_prototype().buffer.from_bytes(np.array([2, 3, 4], dtype="int8").tobytes()) + await arr.store_path.store.set("c/0", buf) + with pytest.raises(ValueError, match="non-zero remainder"): + arr[:] + + +def test_encode_rejects_signed_integer_overflow() -> None: + """Encoding raises when (value - offset) * scale exceeds the target integer range.""" + arr = zarr.create_array( + store={}, + shape=(3,), + dtype="int8", + chunks=(3,), + filters=[ScaleOffset(offset=0, scale=100)], + compressors=None, + fill_value=0, + ) + # 2 * 100 = 200, outside int8 range [-128, 127] + with pytest.raises(ValueError, match="outside the range of dtype int8"): + arr[:] = np.array([0, 1, 2], dtype="int8") + + +def test_encode_rejects_unsigned_integer_underflow() -> None: + """Encoding raises when value - offset underflows an unsigned dtype.""" + arr = zarr.create_array( + store={}, + shape=(3,), + dtype="uint8", + chunks=(3,), + filters=[ScaleOffset(offset=10, scale=1)], + compressors=None, + fill_value=10, + ) + # 5 - 10 = -5, outside uint8 range [0, 255] + with pytest.raises(ValueError, match="outside the range of dtype uint8"): + arr[:] = np.array([10, 5, 20], dtype="uint8") + + +def test_float32_dtype_preserved() -> None: + """float32 arrays survive encode+decode without being promoted to float64.""" + arr = np.arange(100, dtype="float32") + offset = np.float32(5.0) + scale = np.float32(0.25) + encoded = _encode(arr, offset, scale) + assert encoded.dtype == np.dtype("float32") + decoded = _decode(encoded, offset, scale, scale_repr=0.25) + assert decoded.dtype == np.dtype("float32") + + +def test_float_encode_rejects_wider_scalar() -> None: + """A float64 scalar passed with a float32 array must not silently widen the result.""" + arr = np.arange(10, dtype="float32") + # A numpy float64 scalar (not a Python float — NEP 50 exempts those) mixed with a + # float32 ndarray promotes to float64. The codec must reject that. + with pytest.raises(ValueError, match="changed dtype from float32 to float64"): + _encode(arr, np.float64(5.0), np.float64(0.25)) + + +def test_float_decode_rejects_wider_scalar() -> None: + """A float64 scalar passed with a float32 array must not silently widen on decode.""" + arr = np.arange(10, dtype="float32") + with pytest.raises(ValueError, match="changed dtype from float32 to float64"): + _decode(arr, np.float64(5.0), np.float64(0.25), scale_repr=0.25) + + +async def test_decode_rejects_integer_overflow_on_offset_add() -> None: + """Decoding raises when quotient + offset overflows the target integer dtype.""" + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(3,), + dtype="int8", + chunks=(3,), + filters=[ScaleOffset(offset=100, scale=1)], + compressors=None, + fill_value=0, + ) + # encoded=100 → decoded = 100/1 + 100 = 200, outside int8 range + buf = default_buffer_prototype().buffer.from_bytes( + np.array([0, 50, 100], dtype="int8").tobytes() + ) + await arr.store_path.store.set("c/0", buf) + with pytest.raises(ValueError, match="outside the range of dtype int8"): + arr[:] + + +def test_decode_fits_natively_negative_scale() -> None: + """_decode_fits_natively handles negative scale by swapping bounds.""" + # For a negative scale, x // scale flips the relationship between min/max. + # The function should use info.max // scale as the lower bound and info.min // scale + # as the upper bound. + dtype = np.dtype("int16") + # scale=-2 inverts; offset=0 means range is just q_lo..q_hi + assert _decode_fits_natively(dtype, offset=0, scale=-2) is True + # An offset that pushes the range out of bounds returns False + assert _decode_fits_natively(dtype, offset=100000, scale=-2) is False + + +async def test_decode_int_widened_path() -> None: + """When _decode_fits_natively returns False, decode falls through to the widened path.""" + # For uint32 with offset near max, q_hi + offset can exceed uint32 if computed in target dtype. + # The widened path uses int64 arithmetic and range-checks the result. + # We bypass encode by writing raw bytes directly to the store. + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(3,), + dtype="uint32", + chunks=(3,), + # offset large enough that _decode_fits_natively returns False + filters=[ScaleOffset(offset=2**31, scale=1)], + compressors=None, + # fill_value must be >= offset to avoid uint32 underflow during encode + fill_value=2**31, + ) + # Encoded values that, when added to offset, stay within uint32 + buf = default_buffer_prototype().buffer.from_bytes( + np.array([0, 100, 1000], dtype="uint32").tobytes() + ) + await arr.store_path.store.set("c/0", buf) + expected = np.array([2**31, 2**31 + 100, 2**31 + 1000], dtype="uint32") + np.testing.assert_array_equal(arr[:], expected) + + +def test_compute_encoded_size() -> None: + """compute_encoded_size returns the input byte length unchanged (codec is fixed-size).""" + codec = ScaleOffset(offset=0, scale=1) + # The chunk_spec argument is unused; pass any sentinel + assert codec.compute_encoded_size(input_byte_length=100, _chunk_spec=None) == 100 # type: ignore[arg-type] + assert codec.compute_encoded_size(input_byte_length=0, _chunk_spec=None) == 0 # type: ignore[arg-type] From ac667c1a7f25e6fed3b3cd63ac3c241d1ea30cb1 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 30 Apr 2026 17:06:16 -0400 Subject: [PATCH 288/468] chore: automate more of the release process (#3896) * Update release checklist * Automate release process with changelog and downstream test workflows * Trigger based on label * Fix build * Update guidance * Fix build * fix: numcodecs build in downstream * fix: create venv first * fix: install dev group first * fix: include submodules * another isolation change --------- Co-authored-by: Davis Bennett --- .github/ISSUE_TEMPLATE/release-checklist.md | 51 ++++----- .github/workflows/downstream.yml | 108 ++++++++++++++++++++ .github/workflows/prepare_release.yml | 77 ++++++++++++++ docs/contributing.md | 10 ++ 4 files changed, 217 insertions(+), 29 deletions(-) create mode 100644 .github/workflows/downstream.yml create mode 100644 .github/workflows/prepare_release.yml diff --git a/.github/ISSUE_TEMPLATE/release-checklist.md b/.github/ISSUE_TEMPLATE/release-checklist.md index ca973c8c38..5e073cb59f 100644 --- a/.github/ISSUE_TEMPLATE/release-checklist.md +++ b/.github/ISSUE_TEMPLATE/release-checklist.md @@ -16,39 +16,17 @@ assignees: '' **Before release**: -- [ ] Make sure the release branch (e.g., `3.1.x`) is up to date with any backports. -- [ ] Make sure that all pull requests which will be included in the release have been properly documented as changelog files in the [`changes/` directory](https://github.com/zarr-developers/zarr-python/tree/main/changes). -- [ ] Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result to the release branch. - [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/#support-window) to see if the minimum supported version of Python or NumPy needs bumping. -- [ ] Check to ensure that: - - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.py` to find all potential TODOs. - - [ ] All tests pass in the ["Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/test.yml). - - [ ] All tests pass in the ["GPU Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml). - - [ ] All tests pass in the ["Hypothesis" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml). - - [ ] Check that downstream libraries work well (maintainers can make executive decisions about whether all checks are required for this release). - - [ ] numcodecs - - [ ] Xarray (@jhamman @dcherian @TomNicholas) - - Zarr's upstream compatibility is tested via the [Upstream Dev CI worklow](https://github.com/pydata/xarray/actions/workflows/upstream-dev-ci.yaml). - - Click on the most recent workflow and check that the `upstream-dev` job has run and passed. `upstream-dev` is not run on all all workflow runs. - - Check that the expected version of Zarr-Python was tested using the `Version Info` step of the `upstream-dev` job. - - If testing on a branch other than `main` is needed, open a PR modifying https://github.com/pydata/xarray/blob/90ee30943aedba66a37856b2332a41264e288c20/ci/install-upstream-wheels.sh#L56 and add the `run-upstream` label. - - [ ] Titiler.Xarray (@maxrjones) - - [Modify dependencies](https://github.com/developmentseed/titiler/blob/main/src/titiler/xarray/pyproject.toml) for titiler.xarray. - - Modify triggers for running [the test workflow](https://github.com/developmentseed/titiler/blob/61549f2de07b20cca8fb991cfcdc89b23e18ad05/.github/workflows/ci.yml#L5-L7). - - Push the branch to the repository and check for the actions for any failures. +- [ ] Verify that the latest CI workflows on `main` are passing: [Tests](https://github.com/zarr-developers/zarr-python/actions/workflows/test.yml), [GPU Tests](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml), [Hypothesis](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml), [Docs](https://github.com/zarr-developers/zarr-python/actions/workflows/docs.yml), [Lint](https://github.com/zarr-developers/zarr-python/actions/workflows/lint.yml), [Wheels](https://github.com/zarr-developers/zarr-python/actions/workflows/releases.yml). +- [ ] Run the ["Prepare release" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) with the target version. This will build the changelog and open a release PR with the `run-downstream` label. +- [ ] Verify that the [downstream tests](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) (triggered automatically by the `run-downstream` label) pass on the release PR. +- [ ] Review the release PR and verify the changelog in `docs/release-notes.md` looks correct. +- [ ] Merge the release PR. **Release**: -- [ ] Go to https://github.com/zarr-developers/zarr-python/releases. - - [ ] Click "Draft a new release". - - [ ] Choose a version number prefixed with a `v` (e.g. `v0.0.0`). For pre-releases, include the appropriate suffix (e.g. `v0.0.0a1` or `v0.0.0rc2`). - - [ ] Set the target branch to the release branch (e.g., `3.1.x`) - - [ ] Set the description of the release to: `See release notes https://zarr.readthedocs.io/en/stable/release-notes.html#release-0-0-0`, replacing the correct version numbers. For pre-release versions, the URL should omit the pre-release suffix, e.g. "a1" or "rc1". - - [ ] Click on "Generate release notes" to auto-fill the description. - - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too. -- [ ] Verify that release workflows succeeded. - - [ ] The latest version is correct on [PyPI](https://pypi.org/project/zarr/). - - [ ] The stable version is correct on [ReadTheDocs](https://zarr.readthedocs.io/en/stable/). +- [ ] [Draft a new GitHub Release](https://github.com/zarr-developers/zarr-python/releases/new) with tag `vX.Y.Z` targeting `main`. Use "Generate release notes" for the description. +- [ ] Verify the release is published on [PyPI](https://pypi.org/project/zarr/) and [ReadTheDocs](https://zarr.readthedocs.io/en/stable/). **After release**: @@ -57,3 +35,18 @@ assignees: '' --- - [ ] Party :tada: + +--- + +
+Releasing from a branch other than main + +In rare cases (e.g. patch releases for an older minor version), you may need to release from a dedicated release branch (e.g. `3.1.x`): + +- Create the release branch from the appropriate tag if it doesn't already exist. +- Cherry-pick or backport the necessary commits onto the branch. +- Run `towncrier build --version x.y.z` and commit the result to the release branch instead of `main`. +- When drafting the GitHub Release, set the target to the release branch instead of `main`. +- After the release, ensure any relevant changelog updates are also reflected on `main`. + +
diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml new file mode 100644 index 0000000000..849d658016 --- /dev/null +++ b/.github/workflows/downstream.yml @@ -0,0 +1,108 @@ +name: Downstream + +on: + workflow_dispatch: + pull_request: + types: [labeled] + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + xarray: + name: Xarray zarr backend tests + if: github.event_name == 'workflow_dispatch' || github.event.label.name == 'run-downstream' + runs-on: ubuntu-latest + steps: + - name: Check out zarr-python + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + fetch-depth: 0 + persist-credentials: false + + - name: Check out xarray + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + repository: pydata/xarray + path: xarray + persist-credentials: false + + - name: Set up pixi + uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + with: + manifest-path: xarray/pixi.toml + + - name: Install zarr-python from branch + working-directory: xarray + run: pixi run -e test-py313 -- pip install --no-deps .. + + - name: Show versions + working-directory: xarray + run: | + pixi run -e test-py313 -- python -c " + import zarr; print(f'zarr {zarr.__version__}') + import xarray; print(f'xarray {xarray.__version__}') + " + + - name: Run xarray zarr backend tests + working-directory: xarray + run: | + pixi run -e test-py313 -- python -m pytest -x --no-header -q \ + xarray/tests/test_backends.py -k zarr \ + xarray/tests/test_backends_api.py -k zarr \ + xarray/tests/test_backends_datatree.py -k zarr + + numcodecs: + name: numcodecs zarr3 codec tests + if: github.event_name == 'workflow_dispatch' || github.event.label.name == 'run-downstream' + runs-on: ubuntu-latest + steps: + - name: Check out zarr-python + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + fetch-depth: 0 + persist-credentials: false + + - name: Check out numcodecs + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + repository: zarr-developers/numcodecs + fetch-depth: 0 + path: numcodecs + submodules: recursive + persist-credentials: false + + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + with: + python-version: '3.13' + + - name: Install uv + uses: astral-sh/setup-uv@37802adc94f370d6bfd71619e3f0bf239e1f3b78 # v7 + + - name: Install numcodecs with test-zarr-main group + working-directory: numcodecs + run: | + uv venv + uv pip install --group dev + uv sync --group dev --group test-zarr-main + uv pip install --no-build-isolation -e . + + - name: Override zarr-python with branch version + working-directory: numcodecs + run: uv pip install --no-deps .. + + - name: Show versions + working-directory: numcodecs + run: | + uv run python -c " + import zarr; print(f'zarr {zarr.__version__}') + import numcodecs; print(f'numcodecs {numcodecs.__version__}') + " + + - name: Run numcodecs zarr3 tests + working-directory: numcodecs + run: uv run python -m pytest -x --no-header -q tests/test_zarr3.py diff --git a/.github/workflows/prepare_release.yml b/.github/workflows/prepare_release.yml new file mode 100644 index 0000000000..4bccb40092 --- /dev/null +++ b/.github/workflows/prepare_release.yml @@ -0,0 +1,77 @@ +name: Prepare release notes + +on: + workflow_dispatch: + inputs: + version: + description: 'Release version notes (e.g. 3.2.0)' + required: true + type: string + target_branch: + description: 'Branch to target' + required: false + default: 'main' + type: string + +permissions: + contents: write + pull-requests: write + +jobs: + prepare: + name: Build changelog and open PR + runs-on: ubuntu-latest + steps: + - name: Validate inputs + run: | + if [[ ! "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+([-\.][a-zA-Z0-9]+)*$ ]]; then + echo "::error::Invalid version format: '$VERSION'" + exit 1 + fi + if [[ ! "$TARGET_BRANCH" =~ ^[a-zA-Z0-9._/-]+$ ]]; then + echo "::error::Invalid branch name: '$TARGET_BRANCH'" + exit 1 + fi + env: + VERSION: ${{ inputs.version }} + TARGET_BRANCH: ${{ inputs.target_branch }} + + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + ref: ${{ inputs.target_branch }} + fetch-depth: 0 + persist-credentials: false + + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + with: + python-version: '3.12' + + - name: Install towncrier + run: pip install towncrier + + - name: Build changelog + run: towncrier build --version "$VERSION" --yes + env: + VERSION: ${{ inputs.version }} + + - name: Create pull request + uses: peter-evans/create-pull-request@271a8d0340265f705b14b6d32b9829c1cb33d45e # v7.0.8 + with: + branch: release/v${{ inputs.version }} + base: ${{ inputs.target_branch }} + title: "Release v${{ inputs.version }}" + body: | + Automated release preparation for v${{ inputs.version }}. + + This PR was generated by the "Prepare release" workflow. It includes: + - Rendered changelog via `towncrier build --version ${{ inputs.version }}` + - Removal of consumed changelog fragments from `changes/` + + ## Checklist + + - [ ] Review the rendered changelog in `docs/release-notes.md` + - [ ] Downstream tests pass (see [downstream workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml)) + - [ ] Merge this PR, then [draft a GitHub Release](https://github.com/zarr-developers/zarr-python/releases/new) targeting `${{ inputs.target_branch }}` with tag `v${{ inputs.version }}` + commit-message: "chore: build changelog for v${{ inputs.version }}" + labels: run-downstream + delete-branch: true diff --git a/docs/contributing.md b/docs/contributing.md index a1a75d0010..4bba874188 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -339,6 +339,16 @@ Features in `zarr.experimental` carry no stability guarantees. They may be chang Open an issue on GitHub announcing the release using the release checklist template: [https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md). The release checklist includes all steps necessary for the release. +### Preparing a release + +Releases are prepared using the ["Prepare release notes"](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) workflow. To run it: + +1. Go to the [workflow page](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) and click "Run workflow". +2. Enter the release version (e.g. `3.2.0`) and the target branch (defaults to `main`). +3. The workflow will run `towncrier build` to render the changelog, remove consumed fragments from `changes/`, and open a pull request on the `release/v` branch. +4. The release PR is automatically labeled `run-downstream`, which triggers the [downstream test workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) to run Xarray and numcodecs integration tests against the release branch. +5. Review the rendered changelog in `docs/release-notes.md` and verify downstream tests pass before merging. + ## Benchmarks Zarr uses [pytest-benchmark](https://pytest-benchmark.readthedocs.io/en/latest/) for running From 870fabd0f2f94df84698fef1e7f20f59d02d0634 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 30 Apr 2026 17:27:36 -0400 Subject: [PATCH 289/468] chore/3.2.0 release notes (#3927) * docs: label removals as such * docs: remove claim that sharding supports truncated boundary chunks * chore: add more changelog entries * Remove 3722; not wired up * Update 3802.feature.md * Update 3802.feature.md --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3793.misc.md | 1 + changes/3800.misc.md | 1 + changes/3863.bugfix.md | 1 + changes/{3900.misc.md => 3900.removal.md} | 0 changes/{3901.misc.md => 3901.removal.md} | 0 changes/{3902.misc.md => 3902.removal.md} | 0 changes/{3903.misc.md => 3903.removal.md} | 0 7 files changed, 3 insertions(+) create mode 100644 changes/3793.misc.md create mode 100644 changes/3800.misc.md create mode 100644 changes/3863.bugfix.md rename changes/{3900.misc.md => 3900.removal.md} (100%) rename changes/{3901.misc.md => 3901.removal.md} (100%) rename changes/{3902.misc.md => 3902.removal.md} (100%) rename changes/{3903.misc.md => 3903.removal.md} (100%) diff --git a/changes/3793.misc.md b/changes/3793.misc.md new file mode 100644 index 0000000000..1b872dbcc2 --- /dev/null +++ b/changes/3793.misc.md @@ -0,0 +1 @@ +Skip the read-before-write step when a write covers an entire shard, eliminating an unnecessary `get` on full-shard overwrites with the sharding codec. diff --git a/changes/3800.misc.md b/changes/3800.misc.md new file mode 100644 index 0000000000..65497524b3 --- /dev/null +++ b/changes/3800.misc.md @@ -0,0 +1 @@ +Rename the `DimensionNames` type to `DimensionNamesLike` to reflect that it models the wide input type that is narrowed to the `dimension_names` attribute on V3 array metadata, matching the `XLike` naming convention used by other input-narrowing types. diff --git a/changes/3863.bugfix.md b/changes/3863.bugfix.md new file mode 100644 index 0000000000..2902bdf443 --- /dev/null +++ b/changes/3863.bugfix.md @@ -0,0 +1 @@ +Fix handling of `NaT` default fill values for `datetime64` and `timedelta64` data types. Equality checks now use `numpy.isnat` so that the default fill value compares correctly against `NaT`. diff --git a/changes/3900.misc.md b/changes/3900.removal.md similarity index 100% rename from changes/3900.misc.md rename to changes/3900.removal.md diff --git a/changes/3901.misc.md b/changes/3901.removal.md similarity index 100% rename from changes/3901.misc.md rename to changes/3901.removal.md diff --git a/changes/3902.misc.md b/changes/3902.removal.md similarity index 100% rename from changes/3902.misc.md rename to changes/3902.removal.md diff --git a/changes/3903.misc.md b/changes/3903.removal.md similarity index 100% rename from changes/3903.misc.md rename to changes/3903.removal.md From 3ede5e830e03c76d57da5d78775dfbac0f5ea170 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 30 Apr 2026 18:04:27 -0400 Subject: [PATCH 290/468] docs: build 3.2.0 release notes (#3932) * docs: build release notes * docs: fix release notes * fix: whitespace --- changes/2720.doc.md | 1 - changes/3492.doc.md | 1 - changes/3546.misc.md | 1 - changes/3611.bugfix.md | 1 - changes/3679.feature.md | 3 --- changes/3748.feature.md | 1 - changes/3781.feature.md | 1 - changes/3793.misc.md | 1 - changes/3797.bugfix.md | 2 -- changes/3800.misc.md | 1 - changes/3802.feature.md | 16 ----------- changes/3828.misc.md | 2 -- changes/3830.misc.md | 1 - changes/3833.misc.md | 1 - changes/3836.doc.md | 2 -- changes/3837.misc.md | 1 - changes/3845.doc.md | 1 - changes/3846.bugfix.md | 1 - changes/3863.bugfix.md | 1 - changes/3874.feature.md | 1 - changes/3897.misc.md | 2 -- changes/3900.removal.md | 1 - changes/3901.removal.md | 1 - changes/3902.removal.md | 1 - changes/3903.removal.md | 1 - changes/3920.bugfix.md | 1 - docs/release-notes.md | 59 ++++++++++++++++++++++++++++++++++++++++- 27 files changed, 58 insertions(+), 48 deletions(-) delete mode 100644 changes/2720.doc.md delete mode 100644 changes/3492.doc.md delete mode 100644 changes/3546.misc.md delete mode 100644 changes/3611.bugfix.md delete mode 100644 changes/3679.feature.md delete mode 100644 changes/3748.feature.md delete mode 100644 changes/3781.feature.md delete mode 100644 changes/3793.misc.md delete mode 100644 changes/3797.bugfix.md delete mode 100644 changes/3800.misc.md delete mode 100644 changes/3802.feature.md delete mode 100644 changes/3828.misc.md delete mode 100644 changes/3830.misc.md delete mode 100644 changes/3833.misc.md delete mode 100644 changes/3836.doc.md delete mode 100644 changes/3837.misc.md delete mode 100644 changes/3845.doc.md delete mode 100644 changes/3846.bugfix.md delete mode 100644 changes/3863.bugfix.md delete mode 100644 changes/3874.feature.md delete mode 100644 changes/3897.misc.md delete mode 100644 changes/3900.removal.md delete mode 100644 changes/3901.removal.md delete mode 100644 changes/3902.removal.md delete mode 100644 changes/3903.removal.md delete mode 100644 changes/3920.bugfix.md diff --git a/changes/2720.doc.md b/changes/2720.doc.md deleted file mode 100644 index a48b700ca1..0000000000 --- a/changes/2720.doc.md +++ /dev/null @@ -1 +0,0 @@ -Document removal of `zarr.storage.init_group` in v3 migration guide, with replacement using `zarr.open_group`/`zarr.create_group`. diff --git a/changes/3492.doc.md b/changes/3492.doc.md deleted file mode 100644 index 66719c7b50..0000000000 --- a/changes/3492.doc.md +++ /dev/null @@ -1 +0,0 @@ -Document the `threading.max_workers` configuration option in the performance guide. diff --git a/changes/3546.misc.md b/changes/3546.misc.md deleted file mode 100644 index 77fa0acb5f..0000000000 --- a/changes/3546.misc.md +++ /dev/null @@ -1 +0,0 @@ -Upgrade to spec0 compat (python 3.14 max, python 3.12 min). \ No newline at end of file diff --git a/changes/3611.bugfix.md b/changes/3611.bugfix.md deleted file mode 100644 index 8b889d79fc..0000000000 --- a/changes/3611.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix `SyncError` raised when assigning a `zarr.Array` as the value in a `__setitem__` call (e.g. `dst[:] = src` where `src` is a zarr array). The source array is now converted to a NumPy array before entering the async codec pipeline. diff --git a/changes/3679.feature.md b/changes/3679.feature.md deleted file mode 100644 index cdf35382e4..0000000000 --- a/changes/3679.feature.md +++ /dev/null @@ -1,3 +0,0 @@ -Adds a new in-memory storage backend called `ManagedMemoryStore`. Instances of `ManagedMemoryStore` -function similarly to `MemoryStore`, but instances of `ManagedMemoryStore` can be constructed from -a URL like `memory://store`. \ No newline at end of file diff --git a/changes/3748.feature.md b/changes/3748.feature.md deleted file mode 100644 index 5fd94fe0a3..0000000000 --- a/changes/3748.feature.md +++ /dev/null @@ -1 +0,0 @@ -Added `array.read_missing_chunks` configuration option. When set to `False`, reading missing chunks raises a `ChunkNotFoundError` instead of filling them with the array's fill value. diff --git a/changes/3781.feature.md b/changes/3781.feature.md deleted file mode 100644 index 191ca5ed4a..0000000000 --- a/changes/3781.feature.md +++ /dev/null @@ -1 +0,0 @@ -Added `Struct` class (subclass of `Structured`) implementing the zarr-extensions `struct` dtype spec. Uses object-style field format and dict fill values. Legacy `Structured` remains available for backward compatibility. diff --git a/changes/3793.misc.md b/changes/3793.misc.md deleted file mode 100644 index 1b872dbcc2..0000000000 --- a/changes/3793.misc.md +++ /dev/null @@ -1 +0,0 @@ -Skip the read-before-write step when a write covers an entire shard, eliminating an unnecessary `get` on full-shard overwrites with the sharding codec. diff --git a/changes/3797.bugfix.md b/changes/3797.bugfix.md deleted file mode 100644 index c683213c5d..0000000000 --- a/changes/3797.bugfix.md +++ /dev/null @@ -1,2 +0,0 @@ -Fix an issue that prevents the correct parsing of special NumPy ``uint32`` dtypes resulting e.g. -from bit wise operations on ``uint32`` arrays on Windows. diff --git a/changes/3800.misc.md b/changes/3800.misc.md deleted file mode 100644 index 65497524b3..0000000000 --- a/changes/3800.misc.md +++ /dev/null @@ -1 +0,0 @@ -Rename the `DimensionNames` type to `DimensionNamesLike` to reflect that it models the wide input type that is narrowed to the `dimension_names` attribute on V3 array metadata, matching the `XLike` naming convention used by other input-narrowing types. diff --git a/changes/3802.feature.md b/changes/3802.feature.md deleted file mode 100644 index c57a7a98da..0000000000 --- a/changes/3802.feature.md +++ /dev/null @@ -1,16 +0,0 @@ -Add support for rectilinear (variable-sized) chunk grids. This feature is experimental and -must be explicitly enabled via ``zarr.config.set({'array.rectilinear_chunks': True})``. - -Rectilinear chunks can be used through: - -- **Creating arrays**: Pass nested sequences (e.g., ``[[10, 20, 30], [50, 50]]``) to ``chunks`` - in ``zarr.create_array``, ``zarr.from_array``, ``zarr.zeros``, ``zarr.ones``, ``zarr.full``, - ``zarr.open``, and related functions, or to ``chunk_shape`` in ``zarr.create``. -- **Opening existing arrays**: Arrays stored with the ``rectilinear`` chunk grid are read - transparently via ``zarr.open`` and ``zarr.open_array``. -- **Rectilinear sharding**: Shard boundaries can be rectilinear while inner chunks remain regular. - -**Breaking change**: The ``validate`` method on ``BaseCodec`` and ``CodecPipeline`` now receives -a ``ChunkGridMetadata`` instance instead of a ``ChunkGrid`` instance for the ``chunk_grid`` -parameter. Third-party codecs that override ``validate`` and inspect the chunk grid will need to -update their type annotations. No known downstream packages were using this parameter. diff --git a/changes/3828.misc.md b/changes/3828.misc.md deleted file mode 100644 index 8704ecceb6..0000000000 --- a/changes/3828.misc.md +++ /dev/null @@ -1,2 +0,0 @@ -`CodecPipeline.read` and `CodecPipeline.read_batch` now return a tuple of typeddict objects -that each carry information about the request for a chunk from storage. \ No newline at end of file diff --git a/changes/3830.misc.md b/changes/3830.misc.md deleted file mode 100644 index f622038f7e..0000000000 --- a/changes/3830.misc.md +++ /dev/null @@ -1 +0,0 @@ -Optimize the performance of indexing operations when using an array-like indexer on a single dimension. diff --git a/changes/3833.misc.md b/changes/3833.misc.md deleted file mode 100644 index 1f3c87b482..0000000000 --- a/changes/3833.misc.md +++ /dev/null @@ -1 +0,0 @@ -Remove the warning that is emitted when any Numcodecs codec is instantiated. diff --git a/changes/3836.doc.md b/changes/3836.doc.md deleted file mode 100644 index a3138a9a45..0000000000 --- a/changes/3836.doc.md +++ /dev/null @@ -1,2 +0,0 @@ -Corrects the type annotation reported for the `batch_info` parameter in the `CodecPipeline.write` -method docstring. \ No newline at end of file diff --git a/changes/3837.misc.md b/changes/3837.misc.md deleted file mode 100644 index 1a2c6f0e4f..0000000000 --- a/changes/3837.misc.md +++ /dev/null @@ -1 +0,0 @@ -Add the static github actions tool `zizmor` to our CI and pre-commit checks. \ No newline at end of file diff --git a/changes/3845.doc.md b/changes/3845.doc.md deleted file mode 100644 index c478596103..0000000000 --- a/changes/3845.doc.md +++ /dev/null @@ -1 +0,0 @@ -Remove result="ansi" from code blocks in the user guide that were causing empty output cells in the rendered documentation. diff --git a/changes/3846.bugfix.md b/changes/3846.bugfix.md deleted file mode 100644 index bfda1b1693..0000000000 --- a/changes/3846.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix `ZipStore.list()`, `list_dir()`, and `exists()` to auto-open the zip file when called before `open()`, consistent with the existing behavior of `get()` and `set()`. diff --git a/changes/3863.bugfix.md b/changes/3863.bugfix.md deleted file mode 100644 index 2902bdf443..0000000000 --- a/changes/3863.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix handling of `NaT` default fill values for `datetime64` and `timedelta64` data types. Equality checks now use `numpy.isnat` so that the default fill value compares correctly against `NaT`. diff --git a/changes/3874.feature.md b/changes/3874.feature.md deleted file mode 100644 index 592c5b330d..0000000000 --- a/changes/3874.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add `cast_value` and `scale_offset` codecs. \ No newline at end of file diff --git a/changes/3897.misc.md b/changes/3897.misc.md deleted file mode 100644 index 53b2bd9b52..0000000000 --- a/changes/3897.misc.md +++ /dev/null @@ -1,2 +0,0 @@ -Bump the minimum version of `typing-extensions` to 4.13 to support the `extra_items` -keyword argument on `TypedDict` (PEP 728). \ No newline at end of file diff --git a/changes/3900.removal.md b/changes/3900.removal.md deleted file mode 100644 index d38de0ce2e..0000000000 --- a/changes/3900.removal.md +++ /dev/null @@ -1 +0,0 @@ -Remove deprecated `zarr.convenience` and `zarr.creation` modules. \ No newline at end of file diff --git a/changes/3901.removal.md b/changes/3901.removal.md deleted file mode 100644 index d1f08d80eb..0000000000 --- a/changes/3901.removal.md +++ /dev/null @@ -1 +0,0 @@ -Remove the deprecated `zarr_version` parameter from several functions and methods. That parameter is replaced with `zarr_format`. \ No newline at end of file diff --git a/changes/3902.removal.md b/changes/3902.removal.md deleted file mode 100644 index ddfc9813e2..0000000000 --- a/changes/3902.removal.md +++ /dev/null @@ -1 +0,0 @@ -Remove deprecated `Group` methods `array`, `require_dataset`, and `create_dataset`. \ No newline at end of file diff --git a/changes/3903.removal.md b/changes/3903.removal.md deleted file mode 100644 index 7dc0a83177..0000000000 --- a/changes/3903.removal.md +++ /dev/null @@ -1 +0,0 @@ -Remove deprecated `AsyncArray.create` and `Array.create` methods. \ No newline at end of file diff --git a/changes/3920.bugfix.md b/changes/3920.bugfix.md deleted file mode 100644 index 289d12970c..0000000000 --- a/changes/3920.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Use the unit associated with the `Datetime64` data type when creating the default `Nat` scalar value. \ No newline at end of file diff --git a/docs/release-notes.md b/docs/release-notes.md index e79d359e3f..7e3511a0a7 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,6 +2,63 @@ +## 3.2.0 (2026-04-30) + +### Features + +- Adds a new in-memory storage backend called `ManagedMemoryStore`. Instances of `ManagedMemoryStore` + function similarly to `MemoryStore`, but instances of `ManagedMemoryStore` can be constructed from + a URL like `memory://store`. ([#3679](https://github.com/zarr-developers/zarr-python/issues/3679)) +- Added `array.read_missing_chunks` configuration option. When set to `False`, reading missing chunks raises a `ChunkNotFoundError` instead of filling them with the array's fill value. ([#3748](https://github.com/zarr-developers/zarr-python/issues/3748)) +- Added `Struct` class (subclass of `Structured`) implementing the zarr-extensions `struct` dtype spec. Uses object-style field format and dict fill values. Legacy `Structured` remains available for backward compatibility. ([#3781](https://github.com/zarr-developers/zarr-python/issues/3781)) +- Add support for rectilinear (variable-sized) chunk grids. This feature is experimental and + must be explicitly enabled via `zarr.config.set({'array.rectilinear_chunks': True})`. + + Rectilinear chunks can be used through: + + - **Creating arrays**: Pass nested sequences (e.g., `[[10, 20, 30], [50, 50]]`) to `chunks` + in `zarr.create_array`, `zarr.from_array`, `zarr.zeros`, `zarr.ones`, `zarr.full`, + `zarr.open`, and related functions, or to `chunk_shape` in `zarr.create`. + - **Opening existing arrays**: Arrays stored with the `rectilinear` chunk grid are read + transparently via `zarr.open` and `zarr.open_array`. + - **Rectilinear sharding**: Shard boundaries can be rectilinear while inner chunks remain regular. + + **Breaking change**: The `validate` method on `BaseCodec` and `CodecPipeline` now receives + a `ChunkGridMetadata` instance instead of a `ChunkGrid` instance for the `chunk_grid` + parameter. Third-party codecs that override `validate` and inspect the chunk grid will need to + update their type annotations. No known downstream packages were using this parameter. ([#3802](https://github.com/zarr-developers/zarr-python/issues/3802)) + +- Add `cast_value` and `scale_offset` codecs. ([#3874](https://github.com/zarr-developers/zarr-python/issues/3874)) + +### Bugfixes + +- Fix `SyncError` raised when assigning a `zarr.Array` as the value in a `__setitem__` call (e.g. `dst[:] = src` where `src` is a zarr array). The source array is now converted to a NumPy array before entering the async codec pipeline. ([#3611](https://github.com/zarr-developers/zarr-python/issues/3611)) +- Fix an issue that prevents the correct parsing of special NumPy `uint32` dtypes resulting e.g. + from bit wise operations on `uint32` arrays on Windows. ([#3797](https://github.com/zarr-developers/zarr-python/issues/3797)) +- Fix `ZipStore.list()`, `list_dir()`, and `exists()` to auto-open the zip file when called before `open()`, consistent with the existing behavior of `get()` and `set()`. ([#3846](https://github.com/zarr-developers/zarr-python/issues/3846)) +- Fix handling of `NaT` default fill values for `datetime64` and `timedelta64` data types. Equality checks now use `numpy.isnat` so that the default fill value compares correctly against `NaT`. ([#3863](https://github.com/zarr-developers/zarr-python/issues/3863)) +- Use the unit associated with the `Datetime64` data type when creating the default `Nat` scalar value. ([#3920](https://github.com/zarr-developers/zarr-python/issues/3920)) + +### Improved Documentation + +- Document removal of `zarr.storage.init_group` in v3 migration guide, with replacement using `zarr.open_group`/`zarr.create_group`. ([#2720](https://github.com/zarr-developers/zarr-python/issues/2720)) +- Document the `threading.max_workers` configuration option in the performance guide. ([#3492](https://github.com/zarr-developers/zarr-python/issues/3492)) +- Corrects the type annotation reported for the `batch_info` parameter in the `CodecPipeline.write` + method docstring. ([#3836](https://github.com/zarr-developers/zarr-python/issues/3836)) +- Remove result="ansi" from code blocks in the user guide that were causing empty output cells in the rendered documentation. ([#3845](https://github.com/zarr-developers/zarr-python/issues/3845)) + +### Deprecations and Removals + +- Remove deprecated `zarr.convenience` and `zarr.creation` modules. ([#3900](https://github.com/zarr-developers/zarr-python/issues/3900)) +- Remove the deprecated `zarr_version` parameter from several functions and methods. That parameter is replaced with `zarr_format`. ([#3901](https://github.com/zarr-developers/zarr-python/issues/3901)) +- Remove deprecated `Group` methods `array`, `require_dataset`, and `create_dataset`. ([#3902](https://github.com/zarr-developers/zarr-python/issues/3902)) +- Remove deprecated `AsyncArray.create` and `Array.create` methods. ([#3903](https://github.com/zarr-developers/zarr-python/issues/3903)) + +### Misc + +- [#3546](https://github.com/zarr-developers/zarr-python/issues/3546), [#3793](https://github.com/zarr-developers/zarr-python/issues/3793), [#3800](https://github.com/zarr-developers/zarr-python/issues/3800), [#3828](https://github.com/zarr-developers/zarr-python/issues/3828), [#3830](https://github.com/zarr-developers/zarr-python/issues/3830), [#3833](https://github.com/zarr-developers/zarr-python/issues/3833), [#3837](https://github.com/zarr-developers/zarr-python/issues/3837), [#3897](https://github.com/zarr-developers/zarr-python/issues/3897) + + ## 3.1.6 (2026-03-19) ### Features @@ -17,7 +74,7 @@ - Correct the target bytes number for auto-chunking when auto-sharding. ([#3603](https://github.com/zarr-developers/zarr-python/issues/3603)) - Fixed a bug in the sharding codec that prevented nested shard reads in certain cases. ([#3655](https://github.com/zarr-developers/zarr-python/issues/3655)) - Fix obstore `_transform_list_dir` implementation to correctly relativize paths (removing `lstrip` usage). ([#3657](https://github.com/zarr-developers/zarr-python/issues/3657)) -- Raise error when trying to encode :class:`numpy.dtypes.StringDType` with `na_object` set. ([#3695](https://github.com/zarr-developers/zarr-python/issues/3695)) +- Raise error when trying to encode `numpy.dtypes.StringDType` with `na_object` set. ([#3695](https://github.com/zarr-developers/zarr-python/issues/3695)) - `CacheStore`, `LoggingStore` and `LatencyStore` now support with_read_only. ([#3700](https://github.com/zarr-developers/zarr-python/issues/3700)) - Skip chunk coordinate enumeration in resize when the array is only growing, avoiding unbounded memory usage for large arrays. ([#3702](https://github.com/zarr-developers/zarr-python/issues/3702)) - Fix a performance bug in morton curve generation. ([#3705](https://github.com/zarr-developers/zarr-python/issues/3705)) From f8c0c5d97b32f97c1bd231af27078b4efc7e2a1b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 1 May 2026 18:15:43 -0400 Subject: [PATCH 291/468] feat:metadata package (#3919) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat(metadata): scaffold zarr-metadata package structure Co-Authored-By: Claude Opus 4.7 (1M context) * build(metadata): depend on zarr-metadata via local uv workspace source Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add JSON, NamedConfig, NamedRequiredConfig primitives Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add v3 array metadata types Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add v3 consolidated metadata type Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add v3 group metadata type Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): wire up zarr_metadata.v3 re-exports Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add faithful v2 array metadata types Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add v2 group metadata type Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add v2 consolidated metadata type (canonical impl, not spec) Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): wire up zarr_metadata.v2 re-exports Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add ArrayMetadata, GroupMetadata version-polymorphic unions Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add Codec envelope and blosc codec configurations Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add dtype types (DType, LengthBytesConfig, FixedLengthBytesConfig, TimeConfig) Co-Authored-By: Claude Opus 4.7 (1M context) * test(metadata): smoke + structural tests for the package Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(common): re-export JSON, NamedConfig, NamedRequiredConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): re-export v3 types from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): re-export faithful v2 array metadata type Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(codecs): re-export blosc codec configurations from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(abc): re-export CodecJSON from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(dtype): re-export DTypeJSON from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(dtype): re-export LengthBytesConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(dtype): re-export FixedLengthBytesConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(dtype): re-export TimeConfig from zarr-metadata Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): use tuple[int, ...] for fixed-length fields + typed NumcodecsConfig Spec-defined metadata fields with fixed length and no mutation semantics are typed as tuples, not Sequence. Applies to: - v2 ArrayMetadataV2.shape, .chunks - v2 DataTypeV2Structured.shape - v2 ArrayMetadataV2.filters (tuple of codec configs) - v3 RegularChunkGridConfig.chunk_shape - v3 RectilinearChunkGridConfig.chunk_shapes Adds zarr_metadata.v2.codec.NumcodecsConfig, a TypedDict modeling the v2 spec shape for compressors and filters: a required 'id' field plus arbitrary codec-specific extras. ArrayMetadataV2.compressor and .filters now reference this type instead of an untyped Mapping[str, JSON]. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): fix explicit re-exports and complete DateTimeUnit migration Three fixes: 1. Add missing "μs" unit to zarr_metadata.dtype.time.DateTimeUnit so it matches zarr-python's DateTimeUnit. zarr.core.dtype.npy.common.DateTimeUnit now re-exports from zarr-metadata (downstream consumers like zarr.core.dtype.npy.time pick it up transitively). 2. Replace `from X import Y as LegacyName` with `from X import Y` followed by a module-level `LegacyName: TypeAlias = Y` binding. mypy under `strict = true` rejected the renamed-import form under the explicit- re-export check ("Module 'X' does not explicitly export attribute 'Y'"), affecting 13 call sites across the codebase. The TypeAlias form makes the alias a proper type (mypy uses it in annotations) while preserving runtime introspection (`.__annotations__` access on the aliased TypedDict). Affects: - src/zarr/core/dtype/common.py (DTypeJSON) - src/zarr/core/metadata/v2.py (ArrayV2MetadataDict) - src/zarr/core/metadata/v3.py (ArrayMetadataJSON_V3 + 5 others) 3. noqa: UP040 on the TypeAlias bindings. ruff prefers the `type` keyword (PEP 695), but that wraps the alias in a TypeAliasType which breaks `.__annotations__` lookup used by tests. The 12 remaining "unused type: ignore" mypy errors in v3.py are pre-existing (same count on the pre-refactor state) and unrelated to this work. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): extract primitives to common.py to break import cycle Moves JSON, NamedConfig, NamedRequiredConfig out of zarr_metadata/__init__.py into zarr_metadata/common.py. Submodules (v2/*, v3/*) now import from zarr_metadata.common directly, avoiding the circular import that occurred when v2.codec was loaded during __init__.py execution. Also: - v3.array declares RegularChunkGrid/RectilinearChunkGrid as direct TypedDict classes instead of NamedRequiredConfig aliases, simplifying the types and enabling more precise chunk-grid annotations downstream. - v2.consolidated.ConsolidatedMetadataV2.metadata value type widened to GroupMetadataV2 | ArrayMetadataV2 | JSON. - Added spec links to v2/{array,codec} docstrings. zarr_metadata/__init__.py continues to re-export JSON, NamedConfig, NamedRequiredConfig at the top level so zarr.core.common keeps resolving. Co-Authored-By: Claude Opus 4.7 (1M context) * fix(metadata): address review findings Three issues surfaced by final code review: 1. Add py.typed marker to zarr-metadata. Without it, PEP 561 makes type checkers treat zarr-metadata as untyped, cascading into ~44 spurious mypy errors in zarr (subclassing Any, unused type: ignore, etc). 2. RegularChunkGrid.configuration was accidentally typed NotRequired when converted from NamedRequiredConfig to a direct TypedDict class. Per spec, chunk_shape is mandatory. Make configuration required. 3. RectilinearDimSpec was declared as tuples but zarr's compress_rle returned lists, and the to_dict producer built lists. Align producers with the declared type: compress_rle now returns list[int | tuple[int, int]], expand_rle accepts both list and tuple RLE pairs, to_dict builds tuples. The tuple shape is correct per spec: each RLE pair is a JSON array of exactly two elements (size, count) — a fixed-cardinality structure that tuple models more faithfully than a mutable list. Mypy error count now matches main (32) with these fixes in place. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): remove consolidated_metadata from GroupMetadataV3 consolidated_metadata is not in the core Zarr v3 spec as a field on group metadata. It has an (unmerged) extension spec and is implemented by zarr-python, but keeping it out of GroupMetadataV3 is the spec-faithful move. The extra_items=AllowedExtraField on GroupMetadataV3 already permits it to appear at runtime as an extension. ConsolidatedMetadataV3 remains available at zarr_metadata.v3.consolidated for consumers that want to type the extension shape. Also fix two stray lint issues (missing trailing newline in common.py, unused Mapping import in v2/array.py). Co-Authored-By: Claude Opus 4.7 (1M context) * chore(metadata): don't track zarr-metadata's uv.lock zarr-metadata is a library, not an application — its lockfile pins transitive dev versions that shouldn't be fixed in source. Untrack and gitignore. Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add v3 codec types for bytes, crc32c, gzip, zstd, transpose, sharding Adds per-codec TypedDict configurations + name literals + full envelope types for every core v3 codec besides blosc (which is extended in the same style for consistency): - {Codec}CodecName : Literal[""] — the spec "name" value - {Codec}CodecConfiguration : TypedDict — the "configuration" body - {Codec}Codec : NamedRequiredConfig — the full envelope crc32c has no configuration fields, so Crc32cCodec uses NamedConfig (configuration optional) and no Configuration TypedDict is exported. The `V1` suffix is dropped from the Configuration types (except blosc, where V1 + Numcodecs disambiguate two concrete shapes). The other v3 codec specs aren't versioned at the codec level; there's only one shape per codec today, and an incompatible future change would land under a new codec name rather than a v2 of the same name. Also fixes pre-existing v2 test fixtures to include the now-required compressor/fill_value/order/filters fields on ArrayMetadataV2. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): define codec envelope TypedDicts explicitly Each {Codec}Codec envelope type is now an explicit TypedDict class with `name` and `configuration` fields, rather than a NamedRequiredConfig[...] generic alias. Readable at the call site, surfaces the spec structure directly, and allows a real class-level docstring. Also: - Drop BloscCodecConfigurationNumcodecs from zarr-metadata. numcodecs- shape modeling belongs in zarr-python (which implements that shape), not in zarr-metadata (which is spec-only). - Rename BloscCodecConfigurationV1 to BloscCodecConfiguration, matching the unversioned naming used for the other codecs. - Restore BloscConfigV2 locally in zarr-python for the numcodecs shape. Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add Final string constants for codec names and enum-valued fields Each codec now exports SCREAMING_CASE Final constants alongside the Literal types. Downstream packages can reference the spec-defined strings without retyping magic strings. Codec names: BLOSC_CODEC_NAME, BYTES_CODEC_NAME, CRC32C_CODEC_NAME, GZIP_CODEC_NAME, SHARDING_CODEC_NAME, TRANSPOSE_CODEC_NAME, ZSTD_CODEC_NAME. Enum-valued field values: - Blosc: BLOSC_SHUFFLE_{NOSHUFFLE,SHUFFLE,BITSHUFFLE}, BLOSC_CNAME_{LZ4,LZ4HC,BLOSCLZ,SNAPPY,ZLIB,ZSTD} - Bytes: BYTES_ENDIAN_{LITTLE,BIG} (also extracts the existing Literal into a new `Endian` alias) - Sharding: SHARDING_INDEX_LOCATION_{START,END} (and `IndexLocation` Literal alias) Co-Authored-By: Claude Opus 4.7 (1M context) * docs(metadata): say "codec metadata" instead of "codec envelope" Rewords docstrings and test names throughout the package: the {Codec}Codec TypedDict describes a codec's JSON metadata, not a "named-config envelope." Less jargon, consistent with the package name. Identifier names are unchanged (still BloscCodec, GzipCodec, etc.). Also renames v3/array.py chunk-grid docstrings for consistency (Regular/Rectilinear ChunkGrid "metadata" rather than "named-config container"), and updates the README. Co-Authored-By: Claude Opus 4.7 (1M context) * docs(metadata): use single-backtick markdown code formatting Convert all double-backtick RST-style inline code in zarr-metadata docstrings to single-backtick markdown style. The package's documentation will be rendered by mkdocs, which expects markdown, so single backticks render correctly as inline code. Co-Authored-By: Claude Opus 4.7 (1M context) * feat(metadata): add v3 spec data type metadata Models the spec-defined v3 data types from zarr-specs core and zarr-extensions: * `dtype/primitive.py` (NEW) - Final constants and `PrimitiveDTypeName` Literal union for all 14 core v3 primitives (bool, int8..int64, uint8..uint64, float16..float64, complex64, complex128). * `dtype/bytes.py` - adds `BYTES_DTYPE_NAME` and `BytesDTypeName` for the variable-length `bytes` extension; adds `NullTerminatedBytes` envelope TypedDict for `null_terminated_bytes` (zarr-extensions). Retains `FixedLengthBytesConfig` (re-exported by zarr-python). * `dtype/string.py` - adds `STRING_DTYPE_NAME`/`StringDTypeName` for the `string` extension; adds `FixedLengthUtf32` envelope. Retains `LengthBytesConfig`. * `dtype/time.py` - adds `NumpyDatetime64` and `NumpyTimedelta64` envelopes plus name constants/literals. The shared `TimeConfig` body is preserved. * `dtype/struct.py` (NEW) - the `struct` extension type, with `StructField`, `StructConfig`, and `Struct` envelope. Fields hold recursive `DType` values, supporting nested structs. The `r` raw-bytes type from the core spec is parameterised on bit count, not a single literal name, so it isn't given a TypedDict; consumers match it against the wider `DType` alias. Tests updated and extended for the new types and constants. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): per-dtype modules with fill-value types and validators Restructure `zarr_metadata.dtype.*` so each spec data type lives in its own module, mirroring the per-codec layout in `zarr_metadata.codec.*` and the per-dtype directory layout in zarr-extensions. New per-type modules (one per spec data type): bool.py, int8/16/32/64.py, uint8/16/32/64.py, float16/32/64.py, complex64/128.py, bytes.py, string.py, numpy_datetime64.py, numpy_timedelta64.py, struct.py, raw.py Each module exports: - {DTYPE}_DTYPE_NAME (Final str) - {DType}DTypeName (Literal) - For envelope types: a {DType} TypedDict + a {DType}Configuration - {DType}FillValue alias for the JSON shape of `fill_value` Removed `null_terminated_bytes` and `fixed_length_utf32` from zarr-metadata: they are not in zarr-specs or zarr-extensions; they are zarr-python-specific. Their `LengthBytesConfig` and `FixedLengthBytesConfig` TypedDicts now live locally in zarr-python at src/zarr/core/dtype/npy/{string,bytes}.py. zarr.core.dtype.npy.common now imports `DateTimeUnit` from `zarr_metadata.dtype.numpy_datetime64`. zarr.core.dtype.npy.time imports `TimeConfig` (aliased from `NumpyDatetime64Configuration`). NewType + validating-constructor pattern for non-literal spec strings: - HexFloat{16,32,64} for the float hex-string fill values - Base64Bytes for the `bytes` base64 fill value - RawBytesDTypeName for the `r` parameterised name These make spec-format constraints visible to the type system; the matching validating constructors (e.g. `hex_float32`) are the only runtime logic in the package and are minimal regex checks. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): per-grid and per-encoding modules for chunk_grid + chunk_key_encoding Move chunk-grid TypedDicts out of `v3/array.py` into per-type modules, mirroring the per-codec and per-dtype layouts: packages/zarr-metadata/src/zarr_metadata/v3/ ├── chunk_grid/ │ ├── __init__.py │ ├── regular.py # core spec │ └── rectilinear.py # zarr-extensions └── chunk_key_encoding/ ├── __init__.py # ChunkKeySeparator alias ├── default.py # core spec └── v2.py # core spec Each module exports: - {NAME}_NAME (Final str) - {Name} (TypedDict envelope) - {Name}Configuration (TypedDict body) - {Name}Name (Literal type of the `name` field) `v3/array.py` shrinks to just `AllowedExtraField`, `MetadataField`, and `ArrayMetadataV3`. `chunk_grid` and `chunk_key_encoding` fields stay typed as `MetadataField` (str | NamedConfig) -- narrowing them to a specific union belongs in a future validation layer, not in the spec-faithful types layer. Configuration TypedDicts renamed from `*Config` to `*Configuration` to match the dtype/codec naming. zarr.core.metadata.v3 re-exports preserve the legacy `*Config` aliases via `as` imports. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): move codec/ and dtype/ under v3/ Both directories model v3-spec artifacts, so they belong under the v3/ subpackage alongside v3/array, v3/group, v3/consolidated, v3/chunk_grid, and v3/chunk_key_encoding. The principle is now: anything imported from `zarr_metadata.v3.X` is a v3-spec artifact; anything from `zarr_metadata.v2.X` is a v2-spec artifact; only true cross-version primitives sit at the top level (`zarr_metadata.JSON`, `NamedConfig`, `NamedRequiredConfig`, and the `ArrayMetadata`/`GroupMetadata` unions). Path moves: zarr_metadata.codec.* -> zarr_metadata.v3.codec.* zarr_metadata.dtype.* -> zarr_metadata.v3.dtype.* Internal imports inside the moved modules and zarr-python re-export sites updated accordingly. zarr.abc.codec imports the zarr-metadata Codec alias with a private name to avoid colliding with its own runtime `Codec` union (`ArrayArrayCodec | ArrayBytesCodec | BytesBytesCodec`), then re-exports as `CodecJSON`. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(metadata): rename v3/dtype/ -> v3/data_type/ Matches the v3 spec field name `data_type` exactly. All imports inside the package and in zarr-python re-export sites updated accordingly. The `DType` type alias keeps its short name (it's the widely understood abbreviation for "data type JSON shape"); only the module path changes. Co-Authored-By: Claude Opus 4.7 (1M context) * feat: add zarr-metadata package Adds packages/zarr-metadata, a sibling PyPI package that contains spec-defined Zarr v2 and v3 metadata types as pure-typing artifacts (TypedDicts, type aliases, Final string constants, NewType validators). No runtime logic beyond minimal regex validators for spec-format-locked strings (hex floats, base64 bytes, raw-bytes name). Layout (anything imported from `zarr_metadata.v3.X` is a v3-spec artifact; from `zarr_metadata.v2.X` is v2-spec; only true cross-version primitives sit at the top level): zarr_metadata/ ├── common.py # JSON, NamedConfig, NamedRequiredConfig ├── __init__.py # ArrayMetadata, GroupMetadata unions ├── v2/ │ ├── array.py, group.py, consolidated.py, codec.py └── v3/ ├── array.py, group.py, consolidated.py ├── chunk_grid/ {regular, rectilinear} ├── chunk_key_encoding/ {default, v2} ├── codec/ {blosc, bytes, crc32c, gzip, │ sharding, transpose, zstd} └── data_type/ {bool, int8/16/32/64, uint8/16/32/64, float16/32/64, complex64/128, bytes, string, numpy_datetime64, numpy_timedelta64, struct, raw} zarr-python source is unchanged in this branch. zarr-metadata is shipped as an independent package; a follow-up PR will adopt it inside zarr-python once the package is published to PyPI. Co-Authored-By: Claude Opus 4.7 (1M context) * test(metadata): drop tests that don't actually test anything The structural tests constructed dict literals annotated with TypedDict types and asserted that a key we just inserted came back out -- which exercises Python's dict, not the type. The TypedDict has no runtime shape check, so even a type-incompatible dict would pass. Pyright (in CI) is what actually verifies the shapes. Constant-equality tests (e.g. `assert NAME == "name"`) also tested nothing. Kept the validating-constructor tests for hex_float{16,32,64}, base64_bytes, and raw_bytes_dtype_name -- those exercise real regex logic and catch real bugs. Replaced test_imports.py with a single smoke test that confirms the package loads and the top-level union types are reachable. Renamed test_structural.py -> test_validators.py to match what it actually tests. Test count: 47 -> 6, ~750 lines -> 89. Co-Authored-By: Claude Opus 4.7 (1M context) * build(metadata): lower minimum Python to 3.11 zarr-metadata is a typing-only foundational package consumed by libraries; supporting one Python version below the current minimum widens the audience at minimal cost. The only blocker was PEP 695 generic class syntax in `common.py`: class NamedConfig[TName: str, TConfig: ...](TypedDict): Rewritten to the PEP 484 `Generic[T]` form, which works on 3.11+. The two affected classes carry `# noqa: UP046` comments since the ruff rule pushes toward the newer syntax that we deliberately avoid. All other modern features (PEP 604 `X | Y` unions at runtime, `NotRequired`, `extra_items=` via typing_extensions, `ReadOnly`) already work on 3.11. Verified: package imports and all 6 tests pass on Python 3.11. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor: remove generic base metadata * refactor: clean up codecs init * fix: correct v2 structured dtype spec * refactor: drop readonly for numcodecs config * docs: improve docstring * fix: use empty typeddict for crc32c config * fix: remove arbitrary json from consolidated model * fix: don't depend on zarr-metadata yet * fix: typesize is not required * fix: re-wire zarr-metadata up as a dependency for zarr-python * chore: revert changes to src/zarr * chore: mypy ignore the new package * refactor: rename extra field * refactor: we do a little refactoring * test: more dtype tests * chore: add ci * chore: use typing extensions typeddict * fix: unbreak ci * chore: clean up top level exports * chore: clarify extension fields and rename type * allow must_understand: true, and add canonical nan strings --------- Co-authored-by: Claude Opus 4.7 (1M context) --- .github/workflows/zarr-metadata.yml | 99 + .gitignore | 3 + .pre-commit-config.yaml 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packages/zarr-metadata/tests/v3/group/with_extra_field.json create mode 100644 uv.lock diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml new file mode 100644 index 0000000000..1ff0786118 --- /dev/null +++ b/.github/workflows/zarr-metadata.yml @@ -0,0 +1,99 @@ +name: zarr-metadata + +on: + push: + branches: [main] + paths: + - 'packages/zarr-metadata/**' + - '.github/workflows/zarr-metadata.yml' + pull_request: + paths: + - 'packages/zarr-metadata/**' + - '.github/workflows/zarr-metadata.yml' + workflow_dispatch: + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + test: + name: pytest py=${{ matrix.python-version }} + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-metadata + strategy: + fail-fast: false + matrix: + python-version: ['3.11', '3.12', '3.13', '3.14'] + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + with: + enable-cache: true + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + - name: Sync test dependency group + run: uv sync --group test --python ${{ matrix.python-version }} + - name: Run pytest + run: uv run --group test pytest tests + + ruff: + name: ruff + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-metadata + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + - name: Run ruff + run: uvx ruff check . + + pyright: + name: pyright + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-metadata + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + with: + enable-cache: true + - name: Set up Python + run: uv python install 3.11 + - name: Sync test dependency group + run: uv sync --group test --python 3.11 + - name: Run pyright + run: uv run --group test --with pyright pyright src + + zarr-metadata-complete: + name: zarr-metadata complete + needs: [test, ruff, pyright] + if: always() + runs-on: ubuntu-latest + steps: + - name: Check failure + if: | + contains(needs.*.result, 'failure') || + contains(needs.*.result, 'cancelled') + run: exit 1 + - name: Success + run: echo Success! diff --git a/.gitignore b/.gitignore index b79ce264c8..3284865d6c 100644 --- a/.gitignore +++ b/.gitignore @@ -91,3 +91,6 @@ tests/.hypothesis zarr/version.py zarr.egg-info/ + +# zarr-metadata package lockfile (a library, not an app) +packages/zarr-metadata/uv.lock diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d91b35fa4f..6e6c21b581 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -31,7 +31,7 @@ repos: rev: v1.19.1 hooks: - id: mypy - files: src|tests + files: ^(src|tests)/ additional_dependencies: # Package dependencies - packaging diff --git a/packages/zarr-metadata/LICENSE.txt b/packages/zarr-metadata/LICENSE.txt new file mode 100644 index 0000000000..1e8da4d242 --- /dev/null +++ b/packages/zarr-metadata/LICENSE.txt @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2015-2025 Zarr Developers + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md new file mode 100644 index 0000000000..3b78caa796 --- /dev/null +++ b/packages/zarr-metadata/README.md @@ -0,0 +1,52 @@ +# zarr-metadata + +Python type definitions for Zarr v2 and v3 metadata. + +## What this is + +A typed-data package: `TypedDict` definitions and `Literal` aliases for the +JSON shapes specified by the [Zarr v2](https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html) +and [Zarr v3](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) +specifications, plus types for [`zarr-extensions`](https://github.com/zarr-developers/zarr-extensions/) +and a few widely-used-but-unspecified entities (e.g. consolidated metadata). + +## What this is for + +These types describe the JSON shape of Zarr metadata. They are +intended for libraries that **read, write, validate, or transform** +Zarr metadata. Pair them with a runtime validator like +[pydantic](https://docs.pydantic.dev/) to check JSON loaded from disk: + +```python +import json +from pydantic import TypeAdapter +from zarr_metadata.v3.array import ArrayMetadataV3 + +with open("zarr.json", "rb") as f: + raw = json.load(f) + +metadata = TypeAdapter(ArrayMetadataV3).validate_python(raw) +``` + +## What this is *not* + +- Not a parser or builder. There are no `make_array_metadata(...)` factories — + that surface belongs to consumer libraries. +- Not a runtime validator on its own. Pair with `pydantic`, `msgspec`, or + similar to enforce shapes at decode time. + +Even with a runtime validator, these types only describe **structural** +shape — they will not flag *semantically* invalid metadata, like a 3D v3 +array whose `dimension_names` has 4 entries instead of 3. That's a job +for downstream validator routines. + +## Scope + +At minimum, this library supports what Zarr-Python needs: the complete +Zarr v2 and v3 specs, consolidated metadata, and a subset of the metadata +defined in `zarr-extensions`. We are generally open to contributions that +add types for Zarr metadata with a published spec. + +## License + +[MIT](./LICENSE.txt) diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml new file mode 100644 index 0000000000..f24d1ae206 --- /dev/null +++ b/packages/zarr-metadata/pyproject.toml @@ -0,0 +1,68 @@ +[build-system] +requires = ["hatchling>=1.29.0"] +build-backend = "hatchling.build" + +[project] +name = "zarr-metadata" +version = "0.1.0" +description = "Spec-defined metadata types for Zarr v2 and v3." +readme = "README.md" +requires-python = ">=3.11" +license = "MIT" +license-files = ["LICENSE.txt"] +authors = [ + { name = "Davis Bennett", email = "davis.v.bennett@gmail.com" }, +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Typing :: Typed", +] +dependencies = [ + "typing_extensions>=4.13", +] + +[dependency-groups] +test = ["pytest", "pydantic>=2"] + +[tool.hatch.build.targets.wheel] +packages = ["src/zarr_metadata"] + +[tool.ruff] +extend = "../../pyproject.toml" +target-version = "py311" + +[tool.pytest.ini_options] +minversion = "7" +testpaths = ["tests"] +xfail_strict = true +addopts = ["-ra", "--strict-config", "--strict-markers"] +filterwarnings = [ + "error", + # pydantic warns about ReadOnly TypedDict items not being enforced at runtime. + # That's expected here — we rely on type-checker enforcement, not pydantic mutation guards. + "ignore::UserWarning:pydantic._internal._generate_schema", +] + +[tool.numpydoc_validation] +checks = [ + "GL10", + "SS04", + "PR02", + "PR03", + "PR05", + "PR06", +] + +[tool.pyright] +include = ["src"] +enableExperimentalFeatures = true +typeCheckingMode = "strict" +pythonVersion = "3.11" diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py new file mode 100644 index 0000000000..0372373dec --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -0,0 +1,36 @@ +from zarr_metadata._common import NamedConfig +from zarr_metadata.v2.array import ( + ArrayDimensionSeparatorV2, + ArrayMetadataV2, + ArrayOrderV2, + DataTypeMetadataV2, +) +from zarr_metadata.v2.codec import CodecMetadataV2 +from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2 +from zarr_metadata.v3._common import MetadataFieldV3 +from zarr_metadata.v3.array import ArrayMetadataV3, ExtensionFieldV3 +from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 +from zarr_metadata.v3.group import GroupMetadataV3 + +__version__ = "0.1.0" +"""Hardcoded package version. Must match the `version` field in +`pyproject.toml`; the sync is enforced by `tests/test_version.py`.""" + + +__all__ = [ + "ArrayDimensionSeparatorV2", + "ArrayMetadataV2", + "ArrayMetadataV3", + "ArrayOrderV2", + "CodecMetadataV2", + "ConsolidatedMetadataV2", + "ConsolidatedMetadataV3", + "DataTypeMetadataV2", + "ExtensionFieldV3", + "GroupMetadataV2", + "GroupMetadataV3", + "MetadataFieldV3", + "NamedConfig", + "__version__", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/_common.py b/packages/zarr-metadata/src/zarr_metadata/_common.py new file mode 100644 index 0000000000..9aa643e6d0 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/_common.py @@ -0,0 +1,25 @@ +""" +Top-level cross-version primitives for Zarr metadata. + +Version-specific types live under `zarr_metadata.v2` and `zarr_metadata.v3`. +Codec and dtype spec types live under `zarr_metadata.v3.codec` and +`zarr_metadata.v3.data_type`. +""" + +from collections.abc import Mapping +from typing import NotRequired + +from typing_extensions import TypedDict + + +class NamedConfig(TypedDict): + """ + Externally-tagged union member for a metadata field. + + The `configuration` mapping holds arbitrary JSON-encodable values; + it is typed as `Mapping[str, object]` because the type system cannot + express or verify JSON-encodability. + """ + + name: str + configuration: NotRequired[Mapping[str, object]] diff --git a/packages/zarr-metadata/src/zarr_metadata/py.typed b/packages/zarr-metadata/src/zarr_metadata/py.typed new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py new file mode 100644 index 0000000000..06892df48e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py @@ -0,0 +1,21 @@ +"""Zarr v2 metadata types.""" + +from zarr_metadata.v2.array import ( + ArrayDimensionSeparatorV2, + ArrayMetadataV2, + ArrayOrderV2, + DataTypeMetadataV2, +) +from zarr_metadata.v2.codec import CodecMetadataV2 +from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2 + +__all__ = [ + "ArrayDimensionSeparatorV2", + "ArrayMetadataV2", + "ArrayOrderV2", + "CodecMetadataV2", + "ConsolidatedMetadataV2", + "DataTypeMetadataV2", + "GroupMetadataV2", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py new file mode 100644 index 0000000000..4f9f946a12 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -0,0 +1,77 @@ +"""Zarr v2 array metadata types.""" + +from collections.abc import Mapping +from typing import Literal, NotRequired + +from typing_extensions import TypedDict + +from zarr_metadata.v2.codec import CodecMetadataV2 + +DataTypeMetadataV2 = str | tuple[tuple[str, str] | tuple[str, str, tuple[int, ...]], ...] +"""The v2 dtype representation. + +Either a numpy-style dtype string (e.g. `"ChunkGridMetadata` aliases re-exported here are the canonical type +for each grid's permitted JSON shapes. For the underlying +`ChunkGridObject`, `ChunkGridConfiguration`, etc., import directly +from the leaf submodule. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-grids +""" + +from zarr_metadata.v3.chunk_grid.rectilinear import RectilinearChunkGridMetadata +from zarr_metadata.v3.chunk_grid.regular import RegularChunkGridMetadata + +__all__ = [ + "RectilinearChunkGridMetadata", + "RegularChunkGridMetadata", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py new file mode 100644 index 0000000000..e3551e3c72 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/rectilinear.py @@ -0,0 +1,54 @@ +""" +Rectilinear chunk grid (zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear +""" + +from typing import Final, Literal + +from typing_extensions import TypedDict + +RECTILINEAR_CHUNK_GRID_NAME: Final = "rectilinear" +"""The `name` field value of the rectilinear chunk grid.""" + +RectilinearChunkGridName = Literal["rectilinear"] +"""Literal type of the `name` field of the rectilinear chunk grid.""" + +RectilinearDimSpec = int | tuple[int | tuple[int, int], ...] +"""JSON shape for one dimension's rectilinear spec. + +Either a bare integer (uniform shorthand for a regular dimension within +a rectilinear grid), or a tuple of integers and/or `[value, count]` RLE +pairs. +""" + + +class RectilinearChunkGridConfiguration(TypedDict): + """Configuration for the rectilinear chunk grid.""" + + kind: Literal["inline"] + chunk_shapes: tuple[RectilinearDimSpec, ...] + + +class RectilinearChunkGridObject(TypedDict): + """Rectilinear chunk grid metadata in object form.""" + + name: RectilinearChunkGridName + configuration: RectilinearChunkGridConfiguration + + +RectilinearChunkGridMetadata = RectilinearChunkGridObject +"""Permitted JSON shape for rectilinear chunk grid metadata. + +`kind` and `chunk_shapes` are required, so only the object form is valid; +the short-hand-name form is not permitted by the spec for this grid. +""" + +__all__ = [ + "RECTILINEAR_CHUNK_GRID_NAME", + "RectilinearChunkGridConfiguration", + "RectilinearChunkGridMetadata", + "RectilinearChunkGridName", + "RectilinearChunkGridObject", + "RectilinearDimSpec", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py new file mode 100644 index 0000000000..2f7a089934 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_grid/regular.py @@ -0,0 +1,44 @@ +""" +Regular chunk grid (Zarr v3 core spec). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#regular-grids +""" + +from typing import Final, Literal + +from typing_extensions import TypedDict + +REGULAR_CHUNK_GRID_NAME: Final = "regular" +"""The `name` field value of the regular chunk grid.""" + +RegularChunkGridName = Literal["regular"] +"""Literal type of the `name` field of the regular chunk grid.""" + + +class RegularChunkGridConfiguration(TypedDict): + """Configuration for the regular chunk grid.""" + + chunk_shape: tuple[int, ...] + + +class RegularChunkGridObject(TypedDict): + """Regular chunk grid metadata in object form.""" + + name: RegularChunkGridName + configuration: RegularChunkGridConfiguration + + +RegularChunkGridMetadata = RegularChunkGridObject +"""Permitted JSON shape for regular chunk grid metadata. + +`chunk_shape` is required and has no default, so only the object form is +valid; the short-hand-name form is not permitted by the spec for this grid. +""" + +__all__ = [ + "REGULAR_CHUNK_GRID_NAME", + "RegularChunkGridConfiguration", + "RegularChunkGridMetadata", + "RegularChunkGridName", + "RegularChunkGridObject", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py new file mode 100644 index 0000000000..b6774efbe3 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/__init__.py @@ -0,0 +1,25 @@ +""" +Zarr v3 chunk key encoding metadata types. + +Each chunk key encoding lives in its own submodule: + +- `default` -- v3 default encoding (`/`-separated) +- `v2` -- v2-compatibility encoding (`.`-separated by default) + +Both are defined by the v3 core spec. + +The `ChunkKeyEncodingMetadata` aliases re-exported here are the canonical +type for each encoding's permitted JSON shapes. For the underlying +`ChunkKeyEncodingObject`, `ChunkKeyEncodingConfiguration`, etc., import +directly from the leaf submodule. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from zarr_metadata.v3.chunk_key_encoding.default import DefaultChunkKeyEncodingMetadata +from zarr_metadata.v3.chunk_key_encoding.v2 import V2ChunkKeyEncodingMetadata + +__all__ = [ + "DefaultChunkKeyEncodingMetadata", + "V2ChunkKeyEncodingMetadata", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py new file mode 100644 index 0000000000..d69d6af23f --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py @@ -0,0 +1,57 @@ +""" +Default chunk key encoding (Zarr v3 core spec). + +The chunk key for a chunk with grid index `(k, j, i, ...)` is formed +by appending `ckji...` (where `` is `separator`). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +DEFAULT_CHUNK_KEY_ENCODING_NAME: Final = "default" +"""The `name` field value of the default chunk key encoding.""" + +DefaultChunkKeyEncodingName = Literal["default"] +"""Literal type of the `name` field of the default chunk key encoding.""" + +DefaultChunkKeyEncodingSeparator = Literal["/", "."] +"""Permitted `separator` values for the default chunk key encoding. + +Defaults to `"/"` if absent. +""" + + +class DefaultChunkKeyEncodingConfiguration(TypedDict): + """Configuration for the default chunk key encoding. + + `separator` is optional and defaults to `"/"` per spec. + """ + + separator: NotRequired[DefaultChunkKeyEncodingSeparator] + + +class DefaultChunkKeyEncodingObject(TypedDict): + """Default chunk key encoding metadata in object form.""" + + name: DefaultChunkKeyEncodingName + configuration: NotRequired[DefaultChunkKeyEncodingConfiguration] + + +DefaultChunkKeyEncodingMetadata = DefaultChunkKeyEncodingObject | DefaultChunkKeyEncodingName +"""Permitted JSON shapes for the default chunk-key encoding metadata. + +The configuration has no required keys (`separator` defaults to `"/"`), +so the short-hand-name form is permitted in addition to the object form. +""" + +__all__ = [ + "DEFAULT_CHUNK_KEY_ENCODING_NAME", + "DefaultChunkKeyEncodingConfiguration", + "DefaultChunkKeyEncodingMetadata", + "DefaultChunkKeyEncodingName", + "DefaultChunkKeyEncodingObject", + "DefaultChunkKeyEncodingSeparator", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py new file mode 100644 index 0000000000..ce247ca12c --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py @@ -0,0 +1,57 @@ +""" +v2-compatibility chunk key encoding (Zarr v3 core spec). + +Intended only to allow existing v2 arrays to be converted to v3 without +having to rename chunks. Not recommended for new arrays. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +V2_CHUNK_KEY_ENCODING_NAME: Final = "v2" +"""The `name` field value of the v2 chunk key encoding.""" + +V2ChunkKeyEncodingName = Literal["v2"] +"""Literal type of the `name` field of the v2 chunk key encoding.""" + +V2ChunkKeyEncodingSeparator = Literal["/", "."] +"""Permitted `separator` values for the v2 chunk key encoding. + +Defaults to `"."` if absent. +""" + + +class V2ChunkKeyEncodingConfiguration(TypedDict): + """Configuration for the v2 chunk key encoding. + + `separator` is optional and defaults to `"."` per spec. + """ + + separator: NotRequired[V2ChunkKeyEncodingSeparator] + + +class V2ChunkKeyEncodingObject(TypedDict): + """v2-compatibility chunk key encoding metadata in object form.""" + + name: V2ChunkKeyEncodingName + configuration: NotRequired[V2ChunkKeyEncodingConfiguration] + + +V2ChunkKeyEncodingMetadata = V2ChunkKeyEncodingObject | V2ChunkKeyEncodingName +"""Permitted JSON shapes for the v2-compatibility chunk-key encoding metadata. + +The configuration has no required keys (`separator` defaults to `"."`), +so the short-hand-name form is permitted in addition to the object form. +""" + +__all__ = [ + "V2_CHUNK_KEY_ENCODING_NAME", + "V2ChunkKeyEncodingConfiguration", + "V2ChunkKeyEncodingMetadata", + "V2ChunkKeyEncodingName", + "V2ChunkKeyEncodingObject", + "V2ChunkKeyEncodingSeparator", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py new file mode 100644 index 0000000000..8cc819496d --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py @@ -0,0 +1,40 @@ +""" +Zarr v3 codec spec types. + +Each codec defined by the spec or by zarr-extensions has its own submodule +(`blosc`, `bytes`, `cast_value`, `crc32c`, `gzip`, `scale_offset`, +`sharding_indexed`, `transpose`, `zstd`). + +The `CodecMetadata` aliases re-exported here are the canonical type for +each codec's permitted JSON shapes (object form plus, where the spec allows, +a bare-string short-hand form). For the underlying `CodecObject`, +`CodecConfiguration`, etc., import directly from the leaf submodule. + +For the field-level "any codec entry" alias (used in array metadata's +`codecs` list and in sharding's inner pipelines), import `MetadataFieldV3` +from `zarr_metadata.v3`. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/index.html +""" + +from zarr_metadata.v3.codec.blosc import BloscCodecMetadata +from zarr_metadata.v3.codec.bytes import BytesCodecMetadata +from zarr_metadata.v3.codec.cast_value import CastValueCodecMetadata +from zarr_metadata.v3.codec.crc32c import Crc32cCodecMetadata +from zarr_metadata.v3.codec.gzip import GzipCodecMetadata +from zarr_metadata.v3.codec.scale_offset import ScaleOffsetCodecMetadata +from zarr_metadata.v3.codec.sharding_indexed import ShardingIndexedCodecMetadata +from zarr_metadata.v3.codec.transpose import TransposeCodecMetadata +from zarr_metadata.v3.codec.zstd import ZstdCodecMetadata + +__all__ = [ + "BloscCodecMetadata", + "BytesCodecMetadata", + "CastValueCodecMetadata", + "Crc32cCodecMetadata", + "GzipCodecMetadata", + "ScaleOffsetCodecMetadata", + "ShardingIndexedCodecMetadata", + "TransposeCodecMetadata", + "ZstdCodecMetadata", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py new file mode 100644 index 0000000000..69152cee50 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py @@ -0,0 +1,57 @@ +""" +Blosc codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/blosc/index.html +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +BLOSC_CODEC_NAME: Final = "blosc" +"""The `name` field value of the `blosc` codec.""" + +BloscCodecName = Literal["blosc"] +"""Literal type of the `name` field of the `blosc` codec.""" + +BloscShuffle = Literal["noshuffle", "shuffle", "bitshuffle"] +"""Blosc shuffle mode names.""" + +BloscCName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] +"""Blosc compressor identifiers.""" + + +class BloscCodecConfiguration(TypedDict): + """Configuration for the Zarr v3 `blosc` codec.""" + + cname: BloscCName + clevel: int + shuffle: BloscShuffle + blocksize: int + typesize: NotRequired[int] + + +class BloscCodecObject(TypedDict): + """`blosc` codec metadata in object form.""" + + name: BloscCodecName + configuration: BloscCodecConfiguration + + +BloscCodecMetadata = BloscCodecObject +"""Permitted JSON shape for `blosc` codec metadata. + +The configuration has multiple required keys (`cname`, `clevel`, `shuffle`, +`blocksize`), so only the object form is valid; the short-hand-name form +is not permitted by the spec for this codec. +""" + +__all__ = [ + "BLOSC_CODEC_NAME", + "BloscCName", + "BloscCodecConfiguration", + "BloscCodecMetadata", + "BloscCodecName", + "BloscCodecObject", + "BloscShuffle", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py new file mode 100644 index 0000000000..d72f9ac6ea --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py @@ -0,0 +1,53 @@ +""" +Bytes codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/bytes/index.html +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +BYTES_CODEC_NAME: Final = "bytes" +"""The `name` field value of the `bytes` codec.""" + +BytesCodecName = Literal["bytes"] +"""Literal type of the `name` field of the `bytes` codec.""" + +Endian = Literal["little", "big"] +"""Byte order of multi-byte numeric data.""" + + +class BytesCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `bytes` codec. + + The `endian` field is required for multi-byte data types. + """ + + endian: NotRequired[Endian] + + +class BytesCodecObject(TypedDict): + """`bytes` codec metadata in object form.""" + + name: BytesCodecName + configuration: BytesCodecConfiguration + + +BytesCodecMetadata = BytesCodecObject | BytesCodecName +"""Permitted JSON shapes for `bytes` codec metadata. + +The configuration has no required keys (`endian` is conditionally required +at runtime based on data type), so the spec's short-hand-name form is +permitted in addition to the object form. +""" + +__all__ = [ + "BYTES_CODEC_NAME", + "BytesCodecConfiguration", + "BytesCodecMetadata", + "BytesCodecName", + "BytesCodecObject", + "Endian", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py new file mode 100644 index 0000000000..468dab9587 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py @@ -0,0 +1,92 @@ +""" +Cast-value codec types. + +See https://github.com/zarr-developers/zarr-extensions/tree/main/codecs/cast_value +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +from zarr_metadata.v3._common import MetadataFieldV3 + +CAST_VALUE_CODEC_NAME: Final = "cast_value" +"""The `name` field value of the `cast_value` codec.""" + +CastValueCodecName = Literal["cast_value"] +"""Literal type of the `name` field of the `cast_value` codec.""" + +RoundingMode = Literal[ + "nearest-even", + "towards-zero", + "towards-positive", + "towards-negative", + "nearest-away", +] +"""Permitted values for the `rounding` configuration field. + +Defaults to `"nearest-even"` if absent. +""" + +OutOfRangeMode = Literal["clamp", "wrap"] +"""Permitted values for the `out_of_range` configuration field. + +If absent, out-of-range values are an encoding/decoding error. +""" + +ScalarMapEntry = tuple[object, object] +"""A single `[input, output]` mapping in a `scalar_map` direction. + +Each scalar is JSON-encoded per its data type's fill-value rules (so +e.g. `"NaN"` and `"+Infinity"` are permitted). +""" + + +class ScalarMap(TypedDict): + """Optional encode/decode scalar overrides for the cast_value codec.""" + + encode: NotRequired[tuple[ScalarMapEntry, ...]] + decode: NotRequired[tuple[ScalarMapEntry, ...]] + + +class CastValueCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `cast_value` codec. + + `data_type` is the target data type that input values are cast to. It + is the same shape as the top-level array `data_type` field: either a + bare-string primitive name or a `{name, configuration}` envelope. + """ + + data_type: MetadataFieldV3 + rounding: NotRequired[RoundingMode] + out_of_range: NotRequired[OutOfRangeMode] + scalar_map: NotRequired[ScalarMap] + + +class CastValueCodecObject(TypedDict): + """`cast_value` codec metadata in object form.""" + + name: CastValueCodecName + configuration: CastValueCodecConfiguration + + +CastValueCodecMetadata = CastValueCodecObject +"""Permitted JSON shape for `cast_value` codec metadata. + +`configuration.data_type` is required, so only the object form is valid; +the short-hand-name form is not permitted by the spec for this codec. +""" + + +__all__ = [ + "CAST_VALUE_CODEC_NAME", + "CastValueCodecConfiguration", + "CastValueCodecMetadata", + "CastValueCodecName", + "CastValueCodecObject", + "OutOfRangeMode", + "RoundingMode", + "ScalarMap", + "ScalarMapEntry", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py new file mode 100644 index 0000000000..ea35ae5f1d --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py @@ -0,0 +1,50 @@ +""" +CRC32C codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/crc32c/index.html + +The CRC32C codec has no configuration fields, so the `configuration` +key is absent from the metadata. +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +CRC32C_CODEC_NAME: Final = "crc32c" +"""The `name` field value of the `crc32c` codec.""" + +Crc32cCodecName = Literal["crc32c"] +"""Literal type of the `name` field of the `crc32c` codec.""" + + +class Empty(TypedDict, closed=True): # type: ignore[call-arg] + """An empty mapping""" + + +class Crc32cCodecObject(TypedDict): + """`crc32c` codec metadata in object form. + + Per spec the codec has no configuration fields. `configuration` is + optional and, if present, should be an empty mapping. + """ + + name: Crc32cCodecName + configuration: NotRequired[Empty] + + +Crc32cCodecMetadata = Crc32cCodecObject | Crc32cCodecName +"""Permitted JSON shapes for `crc32c` codec metadata. + +The spec's Extension definition allows extensions with no required +configuration to be encoded as a bare short-hand name. CRC32C has no +configuration, so both forms are valid. +""" + + +__all__ = [ + "CRC32C_CODEC_NAME", + "Crc32cCodecMetadata", + "Crc32cCodecName", + "Crc32cCodecObject", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py new file mode 100644 index 0000000000..fb0c2faf3e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py @@ -0,0 +1,50 @@ +""" +Gzip codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/gzip/index.html +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +GZIP_CODEC_NAME: Final = "gzip" +"""The `name` field value of the `gzip` codec.""" + +GzipCodecName = Literal["gzip"] +"""Literal type of the `name` field of the `gzip` codec.""" + + +class GzipCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `gzip` codec. + + `level` is an integer in the range 0-9; 0 disables compression and 9 + is slowest with the best compression ratio. The spec does not mandate + a default. + """ + + level: NotRequired[int] + + +class GzipCodecObject(TypedDict): + """`gzip` codec metadata in object form.""" + + name: GzipCodecName + configuration: GzipCodecConfiguration + + +GzipCodecMetadata = GzipCodecObject | GzipCodecName +"""Permitted JSON shapes for `gzip` codec metadata. + +The configuration has no required keys (`level` has no spec-mandated +default but is `NotRequired`), so the short-hand-name form is permitted. +""" + +__all__ = [ + "GZIP_CODEC_NAME", + "GzipCodecConfiguration", + "GzipCodecMetadata", + "GzipCodecName", + "GzipCodecObject", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/scale_offset.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/scale_offset.py new file mode 100644 index 0000000000..32e824ed67 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/scale_offset.py @@ -0,0 +1,59 @@ +""" +Scale-offset codec types. + +See https://github.com/zarr-developers/zarr-extensions/tree/main/codecs/scale_offset +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +SCALE_OFFSET_CODEC_NAME: Final = "scale_offset" +"""The `name` field value of the `scale_offset` codec.""" + +ScaleOffsetCodecName = Literal["scale_offset"] +"""Literal type of the `name` field of the `scale_offset` codec.""" + + +class ScaleOffsetCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `scale_offset` codec. + + Both fields are optional. A missing `offset` is the additive identity + (e.g. 0 for numeric types); a missing `scale` is the multiplicative + identity (e.g. 1). Each scalar is JSON-encoded per the input array's + fill-value rules, so `"NaN"` and `"+Infinity"` style strings are + permitted in addition to numbers. + """ + + offset: NotRequired[object] + scale: NotRequired[object] + + +class ScaleOffsetCodecObject(TypedDict): + """`scale_offset` codec metadata in object form. + + `configuration` is itself optional per spec — when both `offset` and + `scale` are at their identity defaults, the codec is a no-op and the + entire `configuration` field may be omitted. + """ + + name: ScaleOffsetCodecName + configuration: NotRequired[ScaleOffsetCodecConfiguration] + + +ScaleOffsetCodecMetadata = ScaleOffsetCodecObject | ScaleOffsetCodecName +"""Permitted JSON shapes for `scale_offset` codec metadata. + +The configuration has no required keys (both `offset` and `scale` are +optional, and the configuration itself is optional), so the short-hand-name +form is permitted in addition to the object form. +""" + +__all__ = [ + "SCALE_OFFSET_CODEC_NAME", + "ScaleOffsetCodecConfiguration", + "ScaleOffsetCodecMetadata", + "ScaleOffsetCodecName", + "ScaleOffsetCodecObject", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py new file mode 100644 index 0000000000..c8dd954e3f --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py @@ -0,0 +1,67 @@ +""" +Sharding-indexed codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/sharding-indexed/index.html +""" + +from typing import Final, Literal, NotRequired + +from typing_extensions import TypedDict + +from zarr_metadata.v3._common import MetadataFieldV3 + +SHARDING_INDEXED_CODEC_NAME: Final = "sharding_indexed" +"""The `name` field value of the `sharding_indexed` codec.""" + +ShardingIndexedCodecName = Literal["sharding_indexed"] +"""Literal type of the `name` field of the `sharding_indexed` codec.""" + +IndexLocation = Literal["start", "end"] +"""Position of the shard index within the encoded shard.""" + + +class ShardingIndexedCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `sharding_indexed` codec. + + `chunk_shape` is the shape of inner chunks along each dimension; + it must evenly divide the shard shape. + + `codecs` is the codec pipeline applied to each inner chunk; exactly + one array-to-bytes codec is required. + + `index_codecs` is the codec pipeline applied to the shard index; + it must be deterministic (no variable-size compression). + + `index_location` defaults to `"end"` per the spec. + """ + + chunk_shape: tuple[int, ...] + codecs: tuple[MetadataFieldV3, ...] + index_codecs: tuple[MetadataFieldV3, ...] + index_location: NotRequired[IndexLocation] + + +class ShardingIndexedCodecObject(TypedDict): + """`sharding_indexed` codec metadata in object form.""" + + name: ShardingIndexedCodecName + configuration: ShardingIndexedCodecConfiguration + + +ShardingIndexedCodecMetadata = ShardingIndexedCodecObject +"""Permitted JSON shape for `sharding_indexed` codec metadata. + +The configuration has multiple required keys (`chunk_shape`, `codecs`, +`index_codecs`), so only the object form is valid; the short-hand-name +form is not permitted by the spec for this codec. +""" + +__all__ = [ + "SHARDING_INDEXED_CODEC_NAME", + "IndexLocation", + "ShardingIndexedCodecConfiguration", + "ShardingIndexedCodecMetadata", + "ShardingIndexedCodecName", + "ShardingIndexedCodecObject", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py new file mode 100644 index 0000000000..ac469b356a --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/transpose.py @@ -0,0 +1,49 @@ +""" +Transpose codec types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/transpose/index.html +""" + +from typing import Final, Literal + +from typing_extensions import TypedDict + +TRANSPOSE_CODEC_NAME: Final = "transpose" +"""The `name` field value of the `transpose` codec.""" + +TransposeCodecName = Literal["transpose"] +"""Literal type of the `name` field of the `transpose` codec.""" + + +class TransposeCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `transpose` codec. + + `order` is a permutation of the dimension indices 0..n-1 that + specifies the dimension reordering applied during encoding. + """ + + order: tuple[int, ...] + + +class TransposeCodecObject(TypedDict): + """`transpose` codec metadata in object form.""" + + name: TransposeCodecName + configuration: TransposeCodecConfiguration + + +TransposeCodecMetadata = TransposeCodecObject +"""Permitted JSON shape for `transpose` codec metadata. + +`order` is required, so only the object form is valid; the short-hand-name +form is not permitted by the spec for this codec. +""" + +__all__ = [ + "TRANSPOSE_CODEC_NAME", + "TransposeCodecConfiguration", + "TransposeCodecMetadata", + "TransposeCodecName", + "TransposeCodecObject", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py new file mode 100644 index 0000000000..c0faa64bed --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/zstd.py @@ -0,0 +1,51 @@ +""" +Zstandard codec types. + +See https://github.com/zarr-developers/zarr-specs/pull/256 (unmerged at +time of writing; the configuration shape below reflects the proposed +specification). +""" + +from typing import Final, Literal + +from typing_extensions import TypedDict + +ZSTD_CODEC_NAME: Final = "zstd" +"""The `name` field value of the `zstd` codec.""" + +ZstdCodecName = Literal["zstd"] +"""Literal type of the `name` field of the `zstd` codec.""" + + +class ZstdCodecConfiguration(TypedDict): + """ + Configuration for the Zarr v3 `zstd` codec. + + Both fields are required per the proposed specification. + """ + + level: int + checksum: bool + + +class ZstdCodecObject(TypedDict): + """`zstd` codec metadata in object form.""" + + name: ZstdCodecName + configuration: ZstdCodecConfiguration + + +ZstdCodecMetadata = ZstdCodecObject +"""Permitted JSON shape for `zstd` codec metadata. + +Both `level` and `checksum` are required, so only the object form is +valid; the short-hand-name form is not permitted by the spec for this codec. +""" + +__all__ = [ + "ZSTD_CODEC_NAME", + "ZstdCodecConfiguration", + "ZstdCodecMetadata", + "ZstdCodecName", + "ZstdCodecObject", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py new file mode 100644 index 0000000000..486a0897a5 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py @@ -0,0 +1,43 @@ +"""Zarr v3 consolidated metadata types. + +There is no Zarr v3 specification for consolidated metadata. This module +models the inline-on-group convention used by the reference Python +implementation (and zarrs), where consolidated metadata is embedded as +an extension field on a group's `zarr.json`. + +The shape modeled here (`{kind, must_understand, metadata}` with no `name` +field) reflects the original Zarr v3.0 reading of the extension-field +rules. Under the strict Zarr v3.1 reading, every extension field must +also include a `name: str` key, which would make this shape — and every +real-world consolidated metadata document in the wild — out of spec. +See `ExtensionFieldV3` and +https://github.com/zarr-developers/zarr-specs/issues/371 for the +ongoing discussion. +""" + +from collections.abc import Mapping +from typing import Literal + +from typing_extensions import TypedDict + +from zarr_metadata.v3.array import ArrayMetadataV3 +from zarr_metadata.v3.group import GroupMetadataV3 + + +class ConsolidatedMetadataV3(TypedDict): + """ + Inline consolidated metadata embedded in a v3 group. + + The `metadata` map contains only v3 array and group entries - v2 + entries are excluded by design. Mixing v2 entries into a v3 + consolidated metadata document is invalid per spec. + """ + + kind: Literal["inline"] + must_understand: Literal[False] + metadata: Mapping[str, ArrayMetadataV3 | GroupMetadataV3] + + +__all__ = [ + "ConsolidatedMetadataV3", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py new file mode 100644 index 0000000000..180f9c500d --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/__init__.py @@ -0,0 +1,105 @@ +""" +Zarr v3 data type spec types. + +Each v3 data type has its own submodule: + +- Core primitives: `bool`, `int8`/`16`/`32`/`64`, `uint8`/`16`/`32`/`64`, + `float16`/`32`/`64`, `complex64`/`128`, `raw` (for `r`) +- zarr-extensions: `bytes`, `string`, `numpy_datetime64`, `numpy_timedelta64`, + `struct` + +The two canonical types per dtype are re-exported here: + +- `DataTypeName` -- the literal type of the dtype's `data_type` string + (or, for named-config dtypes, the literal value of their `name` field) +- `FillValue` -- the permitted JSON shape of the `fill_value` field + +Named-config dtypes (`numpy_datetime64`, `numpy_timedelta64`, `struct`) also +expose their envelope TypedDict here. For configuration TypedDicts, branded +`HexFloat` / `Base64Bytes` types, and the corresponding validator +functions, import directly from the leaf submodule. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from zarr_metadata.v3.data_type.bool import BoolDataTypeName, BoolFillValue +from zarr_metadata.v3.data_type.bytes import BytesDataTypeName, BytesFillValue +from zarr_metadata.v3.data_type.complex64 import Complex64DataTypeName, Complex64FillValue +from zarr_metadata.v3.data_type.complex128 import ( + Complex128DataTypeName, + Complex128FillValue, +) +from zarr_metadata.v3.data_type.float16 import Float16DataTypeName, Float16FillValue +from zarr_metadata.v3.data_type.float32 import Float32DataTypeName, Float32FillValue +from zarr_metadata.v3.data_type.float64 import Float64DataTypeName, Float64FillValue +from zarr_metadata.v3.data_type.int8 import Int8DataTypeName, Int8FillValue +from zarr_metadata.v3.data_type.int16 import Int16DataTypeName, Int16FillValue +from zarr_metadata.v3.data_type.int32 import Int32DataTypeName, Int32FillValue +from zarr_metadata.v3.data_type.int64 import Int64DataTypeName, Int64FillValue +from zarr_metadata.v3.data_type.numpy_datetime64 import ( + NumpyDatetime64, + NumpyDatetime64DataTypeName, + NumpyDatetime64FillValue, +) +from zarr_metadata.v3.data_type.numpy_timedelta64 import ( + NumpyTimedelta64, + NumpyTimedelta64DataTypeName, + NumpyTimedelta64FillValue, +) +from zarr_metadata.v3.data_type.raw import RawBytesDataTypeName, RawBytesFillValue +from zarr_metadata.v3.data_type.string import StringDataTypeName, StringFillValue +from zarr_metadata.v3.data_type.struct import ( + Struct, + StructDataTypeName, + StructFillValue, +) +from zarr_metadata.v3.data_type.uint8 import Uint8DataTypeName, Uint8FillValue +from zarr_metadata.v3.data_type.uint16 import Uint16DataTypeName, Uint16FillValue +from zarr_metadata.v3.data_type.uint32 import Uint32DataTypeName, Uint32FillValue +from zarr_metadata.v3.data_type.uint64 import Uint64DataTypeName, Uint64FillValue + +__all__ = [ + "BoolDataTypeName", + "BoolFillValue", + "BytesDataTypeName", + "BytesFillValue", + "Complex64DataTypeName", + "Complex64FillValue", + "Complex128DataTypeName", + "Complex128FillValue", + "Float16DataTypeName", + "Float16FillValue", + "Float32DataTypeName", + "Float32FillValue", + "Float64DataTypeName", + "Float64FillValue", + "Int8DataTypeName", + "Int8FillValue", + "Int16DataTypeName", + "Int16FillValue", + "Int32DataTypeName", + "Int32FillValue", + "Int64DataTypeName", + "Int64FillValue", + "NumpyDatetime64", + "NumpyDatetime64DataTypeName", + "NumpyDatetime64FillValue", + "NumpyTimedelta64", + "NumpyTimedelta64DataTypeName", + "NumpyTimedelta64FillValue", + "RawBytesDataTypeName", + "RawBytesFillValue", + "StringDataTypeName", + "StringFillValue", + "Struct", + "StructDataTypeName", + "StructFillValue", + "Uint8DataTypeName", + "Uint8FillValue", + "Uint16DataTypeName", + "Uint16FillValue", + "Uint32DataTypeName", + "Uint32FillValue", + "Uint64DataTypeName", + "Uint64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py new file mode 100644 index 0000000000..e36613a154 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bool.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `bool` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +BOOL_DATA_TYPE_NAME: Final = "bool" +"""The `data_type` value for the `bool` type.""" + +BoolDataTypeName = Literal["bool"] +"""Literal type of the `data_type` field for `bool`.""" + +BoolFillValue = bool +"""Permitted JSON shape of the `fill_value` field for `bool`: a JSON boolean.""" + + +__all__ = [ + "BOOL_DATA_TYPE_NAME", + "BoolDataTypeName", + "BoolFillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py new file mode 100644 index 0000000000..c7eed64f0f --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/bytes.py @@ -0,0 +1,48 @@ +""" +Zarr `bytes` data type (variable-length raw bytes, zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/bytes +""" + +import re +from typing import Final, Literal, NewType + +BYTES_DATA_TYPE_NAME: Final = "bytes" +"""The `data_type` value for the variable-length `bytes` type.""" + +BytesDataTypeName = Literal["bytes"] +"""Literal type of the `data_type` field for `bytes`.""" + +Base64Bytes = NewType("Base64Bytes", str) +"""A standard-alphabet base64-encoded byte sequence.""" + +_BASE64_RE: Final = re.compile(r"^[A-Za-z0-9+/]*={0,2}$") + + +def base64_bytes(value: str) -> Base64Bytes: + """Validate `value` as a Base64Bytes and brand it. + + Raises ValueError if `value` is not standard-alphabet base64 + (length must be a multiple of 4 once padded; only `A-Z`, `a-z`, + `0-9`, `+`, `/`, and trailing `=` padding are permitted). + """ + if len(value) % 4 != 0 or not _BASE64_RE.fullmatch(value): + raise ValueError(f"Expected standard-alphabet base64, got {value!r}") + return Base64Bytes(value) + + +BytesFillValue = tuple[int, ...] | Base64Bytes +"""Permitted JSON shape of the `fill_value` field for `bytes`. + +Either a JSON array of integers in `[0, 255]` (one per byte), or a +`Base64Bytes` string encoding the byte sequence. +""" + + +__all__ = [ + "BYTES_DATA_TYPE_NAME", + "Base64Bytes", + "BytesDataTypeName", + "BytesFillValue", + "base64_bytes", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py new file mode 100644 index 0000000000..780bbbb02f --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex128.py @@ -0,0 +1,37 @@ +""" +Zarr v3 `complex128` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +from zarr_metadata.v3.data_type.float64 import Float64FillValue + +COMPLEX128_DATA_TYPE_NAME: Final = "complex128" +"""The `data_type` value for the `complex128` type.""" + +Complex128DataTypeName = Literal["complex128"] +"""Literal type of the `data_type` field for `complex128`.""" + +Complex128Component = Float64FillValue +"""One real or imaginary component of a `complex128` fill value. + +Same shape as a `float64` fill value: a JSON number, a named sentinel, +or a `HexFloat64` string. +""" + +Complex128FillValue = tuple[Complex128Component, Complex128Component] +"""Permitted JSON shape of the `fill_value` field for `complex128`. + +A two-element JSON array `[real, imag]` where each component is a +`Complex128Component`. +""" + + +__all__ = [ + "COMPLEX128_DATA_TYPE_NAME", + "Complex128Component", + "Complex128DataTypeName", + "Complex128FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py new file mode 100644 index 0000000000..4aca608899 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/complex64.py @@ -0,0 +1,37 @@ +""" +Zarr v3 `complex64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +from zarr_metadata.v3.data_type.float32 import Float32FillValue + +COMPLEX64_DATA_TYPE_NAME: Final = "complex64" +"""The `data_type` value for the `complex64` type.""" + +Complex64DataTypeName = Literal["complex64"] +"""Literal type of the `data_type` field for `complex64`.""" + +Complex64Component = Float32FillValue +"""One real or imaginary component of a `complex64` fill value. + +Same shape as a `float32` fill value: a JSON number, a named sentinel, +or a `HexFloat32` string. +""" + +Complex64FillValue = tuple[Complex64Component, Complex64Component] +"""Permitted JSON shape of the `fill_value` field for `complex64`. + +A two-element JSON array `[real, imag]` where each component is a +`Complex64Component`. +""" + + +__all__ = [ + "COMPLEX64_DATA_TYPE_NAME", + "Complex64Component", + "Complex64DataTypeName", + "Complex64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py new file mode 100644 index 0000000000..41eec441df --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float16.py @@ -0,0 +1,71 @@ +""" +Zarr v3 `float16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT16_DATA_TYPE_NAME: Final = "float16" +"""The `data_type` value for the `float16` type.""" + +Float16DataTypeName = Literal["float16"] +"""Literal type of the `data_type` field for `float16`.""" + +Float16SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat16 = NewType("HexFloat16", str) +"""A 6-character hex string (`0x` + 4 hex digits) encoding the +unsigned-integer representation of a float16.""" + +_HEX_FLOAT16_RE: Final = re.compile(r"^0x[0-9a-fA-F]{4}$") + + +def hex_float16(value: str) -> HexFloat16: + """Validate `value` as a HexFloat16 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 4 hex + digits. + """ + if not _HEX_FLOAT16_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 4 hex digits, got {value!r}") + return HexFloat16(value) + + +Float16FillValue = float | int | Float16SpecialFillValue | HexFloat16 +"""Permitted JSON shape of the `fill_value` field for `float16`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat16` (`0xYYYY` string encoding +the unsigned-integer representation of the IEEE 754 value). +""" + +CANONICAL_NAN_HEX_FLOAT16: Final = "0x7e00" +"""Canonical hex form of the float16 NaN sentinel `"NaN"`. + +Per spec the named `"NaN"` sentinel denotes the float with sign=0, the +most significant mantissa bit set, and all other mantissa bits zero +(the IEEE 754 default quiet NaN). Other NaN bit patterns must be +encoded with the explicit hex-string form. +""" + +CANONICAL_POSITIVE_INFINITY_HEX_FLOAT16: Final = "0x7c00" +"""Canonical hex form of the float16 `"Infinity"` sentinel.""" + +CANONICAL_NEGATIVE_INFINITY_HEX_FLOAT16: Final = "0xfc00" +"""Canonical hex form of the float16 `"-Infinity"` sentinel.""" + + +__all__ = [ + "CANONICAL_NAN_HEX_FLOAT16", + "CANONICAL_NEGATIVE_INFINITY_HEX_FLOAT16", + "CANONICAL_POSITIVE_INFINITY_HEX_FLOAT16", + "FLOAT16_DATA_TYPE_NAME", + "Float16DataTypeName", + "Float16FillValue", + "Float16SpecialFillValue", + "HexFloat16", + "hex_float16", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py new file mode 100644 index 0000000000..37b7d4f6e8 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float32.py @@ -0,0 +1,71 @@ +""" +Zarr v3 `float32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT32_DATA_TYPE_NAME: Final = "float32" +"""The `data_type` value for the `float32` type.""" + +Float32DataTypeName = Literal["float32"] +"""Literal type of the `data_type` field for `float32`.""" + +Float32SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat32 = NewType("HexFloat32", str) +"""A 10-character hex string (`0x` + 8 hex digits) encoding the +unsigned-integer representation of a float32.""" + +_HEX_FLOAT32_RE: Final = re.compile(r"^0x[0-9a-fA-F]{8}$") + + +def hex_float32(value: str) -> HexFloat32: + """Validate `value` as a HexFloat32 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 8 hex + digits. + """ + if not _HEX_FLOAT32_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 8 hex digits, got {value!r}") + return HexFloat32(value) + + +Float32FillValue = float | int | Float32SpecialFillValue | HexFloat32 +"""Permitted JSON shape of the `fill_value` field for `float32`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat32` (`0xYYYYYYYY` string +encoding the unsigned-integer representation of the IEEE 754 value). +""" + +CANONICAL_NAN_HEX_FLOAT32: Final = "0x7fc00000" +"""Canonical hex form of the float32 NaN sentinel `"NaN"`. + +Per spec the named `"NaN"` sentinel denotes the float with sign=0, the +most significant mantissa bit set, and all other mantissa bits zero +(the IEEE 754 default quiet NaN). Other NaN bit patterns must be +encoded with the explicit hex-string form. +""" + +CANONICAL_POSITIVE_INFINITY_HEX_FLOAT32: Final = "0x7f800000" +"""Canonical hex form of the float32 `"Infinity"` sentinel.""" + +CANONICAL_NEGATIVE_INFINITY_HEX_FLOAT32: Final = "0xff800000" +"""Canonical hex form of the float32 `"-Infinity"` sentinel.""" + + +__all__ = [ + "CANONICAL_NAN_HEX_FLOAT32", + "CANONICAL_NEGATIVE_INFINITY_HEX_FLOAT32", + "CANONICAL_POSITIVE_INFINITY_HEX_FLOAT32", + "FLOAT32_DATA_TYPE_NAME", + "Float32DataTypeName", + "Float32FillValue", + "Float32SpecialFillValue", + "HexFloat32", + "hex_float32", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py new file mode 100644 index 0000000000..9a5cf98288 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/float64.py @@ -0,0 +1,72 @@ +""" +Zarr v3 `float64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +import re +from typing import Final, Literal, NewType + +FLOAT64_DATA_TYPE_NAME: Final = "float64" +"""The `data_type` value for the `float64` type.""" + +Float64DataTypeName = Literal["float64"] +"""Literal type of the `data_type` field for `float64`.""" + +Float64SpecialFillValue = Literal["NaN", "Infinity", "-Infinity"] +"""Named non-finite fill values permitted by the spec for IEEE 754 floats.""" + +HexFloat64 = NewType("HexFloat64", str) +"""An 18-character hex string (`0x` + 16 hex digits) encoding the +unsigned-integer representation of a float64.""" + +_HEX_FLOAT64_RE: Final = re.compile(r"^0x[0-9a-fA-F]{16}$") + + +def hex_float64(value: str) -> HexFloat64: + """Validate `value` as a HexFloat64 and brand it. + + Raises ValueError if `value` is not exactly `0x` followed by 16 hex + digits. + """ + if not _HEX_FLOAT64_RE.fullmatch(value): + raise ValueError(f"Expected '0x' followed by 16 hex digits, got {value!r}") + return HexFloat64(value) + + +Float64FillValue = float | int | Float64SpecialFillValue | HexFloat64 +"""Permitted JSON shape of the `fill_value` field for `float64`. + +Either a JSON number, one of the named non-finite sentinels (`"NaN"`, +`"Infinity"`, `"-Infinity"`), or a `HexFloat64` (`0xYYYYYYYYYYYYYYYY` +string encoding the unsigned-integer representation of the IEEE 754 +value). +""" + +CANONICAL_NAN_HEX_FLOAT64: Final = "0x7ff8000000000000" +"""Canonical hex form of the float64 NaN sentinel `"NaN"`. + +Per spec the named `"NaN"` sentinel denotes the float with sign=0, the +most significant mantissa bit set, and all other mantissa bits zero +(the IEEE 754 default quiet NaN). Other NaN bit patterns must be +encoded with the explicit hex-string form. +""" + +CANONICAL_POSITIVE_INFINITY_HEX_FLOAT64: Final = "0x7ff0000000000000" +"""Canonical hex form of the float64 `"Infinity"` sentinel.""" + +CANONICAL_NEGATIVE_INFINITY_HEX_FLOAT64: Final = "0xfff0000000000000" +"""Canonical hex form of the float64 `"-Infinity"` sentinel.""" + + +__all__ = [ + "CANONICAL_NAN_HEX_FLOAT64", + "CANONICAL_NEGATIVE_INFINITY_HEX_FLOAT64", + "CANONICAL_POSITIVE_INFINITY_HEX_FLOAT64", + "FLOAT64_DATA_TYPE_NAME", + "Float64DataTypeName", + "Float64FillValue", + "Float64SpecialFillValue", + "HexFloat64", + "hex_float64", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py new file mode 100644 index 0000000000..b76f06761a --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int16.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT16_DATA_TYPE_NAME: Final = "int16" +"""The `data_type` value for the `int16` type.""" + +Int16DataTypeName = Literal["int16"] +"""Literal type of the `data_type` field for `int16`.""" + +Int16FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int16`: a JSON integer in [-32768, 32767].""" + + +__all__ = [ + "INT16_DATA_TYPE_NAME", + "Int16DataTypeName", + "Int16FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py new file mode 100644 index 0000000000..7b41ec6c54 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int32.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT32_DATA_TYPE_NAME: Final = "int32" +"""The `data_type` value for the `int32` type.""" + +Int32DataTypeName = Literal["int32"] +"""Literal type of the `data_type` field for `int32`.""" + +Int32FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int32`: a JSON integer in [-2**31, 2**31 - 1].""" + + +__all__ = [ + "INT32_DATA_TYPE_NAME", + "Int32DataTypeName", + "Int32FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py new file mode 100644 index 0000000000..0005675c66 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int64.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT64_DATA_TYPE_NAME: Final = "int64" +"""The `data_type` value for the `int64` type.""" + +Int64DataTypeName = Literal["int64"] +"""Literal type of the `data_type` field for `int64`.""" + +Int64FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int64`: a JSON integer in [-2**63, 2**63 - 1].""" + + +__all__ = [ + "INT64_DATA_TYPE_NAME", + "Int64DataTypeName", + "Int64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py new file mode 100644 index 0000000000..a5a16de761 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/int8.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `int8` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +INT8_DATA_TYPE_NAME: Final = "int8" +"""The `data_type` value for the `int8` type.""" + +Int8DataTypeName = Literal["int8"] +"""Literal type of the `data_type` field for `int8`.""" + +Int8FillValue = int +"""Permitted JSON shape of the `fill_value` field for `int8`: a JSON integer in [-128, 127].""" + + +__all__ = [ + "INT8_DATA_TYPE_NAME", + "Int8DataTypeName", + "Int8FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py new file mode 100644 index 0000000000..243d5fb6f6 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py @@ -0,0 +1,60 @@ +""" +Zarr `numpy.datetime64` data type (zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.datetime64 +""" + +from typing import Final, Literal + +from typing_extensions import ReadOnly, TypedDict + +NUMPY_DATETIME64_DATA_TYPE_NAME: Final = "numpy.datetime64" +"""The `name` field value of the `numpy.datetime64` data type.""" + +NumpyDatetime64DataTypeName = Literal["numpy.datetime64"] +"""Literal type of the `name` field of the `numpy.datetime64` data type.""" + +DateTimeUnit = Literal[ + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" +] +"""Time unit codes used by numpy.datetime64.""" + + +class NumpyDatetime64Configuration(TypedDict): + """ + Configuration for the `numpy.datetime64` data type. + + Attributes + ---------- + unit + A string encoding a unit of time. + scale_factor + The multiplier relative to the unit. + """ + + unit: ReadOnly[DateTimeUnit] + scale_factor: ReadOnly[int] + + +class NumpyDatetime64(TypedDict): + """`numpy.datetime64` data type metadata.""" + + name: NumpyDatetime64DataTypeName + configuration: NumpyDatetime64Configuration + + +NumpyDatetime64FillValue = int | Literal["NaT"] +"""Permitted JSON shape of the `fill_value` field for `numpy.datetime64`. + +Either a JSON integer (count of `unit * scale_factor` since the epoch), +or the string `"NaT"` (equivalent to the integer `-2**63`). +""" + +__all__ = [ + "NUMPY_DATETIME64_DATA_TYPE_NAME", + "DateTimeUnit", + "NumpyDatetime64", + "NumpyDatetime64Configuration", + "NumpyDatetime64DataTypeName", + "NumpyDatetime64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py new file mode 100644 index 0000000000..41e35e7aae --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py @@ -0,0 +1,60 @@ +""" +Zarr `numpy.timedelta64` data type (zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.timedelta64 +""" + +from typing import Final, Literal + +from typing_extensions import ReadOnly, TypedDict + +NUMPY_TIMEDELTA64_DATA_TYPE_NAME: Final = "numpy.timedelta64" +"""The `name` field value of the `numpy.timedelta64` data type.""" + +NumpyTimedelta64DataTypeName = Literal["numpy.timedelta64"] +"""Literal type of the `name` field of the `numpy.timedelta64` data type.""" + +DateTimeUnit = Literal[ + "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" +] +"""Time unit codes used by numpy.timedelta64.""" + + +class NumpyTimedelta64Configuration(TypedDict): + """ + Configuration for the `numpy.timedelta64` data type. + + Attributes + ---------- + unit + A string encoding a unit of time. + scale_factor + The multiplier relative to the unit. + """ + + unit: ReadOnly[DateTimeUnit] + scale_factor: ReadOnly[int] + + +class NumpyTimedelta64(TypedDict): + """`numpy.timedelta64` data type metadata.""" + + name: NumpyTimedelta64DataTypeName + configuration: NumpyTimedelta64Configuration + + +NumpyTimedelta64FillValue = int | Literal["NaT"] +"""Permitted JSON shape of the `fill_value` field for `numpy.timedelta64`. + +Either a JSON integer (a count of `unit * scale_factor`), or the string +`"NaT"` (equivalent to the integer `-2**63`). +""" + +__all__ = [ + "NUMPY_TIMEDELTA64_DATA_TYPE_NAME", + "DateTimeUnit", + "NumpyTimedelta64", + "NumpyTimedelta64Configuration", + "NumpyTimedelta64DataTypeName", + "NumpyTimedelta64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py new file mode 100644 index 0000000000..c9c688c9fa --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/raw.py @@ -0,0 +1,45 @@ +""" +Zarr v3 `r` raw-bytes data type (parameterised by bit count). + +The `data_type` value is a string of the form `r` where `N` is a +positive multiple of 8 (e.g. `r8`, `r16`, `r24`). + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html +""" + +import re +from typing import Final, NewType + +RawBytesDataTypeName = NewType("RawBytesDataTypeName", str) +"""A spec-conformant `r` raw-bytes name (e.g. `"r8"`, `"r16"`).""" + +_RAW_BYTES_RE: Final = re.compile(r"^r(\d+)$") + + +def raw_bytes_dtype_name(value: str) -> RawBytesDataTypeName: + """Validate `value` as a `r` raw-bytes name and brand it. + + Raises ValueError if `value` is not `r` followed by a positive + multiple of 8. + """ + match = _RAW_BYTES_RE.fullmatch(value) + if match is None: + raise ValueError(f"Expected 'r' followed by a positive integer, got {value!r}") + bits = int(match.group(1)) + if bits == 0 or bits % 8 != 0: + raise ValueError(f"Expected 'r' where N is a positive multiple of 8, got {value!r}") + return RawBytesDataTypeName(value) + + +RawBytesFillValue = tuple[int, ...] +"""Permitted JSON shape of the `fill_value` field for `r`. + +A JSON array of N/8 integers in `[0, 255]` (one per byte). +""" + + +__all__ = [ + "RawBytesDataTypeName", + "RawBytesFillValue", + "raw_bytes_dtype_name", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py new file mode 100644 index 0000000000..0a778ccecc --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/string.py @@ -0,0 +1,23 @@ +""" +Zarr `string` data type (variable-length utf-8, zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/string +""" + +from typing import Final, Literal + +STRING_DATA_TYPE_NAME: Final = "string" +"""The `data_type` value for the `string` type.""" + +StringDataTypeName = Literal["string"] +"""Literal type of the `data_type` field for `string`.""" + +StringFillValue = str +"""Permitted JSON shape of the `fill_value` field for `string`: a JSON unicode string.""" + + +__all__ = [ + "STRING_DATA_TYPE_NAME", + "StringDataTypeName", + "StringFillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py new file mode 100644 index 0000000000..284ba8e482 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py @@ -0,0 +1,63 @@ +""" +Zarr `struct` data type (heterogeneous record, zarr-extensions). + +See https://github.com/zarr-developers/zarr-extensions/blob/main/data-types/struct/README.md +""" + +from collections.abc import Mapping +from typing import Final, Literal + +from typing_extensions import ReadOnly, TypedDict + +STRUCT_DATA_TYPE_NAME: Final = "struct" +"""The `name` field value of the `struct` data type.""" + +StructDataTypeName = Literal["struct"] +"""Literal type of the `name` field of the `struct` data type.""" + + +class StructField(TypedDict): + """ + A single field entry inside a structured dtype. + + Attributes + ---------- + name + The field name (must be unique within a struct and non-empty). + data_type + The field's data type. Recursive: may be a bare-string primitive + or a named-config envelope including another `struct`. + """ + + name: ReadOnly[str] + data_type: ReadOnly[object] + + +class StructConfiguration(TypedDict): + """Configuration for the `struct` data type.""" + + fields: ReadOnly[tuple[StructField, ...]] + + +class Struct(TypedDict): + """`struct` data type metadata.""" + + name: StructDataTypeName + configuration: StructConfiguration + + +StructFillValue = Mapping[str, object] +"""Permitted JSON shape of the `fill_value` field for `struct`. + +A JSON object mapping each field name to that field's fill value. Field +fill values are themselves shaped per the field's `data_type`, recursively. +""" + +__all__ = [ + "STRUCT_DATA_TYPE_NAME", + "Struct", + "StructConfiguration", + "StructDataTypeName", + "StructField", + "StructFillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py new file mode 100644 index 0000000000..37e35ec436 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint16.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint16` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT16_DATA_TYPE_NAME: Final = "uint16" +"""The `data_type` value for the `uint16` type.""" + +Uint16DataTypeName = Literal["uint16"] +"""Literal type of the `data_type` field for `uint16`.""" + +Uint16FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint16`: a JSON integer in [0, 65535].""" + + +__all__ = [ + "UINT16_DATA_TYPE_NAME", + "Uint16DataTypeName", + "Uint16FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py new file mode 100644 index 0000000000..f6cd4d447e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint32.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint32` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT32_DATA_TYPE_NAME: Final = "uint32" +"""The `data_type` value for the `uint32` type.""" + +Uint32DataTypeName = Literal["uint32"] +"""Literal type of the `data_type` field for `uint32`.""" + +Uint32FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint32`: a JSON integer in [0, 2**32 - 1].""" + + +__all__ = [ + "UINT32_DATA_TYPE_NAME", + "Uint32DataTypeName", + "Uint32FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py new file mode 100644 index 0000000000..7151d2395a --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint64.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint64` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT64_DATA_TYPE_NAME: Final = "uint64" +"""The `data_type` value for the `uint64` type.""" + +Uint64DataTypeName = Literal["uint64"] +"""Literal type of the `data_type` field for `uint64`.""" + +Uint64FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint64`: a JSON integer in [0, 2**64 - 1].""" + + +__all__ = [ + "UINT64_DATA_TYPE_NAME", + "Uint64DataTypeName", + "Uint64FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py new file mode 100644 index 0000000000..787f1b7866 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/uint8.py @@ -0,0 +1,23 @@ +""" +Zarr v3 `uint8` data type. + +See https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html +""" + +from typing import Final, Literal + +UINT8_DATA_TYPE_NAME: Final = "uint8" +"""The `data_type` value for the `uint8` type.""" + +Uint8DataTypeName = Literal["uint8"] +"""Literal type of the `data_type` field for `uint8`.""" + +Uint8FillValue = int +"""Permitted JSON shape of the `fill_value` field for `uint8`: a JSON integer in [0, 255].""" + + +__all__ = [ + "UINT8_DATA_TYPE_NAME", + "Uint8DataTypeName", + "Uint8FillValue", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py new file mode 100644 index 0000000000..e7396f2615 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -0,0 +1,30 @@ +"""Zarr v3 group metadata types. + +See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#group-metadata +""" + +from collections.abc import Mapping +from typing import Literal, NotRequired + +from typing_extensions import TypedDict + +from zarr_metadata.v3.array import ExtensionFieldV3 + + +class GroupMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[call-arg] + """ + Zarr v3 group metadata document (the `zarr.json` content for a group). + + Extra keys are permitted if they conform to `ExtensionFieldV3`. + + See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#group-metadata + """ + + zarr_format: Literal[3] + node_type: Literal["group"] + attributes: NotRequired[Mapping[str, object]] + + +__all__ = [ + "GroupMetadataV3", +] diff --git a/packages/zarr-metadata/tests/__init__.py b/packages/zarr-metadata/tests/__init__.py new file mode 100644 index 0000000000..d886440736 --- /dev/null +++ b/packages/zarr-metadata/tests/__init__.py @@ -0,0 +1 @@ +"""Tests for zarr-metadata.""" diff --git a/packages/zarr-metadata/tests/test_version.py b/packages/zarr-metadata/tests/test_version.py new file mode 100644 index 0000000000..86b177963b --- /dev/null +++ b/packages/zarr-metadata/tests/test_version.py @@ -0,0 +1,16 @@ +"""Verify that `zarr_metadata.__version__` matches the installed +distribution metadata, which in turn comes from `pyproject.toml`. + +This catches the easy mistake of bumping the version in one place and +forgetting the other. +""" + +from __future__ import annotations + +from importlib.metadata import version + +import zarr_metadata + + +def test_version_matches_distribution_metadata() -> None: + assert zarr_metadata.__version__ == version("zarr-metadata") diff --git a/packages/zarr-metadata/tests/v2/__init__.py b/packages/zarr-metadata/tests/v2/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v2/array/__init__.py b/packages/zarr-metadata/tests/v2/array/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v2/array/blosc_compressor_with_filters.json b/packages/zarr-metadata/tests/v2/array/blosc_compressor_with_filters.json new file mode 100644 index 0000000000..f78add1a0b --- /dev/null +++ b/packages/zarr-metadata/tests/v2/array/blosc_compressor_with_filters.json @@ -0,0 +1,20 @@ +{ + "zarr_format": 2, + "shape": [200], + "chunks": [50], + "dtype": " None: + ADAPTER.validate_python(json.loads(fixture.read_text())) diff --git a/packages/zarr-metadata/tests/v2/consolidated/__init__.py b/packages/zarr-metadata/tests/v2/consolidated/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v2/consolidated/minimal.json b/packages/zarr-metadata/tests/v2/consolidated/minimal.json new file mode 100644 index 0000000000..fa5db0a584 --- /dev/null +++ b/packages/zarr-metadata/tests/v2/consolidated/minimal.json @@ -0,0 +1,4 @@ +{ + "zarr_consolidated_format": 1, + "metadata": {} +} diff --git a/packages/zarr-metadata/tests/v2/consolidated/test_fixtures.py b/packages/zarr-metadata/tests/v2/consolidated/test_fixtures.py new file mode 100644 index 0000000000..9dad66d074 --- /dev/null +++ b/packages/zarr-metadata/tests/v2/consolidated/test_fixtures.py @@ -0,0 +1,20 @@ +"""Decode v2 consolidated metadata fixtures via pydantic.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 + +FIXTURES_DIR = Path(__file__).parent +FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) +ADAPTER = TypeAdapter(ConsolidatedMetadataV2) + + +@pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) +def test_validate(fixture: Path) -> None: + ADAPTER.validate_python(json.loads(fixture.read_text())) diff --git a/packages/zarr-metadata/tests/v2/consolidated/with_array_and_group.json b/packages/zarr-metadata/tests/v2/consolidated/with_array_and_group.json new file mode 100644 index 0000000000..24a859cb1f --- /dev/null +++ b/packages/zarr-metadata/tests/v2/consolidated/with_array_and_group.json @@ -0,0 +1,17 @@ +{ + "zarr_consolidated_format": 1, + "metadata": { + ".zgroup": {"zarr_format": 2}, + "data/.zarray": { + "zarr_format": 2, + "shape": [100], + "chunks": [10], + "dtype": " None: + ADAPTER.validate_python(json.loads(fixture.read_text())) diff --git a/packages/zarr-metadata/tests/v3/__init__.py b/packages/zarr-metadata/tests/v3/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/array/__init__.py b/packages/zarr-metadata/tests/v3/array/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/array/blosc_codec.json b/packages/zarr-metadata/tests/v3/array/blosc_codec.json new file mode 100644 index 0000000000..7681474264 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/blosc_codec.json @@ -0,0 +1,27 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [1024], + "data_type": "int32", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [256]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + { + "name": "blosc", + "configuration": { + "cname": "zstd", + "clevel": 5, + "shuffle": "shuffle", + "blocksize": 0, + "typesize": 4 + } + } + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/datatype_named_config.json b/packages/zarr-metadata/tests/v3/array/datatype_named_config.json new file mode 100644 index 0000000000..b98964f38e --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/datatype_named_config.json @@ -0,0 +1,20 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [10], + "data_type": { + "name": "numpy.datetime64", + "configuration": {"unit": "ns", "scale_factor": 1} + }, + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [10]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/gzip_codec.json b/packages/zarr-metadata/tests/v3/array/gzip_codec.json new file mode 100644 index 0000000000..6c4455dcff --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/gzip_codec.json @@ -0,0 +1,18 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [128], + "data_type": "uint16", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [64]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "gzip", "configuration": {"level": 5}} + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/rectilinear_grid.json b/packages/zarr-metadata/tests/v3/array/rectilinear_grid.json new file mode 100644 index 0000000000..9a33b1469c --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/rectilinear_grid.json @@ -0,0 +1,23 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [100, 100], + "data_type": "float64", + "chunk_grid": { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": [ + [10, 20, 30, 40], + 50 + ] + } + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0.0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/rectilinear_grid_with_rle.json b/packages/zarr-metadata/tests/v3/array/rectilinear_grid_with_rle.json new file mode 100644 index 0000000000..c131554a36 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/rectilinear_grid_with_rle.json @@ -0,0 +1,24 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [60, 30], + "data_type": "int16", + "chunk_grid": { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": [ + [[10, 5], 5, 5], + [15, 15] + ] + } + }, + "chunk_key_encoding": { + "name": "default", + "configuration": {"separator": "/"} + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/regular_grid_default_encoding.json b/packages/zarr-metadata/tests/v3/array/regular_grid_default_encoding.json new file mode 100644 index 0000000000..73eb742d9b --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/regular_grid_default_encoding.json @@ -0,0 +1,18 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [100, 100], + "data_type": "int32", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [10, 10]} + }, + "chunk_key_encoding": { + "name": "default", + "configuration": {"separator": "/"} + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/regular_grid_v2_encoding.json b/packages/zarr-metadata/tests/v3/array/regular_grid_v2_encoding.json new file mode 100644 index 0000000000..6c09fdb954 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/regular_grid_v2_encoding.json @@ -0,0 +1,18 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [50], + "data_type": "uint8", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [25]} + }, + "chunk_key_encoding": { + "name": "v2", + "configuration": {"separator": "."} + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes"} + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/sharding_indexed_codec.json b/packages/zarr-metadata/tests/v3/array/sharding_indexed_codec.json new file mode 100644 index 0000000000..271e4d75a1 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/sharding_indexed_codec.json @@ -0,0 +1,31 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [1024, 1024], + "data_type": "uint16", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [256, 256]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0, + "codecs": [ + { + "name": "sharding_indexed", + "configuration": { + "chunk_shape": [64, 64], + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "gzip", "configuration": {"level": 1}} + ], + "index_codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "crc32c"} + ], + "index_location": "end" + } + } + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/test_fixtures.py b/packages/zarr-metadata/tests/v3/array/test_fixtures.py new file mode 100644 index 0000000000..fccd00d481 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/test_fixtures.py @@ -0,0 +1,27 @@ +"""Decode v3 array metadata fixtures via pydantic. + +Each `*.json` file in this directory is a representative on-disk +`zarr.json` that should validate cleanly as `ArrayMetadataV3`. +Fixtures are named for the variant they exercise (regular vs rectilinear +grid, blosc/gzip/zstd/sharding_indexed codecs, named-config dtypes, optional +fields, extra fields). +""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.array import ArrayMetadataV3 + +FIXTURES_DIR = Path(__file__).parent +FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) +ADAPTER = TypeAdapter(ArrayMetadataV3) + + +@pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) +def test_validate(fixture: Path) -> None: + ADAPTER.validate_python(json.loads(fixture.read_text())) diff --git a/packages/zarr-metadata/tests/v3/array/transpose_and_crc32c_codecs.json b/packages/zarr-metadata/tests/v3/array/transpose_and_crc32c_codecs.json new file mode 100644 index 0000000000..3276d5a471 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/transpose_and_crc32c_codecs.json @@ -0,0 +1,19 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [10, 20, 30], + "data_type": "float32", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [5, 10, 15]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": "NaN", + "codecs": [ + {"name": "transpose", "configuration": {"order": [2, 1, 0]}}, + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "crc32c"} + ] +} diff --git a/packages/zarr-metadata/tests/v3/array/with_extra_field.json b/packages/zarr-metadata/tests/v3/array/with_extra_field.json new file mode 100644 index 0000000000..46a7f0f235 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/with_extra_field.json @@ -0,0 +1,21 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [10], + "data_type": "int32", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [10]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ], + "my_custom_extension": { + "must_understand": false, + "purpose": "exercise the extra_items=ExtensionFieldV3 path" + } +} diff --git a/packages/zarr-metadata/tests/v3/array/with_optionals.json b/packages/zarr-metadata/tests/v3/array/with_optionals.json new file mode 100644 index 0000000000..0c4c60986f --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/with_optionals.json @@ -0,0 +1,24 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [10, 20, 30], + "data_type": "float64", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [5, 10, 15]} + }, + "chunk_key_encoding": { + "name": "default", + "configuration": {"separator": "/"} + }, + "fill_value": "NaN", + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ], + "attributes": { + "description": "fixture exercising optional fields", + "tags": ["test", "metadata"] + }, + "dimension_names": ["t", "y", "x"], + "storage_transformers": [] +} diff --git a/packages/zarr-metadata/tests/v3/array/zstd_codec.json b/packages/zarr-metadata/tests/v3/array/zstd_codec.json new file mode 100644 index 0000000000..03de6a9420 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/array/zstd_codec.json @@ -0,0 +1,18 @@ +{ + "zarr_format": 3, + "node_type": "array", + "shape": [128], + "data_type": "int8", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [64]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes"}, + {"name": "zstd", "configuration": {"level": 3, "checksum": false}} + ] +} diff --git a/packages/zarr-metadata/tests/v3/chunk_grid/__init__.py b/packages/zarr-metadata/tests/v3/chunk_grid/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/__init__.py b/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/cases.json b/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/cases.json new file mode 100644 index 0000000000..c01580c17a --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/cases.json @@ -0,0 +1,32 @@ +{ + "explicit_per_dim": { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": [ + [10, 20, 30, 40], + [50] + ] + } + }, + "uniform_dim_shorthand": { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": [ + [10, 20, 30, 40], + 50 + ] + } + }, + "with_rle_pair": { + "name": "rectilinear", + "configuration": { + "kind": "inline", + "chunk_shapes": [ + [[10, 5], 5, 5], + [15, 15] + ] + } + } +} diff --git a/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/test_fixtures.py b/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/test_fixtures.py new file mode 100644 index 0000000000..cdef26d0a3 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_grid/rectilinear/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate rectilinear chunk grid fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.chunk_grid.rectilinear import RectilinearChunkGridMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_chunk_grid(case: object) -> None: + TypeAdapter(RectilinearChunkGridMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/chunk_grid/regular/__init__.py b/packages/zarr-metadata/tests/v3/chunk_grid/regular/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/chunk_grid/regular/cases.json b/packages/zarr-metadata/tests/v3/chunk_grid/regular/cases.json new file mode 100644 index 0000000000..2ffdef9007 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_grid/regular/cases.json @@ -0,0 +1,14 @@ +{ + "1d": { + "name": "regular", + "configuration": {"chunk_shape": [10]} + }, + "2d": { + "name": "regular", + "configuration": {"chunk_shape": [10, 20]} + }, + "3d": { + "name": "regular", + "configuration": {"chunk_shape": [5, 10, 15]} + } +} diff --git a/packages/zarr-metadata/tests/v3/chunk_grid/regular/test_fixtures.py b/packages/zarr-metadata/tests/v3/chunk_grid/regular/test_fixtures.py new file mode 100644 index 0000000000..9fba28d3ce --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_grid/regular/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate regular chunk grid fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.chunk_grid.regular import RegularChunkGridMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_chunk_grid(case: object) -> None: + TypeAdapter(RegularChunkGridMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/chunk_key_encoding/__init__.py b/packages/zarr-metadata/tests/v3/chunk_key_encoding/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/__init__.py b/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/cases.json b/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/cases.json new file mode 100644 index 0000000000..db9d8f61de --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/cases.json @@ -0,0 +1,14 @@ +{ + "no_configuration": { + "name": "default" + }, + "slash_separator": { + "name": "default", + "configuration": {"separator": "/"} + }, + "dot_separator": { + "name": "default", + "configuration": {"separator": "."} + }, + "short_hand_name": "default" +} diff --git a/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/test_fixtures.py b/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/test_fixtures.py new file mode 100644 index 0000000000..6618df0dd0 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_key_encoding/default/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate default chunk-key encoding fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.chunk_key_encoding.default import DefaultChunkKeyEncodingMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_chunk_key_encoding(case: object) -> None: + TypeAdapter(DefaultChunkKeyEncodingMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/__init__.py b/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/cases.json b/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/cases.json new file mode 100644 index 0000000000..4ba65a6730 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/cases.json @@ -0,0 +1,14 @@ +{ + "no_configuration": { + "name": "v2" + }, + "dot_separator": { + "name": "v2", + "configuration": {"separator": "."} + }, + "slash_separator": { + "name": "v2", + "configuration": {"separator": "/"} + }, + "short_hand_name": "v2" +} diff --git a/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/test_fixtures.py b/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/test_fixtures.py new file mode 100644 index 0000000000..7f43495239 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/chunk_key_encoding/v2/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate v2-compatibility chunk-key encoding fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.chunk_key_encoding.v2 import V2ChunkKeyEncodingMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_chunk_key_encoding(case: object) -> None: + TypeAdapter(V2ChunkKeyEncodingMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/__init__.py b/packages/zarr-metadata/tests/v3/codec/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/blosc/__init__.py b/packages/zarr-metadata/tests/v3/codec/blosc/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/blosc/cases.json b/packages/zarr-metadata/tests/v3/codec/blosc/cases.json new file mode 100644 index 0000000000..20b476764a --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/blosc/cases.json @@ -0,0 +1,21 @@ +{ + "with_typesize": { + "name": "blosc", + "configuration": { + "cname": "zstd", + "clevel": 5, + "shuffle": "shuffle", + "blocksize": 0, + "typesize": 4 + } + }, + "no_typesize": { + "name": "blosc", + "configuration": { + "cname": "lz4", + "clevel": 1, + "shuffle": "noshuffle", + "blocksize": 0 + } + } +} diff --git a/packages/zarr-metadata/tests/v3/codec/blosc/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/blosc/test_fixtures.py new file mode 100644 index 0000000000..bdac8c32b0 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/blosc/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate blosc codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.blosc import BloscCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(BloscCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/bytes/__init__.py b/packages/zarr-metadata/tests/v3/codec/bytes/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/bytes/cases.json b/packages/zarr-metadata/tests/v3/codec/bytes/cases.json new file mode 100644 index 0000000000..f3c8b978f8 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/bytes/cases.json @@ -0,0 +1,15 @@ +{ + "little_endian": { + "name": "bytes", + "configuration": {"endian": "little"} + }, + "big_endian": { + "name": "bytes", + "configuration": {"endian": "big"} + }, + "no_endian": { + "name": "bytes", + "configuration": {} + }, + "short_hand_name": "bytes" +} diff --git a/packages/zarr-metadata/tests/v3/codec/bytes/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/bytes/test_fixtures.py new file mode 100644 index 0000000000..ec725e9ba0 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/bytes/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate bytes codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.bytes import BytesCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(BytesCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/cast_value/__init__.py b/packages/zarr-metadata/tests/v3/codec/cast_value/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/cast_value/cases.json b/packages/zarr-metadata/tests/v3/codec/cast_value/cases.json new file mode 100644 index 0000000000..90771d5f76 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/cast_value/cases.json @@ -0,0 +1,60 @@ +{ + "minimal": { + "name": "cast_value", + "configuration": {"data_type": "uint8"} + }, + "named_config_dtype": { + "name": "cast_value", + "configuration": { + "data_type": { + "name": "numpy.datetime64", + "configuration": {"unit": "ns", "scale_factor": 1} + } + } + }, + "with_rounding": { + "name": "cast_value", + "configuration": { + "data_type": "int16", + "rounding": "towards-zero" + } + }, + "with_out_of_range_clamp": { + "name": "cast_value", + "configuration": { + "data_type": "int8", + "out_of_range": "clamp" + } + }, + "with_out_of_range_wrap": { + "name": "cast_value", + "configuration": { + "data_type": "uint8", + "out_of_range": "wrap" + } + }, + "with_scalar_map_encode_only": { + "name": "cast_value", + "configuration": { + "data_type": "uint8", + "scalar_map": { + "encode": [["NaN", 0]] + } + } + }, + "numpy_compat_full_example": { + "name": "cast_value", + "configuration": { + "data_type": "uint8", + "rounding": "towards-zero", + "out_of_range": "wrap", + "scalar_map": { + "encode": [ + ["NaN", 0], + ["+Infinity", 0], + ["-Infinity", 0] + ] + } + } + } +} diff --git a/packages/zarr-metadata/tests/v3/codec/cast_value/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/cast_value/test_fixtures.py new file mode 100644 index 0000000000..695e25f883 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/cast_value/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate cast_value codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.cast_value import CastValueCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(CastValueCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/crc32c/__init__.py b/packages/zarr-metadata/tests/v3/codec/crc32c/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/crc32c/cases.json b/packages/zarr-metadata/tests/v3/codec/crc32c/cases.json new file mode 100644 index 0000000000..af89eed012 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/crc32c/cases.json @@ -0,0 +1,10 @@ +{ + "no_configuration": { + "name": "crc32c" + }, + "empty_configuration": { + "name": "crc32c", + "configuration": {} + }, + "short_hand_name": "crc32c" +} diff --git a/packages/zarr-metadata/tests/v3/codec/crc32c/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/crc32c/test_fixtures.py new file mode 100644 index 0000000000..906daae6da --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/crc32c/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate crc32c codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.crc32c import Crc32cCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(Crc32cCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/gzip/__init__.py b/packages/zarr-metadata/tests/v3/codec/gzip/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/gzip/cases.json b/packages/zarr-metadata/tests/v3/codec/gzip/cases.json new file mode 100644 index 0000000000..b40cbeeedb --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/gzip/cases.json @@ -0,0 +1,11 @@ +{ + "with_level": { + "name": "gzip", + "configuration": {"level": 5} + }, + "no_level": { + "name": "gzip", + "configuration": {} + }, + "short_hand_name": "gzip" +} diff --git a/packages/zarr-metadata/tests/v3/codec/gzip/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/gzip/test_fixtures.py new file mode 100644 index 0000000000..e198971ee7 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/gzip/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate gzip codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.gzip import GzipCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(GzipCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/scale_offset/__init__.py b/packages/zarr-metadata/tests/v3/codec/scale_offset/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/scale_offset/cases.json b/packages/zarr-metadata/tests/v3/codec/scale_offset/cases.json new file mode 100644 index 0000000000..c96e214007 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/scale_offset/cases.json @@ -0,0 +1,26 @@ +{ + "no_configuration": { + "name": "scale_offset" + }, + "empty_configuration": { + "name": "scale_offset", + "configuration": {} + }, + "offset_only": { + "name": "scale_offset", + "configuration": {"offset": 5} + }, + "scale_only": { + "name": "scale_offset", + "configuration": {"scale": 0.1} + }, + "scale_and_offset": { + "name": "scale_offset", + "configuration": {"offset": 5, "scale": 0.1} + }, + "string_encoded_scalar": { + "name": "scale_offset", + "configuration": {"offset": "NaN"} + }, + "short_hand_name": "scale_offset" +} diff --git a/packages/zarr-metadata/tests/v3/codec/scale_offset/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/scale_offset/test_fixtures.py new file mode 100644 index 0000000000..e0e62b9d56 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/scale_offset/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate scale_offset codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.scale_offset import ScaleOffsetCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(ScaleOffsetCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/sharding_indexed/__init__.py b/packages/zarr-metadata/tests/v3/codec/sharding_indexed/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/sharding_indexed/cases.json b/packages/zarr-metadata/tests/v3/codec/sharding_indexed/cases.json new file mode 100644 index 0000000000..2862dae4a7 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/sharding_indexed/cases.json @@ -0,0 +1,30 @@ +{ + "with_index_location": { + "name": "sharding_indexed", + "configuration": { + "chunk_shape": [64, 64], + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "gzip", "configuration": {"level": 1}} + ], + "index_codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "crc32c"} + ], + "index_location": "end" + } + }, + "no_index_location": { + "name": "sharding_indexed", + "configuration": { + "chunk_shape": [128], + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ], + "index_codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}}, + {"name": "crc32c"} + ] + } + } +} diff --git a/packages/zarr-metadata/tests/v3/codec/sharding_indexed/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/sharding_indexed/test_fixtures.py new file mode 100644 index 0000000000..e3e61e9e4d --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/sharding_indexed/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate sharding_indexed codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.sharding_indexed import ShardingIndexedCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(ShardingIndexedCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/transpose/__init__.py b/packages/zarr-metadata/tests/v3/codec/transpose/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/transpose/cases.json b/packages/zarr-metadata/tests/v3/codec/transpose/cases.json new file mode 100644 index 0000000000..6adcc6948a --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/transpose/cases.json @@ -0,0 +1,6 @@ +{ + "reversed_3d": { + "name": "transpose", + "configuration": {"order": [2, 1, 0]} + } +} diff --git a/packages/zarr-metadata/tests/v3/codec/transpose/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/transpose/test_fixtures.py new file mode 100644 index 0000000000..4bd7c99bc8 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/transpose/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate transpose codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.transpose import TransposeCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(TransposeCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/codec/zstd/__init__.py b/packages/zarr-metadata/tests/v3/codec/zstd/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/codec/zstd/cases.json b/packages/zarr-metadata/tests/v3/codec/zstd/cases.json new file mode 100644 index 0000000000..77733fe054 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/zstd/cases.json @@ -0,0 +1,6 @@ +{ + "default": { + "name": "zstd", + "configuration": {"level": 3, "checksum": false} + } +} diff --git a/packages/zarr-metadata/tests/v3/codec/zstd/test_fixtures.py b/packages/zarr-metadata/tests/v3/codec/zstd/test_fixtures.py new file mode 100644 index 0000000000..a1981211a3 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/codec/zstd/test_fixtures.py @@ -0,0 +1,18 @@ +"""Validate zstd codec fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.codec.zstd import ZstdCodecMetadata + +CASES: dict[str, object] = json.loads((Path(__file__).parent / "cases.json").read_text()) + + +@pytest.mark.parametrize("case", CASES.values(), ids=list(CASES)) +def test_codec(case: object) -> None: + TypeAdapter(ZstdCodecMetadata).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/consolidated/__init__.py b/packages/zarr-metadata/tests/v3/consolidated/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/consolidated/minimal.json b/packages/zarr-metadata/tests/v3/consolidated/minimal.json new file mode 100644 index 0000000000..1f2ab2ad61 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/consolidated/minimal.json @@ -0,0 +1,5 @@ +{ + "kind": "inline", + "must_understand": false, + "metadata": {} +} diff --git a/packages/zarr-metadata/tests/v3/consolidated/test_fixtures.py b/packages/zarr-metadata/tests/v3/consolidated/test_fixtures.py new file mode 100644 index 0000000000..4d9e300bae --- /dev/null +++ b/packages/zarr-metadata/tests/v3/consolidated/test_fixtures.py @@ -0,0 +1,20 @@ +"""Decode v3 consolidated metadata fixtures via pydantic.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 + +FIXTURES_DIR = Path(__file__).parent +FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) +ADAPTER = TypeAdapter(ConsolidatedMetadataV3) + + +@pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) +def test_validate(fixture: Path) -> None: + ADAPTER.validate_python(json.loads(fixture.read_text())) diff --git a/packages/zarr-metadata/tests/v3/consolidated/with_array_and_group.json b/packages/zarr-metadata/tests/v3/consolidated/with_array_and_group.json new file mode 100644 index 0000000000..65ac70f7ac --- /dev/null +++ b/packages/zarr-metadata/tests/v3/consolidated/with_array_and_group.json @@ -0,0 +1,27 @@ +{ + "kind": "inline", + "must_understand": false, + "metadata": { + "child_group": { + "zarr_format": 3, + "node_type": "group" + }, + "child_array": { + "zarr_format": 3, + "node_type": "array", + "shape": [10], + "data_type": "int32", + "chunk_grid": { + "name": "regular", + "configuration": {"chunk_shape": [10]} + }, + "chunk_key_encoding": { + "name": "default" + }, + "fill_value": 0, + "codecs": [ + {"name": "bytes", "configuration": {"endian": "little"}} + ] + } + } +} diff --git a/packages/zarr-metadata/tests/v3/data_type/__init__.py b/packages/zarr-metadata/tests/v3/data_type/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/bool/__init__.py b/packages/zarr-metadata/tests/v3/data_type/bool/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/bool/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/bool/fill_values.json new file mode 100644 index 0000000000..955baa58cc --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/bool/fill_values.json @@ -0,0 +1,4 @@ +{ + "true": true, + "false": false +} diff --git a/packages/zarr-metadata/tests/v3/data_type/bool/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/bool/test_fixtures.py new file mode 100644 index 0000000000..e924015b1d --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/bool/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate bool fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.bool import BoolFillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(BoolFillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/bytes/__init__.py b/packages/zarr-metadata/tests/v3/data_type/bytes/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/bytes/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/bytes/fill_values.json new file mode 100644 index 0000000000..6e55b7313c --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/bytes/fill_values.json @@ -0,0 +1,4 @@ +{ + "tuple": [1, 2, 3], + "base64": "AQID" +} diff --git a/packages/zarr-metadata/tests/v3/data_type/bytes/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/bytes/test_fixtures.py new file mode 100644 index 0000000000..9ee62fb140 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/bytes/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate variable-length bytes fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.bytes import BytesFillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(BytesFillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/bytes/test_validators.py b/packages/zarr-metadata/tests/v3/data_type/bytes/test_validators.py new file mode 100644 index 0000000000..7f41d878f8 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/bytes/test_validators.py @@ -0,0 +1,43 @@ +"""Cover the `base64_bytes` brand validator. + +The pydantic-driven fixture tests don't enforce the base64 alphabet or +length-multiple-of-4 constraint because `Base64Bytes` is a `NewType`, +which pydantic treats as plain `str`. Direct coverage of the validator +function lives here. +""" + +from __future__ import annotations + +import pytest + +from zarr_metadata.v3.data_type.bytes import base64_bytes + +VALID = [ + "", # empty is valid base64 (length 0, multiple of 4) + "AQID", # [1, 2, 3] + "AAAA", # [0, 0, 0] + "////", # [255, 255, 255] + "abcd", + "AB==", # padding + "ABC=", # padding +] +INVALID = [ + "AB", # length 2, not multiple of 4 + "ABC", # length 3, not multiple of 4 + "ABCDE", # length 5 + "AB-D", # url-safe alphabet, not standard + "AB_D", # url-safe alphabet, not standard + "AB!D", # not base64 char + "AB CD", # whitespace +] + + +@pytest.mark.parametrize("value", VALID) +def test_valid(value: str) -> None: + assert base64_bytes(value) == value + + +@pytest.mark.parametrize("value", INVALID) +def test_invalid(value: str) -> None: + with pytest.raises(ValueError, match="standard-alphabet base64"): + base64_bytes(value) diff --git a/packages/zarr-metadata/tests/v3/data_type/complex128/__init__.py b/packages/zarr-metadata/tests/v3/data_type/complex128/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/complex128/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/complex128/fill_values.json new file mode 100644 index 0000000000..c30f15a55c --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/complex128/fill_values.json @@ -0,0 +1,7 @@ +{ + "numeric": [1.5, 2.5], + "zero": [0.0, 0.0], + "with_sentinel_components": ["-Infinity", "NaN"], + "mixed_numeric_and_sentinel": [1.0, "Infinity"], + "with_hex_components": ["0x7ff8000000000000", "0x0000000000000000"] +} diff --git a/packages/zarr-metadata/tests/v3/data_type/complex128/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/complex128/test_fixtures.py new file mode 100644 index 0000000000..3536dc6ef3 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/complex128/test_fixtures.py @@ -0,0 +1,26 @@ +"""Validate complex128 fill-value fixtures. + +A v3 complex fill_value is a two-element JSON array `[real, imag]` where +each component is shaped per the corresponding float's fill value: a +number, one of the named sentinels (`"NaN"`, `"Infinity"`, +`"-Infinity"`), or a hex string of the underlying float's bits. +""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.complex128 import Complex128FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Complex128FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/complex64/__init__.py b/packages/zarr-metadata/tests/v3/data_type/complex64/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/complex64/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/complex64/fill_values.json new file mode 100644 index 0000000000..65d302f496 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/complex64/fill_values.json @@ -0,0 +1,7 @@ +{ + "numeric": [1.5, 2.5], + "zero": [0.0, 0.0], + "with_sentinel_components": ["-Infinity", "NaN"], + "mixed_numeric_and_sentinel": [1.0, "Infinity"], + "with_hex_components": ["0x7fc00000", "0x00000000"] +} diff --git a/packages/zarr-metadata/tests/v3/data_type/complex64/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/complex64/test_fixtures.py new file mode 100644 index 0000000000..83682c74b1 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/complex64/test_fixtures.py @@ -0,0 +1,26 @@ +"""Validate complex64 fill-value fixtures. + +A v3 complex fill_value is a two-element JSON array `[real, imag]` where +each component is shaped per the corresponding float's fill value: a +number, one of the named sentinels (`"NaN"`, `"Infinity"`, +`"-Infinity"`), or a hex string of the underlying float's bits. +""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.complex64 import Complex64FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Complex64FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/float16/__init__.py b/packages/zarr-metadata/tests/v3/data_type/float16/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/float16/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/float16/fill_values.json new file mode 100644 index 0000000000..07034ffba5 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float16/fill_values.json @@ -0,0 +1,8 @@ +{ + "zero": 0.0, + "nan": "NaN", + "infinity": "Infinity", + "neg_infinity": "-Infinity", + "hex_zero": "0x0000", + "hex_signaling_nan": "0x7d00" +} diff --git a/packages/zarr-metadata/tests/v3/data_type/float16/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/float16/test_fixtures.py new file mode 100644 index 0000000000..2241398fb3 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float16/test_fixtures.py @@ -0,0 +1,26 @@ +"""Validate float16 fill-value fixtures. + +A v3 float fill_value is a JSON number, one of the named non-finite +sentinels (`"NaN"`, `"Infinity"`, `"-Infinity"`), or a hex string +(`"0xYYYY"`) encoding the unsigned-integer representation of the IEEE +754 value. +""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.float16 import Float16FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Float16FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/float16/test_validators.py b/packages/zarr-metadata/tests/v3/data_type/float16/test_validators.py new file mode 100644 index 0000000000..c710f27ea4 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float16/test_validators.py @@ -0,0 +1,34 @@ +"""Cover the `hex_float16` brand validator. + +The pydantic-driven fixture tests don't enforce hex format because +`HexFloat16` is a `NewType`, which pydantic treats as plain `str`. +Direct coverage of the validator function lives here. +""" + +from __future__ import annotations + +import pytest + +from zarr_metadata.v3.data_type.float16 import hex_float16 + +VALID = ["0x0000", "0x7c00", "0x7d00", "0xffff", "0xFFFF", "0xAbCd"] +INVALID = [ + "", + "0000", # missing 0x + "0x000", # too short + "0x00000", # too long + "0x000g", # non-hex char + "0X0000", # uppercase X + " 0x0000 ", # whitespace +] + + +@pytest.mark.parametrize("value", VALID) +def test_valid(value: str) -> None: + assert hex_float16(value) == value + + +@pytest.mark.parametrize("value", INVALID) +def test_invalid(value: str) -> None: + with pytest.raises(ValueError, match="Expected '0x'"): + hex_float16(value) diff --git a/packages/zarr-metadata/tests/v3/data_type/float32/__init__.py b/packages/zarr-metadata/tests/v3/data_type/float32/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/float32/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/float32/fill_values.json new file mode 100644 index 0000000000..ed6502f85a --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float32/fill_values.json @@ -0,0 +1,9 @@ +{ + "zero": 0.0, + "nan": "NaN", + "infinity": "Infinity", + "neg_infinity": "-Infinity", + "hex_zero": "0x00000000", + "hex_canonical_nan": "0x7fc00000", + "hex_signaling_nan": "0x7fa00000" +} diff --git a/packages/zarr-metadata/tests/v3/data_type/float32/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/float32/test_fixtures.py new file mode 100644 index 0000000000..bd943bd96e --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float32/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate float32 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.float32 import Float32FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Float32FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/float32/test_validators.py b/packages/zarr-metadata/tests/v3/data_type/float32/test_validators.py new file mode 100644 index 0000000000..e859d91c26 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float32/test_validators.py @@ -0,0 +1,41 @@ +"""Cover the `hex_float32` brand validator. + +The pydantic-driven fixture tests don't enforce hex format because +`HexFloat32` is a `NewType`, which pydantic treats as plain `str`. +Direct coverage of the validator function lives here. +""" + +from __future__ import annotations + +import pytest + +from zarr_metadata.v3.data_type.float32 import hex_float32 + +VALID = [ + "0x00000000", + "0x7fc00000", # canonical NaN + "0x7fa00000", # signaling NaN + "0xffffffff", + "0xFFFFFFFF", + "0xDeadBeef", +] +INVALID = [ + "", + "00000000", # missing 0x + "0x0000000", # too short + "0x000000000", # too long + "0x0000000g", # non-hex char + "0X00000000", # uppercase X + " 0x00000000 ", # whitespace +] + + +@pytest.mark.parametrize("value", VALID) +def test_valid(value: str) -> None: + assert hex_float32(value) == value + + +@pytest.mark.parametrize("value", INVALID) +def test_invalid(value: str) -> None: + with pytest.raises(ValueError, match="Expected '0x'"): + hex_float32(value) diff --git a/packages/zarr-metadata/tests/v3/data_type/float64/__init__.py b/packages/zarr-metadata/tests/v3/data_type/float64/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/float64/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/float64/fill_values.json new file mode 100644 index 0000000000..76da958c63 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float64/fill_values.json @@ -0,0 +1,9 @@ +{ + "zero": 0.0, + "nan": "NaN", + "infinity": "Infinity", + "neg_infinity": "-Infinity", + "hex_zero": "0x0000000000000000", + "hex_canonical_nan": "0x7ff8000000000000", + "hex_signaling_nan": "0x7ff4000000000000" +} diff --git a/packages/zarr-metadata/tests/v3/data_type/float64/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/float64/test_fixtures.py new file mode 100644 index 0000000000..2e4566ae58 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float64/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate float64 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.float64 import Float64FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Float64FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/float64/test_validators.py b/packages/zarr-metadata/tests/v3/data_type/float64/test_validators.py new file mode 100644 index 0000000000..938bf2a1a5 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/float64/test_validators.py @@ -0,0 +1,41 @@ +"""Cover the `hex_float64` brand validator. + +The pydantic-driven fixture tests don't enforce hex format because +`HexFloat64` is a `NewType`, which pydantic treats as plain `str`. +Direct coverage of the validator function lives here. +""" + +from __future__ import annotations + +import pytest + +from zarr_metadata.v3.data_type.float64 import hex_float64 + +VALID = [ + "0x0000000000000000", + "0x7ff8000000000000", # canonical NaN + "0x7ff4000000000000", # signaling NaN + "0xffffffffffffffff", + "0xFFFFFFFFFFFFFFFF", + "0xDeadBeefCafeBabe", +] +INVALID = [ + "", + "0000000000000000", # missing 0x + "0x000000000000000", # too short + "0x00000000000000000", # too long + "0x000000000000000g", # non-hex char + "0X0000000000000000", # uppercase X + " 0x0000000000000000 ", # whitespace +] + + +@pytest.mark.parametrize("value", VALID) +def test_valid(value: str) -> None: + assert hex_float64(value) == value + + +@pytest.mark.parametrize("value", INVALID) +def test_invalid(value: str) -> None: + with pytest.raises(ValueError, match="Expected '0x'"): + hex_float64(value) diff --git a/packages/zarr-metadata/tests/v3/data_type/int16/__init__.py b/packages/zarr-metadata/tests/v3/data_type/int16/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/int16/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/int16/fill_values.json new file mode 100644 index 0000000000..af8304c51b --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int16/fill_values.json @@ -0,0 +1,6 @@ +{ + "zero": 0, + "min": -32768, + "max": 32767, + "negative": -1 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/int16/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/int16/test_fixtures.py new file mode 100644 index 0000000000..2149947c2d --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int16/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate int16 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.int16 import Int16FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Int16FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/int32/__init__.py b/packages/zarr-metadata/tests/v3/data_type/int32/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/int32/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/int32/fill_values.json new file mode 100644 index 0000000000..d0bf317770 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int32/fill_values.json @@ -0,0 +1,6 @@ +{ + "zero": 0, + "min": -2147483648, + "max": 2147483647, + "negative": -1 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/int32/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/int32/test_fixtures.py new file mode 100644 index 0000000000..b1dbb6d370 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int32/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate int32 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.int32 import Int32FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Int32FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/int64/__init__.py b/packages/zarr-metadata/tests/v3/data_type/int64/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/int64/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/int64/fill_values.json new file mode 100644 index 0000000000..a97c5b3f34 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int64/fill_values.json @@ -0,0 +1,6 @@ +{ + "zero": 0, + "min": -9223372036854775808, + "max": 9223372036854775807, + "negative": -1 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/int64/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/int64/test_fixtures.py new file mode 100644 index 0000000000..957bf2296b --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int64/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate int64 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.int64 import Int64FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Int64FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/int8/__init__.py b/packages/zarr-metadata/tests/v3/data_type/int8/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/int8/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/int8/fill_values.json new file mode 100644 index 0000000000..716f347c19 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int8/fill_values.json @@ -0,0 +1,6 @@ +{ + "zero": 0, + "min": -128, + "max": 127, + "negative": -1 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/int8/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/int8/test_fixtures.py new file mode 100644 index 0000000000..ef9438dad0 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/int8/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate int8 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.int8 import Int8FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Int8FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/__init__.py b/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/data_type.json b/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/data_type.json new file mode 100644 index 0000000000..f94c1b45da --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/data_type.json @@ -0,0 +1,7 @@ +{ + "name": "numpy.datetime64", + "configuration": { + "unit": "ns", + "scale_factor": 1 + } +} diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/fill_values.json new file mode 100644 index 0000000000..b628657396 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/fill_values.json @@ -0,0 +1,4 @@ +{ + "int": 12345, + "nat": "NaT" +} diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/test_fixtures.py new file mode 100644 index 0000000000..7609b42d70 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/numpy_datetime64/test_fixtures.py @@ -0,0 +1,26 @@ +"""Validate numpy.datetime64 dtype value and fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.numpy_datetime64 import ( + NumpyDatetime64, + NumpyDatetime64FillValue, +) + +DIR = Path(__file__).parent +FILL_VALUES: dict[str, object] = json.loads((DIR / "fill_values.json").read_text()) + + +def test_data_type() -> None: + TypeAdapter(NumpyDatetime64).validate_python(json.loads((DIR / "data_type.json").read_text())) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(NumpyDatetime64FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/__init__.py b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/data_type.json b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/data_type.json new file mode 100644 index 0000000000..e49ec06e39 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/data_type.json @@ -0,0 +1,7 @@ +{ + "name": "numpy.timedelta64", + "configuration": { + "unit": "s", + "scale_factor": 1 + } +} diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/fill_values.json new file mode 100644 index 0000000000..cd3c94c077 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/fill_values.json @@ -0,0 +1,4 @@ +{ + "int": 42, + "nat": "NaT" +} diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/test_fixtures.py new file mode 100644 index 0000000000..1d4bd86a2d --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/test_fixtures.py @@ -0,0 +1,26 @@ +"""Validate numpy.timedelta64 dtype value and fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.numpy_timedelta64 import ( + NumpyTimedelta64, + NumpyTimedelta64FillValue, +) + +DIR = Path(__file__).parent +FILL_VALUES: dict[str, object] = json.loads((DIR / "fill_values.json").read_text()) + + +def test_data_type() -> None: + TypeAdapter(NumpyTimedelta64).validate_python(json.loads((DIR / "data_type.json").read_text())) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(NumpyTimedelta64FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/raw/__init__.py b/packages/zarr-metadata/tests/v3/data_type/raw/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/raw/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/raw/fill_values.json new file mode 100644 index 0000000000..60cf0760fc --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/raw/fill_values.json @@ -0,0 +1,3 @@ +{ + "all_zero_4_bytes": [0, 0, 0, 0] +} diff --git a/packages/zarr-metadata/tests/v3/data_type/raw/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/raw/test_fixtures.py new file mode 100644 index 0000000000..ee35ebe267 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/raw/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate raw-bytes (`r`) fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.raw import RawBytesFillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(RawBytesFillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/raw/test_validators.py b/packages/zarr-metadata/tests/v3/data_type/raw/test_validators.py new file mode 100644 index 0000000000..c1524aed96 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/raw/test_validators.py @@ -0,0 +1,33 @@ +"""Cover the `raw_bytes_dtype_name` brand validator. + +The pydantic-driven fixture tests don't enforce the `r` shape +because `RawBytesDataTypeName` is a `NewType`, which pydantic treats +as plain `str`. Direct coverage of the validator function lives here. +""" + +from __future__ import annotations + +import pytest + +from zarr_metadata.v3.data_type.raw import raw_bytes_dtype_name + +VALID = ["r8", "r16", "r24", "r256", "r1024"] +INVALID_FORMAT = ["", "8", "R8", "r", "r-8", "r8 ", " r8", "r8r8"] +INVALID_BITS = ["r0", "r1", "r7", "r9", "r15", "r17"] + + +@pytest.mark.parametrize("value", VALID) +def test_valid(value: str) -> None: + assert raw_bytes_dtype_name(value) == value + + +@pytest.mark.parametrize("value", INVALID_FORMAT) +def test_invalid_format(value: str) -> None: + with pytest.raises(ValueError, match="Expected 'r' followed by"): + raw_bytes_dtype_name(value) + + +@pytest.mark.parametrize("value", INVALID_BITS) +def test_invalid_bit_count(value: str) -> None: + with pytest.raises(ValueError, match="positive multiple of 8"): + raw_bytes_dtype_name(value) diff --git a/packages/zarr-metadata/tests/v3/data_type/string/__init__.py b/packages/zarr-metadata/tests/v3/data_type/string/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/string/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/string/fill_values.json new file mode 100644 index 0000000000..d9dfba1658 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/string/fill_values.json @@ -0,0 +1,6 @@ +{ + "empty": "", + "ascii": "hello", + "unicode": "héllo 世界", + "with_escapes": "line1\nline2\t\"quoted\"" +} diff --git a/packages/zarr-metadata/tests/v3/data_type/string/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/string/test_fixtures.py new file mode 100644 index 0000000000..69a8038bdd --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/string/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate string fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.string import StringFillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(StringFillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/struct/__init__.py b/packages/zarr-metadata/tests/v3/data_type/struct/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/struct/data_type.json b/packages/zarr-metadata/tests/v3/data_type/struct/data_type.json new file mode 100644 index 0000000000..999326076e --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/struct/data_type.json @@ -0,0 +1,16 @@ +{ + "name": "struct", + "configuration": { + "fields": [ + {"name": "x", "data_type": "float32"}, + {"name": "y", "data_type": "float32"}, + { + "name": "when", + "data_type": { + "name": "numpy.datetime64", + "configuration": {"unit": "ns", "scale_factor": 1} + } + } + ] + } +} diff --git a/packages/zarr-metadata/tests/v3/data_type/struct/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/struct/fill_values.json new file mode 100644 index 0000000000..e658d70af0 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/struct/fill_values.json @@ -0,0 +1,7 @@ +{ + "all_fields": { + "x": 0.0, + "y": 1.0, + "when": 0 + } +} diff --git a/packages/zarr-metadata/tests/v3/data_type/struct/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/struct/test_fixtures.py new file mode 100644 index 0000000000..15e6257fc1 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/struct/test_fixtures.py @@ -0,0 +1,23 @@ +"""Validate struct dtype value and fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.struct import Struct, StructFillValue + +DIR = Path(__file__).parent +FILL_VALUES: dict[str, object] = json.loads((DIR / "fill_values.json").read_text()) + + +def test_data_type() -> None: + TypeAdapter(Struct).validate_python(json.loads((DIR / "data_type.json").read_text())) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(StructFillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/test_dtype_names.py b/packages/zarr-metadata/tests/v3/data_type/test_dtype_names.py new file mode 100644 index 0000000000..152c1b5fdc --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/test_dtype_names.py @@ -0,0 +1,61 @@ +"""Validate every primitive Zarr v3 data-type name string. + +Primitive dtypes are encoded as bare strings in the `data_type` field of a +v3 array metadata document (e.g. `"int32"`, `"float64"`). Each must +validate as its declared per-dtype `*Name` literal type. +""" + +from __future__ import annotations + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.bool import BOOL_DATA_TYPE_NAME, BoolDataTypeName +from zarr_metadata.v3.data_type.bytes import BYTES_DATA_TYPE_NAME, BytesDataTypeName +from zarr_metadata.v3.data_type.complex64 import COMPLEX64_DATA_TYPE_NAME, Complex64DataTypeName +from zarr_metadata.v3.data_type.complex128 import COMPLEX128_DATA_TYPE_NAME, Complex128DataTypeName +from zarr_metadata.v3.data_type.float16 import FLOAT16_DATA_TYPE_NAME, Float16DataTypeName +from zarr_metadata.v3.data_type.float32 import FLOAT32_DATA_TYPE_NAME, Float32DataTypeName +from zarr_metadata.v3.data_type.float64 import FLOAT64_DATA_TYPE_NAME, Float64DataTypeName +from zarr_metadata.v3.data_type.int8 import INT8_DATA_TYPE_NAME, Int8DataTypeName +from zarr_metadata.v3.data_type.int16 import INT16_DATA_TYPE_NAME, Int16DataTypeName +from zarr_metadata.v3.data_type.int32 import INT32_DATA_TYPE_NAME, Int32DataTypeName +from zarr_metadata.v3.data_type.int64 import INT64_DATA_TYPE_NAME, Int64DataTypeName +from zarr_metadata.v3.data_type.raw import raw_bytes_dtype_name +from zarr_metadata.v3.data_type.string import STRING_DATA_TYPE_NAME, StringDataTypeName +from zarr_metadata.v3.data_type.uint8 import UINT8_DATA_TYPE_NAME, Uint8DataTypeName +from zarr_metadata.v3.data_type.uint16 import UINT16_DATA_TYPE_NAME, Uint16DataTypeName +from zarr_metadata.v3.data_type.uint32 import UINT32_DATA_TYPE_NAME, Uint32DataTypeName +from zarr_metadata.v3.data_type.uint64 import UINT64_DATA_TYPE_NAME, Uint64DataTypeName + +# (name_string, per-dtype literal type) +PRIMITIVE_DTYPES = [ + (BOOL_DATA_TYPE_NAME, BoolDataTypeName), + (INT8_DATA_TYPE_NAME, Int8DataTypeName), + (INT16_DATA_TYPE_NAME, Int16DataTypeName), + (INT32_DATA_TYPE_NAME, Int32DataTypeName), + (INT64_DATA_TYPE_NAME, Int64DataTypeName), + (UINT8_DATA_TYPE_NAME, Uint8DataTypeName), + (UINT16_DATA_TYPE_NAME, Uint16DataTypeName), + (UINT32_DATA_TYPE_NAME, Uint32DataTypeName), + (UINT64_DATA_TYPE_NAME, Uint64DataTypeName), + (FLOAT16_DATA_TYPE_NAME, Float16DataTypeName), + (FLOAT32_DATA_TYPE_NAME, Float32DataTypeName), + (FLOAT64_DATA_TYPE_NAME, Float64DataTypeName), + (COMPLEX64_DATA_TYPE_NAME, Complex64DataTypeName), + (COMPLEX128_DATA_TYPE_NAME, Complex128DataTypeName), + (STRING_DATA_TYPE_NAME, StringDataTypeName), + (BYTES_DATA_TYPE_NAME, BytesDataTypeName), +] + + +@pytest.mark.parametrize(("name", "literal_type"), PRIMITIVE_DTYPES, ids=lambda x: str(x)) +def test_primitive_against_literal(name: str, literal_type: object) -> None: + """The dtype name validates against its declared Literal type.""" + TypeAdapter(literal_type).validate_python(name) + + +@pytest.mark.parametrize("raw_name", ["r8", "r16", "r24", "r256", "r1024"], ids=str) +def test_raw_bytes_name(raw_name: str) -> None: + """`r` names pass the raw_bytes_dtype_name validator.""" + raw_bytes_dtype_name(raw_name) diff --git a/packages/zarr-metadata/tests/v3/data_type/uint16/__init__.py b/packages/zarr-metadata/tests/v3/data_type/uint16/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/uint16/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/uint16/fill_values.json new file mode 100644 index 0000000000..60934f030e --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint16/fill_values.json @@ -0,0 +1,4 @@ +{ + "zero": 0, + "max": 65535 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/uint16/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/uint16/test_fixtures.py new file mode 100644 index 0000000000..f4afaafa8b --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint16/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate uint16 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.uint16 import Uint16FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Uint16FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/uint32/__init__.py b/packages/zarr-metadata/tests/v3/data_type/uint32/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/uint32/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/uint32/fill_values.json new file mode 100644 index 0000000000..1b003f6fab --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint32/fill_values.json @@ -0,0 +1,4 @@ +{ + "zero": 0, + "max": 4294967295 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/uint32/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/uint32/test_fixtures.py new file mode 100644 index 0000000000..cf94a6a829 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint32/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate uint32 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.uint32 import Uint32FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Uint32FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/uint64/__init__.py b/packages/zarr-metadata/tests/v3/data_type/uint64/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/uint64/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/uint64/fill_values.json new file mode 100644 index 0000000000..145703c360 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint64/fill_values.json @@ -0,0 +1,4 @@ +{ + "zero": 0, + "max": 18446744073709551615 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/uint64/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/uint64/test_fixtures.py new file mode 100644 index 0000000000..71851cfeec --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint64/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate uint64 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.uint64 import Uint64FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Uint64FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/data_type/uint8/__init__.py b/packages/zarr-metadata/tests/v3/data_type/uint8/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/data_type/uint8/fill_values.json b/packages/zarr-metadata/tests/v3/data_type/uint8/fill_values.json new file mode 100644 index 0000000000..70e8d5d5bc --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint8/fill_values.json @@ -0,0 +1,4 @@ +{ + "zero": 0, + "max": 255 +} diff --git a/packages/zarr-metadata/tests/v3/data_type/uint8/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/uint8/test_fixtures.py new file mode 100644 index 0000000000..4866753971 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/data_type/uint8/test_fixtures.py @@ -0,0 +1,20 @@ +"""Validate uint8 fill-value fixtures.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.data_type.uint8 import Uint8FillValue + +FILL_VALUES: dict[str, object] = json.loads( + (Path(__file__).parent / "fill_values.json").read_text() +) + + +@pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) +def test_fill_value(case: object) -> None: + TypeAdapter(Uint8FillValue).validate_python(case) diff --git a/packages/zarr-metadata/tests/v3/group/__init__.py b/packages/zarr-metadata/tests/v3/group/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/v3/group/minimal.json b/packages/zarr-metadata/tests/v3/group/minimal.json new file mode 100644 index 0000000000..7e86f1938a --- /dev/null +++ b/packages/zarr-metadata/tests/v3/group/minimal.json @@ -0,0 +1,4 @@ +{ + "zarr_format": 3, + "node_type": "group" +} diff --git a/packages/zarr-metadata/tests/v3/group/test_fixtures.py b/packages/zarr-metadata/tests/v3/group/test_fixtures.py new file mode 100644 index 0000000000..2015d5ce96 --- /dev/null +++ b/packages/zarr-metadata/tests/v3/group/test_fixtures.py @@ -0,0 +1,20 @@ +"""Decode v3 group metadata fixtures via pydantic.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest +from pydantic import TypeAdapter + +from zarr_metadata.v3.group import GroupMetadataV3 + +FIXTURES_DIR = Path(__file__).parent +FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) +ADAPTER = TypeAdapter(GroupMetadataV3) + + +@pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) +def test_validate(fixture: Path) -> None: + ADAPTER.validate_python(json.loads(fixture.read_text())) diff --git a/packages/zarr-metadata/tests/v3/group/with_attributes.json b/packages/zarr-metadata/tests/v3/group/with_attributes.json new file mode 100644 index 0000000000..69804b3db0 --- /dev/null +++ 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"mkdocs-redirects", specifier = ">=1.2.0" }, + { name = "mkdocstrings", specifier = ">=0.29.1" }, + { name = "mkdocstrings-python", specifier = ">=1.16.10" }, + { name = "numcodecs", extras = ["msgpack"] }, + { name = "pytest" }, + { name = "ruff" }, + { name = "s3fs", specifier = ">=2023.10.0" }, + { name = "towncrier" }, +] +remote-tests = [ + { name = "botocore" }, + { name = "coverage", specifier = ">=7.10" }, + { name = "fsspec", specifier = ">=2023.10.0" }, + { name = "hypothesis" }, + { name = "moto", extras = ["s3", "server"] }, + { name = "numpydoc" }, + { name = "obstore", specifier = ">=0.5.1" }, + { name = "pytest" }, + { name = "pytest-accept" }, + { name = "pytest-asyncio" }, + { name = "pytest-benchmark" }, + { name = "pytest-codspeed" }, + { name = "pytest-cov" }, + { name = "pytest-xdist" }, + { name = "requests" }, + { name = "s3fs", specifier = ">=2023.10.0" }, + { name = "tomlkit" }, + { name = "uv" }, +] +test = [ + { name = "coverage", specifier = ">=7.10" }, + { name = "hypothesis" }, + { name = "numpydoc" }, + { name = "pytest" }, + { name = "pytest-accept" }, + { name = "pytest-asyncio" }, + { name = "pytest-benchmark" }, + { name = "pytest-codspeed" }, + { name = "pytest-cov" }, + { name = "pytest-xdist" }, + { name = "tomlkit" }, + { name = "uv" }, +] + +[[package]] +name = "zarr-metadata" +version = "0.1.0" +source = { editable = "packages/zarr-metadata" } +dependencies = [ + { name = "typing-extensions" }, +] + +[package.metadata] +requires-dist = [ + { name = "pytest", marker = "extra == 'test'" }, + { name = "typing-extensions", specifier = ">=4.13" }, +] +provides-extras = ["test"] From ad374b5e8e4a07947b8ca5d72d72887010a7e151 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sun, 3 May 2026 11:08:54 -0400 Subject: [PATCH 292/468] cast_value data type validation was checking the source data type instead of the target data type in the (#3938) "can we use an out of range mode" check. This means a float dtype source and an int dtype target would raise an error, which is incorrect. the fix ensures that we check the _target_ dtype. --- src/zarr/codecs/cast_value.py | 42 +++++++++++++++++++++------- tests/test_codecs/test_cast_value.py | 25 ++++++++++++++++- 2 files changed, 56 insertions(+), 11 deletions(-) diff --git a/src/zarr/codecs/cast_value.py b/src/zarr/codecs/cast_value.py index d8c503464e..adf4886104 100644 --- a/src/zarr/codecs/cast_value.py +++ b/src/zarr/codecs/cast_value.py @@ -54,20 +54,31 @@ class ScalarMap(TypedDict, total=False): # see https://github.com/zarr-developers/zarr-extensions/tree/main/codecs/cast_value -PERMITTED_DATA_TYPE_NAMES: Final[set[str]] = { +CAST_VALUE_INT_DTYPES: Final[set[str]] = { + # signed "int2", "int4", "int8", "int16", "int32", "int64", - "int64uint2", + # unsigned + "uint2", "uint4", "uint8", "uint16", "uint32", "uint64", - "uint64float4_e2m1fn", +} +"""Integer dtype identifiers permitted as the source or target of `cast_value`. + +Membership in this set drives the `out_of_range="wrap"` rule, which the +spec restricts to integral targets that use two's-complement representation +for modular arithmetic. +""" + +CAST_VALUE_FLOAT_DTYPES: Final[set[str]] = { + "float4_e2m1fn", "float6_e2m3fn", "float6_e3m2fn", "float8_e3m4", @@ -82,6 +93,10 @@ class ScalarMap(TypedDict, total=False): "float32", "float64", } +"""Floating-point dtype identifiers permitted as the source or target of `cast_value`.""" + +PERMITTED_DATA_TYPE_NAMES: Final[set[str]] = CAST_VALUE_INT_DTYPES | CAST_VALUE_FLOAT_DTYPES +"""All dtype identifiers the `cast_value` codec is defined for.""" def parse_scalar_map(obj: ScalarMapJSON | ScalarMap) -> ScalarMap: @@ -240,15 +255,22 @@ def validate( dtype: ZDType[TBaseDType, TBaseScalar], chunk_grid: ChunkGridMetadata, ) -> None: - target_name = dtype.to_json(zarr_format=3) - if target_name not in PERMITTED_DATA_TYPE_NAMES: + # `dtype` is the source (the array's dtype); `self.dtype` is the + # cast target. The spec requires both to be permitted, and rules + # like `out_of_range="wrap"` apply to the target. + source_name = dtype.to_json(zarr_format=3) + target_name = self.dtype.to_json(zarr_format=3) + for role, name in (("source", source_name), ("target", target_name)): + if name not in PERMITTED_DATA_TYPE_NAMES: + raise ValueError( + f"The cast_value codec only supports integer and floating-point data types. " + f"Got {role} dtype {name}." + ) + if self.out_of_range == "wrap" and target_name not in CAST_VALUE_INT_DTYPES: raise ValueError( - f"The cast_value codec only supports integer and floating-point data types. " - f"Got dtype {target_name}." + f"out_of_range='wrap' is only valid for integer target types. " + f"Got target dtype {target_name}." ) - target_native = dtype.to_native_dtype() - if self.out_of_range == "wrap" and not np.issubdtype(target_native, np.integer): - raise ValueError("out_of_range='wrap' is only valid for integer target types.") if self.scalar_map is not None: self._validate_scalar_map(dtype, self.dtype) diff --git a/tests/test_codecs/test_cast_value.py b/tests/test_codecs/test_cast_value.py index cb456c0584..5c17124fbd 100644 --- a/tests/test_codecs/test_cast_value.py +++ b/tests/test_codecs/test_cast_value.py @@ -139,7 +139,7 @@ def test_construction_rejects_invalid_target_dtype() -> None: exception_cls=ValueError, ), ExpectErr( - input={"dtype": "float32", "target": "int32", "out_of_range": "wrap"}, + input={"dtype": "int32", "target": "float64", "out_of_range": "wrap"}, msg="only valid for integer", exception_cls=ValueError, ), @@ -165,6 +165,29 @@ def test_validation_rejects_invalid(case: ExpectErr[dict[str, Any]]) -> None: ) +@pytest.mark.parametrize( + ("source_dtype", "target_dtype"), + [ + ("float16", "int8"), + ("float32", "int32"), + ("float64", "int64"), + ("int32", "uint8"), + ], +) +def test_validation_accepts_wrap_with_integer_target(source_dtype: str, target_dtype: str) -> None: + """Regression for #3936: `out_of_range="wrap"` is permitted when the + cast TARGET (not the source array dtype) is an integer type.""" + zarr.create_array( + store={}, + shape=(1,), + dtype=source_dtype, + chunks=(1,), + filters=[CastValue(data_type=target_dtype, out_of_range="wrap")], + compressors=None, + fill_value=0, + ) + + def test_zero_itemsize_raises() -> None: """Variable-length dtypes (itemsize=0) are rejected by compute_encoded_size.""" from zarr.core.array_spec import ArrayConfig, ArraySpec From 021662c87acfd145f87f72fc340dd686d1b375ae Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sun, 3 May 2026 20:39:10 -0400 Subject: [PATCH 293/468] fix: use contextual arrayspec when validating / evolving codecs (#3941) * fix: use contextual arrayspec when validating / evolving codecs * docs: changelog * fix: gate tests depending on presence of compiled backend --- changes/3938.bugfix.md | 4 +++ changes/3941.bugfix.md | 6 ++++ src/zarr/core/codec_pipeline.py | 13 +++++++- src/zarr/core/metadata/v3.py | 16 ++++++++- tests/test_codec_pipeline.py | 50 ++++++++++++++++++++++++++++ tests/test_codecs/test_cast_value.py | 1 + 6 files changed, 88 insertions(+), 2 deletions(-) create mode 100644 changes/3938.bugfix.md create mode 100644 changes/3941.bugfix.md diff --git a/changes/3938.bugfix.md b/changes/3938.bugfix.md new file mode 100644 index 0000000000..9033095d4a --- /dev/null +++ b/changes/3938.bugfix.md @@ -0,0 +1,4 @@ +Fixed a `CastValue` validation bug where the "can we use an out-of-range mode" check +inspected the source dtype instead of the target dtype. This meant arrays with a +float source dtype and an integer target dtype incorrectly raised a `ValueError` +when configured with a `wrap` out-of-range mode. diff --git a/changes/3941.bugfix.md b/changes/3941.bugfix.md new file mode 100644 index 0000000000..91343c4059 --- /dev/null +++ b/changes/3941.bugfix.md @@ -0,0 +1,6 @@ +Fixed a bug where the codec pipeline evolved each codec against the original +array spec instead of the spec produced by upstream array-to-array codecs. This +caused failures whenever an upstream codec changed the dtype between codec +boundaries — e.g. arrays using `CastValue` to convert a single-byte source dtype +(`int8`) to a multi-byte target dtype (`int16`) raised a `ValueError` from +`BytesCodec` about a missing `endian` configuration. diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 4cecc3a6d1..5c26681d6b 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -187,7 +187,18 @@ class BatchedCodecPipeline(CodecPipeline): batch_size: int def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: - return type(self).from_codecs(c.evolve_from_array_spec(array_spec=array_spec) for c in self) + # Each codec must be evolved against the spec it will actually see + # at run-time, not the original array spec. Earlier array->array + # codecs may transform the dtype (e.g. cast_value), so the spec + # threaded into later codecs (the array->bytes serializer and any + # bytes->bytes filters) must reflect those transformations. + evolved: list[Codec] = [] + spec = array_spec + for codec in self: + evolved_codec = codec.evolve_from_array_spec(array_spec=spec) + evolved.append(evolved_codec) + spec = evolved_codec.resolve_metadata(spec) + return type(self).from_codecs(evolved) @classmethod def from_codecs(cls, codecs: Iterable[Codec], *, batch_size: int | None = None) -> Self: diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index a8f2b05518..5750a25c30 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -503,7 +503,21 @@ def __init__( config=ArrayConfig.from_dict({}), # TODO: config is not needed here. prototype=default_buffer_prototype(), # TODO: prototype is not needed here. ) - codecs_parsed = tuple(c.evolve_from_array_spec(array_spec) for c in codecs_parsed_partial) + # Thread the spec through evolution: each codec must be evolved against + # the spec it will actually see at run-time, not the original array spec. + # Earlier array->array codecs may transform the dtype (e.g. cast_value), + # so the spec passed to later codecs must reflect those transformations. + # Per-codec validate() must run before resolve_metadata(), since the + # latter may rely on invariants the former checks (e.g. cast_value + # rejects complex source dtypes that would otherwise crash _do_cast). + evolved: list[Codec] = [] + spec = array_spec + for c in codecs_parsed_partial: + evolved_codec = c.evolve_from_array_spec(spec) + evolved_codec.validate(shape=spec.shape, dtype=spec.dtype, chunk_grid=chunk_grid_parsed) + evolved.append(evolved_codec) + spec = evolved_codec.resolve_metadata(spec) + codecs_parsed = tuple(evolved) validate_codecs(codecs_parsed_partial, data_type) object.__setattr__(self, "shape", shape_parsed) diff --git a/tests/test_codec_pipeline.py b/tests/test_codec_pipeline.py index 48e15b0643..fa41c2867b 100644 --- a/tests/test_codec_pipeline.py +++ b/tests/test_codec_pipeline.py @@ -1,8 +1,10 @@ from __future__ import annotations +import numpy as np import pytest import zarr +from zarr.codecs import BytesCodec, CastValue from zarr.core.array import _get_chunk_spec from zarr.core.buffer.core import default_buffer_prototype from zarr.core.indexing import BasicIndexer @@ -70,3 +72,51 @@ async def test_read_returns_get_results( assert len(results) == len(expected_statuses) for result, expected_status in zip(results, expected_statuses, strict=True): assert result["status"] == expected_status + + +try: + import cast_value_rs # noqa: F401 + + _HAS_CAST_VALUE_RS = True +except ModuleNotFoundError: + _HAS_CAST_VALUE_RS = False + +requires_cast_value_rs = pytest.mark.skipif( + not _HAS_CAST_VALUE_RS, reason="cast-value-rs not installed" +) + + +@requires_cast_value_rs +@pytest.mark.parametrize( + ("source_dtype", "target_dtype"), + [ + # Source is single-byte (no endianness); target is multi-byte (has endianness). + # Without the fix, BytesCodec.evolve_from_array_spec sees the source dtype, + # strips its `endian` to None, and then chokes when the chunk_spec dtype + # gets transformed to the multi-byte target before bytes-decoding. + ("int8", "int16"), + ("uint8", "int32"), + ("int8", "float32"), + # Source is multi-byte; target is single-byte (the reverse direction also + # exercises the spec-threading logic). + ("int16", "int8"), + ], +) +def test_codec_pipeline_threads_dtype_through_evolve(source_dtype: str, target_dtype: str) -> None: + """Regression for #3937: each codec must be evolved against the spec it + will see at runtime, not the original array spec. cast_value transforms + the dtype between AA codecs and the array->bytes serializer.""" + arr = zarr.create_array( + store={}, + shape=(4,), + chunks=(4,), + dtype=source_dtype, + fill_value=0, + filters=[CastValue(data_type=target_dtype)], + serializer=BytesCodec(endian="little"), + compressors=[], + zarr_format=3, + overwrite=True, + ) + arr[:] = np.asarray([0, 1, 2, 3], dtype=source_dtype) + np.testing.assert_array_equal(arr[:], np.asarray([0, 1, 2, 3], dtype=source_dtype)) diff --git a/tests/test_codecs/test_cast_value.py b/tests/test_codecs/test_cast_value.py index 5c17124fbd..361073f96b 100644 --- a/tests/test_codecs/test_cast_value.py +++ b/tests/test_codecs/test_cast_value.py @@ -165,6 +165,7 @@ def test_validation_rejects_invalid(case: ExpectErr[dict[str, Any]]) -> None: ) +@requires_cast_value_rs @pytest.mark.parametrize( ("source_dtype", "target_dtype"), [ From 37ae37b3f5b4c9c5f3577de7dab2f628ffa753f9 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 5 May 2026 00:36:47 -0400 Subject: [PATCH 294/468] fix: defer to fsspec for memory url scheme (#3944) * fix: defer to fsspec for memory url scheme * docs: changelog * test: add test for the memory scheme : memoryfilesystem mapping --- changes/3944.bugfix.md | 4 ++++ src/zarr/storage/_common.py | 2 +- tests/test_store/test_fsspec.py | 12 ++++++++++++ 3 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 changes/3944.bugfix.md diff --git a/changes/3944.bugfix.md b/changes/3944.bugfix.md new file mode 100644 index 0000000000..1fd13d7df3 --- /dev/null +++ b/changes/3944.bugfix.md @@ -0,0 +1,4 @@ +Fixed breakage in existing fsspec-dependent workflows caused by associating the "memory" URL scheme with +instances of `ManagedMemoryStore` instead of fsspec's memory-backed store. After this change, store URLs with a "memory" scheme are handled differently when `fsspec` is installed: +with `fsspec`, a `FsspecStore` backed by a `MemoryFileSystem` is used. Without `fsspec`, +a `ManagedMemoryStore` is used. \ No newline at end of file diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 1aff894119..e4ee0bc4ac 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -369,7 +369,7 @@ async def make_store( return await LocalStore.open(root=store_like, mode=mode, read_only=_read_only) elif isinstance(store_like, str) and parsed is not None: - if parsed.scheme == "memory": + if parsed.scheme == "memory" and not _has_fsspec: # Create or get a ManagedMemoryStore return ManagedMemoryStore(name=parsed.name, path=parsed.path, read_only=_read_only) elif parsed.scheme == "file" or not parsed.scheme: diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 9ef2c0afcd..6e3dc192b8 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -16,6 +16,7 @@ from zarr.core.sync import _collect_aiterator, sync from zarr.errors import ZarrUserWarning from zarr.storage import FsspecStore +from zarr.storage._common import make_store from zarr.storage._fsspec import _make_async from zarr.testing.store import StoreTests @@ -544,3 +545,14 @@ async def test_with_read_only_auto_mkdir(tmp_path: Path) -> None: store_w = FsspecStore.from_url(f"file://{tmp_path}", storage_options={"auto_mkdir": False}) _ = store_w.with_read_only() + + +@pytest.mark.skipif( + parse_version(fsspec.__version__) < parse_version("2024.12.0"), + reason="No AsyncFileSystemWrapper", +) +async def test_memory_scheme() -> None: + """Test that the "memory" scheme creates a `MemoryFileSystem`-backed store""" + store = await make_store("memory://test") + assert isinstance(store, FsspecStore) + assert store.fs.protocol == "memory" From 85890b3bb404fd1d401267c508a2694f5734559e Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 5 May 2026 08:14:16 -0400 Subject: [PATCH 295/468] release : 3.2.1 release notes (#3942) * release:3.2.1 release notes * docs: add changelog entry * docs: remove changelog * Fix date and add link --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3938.bugfix.md | 4 ---- changes/3941.bugfix.md | 6 ------ changes/3944.bugfix.md | 4 ---- docs/release-notes.md | 19 +++++++++++++++++++ 4 files changed, 19 insertions(+), 14 deletions(-) delete mode 100644 changes/3938.bugfix.md delete mode 100644 changes/3941.bugfix.md delete mode 100644 changes/3944.bugfix.md diff --git a/changes/3938.bugfix.md b/changes/3938.bugfix.md deleted file mode 100644 index 9033095d4a..0000000000 --- a/changes/3938.bugfix.md +++ /dev/null @@ -1,4 +0,0 @@ -Fixed a `CastValue` validation bug where the "can we use an out-of-range mode" check -inspected the source dtype instead of the target dtype. This meant arrays with a -float source dtype and an integer target dtype incorrectly raised a `ValueError` -when configured with a `wrap` out-of-range mode. diff --git a/changes/3941.bugfix.md b/changes/3941.bugfix.md deleted file mode 100644 index 91343c4059..0000000000 --- a/changes/3941.bugfix.md +++ /dev/null @@ -1,6 +0,0 @@ -Fixed a bug where the codec pipeline evolved each codec against the original -array spec instead of the spec produced by upstream array-to-array codecs. This -caused failures whenever an upstream codec changed the dtype between codec -boundaries — e.g. arrays using `CastValue` to convert a single-byte source dtype -(`int8`) to a multi-byte target dtype (`int16`) raised a `ValueError` from -`BytesCodec` about a missing `endian` configuration. diff --git a/changes/3944.bugfix.md b/changes/3944.bugfix.md deleted file mode 100644 index 1fd13d7df3..0000000000 --- a/changes/3944.bugfix.md +++ /dev/null @@ -1,4 +0,0 @@ -Fixed breakage in existing fsspec-dependent workflows caused by associating the "memory" URL scheme with -instances of `ManagedMemoryStore` instead of fsspec's memory-backed store. After this change, store URLs with a "memory" scheme are handled differently when `fsspec` is installed: -with `fsspec`, a `FsspecStore` backed by a `MemoryFileSystem` is used. Without `fsspec`, -a `ManagedMemoryStore` is used. \ No newline at end of file diff --git a/docs/release-notes.md b/docs/release-notes.md index 7e3511a0a7..4511c9815e 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,6 +2,25 @@ +## 3.2.1 (2026-05-05) + +### Bugfixes + +- Fixed a `CastValue` validation bug where the "can we use an out-of-range mode" check + inspected the source dtype instead of the target dtype. This meant arrays with a + float source dtype and an integer target dtype incorrectly raised a `ValueError` + when configured with a `wrap` out-of-range mode. ([#3938](https://github.com/zarr-developers/zarr-python/issues/3938)) +- Fixed a bug where the codec pipeline evolved each codec against the original + array spec instead of the spec produced by upstream array-to-array codecs. This + caused failures whenever an upstream codec changed the dtype between codec + boundaries — e.g. arrays using `CastValue` to convert a single-byte source dtype + (`int8`) to a multi-byte target dtype (`int16`) raised a `ValueError` from + `BytesCodec` about a missing `endian` configuration. ([#3941](https://github.com/zarr-developers/zarr-python/issues/3941)) +- Fixed breakage in existing fsspec-dependent workflows caused by associating the "memory" URL scheme with +instances of `ManagedMemoryStore` instead of fsspec's memory-backed store. After this change, store URLs with a "memory" scheme are handled differently when `fsspec` is installed: +with `fsspec`, a `FsspecStore` backed by a `MemoryFileSystem` is used. Without `fsspec`, +a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr-python/issues/3944)) + ## 3.2.0 (2026-04-30) ### Features From 6af3ea49d6c10137c0044a9f78813d79c71b0ac4 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Tue, 5 May 2026 22:20:29 -0400 Subject: [PATCH 296/468] Allow s3 testing in face of "ambient" AWS creds (#3947) --- pyproject.toml | 6 ++++-- tests/test_store/test_fsspec.py | 17 +++++++++++++++-- 2 files changed, 19 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4e3fc109e4..bf617604d8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -365,7 +365,9 @@ ignore = [ python_version = "3.12" ignore_missing_imports = true namespace_packages = false - +pretty = true +show_error_code_links = true +show_error_context = true strict = true warn_unreachable = true enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] @@ -378,7 +380,6 @@ module = [ "tests.test_config", "tests.test_store.test_zip", "tests.test_store.test_local", - "tests.test_store.test_fsspec", "tests.test_store.test_memory", "tests.test_codecs.test_codecs", "tests.test_metadata.*", @@ -394,6 +395,7 @@ strict = false # and fix the errors [[tool.mypy.overrides]] module = [ + "tests.test_store.test_fsspec", "tests.test_group", "tests.test_indexing", "tests.test_properties", diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 6e3dc192b8..142cb3b00d 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -80,7 +80,13 @@ def s3_base() -> Generator[None, None, None]: def get_boto3_client() -> botocore.client.BaseClient: # NB: we use the sync botocore client for setup session = botocore.session.Session() - return session.create_client("s3", endpoint_url=endpoint_url) + + # Prevent IllegalLocationConstraintException by explicitly setting region to + # "us-east-1", which does not require configuring LocationConstraint during + # bucket creation. (It is, in fact, forbidden for that region.) Necessary + # in the face of "ambient" AWS configuration in a development environment + # where the default region might be configured differently. + return session.create_client("s3", endpoint_url=endpoint_url, region_name="us-east-1") @pytest.fixture(autouse=True) @@ -100,7 +106,14 @@ def s3(s3_base: None) -> Generator[s3fs.S3FileSystem, None, None]: client = get_boto3_client() client.create_bucket(Bucket=test_bucket_name, ACL="public-read") s3fs.S3FileSystem.clear_instance_cache() - s3 = s3fs.S3FileSystem(anon=False, client_kwargs={"endpoint_url": endpoint_url}) + s3 = s3fs.S3FileSystem( + anon=False, + client_kwargs={"endpoint_url": endpoint_url}, + # Prevent "AssertionError: Session was never entered" from aiobotocore + # at end of test execution. Using clear_instance_cache is insufficient, + # although still necessary. + skip_instance_cache=True, + ) session = sync(s3.set_session()) s3.invalidate_cache() yield s3 From b4ce0e9547288bf87234756cd57c8382a40cf7d6 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Tue, 5 May 2026 22:46:28 -0400 Subject: [PATCH 297/468] ci: run all of xarray's tests in downstream workflow (#3940) Co-authored-by: Davis Bennett --- .github/workflows/downstream.yml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 849d658016..9b7ce211ab 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -3,7 +3,7 @@ name: Downstream on: workflow_dispatch: pull_request: - types: [labeled] + types: [labeled, synchronize, opened, reopened] permissions: contents: read @@ -15,7 +15,9 @@ concurrency: jobs: xarray: name: Xarray zarr backend tests - if: github.event_name == 'workflow_dispatch' || github.event.label.name == 'run-downstream' + if: | + github.event_name == 'workflow_dispatch' + || contains(github.event.pull_request.labels.*.name, 'run-downstream') runs-on: ubuntu-latest steps: - name: Check out zarr-python @@ -51,14 +53,16 @@ jobs: - name: Run xarray zarr backend tests working-directory: xarray run: | - pixi run -e test-py313 -- python -m pytest -x --no-header -q \ - xarray/tests/test_backends.py -k zarr \ - xarray/tests/test_backends_api.py -k zarr \ - xarray/tests/test_backends_datatree.py -k zarr + pixi run -e test-py313 -- python -m pytest --no-header -q \ + xarray/tests/test_backends.py \ + xarray/tests/test_backends_api.py \ + xarray/tests/test_backends_datatree.py numcodecs: name: numcodecs zarr3 codec tests - if: github.event_name == 'workflow_dispatch' || github.event.label.name == 'run-downstream' + if: | + github.event_name == 'workflow_dispatch' + || contains(github.event.pull_request.labels.*.name, 'run-downstream') runs-on: ubuntu-latest steps: - name: Check out zarr-python From 3d354a8bcd73b457e6b3e744088614238f14cac1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 5 May 2026 20:07:53 -0700 Subject: [PATCH 298/468] chore(deps): bump the actions group across 1 directory with 12 updates (#3930) Bumps the actions group with 12 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/checkout](https://github.com/actions/checkout) | `6.0.1` | `6.0.2` | | [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) | `6.1.0` | `8.1.0` | | [CodSpeedHQ/action](https://github.com/codspeedhq/action) | `4.12.1` | `4.14.0` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `5.3.1` | `6.0.0` | | [actions/cache](https://github.com/actions/cache) | `5.0.4` | `5.0.5` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `3.25.5` | `4.2.2` | | [j178/prek-action](https://github.com/j178/prek-action) | `1.1.1` | `2.0.2` | | [scientific-python/upload-nightly-action](https://github.com/scientific-python/upload-nightly-action) | `0.6.3` | `0.6.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.2` | `0.5.3` | Updates `actions/checkout` from 6.0.1 to 6.0.2 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v6.0.1...de0fac2e4500dabe0009e67214ff5f5447ce83dd) Updates `astral-sh/setup-uv` from 6.1.0 to 8.1.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/v6.1...08807647e7069bb48b6ef5acd8ec9567f424441b) Updates `CodSpeedHQ/action` from 4.12.1 to 4.14.0 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/1c8ae4843586d3ba879736b7f6b7b0c990757fab...658a901452bb54c799643e060733b7afe9121b8d) Updates `codecov/codecov-action` from 5.3.1 to 6.0.0 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v5.3.1...57e3a136b779b570ffcdbf80b3bdc90e7fab3de2) Updates `actions/cache` from 5.0.4 to 5.0.5 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/668228422ae6a00e4ad889ee87cd7109ec5666a7...27d5ce7f107fe9357f9df03efb73ab90386fccae) Updates `github/issue-metrics` from 3.25.5 to 4.2.2 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/67526e7bd8100b870f10b1c120780a8375777b43...c9e9838147fd355dace335ba787f01b6641a400a) Updates `j178/prek-action` from 1.1.1 to 2.0.2 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/0bb87d7f00b0c99306c8bcb8b8beba1eb581c037...cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3) Updates `scientific-python/upload-nightly-action` from 0.6.3 to 0.6.4 - [Release notes](https://github.com/scientific-python/upload-nightly-action/releases) - [Commits](https://github.com/scientific-python/upload-nightly-action/compare/5748273c71e2d8d3a61f3a11a16421c8954f9ecf...e76cfec8a4611fd02808a801b0ff5a7d7c1b2d99) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/bbbca2ddaa5d8feaa63e36b76fdaad77386f024f...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/37930b1c2abaa49bbe596cd826c3c89aef350131...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.2 to 0.5.3 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/71321a20a9ded102f6e9ce5718a2fcec2c4f70d8...b1d7e1fb5de872772f31590499237e7cce841e8e) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 6.0.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 8.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 4.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/cache dependency-version: 5.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.2 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.2 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: scientific-python/upload-nightly-action dependency-version: 0.6.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/check_changelogs.yml | 4 ++-- .github/workflows/codspeed.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 6 +++--- .github/workflows/issue-metrics.yml | 2 +- .github/workflows/lint.yml | 2 +- .github/workflows/nightly_wheels.yml | 2 +- .github/workflows/releases.yml | 8 ++++---- .github/workflows/test.yml | 4 ++-- .github/workflows/zizmor.yml | 2 +- 11 files changed, 18 insertions(+), 18 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 04eb880592..77c03dad0f 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -17,12 +17,12 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0 + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Check changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 8d67cf18d9..848544d03c 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@1c8ae4843586d3ba879736b7f6b7b0c990757fab # v4.12.1 + uses: CodSpeedHQ/action@658a901452bb54c799643e060733b7afe9121b8d # v4.14.0 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 005dfa2af8..6515a2c4c2 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -22,7 +22,7 @@ jobs: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: persist-credentials: false - - uses: astral-sh/setup-uv@f0ec1fc3b38f5e7cd731bb6ce540c5af426746bb # v6.1.0 + - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - run: uv sync --group docs - run: uv run mkdocs build env: diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 777a5c3d64..403441b306 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -76,7 +76,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3 # v5.3.1 + uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: gpu diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index df1ae06c5f..4f9467be7d 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -67,7 +67,7 @@ jobs: # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache - name: Restore cached hypothesis directory id: restore-hypothesis-cache - uses: actions/cache/restore@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4 + uses: actions/cache/restore@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} @@ -87,13 +87,13 @@ jobs: - name: Save cached hypothesis directory id: save-hypothesis-cache if: always() && steps.status.outcome != 'skipped' - uses: actions/cache/save@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5.0.4 + uses: actions/cache/save@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} - name: Upload coverage - uses: codecov/codecov-action@1af58845a975a7985b0beb0cbe6fbbb71a41dbad # v5.5.3 + uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 3746be05ac..14fba5b9ec 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -33,7 +33,7 @@ jobs: echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV" - name: Run issue-metrics tool - uses: github/issue-metrics@67526e7bd8100b870f10b1c120780a8375777b43 # v3.25.5 + uses: github/issue-metrics@c9e9838147fd355dace335ba787f01b6641a400a # v4.2.2 env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index ebcf74b3d7..21a434bd36 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -22,4 +22,4 @@ jobs: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: persist-credentials: false - - uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1.1.1 + - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2.0.2 diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 8446d8fbe4..1f48e9e1b8 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -42,7 +42,7 @@ jobs: run: hatch build - name: Upload nightly wheels - uses: scientific-python/upload-nightly-action@5748273c71e2d8d3a61f3a11a16421c8954f9ecf + uses: scientific-python/upload-nightly-action@e76cfec8a4611fd02808a801b0ff5a7d7c1b2d99 with: artifacts_path: dist anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }} diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 0920b5be12..a6c7202c5b 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -43,7 +43,7 @@ jobs: version: '1.16.5' - name: Build wheel and sdist run: hatch build - - uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 with: name: releases path: dist @@ -53,7 +53,7 @@ jobs: needs: [build_artifacts] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: releases path: dist @@ -76,7 +76,7 @@ jobs: attestations: write # Required for artifact attestation artifact-metadata: write # Required for artifact attestation metadata steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: releases path: dist @@ -85,4 +85,4 @@ jobs: with: subject-path: dist/* - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 + uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 7ff7a8f6ae..03143d3e5b 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -78,7 +78,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage if: ${{ matrix.dependency-set == 'optional' && matrix.os == 'ubuntu-latest' }} - uses: codecov/codecov-action@1af58845a975a7985b0beb0cbe6fbbb71a41dbad # v5.5.3 + uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests @@ -125,7 +125,7 @@ jobs: run: | hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@1af58845a975a7985b0beb0cbe6fbbb71a41dbad # v5.5.3 + uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 19313ab6ec..da19f22421 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -32,4 +32,4 @@ jobs: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@71321a20a9ded102f6e9ce5718a2fcec2c4f70d8 # v0.5.2 + uses: zizmorcore/zizmor-action@b1d7e1fb5de872772f31590499237e7cce841e8e # v0.5.3 From 80d45ca9ad551b26bfff4a65567d806121b4de12 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 6 May 2026 14:44:44 -0400 Subject: [PATCH 299/468] chore: update pre-commit hooks (#3943) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore: update pre-commit hooks updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.4 → v0.15.12](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.4...v0.15.12) - [github.com/codespell-project/codespell: v2.4.1 → v2.4.2](https://github.com/codespell-project/codespell/compare/v2.4.1...v2.4.2) - [github.com/pre-commit/mirrors-mypy: v1.19.1 → v1.20.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.19.1...v1.20.2) - [github.com/scientific-python/cookie: 2026.03.02 → 2026.04.04](https://github.com/scientific-python/cookie/compare/2026.03.02...2026.04.04) - [github.com/zizmorcore/zizmor-pre-commit: v1.23.1 → v1.24.1](https://github.com/zizmorcore/zizmor-pre-commit/compare/v1.23.1...v1.24.1) * chore: fix pre-commit failures --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 10 +++++----- src/zarr/core/array.py | 2 +- src/zarr/core/dtype/npy/structured.py | 5 +++-- src/zarr/storage/_logging.py | 2 +- src/zarr/storage/_wrapper.py | 2 +- tests/test_api.py | 8 ++++---- tests/test_array.py | 2 +- tests/test_codecs/test_numcodecs.py | 10 +++++----- 8 files changed, 21 insertions(+), 20 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6e6c21b581..c9c0e61668 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,13 +11,13 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.4 + rev: v0.15.12 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/codespell-project/codespell - rev: v2.4.1 + rev: v2.4.2 hooks: - id: codespell args: ["-L", "fo,ihs,kake,te", "-S", "fixture"] @@ -28,7 +28,7 @@ repos: exclude: mkdocs.yml - id: trailing-whitespace - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.19.1 + rev: v1.20.2 hooks: - id: mypy files: ^(src|tests)/ @@ -47,7 +47,7 @@ repos: - hypothesis - s3fs - repo: https://github.com/scientific-python/cookie - rev: 2026.03.02 + rev: 2026.04.04 hooks: - id: sp-repo-review - repo: https://github.com/numpy/numpydoc @@ -64,7 +64,7 @@ repos: types: [python] files: ^(src|tests)/ - repo: https://github.com/zizmorcore/zizmor-pre-commit - rev: v1.23.1 + rev: v1.24.1 hooks: - id: zizmor - repo: https://github.com/twisted/towncrier diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 8183a63beb..37f65fce32 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -4816,7 +4816,7 @@ def _parse_keep_array_attr( if serializer == "keep": serializer = "auto" # After resolving "keep" above, chunks is never "keep" at this point. - chunks_out: ChunksLike | Literal["auto"] = chunks # type: ignore[assignment] + chunks_out: ChunksLike | Literal["auto"] = chunks return ( chunks_out, shards, diff --git a/src/zarr/core/dtype/npy/structured.py b/src/zarr/core/dtype/npy/structured.py index d111924e6c..c5ff5b68a3 100644 --- a/src/zarr/core/dtype/npy/structured.py +++ b/src/zarr/core/dtype/npy/structured.py @@ -278,15 +278,16 @@ def _from_json_v2(cls, data: DTypeJSON) -> Self: # structured dtypes are constructed directly from a list of lists # note that we do not handle the object codec here! this will prevent structured # dtypes from containing object dtypes. + name = data["name"] return cls( - fields=tuple( # type: ignore[misc] + fields=tuple( # type: ignore[str-unpack] ( # type: ignore[misc] f_name, get_data_type_from_json( {"name": f_dtype, "object_codec_id": None}, zarr_format=2 ), ) - for f_name, f_dtype in data["name"] + for f_name, f_dtype in name ) ) msg = f"Invalid JSON representation of {cls.__name__}. Got {data!r}, expected a JSON array of arrays" diff --git a/src/zarr/storage/_logging.py b/src/zarr/storage/_logging.py index a4c376c332..5de300c144 100644 --- a/src/zarr/storage/_logging.py +++ b/src/zarr/storage/_logging.py @@ -161,7 +161,7 @@ def __repr__(self) -> str: def __eq__(self, other: object) -> bool: with self.log(other): - return type(self) is type(other) and self._store.__eq__(other._store) # type: ignore[attr-defined] + return type(self) is type(other) and self._store.__eq__(other._store) async def get( self, diff --git a/src/zarr/storage/_wrapper.py b/src/zarr/storage/_wrapper.py index 50fe5c0e59..d8ecfa6d45 100644 --- a/src/zarr/storage/_wrapper.py +++ b/src/zarr/storage/_wrapper.py @@ -83,7 +83,7 @@ def _check_writable(self) -> None: return self._store._check_writable() def __eq__(self, value: object) -> bool: - return type(self) is type(value) and self._store.__eq__(value._store) # type: ignore[attr-defined] + return type(self) is type(value) and self._store.__eq__(value._store) def __str__(self) -> str: return f"wrapping-{self._store}" diff --git a/tests/test_api.py b/tests/test_api.py index d8c4d20f4a..788519969d 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -137,7 +137,7 @@ async def test_array_like_creation( kwargs["fill_value"] = out_fill expect_fill = out_fill elif func is zarr.api.asynchronous.open_like: # type: ignore[comparison-overlap] - if out_fill == "keep": + if out_fill == "keep": # type: ignore[unreachable] expect_fill = ref_fill else: kwargs["fill_value"] = out_fill @@ -161,7 +161,7 @@ async def test_array_like_creation( else: expect_dtype = ref_arr.dtype # type: ignore[assignment] - new_arr = await func(ref_arr, path="foo", zarr_format=zarr_format, **kwargs) # type: ignore[call-arg] + new_arr = await func(ref_arr, path="foo", zarr_format=zarr_format, **kwargs) assert new_arr.shape == expect_shape assert new_arr.chunks == expect_chunks assert new_arr.dtype == expect_dtype @@ -187,7 +187,7 @@ def test_create_array(store: Store, zarr_format: ZarrFormat) -> None: array_w[:] = data_val assert array_w.shape == shape assert array_w.attrs == attrs - assert np.array_equal(array_w[:], np.zeros(shape, dtype=array_w.dtype) + data_val) + assert np.array_equal(array_w[:], np.zeros(shape, dtype=array_w.dtype) + data_val) # type: ignore[unreachable] @pytest.mark.parametrize("write_empty_chunks", [True, False]) @@ -326,7 +326,7 @@ async def test_create_group(store: Store, zarr_format: ZarrFormat) -> None: node = create_group(store, path=path, attributes=attrs, zarr_format=zarr_format) assert isinstance(node, Group) assert node.attrs == attrs - assert node.metadata.zarr_format == zarr_format + assert node.metadata.zarr_format == zarr_format # type: ignore[unreachable] async def test_open_group(memory_store: MemoryStore) -> None: diff --git a/tests/test_array.py b/tests/test_array.py index 132c4c26c3..e5e875a31a 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1770,7 +1770,7 @@ async def test_from_array( assert result.fill_value == new_fill_value assert result.dtype == src_dtype assert result.attrs == new_attributes - assert result.chunks == new_chunks + assert result.chunks == new_chunks # type: ignore[unreachable] @pytest.mark.parametrize("store", ["local"], indirect=True) diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py index eec0ecacae..7d5a0c29c4 100644 --- a/tests/test_codecs/test_numcodecs.py +++ b/tests/test_codecs/test_numcodecs.py @@ -85,7 +85,7 @@ def test_is_numcodec_cls() -> None: @pytest.mark.parametrize("codec_cls", ALL_CODECS) def test_get_codec_class(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None: - assert get_codec_class(codec_cls.codec_name) == codec_cls # type: ignore[comparison-overlap] + assert get_codec_class(codec_cls.codec_name) == codec_cls # type: ignore[comparison-overlap,misc] @pytest.mark.parametrize("codec_class", ALL_CODECS) @@ -240,7 +240,7 @@ def test_generic_checksum(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec try: codec_class()._codec # noqa: B018 except UnknownCodecError as e: # pragma: no cover - pytest.skip(f"{codec_class.codec_name} is not available in numcodecs: {e}") + pytest.skip(f"{codec_class.codec_name} is not available in numcodecs: {e}") # type: ignore[misc] data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16)) @@ -265,11 +265,11 @@ def test_generic_bytes_codec(codec_class: type[_numcodecs._NumcodecsArrayBytesCo codec_class()._codec # noqa: B018 except ValueError as e: # pragma: no cover if "codec not available" in str(e): - pytest.xfail(f"{codec_class.codec_name} is not available: {e}") + pytest.xfail(f"{codec_class.codec_name} is not available: {e}") # type: ignore[misc] else: raise except ImportError as e: # pragma: no cover - pytest.xfail(f"{codec_class.codec_name} is not available: {e}") + pytest.xfail(f"{codec_class.codec_name} is not available: {e}") # type: ignore[misc] data = np.arange(0, 256, dtype="float32").reshape((16, 16)) @@ -347,7 +347,7 @@ def test_codecs_pickleable(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None: try: codec = codec_cls() except UnknownCodecError as e: # pragma: no cover - pytest.skip(f"{codec_cls.codec_name} is not available in numcodecs: {e}") + pytest.skip(f"{codec_cls.codec_name} is not available in numcodecs: {e}") # type: ignore[misc] expected = codec From f9c53d5de48c35ee9c35d91e822040e60e409db9 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 6 May 2026 18:55:51 -0400 Subject: [PATCH 300/468] chore(zarr-metadata): bump version to 0.1.1 (#3949) --- packages/zarr-metadata/pyproject.toml | 2 +- packages/zarr-metadata/src/zarr_metadata/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index f24d1ae206..7fc1382e3a 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "zarr-metadata" -version = "0.1.0" +version = "0.1.1" description = "Spec-defined metadata types for Zarr v2 and v3." readme = "README.md" requires-python = ">=3.11" diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 0372373dec..953bb2e897 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -13,7 +13,7 @@ from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 from zarr_metadata.v3.group import GroupMetadataV3 -__version__ = "0.1.0" +__version__ = "0.1.1" """Hardcoded package version. Must match the `version` field in `pyproject.toml`; the sync is enforced by `tests/test_version.py`.""" From 6e7f2f3f1c104bd26ac84ec6ee51fef9ee59f9ad Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 7 May 2026 15:28:46 -0400 Subject: [PATCH 301/468] refactor: simplify internal chunk representation (#3899) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * refactor: rename guess_chunks to more clearly indicate that it guesses regular chunks * fix: use the same chunk normalization path in all cases Previously rectilinear chunk grids and regular chunk grids normalized chunks inconsistently. This change ensures that chunk specifications are always normalized by the same routines in all cases. This change also ensures that chunks=(-1, ...) consistently normalizes to a full length chunk along that axis. * refactor: use newtype pattern * docs: changelog * fix: handle 0-length arrays * test: test untested cases of chunk normalization * fix: don't accept inane input * test: check error states in normalize_chunks_1d * refactor: make resolvedchunking recursive to support nested sharding * test: add _assert_chunks_equal helper for ChunksTuple Co-Authored-By: Claude Opus 4.7 (1M context) * perf: ChunksTuple uses 1D int64 arrays per axis Switch normalize_chunks_1d to return np.ndarray[tuple[int], np.dtype[np.int64]] instead of tuple[int, ...]. The uniform-chunks branch now constructs in O(1) via np.full, recovering the single-allocation fast path that regressed when the canonical ChunksTuple representation was introduced. Update create_chunk_grid_metadata in v3.py to convert arrays to tuples of ints before passing to is_regular_nd and RectilinearChunkGridMetadata, keeping those downstream functions' signatures unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) * revert: undo out-of-scope v3.py changes from 14788aa The previous commit 14788aa was meant to only touch chunk_grids.py (Tasks 2+3 of the ChunksTuple → int64-array refactor). It also modified create_chunk_grid_metadata in v3.py — that change belongs to a later task with a different approach (widen annotations rather than materialize tuples) and a better perf profile. Restoring v3.py to its pre-14788aa state. The proper v3.py change will land in a follow-up commit. Co-Authored-By: Claude Opus 4.7 (1M context) * fix: cast ChunksTuple elements to int at consumer sites in array.py Co-Authored-By: Claude Opus 4.7 (1M context) * fix: widen is_regular_* annotations and cast ChunksTuple in create_chunk_grid_metadata Accept ndarray[int64] in is_regular_1d/is_regular_nd alongside Sequence[int]. Cast only the first element per axis on the regular path so D ints are allocated rather than N*D. Materialize fully on the rectilinear path because _validate_chunk_shapes checks isinstance(dim_spec, int) which rejects np.int64. Co-Authored-By: Claude Opus 4.7 (1M context) * test: cast ChunksTuple elements to int in create_array_metadata fixture Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite ChunksTuple equality checks and add return-type characterization Use _assert_chunks_equal for the three call sites that compared a tuple of int64 arrays against a tuple of int tuples. Add three small tests asserting that normalize_chunks_1d returns a 1D int64 ndarray for uniform, explicit-list, and -1 sentinel inputs. Co-Authored-By: Claude Opus 4.7 (1M context) * perf: vectorize is_regular_1d for ndarray inputs Per-element Python iteration over a 100K-element int64 array dominated create_array runtime on the (10**8,) chunks=(1000,) regression case (~6 ms in is_regular_nd, downstream of ChunksTuple normalization). Dispatch on np.ndarray and use a single vectorized comparison instead. End-to-end create_array on the regression case: ~7.9 ms -> ~0.6 ms. Promote numpy to a runtime import (was TYPE_CHECKING-only) for the isinstance dispatch. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor: rename ResolvedChunking to ChunkLayout Names the structure (a layout) rather than the operation that produced it. Reads cleanly for both sharded and unsharded cases, fits the recursive inner-layout pattern, and is what one reaches for when reading the code cold. Co-Authored-By: Claude Opus 4.7 (1M context) * chore: add informative error for invalid chunk grid parameter * chore: make tests compact * fix: typos * test: add tests for regular grid helper functions * fix: reject chunks=True * docs: update changelog * docs: remove unneeded changelog entry * test: test for explicit 0-sized chunk length rejection * chore: hoist imports * refactor: add as_regular_shape helper routine * Update src/zarr/core/chunk_grids.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update src/zarr/core/chunk_grids.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update src/zarr/core/array.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * chore: cleanup --------- Co-authored-by: Claude Opus 4.7 (1M context) Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3899.bugfix.md | 7 + src/zarr/core/array.py | 106 ++++------ src/zarr/core/chunk_grids.py | 322 +++++++++++++++++++++-------- src/zarr/core/metadata/v3.py | 39 ++-- tests/conftest.py | 39 ++-- tests/test_array.py | 81 +++++++- tests/test_chunk_grids.py | 244 ++++++++++++++++++---- tests/test_codecs/test_sharding.py | 2 +- tests/test_metadata/test_v3.py | 56 +++++ 9 files changed, 671 insertions(+), 225 deletions(-) create mode 100644 changes/3899.bugfix.md diff --git a/changes/3899.bugfix.md b/changes/3899.bugfix.md new file mode 100644 index 0000000000..e2b2177a39 --- /dev/null +++ b/changes/3899.bugfix.md @@ -0,0 +1,7 @@ +Make chunk normalization properly handle `-1` as a compact representation of the +length of an entire axis. Reject several previously-accepted but ill-defined +chunk specifications: `chunks=True` (previously silently produced size-1 chunks), +chunk tuples shorter than the array's number of dimensions (previously padded to +the array's shape), and `None` as a per-dimension chunk size. These all now +raise informative errors. Also fix chunk handling for 0-length array dimensions, +and add explicit rejection of 0-length chunks. diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 37f65fce32..b7e7fa1b35 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -39,9 +39,13 @@ ) from zarr.core.buffer.cpu import buffer_prototype as cpu_buffer_prototype from zarr.core.chunk_grids import ( + SHARDED_INNER_CHUNK_MAX_BYTES, ChunkGrid, - _auto_partition, - normalize_chunks, + _is_rectilinear_chunks, + as_regular_shape, + guess_chunks, + normalize_chunks_nd, + resolve_outer_and_inner_chunks, ) from zarr.core.chunk_key_encodings import ( ChunkKeyEncoding, @@ -121,10 +125,8 @@ ) from zarr.core.metadata.v3 import ( ChunkGridMetadata, - RectilinearChunkGridMetadata, - RegularChunkGridMetadata, + create_chunk_grid_metadata, parse_node_type_array, - resolve_chunks, ) from zarr.core.sync import sync from zarr.errors import ( @@ -411,8 +413,7 @@ async def _create( if chunks is not None and chunk_shape is not None: raise ValueError("Only one of chunk_shape or chunks can be provided.") - from zarr.core.chunk_grids import _is_rectilinear_chunks - + # Unify the v2 (chunks) and v3 (chunk_shape) parameter names _raw_chunks = chunks if chunks is not None else chunk_shape config_parsed = parse_array_config(config) @@ -438,7 +439,11 @@ async def _create( item_size = 1 if isinstance(dtype_parsed, HasItemSize): item_size = dtype_parsed.item_size - chunk_grid = resolve_chunks(_raw_chunks, shape, item_size) + if _raw_chunks is None: + outer_chunks = guess_chunks(shape, item_size) + else: + outer_chunks = normalize_chunks_nd(_raw_chunks, shape) + chunk_grid = create_chunk_grid_metadata(outer_chunks) result = await cls._create_v3( store_path, shape=shape, @@ -469,10 +474,12 @@ async def _create( item_size = 1 if isinstance(dtype_parsed, HasItemSize): item_size = dtype_parsed.item_size - if chunks: - _chunks = normalize_chunks(chunks, shape, item_size) + _raw = chunks or chunk_shape + if _raw is None: + outer_chunks = guess_chunks(shape, item_size) else: - _chunks = normalize_chunks(chunk_shape, shape, item_size) + outer_chunks = normalize_chunks_nd(_raw, shape) + _chunks = as_regular_shape(outer_chunks) if order is None: order_parsed = config_parsed.order @@ -4385,6 +4392,7 @@ async def init_array( zdtype = parse_dtype(dtype, zarr_format=zarr_format) shape_parsed = parse_shapelike(shape) + item_size = zdtype.item_size if isinstance(zdtype, HasItemSize) else 1 chunk_key_encoding_parsed = _parse_chunk_key_encoding( chunk_key_encoding, zarr_format=zarr_format ) @@ -4397,12 +4405,7 @@ async def init_array( else: await ensure_no_existing_node(store_path, zarr_format=zarr_format) - # Detect rectilinear (nested list) chunks or shards, e.g. [[10, 20, 30], [25, 25]] - from zarr.core.chunk_grids import _is_rectilinear_chunks - - rectilinear_meta: RectilinearChunkGridMetadata | None = None - rectilinear_shards = _is_rectilinear_chunks(shards) - + # Validate rectilinear chunks constraints if _is_rectilinear_chunks(chunks): if zarr_format == 2: raise ValueError("Zarr format 2 does not support rectilinear chunk grids.") @@ -4412,43 +4415,29 @@ async def init_array( "Use rectilinear shards instead: " "chunks=(inner_size, ...), shards=[[shard_sizes], ...]" ) - rectilinear_meta = RectilinearChunkGridMetadata( - chunk_shapes=tuple(tuple(dim_edges) for dim_edges in chunks) + + # Normalize the user's chunks into canonical ChunksTuple form + if chunks is None or chunks == "auto": + chunks_normalized = guess_chunks( + shape_parsed, + item_size, + max_bytes=SHARDED_INNER_CHUNK_MAX_BYTES if shards is not None else None, ) - # Use first chunk size per dim as placeholder for _auto_partition - chunks_flat: tuple[int, ...] | Literal["auto"] = tuple(dim_edges[0] for dim_edges in chunks) else: - # Normalize scalar int to per-dimension tuple (e.g. chunks=100000 for a 1D array) - if isinstance(chunks, int): - chunks = tuple(chunks for _ in shape_parsed) - chunks_flat = cast("tuple[int, ...] | Literal['auto']", chunks) - - # Handle rectilinear shards: shards=[[60, 40, 20], [50, 50]] - # means variable-sized shard boundaries with uniform inner chunks - shards_for_partition: ShardsLike | None = shards - if _is_rectilinear_chunks(shards): - if zarr_format == 2: - raise ValueError("Zarr format 2 does not support rectilinear chunk grids.") - rectilinear_meta = RectilinearChunkGridMetadata( - chunk_shapes=tuple(tuple(dim_edges) for dim_edges in shards) - ) - # Use first shard size per dim as placeholder for _auto_partition - shards_for_partition = tuple(dim_edges[0] for dim_edges in shards) - - item_size = 1 - if isinstance(zdtype, HasItemSize): - item_size = zdtype.item_size + chunks_normalized = normalize_chunks_nd(chunks, shape_parsed) - shard_shape_parsed, chunk_shape_parsed = _auto_partition( + # Resolve chunks + shards into outer_chunks (grid metadata) and + # inner (sub-chunk structure for ShardingCodec, None if no sharding) + outer_chunks, inner = resolve_outer_and_inner_chunks( array_shape=shape_parsed, - shard_shape=shards_for_partition, - chunk_shape=chunks_flat, + chunks=chunks_normalized, + shard_shape=shards, item_size=item_size, ) - chunks_out: tuple[int, ...] + meta: ArrayV2Metadata | ArrayV3Metadata if zarr_format == 2: - if shard_shape_parsed is not None: + if inner is not None: msg = ( "Zarr format 2 arrays can only be created with `shard_shape` set to `None`. " f"Got `shard_shape={shards}` instead." @@ -4472,7 +4461,7 @@ async def init_array( meta = AsyncArray._create_metadata_v2( shape=shape_parsed, dtype=zdtype, - chunks=chunk_shape_parsed, + chunks=as_regular_shape(outer_chunks), dimension_separator=chunk_key_encoding_parsed.separator, fill_value=fill_value, order=order_parsed, @@ -4488,40 +4477,29 @@ async def init_array( dtype=zdtype, ) sub_codecs = cast("tuple[Codec, ...]", (*array_array, array_bytes, *bytes_bytes)) + grid = create_chunk_grid_metadata(outer_chunks) codecs_out: tuple[Codec, ...] - if shard_shape_parsed is not None: + if inner is not None: + inner_chunks_flat = as_regular_shape(inner.outer_chunks) index_location = None if isinstance(shards, dict): index_location = ShardingCodecIndexLocation(shards.get("index_location", None)) if index_location is None: index_location = ShardingCodecIndexLocation.end sharding_codec = ShardingCodec( - chunk_shape=chunk_shape_parsed, codecs=sub_codecs, index_location=index_location + chunk_shape=inner_chunks_flat, codecs=sub_codecs, index_location=index_location ) - # Use rectilinear grid for validation when shards are rectilinear - if rectilinear_shards and rectilinear_meta is not None: - validation_grid: ChunkGridMetadata = rectilinear_meta - else: - validation_grid = RegularChunkGridMetadata(chunk_shape=shard_shape_parsed) sharding_codec.validate( - shape=chunk_shape_parsed, + shape=inner_chunks_flat, dtype=zdtype, - chunk_grid=validation_grid, + chunk_grid=grid, ) codecs_out = (sharding_codec,) - chunks_out = shard_shape_parsed else: - chunks_out = chunk_shape_parsed codecs_out = sub_codecs if order is not None: _warn_order_kwarg() - - grid: ChunkGridMetadata - if rectilinear_meta is not None: - grid = rectilinear_meta - else: - grid = RegularChunkGridMetadata(chunk_shape=chunks_out) meta = AsyncArray._create_metadata_v3( shape=shape_parsed, dtype=zdtype, diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 3d7313cd5d..7459908e0a 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -8,7 +8,16 @@ import warnings from dataclasses import dataclass, field from functools import reduce -from typing import TYPE_CHECKING, Any, Literal, Protocol, TypeGuard, cast, runtime_checkable +from typing import ( + TYPE_CHECKING, + Any, + NamedTuple, + NewType, + Protocol, + TypeGuard, + cast, + runtime_checkable, +) import numpy as np import numpy.typing as npt @@ -27,6 +36,38 @@ from zarr.core.array import ShardsLike from zarr.core.metadata import ArrayMetadata +SHARDED_INNER_CHUNK_MAX_BYTES: int = 1048576 +"""Target ceiling in bytes for the auto-chunking heuristic when sharding is active (1 MiB). + +Applied when `chunks` is left to auto-chunking (`None` or `"auto"`) and `shards` +is not `None`. Explicit chunk sizes are not affected by this value. +""" + +ChunksTuple = NewType("ChunksTuple", tuple[np.ndarray[tuple[int], np.dtype[np.int64]], ...]) +"""Normalized chunk specification: one 1D int64 array of chunk sizes per dimension. + +Produced exclusively by `normalize_chunks_nd` and `guess_chunks`. +Consumers should use this type to ensure they receive validated, +canonical chunk specifications rather than raw user input. +""" + + +class ChunkLayout(NamedTuple): + """Result of resolving user `chunks`/`shards` into grid metadata inputs. + + outer_chunks + Chunk sizes for the chunk grid metadata. When sharding is active + these are the shard sizes; otherwise they are the user's chunk sizes. + inner + Recursive sub-structure inside each chunk. `None` means the chunk is + opaque (no sharding). When present, `inner.outer_chunks` gives the + sub-chunk sizes passed to `ShardingCodec`, and `inner.inner` gives + the next level of nesting (for nested sharding), or `None`. + """ + + outer_chunks: ChunksTuple + inner: ChunkLayout | None = None + @dataclass(frozen=True) class FixedDimension: @@ -319,6 +360,41 @@ def _is_rectilinear_chunks(chunks: Any) -> TypeGuard[Sequence[Sequence[int]]]: return False +def is_regular_1d( + dim_chunks: Sequence[int] | np.ndarray[tuple[int], np.dtype[np.int64]], +) -> bool: + """Check if a single dimension's chunk sizes represent a regular grid. + + A regular dimension has either all chunks the same size, or all + but the last chunk the same size with the last chunk smaller + (boundary chunk). + """ + if len(dim_chunks) <= 1: + return True + first = dim_chunks[0] + if isinstance(dim_chunks, np.ndarray): + # Vectorized comparison avoids per-element Python iteration over int64 arrays. + return bool((dim_chunks[1:-1] == first).all() and dim_chunks[-1] <= first) + for c in dim_chunks[1:-1]: + if c != first: + return False + # Last chunk must be the same size or a smaller boundary chunk + return dim_chunks[-1] <= first + + +def is_regular_nd( + chunks: Iterable[Sequence[int] | np.ndarray[tuple[int], np.dtype[np.int64]]], +) -> bool: + """Check if an N-dimensional chunk specification represents a regular grid.""" + return all(is_regular_1d(d) for d in chunks) + + +def as_regular_shape(chunks: ChunksTuple) -> tuple[int, ...]: + """Flatten a regular ChunksTuple to one int per dimension.""" + assert is_regular_nd(chunks), f"expected regular chunks, got {chunks}" + return tuple(int(dim[0]) for dim in chunks) + + @dataclass(frozen=True) class ChunkGrid: """ @@ -565,7 +641,7 @@ def update_shape(self, new_shape: tuple[int, ...]) -> ChunkGrid: return ChunkGrid(dimensions=dims) -def _guess_chunks( +def _guess_regular_chunks( shape: tuple[int, ...] | int, typesize: int, *, @@ -641,53 +717,115 @@ def _guess_chunks( return tuple(int(x) for x in chunks) -def normalize_chunks(chunks: Any, shape: tuple[int, ...], typesize: int) -> tuple[int, ...]: - """Convenience function to normalize the `chunks` argument for an array - with the given `shape`.""" +def normalize_chunks_1d( + chunks: int | Iterable[object], span: int +) -> np.ndarray[tuple[int], np.dtype[np.int64]]: + """ + Normalize a one-dimensional chunk specification into a 1D int64 array of + chunk sizes that cover the span. - # N.B., expect shape already normalized + `-1` means "one chunk covering the entire span." + For an integer chunk size, all chunks are uniform — the last chunk may + overhang the span. The actual data extent of each chunk is determined + by the chunk grid at runtime, not by this function. + """ + if chunks == -1: + return np.array([span], dtype=np.int64) + if isinstance(chunks, int): + if chunks <= 0: + raise ValueError(f"Chunk size must be positive, got {chunks}") + if span == 0: + return np.array([chunks], dtype=np.int64) + n = ceildiv(span, chunks) + return np.full(n, chunks, dtype=np.int64) + else: + chunk_list = list(chunks) + if not chunk_list: + raise ValueError("Chunk specification must not be empty") + non_int = [ + (idx, c) for idx, c in enumerate(chunk_list) if not isinstance(c, numbers.Integral) + ] + if non_int: + non_int_idxs, non_int_vals = [*zip(*non_int, strict=False)] + raise TypeError( + f"Each chunk size must be an integer; got non-integer element(s) {non_int_vals!r} " + f"at indices {non_int_idxs!r}. Chunk sizes must be declared as a flat sequence of " + f"positive integers (e.g. [3, 3, 1])." + ) + ints: list[int] = [int(c) for c in chunk_list] # type: ignore[call-overload] + if any(c <= 0 for c in ints): + raise ValueError(f"All chunk sizes must be positive, got {ints}") + if sum(ints) != span: + raise ValueError(f"Chunk sizes {ints} do not sum to span {span}") + return np.asarray(ints, dtype=np.int64) + + +def normalize_chunks_nd( + chunks: Any, + shape: tuple[int, ...], +) -> ChunksTuple: + """ + Normalize a chunk specification into a `ChunksTuple`. + + This is a mechanical transformation — no heuristics, no guessing. + Handles `False` ("all data in one chunk"), scalar ints, `-1` sentinels (one chunk + per dimension covering the full span), and explicit per-dimension lists + of chunk sizes (regular or rectilinear). - # handle auto-chunking + For auto-chunking, use `guess_chunks` which returns a + `ChunksTuple` directly. `chunks=None` and `chunks=True` are rejected + here — the caller is responsible for choosing between explicit sizes + and auto-chunking. + """ if chunks is None or chunks is True: - return _guess_chunks(shape, typesize) + raise ValueError( + f'{chunks!r} is not a valid chunk input. Use chunks=None or chunks="auto" from the top-level API for auto-chunking, or pass an int / tuple of ints.' + ) # handle no chunking if chunks is False: - return shape + return ChunksTuple(tuple(np.array([s], dtype=np.int64) for s in shape)) - # handle 1D convenience form + # handle 1D convenience form. bool is excluded above so this only catches actual ints. if isinstance(chunks, numbers.Integral): chunks = tuple(int(chunks) for _ in shape) - # handle dask-style chunks (iterable of iterables) - if all(isinstance(c, (tuple, list)) for c in chunks): - for i, c in enumerate(chunks): - if any(x != y for x, y in itertools.pairwise(c[:-1])) or (len(c) > 1 and c[-1] > c[0]): - raise ValueError( - f"Irregular chunk sizes in dimension {i}: {tuple(c)}. " - "Only uniform chunks (with an optional smaller final chunk) are supported." - ) - chunks = tuple(c[0] for c in chunks) - # handle bad dimensionality - if len(chunks) > len(shape): - raise ValueError("too many dimensions in chunks") - - # handle underspecified chunks - if len(chunks) < len(shape): - # assume chunks across remaining dimensions - chunks += shape[len(chunks) :] - - # handle None or -1 in chunks - if -1 in chunks or None in chunks: - chunks = tuple( - s if c == -1 or c is None else int(c) for s, c in zip(shape, chunks, strict=False) + if len(chunks) != len(shape): + raise ValueError( + f"chunks has {len(chunks)} dimensions but shape has {len(shape)} dimensions" ) - if not all(isinstance(c, numbers.Integral) for c in chunks): - raise TypeError("non integer value in chunks") + return ChunksTuple( + tuple(normalize_chunks_1d(c, span=s) for c, s in zip(chunks, shape, strict=True)) + ) + - return tuple(int(c) for c in chunks) +def guess_chunks( + shape: tuple[int, ...], typesize: int, *, max_bytes: int | None = None +) -> ChunksTuple: + """ + Heuristically determine chunk sizes for an array. + + This is the policy function — it makes opinionated choices about + chunk sizes based on array shape and element size, and returns a + normalized `ChunksTuple`. + + Parameters + ---------- + shape : tuple[int, ...] + Array shape. + typesize : int + Size of one element in bytes. + max_bytes : int or None + Target maximum chunk size in bytes. If None, uses the default + heuristic from `_guess_regular_chunks`. + """ + if max_bytes is not None: + flat = _guess_regular_chunks(shape, typesize, max_bytes=max_bytes) + else: + flat = _guess_regular_chunks(shape, typesize) + return normalize_chunks_nd(flat, shape) def _guess_num_chunks_per_axis_shard( @@ -727,62 +865,76 @@ def _guess_num_chunks_per_axis_shard( return chunks_per_shard -def _auto_partition( +def resolve_outer_and_inner_chunks( *, array_shape: tuple[int, ...], - chunk_shape: tuple[int, ...] | Literal["auto"], + chunks: ChunksTuple, shard_shape: ShardsLike | None, item_size: int, -) -> tuple[tuple[int, ...] | None, tuple[int, ...]]: - """ - Automatically determine the shard shape and chunk shape for an array, given the shape and dtype of the array. - If `shard_shape` is `None` and the chunk_shape is "auto", the chunks will be set heuristically based - on the dtype and shape of the array. - If `shard_shape` is "auto", then the shard shape will be set heuristically from the dtype and shape - of the array; if the `chunk_shape` is also "auto", then the chunks will be set heuristically as well, - given the dtype and shard shape. Otherwise, the chunks will be returned as-is. +) -> ChunkLayout: + """Resolve user `chunks`/`shards` into outer and inner chunk specs. + + Parameters + ---------- + array_shape + The array shape. + chunks + Normalized chunk specification (the user's `chunks=`). + shard_shape + Raw shard specification (the user's `shards=`). + `None` means no sharding, `"auto"` triggers heuristic inference, + a nested sequence is treated as rectilinear shard boundaries, + and anything else is used as a regular shard shape. + item_size + Element size in bytes. + + Returns + ------- + ChunkLayout + `outer_chunks` is the `ChunksTuple` for chunk grid + metadata. `inner` holds the sub-chunk structure for + `ShardingCodec`, or is `None` when sharding is not active. """ if shard_shape is None: - _shards_out: None | tuple[int, ...] = None - if chunk_shape == "auto": - _chunks_out = _guess_chunks(array_shape, item_size) - else: - _chunks_out = chunk_shape - else: - if chunk_shape == "auto": - # aim for a 1MiB chunk - _chunks_out = _guess_chunks(array_shape, item_size, max_bytes=1048576) - else: - _chunks_out = chunk_shape + return ChunkLayout(outer_chunks=chunks) - if shard_shape == "auto": - warnings.warn( - "Automatic shard shape inference is experimental and may change without notice.", - ZarrUserWarning, - stacklevel=2, - ) - _shards_out = () - target_shard_size_bytes = zarr.config.get("array.target_shard_size_bytes", None) - num_chunks_per_shard_axis = ( - _guess_num_chunks_per_axis_shard( - chunk_shape=_chunks_out, - item_size=item_size, - max_bytes=target_shard_size_bytes, - array_shape=array_shape, - ) - if (has_auto_shard := (target_shard_size_bytes is not None)) - else 2 + # Rectilinear shards: normalize the nested sequence directly. + if _is_rectilinear_chunks(shard_shape): + outer = normalize_chunks_nd(shard_shape, array_shape) + return ChunkLayout(outer_chunks=outer, inner=ChunkLayout(outer_chunks=chunks)) + + # Extract the flat chunk shape (first size per dimension) for arithmetic. + chunk_shape_flat = as_regular_shape(chunks) + + if shard_shape == "auto": + warnings.warn( + "Automatic shard shape inference is experimental and may change without notice.", + ZarrUserWarning, + stacklevel=2, + ) + _shards_out: tuple[int, ...] = () + target_shard_size_bytes = zarr.config.get("array.target_shard_size_bytes", None) + num_chunks_per_shard_axis = ( + _guess_num_chunks_per_axis_shard( + chunk_shape=chunk_shape_flat, + item_size=item_size, + max_bytes=target_shard_size_bytes, + array_shape=array_shape, ) - for a_shape, c_shape in zip(array_shape, _chunks_out, strict=True): - # The previous heuristic was `a_shape // c_shape > 8` and now, with target_shard_size_bytes, we only check that the shard size is less than the array size. - can_shard_axis = a_shape // c_shape > 8 if not has_auto_shard else True - if can_shard_axis: - _shards_out += (c_shape * num_chunks_per_shard_axis,) - else: - _shards_out += (c_shape,) - elif isinstance(shard_shape, dict): - _shards_out = tuple(shard_shape["shape"]) - else: - _shards_out = cast("tuple[int, ...]", shard_shape) + if (has_auto_shard := (target_shard_size_bytes is not None)) + else 2 + ) + for a_shape, c_shape in zip(array_shape, chunk_shape_flat, strict=True): + can_shard_axis = a_shape // c_shape > 8 if not has_auto_shard else True + if can_shard_axis: + _shards_out += (c_shape * num_chunks_per_shard_axis,) + else: + _shards_out += (c_shape,) + shard_flat = _shards_out + elif isinstance(shard_shape, dict): + shard_flat = tuple(shard_shape["shape"]) + else: + shard_flat = cast("tuple[int, ...]", shard_shape) - return _shards_out, _chunks_out + outer = normalize_chunks_nd(shard_flat, array_shape) + return ChunkLayout(outer_chunks=outer, inner=ChunkLayout(outer_chunks=chunks)) diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 5750a25c30..c794ee2e87 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -11,6 +11,7 @@ from zarr.abc.metadata import Metadata from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.buffer.core import default_buffer_prototype +from zarr.core.chunk_grids import is_regular_nd from zarr.core.chunk_key_encodings import ( ChunkKeyEncoding, ChunkKeyEncodingLike, @@ -19,7 +20,6 @@ from zarr.core.common import ( JSON, ZARR_JSON, - ChunksLike, DimensionNamesLike, NamedConfig, NamedRequiredConfig, @@ -41,6 +41,7 @@ from typing import Self from zarr.core.buffer import Buffer, BufferPrototype + from zarr.core.chunk_grids import ChunksTuple from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar @@ -371,27 +372,33 @@ def from_dict(cls, data: RectilinearChunkGridMetadataJSON) -> Self: # type: ign ChunkGridMetadata = RegularChunkGridMetadata | RectilinearChunkGridMetadata -def resolve_chunks( - chunks: ChunksLike, - shape: tuple[int, ...], - typesize: int, +def create_chunk_grid_metadata( + chunks: ChunksTuple, ) -> ChunkGridMetadata: - """Construct a chunk grid from user-facing input (e.g. ``create_array(chunks=...)``). + """Construct a chunk grid metadata object from a normalized `ChunksTuple`. - Nested sequences like ``[[10, 20], [5, 5]]`` produce a ``RectilinearChunkGridMetadata``. - Flat inputs like ``(10, 10)`` or a scalar ``int`` produce a ``RegularChunkGridMetadata`` - after normalization via :func:`~zarr.core.chunk_grids.normalize_chunks`. + Regular chunks produce a `RegularChunkGridMetadata`. + Rectilinear chunks produce a `RectilinearChunkGridMetadata`. + + Parameters + ---------- + chunks : ChunksTuple + Normalized chunk specification, as returned by + `normalize_chunks_nd` or `guess_chunks`. See Also -------- parse_chunk_grid : Deserialize a chunk grid from stored JSON metadata. """ - from zarr.core.chunk_grids import _is_rectilinear_chunks, normalize_chunks - - if _is_rectilinear_chunks(chunks): - return RectilinearChunkGridMetadata(chunk_shapes=tuple(tuple(c) for c in chunks)) - - return RegularChunkGridMetadata(chunk_shape=normalize_chunks(chunks, shape, typesize)) + if is_regular_nd(chunks): + # If we know the chunks specification is regular, then we can take the first + # chunk size for each dimension as the chunk shape. + chunk_shape = tuple(int(dim_chunks[0]) for dim_chunks in chunks) + return RegularChunkGridMetadata(chunk_shape=chunk_shape) + else: + return RectilinearChunkGridMetadata( + chunk_shapes=tuple(tuple(int(x) for x in d) for d in chunks) + ) def parse_chunk_grid( @@ -401,7 +408,7 @@ def parse_chunk_grid( See Also -------- - resolve_chunks : Construct a chunk grid from user-facing input. + create_chunk_grid_metadata : Construct a chunk grid from user-facing input. """ if isinstance(data, (RegularChunkGridMetadata, RectilinearChunkGridMetadata)): return data diff --git a/tests/conftest.py b/tests/conftest.py index 6577f8afa0..3515acace0 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -22,7 +22,13 @@ _parse_chunk_encoding_v3, _parse_chunk_key_encoding, ) -from zarr.core.chunk_grids import _auto_partition +from zarr.core.chunk_grids import ( + SHARDED_INNER_CHUNK_MAX_BYTES, + as_regular_shape, + guess_chunks, + normalize_chunks_nd, + resolve_outer_and_inner_chunks, +) from zarr.core.common import ( JSON, DimensionNamesLike, @@ -37,7 +43,7 @@ ) from zarr.core.dtype.common import HasItemSize from zarr.core.metadata.v2 import ArrayV2Metadata -from zarr.core.metadata.v3 import ArrayV3Metadata, RegularChunkGridMetadata +from zarr.core.metadata.v3 import ArrayV3Metadata, create_chunk_grid_metadata from zarr.core.sync import sync from zarr.storage import FsspecStore, LocalStore, MemoryStore, StorePath, ZipStore from zarr.testing.store import LatencyStore @@ -345,10 +351,18 @@ def create_array_metadata( item_size = 1 if isinstance(dtype_parsed, HasItemSize): item_size = dtype_parsed.item_size - shard_shape_parsed, chunk_shape_parsed = _auto_partition( + if chunks == "auto": + chunks_normalized = guess_chunks( + shape_parsed, + item_size, + max_bytes=SHARDED_INNER_CHUNK_MAX_BYTES if shards is not None else None, + ) + else: + chunks_normalized = normalize_chunks_nd(chunks, shape_parsed) + outer_chunks, inner = resolve_outer_and_inner_chunks( array_shape=shape_parsed, + chunks=chunks_normalized, shard_shape=shards, - chunk_shape=chunks, item_size=item_size, ) @@ -356,7 +370,6 @@ def create_array_metadata( order_parsed = zarr_config.get("array.order") else: order_parsed = order - chunks_out: tuple[int, ...] if zarr_format == 2: filters_parsed, compressor_parsed = _parse_chunk_encoding_v2( @@ -366,7 +379,7 @@ def create_array_metadata( return ArrayV2Metadata( shape=shape_parsed, dtype=dtype_parsed, - chunks=chunk_shape_parsed, + chunks=as_regular_shape(outer_chunks), order=order_parsed, dimension_separator=chunk_key_encoding_parsed.separator, fill_value=fill_value, @@ -384,32 +397,32 @@ def create_array_metadata( sub_codecs: tuple[Codec, ...] = (*array_array, array_bytes, *bytes_bytes) codecs_out: tuple[Codec, ...] - if shard_shape_parsed is not None: + if inner is not None: + inner_chunks_flat = as_regular_shape(inner.outer_chunks) index_location = None if isinstance(shards, dict): index_location = ShardingCodecIndexLocation(shards.get("index_location", None)) if index_location is None: index_location = ShardingCodecIndexLocation.end sharding_codec = ShardingCodec( - chunk_shape=chunk_shape_parsed, + chunk_shape=inner_chunks_flat, codecs=sub_codecs, index_location=index_location, ) + validation_grid = create_chunk_grid_metadata(outer_chunks) sharding_codec.validate( - shape=chunk_shape_parsed, + shape=inner_chunks_flat, dtype=dtype_parsed, - chunk_grid=RegularChunkGridMetadata(chunk_shape=shard_shape_parsed), + chunk_grid=validation_grid, ) codecs_out = (sharding_codec,) - chunks_out = shard_shape_parsed else: - chunks_out = chunk_shape_parsed codecs_out = sub_codecs return ArrayV3Metadata( shape=shape_parsed, data_type=dtype_parsed, - chunk_grid={"name": "regular", "configuration": {"chunk_shape": chunks_out}}, + chunk_grid=create_chunk_grid_metadata(outer_chunks), chunk_key_encoding=chunk_key_encoding_parsed, fill_value=fill_value, codecs=codecs_out, diff --git a/tests/test_array.py b/tests/test_array.py index e5e875a31a..51df8d12c6 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -46,7 +46,12 @@ ) from zarr.core.array_spec import ArrayConfig, ArrayConfigParams from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, default_buffer_prototype -from zarr.core.chunk_grids import _auto_partition +from zarr.core.chunk_grids import ( + SHARDED_INNER_CHUNK_MAX_BYTES, + guess_chunks, + normalize_chunks_nd, + resolve_outer_and_inner_chunks, +) from zarr.core.chunk_key_encodings import ChunkKeyEncodingParams from zarr.core.common import JSON, ZarrFormat, ceildiv from zarr.core.dtype import ( @@ -1073,36 +1078,53 @@ def test_auto_partition_auto_shards( where there are 8 or more chunks. """ dtype = np.dtype("uint8") + chunks_normalized = normalize_chunks_nd(chunk_shape, array_shape) with pytest.warns( ZarrUserWarning, match="Automatic shard shape inference is experimental and may change without notice.", ): with zarr.config.set({"array.target_shard_size_bytes": target_shard_size_bytes}): - auto_shards, _ = _auto_partition( + outer_chunks, _ = resolve_outer_and_inner_chunks( array_shape=array_shape, - chunk_shape=chunk_shape, + chunks=chunks_normalized, shard_shape="auto", item_size=dtype.itemsize, ) + auto_shards = tuple(dim[0] for dim in outer_chunks) assert auto_shards == expected_shards def test_auto_partition_auto_shards_with_auto_chunks_should_be_close_to_1MiB() -> None: """ - Test that automatically picking a shard size and a chunk size gives roughly 1MiB chunks. + Test that automatically picking chunk and shard sizes together produces + chunks close to 1 MiB and shards that are a multiple of the chunk size. """ + array_shape = (10_000_000,) + item_size = 1 + # Auto-chunks with sharding use the default inner chunk size target + chunks_normalized = guess_chunks( + array_shape, item_size, max_bytes=SHARDED_INNER_CHUNK_MAX_BYTES + ) + chunk_shape = tuple(dim[0] for dim in chunks_normalized) + chunk_bytes = np.prod(chunk_shape) * item_size + assert chunk_bytes <= SHARDED_INNER_CHUNK_MAX_BYTES + assert chunk_bytes > SHARDED_INNER_CHUNK_MAX_BYTES // 4 # should be in the right ballpark + with pytest.warns( ZarrUserWarning, match="Automatic shard shape inference is experimental and may change without notice.", ): with zarr.config.set({"array.target_shard_size_bytes": 10_000_000}): - _, chunk_shape = _auto_partition( - array_shape=(10_000_000,), - chunk_shape="auto", + outer_chunks, inner = resolve_outer_and_inner_chunks( + array_shape=array_shape, + chunks=chunks_normalized, shard_shape="auto", - item_size=1, + item_size=item_size, ) - assert chunk_shape == (625000,) + assert inner is not None + shard_shape = tuple(dim[0] for dim in outer_chunks) + # Shard dimensions must be multiples of chunk dimensions + assert all(s % c == 0 for s, c in zip(shard_shape, chunk_shape, strict=True)) def test_chunks_and_shards() -> None: @@ -2321,3 +2343,44 @@ def test_with_config_polymorphism() -> None: arr_source_config_dict = arr.with_config(source_config_dict) assert arr_source_config.config == arr_source_config_dict.config + + +@pytest.mark.parametrize( + ("chunk_input", "expected"), + [ + (-1, ((10,),)), + ((-1,), ((10,),)), + ((10,), ((10,),)), + ((5,), ((5, 5),)), + ((3,), ((3, 3, 3, 1),)), + ], + ids=["scalar-neg1", "tuple-neg1", "exact", "half", "remainder"], +) +async def test_create_array_chunks_1d( + chunk_input: int | tuple[int, ...], + expected: tuple[tuple[int, ...], ...], +) -> None: + """Test that chunk normalization produces the expected chunk sizes for 1D arrays.""" + arr = await create_array(store={}, shape=(10,), chunks=chunk_input, dtype="uint8") + assert arr.write_chunk_sizes == expected + + +@pytest.mark.parametrize( + ("chunk_input", "expected"), + [ + (-1, ((10,), (12,), (15,))), + ((3, 4, 5), ((3, 3, 3, 1), (4, 4, 4), (5, 5, 5))), + ((-1, 4, -1), ((10,), (4, 4, 4), (15,))), + ((10, 12, 15), ((10,), (12,), (15,))), + ((7, 3, 2), ((7, 3), (3, 3, 3, 3), (2, 2, 2, 2, 2, 2, 2, 1))), + ], + ids=["all-neg1", "mixed", "neg1-middle", "exact", "remainder"], +) +async def test_create_array_chunks_3d( + chunk_input: int | tuple[int, ...], + expected: tuple[tuple[int, ...], ...], +) -> None: + """Test that chunk normalization produces the expected chunk sizes for 3D arrays.""" + shape = (10, 12, 15) + arr = await create_array(store={}, shape=shape, chunks=chunk_input, dtype="float64") + assert arr.write_chunk_sizes == expected diff --git a/tests/test_chunk_grids.py b/tests/test_chunk_grids.py index 2920b5d6f3..681a599130 100644 --- a/tests/test_chunk_grids.py +++ b/tests/test_chunk_grids.py @@ -1,9 +1,29 @@ +import re from typing import Any import numpy as np import pytest -from zarr.core.chunk_grids import _guess_chunks, normalize_chunks +from tests.test_codecs.conftest import Expect, ExpectErr +from zarr.core.chunk_grids import ( + ChunkLayout, + _guess_regular_chunks, + normalize_chunks_1d, + normalize_chunks_nd, + resolve_outer_and_inner_chunks, +) + + +def _assert_chunks_equal( + actual: tuple[Any, ...], + expected: tuple[tuple[int, ...], ...], +) -> None: + """Compare a ChunksTuple (tuple of np.int64 arrays) against a tuple of int tuples.""" + assert len(actual) == len(expected), f"axis count mismatch: {len(actual)} vs {len(expected)}" + for axis, (a, e) in enumerate(zip(actual, expected, strict=True)): + assert np.array_equal(a, np.asarray(e, dtype=np.int64)), ( + f"axis {axis}: {list(a)} != {list(e)}" + ) @pytest.mark.parametrize( @@ -11,7 +31,7 @@ ) @pytest.mark.parametrize("itemsize", [1, 2, 4]) def test_guess_chunks(shape: tuple[int, ...], itemsize: int) -> None: - chunks = _guess_chunks(shape, itemsize) + chunks = _guess_regular_chunks(shape, itemsize) chunk_size = np.prod(chunks) * itemsize assert isinstance(chunks, tuple) assert len(chunks) == len(shape) @@ -21,43 +41,193 @@ def test_guess_chunks(shape: tuple[int, ...], itemsize: int) -> None: @pytest.mark.parametrize( - ("chunks", "shape", "typesize", "expected"), + ("chunks", "shape", "expected"), [ - ((10,), (100,), 1, (10,)), - ([10], (100,), 1, (10,)), - (10, (100,), 1, (10,)), - ((10, 10), (100, 10), 1, (10, 10)), - (10, (100, 10), 1, (10, 10)), - ((10, None), (100, 10), 1, (10, 10)), - (30, (100, 20, 10), 1, (30, 30, 30)), - ((30,), (100, 20, 10), 1, (30, 20, 10)), - ((30, None), (100, 20, 10), 1, (30, 20, 10)), - ((30, None, None), (100, 20, 10), 1, (30, 20, 10)), - ((30, 20, None), (100, 20, 10), 1, (30, 20, 10)), - ((30, 20, 10), (100, 20, 10), 1, (30, 20, 10)), - # dask-style chunks (uniform with optional smaller final chunk) - (((100, 100, 100), (50, 50)), (300, 100), 1, (100, 50)), - (((100, 100, 50),), (250,), 1, (100,)), - (((100,),), (100,), 1, (100,)), - # auto chunking - (None, (100,), 1, (100,)), - (-1, (100,), 1, (100,)), - ((30, -1, None), (100, 20, 10), 1, (30, 20, 10)), + # 1D cases + ((10,), (100,), ((10,) * 10,)), + ([10], (100,), ((10,) * 10,)), + (10, (100,), ((10,) * 10,)), + # 2D cases + ((10, 10), (100, 10), ((10,) * 10, (10,))), + (10, (100, 10), ((10,) * 10, (10,))), + ((10, -1), (100, 10), ((10,) * 10, (10,))), + # 3D cases + (30, (100, 20, 10), ((30, 30, 30, 30), (30,), (30,))), + ((30, -1, -1), (100, 20, 10), ((30, 30, 30, 30), (20,), (10,))), + ((30, 20, -1), (100, 20, 10), ((30, 30, 30, 30), (20,), (10,))), + ((30, 20, 10), (100, 20, 10), ((30, 30, 30, 30), (20,), (10,))), + # dask-style chunks (explicit per-chunk sizes) + (((100, 100, 100), (50, 50)), (300, 100), ((100, 100, 100), (50, 50))), + (((100, 100, 50),), (250,), ((100, 100, 50),)), + (((100,),), (100,), ((100,),)), + # no chunking (False means each dimension is one chunk spanning the full extent) + (False, (100,), ((100,),)), + (False, (100, 50), ((100,), (50,))), + # sentinel values + (-1, (100,), ((100,),)), + # zero-length dimensions preserve the declared chunk size + (10, (0,), ((10,),)), + ((5, 10), (0, 100), ((5,), (10,) * 10)), + ((5, 10), (20, 0), ((5, 5, 5, 5), (10,))), ], ) def test_normalize_chunks( - chunks: Any, shape: tuple[int, ...], typesize: int, expected: tuple[int, ...] + chunks: Any, shape: tuple[int, ...], expected: tuple[tuple[int, ...], ...] +) -> None: + _assert_chunks_equal(normalize_chunks_nd(chunks, shape), expected) + + +@pytest.mark.parametrize( + ("array_shape", "chunks_input", "shard_shape", "expected_outer", "expected_inner_outer"), + [ + # no sharding: outer = chunks, inner = None + ((100,), (10,), None, ((10,) * 10,), None), + # explicit regular shards + ((100,), (10,), (50,), ((50, 50),), ((10,) * 10,)), + # rectilinear shards + ((100,), (10,), ((60, 40),), ((60, 40),), ((10,) * 10,)), + # dict-style shards + ((100, 100), (10, 10), {"shape": (50, 50)}, ((50, 50), (50, 50)), ((10,) * 10, (10,) * 10)), + ], +) +def test_resolve_outer_and_inner_chunks( + array_shape: tuple[int, ...], + chunks_input: tuple[int, ...], + shard_shape: Any, + expected_outer: tuple[tuple[int, ...], ...], + expected_inner_outer: tuple[tuple[int, ...], ...] | None, +) -> None: + chunks = normalize_chunks_nd(chunks_input, array_shape) + outer_chunks, inner = resolve_outer_and_inner_chunks( + array_shape=array_shape, chunks=chunks, shard_shape=shard_shape, item_size=1 + ) + _assert_chunks_equal(outer_chunks, expected_outer) + if expected_inner_outer is None: + assert inner is None + else: + assert inner is not None + _assert_chunks_equal(inner.outer_chunks, expected_inner_outer) + assert inner.inner is None + + +def test_chunk_layout_nested() -> None: + """Test that ChunkLayout supports recursive nesting for nested sharding.""" + leaf = normalize_chunks_nd((5, 5), (100, 100)) + mid = ChunkLayout( + outer_chunks=normalize_chunks_nd((25, 25), (100, 100)), + inner=ChunkLayout(outer_chunks=leaf), + ) + top = ChunkLayout(outer_chunks=normalize_chunks_nd((50, 50), (100, 100)), inner=mid) + + # Three levels: top -> mid -> leaf + _assert_chunks_equal(top.outer_chunks, ((50, 50), (50, 50))) + assert top.inner is not None + _assert_chunks_equal(top.inner.outer_chunks, ((25,) * 4, (25,) * 4)) + assert top.inner.inner is not None + _assert_chunks_equal(top.inner.inner.outer_chunks, ((5,) * 20, (5,) * 20)) + assert top.inner.inner.inner is None + + +@pytest.mark.parametrize( + "case", + [ + ExpectErr(input=(0, 100), msg="Chunk size must be positive", exception_cls=ValueError), + ExpectErr(input=(-2, 100), msg="Chunk size must be positive", exception_cls=ValueError), + ExpectErr(input=([], 100), msg="must not be empty", exception_cls=ValueError), + ExpectErr(input=([10, -1, 10], 100), msg="must be positive", exception_cls=ValueError), + ExpectErr(input=([10, 0, 10], 20), msg="must be positive", exception_cls=ValueError), + ExpectErr(input=([10, 20], 100), msg="do not sum to span", exception_cls=ValueError), + # Nested/RLE form for a single dim is rejected with offending indices. + ExpectErr( + input=([[3, 3], 1], 7), + msg="non-integer element(s) ([3, 3],) at indices (0,)", + exception_cls=TypeError, + ), + # Multiple non-int elements: all offending indices reported. + ExpectErr( + input=([1, [2, 2], 1, [3]], 9), + msg="non-integer element(s) ([2, 2], [3]) at indices (1, 3)", + exception_cls=TypeError, + ), + # Strings are non-integers and should be reported the same way. + ExpectErr( + input=([2, "3", 5], 10), + msg="non-integer element(s) ('3',) at indices (1,)", + exception_cls=TypeError, + ), + ], + ids=[ + "zero-uniform", + "negative-uniform", + "empty-list", + "negative-element", + "zero-element", + "wrong-sum", + "rle-single-dim", + "multiple-non-ints", + "string-element", + ], +) +def test_normalize_chunks_1d_errors(case: ExpectErr[tuple[Any, int]]) -> None: + """Invalid 1D chunk specifications are rejected with informative error messages.""" + chunks, span = case.input + with pytest.raises(case.exception_cls, match=re.escape(case.msg)): + normalize_chunks_1d(chunks, span=span) + + +@pytest.mark.parametrize( + "case", + [ + ExpectErr( + input=(None, (100,)), + msg="None is not a valid chunk input", + exception_cls=ValueError, + ), + # `True` is rejected explicitly because bool is a subclass of int — without + # this guard, `chunks=True` would silently produce size-1 chunks. + ExpectErr( + input=(True, (100,)), + msg="True is not a valid chunk input", + exception_cls=ValueError, + ), + ExpectErr(input=("foo", (100,)), msg="dimensions", exception_cls=ValueError), + ExpectErr(input=((100, 10), (100,)), msg="dimensions", exception_cls=ValueError), + ExpectErr(input=((10,), (100, 100)), msg="dimensions", exception_cls=ValueError), + # End-to-end: per-dim RLE surfaces through normalize_chunks_nd. + ExpectErr( + input=([[6, 4], [[3, 3], 1]], (10, 10)), + msg="non-integer element(s) ([3, 3],) at indices (0,)", + exception_cls=TypeError, + ), + ], + ids=["none", "true", "string", "too-many-dims", "too-few-dims", "rle-inner-dim"], +) +def test_normalize_chunks_nd_errors(case: ExpectErr[tuple[Any, tuple[int, ...]]]) -> None: + """Invalid N-D chunk specifications are rejected with informative error messages.""" + chunks, shape = case.input + with pytest.raises(case.exception_cls, match=re.escape(case.msg)): + normalize_chunks_nd(chunks, shape) + + +@pytest.mark.parametrize( + "case", + [ + # uniform-chunks branch: one int → broadcast across span via np.full. + Expect(input=(1000, 100_000), expected=[1000] * 100), + # explicit-per-chunk branch. + Expect(input=([10, 20, 30, 40], 100), expected=[10, 20, 30, 40]), + # -1 sentinel branch: one chunk covering the full span. + Expect(input=(-1, 100), expected=[100]), + ], + ids=["uniform", "explicit-list", "full-span-sentinel"], +) +def test_normalize_chunks_1d_returns_int64_array( + case: Expect[tuple[Any, int], list[int]], ) -> None: - assert expected == normalize_chunks(chunks, shape, typesize) - - -def test_normalize_chunks_errors() -> None: - with pytest.raises(ValueError): - normalize_chunks("foo", (100,), 1) - with pytest.raises(ValueError): - normalize_chunks((100, 10), (100,), 1) - # dask-style irregular chunks should raise - with pytest.raises(ValueError, match="Irregular chunk sizes"): - normalize_chunks(((10, 20, 30),), (60,), 1) - with pytest.raises(ValueError, match="Irregular chunk sizes"): - normalize_chunks(((100, 100), (10, 20)), (200, 30), 1) + """Every branch of normalize_chunks_1d must produce a 1D int64 array.""" + chunks, span = case.input + result = normalize_chunks_1d(chunks, span) + assert isinstance(result, np.ndarray) + assert result.dtype == np.int64 + assert result.ndim == 1 + assert result.tolist() == case.expected diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 43d03caf11..233cc4cb77 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -497,7 +497,7 @@ def test_invalid_shard_shape() -> None: {}, shape=(16, 16), shards=(16, 16), - chunks=(9,), + chunks=(9, 9), dtype=np.dtype("uint8"), fill_value=0, ) diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 2bd8488702..07e06cd3fe 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -5,11 +5,13 @@ import json from typing import TYPE_CHECKING +import numpy as np import pytest from tests.conftest import Expect, ExpectFail from tests.test_metadata.conftest import minimal_metadata_dict_v3 from zarr.core.buffer import default_buffer_prototype +from zarr.core.chunk_grids import is_regular_1d, is_regular_nd from zarr.core.config import config from zarr.core.dtype import UInt8 from zarr.core.group import GroupMetadata, parse_node_type @@ -103,6 +105,60 @@ def test_parse_codecs_unknown_raises(monkeypatch: pytest.MonkeyPatch) -> None: parse_codecs([{"name": "unknown"}]) +# --------------------------------------------------------------------------- +# Chunk-grid regularity helpers +# --------------------------------------------------------------------------- + +# Cases used for both list/tuple (Python-sequence path) and ndarray (vectorized +# path) of `is_regular_1d`. Parametrizing the input form ensures both branches +# are exercised by the same suite of edge cases. +_REGULAR_1D_CASES: list[Expect[list[int], bool]] = [ + Expect(input=[], output=True, id="empty"), + Expect(input=[10], output=True, id="single-chunk"), + Expect(input=[10, 10, 10], output=True, id="all-equal"), + Expect(input=[10, 10, 10, 7], output=True, id="smaller-boundary"), + Expect(input=[10, 10, 10, 10], output=True, id="exact-multiple"), + Expect(input=[10, 5, 10], output=False, id="middle-mismatch"), + Expect(input=[10, 10, 10, 12], output=False, id="last-larger"), + # The first chunk anchors the size; later mismatches in the middle fail + # before the boundary check. + Expect(input=[5, 10, 5], output=False, id="middle-larger"), +] + + +@pytest.mark.parametrize("case", _REGULAR_1D_CASES, ids=lambda c: c.id) +def test_is_regular_1d_sequence(case: Expect[list[int], bool]) -> None: + """`is_regular_1d` accepts plain Python sequences and uses the iterative path.""" + # list and tuple both go through the non-ndarray branch. + assert is_regular_1d(case.input) is case.output + assert is_regular_1d(tuple(case.input)) is case.output + + +@pytest.mark.parametrize("case", _REGULAR_1D_CASES, ids=lambda c: c.id) +def test_is_regular_1d_ndarray(case: Expect[list[int], bool]) -> None: + """`is_regular_1d` accepts int64 ndarrays and uses the vectorized path.""" + arr = np.asarray(case.input, dtype=np.int64) + assert is_regular_1d(arr) is case.output + + +@pytest.mark.parametrize( + "case", + [ + Expect(input=[[10, 10, 10], [5, 5]], output=True, id="all-regular"), + Expect(input=[[10, 10, 7], [5, 5, 5, 3]], output=True, id="all-regular-with-boundary"), + Expect(input=[[10, 10, 10], [5, 8, 5]], output=False, id="second-dim-irregular"), + Expect(input=[[10, 5, 10], [5, 5]], output=False, id="first-dim-irregular"), + Expect(input=[], output=True, id="zero-dims"), + ], + ids=lambda c: c.id, +) +def test_is_regular_nd_sequence(case: Expect[list[list[int]], bool]) -> None: + """`is_regular_nd` returns True iff every per-dim spec is regular.""" + assert is_regular_nd(case.input) is case.output + # Same result via ndarray inputs. + assert is_regular_nd([np.asarray(d, dtype=np.int64) for d in case.input]) is case.output + + # --------------------------------------------------------------------------- # Types # --------------------------------------------------------------------------- From 14450013f843c0021c17c95a44457107d8688f20 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Thu, 7 May 2026 18:59:44 -0400 Subject: [PATCH 302/468] Fix V3 time types (#3955) --- src/zarr/core/dtype/npy/time.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index 6a864dc889..c8d2718d52 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -17,7 +17,7 @@ import numpy as np from typing_extensions import ReadOnly -from zarr.core.common import NamedConfig +from zarr.core.common import NamedRequiredConfig from zarr.core.dtype.common import ( DataTypeValidationError, DTypeConfig_V2, @@ -111,14 +111,14 @@ class TimeConfig(TypedDict): scale_factor: ReadOnly[int] -class DateTime64JSON_V3(NamedConfig[Literal["numpy.datetime64"], TimeConfig]): +class DateTime64JSON_V3(NamedRequiredConfig[Literal["numpy.datetime64"], TimeConfig]): """ The JSON representation of the ``numpy.datetime64`` data type in Zarr V3. References ---------- This representation is defined in the ``numpy.datetime64`` - [specification document](https://zarr-specs.readthedocs.io/en/latest/spec/v3/datatypes.html#numpy-datetime64). + [specification document](https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.datetime64). Examples -------- @@ -128,20 +128,20 @@ class DateTime64JSON_V3(NamedConfig[Literal["numpy.datetime64"], TimeConfig]): "configuration": { "unit": "ms", "scale_factor": 1 - } + } } ``` """ -class TimeDelta64JSON_V3(NamedConfig[Literal["numpy.timedelta64"], TimeConfig]): +class TimeDelta64JSON_V3(NamedRequiredConfig[Literal["numpy.timedelta64"], TimeConfig]): """ The JSON representation of the ``TimeDelta64`` data type in Zarr V3. References ---------- This representation is defined in the numpy.timedelta64 - [specification document](https://zarr-specs.readthedocs.io/en/latest/spec/v3/datatypes.html#numpy-timedelta64). + [specification document](https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/numpy.timedelta64). Examples -------- @@ -151,7 +151,7 @@ class TimeDelta64JSON_V3(NamedConfig[Literal["numpy.timedelta64"], TimeConfig]): "configuration": { "unit": "ms", "scale_factor": 1 - } + } } ``` """ From 7c2f372f21b2555e11b2ab52f0e659a0306e5741 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Fri, 8 May 2026 06:05:57 -0400 Subject: [PATCH 303/468] chore: fix ability to run mypy via hatch (#3952) --- pyproject.toml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index bf617604d8..cd7d32c286 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -153,6 +153,9 @@ version.source = "vcs" [tool.hatch.build] hooks.vcs.version-file = "src/zarr/_version.py" +[tool.hatch.envs.dev] +dependency-groups = ["dev"] + [tool.hatch.envs.test] dependency-groups = ["test"] @@ -184,7 +187,6 @@ run-coverage-html = [ ] run = "pytest --ignore tests/benchmarks" run-verbose = "run-coverage --verbose" -run-mypy = "mypy src" run-hypothesis = [ "coverage run --source=src -m pytest -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful* {args:}", "coverage xml", @@ -362,6 +364,7 @@ ignore = [ "tests/**" = ["ANN001", "ANN201", "RUF029", "SIM117", "SIM300"] [tool.mypy] +files = ["src", "tests"] python_version = "3.12" ignore_missing_imports = true namespace_packages = false From 84532cad3bdb27a4e6b21d04ed43baa1cb39d8bd Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 10 May 2026 05:08:49 -0500 Subject: [PATCH 304/468] Fix minor typos (#3957) * Fix docs typos * Fix docstring typos * fix: correct more typos --------- Co-authored-by: Davis Vann Bennett --- docs/contributing.md | 2 +- docs/user-guide/arrays.md | 2 +- docs/user-guide/consolidated_metadata.md | 10 +++++----- docs/user-guide/data_types.md | 2 +- docs/user-guide/experimental.md | 2 +- docs/user-guide/extending.md | 4 ++-- docs/user-guide/gpu.md | 2 +- docs/user-guide/groups.md | 2 +- docs/user-guide/performance.md | 2 +- docs/user-guide/storage.md | 4 ++-- docs/user-guide/v3_migration.md | 2 +- src/zarr/api/asynchronous.py | 4 ++-- src/zarr/api/synchronous.py | 18 +++++++++--------- src/zarr/core/array.py | 24 ++++++++++++------------ src/zarr/core/group.py | 24 ++++++++++++------------ src/zarr/core/sync.py | 2 +- 16 files changed, 53 insertions(+), 53 deletions(-) diff --git a/docs/contributing.md b/docs/contributing.md index 4bba874188..b9c7aa1aa2 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -255,7 +255,7 @@ print("Hello world") #### Building documentation without executing code blocks -Sometimes, you may want the documentation to build quicker. You can disable code block execution by commenting out the [markdown-exec](https://github.com/zarr-developers/zarr-python/blob/884a8c91afcc3efe28b3da952be3b85125c453cb/mkdocs.yml#L132 plugin in the mkdocs configuration file). This will make code blocks and cross references render incorrectly (i.e., expect build warnings), but also reduces build time by ~3x. Be sure to undo the commenting out before opening your pull request. +Sometimes, you may want the documentation to build quicker. You can disable code block execution by commenting out the [markdown-exec plugin](https://github.com/zarr-developers/zarr-python/blob/884a8c91afcc3efe28b3da952be3b85125c453cb/mkdocs.yml#L132) in the mkdocs configuration file. This will make code blocks and cross references render incorrectly (i.e., expect build warnings), but also reduces build time by ~3x. Be sure to undo the commenting out before opening your pull request. ### Changelog diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 6a0ecfda92..4b52629645 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -512,7 +512,7 @@ print(np.all(z.oindex[[0, 2], :] == z[[0, 2], :])) ### Block Indexing -Zarr also support block indexing, which allows selections of whole chunks based on their +Zarr also supports block indexing, which allows selections of whole chunks based on their logical indices along each dimension of an array. For example, this allows selecting a subset of chunk aligned rows and/or columns from a 2-dimensional array. E.g.: diff --git a/docs/user-guide/consolidated_metadata.md b/docs/user-guide/consolidated_metadata.md index c5cd31e5fc..d8066b6846 100644 --- a/docs/user-guide/consolidated_metadata.md +++ b/docs/user-guide/consolidated_metadata.md @@ -17,7 +17,7 @@ If consolidated metadata is present in a Zarr Group's metadata then it is used by default. The initial read to open the group will need to communicate with the store (reading from a file for a [`zarr.storage.LocalStore`][], making a network request for a [`zarr.storage.FsspecStore`][]). After that, any subsequent -metadata reads get child Group or Array nodes will *not* require reads from the store. +metadata reads to get child Group or Array nodes will *not* require reads from the store. In Python, the consolidated metadata is available on the `.consolidated_metadata` attribute of the `GroupMetadata` object. @@ -49,7 +49,7 @@ print(result) ``` If we open that group, the Group's metadata has a `zarr.core.group.ConsolidatedMetadata` -that can be used.: +that can be used: ```python exec="true" session="consolidated_metadata" source="above" result="ansi" from pprint import pprint @@ -58,19 +58,19 @@ import io consolidated = zarr.open_group(store="memory://consolidated-metadata-demo") consolidated_metadata = consolidated.metadata.consolidated_metadata.metadata -# Note: pprint can be users without capturing the output regularly +# Note: pprint can be used without capturing the output regularly output = io.StringIO() pprint(dict(sorted(consolidated_metadata.items())), stream=output, width=60) print(output.getvalue()) ``` -Operations on the group to get children automatically use the consolidated metadata.: +Operations on the group to get children automatically use the consolidated metadata: ```python exec="true" session="consolidated_metadata" source="above" result="ansi" print(consolidated['a']) # no read / HTTP request to the Store is required ``` -With nested groups, the consolidated metadata is available on the children, recursively.: +With nested groups, the consolidated metadata is available on the children, recursively: ```python exec="true" session="consolidated_metadata" source="above" result="ansi" child = group.create_group('child', attributes={'kind': 'child'}) diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md index 3cdafb5f28..3e10845979 100644 --- a/docs/user-guide/data_types.md +++ b/docs/user-guide/data_types.md @@ -262,7 +262,7 @@ here, it's possible to create it yourself: see [Adding New Data Types](#adding-n ### Example Usage -This section will demonstrates the basic usage of Zarr data types. +This section will demonstrate the basic usage of Zarr data types. Create a `ZDType` from a native data type: diff --git a/docs/user-guide/experimental.md b/docs/user-guide/experimental.md index c7f86337a3..1c6d952c7c 100644 --- a/docs/user-guide/experimental.md +++ b/docs/user-guide/experimental.md @@ -4,7 +4,7 @@ This section contains documentation for experimental Zarr Python features. The f ## `CacheStore` -Zarr Python 3.1.4 adds [`zarr.experimental.cache_store.CacheStore`][] provides a dual-store caching implementation +Zarr Python 3.1.4 adds [`zarr.experimental.cache_store.CacheStore`][], which provides a dual-store caching implementation that can be wrapped around any Zarr store to improve performance for repeated data access. This is particularly useful when working with remote stores (e.g., S3, HTTP) where network latency can significantly impact data access speed. diff --git a/docs/user-guide/extending.md b/docs/user-guide/extending.md index 39444135df..cefeb114c5 100644 --- a/docs/user-guide/extending.md +++ b/docs/user-guide/extending.md @@ -78,11 +78,11 @@ Coming soon. ## Custom array buffers -Zarr-python provides control over where and how arrays stored in memory through +Zarr-python provides control over where and how arrays are stored in memory through [`zarr.abc.buffer.Buffer`][]. Currently both CPU (the default) and GPU implementations are provided (see [Using GPUs with Zarr](gpu.md) for more information). You can implement your own buffer classes by implementing the interface defined in [`zarr.abc.buffer.BufferPrototype`][]. ## Other extensions -In the future, Zarr will support writing custom custom data types and chunk grids. +In the future, Zarr will support writing custom data types and chunk grids. diff --git a/docs/user-guide/gpu.md b/docs/user-guide/gpu.md index ff86263cf0..6189f39d3d 100644 --- a/docs/user-guide/gpu.md +++ b/docs/user-guide/gpu.md @@ -7,7 +7,7 @@ Zarr can use GPUs to accelerate your workload by running `zarr.Config.enable_gpu memory as the final stage of the codec pipeline. Data will still be read into or copied to host (CPU) memory for encoding and decoding. - In the future, codecs will be available compressing and decompressing data on + In the future, codecs will be available for compressing and decompressing data on the GPU, avoiding the need to move data between the host and device for compression and decompression. diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index 7664e4c1dc..5faa26a281 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -69,7 +69,7 @@ For more information on groups see the [`zarr.Group` API docs](../api/zarr/group ## Batch Group Creation You can also create multiple groups concurrently with a single function call. [`zarr.create_hierarchy`][] takes -a [`zarr Storage instance`](../api/zarr/storage.md) instance and a dict of `key : metadata` pairs, parses that dict, and +a [`zarr Storage`](../api/zarr/storage.md) instance and a dict of `key : metadata` pairs, parses that dict, and writes metadata documents to storage: ```python exec="true" session="groups" source="above" result="ansi" diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 6d3ec063d2..6514b35a30 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -296,7 +296,7 @@ Zarr arrays and groups can be pickled, as long as the underlying store object ca pickled. With the exception of the `zarr.storage.MemoryStore`, any of the storage classes provided in the `zarr.storage` module can be pickled. -If an array or group is backed by a persistent store such as the a `zarr.storage.LocalStore`, +If an array or group is backed by a persistent store such as a `zarr.storage.LocalStore`, `zarr.storage.ZipStore` or `zarr.storage.FsspecStore` then the store data **are not** pickled. The only thing that is pickled is the necessary parameters to allow the store to re-open any underlying files or databases upon being unpickled. diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index e75cd21381..d5f840ab4b 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -119,7 +119,7 @@ print(array) ### Remote Store -The [`zarr.storage.FsspecStore`][] stores the contents of a Zarr hierarchy in following the same +The [`zarr.storage.FsspecStore`][] stores the contents of a Zarr hierarchy following the same logical layout as the [`LocalStore`][zarr.storage.LocalStore], except the store is assumed to be on a remote storage system such as cloud object storage (e.g. AWS S3, Google Cloud Storage, Azure Blob Store). The [`zarr.storage.FsspecStore`][] is backed by [fsspec](https://filesystem-spec.readthedocs.io) and can support any backend @@ -154,7 +154,7 @@ print(store) ### Memory Store -The [`zarr.storage.MemoryStore`][] an in-memory store that allows for serialization of +The [`zarr.storage.MemoryStore`][] is an in-memory store that allows for serialization of Zarr data (metadata and chunks) to a dictionary: ```python exec="true" session="storage" source="above" result="ansi" diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index b700bf7a25..21386c1522 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -126,7 +126,7 @@ The following sections provide details on breaking changes in Zarr-Python 3. ### The Store class -The Store API has changed significant in Zarr-Python 3. +The Store API has changed significantly in Zarr-Python 3. #### The base store class diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 19b3c0c3fa..bdfb4438dd 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -934,9 +934,9 @@ async def create( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 09397e3d41..97d460a183 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -687,9 +687,9 @@ def create( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like @@ -858,9 +858,9 @@ def create_array( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like @@ -873,7 +873,7 @@ def create_array( filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. + returns another bytestream. Multiple compressors may be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` in [`zarr.config`][zarr.config]. @@ -893,7 +893,7 @@ def create_array( fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory @@ -1042,7 +1042,7 @@ def from_array( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. The default value of ``"keep"`` instructs Zarr to infer ``filters`` from ``data``. If that inference is not possible, Zarr will fall back to the behavior specified by ``"auto"``, @@ -1059,7 +1059,7 @@ def from_array( filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. + returns another bytestream. Multiple compressors may be provided for Zarr format 3. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. @@ -1087,7 +1087,7 @@ def from_array( Fill value for the array. If not specified, defaults to the fill value of the data array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index b7e7fa1b35..2e8ca5445d 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -181,7 +181,7 @@ class DefaultFillValue: A string like ``"auto"`` is ambiguous because such a string is a valid fill value for an array with a string data type. An instance of this class lies outside the space of valid fill values, which means it can - umambiguously express that the default fill value should be used. + unambiguously express that the default fill value should be used. """ @@ -1339,7 +1339,7 @@ def _iter_shard_keys( ------ key: str The storage key of each shard in the selection or in case of no shard - present of each chunk although the latter case as technically incorrect. + present of each chunk although the latter case is technically incorrect. """ # Iterate over the coordinates of chunks in chunk grid space. return _iter_shard_keys( @@ -4079,7 +4079,7 @@ async def from_array( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. The default value of ``"keep"`` instructs Zarr to infer ``filters`` from ``data``. If that inference is not possible, Zarr will fall back to the behavior specified by ``"auto"``, @@ -4096,7 +4096,7 @@ async def from_array( filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. + returns another bytestream. Multiple compressors may be provided for Zarr format 3. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. @@ -4124,7 +4124,7 @@ async def from_array( Fill value for the array. If not specified, defaults to the fill value of the data array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory @@ -4326,9 +4326,9 @@ async def init_array( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like @@ -4354,7 +4354,7 @@ async def init_array( fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory @@ -4576,9 +4576,9 @@ async def create_array( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like @@ -4591,7 +4591,7 @@ async def create_array( filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. + returns another bytestream. Multiple compressors may be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` in [`zarr.config`][zarr.config]. @@ -4611,7 +4611,7 @@ async def create_array( fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 83a9cc6000..cbce1c1ed0 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -1062,9 +1062,9 @@ async def create_array( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like @@ -1077,7 +1077,7 @@ async def create_array( filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. + returns another bytestream. Multiple compressors may be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` in [`zarr.config`][zarr.config]. @@ -1099,7 +1099,7 @@ async def create_array( fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory @@ -2445,9 +2445,9 @@ def create( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like @@ -2460,7 +2460,7 @@ def create( filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. + returns another bytestream. Multiple compressors may be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` in [`zarr.config`][]. @@ -2482,7 +2482,7 @@ def create( fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory @@ -2589,9 +2589,9 @@ def create_array( dict representations of [`zarr.abc.codec.ArrayArrayCodec`][]. For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the - the order if your filters is consistent with the behavior of each filter. + order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default used based on the data + The default value of ``"auto"`` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like @@ -2604,7 +2604,7 @@ def create_array( filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and - returns another bytestream. Multiple compressors my be provided for Zarr format 3. + returns another bytestream. Multiple compressors may be provided for Zarr format 3. If no ``compressors`` are provided, a default set of compressors will be used. These defaults can be changed by modifying the value of ``array.v3_default_compressors`` in [`zarr.config`][zarr.config]. @@ -2626,7 +2626,7 @@ def create_array( fill_value : Any, optional Fill value for the array. order : {"C", "F"}, optional - The memory of the array (default is "C"). + The memory order of the array (default is "C"). For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory diff --git a/src/zarr/core/sync.py b/src/zarr/core/sync.py index 7bcb0bf034..260d4ad841 100644 --- a/src/zarr/core/sync.py +++ b/src/zarr/core/sync.py @@ -198,7 +198,7 @@ def collect_aiterator[T](data: AsyncIterator[T]) -> tuple[T, ...]: class SyncMixin: def _sync[T](self, coroutine: Coroutine[Any, Any, T]) -> T: - # TODO: refactor this to to take *args and **kwargs and pass those to the method + # TODO: refactor this to take *args and **kwargs and pass those to the method # this should allow us to better type the sync wrapper return sync( coroutine, From ad90884910817e75ad762773afa33a610da721ef Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 10 May 2026 21:56:13 +0000 Subject: [PATCH 305/468] chore(deps): bump the actions group with 5 updates (#3951) Bumps the actions group with 5 updates: | Package | From | To | | --- | --- | --- | | [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) | `7.6.0` | `8.1.0` | | [CodSpeedHQ/action](https://github.com/codspeedhq/action) | `4.14.0` | `4.15.0` | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.8.8` | `0.9.5` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.2` | `2.0.3` | | [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) | `7.0.8` | `8.1.1` | Updates `astral-sh/setup-uv` from 7.6.0 to 8.1.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/v7.6...08807647e7069bb48b6ef5acd8ec9567f424441b) Updates `CodSpeedHQ/action` from 4.14.0 to 4.15.0 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/658a901452bb54c799643e060733b7afe9121b8d...c381be0bfd20e844fb45594f6aa182ffcd94545c) Updates `prefix-dev/setup-pixi` from 0.8.8 to 0.9.5 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/19eac09b398e3d0c747adc7921926a6d802df4da...1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0) Updates `j178/prek-action` from 2.0.2 to 2.0.3 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3...6ad80277337ad479fe43bd70701c3f7f8aa74db3) Updates `peter-evans/create-pull-request` from 7.0.8 to 8.1.1 - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/271a8d0340265f705b14b6d32b9829c1cb33d45e...5f6978faf089d4d20b00c7766989d076bb2fc7f1) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 8.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 4.15.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.5 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: peter-evans/create-pull-request dependency-version: 8.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/codspeed.yml | 2 +- .github/workflows/downstream.yml | 4 ++-- .github/workflows/lint.yml | 2 +- .github/workflows/prepare_release.yml | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 848544d03c..7c9d4fd25d 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@658a901452bb54c799643e060733b7afe9121b8d # v4.14.0 + uses: CodSpeedHQ/action@c381be0bfd20e844fb45594f6aa182ffcd94545c # v4.15.0 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 9b7ce211ab..74026233c4 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -34,7 +34,7 @@ jobs: persist-credentials: false - name: Set up pixi - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5 with: manifest-path: xarray/pixi.toml @@ -85,7 +85,7 @@ jobs: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@37802adc94f370d6bfd71619e3f0bf239e1f3b78 # v7 + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Install numcodecs with test-zarr-main group working-directory: numcodecs diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 21a434bd36..d32e75dd0d 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -22,4 +22,4 @@ jobs: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: persist-credentials: false - - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2.0.2 + - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2.0.3 diff --git a/.github/workflows/prepare_release.yml b/.github/workflows/prepare_release.yml index 4bccb40092..4dbedf5b9e 100644 --- a/.github/workflows/prepare_release.yml +++ b/.github/workflows/prepare_release.yml @@ -55,7 +55,7 @@ jobs: VERSION: ${{ inputs.version }} - name: Create pull request - uses: peter-evans/create-pull-request@271a8d0340265f705b14b6d32b9829c1cb33d45e # v7.0.8 + uses: peter-evans/create-pull-request@5f6978faf089d4d20b00c7766989d076bb2fc7f1 # v8.1.1 with: branch: release/v${{ inputs.version }} base: ${{ inputs.target_branch }} From c79425ef5d286e2f13da6035cacc1a39dd54fae1 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 11 May 2026 18:10:38 +0200 Subject: [PATCH 306/468] deprecate blosc enums (#3963) * docs(spec): deprecate BloscShuffle and BloscCname enums Design for steering BloscCodec users toward literal-string parameters, with the enum classes kept importable but deprecated on member access. Canonical: https://gist.github.com/d-v-b/9fd3fe92f82a24c929129f42a6f11f60 Co-Authored-By: Claude Opus 4.7 (1M context) * feat(codecs): deprecate BloscShuffle/BloscCname enums Member access on BloscShuffle / BloscCname now emits DeprecationWarning and returns the equivalent string. BloscCodec stores cname/shuffle as literal strings; passing a real enum.Enum instance to __init__ warns. BloscShuffle.from_int returns a str. Internal call sites in migrate_v3 continue to work because BloscCodec accepts both forms. Co-Authored-By: Claude Opus 4.7 (1M context) * docs: use literal strings for BloscCodec shuffle parameter The BloscShuffle and BloscCname enums are deprecated; update doc examples to the recommended literal-string form. Co-Authored-By: Claude Opus 4.7 (1M context) * chore(changes): add changelog entry for blosc enum deprecation The 0000 filename is a placeholder; rename to the PR number when the pull request is opened. Co-Authored-By: Claude Opus 4.7 (1M context) * docs: drop local copy of blosc enum deprecation spec The design doc is published as a public gist linked from the PR description; the in-tree copy is no longer needed. Co-Authored-By: Claude Opus 4.7 (1M context) * style(codecs): use plain backticks in blosc docstrings Replace Sphinx :class: roles and double-backticks with single backticks in the new docstrings added by the blosc enum deprecation. Co-Authored-By: Claude Opus 4.7 (1M context) * test(codecs): cover blosc error branches Add tests for the ValueError paths in _parse_cname / _parse_shuffle and the AttributeError path in the deprecated-enum metaclass, which codecov reported as uncovered. Drop a few "type: ignore" markers that mypy now flags as unused after the init signature widened. Co-Authored-By: Claude Opus 4.7 (1M context) * test(codecs): use typing.cast instead of type-ignore in blosc tests mypy's per-file (pre-commit) and project-wide views disagree on whether the deliberately-wrong arguments need a type ignore. Using typing.cast keeps both views happy and is more explicit about what each test is asserting. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(codecs): rename blosc literal aliases to Blosc*Literal Rename Shuffle -> BloscShuffleLiteral and CName -> BloscCnameLiteral. The bare Shuffle name collided with numcodecs.Shuffle re-exported from zarr.codecs, which would have caused mkdocstrings cross-refs in the BloscCodec docstring to resolve to the wrong symbol. The Literal suffix also clearly distinguishes the type alias from the deprecated BloscShuffle / BloscCname enum classes. Update the BloscCodec docstring to reference the new names in the Attributes and Parameters sections (Convention A from cast_value.py), with literal values enumerated in prose. Co-Authored-By: Claude Opus 4.7 (1M context) * chore: rename blosc constants * test(codecs): address review feedback on blosc deprecation tests - Parametrize the BloscShuffle / BloscCname member-access warning tests into a single test_blosc_enum_member_access_warns. - Parametrize the cname / shuffle reject-unknown tests into a single test_blosc_codec_rejects_unknown driven by **kwargs. - Parametrize the AttributeError-on-unknown-member tests into a single test_blosc_enum_attribute_error_for_unknown_member. - Add a docstring to every new test explaining what behavior it verifies, so reviewers don't have to read the body to understand the intent. Co-Authored-By: Claude Opus 4.7 (1M context) * test(codecs): parametrize blosc cname/shuffle coverage and JSON roundtrip Backfill missing coverage: previously every test in the blosc suite used only "lz4" or "zstd" for cname and only "bitshuffle" or "shuffle" for shuffle. Add four parametrized tests driven by BLOSC_CNAME / BLOSC_SHUFFLE: - accepts_all_cnames / accepts_all_shuffles: every value in the runtime tuple is accepted by BloscCodec and round-trips on the stored attribute. Catches drift between the BloscCnameLiteral / BloscShuffleLiteral type aliases and their runtime BLOSC_* counterparts. - json_roundtrip_all_cnames / json_roundtrip_all_shuffles: BloscCodec to_dict / from_dict preserves every value. Codec fields are fully specified so the test doesn't trip over tunable-attribute state, which is not part of the JSON form. Co-Authored-By: Claude Opus 4.7 (1M context) * test(codecs): collapse blosc JSON roundtrip tests into one parametrize Replace the cname/shuffle JSON-roundtrip pair with a single parametrized test driven by [("cname", v) for v in BLOSC_CNAME] + [("shuffle", v) for v in BLOSC_SHUFFLE]. They asserted the same property (to_dict / from_dict preserves every literal) on two independent axes, so a single test covers both with clear per-case IDs (e.g. cname-lz4, shuffle-bitshuffle). Co-Authored-By: Claude Opus 4.7 (1M context) * test(codecs): cross-product blosc JSON roundtrip over cname x shuffle Stacked parametrize over BLOSC_CNAME and BLOSC_SHUFFLE so the JSON roundtrip exercises every (cname, shuffle) pair (18 cases instead of 9 in a disjoint union). Drops the **kwargs/dict[str, Any] indirection the disjoint form needed, since the cross-product form passes typed arguments directly. Co-Authored-By: Claude Opus 4.7 (1M context) * Rename 0000.removal.md to 3963.removal.md --------- Co-authored-by: Claude Opus 4.7 (1M context) --- changes/3963.removal.md | 6 ++ docs/quick-start.md | 2 +- docs/user-guide/arrays.md | 4 +- src/zarr/codecs/blosc.py | 180 +++++++++++++++++++++----------- tests/test_codecs/test_blosc.py | 158 ++++++++++++++++++++++++++-- 5 files changed, 276 insertions(+), 74 deletions(-) create mode 100644 changes/3963.removal.md diff --git a/changes/3963.removal.md b/changes/3963.removal.md new file mode 100644 index 0000000000..a83fd53853 --- /dev/null +++ b/changes/3963.removal.md @@ -0,0 +1,6 @@ +The ``BloscShuffle`` and ``BloscCname`` enums (``zarr.codecs.BloscShuffle``, +``zarr.codecs.BloscCname``) are now deprecated. Pass the equivalent literal +string (e.g. ``"zstd"``, ``"bitshuffle"``) when constructing a ``BloscCodec``. +The enum classes remain importable but emit ``DeprecationWarning`` on member +access, and will be removed in a future release. ``BloscCodec.cname`` and +``BloscCodec.shuffle`` are now plain strings rather than enum members. diff --git a/docs/quick-start.md b/docs/quick-start.md index bb7a556b96..27dc8e6045 100644 --- a/docs/quick-start.md +++ b/docs/quick-start.md @@ -58,7 +58,7 @@ z = zarr.create_array( compressors=zarr.codecs.BloscCodec( cname="zstd", clevel=3, - shuffle=zarr.codecs.BloscShuffle.shuffle + shuffle="shuffle" ) ) diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 4b52629645..14122003c0 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -201,7 +201,7 @@ Different compressors can be provided via the `compressors` keyword argument accepted by all array creation functions. For example: ```python exec="true" session="arrays" source="above" result="ansi" -compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=3, shuffle=zarr.codecs.BloscShuffle.bitshuffle) +compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=3, shuffle='bitshuffle') data = np.arange(100000000, dtype='int32').reshape(10000, 10000) z = zarr.create_array(store='data/example-5.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), compressors=compressors) z[:] = data @@ -298,7 +298,7 @@ Here is an example using a delta filter with the Blosc compressor: from zarr.codecs.numcodecs import Delta filters = [Delta(dtype='int32')] -compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=1, shuffle=zarr.codecs.BloscShuffle.shuffle) +compressors = zarr.codecs.BloscCodec(cname='zstd', clevel=1, shuffle='shuffle') data = np.arange(100000000, dtype='int32').reshape(10000, 10000) z = zarr.create_array(store='data/example-9.zarr', shape=data.shape, dtype=data.dtype, chunks=(1000, 1000), filters=filters, compressors=compressors) print(z.info_complete()) diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 62ceff7659..8a20282060 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -1,10 +1,11 @@ from __future__ import annotations import asyncio +import warnings from dataclasses import dataclass, field, replace from enum import Enum from functools import cached_property -from typing import TYPE_CHECKING, Final, Literal, NotRequired, TypedDict +from typing import TYPE_CHECKING, ClassVar, Final, Literal, NotRequired, TypedDict import numcodecs from numcodecs.blosc import Blosc @@ -12,7 +13,7 @@ from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper -from zarr.core.common import JSON, NamedRequiredConfig, parse_enum, parse_named_configuration +from zarr.core.common import JSON, NamedRequiredConfig, parse_named_configuration from zarr.core.dtype.common import HasItemSize if TYPE_CHECKING: @@ -21,19 +22,21 @@ from zarr.core.array_spec import ArraySpec from zarr.core.buffer import Buffer -Shuffle = Literal["noshuffle", "shuffle", "bitshuffle"] +BloscShuffleLiteral = Literal["noshuffle", "shuffle", "bitshuffle"] """The shuffle values permitted for the blosc codec""" -SHUFFLE: Final = ("noshuffle", "shuffle", "bitshuffle") +BLOSC_SHUFFLE: Final = ("noshuffle", "shuffle", "bitshuffle") -CName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] -"""The codec identifiers used in the blosc codec """ +BloscCnameLiteral = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] +"""The codec identifiers used in the blosc codec""" + +BLOSC_CNAME: Final = ("lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd") class BloscConfigV2(TypedDict): """Configuration for the V2 Blosc codec""" - cname: CName + cname: BloscCnameLiteral clevel: int shuffle: int blocksize: int @@ -43,9 +46,9 @@ class BloscConfigV2(TypedDict): class BloscConfigV3(TypedDict): """Configuration for the V3 Blosc codec""" - cname: CName + cname: BloscCnameLiteral clevel: int - shuffle: Shuffle + shuffle: BloscShuffleLiteral blocksize: int typesize: int @@ -56,38 +59,66 @@ class BloscJSON_V3(NamedRequiredConfig[Literal["blosc"], BloscConfigV3]): """ -class BloscShuffle(Enum): +class _DeprecatedStrEnumMeta(type): """ - Enum for shuffle filter used by blosc. + Metaclass for the legacy `BloscShuffle` / `BloscCname` classes. Accessing + a member name (e.g. `BloscShuffle.bitshuffle`) emits a `DeprecationWarning` + and returns the equivalent string. """ - noshuffle = "noshuffle" - shuffle = "shuffle" - bitshuffle = "bitshuffle" + _members: dict[str, str] - @classmethod - def from_int(cls, num: int) -> BloscShuffle: - blosc_shuffle_int_to_str = { + def __getattr__(cls, name: str) -> str: + members: dict[str, str] = type.__getattribute__(cls, "_members") + if name in members: + warnings.warn( + f"{cls.__name__}.{name} is deprecated; pass the string {members[name]!r} instead.", + DeprecationWarning, + stacklevel=2, + ) + return members[name] + raise AttributeError(name) + + +class BloscShuffle(metaclass=_DeprecatedStrEnumMeta): + """ + Deprecated. Pass a literal string (`"noshuffle"`, `"shuffle"`, or + `"bitshuffle"`) directly to `BloscCodec` instead. + """ + + _members: ClassVar[dict[str, str]] = { + "noshuffle": "noshuffle", + "shuffle": "shuffle", + "bitshuffle": "bitshuffle", + } + + @staticmethod + def from_int(num: int) -> BloscShuffleLiteral: + mapping: dict[int, BloscShuffleLiteral] = { 0: "noshuffle", 1: "shuffle", 2: "bitshuffle", } - if num not in blosc_shuffle_int_to_str: + if num not in mapping: raise ValueError(f"Value must be between 0 and 2. Got {num}.") - return BloscShuffle[blosc_shuffle_int_to_str[num]] + return mapping[num] -class BloscCname(Enum): +class BloscCname(metaclass=_DeprecatedStrEnumMeta): """ - Enum for compression library used by blosc. + Deprecated. Pass a literal string (one of `"lz4"`, `"lz4hc"`, + `"blosclz"`, `"snappy"`, `"zlib"`, `"zstd"`) directly to + `BloscCodec` instead. """ - lz4 = "lz4" - lz4hc = "lz4hc" - blosclz = "blosclz" - zstd = "zstd" - snappy = "snappy" - zlib = "zlib" + _members: ClassVar[dict[str, str]] = { + "lz4": "lz4", + "lz4hc": "lz4hc", + "blosclz": "blosclz", + "snappy": "snappy", + "zstd": "zstd", + "zlib": "zlib", + } # See https://zarr.readthedocs.io/en/stable/user-guide/performance.html#configuring-blosc @@ -118,6 +149,34 @@ def parse_blocksize(data: JSON) -> int: raise TypeError(f"Value should be an int. Got {type(data)} instead.") +def _coerce_enum_input(value: object, param_name: str) -> object: + """ + If `value` is a real `enum.Enum` instance, emit a deprecation warning + and return `value.value`. Otherwise return `value` unchanged. + """ + if isinstance(value, Enum): + warnings.warn( + f"Passing an enum to BloscCodec(..., {param_name}=...) is deprecated; " + "pass the equivalent literal string instead.", + DeprecationWarning, + stacklevel=3, + ) + return value.value + return value + + +def _parse_cname(data: object) -> BloscCnameLiteral: + if isinstance(data, str) and data in BLOSC_CNAME: + return data # type: ignore[return-value] + raise ValueError(f"cname must be one of {list(BLOSC_CNAME)!r}. Got {data!r}.") + + +def _parse_shuffle(data: object) -> BloscShuffleLiteral: + if isinstance(data, str) and data in BLOSC_SHUFFLE: + return data # type: ignore[return-value] + raise ValueError(f"shuffle must be one of {list(BLOSC_SHUFFLE)!r}. Got {data!r}.") + + @dataclass(frozen=True) class BloscCodec(BytesBytesCodec): """ @@ -133,12 +192,14 @@ class BloscCodec(BytesBytesCodec): Always False for Blosc codec, as compression produces variable-sized output. typesize : int The data type size in bytes used for shuffle filtering. - cname : BloscCname - The compression algorithm being used (lz4, lz4hc, blosclz, snappy, zlib, or zstd). + cname : BloscCnameLiteral + The compression algorithm being used; one of "lz4", "lz4hc", + "blosclz", "snappy", "zlib", or "zstd". clevel : int The compression level (0-9). - shuffle : BloscShuffle - The shuffle filter mode (noshuffle, shuffle, or bitshuffle). + shuffle : BloscShuffleLiteral + The shuffle filter mode; one of "noshuffle", "shuffle", or + "bitshuffle". blocksize : int The size of compressed blocks in bytes (0 for automatic). @@ -148,13 +209,16 @@ class BloscCodec(BytesBytesCodec): The data type size in bytes. This affects how the shuffle filter processes the data. If None, defaults to 1 and the attribute is marked as tunable. Default: 1. - cname : BloscCname or {'lz4', 'lz4hc', 'blosclz', 'snappy', 'zlib', 'zstd'}, optional - The compression algorithm to use. Default: 'zstd'. + cname : BloscCnameLiteral, optional + The compression algorithm to use; one of "lz4", "lz4hc", "blosclz", + "snappy", "zlib", or "zstd". Default is "zstd". Passing a `BloscCname` + enum is deprecated. clevel : int, optional The compression level, from 0 (no compression) to 9 (maximum compression). Higher values provide better compression at the cost of speed. Default: 5. - shuffle : BloscShuffle or {'noshuffle', 'shuffle', 'bitshuffle'}, optional - The shuffle filter to apply before compression: + shuffle : BloscShuffleLiteral or None, optional + The shuffle filter to apply before compression; one of "noshuffle", + "shuffle", or "bitshuffle": - 'noshuffle': No shuffling - 'shuffle': Byte shuffling (better for typesize > 1) @@ -183,18 +247,13 @@ class BloscCodec(BytesBytesCodec): >>> codec.typesize 1 >>> codec.shuffle - + 'bitshuffle' Create a codec with specific compression settings: >>> codec = BloscCodec(cname='zstd', clevel=9, shuffle='shuffle') >>> codec.cname - - - See Also - -------- - BloscShuffle : Enum for shuffle filter options - BloscCname : Enum for compression algorithm options + 'zstd' """ # This attribute tracks parameters were set to None at init time, and thus tunable @@ -202,38 +261,37 @@ class BloscCodec(BytesBytesCodec): is_fixed_size = False typesize: int - cname: BloscCname + cname: BloscCnameLiteral clevel: int - shuffle: BloscShuffle + shuffle: BloscShuffleLiteral blocksize: int def __init__( self, *, typesize: int | None = None, - cname: BloscCname | CName = BloscCname.zstd, + cname: BloscCname | BloscCnameLiteral = "zstd", clevel: int = 5, - shuffle: BloscShuffle | Shuffle | None = None, + shuffle: BloscShuffle | BloscShuffleLiteral | None = None, blocksize: int = 0, ) -> None: object.__setattr__(self, "_tunable_attrs", set()) - # If typesize was set to None, replace it with a valid typesize - # and flag the typesize attribute as safe to replace later if typesize is None: typesize = 1 self._tunable_attrs.update({"typesize"}) - # If shuffle was set to None, replace it with a valid shuffle - # and flag the shuffle attribute as safe to replace later if shuffle is None: - shuffle = BloscShuffle.bitshuffle + shuffle = "bitshuffle" self._tunable_attrs.update({"shuffle"}) + cname = _coerce_enum_input(cname, "cname") # type: ignore[assignment] + shuffle = _coerce_enum_input(shuffle, "shuffle") # type: ignore[assignment] + typesize_parsed = parse_typesize(typesize) - cname_parsed = parse_enum(cname, BloscCname) + cname_parsed = _parse_cname(cname) clevel_parsed = parse_clevel(clevel) - shuffle_parsed = parse_enum(shuffle, BloscShuffle) + shuffle_parsed = _parse_shuffle(shuffle) blocksize_parsed = parse_blocksize(blocksize) object.__setattr__(self, "typesize", typesize_parsed) @@ -252,9 +310,9 @@ def to_dict(self) -> dict[str, JSON]: "name": "blosc", "configuration": { "typesize": self.typesize, - "cname": self.cname.value, + "cname": self.cname, "clevel": self.clevel, - "shuffle": self.shuffle.value, + "shuffle": self.shuffle, "blocksize": self.blocksize, }, } @@ -276,20 +334,20 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: if "shuffle" in self._tunable_attrs: new_codec = replace( new_codec, - shuffle=(BloscShuffle.bitshuffle if item_size == 1 else BloscShuffle.shuffle), + shuffle=("bitshuffle" if item_size == 1 else "shuffle"), ) return new_codec @cached_property def _blosc_codec(self) -> Blosc: - map_shuffle_str_to_int = { - BloscShuffle.noshuffle: 0, - BloscShuffle.shuffle: 1, - BloscShuffle.bitshuffle: 2, + map_shuffle_str_to_int: dict[BloscShuffleLiteral, int] = { + "noshuffle": 0, + "shuffle": 1, + "bitshuffle": 2, } config_dict: BloscConfigV2 = { - "cname": self.cname.name, # type: ignore[typeddict-item] + "cname": self.cname, "clevel": self.clevel, "shuffle": map_shuffle_str_to_int[self.shuffle], "blocksize": self.blocksize, diff --git a/tests/test_codecs/test_blosc.py b/tests/test_codecs/test_blosc.py index 0201beb8de..f5f13f4d05 100644 --- a/tests/test_codecs/test_blosc.py +++ b/tests/test_codecs/test_blosc.py @@ -1,4 +1,7 @@ +import enum import json +import warnings +from typing import Any, cast import numcodecs import numpy as np @@ -8,7 +11,14 @@ import zarr from zarr.abc.codec import SupportsSyncCodec from zarr.codecs import BloscCodec -from zarr.codecs.blosc import BloscShuffle, Shuffle +from zarr.codecs.blosc import ( + BLOSC_CNAME, + BLOSC_SHUFFLE, + BloscCname, + BloscCnameLiteral, + BloscShuffle, + BloscShuffleLiteral, +) from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.buffer import default_buffer_prototype from zarr.core.dtype import UInt16, get_data_type_from_native_dtype @@ -61,16 +71,26 @@ async def test_blosc_evolve(dtype: str) -> None: assert blosc_configuration_json["shuffle"] == "shuffle" -@pytest.mark.parametrize("shuffle", [None, "bitshuffle", BloscShuffle.shuffle]) +@pytest.mark.parametrize("shuffle", [None, "bitshuffle", "legacy-enum"]) @pytest.mark.parametrize("typesize", [None, 1, 2]) -def test_tunable_attrs_param(shuffle: None | Shuffle | BloscShuffle, typesize: None | int) -> None: +def test_tunable_attrs_param( + shuffle: None | BloscShuffleLiteral | str, typesize: None | int +) -> None: """ - Test that the tunable_attrs parameter is set as expected when creating a BloscCodec, + Test that the tunable_attrs parameter is set as expected when creating a BloscCodec. """ - codec = BloscCodec(typesize=typesize, shuffle=shuffle) + # Materialize BloscShuffle.shuffle via the deprecation shim without + # contaminating the BloscCodec construction below with that warning. + if shuffle == "legacy-enum": + with pytest.warns(DeprecationWarning, match="BloscShuffle.shuffle"): + shuffle_arg: None | BloscShuffleLiteral | str = BloscShuffle.shuffle + else: + shuffle_arg = shuffle + + codec = BloscCodec(typesize=typesize, shuffle=cast(BloscShuffleLiteral | None, shuffle_arg)) - if shuffle is None: - assert codec.shuffle == BloscShuffle.bitshuffle # default shuffle + if shuffle_arg is None: + assert codec.shuffle == "bitshuffle" # default shuffle assert "shuffle" in codec._tunable_attrs if typesize is None: assert codec.typesize == 1 # default typesize @@ -82,7 +102,7 @@ def test_tunable_attrs_param(shuffle: None | Shuffle | BloscShuffle, typesize: N dtype=new_dtype, fill_value=1, prototype=default_buffer_prototype(), - config={}, # type: ignore[arg-type] + config=cast(ArrayConfig, {}), ) evolved_codec = codec.evolve_from_array_spec(array_spec=array_spec) @@ -90,8 +110,8 @@ def test_tunable_attrs_param(shuffle: None | Shuffle | BloscShuffle, typesize: N assert evolved_codec.typesize == new_dtype.item_size else: assert evolved_codec.typesize == codec.typesize - if shuffle is None: - assert evolved_codec.shuffle == BloscShuffle.shuffle + if shuffle_arg is None: + assert evolved_codec.shuffle == "shuffle" else: assert evolved_codec.shuffle == codec.shuffle @@ -135,3 +155,121 @@ def test_blosc_codec_sync_roundtrip() -> None: decoded = codec._decode_sync(encoded, spec) result = np.frombuffer(decoded.as_numpy_array(), dtype="float64") np.testing.assert_array_equal(arr, result) + + +@pytest.mark.parametrize("cname", BLOSC_CNAME) +def test_blosc_codec_accepts_all_cnames(cname: BloscCnameLiteral) -> None: + """ + Every compressor name in BLOSC_CNAME is accepted by BloscCodec and round-trips + to the same value on the stored attribute. Adding a new value to the + BloscCnameLiteral type alias without also adding it to BLOSC_CNAME (or vice + versa) is caught here. + """ + codec = BloscCodec(cname=cname) + assert codec.cname == cname + + +@pytest.mark.parametrize("shuffle", BLOSC_SHUFFLE) +def test_blosc_codec_accepts_all_shuffles(shuffle: BloscShuffleLiteral) -> None: + """ + Every shuffle mode in BLOSC_SHUFFLE is accepted by BloscCodec and round-trips + to the same value on the stored attribute. Adding a new value to the + BloscShuffleLiteral type alias without also adding it to BLOSC_SHUFFLE (or + vice versa) is caught here. + """ + codec = BloscCodec(shuffle=shuffle) + assert codec.shuffle == shuffle + + +@pytest.mark.parametrize("shuffle", BLOSC_SHUFFLE) +@pytest.mark.parametrize("cname", BLOSC_CNAME) +def test_blosc_codec_json_roundtrip(cname: BloscCnameLiteral, shuffle: BloscShuffleLiteral) -> None: + """ + JSON serialization (to_dict / from_dict) preserves every (cname, shuffle) + pair drawn from BLOSC_CNAME x BLOSC_SHUFFLE. Guards against drift in the + codec's V3 JSON form for any combination of compressor and shuffle option. + + The non-varied fields are fully specified so the codec has no tunable + attributes; tunability is not part of the JSON form and would otherwise + cause spurious round-trip mismatches. + """ + codec = BloscCodec(typesize=1, cname=cname, clevel=5, shuffle=shuffle, blocksize=0) + restored = BloscCodec.from_dict(codec.to_dict()) + assert restored == codec + + +@pytest.mark.parametrize( + ("enum_cls", "member", "expected"), + [ + (BloscShuffle, "shuffle", "shuffle"), + (BloscCname, "zstd", "zstd"), + ], +) +def test_blosc_enum_member_access_warns(enum_cls: type, member: str, expected: str) -> None: + """ + Accessing a member on the deprecated BloscShuffle / BloscCname classes + emits a DeprecationWarning and resolves to the equivalent literal string. + """ + match = f"{enum_cls.__name__}.{member}" + with pytest.warns(DeprecationWarning, match=match): + value = getattr(enum_cls, member) + assert value == expected + + +def test_blosc_enum_classes_import_silently() -> None: + """ + Importing the deprecated enum classes by name must not emit a warning; + only member access does. This guards against the blosc module accidentally + triggering its own deprecation warnings when it (or zarr) is imported. + """ + with warnings.catch_warnings(): + warnings.simplefilter("error") + from zarr.codecs.blosc import BloscCname as _BloscCname # noqa: F401 + from zarr.codecs.blosc import BloscShuffle as _BloscShuffle # noqa: F401 + + +def test_blosc_codec_init_with_enum_instance_warns() -> None: + """ + Passing a real `enum.Enum` instance to BloscCodec.__init__ (e.g. an + instance materialized before the deprecation shim was introduced) must + trigger the init-level deprecation warning and still normalize the value + to the corresponding literal string. + """ + + class LegacyShuffle(enum.Enum): + bitshuffle = "bitshuffle" + + class LegacyCname(enum.Enum): + zstd = "zstd" + + with pytest.warns(DeprecationWarning, match="enum"): + codec = BloscCodec( + cname=cast(BloscCname, LegacyCname.zstd), + shuffle=cast(BloscShuffle, LegacyShuffle.bitshuffle), + ) + assert codec.cname == "zstd" + assert codec.shuffle == "bitshuffle" + + +@pytest.mark.parametrize("param", ["cname", "shuffle"]) +def test_blosc_codec_rejects_unknown(param: str) -> None: + """ + BloscCodec.__init__ raises ValueError when given a string outside the + allowed set for `cname` or `shuffle`, and the error message names the + offending parameter. + """ + kwargs: dict[str, Any] = {param: f"not-a-{param}"} + with pytest.raises(ValueError, match=f"{param} must be one of"): + BloscCodec(**kwargs) + + +@pytest.mark.parametrize("enum_cls", [BloscShuffle, BloscCname]) +def test_blosc_enum_attribute_error_for_unknown_member(enum_cls: type) -> None: + """ + Attribute access for a name that is not a known member of the deprecated + enum classes falls through to AttributeError, matching the behavior of a + regular class. + """ + unknown_name = "not_a_member" + with pytest.raises(AttributeError): + getattr(enum_cls, unknown_name) From 1020ca52d585dee1e59a40c980784debc2244044 Mon Sep 17 00:00:00 2001 From: Tom Augspurger Date: Tue, 12 May 2026 09:09:33 -0500 Subject: [PATCH 307/468] BUG: Fix empty Group nodes lacking a "consolidated_metadata" field (#3967) * BUG: Fix empty Group nodes lacking a "consolidated_metadata" field All nodes opened via `open_consolidated` are expected to have a non-null `.metadata.consolidated_metadata`. https://github.com/zarr-developers/zarr-python/issues/3954 showed an example, with a data file written by zarr-python 2.x, where that condition failed to hold. This happened because of a slight difference between how zarr-python 3.x writes consolidated metadata and how zarr-python 2.x wrote it. For leaf `Group` nodes (a `Group` with no `Group` or `Array` children), zarr-python 3.x includes an "empty" `consolidated_metadata` field. In zarr-python 3.x, we include a `consolidated_metadata: metadata: {}` field to indicate that it's empty. zarr-python 2.x *didn't* include that. The fix is to update how we load this type of data. We effectively normalize a node missing consolidated metadata to one that is known not to have consolidated metadata (which is consistent with the idea behind consolidated metadata: just do one metadata read up front). --- changes/3954.bugfix.md | 1 + src/zarr/core/group.py | 20 +++---- tests/test_metadata/test_consolidated.py | 68 ++++++++++++++++++++++++ 3 files changed, 80 insertions(+), 9 deletions(-) create mode 100644 changes/3954.bugfix.md diff --git a/changes/3954.bugfix.md b/changes/3954.bugfix.md new file mode 100644 index 0000000000..1a6c93a8ac --- /dev/null +++ b/changes/3954.bugfix.md @@ -0,0 +1 @@ +Handle missing consolidated metadata in leaf Group nodes. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index cbce1c1ed0..ae18cbaf85 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -235,8 +235,6 @@ def _flat_to_nested( # array metadata of its immediate children. # In the example, the group at `/a/b` will have consolidated metadata # for its children `array-0` and `array-1`. - # - # metadata = dict(metadata) keys = sorted(metadata, key=lambda k: k.count("/")) grouped = { @@ -269,13 +267,17 @@ def _flat_to_nested( # These are already present, either thanks to being an array in the # root, or by being collected as a child in the else clause continue - children_keys = list(children_keys) - # We pop from metadata, since we're *moving* this under group - children = { - child_key.split("/")[-1]: metadata.pop(child_key) - for child_key in children_keys - if child_key != key - } + children: dict[str, ArrayV2Metadata | ArrayV3Metadata | GroupMetadata] = {} + # We pop from metadata, since we're *moving* this under group. + # While doing this, normalize leaf groups to carry empty consolidated metadata. + for child_key in children_keys: + if child_key == key: + continue + child = metadata.pop(child_key) + if isinstance(child, GroupMetadata) and child.consolidated_metadata is None: + child = replace(child, consolidated_metadata=ConsolidatedMetadata(metadata={})) + children[child_key.split("/")[-1]] = child + parent[name] = replace( node, consolidated_metadata=ConsolidatedMetadata(metadata=children) ) diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index 9e8b763ef7..3596d2bcaa 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -51,6 +51,74 @@ async def memory_store_with_hierarchy(memory_store: Store) -> Store: class TestConsolidated: + @pytest.mark.filterwarnings("ignore:Consolidated metadata") + async def test_getitem_consolidated_empty_leaf_group( + self, memory_store: zarr.storage.MemoryStore, zarr_format: ZarrFormat + ) -> None: + # This test writes the bytes directly, rather than using the zarr API, to mimic + # how older versions of zarr-python wrote the consolidated metadata. + # Notably, zarr-python 2.x does not include a + # + # "consolidated_metadata": {"metadata": {}} + # + # field on the leaf group nodes. + if zarr_format == 2: + zmetadata: dict[str, JSON] = { + "metadata": { + ".zattrs": {}, + ".zgroup": {"zarr_format": 2}, + "raw/.zattrs": {}, + "raw/.zgroup": {"zarr_format": 2}, + "raw/varm/.zattrs": {}, + "raw/varm/.zgroup": {"zarr_format": 2}, + }, + "zarr_consolidated_format": 1, + } + await memory_store.set( + ".zgroup", cpu.Buffer.from_bytes(json.dumps({"zarr_format": 2}).encode()) + ) + await memory_store.set(".zattrs", cpu.Buffer.from_bytes(json.dumps({}).encode())) + await memory_store.set( + ".zmetadata", cpu.Buffer.from_bytes(json.dumps(zmetadata).encode()) + ) + + else: + zmetadata = { + "attributes": {}, + "zarr_format": 3, + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": { + "raw": { + "attributes": {}, + "zarr_format": 3, + "node_type": "group", + }, + "raw/varm": { + "attributes": {}, + "zarr_format": 3, + "node_type": "group", + }, + }, + }, + "node_type": "group", + } + await memory_store.set( + "zarr.json", cpu.Buffer.from_bytes(json.dumps(zmetadata).encode()) + ) + + group = await zarr.api.asynchronous.open_consolidated( + store=memory_store, zarr_format=zarr_format + ) + raw = await group.getitem("raw") + assert isinstance(raw, zarr.AsyncGroup) + assert raw.metadata.consolidated_metadata is not None + + varm = await raw.getitem("varm") + assert isinstance(varm, zarr.AsyncGroup) + assert varm.metadata.consolidated_metadata == ConsolidatedMetadata(metadata={}) + async def test_open_consolidated_false_raises(self) -> None: store = zarr.storage.MemoryStore() with pytest.raises(TypeError, match="use_consolidated"): From eac9c86ba48e0de174581be519f219339b16a5ef Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 12 May 2026 22:22:22 +0200 Subject: [PATCH 308/468] fix(zarr-metadata): model stored metadata more closely (#3962) * refactor: bring in types from zarr-metadata * fix: better modelling of Zarr V2 metadata Zarr V2 uses a separate JSON document named `.zattrs` for the attributes of an array or group. This package was inconsistent about how it modelled this fact. The array metadata document type modelled array fields (`shape`, `dtype`, etc), which would be stored in `.zarray`, AND the `attributes` field, which would be stored in `.zattrs`. Thus the array metadata model matched the representation of an array that a program might use, rather than the stored layout. But the group metadata type didn't follow this pattern -- it has no `attributes` field. This PR addresses that inconsistency by adding an `attributes` field to `GroupMetadataV2`. That field is not required. To model the stored representation of V2 data, this PR adds 3 new types: `ZArrayMetadata`, `ZGroupMetadata`, and `ZAttrsMetadata`, that closely model the contents of the `.zarray`, `.zgroup`, and `.zattrs` documents, respectively. This change makes the V2 consolidated metadata type more accurate, as consolidated metadata for Zarr V2 is comprised of inlined metadata documents. * Revert "refactor: bring in types from zarr-metadata" This reverts commit 629e56515d5c2b2f20c7e77e76387db9484d8044. * feat(zarr-metadata): re-export ZArrayMetadata, ZAttrsMetadata, ZGroupMetadata at top level The on-disk file types added in 8b7af90b were importable from the v2 submodule but not from the package root. Add them to the top-level __init__.py so consumers can import them as `zarr_metadata.ZArrayMetadata` etc. Co-Authored-By: Claude Opus 4.7 (1M context) * chore: remove lockfile --------- Co-authored-by: Claude Opus 4.7 (1M context) --- .../src/zarr_metadata/__init__.py | 7 +- .../src/zarr_metadata/v2/__init__.py | 7 +- .../src/zarr_metadata/v2/array.py | 30 +- .../src/zarr_metadata/v2/attributes.py | 20 + .../src/zarr_metadata/v2/consolidated.py | 18 +- .../src/zarr_metadata/v2/group.py | 30 +- .../array/blosc_compressor_with_filters.json | 3 +- .../tests/v2/array/empty_filters_list.json | 3 +- .../v2/array/simple_dtype_no_compressor.json | 3 +- .../tests/v2/array/structured_dtype.json | 3 +- .../tests/v2/array/test_fixtures.py | 9 +- .../v2/consolidated/with_array_and_group.json | 7 +- .../tests/v2/group/test_fixtures.py | 12 +- uv.lock | 4037 ----------------- 14 files changed, 122 insertions(+), 4067 deletions(-) create mode 100644 packages/zarr-metadata/src/zarr_metadata/v2/attributes.py delete mode 100644 uv.lock diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 953bb2e897..3b48e855f5 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -4,10 +4,12 @@ ArrayMetadataV2, ArrayOrderV2, DataTypeMetadataV2, + ZArrayMetadata, ) +from zarr_metadata.v2.attributes import ZAttrsMetadata from zarr_metadata.v2.codec import CodecMetadataV2 from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 -from zarr_metadata.v2.group import GroupMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2, ZGroupMetadata from zarr_metadata.v3._common import MetadataFieldV3 from zarr_metadata.v3.array import ArrayMetadataV3, ExtensionFieldV3 from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 @@ -32,5 +34,8 @@ "GroupMetadataV3", "MetadataFieldV3", "NamedConfig", + "ZArrayMetadata", + "ZAttrsMetadata", + "ZGroupMetadata", "__version__", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py index 06892df48e..4e9a76125b 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py @@ -5,10 +5,12 @@ ArrayMetadataV2, ArrayOrderV2, DataTypeMetadataV2, + ZArrayMetadata, ) +from zarr_metadata.v2.attributes import ZAttrsMetadata from zarr_metadata.v2.codec import CodecMetadataV2 from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 -from zarr_metadata.v2.group import GroupMetadataV2 +from zarr_metadata.v2.group import GroupMetadataV2, ZGroupMetadata __all__ = [ "ArrayDimensionSeparatorV2", @@ -18,4 +20,7 @@ "ConsolidatedMetadataV2", "DataTypeMetadataV2", "GroupMetadataV2", + "ZArrayMetadata", + "ZAttrsMetadata", + "ZGroupMetadata", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 4f9f946a12..9043fd1893 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -39,16 +39,39 @@ """ +class ZArrayMetadata(TypedDict): + """ + On-disk `.zarray` file content. + + Strict shape of the JSON document persisted at `/.zarray` for + a v2 array. User attributes live in a sibling `.zattrs` file and are + NOT part of this type; see `ZAttrsMetadata`. + + See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html + """ + + zarr_format: Literal[2] + shape: tuple[int, ...] + chunks: tuple[int, ...] + dtype: DataTypeMetadataV2 + compressor: CodecMetadataV2 | None + fill_value: object + order: ArrayOrderV2 + filters: tuple[CodecMetadataV2, ...] | None + dimension_separator: NotRequired[ArrayDimensionSeparatorV2] + + class ArrayMetadataV2(TypedDict): """ - Zarr v2 array metadata document. + Zarr v2 array metadata document, in-memory merged form. Models the union of `.zarray` (the spec-defined fields) and `.zattrs` (user attributes). On disk, attributes live in a sibling `.zattrs` file and are not part of `.zarray`; this type folds them in as the `attributes` field so a single TypedDict represents the complete in-memory state of a v2 array node. Consumers that read or write a - real `.zarray` file should split / merge `attributes` accordingly. + real `.zarray` file should split / merge `attributes` accordingly, + or use `ZArrayMetadata` (strict on-disk) plus `ZAttrsMetadata` directly. See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ @@ -62,7 +85,7 @@ class ArrayMetadataV2(TypedDict): order: ArrayOrderV2 filters: tuple[CodecMetadataV2, ...] | None dimension_separator: NotRequired[ArrayDimensionSeparatorV2] - attributes: Mapping[str, object] + attributes: NotRequired[Mapping[str, object]] """User attributes from the sibling `.zattrs` file (not part of `.zarray`). See the class docstring for the rationale behind the merged representation. @@ -74,4 +97,5 @@ class ArrayMetadataV2(TypedDict): "ArrayMetadataV2", "ArrayOrderV2", "DataTypeMetadataV2", + "ZArrayMetadata", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py new file mode 100644 index 0000000000..f260537b80 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py @@ -0,0 +1,20 @@ +"""Zarr v2 user-attributes file content. + +See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html +""" + +from collections.abc import Mapping + +ZAttrsMetadata = Mapping[str, object] +"""On-disk `.zattrs` file content. + +A JSON object holding user-defined attributes for a v2 array or group. +Spec-defined keys for arrays / groups live in sibling `.zarray` / `.zgroup` +files (modeled by `ZArrayMetadata` / `ZGroupMetadata`). This type does not +constrain the keys or values of the attributes mapping. +""" + + +__all__ = [ + "ZAttrsMetadata", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py index 6fb75740bb..61a5527085 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py @@ -10,8 +10,9 @@ from typing_extensions import TypedDict -from zarr_metadata.v2.array import ArrayMetadataV2 -from zarr_metadata.v2.group import GroupMetadataV2 +from zarr_metadata.v2.array import ZArrayMetadata +from zarr_metadata.v2.attributes import ZAttrsMetadata +from zarr_metadata.v2.group import ZGroupMetadata class ConsolidatedMetadataV2(TypedDict): @@ -20,11 +21,20 @@ class ConsolidatedMetadataV2(TypedDict): The `metadata` map uses flat path keys (`"foo/bar/.zarray"`, `"foo/.zattrs"`, etc.) pointing to the JSON contents of the file at - that path. The keys include the filename suffix, not just the node path. + that path. The keys include the filename suffix, not just the node + path; the value's shape is determined by which file the key points at: + + - `/.zarray` -> `ZArrayMetadata` + - `/.zgroup` -> `ZGroupMetadata` + - `/.zattrs` -> `ZAttrsMetadata` + + The TypedDict cannot discriminate the value shape on the key suffix + at the type level; consumers should narrow at runtime by inspecting + `key.endswith(".zarray")` etc. """ zarr_consolidated_format: int - metadata: Mapping[str, GroupMetadataV2 | ArrayMetadataV2] + metadata: Mapping[str, ZArrayMetadata | ZGroupMetadata | ZAttrsMetadata] __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/group.py b/packages/zarr-metadata/src/zarr_metadata/v2/group.py index 2110b9c9fd..5ef9b963d2 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/group.py @@ -3,24 +3,46 @@ See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ -from typing import Literal +from collections.abc import Mapping +from typing import Literal, NotRequired from typing_extensions import TypedDict +class ZGroupMetadata(TypedDict): + """ + On-disk `.zgroup` file content. + + Strict shape of the JSON document persisted at `/.zgroup` for + a v2 group. The spec defines exactly one field. User attributes live + in a sibling `.zattrs` file and are NOT part of this type; see + `ZAttrsMetadata`. + + See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html + """ + + zarr_format: Literal[2] + + class GroupMetadataV2(TypedDict): """ - Zarr v2 group metadata document (the `.zgroup` content). + Zarr v2 group metadata document, in-memory merged form. - Attributes live in a sibling `.zattrs` file, so they are not part - of this dict. + Models the union of `.zgroup` (the spec-defined `zarr_format` field) + and `.zattrs` (user attributes). On disk these are persisted as two + separate files; this type folds them so a single TypedDict represents + the complete in-memory state of a v2 group node. Consumers that read + or write the real on-disk files should use `ZGroupMetadata` (strict + `.zgroup`) plus `ZAttrsMetadata` directly. See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ zarr_format: Literal[2] + attributes: NotRequired[Mapping[str, object]] __all__ = [ "GroupMetadataV2", + "ZGroupMetadata", ] diff --git a/packages/zarr-metadata/tests/v2/array/blosc_compressor_with_filters.json b/packages/zarr-metadata/tests/v2/array/blosc_compressor_with_filters.json index f78add1a0b..d7c01563e0 100644 --- a/packages/zarr-metadata/tests/v2/array/blosc_compressor_with_filters.json +++ b/packages/zarr-metadata/tests/v2/array/blosc_compressor_with_filters.json @@ -15,6 +15,5 @@ "filters": [ {"id": "delta", "dtype": " Date: Thu, 14 May 2026 14:01:38 +0300 Subject: [PATCH 309/468] fix: allow writing to 0-dimensional arrays with sharding (#3966) * fix: allow writing to 0-dimensional arrays with sharding Signed-off-by: NIK-TIGER-BILL * test: directly cover get_chunk_slices_vectorized 0D path Signed-off-by: NIK-TIGER-BILL * fix: ruff unused variable in zero-dim sharding test Signed-off-by: NIK-TIGER-BILL --------- Signed-off-by: NIK-TIGER-BILL Co-authored-by: NIK-TIGER-BILL --- src/zarr/codecs/sharding.py | 10 ++++++++++ tests/test_codecs/test_sharding.py | 28 ++++++++++++++++++++++++++++ 2 files changed, 38 insertions(+) diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 609e32f87d..d0b2cec285 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -171,6 +171,16 @@ def get_chunk_slices_vectorized( valid : ndarray of shape (n_chunks,) Boolean mask indicating which chunks are non-empty. """ + # Handle 0-dimensional arrays (n_dims == 0) + if chunk_coords_array.shape[1] == 0: + # offsets_and_lengths has shape (2,) for 0D, reshape to (1, 2) + offsets_and_lengths = self.offsets_and_lengths.reshape(1, 2) + starts = offsets_and_lengths[:, 0] + lengths = offsets_and_lengths[:, 1] + valid = starts != MAX_UINT_64 + ends = starts + lengths + return starts, ends, valid + # Localize coordinates via modulo (vectorized) shard_shape = np.array(self.offsets_and_lengths.shape[:-1], dtype=np.uint64) localized = chunk_coords_array.astype(np.uint64) % shard_shape diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 233cc4cb77..2325069dd0 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -16,6 +16,7 @@ ShardingCodecIndexLocation, TransposeCodec, ) +from zarr.codecs.sharding import MAX_UINT_64, _ShardIndex from zarr.core.buffer import NDArrayLike, default_buffer_prototype from zarr.storage import StorePath, ZipStore @@ -554,3 +555,30 @@ def test_sharding_mixed_integer_list_indexing(store: Store) -> None: s3 = sharded[0:5, 1, 0:3] assert c3.shape == s3.shape == (5, 3) # type: ignore[union-attr] np.testing.assert_array_equal(c3, s3) + + +def test_sharding_zero_dimensional() -> None: + """Regression test for https://github.com/zarr-developers/zarr-python/issues/3751""" + arr = zarr.create_array({}, shape=(), dtype="f4", chunks=(), shards=()) + arr[()] = 42.0 + assert arr[()] == pytest.approx(42.0) + # Overwriting should also work + arr[()] = 43.0 + assert arr[()] == pytest.approx(43.0) + + +def test_shard_index_get_chunk_slices_vectorized_zero_dimensional() -> None: + """Directly cover the 0-D path in _ShardIndex.get_chunk_slices_vectorized.""" + # For a 0D array offsets_and_lengths has shape (2,) — reshape to (1, 2) inside. + index = _ShardIndex(np.array([10, 4], dtype=np.uint64)) + chunk_coords = np.empty((1, 0), dtype=np.uint64) + starts, ends, valid = index.get_chunk_slices_vectorized(chunk_coords) + np.testing.assert_array_equal(starts, np.array([10], dtype=np.uint64)) + np.testing.assert_array_equal(ends, np.array([14], dtype=np.uint64)) + np.testing.assert_array_equal(valid, np.array([True])) + + # Empty/unwritten chunk case + index_empty = _ShardIndex(np.array([MAX_UINT_64, MAX_UINT_64], dtype=np.uint64)) + starts_e, _ends_e, valid_e = index_empty.get_chunk_slices_vectorized(chunk_coords) + np.testing.assert_array_equal(starts_e, np.array([MAX_UINT_64], dtype=np.uint64)) + np.testing.assert_array_equal(valid_e, np.array([False])) From e815b510057e6b12810e331db9fd3525294bd93b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 14 May 2026 12:29:53 +0000 Subject: [PATCH 310/468] chore(deps): bump the actions group with 2 updates (#3970) Bumps the actions group with 2 updates: [CodSpeedHQ/action](https://github.com/codspeedhq/action) and [actions/labeler](https://github.com/actions/labeler). Updates `CodSpeedHQ/action` from 4.15.0 to 4.15.1 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/c381be0bfd20e844fb45594f6aa182ffcd94545c...3194d9a39c4d46684cb44bf7207fc56626aad8fd) Updates `actions/labeler` from 6.0.1 to 6.1.0 - [Release notes](https://github.com/actions/labeler/releases) - [Commits](https://github.com/actions/labeler/compare/634933edcd8ababfe52f92936142cc22ac488b1b...f27b608878404679385c85cfa523b85ccb86e213) --- updated-dependencies: - dependency-name: CodSpeedHQ/action dependency-version: 4.15.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/labeler dependency-version: 6.1.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/codspeed.yml | 2 +- .github/workflows/needs_release_notes.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 7c9d4fd25d..c9d2060a66 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@c381be0bfd20e844fb45594f6aa182ffcd94545c # v4.15.0 + uses: CodSpeedHQ/action@3194d9a39c4d46684cb44bf7207fc56626aad8fd # v4.15.1 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/needs_release_notes.yml b/.github/workflows/needs_release_notes.yml index 037d7ffa78..1f79725b86 100644 --- a/.github/workflows/needs_release_notes.yml +++ b/.github/workflows/needs_release_notes.yml @@ -21,7 +21,7 @@ jobs: pull-requests: write # Required to add labels to PRs runs-on: ubuntu-latest steps: - - uses: actions/labeler@634933edcd8ababfe52f92936142cc22ac488b1b # v6.0.1 + - uses: actions/labeler@f27b608878404679385c85cfa523b85ccb86e213 # v6.1.0 with: repo-token: ${{ secrets.GITHUB_TOKEN }} sync-labels: true From 7e58df003f528470f06d6fc689099c4f04ef0c95 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 15 May 2026 17:20:00 +0200 Subject: [PATCH 311/468] chore: run mypy from developer environment (#3972) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore: ignore docs/superpowers/ scratch directory * chore: pin python 3.12 on hatch dev env * chore: run mypy from hatch dev env, drop mirrors-mypy hook Replace the pre-commit/mirrors-mypy hook (which maintained its own duplicate dep list) with a `repo: local` hook that runs `hatch run dev:mypy`. The dev hatch env's `dev` group (resolved via uv.lock) becomes the single source of truth for mypy's dependency set. This also unpins numpy from the type-check environment (it was hard-pinned to `numpy==2.1` in the old hook); type fixes that follow keep mypy clean against current numpy stubs: - relax NDArrayLike.reshape/all signatures so np.ndarray structurally satisfies the protocol - widen AsyncGroup.require_array's `dtype` to include None - add narrowly-scoped `# type: ignore` comments with explanatory notes where numpy 2.x stubs are too strict against runtime-valid calls (datetime64 unit f-strings, 'generic' unit sentinel, newbyteorder subclass identity, ZDTypeLike None handling) - drop stale `# type: ignore` comments that are no longer needed * ci: install hatch in lint workflow so mypy hook can run * docs: changelog for mypy-in-dev-env change * refactor: resolve None dtype at create() boundary `create()` accepts `dtype=None` (legacy v2 behavior: an unspecified dtype defaults to float64). Previously this `None` was forwarded untyped into `_create`, which doesn't accept `None` — it only worked because `parse_dtype(None)` -> `np.dtype(None)` happens to resolve to float64. That required a `cast()` to silence mypy. Resolve `None` to `"float64"` explicitly in `create()` before forwarding, so the value passed to `_create` is a real dtype and the cast is no longer needed. No behavior change. * refactor: give NDArrayLike.reshape/all precise signatures The initial fix for numpy-stub conformance widened the NDArrayLike protocol's `reshape` and `all` to `(*args: Any, **kwargs: Any) -> Any`, which erased type information for every consumer of the protocol. Replace with precise signatures that np.ndarray still satisfies structurally: - `reshape(shape: tuple[int, ...], /, *, order=..., copy=...) -> NDArrayLike` — the `Literal[-1]` form was the only thing blocking a precise signature (it straddles numpy's arity-split overloads); it is unused on protocol-typed values, so drop it. `NDBuffer.reshape` keeps its public `-1` support by normalizing `-1` to `(-1,)` before forwarding. - `all(self) -> np.bool_` — the sole caller wraps the result in `bool(...)`, and no-arg is all we use. * chore: remove gitignore for claude docs * chore: restore uv.lock uv.lock was removed in #3962 as unused. The mypy-via-hatch change in this branch makes it load-bearing again: it is the single source of truth that keeps the `dev` hatch environment (and therefore mypy's results) consistent across developer machines and CI. Restore it, regenerated against the current pyproject.toml. * docs: rename changelog entry to PR #3972 * ci: skip mypy hook on pre-commit.ci The mypy hook is now `language: system` and shells out to `hatch run dev:mypy`, which needs the project's hatch dev environment. pre-commit.ci's hosted runners don't have it, so the hook can only fail there. Add it to `ci.skip`; mypy is still covered by the Lint GitHub Actions workflow (which installs hatch) and by local prek runs. * refactor: apply review nitpicks from PR #3972 - Inline the float64 dtype default into the `_create` call instead of reassigning the `dtype` variable. - Move the numpy 2.x stub explanation onto its own line above the code so `# type: ignore` comment lines stay short. Co-Authored-By: Claude Opus 4.7 (1M context) * ci: run mypy via `uv run` so the lockfile is actually honored `hatch run dev:mypy` does not consume `uv.lock` — hatch has no lockfile support and re-resolves the `dev` dependency group from scratch each time it builds the environment. This defeated the PR's goal of a reproducible type-checking environment: contributors with stale or differently-resolved hatch `dev` envs saw different mypy results (e.g. errors from an older `tomlkit` whose `TOMLDocument.__getitem__` was typed `Item | Container` rather than `Any`). Switch the mypy pre-commit hook and the Lint workflow to `uv run --frozen mypy`. `uv` does sync from `uv.lock`, so the committed lockfile becomes the real single source of truth for mypy's dependency set, identical for every contributor and for CI. - .pre-commit-config.yaml: hook entry `hatch run dev:mypy` -> `uv run --frozen mypy` - .github/workflows/lint.yml: install `uv` instead of `hatch` - pyproject.toml / changes: update wording to match Co-Authored-By: Claude Opus 4.7 (1M context) * Apply suggestion from @maxrjones Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * fix: test dtype is None exactly, not via falsy collapse `dtype or "float64"` substitutes the default for any falsy input — empty string, 0, empty Mapping — not just None. Those wouldn't pass ZDTypeLike validation anyway, but the failure mode was "silent substitution to float64" instead of "raise on invalid input". Use an exact `is None` check expressed as a conditional expression. * chore: add .python-version pinning default to 3.12 uv reads `.python-version` to decide which interpreter to use for `uv venv` / `uv sync` / `uv run`. With the mypy hook now running as `uv run --frozen mypy`, pinning the interpreter here keeps the dev env consistent across developer machines — matching the existing `[tool.mypy].python_version = "3.12"` and `requires-python = ">=3.12"` declarations. `.python-version` is not consumed by hatch (its envs declare their own Python via `[tool.hatch.envs.*].python`), so the test matrix (py3.12/3.13/3.14) is unaffected. --------- Co-authored-by: Claude Opus 4.7 (1M context) Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- .github/workflows/lint.yml | 8 + .pre-commit-config.yaml | 30 +- .python-version | 1 + changes/3972.misc.md | 1 + pyproject.toml | 2 +- src/zarr/_compat.py | 2 +- src/zarr/api/asynchronous.py | 3 +- src/zarr/codecs/cast_value.py | 6 +- src/zarr/core/buffer/core.py | 16 +- src/zarr/core/dtype/__init__.py | 2 +- src/zarr/core/dtype/npy/int.py | 18 +- src/zarr/core/dtype/npy/string.py | 3 +- src/zarr/core/dtype/npy/time.py | 21 +- src/zarr/core/group.py | 2 +- tests/test_array.py | 2 +- tests/test_dtype_registry.py | 2 +- uv.lock | 4149 +++++++++++++++++++++++++++++ 17 files changed, 4223 insertions(+), 45 deletions(-) create mode 100644 .python-version create mode 100644 changes/3972.misc.md create mode 100644 uv.lock diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index d32e75dd0d..768e660ec2 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -22,4 +22,12 @@ jobs: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: persist-credentials: false + - name: Set up Python + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + with: + python-version: "3.12" + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + with: + enable-cache: true - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2.0.3 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c9c0e61668..31a74772a0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,11 @@ ci: autoupdate_commit_msg: "chore: update pre-commit hooks" autoupdate_schedule: "monthly" autofix_prs: false - skip: [] # pre-commit.ci only checks for updates, prek runs hooks locally + # mypy runs as a `language: system` hook via `uv run mypy`, which needs `uv` + # and the repo checkout to resolve the dev environment from `uv.lock` — + # unavailable on pre-commit.ci's runners. It is covered instead by the Lint + # GitHub Actions workflow and by local prek runs. + skip: [mypy] default_stages: [pre-commit, pre-push] @@ -27,25 +31,15 @@ repos: - id: check-yaml exclude: mkdocs.yml - id: trailing-whitespace - - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.20.2 + - repo: local hooks: - id: mypy - files: ^(src|tests)/ - additional_dependencies: - # Package dependencies - - packaging - - donfig - - numcodecs - - google-crc32c>=1.5 - - numpy==2.1 # https://github.com/zarr-developers/zarr-python/issues/3780 + https://github.com/zarr-developers/zarr-python/issues/3688 - - typing_extensions - - universal-pathlib - - obstore>=0.5.1 - # Tests - - pytest - - hypothesis - - s3fs + name: mypy + language: system + entry: uv run --frozen mypy + pass_filenames: false + always_run: true + types_or: [python, pyi] - repo: https://github.com/scientific-python/cookie rev: 2026.04.04 hooks: diff --git a/.python-version b/.python-version new file mode 100644 index 0000000000..e4fba21835 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/changes/3972.misc.md b/changes/3972.misc.md new file mode 100644 index 0000000000..60e5f75cca --- /dev/null +++ b/changes/3972.misc.md @@ -0,0 +1 @@ +Run `mypy` via `uv run mypy` instead of `pre-commit`'s isolated venv. The `dev` dependency group in `pyproject.toml`, locked by `uv.lock`, is now the single source of truth for `mypy`'s dependency set, eliminating the duplicate dependency list previously maintained in `.pre-commit-config.yaml` and giving every contributor and CI an identical, reproducible type-checking environment. diff --git a/pyproject.toml b/pyproject.toml index cd7d32c286..f460d31b25 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,6 @@ maintainers = [ { name = "Deepak Cherian" } ] requires-python = ">=3.12" -# If you add a new dependency here, please also add it to .pre-commit-config.yaml dependencies = [ 'packaging>=22.0', 'numpy>=2', @@ -444,6 +443,7 @@ markers = [ [tool.repo-review] ignore = [ "PC111", # fix Python code in documentation - enable later + "PC140", # we run mypy via `uv run mypy`, not via mirrors-mypy "PC170", # use PyGrep hooks - no *.rst files to check "PC180", # for JavaScript - not interested "PC902", # pre-commit.ci custom autofix message - not using autofix diff --git a/src/zarr/_compat.py b/src/zarr/_compat.py index 061e75dbe4..ce6be34c22 100644 --- a/src/zarr/_compat.py +++ b/src/zarr/_compat.py @@ -102,7 +102,7 @@ def _reshape_view(arr: "NDArray[Any]", shape: tuple[int, ...]) -> "NDArray[Any]" If a view cannot be created (the array is not contiguous) on NumPy >= 2.1. """ if Version(np.__version__) >= Version("2.1"): - return arr.reshape(shape, copy=False) # type: ignore[call-overload, no-any-return] + return arr.reshape(shape, copy=False) else: arr.shape = shape return arr diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index bdfb4438dd..7f185535df 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -1049,7 +1049,8 @@ async def create( store_path, shape=shape, chunks=chunks, - dtype=dtype, + # Legacy v2 behavior: an unspecified dtype defaults to float64. + dtype="float64" if dtype is None else dtype, compressor=compressor, fill_value=fill_value, overwrite=overwrite, diff --git a/src/zarr/codecs/cast_value.py b/src/zarr/codecs/cast_value.py index adf4886104..eb8a4de248 100644 --- a/src/zarr/codecs/cast_value.py +++ b/src/zarr/codecs/cast_value.py @@ -300,11 +300,11 @@ def _validate_scalar_map( def _do_cast( self, - arr: np.ndarray, # type: ignore[type-arg] + arr: np.ndarray, *, - target_dtype: np.dtype, # type: ignore[type-arg] + target_dtype: np.dtype, scalar_map: Mapping[str | float | int, str | float | int] | None, - ) -> np.ndarray: # type: ignore[type-arg] + ) -> np.ndarray: if not _HAS_RUST_BACKEND: raise ImportError( "The cast_value codec requires the 'cast-value-rs' package. " diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index 58a59975b7..890c707cd1 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -71,8 +71,13 @@ def __setitem__(self, key: slice, value: Any) -> None: ... def __array__(self) -> npt.NDArray[Any]: ... def reshape( - self, shape: tuple[int, ...] | Literal[-1], *, order: Literal["A", "C", "F"] = ... - ) -> Self: ... + self, + shape: tuple[int, ...], + /, + *, + order: Literal["A", "C", "F"] | None = ..., + copy: bool | None = ..., + ) -> NDArrayLike: ... def view(self, dtype: npt.DTypeLike) -> Self: ... @@ -92,7 +97,7 @@ def transpose(self, axes: SupportsIndex | Sequence[SupportsIndex] | None) -> Sel def ravel(self, order: Literal["K", "A", "C", "F"] = ...) -> Self: ... - def all(self) -> bool: ... + def all(self) -> np.bool_: ... def __eq__(self, other: object) -> Self: # type: ignore[override] """Element-wise equal @@ -502,7 +507,10 @@ def byteorder(self) -> Endian: return Endian(sys.byteorder) def reshape(self, newshape: tuple[int, ...] | Literal[-1]) -> Self: - return self.__class__(self._data.reshape(newshape)) + # numpy accepts a bare -1, but the NDArrayLike protocol only types the + # tuple form; normalize so the forwarded value matches the protocol. + shape = (newshape,) if newshape == -1 else newshape + return self.__class__(self._data.reshape(shape)) def squeeze(self, axis: tuple[int, ...]) -> Self: newshape = tuple(a for i, a in enumerate(self.shape) if i not in axis) diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index 95af6f8389..7e2cd90fd2 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -276,7 +276,7 @@ def parse_dtype( # First attempt to interpret the input as JSON if isinstance(dtype_spec, Mapping | str | Sequence): try: - return get_data_type_from_json(dtype_spec, zarr_format=zarr_format) # type: ignore[arg-type] + return get_data_type_from_json(dtype_spec, zarr_format=zarr_format) except ValueError: # no data type matched this JSON-like input pass diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index e5b8fa6aa1..a68923507b 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -600,7 +600,8 @@ def to_native_dtype(self) -> np.dtypes.Int16DType: The np.dtype('int16') instance. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) + # numpy 2.x stub: newbyteorder widens to base dtype, runtime preserves the concrete subclass + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] @classmethod def _from_json_v2(cls, data: DTypeJSON) -> Self: @@ -762,7 +763,8 @@ def to_native_dtype(self) -> np.dtypes.UInt16DType: The np.dtype('uint16') instance. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) + # numpy 2.x stub: newbyteorder widens to base dtype, runtime preserves the concrete subclass + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] @classmethod def _from_json_v2(cls, data: DTypeJSON) -> Self: @@ -945,7 +947,8 @@ def to_native_dtype(self: Self) -> np.dtypes.Int32DType: The np.dtype('int32') instance. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) + # numpy 2.x stub: newbyteorder widens to base dtype, runtime preserves the concrete subclass + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] @classmethod def _from_json_v2(cls, data: DTypeJSON) -> Self: @@ -1130,7 +1133,8 @@ def to_native_dtype(self) -> np.dtypes.UInt32DType: The NumPy unsigned 32-bit integer dtype. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) + # numpy 2.x stub: newbyteorder widens to base dtype, runtime preserves the concrete subclass + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] @classmethod def _from_json_v2(cls, data: DTypeJSON) -> Self: @@ -1288,7 +1292,8 @@ def to_native_dtype(self) -> np.dtypes.Int64DType: The NumPy signed 64-bit integer dtype. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) + # numpy 2.x stub: newbyteorder widens to base dtype, runtime preserves the concrete subclass + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] @classmethod def _from_json_v2(cls, data: DTypeJSON) -> Self: @@ -1419,7 +1424,8 @@ def to_native_dtype(self) -> np.dtypes.UInt64DType: The native NumPy dtype.eeeeeeeeeeeeeeeee """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls().newbyteorder(byte_order) + # numpy 2.x stub: newbyteorder widens to base dtype, runtime preserves the concrete subclass + return self.dtype_cls().newbyteorder(byte_order) # type: ignore[return-value] @classmethod def _from_json_v2(cls, data: DTypeJSON) -> Self: diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index 069d0b128d..c8ddd5f215 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -172,7 +172,8 @@ def to_native_dtype(self) -> np.dtypes.StrDType[int]: The NumPy data type. """ byte_order = endianness_to_numpy_str(self.endianness) - return self.dtype_cls(self.length).newbyteorder(byte_order) + # numpy 2.x stub: newbyteorder widens to base dtype, runtime preserves the concrete subclass + return self.dtype_cls(self.length).newbyteorder(byte_order) # type: ignore[return-value] @classmethod def _check_json_v2(cls, data: DTypeJSON) -> TypeGuard[FixedLengthUTF32JSON_V2]: diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index c8d2718d52..e55eb08d38 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -537,7 +537,9 @@ def _cast_scalar_unchecked(self, data: TimeDeltaLike) -> np.timedelta64: numpy.timedelta64 The input data cast as a numpy timedelta64 scalar. """ - return self.to_native_dtype().type(data, f"{self.scale_factor}{self.unit}") + # numpy 2.x stub: timedelta64(scalar, formatted_unit_str) is runtime-valid + # but no overload matches the dynamic f-string unit argument. + return self.to_native_dtype().type(data, f"{self.scale_factor}{self.unit}") # type: ignore[call-overload, no-any-return] def cast_scalar(self, data: object) -> np.timedelta64: """ @@ -546,7 +548,8 @@ def cast_scalar(self, data: object) -> np.timedelta64: """ if self._check_scalar(data): if isinstance(data, np.timedelta64) and np.isnat(data): - return np.timedelta64("NaT", self.unit) + # numpy 2.x stub: 'generic' is a runtime-valid unit but not in the Literal overload. + return np.timedelta64("NaT", self.unit) # type: ignore[arg-type] return self._cast_scalar_unchecked(data) msg = ( f"Cannot convert object {data!r} with type {type(data)} to a scalar compatible with the " @@ -561,7 +564,8 @@ def default_scalar(self) -> np.timedelta64: This method provides a default value for the timedelta64 scalar, which is a 'Not-a-Time' (NaT) value. """ - return np.timedelta64("NaT", self.unit) + # numpy 2.x stub: 'generic' is a runtime-valid unit but not in the Literal overload. + return np.timedelta64("NaT", self.unit) # type: ignore[arg-type] def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.timedelta64: """ @@ -585,7 +589,9 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.timedel If the input JSON is not a valid representation of a scalar for this data type. """ if check_json_time(data): - return self.to_native_dtype().type(data, f"{self.scale_factor}{self.unit}") + # numpy 2.x stub: timedelta64(scalar, formatted_unit_str) is runtime-valid + # but no overload matches the dynamic f-string unit argument. + return self.to_native_dtype().type(data, f"{self.scale_factor}{self.unit}") # type: ignore[call-overload, no-any-return] raise TypeError(f"Invalid type: {data}. Expected an integer.") # pragma: no cover @@ -812,7 +818,9 @@ def _cast_scalar_unchecked(self, data: DateTimeLike) -> np.datetime64: numpy.datetime64 The input cast to a NumPy datetime scalar. """ - return self.to_native_dtype().type(data, f"{self.scale_factor}{self.unit}") + # numpy 2.x stub: datetime64(scalar, formatted_unit_str) is runtime-valid + # but no overload matches the dynamic f-string unit argument. + return self.to_native_dtype().type(data, f"{self.scale_factor}{self.unit}") # type: ignore[call-overload, no-any-return] def cast_scalar(self, data: object) -> np.datetime64: """ @@ -851,7 +859,8 @@ def default_scalar(self) -> np.datetime64: The default scalar value, which is a 'Not-a-Time' (NaT) value """ - return np.datetime64("NaT", self.unit) + # numpy 2.x stub: 'generic' is a runtime-valid unit but not in the Literal overload. + return np.datetime64("NaT", self.unit) # type: ignore[arg-type] def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> np.datetime64: """ diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index ae18cbaf85..213b7fb607 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -1166,7 +1166,7 @@ async def require_array( name: str, *, shape: ShapeLike, - dtype: npt.DTypeLike = None, + dtype: npt.DTypeLike | None = None, exact: bool = False, **kwargs: Any, ) -> AnyAsyncArray: diff --git a/tests/test_array.py b/tests/test_array.py index 51df8d12c6..91f0fae1c4 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1792,7 +1792,7 @@ async def test_from_array( assert result.fill_value == new_fill_value assert result.dtype == src_dtype assert result.attrs == new_attributes - assert result.chunks == new_chunks # type: ignore[unreachable] + assert result.chunks == new_chunks @pytest.mark.parametrize("store", ["local"], indirect=True) diff --git a/tests/test_dtype_registry.py b/tests/test_dtype_registry.py index b7ceb502b7..60c6b5db01 100644 --- a/tests/test_dtype_registry.py +++ b/tests/test_dtype_registry.py @@ -82,7 +82,7 @@ def test_match_dtype_string_na_object_error( data_type_registry_fixture: DataTypeRegistry, ) -> None: 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specifier = ">=7.10" }, + { name = "hypothesis" }, + { name = "numpydoc" }, + { name = "pytest" }, + { name = "pytest-accept" }, + { name = "pytest-asyncio" }, + { name = "pytest-benchmark" }, + { name = "pytest-codspeed" }, + { name = "pytest-cov" }, + { name = "pytest-xdist" }, + { name = "tomlkit" }, + { name = "uv" }, +] From b740cf2637588bc4f853a9fa58204265b38f245c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 15 May 2026 23:34:43 +0200 Subject: [PATCH 312/468] feat:get_ranges (#3925) * feat(core): add _coalesce module skeleton with CoalesceOptions and stub * test(core): add failing tests for coalesced_get basic cases * feat(core): implement coalesced_get for basic sequential cases * test(core): cover Offset/Suffix/None and mixed-cluster cases in coalesced_get * feat(core): run coalesced fetches concurrently under max_concurrency * test(core): cover key-missing (start/mid) and fetch-raises in coalesced_get * test(core): cover max_coalesced_bytes cap in coalesced_get * test(core): add coverage-invariant property test for coalesced_get * test(core): drop unused HEAVY_MERGE/NO_MERGE constants Co-Authored-By: Claude Opus 4.7 (1M context) * docs(core): shorten coalesced_get docstring summary line Split the overlong first line into a short numpydoc summary plus an extended description. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(core): drop dead invariant checks in merged-group path After the input split at the top of coalesced_get, merged groups only ever contain RangeByteRequest members. Replace the per-element isinstance filters (and the defensive ``else 0`` sort-key branch) with a single assertion at the top of the merged-group block and direct attribute access. Also remove the unreachable ``if total == 0: return`` guard (``indexed`` is non-empty by construction once we pass the earlier guard). Co-Authored-By: Claude Opus 4.7 (1M context) * test(core): cover key-missing on uncoalescable input Exercise the ``kind == "missing"`` branch in the uncoalescable single-fetch arm for Offset/Suffix/None inputs, which was not hit by existing tests. Co-Authored-By: Claude Opus 4.7 (1M context) * fix(core): cancel pending fetches on early exit and stop-after-miss Two related correctness issues in coalesced_get's drain loop: 1. When the consumer breaks out of the async-for (early exit), the generator's finally block only awaited in-flight tasks rather than cancelling them. That wasted I/O. Cancel first, then gather. 2. The drain loop waited on completion_queue for ``total`` entries, but after a "missing" or "error" we cancel pending tasks -- and cancelled tasks never enqueue a completion. With max_concurrency > 1 this could hang. Rework the drain loop to break out immediately on the first miss/error; the finally block handles cleanup. The new structure also collapses the redundant miss/error branches and removes the now-unused ``total``/``drained``/``stopped`` bookkeeping. Co-Authored-By: Claude Opus 4.7 (1M context) * test(core): cover mid-stream miss with concurrency > 1 Exercises the concurrent path where a missing key is observed while other fetches are still in flight. Uses an asyncio.Event to gate late arrivals until after the miss has been processed, giving the drain loop an opportunity to observe and discard post-stop completions, and verifies the iterator terminates cleanly without hanging or raising. Co-Authored-By: Claude Opus 4.7 (1M context) * test(core): verify consumer-break cancels pending fetches Drives many slow ranges with a small max_concurrency, breaks out of the async-for after the first yield, and verifies that at least one still-running fetch was cancelled rather than being left to run to completion. Cancellation is observed via a counter in the fetch's CancelledError branch. Co-Authored-By: Claude Opus 4.7 (1M context) * fix(core): type coalesced_get as AsyncGenerator coalesced_get is implemented as an async generator (uses yield) and callers need access to aclose() to drive its finally block deterministically. Declaring the return type as AsyncGenerator instead of AsyncIterator exposes aclose()/asend()/athrow() through the type system, matches the runtime object, and lets consumers (e.g. the consumer-break test) avoid type-ignore escape hatches. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(test): drop redundant pytestmark asyncio pyproject asyncio_mode=auto already covers async test dispatch; the explicit pytestmark was a vestige. Co-Authored-By: Claude Opus 4.7 (1M context) * feat(storage): add private SupportsGetRanges protocol * test(storage): add failing tests for FsspecStore.get_ranges * feat(storage): add FsspecStore.get_ranges and coalesce_options kwarg * test(storage): add SupportsGetRanges conformance tests * chore: add towncrier fragment for get_ranges Used 0000.feature.md as a placeholder; rename to {pr-number}.feature.md once the PR is opened. Co-Authored-By: Claude Opus 4.7 (1M context) * docs: drop private-symbol mention from get_ranges changelog The SupportsGetRanges protocol is private; a user-facing release note shouldn't advertise it. Co-Authored-By: Claude Opus 4.7 (1M context) * test: refactor tests * test: skip fsspec-backed get_ranges tests on old fsspec The min_deps CI job pins fsspec to 2023.10.0, which predates AsyncFileSystemWrapper. Wrapping a sync MemoryFileSystem fails there at fixture setup. Guard the affected tests with the same skipif pattern already used in test_fsspec.py. Co-Authored-By: Claude Opus 4.7 (1M context) * Update src/zarr/core/_coalesce.py Co-authored-by: Ilan Gold * Update src/zarr/core/_coalesce.py Co-authored-by: Ilan Gold * Update src/zarr/core/_coalesce.py Co-authored-by: Ilan Gold * chore: lint * refactor: better function design with explicit context * refactor(coalesce): split coalescing from coalesced get * refactor(coalesce): use sequence instead of iterable * Update src/zarr/storage/_fsspec.py Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * refactor: banish typeddict, we are fine with kwargs * refactor: apply suggestions from code review * refactor: use drop queue in favor of as_completed; abort early with FileNotFoundError when get yields None * refactor: define get_ranges on the store abc * Update src/zarr/core/_coalesce.py Co-authored-by: Chuck Daniels * Apply suggestion from @chuckwondo Co-authored-by: Chuck Daniels * Apply suggestion from @chuckwondo Co-authored-by: Chuck Daniels * refactor: use function-scoped defaults * fix: fix failing test * refactor: defaults in one place * hoist imports * Update tests/test_coalesce.py Co-authored-by: Chuck Daniels * Update src/zarr/abc/store.py Co-authored-by: Chuck Daniels * Update src/zarr/core/_coalesce.py Co-authored-by: Chuck Daniels * Update src/zarr/core/_coalesce.py Co-authored-by: Chuck Daniels * Update tests/test_coalesce.py Co-authored-by: Chuck Daniels * apply suggestions from code review * Update src/zarr/core/_coalesce.py Co-authored-by: Chuck Daniels * raise exception group * raise exception group * Update src/zarr/core/_coalesce.py Co-authored-by: Chuck Daniels * Update src/zarr/core/_coalesce.py Co-authored-by: Chuck Daniels --------- Co-authored-by: Claude Opus 4.7 (1M context) Co-authored-by: Ilan Gold Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: Chuck Daniels --- changes/3925.feature.md | 1 + src/zarr/abc/store.py | 63 +- src/zarr/core/_coalesce.py | 222 +++++++ src/zarr/storage/_wrapper.py | 28 +- tests/test_coalesce.py | 674 +++++++++++++++++++++ tests/test_store/test_fsspec_get_ranges.py | 124 ++++ tests/test_store/test_get_ranges.py | 142 +++++ 7 files changed, 1252 insertions(+), 2 deletions(-) create mode 100644 changes/3925.feature.md create mode 100644 src/zarr/core/_coalesce.py create mode 100644 tests/test_coalesce.py create mode 100644 tests/test_store/test_fsspec_get_ranges.py create mode 100644 tests/test_store/test_get_ranges.py diff --git a/changes/3925.feature.md b/changes/3925.feature.md new file mode 100644 index 0000000000..ed07be309c --- /dev/null +++ b/changes/3925.feature.md @@ -0,0 +1 @@ +Add `zarr.abc.store.Store.get_ranges` for concurrent, coalesced multi-range reads from a single key. The method is defined on the `Store` ABC with a default implementation built on `Store.get`, so every store inherits a working version; stores with native multi-range backends (e.g. `FsspecStore`) can override for efficiency. Coalescing knobs (`max_concurrency`, `max_gap_bytes`, `max_coalesced_bytes`) are passed as keyword arguments to `get_ranges`. Failures from underlying fetches surface as a `BaseExceptionGroup` (PEP 654); callers should use `except*` to filter for specific exception types such as `FileNotFoundError`. diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 600df17ee5..3247649f10 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -4,13 +4,14 @@ import json from abc import ABC, abstractmethod from dataclasses import dataclass +from functools import partial from itertools import starmap from typing import TYPE_CHECKING, Literal, Protocol, runtime_checkable from zarr.core.sync import sync if TYPE_CHECKING: - from collections.abc import AsyncGenerator, AsyncIterator, Iterable + from collections.abc import AsyncGenerator, AsyncIterator, Iterable, Sequence from types import TracebackType from typing import Any, Self @@ -616,6 +617,66 @@ async def _get_many( for req in requests: yield (req[0], await self.get(*req)) + async def get_ranges( + self, + key: str, + byte_ranges: Sequence[ByteRequest | None], + *, + prototype: BufferPrototype, + max_concurrency: int = 10, + max_gap_bytes: int = 1 << 20, # 1 MiB + max_coalesced_bytes: int = 16 << 20, # 16 MiB + ) -> AsyncIterator[Sequence[tuple[int, Buffer | None]]]: + """Read many byte ranges from `key`. + + Yields one batch per underlying I/O operation, each a sequence of + `(input_index, Buffer | None)` tuples. Batches across yields arrive in + completion order, not input order. The default implementation built + into `Store` runs the coalescer over `self.get`, so subclasses get a + working implementation for free; stores that have a more efficient + backend (e.g. ranged HTTP, S3 byte-range fetches) should override. + + Parameters + ---------- + key + Storage key to read from. + byte_ranges + Input ranges. `None` means "the whole value". + prototype + Buffer prototype, forwarded to `self.get`. + max_concurrency + Maximum number of merged fetches in flight at once. + max_gap_bytes + Two `RangeByteRequest`s separated by at most this many bytes may + be merged into one fetch. + max_coalesced_bytes + Upper bound on the size of a single merged fetch. + + Raises + ------ + BaseExceptionGroup + Failures from underlying fetches are reported as a + `BaseExceptionGroup` (PEP 654) and should be handled with + `except*`. Inner exceptions include `FileNotFoundError` if any + fetch returns `None` (i.e. `key` is absent), and any exception + raised by `self.get` for the corresponding range. Pending + fetches are cancelled as soon as one task fails, so the group + typically contains a single non-`CancelledError` exception even + under high concurrency. + """ + # Local import: zarr.core._coalesce imports symbols from this module. + from zarr.core._coalesce import coalesced_get + + fetch = partial(self.get, key, prototype) + async for group in coalesced_get( + fetch, + byte_ranges, + max_concurrency=max_concurrency, + max_gap_bytes=max_gap_bytes, + max_coalesced_bytes=max_coalesced_bytes, + ): + yield group + async def getsize(self, key: str) -> int: """ Return the size, in bytes, of a value in a Store. diff --git a/src/zarr/core/_coalesce.py b/src/zarr/core/_coalesce.py new file mode 100644 index 0000000000..bfee9b4052 --- /dev/null +++ b/src/zarr/core/_coalesce.py @@ -0,0 +1,222 @@ +# src/zarr/core/_coalesce.py +from __future__ import annotations + +import asyncio +from typing import TYPE_CHECKING, NamedTuple + +from zarr.abc.store import RangeByteRequest + +if TYPE_CHECKING: + from collections.abc import AsyncGenerator, Awaitable, Callable, Sequence + + from zarr.abc.store import ByteRequest + from zarr.core.buffer import Buffer + + +class _WorkerCtx(NamedTuple): + """Shared state passed to the per-task worker coroutines. + + Bundling these lets the workers declare their dependencies as one + parameter instead of capturing them implicitly via closure. + """ + + fetch: Callable[[ByteRequest | None], Awaitable[Buffer | None]] + semaphore: asyncio.Semaphore + + +async def _fetch_single( + ctx: _WorkerCtx, idx: int, req: ByteRequest | None +) -> Sequence[tuple[int, Buffer | None]]: + """Fetch one byte range. Raises FileNotFoundError if the key is absent.""" + async with ctx.semaphore: + buf = await ctx.fetch(req) + if buf is None: + raise FileNotFoundError + return ((idx, buf),) + + +async def _fetch_group( + ctx: _WorkerCtx, members: list[tuple[int, RangeByteRequest]] +) -> Sequence[tuple[int, Buffer | None]]: + """Fetch one merged byte range and slice it back into per-input buffers. + + `members` must already be sorted by `start`; callers in this module + build it from the sorted mergeable list. Raises `FileNotFoundError` + if the key is absent. + """ + if len(members) == 1: + solo_idx, solo_req = members[0] + return await _fetch_single(ctx, solo_idx, solo_req) + + start = members[0][1].start + end = max(r.end for _, r in members) + async with ctx.semaphore: + big = await ctx.fetch(RangeByteRequest(start, end)) + if big is None: + raise FileNotFoundError + sliced = [(idx, big[r.start - start : r.end - start]) for idx, r in members] + return tuple(sliced) + + +def coalesce_ranges( + byte_ranges: Sequence[ByteRequest | None], + *, + max_gap_bytes: int, + max_coalesced_bytes: int, +) -> tuple[ + list[list[tuple[int, RangeByteRequest]]], + list[tuple[int, ByteRequest | None]], +]: + """Plan a set of byte-range fetches: which inputs merge, which stand alone. + + Pure (no I/O). The result is the I/O plan a caller would execute: each + group corresponds to one fetch of a coalesced byte range, and each + uncoalescable item corresponds to one fetch of the original request. + + All tuning knobs are required keyword arguments. `Store.get_ranges` is + the public entry point and owns the canonical default values; this + function takes them explicitly to avoid duplicating policy. + + Parameters + ---------- + byte_ranges + Input ranges. `None` means "the whole value". + max_gap_bytes + Two `RangeByteRequest`s separated by at most this many bytes may be + merged into one fetch. + max_coalesced_bytes + Upper bound on the size of a single merged fetch. + + Returns + ------- + groups + List of merged groups. Each group is a list of + `(input_index, RangeByteRequest)` pairs sorted by `start`. A + single-element group represents a `RangeByteRequest` that did not + merge with any neighbor. + uncoalescable + List of `(input_index, request)` pairs for inputs that are not + `RangeByteRequest` (`OffsetByteRequest`, `SuffixByteRequest`, + `None`). Indices are preserved from the input order. + + Notes + ----- + Only `RangeByteRequest` inputs participate in coalescing. Two ranges + merge when both: their gap (next `start` minus current group's running + `end`) is `<= max_gap_bytes`, and the resulting merged span is + `<= max_coalesced_bytes`. + """ + indexed = list(enumerate(byte_ranges)) + mergeable = [(i, r) for i, r in indexed if isinstance(r, RangeByteRequest)] + uncoalescable: list[tuple[int, ByteRequest | None]] = [ + (i, r) for i, r in indexed if not isinstance(r, RangeByteRequest) + ] + + # Sort mergeables by start offset, then merge. Track running start/end of the + # current group so each merge step is O(1) instead of O(group size). + mergeable.sort(key=lambda pair: pair[1].start) + groups: list[list[tuple[int, RangeByteRequest]]] = [] + group_start = 0 + group_end = 0 + for pair in mergeable: + _i, r = pair + if groups and r.start - group_end <= max_gap_bytes: + prospective_end = max(group_end, r.end) + if prospective_end - group_start <= max_coalesced_bytes: + groups[-1].append(pair) + group_end = prospective_end + continue + groups.append([pair]) + group_start = r.start + group_end = r.end + + return groups, uncoalescable + + +async def coalesced_get( + fetch: Callable[[ByteRequest | None], Awaitable[Buffer | None]], + byte_ranges: Sequence[ByteRequest | None], + *, + max_concurrency: int, + max_gap_bytes: int, + max_coalesced_bytes: int, +) -> AsyncGenerator[Sequence[tuple[int, Buffer | None]]]: + """Read many byte ranges through `fetch` with coalescing and concurrency. + + Nearby ranges are merged into a single underlying I/O, and merged fetches + are run concurrently. Each yield corresponds to exactly one underlying I/O + operation: a sequence of `(input_index, result)` tuples for all input + ranges served by that I/O. Tuples within a yielded sequence are ordered by + start offset. Yields across groups are in completion order, not input + order. + + All tuning knobs are required keyword arguments. `Store.get_ranges` is + the public entry point and owns the canonical default values; this + function takes them explicitly to avoid duplicating policy. + + Parameters + ---------- + fetch + Callable that reads one byte range and returns a `Buffer` (or `None` + if the underlying key does not exist). Typically constructed via + `functools.partial(store.get, key, prototype)`. + byte_ranges + Input ranges. `None` means "the whole value". + max_concurrency + Maximum number of merged fetches in flight at once. + max_gap_bytes + Forwarded to `coalesce_ranges`. + max_coalesced_bytes + Forwarded to `coalesce_ranges`. + + Yields + ------ + Sequence[tuple[int, Buffer | None]] + Per-I/O batch of `(input_index, result)` tuples. + + Notes + ----- + - Only `RangeByteRequest` inputs are coalesced. `OffsetByteRequest`, + `SuffixByteRequest`, and `None` are each treated as uncoalescable + (one fetch, one single-tuple yield per input). + - Failures from underlying fetches surface as a `BaseExceptionGroup` + (PEP 654). Inner exceptions include `FileNotFoundError` if a fetch + returns `None`, plus any exception `fetch` raises. Pending fetches are + cancelled as soon as one task fails, so the group typically contains a + single non-`CancelledError` exception even under high concurrency. + - Groups completed before the failure remain observable on the yields + preceding the raise. + - `GeneratorExit` raised by `aclose()` is filtered out so the iterator + closes cleanly; callers don't see a group containing only it. + """ + if not byte_ranges: + return + + groups, singles = coalesce_ranges( + byte_ranges, + max_gap_bytes=max_gap_bytes, + max_coalesced_bytes=max_coalesced_bytes, + ) + + ctx = _WorkerCtx(fetch=fetch, semaphore=asyncio.Semaphore(max_concurrency)) + + # Launch all work as tasks. The semaphore bounds actual I/O concurrency. + # TaskGroup wraps task exceptions in BaseExceptionGroup; we propagate the + # group unchanged as part of the public contract (callers handle batch + # failures via `except*` / PEP 654). GeneratorExit (raised when the + # consumer calls aclose()) is filtered out so close completes cleanly. + try: + async with asyncio.TaskGroup() as tg: + tasks = [ + *(tg.create_task(_fetch_group(ctx, group)) for group in groups), + *(tg.create_task(_fetch_single(ctx, i, single)) for i, single in singles), + ] + + for fut in asyncio.as_completed(tasks): + yield await fut + except BaseExceptionGroup as eg: + # Strip GeneratorExits (consumer aclose()) and propagate whatever remains. + _, other_errors = eg.split(GeneratorExit) + + if other_errors is not None: + raise other_errors from None diff --git a/src/zarr/storage/_wrapper.py b/src/zarr/storage/_wrapper.py index d8ecfa6d45..37aeb8166f 100644 --- a/src/zarr/storage/_wrapper.py +++ b/src/zarr/storage/_wrapper.py @@ -3,7 +3,7 @@ from typing import TYPE_CHECKING, cast if TYPE_CHECKING: - from collections.abc import AsyncGenerator, AsyncIterator, Iterable + from collections.abc import AsyncGenerator, AsyncIterator, Iterable, Sequence from types import TracebackType from typing import Any, Self @@ -103,6 +103,32 @@ async def get_partial_values( ) -> list[Buffer | None]: return await self._store.get_partial_values(prototype, key_ranges) + async def get_ranges( + self, + key: str, + byte_ranges: Sequence[ByteRequest | None], + *, + prototype: BufferPrototype, + max_concurrency: int | None = None, + max_gap_bytes: int | None = None, + max_coalesced_bytes: int | None = None, + ) -> AsyncIterator[Sequence[tuple[int, Buffer | None]]]: + """Forward `get_ranges` to the wrapped store. + + Default values for the coalescing kwargs are not declared here; the + wrapped store decides them. `None` means "don't override the wrapped + store's default". + """ + kwargs: dict[str, int] = {} + if max_concurrency is not None: + kwargs["max_concurrency"] = max_concurrency + if max_gap_bytes is not None: + kwargs["max_gap_bytes"] = max_gap_bytes + if max_coalesced_bytes is not None: + kwargs["max_coalesced_bytes"] = max_coalesced_bytes + async for group in self._store.get_ranges(key, byte_ranges, prototype=prototype, **kwargs): + yield group + async def exists(self, key: str) -> bool: return await self._store.exists(key) diff --git a/tests/test_coalesce.py b/tests/test_coalesce.py new file mode 100644 index 0000000000..cb8ff29ec7 --- /dev/null +++ b/tests/test_coalesce.py @@ -0,0 +1,674 @@ +# tests/test_coalesce.py +from __future__ import annotations + +import asyncio +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +import pytest + +from zarr.abc.store import ( + ByteRequest, + OffsetByteRequest, + RangeByteRequest, + SuffixByteRequest, +) +from zarr.core._coalesce import ( + coalesce_ranges, + coalesced_get, +) +from zarr.core.buffer import Buffer, default_buffer_prototype + +if TYPE_CHECKING: + from collections.abc import AsyncIterator, Callable, Mapping, Sequence + + +def _buf(data: bytes) -> Buffer: + return default_buffer_prototype().buffer.from_bytes(data) + + +@dataclass +class FakeFetch: + """Records every call and serves canned bytes from an in-memory blob.""" + + blob: bytes + key_exists: bool = True + raise_on: Callable[[ByteRequest | None], bool] | None = None + calls: list[ByteRequest | None] = field(default_factory=list) + + async def __call__(self, byte_range: ByteRequest | None) -> Buffer | None: + self.calls.append(byte_range) + if not self.key_exists: + return None + if self.raise_on is not None and self.raise_on(byte_range): + raise OSError("injected") + if byte_range is None: + return _buf(self.blob) + if isinstance(byte_range, RangeByteRequest): + return _buf(self.blob[byte_range.start : byte_range.end]) + if isinstance(byte_range, OffsetByteRequest): + return _buf(self.blob[byte_range.offset :]) + if isinstance(byte_range, SuffixByteRequest): + return _buf(self.blob[-byte_range.suffix :]) + raise AssertionError(f"unknown byte_range {byte_range!r}") + + +async def _collect( + agen: AsyncIterator[Sequence[tuple[int, Buffer | None]]], +) -> list[list[tuple[int, Buffer | None]]]: + """Drain an async generator of groups into a list of lists of tuples.""" + return [list(group) async for group in agen] + + +def _contents(groups: list[list[tuple[int, Buffer | None]]]) -> dict[int, bytes]: + """Flatten to {index: bytes}.""" + result: dict[int, bytes] = {} + for group in groups: + for idx, buf in group: + assert buf is not None + result[idx] = buf.to_bytes() + return result + + +# --------------------------------------------------------------------------- +# Shared coalescing-knob bundles. Each is a complete mapping of all three +# kwargs to splat into `coalesced_get`; `coalesce_ranges` ignores +# `max_concurrency`. The leaf functions in `_coalesce.py` require all knobs +# explicitly — `Store.get_ranges` is the public entry point and owns the +# canonical defaults. Tests pick their own values appropriate to the scenario. +# --------------------------------------------------------------------------- + +# Permissive default for tests that don't care about specific thresholds. Mirrors +# `Store.get_ranges`'s public defaults but the test file owns this independently +# of any production constants. +DEFAULT: Mapping[str, int] = { + "max_concurrency": 10, + "max_gap_bytes": 1 << 20, + "max_coalesced_bytes": 16 << 20, +} +"""Permissive defaults; mirrors `Store.get_ranges`'s baseline.""" + +MERGE_GAP_50: Mapping[str, int] = { + "max_concurrency": 10, + "max_gap_bytes": 50, + "max_coalesced_bytes": 1 << 20, +} +"""Merge ranges within 50 bytes of each other.""" + +NO_MERGE: Mapping[str, int] = { + "max_concurrency": 10, + "max_gap_bytes": -1, + "max_coalesced_bytes": 1 << 20, +} +"""No merging: any positive gap is > -1, so no pair ever coalesces.""" + +CAP_50: Mapping[str, int] = { + "max_concurrency": 10, + "max_gap_bytes": 1000, + "max_coalesced_bytes": 50, +} +"""Gap permissive but merged size capped at 50 bytes.""" + + +def _grouping(opts: Mapping[str, int]) -> dict[str, int]: + """Return only the grouping knobs from a full options bundle. + + `coalesce_ranges` rejects `max_concurrency`; this lets test bundles be + full kwargs maps (for `coalesced_get`) and still be passed to the pure + planner via splat. + """ + return {k: v for k, v in opts.items() if k != "max_concurrency"} + + +# A deterministic blob used for content-sensitive cases: byte i == (i % 256). +_INDEXED_BLOB = bytes(i % 256 for i in range(10_000)) + + +# --------------------------------------------------------------------------- +# Parametrized structural/content tests (cases without async timing or errors). +# --------------------------------------------------------------------------- + + +@dataclass(frozen=True) +class StructuralCase: + """One row of the parametrized structure-and-contents table.""" + + id: str + """pytest id for the case.""" + ranges: list[ByteRequest | None] + """Input to coalesced_get.""" + options: Mapping[str, int] + """Coalescing knobs to splat into `coalesced_get`.""" + expected_group_sizes: list[int] + """Sorted list of group tuple-counts (order-independent).""" + expected_contents: dict[int, bytes] | None = None + """{input_index: bytes} to verify bytes, or None to skip the content check.""" + expected_n_fetches: int | None = None + """Exact number of calls to the fetch callable, or None to skip the check.""" + + +_STRUCTURAL_CASES: list[StructuralCase] = [ + StructuralCase( + id="empty-input", + ranges=[], + options=DEFAULT, + expected_group_sizes=[], + expected_n_fetches=0, + ), + StructuralCase( + id="single-range", + ranges=[RangeByteRequest(2, 5)], + options=DEFAULT, + expected_group_sizes=[1], + expected_contents={0: _INDEXED_BLOB[2:5]}, + expected_n_fetches=1, + ), + StructuralCase( + id="disjoint-3-no-merge", + ranges=[ + RangeByteRequest(0, 10), + RangeByteRequest(200, 210), + RangeByteRequest(500, 510), + ], + options=MERGE_GAP_50, + expected_group_sizes=[1, 1, 1], + expected_contents={ + 0: _INDEXED_BLOB[0:10], + 1: _INDEXED_BLOB[200:210], + 2: _INDEXED_BLOB[500:510], + }, + expected_n_fetches=3, + ), + StructuralCase( + id="adjacent-3-one-merged-group", + ranges=[ + RangeByteRequest(0, 5), + RangeByteRequest(10, 15), + RangeByteRequest(20, 25), + ], + options=MERGE_GAP_50, + expected_group_sizes=[3], + expected_contents={ + 0: _INDEXED_BLOB[0:5], + 1: _INDEXED_BLOB[10:15], + 2: _INDEXED_BLOB[20:25], + }, + expected_n_fetches=1, + ), + StructuralCase( + id="two-clusters-one-singleton", + ranges=[ + RangeByteRequest(0, 10), + RangeByteRequest(20, 30), + RangeByteRequest(500, 510), + ], + options=MERGE_GAP_50, + expected_group_sizes=[1, 2], + expected_contents={ + 0: _INDEXED_BLOB[0:10], + 1: _INDEXED_BLOB[20:30], + 2: _INDEXED_BLOB[500:510], + }, + expected_n_fetches=2, + ), + StructuralCase( + id="uncoalescable-mixed-with-range", + ranges=[ + RangeByteRequest(0, 3), + OffsetByteRequest(5), + SuffixByteRequest(2), + None, + ], + options=DEFAULT, + expected_group_sizes=[1, 1, 1, 1], + expected_contents={ + 0: _INDEXED_BLOB[0:3], + 1: _INDEXED_BLOB[5:], + 2: _INDEXED_BLOB[-2:], + 3: _INDEXED_BLOB, + }, + expected_n_fetches=4, + ), + StructuralCase( + id="shuffled-input-indices-preserved", + ranges=[ + RangeByteRequest(500, 510), + RangeByteRequest(0, 10), + RangeByteRequest(200, 210), + RangeByteRequest(300, 310), + ], + options=MERGE_GAP_50, + expected_group_sizes=[1, 1, 1, 1], + expected_contents={ + 0: _INDEXED_BLOB[500:510], + 1: _INDEXED_BLOB[0:10], + 2: _INDEXED_BLOB[200:210], + 3: _INDEXED_BLOB[300:310], + }, + expected_n_fetches=4, + ), + StructuralCase( + id="cap-prevents-merge-of-close-ranges", + # 20 + 20 gap + 20 = 60-byte merged span > cap of 50. + ranges=[RangeByteRequest(0, 20), RangeByteRequest(40, 60)], + options=CAP_50, + expected_group_sizes=[1, 1], + expected_n_fetches=2, + ), + StructuralCase( + id="single-range-larger-than-cap-passes-through", + # Cap only applies to MERGE decisions; a lone oversized range still fetches. + ranges=[RangeByteRequest(0, 200)], + options=CAP_50, + expected_group_sizes=[1], + expected_contents={0: _INDEXED_BLOB[0:200]}, + expected_n_fetches=1, + ), +] + + +@pytest.mark.parametrize("case", _STRUCTURAL_CASES, ids=lambda c: c.id) +async def test_coalescing_structure_and_contents(case: StructuralCase) -> None: + """Group structure, byte contents, and fetch-call count for the deterministic cases.""" + fetch = FakeFetch(_INDEXED_BLOB) + groups = await _collect(coalesced_get(fetch, case.ranges, **case.options)) + + assert sorted(len(g) for g in groups) == sorted(case.expected_group_sizes) + + if case.expected_contents is not None: + assert _contents(groups) == case.expected_contents + + if case.expected_n_fetches is not None: + assert len(fetch.calls) == case.expected_n_fetches + + +# --------------------------------------------------------------------------- +# Focused non-parametrized tests for cases with distinctive assertion shapes. +# --------------------------------------------------------------------------- + + +async def test_within_group_ordering_is_start_offset() -> None: + """Within a merged group, tuples are ordered by start offset, not input order.""" + fetch = FakeFetch(_INDEXED_BLOB) + # Two ranges that merge; one has a later start but is listed first in input. + ranges: list[ByteRequest | None] = [RangeByteRequest(20, 25), RangeByteRequest(0, 5)] + groups = await _collect(coalesced_get(fetch, ranges, **MERGE_GAP_50)) + assert len(groups) == 1 + # Input index 1 (start=0) comes first, then 0 (start=20). + assert [idx for idx, _ in groups[0]] == [1, 0] + + +async def test_adjacent_ranges_fire_single_fetch_spanning_merged_region() -> None: + """Verify the merged fetch covers exactly the span from min-start to max-end.""" + fetch = FakeFetch(_INDEXED_BLOB) + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 5), + RangeByteRequest(10, 15), + RangeByteRequest(20, 25), + ] + await _collect(coalesced_get(fetch, ranges, **MERGE_GAP_50)) + assert len(fetch.calls) == 1 + call = fetch.calls[0] + assert isinstance(call, RangeByteRequest) + assert call.start == 0 + assert call.end == 25 + + +# --------------------------------------------------------------------------- +# Concurrency and cancellation. +# --------------------------------------------------------------------------- + + +async def test_max_concurrency_is_honored() -> None: + """With 10 non-mergeable ranges and max_concurrency=3, peak in-flight must not exceed 3.""" + in_flight = 0 + peak = 0 + lock = asyncio.Lock() + + async def fetch(byte_range: ByteRequest | None) -> Buffer | None: + nonlocal in_flight, peak + async with lock: + in_flight += 1 + peak = max(peak, in_flight) + # give the scheduler a chance to run other tasks + await asyncio.sleep(0.01) + async with lock: + in_flight -= 1 + return _buf(b"x") + + ranges: list[ByteRequest | None] = [RangeByteRequest(i * 1000, i * 1000 + 1) for i in range(10)] + opts: Mapping[str, int] = { + "max_gap_bytes": 0, # force no merging + "max_coalesced_bytes": 1 << 20, + "max_concurrency": 3, + } + async for _group in coalesced_get(fetch, ranges, **opts): + pass + assert peak <= 3 + assert peak >= 2 # must have been some real concurrency + + +async def test_consumer_break_cancels_pending_fetches() -> None: + """Breaking out of the async for should cancel pending fetches rather than let them complete.""" + completed_calls = 0 + cancelled_calls = 0 + + async def fetch(byte_range: ByteRequest | None) -> Buffer | None: + nonlocal completed_calls, cancelled_calls + assert isinstance(byte_range, RangeByteRequest) + start = byte_range.start + try: + # First fetch returns fast so the async-for body runs and can break. + # Later fetches sleep long enough that cancellation has room to land. + await asyncio.sleep(0.001 if start == 0 else 2.0) + except asyncio.CancelledError: + cancelled_calls += 1 + raise + completed_calls += 1 + return _buf(b"x") + + opts: Mapping[str, int] = { + "max_gap_bytes": -1, # no merging + "max_coalesced_bytes": 1 << 20, + "max_concurrency": 3, + } + ranges: list[ByteRequest | None] = [RangeByteRequest(i * 1000, i * 1000 + 1) for i in range(6)] + + agen = coalesced_get(fetch, ranges, **opts) + async for _group in agen: + break + # Explicitly close the generator so its finally block runs (cancelling + # in-flight tasks) before we make assertions. + await agen.aclose() + + # The fast task completes; the remaining tasks are either cancelled while + # sleeping (raising CancelledError into the user try block) or cancelled + # while still waiting on the semaphore (which doesn't enter the try at all). + # Either way, none of them should be allowed to complete. + assert completed_calls == 1 + assert cancelled_calls >= 1 + assert completed_calls + cancelled_calls <= len(ranges) + + +# --------------------------------------------------------------------------- +# Key-missing semantics. +# --------------------------------------------------------------------------- + + +async def test_key_missing_from_first_call_raises() -> None: + """If the very first fetch returns None, the iterator raises an ExceptionGroup containing FileNotFoundError.""" + fetch = FakeFetch(b"x" * 100, key_exists=False) + ranges: list[ByteRequest | None] = [RangeByteRequest(0, 10), RangeByteRequest(20, 30)] + with pytest.RaisesGroup(pytest.RaisesExc(FileNotFoundError)): + await _collect(coalesced_get(fetch, ranges, **DEFAULT)) + + +@pytest.mark.parametrize( + "byte_range", + [OffsetByteRequest(5), SuffixByteRequest(5), None], + ids=["offset", "suffix", "none"], +) +async def test_key_missing_on_uncoalescable_input_raises( + byte_range: ByteRequest | None, +) -> None: + """Uncoalescable inputs take a distinct path; key-missing must still raise (wrapped in a group).""" + fetch = FakeFetch(b"x" * 100, key_exists=False) + with pytest.RaisesGroup(pytest.RaisesExc(FileNotFoundError)): + await _collect(coalesced_get(fetch, [byte_range], **DEFAULT)) + + +async def test_key_missing_mid_stream_raises_after_earlier_groups() -> None: + """If a later fetch returns None, earlier-completed groups yield before the raise.""" + call_count = 0 + + async def fetch(byte_range: ByteRequest | None) -> Buffer | None: + nonlocal call_count + call_count += 1 + # Deterministic: first call serves, second returns None. + await asyncio.sleep(0.01 if call_count == 1 else 0.02) + if call_count >= 2: + return None + return _buf(b"ok") + + opts: Mapping[str, int] = { + "max_gap_bytes": -1, + "max_coalesced_bytes": 1 << 20, + "max_concurrency": 1, # serialize for determinism + } + ranges: list[ByteRequest | None] = [RangeByteRequest(0, 2), RangeByteRequest(100, 102)] + agen = coalesced_get(fetch, ranges, **opts) + first = await anext(agen) + assert len(first) == 1 + with pytest.RaisesGroup(pytest.RaisesExc(FileNotFoundError)): + await anext(agen) + + +async def test_key_missing_mid_stream_with_concurrency_cancels_late_arrivals() -> None: + """ + Under max_concurrency > 1, a mid-stream miss should raise FileNotFoundError + and cancel still-in-flight unrelated tasks rather than wait for them. + """ + late_gate = asyncio.Event() + miss_fired = asyncio.Event() + # Driven by the test body after the first successful yield, so the miss + # task can't race past the start=0 result. + fire_miss = asyncio.Event() + + async def fetch(byte_range: ByteRequest | None) -> Buffer | None: + assert isinstance(byte_range, RangeByteRequest) + start = byte_range.start + if start == 0: + return _buf(b"ok") + if start == 1000: + # Wait for the test to give the green light before returning None. + # This makes ordering deterministic regardless of scheduling. + await asyncio.wait_for(fire_miss.wait(), timeout=5.0) + miss_fired.set() + return None + # Late arrivals would block on this gate; they should be cancelled + # before they ever return. + await asyncio.wait_for(late_gate.wait(), timeout=5.0) + return _buf(b"ok") + + opts: Mapping[str, int] = { + "max_gap_bytes": -1, + "max_coalesced_bytes": 1 << 20, + "max_concurrency": 3, + } + ranges: list[ByteRequest | None] = [RangeByteRequest(i * 1000, i * 1000 + 1) for i in range(7)] + + agen = coalesced_get(fetch, ranges, **opts) + first = await anext(agen) + assert len(first) == 1 + idx, buf = first[0] + assert idx == 0 + assert buf is not None + # Now that #0 has yielded, signal the miss task to return None. + fire_miss.set() + with pytest.RaisesGroup(pytest.RaisesExc(FileNotFoundError)): + await anext(agen) + assert miss_fired.is_set() + # Sanity: late_gate was never set, so the cancellation path is what completed the test. + assert not late_gate.is_set() + + +# --------------------------------------------------------------------------- +# Error propagation. +# --------------------------------------------------------------------------- + + +async def test_fetch_raises_propagates() -> None: + """An exception raised by fetch propagates on the yield that produced the failing group.""" + fetch = FakeFetch( + _INDEXED_BLOB, + raise_on=lambda r: isinstance(r, RangeByteRequest) and r.start >= 100, + ) + opts: Mapping[str, int] = { + "max_gap_bytes": -1, + "max_coalesced_bytes": 1 << 20, + "max_concurrency": 1, + } + ranges: list[ByteRequest | None] = [RangeByteRequest(0, 10), RangeByteRequest(200, 210)] + with pytest.RaisesGroup(pytest.RaisesExc(OSError, match="injected")): + await _collect(coalesced_get(fetch, ranges, **opts)) + + +# --------------------------------------------------------------------------- +# Property-style coverage invariant. +# --------------------------------------------------------------------------- + + +async def test_coverage_invariant_random_inputs() -> None: + """For any random RangeByteRequest input, every input index appears exactly once.""" + import random + + rng = random.Random(42) + fetch = FakeFetch(_INDEXED_BLOB) + + ranges: list[ByteRequest | None] = [] + for _ in range(50): + start = rng.randint(0, 9000) + length = rng.randint(1, 500) + ranges.append(RangeByteRequest(start, start + length)) + + groups = await _collect(coalesced_get(fetch, ranges, **DEFAULT)) + seen: list[int] = [idx for group in groups for idx, _buf in group] + assert sorted(seen) == list(range(len(ranges))) + + flat = _contents(groups) + for i, r in enumerate(ranges): + assert isinstance(r, RangeByteRequest) + assert flat[i] == _INDEXED_BLOB[r.start : r.end] + + +# --------------------------------------------------------------------------- +# Pure-function tests for coalesce_ranges (no async, no fetch). +# --------------------------------------------------------------------------- + + +def test_coalesce_ranges_empty_input() -> None: + groups, uncoalescable = coalesce_ranges([], max_gap_bytes=1 << 20, max_coalesced_bytes=16 << 20) + assert groups == [] + assert uncoalescable == [] + + +def test_coalesce_ranges_separates_coalescable_from_uncoalescable() -> None: + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 10), + OffsetByteRequest(100), + SuffixByteRequest(5), + None, + RangeByteRequest(20, 30), + ] + groups, uncoalescable = coalesce_ranges(ranges, **_grouping(MERGE_GAP_50)) + + # Both range requests fall within MERGE_GAP_50's gap budget. + assert len(groups) == 1 + assert [idx for idx, _ in groups[0]] == [0, 4] + + # Non-RangeByteRequest entries preserve their original input indices. + assert [(idx, type(req).__name__ if req else None) for idx, req in uncoalescable] == [ + (1, "OffsetByteRequest"), + (2, "SuffixByteRequest"), + (3, None), + ] + + +def test_coalesce_ranges_no_merge_when_gap_exceeds_budget() -> None: + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 10), + RangeByteRequest(200, 210), + RangeByteRequest(500, 510), + ] + groups, uncoalescable = coalesce_ranges(ranges, **_grouping(MERGE_GAP_50)) + assert uncoalescable == [] + assert [len(g) for g in groups] == [1, 1, 1] + assert [idx for g in groups for idx, _ in g] == [0, 1, 2] + + +def test_coalesce_ranges_merges_within_gap_budget() -> None: + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 5), + RangeByteRequest(10, 15), + RangeByteRequest(20, 25), + ] + groups, _ = coalesce_ranges(ranges, **_grouping(MERGE_GAP_50)) + assert len(groups) == 1 + assert [idx for idx, _ in groups[0]] == [0, 1, 2] + + +def test_coalesce_ranges_respects_max_coalesced_bytes() -> None: + # Gap budget is permissive (1000), but the merged span would exceed CAP_50's + # 50-byte cap, so the second range starts a new group. + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 30), + RangeByteRequest(40, 80), + ] + groups, _ = coalesce_ranges(ranges, **_grouping(CAP_50)) + assert [len(g) for g in groups] == [1, 1] + + +def test_coalesce_ranges_groups_are_sorted_by_start() -> None: + """Input order is irrelevant; groups always emerge in start-offset order.""" + ranges: list[ByteRequest | None] = [ + RangeByteRequest(500, 510), + RangeByteRequest(0, 10), + RangeByteRequest(20, 30), + RangeByteRequest(200, 210), + ] + groups, _ = coalesce_ranges(ranges, **_grouping(MERGE_GAP_50)) + # First group is the {0-10, 20-30} cluster (from input indices 1, 2). + # Then the {200-210} singleton, then {500-510}. + flat = [idx for g in groups for idx, _ in g] + assert flat == [1, 2, 3, 0] + # Within each group, members are sorted by start. + for g in groups: + starts = [r.start for _, r in g] + assert starts == sorted(starts) + + +def test_coalesce_ranges_overlapping_ranges_merge() -> None: + """Nested/overlapping ranges have a non-positive 'gap' and always merge.""" + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 100), + RangeByteRequest(50, 60), # nested + RangeByteRequest(80, 120), # overlaps + ] + groups, _ = coalesce_ranges(ranges, **_grouping(MERGE_GAP_50)) + assert len(groups) == 1 + assert [idx for idx, _ in groups[0]] == [0, 1, 2] + + +def test_coalesce_ranges_running_end_handles_nesting() -> None: + """A subsequent range fully inside the running span must not extend group_end backwards.""" + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 1000), # group_end=1000 + RangeByteRequest(100, 200), # nested; group_end stays at 1000 + RangeByteRequest(990, 1010), # gap = -10 from running end, still merges + ] + groups, _ = coalesce_ranges(ranges, **_grouping(MERGE_GAP_50)) + assert len(groups) == 1 + assert {idx for idx, _ in groups[0]} == {0, 1, 2} + + +def test_coalesce_ranges_only_uncoalescable_inputs() -> None: + ranges: list[ByteRequest | None] = [None, OffsetByteRequest(10), SuffixByteRequest(5)] + groups, uncoalescable = coalesce_ranges( + ranges, max_gap_bytes=1 << 20, max_coalesced_bytes=16 << 20 + ) + assert groups == [] + assert [idx for idx, _ in uncoalescable] == [0, 1, 2] + + +def test_coalesce_ranges_total_index_coverage() -> None: + """Every input index appears exactly once across groups + uncoalescable.""" + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 10), + None, + RangeByteRequest(15, 25), + OffsetByteRequest(100), + RangeByteRequest(30, 40), + ] + groups, uncoalescable = coalesce_ranges(ranges, **_grouping(MERGE_GAP_50)) + seen = sorted([idx for g in groups for idx, _ in g] + [idx for idx, _ in uncoalescable]) + assert seen == list(range(len(ranges))) diff --git a/tests/test_store/test_fsspec_get_ranges.py b/tests/test_store/test_fsspec_get_ranges.py new file mode 100644 index 0000000000..61d834d22f --- /dev/null +++ b/tests/test_store/test_fsspec_get_ranges.py @@ -0,0 +1,124 @@ +# tests/test_store/test_fsspec_get_ranges.py +"""Lightweight integration tests for FsspecStore.get_ranges using MemoryFileSystem. + +These don't need moto/s3 — they exercise the new method against an in-process +fsspec MemoryFileSystem wrapped in the async wrapper. +""" + +from __future__ import annotations + +import pytest +from packaging.version import parse as parse_version + +from zarr.abc.store import RangeByteRequest +from zarr.core.buffer import Buffer, default_buffer_prototype +from zarr.storage import FsspecStore +from zarr.storage._fsspec import _make_async + +fsspec = pytest.importorskip("fsspec") + +# AsyncFileSystemWrapper (needed to wrap a sync MemoryFileSystem) landed in fsspec 2024.12.0. +# Older versions are pinned by the min-deps CI job, so skip the whole file there. +pytestmark = pytest.mark.skipif( + parse_version(fsspec.__version__) < parse_version("2024.12.0"), + reason="No AsyncFileSystemWrapper", +) + + +@pytest.fixture +def memory_store() -> FsspecStore: + """An FsspecStore backed by fsspec MemoryFileSystem (wrapped async).""" + from fsspec.implementations.memory import MemoryFileSystem + + # Each test gets a clean filesystem; MemoryFileSystem is a singleton per target_options, + # so clear state explicitly. + fs: MemoryFileSystem = MemoryFileSystem() + fs.store.clear() + fs.pseudo_dirs.clear() + async_fs = _make_async(fs) + return FsspecStore(fs=async_fs, path="/root") + + +async def _write(store: FsspecStore, key: str, data: bytes) -> None: + buf = default_buffer_prototype().buffer.from_bytes(data) + await store.set(key, buf) + + +async def test_get_ranges_happy_path(memory_store: FsspecStore) -> None: + blob = bytes(i % 256 for i in range(1024)) + await _write(memory_store, "blob", blob) + proto = default_buffer_prototype() + + ranges = [ + RangeByteRequest(0, 10), + RangeByteRequest(100, 110), + RangeByteRequest(500, 520), + ] + groups: list[list[tuple[int, Buffer | None]]] = [ + list(group) async for group in memory_store.get_ranges("blob", ranges, prototype=proto) + ] + + flat: dict[int, bytes] = {} + for group in groups: + for idx, buf in group: + assert buf is not None + flat[idx] = buf.to_bytes() + + assert flat[0] == blob[0:10] + assert flat[1] == blob[100:110] + assert flat[2] == blob[500:520] + + +async def test_get_ranges_missing_key_raises(memory_store: FsspecStore) -> None: + """A request against a missing key raises BaseExceptionGroup containing FileNotFoundError.""" + proto = default_buffer_prototype() + agen = memory_store.get_ranges("does-not-exist", [RangeByteRequest(0, 10)], prototype=proto) + with pytest.RaisesGroup(pytest.RaisesExc(FileNotFoundError)): + await anext(agen) + + +async def test_get_ranges_forwards_coalescing_kwargs(memory_store: FsspecStore) -> None: + """`max_gap_bytes=-1` forces no merging; we should see three groups for three ranges.""" + blob = bytes(i % 256 for i in range(1024)) + await _write(memory_store, "blob", blob) + proto = default_buffer_prototype() + + ranges = [ + RangeByteRequest(0, 10), + RangeByteRequest(11, 20), # adjacent: would merge under defaults + RangeByteRequest(21, 30), + ] + groups: list[list[tuple[int, Buffer | None]]] = [ + list(group) + async for group in memory_store.get_ranges( + "blob", ranges, prototype=proto, max_gap_bytes=-1 + ) + ] + # With merging disabled, every range becomes its own one-tuple group. + assert sorted(len(g) for g in groups) == [1, 1, 1] + + +async def test_get_ranges_mixed_range_types(memory_store: FsspecStore) -> None: + """Covers RangeByteRequest, OffsetByteRequest, SuffixByteRequest, and None in one call.""" + from zarr.abc.store import ByteRequest, OffsetByteRequest, SuffixByteRequest + + blob = bytes(i % 256 for i in range(512)) + await _write(memory_store, "mixed", blob) + proto = default_buffer_prototype() + + ranges: list[ByteRequest | None] = [ + RangeByteRequest(0, 10), + OffsetByteRequest(500), + SuffixByteRequest(12), + None, + ] + flat: dict[int, bytes] = {} + async for group in memory_store.get_ranges("mixed", ranges, prototype=proto): + for idx, buf in group: + assert buf is not None + flat[idx] = buf.to_bytes() + + assert flat[0] == blob[0:10] + assert flat[1] == blob[500:] + assert flat[2] == blob[-12:] + assert flat[3] == blob diff --git a/tests/test_store/test_get_ranges.py b/tests/test_store/test_get_ranges.py new file mode 100644 index 0000000000..8f0c6a4814 --- /dev/null +++ b/tests/test_store/test_get_ranges.py @@ -0,0 +1,142 @@ +# tests/test_store/test_get_ranges.py +"""Tests for `Store.get_ranges` — the ABC default implementation and wrapper delegation. + +`Store.get_ranges` is defined on the ABC with a default implementation built +on `coalesced_get(self.get, ...)`, so every store inherits a working version. +These tests cover that inherited path and the explicit delegation in +`WrapperStore` (which ensures wrapped stores' optimized overrides are honored). +Store-specific overrides (e.g. `FsspecStore`) have their own test modules. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING + +import pytest + +from zarr.abc.store import RangeByteRequest +from zarr.core.buffer import default_buffer_prototype +from zarr.storage import MemoryStore +from zarr.storage._wrapper import WrapperStore + +if TYPE_CHECKING: + from collections.abc import AsyncIterator, Sequence + + from zarr.abc.store import ByteRequest + from zarr.core.buffer import Buffer, BufferPrototype + + +async def _write(store: MemoryStore, key: str, data: bytes) -> None: + buf = default_buffer_prototype().buffer.from_bytes(data) + await store.set(key, buf) + + +async def test_memory_store_inherits_get_ranges_from_abc() -> None: + """MemoryStore doesn't override `get_ranges`; the ABC default must work end-to-end.""" + store = MemoryStore() + blob = bytes(i % 256 for i in range(512)) + await _write(store, "blob", blob) + + ranges = [RangeByteRequest(0, 10), RangeByteRequest(100, 110)] + proto = default_buffer_prototype() + flat: dict[int, bytes] = {} + async for group in store.get_ranges("blob", ranges, prototype=proto): + for idx, buf in group: + assert buf is not None + flat[idx] = buf.to_bytes() + + assert flat[0] == blob[0:10] + assert flat[1] == blob[100:110] + + +async def test_memory_store_get_ranges_missing_key_raises() -> None: + """A missing key on a default-impl store raises BaseExceptionGroup containing FileNotFoundError.""" + store = MemoryStore() + proto = default_buffer_prototype() + agen = store.get_ranges("does-not-exist", [RangeByteRequest(0, 10)], prototype=proto) + with pytest.RaisesGroup(pytest.RaisesExc(FileNotFoundError)): + await anext(agen) + + +async def test_wrapper_store_delegates_get_ranges() -> None: + """WrapperStore.get_ranges must delegate to the wrapped store, not fall back to the default.""" + + class CountingMemoryStore(MemoryStore): + """Tallies get_ranges invocations so we can assert delegation.""" + + get_ranges_calls: int = 0 + + async def get_ranges( + self, + key: str, + byte_ranges: Sequence[ByteRequest | None], + *, + prototype: BufferPrototype, + max_concurrency: int = 10, + max_gap_bytes: int = 1 << 20, + max_coalesced_bytes: int = 16 << 20, + ) -> AsyncIterator[Sequence[tuple[int, Buffer | None]]]: + type(self).get_ranges_calls += 1 + async for group in super().get_ranges( + key, + byte_ranges, + prototype=prototype, + max_concurrency=max_concurrency, + max_gap_bytes=max_gap_bytes, + max_coalesced_bytes=max_coalesced_bytes, + ): + yield group + + inner = CountingMemoryStore() + blob = b"x" * 100 + await _write(inner, "k", blob) + wrapped = WrapperStore(inner) + + proto = default_buffer_prototype() + groups: list[list[tuple[int, Buffer | None]]] = [ + list(group) + async for group in wrapped.get_ranges("k", [RangeByteRequest(0, 5)], prototype=proto) + ] + + assert CountingMemoryStore.get_ranges_calls == 1 + assert len(groups) == 1 + assert groups[0][0][0] == 0 + + +async def test_wrapper_store_forwards_coalescing_kwargs() -> None: + """Coalescing kwargs flow through WrapperStore to the wrapped store's get_ranges.""" + + class SpyMemoryStore(MemoryStore): + last_max_gap_bytes: int | None = None + + async def get_ranges( + self, + key: str, + byte_ranges: Sequence[ByteRequest | None], + *, + prototype: BufferPrototype, + max_concurrency: int = 10, + max_gap_bytes: int = 1 << 20, + max_coalesced_bytes: int = 16 << 20, + ) -> AsyncIterator[Sequence[tuple[int, Buffer | None]]]: + type(self).last_max_gap_bytes = max_gap_bytes + async for group in super().get_ranges( + key, + byte_ranges, + prototype=prototype, + max_concurrency=max_concurrency, + max_gap_bytes=max_gap_bytes, + max_coalesced_bytes=max_coalesced_bytes, + ): + yield group + + inner = SpyMemoryStore() + await _write(inner, "k", b"y" * 100) + wrapped = WrapperStore(inner) + proto = default_buffer_prototype() + async for _ in wrapped.get_ranges( + "k", [RangeByteRequest(0, 5)], prototype=proto, max_gap_bytes=-1 + ): + pass + + assert SpyMemoryStore.last_max_gap_bytes == -1 From 2e58a7a44c5388ebfa81100fb94f6c215e584dce Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sat, 16 May 2026 17:21:21 +0200 Subject: [PATCH 313/468] chore: remove warning on fixed length utf32 (#3979) --- changes/3979.misc.md | 1 + src/zarr/core/dtype/npy/string.py | 5 +++-- tests/test_dtype/test_npy/test_string.py | 16 ---------------- 3 files changed, 4 insertions(+), 18 deletions(-) create mode 100644 changes/3979.misc.md diff --git a/changes/3979.misc.md b/changes/3979.misc.md new file mode 100644 index 0000000000..3d49547148 --- /dev/null +++ b/changes/3979.misc.md @@ -0,0 +1 @@ +Remove the `UnstableSpecificationWarning` emitted when serializing a `FixedLengthUTF32` data type instance, as a spec for this data type has been published to zarr-extensions. \ No newline at end of file diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index c8ddd5f215..00cde0d99f 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -26,7 +26,6 @@ HasLength, HasObjectCodec, check_dtype_spec_v2, - v3_unstable_dtype_warning, ) from zarr.core.dtype.npy.common import ( check_json_str, @@ -115,6 +114,9 @@ class FixedLengthUTF32( Wraps the ``np.dtypes.StrDType`` data type. Scalars for this data type are instances of ``np.str_``. + The Zarr V3 specification for this data type is defined at + https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/fixed_length_utf32. + Attributes ---------- dtype_cls : Type[np.dtypes.StrDType] @@ -247,7 +249,6 @@ def to_json( if zarr_format == 2: return {"name": self.to_native_dtype().str, "object_codec_id": None} elif zarr_format == 3: - v3_unstable_dtype_warning(self) return { "name": self._zarr_v3_name, "configuration": {"length_bytes": self.length * self.code_point_bytes}, diff --git a/tests/test_dtype/test_npy/test_string.py b/tests/test_dtype/test_npy/test_string.py index 19d202d164..fcc4793281 100644 --- a/tests/test_dtype/test_npy/test_string.py +++ b/tests/test_dtype/test_npy/test_string.py @@ -6,7 +6,6 @@ from tests.test_dtype.test_wrapper import BaseTestZDType from zarr.core.dtype import FixedLengthUTF32 from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING, VariableLengthUTF8 -from zarr.errors import UnstableSpecificationWarning if _NUMPY_SUPPORTS_VLEN_STRING: @@ -125,21 +124,6 @@ class TestFixedLengthUTF32(BaseTestZDType): invalid_scalar_params = (None,) -@pytest.mark.parametrize( - "zdtype", - [ - FixedLengthUTF32(length=10), - ], -) -def test_unstable_dtype_warning(zdtype: FixedLengthUTF32 | VariableLengthUTF8) -> None: - """ - Test that we get a warning when serializing a dtype without a zarr v3 spec to json - when zarr_format is 3 - """ - with pytest.warns(UnstableSpecificationWarning): - zdtype.to_json(zarr_format=3) - - def test_invalid_size() -> None: """ Test that it's impossible to create a data type that has no length From be160fdf3ed66f9cb2d65b864b7e4c9d56d5abc9 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sun, 17 May 2026 22:56:54 +0200 Subject: [PATCH 314/468] misc(zarr-metadata): typed constants and fixes (#3978) * fix: correct bug in bytes + gzip codec metadata object types * feat: add typed constants --- .../src/zarr_metadata/v2/array.py | 14 ++++++++++--- .../v3/chunk_key_encoding/default.py | 6 +++++- .../zarr_metadata/v3/chunk_key_encoding/v2.py | 6 +++++- .../src/zarr_metadata/v3/codec/blosc.py | 12 +++++++++-- .../src/zarr_metadata/v3/codec/bytes.py | 19 +++++++++++++---- .../src/zarr_metadata/v3/codec/cast_value.py | 18 ++++++++++++++-- .../src/zarr_metadata/v3/codec/gzip.py | 21 ++++++++++++------- .../v3/codec/sharding_indexed.py | 6 +++++- .../tests/v3/codec/bytes/cases.json | 3 +++ .../tests/v3/codec/gzip/cases.json | 7 +------ 10 files changed, 84 insertions(+), 28 deletions(-) diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 9043fd1893..04f76c264f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -1,7 +1,7 @@ """Zarr v2 array metadata types.""" from collections.abc import Mapping -from typing import Literal, NotRequired +from typing import Final, Literal, NotRequired from typing_extensions import TypedDict @@ -22,15 +22,18 @@ """ ArrayOrderV2 = Literal["C", "F"] -"""Permitted values for the `order` field of v2 array metadata. +"""Literal type of permitted values for the `order` field of v2 array metadata. `"C"` (row-major) or `"F"` (column-major) — the in-chunk byte layout. See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ +ARRAY_ORDER_V2: Final = ("C", "F") +"""Tuple of permitted values for the `order` field of v2 array metadata.""" + ArrayDimensionSeparatorV2 = Literal[".", "/"] -"""Permitted values for the `dimension_separator` field of v2 array metadata. +"""Literal type of permitted values for the `dimension_separator` field of v2 array metadata. `"."` (legacy default) joins chunk grid coordinates as `0.0`, `0.1`, ... `"/"` joins them as `0/0`, `0/1`, ... yielding nested directories. @@ -38,6 +41,9 @@ See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ +ARRAY_DIMENSION_SEPARATOR_V2: Final = (".", "/") +"""Tuple of permitted values for the `dimension_separator` field of v2 array metadata.""" + class ZArrayMetadata(TypedDict): """ @@ -93,6 +99,8 @@ class ArrayMetadataV2(TypedDict): __all__ = [ + "ARRAY_DIMENSION_SEPARATOR_V2", + "ARRAY_ORDER_V2", "ArrayDimensionSeparatorV2", "ArrayMetadataV2", "ArrayOrderV2", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py index d69d6af23f..c783861b34 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/default.py @@ -18,11 +18,14 @@ """Literal type of the `name` field of the default chunk key encoding.""" DefaultChunkKeyEncodingSeparator = Literal["/", "."] -"""Permitted `separator` values for the default chunk key encoding. +"""Literal type of permitted `separator` values for the default chunk key encoding. Defaults to `"/"` if absent. """ +DEFAULT_CHUNK_KEY_ENCODING_SEPARATOR: Final = ("/", ".") +"""Tuple of permitted values for the `separator` field of the default chunk key encoding.""" + class DefaultChunkKeyEncodingConfiguration(TypedDict): """Configuration for the default chunk key encoding. @@ -49,6 +52,7 @@ class DefaultChunkKeyEncodingObject(TypedDict): __all__ = [ "DEFAULT_CHUNK_KEY_ENCODING_NAME", + "DEFAULT_CHUNK_KEY_ENCODING_SEPARATOR", "DefaultChunkKeyEncodingConfiguration", "DefaultChunkKeyEncodingMetadata", "DefaultChunkKeyEncodingName", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py index ce247ca12c..fef5793626 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py @@ -18,11 +18,14 @@ """Literal type of the `name` field of the v2 chunk key encoding.""" V2ChunkKeyEncodingSeparator = Literal["/", "."] -"""Permitted `separator` values for the v2 chunk key encoding. +"""Literal type of permitted `separator` values for the v2 chunk key encoding. Defaults to `"."` if absent. """ +V2_CHUNK_KEY_ENCODING_SEPARATOR: Final = ("/", ".") +"""Tuple of permitted values for the `separator` field of the v2 chunk key encoding.""" + class V2ChunkKeyEncodingConfiguration(TypedDict): """Configuration for the v2 chunk key encoding. @@ -49,6 +52,7 @@ class V2ChunkKeyEncodingObject(TypedDict): __all__ = [ "V2_CHUNK_KEY_ENCODING_NAME", + "V2_CHUNK_KEY_ENCODING_SEPARATOR", "V2ChunkKeyEncodingConfiguration", "V2ChunkKeyEncodingMetadata", "V2ChunkKeyEncodingName", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py index 69152cee50..5a986c8260 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/blosc.py @@ -15,10 +15,16 @@ """Literal type of the `name` field of the `blosc` codec.""" BloscShuffle = Literal["noshuffle", "shuffle", "bitshuffle"] -"""Blosc shuffle mode names.""" +"""Literal type of blosc shuffle mode names.""" + +BLOSC_SHUFFLE: Final = ("noshuffle", "shuffle", "bitshuffle") +"""Tuple of permitted values for the `shuffle` field of the `blosc` codec.""" BloscCName = Literal["lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd"] -"""Blosc compressor identifiers.""" +"""Literal type of blosc compressor identifiers.""" + +BLOSC_CNAME: Final = ("lz4", "lz4hc", "blosclz", "snappy", "zlib", "zstd") +"""Tuple of permitted values for the `cname` field of the `blosc` codec.""" class BloscCodecConfiguration(TypedDict): @@ -47,7 +53,9 @@ class BloscCodecObject(TypedDict): """ __all__ = [ + "BLOSC_CNAME", "BLOSC_CODEC_NAME", + "BLOSC_SHUFFLE", "BloscCName", "BloscCodecConfiguration", "BloscCodecMetadata", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py index d72f9ac6ea..522cbe10f5 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py @@ -15,7 +15,10 @@ """Literal type of the `name` field of the `bytes` codec.""" Endian = Literal["little", "big"] -"""Byte order of multi-byte numeric data.""" +"""Literal type of byte order of multi-byte numeric data.""" + +ENDIAN: Final = ("little", "big") +"""Tuple of permitted values for the `endian` field of the `bytes` codec.""" class BytesCodecConfiguration(TypedDict): @@ -29,10 +32,16 @@ class BytesCodecConfiguration(TypedDict): class BytesCodecObject(TypedDict): - """`bytes` codec metadata in object form.""" + """`bytes` codec metadata in object form. + + `configuration` is itself optional — when no configuration fields are + set, the entire `configuration` key may be omitted. This matches the + bare-string short-hand form (`BytesCodecName`) at the canonical data + level; both encodings describe a `bytes` codec with default settings. + """ name: BytesCodecName - configuration: BytesCodecConfiguration + configuration: NotRequired[BytesCodecConfiguration] BytesCodecMetadata = BytesCodecObject | BytesCodecName @@ -40,11 +49,13 @@ class BytesCodecObject(TypedDict): The configuration has no required keys (`endian` is conditionally required at runtime based on data type), so the spec's short-hand-name form is -permitted in addition to the object form. +permitted in addition to the object form, and the object form may itself +omit `configuration` entirely. """ __all__ = [ "BYTES_CODEC_NAME", + "ENDIAN", "BytesCodecConfiguration", "BytesCodecMetadata", "BytesCodecName", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py index 468dab9587..17905bf38a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py @@ -23,17 +23,29 @@ "towards-negative", "nearest-away", ] -"""Permitted values for the `rounding` configuration field. +"""Literal type of permitted values for the `rounding` configuration field. Defaults to `"nearest-even"` if absent. """ +ROUNDING_MODE: Final = ( + "nearest-even", + "towards-zero", + "towards-positive", + "towards-negative", + "nearest-away", +) +"""Tuple of permitted values for the `rounding` field of the `cast_value` codec.""" + OutOfRangeMode = Literal["clamp", "wrap"] -"""Permitted values for the `out_of_range` configuration field. +"""Literal type of permitted values for the `out_of_range` configuration field. If absent, out-of-range values are an encoding/decoding error. """ +OUT_OF_RANGE_MODE: Final = ("clamp", "wrap") +"""Tuple of permitted values for the `out_of_range` field of the `cast_value` codec.""" + ScalarMapEntry = tuple[object, object] """A single `[input, output]` mapping in a `scalar_map` direction. @@ -81,6 +93,8 @@ class CastValueCodecObject(TypedDict): __all__ = [ "CAST_VALUE_CODEC_NAME", + "OUT_OF_RANGE_MODE", + "ROUNDING_MODE", "CastValueCodecConfiguration", "CastValueCodecMetadata", "CastValueCodecName", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py index fb0c2faf3e..3b9936f8cd 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/gzip.py @@ -4,7 +4,7 @@ See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/gzip/index.html """ -from typing import Final, Literal, NotRequired +from typing import Final, Literal from typing_extensions import TypedDict @@ -20,11 +20,15 @@ class GzipCodecConfiguration(TypedDict): Configuration for the Zarr v3 `gzip` codec. `level` is an integer in the range 0-9; 0 disables compression and 9 - is slowest with the best compression ratio. The spec does not mandate - a default. + is slowest with the best compression ratio. The codec's compressed + output depends on `level`, so metadata that omits it cannot + reproducibly identify the chunk bytes produced by a writer — `level` + is required for the metadata to fulfill its reproducibility role, + even though the spec text does not mark it required with RFC 2119 + keywords. """ - level: NotRequired[int] + level: int class GzipCodecObject(TypedDict): @@ -34,11 +38,12 @@ class GzipCodecObject(TypedDict): configuration: GzipCodecConfiguration -GzipCodecMetadata = GzipCodecObject | GzipCodecName -"""Permitted JSON shapes for `gzip` codec metadata. +GzipCodecMetadata = GzipCodecObject +"""Permitted JSON shape for `gzip` codec metadata. -The configuration has no required keys (`level` has no spec-mandated -default but is `NotRequired`), so the short-hand-name form is permitted. +`configuration.level` is required (it determines the codec's output bytes +and is therefore part of the metadata's reproducibility contract), so +only the object form is valid; the short-hand-name form is not permitted. """ __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py index c8dd954e3f..93a0774e4e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py @@ -17,7 +17,10 @@ """Literal type of the `name` field of the `sharding_indexed` codec.""" IndexLocation = Literal["start", "end"] -"""Position of the shard index within the encoded shard.""" +"""Literal type of the position of the shard index within the encoded shard.""" + +INDEX_LOCATION: Final = ("start", "end") +"""Tuple of permitted values for the `index_location` field of the `sharding_indexed` codec.""" class ShardingIndexedCodecConfiguration(TypedDict): @@ -58,6 +61,7 @@ class ShardingIndexedCodecObject(TypedDict): """ __all__ = [ + "INDEX_LOCATION", "SHARDING_INDEXED_CODEC_NAME", "IndexLocation", "ShardingIndexedCodecConfiguration", diff --git a/packages/zarr-metadata/tests/v3/codec/bytes/cases.json b/packages/zarr-metadata/tests/v3/codec/bytes/cases.json index f3c8b978f8..0c30d70a67 100644 --- a/packages/zarr-metadata/tests/v3/codec/bytes/cases.json +++ b/packages/zarr-metadata/tests/v3/codec/bytes/cases.json @@ -11,5 +11,8 @@ "name": "bytes", "configuration": {} }, + "no_configuration": { + "name": "bytes" + }, "short_hand_name": "bytes" } diff --git a/packages/zarr-metadata/tests/v3/codec/gzip/cases.json b/packages/zarr-metadata/tests/v3/codec/gzip/cases.json index b40cbeeedb..7d5e1e6f94 100644 --- a/packages/zarr-metadata/tests/v3/codec/gzip/cases.json +++ b/packages/zarr-metadata/tests/v3/codec/gzip/cases.json @@ -2,10 +2,5 @@ "with_level": { "name": "gzip", "configuration": {"level": 5} - }, - "no_level": { - "name": "gzip", - "configuration": {} - }, - "short_hand_name": "gzip" + } } From f2321ec20949bd9b052f116e50e6972e1dd3b1e6 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sun, 17 May 2026 23:34:31 +0200 Subject: [PATCH 315/468] chore: cd workflow (#3935) * chore: cd workflow * chore: remove python script * feat: use `hatch-vcs` + tag workflow (#171) * tag-based releases --------- Co-authored-by: Ilan Gold --- .github/workflows/zarr-metadata-release.yml | 117 ++++++++++++++++++ packages/zarr-metadata/README.md | 28 +++++ packages/zarr-metadata/pyproject.toml | 12 +- .../src/zarr_metadata/__init__.py | 6 +- packages/zarr-metadata/tests/test_version.py | 16 --- 5 files changed, 158 insertions(+), 21 deletions(-) create mode 100644 .github/workflows/zarr-metadata-release.yml delete mode 100644 packages/zarr-metadata/tests/test_version.py diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml new file mode 100644 index 0000000000..809d502f16 --- /dev/null +++ b/.github/workflows/zarr-metadata-release.yml @@ -0,0 +1,117 @@ +name: zarr-metadata release + +on: + workflow_dispatch: + push: + tags: + - 'zarr_metadata-v*' + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: false + +jobs: + build: + name: Build wheel and sdist + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-metadata + steps: + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + persist-credentials: false + fetch-depth: 0 # hatch-vcs needs full history + tags + + - name: Install Hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' + + - name: Build + run: hatch build + + - uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0 + with: + name: zarr-metadata-dist + path: packages/zarr-metadata/dist + + test_artifacts: + name: Test built artifacts + needs: [build] + runs-on: ubuntu-latest + steps: + - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + with: + name: zarr-metadata-dist + path: dist + + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + with: + enable-cache: false + + - name: Set up Python + run: uv python install 3.12 + + - name: Install built wheel and run import smoke test + run: | + wheel=$(ls dist/*.whl) + uv run --with "${wheel}" --python 3.12 --no-project \ + python -c "import zarr_metadata; print('zarr_metadata', zarr_metadata.__version__)" + + upload_pypi: + name: Upload to PyPI + needs: [build, test_artifacts] + if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/zarr_metadata-v') + runs-on: ubuntu-latest + environment: + name: zarr-metadata-releases + url: https://pypi.org/p/zarr-metadata + permissions: + id-token: write # required for OIDC trusted publishing + attestations: write # required for artifact attestations + steps: + - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + with: + name: zarr-metadata-dist + path: dist + + - name: Generate artifact attestation + uses: actions/attest@59d89421af93a897026c735860bf21b6eb4f7b26 # v4.1.0 + with: + subject-path: dist/* + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 + + upload_testpypi: + name: Upload to TestPyPI + needs: [build, test_artifacts] + if: github.event_name == 'workflow_dispatch' + runs-on: ubuntu-latest + environment: + name: zarr-metadata-releases-test + url: https://test.pypi.org/p/zarr-metadata + permissions: + id-token: write + attestations: write + steps: + - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + with: + name: zarr-metadata-dist + path: dist + + - name: Generate artifact attestation + uses: actions/attest@59d89421af93a897026c735860bf21b6eb4f7b26 # v4.1.0 + with: + subject-path: dist/* + + - name: Publish package to TestPyPI + uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 + with: + repository-url: https://test.pypi.org/legacy/ diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md index 3b78caa796..a842e07886 100644 --- a/packages/zarr-metadata/README.md +++ b/packages/zarr-metadata/README.md @@ -47,6 +47,34 @@ Zarr v2 and v3 specs, consolidated metadata, and a subset of the metadata defined in `zarr-extensions`. We are generally open to contributions that add types for Zarr metadata with a published spec. +## Releasing + +The package version is derived from git tags by `hatch-vcs`. Tags must +match the pattern `zarr_metadata-v` (e.g. `zarr_metadata-v0.2.0`) +so they do not collide with the main `zarr-python` release tags. + +To cut a release: + +1. Create and push a tag of the form `zarr_metadata-v` on the + commit you want to publish, e.g.: + ``` + git tag zarr_metadata-v0.2.0 + git push origin zarr_metadata-v0.2.0 + ``` +2. Pushing the tag fires the `zarr-metadata release` workflow, which + builds the wheel/sdist (version resolved from the tag), runs an + install smoke test, and publishes to PyPI via OIDC trusted publishing. + +We intentionally do *not* create a GitHub Release for `zarr-metadata` +versions — GitHub Releases live at the repo level, and a zarr-metadata +release would surface in the zarr-python repo's Releases UI as if it +were a zarr-python release. + +To dry-run a build against TestPyPI, dispatch the workflow manually +(`Actions` → `zarr-metadata release` → `Run workflow`). Manual dispatches +build from the current commit; with no recent tag the version will look +like `0.1.devN`, which is fine for TestPyPI. + ## License [MIT](./LICENSE.txt) diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 7fc1382e3a..70d004fe7b 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -1,10 +1,10 @@ [build-system] -requires = ["hatchling>=1.29.0"] +requires = ["hatchling>=1.29.0", "hatch-vcs"] build-backend = "hatchling.build" [project] name = "zarr-metadata" -version = "0.1.1" +dynamic = ["version"] description = "Spec-defined metadata types for Zarr v2 and v3." readme = "README.md" requires-python = ">=3.11" @@ -32,6 +32,14 @@ dependencies = [ [dependency-groups] test = ["pytest", "pydantic>=2"] +[tool.hatch.version] +source = "vcs" +tag-pattern = '^zarr_metadata-v(?P.+)$' +# `git_describe_command` ensures we get the zarr_metadata tags instead of latest. +# `local_scheme` strips the git commit info so the appending info is just a counter from latest tag. +# test-pypi doesn't accept git commit info in tags, and the count should be enough to distinguish unique runs. +raw-options = { root = "../..", git_describe_command = "git describe --dirty --tags --long --match zarr_metadata-v*", local_scheme = "no-local-version" } + [tool.hatch.build.targets.wheel] packages = ["src/zarr_metadata"] diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 3b48e855f5..cdd8d8e57e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -1,3 +1,5 @@ +from importlib.metadata import version + from zarr_metadata._common import NamedConfig from zarr_metadata.v2.array import ( ArrayDimensionSeparatorV2, @@ -15,9 +17,7 @@ from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 from zarr_metadata.v3.group import GroupMetadataV3 -__version__ = "0.1.1" -"""Hardcoded package version. Must match the `version` field in -`pyproject.toml`; the sync is enforced by `tests/test_version.py`.""" +__version__ = version("zarr-metadata") __all__ = [ diff --git a/packages/zarr-metadata/tests/test_version.py b/packages/zarr-metadata/tests/test_version.py deleted file mode 100644 index 86b177963b..0000000000 --- a/packages/zarr-metadata/tests/test_version.py +++ /dev/null @@ -1,16 +0,0 @@ -"""Verify that `zarr_metadata.__version__` matches the installed -distribution metadata, which in turn comes from `pyproject.toml`. - -This catches the easy mistake of bumping the version in one place and -forgetting the other. -""" - -from __future__ import annotations - -from importlib.metadata import version - -import zarr_metadata - - -def test_version_matches_distribution_metadata() -> None: - assert zarr_metadata.__version__ == version("zarr-metadata") From cdb5846c33fdc217c4ac743a5cdb3e5c54b1868c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sun, 17 May 2026 23:56:50 +0200 Subject: [PATCH 316/468] perf: cache default ArraySpec for regular chunk grids (#3908) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * perf: cache default ArraySpec for regular chunk grids For regular grids, all chunks have the same codec_shape, so we can build the ArraySpec once and reuse it for every chunk — avoiding the per-chunk ChunkGrid.__getitem__ + ArraySpec construction overhead. Adds _get_default_chunk_spec() and uses it in _get_selection and _set_selection. Saves ~5ms per 1000 chunks. Co-Authored-By: Claude Opus 4.6 (1M context) * docs: changelog * refactor: inline creation of default arrayspec --------- Co-authored-by: Claude Opus 4.6 (1M context) --- changes/3908.misc.md | 1 + src/zarr/core/array.py | 30 ++++++++++++++++++++++++++++-- 2 files changed, 29 insertions(+), 2 deletions(-) create mode 100644 changes/3908.misc.md diff --git a/changes/3908.misc.md b/changes/3908.misc.md new file mode 100644 index 0000000000..66717e8444 --- /dev/null +++ b/changes/3908.misc.md @@ -0,0 +1 @@ +Reuse a constant `ArraySpec` during indexing when possible. \ No newline at end of file diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 2e8ca5445d..8e8b9bd181 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -5427,11 +5427,24 @@ async def _get_selection( # reading chunks and decoding them indexed_chunks = list(indexer) + # For regular grids, all chunks share the same ArraySpec, so build it once + # and reuse it to avoid per-chunk ChunkGrid lookups and ArraySpec construction. + regular_grid = chunk_grid.is_regular + if regular_grid: + regular_chunk_spec = ArraySpec( + shape=chunk_grid.chunk_shape, + dtype=metadata.dtype, + fill_value=metadata.fill_value, + config=_config, + prototype=prototype, + ) results = await codec_pipeline.read( [ ( store_path / metadata.encode_chunk_key(chunk_coords), - _get_chunk_spec(metadata, chunk_grid, chunk_coords, _config, prototype), + regular_chunk_spec + if regular_grid + else _get_chunk_spec(metadata, chunk_grid, chunk_coords, _config, prototype), chunk_selection, out_selection, is_complete_chunk, @@ -5770,11 +5783,24 @@ async def _set_selection( _config = replace(_config, order=order) # merging with existing data and encoding chunks + # For regular grids, all chunks share the same ArraySpec, so build it once + # and reuse it to avoid per-chunk ChunkGrid lookups and ArraySpec construction. + regular_grid = chunk_grid.is_regular + if regular_grid: + regular_chunk_spec = ArraySpec( + shape=chunk_grid.chunk_shape, + dtype=metadata.dtype, + fill_value=metadata.fill_value, + config=_config, + prototype=prototype, + ) await codec_pipeline.write( [ ( store_path / metadata.encode_chunk_key(chunk_coords), - _get_chunk_spec(metadata, chunk_grid, chunk_coords, _config, prototype), + regular_chunk_spec + if regular_grid + else _get_chunk_spec(metadata, chunk_grid, chunk_coords, _config, prototype), chunk_selection, out_selection, is_complete_chunk, From 51033fb32f5abe4912db2a22f0fe575d54088981 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 18 May 2026 11:49:11 +0200 Subject: [PATCH 317/468] refactor(sharding): store chunks_per_shard explicitly in _ShardIndex (#3975) * refactor(sharding): store chunks_per_shard explicitly in _ShardIndex _ShardIndex previously inferred the chunk grid shape from offsets_and_lengths.shape[:-1]. For 0-D arrays this collapses the array to rank-1, breaking methods that assume rank >= 2 and forcing a numpy compat cast workaround. Store chunks_per_shard as an explicit NamedTuple field instead. This removes the chunks_per_shard property and its cast, and lets several call sites use the field directly instead of reverse-engineering it. Also fix a latent 0-D bug in is_dense, which iterated offsets_and_lengths assuming rank-2. Closes #3974 Co-Authored-By: Claude Opus 4.7 (1M context) * test: parametrize over dimensionalities * refactor(sharding): store chunks_per_shard explicitly in _ShardIndex _ShardIndex previously inferred the chunk grid shape from offsets_and_lengths.shape[:-1]. For 0-D arrays this collapses the array to rank-1, breaking methods that assume rank >= 2 and forcing a numpy compat cast workaround. Store chunks_per_shard as an explicit NamedTuple field instead. This removes the chunks_per_shard property and its cast, and lets several call sites use the field directly instead of reverse-engineering it. Also fix a latent 0-D bug in is_dense, which iterated offsets_and_lengths assuming rank-2. Tests for get_chunk_slices_vectorized, _ShardReader.__iter__, and is_dense are parametrized over chunk grid ranks (0-D, 1-D, 2-D) so 0-D is exercised as a normal case rather than a special branch. Closes #3974 Co-Authored-By: Claude Opus 4.7 (1M context) * remove is_dense --------- Co-authored-by: Claude Opus 4.7 (1M context) --- changes/3975.misc.md | 1 + src/zarr/codecs/sharding.py | 76 ++++++++++-------------------- tests/test_codecs/test_sharding.py | 45 ++++++++++++------ 3 files changed, 55 insertions(+), 67 deletions(-) create mode 100644 changes/3975.misc.md diff --git a/changes/3975.misc.md b/changes/3975.misc.md new file mode 100644 index 0000000000..b90147988a --- /dev/null +++ b/changes/3975.misc.md @@ -0,0 +1 @@ +Store `chunks_per_shard` explicitly as a field on `_ShardIndex` instead of inferring it from `offsets_and_lengths.shape[:-1]`. The previous derivation collapsed to rank-1 for 0-D arrays, requiring a numpy-compat cast workaround that is now removed. Also removes the unused `_ShardIndex.is_dense` method, which was ported from an earlier prototype and never had any call sites or tests. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index d0b2cec285..8b755cbc37 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -4,7 +4,6 @@ from dataclasses import dataclass, replace from enum import Enum from functools import lru_cache -from operator import itemgetter from typing import TYPE_CHECKING, Any, NamedTuple, cast import numpy as np @@ -123,19 +122,15 @@ async def set_if_not_exists(self, default: Buffer) -> None: class _ShardIndex(NamedTuple): + # the chunk grid shape of a single shard + chunks_per_shard: tuple[int, ...] # dtype uint64, shape (chunks_per_shard_0, chunks_per_shard_1, ..., 2) offsets_and_lengths: npt.NDArray[np.uint64] - @property - def chunks_per_shard(self) -> tuple[int, ...]: - result = tuple(self.offsets_and_lengths.shape[0:-1]) - # The cast is required until https://github.com/numpy/numpy/pull/27211 is merged - return cast("tuple[int, ...]", result) - def _localize_chunk(self, chunk_coords: tuple[int, ...]) -> tuple[int, ...]: return tuple( chunk_i % shard_i - for chunk_i, shard_i in zip(chunk_coords, self.offsets_and_lengths.shape, strict=False) + for chunk_i, shard_i in zip(chunk_coords, self.chunks_per_shard, strict=False) ) def is_all_empty(self) -> bool: @@ -171,25 +166,24 @@ def get_chunk_slices_vectorized( valid : ndarray of shape (n_chunks,) Boolean mask indicating which chunks are non-empty. """ - # Handle 0-dimensional arrays (n_dims == 0) + # Handle 0-dimensional arrays (n_dims == 0): the shard holds a single + # chunk, so every coordinate maps to the same flat entry. if chunk_coords_array.shape[1] == 0: - # offsets_and_lengths has shape (2,) for 0D, reshape to (1, 2) - offsets_and_lengths = self.offsets_and_lengths.reshape(1, 2) - starts = offsets_and_lengths[:, 0] - lengths = offsets_and_lengths[:, 1] - valid = starts != MAX_UINT_64 - ends = starts + lengths - return starts, ends, valid - - # Localize coordinates via modulo (vectorized) - shard_shape = np.array(self.offsets_and_lengths.shape[:-1], dtype=np.uint64) - localized = chunk_coords_array.astype(np.uint64) % shard_shape - - # Build index tuple for advanced indexing - index_tuple = tuple(localized[:, i] for i in range(localized.shape[1])) - - # Fetch all offsets and lengths at once - offsets_and_lengths = self.offsets_and_lengths[index_tuple] + offsets_and_lengths = self.offsets_and_lengths.reshape(-1, 2) + offsets_and_lengths = np.broadcast_to( + offsets_and_lengths, (chunk_coords_array.shape[0], 2) + ) + else: + # Localize coordinates via modulo (vectorized) + shard_shape = np.array(self.chunks_per_shard, dtype=np.uint64) + localized = chunk_coords_array.astype(np.uint64) % shard_shape + + # Build index tuple for advanced indexing + index_tuple = tuple(localized[:, i] for i in range(localized.shape[1])) + + # Fetch all offsets and lengths at once + offsets_and_lengths = self.offsets_and_lengths[index_tuple] + starts = offsets_and_lengths[:, 0] lengths = offsets_and_lengths[:, 1] @@ -211,32 +205,11 @@ def set_chunk_slice(self, chunk_coords: tuple[int, ...], chunk_slice: slice | No chunk_slice.stop - chunk_slice.start, ) - def is_dense(self, chunk_byte_length: int) -> bool: - sorted_offsets_and_lengths = sorted( - [ - (offset, length) - for offset, length in self.offsets_and_lengths - if offset != MAX_UINT_64 - ], - key=itemgetter(0), - ) - - # Are all non-empty offsets unique? - if len( - {offset for offset, _ in sorted_offsets_and_lengths if offset != MAX_UINT_64} - ) != len(sorted_offsets_and_lengths): - return False - - return all( - offset % chunk_byte_length == 0 and length == chunk_byte_length - for offset, length in sorted_offsets_and_lengths - ) - @classmethod def create_empty(cls, chunks_per_shard: tuple[int, ...]) -> _ShardIndex: offsets_and_lengths = np.zeros(chunks_per_shard + (2,), dtype=" int: return int(self.index.offsets_and_lengths.size / 2) def __iter__(self) -> Iterator[tuple[int, ...]]: - return c_order_iter(self.index.offsets_and_lengths.shape[:-1]) + return c_order_iter(self.index.chunks_per_shard) def to_dict_vectorized( self, @@ -298,8 +271,7 @@ def to_dict_vectorized( dict mapping chunk coordinate tuples to Buffer or None """ starts, ends, valid = self.index.get_chunk_slices_vectorized(chunk_coords_array) - chunks_per_shard = tuple(self.index.offsets_and_lengths.shape[:-1]) - chunk_coords_keys = _morton_order_keys(chunks_per_shard) + chunk_coords_keys = _morton_order_keys(self.index.chunks_per_shard) result: dict[tuple[int, ...], Buffer | None] = {} for i, coords in enumerate(chunk_coords_keys): @@ -712,7 +684,7 @@ async def _decode_shard_index( ) # This cannot be None because we have the bytes already index_array = cast(NDBuffer, index_array) - return _ShardIndex(index_array.as_numpy_array()) + return _ShardIndex(chunks_per_shard, index_array.as_numpy_array()) async def _encode_shard_index(self, index: _ShardIndex) -> Buffer: index_bytes = next( diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 2325069dd0..3c1710a51f 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -18,6 +18,7 @@ ) from zarr.codecs.sharding import MAX_UINT_64, _ShardIndex from zarr.core.buffer import NDArrayLike, default_buffer_prototype +from zarr.core.indexing import c_order_iter from zarr.storage import StorePath, ZipStore from ..conftest import ArrayRequest @@ -567,18 +568,32 @@ def test_sharding_zero_dimensional() -> None: assert arr[()] == pytest.approx(43.0) -def test_shard_index_get_chunk_slices_vectorized_zero_dimensional() -> None: - """Directly cover the 0-D path in _ShardIndex.get_chunk_slices_vectorized.""" - # For a 0D array offsets_and_lengths has shape (2,) — reshape to (1, 2) inside. - index = _ShardIndex(np.array([10, 4], dtype=np.uint64)) - chunk_coords = np.empty((1, 0), dtype=np.uint64) - starts, ends, valid = index.get_chunk_slices_vectorized(chunk_coords) - np.testing.assert_array_equal(starts, np.array([10], dtype=np.uint64)) - np.testing.assert_array_equal(ends, np.array([14], dtype=np.uint64)) - np.testing.assert_array_equal(valid, np.array([True])) - - # Empty/unwritten chunk case - index_empty = _ShardIndex(np.array([MAX_UINT_64, MAX_UINT_64], dtype=np.uint64)) - starts_e, _ends_e, valid_e = index_empty.get_chunk_slices_vectorized(chunk_coords) - np.testing.assert_array_equal(starts_e, np.array([MAX_UINT_64], dtype=np.uint64)) - np.testing.assert_array_equal(valid_e, np.array([False])) +def test_shard_index_stores_chunks_per_shard_explicitly() -> None: + """_ShardIndex stores the chunk grid shape as an explicit field.""" + index = _ShardIndex.create_empty((2, 3)) + assert index.chunks_per_shard == (2, 3) + + # 0-D: chunks_per_shard is the empty tuple, distinct from the array's rank + index_0d = _ShardIndex.create_empty(()) + assert index_0d.chunks_per_shard == () + + +@pytest.mark.parametrize("chunks_per_shard", [(), (3,), (2, 3)]) +def test_shard_index_get_chunk_slices_vectorized(chunks_per_shard: tuple[int, ...]) -> None: + """get_chunk_slices_vectorized works uniformly across chunk grid ranks, including 0-D.""" + index = _ShardIndex.create_empty(chunks_per_shard) + # Write the first chunk; leave the rest (if any) empty. + all_coords = list(c_order_iter(chunks_per_shard)) + index.set_chunk_slice(all_coords[0], slice(10, 14)) + + coords_array = np.array(all_coords, dtype=np.uint64).reshape( + len(all_coords), len(chunks_per_shard) + ) + starts, ends, valid = index.get_chunk_slices_vectorized(coords_array) + + expected_valid = np.zeros(len(all_coords), dtype=bool) + expected_valid[0] = True + np.testing.assert_array_equal(valid, expected_valid) + assert starts[0] == 10 + assert ends[0] == 14 + np.testing.assert_array_equal(starts[~expected_valid], MAX_UINT_64) From 8bfcc66ebe173d10e810a057a2deb57f3944999f Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 18 May 2026 17:06:59 +0200 Subject: [PATCH 318/468] docs: update link to developer chat (#3980) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3911ba17b8..45410eeb7b 100644 --- a/README.md +++ b/README.md @@ -72,7 +72,7 @@ Developer Chat - + From 7afdc8d974e7ff3b80c44d17bf105d90987e276a Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 19 May 2026 00:06:42 +0200 Subject: [PATCH 319/468] feat(zarr-metadata): partial metadata types (#3982) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * docs(plan): add Partial* TypedDicts implementation plan Plan for adding ArrayMetadataV3Partial, GroupMetadataV3Partial, ArrayMetadataV2Partial, and GroupMetadataV2Partial to zarr-metadata as siblings of the existing full TypedDicts, plus an equivalence test that prevents drift. * feat(zarr-metadata): add ArrayMetadataV3Partial Sibling TypedDict to ArrayMetadataV3 with total=False, intended for typing dicts that intentionally hold a subset of a complete v3 array metadata document (test fixtures, fragment templates). Drift between the two is prevented by a new equivalence test. * feat(zarr-metadata): add GroupMetadataV3Partial Sibling TypedDict to GroupMetadataV3 with total=False. * feat(zarr-metadata): add ArrayMetadataV2Partial Sibling TypedDict to ArrayMetadataV2 with total=False. * feat(zarr-metadata): add GroupMetadataV2Partial Sibling TypedDict to GroupMetadataV2 with total=False. Added for symmetry with the other v2/v3 *Partial types; the only practical difference from GroupMetadataV2 is that zarr_format becomes optional. * docs(zarr-metadata): align Partial* docstring shapes across all four types After landing all four *Partial classes, the docstrings had drifted into two shapes: ArrayMetadataV2Partial / GroupMetadataV2Partial used the self-contained form (summary → use-case → NotRequired rationale → drift), while GroupMetadataV3Partial deferred its use-case paragraph to ArrayMetadataV3Partial, and ArrayMetadataV3Partial put its drift sentence before the NotRequired rationale. Standardize on the self-contained form with consistent paragraph order so each Partial reads on its own and any future prose edit only needs to touch the one class it concerns. * chore: remove superpowers docs --- .../src/zarr_metadata/__init__.py | 11 +++-- .../src/zarr_metadata/v2/array.py | 42 +++++++++++++++++++ .../src/zarr_metadata/v2/group.py | 31 ++++++++++++++ .../src/zarr_metadata/v3/array.py | 37 ++++++++++++++++ .../src/zarr_metadata/v3/group.py | 29 +++++++++++++ .../tests/test_partial_equivalence.py | 42 +++++++++++++++++++ 6 files changed, 189 insertions(+), 3 deletions(-) create mode 100644 packages/zarr-metadata/tests/test_partial_equivalence.py diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index cdd8d8e57e..dc9bc25c63 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -4,6 +4,7 @@ from zarr_metadata.v2.array import ( ArrayDimensionSeparatorV2, ArrayMetadataV2, + ArrayMetadataV2Partial, ArrayOrderV2, DataTypeMetadataV2, ZArrayMetadata, @@ -11,11 +12,11 @@ from zarr_metadata.v2.attributes import ZAttrsMetadata from zarr_metadata.v2.codec import CodecMetadataV2 from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 -from zarr_metadata.v2.group import GroupMetadataV2, ZGroupMetadata +from zarr_metadata.v2.group import GroupMetadataV2, GroupMetadataV2Partial, ZGroupMetadata from zarr_metadata.v3._common import MetadataFieldV3 -from zarr_metadata.v3.array import ArrayMetadataV3, ExtensionFieldV3 +from zarr_metadata.v3.array import ArrayMetadataV3, ArrayMetadataV3Partial, ExtensionFieldV3 from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 -from zarr_metadata.v3.group import GroupMetadataV3 +from zarr_metadata.v3.group import GroupMetadataV3, GroupMetadataV3Partial __version__ = version("zarr-metadata") @@ -23,7 +24,9 @@ __all__ = [ "ArrayDimensionSeparatorV2", "ArrayMetadataV2", + "ArrayMetadataV2Partial", "ArrayMetadataV3", + "ArrayMetadataV3Partial", "ArrayOrderV2", "CodecMetadataV2", "ConsolidatedMetadataV2", @@ -31,7 +34,9 @@ "DataTypeMetadataV2", "ExtensionFieldV3", "GroupMetadataV2", + "GroupMetadataV2Partial", "GroupMetadataV3", + "GroupMetadataV3Partial", "MetadataFieldV3", "NamedConfig", "ZArrayMetadata", diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 04f76c264f..6673716f6c 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -98,11 +98,53 @@ class ArrayMetadataV2(TypedDict): """ +class ArrayMetadataV2Partial(TypedDict, total=False): + """ + Partial form of `ArrayMetadataV2`: every field is `NotRequired`. + + Field annotations mirror `ArrayMetadataV2` exactly. The only difference is + `total=False`, which makes every key optional at the type level. + + Use this when typing dicts that intentionally hold a subset of a complete + v2 array metadata document — e.g. test fixtures that override only a few + fields of a base template, or callers that build a fragment to be merged + into a complete document elsewhere. + + The `NotRequired[...]` wrappers on `dimension_separator` and `attributes` + are intentional: keeping them preserves byte-identical `__annotations__` + with `ArrayMetadataV2` so the `==` check in + `tests/test_partial_equivalence.py` passes without special-casing those + fields (PEP 655 explicitly permits `NotRequired` inside `total=False`). + + Note: v2 array metadata has no `extra_items` setting (the v2 spec has no + extension-field concept), so this partial inherits the same closed shape. + + Drift between this type and `ArrayMetadataV2` is prevented by + `tests/test_partial_equivalence.py`. + """ + + zarr_format: Literal[2] + shape: tuple[int, ...] + chunks: tuple[int, ...] + dtype: DataTypeMetadataV2 + compressor: CodecMetadataV2 | None + fill_value: object + order: ArrayOrderV2 + filters: tuple[CodecMetadataV2, ...] | None + dimension_separator: NotRequired[ArrayDimensionSeparatorV2] + attributes: NotRequired[Mapping[str, object]] + """User attributes from the sibling `.zattrs` file (not part of `.zarray`). + + See the class docstring for the rationale behind the merged representation. + """ + + __all__ = [ "ARRAY_DIMENSION_SEPARATOR_V2", "ARRAY_ORDER_V2", "ArrayDimensionSeparatorV2", "ArrayMetadataV2", + "ArrayMetadataV2Partial", "ArrayOrderV2", "DataTypeMetadataV2", "ZArrayMetadata", diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/group.py b/packages/zarr-metadata/src/zarr_metadata/v2/group.py index 5ef9b963d2..fd14960a0b 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/group.py @@ -42,7 +42,38 @@ class GroupMetadataV2(TypedDict): attributes: NotRequired[Mapping[str, object]] +class GroupMetadataV2Partial(TypedDict, total=False): + """ + Partial form of `GroupMetadataV2`: every field is `NotRequired`. + + Field annotations mirror `GroupMetadataV2` exactly. The only difference is + `total=False`, which makes every key optional at the type level. + + Use this when typing dicts that intentionally hold a subset of a complete + v2 group metadata document — e.g. test fixtures that override only a few + fields of a base template, or callers that build a fragment to be merged + into a complete document elsewhere. Provided for symmetry with the other + `*Partial` types; the practical effect is that `zarr_format` becomes optional. + + The `NotRequired[...]` wrapper on `attributes` is intentional: keeping it + preserves byte-identical `__annotations__` with `GroupMetadataV2` so the + `==` check in `tests/test_partial_equivalence.py` passes without + special-casing that field (PEP 655 explicitly permits `NotRequired` inside + `total=False`). + + Note: v2 group metadata has no `extra_items` setting (the v2 spec has no + extension-field concept), so this partial inherits the same closed shape. + + Drift between this type and `GroupMetadataV2` is prevented by + `tests/test_partial_equivalence.py`. + """ + + zarr_format: Literal[2] + attributes: NotRequired[Mapping[str, object]] + + __all__ = [ "GroupMetadataV2", + "GroupMetadataV2Partial", "ZGroupMetadata", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index c705430fc2..30bc991f47 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -62,7 +62,44 @@ class ArrayMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[ dimension_names: NotRequired[tuple[str | None, ...]] +class ArrayMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV3): # type: ignore[call-arg] + """ + Partial form of `ArrayMetadataV3`: every field is `NotRequired`. + + Field annotations and `extra_items=` mirror `ArrayMetadataV3` exactly. + The only difference is `total=False`, which makes every key optional + at the type level. + + Use this when typing dicts that intentionally hold a subset of a complete + v3 array metadata document — e.g. test fixtures that override only a few + fields of a base template, or callers that build a fragment to be merged + into a complete document elsewhere. + + The `NotRequired[...]` wrappers on `attributes`, `storage_transformers`, + and `dimension_names` are intentional: keeping them preserves byte-identical + `__annotations__` with `ArrayMetadataV3` so the `==` check in + `tests/test_partial_equivalence.py` passes without special-casing those + fields (PEP 655 explicitly permits `NotRequired` inside `total=False`). + + Drift between this type and `ArrayMetadataV3` is prevented by + `tests/test_partial_equivalence.py`. + """ + + zarr_format: Literal[3] + node_type: Literal["array"] + data_type: MetadataFieldV3 + shape: tuple[int, ...] + chunk_grid: MetadataFieldV3 + chunk_key_encoding: MetadataFieldV3 + fill_value: object + codecs: tuple[MetadataFieldV3, ...] + attributes: NotRequired[Mapping[str, object]] + storage_transformers: NotRequired[tuple[MetadataFieldV3, ...]] + dimension_names: NotRequired[tuple[str | None, ...]] + + __all__ = [ "ArrayMetadataV3", + "ArrayMetadataV3Partial", "ExtensionFieldV3", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py index e7396f2615..e44bf124e3 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -25,6 +25,35 @@ class GroupMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[ attributes: NotRequired[Mapping[str, object]] +class GroupMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV3): # type: ignore[call-arg] + """ + Partial form of `GroupMetadataV3`: every field is `NotRequired`. + + Field annotations and `extra_items=` mirror `GroupMetadataV3` exactly. + The only difference is `total=False`, which makes every key optional + at the type level. + + Use this when typing dicts that intentionally hold a subset of a complete + v3 group metadata document — e.g. test fixtures that override only a few + fields of a base template, or callers that build a fragment to be merged + into a complete document elsewhere. + + The `NotRequired[...]` wrapper on `attributes` is intentional: keeping it + preserves byte-identical `__annotations__` with `GroupMetadataV3` so the + `==` check in `tests/test_partial_equivalence.py` passes without + special-casing that field (PEP 655 explicitly permits `NotRequired` inside + `total=False`). + + Drift between this type and `GroupMetadataV3` is prevented by + `tests/test_partial_equivalence.py`. + """ + + zarr_format: Literal[3] + node_type: Literal["group"] + attributes: NotRequired[Mapping[str, object]] + + __all__ = [ "GroupMetadataV3", + "GroupMetadataV3Partial", ] diff --git a/packages/zarr-metadata/tests/test_partial_equivalence.py b/packages/zarr-metadata/tests/test_partial_equivalence.py new file mode 100644 index 0000000000..995a6a21e1 --- /dev/null +++ b/packages/zarr-metadata/tests/test_partial_equivalence.py @@ -0,0 +1,42 @@ +"""Drift-prevention tests for Partial* TypedDict variants. + +Each *Partial TypedDict in the package must declare the same fields +(with the same annotations) and the same extra_items setting as its +full counterpart. The only intentional difference is total=False +(i.e. every field becomes NotRequired). This test enforces that +invariant so adding a field to the full type without mirroring it +on the partial fails CI. +""" + +from __future__ import annotations + +from typing import Any + +import pytest + +from zarr_metadata.v2.array import ArrayMetadataV2, ArrayMetadataV2Partial +from zarr_metadata.v2.group import GroupMetadataV2, GroupMetadataV2Partial +from zarr_metadata.v3.array import ArrayMetadataV3, ArrayMetadataV3Partial +from zarr_metadata.v3.group import GroupMetadataV3, GroupMetadataV3Partial + +# (full, partial) pairs to check. Add new pairs here as more are introduced. +PAIRS: list[tuple[type, type]] = [ + (ArrayMetadataV3, ArrayMetadataV3Partial), + (GroupMetadataV3, GroupMetadataV3Partial), + (ArrayMetadataV2, ArrayMetadataV2Partial), + (GroupMetadataV2, GroupMetadataV2Partial), +] + + +@pytest.mark.parametrize(("full", "partial"), PAIRS, ids=lambda p: p.__name__) +def test_partial_matches_full(full: Any, partial: Any) -> None: + """Partial TypedDict has identical fields and extra_items, only total differs.""" + assert full.__annotations__ == partial.__annotations__, ( + f"{partial.__name__} fields drifted from {full.__name__}: " + f"full={set(full.__annotations__)}, partial={set(partial.__annotations__)}" + ) + assert getattr(full, "__extra_items__", None) == getattr(partial, "__extra_items__", None), ( + f"{partial.__name__} extra_items differs from {full.__name__}" + ) + assert full.__total__ is True, f"{full.__name__} must be declared with total=True (default)" + assert partial.__total__ is False, f"{partial.__name__} must be declared with total=False" From 7531de5a62ff1e8f008b17d8ba842813e7ae3c57 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 19 May 2026 16:21:12 +0200 Subject: [PATCH 320/468] chore(zarr-metadata): set up a changelog (#3981) * chore: set up changelog * chore: update towncrier CI check to handle subpackages, and improve its behavior --- .github/workflows/check_changelogs.yml | 5 +- ci/check_changelog_entries.py | 47 ++++++++++++----- packages/zarr-metadata/CHANGELOG.md | 66 ++++++++++++++++++++++++ packages/zarr-metadata/changes/README.md | 25 +++++++++ packages/zarr-metadata/pyproject.toml | 12 +++++ 5 files changed, 140 insertions(+), 15 deletions(-) create mode 100644 packages/zarr-metadata/CHANGELOG.md create mode 100644 packages/zarr-metadata/changes/README.md diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 77c03dad0f..d897c82775 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -24,5 +24,8 @@ jobs: - name: Install uv uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - - name: Check changelog entries + - name: Check zarr-python changelog entries run: uv run --no-sync python ci/check_changelog_entries.py + + - name: Check zarr-metadata changelog entries + run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-metadata/changes diff --git a/ci/check_changelog_entries.py b/ci/check_changelog_entries.py index da2700e32a..42d7cc1708 100644 --- a/ci/check_changelog_entries.py +++ b/ci/check_changelog_entries.py @@ -1,12 +1,18 @@ """ Check changelog entries have the correct filename structure. + +Usage: + python check_changelog_entries.py [DIRECTORY] + +DIRECTORY defaults to the repo-root `changes/`. """ import sys from pathlib import Path VALID_CHANGELOG_TYPES = ["feature", "bugfix", "doc", "removal", "misc"] -CHANGELOG_DIRECTORY = (Path(__file__).parent.parent / "changes").resolve() +REPO_ROOT = Path(__file__).parent.parent.resolve() +DEFAULT_DIRECTORY = REPO_ROOT / "changes" def is_int(s: str) -> bool: @@ -18,34 +24,47 @@ def is_int(s: str) -> bool: return True -if __name__ == "__main__": - print(f"Looking for changelog entries in {CHANGELOG_DIRECTORY}") - entries = CHANGELOG_DIRECTORY.glob("*") +def check(directory: Path) -> int: + print(f"Looking for changelog entries in {directory}") + entries = list(directory.glob("*")) entries = [e for e in entries if e.name not in [".gitignore", "README.md"]] print(f"Found {len(entries)} entries") print() bad_suffix = [e for e in entries if e.suffix != ".md"] bad_issue_no = [e for e in entries if not is_int(e.name.split(".")[0])] - bad_type = [e for e in entries if e.name.split(".")[1] not in VALID_CHANGELOG_TYPES] + # Only flag bad_type for files that have already passed the prior two + # checks; otherwise `e.name.split(".")[1]` may raise IndexError on a + # malformed name like `notes.md`. + bad_type = [ + e + for e in entries + if e.suffix == ".md" + and is_int(e.name.split(".")[0]) + and e.name.split(".")[1] not in VALID_CHANGELOG_TYPES + ] - if len(bad_suffix) or len(bad_issue_no) or len(bad_type): - if len(bad_suffix): + if bad_suffix or bad_issue_no or bad_type: + if bad_suffix: print("Changelog entries without .md suffix") print("-------------------------------------") - print("\n".join([p.name for p in bad_suffix])) + print("\n".join(p.name for p in bad_suffix)) print() - if len(bad_issue_no): + if bad_issue_no: print("Changelog entries without integer issue number") print("----------------------------------------------") - print("\n".join([p.name for p in bad_issue_no])) + print("\n".join(p.name for p in bad_issue_no)) print() - if len(bad_type): + if bad_type: print("Changelog entries without valid type") print("------------------------------------") - print("\n".join([p.name for p in bad_type])) + print("\n".join(p.name for p in bad_type)) print(f"Valid types are: {VALID_CHANGELOG_TYPES}") print() - sys.exit(1) + return 1 + return 0 - sys.exit(0) + +if __name__ == "__main__": + directory = Path(sys.argv[1]).resolve() if len(sys.argv) > 1 else DEFAULT_DIRECTORY + sys.exit(check(directory)) diff --git a/packages/zarr-metadata/CHANGELOG.md b/packages/zarr-metadata/CHANGELOG.md new file mode 100644 index 0000000000..9190bfcc45 --- /dev/null +++ b/packages/zarr-metadata/CHANGELOG.md @@ -0,0 +1,66 @@ +# Release notes + + + +## 0.2.0 (2026-05-11) + +### Bugfixes + +- `GzipCodecConfiguration.level` is now required, and `GzipCodecMetadata` + no longer accepts the bare-string `"gzip"` form. The codec's compressed + output depends on `level`, so metadata that omits it cannot reproducibly + identify the chunk bytes produced by a writer. **Breaking** for consumers + that previously typed gzip codec metadata as the bare string or + constructed a `GzipCodecConfiguration` without `level`. + ([#3978](https://github.com/zarr-developers/zarr-python/issues/3978)) +- `BytesCodecObject.configuration` is now `NotRequired`. The configuration + has no required keys (`endian` is conditionally required at runtime + based on data type), so the object form may omit it entirely — matching + the bare-string short-hand. **Soft-breaking** for consumers that + previously relied on `configuration` always being present. + ([#3978](https://github.com/zarr-developers/zarr-python/issues/3978)) +- Better modelling of Zarr v2 stored metadata. Zarr v2 splits a node's + metadata across two JSON documents (`.zarray`/`.zgroup` and `.zattrs`), + but `GroupMetadataV2` had no `attributes` field while `ArrayMetadataV2` + did — an inconsistency. `GroupMetadataV2` now also has an optional + `attributes` field, and `ArrayMetadataV2.attributes` is now + `NotRequired` for symmetry. **Soft-breaking** for consumers that + relied on `ArrayMetadataV2.attributes` always being present. + ([#3962](https://github.com/zarr-developers/zarr-python/issues/3962)) + +### Features + +- Added three new top-level types modelling the **strict on-disk** shape + of Zarr v2 metadata documents: `ZArrayMetadata` (the `.zarray` file), + `ZGroupMetadata` (the `.zgroup` file), and `ZAttrsMetadata` (the + `.zattrs` file). Use these when you want a type that faithfully matches + what's stored on disk; use the merged `ArrayMetadataV2`/`GroupMetadataV2` + when you want the in-memory representation a Python program typically + works with. + ([#3962](https://github.com/zarr-developers/zarr-python/issues/3962)) +- Added typed constants exposing the spec-permitted values of constrained + Literal fields, importable at the per-codec module level. For example, + `from zarr_metadata.v3.codec.bytes import ENDIAN` provides + `("little", "big")` as a tuple, enabling runtime iteration or validator + generation without re-stating the Literal values by hand. + ([#3978](https://github.com/zarr-developers/zarr-python/issues/3978)) + +## 0.1.1 (2026-05-06) + +### Misc + +- First usable release on PyPI. Version 0.1.0 was uploaded then deleted to + reserve the project name; this version is the first one PyPI will install. + No source changes from 0.1.0. + ([#3949](https://github.com/zarr-developers/zarr-python/issues/3949)) + +## 0.1.0 (2026-05-01) + +### Features + +- Initial release. Provides `TypedDict` definitions and `Literal` aliases + for the JSON shapes specified by Zarr v2 and v3 metadata, plus a subset + of `zarr-extensions` types and the un-specified-but-widely-used + consolidated metadata documents. Pair with a runtime validator like + `pydantic` to check JSON loaded from disk. + ([#3919](https://github.com/zarr-developers/zarr-python/issues/3919)) diff --git a/packages/zarr-metadata/changes/README.md b/packages/zarr-metadata/changes/README.md new file mode 100644 index 0000000000..bf0fc85425 --- /dev/null +++ b/packages/zarr-metadata/changes/README.md @@ -0,0 +1,25 @@ +Writing a changelog entry for `zarr-metadata` +--------------------------------------------- + +Fragments in **this** directory are released notes for the `zarr-metadata` +package only — kept separate from the parent zarr-python `changes/` +directory so a PR touching only `packages/zarr-metadata/` produces a +release note for this package only. + +Please put a new file in this directory named `xxxx..md`, where + +- `xxxx` is the pull request number associated with this entry +- `` is one of: + - feature + - bugfix + - doc + - removal + - misc + +Inside the file, please write a short description of what you have +changed, and how it impacts users of `zarr-metadata`. + +A `zarr-metadata` release runs `towncrier build` in `packages/zarr-metadata/`, +which consumes the fragments here and updates `CHANGELOG.md`. Fragments +that describe parent zarr-python changes (not the metadata package) +belong in the top-level `changes/` directory, not here. diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 70d004fe7b..020838261d 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -74,3 +74,15 @@ include = ["src"] enableExperimentalFeatures = true typeCheckingMode = "strict" pythonVersion = "3.11" + +[tool.towncrier] +# Fragments for this package live alongside the package source, separate +# from the parent zarr-python `changes/` directory, so a PR touching only +# `packages/zarr-metadata/` produces a release note for this package only. +directory = "changes" +filename = "CHANGELOG.md" +package = "zarr_metadata" +underlines = ["", "", ""] +title_format = "## {version} ({project_date})" +issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues/{issue})" +start_string = "\n" From 79d5b8fde084b66bfe3c3c2a70fe8a013eb9c55b Mon Sep 17 00:00:00 2001 From: Alden Keefe Sampson Date: Tue, 19 May 2026 11:31:30 -0400 Subject: [PATCH 321/468] Optimize partial shard reads (#3004) * Add performance test of partial shard reads * WIP Consolidate reads of multiple chunks in the same shard Add test and make max gap and max coalesce size config options Code clarity and comments Test that chunk request coalescing reduces calls to store Profile a few values for coalesce_max_gap Update [doc]tests to include new sharding.read.* values document sharded read config options in user-guide/config.rst tweak logic: start new coalesced group if coalescing would exceed `coalesce_max_bytes` previous logic only started a new group if existing group was size already exceeded coalesce_max_bytes. set `mypy_path = "src"` to help pre-commit mypy find imported classes Reorder methods in sharding.py, add docstring + commenting wording docs fix docstring clarification trigger precommit on all python files changed in this pull request trying to get the ruff format that's happening locally during pre-commit to match the pre-commit run that is failing on CI. revert trigger for pre-commit ruff format * Add changes/3004.feature.rst * Consistently return None on failure and test partial shard read failure modes Use range of integers as out_selection not slice in CoordinateIndexer To fix issue when using vindex with repeated indexes in indexer test: improve formatting and add debugging breakpoint in array property tests test: disable hypothesis deadline for test_array_roundtrip to prevent timeout fix: initialize decode buffers with shard_spec.fill_value instead of 0 to fix partial shard holes style: reformat code for improved readability and consistency in sharding.py fix: revert incorrect RangeByteRequest length fix in sharding byte retrieval * Fix and test for case where some chunks in shard are all fill * Self review * Removing profiling code masquerading as a skipped test * revert change to indexing.py, not needed * Add test for duplicate integer indexing into a coalesced group * Undo change to fill value when initializing shard arrays * Undo change to set mypy_path = "src" * Commenting and revert uncessary changes to files for smaller diff * remove now redundant cast * Document runtime config keys * Improve changelog entry and .rst -> .md * .coords -> .chunk_coords in _ChunkCoordsByteSlice dataclass * Update test env in docs/contributing.md * Move `config.get` calls up into `_decode_partial_single` * Ensure no change in behavior when ByteGetter.get returns None + comment * Add test_sharing_unit.py, focusing on coallesce behavior, but with basic tests for other components * Fix typing errors in test_sharing_unit.py * Only use concurrent_map over chunks within a shard if > 1 groups after coalescing * no-op test change to retry CI after unavailable runner failure * Another no-op test change to retry CI after unavailable runner failure * use get_partial_values(), remove explicit coallescing and concurrent_map * cleanup * self review * Unit tests for new get_partial_values implementations * tests: work around mypy not seeing equivalent protocols as equivalent * Re-work to use Store.get_ranges. Simplify significantly. * Add missing assert in test_sharding.py * Remove unit tests that tested now-removed _ShardIndex.is_dense --------- Co-authored-by: Davis Bennett --- changes/3004.feature.md | 4 + src/zarr/codecs/sharding.py | 89 ++++- tests/test_codecs/test_sharding.py | 264 +++++++++++++ tests/test_codecs/test_sharding_unit.py | 488 ++++++++++++++++++++++++ 4 files changed, 828 insertions(+), 17 deletions(-) create mode 100644 changes/3004.feature.md create mode 100644 tests/test_codecs/test_sharding_unit.py diff --git a/changes/3004.feature.md b/changes/3004.feature.md new file mode 100644 index 0000000000..9d3816a50c --- /dev/null +++ b/changes/3004.feature.md @@ -0,0 +1,4 @@ +Optimizes reading multiple chunks from a shard. Serial calls to `Store.get()` +in the sharding codec have been replaced with a single call to +`Store.get_ranges()`, which coalesces nearby byte ranges and fetches them +concurrently. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 8b755cbc37..41f9b7e9c6 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -59,6 +59,7 @@ parse_codecs, ) from zarr.registry import get_ndbuffer_class, get_pipeline_class +from zarr.storage._common import StorePath from zarr.storage._utils import _normalize_byte_range_index if TYPE_CHECKING: @@ -467,7 +468,7 @@ async def _decode_partial_single( all_chunk_coords = {chunk_coords for chunk_coords, *_ in indexed_chunks} # reading bytes of all requested chunks - shard_dict: ShardMapping = {} + shard_dict_maybe: ShardMapping | None if self._is_total_shard(all_chunk_coords, chunks_per_shard): # read entire shard shard_dict_maybe = await self._load_full_shard_maybe( @@ -475,24 +476,18 @@ async def _decode_partial_single( prototype=chunk_spec.prototype, chunks_per_shard=chunks_per_shard, ) - if shard_dict_maybe is None: - return None - shard_dict = shard_dict_maybe else: # read some chunks within the shard - shard_index = await self._load_shard_index_maybe(byte_getter, chunks_per_shard) - if shard_index is None: - return None - shard_dict = {} - for chunk_coords in all_chunk_coords: - chunk_byte_slice = shard_index.get_chunk_slice(chunk_coords) - if chunk_byte_slice: - chunk_bytes = await byte_getter.get( - prototype=chunk_spec.prototype, - byte_range=RangeByteRequest(chunk_byte_slice[0], chunk_byte_slice[1]), - ) - if chunk_bytes: - shard_dict[chunk_coords] = chunk_bytes + shard_dict_maybe = await self._load_partial_shard_maybe( + byte_getter, + chunk_spec.prototype, + chunks_per_shard, + all_chunk_coords, + ) + + if shard_dict_maybe is None: + return None + shard_dict = shard_dict_maybe # decoding chunks and writing them into the output buffer await self.codec_pipeline.read( @@ -779,6 +774,66 @@ async def _load_full_shard_maybe( else None ) + async def _load_partial_shard_maybe( + self, + byte_getter: ByteGetter, + prototype: BufferPrototype, + chunks_per_shard: tuple[int, ...], + all_chunk_coords: set[tuple[int, ...]], + ) -> ShardMapping | None: + """ + Read chunks from `byte_getter` for the case where the read is less than a full shard. + Returns a mapping of chunk coordinates to bytes or None. + """ + shard_index = await self._load_shard_index_maybe(byte_getter, chunks_per_shard) + if shard_index is None: + return None + + # Pair up chunks and their byte ranges as list[tuple[chunk_coord, byte_range]] + chunk_coord_byte_ranges: list[tuple[tuple[int, ...], RangeByteRequest]] = [] + for chunk_coord in all_chunk_coords: + chunk_byte_slice = shard_index.get_chunk_slice(chunk_coord) + if chunk_byte_slice is not None: + chunk_coord_byte_ranges.append( + (chunk_coord, RangeByteRequest(chunk_byte_slice[0], chunk_byte_slice[1])) + ) + + if not chunk_coord_byte_ranges: + return {} + + shard_dict: ShardMutableMapping = {} + if isinstance(byte_getter, StorePath): + # External store: use Store.get_ranges for coalescing + concurrency. + byte_ranges = [byte_range for _, byte_range in chunk_coord_byte_ranges] + try: + async for group in byte_getter.store.get_ranges( + byte_getter.path, byte_ranges, prototype=prototype + ): + for idx, buf in group: + if buf is not None: + chunk_coord, _ = chunk_coord_byte_ranges[idx] + shard_dict[chunk_coord] = buf + except BaseExceptionGroup as eg: + # `Store.get_ranges` raises FileNotFoundError (wrapped in a + # BaseExceptionGroup) if any underlying fetch indicates the key is + # absent. The shard index loaded above, so this typically means a + # race where the shard was deleted mid-read; treat it as "shard + # gone" to match the index-missing branch (return None). Anything + # else in the group (e.g. IO errors) is re-raised. + _, rest = eg.split(FileNotFoundError) + if rest is not None: + raise rest from None + return None + else: + # Any other ByteGetter. In practice only `_ShardingByteGetter` for + # nested sharding, which slices an in-memory buffer (no I/O to coalesce). + for chunk_coord, byte_range in chunk_coord_byte_ranges: + buf = await byte_getter.get(prototype, byte_range) + if buf is not None: + shard_dict[chunk_coord] = buf + + return shard_dict + def compute_encoded_size(self, input_byte_length: int, shard_spec: ArraySpec) -> int: chunks_per_shard = self._get_chunks_per_shard(shard_spec) return input_byte_length + self._shard_index_size(chunks_per_shard) diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 3c1710a51f..b31471337c 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -1,5 +1,6 @@ import pickle from typing import Any +from unittest.mock import AsyncMock import numpy as np import numpy.typing as npt @@ -199,6 +200,269 @@ def test_sharding_partial_read( assert np.all(read_data == 1) +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) +def test_sharding_multiple_chunks_partial_shard_read( + store: Store, + index_location: ShardingCodecIndexLocation, +) -> None: + array_shape = (16, 64) + shard_shape = (8, 32) + chunk_shape = (2, 4) + data = np.arange(np.prod(array_shape), dtype="float32").reshape(array_shape) + + store_mock = AsyncMock(wraps=store, spec=store.__class__) + a = zarr.create_array( + StorePath(store_mock), + shape=data.shape, + chunks=chunk_shape, + shards={"shape": shard_shape, "index_location": index_location}, + compressors=BloscCodec(cname="lz4"), + dtype=data.dtype, + fill_value=1, + ) + a[:] = data + + store_mock.reset_mock() # ignore store calls during array creation + + # Reads 3 (2 full, 1 partial) chunks each from 2 shards (a subset of both shards) + # for a total of 6 chunks accessed + assert np.allclose(a[0, 22:42], np.arange(22, 42, dtype="float32")) + + # 2 shard index reads via store.get() + 2 get_ranges calls (one per shard) + assert store_mock.get.call_count == 2 + assert store_mock.get_ranges.call_count == 2 + + store_mock.reset_mock() + + # Reads 4 chunks from both shards along dimension 0 for a total of 8 chunks accessed + assert np.allclose(a[:, 0], np.arange(0, data.size, array_shape[1], dtype="float32")) + + # 2 shard index reads via store.get() + 2 get_ranges calls (one per shard) + assert store_mock.get.call_count == 2 + assert store_mock.get_ranges.call_count == 2 + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) +def test_sharding_duplicate_read_indexes( + store: Store, + index_location: ShardingCodecIndexLocation, +) -> None: + """ + Check that duplicate index reads are handled correctly when + using get_ranges for chunk data. + """ + array_shape = (15,) + shard_shape = (8,) + chunk_shape = (2,) + data = np.arange(np.prod(array_shape), dtype="float32").reshape(array_shape) + + store_mock = AsyncMock(wraps=store, spec=store.__class__) + a = zarr.create_array( + StorePath(store_mock), + shape=data.shape, + chunks=chunk_shape, + shards={"shape": shard_shape, "index_location": index_location}, + compressors=BloscCodec(cname="lz4"), + dtype=data.dtype, + fill_value=-1, + ) + a[:] = data + + store_mock.reset_mock() # ignore store calls during array creation + + # Read the same index multiple times from two chunks + indexer = [8, 8, 12, 12] + assert np.array_equal(a[indexer], data[indexer]) + + # 1 shard index read via store.get() + 1 get_ranges call + assert store_mock.get.call_count == 1 + assert store_mock.get_ranges.call_count == 1 + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) +def test_sharding_read_empty_chunks_within_non_empty_shard_write_empty_false( + store: Store, index_location: ShardingCodecIndexLocation +) -> None: + """ + Case where + - some, but not all, chunks in the last shard are empty + - the last shard is not complete (array length is not a multiple of shard shape), + this takes us down the partial shard read path + - write_empty_chunks=False so the shard index will have fewer entries than chunks in the shard + """ + # array with mixed empty and non-empty chunks in second shard + data = np.array([ + # shard 0. full 8 elements, all chunks have some non-fill data + 0, 1, 2, 3, 4, 5, 6, 7, + # shard 1. 6 elements (< shard shape) + 2, 0, # chunk 0, written + -9, -9, # chunk 1, all fill, not written + 4, 5 # chunk 2, written + ], dtype="int32") # fmt: off + + spath = StorePath(store) + a = zarr.create_array( + spath, + shape=(14,), + chunks=(2,), + shards={"shape": (8,), "index_location": index_location}, + dtype="int32", + fill_value=-9, + filters=None, + compressors=None, + config={"write_empty_chunks": False}, + ) + a[:] = data + + assert np.array_equal(a[:], data) + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) +def test_sharding_read_empty_chunks_within_empty_shard_write_empty_false( + store: Store, index_location: ShardingCodecIndexLocation +) -> None: + """ + Case where + - all chunks in last shard are empty + - the last shard is not complete (array length is not a multiple of shard shape), + this takes us down the partial shard read path + - write_empty_chunks=False so the shard index will have no entries + """ + fill_value = -99 + shard_size = 8 + data = np.arange(14, dtype="int32") + data[shard_size:] = fill_value # 2nd shard is all fill value + + spath = StorePath(store) + a = zarr.create_array( + spath, + shape=(14,), + chunks=(2,), + shards={"shape": (shard_size,), "index_location": index_location}, + dtype="int32", + fill_value=fill_value, + filters=None, + compressors=None, + config={"write_empty_chunks": False}, + ) + a[:] = data + + assert np.array_equal(a[:], data) + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) +def test_sharding_partial_shard_read__index_load_fails( + store: Store, index_location: ShardingCodecIndexLocation +) -> None: + """Test fill value is returned when the call to the store to load the bytes of the shard's chunk index fails.""" + array_shape = (16,) + shard_shape = (16,) + chunk_shape = (8,) + data = np.arange(np.prod(array_shape), dtype="float32").reshape(array_shape) + fill_value = -999 + + store_mock = AsyncMock(wraps=store, spec=store.__class__) + # loading the index is the first call to .get() so returning None will simulate an index load failure + store_mock.get.return_value = None + + a = zarr.create_array( + StorePath(store_mock), + shape=data.shape, + chunks=chunk_shape, + shards={"shape": shard_shape, "index_location": index_location}, + compressors=BloscCodec(cname="lz4"), + dtype=data.dtype, + fill_value=fill_value, + ) + a[:] = data + + # Read from one of two chunks in a shard to test the partial shard read path + assert a[0] == fill_value + assert a[0] != data[0] + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) +def test_sharding_partial_shard_read__index_chunk_slice_fails( + store: Store, + index_location: ShardingCodecIndexLocation, + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Test fill value is returned when looking up a chunk's byte slice within a shard fails.""" + array_shape = (16,) + shard_shape = (16,) + chunk_shape = (8,) + data = np.arange(np.prod(array_shape), dtype="float32").reshape(array_shape) + fill_value = -999 + + monkeypatch.setattr( + "zarr.codecs.sharding._ShardIndex.get_chunk_slice", + lambda self, chunk_coords: None, + ) + + a = zarr.create_array( + StorePath(store), + shape=data.shape, + chunks=chunk_shape, + shards={"shape": shard_shape, "index_location": index_location}, + compressors=BloscCodec(cname="lz4"), + dtype=data.dtype, + fill_value=fill_value, + ) + a[:] = data + + # Read from one of two chunks in a shard to test the partial shard read path + assert a[0] == fill_value + assert a[0] != data[0] + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) +def test_sharding_partial_shard_read__chunk_load_fails( + store: Store, index_location: ShardingCodecIndexLocation +) -> None: + """Test fill value is returned when the call to the store to load a chunk's bytes fails.""" + array_shape = (16,) + shard_shape = (16,) + chunk_shape = (8,) + data = np.arange(np.prod(array_shape), dtype="float32").reshape(array_shape) + fill_value = -999 + + store_mock = AsyncMock(wraps=store, spec=store.__class__) + + a = zarr.create_array( + StorePath(store_mock), + shape=data.shape, + chunks=chunk_shape, + shards={"shape": shard_shape, "index_location": index_location}, + compressors=BloscCodec(cname="lz4"), + dtype=data.dtype, + fill_value=fill_value, + ) + a[:] = data + + # Set up store mock after array creation to simulate chunk load failure. + # Index loads still succeed (via store.get), but chunk-byte loads fail + # (via store.get_ranges raising BaseExceptionGroup containing FileNotFoundError — + # the same shape Store.get_ranges produces when a key is absent). + store_mock.reset_mock() + + async def fail_chunk_reads(key: str, byte_ranges: Any, **kwargs: Any) -> Any: + raise BaseExceptionGroup("chunk read failed", [FileNotFoundError(key)]) + yield # type: ignore[unreachable] # marks this as an async generator + + store_mock.get_ranges = fail_chunk_reads + + # Read from one of two chunks in a shard to test the partial shard read path + assert a[0] == fill_value + assert a[0] != data[0] + + @pytest.mark.parametrize( "array_fixture", [ diff --git a/tests/test_codecs/test_sharding_unit.py b/tests/test_codecs/test_sharding_unit.py new file mode 100644 index 0000000000..6e022ed9fa --- /dev/null +++ b/tests/test_codecs/test_sharding_unit.py @@ -0,0 +1,488 @@ +import numpy as np +import pytest + +from zarr.codecs.sharding import ( + MAX_UINT_64, + ShardingCodec, + _ShardIndex, + _ShardingByteGetter, + _ShardReader, +) +from zarr.core.buffer import default_buffer_prototype +from zarr.core.buffer.cpu import Buffer +from zarr.storage._common import StorePath +from zarr.storage._memory import MemoryStore + +# ============================================================================ +# _ShardIndex tests +# ============================================================================ + + +def test_shard_index_create_empty() -> None: + """Test that create_empty creates an index filled with MAX_UINT_64.""" + chunks_per_shard = (2, 3) + index = _ShardIndex.create_empty(chunks_per_shard) + + assert index.chunks_per_shard == chunks_per_shard + assert index.offsets_and_lengths.shape == (2, 3, 2) + assert index.offsets_and_lengths.dtype == np.dtype(" None: + """Test create_empty with 1D chunks_per_shard.""" + chunks_per_shard = (4,) + index = _ShardIndex.create_empty(chunks_per_shard) + + assert index.chunks_per_shard == chunks_per_shard + assert index.offsets_and_lengths.shape == (4, 2) + + +def test_shard_index_is_all_empty_true() -> None: + """Test is_all_empty returns True for a freshly created empty index.""" + index = _ShardIndex.create_empty((2, 2)) + assert index.is_all_empty() is True + + +def test_shard_index_is_all_empty_false() -> None: + """Test is_all_empty returns False when at least one chunk is set.""" + index = _ShardIndex.create_empty((2, 2)) + index.set_chunk_slice((0, 0), slice(0, 100)) + assert index.is_all_empty() is False + + +def test_shard_index_get_chunk_slice_empty() -> None: + """Test get_chunk_slice returns None for empty chunks.""" + index = _ShardIndex.create_empty((2, 2)) + assert index.get_chunk_slice((0, 0)) is None + assert index.get_chunk_slice((1, 1)) is None + + +def test_shard_index_get_chunk_slice_set() -> None: + """Test get_chunk_slice returns correct (start, end) tuple after setting.""" + index = _ShardIndex.create_empty((2, 2)) + index.set_chunk_slice((0, 1), slice(100, 200)) + + result = index.get_chunk_slice((0, 1)) + assert result == (100, 200) + + +def test_shard_index_set_chunk_slice() -> None: + """Test set_chunk_slice correctly sets offset and length.""" + index = _ShardIndex.create_empty((3, 3)) + + # Set a chunk slice + index.set_chunk_slice((1, 2), slice(50, 150)) + + # Verify the underlying array + assert index.offsets_and_lengths[1, 2, 0] == 50 # offset + assert index.offsets_and_lengths[1, 2, 1] == 100 # length (150 - 50) + + +def test_shard_index_set_chunk_slice_none() -> None: + """Test set_chunk_slice with None marks chunk as empty.""" + index = _ShardIndex.create_empty((2, 2)) + + # First set a value + index.set_chunk_slice((0, 0), slice(0, 100)) + assert index.get_chunk_slice((0, 0)) == (0, 100) + + # Then clear it + index.set_chunk_slice((0, 0), None) + assert index.get_chunk_slice((0, 0)) is None + assert index.offsets_and_lengths[0, 0, 0] == MAX_UINT_64 + assert index.offsets_and_lengths[0, 0, 1] == MAX_UINT_64 + + +def test_shard_index_get_full_chunk_map() -> None: + """Test get_full_chunk_map returns correct boolean array.""" + index = _ShardIndex.create_empty((2, 3)) + + # Set some chunks + index.set_chunk_slice((0, 0), slice(0, 10)) + index.set_chunk_slice((1, 2), slice(10, 20)) + + chunk_map = index.get_full_chunk_map() + + assert chunk_map.shape == (2, 3) + assert chunk_map.dtype == np.bool_ + assert chunk_map[0, 0] is np.True_ + assert chunk_map[0, 1] is np.False_ + assert chunk_map[0, 2] is np.False_ + assert chunk_map[1, 0] is np.False_ + assert chunk_map[1, 1] is np.False_ + assert chunk_map[1, 2] is np.True_ + + +def test_shard_index_localize_chunk() -> None: + """Test _localize_chunk maps global coords to local shard coords via modulo.""" + index = _ShardIndex.create_empty((2, 3)) + + # Within bounds - should return same coords + assert index._localize_chunk((0, 0)) == (0, 0) + assert index._localize_chunk((1, 2)) == (1, 2) + + # Out of bounds - should wrap via modulo + assert index._localize_chunk((2, 0)) == (0, 0) # 2 % 2 = 0 + assert index._localize_chunk((3, 5)) == (1, 2) # 3 % 2 = 1, 5 % 3 = 2 + assert index._localize_chunk((4, 6)) == (0, 0) # 4 % 2 = 0, 6 % 3 = 0 + + +# ============================================================================ +# _load_partial_shard_maybe tests +# +# These exercise the partial-shard read path against a real MemoryStore wrapped +# in a StorePath (the external-store branch in `_load_partial_shard_maybe`), +# plus one test against a real `_ShardingByteGetter` (the in-memory branch used +# by nested sharding). +# ============================================================================ + + +async def _store_path_with_blob(key: str, blob: bytes) -> StorePath: + """Build a `StorePath` over a fresh `MemoryStore` containing `blob` at `key`.""" + store = MemoryStore() + await store.set(key, Buffer.from_bytes(blob)) + return StorePath(store, key) + + +async def test_load_partial_shard_maybe_index_load_fails() -> None: + """Returns None when the shard key is absent (index load fails).""" + codec = ShardingCodec(chunk_shape=(8,)) + byte_getter = StorePath(MemoryStore(), "missing") + + result = await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=(2,), + all_chunk_coords={(0,)}, + ) + + assert result is None + + +async def test_load_partial_shard_maybe_with_empty_chunks( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Chunks whose index entry is empty are silently skipped.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + + # Index where chunk (1,) is empty; the others point into the stored blob. + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 100)) + index.set_chunk_slice((2,), slice(100, 200)) + index.set_chunk_slice((3,), slice(200, 300)) + + async def mock_load_index( + self: ShardingCodec, byte_getter: StorePath, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + byte_getter = await _store_path_with_blob("shard", b"x" * 300) + + result = await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,), (1,), (2,)}, + ) + + assert result is not None + assert (0,) in result + assert (1,) not in result # empty in index + assert (2,) in result + + +async def test_load_partial_shard_maybe_all_chunks_empty( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Returns an empty dict when all requested chunks are empty (no I/O issued).""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + + # Fully-empty index — `get_chunk_slice` returns None for every coord. + index = _ShardIndex.create_empty(chunks_per_shard) + + async def mock_load_index( + self: ShardingCodec, byte_getter: StorePath, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + # Empty store is fine — we never reach the chunk-read path when all are empty. + byte_getter = StorePath(MemoryStore(), "shard") + + result = await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,), (1,), (2,)}, + ) + + assert result == {} + + +async def test_load_partial_shard_returns_chunk_contents( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Returns the correct bytes for each requested chunk.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 100)) + index.set_chunk_slice((1,), slice(100, 200)) + + async def mock_load_index( + self: ShardingCodec, byte_getter: StorePath, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + blob = b"A" * 100 + b"B" * 100 + byte_getter = await _store_path_with_blob("shard", blob) + + result = await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,), (1,)}, + ) + + assert result is not None + buf_0, buf_1 = result[(0,)], result[(1,)] + assert buf_0 is not None + assert buf_1 is not None + assert buf_0.to_bytes() == b"A" * 100 + assert buf_1.to_bytes() == b"B" * 100 + + +async def test_load_partial_shard_shard_disappears_returns_none( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """If the shard key is missing when chunk reads run, returns None. + + This models a race: the index loaded successfully, but the shard was deleted + before the chunk-byte fetches landed. `Store.get_ranges` surfaces this as a + `BaseExceptionGroup` containing `FileNotFoundError`, which the codec catches + and converts to None to match the index-missing branch's behavior. + """ + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 100)) + + async def mock_load_index( + self: ShardingCodec, byte_getter: StorePath, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + # Store has no value for "shard" — `get_ranges` will raise FileNotFoundError. + byte_getter = StorePath(MemoryStore(), "shard") + + result = await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,)}, + ) + + assert result is None + + +async def test_load_partial_shard_non_fnf_error_propagates( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Non-FileNotFoundError errors from get_ranges are re-raised, not swallowed. + + Our `BaseExceptionGroup.split(FileNotFoundError)` keeps the "shard gone" + behavior for FNF only; anything else (e.g. an OSError from the underlying + fetch) must bubble up. + """ + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 100)) + + async def mock_load_index( + self: ShardingCodec, byte_getter: StorePath, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + # Make the underlying store.get raise OSError. The default Store.get_ranges + # impl routes through self.get; coalesced_get wraps the failure in a + # BaseExceptionGroup, which our code re-raises (minus FNF leaves, of which + # there are none here). + async def boom(*args: object, **kwargs: object) -> Buffer | None: + raise OSError("injected disk error") + + store = MemoryStore() + monkeypatch.setattr(store, "get", boom) + byte_getter = StorePath(store, "shard") + + with pytest.RaisesGroup(pytest.RaisesExc(OSError, match="injected disk error")): + await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,)}, + ) + + +async def test_load_partial_shard_nested_sharding_path( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Nested sharding: byte_getter is a `_ShardingByteGetter` over an in-memory dict.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 100)) + index.set_chunk_slice((1,), slice(100, 200)) + + async def mock_load_index( + self: ShardingCodec, byte_getter: _ShardingByteGetter, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + # The "store" for an inner shard is a dict keyed by outer-chunk coords; the + # byte_getter reads ranges out of one entry of that dict. + blob = b"A" * 100 + b"B" * 100 + shard_dict: dict[tuple[int, ...], Buffer | None] = {(0,): Buffer.from_bytes(blob)} + byte_getter = _ShardingByteGetter(shard_dict, (0,)) + + result = await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,), (1,)}, + ) + + assert result is not None + buf_0, buf_1 = result[(0,)], result[(1,)] + assert buf_0 is not None + assert buf_1 is not None + assert buf_0.to_bytes() == b"A" * 100 + assert buf_1.to_bytes() == b"B" * 100 + + +async def test_load_partial_shard_nested_sharding_missing_outer_chunk( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Nested sharding: outer chunk absent → `_ShardingByteGetter.get` returns None + → chunks are silently skipped, yielding an empty shard_dict.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 100)) + + async def mock_load_index( + self: ShardingCodec, byte_getter: _ShardingByteGetter, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + # Empty outer dict — _ShardingByteGetter.get(...) returns None for any range. + shard_dict: dict[tuple[int, ...], Buffer | None] = {} + byte_getter = _ShardingByteGetter(shard_dict, (0,)) + + result = await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,)}, + ) + + assert result == {} + + +# ============================================================================ +# Supporting class tests (_ShardReader, _is_total_shard) +# ============================================================================ + + +def test_shard_reader_create_empty() -> None: + """Test _ShardReader.create_empty creates reader with empty index.""" + chunks_per_shard = (2, 3) + reader = _ShardReader.create_empty(chunks_per_shard) + + assert reader.index.is_all_empty() + assert len(reader.buf) == 0 + assert len(reader) == 2 * 3 + + +def test_shard_reader_iteration() -> None: + """Test _ShardReader iteration yields all chunk coordinates.""" + chunks_per_shard = (2, 2) + reader = _ShardReader.create_empty(chunks_per_shard) + + coords = list(reader) + + assert len(coords) == 4 + assert (0, 0) in coords + assert (0, 1) in coords + assert (1, 0) in coords + assert (1, 1) in coords + + +def test_shard_reader_getitem_raises_for_empty() -> None: + """Test _ShardReader.__getitem__ raises KeyError for empty chunks.""" + chunks_per_shard = (2,) + reader = _ShardReader.create_empty(chunks_per_shard) + + with pytest.raises(KeyError): + _ = reader[(0,)] + + +def test_is_total_shard_full() -> None: + """Test _is_total_shard returns True when all chunk coords are present.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (2, 2) + all_chunk_coords: set[tuple[int, ...]] = {(0, 0), (0, 1), (1, 0), (1, 1)} + + assert codec._is_total_shard(all_chunk_coords, chunks_per_shard) is True + + +def test_is_total_shard_partial() -> None: + """Test _is_total_shard returns False for partial chunk coords.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (2, 2) + all_chunk_coords: set[tuple[int, ...]] = {(0, 0), (1, 1)} # Missing (0, 1) and (1, 0) + + assert codec._is_total_shard(all_chunk_coords, chunks_per_shard) is False + + +def test_is_total_shard_empty() -> None: + """Test _is_total_shard returns False for empty chunk coords.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (2, 2) + all_chunk_coords: set[tuple[int, ...]] = set() + + assert codec._is_total_shard(all_chunk_coords, chunks_per_shard) is False + + +def test_is_total_shard_1d() -> None: + """Test _is_total_shard works with 1D shards.""" + codec = ShardingCodec(chunk_shape=(8,)) + chunks_per_shard = (4,) + all_chunk_coords: set[tuple[int, ...]] = {(0,), (1,), (2,), (3,)} + + assert codec._is_total_shard(all_chunk_coords, chunks_per_shard) is True + + # Partial + partial_coords: set[tuple[int, ...]] = {(0,), (2,)} + assert codec._is_total_shard(partial_coords, chunks_per_shard) is False From 68c92f6822047934c1d890bbc53ec4eda6ab31bc Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Wed, 20 May 2026 07:03:02 -0400 Subject: [PATCH 322/468] Do not install CuPy on darwin (#3988) --- pyproject.toml | 2 +- uv.lock | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f460d31b25..995053d9b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ remote = [ "obstore>=0.5.1", ] gpu = [ - "cupy-cuda12x", + "cupy-cuda12x; sys_platform != 'darwin'", ] cast-value-rs = ["cast-value-rs"] cli = ["typer"] diff --git a/uv.lock b/uv.lock index eedff80f85..d23f1f2027 100644 --- a/uv.lock +++ b/uv.lock @@ -3945,7 +3945,7 @@ cli = [ { name = "typer" }, ] gpu = [ - { name = "cupy-cuda12x" }, + { name = "cupy-cuda12x", marker = "sys_platform != 'darwin'" }, ] optional = [ { name = "universal-pathlib" }, @@ -4046,7 +4046,7 @@ test = [ [package.metadata] requires-dist = [ { name = "cast-value-rs", marker = "extra == 'cast-value-rs'" }, - { name = "cupy-cuda12x", marker = "extra == 'gpu'" }, + { name = "cupy-cuda12x", marker = "sys_platform != 'darwin' and extra == 'gpu'" }, { name = "donfig", specifier = ">=0.8" }, { name = "fsspec", marker = "extra == 'remote'", specifier = ">=2023.10.0" }, { name = "google-crc32c", specifier = ">=1.5" }, From 6ebc03105ae0e234182e69fde42a4f8bde7fb85a Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 20 May 2026 14:23:58 +0200 Subject: [PATCH 323/468] prepare for 0.2.0 release (#3986) --- packages/zarr-metadata/CHANGELOG.md | 11 ++++++++++- packages/zarr-metadata/pyproject.toml | 13 +++++++++++++ 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/packages/zarr-metadata/CHANGELOG.md b/packages/zarr-metadata/CHANGELOG.md index 9190bfcc45..03e744470b 100644 --- a/packages/zarr-metadata/CHANGELOG.md +++ b/packages/zarr-metadata/CHANGELOG.md @@ -2,7 +2,7 @@ -## 0.2.0 (2026-05-11) +## 0.2.0 (2026-05-19) ### Bugfixes @@ -30,6 +30,15 @@ ### Features +- Added `ArrayMetadataV3Partial`, `GroupMetadataV3Partial`, + `ArrayMetadataV2Partial`, and `GroupMetadataV2Partial` — sibling + TypedDicts to the existing full metadata types, declared with + `total=False` so every field is `NotRequired`. Use these when typing + dicts that intentionally hold a subset of a complete metadata document + (test fixtures, fragment templates, in-progress builders). An + equivalence test pins each `Partial` to the keys and value types of + its full sibling so the two cannot drift. + ([#3982](https://github.com/zarr-developers/zarr-python/issues/3982)) - Added three new top-level types modelling the **strict on-disk** shape of Zarr v2 metadata documents: `ZArrayMetadata` (the `.zarray` file), `ZGroupMetadata` (the `.zgroup` file), and `ZAttrsMetadata` (the diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 020838261d..05667d59e3 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -16,19 +16,32 @@ authors = [ classifiers = [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", + "Intended Audience :: Information Technology", + "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", "Programming Language :: Python :: 3.14", + "Topic :: Scientific/Engineering", + "Topic :: Software Development :: Libraries :: Python Modules", "Typing :: Typed", ] +keywords = ["zarr"] dependencies = [ "typing_extensions>=4.13", ] +[project.urls] +Homepage = "https://github.com/zarr-developers/zarr-python" +Source = "https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-metadata" +Issues = "https://github.com/zarr-developers/zarr-python/issues" +Changelog = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/CHANGELOG.md" +Documentation = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/README.md" + [dependency-groups] test = ["pytest", "pydantic>=2"] From 27abff2920fa543f5f719f4217fc515c4a636408 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Wed, 20 May 2026 15:43:54 -0400 Subject: [PATCH 324/468] Widen ChunksLike type alias (#3990) * Widen ChunksLike type alias Fixes #3869 * Add changelog file. * Prefer if/else statement to if/else expression --- changes/3990.misc.md | 5 +++++ src/zarr/core/array.py | 17 ++++++----------- src/zarr/core/common.py | 2 +- 3 files changed, 12 insertions(+), 12 deletions(-) create mode 100644 changes/3990.misc.md diff --git a/changes/3990.misc.md b/changes/3990.misc.md new file mode 100644 index 0000000000..ff3fcf4cf2 --- /dev/null +++ b/changes/3990.misc.md @@ -0,0 +1,5 @@ +Widen `ChunksLike` type alias to use `Iterable` instead of `Sequence`, and also +remove `None` from the type union. This supports a broader range of types, +removing the necessity to "materialize" iterable values simply to satisfy type +annotations. It also allows use of `ChunksLike` in cases where `None` should +not be permitted. diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 8e8b9bd181..4e9bd6e12f 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -4397,11 +4397,8 @@ async def init_array( chunk_key_encoding, zarr_format=zarr_format ) - if overwrite: - if store_path.store.supports_deletes: - await store_path.delete_dir() - else: - await ensure_no_existing_node(store_path, zarr_format=zarr_format) + if overwrite and store_path.store.supports_deletes: + await store_path.delete_dir() else: await ensure_no_existing_node(store_path, zarr_format=zarr_format) @@ -4417,12 +4414,10 @@ async def init_array( ) # Normalize the user's chunks into canonical ChunksTuple form - if chunks is None or chunks == "auto": - chunks_normalized = guess_chunks( - shape_parsed, - item_size, - max_bytes=SHARDED_INNER_CHUNK_MAX_BYTES if shards is not None else None, - ) + + if chunks == "auto": + max_bytes = None if shards is None else SHARDED_INNER_CHUNK_MAX_BYTES + chunks_normalized = guess_chunks(shape_parsed, item_size, max_bytes=max_bytes) else: chunks_normalized = normalize_chunks_nd(chunks, shape_parsed) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 2279820d7a..eafffa1818 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -37,7 +37,7 @@ BytesLike = bytes | bytearray | memoryview ShapeLike = Iterable[int | np.integer[Any]] | int | np.integer[Any] -ChunksLike = ShapeLike | Sequence[Sequence[int]] | None +ChunksLike = ShapeLike | Iterable[Iterable[int]] # For backwards compatibility ChunkCoords = tuple[int, ...] ZarrFormat = Literal[2, 3] From 5ca1690f1273bb9d1db670f833e5b930ab090f06 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 21 May 2026 19:17:17 +0200 Subject: [PATCH 325/468] fix: match v* when extracting a zarr version from git tags (#3994) * fix: match v* when extracting a zarr version from git tags * test: add test that checks immunity of pyproject.toml-defined git describe invocation against weird tags * test: use simpler test --- pyproject.toml | 6 ++++++ tests/test_version_derivation.py | 34 ++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 tests/test_version_derivation.py diff --git a/pyproject.toml b/pyproject.toml index 995053d9b3..837f2f24ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -148,6 +148,12 @@ omit = [ [tool.hatch] version.source = "vcs" +# Only consider zarr-python's own `v*` tags when deriving the version. Without +# this filter `git describe` matches the most recent tag of any shape, +# including the `zarr_metadata-v*` tags used to release the zarr-metadata +# subpackage — which would make a from-source build report a `0.2.x` version +# instead of `3.x`. +version.raw-options = { git_describe_command = "git describe --dirty --tags --long --match v*" } [tool.hatch.build] hooks.vcs.version-file = "src/zarr/_version.py" diff --git a/tests/test_version_derivation.py b/tests/test_version_derivation.py new file mode 100644 index 0000000000..b9e3e90551 --- /dev/null +++ b/tests/test_version_derivation.py @@ -0,0 +1,34 @@ +"""Sanity check that ``zarr.__version__`` looks like a v3-or-newer release. + +Background: zarr-python derives its version from ``git describe`` via +hatch-vcs. The repo also publishes a separate ``zarr-metadata`` subpackage +that uses ``zarr_metadata-v*`` tags. Without the ``--match v*`` filter in +``[tool.hatch] version.raw-options.git_describe_command``, ``git describe`` +walks back to those subpackage tags and reports a version like ``0.2.0`` for +a from-source build of zarr-python itself — see +https://github.com/zarr-developers/zarr-python/pull/3994. + +This test catches that class of regression: anything that makes zarr-python +report a version lower than the v3 release line. When 4.0 is released, +bump the floor; that's a deliberate, one-line edit at a planned boundary. +""" + +from __future__ import annotations + +from packaging.version import Version + +import zarr + + +def test_version_is_v3_or_newer() -> None: + # Use packaging.Version so we transparently handle hatch-vcs dev suffixes + # like "3.2.2.dev30+gdc5e1825" that appear on any source build past the + # latest v* tag — Version.major returns 3 for that string. + parsed = Version(zarr.__version__) + assert parsed.major >= 3, ( + f"zarr.__version__={zarr.__version__!r} is not on the v3 (or newer) " + f"release line. If this fires on a from-source build, check that " + f"[tool.hatch] version.raw-options.git_describe_command in " + f"pyproject.toml still includes ``--match v*`` so the " + f"``zarr_metadata-v*`` subpackage tags are excluded. See PR #3994." + ) From 093a153dbbb904351234dcb6c85fb4dda36d01d9 Mon Sep 17 00:00:00 2001 From: Ilan Gold Date: Fri, 22 May 2026 08:01:33 -0400 Subject: [PATCH 326/468] feat: subchunk write order (#3826) * feat: subchunk write order * chore: export `SubchunkWriteOrder` * chore: docs * chore: relnote * rename * refactor: no enums * Update docs/user-guide/performance.md Co-authored-by: Davis Bennett * feat: deterministic but random order * fix: make vectorized fetching less reliant on matching order * chore: add hypothesis * refactor: dead code * refactor: more cleanup * don't shard unless there is something to shard * fix: dont mix chunk grid and sharding --------- Co-authored-by: Davis Bennett --- changes/3826.feature.md | 1 + docs/user-guide/performance.md | 7 ++ src/zarr/codecs/__init__.py | 3 +- src/zarr/codecs/sharding.py | 62 ++++++++++--- src/zarr/testing/strategies.py | 64 +++++++++----- tests/test_codecs/test_sharding.py | 137 ++++++++++++++++++++++++++++- 6 files changed, 235 insertions(+), 39 deletions(-) create mode 100644 changes/3826.feature.md diff --git a/changes/3826.feature.md b/changes/3826.feature.md new file mode 100644 index 0000000000..41cc555a92 --- /dev/null +++ b/changes/3826.feature.md @@ -0,0 +1 @@ +Added a `subchunk_write_order` option to `ShardingCodec` to allow for `morton`, `unordered`, `lexicographic`, and `colexicographic` subchunk orderings. \ No newline at end of file diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 6514b35a30..fa98e9466e 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -113,6 +113,13 @@ bytes within chunks of an array may improve the compression ratio, depending on the structure of the data, the compression algorithm used, and which compression filters (e.g., byte-shuffle) have been applied. +### Subchunk memory layout + +The order of chunks **within each shard** can be changed via the `subchunk_write_order` parameter of the `ShardingCodec`. That parameter is a string which must be one of `["morton", "lexicographic", "colexicographic", "unordered"]`. + +By default [`morton`](https://en.wikipedia.org/wiki/Z-order_curve) order provides good spatial locality however [`lexicographic` (i.e., row-major)](https://en.wikipedia.org/wiki/Row-_and_column-major_order), for example, may be better suited to "batched" workflows where some form of sequential reading through a fixed number of outer dimensions is desired. The options are `lexicographic`, `morton`, `unordered` (i.e., random), and `colexicographic`. + + ### Empty chunks It is possible to configure how Zarr handles the storage of chunks that are "empty" diff --git a/src/zarr/codecs/__init__.py b/src/zarr/codecs/__init__.py index 756bd97ed2..9a1b47b351 100644 --- a/src/zarr/codecs/__init__.py +++ b/src/zarr/codecs/__init__.py @@ -29,7 +29,7 @@ Zstd, ) from zarr.codecs.scale_offset import ScaleOffset -from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation +from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation, SubchunkWriteOrder from zarr.codecs.transpose import TransposeCodec from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec from zarr.codecs.zstd import ZstdCodec @@ -47,6 +47,7 @@ "ScaleOffset", "ShardingCodec", "ShardingCodecIndexLocation", + "SubchunkWriteOrder", "TransposeCodec", "VLenBytesCodec", "VLenUTF8Codec", diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 41f9b7e9c6..33c8602ecb 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -4,7 +4,7 @@ from dataclasses import dataclass, replace from enum import Enum from functools import lru_cache -from typing import TYPE_CHECKING, Any, NamedTuple, cast +from typing import TYPE_CHECKING, Any, Literal, NamedTuple, cast import numpy as np import numpy.typing as npt @@ -46,8 +46,6 @@ BasicIndexer, ChunkProjection, SelectorTuple, - _morton_order, - _morton_order_keys, c_order_iter, get_indexer, morton_order_iter, @@ -64,7 +62,7 @@ if TYPE_CHECKING: from collections.abc import Iterator - from typing import Self + from typing import Final, Self from zarr.core.common import JSON from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType @@ -83,6 +81,15 @@ class ShardingCodecIndexLocation(Enum): end = "end" +SubchunkWriteOrder = Literal["morton", "unordered", "lexicographic", "colexicographic"] +SUBCHUNK_WRITE_ORDER: Final[tuple[str, str, str, str]] = ( + "morton", + "unordered", + "lexicographic", + "colexicographic", +) + + def parse_index_location(data: object) -> ShardingCodecIndexLocation: return parse_enum(data, ShardingCodecIndexLocation) @@ -272,14 +279,13 @@ def to_dict_vectorized( dict mapping chunk coordinate tuples to Buffer or None """ starts, ends, valid = self.index.get_chunk_slices_vectorized(chunk_coords_array) - chunk_coords_keys = _morton_order_keys(self.index.chunks_per_shard) result: dict[tuple[int, ...], Buffer | None] = {} - for i, coords in enumerate(chunk_coords_keys): + for i, coords in enumerate(chunk_coords_array): if valid[i]: - result[coords] = self.buf[int(starts[i]) : int(ends[i])] + result[tuple(coords.ravel())] = self.buf[int(starts[i]) : int(ends[i])] else: - result[coords] = None + result[tuple(coords.ravel())] = None return result @@ -293,7 +299,9 @@ class ShardingCodec( chunk_shape: tuple[int, ...] codecs: tuple[Codec, ...] index_codecs: tuple[Codec, ...] + rng: np.random.Generator | None index_location: ShardingCodecIndexLocation = ShardingCodecIndexLocation.end + subchunk_write_order: SubchunkWriteOrder = "morton" def __init__( self, @@ -302,16 +310,24 @@ def __init__( codecs: Iterable[Codec | dict[str, JSON]] = (BytesCodec(),), index_codecs: Iterable[Codec | dict[str, JSON]] = (BytesCodec(), Crc32cCodec()), index_location: ShardingCodecIndexLocation | str = ShardingCodecIndexLocation.end, + subchunk_write_order: SubchunkWriteOrder = "morton", + rng: np.random.Generator | None = None, ) -> None: chunk_shape_parsed = parse_shapelike(chunk_shape) codecs_parsed = parse_codecs(codecs) index_codecs_parsed = parse_codecs(index_codecs) index_location_parsed = parse_index_location(index_location) + if subchunk_write_order not in SUBCHUNK_WRITE_ORDER: + raise ValueError( + f"Unrecognized subchunk write order: {subchunk_write_order}. Only {SUBCHUNK_WRITE_ORDER} are allowed." + ) object.__setattr__(self, "chunk_shape", chunk_shape_parsed) object.__setattr__(self, "codecs", codecs_parsed) object.__setattr__(self, "index_codecs", index_codecs_parsed) object.__setattr__(self, "index_location", index_location_parsed) + object.__setattr__(self, "subchunk_write_order", subchunk_write_order) + object.__setattr__(self, "rng", rng) # Use instance-local lru_cache to avoid memory leaks @@ -324,7 +340,7 @@ def __init__( # todo: typedict return type def __getstate__(self) -> dict[str, Any]: - return self.to_dict() + return {"rng": self.rng, **self.to_dict()} def __setstate__(self, state: dict[str, Any]) -> None: config = state["configuration"] @@ -332,6 +348,7 @@ def __setstate__(self, state: dict[str, Any]) -> None: object.__setattr__(self, "codecs", parse_codecs(config["codecs"])) object.__setattr__(self, "index_codecs", parse_codecs(config["index_codecs"])) object.__setattr__(self, "index_location", parse_index_location(config["index_location"])) + object.__setattr__(self, "rng", state["rng"]) # Use instance-local lru_cache to avoid memory leaks # object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) @@ -509,6 +526,24 @@ async def _decode_partial_single( else: return out + def _subchunk_order_iter( + self, chunks_per_shard: tuple[int, ...], subchunk_write_order: SubchunkWriteOrder + ) -> Iterable[tuple[int, ...]]: + match subchunk_write_order: + case "morton": + subchunk_iter = morton_order_iter(chunks_per_shard) + case "lexicographic": + subchunk_iter = np.ndindex(chunks_per_shard) + case "colexicographic": + subchunk_iter = (c[::-1] for c in np.ndindex(chunks_per_shard[::-1])) + case "unordered": + subchunk_list = list(np.ndindex(chunks_per_shard)) + (self.rng if self.rng is not None else np.random.default_rng()).shuffle( + subchunk_list + ) + subchunk_iter = iter(subchunk_list) + return subchunk_iter + async def _encode_single( self, shard_array: NDBuffer, @@ -526,8 +561,7 @@ async def _encode_single( chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), ) ) - - shard_builder = dict.fromkeys(morton_order_iter(chunks_per_shard)) + shard_builder = dict.fromkeys(self._subchunk_order_iter(chunks_per_shard, "lexicographic")) await self.codec_pipeline.write( [ @@ -570,7 +604,7 @@ async def _encode_partial_single( ) if self._is_complete_shard_write(indexer, chunks_per_shard): - shard_dict = dict.fromkeys(morton_order_iter(chunks_per_shard)) + shard_dict = dict.fromkeys(self._subchunk_order_iter(chunks_per_shard, "lexicographic")) else: shard_reader = await self._load_full_shard_maybe( byte_getter=byte_setter, @@ -580,7 +614,7 @@ async def _encode_partial_single( shard_reader = shard_reader or _ShardReader.create_empty(chunks_per_shard) # Use vectorized lookup for better performance shard_dict = shard_reader.to_dict_vectorized( - np.asarray(_morton_order(chunks_per_shard)) + np.array(list(self._subchunk_order_iter(chunks_per_shard, "lexicographic"))) ) await self.codec_pipeline.write( @@ -619,7 +653,7 @@ async def _encode_shard_dict( template = buffer_prototype.buffer.create_zero_length() chunk_start = 0 - for chunk_coords in morton_order_iter(chunks_per_shard): + for chunk_coords in self._subchunk_order_iter(chunks_per_shard, self.subchunk_write_order): value = map.get(chunk_coords) if value is None: continue diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 1b0ede1148..74d9d7c683 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -13,7 +13,10 @@ import zarr from zarr.abc.store import RangeByteRequest, Store from zarr.codecs.bytes import BytesCodec -from zarr.core.array import Array +from zarr.codecs.crc32c_ import Crc32cCodec +from zarr.codecs.sharding import SUBCHUNK_WRITE_ORDER, ShardingCodec, SubchunkWriteOrder +from zarr.codecs.zstd import ZstdCodec +from zarr.core.array import Array, CompressorsLike, SerializerLike from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding from zarr.core.common import JSON, AccessModeLiteral, ZarrFormat from zarr.core.dtype import get_data_type_from_native_dtype @@ -127,6 +130,9 @@ def dimension_names(draw: st.DrawFn, *, ndim: int | None = None) -> list[None | return draw(st.none() | st.lists(st.none() | simple_text, min_size=ndim, max_size=ndim)) # type: ignore[arg-type] +subchunk_write_orders: st.SearchStrategy[SubchunkWriteOrder] = st.sampled_from(SUBCHUNK_WRITE_ORDER) + + @st.composite def array_metadata( draw: st.DrawFn, @@ -255,6 +261,7 @@ def arrays( arrays: st.SearchStrategy | None = None, attrs: st.SearchStrategy = attrs, zarr_formats: st.SearchStrategy = zarr_formats, + subchunk_write_orders: SearchStrategy[SubchunkWriteOrder] = subchunk_write_orders, open_mode: AccessModeLiteral = "w", ) -> AnyArray: store = draw(stores, label="store") @@ -266,20 +273,11 @@ def arrays( arrays = numpy_arrays(shapes=shapes) nparray = draw(arrays, label="array data") dim_names: None | list[str | None] = None + serializer: SerializerLike = "auto" + compressors_unsearched: CompressorsLike = "auto" # For v3 arrays, optionally use RectilinearChunkGridMetadata chunk_grid_meta: RegularChunkGridMetadata | RectilinearChunkGridMetadata | None = None - shard_shape = None - if zarr_format == 3: - chunk_grid_meta = draw(chunk_grids(shape=nparray.shape), label="chunk grid") - - # Sharding is only supported with regular chunk grids, and has complex - # divisibility constraints that don't play well with hypothesis shrinking. - # Disabled for now — sharding should be tested separately. - - dim_names = draw(dimension_names(ndim=nparray.ndim), label="dimension names") - else: - dim_names = None # test that None works too. fill_value = draw(st.one_of([st.none(), npst.from_dtype(nparray.dtype)])) @@ -295,17 +293,37 @@ def arrays( # - RectilinearChunkGridMetadata -> nested list of ints (triggers rectilinear path) # - v2 -> flat tuple of ints chunks_param: tuple[int, ...] | list[list[int]] - if zarr_format == 3 and chunk_grid_meta is not None: + shard_shape = None + dim_names = None + if zarr_format == 3: + chunk_grid_meta = draw(st.none() | chunk_grids(shape=nparray.shape), label="chunk grid") + dim_names = draw(dimension_names(ndim=nparray.ndim), label="dimension names") if isinstance(chunk_grid_meta, RectilinearChunkGridMetadata): chunks_param = [ list(dim) if isinstance(dim, tuple) else [dim] for dim in chunk_grid_meta.chunk_shapes ] - else: + elif isinstance(chunk_grid_meta, RegularChunkGridMetadata): chunks_param = chunk_grid_meta.chunk_shape + else: + chunks_param = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") + + if all(s > c and c > 1 for s, c in zip(nparray.shape, chunks_param, strict=True)): + shard_shape = draw( + st.none() | shard_shapes(shape=nparray.shape, chunk_shape=chunks_param), + label="shard shape", + ) + if shard_shape is not None: + subchunk_write_order = draw(subchunk_write_orders) + serializer = ShardingCodec( + subchunk_write_order=subchunk_write_order, + codecs=[BytesCodec(), ZstdCodec()], + index_codecs=[BytesCodec(), Crc32cCodec()], + chunk_shape=chunks_param, + ) + compressors_unsearched = None else: chunks_param = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") - a = root.create_array( array_path, shape=nparray.shape, @@ -313,9 +331,10 @@ def arrays( shards=shard_shape, dtype=nparray.dtype, attributes=attributes, - # compressor=compressor, # FIXME + compressors=compressors_unsearched, # FIXME fill_value=fill_value, dimension_names=dim_names, + serializer=serializer, ) assert isinstance(a, Array) @@ -329,12 +348,15 @@ def arrays( # Verify chunks — for rectilinear grids, .chunks raises if zarr_format == 3: - if isinstance(a.metadata.chunk_grid, RectilinearChunkGridMetadata): - assert shard_shape is None - else: - assert isinstance(a.metadata.chunk_grid, RegularChunkGridMetadata) - assert a.metadata.chunk_grid.chunk_shape == a.chunks + assert shard_shape == a.shards + if isinstance(a.metadata.chunk_grid, RegularChunkGridMetadata): + assert a.metadata.chunk_grid.chunk_shape == ( + a.shards if shard_shape is not None else a.chunks + ) assert shard_shape == a.shards + else: + assert isinstance(a.metadata.chunk_grid, RectilinearChunkGridMetadata) + assert shard_shape is None assert a.basename == name, (a.basename, name) assert dict(a.attrs) == expected_attrs diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index b31471337c..74e4a7e0d5 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -1,5 +1,5 @@ import pickle -from typing import Any +from typing import Any, get_args from unittest.mock import AsyncMock import numpy as np @@ -13,14 +13,16 @@ from zarr.abc.store import Store from zarr.codecs import ( BloscCodec, + BytesCodec, + Crc32cCodec, ShardingCodec, ShardingCodecIndexLocation, TransposeCodec, ) -from zarr.codecs.sharding import MAX_UINT_64, _ShardIndex +from zarr.codecs.sharding import MAX_UINT_64, SubchunkWriteOrder, _ShardIndex, _ShardReader from zarr.core.buffer import NDArrayLike, default_buffer_prototype from zarr.core.indexing import c_order_iter -from zarr.storage import StorePath, ZipStore +from zarr.storage import MemoryStore, StorePath, ZipStore from ..conftest import ArrayRequest from .test_codecs import _AsyncArrayProxy, order_from_dim @@ -822,6 +824,135 @@ def test_sharding_mixed_integer_list_indexing(store: Store) -> None: np.testing.assert_array_equal(c3, s3) +async def stored_data_and_get_order( + codec: ShardingCodec, chunks_per_shard: tuple[int, ...] +) -> list[tuple[int, ...]]: + shard_shape = tuple(c * s for c, s in zip(chunks_per_shard, codec.chunk_shape, strict=True)) + store = MemoryStore() + arr = zarr.create_array( + StorePath(store), + shape=shard_shape, + dtype="uint8", + chunks=shard_shape, + serializer=codec, + filters=None, + compressors=None, + fill_value=0, + ) + + arr[:] = np.arange(np.prod(shard_shape), dtype="uint8").reshape(shard_shape) + + shard_buf = await store.get("c/0/0", prototype=default_buffer_prototype()) + if shard_buf is None: + raise RuntimeError("data write failed") + index = (await _ShardReader.from_bytes(shard_buf, codec, chunks_per_shard)).index + offset_to_coord: dict[int, tuple[int, ...]] = dict( + zip( + index.get_chunk_slices_vectorized(np.array(list(np.ndindex(chunks_per_shard))))[ + 0 + ], # start + list(np.ndindex(chunks_per_shard)), # coord + strict=True, + ) + ) + + # The physical write order is recovered by sorting coordinates by start offset. + return [coord for _, coord in sorted(offset_to_coord.items())] + + +@pytest.mark.parametrize( + "subchunk_write_order", + get_args(SubchunkWriteOrder), +) +async def test_encoded_subchunk_write_order(subchunk_write_order: SubchunkWriteOrder) -> None: + """Subchunks must be physically laid out in the shard in the order specified by + ``subchunk_write_order``. We verify this by decoding the shard index and sorting + the chunk coordinates by their byte offset.""" + # Use a non-square chunks_per_shard so all three orderings are distinguishable. + chunks_per_shard = (3, 2) + chunk_shape = (4, 4) + seed = 0 + codec = ShardingCodec( + chunk_shape=chunk_shape, + codecs=[BytesCodec()], + index_codecs=[BytesCodec(), Crc32cCodec()], + index_location=ShardingCodecIndexLocation.end, + subchunk_write_order=subchunk_write_order, + rng=np.random.default_rng(seed=seed), + ) + + actual_order = await stored_data_and_get_order(codec, chunks_per_shard) + if subchunk_write_order != "unordered": + expected_order = list(codec._subchunk_order_iter(chunks_per_shard, subchunk_write_order)) + assert actual_order == expected_order + else: + same_order_same_seed = list( + ShardingCodec( + chunk_shape=chunk_shape, + codecs=[BytesCodec()], + index_codecs=[BytesCodec(), Crc32cCodec()], + index_location=ShardingCodecIndexLocation.end, + subchunk_write_order=subchunk_write_order, + rng=np.random.default_rng(seed=seed), + )._subchunk_order_iter(chunks_per_shard, subchunk_write_order) + ) + assert actual_order == same_order_same_seed + + +async def test_unordered_can_be_seeded() -> None: + orders = [] + chunks_per_shard = (3, 2) + chunk_shape = (4, 4) + seed = 0 + for _ in range(4): + codec = ShardingCodec( + chunk_shape=chunk_shape, + codecs=[BytesCodec()], + index_codecs=[BytesCodec(), Crc32cCodec()], + index_location=ShardingCodecIndexLocation.end, + subchunk_write_order="unordered", + rng=np.random.default_rng(seed=seed), + ) + orders.append(await stored_data_and_get_order(codec, chunks_per_shard)) + assert all(orders[0] == o for o in orders) + + +@pytest.mark.parametrize( + "subchunk_write_order", + get_args(SubchunkWriteOrder), +) +@pytest.mark.parametrize("do_partial", [True, False], ids=["partial", "complete"]) +def test_subchunk_write_order_roundtrip( + subchunk_write_order: SubchunkWriteOrder, do_partial: bool +) -> None: + """Data written with any ``subchunk_write_order`` must round-trip correctly.""" + chunks_per_shard = (3, 2) + chunk_shape = (4, 4) + shard_shape = tuple(c * s for c, s in zip(chunks_per_shard, chunk_shape, strict=True)) + data = np.arange(np.prod(shard_shape), dtype="uint16").reshape(shard_shape) + arr = zarr.create_array( + StorePath(MemoryStore()), + shape=shard_shape, + dtype=data.dtype, + chunks=shard_shape, + serializer=ShardingCodec( + chunk_shape=chunk_shape, + codecs=[BytesCodec()], + subchunk_write_order=subchunk_write_order, + ), + filters=None, + compressors=None, + fill_value=0, + ) + if do_partial: + sub_data = data[: (shard_shape[0] // 2)] + arr[: (shard_shape[0] // 2)] = data[: (shard_shape[0] // 2)] + data = np.vstack([sub_data, np.zeros_like(sub_data)]) + else: + arr[:] = data + np.testing.assert_array_equal(arr[:], data) + + def test_sharding_zero_dimensional() -> None: """Regression test for https://github.com/zarr-developers/zarr-python/issues/3751""" arr = zarr.create_array({}, shape=(), dtype="f4", chunks=(), shards=()) From 1907ad6422d152d280d70ea8d2f3a73fa39b0c9d Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 22 May 2026 15:07:03 +0200 Subject: [PATCH 327/468] prune old string dtype class (#3973) * chore: remove old stringdtype specialized for numpy < 2 * chore: narrow test fn signature * docs: changelog * chore: rename test class * Update changes/3973.removal.md Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- changes/3973.removal.md | 1 + src/zarr/core/dtype/npy/string.py | 154 ++++++----------------- tests/test_array.py | 22 +--- tests/test_codecs/test_vlen.py | 18 +-- tests/test_dtype/test_npy/test_string.py | 101 +++++---------- tests/test_dtype_registry.py | 2 - 6 files changed, 84 insertions(+), 214 deletions(-) create mode 100644 changes/3973.removal.md diff --git a/changes/3973.removal.md b/changes/3973.removal.md new file mode 100644 index 0000000000..c25ac967a2 --- /dev/null +++ b/changes/3973.removal.md @@ -0,0 +1 @@ +Removed the NumPy 1.x implementation of the `VariableLengthUTF8` data type because NumPy 1.x is no longer supported under [SPEC0](https://scientific-python.org/specs/spec-0000/). \ No newline at end of file diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index 00cde0d99f..3beb82c598 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -38,8 +38,6 @@ from zarr.core.common import JSON, ZarrFormat from zarr.core.dtype.wrapper import TBaseDType -_NUMPY_SUPPORTS_VLEN_STRING = hasattr(np.dtypes, "StringDType") - @runtime_checkable class SupportsStr(Protocol): @@ -451,28 +449,31 @@ class VariableLengthUTF8JSON_V2(DTypeConfig_V2[Literal["|O"], Literal["vlen-utf8 """ -# VariableLengthUTF8 is defined in two places, conditioned on the version of NumPy. -# If NumPy 2 is installed, then VariableLengthUTF8 is defined with the NumPy variable length -# string dtype as the native dtype. Otherwise, VariableLengthUTF8 is defined with the NumPy object -# dtype as the native dtype. -class UTF8Base[DType: TBaseDType](ZDType[DType, str], HasObjectCodec): +@dataclass(frozen=True, kw_only=True) +class VariableLengthUTF8(ZDType[np.dtypes.StringDType, str], HasObjectCodec): # type: ignore[type-var] """ - A base class for variable-length UTF-8 string data types. + A Zarr data type for arrays containing variable-length UTF-8 strings. + + Wraps the ``np.dtypes.StringDType`` data type. Scalars for this data type are instances + of ``str``. - Not intended for direct use, but as a base for concrete implementations. Attributes ---------- - object_codec_id : ClassVar[Literal["vlen-utf8"]] + dtype_cls : Type[np.dtypes.StringDType] + The NumPy dtype class for this data type. + _zarr_v3_name : ClassVar[Literal["variable_length_utf8"]] = "variable_length_utf8" + The name of this data type in Zarr V3. + object_codec_id : ClassVar[Literal["vlen-utf8"]] = "vlen-utf8" The object codec ID for this data type. References ---------- - This data type does not have a Zarr V3 specification. + https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/string - The Zarr V2 data type specification can be found [here](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v2/v2.0.rst#data-type-encoding). """ + dtype_cls = np.dtypes.StringDType # type: ignore[assignment] _zarr_v3_name: ClassVar[Literal["string"]] = "string" object_codec_id: ClassVar[Literal["vlen-utf8"]] = "vlen-utf8" @@ -480,7 +481,8 @@ class UTF8Base[DType: TBaseDType](ZDType[DType, str], HasObjectCodec): def from_native_dtype(cls, dtype: TBaseDType) -> Self: """ Create an instance of this data type from a compatible NumPy data type. - + We reject NumPy StringDType instances that have the `na_object` field set, + because this is not representable by the Zarr `string` data type. Parameters ---------- @@ -496,13 +498,33 @@ def from_native_dtype(cls, dtype: TBaseDType) -> Self: ------ DataTypeValidationError If the input is not compatible with this data type. + ValueError + If the input is `numpy.dtypes.StringDType` and has `na_object` set. """ if cls._check_native_dtype(dtype): + if hasattr(dtype, "na_object"): + msg = ( + f"Zarr data type resolution from {dtype} failed. " + "Attempted to resolve a zarr data type from a `numpy.dtypes.StringDType` " + "with `na_object` set, which is not supported." + ) + raise ValueError(msg) return cls() raise DataTypeValidationError( f"Invalid data type: {dtype}. Expected an instance of {cls.dtype_cls}" ) + def to_native_dtype(self) -> np.dtypes.StringDType: + """ + Create a NumPy string dtype from this VariableLengthUTF8 ZDType. + + Returns + ------- + np.dtypes.StringDType + The NumPy string dtype. + """ + return self.dtype_cls() + @classmethod def _check_json_v2( cls, @@ -719,109 +741,3 @@ def cast_scalar(self, data: object) -> str: f"data type {self}." ) raise TypeError(msg) # pragma: no cover - - -if _NUMPY_SUPPORTS_VLEN_STRING: - - @dataclass(frozen=True, kw_only=True) - class VariableLengthUTF8(UTF8Base[np.dtypes.StringDType]): # type: ignore[type-var] - """ - A Zarr data type for arrays containing variable-length UTF-8 strings. - - Wraps the ``np.dtypes.StringDType`` data type. Scalars for this data type are instances - of ``str``. - - - Attributes - ---------- - dtype_cls : Type[np.dtypes.StringDType] - The NumPy dtype class for this data type. - _zarr_v3_name : ClassVar[Literal["variable_length_utf8"]] = "variable_length_utf8" - The name of this data type in Zarr V3. - object_codec_id : ClassVar[Literal["vlen-utf8"]] = "vlen-utf8" - The object codec ID for this data type. - """ - - dtype_cls = np.dtypes.StringDType # type: ignore[assignment] - - @classmethod - def from_native_dtype(cls, dtype: TBaseDType) -> Self: - """ - Create an instance of this data type from a compatible NumPy data type. - We reject NumPy StringDType instances that have the `na_object` field set, - because this is not representable by the Zarr `string` data type. - - Parameters - ---------- - dtype : TBaseDType - The native data type. - - Returns - ------- - Self - An instance of this data type. - - Raises - ------ - DataTypeValidationError - If the input is not compatible with this data type. - ValueError - If the input is `numpy.dtypes.StringDType` and has `na_object` set. - """ - if cls._check_native_dtype(dtype): - if hasattr(dtype, "na_object"): - msg = ( - f"Zarr data type resolution from {dtype} failed. " - "Attempted to resolve a zarr data type from a `numpy.dtypes.StringDType` " - "with `na_object` set, which is not supported." - ) - raise ValueError(msg) - return cls() - raise DataTypeValidationError( - f"Invalid data type: {dtype}. Expected an instance of {cls.dtype_cls}" - ) - - def to_native_dtype(self) -> np.dtypes.StringDType: - """ - Create a NumPy string dtype from this VariableLengthUTF8 ZDType. - - Returns - ------- - np.dtypes.StringDType - The NumPy string dtype. - """ - return self.dtype_cls() - -else: - # Numpy pre-2 does not have a variable length string dtype, so we use the Object dtype instead. - @dataclass(frozen=True, kw_only=True) - class VariableLengthUTF8(UTF8Base[np.dtypes.ObjectDType]): # type: ignore[no-redef] - """ - A Zarr data type for arrays containing variable-length UTF-8 strings. - - Wraps the ``np.dtypes.ObjectDType`` data type. Scalars for this data type are instances - of ``str``. - - - Attributes - ---------- - dtype_cls : Type[np.dtypes.ObjectDType] - The NumPy dtype class for this data type. - _zarr_v3_name : ClassVar[Literal["variable_length_utf8"]] = "variable_length_utf8" - The name of this data type in Zarr V3. - object_codec_id : ClassVar[Literal["vlen-utf8"]] = "vlen-utf8" - The object codec ID for this data type. - """ - - dtype_cls = np.dtypes.ObjectDType - - def to_native_dtype(self) -> np.dtypes.ObjectDType: - """ - Create a NumPy object dtype from this VariableLengthUTF8 ZDType. - - Returns - ------- - np.dtypes.ObjectDType - The NumPy object dtype. - """ - return self.dtype_cls() diff --git a/tests/test_array.py b/tests/test_array.py index 91f0fae1c4..0d6d2d5906 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -69,7 +69,6 @@ ) from zarr.core.dtype.common import ENDIANNESS_STR, EndiannessStr from zarr.core.dtype.npy.common import NUMPY_ENDIANNESS_STR, endianness_from_numpy_str -from zarr.core.dtype.npy.string import UTF8Base from zarr.core.group import AsyncGroup from zarr.core.indexing import BasicIndexer, _iter_grid, _iter_regions from zarr.core.metadata.v2 import ArrayV2Metadata @@ -1981,23 +1980,14 @@ def test_array_repr(store: Store) -> None: assert str(arr) == f"" -class UnknownObjectDtype(UTF8Base[np.dtypes.ObjectDType]): - object_codec_id = "unknown" # type: ignore[assignment] - - def to_native_dtype(self) -> np.dtypes.ObjectDType: - """ - Create a NumPy object dtype from this VariableLengthUTF8 ZDType. +class UnknownObjectCodecDtype(VariableLengthUTF8): + """A data type that requires an object codec with an unknown id, used for error-path tests.""" - Returns - ------- - np.dtypes.ObjectDType - The NumPy object dtype. - """ - return np.dtype("o") # type: ignore[return-value] + object_codec_id = "unknown" # type: ignore[assignment] @pytest.mark.parametrize( - "dtype", [VariableLengthUTF8(), VariableLengthBytes(), UnknownObjectDtype()] + "dtype", [VariableLengthUTF8(), VariableLengthBytes(), UnknownObjectCodecDtype()] ) def test_chunk_encoding_no_object_codec_errors(dtype: ZDType[Any, Any]) -> None: """ @@ -2024,7 +2014,7 @@ def test_unknown_object_codec_default_serializer_v3() -> None: Test that we get a valueerrror when trying to create the default serializer for a data type that requires an unknown object codec """ - dtype = UnknownObjectDtype() + dtype = UnknownObjectCodecDtype() msg = f"Data type {dtype} requires an unknown object codec: {dtype.object_codec_id!r}." with pytest.raises(ValueError, match=re.escape(msg)): default_serializer_v3(dtype) @@ -2035,7 +2025,7 @@ def test_unknown_object_codec_default_filters_v2() -> None: Test that we get a valueerrror when trying to create the default serializer for a data type that requires an unknown object codec """ - dtype = UnknownObjectDtype() + dtype = UnknownObjectCodecDtype() msg = f"Data type {dtype} requires an unknown object codec: {dtype.object_codec_id!r}." with pytest.raises(ValueError, match=re.escape(msg)): default_filters_v2(dtype) diff --git a/tests/test_codecs/test_vlen.py b/tests/test_codecs/test_vlen.py index f3445824b3..3422090a28 100644 --- a/tests/test_codecs/test_vlen.py +++ b/tests/test_codecs/test_vlen.py @@ -10,17 +10,19 @@ from zarr.codecs import ZstdCodec from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec from zarr.core.dtype import get_data_type_from_native_dtype -from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.storage import StorePath -numpy_str_dtypes: list[type | str | None] = [None, str, "str", np.dtypes.StrDType, "S", "U"] -expected_array_string_dtype: np.dtype[Any] -if _NUMPY_SUPPORTS_VLEN_STRING: - numpy_str_dtypes.append(np.dtypes.StringDType) - expected_array_string_dtype = np.dtypes.StringDType() -else: - expected_array_string_dtype = np.dtype("O") +numpy_str_dtypes: list[type | str | None] = [ + None, + str, + "str", + np.dtypes.StrDType, + "S", + "U", + np.dtypes.StringDType, +] +expected_array_string_dtype: np.dtype[Any] = np.dtypes.StringDType() @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") diff --git a/tests/test_dtype/test_npy/test_string.py b/tests/test_dtype/test_npy/test_string.py index fcc4793281..c3b292e5fc 100644 --- a/tests/test_dtype/test_npy/test_string.py +++ b/tests/test_dtype/test_npy/test_string.py @@ -5,79 +5,42 @@ from tests.test_dtype.test_wrapper import BaseTestZDType from zarr.core.dtype import FixedLengthUTF32 -from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING, VariableLengthUTF8 +from zarr.core.dtype.npy.string import VariableLengthUTF8 -if _NUMPY_SUPPORTS_VLEN_STRING: - class TestVariableLengthString(BaseTestZDType): - test_cls = VariableLengthUTF8 # type: ignore[assignment] - valid_dtype = (np.dtypes.StringDType(),) # type: ignore[assignment] - invalid_dtype = ( - np.dtype(np.int8), - np.dtype(np.float64), - np.dtype("|S10"), - ) - valid_json_v2 = ({"name": "|O", "object_codec_id": "vlen-utf8"},) - valid_json_v3 = ("string",) - invalid_json_v2 = ( - "|S10", - "|f8", - "invalid", - ) - invalid_json_v3 = ( - {"name": "variable_length_utf8", "configuration": {"invalid_key": "value"}}, - {"name": "invalid_name"}, - ) - - scalar_v2_params = ((VariableLengthUTF8(), ""), (VariableLengthUTF8(), "hi")) - scalar_v3_params = ( - (VariableLengthUTF8(), ""), - (VariableLengthUTF8(), "hi"), - ) - - cast_value_params = ( - (VariableLengthUTF8(), "", np.str_("")), - (VariableLengthUTF8(), "hi", np.str_("hi")), - ) - # anything can become a string - invalid_scalar_params = (None,) - item_size_params = (VariableLengthUTF8(),) - -else: - - class TestVariableLengthString(BaseTestZDType): # type: ignore[no-redef] - test_cls = VariableLengthUTF8 # type: ignore[assignment] - valid_dtype = (np.dtype("O"),) - invalid_dtype = ( - np.dtype(np.int8), - np.dtype(np.float64), - np.dtype("|S10"), - ) - valid_json_v2 = ({"name": "|O", "object_codec_id": "vlen-utf8"},) - valid_json_v3 = ("string",) - invalid_json_v2 = ( - "|S10", - "|f8", - "invalid", - ) - invalid_json_v3 = ( - {"name": "numpy.variable_length_utf8", "configuration": {"invalid_key": "value"}}, - {"name": "invalid_name"}, - ) +class TestVariableLengthString(BaseTestZDType): + test_cls = VariableLengthUTF8 # type: ignore[assignment] + valid_dtype = (np.dtypes.StringDType(),) # type: ignore[assignment] + invalid_dtype = ( + np.dtype(np.int8), + np.dtype(np.float64), + np.dtype("|S10"), + ) + valid_json_v2 = ({"name": "|O", "object_codec_id": "vlen-utf8"},) + valid_json_v3 = ("string",) + invalid_json_v2 = ( + "|S10", + "|f8", + "invalid", + ) + invalid_json_v3 = ( + {"name": "variable_length_utf8", "configuration": {"invalid_key": "value"}}, + {"name": "invalid_name"}, + ) - scalar_v2_params = ((VariableLengthUTF8(), ""), (VariableLengthUTF8(), "hi")) - scalar_v3_params = ( - (VariableLengthUTF8(), ""), - (VariableLengthUTF8(), "hi"), - ) + scalar_v2_params = ((VariableLengthUTF8(), ""), (VariableLengthUTF8(), "hi")) + scalar_v3_params = ( + (VariableLengthUTF8(), ""), + (VariableLengthUTF8(), "hi"), + ) - cast_value_params = ( - (VariableLengthUTF8(), "", np.str_("")), - (VariableLengthUTF8(), "hi", np.str_("hi")), - ) - # anything can become a string - invalid_scalar_params = (None,) - item_size_params = (VariableLengthUTF8(),) + cast_value_params = ( + (VariableLengthUTF8(), "", np.str_("")), + (VariableLengthUTF8(), "hi", np.str_("hi")), + ) + # anything can become a string + invalid_scalar_params = (None,) + item_size_params = (VariableLengthUTF8(),) class TestFixedLengthUTF32(BaseTestZDType): diff --git a/tests/test_dtype_registry.py b/tests/test_dtype_registry.py index 60c6b5db01..f0946014fc 100644 --- a/tests/test_dtype_registry.py +++ b/tests/test_dtype_registry.py @@ -15,7 +15,6 @@ get_data_type_from_json, ) from zarr.core.dtype.common import unpack_dtype_json -from zarr.core.dtype.npy.string import _NUMPY_SUPPORTS_VLEN_STRING from zarr.dtype import ( # type: ignore[attr-defined] Bool, FixedLengthUTF32, @@ -76,7 +75,6 @@ def test_match_dtype( data_type_registry_fixture.register(wrapper_cls._zarr_v3_name, wrapper_cls) assert isinstance(data_type_registry_fixture.match_dtype(np.dtype(dtype_str)), wrapper_cls) - @pytest.mark.skipif(not _NUMPY_SUPPORTS_VLEN_STRING, reason="requires numpy with T dtype") @staticmethod def test_match_dtype_string_na_object_error( data_type_registry_fixture: DataTypeRegistry, From c0e2afac6e091ea4eaa06bfaad6855536f41bb9d Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 22 May 2026 18:07:38 +0200 Subject: [PATCH 328/468] fix: handle NaN fill_value in array metadata equality (#3999) Frozen dataclass __eq__ compared fill_value directly, so two identical metadata objects with a NaN fill value compared unequal (NaN != NaN under IEEE 754). Compare the JSON-serialized form instead, which treats matching NaN and infinite fill values as equal. Fixes #2929 Co-authored-by: Claude Opus 4.7 (1M context) --- changes/2929.bugfix.md | 3 ++ src/zarr/core/metadata/v2.py | 15 ++++++- src/zarr/core/metadata/v3.py | 13 +++++++ tests/test_metadata/test_v2.py | 54 ++++++++++++++++++++++++++ tests/test_metadata/test_v3.py | 71 +++++++++++++++++++++++++++++++++- 5 files changed, 154 insertions(+), 2 deletions(-) create mode 100644 changes/2929.bugfix.md diff --git a/changes/2929.bugfix.md b/changes/2929.bugfix.md new file mode 100644 index 0000000000..533a5f86c1 --- /dev/null +++ b/changes/2929.bugfix.md @@ -0,0 +1,3 @@ +Fix equality comparison of `ArrayV2Metadata` and `ArrayV3Metadata` objects with a +`NaN` fill value. Such objects are now compared by their JSON-serialized form, so two +otherwise-identical metadata objects with a `NaN` (or infinite) fill value compare equal. diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 8626d480a7..29ed496eb1 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -1,5 +1,6 @@ from __future__ import annotations +import json import warnings from collections.abc import Iterable, Sequence from functools import cached_property @@ -25,7 +26,6 @@ ZDType, ) -import json from dataclasses import dataclass, field, fields, replace import numpy as np @@ -239,6 +239,19 @@ def to_dict(self) -> dict[str, JSON]: return zarray_dict + def __eq__(self, other: object) -> bool: + # The default dataclass __eq__ compares fields directly, which is wrong for a NaN + # fill_value: NaN != NaN under IEEE 754. Comparing the JSON-serialized form instead + # treats matching NaN (and inf) fill values as equal. See issue #2929. + if not isinstance(other, ArrayV2Metadata): + return NotImplemented + return self.to_dict() == other.to_dict() + + def __hash__(self) -> int: + # Hash the JSON-serialized form to stay consistent with __eq__: equal metadata + # must hash equally, which a field-based hash violates for a NaN fill_value. + return hash(json.dumps(self.to_dict(), sort_keys=True)) + def get_chunk_spec( self, _chunk_coords: tuple[int, ...], array_config: ArrayConfig, prototype: BufferPrototype ) -> ArraySpec: diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index c794ee2e87..626c18eb72 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -697,6 +697,19 @@ def to_dict(self) -> dict[str, JSON]: out_dict["data_type"] = dtype_meta.to_json(zarr_format=3) # type: ignore[unreachable] return out_dict + def __eq__(self, other: object) -> bool: + # The default dataclass __eq__ compares fields directly, which is wrong for a NaN + # fill_value: NaN != NaN under IEEE 754. Comparing the JSON-serialized form instead + # treats matching NaN (and inf) fill values as equal. See issue #2929. + if not isinstance(other, ArrayV3Metadata): + return NotImplemented + return self.to_dict() == other.to_dict() + + def __hash__(self) -> int: + # Hash the JSON-serialized form to stay consistent with __eq__: equal metadata + # must hash equally, which a field-based hash violates for a NaN fill_value. + return hash(json.dumps(self.to_dict(), sort_keys=True)) + def update_shape(self, shape: tuple[int, ...]) -> Self: chunk_grid = self.chunk_grid if isinstance(chunk_grid, RectilinearChunkGridMetadata): diff --git a/tests/test_metadata/test_v2.py b/tests/test_metadata/test_v2.py index 8c3082e924..d1a1ca00b4 100644 --- a/tests/test_metadata/test_v2.py +++ b/tests/test_metadata/test_v2.py @@ -308,6 +308,60 @@ def test_from_dict_extra_fields() -> None: assert result == expected +def test_eq_nan_fill_value() -> None: + """Two metadata objects with an identical NaN fill_value compare equal. + + NaN is not equal to itself under IEEE 754, so the default dataclass __eq__ + reports two otherwise-identical metadata objects as unequal. Metadata + equality must treat matching NaN fill values as equal (see issue #2929). + """ + a = ArrayV2Metadata( + shape=(8,), dtype=Float64(), chunks=(8,), fill_value=np.float64("nan"), order="C" + ) + b = ArrayV2Metadata( + shape=(8,), dtype=Float64(), chunks=(8,), fill_value=np.float64("nan"), order="C" + ) + assert a == b + + +def test_eq_distinct_fill_value() -> None: + """Metadata objects that differ only in fill_value do not compare equal.""" + a = ArrayV2Metadata(shape=(8,), dtype=Float64(), chunks=(8,), fill_value=0.0, order="C") + b = ArrayV2Metadata(shape=(8,), dtype=Float64(), chunks=(8,), fill_value=1.0, order="C") + assert a != b + + +@pytest.mark.parametrize("fill_value", [np.float64("inf"), np.float64("-inf")]) +def test_eq_inf_fill_value(fill_value: np.float64) -> None: + """Two metadata objects with an identical infinite fill_value compare equal.""" + a = ArrayV2Metadata(shape=(8,), dtype=Float64(), chunks=(8,), fill_value=fill_value, order="C") + b = ArrayV2Metadata(shape=(8,), dtype=Float64(), chunks=(8,), fill_value=fill_value, order="C") + assert a == b + + +def test_hash_consistent_with_eq_nan_fill_value() -> None: + """Equal metadata objects with a NaN fill_value hash equal. + + NaN hashes by identity, so a field-based hash would break the + ``a == b implies hash(a) == hash(b)`` invariant for objects that compare + equal under the to_dict-based __eq__. + """ + a = ArrayV2Metadata( + shape=(8,), dtype=Float64(), chunks=(8,), fill_value=np.float64("nan"), order="C" + ) + b = ArrayV2Metadata( + shape=(8,), dtype=Float64(), chunks=(8,), fill_value=np.float64("nan"), order="C" + ) + assert a == b + assert hash(a) == hash(b) + + +def test_eq_non_metadata() -> None: + """Comparison against a non-metadata object returns False rather than erroring.""" + a = ArrayV2Metadata(shape=(8,), dtype=Float64(), chunks=(8,), fill_value=0.0, order="C") + assert a != object() + + def test_zstd_checksum() -> None: compressor_config: dict[str, JSON] = {"id": "zstd", "level": 5, "checksum": False} arr = zarr.create_array( diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index 07e06cd3fe..f8f8fc56ff 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -13,8 +13,9 @@ from zarr.core.buffer import default_buffer_prototype from zarr.core.chunk_grids import is_regular_1d, is_regular_nd from zarr.core.config import config -from zarr.core.dtype import UInt8 +from zarr.core.dtype import Float64, UInt8 from zarr.core.group import GroupMetadata, parse_node_type +from zarr.core.metadata.v2 import ArrayV2Metadata from zarr.core.metadata.v3 import ( ARRAY_METADATA_KEYS, ArrayMetadataJSON_V3, @@ -335,6 +336,74 @@ def test_init_extra_fields_collision() -> None: ) +# --------------------------------------------------------------------------- +# Equality +# --------------------------------------------------------------------------- + + +def test_eq_nan_fill_value() -> None: + """Two metadata objects with an identical NaN fill_value compare equal. + + NaN is not equal to itself under IEEE 754, so the default dataclass __eq__ + reports two otherwise-identical metadata objects as unequal. Metadata + equality must treat matching NaN fill values as equal (see issue #2929). + """ + a = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value="NaN")) # type: ignore[arg-type] + b = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value="NaN")) # type: ignore[arg-type] + assert a == b + + +def test_eq_distinct_fill_value() -> None: + """Metadata objects that differ only in fill_value do not compare equal.""" + a = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value=0.0)) # type: ignore[arg-type] + b = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value=1.0)) # type: ignore[arg-type] + assert a != b + + +@pytest.mark.parametrize("fill_value", ["Infinity", "-Infinity"]) +def test_eq_inf_fill_value(fill_value: str) -> None: + """Two metadata objects with an identical infinite fill_value compare equal.""" + a = ArrayV3Metadata.from_dict( + minimal_metadata_dict_v3(data_type="float64", fill_value=fill_value) # type: ignore[arg-type] + ) + b = ArrayV3Metadata.from_dict( + minimal_metadata_dict_v3(data_type="float64", fill_value=fill_value) # type: ignore[arg-type] + ) + assert a == b + + +def test_hash_consistent_with_eq_nan_fill_value() -> None: + """Equal metadata objects with a NaN fill_value hash equal. + + NaN hashes by identity, so a field-based hash would break the + ``a == b implies hash(a) == hash(b)`` invariant for objects that compare + equal under the to_dict-based __eq__. + """ + a = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value="NaN")) # type: ignore[arg-type] + b = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value="NaN")) # type: ignore[arg-type] + assert a == b + assert hash(a) == hash(b) + + +def test_eq_non_metadata() -> None: + """Comparison against a non-metadata object returns False rather than erroring.""" + a = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value=0.0)) # type: ignore[arg-type] + assert a != object() + + +def test_eq_across_zarr_formats() -> None: + """A v2 and v3 metadata describing the same array do not compare equal. + + Each __eq__ guards on its own concrete type and returns NotImplemented + otherwise, so the two versions are never equal even when they describe the + same array. + """ + v3 = ArrayV3Metadata.from_dict(minimal_metadata_dict_v3(data_type="float64", fill_value=0.0)) # type: ignore[arg-type] + v2 = ArrayV2Metadata(shape=(4, 4), dtype=Float64(), chunks=(4, 4), fill_value=0.0, order="C") + assert v2 != v3 + assert v3 != v2 + + # --------------------------------------------------------------------------- # JSON indent # --------------------------------------------------------------------------- From 1cda98117765f8de2b9dfe9a116969c6b529ea50 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Tue, 26 May 2026 16:23:30 -0400 Subject: [PATCH 329/468] Run doctests via pytest and fix broken doctests. (#4000) * Run doctests via pytest and fix broken doctests. Fixes #3498 * Add changes file for PR * Ignore cli sources for doctests * Prefer store={} to MemoryStore in doctests --- changes/4000.misc.md | 1 + pyproject.toml | 5 +- src/zarr/abc/store.py | 47 ++- src/zarr/api/synchronous.py | 76 ++-- src/zarr/codecs/numcodecs/_codecs.py | 16 +- src/zarr/core/array.py | 559 ++++++++++++++------------- src/zarr/core/group.py | 132 +++---- src/zarr/storage/_local.py | 54 ++- src/zarr/storage/_memory.py | 53 ++- 9 files changed, 488 insertions(+), 455 deletions(-) create mode 100644 changes/4000.misc.md diff --git a/changes/4000.misc.md b/changes/4000.misc.md new file mode 100644 index 0000000000..17d48d3016 --- /dev/null +++ b/changes/4000.misc.md @@ -0,0 +1 @@ +Run all doctests via pytest and fix all broken doctests. diff --git a/pyproject.toml b/pyproject.toml index 837f2f24ab..e342e8305c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -414,7 +414,7 @@ ignore_errors = true [tool.pytest.ini_options] minversion = "7" -testpaths = ["tests", "docs/user-guide"] +testpaths = ["src", "tests", "docs/user-guide"] log_cli_level = "INFO" log_level = "INFO" xfail_strict = true @@ -430,6 +430,9 @@ addopts = [ "--benchmark-disable", # benchmark routines run as tests without benchmarking instrumentation "--durations", "10", "-ra", "--strict-config", "--strict-markers", + "--doctest-modules", + "--ignore=tests/test_regression/scripts", + "--ignore=src/zarr/_cli", ] filterwarnings = [ "error", diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 3247649f10..ab58acf59f 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -256,12 +256,20 @@ async def _get_bytes( Examples -------- - >>> store = await MemoryStore.open() - >>> await store.set("data", Buffer.from_bytes(b"hello world")) - >>> data = await store.get_bytes("data", prototype=default_buffer_prototype()) - >>> print(data) + >>> async def example(): + ... from zarr.core.buffer.cpu import Buffer + ... from zarr.storage import MemoryStore + ... + ... store = await MemoryStore.open() + ... await store.set("data", Buffer.from_bytes(b"hello world")) + ... # No need to specify prototype for MemoryStore + ... return await store._get_bytes("data") + + >>> import asyncio + >>> asyncio.run(example()) b'hello world' """ + buffer = await self.get(key, prototype, byte_range) if buffer is None: raise FileNotFoundError(key) @@ -309,10 +317,11 @@ def _get_bytes_sync( Examples -------- + >>> from zarr.core.buffer.cpu import Buffer + >>> from zarr.storage import MemoryStore >>> store = MemoryStore() - >>> await store.set("data", Buffer.from_bytes(b"hello world")) - >>> data = store.get_bytes_sync("data", prototype=default_buffer_prototype()) - >>> print(data) + >>> store.set_sync("data", Buffer.from_bytes(b"hello world")) + >>> store._get_bytes_sync("data") # No need to specify prototype for MemoryStore b'hello world' """ @@ -358,11 +367,18 @@ async def _get_json( Examples -------- - >>> store = await MemoryStore.open() - >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> data = await store.get_json("zarr.json", prototype=default_buffer_prototype()) - >>> print(data) + >>> async def example(): + ... from zarr.core.buffer.cpu import Buffer + ... from zarr.storage import MemoryStore + ... + ... store = await MemoryStore.open() + ... metadata = {"zarr_format": 3, "node_type": "array"} + ... await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + ... # No need to specify prototype for MemoryStore + ... return await store._get_json("zarr.json") + + >>> import asyncio + >>> asyncio.run(example()) {'zarr_format': 3, 'node_type': 'array'} """ @@ -414,11 +430,12 @@ def _get_json_sync( Examples -------- + >>> from zarr.core.buffer.cpu import Buffer + >>> from zarr.storage import MemoryStore >>> store = MemoryStore() >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> data = store.get_json_sync("zarr.json", prototype=default_buffer_prototype()) - >>> print(data) + >>> store.set_sync("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> store._get_json_sync("zarr.json") # No need to specify prototype for MemoryStore {'zarr_format': 3, 'node_type': 'array'} """ diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 97d460a183..8386427b3f 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -1126,63 +1126,45 @@ def from_array( -------- Create an array from an existing Array: - ```python - import zarr - store = zarr.storage.MemoryStore() - store2 = zarr.storage.LocalStore('example_from_array.zarr') - arr = zarr.create_array( - store=store, - shape=(100,100), - chunks=(10,10), - dtype='int32', - fill_value=0) - arr2 = zarr.from_array(store2, data=arr, overwrite=True) - # - ``` + >>> import asyncio + >>> import zarr + >>> store = zarr.storage.LocalStore("example_from_array.zarr") + >>> arr = zarr.create_array( + ... store={}, + ... shape=(100,100), + ... chunks=(10,10), + ... dtype="int32", + ... fill_value=0 + ... ) + >>> arr2 = zarr.from_array(store, data=arr, overwrite=True) + >>> arr2 + + >>> asyncio.run(store.clear()) # Remove files generated by test Create an array from an existing NumPy array: - ```python - import zarr - import numpy as np - arr3 = zarr.from_array( - zarr.storage.MemoryStore(), - data=np.arange(10000, dtype='i4').reshape(100, 100), - ) - # - ``` + >>> import numpy as np + >>> zarr.from_array({}, data=np.arange(10000, dtype="i4").reshape(100, 100)) + Create an array from any array-like object: - ```python - import zarr - arr4 = zarr.from_array( - zarr.storage.MemoryStore(), - data=[[1, 2], [3, 4]], - ) - # - arr4[...] - # array([[1, 2],[3, 4]]) - ``` + >>> arr3 = zarr.from_array({}, data=[[1, 2], [3, 4]]) + >>> arr3 + + >>> arr3[...] + array([[1, 2], [3, 4]]) Create an array from an existing Array without copying the data: - ```python - import zarr - arr4 = zarr.from_array( - zarr.storage.MemoryStore(), - data=[[1, 2], [3, 4]], - ) - arr5 = zarr.from_array( - zarr.storage.MemoryStore(), - data=arr4, - write_data=False, - ) - # - arr5[...] - # array([[0, 0],[0, 0]]) - ``` + >>> arr4 = zarr.from_array({}, data=[[1, 2], [3, 4]]) + >>> arr5 = zarr.from_array({}, data=arr4, write_data=False) + >>> arr5 + + >>> arr5[...] + array([[0, 0], [0, 0]]) """ + return Array( sync( zarr.core.array.from_array( diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py index 06c085ad2a..1be1381a08 100644 --- a/src/zarr/codecs/numcodecs/_codecs.py +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -8,14 +8,16 @@ import zarr import zarr.codecs.numcodecs as numcodecs +store = zarr.storage.MemoryStore() array = zarr.create_array( - store="data_numcodecs.zarr", - shape=(1024, 1024), - chunks=(64, 64), - dtype="uint32", - filters=[numcodecs.Delta(dtype="uint32")], - compressors=[numcodecs.BZ2(level=5)], - overwrite=True) + store=store, + shape=(1024, 1024), + chunks=(64, 64), + dtype="uint32", + filters=[numcodecs.Delta(dtype="uint32")], + compressors=[numcodecs.BZ2(level=5)], + overwrite=True +) array[:] = np.arange(np.prod(array.shape), dtype=array.dtype).reshape(*array.shape) ``` diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 4e9bd6e12f..366c19bb0c 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -847,10 +847,11 @@ def read_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Examples -------- - >>> arr = zarr.create_array(store, shape=(100, 80), chunks=(30, 40)) + >>> arr = zarr.create_array({}, dtype="i1", shape=(100, 80), chunks=(30, 40)) >>> arr.read_chunk_sizes ((30, 30, 30, 10), (40, 40)) """ + from zarr.codecs.sharding import ShardingCodec codecs: tuple[Codec, ...] = getattr(self.metadata, "codecs", ()) @@ -876,10 +877,12 @@ def write_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Examples -------- - >>> arr = zarr.create_array(store, shape=(100, 80), chunks=(30, 40)) + >>> import zarr.storage + >>> arr = zarr.create_array({}, dtype="i1", shape=(100, 80), chunks=(30, 40)) >>> arr.write_chunk_sizes ((30, 30, 30, 10), (40, 40)) """ + return self._chunk_grid.chunk_sizes @property @@ -1453,26 +1456,25 @@ async def getitem( Examples -------- - ```python - import asyncio - import zarr.api.asynchronous - - async def example(): - store = zarr.storage.MemoryStore() - async_arr = await zarr.api.asynchronous.create_array( - store=store, - shape=(100,100), - chunks=(10,10), - dtype='i4', - fill_value=0) - result = await async_arr.getitem((0,1)) - print(result) - #> 0 - return result - - value = asyncio.run(example()) - ``` + >>> async def example(): + ... import zarr.api.asynchronous + ... import zarr.storage + ... + ... async_arr = await zarr.api.asynchronous.create_array( + ... store={}, + ... shape=(100,100), + ... chunks=(10,10), + ... dtype="i4", + ... fill_value=0, + ... ) + ... + ... return await async_arr.getitem((0, 1)) + + >>> import asyncio + >>> asyncio.run(example()) + np.int32(0) """ + return await _getitem( self.store_path, self.metadata, @@ -1730,20 +1732,25 @@ def info(self) -> Any: Examples -------- - - >>> arr = await zarr.api.asynchronous.create( - ... path="array", shape=(3, 4, 5), chunks=(2, 2, 2)) + >>> import asyncio + >>> arr = asyncio.run( + ... zarr.api.asynchronous.create( + ... path="array", shape=(3, 4, 5), chunks=(2, 2, 2) + ... ) ... ) >>> arr.info Type : Array Zarr format : 3 - Data type : DataType.float64 + Data type : Float64(endianness='little') + Fill value : 0.0 Shape : (3, 4, 5) Chunk shape : (2, 2, 2) Order : C Read-only : False Store type : MemoryStore - Codecs : [{'endian': }] + Filters : () + Serializer : BytesCodec(endian=) + Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 480 """ return self._info() @@ -2002,7 +2009,8 @@ def read_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Examples -------- - >>> arr = zarr.open_array(store) + >>> import zarr + >>> arr = zarr.create_array({}, dtype="i1", shape=(100, 80), chunks=(30, 40)) >>> arr.read_chunk_sizes ((30, 30, 30, 10), (40, 40)) """ @@ -2025,7 +2033,8 @@ def write_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Examples -------- - >>> arr = zarr.open_array(store) + >>> import zarr + >>> arr = zarr.create_array({}, dtype="i1", shape=(100, 80), chunks=(30, 40)) >>> arr.write_chunk_sizes ((30, 30, 30, 10), (40, 40)) """ @@ -2255,7 +2264,7 @@ def nchunks_initialized(self) -> int: Examples -------- - >>> arr = zarr.create_array(store={}, shape=(10,), chunks=(1,), shards=(2,)) + >>> arr = zarr.create_array(store={}, dtype="i1", shape=(10,), chunks=(1,), shards=(2,)) >>> arr.nchunks_initialized 0 >>> arr[:5] = 1 @@ -2277,11 +2286,11 @@ def _nshards_initialized(self) -> int: Examples -------- - >>> arr = await zarr.create(shape=(10,), chunks=(2,)) + >>> arr = zarr.create(shape=(10,), chunks=(2,)) >>> arr._nshards_initialized 0 >>> arr[:5] = 1 - >>> arr._nshard_initialized + >>> arr._nshards_initialized 3 """ return sync(self.async_array._nshards_initialized()) @@ -2449,66 +2458,66 @@ def __getitem__(self, selection: Selection) -> NDArrayLikeOrScalar: Examples -------- - Setup a 1-dimensional array:: + Setup a 1-dimensional array: >>> import zarr >>> import numpy as np >>> data = np.arange(100, dtype="uint16") >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=(10,), - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=(10,), + ... dtype=data.dtype, + ... ) >>> z[:] = data - Retrieve a single item:: + Retrieve a single item: >>> z[5] - 5 + array(5, dtype=uint16) - Retrieve a region via slicing:: + Retrieve a region via slicing: >>> z[:5] - array([0, 1, 2, 3, 4]) + array([0, 1, 2, 3, 4], dtype=uint16) >>> z[-5:] - array([95, 96, 97, 98, 99]) + array([95, 96, 97, 98, 99], dtype=uint16) >>> z[5:10] - array([5, 6, 7, 8, 9]) + array([5, 6, 7, 8, 9], dtype=uint16) >>> z[5:10:2] - array([5, 7, 9]) + array([5, 7, 9], dtype=uint16) >>> z[::2] - array([ 0, 2, 4, ..., 94, 96, 98]) + array([ 0, 2, 4, ..., 94, 96, 98], dtype=uint16) - Load the entire array into memory:: + Load the entire array into memory: >>> z[...] - array([ 0, 1, 2, ..., 97, 98, 99]) + array([ 0, 1, 2, ..., 97, 98, 99], dtype=uint16) - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> data = np.arange(100, dtype="uint16").reshape(10, 10) >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=(10, 10), - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=(10, 10), + ... dtype=data.dtype, + ... ) >>> z[:] = data - Retrieve an item:: + Retrieve an item: >>> z[2, 2] - 22 + array(22, dtype=uint16) - Retrieve a region via slicing:: + Retrieve a region via slicing: >>> z[1:3, 1:3] array([[11, 12], - [21, 22]]) + [21, 22]], dtype=uint16) >>> z[1:3, :] array([[10, 11, 12, 13, 14, 15, 16, 17, 18, 19], - [20, 21, 22, 23, 24, 25, 26, 27, 28, 29]]) + [20, 21, 22, 23, 24, 25, 26, 27, 28, 29]], dtype=uint16) >>> z[:, 1:3] array([[ 1, 2], [11, 12], @@ -2519,19 +2528,19 @@ def __getitem__(self, selection: Selection) -> NDArrayLikeOrScalar: [61, 62], [71, 72], [81, 82], - [91, 92]]) + [91, 92]], dtype=uint16) >>> z[0:5:2, 0:5:2] array([[ 0, 2, 4], [20, 22, 24], - [40, 42, 44]]) + [40, 42, 44]], dtype=uint16) >>> z[::2, ::2] array([[ 0, 2, 4, 6, 8], [20, 22, 24, 26, 28], [40, 42, 44, 46, 48], [60, 62, 64, 66, 68], - [80, 82, 84, 86, 88]]) + [80, 82, 84, 86, 88]], dtype=uint16) - Load the entire array into memory:: + Load the entire array into memory: >>> z[...] array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9], @@ -2543,7 +2552,7 @@ def __getitem__(self, selection: Selection) -> NDArrayLikeOrScalar: [60, 61, 62, 63, 64, 65, 66, 67, 68, 69], [70, 71, 72, 73, 74, 75, 76, 77, 78, 79], [80, 81, 82, 83, 84, 85, 86, 87, 88, 89], - [90, 91, 92, 93, 94, 95, 96, 97, 98, 99]]) + [90, 91, 92, 93, 94, 95, 96, 97, 98, 99]], dtype=uint16) Notes ----- @@ -2576,8 +2585,8 @@ def __getitem__(self, selection: Selection) -> NDArrayLikeOrScalar: [get_orthogonal_selection][zarr.Array.get_orthogonal_selection], [set_orthogonal_selection][zarr.Array.set_orthogonal_selection], [get_block_selection][zarr.Array.get_block_selection], [set_block_selection][zarr.Array.set_block_selection], [vindex][zarr.Array.vindex], [oindex][zarr.Array.oindex], [blocks][zarr.Array.blocks], [__setitem__][zarr.Array.__setitem__] - """ + fields, pure_selection = pop_fields(selection) if is_pure_fancy_indexing(pure_selection, self.ndim): return self.vindex[cast("CoordinateSelection | MaskSelection", selection)] @@ -2599,43 +2608,43 @@ def __setitem__(self, selection: Selection, value: npt.ArrayLike) -> None: Examples -------- - Setup a 1-dimensional array:: + Setup a 1-dimensional array: >>> import zarr >>> z = zarr.zeros( - >>> shape=(100,), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(5,), - >>> dtype="i4", - >>> ) + ... shape=(100,), + ... store={}, + ... chunk_shape=(5,), + ... dtype="i4", + ... ) - Set all array elements to the same scalar value:: + Set all array elements to the same scalar value: >>> z[...] = 42 >>> z[...] - array([42, 42, 42, ..., 42, 42, 42]) + array([42, 42, 42, ..., 42, 42, 42], dtype=int32) - Set a portion of the array:: + Set a portion of the array: >>> z[:10] = np.arange(10) >>> z[-10:] = np.arange(10)[::-1] >>> z[...] - array([ 0, 1, 2, ..., 2, 1, 0]) + array([ 0, 1, 2, ..., 2, 1, 0], dtype=int32) - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> z = zarr.zeros( - >>> shape=(5, 5), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(5, 5), - >>> dtype="i4", - >>> ) + ... shape=(5, 5), + ... store={}, + ... chunk_shape=(5, 5), + ... dtype="i4", + ... ) - Set all array elements to the same scalar value:: + Set all array elements to the same scalar value: >>> z[...] = 42 - Set a portion of the array:: + Set a portion of the array: >>> z[0, :] = np.arange(z.shape[1]) >>> z[:, 0] = np.arange(z.shape[0]) @@ -2644,7 +2653,7 @@ def __setitem__(self, selection: Selection, value: npt.ArrayLike) -> None: [ 1, 42, 42, 42, 42], [ 2, 42, 42, 42, 42], [ 3, 42, 42, 42, 42], - [ 4, 42, 42, 42, 42]]) + [ 4, 42, 42, 42, 42]], dtype=int32) Notes ----- @@ -2711,8 +2720,8 @@ def get_basic_selection( Parameters ---------- - selection : tuple - A tuple specifying the requested item or region for each dimension of the + selection : BasicSelection + A selection specifying the requested item or region for each dimension of the array. May be any combination of int and/or slice or ellipsis for multidimensional arrays. out : NDBuffer, optional If given, load the selected data directly into this buffer. @@ -2729,67 +2738,67 @@ def get_basic_selection( Examples -------- - Setup a 1-dimensional array:: + Setup a 1-dimensional array: >>> import zarr >>> import numpy as np >>> data = np.arange(100, dtype="uint16") >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=(3,), - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=(3,), + ... dtype=data.dtype, + ... ) >>> z[:] = data - Retrieve a single item:: + Retrieve a single item: >>> z.get_basic_selection(5) - 5 + np.uint16(5) - Retrieve a region via slicing:: + Retrieve a region via slicing: >>> z.get_basic_selection(slice(5)) - array([0, 1, 2, 3, 4]) + array([0, 1, 2, 3, 4], dtype=uint16) >>> z.get_basic_selection(slice(-5, None)) - array([95, 96, 97, 98, 99]) + array([95, 96, 97, 98, 99], dtype=uint16) >>> z.get_basic_selection(slice(5, 10)) - array([5, 6, 7, 8, 9]) + array([5, 6, 7, 8, 9], dtype=uint16) >>> z.get_basic_selection(slice(5, 10, 2)) - array([5, 7, 9]) + array([5, 7, 9], dtype=uint16) >>> z.get_basic_selection(slice(None, None, 2)) - array([ 0, 2, 4, ..., 94, 96, 98]) + array([ 0, 2, 4, ..., 94, 96, 98], dtype=uint16) - Setup a 3-dimensional array:: + Setup a 3-dimensional array: >>> data = np.arange(1000).reshape(10, 10, 10) >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=(5, 5, 5), - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=(5, 5, 5), + ... dtype=data.dtype, + ... ) >>> z[:] = data - Retrieve an item:: + Retrieve an item: >>> z.get_basic_selection((1, 2, 3)) - 123 + np.int64(123) - Retrieve a region via slicing and Ellipsis:: + Retrieve a region via slicing and Ellipsis: >>> z.get_basic_selection((slice(1, 3), slice(1, 3), 0)) array([[110, 120], [210, 220]]) - >>> z.get_basic_selection(0, (slice(1, 3), slice(None))) + >>> z.get_basic_selection((0, slice(1, 3), slice(None))) array([[10, 11, 12, 13, 14, 15, 16, 17, 18, 19], [20, 21, 22, 23, 24, 25, 26, 27, 28, 29]]) - >>> z.get_basic_selection((..., 5)) - array([[ 2 12 22 32 42 52 62 72 82 92] - [102 112 122 132 142 152 162 172 182 192] + >>> z.get_basic_selection((..., 2)) + array([[ 2, 12, 22, 32, 42, 52, 62, 72, 82, 92], + [102, 112, 122, 132, 142, 152, 162, 172, 182, 192], ... - [802 812 822 832 842 852 862 872 882 892] - [902 912 922 932 942 952 962 972 982 992]] + [802, 812, 822, 832, 842, 852, 862, 872, 882, 892], + [902, 912, 922, 932, 942, 952, 962, 972, 982, 992]]) Notes ----- @@ -2856,43 +2865,43 @@ def set_basic_selection( Examples -------- - Setup a 1-dimensional array:: + Setup a 1-dimensional array: >>> import zarr >>> z = zarr.zeros( - >>> shape=(100,), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(100,), - >>> dtype="i4", - >>> ) + ... shape=(100,), + ... store={}, + ... chunk_shape=(100,), + ... dtype="i4", + ... ) - Set all array elements to the same scalar value:: + Set all array elements to the same scalar value: >>> z.set_basic_selection(..., 42) >>> z[...] - array([42, 42, 42, ..., 42, 42, 42]) + array([42, 42, 42, ..., 42, 42, 42], dtype=int32) - Set a portion of the array:: + Set a portion of the array: >>> z.set_basic_selection(slice(10), np.arange(10)) >>> z.set_basic_selection(slice(-10, None), np.arange(10)[::-1]) >>> z[...] - array([ 0, 1, 2, ..., 2, 1, 0]) + array([ 0, 1, 2, ..., 2, 1, 0], dtype=int32) - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> z = zarr.zeros( - >>> shape=(5, 5), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(5, 5), - >>> dtype="i4", - >>> ) + ... shape=(5, 5), + ... store={}, + ... chunk_shape=(5, 5), + ... dtype="i4", + ... ) - Set all array elements to the same scalar value:: + Set all array elements to the same scalar value: >>> z.set_basic_selection(..., 42) - Set a portion of the array:: + Set a portion of the array: >>> z.set_basic_selection((0, slice(None)), np.arange(z.shape[1])) >>> z.set_basic_selection((slice(None), 0), np.arange(z.shape[0])) @@ -2901,7 +2910,7 @@ def set_basic_selection( [ 1, 42, 42, 42, 42], [ 2, 42, 42, 42, 42], [ 3, 42, 42, 42, 42], - [ 4, 42, 42, 42, 42]]) + [ 4, 42, 42, 42, 42]], dtype=int32) Notes ----- @@ -2967,21 +2976,21 @@ def get_orthogonal_selection( Examples -------- - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> import zarr >>> import numpy as np >>> data = np.arange(100).reshape(10, 10) >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=data.shape, - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=data.shape, + ... dtype=data.dtype, + ... ) >>> z[:] = data Retrieve rows and columns via any combination of int, slice, integer array and/or - Boolean array:: + Boolean array: >>> z.get_orthogonal_selection(([1, 4], slice(None))) array([[10, 11, 12, 13, 14, 15, 16, 17, 18, 19], @@ -3008,7 +3017,7 @@ def get_orthogonal_selection( [41, 44]]) For convenience, the orthogonal selection functionality is also available via the - `oindex` property, e.g.:: + `oindex` property, e.g.: >>> z.oindex[[1, 4], :] array([[10, 11, 12, 13, 14, 15, 16, 17, 18, 19], @@ -3091,18 +3100,18 @@ def set_orthogonal_selection( Examples -------- - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> import zarr >>> z = zarr.zeros( - >>> shape=(5, 5), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(5, 5), - >>> dtype="i4", - >>> ) + ... shape=(5, 5), + ... store={}, + ... chunk_shape=(5, 5), + ... dtype="i4", + ... ) - Set data for a selection of rows:: + Set data for a selection of rows: >>> z.set_orthogonal_selection(([1, 4], slice(None)), 1) >>> z[...] @@ -3110,9 +3119,9 @@ def set_orthogonal_selection( [1, 1, 1, 1, 1], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], - [1, 1, 1, 1, 1]]) + [1, 1, 1, 1, 1]], dtype=int32) - Set data for a selection of columns:: + Set data for a selection of columns: >>> z.set_orthogonal_selection((slice(None), [1, 4]), 2) >>> z[...] @@ -3120,9 +3129,9 @@ def set_orthogonal_selection( [1, 2, 1, 1, 2], [0, 2, 0, 0, 2], [0, 2, 0, 0, 2], - [1, 2, 1, 1, 2]]) + [1, 2, 1, 1, 2]], dtype=int32) - Set data for a selection of rows and columns:: + Set data for a selection of rows and columns: >>> z.set_orthogonal_selection(([1, 4], [1, 4]), 3) >>> z[...] @@ -3130,9 +3139,9 @@ def set_orthogonal_selection( [1, 3, 1, 1, 3], [0, 2, 0, 0, 2], [0, 2, 0, 0, 2], - [1, 3, 1, 1, 3]]) + [1, 3, 1, 1, 3]], dtype=int32) - Set data from a 2D array:: + Set data from a 2D array: >>> values = np.arange(10).reshape(2, 5) >>> z.set_orthogonal_selection(([0, 3], ...), values) @@ -3141,10 +3150,9 @@ def set_orthogonal_selection( [1, 3, 1, 1, 3], [0, 2, 0, 0, 2], [5, 6, 7, 8, 9], - [1, 3, 1, 1, 3]]) + [1, 3, 1, 1, 3]], dtype=int32) - For convenience, this functionality is also available via the `oindex` property. - E.g.:: + For convenience, this functionality is also available via the `oindex` property: >>> z.oindex[[1, 4], [1, 4]] = 4 >>> z[...] @@ -3152,7 +3160,7 @@ def set_orthogonal_selection( [1, 4, 1, 1, 4], [0, 2, 0, 0, 2], [5, 6, 7, 8, 9], - [1, 4, 1, 1, 4]]) + [1, 4, 1, 1, 4]], dtype=int32) Notes ----- @@ -3214,20 +3222,20 @@ def get_mask_selection( Examples -------- - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> import zarr >>> import numpy as np >>> data = np.arange(100).reshape(10, 10) >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=data.shape, - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=data.shape, + ... dtype=data.dtype, + ... ) >>> z[:] = data - Retrieve items by specifying a mask:: + Retrieve items by specifying a mask: >>> sel = np.zeros_like(z, dtype=bool) >>> sel[1, 1] = True @@ -3236,7 +3244,7 @@ def get_mask_selection( array([11, 44]) For convenience, the mask selection functionality is also available via the - `vindex` property, e.g.:: + `vindex` property: >>> z.vindex[sel] array([11, 44]) @@ -3297,17 +3305,17 @@ def set_mask_selection( Examples -------- - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> import zarr >>> z = zarr.zeros( - >>> shape=(5, 5), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(5, 5), - >>> dtype="i4", - >>> ) + ... shape=(5, 5), + ... store={}, + ... chunk_shape=(5, 5), + ... dtype="i4", + ... ) - Set data for a selection of items:: + Set data for a selection of items: >>> sel = np.zeros_like(z, dtype=bool) >>> sel[1, 1] = True @@ -3318,10 +3326,9 @@ def set_mask_selection( [0, 1, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], - [0, 0, 0, 0, 1]]) + [0, 0, 0, 0, 1]], dtype=int32) - For convenience, this functionality is also available via the `vindex` property. - E.g.:: + For convenience, this functionality is also available via the `vindex` property: >>> z.vindex[sel] = 2 >>> z[...] @@ -3329,7 +3336,7 @@ def set_mask_selection( [0, 2, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], - [0, 0, 0, 0, 2]]) + [0, 0, 0, 0, 2]], dtype=int32) Notes ----- @@ -3388,29 +3395,29 @@ def get_coordinate_selection( Examples -------- - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> import zarr >>> import numpy as np >>> data = np.arange(0, 100, dtype="uint16").reshape((10, 10)) >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=(3, 3), - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=(3, 3), + ... dtype=data.dtype, + ... ) >>> z[:] = data - Retrieve items by specifying their coordinates:: + Retrieve items by specifying their coordinates: >>> z.get_coordinate_selection(([1, 4], [1, 4])) - array([11, 44]) + array([11, 44], dtype=uint16) For convenience, the coordinate selection functionality is also available via the - `vindex` property, e.g.:: + `vindex` property: >>> z.vindex[[1, 4], [1, 4]] - array([11, 44]) + array([11, 44], dtype=uint16) Notes ----- @@ -3478,17 +3485,17 @@ def set_coordinate_selection( Examples -------- - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> import zarr >>> z = zarr.zeros( - >>> shape=(5, 5), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(5, 5), - >>> dtype="i4", - >>> ) + ... shape=(5, 5), + ... store={}, + ... chunk_shape=(5, 5), + ... dtype="i4", + ... ) - Set data for a selection of items:: + Set data for a selection of items: >>> z.set_coordinate_selection(([1, 4], [1, 4]), 1) >>> z[...] @@ -3496,10 +3503,9 @@ def set_coordinate_selection( [0, 1, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], - [0, 0, 0, 0, 1]]) + [0, 0, 0, 0, 1]], dtype=int32) - For convenience, this functionality is also available via the `vindex` property. - E.g.:: + For convenience, this functionality is also available via the `vindex` property: >>> z.vindex[[1, 4], [1, 4]] = 2 >>> z[...] @@ -3507,7 +3513,7 @@ def set_coordinate_selection( [0, 2, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], - [0, 0, 0, 0, 2]]) + [0, 0, 0, 0, 2]], dtype=int32) Notes ----- @@ -3590,40 +3596,40 @@ def get_block_selection( Examples -------- - Setup a 2-dimensional array:: + Setup a 2-dimensional array: >>> import zarr >>> import numpy as np >>> data = np.arange(0, 100, dtype="uint16").reshape((10, 10)) >>> z = zarr.create_array( - >>> StorePath(MemoryStore(mode="w")), - >>> shape=data.shape, - >>> chunks=(3, 3), - >>> dtype=data.dtype, - >>> ) + ... {}, + ... shape=data.shape, + ... chunks=(3, 3), + ... dtype=data.dtype, + ... ) >>> z[:] = data - Retrieve items by specifying their block coordinates:: + Retrieve items by specifying their block coordinates: >>> z.get_block_selection((1, slice(None))) array([[30, 31, 32, 33, 34, 35, 36, 37, 38, 39], [40, 41, 42, 43, 44, 45, 46, 47, 48, 49], - [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]]) + [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]], dtype=uint16) - Which is equivalent to:: + Which is equivalent to: >>> z[3:6, :] array([[30, 31, 32, 33, 34, 35, 36, 37, 38, 39], [40, 41, 42, 43, 44, 45, 46, 47, 48, 49], - [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]]) + [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]], dtype=uint16) For convenience, the block selection functionality is also available via the - `blocks` property, e.g.:: + `blocks` property: >>> z.blocks[1] array([[30, 31, 32, 33, 34, 35, 36, 37, 38, 39], [40, 41, 42, 43, 44, 45, 46, 47, 48, 49], - [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]]) + [50, 51, 52, 53, 54, 55, 56, 57, 58, 59]], dtype=uint16) Notes ----- @@ -3633,13 +3639,12 @@ def get_block_selection( Slices are supported. However, only with a step size of one. - Block index arrays may be multidimensional to index multidimensional arrays. - For example:: + Block index arrays may be multidimensional to index multidimensional arrays: >>> z.blocks[0, 1:3] array([[ 3, 4, 5, 6, 7, 8], [13, 14, 15, 16, 17, 18], - [23, 24, 25, 26, 27, 28]]) + [23, 24, 25, 26, 27, 28]], dtype=uint16) Related ------- @@ -3691,17 +3696,17 @@ def set_block_selection( Examples -------- - Set up a 2-dimensional array:: + Set up a 2-dimensional array: >>> import zarr >>> z = zarr.zeros( - >>> shape=(6, 6), - >>> store=StorePath(MemoryStore(mode="w")), - >>> chunk_shape=(2, 2), - >>> dtype="i4", - >>> ) + ... shape=(6, 6), + ... store={}, + ... chunk_shape=(2, 2), + ... dtype="i4", + ... ) - Set data for a selection of items:: + Set data for a selection of items: >>> z.set_block_selection((1, 0), 1) >>> z[...] @@ -3710,10 +3715,9 @@ def set_block_selection( [1, 1, 0, 0, 0, 0], [1, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], - [0, 0, 0, 0, 0, 0]]) + [0, 0, 0, 0, 0, 0]], dtype=int32) - For convenience, this functionality is also available via the `blocks` property. - E.g.:: + For convenience, this functionality is also available via the `blocks` property: >>> z.blocks[2, 1] = 4 >>> z[...] @@ -3722,7 +3726,7 @@ def set_block_selection( [1, 1, 0, 0, 0, 0], [1, 1, 0, 0, 0, 0], [0, 0, 4, 4, 0, 0], - [0, 0, 4, 4, 0, 0]]) + [0, 0, 4, 4, 0, 0]], dtype=int32) >>> z.blocks[:, 2] = 7 >>> z[...] @@ -3731,7 +3735,7 @@ def set_block_selection( [1, 1, 0, 0, 7, 7], [1, 1, 0, 0, 7, 7], [0, 0, 4, 4, 7, 7], - [0, 0, 4, 4, 7, 7]]) + [0, 0, 4, 4, 7, 7]], dtype=int32) Notes ----- @@ -3849,7 +3853,7 @@ def append(self, data: npt.ArrayLike, axis: int = 0) -> tuple[int, ...]: -------- >>> import numpy as np >>> import zarr - >>> a = np.arange(10000000, dtype='i4').reshape(10000, 1000) + >>> a = np.arange(10000000, dtype="i4").reshape(10000, 1000) >>> z = zarr.array(a, chunks=(1000, 100)) >>> z.shape (10000, 1000) @@ -3913,13 +3917,16 @@ def info(self) -> Any: >>> arr.info Type : Array Zarr format : 3 - Data type : DataType.float32 + Data type : Float32(endianness='little') + Fill value : 0.0 Shape : (10,) Chunk shape : (2,) Order : C Read-only : False Store type : MemoryStore - Codecs : [BytesCodec(endian=)] + Filters : () + Serializer : BytesCodec(endian=) + Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 40 """ return self.async_array.info @@ -4161,48 +4168,49 @@ async def from_array( Examples -------- - Create an array from an existing Array:: + Create an array from an existing Array: + >>> import asyncio >>> import zarr - >>> store = zarr.storage.MemoryStore() - >>> store2 = zarr.storage.LocalStore('example.zarr') + >>> store = zarr.storage.LocalStore("example.zarr") >>> arr = zarr.create_array( - >>> store=store, - >>> shape=(100,100), - >>> chunks=(10,10), - >>> dtype='int32', - >>> fill_value=0) - >>> arr2 = await zarr.api.asynchronous.from_array(store2, data=arr) + ... store={}, + ... shape=(100,100), + ... chunks=(10,10), + ... dtype="int32", + ... fill_value=0, + ... ) + + >>> arr2 = asyncio.run(from_array(store, data=arr, overwrite=True)) + >>> arr2 + >>> asyncio.run(store.clear()) # Remove files generated by test + + Create an array from an existing NumPy array: - Create an array from an existing NumPy array:: - - >>> arr3 = await zarr.api.asynchronous.from_array( - >>> zarr.storage.MemoryStore(), - >>> data=np.arange(10000, dtype='i4').reshape(100, 100), - >>> ) - - - Create an array from any array-like object:: - - >>> arr4 = await zarr.api.asynchronous.from_array( - >>> zarr.storage.MemoryStore(), - >>> data=[[1, 2], [3, 4]], - >>> ) - - >>> await arr4.getitem(...) - array([[1, 2],[3, 4]]) - - Create an array from an existing Array without copying the data:: - - >>> arr5 = await zarr.api.asynchronous.from_array( - >>> zarr.storage.MemoryStore(), - >>> data=Array(arr4), - >>> write_data=False, - >>> ) - - >>> await arr5.getitem(...) - array([[0, 0],[0, 0]]) + >>> arr3 = asyncio.run( + ... from_array({}, data=np.arange(10000, dtype="i4").reshape(100, 100)) + ... ) + >>> arr3 + + + Create an array from any array-like object: + + >>> arr4 = asyncio.run(from_array({}, data=[[1, 2], [3, 4]])) + >>> arr4 + + >>> asyncio.run(arr4.getitem(...)) + array([[1, 2], + [3, 4]]) + + Create an array from an existing Array without copying the data: + + >>> arr5 = asyncio.run(from_array({}, data=Array(arr4), write_data=False)) + >>> arr5 + + >>> asyncio.run(arr5.getitem(...)) + array([[0, 0], + [0, 0]]) """ mode: Literal["a"] = "a" config_parsed = parse_array_config(config) @@ -4645,15 +4653,18 @@ async def create_array( Examples -------- + >>> import asyncio >>> import zarr - >>> store = zarr.storage.MemoryStore(mode='w') - >>> async_arr = await zarr.api.asynchronous.create_array( - >>> store=store, - >>> shape=(100,100), - >>> chunks=(10,10), - >>> dtype='i4', - >>> fill_value=0) - + >>> asyncio.run( + ... zarr.api.asynchronous.create_array( + ... store={}, + ... shape=(100,100), + ... chunks=(10,10), + ... dtype="i4", + ... fill_value=0 + ... ) + ... ) + """ data_parsed, shape_parsed, dtype_parsed = _parse_data_params( data=data, shape=shape, dtype=dtype @@ -5067,7 +5078,7 @@ def _parse_data_params( shape_out = shape if dtype is None: msg = ( - "The data parameter was set to None, but dtype was not specified." + "The data parameter was set to None, but dtype was not specified. " "Either provide an array-like value for data, or specify dtype." ) raise ValueError(msg) diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 213b7fb607..de8c8e9a68 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -1898,12 +1898,13 @@ def __delitem__(self, key: str) -> None: Examples -------- >>> import zarr - >>> group = Group.from_store(zarr.storage.MemoryStore() - >>> group.create_array(name="subarray", shape=(10,), chunks=(10,)) + >>> group = Group.from_store(zarr.storage.MemoryStore()) + >>> a = group.create_array(name="subarray", dtype="i1", shape=(10,), chunks=(10,)) >>> del group["subarray"] >>> "subarray" in group False """ + self._sync(self._async_group.delitem(key)) def __iter__(self) -> Iterator[str]: @@ -1914,14 +1915,10 @@ def __iter__(self) -> Iterator[str]: >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') - >>> d1 = g1.create_array('baz', shape=(10,), chunks=(10,)) - >>> d2 = g1.create_array('quux', shape=(10,), chunks=(10,)) - >>> for name in g1: - ... print(name) - baz - bar - foo - quux + >>> d1 = g1.create_array('baz', dtype="i1", shape=(10,), chunks=(10,)) + >>> d2 = g1.create_array('quux', dtype="i1", shape=(10,), chunks=(10,)) + >>> sorted(g1) + ['bar', 'baz', 'foo', 'quux'] """ yield from self.keys() @@ -1944,11 +1941,12 @@ def __setitem__(self, key: str, value: Any) -> None: Examples -------- + >>> import numpy as np >>> import zarr >>> group = zarr.group() - >>> group["foo"] = zarr.zeros((10,)) + >>> group["foo"] = np.array(zarr.zeros((10,))) >>> group["foo"] - + """ self._sync(self._async_group.setitem(key, value)) @@ -1960,10 +1958,15 @@ async def update_attributes_async(self, new_attributes: dict[str, Any]) -> Group Examples -------- - >>> import zarr - >>> group = zarr.group() - >>> await group.update_attributes_async({"foo": "bar"}) - >>> group.attrs.asdict() + >>> async def example(): + ... import zarr + ... + ... group = zarr.group() + ... new_group = await group.update_attributes_async({"foo": "bar"}) + ... return new_group.attrs.asdict() + + >>> import asyncio + >>> asyncio.run(example()) {'foo': 'bar'} """ new_metadata = replace(self.metadata, attributes=new_attributes) @@ -2062,8 +2065,7 @@ def update_attributes(self, new_attributes: dict[str, Any]) -> Group: Examples -------- >>> import zarr - >>> group = zarr.group() - >>> group.update_attributes({"foo": "bar"}) + >>> group = zarr.group().update_attributes({"foo": "bar"}) >>> group.attrs.asdict() {'foo': 'bar'} """ @@ -2169,19 +2171,17 @@ def create_hierarchy( >>> import zarr >>> from zarr.core.group import GroupMetadata >>> root = zarr.create_group(store={}) - >>> for key, val in root.create_hierarchy({'a/b/c': GroupMetadata()}): - ... print(key, val) - ... - - - + >>> sorted(root.create_hierarchy({'a/b/c': GroupMetadata()})) + [('a', ), + ('a/b', ), + ('a/b/c', )] """ for key, node in self._sync_iter( self._async_group.create_hierarchy(nodes, overwrite=overwrite) ): yield (key, _parse_async_node(node)) - def keys(self) -> Generator[str, None]: + def keys(self) -> Generator[str]: """Return an iterator over group member names. Examples @@ -2190,14 +2190,10 @@ def keys(self) -> Generator[str, None]: >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') >>> g3 = g1.create_group('bar') - >>> d1 = g1.create_array('baz', shape=(10,), chunks=(10,)) - >>> d2 = g1.create_array('quux', shape=(10,), chunks=(10,)) - >>> for name in g1.keys(): - ... print(name) - baz - bar - foo - quux + >>> d1 = g1.create_array('baz', dtype="i1", shape=(10,), chunks=(10,)) + >>> d2 = g1.create_array('quux', dtype="i1", shape=(10,), chunks=(10,)) + >>> sorted(g1.keys()) + ['bar', 'baz', 'foo', 'quux'] """ yield from self._sync_iter(self._async_group.keys()) @@ -2209,14 +2205,13 @@ def __contains__(self, member: str) -> bool: >>> import zarr >>> g1 = zarr.group() >>> g2 = g1.create_group('foo') - >>> d1 = g1.create_array('bar', shape=(10,), chunks=(10,)) + >>> d1 = g1.create_array('bar', dtype="i1", shape=(10,), chunks=(10,)) >>> 'foo' in g1 True >>> 'bar' in g1 True >>> 'baz' in g1 False - """ return self._sync(self._async_group.contains(member)) @@ -2227,10 +2222,9 @@ def groups(self) -> Generator[tuple[str, Group], None]: -------- >>> import zarr >>> group = zarr.group() - >>> group.create_group("subgroup") - >>> for name, subgroup in group.groups(): - ... print(name, subgroup) - subgroup + >>> subgroup = group.create_group("subgroup") + >>> list(group.groups()) + [('subgroup', )] """ for name, async_group in self._sync_iter(self._async_group.groups()): yield name, Group(async_group) @@ -2242,10 +2236,9 @@ def group_keys(self) -> Generator[str, None]: -------- >>> import zarr >>> group = zarr.group() - >>> group.create_group("subgroup") - >>> for name in group.group_keys(): - ... print(name) - subgroup + >>> subgroup = group.create_group("subgroup") + >>> list(group.group_keys()) + ['subgroup'] """ for name, _ in self.groups(): yield name @@ -2257,10 +2250,9 @@ def group_values(self) -> Generator[Group, None]: -------- >>> import zarr >>> group = zarr.group() - >>> group.create_group("subgroup") - >>> for subgroup in group.group_values(): - ... print(subgroup) - + >>> subgroup = group.create_group("subgroup") + >>> list(group.group_values()) + [] """ for _, group in self.groups(): yield group @@ -2272,10 +2264,9 @@ def arrays(self) -> Generator[tuple[str, AnyArray], None]: -------- >>> import zarr >>> group = zarr.group() - >>> group.create_array("subarray", shape=(10,), chunks=(10,)) - >>> for name, subarray in group.arrays(): - ... print(name, subarray) - subarray + >>> subarray = group.create_array("subarray", dtype="i1", shape=(10,), chunks=(10,)) + >>> list(group.arrays()) + [('subarray', )] """ for name, async_array in self._sync_iter(self._async_group.arrays()): yield name, Array(async_array) @@ -2287,10 +2278,9 @@ def array_keys(self) -> Generator[str, None]: -------- >>> import zarr >>> group = zarr.group() - >>> group.create_array("subarray", shape=(10,), chunks=(10,)) - >>> for name in group.array_keys(): - ... print(name) - subarray + >>> subarray = group.create_array("subarray", dtype="i1", shape=(10,), chunks=(10,)) + >>> list(group.array_keys()) + ['subarray'] """ for name, _ in self.arrays(): @@ -2303,10 +2293,9 @@ def array_values(self) -> Generator[AnyArray, None]: -------- >>> import zarr >>> group = zarr.group() - >>> group.create_array("subarray", shape=(10,), chunks=(10,)) - >>> for subarray in group.array_values(): - ... print(subarray) - + >>> subarray = group.create_array("subarray", dtype="i1", shape=(10,), chunks=(10,)) + >>> list(group.array_values()) + [] """ for _, array in self.arrays(): yield array @@ -2363,7 +2352,7 @@ def create_group(self, name: str, **kwargs: Any) -> Group: >>> group = zarr.group() >>> subgroup = group.create_group("subgroup") >>> subgroup - + """ return Group(self._sync(self._async_group.create_group(name, **kwargs))) @@ -2929,21 +2918,24 @@ async def create_hierarchy( Yields ------ tuple[str, AsyncGroup | AsyncArray] - This function yields (path, node) pairs, in the order the nodes were created. + Yields (path, node) pairs, in the order the nodes were created. Examples -------- - >>> from zarr.api.asynchronous import create_hierarchy - >>> from zarr.storage import MemoryStore - >>> from zarr.core.group import GroupMetadata + >>> async def example(): + ... from zarr.api.asynchronous import create_hierarchy + ... from zarr.core.group import GroupMetadata + ... from zarr.storage import MemoryStore + ... + ... store = MemoryStore() + ... nodes = {'a': GroupMetadata(attributes={'name': 'leaf'})} + ... return sorted([x async for x in create_hierarchy(store=store, nodes=nodes)]) + >>> import asyncio - >>> store = MemoryStore() - >>> nodes = {'a': GroupMetadata(attributes={'name': 'leaf'})} - >>> async def run(): - ... print(dict([x async for x in create_hierarchy(store=store, nodes=nodes)])) - >>> asyncio.run(run()) - # {'a': , '': } + >>> asyncio.run(example()) + [('', ), ('a', )] """ + # normalize the keys to be valid paths nodes_normed_keys = _normalize_path_keys(nodes) diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 96f1e61746..038de4fef8 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -397,13 +397,20 @@ async def _get_bytes( Examples -------- - >>> store = await LocalStore.open("data") - >>> await store.set("data", Buffer.from_bytes(b"hello")) - >>> # No need to specify prototype for LocalStore - >>> data = await store.get_bytes("data") - >>> print(data) + >>> async def example(): + ... import json + ... from zarr.core.buffer.cpu import Buffer + ... + ... store = await LocalStore.open("data") + ... await store.set("data", Buffer.from_bytes(b"hello")) + ... # No need to specify prototype for LocalStore + ... return await store._get_bytes("data") + + >>> import asyncio + >>> asyncio.run(example()) b'hello' """ + if prototype is None: prototype = default_buffer_prototype() return await super()._get_bytes(key, prototype=prototype, byte_range=byte_range) @@ -453,13 +460,14 @@ def _get_bytes_sync( Examples -------- + >>> from zarr.core.buffer.cpu import Buffer >>> store = LocalStore("data") - >>> store.set("data", Buffer.from_bytes(b"hello")) + >>> store.set_sync("data", Buffer.from_bytes(b"hello")) >>> # No need to specify prototype for LocalStore - >>> data = store.get_bytes("data") - >>> print(data) + >>> store._get_bytes_sync("data") b'hello' """ + if prototype is None: prototype = default_buffer_prototype() return super()._get_bytes_sync(key, prototype=prototype, byte_range=byte_range) @@ -510,15 +518,21 @@ async def _get_json( Examples -------- - >>> store = await LocalStore.open("data") - >>> import json - >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> # No need to specify prototype for LocalStore - >>> data = await store.get_json("zarr.json") - >>> print(data) + >>> async def example(): + ... import json + ... from zarr.core.buffer.cpu import Buffer + ... + ... store = await LocalStore.open("data") + ... metadata = {"zarr_format": 3, "node_type": "array"} + ... await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + ... # No need to specify prototype for LocalStore + ... return await store._get_json("zarr.json") + + >>> import asyncio + >>> asyncio.run(example()) {'zarr_format': 3, 'node_type': 'array'} """ + if prototype is None: prototype = default_buffer_prototype() return await super()._get_json(key, prototype=prototype, byte_range=byte_range) @@ -573,15 +587,15 @@ def _get_json_sync( Examples -------- - >>> store = LocalStore("data") >>> import json + >>> from zarr.core.buffer.cpu import Buffer + >>> store = LocalStore("data") >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> # No need to specify prototype for LocalStore - >>> data = store.get_json("zarr.json") - >>> print(data) + >>> store.set_sync("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> store._get_json_sync("zarr.json") # No need to specify prototype for LocalStore {'zarr_format': 3, 'node_type': 'array'} """ + if prototype is None: prototype = default_buffer_prototype() return super()._get_json_sync(key, prototype=prototype, byte_range=byte_range) diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index bd91029732..121fcdab7f 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -266,13 +266,19 @@ async def _get_bytes( Examples -------- - >>> store = await MemoryStore.open() - >>> await store.set("data", Buffer.from_bytes(b"hello")) - >>> # No need to specify prototype for MemoryStore - >>> data = await store.get_bytes("data") - >>> print(data) + >>> async def example(): + ... from zarr.core.buffer.cpu import Buffer + ... + ... store = await MemoryStore.open() + ... await store.set("data", Buffer.from_bytes(b"hello")) + ... # No need to specify prototype for MemoryStore + ... return await store._get_bytes("data") + + >>> import asyncio + >>> asyncio.run(example()) b'hello' """ + if prototype is None: prototype = default_buffer_prototype() return await super()._get_bytes(key, prototype=prototype, byte_range=byte_range) @@ -322,11 +328,10 @@ def _get_bytes_sync( Examples -------- + >>> from zarr.core.buffer.cpu import Buffer >>> store = MemoryStore() - >>> store.set("data", Buffer.from_bytes(b"hello")) - >>> # No need to specify prototype for MemoryStore - >>> data = store.get_bytes("data") - >>> print(data) + >>> store.set_sync("data", Buffer.from_bytes(b"hello")) + >>> store._get_bytes_sync("data") # No need to specify prototype for MemoryStore b'hello' """ if prototype is None: @@ -379,15 +384,21 @@ async def _get_json( Examples -------- - >>> store = await MemoryStore.open() - >>> import json - >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> # No need to specify prototype for MemoryStore - >>> data = await store.get_json("zarr.json") - >>> print(data) + >>> async def example(): + ... import json + ... from zarr.core.buffer.cpu import Buffer + ... + ... store = await MemoryStore.open() + ... metadata = {"zarr_format": 3, "node_type": "array"} + ... await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + ... # No need to specify prototype for MemoryStore + ... return await store._get_json("zarr.json") + + >>> import asyncio + >>> asyncio.run(example()) {'zarr_format': 3, 'node_type': 'array'} """ + if prototype is None: prototype = default_buffer_prototype() return await super()._get_json(key, prototype=prototype, byte_range=byte_range) @@ -442,15 +453,15 @@ def _get_json_sync( Examples -------- - >>> store = MemoryStore() >>> import json + >>> from zarr.core.buffer.cpu import Buffer + >>> store = MemoryStore() >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> # No need to specify prototype for MemoryStore - >>> data = store.get_json("zarr.json") - >>> print(data) + >>> store.set_sync("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) + >>> store._get_json_sync("zarr.json") # No need to specify prototype for MemoryStore {'zarr_format': 3, 'node_type': 'array'} """ + if prototype is None: prototype = default_buffer_prototype() return super()._get_json_sync(key, prototype=prototype, byte_range=byte_range) From ff6da8f99adcd76a23bca960649f8fd75fc3da5b Mon Sep 17 00:00:00 2001 From: josh-ag2 Date: Thu, 28 May 2026 10:50:30 -0400 Subject: [PATCH 330/468] fix(FsspecStore): close owned async filesystem on store.close() (#4003) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix(FsspecStore): close owned async filesystem on store.close() FsspecStore.from_url() and from_mapper() create their own async filesystem instance that zarr is responsible for — but Store.close() never cleaned it up, leaving the underlying aiohttp ClientSession open until garbage collection. This produced "Unclosed client session" ResourceWarnings from aiohttp, and in environments where the finalizer ran on the wrong event loop (e.g. Python 3.12+ with eager_start=True) it could raise RuntimeError. Changes: - Add _close_fs() async helper: calls fs.set_session() then client.close() for filesystems that expose set_session() (e.g. s3fs); no-op for all others. - Add _owns_fs: bool to FsspecStore.__init__ (default False). Set True in from_url() unconditionally; set True in from_mapper() only when _make_async() produced a new instance (sync→async wrap). Direct construction and from_upath() leave _owns_fs=False — the caller supplied the fs and remains responsible for it. - Override close() to invoke zarr_sync(_close_fs(self.fs)) before calling super().close(), guarded by _owns_fs and a bare except so it can never raise from a destructor path. Tests: - Update pytestmark comment (the filter stays for GC-path warnings). - test_from_url_owns_filesystem / test_from_url_close_releases_store - test_direct_construction_does_not_own_filesystem - test_from_upath_does_not_own_filesystem - test_from_mapper_does_not_own_already_async_filesystem - test_from_mapper_owns_wrapped_sync_filesystem - test_close_fs_closes_s3_client / test_close_fs_no_op_for_fs_without_set_session Co-Authored-By: Claude Sonnet 4.6 * fix lint: use contextlib.suppress instead of try/except/pass (SIM105) * add towncrier release note for #4003 * changes: expand 4003 release note to document fix scope and s3fs limitation Co-Authored-By: Claude Sonnet 4.6 * fix(FsspecStore): propagate fs ownership through with_read_only Addresses roborev review findings on the filesystem-ownership change: - with_read_only() transferred fs ownership: it built the derived store with _owns_fs=False while sharing the same fs. In the common from_url(...).with_read_only() chain the only owner (the unreferenced source) was GC'd without close(), reintroducing the unclosed-session leak. Ownership now transfers to the surviving store and is cleared on the source to avoid a double-close. Covered by a new test. - close() now logs at debug before suppressing, so a regression in the close path stays observable instead of silently reverting to leaking. - Documented that set_session() lazily creates a session, so closing a store that never did I/O may instantiate one purely to close it (accepted best-effort behavior). Co-Authored-By: Claude Opus 4.7 --------- Co-authored-by: Claude Sonnet 4.6 Co-authored-by: Davis Bennett --- changes/4003.bugfix.md | 19 ++++ src/zarr/storage/_fsspec.py | 61 ++++++++++++- tests/test_store/test_fsspec.py | 149 +++++++++++++++++++++++++++++++- 3 files changed, 224 insertions(+), 5 deletions(-) create mode 100644 changes/4003.bugfix.md diff --git a/changes/4003.bugfix.md b/changes/4003.bugfix.md new file mode 100644 index 0000000000..36327b55df --- /dev/null +++ b/changes/4003.bugfix.md @@ -0,0 +1,19 @@ +`FsspecStore.from_url()` and `from_mapper()` now close the async filesystem +they create when `store.close()` is called. Previously the underlying aiohttp +`ClientSession` was left open until garbage collection, producing +`"Unclosed client session"` `ResourceWarning`s from aiohttp. + +The fix introduces `FsspecStore._owns_fs`, a boolean that is ``True`` only when +`FsspecStore` itself created the filesystem (via `from_url` or `from_mapper` +when a sync→async conversion was performed). When `_owns_fs` is ``True``, +`store.close()` calls the new `_close_fs()` helper, which invokes +`fs.set_session()` and closes the returned client. Callers who supply their own +filesystem instance to `FsspecStore()` directly remain responsible for its +lifecycle; `_owns_fs` is ``False`` for those stores. + +**Scope note**: This fix closes the S3 client session that is active at the time +`store.close()` is called. Some S3-backed filesystem implementations (e.g. +s3fs with ``cache_regions=True``) may internally refresh and replace their +client during I/O operations, abandoning prior sessions before ``store.close()`` +is invoked. Those intermediate sessions are outside the scope of this fix and +are an issue in the upstream filesystem library. diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 14386d1aac..29201a6fee 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -3,6 +3,7 @@ import json import warnings from contextlib import suppress +from logging import getLogger from typing import TYPE_CHECKING, Any from packaging.version import parse as parse_version @@ -18,6 +19,8 @@ from zarr.errors import ZarrUserWarning from zarr.storage._utils import _dereference_path +logger = getLogger(__name__) + if TYPE_CHECKING: from collections.abc import AsyncIterator, Iterable @@ -35,6 +38,26 @@ ) +async def _close_fs(fs: AsyncFileSystem) -> None: + """ + Best-effort async close of an fsspec async filesystem owned by FsspecStore. + + For filesystems that expose ``set_session()`` (e.g. s3fs) the underlying + aiohttp ``ClientSession`` is closed explicitly, which prevents + "Unclosed client session" ``ResourceWarning``s from aiohttp. For all + other filesystem types the call is a no-op (not every implementation + manages an HTTP session directly). + + Note that ``set_session()`` lazily creates a session if none exists yet, so + closing a store that never performed any I/O may instantiate a session + purely to close it. This is accepted best-effort behavior; fsspec does not + expose a stable, cross-implementation way to test for an existing session. + """ + if hasattr(fs, "set_session"): + session = await fs.set_session() + await session.close() + + def _make_async(fs: AbstractFileSystem) -> AsyncFileSystem: """Convert a sync FSSpec filesystem to an async FFSpec filesystem @@ -129,6 +152,9 @@ def __init__( self.fs = fs self.path = path self.allowed_exceptions = allowed_exceptions + # True only when this store created fs itself (from_url / from_mapper with new instance). + # Callers who supply their own fs remain responsible for its lifecycle. + self._owns_fs: bool = False if not self.fs.async_impl: raise TypeError("Filesystem needs to support async operations.") @@ -194,13 +220,17 @@ def from_mapper( ------- FsspecStore """ - fs = _make_async(fs_map.fs) - return cls( + original_fs = fs_map.fs + fs = _make_async(original_fs) + store = cls( fs=fs, path=fs_map.root, read_only=read_only, allowed_exceptions=allowed_exceptions, ) + # _make_async returns a new instance when converting sync→async; own it. + store._owns_fs = fs is not original_fs + return store @classmethod def from_url( @@ -242,16 +272,39 @@ def from_url( if not fs.async_impl: fs = _make_async(fs) - return cls(fs=fs, path=path, read_only=read_only, allowed_exceptions=allowed_exceptions) + store = cls(fs=fs, path=path, read_only=read_only, allowed_exceptions=allowed_exceptions) + store._owns_fs = True + return store def with_read_only(self, read_only: bool = False) -> FsspecStore: # docstring inherited - return type(self)( + new_store = type(self)( fs=self.fs, path=self.path, allowed_exceptions=self.allowed_exceptions, read_only=read_only, ) + # The derived store shares the same fs. Transfer ownership so the + # surviving store closes it, and clear ours to avoid a double-close. + # Otherwise the common ``from_url(...).with_read_only()`` chain would + # drop the only owner (the unreferenced source) and leak the session. + new_store._owns_fs = self._owns_fs + self._owns_fs = False + return new_store + + def close(self) -> None: + # docstring inherited + if self._owns_fs: + from zarr.core.sync import sync as zarr_sync + + # Best-effort: a failure to release the session must not block close(), + # but log it so a genuine regression in the close path stays observable + # rather than silently reverting to the leaking behavior. + try: + zarr_sync(_close_fs(self.fs)) + except Exception: + logger.debug("Failed to close owned filesystem %r", self.fs, exc_info=True) + super().close() async def clear(self) -> None: # docstring inherited diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 142cb3b00d..8006470174 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -36,7 +36,9 @@ pytest.mark.filterwarnings( re.escape("ignore:datetime.datetime.utcnow() is deprecated:DeprecationWarning") ), - # TODO: fix these warnings + # FsspecStore.from_url() and from_mapper() now close the aiohttp session on store.close(). + # This filter covers stores that are GC'd without an explicit close() call, and any + # residual sessions from aiobotocore's ClientCreatorContext (a separate upstream issue). pytest.mark.filterwarnings("ignore:Unclosed client session:ResourceWarning"), pytest.mark.filterwarnings( "ignore:coroutine 'ClientCreatorContext.__aexit__' was never awaited:RuntimeWarning" @@ -283,6 +285,75 @@ async def test_delete_dir_unsupported_deletes(self, store: FsspecStore) -> None: ): await store.delete_dir("test_prefix") + # ── Filesystem lifecycle (ownership) ────────────────────────────────────── + + def test_from_url_owns_filesystem(self) -> None: + """FsspecStore.from_url() creates the async fs; it must own it.""" + store = FsspecStore.from_url( + f"s3://{test_bucket_name}/lifecycle/", + storage_options={"endpoint_url": endpoint_url, "anon": False}, + ) + assert store._owns_fs + store.close() + + async def test_from_url_close_releases_store(self) -> None: + """ + close() on a from_url() store must succeed without error and mark the + store as closed. For the owned filesystem, _close_fs() is invoked to + release the underlying S3 client / aiohttp connection pool. + """ + store = FsspecStore.from_url( + f"s3://{test_bucket_name}/lifecycle/", + storage_options={"endpoint_url": endpoint_url, "anon": False}, + ) + # Materialise the S3 client and connection pool. + await store.set("probe", cpu.Buffer.from_bytes(b"x")) + + store.close() + + assert not store._is_open + + def test_direct_construction_does_not_own_filesystem(self) -> None: + """Direct FsspecStore() must not claim ownership — the caller owns the fs.""" + try: + from fsspec import url_to_fs + except ImportError: + from fsspec.core import url_to_fs + fs, path = url_to_fs( + f"s3://{test_bucket_name}", endpoint_url=endpoint_url, anon=False, asynchronous=True + ) + store = FsspecStore(fs=fs, path=path) + assert not store._owns_fs + + @pytest.mark.skipif( + parse_version(fsspec.__version__) < parse_version("2024.03.01"), + reason="Prior bug in from_upath", + ) + def test_from_upath_does_not_own_filesystem(self) -> None: + """from_upath() uses the UPath's existing fs; the store must not own it.""" + upath = pytest.importorskip("upath") + path = upath.UPath( + f"s3://{test_bucket_name}/foo/bar/", + endpoint_url=endpoint_url, + anon=False, + asynchronous=True, + ) + store = FsspecStore.from_upath(path) + assert not store._owns_fs + + def test_from_mapper_does_not_own_already_async_filesystem(self) -> None: + """from_mapper() with an already-async fs must not claim ownership.""" + s3_filesystem = s3fs.S3FileSystem( + asynchronous=True, + endpoint_url=endpoint_url, + anon=False, + skip_instance_cache=True, + ) + mapper = s3_filesystem.get_mapper(f"s3://{test_bucket_name}/") + store = FsspecStore.from_mapper(mapper) + # _make_async returns the same instance for an already-async fs. + assert not store._owns_fs + def array_roundtrip(store: FsspecStore) -> None: """ @@ -512,6 +583,82 @@ def test_open_s3map_raises() -> None: zarr.open(store=mapper, storage_options={"anon": True}, mode="w", shape=(3, 3)) +async def test_close_fs_closes_s3_client() -> None: + """ + _close_fs() must call set_session() and then close() on the returned + S3 client. This is verified with mocks to avoid a real S3 connection. + """ + from unittest.mock import AsyncMock + + from zarr.storage._fsspec import _close_fs + + mock_client = AsyncMock() + mock_fs = AsyncMock() + mock_fs.set_session = AsyncMock(return_value=mock_client) + + await _close_fs(mock_fs) + + mock_fs.set_session.assert_called_once() + mock_client.close.assert_called_once() + + +async def test_close_fs_no_op_for_fs_without_set_session() -> None: + """_close_fs() must be a no-op for filesystems that don't expose set_session().""" + from unittest.mock import AsyncMock + + from zarr.storage._fsspec import _close_fs + + mock_fs = AsyncMock(spec=[]) # empty spec — no set_session attribute + await _close_fs(mock_fs) # must not raise + + +@pytest.mark.skipif( + parse_version(fsspec.__version__) < parse_version("2024.12.0"), + reason="No AsyncFileSystemWrapper", +) +def test_from_mapper_owns_wrapped_sync_filesystem(tmp_path: pathlib.Path) -> None: + """ + from_mapper() with a sync fs must wrap it in AsyncFileSystemWrapper and + claim ownership so that close() cleans it up. + + The local filesystem is synchronous; _make_async() produces a new + AsyncFileSystemWrapper instance — a different object from the original fs. + """ + import fsspec as _fsspec + from fsspec.implementations.asyn_wrapper import AsyncFileSystemWrapper + + fs = _fsspec.filesystem("file", auto_mkdir=True) + mapper = fs.get_mapper(str(tmp_path)) + store = FsspecStore.from_mapper(mapper) + assert isinstance(store.fs, AsyncFileSystemWrapper) + assert store._owns_fs + + +@pytest.mark.skipif( + parse_version(fsspec.__version__) < parse_version("2024.12.0"), + reason="No AsyncFileSystemWrapper", +) +def test_with_read_only_transfers_filesystem_ownership(tmp_path: pathlib.Path) -> None: + """ + with_read_only() must transfer fs ownership to the derived store and clear + it on the source, so the surviving store closes the shared fs exactly once. + + In the common ``from_url(...).with_read_only()`` chain the source store is + immediately unreferenced; if ownership were not transferred, the only owner + would be garbage-collected without close() and the session would leak. + """ + source = FsspecStore.from_url(f"file://{tmp_path}", storage_options={"auto_mkdir": False}) + assert source._owns_fs + + derived = source.with_read_only(read_only=True) + + # Ownership moved to the survivor; the source no longer owns it (no double-close). + assert derived._owns_fs + assert not source._owns_fs + # The derived store shares the same underlying fs. + assert derived.fs is source.fs + + @pytest.mark.parametrize("asynchronous", [True, False]) def test_make_async(asynchronous: bool) -> None: s3_filesystem = s3fs.S3FileSystem( From 6ce787d1ee9a23fed07753a6e0e89fd7951fdb9d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 29 May 2026 16:15:59 +0000 Subject: [PATCH 331/468] chore(deps): bump the actions group across 1 directory with 8 updates (#4014) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/downstream.yml | 2 +- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/issue-metrics.yml | 2 +- .github/workflows/lint.yml | 2 +- .github/workflows/test.yml | 4 ++-- .github/workflows/zarr-metadata-release.yml | 12 ++++++------ .github/workflows/zizmor.yml | 2 +- 8 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 74026233c4..3eb6898895 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -34,7 +34,7 @@ jobs: persist-credentials: false - name: Set up pixi - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0 # v0.9.5 + uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6 with: manifest-path: xarray/pixi.toml diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 403441b306..333769cb9e 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -76,7 +76,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: gpu diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 4f9467be7d..a456b2aa0a 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -93,7 +93,7 @@ jobs: key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} - name: Upload coverage - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 14fba5b9ec..510849ef3e 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -33,7 +33,7 @@ jobs: echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV" - name: Run issue-metrics tool - uses: github/issue-metrics@c9e9838147fd355dace335ba787f01b6641a400a # v4.2.2 + uses: github/issue-metrics@1e38d5e62363e14db8019ed7d106b9855bdba6cc # v4.2.7 env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 768e660ec2..fec211b4dd 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -30,4 +30,4 @@ jobs: uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 with: enable-cache: true - - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2.0.3 + - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 03143d3e5b..62e571856b 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -78,7 +78,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage if: ${{ matrix.dependency-set == 'optional' && matrix.os == 'ubuntu-latest' }} - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests @@ -125,7 +125,7 @@ jobs: run: | hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0 + uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index 809d502f16..9639fcfdd3 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -35,7 +35,7 @@ jobs: - name: Build run: hatch build - - uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 with: name: zarr-metadata-dist path: packages/zarr-metadata/dist @@ -45,7 +45,7 @@ jobs: needs: [build] runs-on: ubuntu-latest steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: zarr-metadata-dist path: dist @@ -76,7 +76,7 @@ jobs: id-token: write # required for OIDC trusted publishing attestations: write # required for artifact attestations steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: zarr-metadata-dist path: dist @@ -87,7 +87,7 @@ jobs: subject-path: dist/* - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 + uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 upload_testpypi: name: Upload to TestPyPI @@ -101,7 +101,7 @@ jobs: id-token: write attestations: write steps: - - uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0 + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 with: name: zarr-metadata-dist path: dist @@ -112,6 +112,6 @@ jobs: subject-path: dist/* - name: Publish package to TestPyPI - uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0 + uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 with: repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index da19f22421..7ac4fe5d0e 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -32,4 +32,4 @@ jobs: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@b1d7e1fb5de872772f31590499237e7cce841e8e # v0.5.3 + uses: zizmorcore/zizmor-action@5f14fd08f7cf1cb1609c1e344975f152c7ee938d # v0.5.6 From e1185ef67ac82c6f4729d409cf546e7cd9953291 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lo=C3=AFc=20Houpert?= <10154151+lhoupert@users.noreply.github.com> Date: Tue, 2 Jun 2026 10:32:52 +0100 Subject: [PATCH 332/468] fix: use hatch's `default` env so the uv installer is inherited (#4023) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix: use hatch's `default` env so the uv installer is inherited `[tool.hatch.envs.defaults]` (plural) is a standalone environment that nothing inherits from — hatch's base environment is `default` (singular). As written, `installer = "uv"` never applied to `test`, `docs`, etc., so those envs fell back to the `virtualenv` backend. This breaks contributors whose Python is uv-managed: hatch hands the `~/.local/bin/pythonX.Y` symlink to virtualenv, which mis-relocates the python-build-standalone interpreter (`sys.base_prefix = '/install'`, `ModuleNotFoundError: No module named 'encodings'`). Creating the env with `uv venv` relocates it correctly. Renaming to `default` makes the intended uv installer apply to all envs. Co-Authored-By: Claude Opus 4.8 * ci: install uv in hatch-based workflows so the uv installer works Activating `installer = "uv"` (via the `default` env fix) means hatch now needs a uv binary to create/sync the test, gputest and hypothesis envs. These workflows install hatch via the `pypa/hatch` action (a pyapp build with its own bundled Python) but never set up uv, so hatch fell back to provisioning uv through its pyapp runtime — whose `pip` has a `python3.12` shebang that doesn't exist on non-3.12 runners: .../pyapp/hatch/.../python/bin/python3.12: No such file or directory Process completed with exit code 126 Add the repo's standard `astral-sh/setup-uv` step (already used by docs/lint workflows) before "Install Hatch" so hatch finds uv on PATH and uses it directly. With uv available, `uv venv --python ` selects the correct interpreter, so the root `.python-version` (3.12, for the dev env) no longer interferes with the 3.13/3.14 matrix envs. Co-Authored-By: Claude Opus 4.8 * ci: point hatch at the setup-uv binary to skip its broken uv bootstrap Installing uv on PATH is not enough: hatch only skips provisioning its internal `hatch-uv` env when an explicit uv path is set. Otherwise it bootstraps uv via its bundled pyapp `pip` (shebang `python3.12`), which fails on non-3.12 runners with exit code 126. Set `HATCH_ENV_TYPE_VIRTUAL_UV_PATH=uv` so hatch uses the uv provided by astral-sh/setup-uv directly instead of bootstrapping. Verified locally: with the explicit path set, `hatch env create` succeeds. Co-Authored-By: Claude Opus 4.8 * ci(test): install hatch via pip instead of the pyapp action The macOS jobs failed even with uv on PATH: hatch's pyapp (standalone) build on macOS has a `pip` whose shebang points at a non-existent `python3.12`, and activating the uv installer makes hatch invoke it (`exit code 126`). Linux pyapp builds are unaffected, which is why the GPU and Hypothesis (Linux) workflows pass. Install hatch with `python -m pip install hatch==1.16.5` (the method the contributing docs already document) so hatch runs on the runner's normal Python with a working pip on every OS. uv (from setup-uv) is still used as the env installer. Co-Authored-By: Claude Opus 4.8 --------- Co-authored-by: Claude Opus 4.8 --- .github/workflows/gpu_test.yml | 4 ++++ .github/workflows/hypothesis.yaml | 4 ++++ .github/workflows/test.yml | 29 +++++++++++++++++------------ pyproject.toml | 2 +- 4 files changed, 26 insertions(+), 13 deletions(-) diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 333769cb9e..c03318d649 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -12,6 +12,8 @@ on: env: LD_LIBRARY_PATH: /usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/lib64 + # Use the uv from astral-sh/setup-uv instead of hatch's bundled (pyapp) uv. + HATCH_ENV_TYPE_VIRTUAL_UV_PATH: uv permissions: contents: read @@ -59,6 +61,8 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: 'pip' + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index a456b2aa0a..bc711c8490 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -18,6 +18,8 @@ concurrency: env: FORCE_COLOR: 3 + # Use the uv from astral-sh/setup-uv instead of hatch's bundled (pyapp) uv. + HATCH_ENV_TYPE_VIRTUAL_UV_PATH: uv jobs: @@ -54,6 +56,8 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: 'pip' + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 62e571856b..142290d109 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,6 +13,11 @@ on: permissions: contents: read +env: + # Use the uv from astral-sh/setup-uv; without an explicit path hatch + # bootstraps its own (pyapp) uv, which fails on non-3.12 runners. + HATCH_ENV_TYPE_VIRTUAL_UV_PATH: uv + concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true @@ -60,10 +65,10 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: 'pip' + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Install Hatch - uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc - with: - version: '1.16.5' + run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env env: HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} @@ -109,10 +114,10 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: 'pip' + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Install Hatch - uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc - with: - version: '1.16.5' + run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env env: HATCH_ENV: ${{ matrix.dependency-set }} @@ -144,10 +149,10 @@ jobs: with: python-version: '3.13' cache: 'pip' + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Install Hatch - uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc - with: - version: '1.16.5' + run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env run: | hatch run doctest:pip list @@ -168,10 +173,10 @@ jobs: with: python-version: '3.13' cache: 'pip' + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - name: Install Hatch - uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc - with: - version: '1.16.5' + run: python -m pip install hatch==1.16.5 - name: Run Benchmarks run: | hatch env run --env "test.py3.13-minimal" run-benchmark diff --git a/pyproject.toml b/pyproject.toml index e342e8305c..81a4461978 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -257,7 +257,7 @@ extra-dependencies = [ 'obstore==0.5.*', ] -[tool.hatch.envs.defaults] +[tool.hatch.envs.default] installer = "uv" [tool.hatch.envs.docs] From 8932bbe0e2d99cc2117af1e464731712378f3e06 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 09:53:51 +0000 Subject: [PATCH 333/468] chore: update pre-commit hooks (#4024) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.12 → v0.15.15](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.12...v0.15.15) - [github.com/zizmorcore/zizmor-pre-commit: v1.24.1 → v1.25.2](https://github.com/zizmorcore/zizmor-pre-commit/compare/v1.24.1...v1.25.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 31a74772a0..fb2e8c3c6f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.12 + rev: v0.15.15 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -58,7 +58,7 @@ repos: types: [python] files: ^(src|tests)/ - repo: https://github.com/zizmorcore/zizmor-pre-commit - rev: v1.24.1 + rev: v1.25.2 hooks: - id: zizmor - repo: https://github.com/twisted/towncrier From 0b2eda4b44a50f98c44d0d30c38404696036c622 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 2 Jun 2026 21:42:24 +0200 Subject: [PATCH 334/468] docs: test more code snippets in docs (#4018) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * docs: spec for closing the silently-unexecuted docs-block gap (#4016) Design for fixing issue #4016 (invalid create_array(mode="w") in docs) and preventing recurrence: per-case remediation of the 12 non-executed python blocks (S3 via moto, config blocks via exec="true", GPU via the gpu marker, explicit opt-out for non-Python blocks) plus a guard test asserting every docs python block is either executed or explicitly opted out with a reason. Co-Authored-By: Claude Opus 4.8 (1M context) * docs: unify docs-block marker model (s3 + gpu) in #4016 spec Replace the bespoke hidden-moto-setup-block approach for the S3 example with a marker-bound model: a block declares markers="s3"/"gpu" on the fence, and the harness binds each marker to the infra/env it needs (s3 -> moto fixture in the default doctest env; gpu -> gputest env via pytest -m gpu). Symmetric declaration; the asymmetry is only in what each marker resolves to. Co-Authored-By: Claude Opus 4.8 (1M context) * docs: link spec to upstream issue #4017 Co-Authored-By: Claude Opus 4.8 (1M context) * docs: implementation plan for docs-block validation (#4016, #4017) Co-Authored-By: Claude Opus 4.8 (1M context) * test: spike s3 default-endpoint mechanism for docs (no storage_options) Result: A-env-var A bare zarr.create_array("s3://bucket/key", ...) with NO storage_options reaches a moto server when AWS_ENDPOINT_URL is set process-wide. s3fs/ aiobotocore honor the env var, so the visible docs block can stay clean. Caveat: moto[s3,server] currently lives only in the 'remote-tests' dependency group, not 'test'; the doctest hatch env (dependency-groups= ['test']) does NOT have moto installed. The downstream real-fixture task must add moto[s3,server] (and requests) to the doctest env extras. Co-Authored-By: Claude Opus 4.8 (1M context) * test: register s3 pytest marker * test: parse markers= on docs blocks and add moto s3 fixture binding Co-Authored-By: Claude Opus 4.8 (1M context) * docs: fix invalid s3 create_array example and run it against moto (#4016) Co-Authored-By: Claude Opus 4.8 (1M context) * docs: execute config-setting examples in performance.md and arrays.md Co-Authored-By: Claude Opus 4.8 (1M context) * docs: make cli zarr.open example runnable against a local store * docs: execute gpu example under the gpu marker Co-Authored-By: Claude Opus 4.8 (1M context) * docs: fix exec=on typo and explicitly opt out non-runnable blocks Co-Authored-By: Claude Opus 4.8 (1M context) * docs: make dask performance example runnable (or opt out if dask absent) * docs: record plan corrections from execution (spike result, gpu marker mechanism) Co-Authored-By: Claude Opus 4.8 (1M context) * test: guard that every docs python block is executed or opted out (#4017) Co-Authored-By: Claude Opus 4.8 (1M context) * docs: separate `test` flag from `exec` so infra-bound examples don't break the build markdown-exec's `exec="true"` means "run at build to render output"; build runners have no GPU/cupy and no moto server, so tagging the GPU/S3 examples exec="true" made `mkdocs build --strict` abort. Introduce a separate `test="true"` flag that our tests/test_docs.py harness keys on (markdown-exec ignores it): a block is validated if exec="true" OR test="true". The GPU and S3 examples become test="true" (+markers) and are no longer run at build. Also: a test="true"-only python fence placed before an exec="true" block of the same page disrupts markdown-exec's build execution of the later block (the quickstart ZipStore example failed with FileNotFoundError). Move the S3 example to the end of quick-start.md so no shared-session exec block follows it; document the constraint in the guard docstring and the design spec. Verified: full docs test suite green (57 passed, 2 skipped), `mkdocs build --strict` exits 0, prek (ruff/mypy/...) clean. Co-Authored-By: Claude Opus 4.8 (1M context) * docs: add news fragment for docs-block validation (#4016, #4017) Co-Authored-By: Claude Opus 4.8 (1M context) * test: harden docs_s3_backend teardown and make cli example idempotent Address roborev branch-review findings (job 186): - Medium: moto-api reset POST ran before server.stop()/env restore in the finally block; if it raised, the fixed-port server thread leaked and AWS_ENDPOINT_URL was left dangling. Nest the reset in its own try/finally so server.stop() and env restoration always run. - Low: f"{S3_ENDPOINT}/moto-api/reset" double-slashed (constant ends in /); drop the extra slash. - Low: AWS_SECRET_ACCESS_KEY/AWS_ACCESS_KEY_ID were setdefault'd but never restored; save/restore all three mutated env vars uniformly. - Low: cli.md create_array lacked overwrite=True, non-idempotent across local runs; add it. Verified: full docs suite green (57 passed, 2 skipped), s3+cli pass on repeated runs, mkdocs build --strict exits 0, prek clean. Co-Authored-By: Claude Opus 4.8 (1M context) * test: actually run the gpu docs example on GPU; align collector/guard scope Address roborev branch-review findings (job 188): - Medium: the gpu docs example ran in NO environment. The gputest env lacks pytest-examples, so test_docs.py's module-level importorskip("pytest_examples") skipped the whole module under `pytest -m gpu` -- the gpu case was never collected even on GPU hardware, yet the guard reported it "validated" via test="true". Add pytest-examples to the gputest env; confirmed gpu-demo now collects under `hatch -e gputest run pytest -m gpu --co`. - Low: _session_params (collection) didn't exclude docs/superpowers/ while the guard did -- an asymmetry that could run a cache-doc block as a real test without the guard flagging it. Extract a shared _is_published_docs() helper used by both, so collection and guard agree on scope. Verified: doctest suite green (57 passed, 2 skipped), gpu-demo collectable in gputest, mkdocs build --strict exits 0, prek clean. Co-Authored-By: Claude Opus 4.8 (1M context) * test: enforce test-only block placement; drop redundant marker round-trip Address roborev branch-review findings (job 190): - Low: the "test=true-only block must not precede an exec=true block on the same page" constraint was documented but unenforced (only caught by mkdocs --strict). Add test_test_only_blocks_come_last, which fails fast/locally when a test-only block has a smaller start_line than a later same-file exec=true block. Negative- checked: it catches an exec block added after the gpu test-only block. - Low: _markers_for built pytest.MarkDecorator objects that _session_params immediately reduced to .name and rebuilt; replace with _marker_names returning raw strings, building decorators once at param time. Verified: doctest suite green (58 passed, 2 skipped), placement test passes and fails on a planted violation, prek clean, mkdocs build --strict exits 0. Co-Authored-By: Claude Opus 4.8 (1M context) * ci: make docs build strict; correct placement-hazard scope Address roborev branch-review finding (job 192): the placement guard's docstring claimed any non-exec="true" python fence before an exec="true" block breaks the build, but the guard only checked test="true" blocks, leaving exec="false"-before- exec="true" arrangements (data_types.md, performance.md) unguarded. Investigation (experiments + markdown-exec's SuperFences integration) established the real mechanism: a non-executed python fence (test="true" OR exec="false") before an exec="true" block disrupts build-time execution of a later *state-dependent* block (needs a cross-block dependency to surface, which is why the standalone exec="true" blocks under those exec="false" opt-outs build fine). CI ran non-strict `mkdocs build`, so such a failure would have merged as a silent warning. - ci/docs.yml: `mkdocs build` -> `mkdocs build --strict` so any build-time exec failure (including the exec="false" case) fails CI authoritatively. Verified: a clean build currently emits zero warnings, so --strict passes today. - Narrow the placement guard's docstring and the spec to the real (state-dependent) mechanism, and frame test_test_only_blocks_come_last as a conservative fast-feedback convention with --strict as the authoritative check -- no longer over-claiming. Verified: docs suite green (58 passed, 2 skipped), `mkdocs build --strict` exits 0, prek clean. Co-Authored-By: Claude Opus 4.8 (1M context) * docs: remove design spec/plan caches from version control The spec and implementation plan under docs/superpowers/ were working artifacts, not published documentation (they were never in the mkdocs nav). The spec is preserved in a public gist; the plan is a local execution record. Remove both from the repo and drop the now-stale spec path from the test_docs.py module docstring. Co-Authored-By: Claude Opus 4.8 (1M context) * test: drop superpowers-docs exclusion now that those files are gone The _is_published_docs helper existed only to skip docs/superpowers/ design-doc caches; those files are no longer in the repo, so the helper and its three call sites were dead code referencing a nonexistent directory. Remove them — every find_examples(DOCS_ROOT) result is now published docs. Co-Authored-By: Claude Opus 4.8 (1M context) * test: share one moto S3 backend across fsspec and docs tests Both test_store/test_fsspec.py and test_docs.py stood up their own moto ThreadedMotoServer (ports 5555 and 5556). Extract a single session-scoped `moto_server` fixture + MOTO_ENDPOINT_URL constant into tests/conftest.py and have both consumers reuse it: - test_fsspec.py: s3_base now returns the shared moto_server; its per-test `s3` fixture (bucket "test", explicit endpoint, event-loop cleanup) is unchanged. - test_docs.py: docs_s3_backend depends on moto_server and adds only its docs-specific layer (process-wide AWS_ENDPOINT_URL + "example-bucket"); it no longer owns the server lifecycle. One server now serves the whole session; each consumer creates and moto-api-resets its own bucket. Verified: test_fsspec.py (96 passed), the docs suite (58 passed), both together in one session (154 passed), and the full standard suite in the optional env (5956 passed); prek clean. Co-Authored-By: Claude Opus 4.8 (1M context) * docs: document the exec vs test code-block distinction for contributors The contributing guide explained exec="true" but said nothing about test="true", the exec="false"+reason opt-out, the guard that requires one of them, or the placement constraint -- so a contributor could write a bare block and hit the guard with no explanation. Add a "Validating code blocks: exec vs test" section covering: - exec="true" (build-render) vs test="true" (validate-only) and when to use each - the exec="false" reason="..." opt-out and the test_no_unvalidated_blocks guard - markers="gpu"/"s3" for infra-bound blocks - the placement rule (test-only blocks come last) + --strict CI Attribute examples are shown as inline code rather than nested ```python fences, so pytest-examples' find_examples never mistakes the teaching examples for real blocks (verified: only the two genuine blocks in contributing.md are collected). Co-Authored-By: Claude Opus 4.8 (1M context) --------- Co-authored-by: Claude Opus 4.8 (1M context) --- .github/workflows/docs.yml | 5 +- changes/4016.bugfix.md | 1 + docs/contributing.md | 64 ++++++- docs/quick-start.md | 26 +-- docs/user-guide/arrays.md | 2 +- docs/user-guide/cli.md | 8 +- docs/user-guide/data_types.md | 2 +- docs/user-guide/examples/custom_dtype.md | 2 +- docs/user-guide/gpu.md | 2 +- docs/user-guide/performance.md | 6 +- docs/user-guide/v3_migration.md | 2 +- pyproject.toml | 8 +- tests/conftest.py | 28 +++ tests/test_docs.py | 230 +++++++++++++++++++---- tests/test_store/test_fsspec.py | 30 ++- 15 files changed, 328 insertions(+), 88 deletions(-) create mode 100644 changes/4016.bugfix.md diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6515a2c4c2..fb5487ada4 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -24,7 +24,10 @@ jobs: persist-credentials: false - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 - run: uv sync --group docs - - run: uv run mkdocs build + # --strict turns warnings into errors, so a docs code block that fails to execute + # at build time (e.g. a non-exec python fence disrupting a later exec="true" block) + # fails CI instead of merging as a silent warning. + - run: uv run mkdocs build --strict env: DISABLE_MKDOCS_2_WARNING: "true" NO_MKDOCS_2_WARNING: "true" diff --git a/changes/4016.bugfix.md b/changes/4016.bugfix.md new file mode 100644 index 0000000000..01984110f7 --- /dev/null +++ b/changes/4016.bugfix.md @@ -0,0 +1 @@ +Fixed an invalid `zarr.create_array` example in the quick-start documentation (it passed an unsupported `mode` argument) and made the cloud-storage example execute against a mock S3 backend in CI. Added a test ensuring every Python code block in the documentation is either executed or explicitly opted out with a documented reason, so an invalid example can no longer go untested. diff --git a/docs/contributing.md b/docs/contributing.md index b9c7aa1aa2..e4906f6db5 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -12,7 +12,7 @@ If you find a bug, please raise a [GitHub issue](https://github.com/zarr-develop 1. A minimal, self-contained snippet of Python code reproducing the problem. You can format the code nicely using markdown, e.g.: -```python +```python exec="false" reason="illustrative pseudocode with a '# etc.' placeholder, not runnable" import zarr g = zarr.group() # etc. @@ -225,10 +225,10 @@ hatch --env docs run serve #### Adding executable code blocks in the documentation -Zarr uses [Markdown Exec](https://pawamoy.github.io/markdown-exec/usage/) to execute code blocks in Markdown files. Add `exec="on"` to a code block header for it to be executed when the docs are built. For example: +Zarr uses [Markdown Exec](https://pawamoy.github.io/markdown-exec/usage/) to execute code blocks in Markdown files. Add `exec="true"` to a code block header for it to be executed when the docs are built. For example: ````md -```python exec="on" +```python exec="true" print("Hello world") ``` ```` @@ -253,6 +253,64 @@ renders as: print("Hello world") ``` +#### Validating code blocks: `exec` vs `test` + +Every Python code block in the documentation is checked by a test +(`tests/test_docs.py`) so that examples cannot quietly rot — the bug that motivated +this was an example calling `zarr.create_array(..., mode="w")`, an argument that does +not exist, which went unnoticed because nothing ran it. A block declares *how* it is +validated using one of two independent attributes: + + - **`exec="true"`** — Markdown Exec runs the block **at docs-build time to render its + output** into the page. This is the attribute described above; it is also what the + test suite executes. Use it for ordinary examples whose output should appear in the + docs. + - **`test="true"`** — the block is **run by the test suite only**, *not* at build time. + Use this for an example that should be validated but cannot run in the docs-build + environment — for example one that needs a GPU or a cloud backend. Markdown Exec + leaves a `test="true"` block as a static, syntax-highlighted snippet (it never + executes it), while the test suite still runs it (see the marker note below). + +A block may carry both (`exec="true" test="true"`), though in practice `exec="true"` +already implies it is tested, so you rarely need `test="true"` alongside it. + +The two attributes are kept separate on purpose: `exec=` controls *build-time rendering* +and `test=` controls *test-time validation*. Tagging a GPU/cloud example `exec="true"` +would make `mkdocs build` try to run it on a machine without that infrastructure and fail +the build; `test="true"` lets it be validated without being built. + +##### Opting a block out of validation + +A handful of blocks genuinely cannot run and are not executable Python — a REPL +transcript, a deliberately-incorrect "before" snippet, a `--8<--` file include. Mark +these explicitly by opening the fence with +`exec="false" reason="REPL output transcript, not executable source"` (supply a reason +that fits the block). + +`exec="false"` with a non-empty `reason` is an explicit, greppable opt-out. A test +(`test_no_unvalidated_blocks`) requires **every** Python block to be either `exec="true"`, +`test="true"`, or `exec="false"` with a reason — so a block can never silently skip +validation. A bare ` ```python ` fence, or a typo like `exec="on"`, fails that test. + +##### Marker-bound blocks (GPU, S3) + +A `test="true"` block that needs special infrastructure declares a pytest marker with +`markers="..."`, which binds it to that infrastructure in the test suite: + + - `markers="gpu"` — run only under `pytest -m gpu` (the GPU CI environment); skipped + elsewhere via `importorskip("cupy")`. + - `markers="s3"` — run against a mock S3 (moto) backend supplied by a test fixture, so + the example can use a bare `s3://…` URL with no test-only connection details on show. + +##### Placement of `test="true"` blocks + +Because Markdown Exec does not execute a `test="true"` (or `exec="false"`) block, placing +one *before* an `exec="true"` block on the same page can disrupt the build-time execution +of that later block. Put `test="true"` blocks **after** all `exec="true"` blocks on the +page (or on a page where they are the only Python block). The `test_test_only_blocks_come_last` +test enforces this, and the CI docs build runs with `--strict` so any such breakage fails +the build rather than passing as a warning. + #### Building documentation without executing code blocks Sometimes, you may want the documentation to build quicker. You can disable code block execution by commenting out the [markdown-exec plugin](https://github.com/zarr-developers/zarr-python/blob/884a8c91afcc3efe28b3da952be3b85125c453cb/mkdocs.yml#L132) in the mkdocs configuration file. This will make code blocks and cross references render incorrectly (i.e., expect build warnings), but also reduces build time by ~3x. Be sure to undo the commenting out before opening your pull request. diff --git a/docs/quick-start.md b/docs/quick-start.md index 27dc8e6045..0bad4f2e34 100644 --- a/docs/quick-start.md +++ b/docs/quick-start.md @@ -127,18 +127,6 @@ be done in a separate step. Zarr supports persistent storage to disk or cloud-compatible backends. While examples above utilized a [`zarr.storage.LocalStore`][], a number of other storage options are available. -Zarr integrates seamlessly with cloud object storage such as Amazon S3 and Google Cloud Storage -using external libraries like [s3fs](https://s3fs.readthedocs.io) or -[gcsfs](https://gcsfs.readthedocs.io): - -```python - -import s3fs - -z = zarr.create_array("s3://example-bucket/foo", mode="w", shape=(100, 100), chunks=(10, 10), dtype="f4") -z[:, :] = np.random.random((100, 100)) -``` - A single-file store can also be created using the [`zarr.storage.ZipStore`][]: ```python exec="true" session="quickstart" source="above" @@ -173,4 +161,18 @@ z = zarr.open_array(store, mode='r') print(z[:]) ``` +Zarr also integrates seamlessly with cloud object storage such as Amazon S3 and Google +Cloud Storage using external libraries like [s3fs](https://s3fs.readthedocs.io) or +[gcsfs](https://gcsfs.readthedocs.io): + +```python test="true" session="s3demo" markers="s3" source="above" +import zarr +import numpy as np + +z = zarr.create_array( + "s3://example-bucket/foo", shape=(100, 100), chunks=(10, 10), dtype="f4" +) +z[:, :] = np.random.random((100, 100)) +``` + Read more about Zarr's storage options in the [User Guide](user-guide/index.md). diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 14122003c0..dd1788b7d2 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -619,7 +619,7 @@ Without the `shards` argument, there would be 10,000 chunks stored as individual Because the feature is still stabilizing, it is disabled by default and must be explicitly enabled: - ```python + ```python exec="true" session="arrays-rectilinear" import zarr zarr.config.set({"array.rectilinear_chunks": True}) ``` diff --git a/docs/user-guide/cli.md b/docs/user-guide/cli.md index fc812c1a20..13fcb6f1b6 100644 --- a/docs/user-guide/cli.md +++ b/docs/user-guide/cli.md @@ -45,9 +45,13 @@ This will write new `zarr.json` files to `input.zarr`, leaving the existing v2 m To open the array/group using the new metadata use: -```python +```python exec="true" session="cli-open" source="above" import zarr -zarr_with_v3_metadata = zarr.open('path/to/input.zarr', zarr_format=3) + +# create a small array to open (stands in for the migrated store) +zarr.create_array("data/cli-demo.zarr", shape=(4, 4), chunks=(2, 2), dtype="i4", overwrite=True) + +zarr_with_v3_metadata = zarr.open("data/cli-demo.zarr", zarr_format=3) ``` Once you are happy with the conversion, you can run the following to remove the old v2 metadata: diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md index 3e10845979..6f6bb05033 100644 --- a/docs/user-guide/data_types.md +++ b/docs/user-guide/data_types.md @@ -360,7 +360,7 @@ print(type(a.dtype)) But if we inspect the metadata for the array, we can see the Zarr data type object: -```python +```python exec="false" reason="REPL output transcript, not executable source" type(a.metadata.data_type) ``` diff --git a/docs/user-guide/examples/custom_dtype.md b/docs/user-guide/examples/custom_dtype.md index d6736e25dd..391407b822 100644 --- a/docs/user-guide/examples/custom_dtype.md +++ b/docs/user-guide/examples/custom_dtype.md @@ -2,6 +2,6 @@ ## Source Code -```python +```python exec="false" reason="pymdownx snippet include directive, not python source" --8<-- "examples/custom_dtype/custom_dtype.py" ``` diff --git a/docs/user-guide/gpu.md b/docs/user-guide/gpu.md index 6189f39d3d..6c26c3e564 100644 --- a/docs/user-guide/gpu.md +++ b/docs/user-guide/gpu.md @@ -16,7 +16,7 @@ Zarr can use GPUs to accelerate your workload by running `zarr.Config.enable_gpu [`zarr.config`][] configures Zarr to use GPU memory for the data buffers used internally by Zarr via `enable_gpu()`. -```python +```python test="true" session="gpu-demo" markers="gpu" source="above" import zarr import cupy as cp zarr.config.enable_gpu() diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index fa98e9466e..3357913557 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -204,7 +204,7 @@ determines the maximum number of concurrent I/O operations. The default value is 10, which is a conservative value. You may get improved performance by tuning the concurrency limit. You can adjust this value based on your specific needs: -```python +```python exec="true" session="perf-concurrency" import zarr # Set concurrency for the current session @@ -234,7 +234,7 @@ By default it is `None`, which lets Python choose the pool size (typically You can set it explicitly when you want more predictable resource usage: -```python +```python exec="true" session="perf-workers" import zarr zarr.config.set({'threading.max_workers': 8}) @@ -260,7 +260,7 @@ For example, if you're running Dask with 10 threads and Zarr's default concurren **Recommendation**: When using Dask with many threads, configure Zarr's concurrency settings: -```python +```python exec="false" reason="requires dask, which is not in the docs test environment" import zarr import dask.array as da diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index 21386c1522..1680547d93 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -39,7 +39,7 @@ the following actions in order: - `numcodecs.*` will no longer be available in `zarr.*`. To migrate, import codecs directly from `numcodecs`: - ```python + ```python exec="false" reason="intentionally shows the old/incorrect import for contrast" from numcodecs import Blosc # instead of: # from zarr import Blosc diff --git a/pyproject.toml b/pyproject.toml index 81a4461978..23eba4e643 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -204,6 +204,10 @@ list-env = "pip list" template = "test" extra-dependencies = [ "universal_pathlib", + # Needed so tests/test_docs.py is collectable under `pytest -m gpu`; otherwise its + # module-level importorskip("pytest_examples") skips the whole module and the gpu + # docs example is never executed on GPU hardware. + "pytest-examples", ] features = ["gpu"] @@ -277,9 +281,8 @@ readthedocs = "rm -rf $READTHEDOCS_OUTPUT/html && cp -r site $READTHEDOCS_OUTPUT [tool.hatch.envs.doctest] description = "Test environment for validating executable code blocks in documentation" features = ['remote'] -dependency-groups = ['test'] +dependency-groups = ['remote-tests'] extra-dependencies = [ - "s3fs>=2023.10.0", "pytest-examples", ] @@ -446,6 +449,7 @@ filterwarnings = [ markers = [ "asyncio: mark test as asyncio test", "gpu: mark a test as requiring CuPy and GPU", + "s3: mark a test as requiring a (mock) S3 backend via moto", "slow_hypothesis: slow hypothesis tests", ] diff --git a/tests/conftest.py b/tests/conftest.py index 3515acace0..3402eb7063 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -531,3 +531,31 @@ def deep_nan_equal(a: object, b: object) -> bool: if isinstance(a, Sequence) and isinstance(b, Sequence): return all(deep_nan_equal(a[i], b[i]) for i in range(len(a))) return nan_equal(a, b) + + +# Shared mock-S3 (moto) backend. A single server is reused across the whole test session by +# every test that needs S3 -- both the fsspec store tests and the documentation examples -- +# instead of each module standing up its own. Consumers create their own buckets and choose +# how the endpoint reaches the client (explicit storage_options vs. the AWS_ENDPOINT_URL +# env var) on top of this fixture. +MOTO_SERVER_PORT = 5555 +MOTO_ENDPOINT_URL = f"http://127.0.0.1:{MOTO_SERVER_PORT}/" + + +@pytest.fixture(scope="session") +def moto_server() -> Generator[str, None, None]: + """Start a session-scoped moto S3 server and yield its endpoint URL. + + importorskip lives inside the fixture so moto is only required when a test actually + requests an S3 backend, not for the whole test session.""" + moto_server_mod = pytest.importorskip("moto.moto_server.threaded_moto_server") + + server = moto_server_mod.ThreadedMotoServer(ip_address="127.0.0.1", port=MOTO_SERVER_PORT) + server.start() + # moto needs *some* credentials present; use throwaway values if the environment has none. + os.environ.setdefault("AWS_SECRET_ACCESS_KEY", "foo") + os.environ.setdefault("AWS_ACCESS_KEY_ID", "foo") + try: + yield MOTO_ENDPOINT_URL + finally: + server.stop() diff --git a/tests/test_docs.py b/tests/test_docs.py index d467e478e8..02dca225b0 100644 --- a/tests/test_docs.py +++ b/tests/test_docs.py @@ -1,95 +1,243 @@ """ Tests for executable code blocks in markdown documentation. -This module uses pytest-examples to validate that all Python code examples -with exec="true" in the documentation execute successfully. +This module uses pytest-examples to validate Python code examples in the docs. A block is +validated if it renders output at build (exec="true") or is explicitly marked for testing +(test="true"). The two flags are separate on purpose: exec= drives markdown-exec's +build-time rendering, while test= lets a block be validated without being run at build +(e.g. gpu/s3 examples the build environment cannot run). The test_no_unvalidated_blocks +guard ensures every python block declares one of those, or an explicit exec="false" opt-out +with a reason, so a block can never silently skip validation. """ from __future__ import annotations +import os from collections import defaultdict from pathlib import Path +from typing import TYPE_CHECKING, Any import pytest pytest.importorskip("pytest_examples") from pytest_examples import CodeExample, EvalExample, find_examples -# Find all markdown files with executable code blocks +if TYPE_CHECKING: + from collections.abc import Generator + DOCS_ROOT = Path(__file__).parent.parent / "docs" SOURCES_ROOT = Path(__file__).parent.parent / "src" / "zarr" -def find_markdown_files_with_exec() -> list[Path]: - """Find all markdown files containing exec="true" code blocks.""" - markdown_files = [] +def name_example(path: str, session: str) -> str: + """Generate a readable name for a test case from file path and session.""" + file = Path(path) + try: + file = file.relative_to(DOCS_ROOT) + except ValueError: + # Path is outside DOCS_ROOT (e.g. a tmp_path fixture in unit tests); use the + # bare file name rather than an absolute path for a stable, readable id. + file = Path(file.name) + return f"{file}:{session}" - for md_file in DOCS_ROOT.rglob("*.md"): - try: - content = md_file.read_text(encoding="utf-8") - if 'exec="true"' in content: - markdown_files.append(md_file) - except Exception: - # Skip files that can't be read + +def _marker_names(settings: dict[str, str]) -> list[str]: + """Parse a block's markers="a b" attribute into a list of marker names.""" + return [name for name in settings.get("markers", "").split() if name] + + +def _is_tested(settings: dict[str, str]) -> bool: + """A block is validated by our pytest harness if it is run at build to render output + (exec="true") OR explicitly marked for testing (test="true"). The two flags are + separate on purpose: exec= drives markdown-exec's build-time rendering, while test= + lets a block be validated without being run at build (e.g. gpu/s3 blocks, which the + build environment cannot run).""" + return settings.get("exec") == "true" or settings.get("test") == "true" + + +def _session_params(root: Path) -> list[Any]: + """Group tested examples (exec="true" or test="true") by (file, session) and emit one + pytest.param per session, carrying the union of markers declared by that session's + blocks.""" + sessions: defaultdict[tuple[str, str], list[CodeExample]] = defaultdict(list) + marks_by_session: defaultdict[tuple[str, str], set[str]] = defaultdict(set) + + for example in find_examples(str(root)): + settings = example.prefix_settings() + if not _is_tested(settings): continue + session_name = settings.get("session", "_default") + key = (str(example.path), session_name) + sessions[key].append(example) + marks_by_session[key].update(_marker_names(settings)) - return sorted(markdown_files) + params = [] + for key in sorted(sessions.keys(), key=lambda x: (x[0], x[1])): + marks = tuple(getattr(pytest.mark, name) for name in sorted(marks_by_session[key])) + params.append(pytest.param(key, marks=marks, id=name_example(key[0], key[1]))) + return params -def group_examples_by_session() -> list[tuple[str, str]]: - """ - Group examples by their session and file, maintaining order. +S3_BUCKET = "example-bucket" - Returns a list of session_key tuples where session_key is - (file_path, session_name). - """ - all_examples = list(find_examples(DOCS_ROOT)) - # Group by file and session - sessions = defaultdict(list) +@pytest.fixture +def docs_s3_backend(moto_server: str) -> Generator[None, None, None]: + """Point docs S3 examples at the shared moto server (tests/conftest.py) via a + process-wide AWS_ENDPOINT_URL, so a block can use a bare s3:// URL with no + storage_options (see spike in the design notes). The server lifecycle belongs to the + session-scoped `moto_server` fixture; this fixture only adds the docs-specific + endpoint env var and a fresh bucket, and restores both on teardown.""" + s3fs = pytest.importorskip("s3fs") + botocore = pytest.importorskip("botocore") + requests = pytest.importorskip("requests") - for example in all_examples: + prev_endpoint = os.environ.get("AWS_ENDPOINT_URL") + os.environ["AWS_ENDPOINT_URL"] = moto_server + + session = botocore.session.Session() + client = session.create_client("s3", endpoint_url=moto_server, region_name="us-east-1") + client.create_bucket(Bucket=S3_BUCKET) + client.close() + s3fs.S3FileSystem.clear_instance_cache() + try: + yield + finally: + # Reset moto state and restore AWS_ENDPOINT_URL; the shared server keeps running + # (the moto_server fixture stops it at session end). + try: + requests.post(f"{moto_server}moto-api/reset") + finally: + if prev_endpoint is None: + os.environ.pop("AWS_ENDPOINT_URL", None) + else: + os.environ["AWS_ENDPOINT_URL"] = prev_endpoint + + +def test_markers_attribute_is_parsed(tmp_path: Path) -> None: + """A test="true" block tagged markers="s3" must surface that marker on its + parametrized case, so pytest can gate/bind it (e.g. attach the moto fixture). + Uses test="true" (not exec="true") because marker-bound blocks are validated by the + harness without being run at build time.""" + md = tmp_path / "ex.md" + md.write_text( + '```python test="true" session="demo" markers="s3"\nimport zarr\n```\n', + encoding="utf-8", + ) + params = _session_params(md.parent) + assert len(params) == 1 + marks = params[0].marks + assert any(m.name == "s3" for m in marks) + + +def test_no_unvalidated_blocks() -> None: + """Every python code block in docs/ must declare its validation state: exec="true" + (run at build to render output), test="true" (validated by this harness without being + run at build), or exec="false" with a reason (explicit, documented opt-out). A bare or + mistyped fence (e.g. exec="on") fails here, so a block can never silently opt out of + validation -- the gap that hid the invalid create_array(mode="w") example in #4016. + + A separate placement constraint is enforced by test_test_only_blocks_come_last.""" + offenders: list[str] = [] + for example in find_examples(str(DOCS_ROOT)): + rel = Path(example.path).relative_to(DOCS_ROOT) settings = example.prefix_settings() - if settings.get("exec") != "true": + exec_val = settings.get("exec") + loc = f"{rel}:{example.start_line}" + # Validated either by build-render (exec="true") or by the test harness + # (test="true"). + if _is_tested(settings): + continue + # Explicit, documented opt-out from execution. + if exec_val == "false" and settings.get("reason", "").strip(): continue + offenders.append( + f"{loc} (exec={exec_val!r}, test={settings.get('test')!r}, " + f"reason={settings.get('reason')!r})" + ) - # Use file path and session name as key - file_path = example.path - session_name = settings.get("session", "_default") - session_key = (str(file_path), session_name) + assert not offenders, ( + 'Docs python blocks must be exec="true", test="true", or exec="false" with a ' + "reason:\n" + "\n".join(offenders) + ) - sessions[session_key].append(example) - # Return sorted list of session keys for consistent test ordering - return sorted(sessions.keys(), key=lambda x: (x[0], x[1])) +def test_test_only_blocks_come_last() -> None: + """A conservative placement convention: a test="true"-only block must come after every + exec="true" block in the same file. + Mechanism (established by experiment + markdown-exec's SuperFences integration): a + python fence that markdown-exec does not execute -- i.e. one lacking exec="true", + whether test="true" or exec="false" -- placed before an exec="true" block disrupts + markdown-exec's build-time execution of a *later, state-dependent* block. Observed: a + non-exec python fence inserted before the quickstart ZipStore write/read pair made the + read block fail with FileNotFoundError (the write never took effect), aborting + `mkdocs build --strict`. The effect needs a cross-block dependency to surface, so it + does not affect the standalone exec="true" blocks in e.g. data_types.md/performance.md + that already have exec="false" opt-out blocks above them. -def name_example(path: str, session: str) -> str: - """Generate a readable name for a test case from file path and session.""" - return f"{Path(path).relative_to(DOCS_ROOT)}:{session}" + Because we cannot statically tell which later blocks are state-dependent, this guard + enforces the simple, safe convention only for the blocks we author this way + (test="true" marker-bound examples like s3/gpu). It is NOT a complete build-hazard + check -- the authoritative check is `mkdocs build --strict` (the docs:check CI job), + which catches the exec="false" case too. This guard just turns the common test-only + case into a fast, local failure.""" + # Collect, per published-docs file, the start lines of test-only and exec blocks. + test_only: defaultdict[str, list[int]] = defaultdict(list) + exec_lines: defaultdict[str, list[int]] = defaultdict(list) + for example in find_examples(str(DOCS_ROOT)): + settings = example.prefix_settings() + path = str(example.path) + if settings.get("exec") == "true": + exec_lines[path].append(example.start_line) + elif settings.get("test") == "true": + test_only[path].append(example.start_line) + + offenders: list[str] = [] + for path, only_lines in test_only.items(): + rel = Path(path).relative_to(DOCS_ROOT) + last_exec = max(exec_lines.get(path, [0])) + offenders.extend( + f'{rel}:{line} (test="true" block precedes an exec="true" block at line {last_exec})' + for line in only_lines + if line < last_exec + ) + + assert not offenders, ( + 'A test="true"-only block must come after every exec="true" block in the same ' + 'file: a non-executed python fence before an exec="true" block can disrupt ' + "markdown-exec's build-time execution of a later state-dependent block (see this " + "test's docstring):\n" + "\n".join(offenders) + ) # Get all example sessions -@pytest.mark.parametrize( - "session_key", group_examples_by_session(), ids=lambda v: name_example(v[0], v[1]) -) +@pytest.mark.parametrize("session_key", _session_params(DOCS_ROOT)) def test_documentation_examples( session_key: tuple[str, str], eval_example: EvalExample, + request: pytest.FixtureRequest, ) -> None: """ - Test that all exec="true" code examples in documentation execute successfully. + Test that all validated code examples (exec="true" or test="true") in documentation + execute successfully. This test groups examples by session (file + session name) and runs them sequentially in the same execution context, allowing code to build on previous examples. This test uses pytest-examples to: - - Find all code examples with exec="true" in markdown files + - Find all code examples marked exec="true" or test="true" in markdown files - Group them by session - Execute them in order within the same context - Verify no exceptions are raised """ + if request.node.get_closest_marker("gpu") is not None: + pytest.importorskip("cupy") + + if request.node.get_closest_marker("s3") is not None: + request.getfixturevalue("docs_s3_backend") + file_path, session_name = session_key # Get examples for this session @@ -97,7 +245,7 @@ def test_documentation_examples( examples = [] for example in all_examples: settings = example.prefix_settings() - if settings.get("exec") != "true": + if not _is_tested(settings): continue if str(example.path) == file_path and settings.get("session", "_default") == session_name: examples.append(example) diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 8006470174..9efee40d7a 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -1,7 +1,6 @@ from __future__ import annotations import json -import os import re from typing import TYPE_CHECKING, Any @@ -10,6 +9,7 @@ from packaging.version import parse as parse_version import zarr.api.asynchronous +from tests.conftest import MOTO_ENDPOINT_URL from zarr import Array from zarr.abc.store import OffsetByteRequest from zarr.core.buffer import Buffer, cpu, default_buffer_prototype @@ -52,31 +52,23 @@ fsspec = pytest.importorskip("fsspec") s3fs = pytest.importorskip("s3fs") requests = pytest.importorskip("requests") -moto_server = pytest.importorskip("moto.moto_server.threaded_moto_server") -moto = pytest.importorskip("moto") +# Skip this module entirely when moto is absent; the server itself comes from the shared +# `moto_server` fixture in tests/conftest.py. +pytest.importorskip("moto") botocore = pytest.importorskip("botocore") # ### amended from s3fs ### # test_bucket_name = "test" secure_bucket_name = "test-secure" -port = 5555 -endpoint_url = f"http://127.0.0.1:{port}/" +# The moto server itself is the session-scoped `moto_server` fixture in tests/conftest.py; +# this module reuses its endpoint rather than standing up its own server. +endpoint_url = MOTO_ENDPOINT_URL -@pytest.fixture(scope="module") -def s3_base() -> Generator[None, None, None]: - # writable local S3 system - - # This fixture is module-scoped, meaning that we can reuse the MotoServer across all tests - server = moto_server.ThreadedMotoServer(ip_address="127.0.0.1", port=port) - server.start() - if "AWS_SECRET_ACCESS_KEY" not in os.environ: - os.environ["AWS_SECRET_ACCESS_KEY"] = "foo" - if "AWS_ACCESS_KEY_ID" not in os.environ: - os.environ["AWS_ACCESS_KEY_ID"] = "foo" - - yield - server.stop() +@pytest.fixture +def s3_base(moto_server: str) -> str: + """Reuse the shared session-scoped moto server (see tests/conftest.py).""" + return moto_server def get_boto3_client() -> botocore.client.BaseClient: From fe229107f9915f05817f7a664d3550695ff9ca44 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 22:56:38 +0200 Subject: [PATCH 335/468] chore(deps-dev): bump uv in the uv group across 1 directory (#4019) Bumps the uv group with 1 update in the / directory: [uv](https://github.com/astral-sh/uv). Updates `uv` from 0.11.14 to 0.11.15 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.11.14...0.11.15) --- updated-dependencies: - dependency-name: uv dependency-version: 0.11.15 dependency-type: direct:development ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- uv.lock | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/uv.lock b/uv.lock index d23f1f2027..8f06e43cb6 100644 --- a/uv.lock +++ b/uv.lock @@ -3661,28 +3661,28 @@ wheels = [ [[package]] name = "uv" -version = "0.11.14" -source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/30/a3/be4a946c7c2fc4094c020c8f7d8bd0a739bad55ebe4e2817d6e2b1bc6bff/uv-0.11.14.tar.gz", hash = "sha256:0ea006a117b586b2681b6dfd9703a540d2ad2a136ec0f48d272767e599cc3dfb", size = 4130699, upload-time = "2026-05-12T18:00:37.321Z" } -wheels = [ - { url = "https://files.pythonhosted.org/packages/f7/15/9b2138b16eb1fa8c2cd84b1037ad10c38b3acc36ce96c6d27000bfb7e716/uv-0.11.14-py3-none-linux_armv6l.whl", hash = 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2026 12:08:59 +0200 Subject: [PATCH 336/468] refactor: remove random subchunk ordering (#4011) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat: subchunk write order (#3826) * feat: subchunk write order * chore: export `SubchunkWriteOrder` * chore: docs * chore: relnote * rename * refactor: no enums * Update docs/user-guide/performance.md Co-authored-by: Davis Bennett * feat: deterministic but random order * fix: make vectorized fetching less reliant on matching order * chore: add hypothesis * refactor: dead code * refactor: more cleanup * don't shard unless there is something to shard * fix: dont mix chunk grid and sharding --------- Co-authored-by: Davis Bennett (cherry picked from commit 093a153dbbb904351234dcb6c85fb4dda36d01d9) * refactor: unordered subchunk order means no-promise, not random Co-Authored-By: Claude Opus 4.7 (1M context) * test: pin subchunk_write_order survival through pickle Co-Authored-By: Claude Opus 4.7 (1M context) * refactor: remove rng from ShardingCodec; carry subchunk_write_order through pickle Co-Authored-By: Claude Opus 4.7 (1M context) * docs: describe unordered subchunk order as no-guarantee, drop rng Co-Authored-By: Claude Opus 4.7 (1M context) * test: drive sharding strategy through serializer to exercise subchunk_write_order The hypothesis arrays() strategy passed both shards= and a ShardingCodec serializer, which nested the codecs and left subchunk_write_order governing only a 1-element inner grid. Drive sharding through the serializer alone. Co-Authored-By: Claude Opus 4.7 (1M context) * harden: guard _subchunk_order_iter; document write-order is not persisted Co-Authored-By: Claude Opus 4.7 (1M context) * cleanup: use np.ndindex for immaterial intermediate order; drop stale FIXME Co-Authored-By: Claude Opus 4.7 (1M context) * polish: guard scalar arrays in sharding strategy; align doc value ordering Co-Authored-By: Claude Opus 4.7 (1M context) * Revert strategies.py changes — unrelated to this PR These changes were patching a latent bug in `arrays()` where ShardingCodec-as-serializer was being double-stacked with `shards=...`, producing nested sharding. Splitting to a follow-up PR so this one stays focused on removing the `rng`/random-subchunk-order surface. Co-Authored-By: Claude Opus 4.7 (1M context) --------- Co-authored-by: Ilan Gold Co-authored-by: Claude Opus 4.7 (1M context) --- changes/3826.feature.md | 2 +- docs/user-guide/performance.md | 4 +-- src/zarr/codecs/sharding.py | 35 ++++++++++++--------- tests/test_codecs/test_sharding.py | 50 ++++++++---------------------- 4 files changed, 37 insertions(+), 54 deletions(-) diff --git a/changes/3826.feature.md b/changes/3826.feature.md index 41cc555a92..8909e777c5 100644 --- a/changes/3826.feature.md +++ b/changes/3826.feature.md @@ -1 +1 @@ -Added a `subchunk_write_order` option to `ShardingCodec` to allow for `morton`, `unordered`, `lexicographic`, and `colexicographic` subchunk orderings. \ No newline at end of file +Added a `subchunk_write_order` option to `ShardingCodec` to control the physical order of subchunks within a shard. Supported values are `morton`, `unordered`, `lexicographic`, and `colexicographic`. `unordered` makes no guarantee about subchunk layout. This setting affects only on-disk layout, not the data read back, and is not persisted in array metadata: it applies per codec instance and is not recovered when reopening a sharded array. diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 3357913557..685ce7fe7e 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -115,9 +115,9 @@ filters (e.g., byte-shuffle) have been applied. ### Subchunk memory layout -The order of chunks **within each shard** can be changed via the `subchunk_write_order` parameter of the `ShardingCodec`. That parameter is a string which must be one of `["morton", "lexicographic", "colexicographic", "unordered"]`. +The order of chunks **within each shard** can be changed via the `subchunk_write_order` parameter of the `ShardingCodec`. That parameter is a string which must be one of `["morton", "unordered", "lexicographic", "colexicographic"]`. -By default [`morton`](https://en.wikipedia.org/wiki/Z-order_curve) order provides good spatial locality however [`lexicographic` (i.e., row-major)](https://en.wikipedia.org/wiki/Row-_and_column-major_order), for example, may be better suited to "batched" workflows where some form of sequential reading through a fixed number of outer dimensions is desired. The options are `lexicographic`, `morton`, `unordered` (i.e., random), and `colexicographic`. +By default [`morton`](https://en.wikipedia.org/wiki/Z-order_curve) order provides good spatial locality. [`lexicographic` (i.e., row-major)](https://en.wikipedia.org/wiki/Row-_and_column-major_order), for example, may be better suited to "batched" workflows where some form of sequential reading through a fixed number of outer dimensions is desired, and `colexicographic` is its reverse. `unordered` makes no guarantee about the order in which subchunks are laid out within a shard. ### Empty chunks diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 33c8602ecb..657484e9af 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -294,12 +294,16 @@ def to_dict_vectorized( class ShardingCodec( ArrayBytesCodec, ArrayBytesCodecPartialDecodeMixin, ArrayBytesCodecPartialEncodeMixin ): - """Sharding codec""" + """Sharding codec. + + `subchunk_write_order` controls the physical order of subchunks within a shard. It is a + write-time setting only: it is not stored in array metadata, so reopening a sharded array + does not recover it (the setting reverts to the `morton` default per codec instance). + """ chunk_shape: tuple[int, ...] codecs: tuple[Codec, ...] index_codecs: tuple[Codec, ...] - rng: np.random.Generator | None index_location: ShardingCodecIndexLocation = ShardingCodecIndexLocation.end subchunk_write_order: SubchunkWriteOrder = "morton" @@ -311,7 +315,6 @@ def __init__( index_codecs: Iterable[Codec | dict[str, JSON]] = (BytesCodec(), Crc32cCodec()), index_location: ShardingCodecIndexLocation | str = ShardingCodecIndexLocation.end, subchunk_write_order: SubchunkWriteOrder = "morton", - rng: np.random.Generator | None = None, ) -> None: chunk_shape_parsed = parse_shapelike(chunk_shape) codecs_parsed = parse_codecs(codecs) @@ -327,7 +330,6 @@ def __init__( object.__setattr__(self, "index_codecs", index_codecs_parsed) object.__setattr__(self, "index_location", index_location_parsed) object.__setattr__(self, "subchunk_write_order", subchunk_write_order) - object.__setattr__(self, "rng", rng) # Use instance-local lru_cache to avoid memory leaks @@ -340,7 +342,9 @@ def __init__( # todo: typedict return type def __getstate__(self) -> dict[str, Any]: - return {"rng": self.rng, **self.to_dict()} + # `subchunk_write_order` is not part of codec metadata (`to_dict`), so carry it + # explicitly to survive a pickle round-trip (otherwise it reverts to `morton`). + return {"subchunk_write_order": self.subchunk_write_order, **self.to_dict()} def __setstate__(self, state: dict[str, Any]) -> None: config = state["configuration"] @@ -348,7 +352,7 @@ def __setstate__(self, state: dict[str, Any]) -> None: object.__setattr__(self, "codecs", parse_codecs(config["codecs"])) object.__setattr__(self, "index_codecs", parse_codecs(config["index_codecs"])) object.__setattr__(self, "index_location", parse_index_location(config["index_location"])) - object.__setattr__(self, "rng", state["rng"]) + object.__setattr__(self, "subchunk_write_order", state["subchunk_write_order"]) # Use instance-local lru_cache to avoid memory leaks # object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) @@ -537,11 +541,11 @@ def _subchunk_order_iter( case "colexicographic": subchunk_iter = (c[::-1] for c in np.ndindex(chunks_per_shard[::-1])) case "unordered": - subchunk_list = list(np.ndindex(chunks_per_shard)) - (self.rng if self.rng is not None else np.random.default_rng()).shuffle( - subchunk_list - ) - subchunk_iter = iter(subchunk_list) + # "unordered" promises no particular layout; today it happens to be + # lexicographic, but callers must not rely on that. + subchunk_iter = np.ndindex(chunks_per_shard) + case _: + raise ValueError(f"Unrecognized subchunk write order: {subchunk_write_order!r}.") return subchunk_iter async def _encode_single( @@ -561,7 +565,9 @@ async def _encode_single( chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), ) ) - shard_builder = dict.fromkeys(self._subchunk_order_iter(chunks_per_shard, "lexicographic")) + # The key order of this intermediate dict is immaterial; the physical layout is + # decided later by the `subchunk_write_order` loop in `_encode_shard_dict`. + shard_builder = dict.fromkeys(np.ndindex(chunks_per_shard)) await self.codec_pipeline.write( [ @@ -604,7 +610,8 @@ async def _encode_partial_single( ) if self._is_complete_shard_write(indexer, chunks_per_shard): - shard_dict = dict.fromkeys(self._subchunk_order_iter(chunks_per_shard, "lexicographic")) + # Intermediate key order is immaterial (see `_encode_single`). + shard_dict = dict.fromkeys(np.ndindex(chunks_per_shard)) else: shard_reader = await self._load_full_shard_maybe( byte_getter=byte_setter, @@ -614,7 +621,7 @@ async def _encode_partial_single( shard_reader = shard_reader or _ShardReader.create_empty(chunks_per_shard) # Use vectorized lookup for better performance shard_dict = shard_reader.to_dict_vectorized( - np.array(list(self._subchunk_order_iter(chunks_per_shard, "lexicographic"))) + np.array(list(np.ndindex(chunks_per_shard))) ) await self.codec_pipeline.write( diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 74e4a7e0d5..856d29ef7a 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -669,9 +669,17 @@ async def test_delete_empty_shards(store: Store) -> None: def test_pickle() -> None: + """ShardingCodec round-trips through pickle, including the non-serialized + ``subchunk_write_order`` (which ``to_dict`` omits and which must not silently + revert to the ``morton`` default).""" codec = ShardingCodec(chunk_shape=(8, 8)) assert pickle.loads(pickle.dumps(codec)) == codec + ordered = ShardingCodec(chunk_shape=(8, 8), subchunk_write_order="lexicographic") + restored = pickle.loads(pickle.dumps(ordered)) + assert restored == ordered + assert restored.subchunk_write_order == "lexicographic" + @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) @pytest.mark.parametrize( @@ -867,54 +875,22 @@ async def stored_data_and_get_order( async def test_encoded_subchunk_write_order(subchunk_write_order: SubchunkWriteOrder) -> None: """Subchunks must be physically laid out in the shard in the order specified by ``subchunk_write_order``. We verify this by decoding the shard index and sorting - the chunk coordinates by their byte offset.""" - # Use a non-square chunks_per_shard so all three orderings are distinguishable. + the chunk coordinates by their byte offset. ``unordered`` makes no stable-order + promise, but is deterministic in this implementation, so it is checked the same way.""" + # Use a non-square chunks_per_shard so all orderings are distinguishable. chunks_per_shard = (3, 2) chunk_shape = (4, 4) - seed = 0 codec = ShardingCodec( chunk_shape=chunk_shape, codecs=[BytesCodec()], index_codecs=[BytesCodec(), Crc32cCodec()], index_location=ShardingCodecIndexLocation.end, subchunk_write_order=subchunk_write_order, - rng=np.random.default_rng(seed=seed), ) actual_order = await stored_data_and_get_order(codec, chunks_per_shard) - if subchunk_write_order != "unordered": - expected_order = list(codec._subchunk_order_iter(chunks_per_shard, subchunk_write_order)) - assert actual_order == expected_order - else: - same_order_same_seed = list( - ShardingCodec( - chunk_shape=chunk_shape, - codecs=[BytesCodec()], - index_codecs=[BytesCodec(), Crc32cCodec()], - index_location=ShardingCodecIndexLocation.end, - subchunk_write_order=subchunk_write_order, - rng=np.random.default_rng(seed=seed), - )._subchunk_order_iter(chunks_per_shard, subchunk_write_order) - ) - assert actual_order == same_order_same_seed - - -async def test_unordered_can_be_seeded() -> None: - orders = [] - chunks_per_shard = (3, 2) - chunk_shape = (4, 4) - seed = 0 - for _ in range(4): - codec = ShardingCodec( - chunk_shape=chunk_shape, - codecs=[BytesCodec()], - index_codecs=[BytesCodec(), Crc32cCodec()], - index_location=ShardingCodecIndexLocation.end, - subchunk_write_order="unordered", - rng=np.random.default_rng(seed=seed), - ) - orders.append(await stored_data_and_get_order(codec, chunks_per_shard)) - assert all(orders[0] == o for o in orders) + expected_order = list(codec._subchunk_order_iter(chunks_per_shard, subchunk_write_order)) + assert actual_order == expected_order @pytest.mark.parametrize( From b9d396460da369bea86f4bd978d3746f7a41076b Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Sat, 6 Jun 2026 21:21:40 +0200 Subject: [PATCH 337/468] fix: make xarray downstream tests work (#4043) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * ci: restrict xarray downstream job to the test-py313 pixi environment setup-pixi installs every environment in xarray's manifest by default, which drags in `mypy-upstream`. That environment builds numcodecs from git and fails under newer pixi with `meson-python: error: Unknown option "pixi-conda-environment"`, breaking the job before any test runs — even though all our steps only use `test-py313`. Limit installation to the one environment we actually use. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- .github/workflows/downstream.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 3eb6898895..71784c358d 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -37,6 +37,13 @@ jobs: uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6 with: manifest-path: xarray/pixi.toml + # Only install the environment our steps use. Installing every + # environment in xarray's manifest (the default) drags in + # `mypy-upstream`, which builds numcodecs from git and fails under + # newer pixi with `meson-python: error: Unknown option + # "pixi-conda-environment"` — unrelated to the zarr-python branch + # under test. + environments: test-py313 - name: Install zarr-python from branch working-directory: xarray From 96a62b51f8fe86eeb056eee1684eef94b4114e35 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 8 Jun 2026 22:26:59 -0400 Subject: [PATCH 338/468] test: add property tests for block and mask indexing (#4054) * test: add property tests for block and mask indexing * test: reuse basic_indices in block_indices strategy * test: take chunk_grid_shape as input in block_indices strategy --- changes/4054.misc.md | 1 + src/zarr/testing/strategies.py | 61 ++++++++++++++++++++++++++++++++++ tests/test_properties.py | 61 ++++++++++++++++++++++++++++++++++ 3 files changed, 123 insertions(+) create mode 100644 changes/4054.misc.md diff --git a/changes/4054.misc.md b/changes/4054.misc.md new file mode 100644 index 0000000000..4aa9435b84 --- /dev/null +++ b/changes/4054.misc.md @@ -0,0 +1 @@ +Add Hypothesis property tests for block and mask indexing (`test_block_indexing`, `test_mask_indexing`), along with a `block_indices` strategy in `zarr.testing.strategies`. These extend the existing randomized indexing coverage (basic, orthogonal, and vectorized) to the block and mask selection methods. diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 74d9d7c683..7d6556a359 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -591,6 +591,67 @@ def orthogonal_indices( return tuple(zindexer), tuple(np.broadcast_arrays(*npindexer)) +@st.composite +def block_indices( + draw: st.DrawFn, *, chunk_grid_shape: tuple[int, ...], chunks: tuple[int, ...] +) -> tuple[tuple[int | slice, ...], tuple[slice, ...]]: + """ + Strategy for block-selection indexers over a *regular* chunk grid. + + Block indexing is basic indexing applied to the block grid (the grid of + chunks), so each axis is drawn with ``basic_indices`` over that axis's chunk + count from ``chunk_grid_shape`` (e.g. ``Array.cdata_shape``), mirroring how + ``orthogonal_indices`` reuses ``basic_indices`` per axis. Block indexing only + supports integers and step-1 slices whose start references an existing chunk, + so strided slices and slices starting at the grid edge are filtered out. The + array-space translation assumes a regular (uniform) chunk grid; an over-long + stop into a smaller last chunk is left for numpy to clamp when the oracle is + applied. + + Returns + ------- + block_indexer + A per-axis tuple of ints / step-1 slices addressing whole chunks, + suitable for ``Array.blocks`` / ``get_block_selection`` / ``set_block_selection``. + array_indexer + The equivalent array-space selection (a tuple of slices) for indexing + the corresponding numpy array, used as the comparison oracle. + """ + + def supported(nchunks: int) -> Callable[[tuple[Any, ...]], bool]: + # Block indexing only accepts step-1 slices whose start references an + # existing chunk (a slice starting at nchunks raises, unlike numpy). + def predicate(value: tuple[Any, ...]) -> bool: + dim_sel = value[0] + if isinstance(dim_sel, slice): + if dim_sel.step not in (None, 1): + return False + start = dim_sel.start or 0 + return 0 <= (start + nchunks if start < 0 else start) < nchunks + return True + + return predicate + + block_indexer: list[int | slice] = [] + array_indexer: list[slice] = [] + for chunk, nchunks in zip(chunks, chunk_grid_shape, strict=True): + (dim_sel,) = draw( + basic_indices(min_dims=1, shape=(nchunks,), allow_ellipsis=False) + # normalize bare ints / slices to a 1-tuple, skip the empty tuple + .map(lambda x: (x,) if not isinstance(x, tuple) else x) + .filter(bool) + .filter(supported(nchunks)) + ) + block_indexer.append(dim_sel) + if isinstance(dim_sel, slice): + start, stop, _ = dim_sel.indices(nchunks) + array_indexer.append(slice(start * chunk, stop * chunk)) + else: + block = dim_sel % nchunks + array_indexer.append(slice(block * chunk, (block + 1) * chunk)) + return tuple(block_indexer), tuple(array_indexer) + + def key_ranges( keys: SearchStrategy[str] = node_names, max_size: int = sys.maxsize ) -> SearchStrategy[list[tuple[str, RangeByteRequest]]]: diff --git a/tests/test_properties.py b/tests/test_properties.py index 0e5dcf77b0..994510aca0 100644 --- a/tests/test_properties.py +++ b/tests/test_properties.py @@ -25,7 +25,9 @@ array_metadata, arrays, basic_indices, + block_indices, complex_rectilinear_arrays, + np_array_and_chunks, numpy_arrays, orthogonal_indices, rectilinear_arrays, @@ -230,6 +232,65 @@ async def test_vindex(data: st.DataObject) -> None: # note: async vindex setitem not yet implemented +@settings(deadline=None) +@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") +@given(data=st.data()) +def test_mask_indexing(data: st.DataObject) -> None: + zarray = data.draw(st.one_of(simple_arrays(), rectilinear_arrays())) + nparray = zarray[:] + mask = data.draw(npst.arrays(dtype=np.bool_, shape=st.just(nparray.shape))) + + expected = nparray[mask] + + # sync get, via both the dedicated method and the vindex interface + assert_array_equal(expected, zarray.get_mask_selection(mask)) + assert_array_equal(expected, zarray.vindex[mask]) + + # sync set, via both interfaces + assume(zarray.shards is None) # GH2834 + new_data = data.draw(numpy_arrays(shapes=st.just(expected.shape), dtype=nparray.dtype)) + nparray[mask] = new_data + zarray.set_mask_selection(mask, new_data) + assert_array_equal(nparray, zarray[:]) + + zarray.vindex[mask] = new_data + assert_array_equal(nparray, zarray[:]) + + +@settings(deadline=None) +@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") +@given(data=st.data()) +def test_block_indexing(data: st.DataObject) -> None: + # Block indexing addresses whole chunks on a regular grid; the array-space + # oracle in block_indices() assumes regular, unsharded chunks, so build the + # array directly from a regular chunking rather than drawing one that might + # be rectilinear or sharded. + nparray, chunks = data.draw( + np_array_and_chunks(arrays=numpy_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1))) + ) + store = data.draw(stores) + zarray = zarr.create_array(store=store, shape=nparray.shape, chunks=chunks, dtype=nparray.dtype) + zarray[...] = nparray + + block_indexer, array_indexer = data.draw( + block_indices(chunk_grid_shape=zarray.cdata_shape, chunks=chunks) + ) + expected = nparray[array_indexer] + + # sync get, via both the .blocks interface and the dedicated method + assert_array_equal(expected, zarray.blocks[block_indexer]) + assert_array_equal(expected, zarray.get_block_selection(block_indexer)) + + # sync set, via both interfaces + new_data = data.draw(numpy_arrays(shapes=st.just(expected.shape), dtype=nparray.dtype)) + nparray[array_indexer] = new_data + zarray.blocks[block_indexer] = new_data + assert_array_equal(nparray, zarray[:]) + + zarray.set_block_selection(block_indexer, new_data) + assert_array_equal(nparray, zarray[:]) + + @given(store=stores, meta=array_metadata()) # type: ignore[misc] @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") async def test_roundtrip_array_metadata_from_store( From 0b431e667ae027b30e59f79a6544600a6affa3bb Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Tue, 9 Jun 2026 17:43:43 +0200 Subject: [PATCH 339/468] refactor: use backported sentinel type (#4046) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * refactor: use backported stdlib sentinel type * docs: changelog * chore: rename changelog --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- changes/4046.misc.md | 1 + pyproject.toml | 4 ++-- src/zarr/core/array.py | 40 ++++++++++++++++++---------------------- uv.lock | 2 +- 4 files changed, 22 insertions(+), 25 deletions(-) create mode 100644 changes/4046.misc.md diff --git a/changes/4046.misc.md b/changes/4046.misc.md new file mode 100644 index 0000000000..96c0c7d78a --- /dev/null +++ b/changes/4046.misc.md @@ -0,0 +1 @@ +Replace the internal `DefaultFillValue` sentinel class with a `typing_extensions.Sentinel`, and raise the minimum `typing_extensions` version to 4.14. diff --git a/pyproject.toml b/pyproject.toml index 23eba4e643..9f6005f981 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ dependencies = [ 'numpy>=2', 'numcodecs>=0.14', 'google-crc32c>=1.5', - 'typing_extensions>=4.13', + 'typing_extensions>=4.14', 'donfig>=0.8', ] @@ -256,7 +256,7 @@ extra-dependencies = [ 'fsspec==2023.10.0', 's3fs==2023.10.0', 'universal_pathlib==0.2.0', - 'typing_extensions==4.13.*', + 'typing_extensions==4.14.*', 'donfig==0.8.*', 'obstore==0.5.*', ] diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 366c19bb0c..9740f575a0 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -18,7 +18,7 @@ from warnings import warn import numpy as np -from typing_extensions import deprecated +from typing_extensions import Sentinel, deprecated import zarr from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec @@ -162,7 +162,6 @@ # Array and AsyncArray are defined in the base ``zarr`` namespace __all__ = [ "DEFAULT_FILL_VALUE", - "DefaultFillValue", "create_codec_pipeline", "parse_array_metadata", ] @@ -170,22 +169,19 @@ logger = getLogger(__name__) -class DefaultFillValue: - """ - Sentinel class to indicate that the default fill value should be used. - - This class exists because conventional values used to convey "defaultness" like ``None`` or - ``"auto"` are ambiguous when specifying the fill value parameter of a Zarr array. - The value ``None`` is ambiguous because it is a valid fill value for Zarr V2 - (resulting in ``"fill_value": null`` in array metadata). - A string like ``"auto"`` is ambiguous because such a string is a valid fill value for an array - with a string data type. - An instance of this class lies outside the space of valid fill values, which means it can - unambiguously express that the default fill value should be used. - """ - +DEFAULT_FILL_VALUE = Sentinel("DEFAULT_FILL_VALUE") +""" +Sentinel indicating that the default fill value should be used. -DEFAULT_FILL_VALUE = DefaultFillValue() +This sentinel exists because conventional values used to convey "defaultness" like `None` or +`"auto"` are ambiguous when specifying the fill value parameter of a Zarr array. +The value `None` is ambiguous because it is a valid fill value for Zarr V2 +(resulting in `"fill_value": null` in array metadata). +A string like `"auto"` is ambiguous because such a string is a valid fill value for an array +with a string data type. +This sentinel lies outside the space of valid fill values, which means it can +unambiguously express that the default fill value should be used. +""" def _chunk_sizes_from_shape( @@ -541,9 +537,9 @@ def _create_metadata_v3( else: chunk_key_encoding_parsed = chunk_key_encoding - if isinstance(fill_value, DefaultFillValue) or fill_value is None: - # Use dtype's default scalar for DefaultFillValue sentinel - # For v3, None is converted to DefaultFillValue behavior + if fill_value is DEFAULT_FILL_VALUE or fill_value is None: + # Use dtype's default scalar for the DEFAULT_FILL_VALUE sentinel + # For v3, None is converted to DEFAULT_FILL_VALUE behavior fill_value_parsed = dtype.default_scalar() else: fill_value_parsed = fill_value @@ -625,8 +621,8 @@ def _create_metadata_v2( if dimension_separator is None: dimension_separator = "." - # Handle DefaultFillValue sentinel - if isinstance(fill_value, DefaultFillValue): + # Handle the DEFAULT_FILL_VALUE sentinel + if fill_value is DEFAULT_FILL_VALUE: fill_value_parsed: Any = dtype.default_scalar() else: # For v2, preserve None as-is (backward compatibility) diff --git a/uv.lock b/uv.lock index 8f06e43cb6..de7dfed316 100644 --- a/uv.lock +++ b/uv.lock @@ -4055,7 +4055,7 @@ requires-dist = [ { name = "obstore", marker = "extra == 'remote'", specifier = ">=0.5.1" }, { name = "packaging", specifier = ">=22.0" }, { name = "typer", marker = "extra == 'cli'" }, - { name = "typing-extensions", specifier = ">=4.13" }, + { name = "typing-extensions", specifier = ">=4.14" }, { name = "universal-pathlib", marker = "extra == 'optional'" }, ] provides-extras = ["cast-value-rs", "cli", "gpu", "optional", "remote"] From 07346660f50e41b5e60adbb517e63a2b4449957b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 10 Jun 2026 16:37:32 +0200 Subject: [PATCH 340/468] chore(deps): bump aiohttp in the uv group across 1 directory (#4031) --- updated-dependencies: - dependency-name: aiohttp dependency-version: 3.14.0 dependency-type: indirect ... 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`mypy-upstream`, which sources numcodecs from git and fails under newer pixi with `meson-python: error: Unknown option "pixi-conda-environment"` during the solve — before any test runs. Setting `environments: test-py313` makes setup-pixi run `pixi install -e test-py313`, which never solves that environment. Co-Authored-By: Claude Opus 4.8 * ci: run xarray downstream tests via uv instead of pixi pixi has no committed lockfile in pydata/xarray, so `pixi install` solves the entire manifest regardless of `-e ` — including the `mypy-upstream` environment, which sources numcodecs from git and fails to build under newer pixi with `meson-python: error: Unknown option "pixi-conda-environment"`. The job died at environment setup before any test ran, and the per-environment flag (the previously reverted approach) does not avoid the failing solve. Install xarray with uv from its checkout instead — the `dev` dependency group for pytest tooling plus the `io`/`parallel`/`accel` extras for the zarr-relevant backends — then override zarr with the branch build. Tests needing an uninstalled backend skip via xarray's `requires_*` markers. Co-Authored-By: Claude Opus 4.8 --------- Co-authored-by: Claude Opus 4.8 --- .github/workflows/downstream.yml | 40 ++++++++++++++++++++------------ 1 file changed, 25 insertions(+), 15 deletions(-) diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 71784c358d..ec792163df 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -33,26 +33,36 @@ jobs: path: xarray persist-credentials: false - - name: Set up pixi - uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6 + # We install xarray with plain pip/uv rather than pixi. pixi solves + # xarray's entire manifest (it has no committed lockfile), which drags in + # the `mypy-upstream` environment; that environment sources numcodecs from + # git and fails to build under newer pixi with + # `meson-python: error: Unknown option "pixi-conda-environment"`, breaking + # the job before any test runs. Tests that need a backend we don't install + # are skipped via xarray's `requires_*` markers, not failed. + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: - manifest-path: xarray/pixi.toml - # Only install the environment our steps use. Installing every - # environment in xarray's manifest (the default) drags in - # `mypy-upstream`, which builds numcodecs from git and fails under - # newer pixi with `meson-python: error: Unknown option - # "pixi-conda-environment"` — unrelated to the zarr-python branch - # under test. - environments: test-py313 - - - name: Install zarr-python from branch + python-version: '3.13' + + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + + - name: Install xarray and test dependencies working-directory: xarray - run: pixi run -e test-py313 -- pip install --no-deps .. + run: | + uv venv + # xarray's pytest tooling lives in the PEP 735 `dev` dependency group; + # the zarr-relevant backends come from the `io` and `parallel` extras. + uv pip install --group dev ".[io,parallel,accel]" + + - name: Override zarr-python with branch version + working-directory: xarray + run: uv pip install --no-deps .. - name: Show versions working-directory: xarray run: | - pixi run -e test-py313 -- python -c " + uv run python -c " import zarr; print(f'zarr {zarr.__version__}') import xarray; print(f'xarray {xarray.__version__}') " @@ -60,7 +70,7 @@ jobs: - name: Run xarray zarr backend tests working-directory: xarray run: | - pixi run -e test-py313 -- python -m pytest --no-header -q \ + uv run python -m pytest --no-header -q \ xarray/tests/test_backends.py \ xarray/tests/test_backends_api.py \ xarray/tests/test_backends_datatree.py From 467dda7b60d840db37dc0dcaeaf51af3aff709c7 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 10 Jun 2026 21:46:28 +0200 Subject: [PATCH 342/468] chore: indexing test cleanup (#4001) * docs: design spec for indexing test cleanup Plan to consolidate and speed up tests/test_indexing.py: shrink oversized arrays (>=3 chunks/axis, partial edge), replace np.random selection loops with hand-picked parametrized cases via the Expect/ExpectFail dataclasses, one-behavior-per-test isolation, and docstrings throughout. Includes a prerequisite step deduplicating the two divergent Expect dataclass pairs (tests/conftest.py vs tests/test_codecs/conftest.py) onto one canonical pair. Co-Authored-By: Claude Opus 4.7 (1M context) * docs: implementation plan for indexing test cleanup Task-by-task plan: Expect dataclass dedup (Part 0) then per-family rewrites of tests/test_indexing.py to parametrized Expect/ExpectFail cases on smaller arrays (Part 1), with final verification and speed measurement (Part 2). Co-Authored-By: Claude Opus 4.7 (1M context) * test: make canonical Expect/ExpectFail frozen Prepares for deduplicating the second Expect pair in test_codecs/conftest.py. Co-Authored-By: Claude Opus 4.7 (1M context) * test: migrate test_chunk_grids to canonical Expect/ExpectFail Co-Authored-By: Claude Opus 4.7 (1M context) * test: migrate test_cast_value to canonical Expect/ExpectFail Co-Authored-By: Claude Opus 4.7 (1M context) * test: migrate test_scale_offset to canonical Expect/ExpectFail Co-Authored-By: Claude Opus 4.7 (1M context) * test: delete duplicate Expect dataclasses in test_codecs/conftest.py All consumers now use the canonical Expect/ExpectFail from tests/conftest.py. Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite orthogonal 1d bool indexing as parametrized cases Smaller array (30 elems, chunks of 7), hand-picked deterministic masks replacing np.random sparsity sweep, error paths split into their own test. Co-Authored-By: Claude Opus 4.7 (1M context) * docs: add Task 0.6 (optional ExpectFail.msg + raises helper) Structural fix for the msg="" footgun discovered during Task 1.1: msg becomes optional and regex-matched via a case.raises() helper, with an escape flag. Co-Authored-By: Claude Opus 4.7 (1M context) * test: make ExpectFail.msg optional with a raises() helper msg defaults to None (assert exception type only) and is treated as a regex, with an escape flag for literal messages. Removes the msg="" footgun that the repo's filterwarnings=["error"] config turned into a failure. Co-Authored-By: Claude Opus 4.7 (1M context) * test: clearer single-true mask idiom in orthogonal 1d exemplar np.arange(30) == 7 reads better than np.eye(1, 30, 7)[0]; matters because the other indexing families copy this exemplar. Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite orthogonal 1d int indexing as parametrized cases Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite orthogonal 2d indexing as parametrized cases Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite orthogonal 3d indexing as parametrized cases Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite set-orthogonal indexing family as parametrized cases Reuses the get-orthogonal case tables; deletes the per-dimensionality set helpers. Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite basic 1d/2d selection families as parametrized cases Co-Authored-By: Claude Opus 4.7 (1M context) * test: restore basic-indexing integer-list rejection coverage The basic-selection rewrite dropped two assertions that get_basic_selection rejects integer-list selections (1D direct, 2D nested in a tuple); restore them as dedicated get-only tests, since z[...] falls back to fancy indexing. Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite coordinate selection family as parametrized cases Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite block selection family as parametrized cases Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite mask selection family as parametrized cases Co-Authored-By: Claude Opus 4.7 (1M context) * test: shrink arrays in selection_out and numpy-equivalence tests Co-Authored-By: Claude Opus 4.7 (1M context) * test: add behavior docstrings to remaining indexing tests Co-Authored-By: Claude Opus 4.7 (1M context) * test: drop redundant pytest.mark.asyncio decorators asyncio_mode = "auto" already collects async test functions; the explicit marks were no-ops. Co-Authored-By: Claude Opus 4.7 (1M context) * docs: add changelog fragment for indexing test cleanup Rename XXXX.misc.md to the PR number when the PR is opened. Co-Authored-By: Claude Opus 4.7 (1M context) * test: explain msg=None on the basic-1d string bad case Co-Authored-By: Claude Opus 4.7 (1M context) * docs: remove LLM plans * docs: rename changelog --------- Co-authored-by: Claude Opus 4.7 (1M context) --- changes/4001.misc.md | 1 + tests/conftest.py | 23 +- tests/test_chunk_grids.py | 110 +- tests/test_codecs/conftest.py | 20 - tests/test_codecs/test_cast_value.py | 114 +- tests/test_codecs/test_scale_offset.py | 75 +- tests/test_indexing.py | 1748 ++++++++++++------------ tests/test_metadata/test_v3.py | 5 +- 8 files changed, 1074 insertions(+), 1022 deletions(-) create mode 100644 changes/4001.misc.md delete mode 100644 tests/test_codecs/conftest.py diff --git a/changes/4001.misc.md b/changes/4001.misc.md new file mode 100644 index 0000000000..1f44b551ed --- /dev/null +++ b/changes/4001.misc.md @@ -0,0 +1 @@ +Consolidated the array indexing test suite (`tests/test_indexing.py`): the loop-and-`np.random` based selection tests were rewritten as deterministic, parametrized `Expect`/`ExpectFail` cases on small arrays, error paths were split into their own named tests, and the two divergent `Expect` test-case dataclass pairs were unified onto the canonical one in `tests/conftest.py` (whose `ExpectFail` now has an optional regex `msg` and a `raises()` helper). Test-only change with no effect on the public API. diff --git a/tests/conftest.py b/tests/conftest.py index 3402eb7063..207fba0a44 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -3,6 +3,7 @@ import math import os import pathlib +import re import sys from collections.abc import Mapping, Sequence from dataclasses import dataclass, field @@ -50,6 +51,7 @@ if TYPE_CHECKING: from collections.abc import Generator + from contextlib import AbstractContextManager from typing import Any, Literal from _pytest.compat import LEGACY_PATH @@ -64,7 +66,7 @@ from zarr.core.dtype.wrapper import ZDType -@dataclass +@dataclass(frozen=True) class Expect[TIn, TOut]: """A test case with explicit input, expected output, and a human-readable id.""" @@ -73,14 +75,27 @@ class Expect[TIn, TOut]: id: str -@dataclass +@dataclass(frozen=True) class ExpectFail[TIn]: - """A test case that should raise an exception.""" + """A test case that should raise an exception. + + `msg` is a regex matched against the exception text (pytest's native + `match=` semantics). Leave it `None` to assert only the exception type. Set + `escape=True` when `msg` is a literal that contains regex metacharacters + such as `(`, `[`, or `.`; `escape` has no effect when `msg` is `None`. + """ input: TIn exception: type[Exception] id: str - msg: str + msg: str | None = None + escape: bool = False + + def raises(self) -> AbstractContextManager[pytest.ExceptionInfo[Exception]]: + if self.msg is None: + return pytest.raises(self.exception) + pattern = re.escape(self.msg) if self.escape else self.msg + return pytest.raises(self.exception, match=pattern) async def parse_store( diff --git a/tests/test_chunk_grids.py b/tests/test_chunk_grids.py index 681a599130..b730a43901 100644 --- a/tests/test_chunk_grids.py +++ b/tests/test_chunk_grids.py @@ -1,10 +1,9 @@ -import re from typing import Any import numpy as np import pytest -from tests.test_codecs.conftest import Expect, ExpectErr +from tests.conftest import Expect, ExpectFail from zarr.core.chunk_grids import ( ChunkLayout, _guess_regular_chunks, @@ -131,81 +130,104 @@ def test_chunk_layout_nested() -> None: @pytest.mark.parametrize( "case", [ - ExpectErr(input=(0, 100), msg="Chunk size must be positive", exception_cls=ValueError), - ExpectErr(input=(-2, 100), msg="Chunk size must be positive", exception_cls=ValueError), - ExpectErr(input=([], 100), msg="must not be empty", exception_cls=ValueError), - ExpectErr(input=([10, -1, 10], 100), msg="must be positive", exception_cls=ValueError), - ExpectErr(input=([10, 0, 10], 20), msg="must be positive", exception_cls=ValueError), - ExpectErr(input=([10, 20], 100), msg="do not sum to span", exception_cls=ValueError), + ExpectFail( + input=(0, 100), + exception=ValueError, + id="zero-uniform", + msg="Chunk size must be positive", + ), + ExpectFail( + input=(-2, 100), + exception=ValueError, + id="negative-uniform", + msg="Chunk size must be positive", + ), + ExpectFail(input=([], 100), exception=ValueError, id="empty-list", msg="must not be empty"), + ExpectFail( + input=([10, -1, 10], 100), + exception=ValueError, + id="negative-element", + msg="must be positive", + ), + ExpectFail( + input=([10, 0, 10], 20), exception=ValueError, id="zero-element", msg="must be positive" + ), + ExpectFail( + input=([10, 20], 100), exception=ValueError, id="wrong-sum", msg="do not sum to span" + ), # Nested/RLE form for a single dim is rejected with offending indices. - ExpectErr( + ExpectFail( input=([[3, 3], 1], 7), + exception=TypeError, + id="rle-single-dim", msg="non-integer element(s) ([3, 3],) at indices (0,)", - exception_cls=TypeError, + escape=True, ), # Multiple non-int elements: all offending indices reported. - ExpectErr( + ExpectFail( input=([1, [2, 2], 1, [3]], 9), + exception=TypeError, + id="multiple-non-ints", msg="non-integer element(s) ([2, 2], [3]) at indices (1, 3)", - exception_cls=TypeError, + escape=True, ), # Strings are non-integers and should be reported the same way. - ExpectErr( + ExpectFail( input=([2, "3", 5], 10), + exception=TypeError, + id="string-element", msg="non-integer element(s) ('3',) at indices (1,)", - exception_cls=TypeError, + escape=True, ), ], - ids=[ - "zero-uniform", - "negative-uniform", - "empty-list", - "negative-element", - "zero-element", - "wrong-sum", - "rle-single-dim", - "multiple-non-ints", - "string-element", - ], + ids=lambda c: c.id, ) -def test_normalize_chunks_1d_errors(case: ExpectErr[tuple[Any, int]]) -> None: +def test_normalize_chunks_1d_errors(case: ExpectFail[tuple[Any, int]]) -> None: """Invalid 1D chunk specifications are rejected with informative error messages.""" chunks, span = case.input - with pytest.raises(case.exception_cls, match=re.escape(case.msg)): + with case.raises(): normalize_chunks_1d(chunks, span=span) @pytest.mark.parametrize( "case", [ - ExpectErr( + ExpectFail( input=(None, (100,)), + exception=ValueError, + id="none", msg="None is not a valid chunk input", - exception_cls=ValueError, ), # `True` is rejected explicitly because bool is a subclass of int — without # this guard, `chunks=True` would silently produce size-1 chunks. - ExpectErr( + ExpectFail( input=(True, (100,)), + exception=ValueError, + id="true", msg="True is not a valid chunk input", - exception_cls=ValueError, ), - ExpectErr(input=("foo", (100,)), msg="dimensions", exception_cls=ValueError), - ExpectErr(input=((100, 10), (100,)), msg="dimensions", exception_cls=ValueError), - ExpectErr(input=((10,), (100, 100)), msg="dimensions", exception_cls=ValueError), + ExpectFail(input=("foo", (100,)), exception=ValueError, id="string", msg="dimensions"), + ExpectFail( + input=((100, 10), (100,)), exception=ValueError, id="too-many-dims", msg="dimensions" + ), + ExpectFail( + input=((10,), (100, 100)), exception=ValueError, id="too-few-dims", msg="dimensions" + ), # End-to-end: per-dim RLE surfaces through normalize_chunks_nd. - ExpectErr( + ExpectFail( input=([[6, 4], [[3, 3], 1]], (10, 10)), + exception=TypeError, + id="rle-inner-dim", msg="non-integer element(s) ([3, 3],) at indices (0,)", - exception_cls=TypeError, + escape=True, ), ], - ids=["none", "true", "string", "too-many-dims", "too-few-dims", "rle-inner-dim"], + ids=lambda c: c.id, ) -def test_normalize_chunks_nd_errors(case: ExpectErr[tuple[Any, tuple[int, ...]]]) -> None: +def test_normalize_chunks_nd_errors(case: ExpectFail[tuple[Any, tuple[int, ...]]]) -> None: """Invalid N-D chunk specifications are rejected with informative error messages.""" chunks, shape = case.input - with pytest.raises(case.exception_cls, match=re.escape(case.msg)): + with case.raises(): normalize_chunks_nd(chunks, shape) @@ -213,13 +235,13 @@ def test_normalize_chunks_nd_errors(case: ExpectErr[tuple[Any, tuple[int, ...]]] "case", [ # uniform-chunks branch: one int → broadcast across span via np.full. - Expect(input=(1000, 100_000), expected=[1000] * 100), + Expect(input=(1000, 100_000), output=[1000] * 100, id="uniform"), # explicit-per-chunk branch. - Expect(input=([10, 20, 30, 40], 100), expected=[10, 20, 30, 40]), + Expect(input=([10, 20, 30, 40], 100), output=[10, 20, 30, 40], id="explicit-list"), # -1 sentinel branch: one chunk covering the full span. - Expect(input=(-1, 100), expected=[100]), + Expect(input=(-1, 100), output=[100], id="full-span-sentinel"), ], - ids=["uniform", "explicit-list", "full-span-sentinel"], + ids=lambda c: c.id, ) def test_normalize_chunks_1d_returns_int64_array( case: Expect[tuple[Any, int], list[int]], @@ -230,4 +252,4 @@ def test_normalize_chunks_1d_returns_int64_array( assert isinstance(result, np.ndarray) assert result.dtype == np.int64 assert result.ndim == 1 - assert result.tolist() == case.expected + assert result.tolist() == case.output diff --git a/tests/test_codecs/conftest.py b/tests/test_codecs/conftest.py deleted file mode 100644 index b654ab1ec0..0000000000 --- a/tests/test_codecs/conftest.py +++ /dev/null @@ -1,20 +0,0 @@ -from __future__ import annotations - -from dataclasses import dataclass - - -@dataclass(frozen=True) -class Expect[TIn, TOut]: - """Model an input and an expected output value for a test case.""" - - input: TIn - expected: TOut - - -@dataclass(frozen=True) -class ExpectErr[TIn]: - """Model an input and an expected error message for a test case.""" - - input: TIn - msg: str - exception_cls: type[Exception] diff --git a/tests/test_codecs/test_cast_value.py b/tests/test_codecs/test_cast_value.py index 361073f96b..c43edb76e8 100644 --- a/tests/test_codecs/test_cast_value.py +++ b/tests/test_codecs/test_cast_value.py @@ -6,7 +6,7 @@ import pytest import zarr -from tests.test_codecs.conftest import Expect, ExpectErr +from tests.conftest import Expect, ExpectFail from zarr.codecs.cast_value import CastValue try: @@ -31,7 +31,8 @@ [ Expect( input=CastValue(data_type="uint8"), - expected={"name": "cast_value", "configuration": {"data_type": "uint8"}}, + output={"name": "cast_value", "configuration": {"data_type": "uint8"}}, + id="minimal", ), Expect( input=CastValue( @@ -40,7 +41,7 @@ out_of_range="clamp", scalar_map={"encode": [("NaN", 0)]}, ), - expected={ + output={ "name": "cast_value", "configuration": { "data_type": "uint8", @@ -49,13 +50,14 @@ "scalar_map": {"encode": [("NaN", 0)]}, }, }, + id="full", ), ], - ids=["minimal", "full"], + ids=lambda c: c.id, ) def test_to_dict(case: Expect[CastValue, dict[str, Any]]) -> None: """to_dict produces the expected JSON structure.""" - assert case.input.to_dict() == case.expected + assert case.input.to_dict() == case.output @pytest.mark.parametrize( @@ -63,7 +65,8 @@ def test_to_dict(case: Expect[CastValue, dict[str, Any]]) -> None: [ Expect( input={"name": "cast_value", "configuration": {"data_type": "float32"}}, - expected=("float32", "nearest-even", None), + output=("float32", "nearest-even", None), + id="defaults", ), Expect( input={ @@ -74,15 +77,16 @@ def test_to_dict(case: Expect[CastValue, dict[str, Any]]) -> None: "out_of_range": "clamp", }, }, - expected=("int16", "towards-zero", "clamp"), + output=("int16", "towards-zero", "clamp"), + id="explicit", ), ], - ids=["defaults", "explicit"], + ids=lambda c: c.id, ) def test_from_dict(case: Expect[dict[str, Any], tuple[str, str, str | None]]) -> None: """from_dict deserializes configuration with correct values and defaults.""" codec = CastValue.from_dict(case.input) - dtype_name, rounding, out_of_range = case.expected + dtype_name, rounding, out_of_range = case.output assert codec.dtype.to_native_dtype() == np.dtype(dtype_name) assert codec.rounding == rounding assert codec.out_of_range == out_of_range @@ -133,22 +137,24 @@ def test_construction_rejects_invalid_target_dtype() -> None: @pytest.mark.parametrize( "case", [ - ExpectErr( + ExpectFail( input={"dtype": "complex128", "target": "float64"}, msg="only supports integer and floating-point", - exception_cls=ValueError, + exception=ValueError, + id="complex-source", ), - ExpectErr( + ExpectFail( input={"dtype": "int32", "target": "float64", "out_of_range": "wrap"}, msg="only valid for integer", - exception_cls=ValueError, + exception=ValueError, + id="wrap-float-target", ), ], - ids=["complex-source", "wrap-float-target"], + ids=lambda c: c.id, ) -def test_validation_rejects_invalid(case: ExpectErr[dict[str, Any]]) -> None: +def test_validation_rejects_invalid(case: ExpectFail[dict[str, Any]]) -> None: """Invalid dtype or out_of_range combinations are rejected at array creation.""" - with pytest.raises(case.exception_cls, match=case.msg): + with case.raises(): zarr.create_array( store={}, shape=(10,), @@ -216,14 +222,14 @@ def test_zero_itemsize_raises() -> None: @pytest.mark.parametrize( "case", [ - Expect(input=("float64", "float32"), expected=np.arange(50, dtype="float64")), - Expect(input=("float32", "float64"), expected=np.arange(50, dtype="float32")), - Expect(input=("int32", "int64"), expected=np.arange(50, dtype="int32")), - Expect(input=("int64", "int16"), expected=np.arange(50, dtype="int64")), - Expect(input=("float64", "int32"), expected=np.arange(50, dtype="float64")), - Expect(input=("int32", "float64"), expected=np.arange(50, dtype="int32")), + Expect(input=("float64", "float32"), output=np.arange(50, dtype="float64"), id="f64→f32"), + Expect(input=("float32", "float64"), output=np.arange(50, dtype="float32"), id="f32→f64"), + Expect(input=("int32", "int64"), output=np.arange(50, dtype="int32"), id="i32→i64"), + Expect(input=("int64", "int16"), output=np.arange(50, dtype="int64"), id="i64→i16"), + Expect(input=("float64", "int32"), output=np.arange(50, dtype="float64"), id="f64→i32"), + Expect(input=("int32", "float64"), output=np.arange(50, dtype="int32"), id="i32→f64"), ], - ids=["f64→f32", "f32→f64", "i32→i64", "i64→i16", "f64→i32", "i32→f64"], + ids=lambda c: c.id, ) def test_encode_decode_roundtrip( case: Expect[tuple[str, str], np.ndarray[Any, np.dtype[Any]]], @@ -241,8 +247,8 @@ def test_encode_decode_roundtrip( compressors=None, fill_value=0, ) - arr[:] = case.expected - np.testing.assert_array_equal(arr[:], case.expected) + arr[:] = case.output + np.testing.assert_array_equal(arr[:], case.output) @requires_cast_value_rs @@ -251,10 +257,11 @@ def test_encode_decode_roundtrip( [ Expect( input=np.array([1.7, -1.7, 2.5, -2.5], dtype="float64"), - expected=np.array([1, -1, 2, -2], dtype="float64"), + output=np.array([1, -1, 2, -2], dtype="float64"), + id="towards-zero", ), ], - ids=["towards-zero"], + ids=lambda c: c.id, ) def test_float_to_int_rounding( case: Expect[np.ndarray[Any, np.dtype[Any]], np.ndarray[Any, np.dtype[Any]]], @@ -272,7 +279,7 @@ def test_float_to_int_rounding( fill_value=0, ) arr[:] = case.input - np.testing.assert_array_equal(arr[:], case.expected) + np.testing.assert_array_equal(arr[:], case.output) @requires_cast_value_rs @@ -281,10 +288,11 @@ def test_float_to_int_rounding( [ Expect( input=np.array([0, 200, -200], dtype="int32"), - expected=np.array([0, 127, -128], dtype="int32"), + output=np.array([0, 127, -128], dtype="int32"), + id="int32→int8", ), ], - ids=["int32→int8"], + ids=lambda c: c.id, ) def test_out_of_range_clamp( case: Expect[np.ndarray[Any, np.dtype[Any]], np.ndarray[Any, np.dtype[Any]]], @@ -302,7 +310,7 @@ def test_out_of_range_clamp( fill_value=0, ) arr[:] = case.input - np.testing.assert_array_equal(arr[:], case.expected) + np.testing.assert_array_equal(arr[:], case.output) def test_compute_encoded_size() -> None: @@ -355,55 +363,54 @@ def test_scalar_map_encode_decode_roundtrip() -> None: @pytest.mark.parametrize( "case", [ - ExpectErr( + ExpectFail( input={ "dtype": "int32", "target": "int8", "scalar_map": {"encode": [("NaN", 0)]}, }, msg="not representable in dtype int32", - exception_cls=ValueError, + exception=ValueError, + id="nan-key-for-int-source", ), - ExpectErr( + ExpectFail( input={ "dtype": "int32", "target": "float64", "scalar_map": {"decode": [(0, "NaN")]}, }, msg="not representable in dtype int32", - exception_cls=ValueError, + exception=ValueError, + id="nan-value-for-int-decode-target", ), - ExpectErr( + ExpectFail( input={ "dtype": "float64", "target": "int8", "scalar_map": {"encode": [("NaN", 999)]}, }, msg="not representable in dtype int8", - exception_cls=ValueError, + exception=ValueError, + id="encode-value-out-of-range", ), - ExpectErr( + ExpectFail( input={ "dtype": "float64", "target": "int8", "scalar_map": {"encode": [("NaN", 1.5)]}, }, msg="not representable in dtype int8", - exception_cls=ValueError, + exception=ValueError, + id="encode-value-not-integer", ), ], - ids=[ - "nan-key-for-int-source", - "nan-value-for-int-decode-target", - "encode-value-out-of-range", - "encode-value-not-integer", - ], + ids=lambda c: c.id, ) -def test_scalar_map_validation_rejects_invalid(case: ExpectErr[dict[str, Any]]) -> None: +def test_scalar_map_validation_rejects_invalid(case: ExpectFail[dict[str, Any]]) -> None: """Invalid scalar_map entries are rejected at array creation.""" import zarr - with pytest.raises(case.exception_cls, match=case.msg): + with case.raises(): zarr.create_array( store={}, shape=(10,), @@ -450,20 +457,23 @@ def test_combined_with_scale_offset() -> None: [ Expect( input={"encode": [("NaN", 0)]}, - expected={"encode": {"NaN": 0}}, + output={"encode": {"NaN": 0}}, + id="encode-only", ), Expect( input={"encode": [("NaN", 0)], "decode": [(0, "NaN")]}, - expected={"encode": {"NaN": 0}, "decode": {0: "NaN"}}, + output={"encode": {"NaN": 0}, "decode": {0: "NaN"}}, + id="both-directions", ), Expect( input={"encode": {"NaN": 0}}, - expected={"encode": {"NaN": 0}}, + output={"encode": {"NaN": 0}}, + id="already-normalized", ), ], - ids=["encode-only", "both-directions", "already-normalized"], + ids=lambda c: c.id, ) def test_parse_scalar_map(case: Expect[Any, Any]) -> None: from zarr.codecs.cast_value import parse_scalar_map - assert parse_scalar_map(case.input) == case.expected + assert parse_scalar_map(case.input) == case.output diff --git a/tests/test_codecs/test_scale_offset.py b/tests/test_codecs/test_scale_offset.py index 99a5e3b99d..513caf463a 100644 --- a/tests/test_codecs/test_scale_offset.py +++ b/tests/test_codecs/test_scale_offset.py @@ -6,7 +6,7 @@ import pytest import zarr -from tests.test_codecs.conftest import Expect, ExpectErr +from tests.conftest import Expect, ExpectFail from zarr.codecs.scale_offset import ( ScaleOffset, _decode, @@ -24,42 +24,46 @@ @pytest.mark.parametrize( "case", [ - Expect(input=ScaleOffset(), expected={"name": "scale_offset"}), + Expect(input=ScaleOffset(), output={"name": "scale_offset"}, id="default"), Expect( input=ScaleOffset(offset=5), - expected={"name": "scale_offset", "configuration": {"offset": 5}}, + output={"name": "scale_offset", "configuration": {"offset": 5}}, + id="offset-only", ), Expect( input=ScaleOffset(scale=0.1), - expected={"name": "scale_offset", "configuration": {"scale": 0.1}}, + output={"name": "scale_offset", "configuration": {"scale": 0.1}}, + id="scale-only", ), Expect( input=ScaleOffset(offset=5, scale=0.1), - expected={"name": "scale_offset", "configuration": {"offset": 5, "scale": 0.1}}, + output={"name": "scale_offset", "configuration": {"offset": 5, "scale": 0.1}}, + id="both", ), ], - ids=["default", "offset-only", "scale-only", "both"], + ids=lambda c: c.id, ) def test_to_dict(case: Expect[ScaleOffset, dict[str, Any]]) -> None: """to_dict produces the expected JSON structure.""" - assert case.input.to_dict() == case.expected + assert case.input.to_dict() == case.output @pytest.mark.parametrize( "case", [ - Expect(input={"name": "scale_offset"}, expected=(0, 1)), + Expect(input={"name": "scale_offset"}, output=(0, 1), id="no-config"), Expect( input={"name": "scale_offset", "configuration": {"offset": 3, "scale": 2}}, - expected=(3, 2), + output=(3, 2), + id="with-config", ), ], - ids=["no-config", "with-config"], + ids=lambda c: c.id, ) def test_from_dict(case: Expect[dict[str, Any], tuple[int | float, int | float]]) -> None: """from_dict deserializes configuration with correct values and defaults.""" codec = ScaleOffset.from_dict(case.input) - expected_offset, expected_scale = case.expected + expected_offset, expected_scale = case.output assert codec.offset == expected_offset assert codec.scale == expected_scale @@ -79,38 +83,42 @@ def test_serialization_roundtrip() -> None: @pytest.mark.parametrize( "case", [ - ExpectErr( + ExpectFail( input={"offset": [1, 2]}, + exception=TypeError, + id="list-offset", msg="offset must be a number or string", - exception_cls=TypeError, ), - ExpectErr( - input={"scale": [1, 2]}, msg="scale must be a number or string", exception_cls=TypeError + ExpectFail( + input={"scale": [1, 2]}, + exception=TypeError, + id="list-scale", + msg="scale must be a number or string", ), ], - ids=["list-offset", "list-scale"], + ids=lambda c: c.id, ) -def test_construction_rejects_non_numeric(case: ExpectErr[dict[str, Any]]) -> None: +def test_construction_rejects_non_numeric(case: ExpectFail[dict[str, Any]]) -> None: """Non-numeric offset or scale is rejected at construction time.""" - with pytest.raises(case.exception_cls, match=case.msg): + with case.raises(): ScaleOffset(**case.input) @pytest.mark.parametrize( "case", [ - Expect(input={"offset": 5, "scale": 2}, expected=(5, 2)), - Expect(input={"offset": 0.5, "scale": 0.1}, expected=(0.5, 0.1)), + Expect(input={"offset": 5, "scale": 2}, output=(5, 2), id="int"), + Expect(input={"offset": 0.5, "scale": 0.1}, output=(0.5, 0.1), id="float"), ], - ids=["int", "float"], + ids=lambda c: c.id, ) def test_construction_accepts_numeric( case: Expect[dict[str, Any], tuple[int | float, int | float]], ) -> None: """Integer and float values are accepted for both parameters.""" codec = ScaleOffset(**case.input) - assert codec.offset == case.expected[0] - assert codec.scale == case.expected[1] + assert codec.offset == case.output[0] + assert codec.scale == case.output[1] # --------------------------------------------------------------------------- @@ -259,28 +267,31 @@ def test_rejects_zero_scale() -> None: @pytest.mark.parametrize( "case", [ - ExpectErr( + ExpectFail( input={"dtype": "int32", "offset": 1.5, "scale": 1}, + exception=ValueError, + id="float-offset-for-int", msg="offset value 1.5 is not representable", - exception_cls=ValueError, ), - ExpectErr( + ExpectFail( input={"dtype": "int32", "offset": 0, "scale": 0.5}, + exception=ValueError, + id="float-scale-for-int", msg="scale value 0.5 is not representable", - exception_cls=ValueError, ), - ExpectErr( + ExpectFail( input={"dtype": "int16", "offset": "NaN", "scale": 1}, + exception=ValueError, + id="nan-offset-for-int", msg="offset value 'NaN' is not representable", - exception_cls=ValueError, ), ], - ids=["float-offset-for-int", "float-scale-for-int", "nan-offset-for-int"], + ids=lambda c: c.id, ) -def test_rejects_unrepresentable_scale_offset(case: ExpectErr[dict[str, Any]]) -> None: +def test_rejects_unrepresentable_scale_offset(case: ExpectFail[dict[str, Any]]) -> None: """Scale/offset values that can't be represented in the array dtype are rejected.""" - with pytest.raises(case.exception_cls, match=case.msg): + with case.raises(): zarr.create_array( store={}, shape=(10,), diff --git a/tests/test_indexing.py b/tests/test_indexing.py index c45942eee7..a9358e4fcf 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -11,6 +11,7 @@ from numpy.testing import assert_array_equal import zarr +from tests.conftest import Expect, ExpectFail from zarr import Array from zarr.core.buffer import default_buffer_prototype from zarr.core.indexing import ( @@ -102,6 +103,7 @@ def set_sync(self, key: str, value: Buffer) -> None: def test_normalize_integer_selection() -> None: + """normalize_integer_selection handles positive/negative indices and raises IndexError for out-of-bounds values.""" assert 1 == normalize_integer_selection(1, 100) assert 99 == normalize_integer_selection(-1, 100) with pytest.raises(IndexError): @@ -113,6 +115,7 @@ def test_normalize_integer_selection() -> None: def test_replace_ellipsis() -> None: + """replace_ellipsis expands Ellipsis to full slice(None) selections for 1D and 2D shapes.""" # 1D, single item assert (0,) == replace_ellipsis(0, (100,)) @@ -161,6 +164,7 @@ def test_replace_ellipsis() -> None: ) @pytest.mark.parametrize("use_out", [True, False]) def test_get_basic_selection_0d(store: StorePath, use_out: bool, value: Any, dtype: Any) -> None: + """get_basic_selection on a 0-dimensional array returns the scalar value via Ellipsis and (), including the `out` buffer path.""" # setup arr_np = np.array(value, dtype=dtype) arr_z = zarr_array_from_numpy_array(store, arr_np) @@ -201,77 +205,70 @@ def test_get_basic_selection_0d(store: StorePath, use_out: bool, value: Any, dty # assert_array_equal(a[["foo", "bar"]], c) -basic_selections_1d: list[BasicSelection] = [ - # single value - 42, - -1, - # slices - slice(0, 1050), - slice(50, 150), - slice(0, 2000), - slice(-150, -50), - slice(-2000, 2000), - slice(0, 0), # empty result - slice(-1, 0), # empty result - # total selections - slice(None), - Ellipsis, - (), - (Ellipsis, slice(None)), - # slice with step - slice(None), - slice(None, None), - slice(None, None, 1), - slice(None, None, 10), - slice(None, None, 100), - slice(None, None, 1000), - slice(None, None, 10000), - slice(0, 1050), - slice(0, 1050, 1), - slice(0, 1050, 10), - slice(0, 1050, 100), - slice(0, 1050, 1000), - slice(0, 1050, 10000), - slice(1, 31, 3), - slice(1, 31, 30), - slice(1, 31, 300), - slice(81, 121, 3), - slice(81, 121, 30), - slice(81, 121, 300), - slice(50, 150), - slice(50, 150, 1), - slice(50, 150, 10), +_BASIC_1D_CASES: list[Expect[BasicSelection, None]] = [ + Expect(input=5, output=None, id="single-positive"), + Expect(input=-1, output=None, id="single-negative"), + Expect(input=slice(3, 18), output=None, id="bounded-slice"), + Expect(input=slice(0, 100), output=None, id="over-bounds-slice"), + Expect(input=slice(-18, -3), output=None, id="negative-slice"), + Expect(input=slice(0, 0), output=None, id="empty-slice"), + Expect(input=slice(-1, 0), output=None, id="empty-negative-slice"), + Expect(input=slice(None), output=None, id="full-slice"), + Expect(input=Ellipsis, output=None, id="ellipsis"), + Expect(input=(), output=None, id="empty-tuple"), + Expect(input=(Ellipsis, slice(None)), output=None, id="ellipsis-slice"), + Expect(input=slice(None, None, 3), output=None, id="stride-3"), + Expect(input=slice(3, 27, 5), output=None, id="bounded-stride"), ] -basic_selections_1d_bad = [ - # only positive step supported - slice(None, None, -1), - slice(None, None, -10), - slice(None, None, -100), - slice(None, None, -1000), - slice(None, None, -10000), - slice(1050, -1, -1), - slice(1050, -1, -10), - slice(1050, -1, -100), - slice(1050, -1, -1000), - slice(1050, -1, -10000), - slice(1050, 0, -1), - slice(1050, 0, -10), - slice(1050, 0, -100), - slice(1050, 0, -1000), - slice(1050, 0, -10000), - slice(150, 50, -1), - slice(150, 50, -10), - slice(31, 1, -3), - slice(121, 81, -3), - slice(-1, 0, -1), - # bad stuff - 2.3, - "foo", - b"xxx", - None, - (0, 0), - (slice(None), slice(None)), +_BASIC_1D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail( + input=slice(None, None, -1), + exception=IndexError, + id="negative-step", + msg="only slices with step >= 1 are supported", + ), + ExpectFail( + input=2.3, + exception=IndexError, + id="float", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), + # get_basic_selection and z[...] word their errors differently for a string + # selection, so this case asserts only the exception type (msg=None). + ExpectFail( + input="foo", + exception=IndexError, + id="string", + msg=None, + ), + ExpectFail( + input=b"xxx", + exception=IndexError, + id="bytes", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), + ExpectFail( + input=None, + exception=IndexError, + id="none", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), + ExpectFail( + input=(0, 0), + exception=IndexError, + id="tuple-too-many", + msg="too many indices for array; expected 1, got 2", + ), + ExpectFail( + input=(slice(None), slice(None)), + exception=IndexError, + id="two-slices", + msg="too many indices for array; expected 1, got 2", + ), ] @@ -292,99 +289,133 @@ def _test_get_basic_selection( assert_array_equal(expect, b.as_numpy_array()) -# noinspection PyStatementEffect -def test_get_basic_selection_1d(store: StorePath) -> None: - # setup - a = np.arange(1050, dtype=int) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) +@pytest.mark.parametrize("case", _BASIC_1D_CASES, ids=lambda c: c.id) +def test_get_basic_selection_1d(store: StorePath, case: Expect[BasicSelection, None]) -> None: + """Basic getitem on a 1D array matches numpy for ints, slices, strides, and full selections.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_get_basic_selection(a, z, case.input) + + +@pytest.mark.parametrize("case", _BASIC_1D_BAD_CASES, ids=lambda c: c.id) +def test_get_basic_selection_1d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """Basic getitem on a 1D array rejects negative steps and invalid index types with IndexError.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.get_basic_selection(case.input) + with case.raises(): + z[case.input] + + +_BASIC_2D_CASES: list[Expect[BasicSelection, None]] = [ + Expect(input=5, output=None, id="single-row"), + Expect(input=-1, output=None, id="single-row-neg"), + Expect(input=(5, slice(None)), output=None, id="row-and-full-col"), + Expect(input=(slice(None), 3), output=None, id="single-col"), + Expect(input=(slice(None), -1), output=None, id="single-col-neg"), + Expect(input=slice(None), output=None, id="full"), + Expect(input=slice(2, 9), output=None, id="row-slice"), + Expect(input=slice(0, 0), output=None, id="empty-row-slice"), + Expect(input=(slice(2, 9), slice(1, 4)), output=None, id="2d-slice"), + Expect(input=(slice(0, 12, 3), slice(0, 5, 2)), output=None, id="strided-2d-slice"), + Expect(input=Ellipsis, output=None, id="ellipsis"), + Expect(input=(), output=None, id="empty-tuple"), +] - for selection in basic_selections_1d: - _test_get_basic_selection(a, z, selection) +_BASIC_2D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail( + input=2.3, + exception=IndexError, + id="float", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), + ExpectFail( + input="foo", + exception=IndexError, + id="string", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), + ExpectFail( + input=None, + exception=IndexError, + id="none", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), + ExpectFail( + input=(2.3, slice(None)), + exception=IndexError, + id="float-in-tuple", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), + ExpectFail( + input=slice(None, None, -1), + exception=IndexError, + id="negative-step", + msg="only slices with step >= 1 are supported", + ), + ExpectFail( + input=(slice(None), slice(None), slice(None)), + exception=IndexError, + id="too-many-dims", + msg="too many indices for array; expected 2, got 3", + ), + ExpectFail( + input=[0, 1], + exception=IndexError, + id="integer-list", + msg="unsupported selection item for basic indexing; expected integer or slice, got ", + escape=True, + ), +] - for selection_bad in basic_selections_1d_bad: - with pytest.raises(IndexError): - z.get_basic_selection(selection_bad) # type: ignore[arg-type] - with pytest.raises(IndexError): - z[selection_bad] # type: ignore[index] - with pytest.raises(IndexError): - z.get_basic_selection([1, 0]) # type: ignore[arg-type] - - -basic_selections_2d: list[BasicSelection] = [ - # single row - 42, - -1, - (42, slice(None)), - (-1, slice(None)), - # single col - (slice(None), 4), - (slice(None), -1), - # row slices - slice(None), - slice(0, 1000), - slice(250, 350), - slice(0, 2000), - slice(-350, -250), - slice(0, 0), # empty result - slice(-1, 0), # empty result - slice(-2000, 0), - slice(-2000, 2000), - # 2D slices - (slice(None), slice(1, 5)), - (slice(250, 350), slice(None)), - (slice(250, 350), slice(1, 5)), - (slice(250, 350), slice(-5, -1)), - (slice(250, 350), slice(-50, 50)), - (slice(250, 350, 10), slice(1, 5)), - (slice(250, 350), slice(1, 5, 2)), - (slice(250, 350, 33), slice(1, 5, 3)), - # total selections - (slice(None), slice(None)), - Ellipsis, - (), - (Ellipsis, slice(None)), - (Ellipsis, slice(None), slice(None)), -] +@pytest.mark.parametrize("case", _BASIC_2D_CASES, ids=lambda c: c.id) +def test_get_basic_selection_2d(store: StorePath, case: Expect[BasicSelection, None]) -> None: + """Basic getitem on a 2D array matches numpy for rows, cols, slices, and strides.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_get_basic_selection(a, z, case.input) -basic_selections_2d_bad = [ - # bad stuff - 2.3, - "foo", - b"xxx", - None, - (2.3, slice(None)), - # only positive step supported - slice(None, None, -1), - (slice(None, None, -1), slice(None)), - (0, 0, 0), - (slice(None), slice(None), slice(None)), -] +@pytest.mark.parametrize("case", _BASIC_2D_BAD_CASES, ids=lambda c: c.id) +def test_get_basic_selection_2d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """Basic getitem on a 2D array rejects malformed selections with IndexError.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + with case.raises(): + z.get_basic_selection(case.input) -# noinspection PyStatementEffect -def test_get_basic_selection_2d(store: StorePath) -> None: - # setup - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - for selection in basic_selections_2d: - _test_get_basic_selection(a, z, selection) +def test_basic_2d_fancy_fallback(store: StorePath) -> None: + """Indexing a 2D array with paired integer lists falls back to fancy (vectorized) indexing.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + np.testing.assert_array_equal(z[([0, 1], [0, 1])], a[([0, 1], [0, 1])]) + + +def test_get_basic_selection_1d_rejects_integer_list(store: StorePath) -> None: + """get_basic_selection on a 1D array rejects an integer list (basic indexing is int/slice only).""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with pytest.raises(IndexError, match="unsupported selection item for basic indexing"): + z.get_basic_selection([1, 0]) - bad_selections = basic_selections_2d_bad + [ - # integer arrays - [0, 1], - (slice(None), [0, 1]), - ] - for selection_bad in bad_selections: - with pytest.raises(IndexError): - z.get_basic_selection(selection_bad) # type: ignore[arg-type] - # check fallback on fancy indexing - fancy_selection = ([0, 1], [0, 1]) - np.testing.assert_array_equal(z[fancy_selection], [0, 11]) + +def test_get_basic_selection_2d_rejects_list_in_tuple(store: StorePath) -> None: + """get_basic_selection on a 2D array rejects a list nested in an index tuple.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + with pytest.raises(IndexError, match="unsupported selection item for basic indexing"): + z.get_basic_selection((slice(None), [0, 1])) def test_fancy_indexing_fallback_on_get_setitem(store: StorePath) -> None: + """Paired integer-list indexing falls back to vectorized (fancy) get and set via `__getitem__`/`__setitem__`.""" z = zarr_array_from_numpy_array(store, np.zeros((20, 20))) z[[1, 2, 3], [1, 2, 3]] = 1 np.testing.assert_array_equal( @@ -444,6 +475,7 @@ def test_orthogonal_indexing_fallback_on_getitem_2d( def test_setitem_zarr_array_as_value() -> None: + """Assigning a zarr array as a value in `__setitem__` does not raise a SyncError (regression for GH3611).""" # Regression test for https://github.com/zarr-developers/zarr-python/issues/3611 # Assigning a zarr Array as the value used to raise # SyncError("Calling sync() from within a running loop") because the codec @@ -463,6 +495,7 @@ def test_setitem_zarr_array_as_value() -> None: @pytest.mark.skip(reason="fails on ubuntu, windows; numpy=2.2; in CI") def test_setitem_repeated_index(): + """oindex assignment with repeated indices writes the last value for each duplicated index position.""" array = zarr.array(data=np.zeros((4,)), chunks=(1,)) indexer = np.array([-1, -1, 0, 0]) array.oindex[(indexer,)] = [0, 1, 2, 3] @@ -548,6 +581,7 @@ def test_orthogonal_indexing_fallback_on_setitem_2d( def test_fancy_indexing_doesnt_mix_with_implicit_slicing(store: StorePath) -> None: + """Fancy indexing that would require implicit slicing over an unspecified axis raises IndexError on a 3D array.""" z2 = zarr_array_from_numpy_array(store, np.zeros((5, 5, 5))) with pytest.raises(IndexError): z2[[1, 2, 3], [1, 2, 3]] = 2 @@ -571,6 +605,7 @@ def test_fancy_indexing_doesnt_mix_with_implicit_slicing(store: StorePath) -> No def test_set_basic_selection_0d( store: StorePath, value: Any, dtype: str | list[tuple[str, str]] ) -> None: + """set_basic_selection and `__setitem__` write scalar values correctly to a 0-dimensional array.""" arr_np = np.array(value, dtype=dtype) arr_np_zeros = np.zeros_like(arr_np, dtype=dtype) arr_z = zarr_array_from_numpy_array(store, arr_np_zeros) @@ -611,187 +646,279 @@ def _test_get_orthogonal_selection( assert_array_equal(expect, actual) -# noinspection PyStatementEffect -def test_get_orthogonal_selection_1d_bool(store: StorePath) -> None: - # setup - a = np.arange(1050, dtype=int) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: - ix = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - _test_get_orthogonal_selection(a, z, ix) - - # test errors - with pytest.raises(IndexError): - z.oindex[np.zeros(50, dtype=bool)] # too short - with pytest.raises(IndexError): - z.oindex[np.zeros(2000, dtype=bool)] # too long - with pytest.raises(IndexError): - # too many dimensions - z.oindex[[[True, False], [False, True]]] # type: ignore[index] - - -# noinspection PyStatementEffect -def test_get_orthogonal_selection_1d_int(store: StorePath) -> None: - # setup - a = np.arange(550, dtype=int) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.01: - # sorted integer arrays - ix = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - ix.sort() - _test_get_orthogonal_selection(a, z, ix) - - selections = basic_selections_1d + [ - # test wraparound - [0, 3, 10, -23, -12, -1], - # explicit test not sorted - [3, 105, 23, 127], - ] - for selection in selections: - _test_get_orthogonal_selection(a, z, selection) +_ORTHO_1D_BOOL_CASES: list[Expect[OrthogonalSelection, None]] = [ + Expect(input=np.zeros(30, dtype=bool), output=None, id="empty-mask"), + Expect(input=np.ones(30, dtype=bool), output=None, id="full-mask"), + Expect(input=np.arange(30) % 2 == 0, output=None, id="alternating-mask"), + Expect(input=np.arange(30) == 7, output=None, id="single-true"), + Expect( + input=np.isin(np.arange(30), [0, 1, 8, 15, 29]), + output=None, + id="sparse-cross-chunk", + ), +] - bad_selections = basic_selections_1d_bad + [ - [a.shape[0] + 1], # out of bounds - [-(a.shape[0] + 1)], # out of bounds - [[2, 4], [6, 8]], # too many dimensions - ] - for bad_selection in bad_selections: - with pytest.raises(IndexError): - z.get_orthogonal_selection(bad_selection) # type: ignore[arg-type] - with pytest.raises(IndexError): - z.oindex[bad_selection] # type: ignore[index] +_ORTHO_1D_BOOL_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail( + input=np.zeros(5, dtype=bool), + exception=IndexError, + id="mask-too-short", + msg="wrong length for dimension; expected 30, got 5", + ), + ExpectFail( + input=np.zeros(50, dtype=bool), + exception=IndexError, + id="mask-too-long", + msg="wrong length for dimension; expected 30, got 50", + ), + ExpectFail( + input=[[True, False], [False, True]], + exception=IndexError, + id="mask-too-many-dims", + msg="must be 1-dimensional only", + ), +] -def _test_get_orthogonal_selection_2d( - a: npt.NDArray[Any], z: Array, ix0: npt.NDArray[np.bool], ix1: npt.NDArray[np.bool] +@pytest.mark.parametrize("case", _ORTHO_1D_BOOL_CASES, ids=lambda c: c.id) +def test_get_orthogonal_selection_1d_bool( + store: StorePath, case: Expect[OrthogonalSelection, None] ) -> None: - selections = [ - # index both axes with array - (ix0, ix1), - # mixed indexing with array / slice - (ix0, slice(1, 5)), - (ix0, slice(1, 5, 2)), - (slice(250, 350), ix1), - (slice(250, 350, 10), ix1), - # mixed indexing with array / int - (ix0, 4), - (42, ix1), - ] - for selection in selections: - _test_get_orthogonal_selection(a, z, selection) - - -# noinspection PyStatementEffect -def test_get_orthogonal_selection_2d(store: StorePath) -> None: - # setup - a = np.arange(5400, dtype=int).reshape(600, 9) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.01: - # boolean arrays - ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) - _test_get_orthogonal_selection_2d(a, z, ix0, ix1) + """oindex with a 1D boolean mask matches numpy across chunk boundaries.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_get_orthogonal_selection(a, z, case.input) + + +@pytest.mark.parametrize("case", _ORTHO_1D_BOOL_BAD_CASES, ids=lambda c: c.id) +def test_get_orthogonal_selection_1d_bool_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """oindex rejects masks of the wrong length or dimensionality with IndexError.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.oindex[case.input] + + +_ORTHO_1D_INT_CASES: list[Expect[OrthogonalSelection, None]] = [ + Expect(input=[0, 8, 15, 29], output=None, id="sorted"), + Expect(input=[3, 29, 1, 16], output=None, id="unsorted"), + Expect(input=[2, 2, 8, 8], output=None, id="duplicates"), + Expect(input=[0, 3, 10, -23, -12, -1], output=None, id="wraparound"), + Expect(input=[15], output=None, id="single"), +] - # mixed int array / bool array - selections = ( - (ix0, np.nonzero(ix1)[0]), - (np.nonzero(ix0)[0], ix1), - ) - for selection in selections: - _test_get_orthogonal_selection(a, z, selection) +_ORTHO_1D_INT_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail( + input=[31], + exception=IndexError, + id="out-of-bounds-high", + msg="index out of bounds for dimension with length 30", + ), + ExpectFail( + input=[-31], + exception=IndexError, + id="out-of-bounds-low", + msg="index out of bounds for dimension with length 30", + ), + ExpectFail( + input=[[2, 4], [6, 8]], + exception=IndexError, + id="too-many-dims", + msg="integer arrays in an orthogonal selection must be 1-dimensional only", + ), +] - # sorted integer arrays - ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) - ix0.sort() - ix1.sort() - _test_get_orthogonal_selection_2d(a, z, ix0, ix1) - for selection_2d in basic_selections_2d: - _test_get_orthogonal_selection(a, z, selection_2d) +@pytest.mark.parametrize("case", _ORTHO_1D_INT_CASES, ids=lambda c: c.id) +def test_get_orthogonal_selection_1d_int( + store: StorePath, case: Expect[OrthogonalSelection, None] +) -> None: + """oindex with a 1D integer array matches numpy, including wraparound and duplicates.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_get_orthogonal_selection(a, z, case.input) + + +@pytest.mark.parametrize("case", _ORTHO_1D_INT_BAD_CASES, ids=lambda c: c.id) +def test_get_orthogonal_selection_1d_int_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """oindex rejects out-of-bounds or multi-dimensional integer selections with IndexError.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.get_orthogonal_selection(case.input) + with case.raises(): + z.oindex[case.input] + + +_ORTHO_2D_IX0_BOOL = np.isin(np.arange(12), [0, 5, 11]) # rows 0, 5, 11 +_ORTHO_2D_IX1_BOOL = np.array([True, False, True, False, True]) # cols 0, 2, 4 +_ORTHO_2D_IX0_INT = np.array([0, 5, 11]) +_ORTHO_2D_IX1_INT = np.array([0, 2, 4]) + +_ORTHO_2D_CASES: list[Expect[OrthogonalSelection, None]] = [ + Expect(input=(_ORTHO_2D_IX0_BOOL, _ORTHO_2D_IX1_BOOL), output=None, id="both-bool"), + Expect(input=(_ORTHO_2D_IX0_BOOL, slice(1, 4)), output=None, id="bool-slice"), + Expect(input=(_ORTHO_2D_IX0_BOOL, slice(0, 5, 2)), output=None, id="bool-strided-slice"), + Expect(input=(slice(2, 9), _ORTHO_2D_IX1_BOOL), output=None, id="slice-bool"), + Expect(input=(slice(0, 12, 4), _ORTHO_2D_IX1_BOOL), output=None, id="strided-slice-bool"), + Expect(input=(_ORTHO_2D_IX0_BOOL, 3), output=None, id="bool-int"), + Expect(input=(7, _ORTHO_2D_IX1_BOOL), output=None, id="int-bool"), + Expect(input=(_ORTHO_2D_IX0_INT, _ORTHO_2D_IX1_INT), output=None, id="both-int"), + Expect(input=(_ORTHO_2D_IX0_INT, _ORTHO_2D_IX1_BOOL), output=None, id="int-array-bool-array"), + Expect(input=(_ORTHO_2D_IX0_BOOL, _ORTHO_2D_IX1_INT), output=None, id="bool-array-int-array"), + Expect(input=7, output=None, id="single-row"), + Expect(input=(slice(None), 3), output=None, id="single-col"), + Expect(input=(slice(None), slice(None)), output=None, id="full"), + Expect(input=slice(2, 9), output=None, id="row-slice"), +] - for selection_2d_bad in basic_selections_2d_bad: - with pytest.raises(IndexError): - z.get_orthogonal_selection(selection_2d_bad) # type: ignore[arg-type] - with pytest.raises(IndexError): - z.oindex[selection_2d_bad] # type: ignore[index] +_ORTHO_2D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail( + input=2.3, + exception=IndexError, + id="float-index", + msg="unsupported selection item for orthogonal indexing", + ), + # get_orthogonal_selection and oindex raise different messages for a string + # selection, so assert only the exception type. + ExpectFail( + input="foo", + exception=IndexError, + id="string-index", + msg=None, + ), + ExpectFail( + input=None, + exception=IndexError, + id="none-index", + msg="unsupported selection item for orthogonal indexing", + ), + ExpectFail( + input=slice(None, None, -1), + exception=IndexError, + id="negative-step", + msg="only slices with step >= 1 are supported", + ), + ExpectFail( + input=(0, 0, 0), + exception=IndexError, + id="too-many-dims", + msg="too many indices for array", + ), +] -def _test_get_orthogonal_selection_3d( - a: npt.NDArray, - z: Array, - ix0: npt.NDArray[np.bool], - ix1: npt.NDArray[np.bool], - ix2: npt.NDArray[np.bool], +@pytest.mark.parametrize("case", _ORTHO_2D_CASES, ids=lambda c: c.id) +def test_get_orthogonal_selection_2d( + store: StorePath, case: Expect[OrthogonalSelection, None] ) -> None: - selections = [ - # single value - (60, 15, 4), - (-1, -1, -1), - # index all axes with array - (ix0, ix1, ix2), - # mixed indexing with single array / slices - (ix0, slice(10, 20), slice(1, 5)), - (slice(30, 50), ix1, slice(1, 5)), - (slice(30, 50), slice(10, 20), ix2), - (ix0, slice(10, 20, 5), slice(1, 5, 2)), - (slice(30, 50, 3), ix1, slice(1, 5, 2)), - (slice(30, 50, 3), slice(10, 20, 5), ix2), - # mixed indexing with single array / ints - (ix0, 15, 4), - (60, ix1, 4), - (60, 15, ix2), - # mixed indexing with single array / slice / int - (ix0, slice(10, 20), 4), - (15, ix1, slice(1, 5)), - (slice(30, 50), 15, ix2), - # mixed indexing with two array / slice - (ix0, ix1, slice(1, 5)), - (slice(30, 50), ix1, ix2), - (ix0, slice(10, 20), ix2), - # mixed indexing with two array / integer - (ix0, ix1, 4), - (15, ix1, ix2), - (ix0, 15, ix2), - ] - for selection in selections: - _test_get_orthogonal_selection(a, z, selection) + """oindex on a 2D array matches numpy for array/slice/int combinations per axis.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_get_orthogonal_selection(a, z, case.input) + + +@pytest.mark.parametrize("case", _ORTHO_2D_BAD_CASES, ids=lambda c: c.id) +def test_get_orthogonal_selection_2d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """oindex on a 2D array rejects malformed selections with IndexError.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + with case.raises(): + z.get_orthogonal_selection(case.input) + with case.raises(): + z.oindex[case.input] + + +_ORTHO_3D_IX0_BOOL = np.isin(np.arange(7), [0, 3, 6]) # axis 0 +_ORTHO_3D_IX1_BOOL = np.isin(np.arange(6), [0, 2, 5]) # axis 1 +_ORTHO_3D_IX2_BOOL = np.isin(np.arange(10), [0, 4, 9]) # axis 2 +_ORTHO_3D_IX0_INT = np.array([0, 3, 6]) +_ORTHO_3D_IX1_INT = np.array([0, 2, 5]) +_ORTHO_3D_IX2_INT = np.array([0, 4, 9]) + +_ORTHO_3D_CASES: list[Expect[OrthogonalSelection, None]] = [ + # single value + Expect(input=(5, 3, 8), output=None, id="single-value"), + Expect(input=(-1, -1, -1), output=None, id="all-negative"), + # index all axes with arrays + Expect( + input=(_ORTHO_3D_IX0_BOOL, _ORTHO_3D_IX1_BOOL, _ORTHO_3D_IX2_BOOL), + output=None, + id="three-bool-arrays", + ), + Expect( + input=(_ORTHO_3D_IX0_INT, _ORTHO_3D_IX1_INT, _ORTHO_3D_IX2_INT), + output=None, + id="three-int-arrays", + ), + # mixed indexing with single array / slices + Expect( + input=(_ORTHO_3D_IX0_BOOL, slice(1, 5), slice(2, 9)), output=None, id="array-slice-slice" + ), + Expect( + input=(slice(1, 6), _ORTHO_3D_IX1_BOOL, slice(2, 9)), output=None, id="slice-array-slice" + ), + Expect( + input=(slice(1, 6), slice(1, 5), _ORTHO_3D_IX2_BOOL), output=None, id="slice-slice-array" + ), + Expect( + input=(_ORTHO_3D_IX0_BOOL, slice(0, 6, 2), slice(0, 10, 3)), + output=None, + id="array-strided-strided", + ), + Expect( + input=(slice(0, 7, 2), _ORTHO_3D_IX1_BOOL, slice(0, 10, 3)), + output=None, + id="strided-array-strided", + ), + Expect( + input=(slice(0, 7, 2), slice(0, 6, 2), _ORTHO_3D_IX2_BOOL), + output=None, + id="strided-strided-array", + ), + # mixed indexing with single array / ints + Expect(input=(_ORTHO_3D_IX0_BOOL, 3, 8), output=None, id="array-int-int"), + Expect(input=(5, _ORTHO_3D_IX1_BOOL, 8), output=None, id="int-array-int"), + Expect(input=(5, 3, _ORTHO_3D_IX2_BOOL), output=None, id="int-int-array"), + # mixed indexing with single array / slice / int + Expect(input=(_ORTHO_3D_IX0_BOOL, slice(1, 5), 8), output=None, id="array-slice-int"), + Expect(input=(5, _ORTHO_3D_IX1_BOOL, slice(2, 9)), output=None, id="int-array-slice"), + Expect(input=(slice(1, 6), 3, _ORTHO_3D_IX2_BOOL), output=None, id="slice-int-array"), + # mixed indexing with two arrays / slice + Expect( + input=(_ORTHO_3D_IX0_BOOL, _ORTHO_3D_IX1_BOOL, slice(2, 9)), + output=None, + id="two-arrays-slice", + ), + Expect( + input=(slice(1, 6), _ORTHO_3D_IX1_BOOL, _ORTHO_3D_IX2_BOOL), + output=None, + id="slice-two-arrays", + ), + Expect( + input=(_ORTHO_3D_IX0_BOOL, slice(1, 5), _ORTHO_3D_IX2_BOOL), + output=None, + id="array-slice-array", + ), + # mixed indexing with two arrays / integer + Expect(input=(_ORTHO_3D_IX0_BOOL, _ORTHO_3D_IX1_BOOL, 8), output=None, id="two-arrays-int"), + Expect(input=(5, _ORTHO_3D_IX1_BOOL, _ORTHO_3D_IX2_BOOL), output=None, id="int-two-arrays"), + Expect(input=(_ORTHO_3D_IX0_BOOL, 3, _ORTHO_3D_IX2_BOOL), output=None, id="array-int-array"), +] -def test_get_orthogonal_selection_3d(store: StorePath) -> None: - # setup - a = np.arange(32400, dtype=int).reshape(120, 30, 9) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(60, 20, 3)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.01: - # boolean arrays - ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) - ix2 = np.random.binomial(1, 0.5, size=a.shape[2]).astype(bool) - _test_get_orthogonal_selection_3d(a, z, ix0, ix1, ix2) - - # sorted integer arrays - ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) - ix2 = np.random.choice(a.shape[2], size=int(a.shape[2] * 0.5), replace=True) - ix0.sort() - ix1.sort() - ix2.sort() - _test_get_orthogonal_selection_3d(a, z, ix0, ix1, ix2) +@pytest.mark.parametrize("case", _ORTHO_3D_CASES, ids=lambda c: c.id) +def test_get_orthogonal_selection_3d( + store: StorePath, case: Expect[OrthogonalSelection, None] +) -> None: + """oindex on a 3D array matches numpy for array/slice/int combinations per axis.""" + a = np.arange(420, dtype=int).reshape(7, 6, 10) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(3, 2, 4)) + _test_get_orthogonal_selection(a, z, case.input) def test_orthogonal_indexing_edge_cases(store: StorePath) -> None: + """oindex on a shape-(1, 2, 3) array correctly handles mixing integer, slice, int-list, and bool-list indexers per axis.""" a = np.arange(6).reshape(1, 2, 3) z = zarr_array_from_numpy_array(store, a, chunk_shape=(1, 2, 3)) @@ -824,30 +951,19 @@ def _test_set_orthogonal_selection( assert_array_equal(a, z[:]) -def test_set_orthogonal_selection_1d(store: StorePath) -> None: - # setup - v = np.arange(550, dtype=int) - a = np.empty(v.shape, dtype=int) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) - - # test with different degrees of sparseness - np.random.seed(42) - for p in 0.5, 0.01: - # boolean arrays - ix = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - _test_set_orthogonal_selection(v, a, z, ix) - - # sorted integer arrays - ix = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - ix.sort() - _test_set_orthogonal_selection(v, a, z, ix) - - # basic selections - for selection in basic_selections_1d: - _test_set_orthogonal_selection(v, a, z, selection) +@pytest.mark.parametrize("case", _ORTHO_1D_BOOL_CASES + _ORTHO_1D_INT_CASES, ids=lambda c: c.id) +def test_set_orthogonal_selection_1d( + store: StorePath, case: Expect[OrthogonalSelection, None] +) -> None: + """set_orthogonal_selection on a 1D array round-trips through numpy for masks and int arrays.""" + v = np.arange(30, dtype=int) + a = np.empty_like(v) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_set_orthogonal_selection(v, a, z, case.input) def test_set_item_1d_last_two_chunks(store: StorePath): + """Regression for GH2849: `__setitem__` correctly writes to the last two chunks of a 1D array and to 0-dimensional scalar arrays.""" # regression test for GH2849 g = zarr.open_group(store=store, zarr_format=3, mode="w") a = g.create_array("bar", shape=(10,), chunks=(3,), dtype=int) @@ -866,110 +982,30 @@ def test_set_item_1d_last_two_chunks(store: StorePath): np.testing.assert_equal(z["zoo"][()], np.array(1)) -def _test_set_orthogonal_selection_2d( - v: npt.NDArray[np.int_], - a: npt.NDArray[np.int_], - z: Array, - ix0: npt.NDArray[np.bool], - ix1: npt.NDArray[np.bool], +@pytest.mark.parametrize("case", _ORTHO_2D_CASES, ids=lambda c: c.id) +def test_set_orthogonal_selection_2d( + store: StorePath, case: Expect[OrthogonalSelection, None] ) -> None: - selections = [ - # index both axes with array - (ix0, ix1), - # mixed indexing with array / slice or int - (ix0, slice(1, 5)), - (slice(250, 350), ix1), - (ix0, 4), - (42, ix1), - ] - for selection in selections: - _test_set_orthogonal_selection(v, a, z, selection) - - -def test_set_orthogonal_selection_2d(store: StorePath) -> None: - # setup - v = np.arange(5400, dtype=int).reshape(600, 9) + """set_orthogonal_selection on a 2D array round-trips through numpy.""" + v = np.arange(60, dtype=int).reshape(12, 5) a = np.empty_like(v) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.01: - # boolean arrays - ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) - _test_set_orthogonal_selection_2d(v, a, z, ix0, ix1) - - # sorted integer arrays - ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) - ix0.sort() - ix1.sort() - _test_set_orthogonal_selection_2d(v, a, z, ix0, ix1) - - for selection in basic_selections_2d: - _test_set_orthogonal_selection(v, a, z, selection) - - -def _test_set_orthogonal_selection_3d( - v: npt.NDArray[np.int_], - a: npt.NDArray[np.int_], - z: Array, - ix0: npt.NDArray[np.bool], - ix1: npt.NDArray[np.bool], - ix2: npt.NDArray[np.bool], -) -> None: - selections = ( - # single value - (60, 15, 4), - (-1, -1, -1), - # index all axes with bool array - (ix0, ix1, ix2), - # mixed indexing with single bool array / slice or int - (ix0, slice(10, 20), slice(1, 5)), - (slice(30, 50), ix1, slice(1, 5)), - (slice(30, 50), slice(10, 20), ix2), - (ix0, 15, 4), - (60, ix1, 4), - (60, 15, ix2), - (ix0, slice(10, 20), 4), - (slice(30, 50), ix1, 4), - (slice(30, 50), 15, ix2), - # indexing with two arrays / slice - (ix0, ix1, slice(1, 5)), - # indexing with two arrays / integer - (ix0, ix1, 4), - ) - for selection in selections: - _test_set_orthogonal_selection(v, a, z, selection) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_set_orthogonal_selection(v, a, z, case.input) -def test_set_orthogonal_selection_3d(store: StorePath) -> None: - # setup - v = np.arange(32400, dtype=int).reshape(120, 30, 9) +@pytest.mark.parametrize("case", _ORTHO_3D_CASES, ids=lambda c: c.id) +def test_set_orthogonal_selection_3d( + store: StorePath, case: Expect[OrthogonalSelection, None] +) -> None: + """set_orthogonal_selection on a 3D array round-trips through numpy.""" + v = np.arange(420, dtype=int).reshape(7, 6, 10) a = np.empty_like(v) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(60, 20, 3)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.01: - # boolean arrays - ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) - ix2 = np.random.binomial(1, 0.5, size=a.shape[2]).astype(bool) - _test_set_orthogonal_selection_3d(v, a, z, ix0, ix1, ix2) - - # sorted integer arrays - ix0 = np.random.choice(a.shape[0], size=int(a.shape[0] * p), replace=True) - ix1 = np.random.choice(a.shape[1], size=int(a.shape[1] * 0.5), replace=True) - ix2 = np.random.choice(a.shape[2], size=int(a.shape[2] * 0.5), replace=True) - ix0.sort() - ix1.sort() - ix2.sort() - _test_set_orthogonal_selection_3d(v, a, z, ix0, ix1, ix2) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(3, 2, 4)) + _test_set_orthogonal_selection(v, a, z, case.input) def test_orthogonal_indexing_fallback_on_get_setitem(store: StorePath) -> None: + """Paired integer-list indexing on a 2D array falls back to orthogonal get and set via `__getitem__`/`__setitem__`.""" z = zarr_array_from_numpy_array(store, np.zeros((20, 20))) z[[1, 2, 3], [1, 2, 3]] = 1 np.testing.assert_array_equal( @@ -1000,118 +1036,135 @@ def _test_get_coordinate_selection( assert_array_equal(expect, actual) -coordinate_selections_1d_bad = [ - # slice not supported - slice(5, 15), - slice(None), - Ellipsis, - # bad stuff - 2.3, - "foo", - b"xxx", - None, - (0, 0), - (slice(None), slice(None)), +_COORD_1D_CASES: list[Expect[CoordinateSelection, None]] = [ + Expect(input=5, output=None, id="single"), + Expect(input=-1, output=None, id="single-negative"), + Expect(input=[0, 3, 10, -23, -12, -1], output=None, id="wraparound"), + Expect(input=[3, 25, 8, 17], output=None, id="out-of-order"), + Expect(input=[1, 8, 15, 29], output=None, id="sorted"), + Expect(input=[29, 15, 8, 1], output=None, id="reversed"), + Expect(input=[2, 2, 8, 8], output=None, id="duplicates"), + Expect(input=np.array([[2, 4], [6, 8]]), output=None, id="multi-dim"), ] +# get_coordinate_selection and vindex word their errors differently for these +# invalid-type inputs, so these cases assert only the exception type (msg=None). +_COORD_1D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail(input=slice(5, 15), exception=IndexError, id="slice", msg=None), + ExpectFail(input=slice(None), exception=IndexError, id="full-slice", msg=None), + ExpectFail(input=Ellipsis, exception=IndexError, id="ellipsis", msg=None), + ExpectFail(input=2.3, exception=IndexError, id="float", msg=None), + ExpectFail(input="foo", exception=IndexError, id="string", msg=None), + ExpectFail(input=b"xxx", exception=IndexError, id="bytes", msg=None), + ExpectFail(input=None, exception=IndexError, id="none", msg=None), + ExpectFail(input=(0, 0), exception=IndexError, id="tuple-pair", msg=None), + ExpectFail(input=(slice(None), slice(None)), exception=IndexError, id="two-slices", msg=None), + ExpectFail( + input=[31], + exception=IndexError, + id="out-of-bounds-high", + msg="index out of bounds for dimension with length 30", + ), + ExpectFail( + input=[-31], + exception=IndexError, + id="out-of-bounds-low", + msg="index out of bounds for dimension with length 30", + ), +] -# noinspection PyStatementEffect -def test_get_coordinate_selection_1d(store: StorePath) -> None: - # setup - a = np.arange(1050, dtype=int) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) +_COORD_2D_IX0 = np.array([0, 5, 11, 2, 8]) +_COORD_2D_IX1 = np.array([1, 3, 4, 0, 2]) + +_COORD_2D_CASES: list[Expect[CoordinateSelection, None]] = [ + Expect(input=(5, 4), output=None, id="single"), + Expect(input=(-1, -1), output=None, id="single-negative"), + Expect(input=(_COORD_2D_IX0, _COORD_2D_IX1), output=None, id="both-arrays"), + # scalar broadcasts in coordinate indexing (numpy and zarr agree) + Expect(input=(np.array([0, 5, 11]), 4), output=None, id="array-int"), + Expect(input=(7, np.array([0, 2, 4])), output=None, id="int-array"), + Expect(input=([3, 3, 4, 2, 5], [1, 3, 4, 0, 2]), output=None, id="not-monotonic-first"), + Expect(input=([1, 1, 2, 2, 5], [1, 3, 2, 1, 0]), output=None, id="not-monotonic-second"), + Expect( + input=(np.array([[1, 1, 2], [2, 2, 5]]), np.array([[1, 3, 2], [1, 0, 0]])), + output=None, + id="multi-dim", + ), +] - np.random.seed(42) - # test with different degrees of sparseness - for p in 2, 0.5, 0.1, 0.01: - n = int(a.size * p) - ix = np.random.choice(a.shape[0], size=n, replace=True) - _test_get_coordinate_selection(a, z, ix) - ix.sort() - _test_get_coordinate_selection(a, z, ix) - ix = ix[::-1] - _test_get_coordinate_selection(a, z, ix) +_COORD_2D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail( + input=(slice(5, 15), [1, 2, 3]), + exception=IndexError, + id="slice-with-array", + msg=None, + ), + ExpectFail( + input=([1, 2, 3], slice(5, 15)), + exception=IndexError, + id="array-with-slice", + msg=None, + ), + ExpectFail( + input=(Ellipsis, [1, 2, 3]), + exception=IndexError, + id="ellipsis-with-array", + msg=None, + ), + ExpectFail(input=Ellipsis, exception=IndexError, id="ellipsis", msg=None), + ExpectFail( + input=(np.array([12]), np.array([0])), + exception=IndexError, + id="out-of-bounds-axis0", + msg="index out of bounds for dimension with length 12", + ), + ExpectFail( + input=(np.array([0]), np.array([5])), + exception=IndexError, + id="out-of-bounds-axis1", + msg="index out of bounds for dimension with length 5", + ), +] - selections = [ - # test single item - 42, - -1, - # test wraparound - [0, 3, 10, -23, -12, -1], - # test out of order - [3, 105, 23, 127], # not monotonically increasing - # test multi-dimensional selection - np.array([[2, 4], [6, 8]]), - ] - for selection in selections: - _test_get_coordinate_selection(a, z, selection) - # test errors - bad_selections = coordinate_selections_1d_bad + [ - [a.shape[0] + 1], # out of bounds - [-(a.shape[0] + 1)], # out of bounds - ] - for selection in bad_selections: - with pytest.raises(IndexError): - z.get_coordinate_selection(selection) # type: ignore[arg-type] - with pytest.raises(IndexError): - z.vindex[selection] # type: ignore[index] +@pytest.mark.parametrize("case", _COORD_1D_CASES, ids=lambda c: c.id) +def test_get_coordinate_selection_1d( + store: StorePath, case: Expect[CoordinateSelection, None] +) -> None: + """vindex and get_coordinate_selection on a 1D array match numpy for int, list, and multi-dim selections.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_get_coordinate_selection(a, z, case.input) + + +@pytest.mark.parametrize("case", _COORD_1D_BAD_CASES, ids=lambda c: c.id) +def test_get_coordinate_selection_1d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """get_coordinate_selection and vindex both raise IndexError for invalid 1D selections.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.get_coordinate_selection(case.input) # type: ignore[arg-type] + with case.raises(): + z.vindex[case.input] # type: ignore[index] + + +@pytest.mark.parametrize("case", _COORD_2D_CASES, ids=lambda c: c.id) +def test_get_coordinate_selection_2d( + store: StorePath, case: Expect[CoordinateSelection, None] +) -> None: + """vindex and get_coordinate_selection on a 2D array match numpy for coordinate selections.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_get_coordinate_selection(a, z, case.input) -def test_get_coordinate_selection_2d(store: StorePath) -> None: - # setup - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - - np.random.seed(42) - ix0: npt.ArrayLike - ix1: npt.ArrayLike - # test with different degrees of sparseness - for p in 2, 0.5, 0.1, 0.01: - n = int(a.size * p) - ix0 = np.random.choice(a.shape[0], size=n, replace=True) - ix1 = np.random.choice(a.shape[1], size=n, replace=True) - selections = [ - # single value - (42, 4), - (-1, -1), - # index both axes with array - (ix0, ix1), - # mixed indexing with array / int - (ix0, 4), - (42, ix1), - (42, 4), - ] - for selection in selections: - _test_get_coordinate_selection(a, z, selection) - - # not monotonically increasing (first dim) - ix0 = [3, 3, 4, 2, 5] - ix1 = [1, 3, 5, 7, 9] - _test_get_coordinate_selection(a, z, (ix0, ix1)) - - # not monotonically increasing (second dim) - ix0 = [1, 1, 2, 2, 5] - ix1 = [1, 3, 2, 1, 0] - _test_get_coordinate_selection(a, z, (ix0, ix1)) - - # multi-dimensional selection - ix0 = np.array([[1, 1, 2], [2, 2, 5]]) - ix1 = np.array([[1, 3, 2], [1, 0, 0]]) - _test_get_coordinate_selection(a, z, (ix0, ix1)) - - selection = slice(5, 15), [1, 2, 3] - with pytest.raises(IndexError): - z.get_coordinate_selection(selection) # type:ignore[arg-type] - selection = [1, 2, 3], slice(5, 15) - with pytest.raises(IndexError): - z.get_coordinate_selection(selection) # type:ignore[arg-type] - selection = Ellipsis, [1, 2, 3] - with pytest.raises(IndexError): - z.get_coordinate_selection(selection) # type:ignore[arg-type] - selection = Ellipsis - with pytest.raises(IndexError): - z.get_coordinate_selection(selection) # type:ignore[arg-type] +@pytest.mark.parametrize("case", _COORD_2D_BAD_CASES, ids=lambda c: c.id) +def test_get_coordinate_selection_2d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """get_coordinate_selection raises IndexError when slices or Ellipsis appear in a 2D coordinate selection.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + with case.raises(): + z.get_coordinate_selection(case.input) # type: ignore[arg-type] def _test_set_coordinate_selection( @@ -1131,59 +1184,26 @@ def _test_set_coordinate_selection( assert_array_equal(a, z[:]) -def test_set_coordinate_selection_1d(store: StorePath) -> None: - # setup - v = np.arange(550, dtype=int) - a = np.empty(v.shape, dtype=v.dtype) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.01: - n = int(a.size * p) - ix = np.random.choice(a.shape[0], size=n, replace=True) - _test_set_coordinate_selection(v, a, z, ix) - - # multi-dimensional selection - ix = np.array([[2, 4], [6, 8]]) - _test_set_coordinate_selection(v, a, z, ix) - - for selection in coordinate_selections_1d_bad: - with pytest.raises(IndexError): - z.set_coordinate_selection(selection, 42) # type:ignore[arg-type] - with pytest.raises(IndexError): - z.vindex[selection] = 42 # type:ignore[index] +@pytest.mark.parametrize("case", _COORD_1D_CASES, ids=lambda c: c.id) +def test_set_coordinate_selection_1d( + store: StorePath, case: Expect[CoordinateSelection, None] +) -> None: + """set_coordinate_selection and vindex assignment on a 1D array round-trip through numpy.""" + v = np.arange(30, dtype=int) + a = np.empty_like(v) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_set_coordinate_selection(v, a, z, case.input) -def test_set_coordinate_selection_2d(store: StorePath) -> None: - # setup - v = np.arange(5400, dtype=int).reshape(600, 9) +@pytest.mark.parametrize("case", _COORD_2D_CASES, ids=lambda c: c.id) +def test_set_coordinate_selection_2d( + store: StorePath, case: Expect[CoordinateSelection, None] +) -> None: + """set_coordinate_selection and vindex assignment on a 2D array round-trip through numpy.""" + v = np.arange(60, dtype=int).reshape(12, 5) a = np.empty_like(v) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.01: - n = int(a.size * p) - ix0 = np.random.choice(a.shape[0], size=n, replace=True) - ix1 = np.random.choice(a.shape[1], size=n, replace=True) - - selections = ( - (42, 4), - (-1, -1), - # index both axes with array - (ix0, ix1), - # mixed indexing with array / int - (ix0, 4), - (42, ix1), - ) - for selection in selections: - _test_set_coordinate_selection(v, a, z, selection) - - # multi-dimensional selection - ix0 = np.array([[1, 2, 3], [4, 5, 6]]) - ix1 = np.array([[1, 3, 2], [2, 0, 5]]) - _test_set_coordinate_selection(v, a, z, (ix0, ix1)) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_set_coordinate_selection(v, a, z, case.input) def _test_get_block_selection( @@ -1199,122 +1219,84 @@ def _test_get_block_selection( assert_array_equal(expect, actual) -block_selections_1d: list[BasicSelection] = [ - # test single item - 0, - 5, - # test wraparound - -1, - -4, - # test slice - slice(5), - slice(None, 3), - slice(5, 6), - slice(-3, -1), - slice(None), # Full slice +_BLOCK_1D_CASES: list[Expect[BasicSelection, slice]] = [ + Expect(input=0, output=slice(0, 7), id="block-0"), + Expect(input=2, output=slice(14, 21), id="block-mid"), + Expect(input=4, output=slice(28, 30), id="block-last"), + Expect(input=-1, output=slice(28, 30), id="block-neg-1"), + Expect(input=-2, output=slice(21, 28), id="block-neg-2"), + Expect(input=slice(3), output=slice(0, 21), id="slice-to-3"), + Expect(input=slice(None, 2), output=slice(0, 14), id="slice-none-2"), + Expect(input=slice(1, 2), output=slice(7, 14), id="slice-1-2"), + Expect(input=slice(-2, -1), output=slice(21, 28), id="slice-neg"), + Expect(input=slice(None), output=slice(0, 30), id="full"), ] -block_selections_1d_array_projection: list[slice] = [ - # test single item - slice(100), - slice(500, 600), - # test wraparound - slice(1000, None), - slice(700, 800), - # test slice - slice(500), - slice(None, 300), - slice(500, 600), - slice(800, 1000), - slice(None), +_BLOCK_1D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail(input=slice(3, 8, 2), exception=IndexError, id="strided-slice"), + ExpectFail(input=2.3, exception=IndexError, id="float"), + ExpectFail(input=b"xxx", exception=IndexError, id="bytes"), + ExpectFail(input=None, exception=IndexError, id="none"), + ExpectFail(input=(0, 0), exception=IndexError, id="tuple-pair"), + ExpectFail(input=(slice(None), slice(None)), exception=IndexError, id="two-slices"), + ExpectFail(input=[0, 5, 3], exception=IndexError, id="int-list"), + ExpectFail(input=5, exception=IndexError, id="out-of-bounds-high"), + ExpectFail(input=-6, exception=IndexError, id="out-of-bounds-low"), ] -block_selections_1d_bad = [ - # slice not supported - slice(3, 8, 2), - # bad stuff - 2.3, - # "foo", # TODO - b"xxx", - None, - (0, 0), - (slice(None), slice(None)), - [0, 5, 3], +_BLOCK_2D_CASES: list[Expect[BasicSelection, tuple[slice, slice]]] = [ + Expect(input=(0, 0), output=(slice(0, 5), slice(0, 2)), id="single-00"), + Expect(input=(1, 1), output=(slice(5, 10), slice(2, 4)), id="single-mid"), + Expect(input=(-1, -1), output=(slice(10, 12), slice(4, 5)), id="neg"), + Expect(input=(slice(0, 2), 0), output=(slice(0, 10), slice(0, 2)), id="slice-rows"), + Expect(input=(2, slice(1, 3)), output=(slice(10, 12), slice(2, 5)), id="slice-cols"), + Expect(input=(slice(0, 2), slice(0, 2)), output=(slice(0, 10), slice(0, 4)), id="both-slices"), + Expect(input=(slice(None), slice(None)), output=(slice(0, 12), slice(0, 5)), id="full"), ] +_BLOCK_2D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail(input=(slice(5, 15), [1, 2, 3]), exception=IndexError, id="slice-with-array"), + ExpectFail(input=(Ellipsis, [1, 2, 3]), exception=IndexError, id="ellipsis-with-array"), + ExpectFail(input=(slice(15, 20), slice(None)), exception=IndexError, id="out-of-bounds"), +] -def test_get_block_selection_1d(store: StorePath) -> None: - # setup - a = np.arange(1050, dtype=int) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) - for selection, expected_idx in zip( - block_selections_1d, block_selections_1d_array_projection, strict=True - ): - _test_get_block_selection(a, z, selection, expected_idx) +@pytest.mark.parametrize("case", _BLOCK_1D_CASES, ids=lambda c: c.id) +def test_get_block_selection_1d(store: StorePath, case: Expect[BasicSelection, slice]) -> None: + """get_block_selection / .blocks on a 1D array selects whole chunks matching the array slice.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_get_block_selection(a, z, case.input, case.output) - bad_selections = block_selections_1d_bad + [ - z._chunk_grid.get_nchunks() + 1, # out of bounds - -(z._chunk_grid.get_nchunks() + 1), # out of bounds - ] - for selection_bad in bad_selections: - with pytest.raises(IndexError): - z.get_block_selection(selection_bad) # type:ignore[arg-type] - with pytest.raises(IndexError): - z.blocks[selection_bad] # type:ignore[index] - - -block_selections_2d: list[BasicSelection] = [ - # test single item - (0, 0), - (1, 2), - # test wraparound - (-1, -1), - (-3, -2), - # test slice - (slice(1), slice(2)), - (slice(None, 2), slice(-2, -1)), - (slice(2, 3), slice(-2, None)), - (slice(-3, -1), slice(-3, -2)), - (slice(None), slice(None)), # Full slice -] - -block_selections_2d_array_projection: list[tuple[slice, slice]] = [ - # test single item - (slice(300), slice(3)), - (slice(300, 600), slice(6, 9)), - # test wraparound - (slice(900, None), slice(9, None)), - (slice(300, 600), slice(6, 9)), - # test slice - (slice(300), slice(6)), - (slice(None, 600), slice(6, 9)), - (slice(600, 900), slice(6, None)), - (slice(300, 900), slice(3, 6)), - (slice(None), slice(None)), # Full slice -] +@pytest.mark.parametrize("case", _BLOCK_1D_BAD_CASES, ids=lambda c: c.id) +def test_get_block_selection_1d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """get_block_selection / .blocks on a 1D array rejects invalid block selections with IndexError.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.get_block_selection(case.input) + with case.raises(): + z.blocks[case.input] -def test_get_block_selection_2d(store: StorePath) -> None: - # setup - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) +@pytest.mark.parametrize("case", _BLOCK_2D_CASES, ids=lambda c: c.id) +def test_get_block_selection_2d( + store: StorePath, case: Expect[BasicSelection, tuple[slice, slice]] +) -> None: + """get_block_selection / .blocks on a 2D array selects whole chunk regions matching the array slices.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_get_block_selection(a, z, case.input, case.output) - for selection, expected_idx in zip( - block_selections_2d, block_selections_2d_array_projection, strict=True - ): - _test_get_block_selection(a, z, selection, expected_idx) - selection = slice(5, 15), [1, 2, 3] - with pytest.raises(IndexError): - z.get_block_selection(selection) - selection = Ellipsis, [1, 2, 3] - with pytest.raises(IndexError): - z.get_block_selection(selection) - selection = slice(15, 20), slice(None) - with pytest.raises(IndexError): # out of bounds - z.get_block_selection(selection) +@pytest.mark.parametrize("case", _BLOCK_2D_BAD_CASES, ids=lambda c: c.id) +def test_get_block_selection_2d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """get_block_selection on a 2D array rejects invalid or out-of-bounds block selections with IndexError.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + with case.raises(): + z.get_block_selection(case.input) def _test_set_block_selection( @@ -1322,7 +1304,7 @@ def _test_set_block_selection( a: npt.NDArray[Any], z: zarr.Array, selection: BasicSelection, - expected_idx: slice, + expected_idx: slice | tuple[slice, ...], ) -> None: for value in 42, v[expected_idx], v[expected_idx].tolist(): # setup expectation @@ -1338,44 +1320,44 @@ def _test_set_block_selection( assert_array_equal(a, z[:]) -def test_set_block_selection_1d(store: StorePath) -> None: - # setup - v = np.arange(1050, dtype=int) - a = np.empty(v.shape, dtype=v.dtype) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) +@pytest.mark.parametrize("case", _BLOCK_1D_CASES, ids=lambda c: c.id) +def test_set_block_selection_1d(store: StorePath, case: Expect[BasicSelection, slice]) -> None: + """set_block_selection / .blocks assignment on a 1D array round-trips through numpy for each block selection.""" + v = np.arange(30, dtype=int) + a = np.empty_like(v) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_set_block_selection(v, a, z, case.input, case.output) - for selection, expected_idx in zip( - block_selections_1d, block_selections_1d_array_projection, strict=True - ): - _test_set_block_selection(v, a, z, selection, expected_idx) - for selection_bad in block_selections_1d_bad: - with pytest.raises(IndexError): - z.set_block_selection(selection_bad, 42) # type:ignore[arg-type] - with pytest.raises(IndexError): - z.blocks[selection_bad] = 42 # type:ignore[index] +@pytest.mark.parametrize("case", _BLOCK_1D_BAD_CASES, ids=lambda c: c.id) +def test_set_block_selection_1d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """set_block_selection / .blocks assignment on a 1D array rejects invalid block selections with IndexError.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.set_block_selection(case.input, 42) + with case.raises(): + z.blocks[case.input] = 42 -def test_set_block_selection_2d(store: StorePath) -> None: - # setup - v = np.arange(10000, dtype=int).reshape(1000, 10) - a = np.empty(v.shape, dtype=v.dtype) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) +@pytest.mark.parametrize("case", _BLOCK_2D_CASES, ids=lambda c: c.id) +def test_set_block_selection_2d( + store: StorePath, case: Expect[BasicSelection, tuple[slice, slice]] +) -> None: + """set_block_selection / .blocks assignment on a 2D array round-trips through numpy for each block selection.""" + v = np.arange(60, dtype=int).reshape(12, 5) + a = np.empty_like(v) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_set_block_selection(v, a, z, case.input, case.output) - for selection, expected_idx in zip( - block_selections_2d, block_selections_2d_array_projection, strict=True - ): - _test_set_block_selection(v, a, z, selection, expected_idx) - selection = slice(5, 15), [1, 2, 3] - with pytest.raises(IndexError): - z.set_block_selection(selection, 42) - selection = Ellipsis, [1, 2, 3] - with pytest.raises(IndexError): - z.set_block_selection(selection, 42) - selection = slice(15, 20), slice(None) - with pytest.raises(IndexError): # out of bounds - z.set_block_selection(selection, 42) +@pytest.mark.parametrize("case", _BLOCK_2D_BAD_CASES, ids=lambda c: c.id) +def test_set_block_selection_2d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """set_block_selection on a 2D array rejects invalid or out-of-bounds block selections with IndexError.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + with case.raises(): + z.set_block_selection(case.input, 42) def _test_get_mask_selection(a: npt.NDArray[Any], z: Array, selection: npt.NDArray) -> None: @@ -1388,65 +1370,99 @@ def _test_get_mask_selection(a: npt.NDArray[Any], z: Array, selection: npt.NDArr assert_array_equal(expect, actual) -mask_selections_1d_bad = [ - # slice not supported - slice(5, 15), - slice(None), - Ellipsis, - # bad stuff - 2.3, - "foo", - b"xxx", - None, - (0, 0), - (slice(None), slice(None)), +_MASK_1D_CASES: list[Expect[Any, None]] = [ + Expect(input=np.zeros(30, dtype=bool), output=None, id="all-false"), + Expect(input=np.ones(30, dtype=bool), output=None, id="all-true"), + Expect(input=np.arange(30) % 2 == 0, output=None, id="alternating"), + Expect( + input=np.isin(np.arange(30), [0, 7, 14, 29]), + output=None, + id="sparse-cross-chunk", + ), ] +# msg=None for all 1d bad cases: get_mask_selection and vindex raise different +# messages for the same input, so no single substring satisfies both assertions. +_MASK_1D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail(input=slice(5, 15), exception=IndexError, id="slice"), + ExpectFail(input=slice(None), exception=IndexError, id="full-slice"), + ExpectFail(input=Ellipsis, exception=IndexError, id="ellipsis"), + ExpectFail(input=2.3, exception=IndexError, id="float"), + ExpectFail(input="foo", exception=IndexError, id="string"), + ExpectFail(input=b"xxx", exception=IndexError, id="bytes"), + ExpectFail(input=None, exception=IndexError, id="none"), + ExpectFail(input=(0, 0), exception=IndexError, id="tuple-pair"), + ExpectFail(input=(slice(None), slice(None)), exception=IndexError, id="two-slices"), + ExpectFail(input=np.zeros(5, dtype=bool), exception=IndexError, id="mask-too-short"), + ExpectFail(input=np.zeros(50, dtype=bool), exception=IndexError, id="mask-too-long"), + ExpectFail(input=[[True, False], [False, True]], exception=IndexError, id="too-many-dims"), +] -# noinspection PyStatementEffect -def test_get_mask_selection_1d(store: StorePath) -> None: - # setup - a = np.arange(1050, dtype=int) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: - ix = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - _test_get_mask_selection(a, z, ix) - - # test errors - bad_selections = mask_selections_1d_bad + [ - np.zeros(50, dtype=bool), # too short - np.zeros(2000, dtype=bool), # too long - [[True, False], [False, True]], # too many dimensions - ] - for selection in bad_selections: - with pytest.raises(IndexError): - z.get_mask_selection(selection) # type: ignore[arg-type] - with pytest.raises(IndexError): - z.vindex[selection] # type:ignore[index] +def _make_sparse_2d_mask() -> npt.NDArray[np.bool_]: + """Build a deterministic sparse (12, 5) boolean mask with Trues at (0,0), (5,2), (11,4), (2,3).""" + mask = np.zeros((12, 5), dtype=bool) + for r, c in [(0, 0), (5, 2), (11, 4), (2, 3)]: + mask[r, c] = True + return mask + + +_MASK_2D_CASES: list[Expect[Any, None]] = [ + Expect(input=np.zeros((12, 5), dtype=bool), output=None, id="all-false"), + Expect(input=np.ones((12, 5), dtype=bool), output=None, id="all-true"), + Expect( + input=(np.add.outer(np.arange(12), np.arange(5)) % 2).astype(bool), + output=None, + id="checkerboard", + ), + Expect( + input=_make_sparse_2d_mask(), + output=None, + id="sparse", + ), +] +_MASK_2D_BAD_CASES: list[ExpectFail[Any]] = [ + ExpectFail(input=np.zeros((12, 3), dtype=bool), exception=IndexError, id="too-few-cols"), + ExpectFail(input=np.zeros((20, 5), dtype=bool), exception=IndexError, id="too-many-rows"), + ExpectFail(input=[True, False], exception=IndexError, id="wrong-ndim"), +] -# noinspection PyStatementEffect -def test_get_mask_selection_2d(store: StorePath) -> None: - # setup - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: - ix = np.random.binomial(1, p, size=a.size).astype(bool).reshape(a.shape) - _test_get_mask_selection(a, z, ix) +@pytest.mark.parametrize("case", _MASK_1D_CASES, ids=lambda c: c.id) +def test_get_mask_selection_1d(store: StorePath, case: Expect[Any, None]) -> None: + """get_mask_selection / vindex / getitem on a 1D array match numpy for boolean masks.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_get_mask_selection(a, z, case.input) - # test errors - with pytest.raises(IndexError): - z.vindex[np.zeros((1000, 5), dtype=bool)] # too short - with pytest.raises(IndexError): - z.vindex[np.zeros((2000, 10), dtype=bool)] # too long - with pytest.raises(IndexError): - z.vindex[[True, False]] # wrong no. dimensions + +@pytest.mark.parametrize("case", _MASK_1D_BAD_CASES, ids=lambda c: c.id) +def test_get_mask_selection_1d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """get_mask_selection / vindex on a 1D array reject non-boolean-mask and mis-shaped selections.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.get_mask_selection(case.input) # type: ignore[arg-type] + with case.raises(): + z.vindex[case.input] # type: ignore[index] + + +@pytest.mark.parametrize("case", _MASK_2D_CASES, ids=lambda c: c.id) +def test_get_mask_selection_2d(store: StorePath, case: Expect[Any, None]) -> None: + """get_mask_selection / vindex / getitem on a 2D array match numpy for boolean masks.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_get_mask_selection(a, z, case.input) + + +@pytest.mark.parametrize("case", _MASK_2D_BAD_CASES, ids=lambda c: c.id) +def test_get_mask_selection_2d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """vindex on a 2D array rejects masks of the wrong shape or dimensionality.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + with case.raises(): + z.vindex[case.input] # type: ignore[index] def _test_set_mask_selection( @@ -1465,46 +1481,44 @@ def _test_set_mask_selection( assert_array_equal(a, z[:]) -def test_set_mask_selection_1d(store: StorePath) -> None: - # setup - v = np.arange(1050, dtype=int) +@pytest.mark.parametrize("case", _MASK_1D_CASES, ids=lambda c: c.id) +def test_set_mask_selection_1d(store: StorePath, case: Expect[Any, None]) -> None: + """set_mask_selection / vindex / setitem on a 1D array match numpy for boolean masks.""" + v = np.arange(30, dtype=int) a = np.empty_like(v) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + _test_set_mask_selection(v, a, z, case.input) - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: - ix = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - _test_set_mask_selection(v, a, z, ix) - for selection in mask_selections_1d_bad: - with pytest.raises(IndexError): - z.set_mask_selection(selection, 42) # type: ignore[arg-type] - with pytest.raises(IndexError): - z.vindex[selection] = 42 # type: ignore[index] +@pytest.mark.parametrize("case", _MASK_1D_BAD_CASES, ids=lambda c: c.id) +def test_set_mask_selection_1d_raises(store: StorePath, case: ExpectFail[Any]) -> None: + """set_mask_selection / vindex on a 1D array reject non-boolean-mask and mis-shaped selections.""" + a = np.arange(30, dtype=int) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) + with case.raises(): + z.set_mask_selection(case.input, 42) # type: ignore[arg-type] + with case.raises(): + z.vindex[case.input] = 42 # type: ignore[index] -def test_set_mask_selection_2d(store: StorePath) -> None: - # setup - v = np.arange(10000, dtype=int).reshape(1000, 10) +@pytest.mark.parametrize("case", _MASK_2D_CASES, ids=lambda c: c.id) +def test_set_mask_selection_2d(store: StorePath, case: Expect[Any, None]) -> None: + """set_mask_selection / vindex / setitem on a 2D array match numpy for boolean masks.""" + v = np.arange(60, dtype=int).reshape(12, 5) a = np.empty_like(v) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: - ix = np.random.binomial(1, p, size=a.size).astype(bool).reshape(a.shape) - _test_set_mask_selection(v, a, z, ix) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + _test_set_mask_selection(v, a, z, case.input) def test_get_selection_out(store: StorePath) -> None: + """get_*_selection writes results into a provided out buffer, matching numpy.""" # basic selections - a = np.arange(1050) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) + a = np.arange(30) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(7,)) selections = [ - slice(50, 150), - slice(0, 1050), + slice(5, 15), + slice(0, 30), slice(1, 2), ] for selection in selections: @@ -1517,57 +1531,47 @@ def test_get_selection_out(store: StorePath) -> None: z.get_basic_selection(Ellipsis, out=[]) # type: ignore[arg-type] # orthogonal selections - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: - ix0 = np.random.binomial(1, p, size=a.shape[0]).astype(bool) - ix1 = np.random.binomial(1, 0.5, size=a.shape[1]).astype(bool) - selections = [ - # index both axes with array - (ix0, ix1), - # mixed indexing with array / slice - (ix0, slice(1, 5)), - (slice(250, 350), ix1), - # mixed indexing with array / int - (ix0, 4), - (42, ix1), - # mixed int array / bool array - (ix0, np.nonzero(ix1)[0]), - (np.nonzero(ix0)[0], ix1), - ] - for selection in selections: - expect = oindex(a, selection) - out = get_ndbuffer_class().from_numpy_array(np.zeros(expect.shape, dtype=expect.dtype)) - z.get_orthogonal_selection(selection, out=out) - assert_array_equal(expect, out.as_numpy_array()[:]) + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + selections = [ + # index both axes with bool array + (_ORTHO_2D_IX0_BOOL, _ORTHO_2D_IX1_BOOL), + # mixed indexing with bool array / slice + (_ORTHO_2D_IX0_BOOL, slice(1, 4)), + (slice(2, 9), _ORTHO_2D_IX1_BOOL), + # mixed indexing with bool array / int + (_ORTHO_2D_IX0_BOOL, 3), + (7, _ORTHO_2D_IX1_BOOL), + # mixed int array / bool array + (_ORTHO_2D_IX0_BOOL, _ORTHO_2D_IX1_INT), + (_ORTHO_2D_IX0_INT, _ORTHO_2D_IX1_BOOL), + ] + for selection in selections: + expect = oindex(a, selection) + out = get_ndbuffer_class().from_numpy_array(np.zeros(expect.shape, dtype=expect.dtype)) + z.get_orthogonal_selection(selection, out=out) + assert_array_equal(expect, out.as_numpy_array()[:]) # coordinate selections - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) - np.random.seed(42) - # test with different degrees of sparseness - for p in 0.5, 0.1, 0.01: - n = int(a.size * p) - ix0 = np.random.choice(a.shape[0], size=n, replace=True) - ix1 = np.random.choice(a.shape[1], size=n, replace=True) - selections = [ - # index both axes with array - (ix0, ix1), - # mixed indexing with array / int - (ix0, 4), - (42, ix1), - ] - for selection in selections: - expect = a[selection] - out = get_ndbuffer_class().from_numpy_array(np.zeros(expect.shape, dtype=expect.dtype)) - z.get_coordinate_selection(selection, out=out) - assert_array_equal(expect, out.as_numpy_array()[:]) + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) + selections = [ + # index both axes with array + (np.array([0, 5, 11]), np.array([0, 2, 4])), + # mixed indexing with array / int + (np.array([0, 5, 11]), 3), + (7, np.array([0, 2, 4])), + ] + for selection in selections: + expect = a[selection] + out = get_ndbuffer_class().from_numpy_array(np.zeros(expect.shape, dtype=expect.dtype)) + z.get_coordinate_selection(selection, out=out) + assert_array_equal(expect, out.as_numpy_array()[:]) @pytest.mark.xfail(reason="fields are not supported in v3") def test_get_selections_with_fields(store: StorePath) -> None: + """Would verify that basic, orthogonal, coordinate, and mask selections with structured-array `fields` arguments return the correct sub-fields (xfail: fields unsupported in v3).""" a = np.array( [("aaa", 1, 4.2), ("bbb", 2, 8.4), ("ccc", 3, 12.6)], dtype=[("foo", "S3"), ("bar", "i4"), ("baz", "f8")], @@ -1676,6 +1680,7 @@ def test_get_selections_with_fields(store: StorePath) -> None: @pytest.mark.xfail(reason="fields are not supported in v3") def test_set_selections_with_fields(store: StorePath) -> None: + """Would verify that basic, orthogonal, coordinate, and mask set-selections with structured-array `fields` correctly write individual fields and reject multi-field assignment (xfail: fields unsupported in v3).""" v = np.array( [("aaa", 1, 4.2), ("bbb", 2, 8.4), ("ccc", 3, 12.6)], dtype=[("foo", "S3"), ("bar", "i4"), ("baz", "f8")], @@ -1761,6 +1766,7 @@ def test_set_selections_with_fields(store: StorePath) -> None: def test_slice_selection_uints() -> None: + """make_slice_selection accepts unsigned integer indices without error and produces correct shape.""" arr = np.arange(24).reshape((4, 6)) idx = np.uint64(3) slice_sel = make_slice_selection((idx,)) @@ -1768,6 +1774,7 @@ def test_slice_selection_uints() -> None: def test_numpy_int_indexing(store: StorePath) -> None: + """Indexing with a plain Python int and with `np.int64` both return the correct scalar element.""" a = np.arange(1050) z = zarr_array_from_numpy_array(store, a, chunk_shape=(100,)) assert a[42] == z[42] @@ -1802,6 +1809,7 @@ def test_numpy_int_indexing(store: StorePath) -> None: async def test_accessed_chunks( shape: tuple[int, ...], chunks: tuple[int, ...], ops: list[tuple[str, tuple[slice, ...]]] ) -> None: + """Only the chunks intersected by a slice selection are read or written, verified via a `CountingDict` store.""" # Test that only the required chunks are accessed during basic selection operations # shape: array shape # chunks: chunk size @@ -1858,22 +1866,23 @@ async def test_accessed_chunks( [1, ...], [slice(None)], [1, 3], - [[1, 2, 3], 9], - [np.arange(1000)], - [slice(5, 15)], - [slice(2, 4), 4], + [[1, 2, 3], 4], + [np.arange(12)], + [slice(2, 9)], + [slice(1, 3), 3], [[1, 3]], # mask selection - [np.tile([True, False], (1000, 5))], - [np.full((1000, 10), False)], + [np.tile([True, False, True, False, True], (12, 1))], + [np.full((12, 5), False)], # coordinate selection - [[1, 2, 3, 4], [5, 6, 7, 8]], - [[100, 200, 300], [4, 5, 6]], + [[1, 2, 3, 4], [0, 1, 2, 3]], + [[10, 11, 5], [4, 0, 2]], ], ) def test_indexing_equals_numpy(store: StorePath, selection: Selection) -> None: - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) + """Indexing a zarr array with assorted basic/mask/coordinate selections matches numpy.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) # note: in python 3.10 a[*selection] is not valid unpacking syntax expected = a[*selection,] actual = z[*selection,] @@ -1883,17 +1892,18 @@ def test_indexing_equals_numpy(store: StorePath, selection: Selection) -> None: @pytest.mark.parametrize( "selection", [ - [np.tile([True, False], 500), np.tile([True, False], 5)], - [np.full(1000, False), np.tile([True, False], 5)], - [np.full(1000, True), np.full(10, True)], - [np.full(1000, True), [True, False] * 5], + [np.tile([True, False], 6), np.tile([True, False, True, False, True], 1)], + [np.full(12, False), np.array([True, False, True, False, True])], + [np.full(12, True), np.full(5, True)], + [np.full(12, True), [True, False, True, False, True]], ], ) def test_orthogonal_bool_indexing_like_numpy_ix( store: StorePath, selection: list[npt.ArrayLike] ) -> None: - a = np.arange(10000, dtype=int).reshape(1000, 10) - z = zarr_array_from_numpy_array(store, a, chunk_shape=(300, 3)) + """Orthogonal boolean indexing on each axis matches numpy's np.ix_ semantics.""" + a = np.arange(60, dtype=int).reshape(12, 5) + z = zarr_array_from_numpy_array(store, a, chunk_shape=(5, 2)) expected = a[np.ix_(*selection)] # note: in python 3.10 z[*selection] is not valid unpacking syntax actual = z[*selection,] @@ -1951,6 +1961,7 @@ def test_iter_grid_invalid() -> None: def test_indexing_with_zarr_array(store: StorePath) -> None: + """Regression for GH2133: indexing a zarr array with another zarr array (boolean or integer) as the indexer produces the same result as indexing with the equivalent numpy array.""" # regression test for https://github.com/zarr-developers/zarr-python/issues/2133 a = np.arange(10) za = zarr.array(a, chunks=2, store=store, path="a") @@ -1970,6 +1981,7 @@ def test_indexing_with_zarr_array(store: StorePath) -> None: @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) @pytest.mark.parametrize("shape", [(0, 2, 3), (0,), (3, 0)]) def test_zero_sized_chunks(store: StorePath, shape: list[int]) -> None: + """Arrays with zero-extent dimensions can be created and indexed without error; reading back returns the fill value.""" # Chunk sizes must be >= 1 per spec; use 1 for zero-extent dimensions. chunks = tuple(max(1, s) for s in shape) z = zarr.create_array(store=store, shape=shape, chunks=chunks, zarr_format=3, dtype="f8") @@ -1979,6 +1991,7 @@ def test_zero_sized_chunks(store: StorePath, shape: list[int]) -> None: @pytest.mark.parametrize("store", ["memory"], indirect=["store"]) def test_vectorized_indexing_incompatible_shape(store) -> None: + """Regression for GH2469: vectorized set-indexing raises ValueError when the value shape is incompatible with the indexer shape.""" # GH2469 shape = (4, 4) chunks = (2, 2) @@ -1996,6 +2009,7 @@ def test_vectorized_indexing_incompatible_shape(store) -> None: def test_iter_chunk_regions(): + """_iter_chunk_regions yields slices that exactly cover each chunk, and reading/writing each region round-trips correctly.""" chunks = (2, 3) a = zarr.create((10, 10), chunks=chunks) a[:] = 1 @@ -2106,8 +2120,8 @@ class TestAsync: (np.array([False, False]), np.empty(shape=(0, 2), dtype="i8")), ], ) - @pytest.mark.asyncio async def test_async_oindex(self, store, indexer, expected): + """The async `oindex.getitem` interface returns the correct orthogonally-indexed result for int, slice, ellipsis, array, and boolean indexers.""" z = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") z[...] = np.array([[1, 2], [3, 4]]) async_zarr = z._async_array @@ -2115,8 +2129,8 @@ async def test_async_oindex(self, store, indexer, expected): result = await async_zarr.oindex.getitem(indexer) assert_array_equal(result, expected) - @pytest.mark.asyncio async def test_async_oindex_with_zarr_array(self, store): + """The async `oindex.getitem` interface accepts a zarr boolean array as the indexer and returns the correct rows.""" group = zarr.create_group(store=store, zarr_format=3) z1 = group.create_array(name="z1", shape=(2, 2), chunks=(1, 1), dtype="i8") @@ -2139,8 +2153,8 @@ async def test_async_oindex_with_zarr_array(self, store): (np.array([[False, True], [False, True]]), np.array([2, 4])), ], ) - @pytest.mark.asyncio async def test_async_vindex(self, store, indexer, expected): + """The async `vindex.getitem` interface returns the correct vectorized-indexed result for coordinate and boolean indexers.""" z = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") z[...] = np.array([[1, 2], [3, 4]]) async_zarr = z._async_array @@ -2148,8 +2162,8 @@ async def test_async_vindex(self, store, indexer, expected): result = await async_zarr.vindex.getitem(indexer) assert_array_equal(result, expected) - @pytest.mark.asyncio async def test_async_vindex_with_zarr_array(self, store): + """The async `vindex.getitem` interface accepts a zarr 2D boolean array as the indexer and returns the correct elements.""" group = zarr.create_group(store=store, zarr_format=3) z1 = group.create_array(name="z1", shape=(2, 2), chunks=(1, 1), dtype="i8") @@ -2164,8 +2178,8 @@ async def test_async_vindex_with_zarr_array(self, store): expected = np.array([2, 4]) assert_array_equal(result, expected) - @pytest.mark.asyncio async def test_async_invalid_indexer(self, store): + """The async `vindex.getitem` and `oindex.getitem` interfaces raise IndexError when given an unsupported indexer type.""" z = zarr.create_array(store=store, shape=(2, 2), chunks=(1, 1), zarr_format=3, dtype="i8") z[...] = np.array([[1, 2], [3, 4]]) async_zarr = z._async_array diff --git a/tests/test_metadata/test_v3.py b/tests/test_metadata/test_v3.py index f8f8fc56ff..d1e156e500 100644 --- a/tests/test_metadata/test_v3.py +++ b/tests/test_metadata/test_v3.py @@ -282,7 +282,6 @@ def test_array_metadata_roundtrip(case: Expect[dict[str, Any], dict[str, Any]]) ExpectFail( input={"data_type": "uint8", "fill_value": {}}, exception=TypeError, - msg=".*", id="invalid_fill_value_type", ), ], @@ -291,7 +290,7 @@ def test_array_metadata_roundtrip(case: Expect[dict[str, Any], dict[str, Any]]) def test_array_metadata_from_dict_fails(case: ExpectFail[dict[str, Any]]) -> None: """from_dict rejects invalid metadata documents.""" d = minimal_metadata_dict_v3(**case.input) - with pytest.raises(case.exception, match=case.msg): + with case.raises(): ArrayV3Metadata.from_dict(d) # type: ignore[arg-type] @@ -315,7 +314,7 @@ def test_array_metadata_from_dict_fails(case: ExpectFail[dict[str, Any]]) -> Non ) def test_array_metadata_extra_fields_rejected(case: ExpectFail[dict[str, Any]]) -> None: """from_dict rejects extra fields that don't conform to the spec.""" - with pytest.raises(case.exception, match=case.msg): + with case.raises(): ArrayV3Metadata.from_dict(case.input) From 4bfe00b373cfef6591fa7dc202e7496d69917d0c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 10 Jun 2026 22:14:03 +0200 Subject: [PATCH 343/468] refactor/consolidated JSON IO routines (#3998) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat: add free functions for JSON document I/O Add four free functions for moving JSON documents in and out of stores, plus a thin StorePath.get_json wrapper: - buffer_to_json / json_to_buffer: convert between a Buffer and a parsed JSON value. The buffer prototype and the serialization policy (indent from config, allow_nan=True) live here, in one place. - get_json / set_json: compose those with Store.get / Store.set. get_json returns None for a missing key, matching what most callers want; callers needing presence check for None themselves. These are free functions, not Store ABC methods, so stores cannot (and need not) override them and the Store contract gains no dependency on the buffer prototype or global config. Subsequent commits sweep the hand-rolled JSON I/O sites onto these and delete the old private _get_bytes/_get_json store methods. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor: route JSON document I/O through the free functions Sweep the hand-rolled `json.dumps`/`json.loads` + buffer construction in the metadata write paths and the metadata/node read paths onto the free functions added in the previous commit. Write sites (`to_buffer_dict` in group/metadata) now call `json_to_buffer`, which centralizes the `json_indent`/`allow_nan=True` serialization policy. Read sites parse buffers through `buffer_to_json_object`, a new helper that narrows the parsed `JSON` to `dict[str, JSON]` once (every metadata document is an object) rather than relying on `json.loads` returning `Any`. The compact (no-indent) consolidated-metadata blob in `GroupMetadata.to_buffer_dict` is intentionally left as a raw `json.dumps` to preserve its byte layout, and `_read_metadata_v2` keeps its `asyncio.gather` of three `store.get` calls. Co-Authored-By: Claude Opus 4.7 * refactor: remove the unused private JSON/bytes store methods `Store._get_bytes`, `_get_bytes_sync`, `_get_json`, and `_get_json_sync` had no production callers — the metadata read/write paths now go through the free functions in `zarr.core._json`. Delete the four ABC methods, the eight per-store overrides on `LocalStore`/`MemoryStore` (which existed only to make the `prototype` argument optional), and the tests that exercised them (the shared `StoreTests` methods plus the per-store prototype=None tests). Drop the now-unused `json`/`sync`/`Any` imports they pulled in. These methods were always private; removing them is not a public API change. Co-Authored-By: Claude Opus 4.7 * doc: add changelog fragment for the JSON I/O refactor Co-Authored-By: Claude Opus 4.7 * refactor: make json_to_buffer pure (no config read) `json_to_buffer` (and `set_json`) now take the JSON encoding parameters `indent` and `allow_nan` as explicit keyword arguments instead of reading `config.get("json_indent")` internally. The functions in `zarr.core._json` are now pure: they depend only on their arguments, not the global config. Each `to_buffer_dict` caller (group, metadata v2/v3) reads `config.get("json_indent")` and passes it as `indent=`. This re-localizes the config read to the metadata layer that owns the policy, and keeps the I/O helpers free of any config dependency. With `indent` now explicit, the compact consolidated-metadata blob in `GroupMetadata.to_buffer_dict` also routes through `json_to_buffer` (indent defaults to None == compact), removing the last raw `json.dumps` in that method and the `json` import from group.py. Output bytes are unchanged (the consolidated/metadata regression tests pass). Co-Authored-By: Claude Opus 4.7 * doc: rename changelog fragment to PR number 3998 Co-Authored-By: Claude Opus 4.7 * test: cover the malformed-metadata branches in contains_array/group The except clauses in `contains_array`, `contains_group`, and `_contains_node_v3` (widened to catch `TypeError` in the JSON I/O refactor) had no test exercising them — a stored `zarr.json` that is malformed bytes, valid-but-non-object JSON, or an object missing `node_type` now has a test asserting each function reports the node as absent. One test per failure mode; the two `contains_*` functions are parametrized over `func`. Co-Authored-By: Claude Opus 4.7 * Update src/zarr/core/_json.py Co-authored-by: Chuck Daniels * fix: missing import * doc: address review nits on _json.py docstrings Add a Parameters section to buffer_to_json_object and drop the redundant type annotations from the numpydoc Parameters sections, per review feedback on #3998. Co-Authored-By: Claude Opus 4.7 (1M context) --------- Co-authored-by: Claude Opus 4.7 (1M context) Co-authored-by: Chuck Daniels --- changes/3998.misc.md | 1 + src/zarr/abc/store.py | 225 ----------------------------- src/zarr/core/_json.py | 133 +++++++++++++++++ src/zarr/core/array.py | 8 +- src/zarr/core/group.py | 48 +++---- src/zarr/core/metadata/v2.py | 11 +- src/zarr/core/metadata/v3.py | 12 +- src/zarr/storage/_common.py | 33 ++++- src/zarr/storage/_local.py | 246 +------------------------------- src/zarr/storage/_memory.py | 241 ------------------------------- src/zarr/testing/store.py | 41 ------ tests/test_json.py | 116 +++++++++++++++ tests/test_store/test_core.py | 77 +++++++++- tests/test_store/test_local.py | 54 ------- tests/test_store/test_memory.py | 99 ------------- 15 files changed, 378 insertions(+), 967 deletions(-) create mode 100644 changes/3998.misc.md create mode 100644 src/zarr/core/_json.py create mode 100644 tests/test_json.py diff --git a/changes/3998.misc.md b/changes/3998.misc.md new file mode 100644 index 0000000000..bacfa93a8b --- /dev/null +++ b/changes/3998.misc.md @@ -0,0 +1 @@ +Centralized JSON document I/O behind free functions in `zarr.core._json` and removed the unused private `Store._get_bytes`/`_get_json` methods and their per-store overrides. diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index ab58acf59f..304d0cddb5 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -1,15 +1,12 @@ from __future__ import annotations import asyncio -import json from abc import ABC, abstractmethod from dataclasses import dataclass from functools import partial from itertools import starmap from typing import TYPE_CHECKING, Literal, Protocol, runtime_checkable -from zarr.core.sync import sync - if TYPE_CHECKING: from collections.abc import AsyncGenerator, AsyncIterator, Iterable, Sequence from types import TracebackType @@ -219,228 +216,6 @@ async def get( """ ... - async def _get_bytes( - self, key: str, *, prototype: BufferPrototype, byte_range: ByteRequest | None = None - ) -> bytes: - """ - Retrieve raw bytes from the store asynchronously. - - This is a convenience method that wraps ``get()`` and converts the result - to bytes. Use this when you need the raw byte content of a stored value. - - Parameters - ---------- - key : str - The key identifying the data to retrieve. - prototype : BufferPrototype - The buffer prototype to use for reading the data. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. - - Returns - ------- - bytes - The raw bytes stored at the given key. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - - See Also - -------- - get : Lower-level method that returns a Buffer object. - get_bytes : Synchronous version of this method. - get_json : Asynchronous method for retrieving and parsing JSON data. - - Examples - -------- - >>> async def example(): - ... from zarr.core.buffer.cpu import Buffer - ... from zarr.storage import MemoryStore - ... - ... store = await MemoryStore.open() - ... await store.set("data", Buffer.from_bytes(b"hello world")) - ... # No need to specify prototype for MemoryStore - ... return await store._get_bytes("data") - - >>> import asyncio - >>> asyncio.run(example()) - b'hello world' - """ - - buffer = await self.get(key, prototype, byte_range) - if buffer is None: - raise FileNotFoundError(key) - return buffer.to_bytes() - - def _get_bytes_sync( - self, key: str = "", *, prototype: BufferPrototype, byte_range: ByteRequest | None = None - ) -> bytes: - """ - Retrieve raw bytes from the store synchronously. - - This is a synchronous wrapper around ``get_bytes()``. It should only - be called from non-async code. For async contexts, use ``get_bytes()`` - instead. - - Parameters - ---------- - key : str, optional - The key identifying the data to retrieve. Defaults to an empty string. - prototype : BufferPrototype - The buffer prototype to use for reading the data. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. - - Returns - ------- - bytes - The raw bytes stored at the given key. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - - Warnings - -------- - Do not call this method from async functions. Use ``get_bytes()`` instead - to avoid blocking the event loop. - - See Also - -------- - get_bytes : Asynchronous version of this method. - get_json_sync : Synchronous method for retrieving and parsing JSON data. - - Examples - -------- - >>> from zarr.core.buffer.cpu import Buffer - >>> from zarr.storage import MemoryStore - >>> store = MemoryStore() - >>> store.set_sync("data", Buffer.from_bytes(b"hello world")) - >>> store._get_bytes_sync("data") # No need to specify prototype for MemoryStore - b'hello world' - """ - - return sync(self._get_bytes(key, prototype=prototype, byte_range=byte_range)) - - async def _get_json( - self, key: str, *, prototype: BufferPrototype, byte_range: ByteRequest | None = None - ) -> Any: - """ - Retrieve and parse JSON data from the store asynchronously. - - This is a convenience method that retrieves bytes from the store and - parses them as JSON. - - Parameters - ---------- - key : str - The key identifying the JSON data to retrieve. - prototype : BufferPrototype - The buffer prototype to use for reading the data. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. - Note: Using byte ranges with JSON may result in invalid JSON. - - Returns - ------- - Any - The parsed JSON data. This follows the behavior of ``json.loads()`` and - can be any JSON-serializable type: dict, list, str, int, float, bool, or None. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - json.JSONDecodeError - If the stored data is not valid JSON. - - See Also - -------- - get_bytes : Method for retrieving raw bytes. - get_json_sync : Synchronous version of this method. - - Examples - -------- - >>> async def example(): - ... from zarr.core.buffer.cpu import Buffer - ... from zarr.storage import MemoryStore - ... - ... store = await MemoryStore.open() - ... metadata = {"zarr_format": 3, "node_type": "array"} - ... await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - ... # No need to specify prototype for MemoryStore - ... return await store._get_json("zarr.json") - - >>> import asyncio - >>> asyncio.run(example()) - {'zarr_format': 3, 'node_type': 'array'} - """ - - return json.loads(await self._get_bytes(key, prototype=prototype, byte_range=byte_range)) - - def _get_json_sync( - self, key: str = "", *, prototype: BufferPrototype, byte_range: ByteRequest | None = None - ) -> Any: - """ - Retrieve and parse JSON data from the store synchronously. - - This is a synchronous wrapper around ``get_json()``. It should only - be called from non-async code. For async contexts, use ``get_json()`` - instead. - - Parameters - ---------- - key : str, optional - The key identifying the JSON data to retrieve. Defaults to an empty string. - prototype : BufferPrototype - The buffer prototype to use for reading the data. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Can be a ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest``. - Note: Using byte ranges with JSON may result in invalid JSON. - - Returns - ------- - Any - The parsed JSON data. This follows the behavior of ``json.loads()`` and - can be any JSON-serializable type: dict, list, str, int, float, bool, or None. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - json.JSONDecodeError - If the stored data is not valid JSON. - - Warnings - -------- - Do not call this method from async functions. Use ``get_json()`` instead - to avoid blocking the event loop. - - See Also - -------- - get_json : Asynchronous version of this method. - get_bytes_sync : Synchronous method for retrieving raw bytes without parsing. - - Examples - -------- - >>> from zarr.core.buffer.cpu import Buffer - >>> from zarr.storage import MemoryStore - >>> store = MemoryStore() - >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> store.set_sync("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> store._get_json_sync("zarr.json") # No need to specify prototype for MemoryStore - {'zarr_format': 3, 'node_type': 'array'} - """ - - return sync(self._get_json(key, prototype=prototype, byte_range=byte_range)) - @abstractmethod async def get_partial_values( self, diff --git a/src/zarr/core/_json.py b/src/zarr/core/_json.py new file mode 100644 index 0000000000..efe8152a4f --- /dev/null +++ b/src/zarr/core/_json.py @@ -0,0 +1,133 @@ +"""Helpers for moving JSON documents in and out of zarr stores. + +These are free functions, deliberately not methods on the ``Store`` ABC: +reading and writing JSON is a composition of the store's ``get``/``set`` +primitives with a buffer/JSON conversion, not part of the store contract. +Keeping them as functions means stores cannot (and need not) override them, +and the ``Store`` definition stays free of any dependency on the buffer +prototype. + +These functions are pure: the JSON encoding parameters (``indent``, +``allow_nan``) are explicit arguments rather than read from the global config. +Callers that want zarr's configured indentation pass +``indent=config.get("json_indent")``. + +Two layers: + +- ``buffer_to_json`` / ``json_to_buffer`` convert between a ``Buffer`` and a + parsed JSON value. The buffer prototype lives here, at buffer construction, + where it is meaningful. +- ``get_json`` / ``set_json`` compose those with ``Store.get`` / ``Store.set``. + ``get_json`` returns ``None`` for a missing key (the contract most callers + want); callers that require presence check for ``None`` themselves. +""" + +from __future__ import annotations + +import json +from typing import TYPE_CHECKING, cast + +from zarr.core.buffer import default_buffer_prototype + +if TYPE_CHECKING: + from zarr.abc.store import ByteRequest, Store + from zarr.core.buffer import Buffer, BufferPrototype + from zarr.core.common import JSON + + +def buffer_to_json(buffer: Buffer) -> JSON: + """Parse the contents of a `Buffer` as a JSON value.""" + # json.loads is typed as returning Any; the result is by definition JSON. + return cast("JSON", json.loads(buffer.to_bytes())) + + +def buffer_to_json_object(buffer: Buffer) -> dict[str, JSON]: + """Parse the contents of a `Buffer` as a JSON object (a `dict`). + + Every metadata document zarr reads is a JSON object, so this narrows the + `JSON` union to `dict[str, JSON]` once, here, instead of at each call site. + + Parameters + ---------- + buffer + The buffer whose contents are parsed as a JSON object. + + Raises + ------ + TypeError + If the parsed value is not a JSON object. + """ + obj = buffer_to_json(buffer) + if not isinstance(obj, dict): + raise TypeError(f"Expected a JSON object, got {type(obj).__name__}.") + return obj + + +def json_to_buffer( + obj: JSON, + *, + prototype: BufferPrototype | None = None, + indent: int | None = None, + allow_nan: bool = True, +) -> Buffer: + """Serialize a JSON value into a `Buffer`. + + Parameters + ---------- + obj + The JSON-serializable value to encode. + prototype + The buffer prototype to construct the result with. Defaults to + `default_buffer_prototype()`. + indent + Indentation passed to `json.dumps`. `None` (the default) writes + without newline indentation, using json's default separators. + Callers that want zarr's configured indentation pass + `indent=config.get("json_indent")`. + allow_nan + Whether to permit `NaN`/`Infinity` in the output, passed to + `json.dumps`. + """ + if prototype is None: + prototype = default_buffer_prototype() + return prototype.buffer.from_bytes(json.dumps(obj, indent=indent, allow_nan=allow_nan).encode()) + + +async def get_json(store: Store, key: str, *, byte_range: ByteRequest | None = None) -> JSON | None: + """Read and parse the JSON document at `key`, or `None` if it is absent. + + Parameters + ---------- + store + The store to read from. + key + The key identifying the JSON document. + byte_range + If given, read only this portion of the value. Note that a partial + read of a JSON document may not be valid JSON. + + Returns + ------- + JSON or None + The parsed JSON value, or `None` if `key` does not exist. + """ + buffer = await store.get(key, default_buffer_prototype(), byte_range) + return None if buffer is None else buffer_to_json(buffer) + + +async def set_json( + store: Store, + key: str, + obj: JSON, + *, + prototype: BufferPrototype | None = None, + indent: int | None = None, + allow_nan: bool = True, +) -> None: + """Serialize `obj` as JSON and write it to `key` in `store`. + + `indent` and `allow_nan` are forwarded to `json_to_buffer`. + """ + await store.set( + key, json_to_buffer(obj, prototype=prototype, indent=indent, allow_nan=allow_nan) + ) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 9740f575a0..d15c70064b 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1,6 +1,5 @@ from __future__ import annotations -import json import warnings from asyncio import gather from collections.abc import Iterable, Mapping, Sequence @@ -28,6 +27,7 @@ from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec from zarr.codecs.zstd import ZstdCodec from zarr.core._info import ArrayInfo +from zarr.core._json import buffer_to_json_object from zarr.core.array_spec import ArrayConfig, ArrayConfigLike, ArraySpec, parse_array_config from zarr.core.attributes import Attributes from zarr.core.buffer import ( @@ -285,13 +285,13 @@ async def get_array_metadata( if zarr_format == 2: # V2 arrays are comprised of a .zarray and .zattrs objects assert zarray_bytes is not None - metadata_dict = json.loads(zarray_bytes.to_bytes()) - zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {} + metadata_dict = buffer_to_json_object(zarray_bytes) + zattrs_dict = buffer_to_json_object(zattrs_bytes) if zattrs_bytes is not None else {} metadata_dict["attributes"] = zattrs_dict else: # V3 arrays are comprised of a zarr.json object assert zarr_json_bytes is not None - metadata_dict = json.loads(zarr_json_bytes.to_bytes()) + metadata_dict = buffer_to_json_object(zarr_json_bytes) parse_node_type_array(metadata_dict.get("node_type")) diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index de8c8e9a68..44eefb3786 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -2,7 +2,6 @@ import asyncio import itertools -import json import logging import unicodedata import warnings @@ -18,6 +17,7 @@ from zarr.abc.metadata import Metadata from zarr.abc.store import Store, set_or_delete from zarr.core._info import GroupInfo +from zarr.core._json import buffer_to_json_object, json_to_buffer from zarr.core.array import ( DEFAULT_FILL_VALUE, Array, @@ -356,21 +356,15 @@ class GroupMetadata(Metadata): node_type: Literal["group"] = field(default="group", init=False) def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: - json_indent = config.get("json_indent") + indent = config.get("json_indent") if self.zarr_format == 3: - return { - ZARR_JSON: prototype.buffer.from_bytes( - json.dumps(self.to_dict(), indent=json_indent, allow_nan=True).encode() - ) - } + return {ZARR_JSON: json_to_buffer(self.to_dict(), prototype=prototype, indent=indent)} else: items = { - ZGROUP_JSON: prototype.buffer.from_bytes( - json.dumps({"zarr_format": self.zarr_format}, indent=json_indent).encode() - ), - ZATTRS_JSON: prototype.buffer.from_bytes( - json.dumps(self.attributes, indent=json_indent, allow_nan=True).encode() + ZGROUP_JSON: json_to_buffer( + {"zarr_format": self.zarr_format}, prototype=prototype, indent=indent ), + ZATTRS_JSON: json_to_buffer(self.attributes, prototype=prototype, indent=indent), } if self.consolidated_metadata: d = { @@ -395,10 +389,9 @@ def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: }, } - items[ZMETADATA_V2_JSON] = prototype.buffer.from_bytes( - json.dumps( - {"metadata": d, "zarr_consolidated_format": 1}, allow_nan=True - ).encode() + # The consolidated metadata blob is written compactly (no indent). + items[ZMETADATA_V2_JSON] = json_to_buffer( + {"metadata": d, "zarr_consolidated_format": 1}, prototype=prototype ) return items @@ -626,13 +619,13 @@ def _from_bytes_v2( consolidated_metadata_bytes: Buffer | None, ) -> AsyncGroup: # V2 groups are comprised of a .zgroup and .zattrs objects - zgroup = json.loads(zgroup_bytes.to_bytes()) - zattrs = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {} - group_metadata = {**zgroup, "attributes": zattrs} + zgroup = buffer_to_json_object(zgroup_bytes) + zattrs = buffer_to_json_object(zattrs_bytes) if zattrs_bytes is not None else {} + group_metadata: dict[str, Any] = {**zgroup, "attributes": zattrs} if consolidated_metadata_bytes is not None: - v2_consolidated_metadata = json.loads(consolidated_metadata_bytes.to_bytes()) - v2_consolidated_metadata = v2_consolidated_metadata["metadata"] + v2_consolidated_doc = buffer_to_json_object(consolidated_metadata_bytes) + v2_consolidated_metadata = cast("dict[str, Any]", v2_consolidated_doc["metadata"]) # We already read zattrs and zgroup. Should we ignore these? v2_consolidated_metadata.pop(".zattrs", None) v2_consolidated_metadata.pop(".zgroup", None) @@ -667,7 +660,7 @@ def _from_bytes_v3( zarr_json_bytes: Buffer, use_consolidated: bool | None, ) -> AsyncGroup: - group_metadata = json.loads(zarr_json_bytes.to_bytes()) + group_metadata = buffer_to_json_object(zarr_json_bytes) if use_consolidated and group_metadata.get("consolidated_metadata") is None: msg = f"Consolidated metadata requested with 'use_consolidated=True' but not found in '{store_path.path}'." raise ValueError(msg) @@ -3368,9 +3361,7 @@ async def _read_metadata_v3(store: Store, path: str) -> ArrayV3Metadata | GroupM ) if zarr_json_bytes is None: raise FileNotFoundError(path) - else: - zarr_json = json.loads(zarr_json_bytes.to_bytes()) - return _build_metadata_v3(zarr_json) + return _build_metadata_v3(buffer_to_json_object(zarr_json_bytes)) async def _read_metadata_v2(store: Store, path: str) -> ArrayV2Metadata | GroupMetadata: @@ -3387,22 +3378,23 @@ async def _read_metadata_v2(store: Store, path: str) -> ArrayV2Metadata | GroupM store.get(_join_paths([path, ZATTRS_JSON]), prototype=default_buffer_prototype()), ) + zattrs: dict[str, JSON] if zattrs_bytes is None: zattrs = {} else: - zattrs = json.loads(zattrs_bytes.to_bytes()) + zattrs = buffer_to_json_object(zattrs_bytes) # TODO: decide how to handle finding both array and group metadata. The spec does not seem to # consider this situation. A practical approach would be to ignore that combination, and only # return the array metadata. if zarray_bytes is not None: - zmeta = json.loads(zarray_bytes.to_bytes()) + zmeta = buffer_to_json_object(zarray_bytes) else: if zgroup_bytes is None: # neither .zarray or .zgroup were found results in KeyError raise FileNotFoundError(path) else: - zmeta = json.loads(zgroup_bytes.to_bytes()) + zmeta = buffer_to_json_object(zgroup_bytes) return _build_metadata_v2(zmeta, zattrs) diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 29ed496eb1..ac32521239 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -30,6 +30,7 @@ import numpy as np +from zarr.core._json import json_to_buffer from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.chunk_key_encodings import parse_separator from zarr.core.common import ( @@ -140,14 +141,10 @@ def shards(self) -> tuple[int, ...] | None: def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: zarray_dict = self.to_dict() zattrs_dict = zarray_dict.pop("attributes", {}) - json_indent = config.get("json_indent") + indent = config.get("json_indent") return { - ZARRAY_JSON: prototype.buffer.from_bytes( - json.dumps(zarray_dict, indent=json_indent, allow_nan=True).encode() - ), - ZATTRS_JSON: prototype.buffer.from_bytes( - json.dumps(zattrs_dict, indent=json_indent, allow_nan=True).encode() - ), + ZARRAY_JSON: json_to_buffer(zarray_dict, prototype=prototype, indent=indent), + ZATTRS_JSON: json_to_buffer(zattrs_dict, prototype=prototype, indent=indent), } @classmethod diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 626c18eb72..9eaccc5076 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -9,6 +9,7 @@ from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec, BytesBytesCodec, Codec from zarr.abc.metadata import Metadata +from zarr.core._json import json_to_buffer from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.buffer.core import default_buffer_prototype from zarr.core.chunk_grids import is_regular_nd @@ -289,8 +290,6 @@ class RectilinearChunkGridMetadata(Metadata): chunk_shapes: tuple[int | tuple[int, ...], ...] def __post_init__(self) -> None: - from zarr.core.config import config - if not config.get("array.rectilinear_chunks"): raise ValueError( "Rectilinear chunk grids are experimental and disabled by default. " @@ -606,13 +605,8 @@ def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: return self.chunk_key_encoding.encode_chunk_key(chunk_coords) def to_buffer_dict(self, prototype: BufferPrototype) -> dict[str, Buffer]: - json_indent = config.get("json_indent") - d = self.to_dict() - return { - ZARR_JSON: prototype.buffer.from_bytes( - json.dumps(d, allow_nan=True, indent=json_indent).encode() - ) - } + indent = config.get("json_indent") + return {ZARR_JSON: json_to_buffer(self.to_dict(), prototype=prototype, indent=indent)} @classmethod def from_dict(cls, data: dict[str, JSON]) -> Self: diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index e4ee0bc4ac..1e13a9ac3f 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -12,6 +12,7 @@ SupportsGetSync, SupportsSetSync, ) +from zarr.core._json import buffer_to_json_object, get_json from zarr.core.buffer import Buffer, default_buffer_prototype from zarr.core.common import ( ANY_ACCESS_MODE, @@ -34,6 +35,7 @@ if TYPE_CHECKING: from zarr.core.buffer import BufferPrototype + from zarr.core.common import JSON class StorePath: @@ -161,6 +163,23 @@ async def get( prototype = default_buffer_prototype() return await self.store.get(self.path, prototype=prototype, byte_range=byte_range) + async def get_json(self, *, byte_range: ByteRequest | None = None) -> JSON | None: + """ + Read and parse the JSON document at this path, or None if it is absent. + + Parameters + ---------- + byte_range : ByteRequest, optional + If given, read only this portion of the value. Note that a partial + read of a JSON document may not be valid JSON. + + Returns + ------- + JSON or None + The parsed JSON value, or None if this path does not exist. + """ + return await get_json(self.store, self.path, byte_range=byte_range) + async def set(self, value: Buffer) -> None: """ Write bytes to the store. @@ -521,14 +540,14 @@ async def _contains_node_v3(store_path: StorePath) -> Literal["array", "group", # if no metadata document could be loaded, then we just return "nothing" if extant_meta_bytes is not None: try: - extant_meta_json = json.loads(extant_meta_bytes.to_bytes()) + extant_meta_json = buffer_to_json_object(extant_meta_bytes) # avoid constructing a full metadata document here in the name of speed. if extant_meta_json["node_type"] == "array": result = "array" elif extant_meta_json["node_type"] == "group": result = "group" - except (KeyError, json.JSONDecodeError): - # either of these errors is consistent with no array or group present. + except (KeyError, TypeError, json.JSONDecodeError): + # any of these errors is consistent with no array or group present. pass return result @@ -592,11 +611,11 @@ async def contains_array(store_path: StorePath, zarr_format: ZarrFormat) -> bool return False else: try: - extant_meta_json = json.loads(extant_meta_bytes.to_bytes()) + extant_meta_json = buffer_to_json_object(extant_meta_bytes) # we avoid constructing a full metadata document here in the name of speed. if extant_meta_json["node_type"] == "array": return True - except (ValueError, KeyError): + except (ValueError, KeyError, TypeError): return False elif zarr_format == 2: return await (store_path / ZARRAY_JSON).exists() @@ -629,10 +648,10 @@ async def contains_group(store_path: StorePath, zarr_format: ZarrFormat) -> bool return False else: try: - extant_meta_json = json.loads(extant_meta_bytes.to_bytes()) + extant_meta_json = buffer_to_json_object(extant_meta_bytes) # we avoid constructing a full metadata document here in the name of speed. result: bool = extant_meta_json["node_type"] == "group" - except (ValueError, KeyError): + except (ValueError, KeyError, TypeError): return False else: return result diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 038de4fef8..3d9882d3db 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -8,7 +8,7 @@ import sys import uuid from pathlib import Path -from typing import TYPE_CHECKING, Any, BinaryIO, Literal, Self +from typing import TYPE_CHECKING, BinaryIO, Literal, Self from zarr.abc.store import ( ByteRequest, @@ -356,250 +356,6 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: except (FileNotFoundError, NotADirectoryError): pass - async def _get_bytes( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> bytes: - """ - Retrieve raw bytes from the local store asynchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - - Returns - ------- - bytes - The raw bytes stored at the given key. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - - See Also - -------- - Store.get_bytes : Base implementation with full documentation. - get_bytes_sync : Synchronous version of this method. - - Examples - -------- - >>> async def example(): - ... import json - ... from zarr.core.buffer.cpu import Buffer - ... - ... store = await LocalStore.open("data") - ... await store.set("data", Buffer.from_bytes(b"hello")) - ... # No need to specify prototype for LocalStore - ... return await store._get_bytes("data") - - >>> import asyncio - >>> asyncio.run(example()) - b'hello' - """ - - if prototype is None: - prototype = default_buffer_prototype() - return await super()._get_bytes(key, prototype=prototype, byte_range=byte_range) - - def _get_bytes_sync( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> bytes: - """ - Retrieve raw bytes from the local store synchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - - Returns - ------- - bytes - The raw bytes stored at the given key. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - - Warnings - -------- - Do not call this method from async functions. Use ``get_bytes()`` instead. - - See Also - -------- - Store.get_bytes_sync : Base implementation with full documentation. - get_bytes : Asynchronous version of this method. - - Examples - -------- - >>> from zarr.core.buffer.cpu import Buffer - >>> store = LocalStore("data") - >>> store.set_sync("data", Buffer.from_bytes(b"hello")) - >>> # No need to specify prototype for LocalStore - >>> store._get_bytes_sync("data") - b'hello' - """ - - if prototype is None: - prototype = default_buffer_prototype() - return super()._get_bytes_sync(key, prototype=prototype, byte_range=byte_range) - - async def _get_json( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> Any: - """ - Retrieve and parse JSON data from the local store asynchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_json`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the JSON data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Note: Using byte ranges with JSON may result in invalid JSON. - - Returns - ------- - Any - The parsed JSON data. This follows the behavior of ``json.loads()`` and - can be any JSON-serializable type: dict, list, str, int, float, bool, or None. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - json.JSONDecodeError - If the stored data is not valid JSON. - - See Also - -------- - Store.get_json : Base implementation with full documentation. - get_json_sync : Synchronous version of this method. - get_bytes : Method for retrieving raw bytes without parsing. - - Examples - -------- - >>> async def example(): - ... import json - ... from zarr.core.buffer.cpu import Buffer - ... - ... store = await LocalStore.open("data") - ... metadata = {"zarr_format": 3, "node_type": "array"} - ... await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - ... # No need to specify prototype for LocalStore - ... return await store._get_json("zarr.json") - - >>> import asyncio - >>> asyncio.run(example()) - {'zarr_format': 3, 'node_type': 'array'} - """ - - if prototype is None: - prototype = default_buffer_prototype() - return await super()._get_json(key, prototype=prototype, byte_range=byte_range) - - def _get_json_sync( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> Any: - """ - Retrieve and parse JSON data from the local store synchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_json`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the JSON data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Note: Using byte ranges with JSON may result in invalid JSON. - - Returns - ------- - Any - The parsed JSON data. This follows the behavior of ``json.loads()`` and - can be any JSON-serializable type: dict, list, str, int, float, bool, or None. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - json.JSONDecodeError - If the stored data is not valid JSON. - - Warnings - -------- - Do not call this method from async functions. Use ``get_json()`` instead. - - See Also - -------- - Store.get_json_sync : Base implementation with full documentation. - get_json : Asynchronous version of this method. - get_bytes_sync : Method for retrieving raw bytes without parsing. - - Examples - -------- - >>> import json - >>> from zarr.core.buffer.cpu import Buffer - >>> store = LocalStore("data") - >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> store.set_sync("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> store._get_json_sync("zarr.json") # No need to specify prototype for LocalStore - {'zarr_format': 3, 'node_type': 'array'} - """ - - if prototype is None: - prototype = default_buffer_prototype() - return super()._get_json_sync(key, prototype=prototype, byte_range=byte_range) - async def move(self, dest_root: Path | str) -> None: """ Move the store to another path. The old root directory is deleted. diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index 121fcdab7f..e867706155 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -225,247 +225,6 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: for key in keys_unique: yield key - async def _get_bytes( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> bytes: - """ - Retrieve raw bytes from the memory store asynchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - - Returns - ------- - bytes - The raw bytes stored at the given key. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - - See Also - -------- - Store.get_bytes : Base implementation with full documentation. - get_bytes_sync : Synchronous version of this method. - - Examples - -------- - >>> async def example(): - ... from zarr.core.buffer.cpu import Buffer - ... - ... store = await MemoryStore.open() - ... await store.set("data", Buffer.from_bytes(b"hello")) - ... # No need to specify prototype for MemoryStore - ... return await store._get_bytes("data") - - >>> import asyncio - >>> asyncio.run(example()) - b'hello' - """ - - if prototype is None: - prototype = default_buffer_prototype() - return await super()._get_bytes(key, prototype=prototype, byte_range=byte_range) - - def _get_bytes_sync( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> bytes: - """ - Retrieve raw bytes from the memory store synchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_bytes`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - - Returns - ------- - bytes - The raw bytes stored at the given key. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - - Warnings - -------- - Do not call this method from async functions. Use ``get_bytes()`` instead. - - See Also - -------- - Store.get_bytes_sync : Base implementation with full documentation. - get_bytes : Asynchronous version of this method. - - Examples - -------- - >>> from zarr.core.buffer.cpu import Buffer - >>> store = MemoryStore() - >>> store.set_sync("data", Buffer.from_bytes(b"hello")) - >>> store._get_bytes_sync("data") # No need to specify prototype for MemoryStore - b'hello' - """ - if prototype is None: - prototype = default_buffer_prototype() - return super()._get_bytes_sync(key, prototype=prototype, byte_range=byte_range) - - async def _get_json( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> Any: - """ - Retrieve and parse JSON data from the memory store asynchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_json`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the JSON data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Note: Using byte ranges with JSON may result in invalid JSON. - - Returns - ------- - Any - The parsed JSON data. This follows the behavior of ``json.loads()`` and - can be any JSON-serializable type: dict, list, str, int, float, bool, or None. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - json.JSONDecodeError - If the stored data is not valid JSON. - - See Also - -------- - Store.get_json : Base implementation with full documentation. - get_json_sync : Synchronous version of this method. - get_bytes : Method for retrieving raw bytes without parsing. - - Examples - -------- - >>> async def example(): - ... import json - ... from zarr.core.buffer.cpu import Buffer - ... - ... store = await MemoryStore.open() - ... metadata = {"zarr_format": 3, "node_type": "array"} - ... await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - ... # No need to specify prototype for MemoryStore - ... return await store._get_json("zarr.json") - - >>> import asyncio - >>> asyncio.run(example()) - {'zarr_format': 3, 'node_type': 'array'} - """ - - if prototype is None: - prototype = default_buffer_prototype() - return await super()._get_json(key, prototype=prototype, byte_range=byte_range) - - def _get_json_sync( - self, - key: str = "", - *, - prototype: BufferPrototype | None = None, - byte_range: ByteRequest | None = None, - ) -> Any: - """ - Retrieve and parse JSON data from the memory store synchronously. - - This is a convenience override that makes the ``prototype`` parameter optional - by defaulting to the standard buffer prototype. See the base ``Store.get_json`` - for full documentation. - - Parameters - ---------- - key : str, optional - The key identifying the JSON data to retrieve. Defaults to an empty string. - prototype : BufferPrototype, optional - The buffer prototype to use for reading the data. If None, uses - ``default_buffer_prototype()``. - byte_range : ByteRequest, optional - If specified, only retrieve a portion of the stored data. - Note: Using byte ranges with JSON may result in invalid JSON. - - Returns - ------- - Any - The parsed JSON data. This follows the behavior of ``json.loads()`` and - can be any JSON-serializable type: dict, list, str, int, float, bool, or None. - - Raises - ------ - FileNotFoundError - If the key does not exist in the store. - json.JSONDecodeError - If the stored data is not valid JSON. - - Warnings - -------- - Do not call this method from async functions. Use ``get_json()`` instead. - - See Also - -------- - Store.get_json_sync : Base implementation with full documentation. - get_json : Asynchronous version of this method. - get_bytes_sync : Method for retrieving raw bytes without parsing. - - Examples - -------- - >>> import json - >>> from zarr.core.buffer.cpu import Buffer - >>> store = MemoryStore() - >>> metadata = {"zarr_format": 3, "node_type": "array"} - >>> store.set_sync("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode())) - >>> store._get_json_sync("zarr.json") # No need to specify prototype for MemoryStore - {'zarr_format': 3, 'node_type': 'array'} - """ - - if prototype is None: - prototype = default_buffer_prototype() - return super()._get_json_sync(key, prototype=prototype, byte_range=byte_range) - class GpuMemoryStore(MemoryStore): """ diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index a0bbe6b4b2..81024c85c8 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -1,7 +1,6 @@ from __future__ import annotations import asyncio -import json import pickle from abc import abstractmethod from typing import TYPE_CHECKING, Self @@ -558,46 +557,6 @@ async def test_set_if_not_exists(self, store: S) -> None: result = await store.get("k2", default_buffer_prototype()) assert result == new - async def test_get_bytes(self, store: S) -> None: - """ - Test that the get_bytes method reads bytes. - """ - data = b"hello world" - key = "zarr.json" - await self.set(store, key, self.buffer_cls.from_bytes(data)) - assert await store._get_bytes(key, prototype=default_buffer_prototype()) == data - with pytest.raises(FileNotFoundError): - await store._get_bytes("nonexistent_key", prototype=default_buffer_prototype()) - - def test_get_bytes_sync(self, store: S) -> None: - """ - Test that the get_bytes_sync method reads bytes. - """ - data = b"hello world" - key = "zarr.json" - sync(self.set(store, key, self.buffer_cls.from_bytes(data))) - assert store._get_bytes_sync(key, prototype=default_buffer_prototype()) == data - - async def test_get_json(self, store: S) -> None: - """ - Test that the get_json method reads json. - """ - data = {"foo": "bar"} - data_bytes = json.dumps(data).encode("utf-8") - key = "zarr.json" - await self.set(store, key, self.buffer_cls.from_bytes(data_bytes)) - assert await store._get_json(key, prototype=default_buffer_prototype()) == data - - def test_get_json_sync(self, store: S) -> None: - """ - Test that the get_json method reads json. - """ - data = {"foo": "bar"} - data_bytes = json.dumps(data).encode("utf-8") - key = "zarr.json" - sync(self.set(store, key, self.buffer_cls.from_bytes(data_bytes))) - assert store._get_json_sync(key, prototype=default_buffer_prototype()) == data - # ------------------------------------------------------------------- # Synchronous store methods (SupportsSyncStore protocol) # ------------------------------------------------------------------- diff --git a/tests/test_json.py b/tests/test_json.py new file mode 100644 index 0000000000..17a8c631d5 --- /dev/null +++ b/tests/test_json.py @@ -0,0 +1,116 @@ +from __future__ import annotations + +import math +from typing import TYPE_CHECKING + +import pytest + +from zarr.core._json import ( + buffer_to_json, + buffer_to_json_object, + get_json, + json_to_buffer, + set_json, +) +from zarr.core.buffer import cpu, default_buffer_prototype +from zarr.storage import MemoryStore +from zarr.storage._common import StorePath + +if TYPE_CHECKING: + from zarr.core.common import JSON + + +def test_json_to_buffer_round_trips() -> None: + """`buffer_to_json` inverts `json_to_buffer` for an arbitrary JSON value.""" + obj: JSON = {"zarr_format": 3, "node_type": "group", "attributes": {"a": [1, 2, 3]}} + buffer = json_to_buffer(obj) + assert buffer_to_json(buffer) == obj + + +def test_json_to_buffer_uses_given_prototype() -> None: + """`json_to_buffer` constructs the buffer from the supplied prototype.""" + prototype = default_buffer_prototype() + buffer = json_to_buffer({"x": 1}, prototype=prototype) + assert isinstance(buffer, prototype.buffer) + + +def test_json_to_buffer_allows_nan_by_default() -> None: + """`json_to_buffer` permits NaN by default (writes it as `NaN`).""" + buffer = json_to_buffer({"fill_value": math.nan}) + decoded = buffer_to_json(buffer) + assert isinstance(decoded, dict) + assert math.isnan(decoded["fill_value"]) + + +def test_json_to_buffer_allow_nan_false_rejects_nan() -> None: + """`json_to_buffer(allow_nan=False)` raises on a non-finite value.""" + with pytest.raises(ValueError, match="Out of range float"): + json_to_buffer({"fill_value": math.nan}, allow_nan=False) + + +def test_json_to_buffer_indent_controls_formatting() -> None: + """`json_to_buffer(indent=...)` controls whitespace in the serialized bytes.""" + obj: JSON = {"a": 1, "b": 2} + compact = json_to_buffer(obj).to_bytes() + indented = json_to_buffer(obj, indent=2).to_bytes() + assert b"\n" not in compact + assert b"\n" in indented + # both still round-trip to the same value + assert buffer_to_json(json_to_buffer(obj, indent=2)) == obj + + +async def test_get_json_reads_existing_key() -> None: + """`get_json` returns the parsed document stored at an existing key.""" + store = MemoryStore() + obj: JSON = {"zarr_format": 3, "node_type": "array"} + await set_json(store, "zarr.json", obj) + assert await get_json(store, "zarr.json") == obj + + +async def test_get_json_returns_none_for_missing_key() -> None: + """`get_json` returns None (rather than raising) when the key is absent.""" + store = MemoryStore() + assert await get_json(store, "does-not-exist") is None + + +async def test_set_json_then_get_json_round_trips() -> None: + """`set_json` followed by `get_json` returns the original value.""" + store = MemoryStore() + obj: JSON = {"a": 1, "b": [2, 3], "c": {"d": None}} + await set_json(store, "doc.json", obj) + assert await get_json(store, "doc.json") == obj + + +async def test_storepath_get_json_reads_existing_key() -> None: + """`StorePath.get_json` reads and parses the document at its own path.""" + store = MemoryStore() + obj: JSON = {"zarr_format": 2} + await set_json(store, "group/.zgroup", obj) + sp = StorePath(store, "group/.zgroup") + assert await sp.get_json() == obj + + +async def test_storepath_get_json_returns_none_for_missing() -> None: + """`StorePath.get_json` returns None when its path is absent.""" + store = MemoryStore() + sp = StorePath(store, "missing") + assert await sp.get_json() is None + + +def test_buffer_to_json_on_cpu_buffer() -> None: + """`buffer_to_json` works on a plain CPU buffer built from raw bytes.""" + buffer = cpu.Buffer.from_bytes(b'{"hello": "world"}') + assert buffer_to_json(buffer) == {"hello": "world"} + + +def test_buffer_to_json_object_returns_dict() -> None: + """`buffer_to_json_object` returns the parsed object as a dict.""" + buffer = cpu.Buffer.from_bytes(b'{"node_type": "group"}') + assert buffer_to_json_object(buffer) == {"node_type": "group"} + + +def test_buffer_to_json_object_rejects_non_object() -> None: + """`buffer_to_json_object` raises TypeError when the document is not an object.""" + buffer = cpu.Buffer.from_bytes(b"[1, 2, 3]") + with pytest.raises(TypeError, match="Expected a JSON object"): + buffer_to_json_object(buffer) diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index e673bfd40b..f2c81b87f9 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -1,5 +1,5 @@ import tempfile -from collections.abc import Callable, Generator +from collections.abc import Awaitable, Callable, Generator from pathlib import Path from typing import Any, Literal @@ -8,9 +8,15 @@ import zarr from zarr import Group -from zarr.core.common import AccessModeLiteral, ZarrFormat +from zarr.core.buffer import cpu +from zarr.core.common import ZARR_JSON, AccessModeLiteral, ZarrFormat from zarr.storage import FsspecStore, LocalStore, MemoryStore, StoreLike, StorePath, ZipStore -from zarr.storage._common import contains_array, contains_group, make_store_path +from zarr.storage._common import ( + _contains_node_v3, + contains_array, + contains_group, + make_store_path, +) from zarr.storage._utils import ( _join_paths, _normalize_path_keys, @@ -19,6 +25,9 @@ normalize_path, ) +# contains_array and contains_group share this signature. +_ContainsFunc = Callable[[StorePath, ZarrFormat], Awaitable[bool]] + @pytest.fixture( params=["none", "temp_dir_str", "temp_dir_path", "store_path", "memory_store", "dict"] @@ -75,15 +84,69 @@ async def test_contains_array( @pytest.mark.parametrize("func", [contains_array, contains_group]) -async def test_contains_invalid_format_raises( - local_store: LocalStore, func: Callable[[Any], Any] -) -> None: +async def test_contains_invalid_format_raises(local_store: LocalStore, func: _ContainsFunc) -> None: """ Test contains_group and contains_array raise errors for invalid zarr_formats """ store_path = StorePath(local_store) with pytest.raises(ValueError): - assert await func(store_path, zarr_format="3.0") # type: ignore[call-arg] + assert await func(store_path, "3.0") # type: ignore[arg-type] + + +async def _write_zarr_json(store_path: StorePath, data: bytes) -> None: + """Write raw bytes to the v3 metadata key under `store_path`.""" + await (store_path / ZARR_JSON).set(cpu.Buffer.from_bytes(data)) + + +@pytest.mark.parametrize("func", [contains_array, contains_group]) +async def test_contains_malformed_json_returns_false( + local_store: LocalStore, func: _ContainsFunc +) -> None: + """A v3 metadata document that is not valid JSON reads as 'not present'.""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b"{not valid json") + assert await func(store_path, 3) is False + + +@pytest.mark.parametrize("func", [contains_array, contains_group]) +async def test_contains_non_object_json_returns_false( + local_store: LocalStore, func: _ContainsFunc +) -> None: + """A v3 metadata document that is valid JSON but not an object reads as 'not present'.""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b"[1, 2, 3]") + assert await func(store_path, 3) is False + + +@pytest.mark.parametrize("func", [contains_array, contains_group]) +async def test_contains_missing_node_type_returns_false( + local_store: LocalStore, func: _ContainsFunc +) -> None: + """A v3 metadata document with no 'node_type' key reads as 'not present'.""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b'{"zarr_format": 3}') + assert await func(store_path, 3) is False + + +async def test_contains_node_v3_malformed_json_returns_nothing(local_store: LocalStore) -> None: + """`_contains_node_v3` returns 'nothing' when the document is not valid JSON.""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b"{not valid json") + assert await _contains_node_v3(store_path) == "nothing" + + +async def test_contains_node_v3_non_object_json_returns_nothing(local_store: LocalStore) -> None: + """`_contains_node_v3` returns 'nothing' when the document is not a JSON object.""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b"[1, 2, 3]") + assert await _contains_node_v3(store_path) == "nothing" + + +async def test_contains_node_v3_missing_node_type_returns_nothing(local_store: LocalStore) -> None: + """`_contains_node_v3` returns 'nothing' when the document lacks a 'node_type' key.""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b'{"zarr_format": 3}') + assert await _contains_node_v3(store_path) == "nothing" @pytest.mark.parametrize("path", [None, "", "bar"]) diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index bdc9b48121..6756bc83d9 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -1,9 +1,7 @@ from __future__ import annotations -import json import pathlib import re -from typing import TYPE_CHECKING import numpy as np import pytest @@ -11,15 +9,11 @@ import zarr from zarr import create_array from zarr.core.buffer import Buffer, cpu -from zarr.core.sync import sync from zarr.storage import LocalStore from zarr.storage._local import _atomic_write from zarr.testing.store import StoreTests from zarr.testing.utils import assert_bytes_equal -if TYPE_CHECKING: - from zarr.core.buffer import BufferPrototype - class TestLocalStore(StoreTests[LocalStore, cpu.Buffer]): store_cls = LocalStore @@ -114,54 +108,6 @@ async def test_move( ): await store2.move(destination) - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - async def test_get_bytes_with_prototype_none( - self, store: LocalStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_bytes works with prototype=None.""" - data = b"hello world" - key = "test_key" - await self.set(store, key, self.buffer_cls.from_bytes(data)) - - result = await store._get_bytes(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - def test_get_bytes_sync_with_prototype_none( - self, store: LocalStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_bytes_sync works with prototype=None.""" - data = b"hello world" - key = "test_key" - sync(self.set(store, key, self.buffer_cls.from_bytes(data))) - - result = store._get_bytes_sync(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - async def test_get_json_with_prototype_none( - self, store: LocalStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_json works with prototype=None.""" - data = {"foo": "bar", "number": 42} - key = "test.json" - await self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode())) - - result = await store._get_json(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - def test_get_json_sync_with_prototype_none( - self, store: LocalStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_json_sync works with prototype=None.""" - data = {"foo": "bar", "number": 42} - key = "test.json" - sync(self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode()))) - - result = store._get_json_sync(key, prototype=buffer_cls) - assert result == data - @pytest.mark.parametrize("exclusive", [True, False]) def test_atomic_write_successful(tmp_path: pathlib.Path, exclusive: bool) -> None: diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 92e292bef1..1e3ee89e92 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -1,6 +1,5 @@ from __future__ import annotations -import json import re from typing import TYPE_CHECKING, Any @@ -10,14 +9,12 @@ import zarr from zarr.core.buffer import Buffer, cpu, gpu -from zarr.core.sync import sync from zarr.errors import ZarrUserWarning from zarr.storage import GpuMemoryStore, ManagedMemoryStore, MemoryStore from zarr.testing.store import StoreTests from zarr.testing.utils import gpu_test if TYPE_CHECKING: - from zarr.core.buffer import BufferPrototype from zarr.core.common import ZarrFormat @@ -79,54 +76,6 @@ async def test_deterministic_size( np.testing.assert_array_equal(a[:3], 1) np.testing.assert_array_equal(a[3:], 0) - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - async def test_get_bytes_with_prototype_none( - self, store: MemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_bytes works with prototype=None.""" - data = b"hello world" - key = "test_key" - await self.set(store, key, self.buffer_cls.from_bytes(data)) - - result = await store._get_bytes(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - def test_get_bytes_sync_with_prototype_none( - self, store: MemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_bytes_sync works with prototype=None.""" - data = b"hello world" - key = "test_key" - sync(self.set(store, key, self.buffer_cls.from_bytes(data))) - - result = store._get_bytes_sync(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - async def test_get_json_with_prototype_none( - self, store: MemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_json works with prototype=None.""" - data = {"foo": "bar", "number": 42} - key = "test.json" - await self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode())) - - result = await store._get_json(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - def test_get_json_sync_with_prototype_none( - self, store: MemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_json_sync works with prototype=None.""" - data = {"foo": "bar", "number": 42} - key = "test.json" - sync(self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode()))) - - result = store._get_json_sync(key, prototype=buffer_cls) - assert result == data - # TODO: fix this warning @pytest.mark.filterwarnings("ignore:Unclosed client session:ResourceWarning") @@ -324,54 +273,6 @@ async def test_deterministic_size( np.testing.assert_array_equal(a[:3], 1) np.testing.assert_array_equal(a[3:], 0) - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - async def test_get_bytes_with_prototype_none( - self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_bytes works with prototype=None.""" - data = b"hello world" - key = "test_key" - await self.set(store, key, self.buffer_cls.from_bytes(data)) - - result = await store._get_bytes(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - def test_get_bytes_sync_with_prototype_none( - self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_bytes_sync works with prototype=None.""" - data = b"hello world" - key = "test_key" - sync(self.set(store, key, self.buffer_cls.from_bytes(data))) - - result = store._get_bytes_sync(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - async def test_get_json_with_prototype_none( - self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_json works with prototype=None.""" - data = {"foo": "bar", "number": 42} - key = "test.json" - await self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode())) - - result = await store._get_json(key, prototype=buffer_cls) - assert result == data - - @pytest.mark.parametrize("buffer_cls", [None, cpu.buffer_prototype]) - def test_get_json_sync_with_prototype_none( - self, store: ManagedMemoryStore, buffer_cls: None | BufferPrototype - ) -> None: - """Test that get_json_sync works with prototype=None.""" - data = {"foo": "bar", "number": 42} - key = "test.json" - sync(self.set(store, key, self.buffer_cls.from_bytes(json.dumps(data).encode()))) - - result = store._get_json_sync(key, prototype=buffer_cls) - assert result == data - def test_from_url(self, store: ManagedMemoryStore) -> None: """Test that from_url creates a store sharing the same dict.""" url = str(store) From e5fb84f67e077fba9049aab10b630553b5a57ee7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 11 Jun 2026 11:49:37 +0200 Subject: [PATCH 344/468] chore(deps): bump the actions group with 3 updates (#4058) Bumps the actions group with 3 updates: [actions/checkout](https://github.com/actions/checkout), [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) and [CodSpeedHQ/action](https://github.com/codspeedhq/action). Updates `actions/checkout` from 6.0.2 to 6.0.3 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/de0fac2e4500dabe0009e67214ff5f5447ce83dd...df4cb1c069e1874edd31b4311f1884172cec0e10) Updates `astral-sh/setup-uv` from 8.1.0 to 8.2.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/08807647e7069bb48b6ef5acd8ec9567f424441b...fac544c07dec837d0ccb6301d7b5580bf5edae39) Updates `CodSpeedHQ/action` from 4.15.1 to 4.17.0 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/3194d9a39c4d46684cb44bf7207fc56626aad8fd...9d332c4d90b43981c3e55ae8e38e68709996240f) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 6.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 8.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 4.17.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 4 ++-- .github/workflows/codspeed.yml | 4 ++-- .github/workflows/docs.yml | 4 ++-- .github/workflows/downstream.yml | 12 ++++++------ .github/workflows/gpu_test.yml | 4 ++-- .github/workflows/hypothesis.yaml | 4 ++-- .github/workflows/lint.yml | 4 ++-- .github/workflows/nightly_wheels.yml | 2 +- .github/workflows/prepare_release.yml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/test.yml | 16 ++++++++-------- .github/workflows/zarr-metadata-release.yml | 4 ++-- .github/workflows/zarr-metadata.yml | 12 ++++++------ .github/workflows/zizmor.yml | 2 +- 14 files changed, 38 insertions(+), 38 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index d897c82775..10a21d21c3 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -17,12 +17,12 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Check zarr-python changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index c9d2060a66..4e20b5efa7 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -23,7 +23,7 @@ jobs: github.event_name == 'workflow_dispatch' || (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark')) steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 persist-credentials: false @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@3194d9a39c4d46684cb44bf7207fc56626aad8fd # v4.15.1 + uses: CodSpeedHQ/action@9d332c4d90b43981c3e55ae8e38e68709996240f # v4.17.0 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index fb5487ada4..ab745beec1 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -19,10 +19,10 @@ jobs: name: Check docs runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false - - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - run: uv sync --group docs # --strict turns warnings into errors, so a docs code block that fails to execute # at build time (e.g. a non-exec python fence disrupting a later exec="true" block) diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index ec792163df..08bfcf2139 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -21,13 +21,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out zarr-python - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 persist-credentials: false - name: Check out xarray - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: repository: pydata/xarray path: xarray @@ -45,7 +45,7 @@ jobs: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install xarray and test dependencies working-directory: xarray @@ -83,13 +83,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out zarr-python - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 persist-credentials: false - name: Check out numcodecs - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: repository: zarr-developers/numcodecs fetch-depth: 0 @@ -102,7 +102,7 @@ jobs: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install numcodecs with test-zarr-main group working-directory: numcodecs diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index c03318d649..27c95762d6 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -34,7 +34,7 @@ jobs: python-version: ['3.12'] steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 # grab all branches and tags persist-credentials: false @@ -62,7 +62,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index bc711c8490..92907f45e1 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -39,7 +39,7 @@ jobs: dependency-set: ["optional"] steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false - name: Set HYPOTHESIS_PROFILE based on trigger @@ -57,7 +57,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index fec211b4dd..32e521377d 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -19,7 +19,7 @@ jobs: name: Lint runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false - name: Set up Python @@ -27,7 +27,7 @@ jobs: with: python-version: "3.12" - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 with: enable-cache: true - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4 diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 1f48e9e1b8..6ef6c28994 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: submodules: true fetch-depth: 0 diff --git a/.github/workflows/prepare_release.yml b/.github/workflows/prepare_release.yml index 4dbedf5b9e..57ae10ff0d 100644 --- a/.github/workflows/prepare_release.yml +++ b/.github/workflows/prepare_release.yml @@ -36,7 +36,7 @@ jobs: VERSION: ${{ inputs.version }} TARGET_BRANCH: ${{ inputs.target_branch }} - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: ref: ${{ inputs.target_branch }} fetch-depth: 0 diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index a6c7202c5b..43436de947 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -26,7 +26,7 @@ jobs: fail-fast: false steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: submodules: true fetch-depth: 0 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 142290d109..9b5f98a2d2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -56,7 +56,7 @@ jobs: runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 # grab all branches and tags persist-credentials: false @@ -66,7 +66,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -105,7 +105,7 @@ jobs: - python-version: "3.12" dependency-set: upstream steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 persist-credentials: false @@ -115,7 +115,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -140,7 +140,7 @@ jobs: name: doctests runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3 persist-credentials: false @@ -150,7 +150,7 @@ jobs: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -164,7 +164,7 @@ jobs: name: Benchmark smoke test runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: fetch-depth: 0 persist-credentials: false @@ -174,7 +174,7 @@ jobs: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Run Benchmarks diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index 9639fcfdd3..cd4e408906 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -22,7 +22,7 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false fetch-depth: 0 # hatch-vcs needs full history + tags @@ -51,7 +51,7 @@ jobs: path: dist - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 with: enable-cache: false diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml index 1ff0786118..3081abf094 100644 --- a/.github/workflows/zarr-metadata.yml +++ b/.github/workflows/zarr-metadata.yml @@ -32,11 +32,11 @@ jobs: matrix: python-version: ['3.11', '3.12', '3.13', '3.14'] steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 with: enable-cache: true - name: Set up Python ${{ matrix.python-version }} @@ -54,11 +54,11 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Run ruff run: uvx ruff check . @@ -70,11 +70,11 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 with: enable-cache: true - name: Set up Python diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 7ac4fe5d0e..869f76dcc1 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -27,7 +27,7 @@ jobs: security-events: write # Required by zizmor-action to upload SARIF files steps: - name: Checkout repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 with: persist-credentials: false From 3d8746a0b3b257b26ea61f3f7fefb7581aad70f8 Mon Sep 17 00:00:00 2001 From: Chuck Daniels Date: Thu, 11 Jun 2026 06:06:14 -0400 Subject: [PATCH 345/468] Modify custom dtype example to use only public API (#4052) * Move DataTypeValidationError to zarr.errors Internally change all imports of DataTypeValidationError to import from zarr.errors and deprecate imports of DataTypeValidationError from all other modules. * Import ZDType, data_type_registry from zarr.dtype * Re-export common types from zarr.types * Re-export check_dtype_spec_v2 from zarr.dtype * Add change file for PR 4052 --------- Co-authored-by: Davis Bennett --- changes/4052.doc.md | 21 ++++++++++ examples/custom_dtype/custom_dtype.py | 48 ++++++++++++++--------- src/zarr/core/dtype/__init__.py | 22 ++++++++--- src/zarr/core/dtype/common.py | 15 ++++++- src/zarr/core/dtype/npy/bool.py | 2 +- src/zarr/core/dtype/npy/bytes.py | 2 +- src/zarr/core/dtype/npy/complex.py | 2 +- src/zarr/core/dtype/npy/float.py | 2 +- src/zarr/core/dtype/npy/int.py | 2 +- src/zarr/core/dtype/npy/string.py | 2 +- src/zarr/core/dtype/npy/structured.py | 2 +- src/zarr/core/dtype/npy/time.py | 2 +- src/zarr/core/dtype/registry.py | 6 +-- src/zarr/dtype.py | 21 +++++++++- src/zarr/errors.py | 4 ++ src/zarr/types.py | 15 +++++++ tests/package_with_entrypoint/__init__.py | 3 +- tests/test_errors.py | 23 +++++++++++ 18 files changed, 154 insertions(+), 40 deletions(-) create mode 100644 changes/4052.doc.md diff --git a/changes/4052.doc.md b/changes/4052.doc.md new file mode 100644 index 0000000000..90b4679db5 --- /dev/null +++ b/changes/4052.doc.md @@ -0,0 +1,21 @@ +Updated the custom dtype example in `examples/custom_dtype/custom_dtype.py` to +use only the public API, eliminating all non-public imports, illustrating what +users should do. + +To better support this, the following types and functions were made available +from public modules: + +| Type/Function | Non-public module | Public module | +| ------------------------- | ------------------------ | ------------- | +| `DataTypeValidationError` | `zarr.core.dtype.common` | `zarr.errors` | +| `JSON` | `zarr.core.common` | `zarr.types` | +| `ZarrFormat` | `zarr.core.common` | `zarr.types` | +| `DTypeConfig_V2` | `zarr.core.dtype.common` | `zarr.types` | +| `DTypeJSON` | `zarr.core.dtype.common` | `zarr.types` | +| `DTypeSpec_V2` | `zarr.core.dtype.common` | `zarr.dtype` | +| `check_dtype_spec_v2` | `zarr.core.dtype.common` | `zarr.dtype` | + +`DataTypeValidationError` was *moved* to `zarr.errors`. Importing it from +`zarr.core.dtype.common` (its original location), `zarr.core.dtype`, or +`zarr.dtype` still works but now raises a `ZarrDeprecationWarning`. The remaining +types and functions are simply re-exported from the listed public module. diff --git a/examples/custom_dtype/custom_dtype.py b/examples/custom_dtype/custom_dtype.py index a13283a681..53acb70f52 100644 --- a/examples/custom_dtype/custom_dtype.py +++ b/examples/custom_dtype/custom_dtype.py @@ -22,14 +22,9 @@ import pytest import zarr -from zarr.core.common import JSON, ZarrFormat -from zarr.core.dtype import ZDType, data_type_registry -from zarr.core.dtype.common import ( - DataTypeValidationError, - DTypeConfig_V2, - DTypeJSON, - check_dtype_spec_v2, -) +from zarr.dtype import ZDType, check_dtype_spec_v2, data_type_registry +from zarr.errors import DataTypeValidationError +from zarr.types import JSON, DTypeConfig_V2, DTypeJSON, ZarrFormat # This is the int2 array data type int2_dtype_cls = type(np.dtype("int2")) @@ -120,7 +115,7 @@ def _from_json_v3(cls: type[Self], data: DTypeJSON) -> Self: msg = f"Invalid JSON representation of {cls.__name__}. Got {data!r}, expected the string {cls._zarr_v3_name!r}" raise DataTypeValidationError(msg) - @overload # type: ignore[override] + @overload def to_json(self, zarr_format: Literal[2]) -> DTypeConfig_V2[Literal["int2"], None]: ... @overload @@ -145,7 +140,7 @@ def to_json( """ if zarr_format == 2: return {"name": "int2", "object_codec_id": None} - elif zarr_format == 3: + if zarr_format == 3: return self._zarr_v3_name raise ValueError(f"zarr_format must be 2 or 3, got {zarr_format}") # pragma: no cover @@ -191,9 +186,11 @@ def to_json_scalar(self, data: object, *, zarr_format: ZarrFormat) -> int: """ # We could add a type check here, but we don't need to for this example val: int = int(data) # type: ignore[call-overload] - if val not in (-2, -1, 0, 1): - raise ValueError("Invalid value. Expected -2, -1, 0, or 1.") - return val + + if val in {-2, -1, 0, 1}: + return val + + raise ValueError("Invalid value. Expected -2, -1, 0, or 1.") def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> ml_dtypes.int2: """ @@ -220,7 +217,11 @@ def from_json_scalar(self, data: JSON, *, zarr_format: ZarrFormat) -> ml_dtypes. def test_custom_dtype(tmp_path: Path, zarr_format: ZarrFormat) -> None: # create array and write values z_w = zarr.create_array( - store=tmp_path, shape=(4,), dtype="int2", zarr_format=zarr_format, compressors=None + store=tmp_path, + shape=(4,), + dtype="int2", + zarr_format=zarr_format, + compressors=None, ) z_w[:] = [-1, -2, 0, 1] @@ -230,10 +231,7 @@ def test_custom_dtype(tmp_path: Path, zarr_format: ZarrFormat) -> None: print(z_r.info_complete()) # look at the array metadata - if zarr_format == 2: - meta_file = tmp_path / ".zarray" - else: - meta_file = tmp_path / "zarr.json" + meta_file = tmp_path / (".zarray" if zarr_format == 2 else "zarr.json") print(json.dumps(json.loads(meta_file.read_text()), indent=2)) @@ -242,4 +240,16 @@ def test_custom_dtype(tmp_path: Path, zarr_format: ZarrFormat) -> None: # Without the dummy configuration file, at test time pytest will attempt to use the # configuration file in the project root, which will error because Zarr is using some # plugins that are not installed in this example. - sys.exit(pytest.main(["-s", __file__, f"-c {__file__}"])) + sys.exit( + pytest.main( + [ + "-s", + __file__, + f"-c {__file__}", + # Suppress: "PytestAssertRewriteWarning: Module already imported so + # cannot be rewritten; zarr" + "-W", + "ignore::pytest.PytestAssertRewriteWarning", + ] + ) + ) diff --git a/src/zarr/core/dtype/__init__.py b/src/zarr/core/dtype/__init__.py index 7e2cd90fd2..d1dbd6e2c8 100644 --- a/src/zarr/core/dtype/__init__.py +++ b/src/zarr/core/dtype/__init__.py @@ -3,10 +3,6 @@ from collections.abc import Sequence from typing import TYPE_CHECKING, Final -from zarr.core.dtype.common import ( - DataTypeValidationError, - DTypeJSON, -) from zarr.core.dtype.npy.bool import Bool from zarr.core.dtype.npy.bytes import ( NullTerminatedBytes, @@ -39,6 +35,7 @@ if TYPE_CHECKING: from zarr.core.common import ZarrFormat + from zarr.core.dtype.common import DTypeJSON from collections.abc import Mapping @@ -61,7 +58,6 @@ "Complex64", "Complex128", "DataTypeRegistry", - "DataTypeValidationError", "DateTime64", "DateTime64JSON_V2", "DateTime64JSON_V3", @@ -287,3 +283,19 @@ def parse_dtype( # otherwise, we have either a numpy dtype string, or a zarr v3 dtype string, and in either case # we can create a native dtype from it, and do the dtype inference from that return get_data_type_from_native_dtype(dtype_spec) # type: ignore[arg-type] + + +def __getattr__(name: str) -> object: + if name == "DataTypeValidationError": + import warnings + + from zarr.errors import DataTypeValidationError, ZarrDeprecationWarning + + warnings.warn( + "Importing DataTypeValidationError from zarr.core.dtype is deprecated. " + "Use zarr.errors.DataTypeValidationError instead.", + ZarrDeprecationWarning, + stacklevel=2, + ) + return DataTypeValidationError + raise AttributeError(f"module {__name__!r} has no attribute {name!r}") diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index 87e46b53d2..76d763d267 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -146,7 +146,20 @@ def unpack_dtype_json(data: DTypeSpec_V2 | DTypeSpec_V3) -> DTypeJSON: return data -class DataTypeValidationError(ValueError): ... +def __getattr__(name: str) -> object: + if name == "DataTypeValidationError": + import warnings + + from zarr.errors import DataTypeValidationError, ZarrDeprecationWarning + + warnings.warn( + "Importing DataTypeValidationError from zarr.core.dtype.common is deprecated. " + "Use zarr.errors.DataTypeValidationError or zarr.dtype.DataTypeValidationError instead.", + ZarrDeprecationWarning, + stacklevel=2, + ) + return DataTypeValidationError + raise AttributeError(f"module {__name__!r} has no attribute {name!r}") class ScalarTypeValidationError(ValueError): ... diff --git a/src/zarr/core/dtype/npy/bool.py b/src/zarr/core/dtype/npy/bool.py index 3e7f5b72f0..f92476a455 100644 --- a/src/zarr/core/dtype/npy/bool.py +++ b/src/zarr/core/dtype/npy/bool.py @@ -6,13 +6,13 @@ import numpy as np from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasItemSize, check_dtype_spec_v2, ) from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index 2cf5985d69..af8fa7a272 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -9,7 +9,6 @@ from zarr.core.common import JSON, NamedConfig, ZarrFormat from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasItemSize, @@ -20,6 +19,7 @@ ) from zarr.core.dtype.npy.common import check_json_str from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr.errors import DataTypeValidationError BytesLike = np.bytes_ | str | bytes | int diff --git a/src/zarr/core/dtype/npy/complex.py b/src/zarr/core/dtype/npy/complex.py index 76a0f05869..0286d42380 100644 --- a/src/zarr/core/dtype/npy/complex.py +++ b/src/zarr/core/dtype/npy/complex.py @@ -13,7 +13,6 @@ import numpy as np from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasEndianness, @@ -32,6 +31,7 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/npy/float.py b/src/zarr/core/dtype/npy/float.py index 668e169d8b..d041416b81 100644 --- a/src/zarr/core/dtype/npy/float.py +++ b/src/zarr/core/dtype/npy/float.py @@ -6,7 +6,6 @@ import numpy as np from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasEndianness, @@ -26,6 +25,7 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/npy/int.py b/src/zarr/core/dtype/npy/int.py index a68923507b..c18fd01dd8 100644 --- a/src/zarr/core/dtype/npy/int.py +++ b/src/zarr/core/dtype/npy/int.py @@ -15,7 +15,6 @@ import numpy as np from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasEndianness, @@ -30,6 +29,7 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/npy/string.py b/src/zarr/core/dtype/npy/string.py index 3beb82c598..3f84e8123f 100644 --- a/src/zarr/core/dtype/npy/string.py +++ b/src/zarr/core/dtype/npy/string.py @@ -18,7 +18,6 @@ from zarr.core.common import NamedConfig from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasEndianness, @@ -33,6 +32,7 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import ZDType +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/npy/structured.py b/src/zarr/core/dtype/npy/structured.py index c5ff5b68a3..b865998e52 100644 --- a/src/zarr/core/dtype/npy/structured.py +++ b/src/zarr/core/dtype/npy/structured.py @@ -8,7 +8,6 @@ from zarr.core.common import NamedConfig from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasItemSize, @@ -23,6 +22,7 @@ check_json_str, ) from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/npy/time.py b/src/zarr/core/dtype/npy/time.py index e55eb08d38..4efa0be7bb 100644 --- a/src/zarr/core/dtype/npy/time.py +++ b/src/zarr/core/dtype/npy/time.py @@ -19,7 +19,6 @@ from zarr.core.common import NamedRequiredConfig from zarr.core.dtype.common import ( - DataTypeValidationError, DTypeConfig_V2, DTypeJSON, HasEndianness, @@ -34,6 +33,7 @@ get_endianness_from_numpy_dtype, ) from zarr.core.dtype.wrapper import TBaseDType, ZDType +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from zarr.core.common import JSON, ZarrFormat diff --git a/src/zarr/core/dtype/registry.py b/src/zarr/core/dtype/registry.py index 315945cf4e..0a9b2aa64a 100644 --- a/src/zarr/core/dtype/registry.py +++ b/src/zarr/core/dtype/registry.py @@ -6,15 +6,13 @@ import numpy as np -from zarr.core.dtype.common import ( - DataTypeValidationError, - DTypeJSON, -) +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from importlib.metadata import EntryPoint from zarr.core.common import ZarrFormat + from zarr.core.dtype.common import DTypeJSON from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType diff --git a/src/zarr/dtype.py b/src/zarr/dtype.py index f75219aab8..0c271b6c90 100644 --- a/src/zarr/dtype.py +++ b/src/zarr/dtype.py @@ -2,7 +2,6 @@ Bool, Complex64, Complex128, - DataTypeValidationError, DateTime64, DateTime64JSON_V2, DateTime64JSON_V3, @@ -45,12 +44,13 @@ parse_data_type, # noqa: F401 parse_dtype, ) +from zarr.core.dtype.common import DTypeSpec_V2, check_dtype_spec_v2 __all__ = [ "Bool", "Complex64", "Complex128", - "DataTypeValidationError", + "DTypeSpec_V2", "DateTime64", "DateTime64JSON_V2", "DateTime64JSON_V3", @@ -87,6 +87,23 @@ "VariableLengthUTF8", "VariableLengthUTF8JSON_V2", "ZDType", + "check_dtype_spec_v2", "data_type_registry", "parse_dtype", ] + + +def __getattr__(name: str) -> object: + if name == "DataTypeValidationError": + import warnings + + from zarr.errors import DataTypeValidationError, ZarrDeprecationWarning + + warnings.warn( + "Importing DataTypeValidationError from zarr.dtype is deprecated. " + "Use zarr.errors.DataTypeValidationError instead.", + ZarrDeprecationWarning, + stacklevel=2, + ) + return DataTypeValidationError + raise AttributeError(f"module {__name__!r} has no attribute {name!r}") diff --git a/src/zarr/errors.py b/src/zarr/errors.py index 5a6bb54bef..781bebe534 100644 --- a/src/zarr/errors.py +++ b/src/zarr/errors.py @@ -7,6 +7,7 @@ "ContainsArrayAndGroupError", "ContainsArrayError", "ContainsGroupError", + "DataTypeValidationError", "GroupNotFoundError", "MetadataValidationError", "NegativeStepError", @@ -84,6 +85,9 @@ class ContainsArrayAndGroupError(BaseZarrError): ) +class DataTypeValidationError(ValueError): ... + + class MetadataValidationError(BaseZarrError): """Raised when the Zarr metadata is invalid in some way""" diff --git a/src/zarr/types.py b/src/zarr/types.py index c159d5d5f2..8b77d344b2 100644 --- a/src/zarr/types.py +++ b/src/zarr/types.py @@ -1,6 +1,8 @@ from typing import Any from zarr.core.array import Array, AsyncArray +from zarr.core.common import JSON, ZarrFormat +from zarr.core.dtype.common import DTypeConfig_V2, DTypeJSON from zarr.core.metadata.v2 import ArrayV2Metadata from zarr.core.metadata.v3 import ArrayV3Metadata @@ -21,3 +23,16 @@ type ArrayV3 = Array[ArrayV3Metadata] """A Zarr format 3 `Array`""" + +__all__ = ( + "JSON", + "AnyArray", + "AnyAsyncArray", + "ArrayV2", + "ArrayV3", + "AsyncArrayV2", + "AsyncArrayV3", + "DTypeConfig_V2", + "DTypeJSON", + "ZarrFormat", +) diff --git a/tests/package_with_entrypoint/__init__.py b/tests/package_with_entrypoint/__init__.py index 7b5dfb5a1e..23afcf1dc2 100644 --- a/tests/package_with_entrypoint/__init__.py +++ b/tests/package_with_entrypoint/__init__.py @@ -9,8 +9,8 @@ from zarr.abc.codec import ArrayBytesCodec, CodecInput, CodecPipeline from zarr.codecs import BytesCodec from zarr.core.buffer import Buffer, NDBuffer -from zarr.core.dtype.common import DataTypeValidationError, DTypeJSON, DTypeSpec_V2 from zarr.core.dtype.npy.bool import Bool +from zarr.errors import DataTypeValidationError if TYPE_CHECKING: from collections.abc import Iterable @@ -18,6 +18,7 @@ from zarr.core.array_spec import ArraySpec from zarr.core.common import ZarrFormat + from zarr.core.dtype.common import DTypeJSON, DTypeSpec_V2 class TestEntrypointCodec(ArrayBytesCodec): diff --git a/tests/test_errors.py b/tests/test_errors.py index ccc9e597bb..17dbada9f4 100644 --- a/tests/test_errors.py +++ b/tests/test_errors.py @@ -1,13 +1,17 @@ """Test errors""" +import pytest + from zarr.errors import ( ArrayNotFoundError, ContainsArrayAndGroupError, ContainsArrayError, ContainsGroupError, + DataTypeValidationError, GroupNotFoundError, MetadataValidationError, NodeTypeValidationError, + ZarrDeprecationWarning, ) @@ -76,3 +80,22 @@ def test_node_type_validation_error() -> None: """ err = NodeTypeValidationError("a", "b", "c") assert str(err) == "Invalid value for 'a'. Expected 'b'. Got 'c'." + + +@pytest.mark.parametrize( + "module_name", + [ + "zarr.core.dtype.common", + "zarr.core.dtype", + "zarr.dtype", + ], +) +def test_data_type_validation_error_deprecated_import(module_name: str) -> None: + import importlib + + module = importlib.import_module(module_name) + + with pytest.warns(ZarrDeprecationWarning, match=f"{module_name}"): + cls = module.DataTypeValidationError + + assert cls is DataTypeValidationError From ea76ec85c45f1fe503bd324985b329a75adc0d80 Mon Sep 17 00:00:00 2001 From: Siddhant Tibrewal Date: Thu, 11 Jun 2026 14:44:47 +0200 Subject: [PATCH 346/468] fix: copy attributes passed from the user to avoid mutation (#4060) * fix: copy attributes passed from the user to avoid mutation * fix: copy attributes passed from the user to avoid mutation --------- Co-authored-by: Davis Bennett --- changes/4059.bugfix.md | 1 + src/zarr/core/group.py | 2 +- src/zarr/core/metadata/common.py | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 changes/4059.bugfix.md diff --git a/changes/4059.bugfix.md b/changes/4059.bugfix.md new file mode 100644 index 0000000000..16fb582f65 --- /dev/null +++ b/changes/4059.bugfix.md @@ -0,0 +1 @@ +Prevents mutation of the attributes dict provided by the user by copying them instead of keeping the reference diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 44eefb3786..52eaa3e144 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -105,7 +105,7 @@ def parse_attributes(data: Any) -> dict[str, Any]: if data is None: return {} elif isinstance(data, dict) and all(isinstance(k, str) for k in data): - return data + return dict(data) msg = f"Expected dict with string keys. Got {type(data)} instead." raise TypeError(msg) diff --git a/src/zarr/core/metadata/common.py b/src/zarr/core/metadata/common.py index 44d3eb292b..6367bdb28a 100644 --- a/src/zarr/core/metadata/common.py +++ b/src/zarr/core/metadata/common.py @@ -10,4 +10,4 @@ def parse_attributes(data: dict[str, JSON] | None) -> dict[str, JSON]: if data is None: return {} - return data + return dict(data) From 205f5f81b791e74dcdd9b5b4d5dedca4b9f1b68c Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 11 Jun 2026 20:36:42 -0400 Subject: [PATCH 347/468] docs: add core-developer self-merge policy (#4053) * docs: add core-developer self-merge policy for low-risk PRs * docs: specify emergency fixes, low-blast radius bug fixes, and new experimental features * docs: add changelog entry * docs: make self-merge policy less prescriptive * Apply suggestion about pinging other devs --------- Co-authored-by: Davis Bennett --- changes/4053.doc.md | 1 + docs/contributing.md | 46 +++++++++++++++++++++++++++++--------------- 2 files changed, 31 insertions(+), 16 deletions(-) create mode 100644 changes/4053.doc.md diff --git a/changes/4053.doc.md b/changes/4053.doc.md new file mode 100644 index 0000000000..3220b2b4ec --- /dev/null +++ b/changes/4053.doc.md @@ -0,0 +1 @@ +Document a self-merge policy in the contributor guide, describing when a core developer may merge their own pull request without a second reviewer and which changes warrant more caution. diff --git a/docs/contributing.md b/docs/contributing.md index e4906f6db5..750f7c7a65 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -327,7 +327,11 @@ Alternatively, you can manually create the files in the `changes` directory usin See the [towncrier](https://towncrier.readthedocs.io/en/stable/tutorial.html) docs for more. -## Merging pull requests +## Project governance + +This section documents the processes that core developers follow to maintain the project. The current core developers are listed in [`TEAM.md`](https://github.com/zarr-developers/zarr-python/blob/main/TEAM.md). + +### Merging pull requests Pull requests submitted by an external contributor should be reviewed and approved by at least one core developer before being merged. Ideally, pull requests submitted by a core developer should be reviewed and approved by at least one other core developer before being merged. @@ -335,6 +339,31 @@ Pull requests should not be merged until all CI checks have passed (GitHub Actio Before merging, the milestone must be set to decide whether a PR will be in the next patch, minor, or major release. The next section explains which types of changes go in each release. +### Self-merging pull requests + +The default is that a pull request opened by a core developer is reviewed and approved by at least one other core developer before it is merged. We trust core developers to use their judgment, though, and we would rather bias toward action than make routine changes wait on review they do not really need. + +So a core developer may merge their own pull request whenever they judge the change to be low-risk, provided the standard merge requirements are met — CI is green against code that has had the latest `main` merged in, a changelog fragment has been added, and the milestone is set — and other core developers have had a fair chance to weigh in. As a rule of thumb, leave the pull request open for a few days before self-merging, unless it is genuinely trivial or time-sensitive. If you are confident a change is fine, merge it; if you have real doubts, ask for a review. It is generally advisable to ping another developer in the PR description for awareness about the direction, even if you choose not to request a formal review. + +Some changes warrant more caution, and a second reviewer is usually worth seeking even when you could self-merge: changes to the public API, anything touching data-format or on-disk compatibility, and performance-sensitive code. These are the most expensive to get wrong and the hardest to reverse. Reverts, by contrast, are cheap — if a self-merged change turns out to be a mistake, reverting it is itself a low-risk change that any core developer can make, and the reworked version can go through normal review. When something recently merged is actively causing harm — a broken `main`, a release blocker, or data corruption — fix it fast and request review after the fact rather than waiting. + +This policy exists to lower the cost of routine work and to help newer core developers grow comfortable merging changes. It is not a license to merge past an unresolved objection: if another core developer asks to review a change, give them that chance. + +### Release procedure + +Open an issue on GitHub announcing the release using the release checklist template: +[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md). The release checklist includes all steps necessary for the release. + +#### Preparing a release + +Releases are prepared using the ["Prepare release notes"](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) workflow. To run it: + +1. Go to the [workflow page](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) and click "Run workflow". +2. Enter the release version (e.g. `3.2.0`) and the target branch (defaults to `main`). +3. The workflow will run `towncrier build` to render the changelog, remove consumed fragments from `changes/`, and open a pull request on the `release/v` branch. +4. The release PR is automatically labeled `run-downstream`, which triggers the [downstream test workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) to run Xarray and numcodecs integration tests against the release branch. +5. Review the rendered changelog in `docs/release-notes.md` and verify downstream tests pass before merging. + ## Compatibility and versioning policies ### Versioning @@ -392,21 +421,6 @@ We aim to either **promote** or **remove** experimental features within **6 mont Features in `zarr.experimental` carry no stability guarantees. They may be changed or removed in any release, including patch releases. If you depend on an experimental feature, pin your `zarr-python` version accordingly. -## Release procedure - -Open an issue on GitHub announcing the release using the release checklist template: -[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md). The release checklist includes all steps necessary for the release. - -### Preparing a release - -Releases are prepared using the ["Prepare release notes"](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) workflow. To run it: - -1. Go to the [workflow page](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) and click "Run workflow". -2. Enter the release version (e.g. `3.2.0`) and the target branch (defaults to `main`). -3. The workflow will run `towncrier build` to render the changelog, remove consumed fragments from `changes/`, and open a pull request on the `release/v` branch. -4. The release PR is automatically labeled `run-downstream`, which triggers the [downstream test workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) to run Xarray and numcodecs integration tests against the release branch. -5. Review the rendered changelog in `docs/release-notes.md` and verify downstream tests pass before merging. - ## Benchmarks Zarr uses [pytest-benchmark](https://pytest-benchmark.readthedocs.io/en/latest/) for running From 97d781bed6d7e0cd178eb143cf493a1c6c8a5750 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 12 Jun 2026 11:42:06 +0200 Subject: [PATCH 348/468] fix![zarr-metadata]: define JSONValue type, and narrow object annotations to use JSONValue (#4037) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore: define JSONValue type, and narrow object annotations to use JSONValue * fix: apply JSONValue more extensively, and correct dtype data types * Delete packages/zarr-metadata/.claude/hooks/.logs/hook-log.jsonl * Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * fix: export JSONValue * docs: add changelog entry --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- packages/zarr-metadata/changes/4037.misc.md | 1 + .../src/zarr_metadata/__init__.py | 3 ++- .../src/zarr_metadata/_common.py | 19 +++++++++++++++---- .../src/zarr_metadata/v2/array.py | 11 ++++++----- .../src/zarr_metadata/v2/attributes.py | 4 +++- .../src/zarr_metadata/v2/codec.py | 4 +++- .../src/zarr_metadata/v2/group.py | 6 ++++-- .../src/zarr_metadata/v3/array.py | 11 ++++++----- .../src/zarr_metadata/v3/codec/cast_value.py | 3 ++- .../zarr_metadata/v3/codec/scale_offset.py | 6 ++++-- .../src/zarr_metadata/v3/data_type/struct.py | 7 +++++-- .../src/zarr_metadata/v3/group.py | 5 +++-- 12 files changed, 54 insertions(+), 26 deletions(-) create mode 100644 packages/zarr-metadata/changes/4037.misc.md diff --git a/packages/zarr-metadata/changes/4037.misc.md b/packages/zarr-metadata/changes/4037.misc.md new file mode 100644 index 0000000000..fee5c69cca --- /dev/null +++ b/packages/zarr-metadata/changes/4037.misc.md @@ -0,0 +1 @@ +Introduces a new `JSONValue` type that models python objects that serialize directly to JSON. This type is used to annotate the contents of `attributes` and `fill_value` fields, replacing the use of the overly wide `object` type. This is technically a breaking change. \ No newline at end of file diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index dc9bc25c63..7c6461500e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -1,6 +1,6 @@ from importlib.metadata import version -from zarr_metadata._common import NamedConfig +from zarr_metadata._common import JSONValue, NamedConfig from zarr_metadata.v2.array import ( ArrayDimensionSeparatorV2, ArrayMetadataV2, @@ -37,6 +37,7 @@ "GroupMetadataV2Partial", "GroupMetadataV3", "GroupMetadataV3Partial", + "JSONValue", "MetadataFieldV3", "NamedConfig", "ZArrayMetadata", diff --git a/packages/zarr-metadata/src/zarr_metadata/_common.py b/packages/zarr-metadata/src/zarr_metadata/_common.py index 9aa643e6d0..f6064d863f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_common.py +++ b/packages/zarr-metadata/src/zarr_metadata/_common.py @@ -9,7 +9,19 @@ from collections.abc import Mapping from typing import NotRequired -from typing_extensions import TypedDict +from typing_extensions import TypeAliasType, TypedDict + +JSONValue = TypeAliasType( + "JSONValue", + "int | float | bool | None | str | list[JSONValue] | tuple[JSONValue, ...] | Mapping[str, JSONValue]", # type: ignore[reportInvalidTypeForm] +) +"""A recursive type alias for JSON-encodable values. + +Defined via `TypeAliasType` (rather than a plain `TypeAlias`) so the +self-reference is a named recursion point that pydantic can resolve when +building a `TypeAdapter`; a bare recursive `TypeAlias` raises +`PydanticUserError`/`RecursionError` at validation time. +""" class NamedConfig(TypedDict): @@ -17,9 +29,8 @@ class NamedConfig(TypedDict): Externally-tagged union member for a metadata field. The `configuration` mapping holds arbitrary JSON-encodable values; - it is typed as `Mapping[str, object]` because the type system cannot - express or verify JSON-encodability. + it is typed as `Mapping[str, JSONValue]`. """ name: str - configuration: NotRequired[Mapping[str, object]] + configuration: NotRequired[Mapping[str, JSONValue]] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 6673716f6c..999c341dc7 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -5,6 +5,7 @@ from typing_extensions import TypedDict +from zarr_metadata._common import JSONValue from zarr_metadata.v2.codec import CodecMetadataV2 DataTypeMetadataV2 = str | tuple[tuple[str, str] | tuple[str, str, tuple[int, ...]], ...] @@ -61,7 +62,7 @@ class ZArrayMetadata(TypedDict): chunks: tuple[int, ...] dtype: DataTypeMetadataV2 compressor: CodecMetadataV2 | None - fill_value: object + fill_value: JSONValue order: ArrayOrderV2 filters: tuple[CodecMetadataV2, ...] | None dimension_separator: NotRequired[ArrayDimensionSeparatorV2] @@ -87,11 +88,11 @@ class ArrayMetadataV2(TypedDict): chunks: tuple[int, ...] dtype: DataTypeMetadataV2 compressor: CodecMetadataV2 | None - fill_value: object + fill_value: JSONValue order: ArrayOrderV2 filters: tuple[CodecMetadataV2, ...] | None dimension_separator: NotRequired[ArrayDimensionSeparatorV2] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] """User attributes from the sibling `.zattrs` file (not part of `.zarray`). See the class docstring for the rationale behind the merged representation. @@ -128,11 +129,11 @@ class ArrayMetadataV2Partial(TypedDict, total=False): chunks: tuple[int, ...] dtype: DataTypeMetadataV2 compressor: CodecMetadataV2 | None - fill_value: object + fill_value: JSONValue order: ArrayOrderV2 filters: tuple[CodecMetadataV2, ...] | None dimension_separator: NotRequired[ArrayDimensionSeparatorV2] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] """User attributes from the sibling `.zattrs` file (not part of `.zarray`). See the class docstring for the rationale behind the merged representation. diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py index f260537b80..18b8ded9da 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py @@ -5,7 +5,9 @@ from collections.abc import Mapping -ZAttrsMetadata = Mapping[str, object] +from zarr_metadata._common import JSONValue + +ZAttrsMetadata = Mapping[str, JSONValue] """On-disk `.zattrs` file content. A JSON object holding user-defined attributes for a v2 array or group. diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/codec.py b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py index 5b42432e8c..6d194b7e29 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/codec.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py @@ -7,8 +7,10 @@ from typing_extensions import TypedDict +from zarr_metadata._common import JSONValue -class CodecMetadataV2(TypedDict, extra_items=object): # type: ignore[call-arg] + +class CodecMetadataV2(TypedDict, extra_items=JSONValue): # type: ignore[call-arg] """ A numcodecs configuration dict, used as a v2 compressor or filter. diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/group.py b/packages/zarr-metadata/src/zarr_metadata/v2/group.py index fd14960a0b..5f456fe8d3 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/group.py @@ -8,6 +8,8 @@ from typing_extensions import TypedDict +from zarr_metadata._common import JSONValue + class ZGroupMetadata(TypedDict): """ @@ -39,7 +41,7 @@ class GroupMetadataV2(TypedDict): """ zarr_format: Literal[2] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] class GroupMetadataV2Partial(TypedDict, total=False): @@ -69,7 +71,7 @@ class GroupMetadataV2Partial(TypedDict, total=False): """ zarr_format: Literal[2] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] __all__ = [ diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index 30bc991f47..d9cea4aef4 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -5,10 +5,11 @@ from typing_extensions import TypedDict +from zarr_metadata._common import JSONValue from zarr_metadata.v3._common import MetadataFieldV3 -class ExtensionFieldV3(TypedDict, extra_items=object): # type: ignore[call-arg] +class ExtensionFieldV3(TypedDict, extra_items=JSONValue): # type: ignore[call-arg] """ Required shape of any extension field on a v3 metadata document. @@ -55,9 +56,9 @@ class ArrayMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[ shape: tuple[int, ...] chunk_grid: MetadataFieldV3 chunk_key_encoding: MetadataFieldV3 - fill_value: object + fill_value: JSONValue codecs: tuple[MetadataFieldV3, ...] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] storage_transformers: NotRequired[tuple[MetadataFieldV3, ...]] dimension_names: NotRequired[tuple[str | None, ...]] @@ -91,9 +92,9 @@ class ArrayMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV shape: tuple[int, ...] chunk_grid: MetadataFieldV3 chunk_key_encoding: MetadataFieldV3 - fill_value: object + fill_value: JSONValue codecs: tuple[MetadataFieldV3, ...] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] storage_transformers: NotRequired[tuple[MetadataFieldV3, ...]] dimension_names: NotRequired[tuple[str | None, ...]] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py index 17905bf38a..fd6fb2ee4a 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py @@ -8,6 +8,7 @@ from typing_extensions import TypedDict +from zarr_metadata._common import JSONValue from zarr_metadata.v3._common import MetadataFieldV3 CAST_VALUE_CODEC_NAME: Final = "cast_value" @@ -46,7 +47,7 @@ OUT_OF_RANGE_MODE: Final = ("clamp", "wrap") """Tuple of permitted values for the `out_of_range` field of the `cast_value` codec.""" -ScalarMapEntry = tuple[object, object] +ScalarMapEntry = tuple[JSONValue, JSONValue] """A single `[input, output]` mapping in a `scalar_map` direction. Each scalar is JSON-encoded per its data type's fill-value rules (so diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/scale_offset.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/scale_offset.py index 32e824ed67..9701db8497 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/scale_offset.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/scale_offset.py @@ -8,6 +8,8 @@ from typing_extensions import TypedDict +from zarr_metadata._common import JSONValue + SCALE_OFFSET_CODEC_NAME: Final = "scale_offset" """The `name` field value of the `scale_offset` codec.""" @@ -26,8 +28,8 @@ class ScaleOffsetCodecConfiguration(TypedDict): permitted in addition to numbers. """ - offset: NotRequired[object] - scale: NotRequired[object] + offset: NotRequired[JSONValue] + scale: NotRequired[JSONValue] class ScaleOffsetCodecObject(TypedDict): diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py index 284ba8e482..282bcc83d6 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py @@ -9,6 +9,9 @@ from typing_extensions import ReadOnly, TypedDict +from zarr_metadata._common import JSONValue +from zarr_metadata.v3._common import MetadataFieldV3 + STRUCT_DATA_TYPE_NAME: Final = "struct" """The `name` field value of the `struct` data type.""" @@ -30,7 +33,7 @@ class StructField(TypedDict): """ name: ReadOnly[str] - data_type: ReadOnly[object] + data_type: ReadOnly[MetadataFieldV3] class StructConfiguration(TypedDict): @@ -46,7 +49,7 @@ class Struct(TypedDict): configuration: StructConfiguration -StructFillValue = Mapping[str, object] +StructFillValue = Mapping[str, JSONValue] """Permitted JSON shape of the `fill_value` field for `struct`. A JSON object mapping each field name to that field's fill value. Field diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py index e44bf124e3..27186b6059 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -8,6 +8,7 @@ from typing_extensions import TypedDict +from zarr_metadata._common import JSONValue from zarr_metadata.v3.array import ExtensionFieldV3 @@ -22,7 +23,7 @@ class GroupMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[ zarr_format: Literal[3] node_type: Literal["group"] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] class GroupMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV3): # type: ignore[call-arg] @@ -50,7 +51,7 @@ class GroupMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV zarr_format: Literal[3] node_type: Literal["group"] - attributes: NotRequired[Mapping[str, object]] + attributes: NotRequired[Mapping[str, JSONValue]] __all__ = [ From 88ed0acc33e943e7e01629d1c40a8677759eaa85 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 12 Jun 2026 12:23:04 +0200 Subject: [PATCH 349/468] perf: cache lexicographic chunk coords in sharding codec (#4012) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * perf: cache lexicographic chunk coords in sharding codec The subchunk_write_order feature (#3826) regressed sharded write performance: _encode_partial_single rebuilt the full per-shard chunk coordinate grid on every write via `np.array(list(_subchunk_order_iter(..., "lexicographic")))`, and `to_dict_vectorized` rebuilt a tuple key per row with `tuple(coords.ravel())`. For a single-chunk write into a shard with tens of thousands of chunks this roughly doubled write time (~22ms -> ~40ms on test_sharded_morton_write_single_chunk, matching the -44% CodSpeed regression). Add cached `_lexicographic_order` (array) and `_lexicographic_order_keys` (tuples) helpers in indexing.py, mirroring `_morton_order`/`_morton_order_keys`, and pass the cached keys into `to_dict_vectorized` instead of deriving them row-by-row. This restores write throughput to the pre-#3826 baseline while preserving identical chunk ordering (verified equal to np.ndindex across shapes including 0-d and empty). Co-Authored-By: Claude Opus 4.7 (1M context) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * refactor(sharding): derive coords inside to_dict_vectorized Address review feedback: `_ShardReader.to_dict_vectorized` took the lexicographic coordinate array and key tuples as parameters, even though the reader already knows its own `chunks_per_shard` and both structures are `lru_cache`d. Thread nothing in — fetch them inside the method via `_lexicographic_order`/`_lexicographic_order_keys`. Same cache, so no perf change; the call site collapses to `to_dict_vectorized()`. Add a unit test covering the method directly across 0-d, 1-d, and 2-d shard grids: present chunks map to their stored bytes, empty chunks to None, and every lexicographic coordinate appears as a key. Co-Authored-By: Claude Opus 4.8 (1M context) * Update src/zarr/core/indexing.py Co-authored-by: Ilan Gold * refactor(sharding): drop redundant lexicographic_order_iter Address review feedback from @ilan-gold and @chuckwondo on the `lexicographic_order_iter` helper. `lexicographic_order_iter` returned a *lazy* iterator over an *eagerly-built, cached* tuple (`_lexicographic_order_keys`), which chuckwondo rightly flagged as confusing — and its output is byte-for-byte identical to the pre-existing, genuinely-lazy `c_order_iter` (verified across 0-d, empty, and N-d shapes). So the name promised laziness the implementation didn't provide, over a sequence we could already produce. Remove the wrapper and use the cached `_lexicographic_order_keys` tuple directly at the two `dict.fromkeys` call sites and in `_subchunk_order_iter`. This keeps the eager/cached coordinate tuples — which is the actual optimization: `dict.fromkeys` over the cached tuple is ~1.4x faster than over lazy `c_order_iter` at 32^3 (≈900us vs ≈1300us), because the cache amortizes tuple construction across repeated writes to same-shaped shards. Switching to `c_order_iter` would have reintroduced that cost, so it is deliberately not used here. Also drop the now-dead `tuple()` wrap in `morton_order_iter` (its argument is typed `tuple[int, ...]` and every caller passes one), per ilan-gold. Co-Authored-By: Claude Opus 4.8 (1M context) * refactor(indexing): prefer lexicographic_order_iter, soft-deprecate c_order_iter `c_order_iter` names a memory layout ("C order") rather than what the iterator actually yields. Reintroduce `lexicographic_order_iter` as the clearer name for the same row-major coordinate sequence, and make `c_order_iter` a thin alias that delegates to it, with a docstring note steering new code to the preferred name. No runtime warning — these are internal helpers. `lexicographic_order_iter` keeps the eager/cached implementation (iter over the lru_cached `_lexicographic_order_keys` tuple), which is ~1.4x faster than the old lazy `itertools.product` on the `dict.fromkeys` shard-write path and is the optimization this branch exists to deliver. The alias therefore changes `c_order_iter` from lazy to eager/cached; all in-repo callers (_ShardReader.__iter__, _is_total_shard, _subchunk_order_iter, and two tests) are migrated to `lexicographic_order_iter`, so nothing in-tree relies on the old laziness. Output is unchanged: lexicographic_order_iter, the c_order_iter alias, and np.ndindex all agree across 0-d, empty, and N-d shapes. Co-Authored-By: Claude Opus 4.8 (1M context) * refactor(indexing): make lexicographic_order_iter the lazy primitive Per review from @mkitti: invert the relationship between the lazy iterator and the eagerly-collected tuple. `lexicographic_order_iter` is now a genuine lazy generator over the chunk-grid coordinates, and `_lexicographic_order_keys` collects it into a cached tuple — the eager version is "collect the lazy one", not the other way around. Previously lexicographic_order_iter returned iter() over the cached tuple, so any consumer that only needed a prefix still paid to materialize the entire grid. _is_total_shard does exactly that — an early-exit `all(coord in set for coord in ...)` — and on a cold cache for a 32^3 shard whose first coordinate is absent this dropped from ~15.8ms to ~24us (the lazy generator builds one coordinate and bails). The hot path is unchanged: the two dict.fromkeys sites consume the full grid and use the cached `_lexicographic_order_keys` tuple directly (~0.9ms at 32^3), so the regression fix this branch delivers is intact. This also resolves @chuckwondo's point — the iterator is now actually lazy rather than a thin wrapper over eager data. Co-authored-by: Mark Kittisopikul Co-Authored-By: Claude Opus 4.8 (1M context) * refactor(indexing): make morton_order_iter the lazy primitive too Per @mkitti: the morton pair was backwards in the same way the lexicographic pair was. Invert it to match — `morton_order_iter` is now the lazy generator primitive and `_morton_order_keys` collects it into a cached tuple, mirroring `lexicographic_order_iter` / `_lexicographic_order_keys`. No behavioral change for the in-tree consumers (all fully consume the sequence) and the Z-order is identical; this keeps the two coordinate- order families symmetric and gives morton the same lazy/early-exit option lexicographic now has. Co-authored-by: Mark Kittisopikul Co-Authored-By: Claude Opus 4.8 (1M context) * refactor(indexing): expose chunk-order coordinates as cached sequences Replace the morton/lexicographic order iterators (and the c_order_iter alias) with two cached, numpy-backed sequences: `morton_order_coords(shape)` and `lexicographic_order_coords(shape)`, each returning the grid coordinates in that order as a tuple of coordinate tuples. This addresses several points from review: - The earlier "lazy primitive" inversion de-optimized the hot write path: `morton_order_iter` rebuilt every coordinate tuple from the array on each call, and that path runs in `_encode_shard_dict` on every shard write (~16ms/write at 32^3 chunks-per-shard). The coords are a finite set of known length reused in full, so they are an indexable sequence built once and cached, not a lazily-rebuilt generator. (per @mkitti) - `lexicographic_order_iter` was never genuinely lazy — `_lexicographic_order` materializes the whole `np.indices` grid up front — so the early-exit framing was inaccurate. (per @Copilot, @chuckwondo) - Two functions differing only in caching vs laziness was redundant (per @ilan-gold); there is now one sequence per order. `_ShardReader.__iter__` wraps it in `iter()`, the only site that needs an iterator. - `_is_total_shard` no longer iterates the order at all: `all_chunk_coords` is always a subset of the shard grid (guaranteed by `validate`'s shard/chunk divisibility check), so a count check proves totality. A subset assertion documents the invariant. Coordinates are Python int tuples because every consumer uses them as dict keys / set members, which numpy arrays cannot be (unhashable, mutable); the numpy array is kept only for the vectorized index lookup in `to_dict_vectorized`. The per-shape cache holds ~prod(chunks_per_shard) tuples (~0.07% of shard size for multi-GB shards with (64,64,64) chunks), capped at 16 shapes per order. Co-authored-by: Mark Kittisopikul Co-Authored-By: Claude Opus 4.8 (1M context) * test(bench): add warm-cache shard-write benchmark The existing test_sharded_morton_write_single_chunk clears the chunk-order cache before every iteration, so it only measures the cold grid-build cost. That made it blind to a regression where the per-shard coordinate tuples were rebuilt on every write instead of being reused from the cache — the cold benchmark could not distinguish the two (both pay the build each iteration). Add test_sharded_morton_write_single_chunk_warm_cache, which warms the cache once and then times repeated same-shape writes — the amortized regime the cache exists to optimize (many shards of one shape per array). Verified it discriminates: with the cached sequence it is ~4x faster than the cold benchmark, and a rebuild-every-write regression shows up as a ~4x slowdown here while staying invisible to the cold benchmark. Co-Authored-By: Claude Opus 4.8 (1M context) * docs: update changelog for full-shard write coverage The fix caches the per-shard coordinate grid for every shard write, not only partial writes, and the win is amortized across repeated writes to same-shaped shards. Reword the note accordingly; keep it user-facing (the internal indexing helper refactor is not part of the public API). Co-Authored-By: Claude Opus 4.8 (1M context) * perf: build order-coord tuples via .tolist(); document dual representation `morton_order_coords` / `lexicographic_order_coords` built their tuple-of- tuples with a row-by-row `tuple(int(x) for x in row)` comprehension. Using `map(tuple, arr.tolist())` instead does the int conversion in a single C-level call, producing byte-identical native-int tuples ~8-9x faster (~16ms -> ~1.9ms cold build at 32^3). It is a per-shape cached build, so this only speeds the first write to each shard shape, but it is free. Also document in `to_dict_vectorized` why the chunk coordinates are needed in two forms — a numpy array for the vectorized index lookup and hashable tuples for the dict keys — since numpy rows are unhashable and a tuple list can't be used for the vectorized modulo/advanced-indexing. Co-Authored-By: Claude Opus 4.8 (1M context) * perf,test: address code-review findings in the sharding coord cache - Drop the O(n_chunks) assert in _is_total_shard. It built a fresh set(lexicographic_order_coords(...)) on every partial read/write to check an invariant `validate` already guarantees, regressing the very partial-access hot path this PR optimizes (~673us vs ~112ns at 32^3 chunks-per-shard) and vanishing under -O. The invariant is documented in the comment; the count check alone proves totality. - Cache the colexicographic subchunk order. The colex branch of _subchunk_order_iter rebuilt the grid via uncached np.ndindex on every write while its morton/lexicographic siblings hit the cache; add colexicographic_order_coords (cached, derived from lexicographic_order_coords of the reversed shape) and use it. - Fix two benchmark docstrings: the cold benchmark now clears the lexicographic caches too (the write path builds that grid via dict.fromkeys / to_dict_vectorized, so a morton-only clear left it warm and under-reported the cold cost); the warm benchmark docstring now describes what it actually exercises (repeated writes to one shard, which reuse the cache identically to writes across same-shaped shards). Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: Claude Opus 4.7 (1M context) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ilan Gold Co-authored-by: Mark Kittisopikul --- changes/4001.misc.md | 7 ++- src/zarr/codecs/sharding.py | 73 ++++++++++++++--------- src/zarr/core/indexing.py | 70 +++++++++++++++++----- tests/benchmarks/test_indexing.py | 94 +++++++++++++++++++++++++----- tests/test_codecs/test_codecs.py | 14 ++--- tests/test_codecs/test_sharding.py | 40 ++++++++++++- 6 files changed, 229 insertions(+), 69 deletions(-) diff --git a/changes/4001.misc.md b/changes/4001.misc.md index 1f44b551ed..adbba988d9 100644 --- a/changes/4001.misc.md +++ b/changes/4001.misc.md @@ -1 +1,6 @@ -Consolidated the array indexing test suite (`tests/test_indexing.py`): the loop-and-`np.random` based selection tests were rewritten as deterministic, parametrized `Expect`/`ExpectFail` cases on small arrays, error paths were split into their own named tests, and the two divergent `Expect` test-case dataclass pairs were unified onto the canonical one in `tests/conftest.py` (whose `ExpectFail` now has an optional regex `msg` and a `raises()` helper). Test-only change with no effect on the public API. +Restore sharding write performance for shards with many inner chunks. The +`subchunk_write_order` feature inadvertently rebuilt the per-shard chunk +coordinate grid (up to tens of thousands of coordinate tuples) on every shard +write. These coordinates are now computed once per shard shape and cached, so +repeated writes to same-shaped shards reuse them, restoring write throughput to +its previous level. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 657484e9af..442567fe0a 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -46,9 +46,11 @@ BasicIndexer, ChunkProjection, SelectorTuple, - c_order_iter, + _lexicographic_order, + colexicographic_order_coords, get_indexer, - morton_order_iter, + lexicographic_order_coords, + morton_order_coords, ) from zarr.core.metadata.v3 import ( ChunkGridMetadata, @@ -261,31 +263,42 @@ def __len__(self) -> int: return int(self.index.offsets_and_lengths.size / 2) def __iter__(self) -> Iterator[tuple[int, ...]]: - return c_order_iter(self.index.chunks_per_shard) + return iter(lexicographic_order_coords(self.index.chunks_per_shard)) - def to_dict_vectorized( - self, - chunk_coords_array: npt.NDArray[np.integer[Any]], - ) -> dict[tuple[int, ...], Buffer | None]: + def to_dict_vectorized(self) -> dict[tuple[int, ...], Buffer | None]: """Build a dict of chunk coordinates to buffers using vectorized lookup. - Parameters - ---------- - chunk_coords_array : ndarray of shape (n_chunks, n_dims) - Array of chunk coordinates for vectorized index lookup. + The full per-shard chunk coordinate grid (both the array used for the + vectorized index lookup and the plain tuples used as dict keys) is + cached on `chunks_per_shard`, so neither is rebuilt on every call. For a + shard with tens of thousands of chunks this avoids reconstructing that + many tuples on every partial write. Returns ------- dict mapping chunk coordinate tuples to Buffer or None """ + chunks_per_shard = self.index.chunks_per_shard + # The same chunk-grid coordinates are needed in two forms, and neither can + # stand in for the other: + # - `chunk_coords_array`: an (n_chunks, n_dims) numpy array, fed to the + # vectorized index lookup, which does modulo + advanced indexing on it. + # A list of tuples can't be used for that without first being arrayified. + # - `chunk_coords_keys`: the same coordinates as hashable Python tuples, + # used as the result dict's keys. numpy array rows are unhashable + # (mutable), so they can't key a dict. + # Both are cached per shape (see indexing.py), so neither is rebuilt here; + # row i of the array and key i refer to the same chunk. + chunk_coords_array = _lexicographic_order(chunks_per_shard) + chunk_coords_keys = lexicographic_order_coords(chunks_per_shard) starts, ends, valid = self.index.get_chunk_slices_vectorized(chunk_coords_array) result: dict[tuple[int, ...], Buffer | None] = {} - for i, coords in enumerate(chunk_coords_array): + for i, coords in enumerate(chunk_coords_keys): if valid[i]: - result[tuple(coords.ravel())] = self.buf[int(starts[i]) : int(ends[i])] + result[coords] = self.buf[int(starts[i]) : int(ends[i])] else: - result[tuple(coords.ravel())] = None + result[coords] = None return result @@ -533,13 +546,14 @@ async def _decode_partial_single( def _subchunk_order_iter( self, chunks_per_shard: tuple[int, ...], subchunk_write_order: SubchunkWriteOrder ) -> Iterable[tuple[int, ...]]: + subchunk_iter: Iterable[tuple[int, ...]] match subchunk_write_order: case "morton": - subchunk_iter = morton_order_iter(chunks_per_shard) + subchunk_iter = morton_order_coords(chunks_per_shard) case "lexicographic": - subchunk_iter = np.ndindex(chunks_per_shard) + subchunk_iter = lexicographic_order_coords(chunks_per_shard) case "colexicographic": - subchunk_iter = (c[::-1] for c in np.ndindex(chunks_per_shard[::-1])) + subchunk_iter = colexicographic_order_coords(chunks_per_shard) case "unordered": # "unordered" promises no particular layout; today it happens to be # lexicographic, but callers must not rely on that. @@ -565,9 +579,7 @@ async def _encode_single( chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), ) ) - # The key order of this intermediate dict is immaterial; the physical layout is - # decided later by the `subchunk_write_order` loop in `_encode_shard_dict`. - shard_builder = dict.fromkeys(np.ndindex(chunks_per_shard)) + shard_builder = dict.fromkeys(lexicographic_order_coords(chunks_per_shard)) await self.codec_pipeline.write( [ @@ -610,8 +622,7 @@ async def _encode_partial_single( ) if self._is_complete_shard_write(indexer, chunks_per_shard): - # Intermediate key order is immaterial (see `_encode_single`). - shard_dict = dict.fromkeys(np.ndindex(chunks_per_shard)) + shard_dict = dict.fromkeys(lexicographic_order_coords(chunks_per_shard)) else: shard_reader = await self._load_full_shard_maybe( byte_getter=byte_setter, @@ -619,10 +630,10 @@ async def _encode_partial_single( chunks_per_shard=chunks_per_shard, ) shard_reader = shard_reader or _ShardReader.create_empty(chunks_per_shard) - # Use vectorized lookup for better performance - shard_dict = shard_reader.to_dict_vectorized( - np.array(list(np.ndindex(chunks_per_shard))) - ) + # Use vectorized lookup for better performance. The lexicographic + # coordinate array and keys are cached, so neither is rebuilt on + # every write. + shard_dict = shard_reader.to_dict_vectorized() await self.codec_pipeline.write( [ @@ -692,9 +703,13 @@ async def _encode_shard_dict( def _is_total_shard( self, all_chunk_coords: set[tuple[int, ...]], chunks_per_shard: tuple[int, ...] ) -> bool: - return len(all_chunk_coords) == product(chunks_per_shard) and all( - chunk_coords in all_chunk_coords for chunk_coords in c_order_iter(chunks_per_shard) - ) + # `all_chunk_coords` comes from an indexer over this shard's chunk grid, so + # it is always a subset of that grid (`validate` requires the shard shape to + # be divisible by the inner chunk shape, so the indexer cannot produce an + # out-of-grid coordinate). A subset whose size equals the grid's is the + # whole grid, so the count check alone proves totality — no need to build + # and membership-test the full coordinate set on this hot path. + return len(all_chunk_coords) == product(chunks_per_shard) def _is_complete_shard_write( self, diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index cb81164209..d205d49a11 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -1521,19 +1521,19 @@ def decode_morton_vectorized( @lru_cache(maxsize=16) -def _morton_order(chunk_shape: tuple[int, ...]) -> npt.NDArray[np.intp]: - n_total = product(chunk_shape) - n_dims = len(chunk_shape) +def _morton_order(shape: tuple[int, ...]) -> npt.NDArray[np.intp]: + n_total = product(shape) + n_dims = len(shape) if n_total == 0: out = np.empty((0, n_dims), dtype=np.intp) out.flags.writeable = False return out # Ceiling hypercube: smallest power-of-2 hypercube whose Morton codes span - # all valid coordinates in chunk_shape. (c-1).bit_length() gives the number + # all valid coordinates in shape. (c-1).bit_length() gives the number # of bits needed to index c values (0 for singleton dims). n_z = 2**total_bits # is the size of this hypercube. - total_bits = sum((c - 1).bit_length() for c in chunk_shape) + total_bits = sum((c - 1).bit_length() for c in shape) n_z = 1 << total_bits if total_bits > 0 else 1 # Decode all Morton codes in the ceiling hypercube, then filter to valid coords. @@ -1544,8 +1544,8 @@ def _morton_order(chunk_shape: tuple[int, ...]) -> npt.NDArray[np.intp]: # Ceiling strategy: decode all n_z codes vectorized, filter in-bounds. # Works well when the overgeneration ratio n_z/n_total is small (≤4). z_values = np.arange(n_z, dtype=np.intp) - all_coords = decode_morton_vectorized(z_values, chunk_shape) - shape_arr = np.array(chunk_shape, dtype=np.intp) + all_coords = decode_morton_vectorized(z_values, shape) + shape_arr = np.array(shape, dtype=np.intp) valid_mask = np.all(all_coords < shape_arr, axis=1) order = all_coords[valid_mask] else: @@ -1554,11 +1554,11 @@ def _morton_order(chunk_shape: tuple[int, ...]) -> npt.NDArray[np.intp]: # larger overgeneration penalty for near-miss shapes like (33,33,33). # Cost: O(n_total * bits) encode + O(n_total log n_total) sort, # vs O(n_z * bits) = O(8 * n_total * bits) for ceiling. - grids = np.meshgrid(*[np.arange(c, dtype=np.intp) for c in chunk_shape], indexing="ij") + grids = np.meshgrid(*[np.arange(c, dtype=np.intp) for c in shape], indexing="ij") all_coords = np.stack([g.ravel() for g in grids], axis=1) # Encode all coordinates to Morton codes (vectorized). - bits_per_dim = tuple((c - 1).bit_length() for c in chunk_shape) + bits_per_dim = tuple((c - 1).bit_length() for c in shape) max_coord_bits = max(bits_per_dim) z_codes = np.zeros(n_total, dtype=np.intp) output_bit = 0 @@ -1576,16 +1576,56 @@ def _morton_order(chunk_shape: tuple[int, ...]) -> npt.NDArray[np.intp]: @lru_cache(maxsize=16) -def _morton_order_keys(chunk_shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: - return tuple(tuple(int(x) for x in row) for row in _morton_order(chunk_shape)) +def morton_order_coords(shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: + # The grid coordinates in Morton (Z) order, as a cached sequence. The + # coordinate set of a finite grid has a known length and is reused in full on + # every shard write, so it is built once (vectorized, via `_morton_order`) and + # cached per shape rather than recomputed. Indexable and `len`-able; iterate it + # directly where an iterator is needed. + # + # `.tolist()` converts the whole array to native Python ints in one C-level + # call; building the tuples row-by-row with `int(x)` is ~9x slower. + return tuple(map(tuple, _morton_order(shape).tolist())) -def morton_order_iter(chunk_shape: tuple[int, ...]) -> Iterator[tuple[int, ...]]: - return iter(_morton_order_keys(tuple(chunk_shape))) +@lru_cache(maxsize=16) +def _lexicographic_order(shape: tuple[int, ...]) -> npt.NDArray[np.intp]: + # Lexicographic (C-order) coordinates, computed vectorized and cached so that + # the sharding codec's per-shard chunk grid is not rebuilt on every call. + # Equivalent to `np.array(list(np.ndindex(shape)))` but without the + # Python-level iteration over every coordinate. + n_dims = len(shape) + if n_dims == 0: + # A 0-d shard holds a single chunk addressed by the empty coordinate, so + # the coordinate array has one row and zero columns. np.indices(()) cannot + # express this, so build it directly. Matches list(np.ndindex(())) == [()]. + order = np.empty((1, 0), dtype=np.intp) + else: + order = np.indices(shape, dtype=np.intp).reshape(n_dims, -1).T + order.flags.writeable = False + return order -def c_order_iter(chunks_per_shard: tuple[int, ...]) -> Iterator[tuple[int, ...]]: - return itertools.product(*(range(x) for x in chunks_per_shard)) +@lru_cache(maxsize=16) +def lexicographic_order_coords(shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: + # The grid coordinates in lexicographic (row-major / C) order, as a cached + # sequence. The coordinate set of a finite grid has a known length and is + # reused in full on every shard write, so it is built once (vectorized, via + # `_lexicographic_order`) and cached per shape. Indexable and `len`-able; + # iterate it directly where an iterator is needed. + # + # `.tolist()` converts the whole array to native Python ints in one C-level + # call; building the tuples row-by-row with `int(x)` is ~9x slower. + return tuple(map(tuple, _lexicographic_order(shape).tolist())) + + +@lru_cache(maxsize=16) +def colexicographic_order_coords(shape: tuple[int, ...]) -> tuple[tuple[int, ...], ...]: + # The grid coordinates in colexicographic (column-major / F) order, as a cached + # sequence: the first axis varies fastest. Equivalent to reversing each axis, + # taking lexicographic order, and reversing the coordinates back. Cached per + # shape like its siblings so shard writes don't rebuild it. + return tuple(c[::-1] for c in lexicographic_order_coords(shape[::-1])) def get_indexer( diff --git a/tests/benchmarks/test_indexing.py b/tests/benchmarks/test_indexing.py index 385a85b5b5..c9b80f9ff6 100644 --- a/tests/benchmarks/test_indexing.py +++ b/tests/benchmarks/test_indexing.py @@ -74,7 +74,7 @@ def test_sharded_morton_indexing( The Morton order cache is cleared before each iteration to measure the full computation cost. """ - from zarr.core.indexing import _morton_order, _morton_order_keys + from zarr.core.indexing import _morton_order, morton_order_coords # Create array where each shard contains many small chunks # e.g., shards=(32,32,32) with chunks=(2,2,2) means 16x16x16 = 4096 chunks per shard @@ -98,7 +98,7 @@ def test_sharded_morton_indexing( def read_with_cache_clear() -> None: _morton_order.cache_clear() - _morton_order_keys.cache_clear() + morton_order_coords.cache_clear() getitem(data, indexer) benchmark(read_with_cache_clear) @@ -126,7 +126,7 @@ def test_sharded_morton_indexing_large( the Morton order computation a more significant portion of total time. The Morton order cache is cleared before each iteration. """ - from zarr.core.indexing import _morton_order, _morton_order_keys + from zarr.core.indexing import _morton_order, morton_order_coords # 1x1x1 chunks means chunks_per_shard equals shard shape shape = tuple(s * 2 for s in shards) # 2 shards per dimension @@ -149,7 +149,7 @@ def test_sharded_morton_indexing_large( def read_with_cache_clear() -> None: _morton_order.cache_clear() - _morton_order_keys.cache_clear() + morton_order_coords.cache_clear() getitem(data, indexer) benchmark(read_with_cache_clear) @@ -169,7 +169,7 @@ def test_sharded_morton_single_chunk( computing the full Morton order, making the optimization impact clear. The Morton order cache is cleared before each iteration. """ - from zarr.core.indexing import _morton_order, _morton_order_keys + from zarr.core.indexing import _morton_order, morton_order_coords # 1x1x1 chunks means chunks_per_shard equals shard shape shape = tuple(s * 2 for s in shards) # 2 shards per dimension @@ -192,13 +192,13 @@ def test_sharded_morton_single_chunk( def read_with_cache_clear() -> None: _morton_order.cache_clear() - _morton_order_keys.cache_clear() + morton_order_coords.cache_clear() getitem(data, indexer) benchmark(read_with_cache_clear) -# Benchmark for morton_order_iter directly (no I/O) +# Benchmark for morton_order_coords directly (no I/O) morton_iter_shapes = ( (8, 8, 8), # 512 elements (power-of-2) (10, 10, 10), # 1000 elements (non-power-of-2) @@ -211,23 +211,23 @@ def read_with_cache_clear() -> None: @pytest.mark.parametrize("shape", morton_iter_shapes, ids=str) -def test_morton_order_iter( +def test_morton_order( shape: tuple[int, ...], benchmark: BenchmarkFixture, ) -> None: - """Benchmark morton_order_iter directly without I/O. + """Benchmark morton_order_coords directly without I/O. This isolates the Morton order computation to measure the optimization impact without array read/write overhead. The cache is cleared before each iteration. """ - from zarr.core.indexing import _morton_order, _morton_order_keys, morton_order_iter + from zarr.core.indexing import _morton_order, morton_order_coords def compute_morton_order() -> None: _morton_order.cache_clear() - _morton_order_keys.cache_clear() - # Consume the iterator to force computation - list(morton_order_iter(shape)) + morton_order_coords.cache_clear() + # Build the full sequence to force computation + list(morton_order_coords(shape)) benchmark(compute_morton_order) @@ -250,7 +250,12 @@ def test_sharded_morton_write_single_chunk( """ import numpy as np - from zarr.core.indexing import _morton_order, _morton_order_keys + from zarr.core.indexing import ( + _lexicographic_order, + _morton_order, + lexicographic_order_coords, + morton_order_coords, + ) # 1x1x1 chunks means chunks_per_shard equals shard shape shape = tuple(s * 2 for s in shards) # 2 shards per dimension @@ -272,8 +277,67 @@ def test_sharded_morton_write_single_chunk( indexer = (slice(1), slice(1), slice(1)) def write_with_cache_clear() -> None: + # Clear every coordinate cache the write path touches, not just morton: + # the sharded write also builds the lexicographic grid (dict.fromkeys / + # to_dict_vectorized), so a partial clear would leave that path warm and + # under-report the cold build cost. _morton_order.cache_clear() - _morton_order_keys.cache_clear() + morton_order_coords.cache_clear() + _lexicographic_order.cache_clear() + lexicographic_order_coords.cache_clear() data[indexer] = write_data benchmark(write_with_cache_clear) + + +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("shards", large_morton_shards, ids=str) +def test_sharded_morton_write_single_chunk_warm_cache( + store: Store, + shards: tuple[int, ...], + benchmark: BenchmarkFixture, +) -> None: + """Benchmark a single-chunk shard write with the chunk-order cache warm. + + Unlike ``test_sharded_morton_write_single_chunk``, this does NOT clear the + order cache between iterations: it warms the cache once, then repeatedly + writes the same single chunk. This isolates the amortized per-write cost the + cache exists to optimize — the regime where the coordinate grid was already + built (by an earlier write to this shard, or to any same-shaped shard) and is + reused rather than rebuilt. Repeated writes to one shard and writes spread + across many same-shaped shards exercise that cache reuse identically. + + This is the regime the cold benchmark cannot see. A regression that rebuilds + the per-shard coordinate tuples on every write (rather than reusing the + cached sequence) is invisible to the cold benchmark but shows up here. + """ + import numpy as np + + from zarr.core.indexing import _morton_order, morton_order_coords + + shape = tuple(s * 2 for s in shards) # 2 shards per dimension + chunks = (1,) * 3 # 1x1x1 chunks: chunks_per_shard = shards + + data = create_array( + store=store, + shape=shape, + dtype="uint8", + chunks=chunks, + shards=shards, + compressors=None, + filters=None, + fill_value=0, + ) + + write_data = np.ones((1, 1, 1), dtype="uint8") + indexer = (slice(1), slice(1), slice(1)) + + # Warm the cache once up front; the timed writes then hit the warm path. + _morton_order.cache_clear() + morton_order_coords.cache_clear() + data[indexer] = write_data + + def write_warm() -> None: + data[indexer] = write_data + + benchmark(write_warm) diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index 6e3e3f6d28..b88aa6f507 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -18,7 +18,7 @@ TransposeCodec, ) from zarr.core.buffer import default_buffer_prototype -from zarr.core.indexing import BasicSelection, decode_morton, morton_order_iter +from zarr.core.indexing import BasicSelection, decode_morton, morton_order_coords from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.dtype import UInt8 from zarr.errors import ZarrUserWarning @@ -173,8 +173,8 @@ def test_open(store: Store) -> None: def test_morton_exact_order() -> None: """Test exact morton ordering for power-of-2 shapes.""" - assert list(morton_order_iter((2, 2))) == [(0, 0), (1, 0), (0, 1), (1, 1)] - assert list(morton_order_iter((2, 2, 2))) == [ + assert list(morton_order_coords((2, 2))) == [(0, 0), (1, 0), (0, 1), (1, 1)] + assert list(morton_order_coords((2, 2, 2))) == [ (0, 0, 0), (1, 0, 0), (0, 1, 0), @@ -184,7 +184,7 @@ def test_morton_exact_order() -> None: (0, 1, 1), (1, 1, 1), ] - assert list(morton_order_iter((2, 2, 2, 2))) == [ + assert list(morton_order_coords((2, 2, 2, 2))) == [ (0, 0, 0, 0), (1, 0, 0, 0), (0, 1, 0, 0), @@ -223,12 +223,12 @@ def test_morton_exact_order() -> None: ], ) def test_morton_is_permutation(shape: tuple[int, ...]) -> None: - """Test that morton_order_iter produces every valid coordinate exactly once.""" + """Test that morton_order_coords produces every valid coordinate exactly once.""" import itertools from zarr.core.common import product - order = list(morton_order_iter(shape)) + order = list(morton_order_coords(shape)) expected_len = product(shape) # completeness: every valid coordinate is present assert len(order) == expected_len @@ -257,7 +257,7 @@ def test_morton_ordering(shape: tuple[int, ...]) -> None: so the ordering should be exactly decode_morton(0), decode_morton(1), ... """ - order = list(morton_order_iter(shape)) + order = list(morton_order_coords(shape)) for i, coord in enumerate(order): assert coord == decode_morton(i, shape) diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 856d29ef7a..2a2dbc1c0a 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -21,7 +21,7 @@ ) from zarr.codecs.sharding import MAX_UINT_64, SubchunkWriteOrder, _ShardIndex, _ShardReader from zarr.core.buffer import NDArrayLike, default_buffer_prototype -from zarr.core.indexing import c_order_iter +from zarr.core.indexing import lexicographic_order_coords from zarr.storage import MemoryStore, StorePath, ZipStore from ..conftest import ArrayRequest @@ -954,7 +954,7 @@ def test_shard_index_get_chunk_slices_vectorized(chunks_per_shard: tuple[int, .. """get_chunk_slices_vectorized works uniformly across chunk grid ranks, including 0-D.""" index = _ShardIndex.create_empty(chunks_per_shard) # Write the first chunk; leave the rest (if any) empty. - all_coords = list(c_order_iter(chunks_per_shard)) + all_coords = list(lexicographic_order_coords(chunks_per_shard)) index.set_chunk_slice(all_coords[0], slice(10, 14)) coords_array = np.array(all_coords, dtype=np.uint64).reshape( @@ -968,3 +968,39 @@ def test_shard_index_get_chunk_slices_vectorized(chunks_per_shard: tuple[int, .. assert starts[0] == 10 assert ends[0] == 14 np.testing.assert_array_equal(starts[~expected_valid], MAX_UINT_64) + + +@pytest.mark.parametrize("chunks_per_shard", [(), (3,), (2, 3)]) +def test_shard_reader_to_dict_vectorized(chunks_per_shard: tuple[int, ...]) -> None: + """to_dict_vectorized derives its own coords and maps present chunks to buffers, empty to None. + + The reader is given the full per-shard chunk grid implicitly (it reads + ``chunks_per_shard`` off its own index), so the result must contain every + lexicographic coordinate as a key, with the stored bytes for present chunks + and ``None`` for empty ones. + """ + all_coords = list(lexicographic_order_coords(chunks_per_shard)) + # Lay two chunks back-to-back in the buffer; leave the rest (if any) empty. + payload = b"abcdXY" + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice(all_coords[0], slice(0, 4)) + present = {all_coords[0]: payload[0:4]} + if len(all_coords) > 1: + index.set_chunk_slice(all_coords[1], slice(4, 6)) + present[all_coords[1]] = payload[4:6] + + reader = _ShardReader() + reader.index = index + reader.buf = default_buffer_prototype().buffer.from_bytes(payload) + + result = reader.to_dict_vectorized() + + # Every lexicographic coordinate is present as a key, in order. + assert list(result.keys()) == all_coords + for coords in all_coords: + buf = result[coords] + if coords in present: + assert buf is not None + assert buf.to_bytes() == present[coords] + else: + assert buf is None From be62f5af84e2b012e596eb215348333daf9a53c6 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 12 Jun 2026 17:16:38 +0200 Subject: [PATCH 350/468] deprecate more enums (#3968) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * refactor(codecs): extract shared enum-deprecation helpers Pulls _DeprecatedStrEnumMeta and _coerce_enum_input out into a private shared module so bytes.py and sharding.py can reuse the pattern introduced for blosc in #3963. _coerce_enum_input gains a codec_name parameter so the warning text names the actual codec instead of being hard-coded to BloscCodec. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(codecs): use shared enum-deprecation helpers in blosc Removes the local _DeprecatedStrEnumMeta and _coerce_enum_input definitions from blosc.py in favor of the shared versions in zarr.codecs._deprecated_enum. Pure refactor — behavior is covered by the existing tests. Co-Authored-By: Claude Opus 4.7 (1M context) * feat(codecs): deprecate Endian enum Member access on Endian now emits DeprecationWarning and returns the equivalent string. BytesCodec stores endian as a literal string; passing a real enum.Enum instance to __init__ warns. Removes the module-level default_system_endian binding; BytesCodec defaults to sys.byteorder directly. Co-Authored-By: Claude Opus 4.7 (1M context) * fixup(codecs): restore spec form for Endian deprecation Two spec deviations from the previous commit: - Test exercises the metaclass __getattr__ path via getattr(...) per spec, with # noqa: B009 to silence ruff. - Restore the # type: ignore[arg-type] on newbyteorder (documents numpy bug #26473). The transient comparison-overlap mypy error resolves in the next task when NDBuffer.byteorder widens to EndianLiteral. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(buffer): widen NDBuffer.byteorder to EndianLiteral Returns the literal string directly instead of the deprecated Endian enum. The Endian enum is being phased out (see preceding commit). Co-Authored-By: Claude Opus 4.7 (1M context) * chore(codecs): drop now-unused type-ignore in BytesCodec._encode_sync After widening NDBuffer.byteorder to EndianLiteral, the # type: ignore[arg-type] on newbyteorder(self.endian) is flagged as unused-ignore. mypy passes without it, so drop it along with the comment referencing numpy issue #26473. Co-Authored-By: Claude Opus 4.7 (1M context) * feat(codecs): deprecate ShardingCodecIndexLocation enum Member access on ShardingCodecIndexLocation now emits DeprecationWarning and returns the equivalent string. ShardingCodec stores index_location as a literal string; passing a real enum.Enum instance to __init__ warns. Co-Authored-By: Claude Opus 4.7 (1M context) * test: rewrite sharding-test parametrize decorators to literal strings Pre-existing parametrize decorators referencing ShardingCodecIndexLocation.start/.end triggered DeprecationWarning at collection time, which pyproject.toml promotes to an error. Rewrites the decorators and function-signature annotations to use literal strings and IndexLocationLiteral. Restores the original ShardingCodec import path (zarr.codecs, not zarr.codecs.sharding) that the previous commit accidentally consolidated. Also widens ShardsConfigParam.index_location to accept IndexLocationLiteral so that the rewritten test signatures pass mypy cleanly without introducing new type errors. This subsumes part of Task 7 from the implementation plan; the rest of Task 7 (conftest.py, test_info.py) is unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor(core): use IndexLocationLiteral in array module Replaces ShardingCodecIndexLocation references in array.py with the literal-string alias and the _parse_index_location helper. Updates two docstring examples to reflect BytesCodec's new repr after the Endian deprecation. Co-Authored-By: Claude Opus 4.7 (1M context) * test: use literal strings for sharding/endian in conftest + test_info Replaces ShardingCodecIndexLocation in conftest.py with the literal-string alias and the _parse_index_location helper, mirroring Task 5's rewrite of the analogous call site in array.py. Updates two BytesCodec repr expectations in test_info.py to match the new repr after the Endian deprecation. Co-Authored-By: Claude Opus 4.7 (1M context) * chore(changes): add changelog entry for Endian + sharding enum deprecation The 0000 filename is a placeholder; rename to the PR number when the pull request is opened. Co-Authored-By: Claude Opus 4.7 (1M context) * chore(changes): document NDBuffer.byteorder and default_system_endian removals Independent review pointed out that the changelog covered only the enum deprecations themselves and missed two user-visible side effects: NDBuffer.byteorder's return type widening, and the removal of the module-level default_system_endian binding from zarr.codecs.bytes. Co-Authored-By: Claude Opus 4.7 (1M context) * test(codecs): tighten deprecation-warning patterns and cover legacy idiom Three targeted improvements from independent review: - Replace match="enum" / match="ClassName.member" with anchored regex patterns (raw strings, escaped dots, "Passing an enum to " prefix). The previous patterns matched any deprecation warning that happened to include the substring "enum" or the class name with any trailing character. - Add test_*_codec_init_with_deprecated_class_member for both BytesCodec and ShardingCodec. The existing init_with_enum_instance_warns test exercises _coerce_enum_input via a foreign Enum subclass, but the realistic legacy idiom -- Codec(param=DeprecatedClass.member) -- went through the metaclass __getattr__ path with no direct coverage. - Strengthen the JSON-roundtrip tests: assert the wire-shape literal (the index_location field for sharding; the full {name, configuration} dict for bytes) in addition to the round-trip equality check, so a regression in to_dict's representation surfaces directly. Committed with --no-verify because the per-file pre-commit mypy hook produces false-positive unused-ignore / no-any-return errors on these files (see feedback_prek_all_files_for_mypy memory). The repo-wide mypy check via "prek run --all-files" is clean. Co-Authored-By: Claude Opus 4.7 (1M context) * refactor: drop _parse_index_location cross-module imports ShardingCodec.__init__ already validates index_location via _parse_index_location, so the eager parse at the call sites in array.py's init_array and conftest.py's create_array_metadata was duplicating validation. Replace it with a cast at each call site, which is a more honest local statement of "I trust this dict value is well-shaped; the codec will reject it if not." Side benefit: drops the underscore-prefixed cross-module import, which was a small abstraction leak. The dead-feeling `if index_location is None` fallback after the dict branch was unreachable in the dict case after Task 5/7 (because _parse_index_location either returned a literal or raised), and is now folded into the initial-default assignment. Co-Authored-By: Claude Opus 4.7 (1M context) * test(codecs): cover bytes evolve_from_array_spec and init_array dict-shards Two coverage gaps codecov flagged on this PR: - BytesCodec.evolve_from_array_spec's structured-dtype branch with multi-byte fields and missing endian. The branch is the legacy back-compat for zarr v2 implicit-little-endian structured arrays. Adds a test that asserts both the UserWarning and the resulting endian="little". Also adds a companion test for the structured- single-byte-fields branch that clears endian, for symmetry. - init_array's isinstance(shards, dict) branch in the sharding path. Existing sharding tests do pass dict-shaped shards through zarr.create_array, but coverage tooling in some CI environments didn't credit the patch-introduced cast line as exercised. Adds a focused MemoryStore-backed test that runs zarr.create_array with a ShardsConfigParam-shaped dict and asserts the resulting ShardingCodec.index_location matches the requested literal. Committed with --no-verify because the per-file pre-commit mypy hook produces false-positive unused-ignore / no-any-return errors on these files. The repo-wide mypy check via "prek run --all-files" is clean (see feedback_prek_all_files_for_mypy memory). Co-Authored-By: Claude Opus 4.7 (1M context) * refactor: rename IndexLocationLiteral to IndexLocation zarr-metadata uses IndexLocation (no Literal suffix) for the same type alias. Match that name in zarr-python so the two packages stay synchronized. No collision with the deprecated ShardingCodecIndexLocation shim class since the names differ. The corresponding rename for EndianLiteral -> Endian is not done in this branch because Endian is already taken by the deprecated shim class. Co-Authored-By: Claude Opus 4.7 (1M context) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * docs: clarify that _coerce_enum_input only fires for foreign enum instances Co-Authored-By: Claude Fable 5 * docs: rename changelog --------- Signed-off-by: dependabot[bot] Co-authored-by: Claude Opus 4.7 (1M context) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- changes/3968.removal.md | 17 +++ src/zarr/codecs/_deprecated_enum.py | 59 ++++++++ src/zarr/codecs/blosc.py | 44 +----- src/zarr/codecs/bytes.py | 46 ++++--- src/zarr/codecs/sharding.py | 46 ++++--- src/zarr/core/array.py | 16 +-- src/zarr/core/buffer/core.py | 12 +- tests/conftest.py | 8 +- tests/test_codecs/test_bytes.py | 173 +++++++++++++++++++++++ tests/test_codecs/test_sharding.py | 206 +++++++++++++++++++++++----- tests/test_info.py | 4 +- 11 files changed, 499 insertions(+), 132 deletions(-) create mode 100644 changes/3968.removal.md create mode 100644 src/zarr/codecs/_deprecated_enum.py create mode 100644 tests/test_codecs/test_bytes.py diff --git a/changes/3968.removal.md b/changes/3968.removal.md new file mode 100644 index 0000000000..075e4a15a9 --- /dev/null +++ b/changes/3968.removal.md @@ -0,0 +1,17 @@ +The ``Endian`` (``zarr.codecs.bytes.Endian``) and ``ShardingCodecIndexLocation`` +(``zarr.codecs.ShardingCodecIndexLocation``) enums are now deprecated. Pass the +equivalent literal string instead (e.g. ``"little"`` / ``"big"``, ``"start"`` / +``"end"``). The enum classes remain importable but emit ``DeprecationWarning`` +on member access, and will be removed in a future release. ``BytesCodec.endian`` +and ``ShardingCodec.index_location`` are now plain strings rather than enum +members. + +Two follow-on changes from this deprecation: + +- ``NDBuffer.byteorder`` now returns a literal string (``"little"`` or + ``"big"``) rather than an ``Endian`` member. Subclasses overriding this + property should update their return type. +- The module-level binding ``zarr.codecs.bytes.default_system_endian`` was + removed. ``BytesCodec()`` continues to default to ``sys.byteorder``; + external callers that imported ``default_system_endian`` should use + ``sys.byteorder`` directly. diff --git a/src/zarr/codecs/_deprecated_enum.py b/src/zarr/codecs/_deprecated_enum.py new file mode 100644 index 0000000000..5538ae26f6 --- /dev/null +++ b/src/zarr/codecs/_deprecated_enum.py @@ -0,0 +1,59 @@ +"""Helpers for deprecating string-valued enums in favor of literal strings. + +See PR #3963 for context on the deprecation pattern. +""" + +from __future__ import annotations + +import warnings +from enum import Enum + + +class _DeprecatedStrEnumMeta(type): + """ + Metaclass for legacy enum-like classes. Accessing a member name on the + class (e.g. `LegacyShim.foo`) emits a `DeprecationWarning` and returns + the equivalent string. Members are declared by setting a `_members` + class attribute mapping each member name to its string value. + """ + + _members: dict[str, str] + + def __getattr__(cls, name: str) -> str: + members: dict[str, str] = type.__getattribute__(cls, "_members") + if name in members: + warnings.warn( + f"{cls.__name__}.{name} is deprecated; pass the string {members[name]!r} instead.", + DeprecationWarning, + stacklevel=2, + ) + return members[name] + raise AttributeError(name) + + +def _coerce_enum_input(value: object, param_name: str, codec_name: str) -> object: + """ + If `value` is a real `enum.Enum` instance, emit a deprecation warning + naming `codec_name` and return `value.value`. Otherwise return `value` + unchanged. The third argument lets the warning text name the actual + codec (e.g. `BloscCodec`, `BytesCodec`, `ShardingCodec`). + + Note that zarr's own legacy classes (e.g. `ShardingCodecIndexLocation`) + never reach the `Enum` branch here: they no longer inherit from `Enum`, + and member access on them already returns a plain string (with its own + warning) via `_DeprecatedStrEnumMeta`. This branch exists for enum + instances defined *outside* zarr — in particular `str`-mixin enums that + downstream code defined to mirror zarr's old enums, which the old + `parse_enum`-based codepath accepted because they are `str` instances. + Coercing them to `value.value` keeps the stored attribute a plain string + and gives those callers a migration warning. + """ + if isinstance(value, Enum): + warnings.warn( + f"Passing an enum to {codec_name}(..., {param_name}=...) is deprecated; " + "pass the equivalent literal string instead.", + DeprecationWarning, + stacklevel=3, + ) + return value.value + return value diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 8a20282060..087de716fc 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -1,9 +1,7 @@ from __future__ import annotations import asyncio -import warnings from dataclasses import dataclass, field, replace -from enum import Enum from functools import cached_property from typing import TYPE_CHECKING, ClassVar, Final, Literal, NotRequired, TypedDict @@ -12,6 +10,7 @@ from packaging.version import Version from zarr.abc.codec import BytesBytesCodec +from zarr.codecs._deprecated_enum import _coerce_enum_input, _DeprecatedStrEnumMeta from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, NamedRequiredConfig, parse_named_configuration from zarr.core.dtype.common import HasItemSize @@ -59,27 +58,6 @@ class BloscJSON_V3(NamedRequiredConfig[Literal["blosc"], BloscConfigV3]): """ -class _DeprecatedStrEnumMeta(type): - """ - Metaclass for the legacy `BloscShuffle` / `BloscCname` classes. Accessing - a member name (e.g. `BloscShuffle.bitshuffle`) emits a `DeprecationWarning` - and returns the equivalent string. - """ - - _members: dict[str, str] - - def __getattr__(cls, name: str) -> str: - members: dict[str, str] = type.__getattribute__(cls, "_members") - if name in members: - warnings.warn( - f"{cls.__name__}.{name} is deprecated; pass the string {members[name]!r} instead.", - DeprecationWarning, - stacklevel=2, - ) - return members[name] - raise AttributeError(name) - - class BloscShuffle(metaclass=_DeprecatedStrEnumMeta): """ Deprecated. Pass a literal string (`"noshuffle"`, `"shuffle"`, or @@ -149,22 +127,6 @@ def parse_blocksize(data: JSON) -> int: raise TypeError(f"Value should be an int. Got {type(data)} instead.") -def _coerce_enum_input(value: object, param_name: str) -> object: - """ - If `value` is a real `enum.Enum` instance, emit a deprecation warning - and return `value.value`. Otherwise return `value` unchanged. - """ - if isinstance(value, Enum): - warnings.warn( - f"Passing an enum to BloscCodec(..., {param_name}=...) is deprecated; " - "pass the equivalent literal string instead.", - DeprecationWarning, - stacklevel=3, - ) - return value.value - return value - - def _parse_cname(data: object) -> BloscCnameLiteral: if isinstance(data, str) and data in BLOSC_CNAME: return data # type: ignore[return-value] @@ -285,8 +247,8 @@ def __init__( shuffle = "bitshuffle" self._tunable_attrs.update({"shuffle"}) - cname = _coerce_enum_input(cname, "cname") # type: ignore[assignment] - shuffle = _coerce_enum_input(shuffle, "shuffle") # type: ignore[assignment] + cname = _coerce_enum_input(cname, "cname", "BloscCodec") # type: ignore[assignment] + shuffle = _coerce_enum_input(shuffle, "shuffle", "BloscCodec") # type: ignore[assignment] typesize_parsed = parse_typesize(typesize) cname_parsed = _parse_cname(cname) diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index 48f8b57c49..1c67c65e98 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -3,12 +3,12 @@ import sys import warnings from dataclasses import dataclass, replace -from enum import Enum -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, ClassVar, Final, Literal from zarr.abc.codec import ArrayBytesCodec +from zarr.codecs._deprecated_enum import _coerce_enum_input, _DeprecatedStrEnumMeta from zarr.core.buffer import Buffer, NDBuffer -from zarr.core.common import JSON, parse_enum, parse_named_configuration +from zarr.core.common import JSON, parse_named_configuration from zarr.core.dtype.common import HasEndianness from zarr.core.dtype.npy.structured import Struct @@ -18,16 +18,25 @@ from zarr.core.array_spec import ArraySpec -class Endian(Enum): +EndianLiteral = Literal["little", "big"] +"""Byte order of multi-byte numeric data.""" + +ENDIAN: Final = ("little", "big") + + +class Endian(metaclass=_DeprecatedStrEnumMeta): """ - Enum for endian type used by bytes codec. + Deprecated. Pass a literal string (`"little"` or `"big"`) directly to + `BytesCodec` instead. """ - big = "big" - little = "little" + _members: ClassVar[dict[str, str]] = {"little": "little", "big": "big"} -default_system_endian = Endian(sys.byteorder) +def _parse_endian(data: object) -> EndianLiteral: + if isinstance(data, str) and data in ENDIAN: + return data # type: ignore[return-value] + raise ValueError(f"endian must be one of {list(ENDIAN)!r}. Got {data!r}.") @dataclass(frozen=True) @@ -36,10 +45,14 @@ class BytesCodec(ArrayBytesCodec): is_fixed_size = True - endian: Endian | None + endian: EndianLiteral | None - def __init__(self, *, endian: Endian | str | None = default_system_endian) -> None: - endian_parsed = None if endian is None else parse_enum(endian, Endian) + def __init__(self, *, endian: Endian | EndianLiteral | None = sys.byteorder) -> None: + if endian is None: + endian_parsed: EndianLiteral | None = None + else: + coerced = _coerce_enum_input(endian, "endian", "BytesCodec") + endian_parsed = _parse_endian(coerced) object.__setattr__(self, "endian", endian_parsed) @@ -55,7 +68,7 @@ def to_dict(self) -> dict[str, JSON]: if self.endian is None: return {"name": "bytes"} else: - return {"name": "bytes", "configuration": {"endian": self.endian.value}} + return {"name": "bytes", "configuration": {"endian": self.endian}} def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: if isinstance(array_spec.dtype, Struct): @@ -67,7 +80,7 @@ def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: UserWarning, stacklevel=2, ) - return replace(self, endian=Endian.little) + return replace(self, endian="little") else: if self.endian is not None: return replace(self, endian=None) @@ -85,8 +98,7 @@ def _decode_sync( chunk_bytes: Buffer, chunk_spec: ArraySpec, ) -> NDBuffer: - # TODO: remove endianness enum in favor of literal union - endian_str = self.endian.value if self.endian is not None else None + endian_str = self.endian if isinstance(chunk_spec.dtype, HasEndianness): dtype = replace(chunk_spec.dtype, endianness=endian_str).to_native_dtype() # type: ignore[call-arg] else: @@ -121,9 +133,7 @@ def _encode_sync( and self.endian is not None and self.endian != chunk_array.byteorder ): - # type-ignore is a numpy bug - # see https://github.com/numpy/numpy/issues/26473 - new_dtype = chunk_array.dtype.newbyteorder(self.endian.name) # type: ignore[arg-type] + new_dtype = chunk_array.dtype.newbyteorder(self.endian) chunk_array = chunk_array.astype(new_dtype) nd_array = chunk_array.as_ndarray_like() diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 442567fe0a..1fe24719c9 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -2,9 +2,8 @@ from collections.abc import Iterable, Mapping, MutableMapping, Sequence from dataclasses import dataclass, replace -from enum import Enum from functools import lru_cache -from typing import TYPE_CHECKING, Any, Literal, NamedTuple, cast +from typing import TYPE_CHECKING, Any, ClassVar, Final, Literal, NamedTuple, cast import numpy as np import numpy.typing as npt @@ -23,6 +22,7 @@ RangeByteRequest, SuffixByteRequest, ) +from zarr.codecs._deprecated_enum import _coerce_enum_input, _DeprecatedStrEnumMeta from zarr.codecs.bytes import BytesCodec from zarr.codecs.crc32c_ import Crc32cCodec from zarr.core.array_spec import ArrayConfig, ArraySpec @@ -36,7 +36,6 @@ from zarr.core.chunk_grids import ChunkGrid from zarr.core.common import ( ShapeLike, - parse_enum, parse_named_configuration, parse_shapelike, product, @@ -64,7 +63,7 @@ if TYPE_CHECKING: from collections.abc import Iterator - from typing import Final, Self + from typing import Self from zarr.core.common import JSON from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType @@ -74,13 +73,19 @@ ShardMutableMapping = MutableMapping[tuple[int, ...], Buffer | None] -class ShardingCodecIndexLocation(Enum): +IndexLocation = Literal["start", "end"] +"""Position of the shard index within the encoded shard.""" + +INDEX_LOCATION: Final = ("start", "end") + + +class ShardingCodecIndexLocation(metaclass=_DeprecatedStrEnumMeta): """ - Enum for index location used by the sharding codec. + Deprecated. Pass a literal string (`"start"` or `"end"`) directly to + `ShardingCodec` instead. """ - start = "start" - end = "end" + _members: ClassVar[dict[str, str]] = {"start": "start", "end": "end"} SubchunkWriteOrder = Literal["morton", "unordered", "lexicographic", "colexicographic"] @@ -92,8 +97,10 @@ class ShardingCodecIndexLocation(Enum): ) -def parse_index_location(data: object) -> ShardingCodecIndexLocation: - return parse_enum(data, ShardingCodecIndexLocation) +def _parse_index_location(data: object) -> IndexLocation: + if isinstance(data, str) and data in INDEX_LOCATION: + return data # type: ignore[return-value] + raise ValueError(f"index_location must be one of {list(INDEX_LOCATION)!r}. Got {data!r}.") @dataclass(frozen=True) @@ -233,7 +240,7 @@ async def from_bytes( shard_index_size = codec._shard_index_size(chunks_per_shard) obj = cls() obj.buf = buf - if codec.index_location == ShardingCodecIndexLocation.start: + if codec.index_location == "start": shard_index_bytes = obj.buf[:shard_index_size] else: shard_index_bytes = obj.buf[-shard_index_size:] @@ -317,7 +324,7 @@ class ShardingCodec( chunk_shape: tuple[int, ...] codecs: tuple[Codec, ...] index_codecs: tuple[Codec, ...] - index_location: ShardingCodecIndexLocation = ShardingCodecIndexLocation.end + index_location: IndexLocation = "end" subchunk_write_order: SubchunkWriteOrder = "morton" def __init__( @@ -326,13 +333,16 @@ def __init__( chunk_shape: ShapeLike, codecs: Iterable[Codec | dict[str, JSON]] = (BytesCodec(),), index_codecs: Iterable[Codec | dict[str, JSON]] = (BytesCodec(), Crc32cCodec()), - index_location: ShardingCodecIndexLocation | str = ShardingCodecIndexLocation.end, + index_location: ShardingCodecIndexLocation | IndexLocation = "end", subchunk_write_order: SubchunkWriteOrder = "morton", ) -> None: chunk_shape_parsed = parse_shapelike(chunk_shape) codecs_parsed = parse_codecs(codecs) index_codecs_parsed = parse_codecs(index_codecs) - index_location_parsed = parse_index_location(index_location) + index_location_coerced = _coerce_enum_input( + index_location, "index_location", "ShardingCodec" + ) + index_location_parsed = _parse_index_location(index_location_coerced) if subchunk_write_order not in SUBCHUNK_WRITE_ORDER: raise ValueError( f"Unrecognized subchunk write order: {subchunk_write_order}. Only {SUBCHUNK_WRITE_ORDER} are allowed." @@ -364,7 +374,7 @@ def __setstate__(self, state: dict[str, Any]) -> None: object.__setattr__(self, "chunk_shape", parse_shapelike(config["chunk_shape"])) object.__setattr__(self, "codecs", parse_codecs(config["codecs"])) object.__setattr__(self, "index_codecs", parse_codecs(config["index_codecs"])) - object.__setattr__(self, "index_location", parse_index_location(config["index_location"])) + object.__setattr__(self, "index_location", _parse_index_location(config["index_location"])) object.__setattr__(self, "subchunk_write_order", state["subchunk_write_order"]) # Use instance-local lru_cache to avoid memory leaks @@ -388,7 +398,7 @@ def to_dict(self) -> dict[str, JSON]: "chunk_shape": self.chunk_shape, "codecs": tuple(s.to_dict() for s in self.codecs), "index_codecs": tuple(s.to_dict() for s in self.index_codecs), - "index_location": self.index_location.value, + "index_location": self.index_location, }, } @@ -688,7 +698,7 @@ async def _encode_shard_dict( return None index_bytes = await self._encode_shard_index(index) - if self.index_location == ShardingCodecIndexLocation.start: + if self.index_location == "start": empty_chunks_mask = index.offsets_and_lengths[..., 0] == MAX_UINT_64 index.offsets_and_lengths[~empty_chunks_mask, 0] += len(index_bytes) index_bytes = await self._encode_shard_index( @@ -799,7 +809,7 @@ async def _load_shard_index_maybe( self, byte_getter: ByteGetter, chunks_per_shard: tuple[int, ...] ) -> _ShardIndex | None: shard_index_size = self._shard_index_size(chunks_per_shard) - if self.index_location == ShardingCodecIndexLocation.start: + if self.index_location == "start": index_bytes = await byte_getter.get( prototype=numpy_buffer_prototype(), byte_range=RangeByteRequest(0, shard_index_size), diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index d15c70064b..2c2a4622e3 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -153,7 +153,7 @@ from zarr.abc.codec import CodecPipeline from zarr.abc.store import Store - from zarr.codecs.sharding import ShardingCodecIndexLocation + from zarr.codecs.sharding import IndexLocation from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar from zarr.storage import StoreLike from zarr.types import AnyArray, AnyAsyncArray, ArrayV2, ArrayV3, AsyncArrayV2, AsyncArrayV3 @@ -1745,7 +1745,7 @@ def info(self) -> Any: Read-only : False Store type : MemoryStore Filters : () - Serializer : BytesCodec(endian=) + Serializer : BytesCodec(endian='little') Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 480 """ @@ -3921,7 +3921,7 @@ def info(self) -> Any: Read-only : False Store type : MemoryStore Filters : () - Serializer : BytesCodec(endian=) + Serializer : BytesCodec(endian='little') Compressors : (ZstdCodec(level=0, checksum=False),) No. bytes : 40 """ @@ -4006,7 +4006,7 @@ async def _shards_initialized( class ShardsConfigParam(TypedDict): shape: tuple[int, ...] - index_location: ShardingCodecIndexLocation | None + index_location: IndexLocation | None type ShardsLike = tuple[int, ...] | Sequence[Sequence[int]] | ShardsConfigParam | Literal["auto"] @@ -4392,7 +4392,7 @@ async def init_array( if zarr_format is None: zarr_format = _default_zarr_format() - from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation + from zarr.codecs.sharding import ShardingCodec zdtype = parse_dtype(dtype, zarr_format=zarr_format) shape_parsed = parse_shapelike(shape) @@ -4480,11 +4480,9 @@ async def init_array( codecs_out: tuple[Codec, ...] if inner is not None: inner_chunks_flat = as_regular_shape(inner.outer_chunks) - index_location = None + index_location: IndexLocation = "end" if isinstance(shards, dict): - index_location = ShardingCodecIndexLocation(shards.get("index_location", None)) - if index_location is None: - index_location = ShardingCodecIndexLocation.end + index_location = cast("IndexLocation", shards.get("index_location", "end")) sharding_codec = ShardingCodec( chunk_shape=inner_chunks_flat, codecs=sub_codecs, index_location=index_location ) diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index 890c707cd1..497543f88f 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -21,7 +21,7 @@ from collections.abc import Iterable, Sequence from typing import Self - from zarr.codecs.bytes import Endian + from zarr.codecs.bytes import EndianLiteral from zarr.core.common import BytesLike # Everything here is imported into ``zarr.core.buffer`` namespace. @@ -496,15 +496,13 @@ def shape(self) -> tuple[int, ...]: return self._data.shape @property - def byteorder(self) -> Endian: - from zarr.codecs.bytes import Endian - + def byteorder(self) -> EndianLiteral: if self.dtype.byteorder == "<": - return Endian.little + return "little" elif self.dtype.byteorder == ">": - return Endian.big + return "big" else: - return Endian(sys.byteorder) + return sys.byteorder def reshape(self, newshape: tuple[int, ...] | Literal[-1]) -> Self: # numpy accepts a bare -1, but the NDArrayLike protocol only types the diff --git a/tests/conftest.py b/tests/conftest.py index 207fba0a44..031c4a4283 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -17,7 +17,7 @@ import zarr.registry from zarr import AsyncGroup, config from zarr.abc.store import Store -from zarr.codecs.sharding import ShardingCodec, ShardingCodecIndexLocation +from zarr.codecs.sharding import IndexLocation, ShardingCodec from zarr.core.array import ( _parse_chunk_encoding_v2, _parse_chunk_encoding_v3, @@ -414,11 +414,9 @@ def create_array_metadata( codecs_out: tuple[Codec, ...] if inner is not None: inner_chunks_flat = as_regular_shape(inner.outer_chunks) - index_location = None + index_location: IndexLocation = "end" if isinstance(shards, dict): - index_location = ShardingCodecIndexLocation(shards.get("index_location", None)) - if index_location is None: - index_location = ShardingCodecIndexLocation.end + index_location = cast("IndexLocation", shards.get("index_location", "end")) sharding_codec = ShardingCodec( chunk_shape=inner_chunks_flat, codecs=sub_codecs, diff --git a/tests/test_codecs/test_bytes.py b/tests/test_codecs/test_bytes.py new file mode 100644 index 0000000000..25c786a405 --- /dev/null +++ b/tests/test_codecs/test_bytes.py @@ -0,0 +1,173 @@ +"""Tests for `BytesCodec` and the deprecation of the `Endian` enum.""" + +from __future__ import annotations + +import enum +import sys +import warnings +from typing import Any, cast + +import pytest + +from zarr.codecs.bytes import ( + ENDIAN, + BytesCodec, + Endian, + EndianLiteral, +) +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import default_buffer_prototype +from zarr.core.dtype.npy.int import Int8, Int32 +from zarr.core.dtype.npy.structured import Struct + + +@pytest.mark.parametrize("endian", ENDIAN) +def test_bytes_codec_accepts_all_endians(endian: EndianLiteral) -> None: + """ + Every endian value in ENDIAN is accepted by BytesCodec and round-trips + to the same value on the stored attribute. Catches drift between the + EndianLiteral type alias and the runtime ENDIAN tuple. + """ + codec = BytesCodec(endian=endian) + assert codec.endian == endian + + +@pytest.mark.parametrize("endian", ENDIAN) +def test_bytes_codec_json_roundtrip(endian: EndianLiteral) -> None: + """ + BytesCodec.to_dict produces the spec-defined wire shape and the + round-trip through from_dict preserves equality. Asserting the literal + JSON shape catches drift between BytesCodec's runtime representation and + the codec's V3 on-disk form. + """ + codec = BytesCodec(endian=endian) + assert codec.to_dict() == {"name": "bytes", "configuration": {"endian": endian}} + restored = BytesCodec.from_dict(codec.to_dict()) + assert restored == codec + + +@pytest.mark.parametrize( + ("member", "expected"), + [("little", "little"), ("big", "big")], +) +def test_endian_member_access_warns(member: str, expected: str) -> None: + """ + Accessing a member on the deprecated `Endian` class emits a + `DeprecationWarning` and resolves to the equivalent literal string. + """ + with pytest.warns(DeprecationWarning, match=rf"Endian\.{member}"): + value = getattr(Endian, member) + assert value == expected + + +def test_endian_class_imports_silently() -> None: + """ + Importing the deprecated `Endian` class by name must not emit a warning; + only member access does. Guards against `bytes.py` accidentally + triggering its own deprecation warnings at import time. + """ + with warnings.catch_warnings(): + warnings.simplefilter("error") + from zarr.codecs.bytes import Endian as _Endian # noqa: F401 + + +def test_bytes_codec_init_with_enum_instance_warns() -> None: + """ + Passing a foreign `enum.Enum` instance to `BytesCodec.__init__` triggers + the init-level deprecation warning (from `_coerce_enum_input`) and + normalizes the value to the corresponding literal string. Covers the + case where a downstream package defined its own enum-shaped class to + bridge between zarr's old API and its own. + """ + + class LegacyEndian(enum.Enum): + little = "little" + + with pytest.warns(DeprecationWarning, match=r"Passing an enum to BytesCodec"): + codec = BytesCodec(endian=cast(Endian, LegacyEndian.little)) + assert codec.endian == "little" + + +def test_bytes_codec_init_with_deprecated_class_member() -> None: + """ + The realistic legacy-upgrade idiom: `BytesCodec(endian=Endian.little)`. + Member access on `Endian` emits one `DeprecationWarning` (from the + metaclass) and resolves to the bare string, which `BytesCodec` then + accepts without further warning. No second warning from + `_coerce_enum_input` because the metaclass already produced a string. + + The `cast` is necessary because the metaclass `__getattr__` is typed + as returning `str`, which does not statically match the codec's + `EndianLiteral` parameter even though the runtime value does. + """ + with pytest.warns(DeprecationWarning, match=r"Endian\.little"): + codec = BytesCodec(endian=cast(EndianLiteral, Endian.little)) + assert codec.endian == "little" + + +def test_bytes_codec_rejects_unknown_endian() -> None: + """ + `BytesCodec.__init__` raises `ValueError` when given a string outside + `ENDIAN`, and the error message names the offending parameter. + """ + kwargs: dict[str, Any] = {"endian": "north"} + with pytest.raises(ValueError, match="endian must be one of"): + BytesCodec(**kwargs) + + +def test_endian_attribute_error_for_unknown_member() -> None: + """ + Attribute access for a name that is not a known member of the + deprecated `Endian` class falls through to `AttributeError`, matching + the behavior of a regular class. + """ + with pytest.raises(AttributeError): + getattr(Endian, "not_a_member") # noqa: B009 + + +def test_bytes_codec_default_endian_matches_system() -> None: + """ + Constructing `BytesCodec()` with no arguments yields a codec whose + `endian` matches `sys.byteorder`. This replaces the previous + `default_system_endian = Endian(sys.byteorder)` module-level binding. + """ + codec = BytesCodec() + assert codec.endian == sys.byteorder + + +def _make_array_spec(dtype: Any) -> ArraySpec: + """Build a minimal ArraySpec around the given dtype for codec.evolve testing.""" + return ArraySpec( + shape=(1,), + dtype=dtype, + fill_value=0, + config=cast(ArrayConfig, {}), + prototype=default_buffer_prototype(), + ) + + +def test_bytes_codec_evolve_structured_multi_byte_fields_warns_and_defaults() -> None: + """ + BytesCodec(endian=None).evolve_from_array_spec(spec) with a structured dtype + whose fields contain multi-byte members emits a UserWarning about the + missing endian and returns a codec with endian set to "little" for legacy + compatibility. + """ + codec = BytesCodec(endian=None) + dtype = Struct(fields=(("a", Int32()), ("b", Int32()))) + spec = _make_array_spec(dtype) + with pytest.warns(UserWarning, match=r"Missing 'endian' for structured dtype"): + evolved = codec.evolve_from_array_spec(spec) + assert evolved.endian == "little" + + +def test_bytes_codec_evolve_structured_single_byte_fields_clears_endian() -> None: + """ + For a structured dtype whose fields are all single-byte, BytesCodec drops + its endian on evolve (endian is meaningless for single-byte content). + """ + codec = BytesCodec(endian="little") + dtype = Struct(fields=(("a", Int8()), ("b", Int8()))) + spec = _make_array_spec(dtype) + evolved = codec.evolve_from_array_spec(spec) + assert evolved.endian is None diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 2a2dbc1c0a..e62334f5d3 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -1,5 +1,7 @@ +import enum import pickle -from typing import Any, get_args +import warnings +from typing import Any, cast, get_args from unittest.mock import AsyncMock import numpy as np @@ -16,12 +18,20 @@ BytesCodec, Crc32cCodec, ShardingCodec, - ShardingCodecIndexLocation, TransposeCodec, ) -from zarr.codecs.sharding import MAX_UINT_64, SubchunkWriteOrder, _ShardIndex, _ShardReader +from zarr.codecs.sharding import ( + INDEX_LOCATION, + MAX_UINT_64, + IndexLocation, + ShardingCodecIndexLocation, + SubchunkWriteOrder, + _ShardIndex, + _ShardReader, +) from zarr.core.buffer import NDArrayLike, default_buffer_prototype from zarr.core.indexing import lexicographic_order_coords +from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.storage import MemoryStore, StorePath, ZipStore from ..conftest import ArrayRequest @@ -43,7 +53,7 @@ def test_sharding( store: Store, array_fixture: npt.NDArray[Any], - index_location: ShardingCodecIndexLocation, + index_location: IndexLocation, offset: int, ) -> None: """ @@ -81,7 +91,7 @@ def test_sharding( @pytest.mark.parametrize("offset", [0, 10]) def test_sharding_scalar( store: Store, - index_location: ShardingCodecIndexLocation, + index_location: IndexLocation, offset: int, ) -> None: """ @@ -115,7 +125,7 @@ def test_sharding_scalar( indirect=["array_fixture"], ) def test_sharding_partial( - store: Store, array_fixture: npt.NDArray[Any], index_location: ShardingCodecIndexLocation + store: Store, array_fixture: npt.NDArray[Any], index_location: IndexLocation ) -> None: data = array_fixture spath = StorePath(store) @@ -151,7 +161,7 @@ def test_sharding_partial( indirect=["array_fixture"], ) def test_sharding_partial_readwrite( - store: Store, array_fixture: npt.NDArray[Any], index_location: ShardingCodecIndexLocation + store: Store, array_fixture: npt.NDArray[Any], index_location: IndexLocation ) -> None: data = array_fixture spath = StorePath(store) @@ -183,7 +193,7 @@ def test_sharding_partial_readwrite( @pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_partial_read( - store: Store, array_fixture: npt.NDArray[Any], index_location: ShardingCodecIndexLocation + store: Store, array_fixture: npt.NDArray[Any], index_location: IndexLocation ) -> None: data = array_fixture spath = StorePath(store) @@ -206,7 +216,7 @@ def test_sharding_partial_read( @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_multiple_chunks_partial_shard_read( store: Store, - index_location: ShardingCodecIndexLocation, + index_location: IndexLocation, ) -> None: array_shape = (16, 64) shard_shape = (8, 32) @@ -249,7 +259,7 @@ def test_sharding_multiple_chunks_partial_shard_read( @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_duplicate_read_indexes( store: Store, - index_location: ShardingCodecIndexLocation, + index_location: IndexLocation, ) -> None: """ Check that duplicate index reads are handled correctly when @@ -286,7 +296,7 @@ def test_sharding_duplicate_read_indexes( @pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_read_empty_chunks_within_non_empty_shard_write_empty_false( - store: Store, index_location: ShardingCodecIndexLocation + store: Store, index_location: IndexLocation ) -> None: """ Case where @@ -325,7 +335,7 @@ def test_sharding_read_empty_chunks_within_non_empty_shard_write_empty_false( @pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_read_empty_chunks_within_empty_shard_write_empty_false( - store: Store, index_location: ShardingCodecIndexLocation + store: Store, index_location: IndexLocation ) -> None: """ Case where @@ -359,7 +369,7 @@ def test_sharding_read_empty_chunks_within_empty_shard_write_empty_false( @pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_partial_shard_read__index_load_fails( - store: Store, index_location: ShardingCodecIndexLocation + store: Store, index_location: IndexLocation ) -> None: """Test fill value is returned when the call to the store to load the bytes of the shard's chunk index fails.""" array_shape = (16,) @@ -392,7 +402,7 @@ def test_sharding_partial_shard_read__index_load_fails( @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_partial_shard_read__index_chunk_slice_fails( store: Store, - index_location: ShardingCodecIndexLocation, + index_location: IndexLocation, monkeypatch: pytest.MonkeyPatch, ) -> None: """Test fill value is returned when looking up a chunk's byte slice within a shard fails.""" @@ -426,7 +436,7 @@ def test_sharding_partial_shard_read__index_chunk_slice_fails( @pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_partial_shard_read__chunk_load_fails( - store: Store, index_location: ShardingCodecIndexLocation + store: Store, index_location: IndexLocation ) -> None: """Test fill value is returned when the call to the store to load a chunk's bytes fails.""" array_shape = (16,) @@ -475,7 +485,7 @@ async def fail_chunk_reads(key: str, byte_ranges: Any, **kwargs: Any) -> Any: @pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) def test_sharding_partial_overwrite( - store: Store, array_fixture: npt.NDArray[Any], index_location: ShardingCodecIndexLocation + store: Store, array_fixture: npt.NDArray[Any], index_location: IndexLocation ) -> None: data = array_fixture[:10, :10, :10] spath = StorePath(store) @@ -526,8 +536,8 @@ def test_sharding_partial_overwrite( def test_nested_sharding( store: Store, array_fixture: npt.NDArray[Any], - outer_index_location: ShardingCodecIndexLocation, - inner_index_location: ShardingCodecIndexLocation, + outer_index_location: IndexLocation, + inner_index_location: IndexLocation, ) -> None: data = array_fixture spath = StorePath(store) @@ -574,8 +584,8 @@ def test_nested_sharding( def test_nested_sharding_create_array( store: Store, array_fixture: npt.NDArray[Any], - outer_index_location: ShardingCodecIndexLocation, - inner_index_location: ShardingCodecIndexLocation, + outer_index_location: IndexLocation, + inner_index_location: IndexLocation, ) -> None: data = array_fixture spath = StorePath(store) @@ -682,12 +692,8 @@ def test_pickle() -> None: @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -@pytest.mark.parametrize( - "index_location", [ShardingCodecIndexLocation.start, ShardingCodecIndexLocation.end] -) -async def test_sharding_with_empty_inner_chunk( - store: Store, index_location: ShardingCodecIndexLocation -) -> None: +@pytest.mark.parametrize("index_location", ["start", "end"]) +async def test_sharding_with_empty_inner_chunk(store: Store, index_location: IndexLocation) -> None: data = np.arange(0, 16 * 16, dtype="uint32").reshape((16, 16)) fill_value = 1 @@ -709,13 +715,10 @@ async def test_sharding_with_empty_inner_chunk( @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -@pytest.mark.parametrize( - "index_location", - [ShardingCodecIndexLocation.start, ShardingCodecIndexLocation.end], -) +@pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize("chunks_per_shard", [(5, 2), (2, 5), (5, 5)]) async def test_sharding_with_chunks_per_shard( - store: Store, index_location: ShardingCodecIndexLocation, chunks_per_shard: tuple[int] + store: Store, index_location: IndexLocation, chunks_per_shard: tuple[int] ) -> None: chunk_shape = (2, 1) shape = tuple(x * y for x, y in zip(chunks_per_shard, chunk_shape, strict=False)) @@ -884,7 +887,7 @@ async def test_encoded_subchunk_write_order(subchunk_write_order: SubchunkWriteO chunk_shape=chunk_shape, codecs=[BytesCodec()], index_codecs=[BytesCodec(), Crc32cCodec()], - index_location=ShardingCodecIndexLocation.end, + index_location="end", subchunk_write_order=subchunk_write_order, ) @@ -929,6 +932,145 @@ def test_subchunk_write_order_roundtrip( np.testing.assert_array_equal(arr[:], data) +# --- Tests for ShardingCodecIndexLocation deprecation --- + + +@pytest.mark.parametrize("location", INDEX_LOCATION) +def test_sharding_codec_accepts_all_index_locations(location: IndexLocation) -> None: + """ + Every value in INDEX_LOCATION is accepted by ShardingCodec and round-trips + to the same value on the stored attribute. Catches drift between the + IndexLocation type alias and the runtime INDEX_LOCATION tuple. + """ + codec = ShardingCodec(chunk_shape=(1,), index_location=location) + assert codec.index_location == location + + +@pytest.mark.parametrize("location", INDEX_LOCATION) +def test_sharding_codec_json_roundtrip_index_location( + location: IndexLocation, +) -> None: + """ + ShardingCodec.to_dict writes index_location as the bare literal string, + and the round-trip through from_dict preserves equality. Asserting the + on-disk index_location value (not just the round-trip) catches drift + between ShardingCodec's runtime representation and the V3 wire form. + """ + codec = ShardingCodec(chunk_shape=(1,), index_location=location) + serialized = codec.to_dict() + assert serialized["configuration"]["index_location"] == location # type: ignore[index, call-overload] + restored = ShardingCodec.from_dict(serialized) + assert restored == codec + + +@pytest.mark.parametrize( + ("member", "expected"), + [("start", "start"), ("end", "end")], +) +def test_sharding_index_location_member_access_warns(member: str, expected: str) -> None: + """ + Accessing a member on the deprecated ShardingCodecIndexLocation class + emits a DeprecationWarning and resolves to the equivalent literal string. + """ + with pytest.warns(DeprecationWarning, match=rf"ShardingCodecIndexLocation\.{member}"): + value = getattr(ShardingCodecIndexLocation, member) + assert value == expected + + +def test_sharding_index_location_class_imports_silently() -> None: + """ + Importing the deprecated ShardingCodecIndexLocation class by name must not + emit a warning; only member access does. + """ + with warnings.catch_warnings(): + warnings.simplefilter("error") + from zarr.codecs.sharding import ( # noqa: F401 + ShardingCodecIndexLocation as _SCIL, + ) + + +def test_sharding_codec_init_with_enum_instance_warns() -> None: + """ + Passing a foreign enum.Enum instance to ShardingCodec.__init__ triggers + the init-level deprecation warning (from _coerce_enum_input) and + normalizes the value to the corresponding literal string. Covers the + case where a downstream package defined its own enum-shaped class to + bridge between zarr's old API and its own. + """ + + class LegacyIndexLocation(enum.Enum): + end = "end" + + with pytest.warns(DeprecationWarning, match=r"Passing an enum to ShardingCodec"): + codec = ShardingCodec( + chunk_shape=(1,), + index_location=cast(ShardingCodecIndexLocation, LegacyIndexLocation.end), + ) + assert codec.index_location == "end" + + +def test_sharding_codec_init_with_deprecated_class_member() -> None: + """ + The realistic legacy-upgrade idiom: ShardingCodec(index_location=ShardingCodecIndexLocation.end). + Member access on ShardingCodecIndexLocation emits one DeprecationWarning + (from the metaclass) and resolves to the bare string, which ShardingCodec + then accepts without further warning. No second warning from + _coerce_enum_input because the metaclass already produced a string. + + The cast is necessary because the metaclass __getattr__ is typed as + returning str, which does not statically match the codec's + IndexLocation parameter even though the runtime value does. + """ + with pytest.warns(DeprecationWarning, match=r"ShardingCodecIndexLocation\.end"): + codec = ShardingCodec( + chunk_shape=(1,), + index_location=cast(IndexLocation, ShardingCodecIndexLocation.end), + ) + assert codec.index_location == "end" + + +def test_sharding_codec_rejects_unknown_index_location() -> None: + """ + ShardingCodec.__init__ raises ValueError when index_location is outside + INDEX_LOCATION, and the error message names the offending parameter. + """ + kwargs: dict[str, Any] = {"chunk_shape": (1,), "index_location": "middle"} + with pytest.raises(ValueError, match="index_location must be one of"): + ShardingCodec(**kwargs) + + +def test_sharding_index_location_attribute_error_for_unknown_member() -> None: + """ + Attribute access for a name that is not a known member of the deprecated + ShardingCodecIndexLocation class falls through to AttributeError. + """ + with pytest.raises(AttributeError): + getattr(ShardingCodecIndexLocation, "not_a_member") # noqa: B009 + + +@pytest.mark.parametrize("index_location", INDEX_LOCATION) +def test_create_array_with_dict_shards_index_location( + index_location: IndexLocation, +) -> None: + """ + zarr.create_array accepts a `ShardsConfigParam`-shaped dict for `shards` + with an explicit `index_location`, and the resulting sharding codec + stores that value. Covers the `isinstance(shards, dict)` branch in + init_array that the tuple-shaped `shards` form doesn't reach. + """ + arr = zarr.create_array( + store={}, + shape=(8,), + chunks=(2,), + shards={"shape": (4,), "index_location": index_location}, + dtype="uint8", + ) + assert isinstance(arr.metadata, ArrayV3Metadata) # needed for mypy + sharding = arr.metadata.codecs[0] + assert isinstance(sharding, ShardingCodec) + assert sharding.index_location == index_location + + def test_sharding_zero_dimensional() -> None: """Regression test for https://github.com/zarr-developers/zarr-python/issues/3751""" arr = zarr.create_array({}, shape=(), dtype="f4", chunks=(), shards=()) diff --git a/tests/test_info.py b/tests/test_info.py index 28c8803c83..08f2318dc2 100644 --- a/tests/test_info.py +++ b/tests/test_info.py @@ -74,7 +74,7 @@ def test_array_info(zarr_format: ZarrFormat) -> None: Read-only : True Store type : MemoryStore Filters : () - Serializer : BytesCodec(endian=) + Serializer : BytesCodec(endian='little') Compressors : ()""") @@ -117,7 +117,7 @@ def test_array_info_complete( Read-only : True Store type : MemoryStore Filters : () - Serializer : BytesCodec(endian=) + Serializer : BytesCodec(endian='little') Compressors : () No. bytes : {count_bytes} ({count_bytes_formatted}) No. bytes stored : {count_bytes_stored} ({count_bytes_stored_formatted}) From 971d30dfb414318513b5278055f2d7bae5644fd2 Mon Sep 17 00:00:00 2001 From: Zack Koppert Date: Fri, 12 Jun 2026 10:19:40 -0700 Subject: [PATCH 351/468] fix: update OSPO action references to canonical org path (#3856) The OSPO actions have moved from github/ to github-community-projects/. Update workflow references to use the canonical org path. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/issue-metrics.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 510849ef3e..9c29f2eb2a 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -33,7 +33,7 @@ jobs: echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV" - name: Run issue-metrics tool - uses: github/issue-metrics@1e38d5e62363e14db8019ed7d106b9855bdba6cc # v4.2.7 + uses: github-community-projects/issue-metrics@1e38d5e62363e14db8019ed7d106b9855bdba6cc # v4.2.7 env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' From 0bb8ceb0f1b3dcf5e4757821086a7eaf440e4c07 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Jun 2026 18:50:25 +0200 Subject: [PATCH 352/468] chore(deps): bump tornado in the uv group across 1 directory (#4062) Bumps the uv group with 1 update in the / directory: [tornado](https://github.com/tornadoweb/tornado). 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[Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore(deps): pin dev tooling for reproducible CI The hatch test envs and bare `uv run` resolve [dependency-groups] fresh from PyPI and ignore uv.lock, so an unrelated upstream tooling release can break CI without any change on our side (e.g. the pytest 9.1.0 `duplicate parametrization` regression, pytest-dev/pytest#14591). Pin dev *tooling* (pytest & plugins, coverage, hypothesis, mypy, ruff, mkdocs*, towncrier, moto, ...) to exact versions. Leave runtime/ integration deps (fsspec, obstore, s3fs, botocore, numcodecs, universal-pathlib) floating so the `optional` test matrix keeps exercising their latest releases; the `min_deps`/`upstream` envs cover the floor and bleeding edge. Also: - Add a focused `release` dependency group as the single source of truth for the towncrier pin; `docs` includes it. prepare_release.yml now runs `uv run --only-group release towncrier build` instead of an unpinned `pip install towncrier`. - Add a `uv` dependabot ecosystem so the pins and uv.lock get weekly update PRs instead of silently rotting. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- .github/dependabot.yml | 13 +++ .github/workflows/prepare_release.yml | 11 +-- pyproject.toml | 68 +++++++------ uv.lock | 136 +++++++++++++------------- 4 files changed, 127 insertions(+), 101 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index c6ab07e397..87e80ce7e5 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -12,6 +12,19 @@ updates: - "*" cooldown: default-days: 7 + # Keep the pinned dev tooling in pyproject.toml's [dependency-groups] and the + # uv.lock current. Without this the exact pins (e.g. pytest) would never be + # bumped automatically and would silently rot. + - package-ecosystem: "uv" + directory: "/" + schedule: + interval: "weekly" + groups: + python-dependencies: + patterns: + - "*" + cooldown: + default-days: 7 - package-ecosystem: "github-actions" directory: "/" target-branch: "support/v2" diff --git a/.github/workflows/prepare_release.yml b/.github/workflows/prepare_release.yml index 57ae10ff0d..b0f1000529 100644 --- a/.github/workflows/prepare_release.yml +++ b/.github/workflows/prepare_release.yml @@ -42,15 +42,12 @@ jobs: fetch-depth: 0 persist-credentials: false - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 - with: - python-version: '3.12' - - - name: Install towncrier - run: pip install towncrier + - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - name: Build changelog - run: towncrier build --version "$VERSION" --yes + # Use the pinned towncrier from the `release` dependency group (single + # source of truth) rather than an unpinned standalone install. + run: uv run --only-group release towncrier build --version "$VERSION" --yes env: VERSION: ${{ inputs.version }} diff --git a/pyproject.toml b/pyproject.toml index 9f6005f981..08e49e8255 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -83,20 +83,29 @@ Discussions = "https://github.com/zarr-developers/zarr-python/discussions" documentation = "https://zarr.readthedocs.io/" homepage = "https://github.com/zarr-developers/zarr-python" +# Dev *tooling* is pinned to exact versions for reproducible CI: the hatch envs +# (see `tool.hatch.envs.*`) and bare `uv run` resolve these groups fresh from +# PyPI and do NOT consult uv.lock, so an unrelated tooling release can break CI +# without any change on our side (e.g. the pytest 9.1.0 `duplicate +# parametrization` regression). Runtime/integration deps (fsspec, obstore, s3fs, +# botocore, numcodecs, universal-pathlib) are intentionally left floating so the +# `optional` test matrix keeps exercising their latest releases; their floor and +# bleeding edge are covered by the `min_deps` and `upstream` hatch envs. Bump the +# pins deliberately, e.g. via dependabot or `uv lock --upgrade`. [dependency-groups] test = [ - "coverage>=7.10", - "pytest", - "pytest-asyncio", - "pytest-cov", - "pytest-accept", - "numpydoc", - "hypothesis", - "pytest-xdist", - "pytest-benchmark", - "pytest-codspeed", - "tomlkit", - "uv", + "coverage==7.14.0", + "pytest==9.0.3", + "pytest-asyncio==1.3.0", + "pytest-cov==7.1.0", + "pytest-accept==0.2.3", + "numpydoc==1.10.0", + "hypothesis==6.152.7", + "pytest-xdist==3.8.0", + "pytest-benchmark==5.2.3", + "pytest-codspeed==5.0.1", + "tomlkit==0.15.0", + "uv==0.11.15", ] remote-tests = [ {include-group = "test"}, @@ -104,35 +113,38 @@ remote-tests = [ "obstore>=0.5.1", "botocore", "s3fs>=2023.10.0", - "moto[s3,server]", - "requests", + "moto[s3,server]==5.2.1", + "requests==2.34.1", +] +release = [ + "towncrier==25.8.0", ] docs = [ # Doc building - "mkdocs-material[imaging]>=9.6.14", - "mkdocs>=1.6.1,<2", - "mkdocstrings>=0.29.1", - "mkdocstrings-python>=1.16.10", - "mike>=2.1.3", - "mkdocs-jupyter>=0.25.1", - "mkdocs-redirects>=1.2.0", - "markdown-exec[ansi]", - "griffe-inherited-docstrings", - "ruff", + "mkdocs-material[imaging]==9.7.6", + "mkdocs==1.6.1", + "mkdocstrings==1.0.4", + "mkdocstrings-python==2.0.3", + "mike==2.2.0", + "mkdocs-jupyter==0.26.3", + "mkdocs-redirects==1.2.3", + "markdown-exec[ansi]==1.12.1", + "griffe-inherited-docstrings==1.1.3", + "ruff==0.15.12", # Changelog generation - "towncrier", + {include-group = "release"}, # Optional dependencies to run examples "numcodecs[msgpack]", "s3fs>=2023.10.0", - "astroid<4", - "pytest", + "astroid==3.3.11", + "pytest==9.0.3", ] dev = [ {include-group = "test"}, {include-group = "remote-tests"}, {include-group = "docs"}, "universal-pathlib", - "mypy", + "mypy==2.1.0", ] [tool.coverage.report] diff --git a/uv.lock b/uv.lock index 39eebfb270..e4ab5681ac 100644 --- a/uv.lock +++ b/uv.lock @@ -4023,6 +4023,9 @@ docs = [ { name = "s3fs" }, { name = "towncrier" }, ] +release = [ + { name = "towncrier" }, +] remote-tests = [ { name = "botocore" }, { name = "coverage" }, @@ -4077,88 +4080,89 @@ provides-extras = ["cast-value-rs", "cli", "gpu", "optional", "remote"] [package.metadata.requires-dev] dev = [ - { name = "astroid", specifier = "<4" }, + { name = "astroid", specifier = "==3.3.11" }, { name = "botocore" }, - { name = "coverage", specifier = ">=7.10" }, + { name = "coverage", specifier = "==7.14.0" }, { name = "fsspec", specifier = ">=2023.10.0" }, - { name = "griffe-inherited-docstrings" }, - { name = "hypothesis" }, - { name = "markdown-exec", extras = ["ansi"] }, - { name = "mike", specifier = ">=2.1.3" }, - { name = "mkdocs", specifier = ">=1.6.1,<2" }, - { name = "mkdocs-jupyter", specifier = ">=0.25.1" }, - { name = "mkdocs-material", extras = ["imaging"], specifier = ">=9.6.14" }, - { name = "mkdocs-redirects", specifier = ">=1.2.0" }, - { name = "mkdocstrings", specifier = ">=0.29.1" }, - { name = "mkdocstrings-python", specifier = ">=1.16.10" }, - { name = "moto", extras = ["s3", "server"] }, - { name = "mypy" }, + { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, + { name = "hypothesis", specifier = "==6.152.7" }, + { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.1" }, + { name = "mike", specifier = "==2.2.0" }, + { name = "mkdocs", specifier = "==1.6.1" }, + { name = "mkdocs-jupyter", specifier = "==0.26.3" }, + { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.6" }, + { name = "mkdocs-redirects", specifier = "==1.2.3" }, + { name = "mkdocstrings", specifier = "==1.0.4" }, + { name = "mkdocstrings-python", specifier = "==2.0.3" }, + { name = "moto", extras = ["s3", "server"], specifier = "==5.2.1" }, + { name = "mypy", specifier = "==2.1.0" }, { name = "numcodecs", extras = ["msgpack"] }, - { name = "numpydoc" }, + { name = "numpydoc", specifier = "==1.10.0" }, { name = "obstore", specifier = ">=0.5.1" }, - { name = "pytest" }, - { name = "pytest-accept" }, - { name = "pytest-asyncio" }, - { name = "pytest-benchmark" }, - { name = "pytest-codspeed" }, - { name = "pytest-cov" }, - { name = "pytest-xdist" }, - { name = "requests" }, - { name = "ruff" }, + { name = "pytest", specifier = "==9.0.3" }, + { name = "pytest-accept", specifier = "==0.2.3" }, + { name = "pytest-asyncio", specifier = "==1.3.0" }, + { name = "pytest-benchmark", specifier = "==5.2.3" }, + { name = "pytest-codspeed", specifier = "==5.0.1" }, + { name = "pytest-cov", specifier = "==7.1.0" }, + { name = "pytest-xdist", specifier = "==3.8.0" }, + { name = "requests", specifier = "==2.34.1" }, + { name = "ruff", specifier = "==0.15.12" }, { name = "s3fs", specifier = ">=2023.10.0" }, - { name = "tomlkit" }, - { name = "towncrier" }, + { name = "tomlkit", specifier = "==0.15.0" }, + { name = "towncrier", specifier = "==25.8.0" }, { name = "universal-pathlib" }, - { name = "uv" }, + { name = "uv", specifier = "==0.11.15" }, ] docs = [ - { name = "astroid", specifier = "<4" }, - { name = "griffe-inherited-docstrings" }, - { name = "markdown-exec", extras = ["ansi"] }, - { name = "mike", specifier = ">=2.1.3" }, - { name = "mkdocs", specifier = ">=1.6.1,<2" }, - { name = "mkdocs-jupyter", specifier = ">=0.25.1" }, - { name = "mkdocs-material", extras = ["imaging"], specifier = ">=9.6.14" }, - { name = "mkdocs-redirects", specifier = ">=1.2.0" }, - { name = "mkdocstrings", specifier = ">=0.29.1" }, - { name = "mkdocstrings-python", specifier = ">=1.16.10" }, + { name = "astroid", specifier = "==3.3.11" }, + { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, + { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.1" }, + { name = "mike", specifier = "==2.2.0" }, + { name = "mkdocs", specifier = "==1.6.1" }, + { name = "mkdocs-jupyter", specifier = "==0.26.3" }, + { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.6" }, + { name = "mkdocs-redirects", specifier = "==1.2.3" }, + { name = "mkdocstrings", specifier = "==1.0.4" }, + { name = "mkdocstrings-python", specifier = "==2.0.3" }, { name = "numcodecs", extras = ["msgpack"] }, - { name = "pytest" }, - { name = "ruff" }, + { name = "pytest", specifier = "==9.0.3" }, + { name = "ruff", specifier = "==0.15.12" }, { name = "s3fs", specifier = ">=2023.10.0" }, - { name = "towncrier" }, + { name = "towncrier", specifier = "==25.8.0" }, ] +release = [{ name = "towncrier", specifier = "==25.8.0" }] remote-tests = [ { name = "botocore" }, - { name = "coverage", specifier = ">=7.10" }, + { name = "coverage", specifier = "==7.14.0" }, { name = "fsspec", specifier = ">=2023.10.0" }, - { name = "hypothesis" }, - { name = "moto", extras = ["s3", "server"] }, - { name = "numpydoc" }, + { name = "hypothesis", specifier = "==6.152.7" }, + { name = "moto", extras = ["s3", "server"], specifier = "==5.2.1" }, + { name = "numpydoc", specifier = "==1.10.0" }, { name = "obstore", specifier = ">=0.5.1" }, - { name = "pytest" }, - { name = "pytest-accept" }, - { name = "pytest-asyncio" }, - { name = "pytest-benchmark" }, - { name = "pytest-codspeed" }, - { name = "pytest-cov" }, - { name = "pytest-xdist" }, - { name = "requests" }, + { name = "pytest", specifier = "==9.0.3" }, + { name = "pytest-accept", specifier = "==0.2.3" }, + { name = "pytest-asyncio", specifier = "==1.3.0" }, + { name = "pytest-benchmark", specifier = "==5.2.3" }, + { name = "pytest-codspeed", specifier = "==5.0.1" }, + { name = "pytest-cov", specifier = "==7.1.0" }, + { name = "pytest-xdist", specifier = "==3.8.0" }, + { name = "requests", specifier = "==2.34.1" }, { name = "s3fs", specifier = ">=2023.10.0" }, - { name = "tomlkit" }, - { name = "uv" }, + { name = "tomlkit", specifier = "==0.15.0" }, + { name = "uv", specifier = "==0.11.15" }, ] test = [ - { name = "coverage", specifier = ">=7.10" }, - { name = "hypothesis" }, - { name = "numpydoc" }, - { name = "pytest" }, - { name = "pytest-accept" }, - { name = "pytest-asyncio" }, - { name = "pytest-benchmark" }, - { name = "pytest-codspeed" }, - { name = "pytest-cov" }, - { name = "pytest-xdist" }, - { name = "tomlkit" }, - { name = "uv" }, + { name = "coverage", specifier = "==7.14.0" }, + { name = "hypothesis", specifier = "==6.152.7" }, + { name = "numpydoc", specifier = "==1.10.0" }, + { name = "pytest", specifier = "==9.0.3" }, + { name = "pytest-accept", specifier = "==0.2.3" }, + { name = "pytest-asyncio", specifier = "==1.3.0" }, + { name = "pytest-benchmark", specifier = "==5.2.3" }, + { name = "pytest-codspeed", specifier = "==5.0.1" }, + { name = "pytest-cov", specifier = "==7.1.0" }, + { name = "pytest-xdist", specifier = "==3.8.0" }, + { name = "tomlkit", specifier = "==0.15.0" }, + { name = "uv", specifier = "==0.11.15" }, ] From c284b2e974f20abbdb47141c46e72fe3349c22b4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 16 Jun 2026 11:06:24 +0200 Subject: [PATCH 354/468] chore(deps): bump codecov/codecov-action in the actions group (#4071) Bumps the actions group with 1 update: [codecov/codecov-action](https://github.com/codecov/codecov-action). Updates `codecov/codecov-action` from 6.0.1 to 7.0.0 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/e79a6962e0d4c0c17b229090214935d2e33f8354...fb8b3582c8e4def4969c97caa2f19720cb33a72f) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/test.yml | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 27c95762d6..f27307efff 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -80,7 +80,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 + uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: gpu diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 92907f45e1..d15b5b1405 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -97,7 +97,7 @@ jobs: key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} - name: Upload coverage - uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 + uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9b5f98a2d2..51ce958f90 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -83,7 +83,7 @@ jobs: hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage if: ${{ matrix.dependency-set == 'optional' && matrix.os == 'ubuntu-latest' }} - uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 + uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests @@ -130,7 +130,7 @@ jobs: run: | hatch env run --env "$HATCH_ENV" run-coverage - name: Upload coverage - uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1 + uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0 with: token: ${{ secrets.CODECOV_TOKEN }} flags: tests From bad558d52f2c4b2c40e8447d744b9a156394366a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 16 Jun 2026 11:34:43 +0200 Subject: [PATCH 355/468] chore(deps): bump the python-dependencies group with 14 updates (#4072) Bumps the python-dependencies group with 14 updates: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.4.4` | `2.4.6` | | [obstore](https://github.com/geospatial-jeff/pyasyncio-benchmark) | `0.9.4` | `0.10.0` | | [cupy-cuda12x](https://github.com/cupy/cupy) | `14.0.1` | `14.1.1` | | [typer](https://github.com/fastapi/typer) | `0.25.1` | `0.26.7` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.14.0` | `7.14.1` | | [pytest-asyncio](https://github.com/pytest-dev/pytest-asyncio) | `1.3.0` | `1.4.0` | | [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.152.7` | `6.155.2` | | [pytest-codspeed](https://github.com/CodSpeedHQ/pytest-codspeed) | `5.0.1` | `5.0.3` | | [uv](https://github.com/astral-sh/uv) | `0.11.15` | `0.11.19` | | [moto[s3,server]](https://github.com/getmoto/moto) | `5.2.1` | `5.2.2` | | [requests](https://github.com/psf/requests) | `2.34.1` | `2.34.2` | | [mkdocstrings-python](https://github.com/mkdocstrings/python) | `2.0.3` | `2.0.4` | | [ruff](https://github.com/astral-sh/ruff) | `0.15.12` | `0.15.16` | | [astroid](https://github.com/pylint-dev/astroid) | `3.3.11` | `4.1.2` | Updates `numpy` from 2.4.4 to 2.4.6 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.4.4...v2.4.6) Updates `obstore` from 0.9.4 to 0.10.0 - [Commits](https://github.com/geospatial-jeff/pyasyncio-benchmark/commits) Updates `cupy-cuda12x` from 14.0.1 to 14.1.1 - [Release notes](https://github.com/cupy/cupy/releases) - [Commits](https://github.com/cupy/cupy/compare/v14.0.1...v14.1.1) Updates `typer` from 0.25.1 to 0.26.7 - [Release notes](https://github.com/fastapi/typer/releases) - [Changelog](https://github.com/fastapi/typer/blob/master/docs/release-notes.md) - [Commits](https://github.com/fastapi/typer/compare/0.25.1...0.26.7) Updates `coverage` from 7.14.0 to 7.14.1 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](https://github.com/coveragepy/coveragepy/compare/7.14.0...7.14.1) Updates `pytest-asyncio` from 1.3.0 to 1.4.0 - [Release notes](https://github.com/pytest-dev/pytest-asyncio/releases) - [Commits](https://github.com/pytest-dev/pytest-asyncio/compare/v1.3.0...v1.4.0) Updates `hypothesis` from 6.152.7 to 6.155.2 - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.152.7...v6.155.2) Updates `pytest-codspeed` from 5.0.1 to 5.0.3 - [Release notes](https://github.com/CodSpeedHQ/pytest-codspeed/releases) - [Changelog](https://github.com/CodSpeedHQ/pytest-codspeed/blob/master/CHANGELOG.md) - [Commits](https://github.com/CodSpeedHQ/pytest-codspeed/compare/v5.0.1...v5.0.3) Updates `uv` from 0.11.15 to 0.11.19 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.11.15...0.11.19) Updates `moto[s3,server]` from 5.2.1 to 5.2.2 - [Release notes](https://github.com/getmoto/moto/releases) - [Changelog](https://github.com/getmoto/moto/blob/master/CHANGELOG.md) - [Commits](https://github.com/getmoto/moto/compare/5.2.1...5.2.2) Updates `requests` from 2.34.1 to 2.34.2 - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](https://github.com/psf/requests/compare/v2.34.1...v2.34.2) Updates `mkdocstrings-python` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/mkdocstrings/python/releases) - [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md) - [Commits](https://github.com/mkdocstrings/python/compare/2.0.3...2.0.4) Updates `ruff` from 0.15.12 to 0.15.16 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.15.12...0.15.16) Updates `astroid` from 3.3.11 to 4.1.2 - [Release notes](https://github.com/pylint-dev/astroid/releases) - [Changelog](https://github.com/pylint-dev/astroid/blob/main/ChangeLog) - [Commits](https://github.com/pylint-dev/astroid/compare/v3.3.11...v4.1.2) --- updated-dependencies: - dependency-name: numpy dependency-version: 2.4.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: obstore dependency-version: 0.10.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: cupy-cuda12x dependency-version: 14.1.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: typer dependency-version: 0.26.7 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: coverage dependency-version: 7.14.1 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: pytest-asyncio dependency-version: 1.4.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: hypothesis dependency-version: 6.155.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: pytest-codspeed dependency-version: 5.0.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: uv dependency-version: 0.11.19 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: moto[s3,server] dependency-version: 5.2.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: requests dependency-version: 2.34.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: mkdocstrings-python dependency-version: 2.0.4 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.15.16 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: astroid dependency-version: 4.1.2 dependency-type: direct:development update-type: version-update:semver-major dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- pyproject.toml | 20 +- uv.lock | 604 +++++++++++++++++++++++++------------------------ 2 files changed, 313 insertions(+), 311 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 08e49e8255..9b372192e9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -94,18 +94,18 @@ homepage = "https://github.com/zarr-developers/zarr-python" # pins deliberately, e.g. via dependabot or `uv lock --upgrade`. [dependency-groups] test = [ - "coverage==7.14.0", + "coverage==7.14.1", "pytest==9.0.3", - "pytest-asyncio==1.3.0", + "pytest-asyncio==1.4.0", "pytest-cov==7.1.0", "pytest-accept==0.2.3", "numpydoc==1.10.0", - "hypothesis==6.152.7", + "hypothesis==6.155.2", "pytest-xdist==3.8.0", "pytest-benchmark==5.2.3", - "pytest-codspeed==5.0.1", + "pytest-codspeed==5.0.3", "tomlkit==0.15.0", - "uv==0.11.15", + "uv==0.11.19", ] remote-tests = [ {include-group = "test"}, @@ -113,8 +113,8 @@ remote-tests = [ "obstore>=0.5.1", "botocore", "s3fs>=2023.10.0", - "moto[s3,server]==5.2.1", - "requests==2.34.1", + "moto[s3,server]==5.2.2", + "requests==2.34.2", ] release = [ "towncrier==25.8.0", @@ -124,19 +124,19 @@ docs = [ "mkdocs-material[imaging]==9.7.6", "mkdocs==1.6.1", "mkdocstrings==1.0.4", - "mkdocstrings-python==2.0.3", + "mkdocstrings-python==2.0.4", "mike==2.2.0", "mkdocs-jupyter==0.26.3", "mkdocs-redirects==1.2.3", "markdown-exec[ansi]==1.12.1", "griffe-inherited-docstrings==1.1.3", - 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[tornado](https://github.com/tornadoweb/tornado) from 6.5.6 to 6.5.7. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](https://github.com/tornadoweb/tornado/compare/v6.5.6...v6.5.7) --- updated-dependencies: - dependency-name: tornado dependency-version: 6.5.7 dependency-type: indirect ... 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[Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pyca/cryptography/compare/48.0.0...48.0.1) --- updated-dependencies: - dependency-name: cryptography dependency-version: 48.0.1 dependency-type: indirect ... 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[j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: storage byte-range clamp, logging generator, getsize_prefix, zip close, codec order validation - storage/_utils.py: clamp SuffixByteRequest start to max(0, ...) so suffix > len(data) returns all available bytes (B1) - storage/_logging.py: materialise key_ranges into a list before building the log hint string, preventing one-shot generator exhaustion (B2) - abc/store.py: normalise getsize_prefix argument to end with "/" before calling list_prefix, matching delete_dir/is_empty behaviour so sibling keys are not over-counted (B3) - storage/_zip.py: guard ZipStore.close() with an early return when the store was never opened, avoiding AttributeError on missing _lock (B4) - core/codec_pipeline.py: add the missing raise TypeError(msg) in the BytesBytesCodec-after-ArrayArrayCodec branch of codecs_from_list (B5) Add regression tests for all five fixes. Co-Authored-By: Claude Fable 5 * test: strengthen property/stateful tests to catch the five bugfixes Augment the existing property-based test infrastructure (and convert two example-based regression tests to property tests) so that each of the five bugs fixed in this PR is caught by a property/stateful test, verified red-green against the pre-fix source: - B1 (suffix clamp): broaden the `key_ranges` strategy to emit SuffixByteRequest / OffsetByteRequest / None with bounds that can exceed the value length, and give the stateful `get_partial_values` rule an independent oracle for every ByteRequest variant. - B2 (generator exhaustion): the shared `StoreTests.test_get_partial_values` now passes `key_ranges` as a one-shot generator and asserts one result per request, so a store/wrapper that exhausts the iterable early is caught (previously masked because the expected loop was driven by the observed count). The stateful rule likewise passes a generator. - B3 (getsize_prefix sibling over-counting): add a `getsize_prefix` rule to the store state machine that asserts only keys under `node/` are counted. - B4 (ZipStore.close before open): replace the two example-based regression tests with a stateful lifecycle machine asserting `close()` never raises, regardless of open/IO history. - B5 (missing raise in codec order validation): replace the single example with a property test over random {AA,AB,BB} codec orderings whose expected outcome (TypeError / ValueError / ok) is modelled independently. Co-Authored-By: Claude Opus 4.8 (1M context) * test: consolidate the five bugfix regressions into property/shared tests Make each of the five bugs fixed in this PR catchable by a property/stateful or shared-harness test (verified red-green against the pre-fix source), and remove the per-store special-case tests whose coverage is now subsumed: - B1 (suffix clamp): broaden the `key_ranges` strategy to emit SuffixByteRequest / OffsetByteRequest / None with bounds that can exceed the value length, and give the stateful `get_partial_values` rule an independent oracle for every ByteRequest variant. The pure-function unit test `TestNormalizeByteRangeIndex` is kept as a fast deterministic guard. - B2 (generator exhaustion): the shared `StoreTests.test_get_partial_values` now passes `key_ranges` as a one-shot generator and asserts one result per request, so any store/wrapper that exhausts the iterable early is caught across all stores. The logging-only regression test is removed as redundant. - B3 (getsize_prefix sibling over-counting): the shared `StoreTests.test_getsize_prefix` now includes a sibling key ("cc/0") that must be excluded, covering every store deterministically. Add a matching `getsize_prefix` rule to the store state machine. The memory-only regression test is removed as redundant. - B4 (ZipStore.close before open): replace the two example-based regression tests with a stateful lifecycle machine asserting `close()` never raises, regardless of open/IO history. - B5 (missing raise in codec order validation): replace the single example with a property test over random {AA,AB,BB} codec orderings whose expected outcome (TypeError / ValueError / ok) is modelled independently. Co-Authored-By: Claude Opus 4.8 (1M context) * fix(fsspec): make get_partial_values robust to one-shot key_ranges FsspecStore.get_partial_values guarded its body with a bare `if key_ranges:` before materialising the argument. Because `key_ranges` is typed as a generic Iterable, a one-shot generator is always truthy even when empty, so the `else: return []` fast path was unreachable for generator inputs (it happened to be harmless only because fsspec's _cat_ranges returns [] for empty input). Materialise `key_ranges` into a list first, then check `if not key_ranges`, matching the iterable contract for any Iterable (list or generator). Also enable mypy's `truthy-iterable` error code, which flags exactly this class of bug (truthiness test on a non-Collection Iterable). There are no existing violations in src/zarr or tests, so this is a zero-cost guard against recurrence. Co-Authored-By: Claude Opus 4.8 (1M context) * docs: add changelog fragment for the storage and codec bugfixes Co-Authored-By: Claude Opus 4.8 (1M context) * docs: clarify SuffixByteRequest changelog entry The pre-fix MemoryStore behavior returned incorrect data (a wrong slice via a negative start index), not merely fewer bytes; note the HTTP suffix-range semantics that define the correct behavior. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 --- changes/4074.bugfix.md | 7 +++ pyproject.toml | 2 +- src/zarr/abc/store.py | 2 + src/zarr/core/codec_pipeline.py | 1 + src/zarr/storage/_fsspec.py | 47 ++++++++++---------- src/zarr/storage/_logging.py | 1 + src/zarr/storage/_utils.py | 2 +- src/zarr/storage/_zip.py | 2 + src/zarr/testing/stateful.py | 53 ++++++++++++++++++++--- src/zarr/testing/store.py | 23 +++++++--- src/zarr/testing/strategies.py | 31 +++++++++---- tests/test_codec_pipeline.py | 77 ++++++++++++++++++++++++++++++++- tests/test_store/test_utils.py | 33 +++++++++++++- tests/test_store/test_zip.py | 72 ++++++++++++++++++++++++++++++ 14 files changed, 305 insertions(+), 48 deletions(-) create mode 100644 changes/4074.bugfix.md diff --git a/changes/4074.bugfix.md b/changes/4074.bugfix.md new file mode 100644 index 0000000000..d55a52b887 --- /dev/null +++ b/changes/4074.bugfix.md @@ -0,0 +1,7 @@ +Fixed several storage and codec bugs: + +- Reading a value with a `SuffixByteRequest` larger than the value now correctly returns the whole value (matching HTTP `bytes=-N` suffix-range semantics), instead of silently returning incorrect data for `MemoryStore`. +- `LoggingStore.get_partial_values` and `FsspecStore.get_partial_values` no longer return empty results when `key_ranges` is passed as a one-shot iterable (e.g. a generator). +- `Store.getsize_prefix` no longer over-counts sibling keys that merely share a string prefix (e.g. `getsize_prefix("foo")` no longer includes keys under `foobar/`). +- `ZipStore.close()` no longer raises `AttributeError` when the store was created but never opened (including when used as a context manager without any I/O). +- `codecs_from_list` now raises a descriptive `TypeError` when a `BytesBytesCodec` immediately follows an `ArrayArrayCodec`, instead of a misleading "Required ArrayBytesCodec was not found" `ValueError`. diff --git a/pyproject.toml b/pyproject.toml index 9b372192e9..6f6c7265a5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -393,7 +393,7 @@ show_error_code_links = true show_error_context = true strict = true warn_unreachable = true -enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] +enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool", "truthy-iterable"] [[tool.mypy.overrides]] module = [ diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 304d0cddb5..7c187594df 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -536,6 +536,8 @@ async def getsize_prefix(self, prefix: str) -> int: from zarr.core.common import concurrent_map from zarr.core.config import config + if prefix != "" and not prefix.endswith("/"): + prefix += "/" keys = [(x,) async for x in self.list_prefix(prefix)] limit = config.get("async.concurrency") sizes = await concurrent_map(keys, self.getsize, limit=limit) diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 5c26681d6b..032703fc03 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -679,6 +679,7 @@ def codecs_from_list( "must be preceded by either another BytesBytesCodec, or an ArrayBytesCodec. " f"Got {type(prev_codec)} instead." ) + raise TypeError(msg) bytes_bytes += (cur_codec,) else: raise TypeError diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 29201a6fee..89d788af1a 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -424,30 +424,31 @@ async def get_partial_values( key_ranges: Iterable[tuple[str, ByteRequest | None]], ) -> list[Buffer | None]: # docstring inherited - if key_ranges: - # _cat_ranges expects a list of paths, start, and end ranges, so we need to reformat each ByteRequest. - key_ranges = list(key_ranges) - paths: list[str] = [] - starts: list[int | None] = [] - stops: list[int | None] = [] - for key, byte_range in key_ranges: - paths.append(_dereference_path(self.path, key)) - if byte_range is None: - starts.append(None) - stops.append(None) - elif isinstance(byte_range, RangeByteRequest): - starts.append(byte_range.start) - stops.append(byte_range.end) - elif isinstance(byte_range, OffsetByteRequest): - starts.append(byte_range.offset) - stops.append(None) - elif isinstance(byte_range, SuffixByteRequest): - starts.append(-byte_range.suffix) - stops.append(None) - else: - raise ValueError(f"Unexpected byte_range, got {byte_range}.") - else: + # Materialise first: key_ranges may be a one-shot iterable, so a bare + # truthiness check (e.g. `if key_ranges`) would be unreliable for an + # empty generator. _cat_ranges also expects lists of paths/starts/stops. + key_ranges = list(key_ranges) + if not key_ranges: return [] + paths: list[str] = [] + starts: list[int | None] = [] + stops: list[int | None] = [] + for key, byte_range in key_ranges: + paths.append(_dereference_path(self.path, key)) + if byte_range is None: + starts.append(None) + stops.append(None) + elif isinstance(byte_range, RangeByteRequest): + starts.append(byte_range.start) + stops.append(byte_range.end) + elif isinstance(byte_range, OffsetByteRequest): + starts.append(byte_range.offset) + stops.append(None) + elif isinstance(byte_range, SuffixByteRequest): + starts.append(-byte_range.suffix) + stops.append(None) + else: + raise ValueError(f"Unexpected byte_range, got {byte_range}.") # TODO: expectations for exceptions or missing keys? res = await self.fs._cat_ranges(paths, starts, stops, on_error="return") # the following is an s3-specific condition we probably don't want to leak diff --git a/src/zarr/storage/_logging.py b/src/zarr/storage/_logging.py index 5de300c144..c6f58ccd61 100644 --- a/src/zarr/storage/_logging.py +++ b/src/zarr/storage/_logging.py @@ -179,6 +179,7 @@ async def get_partial_values( key_ranges: Iterable[tuple[str, ByteRequest | None]], ) -> list[Buffer | None]: # docstring inherited + key_ranges = list(key_ranges) keys = ",".join([k[0] for k in key_ranges]) with self.log(keys): return await self._store.get_partial_values(prototype=prototype, key_ranges=key_ranges) diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index 1f8e9b0a29..b100f862cf 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -153,7 +153,7 @@ def _normalize_byte_range_index(data: Buffer, byte_range: ByteRequest | None) -> start = byte_range.offset stop = len(data) + 1 elif isinstance(byte_range, SuffixByteRequest): - start = len(data) - byte_range.suffix + start = max(0, len(data) - byte_range.suffix) stop = len(data) + 1 else: raise ValueError(f"Unexpected byte_range, got {byte_range}.") diff --git a/src/zarr/storage/_zip.py b/src/zarr/storage/_zip.py index 897797e999..430b0c3e2a 100644 --- a/src/zarr/storage/_zip.py +++ b/src/zarr/storage/_zip.py @@ -120,6 +120,8 @@ def __setstate__(self, state: dict[str, Any]) -> None: def close(self) -> None: # docstring inherited + if not self._is_open: + return super().close() with self._lock: self._zf.close() diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index d6c43f4ecc..9817ebd618 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -1,6 +1,6 @@ import builtins import functools -from collections.abc import Callable +from collections.abc import Callable, Iterable from typing import Any, cast import hypothesis.extra.numpy as npst @@ -18,7 +18,12 @@ import zarr from zarr import Array -from zarr.abc.store import Store +from zarr.abc.store import ( + OffsetByteRequest, + RangeByteRequest, + Store, + SuffixByteRequest, +) from zarr.codecs.bytes import BytesCodec from zarr.core.buffer import Buffer, BufferPrototype, cpu, default_buffer_prototype from zarr.core.sync import SyncMixin @@ -460,7 +465,7 @@ def get(self, key: str, prototype: BufferPrototype) -> Buffer | None: return self._sync(self.store.get(key, prototype=prototype)) def get_partial_values( - self, key_ranges: builtins.list[Any], prototype: BufferPrototype + self, key_ranges: Iterable[Any], prototype: BufferPrototype ) -> builtins.list[Buffer | None]: return self._sync(self.store.get_partial_values(prototype=prototype, key_ranges=key_ranges)) @@ -476,6 +481,9 @@ def clear(self) -> None: def exists(self, key: str) -> bool: return self._sync(self.store.exists(key)) + def getsize_prefix(self, prefix: str) -> int: + return self._sync(self.store.getsize_prefix(prefix)) + def list_dir(self, prefix: str) -> None: raise NotImplementedError @@ -555,7 +563,9 @@ def get_partial_values(self, data: DataObject) -> None: key_ranges(keys=st.sampled_from(sorted(self.model.keys())), max_size=MAX_BINARY_SIZE) ) note(f"(get partial) {key_range=}") - obs_maybe = self.store.get_partial_values(key_range, self.prototype) + # Pass a one-shot generator rather than a list: stores (and wrappers such + # as LoggingStore) must not exhaust the iterable before using it. + obs_maybe = self.store.get_partial_values((kr for kr in key_range), self.prototype) observed = [] for obs in obs_maybe: @@ -565,9 +575,23 @@ def get_partial_values(self, data: DataObject) -> None: model_vals_ls = [] for key, byte_range in key_range: - start = byte_range.start - stop = byte_range.end - model_vals_ls.append(self.model[key][start:stop]) + # Independently model each ByteRequest variant (do NOT reuse the + # store's _normalize_byte_range_index helper, so this stays an + # independent oracle). Bounds may exceed the value length. + value = self.model[key] + n = len(value) + if byte_range is None: + expected = value[:] + elif isinstance(byte_range, RangeByteRequest): + expected = value[byte_range.start : byte_range.end] + elif isinstance(byte_range, OffsetByteRequest): + expected = value[byte_range.offset :] + elif isinstance(byte_range, SuffixByteRequest): + # "last suffix bytes"; suffix > n means the whole value. + expected = value[max(0, n - byte_range.suffix) :] + else: + raise AssertionError(f"unexpected byte_range {byte_range!r}") + model_vals_ls.append(expected) assert all( obs == exp.to_bytes() for obs, exp in zip(observed, model_vals_ls, strict=True) @@ -612,6 +636,21 @@ def exists(self, key: str) -> None: assert self.store.exists(key) == (key in self.model) + @precondition(lambda self: len(self.model.keys()) > 0) + @rule(data=st.data()) + def getsize_prefix(self, data: DataObject) -> None: + # Measure the size under the first path segment of some existing key. + # getsize_prefix(node) must count only keys under the directory "node/", + # not sibling keys that merely share the string prefix (e.g. measuring + # "a" must not include a sibling key "ab/..."). + key = data.draw(st.sampled_from(sorted(self.model.keys()))) + node = key.split("/")[0] + note(f"(getsize_prefix) {node=}") + + observed = self.store.getsize_prefix(node) + expected = sum(len(value) for k, value in self.model.items() if k.startswith(node + "/")) + assert observed == expected, (observed, expected, node) + @invariant() def check_paths_equal(self) -> None: note("Checking that paths are equal") diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index 81024c85c8..11ceeee83a 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -299,10 +299,16 @@ async def test_getsize(self, store: S, key: str, data: bytes) -> None: async def test_getsize_prefix(self, store: S) -> None: """ Test the result of store.getsize_prefix(). + + Includes a sibling key ("cc/0") that shares the string prefix "c" but + belongs to a different directory: getsize_prefix("c") must not count it, + i.e. the prefix is matched as a directory ("c/...") not a raw substring. """ data_buf = self.buffer_cls.from_bytes(b"\x01\x02\x03\x04") keys = ["c/0/0", "c/0/1", "c/1/0", "c/1/1"] - keys_values = [(k, data_buf) for k in keys] + # Sibling directory sharing the "c" string prefix; must be excluded. + sibling_keys = ["cc/0"] + keys_values = [(k, data_buf) for k in keys + sibling_keys] await store._set_many(keys_values) expected = len(data_buf) * len(keys) observed = await store.getsize_prefix("c") @@ -370,11 +376,19 @@ async def test_get_partial_values( for key, _ in key_ranges: await self.set(store, key, self.buffer_cls.from_bytes(bytes(key, encoding="utf-8"))) - # read back just part of it + # read back just part of it. Pass key_ranges as a one-shot generator + # (a valid Iterable per the method signature) to ensure stores and + # wrappers do not exhaust the iterable before handing it to the backend. observed_maybe = await store.get_partial_values( - prototype=default_buffer_prototype(), key_ranges=key_ranges + prototype=default_buffer_prototype(), + key_ranges=(kr for kr in key_ranges), ) + # One result must be returned per requested key range. Checking this + # explicitly guards against a store/wrapper exhausting the key_ranges + # iterable early and silently returning fewer (or no) results. + assert len(observed_maybe) == len(key_ranges) + observed: list[Buffer] = [] expected: list[Buffer] = [] @@ -382,8 +396,7 @@ async def test_get_partial_values( assert obs is not None observed.append(obs) - for idx in range(len(observed)): - key, byte_range = key_ranges[idx] + for key, byte_range in key_ranges: result = await store.get( key, prototype=default_buffer_prototype(), byte_range=byte_range ) diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 7d6556a359..0ef1ba99bb 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -11,7 +11,13 @@ from hypothesis.strategies import SearchStrategy import zarr -from zarr.abc.store import RangeByteRequest, Store +from zarr.abc.store import ( + ByteRequest, + OffsetByteRequest, + RangeByteRequest, + Store, + SuffixByteRequest, +) from zarr.codecs.bytes import BytesCodec from zarr.codecs.crc32c_ import Crc32cCodec from zarr.codecs.sharding import SUBCHUNK_WRITE_ORDER, ShardingCodec, SubchunkWriteOrder @@ -654,22 +660,29 @@ def predicate(value: tuple[Any, ...]) -> bool: def key_ranges( keys: SearchStrategy[str] = node_names, max_size: int = sys.maxsize -) -> SearchStrategy[list[tuple[str, RangeByteRequest]]]: +) -> SearchStrategy[list[tuple[str, ByteRequest | None]]]: """ Function to generate key_ranges strategy for get_partial_values() returns list strategy w/ form:: - [(key, (range_start, range_end)), - (key, (range_start, range_end)),...] + [(key, byte_request), + (key, byte_request),...] + + where ``byte_request`` is ``None`` or any of the concrete ``ByteRequest`` + subtypes. The bounds are drawn independently of each value's length, so the + offsets/suffixes routinely exceed the data and exercise the clamping logic + in ``_normalize_byte_range_index``. """ - def make_request(start: int, length: int) -> RangeByteRequest: + def make_range(start: int, length: int) -> RangeByteRequest: return RangeByteRequest(start, end=min(start + length, max_size)) - byte_ranges = st.builds( - make_request, - start=st.integers(min_value=0, max_value=max_size), - length=st.integers(min_value=0, max_value=max_size), + bound = st.integers(min_value=0, max_value=max_size) + byte_ranges: SearchStrategy[ByteRequest | None] = st.one_of( + st.none(), + st.builds(make_range, start=bound, length=bound), + st.builds(OffsetByteRequest, offset=bound), + st.builds(SuffixByteRequest, suffix=bound), ) key_tuple = st.tuples(keys, byte_ranges) return st.lists(key_tuple, min_size=1, max_size=10) diff --git a/tests/test_codec_pipeline.py b/tests/test_codec_pipeline.py index fa41c2867b..4d596164db 100644 --- a/tests/test_codec_pipeline.py +++ b/tests/test_codec_pipeline.py @@ -1,15 +1,28 @@ from __future__ import annotations +from typing import TYPE_CHECKING + import numpy as np import pytest +pytest.importorskip("hypothesis") + +import hypothesis.strategies as st +from hypothesis import given + import zarr -from zarr.codecs import BytesCodec, CastValue +from zarr.codecs import BytesCodec, CastValue, GzipCodec, TransposeCodec from zarr.core.array import _get_chunk_spec from zarr.core.buffer.core import default_buffer_prototype +from zarr.core.codec_pipeline import codecs_from_list from zarr.core.indexing import BasicIndexer from zarr.storage import MemoryStore +if TYPE_CHECKING: + from collections.abc import Callable + + from zarr.abc.codec import Codec + @pytest.mark.parametrize( ("write_slice", "read_slice", "expected_statuses"), @@ -120,3 +133,65 @@ def test_codec_pipeline_threads_dtype_through_evolve(source_dtype: str, target_d ) arr[:] = np.asarray([0, 1, 2, 3], dtype=source_dtype) np.testing.assert_array_equal(arr[:], np.asarray([0, 1, 2, 3], dtype=source_dtype)) + + +# Property-based check of codecs_from_list ordering validation. +# +# Valid codec orderings are exactly: (ArrayArrayCodec)* (ArrayBytesCodec) +# (BytesBytesCodec)*. codecs_from_list walks adjacent pairs and must raise +# TypeError the moment a codec appears in a structurally invalid position -- +# notably, a BytesBytesCodec immediately following an ArrayArrayCodec with no +# ArrayBytesCodec in between (which previously built an error message but never +# raised it, falling through to an unrelated ValueError instead). +_AA = "AA" # ArrayArrayCodec -> TransposeCodec +_AB = "AB" # ArrayBytesCodec -> BytesCodec +_BB = "BB" # BytesBytesCodec -> GzipCodec + +_CODEC_FACTORY: dict[str, Callable[[], Codec]] = { + _AA: lambda: TransposeCodec(order=(0, 1)), + _AB: BytesCodec, + _BB: GzipCodec, +} + + +def _expected_codec_order_outcome(labels: list[str]) -> str: + """Independently predict codecs_from_list's outcome: 'TypeError', + 'ValueError' or 'ok', mirroring its left-to-right scan and the order in + which it checks ordering violations (TypeError) vs. the ArrayBytes-count + constraints (ValueError).""" + prev = None + seen_array_bytes = False + for cur in labels: + if cur == _AA: + if prev in (_AB, _BB): + return "TypeError" + elif cur == _AB: + if prev == _BB: + return "TypeError" + if seen_array_bytes: + return "ValueError" # two ArrayBytesCodecs + seen_array_bytes = True + else: # _BB + if prev == _AA: + return "TypeError" + prev = cur + if not seen_array_bytes: + return "ValueError" # Required ArrayBytesCodec was not found + return "ok" + + +@given(labels=st.lists(st.sampled_from([_AA, _AB, _BB]), min_size=1, max_size=5)) +def test_codecs_from_list_outcome_matches_order_rules(labels: list[str]) -> None: + codecs = [_CODEC_FACTORY[label]() for label in labels] + expected = _expected_codec_order_outcome(labels) + if expected == "TypeError": + with pytest.raises(TypeError): + codecs_from_list(codecs) + elif expected == "ValueError": + with pytest.raises(ValueError): + codecs_from_list(codecs) + else: + # Valid ordering: must classify without raising. + aa, _ab, bb = codecs_from_list(codecs) + assert labels.count(_AA) == len(aa) + assert labels.count(_BB) == len(bb) diff --git a/tests/test_store/test_utils.py b/tests/test_store/test_utils.py index b1934e7eae..291526fab8 100644 --- a/tests/test_store/test_utils.py +++ b/tests/test_store/test_utils.py @@ -5,7 +5,9 @@ import pytest -from zarr.storage._utils import ParsedStoreUrl, parse_store_url +from zarr.abc.store import SuffixByteRequest +from zarr.core.buffer.core import default_buffer_prototype +from zarr.storage._utils import ParsedStoreUrl, _normalize_byte_range_index, parse_store_url class TestParseStoreUrl: @@ -95,3 +97,32 @@ def test_drive_letter_not_special_on_non_windows(self, url: str) -> None: result = parse_store_url(url) # urlparse interprets the drive letter as a scheme assert result.scheme == "c" + + +class TestNormalizeByteRangeIndex: + """Tests for _normalize_byte_range_index.""" + + def test_suffix_larger_than_data_returns_all_bytes(self) -> None: + """Regression: SuffixByteRequest with suffix > len(data) must not produce a + negative start index that causes numpy to return fewer bytes than available.""" + prototype = default_buffer_prototype() + data = prototype.buffer.from_bytes(b"hello") # 5 bytes + byte_range = SuffixByteRequest(suffix=7) + start, stop = _normalize_byte_range_index(data, byte_range) + assert start == 0, f"start should be 0 (clamped), got {start}" + result = data[start:stop] + assert len(result) == 5, f"expected all 5 bytes, got {len(result)}" + + def test_suffix_exact_length(self) -> None: + """SuffixByteRequest with suffix == len(data) returns all bytes.""" + prototype = default_buffer_prototype() + data = prototype.buffer.from_bytes(b"hello") + start, _stop = _normalize_byte_range_index(data, SuffixByteRequest(suffix=5)) + assert start == 0 + + def test_suffix_shorter_than_data(self) -> None: + """SuffixByteRequest with suffix < len(data) returns the last n bytes.""" + prototype = default_buffer_prototype() + data = prototype.buffer.from_bytes(b"hello") + start, _stop = _normalize_byte_range_index(data, SuffixByteRequest(suffix=3)) + assert start == 2 diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py index be51bcedcb..ed69114b51 100644 --- a/tests/test_store/test_zip.py +++ b/tests/test_store/test_zip.py @@ -8,11 +8,20 @@ import numpy as np import pytest +from hypothesis import settings +from hypothesis.stateful import ( + RuleBasedStateMachine, + initialize, + precondition, + rule, + run_state_machine_as_test, +) import zarr from zarr import create_array from zarr.core.buffer import Buffer, cpu, default_buffer_prototype from zarr.core.group import Group +from zarr.core.sync import sync from zarr.storage import ZipStore from zarr.testing.store import StoreTests @@ -177,3 +186,66 @@ async def test_move(self, tmp_path: Path) -> None: assert destination.exists() assert not origin.exists() assert np.array_equal(array[...], np.arange(10)) + + +class ZipStoreLifecycleMachine(RuleBasedStateMachine): + """Drive a ZipStore through construct / open / write / close transitions. + + Invariant under test: a constructed ZipStore can always be closed without + raising, regardless of whether it was ever opened or did any I/O. This is a + property-based generalization of the former example-based regression tests + for ZipStore.close() being called on a never-opened store (which raised + AttributeError because ``_lock`` is created lazily in ``_sync_open``). + """ + + def __init__(self, tmp_path: Path) -> None: + super().__init__() + self._tmp_path = tmp_path + self._counter = 0 + self.store: ZipStore | None = None + self._opened = False + + @initialize() + def start(self) -> None: + self.store = None + self._opened = False + + @precondition(lambda self: self.store is None) + @rule() + def construct(self) -> None: + # Fresh path each time so mode="w" never clobbers a closed archive. + self._counter += 1 + self.store = ZipStore(self._tmp_path / f"s{self._counter}.zip", mode="w") + self._opened = False + + @precondition(lambda self: self.store is not None and not self._opened) + @rule() + def open(self) -> None: + assert self.store is not None + self.store._sync_open() + self._opened = True + + @precondition(lambda self: self.store is not None and not self._opened) + @rule() + def write(self) -> None: + assert self.store is not None + # store.set auto-opens the store. + sync(self.store.set("a", cpu.Buffer.from_bytes(b"hi"))) + self._opened = True + + @precondition(lambda self: self.store is not None) + @rule() + def close(self) -> None: + assert self.store is not None + # The property under test: close() must never raise, even with no + # prior open or I/O. + self.store.close() + self.store = None + self._opened = False + + +def test_zipstore_close_lifecycle(tmp_path: Path) -> None: + run_state_machine_as_test( # type: ignore[no-untyped-call] + lambda: ZipStoreLifecycleMachine(tmp_path), + settings=settings(max_examples=50, deadline=None), + ) From 122d974edef7e61676ee6524d7316d41c74f0f55 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jun 2026 14:26:25 +0200 Subject: [PATCH 360/468] chore(deps): bump bleach from 6.3.0 to 6.4.0 (#4081) Bumps [bleach](https://github.com/mozilla/bleach) from 6.3.0 to 6.4.0. - [Changelog](https://github.com/mozilla/bleach/blob/main/CHANGES) - [Commits](https://github.com/mozilla/bleach/compare/v6.3.0...v6.4.0) --- updated-dependencies: - dependency-name: bleach dependency-version: 6.4.0 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- uv.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/uv.lock b/uv.lock index dedaf964fa..5efa31e2d9 100644 --- a/uv.lock +++ b/uv.lock @@ -339,14 +339,14 @@ wheels = [ [[package]] name = "bleach" -version = "6.3.0" +version = "6.4.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "webencodings" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/07/18/3c8523962314be6bf4c8989c79ad9531c825210dd13a8669f6b84336e8bd/bleach-6.3.0.tar.gz", hash = "sha256:6f3b91b1c0a02bb9a78b5a454c92506aa0fdf197e1d5e114d2e00c6f64306d22", size = 203533, upload-time = "2025-10-27T17:57:39.211Z" } +sdist = { url = "https://files.pythonhosted.org/packages/48/3c/e12ac860709702bd5ebeb9b56a4fe334f1001246ee1b8f2b7ee28912df7d/bleach-6.4.0.tar.gz", hash = "sha256:4202482733d85cedd04e59fcb2f89f4e4c7c385a78d3c3c23c30446843a37452", size = 204857, upload-time = "2026-06-05T13:01:13.734Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/cd/3a/577b549de0cc09d95f11087ee63c739bba856cd3952697eec4c4bb91350a/bleach-6.3.0-py3-none-any.whl", hash = "sha256:fe10ec77c93ddf3d13a73b035abaac7a9f5e436513864ccdad516693213c65d6", size = 164437, upload-time = "2025-10-27T17:57:37.538Z" }, + { url = "https://files.pythonhosted.org/packages/58/9d/40b6267367182187139a4000b82a3b287d84d745bccd808e75d916920e9d/bleach-6.4.0-py3-none-any.whl", hash = "sha256:4b6b6a54fff2e69a3dde9d21cc6301220bee3c3cb792187d11403fd795031081", size = 165109, upload-time = "2026-06-05T13:01:12.504Z" }, ] [package.optional-dependencies] From 98c3a5c5e4e592b9b0a89991ab75e81835430622 Mon Sep 17 00:00:00 2001 From: Alden Keefe Sampson Date: Thu, 18 Jun 2026 10:32:59 -0400 Subject: [PATCH 361/468] Control sharding codec read coalescing with ArrayConfig and runtime config options (#3987) * feat: add sharding.read.* coalescing runtime config options * add changes/3987.feature.md * Add coalesce options to ArrayConfig with defaults from global config * Fix missing api ref in changes/3987.feature.md * unit tests for parse_int * Fix typeddict-item lint in sharding unit test The merge of #3968 ("deprecate more enums") retyped ShardsConfigParam.index_location to IndexLocation (Literal["start", "end"]), so the deprecated ShardingCodecIndexLocation.end member (now a plain str) no longer satisfies it. Pass the literal "end" directly, as the deprecation instructs. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Co-authored-by: Davis Bennett Co-authored-by: Claude Opus 4.8 (1M context) --- changes/3987.feature.md | 1 + docs/user-guide/config.md | 1 + src/zarr/codecs/sharding.py | 14 +- src/zarr/core/array_spec.py | 30 ++++- src/zarr/core/common.py | 6 + src/zarr/core/config.py | 2 + tests/test_codecs/test_sharding_unit.py | 163 ++++++++++++++++++++++++ tests/test_common.py | 13 ++ tests/test_config.py | 24 +++- 9 files changed, 250 insertions(+), 4 deletions(-) create mode 100644 changes/3987.feature.md diff --git a/changes/3987.feature.md b/changes/3987.feature.md new file mode 100644 index 0000000000..2492b4d7dd --- /dev/null +++ b/changes/3987.feature.md @@ -0,0 +1 @@ +Two new fields on `ArrayConfig` control how the sharding codec coalesces partial-shard reads: `sharding_coalesce_max_gap_bytes` (default 1 MiB) and `sharding_coalesce_max_bytes` (default 16 MiB). When reading multiple chunks from the same shard, nearby byte ranges are merged into a single request to the store if separated by no more than `sharding_coalesce_max_gap_bytes` and the merged read stays within `sharding_coalesce_max_bytes`. Defaults are seeded from the matching `array.sharding_coalesce_max_gap_bytes` / `array.sharding_coalesce_max_bytes` keys in [`zarr.config`][] at array-creation time, and can be overridden per array by passing `config={...}` to [`zarr.create_array`][]. diff --git a/docs/user-guide/config.md b/docs/user-guide/config.md index 8a8fa94c3d..71c021b070 100644 --- a/docs/user-guide/config.md +++ b/docs/user-guide/config.md @@ -35,6 +35,7 @@ Configuration options include the following: - Async and threading options, e.g. `async.concurrency` and `threading.max_workers` - Selections of implementations of codecs, codec pipelines and buffers - Enabling GPU support with `zarr.config.enable_gpu()`. See GPU support for more. +- Control request merging when reading multiple chunks from the same shard with `array.sharding_coalesce_max_gap_bytes` and `array.sharding_coalesce_max_bytes`. Reads of nearby chunks are coalesced into a single request to the store when separated by at most `sharding_coalesce_max_gap_bytes` and the resulting merged read is no larger than `sharding_coalesce_max_bytes`. For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, first register the implementations in the registry and then select them in the config. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 1fe24719c9..332aab3351 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -527,6 +527,8 @@ async def _decode_partial_single( chunk_spec.prototype, chunks_per_shard, all_chunk_coords, + max_gap_bytes=shard_spec.config.sharding_coalesce_max_gap_bytes, + max_coalesced_bytes=shard_spec.config.sharding_coalesce_max_bytes, ) if shard_dict_maybe is None: @@ -846,10 +848,16 @@ async def _load_partial_shard_maybe( prototype: BufferPrototype, chunks_per_shard: tuple[int, ...], all_chunk_coords: set[tuple[int, ...]], + max_gap_bytes: int, + max_coalesced_bytes: int, ) -> ShardMapping | None: """ Read chunks from `byte_getter` for the case where the read is less than a full shard. Returns a mapping of chunk coordinates to bytes or None. + + `max_gap_bytes` and `max_coalesced_bytes` are forwarded to + `Store.get_ranges` to control byte-range coalescing across the requested + chunks. """ shard_index = await self._load_shard_index_maybe(byte_getter, chunks_per_shard) if shard_index is None: @@ -873,7 +881,11 @@ async def _load_partial_shard_maybe( byte_ranges = [byte_range for _, byte_range in chunk_coord_byte_ranges] try: async for group in byte_getter.store.get_ranges( - byte_getter.path, byte_ranges, prototype=prototype + byte_getter.path, + byte_ranges, + prototype=prototype, + max_gap_bytes=max_gap_bytes, + max_coalesced_bytes=max_coalesced_bytes, ): for idx, buf in group: if buf is not None: diff --git a/src/zarr/core/array_spec.py b/src/zarr/core/array_spec.py index 2b5eb0191c..89163f7d83 100644 --- a/src/zarr/core/array_spec.py +++ b/src/zarr/core/array_spec.py @@ -7,6 +7,7 @@ MemoryOrder, parse_bool, parse_fill_value, + parse_int, parse_order, parse_shapelike, ) @@ -29,6 +30,8 @@ class ArrayConfigParams(TypedDict): order: NotRequired[MemoryOrder] write_empty_chunks: NotRequired[bool] read_missing_chunks: NotRequired[bool] + sharding_coalesce_max_gap_bytes: NotRequired[int] + sharding_coalesce_max_bytes: NotRequired[int] @dataclass(frozen=True) @@ -45,22 +48,42 @@ class ArrayConfig: read_missing_chunks : bool If True, missing chunks will be filled with the array's fill value on read. If False, reading missing chunks will raise a ``ChunkNotFoundError``. + sharding_coalesce_max_gap_bytes : int + When reading multiple chunks from the same shard, nearby byte ranges + separated by no more than this many bytes are coalesced into a single + request to the store. + sharding_coalesce_max_bytes : int + Requests will not be coalesced if doing so would exceed this byte size. """ order: MemoryOrder write_empty_chunks: bool read_missing_chunks: bool + sharding_coalesce_max_gap_bytes: int + sharding_coalesce_max_bytes: int def __init__( - self, order: MemoryOrder, write_empty_chunks: bool, *, read_missing_chunks: bool = True + self, + order: MemoryOrder, + write_empty_chunks: bool, + *, + read_missing_chunks: bool = True, + sharding_coalesce_max_gap_bytes: int = 1 << 20, # 1 MiB + sharding_coalesce_max_bytes: int = 16 << 20, # 16 MiB ) -> None: order_parsed = parse_order(order) write_empty_chunks_parsed = parse_bool(write_empty_chunks) read_missing_chunks_parsed = parse_bool(read_missing_chunks) + sharding_coalesce_max_gap_bytes_parsed = parse_int(sharding_coalesce_max_gap_bytes) + sharding_coalesce_max_bytes_parsed = parse_int(sharding_coalesce_max_bytes) object.__setattr__(self, "order", order_parsed) object.__setattr__(self, "write_empty_chunks", write_empty_chunks_parsed) object.__setattr__(self, "read_missing_chunks", read_missing_chunks_parsed) + object.__setattr__( + self, "sharding_coalesce_max_gap_bytes", sharding_coalesce_max_gap_bytes_parsed + ) + object.__setattr__(self, "sharding_coalesce_max_bytes", sharding_coalesce_max_bytes_parsed) @classmethod def from_dict(cls, data: ArrayConfigParams) -> Self: @@ -72,7 +95,8 @@ def from_dict(cls, data: ArrayConfigParams) -> Self: kwargs_out: ArrayConfigParams = {} for f in fields(ArrayConfig): field_name = cast( - "Literal['order', 'write_empty_chunks', 'read_missing_chunks']", f.name + "Literal['order', 'write_empty_chunks', 'read_missing_chunks', 'sharding_coalesce_max_gap_bytes', 'sharding_coalesce_max_bytes']", + f.name, ) if field_name not in data: kwargs_out[field_name] = zarr_config.get(f"array.{field_name}") @@ -88,6 +112,8 @@ def to_dict(self) -> ArrayConfigParams: "order": self.order, "write_empty_chunks": self.write_empty_chunks, "read_missing_chunks": self.read_missing_chunks, + "sharding_coalesce_max_gap_bytes": self.sharding_coalesce_max_gap_bytes, + "sharding_coalesce_max_bytes": self.sharding_coalesce_max_bytes, } diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index eafffa1818..570e3dfdc3 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -217,6 +217,12 @@ def parse_bool(data: Any) -> bool: raise ValueError(f"Expected bool, got {data} instead.") +def parse_int(data: Any) -> int: + if isinstance(data, int) and not isinstance(data, bool): + return data + raise ValueError(f"Expected int, got {data} instead.") + + def _warn_write_empty_chunks_kwarg() -> None: # TODO: link to docs page on array configuration in this message msg = ( diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 7dcbc78e31..08d2a50ace 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -99,6 +99,8 @@ def enable_gpu(self) -> ConfigSet: "read_missing_chunks": True, "target_shard_size_bytes": None, "rectilinear_chunks": False, + "sharding_coalesce_max_gap_bytes": 1 << 20, # 1 MiB + "sharding_coalesce_max_bytes": 16 << 20, # 16 MiB }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, diff --git a/tests/test_codecs/test_sharding_unit.py b/tests/test_codecs/test_sharding_unit.py index 6e022ed9fa..2e3872e7a6 100644 --- a/tests/test_codecs/test_sharding_unit.py +++ b/tests/test_codecs/test_sharding_unit.py @@ -1,3 +1,8 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING, cast +from unittest.mock import AsyncMock + import numpy as np import pytest @@ -10,9 +15,14 @@ ) from zarr.core.buffer import default_buffer_prototype from zarr.core.buffer.cpu import Buffer +from zarr.core.config import config from zarr.storage._common import StorePath from zarr.storage._memory import MemoryStore +if TYPE_CHECKING: + from zarr.core.array import ShardsConfigParam + from zarr.core.array_spec import ArrayConfigParams + # ============================================================================ # _ShardIndex tests # ============================================================================ @@ -155,6 +165,8 @@ async def test_load_partial_shard_maybe_index_load_fails() -> None: prototype=default_buffer_prototype(), chunks_per_shard=(2,), all_chunk_coords={(0,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) assert result is None @@ -187,6 +199,8 @@ async def mock_load_index( prototype=default_buffer_prototype(), chunks_per_shard=chunks_per_shard, all_chunk_coords={(0,), (1,), (2,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) assert result is not None @@ -220,6 +234,8 @@ async def mock_load_index( prototype=default_buffer_prototype(), chunks_per_shard=chunks_per_shard, all_chunk_coords={(0,), (1,), (2,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) assert result == {} @@ -251,6 +267,8 @@ async def mock_load_index( prototype=default_buffer_prototype(), chunks_per_shard=chunks_per_shard, all_chunk_coords={(0,), (1,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) assert result is not None @@ -292,6 +310,8 @@ async def mock_load_index( prototype=default_buffer_prototype(), chunks_per_shard=chunks_per_shard, all_chunk_coords={(0,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) assert result is None @@ -336,6 +356,8 @@ async def boom(*args: object, **kwargs: object) -> Buffer | None: prototype=default_buffer_prototype(), chunks_per_shard=chunks_per_shard, all_chunk_coords={(0,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) @@ -368,6 +390,8 @@ async def mock_load_index( prototype=default_buffer_prototype(), chunks_per_shard=chunks_per_shard, all_chunk_coords={(0,), (1,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) assert result is not None @@ -405,6 +429,8 @@ async def mock_load_index( prototype=default_buffer_prototype(), chunks_per_shard=chunks_per_shard, all_chunk_coords={(0,)}, + max_gap_bytes=1 << 20, + max_coalesced_bytes=16 << 20, ) assert result == {} @@ -486,3 +512,140 @@ def test_is_total_shard_1d() -> None: # Partial partial_coords: set[tuple[int, ...]] = {(0,), (2,)} assert codec._is_total_shard(partial_coords, chunks_per_shard) is False + + +# ============================================================================ +# Coalescing config option tests +# +# Assert that the `array.sharding_coalesce_max_gap_bytes` and +# `array.sharding_coalesce_max_bytes` global config keys flow through +# `ArrayConfig` to `Store.get_ranges` as `max_gap_bytes` / +# `max_coalesced_bytes` kwargs, and that per-array `config={...}` overrides +# the global default. +# ============================================================================ + + +def _trigger_partial_shard_read(array_config: ArrayConfigParams | None = None) -> AsyncMock: + """Build a sharded array on a mocked `MemoryStore`, trigger a partial-shard + read via the public read path, and return the `get_ranges` mock. + """ + import zarr + + chunk_shape = (2,) + shard_shape = (8,) + data = np.arange(8, dtype="int32") + + store = MemoryStore() + store_mock = AsyncMock(wraps=store, spec=store.__class__) + + shards: ShardsConfigParam = { + "shape": shard_shape, + "index_location": "end", + } + a = zarr.create_array( + StorePath(store_mock), + shape=(8,), + chunks=chunk_shape, + shards=shards, + dtype=data.dtype, + fill_value=-1, + config=array_config, + ) + a[:] = data + + store_mock.reset_mock() + + # Read a strict subset of chunks to take the partial-shard read path. + _ = a[0:4] + + return cast(AsyncMock, store_mock.get_ranges) + + +def test_load_partial_shard_forwards_global_config_to_get_ranges() -> None: + """Global `array.sharding_coalesce_*` values flow into ArrayConfig at + array-creation time and are forwarded to `Store.get_ranges`.""" + with config.set( + { + "array.sharding_coalesce_max_gap_bytes": 4242, + "array.sharding_coalesce_max_bytes": 424242, + } + ): + get_ranges_mock = _trigger_partial_shard_read() + + assert get_ranges_mock.call_count >= 1 + for call in get_ranges_mock.call_args_list: + kwargs = call.kwargs + assert kwargs["max_gap_bytes"] == 4242 + assert kwargs["max_coalesced_bytes"] == 424242 + + +def test_load_partial_shard_per_array_config_overrides_global() -> None: + """Per-array `config={...}` passed to `create_array` takes precedence over + the global config and is forwarded to `Store.get_ranges`.""" + with config.set( + { + "array.sharding_coalesce_max_gap_bytes": 4242, + "array.sharding_coalesce_max_bytes": 424242, + } + ): + get_ranges_mock = _trigger_partial_shard_read( + array_config={ + "sharding_coalesce_max_gap_bytes": 99, + "sharding_coalesce_max_bytes": 9999, + }, + ) + + assert get_ranges_mock.call_count >= 1 + for call in get_ranges_mock.call_args_list: + kwargs = call.kwargs + assert kwargs["max_gap_bytes"] == 99 + assert kwargs["max_coalesced_bytes"] == 9999 + + +def test_load_partial_shard_uses_config_defaults() -> None: + """Without explicit config, defaults from `zarr.config` are forwarded.""" + get_ranges_mock = _trigger_partial_shard_read() + + assert get_ranges_mock.call_count >= 1 + for call in get_ranges_mock.call_args_list: + kwargs = call.kwargs + assert kwargs["max_gap_bytes"] == config.get("array.sharding_coalesce_max_gap_bytes") + assert kwargs["max_coalesced_bytes"] == config.get("array.sharding_coalesce_max_bytes") + + +async def test_load_partial_shard_explicit_kwargs_passthrough( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """`_load_partial_shard_maybe` forwards its explicit kwargs to `get_ranges`.""" + codec = ShardingCodec(chunk_shape=(2,)) + chunks_per_shard = (4,) + + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 100)) + index.set_chunk_slice((2,), slice(200, 300)) + + store = MemoryStore() + await store.set("shard", Buffer.from_bytes(b"x" * 300)) + store_mock = AsyncMock(wraps=store, spec=store.__class__) + byte_getter = StorePath(store_mock, "shard") + + async def mock_load_index( + self: ShardingCodec, byte_getter: StorePath, cps: tuple[int, ...] + ) -> _ShardIndex: + return index + + monkeypatch.setattr(ShardingCodec, "_load_shard_index_maybe", mock_load_index) + + await codec._load_partial_shard_maybe( + byte_getter=byte_getter, + prototype=default_buffer_prototype(), + chunks_per_shard=chunks_per_shard, + all_chunk_coords={(0,), (2,)}, + max_gap_bytes=12345, + max_coalesced_bytes=67890, + ) + + store_mock.get_ranges.assert_called_once() + kwargs = store_mock.get_ranges.call_args.kwargs + assert kwargs["max_gap_bytes"] == 12345 + assert kwargs["max_coalesced_bytes"] == 67890 diff --git a/tests/test_common.py b/tests/test_common.py index 0dedde1d6b..2fe0743e14 100644 --- a/tests/test_common.py +++ b/tests/test_common.py @@ -9,6 +9,7 @@ from zarr.core.common import ( ANY_ACCESS_MODE, AccessModeLiteral, + parse_int, parse_name, parse_shapelike, product, @@ -72,6 +73,18 @@ def test_parse_indexing_order_invalid(data: Any) -> None: parse_indexing_order(data) +@pytest.mark.parametrize("data", ["1", 1.0, True, False, None, [1], (1,)]) +def test_parse_int_invalid(data: Any) -> None: + """Non-int values (including bools, which are int subclasses) are rejected.""" + with pytest.raises(ValueError, match="Expected int"): + parse_int(data) + + +@pytest.mark.parametrize("data", [0, 1, -1, 2**63]) +def test_parse_int_valid(data: int) -> None: + assert parse_int(data) == data + + @pytest.mark.parametrize("data", ["C", "F"]) def parse_indexing_order_valid(data: Literal["C", "F"]) -> None: assert parse_indexing_order(data) == data diff --git a/tests/test_config.py b/tests/test_config.py index 4e293e968f..a758378dc7 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -1,3 +1,4 @@ +import inspect import os from collections.abc import Iterable from typing import Any @@ -17,7 +18,7 @@ Crc32cCodec, ShardingCodec, ) -from zarr.core.array_spec import ArraySpec +from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.buffer import NDBuffer from zarr.core.buffer.core import Buffer from zarr.core.codec_pipeline import BatchedCodecPipeline @@ -56,6 +57,8 @@ def test_config_defaults_set() -> None: "read_missing_chunks": True, "target_shard_size_bytes": None, "rectilinear_chunks": False, + "sharding_coalesce_max_gap_bytes": 1 << 20, + "sharding_coalesce_max_bytes": 16 << 20, }, "async": {"concurrency": 10, "timeout": None}, "threading": {"max_workers": None}, @@ -109,6 +112,25 @@ def test_config_defaults_set() -> None: assert config.get("json_indent") == 2 +def test_array_config_init_defaults_match_global_config() -> None: + """Each `ArrayConfig.__init__` parameter that has a default must match the + value of `array.` in the global config. Catches drift between + the two sources of truth.""" + params = inspect.signature(ArrayConfig.__init__).parameters + has_defaults = { + name: p.default + for name, p in params.items() + if name != "self" and p.default is not inspect.Parameter.empty + } + assert has_defaults, "expected at least one default to check" + for name, default in has_defaults.items(): + assert default == config.get(f"array.{name}"), ( + f"ArrayConfig.__init__ default for {name!r} ({default!r}) does not " + f"match global config value for 'array.{name}' " + f"({config.get(f'array.{name}')!r})" + ) + + @pytest.mark.parametrize( ("key", "old_val", "new_val"), [("array.order", "C", "F"), ("async.concurrency", 10, 128), ("json_indent", 2, 0)], From 6c3624554b255aec1e89871a3dc640b0bffe9f24 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jun 2026 14:49:47 +0000 Subject: [PATCH 362/468] chore(deps-dev): bump the python-dependencies group across 1 directory with 2 updates (#4080) Bumps the python-dependencies group with 2 updates in the / directory: [obstore](https://github.com/geospatial-jeff/pyasyncio-benchmark) and [uv](https://github.com/astral-sh/uv). Updates `obstore` from 0.10.0 to 0.10.1 - [Commits](https://github.com/geospatial-jeff/pyasyncio-benchmark/commits) Updates `uv` from 0.11.19 to 0.11.20 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.11.19...0.11.20) --- updated-dependencies: - dependency-name: obstore dependency-version: 0.10.1 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: uv dependency-version: 0.11.20 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- pyproject.toml | 2 +- uv.lock | 134 ++++++++++++++++++++++++------------------------- 2 files changed, 68 insertions(+), 68 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6f6c7265a5..493b18822a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -105,7 +105,7 @@ test = [ "pytest-benchmark==5.2.3", "pytest-codspeed==5.0.3", "tomlkit==0.15.0", - "uv==0.11.19", + "uv==0.11.20", ] remote-tests = [ {include-group = "test"}, diff --git a/uv.lock b/uv.lock index 5efa31e2d9..adc71bae62 100644 --- a/uv.lock +++ b/uv.lock @@ -2259,52 +2259,52 @@ wheels = [ [[package]] name = "obstore" -version = "0.10.0" +version = "0.10.1" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "typing-extensions", marker = "python_full_version < '3.13'" }, ] -sdist = { url = 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}, { name = "pytest-xdist", specifier = "==3.8.0" }, { name = "tomlkit", specifier = "==0.15.0" }, - { name = "uv", specifier = "==0.11.19" }, + { name = "uv", specifier = "==0.11.20" }, ] From ed60e132c929c5e9a17f595f3f4abb0ffd85eddf Mon Sep 17 00:00:00 2001 From: Justus Magin Date: Thu, 18 Jun 2026 21:51:55 +0200 Subject: [PATCH 363/468] allow roundtripping the `BytesCodec` (#3417) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * rename test_endian.py to test_bytes.py * tests for `BytesCodec.to_dict` * tests for `from_dict` and roundtripping * don't use the system's default in `from_dict` * changelog * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: consolidate endian tests into one config-parameterized test test_endian and test_endian_write tested the same property — the bytes codec serializes multi-byte data correctly given an input configuration — differing only in the input array's byte order, which test_endian fixed to native (i.e. a slice of test_endian_write's matrix). Merge them into a single test parameterized over the configuration: input dtype byte order (>u2 / * test: use Expect/ExpectFail helpers for bytes codec dict tests - to_dict and from_dict are inverses over the same (endian, wire-dict) table; express that with a single shared list of `Expect` cases instead of two duplicated parametrize tables. - rejects_unknown_endian now uses `ExpectFail`, matching the error-table idiom used elsewhere (e.g. test_chunk_grids). - Move the annotation-only `Store` import into a TYPE_CHECKING block (TC001), a latent issue from combining `from __future__ import annotations` with the integration tests during the earlier merge. Co-Authored-By: Claude Opus 4.8 (1M context) * doc: note from_dict behavior change in changelog Clarify that the fix alters BytesCodec.from_dict: a missing `endian` configuration is now interpreted as endian=None (what to_dict emits) rather than the system's native byte order. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: Davis Bennett Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- changes/3417.bugfix.md | 4 + src/zarr/codecs/bytes.py | 1 + tests/test_codecs/test_bytes.py | 140 +++++++++++++++++++++++++++++-- tests/test_codecs/test_endian.py | 89 -------------------- 4 files changed, 138 insertions(+), 96 deletions(-) create mode 100644 changes/3417.bugfix.md delete mode 100644 tests/test_codecs/test_endian.py diff --git a/changes/3417.bugfix.md b/changes/3417.bugfix.md new file mode 100644 index 0000000000..be5b44f3e9 --- /dev/null +++ b/changes/3417.bugfix.md @@ -0,0 +1,4 @@ +Fixed `BytesCodec.from_dict` so that `BytesCodec` instances roundtrip to / from +their dict representation. `BytesCodec.from_dict` now interprets a missing +`endian` configuration as `endian=None` (matching what `BytesCodec.to_dict` +emits), instead of falling back to the system's native byte order. diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index 1c67c65e98..240c077627 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -62,6 +62,7 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: data, "bytes", require_configuration=False ) configuration_parsed = configuration_parsed or {} + configuration_parsed.setdefault("endian", None) return cls(**configuration_parsed) # type: ignore[arg-type] def to_dict(self) -> dict[str, JSON]: diff --git a/tests/test_codecs/test_bytes.py b/tests/test_codecs/test_bytes.py index 25c786a405..03dd0b40c6 100644 --- a/tests/test_codecs/test_bytes.py +++ b/tests/test_codecs/test_bytes.py @@ -5,10 +5,14 @@ import enum import sys import warnings -from typing import Any, cast +from typing import TYPE_CHECKING, Any, Literal, cast +import numpy as np import pytest +import zarr +from tests.conftest import Expect, ExpectFail +from zarr.abc.codec import SupportsSyncCodec from zarr.codecs.bytes import ( ENDIAN, BytesCodec, @@ -16,9 +20,83 @@ EndianLiteral, ) from zarr.core.array_spec import ArrayConfig, ArraySpec -from zarr.core.buffer import default_buffer_prototype +from zarr.core.buffer import NDBuffer, default_buffer_prototype +from zarr.core.dtype import get_data_type_from_native_dtype from zarr.core.dtype.npy.int import Int8, Int32 from zarr.core.dtype.npy.structured import Struct +from zarr.storage import StorePath + +from .test_codecs import _AsyncArrayProxy + +if TYPE_CHECKING: + from zarr.abc.store import Store + + +@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) +@pytest.mark.parametrize("input_dtype", [">u2", "u2", " None: + """ + The `bytes` codec stores multi-byte data in the byte order configured on the + codec, regardless of the input array's byte order, and reads it back to the + original values. The input-dtype/store-endian cross-product exercises the + encode-side byteswap (input byte order != store byte order) and the no-op + case alike. Compression is disabled so the stored chunk is the codec's raw + output and its byte layout can be asserted directly. + """ + data = np.arange(0, 256, dtype=input_dtype).reshape((16, 16)) + path = "endian" + spath = StorePath(store, path) + a = await zarr.api.asynchronous.create_array( + spath, + shape=data.shape, + chunks=(16, 16), + dtype="uint16", + fill_value=0, + compressors=None, + serializer=BytesCodec(endian=store_endian), + ) + + await _AsyncArrayProxy(a)[:, :].set(data) + + # The stored chunk is laid out in the byte order configured on the codec. + stored = await store.get(f"{path}/c/0/0", prototype=default_buffer_prototype()) + assert stored is not None + expected_dtype = ">u2" if store_endian == "big" else " None: + assert isinstance(BytesCodec(), SupportsSyncCodec) + + +def test_bytes_codec_sync_roundtrip() -> None: + codec = BytesCodec() + arr = np.arange(100, dtype="float64") + zdtype = get_data_type_from_native_dtype(arr.dtype) + spec = ArraySpec( + shape=arr.shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + nd_buf: NDBuffer = default_buffer_prototype().nd_buffer.from_numpy_array(arr) + + codec = codec.evolve_from_array_spec(spec) + + encoded = codec._encode_sync(nd_buf, spec) + assert encoded is not None + decoded = codec._decode_sync(encoded, spec) + np.testing.assert_array_equal(arr, decoded.as_numpy_array()) @pytest.mark.parametrize("endian", ENDIAN) @@ -46,6 +124,43 @@ def test_bytes_codec_json_roundtrip(endian: EndianLiteral) -> None: assert restored == codec +# to_dict and from_dict are inverses over this (endian setting, wire dict) mapping: +# to_dict turns the endian setting into the dict; from_dict recovers it. +_ENDIAN_DICT_CASES: list[Expect[EndianLiteral | None, dict[str, Any]]] = [ + Expect( + input="little", + output={"name": "bytes", "configuration": {"endian": "little"}}, + id="little", + ), + Expect( + input="big", + output={"name": "bytes", "configuration": {"endian": "big"}}, + id="big", + ), + Expect(input=None, output={"name": "bytes"}, id="missing"), +] + + +@pytest.mark.parametrize("case", _ENDIAN_DICT_CASES, ids=lambda c: c.id) +def test_to_dict(case: Expect[EndianLiteral | None, dict[str, Any]]) -> None: + assert BytesCodec(endian=case.input).to_dict() == case.output + + +@pytest.mark.parametrize("case", _ENDIAN_DICT_CASES, ids=lambda c: c.id) +def test_from_dict(case: Expect[EndianLiteral | None, dict[str, Any]]) -> None: + assert BytesCodec.from_dict(case.output).endian == case.input + + +@pytest.mark.parametrize("endian", ["little", "big", pytest.param(None, id="missing")]) +def test_roundtrip(endian: EndianLiteral | None) -> None: + codec = BytesCodec(endian=endian) + + encoded = codec.to_dict() + roundtripped = BytesCodec.from_dict(encoded) + + assert codec == roundtripped + + @pytest.mark.parametrize( ("member", "expected"), [("little", "little"), ("big", "big")], @@ -105,14 +220,25 @@ def test_bytes_codec_init_with_deprecated_class_member() -> None: assert codec.endian == "little" -def test_bytes_codec_rejects_unknown_endian() -> None: +@pytest.mark.parametrize( + "case", + [ + ExpectFail( + input="north", + exception=ValueError, + id="unknown-string", + msg="endian must be one of", + ), + ], + ids=lambda c: c.id, +) +def test_bytes_codec_rejects_unknown_endian(case: ExpectFail[Any]) -> None: """ - `BytesCodec.__init__` raises `ValueError` when given a string outside + `BytesCodec.__init__` raises `ValueError` when given a value outside `ENDIAN`, and the error message names the offending parameter. """ - kwargs: dict[str, Any] = {"endian": "north"} - with pytest.raises(ValueError, match="endian must be one of"): - BytesCodec(**kwargs) + with case.raises(): + BytesCodec(endian=case.input) def test_endian_attribute_error_for_unknown_member() -> None: diff --git a/tests/test_codecs/test_endian.py b/tests/test_codecs/test_endian.py deleted file mode 100644 index c505cee828..0000000000 --- a/tests/test_codecs/test_endian.py +++ /dev/null @@ -1,89 +0,0 @@ -from typing import Literal - -import numpy as np -import pytest - -import zarr -from zarr.abc.codec import SupportsSyncCodec -from zarr.abc.store import Store -from zarr.codecs import BytesCodec -from zarr.core.array_spec import ArrayConfig, ArraySpec -from zarr.core.buffer import NDBuffer, default_buffer_prototype -from zarr.core.dtype import get_data_type_from_native_dtype -from zarr.storage import StorePath - -from .test_codecs import _AsyncArrayProxy - - -@pytest.mark.filterwarnings("ignore:The endianness of the requested serializer") -@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -@pytest.mark.parametrize("endian", ["big", "little"]) -async def test_endian(store: Store, endian: Literal["big", "little"]) -> None: - data = np.arange(0, 256, dtype="uint16").reshape((16, 16)) - path = "endian" - spath = StorePath(store, path) - a = await zarr.api.asynchronous.create_array( - spath, - shape=data.shape, - chunks=(16, 16), - dtype=data.dtype, - fill_value=0, - chunk_key_encoding={"name": "v2", "separator": "."}, - serializer=BytesCodec(endian=endian), - ) - - await _AsyncArrayProxy(a)[:, :].set(data) - readback_data = await _AsyncArrayProxy(a)[:, :].get() - assert np.array_equal(data, readback_data) - - -def test_bytes_codec_supports_sync() -> None: - assert isinstance(BytesCodec(), SupportsSyncCodec) - - -def test_bytes_codec_sync_roundtrip() -> None: - codec = BytesCodec() - arr = np.arange(100, dtype="float64") - zdtype = get_data_type_from_native_dtype(arr.dtype) - spec = ArraySpec( - shape=arr.shape, - dtype=zdtype, - fill_value=zdtype.cast_scalar(0), - config=ArrayConfig(order="C", write_empty_chunks=True), - prototype=default_buffer_prototype(), - ) - nd_buf: NDBuffer = default_buffer_prototype().nd_buffer.from_numpy_array(arr) - - codec = codec.evolve_from_array_spec(spec) - - encoded = codec._encode_sync(nd_buf, spec) - assert encoded is not None - decoded = codec._decode_sync(encoded, spec) - np.testing.assert_array_equal(arr, decoded.as_numpy_array()) - - -@pytest.mark.filterwarnings("ignore:The endianness of the requested serializer") -@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -@pytest.mark.parametrize("dtype_input_endian", [">u2", "u2", " None: - data = np.arange(0, 256, dtype=dtype_input_endian).reshape((16, 16)) - path = "endian" - spath = StorePath(store, path) - a = await zarr.api.asynchronous.create_array( - spath, - shape=data.shape, - chunks=(16, 16), - dtype="uint16", - fill_value=0, - chunk_key_encoding={"name": "v2", "separator": "."}, - serializer=BytesCodec(endian=dtype_store_endian), - ) - - await _AsyncArrayProxy(a)[:, :].set(data) - readback_data = await _AsyncArrayProxy(a)[:, :].get() - assert np.array_equal(data, readback_data) From aa8663a49676fb0dbdd1a21b82be78eb3c29f596 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 19 Jun 2026 14:48:35 +0200 Subject: [PATCH 364/468] feat![zarr-metadata]: extensive top-level exports (#4083) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat(zarr-metadata): promote curated front door to top-level public API Promote a curated set of names to the top-level `zarr_metadata` namespace so consumers can import spec types directly (e.g. `from zarr_metadata import ArrayMetadataV3, ShardingIndexLocation, BLOSC_CNAME`). Deep submodule paths continue to work unchanged. Several promoted names get clearer spellings now that they appear bare at the top level: `Endian`->`Endianness`, `IndexLocation`->`ShardingIndexLocation`, `RoundingMode`->`CastRoundingMode`, `OutOfRangeMode`->`CastOutOfRangeMode`, `DateTimeUnit`->`NumpyTimeUnit`, `NamedConfig`->`NamedConfigV3`, and `MetadataFieldV3`->`MetadataV3` (matching the name `zarrs` uses for this `name`-or-`{name, configuration}` shape). Also adds the `NUMPY_TIME_UNIT` runtime constant paired with the `NumpyTimeUnit` Literal. Scoped to packages/zarr-metadata only; no zarr-python changes, so no deprecation shims are needed (zarr-python does not yet depend on zarr-metadata). A follow-up zarr-python PR will consume these names. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- .../zarr-metadata/changes/4083.feature.md | 21 ++ .../src/zarr_metadata/__init__.py | 295 +++++++++++++++++- .../src/zarr_metadata/_common.py | 2 +- .../src/zarr_metadata/v3/__init__.py | 4 +- .../src/zarr_metadata/v3/_common.py | 8 +- .../src/zarr_metadata/v3/array.py | 22 +- .../src/zarr_metadata/v3/codec/__init__.py | 2 +- .../src/zarr_metadata/v3/codec/bytes.py | 10 +- .../src/zarr_metadata/v3/codec/cast_value.py | 24 +- .../v3/codec/sharding_indexed.py | 16 +- .../v3/data_type/numpy_datetime64.py | 6 +- .../v3/data_type/numpy_timedelta64.py | 26 +- .../src/zarr_metadata/v3/data_type/struct.py | 4 +- .../zarr-metadata/tests/test_public_api.py | 215 +++++++++++++ .../numpy_timedelta64/test_fixtures.py | 7 + 15 files changed, 606 insertions(+), 56 deletions(-) create mode 100644 packages/zarr-metadata/changes/4083.feature.md create mode 100644 packages/zarr-metadata/tests/test_public_api.py diff --git a/packages/zarr-metadata/changes/4083.feature.md b/packages/zarr-metadata/changes/4083.feature.md new file mode 100644 index 0000000000..c383495c1a --- /dev/null +++ b/packages/zarr-metadata/changes/4083.feature.md @@ -0,0 +1,21 @@ +Promoted a curated "front door" of names to the top-level `zarr_metadata` +namespace, so consumers can write e.g. `from zarr_metadata import +ArrayMetadataV3, ShardingIndexLocation, BLOSC_CNAME` instead of importing from +deep submodule paths. The front door covers every metadata-document TypedDict, +each codec/chunk-grid/chunk-key-encoding canonical type, the full data-type +trio for every dtype, and every constant + `Literal` pair. Deep submodule paths +continue to work unchanged. + +Several promoted names were given clearer, less ambiguous spellings than their +deep-module names, since they now appear bare at the top level: +`Endian`/`ENDIAN` → `Endianness`/`ENDIANNESS`, +`IndexLocation`/`INDEX_LOCATION` → `ShardingIndexLocation`/`SHARDING_INDEX_LOCATION`, +`RoundingMode`/`ROUNDING_MODE` → `CastRoundingMode`/`CAST_ROUNDING_MODE`, +`OutOfRangeMode`/`OUT_OF_RANGE_MODE` → `CastOutOfRangeMode`/`CAST_OUT_OF_RANGE_MODE`, +`DateTimeUnit` → `NumpyTimeUnit`, +`NamedConfig` → `NamedConfigV3`, and +`MetadataFieldV3` → `MetadataV3` (matching the name `zarrs` uses for this +`name`-or-`{name, configuration}` shape). + +Also added the `NUMPY_TIME_UNIT` runtime constant (a `Final` tuple paired with +the `NumpyTimeUnit` Literal) in `zarr_metadata.v3.data_type.numpy_timedelta64`. diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 7c6461500e..46949570a2 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -1,7 +1,9 @@ from importlib.metadata import version -from zarr_metadata._common import JSONValue, NamedConfig +from zarr_metadata._common import JSONValue, NamedConfigV3 from zarr_metadata.v2.array import ( + ARRAY_DIMENSION_SEPARATOR_V2, + ARRAY_ORDER_V2, ArrayDimensionSeparatorV2, ArrayMetadataV2, ArrayMetadataV2Partial, @@ -13,35 +15,320 @@ from zarr_metadata.v2.codec import CodecMetadataV2 from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 from zarr_metadata.v2.group import GroupMetadataV2, GroupMetadataV2Partial, ZGroupMetadata -from zarr_metadata.v3._common import MetadataFieldV3 +from zarr_metadata.v3._common import MetadataV3 from zarr_metadata.v3.array import ArrayMetadataV3, ArrayMetadataV3Partial, ExtensionFieldV3 +from zarr_metadata.v3.chunk_grid.rectilinear import ( + RECTILINEAR_CHUNK_GRID_NAME, + RectilinearChunkGridMetadata, + RectilinearChunkGridName, +) +from zarr_metadata.v3.chunk_grid.regular import ( + REGULAR_CHUNK_GRID_NAME, + RegularChunkGridMetadata, + RegularChunkGridName, +) +from zarr_metadata.v3.chunk_key_encoding.default import ( + DEFAULT_CHUNK_KEY_ENCODING_NAME, + DEFAULT_CHUNK_KEY_ENCODING_SEPARATOR, + DefaultChunkKeyEncodingMetadata, + DefaultChunkKeyEncodingName, + DefaultChunkKeyEncodingSeparator, +) +from zarr_metadata.v3.chunk_key_encoding.v2 import ( + V2_CHUNK_KEY_ENCODING_NAME, + V2_CHUNK_KEY_ENCODING_SEPARATOR, + V2ChunkKeyEncodingMetadata, + V2ChunkKeyEncodingName, + V2ChunkKeyEncodingSeparator, +) +from zarr_metadata.v3.codec.blosc import ( + BLOSC_CNAME, + BLOSC_CODEC_NAME, + BLOSC_SHUFFLE, + BloscCName, + BloscCodecMetadata, + BloscCodecName, + BloscShuffle, +) +from zarr_metadata.v3.codec.bytes import ( + BYTES_CODEC_NAME, + ENDIANNESS, + BytesCodecMetadata, + BytesCodecName, + Endianness, +) +from zarr_metadata.v3.codec.cast_value import ( + CAST_OUT_OF_RANGE_MODE, + CAST_ROUNDING_MODE, + CAST_VALUE_CODEC_NAME, + CastOutOfRangeMode, + CastRoundingMode, + CastValueCodecMetadata, + CastValueCodecName, +) +from zarr_metadata.v3.codec.crc32c import CRC32C_CODEC_NAME, Crc32cCodecMetadata, Crc32cCodecName +from zarr_metadata.v3.codec.gzip import GZIP_CODEC_NAME, GzipCodecMetadata, GzipCodecName +from zarr_metadata.v3.codec.scale_offset import ( + SCALE_OFFSET_CODEC_NAME, + ScaleOffsetCodecMetadata, + ScaleOffsetCodecName, +) +from zarr_metadata.v3.codec.sharding_indexed import ( + SHARDING_INDEX_LOCATION, + SHARDING_INDEXED_CODEC_NAME, + ShardingIndexedCodecMetadata, + ShardingIndexedCodecName, + ShardingIndexLocation, +) +from zarr_metadata.v3.codec.transpose import ( + TRANSPOSE_CODEC_NAME, + TransposeCodecMetadata, + TransposeCodecName, +) +from zarr_metadata.v3.codec.zstd import ZSTD_CODEC_NAME, ZstdCodecMetadata, ZstdCodecName from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 +from zarr_metadata.v3.data_type.bool import ( + BOOL_DATA_TYPE_NAME, + BoolDataTypeName, + BoolFillValue, +) +from zarr_metadata.v3.data_type.bytes import ( + BYTES_DATA_TYPE_NAME, + BytesDataTypeName, + BytesFillValue, +) +from zarr_metadata.v3.data_type.complex64 import ( + COMPLEX64_DATA_TYPE_NAME, + Complex64DataTypeName, + Complex64FillValue, +) +from zarr_metadata.v3.data_type.complex128 import ( + COMPLEX128_DATA_TYPE_NAME, + Complex128DataTypeName, + Complex128FillValue, +) +from zarr_metadata.v3.data_type.float16 import ( + FLOAT16_DATA_TYPE_NAME, + Float16DataTypeName, + Float16FillValue, +) +from zarr_metadata.v3.data_type.float32 import ( + FLOAT32_DATA_TYPE_NAME, + Float32DataTypeName, + Float32FillValue, +) +from zarr_metadata.v3.data_type.float64 import ( + FLOAT64_DATA_TYPE_NAME, + Float64DataTypeName, + Float64FillValue, +) +from zarr_metadata.v3.data_type.int8 import ( + INT8_DATA_TYPE_NAME, + Int8DataTypeName, + Int8FillValue, +) +from zarr_metadata.v3.data_type.int16 import ( + INT16_DATA_TYPE_NAME, + Int16DataTypeName, + Int16FillValue, +) +from zarr_metadata.v3.data_type.int32 import ( + INT32_DATA_TYPE_NAME, + Int32DataTypeName, + Int32FillValue, +) +from zarr_metadata.v3.data_type.int64 import ( + INT64_DATA_TYPE_NAME, + Int64DataTypeName, + Int64FillValue, +) +from zarr_metadata.v3.data_type.numpy_datetime64 import ( + NUMPY_DATETIME64_DATA_TYPE_NAME, + NumpyDatetime64DataTypeName, + NumpyDatetime64FillValue, +) +from zarr_metadata.v3.data_type.numpy_timedelta64 import ( + NUMPY_TIME_UNIT, + NUMPY_TIMEDELTA64_DATA_TYPE_NAME, + NumpyTimedelta64DataTypeName, + NumpyTimedelta64FillValue, + NumpyTimeUnit, +) +from zarr_metadata.v3.data_type.raw import RawBytesDataTypeName, RawBytesFillValue +from zarr_metadata.v3.data_type.string import ( + STRING_DATA_TYPE_NAME, + StringDataTypeName, + StringFillValue, +) +from zarr_metadata.v3.data_type.struct import ( + STRUCT_DATA_TYPE_NAME, + StructDataTypeName, + StructFillValue, +) +from zarr_metadata.v3.data_type.uint8 import ( + UINT8_DATA_TYPE_NAME, + Uint8DataTypeName, + Uint8FillValue, +) +from zarr_metadata.v3.data_type.uint16 import ( + UINT16_DATA_TYPE_NAME, + Uint16DataTypeName, + Uint16FillValue, +) +from zarr_metadata.v3.data_type.uint32 import ( + UINT32_DATA_TYPE_NAME, + Uint32DataTypeName, + Uint32FillValue, +) +from zarr_metadata.v3.data_type.uint64 import ( + UINT64_DATA_TYPE_NAME, + Uint64DataTypeName, + Uint64FillValue, +) from zarr_metadata.v3.group import GroupMetadataV3, GroupMetadataV3Partial __version__ = version("zarr-metadata") __all__ = [ + "ARRAY_DIMENSION_SEPARATOR_V2", + "ARRAY_ORDER_V2", + "BLOSC_CNAME", + "BLOSC_CODEC_NAME", + "BLOSC_SHUFFLE", + "BOOL_DATA_TYPE_NAME", + "BYTES_CODEC_NAME", + "BYTES_DATA_TYPE_NAME", + "CAST_OUT_OF_RANGE_MODE", + "CAST_ROUNDING_MODE", + "CAST_VALUE_CODEC_NAME", + "COMPLEX64_DATA_TYPE_NAME", + "COMPLEX128_DATA_TYPE_NAME", + "CRC32C_CODEC_NAME", + "DEFAULT_CHUNK_KEY_ENCODING_NAME", + "DEFAULT_CHUNK_KEY_ENCODING_SEPARATOR", + "ENDIANNESS", + "FLOAT16_DATA_TYPE_NAME", + "FLOAT32_DATA_TYPE_NAME", + "FLOAT64_DATA_TYPE_NAME", + "GZIP_CODEC_NAME", + "INT8_DATA_TYPE_NAME", + "INT16_DATA_TYPE_NAME", + "INT32_DATA_TYPE_NAME", + "INT64_DATA_TYPE_NAME", + "NUMPY_DATETIME64_DATA_TYPE_NAME", + "NUMPY_TIMEDELTA64_DATA_TYPE_NAME", + "NUMPY_TIME_UNIT", + "RECTILINEAR_CHUNK_GRID_NAME", + "REGULAR_CHUNK_GRID_NAME", + "SCALE_OFFSET_CODEC_NAME", + "SHARDING_INDEXED_CODEC_NAME", + "SHARDING_INDEX_LOCATION", + "STRING_DATA_TYPE_NAME", + "STRUCT_DATA_TYPE_NAME", + "TRANSPOSE_CODEC_NAME", + "UINT8_DATA_TYPE_NAME", + "UINT16_DATA_TYPE_NAME", + "UINT32_DATA_TYPE_NAME", + "UINT64_DATA_TYPE_NAME", + "V2_CHUNK_KEY_ENCODING_NAME", + "V2_CHUNK_KEY_ENCODING_SEPARATOR", + "ZSTD_CODEC_NAME", "ArrayDimensionSeparatorV2", "ArrayMetadataV2", "ArrayMetadataV2Partial", "ArrayMetadataV3", "ArrayMetadataV3Partial", "ArrayOrderV2", + "BloscCName", + "BloscCodecMetadata", + "BloscCodecName", + "BloscShuffle", + "BoolDataTypeName", + "BoolFillValue", + "BytesCodecMetadata", + "BytesCodecName", + "BytesDataTypeName", + "BytesFillValue", + "CastOutOfRangeMode", + "CastRoundingMode", + "CastValueCodecMetadata", + "CastValueCodecName", "CodecMetadataV2", + "Complex64DataTypeName", + "Complex64FillValue", + "Complex128DataTypeName", + "Complex128FillValue", "ConsolidatedMetadataV2", "ConsolidatedMetadataV3", + "Crc32cCodecMetadata", + "Crc32cCodecName", "DataTypeMetadataV2", + "DefaultChunkKeyEncodingMetadata", + "DefaultChunkKeyEncodingName", + "DefaultChunkKeyEncodingSeparator", + "Endianness", "ExtensionFieldV3", + "Float16DataTypeName", + "Float16FillValue", + "Float32DataTypeName", + "Float32FillValue", + "Float64DataTypeName", + "Float64FillValue", "GroupMetadataV2", "GroupMetadataV2Partial", "GroupMetadataV3", "GroupMetadataV3Partial", + "GzipCodecMetadata", + "GzipCodecName", + "Int8DataTypeName", + "Int8FillValue", + "Int16DataTypeName", + "Int16FillValue", + "Int32DataTypeName", + "Int32FillValue", + "Int64DataTypeName", + "Int64FillValue", "JSONValue", - "MetadataFieldV3", - "NamedConfig", + "MetadataV3", + "NamedConfigV3", + "NumpyDatetime64DataTypeName", + "NumpyDatetime64FillValue", + "NumpyTimeUnit", + "NumpyTimedelta64DataTypeName", + "NumpyTimedelta64FillValue", + "RawBytesDataTypeName", + "RawBytesFillValue", + "RectilinearChunkGridMetadata", + "RectilinearChunkGridName", + "RegularChunkGridMetadata", + "RegularChunkGridName", + "ScaleOffsetCodecMetadata", + "ScaleOffsetCodecName", + "ShardingIndexLocation", + "ShardingIndexedCodecMetadata", + "ShardingIndexedCodecName", + "StringDataTypeName", + "StringFillValue", + "StructDataTypeName", + "StructFillValue", + "TransposeCodecMetadata", + "TransposeCodecName", + "Uint8DataTypeName", + "Uint8FillValue", + "Uint16DataTypeName", + "Uint16FillValue", + "Uint32DataTypeName", + "Uint32FillValue", + "Uint64DataTypeName", + "Uint64FillValue", + "V2ChunkKeyEncodingMetadata", + "V2ChunkKeyEncodingName", + "V2ChunkKeyEncodingSeparator", "ZArrayMetadata", "ZAttrsMetadata", "ZGroupMetadata", + "ZstdCodecMetadata", + "ZstdCodecName", "__version__", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/_common.py b/packages/zarr-metadata/src/zarr_metadata/_common.py index f6064d863f..598a12e80c 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_common.py +++ b/packages/zarr-metadata/src/zarr_metadata/_common.py @@ -24,7 +24,7 @@ """ -class NamedConfig(TypedDict): +class NamedConfigV3(TypedDict): """ Externally-tagged union member for a metadata field. diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py index 7699aa744d..c897f20d52 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py @@ -1,6 +1,6 @@ """Zarr v3 metadata types.""" -from zarr_metadata.v3._common import MetadataFieldV3 +from zarr_metadata.v3._common import MetadataV3 from zarr_metadata.v3.array import ArrayMetadataV3, ExtensionFieldV3 from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 from zarr_metadata.v3.group import GroupMetadataV3 @@ -10,5 +10,5 @@ "ConsolidatedMetadataV3", "ExtensionFieldV3", "GroupMetadataV3", - "MetadataFieldV3", + "MetadataV3", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/_common.py b/packages/zarr-metadata/src/zarr_metadata/v3/_common.py index 8d8e21616a..3424587a43 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/_common.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/_common.py @@ -2,12 +2,12 @@ This module is private (underscore-prefixed) and exists to avoid circular imports between leaf modules and sub-package `__init__.py` re-exports. -Public consumers should import `MetadataFieldV3` from `zarr_metadata.v3`. +Public consumers should import `MetadataV3` from `zarr_metadata.v3`. """ -from zarr_metadata._common import NamedConfig +from zarr_metadata._common import NamedConfigV3 -MetadataFieldV3 = str | NamedConfig +MetadataV3 = str | NamedConfigV3 """The JSON shape of any v3 metadata extension-point entry: either a bare short-hand name string or a `{name, configuration}` envelope. @@ -19,5 +19,5 @@ __all__ = [ - "MetadataFieldV3", + "MetadataV3", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index d9cea4aef4..a8b0fa3358 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -6,7 +6,7 @@ from typing_extensions import TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v3._common import MetadataFieldV3 +from zarr_metadata.v3._common import MetadataV3 class ExtensionFieldV3(TypedDict, extra_items=JSONValue): # type: ignore[call-arg] @@ -52,14 +52,14 @@ class ArrayMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[ zarr_format: Literal[3] node_type: Literal["array"] - data_type: MetadataFieldV3 + data_type: MetadataV3 shape: tuple[int, ...] - chunk_grid: MetadataFieldV3 - chunk_key_encoding: MetadataFieldV3 + chunk_grid: MetadataV3 + chunk_key_encoding: MetadataV3 fill_value: JSONValue - codecs: tuple[MetadataFieldV3, ...] + codecs: tuple[MetadataV3, ...] attributes: NotRequired[Mapping[str, JSONValue]] - storage_transformers: NotRequired[tuple[MetadataFieldV3, ...]] + storage_transformers: NotRequired[tuple[MetadataV3, ...]] dimension_names: NotRequired[tuple[str | None, ...]] @@ -88,14 +88,14 @@ class ArrayMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV zarr_format: Literal[3] node_type: Literal["array"] - data_type: MetadataFieldV3 + data_type: MetadataV3 shape: tuple[int, ...] - chunk_grid: MetadataFieldV3 - chunk_key_encoding: MetadataFieldV3 + chunk_grid: MetadataV3 + chunk_key_encoding: MetadataV3 fill_value: JSONValue - codecs: tuple[MetadataFieldV3, ...] + codecs: tuple[MetadataV3, ...] attributes: NotRequired[Mapping[str, JSONValue]] - storage_transformers: NotRequired[tuple[MetadataFieldV3, ...]] + storage_transformers: NotRequired[tuple[MetadataV3, ...]] dimension_names: NotRequired[tuple[str | None, ...]] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py index 8cc819496d..b4f357117f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py @@ -11,7 +11,7 @@ `CodecConfiguration`, etc., import directly from the leaf submodule. For the field-level "any codec entry" alias (used in array metadata's -`codecs` list and in sharding's inner pipelines), import `MetadataFieldV3` +`codecs` list and in sharding's inner pipelines), import `MetadataV3` from `zarr_metadata.v3`. See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/index.html diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py index 522cbe10f5..04e746f898 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/bytes.py @@ -14,10 +14,10 @@ BytesCodecName = Literal["bytes"] """Literal type of the `name` field of the `bytes` codec.""" -Endian = Literal["little", "big"] +Endianness = Literal["little", "big"] """Literal type of byte order of multi-byte numeric data.""" -ENDIAN: Final = ("little", "big") +ENDIANNESS: Final = ("little", "big") """Tuple of permitted values for the `endian` field of the `bytes` codec.""" @@ -28,7 +28,7 @@ class BytesCodecConfiguration(TypedDict): The `endian` field is required for multi-byte data types. """ - endian: NotRequired[Endian] + endian: NotRequired[Endianness] class BytesCodecObject(TypedDict): @@ -55,10 +55,10 @@ class BytesCodecObject(TypedDict): __all__ = [ "BYTES_CODEC_NAME", - "ENDIAN", + "ENDIANNESS", "BytesCodecConfiguration", "BytesCodecMetadata", "BytesCodecName", "BytesCodecObject", - "Endian", + "Endianness", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py index fd6fb2ee4a..7e9b071669 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py @@ -9,7 +9,7 @@ from typing_extensions import TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v3._common import MetadataFieldV3 +from zarr_metadata.v3._common import MetadataV3 CAST_VALUE_CODEC_NAME: Final = "cast_value" """The `name` field value of the `cast_value` codec.""" @@ -17,7 +17,7 @@ CastValueCodecName = Literal["cast_value"] """Literal type of the `name` field of the `cast_value` codec.""" -RoundingMode = Literal[ +CastRoundingMode = Literal[ "nearest-even", "towards-zero", "towards-positive", @@ -29,7 +29,7 @@ Defaults to `"nearest-even"` if absent. """ -ROUNDING_MODE: Final = ( +CAST_ROUNDING_MODE: Final = ( "nearest-even", "towards-zero", "towards-positive", @@ -38,13 +38,13 @@ ) """Tuple of permitted values for the `rounding` field of the `cast_value` codec.""" -OutOfRangeMode = Literal["clamp", "wrap"] +CastOutOfRangeMode = Literal["clamp", "wrap"] """Literal type of permitted values for the `out_of_range` configuration field. If absent, out-of-range values are an encoding/decoding error. """ -OUT_OF_RANGE_MODE: Final = ("clamp", "wrap") +CAST_OUT_OF_RANGE_MODE: Final = ("clamp", "wrap") """Tuple of permitted values for the `out_of_range` field of the `cast_value` codec.""" ScalarMapEntry = tuple[JSONValue, JSONValue] @@ -71,9 +71,9 @@ class CastValueCodecConfiguration(TypedDict): bare-string primitive name or a `{name, configuration}` envelope. """ - data_type: MetadataFieldV3 - rounding: NotRequired[RoundingMode] - out_of_range: NotRequired[OutOfRangeMode] + data_type: MetadataV3 + rounding: NotRequired[CastRoundingMode] + out_of_range: NotRequired[CastOutOfRangeMode] scalar_map: NotRequired[ScalarMap] @@ -93,15 +93,15 @@ class CastValueCodecObject(TypedDict): __all__ = [ + "CAST_OUT_OF_RANGE_MODE", + "CAST_ROUNDING_MODE", "CAST_VALUE_CODEC_NAME", - "OUT_OF_RANGE_MODE", - "ROUNDING_MODE", + "CastOutOfRangeMode", + "CastRoundingMode", "CastValueCodecConfiguration", "CastValueCodecMetadata", "CastValueCodecName", "CastValueCodecObject", - "OutOfRangeMode", - "RoundingMode", "ScalarMap", "ScalarMapEntry", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py index 93a0774e4e..a1488f7c30 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py @@ -8,7 +8,7 @@ from typing_extensions import TypedDict -from zarr_metadata.v3._common import MetadataFieldV3 +from zarr_metadata.v3._common import MetadataV3 SHARDING_INDEXED_CODEC_NAME: Final = "sharding_indexed" """The `name` field value of the `sharding_indexed` codec.""" @@ -16,10 +16,10 @@ ShardingIndexedCodecName = Literal["sharding_indexed"] """Literal type of the `name` field of the `sharding_indexed` codec.""" -IndexLocation = Literal["start", "end"] +ShardingIndexLocation = Literal["start", "end"] """Literal type of the position of the shard index within the encoded shard.""" -INDEX_LOCATION: Final = ("start", "end") +SHARDING_INDEX_LOCATION: Final = ("start", "end") """Tuple of permitted values for the `index_location` field of the `sharding_indexed` codec.""" @@ -40,9 +40,9 @@ class ShardingIndexedCodecConfiguration(TypedDict): """ chunk_shape: tuple[int, ...] - codecs: tuple[MetadataFieldV3, ...] - index_codecs: tuple[MetadataFieldV3, ...] - index_location: NotRequired[IndexLocation] + codecs: tuple[MetadataV3, ...] + index_codecs: tuple[MetadataV3, ...] + index_location: NotRequired[ShardingIndexLocation] class ShardingIndexedCodecObject(TypedDict): @@ -61,9 +61,9 @@ class ShardingIndexedCodecObject(TypedDict): """ __all__ = [ - "INDEX_LOCATION", "SHARDING_INDEXED_CODEC_NAME", - "IndexLocation", + "SHARDING_INDEX_LOCATION", + "ShardingIndexLocation", "ShardingIndexedCodecConfiguration", "ShardingIndexedCodecMetadata", "ShardingIndexedCodecName", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py index 243d5fb6f6..8784160f71 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_datetime64.py @@ -14,7 +14,7 @@ NumpyDatetime64DataTypeName = Literal["numpy.datetime64"] """Literal type of the `name` field of the `numpy.datetime64` data type.""" -DateTimeUnit = Literal[ +NumpyTimeUnit = Literal[ "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" ] """Time unit codes used by numpy.datetime64.""" @@ -32,7 +32,7 @@ class NumpyDatetime64Configuration(TypedDict): The multiplier relative to the unit. """ - unit: ReadOnly[DateTimeUnit] + unit: ReadOnly[NumpyTimeUnit] scale_factor: ReadOnly[int] @@ -52,9 +52,9 @@ class NumpyDatetime64(TypedDict): __all__ = [ "NUMPY_DATETIME64_DATA_TYPE_NAME", - "DateTimeUnit", "NumpyDatetime64", "NumpyDatetime64Configuration", "NumpyDatetime64DataTypeName", "NumpyDatetime64FillValue", + "NumpyTimeUnit", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py index 41e35e7aae..f5c8c77bf8 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/numpy_timedelta64.py @@ -14,11 +14,30 @@ NumpyTimedelta64DataTypeName = Literal["numpy.timedelta64"] """Literal type of the `name` field of the `numpy.timedelta64` data type.""" -DateTimeUnit = Literal[ +NumpyTimeUnit = Literal[ "Y", "M", "W", "D", "h", "m", "s", "ms", "us", "μs", "ns", "ps", "fs", "as", "generic" ] """Time unit codes used by numpy.timedelta64.""" +NUMPY_TIME_UNIT: Final = ( + "Y", + "M", + "W", + "D", + "h", + "m", + "s", + "ms", + "us", + "μs", + "ns", + "ps", + "fs", + "as", + "generic", +) +"""Runtime tuple of the permitted `numpy.timedelta64`/`numpy.datetime64` unit strings.""" + class NumpyTimedelta64Configuration(TypedDict): """ @@ -32,7 +51,7 @@ class NumpyTimedelta64Configuration(TypedDict): The multiplier relative to the unit. """ - unit: ReadOnly[DateTimeUnit] + unit: ReadOnly[NumpyTimeUnit] scale_factor: ReadOnly[int] @@ -52,7 +71,8 @@ class NumpyTimedelta64(TypedDict): __all__ = [ "NUMPY_TIMEDELTA64_DATA_TYPE_NAME", - "DateTimeUnit", + "NUMPY_TIME_UNIT", + "NumpyTimeUnit", "NumpyTimedelta64", "NumpyTimedelta64Configuration", "NumpyTimedelta64DataTypeName", diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py index 282bcc83d6..5291e5c309 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py @@ -10,7 +10,7 @@ from typing_extensions import ReadOnly, TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v3._common import MetadataFieldV3 +from zarr_metadata.v3._common import MetadataV3 STRUCT_DATA_TYPE_NAME: Final = "struct" """The `name` field value of the `struct` data type.""" @@ -33,7 +33,7 @@ class StructField(TypedDict): """ name: ReadOnly[str] - data_type: ReadOnly[MetadataFieldV3] + data_type: ReadOnly[MetadataV3] class StructConfiguration(TypedDict): diff --git a/packages/zarr-metadata/tests/test_public_api.py b/packages/zarr-metadata/tests/test_public_api.py new file mode 100644 index 0000000000..d3270579c3 --- /dev/null +++ b/packages/zarr-metadata/tests/test_public_api.py @@ -0,0 +1,215 @@ +"""Test that the curated front-door names are accessible from the top-level zarr_metadata package.""" + +import re +from typing import get_args + +import zarr_metadata as zm + + +def _group_rank(s: str) -> int: + """RUF022 groups `__all__` as: SCREAMING_SNAKE (0), then TitleCase (1), then dunders (2). + + The exact intra-group ordering is ruff's own natural sort and is enforced by + ruff itself (pre-commit + CI); this test only asserts the grouping, not the + fragile tie-breaking, so it can't drift out of sync with ruff's implementation. + """ + if s.startswith("__") and s.endswith("__"): + return 2 + stripped = re.sub(r"[\d_]", "", s) + return 0 if stripped.isupper() else 1 + + +EXPECTED = [ + # Category A — metadata-document types + "ArrayMetadataV2", + "ArrayMetadataV2Partial", + "ZArrayMetadata", + "GroupMetadataV2", + "GroupMetadataV2Partial", + "ZGroupMetadata", + "ConsolidatedMetadataV2", + "ZAttrsMetadata", + "CodecMetadataV2", + "ArrayMetadataV3", + "ArrayMetadataV3Partial", + "ExtensionFieldV3", + "GroupMetadataV3", + "GroupMetadataV3Partial", + "ConsolidatedMetadataV3", + "NamedConfigV3", + "MetadataV3", + "JSONValue", + # v2 data-type encoding union + "DataTypeMetadataV2", + # Category B — codec canonical unions + "BloscCodecMetadata", + "BytesCodecMetadata", + "CastValueCodecMetadata", + "Crc32cCodecMetadata", + "GzipCodecMetadata", + "ScaleOffsetCodecMetadata", + "ShardingIndexedCodecMetadata", + "TransposeCodecMetadata", + "ZstdCodecMetadata", + # Category C — grid/key canonical unions + "RegularChunkGridMetadata", + "RectilinearChunkGridMetadata", + "DefaultChunkKeyEncodingMetadata", + "V2ChunkKeyEncodingMetadata", + # Category D — dtype trios + # bool + "BoolDataTypeName", + "BOOL_DATA_TYPE_NAME", + "BoolFillValue", + # int8/16/32/64 + "Int8DataTypeName", + "INT8_DATA_TYPE_NAME", + "Int8FillValue", + "Int16DataTypeName", + "INT16_DATA_TYPE_NAME", + "Int16FillValue", + "Int32DataTypeName", + "INT32_DATA_TYPE_NAME", + "Int32FillValue", + "Int64DataTypeName", + "INT64_DATA_TYPE_NAME", + "Int64FillValue", + # uint8/16/32/64 (actual casing is Uint, not UInt) + "Uint8DataTypeName", + "UINT8_DATA_TYPE_NAME", + "Uint8FillValue", + "Uint16DataTypeName", + "UINT16_DATA_TYPE_NAME", + "Uint16FillValue", + "Uint32DataTypeName", + "UINT32_DATA_TYPE_NAME", + "Uint32FillValue", + "Uint64DataTypeName", + "UINT64_DATA_TYPE_NAME", + "Uint64FillValue", + # float16/32/64 + "Float16DataTypeName", + "FLOAT16_DATA_TYPE_NAME", + "Float16FillValue", + "Float32DataTypeName", + "FLOAT32_DATA_TYPE_NAME", + "Float32FillValue", + "Float64DataTypeName", + "FLOAT64_DATA_TYPE_NAME", + "Float64FillValue", + # complex64/128 + "Complex64DataTypeName", + "COMPLEX64_DATA_TYPE_NAME", + "Complex64FillValue", + "Complex128DataTypeName", + "COMPLEX128_DATA_TYPE_NAME", + "Complex128FillValue", + # bytes + "BytesDataTypeName", + "BYTES_DATA_TYPE_NAME", + "BytesFillValue", + # string + "StringDataTypeName", + "STRING_DATA_TYPE_NAME", + "StringFillValue", + # numpy_datetime64 + "NumpyDatetime64DataTypeName", + "NUMPY_DATETIME64_DATA_TYPE_NAME", + "NumpyDatetime64FillValue", + # numpy_timedelta64 + "NumpyTimedelta64DataTypeName", + "NUMPY_TIMEDELTA64_DATA_TYPE_NAME", + "NumpyTimedelta64FillValue", + # struct + "StructDataTypeName", + "STRUCT_DATA_TYPE_NAME", + "StructFillValue", + # raw (no _DATA_TYPE_NAME constant) + "RawBytesDataTypeName", + "RawBytesFillValue", + # Category E — constant+Literal pairs + "ARRAY_ORDER_V2", + "ArrayOrderV2", + "ARRAY_DIMENSION_SEPARATOR_V2", + "ArrayDimensionSeparatorV2", + "ENDIANNESS", + "Endianness", + "BYTES_CODEC_NAME", + "BytesCodecName", + "BLOSC_CODEC_NAME", + "BloscCodecName", + "BLOSC_CNAME", + "BloscCName", + "BLOSC_SHUFFLE", + "BloscShuffle", + "CAST_ROUNDING_MODE", + "CastRoundingMode", + "CAST_OUT_OF_RANGE_MODE", + "CastOutOfRangeMode", + "CAST_VALUE_CODEC_NAME", + "CastValueCodecName", + "CRC32C_CODEC_NAME", + "Crc32cCodecName", + "GZIP_CODEC_NAME", + "GzipCodecName", + "SCALE_OFFSET_CODEC_NAME", + "ScaleOffsetCodecName", + "SHARDING_INDEX_LOCATION", + "ShardingIndexLocation", + "SHARDING_INDEXED_CODEC_NAME", + "ShardingIndexedCodecName", + "TRANSPOSE_CODEC_NAME", + "TransposeCodecName", + "ZSTD_CODEC_NAME", + "ZstdCodecName", + "REGULAR_CHUNK_GRID_NAME", + "RegularChunkGridName", + "RECTILINEAR_CHUNK_GRID_NAME", + "RectilinearChunkGridName", + "DEFAULT_CHUNK_KEY_ENCODING_NAME", + "DefaultChunkKeyEncodingName", + "DEFAULT_CHUNK_KEY_ENCODING_SEPARATOR", + "DefaultChunkKeyEncodingSeparator", + "V2_CHUNK_KEY_ENCODING_NAME", + "V2ChunkKeyEncodingName", + "V2_CHUNK_KEY_ENCODING_SEPARATOR", + "V2ChunkKeyEncodingSeparator", + "NUMPY_TIME_UNIT", + "NumpyTimeUnit", +] + + +def test_front_door_names_public() -> None: + missing = [n for n in EXPECTED if n not in zm.__all__ or not hasattr(zm, n)] + assert not missing, f"missing from top-level API: {missing}" + + +def test_front_door_is_exactly_expected() -> None: + """`__all__` must contain exactly the curated names (plus `__version__`). + + Guards against a name being promoted to the front door without a + corresponding, deliberate entry in `EXPECTED` — i.e. an accidental + addition to the public API surface. + """ + assert set(zm.__all__) - {"__version__"} == set(EXPECTED) + + +def test_all_is_grouped_and_unique() -> None: + ranks = [_group_rank(n) for n in zm.__all__] + assert ranks == sorted(ranks), "`__all__` groups out of order (SCREAMING, TitleCase, dunder)" + assert len(zm.__all__) == len(set(zm.__all__)) + + +def test_promoted_pairs_drift() -> None: + pairs = [ + (zm.ENDIANNESS, zm.Endianness), + (zm.BLOSC_CNAME, zm.BloscCName), + (zm.BLOSC_SHUFFLE, zm.BloscShuffle), + (zm.SHARDING_INDEX_LOCATION, zm.ShardingIndexLocation), + (zm.NUMPY_TIME_UNIT, zm.NumpyTimeUnit), + (zm.CAST_ROUNDING_MODE, zm.CastRoundingMode), + (zm.CAST_OUT_OF_RANGE_MODE, zm.CastOutOfRangeMode), + (zm.ARRAY_ORDER_V2, zm.ArrayOrderV2), + ] + for const, lit in pairs: + assert set(const) == set(get_args(lit)) diff --git a/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/test_fixtures.py b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/test_fixtures.py index 1d4bd86a2d..2a6c651582 100644 --- a/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/test_fixtures.py +++ b/packages/zarr-metadata/tests/v3/data_type/numpy_timedelta64/test_fixtures.py @@ -4,13 +4,16 @@ import json from pathlib import Path +from typing import get_args import pytest from pydantic import TypeAdapter from zarr_metadata.v3.data_type.numpy_timedelta64 import ( + NUMPY_TIME_UNIT, NumpyTimedelta64, NumpyTimedelta64FillValue, + NumpyTimeUnit, ) DIR = Path(__file__).parent @@ -24,3 +27,7 @@ def test_data_type() -> None: @pytest.mark.parametrize("case", FILL_VALUES.values(), ids=list(FILL_VALUES)) def test_fill_value(case: object) -> None: TypeAdapter(NumpyTimedelta64FillValue).validate_python(case) + + +def test_time_unit_constant_matches_literal() -> None: + assert set(NUMPY_TIME_UNIT) == set(get_args(NumpyTimeUnit)) From 4e79f1bca6cb0fb4a1e763ae8b2706a17d0fde7e Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 19 Jun 2026 15:11:34 +0200 Subject: [PATCH 365/468] zarr metadata 0.3.0 (#4084) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore(zarr-metadata): render 0.3.0 changelog Co-Authored-By: Claude Opus 4.7 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.7 (1M context) --- packages/zarr-metadata/CHANGELOG.md | 28 +++++++++++++++++++ packages/zarr-metadata/changes/4037.misc.md | 1 - .../zarr-metadata/changes/4083.feature.md | 21 -------------- 3 files changed, 28 insertions(+), 22 deletions(-) delete mode 100644 packages/zarr-metadata/changes/4037.misc.md delete mode 100644 packages/zarr-metadata/changes/4083.feature.md diff --git a/packages/zarr-metadata/CHANGELOG.md b/packages/zarr-metadata/CHANGELOG.md index 03e744470b..a3ff1177a0 100644 --- a/packages/zarr-metadata/CHANGELOG.md +++ b/packages/zarr-metadata/CHANGELOG.md @@ -2,6 +2,34 @@ +## 0.3.0 (2026-06-19) + +### Deprecations and Removals + +- Introduces a new `JSONValue` type that models python objects that serialize directly to JSON. This type is used to annotate the contents of `attributes` and `fill_value` fields, replacing the use of the overly wide `object` type. This is technically a breaking change. ([#4037](https://github.com/zarr-developers/zarr-python/issues/4037)) +- Promoted a curated "front door" of names to the top-level `zarr_metadata` + namespace, so consumers can write e.g. `from zarr_metadata import + ArrayMetadataV3, ShardingIndexLocation, BLOSC_CNAME` instead of importing from + deep submodule paths. The front door covers every metadata-document TypedDict, + each codec/chunk-grid/chunk-key-encoding canonical type, the full data-type + trio for every dtype, and every constant + `Literal` pair. Deep submodule paths + continue to work unchanged. + + Several promoted names were given clearer, less ambiguous spellings than their + deep-module names, since they now appear bare at the top level: + `Endian`/`ENDIAN` → `Endianness`/`ENDIANNESS`, + `IndexLocation`/`INDEX_LOCATION` → `ShardingIndexLocation`/`SHARDING_INDEX_LOCATION`, + `RoundingMode`/`ROUNDING_MODE` → `CastRoundingMode`/`CAST_ROUNDING_MODE`, + `OutOfRangeMode`/`OUT_OF_RANGE_MODE` → `CastOutOfRangeMode`/`CAST_OUT_OF_RANGE_MODE`, + `DateTimeUnit` → `NumpyTimeUnit`, + `NamedConfig` → `NamedConfigV3`, and + `MetadataFieldV3` → `MetadataV3` (matching the name `zarrs` uses for this + `name`-or-`{name, configuration}` shape). + + Also added the `NUMPY_TIME_UNIT` runtime constant (a `Final` tuple paired with + the `NumpyTimeUnit` Literal) in `zarr_metadata.v3.data_type.numpy_timedelta64`. ([#4083](https://github.com/zarr-developers/zarr-python/issues/4083)) + + ## 0.2.0 (2026-05-19) ### Bugfixes diff --git a/packages/zarr-metadata/changes/4037.misc.md b/packages/zarr-metadata/changes/4037.misc.md deleted file mode 100644 index fee5c69cca..0000000000 --- a/packages/zarr-metadata/changes/4037.misc.md +++ /dev/null @@ -1 +0,0 @@ -Introduces a new `JSONValue` type that models python objects that serialize directly to JSON. This type is used to annotate the contents of `attributes` and `fill_value` fields, replacing the use of the overly wide `object` type. This is technically a breaking change. \ No newline at end of file diff --git a/packages/zarr-metadata/changes/4083.feature.md b/packages/zarr-metadata/changes/4083.feature.md deleted file mode 100644 index c383495c1a..0000000000 --- a/packages/zarr-metadata/changes/4083.feature.md +++ /dev/null @@ -1,21 +0,0 @@ -Promoted a curated "front door" of names to the top-level `zarr_metadata` -namespace, so consumers can write e.g. `from zarr_metadata import -ArrayMetadataV3, ShardingIndexLocation, BLOSC_CNAME` instead of importing from -deep submodule paths. The front door covers every metadata-document TypedDict, -each codec/chunk-grid/chunk-key-encoding canonical type, the full data-type -trio for every dtype, and every constant + `Literal` pair. Deep submodule paths -continue to work unchanged. - -Several promoted names were given clearer, less ambiguous spellings than their -deep-module names, since they now appear bare at the top level: -`Endian`/`ENDIAN` → `Endianness`/`ENDIANNESS`, -`IndexLocation`/`INDEX_LOCATION` → `ShardingIndexLocation`/`SHARDING_INDEX_LOCATION`, -`RoundingMode`/`ROUNDING_MODE` → `CastRoundingMode`/`CAST_ROUNDING_MODE`, -`OutOfRangeMode`/`OUT_OF_RANGE_MODE` → `CastOutOfRangeMode`/`CAST_OUT_OF_RANGE_MODE`, -`DateTimeUnit` → `NumpyTimeUnit`, -`NamedConfig` → `NamedConfigV3`, and -`MetadataFieldV3` → `MetadataV3` (matching the name `zarrs` uses for this -`name`-or-`{name, configuration}` shape). - -Also added the `NUMPY_TIME_UNIT` runtime constant (a `Final` tuple paired with -the `NumpyTimeUnit` Literal) in `zarr_metadata.v3.data_type.numpy_timedelta64`. From 4427290f47707f2fcfc55f3e430abf744d6abfc1 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 22 Jun 2026 11:55:27 +0200 Subject: [PATCH 366/468] Claude/py312 modernizations (#4087) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Python 3.12 modernizations: itertools.batched, collections.abc.Buffer, math.prod, pathlib - Replace hand-rolled batched() in codec_pipeline.py with itertools.batched (stdlib 3.12+) - Replace typing_extensions.Buffer with collections.abc.Buffer in crc32c_.py - Remove unused ParamSpec / P from core/sync.py - Replace functools.reduce(operator.mul) with math.prod in common.product(), indexing.py CoordinateIndexer.__init__, array.AsyncArray.size, and chunk_grids._guess_num_chunks_per_axis_shard - Replace os.path.exists / os.path.getsize with pathlib equivalents in storage/_local.py Co-Authored-By: Claude Fable 5 --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 --- src/zarr/codecs/crc32c_.py | 10 +++------- src/zarr/core/array.py | 3 ++- src/zarr/core/chunk_grids.py | 2 +- src/zarr/core/codec_pipeline.py | 10 +--------- src/zarr/core/common.py | 4 +--- src/zarr/core/indexing.py | 6 +++--- src/zarr/core/sync.py | 4 ---- src/zarr/storage/_local.py | 4 ++-- 8 files changed, 13 insertions(+), 30 deletions(-) diff --git a/src/zarr/codecs/crc32c_.py b/src/zarr/codecs/crc32c_.py index ebe2ac8f7a..7d41e11637 100644 --- a/src/zarr/codecs/crc32c_.py +++ b/src/zarr/codecs/crc32c_.py @@ -1,11 +1,11 @@ from __future__ import annotations +from collections.abc import Buffer as ABCBuffer from dataclasses import dataclass from typing import TYPE_CHECKING, cast import google_crc32c import numpy as np -import typing_extensions from zarr.abc.codec import BytesBytesCodec from zarr.core.common import JSON, parse_named_configuration @@ -41,9 +41,7 @@ def _decode_sync( inner_bytes = data[:-4] # Need to do a manual cast until https://github.com/numpy/numpy/issues/26783 is resolved - computed_checksum = np.uint32( - google_crc32c.value(cast("typing_extensions.Buffer", inner_bytes)) - ).tobytes() + computed_checksum = np.uint32(google_crc32c.value(cast(ABCBuffer, inner_bytes))).tobytes() stored_checksum = bytes(crc32_bytes) if computed_checksum != stored_checksum: raise ValueError( @@ -65,9 +63,7 @@ def _encode_sync( ) -> Buffer | None: data = chunk_bytes.as_numpy_array() # Calculate the checksum and "cast" it to a numpy array - checksum = np.array( - [google_crc32c.value(cast("typing_extensions.Buffer", data))], dtype=np.uint32 - ) + checksum = np.array([google_crc32c.value(cast(ABCBuffer, data))], dtype=np.uint32) # Append the checksum (as bytes) to the data return chunk_spec.prototype.buffer.from_array_like(np.append(data, checksum.view("B"))) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 2c2a4622e3..977520b12e 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -1,5 +1,6 @@ from __future__ import annotations +import math import warnings from asyncio import gather from collections.abc import Iterable, Mapping, Sequence @@ -905,7 +906,7 @@ def size(self) -> int: int Total number of elements in the array """ - return np.prod(self.metadata.shape).item() + return math.prod(self.metadata.shape) @property def filters(self) -> tuple[Numcodec, ...] | tuple[ArrayArrayCodec, ...]: diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 7459908e0a..2cb9762775 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -852,7 +852,7 @@ def _guess_num_chunks_per_axis_shard( ------- The number of chunks per axis. """ - bytes_per_chunk = np.prod(chunk_shape) * item_size + bytes_per_chunk = math.prod(chunk_shape) * item_size if max_bytes < bytes_per_chunk: return 1 num_axes = len(chunk_shape) diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 032703fc03..23ecb0e255 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -1,7 +1,7 @@ from __future__ import annotations from dataclasses import dataclass, field -from itertools import islice, pairwise +from itertools import batched, pairwise from typing import TYPE_CHECKING, Any from warnings import warn @@ -42,14 +42,6 @@ def _unzip2[T, U](iterable: Iterable[tuple[T, U]]) -> tuple[list[T], list[U]]: return (out0, out1) -def batched[T](iterable: Iterable[T], n: int) -> Iterable[tuple[T, ...]]: - if n < 1: - raise ValueError("n must be at least one") - it = iter(iterable) - while batch := tuple(islice(it, n)): - yield batch - - def resolve_batched(codec: Codec, chunk_specs: Iterable[ArraySpec]) -> Iterable[ArraySpec]: return [codec.resolve_metadata(chunk_spec) for chunk_spec in chunk_specs] diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 570e3dfdc3..20664e553e 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -1,9 +1,7 @@ from __future__ import annotations import asyncio -import functools import math -import operator import warnings from collections.abc import Iterable, Mapping, Sequence from enum import Enum @@ -83,7 +81,7 @@ class NamedRequiredConfig[TName: str, TConfig: Mapping[str, object]](TypedDict): def product(tup: tuple[int, ...]) -> int: - return functools.reduce(operator.mul, tup, 1) + return math.prod(tup) def ceildiv(a: float, b: float) -> int: diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index d205d49a11..f6eb495cd9 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -1,12 +1,12 @@ from __future__ import annotations import itertools +import math import numbers -import operator from collections.abc import Iterator, Sequence from dataclasses import dataclass from enum import Enum -from functools import lru_cache, reduce +from functools import lru_cache from types import EllipsisType from typing import ( TYPE_CHECKING, @@ -1187,7 +1187,7 @@ def __init__( cdata_shape = (1,) else: cdata_shape = tuple(g.nchunks for g in dim_grids) - nchunks = reduce(operator.mul, cdata_shape, 1) + nchunks = math.prod(cdata_shape) # some initial normalization selection_normalized = cast("CoordinateSelectionNormalized", ensure_tuple(selection)) diff --git a/src/zarr/core/sync.py b/src/zarr/core/sync.py index 260d4ad841..160950ba64 100644 --- a/src/zarr/core/sync.py +++ b/src/zarr/core/sync.py @@ -8,8 +8,6 @@ from concurrent.futures import ThreadPoolExecutor, wait from typing import TYPE_CHECKING -from typing_extensions import ParamSpec - from zarr.core.config import config if TYPE_CHECKING: @@ -19,8 +17,6 @@ logger = logging.getLogger(__name__) -P = ParamSpec("P") - # From https://github.com/fsspec/filesystem_spec/blob/master/fsspec/asyn.py iothread: list[threading.Thread | None] = [None] # dedicated IO thread diff --git a/src/zarr/storage/_local.py b/src/zarr/storage/_local.py index 3d9882d3db..1627c1a6b5 100644 --- a/src/zarr/storage/_local.py +++ b/src/zarr/storage/_local.py @@ -363,10 +363,10 @@ async def move(self, dest_root: Path | str) -> None: if isinstance(dest_root, str): dest_root = Path(dest_root) os.makedirs(dest_root.parent, exist_ok=True) - if os.path.exists(dest_root): + if dest_root.exists(): raise FileExistsError(f"Destination root {dest_root} already exists.") shutil.move(self.root, dest_root) self.root = dest_root async def getsize(self, key: str) -> int: - return os.path.getsize(self.root / key) + return (self.root / key).stat().st_size From bba0d0fcc8bb19fb92e08182f6a67566b9618ad3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jun 2026 10:07:42 +0000 Subject: [PATCH 367/468] chore(deps): bump CodSpeedHQ/action in the actions group (#4079) Bumps the actions group with 1 update: [CodSpeedHQ/action](https://github.com/codspeedhq/action). Updates `CodSpeedHQ/action` from 4.17.0 to 4.17.5 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/9d332c4d90b43981c3e55ae8e38e68709996240f...c145068895e045cc725ee76fcd2307624b65c3af) --- updated-dependencies: - dependency-name: CodSpeedHQ/action dependency-version: 4.17.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/codspeed.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 4e20b5efa7..115b9d0bf7 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@9d332c4d90b43981c3e55ae8e38e68709996240f # v4.17.0 + uses: CodSpeedHQ/action@c145068895e045cc725ee76fcd2307624b65c3af # v4.17.5 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed From 4862895047140b86851b7ef181120d5e117559a9 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Mon, 22 Jun 2026 06:20:22 -0400 Subject: [PATCH 368/468] chore: add rectilinear hypothesis block indexing tests (#4075) * chore: extend hypothesis block indexing tests for rectilinear grids * Simplify * retain coverage --------- Co-authored-by: Davis Bennett --- changes/4073.misc.md | 1 + src/zarr/testing/strategies.py | 96 +++++++++++++++++++++++++++++----- tests/test_properties.py | 24 ++++----- 3 files changed, 93 insertions(+), 28 deletions(-) create mode 100644 changes/4073.misc.md diff --git a/changes/4073.misc.md b/changes/4073.misc.md new file mode 100644 index 0000000000..bcc6b8281e --- /dev/null +++ b/changes/4073.misc.md @@ -0,0 +1 @@ +Extend the `test_block_indexing` Hypothesis property test to cover rectilinear chunk grids and sharded regular grids, and generalize the `block_indices` strategy in `zarr.testing.strategies` to build its array-space oracle from cumulative chunk offsets (`chunk_sizes` parameter) instead of a uniform chunk size. diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 0ef1ba99bb..f2c83677cc 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -1,3 +1,4 @@ +import itertools import math import sys from collections.abc import Callable, Mapping @@ -599,20 +600,30 @@ def orthogonal_indices( @st.composite def block_indices( - draw: st.DrawFn, *, chunk_grid_shape: tuple[int, ...], chunks: tuple[int, ...] + draw: st.DrawFn, *, chunk_sizes: tuple[tuple[int, ...], ...] ) -> tuple[tuple[int | slice, ...], tuple[slice, ...]]: """ - Strategy for block-selection indexers over a *regular* chunk grid. + Strategy for block-selection indexers over a chunk grid. Block indexing is basic indexing applied to the block grid (the grid of chunks), so each axis is drawn with ``basic_indices`` over that axis's chunk - count from ``chunk_grid_shape`` (e.g. ``Array.cdata_shape``), mirroring how - ``orthogonal_indices`` reuses ``basic_indices`` per axis. Block indexing only - supports integers and step-1 slices whose start references an existing chunk, - so strided slices and slices starting at the grid edge are filtered out. The - array-space translation assumes a regular (uniform) chunk grid; an over-long - stop into a smaller last chunk is left for numpy to clamp when the oracle is - applied. + count, mirroring how ``orthogonal_indices`` reuses ``basic_indices`` per + axis. ``chunk_sizes`` gives the per-chunk data sizes of the array's *outer* + (block) grid for every axis — i.e. ``Array.write_chunk_sizes``, the grid that + ``Array.blocks`` addresses (the shard grid when sharding is used). For + example ``(3, 3, 3, 1)`` for a length-10 axis with a regular chunk size of 3, + or the explicit edges of a rectilinear axis; ``nchunks`` for an axis is + ``len(chunk_sizes[axis])``. + + The array-space translation uses the cumulative sum of those sizes, matching + ``BlockIndexer``'s use of ``dim_grid.chunk_offset``. Because the sizes are + clipped to the array extent, the final offset equals the extent and the + translation is exact for regular (uniform), rectilinear, and sharded grids + alike. + + Block indexing only supports integers and step-1 slices whose start + references an existing chunk, so strided slices and slices starting at the + grid edge are filtered out. Returns ------- @@ -640,24 +651,83 @@ def predicate(value: tuple[Any, ...]) -> bool: block_indexer: list[int | slice] = [] array_indexer: list[slice] = [] - for chunk, nchunks in zip(chunks, chunk_grid_shape, strict=True): - (dim_sel,) = draw( + for sizes in chunk_sizes: + nchunks = len(sizes) + # offsets[i] is the array-space start of chunk i; length nchunks + 1. + offsets = list(itertools.accumulate(sizes, initial=0)) + dim_strategy = ( basic_indices(min_dims=1, shape=(nchunks,), allow_ellipsis=False) # normalize bare ints / slices to a 1-tuple, skip the empty tuple .map(lambda x: (x,) if not isinstance(x, tuple) else x) .filter(bool) .filter(supported(nchunks)) ) + # basic_indices draws slices far more often than bare integers, so the + # integer (single-block) branch below would only be hit on rare draws. + # Union in an explicit integer so it is reliably exercised — keeping + # coverage deterministic under the derandomized ``ci`` Hypothesis profile. + (dim_sel,) = draw( + dim_strategy | st.integers(min_value=0, max_value=nchunks - 1).map(lambda i: (i,)) + ) block_indexer.append(dim_sel) if isinstance(dim_sel, slice): start, stop, _ = dim_sel.indices(nchunks) - array_indexer.append(slice(start * chunk, stop * chunk)) + array_indexer.append(slice(offsets[start], offsets[stop])) else: block = dim_sel % nchunks - array_indexer.append(slice(block * chunk, (block + 1) * chunk)) + array_indexer.append(slice(offsets[block], offsets[block + 1])) return tuple(block_indexer), tuple(array_indexer) +@st.composite +def block_test_arrays( + draw: st.DrawFn, +) -> tuple[Array[Any], np.ndarray[Any, Any]]: + """Draw an array for block-indexing property tests, with its source contents. + + Two arms, selected with equal probability: + + - **regular**: a regular chunk grid, optionally wrapped in sharding. + - **rectilinear**: a variable (rectilinear) chunk grid, always unsharded. + + Returns ``(zarray, nparray)``. The per-axis block sizes the oracle needs are + ``zarray.write_chunk_sizes`` — the array's *outer* (block / shard) grid, which + is exactly the grid ``Array.blocks`` addresses; the caller reads it directly. + """ + chunks: tuple[int, ...] | list[list[int]] + if draw(st.booleans()): + # regular arm, optionally sharded + nparray, chunks = draw( + np_array_and_chunks( + arrays=numpy_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1)) + ) + ) + # min_side=1 chunking guarantees shape // chunk >= 1 on every axis, which + # shard_shapes requires. + shards = draw(st.none() | shard_shapes(shape=nparray.shape, chunk_shape=chunks)) + event("block regular sharded" if shards is not None else "block regular unsharded") + rectilinear = False + else: + # rectilinear arm, always unsharded + event("block rectilinear") + shape = draw(_rectilinear_shapes) + chunks = draw(rectilinear_chunks(shape=shape)) + nparray = draw(numpy_arrays(shapes=st.just(shape), dtype=draw(dtypes()))) + shards, rectilinear = None, True + + store = draw(stores) + with zarr.config.set({"array.rectilinear_chunks": rectilinear}): + zarray = zarr.create_array( + store=store, + shape=nparray.shape, + chunks=chunks, + shards=shards, + dtype=nparray.dtype, + ) + zarray[...] = nparray + return zarray, nparray + + def key_ranges( keys: SearchStrategy[str] = node_names, max_size: int = sys.maxsize ) -> SearchStrategy[list[tuple[str, ByteRequest | None]]]: diff --git a/tests/test_properties.py b/tests/test_properties.py index 994510aca0..3f71fdf493 100644 --- a/tests/test_properties.py +++ b/tests/test_properties.py @@ -26,8 +26,8 @@ arrays, basic_indices, block_indices, + block_test_arrays, complex_rectilinear_arrays, - np_array_and_chunks, numpy_arrays, orthogonal_indices, rectilinear_arrays, @@ -261,27 +261,21 @@ def test_mask_indexing(data: st.DataObject) -> None: @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") @given(data=st.data()) def test_block_indexing(data: st.DataObject) -> None: - # Block indexing addresses whole chunks on a regular grid; the array-space - # oracle in block_indices() assumes regular, unsharded chunks, so build the - # array directly from a regular chunking rather than drawing one that might - # be rectilinear or sharded. - nparray, chunks = data.draw( - np_array_and_chunks(arrays=numpy_arrays(shapes=npst.array_shapes(max_dims=4, min_side=1))) - ) - store = data.draw(stores) - zarray = zarr.create_array(store=store, shape=nparray.shape, chunks=chunks, dtype=nparray.dtype) - zarray[...] = nparray + # Block indexing addresses whole inner chunks. block_indices() builds its + # array-space oracle from cumulative chunk offsets, so it works for regular + # (uniform), rectilinear, and sharded grids alike; block_test_arrays draws + # across that matrix (rectilinear + sharded is unsupported and not drawn). + zarray, nparray = data.draw(block_test_arrays()) - block_indexer, array_indexer = data.draw( - block_indices(chunk_grid_shape=zarray.cdata_shape, chunks=chunks) - ) + block_indexer, array_indexer = data.draw(block_indices(chunk_sizes=zarray.write_chunk_sizes)) expected = nparray[array_indexer] # sync get, via both the .blocks interface and the dedicated method assert_array_equal(expected, zarray.blocks[block_indexer]) assert_array_equal(expected, zarray.get_block_selection(block_indexer)) - # sync set, via both interfaces + # sync set, via both interfaces; sharded set is broken upstream (GH2834) + assume(zarray.shards is None) new_data = data.draw(numpy_arrays(shapes=st.just(expected.shape), dtype=nparray.dtype)) nparray[array_indexer] = new_data zarray.blocks[block_indexer] = new_data From 5fe6327631fd9a94fda4cfbe075b4c801e685c8e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jun 2026 10:41:08 +0000 Subject: [PATCH 369/468] chore(deps): bump pydantic-settings from 2.14.1 to 2.14.2 (#4089) Bumps [pydantic-settings](https://github.com/pydantic/pydantic-settings) from 2.14.1 to 2.14.2. - [Release notes](https://github.com/pydantic/pydantic-settings/releases) - [Commits](https://github.com/pydantic/pydantic-settings/compare/v2.14.1...v2.14.2) --- updated-dependencies: - dependency-name: pydantic-settings dependency-version: 2.14.2 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- uv.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/uv.lock b/uv.lock index adc71bae62..e9a5d6aced 100644 --- a/uv.lock +++ b/uv.lock @@ -2793,16 +2793,16 @@ wheels = [ [[package]] name = "pydantic-settings" -version = "2.14.1" +version = "2.14.2" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "pydantic" }, { name = "python-dotenv" }, { name = "typing-inspection" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/07/60/1d1e59c9c90d54591469ada7d268251f71c24bdb765f1a8a832cee8c6653/pydantic_settings-2.14.1.tar.gz", hash = "sha256:e874d3bec7e787b0c9958277956ed9b4dd5de6a80e162188fdaff7c5e26fd5fa", size = 235551, upload-time = "2026-05-08T13:40:06.542Z" } +sdist = { url = "https://files.pythonhosted.org/packages/5c/b5/8f48e906c3e0205276e8bd8cb7512217a87b2685304d64be27cad5b3019f/pydantic_settings-2.14.2.tar.gz", hash = "sha256:c19dd64b19097f1de80184f0cc7b0272a13ae6e170cbf240a3e27e381ed14a5f", size = 237700, upload-time = "2026-06-19T13:44:56.324Z" } wheels = [ - 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[Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * ci: restrict dependabot uv updates to direct dependencies Stop Dependabot from opening standalone PRs to bump transitive deps in uv.lock. With `allow: dependency-type: direct`, updates are limited to dependencies declared in pyproject.toml; uv.lock is regenerated only as a side effect of those direct bumps. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- .github/dependabot.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 87e80ce7e5..849d44efc9 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -15,8 +15,14 @@ updates: # Keep the pinned dev tooling in pyproject.toml's [dependency-groups] and the # uv.lock current. Without this the exact pins (e.g. pytest) would never be # bumped automatically and would silently rot. + # + # `allow: dependency-type: direct` restricts updates to dependencies declared + # in pyproject.toml. Transitive deps in uv.lock are then only updated as a + # side effect of a direct bump, never via a standalone PR. - package-ecosystem: "uv" directory: "/" + allow: + - dependency-type: "direct" schedule: interval: "weekly" groups: From 486f26a0a9d670831ac38b67bc56c691fc80e5a1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jun 2026 11:22:41 +0000 Subject: [PATCH 371/468] chore(deps): bump msgpack from 1.1.2 to 1.2.1 (#4088) Bumps [msgpack](https://github.com/msgpack/msgpack-python) from 1.1.2 to 1.2.1. - [Release notes](https://github.com/msgpack/msgpack-python/releases) - [Changelog](https://github.com/msgpack/msgpack-python/blob/main/CHANGELOG.md) - [Commits](https://github.com/msgpack/msgpack-python/compare/v1.1.2...v1.2.1) --- updated-dependencies: - dependency-name: msgpack dependency-version: 1.2.1 dependency-type: indirect ... 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Mon, 22 Jun 2026 19:00:53 +0200 Subject: [PATCH 372/468] test: pytest cleanups / modernization (#4093) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: modernize pytest usage (tmp_path, auto asyncio, stable ids, monkeypatch) - Migrate legacy `tmpdir`/`_pytest.compat.LEGACY_PATH` fixtures to the stdlib `tmp_path: pathlib.Path` fixture across conftest and tests; remove the private `_pytest.compat` import and fix an inverted annotation. - Remove redundant `@pytest.mark.asyncio` decorators (asyncio_mode="auto" collects async tests automatically) and drop the now-unused `asyncio` and `s3` entries from the pyproject markers list. - Give `test_docstring_consistent_parameters` stable, human-readable parametrize ids via `pytest.param(..., id=...)`. - Use `monkeypatch.setenv` (auto-restored) instead of manual env save/restore in `tests/test_docs.py`. Co-Authored-By: Claude Opus 4.8 (1M context) * test: restore s3 pytest marker dropped in error The previous commit removed the `s3` marker from pyproject, but it is still applied dynamically to doc-example tests (e.g. the `markers="s3"` block in docs/quick-start.md, via getattr(pytest.mark, name) in tests/test_docs.py). Under `--strict-markers` the unknown mark is escalated to a collection error, breaking the doctests, py=3.12, and "Test complete" CI jobs. The `asyncio` marker removal is kept since pytest-asyncio's auto mode registers that marker itself. Co-Authored-By: Claude Opus 4.8 (1M context) --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- pyproject.toml | 1 - tests/conftest.py | 29 ++++++++++++++--------------- tests/test_api.py | 7 +++---- tests/test_api/test_synchronous.py | 10 ++++++---- tests/test_buffer.py | 5 ----- tests/test_docs.py | 20 +++++++------------- tests/test_group.py | 7 +++---- tests/test_properties.py | 4 ---- tests/test_store/test_core.py | 9 ++++----- tests/test_store/test_local.py | 4 ++-- 10 files changed, 39 insertions(+), 57 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 493b18822a..02e66c67e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -459,7 +459,6 @@ filterwarnings = [ "ignore:Exception ignored ((on calling weakref callback)|(in[\\s\\S]*Session was never entered)):pytest.PytestUnraisableExceptionWarning", ] markers = [ - "asyncio: mark test as asyncio test", "gpu: mark a test as requiring CuPy and GPU", "s3: mark a test as requiring a (mock) S3 backend via moto", "slow_hypothesis: slow hypothesis tests", diff --git a/tests/conftest.py b/tests/conftest.py index 031c4a4283..c02daf7663 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -54,8 +54,6 @@ from contextlib import AbstractContextManager from typing import Any, Literal - from _pytest.compat import LEGACY_PATH - from zarr.abc.codec import Codec from zarr.core.array import CompressorsLike, FiltersLike, SerializerLike, ShardsLike from zarr.core.chunk_key_encodings import ( @@ -121,14 +119,14 @@ def path_type(request: pytest.FixtureRequest) -> Any: # todo: harmonize this with local_store fixture @pytest.fixture -async def store_path(tmpdir: LEGACY_PATH) -> StorePath: - store = await LocalStore.open(str(tmpdir)) +async def store_path(tmp_path: pathlib.Path) -> StorePath: + store = await LocalStore.open(str(tmp_path)) return StorePath(store) @pytest.fixture -async def local_store(tmpdir: LEGACY_PATH) -> LocalStore: - return await LocalStore.open(str(tmpdir)) +async def local_store(tmp_path: pathlib.Path) -> LocalStore: + return await LocalStore.open(str(tmp_path)) @pytest.fixture @@ -142,26 +140,27 @@ async def memory_store() -> MemoryStore: @pytest.fixture -async def zip_store(tmpdir: LEGACY_PATH) -> ZipStore: - return await ZipStore.open(str(tmpdir / "zarr.zip"), mode="w") +async def zip_store(tmp_path: pathlib.Path) -> ZipStore: + return await ZipStore.open(str(tmp_path / "zarr.zip"), mode="w") @pytest.fixture -async def store(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> Store: +async def store(request: pytest.FixtureRequest, tmp_path: pathlib.Path) -> Store: param = request.param - return await parse_store(param, str(tmpdir)) + return await parse_store(param, str(tmp_path)) @pytest.fixture -async def store2(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> Store: +async def store2(request: pytest.FixtureRequest, tmp_path: pathlib.Path) -> Store: """Fixture to create a second store for testing copy operations between stores""" param = request.param - store2_path = tmpdir.mkdir("store2") + store2_path = tmp_path / "store2" + store2_path.mkdir() return await parse_store(param, str(store2_path)) @pytest.fixture(params=["local", "memory", "zip"]) -def sync_store(request: pytest.FixtureRequest, tmp_path: LEGACY_PATH) -> Store: +def sync_store(request: pytest.FixtureRequest, tmp_path: pathlib.Path) -> Store: result = sync(parse_store(request.param, str(tmp_path))) if not isinstance(result, Store): raise TypeError(f"Wrong store class returned by test fixture! got {result} instead") @@ -176,10 +175,10 @@ class AsyncGroupRequest: @pytest.fixture -async def async_group(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> AsyncGroup: +async def async_group(request: pytest.FixtureRequest, tmp_path: pathlib.Path) -> AsyncGroup: param: AsyncGroupRequest = request.param - store = await parse_store(param.store, str(tmpdir)) + store = await parse_store(param.store, str(tmp_path)) return await AsyncGroup.from_store( store, attributes=param.attributes, diff --git a/tests/test_api.py b/tests/test_api.py index 788519969d..121f02c7b2 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -293,7 +293,6 @@ def test_open_array_rectilinear_chunks(tmp_path: Path) -> None: assert z.read_chunk_sizes == ((3, 3, 4), (5, 5)) -@pytest.mark.asyncio async def test_async_array_open_array_not_found() -> None: """Test that AsyncArray.open raises ArrayNotFoundError when array doesn't exist""" store = MemoryStore() @@ -352,16 +351,16 @@ async def test_open_group(memory_store: MemoryStore) -> None: @pytest.mark.parametrize("zarr_format", [None, 2, 3]) -async def test_open_group_unspecified_version(tmpdir: Path, zarr_format: ZarrFormat) -> None: +async def test_open_group_unspecified_version(tmp_path: Path, zarr_format: ZarrFormat) -> None: """Regression test for https://github.com/zarr-developers/zarr-python/issues/2175""" # create a group with specified zarr format (could be 2, 3, or None) _ = await zarr.api.asynchronous.open_group( - store=str(tmpdir), mode="w", zarr_format=zarr_format, attributes={"foo": "bar"} + store=str(tmp_path), mode="w", zarr_format=zarr_format, attributes={"foo": "bar"} ) # now open that group without specifying the format - g2 = await zarr.api.asynchronous.open_group(store=str(tmpdir), mode="r") + g2 = await zarr.api.asynchronous.open_group(store=str(tmp_path), mode="r") assert g2.attrs == {"foo": "bar"} diff --git a/tests/test_api/test_synchronous.py b/tests/test_api/test_synchronous.py index 9e4aab438d..9b15ec32f6 100644 --- a/tests/test_api/test_synchronous.py +++ b/tests/test_api/test_synchronous.py @@ -44,7 +44,7 @@ def test_docstrings_match(callable_name: str) -> None: @pytest.mark.parametrize( ("parameter_name", "array_creation_routines"), [ - ( + pytest.param( ("store", "path"), ( asynchronous.create_array, @@ -54,8 +54,9 @@ def test_docstrings_match(callable_name: str) -> None: zarr.AsyncGroup.create_array, zarr.Group.create_array, ), + id="store-path-create_array_group", ), - ( + pytest.param( ( "store", "path", @@ -65,8 +66,9 @@ def test_docstrings_match(callable_name: str) -> None: synchronous.create, zarr.Group.create, ), + id="store-path-create", ), - ( + pytest.param( ( ( "filters", @@ -87,9 +89,9 @@ def test_docstrings_match(callable_name: str) -> None: zarr.AsyncGroup.create_array, zarr.Group.create_array, ), + id="encoding-params-create_and_array", ), ], - ids=str, ) def test_docstring_consistent_parameters( parameter_name: str, array_creation_routines: tuple[Callable[[Any], Any], ...] diff --git a/tests/test_buffer.py b/tests/test_buffer.py index b50e5abb67..b4a16ed1de 100644 --- a/tests/test_buffer.py +++ b/tests/test_buffer.py @@ -44,7 +44,6 @@ def test_nd_array_like(xp: types.ModuleType) -> None: assert isinstance(ary, NDArrayLike) -@pytest.mark.asyncio async def test_async_array_prototype() -> None: """Test the use of a custom buffer prototype""" @@ -73,7 +72,6 @@ async def test_async_array_prototype() -> None: @gpu_test -@pytest.mark.asyncio async def test_async_array_gpu_prototype() -> None: """Test the use of the GPU buffer prototype""" @@ -97,7 +95,6 @@ async def test_async_array_gpu_prototype() -> None: assert cp.array_equal(expect, got) -@pytest.mark.asyncio async def test_codecs_use_of_prototype() -> None: expect = np.zeros((10, 10), dtype="uint16", order="F") a = await zarr.api.asynchronous.create_array( @@ -126,7 +123,6 @@ async def test_codecs_use_of_prototype() -> None: @gpu_test -@pytest.mark.asyncio async def test_codecs_use_of_gpu_prototype() -> None: expect = cp.zeros((10, 10), dtype="uint16", order="F") a = await zarr.api.asynchronous.create_array( @@ -155,7 +151,6 @@ async def test_codecs_use_of_gpu_prototype() -> None: @gpu_test -@pytest.mark.asyncio async def test_sharding_use_of_gpu_prototype() -> None: with zarr.config.enable_gpu(): expect = cp.zeros((10, 10), dtype="uint16", order="F") diff --git a/tests/test_docs.py b/tests/test_docs.py index 02dca225b0..9c42a0521a 100644 --- a/tests/test_docs.py +++ b/tests/test_docs.py @@ -12,7 +12,6 @@ from __future__ import annotations -import os from collections import defaultdict from pathlib import Path from typing import TYPE_CHECKING, Any @@ -82,7 +81,9 @@ def _session_params(root: Path) -> list[Any]: @pytest.fixture -def docs_s3_backend(moto_server: str) -> Generator[None, None, None]: +def docs_s3_backend( + moto_server: str, monkeypatch: pytest.MonkeyPatch +) -> Generator[None, None, None]: """Point docs S3 examples at the shared moto server (tests/conftest.py) via a process-wide AWS_ENDPOINT_URL, so a block can use a bare s3:// URL with no storage_options (see spike in the design notes). The server lifecycle belongs to the @@ -92,8 +93,7 @@ def docs_s3_backend(moto_server: str) -> Generator[None, None, None]: botocore = pytest.importorskip("botocore") requests = pytest.importorskip("requests") - prev_endpoint = os.environ.get("AWS_ENDPOINT_URL") - os.environ["AWS_ENDPOINT_URL"] = moto_server + monkeypatch.setenv("AWS_ENDPOINT_URL", moto_server) session = botocore.session.Session() client = session.create_client("s3", endpoint_url=moto_server, region_name="us-east-1") @@ -103,15 +103,9 @@ def docs_s3_backend(moto_server: str) -> Generator[None, None, None]: try: yield finally: - # Reset moto state and restore AWS_ENDPOINT_URL; the shared server keeps running - # (the moto_server fixture stops it at session end). - try: - requests.post(f"{moto_server}moto-api/reset") - finally: - if prev_endpoint is None: - os.environ.pop("AWS_ENDPOINT_URL", None) - else: - os.environ["AWS_ENDPOINT_URL"] = prev_endpoint + # Reset moto state; AWS_ENDPOINT_URL is restored automatically by monkeypatch. + # The shared server keeps running (the moto_server fixture stops it at session end). + requests.post(f"{moto_server}moto-api/reset") def test_markers_attribute_is_parsed(tmp_path: Path) -> None: diff --git a/tests/test_group.py b/tests/test_group.py index e05df0dfcb..692b88c8af 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -54,17 +54,16 @@ from .conftest import meta_from_array, parse_store if TYPE_CHECKING: + import pathlib from collections.abc import Callable - from _pytest.compat import LEGACY_PATH - from zarr.core.buffer.core import Buffer from zarr.core.common import JSON, ZarrFormat @pytest.fixture(params=["local", "memory", "zip"]) -async def store(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> Store: - result = await parse_store(request.param, str(tmpdir)) +async def store(request: pytest.FixtureRequest, tmp_path: pathlib.Path) -> Store: + result = await parse_store(request.param, str(tmp_path)) if not isinstance(result, Store): raise TypeError(f"Wrong store class returned by test fixture! got {result} instead") return result diff --git a/tests/test_properties.py b/tests/test_properties.py index 3f71fdf493..33888bfd4e 100644 --- a/tests/test_properties.py +++ b/tests/test_properties.py @@ -119,7 +119,6 @@ def test_array_creates_implicit_groups(array): # this decorator removes timeout; not ideal but it should avoid intermittent CI failures -@pytest.mark.asyncio @settings(deadline=None) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") @given(data=st.data()) @@ -146,7 +145,6 @@ async def test_basic_indexing(data: st.DataObject) -> None: # TODO test async setitem? -@pytest.mark.asyncio @settings(deadline=None) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") @given(data=st.data()) @@ -156,7 +154,6 @@ async def test_basic_indexing_complex_rectilinear(data: st.DataObject) -> None: assert_array_equal(nparray[indexer], zarray[indexer]) -@pytest.mark.asyncio @given(data=st.data()) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") async def test_oindex(data: st.DataObject) -> None: @@ -193,7 +190,6 @@ async def test_oindex(data: st.DataObject) -> None: # note: async oindex setitem not yet implemented -@pytest.mark.asyncio @given(data=st.data()) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") async def test_vindex(data: st.DataObject) -> None: diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index f2c81b87f9..0ba0330d08 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -4,7 +4,6 @@ from typing import Any, Literal import pytest -from _pytest.compat import LEGACY_PATH import zarr from zarr import Group @@ -163,7 +162,7 @@ async def test_make_store_path_none(path: str) -> None: @pytest.mark.parametrize("store_type", [str, Path]) @pytest.mark.parametrize("mode", ["r", "w"]) async def test_make_store_path_local( - tmpdir: LEGACY_PATH, + tmp_path: Path, store_type: type[str] | type[Path] | type[LocalStore], path: str, mode: AccessModeLiteral, @@ -171,10 +170,10 @@ async def test_make_store_path_local( """ Test the various ways of invoking make_store_path that create a LocalStore """ - store_like = store_type(str(tmpdir)) + store_like = store_type(str(tmp_path)) store_path = await make_store_path(store_like, path=path, mode=mode) assert isinstance(store_path.store, LocalStore) - assert Path(store_path.store.root) == Path(tmpdir) + assert Path(store_path.store.root) == Path(tmp_path) assert store_path.path == normalize_path(path) assert store_path.read_only == (mode == "r") @@ -336,7 +335,7 @@ def test_relativize_path_invalid() -> None: _relativize_path(path="a/b/c", prefix="b") -def test_different_open_mode(tmp_path: LEGACY_PATH) -> None: +def test_different_open_mode(tmp_path: Path) -> None: # Test with a store that implements .with_read_only() store = MemoryStore() zarr.create((100,), store=store, zarr_format=2, path="a") diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index 6756bc83d9..c4536e5c49 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -29,8 +29,8 @@ async def set(self, store: LocalStore, key: str, value: Buffer) -> None: (store.root / key).write_bytes(value.to_bytes()) @pytest.fixture - def store_kwargs(self, tmpdir: str) -> dict[str, str]: - return {"root": str(tmpdir)} + def store_kwargs(self, tmp_path: pathlib.Path) -> dict[str, str]: + return {"root": str(tmp_path)} def test_store_repr(self, store: LocalStore) -> None: assert str(store) == f"file://{store.root.as_posix()}" From 22818d9624355856672ae7a915abae20a462315d Mon Sep 17 00:00:00 2001 From: Zamuldinov Nikita <59732804+NIK-TIGER-BILL@users.noreply.github.com> Date: Tue, 23 Jun 2026 22:32:49 +0300 Subject: [PATCH 373/468] fix(testing): correct delete_dir prefix matching in stateful tests (#4002) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix(testing): correct delete_dir prefix matching in stateful tests Fix flaky stateful test bookkeeping when delete_dir matches string prefixes instead of true directory descendants. A path such as 6/faNT... could be incorrectly removed when deleting 6/f. Closes #3977 Signed-off-by: NIK-TIGER-BILL * fix: address review comment — remove standalone regression test per maintainer feedback Signed-off-by: NIK-TIGER-BILL * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: NIK-TIGER-BILL Co-authored-by: NIK-TIGER-BILL Co-authored-by: Davis Bennett Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- changes/3977.bugfix.md | 1 + src/zarr/testing/stateful.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 changes/3977.bugfix.md diff --git a/changes/3977.bugfix.md b/changes/3977.bugfix.md new file mode 100644 index 0000000000..6a8d9b4244 --- /dev/null +++ b/changes/3977.bugfix.md @@ -0,0 +1 @@ +Fix flaky stateful test bookkeeping when `delete_dir` matches string prefixes instead of true directory descendants. Previously a path such as `6/faNT…` could be incorrectly removed when deleting `6/f`. (See [issue #3977](https://github.com/zarr-developers/zarr-python/issues/3977).) diff --git a/src/zarr/testing/stateful.py b/src/zarr/testing/stateful.py index 9817ebd618..9105b8234e 100644 --- a/src/zarr/testing/stateful.py +++ b/src/zarr/testing/stateful.py @@ -311,7 +311,7 @@ def delete_dir(self, data: DataObject) -> None: matches = set() for node in self.all_groups | self.all_arrays: - if node.startswith(path): + if node == path or node.startswith(path + "/"): matches.add(node) self.all_groups = self.all_groups - matches self.all_arrays = self.all_arrays - matches From fd6189bae9d4beb1127dd68c06a9526ad0940947 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 25 Jun 2026 11:05:33 +0200 Subject: [PATCH 374/468] chore(deps): bump the actions group with 3 updates (#4097) Bumps the actions group with 3 updates: [actions/checkout](https://github.com/actions/checkout), [CodSpeedHQ/action](https://github.com/codspeedhq/action) and [github-community-projects/issue-metrics](https://github.com/github-community-projects/issue-metrics). Updates `actions/checkout` from 6.0.3 to 7.0.0 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/df4cb1c069e1874edd31b4311f1884172cec0e10...9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0) Updates `CodSpeedHQ/action` from 4.17.5 to 4.17.6 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/c145068895e045cc725ee76fcd2307624b65c3af...63f3e98b61959fe67f146a3ff022e4136fe9bb9c) Updates `github-community-projects/issue-metrics` from 4.2.7 to 4.2.8 - [Release notes](https://github.com/github-community-projects/issue-metrics/releases) - [Commits](https://github.com/github-community-projects/issue-metrics/compare/1e38d5e62363e14db8019ed7d106b9855bdba6cc...44173f9e0a3b2144a777a10a340e4c09a25ac9f8) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 4.17.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github-community-projects/issue-metrics dependency-version: 4.2.8 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 2 +- .github/workflows/codspeed.yml | 4 ++-- .github/workflows/docs.yml | 2 +- .github/workflows/downstream.yml | 8 ++++---- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/issue-metrics.yml | 2 +- .github/workflows/lint.yml | 2 +- .github/workflows/nightly_wheels.yml | 2 +- .github/workflows/prepare_release.yml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/test.yml | 8 ++++---- .github/workflows/zarr-metadata-release.yml | 2 +- .github/workflows/zarr-metadata.yml | 6 +++--- .github/workflows/zizmor.yml | 2 +- 15 files changed, 24 insertions(+), 24 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 10a21d21c3..25034b868d 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -17,7 +17,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 115b9d0bf7..a77e99bc28 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -23,7 +23,7 @@ jobs: github.event_name == 'workflow_dispatch' || (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark')) steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 persist-credentials: false @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@c145068895e045cc725ee76fcd2307624b65c3af # v4.17.5 + uses: CodSpeedHQ/action@63f3e98b61959fe67f146a3ff022e4136fe9bb9c # v4.17.6 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ab745beec1..59eca8d9b9 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -19,7 +19,7 @@ jobs: name: Check docs runs-on: ubuntu-latest steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index 08bfcf2139..c592fb3cd6 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -21,13 +21,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out zarr-python - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 persist-credentials: false - name: Check out xarray - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: pydata/xarray path: xarray @@ -83,13 +83,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out zarr-python - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 persist-credentials: false - name: Check out numcodecs - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: zarr-developers/numcodecs fetch-depth: 0 diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index f27307efff..60c871cb15 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -34,7 +34,7 @@ jobs: python-version: ['3.12'] steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 # grab all branches and tags persist-credentials: false diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index d15b5b1405..b1262cee06 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -39,7 +39,7 @@ jobs: dependency-set: ["optional"] steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - name: Set HYPOTHESIS_PROFILE based on trigger diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 9c29f2eb2a..53860d21c8 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -33,7 +33,7 @@ jobs: echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV" - name: Run issue-metrics tool - uses: github-community-projects/issue-metrics@1e38d5e62363e14db8019ed7d106b9855bdba6cc # v4.2.7 + uses: github-community-projects/issue-metrics@44173f9e0a3b2144a777a10a340e4c09a25ac9f8 # v4.2.8 env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 32e521377d..d60c9f59b4 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -19,7 +19,7 @@ jobs: name: Lint runs-on: ubuntu-latest steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - name: Set up Python diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 6ef6c28994..85f07cc8a1 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: submodules: true fetch-depth: 0 diff --git a/.github/workflows/prepare_release.yml b/.github/workflows/prepare_release.yml index b0f1000529..d558779bf2 100644 --- a/.github/workflows/prepare_release.yml +++ b/.github/workflows/prepare_release.yml @@ -36,7 +36,7 @@ jobs: VERSION: ${{ inputs.version }} TARGET_BRANCH: ${{ inputs.target_branch }} - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: ref: ${{ inputs.target_branch }} fetch-depth: 0 diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 43436de947..c930eea689 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -26,7 +26,7 @@ jobs: fail-fast: false steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: submodules: true fetch-depth: 0 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 51ce958f90..a75974f6c9 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -56,7 +56,7 @@ jobs: runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 # grab all branches and tags persist-credentials: false @@ -105,7 +105,7 @@ jobs: - python-version: "3.12" dependency-set: upstream steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 persist-credentials: false @@ -140,7 +140,7 @@ jobs: name: doctests runs-on: ubuntu-latest steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3 persist-credentials: false @@ -164,7 +164,7 @@ jobs: name: Benchmark smoke test runs-on: ubuntu-latest steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: fetch-depth: 0 persist-credentials: false diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index cd4e408906..689d3392ba 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -22,7 +22,7 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false fetch-depth: 0 # hatch-vcs needs full history + tags diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml index 3081abf094..95e8251227 100644 --- a/.github/workflows/zarr-metadata.yml +++ b/.github/workflows/zarr-metadata.yml @@ -32,7 +32,7 @@ jobs: matrix: python-version: ['3.11', '3.12', '3.13', '3.14'] steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - name: Install uv @@ -54,7 +54,7 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - name: Install uv @@ -70,7 +70,7 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - name: Install uv diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 869f76dcc1..2b08f619f0 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -27,7 +27,7 @@ jobs: security-events: write # Required by zizmor-action to upload SARIF files steps: - name: Checkout repository - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false From 60db6d62060a5e02df501ca3e11d8af68cc9bcb8 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 25 Jun 2026 21:58:07 +0200 Subject: [PATCH 375/468] Remove struct unstable warning (#4100) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: don't warn on the spec'd "struct" data type in v3 The `struct` data type now has a stable Zarr V3 specification (zarr-extensions/data-types/struct), so serializing it no longer warrants an UnstableSpecificationWarning. The legacy `structured` alias and the unspecified bytes data types (null_terminated_bytes, raw_bytes, variable_length_bytes) continue to warn. Co-Authored-By: Claude Opus 4.8 (1M context) Claude-Session: https://claude.ai/code/session_019rRWaxXfZ3ZmbiZYWZoDBP * docs: add changelog fragment for struct warning fix Co-Authored-By: Claude Opus 4.8 (1M context) Claude-Session: https://claude.ai/code/session_019rRWaxXfZ3ZmbiZYWZoDBP --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- changes/202.bugfix.md | 1 + src/zarr/core/dtype/npy/structured.py | 4 +++- 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 changes/202.bugfix.md diff --git a/changes/202.bugfix.md b/changes/202.bugfix.md new file mode 100644 index 0000000000..9c9bd40f21 --- /dev/null +++ b/changes/202.bugfix.md @@ -0,0 +1 @@ +Stop emitting an `UnstableSpecificationWarning` when serializing the `struct` data type to Zarr V3 metadata. The `struct` data type now has a stable Zarr V3 specification. The legacy `structured` alias and the unspecified `null_terminated_bytes`, `raw_bytes`, and `variable_length_bytes` data types continue to warn. diff --git a/src/zarr/core/dtype/npy/structured.py b/src/zarr/core/dtype/npy/structured.py index b865998e52..dcc523d1d2 100644 --- a/src/zarr/core/dtype/npy/structured.py +++ b/src/zarr/core/dtype/npy/structured.py @@ -589,7 +589,9 @@ def to_json(self, zarr_format: ZarrFormat) -> StructuredJSON_V2 | StructJSON_V3: ] return {"name": fields_v2, "object_codec_id": None} elif zarr_format == 3: - v3_unstable_dtype_warning(self) + # The "struct" data type has a stable Zarr V3 specification + # (https://github.com/zarr-developers/zarr-extensions/tree/main/data-types/struct), + # so unlike the legacy "structured" alias it does not emit an unstable-spec warning. fields_v3 = [ {"name": f_name, "data_type": f_dtype.to_json(zarr_format=zarr_format)} for f_name, f_dtype in self.fields From 036ede74a38a0fad432768a2cec0937d20941a7d Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 25 Jun 2026 22:11:25 +0200 Subject: [PATCH 376/468] chore: test correctness fixes (#4094) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: correctness fixes for test-suite audit (Section A) - Move downstream `gpu` pytest marker registration from `src/zarr/testing/conftest.py` into the pytest11 plugin entry point `src/zarr/testing/__init__.py` (the conftest was never loaded by downstream consumers of StoreTests under --strict-markers). Delete the now-dead conftest and drop its `[tool.coverage.run] omit` entry. As a side benefit, `assert_bytes_equal` is now imported only when pytest is available (it imports pytest), matching StoreTests. - Add verified `match=` regexes to broad/bare `pytest.raises` in tests/test_api.py (test_create float shape/chunks, test_save_errors, test_save no-arrays), tests/test_group.py (KeyError key names, require_group TypeError), and tests/test_store/test_core.py (invalid zarr_format, make_store_path type, normalize_path). Each message was confirmed against the actual code. - Remove `hasattr(cached_store, "_is_key_fresh")`-guarded assertions in tests/test_experimental/test_cache_store.py that could silently no-op; `_is_key_fresh` exists on CacheStore, so assert it directly. - Add `reason=` to the two reason-less xfail marks in tests/test_indexing.py (structured dtypes unsupported in v3). The unconditional env-specific skip is left as-is (the operation is broadly broken, including locally, so no correct skipif condition exists). Co-Authored-By: Claude Opus 4.8 (1M context) * test: don't xfail * docs: drop stale zarr.testing.conftest API page conftest.py was removed from zarr.testing in this branch, but the auto-API page, its mkdocs nav entry, and the testing index link still referenced it, breaking `mkdocs build --strict`. Co-Authored-By: Claude Opus 4.8 (1M context) Claude-Session: https://claude.ai/code/session_019rRWaxXfZ3ZmbiZYWZoDBP --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Opus 4.8 (1M context) --- docs/api/zarr/testing/conftest.md | 3 --- docs/api/zarr/testing/index.md | 1 - mkdocs.yml | 1 - pyproject.toml | 1 - src/zarr/testing/__init__.py | 14 ++++++++++- src/zarr/testing/conftest.py | 9 ------- tests/test_api.py | 16 ++++++------ tests/test_experimental/test_cache_store.py | 27 ++++++--------------- tests/test_group.py | 12 ++++----- tests/test_indexing.py | 18 ++++++++------ tests/test_store/test_core.py | 6 ++--- 11 files changed, 50 insertions(+), 58 deletions(-) delete mode 100644 docs/api/zarr/testing/conftest.md delete mode 100644 src/zarr/testing/conftest.py diff --git a/docs/api/zarr/testing/conftest.md b/docs/api/zarr/testing/conftest.md deleted file mode 100644 index 67cecfd9b8..0000000000 --- a/docs/api/zarr/testing/conftest.md +++ /dev/null @@ -1,3 +0,0 @@ -## Conftest - -::: zarr.testing.conftest diff --git a/docs/api/zarr/testing/index.md b/docs/api/zarr/testing/index.md index 4ef56ec69c..ab5dd1daa0 100644 --- a/docs/api/zarr/testing/index.md +++ b/docs/api/zarr/testing/index.md @@ -5,7 +5,6 @@ title: testing See the following sub-modules: - [buffer](./buffer.md) -- [conftest](./conftest.md) - [stateful](./stateful.md) - [store](./store.md) - [strategies](./strategies.md) diff --git a/mkdocs.yml b/mkdocs.yml index 7a4bfa35ef..e4e757e630 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -66,7 +66,6 @@ nav: - Testing: - api/zarr/testing/index.md - api/zarr/testing/buffer.md - - api/zarr/testing/conftest.md - api/zarr/testing/stateful.md - api/zarr/testing/store.md - api/zarr/testing/strategies.md diff --git a/pyproject.toml b/pyproject.toml index 02e66c67e8..6a7238ff8f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -155,7 +155,6 @@ exclude_also = [ [tool.coverage.run] omit = [ "bench/compress_normal.py", - "src/zarr/testing/conftest.py", # only for downstream projects ] [tool.hatch] diff --git a/src/zarr/testing/__init__.py b/src/zarr/testing/__init__.py index 21a3572846..823c508052 100644 --- a/src/zarr/testing/__init__.py +++ b/src/zarr/testing/__init__.py @@ -1,16 +1,28 @@ import importlib.util import warnings +from typing import TYPE_CHECKING from zarr.errors import ZarrUserWarning if importlib.util.find_spec("pytest") is not None: from zarr.testing.store import StoreTests + from zarr.testing.utils import assert_bytes_equal else: warnings.warn( "pytest not installed, skipping test suite", category=ZarrUserWarning, stacklevel=2 ) -from zarr.testing.utils import assert_bytes_equal +if TYPE_CHECKING: + import pytest + + +def pytest_configure(config: "pytest.Config") -> None: + # The tests in zarr.testing are intended to be run by downstream projects. + # To allow those downstream projects to run with `--strict-markers`, we need + # to register an entry point with pytest11 and register our "plugin" with it, + # which just registers the markers used in zarr.testing + config.addinivalue_line("markers", "gpu: mark a test as requiring CuPy and GPU") + # TODO: import public buffer tests? diff --git a/src/zarr/testing/conftest.py b/src/zarr/testing/conftest.py deleted file mode 100644 index 59c148e0ec..0000000000 --- a/src/zarr/testing/conftest.py +++ /dev/null @@ -1,9 +0,0 @@ -import pytest - - -def pytest_configure(config: pytest.Config) -> None: - # The tests in zarr.testing are intended to be run by downstream projects. - # To allow those downstream projects to run with `--strict-markers`, we need - # to register an entry point with pytest11 and register our "plugin" with it, - # which just registers the markers used in zarr.testing - config.addinivalue_line("markers", "gpu: mark a test as requiring CuPy and GPU") diff --git a/tests/test_api.py b/tests/test_api.py index 121f02c7b2..503aeee405 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -75,11 +75,11 @@ def test_create(memory_store: Store) -> None: assert z.chunks == (40,) # create array with float shape - with pytest.raises(TypeError): + with pytest.raises(TypeError, match="Expected an iterable of integers"): z = create(shape=(400.5, 100), store=store, overwrite=True) # type: ignore[arg-type] # create array with float chunk shape - with pytest.raises(TypeError): + with pytest.raises(TypeError, match="'float' object is not iterable"): z = create(shape=(400, 100), chunks=(16, 16.5), store=store, overwrite=True) # type: ignore[arg-type] @@ -378,7 +378,7 @@ def test_save(store: Store, n_args: int, n_kwargs: int, path: None | str) -> Non kwargs = {f"arg_{i}": data for i in range(n_kwargs)} if n_kwargs == 0 and n_args == 0: - with pytest.raises(ValueError): + with pytest.raises(ValueError, match="at least one array must be provided"): save(store, path=path) elif n_args == 1 and n_kwargs == 0: save(store, *args, path=path) @@ -397,17 +397,19 @@ def test_save(store: Store, n_args: int, n_kwargs: int, path: None | str) -> Non def test_save_errors() -> None: - with pytest.raises(ValueError): + with pytest.raises(ValueError, match="at least one array must be provided"): # no arrays provided save_group("data/group.zarr") - with pytest.raises(TypeError): + with pytest.raises(TypeError, match="missing 1 required positional argument: 'arr'"): # no array provided save_array("data/group.zarr") # type: ignore[call-arg] - with pytest.raises(ValueError): + with pytest.raises(ValueError, match="at least one array must be provided"): # no arrays provided save("data/group.zarr") a = np.arange(10) - with pytest.raises(TypeError): + with pytest.raises( + TypeError, match="Keyword argument 'mode' must be a numpy or other NDArrayLike array" + ): # mode is no valid argument and would get handled as an array zarr.save("data/example.zarr", a, mode="w") diff --git a/tests/test_experimental/test_cache_store.py b/tests/test_experimental/test_cache_store.py index fc17ccd5e1..5ad56a4335 100644 --- a/tests/test_experimental/test_cache_store.py +++ b/tests/test_experimental/test_cache_store.py @@ -131,21 +131,14 @@ async def test_cache_expiration(self) -> None: test_data = CPUBuffer.from_bytes(b"expiring data") await cached_store.set("expire_key", test_data) - # Should be fresh initially (if _is_key_fresh method exists) - if hasattr(cached_store, "_is_key_fresh"): - assert cached_store._is_key_fresh("expire_key") - - # Wait for expiration - await asyncio.sleep(1.1) - - # Should now be stale - assert not cached_store._is_key_fresh("expire_key") - else: - # Skip freshness check if method doesn't exist - await asyncio.sleep(1.1) - # Just verify the data is still accessible - result = await cached_store.get("expire_key", default_buffer_prototype()) - assert result is not None + # Should be fresh initially + assert cached_store._is_key_fresh("expire_key") + + # Wait for expiration + await asyncio.sleep(1.1) + + # Should now be stale + assert not cached_store._is_key_fresh("expire_key") async def test_cache_set_data_false(self, source_store: Store, cache_store: Store) -> None: """Test behavior when cache_set_data=False.""" @@ -225,10 +218,6 @@ async def test_stale_cache_refresh(self) -> None: async def test_infinity_max_age(self, cached_store: CacheStore) -> None: """Test that 'infinity' max_age means cache never expires.""" - # Skip test if _is_key_fresh method doesn't exist - if not hasattr(cached_store, "_is_key_fresh"): - pytest.skip("_is_key_fresh method not implemented") - test_data = CPUBuffer.from_bytes(b"eternal data") await cached_store.set("eternal_key", test_data) diff --git a/tests/test_group.py b/tests/test_group.py index 692b88c8af..bc80e19e86 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -395,7 +395,7 @@ def test_group_getitem(store: Store, zarr_format: ZarrFormat, consolidated: bool assert group["subgroup"]["subarray"] == subsubarray assert group["subgroup/subarray"] == subsubarray - with pytest.raises(KeyError): + with pytest.raises(KeyError, match="nope"): group["nope"] with pytest.raises(KeyError, match="subarray/subsubarray"): @@ -483,11 +483,11 @@ def test_group_delitem(store: Store, zarr_format: ZarrFormat, consolidated: bool assert group["subarray"] == subarray del group["subgroup"] - with pytest.raises(KeyError): + with pytest.raises(KeyError, match="subgroup"): group["subgroup"] del group["subarray"] - with pytest.raises(KeyError): + with pytest.raises(KeyError, match="subarray"): group["subarray"] @@ -1060,7 +1060,7 @@ async def test_asyncgroup_getitem(store: Store, zarr_format: ZarrFormat) -> None assert await agroup.getitem(sub_group_path) == sub_group # check that asking for a nonexistent key raises KeyError - with pytest.raises(KeyError): + with pytest.raises(KeyError, match="foo"): await agroup.getitem("foo") @@ -1316,7 +1316,7 @@ async def test_require_group(store: LocalStore | MemoryStore, zarr_format: ZarrF # await root.require_group("foo", overwrite=True) # test that requiring a group where an array is fails - with pytest.raises(TypeError): + with pytest.raises(TypeError, match="Incompatible object"): await foo_group.require_group("bar") @@ -1650,7 +1650,7 @@ def test_delitem_removes_children(store: Store, zarr_format: ZarrFormat) -> None arr = g1.create_array("0/0/0", shape=(1,), dtype="uint8") arr[:] = 1 del g1["0"] - with pytest.raises(KeyError): + with pytest.raises(KeyError, match="0/0"): g1["0/0"] diff --git a/tests/test_indexing.py b/tests/test_indexing.py index a9358e4fcf..3d80f6364c 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -158,7 +158,9 @@ def test_replace_ellipsis() -> None: [ (42, "uint8"), pytest.param( - (b"aaa", 1, 4.2), [("foo", "S3"), ("bar", "i4"), ("baz", "f8")], marks=pytest.mark.xfail + (b"aaa", 1, 4.2), + [("foo", "S3"), ("bar", "i4"), ("baz", "f8")], + marks=pytest.mark.filterwarnings("ignore::zarr.errors.UnstableSpecificationWarning"), ), ], ) @@ -171,8 +173,8 @@ def test_get_basic_selection_0d(store: StorePath, use_out: bool, value: Any, dty assert_array_equal(arr_np, arr_z.get_basic_selection(Ellipsis)) assert_array_equal(arr_np, arr_z[...]) - assert value == arr_z.get_basic_selection(()) - assert value == arr_z[()] + assert arr_np[()] == arr_z.get_basic_selection(()) + assert arr_np[()] == arr_z[()] if use_out: # test out param @@ -598,7 +600,9 @@ def test_fancy_indexing_doesnt_mix_with_implicit_slicing(store: StorePath) -> No [ (42, "uint8"), pytest.param( - (b"aaa", 1, 4.2), [("foo", "S3"), ("bar", "i4"), ("baz", "f8")], marks=pytest.mark.xfail + (b"aaa", 1, 4.2), + [("foo", "S3"), ("bar", "i4"), ("baz", "f8")], + marks=pytest.mark.filterwarnings("ignore::zarr.errors.UnstableSpecificationWarning"), ), ], ) @@ -612,11 +616,11 @@ def test_set_basic_selection_0d( assert_array_equal(arr_np_zeros, arr_z) arr_z.set_basic_selection(Ellipsis, value) - assert_array_equal(value, arr_z) - arr_z[...] = 0 + assert_array_equal(arr_np, arr_z) + arr_z[...] = arr_np_zeros[()] assert_array_equal(arr_np_zeros, arr_z) arr_z[...] = value - assert_array_equal(value, arr_z) + assert_array_equal(arr_np, arr_z) # todo: uncomment the structured array tests when we can make them pass, # or delete them if we formally decide not to support structured dtypes. diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index 0ba0330d08..ae64e17ee0 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -88,7 +88,7 @@ async def test_contains_invalid_format_raises(local_store: LocalStore, func: _Co Test contains_group and contains_array raise errors for invalid zarr_formats """ store_path = StorePath(local_store) - with pytest.raises(ValueError): + with pytest.raises(ValueError, match="Invalid zarr_format provided. Got 3.0, expected 2 or 3"): assert await func(store_path, "3.0") # type: ignore[arg-type] @@ -214,7 +214,7 @@ async def test_make_store_path_invalid() -> None: """ Test that invalid types raise TypeError """ - with pytest.raises(TypeError): + with pytest.raises(TypeError, match="Unsupported type for store_like: 'int'"): await make_store_path(1) @@ -262,7 +262,7 @@ def test_normalize_path_none() -> None: @pytest.mark.parametrize("path", [".", ".."]) def test_normalize_path_invalid(path: str) -> None: - with pytest.raises(ValueError): + with pytest.raises(ValueError, match="is invalid because its string representation contains"): normalize_path(path) From 8ebd1cca10b0a57d8c56eb71ff0457f4d7aea8d7 Mon Sep 17 00:00:00 2001 From: Vincent Gao Date: Fri, 26 Jun 2026 16:14:48 +0200 Subject: [PATCH 377/468] Fix scalar array save and load (#4103) --- changes/3469.bugfix.md | 1 + src/zarr/api/asynchronous.py | 4 ++-- tests/test_api.py | 16 ++++++++++++++++ 3 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 changes/3469.bugfix.md diff --git a/changes/3469.bugfix.md b/changes/3469.bugfix.md new file mode 100644 index 0000000000..eb56e87476 --- /dev/null +++ b/changes/3469.bugfix.md @@ -0,0 +1 @@ +Fixed `save_array`, `Group.__setitem__`, and `load` for 0-dimensional arrays. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 7f185535df..1908a1a11e 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -304,7 +304,7 @@ async def load( obj = await open(store=store, path=path, zarr_format=zarr_format) if isinstance(obj, AsyncArray): - return await obj.getitem(slice(None)) + return await obj.getitem(Ellipsis) else: raise NotImplementedError("loading groups not yet supported") @@ -482,7 +482,7 @@ async def save_array( overwrite=overwrite, **kwargs, ) - await new.setitem(slice(None), arr) + await new.setitem(Ellipsis, arr) async def save_group( diff --git a/tests/test_api.py b/tests/test_api.py index 503aeee405..1b4414ae63 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -396,6 +396,22 @@ def test_save(store: Store, n_args: int, n_kwargs: int, path: None | str) -> Non assert group.nmembers() == n_args + n_kwargs +@pytest.mark.parametrize( + "data", + [ + np.array(42, dtype=np.int64), + np.array("teststr", dtype=np.bytes_), + ], +) +@pytest.mark.filterwarnings("ignore::zarr.errors.UnstableSpecificationWarning") +def test_group_setitem_loads_scalar_arrays(sync_store: Store, data: np.ndarray) -> None: + root = zarr.open_group(store=sync_store) + root["test"] = data + + assert_array_equal(root["test"][...], data) + assert_array_equal(zarr.load(store=sync_store, path="test"), data) + + def test_save_errors() -> None: with pytest.raises(ValueError, match="at least one array must be provided"): # no arrays provided From e29ddd2f91ec3b42df13a2945c986dccf0f596a9 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Fri, 26 Jun 2026 14:02:56 -0400 Subject: [PATCH 378/468] docs: add reviewer guidance and author attestation to PR template (#4106) * docs: add reviewer guidance and author attestation to PR template * docs: recommend conventional commits style PR titles * docs: change example --- .github/PULL_REQUEST_TEMPLATE.md | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index c36428b300..1d12aa02eb 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,6 +1,24 @@ -[Description of PR] + + +## Summary + +[Describe what this PR changes and why, in your own words.] + +## For reviewers + +[What would you most value a second look at? What are you already confident in? For a refactor, say whether behavior is meant to be unchanged.] + +## Author attestation + +- [ ] I am a human, these are my changes, and I have reviewed and understood every change and can explain why each is correct. + +AI coding assistance is welcome, but a human must be the author and is responsible for the contents of the PR. The description and any review responses must be in your own words. Please read [AI-assisted contributions](https://zarr.readthedocs.io/en/stable/contributing/#ai-assisted-contributions) before opening. + +## TODO -TODO: * [ ] Add unit tests and/or doctests in docstrings * [ ] Add docstrings and API docs for any new/modified user-facing classes and functions * [ ] New/modified features documented in `docs/user-guide/*.md` From 1ab9953d08d24f58a51260958dc8f27bb38f44b9 Mon Sep 17 00:00:00 2001 From: Zamuldinov Nikita <59732804+NIK-TIGER-BILL@users.noreply.github.com> Date: Wed, 1 Jul 2026 16:18:20 +0300 Subject: [PATCH 379/468] docs: document zarr.errors changes in the v3 migration guide (#4110) Signed-off-by: NIK-TIGER-BILL Co-authored-by: NIK-TIGER-BILL --- changes/3009.doc.md | 1 + docs/user-guide/v3_migration.md | 6 ++++++ 2 files changed, 7 insertions(+) create mode 100644 changes/3009.doc.md diff --git a/changes/3009.doc.md b/changes/3009.doc.md new file mode 100644 index 0000000000..777672b77b --- /dev/null +++ b/changes/3009.doc.md @@ -0,0 +1 @@ +Document the changes to `zarr.errors` in the 3.0 migration guide, including the removal of v2 exception classes and the introduction of `NodeNotFoundError`. diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index 1680547d93..5192179550 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -47,6 +47,12 @@ the following actions in order: - The `zarr.v3_api_available` feature flag is being removed. In Zarr-Python 3 the v3 API is always available, so you shouldn't need to use this flag. + - `zarr.errors` has been consolidated. Several exception classes from + Zarr-Python 2 (such as `zarr.errors.PathNotFoundError`) have been removed + or replaced. For example, missing nodes now raise `zarr.errors.NodeNotFoundError` + (which subclasses both `BaseZarrError` and `FileNotFoundError`) instead of + `zarr.errors.PathNotFoundError`. Review any code that catches exceptions + from `zarr.errors` after migrating. - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) From 4b68c2c260a363283595b753b486ad8e92214813 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 2 Jul 2026 16:39:15 -0400 Subject: [PATCH 380/468] refactor(testing): call super().__init__ in LatencyStore (#4102) Co-authored-by: Davis Bennett --- src/zarr/testing/store.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index 11ceeee83a..fb87a69a09 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -628,9 +628,9 @@ class LatencyStore(WrapperStore[Store]): set_latency: float def __init__(self, store: Store, *, get_latency: float = 0, set_latency: float = 0) -> None: + super().__init__(store) self.get_latency = float(get_latency) self.set_latency = float(set_latency) - self._store = store def _with_store(self, store: Store) -> Self: return type(self)(store, get_latency=self.get_latency, set_latency=self.set_latency) From 5236a0355cdbbac40a02de681b8c1cd0a0a07d3c Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Fri, 3 Jul 2026 10:29:48 +0200 Subject: [PATCH 381/468] Claude/internal simplifications (#4105) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * refactor: dedupe overwrite-check logic in array creation Extract the repeated "delete existing node if overwriting (and the store supports deletes), otherwise enforce no existing node" dance into a single private helper `_prepare_overwrite`, used by `_create_v3`, `_create_v2`, and `_create_array_metadata`. Co-Authored-By: Claude Fable 5 * refactor: inline single-caller get-selection wrappers The module-level `_get_orthogonal_selection`, `_get_mask_selection`, and `_get_coordinate_selection` helpers each constructed an indexer and delegated to `_get_selection`, and each had exactly one caller (the corresponding `AsyncArray.get_*_selection` method). Inline the indexer construction into those methods and delete the wrappers. Co-Authored-By: Claude Fable 5 * refactor: unify zarr-dtype access via metadata.dtype `ArrayV2Metadata.dtype` and `ArrayV3Metadata.dtype` (the latter an alias for `data_type`) both already return the zarr dtype object, so the repeated `metadata.dtype if zarr_format == 2 else metadata.data_type` dispatch in `AsyncArray._zdtype`, `_get_selection`, and `_set_selection` collapses to a single `metadata.dtype` access. Co-Authored-By: Claude Fable 5 * refactor: make Array.cdata_shape delegate to _chunk_grid_shape `Array.cdata_shape` and `Array._chunk_grid_shape` had identical bodies; the public `cdata_shape` now delegates to `_chunk_grid_shape` instead of duplicating the access. Co-Authored-By: Claude Fable 5 * refactor: inline no-op default_filters_v3 `default_filters_v3` unconditionally returned an empty tuple. Inline that empty tuple at its two call sites (with a short comment) and delete the function. Co-Authored-By: Claude Fable 5 * refactor: dedupe contains_group V3 branch via _contains_node_v3 The V3 branch of `contains_group` re-implemented the node-type detection that `_contains_node_v3` already performs. Replace it with `(await _contains_node_v3(store_path)) == "group"`, which is behaviorally identical for all cases (missing document, array, group, malformed/non-object JSON, and missing node_type key all map to the same result). `contains_array` is intentionally left unchanged: its V3 branch falls through to a `ValueError` when a *group* node is present, which `_contains_node_v3` does not reproduce, so swapping it would change observable behavior. Co-Authored-By: Claude Fable 5 * refactor: extract not-yet-implemented kwarg warning helper `open_group` and `create` each had repeated `if x is not None: warnings.warn(f"...not yet implemented...")` blocks. Extract a `_warn_unimplemented_kwargs` helper taking a name->value mapping. The helper uses stacklevel=3 to compensate for the extra call frame, so the warning still points at the same call site (verified: identical message, category, source location, and emission order). Co-Authored-By: Claude Fable 5 * refactor: fold fill_value extraction into _like_args `_like_args` now records the source array's fill_value, so `empty_like`, `full_like`, and `open_like` no longer need to re-check isinstance and setdefault it. `ones_like`/`zeros_like` drop the inherited fill_value (they supply their own), preserving exact prior behavior including the existing duplicate-keyword TypeError when an explicit fill_value is passed. Update the `_like_args` unit test to include the new key. Co-Authored-By: Claude Fable 5 * fix: catch UnicodeDecodeError in _contains_node_v3 Routing `contains_group` through the shared `_contains_node_v3` helper narrowed the exception handling from `(ValueError, KeyError, TypeError)` to `(KeyError, TypeError, json.JSONDecodeError)`. A non-UTF-8 `zarr.json` makes `json.loads` raise `UnicodeDecodeError` (a `ValueError` subclass that is not `json.JSONDecodeError`), so `contains_group` would raise instead of returning `False` as it did before. Broaden the guard to `ValueError`, which covers both malformed JSON and non-UTF-8 bytes, exactly matching the previous behavior (and aligning `ensure_no_existing_node`, which also routes through this helper). Add regression tests for the non-UTF-8 case across `contains_array`, `contains_group`, and `_contains_node_v3`. Assisted-by: ClaudeCode:claude-opus-4.8 --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 --- src/zarr/api/asynchronous.py | 72 +++++--- src/zarr/core/array.py | 276 +++++----------------------- src/zarr/storage/_common.py | 20 +- tests/test_api/test_asynchronous.py | 1 + tests/test_store/test_core.py | 17 ++ 5 files changed, 115 insertions(+), 271 deletions(-) diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 1908a1a11e..54fefaa041 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -108,6 +108,19 @@ def _infer_overwrite(mode: AccessModeLiteral) -> bool: return mode in _OVERWRITE_MODES +def _warn_unimplemented_kwargs(kwargs: dict[str, Any]) -> None: + """ + Emit a "not yet implemented" warning for each provided keyword argument that is not None. + + ``kwargs`` maps a keyword argument name to its supplied value. The ``stacklevel`` is chosen + so the warning points at the caller of the public API function (the same location as an + inline ``warnings.warn(..., stacklevel=2)`` would). + """ + for name, value in kwargs.items(): + if value is not None: + warnings.warn(f"{name} is not yet implemented", ZarrRuntimeWarning, stacklevel=3) + + def _get_shape_chunks(a: ArrayLike | Any) -> tuple[tuple[int, ...] | None, tuple[int, ...] | None]: """Helper function to get the shape and chunks from an array-like object""" shape = None @@ -134,6 +147,7 @@ class _LikeArgs(TypedDict): filters: NotRequired[tuple[Numcodec, ...] | None] compressor: NotRequired[CompressorLikev2] codecs: NotRequired[tuple[Codec, ...]] + fill_value: NotRequired[Any] def _like_args(a: ArrayLike) -> _LikeArgs: @@ -151,6 +165,7 @@ def _like_args(a: ArrayLike) -> _LikeArgs: new["dtype"] = a.dtype if isinstance(a, AsyncArray | Array): + new["fill_value"] = a.metadata.fill_value if isinstance(a.metadata, ArrayV2Metadata): new["order"] = a.order new["compressor"] = a.metadata.compressor @@ -813,14 +828,14 @@ async def open_group( The new group. """ - if cache_attrs is not None: - warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if synchronizer is not None: - warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if meta_array is not None: - warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if chunk_store is not None: - warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2) + _warn_unimplemented_kwargs( + { + "cache_attrs": cache_attrs, + "synchronizer": synchronizer, + "meta_array": meta_array, + "chunk_store": chunk_store, + } + ) store_path = await make_store_path(store, mode=mode, storage_options=storage_options, path=path) if attributes is None: @@ -1010,20 +1025,17 @@ async def create( if zarr_format is None: zarr_format = _default_zarr_format() - if synchronizer is not None: - warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if chunk_store is not None: - warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if cache_metadata is not None: - warnings.warn("cache_metadata is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if cache_attrs is not None: - warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if object_codec is not None: - warnings.warn("object_codec is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if read_only is not None: - warnings.warn("read_only is not yet implemented", ZarrRuntimeWarning, stacklevel=2) - if meta_array is not None: - warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2) + _warn_unimplemented_kwargs( + { + "synchronizer": synchronizer, + "chunk_store": chunk_store, + "cache_metadata": cache_metadata, + "cache_attrs": cache_attrs, + "object_codec": object_codec, + "read_only": read_only, + "meta_array": meta_array, + } + ) if write_empty_chunks is not None: _warn_write_empty_chunks_kwarg() @@ -1111,8 +1123,6 @@ async def empty_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: and these are not guaranteed to be stable from one access to the next. """ like_kwargs = _like_args(a) | kwargs - if isinstance(a, (AsyncArray | Array)): - like_kwargs.setdefault("fill_value", a.metadata.fill_value) return await empty(**like_kwargs) # type: ignore[arg-type] @@ -1155,8 +1165,6 @@ async def full_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: The new array. """ like_kwargs = _like_args(a) | kwargs - if isinstance(a, (AsyncArray | Array)): - like_kwargs.setdefault("fill_value", a.metadata.fill_value) return await full(**like_kwargs) # type: ignore[arg-type] @@ -1194,7 +1202,10 @@ async def ones_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: Array The new array. """ - like_kwargs = _like_args(a) | kwargs + like_args = _like_args(a) + # `ones` supplies its own fill_value, so drop any inherited from `a`. + like_args.pop("fill_value", None) + like_kwargs = like_args | kwargs return await ones(**like_kwargs) # type: ignore[arg-type] @@ -1270,8 +1281,6 @@ async def open_like(a: ArrayLike, path: str, **kwargs: Any) -> AnyAsyncArray: The opened array. """ like_kwargs = _like_args(a) | kwargs - if isinstance(a, (AsyncArray | Array)): - like_kwargs.setdefault("fill_value", a.metadata.fill_value) return await open_array(path=path, **like_kwargs) # type: ignore[arg-type] @@ -1309,5 +1318,8 @@ async def zeros_like(a: ArrayLike, **kwargs: Any) -> AnyAsyncArray: Array The new array. """ - like_kwargs = _like_args(a) | kwargs + like_args = _like_args(a) + # `zeros` supplies its own fill_value, so drop any inherited from `a`. + like_args.pop("fill_value", None) + like_kwargs = like_args | kwargs return await zeros(**like_kwargs) # type: ignore[arg-type] diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 977520b12e..ea7d125b10 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -299,6 +299,22 @@ async def get_array_metadata( return metadata_dict +async def _prepare_overwrite( + store_path: StorePath, *, zarr_format: ZarrFormat, overwrite: bool +) -> None: + """ + Prepare a store path for writing a new node. + + If ``overwrite`` is true and the store supports deletes, any existing node at + ``store_path`` is deleted. Otherwise, the absence of an existing node is enforced + (raising if one is present). + """ + if overwrite and store_path.store.supports_deletes: + await store_path.delete_dir() + else: + await ensure_no_existing_node(store_path, zarr_format=zarr_format) + + @dataclass(frozen=True) class AsyncArray[T_ArrayMetadata: (ArrayV2Metadata, ArrayV3Metadata)]: """ @@ -524,7 +540,8 @@ def _create_metadata_v3( shape = parse_shapelike(shape) if codecs is None: - filters = default_filters_v3(dtype) + # no data types have default filters + filters = () serializer = default_serializer_v3(dtype) compressors = default_compressors_v3(dtype) @@ -577,13 +594,7 @@ async def _create_v3( attributes: dict[str, JSON] | None = None, overwrite: bool = False, ) -> AsyncArrayV3: - if overwrite: - if store_path.store.supports_deletes: - await store_path.delete_dir() - else: - await ensure_no_existing_node(store_path, zarr_format=3) - else: - await ensure_no_existing_node(store_path, zarr_format=3) + await _prepare_overwrite(store_path, zarr_format=3, overwrite=overwrite) if isinstance(chunk_key_encoding, tuple): chunk_key_encoding = ( @@ -658,13 +669,7 @@ async def _create_v2( attributes: dict[str, JSON] | None = None, overwrite: bool = False, ) -> AsyncArrayV2: - if overwrite: - if store_path.store.supports_deletes: - await store_path.delete_dir() - else: - await ensure_no_existing_node(store_path, zarr_format=2) - else: - await ensure_no_existing_node(store_path, zarr_format=2) + await _prepare_overwrite(store_path, zarr_format=2, overwrite=overwrite) compressor_parsed: CompressorLikev2 if compressor == "auto": @@ -970,10 +975,9 @@ def _zdtype(self) -> ZDType[TBaseDType, TBaseScalar]: """ The zarr-specific representation of the array data type """ - if self.metadata.zarr_format == 2: - return self.metadata.dtype - else: - return self.metadata.data_type + # `dtype` returns the zarr dtype object for both v2 and v3 metadata + # (on v3 it is an alias for `data_type`). + return self.metadata.dtype @property def dtype(self) -> TBaseDType: @@ -1490,13 +1494,16 @@ async def get_orthogonal_selection( fields: Fields | None = None, prototype: BufferPrototype | None = None, ) -> NDArrayLikeOrScalar: - return await _get_orthogonal_selection( + if prototype is None: + prototype = default_buffer_prototype() + indexer = OrthogonalIndexer(selection, self.metadata.shape, self._chunk_grid) + return await _get_selection( self.store_path, self.metadata, self.codec_pipeline, self.config, self._chunk_grid, - selection, + indexer=indexer, out=out, fields=fields, prototype=prototype, @@ -1510,13 +1517,16 @@ async def get_mask_selection( fields: Fields | None = None, prototype: BufferPrototype | None = None, ) -> NDArrayLikeOrScalar: - return await _get_mask_selection( + if prototype is None: + prototype = default_buffer_prototype() + indexer = MaskIndexer(mask, self.metadata.shape, self._chunk_grid) + return await _get_selection( self.store_path, self.metadata, self.codec_pipeline, self.config, self._chunk_grid, - mask, + indexer=indexer, out=out, fields=fields, prototype=prototype, @@ -1530,17 +1540,24 @@ async def get_coordinate_selection( fields: Fields | None = None, prototype: BufferPrototype | None = None, ) -> NDArrayLikeOrScalar: - return await _get_coordinate_selection( + if prototype is None: + prototype = default_buffer_prototype() + indexer = CoordinateIndexer(selection, self.metadata.shape, self._chunk_grid) + out_array = await _get_selection( self.store_path, self.metadata, self.codec_pipeline, self.config, self._chunk_grid, - selection, + indexer=indexer, out=out, fields=fields, prototype=prototype, ) + if hasattr(out_array, "shape"): + # restore shape + out_array = cast("NDArrayLikeOrScalar", np.array(out_array).reshape(indexer.sel_shape)) + return out_array async def _save_metadata(self, metadata: ArrayMetadata, ensure_parents: bool = False) -> None: """ @@ -2166,7 +2183,7 @@ def cdata_shape(self) -> tuple[int, ...]: When sharding is used, this counts inner chunks (not shards) per dimension. """ - return self.async_array._chunk_grid_shape + return self._chunk_grid_shape @property def _chunk_grid_shape(self) -> tuple[int, ...]: @@ -4402,10 +4419,7 @@ async def init_array( chunk_key_encoding, zarr_format=zarr_format ) - if overwrite and store_path.store.supports_deletes: - await store_path.delete_dir() - else: - await ensure_no_existing_node(store_path, zarr_format=zarr_format) + await _prepare_overwrite(store_path, zarr_format=zarr_format, overwrite=overwrite) # Validate rectilinear chunks constraints if _is_rectilinear_chunks(chunks): @@ -4832,15 +4846,6 @@ def _parse_chunk_key_encoding( return result -def default_filters_v3(dtype: ZDType[Any, Any]) -> tuple[ArrayArrayCodec, ...]: - """ - Given a data type, return the default filters for that data type. - - This is an empty tuple. No data types have default filters. - """ - return () - - def default_compressors_v3(dtype: ZDType[Any, Any]) -> tuple[BytesBytesCodec, ...]: """ Given a data type, return the default compressors for that data type. @@ -4993,7 +4998,8 @@ def _parse_chunk_encoding_v3( if filters is None: out_array_array: tuple[ArrayArrayCodec, ...] = () elif filters == "auto": - out_array_array = default_filters_v3(dtype) + # no data types have default filters + out_array_array = () else: maybe_array_array: Iterable[Codec | dict[str, JSON]] if isinstance(filters, dict | Codec): @@ -5388,11 +5394,8 @@ async def _get_selection( NDArrayLikeOrScalar The selected data. """ - # Get dtype from metadata - if metadata.zarr_format == 2: - zdtype = metadata.dtype - else: - zdtype = metadata.data_type + # `dtype` returns the zarr dtype object for both v2 and v3 metadata. + zdtype = metadata.dtype dtype = zdtype.to_native_dtype() # Determine memory order @@ -5522,182 +5525,6 @@ async def _getitem( ) -async def _get_orthogonal_selection( - store_path: StorePath, - metadata: ArrayMetadata, - codec_pipeline: CodecPipeline, - config: ArrayConfig, - chunk_grid: ChunkGrid, - selection: OrthogonalSelection, - *, - out: NDBuffer | None = None, - fields: Fields | None = None, - prototype: BufferPrototype | None = None, -) -> NDArrayLikeOrScalar: - """ - Get an orthogonal selection from the array. - - Parameters - ---------- - store_path : StorePath - The store path of the array. - metadata : ArrayMetadata - The array metadata. - codec_pipeline : CodecPipeline - The codec pipeline for encoding/decoding. - config : ArrayConfig - The array configuration. - chunk_grid : ChunkGrid - The chunk grid. - selection : OrthogonalSelection - The orthogonal selection specification. - out : NDBuffer | None, optional - An output buffer to write the data to. - fields : Fields | None, optional - Fields to select from structured arrays. - prototype : BufferPrototype | None, optional - A buffer prototype to use for the retrieved data. - - Returns - ------- - NDArrayLikeOrScalar - The selected data. - """ - if prototype is None: - prototype = default_buffer_prototype() - indexer = OrthogonalIndexer(selection, metadata.shape, chunk_grid) - return await _get_selection( - store_path, - metadata, - codec_pipeline, - config, - chunk_grid, - indexer=indexer, - out=out, - fields=fields, - prototype=prototype, - ) - - -async def _get_mask_selection( - store_path: StorePath, - metadata: ArrayMetadata, - codec_pipeline: CodecPipeline, - config: ArrayConfig, - chunk_grid: ChunkGrid, - mask: MaskSelection, - *, - out: NDBuffer | None = None, - fields: Fields | None = None, - prototype: BufferPrototype | None = None, -) -> NDArrayLikeOrScalar: - """ - Get a mask selection from the array. - - Parameters - ---------- - store_path : StorePath - The store path of the array. - metadata : ArrayMetadata - The array metadata. - codec_pipeline : CodecPipeline - The codec pipeline for encoding/decoding. - config : ArrayConfig - The array configuration. - chunk_grid : ChunkGrid - The chunk grid. - mask : MaskSelection - The boolean mask specifying the selection. - out : NDBuffer | None, optional - An output buffer to write the data to. - fields : Fields | None, optional - Fields to select from structured arrays. - prototype : BufferPrototype | None, optional - A buffer prototype to use for the retrieved data. - - Returns - ------- - NDArrayLikeOrScalar - The selected data. - """ - if prototype is None: - prototype = default_buffer_prototype() - indexer = MaskIndexer(mask, metadata.shape, chunk_grid) - return await _get_selection( - store_path, - metadata, - codec_pipeline, - config, - chunk_grid, - indexer=indexer, - out=out, - fields=fields, - prototype=prototype, - ) - - -async def _get_coordinate_selection( - store_path: StorePath, - metadata: ArrayMetadata, - codec_pipeline: CodecPipeline, - config: ArrayConfig, - chunk_grid: ChunkGrid, - selection: CoordinateSelection, - *, - out: NDBuffer | None = None, - fields: Fields | None = None, - prototype: BufferPrototype | None = None, -) -> NDArrayLikeOrScalar: - """ - Get a coordinate selection from the array. - - Parameters - ---------- - store_path : StorePath - The store path of the array. - metadata : ArrayMetadata - The array metadata. - codec_pipeline : CodecPipeline - The codec pipeline for encoding/decoding. - config : ArrayConfig - The array configuration. - chunk_grid : ChunkGrid - The chunk grid. - selection : CoordinateSelection - The coordinate selection specification. - out : NDBuffer | None, optional - An output buffer to write the data to. - fields : Fields | None, optional - Fields to select from structured arrays. - prototype : BufferPrototype | None, optional - A buffer prototype to use for the retrieved data. - - Returns - ------- - NDArrayLikeOrScalar - The selected data. - """ - if prototype is None: - prototype = default_buffer_prototype() - indexer = CoordinateIndexer(selection, metadata.shape, chunk_grid) - out_array = await _get_selection( - store_path, - metadata, - codec_pipeline, - config, - chunk_grid, - indexer=indexer, - out=out, - fields=fields, - prototype=prototype, - ) - - if hasattr(out_array, "shape"): - # restore shape - out_array = cast("NDArrayLikeOrScalar", np.array(out_array).reshape(indexer.sel_shape)) - return out_array - - async def _set_selection( store_path: StorePath, metadata: ArrayMetadata, @@ -5734,11 +5561,8 @@ async def _set_selection( fields : Fields | None, optional Fields to select from structured arrays. """ - # Get dtype from metadata - if metadata.zarr_format == 2: - zdtype = metadata.dtype - else: - zdtype = metadata.data_type + # `dtype` returns the zarr dtype object for both v2 and v3 metadata. + zdtype = metadata.dtype dtype = zdtype.to_native_dtype() # check fields are sensible diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 1e13a9ac3f..7e9c035c69 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -1,7 +1,6 @@ from __future__ import annotations import importlib.util -import json from pathlib import Path from typing import TYPE_CHECKING, Any, Literal, Self @@ -546,8 +545,10 @@ async def _contains_node_v3(store_path: StorePath) -> Literal["array", "group", result = "array" elif extant_meta_json["node_type"] == "group": result = "group" - except (KeyError, TypeError, json.JSONDecodeError): - # any of these errors is consistent with no array or group present. + except (KeyError, TypeError, ValueError): + # any of these errors is consistent with no array or group present. `ValueError` + # covers both malformed JSON (`json.JSONDecodeError`) and non-UTF-8 bytes + # (`UnicodeDecodeError`), each a `ValueError` subclass. pass return result @@ -643,18 +644,7 @@ async def contains_group(store_path: StorePath, zarr_format: ZarrFormat) -> bool """ if zarr_format == 3: - extant_meta_bytes = await (store_path / ZARR_JSON).get() - if extant_meta_bytes is None: - return False - else: - try: - extant_meta_json = buffer_to_json_object(extant_meta_bytes) - # we avoid constructing a full metadata document here in the name of speed. - result: bool = extant_meta_json["node_type"] == "group" - except (ValueError, KeyError, TypeError): - return False - else: - return result + return (await _contains_node_v3(store_path)) == "group" elif zarr_format == 2: return await (store_path / ZGROUP_JSON).exists() msg = f"Invalid zarr_format provided. Got {zarr_format}, expected 2 or 3" # type: ignore[unreachable] diff --git a/tests/test_api/test_asynchronous.py b/tests/test_api/test_asynchronous.py index 362195e858..6ebec36bbd 100644 --- a/tests/test_api/test_asynchronous.py +++ b/tests/test_api/test_asynchronous.py @@ -75,6 +75,7 @@ def test_get_shape_chunks( "chunks": (10,), "shape": (100,), "dtype": np.dtype("f8"), + "fill_value": np.float64(0.0), "compressor": None, "filters": None, "order": "C", diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index ae64e17ee0..d2784e1b4b 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -127,6 +127,16 @@ async def test_contains_missing_node_type_returns_false( assert await func(store_path, 3) is False +@pytest.mark.parametrize("func", [contains_array, contains_group]) +async def test_contains_non_utf8_bytes_returns_false( + local_store: LocalStore, func: _ContainsFunc +) -> None: + """A v3 metadata document that is not valid UTF-8 reads as 'not present' (not an error).""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b"\x80\x81\x82\x83") + assert await func(store_path, 3) is False + + async def test_contains_node_v3_malformed_json_returns_nothing(local_store: LocalStore) -> None: """`_contains_node_v3` returns 'nothing' when the document is not valid JSON.""" store_path = StorePath(local_store, path="foo") @@ -148,6 +158,13 @@ async def test_contains_node_v3_missing_node_type_returns_nothing(local_store: L assert await _contains_node_v3(store_path) == "nothing" +async def test_contains_node_v3_non_utf8_bytes_returns_nothing(local_store: LocalStore) -> None: + """`_contains_node_v3` returns 'nothing' when the document is not valid UTF-8.""" + store_path = StorePath(local_store, path="foo") + await _write_zarr_json(store_path, b"\x80\x81\x82\x83") + assert await _contains_node_v3(store_path) == "nothing" + + @pytest.mark.parametrize("path", [None, "", "bar"]) async def test_make_store_path_none(path: str) -> None: """ From 179f2ff32bf51067d89dcd41a724451fe0329bb8 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Mon, 6 Jul 2026 09:41:52 +0200 Subject: [PATCH 382/468] Fix minor documentation issues (#4120) Assisted-by: GitHub Copilot (GPT-5.3-Codex) --- docs/contributing.md | 2 +- docs/release-notes.md | 8 ++++---- src/zarr/core/dtype/npy/bytes.py | 2 +- src/zarr/core/group.py | 2 +- tests/test_array.py | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/contributing.md b/docs/contributing.md index 750f7c7a65..084916d584 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -396,7 +396,7 @@ Zarr developers should make changes as smooth as possible for users. This means The Zarr library is an implementation of a file format standard defined externally -- see the [Zarr specifications website](https://zarr-specs.readthedocs.io) for the list of Zarr file format specifications. -If an existing Zarr format version changes, or a new version of the Zarr format is released, then the Zarr library will generally require changes. It is very likely that a new Zarr format will require extensive breaking changes to the Zarr library, and so support for a new Zarr format in the Zarr library will almost certainly come in new `major` release. When the Zarr library adds support for a new Zarr format, there may be a period of accelerated changes as developers refine newly added APIs and deprecate old APIs. In such a transitional phase breaking changes may be more frequent than usual. +If an existing Zarr format version changes, or a new version of the Zarr format is released, then the Zarr library will generally require changes. It is very likely that a new Zarr format will require extensive breaking changes to the Zarr library, and so support for a new Zarr format in the Zarr library will almost certainly come in a new `major` release. When the Zarr library adds support for a new Zarr format, there may be a period of accelerated changes as developers refine newly added APIs and deprecate old APIs. In such a transitional phase breaking changes may be more frequent than usual. ## Experimental API policy diff --git a/docs/release-notes.md b/docs/release-notes.md index 4511c9815e..93cf1e73b6 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -536,18 +536,18 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Test `getsize()` and `getsize_prefix()` in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Test that a `ValueError` is raised for invalid byte range syntax in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Separate instantiating and opening a store in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Add a test for using Stores as a context managers in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Add a test for using Stores as context managers in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Implemented `LoggingStore.open()`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - `LoggingStore` is now a generic class. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Change StoreTest's `test_store_repr`, `test_store_supports_writes`, `test_store_supports_partial_writes`, and `test_store_supports_listing` - to to be implemented using `@abstractmethod`, rather raising `NotImplementedError`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) + to be implemented using `@abstractmethod`, rather than raising `NotImplementedError`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Test the error raised for invalid buffer arguments in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Test that data can be written to a store that's not yet open using the store.set method in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Adds a new function `init_array` for initializing an array in storage, and refactors `create_array` to use `init_array`. `create_array` takes two new parameters: `data`, an optional array-like object, and `write_data`, a bool which defaults to `True`. If `data` is given to `create_array`, then the `dtype` and `shape` attributes of `data` are used to define the - corresponding attributes of the resulting Zarr array. Additionally, if `data` given and `write_data` is `True`, + corresponding attributes of the resulting Zarr array. Additionally, if `data` is given and `write_data` is `True`, then the values in `data` will be written to the newly created array. ([#2761](https://github.com/zarr-developers/zarr-python/issues/2761)) ### Bugfixes @@ -559,7 +559,7 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Use stdout rather than stderr as the default stream for `LoggingStore`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Match the errors raised by read only stores in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) - Fixed `ZipStore` to make sure the correct attributes are saved when instances are pickled. - This fixes a previous bug that prevent using `ZipStore` with a `ProcessPoolExecutor`. ([#2762](https://github.com/zarr-developers/zarr-python/issues/2762)) + This fixes a previous bug that prevented using `ZipStore` with a `ProcessPoolExecutor`. ([#2762](https://github.com/zarr-developers/zarr-python/issues/2762)) - Updated the optional test dependencies to include `botocore` and `fsspec`. ([#2768](https://github.com/zarr-developers/zarr-python/issues/2768)) - Fixed the fsspec tests to skip if `botocore` is not installed. Previously they would have failed with an import error. ([#2768](https://github.com/zarr-developers/zarr-python/issues/2768)) diff --git a/src/zarr/core/dtype/npy/bytes.py b/src/zarr/core/dtype/npy/bytes.py index af8fa7a272..e60f3c6c48 100644 --- a/src/zarr/core/dtype/npy/bytes.py +++ b/src/zarr/core/dtype/npy/bytes.py @@ -1069,7 +1069,7 @@ def _from_json_v2(cls, data: DTypeJSON) -> Self: Raises ------ DataTypeValidationError - If the input data is not a valid representation of this class class. + If the input data is not a valid representation of this class. """ if cls._check_json_v2(data): diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 52eaa3e144..0aaf89234e 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -3065,7 +3065,7 @@ async def create_nodes( """ # Note: the only way to alter this value is via the config. If that's undesirable for some reason, - # then we should consider adding a keyword argument this this function + # then we should consider adding a keyword argument to this function semaphore = asyncio.Semaphore(config.get("async.concurrency")) create_tasks: list[Coroutine[None, None, str]] = [] diff --git a/tests/test_array.py b/tests/test_array.py index 0d6d2d5906..89d7547e78 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1684,7 +1684,7 @@ def test_default_endianness( store: Store, zarr_format: ZarrFormat, endianness: EndiannessStr ) -> None: """ - Test that that endianness is correctly set when creating an array when not specifying a serializer + Test that endianness is correctly set when creating an array when not specifying a serializer. """ dtype = Int16(endianness=endianness) arr = zarr.create_array(store=store, shape=(1,), dtype=dtype, zarr_format=zarr_format) From 1d06a821d18e3f21146d0a4274d8f3dba3847db0 Mon Sep 17 00:00:00 2001 From: Myk <49292718+oldrobotdev@users.noreply.github.com> Date: Mon, 6 Jul 2026 11:36:11 +0200 Subject: [PATCH 383/468] fix: keep element order when writing F-contiguous chunks with vlen codecs (#4116) * fix: keep element order when writing F-contiguous chunks with vlen codecs The numcodecs vlen codecs flatten their input with order='A', so an F-contiguous object-dtype chunk is encoded in transposed element order while decode reshapes in C order, silently scrambling the round-trip. Make both vlen codec wrappers pass a C-contiguous array to numcodecs; this copies only the object-pointer array and only when the chunk is not already C-contiguous. * docs: add changelog entry * fix: keep element order for numcodecs filter codecs too The generic numcodecs adapter codecs pass the chunk to numcodecs unchanged, so F-contiguous chunks hit the same order='A' flattening as the vlen codecs: Delta, FixedScaleOffset and PackBits all round-trip transposed data for an F-contiguous chunk that exactly covers the selection. Apply the same C-contiguity normalization in the array-array and array-bytes adapter encode paths. --------- Co-authored-by: Davis Bennett --- changes/4116.bugfix.md | 1 + src/zarr/codecs/numcodecs/_codecs.py | 8 +++++-- src/zarr/codecs/vlen_utf8.py | 8 +++++-- tests/test_codecs/test_numcodecs.py | 34 ++++++++++++++++++++++++++++ tests/test_codecs/test_vlen.py | 31 ++++++++++++++++++++++++- 5 files changed, 77 insertions(+), 5 deletions(-) create mode 100644 changes/4116.bugfix.md diff --git a/changes/4116.bugfix.md b/changes/4116.bugfix.md new file mode 100644 index 0000000000..e99eac8c95 --- /dev/null +++ b/changes/4116.bugfix.md @@ -0,0 +1 @@ +Fixed writing Fortran-ordered (F-contiguous) arrays through the variable-length string and bytes codecs and through numcodecs array-array filters such as `Delta`, `FixedScaleOffset` and `PackBits`. Chunks are now passed to numcodecs as C-contiguous arrays, so elements are no longer stored in transposed order. diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py index 1be1381a08..9c967fdbdd 100644 --- a/src/zarr/codecs/numcodecs/_codecs.py +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -162,7 +162,9 @@ async def _decode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> N return chunk_spec.prototype.nd_buffer.from_ndarray_like(out.reshape(chunk_spec.shape)) async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: - chunk_ndarray = chunk_data.as_ndarray_like() + # numcodecs codecs flatten with order="A", so an F-contiguous chunk + # would be encoded in transposed element order (gh-3558) + chunk_ndarray = np.ascontiguousarray(chunk_data.as_ndarray_like()) out = await asyncio.to_thread(self._codec.encode, chunk_ndarray) return chunk_spec.prototype.nd_buffer.from_ndarray_like(out) @@ -177,7 +179,9 @@ async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> NDB return chunk_spec.prototype.nd_buffer.from_ndarray_like(out.reshape(chunk_spec.shape)) async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> Buffer: - chunk_ndarray = chunk_data.as_ndarray_like() + # numcodecs codecs flatten with order="A", so an F-contiguous chunk + # would be encoded in transposed element order (gh-3558) + chunk_ndarray = np.ascontiguousarray(chunk_data.as_ndarray_like()) out = await asyncio.to_thread(self._codec.encode, chunk_ndarray) return chunk_spec.prototype.buffer.from_bytes(out) diff --git a/src/zarr/codecs/vlen_utf8.py b/src/zarr/codecs/vlen_utf8.py index a10cb7c335..078e6032fc 100644 --- a/src/zarr/codecs/vlen_utf8.py +++ b/src/zarr/codecs/vlen_utf8.py @@ -67,8 +67,10 @@ def _encode_sync( chunk_spec: ArraySpec, ) -> Buffer | None: assert isinstance(chunk_array, NDBuffer) + # numcodecs vlen codecs flatten with order="A", so an F-contiguous chunk + # would be encoded in transposed element order (gh-3558) return chunk_spec.prototype.buffer.from_bytes( - _vlen_utf8_codec.encode(chunk_array.as_numpy_array()) + _vlen_utf8_codec.encode(np.ascontiguousarray(chunk_array.as_numpy_array())) ) async def _encode_single( @@ -125,8 +127,10 @@ def _encode_sync( chunk_spec: ArraySpec, ) -> Buffer | None: assert isinstance(chunk_array, NDBuffer) + # numcodecs vlen codecs flatten with order="A", so an F-contiguous chunk + # would be encoded in transposed element order (gh-3558) return chunk_spec.prototype.buffer.from_bytes( - _vlen_bytes_codec.encode(chunk_array.as_numpy_array()) + _vlen_bytes_codec.encode(np.ascontiguousarray(chunk_array.as_numpy_array())) ) async def _encode_single( diff --git a/tests/test_codecs/test_numcodecs.py b/tests/test_codecs/test_numcodecs.py index 7d5a0c29c4..99cd89492f 100644 --- a/tests/test_codecs/test_numcodecs.py +++ b/tests/test_codecs/test_numcodecs.py @@ -163,6 +163,40 @@ def test_generic_filter( np.testing.assert_array_equal(data, b[:, :]) +@pytest.mark.parametrize( + ("codec_class", "codec_config", "dtype"), + [ + (_numcodecs.Delta, {"dtype": "int64"}, "int64"), + (_numcodecs.FixedScaleOffset, {"offset": 0, "scale": 1}, "int64"), + (_numcodecs.PackBits, {}, "bool"), + ], + ids=["delta", "fixedscaleoffset", "packbits"], +) +def test_generic_filter_f_contiguous( + codec_class: type[_numcodecs._NumcodecsArrayArrayCodec], + codec_config: dict[str, JSON], + dtype: str, +) -> None: + # gh-3558: F-contiguous chunks were handed to numcodecs filters as is, and + # numcodecs flattens in memory order, so the elements came back transposed + if dtype == "bool": + data = np.asfortranarray(np.tril(np.ones((16, 16), dtype=bool))) + else: + data = np.asfortranarray(np.arange(256, dtype=dtype).reshape(16, 16)) + + a = create_array( + {}, + shape=data.shape, + chunks=(16, 16), + dtype=data.dtype, + fill_value=0, + filters=[codec_class(**codec_config)], + ) + + a[:, :] = data + np.testing.assert_array_equal(data, a[:, :]) + + def test_generic_filter_bitround() -> None: data = np.linspace(0, 1, 256, dtype="float32").reshape((16, 16)) diff --git a/tests/test_codecs/test_vlen.py b/tests/test_codecs/test_vlen.py index 3422090a28..6729a68af9 100644 --- a/tests/test_codecs/test_vlen.py +++ b/tests/test_codecs/test_vlen.py @@ -9,7 +9,7 @@ from zarr.abc.store import Store from zarr.codecs import ZstdCodec from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec -from zarr.core.dtype import get_data_type_from_native_dtype +from zarr.core.dtype import VariableLengthBytes, get_data_type_from_native_dtype from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.storage import StorePath @@ -67,6 +67,35 @@ def test_vlen_string( assert a.dtype == data.dtype +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("chunks", [(3, 3), (2, 2)]) +def test_vlen_string_f_contiguous(store: Store, chunks: tuple[int, int]) -> None: + # gh-3558: F-contiguous chunks were encoded in transposed element order + data = np.asarray( + np.array([f"S{i:05}" for i in range(9)], dtype=object).reshape(3, 3), order="F" + ) + sp = StorePath(store, path="string-f-contiguous") + a = zarr.create_array(sp, shape=data.shape, chunks=chunks, dtype=str, fill_value="") + a[:, :] = data + assert np.array_equal(data, np.asarray(a[:, :], dtype=object)) + + +@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") +@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) +@pytest.mark.parametrize("chunks", [(3, 3), (2, 2)]) +def test_vlen_bytes_f_contiguous(store: Store, chunks: tuple[int, int]) -> None: + # gh-3558: F-contiguous chunks were encoded in transposed element order + data = np.asarray( + np.array([b"%05d" % i for i in range(9)], dtype=object).reshape(3, 3), order="F" + ) + sp = StorePath(store, path="bytes-f-contiguous") + a = zarr.create_array( + sp, shape=data.shape, chunks=chunks, dtype=VariableLengthBytes(), fill_value=b"" + ) + a[:, :] = data + assert np.array_equal(data, np.asarray(a[:, :], dtype=object)) + + def test_vlen_utf8_codec_supports_sync() -> None: assert isinstance(VLenUTF8Codec(), SupportsSyncCodec) From a84949a094cd31d43c7701b197e107bda0cd4951 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Mon, 6 Jul 2026 12:56:57 +0200 Subject: [PATCH 384/468] test: consolidate vlen F-contiguous regression tests (#4122) Follow-up test-quality cleanup for the gh-3558 fix (#4116): - Merge test_vlen_string_f_contiguous and test_vlen_bytes_f_contiguous into one test parametrized over (dtype, fill_value, elements), matching the parametrized style of test_vlen_string in the same file. - Drop the chunks=(2,2) case: with (3,3) data it produces only partial chunks, which the codec pipeline recopies to C order before encoding, so it never exercised the F-contiguous path it claimed to cover. Use chunks == shape (a single complete chunk) so the F-contiguous buffer reaches the codec untouched. - Build the F-contiguous input directly via reshape(order="F") instead of wrapping a C-order reshape in np.asarray(..., order="F"), and assert data.flags.f_contiguous so a future simplification can't silently defeat the regression guard. - Add a docstring stating the verified behavior. Assisted-by: ClaudeCode:claude-opus-4.8 --- tests/test_codecs/test_vlen.py | 43 +++++++++++++++++----------------- 1 file changed, 21 insertions(+), 22 deletions(-) diff --git a/tests/test_codecs/test_vlen.py b/tests/test_codecs/test_vlen.py index 6729a68af9..c2c2c9b201 100644 --- a/tests/test_codecs/test_vlen.py +++ b/tests/test_codecs/test_vlen.py @@ -9,7 +9,7 @@ from zarr.abc.store import Store from zarr.codecs import ZstdCodec from zarr.codecs.vlen_utf8 import VLenBytesCodec, VLenUTF8Codec -from zarr.core.dtype import VariableLengthBytes, get_data_type_from_native_dtype +from zarr.core.dtype import get_data_type_from_native_dtype from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.storage import StorePath @@ -67,30 +67,29 @@ def test_vlen_string( assert a.dtype == data.dtype -@pytest.mark.parametrize("store", ["memory"], indirect=["store"]) -@pytest.mark.parametrize("chunks", [(3, 3), (2, 2)]) -def test_vlen_string_f_contiguous(store: Store, chunks: tuple[int, int]) -> None: - # gh-3558: F-contiguous chunks were encoded in transposed element order - data = np.asarray( - np.array([f"S{i:05}" for i in range(9)], dtype=object).reshape(3, 3), order="F" - ) - sp = StorePath(store, path="string-f-contiguous") - a = zarr.create_array(sp, shape=data.shape, chunks=chunks, dtype=str, fill_value="") - a[:, :] = data - assert np.array_equal(data, np.asarray(a[:, :], dtype=object)) - - @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") @pytest.mark.parametrize("store", ["memory"], indirect=["store"]) -@pytest.mark.parametrize("chunks", [(3, 3), (2, 2)]) -def test_vlen_bytes_f_contiguous(store: Store, chunks: tuple[int, int]) -> None: - # gh-3558: F-contiguous chunks were encoded in transposed element order - data = np.asarray( - np.array([b"%05d" % i for i in range(9)], dtype=object).reshape(3, 3), order="F" - ) - sp = StorePath(store, path="bytes-f-contiguous") +@pytest.mark.parametrize( + ("dtype", "fill_value", "elements"), + [ + pytest.param("string", "", [f"S{i:05}" for i in range(9)], id="string"), + pytest.param("variable_length_bytes", b"", [b"%05d" % i for i in range(9)], id="bytes"), + ], +) +def test_vlen_f_contiguous( + store: Store, dtype: str, fill_value: str | bytes, elements: list[str] | list[bytes] +) -> None: + """An F-contiguous chunk written through a vlen codec round-trips in the original + element order rather than the transposed memory order (gh-3558).""" + # reshape(order="F") gives an F-contiguous view directly, so the whole-array write + # below hands an F-contiguous chunk to the codec; assert it to guard the precondition. + data = np.array(elements, dtype=object).reshape((3, 3), order="F") + assert data.flags.f_contiguous + sp = StorePath(store, path="vlen-f-contiguous") + # chunks == shape so the write is a single complete chunk, which the codec pipeline + # forwards to the codec untouched; a partial-chunk layout would be recopied to C order. a = zarr.create_array( - sp, shape=data.shape, chunks=chunks, dtype=VariableLengthBytes(), fill_value=b"" + sp, shape=data.shape, chunks=data.shape, dtype=dtype, fill_value=fill_value ) a[:, :] = data assert np.array_equal(data, np.asarray(a[:, :], dtype=object)) From 6f213bd72c5663eca57478551775b17e2f0f1e41 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Jul 2026 11:07:28 +0000 Subject: [PATCH 385/468] chore(deps): bump the actions group with 5 updates (#4114) Bumps the actions group with 5 updates: | Package | From | To | | --- | --- | --- | | [CodSpeedHQ/action](https://github.com/codspeedhq/action) | `4.17.6` | `4.18.1` | | [actions/setup-python](https://github.com/actions/setup-python) | `6.2.0` | `6.3.0` | | [actions/cache/restore](https://github.com/actions/cache) | `5.0.5` | `6.1.0` | | [actions/cache/save](https://github.com/actions/cache) | `5.0.5` | `6.1.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.6` | `0.5.7` | Updates `CodSpeedHQ/action` from 4.17.6 to 4.18.1 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/63f3e98b61959fe67f146a3ff022e4136fe9bb9c...a4a36bb07c0638b0b4ca52bf1f3dad1b4289e52f) Updates `actions/setup-python` from 6.2.0 to 6.3.0 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/a309ff8b426b58ec0e2a45f0f869d46889d02405...ece7cb06caefa5fff74198d8649806c4678c61a1) Updates `actions/cache/restore` from 5.0.5 to 6.1.0 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/27d5ce7f107fe9357f9df03efb73ab90386fccae...55cc8345863c7cc4c66a329aec7e433d2d1c52a9) Updates `actions/cache/save` from 5.0.5 to 6.1.0 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/27d5ce7f107fe9357f9df03efb73ab90386fccae...55cc8345863c7cc4c66a329aec7e433d2d1c52a9) Updates `zizmorcore/zizmor-action` from 0.5.6 to 0.5.7 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/5f14fd08f7cf1cb1609c1e344975f152c7ee938d...192e21d79ab29983730a13d1382995c2307fbcaa) --- updated-dependencies: - dependency-name: CodSpeedHQ/action dependency-version: 4.18.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: actions/setup-python dependency-version: 6.3.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: actions/cache/restore dependency-version: 6.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/cache/save dependency-version: 6.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett --- .github/workflows/codspeed.yml | 2 +- .github/workflows/downstream.yml | 4 ++-- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 6 +++--- .github/workflows/lint.yml | 2 +- .github/workflows/nightly_wheels.yml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/test.yml | 8 ++++---- .github/workflows/zizmor.yml | 2 +- 9 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index a77e99bc28..1d8e847ec5 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@63f3e98b61959fe67f146a3ff022e4136fe9bb9c # v4.17.6 + uses: CodSpeedHQ/action@a4a36bb07c0638b0b4ca52bf1f3dad1b4289e52f # v4.18.1 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index c592fb3cd6..d8aa2907be 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -40,7 +40,7 @@ jobs: # `meson-python: error: Unknown option "pixi-conda-environment"`, breaking # the job before any test runs. Tests that need a backend we don't install # are skipped via xarray's `requires_*` markers, not failed. - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: '3.13' @@ -97,7 +97,7 @@ jobs: submodules: recursive persist-credentials: false - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: '3.13' diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index 60c871cb15..f2bf4907fa 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -57,7 +57,7 @@ jobs: echo $LD_LIBRARY_PATH nvcc -V - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index b1262cee06..950714e098 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -52,7 +52,7 @@ jobs: echo "HYPOTHESIS_PROFILE=ci" >> $GITHUB_ENV fi - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -71,7 +71,7 @@ jobs: # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache - name: Restore cached hypothesis directory id: restore-hypothesis-cache - uses: actions/cache/restore@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5 + uses: actions/cache/restore@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} @@ -91,7 +91,7 @@ jobs: - name: Save cached hypothesis directory id: save-hypothesis-cache if: always() && steps.status.outcome != 'skipped' - uses: actions/cache/save@27d5ce7f107fe9357f9df03efb73ab90386fccae # v5.0.5 + uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 with: path: .hypothesis/ key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }} diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index d60c9f59b4..287c76e7b6 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -23,7 +23,7 @@ jobs: with: persist-credentials: false - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: "3.12" - name: Install uv diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 85f07cc8a1..0a0cafd425 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -28,7 +28,7 @@ jobs: fetch-depth: 0 persist-credentials: false - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 name: Install Python with: python-version: '3.14' diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index c930eea689..6b5895a413 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -32,7 +32,7 @@ jobs: fetch-depth: 0 persist-credentials: false - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 name: Install Python with: python-version: '3.12' diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a75974f6c9..7bc43512b5 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -61,7 +61,7 @@ jobs: fetch-depth: 0 # grab all branches and tags persist-credentials: false - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -110,7 +110,7 @@ jobs: fetch-depth: 0 persist-credentials: false - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' @@ -145,7 +145,7 @@ jobs: fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3 persist-credentials: false - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: '3.13' cache: 'pip' @@ -169,7 +169,7 @@ jobs: fetch-depth: 0 persist-credentials: false - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 with: python-version: '3.13' cache: 'pip' diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 2b08f619f0..6250426bae 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -32,4 +32,4 @@ jobs: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@5f14fd08f7cf1cb1609c1e344975f152c7ee938d # v0.5.6 + uses: zizmorcore/zizmor-action@192e21d79ab29983730a13d1382995c2307fbcaa # v0.5.7 From 6876120896509b753b3890cbbef795765c7063d7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Jul 2026 09:39:59 -0400 Subject: [PATCH 386/468] chore(deps): bump joserfc from 1.6.5 to 1.6.8 (#4123) Bumps [joserfc](https://github.com/authlib/joserfc) from 1.6.5 to 1.6.8. - [Release notes](https://github.com/authlib/joserfc/releases) - [Changelog](https://github.com/authlib/joserfc/blob/main/docs/changelog.rst) - [Commits](https://github.com/authlib/joserfc/compare/1.6.5...1.6.8) --- updated-dependencies: - dependency-name: joserfc dependency-version: 1.6.8 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- uv.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/uv.lock b/uv.lock index 799ea6e45a..9bb186b8f7 100644 --- a/uv.lock +++ b/uv.lock @@ -1288,14 +1288,14 @@ wheels = [ [[package]] name = "joserfc" -version = "1.6.5" +version = "1.6.8" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "cryptography" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/3b/dc/5f768c2e391e9afabe5d18e3221346deb5fb6338565f1ccc9e7c6d7befdd/joserfc-1.6.5.tar.gz", hash = "sha256:1482a7db78fb4602e44ed89e51b599d052e091288c7c532c5b694e20149dec48", size = 231881, upload-time = "2026-05-06T04:58:13.408Z" } +sdist = { url = "https://files.pythonhosted.org/packages/5d/ac/d4fd5b30f82900eac60d765f179f0ba005825ac462cc8ced6e13ec685ab3/joserfc-1.6.8.tar.gz", hash = "sha256:878620c553a6ebdd76ccdc356782fee3f735f21a356d079a546b42a4670ace5f", size = 232930, upload-time = "2026-05-27T03:22:37.819Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/54/3b/ad1cb22e75c963b1f07c8a2329bf47227ce7e4361df5eb2fb101b2ce33ef/joserfc-1.6.5-py3-none-any.whl", hash = "sha256:e9878a0f8243fe7b95e11fdda81374ca9f7a689e302751579d3dfdeec559675e", size = 70464, upload-time = "2026-05-06T04:58:11.668Z" }, + { url = "https://files.pythonhosted.org/packages/98/8c/5cdce2cf3ce8155849baf9a5e2ce77e89dc87ec3bdb38259e5d85fbc45bd/joserfc-1.6.8-py3-none-any.whl", hash = "sha256:22fb31a69094a5e6f44632002a9df2c30c941fc6c8ce1b037e92c03de954cf9f", size = 70927, upload-time = "2026-05-27T03:22:35.796Z" }, ] [[package]] From a4d6a69880c464f820e12df44e01c4789323a9f0 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 8 Jul 2026 13:42:30 +0200 Subject: [PATCH 387/468] chore: update pre-commit hooks (#4125) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.15 → v0.15.20](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.15...v0.15.20) - [github.com/scientific-python/cookie: 2026.04.04 → 2026.06.18](https://github.com/scientific-python/cookie/compare/2026.04.04...2026.06.18) - [github.com/numpy/numpydoc: v1.10.0 → v1.11.0rc0](https://github.com/numpy/numpydoc/compare/v1.10.0...v1.11.0rc0) - [github.com/zizmorcore/zizmor-pre-commit: v1.25.2 → v1.26.1](https://github.com/zizmorcore/zizmor-pre-commit/compare/v1.25.2...v1.26.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fb2e8c3c6f..e08c98abca 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.15 + rev: v0.15.20 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] @@ -41,11 +41,11 @@ repos: always_run: true types_or: [python, pyi] - repo: https://github.com/scientific-python/cookie - rev: 2026.04.04 + rev: 2026.06.18 hooks: - id: sp-repo-review - repo: https://github.com/numpy/numpydoc - rev: v1.10.0 + rev: v1.11.0rc0 hooks: - id: numpydoc-validation - repo: local @@ -58,7 +58,7 @@ repos: types: [python] files: ^(src|tests)/ - repo: https://github.com/zizmorcore/zizmor-pre-commit - rev: v1.25.2 + rev: v1.26.1 hooks: - id: zizmor - repo: https://github.com/twisted/towncrier From a259ec141bbbdfa4ea48831ac076850ef24035fc Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Wed, 8 Jul 2026 13:53:31 +0200 Subject: [PATCH 388/468] Remove broken badge (#4121) * Remove broken badge It relies on a CI workflow that had been removed in 2024 by 9e3e8c0. It's unclear whether it should be replaced by a different CI workflow, and if so which one. * Horizontal layout for badges, to save space * Remove Funding Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: Davis Bennett --- README.md | 99 +++++-------------------------------------------------- 1 file changed, 8 insertions(+), 91 deletions(-) diff --git a/README.md b/README.md index 45410eeb7b..fb0890d18c 100644 --- a/README.md +++ b/README.md @@ -4,97 +4,14 @@ # Zarr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Latest Release - - latest release - -
- - latest release - -
Package Status - - status - -
License - - license - -
Build Status - - build status - -
Pre-commit Status - - pre-commit status - -
Coverage - - coverage - -
Downloads - - pypi downloads - -
Developer Chat - - - -
Funding - - CZI's Essential Open Source Software for Science - -
Citation - - DOI - -
+[![Latest Release](https://badge.fury.io/py/zarr.svg)](https://pypi.org/project/zarr/) +[![CondaForge](https://anaconda.org/conda-forge/zarr/badges/version.svg)](https://anaconda.org/anaconda/zarr/) +[![Package Status](https://img.shields.io/pypi/status/zarr.svg)](https://pypi.org/project/zarr/) +[![License](https://img.shields.io/pypi/l/zarr.svg)](https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt) +[![Coverage](https://codecov.io/gh/zarr-developers/zarr-python/branch/main/graph/badge.svg)](https://codecov.io/gh/zarr-developers/zarr-python) +[![Downloads](https://pepy.tech/badge/zarr)](https://zarr.readthedocs.io) +[![Developer Chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://ossci.zulipchat.com/#narrow/channel/423692-Zarr-Python) +[![Citation](https://zenodo.org/badge/DOI/10.5281/zenodo.3773450.svg)](https://doi.org/10.5281/zenodo.3773450) ## What is it? From aedb360e27ca9795e6376ce0c14fa934d8385b2f Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Wed, 8 Jul 2026 15:32:28 +0200 Subject: [PATCH 389/468] docs: fix CacheStore max_age_seconds docstring default (#4133) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * docs: fix CacheStore max_age_seconds docstring default The docstring documented max_age_seconds as 'int | None' with a default of None, but the signature defaults to "infinity" and None is rejected by validation. Also note that cache_store must support deletes. Co-Authored-By: Claude Fable 5 --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 --- changes/4133.doc.md | 1 + src/zarr/experimental/cache_store.py | 9 +++++---- 2 files changed, 6 insertions(+), 4 deletions(-) create mode 100644 changes/4133.doc.md diff --git a/changes/4133.doc.md b/changes/4133.doc.md new file mode 100644 index 0000000000..9690318b46 --- /dev/null +++ b/changes/4133.doc.md @@ -0,0 +1 @@ +Fixed the documented default of ``max_age_seconds`` in the ``CacheStore`` docstring: the default is ``"infinity"`` (no expiration), not ``None``, which is rejected. Also noted that ``cache_store`` must support deletes. diff --git a/src/zarr/experimental/cache_store.py b/src/zarr/experimental/cache_store.py index 1535b42f67..dd50693ad9 100644 --- a/src/zarr/experimental/cache_store.py +++ b/src/zarr/experimental/cache_store.py @@ -52,10 +52,11 @@ class CacheStore(WrapperStore[Store]): store : Store The underlying store to wrap with caching cache_store : Store - The store to use for caching (can be any Store implementation) - max_age_seconds : int | None, optional - Maximum age of cached entries in seconds. None means no expiration. - Default is None. + The store to use for caching (can be any Store implementation that + supports deletes) + max_age_seconds : int or "infinity", optional + Maximum age of cached entries in seconds. The string "infinity" means + entries never expire. Default is "infinity". max_size : int | None, optional Maximum size of the cache in bytes. When exceeded, least recently used items are evicted. None means unlimited size. Default is None. From 8db2684f92bda15857fda689cb969f86f455bde2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 9 Jul 2026 07:33:05 +0200 Subject: [PATCH 390/468] chore(deps): bump the actions group with 3 updates (#4135) Bumps the actions group with 3 updates: [scientific-python/issue-from-pytest-log-action](https://github.com/scientific-python/issue-from-pytest-log-action), [j178/prek-action](https://github.com/j178/prek-action) and [actions/attest](https://github.com/actions/attest). Updates `scientific-python/issue-from-pytest-log-action` from 1.5.0 to 1.6.0 - [Release notes](https://github.com/scientific-python/issue-from-pytest-log-action/releases) - [Commits](https://github.com/scientific-python/issue-from-pytest-log-action/compare/8e905db353437cda1d6a773de245343fbfc940dd...87351a8f864e969567cda22a25a2f214cbe2340f) Updates `j178/prek-action` from 2.0.4 to 2.0.5 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/bdca6f102f98e2b4c7029491a53dfd366469e33d...e98a699c41eb69ab013a45817a0406469a748f8d) Updates `actions/attest` from 4.1.0 to 4.1.1 - [Release notes](https://github.com/actions/attest/releases) - [Changelog](https://github.com/actions/attest/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest/compare/59d89421af93a897026c735860bf21b6eb4f7b26...a1948c3f048ba23858d222213b7c278aabede763) --- updated-dependencies: - dependency-name: scientific-python/issue-from-pytest-log-action dependency-version: 1.6.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/attest dependency-version: 4.1.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/lint.yml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/zarr-metadata-release.yml | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 950714e098..01212dfb56 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -109,7 +109,7 @@ jobs: && steps.status.outcome == 'failure' && github.event_name == 'schedule' && github.repository_owner == 'zarr-developers' - uses: scientific-python/issue-from-pytest-log-action@8e905db353437cda1d6a773de245343fbfc940dd # v1.5.0 + uses: scientific-python/issue-from-pytest-log-action@87351a8f864e969567cda22a25a2f214cbe2340f # v1.6.0 with: log-path: output-${{ matrix.python-version }}-log.jsonl issue-title: "Nightly Hypothesis tests failed" diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 287c76e7b6..8190b1e061 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -30,4 +30,4 @@ jobs: uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 with: enable-cache: true - - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4 + - uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2.0.5 diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 6b5895a413..4d460f4a56 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -81,7 +81,7 @@ jobs: name: releases path: dist - name: Generate artifact attestation - uses: actions/attest@59d89421af93a897026c735860bf21b6eb4f7b26 # v4.1.0 + uses: actions/attest@a1948c3f048ba23858d222213b7c278aabede763 # v4.1.1 with: subject-path: dist/* - name: Publish package to PyPI diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index 689d3392ba..db05489798 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -82,7 +82,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@59d89421af93a897026c735860bf21b6eb4f7b26 # v4.1.0 + uses: actions/attest@a1948c3f048ba23858d222213b7c278aabede763 # v4.1.1 with: subject-path: dist/* @@ -107,7 +107,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@59d89421af93a897026c735860bf21b6eb4f7b26 # v4.1.0 + uses: actions/attest@a1948c3f048ba23858d222213b7c278aabede763 # v4.1.1 with: subject-path: dist/* From 434c7fbc2b30b306082bc8f8259137e58cd5d5e9 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 9 Jul 2026 08:47:57 +0200 Subject: [PATCH 391/468] ci: stop dependabot updates targeting support/v2 (#4136) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * ci: stop dependabot updates targeting support/v2 The support/v2 branch's CI is failing for reasons unrelated to actions bumps (numpy 2.5 deprecation, Windows azurite SSL errors, RTD build), so the weekly dependabot PRs against it are pure noise. Remove the target-branch entry so dependabot only tracks main. Assisted-by: ClaudeCode:claude-fable-5 --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/dependabot.yml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 849d44efc9..0c794d9b08 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -31,14 +31,3 @@ updates: - "*" cooldown: default-days: 7 - - package-ecosystem: "github-actions" - directory: "/" - target-branch: "support/v2" - schedule: - interval: "weekly" - groups: - actions: - patterns: - - "*" - cooldown: - default-days: 7 From 79486f7f42f64c50a9655d3ef3cea39a144dc4b2 Mon Sep 17 00:00:00 2001 From: Davis Bennett Date: Thu, 9 Jul 2026 11:49:22 +0200 Subject: [PATCH 392/468] docs: fix errors and improve consistency across the documentation (#4132) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * docs: fix errors and improve consistency across the documentation A full review of the documentation, verified by executing every runnable snippet against the current source. Highlights: Correctness: - performance.md: fix three claims contradicted by the page's own rendered output (memory-order/compression, inverted write_empty_chunks conclusion, wrong async.concurrency and threading.max_workers defaults); update stale MemoryStore pickle claim - Make three invisible exec blocks visible (rectilinear enable snippet in arrays.md, two config snippets in performance.md) - storage.md: fix the explicit-S3-filesystem example (endpoint_url misuse, missing bucket path) - config.md: show true defaults (earlier example no longer leaks array.order into the session); fix codecs.bytes key - arrays.md: document all five ArrayConfig options; correct memory:// store description; fix wrong column-index comments; remove orphaned example - v3_migration.md: remove Group.move and dimension_separator from not-yet-ported lists (both work); fix truncated store table row; update lapsed 2.x support-window and stale work-in-progress framing - cli.md: document the required cli extra; fix dry-run output; name the equivalent functions in zarr.metadata.migrate_v3 - installation.md: correct typing_extensions minimum; document all optional dependency groups (remote, gpu, cli, optional, cast-value-rs) - gpu.md: fix nonexistent zarr.Config.enable_gpu; add installation guidance - contributing.md: fix docs build output dir and serve URL; drop outdated doctest note - extending.md: custom data types are supported now, not future work - data_types.md: remove stray doctest output from a source block; use public zarr.dtype import; drop dead warnings-suppression boilerplate - quick-start.md: fix result="html" on a Python-repr output block Usability: - Reorder the user-guide nav into a beginner-to-advanced progression - quick-start.md: add H1 and heading hierarchy, remote-storage install note, and a Next steps section - user-guide/index.md: list the CLI, experimental, and examples pages - groups.md: explain group/create_group/open_group; document member enumeration and deletion - attributes.md: document bulk updates via update_attributes and deletion - consolidated_metadata.md: document the public use_consolidated knob - glossary.md: add Group, Attributes, and Consolidated Metadata entries; cover v2 metadata documents - Add cross-links between related pages throughout; replace "Coming soon" stubs with links to existing content - experimental.md: nest CacheStore sections properly; link the experimental API policy - release-notes.md: normalize version headings and dates Co-Authored-By: Claude Fable 5 * docs: add changelog fragment for #4132 Co-Authored-By: Claude Fable 5 * docs: standardize on American spelling (behaviour -> behavior) Co-Authored-By: Claude Fable 5 * docs: render test="true" and exec="false" fences as code blocks Markdown Exec's superfences fence only claims exec="true" blocks. Fences carrying the repo's other validation markers (test="true", exec="false") failed superfences validation entirely and their contents spilled into the page as raw markdown -- most visibly the custom dtype example, where the included script's PEP 723 header rendered as a series of headings. The GPU page, the quick-start S3 example, and the exec="false" opt-out blocks were equally affected. Add an MkDocs hook that registers a second python fence, tried when Markdown Exec's declines, which strips the validation attributes and delegates to the standard superfences highlighter. Co-Authored-By: Claude Fable 5 * docs: convert rectilinear chunks notebook to a markdown example page The notebook rendered oddly via mkdocs-jupyter: the PEP 723 dependency header appeared as the first code cell, a bare ConfigSet repr leaked into the output, and the page styling did not match the rest of the site. Since the example cannot execute at build time anyway (it requires an xarray fork with rectilinear chunk grid support plus remote data), convert it to a markdown page in the same style as the custom dtype example, with the captured outputs shown as static blocks and an admonition explaining the requirements. The page URL is unchanged. With no notebooks left in the docs, also drop the mkdocs-jupyter plugin and dependency. Co-Authored-By: Claude Fable 5 * docs: shorten custom dtype example title to "Custom Data Type" Co-Authored-By: Claude Fable 5 * docs: restructure API reference nav to distinguish classes from modules The API nav was a flat list whose labels came from each page's first mkdocstrings heading, mixing classes (Array), modules (codecs), and function groups (create) with no visual distinction, plus accidental labels like a title-cased Cpu, two literal Index entries, and an API section nested under API Reference. Group the nav into Classes / Functions / Modules with explicit titles: classes as zarr.Array and zarr.Group, function pages as Creating/Opening/ Saving/Loading, and modules by their dotted import path (zarr.storage, zarr.abc.store, ...), so the naming convention itself distinguishes the kinds. Also give the four subpackage index pages consistent titles. Page URLs are unchanged. Co-Authored-By: Claude Fable 5 * docs: flatten API reference nav with kind annotations Users browsing the API reference don't know in advance whether the thing they want is a class, function, or module, so grouping the nav by kind made them guess. Flatten the list back and annotate each entry with its kind instead: zarr.Array (class), Creating (functions), zarr.storage (module). Nesting is kept only where it means containment (the abc, api, buffer, and testing subpackages); their children are unannotated since context makes them modules. Co-Authored-By: Claude Fable 5 * docs: use bare function-page names from main in the API nav create/open/save/load, as on main, rather than invented verb labels; the (functions) annotation carries the kind. Co-Authored-By: Claude Fable 5 * docs: render API nav identifiers in monospace Material passes nav titles through as HTML, so wrap the identifier part of each API reference nav label in , keeping the (class)/(functions)/ (module) annotations in regular type. Verified the HTML is not escaped in the sidebar, is stripped from the browser , and behaves in search like any backticked heading. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: one API nav entry per function, mirroring the flat zarr namespace The create/open/save/load pages grouped functions by verb, an organization that doesn't exist in the codebase -- all of these are top-level names in the flat zarr namespace. Replace them with one page and one nav entry per function (zarr.create_array, zarr.open_group, ...), alphabetized case- insensitively alongside the classes and modules, so zarr.Array (class) sits next to zarr.array (function). This also adds previously undocumented public functions to the API reference: zarr.consolidate_metadata and zarr.print_debug_info. The unimplemented copy/copy_all/copy_store stubs and the deprecated zarr.tree are deliberately excluded. Old create/open/save/load URLs redirect to representative function pages. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * docs: use mkdocstrings symbol badges for kind annotations in API nav The spelled-out (function)/(module)/(class) annotations made 8 of 41 monospace nav entries wrap to two lines. Replace them with the compact func/mod/class doc-symbol badges that mkdocstrings already renders in every page's table of contents, joined to the name with a non-breaking space so badge and name never separate. Verified in the rendered site: no wrapped entries, badge CSS loads globally, and function-page titles render as e.g. 'func zarr.open_group'. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> --- changes/4132.doc.md | 6 + docs/api/zarr/abc/index.md | 18 +- docs/api/zarr/api/index.md | 4 +- docs/api/zarr/buffer/index.md | 4 + docs/api/zarr/create.md | 19 - docs/api/zarr/functions/array.md | 5 + .../zarr/functions/consolidate_metadata.md | 5 + docs/api/zarr/functions/create.md | 5 + docs/api/zarr/functions/create_array.md | 5 + docs/api/zarr/functions/create_group.md | 5 + docs/api/zarr/functions/create_hierarchy.md | 5 + docs/api/zarr/functions/empty.md | 5 + docs/api/zarr/functions/empty_like.md | 5 + docs/api/zarr/functions/from_array.md | 5 + docs/api/zarr/functions/full.md | 5 + docs/api/zarr/functions/full_like.md | 5 + docs/api/zarr/functions/group.md | 5 + docs/api/zarr/{ => functions}/load.md | 2 +- docs/api/zarr/functions/ones.md | 5 + docs/api/zarr/functions/ones_like.md | 5 + docs/api/zarr/functions/open.md | 5 + docs/api/zarr/functions/open_array.md | 5 + docs/api/zarr/functions/open_consolidated.md | 5 + docs/api/zarr/functions/open_group.md | 5 + docs/api/zarr/functions/open_like.md | 5 + docs/api/zarr/functions/print_debug_info.md | 5 + docs/api/zarr/functions/save.md | 5 + docs/api/zarr/functions/save_array.md | 5 + docs/api/zarr/functions/save_group.md | 5 + docs/api/zarr/functions/zeros.md | 5 + docs/api/zarr/functions/zeros_like.md | 5 + docs/api/zarr/index.md | 8 +- docs/api/zarr/open.md | 9 - docs/api/zarr/save.md | 7 - docs/api/zarr/testing/index.md | 14 +- docs/contributing.md | 17 +- docs/index.md | 6 +- docs/quick-start.md | 37 +- docs/release-notes.md | 10 +- docs/user-guide/arrays.md | 67 +-- docs/user-guide/attributes.md | 28 +- docs/user-guide/cli.md | 26 +- docs/user-guide/config.md | 16 +- docs/user-guide/consolidated_metadata.md | 32 +- docs/user-guide/data_types.md | 35 +- .../examples/rectilinear_chunks.ipynb | 428 -------------- .../user-guide/examples/rectilinear_chunks.md | 173 ++++++ docs/user-guide/experimental.md | 45 +- docs/user-guide/extending.md | 18 +- docs/user-guide/glossary.md | 35 +- docs/user-guide/gpu.md | 42 +- docs/user-guide/groups.md | 52 +- docs/user-guide/index.md | 13 +- docs/user-guide/installation.md | 16 +- docs/user-guide/performance.md | 69 +-- docs/user-guide/storage.md | 23 +- docs/user-guide/v3_migration.md | 36 +- examples/custom_dtype/README.md | 13 +- mkdocs.yml | 108 ++-- mkdocs_hooks.py | 82 +++ pyproject.toml | 1 - uv.lock | 536 ------------------ 62 files changed, 900 insertions(+), 1280 deletions(-) create mode 100644 changes/4132.doc.md delete mode 100644 docs/api/zarr/create.md create mode 100644 docs/api/zarr/functions/array.md create mode 100644 docs/api/zarr/functions/consolidate_metadata.md create mode 100644 docs/api/zarr/functions/create.md create mode 100644 docs/api/zarr/functions/create_array.md create mode 100644 docs/api/zarr/functions/create_group.md create mode 100644 docs/api/zarr/functions/create_hierarchy.md create mode 100644 docs/api/zarr/functions/empty.md create mode 100644 docs/api/zarr/functions/empty_like.md create mode 100644 docs/api/zarr/functions/from_array.md create mode 100644 docs/api/zarr/functions/full.md create mode 100644 docs/api/zarr/functions/full_like.md create mode 100644 docs/api/zarr/functions/group.md rename docs/api/zarr/{ => functions}/load.md (57%) create mode 100644 docs/api/zarr/functions/ones.md create mode 100644 docs/api/zarr/functions/ones_like.md create mode 100644 docs/api/zarr/functions/open.md create mode 100644 docs/api/zarr/functions/open_array.md create mode 100644 docs/api/zarr/functions/open_consolidated.md create mode 100644 docs/api/zarr/functions/open_group.md create mode 100644 docs/api/zarr/functions/open_like.md create mode 100644 docs/api/zarr/functions/print_debug_info.md create mode 100644 docs/api/zarr/functions/save.md create mode 100644 docs/api/zarr/functions/save_array.md create mode 100644 docs/api/zarr/functions/save_group.md create mode 100644 docs/api/zarr/functions/zeros.md create mode 100644 docs/api/zarr/functions/zeros_like.md delete mode 100644 docs/api/zarr/open.md delete mode 100644 docs/api/zarr/save.md delete mode 100644 docs/user-guide/examples/rectilinear_chunks.ipynb create mode 100644 docs/user-guide/examples/rectilinear_chunks.md create mode 100644 mkdocs_hooks.py diff --git a/changes/4132.doc.md b/changes/4132.doc.md new file mode 100644 index 0000000000..3325c82f43 --- /dev/null +++ b/changes/4132.doc.md @@ -0,0 +1,6 @@ +Fixed many documentation errors found in a full review of the user guide, including +prose contradicted by rendered example output on the performance page, invisible +code blocks, an incorrect S3 example, stale "not yet implemented" claims in the +v3 migration guide, and undocumented optional dependency groups. Also improved +navigation order, cross-linking between pages, and coverage of group member +enumeration, bulk attribute updates, and the `use_consolidated` keyword. diff --git a/docs/api/zarr/abc/index.md b/docs/api/zarr/abc/index.md index 7c2fb2ef13..7e15cb2a51 100644 --- a/docs/api/zarr/abc/index.md +++ b/docs/api/zarr/abc/index.md @@ -1,7 +1,13 @@ -## Abstract base classes +--- +title: zarr.abc +--- -- **[buffer](./buffer.md)** - Providing access to underlying memory via [buffers](https://docs.python.org/3/c-api/buffer.html) -- **[codec](./codec.md)** - Expressing [zarr codecs](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-encoding) -- **[metadata](./metadata.md)** - Creating metadata classes compatible with the Zarr API -- **[numcodec](./numcodec.md)** - Protocols and classes for modeling codec interface used by numcodecs -- **[store](./store.md)** - ABC for implementing Zarr stores and managing getting and setting bytes in a store \ No newline at end of file +# zarr.abc + +Abstract base classes for extending Zarr-Python. + +- **[zarr.abc.buffer](./buffer.md)** - Providing access to underlying memory via [buffers](https://docs.python.org/3/c-api/buffer.html) +- **[zarr.abc.codec](./codec.md)** - Expressing [zarr codecs](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-encoding) +- **[zarr.abc.metadata](./metadata.md)** - Creating metadata classes compatible with the Zarr API +- **[zarr.abc.numcodec](./numcodec.md)** - Protocols and classes for modeling codec interface used by numcodecs +- **[zarr.abc.store](./store.md)** - ABC for implementing Zarr stores and managing getting and setting bytes in a store diff --git a/docs/api/zarr/api/index.md b/docs/api/zarr/api/index.md index 75b4fff62b..7fac5e766a 100644 --- a/docs/api/zarr/api/index.md +++ b/docs/api/zarr/api/index.md @@ -1,5 +1,7 @@ --- -title: API +title: zarr.api --- +# zarr.api + Zarr provides both an [async](./asynchronous.md) and a [sync](./synchronous.md) API. See those pages for more details. diff --git a/docs/api/zarr/buffer/index.md b/docs/api/zarr/buffer/index.md index 0b303781e1..ebbb9e1c99 100644 --- a/docs/api/zarr/buffer/index.md +++ b/docs/api/zarr/buffer/index.md @@ -1,3 +1,7 @@ +--- +title: zarr.buffer +--- + Zarr provides buffer classes for both the [cpu](./cpu.md) and [gpu](./gpu.md). Generic buffer functionality is also detailed below. ::: zarr.buffer diff --git a/docs/api/zarr/create.md b/docs/api/zarr/create.md deleted file mode 100644 index 971e9c293c..0000000000 --- a/docs/api/zarr/create.md +++ /dev/null @@ -1,19 +0,0 @@ ---- -title: create ---- - -::: zarr.array -::: zarr.create -::: zarr.create_array -::: zarr.create_group -::: zarr.create_hierarchy -::: zarr.empty -::: zarr.empty_like -::: zarr.full -::: zarr.full_like -::: zarr.from_array -::: zarr.group -::: zarr.ones -::: zarr.ones_like -::: zarr.zeros -::: zarr.zeros_like diff --git a/docs/api/zarr/functions/array.md b/docs/api/zarr/functions/array.md new file mode 100644 index 0000000000..ff7242005c --- /dev/null +++ b/docs/api/zarr/functions/array.md @@ -0,0 +1,5 @@ +--- +title: zarr.array +--- + +::: zarr.array diff --git a/docs/api/zarr/functions/consolidate_metadata.md b/docs/api/zarr/functions/consolidate_metadata.md new file mode 100644 index 0000000000..946531f028 --- /dev/null +++ b/docs/api/zarr/functions/consolidate_metadata.md @@ -0,0 +1,5 @@ +--- +title: zarr.consolidate_metadata +--- + +::: zarr.consolidate_metadata diff --git a/docs/api/zarr/functions/create.md b/docs/api/zarr/functions/create.md new file mode 100644 index 0000000000..b43094eaba --- /dev/null +++ b/docs/api/zarr/functions/create.md @@ -0,0 +1,5 @@ +--- +title: zarr.create +--- + +::: zarr.create diff --git a/docs/api/zarr/functions/create_array.md b/docs/api/zarr/functions/create_array.md new file mode 100644 index 0000000000..a9f4a24bd0 --- /dev/null +++ b/docs/api/zarr/functions/create_array.md @@ -0,0 +1,5 @@ +--- +title: zarr.create_array +--- + +::: zarr.create_array diff --git a/docs/api/zarr/functions/create_group.md b/docs/api/zarr/functions/create_group.md new file mode 100644 index 0000000000..50beb0674c --- /dev/null +++ b/docs/api/zarr/functions/create_group.md @@ -0,0 +1,5 @@ +--- +title: zarr.create_group +--- + +::: zarr.create_group diff --git a/docs/api/zarr/functions/create_hierarchy.md b/docs/api/zarr/functions/create_hierarchy.md new file mode 100644 index 0000000000..38938ffee2 --- /dev/null +++ b/docs/api/zarr/functions/create_hierarchy.md @@ -0,0 +1,5 @@ +--- +title: zarr.create_hierarchy +--- + +::: zarr.create_hierarchy diff --git a/docs/api/zarr/functions/empty.md b/docs/api/zarr/functions/empty.md new file mode 100644 index 0000000000..aff67bb9ed --- /dev/null +++ b/docs/api/zarr/functions/empty.md @@ -0,0 +1,5 @@ +--- +title: zarr.empty +--- + +::: zarr.empty diff --git a/docs/api/zarr/functions/empty_like.md b/docs/api/zarr/functions/empty_like.md new file mode 100644 index 0000000000..9e2fbd26a5 --- /dev/null +++ b/docs/api/zarr/functions/empty_like.md @@ -0,0 +1,5 @@ +--- +title: zarr.empty_like +--- + +::: zarr.empty_like diff --git a/docs/api/zarr/functions/from_array.md b/docs/api/zarr/functions/from_array.md new file mode 100644 index 0000000000..7ab8179b05 --- /dev/null +++ b/docs/api/zarr/functions/from_array.md @@ -0,0 +1,5 @@ +--- +title: zarr.from_array +--- + +::: zarr.from_array diff --git a/docs/api/zarr/functions/full.md b/docs/api/zarr/functions/full.md new file mode 100644 index 0000000000..d6c60de2d5 --- /dev/null +++ b/docs/api/zarr/functions/full.md @@ -0,0 +1,5 @@ +--- +title: zarr.full +--- + +::: zarr.full diff --git a/docs/api/zarr/functions/full_like.md b/docs/api/zarr/functions/full_like.md new file mode 100644 index 0000000000..eb5c162f76 --- /dev/null +++ b/docs/api/zarr/functions/full_like.md @@ -0,0 +1,5 @@ +--- +title: zarr.full_like +--- + +::: zarr.full_like diff --git a/docs/api/zarr/functions/group.md b/docs/api/zarr/functions/group.md new file mode 100644 index 0000000000..3048218f6b --- /dev/null +++ b/docs/api/zarr/functions/group.md @@ -0,0 +1,5 @@ +--- +title: zarr.group +--- + +::: zarr.group diff --git a/docs/api/zarr/load.md b/docs/api/zarr/functions/load.md similarity index 57% rename from docs/api/zarr/load.md rename to docs/api/zarr/functions/load.md index d6463ca976..aa004076ab 100644 --- a/docs/api/zarr/load.md +++ b/docs/api/zarr/functions/load.md @@ -1,5 +1,5 @@ --- -title: load +title: zarr.load --- ::: zarr.load diff --git a/docs/api/zarr/functions/ones.md b/docs/api/zarr/functions/ones.md new file mode 100644 index 0000000000..b7757da1bc --- /dev/null +++ b/docs/api/zarr/functions/ones.md @@ -0,0 +1,5 @@ +--- +title: zarr.ones +--- + +::: zarr.ones diff --git a/docs/api/zarr/functions/ones_like.md b/docs/api/zarr/functions/ones_like.md new file mode 100644 index 0000000000..cffccb10ef --- /dev/null +++ b/docs/api/zarr/functions/ones_like.md @@ -0,0 +1,5 @@ +--- +title: zarr.ones_like +--- + +::: zarr.ones_like diff --git a/docs/api/zarr/functions/open.md b/docs/api/zarr/functions/open.md new file mode 100644 index 0000000000..3d75977395 --- /dev/null +++ b/docs/api/zarr/functions/open.md @@ -0,0 +1,5 @@ +--- +title: zarr.open +--- + +::: zarr.open diff --git a/docs/api/zarr/functions/open_array.md b/docs/api/zarr/functions/open_array.md new file mode 100644 index 0000000000..f40da1bd5d --- /dev/null +++ b/docs/api/zarr/functions/open_array.md @@ -0,0 +1,5 @@ +--- +title: zarr.open_array +--- + +::: zarr.open_array diff --git a/docs/api/zarr/functions/open_consolidated.md b/docs/api/zarr/functions/open_consolidated.md new file mode 100644 index 0000000000..de71cf7662 --- /dev/null +++ b/docs/api/zarr/functions/open_consolidated.md @@ -0,0 +1,5 @@ +--- +title: zarr.open_consolidated +--- + +::: zarr.open_consolidated diff --git a/docs/api/zarr/functions/open_group.md b/docs/api/zarr/functions/open_group.md new file mode 100644 index 0000000000..4944e94e06 --- /dev/null +++ b/docs/api/zarr/functions/open_group.md @@ -0,0 +1,5 @@ +--- +title: zarr.open_group +--- + +::: zarr.open_group diff --git a/docs/api/zarr/functions/open_like.md b/docs/api/zarr/functions/open_like.md new file mode 100644 index 0000000000..1aea075a81 --- /dev/null +++ b/docs/api/zarr/functions/open_like.md @@ -0,0 +1,5 @@ +--- +title: zarr.open_like +--- + +::: zarr.open_like diff --git a/docs/api/zarr/functions/print_debug_info.md b/docs/api/zarr/functions/print_debug_info.md new file mode 100644 index 0000000000..c98329f893 --- /dev/null +++ b/docs/api/zarr/functions/print_debug_info.md @@ -0,0 +1,5 @@ +--- +title: zarr.print_debug_info +--- + +::: zarr.print_debug_info diff --git a/docs/api/zarr/functions/save.md b/docs/api/zarr/functions/save.md new file mode 100644 index 0000000000..6c8eae410f --- /dev/null +++ b/docs/api/zarr/functions/save.md @@ -0,0 +1,5 @@ +--- +title: zarr.save +--- + +::: zarr.save diff --git a/docs/api/zarr/functions/save_array.md b/docs/api/zarr/functions/save_array.md new file mode 100644 index 0000000000..58a6d5143d --- /dev/null +++ b/docs/api/zarr/functions/save_array.md @@ -0,0 +1,5 @@ +--- +title: zarr.save_array +--- + +::: zarr.save_array diff --git a/docs/api/zarr/functions/save_group.md b/docs/api/zarr/functions/save_group.md new file mode 100644 index 0000000000..ba66a70563 --- /dev/null +++ b/docs/api/zarr/functions/save_group.md @@ -0,0 +1,5 @@ +--- +title: zarr.save_group +--- + +::: zarr.save_group diff --git a/docs/api/zarr/functions/zeros.md b/docs/api/zarr/functions/zeros.md new file mode 100644 index 0000000000..d43e8d913b --- /dev/null +++ b/docs/api/zarr/functions/zeros.md @@ -0,0 +1,5 @@ +--- +title: zarr.zeros +--- + +::: zarr.zeros diff --git a/docs/api/zarr/functions/zeros_like.md b/docs/api/zarr/functions/zeros_like.md new file mode 100644 index 0000000000..5adf1a23b3 --- /dev/null +++ b/docs/api/zarr/functions/zeros_like.md @@ -0,0 +1,5 @@ +--- +title: zarr.zeros_like +--- + +::: zarr.zeros_like diff --git a/docs/api/zarr/index.md b/docs/api/zarr/index.md index 194edb7913..f691c4599a 100644 --- a/docs/api/zarr/index.md +++ b/docs/api/zarr/index.md @@ -14,13 +14,13 @@ Complete reference documentation for the Zarr-Python API. - **[Array](array.md)** - The main Zarr array class for N-dimensional data - **[Group](group.md)** - Hierarchical organization of arrays and subgroups -- **[Create](create.md)** - Functions for creating new arrays and groups -- **[Open](open.md)** - Opening existing Zarr stores and arrays +- **[create_array](functions/create_array.md)** and **[create_group](functions/create_group.md)** - Creating new arrays and groups +- **[open](functions/open.md)**, **[open_array](functions/open_array.md)**, and **[open_group](functions/open_group.md)** - Opening existing Zarr stores, arrays, and groups ### Data Operations -- **[Load](load.md)** - Loading data from Zarr stores -- **[Save](save.md)** - Saving data to Zarr format +- **[load](functions/load.md)** - Loading data from Zarr stores +- **[save](functions/save.md)** - Saving data to Zarr format ### Data Types and Configuration diff --git a/docs/api/zarr/open.md b/docs/api/zarr/open.md deleted file mode 100644 index c59f896129..0000000000 --- a/docs/api/zarr/open.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -title: open ---- - -::: zarr.open -::: zarr.open_array -::: zarr.open_consolidated -::: zarr.open_group -::: zarr.open_like diff --git a/docs/api/zarr/save.md b/docs/api/zarr/save.md deleted file mode 100644 index c611d10a4c..0000000000 --- a/docs/api/zarr/save.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: save ---- - -::: zarr.save -::: zarr.save_array -::: zarr.save_group diff --git a/docs/api/zarr/testing/index.md b/docs/api/zarr/testing/index.md index ab5dd1daa0..2b48ad349f 100644 --- a/docs/api/zarr/testing/index.md +++ b/docs/api/zarr/testing/index.md @@ -1,11 +1,13 @@ --- -title: testing +title: zarr.testing --- +# zarr.testing + See the following sub-modules: -- [buffer](./buffer.md) -- [stateful](./stateful.md) -- [store](./store.md) -- [strategies](./strategies.md) -- [utils](./utils.md) +- [zarr.testing.buffer](./buffer.md) +- [zarr.testing.stateful](./stateful.md) +- [zarr.testing.store](./store.md) +- [zarr.testing.strategies](./strategies.md) +- [zarr.testing.utils](./utils.md) diff --git a/docs/contributing.md b/docs/contributing.md index 084916d584..eaab26fbc7 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -18,9 +18,9 @@ g = zarr.group() # etc. ``` -2. An explanation of why the current behaviour is wrong/not desired, and what you expect instead. +2. An explanation of why the current behavior is wrong/not desired, and what you expect instead. -3. Information about the version of Zarr, along with versions of dependencies and the Python interpreter, and installation information. The version of Zarr can be obtained from the `zarr.__version__` property. Please also state how Zarr was installed, e.g., "installed via pip into a virtual environment", or "installed using conda". Information about other packages installed can be obtained by executing `pip freeze` (if using pip to install packages) or `conda env export` (if using conda to install packages) from the operating system command prompt. The version of the Python interpreter can be obtained by running a Python interactive session, e.g.: +3. Information about the version of Zarr, along with versions of dependencies and the Python interpreter, and installation information. The version of Zarr can be obtained from the `zarr.__version__` attribute. Please also state how Zarr was installed, e.g., "installed via pip into a virtual environment", or "installed using conda". Information about other packages installed can be obtained by executing `pip freeze` (if using pip to install packages) or `conda env export` (if using conda to install packages) from the operating system command prompt. The version of the Python interpreter can be obtained by running a Python interactive session, e.g.: ```console python @@ -133,8 +133,6 @@ hatch env run --env test.py3.12-optional run All tests are automatically run via GitHub Actions for every pull request and must pass before code can be accepted. Test coverage is also collected automatically via the Codecov service. -> **Note:** Previous versions of Zarr-Python made extensive use of doctests. These tests were not maintained during the 3.0 refactor but may be brought back in the future. See issue #2614 for more details. - ### Code standards - using prek All code must conform to the PEP8 standard. Regarding line length, lines up to 100 characters are allowed, although please try to keep under 90 wherever possible. @@ -215,9 +213,9 @@ The documentation can be built locally by running: hatch --env docs run build ``` -The resulting built documentation will be available in the `docs/_build/html` folder. +The resulting built documentation will be available in the `site` folder. -Hatch can also be used to serve continuously updating version of the documentation during development at [http://0.0.0.0:8000/](http://0.0.0.0:8000/). This can be done by running: +Hatch can also be used to serve continuously updating version of the documentation during development at [http://127.0.0.1:8000/](http://127.0.0.1:8000/). This can be done by running: ```bash hatch --env docs run serve @@ -292,6 +290,11 @@ that fits the block). `test="true"`, or `exec="false"` with a reason — so a block can never silently skip validation. A bare ` ```python ` fence, or a typo like `exec="on"`, fails that test. +Markdown Exec only renders `exec="true"` fences; the `mkdocs_hooks.py` hook at the +repository root makes `test="true"` and `exec="false"` fences render as ordinary +highlighted code blocks. Without it, these fences would fail superfences parsing and +their contents would spill into the page as raw markdown. + ##### Marker-bound blocks (GPU, S3) A `test="true"` block that needs special infrastructure declares a pytest marker with @@ -382,7 +385,7 @@ Releases are classified by the library changes contained in that release. This c Minor releases are safe for most users and downstream projects to adopt. -* **patch** releases (for example, `3.1.0` -> `3.1.1`) are for changes that contain no breaking or behaviour changes for downstream projects or users. Examples of changes suitable for a patch release are bugfixes and documentation improvements. +* **patch** releases (for example, `3.1.0` -> `3.1.1`) are for changes that contain no breaking or behavior changes for downstream projects or users. Examples of changes suitable for a patch release are bugfixes and documentation improvements. Users should always feel safe upgrading to the latest patch release. diff --git a/docs/index.md b/docs/index.md index b8c2b07ee7..1ec5e93c75 100644 --- a/docs/index.md +++ b/docs/index.md @@ -30,7 +30,7 @@ pip install zarr or `conda`: ```bash -conda install --channel conda-forge zarr +conda install -c conda-forge zarr ``` ## Navigating the documentation @@ -45,14 +45,14 @@ conda install --channel conda-forge zarr introduction to Zarr's main concepts and links to additional tutorials. -- [:material-book-open:{ .lg .middle } __User guide__](user-guide/installation.md) +- [:material-book-open:{ .lg .middle } __User guide__](user-guide/index.md) --- A detailed guide for how to use Zarr-Python. -- [:material-api:{ .lg .middle } __API Reference__](api/zarr/open.md) +- [:material-api:{ .lg .middle } __API Reference__](api/zarr/index.md) --- diff --git a/docs/quick-start.md b/docs/quick-start.md index 0bad4f2e34..29232d2a04 100644 --- a/docs/quick-start.md +++ b/docs/quick-start.md @@ -1,7 +1,11 @@ -This section will help you get up and running with +# Quick start + +This page will help you get up and running with the Zarr library in Python to efficiently manage and analyze multi-dimensional arrays. +Zarr must be installed first -- see the [installation guide](user-guide/installation.md) +if you have not installed it yet. -### Creating an Array +## Creating an Array To get started, you can create a simple Zarr array: @@ -42,12 +46,12 @@ Here, we created a 2D array of shape `(100, 100)`, chunked into blocks of `(10, 10)`, and filled it with random floating-point data. This array was written to a `LocalStore` in the `data/example-1.zarr` directory. -#### Compression and Filters +### Compression and Filters Zarr supports data compression and filters. For example, to use Blosc compression: -```python exec="true" session="quickstart" source="above" result="code" +```python exec="true" session="quickstart" source="above" result="ansi" # Create a 2D Zarr array with Blosc compression z = zarr.create_array( @@ -70,7 +74,7 @@ print(z.info) This compresses the data using the Blosc codec with shuffle enabled for better compression. -### Hierarchical Groups +## Hierarchical Groups Zarr allows you to create hierarchical groups, similar to directories: @@ -94,12 +98,12 @@ print(root.tree()) This creates a group hierarchy with a group (`foo`) and two arrays (`bar` and `spam`). -#### Batch Hierarchy Creation +### Batch Hierarchy Creation Zarr provides tools for creating a collection of arrays and groups with a single function call. Suppose we want to copy existing groups and arrays into a new storage backend: -```python exec="true" session="quickstart" source="above" result="html" +```python exec="true" session="quickstart" source="above" result="code" # Create nested groups and add arrays root = zarr.group("data/example-4.zarr", attributes={'name': 'root'}) @@ -122,7 +126,7 @@ assert new_root.attrs == root.attrs Note that [`zarr.create_hierarchy`][] will only initialize arrays and groups -- copying array data must be done in a separate step. -### Persistent Storage +## Persistent Storage Zarr supports persistent storage to disk or cloud-compatible backends. While examples above utilized a [`zarr.storage.LocalStore`][], a number of other storage options are available. @@ -150,7 +154,7 @@ store.close() To open an existing array from a ZIP file: -```python exec="true" session="quickstart" source="above" result="code" +```python exec="true" session="quickstart" source="above" result="ansi" # Open the ZipStore in read-only mode store = zarr.storage.ZipStore("data/example-5.zip", read_only=True) @@ -163,7 +167,9 @@ print(z[:]) Zarr also integrates seamlessly with cloud object storage such as Amazon S3 and Google Cloud Storage using external libraries like [s3fs](https://s3fs.readthedocs.io) or -[gcsfs](https://gcsfs.readthedocs.io): +[gcsfs](https://gcsfs.readthedocs.io). Remote storage support requires the `remote` +optional dependencies (`pip install "zarr[remote]"`) as well as a filesystem library +for your storage service, such as `s3fs` for S3: ```python test="true" session="s3demo" markers="s3" source="above" import zarr @@ -175,4 +181,13 @@ z = zarr.create_array( z[:, :] = np.random.random((100, 100)) ``` -Read more about Zarr's storage options in the [User Guide](user-guide/index.md). +See the [Remote Store](user-guide/storage.md#remote-store) section of the storage guide +for more detail, including how to configure the underlying filesystem with `storage_options`. + +## Next steps + +This page only scratches the surface. Continue with the [User Guide](user-guide/index.md), in particular: + +- **[Arrays](user-guide/arrays.md)** - creating, reading, and writing arrays in depth +- **[Groups](user-guide/groups.md)** - organizing arrays into hierarchies +- **[Storage](user-guide/storage.md)** - the full range of local, remote, and in-memory storage options diff --git a/docs/release-notes.md b/docs/release-notes.md index 93cf1e73b6..3ba870ac92 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -114,9 +114,9 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - [#3562](https://github.com/zarr-developers/zarr-python/issues/3562), [#3605](https://github.com/zarr-developers/zarr-python/issues/3605), [#3619](https://github.com/zarr-developers/zarr-python/issues/3619), [#3623](https://github.com/zarr-developers/zarr-python/issues/3623), [#3636](https://github.com/zarr-developers/zarr-python/issues/3636), [#3648](https://github.com/zarr-developers/zarr-python/issues/3648), [#3656](https://github.com/zarr-developers/zarr-python/issues/3656), [#3658](https://github.com/zarr-developers/zarr-python/issues/3658), [#3673](https://github.com/zarr-developers/zarr-python/issues/3673), [#3704](https://github.com/zarr-developers/zarr-python/issues/3704), [#3706](https://github.com/zarr-developers/zarr-python/issues/3706), [#3708](https://github.com/zarr-developers/zarr-python/issues/3708), [#3712](https://github.com/zarr-developers/zarr-python/issues/3712), [#3713](https://github.com/zarr-developers/zarr-python/issues/3713), [#3717](https://github.com/zarr-developers/zarr-python/issues/3717), [#3721](https://github.com/zarr-developers/zarr-python/issues/3721), [#3728](https://github.com/zarr-developers/zarr-python/issues/3728), [#3778](https://github.com/zarr-developers/zarr-python/issues/3778) -## zarr 3.1.5 (2025-11-21) +## 3.1.5 (2025-11-21) -## Bugfixes +### Bugfixes - Fix formatting errors in the release notes section of the docs. ([#3594](https://github.com/zarr-developers/zarr-python/issues/3594)) @@ -153,7 +153,7 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - [#3515](https://github.com/zarr-developers/zarr-python/issues/3515), [#3532](https://github.com/zarr-developers/zarr-python/issues/3532), [#3533](https://github.com/zarr-developers/zarr-python/issues/3533), [#3553](https://github.com/zarr-developers/zarr-python/issues/3553) -## zarr 3.1.3 (2025-09-18) +## 3.1.3 (2025-09-18) ### Features @@ -576,7 +576,7 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr parameters of those instances. `ChunkKeyEncodingLike` should be used by high-level functions to provide a convenient way for creating `ChunkKeyEncoding` objects. ([#2763](https://github.com/zarr-developers/zarr-python/issues/2763)) -## 3.0.1 (Jan. 17, 2025) +## 3.0.1 (2025-01-17) * Implement `zarr.from_array` using concurrent streaming ([#2622](https://github.com/zarr-developers/zarr-python/issues/2622)). @@ -604,7 +604,7 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr * Speed up hypothesis tests ([#2650](https://github.com/zarr-developers/zarr-python/issues/2650)). * Remove multiple imports for an import name ([#2723](https://github.com/zarr-developers/zarr-python/issues/2723)). -## 3.0.0 (Jan. 9, 2025) +## 3.0.0 (2025-01-09) 3.0.0 is a new major release of Zarr-Python, with many breaking changes. See the [v3 migration guide](user-guide/v3_migration.md) for a listing of what's changed. diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index dd1788b7d2..51b2fa1a17 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -8,8 +8,6 @@ Zarr has several functions for creating arrays. For example: import shutil shutil.rmtree('data', ignore_errors=True) import numpy as np - -np.random.seed(0) ``` ```python exec="true" session="arrays" source="above" result="ansi" @@ -21,12 +19,16 @@ print(z) The code above creates a 2-dimensional array of 32-bit integers with 10000 rows and 10000 columns, divided into chunks where each chunk has 1000 rows and 1000 columns (and so there will be 100 chunks in total). The data is written to an -in-memory store (see [`zarr.storage.MemoryStore`][] for more details). See -[Persistent arrays](#persistent-arrays) for details on storing arrays in other stores, -and see [Data types](data_types.md) for an in-depth look at the data types supported -by Zarr. - -See the [creation API documentation](../api/zarr/create.md) for more detailed information about +in-memory store: when `fsspec` is installed, a `memory://` URL resolves to a +[`zarr.storage.FsspecStore`][] backed by fsspec's in-memory filesystem; otherwise a +[`zarr.storage.ManagedMemoryStore`][] is used. See the [Storage guide](storage.md) +for more details on stores, and +[Persistent arrays](#persistent-arrays) for details on storing arrays in other stores. +See [Data types](data_types.md) for an in-depth look at the data types supported +by Zarr, and [Chunk size and shape](performance.md#chunk-size-and-shape) in the +performance guide for guidance on choosing chunk shapes. + +See the [`zarr.create_array`][] API documentation for more detailed information about creating arrays. ## Reading and writing data @@ -128,7 +130,7 @@ A Zarr array can be resized, which means that any of its dimensions can be increased or decreased in length. For example: ```python exec="true" session="arrays" source="above" result="ansi" -z = zarr.create_array(store='data/example-3.zarr', shape=(10000, 10000), dtype='int32',chunks=(1000, 1000)) +z = zarr.create_array(store='data/example-3.zarr', shape=(10000, 10000), dtype='int32', chunks=(1000, 1000)) z[:] = 42 print(f"Original shape: {z.shape}") z.resize((20000, 10000)) @@ -157,13 +159,15 @@ print(f"Shape after second append: {z.shape}") Zarr arrays are parametrized with a configuration that determines certain aspects of array behavior. -We currently support three configuration options for arrays: `write_empty_chunks`, `read_missing_chunks`, and `order`. +We currently support five configuration options for arrays: `order`, `write_empty_chunks`, `read_missing_chunks`, `sharding_coalesce_max_gap_bytes`, and `sharding_coalesce_max_bytes`. | field | type | default | description | | - | - | - | - | +| `order` | `Literal["C", "F"]` | `"C"` | The memory layout of arrays returned when reading data from the store. | `write_empty_chunks` | `bool` | `False` | Controls whether empty chunks are written to storage. See [Empty chunks](performance.md#empty-chunks). | `read_missing_chunks` | `bool` | `True` | Controls whether missing chunks are filled with the array's fill value on read. If `False`, reading missing chunks raises a [`ChunkNotFoundError`][zarr.errors.ChunkNotFoundError]. -| `order` | `Literal["C", "F"]` | `"C"` | The memory layout of arrays returned when reading data from the store. +| `sharding_coalesce_max_gap_bytes` | `int` | `1048576` (1 MiB) | When reading multiple chunks from the same shard, nearby byte ranges separated by no more than this many bytes are coalesced into a single request to the store. +| `sharding_coalesce_max_bytes` | `int` | `16777216` (16 MiB) | Requests will not be coalesced if doing so would exceed this byte size. !!! info The Zarr V3 spec states that readers should interpret an uninitialized chunk as containing the @@ -266,19 +270,6 @@ z = zarr.create_array(store='data/example-7.zarr', shape=data.shape, dtype=data. print(f"Compressors: {z.compressors}") ``` -To disable compression, set `compressors=None` when creating an array, e.g.: - -```python exec="true" session="arrays" source="above" result="ansi" -z = zarr.create_array( - store='data/example-8.zarr', - shape=(100000000,), - chunks=(1000000,), - dtype='int32', - compressors=None -) -print(f"Compressors: {z.compressors}") -``` - ## Filters In some cases, compression can be improved by transforming the data in some @@ -461,11 +452,11 @@ print(z.get_orthogonal_selection(([0, 2], slice(None)))) # select first and thi ``` ```python exec="true" session="arrays" source="above" result="ansi" -print(z.get_orthogonal_selection((slice(None), [1, 3]))) # select second and fourth columns) +print(z.get_orthogonal_selection((slice(None), [1, 3]))) # select second and fourth columns ``` ```python exec="true" session="arrays" source="above" result="ansi" -print(z.get_orthogonal_selection(([0, 2], [1, 3]))) # select rows [0, 2] and columns [1, 4] +print(z.get_orthogonal_selection(([0, 2], [1, 3]))) # select rows [0, 2] and columns [1, 3] ``` Data can also be modified, e.g.: @@ -489,7 +480,7 @@ print(z.oindex[:, [1, 3]]) # select second and fourth columns ``` ```python exec="true" session="arrays" source="above" result="ansi" -print(z.oindex[[0, 2], [1, 3]]) # select rows [0, 2] and columns [1, 4] +print(z.oindex[[0, 2], [1, 3]]) # select rows [0, 2] and columns [1, 3] ``` ```python exec="true" session="arrays" source="above" result="ansi" @@ -510,7 +501,7 @@ z[:] = data print(np.all(z.oindex[[0, 2], :] == z[[0, 2], :])) ``` -### Block Indexing +### Block indexing Zarr also supports block indexing, which allows selections of whole chunks based on their logical indices along each dimension of an array. For example, this allows selecting @@ -575,15 +566,6 @@ Any combination of integer and slice can be used for block indexing: print(z.blocks[2, 1:3]) ``` -```python exec="true" session="arrays" source="above" result="ansi" -root = zarr.create_group('data/example-19.zarr') -foo = root.create_array(name='foo', shape=(1000, 100), chunks=(10, 10), dtype='float32') -bar = root.create_array(name='bar', shape=(100,), dtype='int32') -foo[:, :] = np.random.random((1000, 100)) -bar[:] = np.arange(100) -print(root.tree()) -``` - ## Sharding Using small chunk shapes in very large arrays can lead to a very large number of chunks. @@ -596,7 +578,9 @@ This allows individual chunks to be read independently. However, when writing data, a full shard must be written in one go for optimal performance and to avoid concurrency issues. That means that shards are the units of writing and chunks are the units of reading. -Users need to configure the chunk and shard shapes accordingly. +Users need to configure the chunk and shard shapes accordingly. For guidance on +choosing chunk and shard shapes, see [Sharding](performance.md#sharding) in the +performance guide. Sharded arrays can be created by providing the `shards` parameter to [`zarr.create_array`][]. @@ -619,7 +603,7 @@ Without the `shards` argument, there would be 10,000 chunks stored as individual Because the feature is still stabilizing, it is disabled by default and must be explicitly enabled: - ```python exec="true" session="arrays-rectilinear" + ```python exec="true" session="arrays" source="above" import zarr zarr.config.set({"array.rectilinear_chunks": True}) ``` @@ -641,7 +625,6 @@ To create an array with rectilinear chunks, pass a nested list to the `chunks` parameter where each inner list gives the chunk sizes along one dimension: ```python exec="true" session="arrays" source="above" result="ansi" -zarr.config.set({"array.rectilinear_chunks": True}) z = zarr.create_array( store=zarr.storage.MemoryStore(), shape=(60, 100), @@ -775,9 +758,9 @@ pairs are accepted: When writing, Zarr automatically compresses repeated values into RLE format. -## Missing features in 3.0 +## Features not yet ported to Zarr-Python 3 -The following features have not been ported to 3.0 yet. +The following Zarr-Python 2 features are not yet available in Zarr-Python 3. ### Copying and migrating data diff --git a/docs/user-guide/attributes.md b/docs/user-guide/attributes.md index d5961ed38a..96a5d67584 100644 --- a/docs/user-guide/attributes.md +++ b/docs/user-guide/attributes.md @@ -32,5 +32,29 @@ print(z.attrs['baz']) print(z.attrs['qux']) ``` -Internally Zarr uses JSON to store array attributes, so attribute values must be -JSON serializable. +Attributes can be deleted with the `del` operator: + +```python exec="true" session="attributes" source="above" result="ansi" +del z.attrs['baz'] +print(sorted(z.attrs)) +``` + +Note that each attribute assignment or deletion writes the node's metadata +document back to the store. To change several attributes in a single write, +use [`zarr.Array.update_attributes`][] (or [`zarr.Group.update_attributes`][] +for groups), which merges the given dict into the existing attributes and +returns the updated array or group: + +```python exec="true" session="attributes" source="above" result="ansi" +z = z.update_attributes({'baz': 43, 'quux': True}) +print(sorted(z.attrs)) +``` + +Internally Zarr uses JSON to store array and group attributes, so attribute +values must be JSON serializable. + +When working with hierarchies that contain many arrays and groups, reading the +attributes of each node separately can be slow. See +[Consolidated metadata](consolidated_metadata.md) for a way to store the +metadata (including attributes) of all nodes in a hierarchy in a single +document. diff --git a/docs/user-guide/cli.md b/docs/user-guide/cli.md index 13fcb6f1b6..77f50f5eaf 100644 --- a/docs/user-guide/cli.md +++ b/docs/user-guide/cli.md @@ -2,9 +2,22 @@ Zarr-Python provides a command-line interface that enables: -- migration of Zarr v2 metadata to v3 +- migration of Zarr v2 metadata to v3 (see the [3.0 Migration Guide](v3_migration.md) for + migrating your *code* from the Zarr-Python 2 API to the Zarr-Python 3 API) - removal of v2 or v3 metadata +## Installation + +The command-line interface requires the `cli` optional dependencies. Install them with: + +```bash +pip install "zarr[cli]" +``` + +Without this extra, running `zarr` in a terminal will fail with `ModuleNotFoundError`. + +## Getting help + To see available commands run the following in a terminal: ```bash @@ -83,7 +96,7 @@ zarr remove-metadata v3 path/to/input.zarr By default, this will only allow removal of metadata if a valid alternative exists. For example, you can't remove v2 metadata unless v3 metadata exists at that location. -To override this behaviour use `--force`: +To override this behavior use `--force`: ```bash zarr remove-metadata v3 path/to/input.zarr --force @@ -98,7 +111,7 @@ or modifying any files. zarr migrate v3 path/to/input.zarr --dry-run Dry run enabled - no new files will be created or changed. Log of files that would be created on a real run: -Saving metadata to path/to/input.zarr/zarr.json +Saving metadata to file://path/to/input.zarr/zarr.json ``` ## Verbose @@ -113,5 +126,8 @@ zarr --verbose remove-metadata v2 path/to/input.zarr ## Equivalent functions -All features of the command-line interface are also available via functions under -`zarr.metadata`. \ No newline at end of file +All features of the command-line interface are also available as functions in the +`zarr.metadata.migrate_v3` module: +[`migrate_v2_to_v3`][zarr.metadata.migrate_v3.migrate_v2_to_v3] and +[`remove_metadata`][zarr.metadata.migrate_v3.remove_metadata]. +See the [`zarr.metadata` API reference](../api/zarr/metadata.md) for details. diff --git a/docs/user-guide/config.md b/docs/user-guide/config.md index 71c021b070..d1a70a14b0 100644 --- a/docs/user-guide/config.md +++ b/docs/user-guide/config.md @@ -6,14 +6,22 @@ is based on the [donfig](https://github.com/pytroll/donfig) Python library. Configuration values can be set using code like the following: ```python exec="true" session="config" source="above" result="ansi" - import zarr +zarr.config.set({'array.order': 'F'}) + print(zarr.config.get('array.order')) ``` +`zarr.config.set` can also be used as a context manager, which restores the +previous configuration on exit, and `zarr.config.reset` restores the default +configuration: + ```python exec="true" session="config" source="above" result="ansi" -zarr.config.set({'array.order': 'F'}) +zarr.config.reset() + +with zarr.config.set({'array.order': 'F'}): + print(zarr.config.get('array.order')) print(zarr.config.get('array.order')) ``` @@ -34,13 +42,13 @@ Configuration options include the following: - Whether missing chunks are filled with the array's fill value on read `array.read_missing_chunks` (default `True`). Set to `False` to raise a [`ChunkNotFoundError`][zarr.errors.ChunkNotFoundError] instead. - Async and threading options, e.g. `async.concurrency` and `threading.max_workers` - Selections of implementations of codecs, codec pipelines and buffers -- Enabling GPU support with `zarr.config.enable_gpu()`. See GPU support for more. +- Enabling GPU support with `zarr.config.enable_gpu()`. See [GPU support](gpu.md) for more. - Control request merging when reading multiple chunks from the same shard with `array.sharding_coalesce_max_gap_bytes` and `array.sharding_coalesce_max_bytes`. Reads of nearby chunks are coalesced into a single request to the store when separated by at most `sharding_coalesce_max_gap_bytes` and the resulting merged read is no larger than `sharding_coalesce_max_bytes`. For selecting custom implementations of codecs, pipelines, buffers and ndbuffers, first register the implementations in the registry and then select them in the config. For example, an implementation of the bytes codec in a class `'custompackage.NewBytesCodec'`, -requires the value of `codecs.bytes.name` to be `'custompackage.NewBytesCodec'`. +requires the value of `codecs.bytes` to be `'custompackage.NewBytesCodec'`. This is the current default configuration: diff --git a/docs/user-guide/consolidated_metadata.md b/docs/user-guide/consolidated_metadata.md index d8066b6846..7030ed6cbc 100644 --- a/docs/user-guide/consolidated_metadata.md +++ b/docs/user-guide/consolidated_metadata.md @@ -5,7 +5,7 @@ stores. [zarr-specs#309](https://github.com/zarr-developers/zarr-specs/pull/309) has proposed a formal extension to the v3 specification to support consolidated metadata. -Zarr-Python implements the [Consolidated Metadata](https://github.com/zarr-developers/zarr-specs/pull/309) for v2 and v3 stores. +Zarr-Python implements the Consolidated Metadata feature for both the v2 and v3 formats. Consolidated metadata can reduce the time needed to load the metadata for an entire hierarchy, especially when the metadata is being served over a network. Consolidated metadata essentially stores all the metadata for a hierarchy in the @@ -48,8 +48,8 @@ result = zarr.consolidate_metadata("memory://consolidated-metadata-demo") print(result) ``` -If we open that group, the Group's metadata has a `zarr.core.group.ConsolidatedMetadata` -that can be used: +If we open that group, the Group's metadata includes a `ConsolidatedMetadata` object +holding the metadata for every child node, which can be used: ```python exec="true" session="consolidated_metadata" source="above" result="ansi" from pprint import pprint @@ -58,7 +58,6 @@ import io consolidated = zarr.open_group(store="memory://consolidated-metadata-demo") consolidated_metadata = consolidated.metadata.consolidated_metadata.metadata -# Note: pprint can be used without capturing the output regularly output = io.StringIO() pprint(dict(sorted(consolidated_metadata.items())), stream=output, width=60) print(output.getvalue()) @@ -74,7 +73,7 @@ With nested groups, the consolidated metadata is available on the children, recu ```python exec="true" session="consolidated_metadata" source="above" result="ansi" child = group.create_group('child', attributes={'kind': 'child'}) -grandchild = child.create_group('child', attributes={'kind': 'grandchild'}) +grandchild = child.create_group('grandchild', attributes={'kind': 'grandchild'}) consolidated = zarr.consolidate_metadata("memory://consolidated-metadata-demo") output = io.StringIO() @@ -86,9 +85,26 @@ print(output.getvalue()) The keys in the consolidated metadata are sorted prior to writing. Keys are sorted in ascending order by path depth, where a path is defined as a sequence of strings joined by `"/"`. For keys with the same path length, lexicographic - order is used to break the tie. This behaviour ensures deterministic metadata + order is used to break the tie. This behavior ensures deterministic metadata output for a given group. +### Controlling the use of consolidated metadata + +By default, [`zarr.open_group`][] uses consolidated metadata if it is present, and +falls back to reading metadata from the store otherwise. This behavior can be +controlled with the `use_consolidated` keyword. Pass `use_consolidated=False` to +ignore consolidated metadata and always read the metadata of child nodes directly +from the store: + +```python exec="true" session="consolidated_metadata" source="above" result="ansi" +group = zarr.open_group(store="memory://consolidated-metadata-demo", use_consolidated=False) +print(group.metadata.consolidated_metadata) +``` + +Passing `use_consolidated=True` instead raises an error if consolidated metadata is +not found, which is useful when reading over a network, where relying on many +per-node metadata requests would be slow. + ## Synchronization and Concurrency Consolidated metadata is intended for read-heavy use cases on slowly changing @@ -99,7 +115,9 @@ removed, or modified, consolidated metadata may not be desirable. would need to be re-consolidated to keep it in sync with the store. 2. Readers using consolidated metadata will regularly see a "past" version of the metadata, at the time they read the root node with its consolidated - metadata. + metadata. Readers who need the latest view of a changing hierarchy can pass + `use_consolidated=False` to [`zarr.open_group`][] to always read child + metadata directly from the store. ## Stores Without Support for Consolidated Metadata diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md index 6f6bb05033..642a09d714 100644 --- a/docs/user-guide/data_types.md +++ b/docs/user-guide/data_types.md @@ -1,6 +1,6 @@ # Array data types -## Zarr's Data Type Model +## Zarr's data type model Zarr is designed for interoperability with NumPy, so if you are familiar with NumPy or any other N-dimensional array library, Zarr's model for array data types should seem familiar. However, Zarr @@ -14,7 +14,7 @@ which adds some unique aspects to the Zarr data type model. The following sections explain Zarr's data type model in greater detail and demonstrate the Zarr Python APIs for working with Zarr data types. -### Array Data Types +### Array data types Every Zarr array has a data type, which defines the meaning of the array's elements. An array's data type is encoded in the JSON metadata for the array. This means that the data type of an array must be @@ -38,10 +38,10 @@ For the boolean data type, the scalar encoding is simple—booleans are natively JSON, so Zarr saves booleans as JSON booleans. Other scalars, like floats or raw bytes, have more elaborate encoding schemes, and in some cases, this scheme depends on the Zarr format version. -## Data Types in Zarr Version 2 +## Data types in Zarr version 2 Version 2 of the Zarr format defined its data types relative to -[NumPy's data types](https://numpy.org/doc/2.1/reference/arrays.dtypes.html#data-type-objects-dtype), +[NumPy's data types](https://numpy.org/doc/stable/reference/arrays.dtypes.html#data-type-objects-dtype), and added a few non-NumPy data types as well. With one exception ([structured data types](#structured-data-type)), the Zarr V2 JSON identifier for a data type is just the NumPy `str` attribute of that data type: @@ -64,7 +64,7 @@ print(dtype_meta) !!! note The `<` character in the data type metadata encodes the - [endianness](https://numpy.org/doc/2.2/reference/generated/numpy.dtype.byteorder.html), + [endianness](https://numpy.org/doc/stable/reference/generated/numpy.dtype.byteorder.html), or "byte order," of the data type. As per the NumPy model, in Zarr version 2 each data type has an endianness where applicable. However, Zarr version 3 data types do not store endianness information. @@ -72,7 +72,7 @@ print(dtype_meta) There are two special cases to consider: ["structured" data types](#structured-data-type), and ["object"](#object-data-type) data types. -### Structured Data Type +### Structured data type NumPy allows the construction of a so-called "structured" data types comprised of ordered collections of named fields, where each field is itself a distinct NumPy data type. See the NumPy documentation @@ -101,7 +101,7 @@ dtype_meta = json.loads(store['.zarray'].to_bytes())["dtype"] print(dtype_meta) ``` -### Object Data Type +### Object data type The NumPy "object" type is essentially an array of references to arbitrary Python objects. It can model arrays of variable-length UTF-8 strings, arrays of variable-length byte strings, or @@ -129,7 +129,7 @@ Although this fact can be ignored for many simple numeric data types, any compre Zarr V2 data types must either reject the "object" data types or include the "object codec" identifier in the JSON form of the basic data type model. -## Data Types in Zarr Version 3 +## Data types in Zarr version 3 The NumPy-based Zarr V2 data type representation was effective for simple data types but struggled with more complex data types, like "object" and "structured" data types. To address these limitations, @@ -159,7 +159,7 @@ Zarr V3 introduced several key changes to how data types are represented: For more about data types in Zarr V3, see the [V3 specification](https://zarr-specs.readthedocs.io/en/latest/v3/data-types/index.html). -## Data Types in Zarr Python +## Data types in Zarr Python The two Zarr formats that Zarr Python supports specify data types in different ways: data types in Zarr version 2 are encoded as NumPy-compatible strings (or lists, in the case of structured data @@ -191,7 +191,7 @@ API for the following operations: The following section lists the data types built in to Zarr Python. With a few exceptions, Zarr Python supports nearly all of the data types in NumPy. If you need a data type that is not listed -here, it's possible to create it yourself: see [Adding New Data Types](#adding-new-data-types). +here, it's possible to create it yourself: see [Adding new data types](#adding-new-data-types). #### Boolean - [Boolean][zarr.dtype.Bool] @@ -260,14 +260,14 @@ here, it's possible to create it yourself: see [Adding New Data Types](#adding-n explicit `endian` parameter. If omitted, Zarr Python assumes little-endian for legacy compatibility but emits a warning. -### Example Usage +### Example usage This section will demonstrate the basic usage of Zarr data types. Create a `ZDType` from a native data type: ```python exec="true" session="data_types" source="above" -from zarr.core.dtype import Int8 +from zarr.dtype import Int8 import numpy as np int8 = Int8.from_native_dtype(np.dtype('int8')) ``` @@ -291,7 +291,6 @@ Serialize to JSON for Zarr V2: ```python exec="true" session="data_types" source="above" result="ansi" json_v2 = int8.to_json(zarr_format=2) print(json_v2) -{'name': '|i1', 'object_codec_id': None} ``` !!! note @@ -324,7 +323,7 @@ scalar_value = int8.from_json_scalar(42, zarr_format=3) assert scalar_value == np.int8(42) ``` -### Adding New Data Types +### Adding new data types Each Zarr data type is a separate Python class that inherits from [ZDType][zarr.dtype.ZDType]. You can define a custom data type by @@ -332,7 +331,7 @@ writing your own subclass of [ZDType][zarr.dtype.ZDType] and adding your data type to the data type registry. To see an executable demonstration of this process, see the [`custom_dtype` example](../user-guide/examples/custom_dtype.md). -### Data Type Resolution +### Data type resolution Although Zarr Python uses a different data type model from NumPy, you can still define a Zarr array with a NumPy data type object: @@ -375,16 +374,14 @@ For simple data types like `int`, the solution could be extremely simple: just maintain a lookup table that maps a NumPy data type to the Zarr data type equivalent. But not all data types are so simple. Consider this case: -```python exec="true" session="data_types" source="above" +```python exec="true" session="data_types" source="above" result="ansi" from zarr import create_array -import warnings import numpy as np -warnings.simplefilter("ignore", category=FutureWarning) a = create_array({}, shape=(10,), dtype=[('a', 'f8'), ('b', 'i8')]) print(a.dtype) # this is the NumPy data type ``` -```python exec="true" session="data_types" source="above" +```python exec="true" session="data_types" source="above" result="ansi" print(a.metadata.data_type) # this is the Zarr data type ``` diff --git a/docs/user-guide/examples/rectilinear_chunks.ipynb b/docs/user-guide/examples/rectilinear_chunks.ipynb deleted file mode 100644 index a2dd636ee8..0000000000 --- a/docs/user-guide/examples/rectilinear_chunks.ipynb +++ /dev/null @@ -1,428 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "da9139cc", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:20.792275Z", - "iopub.status.busy": "2026-03-30T13:18:20.792050Z", - "iopub.status.idle": "2026-03-30T13:18:20.801655Z", - "shell.execute_reply": "2026-03-30T13:18:20.797952Z", - "shell.execute_reply.started": "2026-03-30T13:18:20.792253Z" - } - }, - "outputs": [], - "source": [ - "# /// script\n", - "# requires-python = \">=3.12\"\n", - "# dependencies = [\n", - "# \"dask\",\n", - "# \"healpix-geo\",\n", - "# \"matplotlib\",\n", - "# \"numpy\",\n", - "# \"obstore\",\n", - "# \"xarray\",\n", - "# \"zarr\",\n", - "# ]\n", - "#\n", - "# [tool.uv.sources]\n", - "# zarr = { git = \"https://github.com/zarr-developers/zarr-python\", branch = \"main\" }\n", - "# xarray = { git = \"https://github.com/maxrjones/xarray\", branch = \"poc/unified-zarr-chunk-grid\" }\n", - "# ///" - ] - }, - { - "cell_type": "markdown", - "id": "71gnhfq4pfe", - "metadata": {}, - "source": [ - "# Rectilinear Chunk Grids\n", - "\n", - "This notebook demonstrates the unified chunk grid implementation from [#3802](https://github.com/zarr-developers/zarr-python/pull/3802), which adds support for rectilinear (variable) chunk grids.\n", - "\n", - "Note that it requires installing from a fork of Xarray; this will ideally be incorporated in the codebase and included in a future Xarray release.\n", - "\n", - "Rectilinear grids allow different chunk sizes along each dimension, which is useful for data that doesn't partition evenly. For example, sparse HEALPix cells grouped by parent tile, boundary-padded HPC arrays, or ingesting existing variable-chunked datasets via VirtualiZarr." - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "9e9nyjdx06f", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:20.802629Z", - "iopub.status.busy": "2026-03-30T13:18:20.802471Z", - "iopub.status.idle": "2026-03-30T13:18:21.183147Z", - "shell.execute_reply": "2026-03-30T13:18:21.182751Z", - "shell.execute_reply.started": "2026-03-30T13:18:20.802615Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": [ - "<donfig.config_obj.ConfigSet at 0x10d8f4ec0>" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import tempfile\n", - "from pathlib import Path\n", - "import json\n", - "\n", - "import numpy as np\n", - "import xarray as xr\n", - "from healpix_geo import nested\n", - "from obstore.store import HTTPStore\n", - "\n", - "import zarr\n", - "from zarr.storage import ObjectStore\n", - "\n", - "zarr.config.set({'async.concurrency': 128}) # Increase concurrency for better performance with obstore\n", - "zarr.config.set({\"array.rectilinear_chunks\": True}) # Opt-in to rectilinear chunks\n" - ] - }, - { - "cell_type": "markdown", - "id": "kj1o9xik9l", - "metadata": {}, - "source": [ - "## 1. Inspect HEALPix dataset\n", - "\n", - "Load the remote Zarr store to understand the data structure before chunking it." - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "v6cot74r1gq", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:21.183653Z", - "iopub.status.busy": "2026-03-30T13:18:21.183505Z", - "iopub.status.idle": "2026-03-30T13:18:22.028419Z", - "shell.execute_reply": "2026-03-30T13:18:22.027356Z", - "shell.execute_reply.started": "2026-03-30T13:18:21.183644Z" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Members: [('cell_ids', <Array object_store://HTTPStore(\"https://data-taos.ifremer.fr/GRID4EARTH/no_chunk_healpix.zarr\")/cell_ids shape=(222442,) dtype=int64>), ('da', <Array object_store://HTTPStore(\"https://data-taos.ifremer.fr/GRID4EARTH/no_chunk_healpix.zarr\")/da shape=(222442,) dtype=float32>)]\n", - "Attrs: {}\n", - "Write chunk sizes: ((55611, 55611, 55611, 55609),)\n" - ] - } - ], - "source": [ - "ob_store = HTTPStore.from_url(\"https://data-taos.ifremer.fr/GRID4EARTH/no_chunk_healpix.zarr\")\n", - "store = ObjectStore(ob_store)\n", - "g = zarr.open_group(store, mode=\"r\", zarr_format=2, use_consolidated=True)\n", - "arr = g['da']\n", - "\n", - "print(\"Members:\", list(g.members()))\n", - "print(\"Attrs:\", dict(g.attrs))\n", - "print(\"Write chunk sizes:\", arr.write_chunk_sizes)" - ] - }, - { - "cell_type": "markdown", - "id": "wmuqi66d46", - "metadata": {}, - "source": [ - "## 2. HEALPix-style variable chunking\n", - "\n", - "Inspired by [this use case](https://github.com/zarr-developers/zarr-python/pull/3534#issuecomment-3848669859): HEALPix grids where cells are grouped by parent tile at a coarser resolution level, producing variable-sized chunks along the cell dimension when accounting for sparsity." - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "90bc91b9", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:22.029842Z", - "iopub.status.busy": "2026-03-30T13:18:22.029258Z", - "iopub.status.idle": "2026-03-30T13:18:23.629597Z", - "shell.execute_reply": "2026-03-30T13:18:23.628896Z", - "shell.execute_reply.started": "2026-03-30T13:18:22.029824Z" - } - }, - "outputs": [], - "source": [ - "da = xr.open_zarr(\n", - " store,\n", - " zarr_format=2,\n", - " consolidated=True,\n", - ")" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "0d7785b0-d72f-4ef8-8a57-91d61f07be96", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:23.630244Z", - "iopub.status.busy": "2026-03-30T13:18:23.629978Z", - "iopub.status.idle": "2026-03-30T13:18:23.633850Z", - "shell.execute_reply": "2026-03-30T13:18:23.632930Z", - "shell.execute_reply.started": "2026-03-30T13:18:23.630232Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": [ - "10" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "depth = da.cell_ids.attrs['level']\n", - "depth" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "72c80224-dcac-4724-8caf-5717b29a25d5", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:23.634211Z", - "iopub.status.busy": "2026-03-30T13:18:23.634119Z", - "iopub.status.idle": "2026-03-30T13:18:23.642291Z", - "shell.execute_reply": "2026-03-30T13:18:23.641668Z", - "shell.execute_reply.started": "2026-03-30T13:18:23.634203Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": [ - "array([ 25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603,\n", - " 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879,\n", - " 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096,\n", - " 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096,\n", - " 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714,\n", - " 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438,\n", - " 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23])" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "new_depth = depth-6\n", - "parents = nested.zoom_to(da.cell_ids, depth=depth, new_depth=new_depth)\n", - "_, chunk_sizes =np.unique(parents, return_counts=True)\n", - "chunk_sizes" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "a79a281b-ca74-49c3-a467-60490a4ad63e", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:23.642721Z", - "iopub.status.busy": "2026-03-30T13:18:23.642622Z", - "iopub.status.idle": "2026-03-30T13:18:23.649165Z", - "shell.execute_reply": "2026-03-30T13:18:23.648723Z", - "shell.execute_reply.started": "2026-03-30T13:18:23.642712Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": [ - "Frozen({'cell_ids': (25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096, 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096, 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714, 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23)})" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "da = da.chunk({\"cell_ids\": tuple(chunk_sizes.tolist())})\n", - "da.chunks" - ] - }, - { - "cell_type": "markdown", - "id": "bsp6y7otkzb", - "metadata": {}, - "source": [ - "## 3. Write as rectilinear Zarr V3\n", - "\n", - "Write the variable-chunked dataset to a local Zarr V3 store with rectilinear chunk grids enabled." - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "id": "ribguojdr0s", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:23.649823Z", - "iopub.status.busy": "2026-03-30T13:18:23.649737Z", - "iopub.status.idle": "2026-03-30T13:18:24.089390Z", - "shell.execute_reply": "2026-03-30T13:18:24.088640Z", - "shell.execute_reply.started": "2026-03-30T13:18:23.649815Z" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Written to: /var/folders/70/hc_nynms54d8lp67z4rsfctc0000gp/T/tmp6dibcrho/healpix_rectilinear.zarr\n" - ] - } - ], - "source": [ - "output_path = Path(tempfile.mkdtemp()) / \"healpix_rectilinear.zarr\"\n", - "\n", - "encoding = {\n", - " \"da\": {\"chunks\": [chunk_sizes.tolist()]},\n", - " \"cell_ids\": {\"chunks\": [chunk_sizes.tolist()]},\n", - "}\n", - "\n", - "da.to_zarr(output_path, zarr_format=3, mode=\"w\", encoding=encoding, consolidated=False)\n", - "\n", - "print(f\"Written to: {output_path}\")" - ] - }, - { - "cell_type": "markdown", - "id": "rbfm1hn63g9", - "metadata": {}, - "source": [ - "## 4. Verify rectilinear metadata\n", - "\n", - "Inspect the output store to confirm the chunk grid is serialized as `\"rectilinear\"` in `zarr.json`,\n", - "following the [rectilinear chunk grid extension spec](https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear).\n", - "\n", - "Key things to look for in `chunk_grid`:\n", - "- **`name`**: `\"rectilinear\"` (the extension identifier)\n", - "- **`configuration.kind`**: `\"inline\"` (edge lengths stored directly in metadata)\n", - "- **`configuration.chunk_shapes`**: one entry per dimension — here a single list for the 1D `cell_ids` axis. Each element is either:\n", - " - a **bare integer** for a unique edge length (e.g., `25`, `645`)\n", - " - a **`[value, count]` array** using [run-length encoding](https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear#run-length-encoding) for consecutive repeated sizes (e.g., `[4096, 4]` means four consecutive chunks of size 4096)" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "mpdn5hxp7lp", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:24.090312Z", - "iopub.status.busy": "2026-03-30T13:18:24.090192Z", - "iopub.status.idle": "2026-03-30T13:18:24.093595Z", - "shell.execute_reply": "2026-03-30T13:18:24.092908Z", - "shell.execute_reply.started": "2026-03-30T13:18:24.090303Z" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{'name': 'rectilinear', 'configuration': {'kind': 'inline', 'chunk_shapes': [[25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, [4096, 2], 3327, 4047, [4096, 2], 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, [4096, 4], 3515, 1395, 4096, 3622, [4096, 2], 3875, [4096, 5], 2034, 4096, 358, 3991, [4096, 4], 2714, 1210, [4096, 4], 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23]]}}\n" - ] - } - ], - "source": [ - "\n", - "# Read the zarr.json for the 'da' array\n", - "da_meta_path = output_path / \"da\" / \"zarr.json\"\n", - "meta = json.loads(da_meta_path.read_text())\n", - "print(meta['chunk_grid'])" - ] - }, - { - "cell_type": "markdown", - "id": "inz7s8ugu2c", - "metadata": {}, - "source": [ - "## 5. Round-trip verification\n", - "\n", - "Read the rectilinear store back and confirm the chunk sizes are preserved." - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "308gxly6r3j", - "metadata": { - "execution": { - "iopub.execute_input": "2026-03-30T13:18:24.094252Z", - "iopub.status.busy": "2026-03-30T13:18:24.094013Z", - "iopub.status.idle": "2026-03-30T13:18:24.117313Z", - "shell.execute_reply": "2026-03-30T13:18:24.116670Z", - "shell.execute_reply.started": "2026-03-30T13:18:24.094242Z" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Round-trip chunk sizes: Frozen({'cell_ids': (25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096, 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096, 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714, 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23)})\n" - ] - } - ], - "source": [ - "roundtrip = xr.open_zarr(output_path, zarr_format=3, consolidated=False)\n", - "\n", - "print(\"Round-trip chunk sizes:\", roundtrip.chunks)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "e8d42341-c242-44f5-ad6a-491370e3ffab", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/user-guide/examples/rectilinear_chunks.md b/docs/user-guide/examples/rectilinear_chunks.md new file mode 100644 index 0000000000..098cdf1e2f --- /dev/null +++ b/docs/user-guide/examples/rectilinear_chunks.md @@ -0,0 +1,173 @@ +# Rectilinear Chunk Grids + +This example demonstrates rectilinear (variable-sized) chunk grids, introduced in +[#3802](https://github.com/zarr-developers/zarr-python/pull/3802). Rectilinear grids +allow different chunk sizes along each dimension, which is useful for data that +doesn't partition evenly — for example, sparse HEALPix cells grouped by parent tile, +boundary-padded HPC arrays, or ingesting existing variable-chunked datasets via +VirtualiZarr. See [Rectilinear (variable) chunk grids](../arrays.md#rectilinear-variable-chunk-grids) +in the arrays guide for an introduction to the feature. + +The example chunks a HEALPix dataset by parent tile, writes it as a Zarr v3 array +with a rectilinear chunk grid, and verifies the round trip through +[Xarray](https://xarray.dev). + +!!! warning "Experimental" + Rectilinear chunk grids are an experimental feature and may change in future + releases. In addition, this example currently requires + [a fork of Xarray](https://github.com/maxrjones/xarray/tree/poc/unified-zarr-chunk-grid) + with rectilinear chunk grid support (this will ideally be incorporated into a + future Xarray release), as well as the `dask`, `healpix-geo`, and `obstore` + packages, and it reads an example dataset from a remote server. For these + reasons the code on this page is not executed when the documentation is built; + the outputs shown were captured from a live run. + +## Setup + +Rectilinear chunk grids are disabled by default and must be explicitly enabled via +the `array.rectilinear_chunks` configuration option: + +```python exec="false" reason="requires an xarray fork with rectilinear chunk grid support and remote example data" +import json +import tempfile +from pathlib import Path + +import numpy as np +import xarray as xr +from healpix_geo import nested +from obstore.store import HTTPStore + +import zarr +from zarr.storage import ObjectStore + +# Increase concurrency for better performance with obstore +zarr.config.set({'async.concurrency': 128}) +# Opt in to rectilinear chunks +zarr.config.set({'array.rectilinear_chunks': True}) +``` + +## Inspect the HEALPix dataset + +Load the remote Zarr store to understand the data structure before chunking it: + +```python exec="false" reason="requires an xarray fork with rectilinear chunk grid support and remote example data" +ob_store = HTTPStore.from_url("https://data-taos.ifremer.fr/GRID4EARTH/no_chunk_healpix.zarr") +store = ObjectStore(ob_store) +g = zarr.open_group(store, mode="r", zarr_format=2, use_consolidated=True) +arr = g['da'] + +print("Members:", list(g.members())) +print("Attrs:", dict(g.attrs)) +print("Write chunk sizes:", arr.write_chunk_sizes) +``` + +```text +Members: [('cell_ids', <Array object_store://HTTPStore("https://data-taos.ifremer.fr/GRID4EARTH/no_chunk_healpix.zarr")/cell_ids shape=(222442,) dtype=int64>), ('da', <Array object_store://HTTPStore("https://data-taos.ifremer.fr/GRID4EARTH/no_chunk_healpix.zarr")/da shape=(222442,) dtype=float32>)] +Attrs: {} +Write chunk sizes: ((55611, 55611, 55611, 55609),) +``` + +## HEALPix-style variable chunking + +Inspired by [this use case](https://github.com/zarr-developers/zarr-python/pull/3534#issuecomment-3848669859): +HEALPix grids where cells are grouped by parent tile at a coarser resolution level, +producing variable-sized chunks along the cell dimension when accounting for sparsity. + +```python exec="false" reason="requires an xarray fork with rectilinear chunk grid support and remote example data" +da = xr.open_zarr( + store, + zarr_format=2, + consolidated=True, +) + +depth = da.cell_ids.attrs['level'] +new_depth = depth - 6 +parents = nested.zoom_to(da.cell_ids, depth=depth, new_depth=new_depth) +_, chunk_sizes = np.unique(parents, return_counts=True) +print(chunk_sizes) +``` + +```text +[ 25 645 1510 2363 3203 74 769 3963 4096 233 1603 2450 4096 4096 + 3327 4047 4096 4096 1278 2113 4096 3879 4096 3842 2173 983 4046 2187 + 4095 1369 4096 4096 4096 4096 3515 1395 4096 3622 4096 4096 3875 4096 + 4096 4096 4096 4096 2034 4096 358 3991 4096 4096 4096 4096 2714 1210 + 4096 4096 4096 4096 92 3826 4096 2629 4096 1438 4096 353 4078 3410 + 2407 226 132 2738 1223 23] +``` + +Rechunk the dataset with these variable-sized chunks: + +```python exec="false" reason="requires an xarray fork with rectilinear chunk grid support and remote example data" +da = da.chunk({"cell_ids": tuple(chunk_sizes.tolist())}) +print(da.chunks) +``` + +```text +Frozen({'cell_ids': (25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096, 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096, 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714, 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23)}) +``` + +## Write as rectilinear Zarr v3 + +Write the variable-chunked dataset to a local Zarr v3 store with rectilinear chunk +grids enabled: + +```python exec="false" reason="requires an xarray fork with rectilinear chunk grid support and remote example data" +output_path = Path(tempfile.mkdtemp()) / "healpix_rectilinear.zarr" + +encoding = { + "da": {"chunks": [chunk_sizes.tolist()]}, + "cell_ids": {"chunks": [chunk_sizes.tolist()]}, +} + +da.to_zarr(output_path, zarr_format=3, mode="w", encoding=encoding, consolidated=False) + +print(f"Written to: {output_path}") +``` + +```text +Written to: /var/folders/.../T/tmp6dibcrho/healpix_rectilinear.zarr +``` + +## Verify the rectilinear metadata + +Inspect the output store to confirm the chunk grid is serialized as `"rectilinear"` +in `zarr.json`, following the +[rectilinear chunk grid extension spec](https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear). + +Key things to look for in `chunk_grid`: + +- **`name`**: `"rectilinear"` (the extension identifier) +- **`configuration.kind`**: `"inline"` (edge lengths stored directly in metadata) +- **`configuration.chunk_shapes`**: one entry per dimension — here a single list for + the 1D `cell_ids` axis. Each element is either: + - a **bare integer** for a unique edge length (e.g., `25`, `645`) + - a **`[value, count]` array** using + [run-length encoding](https://github.com/zarr-developers/zarr-extensions/tree/main/chunk-grids/rectilinear#run-length-encoding) + for consecutive repeated sizes (e.g., `[4096, 4]` means four consecutive chunks + of size 4096) + +```python exec="false" reason="requires an xarray fork with rectilinear chunk grid support and remote example data" +# Read the zarr.json for the 'da' array +da_meta_path = output_path / "da" / "zarr.json" +meta = json.loads(da_meta_path.read_text()) +print(meta['chunk_grid']) +``` + +```text +{'name': 'rectilinear', 'configuration': {'kind': 'inline', 'chunk_shapes': [[25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, [4096, 2], 3327, 4047, [4096, 2], 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, [4096, 4], 3515, 1395, 4096, 3622, [4096, 2], 3875, [4096, 5], 2034, 4096, 358, 3991, [4096, 4], 2714, 1210, [4096, 4], 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23]]}} +``` + +## Round-trip verification + +Read the rectilinear store back and confirm the chunk sizes are preserved: + +```python exec="false" reason="requires an xarray fork with rectilinear chunk grid support and remote example data" +roundtrip = xr.open_zarr(output_path, zarr_format=3, consolidated=False) + +print("Round-trip chunk sizes:", roundtrip.chunks) +``` + +```text +Round-trip chunk sizes: Frozen({'cell_ids': (25, 645, 1510, 2363, 3203, 74, 769, 3963, 4096, 233, 1603, 2450, 4096, 4096, 3327, 4047, 4096, 4096, 1278, 2113, 4096, 3879, 4096, 3842, 2173, 983, 4046, 2187, 4095, 1369, 4096, 4096, 4096, 4096, 3515, 1395, 4096, 3622, 4096, 4096, 3875, 4096, 4096, 4096, 4096, 4096, 2034, 4096, 358, 3991, 4096, 4096, 4096, 4096, 2714, 1210, 4096, 4096, 4096, 4096, 92, 3826, 4096, 2629, 4096, 1438, 4096, 353, 4078, 3410, 2407, 226, 132, 2738, 1223, 23)}) +``` diff --git a/docs/user-guide/experimental.md b/docs/user-guide/experimental.md index 1c6d952c7c..a50be394c2 100644 --- a/docs/user-guide/experimental.md +++ b/docs/user-guide/experimental.md @@ -1,6 +1,8 @@ # Experimental features -This section contains documentation for experimental Zarr Python features. The features described here are exciting and potentially useful, but also volatile -- we might change them at any time. Take this into account if you consider depending on these features. +This section contains documentation for experimental Zarr Python features. The features described here are exciting and potentially useful, but also volatile -- we might change them at any time. Take this into account if you consider depending on these features. See the +[experimental API policy](../contributing.md#experimental-api-policy) for the stability +guarantees (or lack thereof) that apply to everything documented on this page. ## `CacheStore` @@ -16,10 +18,11 @@ when the cache reaches its maximum size. Because the `CacheStore` uses an ordinary Zarr `Store` object as the caching layer, you can reuse the data stored in the cache later. -> **Note:** The CacheStore is a wrapper store that maintains compatibility with the full -> `zarr.abc.store.Store` API while adding transparent caching functionality. +!!! note + The CacheStore is a wrapper store that maintains compatibility with the full + `zarr.abc.store.Store` API while adding transparent caching functionality. -## Basic Usage +### Basic Usage Creating a CacheStore requires both a source store and a cache store. The cache store can be any Store implementation, providing flexibility in cache persistence: @@ -51,7 +54,7 @@ zarr_array[:] = np.random.random((100, 100)) The dual-store architecture allows you to use different store types for source and cache, such as a remote store for source data and a local store for persistent caching. -## Performance Benefits +### Performance Benefits The CacheStore provides significant performance improvements for repeated data access: @@ -79,20 +82,15 @@ print(f"Speedup is {speedup}") Cache effectiveness is particularly pronounced with repeated access to the same data chunks. -## Cache Configuration +### Cache Configuration The CacheStore can be configured with several parameters: -**max_size**: Controls the maximum size of cached data in bytes +**max_size**: Controls the maximum size of cached data in bytes. The +[Basic Usage](#basic-usage) example above sets a 256MB limit with +`max_size=256*1024*1024`: ```python exec="true" session="experimental" source="above" -# 256MB cache with size limit -cache = CacheStore( - store=source_store, - cache_store=cache_store, - max_size=256*1024*1024 -) - # Unlimited cache size (use with caution) cache = CacheStore( store=source_store, @@ -137,14 +135,15 @@ cache = CacheStore( ) ``` -## Cache Statistics +### Cache Statistics The CacheStore provides statistics to monitor cache performance and state: ```python exec="true" session="experimental" source="above" # Access some data to generate cache activity -data = zarr_array[0:50, 0:50] # First access - cache miss -data = zarr_array[0:50, 0:50] # Second access - cache hit +# (these chunks were already cached by the reads above, so both accesses are cache hits) +data = zarr_array[0:50, 0:50] +data = zarr_array[0:50, 0:50] # Get comprehensive cache information info = cached_store.cache_info() @@ -159,7 +158,7 @@ print(info['cache_set_data']) The `cache_info()` method returns a dictionary with detailed information about the cache state. -## Cache Management +### Cache Management The CacheStore provides methods for manual cache management: @@ -177,7 +176,7 @@ assert info['current_size'] == 0 The `clear_cache()` method is an async method that clears both the cache store (if it supports the `clear` method) and all internal tracking data. -## Best Practices +### Best Practices 1. **Choose appropriate cache store**: Use MemoryStore for fast temporary caching or LocalStore for persistent caching 2. **Size the cache appropriately**: Set `max_size` based on available storage and expected data access patterns @@ -186,12 +185,12 @@ The `clear_cache()` method is an async method that clears both the cache store 5. **Consider data locality**: Group related data accesses together to improve cache efficiency 6. **Set appropriate expiration**: Use `max_age_seconds` for time-sensitive data or "infinity" for static data -## Working with Different Store Types +### Working with Different Store Types The CacheStore can wrap any store that implements the `zarr.abc.store.Store` interface and use any store type for the cache backend: -### Local Store with Memory Cache +#### Local Store with Memory Cache ```python exec="true" session="experimental-memory-cache" source="above" from zarr.storage import LocalStore, MemoryStore @@ -208,7 +207,7 @@ cached_store = CacheStore( ) ``` -### Memory Store with Persistent Cache +#### Memory Store with Persistent Cache ```python exec="true" session="experimental-local-cache" source="above" from tempfile import mkdtemp @@ -228,7 +227,7 @@ cached_store = CacheStore( The dual-store architecture provides flexibility in choosing the best combination of source and cache stores for your specific use case. -## Examples from Real Usage +### Examples from Real Usage Here's a complete example demonstrating cache effectiveness: diff --git a/docs/user-guide/extending.md b/docs/user-guide/extending.md index cefeb114c5..8602ec8c3b 100644 --- a/docs/user-guide/extending.md +++ b/docs/user-guide/extending.md @@ -50,8 +50,8 @@ Custom codecs should also implement the following methods: To use custom codecs in Zarr, they need to be registered using the [entrypoint mechanism](https://packaging.python.org/en/latest/specifications/entry-points/). Commonly, entrypoints are declared in the `pyproject.toml` of your package under the -`[project.entry-points."zarr.codecs"]` section. Zarr will automatically discover and -load all codecs registered with the entrypoint mechanism from imported modules. +`[project.entry-points."zarr.codecs"]` section. Zarr will automatically discover +all codecs registered via the entrypoint mechanism in installed packages. ```toml [project.entry-points."zarr.codecs"] @@ -74,7 +74,8 @@ implementation. ## Custom stores -Coming soon. +Custom stores can be created by implementing the [`zarr.abc.store.Store`][] interface. +See [developing custom stores](storage.md#developing-custom-stores) for more information. ## Custom array buffers @@ -82,7 +83,16 @@ Zarr-python provides control over where and how arrays are stored in memory thro [`zarr.abc.buffer.Buffer`][]. Currently both CPU (the default) and GPU implementations are provided (see [Using GPUs with Zarr](gpu.md) for more information). You can implement your own buffer classes by implementing the interface defined in [`zarr.abc.buffer.BufferPrototype`][]. +Like codecs, custom buffer implementations can be registered via entrypoints, using the +`zarr.buffer` and `zarr.ndbuffer` entrypoint groups. + +## Custom data types + +Zarr supports user-defined data types. See the +[data types documentation](data_types.md) for an explanation of how Zarr Python +models data types and how to write your own, and the +[custom data type example](examples/custom_dtype.md) for a complete worked example. ## Other extensions -In the future, Zarr will support writing custom data types and chunk grids. +In the future, Zarr will support writing custom chunk grids. diff --git a/docs/user-guide/glossary.md b/docs/user-guide/glossary.md index 3eb63925cc..dde08388a1 100644 --- a/docs/user-guide/glossary.md +++ b/docs/user-guide/glossary.md @@ -9,12 +9,18 @@ This page defines key terms used throughout the zarr-python documentation and AP An N-dimensional typed array stored in a Zarr [store](#store). An array's [metadata](#metadata) defines its shape, data type, chunk layout, and codecs. +### Group + +A container for [arrays](#array) and other groups, enabling hierarchical +organization of data — similar to directories in a file system, or groups in +HDF5. Like arrays, each group has its own [metadata](#metadata) and +[attributes](#attributes). See the [groups documentation](groups.md). + ### Chunk The fundamental unit of data in a Zarr array. An array is divided into chunks -along each dimension according to the [chunk grid](#chunk-grid), which is currently -part of Zarr's private API. Each chunk is independently compressed and encoded -through the array's [codec](#codec) pipeline. +along each dimension according to the [chunk grid](#chunk-grid). Each chunk is +independently compressed and encoded through the array's [codec](#codec) pipeline. When [sharding](#shard) is used, "chunk" refers to the inner chunks within each shard, because those are the compressible units. The chunks are the smallest units @@ -52,7 +58,8 @@ not the inner chunk boundaries. The inner chunk shape is defined within the grid. [`Array.chunks`][zarr.Array.chunks] returns the chunk shape for regular grids. For all grid types, `Array.read_chunk_sizes` and `Array.write_chunk_sizes` return the per-dimension chunk sizes in dask-style `tuple[tuple[int, ...], ...]` -format. +format. Note that while the chunk grid is a public concept of the Zarr format, +the classes zarr-python uses to model chunk grids are currently private API. ### Shard @@ -88,12 +95,28 @@ file) in the store, addressed by a key derived from its grid coordinates. ### Metadata -The JSON document (`zarr.json`) that describes an [array](#array) or group. For -arrays, metadata includes the shape, data type, [chunk grid](#chunk-grid), fill +The JSON document that describes an [array](#array) or [group](#group). In Zarr +format 3 this is a single `zarr.json` document; Zarr format 2 stores the +equivalent information in separate `.zarray`, `.zgroup`, and `.zattrs` documents. +For arrays, metadata includes the shape, data type, [chunk grid](#chunk-grid), fill value, and [codec](#codec) pipeline. Metadata is stored alongside the data in the [store](#store). Zarr-Python does not yet expose its internal metadata representation as part of its public API. +### Attributes + +User-defined key-value pairs (any JSON-serializable values) attached to an +[array](#array) or [group](#group). Attributes are stored in the +[metadata](#metadata) document. See the +[attributes documentation](attributes.md). + +### Consolidated Metadata + +A copy of the [metadata](#metadata) of every array and group in a hierarchy, +stored in the metadata of the root group so that the entire hierarchy can be +inspected with a single read from the [store](#store). See the +[consolidated metadata documentation](consolidated_metadata.md). + ## Codecs ### Codec diff --git a/docs/user-guide/gpu.md b/docs/user-guide/gpu.md index 6c26c3e564..26d1c114b0 100644 --- a/docs/user-guide/gpu.md +++ b/docs/user-guide/gpu.md @@ -1,6 +1,6 @@ # Using GPUs with Zarr -Zarr can use GPUs to accelerate your workload by running `zarr.Config.enable_gpu`. +Zarr can use GPUs to accelerate your workload by running `zarr.config.enable_gpu()`. !!! note `zarr-python` currently supports reading the ndarray data into device (GPU) @@ -11,20 +11,50 @@ Zarr can use GPUs to accelerate your workload by running `zarr.Config.enable_gpu the GPU, avoiding the need to move data between the host and device for compression and decompression. +## Installation + +Zarr's GPU support requires [CuPy](https://cupy.dev), which in turn requires a +CUDA-compatible NVIDIA GPU. CuPy can be installed alongside Zarr with the `gpu` +extra (see [Installation](installation.md) for the other optional dependency groups): + +```console +pip install "zarr[gpu]" +``` + +This installs the `cupy-cuda12x` package. If you need a CuPy build for a different +CUDA version, see the [CuPy installation guide](https://docs.cupy.dev/en/stable/install.html) +and install the appropriate package yourself. + ## Reading data into device memory -[`zarr.config`][] configures Zarr to use GPU memory for the data -buffers used internally by Zarr via `enable_gpu()`. +Calling `zarr.config.enable_gpu()` configures Zarr to use GPU memory for the data +buffers used internally by Zarr: ```python test="true" session="gpu-demo" markers="gpu" source="above" import zarr import cupy as cp + zarr.config.enable_gpu() z = zarr.create_array( store="memory://gpu-demo", shape=(100, 100), chunks=(10, 10), dtype="float32", ) -type(z[:10, :10]) -# cupy.ndarray +assert isinstance(z[:10, :10], cp.ndarray) +``` + +Note that the arrays returned by reads are of type `cupy.ndarray` rather than +NumPy arrays. + +`zarr.config.enable_gpu()` returns a [donfig](https://donfig.readthedocs.io/en/latest/) +`ConfigSet`, which can be used as a context manager to enable GPU support for a +limited scope: + +```python test="true" session="gpu-demo" markers="gpu" source="above" +with zarr.config.enable_gpu(): + data = z[:10, :10] +assert isinstance(data, cp.ndarray) ``` -Note that the output type is a `cupy.ndarray` rather than a NumPy array. +Under the hood, `enable_gpu()` selects the GPU-backed buffer classes +`zarr.buffer.gpu.Buffer` and `zarr.buffer.gpu.NDBuffer` via the `buffer` and +`ndbuffer` configuration keys. See [Custom array buffers](extending.md#custom-array-buffers) +for more on Zarr's buffer classes, including how to implement your own. diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index 5faa26a281..a2b40dfe8a 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -4,7 +4,7 @@ Zarr supports hierarchical organization of arrays via groups. As with arrays, groups can be stored in memory, on disk, or via other storage systems that support a similar interface. -To create a group, use the [`zarr.group`][] function: +To create a group, use the [`zarr.create_group`][] function: ```python exec="true" session="groups" source="above" result="ansi" import zarr @@ -12,6 +12,13 @@ root = zarr.create_group(store="memory://groups-demo") print(root) ``` +Zarr-Python provides three related functions for making groups: +[`zarr.create_group`][] creates a new group; [`zarr.open_group`][] creates or +re-opens a group depending on its `mode` argument (see below); and +[`zarr.group`][], which is kept for compatibility with Zarr-Python 2, is +equivalent to calling [`zarr.open_group`][] with `mode='a'` (or `mode='w'` +when `overwrite=True`). + Groups have a similar API to the Group class from [h5py](https://www.h5py.org/). For example, groups can contain other groups: ```python exec="true" session="groups" source="above" @@ -26,7 +33,8 @@ z1 = bar.create_array(name='baz', shape=(10000, 10000), chunks=(1000, 1000), dty print(z1) ``` -Members of a group can be accessed via the suffix notation, e.g.: +Members of a group can be accessed with square-bracket item access, like a +Python `dict`, e.g.: ```python exec="true" session="groups" source="above" result="ansi" print(root['foo']) @@ -66,10 +74,46 @@ print(z) For more information on groups see the [`zarr.Group` API docs](../api/zarr/group.md). -## Batch Group Creation +## Exploring group contents + +Groups also support a dict-like interface for enumerating their contents. The +[`zarr.Group.keys`][] method iterates over member names, and the `in` operator +tests for membership: + +```python exec="true" session="groups" source="above" result="ansi" +print(list(root.keys())) +print('foo' in root) +``` + +The [`zarr.Group.members`][] method returns `(name, member)` pairs for the +arrays and groups contained in a group: + +```python exec="true" session="groups" source="above" result="ansi" +for name, member in root.members(): + print(name, member) +``` + +By default only immediate members are returned. Pass `max_depth=None` to +recursively traverse the whole hierarchy below a group: + +```python exec="true" session="groups" source="above" result="ansi" +for name, member in root.members(max_depth=None): + print(name, member) +``` + +Members can be deleted with the `del` operator, which removes the member's +metadata and data from the store: + +```python exec="true" session="groups" source="above" result="ansi" +del root['foo/bar/baz'] +for name, member in root.members(max_depth=None): + print(name, member) +``` + +## Batch group creation You can also create multiple groups concurrently with a single function call. [`zarr.create_hierarchy`][] takes -a [`zarr Storage`](../api/zarr/storage.md) instance and a dict of `key : metadata` pairs, parses that dict, and +a [`Store`](../api/zarr/storage.md) instance and a dict of `key : metadata` pairs, parses that dict, and writes metadata documents to storage: ```python exec="true" session="groups" source="above" result="ansi" diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md index ff6e354d80..6b9a547776 100644 --- a/docs/user-guide/index.md +++ b/docs/user-guide/index.md @@ -7,7 +7,7 @@ Welcome to the user guide, where you can learn more about using Zarr-Python! New to Zarr-Python? Start here: - **[Installation](installation.md)** - Install Zarr-Python -- **[Quick-start](../quick-start.md)** - Quick overview of core functionality +- **[Quick start](../quick-start.md)** - Quick overview of core functionality ## Core Concepts @@ -15,7 +15,7 @@ Learn the essential building blocks: - **[Arrays](arrays.md)** - Learn the fundamentals of working with arrays - **[Groups](groups.md)** - Organize your data with groups -- **[Attributes](attributes.md)** - Configure metadata to your data structures +- **[Attributes](attributes.md)** - Attach metadata to your arrays and groups - **[Storage](storage.md)** - Learn how data is stored and accessed ## Configuration & Setup @@ -23,6 +23,7 @@ Learn the essential building blocks: Customize your experience: - **[Runtime Configuration](config.md)** - Configure Zarr-Python for your needs +- **[Command-Line Interface](cli.md)** - Migrate and manage Zarr metadata from the terminal - **[V3 Migration](v3_migration.md)** - Upgrading from version 2 to version 3 ## Advanced Topics @@ -34,6 +35,14 @@ Take your skills to the next level: - **[GPU](gpu.md)** - Leverage GPU acceleration - **[Extending](extending.md)** - Extend functionality with custom code - **[Consolidated Metadata](consolidated_metadata.md)** - Advanced metadata management +- **[Experimental Features](experimental.md)** - Preview features that may change at any time + +## Examples + +Worked, end-to-end examples: + +- **[Custom Data Type](examples/custom_dtype.md)** - Extend Zarr-Python with a user-defined data type +- **[Rectilinear Chunk Grids](examples/rectilinear_chunks.md)** - Use variable-sized chunks along each dimension ## Reference diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md index c902acf171..4af7667a44 100644 --- a/docs/user-guide/installation.md +++ b/docs/user-guide/installation.md @@ -9,7 +9,7 @@ Required dependencies include: - [numpy](https://numpy.org) (2.0 or later) - [numcodecs](https://numcodecs.readthedocs.io) (0.14 or later) - [google-crc32c](https://github.com/googleapis/python-crc32c) (1.5 or later) -- [typing_extensions](https://typing-extensions.readthedocs.io) (4.9 or later) +- [typing_extensions](https://typing-extensions.readthedocs.io) (4.14 or later) - [donfig](https://donfig.readthedocs.io) (0.8 or later) ## pip @@ -23,10 +23,11 @@ pip install zarr There are a number of optional dependency groups you can install for extra functionality. These can be installed using `pip install "zarr[<extra>]"`, e.g. `pip install "zarr[gpu]"` -- `gpu`: support for GPUs -- `remote`: support for reading/writing to remote data stores - -Additional optional dependencies include `universal_pathlib`. These must be installed separately. +- `remote`: support for reading/writing to remote data stores (fsspec, obstore) +- `gpu`: support for GPUs (cupy) +- `cli`: support for the `zarr` [command-line interface](cli.md) (typer) +- `optional`: support for path-like access to local and remote stores (universal-pathlib) +- `cast-value-rs`: support for the `cast_value` codec (cast-value-rs) ## conda @@ -39,7 +40,7 @@ conda install -c conda-forge zarr Conda does not support optional dependencies, so you will have to manually install any packages needed to enable extra functionality. -# Nightly wheels +## Nightly wheels Development wheels are built nightly and published to the [scientific-python-nightly-wheels](https://anaconda.org/scientific-python-nightly-wheels) index. To install the latest nightly build: @@ -48,6 +49,7 @@ pip install --pre --extra-index-url https://pypi.anaconda.org/scientific-python- ``` Note that nightly wheels may be unstable and are intended for testing purposes. + ## Dependency support Zarr has endorsed [Scientific-Python SPEC 0](https://scientific-python.org/specs/spec-0000/) and now follows the version support window as outlined below: @@ -57,4 +59,4 @@ Zarr has endorsed [Scientific-Python SPEC 0](https://scientific-python.org/specs ## Development -To install the latest development version of Zarr, see the contributing guide. +To install the latest development version of Zarr, see the [contributing guide](../contributing.md). diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 685ce7fe7e..818386578c 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -81,37 +81,38 @@ z6 = zarr.create_array(store={}, shape=(10000, 10000, 1000), shards=(1000, 1000, print(z6.info) ``` -`shards` can be `"auto"` as well, in which case the `array.target_shard_size_bytes` setting can be used to control the size of shards (i.e., the size of the chunks cumulatively and uncompressed within the shard will be as close to, without being bigger than, `array.target_shard_size_bytes`); otherwise, a default is used. +`shards` can be `"auto"` as well, in which case Zarr chooses a shard shape for you. +The `array.target_shard_size_bytes` configuration setting controls this choice: the +cumulative uncompressed size of the chunks within each shard will be as close as +possible to, without exceeding, that target. If the setting is `None` (the default), +Zarr falls back to a built-in heuristic for choosing the shard shape. ### Chunk memory layout -The order of bytes **within each chunk** of an array can be changed via the -`order` config option, to use either C or Fortran layout. For -multi-dimensional arrays, these two layouts may provide different compression -ratios, depending on the correlation structure within the data. E.g.: +The memory layout of the in-memory arrays that Zarr produces and consumes can be +changed via the `order` config option, to use either C or Fortran layout. This can +matter for performance when the data is passed to other libraries that expect a +particular memory layout. E.g.: ```python exec="true" session="performance" source="above" result="ansi" import numpy as np -a = np.arange(100000000, dtype='int32').reshape(10000, 10000).T -c = zarr.create_array(store={}, shape=a.shape, chunks=(1000, 1000), dtype=a.dtype, config={'order': 'C'}) -c[:] = a -print(c.info_complete()) +c = zarr.create_array(store={}, shape=(10000, 10000), chunks=(1000, 1000), dtype='int32', config={'order': 'C'}) +print(c[:100, :100].flags.c_contiguous) ``` ```python exec="true" session="performance" source="above" result="ansi" with zarr.config.set({'array.order': 'F'}): - f = zarr.create_array(store={}, shape=a.shape, chunks=(1000, 1000), dtype=a.dtype) - f[:] = a -print(f.info_complete()) - + f = zarr.create_array(store={}, shape=(10000, 10000), chunks=(1000, 1000), dtype='int32') +print(f[:100, :100].flags.f_contiguous) ``` -In the above example, Fortran order gives a better compression ratio. This is an -artificial example but illustrates the general point that changing the order of -bytes within chunks of an array may improve the compression ratio, depending on -the structure of the data, the compression algorithm used, and which compression -filters (e.g., byte-shuffle) have been applied. +Note that for Zarr format 3 arrays the `order` option only affects the in-memory +layout: the bytes written to storage are identical for both settings. The layout of +the serialized data is instead determined by the array's codecs (e.g. the transpose +codec), which can change how well the data compresses depending on the correlation +structure within the data and which compression filters (e.g., byte-shuffle) have +been applied. ### Subchunk memory layout @@ -142,7 +143,7 @@ assert arr.config.write_empty_chunks == False ``` The following example illustrates the effect of the `write_empty_chunks` flag on -the time required to write an array with different values.: +the time required to write an array with different values: ```python exec="true" session="performance" source="above" result="ansi" import zarr @@ -182,12 +183,17 @@ for write_empty_chunks in (True, False): print(f'\nwrite_empty_chunks={write_empty_chunks}:\n\tRandom Data: {full[0]:.4f}s, {full[1]} objects stored\n\t Empty Data: {empty[0]:.4f}s, {empty[1]} objects stored\n') ``` -In this example, writing random data is slightly slower with `write_empty_chunks=True`, -but writing empty data is substantially faster and generates far fewer objects in storage. +In this example, writing random data is slightly slower with `write_empty_chunks=False`, +because every chunk must be checked for emptiness before it is stored. Writing empty +data with `write_empty_chunks=False` is substantially faster, however, and stores no +objects at all. ### Changing chunk shapes (rechunking) -Coming soon. +Zarr-Python does not yet provide a built-in way to change the chunk shape of an +existing array in place. Arrays can, however, be resized and appended to along any +dimension — see [Resizing and appending](arrays.md#resizing-and-appending) — and data +can be copied to a new array created with the desired chunk shape. ## Parallel computing and synchronization @@ -204,7 +210,7 @@ determines the maximum number of concurrent I/O operations. The default value is 10, which is a conservative value. You may get improved performance by tuning the concurrency limit. You can adjust this value based on your specific needs: -```python exec="true" session="perf-concurrency" +```python exec="true" session="perf-concurrency" source="above" import zarr # Set concurrency for the current session @@ -234,7 +240,7 @@ By default it is `None`, which lets Python choose the pool size (typically You can set it explicitly when you want more predictable resource usage: -```python exec="true" session="perf-workers" +```python exec="true" session="perf-workers" source="above" import zarr zarr.config.set({'threading.max_workers': 8}) @@ -256,7 +262,7 @@ concurrently. total_concurrency ≈ dask_threads × zarr_async_concurrency ``` -For example, if you're running Dask with 10 threads and Zarr's default concurrency of 64, you could potentially have up to 640 concurrent operations, which may overwhelm your storage system or cause memory issues. +For example, if you're running Dask with 10 threads and Zarr's default concurrency of 10, you could potentially have up to 100 concurrent operations, which may overwhelm your storage system or cause memory issues. **Recommendation**: When using Dask with many threads, configure Zarr's concurrency settings: @@ -283,7 +289,7 @@ result = arr.mean(axis=0).compute() **Configuration guidelines for Dask workloads**: - `async.concurrency`: Controls the maximum number of concurrent async I/O operations. Start with a lower value (e.g., 4-8) when using many Dask threads. -- `threading.max_workers`: Controls Zarr's internal thread pool size for blocking operations (defaults to CPU count). Reduce this to avoid thread contention with Dask's scheduler. +- `threading.max_workers`: Controls Zarr's internal thread pool size for blocking operations (defaults to `None`, letting Python choose the pool size). Reduce this to avoid thread contention with Dask's scheduler. You may need to experiment with different values to find the optimal balance for your workload. Monitor your system's resource usage and adjust these settings based on whether your storage system or CPU is the bottleneck. @@ -300,14 +306,17 @@ When writing to the same chunks from multiple processes, you should use external ## Pickle support Zarr arrays and groups can be pickled, as long as the underlying store object can be -pickled. With the exception of the `zarr.storage.MemoryStore`, any of the -storage classes provided in the `zarr.storage` module can be pickled. +pickled. All of the storage classes provided in the `zarr.storage` module can be pickled. If an array or group is backed by a persistent store such as a `zarr.storage.LocalStore`, `zarr.storage.ZipStore` or `zarr.storage.FsspecStore` then the store data **are not** pickled. The only thing that is pickled is the necessary parameters to allow the store to re-open any underlying files or databases upon being unpickled. +Note that pickling a `zarr.storage.MemoryStore` copies the data it holds into the +pickle stream: unpickling produces an independent in-memory copy, so a `MemoryStore` +cannot be used to share data between processes. + E.g., pickle/unpickle a local store array: ```python exec="true" session="performance" source="above" result="ansi" @@ -320,7 +329,3 @@ z2 = pickle.loads(s) assert z1 == z2 print(np.all(z1[:] == z2[:])) ``` - -## Configuring Blosc - -Coming soon. diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index d5f840ab4b..d32fe217c9 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -18,13 +18,13 @@ being created automatically: ```python exec="true" session="storage" source="above" result="ansi" import zarr -# Implicitly create a writable LocalStore +# Implicitly creates a writable LocalStore group = zarr.create_group(store='data/foo/bar') print(group) ``` ```python exec="true" session="storage" source="above" result="ansi" -# Implicitly create a read-only FsspecStore +# Implicitly creates a read-only FsspecStore # Note: requires s3fs to be installed group = zarr.open_group( store='s3://noaa-nwm-retro-v2-zarr-pds', @@ -138,24 +138,25 @@ print(group) ``` The type of filesystem (e.g. S3, https, etc..) is inferred from the scheme of the url (e.g. s3 for "**s3**://noaa-nwm-retro-v2-zarr-pds"). -In case a specific filesystem is needed, one can explicitly create it. For example to create an S3 filesystem: +In case a specific filesystem is needed, one can explicitly create it. For example to create an S3 filesystem +(note that the filesystem must be created with `asynchronous=True`): ```python exec="true" session="storage" source="above" result="ansi" # Note: requires s3fs to be installed import fsspec -fs = fsspec.filesystem( - 's3', anon=True, asynchronous=True, - client_kwargs={'endpoint_url': "https://noaa-nwm-retro-v2-zarr-pds.s3.amazonaws.com"} -) -store = zarr.storage.FsspecStore(fs) +fs = fsspec.filesystem('s3', anon=True, asynchronous=True) +store = zarr.storage.FsspecStore(fs, path='noaa-nwm-retro-v2-zarr-pds', read_only=True) print(store) ``` +When using an S3-compatible service other than AWS, pass the service endpoint to the +filesystem via `client_kwargs={'endpoint_url': 'https://...'}`. + ### Memory Store -The [`zarr.storage.MemoryStore`][] is an in-memory store that allows for serialization of -Zarr data (metadata and chunks) to a dictionary: +The [`zarr.storage.MemoryStore`][] stores Zarr data (metadata and chunks) in an +in-memory dictionary: ```python exec="true" session="storage" source="above" result="ansi" data = {} @@ -199,3 +200,5 @@ print(group.info) Zarr-Python [`zarr.abc.store.Store`][] API is meant to be extended. The Store Abstract Base Class includes all of the methods needed to be a fully operational store in Zarr Python. Zarr also provides a test harness for custom stores: [`zarr.testing.store.StoreTests`][]. +See the [Custom stores](extending.md#custom-stores) section of the extending guide for +more on implementing your own store. diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index 5192179550..6d9d516ebe 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -16,6 +16,12 @@ migrate your code from version 2 to version 3. If we have missed anything, pleas open a [GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new) so we can improve this guide. +!!! tip + This page is about migrating your *code* from the Zarr-Python 2 API to the + Zarr-Python 3 API. If you want to migrate the *metadata* of stored data from + Zarr format 2 to Zarr format 3, see the `zarr migrate` command described in + the [command-line interface documentation](cli.md). + ## Compatibility target The goals described above necessitated some breaking changes to the API (hence the @@ -62,14 +68,14 @@ the following actions in order: * `zarr.codecs` has changed, see "Codecs" section below for more information * `zarr.context` has gone, with no replacement * `zarr.core` remains but should be considered private API - * `zarr.hierarchy` has gone, with no replacement (use `zarr.Group` inplace of `zarr.hierarchy.Group`) + * `zarr.hierarchy` has gone, with no replacement (use `zarr.Group` in place of `zarr.hierarchy.Group`) * `zarr.indexing` has gone, with no replacement * `zarr.meta` has gone, with no replacement * `zarr.meta_v1` has gone, with no replacement * `zarr.sync` has gone, with no replacement * `zarr.types` has gone, with no replacement * `zarr.util` has gone, with no replacement - * `zarr.n5` has gone, see below for an alternative N5 options + * `zarr.n5` has gone, see below for an alternative N5 option 3. Test that your package works with version 3. 4. Update the pin to include `zarr>=3,<4`. @@ -77,8 +83,9 @@ the following actions in order: ## Zarr-Python 2 support window Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for -its performance improvements and new features. Security and bug fixes will be made to -the 2.x series for at least six months following the first Zarr-Python 3 release. +its performance improvements and new features. Security and bug fixes were made to +the 2.x series for six months following the first Zarr-Python 3 release (January 2025); +the 2.x series is no longer actively maintained. If you need to use the latest Zarr-Python 2 release, you can install it with: ```console @@ -157,11 +164,9 @@ The following stores have been renamed or changed: | `DirectoryStore` | [`zarr.storage.LocalStore`][] | | `FSStore` | [`zarr.storage.FsspecStore`][] | | `TempStore` | Use [`tempfile.TemporaryDirectory`][] with [`LocalStore`][zarr.storage.LocalStore] | -| `zarr. - A number of deprecated stores were also removed. -See issue #1274 for more details on the removal of these stores. +See [issue #1274](https://github.com/zarr-developers/zarr-python/issues/1274) for more details on the removal of these stores. - `N5Store` - see https://github.com/zarr-developers/n5py for an alternative interface to N5 formatted data. @@ -175,7 +180,7 @@ See issue #1274 for more details on the removal of these stores. The latter five stores in this list do not have an equivalent in Zarr-Python 3. If you are interested in developing a custom store that targets these backends, see -[developing custom stores](storage.md/#developing-custom-stores) or open an +[developing custom stores](storage.md#developing-custom-stores) or open an [issue](https://github.com/zarr-developers/zarr-python/issues) to discuss your use case. ### Codecs @@ -205,23 +210,21 @@ When installing using `pip`: (e.g. [`zarr.create`][], [`zarr.open`][], [`zarr.group`][], [`zarr.array`][]) has been removed. Use `zarr_format` instead. -## 🚧 Work in Progress 🚧 +## Unimplemented Zarr-Python 2 features -Zarr-Python 3 is still under active development, and is not yet fully complete. -The following list summarizes areas of the codebase that we expect to build out -after the 3.0.0 release. If features listed below are important to your use case +A few features of Zarr-Python 2 remain unimplemented in Zarr-Python 3. +If any of the features listed below are important to your use case of Zarr-Python, please open (or comment on) a [GitHub issue](https://github.com/zarr-developers/zarr-python/issues/new). -The following functions / methods have not been ported to Zarr-Python 3 yet: +The following functions / methods have not been ported to Zarr-Python 3: - `zarr.copy` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) - `zarr.copy_all` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) - `zarr.copy_store` ([issue #2407](https://github.com/zarr-developers/zarr-python/issues/2407)) -- `zarr.Group.move` ([issue #2108](https://github.com/zarr-developers/zarr-python/issues/2108)) The following features (corresponding to function arguments to functions in - `zarr`) have not been ported to Zarr-Python 3 yet. Using these features + `zarr`) have not been ported to Zarr-Python 3. Using these features will raise a warning or a `NotImplementedError`: - `cache_attrs` @@ -230,10 +233,9 @@ The following features (corresponding to function arguments to functions in - `meta_array` - `object_codec` ([issue #2617](https://github.com/zarr-developers/zarr-python/issues/2617)) - `synchronizer` ([issue #1596](https://github.com/zarr-developers/zarr-python/issues/1596)) -- `dimension_separator` The following features that were supported by Zarr-Python 2 have not been ported - to Zarr-Python 3 yet: + to Zarr-Python 3: - Object dtypes ([issue #2616](https://github.com/zarr-developers/zarr-python/issues/2616)) - Ragged arrays ([issue #2618](https://github.com/zarr-developers/zarr-python/issues/2618)) diff --git a/examples/custom_dtype/README.md b/examples/custom_dtype/README.md index c0722d0661..266f398ca8 100644 --- a/examples/custom_dtype/README.md +++ b/examples/custom_dtype/README.md @@ -1,4 +1,4 @@ -# Custom Data Type Example +# Custom Data Type This example demonstrates how to extend Zarr Python by defining a new data type. @@ -11,12 +11,17 @@ The example shows how to: ## Running the Example +The script declares its dependencies inline +([PEP 723](https://peps.python.org/pep-0723/)), so the easiest way to run it is +with [uv](https://docs.astral.sh/uv/), which installs them automatically: + ```bash -python examples/custom_dtype/custom_dtype.py +uv run examples/custom_dtype/custom_dtype.py ``` -Or run with uv: +Alternatively, run it with plain Python, in which case you must first install +`zarr`, `ml_dtypes`, and `pytest` yourself: ```bash -uv run examples/custom_dtype/custom_dtype.py +python examples/custom_dtype/custom_dtype.py ``` diff --git a/mkdocs.yml b/mkdocs.yml index e4e757e630..46bfc1764c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -17,61 +17,86 @@ nav: - user-guide/arrays.md - user-guide/groups.md - user-guide/attributes.md + - user-guide/data_types.md - user-guide/storage.md - user-guide/config.md - - user-guide/cli.md - - user-guide/v3_migration.md - - user-guide/data_types.md - user-guide/performance.md + - user-guide/cli.md - user-guide/extending.md - user-guide/gpu.md - user-guide/consolidated_metadata.md - user-guide/experimental.md + - user-guide/v3_migration.md - user-guide/glossary.md - Examples: - user-guide/examples/custom_dtype.md - - user-guide/examples/rectilinear_chunks.ipynb + - user-guide/examples/rectilinear_chunks.md - API Reference: - api/zarr/index.md - - api/zarr/array.md - - api/zarr/group.md - - api/zarr/create.md - - api/zarr/dtype.md - - api/zarr/load.md - - api/zarr/open.md - - api/zarr/save.md - - api/zarr/codecs.md - - api/zarr/codecs/numcodecs.md - - api/zarr/config.md - - api/zarr/errors.md - - api/zarr/metadata.md - - api/zarr/registry.md - - api/zarr/storage.md - - api/zarr/experimental.md - - ABC: + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc</code>': - api/zarr/abc/index.md - - api/zarr/abc/buffer.md - - api/zarr/abc/codec.md - - api/zarr/abc/numcodec.md - - api/zarr/abc/metadata.md - - api/zarr/abc/store.md - - API: + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc.buffer</code>': api/zarr/abc/buffer.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc.codec</code>': api/zarr/abc/codec.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc.metadata</code>': api/zarr/abc/metadata.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc.numcodec</code>': api/zarr/abc/numcodec.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc.store</code>': api/zarr/abc/store.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.api</code>': - api/zarr/api/index.md - - api/zarr/api/asynchronous.md - - api/zarr/api/synchronous.md - - Buffer: + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.api.asynchronous</code>': api/zarr/api/asynchronous.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.api.synchronous</code>': api/zarr/api/synchronous.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-class"></code> <code>zarr.Array</code>': api/zarr/array.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.array</code>': api/zarr/functions/array.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.buffer</code>': - api/zarr/buffer/index.md - - api/zarr/buffer/cpu.md - - api/zarr/buffer/gpu.md - - Testing: + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.buffer.cpu</code>': api/zarr/buffer/cpu.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.buffer.gpu</code>': api/zarr/buffer/gpu.md + - 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'<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.dtype</code>': api/zarr/dtype.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.empty</code>': api/zarr/functions/empty.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.empty_like</code>': api/zarr/functions/empty_like.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.errors</code>': api/zarr/errors.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.experimental</code>': api/zarr/experimental.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.from_array</code>': api/zarr/functions/from_array.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.full</code>': api/zarr/functions/full.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.full_like</code>': api/zarr/functions/full_like.md + - 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'<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros</code>': api/zarr/functions/zeros.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros_like</code>': api/zarr/functions/zeros_like.md - release-notes.md - contributing.md +hooks: + - mkdocs_hooks.py + watch: - src/zarr - docs @@ -128,11 +153,6 @@ extra_css: plugins: - autorefs - search - - mkdocs-jupyter: - include: ["docs/user-guide/examples/*.ipynb"] - execute: false - ignore_h1_titles: true - show_input: true - markdown-exec - mkdocstrings: enable_inventory: true @@ -217,6 +237,10 @@ plugins: 'developers/index.html.md': 'contributing.md' 'developers/roadmap.html.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' 'api.md': 'api/zarr/index.md' + 'api/zarr/create.md': 'api/zarr/functions/create.md' + 'api/zarr/open.md': 'api/zarr/functions/open.md' + 'api/zarr/save.md': 'api/zarr/functions/save.md' + 'api/zarr/load.md': 'api/zarr/functions/load.md' 'api/zarr/metadata/migrate_v3.md': 'api/zarr/metadata.md' # Based on https://github.com/developmentseed/titiler/blob/50934c929cca2fa8d3c408d239015f8da429c6a8/docs/mkdocs.yml#L115-L140 diff --git a/mkdocs_hooks.py b/mkdocs_hooks.py new file mode 100644 index 0000000000..88368926b9 --- /dev/null +++ b/mkdocs_hooks.py @@ -0,0 +1,82 @@ +"""MkDocs hook that renders validation-marked code fences as ordinary code blocks. + +The docs validation convention (see ``tests/test_docs.py`` and the contributing +guide) requires every python fence to carry ``exec="true"``, ``test="true"``, or +``exec="false" reason="..."``. Markdown Exec's superfences fence only claims +``exec="true"`` blocks; without this hook the remaining marked fences fail +superfences validation and their contents spill into the page as raw markdown +(e.g. the PEP 723 header of the custom dtype example rendered as headings). + +This hook registers a second ``python`` fence, tried when Markdown Exec's +declines, that strips the validation attributes and delegates to the standard +superfences highlighter so the block renders exactly like a plain code fence. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +if TYPE_CHECKING: + from markdown import Markdown + from mkdocs.config.defaults import MkDocsConfig + +# Mirrors markdown_exec's _to_bool: everything but these means "true". +_FALSY = {"", "no", "off", "false", "0"} + + +def _validator( + language: str, + inputs: dict[str, str], + options: dict[str, Any], + attrs: dict[str, Any], + md: Markdown, +) -> bool: + """Claim fences marked test="true" or exec="false"; leave the rest alone.""" + if "exec" not in inputs and "test" not in inputs: + # Plain fence: let the default superfences pathway highlight it. + return False + if str(inputs.get("exec", "false")).lower() not in _FALSY: + # Executable fence: Markdown Exec's own custom fence handles it. + return False + # Consume the validation attributes so they don't leak into the output. + inputs.clear() + return True + + +def _formatter( + source: str, + language: str, + css_class: str, + options: dict[str, Any], + md: Markdown, + classes: list[str] | None = None, + id_value: str = "", + attrs: dict[str, Any] | None = None, + **kwargs: Any, +) -> str: + """Render with the same highlighter superfences uses for plain fences.""" + fenced = md.preprocessors["fenced_code_block"] + fenced.get_hl_settings() + return fenced.highlight( + src=source, + language=language, + options={}, + md=md, + classes=classes, + id_value=id_value, + attrs=attrs or {}, + ) + + +def on_config(config: MkDocsConfig) -> MkDocsConfig: + superfences = config.setdefault("mdx_configs", {}).setdefault("pymdownx.superfences", {}) + custom_fences = superfences.setdefault("custom_fences", []) + custom_fences.append( + { + "name": "python", + "class": "python", + "validator": _validator, + "format": _formatter, + } + ) + return config diff --git a/pyproject.toml b/pyproject.toml index 6a7238ff8f..1ecfb6a62f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -126,7 +126,6 @@ docs = [ "mkdocstrings==1.0.4", "mkdocstrings-python==2.0.4", "mike==2.2.0", - 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{ name = "mkdocs-jupyter", specifier = "==0.26.3" }, { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.6" }, { name = "mkdocs-redirects", specifier = "==1.2.3" }, { name = "mkdocstrings", specifier = "==1.0.4" }, @@ -4130,7 +3595,6 @@ docs = [ { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.1" }, { name = "mike", specifier = "==2.2.0" }, { name = "mkdocs", specifier = "==1.6.1" }, - { name = "mkdocs-jupyter", specifier = "==0.26.3" }, { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.6" }, { name = "mkdocs-redirects", specifier = "==1.2.3" }, { name = "mkdocstrings", specifier = "==1.0.4" }, From 9bc5b0a1b06836e0e41ca5e1509ac36ca5634aa9 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 9 Jul 2026 15:19:19 +0200 Subject: [PATCH 393/468] test: pass a list, not a generator, to parametrize in test_docs (#4138) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: pass a list, not a generator, to parametrize in test_docs pytest 9.1 deprecated passing a non-Collection iterable to @pytest.mark.parametrize (PytestRemovedIn10Warning). find_examples() returns a generator, and with filterwarnings=error that deprecation becomes a hard collection error, breaking the doctests env under pytest 9.1.1 (e.g. the #4137 dependency bump). Materialize it to a list, matching the existing list(find_examples(...)) usage elsewhere in this module. Assisted-by: ClaudeCode:claude-opus-4-8 * doc: add changelog fragment for test_docs parametrize fix Assisted-by: ClaudeCode:claude-opus-4-8 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- changes/4138.misc.md | 1 + tests/test_docs.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 changes/4138.misc.md diff --git a/changes/4138.misc.md b/changes/4138.misc.md new file mode 100644 index 0000000000..2cf0365bb9 --- /dev/null +++ b/changes/4138.misc.md @@ -0,0 +1 @@ +Pass a list rather than a generator to `pytest.mark.parametrize` in `tests/test_docs.py`, so the test suite collects cleanly under pytest 9.1 (which deprecates non-Collection iterables and, under `filterwarnings = error`, turns that into a collection error). diff --git a/tests/test_docs.py b/tests/test_docs.py index 9c42a0521a..0ed429f173 100644 --- a/tests/test_docs.py +++ b/tests/test_docs.py @@ -254,7 +254,7 @@ def test_documentation_examples( module_globals.update(result) -@pytest.mark.parametrize("example", find_examples(str(SOURCES_ROOT)), ids=str) +@pytest.mark.parametrize("example", list(find_examples(str(SOURCES_ROOT))), ids=str) def test_docstrings(example: CodeExample, eval_example: EvalExample) -> None: """Test our docstring examples.""" if example.path.name == "config.py" and "your.module" in example.source: From 31817c681dc747d4d723af072e9562c624def553 Mon Sep 17 00:00:00 2001 From: Sai Asish Y <say.apm35@gmail.com> Date: Thu, 9 Jul 2026 08:13:14 -0700 Subject: [PATCH 394/468] docs: clarify difference between load and open in docstrings (#3984) * docs: clarify difference between load and open in docstrings * docs: add changelog entry for load/open clarification * docs: rename changelog entry to match PR number * docs: clarify load returns configured buffer prototype, not always NumPy Signed-off-by: Sai Asish Y <say.apm35@gmail.com> --------- Signed-off-by: Sai Asish Y <say.apm35@gmail.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- changes/3984.doc.md | 4 ++++ src/zarr/api/asynchronous.py | 21 ++++++++++++++++++++- src/zarr/api/synchronous.py | 21 ++++++++++++++++++++- 3 files changed, 44 insertions(+), 2 deletions(-) create mode 100644 changes/3984.doc.md diff --git a/changes/3984.doc.md b/changes/3984.doc.md new file mode 100644 index 0000000000..1b92fb8e74 --- /dev/null +++ b/changes/3984.doc.md @@ -0,0 +1,4 @@ +Clarify the difference between `zarr.load` and `zarr.open` in their docstrings. +`load` eagerly reads data into an in-memory array, while `open` returns a +lazy `Array` or `Group` backed by the store, with `See Also` cross-references +linking the two. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index 54fefaa041..c751d6a31c 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -309,12 +309,20 @@ async def load( See Also -------- - save + save, open Notes ----- If loading data from a group of arrays, data will not be immediately loaded into memory. Rather, arrays will be loaded into memory as they are requested. + + Unlike [`open`][zarr.open], which returns a lazy [`Array`][zarr.Array] or + [`Group`][zarr.Group] backed by the store, `load` eagerly reads the data and + returns it as an in-memory array (or a dict of arrays for a group). + The array type is NumPy by default, but follows the configured + buffer prototype (for example, CuPy for GPU use cases). + Use `open` when you want to read or write data incrementally without loading it + all into memory. """ obj = await open(store=store, path=path, zarr_format=zarr_format) @@ -362,6 +370,17 @@ async def open( ------- z : array or group Return type depends on what exists in the given store. + + See Also + -------- + load + + Notes + ----- + `open` returns a lazy [`Array`][zarr.Array] or [`Group`][zarr.Group] backed by + the store, so data is read and written incrementally. Use [`load`][zarr.load] + instead when you want the data eagerly read into an in-memory array (a + NumPy array by default). """ if mode is None: diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 8386427b3f..3231837a04 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -161,12 +161,20 @@ def load( See Also -------- - save, savez + save, savez, open Notes ----- If loading data from a group of arrays, data will not be immediately loaded into memory. Rather, arrays will be loaded into memory as they are requested. + + Unlike [`open`][zarr.open], which returns a lazy [`Array`][zarr.Array] or + [`Group`][zarr.Group] backed by the store, `load` eagerly reads the data and + returns it as an in-memory array (or a dict of arrays for a group). + The array type is NumPy by default, but follows the configured + buffer prototype (for example, CuPy for GPU use cases). + Use `open` when you want to read or write data incrementally without loading it + all into memory. """ return sync(async_api.load(store=store, zarr_format=zarr_format, path=path)) @@ -209,6 +217,17 @@ def open( ------- z : array or group Return type depends on what exists in the given store. + + See Also + -------- + load + + Notes + ----- + `open` returns a lazy [`Array`][zarr.Array] or [`Group`][zarr.Group] backed by + the store, so data is read and written incrementally. Use [`load`][zarr.load] + instead when you want the data eagerly read into an in-memory array (a + NumPy array by default). """ obj = sync( async_api.open( From c9ca0b957f9fb3d6e9249c2c4899b77c6ab3cc44 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 10 Jul 2026 12:52:02 +0000 Subject: [PATCH 395/468] chore(deps): bump the python-dependencies group across 1 directory with 13 updates (#4137) Bumps the python-dependencies group with 12 updates in the / directory: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.4.6` | `2.5.0` | | [typing-extensions](https://github.com/python/typing_extensions) | `4.15.0` | `4.16.0` | | [fsspec](https://github.com/fsspec/filesystem_spec) | `2026.4.0` | `2026.6.0` | | [obstore](https://github.com/geospatial-jeff/pyasyncio-benchmark) | `0.10.1` | `0.11.0` | | [typer](https://github.com/fastapi/typer) | `0.26.7` | `0.26.8` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.14.1` | `7.14.3` | | [pytest](https://github.com/pytest-dev/pytest) | `9.0.3` | `9.1.1` | | [pytest-accept](https://github.com/max-sixty/pytest-accept) | `0.2.3` | `0.3.0` | | [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.155.2` | `6.155.7` | | [uv](https://github.com/astral-sh/uv) | `0.11.20` | `0.11.26` | | [mkdocstrings-python](https://github.com/mkdocstrings/python) | `2.0.4` | `2.0.5` | | [ruff](https://github.com/astral-sh/ruff) | `0.15.16` | `0.15.20` | Updates `numpy` from 2.4.6 to 2.5.0 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.4.6...v2.5.0) Updates `typing-extensions` from 4.15.0 to 4.16.0 - [Release notes](https://github.com/python/typing_extensions/releases) - [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md) - [Commits](https://github.com/python/typing_extensions/compare/4.15.0...4.16.0) Updates `fsspec` from 2026.4.0 to 2026.6.0 - [Commits](https://github.com/fsspec/filesystem_spec/compare/2026.4.0...2026.6.0) Updates `obstore` from 0.10.1 to 0.11.0 - [Commits](https://github.com/geospatial-jeff/pyasyncio-benchmark/commits) Updates `typer` from 0.26.7 to 0.26.8 - [Release notes](https://github.com/fastapi/typer/releases) - [Changelog](https://github.com/fastapi/typer/blob/master/docs/release-notes.md) - [Commits](https://github.com/fastapi/typer/compare/0.26.7...0.26.8) Updates `coverage` from 7.14.1 to 7.14.3 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](https://github.com/coveragepy/coveragepy/compare/7.14.1...7.14.3) Updates `pytest` from 9.0.3 to 9.1.1 - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/9.0.3...9.1.1) Updates `pytest-accept` from 0.2.3 to 0.3.0 - [Release notes](https://github.com/max-sixty/pytest-accept/releases) - [Changelog](https://github.com/max-sixty/pytest-accept/blob/main/CHANGELOG.md) - [Commits](https://github.com/max-sixty/pytest-accept/compare/0.2.3...0.3.0) Updates `hypothesis` from 6.155.2 to 6.155.7 - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/v6.155.2...v6.155.7) Updates `uv` from 0.11.20 to 0.11.26 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.11.20...0.11.26) Updates `s3fs` from 2026.4.0 to 2026.6.0 - [Changelog](https://github.com/fsspec/s3fs/blob/main/release-procedure.md) - [Commits](https://github.com/fsspec/s3fs/commits) Updates `mkdocstrings-python` from 2.0.4 to 2.0.5 - [Release notes](https://github.com/mkdocstrings/python/releases) - [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md) - [Commits](https://github.com/mkdocstrings/python/compare/2.0.4...2.0.5) Updates `ruff` from 0.15.16 to 0.15.20 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.15.16...0.15.20) --- updated-dependencies: - dependency-name: numpy dependency-version: 2.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: typing-extensions dependency-version: 4.16.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: fsspec dependency-version: 2026.6.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: obstore dependency-version: 0.11.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: typer dependency-version: 0.26.8 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: coverage dependency-version: 7.14.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: pytest dependency-version: 9.1.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: pytest-accept dependency-version: 0.3.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: hypothesis dependency-version: 6.155.7 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: uv dependency-version: 0.11.26 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: s3fs dependency-version: 2026.6.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: mkdocstrings-python dependency-version: 2.0.5 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.15.20 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- pyproject.toml | 16 +- uv.lock | 494 +++++++++++++++++++++++-------------------------- 2 files changed, 236 insertions(+), 274 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1ecfb6a62f..255d546276 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -94,18 +94,18 @@ homepage = "https://github.com/zarr-developers/zarr-python" # pins deliberately, e.g. via dependabot or `uv lock --upgrade`. [dependency-groups] test = [ - "coverage==7.14.1", - "pytest==9.0.3", + "coverage==7.14.3", + "pytest==9.1.1", "pytest-asyncio==1.4.0", "pytest-cov==7.1.0", - "pytest-accept==0.2.3", + "pytest-accept==0.3.0", "numpydoc==1.10.0", - "hypothesis==6.155.2", + "hypothesis==6.155.7", "pytest-xdist==3.8.0", "pytest-benchmark==5.2.3", "pytest-codspeed==5.0.3", "tomlkit==0.15.0", - "uv==0.11.20", + "uv==0.11.26", ] remote-tests = [ {include-group = "test"}, @@ -124,19 +124,19 @@ docs = [ "mkdocs-material[imaging]==9.7.6", "mkdocs==1.6.1", "mkdocstrings==1.0.4", - "mkdocstrings-python==2.0.4", + "mkdocstrings-python==2.0.5", "mike==2.2.0", "mkdocs-redirects==1.2.3", "markdown-exec[ansi]==1.12.1", "griffe-inherited-docstrings==1.1.3", - "ruff==0.15.16", + "ruff==0.15.20", # Changelog generation {include-group = "release"}, # Optional dependencies to run examples "numcodecs[msgpack]", "s3fs>=2023.10.0", "astroid==4.1.2", - "pytest==9.0.3", + "pytest==9.1.1", ] dev = [ {include-group = "test"}, 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{ name = "ruff", specifier = "==0.15.16" }, + { name = "ruff", specifier = "==0.15.20" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "tomlkit", specifier = "==0.15.0" }, { name = "towncrier", specifier = "==25.8.0" }, { name = "universal-pathlib" }, - { name = "uv", specifier = "==0.11.20" }, + { name = "uv", specifier = "==0.11.26" }, ] docs = [ { name = "astroid", specifier = "==4.1.2" }, @@ -3598,24 +3560,24 @@ docs = [ { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.6" }, { name = "mkdocs-redirects", specifier = "==1.2.3" }, { name = "mkdocstrings", specifier = "==1.0.4" }, - { name = "mkdocstrings-python", specifier = "==2.0.4" }, + { name = "mkdocstrings-python", specifier = "==2.0.5" }, { name = "numcodecs", extras = ["msgpack"] }, - { name = "pytest", specifier = "==9.0.3" }, - { name = "ruff", specifier = "==0.15.16" }, + { name = "pytest", specifier = "==9.1.1" }, + { name = "ruff", specifier = "==0.15.20" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "towncrier", specifier = "==25.8.0" }, ] release = [{ name = "towncrier", specifier = "==25.8.0" }] remote-tests = [ { name = "botocore" }, - { name = "coverage", specifier = "==7.14.1" }, + { name = "coverage", specifier = "==7.14.3" }, { name = "fsspec", specifier = ">=2023.10.0" }, - { name = "hypothesis", specifier = "==6.155.2" }, + { name = "hypothesis", specifier = "==6.155.7" }, { name = "moto", extras = ["s3", "server"], specifier = "==5.2.2" }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "obstore", specifier = ">=0.5.1" }, - { name = "pytest", specifier = "==9.0.3" }, - { name = "pytest-accept", specifier = "==0.2.3" }, + { name = "pytest", specifier = "==9.1.1" }, + { name = "pytest-accept", specifier = "==0.3.0" }, { name = "pytest-asyncio", specifier = "==1.4.0" }, { name = "pytest-benchmark", specifier = "==5.2.3" }, { name = "pytest-codspeed", specifier = "==5.0.3" }, @@ -3624,19 +3586,19 @@ remote-tests = [ { name = "requests", specifier = "==2.34.2" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "tomlkit", specifier = "==0.15.0" }, - { name = "uv", specifier = "==0.11.20" }, + { name = "uv", specifier = "==0.11.26" }, ] test = [ - { name = "coverage", specifier = "==7.14.1" }, - { name = "hypothesis", specifier = "==6.155.2" }, + { name = "coverage", specifier = "==7.14.3" }, + { name = "hypothesis", specifier = "==6.155.7" }, { name = "numpydoc", specifier = "==1.10.0" }, - { name = "pytest", specifier = "==9.0.3" }, - { name = "pytest-accept", specifier = "==0.2.3" }, + { name = "pytest", specifier = "==9.1.1" }, + { name = "pytest-accept", specifier = "==0.3.0" }, { name = "pytest-asyncio", specifier = "==1.4.0" }, { name = "pytest-benchmark", specifier = "==5.2.3" }, { name = "pytest-codspeed", specifier = "==5.0.3" }, { name = "pytest-cov", specifier = "==7.1.0" }, { name = "pytest-xdist", specifier = "==3.8.0" }, { name = "tomlkit", specifier = "==0.15.0" }, - { name = "uv", specifier = "==0.11.20" }, + { name = "uv", specifier = "==0.11.26" }, ] From 13279cac07e80c9142d8f7ad55cfcdb881d16a8e Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Fri, 10 Jul 2026 16:49:19 +0200 Subject: [PATCH 396/468] test: bind moto server to an ephemeral port to fix xdist deadlock (#4139) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: bind moto server to an ephemeral port to fix xdist deadlock The session-scoped moto_server fixture bound a fixed port (5555). Under pytest-xdist, session-scoped fixtures run once per worker, so concurrent workers raced to bind the same port. The losers blocked forever inside ThreadedMotoServer.start(): its werkzeug thread dies on "Address already in use" before setting the ready event that start() waits on, and the wait has no timeout. Any multi-worker run whose s3 tests landed on 2+ workers deadlocked near the end of the suite at 0% CPU. CI never saw this because it runs the suite single-process. Bind port 0 instead and yield the actual endpoint from the fixture. Since the endpoint is now only known at runtime, test_fsspec.py's module-level endpoint_url constant becomes an endpoint_url fixture (replacing the s3_base alias), and its consumers take it as a parameter. With this fix the full suite completes in ~1 minute under -n auto on a 10-core machine, where it previously hung indefinitely. Assisted-by: ClaudeCode:claude-fable-5 * doc: add changelog fragment for moto ephemeral-port fix Assisted-by: ClaudeCode:claude-fable-5 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- changes/214.misc.md | 1 + tests/conftest.py | 14 +++++++--- tests/test_store/test_fsspec.py | 45 ++++++++++++++++----------------- 3 files changed, 33 insertions(+), 27 deletions(-) create mode 100644 changes/214.misc.md diff --git a/changes/214.misc.md b/changes/214.misc.md new file mode 100644 index 0000000000..8611362e84 --- /dev/null +++ b/changes/214.misc.md @@ -0,0 +1 @@ +Bind the shared moto S3 test server to an ephemeral port instead of a fixed one. The fixed port deadlocked `pytest -n auto`: session-scoped fixtures run once per xdist worker, so concurrent workers raced to bind the same port and the losers blocked forever in `ThreadedMotoServer.start()`. diff --git a/tests/conftest.py b/tests/conftest.py index c02daf7663..ec8f07b0e8 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -550,24 +550,30 @@ def deep_nan_equal(a: object, b: object) -> bool: # instead of each module standing up its own. Consumers create their own buckets and choose # how the endpoint reaches the client (explicit storage_options vs. the AWS_ENDPOINT_URL # env var) on top of this fixture. -MOTO_SERVER_PORT = 5555 -MOTO_ENDPOINT_URL = f"http://127.0.0.1:{MOTO_SERVER_PORT}/" @pytest.fixture(scope="session") def moto_server() -> Generator[str, None, None]: """Start a session-scoped moto S3 server and yield its endpoint URL. + The server binds an ephemeral port (port=0), so the endpoint is only known at + runtime; consumers must take it from this fixture rather than a constant. A fixed + port deadlocks under pytest-xdist: session-scoped fixtures run once per *worker*, so + concurrent workers race to bind the same port, and the losers block forever inside + ThreadedMotoServer.start(), whose server thread dies on "Address already in use" + before ever setting the ready event that start() waits on. + importorskip lives inside the fixture so moto is only required when a test actually requests an S3 backend, not for the whole test session.""" moto_server_mod = pytest.importorskip("moto.moto_server.threaded_moto_server") - server = moto_server_mod.ThreadedMotoServer(ip_address="127.0.0.1", port=MOTO_SERVER_PORT) + server = moto_server_mod.ThreadedMotoServer(ip_address="127.0.0.1", port=0) server.start() + host, port = server.get_host_and_port() # moto needs *some* credentials present; use throwaway values if the environment has none. os.environ.setdefault("AWS_SECRET_ACCESS_KEY", "foo") os.environ.setdefault("AWS_ACCESS_KEY_ID", "foo") try: - yield MOTO_ENDPOINT_URL + yield f"http://{host}:{port}/" finally: server.stop() diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 9efee40d7a..898d49ec08 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -9,7 +9,6 @@ from packaging.version import parse as parse_version import zarr.api.asynchronous -from tests.conftest import MOTO_ENDPOINT_URL from zarr import Array from zarr.abc.store import OffsetByteRequest from zarr.core.buffer import Buffer, cpu, default_buffer_prototype @@ -60,18 +59,18 @@ # ### amended from s3fs ### # test_bucket_name = "test" secure_bucket_name = "test-secure" -# The moto server itself is the session-scoped `moto_server` fixture in tests/conftest.py; -# this module reuses its endpoint rather than standing up its own server. -endpoint_url = MOTO_ENDPOINT_URL @pytest.fixture -def s3_base(moto_server: str) -> str: - """Reuse the shared session-scoped moto server (see tests/conftest.py).""" +def endpoint_url(moto_server: str) -> str: + """Endpoint of the shared session-scoped moto server (see tests/conftest.py). + + A fixture rather than a module-level constant because the server binds an ephemeral + port, so the endpoint is only known once the server is running.""" return moto_server -def get_boto3_client() -> botocore.client.BaseClient: +def get_boto3_client(endpoint_url: str) -> botocore.client.BaseClient: # NB: we use the sync botocore client for setup session = botocore.session.Session() @@ -84,7 +83,7 @@ def get_boto3_client() -> botocore.client.BaseClient: @pytest.fixture(autouse=True) -def s3(s3_base: None) -> Generator[s3fs.S3FileSystem, None, None]: +def s3(endpoint_url: str) -> Generator[s3fs.S3FileSystem, None, None]: """ Quoting Martin Durant: pytest-asyncio creates a new event loop for each async test. @@ -97,7 +96,7 @@ def s3(s3_base: None) -> Generator[s3fs.S3FileSystem, None, None]: https://github.com/zarr-developers/zarr-python/pull/1785#discussion_r1634856207 """ - client = get_boto3_client() + client = get_boto3_client(endpoint_url) client.create_bucket(Bucket=test_bucket_name, ACL="public-read") s3fs.S3FileSystem.clear_instance_cache() s3 = s3fs.S3FileSystem( @@ -119,7 +118,7 @@ def s3(s3_base: None) -> Generator[s3fs.S3FileSystem, None, None]: # ### end from s3fs ### # -async def test_basic() -> None: +async def test_basic(endpoint_url: str) -> None: store = FsspecStore.from_url( f"s3://{test_bucket_name}/foo/spam/", storage_options={"endpoint_url": endpoint_url, "anon": False}, @@ -146,7 +145,7 @@ class TestFsspecStoreS3(StoreTests[FsspecStore, cpu.Buffer]): buffer_cls = cpu.Buffer @pytest.fixture - def store_kwargs(self) -> dict[str, str | bool]: + def store_kwargs(self, endpoint_url: str) -> dict[str, str | bool]: try: from fsspec import url_to_fs except ImportError: @@ -184,7 +183,7 @@ def test_store_supports_writes(self, store: FsspecStore) -> None: def test_store_supports_listing(self, store: FsspecStore) -> None: assert store.supports_listing - async def test_fsspec_store_from_uri(self, store: FsspecStore) -> None: + async def test_fsspec_store_from_uri(self, store: FsspecStore, endpoint_url: str) -> None: storage_options = { "endpoint_url": endpoint_url, "anon": False, @@ -237,7 +236,7 @@ async def test_fsspec_store_from_uri(self, store: FsspecStore) -> None: parse_version(fsspec.__version__) < parse_version("2024.03.01"), reason="Prior bug in from_upath", ) - def test_from_upath(self) -> None: + def test_from_upath(self, endpoint_url: str) -> None: upath = pytest.importorskip("upath") path = upath.UPath( f"s3://{test_bucket_name}/foo/bar/", @@ -250,7 +249,7 @@ def test_from_upath(self) -> None: assert result.fs.asynchronous assert result.path == f"{test_bucket_name}/foo/bar" - def test_init_warns_if_fs_asynchronous_is_false(self) -> None: + def test_init_warns_if_fs_asynchronous_is_false(self, endpoint_url: str) -> None: try: from fsspec import url_to_fs except ImportError: @@ -279,7 +278,7 @@ async def test_delete_dir_unsupported_deletes(self, store: FsspecStore) -> None: # ── Filesystem lifecycle (ownership) ────────────────────────────────────── - def test_from_url_owns_filesystem(self) -> None: + def test_from_url_owns_filesystem(self, endpoint_url: str) -> None: """FsspecStore.from_url() creates the async fs; it must own it.""" store = FsspecStore.from_url( f"s3://{test_bucket_name}/lifecycle/", @@ -288,7 +287,7 @@ def test_from_url_owns_filesystem(self) -> None: assert store._owns_fs store.close() - async def test_from_url_close_releases_store(self) -> None: + async def test_from_url_close_releases_store(self, endpoint_url: str) -> None: """ close() on a from_url() store must succeed without error and mark the store as closed. For the owned filesystem, _close_fs() is invoked to @@ -305,7 +304,7 @@ async def test_from_url_close_releases_store(self) -> None: assert not store._is_open - def test_direct_construction_does_not_own_filesystem(self) -> None: + def test_direct_construction_does_not_own_filesystem(self, endpoint_url: str) -> None: """Direct FsspecStore() must not claim ownership — the caller owns the fs.""" try: from fsspec import url_to_fs @@ -321,7 +320,7 @@ def test_direct_construction_does_not_own_filesystem(self) -> None: parse_version(fsspec.__version__) < parse_version("2024.03.01"), reason="Prior bug in from_upath", ) - def test_from_upath_does_not_own_filesystem(self) -> None: + def test_from_upath_does_not_own_filesystem(self, endpoint_url: str) -> None: """from_upath() uses the UPath's existing fs; the store must not own it.""" upath = pytest.importorskip("upath") path = upath.UPath( @@ -333,7 +332,7 @@ def test_from_upath_does_not_own_filesystem(self) -> None: store = FsspecStore.from_upath(path) assert not store._owns_fs - def test_from_mapper_does_not_own_already_async_filesystem(self) -> None: + def test_from_mapper_does_not_own_already_async_filesystem(self, endpoint_url: str) -> None: """from_mapper() with an already-async fs must not claim ownership.""" s3_filesystem = s3fs.S3FileSystem( asynchronous=True, @@ -501,7 +500,7 @@ def test_wrap_sync_filesystem_raises(tmp_path: pathlib.Path) -> None: parse_version(fsspec.__version__) < parse_version("2024.12.0"), reason="No AsyncFileSystemWrapper", ) -def test_no_wrap_async_filesystem() -> None: +def test_no_wrap_async_filesystem(endpoint_url: str) -> None: """An async fs should not be wrapped automatically; fsspec's s3 filesystem is such an fs""" from fsspec.implementations.asyn_wrapper import AsyncFileSystemWrapper @@ -551,7 +550,7 @@ def test_open_fsmap_file_raises(tmp_path: pathlib.Path) -> None: @pytest.mark.parametrize("asynchronous", [True, False]) -def test_open_fsmap_s3(asynchronous: bool) -> None: +def test_open_fsmap_s3(asynchronous: bool, endpoint_url: str) -> None: s3_filesystem = s3fs.S3FileSystem( asynchronous=asynchronous, endpoint_url=endpoint_url, anon=False ) @@ -559,7 +558,7 @@ def test_open_fsmap_s3(asynchronous: bool) -> None: array_roundtrip(mapper) -def test_open_s3map_raises() -> None: +def test_open_s3map_raises(endpoint_url: str) -> None: with pytest.raises(TypeError, match="Unsupported type for store_like:.*"): zarr.open(store=0, mode="w", shape=(3, 3)) s3_filesystem = s3fs.S3FileSystem(asynchronous=True, endpoint_url=endpoint_url, anon=False) @@ -652,7 +651,7 @@ def test_with_read_only_transfers_filesystem_ownership(tmp_path: pathlib.Path) - @pytest.mark.parametrize("asynchronous", [True, False]) -def test_make_async(asynchronous: bool) -> None: +def test_make_async(asynchronous: bool, endpoint_url: str) -> None: s3_filesystem = s3fs.S3FileSystem( asynchronous=asynchronous, endpoint_url=endpoint_url, anon=False ) From b4179e4dcbf787c987723007af191e87295e4276 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Mon, 13 Jul 2026 14:46:06 +0200 Subject: [PATCH 397/468] test: enable pytest strict mode, fix duplicate parametrization ids, and add 10m timeout to individual tests (#4140) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: bind moto server to an ephemeral port to fix xdist deadlock The session-scoped moto_server fixture bound a fixed port (5555). Under pytest-xdist, session-scoped fixtures run once per worker, so concurrent workers raced to bind the same port. The losers blocked forever inside ThreadedMotoServer.start(): its werkzeug thread dies on "Address already in use" before setting the ready event that start() waits on, and the wait has no timeout. Any multi-worker run whose s3 tests landed on 2+ workers deadlocked near the end of the suite at 0% CPU. CI never saw this because it runs the suite single-process. Bind port 0 instead and yield the actual endpoint from the fixture. Since the endpoint is now only known at runtime, test_fsspec.py's module-level endpoint_url constant becomes an endpoint_url fixture (replacing the s3_base alias), and its consumers take it as a parameter. With this fix the full suite completes in ~1 minute under -n auto on a 10-core machine, where it previously hung indefinitely. Assisted-by: ClaudeCode:claude-fable-5 * doc: add changelog fragment for moto ephemeral-port fix Assisted-by: ClaudeCode:claude-fable-5 * test: enable pytest strict mode and fix duplicate parametrization ids Adopt pytest 9's `strict = true` config option, which enables strict_config, strict_markers, strict_xfail, strict_parametrization_ids, and future strictness options. This replaces the --strict-config and --strict-markers addopts flags (which pytest silently ignored when passed via addopts before 9.1, pytest#14442) and the separate xfail_strict setting. minversion is bumped to 9 accordingly. strict_parametrization_ids surfaced seven parametrizations whose ids collided, which pytest previously deduplicated silently: - test_common.py paired float("inf") with np.inf (and -inf/nan), but np.inf IS a Python float, so three cases per test ran twice and the intended numpy-scalar coverage did not exist. Use np.float64 scalars with explicit ids, restoring the intended coverage. - test_int.py deliberately includes np.dtype("i")/np.dtype("I"), which compare equal to one of the explicit-endian dtypes and stringify identically. The class-fixture hook in test_dtype/conftest now suffixes colliding ids with their index instead of relying on pytest's silent deduplication. - test_group.py test_consistent_signatures id'd both create_hierarchy pairs identically; ids now include module and qualname. - test_array.py ("a" vs b"a"), test_vlen.py (str vs "str"), and test_metadata/test_v2.py (3 vs "3") get explicit ids for the colliding member. Assisted-by: ClaudeCode:claude-fable-5 * doc: add changelog fragment for pytest strict mode Assisted-by: ClaudeCode:claude-fable-5 * test: arm faulthandler watchdog to turn deadlocks into loud failures Set faulthandler_timeout=600 with faulthandler_exit_on_timeout (new in pytest 9): if a single test exceeds 10 minutes, every thread's traceback is dumped and the run is killed, instead of hanging indefinitely with no diagnostics. Motivated by the moto fixed-port deadlock, which hung local -n auto runs at ~98% for hours and required manual kill -ABRT forensics to diagnose; with this watchdog the same bug would have failed in 10 minutes with the offending stack in the log. The ceiling is ~30x the slowest legitimate test (~20s locally) to stay clear of slow CI runners, coverage overhead, and nightly stateful hypothesis runs. Assisted-by: ClaudeCode:claude-fable-5 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- changes/215.misc.md | 1 + pyproject.toml | 16 +++++++++++++--- tests/test_array.py | 3 ++- tests/test_codecs/test_vlen.py | 6 ++++-- tests/test_dtype/conftest.py | 18 +++++++++++++++++- tests/test_dtype/test_npy/test_common.py | 19 +++++++++++-------- tests/test_group.py | 3 +++ tests/test_metadata/test_v2.py | 3 ++- 8 files changed, 53 insertions(+), 16 deletions(-) create mode 100644 changes/215.misc.md diff --git a/changes/215.misc.md b/changes/215.misc.md new file mode 100644 index 0000000000..f8df7cc632 --- /dev/null +++ b/changes/215.misc.md @@ -0,0 +1 @@ +Enable pytest's `strict = true` config option (strict config, markers, xfail, and parametrization ids), replacing the `--strict-config`/`--strict-markers` addopts flags that pytest silently ignored before 9.1, and fix the seven duplicate parametrization ids it surfaced — including restoring float-JSON roundtrip cases that were meant to cover numpy scalars but ran plain-float cases twice instead. Also arm pytest's faulthandler watchdog (`faulthandler_timeout = 600` with `faulthandler_exit_on_timeout`) so a deadlocked test dumps every thread's traceback and fails the run instead of hanging indefinitely. diff --git a/pyproject.toml b/pyproject.toml index 255d546276..081ddefdfb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -426,11 +426,21 @@ module = [ ignore_errors = true [tool.pytest.ini_options] -minversion = "7" +minversion = "9" testpaths = ["src", "tests", "docs/user-guide"] log_cli_level = "INFO" log_level = "INFO" -xfail_strict = true +# Enables strict_config, strict_markers, strict_xfail, strict_parametrization_ids, and +# any strictness options added in future pytest releases. Note that the equivalent +# `--strict-config`/`--strict-markers` flags were silently ignored when passed via +# addopts before pytest 9.1 (pytest#14442), so this option is the reliable spelling. +strict = true +# Turn deadlocks into loud failures: if a single test exceeds this many seconds, dump +# every thread's traceback and kill the run (exit_on_timeout is new in pytest 9). Sized +# far above the slowest legitimate test (~20s locally; slower under coverage/Windows/ +# nightly stateful-hypothesis runs) so only a genuine hang can trip it. +faulthandler_timeout = 600 +faulthandler_exit_on_timeout = true asyncio_mode = "auto" asyncio_default_fixture_loop_scope = "function" doctest_optionflags = [ @@ -442,7 +452,7 @@ addopts = [ "--benchmark-columns", "min,mean,stddev,outliers,rounds,iterations", "--benchmark-disable", # benchmark routines run as tests without benchmarking instrumentation "--durations", "10", - "-ra", "--strict-config", "--strict-markers", + "-ra", "--doctest-modules", "--ignore=tests/test_regression/scripts", "--ignore=src/zarr/_cli", diff --git a/tests/test_array.py b/tests/test_array.py index 89d7547e78..4faf99eb9e 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1693,7 +1693,8 @@ def test_default_endianness( assert endianness_from_numpy_str(byte_order) == endianness # type: ignore[arg-type] -@pytest.mark.parametrize("value", [1, 1.4, "a", b"a", np.array(1)]) +# The explicit id for b"a" avoids colliding with the auto-generated id for "a". +@pytest.mark.parametrize("value", [1, 1.4, "a", pytest.param(b"a", id="a-bytes"), np.array(1)]) @pytest.mark.parametrize("zarr_format", [2, 3]) @pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") def test_scalar_array(value: Any, zarr_format: ZarrFormat) -> None: diff --git a/tests/test_codecs/test_vlen.py b/tests/test_codecs/test_vlen.py index c2c2c9b201..b90ad88ddc 100644 --- a/tests/test_codecs/test_vlen.py +++ b/tests/test_codecs/test_vlen.py @@ -13,10 +13,12 @@ from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.storage import StorePath -numpy_str_dtypes: list[type | str | None] = [ +# The explicit id for the "str" literal avoids colliding with the auto-generated id for +# the `str` builtin. +numpy_str_dtypes: list[Any] = [ None, str, - "str", + pytest.param("str", id="str-literal"), np.dtypes.StrDType, "S", "U", diff --git a/tests/test_dtype/conftest.py b/tests/test_dtype/conftest.py index 4c585bfdf6..100b9df226 100644 --- a/tests/test_dtype/conftest.py +++ b/tests/test_dtype/conftest.py @@ -1,5 +1,6 @@ # Generate a collection of zdtype instances for use in testing. import warnings +from collections import Counter from typing import Any import numpy as np @@ -64,4 +65,19 @@ class TestB(TestExample): for fixture_name in metafunc.fixturenames: if hasattr(metafunc.cls, fixture_name): params = getattr(metafunc.cls, fixture_name) - metafunc.parametrize(fixture_name, params, scope="class", ids=str) + metafunc.parametrize( + fixture_name, params, scope="class", ids=_unique_ids([str(p) for p in params]) + ) + + +def _unique_ids(ids: list[str]) -> list[str]: + """Suffix repeated ids with their positional index so every id is unique. + + Distinct parameters can stringify identically: for example `np.dtype("i")` and + `np.dtype("<i4")` both render as `int32` on little-endian platforms, but they are + deliberately distinct test cases. Pytest used to deduplicate colliding ids silently; + `strict_parametrization_ids` makes them a collection error, so we disambiguate + explicitly. Ids that are already unique are left untouched. + """ + counts = Counter(ids) + return [f"{id_}-{idx}" if counts[id_] > 1 else id_ for idx, id_ in enumerate(ids)] diff --git a/tests/test_dtype/test_npy/test_common.py b/tests/test_dtype/test_npy/test_common.py index d8912a70ec..b7e4e875ad 100644 --- a/tests/test_dtype/test_npy/test_common.py +++ b/tests/test_dtype/test_npy/test_common.py @@ -36,14 +36,17 @@ from zarr.core.common import JSON, ZarrFormat -json_float_v2_roundtrip_cases: tuple[tuple[JSONFloatV2, float | np.floating[Any]], ...] = ( - ("Infinity", float("inf")), - ("Infinity", np.inf), - ("-Infinity", float("-inf")), - ("-Infinity", -np.inf), - ("NaN", float("nan")), - ("NaN", np.nan), - (1.0, 1.0), +# Each special value is tested as both a Python float and a numpy scalar. The explicit +# ids are load-bearing: np.float64("inf") stringifies identically to float("inf"), so +# without them these parameter sets would produce duplicate test ids. +json_float_v2_roundtrip_cases: tuple[Any, ...] = ( + pytest.param("Infinity", float("inf"), id="Infinity-float"), + pytest.param("Infinity", np.float64("inf"), id="Infinity-float64"), + pytest.param("-Infinity", float("-inf"), id="-Infinity-float"), + pytest.param("-Infinity", np.float64("-inf"), id="-Infinity-float64"), + pytest.param("NaN", float("nan"), id="NaN-float"), + pytest.param("NaN", np.float64("nan"), id="NaN-float64"), + pytest.param(1.0, 1.0, id="1.0-1.0"), ) json_float_v3_cases = json_float_v2_roundtrip_cases diff --git a/tests/test_group.py b/tests/test_group.py index bc80e19e86..1acd5551ca 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -1713,6 +1713,9 @@ def test_create_nodes_concurrency_limit(store: MemoryStore) -> None: (zarr.core.group.create_rooted_hierarchy, zarr.core.sync_group.create_rooted_hierarchy), (zarr.core.group.get_node, zarr.core.sync_group.get_node), ], + # The default ids (from __name__) collide: the method pair and the module-level pair + # for create_hierarchy would both be id'd "create_hierarchy-create_hierarchy". + ids=lambda func: f"{func.__module__.rsplit('.', maxsplit=1)[-1]}.{func.__qualname__}", ) def test_consistent_signatures( a_func: Callable[[object], object], b_func: Callable[[object], object] diff --git a/tests/test_metadata/test_v2.py b/tests/test_metadata/test_v2.py index d1a1ca00b4..0f280f0401 100644 --- a/tests/test_metadata/test_v2.py +++ b/tests/test_metadata/test_v2.py @@ -29,7 +29,8 @@ def test_parse_zarr_format_valid() -> None: assert parse_zarr_format(2) == 2 -@pytest.mark.parametrize("data", [None, 1, 3, 4, 5, "3"]) +# The explicit id for "3" avoids colliding with the auto-generated id for the int 3. +@pytest.mark.parametrize("data", [None, 1, 3, 4, 5, pytest.param("3", id="3-str")]) def test_parse_zarr_format_invalid(data: Any) -> None: with pytest.raises(ValueError, match=f"Invalid value. Expected 2. Got {data}"): parse_zarr_format(data) From fe50301564b6f5ca6552b5ca411a793682163760 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Mon, 13 Jul 2026 18:43:53 +0200 Subject: [PATCH 398/468] perf: use sync methods for chunk encoding / decoding (#3885) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat: define `PreparedWrite` and `SupportsChunkPacking` data structures `PreparedWrite` models a set of per-chunk changes that would be applied to a stored chunk. `SupportsChunkPacking` is a protocol for array -> bytes codecs that can use `PreparedWrite` objects to update an existing chunk. * feat: new codec pipeline that uses sync path * feat: complete second codecpipeline * fix: handle rectilinear chunks * fixup * feat: SupportsSetRange protocol + sync byte-range writes Adds a SupportsSetRange protocol to zarr.abc.store for stores that allow overwriting a byte range within an existing value. Implementations are added for LocalStore (using file-handle seek+write) and MemoryStore (in-memory bytearray slice assignment). This is the prerequisite for the partial-shard write fast path in ShardingCodec, which can patch individual inner-chunk slots without rewriting the entire shard blob when the inner codec chain is fixed-size. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat: add sync codec methods to V2 and numcodecs codecs V2Codec, BytesCodec, BloscCodec, etc. previously only implemented the async _decode_single / _encode_single methods. Add their sync counterparts (_decode_sync / _encode_sync) so that the upcoming SyncCodecPipeline can dispatch through them without spinning up an event loop. For codecs that wrap external compressors (numcodecs.Zstd, numcodecs.Blosc, the V2 fallback chain), the sync versions just call the underlying compressor's blocking API directly instead of routing through asyncio.to_thread. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat: SyncCodecPipeline — synchronous codec pipeline with per-chunk parallelism Adds SyncCodecPipeline alongside BatchedCodecPipeline. The new pipeline runs codecs through their sync entry points (_decode_sync / _encode_sync) and dispatches per-chunk work to a module-level thread pool sized by the codec_pipeline.max_workers config (default = os.cpu_count()). Each chunk's full lifecycle (fetch + decode + scatter for reads; get-existing + merge + encode + set/delete for writes) runs as one pool task — overlapping IO of one chunk with compute of another. Scatter into the shared output buffer is thread-safe because chunks have non-overlapping output selections. The async wrappers (read/write) detect SupportsGetSync/SupportsSetSync stores and dispatch to the sync fast path, passing the configured max_workers. Other stores fall through to the async path, which still uses asyncio.concurrent_map at async.concurrency. Notes on perf: - Default (None → cpu_count) is tuned for chunks ≥ ~512 KB. - Small chunks (≤ 64 KB) regress 1.5-3x because pool dispatch overhead (~30-50 µs/task) dominates per-chunk work. Workaround: zarr.config.set({"codec_pipeline.max_workers": 1}). - For large chunks on local/memory stores, IO+compute parallelism yields 1.7-2.5x over BatchedCodecPipeline on direct-API reads and ~2.5x on roundtrip. ChunkTransform encapsulates the sync codec chain. It caches resolved ArraySpecs across calls with the same chunk_spec — combined with the constant-ArraySpec optimization in indexing, hot-path overhead is minimized. Includes test scaffolding for the new pipeline (test_sync_codec_pipeline) and config plumbing for the max_workers key. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat: partial-shard write support in ShardingCodec Adds _encode_partial_sync and _decode_partial_sync to ShardingCodec. For fixed-size inner codec chains and stores that implement SupportsSetRange, partial writes patch individual inner-chunk slots in-place instead of rewriting the whole shard: - Reads existing shard index (one byte-range get). - For each affected inner chunk: decodes the slot, merges the new region, re-encodes. - Writes each modified slot at its deterministic byte offset, then rewrites just the index. For variable-size inner codecs (e.g. with compression) or stores that don't support byte-range writes, falls through to a full-shard rewrite matching BatchedCodecPipeline semantics. The partial-decode path computes a ReadPlan from the shard index and issues one byte-range get per overlapping chunk, decoding only what the read selection touches. Both paths are dispatched from SyncCodecPipeline via the existing supports_partial_decode / supports_partial_encode protocol checks. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test: codec invariants + pipeline parity matrix Two new test files: test_codec_invariants — asserts contract-level properties that every codec / shard / buffer combination must satisfy: round-trip exactness, prototype propagation, fill-value handling, all-empty shard handling. test_pipeline_parity — exhaustive matrix asserting that SyncCodecPipeline and BatchedCodecPipeline produce semantically identical results across codec configs, layouts (including nested sharding), write sequences, and write_empty_chunks settings. Three checks per cell: 1. Same array contents on read. 2. Same set of store keys after writes. 3. Each pipeline reads the other's output identically (catches layout-divergence bugs). These tests pinned the design throughout the SyncCodecPipeline + partial-shard development. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: gitignore local agent/planning notes Adds .gitignore entries for .claude/, CLAUDE.md, and docs/superpowers/ so local IDE/agent planning artifacts don't get committed by accident. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: remove unused PreparedWrite and SupportsChunkCodec Both were exported from zarr.abc.codec.__all__ but never referenced by either codec pipeline or any test. Artifacts of an earlier design iteration superseded by the current SyncCodecPipeline. Also remove now-unused imports of `dataclass` and `ChunkProjection` that were only needed by the deleted symbols. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: remove stale phased-pipeline test files Both tests/test_phased_codec_pipeline.py and tests/test_pipeline_benchmark.py import PhasedCodecPipeline, which no longer exists in src/. Each failed at collection. The benchmarking intent of test_pipeline_benchmark.py is replaced by extensions to tests/benchmarks/test_e2e.py later in this branch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor: rename SyncCodecPipeline to FusedCodecPipeline The new name describes what the pipeline does (fuses fetch+decode+scatter into one task per chunk) rather than the implementation detail of using sync codec entry points. The name also stays accurate when this pipeline gains a remote-store / async fast path in a future change. Mechanical rename across the class, register_pipeline call, dotted-path strings used by zarr.config, isinstance checks, parametrize values, and docstrings. tests/test_sync_pipeline.py renamed to tests/test_fused_pipeline.py. Nothing on this branch is released, so no deprecation alias is needed. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor: lift _merge_chunk_array to module level The BatchedCodecPipeline and FusedCodecPipeline classes had identical copies of _merge_chunk_array (one method, one staticmethod). Extract once as a module-level free function and call from both. No new base class or mixin is introduced. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor: extract _async_read_fallback to module level Both BatchedCodecPipeline.read_batch (non-partial-decode branch) and FusedCodecPipeline.read (async fallback) duplicate the same sequence: concurrent_map(get) -> pipeline.decode -> scatter into out. Lift to a module-level free function and call from both. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor: extract _async_write_fallback to module level Both BatchedCodecPipeline.write_batch (non-partial-encode branch) and FusedCodecPipeline.write (async fallback) duplicate the same sequence: read existing bytes -> decode -> merge -> encode -> set/delete. Lift to a module-level free function and call from both. After this change, neither pipeline class carries _merge_chunk_array, nor the duplicated read/write fallback bodies. Each class is reduced to its constructor, fast-path methods, and thin async dispatch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(bench): parametrize test_e2e over both codec pipelines Adds a `pipeline` fixture with values ["batched", "fused"] that swaps codec_pipeline.path for the duration of each benchmark. Both test_write_array and test_read_array now produce one benchmark cell per (compression x layout x store x pipeline). CodSpeed will report comparable numbers for both pipelines on the same workloads. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(bench): parametrize test_e2e over a synthetic latency dimension Adds `latency in {0, 0.001, 0.05, 0.2}` and a bench_store fixture that wraps the underlying memory store in zarr.testing.store.LatencyStore when latency > 0. Local-store cells skip nonzero latency — adding synthetic latency on top of a real filesystem double-counts and is not the intended measurement. Combined with the pipeline parameter, the matrix now produces comparable benchmark numbers for {Batched, Fused} x {0, 1ms, 50ms, 200ms} on memory-shaped operation. The numbers are signal under one simple model of remote latency, not absolute predictions of S3 behavior. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: restore deleted comments in V2Codec._decode_sync Commit 7f45aba9 (which converted _decode_single -> _decode_sync) dropped two explanatory comment blocks from the dtype-handling branches in V2Codec.decode. Both comments document non-obvious WHY: - The TypeError catch is for chunks whose stored dtype doesn't match the array spec dtype (e.g. string dtype vs object array). - The elif branch fires when filters were tampered with: an object array needs an object codec in the filter chain to be read correctly. These were removed as drive-by cleanup during the sync-method rename without intent to delete the substance. Restoring verbatim. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: explain non-obvious behaviors in sharding sync methods Add docstring substance and a couple of inline notes to the new sync methods on ShardingCodec that landed on this branch. Concretely: - _decode_sync / _encode_sync: explain how each relates to the async counterpart and the partial-* variants, and why inner chunks are iterated in Morton order on the encode path. - _encode_shard_dict_sync: explain the two-pass offset shift in the index-at-start branch (offsets are written relative to the data section, then bumped by len(index_bytes)) and the MAX_UINT_64 empty-chunk sentinel that must not be touched. - _encode_partial_sync byte-range path: explain WHY morton-rank determines byte offset deterministically (fixed-size inner chunks = every slot at a stable offset regardless of which others are present); this is the load-bearing invariant for the byte-range fast path. - _decode_partial_sync: docstring now lists the two sub-paths (full-shard fetch vs. index-then-byte-ranges) and the reason the full-shard branch exists (one round trip beats N+1 small ones). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: convert RST inline literals to Markdown-style backticks Docstrings added on this branch used RST-style ``literal`` markup (double-backticks). Convert to Markdown-style `literal` (single backticks) so the docstrings render correctly in Markdown-aware viewers without needing a separate RST-to-Markdown step. Two cases worth calling out: - src/zarr/core/codec_pipeline.py and src/zarr/codecs/sharding.py: every ``literal`` in these files came in on this branch, so the conversion is global within those files. - src/zarr/abc/store.py and src/zarr/core/array.py: only docstrings added on this branch are converted; pre-existing RST-style literals from main are left alone (out of scope). Also converted one .. note:: directive in src/zarr/core/array.py (the regular_chunk_array_spec helper) to a Markdown blockquote, since that directive was added on this branch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * perf: memoize encoded inner chunk for scalar complete-shard writes (#177) In ShardingCodec._encode_partial_sync's full-shard-rewrite loop, a scalar broadcast value produces byte-for-byte identical results for every complete inner chunk (same fill, same empty-check, same encoded bytes). Compute that outcome once and reuse it across all complete chunks instead of re-merging, re-checking write_empty_chunks, and re-encoding tens of thousands of identical chunks. Incomplete edge chunks still merge against their own data individually. Target case (fused, memory, chunks=100/shards=1M, no compression): write 92.26ms -> 21.59ms (4.3x). Pipeline parity (byte-identical to batched) and 956 tests pass under the fused pipeline; adversarial partial-overwrite/ edge/compression/2D/aliasing checks pass. Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * perf+fix: bulk whole-shard read + repair _ShardIndex construction post-merge Two things, both scoped to the sync sharding read path: 1. Fix: main's #3975 made _ShardIndex a 2-field NamedTuple (chunks_per_shard, offsets_and_lengths), but the Fused sync methods still constructed it with one arg, erroring on every Fused sharded read. Pass chunks_per_shard through in _decode_shard_index_sync and the byte-range write path. 2. Perf: _decode_full_shard_bulk + _ShardIndex.is_dense. A whole-shard read of a dense, fixed-size, uncompressed shard is reconstructed by reshaping/scattering the data section in bulk, replacing the per-chunk decode/index/projection loop (~78% of a full read). Chunk positions are read from the stored index, so it is correct for any subchunk_write_order. Falls through to the per-chunk path for compression/filters, non-dense shards, and any read whose output shape != the shard shape (strided/partial/fancy). Full read (memory, 10000 chunks/shard, uint8): ~291ms -> ~21ms (13.9x vs Batched). Verified: 0 new test failures vs the merge baseline; full reads correct across dtypes and 2D; partial/strided/gzip fall through. (Pre-existing Fused x subchunk_write_order gaps remain, tracked separately.) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix: FusedCodecPipeline honors subchunk_write_order + coalesced partial reads Three integration gaps surfaced when the Fused pipeline met main's new subchunk_write_order (#3826), partial-read coalescing (#3004), and _ShardIndex refactor. Under Fused these caused 25 sharding/parity failures (data was correct in the partial-read cases; the failures were write-order layout + IO-pattern divergence). Fixes: 1. Write order: _encode_shard_dict_sync laid out chunks in hardcoded morton order, ignoring subchunk_write_order. Now iterates _subchunk_order_iter(self.subchunk_write_order), matching the async _encode_shard_dict. Fixes lexicographic/colexicographic/unordered storage. 2. Coalesced sync partial reads: add Store.get_ranges_sync (a synchronous, coalescing counterpart of get_ranges, reusing coalesce_ranges) and ShardingCodec._load_partial_shard_maybe_sync; route _decode_partial_sync's partial branch through it. Sync stores now get #3004's byte-range coalescing without an event loop (fewer, merged reads). 3. Non-sync fallback: FusedCodecPipeline.read now routes non-sync stores (e.g. ZipStore) through the async partial-decode path when the AB codec supports it, instead of _async_read_fallback's whole-shard get(). Matches Batched's IO behavior; avoids over-reading whole shards on partial reads. Tests: the #3004 partial-read tests are made pipeline-aware (assert the active method family: get/get_ranges vs get_sync/get_ranges_sync, gated on store sync support). 573 sharding+parity+pipeline+indexing and 657 codec tests pass under BOTH pipelines (was 25 failing under Fused). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix: address roborev review (job 222) — Fused sharding correctness HIGH (sharding.py, byte-range write fast path): derived each chunk's physical slot from self.subchunk_write_order instead of hardcoded morton order, and excluded 'unordered' (no recoverable rank -> falls through to the index-driven full-rewrite path). A partial write into a dense shard first written with a non-default order no longer corrupts data via wrong byte offsets. HIGH (sharding.py, _decode_full_shard_bulk): build the read-view dtype from the BytesCodec's endian (as BytesCodec._decode_sync does), not the dtype's native endianness. A big-endian shard read on a little-endian host (or vice versa) now decodes correctly instead of silently reinterpreting bytes. MEDIUM (sharding.py, _decode_full_shard_bulk): the bulk fast path now requires the inner chain to be exactly one BytesCodec, excluding crc-bearing shards. The bulk path can't verify per-chunk checksums, so crc shards fall through to the per-chunk path and keep their corruption detection. LOW (codec_pipeline.py, ChunkTransform._resolve_specs): key the resolved-spec cache on the frozen, hashable ArraySpec value instead of (shape, id()), which could collide after id reuse. LOW (codec_pipeline.py, _get_pool): don't shutdown(wait=False) the old pool on grow — a concurrent in-flight pool.map could hit 'cannot schedule new futures after shutdown'. The orphaned pool drains and is GC'd. Tests: extended test_pipeline_parity with big-endian + crc32c codec configs and a dedicated subchunk_write_order x index_location parity test (asserts identical contents always, identical bytes for deterministic orders). Verified each new test fails when its corresponding fix is reverted. 1219 tests pass under both pipelines; mypy clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: correct FusedCodecPipeline framing — sync scheduling, not IO/compute separation The class docstring claimed it 'separates IO from compute', then immediately said the ShardingCodec does IO internally — self-contradictory and misleading. The actual win is replacing per-chunk ASYNC scheduling with synchronous, batched/coalesced execution; the sharding codec still owns its storage IO (the zarrs model, unlike tensorstore's storage-free codecs). Rewrite the docstring to state this plainly and note that a storage-free codec is a possible future direction, not what this pipeline does. No behavior change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor: stop hard-coding assumptions about the 'unordered' write order After merging #4011 (which made 'unordered' deterministic and warns callers not to rely on its layout), drop the two places my earlier fixes special-cased it by name: - Byte-range write fast path: remove the 'subchunk_write_order != unordered' gate. The rank map is derived from _subchunk_order_iter(self.subchunk_write_ order), which is the single source of truth for physical layout — correct for every order without a name check. _subchunk_order_iter is the only place that knows a given order's layout. - Parity test: assert byte-equality across pipelines for ALL orders, not just 'deterministic' ones. The check verifies the two pipelines AGREE (they share _subchunk_order_iter), which holds whatever an order resolves to; it makes no assumption about what 'unordered' means. 540 parity+sharding and 862 codec/indexing tests pass under both pipelines; mypy clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat: make FusedCodecPipeline the default codec pipeline Flip codec_pipeline.path default from BatchedCodecPipeline to FusedCodecPipeline. Fused runs codec compute synchronously/in bulk and gives large speedups on sharded workloads (up to ~24x write / ~14x read on many-chunks-per-shard, more with compression) and no regressions on compute-bound cases; it falls back to the async path for non-sync stores. Batched remains selectable via config. Test fallout from the flip (all behavior, not stale-assertion churn): - test_config_defaults_set: expected default path updated. - test_config_codec_implementation: the mock codec now also overrides _encode_sync, so it records a call regardless of which pipeline is default (Fused uses the sync entry point). - StoreExpectingTestBuffer (zarr.testing.buffer): added set_sync/get_sync that mirror the async buffer-type guards, so the 'all buffers are TestBuffer' invariant is checked on the sync write path too. Verified Fused correctly threads a custom BufferPrototype (sharded writes store TestBuffer instances) — the test simply wasn't exercising the sync path before. Full suite: 6346 passed, 0 failed under the new default. NOTE: changelog fragment filename is a PLACEHOLDER — rename changes/PLACEHOLDER-fused-default.feature.md to changes/<PR#>.feature.md once the PR number is known (towncrier keys fragments by issue/PR number). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix: ShardingCodec inner pipeline follows the configured default, not hard-coded Batched The codec_pipeline property hard-coded BatchedCodecPipeline.from_codecs(). main resolves it against the registry via get_pipeline_class() (#2179); the branch carried an older hard-coded version and the main-merge kept the branch side. With FusedCodecPipeline now the default this left the inner sub-chunk pipeline stuck on Batched while the outer array used Fused — an inconsistency, and stale relative to main. Restore get_pipeline_class().from_codecs(), matching the rest of this module (which already uses get_pipeline_class elsewhere). Verified: sharding + parity + pipeline (596) and codecs+array+indexing+properties (2161) pass; nested sharding roundtrips correctly under both pipelines; no functional BatchedCodecPipeline references remain in sharding.py. mypy clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix: Fused async decode/encode must evolve codec specs (HIGH-2) + shared CodecPipelineTests HIGH-2: FusedCodecPipeline.decode()/encode() (the async fallback for non-sync stores) reused one flat chunk_spec across every codec stage instead of evolving it per codec via resolve_metadata. Spec-changing array->array codecs broke: TransposeCodec crashed on read (could not broadcast (2,2) into (2,4)); cast_value/scale_offset would silently corrupt. Reachable on the DEFAULT pipeline for every non-sync store (S3/GCS/fsspec/zip). Fix, without re-duplicating spec logic (the duplication caused the bug): - Extract resolve_aa_specs(): single source of truth for per-stage spec evolution (forward-thread resolve_metadata over the AA codecs). Pure metadata. - Add AsyncChunkTransform: per-chunk ASYNC mirror of ChunkTransform, driving the codecs' async _decode_single/_encode_single with the correct per-stage spec. No mini-batch concept (that stays a BatchedCodecPipeline concern). - ChunkTransform._resolve_specs delegates to resolve_aa_specs. - Fused.decode()/encode() loop per chunk through AsyncChunkTransform. Also harden the sharding byte-range WRITE fast path: take chunk offsets from the stored shard index, not from the live subchunk_write_order (which is not recoverable on reopen by design). New tests/test_codec_pipeline_suite.py: xUnit CodecPipelineTests base run as TestBatchedPipeline and TestFusedPipeline over a sync (MemoryStore) AND a non-sync (LatencyStore) store axis. Reproduces HIGH-2 automatically. 140 pass; mypy clean; original ZipStore+transpose crash now roundtrips. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: dedupe codec-pipeline tests against the shared CodecPipelineTests suite The shared suite runs every pipeline-agnostic behavior test against BOTH pipelines x both store paths, so per-file copies of the same behavior are redundant. Remove confirmed duplicates; keep tests that exercise something the suite does not. - Strengthen the suite's write_empty_chunks tests to also assert chunk-key presence/absence (absorbing the old _no_store / _persists coverage). - test_codec_pipeline.py: drop the 8 behavior duplicates now in the suite. KEEP test_read_returns_get_results (low-level pipeline.read GetResult API), test_write_empty_chunks_false_no_store (store-key shape), and test_codec_pipeline_threads_dtype_through_evolve (#3937 regression). - test_fused_pipeline.py: drop the array-level streaming read/write tests and test_partial_shard_write_roundtrip_correctness (array behavior, suite-covered). KEEP all pipeline-API / Fused-internal tests (construction, evolve, low-level write/read(_sync) roundtrips, sync-write/async-read interop, ChunkTransform encode/decode, set_range, inner_codecs_fixed_size, byte-range fast path). 740 pass across suite + codec_pipeline + fused + sync + invariants + parity + sharding; ruff + mypy clean. No coverage removed without a verified equivalent. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: unify the create/write/read suite tests into one Scenario-parametrized test The bulk of CodecPipelineTests followed one shape: create an array, apply some writes, optionally assert which chunk keys exist, then assert reads come back correct. Capture those variables in a frozen Scenario dataclass (array_kwargs, writes, reads, keys_present/absent) and drive them all through a single parametrized test_scenario. Correctness is checked against a numpy reference the scenario derives from its own writes, so cases don't hand-maintain expected values. 18 scenarios cover the same matrix (layouts, gzip, transpose spec-evolution, nested sharding, partial-shard overwrite, write_empty key presence/absence) x both pipelines x sync/async stores. Kept as separate focused tests the two cases that don't fit the shape: test_read_missing_chunks_false_raises (asserts an exception) and test_partial_write_after_reopen_is_correct (has an extra reopen step). Verified the parametrized form keeps its regression-guard value: reverting the HIGH-2 spec-evolution fix still fails test_scenario[async-transpose]. 670 pass across pipeline + sharding suites; ruff + mypy clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: prune test_fused_pipeline.py to its irreducible Fused-specific core The Fused test file had accumulated tests that either duplicated the pipeline-agnostic CodecPipelineTests suite or were misfiled. Triage: - async roundtrip / missing-chunk-fill / partial-shard-write dups: removed; the shared test_scenario covers these across both pipelines x sync/async stores. Added float32 and zstd Scenarios first so the dtype/codec coverage the dups carried transfers to the shared matrix (no net coverage loss). - store set_range / SupportsSetRange tests: already covered (more thoroughly, parametrized) in tests/test_store/test_memory.py; removed as dups. - ShardingCodec._inner_codecs_fixed_size tests: moved to tests/test_codecs/test_sharding_unit.py where the sharding internals live. What stays is genuinely Fused-only and cannot be pipeline-agnostic: the synchronous API (write_sync / read_sync / _sync_transform) which Batched has no equivalent of, and the byte-range fast-path assertions (set_range_sync fires / falls back) which test a Fused-only optimization. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test: dissolve test_codec_invariants.py, redistributing by subject The "invariants" file grouped tests by their shared motivation (a design doc) rather than by what they test, which is the wrong axis -- it mixed pipeline-agnostic behavior, Fused-only internals, and a per-codec property into one file. Sorted each test into the home its subject implies: Pipeline-agnostic behavior -> CodecPipelineTests (runs on BOTH pipelines x sync/async stores via the existing fixtures): - S2 empty-chunk skipping under default config -> a Scenario (keys_absent). - S2 shard deleted after overwrite-to-fill -> a base-class method (it needs a mid-sequence key assertion the Scenario shape can't express). - C3 no isinstance(ShardingCodec) branching in read/write -> a base-class method that resolves the subclass's configured pipeline and source-scans it. Fused-only (byte-range fast path / ChunkTransform internals) -> test_fused_pipeline.py: - S3 fast path skipped when write_empty_chunks=False (the unique complement of the existing uses-set-range test; the write_empty_chunks=True case was a dup and is dropped). - B1 byte-range path copies read-only LocalStore buffers before mutating. - C2 ChunkTransform passes each codec the runtime chunk_spec prototype. Per-codec contract -> tests/test_codecs/test_codecs.py: - C1 resolve_metadata only mutates shape (prototype/dtype/fill_value/config stable across the chain) -- a property of individual codecs, no pipeline. Dropped as a pure duplicate (already in test_store/test_memory.py): - test_supports_set_range_is_runtime_checkable. No coverage lost: every kept test moved, and the two genuinely-shared behaviors now run on both pipelines instead of only whichever was default. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test: drop redundant read-parity matrix, move partial-read coverage to shared suite test_pipeline_read_parity checked Fused vs Batched partial reads against *each other*. The shared CodecPipelineTests suite already reads partial/strided selections from sharded arrays against a numpy reference on BOTH pipelines -- which is strictly stronger (it would catch both pipelines diverging from the spec in the same way, which a pipeline-vs-pipeline check cannot). The one sliver read-parity covered that the shared suite didn't was scalar single-element reads from a sharded array (the sharding codec's partial-decode path). Added two Scenarios (sharded-scalar-reads-1d / -2d) to capture it. Verified they exercise the partial-decode path on both pipelines: the default Fused pipeline routes a scalar sharded read through _decode_partial_sync, the Batched pipeline through _decode_partial_single -- so both variants are now checked against numpy, not just against each other. Kept in test_pipeline_parity.py the two checks the per-pipeline suite cannot express, because its two subclasses run in isolation and never see each other's output: - test_pipeline_parity: cross-read interop (write under A, read whole under B) + cross-pipeline store-key-set equality. - test_pipeline_parity_subchunk_write_order: byte-identical shard output across pipelines for every subchunk_write_order x index_location. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test: rename test_sync_codec_pipeline -> test_chunk_transform; drop cross-file dup The file named test_sync_codec_pipeline.py tested no pipeline -- it is the unit test suite for ChunkTransform (the per-chunk synchronous codec chain that FusedCodecPipeline uses internally). "sync codec pipeline" was an earlier name for the Fused pipeline; the filename had outlived it. Renamed to test_chunk_transform.py (git mv preserves history) and added a module docstring naming what it actually covers. Also removed test_sync_transform_encode_decode_roundtrip from test_fused_pipeline.py: it was a weaker cross-file duplicate of this file's test_encode_decode_roundtrip (which covers the same encode->decode->compare over five codec chains rather than just bytes-only). Its one extra assertion -- that evolve_from_array_spec populates _sync_transform -- is already covered by test_evolve_from_array_spec in the Fused file. test_codec_pipeline.py left as-is: all three tests are correctly placed and cover things the Scenario suite can't (the low-level pipeline.read GetResult API, a plain dict store, and the #3937 cast_value dtype-threading regression). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * feat: remove byte-range-write support pending store-interface decision The byte-range-write machinery works, but the right store interface for it is still undecided, so it is removed from this PR and will return once that lands. Removed: - SupportsSetRange protocol (abc/store.py) and its __all__ export. - MemoryStore.set_range / set_range_sync / _set_range_impl and the SupportsSetRange base (storage/_memory.py). - LocalStore.set_range / set_range_sync, the _put_range helper, and the SupportsSetRange base (storage/_local.py). - The sharding codec's byte-range-write fast path in _encode_partial_sync; partial shard writes now always take the full-shard-rewrite path (identical to BatchedCodecPipeline, verified by the pipeline-parity suite). Also dropped the now-dead _chunk_byte_offset helper it relied on. - changes/3907.feature.md (the byte-range-writes changelog note). The byte-range-READ changelog (3004) is unrelated and kept. Byte-range READS (ByteRequest, get(byte_range=), get_ranges coalescing, the read-side bulk shard decode) are untouched -- this only removes writes. The known-good tests that exercise byte-range writes are commented out (not deleted) in test_store/test_memory.py, test_store/test_local.py, and test_fused_pipeline.py, to restore once the store design is settled. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor: remove dead _get_default_chunk_spec helper PR-added module-level helper in array.py with zero callers — an ArraySpec-reuse optimization that was never wired up. Plain function, no protocol role, safe to drop. Verified: no references anywhere in src/ or tests/, and the full array/sharding/pipeline suites stay green. Note: ShardingCodec._encode_sync, though never *called*, is NOT dead — it is a required member of the runtime_checkable SupportsSyncCodec protocol. Removing it drops ShardingCodec from SupportsSyncCodec and breaks the sync read-fallback routing (16 test failures), so it stays. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs: correct ShardingCodec._encode_sync docstring re: write order The docstring claimed _encode_sync "iterates inner chunks in Morton order — that's the canonical layout the shard index expects", which is wrong and a latent footgun: it implies the method imposes a morton physical layout. It does not. The morton iteration only populates an intermediate dict whose key order is immaterial; the on-disk layout is decided downstream by the subchunk_write_order loop in _encode_shard_dict_sync (same as the async _encode_single sibling). Also clarified that this method IS reached — via nested sharding, where an inner ShardingCodec is encoded through the outer codec's ChunkTransform. (It is not called for top-level sharded writes, which route through _encode_partial_sync.) Verified empirically: routing through nested _encode_sync, all three subchunk_write_order values roundtrip correctly AND morton vs lexicographic produce physically different bytes — i.e. the order is honored, not ignored. Behavior unchanged; docstring only. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor: remove unused ShardingCodec._load_shard_index wrapper PR-added thin wrapper (`_load_shard_index_maybe(...) or _ShardIndex.create_empty(...)`) with zero invocations anywhere in src/ or tests/. Unlike _encode_sync, this is genuinely removable: confirmed it is NOT a member of any runtime_checkable protocol or ABC (no reference in src/zarr/abc/, not a base-class override) and is reached by no dynamic dispatch (no getattr / string reference). main has no _load_shard_index* methods at all, so it was introduced and left unused by this PR. The _maybe and _maybe_sync variants it wrapped remain and are used. Verified: full sharding + nested-sharding + parity + pipeline suites stay green, ruff + mypy clean. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs: drop stale set_range_sync mention from FusedCodecPipeline docstring The FusedCodecPipeline class docstring still described sharded writes as using "byte-range writes via set_range_sync" — but byte-range-write support was removed from this PR (set_range_sync / SupportsSetRange are gone). Sharded writes now take the codec's synchronous full-shard-rewrite path. Docstring only; no behavior change. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs: use plain single backticks in docstrings, not RST double-backticks This branch's docstrings/comments had introduced RST-style ``double-backtick`` inline literals, which this project does not use (plain single backticks only — no RST roles or double-backticks). Converted the 25 occurrences across the sharding codec, codec_pipeline, and fsspec store docstrings/comments to single backticks. Style only; no behavior change. Also confirmed (via git blame, this-branch lines only) there are no remaining references to removed/outdated designs: the byte-range-write (set_range) mentions and the "separating IO from compute" framing were already corrected earlier in this branch. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * feat: default codec_pipeline.max_workers to 1 (sequential), threading opt-in Pairs with the FusedCodecPipeline default: keep the new pipeline, but do NOT enable threading by default. `max_workers=None` (auto -> cpu_count) spawned a thread pool on every read/write, which is a behavior change with real downstream risk — it runs custom stores/codecs concurrently (thread-safety) and can oversubscribe many-core nodes whose workloads already parallelize at the dask/MPI layer. The default is now 1 (fully sequential: the pool is never created when max_workers <= 1). Parallelism is opt-in via `codec_pipeline.max_workers` (positive int, or None for auto). Updates _resolve_max_workers docstring and the config-defaults test accordingly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * perf: vectorize shard_dict build in _encode_partial_sync (fix write regression) CodSpeed flagged test_sharded_morton_write_single_chunk regressing ~38-39% (writing one 1x1x1 chunk into a 32^3 = 32768-chunk shard). Both main and this branch do a full shard rewrite for a partial write, so the rewrite itself is not the regression — and it is NOT the removed byte-range fast path (that path was gated out here anyway: write_empty_chunks defaults to False -> skip_empty=True). The cause: the sync _encode_partial_sync rebuilt the in-memory shard_dict with a per-coordinate __getitem__ loop over all 32768 chunks (O(n_chunks) Python overhead + try/except per chunk), whereas main's async _encode_partial_single builds the same dict with a single vectorized index lookup via _ShardReader.to_dict_vectorized. Switched the sync path to to_dict_vectorized (a plain, non-async method; _shard_reader_from_bytes_sync already returns a _ShardReader), matching the async path. The dict's key order is immaterial (the physical layout is decided downstream by the subchunk_write_order loop in _encode_shard_dict_sync), so the merge loop — which looks up by coordinate, not order — is unaffected. Local micro-benchmark (32^3 shard, single 1x1x1 chunk write): 59.4 -> 40.0 ms/write (~1.5x), matching the CodSpeed delta. Correctness: full sharding + pipeline-parity suites pass (581), so Fused still matches Batched byte-for-byte. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * fix: thread spec forward in FusedCodecPipeline.evolve_from_array_spec The deps=optional CI job (where cast_value_rs is installed) failed test_codec_pipeline_threads_dtype_through_evolve and several test_cast_value tests with "Invalid endianness: None" / "endian needs to be specified for multi-byte data types". Root cause: FusedCodecPipeline.evolve_from_array_spec evolved EVERY codec against the same original array_spec: evolved = tuple(c.evolve_from_array_spec(array_spec=array_spec) for c in self.codecs) When an array->array codec widens the dtype (e.g. cast_value int8 -> int16), the BytesCodec serializer was still evolved against the single-byte SOURCE dtype, so it stripped its `endian` to None (bytes.py treats single-byte dtypes as having no endianness) and then failed at decode time on the multi-byte data. BatchedCodecPipeline.evolve_from_array_spec already threads the spec forward (spec = evolved_codec.resolve_metadata(spec)); the Fused version did not. Fixed by mirroring the Batched threading. Also added test_evolve_threads_spec_preserving_serializer_endian: a dependency-free regression test (uses a minimal dtype-widening AA codec stub, no cast_value_rs) that runs on BOTH pipelines via the pipeline_class fixture. It fails on [sync] without this fix and passes with it — closing the gap where the only coverage required an optional dep and thus ran in no default env. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor: extract shared pipeline logic into freestanding functions The endian bug fixed in the previous commit existed because the two codec pipelines duplicated the same conceptual logic and one copy drifted: Batched's evolve_from_array_spec threaded the spec forward correctly, Fused's did not. Duplicated logic that can silently diverge is a standing bug source, so extract the drift-prone pieces into single sources of truth that both pipelines delegate to (mirroring the existing resolve_aa_specs precedent): - evolve_codecs(codecs, array_spec): the construction-time spec-threading loop. Both BatchedCodecPipeline and FusedCodecPipeline.evolve_from_array_spec now call it. There is now exactly one place this logic lives, so it cannot drift. - pipeline_supports_partial_decode / _encode(ab, *, aa, bb, require_no_aa_bb): the partial-decode/encode predicate. Both pipelines delegate. The two pass DIFFERENT require_no_aa_bb values (Batched True, Fused False) — that divergence is pre-existing and deliberately preserved here (not silently unified); it is now explicit at the call sites and documented in one function instead of being buried in two slightly-different inline isinstance checks. Behavior-preserving: each pipeline computes exactly what it did before. Left the trivial fan-out loops (validate, compute_encoded_size) as-is — deduping those would require changing the CodecPipeline ABC contract (abstract -> concrete) for near-zero drift benefit. Full pipeline/sharding/parity suites + the dtype-evolve regression test pass; ruff + mypy clean. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test: cover the max_workers>1 thread-pool path and concurrent decode The pool dispatch in read_sync/write_sync (codec_pipeline.max_workers > 1) had zero functional test coverage — only config-default assertions existed — even though threading is the opt-in we point users at. Adds: - an end-to-end multi-chunk read/write roundtrip with max_workers=4 (verified the pool dispatch actually fires, not the sequential branch); - worker-exception propagation tests for both write_sync (list-consumed pool.map) and read_sync (tuple-consumed pool.map): a store error raised in a pool worker must surface to the caller; - a concurrent-decode test: transpose filter (so ChunkTransform._resolve_specs cache traffic actually occurs — with no AA codecs the cache is bypassed), pool workers decoding concurrently, plus an outer thread pool issuing overlapping reads. Pins correctness under concurrency around the shared transform's mutable cache. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test: add zarr v2 scenarios to the shared codec-pipeline suite zarr_format=2 appeared in none of the pipeline test files: v2 arrays were only exercised implicitly through whichever pipeline is the global default. v2 goes through the V2Codec wrapper (numcodecs filters + compressor) — a different codec path than the v3 AA/AB/BB chain, with its own _encode_sync/_decode_sync under FusedCodecPipeline — so it deserves explicit coverage on BOTH pipelines and BOTH store kinds (sync fast path + async fallback). Adds v2-roundtrip (uncompressed) and v2-gzip-roundtrip (numcodecs.GZip — the v2 compressor spelling; v3 codec configs are rejected for v2 arrays) to SCENARIOS. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * perf: encode the shard index once, via a shared layout helper Both _encode_shard_dict_sync and the async _encode_shard_dict encoded the shard index TWICE when index_location=start: encode to learn the length, shift the present chunks' offsets by it, then re-encode with corrected offsets. The index size is knowable without encoding — _shard_index_size() is already the byte- exact contract every index read path relies on (reads slice exactly that many bytes) — so the layout can use absolute offsets from the start and the index is encoded once. Saves a full index encode (including its crc32c over the offsets array) per shard write with index_location=start. The layout loop was also duplicated between the sync and async versions — the same drift surface that produced the evolve_from_array_spec endian bug. Both now delegate to a shared pure _build_shard_layout (offset math lives once) and _assemble_shard. A runtime guard verifies the encoded index length matches _shard_index_size rather than silently corrupting offsets if someone ever configures variable-size index codecs. Verified: 606 tests pass including the pipeline-parity byte-identical shard assertions across index_location=start/end and every subchunk_write_order, and the sharded reopen tests — the on-disk layout is unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test: pin read_missing_chunks=False semantics on sharded arrays read_missing_chunks exists to help consumers distinguish a transport error from a truly missing chunk. That distinction is a STORE-KEY-level concept: a missing shard key raises ChunkNotFoundError. It does not cleanly apply to inner subchunks of a shard that was fetched successfully — there is no transport ambiguity there; the shard index simply records the subchunk as absent — so those fill with the fill value rather than raising. Both pipelines already implement exactly this (verified empirically), but nothing pinned it, so the asymmetry vs unsharded arrays read as a bug in review. This adds a shared-suite test (both pipelines x sync/async stores) asserting both sides: missing shard key raises; missing inner subchunk of an existing shard fills. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * Ig/fused additions (#180) * chore: add parallelism TODOs * perf: non-sharded reads * chore: code duplication * fix: arguments dont spread themselves! * fix: bring in suggested guard * perf: don't block on pool ops * chore: docstring + materialize early --------- Co-authored-by: ilan-gold <ilanbassgold@gmail.com> * perf: sync IO for sharding byte getters; evolve the nested inner pipeline Addresses the open question on this PR about sync/async byte getters, benchmark-guided as discussed. _ShardingByteGetter/_ShardingByteSetter are in-memory dict wrappers but presented only an async API, so the nested codec_pipeline.read over inner chunks fell to the async fallback: one concurrent_map coroutine per inner chunk for a dict lookup (~2.1 us/chunk pure asyncio overhead, ~8.8 ms per 4096-chunk shard). On top of that, the nested pipeline (ShardingCodec.codec_pipeline) is built by from_codecs and never evolved, so its sync transform was always None — inner chunks also paid per-chunk AsyncChunkTransform coroutines, and the decode_sync/encode_sync fallback improvements in this PR could not reach them. Changes: - SyncByteGetter / SyncByteSetter runtime protocols in zarr.abc.store (resurrecting the design from the original perf/prepared-write experiments, same names and shape). StorePath matches structurally but is still gated on its STORE's sync support; the protocols gate non-StorePath byte getters. - _ShardingByteGetter/Setter implement get_sync/set_sync/delete_sync; the async methods delegate to the sync ones (single implementation). - ShardingCodec._get_inner_pipeline(shard_spec): the nested pipeline evolved against the inner chunk spec (threads specs through the inner chain AND builds the sync transform). The four nested read/write call sites use it. - FusedCodecPipeline.read/write gates accept non-StorePath SyncByteGetter/ SyncByteSetter, so nested inner-chunk IO takes read_sync/write_sync. - _decode_shard_index/_encode_shard_index delegate to their sync twins (pure compute; kills a per-shard AsyncChunkTransform round-trip and a sync/async duplication). Benchmark (4096 inner chunks per shard, LatencyStore@0 i.e. the async-fallback path = sharded data on remote stores), vs this PR's head: uncompressed read: 44.2 -> 28.9 ms (1.53x) gzip read: 182.0 -> 50.9 ms (3.6x) writes: unchanged (~34 / ~70 ms) — already optimized by this PR's encode_sync fallback (whole-shard sync encode, no byte setters involved). Adds a regression test asserting sharded fallback reads route inner chunks through the sync fast path (read_sync engaged, zero AsyncChunkTransform calls); verified it fails if the gate is removed. Full sharding + parity + pipeline suites pass (619). Assisted-by: ClaudeCode:claude-fable-5 * fix: root-cause the cross-file test flake (pytest-asyncio loop leak); cache inner pipeline The pipeline test suites have failed intermittently all along on an arbitrary test that passes in isolation. Root cause (allocation site verified with PYTHONTRACEMALLOC): pytest-asyncio implicitly creates an event loop in _get_event_loop_no_warn during fixture setup/teardown and never closes it. When GC reclaims that loop — or its self-pipe socketpair — mid-test, pytest's unraisable hook converts the ResourceWarning into a failure of whichever unrelated test happens to be running. The sync-bytegetter change increased per-shard-op allocation churn enough to make this near-deterministic, which is how it was finally traced. Two changes: - pyproject filterwarnings: narrowly ignore the two unraisable shapes (BaseEventLoop.__del__, AF_UNIX socketpair), mirroring the existing s3fs/aiobotocore entry. Not zarr's loops. - ShardingCodec._get_inner_pipeline is now memoized per (pipeline class, shard_spec) — evolving built a ChunkTransform on every shard operation. The pipeline class is part of the key so codec_pipeline.path config changes are still honored. Battery that previously failed ~every run now passes 3x consecutively (635). Assisted-by: ClaudeCode:claude-fable-5 * refactor: dedupe sharding sync/async mirrors; fix un-threaded inner-chain evolve Continues the anti-skew work: where the sync and async sharding paths implemented the same logic twice, extract a single source of truth so the copies cannot drift (the mechanism behind the pipeline-level endian bug). - _get_inner_chunk_transform / _get_index_chunk_transform now evolve their codec chains via evolve_codecs (spec THREADED forward). Both previously evolved every codec against the same unthreaded spec — the exact bug shape that stripped BytesCodec.endian at the pipeline level, latent here for any spec-changing inner codec. Both are also now actually memoized (the inner transform's docstring claimed a cache that did not exist; transforms were rebuilt per call). - New regression test (dependency-free dtype-widening stub codec) asserting the inner serializer keeps its endian; verified it fails on the unthreaded version. - _shard_index_byte_range(): the index-location byte-range arithmetic existed verbatim in both _load_shard_index_maybe and its _sync twin; now one helper. - _pair_chunks_with_byte_ranges(): the chunk-coord/byte-range pairing loop existed verbatim in both _load_partial_shard_maybe and its _sync twin; now one helper. Deliberately NOT unified: the small hand-rolled loops remaining in _decode_sync/_encode_sync vs their async twins. Post sync-bytegetter work the async versions are thin delegations to the (shared, evolved) nested pipeline, so the heavy machinery — evolve, transforms, layout, index codecs — is already single-sourced; force-merging the residual loops would couple different missing-chunk/concurrency semantics for little drift-surface gain. The pipeline-parity suite guards their behavioral equivalence. Full battery passes twice (636); ruff + mypy clean. Assisted-by: ClaudeCode:claude-fable-5 * refactor: canonical chunk write-state functions; fix complete-chunk merge copy Prototype of the "chunk state algebra" direction: the write-side state logic (maybe-read existing -> merge -> empty-normalize -> encode-or-elide) existed in four places with divergent inline conventions. It is now three canonical functions in codec_pipeline.py: - chunk_is_empty(): THE write_empty_chunks normalization rule (all-fill chunk normalizes to missing), previously five scattered inline all_equal checks. - encode_or_elide_chunk(): normalize-empty + encode; None = must not be stored. - merge_and_encode_chunk(): the full single-chunk write transition. Used by the fused _write_one and both branches of the sharding _encode_partial_sync loop (including the scalar-broadcast memoization, which now memoizes the canonical function's result). _encode_sync uses encode_or_elide_chunk. Unification found a real perf bug: _merge_chunk_array's complete-chunk early return required value.shape == chunk_spec.shape, which never holds for multi-chunk writes — so every complete chunk of every multi-chunk fused write paid a create+fill+copy. (Sharding's hand-rolled loop bypassed this with a view, which is itself how the two copies had drifted.) The guard now returns value[out_selection] whenever it is exactly chunk-shaped. Measured, two A/B passes: unsharded full write (1000 chunks) ~1.5x faster; bulk partial shard write (900 complete inner chunks) ~1.4x faster; sharded single-chunk write unchanged. Callers pass existing=None for complete chunks so fully-overwritten data is never decoded. Also removed the last divergent missing-chunk conventions: _decode_sync's try/except KeyError is now .get() -> None (None is the single "missing" convention), and the dead skip_empty/fill_value prologues are gone. 1945 tests pass including pipeline-parity byte-identical assertions; ruff + mypy clean. Assisted-by: ClaudeCode:claude-fable-5 * refactor: canonical chunk read functions (decode_and_scatter / scatter_chunk) The read twin of merge_and_encode_chunk: the fill-on-missing scatter logic existed in five places (fused _read_one, partial-decode _read_one, the async fallback scatter loop, and the two sharding decode tails) with two different missing conventions (None vs try/except KeyError) and three fill spellings (precomputed batch fill, raw shard_spec.fill_value, inline or-default). Now two canonical functions in codec_pipeline.py: - scatter_chunk(): scatter an already-selected region; None = missing -> scatter fill, return a "missing" GetResult. POLICY-FREE on purpose: whether missing is an error (read_missing_chunks=False) is decided at the array layer from the top-level statuses — which is exactly what makes missing INNER chunks of a present shard fill rather than raise (the sharding codec discards the nested statuses). That semantic, previously implicit in which loop happened to run, is now written down where the rule lives. - decode_and_scatter_chunk(): decode (None = missing) -> select -> scatter. All five sites converted; the last try/except KeyError missing-convention is gone (Mapping.get works for both _ShardReader and plain dicts). Read benchmarks A/B neutral-to-marginally-better on all paths (unsharded full, sharded full/partial, half-missing fill). 786 tests pass including pipeline-parity and indexing; ruff + mypy clean. Assisted-by: ClaudeCode:claude-fable-5 * test: property tests asserting fast paths equal general paths Add tests/test_fastpath_equivalence.py with four hypothesis properties, one per fast path on the branch: - _merge_chunk_array complete-chunk view == general merge path (and independent of existing chunk content) - ShardingCodec._decode_full_shard_bulk == _decode_sync for dense uncompressed shards across dtypes, endianness, subchunk write order, and index location (asserts the bulk path actually applies, so the test cannot pass vacuously) - scalar writes leave the store byte-identical to equivalent broadcast array writes (pins the sharded scalar-broadcast memoization) - Store.get_ranges_sync coalesced reads == one get_sync per range, for arbitrary gap/coalesce limits and Range/Offset/Suffix/None requests Each was verified to catch its bug class by temporary fault injection: dropping the bulk decode's endian handling and shifting the coalesce re-slice offset by one both produced shrunk falsifying examples. Assisted-by: ClaudeCode:claude-fable-5 * fix: address open review findings across sharding, pipeline, and tests Code fixes: - ShardingCodec.evolve_from_array_spec now threads the spec through the inner chain via evolve_codecs. The unthreaded evolve survived on the real array-creation path after the transform builders were fixed, baking an endian-stripped BytesCodec into the evolved instance behind any dtype-changing inner codec. Regression test goes through evolve_from_array_spec and then builds the inner transform. - Async _decode_shard_index/_encode_shard_index fall back to the async pipeline when an index codec is not sync-capable, instead of failing every path for third-party async-only index codecs. - Removed the redundant hand-rolled dict caches inside the chunk transform builders; the instance-local lru_cache wrappers are the single memoization mechanism. _shard_index_size is now lru_cached too. - The encoded-index-size guard lives once, in _assemble_shard, instead of duplicated in the sync and async encoders. - _get_inner_pipeline cache key includes codec_pipeline.batch_size, which from_codecs captures at construction. - Coordinate arrays built via np.indices instead of np.array(list(np.ndindex(...))) in the partial-write loaders. - _merge_chunk_array docstring states the view-aliasing contract; the guard comment sits on the check it annotates. - The socketpair unraisable filter covers family=(1|2) (Windows emulates socketpair with AF_INET), and its comment owns the tradeoff that the patterns cannot scope to pytest-asyncio. Test hardening: - Pool tests assert the pool branch actually fires (_resolve_max_workers + a _get_pool spy) instead of silently degrading to the sequential branch on a config regression; the concurrent-read test re-opens the array each round so readers race a cold spec cache. - New direct test pins the SyncByteSetter write gate in FusedCodecPipeline.write (verified to fail with the gate removed). - New test pins the merge fast path's view-aliasing + source-unmutated contract end-to-end on both pipelines. - read_missing_chunks=False sharded test asserts both halves of the asymmetry against the same partially-written array. - v2 scenario with a numcodecs Delta filter covers the V2Codec filter branch; _chunk_keys recognizes v2 metadata keys. Assisted-by: ClaudeCode:claude-fable-5 * doc: add changelog entries for PR #3885 Rename the fused-default placeholder to the PR-numbered 3885.feature.md and add a second feature entry for the new SyncByteGetter/SyncByteSetter protocols and Store.get_ranges_sync. Assisted-by: ClaudeCode:claude-opus-4.8 * test: cover async fallback paths orphaned by the Fused default Making FusedCodecPipeline the default left the async (Batched) mirror paths and the new sync-IO error paths exercised only narrowly, dropping project coverage. Add targeted tests for the reachable gaps: - AsyncChunkTransform.decode_chunk/encode_chunk == ChunkTransform across aa/ab/bb codec combinations (the async per-chunk chain the default sync path never runs), plus FusedCodecPipeline.encode/decode None-chunk passthrough. - ShardingCodec._decode_single/_encode_single whole-shard round-trip and all-empty branches. The codec advertises partial decode/encode, so the pipeline always picks the partial methods; these whole-shard async methods are reached only via the direct ArrayBytesCodec API. - Async-only index codec fallback in _decode_shard_index/ _encode_shard_index (#269), via a test-only async-only ArrayBytesCodec stub that is not SupportsSyncCodec. - Store.get_ranges_sync happy path, missing-key BaseExceptionGroup, and the non-sync-store TypeError. Local merged coverage on the touched files: codec_pipeline.py 85.4->92.2%, sharding.py 92.4->96.7%, abc/store.py 93.8->95.3%. Assisted-by: ClaudeCode:claude-opus-4.8 * refactor: move reused functions around chunks into standalone file * refactor: use more helpful name and remove comment * refactor: move more * refactor: move more * Ig/as completed read (#194) * perf: use `as_completed` * refactor: unfiy branches * refactor: `concurrent_iter` only handles running * add note * add note about blocking * chore: latency distribution in store * refactor: as_completed reading * perf: as_completed writes * chore: remove dead code * fix: use concurrent_map * fix: remove unnecessary list * fix: revert use of concurrent_map --------- Co-authored-by: ilan-gold <ilanbassgold@gmail.com> * fix: bulk shard decode must not serve reordering reads in natural order `ShardingCodec._decode_full_shard_bulk_if_uncompressed` gated the vectorized whole-shard fast path on `indexer.shape == shard_spec.shape`. For a `CoordinateIndexer` (vindex / integer-array oindex), `.shape` is the flattened point count, which can equal the shard shape by coincidence (trivially in 1-D). Such a selection then passed the gate and the bulk path returned the shard in natural order, silently dropping the reordering — data corruption on uncompressed, crc-free shards. Gate instead on `sel_shape`: a gather indexer exposes it, a contiguous full read (BasicIndexer, or a non-gathering OrthogonalIndexer from `arr[:]`) does not. `isinstance(indexer, BasicIndexer)` would be too strict — `arr[:]` produces an OrthogonalIndexer and must keep the fast path. Regression guard: test_reordering_read_on_uncompressed_shard_honors_selection exercises the end-to-end read path (where the gate lives), which the BasicIndexer-only bulk-decode parity test could not reach. The `arrays()` hypothesis strategy now also samples the uncompressed single-BytesCodec sharding config (via `sharding_inner_codecs`) so the fast path is covered under randomized indexing going forward. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix: make ChunkTransform spec cache torn-read-safe under threading A `ChunkTransform` is shared across thread-pool workers (read_sync / write_sync with max_workers > 1). Its `_resolve_specs` cache stored the key and the resolved specs in three separate fields, written non-atomically: a worker could observe a freshly-set key paired with the previous (or None) specs, returning the wrong codec chain for a chunk_spec — silent corruption with mixed specs, or a tripped assert. Collapse the cache into a single `(key, aa_specs, ab_spec)` tuple field replaced with one atomic attribute write. Under the GIL a reader now sees either the complete old entry or the complete new one, never a torn mix; worst case is a recompute, never a wrong result. Regression guard: test_shared_transform_decode_alternating_specs pins the single-slot eviction/refill correctness that underpins the atomicity (it fails if specs go stale on eviction). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * fix: default Codec.is_fixed_size so sharded vlen/numcodecs reads don't crash `ShardingCodec._inner_codecs_fixed_size` reads `c.is_fixed_size` on every inner codec to gate the bulk-decode fast path. `is_fixed_size` was declared on the Codec ABC as a bare annotation with no default, so codecs that never set it — VLenUTF8Codec, VLenBytesCodec, the numcodecs wrappers — raised AttributeError, crashing every sharded read whose inner chain included such a codec under the default (Fused) pipeline. Give the ABC a conservative default `is_fixed_size = False`. It stays a class attribute (not a dataclass field; fixed-size codecs still override with True), and treating an unknown codec as not-fixed-size only disables the size-dependent fast path, never correctness. Regression guard: test_sharding_vlen_inner_codec_roundtrip (Fused + Batched). Uses StringDType to force the VLenUTF8 inner chain — a fixed-width <U dtype would use BytesCodec and not reproduce. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * refactor: drop unreachable None branch in _async_write_fallback `_merge_chunk_array` always returns a real NDBuffer, so the merged-chunk list never contains None and the `if chunk_array is None` branch (with its `# type: ignore[unreachable]`) was dead. Replace the loop with a comprehension that applies only the empty-chunk normalization. mypy confirms no unused-ignore error, so the branch really was the only unreachable code there. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * feat: keep BatchedCodecPipeline as the default; FusedCodecPipeline is opt-in Move slowly on the new pipeline: revert the default back to BatchedCodecPipeline so behavior is unchanged for existing users, and let early adopters opt into FusedCodecPipeline via codec_pipeline.path. Nothing else about the Fused pipeline changes. - config: default codec_pipeline.path back to BatchedCodecPipeline. Keep the codec_pipeline.max_workers=1 entry (only read by Fused; harmless and inert under Batched) so opting in gets a sane sequential default. - test_config: update the defaults snapshot and the stale "the default" comment. - test_fastpath_equivalence: test_scalar_write_equals_broadcast_write relied on Fused being the default to exercise the scalar-broadcast memoization; set the pipeline explicitly so it still pins that path. - changelog: describe FusedCodecPipeline as opt-in, not the default. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: remove commented-out byte-range-write fast-path tests The sharding codec's byte-range-write fast path (set_range_sync) was removed from this PR pending a store-interface decision, leaving four partial-shard-write tests commented out. Per review, drop the dead block rather than carry it: it references a removed code path and would need rewriting against whatever interface eventually lands. The tests live in git history if needed when that design returns. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * apply changes from code review * refactor: drop dead sel_shape reshape in _decode_partial_sync bulk path `_decode_full_shard_bulk_if_uncompressed` returns None for any gather indexer (it gates on `sel_shape is not None`), so when the total-shard bulk path gets a non-None result the indexer cannot have `sel_shape` — making the `hasattr(indexer, "sel_shape")` reshape branch unreachable. It was a leftover from before the bulk-decode gather gate (the vindex corruption fix). Surfaced by coverage. Behavior-neutral. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: document the experimental FusedCodecPipeline Add a section to the experimental-features user guide explaining the opt-in synchronous codec pipeline: what it does (removes per-chunk async scheduling overhead), when it helps (low-latency stores like MemoryStore and LocalStore; transparent async fallback otherwise), how to opt in via codec_pipeline.path, and the codec_pipeline.max_workers threading knob. All code blocks are exec="true" so they run at docs build time. Verified with a strict mkdocs build (no broken cross-references). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Update docs/user-guide/experimental.md Co-authored-by: Ilan Gold <ilanbassgold@gmail.com> * Update docs/user-guide/experimental.md Co-authored-by: Ilan Gold <ilanbassgold@gmail.com> * Update src/zarr/codecs/sharding.py Co-authored-by: Ilan Gold <ilanbassgold@gmail.com> * Update src/zarr/codecs/sharding.py Co-authored-by: Ilan Gold <ilanbassgold@gmail.com> * Update src/zarr/codecs/sharding.py Co-authored-by: Ilan Gold <ilanbassgold@gmail.com> * fix: syntax, missing import * perf: benchmarking non-repeated values (#205) * refactor codecs * codec fixes + threading switch + benchmark reversion for defaults (#211) * refactor codecs * threading + benchmark cleanups * docs: clarify default-pipeline behavior in 3885 changelog fragments Soften the overstated 'default pipeline is unchanged' claim to note it holds for standard configurations, and add a bugfix fragment for the sharding inner-codec spec-evolution fix (#2179) that also runs on the default BatchedCodecPipeline. Assisted-by: ClaudeCode:claude-opus-4.8 * fix: test * fix: lint --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com> Co-authored-by: ilan-gold <ilanbassgold@gmail.com> --- .gitignore | 4 + changes/3885.bugfix.md | 1 + changes/3885.feature.1.md | 1 + changes/3885.feature.md | 1 + docs/user-guide/experimental.md | 87 ++ pyproject.toml | 12 + src/zarr/abc/codec.py | 10 +- src/zarr/abc/store.py | 96 ++ src/zarr/codecs/_v2.py | 26 +- src/zarr/codecs/numcodecs/_codecs.py | 50 +- src/zarr/codecs/sharding.py | 929 ++++++++++++-- src/zarr/core/array.py | 29 +- src/zarr/core/chunk_utils.py | 359 ++++++ src/zarr/core/codec_pipeline.py | 1123 ++++++++++++----- src/zarr/core/common.py | 43 +- src/zarr/core/config.py | 8 + src/zarr/storage/_fsspec.py | 10 +- src/zarr/testing/buffer.py | 24 + src/zarr/testing/store.py | 30 +- src/zarr/testing/strategies.py | 16 +- tests/benchmarks/test_e2e.py | 154 ++- tests/conftest.py | 2 +- ...ec_pipeline.py => test_chunk_transform.py} | 31 +- tests/test_codec_pipeline.py | 142 ++- tests/test_codec_pipeline_suite.py | 582 +++++++++ tests/test_codecs/test_codecs.py | 38 + tests/test_codecs/test_sharding.py | 133 +- tests/test_codecs/test_sharding_unit.py | 265 +++- tests/test_config.py | 12 +- tests/test_fastpath_equivalence.py | 382 ++++++ tests/test_fused_pipeline.py | 684 ++++++++++ tests/test_pipeline_parity.py | 420 ++++++ tests/test_store/test_get_ranges.py | 41 + tests/test_store/test_local.py | 52 + tests/test_store/test_memory.py | 53 + 35 files changed, 5378 insertions(+), 472 deletions(-) create mode 100644 changes/3885.bugfix.md create mode 100644 changes/3885.feature.1.md create mode 100644 changes/3885.feature.md create mode 100644 src/zarr/core/chunk_utils.py rename tests/{test_sync_codec_pipeline.py => test_chunk_transform.py} (82%) create mode 100644 tests/test_codec_pipeline_suite.py create mode 100644 tests/test_fastpath_equivalence.py create mode 100644 tests/test_fused_pipeline.py create mode 100644 tests/test_pipeline_parity.py diff --git a/.gitignore b/.gitignore index 3284865d6c..59b6632a3c 100644 --- a/.gitignore +++ b/.gitignore @@ -92,5 +92,9 @@ tests/.hypothesis zarr/version.py zarr.egg-info/ +# Local agent / planning notes (not versioned) +.claude/ +CLAUDE.md +docs/superpowers/ # zarr-metadata package lockfile (a library, not an app) packages/zarr-metadata/uv.lock diff --git a/changes/3885.bugfix.md b/changes/3885.bugfix.md new file mode 100644 index 0000000000..d4c1dd5c03 --- /dev/null +++ b/changes/3885.bugfix.md @@ -0,0 +1 @@ +Fixed inner-codec spec evolution for sharded arrays. The sharding codec now threads the array spec through its inner codec chain when evolving codecs, so a codec that changes the dtype upstream of `BytesCodec` no longer leaves the inner chain evolved against the wrong spec (which previously failed at decode time). This runs on the default `BatchedCodecPipeline` as well. Standard inner chains (`[BytesCodec]`, `[BytesCodec, ZstdCodec]`, transpose + bytes) are byte-identical to before. Restores the behavior of #2179. diff --git a/changes/3885.feature.1.md b/changes/3885.feature.1.md new file mode 100644 index 0000000000..0a51ba6844 --- /dev/null +++ b/changes/3885.feature.1.md @@ -0,0 +1 @@ +Added `SyncByteGetter` and `SyncByteSetter` runtime-checkable protocols and a `get_ranges_sync` method on the `Store` ABC. These let custom byte getters/setters opt into the synchronous codec pipeline's fast path for in-memory IO, which the sharding codec uses for its inner chunks. diff --git a/changes/3885.feature.md b/changes/3885.feature.md new file mode 100644 index 0000000000..13010f521e --- /dev/null +++ b/changes/3885.feature.md @@ -0,0 +1 @@ +Added `FusedCodecPipeline`, an opt-in codec pipeline that runs codec compute synchronously and in bulk (avoiding the per-chunk async scheduling overhead of the default `BatchedCodecPipeline`), giving large speedups for sharded arrays (up to ~24x writes / ~14x reads on many-chunks-per-shard layouts, more with compression) and no regressions on compute-bound workloads. The default `BatchedCodecPipeline` is unchanged for standard configurations, so existing code keeps working unless you opt in; enable the new pipeline with `zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"})`. diff --git a/docs/user-guide/experimental.md b/docs/user-guide/experimental.md index a50be394c2..a70ee923fe 100644 --- a/docs/user-guide/experimental.md +++ b/docs/user-guide/experimental.md @@ -4,6 +4,93 @@ This section contains documentation for experimental Zarr Python features. The f [experimental API policy](../contributing.md#experimental-api-policy) for the stability guarantees (or lack thereof) that apply to everything documented on this page. +## `FusedCodecPipeline` + +A *codec pipeline* is the machinery that turns chunks of array data into stored bytes and back, by running the configured codecs (filters, serializer, compressors) and performing the storage IO. +The default pipeline, `BatchedCodecPipeline`, schedules both the IO and codec work asynchronously -- roughly one coroutine per chunk operation. + +`FusedCodecPipeline` is an experimental alternative that runs codec compute and synchronous IO *synchronously*, avoiding that per-chunk async scheduling overhead and nasty [`asyncio.to_thread` overhead](https://github.com/python/cpython/issues/136084). +On real workloads the scheduling cost can dominate the actual codec work, so removing it is a significant speedup -- especially for **sharded arrays**, where a single shard read or write involves many inner chunks. + +> **Note:** The win is *not* a faster compressor or a different on-disk format -- the bytes written are +> identical. It is purely the removal of async scheduling overhead, plus a few vectorized fast paths +> for dense, uncompressed shards i.e., removing compute where it is not needed. + +### When it helps + +There are two main benefits in this new pipeline: + +1. When storage IO is fast enough that the *scheduling* overhead, not the IO itself, is the bottleneck. That means **low-latency stores** that are themselves synchronous -- in particular [`zarr.storage.MemoryStore`][] and [`zarr.storage.LocalStore`][]. + +2. Whenever codec work that is truly synchronous will not need the overhead of `async` scheduling i.e., inner-chunk codec work in sharding using something like `zstd`. We also now make use of `asyncio.as_completed` so that IO from asynchronous sources can begin decompression immediately. + +### Opting in + +`FusedCodecPipeline` is opt-in: the default pipeline is unchanged, so existing code behaves exactly as +before. Select it through the [runtime configuration](config.md), by setting `codec_pipeline.path`: + +```python exec="true" session="experimental-fused" source="above" result="ansi" +import zarr + +zarr.config.set( + {"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"} +) +``` + +You can set this globally as above (affecting every array created or opened afterwards), or scope it to +a block of code using `zarr.config.set` as a context manager: + +```python exec="true" session="experimental-fused" source="above" +import numpy as np +import zarr +from zarr.storage import MemoryStore + +with zarr.config.set( + {"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"} +): + # A sharded array on an in-memory store -- the low-latency case the + # synchronous pipeline targets. + arr = zarr.create_array( + store=MemoryStore(), + shape=(1000, 1000), + chunks=(100, 100), + shards=(1000, 1000), + dtype="float32", + ) + arr[:] = np.random.random((1000, 1000)).astype("float32") + result = arr[:] + +print(result.shape) +``` + +To return to the default pipeline, set `codec_pipeline.path` back to the batched implementation: + +```python exec="true" session="experimental-fused" source="above" +import zarr + +zarr.config.set( + {"codec_pipeline.path": "zarr.core.codec_pipeline.BatchedCodecPipeline"} +) +``` + +### Threading + +By default the synchronous pipeline runs fully threaded i.e., `os.cpu_count()`. +For memory-backed workflows, you may find that setting `max_workers` to 1 helps (since requests for data from the store are GIL-locked, unlike, say, file-backed i/o). + +```python exec="true" session="experimental-fused" source="above" +import zarr + +# Use a fixed-size thread pool for codec compute. +zarr.config.set({"codec_pipeline.max_workers": 8}) + +# Or "auto", sized to the number of CPUs. +zarr.config.set({"codec_pipeline.max_workers": None}) +``` + +On many-core nodes a pool sized to `cpu_count` can oversubscribe workloads that already parallelize at a higher level (e.g. Dask). +`codec_pipeline.max_workers` only affects `FusedCodecPipeline`; the default `BatchedCodecPipeline` ignores it. + ## `CacheStore` Zarr Python 3.1.4 adds [`zarr.experimental.cache_store.CacheStore`][], which provides a dual-store caching implementation diff --git a/pyproject.toml b/pyproject.toml index 081ddefdfb..727071b5a3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -465,6 +465,18 @@ filterwarnings = [ # collected without being entered. This is a known issue in s3fs/aiobotocore, and pytest # per-test filterwarnings markers can't catch it (https://github.com/pytest-dev/pytest/issues/14096). "ignore:Exception ignored ((on calling weakref callback)|(in[\\s\\S]*Session was never entered)):pytest.PytestUnraisableExceptionWarning", + # pytest-asyncio implicitly creates an event loop in _get_event_loop_no_warn during + # fixture setup/teardown and never closes it (allocation site verified with + # PYTHONTRACEMALLOC: pytest_asyncio/plugin.py). When the garbage collector reclaims + # that loop (and its self-pipe socketpair: AF_UNIX family=1 on POSIX, emulated with + # AF_INET family=2 on Windows) mid-test, the unraisable hook fails whichever unrelated + # test happens to be running — the long-standing "random cross-file failure" in the + # pipeline suites. The message contains only the __del__ repr, so these patterns cannot + # scope to pytest-asyncio specifically: a loop/socketpair leak in zarr's own sync + # machinery would also be silenced. Accepted tradeoff — revisit if zarr.core.sync grows + # loop-lifecycle changes. + "ignore:Exception ignored in[\\s\\S]*<function BaseEventLoop.__del__:pytest.PytestUnraisableExceptionWarning", + "ignore:Exception ignored in[\\s\\S]*<socket.socket fd=\\d+, family=(1|2), type=1:pytest.PytestUnraisableExceptionWarning", ] markers = [ "gpu: mark a test as requiring CuPy and GPU", diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index eed2119aff..61c5dc9948 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -93,7 +93,15 @@ class BaseCodec[CI: CodecInput, CO: CodecOutput](Metadata): ArrayArrayCodec, ArrayBytesCodec or BytesBytesCodec for subclassing. """ - is_fixed_size: bool + # Whether this codec's encoded output is a fixed size given a fixed input + # size. Defaults to False (the conservative answer): a codec that does not + # explicitly opt in is treated as variable-size, which only disables + # size-dependent fast paths (e.g. the sharding bulk-decode), never + # correctness. Codecs with genuinely fixed-size output (BytesCodec, + # TransposeCodec, ...) override this with True. The default also keeps + # third-party / variable-length codecs (VLenUTF8, numcodecs wrappers) that + # never set the attribute from raising AttributeError where it is read. + is_fixed_size: bool = False @abstractmethod def compute_encoded_size(self, input_byte_length: int, chunk_spec: ArraySpec) -> int: diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index 7c187594df..c60d2468c5 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -22,6 +22,8 @@ "SupportsGetSync", "SupportsSetSync", "SupportsSyncStore", + "SyncByteGetter", + "SyncByteSetter", "set_or_delete", ] @@ -469,6 +471,73 @@ async def get_ranges( ): yield group + def get_ranges_sync( + self, + key: str, + byte_ranges: Sequence[ByteRequest | None], + *, + prototype: BufferPrototype, + max_gap_bytes: int = 1 << 20, # 1 MiB + max_coalesced_bytes: int = 16 << 20, # 16 MiB + ) -> Sequence[tuple[int, Buffer | None]]: + """Synchronous, coalescing counterpart of `get_ranges`. + + Plans merged fetches with the same `coalesce_ranges` policy as the async + path, then issues one synchronous `get_sync` per merged group (or per + uncoalescable request) and slices results back into per-input buffers. + Used by the sync codec pipeline's partial-shard reads so they get the + same byte-range coalescing as the async path, without an event loop. + + Returns a list of `(input_index, Buffer | None)`. Raises + `BaseExceptionGroup` containing a `FileNotFoundError` if the key is + absent (matching `get_ranges`), so callers can handle a deleted shard + uniformly across the sync and async paths. + + Requires the store to implement `get_sync` (`SupportsGetSync`). + """ + from zarr.core._coalesce import coalesce_ranges + + if not isinstance(self, SupportsGetSync): + raise TypeError(f"{type(self).__name__} does not support synchronous reads") + + groups, uncoalescable = coalesce_ranges( + byte_ranges, max_gap_bytes=max_gap_bytes, max_coalesced_bytes=max_coalesced_bytes + ) + results: list[tuple[int, Buffer | None]] = [] + errors: list[BaseException] = [] + + def _get(req: ByteRequest | None) -> Buffer | None: + return self.get_sync(key, prototype=prototype, byte_range=req) + + for idx, req in uncoalescable: + buf = _get(req) + if buf is None: + errors.append(FileNotFoundError(key)) + else: + results.append((idx, buf)) + + for members in groups: + if len(members) == 1: + solo_idx, solo_req = members[0] + buf = _get(solo_req) + if buf is None: + errors.append(FileNotFoundError(key)) + else: + results.append((solo_idx, buf)) + continue + start = members[0][1].start + end = max(r.end for _, r in members) + big = _get(RangeByteRequest(start, end)) + if big is None: + errors.append(FileNotFoundError(key)) + continue + for member_idx, r in members: + results.append((member_idx, big[r.start - start : r.end - start])) + + if errors: + raise BaseExceptionGroup("chunk read failed", errors) + return results + async def getsize(self, key: str) -> int: """ Return the size, in bytes, of a value in a Store. @@ -564,6 +633,33 @@ async def delete(self) -> None: ... async def set_if_not_exists(self, default: Buffer) -> None: ... +@runtime_checkable +class SyncByteGetter(Protocol): + """A `ByteGetter` that can also fetch synchronously, without an event loop. + + Non-StorePath byte getters (e.g. the sharding codec's in-memory + `_ShardingByteGetter`) implement this so a synchronous codec pipeline can + take its sync fast path on them instead of scheduling one coroutine per + chunk. Note that `StorePath` also *has* a `get_sync` method (so it matches + this protocol structurally) but it only works when its store supports + synchronous IO — callers gate `StorePath` on the store's `SupportsGetSync` + instead of on this protocol. + """ + + def get_sync( + self, prototype: BufferPrototype | None = None, byte_range: ByteRequest | None = None + ) -> Buffer | None: ... + + +@runtime_checkable +class SyncByteSetter(SyncByteGetter, Protocol): + """A `ByteSetter` that can also write synchronously. See `SyncByteGetter`.""" + + def set_sync(self, value: Buffer) -> None: ... + + def delete_sync(self) -> None: ... + + @runtime_checkable class SupportsGetSync(Protocol): def get_sync( diff --git a/src/zarr/codecs/_v2.py b/src/zarr/codecs/_v2.py index 3c6c99c21c..7fdf408d1d 100644 --- a/src/zarr/codecs/_v2.py +++ b/src/zarr/codecs/_v2.py @@ -23,7 +23,7 @@ class V2Codec(ArrayBytesCodec): is_fixed_size = False - async def _decode_single( + def _decode_sync( self, chunk_bytes: Buffer, chunk_spec: ArraySpec, @@ -31,14 +31,14 @@ async def _decode_single( cdata = chunk_bytes.as_array_like() # decompress if self.compressor: - chunk = await asyncio.to_thread(self.compressor.decode, cdata) + chunk = self.compressor.decode(cdata) else: chunk = cdata # apply filters if self.filters: for f in reversed(self.filters): - chunk = await asyncio.to_thread(f.decode, chunk) + chunk = f.decode(chunk) # view as numpy array with correct dtype chunk = ensure_ndarray_like(chunk) @@ -70,7 +70,7 @@ async def _decode_single( return get_ndbuffer_class().from_ndarray_like(chunk) - async def _encode_single( + def _encode_sync( self, chunk_array: NDBuffer, chunk_spec: ArraySpec, @@ -83,18 +83,32 @@ async def _encode_single( # apply filters if self.filters: for f in self.filters: - chunk = await asyncio.to_thread(f.encode, chunk) + chunk = f.encode(chunk) # check object encoding if ensure_ndarray_like(chunk).dtype == object: raise RuntimeError("cannot write object array without object codec") # compress if self.compressor: - cdata = await asyncio.to_thread(self.compressor.encode, chunk) + cdata = self.compressor.encode(chunk) else: cdata = chunk cdata = ensure_bytes(cdata) return chunk_spec.prototype.buffer.from_bytes(cdata) + async def _decode_single( + self, + chunk_bytes: Buffer, + chunk_spec: ArraySpec, + ) -> NDBuffer: + return await asyncio.to_thread(self._decode_sync, chunk_bytes, chunk_spec) + + async def _encode_single( + self, + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + ) -> Buffer | None: + return await asyncio.to_thread(self._encode_sync, chunk_array, chunk_spec) + def compute_encoded_size(self, _input_byte_length: int, _chunk_spec: ArraySpec) -> int: raise NotImplementedError diff --git a/src/zarr/codecs/numcodecs/_codecs.py b/src/zarr/codecs/numcodecs/_codecs.py index 9c967fdbdd..f44c35964c 100644 --- a/src/zarr/codecs/numcodecs/_codecs.py +++ b/src/zarr/codecs/numcodecs/_codecs.py @@ -47,7 +47,7 @@ if TYPE_CHECKING: from zarr.abc.numcodec import Numcodec from zarr.core.array_spec import ArraySpec - from zarr.core.buffer import Buffer, BufferPrototype, NDBuffer + from zarr.core.buffer import Buffer, NDBuffer CODEC_PREFIX = "numcodecs." @@ -134,57 +134,67 @@ class _NumcodecsBytesBytesCodec(_NumcodecsCodec, BytesBytesCodec): def __init__(self, **codec_config: JSON) -> None: super().__init__(**codec_config) - async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> Buffer: - return await asyncio.to_thread( - as_numpy_array_wrapper, - self._codec.decode, - chunk_data, - chunk_spec.prototype, - ) + def _decode_sync(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> Buffer: + return as_numpy_array_wrapper(self._codec.decode, chunk_data, chunk_spec.prototype) - def _encode(self, chunk_data: Buffer, prototype: BufferPrototype) -> Buffer: + def _encode_sync(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> Buffer: encoded = self._codec.encode(chunk_data.as_array_like()) if isinstance(encoded, np.ndarray): # Required for checksum codecs - return prototype.buffer.from_bytes(encoded.tobytes()) - return prototype.buffer.from_bytes(encoded) + return chunk_spec.prototype.buffer.from_bytes(encoded.tobytes()) + return chunk_spec.prototype.buffer.from_bytes(encoded) + + async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> Buffer: + return await asyncio.to_thread(self._decode_sync, chunk_data, chunk_spec) async def _encode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> Buffer: - return await asyncio.to_thread(self._encode, chunk_data, chunk_spec.prototype) + return await asyncio.to_thread(self._encode_sync, chunk_data, chunk_spec) class _NumcodecsArrayArrayCodec(_NumcodecsCodec, ArrayArrayCodec): def __init__(self, **codec_config: JSON) -> None: super().__init__(**codec_config) - async def _decode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: + def _decode_sync(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: chunk_ndarray = chunk_data.as_ndarray_like() - out = await asyncio.to_thread(self._codec.decode, chunk_ndarray) + out = self._codec.decode(chunk_ndarray) return chunk_spec.prototype.nd_buffer.from_ndarray_like(out.reshape(chunk_spec.shape)) - async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: + def _encode_sync(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: # numcodecs codecs flatten with order="A", so an F-contiguous chunk # would be encoded in transposed element order (gh-3558) chunk_ndarray = np.ascontiguousarray(chunk_data.as_ndarray_like()) - out = await asyncio.to_thread(self._codec.encode, chunk_ndarray) + out = self._codec.encode(chunk_ndarray) return chunk_spec.prototype.nd_buffer.from_ndarray_like(out) + async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: + return await asyncio.to_thread(self._encode_sync, chunk_data, chunk_spec) + + async def _decode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer: + return await asyncio.to_thread(self._decode_sync, chunk_data, chunk_spec) + class _NumcodecsArrayBytesCodec(_NumcodecsCodec, ArrayBytesCodec): def __init__(self, **codec_config: JSON) -> None: super().__init__(**codec_config) - async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + def _decode_sync(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> NDBuffer: chunk_bytes = chunk_data.to_bytes() - out = await asyncio.to_thread(self._codec.decode, chunk_bytes) + out = self._codec.decode(chunk_bytes) return chunk_spec.prototype.nd_buffer.from_ndarray_like(out.reshape(chunk_spec.shape)) - async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> Buffer: + def _encode_sync(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> Buffer: # numcodecs codecs flatten with order="A", so an F-contiguous chunk # would be encoded in transposed element order (gh-3558) chunk_ndarray = np.ascontiguousarray(chunk_data.as_ndarray_like()) - out = await asyncio.to_thread(self._codec.encode, chunk_ndarray) + out = self._codec.encode(chunk_ndarray) return chunk_spec.prototype.buffer.from_bytes(out) + async def _encode_single(self, chunk_data: NDBuffer, chunk_spec: ArraySpec) -> Buffer: + return await asyncio.to_thread(self._encode_sync, chunk_data, chunk_spec) + + async def _decode_single(self, chunk_data: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + return await asyncio.to_thread(self._decode_sync, chunk_data, chunk_spec) + # bytes-to-bytes codecs class Blosc(_NumcodecsBytesBytesCodec, codec_name="blosc"): diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 332aab3351..2d4d63d400 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -3,7 +3,7 @@ from collections.abc import Iterable, Mapping, MutableMapping, Sequence from dataclasses import dataclass, replace from functools import lru_cache -from typing import TYPE_CHECKING, Any, ClassVar, Final, Literal, NamedTuple, cast +from typing import TYPE_CHECKING, Any, ClassVar, Final, Literal, NamedTuple import numpy as np import numpy.typing as npt @@ -14,13 +14,16 @@ ArrayBytesCodecPartialEncodeMixin, Codec, CodecPipeline, + SupportsSyncCodec, ) from zarr.abc.store import ( ByteGetter, ByteRequest, ByteSetter, RangeByteRequest, + Store, SuffixByteRequest, + SupportsGetSync, ) from zarr.codecs._deprecated_enum import _coerce_enum_input, _DeprecatedStrEnumMeta from zarr.codecs.bytes import BytesCodec @@ -34,12 +37,21 @@ numpy_buffer_prototype, ) from zarr.core.chunk_grids import ChunkGrid +from zarr.core.chunk_utils import ( + ChunkTransform, + decode_and_scatter_chunk, + encode_or_elide_chunk, + evolve_codecs, + merge_and_encode_chunk, +) from zarr.core.common import ( ShapeLike, parse_named_configuration, parse_shapelike, product, ) +from zarr.core.config import config as zarr_config +from zarr.core.dtype.common import HasEndianness from zarr.core.dtype.npy.int import UInt64 from zarr.core.indexing import ( BasicIndexer, @@ -105,13 +117,21 @@ def _parse_index_location(data: object) -> IndexLocation: @dataclass(frozen=True) class _ShardingByteGetter(ByteGetter): + """In-memory byte getter for one inner chunk of a shard. + + Implements `SyncByteGetter` (dict access needs no event loop), so the + synchronous codec pipeline takes its sync fast path on inner chunks + instead of scheduling one coroutine per chunk; the async `get` simply + delegates to `get_sync`. + """ + shard_dict: ShardMapping chunk_coords: tuple[int, ...] - async def get( - self, prototype: BufferPrototype, byte_range: ByteRequest | None = None + def get_sync( + self, prototype: BufferPrototype | None = None, byte_range: ByteRequest | None = None ) -> Buffer | None: - assert prototype == default_buffer_prototype(), ( + assert prototype is None or prototype == default_buffer_prototype(), ( f"prototype is not supported within shards currently. diff: {prototype} != {default_buffer_prototype()}" ) value = self.shard_dict.get(self.chunk_coords) @@ -122,17 +142,33 @@ async def get( start, stop = _normalize_byte_range_index(value, byte_range) return value[start:stop] + async def get( + self, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Buffer | None: + return self.get_sync(prototype, byte_range) + @dataclass(frozen=True) class _ShardingByteSetter(_ShardingByteGetter, ByteSetter): + """In-memory byte setter for one inner chunk of a shard. + + Implements `SyncByteSetter`; the async methods delegate to the sync ones. + """ + shard_dict: ShardMutableMapping + def set_sync(self, value: Buffer) -> None: + self.shard_dict[self.chunk_coords] = value + + def delete_sync(self) -> None: + del self.shard_dict[self.chunk_coords] + async def set(self, value: Buffer, byte_range: ByteRequest | None = None) -> None: assert byte_range is None, "byte_range is not supported within shards" - self.shard_dict[self.chunk_coords] = value + self.set_sync(value) async def delete(self) -> None: - del self.shard_dict[self.chunk_coords] + self.delete_sync() async def set_if_not_exists(self, default: Buffer) -> None: self.shard_dict.setdefault(self.chunk_coords, default) @@ -156,6 +192,24 @@ def is_all_empty(self) -> bool: def get_full_chunk_map(self) -> npt.NDArray[np.bool_]: return np.not_equal(self.offsets_and_lengths[..., 0], MAX_UINT_64) + def is_dense(self, chunk_byte_length: int) -> bool: + """True when every chunk is present, fixed-length, and uniquely placed. + + Used to gate the vectorized whole-shard decode: a dense fixed-size shard + is a regular grid of equal-length payloads, so it can be reshaped/scattered + in bulk rather than decoded chunk-by-chunk. + """ + offsets = self.offsets_and_lengths[..., 0].reshape(-1) + lengths = self.offsets_and_lengths[..., 1].reshape(-1) + # all present + if bool(np.any(offsets == MAX_UINT_64)): + return False + # all the same fixed length + if not bool(np.all(lengths == chunk_byte_length)): + return False + # offsets unique (no two chunks share a slot) + return int(np.unique(offsets).size) == int(offsets.size) + def get_chunk_slice(self, chunk_coords: tuple[int, ...]) -> tuple[int, int] | None: localized_chunk = self._localize_chunk(chunk_coords) chunk_start, chunk_len = self.offsets_and_lengths[localized_chunk] @@ -321,6 +375,8 @@ class ShardingCodec( does not recover it (the setting reverts to the `morton` default per codec instance). """ + is_fixed_size = False + chunk_shape: tuple[int, ...] codecs: tuple[Codec, ...] index_codecs: tuple[Codec, ...] @@ -362,6 +418,13 @@ def __init__( # object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) object.__setattr__(self, "_get_index_chunk_spec", lru_cache()(self._get_index_chunk_spec)) object.__setattr__(self, "_get_chunks_per_shard", lru_cache()(self._get_chunks_per_shard)) + object.__setattr__(self, "_shard_index_size", lru_cache()(self._shard_index_size)) + object.__setattr__( + self, "_get_inner_chunk_transform", lru_cache()(self._get_inner_chunk_transform) + ) + object.__setattr__( + self, "_get_index_chunk_transform", lru_cache()(self._get_index_chunk_transform) + ) # todo: typedict return type def __getstate__(self) -> dict[str, Any]: @@ -381,6 +444,13 @@ def __setstate__(self, state: dict[str, Any]) -> None: # object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) object.__setattr__(self, "_get_index_chunk_spec", lru_cache()(self._get_index_chunk_spec)) object.__setattr__(self, "_get_chunks_per_shard", lru_cache()(self._get_chunks_per_shard)) + object.__setattr__(self, "_shard_index_size", lru_cache()(self._shard_index_size)) + object.__setattr__( + self, "_get_inner_chunk_transform", lru_cache()(self._get_inner_chunk_transform) + ) + object.__setattr__( + self, "_get_index_chunk_transform", lru_cache()(self._get_index_chunk_transform) + ) @classmethod def from_dict(cls, data: dict[str, JSON]) -> Self: @@ -391,6 +461,41 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: def codec_pipeline(self) -> CodecPipeline: return get_pipeline_class().from_codecs(self.codecs) + def _get_inner_pipeline(self, shard_spec: ArraySpec) -> CodecPipeline: + """The nested pipeline for inner-chunk IO, evolved against the inner + chunk spec. + + Evolving matters for two reasons: it threads the spec through the inner + codec chain (spec-changing codecs see the spec they will actually + operate on), and — for a synchronous pipeline — it builds the sync + transform, so inner-chunk IO over the (sync-capable) sharding byte + getters takes the pipeline's sync fast path instead of scheduling one + coroutine per inner chunk. The bare `codec_pipeline` property returns an + unevolved pipeline, which a synchronous pipeline can only run through + its async fallback. + + Memoized per (pipeline class, batch size, shard_spec): evolving builds + a ChunkTransform, which is wasteful to redo on every shard operation. + The pipeline class and batch size participate in the key so the + `codec_pipeline.path` and `codec_pipeline.batch_size` configs are still + honored after the first use (`from_codecs` captures batch_size at + construction). A benign construction race between threads is possible + (last writer wins) — same as the other caches here. + """ + cache: dict[tuple[type[CodecPipeline], int, ArraySpec], CodecPipeline] | None = getattr( + self, "_inner_pipeline_cache", None + ) + if cache is None: + cache = {} + object.__setattr__(self, "_inner_pipeline_cache", cache) + key = (get_pipeline_class(), zarr_config.get("codec_pipeline.batch_size"), shard_spec) + pipeline = cache.get(key) + if pipeline is None: + chunk_spec = self._get_chunk_spec(shard_spec) + pipeline = self.codec_pipeline.evolve_from_array_spec(chunk_spec) + cache[key] = pipeline + return pipeline + def to_dict(self) -> dict[str, JSON]: return { "name": "sharding_indexed", @@ -403,8 +508,27 @@ def to_dict(self) -> dict[str, JSON]: } def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: + """Thread the spec through the inner chain. + + Each codec is evolved against the spec produced by the previous one. + Evolving every codec against the same unthreaded spec is the bug shape that + strips `BytesCodec.endian` behind a dtype-changing codec — and this + method runs on the real array-creation path, baking the damaged chain + into the evolved instance before the transform builders ever run. + + Parameters + ---------- + array_spec + The base spec to be evolved as we thread it. + + Returns + ------- + This codec with the evolved code chain. + """ + from zarr.core.chunk_utils import evolve_codecs + shard_spec = self._get_chunk_spec(array_spec) - evolved_codecs = tuple(c.evolve_from_array_spec(array_spec=shard_spec) for c in self.codecs) + evolved_codecs = evolve_codecs(self.codecs, shard_spec) if evolved_codecs != self.codecs: return replace(self, codecs=evolved_codecs) return self @@ -439,6 +563,383 @@ def validate( f"divisible by the shard's inner chunk size {inner}." ) + def _get_inner_chunk_transform(self, shard_spec: ArraySpec) -> Any: + """The synchronous transform for the inner codec chain. + + Memoized by the instance-local `lru_cache` wrapping installed in + `__init__`/`__setstate__` (the single cache mechanism for these + builders — do not add another layer inside the body). + + Codecs are evolved with the spec THREADED forward (`evolve_codecs`): + each inner codec is evolved against the spec produced by the previous + one, not the original chunk spec. Evolving every codec against the same + unthreaded spec is the bug shape that stripped `BytesCodec.endian` at + the pipeline level (see `evolve_codecs`) — the inner chain must use the + same single source of truth. + """ + + chunk_spec = self._get_chunk_spec(shard_spec) + return ChunkTransform(codecs=evolve_codecs(self.codecs, chunk_spec)) + + def _get_index_chunk_transform(self, chunks_per_shard: tuple[int, ...]) -> Any: + """The synchronous transform for the index codec chain. + + Memoized via instance-local `lru_cache`. + """ + + index_spec = self._get_index_chunk_spec(chunks_per_shard) + return ChunkTransform(codecs=evolve_codecs(self.index_codecs, index_spec)) + + def _decode_shard_index_sync( + self, index_bytes: Buffer, chunks_per_shard: tuple[int, ...] + ) -> _ShardIndex: + """Decode shard index synchronously using ChunkTransform.""" + index_transform = self._get_index_chunk_transform(chunks_per_shard) + index_spec = self._get_index_chunk_spec(chunks_per_shard) + index_array = index_transform.decode_chunk(index_bytes, index_spec) + return _ShardIndex(chunks_per_shard, index_array.as_numpy_array()) + + def _encode_shard_index_sync(self, index: _ShardIndex) -> Buffer: + """Encode shard index synchronously using ChunkTransform.""" + index_transform = self._get_index_chunk_transform(index.chunks_per_shard) + index_spec = self._get_index_chunk_spec(index.chunks_per_shard) + index_nd = get_ndbuffer_class().from_numpy_array(index.offsets_and_lengths) + result: Buffer | None = index_transform.encode_chunk(index_nd, index_spec) + assert result is not None + return result + + def _shard_reader_from_bytes_sync( + self, buf: Buffer, chunks_per_shard: tuple[int, ...] + ) -> _ShardReader: + """Sync version of _ShardReader.from_bytes.""" + shard_index_size = self._shard_index_size(chunks_per_shard) + if self.index_location == "start": + shard_index_bytes = buf[:shard_index_size] + else: + shard_index_bytes = buf[-shard_index_size:] + index = self._decode_shard_index_sync(shard_index_bytes, chunks_per_shard) + reader = _ShardReader() + reader.buf = buf + reader.index = index + return reader + + def _decode_sync( + self, + shard_bytes: Buffer, + shard_spec: ArraySpec, + ) -> NDBuffer: + """Decode a full shard synchronously. + + Sync counterpart to `_decode_single`. Same semantics (decode every + inner chunk and assemble the full shard array) but routes through + `ChunkTransform` instead of the async codec pipeline, so it can + run on the sync codec-pipeline fast path without an event loop. + + For a partial read where the caller only needs a slice of the shard, + use `_decode_partial_sync` instead — it fetches only the byte + ranges that overlap the selection. + + This method does not parallelize decompression, but should. + See TODO: make issue for handling subchunk parallelism + """ + shard_shape = shard_spec.shape + chunk_shape = self.chunk_shape + chunks_per_shard = self._get_chunks_per_shard(shard_spec) + chunk_spec = self._get_chunk_spec(shard_spec) + inner_transform = self._get_inner_chunk_transform(shard_spec) + + indexer = BasicIndexer( + tuple(slice(0, s) for s in shard_shape), + shape=shard_shape, + chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), + ) + + out = chunk_spec.prototype.nd_buffer.empty( + shape=shard_shape, + dtype=shard_spec.dtype.to_native_dtype(), + order=shard_spec.order, + ) + + shard_dict = self._shard_reader_from_bytes_sync(shard_bytes, chunks_per_shard) + + if shard_dict.index.is_all_empty(): + out.fill(shard_spec.fill_value) + return out + + for chunk_coords, chunk_selection, out_selection, _ in indexer: + # the GetResult status is discarded: missing INNER chunks of a + # present shard always fill (read_missing_chunks is a store-key + # level promise, applied to top-level statuses at the array layer) + decode_and_scatter_chunk( + shard_dict.get(chunk_coords), + out, + chunk_spec=chunk_spec, + chunk_selection=chunk_selection, + out_selection=out_selection, + drop_axes=(), + decode=inner_transform.decode_chunk, + ) + + return out + + def _encode_sync( + self, + shard_array: NDBuffer, + shard_spec: ArraySpec, + ) -> Buffer | None: + """Encode a full shard synchronously. + + Sync counterpart to `_encode_single`. This is reached when a + `ShardingCodec` is an *inner* codec of another sharding codec (nested + sharding): the outer codec encodes each inner chunk through its + `ChunkTransform`, which calls this method on the inner `ShardingCodec`. + + Each inner chunk is encoded through the inner `ChunkTransform` and + collected into an intermediate `dict`. The dict's key order is + immaterial — the physical on-disk layout is decided downstream by the + `subchunk_write_order` loop in `_encode_shard_dict_sync` (this method + does NOT impose a layout). Empty inner chunks become `None` entries when + `write_empty_chunks` is False, signalling `_encode_shard_dict_sync` to + elide them from the data section and mark them empty in the shard index. + + Returns `None` if every inner chunk was elided (an all-empty shard) — + callers treat that as "delete the shard key". + + This method does not parallelize compression, but should. + See TODO: make issue for handling subchunk parallelism + + For a partial write that only touches some inner chunks, use + `_encode_partial_sync` instead. + """ + shard_shape = shard_spec.shape + chunks_per_shard = self._get_chunks_per_shard(shard_spec) + chunk_spec = self._get_chunk_spec(shard_spec) + inner_transform = self._get_inner_chunk_transform(shard_spec) + + indexer = BasicIndexer( + tuple(slice(0, s) for s in shard_shape), + shape=shard_shape, + chunk_grid=ChunkGrid.from_sizes(shard_shape, self.chunk_shape), + ) + + # Key order here is immaterial; _encode_shard_dict_sync lays the present + # chunks out in subchunk_write_order. + shard_builder: dict[tuple[int, ...], Buffer | None] = dict.fromkeys( + lexicographic_order_coords(chunks_per_shard) + ) + + for chunk_coords, _chunk_selection, out_selection, _ in indexer: + # None = chunk normalized to missing (see encode_or_elide_chunk) + shard_builder[chunk_coords] = encode_or_elide_chunk( + shard_array[out_selection], chunk_spec, inner_transform.encode_chunk + ) + + return self._encode_shard_dict_sync( + shard_builder, + chunks_per_shard=chunks_per_shard, + buffer_prototype=default_buffer_prototype(), + ) + + def _encode_partial_sync( + self, + byte_setter: Any, + value: NDBuffer, + selection: SelectorTuple, + shard_spec: ArraySpec, + ) -> None: + """Sync equivalent of `_encode_partial_single`. + + Receives the source data for the written region (not a pre-merged + shard array) and the selection within the shard, matching the + calling convention of the async partial-encode path used by + `BatchedCodecPipeline`. + + This method does not parallelize compression, but should. + See TODO: make issue for handling subchunk parallelism + + Loads the existing shard, merges the written region into the affected + inner chunks, and rewrites the whole shard. + """ + shard_shape = shard_spec.shape + chunks_per_shard = self._get_chunks_per_shard(shard_spec) + chunk_spec = self._get_chunk_spec(shard_spec) + inner_transform = self._get_inner_chunk_transform(shard_spec) + + indexer = list( + get_indexer( + selection, + shape=shard_shape, + chunk_grid=ChunkGrid.from_sizes(shard_shape, self.chunk_shape), + ) + ) + + is_complete = self._is_complete_shard_write(indexer, chunks_per_shard) + + is_scalar = len(value.shape) == 0 + + # Load existing inner-chunk bytes into a dict (same structure as + # the async path's shard_dict). + if is_complete: + shard_dict: dict[tuple[int, ...], Buffer | None] = dict.fromkeys( + lexicographic_order_coords(chunks_per_shard) + ) + else: + existing_bytes = byte_setter.get_sync(prototype=shard_spec.prototype) + if existing_bytes is not None: + shard_reader_fb = self._shard_reader_from_bytes_sync( + existing_bytes, chunks_per_shard + ) + # Build the dict with one vectorized index lookup over all chunks, + # matching the async _encode_partial_single path. A per-coordinate + # __getitem__ loop here is O(n_chunks) Python overhead that dominates + # partial writes into shards with many inner chunks. The coordinate + # array and keys are cached on the reader, so neither is rebuilt here. + shard_dict = shard_reader_fb.to_dict_vectorized() + else: + shard_dict = dict.fromkeys(lexicographic_order_coords(chunks_per_shard)) + + # Merge, encode, and store each affected inner chunk into shard_dict via + # the canonical merge_and_encode_chunk (None = normalized to missing). + # + # Scalar fast path: when the written value is a scalar broadcast, every + # *complete* inner chunk is byte-for-byte identical — same fill, same + # empty-check, same encoded bytes. Compute that outcome once and reuse it + # for all complete chunks instead of re-merging, re-checking, and + # re-encoding tens of thousands of identical chunks. Incomplete (edge) + # chunks still merge against their own existing data individually. + # `_sentinel` distinguishes "not computed yet" from a memoized `None` + # (an empty chunk). + _sentinel = object() + scalar_complete_result: Buffer | None | object = _sentinel + + for chunk_coords, chunk_sel, out_sel, is_complete_chunk in indexer: + if is_scalar and is_complete_chunk: + if scalar_complete_result is _sentinel: + scalar_complete_result = merge_and_encode_chunk( + None, + value, + chunk_spec=chunk_spec, + chunk_selection=chunk_sel, + out_selection=out_sel, + is_complete=is_complete_chunk, + drop_axes=(), + decode=inner_transform.decode_chunk, + encode=inner_transform.encode_chunk, + ) + shard_dict[chunk_coords] = scalar_complete_result # type: ignore[assignment] + continue + + # A complete chunk fully overwrites: skip decoding what it replaces. + existing_raw = None if is_complete_chunk else shard_dict.get(chunk_coords) + shard_dict[chunk_coords] = merge_and_encode_chunk( + existing_raw, + value, + chunk_spec=chunk_spec, + chunk_selection=chunk_sel, + out_selection=out_sel, + is_complete=is_complete_chunk, + drop_axes=(), + decode=inner_transform.decode_chunk, + encode=inner_transform.encode_chunk, + ) + + blob = self._encode_shard_dict_sync( + shard_dict, + chunks_per_shard=chunks_per_shard, + buffer_prototype=default_buffer_prototype(), + ) + if blob is None: + byte_setter.delete_sync() + else: + byte_setter.set_sync(blob) + + def _build_shard_layout( + self, + shard_dict: ShardMapping, + chunks_per_shard: tuple[int, ...], + ) -> tuple[_ShardIndex, list[Buffer]] | None: + """Lay out the present inner chunks of a shard. Pure compute, no IO. + + Packs the encoded inner chunks (in the codec's `subchunk_write_order`) + into a contiguous data section and builds a shard index pointing each + present chunk at its ABSOLUTE byte offset within the final blob: when + the index is stored at the start, offsets are pre-shifted by the index + size (known without encoding — the index codecs are fixed-size, which + every index read path already relies on), so the index can be encoded + exactly once by the caller. + + Returns `(index, data_buffers)`, or `None` for an all-empty shard (no + chunks present). Shared by the sync and async `_encode_shard_dict*` so + the layout/offset logic cannot drift between them. + """ + index = _ShardIndex.create_empty(chunks_per_shard) + buffers: list[Buffer] = [] + chunk_start = ( + self._shard_index_size(chunks_per_shard) if self.index_location == "start" else 0 + ) + + for chunk_coords in self._subchunk_order_iter(chunks_per_shard, self.subchunk_write_order): + value = shard_dict.get(chunk_coords) + if value is None or len(value) == 0: + continue + chunk_length = len(value) + buffers.append(value) + index.set_chunk_slice(chunk_coords, slice(chunk_start, chunk_start + chunk_length)) + chunk_start += chunk_length + + if len(buffers) == 0: + return None + return index, buffers + + def _assemble_shard( + self, + index_bytes: Buffer, + buffers: list[Buffer], + buffer_prototype: BufferPrototype, + *, + chunks_per_shard: tuple[int, ...], + ) -> Buffer: + """Concatenate the encoded index and data buffers into the shard blob. + + The layout from `_build_shard_layout` already assumes the index size, so + the encoded index length must match `_shard_index_size` exactly — guard + that assumption rather than silently corrupt offsets. The guard lives + here, once, for both the sync and async encode paths. + """ + if len(index_bytes) != self._shard_index_size(chunks_per_shard): + raise RuntimeError( + "encoded shard index size does not match _shard_index_size; " + "variable-size index codecs are not supported" + ) + if self.index_location == "start": + buffers.insert(0, index_bytes) + else: + buffers.append(index_bytes) + template = buffer_prototype.buffer.create_zero_length() + return template.combine(buffers) + + def _encode_shard_dict_sync( + self, + shard_dict: ShardMapping, + chunks_per_shard: tuple[int, ...], + buffer_prototype: BufferPrototype, + ) -> Buffer | None: + """Sync version of _encode_shard_dict. + + Layout via the shared `_build_shard_layout` (offsets already absolute), + then a single index encode and concatenation. + + Returns `None` for an all-empty shard (no chunks present). + """ + layout = self._build_shard_layout(shard_dict, chunks_per_shard) + if layout is None: + return None + index, buffers = layout + index_bytes = self._encode_shard_index_sync(index) + return self._assemble_shard( + index_bytes, buffers, buffer_prototype, chunks_per_shard=chunks_per_shard + ) + async def _decode_single( self, shard_bytes: Buffer, @@ -468,7 +969,7 @@ async def _decode_single( return out # decoding chunks and writing them into the output buffer - await self.codec_pipeline.read( + await self._get_inner_pipeline(shard_spec).read( [ ( _ShardingByteGetter(shard_dict, chunk_coords), @@ -536,7 +1037,7 @@ async def _decode_partial_single( shard_dict = shard_dict_maybe # decoding chunks and writing them into the output buffer - await self.codec_pipeline.read( + await self._get_inner_pipeline(shard_spec).read( [ ( _ShardingByteGetter(shard_dict, chunk_coords), @@ -574,6 +1075,201 @@ def _subchunk_order_iter( raise ValueError(f"Unrecognized subchunk write order: {subchunk_write_order!r}.") return subchunk_iter + def _decode_full_shard_bulk_if_uncompressed( + self, + shard_bytes: Buffer, + shard_spec: ArraySpec, + indexer: Any, + ) -> NDBuffer | None: + """Vectorized whole-shard decode for dense, fixed-size, uncompressed shards. + + Returns the assembled shard array, or None if the fast path does not + apply (so the caller falls back to the per-chunk loop). Conditions: + - inner codec chain is fixed-size (no compression / variable-length); + - the inner codec chain is exactly a single BytesCodec — decode is a + dtype/endian view with no reordering. A trailing crc32c is NOT accepted + (the bulk path can't verify per-chunk checksums, so crc shards keep the + per-chunk path's corruption detection); + - the stored index is dense (every chunk present, equal fixed length, + contiguous) so the data section is a regular grid of chunk payloads. + + Chunk positions are read from the stored index, so this is correct for + any `subchunk_write_order` (morton / lexicographic / colexicographic / + unordered). The on-disk byte order is taken from the BytesCodec's + `endian`, so big- and little-endian shards both decode correctly. + """ + # --- gate on a trivial, fixed-size inner codec chain --- + if not self._inner_codecs_fixed_size: + return None + # The inner chain must be exactly a single BytesCodec (a dtype/endian + # view, no reordering). A trailing Crc32cCodec is excluded on purpose: + # the bulk path would have to strip-and-discard the per-chunk checksum + # bytes, silently dropping the corruption detection the per-chunk path + # enforces (Crc32cCodec._decode_sync raises on mismatch). crc-protected + # shards therefore fall through to the per-chunk path. + if len(self.codecs) != 1 or not isinstance(self.codecs[0], BytesCodec): + return None + ab_codec = self.codecs[0] + + chunks_per_shard = self._get_chunks_per_shard(shard_spec) + chunk_spec = self._get_chunk_spec(shard_spec) + n_chunks = product(chunks_per_shard) + if n_chunks == 0: + return None + + # Only valid for a plain contiguous full-shard read, where each chunk + # lands at its natural grid position. The `sel_shape` check is + # load-bearing: a gather indexer (CoordinateIndexer, from vindex / an + # oindex with an integer-array selection) reorders points and exposes + # `sel_shape`, but its `.shape` is the FLATTENED point count, which can + # equal the shard shape by coincidence (trivially in 1-D). Gating on + # shape alone lets such a selection through, and the bulk path then + # returns the shard in natural order, silently dropping the reordering. + # A contiguous full read (BasicIndexer, or a non-gathering + # OrthogonalIndexer from `arr[:]`) has no `sel_shape` and is served here. + # Anything that gathers must fall through to the per-chunk path so + # chunk_selection / out_selection are honored. + if getattr(indexer, "sel_shape", None) is not None: + return None + if tuple(indexer.shape) != tuple(shard_spec.shape): + return None + chunk_byte_length = self._inner_chunk_byte_length(chunk_spec) + + shard_index_size = self._shard_index_size(chunks_per_shard) + if len(shard_bytes) != n_chunks * chunk_byte_length + shard_index_size: + return None # not a dense fixed-size shard + + # --- decode the index; require dense layout --- + if self.index_location == "start": + index_bytes = shard_bytes[:shard_index_size] + else: + index_bytes = shard_bytes[-shard_index_size:] + index = self._decode_shard_index_sync(index_bytes, chunks_per_shard) + if not index.is_dense(chunk_byte_length): + return None + + # --- bulk reconstruct --- + # The index gives each chunk's absolute byte offset within the blob; with + # a dense, crc-free, fixed-size layout the payload length is exactly the + # encoded item-bytes of one chunk. + native_dtype = shard_spec.dtype.to_native_dtype() + raw = shard_bytes.as_numpy_array().view(np.uint8) + payload = chunk_byte_length + cs = self.chunk_shape + + # On-disk byte order is carried by the BytesCodec's `endian`, NOT by the + # data type (zarr v3). Build the read-view dtype from the codec's endian + # exactly as BytesCodec._decode_sync does, so a big-endian shard read on a + # little-endian host (or vice versa) is interpreted correctly. Assigning + # into the native-dtype `out` then performs any needed byteswap. `endian` + # is now a plain Literal['little', 'big'] | None string (no longer an enum). + endian_str = ab_codec.endian + if isinstance(chunk_spec.dtype, HasEndianness): + stored_dtype = replace(chunk_spec.dtype, endianness=endian_str).to_native_dtype() # type: ignore[call-arg] + else: + stored_dtype = chunk_spec.dtype.to_native_dtype() + + offsets = index.offsets_and_lengths[..., 0].reshape(-1) # localized coords, C-order + coords_c = list(np.ndindex(chunks_per_shard)) + out = shard_spec.prototype.nd_buffer.empty( + shape=indexer.shape, dtype=native_dtype, order=shard_spec.order + ) + for flat, coord in enumerate(coords_c): + start = int(offsets[flat]) + chunk = raw[start : start + payload].view(stored_dtype).reshape(cs) + sel = tuple(slice(c * s, c * s + s) for c, s in zip(coord, cs, strict=True)) + out[sel] = chunk + return out + + def _decode_partial_sync( + self, + byte_getter: Any, + selection: SelectorTuple, + shard_spec: ArraySpec, + ) -> NDBuffer | None: + """Sync equivalent of `_decode_partial_single`. + + Reads only the inner-chunk byte ranges that overlap `selection` + (plus the shard index) and decodes them through the inner codec + chain. The store must support `get_sync` with byte ranges. + + This method does not parallelize decompression, but should. + See TODO: make issue for handling subchunk parallelism + + Two sub-paths: + - If `selection` covers the entire shard, just fetch the whole + blob — that's strictly cheaper than two round trips (index, then + data) plus the per-chunk overhead of partial fetches. + - Otherwise fetch the index alone, look up only the byte slices of + the inner chunks the selection touches, fetch those, and decode. + """ + shard_shape = shard_spec.shape + chunk_shape = self.chunk_shape + chunks_per_shard = self._get_chunks_per_shard(shard_spec) + chunk_spec = self._get_chunk_spec(shard_spec) + inner_transform = self._get_inner_chunk_transform(shard_spec) + + indexer = get_indexer( + selection, + shape=shard_shape, + chunk_grid=ChunkGrid.from_sizes(shard_shape, chunk_shape), + ) + + out = shard_spec.prototype.nd_buffer.empty( + shape=indexer.shape, + dtype=shard_spec.dtype.to_native_dtype(), + order=shard_spec.order, + ) + + indexed_chunks = list(indexer) + all_chunk_coords = {chunk_coords for chunk_coords, *_ in indexed_chunks} + + # Read just the inner chunks we need. + if self._is_total_shard(all_chunk_coords, chunks_per_shard): + shard_bytes = byte_getter.get_sync(prototype=chunk_spec.prototype) + if shard_bytes is None: + return None + bulk = self._decode_full_shard_bulk_if_uncompressed(shard_bytes, shard_spec, indexer) + if bulk is not None: + # The bulk path only fires for a contiguous full-shard read (it + # returns None for any gather indexer that exposes `sel_shape`), + # so the result is already shard-shaped — no reshape needed. + return bulk + shard_reader = self._shard_reader_from_bytes_sync(shard_bytes, chunks_per_shard) + shard_dict: ShardMapping = shard_reader + else: + # Partial read: fetch only the touched inner chunks, coalescing + # adjacent byte ranges (mirrors the async _load_partial_shard_maybe + # / #3004). Returns None if the shard is absent. + partial = self._load_partial_shard_maybe_sync( + byte_getter, + chunk_spec.prototype, + chunks_per_shard, + all_chunk_coords, + max_gap_bytes=shard_spec.config.sharding_coalesce_max_gap_bytes, + max_coalesced_bytes=shard_spec.config.sharding_coalesce_max_bytes, + ) + if partial is None: + return None + shard_dict = partial + + # Decode each needed inner chunk and scatter into out (statuses + # discarded: missing inner chunks fill, see _decode_sync). + for chunk_coords, chunk_selection, out_selection, _ in indexed_chunks: + decode_and_scatter_chunk( + shard_dict.get(chunk_coords), + out, + chunk_spec=chunk_spec, + chunk_selection=chunk_selection, + out_selection=out_selection, + drop_axes=(), + decode=inner_transform.decode_chunk, + ) + + if hasattr(indexer, "sel_shape"): + return out.reshape(indexer.sel_shape) + return out + async def _encode_single( self, shard_array: NDBuffer, @@ -593,7 +1289,7 @@ async def _encode_single( ) shard_builder = dict.fromkeys(lexicographic_order_coords(chunks_per_shard)) - await self.codec_pipeline.write( + await self._get_inner_pipeline(shard_spec).write( [ ( _ShardingByteSetter(shard_builder, chunk_coords), @@ -647,7 +1343,7 @@ async def _encode_partial_single( # every write. shard_dict = shard_reader.to_dict_vectorized() - await self.codec_pipeline.write( + await self._get_inner_pipeline(shard_spec).write( [ ( _ShardingByteSetter(shard_dict, chunk_coords), @@ -677,40 +1373,17 @@ async def _encode_shard_dict( chunks_per_shard: tuple[int, ...], buffer_prototype: BufferPrototype, ) -> Buffer | None: - index = _ShardIndex.create_empty(chunks_per_shard) - - buffers = [] - - template = buffer_prototype.buffer.create_zero_length() - chunk_start = 0 - for chunk_coords in self._subchunk_order_iter(chunks_per_shard, self.subchunk_write_order): - value = map.get(chunk_coords) - if value is None: - continue - - if len(value) == 0: - continue - - chunk_length = len(value) - buffers.append(value) - index.set_chunk_slice(chunk_coords, slice(chunk_start, chunk_start + chunk_length)) - chunk_start += chunk_length - - if len(buffers) == 0: + """Layout via the shared `_build_shard_layout` (offsets already + absolute), then a single index encode and concatenation. Async twin of + `_encode_shard_dict_sync`.""" + layout = self._build_shard_layout(map, chunks_per_shard) + if layout is None: return None - + index, buffers = layout index_bytes = await self._encode_shard_index(index) - if self.index_location == "start": - empty_chunks_mask = index.offsets_and_lengths[..., 0] == MAX_UINT_64 - index.offsets_and_lengths[~empty_chunks_mask, 0] += len(index_bytes) - index_bytes = await self._encode_shard_index( - index - ) # encode again with corrected offsets - buffers.insert(0, index_bytes) - else: - buffers.append(index_bytes) - - return template.combine(buffers) + return self._assemble_shard( + index_bytes, buffers, buffer_prototype, chunks_per_shard=chunks_per_shard + ) def _is_total_shard( self, all_chunk_coords: set[tuple[int, ...]], chunks_per_shard: tuple[int, ...] @@ -733,23 +1406,35 @@ def _is_complete_shard_write( is_complete_chunk for *_, is_complete_chunk in indexed_chunks ) + def _index_codecs_sync_capable(self) -> bool: + return all(isinstance(c, SupportsSyncCodec) for c in self.index_codecs) + async def _decode_shard_index( self, index_bytes: Buffer, chunks_per_shard: tuple[int, ...] ) -> _ShardIndex: + # Pure compute (the bytes are already in hand): delegate to the sync + # implementation instead of spinning up a pipeline + per-call + # AsyncChunkTransform for a tiny fixed-size decode. The default + # (bytes + crc32c) index chain is sync-capable; an async-only + # third-party index codec falls back to the full async pipeline, which + # the synchronous read paths cannot use but this async path still can. + if self._index_codecs_sync_capable(): + return self._decode_shard_index_sync(index_bytes, chunks_per_shard) index_array = next( iter( await get_pipeline_class() .from_codecs(self.index_codecs) - .decode( - [(index_bytes, self._get_index_chunk_spec(chunks_per_shard))], - ) + .decode([(index_bytes, self._get_index_chunk_spec(chunks_per_shard))]) ) ) - # This cannot be None because we have the bytes already - index_array = cast(NDBuffer, index_array) + assert index_array is not None # the bytes are already in hand return _ShardIndex(chunks_per_shard, index_array.as_numpy_array()) async def _encode_shard_index(self, index: _ShardIndex) -> Buffer: + # Pure compute: delegate to the sync implementation, with the same + # async-pipeline fallback as _decode_shard_index. + if self._index_codecs_sync_capable(): + return self._encode_shard_index_sync(index) index_bytes = next( iter( await get_pipeline_class() @@ -760,12 +1445,11 @@ async def _encode_shard_index(self, index: _ShardIndex) -> Buffer: get_ndbuffer_class().from_numpy_array(index.offsets_and_lengths), self._get_index_chunk_spec(index.chunks_per_shard), ) - ], + ] ) ) ) assert index_bytes is not None - assert isinstance(index_bytes, Buffer) return index_bytes def _shard_index_size(self, chunks_per_shard: tuple[int, ...]) -> int: @@ -807,30 +1491,48 @@ def _get_chunks_per_shard(self, shard_spec: ArraySpec) -> tuple[int, ...]: ) ) + def _shard_index_byte_range( + self, chunks_per_shard: tuple[int, ...] + ) -> RangeByteRequest | SuffixByteRequest: + """Byte range of the shard index within the shard blob. + + Single source of truth for the index-location arithmetic, shared by the + sync and async index loaders so they cannot drift. + """ + shard_index_size = self._shard_index_size(chunks_per_shard) + if self.index_location == "start": + return RangeByteRequest(0, shard_index_size) + return SuffixByteRequest(shard_index_size) + + @staticmethod + def _pair_chunks_with_byte_ranges( + shard_index: _ShardIndex, all_chunk_coords: set[tuple[int, ...]] + ) -> list[tuple[tuple[int, ...], RangeByteRequest]]: + """Pair each requested chunk coord with its byte range in the shard. + + Coords whose chunk is absent from the index are omitted. Shared by the + sync and async partial-shard loaders. + """ + chunk_coord_byte_ranges: list[tuple[tuple[int, ...], RangeByteRequest]] = [] + for chunk_coord in all_chunk_coords: + chunk_byte_slice = shard_index.get_chunk_slice(chunk_coord) + if chunk_byte_slice is not None: + chunk_coord_byte_ranges.append( + (chunk_coord, RangeByteRequest(chunk_byte_slice[0], chunk_byte_slice[1])) + ) + return chunk_coord_byte_ranges + async def _load_shard_index_maybe( self, byte_getter: ByteGetter, chunks_per_shard: tuple[int, ...] ) -> _ShardIndex | None: - shard_index_size = self._shard_index_size(chunks_per_shard) - if self.index_location == "start": - index_bytes = await byte_getter.get( - prototype=numpy_buffer_prototype(), - byte_range=RangeByteRequest(0, shard_index_size), - ) - else: - index_bytes = await byte_getter.get( - prototype=numpy_buffer_prototype(), byte_range=SuffixByteRequest(shard_index_size) - ) + index_bytes = await byte_getter.get( + prototype=numpy_buffer_prototype(), + byte_range=self._shard_index_byte_range(chunks_per_shard), + ) if index_bytes is not None: return await self._decode_shard_index(index_bytes, chunks_per_shard) return None - async def _load_shard_index( - self, byte_getter: ByteGetter, chunks_per_shard: tuple[int, ...] - ) -> _ShardIndex: - return ( - await self._load_shard_index_maybe(byte_getter, chunks_per_shard) - ) or _ShardIndex.create_empty(chunks_per_shard) - async def _load_full_shard_maybe( self, byte_getter: ByteGetter, prototype: BufferPrototype, chunks_per_shard: tuple[int, ...] ) -> _ShardReader | None: @@ -842,6 +1544,19 @@ async def _load_full_shard_maybe( else None ) + @property + def _inner_codecs_fixed_size(self) -> bool: + """True when all inner codecs produce fixed-size output (no compression).""" + return all(c.is_fixed_size for c in self.codecs) + + def _inner_chunk_byte_length(self, chunk_spec: ArraySpec) -> int: + """Encoded byte length of a single inner chunk. Only valid when _inner_codecs_fixed_size.""" + raw_byte_length = 1 + for s in self.chunk_shape: + raw_byte_length *= s + raw_byte_length *= chunk_spec.dtype.item_size # type: ignore[attr-defined] + return int(self.codec_pipeline.compute_encoded_size(raw_byte_length, chunk_spec)) + async def _load_partial_shard_maybe( self, byte_getter: ByteGetter, @@ -863,14 +1578,7 @@ async def _load_partial_shard_maybe( if shard_index is None: return None - # Pair up chunks and their byte ranges as list[tuple[chunk_coord, byte_range]] - chunk_coord_byte_ranges: list[tuple[tuple[int, ...], RangeByteRequest]] = [] - for chunk_coord in all_chunk_coords: - chunk_byte_slice = shard_index.get_chunk_slice(chunk_coord) - if chunk_byte_slice is not None: - chunk_coord_byte_ranges.append( - (chunk_coord, RangeByteRequest(chunk_byte_slice[0], chunk_byte_slice[1])) - ) + chunk_coord_byte_ranges = self._pair_chunks_with_byte_ranges(shard_index, all_chunk_coords) if not chunk_coord_byte_ranges: return {} @@ -912,6 +1620,77 @@ async def _load_partial_shard_maybe( return shard_dict + def _load_shard_index_maybe_sync( + self, byte_getter: Any, chunks_per_shard: tuple[int, ...] + ) -> _ShardIndex | None: + """Sync counterpart of `_load_shard_index_maybe`.""" + index_bytes = byte_getter.get_sync( + prototype=numpy_buffer_prototype(), + byte_range=self._shard_index_byte_range(chunks_per_shard), + ) + if index_bytes is not None: + return self._decode_shard_index_sync(index_bytes, chunks_per_shard) + return None + + def _load_partial_shard_maybe_sync( + self, + byte_getter: Any, + prototype: BufferPrototype, + chunks_per_shard: tuple[int, ...], + all_chunk_coords: set[tuple[int, ...]], + *, + max_gap_bytes: int, + max_coalesced_bytes: int, + ) -> ShardMapping | None: + """Sync counterpart of `_load_partial_shard_maybe` (the #3004 read path). + + Reads the shard index, then fetches only the touched inner chunks via the + store's coalescing `get_ranges_sync` (merging adjacent ranges into fewer + reads), matching the async path's IO shape without an event loop. + `max_gap_bytes` and `max_coalesced_bytes` control the coalescing, forwarded + from the array's `sharding_coalesce_*` config exactly as the async path. + """ + shard_index = self._load_shard_index_maybe_sync(byte_getter, chunks_per_shard) + if shard_index is None: + return None + + chunk_coord_byte_ranges = self._pair_chunks_with_byte_ranges(shard_index, all_chunk_coords) + + if not chunk_coord_byte_ranges: + return {} + + shard_dict: ShardMutableMapping = {} + store = byte_getter.store if hasattr(byte_getter, "store") else None + if isinstance(store, Store) and isinstance(store, SupportsGetSync): + # External store: coalesce via get_ranges_sync (mirrors get_ranges). + byte_ranges = [byte_range for _, byte_range in chunk_coord_byte_ranges] + try: + for idx, buf in store.get_ranges_sync( + byte_getter.path, + byte_ranges, + prototype=prototype, + max_gap_bytes=max_gap_bytes, + max_coalesced_bytes=max_coalesced_bytes, + ): + if buf is not None: + chunk_coord, _ = chunk_coord_byte_ranges[idx] + shard_dict[chunk_coord] = buf + except BaseExceptionGroup as eg: + # Mirror the async path: a FileNotFoundError means the shard was + # deleted mid-read -> treat as "gone" (None). Re-raise anything else. + _, rest = eg.split(FileNotFoundError) + if rest is not None: + raise rest from None + return None + else: + # Nested sharding: an in-memory _ShardingByteGetter, no IO to coalesce. + for chunk_coord, byte_range in chunk_coord_byte_ranges: + buf = byte_getter.get_sync(prototype=prototype, byte_range=byte_range) + if buf is not None: + shard_dict[chunk_coord] = buf + + return shard_dict + def compute_encoded_size(self, input_byte_length: int, shard_spec: ArraySpec) -> int: chunks_per_shard = self._get_chunks_per_shard(shard_spec) return input_byte_length + self._shard_index_size(chunks_per_shard) diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index ea7d125b10..2bf761bd3d 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -228,10 +228,35 @@ def create_codec_pipeline(metadata: ArrayMetadata, *, store: Store | None = None pass if isinstance(metadata, ArrayV3Metadata): - return get_pipeline_class().from_codecs(metadata.codecs) + pipeline = get_pipeline_class().from_codecs(metadata.codecs) + from zarr.core.metadata.v3 import RegularChunkGridMetadata + + # Use the regular chunk shape if available, otherwise use a + # placeholder. The ChunkTransform is shape-agnostic — the actual + # chunk shape is passed per-call at decode/encode time. + if isinstance(metadata.chunk_grid, RegularChunkGridMetadata): + chunk_shape = metadata.chunk_grid.chunk_shape + else: + chunk_shape = (1,) * len(metadata.shape) + chunk_spec = ArraySpec( + shape=chunk_shape, + dtype=metadata.data_type, + fill_value=metadata.fill_value, + config=ArrayConfig.from_dict({}), + prototype=default_buffer_prototype(), + ) + return pipeline.evolve_from_array_spec(chunk_spec) elif isinstance(metadata, ArrayV2Metadata): v2_codec = V2Codec(filters=metadata.filters, compressor=metadata.compressor) - return get_pipeline_class().from_codecs([v2_codec]) + pipeline = get_pipeline_class().from_codecs([v2_codec]) + chunk_spec = ArraySpec( + shape=metadata.chunks, + dtype=metadata.dtype, + fill_value=metadata.fill_value, + config=ArrayConfig.from_dict({"order": metadata.order}), + prototype=default_buffer_prototype(), + ) + return pipeline.evolve_from_array_spec(chunk_spec) raise TypeError # pragma: no cover diff --git a/src/zarr/core/chunk_utils.py b/src/zarr/core/chunk_utils.py new file mode 100644 index 0000000000..ee42e60cce --- /dev/null +++ b/src/zarr/core/chunk_utils.py @@ -0,0 +1,359 @@ +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, Any, cast + +from zarr.abc.codec import GetResult, SupportsSyncCodec +from zarr.core.indexing import is_scalar + +if TYPE_CHECKING: + from collections.abc import Callable, Iterable + + from zarr.abc.codec import Codec + from zarr.core.array_spec import ArraySpec + from zarr.core.buffer import Buffer, NDBuffer + from zarr.core.indexing import SelectorTuple + + +def evolve_codecs(codecs: Iterable[Codec], array_spec: ArraySpec) -> tuple[Codec, ...]: + """Evolve a codec chain against ``array_spec``, threading the spec forward. + + Each codec is evolved against the spec produced by the previous one — NOT + the original ``array_spec`` — because earlier array->array codecs may + transform the chunk spec (e.g. ``cast_value`` widening int8 -> int16). A + later codec (notably the array->bytes serializer) must be evolved against + the spec it will actually see at run time; evolving every codec against the + unthreaded original spec would, for example, strip a ``BytesCodec``'s + ``endian`` (it sees the single-byte source dtype) and then fail at decode + time on the multi-byte target. + + This is the single source of truth for pipeline-construction-time codec + evolution, shared by every ``CodecPipeline.evolve_from_array_spec``. (The + per-chunk decode/encode counterpart is ``resolve_aa_specs``.) + """ + evolved: list[Codec] = [] + spec = array_spec + for codec in codecs: + evolved_codec = codec.evolve_from_array_spec(array_spec=spec) + evolved.append(evolved_codec) + spec = evolved_codec.resolve_metadata(spec) + return tuple(evolved) + + +def encode_or_elide_chunk( + chunk_array: NDBuffer, + chunk_spec: ArraySpec, + encode: Callable[[NDBuffer, ArraySpec], Buffer | None], +) -> Buffer | None: + """Encode a merged chunk, normalizing empties to missing. + + Returns the bytes to store, or ``None`` meaning the chunk must NOT be + stored (either it normalized to empty per `chunk_is_empty`, or the codec + chain elided it). ``None`` is the single "missing" convention shared by + the chunk write paths and the shard dicts. + """ + + if chunk_is_empty(chunk_array, chunk_spec): + return None + return encode(chunk_array, chunk_spec) + + +def fill_value_or_default(chunk_spec: ArraySpec) -> Any: + fill_value = chunk_spec.fill_value + if fill_value is None: + # Zarr V2 allowed `fill_value` to be null in the metadata. + # Zarr V3 requires it to be set. This has already been + # validated when decoding the metadata, but we support reading + # Zarr V2 data and need to support the case where fill_value + # is None. + return chunk_spec.dtype.default_scalar() + else: + return fill_value + + +def chunk_is_empty(chunk_array: NDBuffer, chunk_spec: ArraySpec) -> bool: + """THE empty-chunk normalization rule, in one place. + + With ``write_empty_chunks=False`` (the default), a chunk whose decoded + content equals the fill value normalizes to *missing*: it must not be + stored, and readers reconstruct it from the fill value. Every write path + (fused, async fallback, shard inner chunks) must apply this same rule — + scattering inline ``all_equal`` checks is how the rule drifts. + """ + return not chunk_spec.config.write_empty_chunks and chunk_array.all_equal( + fill_value_or_default(chunk_spec) + ) + + +def scatter_chunk( + selected: NDBuffer | None, + out: NDBuffer, + *, + chunk_spec: ArraySpec, + out_selection: SelectorTuple, + drop_axes: tuple[int, ...], +) -> GetResult: + """Scatter one chunk's (already-selected) decoded region into ``out``. + + ``None`` = the chunk is missing: the fill value is scattered instead and a + ``missing`` status is returned. POLICY-FREE by design: whether a missing + chunk is an error (``read_missing_chunks=False``) is decided by the array + layer from the returned statuses — which is also what makes missing INNER + chunks of a present shard fill rather than raise (the sharding codec + discards the nested read's statuses; only top-level statuses reach the + array layer). + """ + if selected is None: + out[out_selection] = fill_value_or_default(chunk_spec) + return GetResult(status="missing") + if drop_axes: + selected = selected.squeeze(axis=drop_axes) + out[out_selection] = selected + return GetResult(status="present") + + +def _merge_chunk_array( + existing_chunk_array: NDBuffer | None, + value: NDBuffer, + out_selection: SelectorTuple, + chunk_spec: ArraySpec, + chunk_selection: SelectorTuple, + is_complete_chunk: bool, + drop_axes: tuple[int, ...], +) -> NDBuffer: + """Merge `value` into a full-chunk-shaped NDBuffer at `chunk_selection`. + + If `is_complete_chunk` and `value[out_selection]` is exactly chunk-shaped, + that VIEW of the caller's `value` is returned without copying — callers + (and the codecs they pass it to) must treat it as read-only, since + mutating it would corrupt the user's source array. Otherwise, a writable + buffer is materialized — either from `existing_chunk_array.copy()` if + one was read from the store, or freshly allocated and filled with the + chunk's fill value — and the relevant slice of `value` is written into it. + """ + if is_complete_chunk and value.shape != (): + selected = value[out_selection] + # The shape check guards against a partial edge chunk arriving with + # is_complete_chunk=True, and against dropped axes (size-1 integer + # dims), where the selection is not exactly chunk-shaped. + if selected.shape == chunk_spec.shape: + return selected + if existing_chunk_array is None: + chunk_array = chunk_spec.prototype.nd_buffer.create( + shape=chunk_spec.shape, + dtype=chunk_spec.dtype.to_native_dtype(), + order=chunk_spec.order, + fill_value=fill_value_or_default(chunk_spec), + ) + else: + chunk_array = existing_chunk_array.copy() + if chunk_selection == () or is_scalar( + value.as_ndarray_like(), chunk_spec.dtype.to_native_dtype() + ): + chunk_value = value + else: + chunk_value = value[out_selection] + if drop_axes: + item = tuple( + None if idx in drop_axes else slice(None) for idx in range(chunk_spec.ndim) + ) + chunk_value = chunk_value[item] + chunk_array[chunk_selection] = chunk_value + return chunk_array + + +def merge_and_encode_chunk( + existing_bytes: Buffer | None, + value: NDBuffer, + *, + chunk_spec: ArraySpec, + chunk_selection: SelectorTuple, + out_selection: SelectorTuple, + is_complete: bool, + drop_axes: tuple[int, ...], + decode: Callable[[Buffer, ArraySpec], NDBuffer], + encode: Callable[[NDBuffer, ArraySpec], Buffer | None], +) -> Buffer | None: + """The canonical single-chunk write: merge, normalize, encode. + + decode existing (``None`` = chunk currently missing) -> merge ``value`` at + ``chunk_selection`` -> normalize empties to missing -> encode. Returns the + bytes to store or ``None`` = do not store / delete. This is the one + state-transition every per-chunk write path expresses; only the IO around + it (where ``existing_bytes`` comes from, where the result goes) differs. + """ + + existing_array = decode(existing_bytes, chunk_spec) if existing_bytes is not None else None + merged = _merge_chunk_array( + existing_array, value, out_selection, chunk_spec, chunk_selection, is_complete, drop_axes + ) + return encode_or_elide_chunk(merged, chunk_spec, encode) + + +def decode_and_scatter_chunk( + chunk_bytes: Buffer | None, + out: NDBuffer, + *, + chunk_spec: ArraySpec, + chunk_selection: SelectorTuple, + out_selection: SelectorTuple, + drop_axes: tuple[int, ...], + decode: Callable[[Buffer, ArraySpec], NDBuffer], +) -> GetResult: + """The canonical single-chunk read: decode stored bytes (``None`` = + missing), select, and scatter into ``out`` via `scatter_chunk`. The read + twin of `merge_and_encode_chunk`. + """ + if chunk_bytes is None: + return scatter_chunk( + None, out, chunk_spec=chunk_spec, out_selection=out_selection, drop_axes=drop_axes + ) + selected = decode(chunk_bytes, chunk_spec)[chunk_selection] + return scatter_chunk( + selected, out, chunk_spec=chunk_spec, out_selection=out_selection, drop_axes=drop_axes + ) + + +@dataclass(slots=True, kw_only=True) +class ChunkTransform: + """A synchronous codec chain. + + Provides `encode_chunk` and `decode_chunk` for pure-compute codec + operations (no IO, no threading, no batching). The `chunk_spec` is + supplied per call so the same transform can be reused across chunks + with different shapes, prototypes, etc. + + All codecs must implement `SupportsSyncCodec`. Construction will + raise `TypeError` if any codec does not. + """ + + codecs: tuple[Codec, ...] + + _aa_codecs: tuple[SupportsSyncCodec[NDBuffer, NDBuffer], ...] = field( + init=False, repr=False, compare=False + ) + _ab_codec: SupportsSyncCodec[NDBuffer, Buffer] = field(init=False, repr=False, compare=False) + _bb_codecs: tuple[SupportsSyncCodec[Buffer, Buffer], ...] = field( + init=False, repr=False, compare=False + ) + + def __post_init__(self) -> None: + from zarr.core.codec_pipeline import codecs_from_list + + non_sync = [c for c in self.codecs if not isinstance(c, SupportsSyncCodec)] + if non_sync: + names = ", ".join(type(c).__name__ for c in non_sync) + raise TypeError( + f"All codecs must implement SupportsSyncCodec. The following do not: {names}" + ) + + aa, ab, bb = codecs_from_list(list(self.codecs)) + # SupportsSyncCodec was verified above; the cast is purely for mypy. + self._aa_codecs = cast("tuple[SupportsSyncCodec[NDBuffer, NDBuffer], ...]", tuple(aa)) + self._ab_codec = cast("SupportsSyncCodec[NDBuffer, Buffer]", ab) + self._bb_codecs = cast("tuple[SupportsSyncCodec[Buffer, Buffer], ...]", tuple(bb)) + + # The whole cache entry — (key, aa_specs, ab_spec) — is stored as ONE field + # and replaced with a single attribute write. A `ChunkTransform` is shared + # across thread-pool workers (read_sync/write_sync with max_workers > 1), and + # storing the key separately from the specs would race: a worker could read a + # freshly-set key while the matching specs were still the previous (or None) + # value. A single tuple assignment is atomic under the GIL, so a reader sees + # either the complete old entry or the complete new one — never a torn mix. + _cache: tuple[ArraySpec, tuple[ArraySpec, ...], ArraySpec] | None = field( + init=False, repr=False, compare=False, default=None + ) + + def _resolve_specs(self, chunk_spec: ArraySpec) -> tuple[tuple[ArraySpec, ...], ArraySpec]: + """Return per-AA-codec input specs and the AB spec for `chunk_spec`. + + The resolved chain depends only on the value of `chunk_spec`, so we cache + it keyed on `chunk_spec` itself (ArraySpec is a frozen, hashable dataclass + — value identity). Keying on `id(chunk_spec)` would be unsafe: ids are + recycled after garbage collection, so a freed spec's id reused by a + different spec (same shape, different prototype/dtype/config) could yield + a stale hit. Value identity avoids that entirely. + + Thread-safety: a benign construction race is possible (two workers with + different specs may each compute and overwrite the single-entry cache — + last writer wins), but a torn read is not, because the entry is written + atomically as one tuple. Worst case is a recompute, never a wrong result. + """ + from zarr.core.codec_pipeline import resolve_aa_specs + + if not self._aa_codecs: + return (), chunk_spec + cache = self._cache + if cache is not None and cache[0] == chunk_spec: + return cache[1], cache[2] + + aa_specs_t, spec = resolve_aa_specs(cast("tuple[Codec, ...]", self._aa_codecs), chunk_spec) + self._cache = (chunk_spec, aa_specs_t, spec) + return aa_specs_t, spec + + def decode_chunk(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + """Decode a single chunk through the full codec chain, synchronously. + + Pure compute -- no IO. + + Parameters + ---------- + chunk_bytes : Buffer + The encoded chunk bytes. + chunk_spec : ArraySpec + The array spec describing shape, dtype, fill value, and codec + configuration for this chunk. + """ + aa_specs, ab_spec = self._resolve_specs(chunk_spec) + + data: Buffer = chunk_bytes + for bb_codec in reversed(self._bb_codecs): + data = bb_codec._decode_sync(data, ab_spec) + + chunk_array: NDBuffer = self._ab_codec._decode_sync(data, ab_spec) + + for aa_codec, aa_spec in zip(reversed(self._aa_codecs), reversed(aa_specs), strict=True): + chunk_array = aa_codec._decode_sync(chunk_array, aa_spec) + + return chunk_array + + def encode_chunk(self, chunk_array: NDBuffer, chunk_spec: ArraySpec) -> Buffer | None: + """Encode a single chunk through the full codec chain, synchronously. + + Pure compute -- no IO. + + Parameters + ---------- + chunk_array : NDBuffer + The chunk data to encode. + chunk_spec : ArraySpec + The array spec describing shape, dtype, fill value, and codec + configuration for this chunk. + """ + aa_specs, ab_spec = self._resolve_specs(chunk_spec) + + aa_data: NDBuffer = chunk_array + for aa_codec, aa_spec in zip(self._aa_codecs, aa_specs, strict=True): + aa_result = aa_codec._encode_sync(aa_data, aa_spec) + if aa_result is None: + return None + aa_data = aa_result + + ab_result = self._ab_codec._encode_sync(aa_data, ab_spec) + if ab_result is None: + return None + + bb_data: Buffer = ab_result + for bb_codec in self._bb_codecs: + bb_result = bb_codec._encode_sync(bb_data, ab_spec) + if bb_result is None: + return None + bb_data = bb_result + + return bb_data + + def compute_encoded_size(self, byte_length: int, array_spec: ArraySpec) -> int: + for codec in self.codecs: + byte_length = codec.compute_encoded_size(byte_length, array_spec) + array_spec = codec.resolve_metadata(array_spec) + return byte_length diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 23ecb0e255..2e3f1ed122 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -1,8 +1,11 @@ from __future__ import annotations +import asyncio +import threading +from concurrent.futures import ThreadPoolExecutor from dataclasses import dataclass, field from itertools import batched, pairwise -from typing import TYPE_CHECKING, Any +from typing import TYPE_CHECKING, Any, cast from warnings import warn from zarr.abc.codec import ( @@ -14,25 +17,76 @@ Codec, CodecPipeline, GetResult, - SupportsSyncCodec, ) -from zarr.core.common import concurrent_map +from zarr.core.chunk_utils import ( + ChunkTransform, + _merge_chunk_array, + chunk_is_empty, + decode_and_scatter_chunk, + evolve_codecs, + fill_value_or_default, + merge_and_encode_chunk, + scatter_chunk, +) +from zarr.core.common import concurrent_iter, concurrent_map from zarr.core.config import config -from zarr.core.indexing import SelectorTuple, is_scalar from zarr.errors import ZarrUserWarning from zarr.registry import register_pipeline if TYPE_CHECKING: - from collections.abc import Iterable, Iterator + from collections.abc import Iterable, Iterator, Sequence from typing import Self from zarr.abc.store import ByteGetter, ByteSetter from zarr.core.array_spec import ArraySpec from zarr.core.buffer import Buffer, BufferPrototype, NDBuffer from zarr.core.dtype.wrapper import TBaseDType, TBaseScalar, ZDType + from zarr.core.indexing import SelectorTuple from zarr.core.metadata.v3 import ChunkGridMetadata +_pool: ThreadPoolExecutor | None = None +_pool_size: int = 0 +_pool_lock = threading.Lock() + + +def _resolve_max_workers() -> int: + """Helper for getting the maximum number of workers available to the `FusedCodecPipeline`""" + import os as _os + + cfg = config.get("codec_pipeline.max_workers", default=None) + if cfg is None: + return _os.cpu_count() or 1 + return max(1, int(cfg)) + + +def _get_pool(max_workers: int) -> ThreadPoolExecutor: + """Get or create the module-level thread pool, sized to `max_workers`. + + The pool grows on demand — if a request arrives for more workers than the + current pool has, it is replaced with a larger one. The previous pool is NOT + shut down here: another thread may be holding a reference to it and about to + submit (`shutdown` would make its `pool.map` raise "cannot schedule new + futures after shutdown"). The orphaned pool finishes its in-flight tasks and + is garbage-collected once no caller references it. The pool only grows, never + shrinks (a shrink request reuses the larger pool, leaving workers idle). + + Callers that want sequential execution should not call this — they + should run the task list inline. `max_workers` must be >= 1. + """ + global _pool, _pool_size + if max_workers < 1: + raise ValueError(f"max_workers must be >= 1, got {max_workers}") + if _pool is None or _pool_size < max_workers: + with _pool_lock: + if _pool is None or _pool_size < max_workers: + # Replace without shutting down the old pool (see docstring): + # avoids a race with a concurrent in-flight pool.map on it. + _pool = ThreadPoolExecutor(max_workers=max_workers) + _pool_size = max_workers + return _pool + + def _unzip2[T, U](iterable: Iterable[tuple[T, U]]) -> tuple[list[T], list[U]]: out0: list[T] = [] out1: list[U] = [] @@ -46,123 +100,423 @@ def resolve_batched(codec: Codec, chunk_specs: Iterable[ArraySpec]) -> Iterable[ return [codec.resolve_metadata(chunk_spec) for chunk_spec in chunk_specs] -def fill_value_or_default(chunk_spec: ArraySpec) -> Any: - fill_value = chunk_spec.fill_value - if fill_value is None: - # Zarr V2 allowed `fill_value` to be null in the metadata. - # Zarr V3 requires it to be set. This has already been - # validated when decoding the metadata, but we support reading - # Zarr V2 data and need to support the case where fill_value - # is None. - return chunk_spec.dtype.default_scalar() +def resolve_aa_specs( + aa_codecs: tuple[Codec, ...], chunk_spec: ArraySpec +) -> tuple[tuple[ArraySpec, ...], ArraySpec]: + """Resolve the per-stage chunk specs for a single chunk's codec chain. + + Threads `chunk_spec` forward through the array->array codecs via + `resolve_metadata` (each codec sees the spec produced by the previous one), + returning `(aa_specs, ab_spec)`: + + * `aa_specs[i]` is the spec the i-th AA codec operates on (its *input* on + encode / *output* on decode); + * `ab_spec` is the spec after all AA codecs — what the array->bytes codec + and the bytes->bytes codecs operate on. + + This is the single source of truth for per-stage spec evolution, shared by + the synchronous `ChunkTransform` and the asynchronous + `AsyncChunkTransform`. It is pure metadata (only `resolve_metadata`), so + it places no synchronous-codec requirement on the codecs. + """ + aa_specs: list[ArraySpec] = [] + spec = chunk_spec + for aa_codec in aa_codecs: + aa_specs.append(spec) + spec = aa_codec.resolve_metadata(spec) + return tuple(aa_specs), spec + + +def pipeline_supports_partial_decode( + array_bytes_codec: ArrayBytesCodec, + *, + array_array_codecs: tuple[ArrayArrayCodec, ...], + bytes_bytes_codecs: tuple[BytesBytesCodec, ...], + require_no_aa_bb: bool, +) -> bool: + """Whether a codec pipeline can decode a partial selection without a full read. + + Requires the array->bytes codec to implement + ``ArrayBytesCodecPartialDecodeMixin``. When ``require_no_aa_bb`` is True it + additionally requires no array->array / bytes->bytes codecs, because those + can change the slice<->byte-range correspondence (an AA codec can make the + selection non-contiguous, a BB codec can rewrite the bytes), making partial + decode infeasible. + + NOTE: the two pipelines currently pass different ``require_no_aa_bb`` values + (Batched: True; Fused: False). That divergence is intentional-for-now and + tracked separately; this function centralizes the predicate without changing + either pipeline's behavior. + """ + if require_no_aa_bb and (len(array_array_codecs) + len(bytes_bytes_codecs)) != 0: + return False + return isinstance(array_bytes_codec, ArrayBytesCodecPartialDecodeMixin) + + +def pipeline_supports_partial_encode( + array_bytes_codec: ArrayBytesCodec, + *, + array_array_codecs: tuple[ArrayArrayCodec, ...], + bytes_bytes_codecs: tuple[BytesBytesCodec, ...], + require_no_aa_bb: bool, +) -> bool: + """Whether a codec pipeline can encode a partial selection without a full rewrite. + + Mirror of ``pipeline_supports_partial_decode`` for encoding. See its note re: + the per-pipeline ``require_no_aa_bb`` divergence. + """ + if require_no_aa_bb and (len(array_array_codecs) + len(bytes_bytes_codecs)) != 0: + return False + return isinstance(array_bytes_codec, ArrayBytesCodecPartialEncodeMixin) + + +async def _fetch_and_decode_as_completed( + batch: Sequence[tuple[ByteGetter | None, ArraySpec]], + transform: ChunkTransform, +) -> list[NDBuffer | None]: + """Concurrently fetch each chunk's bytes and decode it as fetches complete. + + Decoding overlaps with in-flight fetches: each chunk is decoded the moment + its bytes arrive (in a thread pool when one is available, otherwise inline) + rather than waiting for the whole batch to land. A `None` byte getter fetches + nothing and decodes to `None`. Results are returned in input order. + """ + max_workers = _resolve_max_workers() + pool = _get_pool(max_workers) if max_workers > 1 else None + loop = asyncio.get_running_loop() + decode_futures: list[asyncio.Future[NDBuffer | None]] = [loop.create_future() for _ in batch] + + async def _fetch( + idx: int, byte_getter: ByteGetter | None, prototype: BufferPrototype + ) -> tuple[int, Buffer | None]: + return idx, None if byte_getter is None else await byte_getter.get(prototype) + + def _decode(buffer: Buffer | None, chunk_spec: ArraySpec) -> NDBuffer | None: + return None if buffer is None else transform.decode_chunk(buffer, chunk_spec) + + fetch_tasks = concurrent_iter( + [ + (idx, byte_getter, chunk_spec.prototype) + for idx, (byte_getter, chunk_spec) in enumerate(batch) + ], + _fetch, + config.get("async.concurrency"), + ) + for fetch_coro in asyncio.as_completed(fetch_tasks): + idx, buffer = await fetch_coro + chunk_spec = batch[idx][1] + # Bridge both paths to asyncio.Future so the final collection loop + # can `await` uniformly without blocking the event loop. For the + # pool path that means `wrap_future` (not `pool.submit(...).result()`, + # which would block the loop thread for the duration of every decode + # — freezing any unrelated coroutines sharing this loop). + if pool is None: + decode_futures[idx].set_result(_decode(buffer, chunk_spec)) + else: + decode_futures[idx] = asyncio.wrap_future(pool.submit(_decode, buffer, chunk_spec)) + + return await asyncio.gather(*decode_futures) + + +async def _encode_and_write_as_completed( + batch: Sequence[tuple[ByteSetter, NDBuffer | None, ArraySpec]], + transform: ChunkTransform, +) -> None: + """Encode each chunk and write it out as encodes complete. + + The reverse of `_fetch_and_decode_as_completed`: each chunk is encoded (in a + thread pool when one is available, otherwise inline) and its write is launched + the moment that chunk's encode finishes — overlapping IO writes with + still-running encodes rather than waiting for the whole batch to encode. + A `None` chunk array encodes to `None` and is `delete`d. Writes are bounded + by `async.concurrency`. + """ + max_workers = _resolve_max_workers() + pool = _get_pool(max_workers) if max_workers > 1 else None + loop = asyncio.get_running_loop() + semaphore = asyncio.Semaphore(config.get("async.concurrency")) + + def _encode( + idx: int, chunk_array: NDBuffer | None, chunk_spec: ArraySpec + ) -> tuple[int, Buffer | None]: + return idx, None if chunk_array is None else transform.encode_chunk(chunk_array, chunk_spec) + + async def _write(idx: int, chunk_bytes: Buffer | None) -> None: + byte_setter = batch[idx][0] + async with semaphore: + if chunk_bytes is None: + await byte_setter.delete() + else: + await byte_setter.set(chunk_bytes) + + # Submit every encode up front. The pool path bridges to asyncio.Future via + # `wrap_future` (not `pool.submit(...).result()`, which would block the loop + # thread); the inline path resolves immediately. + encode_futures: list[asyncio.Future[tuple[int, Buffer | None]]] = [] + for idx, (_, chunk_array, chunk_spec) in enumerate(batch): + if pool is None: + fut: asyncio.Future[tuple[int, Buffer | None]] = loop.create_future() + fut.set_result(_encode(idx, chunk_array, chunk_spec)) + else: + fut = asyncio.wrap_future(pool.submit(_encode, idx, chunk_array, chunk_spec)) + encode_futures.append(fut) + + # Kick off each chunk's write the instant its encode lands, so writes of + # already-compressed chunks proceed while the rest are still encoding. + write_tasks: list[asyncio.Task[None]] = [] + for encode_coro in asyncio.as_completed(encode_futures): + idx, chunk_bytes = await encode_coro + write_tasks.append(asyncio.ensure_future(_write(idx, chunk_bytes))) + await asyncio.gather(*write_tasks) + + +async def _async_read_fallback( + pipeline: CodecPipeline, + batch: list[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], + out: NDBuffer, + drop_axes: tuple[int, ...], +) -> tuple[GetResult, ...]: + """Async fallback read used when no fast-path is available. + + Fetches every chunk's bytes via `concurrent_map` (sized by + `async.concurrency`), decodes the batch through `pipeline.decode`, + then scatters each decoded chunk into `out` at its `out_selection`. + + Used by both `BatchedCodecPipeline.read_batch` (non-partial-decode + branch) and `FusedCodecPipeline.read` (when the store is not a + `SupportsGetSync` / sync transform is unavailable). + """ + + chunk_array_batch: list[NDBuffer | None] + + if isinstance(pipeline, FusedCodecPipeline) and pipeline.sync_transform is not None: + chunk_array_batch = await _fetch_and_decode_as_completed( + [(byte_getter, chunk_spec) for byte_getter, chunk_spec, *_ in batch], + pipeline.sync_transform, + ) else: - return fill_value + chunk_bytes_batch = await concurrent_map( + [(byte_getter, array_spec.prototype) for byte_getter, array_spec, *_ in batch], + lambda byte_getter, prototype: byte_getter.get(prototype), + config.get("async.concurrency"), + ) + chunk_array_batch = list( + await pipeline.decode( + [ + (chunk_bytes, chunk_spec) + for chunk_bytes, (_, chunk_spec, *_) in zip( + chunk_bytes_batch, batch, strict=False + ) + ], + ) + ) + + results: list[GetResult] = [] + for chunk_array, (_, chunk_spec, chunk_selection, out_selection, _) in zip( + chunk_array_batch, batch, strict=True + ): + selected = None if chunk_array is None else chunk_array[chunk_selection] + results.append( + scatter_chunk( + selected, + out, + chunk_spec=chunk_spec, + out_selection=out_selection, + drop_axes=drop_axes, + ) + ) + return tuple(results) + + +async def _async_write_fallback( + pipeline: CodecPipeline, + batch: list[tuple[ByteSetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], + value: NDBuffer, + drop_axes: tuple[int, ...], +) -> None: + """Async fallback write used when no fast-path is available. + + For each chunk in `batch`: read its existing bytes from the store + (skipping the read for complete chunks), decode the batch via + `pipeline.decode`, merge `value` into each decoded chunk via + `_merge_chunk_array`, drop chunks that are all-fill when + `write_empty_chunks` is False, encode the surviving chunks via + `pipeline.encode`, then `set` the encoded bytes (or `delete` + if encoding produced `None` or the chunk dropped). + + Used by both `BatchedCodecPipeline.write_batch` (non-partial-encode + branch) and `FusedCodecPipeline.write` (when the store is not a + `SupportsSetSync` / sync transform is unavailable). + """ + + if use_sync := ( + isinstance(pipeline, FusedCodecPipeline) and pipeline.sync_transform is not None + ): + # Read each chunk's existing bytes (skipping complete chunks) and decode + # as fetches complete, overlapping the sync decode with in-flight reads. + chunk_array_decoded: Iterable[NDBuffer | None] = await _fetch_and_decode_as_completed( + [ + (None if is_complete_chunk else byte_setter, chunk_spec) + for byte_setter, chunk_spec, _, _, is_complete_chunk in batch + ], + pipeline.sync_transform, + ) + else: + + async def _read_key( + byte_setter: ByteSetter | None, prototype: BufferPrototype + ) -> Buffer | None: + if byte_setter is None: + return None + return await byte_setter.get(prototype=prototype) + + chunk_bytes_batch: Iterable[Buffer | None] = await concurrent_map( + [ + ( + None if is_complete_chunk else byte_setter, + chunk_spec.prototype, + ) + for byte_setter, chunk_spec, chunk_selection, _, is_complete_chunk in batch + ], + _read_key, + config.get("async.concurrency"), + ) + chunk_array_decoded = await pipeline.decode( + [ + (chunk_bytes, chunk_spec) + for chunk_bytes, (_, chunk_spec, *_) in zip(chunk_bytes_batch, batch, strict=False) + ], + ) + chunk_array_merged = [ + _merge_chunk_array( + chunk_array, + value, + out_selection, + chunk_spec, + chunk_selection, + is_complete_chunk, + drop_axes, + ) + for chunk_array, ( + _, + chunk_spec, + chunk_selection, + out_selection, + is_complete_chunk, + ) in zip(chunk_array_decoded, batch, strict=False) + ] + # _merge_chunk_array always returns a real NDBuffer (never None), so the only + # way a chunk drops to None here is the empty-chunk normalization. + chunk_array_batch: list[NDBuffer | None] = [ + None if chunk_is_empty(chunk_array, chunk_spec) else chunk_array + for chunk_array, (_, chunk_spec, *_) in zip(chunk_array_merged, batch, strict=False) + ] + + if use_sync: + sync_transform = cast(FusedCodecPipeline, pipeline).sync_transform + assert sync_transform is not None + await _encode_and_write_as_completed( + [ + (byte_setter, chunk_array, chunk_spec) + for chunk_array, (byte_setter, chunk_spec, *_) in zip( + chunk_array_batch, batch, strict=False + ) + ], + sync_transform, + ) + else: + chunk_bytes_batch = await pipeline.encode( + [ + (chunk_array, chunk_spec) + for chunk_array, (_, chunk_spec, *_) in zip(chunk_array_batch, batch, strict=False) + ], + ) + + async def _write_key(byte_setter: ByteSetter, chunk_bytes: Buffer | None) -> None: + if chunk_bytes is None: + await byte_setter.delete() + else: + await byte_setter.set(chunk_bytes) + + await concurrent_map( + [ + (byte_setter, chunk_bytes) + for chunk_bytes, (byte_setter, *_) in zip(chunk_bytes_batch, batch, strict=False) + ], + _write_key, + config.get("async.concurrency"), + ) @dataclass(slots=True, kw_only=True) -class ChunkTransform: - """A synchronous codec chain bound to an ArraySpec. +class AsyncChunkTransform: + """A per-chunk asynchronous codec chain — the async mirror of ChunkTransform. - Provides `encode` and `decode` for pure-compute codec operations - (no IO, no threading, no batching). + Decodes/encodes a SINGLE chunk through the full codec chain, awaiting each + codec's per-chunk async method (`_decode_single`/`_encode_single`) with the + correctly-evolved per-stage spec (via the shared `resolve_aa_specs`). - All codecs must implement `SupportsSyncCodec`. Construction will - raise `TypeError` if any codec does not. + Unlike ChunkTransform it places no `SupportsSyncCodec` requirement on the + codecs, so it works for async-only codecs. Unlike the batched codec API it + operates on one chunk at a time — the mini-batch fan-out is a + BatchedCodecPipeline concern and deliberately not reintroduced here. """ codecs: tuple[Codec, ...] - array_spec: ArraySpec - # (sync codec, input_spec) pairs in pipeline order. - _aa_codecs: tuple[tuple[SupportsSyncCodec[NDBuffer, NDBuffer], ArraySpec], ...] = field( - init=False, repr=False, compare=False - ) - _ab_codec: SupportsSyncCodec[NDBuffer, Buffer] = field(init=False, repr=False, compare=False) - _ab_spec: ArraySpec = field(init=False, repr=False, compare=False) - _bb_codecs: tuple[SupportsSyncCodec[Buffer, Buffer], ...] = field( - init=False, repr=False, compare=False - ) + _aa_codecs: tuple[ArrayArrayCodec, ...] = field(init=False, repr=False, compare=False) + _ab_codec: ArrayBytesCodec = field(init=False, repr=False, compare=False) + _bb_codecs: tuple[BytesBytesCodec, ...] = field(init=False, repr=False, compare=False) def __post_init__(self) -> None: - non_sync = [c for c in self.codecs if not isinstance(c, SupportsSyncCodec)] - if non_sync: - names = ", ".join(type(c).__name__ for c in non_sync) - raise TypeError( - f"All codecs must implement SupportsSyncCodec. The following do not: {names}" - ) - aa, ab, bb = codecs_from_list(list(self.codecs)) - - aa_codecs: list[tuple[SupportsSyncCodec[NDBuffer, NDBuffer], ArraySpec]] = [] - spec = self.array_spec - for aa_codec in aa: - assert isinstance(aa_codec, SupportsSyncCodec) - aa_codecs.append((aa_codec, spec)) - spec = aa_codec.resolve_metadata(spec) - - self._aa_codecs = tuple(aa_codecs) - assert isinstance(ab, SupportsSyncCodec) + self._aa_codecs = aa self._ab_codec = ab - self._ab_spec = spec - bb_sync: list[SupportsSyncCodec[Buffer, Buffer]] = [] - for bb_codec in bb: - assert isinstance(bb_codec, SupportsSyncCodec) - bb_sync.append(bb_codec) - self._bb_codecs = tuple(bb_sync) - - def decode( - self, - chunk_bytes: Buffer, - ) -> NDBuffer: - """Decode a single chunk through the full codec chain, synchronously. + self._bb_codecs = bb + + async def decode_chunk(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + """Decode one chunk through the chain (bb -> ab -> aa), async.""" + aa_specs, ab_spec = resolve_aa_specs(self._aa_codecs, chunk_spec) - Pure compute -- no IO. - """ data: Buffer = chunk_bytes for bb_codec in reversed(self._bb_codecs): - data = bb_codec._decode_sync(data, self._ab_spec) + data = await bb_codec._decode_single(data, ab_spec) - chunk_array: NDBuffer = self._ab_codec._decode_sync(data, self._ab_spec) + chunk_array: NDBuffer = await self._ab_codec._decode_single(data, ab_spec) - for aa_codec, spec in reversed(self._aa_codecs): - chunk_array = aa_codec._decode_sync(chunk_array, spec) + for aa_codec, aa_spec in zip(reversed(self._aa_codecs), reversed(aa_specs), strict=True): + chunk_array = await aa_codec._decode_single(chunk_array, aa_spec) return chunk_array - def encode( - self, - chunk_array: NDBuffer, - ) -> Buffer | None: - """Encode a single chunk through the full codec chain, synchronously. + async def encode_chunk(self, chunk_array: NDBuffer, chunk_spec: ArraySpec) -> Buffer | None: + """Encode one chunk through the chain (aa -> ab -> bb), async. - Pure compute -- no IO. + Returns None if any stage drops the chunk (e.g. an all-fill chunk under + write_empty_chunks=False), matching ChunkTransform.encode_chunk. """ + aa_specs, ab_spec = resolve_aa_specs(self._aa_codecs, chunk_spec) + aa_data: NDBuffer = chunk_array - for aa_codec, spec in self._aa_codecs: - aa_result = aa_codec._encode_sync(aa_data, spec) + for aa_codec, aa_spec in zip(self._aa_codecs, aa_specs, strict=True): + aa_result = await aa_codec._encode_single(aa_data, aa_spec) if aa_result is None: return None aa_data = aa_result - ab_result = self._ab_codec._encode_sync(aa_data, self._ab_spec) + ab_result = await self._ab_codec._encode_single(aa_data, ab_spec) if ab_result is None: return None bb_data: Buffer = ab_result for bb_codec in self._bb_codecs: - bb_result = bb_codec._encode_sync(bb_data, self._ab_spec) + bb_result = await bb_codec._encode_single(bb_data, ab_spec) if bb_result is None: return None bb_data = bb_result return bb_data - def compute_encoded_size(self, byte_length: int, array_spec: ArraySpec) -> int: - for codec in self.codecs: - byte_length = codec.compute_encoded_size(byte_length, array_spec) - array_spec = codec.resolve_metadata(array_spec) - return byte_length - @dataclass(frozen=True) class BatchedCodecPipeline(CodecPipeline): @@ -179,18 +533,7 @@ class BatchedCodecPipeline(CodecPipeline): batch_size: int def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: - # Each codec must be evolved against the spec it will actually see - # at run-time, not the original array spec. Earlier array->array - # codecs may transform the dtype (e.g. cast_value), so the spec - # threaded into later codecs (the array->bytes serializer and any - # bytes->bytes filters) must reflect those transformations. - evolved: list[Codec] = [] - spec = array_spec - for codec in self: - evolved_codec = codec.evolve_from_array_spec(array_spec=spec) - evolved.append(evolved_codec) - spec = evolved_codec.resolve_metadata(spec) - return type(self).from_codecs(evolved) + return type(self).from_codecs(evolve_codecs(self, array_spec)) @classmethod def from_codecs(cls, codecs: Iterable[Codec], *, batch_size: int | None = None) -> Self: @@ -205,34 +548,22 @@ def from_codecs(cls, codecs: Iterable[Codec], *, batch_size: int | None = None) @property def supports_partial_decode(self) -> bool: - """Determines whether the codec pipeline supports partial decoding. - - Currently, only codec pipelines with a single ArrayBytesCodec that supports - partial decoding can support partial decoding. This limitation is due to the fact - that ArrayArrayCodecs can change the slice selection leading to non-contiguous - slices and BytesBytesCodecs can change the chunk bytes in a way that slice - selections cannot be attributed to byte ranges anymore which renders partial - decoding infeasible. - - This limitation may softened in the future.""" - return (len(self.array_array_codecs) + len(self.bytes_bytes_codecs)) == 0 and isinstance( - self.array_bytes_codec, ArrayBytesCodecPartialDecodeMixin + # Only a single ArrayBytesCodec that supports partial decoding, and no + # AA/BB codecs (they break the slice<->byte-range correspondence). + return pipeline_supports_partial_decode( + self.array_bytes_codec, + array_array_codecs=self.array_array_codecs, + bytes_bytes_codecs=self.bytes_bytes_codecs, + require_no_aa_bb=True, ) @property def supports_partial_encode(self) -> bool: - """Determines whether the codec pipeline supports partial encoding. - - Currently, only codec pipelines with a single ArrayBytesCodec that supports - partial encoding can support partial encoding. This limitation is due to the fact - that ArrayArrayCodecs can change the slice selection leading to non-contiguous - slices and BytesBytesCodecs can change the chunk bytes in a way that slice - selections cannot be attributed to byte ranges anymore which renders partial - encoding infeasible. - - This limitation may softened in the future.""" - return (len(self.array_array_codecs) + len(self.bytes_bytes_codecs)) == 0 and isinstance( - self.array_bytes_codec, ArrayBytesCodecPartialEncodeMixin + return pipeline_supports_partial_encode( + self.array_bytes_codec, + array_array_codecs=self.array_array_codecs, + bytes_bytes_codecs=self.bytes_bytes_codecs, + require_no_aa_bb=True, ) def __iter__(self) -> Iterator[Codec]: @@ -359,8 +690,8 @@ async def read_batch( out: NDBuffer, drop_axes: tuple[int, ...] = (), ) -> tuple[GetResult, ...]: - results: list[GetResult] = [] if self.supports_partial_decode: + results: list[GetResult] = [] batch_info_list = list(batch_info) chunk_array_batch = await self.decode_partial_batch( [ @@ -379,81 +710,8 @@ async def read_batch( else: out[out_selection] = fill_value_or_default(chunk_spec) results.append(GetResult(status="missing")) - else: - batch_info_list = list(batch_info) - chunk_bytes_batch = await concurrent_map( - [ - (byte_getter, array_spec.prototype) - for byte_getter, array_spec, *_ in batch_info_list - ], - lambda byte_getter, prototype: byte_getter.get(prototype), - config.get("async.concurrency"), - ) - chunk_array_batch = await self.decode_batch( - [ - (chunk_bytes, chunk_spec) - for chunk_bytes, (_, chunk_spec, *_) in zip( - chunk_bytes_batch, batch_info_list, strict=False - ) - ], - ) - for chunk_array, (_, chunk_spec, chunk_selection, out_selection, _) in zip( - chunk_array_batch, batch_info_list, strict=False - ): - if chunk_array is not None: - tmp = chunk_array[chunk_selection] - if drop_axes: - tmp = tmp.squeeze(axis=drop_axes) - out[out_selection] = tmp - results.append(GetResult(status="present")) - else: - out[out_selection] = fill_value_or_default(chunk_spec) - results.append(GetResult(status="missing")) - return tuple(results) - - def _merge_chunk_array( - self, - existing_chunk_array: NDBuffer | None, - value: NDBuffer, - out_selection: SelectorTuple, - chunk_spec: ArraySpec, - chunk_selection: SelectorTuple, - is_complete_chunk: bool, - drop_axes: tuple[int, ...], - ) -> NDBuffer: - if ( - is_complete_chunk - and value.shape == chunk_spec.shape - # Guard that this is not a partial chunk at the end with is_complete_chunk=True - and value[out_selection].shape == chunk_spec.shape - ): - return value - if existing_chunk_array is None: - chunk_array = chunk_spec.prototype.nd_buffer.create( - shape=chunk_spec.shape, - dtype=chunk_spec.dtype.to_native_dtype(), - order=chunk_spec.order, - fill_value=fill_value_or_default(chunk_spec), - ) - else: - chunk_array = existing_chunk_array.copy() # make a writable copy - if chunk_selection == () or is_scalar( - value.as_ndarray_like(), chunk_spec.dtype.to_native_dtype() - ): - chunk_value = value - else: - chunk_value = value[out_selection] - # handle missing singleton dimensions - if drop_axes: - item = tuple( - None # equivalent to np.newaxis - if idx in drop_axes - else slice(None) - for idx in range(chunk_spec.ndim) - ) - chunk_value = chunk_value[item] - chunk_array[chunk_selection] = chunk_value - return chunk_array + return tuple(results) + return await _async_read_fallback(self, list(batch_info), out, drop_axes) async def write_batch( self, @@ -478,93 +736,8 @@ async def write_batch( ], ) - else: - # Read existing bytes if not total slice - async def _read_key( - byte_setter: ByteSetter | None, prototype: BufferPrototype - ) -> Buffer | None: - if byte_setter is None: - return None - return await byte_setter.get(prototype=prototype) - - chunk_bytes_batch: Iterable[Buffer | None] - chunk_bytes_batch = await concurrent_map( - [ - ( - None if is_complete_chunk else byte_setter, - chunk_spec.prototype, - ) - for byte_setter, chunk_spec, chunk_selection, _, is_complete_chunk in batch_info - ], - _read_key, - config.get("async.concurrency"), - ) - chunk_array_decoded = await self.decode_batch( - [ - (chunk_bytes, chunk_spec) - for chunk_bytes, (_, chunk_spec, *_) in zip( - chunk_bytes_batch, batch_info, strict=False - ) - ], - ) - - chunk_array_merged = [ - self._merge_chunk_array( - chunk_array, - value, - out_selection, - chunk_spec, - chunk_selection, - is_complete_chunk, - drop_axes, - ) - for chunk_array, ( - _, - chunk_spec, - chunk_selection, - out_selection, - is_complete_chunk, - ) in zip(chunk_array_decoded, batch_info, strict=False) - ] - chunk_array_batch: list[NDBuffer | None] = [] - for chunk_array, (_, chunk_spec, *_) in zip( - chunk_array_merged, batch_info, strict=False - ): - if chunk_array is None: - chunk_array_batch.append(None) # type: ignore[unreachable] - else: - if not chunk_spec.config.write_empty_chunks and chunk_array.all_equal( - fill_value_or_default(chunk_spec) - ): - chunk_array_batch.append(None) - else: - chunk_array_batch.append(chunk_array) - - chunk_bytes_batch = await self.encode_batch( - [ - (chunk_array, chunk_spec) - for chunk_array, (_, chunk_spec, *_) in zip( - chunk_array_batch, batch_info, strict=False - ) - ], - ) - - async def _write_key(byte_setter: ByteSetter, chunk_bytes: Buffer | None) -> None: - if chunk_bytes is None: - await byte_setter.delete() - else: - await byte_setter.set(chunk_bytes) - - await concurrent_map( - [ - (byte_setter, chunk_bytes) - for chunk_bytes, (byte_setter, *_) in zip( - chunk_bytes_batch, batch_info, strict=False - ) - ], - _write_key, - config.get("async.concurrency"), - ) + return + await _async_write_fallback(self, list(batch_info), value, drop_axes) async def decode( self, @@ -624,11 +797,13 @@ def codecs_from_list( ) -> tuple[tuple[ArrayArrayCodec, ...], ArrayBytesCodec, tuple[BytesBytesCodec, ...]]: from zarr.codecs.sharding import ShardingCodec + codecs = tuple(codecs) # materialize to avoid generator consumption issues + array_array: tuple[ArrayArrayCodec, ...] = () array_bytes_maybe: ArrayBytesCodec | None = None bytes_bytes: tuple[BytesBytesCodec, ...] = () - if any(isinstance(codec, ShardingCodec) for codec in codecs) and len(tuple(codecs)) > 1: + if any(isinstance(codec, ShardingCodec) for codec in codecs) and len(codecs) > 1: warn( "Combining a `sharding_indexed` codec disables partial reads and " "writes, which may lead to inefficient performance.", @@ -683,3 +858,387 @@ def codecs_from_list( register_pipeline(BatchedCodecPipeline) + + +@dataclass(frozen=True) +class FusedCodecPipeline(CodecPipeline): + """Codec pipeline that runs codec compute synchronously, in bulk. + + This is an opt-in alternative to `BatchedCodecPipeline`. The win is NOT + "separating IO from compute" — the codecs (notably `ShardingCodec`) still + perform their own storage IO. The win is replacing the batched pipeline's + per-chunk *async scheduling* (≈one coroutine per chunk, which dominates real + codec work) with synchronous, batched/coalesced execution: + + 1. When every codec implements `SupportsSyncCodec`, a `ChunkTransform` + runs the codec chain synchronously (no event loop, no per-chunk coroutine) + — optionally across a thread pool for CPU-heavy decode/encode. + 2. Sharded reads use the codec's synchronous IO methods: byte-range reads + coalesced via `Store.get_ranges_sync`, and a vectorized whole-shard bulk + decode for dense, fixed-size, uncompressed shards. Sharded writes go + through the codec's synchronous full-shard-rewrite path. + 3. When the store lacks synchronous IO (e.g. ZipStore) the pipeline falls + back to the async path, equivalent to `BatchedCodecPipeline`. + + IO ownership: the sharding codec holds the byte getter/setter and reads/ + writes storage directly (the same model as zarrs; unlike tensorstore, which + keeps codecs storage-free). A storage-free codec is a possible future + direction (see the pure-codec design notes) but is explicitly NOT what this + pipeline does. + """ + + codecs: tuple[Codec, ...] + array_array_codecs: tuple[ArrayArrayCodec, ...] + array_bytes_codec: ArrayBytesCodec + bytes_bytes_codecs: tuple[BytesBytesCodec, ...] + sync_transform: ChunkTransform | None + batch_size: int + + @classmethod + def from_codecs(cls, codecs: Iterable[Codec], *, batch_size: int | None = None) -> Self: + codec_list = tuple(codecs) + aa, ab, bb = codecs_from_list(codec_list) + + if batch_size is None: + batch_size = config.get("codec_pipeline.batch_size") + + return cls( + codecs=codec_list, + array_array_codecs=aa, + array_bytes_codec=ab, + bytes_bytes_codecs=bb, + sync_transform=None, + batch_size=batch_size, + ) + + def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: + evolved_codecs = evolve_codecs(self.codecs, array_spec) + aa, ab, bb = codecs_from_list(evolved_codecs) + + try: + sync_transform: ChunkTransform | None = ChunkTransform(codecs=evolved_codecs) + except TypeError: + sync_transform = None + + return type(self)( + codecs=evolved_codecs, + array_array_codecs=aa, + array_bytes_codec=ab, + bytes_bytes_codecs=bb, + sync_transform=sync_transform, + batch_size=self.batch_size, + ) + + def __iter__(self) -> Iterator[Codec]: + return iter(self.codecs) + + @property + def supports_partial_decode(self) -> bool: + # NOTE: unlike BatchedCodecPipeline this does NOT require the AA/BB codec + # lists to be empty (require_no_aa_bb=False). That divergence is tracked + # separately; see pipeline_supports_partial_decode. + return pipeline_supports_partial_decode( + self.array_bytes_codec, + array_array_codecs=self.array_array_codecs, + bytes_bytes_codecs=self.bytes_bytes_codecs, + require_no_aa_bb=False, + ) + + @property + def supports_partial_encode(self) -> bool: + return pipeline_supports_partial_encode( + self.array_bytes_codec, + array_array_codecs=self.array_array_codecs, + bytes_bytes_codecs=self.bytes_bytes_codecs, + require_no_aa_bb=False, + ) + + def validate( + self, + *, + shape: tuple[int, ...], + dtype: ZDType[TBaseDType, TBaseScalar], + chunk_grid: ChunkGridMetadata, + ) -> None: + for codec in self.codecs: + codec.validate(shape=shape, dtype=dtype, chunk_grid=chunk_grid) + + def compute_encoded_size(self, byte_length: int, array_spec: ArraySpec) -> int: + for codec in self: + byte_length = codec.compute_encoded_size(byte_length, array_spec) + array_spec = codec.resolve_metadata(array_spec) + return byte_length + + # -- async decode/encode (required by ABC) and sync versions -- + + async def decode( + self, + chunk_bytes_and_specs: Iterable[tuple[Buffer | None, ArraySpec]], + ) -> Iterable[NDBuffer | None]: + # Decode each chunk through AsyncChunkTransform, which threads the + # per-stage spec correctly (via resolve_aa_specs). This is the single + # source of truth for async per-chunk decode; earlier this method + # reused one flat `chunk_specs` across every codec stage, which silently + # corrupted/crashed spec-changing codecs (transpose/cast/scale_offset) + # on the async fallback path. + async_transform = AsyncChunkTransform(codecs=self.codecs) + out: list[NDBuffer | None] = [] + for chunk_bytes, chunk_spec in chunk_bytes_and_specs: + if chunk_bytes is None: + out.append(None) + else: + out.append(await async_transform.decode_chunk(chunk_bytes, chunk_spec)) + return out + + async def encode( + self, + chunk_arrays_and_specs: Iterable[tuple[NDBuffer | None, ArraySpec]], + ) -> Iterable[Buffer | None]: + async_transform = AsyncChunkTransform(codecs=self.codecs) + out: list[Buffer | None] = [] + for chunk_array, chunk_spec in chunk_arrays_and_specs: + if chunk_array is None: + out.append(None) + else: + out.append(await async_transform.encode_chunk(chunk_array, chunk_spec)) + return out + + # -- sync read/write -- + + def read_sync( + self, + batch_info: Iterable[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], + out: NDBuffer, + drop_axes: tuple[int, ...] = (), + max_workers: int = 1, + ) -> tuple[GetResult, ...]: + """Synchronous read: fetch -> decode -> scatter, per chunk. + + When `max_workers > 1` and there are multiple chunks, each + chunk's full lifecycle (fetch + decode + scatter) runs as one + task on a thread pool sized to `max_workers` — overlapping IO + of one chunk with decode/scatter of another. Scatter is + thread-safe because the chunks have non-overlapping output + selections. + + `max_workers=1` runs everything sequentially in the calling + thread (no pool involvement). + + Mirrors `BatchedCodecPipeline.read_batch`: when the AB codec + supports partial decoding (e.g. sharding), the codec handles its + own IO and only fetches the inner-chunk byte ranges that overlap + the read selection. Otherwise the pipeline fetches the full + blob and decodes the whole chunk. + """ + assert self.sync_transform is not None + transform = self.sync_transform + + batch = list(batch_info) + if not batch: + return () + + # Partial-decode fast path: the AB codec owns IO (read only the + # byte ranges needed for the requested selection). Same condition + # and dispatch as BatchedCodecPipeline.read_batch. + if self.supports_partial_decode: + codec = self.array_bytes_codec + assert hasattr(codec, "_decode_partial_sync") + + def _read_one( + item: tuple[Any, ArraySpec, SelectorTuple, SelectorTuple, bool], + ) -> GetResult: + byte_getter, chunk_spec, chunk_selection, out_selection, _ = item + # the partial decode returns the already-selected region + decoded = codec._decode_partial_sync(byte_getter, chunk_selection, chunk_spec) + return scatter_chunk( + decoded, + out, + chunk_spec=chunk_spec, + out_selection=out_selection, + drop_axes=drop_axes, + ) + + else: + # Per-chunk fused path: fetch + decode + scatter as one task. + def _read_one( + item: tuple[Any, ArraySpec, SelectorTuple, SelectorTuple, bool], + ) -> GetResult: + byte_getter, chunk_spec, chunk_selection, out_selection, _ = item + raw = byte_getter.get_sync(prototype=chunk_spec.prototype) + return decode_and_scatter_chunk( + raw, + out, + chunk_spec=chunk_spec, + chunk_selection=chunk_selection, + out_selection=out_selection, + drop_axes=drop_axes, + decode=transform.decode_chunk, + ) + + if max_workers > 1 and len(batch) > 1: + pool = _get_pool(max_workers) + return tuple(pool.map(_read_one, batch)) + return tuple(_read_one(item) for item in batch) + + def write_sync( + self, + batch_info: Iterable[tuple[ByteSetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], + value: NDBuffer, + drop_axes: tuple[int, ...] = (), + max_workers: int = 1, + ) -> None: + """Synchronous write: fetch existing -> merge+encode -> store. + + When `max_workers > 1` and there are multiple chunks, each + chunk's full lifecycle (get-existing + merge + encode + set/delete) + runs as one task on a thread pool sized to `max_workers` — + overlapping IO of one chunk with compute of another. + + `max_workers=1` runs everything sequentially in the calling + thread (no pool involvement). + + When the codec pipeline supports partial encoding (e.g. a + sharding codec with no outer AA/BB codecs), the AB codec handles + the full write cycle — reading existing data, merging, encoding, + and writing — matching the async `BatchedCodecPipeline` path. + """ + assert self.sync_transform is not None + transform = self.sync_transform + + batch = list(batch_info) + if not batch: + return + + # Partial-encode path: the AB codec owns IO (read, merge, encode, + # write). Same condition and calling convention as + # BatchedCodecPipeline.write_batch. + if self.supports_partial_encode: + codec = self.array_bytes_codec + assert hasattr(codec, "_encode_partial_sync") + scalar = len(value.shape) == 0 + + def _write_one( + item: tuple[Any, ArraySpec, SelectorTuple, SelectorTuple, bool], + ) -> None: + bs, chunk_spec, chunk_selection, out_selection, _is_complete = item + chunk_value = value if scalar else value[out_selection] + codec._encode_partial_sync(bs, chunk_value, chunk_selection, chunk_spec) + + else: + # Per-chunk fused path: get-existing + merge + encode + set/delete as one task. + def _write_one( + item: tuple[Any, ArraySpec, SelectorTuple, SelectorTuple, bool], + ) -> None: + bs, chunk_spec, chunk_selection, out_selection, is_complete = item + existing_bytes: Buffer | None = None + if not is_complete: + existing_bytes = bs.get_sync(prototype=chunk_spec.prototype) + + encoded = merge_and_encode_chunk( + existing_bytes, + value, + chunk_spec=chunk_spec, + chunk_selection=chunk_selection, + out_selection=out_selection, + is_complete=is_complete, + drop_axes=drop_axes, + decode=transform.decode_chunk, + encode=transform.encode_chunk, + ) + if encoded is None: + bs.delete_sync() + else: + bs.set_sync(encoded) + + if max_workers > 1 and len(batch) > 1: + pool = _get_pool(max_workers) + list(pool.map(_write_one, batch)) + else: + for item in batch: + _write_one(item) + + # -- async read/write -- + + async def read( + self, + batch_info: Iterable[tuple[ByteGetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], + out: NDBuffer, + drop_axes: tuple[int, ...] = (), + ) -> tuple[GetResult, ...]: + batch = list(batch_info) + if not batch: + return () + + # Fast path: sync transform plus synchronous IO. For StorePath the gate + # is on the STORE's sync support (StorePath always has a get_sync + # method, but it only works when its store does); for other byte + # getters (e.g. the sharding codec's in-memory _ShardingByteGetter) the + # SyncByteGetter protocol is the gate. + from zarr.abc.store import SupportsGetSync, SyncByteGetter + from zarr.storage._common import StorePath + + first_bg = batch[0][0] + if self.sync_transform is not None and ( + (isinstance(first_bg, StorePath) and isinstance(first_bg.store, SupportsGetSync)) + or (not isinstance(first_bg, StorePath) and isinstance(first_bg, SyncByteGetter)) + ): + return self.read_sync(batch, out, drop_axes, max_workers=_resolve_max_workers()) + + # Non-sync store (e.g. ZipStore): can't use the sync fast path. But if the + # array-bytes codec supports partial decoding (sharding), still route + # through the async partial-decode path — it fetches only the needed + # inner-chunk byte ranges (coalesced via get_ranges), matching + # BatchedCodecPipeline. Without this, the whole-shard _async_read_fallback + # below would over-read and diverge from the batched pipeline's IO. + if self.supports_partial_decode: + assert isinstance(self.array_bytes_codec, ArrayBytesCodecPartialDecodeMixin) + chunk_array_batch = await self.array_bytes_codec.decode_partial( + [ + (byte_getter, chunk_selection, chunk_spec) + for byte_getter, chunk_spec, chunk_selection, *_ in batch + ] + ) + results: list[GetResult] = [] + for chunk_array, (_, chunk_spec, _, out_selection, _) in zip( + chunk_array_batch, batch, strict=False + ): + if chunk_array is not None: + if drop_axes: + chunk_array = chunk_array.squeeze(axis=drop_axes) + out[out_selection] = chunk_array + results.append(GetResult(status="present")) + else: + out[out_selection] = fill_value_or_default(chunk_spec) + results.append(GetResult(status="missing")) + return tuple(results) + + return await _async_read_fallback(self, batch, out, drop_axes) + + async def write( + self, + batch_info: Iterable[tuple[ByteSetter, ArraySpec, SelectorTuple, SelectorTuple, bool]], + value: NDBuffer, + drop_axes: tuple[int, ...] = (), + ) -> None: + batch = list(batch_info) + if not batch: + return + + # Fast path: sync transform plus synchronous IO. Mirrors `read`: gate + # StorePath on the store's sync support, other byte setters (e.g. the + # sharding codec's in-memory _ShardingByteSetter) on SyncByteSetter. + from zarr.abc.store import SupportsSetSync, SyncByteSetter + from zarr.storage._common import StorePath + + first_bs = batch[0][0] + if self.sync_transform is not None and ( + (isinstance(first_bs, StorePath) and isinstance(first_bs.store, SupportsSetSync)) + or (not isinstance(first_bs, StorePath) and isinstance(first_bs, SyncByteSetter)) + ): + self.write_sync(batch, value, drop_axes, max_workers=_resolve_max_workers()) + return + + await _async_write_fallback(self, batch, value, drop_axes) + + +register_pipeline(FusedCodecPipeline) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 20664e553e..4114cb7645 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -5,7 +5,6 @@ import warnings from collections.abc import Iterable, Mapping, Sequence from enum import Enum -from itertools import starmap from typing import ( TYPE_CHECKING, Any, @@ -90,22 +89,46 @@ def ceildiv(a: float, b: float) -> int: return math.ceil(a / b) -async def concurrent_map[T: tuple[Any, ...], V]( +def concurrent_iter[T: tuple[Any, ...], V]( items: Iterable[T], func: Callable[..., Awaitable[V]], limit: int | None = None, -) -> list[V]: +) -> Iterator[asyncio.Task[V]]: + """Launch `func(*item)` for each item concurrently, returning the tasks. + + When `limit` is set, no more than `limit` calls are in flight at once. + Tasks are returned in input order; callers that want completion order + should wrap the result in `asyncio.as_completed`. + + Note on `ensure_future`: when the result is passed to `asyncio.gather` or + `asyncio.as_completed`, those already wrap awaitables into tasks, so the + `ensure_future` here is redundant. It matters for callers that iterate and + await tasks one at a time — without eager scheduling, each coroutine would + only start when individually awaited, serializing the work and defeating + the semaphore. It also makes the return type honest (real `Task`s support + `.cancel()`, `.done()`, callbacks) rather than bare coroutines. + + See https://docs.python.org/3/library/asyncio-task.html#coroutines: + "Note that simply calling a coroutine will not schedule it to be executed:" + """ if limit is None: - return await asyncio.gather(*list(starmap(func, items))) + return (asyncio.ensure_future(func(*item)) for item in items) - else: - sem = asyncio.Semaphore(limit) + sem = asyncio.Semaphore(limit) + + async def run(item: T) -> V: + async with sem: + return await func(*item) + + return (asyncio.ensure_future(run(item)) for item in items) - async def run(item: tuple[Any]) -> V: - async with sem: - return await func(*item) - return await asyncio.gather(*[asyncio.ensure_future(run(item)) for item in items]) +async def concurrent_map[T: tuple[Any, ...], V]( + items: Iterable[T], + func: Callable[..., Awaitable[V]], + limit: int | None = None, +) -> list[V]: + return await asyncio.gather(*concurrent_iter(items, func, limit)) def enum_names[E: Enum](enum: type[E]) -> Iterator[str]: diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 08d2a50ace..42c5ed3b60 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -106,8 +106,16 @@ def enable_gpu(self) -> ConfigSet: "threading": {"max_workers": None}, "json_indent": 2, "codec_pipeline": { + # FusedCodecPipeline is the faster synchronous pipeline, but it stays + # opt-in for now so behavior is unchanged for existing users. Early + # adopters can switch with + # zarr.config.set( + # {"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"} + # ) "path": "zarr.core.codec_pipeline.BatchedCodecPipeline", "batch_size": 1, + # Only read by FusedCodecPipeline (BatchedCodecPipeline ignores it). + "max_workers": None, }, "codecs": { "blosc": "zarr.codecs.blosc.BloscCodec", diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 89d788af1a..617980ac19 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -42,13 +42,13 @@ async def _close_fs(fs: AsyncFileSystem) -> None: """ Best-effort async close of an fsspec async filesystem owned by FsspecStore. - For filesystems that expose ``set_session()`` (e.g. s3fs) the underlying - aiohttp ``ClientSession`` is closed explicitly, which prevents - "Unclosed client session" ``ResourceWarning``s from aiohttp. For all + For filesystems that expose `set_session()` (e.g. s3fs) the underlying + aiohttp `ClientSession` is closed explicitly, which prevents + "Unclosed client session" `ResourceWarning`s from aiohttp. For all other filesystem types the call is a no-op (not every implementation manages an HTTP session directly). - Note that ``set_session()`` lazily creates a session if none exists yet, so + Note that `set_session()` lazily creates a session if none exists yet, so closing a store that never performed any I/O may instantiate a session purely to close it. This is accepted best-effort behavior; fsspec does not expose a stable, cross-implementation way to test for an existing session. @@ -286,7 +286,7 @@ def with_read_only(self, read_only: bool = False) -> FsspecStore: ) # The derived store shares the same fs. Transfer ownership so the # surviving store closes it, and clear ours to avoid a double-close. - # Otherwise the common ``from_url(...).with_read_only()`` chain would + # Otherwise the common `from_url(...).with_read_only()` chain would # drop the only owner (the unreferenced source) and leak the session. new_store._owns_fs = self._owns_fs self._owns_fs = False diff --git a/src/zarr/testing/buffer.py b/src/zarr/testing/buffer.py index 6096ece2f8..f666801694 100644 --- a/src/zarr/testing/buffer.py +++ b/src/zarr/testing/buffer.py @@ -13,6 +13,8 @@ from collections.abc import Iterable from typing import Self + from zarr.abc.store import ByteRequest + __all__ = [ "NDBufferUsingTestNDArrayLike", @@ -72,6 +74,13 @@ async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None assert isinstance(value, TestBuffer) await super().set(key, value, byte_range) + def set_sync(self, key: str, value: Buffer) -> None: + # Synchronous counterpart of `set`, used by FusedCodecPipeline. Mirror the + # same buffer-type guard so the invariant holds whichever pipeline writes. + if "json" not in key: + assert isinstance(value, TestBuffer) + super().set_sync(key, value) + async def get( self, key: str, @@ -84,3 +93,18 @@ async def get( if ret is not None: assert isinstance(ret, prototype.buffer) return ret + + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + # Synchronous counterpart of `get`, used by FusedCodecPipeline. + if "json" not in key and prototype is not None: + assert prototype.buffer is TestBuffer + ret = super().get_sync(key=key, prototype=prototype, byte_range=byte_range) + if ret is not None and prototype is not None: + assert isinstance(ret, prototype.buffer) + return ret diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index fb87a69a09..80a0996ca6 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -5,6 +5,8 @@ from abc import abstractmethod from typing import TYPE_CHECKING, Self +import numpy as np + from zarr.storage import WrapperStore if TYPE_CHECKING: @@ -624,13 +626,31 @@ class LatencyStore(WrapperStore[Store]): performance testing. """ - get_latency: float - set_latency: float + _get_latency: float | tuple[float, float] + _set_latency: float | tuple[float, float] - def __init__(self, store: Store, *, get_latency: float = 0, set_latency: float = 0) -> None: + def __init__( + self, + store: Store, + *, + get_latency: float | tuple[float, float] = 0, + set_latency: float | tuple[float, float] = 0, + ) -> None: super().__init__(store) - self.get_latency = float(get_latency) - self.set_latency = float(set_latency) + self._get_latency = get_latency if isinstance(get_latency, tuple) else float(get_latency) + self._set_latency = set_latency if isinstance(set_latency, tuple) else float(set_latency) + + @property + def get_latency(self) -> float: + if isinstance(self._get_latency, float): + return self._get_latency + return max(0.0, np.random.normal(loc=self._get_latency[0], scale=self._get_latency[1])) + + @property + def set_latency(self) -> float: + if isinstance(self._set_latency, float): + return self._set_latency + return max(0.0, np.random.normal(loc=self._set_latency[0], scale=self._set_latency[1])) def _with_store(self, store: Store) -> Self: return type(self)(store, get_latency=self.get_latency, set_latency=self.set_latency) diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index f2c83677cc..99e81b0389 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -139,6 +139,19 @@ def dimension_names(draw: st.DrawFn, *, ndim: int | None = None) -> list[None | subchunk_write_orders: st.SearchStrategy[SubchunkWriteOrder] = st.sampled_from(SUBCHUNK_WRITE_ORDER) +# Inner codec chains for a ShardingCodec. We MUST sample the uncompressed, +# single-BytesCodec configuration (no Zstd) — that is the only configuration in +# which the FusedCodecPipeline's vectorized whole-shard "bulk decode" fast path +# engages, so it is the only one that can exercise (and regress-guard) that path +# against arbitrary indexing. Freezing the inner codecs to [BytesCodec, ZstdCodec] +# silently disables the fast path under every property test. +sharding_inner_codecs: st.SearchStrategy[list[BytesCodec | ZstdCodec]] = st.sampled_from( + [ + [BytesCodec()], + [BytesCodec(), ZstdCodec()], + ] +) + @st.composite def array_metadata( @@ -322,9 +335,10 @@ def arrays( ) if shard_shape is not None: subchunk_write_order = draw(subchunk_write_orders) + inner_codecs = draw(sharding_inner_codecs, label="sharding inner codecs") serializer = ShardingCodec( subchunk_write_order=subchunk_write_order, - codecs=[BytesCodec(), ZstdCodec()], + codecs=inner_codecs, index_codecs=[BytesCodec(), Crc32cCodec()], chunk_shape=chunks_param, ) diff --git a/tests/benchmarks/test_e2e.py b/tests/benchmarks/test_e2e.py index 65d0e65ac9..9d60d9a2fb 100644 --- a/tests/benchmarks/test_e2e.py +++ b/tests/benchmarks/test_e2e.py @@ -4,51 +4,144 @@ from __future__ import annotations -from typing import TYPE_CHECKING +import platform +import subprocess +from functools import lru_cache +from operator import getitem, setitem +from typing import TYPE_CHECKING, Any, Literal + +import numpy as np +import pytest +import zarr from tests.benchmarks.common import Layout +from zarr import create_array +from zarr.core.config import config as zarr_config +from zarr.testing.store import LatencyStore + + +def clear_cache() -> None: + if platform.system() == "Darwin": + subprocess.call(["sync", "&&", "sudo", "purge"]) + elif platform.system() == "Linux": + subprocess.call(["sudo", "sh", "-c", "sync; echo 3 > /proc/sys/vm/drop_caches"]) + else: + raise Exception("Unsupported platform") # noqa: TRY002 + if TYPE_CHECKING: + from collections.abc import Callable, Iterator + from types import EllipsisType + from pytest_benchmark.fixture import BenchmarkFixture from zarr.abc.store import Store from zarr.core.common import NamedConfig -from operator import getitem, setitem -from typing import Any, Literal -import pytest -from zarr import create_array +@lru_cache +def _data(shape: tuple[int]) -> np.ndarray: + n = shape[0] + period = 256 + noise_level = 1 + pattern = (np.sin(np.linspace(0, 2 * np.pi, period)) * 50 + 128).round().astype(np.uint8) + data = np.tile(pattern, int(np.ceil(n / period)))[:n].astype(np.int16) + data += np.random.randint(-noise_level, noise_level + 1, size=n, dtype=np.int16) + return np.clip(data, 0, 255).astype(np.uint8) -CompressorName = Literal["gzip"] | None + +CompressorName = Literal["zstd"] | None compressors: dict[CompressorName, NamedConfig[Any, Any] | None] = { None: None, - "gzip": {"name": "gzip", "configuration": {"level": 1}}, + # Default v3 + "zstd": {"name": "zstd", "configuration": {"level": 0, "checksum": False}}, } layouts: tuple[Layout, ...] = ( # No shards, just 1000 chunks - Layout(shape=(1_000_000,), chunks=(1000,), shards=None), + Layout(shape=(100_000_000,), chunks=(100_000,), shards=None), # 1:1 chunk:shard shape, should measure overhead of sharding - Layout(shape=(1_000_000,), chunks=(1000,), shards=(1000,)), - # One shard with all the chunks, should measure overhead of handling inner shard chunks - Layout(shape=(1_000_000,), chunks=(100,), shards=(10000 * 100,)), + Layout(shape=(100_000_000,), chunks=(100_000,), shards=(100_000,)), + # One shard with all the chunks, should measure over/under-head of handling inner shard chunks + Layout(shape=(100_000_000,), chunks=(100_000,), shards=(100_000 * 1_000,)), + # Mixed layout balancing inner vs. outer concurrency (likely the most real-world case) + Layout(shape=(1_000_000_000,), chunks=(100_000,), shards=(100_000 * 100,)), ) +_PIPELINE_SETTINGS = { + "batched": {"codec_pipeline.path": "zarr.core.codec_pipeline.BatchedCodecPipeline"}, + "fused_full_threaded": { + "codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline", + "codec_pipeline.max_workers": None, + }, + "fused_single_threaded": { + "codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline", + "codec_pipeline.max_workers": 1, + }, +} + +_LATENCY_VALUES = (0, 0.03) -@pytest.mark.parametrize("compression_name", [None, "gzip"]) + +@pytest.fixture(params=_LATENCY_VALUES, ids=lambda v: f"latency={v}") +def latency(request: pytest.FixtureRequest) -> float: + return request.param # type: ignore[no-any-return] + + +@pytest.fixture +def bench_store(store: Store, latency: float, request: pytest.FixtureRequest) -> Store: + """Wraps the underlying store in LatencyStore when latency > 0. + + Local-store cases skip nonzero latency — synthetic latency on top of + a real LocalStore is double-counting; latency simulation only applies + to the in-process memory store. + """ + callspec = getattr(request.node, "callspec", None) + store_kind = callspec.params.get("store", "memory") if callspec is not None else "memory" + if latency > 0: + if store_kind == "local": + pytest.skip("latency injection only applies to in-memory store") + return LatencyStore( + store, get_latency=(latency, latency * 1.2), set_latency=(latency, latency * 1.2) + ) + if store_kind == "memory": + pytest.skip("memory store doesn't offer much over local without latency") + return store + + +@pytest.fixture(params=["batched"]) # , "fused_full_threaded", "fused_single_threaded"]) +def pipeline(request: pytest.FixtureRequest) -> Iterator[str]: + """Set ``codec_pipeline.path`` for the duration of the benchmark. + + Yields the pipeline name so each parametrize cell has a distinct + benchmark id. + """ + name = request.param + with zarr_config.set(_PIPELINE_SETTINGS[name]): + yield name + + +@pytest.mark.parametrize( + "get_data", [lambda shape: 1, lambda shape: _data(shape)], ids=["repeated", "semi_random"] +) +@pytest.mark.parametrize("compression_name", ["zstd", None]) @pytest.mark.parametrize("layout", layouts, ids=str) -@pytest.mark.parametrize("store", ["memory", "local"], indirect=["store"]) +@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) def test_write_array( - store: Store, layout: Layout, compression_name: CompressorName, benchmark: BenchmarkFixture + bench_store: Store, + layout: Layout, + compression_name: CompressorName, + pipeline: str, + benchmark: BenchmarkFixture, + get_data: Callable[[tuple[int]], np.ndarray | int], ) -> None: """ Test the time required to fill an array with a single value """ arr = create_array( - store, + bench_store, dtype="uint8", shape=layout.shape, chunks=layout.chunks, @@ -57,20 +150,32 @@ def test_write_array( fill_value=0, ) - benchmark(setitem, arr, Ellipsis, 1) + def setup() -> tuple[tuple[zarr.Array, EllipsisType, int | np.ndarray], dict]: # type: ignore[type-arg] + clear_cache() + return (arr, Ellipsis, get_data(layout.shape)), {} # type: ignore[arg-type] + + benchmark.pedantic(setitem, setup=setup, rounds=3) # type: ignore[no-untyped-call] -@pytest.mark.parametrize("compression_name", [None, "gzip"]) +@pytest.mark.parametrize( + "get_data", [lambda shape: 1, lambda shape: _data(shape)], ids=["repeated", "semi_random"] +) +@pytest.mark.parametrize("compression_name", ["zstd", None]) @pytest.mark.parametrize("layout", layouts, ids=str) -@pytest.mark.parametrize("store", ["memory", "local"], indirect=["store"]) +@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) def test_read_array( - store: Store, layout: Layout, compression_name: CompressorName, benchmark: BenchmarkFixture + bench_store: Store, + layout: Layout, + compression_name: CompressorName, + pipeline: str, + benchmark: BenchmarkFixture, + get_data: Callable[[tuple[int]], np.ndarray | int], ) -> None: """ Test the time required to fill an array with a single value """ arr = create_array( - store, + bench_store, dtype="uint8", shape=layout.shape, chunks=layout.chunks, @@ -78,5 +183,10 @@ def test_read_array( compressors=compressors[compression_name], # type: ignore[arg-type] fill_value=0, ) - arr[:] = 1 - benchmark(getitem, arr, Ellipsis) + arr[:] = get_data(layout.shape) # type: ignore[arg-type] + + def setup() -> tuple[tuple[zarr.Array, EllipsisType], dict]: # type: ignore[type-arg] + clear_cache() + return (arr, Ellipsis), {} + + benchmark.pedantic(getitem, setup=setup, rounds=3) # type: ignore[no-untyped-call] diff --git a/tests/conftest.py b/tests/conftest.py index ec8f07b0e8..7ccf9958e7 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -108,7 +108,7 @@ async def parse_store( if store == "zip": return await ZipStore.open(f"{path}/zarr.zip", mode="w") if store == "memory_get_latency": - return LatencyStore(MemoryStore(), get_latency=0.0001, set_latency=0) + return LatencyStore(MemoryStore(), get_latency=0.0001, set_latency=0.0) raise AssertionError diff --git a/tests/test_sync_codec_pipeline.py b/tests/test_chunk_transform.py similarity index 82% rename from tests/test_sync_codec_pipeline.py rename to tests/test_chunk_transform.py index 1bfde7c837..d2a2b39c41 100644 --- a/tests/test_sync_codec_pipeline.py +++ b/tests/test_chunk_transform.py @@ -1,3 +1,13 @@ +"""Unit tests for ChunkTransform -- the per-chunk synchronous codec chain. + +ChunkTransform is the data structure FusedCodecPipeline uses to encode/decode a +single chunk through a sequence of codecs synchronously. These tests exercise it +directly (no pipeline, no store): construction and its rejection of codecs that +lack a synchronous implementation, encode/decode roundtrips across codec chains, +compute_encoded_size, and None short-circuiting when an array->array codec +returns None. End-to-end pipeline behavior lives in the pipeline test modules. +""" + from __future__ import annotations from typing import Any @@ -13,7 +23,7 @@ from zarr.codecs.zstd import ZstdCodec from zarr.core.array_spec import ArrayConfig, ArraySpec from zarr.core.buffer import Buffer, NDBuffer, default_buffer_prototype -from zarr.core.codec_pipeline import ChunkTransform +from zarr.core.chunk_utils import ChunkTransform from zarr.core.dtype import get_data_type_from_native_dtype @@ -58,8 +68,8 @@ def _make_nd_buffer(arr: np.ndarray[Any, np.dtype[Any]]) -> NDBuffer: ) def test_construction(shape: tuple[int, ...], codecs: tuple[Codec, ...]) -> None: """Construction succeeds when all codecs implement SupportsSyncCodec.""" - spec = _make_array_spec(shape, np.dtype("float64")) - ChunkTransform(codecs=codecs, array_spec=spec) + _ = _make_array_spec(shape, np.dtype("float64")) + ChunkTransform(codecs=codecs) @pytest.mark.parametrize( @@ -72,9 +82,9 @@ def test_construction(shape: tuple[int, ...], codecs: tuple[Codec, ...]) -> None ) def test_construction_rejects_non_sync(shape: tuple[int, ...], codecs: tuple[Codec, ...]) -> None: """Construction raises TypeError when any codec lacks SupportsSyncCodec.""" - spec = _make_array_spec(shape, np.dtype("float64")) + _ = _make_array_spec(shape, np.dtype("float64")) with pytest.raises(TypeError, match="AsyncOnlyCodec"): - ChunkTransform(codecs=codecs, array_spec=spec) + ChunkTransform(codecs=codecs) @pytest.mark.parametrize( @@ -96,12 +106,12 @@ def test_encode_decode_roundtrip( ) -> None: """Data survives a full encode/decode cycle.""" spec = _make_array_spec(arr.shape, arr.dtype) - chain = ChunkTransform(codecs=codecs, array_spec=spec) + chain = ChunkTransform(codecs=codecs) nd_buf = _make_nd_buffer(arr) - encoded = chain.encode(nd_buf) + encoded = chain.encode_chunk(nd_buf, spec) assert encoded is not None - decoded = chain.decode(encoded) + decoded = chain.decode_chunk(encoded, spec) np.testing.assert_array_equal(arr, decoded.as_numpy_array()) @@ -122,7 +132,7 @@ def test_compute_encoded_size( ) -> None: """compute_encoded_size returns the correct byte length.""" spec = _make_array_spec(shape, np.dtype("float64")) - chain = ChunkTransform(codecs=codecs, array_spec=spec) + chain = ChunkTransform(codecs=codecs) assert chain.compute_encoded_size(input_size, spec) == expected_size @@ -138,8 +148,7 @@ def _encode_sync(self, chunk_array: NDBuffer, chunk_spec: ArraySpec) -> NDBuffer spec = _make_array_spec((3, 4), np.dtype("float64")) chain = ChunkTransform( codecs=(NoneReturningAACodec(order=(1, 0)), BytesCodec()), - array_spec=spec, ) arr = np.arange(12, dtype="float64").reshape(3, 4) nd_buf = _make_nd_buffer(arr) - assert chain.encode(nd_buf) is None + assert chain.encode_chunk(nd_buf, spec) is None diff --git a/tests/test_codec_pipeline.py b/tests/test_codec_pipeline.py index 4d596164db..b069792fd8 100644 --- a/tests/test_codec_pipeline.py +++ b/tests/test_codec_pipeline.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Any import numpy as np import pytest @@ -15,34 +15,57 @@ from zarr.core.array import _get_chunk_spec from zarr.core.buffer.core import default_buffer_prototype from zarr.core.codec_pipeline import codecs_from_list +from zarr.core.config import config as zarr_config from zarr.core.indexing import BasicIndexer from zarr.storage import MemoryStore if TYPE_CHECKING: - from collections.abc import Callable + from collections.abc import Callable, Generator from zarr.abc.codec import Codec +@pytest.fixture(autouse=True) +def _enable_rectilinear_chunks() -> Generator[None]: + """Enable rectilinear chunks for all tests in this module.""" + with zarr_config.set({"array.rectilinear_chunks": True}): + yield + + +pipeline_paths = [ + "zarr.core.codec_pipeline.BatchedCodecPipeline", + "zarr.core.codec_pipeline.FusedCodecPipeline", +] + + +@pytest.fixture(params=pipeline_paths, ids=["batched", "sync"]) +def pipeline_class(request: pytest.FixtureRequest) -> Generator[str]: + """Temporarily set the codec pipeline class for the test.""" + path = request.param + with zarr_config.set({"codec_pipeline.path": path}): + yield path + + +# --------------------------------------------------------------------------- +# GetResult status tests (low-level pipeline API) +# --------------------------------------------------------------------------- + + @pytest.mark.parametrize( ("write_slice", "read_slice", "expected_statuses"), [ - # Write all chunks, read all — all present (slice(None), slice(None), ("present", "present", "present")), - # Write first chunk only, read all — first present, rest missing (slice(0, 2), slice(None), ("present", "missing", "missing")), - # Write nothing, read all — all missing (None, slice(None), ("missing", "missing", "missing")), ], ) async def test_read_returns_get_results( + pipeline_class: str, write_slice: slice | None, read_slice: slice, expected_statuses: tuple[str, ...], ) -> None: - """ - Test that CodecPipeline.read returns a tuple of GetResult with correct statuses. - """ + """CodecPipeline.read returns GetResult with correct statuses.""" store = MemoryStore() arr = zarr.open_array(store, mode="w", shape=(6,), chunks=(2,), dtype="int64", fill_value=-1) @@ -87,6 +110,34 @@ async def test_read_returns_get_results( assert result["status"] == expected_status +# --------------------------------------------------------------------------- +# write_empty_chunks / read_missing_chunks config tests +# --------------------------------------------------------------------------- + + +async def test_write_empty_chunks_false_no_store(pipeline_class: str) -> None: + """With write_empty_chunks=False, fill_value-only chunks should not be stored.""" + store: dict[str, Any] = {} + arr = zarr.create_array( + store=store, + shape=(20,), + dtype="float64", + chunks=(10,), + shards=None, + compressors=None, + fill_value=0.0, + config={"write_empty_chunks": False}, + ) + arr[:] = 0.0 # all fill_value + + # Chunks should NOT be persisted + assert "c/0" not in store + assert "c/1" not in store + + # But reading should still return fill values + np.testing.assert_array_equal(arr[:], np.zeros(20, dtype="float64")) + + try: import cast_value_rs # noqa: F401 @@ -135,6 +186,81 @@ def test_codec_pipeline_threads_dtype_through_evolve(source_dtype: str, target_d np.testing.assert_array_equal(arr[:], np.asarray([0, 1, 2, 3], dtype=source_dtype)) +def test_evolve_threads_spec_preserving_serializer_endian(pipeline_class: str) -> None: + """Regression for #3937, dependency-free variant. + + `evolve_from_array_spec` must thread the spec FORWARD through the codec chain: + each codec is evolved against the spec produced by the previous one, not the + original array spec. An array->array codec that widens the dtype from a + single-byte type (no endianness) to a multi-byte type means the BytesCodec + serializer must be evolved against the *widened* dtype — otherwise it sees + the single-byte source, strips its `endian` to None, and later fails to + decode the multi-byte data. + + The original regression test for this needs `cast_value_rs` (so it only runs + in the optional-deps CI job). This variant uses a minimal dtype-widening AA + codec stub, so it runs everywhere and on both pipelines via `pipeline_class`. + """ + from dataclasses import dataclass + + from zarr.abc.codec import ArrayArrayCodec + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.dtype import get_data_type_from_native_dtype + from zarr.registry import get_pipeline_class + + @dataclass(frozen=True) + class _WidenToInt16(ArrayArrayCodec): + """Test-only AA codec: reports the encoded dtype as int16 (no real encode).""" + + is_fixed_size = True + + def to_dict(self) -> dict[str, Any]: + return {"name": "_widen_to_int16"} + + @classmethod + def from_dict(cls, data: dict[str, Any]) -> _WidenToInt16: + return cls() + + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + from dataclasses import replace + + return replace(chunk_spec, dtype=get_data_type_from_native_dtype(np.dtype("int16"))) + + def compute_encoded_size(self, input_byte_length: int, _spec: ArraySpec) -> int: + return input_byte_length + + async def _decode_single(self, chunk_array: Any, chunk_spec: ArraySpec) -> Any: + return chunk_array # pragma: no cover + + async def _encode_single(self, chunk_array: Any, chunk_spec: ArraySpec) -> Any: + return chunk_array # pragma: no cover + + zdtype = get_data_type_from_native_dtype(np.dtype("int8")) # single-byte source + spec = ArraySpec( + shape=(4,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=False), + prototype=default_buffer_prototype(), + ) + + from zarr.core.codec_pipeline import BatchedCodecPipeline, FusedCodecPipeline + + pipeline = get_pipeline_class().from_codecs((_WidenToInt16(), BytesCodec(endian="little"))) + evolved = pipeline.evolve_from_array_spec(spec) + # Both concrete pipelines expose `array_bytes_codec`; narrow off the ABC. + assert isinstance(evolved, (BatchedCodecPipeline, FusedCodecPipeline)) + serializer = evolved.array_bytes_codec + + # The serializer must keep its little-endian setting: it is evolved against + # the widened (int16) dtype, not the single-byte source. + assert isinstance(serializer, BytesCodec) + assert serializer.endian is not None, ( + "BytesCodec serializer lost its `endian` — evolve_from_array_spec did not " + "thread the dtype-widening AA codec's spec into the serializer" + ) + + # Property-based check of codecs_from_list ordering validation. # # Valid codec orderings are exactly: (ArrayArrayCodec)* (ArrayBytesCodec) diff --git a/tests/test_codec_pipeline_suite.py b/tests/test_codec_pipeline_suite.py new file mode 100644 index 0000000000..07e1aa2ec4 --- /dev/null +++ b/tests/test_codec_pipeline_suite.py @@ -0,0 +1,582 @@ +"""Shared codec-pipeline behavior suite, run against EVERY codec pipeline. + +The defining property of a codec pipeline is that the array semantics it +produces must be identical no matter which pipeline is configured. To make +"one pipeline diverges from the others" structurally hard to ship, every +pipeline-agnostic behavior test lives as a method on ``CodecPipelineTests`` and +is instantiated once per pipeline (``TestBatchedPipeline`` / ``TestFusedPipeline``). + +Each test also runs over a *store axis* that exercises both code paths the +synchronous pipelines branch on: + +* ``sync`` -> ``MemoryStore`` (supports ``get_sync``/``set_sync``: fast path) +* ``async`` -> ``LatencyStore(MemoryStore())`` (NOT sync-capable: async fallback) + +The async axis is deliberate: a regression that only affects the async fallback +of the default pipeline (e.g. a codec-spec-evolution bug that surfaces only on +remote stores) is invisible if every test runs on MemoryStore. Running the same +battery over a non-sync store closes that gap. + +Pipeline-specific tests (construction, ``from_codecs``, the byte-range write +fast path, etc.) stay in their own modules; only behavior that ALL pipelines +must share belongs here. +""" + +from __future__ import annotations + +from dataclasses import dataclass +from typing import TYPE_CHECKING, Any + +import numcodecs +import numpy as np +import pytest + +import zarr +from zarr.codecs import BytesCodec, GzipCodec, ShardingCodec, TransposeCodec +from zarr.core.config import config as zarr_config +from zarr.errors import ChunkNotFoundError +from zarr.storage import MemoryStore +from zarr.testing.store import LatencyStore + +if TYPE_CHECKING: + from collections.abc import Iterator + + from zarr.abc.store import Store + from zarr.codecs.sharding import SubchunkWriteOrder + + +# --- store axis: a sync store and a non-sync (async-fallback) store ---------- + +STORE_KINDS = ["sync", "async"] + + +def _make_store(kind: str) -> Store: + if kind == "sync": + # MemoryStore supports get_sync/set_sync -> synchronous fast path. + return MemoryStore() + if kind == "async": + # LatencyStore is NOT SupportsGetSync/SupportsSetSync, so a synchronous + # pipeline must fall back to its async path. Zero latency keeps it fast. + return LatencyStore(MemoryStore(), get_latency=0.0, set_latency=0.0) + raise AssertionError(kind) + + +# --- scenario model ---------------------------------------------------------- +# +# Most pipeline behavior tests have one shape: +# create an array, apply some writes, (optionally) assert which chunk keys +# exist, then assert reads come back correct. A Scenario captures exactly those +# variables so one parametrized test covers them all. Correctness is checked +# against a numpy reference array that the scenario mutates in lock-step with +# the zarr array, so cases don't hand-maintain expected values. + + +@dataclass(frozen=True) +class Scenario: + id: str + array_kwargs: dict[str, Any] + # (selection, value) writes applied in order. value may be a scalar or array. + writes: tuple[tuple[Any, Any], ...] = () + # selections to read back and check against the reference. () means "read all". + reads: tuple[Any, ...] = (slice(None),) + # substrings of chunk keys that must be present / absent after the writes. + # Only checked on the sync store (key layout is identical across stores, but + # we keep it to one axis to avoid asserting store internals twice). + keys_present: tuple[str, ...] = () + keys_absent: tuple[str, ...] = () + + def reference(self) -> np.ndarray: + """The numpy array the scenario's writes should produce, starting from + the array's fill value.""" + kw = self.array_kwargs + shape = kw["shape"] + dtype = np.dtype(kw["dtype"]) + fill = kw.get("fill_value", 0) + ref = np.full(shape, fill, dtype=dtype) + for sel, value in self.writes: + ref[sel] = value + return ref + + +def _val(n: int, dtype: str, offset: int = 1) -> np.ndarray: + return np.arange(offset, offset + n, dtype=dtype) + + +# Common dtype/chunk presets reused below. +_F64 = {"dtype": "float64", "fill_value": 0.0} +_I32 = {"dtype": "int32", "fill_value": -1} + +SCENARIOS: tuple[Scenario, ...] = ( + # --- full-array roundtrips across layouts/codecs ------------------------ + Scenario( + "1d-unsharded-roundtrip", + {"shape": (100,), "chunks": (10,), "shards": None, "compressors": None, **_F64}, + writes=((slice(None), _val(100, "float64")),), + ), + Scenario( + "1d-sharded-roundtrip", + {"shape": (100,), "chunks": (10,), "shards": (100,), "compressors": None, **_F64}, + writes=((slice(None), _val(100, "float64")),), + ), + Scenario( + "1d-multi-chunk-shard-roundtrip", + {"shape": (100,), "chunks": (10,), "shards": (50,), "compressors": None, **_F64}, + writes=((slice(None), _val(100, "float64")),), + ), + Scenario( + "2d-unsharded-roundtrip", + {"shape": (10, 20), "chunks": (5, 10), "shards": None, "compressors": None, **_I32}, + writes=((slice(None), np.arange(200, dtype="int32").reshape(10, 20)),), + ), + Scenario( + "2d-sharded-roundtrip", + {"shape": (20, 20), "chunks": (5, 5), "shards": (10, 10), "compressors": None, **_I32}, + writes=((slice(None), np.arange(400, dtype="int32").reshape(20, 20)),), + ), + Scenario( + "1d-gzip-roundtrip", + { + "shape": (100,), + "chunks": (10,), + "shards": None, + "compressors": {"name": "gzip", "configuration": {"level": 1}}, + **_F64, + }, + writes=((slice(None), _val(100, "float64")),), + ), + Scenario( + "1d-zstd-roundtrip", + { + "shape": (100,), + "chunks": (10,), + "shards": None, + "compressors": {"name": "zstd", "configuration": {"level": 1}}, + **_F64, + }, + writes=((slice(None), _val(100, "float64")),), + ), + Scenario( + "1d-float32-roundtrip", + { + "shape": (50,), + "chunks": (10,), + "shards": None, + "compressors": None, + "dtype": "float32", + "fill_value": 0.0, + }, + writes=((slice(None), _val(50, "float32")),), + ), + # zarr v2 goes through the V2Codec wrapper (filters + compressor), a + # different codec path than the v3 AA/AB/BB chain — and a different sync + # implementation under FusedCodecPipeline. Without these scenarios, v2 was + # only exercised implicitly via whichever pipeline is the global default. + Scenario( + "v2-roundtrip", + { + "shape": (100,), + "chunks": (10,), + "shards": None, + "compressors": None, + "zarr_format": 2, + **_F64, + }, + writes=((slice(None), _val(100, "float64")),), + ), + Scenario( + "v2-gzip-roundtrip", + { + "shape": (100,), + "chunks": (10,), + "shards": None, + "compressors": numcodecs.GZip(level=1), + "zarr_format": 2, + **_F64, + }, + writes=((slice(None), _val(100, "float64")),), + ), + # v2 filters are the other half of the V2Codec wrapper (numcodecs + # array->array filters, a distinct branch from the compressor in + # _encode_sync/_decode_sync). + Scenario( + "v2-filter-gzip-roundtrip", + { + "shape": (100,), + "chunks": (10,), + "shards": None, + "filters": numcodecs.Delta(dtype="float64"), + "compressors": numcodecs.GZip(level=1), + "zarr_format": 2, + **_F64, + }, + writes=((slice(None), _val(100, "float64")),), + ), + # --- read unwritten chunks -> fill value -------------------------------- + Scenario( + "missing-chunks-fill", + { + "shape": (100,), + "chunks": (10,), + "shards": None, + "compressors": None, + "dtype": "float64", + "fill_value": -7.0, + }, + writes=(), + ), + Scenario( + "missing-chunks-fill-sharded", + { + "shape": (100,), + "chunks": (10,), + "shards": (100,), + "compressors": None, + "dtype": "float64", + "fill_value": -7.0, + }, + writes=(), + ), + # --- partial write, varied read selections ------------------------------ + Scenario( + "partial-write-full-read", + {"shape": (100,), "chunks": (10,), "shards": None, "compressors": None, **_F64}, + writes=((slice(5, 15), _val(10, "float64")),), + reads=(slice(None),), + ), + Scenario( + "full-write-strided-read", + {"shape": (100,), "chunks": (10,), "shards": None, "compressors": None, **_F64}, + writes=((slice(None), _val(100, "float64")),), + reads=(np.s_[::3], np.s_[10:20]), + ), + Scenario( + "partial-write-partial-read-sharded", + {"shape": (100,), "chunks": (10,), "shards": (100,), "compressors": None, **_F64}, + writes=((slice(20, 70), _val(50, "float64")),), + reads=(np.s_[30:60], slice(None)), + ), + # scalar single-element reads from a sharded array hit the sharding codec's + # partial-decode path (_decode_partial_single), distinct from slice reads. + Scenario( + "sharded-scalar-reads-1d", + {"shape": (100,), "chunks": (10,), "shards": (50,), "compressors": None, **_F64}, + writes=((slice(None), _val(100, "float64")),), + reads=(np.s_[0], np.s_[50], np.s_[99], np.s_[::3]), + ), + Scenario( + "sharded-scalar-reads-2d", + {"shape": (20, 20), "chunks": (5, 5), "shards": (10, 10), "compressors": None, **_I32}, + writes=((slice(None), np.arange(400, dtype="int32").reshape(20, 20)),), + reads=(np.s_[0, 0], np.s_[10, 10], np.s_[19, 19]), + ), + # --- spec-changing codec (transpose): the async-spec-evolution guard ---- + Scenario( + "transpose", + { + "shape": (8, 12), + "chunks": (2, 4), + "shards": None, + "filters": [TransposeCodec(order=(1, 0))], + "serializer": BytesCodec(), + **_I32, + }, + writes=((slice(None), np.arange(96, dtype="int32").reshape(8, 12)),), + reads=(slice(None), np.s_[1:7, 2:10]), + ), + Scenario( + "transpose-gzip", + { + "shape": (8, 12), + "chunks": (2, 4), + "shards": None, + "filters": [TransposeCodec(order=(1, 0))], + "serializer": BytesCodec(), + "compressors": GzipCodec(level=1), + **_I32, + }, + writes=((slice(None), np.arange(96, dtype="int32").reshape(8, 12)),), + reads=(slice(None), np.s_[1:7, 2:10]), + ), + # --- nested sharding ---------------------------------------------------- + Scenario( + "nested-sharding", + { + "shape": (20, 20), + "chunks": (10, 10), + "shards": None, + "compressors": None, + **_I32, + "fill_value": 0, + "serializer": ShardingCodec( + chunk_shape=(10, 10), codecs=[ShardingCodec(chunk_shape=(5, 5))] + ), + }, + writes=((slice(None), np.arange(400, dtype="int32").reshape(20, 20)),), + ), + # --- partial overwrite of an existing shard (merge) --------------------- + Scenario( + "partial-shard-overwrite", + { + "shape": (40,), + "chunks": (4,), + "shards": (40,), + "compressors": None, + **_I32, + "config": {"write_empty_chunks": True}, + }, + writes=( + (slice(None), np.arange(40, dtype="int32")), + (slice(7, 18), _val(11, "int32", 700)), + ), + ), + # --- write_empty_chunks: storage-key presence/absence ------------------- + Scenario( + "write-empty-false-omits-fill-chunk", + { + "shape": (20,), + "chunks": (10,), + "shards": None, + "compressors": None, + **_F64, + "config": {"write_empty_chunks": False}, + }, + writes=((slice(0, 10), _val(10, "float64")), (slice(10, 20), np.zeros(10, "float64"))), + keys_present=("c/0",), + keys_absent=("c/1",), + ), + Scenario( + "write-empty-true-persists-fill-chunk", + { + "shape": (20,), + "chunks": (10,), + "shards": None, + "compressors": None, + **_F64, + "config": {"write_empty_chunks": True}, + }, + writes=((slice(None), np.zeros(20, "float64")),), + keys_present=("c/0", "c/1"), + ), + # default config (no explicit write_empty_chunks) must still skip fill chunks + Scenario( + "default-config-omits-fill-chunk", + {"shape": (20,), "chunks": (10,), "shards": None, "compressors": None, **_F64}, + writes=((slice(10, 20), np.zeros(10, "float64")),), + keys_absent=("c/1",), + ), +) + + +class CodecPipelineTests: + """Behavior every codec pipeline must satisfy, on sync and async stores. + + Subclasses set ``pipeline_path`` to the fully-qualified pipeline class. + """ + + pipeline_path: str + + @pytest.fixture(autouse=True) + def _use_pipeline(self) -> Iterator[None]: + with zarr_config.set({"codec_pipeline.path": self.pipeline_path}): + yield + + @pytest.fixture(params=STORE_KINDS) + def store(self, request: pytest.FixtureRequest) -> Store: + return _make_store(request.param) + + @staticmethod + def _chunk_keys(store: Store) -> set[str]: + """All non-metadata keys currently in the store (v3 and v2 metadata).""" + import asyncio + + def _is_metadata(key: str) -> bool: + tail = key.rsplit("/", 1)[-1] + return tail in ("zarr.json", ".zarray", ".zattrs", ".zgroup", ".zmetadata") + + async def _list() -> set[str]: + return {k async for k in store.list() if not _is_metadata(k)} + + return asyncio.run(_list()) + + # -- the common shape: create -> write -> [assert keys] -> assert reads ---- + + @pytest.mark.parametrize("scenario", SCENARIOS, ids=lambda s: s.id) + def test_scenario(self, store: Store, scenario: Scenario) -> None: + """Create an array, apply the scenario's writes, optionally assert which + chunk keys exist, then assert each read selection matches a numpy + reference. Run against every pipeline (subclass) and store kind (fixture). + """ + arr = zarr.create_array(store=store, **scenario.array_kwargs) + for sel, value in scenario.writes: + arr[sel] = value + + ref = scenario.reference() + for sel in scenario.reads: + np.testing.assert_array_equal( + arr[sel], ref[sel], err_msg=f"{scenario.id}: read {sel!r} mismatch" + ) + + if scenario.keys_present or scenario.keys_absent: + keys = self._chunk_keys(store) + for present in scenario.keys_present: + assert any(present in k for k in keys), (present, keys) + for absent in scenario.keys_absent: + assert not any(absent in k for k in keys), (absent, keys) + + # -- outliers that don't fit the create/write/read scenario shape ---------- + + def test_read_missing_chunks_false_raises(self, store: Store) -> None: + """read_missing_chunks=False makes reading an unwritten chunk an error, + not a fill — a different assertion (raises) than the scenario shape.""" + arr = zarr.create_array( + store=store, + shape=(20,), + dtype="float64", + chunks=(10,), + shards=None, + compressors=None, + fill_value=0.0, + config={"read_missing_chunks": False}, + ) + with pytest.raises(ChunkNotFoundError): + arr[:] + + def test_read_missing_chunks_false_sharded_semantics(self, store: Store) -> None: + """read_missing_chunks=False is a STORE-KEY-level promise on sharded arrays. + + The config exists to help consumers distinguish a transport error from a + truly missing chunk. That distinction applies to store keys: a missing + SHARD key raises ChunkNotFoundError. It does not cleanly apply to inner + subchunks of a shard that was fetched successfully — there is no + transport ambiguity there, the shard index simply records the subchunk + as absent — so missing inner subchunks fill with the fill value rather + than raising. This pins that asymmetry as intentional. + """ + arr = zarr.create_array( + store=store, + shape=(100,), + dtype="float64", + chunks=(10,), + shards=(50,), + compressors=None, + fill_value=-1.0, + config={"read_missing_chunks": False}, + ) + # No shard key exists yet: reading is a missing-store-key error. + with pytest.raises(ChunkNotFoundError): + arr[:] + + # Write one inner chunk of the first shard. The shard key now exists, + # but most inner subchunks are absent from its index. + arr[20:30] = np.arange(10, dtype="float64") + + # Reading across written + absent inner subchunks of the EXISTING shard + # fills rather than raises. + out = arr[15:35] + expected = np.full(20, -1.0) + expected[5:15] = np.arange(10, dtype="float64") + np.testing.assert_array_equal(out, expected) + + # Both halves of the asymmetry in ONE read against the SAME partially + # written array: shard 0 exists (absent subchunks fill), shard 1 has no + # store key (raises) — pins that the raise still fires once some shard + # exists, and not only on a fully-empty array. + with pytest.raises(ChunkNotFoundError): + arr[:] + with pytest.raises(ChunkNotFoundError): + arr[45:55] # spans the existing and the missing shard + + @pytest.mark.parametrize("subchunk_write_order", ["morton", "lexicographic", "colexicographic"]) + def test_partial_write_after_reopen_is_correct( + self, store: Store, subchunk_write_order: SubchunkWriteOrder + ) -> None: + """Has an extra step the scenario shape lacks — a REOPEN between writes. + + Reopening a sharded array and partially overwriting it must read back + correctly regardless of the original subchunk_write_order. subchunk_write_ + order is intentionally NOT recoverable on reopen, so chunk locations on a + write to an existing shard must come from the STORED shard index, not the + (now-default) live order. A non-square inner grid makes the orders + physically distinct, so a wrong offset would corrupt data and fail here. + """ + shape, shard, inner = (6, 4), (6, 4), (2, 2) + arr = zarr.create_array( + store=store, + shape=shape, + dtype="int32", + chunks=shard, + fill_value=-1, + compressors=None, + config={"write_empty_chunks": True}, + serializer=ShardingCodec( + chunk_shape=inner, codecs=[BytesCodec()], subchunk_write_order=subchunk_write_order + ), + ) + ref = np.arange(24, dtype="int32").reshape(shape) + arr[:] = ref + + reopened = zarr.open_array(store=store, mode="r+") + reopened[1:5, 0:3] = 777 # partial overwrite into the existing shard + ref[1:5, 0:3] = 777 + np.testing.assert_array_equal(reopened[:], ref) + + def test_empty_shard_deleted_after_overwrite_to_fill(self, store: Store) -> None: + """A shard written with real data and then fully overwritten back to the + fill value must have its store key deleted, not left as a stale blob. + + This has a mid-sequence key assertion (present after write 1, absent + after write 2) that the create/write/read scenario shape can't express. + """ + arr = zarr.create_array( + store=store, + shape=(16,), + chunks=(4,), + shards=(8,), + dtype="float64", + compressors=None, + fill_value=0.0, + ) + arr[0:8] = np.arange(8, dtype="float64") + 1 + assert any("c/0" in k for k in self._chunk_keys(store)) + arr[0:8] = 0.0 + assert not any("c/0" in k for k in self._chunk_keys(store)), ( + "shard should be deleted when fully overwritten to fill value" + ) + + def test_read_write_methods_do_not_branch_on_sharding_codec_type(self) -> None: + """Pipeline read/write must dispatch on supports_partial_encode/decode, + not isinstance(ShardingCodec) — a static guard against type-branching. + + Scoped to this pipeline's own read/write methods (other helpers, e.g. + metadata validation, may legitimately isinstance-check ShardingCodec). + """ + import inspect + import re + + from zarr.registry import get_pipeline_class + + # The autouse _use_pipeline fixture has set codec_pipeline.path to this + # subclass's pipeline; resolve the class it points at and guard that. + # reload_config=False so the fixture's config override is honored + # (reload_config=True re-reads the base config, ignoring the override). + cls = get_pipeline_class(reload_config=False) + + pattern = re.compile(r"isinstance\s*\([^)]*ShardingCodec[^)]*\)") + for method_name in ("read", "write", "read_sync", "write_sync"): + method = getattr(cls, method_name, None) + if method is None: + continue + matches = pattern.findall(inspect.getsource(method)) + assert not matches, ( + f"{cls.__name__}.{method_name} contains an isinstance check on " + f"ShardingCodec; use supports_partial_encode/decode instead. " + f"Matches: {matches}" + ) + + +class TestBatchedPipeline(CodecPipelineTests): + pipeline_path = "zarr.core.codec_pipeline.BatchedCodecPipeline" + + +class TestFusedPipeline(CodecPipelineTests): + pipeline_path = "zarr.core.codec_pipeline.FusedCodecPipeline" diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index b88aa6f507..01ac02920f 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -402,3 +402,41 @@ async def test_resize(store: Store) -> None: assert await store.get(f"{path}/0.1", prototype=default_buffer_prototype()) is not None assert await store.get(f"{path}/1.0", prototype=default_buffer_prototype()) is None assert await store.get(f"{path}/1.1", prototype=default_buffer_prototype()) is None + + +def _resolve_metadata_codecs() -> list[Codec]: + from zarr.codecs.crc32c_ import Crc32cCodec + from zarr.codecs.zstd import ZstdCodec + + return [ + BytesCodec(), + GzipCodec(level=1), + TransposeCodec(order=(0,)), + Crc32cCodec(), + ZstdCodec(level=1), + ] + + +@pytest.mark.parametrize("codec", _resolve_metadata_codecs(), ids=lambda c: type(c).__name__) +def test_resolve_metadata_only_mutates_shape(codec: Codec) -> None: + """A codec's resolve_metadata may change a chunk's `shape` but must leave the + prototype, dtype, fill_value, and config untouched -- the pipeline relies on + those being stable across the codec chain. + """ + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.dtype import get_data_type_from_native_dtype + + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + spec_in = ArraySpec( + shape=(10,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0.0), + config=ArrayConfig(order="C", write_empty_chunks=False), + prototype=default_buffer_prototype(), + ) + spec_out = codec.resolve_metadata(spec_in) + name = type(codec).__name__ + assert spec_out.prototype is spec_in.prototype, f"{name} changed prototype" + assert spec_out.dtype == spec_in.dtype, f"{name} changed dtype" + assert spec_out.fill_value == spec_in.fill_value, f"{name} changed fill_value" + assert spec_out.config == spec_in.config, f"{name} changed config" diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index e62334f5d3..9e6bebd8df 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -38,6 +38,64 @@ from .test_codecs import _AsyncArrayProxy, order_from_dim +def _reads_are_sync(store_mock: AsyncMock) -> bool: + """True when the partial-shard read for this store+pipeline goes through the + synchronous methods (get_sync / get_ranges_sync). That requires BOTH the + configured pipeline to be the sync (Fused) one AND the store to support sync + reads — a Fused read against a non-sync store (e.g. ZipStore) falls back to + the async path. Lets the partial-shard-read tests assert the same intent + against whichever method family is actually exercised.""" + from zarr.abc.store import SupportsGetSync + from zarr.core.config import config + + pipeline_is_sync = "Fused" in config.get("codec_pipeline.path") + # store_mock wraps the real store; check the wrapped class for sync support. + wrapped = getattr(store_mock, "_mock_wraps", store_mock) + return pipeline_is_sync and isinstance(wrapped, SupportsGetSync) + + +def _index_read_count(store_mock: AsyncMock) -> int: + """Number of shard-index reads, regardless of sync/async pipeline.""" + method = store_mock.get_sync if _reads_are_sync(store_mock) else store_mock.get + return int(method.call_count) + + +def _range_read_count(store_mock: AsyncMock) -> int: + """Number of coalesced chunk-data reads, regardless of sync/async pipeline.""" + method = store_mock.get_ranges_sync if _reads_are_sync(store_mock) else store_mock.get_ranges + return int(method.call_count) + + +def _fail_index_read(store_mock: AsyncMock) -> None: + """Simulate the shard-index load returning nothing, for the active path.""" + if _reads_are_sync(store_mock): + store_mock.get_sync.return_value = None + else: + store_mock.get.return_value = None + + +def _fail_chunk_reads( + store_mock: AsyncMock, key_absent_exc: type[Exception] = FileNotFoundError +) -> None: + """Simulate chunk-data loads failing (key absent), for the active path. + + Async get_ranges raises a BaseExceptionGroup; the sync get_ranges_sync mirrors + that contract, so both inject a FileNotFoundError-bearing group.""" + if _reads_are_sync(store_mock): + + def fail_sync(key: str, byte_ranges: Any, **kwargs: Any) -> Any: + raise BaseExceptionGroup("chunk read failed", [key_absent_exc(key)]) + + store_mock.get_ranges_sync = fail_sync + else: + + async def fail_async(key: str, byte_ranges: Any, **kwargs: Any) -> Any: + raise BaseExceptionGroup("chunk read failed", [key_absent_exc(key)]) + yield # type: ignore[unreachable] # marks this as an async generator + + store_mock.get_ranges = fail_async + + @pytest.mark.parametrize("store", ["local", "memory", "zip"], indirect=["store"]) @pytest.mark.parametrize("index_location", ["start", "end"]) @pytest.mark.parametrize( @@ -241,18 +299,18 @@ def test_sharding_multiple_chunks_partial_shard_read( # for a total of 6 chunks accessed assert np.allclose(a[0, 22:42], np.arange(22, 42, dtype="float32")) - # 2 shard index reads via store.get() + 2 get_ranges calls (one per shard) - assert store_mock.get.call_count == 2 - assert store_mock.get_ranges.call_count == 2 + # 2 shard index reads + 2 coalesced chunk-data reads (one per shard) + assert _index_read_count(store_mock) == 2 + assert _range_read_count(store_mock) == 2 store_mock.reset_mock() # Reads 4 chunks from both shards along dimension 0 for a total of 8 chunks accessed assert np.allclose(a[:, 0], np.arange(0, data.size, array_shape[1], dtype="float32")) - # 2 shard index reads via store.get() + 2 get_ranges calls (one per shard) - assert store_mock.get.call_count == 2 - assert store_mock.get_ranges.call_count == 2 + # 2 shard index reads + 2 coalesced chunk-data reads (one per shard) + assert _index_read_count(store_mock) == 2 + assert _range_read_count(store_mock) == 2 @pytest.mark.parametrize("index_location", ["start", "end"]) @@ -288,9 +346,9 @@ def test_sharding_duplicate_read_indexes( indexer = [8, 8, 12, 12] assert np.array_equal(a[indexer], data[indexer]) - # 1 shard index read via store.get() + 1 get_ranges call - assert store_mock.get.call_count == 1 - assert store_mock.get_ranges.call_count == 1 + # 1 shard index read + 1 coalesced chunk-data read + assert _index_read_count(store_mock) == 1 + assert _range_read_count(store_mock) == 1 @pytest.mark.parametrize("index_location", ["start", "end"]) @@ -379,8 +437,6 @@ def test_sharding_partial_shard_read__index_load_fails( fill_value = -999 store_mock = AsyncMock(wraps=store, spec=store.__class__) - # loading the index is the first call to .get() so returning None will simulate an index load failure - store_mock.get.return_value = None a = zarr.create_array( StorePath(store_mock), @@ -393,6 +449,10 @@ def test_sharding_partial_shard_read__index_load_fails( ) a[:] = data + # Loading the index returns None -> simulate an index load failure, on + # whichever read method the active pipeline uses (get / get_sync). + _fail_index_read(store_mock) + # Read from one of two chunks in a shard to test the partial shard read path assert a[0] == fill_value assert a[0] != data[0] @@ -459,16 +519,12 @@ def test_sharding_partial_shard_read__chunk_load_fails( a[:] = data # Set up store mock after array creation to simulate chunk load failure. - # Index loads still succeed (via store.get), but chunk-byte loads fail - # (via store.get_ranges raising BaseExceptionGroup containing FileNotFoundError — - # the same shape Store.get_ranges produces when a key is absent). + # Index loads still succeed, but chunk-byte loads fail (the coalesced range + # read raises a BaseExceptionGroup containing FileNotFoundError — the same + # shape produced when a key is absent), on whichever read method the active + # pipeline uses (get_ranges / get_ranges_sync). store_mock.reset_mock() - - async def fail_chunk_reads(key: str, byte_ranges: Any, **kwargs: Any) -> Any: - raise BaseExceptionGroup("chunk read failed", [FileNotFoundError(key)]) - yield # type: ignore[unreachable] # marks this as an async generator - - store_mock.get_ranges = fail_chunk_reads + _fail_chunk_reads(store_mock) # Read from one of two chunks in a shard to test the partial shard read path assert a[0] == fill_value @@ -1112,6 +1168,43 @@ def test_shard_index_get_chunk_slices_vectorized(chunks_per_shard: tuple[int, .. np.testing.assert_array_equal(starts[~expected_valid], MAX_UINT_64) +@pytest.mark.filterwarnings("ignore::zarr.core.dtype.common.UnstableSpecificationWarning") +@pytest.mark.parametrize( + "pipeline_path", + [ + "zarr.core.codec_pipeline.FusedCodecPipeline", + "zarr.core.codec_pipeline.BatchedCodecPipeline", + ], +) +def test_sharding_vlen_inner_codec_roundtrip(pipeline_path: str) -> None: + """A sharded array whose inner codec chain is a variable-length codec + (VLenUTF8) must round-trip under either pipeline. + + Regression: the Fused pipeline's bulk-decode gate calls `c.is_fixed_size` + on every inner codec. `is_fixed_size` is declared on the Codec ABC but had + no default, so codecs that don't set it (VLenUTF8/VLenBytes, numcodecs + wrappers) raised AttributeError on read — crashing every sharded read whose + inner chain included such a codec. + """ + # The variable-length StringDType resolves to a VLenUTF8Codec inner chain + # (a fixed-width <U dtype would use BytesCodec, which has is_fixed_size). + data = np.array(["aa", "bbbb", "c", "dddddd", "ee", "f"], dtype=np.dtypes.StringDType()) + with zarr.config.set({"codec_pipeline.path": pipeline_path}): + arr = zarr.create_array( + store=MemoryStore(), + shape=(6,), + chunks=(2,), + shards=(6,), + dtype=data.dtype, + fill_value="", + ) + arr[:] = data + # full read (would hit the bulk-decode gate under Fused) ... + assert np.array_equal(arr[:], data) + # ... and a reordering read (partial-decode path) + assert np.array_equal(arr.vindex[np.array([5, 4, 3, 2, 1, 0])], data[[5, 4, 3, 2, 1, 0]]) + + @pytest.mark.parametrize("chunks_per_shard", [(), (3,), (2, 3)]) def test_shard_reader_to_dict_vectorized(chunks_per_shard: tuple[int, ...]) -> None: """to_dict_vectorized derives its own coords and maps present chunks to buffers, empty to None. diff --git a/tests/test_codecs/test_sharding_unit.py b/tests/test_codecs/test_sharding_unit.py index 2e3872e7a6..34d468fa05 100644 --- a/tests/test_codecs/test_sharding_unit.py +++ b/tests/test_codecs/test_sharding_unit.py @@ -1,11 +1,17 @@ from __future__ import annotations -from typing import TYPE_CHECKING, cast +import asyncio +from dataclasses import dataclass, replace +from typing import TYPE_CHECKING, Any, cast from unittest.mock import AsyncMock import numpy as np import pytest +from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec +from zarr.codecs.bytes import BytesCodec +from zarr.codecs.crc32c_ import Crc32cCodec +from zarr.codecs.gzip import GzipCodec from zarr.codecs.sharding import ( MAX_UINT_64, ShardingCodec, @@ -13,9 +19,13 @@ _ShardingByteGetter, _ShardReader, ) -from zarr.core.buffer import default_buffer_prototype +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import Buffer as ABCBuffer +from zarr.core.buffer import NDBuffer, default_buffer_prototype from zarr.core.buffer.cpu import Buffer +from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer from zarr.core.config import config +from zarr.core.dtype import get_data_type_from_native_dtype from zarr.storage._common import StorePath from zarr.storage._memory import MemoryStore @@ -514,6 +524,257 @@ def test_is_total_shard_1d() -> None: assert codec._is_total_shard(partial_coords, chunks_per_shard) is False +# ============================================================================ +# _inner_codecs_fixed_size tests +# ============================================================================ + + +def test_inner_codecs_fixed_size_no_compression() -> None: + """Inner codecs without compression should be fixed-size.""" + codec = ShardingCodec(chunk_shape=(10,), codecs=[BytesCodec()]) + assert codec._inner_codecs_fixed_size is True + + +def test_inner_codecs_fixed_size_with_compression() -> None: + """Inner codecs with compression should NOT be fixed-size.""" + codec = ShardingCodec(chunk_shape=(10,), codecs=[BytesCodec(), GzipCodec()]) + assert codec._inner_codecs_fixed_size is False + + +# ============================================================================ +# inner-chain spec threading +# ============================================================================ + + +@dataclass(frozen=True) +class _WidenToInt16(ArrayArrayCodec): + """Test-only sync-capable AA codec that reports its output dtype as int16.""" + + is_fixed_size = True + + def to_dict(self) -> dict[str, Any]: + return {"name": "_widen_to_int16"} + + @classmethod + def from_dict(cls, data: dict[str, Any]) -> _WidenToInt16: + return cls() + + def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: + return replace(chunk_spec, dtype=get_data_type_from_native_dtype(np.dtype("int16"))) + + def compute_encoded_size(self, input_byte_length: int, _spec: ArraySpec) -> int: + return input_byte_length + + def _encode_sync(self, chunk_array: Any, chunk_spec: ArraySpec) -> Any: + return chunk_array # pragma: no cover + + def _decode_sync(self, chunk_array: Any, chunk_spec: ArraySpec) -> Any: + return chunk_array # pragma: no cover + + async def _encode_single(self, chunk_array: Any, chunk_spec: ArraySpec) -> Any: + return chunk_array # pragma: no cover + + async def _decode_single(self, chunk_array: Any, chunk_spec: ArraySpec) -> Any: + return chunk_array # pragma: no cover + + +def _int8_spec(shape: tuple[int, ...]) -> ArraySpec: + zdtype = get_data_type_from_native_dtype(np.dtype("int8")) # single-byte source + return ArraySpec( + shape=shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=False), + prototype=default_buffer_prototype(), + ) + + +def test_inner_chunk_transform_threads_spec() -> None: + """The inner codec chain must be evolved with the spec threaded forward. + + A dtype-widening inner array->array codec means the BytesCodec serializer + is evolved against the WIDENED dtype, not the single-byte source — + otherwise it strips its `endian` to None and fails to decode multi-byte + inner chunks. Same contract as the pipeline-level `evolve_codecs` + regression test, applied to `_get_inner_chunk_transform`. + """ + codec = ShardingCodec(chunk_shape=(4,), codecs=[_WidenToInt16(), BytesCodec(endian="little")]) + shard_spec = _int8_spec((8,)) + + transform = codec._get_inner_chunk_transform(shard_spec) + serializer = transform._ab_codec + assert isinstance(serializer, BytesCodec) + assert serializer.endian is not None, ( + "inner BytesCodec lost its `endian` — _get_inner_chunk_transform did not " + "thread the dtype-widening codec's spec into the serializer" + ) + + +def test_evolve_from_array_spec_threads_spec() -> None: + """`ShardingCodec.evolve_from_array_spec` must thread the spec through the + inner chain, like `_get_inner_chunk_transform` does. + + This method runs EARLIER, on the real array-creation path (the outer + pipeline evolves the sharding codec itself), so an unthreaded evolve here + bakes an endian-stripped BytesCodec into the evolved instance's `codecs` + before the transform builders ever run — and the later threaded evolve then + raises instead of recovering. Calling `_get_inner_chunk_transform` on the + EVOLVED instance pins the full real path. + """ + codec = ShardingCodec(chunk_shape=(4,), codecs=[_WidenToInt16(), BytesCodec(endian="little")]) + # the array spec the OUTER pipeline evolves the sharding codec against + array_spec = _int8_spec((8,)) + + evolved = codec.evolve_from_array_spec(array_spec) + inner_serializer = next(c for c in evolved.codecs if isinstance(c, BytesCodec)) + assert inner_serializer.endian is not None, ( + "evolve_from_array_spec evolved the inner BytesCodec against the " + "un-widened spec, stripping its `endian`" + ) + + # and the evolved instance must still build a working inner transform + transform = evolved._get_inner_chunk_transform(array_spec) + serializer = transform._ab_codec + assert isinstance(serializer, BytesCodec) + assert serializer.endian is not None + + +# ============================================================================ +# async whole-shard codec methods +# +# `ShardingCodec` advertises partial decode/encode, so the codec pipeline +# always routes sharded reads/writes through `_decode_partial_single` / +# `_encode_partial_single`. The whole-shard async methods `_decode_single` / +# `_encode_single` are reached only via the direct `ArrayBytesCodec` API (e.g. +# a consumer that calls the codec outside a pipeline), so they get no coverage +# from end-to-end array tests. Pin them with a direct round-trip. +# ============================================================================ + + +@pytest.mark.parametrize("write_empty_chunks", [True, False]) +def test_decode_single_encode_single_roundtrip(write_empty_chunks: bool) -> None: + """`ShardingCodec._encode_single` then `_decode_single` round-trips a whole + shard. Covers the async whole-shard path the pipeline bypasses in favor of + the partial methods.""" + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + spec = ArraySpec( + shape=(50,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=write_empty_chunks), + prototype=default_buffer_prototype(), + ) + codec = ShardingCodec(chunk_shape=(10,), codecs=[BytesCodec()]) + data = np.arange(50, dtype="float64") + value = CPUNDBuffer.from_numpy_array(data) + + encoded = asyncio.run(codec._encode_single(value, spec)) + assert encoded is not None # data is non-empty -> a shard is always produced + decoded = asyncio.run(codec._decode_single(encoded, spec)) + np.testing.assert_array_equal(decoded.as_numpy_array(), data) + + +def test_encode_single_all_empty_returns_none() -> None: + """`_encode_single` of an all-fill shard under write_empty_chunks=False + elides every inner chunk and returns None (the all-empty branch).""" + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + spec = ArraySpec( + shape=(50,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=False), + prototype=default_buffer_prototype(), + ) + codec = ShardingCodec(chunk_shape=(10,), codecs=[BytesCodec()]) + fill = CPUNDBuffer.from_numpy_array(np.zeros(50, dtype="float64")) + + assert asyncio.run(codec._encode_single(fill, spec)) is None + + +def test_decode_single_all_empty_fills() -> None: + """`_decode_single` of a shard whose index is all-empty fills the output + with the fill value (the is_all_empty fast path).""" + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + spec = ArraySpec( + shape=(50,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(-1.0), + config=ArrayConfig(order="C", write_empty_chunks=False), + prototype=default_buffer_prototype(), + ) + codec = ShardingCodec(chunk_shape=(10,), codecs=[BytesCodec()]) + # an empty shard is just the encoded empty index + empty_index = asyncio.run(codec._encode_shard_index(_ShardIndex.create_empty((5,)))) + decoded = asyncio.run(codec._decode_single(empty_index, spec)) + np.testing.assert_array_equal(decoded.as_numpy_array(), np.full(50, -1.0)) + + +# ============================================================================ +# async-only index codec fallback (#269) +# +# `_decode_shard_index` / `_encode_shard_index` delegate to their sync twins +# when every index codec is sync-capable, and otherwise fall back to the async +# pipeline. The default index chain (bytes + crc32c) is sync-capable, so the +# fallback is exercised only by an async-only index codec. +# ============================================================================ + + +class _AsyncOnlyBytesCodec(ArrayBytesCodec): + """An array<->bytes codec that implements ONLY the async per-chunk methods. + + Wraps a real `BytesCodec` for the actual conversion but deliberately omits + `_encode_sync`/`_decode_sync`, so it is NOT a `SupportsSyncCodec`. Used as + an index codec to force the async-pipeline fallback in + `_decode_shard_index`/`_encode_shard_index`. + """ + + _inner = BytesCodec() + + def to_dict(self) -> dict[str, Any]: + return {"name": "_async_only_bytes"} + + @classmethod + def from_dict(cls, data: dict[str, Any]) -> _AsyncOnlyBytesCodec: + return cls() + + def evolve_from_array_spec(self, array_spec: ArraySpec) -> _AsyncOnlyBytesCodec: + return self + + def compute_encoded_size(self, input_byte_length: int, _spec: ArraySpec) -> int: + return input_byte_length + + async def _decode_single(self, chunk_bytes: ABCBuffer, chunk_spec: ArraySpec) -> NDBuffer: + return await self._inner._decode_single(chunk_bytes, chunk_spec) + + async def _encode_single(self, chunk_array: NDBuffer, chunk_spec: ArraySpec) -> ABCBuffer: + result = await self._inner._encode_single(chunk_array, chunk_spec) + assert result is not None + return result + + +def test_shard_index_async_fallback_for_async_only_index_codec() -> None: + """An async-only index codec is not sync-capable, so `_encode_shard_index` + and `_decode_shard_index` must take the async-pipeline fallback (#269) + instead of the sync twins — and still round-trip.""" + from zarr.abc.codec import SupportsSyncCodec + + codec = ShardingCodec( + chunk_shape=(10,), + codecs=[BytesCodec()], + index_codecs=[_AsyncOnlyBytesCodec(), Crc32cCodec()], + ) + assert not codec._index_codecs_sync_capable() + assert not isinstance(_AsyncOnlyBytesCodec(), SupportsSyncCodec) + + chunks_per_shard = (5,) + index = _ShardIndex.create_empty(chunks_per_shard) + index.set_chunk_slice((0,), slice(0, 42)) + + encoded = asyncio.run(codec._encode_shard_index(index)) + decoded = asyncio.run(codec._decode_shard_index(encoded, chunks_per_shard)) + np.testing.assert_array_equal(decoded.offsets_and_lengths, index.offsets_and_lengths) + + # ============================================================================ # Coalescing config option tests # diff --git a/tests/test_config.py b/tests/test_config.py index a758378dc7..47f71a798e 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -66,6 +66,7 @@ def test_config_defaults_set() -> None: "codec_pipeline": { "path": "zarr.core.codec_pipeline.BatchedCodecPipeline", "batch_size": 1, + "max_workers": None, }, "codecs": { "blosc": "zarr.codecs.blosc.BloscCodec", @@ -156,7 +157,7 @@ def test_config_codec_pipeline_class(store: Store) -> None: # has default value assert get_pipeline_class().__name__ != "" - config.set({"codec_pipeline.name": "zarr.core.codec_pipeline.BatchedCodecPipeline"}) + config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.BatchedCodecPipeline"}) assert get_pipeline_class() == zarr.core.codec_pipeline.BatchedCodecPipeline _mock = Mock() @@ -211,10 +212,19 @@ def test_config_codec_implementation(store: Store) -> None: _mock = Mock() class MockBloscCodec(BloscCodec): + # Record a call from whichever encode entry point the active codec + # pipeline uses: the async `_encode_single` (BatchedCodecPipeline, the + # default) or the synchronous `_encode_sync` (FusedCodecPipeline). + # Overriding both keeps this test ("the configured codec is actually + # used") independent of which pipeline is the default. async def _encode_single(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> Buffer | None: _mock.call() return None + def _encode_sync(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> Buffer | None: + _mock.call() + return None + register_codec("blosc", MockBloscCodec) with config.set({"codecs.blosc": fully_qualified_name(MockBloscCodec)}): assert get_codec_class("blosc") == MockBloscCodec diff --git a/tests/test_fastpath_equivalence.py b/tests/test_fastpath_equivalence.py new file mode 100644 index 0000000000..317b8742f1 --- /dev/null +++ b/tests/test_fastpath_equivalence.py @@ -0,0 +1,382 @@ +"""Property tests: every fast path must equal the general path. + +The codec pipelines contain fast paths that skip work whose result is known — +the complete-chunk merge view, the vectorized whole-shard bulk decode, the +scalar-broadcast write memoization, byte-range coalescing. Each is only safe if +it produces results identical to the general path it bypasses. These tests pin +that equivalence on randomized inputs, so a fast path that silently diverges +(the bug class behind the bulk-decode endianness fix) fails here instead of +corrupting data downstream. + +Convention for new fast paths: a fast path is "skip work whose result is +known", never "a different algorithm" — and it ships with a property test in +this module asserting equality with the general path. +""" + +from __future__ import annotations + +from typing import Any + +import hypothesis.extra.numpy as npst +import hypothesis.strategies as st +import numpy as np +from hypothesis import given, settings + +import zarr +from zarr.abc.store import OffsetByteRequest, RangeByteRequest, SuffixByteRequest +from zarr.codecs.bytes import BytesCodec +from zarr.codecs.sharding import ShardingCodec +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import default_buffer_prototype +from zarr.core.buffer.cpu import Buffer as CPUBuffer +from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer +from zarr.core.chunk_grids import ChunkGrid +from zarr.core.chunk_utils import _merge_chunk_array +from zarr.core.dtype import get_data_type_from_native_dtype +from zarr.core.indexing import BasicIndexer +from zarr.storage import MemoryStore + +_DTYPES = st.sampled_from(["uint8", "int16", "float32"]) + + +def _spec(shape: tuple[int, ...], dtype: str, *, write_empty_chunks: bool = True) -> ArraySpec: + zdtype = get_data_type_from_native_dtype(np.dtype(dtype)) + return ArraySpec( + shape=shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=write_empty_chunks), + prototype=default_buffer_prototype(), + ) + + +# --------------------------------------------------------------------------- +# _merge_chunk_array: the complete-chunk early return (a view of +# value[out_selection]) must equal the general create/copy + setitem path. +# --------------------------------------------------------------------------- + + +@st.composite +def _merge_cases(draw: st.DrawFn) -> tuple[np.ndarray, tuple[int, ...], tuple[slice, ...]]: + ndim = draw(st.integers(1, 3)) + chunk_shape = tuple(draw(st.integers(1, 5)) for _ in range(ndim)) + n_blocks = draw(st.integers(1, 3)) + dtype = draw(_DTYPES) + # value spans n_blocks chunk-sized blocks along axis 0; out_selection picks one + value_shape = (chunk_shape[0] * n_blocks, *chunk_shape[1:]) + value = draw(npst.arrays(dtype=np.dtype(dtype), shape=value_shape)) + block = draw(st.integers(0, n_blocks - 1)) + out_selection = ( + slice(block * chunk_shape[0], (block + 1) * chunk_shape[0]), + *(slice(0, s) for s in chunk_shape[1:]), + ) + return value, chunk_shape, out_selection + + +@settings(max_examples=200, deadline=None) +@given(case=_merge_cases(), with_existing=st.booleans()) +def test_merge_complete_chunk_equals_general_path( + case: tuple[np.ndarray, tuple[int, ...], tuple[slice, ...]], with_existing: bool +) -> None: + """The is_complete_chunk fast path (return a view of value[out_selection]) + must produce exactly what the general merge path produces — and a complete + write must be independent of any existing chunk content.""" + value_np, chunk_shape, out_selection = case + spec = _spec(chunk_shape, str(value_np.dtype)) + value = CPUNDBuffer.from_numpy_array(value_np) + chunk_selection = tuple(slice(0, s) for s in chunk_shape) + + existing = None + if with_existing: + existing = CPUNDBuffer.from_numpy_array(np.full(chunk_shape, 7, dtype=value_np.dtype)) + + fast = _merge_chunk_array(existing, value, out_selection, spec, chunk_selection, True, ()) + general = _merge_chunk_array(existing, value, out_selection, spec, chunk_selection, False, ()) + np.testing.assert_array_equal(fast.as_numpy_array(), general.as_numpy_array()) + np.testing.assert_array_equal(fast.as_numpy_array(), value_np[out_selection]) + + +# --------------------------------------------------------------------------- +# _decode_full_shard_bulk_if_uncompressed: the vectorized dense-shard decode must equal the +# general per-chunk decode (_decode_sync), across dtypes, endianness, write +# orders, and index locations. This is the bug class of the historical +# bulk-decode endianness fix. +# --------------------------------------------------------------------------- + + +@st.composite +def _shard_cases(draw: st.DrawFn) -> dict[str, Any]: + ndim = draw(st.integers(1, 2)) + chunk_shape = tuple(draw(st.integers(1, 4)) for _ in range(ndim)) + grid = tuple(draw(st.integers(1, 3)) for _ in range(ndim)) + shard_shape = tuple(c * g for c, g in zip(chunk_shape, grid, strict=True)) + dtype = draw(_DTYPES) + data = draw(npst.arrays(dtype=np.dtype(dtype), shape=shard_shape)) + return { + "chunk_shape": chunk_shape, + "shard_shape": shard_shape, + "data": data, + "endian": draw(st.sampled_from(["little", "big"])), + "index_location": draw(st.sampled_from(["start", "end"])), + "subchunk_write_order": draw( + st.sampled_from(["morton", "lexicographic", "colexicographic", "unordered"]) + ), + } + + +@settings(max_examples=100, deadline=None) +@given(case=_shard_cases()) +def test_bulk_shard_decode_equals_general_decode(case: dict[str, Any]) -> None: + """For dense fixed-size uncompressed shards, the vectorized bulk decode must + reproduce the general per-chunk decode exactly, whatever the endianness, + subchunk write order, or index location.""" + codec = ShardingCodec( + chunk_shape=case["chunk_shape"], + codecs=[BytesCodec(endian=case["endian"])], + index_location=case["index_location"], + subchunk_write_order=case["subchunk_write_order"], + ) + spec = _spec(case["shard_shape"], str(case["data"].dtype), write_empty_chunks=True) + blob = codec._encode_sync(CPUNDBuffer.from_numpy_array(case["data"]), spec) + assert blob is not None # write_empty_chunks=True -> dense, never elided + + general = codec._decode_sync(blob, spec) + indexer = BasicIndexer( + tuple(slice(0, s) for s in case["shard_shape"]), + shape=case["shard_shape"], + chunk_grid=ChunkGrid.from_sizes(case["shard_shape"], case["chunk_shape"]), + ) + bulk = codec._decode_full_shard_bulk_if_uncompressed(blob, spec, indexer) + # the fast path must APPLY for this dense uncompressed configuration — + # a vacuous None would silently stop testing the equivalence + assert bulk is not None + np.testing.assert_array_equal(bulk.as_numpy_array(), general.as_numpy_array()) + np.testing.assert_array_equal(general.as_numpy_array(), case["data"]) + + +def test_merge_complete_chunk_returns_view_and_write_does_not_mutate_source() -> None: + """The complete-chunk merge fast path returns a VIEW of the caller's value + (no copy — that is the perf win), and a multi-chunk write through either + pipeline leaves the user's source array untouched. + + Pins both halves of the aliasing contract: a future "defensive copy" + refactor that silently reintroduces the per-chunk create/fill/copy breaks + the first assertion, and an in-place-mutating codec that corrupts the + user's array through the shared view breaks the second. + """ + # the fast path must return a view aliasing `value`, not a copy + value_np = np.arange(30, dtype="uint16") + spec = _spec((10,), "uint16") + value = CPUNDBuffer.from_numpy_array(value_np) + merged = _merge_chunk_array(None, value, (slice(10, 20),), spec, (slice(0, 10),), True, ()) + assert np.shares_memory(merged.as_numpy_array(), value_np), ( + "complete-chunk merge no longer returns a view of the caller's value" + ) + + # end-to-end: the source array is byte-identical after a multi-chunk write + for pipeline_path in ( + "zarr.core.codec_pipeline.FusedCodecPipeline", + "zarr.core.codec_pipeline.BatchedCodecPipeline", + ): + with zarr.config.set({"codec_pipeline.path": pipeline_path}): + arr = zarr.create_array( + store=MemoryStore(), + shape=(30,), + chunks=(10,), + dtype="uint16", + compressors=None, + fill_value=0, + ) + source = np.arange(30, dtype="uint16") + snapshot = source.copy() + arr[:] = source + np.testing.assert_array_equal(source, snapshot, err_msg=pipeline_path) + np.testing.assert_array_equal(arr[:], snapshot, err_msg=pipeline_path) + + +# --------------------------------------------------------------------------- +# Whole-shard bulk decode under arbitrary indexing: the bulk decode only fires +# for a *contiguous full-shard* read, but it is reached through the partial-read +# path (`_decode_partial_sync`), whose only gate is `indexer.shape == +# shard_spec.shape`. A reordering coordinate/orthogonal selection that happens +# to touch every chunk (so the flattened point count equals the shard shape) +# must NOT be served by the bulk path in natural order — it must honor the +# selection. This pins the END-TO-END read (the gate lives in the array read +# path, not in `_decode_full_shard_bulk_if_uncompressed` itself), which +# `test_bulk_shard_decode_equals_general_decode` (BasicIndexer only) cannot +# reach. See the vindex-on-uncompressed-shard corruption bug. +# --------------------------------------------------------------------------- + + +@st.composite +def _uncompressed_shard_index_cases(draw: st.DrawFn) -> dict[str, Any]: + # 1-D is where the trigger is easiest: a CoordinateIndexer's `.shape` is the + # flattened point count, which equals a 1-D shard shape exactly when the + # selection visits `shard_len` points. + chunk = draw(st.integers(1, 4)) + grid = draw(st.integers(1, 4)) + shard_len = chunk * grid + dtype = draw(_DTYPES) + data = draw(npst.arrays(dtype=np.dtype(dtype), shape=(shard_len,))) + perm = draw(st.permutations(list(range(shard_len)))) + return { + "chunk": chunk, + "shard_len": shard_len, + "data": data, + "perm": np.array(perm), + "endian": draw(st.sampled_from(["little", "big"])), + "index_location": draw(st.sampled_from(["start", "end"])), + "subchunk_write_order": draw( + st.sampled_from(["morton", "lexicographic", "colexicographic", "unordered"]) + ), + } + + +@settings(max_examples=200, deadline=None) +@given(case=_uncompressed_shard_index_cases()) +def test_reordering_read_on_uncompressed_shard_honors_selection(case: dict[str, Any]) -> None: + """A reordering vindex/oindex over a full uncompressed shard must return the + permuted data, not the shard in natural order — under the Fused pipeline + (where the bulk-decode fast path engages) exactly as under numpy.""" + perm = case["perm"] + data = case["data"] + serializer = BytesCodec(endian=case["endian"]) + + with zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): + arr = zarr.create_array( + store=MemoryStore(), + shape=(case["shard_len"],), + chunks=(case["chunk"],), + shards=(case["shard_len"],), + dtype=data.dtype, + serializer=serializer, + compressors=None, + filters=None, + fill_value=0, + ) + arr[:] = data + + # vindex with a full-coverage permutation: flattened point count == + # shard shape, so the buggy gate would mis-classify this as a contiguous + # full-shard read and return data unpermuted. + np.testing.assert_array_equal(arr.vindex[perm], data[perm]) + # oindex with a single reordering index list along the only axis. + np.testing.assert_array_equal(arr.oindex[perm], data[perm]) + + +# --------------------------------------------------------------------------- +# Scalar-broadcast write memoization: writing a scalar must produce the same +# STORED BYTES as writing the equivalent broadcast array. +# --------------------------------------------------------------------------- + + +@st.composite +def _scalar_cases(draw: st.DrawFn) -> dict[str, Any]: + n_chunks = draw(st.integers(2, 6)) + chunk = draw(st.integers(2, 6)) + shape = n_chunks * chunk + start = draw(st.integers(0, shape - 1)) + stop = draw(st.integers(start + 1, shape)) + return { + "shape": shape, + "chunk": chunk, + "sel": slice(start, stop), + "scalar": draw(st.integers(0, 255)), + "write_empty_chunks": draw(st.booleans()), + "sharded": draw(st.booleans()), + } + + +@settings(max_examples=100, deadline=None) +@given(case=_scalar_cases()) +def test_scalar_write_equals_broadcast_write(case: dict[str, Any]) -> None: + """arr[sel] = scalar and arr[sel] = full(sel_shape, scalar) must leave the + store byte-identical (pins the scalar-broadcast memoization in the sharded + partial-write path, incl. its empty-chunk normalization).""" + + def build() -> tuple[MemoryStore, zarr.Array[Any]]: + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(case["shape"],), + chunks=(case["chunk"],), + shards=(case["shape"],) if case["sharded"] else None, + dtype="uint8", + compressors=None, + fill_value=0, + config={"write_empty_chunks": case["write_empty_chunks"]}, + ) + return store, arr + + # The scalar-broadcast memoization lives in the Fused sync write path; pin it + # explicitly since Fused is no longer the default pipeline. + with zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): + store_a, arr_a = build() + arr_a[case["sel"]] = case["scalar"] + + store_b, arr_b = build() + n = case["sel"].stop - case["sel"].start + arr_b[case["sel"]] = np.full(n, case["scalar"], dtype="uint8") + + keys_a = {k: bytes(v.to_bytes()) for k, v in store_a._store_dict.items()} + keys_b = {k: bytes(v.to_bytes()) for k, v in store_b._store_dict.items()} + assert keys_a == keys_b + + +# --------------------------------------------------------------------------- +# get_ranges_sync coalescing: merged fetches must return exactly what +# individual per-range gets return, for any gap/coalesce limits. +# --------------------------------------------------------------------------- + + +@st.composite +def _range_cases(draw: st.DrawFn) -> dict[str, Any]: + blob_len = draw(st.integers(1, 200)) + n = draw(st.integers(1, 8)) + ranges: list[RangeByteRequest | OffsetByteRequest | SuffixByteRequest | None] = [] + for _ in range(n): + kind = draw(st.sampled_from(["range", "offset", "suffix", "none"])) + if kind == "range": + start = draw(st.integers(0, blob_len - 1)) + end = draw(st.integers(start + 1, blob_len)) + ranges.append(RangeByteRequest(start, end)) + elif kind == "offset": + ranges.append(OffsetByteRequest(draw(st.integers(0, blob_len - 1)))) + elif kind == "suffix": + ranges.append(SuffixByteRequest(draw(st.integers(1, blob_len)))) + else: + ranges.append(None) + return { + "blob": draw(st.binary(min_size=blob_len, max_size=blob_len)), + "ranges": ranges, + "max_gap": draw(st.integers(0, 64)), + "max_coalesced": draw(st.integers(1, 512)), + } + + +@settings(max_examples=200, deadline=None) +@given(case=_range_cases()) +def test_get_ranges_sync_equals_individual_gets(case: dict[str, Any]) -> None: + """Coalesced byte-range reads must return exactly what one get_sync per + range returns — for any gap/coalesce limits (the offset re-slicing math is + where a coalescing bug would corrupt data).""" + store = MemoryStore() + store._is_open = True + proto = default_buffer_prototype() + store._store_dict["k"] = CPUBuffer.from_bytes(case["blob"]) + + expected = [store.get_sync("k", prototype=proto, byte_range=r) for r in case["ranges"]] + + got: dict[int, bytes | None] = {} + for idx, buf in store.get_ranges_sync( + "k", + case["ranges"], + prototype=proto, + max_gap_bytes=case["max_gap"], + max_coalesced_bytes=case["max_coalesced"], + ): + got[idx] = None if buf is None else bytes(buf.to_bytes()) + + for i, exp in enumerate(expected): + exp_bytes = None if exp is None else bytes(exp.to_bytes()) + assert got.get(i) == exp_bytes, f"range {i} ({case['ranges'][i]!r}) mismatch" diff --git a/tests/test_fused_pipeline.py b/tests/test_fused_pipeline.py new file mode 100644 index 0000000000..73c2c6e1c3 --- /dev/null +++ b/tests/test_fused_pipeline.py @@ -0,0 +1,684 @@ +"""Tests for FusedCodecPipeline -- the per-chunk-fused codec pipeline.""" + +from __future__ import annotations + +from typing import Any + +import numpy as np +import pytest + +import zarr +from zarr.codecs.bytes import BytesCodec +from zarr.codecs.gzip import GzipCodec +from zarr.codecs.transpose import TransposeCodec +from zarr.codecs.zstd import ZstdCodec +from zarr.core.codec_pipeline import FusedCodecPipeline +from zarr.core.config import config as zarr_config +from zarr.storage import MemoryStore, StorePath + + +@pytest.mark.parametrize( + "codecs", + [ + (BytesCodec(),), + (BytesCodec(), GzipCodec(level=1)), + (BytesCodec(), ZstdCodec(level=1)), + (TransposeCodec(order=(1, 0)), BytesCodec()), + (TransposeCodec(order=(1, 0)), BytesCodec(), ZstdCodec(level=1)), + ], + ids=["bytes-only", "gzip", "zstd", "transpose", "transpose+zstd"], +) +def test_construction(codecs: tuple[Any, ...]) -> None: + """FusedCodecPipeline can be constructed from valid codec combinations.""" + pipeline = FusedCodecPipeline.from_codecs(codecs) + assert pipeline.codecs == codecs + + +def test_evolve_from_array_spec() -> None: + """evolve_from_array_spec creates a sync transform.""" + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.dtype import get_data_type_from_native_dtype + + pipeline = FusedCodecPipeline.from_codecs((BytesCodec(),)) + assert pipeline.sync_transform is None + + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + spec = ArraySpec( + shape=(100,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + evolved = pipeline.evolve_from_array_spec(spec) + assert evolved.sync_transform is not None + + +# --------------------------------------------------------------------------- +# Sync path tests +# +# These exercise FusedCodecPipeline's synchronous API (write_sync / read_sync / +# sync_transform), which has no equivalent on BatchedCodecPipeline -- so they +# cannot live in the pipeline-agnostic CodecPipelineTests suite. The async +# roundtrip / fill-value behaviour is covered there (test_scenario) across both +# pipelines and sync/async stores. +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("dtype", "shape"), + [ + ("float64", (100,)), + ("float32", (50,)), + ("int32", (200,)), + ("float64", (10, 10)), + ], + ids=["f64-1d", "f32-1d", "i32-1d", "f64-2d"], +) +def test_read_write_sync_roundtrip(dtype: str, shape: tuple[int, ...]) -> None: + """Data written via write_sync can be read back via read_sync.""" + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer + from zarr.core.dtype import get_data_type_from_native_dtype + + store = MemoryStore() + zdtype = get_data_type_from_native_dtype(np.dtype(dtype)) + spec = ArraySpec( + shape=shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + + pipeline = FusedCodecPipeline.from_codecs((BytesCodec(),)) + pipeline = pipeline.evolve_from_array_spec(spec) + + data = np.arange(int(np.prod(shape)), dtype=dtype).reshape(shape) + value = CPUNDBuffer.from_numpy_array(data) + chunk_selection = tuple(slice(0, s) for s in shape) + out_selection = chunk_selection + store_path = StorePath(store, "c/0") + + # Write sync + pipeline.write_sync( + [(store_path, spec, chunk_selection, out_selection, True)], + value, + ) + + # Read sync + out = CPUNDBuffer.from_numpy_array(np.zeros(shape, dtype=dtype)) + pipeline.read_sync( + [(store_path, spec, chunk_selection, out_selection, True)], + out, + ) + + np.testing.assert_array_equal(data, out.as_numpy_array()) + + +def test_read_sync_missing_chunk_fills() -> None: + """Sync read of a missing chunk fills with the fill value.""" + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer + from zarr.core.dtype import get_data_type_from_native_dtype + + store = MemoryStore() + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + spec = ArraySpec( + shape=(10,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(42.0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + + pipeline = FusedCodecPipeline.from_codecs((BytesCodec(),)) + pipeline = pipeline.evolve_from_array_spec(spec) + + out = CPUNDBuffer.from_numpy_array(np.zeros(10, dtype="float64")) + store_path = StorePath(store, "c/0") + chunk_sel = (slice(0, 10),) + + pipeline.read_sync( + [(store_path, spec, chunk_sel, chunk_sel, True)], + out, + ) + + np.testing.assert_array_equal(out.as_numpy_array(), np.full(10, 42.0)) + + +def test_sync_write_async_read_roundtrip() -> None: + """Data written via write_sync can be read back via async read.""" + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer + from zarr.core.dtype import get_data_type_from_native_dtype + from zarr.core.sync import sync + + store = MemoryStore() + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + spec = ArraySpec( + shape=(100,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + + pipeline = FusedCodecPipeline.from_codecs((BytesCodec(),)) + pipeline = pipeline.evolve_from_array_spec(spec) + + data = np.arange(100, dtype="float64") + value = CPUNDBuffer.from_numpy_array(data) + chunk_sel = (slice(0, 100),) + store_path = StorePath(store, "c/0") + + # Write sync + pipeline.write_sync( + [(store_path, spec, chunk_sel, chunk_sel, True)], + value, + ) + + # Read async + out = CPUNDBuffer.from_numpy_array(np.zeros(100, dtype="float64")) + sync( + pipeline.read( + [(store_path, spec, chunk_sel, chunk_sel, True)], + out, + ) + ) + + +def test_chunk_transform_uses_runtime_prototype() -> None: + """ChunkTransform must pass each codec the prototype from the runtime chunk_spec, + not one captured at evolve time. Constructs ChunkTransform directly (a + Fused-internal data structure with no BatchedCodecPipeline equivalent). + """ + from zarr.abc.codec import BytesBytesCodec + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import Buffer, BufferPrototype, default_buffer_prototype + from zarr.core.chunk_utils import ChunkTransform + from zarr.core.dtype import get_data_type_from_native_dtype + + class _PrototypeRecordingCodec(BytesBytesCodec): # type: ignore[misc,unused-ignore] + """A no-op BB codec that records the prototype it was called with.""" + + is_fixed_size = True + seen_prototypes: list[object] + + def __init__(self) -> None: + object.__setattr__(self, "seen_prototypes", []) + + def to_dict(self) -> dict[str, Any]: + return {"name": "_prototype_recording", "configuration": {}} + + @classmethod + def from_dict(cls, data: dict[str, Any]) -> _PrototypeRecordingCodec: + return cls() + + def compute_encoded_size(self, input_byte_length: int, _spec: ArraySpec) -> int: + return input_byte_length + + def _encode_sync(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> Buffer | None: + self.seen_prototypes.append(chunk_spec.prototype) + return chunk_bytes + + def _decode_sync(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> Buffer: + self.seen_prototypes.append(chunk_spec.prototype) + return chunk_bytes + + async def _encode_single(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> Buffer | None: + return self._encode_sync(chunk_bytes, chunk_spec) + + async def _decode_single(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> Buffer: + return self._decode_sync(chunk_bytes, chunk_spec) + + recording = _PrototypeRecordingCodec() + transform = ChunkTransform(codecs=(BytesCodec(), recording)) + + zdtype = get_data_type_from_native_dtype(np.dtype("float64")) + + def _spec(prototype: BufferPrototype) -> ArraySpec: + return ArraySpec( + shape=(10,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0.0), + config=ArrayConfig(order="C", write_empty_chunks=False), + prototype=prototype, + ) + + proto_default = default_buffer_prototype() + # A distinct BufferPrototype instance with the same buffer/nd_buffer types -- + # fails an identity check but works at runtime. + proto_other = BufferPrototype(buffer=proto_default.buffer, nd_buffer=proto_default.nd_buffer) + assert proto_other is not proto_default + + arr = proto_default.nd_buffer.from_numpy_array(np.arange(10, dtype="float64")) + transform.encode_chunk(arr, _spec(proto_default)) + transform.encode_chunk(arr, _spec(proto_other)) + + assert recording.seen_prototypes[0] is proto_default + assert recording.seen_prototypes[1] is proto_other, ( + "ChunkTransform did not pass the runtime prototype to the codec" + ) + + +# --------------------------------------------------------------------------- +# Thread-pool (max_workers > 1) tests +# +# The pool dispatch in read_sync/write_sync is Fused-only and off by default +# (codec_pipeline.max_workers defaults to 1 == sequential). These tests opt in +# and exercise the pool path end-to-end, exception propagation from workers, +# and concurrent decode through the shared ChunkTransform. +# --------------------------------------------------------------------------- + +_FUSED_POOL_CONFIG = { + "codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline", + "codec_pipeline.max_workers": 4, +} + + +def test_read_write_with_thread_pool() -> None: + """With max_workers > 1, multi-chunk reads and writes dispatch through the + thread pool (pool.map in read_sync/write_sync) and produce the same results + as sequential execution. + + The `_get_pool` spy pins that the pool branch actually fires: without it, + a config-resolution regression (renamed key, `_resolve_max_workers` + returning 1) would silently degrade all the pool tests into re-testing the + sequential branch while staying green. + """ + from unittest.mock import patch + + import zarr.core.codec_pipeline as cp_mod + + with zarr_config.set(_FUSED_POOL_CONFIG): + assert cp_mod._resolve_max_workers() == 4, ( + "codec_pipeline.max_workers config did not reach _resolve_max_workers" + ) + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(100,), + chunks=(10,), + dtype="float64", + compressors=None, + fill_value=0.0, + ) + assert isinstance(arr._async_array.codec_pipeline, FusedCodecPipeline) + data = np.arange(100, dtype="float64") + with patch.object(cp_mod, "_get_pool", wraps=cp_mod._get_pool) as pool_spy: + arr[:] = data # 10 chunks -> pool dispatch in write_sync + assert pool_spy.call_count >= 1, "multi-chunk write did not take the pool branch" + writes = pool_spy.call_count + np.testing.assert_array_equal(arr[:], data) # pool dispatch in read_sync + assert pool_spy.call_count > writes, "multi-chunk read did not take the pool branch" + arr[5:25] = 7.0 # partial write: merge path through the pool + data[5:25] = 7.0 + np.testing.assert_array_equal(arr[:], data) + + +def test_thread_pool_write_worker_exception_propagates() -> None: + """A store error raised inside a pool worker during write_sync surfaces to + the caller (write_sync consumes pool.map, so worker exceptions re-raise).""" + from unittest.mock import patch + + with zarr_config.set(_FUSED_POOL_CONFIG): + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(100,), + chunks=(10,), + dtype="float64", + compressors=None, + fill_value=0.0, + ) + with ( + patch.object(store, "set_sync", side_effect=RuntimeError("simulated store error")), + pytest.raises(RuntimeError, match="simulated store error"), + ): + arr[:] = np.arange(100, dtype="float64") + + +def test_thread_pool_read_worker_exception_propagates() -> None: + """A store error raised inside a pool worker during read_sync surfaces to + the caller (read_sync consumes pool.map into a tuple).""" + from unittest.mock import patch + + with zarr_config.set(_FUSED_POOL_CONFIG): + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(100,), + chunks=(10,), + dtype="float64", + compressors=None, + fill_value=0.0, + ) + arr[:] = np.arange(100, dtype="float64") + with ( + patch.object(store, "get_sync", side_effect=RuntimeError("simulated store error")), + pytest.raises(RuntimeError, match="simulated store error"), + ): + arr[:] + + +def test_concurrent_reads_shared_transform_with_pool() -> None: + """Concurrent decode through the shared ChunkTransform produces correct data. + + The transform's `_resolve_specs` cache is shared mutable state. With no + array->array codecs the cache is bypassed entirely, so this uses a transpose + filter to force cache traffic, max_workers=4 so pool workers decode chunks + concurrently, and an outer thread pool so multiple reads are in flight at + once. Each round RE-OPENS the array so the shared transform starts with a + cold spec cache and the concurrent readers race the non-atomic first fill — + reading through a single pre-warmed handle would only ever exercise cache + hits. This pins correctness under concurrency (it cannot prove the absence + of a race, but a torn cache would corrupt results here). + """ + from concurrent.futures import ThreadPoolExecutor + + with zarr_config.set(_FUSED_POOL_CONFIG): + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(40, 40), + chunks=(5, 5), + dtype="int32", + filters=[TransposeCodec(order=(1, 0))], + serializer=BytesCodec(), + compressors=None, + fill_value=-1, + ) + data = np.arange(1600, dtype="int32").reshape(40, 40) + arr[:] = data + + for _ in range(5): # several rounds, each racing a cold cache + fresh = zarr.open_array(store=store, mode="r") + + def read_row_block(i: int, handle: zarr.Array[Any] = fresh) -> np.ndarray: + return np.asarray(handle[i * 4 : (i + 1) * 4, :]) + + with ThreadPoolExecutor(max_workers=8) as ex: + futures = {ex.submit(read_row_block, i): i for i in range(10)} + for fut, i in futures.items(): + np.testing.assert_array_equal(fut.result(), data[i * 4 : (i + 1) * 4, :]) + + +def test_shared_transform_decode_alternating_specs() -> None: + """A single ChunkTransform must decode chunks of DIFFERENT specs correctly + when calls alternate, exercising eviction/refill of its single-entry + `_resolve_specs` cache. + + The two specs differ in shape, so each call evicts the other's cached entry. + A transpose filter forces the cache to be used (with no AA codec the cache is + bypassed). The cache entry is stored as one atomic tuple precisely so a + concurrent reader can never observe a key paired with another spec's resolved + chain; this test pins the sequential eviction/refill correctness that + underpins that guarantee. (The concurrent counterpart is + `test_concurrent_reads_shared_transform_with_pool`.) + """ + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer + from zarr.core.chunk_utils import ChunkTransform + from zarr.core.dtype import get_data_type_from_native_dtype + + def _spec(shape: tuple[int, ...]) -> ArraySpec: + zdtype = get_data_type_from_native_dtype(np.dtype("int32")) + return ArraySpec( + shape=shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + + transform = ChunkTransform(codecs=(TransposeCodec(order=(1, 0)), BytesCodec())) + + # two distinct specs (different shapes) sharing the one transform + cache slot + cases = [] + for shape in [(5, 7), (3, 11)]: + spec = _spec(shape) + arr = np.arange(int(np.prod(shape)), dtype="int32").reshape(shape) + encoded = transform.encode_chunk(CPUNDBuffer.from_numpy_array(arr), spec) + assert encoded is not None + cases.append((spec, encoded, arr)) + + # Alternate specs so every call evicts and refills the single cache slot. + for i in range(20): + spec, encoded, expected = cases[i % len(cases)] + got = transform.decode_chunk(encoded, spec).as_numpy_array() + np.testing.assert_array_equal(got, expected) + + +def test_sharded_fallback_inner_chunks_avoid_async_transform() -> None: + """Inner chunks of a shard on a NON-sync store decode through the sync + ChunkTransform, not per-chunk AsyncChunkTransform coroutines. + + The sharding byte getters are in-memory dict wrappers; they implement + SyncByteGetter/SyncByteSetter, and the nested inner pipeline is evolved + (so its sync transform exists), letting the nested read/write take the + sync fast path. Without this, every inner chunk pays a coroutine for a + dict lookup plus an async per-chunk transform — measured at 1.5x (raw) to + 3.6x (gzip) of sharded fallback read time. + """ + from unittest.mock import patch + + from zarr.core.codec_pipeline import AsyncChunkTransform + from zarr.testing.store import LatencyStore + + calls = {"decode": 0, "encode": 0} + orig_decode = AsyncChunkTransform.decode_chunk + orig_encode = AsyncChunkTransform.encode_chunk + + async def spy_decode(self: Any, *args: Any, **kwargs: Any) -> Any: + calls["decode"] += 1 + return await orig_decode(self, *args, **kwargs) + + async def spy_encode(self: Any, *args: Any, **kwargs: Any) -> Any: + calls["encode"] += 1 + return await orig_encode(self, *args, **kwargs) + + # LatencyStore is not sync-capable -> the OUTER pipeline takes the async + # fallback; the INNER chunks go over the sharding byte getters. + store = LatencyStore(MemoryStore(), get_latency=0.0, set_latency=0.0) + arr = zarr.create_array( + store=store, + shape=(100,), + chunks=(10,), + shards=(50,), + dtype="uint8", + compressors=None, + fill_value=0, + ) + if not isinstance(arr._async_array.codec_pipeline, FusedCodecPipeline): + pytest.skip("sync fast path for inner chunks is specific to FusedCodecPipeline") + + data = np.arange(100, dtype="uint8") + sync_calls = {"read_sync": 0} + orig_read_sync = FusedCodecPipeline.read_sync + + def spy_read_sync(self: Any, *args: Any, **kwargs: Any) -> Any: + sync_calls["read_sync"] += 1 + return orig_read_sync(self, *args, **kwargs) + + with ( + patch.object(AsyncChunkTransform, "decode_chunk", spy_decode), + patch.object(AsyncChunkTransform, "encode_chunk", spy_encode), + patch.object(FusedCodecPipeline, "read_sync", spy_read_sync), + ): + arr[:] = data + out = np.asarray(arr[:]) + + np.testing.assert_array_equal(out, data) + assert calls == {"decode": 0, "encode": 0}, ( + f"inner chunks went through per-chunk AsyncChunkTransform coroutines: {calls}" + ) + # The outer store is not sync-capable, so any read_sync calls are the + # NESTED pipeline taking the sync fast path over the sharding byte getters + # (the SyncByteGetter gate). Without the gate, inner chunks go through + # concurrent_map with one coroutine per chunk. (Writes don't appear here: + # the fallback write encodes whole shards through the outer sync transform + # -> ShardingCodec._encode_sync, never touching the nested byte setters.) + assert sync_calls["read_sync"] >= 1, "nested read did not take the sync fast path" + + +def test_write_over_sync_byte_setter_takes_sync_path() -> None: + """`FusedCodecPipeline.write` routes a non-StorePath `SyncByteSetter` (the + sharding codec's `_ShardingByteSetter`) through `write_sync`. + + This is the write-side twin of the SyncByteGetter gate: the read test + above cannot guard it because fallback whole-array writes encode shards + via `_encode_sync` and never touch the nested byte setters. The nested + `write` over `_ShardingByteSetter` is reached from the async shard encode + paths (`_encode_single`/`_encode_partial_single`), so pin the gate + directly: without it, this write degrades to the async fallback (one + coroutine per inner chunk for an in-memory dict store). + """ + import asyncio + from unittest.mock import patch + + from zarr.codecs.sharding import _ShardingByteSetter + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.dtype import get_data_type_from_native_dtype + + zdtype = get_data_type_from_native_dtype(np.dtype("uint8")) + spec = ArraySpec( + shape=(10,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + pipeline = FusedCodecPipeline.from_codecs([BytesCodec()]).evolve_from_array_spec(spec) + assert pipeline.sync_transform is not None + + shard_dict: dict[tuple[int, ...], Any] = {} + setter = _ShardingByteSetter(shard_dict, (0,)) + value = default_buffer_prototype().nd_buffer.from_numpy_array(np.arange(10, dtype="uint8")) + + sync_calls = {"write_sync": 0} + orig_write_sync = FusedCodecPipeline.write_sync + + def spy_write_sync(self: Any, *args: Any, **kwargs: Any) -> Any: + sync_calls["write_sync"] += 1 + return orig_write_sync(self, *args, **kwargs) + + sel = (slice(0, 10),) + with patch.object(FusedCodecPipeline, "write_sync", spy_write_sync): + asyncio.run(pipeline.write([(setter, spec, sel, sel, True)], value)) + + assert sync_calls["write_sync"] >= 1, ( + "write over a SyncByteSetter did not take the sync fast path" + ) + written = shard_dict[(0,)] + np.testing.assert_array_equal( + np.frombuffer(written.to_bytes(), dtype="uint8"), np.arange(10, dtype="uint8") + ) + + +# --------------------------------------------------------------------------- +# AsyncChunkTransform: the async per-chunk codec chain used on the async +# fallback path. It is the async mirror of ChunkTransform, so it must produce +# identical bytes/arrays. The default (Fused, sync-store) path never uses it; +# these tests drive it directly over multi-codec chains so the aa/bb loops and +# the all-fill drop branch are exercised. +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + "codecs", + [ + (BytesCodec(),), + (BytesCodec(), GzipCodec(level=1)), + (TransposeCodec(order=(1, 0)), BytesCodec()), + (TransposeCodec(order=(1, 0)), BytesCodec(), ZstdCodec(level=1)), + ], + ids=["bytes-only", "bb", "aa", "aa+ab+bb"], +) +def test_async_chunk_transform_matches_sync(codecs: tuple[Any, ...]) -> None: + """`AsyncChunkTransform.decode_chunk`/`encode_chunk` must round-trip and + produce exactly what the synchronous `ChunkTransform` produces, across + array->array, array->bytes, and bytes->bytes codec combinations. + + This is the async mirror of the codecs the default pipeline runs + synchronously; a divergence here corrupts data only on the async fallback + path (remote stores), which no end-to-end test of the default pipeline + touches. + """ + import asyncio + + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer + from zarr.core.chunk_utils import ChunkTransform, evolve_codecs + from zarr.core.codec_pipeline import AsyncChunkTransform + from zarr.core.dtype import get_data_type_from_native_dtype + + shape = (4, 4) + zdtype = get_data_type_from_native_dtype(np.dtype("int32")) + spec = ArraySpec( + shape=shape, + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + evolved = evolve_codecs(codecs, spec) + sync_t = ChunkTransform(codecs=evolved) + async_t = AsyncChunkTransform(codecs=evolved) + + data = np.arange(16, dtype="int32").reshape(shape) + value = CPUNDBuffer.from_numpy_array(data) + + sync_bytes = sync_t.encode_chunk(value, spec) + async_bytes = asyncio.run(async_t.encode_chunk(value, spec)) + assert sync_bytes is not None + assert async_bytes is not None + np.testing.assert_array_equal(async_bytes.to_bytes(), sync_bytes.to_bytes()) + + sync_arr = sync_t.decode_chunk(async_bytes, spec) + async_arr = asyncio.run(async_t.decode_chunk(async_bytes, spec)) + np.testing.assert_array_equal(async_arr.as_numpy_array(), sync_arr.as_numpy_array()) + np.testing.assert_array_equal(async_arr.as_numpy_array(), data) + + +def test_async_decode_encode_passes_through_none_chunks() -> None: + """`FusedCodecPipeline.decode`/`encode` (the async batch entry points used + on the fallback path) map a None chunk to None and leave real chunks + untouched — pins the None-passthrough branch the default sync path skips.""" + import asyncio + + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer + from zarr.core.dtype import get_data_type_from_native_dtype + + zdtype = get_data_type_from_native_dtype(np.dtype("int32")) + spec = ArraySpec( + shape=(4,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + pipeline = FusedCodecPipeline.from_codecs([BytesCodec()]).evolve_from_array_spec(spec) + + data = np.arange(4, dtype="int32") + value = CPUNDBuffer.from_numpy_array(data) + + # encode a real chunk and a None chunk together + encoded = list(asyncio.run(pipeline.encode([(value, spec), (None, spec)]))) + assert encoded[1] is None + assert encoded[0] is not None + + # decode the real chunk and a None chunk together + decoded = list(asyncio.run(pipeline.decode([(encoded[0], spec), (None, spec)]))) + assert decoded[1] is None + assert decoded[0] is not None + np.testing.assert_array_equal(decoded[0].as_numpy_array(), data) diff --git a/tests/test_pipeline_parity.py b/tests/test_pipeline_parity.py new file mode 100644 index 0000000000..717f0f48f1 --- /dev/null +++ b/tests/test_pipeline_parity.py @@ -0,0 +1,420 @@ +"""Pipeline parity test — exhaustive matrix of read/write scenarios. + +For every cell of the matrix (codec config x layout x operation +sequence x runtime config), assert that ``FusedCodecPipeline`` and +``BatchedCodecPipeline`` produce semantically identical results: + + * Same returned array contents on read. + * Same set of store keys after writes (catches divergent empty-shard + handling: one pipeline deletes, the other writes an empty blob). + * Reading each pipeline's store contents through the *other* pipeline + yields the same array (catches "wrote a layout that only one + pipeline can read" bugs). + +Pipeline-divergence bugs (e.g. one pipeline writes a dense shard +layout while the other writes a compact layout) fail this test +loudly with a clear diff, instead of waiting for a downstream +test to trip over the symptom. + +Byte-for-byte equality of store contents is intentionally NOT +checked: codecs like gzip embed the wall-clock timestamp in their +output, so two compressions of the same data done at different +seconds produce different bytes despite being semantically +identical. + +The matrix axes are: + + * codec chain — bytes-only, gzip, with/without sharding + * layout — chunk_shape, shard_shape (None for no sharding) + * write sequence — full overwrite, partial in middle, scalar to one + cell, multiple overlapping writes, sequence ending in fill values + * runtime config — write_empty_chunks True/False +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +import numpy as np +import pytest + +import zarr +from zarr.codecs.bytes import BytesCodec +from zarr.codecs.crc32c_ import Crc32cCodec +from zarr.codecs.gzip import GzipCodec +from zarr.codecs.sharding import ( + SUBCHUNK_WRITE_ORDER, + IndexLocation, + ShardingCodec, + SubchunkWriteOrder, +) +from zarr.core.config import config as zarr_config +from zarr.storage import MemoryStore + +if TYPE_CHECKING: + from collections.abc import Callable, Iterator + + +# --------------------------------------------------------------------------- +# Reference helpers +# --------------------------------------------------------------------------- + + +def _store_snapshot(store: MemoryStore) -> dict[str, bytes]: + """Return {key: bytes} for every entry in the store.""" + return {k: bytes(v.to_bytes()) for k, v in store._store_dict.items()} + + +# --------------------------------------------------------------------------- +# Matrix definitions +# --------------------------------------------------------------------------- + + +# Each codec config is (filters, serializer, compressors). We only vary the +# pieces that actually affect the pipeline. compressors=None means a +# fixed-size chain (the byte-range fast path is eligible when sharded). +CodecConfig = dict[str, Any] + +CODEC_CONFIGS: list[tuple[str, CodecConfig]] = [ + ("bytes-only", {"compressors": None}), + ("gzip", {"compressors": GzipCodec(level=1)}), + # Big-endian serializer: the on-disk byte order is carried by the BytesCodec, + # not the dtype. Guards the bulk whole-shard decode against ignoring endian + # (it would otherwise reinterpret big-endian bytes as native — silent + # corruption). dtype is int32 so endianness is observable. + ( + "bytes-big-endian", + {"compressors": None, "serializer": BytesCodec(endian="big"), "dtype": "int32"}, + ), + # crc32c as a bytes->bytes codec after the serializer: the bulk fast path + # must NOT silently drop checksum verification (it falls through to the + # per-chunk path). Parity still requires identical bytes + contents across + # pipelines. (crc32c is a BytesBytesCodec, so it goes in `compressors`.) + ( + "bytes-crc32c", + {"compressors": [Crc32cCodec()], "serializer": BytesCodec(), "dtype": "int32"}, + ), +] + + +# (id, kwargs) — chunks/shards layout. kwargs are passed to create_array. +LayoutConfig = dict[str, Any] + +LAYOUT_CONFIGS: list[tuple[str, LayoutConfig]] = [ + ("1d-unsharded", {"shape": (100,), "chunks": (10,), "shards": None}), + ("1d-1chunk-per-shard", {"shape": (100,), "chunks": (10,), "shards": (10,)}), + ("1d-multi-chunk-per-shard", {"shape": (100,), "chunks": (10,), "shards": (50,)}), + ("2d-unsharded", {"shape": (20, 20), "chunks": (5, 5), "shards": None}), + ("2d-sharded", {"shape": (20, 20), "chunks": (5, 5), "shards": (10, 10)}), + # Nested sharding: outer chunk (10,10) sharded into inner chunks (5,5). + # Restricted to bytes-only codec because combining an outer ShardingCodec + # with a compressor (gzip) triggers a ZarrUserWarning and results in a + # checksum mismatch inside the inner shard index — a known limitation, not + # a pipeline-parity bug. The bytes-only path still exercises the full + # two-level shard encoding/decoding in both pipelines. + ( + "2d-nested-sharded", + { + "shape": (20, 20), + "chunks": (10, 10), + "shards": None, + "serializer": ShardingCodec( + chunk_shape=(10, 10), + codecs=[ShardingCodec(chunk_shape=(5, 5))], + ), + # Only run with the bytes-only codec config; gzip is incompatible + # with nested sharding (see comment above). + "_codec_ids": {"bytes-only"}, + }, + ), +] + + +WriteOp = tuple[Any, Any] # (selection, value) +WriteSequence = tuple[str, list[WriteOp]] + + +def _full_overwrite(shape: tuple[int, ...]) -> list[WriteOp]: + return [((slice(None),) * len(shape), np.arange(int(np.prod(shape))).reshape(shape) + 1)] + + +def _partial_middle(shape: tuple[int, ...]) -> list[WriteOp]: + if len(shape) == 1: + n = shape[0] + return [((slice(n // 4, 3 * n // 4),), 7)] + # 2D: write a centered block + rs = slice(shape[0] // 4, 3 * shape[0] // 4) + cs = slice(shape[1] // 4, 3 * shape[1] // 4) + return [((rs, cs), 7)] + + +def _scalar_one_cell(shape: tuple[int, ...]) -> list[WriteOp]: + if len(shape) == 1: + return [((shape[0] // 2,), 99)] + return [((shape[0] // 2, shape[1] // 2), 99)] + + +def _overlapping(shape: tuple[int, ...]) -> list[WriteOp]: + if len(shape) == 1: + n = shape[0] + return [ + ((slice(0, n // 2),), 1), + ((slice(n // 4, 3 * n // 4),), 2), + ((slice(n // 2, n),), 3), + ] + rs1, cs1 = slice(0, shape[0] // 2), slice(0, shape[1] // 2) + rs2, cs2 = slice(shape[0] // 4, 3 * shape[0] // 4), slice(shape[1] // 4, 3 * shape[1] // 4) + return [((rs1, cs1), 1), ((rs2, cs2), 2)] + + +def _ends_in_fill(shape: tuple[int, ...]) -> list[WriteOp]: + """Write something then overwrite it with fill — exercises empty-chunk handling.""" + full = (slice(None),) * len(shape) + return [(full, 5), (full, 0)] + + +def _ends_in_partial_fill(shape: tuple[int, ...]) -> list[WriteOp]: + """Write data, then overwrite half with fill — some chunks become empty.""" + full: tuple[slice, ...] + half: tuple[slice, ...] + if len(shape) == 1: + full = (slice(None),) + half = (slice(0, shape[0] // 2),) + else: + full = (slice(None), slice(None)) + half = (slice(0, shape[0] // 2), slice(None)) + return [(full, 5), (half, 0)] + + +SEQUENCES: list[tuple[str, Callable[[tuple[int, ...]], list[WriteOp]]]] = [ + ("full-overwrite", _full_overwrite), + ("partial-middle", _partial_middle), + ("scalar-one-cell", _scalar_one_cell), + ("overlapping", _overlapping), + ("ends-in-fill", _ends_in_fill), + ("ends-in-partial-fill", _ends_in_partial_fill), +] + + +WRITE_EMPTY_CHUNKS = [False, True] + + +# --------------------------------------------------------------------------- +# Matrix iteration (pruned) +# --------------------------------------------------------------------------- + + +def _matrix() -> Iterator[Any]: + for codec_id, codec_kwargs in CODEC_CONFIGS: + for layout_id, layout in LAYOUT_CONFIGS: + allowed = layout.get("_codec_ids") + if allowed is not None and codec_id not in allowed: + continue + for seq_id, seq_fn in SEQUENCES: + for wec in WRITE_EMPTY_CHUNKS: + yield pytest.param( + codec_kwargs, + layout, + seq_fn, + wec, + id=f"{layout_id}-{codec_id}-{seq_id}-wec{wec}", + ) + + +# --------------------------------------------------------------------------- +# The parity test +# --------------------------------------------------------------------------- + + +def _write_under_pipeline( + pipeline_path: str, + codec_kwargs: CodecConfig, + layout: LayoutConfig, + sequence: list[WriteOp], + write_empty_chunks: bool, +) -> tuple[MemoryStore, Any]: + """Apply a sequence of writes via the chosen pipeline. + + Returns (store with the written data, final array contents read back). + """ + # Strip private metadata keys (e.g. "_codec_ids") before passing to create_array. + array_layout = {k: v for k, v in layout.items() if not k.startswith("_")} + # dtype defaults to float64 but a codec config may override it (e.g. an + # endian-sensitive int dtype). Merge so the override wins without a dup kwarg. + create_kwargs = {"dtype": "float64", **array_layout, **codec_kwargs} + store = MemoryStore() + with zarr_config.set({"codec_pipeline.path": pipeline_path}): + arr = zarr.create_array( + store=store, + fill_value=0, + config={"write_empty_chunks": write_empty_chunks}, + **create_kwargs, + ) + for sel, val in sequence: + arr[sel] = val + contents = arr[...] + return store, contents + + +def _read_under_pipeline(pipeline_path: str, store: MemoryStore) -> Any: + """Re-open an existing store under the chosen pipeline and read it whole.""" + with zarr_config.set({"codec_pipeline.path": pipeline_path}): + arr = zarr.open_array(store=store, mode="r") + return arr[...] + + +_BATCHED = "zarr.core.codec_pipeline.BatchedCodecPipeline" +_FUSED = "zarr.core.codec_pipeline.FusedCodecPipeline" + + +@pytest.mark.parametrize( + ("codec_kwargs", "layout", "sequence_fn", "write_empty_chunks"), + list(_matrix()), +) +def test_pipeline_parity( + codec_kwargs: CodecConfig, + layout: LayoutConfig, + sequence_fn: Callable[[tuple[int, ...]], list[WriteOp]], + write_empty_chunks: bool, +) -> None: + """FusedCodecPipeline must be semantically identical to BatchedCodecPipeline. + + Three checks, in order of decreasing diagnostic value: + + 1. Both pipelines return the same array contents after the same + write sequence (catches semantic correctness bugs). + 2. Both pipelines produce the same set of store keys (catches + empty-shard divergence: one deletes, the other doesn't). + 3. Each pipeline can correctly read the *other* pipeline's + output (catches layout-divergence bugs that would prevent + interop, e.g. dense vs compact shard layouts). + + Byte-for-byte store equality is intentionally not checked: codecs + like gzip embed wall-clock timestamps that vary between runs. + """ + sequence = sequence_fn(layout["shape"]) + + batched_store, batched_arr = _write_under_pipeline( + _BATCHED, codec_kwargs, layout, sequence, write_empty_chunks + ) + sync_store, sync_arr = _write_under_pipeline( + _FUSED, codec_kwargs, layout, sequence, write_empty_chunks + ) + + # 1. Array contents must agree. + np.testing.assert_array_equal( + sync_arr, + batched_arr, + err_msg="FusedCodecPipeline returned different array contents than BatchedCodecPipeline", + ) + + # 2. Store key sets must agree. + batched_keys = set(batched_store._store_dict) - {"zarr.json"} + sync_keys = set(sync_store._store_dict) - {"zarr.json"} + assert sync_keys == batched_keys, ( + f"Pipelines disagree on which store keys exist.\n" + f" only in batched: {sorted(batched_keys - sync_keys)}\n" + f" only in sync: {sorted(sync_keys - batched_keys)}" + ) + + # 3. Cross-read: each pipeline must correctly read the other's output. + sync_reads_batched = _read_under_pipeline(_FUSED, batched_store) + batched_reads_sync = _read_under_pipeline(_BATCHED, sync_store) + np.testing.assert_array_equal( + sync_reads_batched, + batched_arr, + err_msg="FusedCodecPipeline could not correctly read BatchedCodecPipeline's output", + ) + np.testing.assert_array_equal( + batched_reads_sync, + sync_arr, + err_msg="BatchedCodecPipeline could not correctly read FusedCodecPipeline's output", + ) + + +# --------------------------------------------------------------------------- +# Partial-read parity across subchunk write orders +# --------------------------------------------------------------------------- +# +# Note: general partial-read coverage (scalar single-element and strided reads +# from sharded arrays, which hit the sharding codec's partial-decode path) lives +# in tests/test_codec_pipeline_suite.py as Scenarios. Those run each pipeline +# against a numpy reference -- strictly stronger than checking the two pipelines +# only against each other, and they cover both the sync (_decode_partial_sync) +# and async (_decode_partial_single) partial-decode variants. What remains here +# is the cross-pipeline byte-identical-layout check, which the per-pipeline +# suite structurally cannot express. + + +@pytest.mark.parametrize("subchunk_write_order", SUBCHUNK_WRITE_ORDER) +@pytest.mark.parametrize("index_location", ["start", "end"]) +def test_pipeline_parity_subchunk_write_order( + subchunk_write_order: SubchunkWriteOrder, index_location: IndexLocation +) -> None: + """Both pipelines must agree across every subchunk_write_order, including a + PARTIAL write into an already-dense fixed-size shard. + + This is the regression net for the byte-range write fast path, which derives + each chunk's physical slot from its rank in subchunk_write_order. A wrong + (e.g. hardcoded morton) assumption corrupts non-default orders silently, so + we assert both identical contents AND identical stored bytes across pipelines. + write_empty_chunks=True keeps every slot present, making the shard dense and + the byte-range write path eligible. + """ + # 2D, fixed-size (no compression). The shard (array `chunks`) must hold + # MULTIPLE inner chunks, and be non-square, so morton / lexicographic / + # colexicographic produce physically DIFFERENT layouts — with one inner + # chunk per shard all orders coincide and a wrong-order bug is invisible. + # inner chunk = (2, 2); shard = (6, 4) -> a 3x2 grid of inner chunks. + shape, shard_shape, inner_chunk = (12, 8), (6, 4), (2, 2) + serializer = ShardingCodec( + chunk_shape=inner_chunk, + codecs=[BytesCodec()], + index_location=index_location, + subchunk_write_order=subchunk_write_order, + ) + ref = np.arange(int(np.prod(shape)), dtype="int32").reshape(shape) + + def run(pipeline_path: str) -> tuple[dict[str, bytes], Any]: + store = MemoryStore() + with zarr_config.set({"codec_pipeline.path": pipeline_path}): + arr = zarr.create_array( + store=store, + shape=shape, + chunks=shard_shape, # array "chunks" == shard size for a ShardingCodec serializer + dtype="int32", + fill_value=-1, + serializer=serializer, + compressors=None, + config={"write_empty_chunks": True}, + ) + arr[:] = ref # dense full write + arr[3:9, 1:6] = 777 # partial write INTO the dense shard + contents = arr[...] + return _store_snapshot(store), contents + + batched_bytes, batched_contents = run(_BATCHED) + sync_bytes, sync_contents = run(_FUSED) + + # Contents must always match across pipelines and equal the reference — + # this catches a wrong-order byte-range write (it corrupts the data). + expected = ref.copy() + expected[3:9, 1:6] = 777 + np.testing.assert_array_equal(batched_contents, expected) + np.testing.assert_array_equal( + sync_contents, + batched_contents, + err_msg=f"pipeline contents diverged for subchunk_write_order={subchunk_write_order!r}", + ) + # The two pipelines must also produce byte-identical shards — a stronger + # check that they agree on physical layout. This holds for EVERY order + # (without special-casing any by name): both pipelines lay chunks out via + # the same `_subchunk_order_iter`, so for a given codec instance they must + # land on the same bytes whatever that order resolves to. We make no + # assumption here about what any particular order "means" — only that the + # two implementations agree. + assert sync_bytes == batched_bytes, ( + f"pipelines wrote different bytes for subchunk_write_order={subchunk_write_order!r} " + f"(index_location={index_location!r}) — byte-range write fast path likely assumed " + f"the wrong physical chunk order" + ) diff --git a/tests/test_store/test_get_ranges.py b/tests/test_store/test_get_ranges.py index 8f0c6a4814..f04251adf4 100644 --- a/tests/test_store/test_get_ranges.py +++ b/tests/test_store/test_get_ranges.py @@ -18,6 +18,7 @@ from zarr.core.buffer import default_buffer_prototype from zarr.storage import MemoryStore from zarr.storage._wrapper import WrapperStore +from zarr.testing.store import LatencyStore if TYPE_CHECKING: from collections.abc import AsyncIterator, Sequence @@ -58,6 +59,46 @@ async def test_memory_store_get_ranges_missing_key_raises() -> None: await anext(agen) +def test_get_ranges_sync_reads_multiple_ranges() -> None: + """The synchronous `get_ranges_sync` on a sync-capable store returns each + requested range, mirroring the async `get_ranges` happy path.""" + import asyncio + + store = MemoryStore() + blob = bytes(i % 256 for i in range(512)) + asyncio.run(_write(store, "blob", blob)) + + ranges = [RangeByteRequest(0, 10), RangeByteRequest(100, 110)] + proto = default_buffer_prototype() + flat: dict[int, bytes] = {} + for idx, buf in store.get_ranges_sync("blob", ranges, prototype=proto): + assert buf is not None + flat[idx] = buf.to_bytes() + + assert flat[0] == blob[0:10] + assert flat[1] == blob[100:110] + + +def test_get_ranges_sync_missing_key_raises() -> None: + """A missing key makes `get_ranges_sync` raise a BaseExceptionGroup + containing FileNotFoundError — the same contract as async `get_ranges`, so + callers handle a deleted shard uniformly across sync and async paths.""" + store = MemoryStore() + proto = default_buffer_prototype() + with pytest.RaisesGroup(pytest.RaisesExc(FileNotFoundError)): + store.get_ranges_sync("does-not-exist", [RangeByteRequest(0, 10)], prototype=proto) + + +def test_get_ranges_sync_on_non_sync_store_raises_type_error() -> None: + """`get_ranges_sync` requires the store to support synchronous reads + (`SupportsGetSync`); a non-sync store raises TypeError rather than silently + falling back.""" + store = LatencyStore(MemoryStore(), get_latency=0.0, set_latency=0.0) + proto = default_buffer_prototype() + with pytest.raises(TypeError, match="does not support synchronous reads"): + store.get_ranges_sync("k", [RangeByteRequest(0, 10)], prototype=proto) + + async def test_wrapper_store_delegates_get_ranges() -> None: """WrapperStore.get_ranges must delegate to the wrapped store, not fall back to the default.""" diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index c4536e5c49..f65f618d65 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -108,6 +108,58 @@ async def test_move( ): await store2.move(destination) + # --- byte-range-write tests: disabled --- + # Byte-range-write support (set_range / set_range_sync / SupportsSetRange) + # was removed from this PR pending a decision on the store interface. These + # tests are known-good and kept commented out to restore once that lands. + # def test_supports_set_range(self, store: LocalStore) -> None: + # """LocalStore should implement SupportsSetRange.""" + # assert isinstance(store, SupportsSetRange) + # + # @pytest.mark.parametrize( + # ("start", "patch", "expected"), + # [ + # (0, b"XX", b"XXAAAAAAAA"), + # (3, b"XX", b"AAAXXAAAAA"), + # (8, b"XX", b"AAAAAAAAXX"), + # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), + # (5, b"B", b"AAAAABAAAA"), + # (0, b"BCDE", b"BCDEAAAAAA"), + # ], + # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], + # ) + # async def test_set_range( + # self, store: LocalStore, start: int, patch: bytes, expected: bytes + # ) -> None: + # """set_range should overwrite bytes at the given offset.""" + # await store.set("test/key", cpu.Buffer.from_bytes(b"AAAAAAAAAA")) + # await store.set_range("test/key", cpu.Buffer.from_bytes(patch), start=start) + # result = await store.get("test/key", prototype=cpu.buffer_prototype) + # assert result is not None + # assert result.to_bytes() == expected + # + # @pytest.mark.parametrize( + # ("start", "patch", "expected"), + # [ + # (0, b"XX", b"XXAAAAAAAA"), + # (3, b"XX", b"AAAXXAAAAA"), + # (8, b"XX", b"AAAAAAAAXX"), + # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), + # (5, b"B", b"AAAAABAAAA"), + # (0, b"BCDE", b"BCDEAAAAAA"), + # ], + # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], + # ) + # def test_set_range_sync( + # self, store: LocalStore, start: int, patch: bytes, expected: bytes + # ) -> None: + # """set_range_sync should overwrite bytes at the given offset.""" + # sync(store.set("test/key", cpu.Buffer.from_bytes(b"AAAAAAAAAA"))) + # store.set_range_sync("test/key", cpu.Buffer.from_bytes(patch), start=start) + # result = store.get_sync(key="test/key", prototype=cpu.buffer_prototype) + # assert result is not None + # assert result.to_bytes() == expected + @pytest.mark.parametrize("exclusive", [True, False]) def test_atomic_write_successful(tmp_path: pathlib.Path, exclusive: bool) -> None: diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 1e3ee89e92..35504718a7 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -76,6 +76,59 @@ async def test_deterministic_size( np.testing.assert_array_equal(a[:3], 1) np.testing.assert_array_equal(a[3:], 0) + # --- byte-range-write tests: disabled --- + # Byte-range-write support (set_range / set_range_sync / SupportsSetRange) + # was removed from this PR pending a decision on the store interface. These + # tests are known-good and kept commented out to restore once that lands. + # def test_supports_set_range(self, store: MemoryStore) -> None: + # """MemoryStore should implement SupportsSetRange.""" + # assert isinstance(store, SupportsSetRange) + # + # @pytest.mark.parametrize( + # ("start", "patch", "expected"), + # [ + # (0, b"XX", b"XXAAAAAAAA"), + # (3, b"XX", b"AAAXXAAAAA"), + # (8, b"XX", b"AAAAAAAAXX"), + # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), + # (5, b"B", b"AAAAABAAAA"), + # (0, b"BCDE", b"BCDEAAAAAA"), + # ], + # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], + # ) + # async def test_set_range( + # self, store: MemoryStore, start: int, patch: bytes, expected: bytes + # ) -> None: + # """set_range should overwrite bytes at the given offset.""" + # await store.set("test/key", cpu.Buffer.from_bytes(b"AAAAAAAAAA")) + # await store.set_range("test/key", cpu.Buffer.from_bytes(patch), start=start) + # result = await store.get("test/key", prototype=cpu.buffer_prototype) + # assert result is not None + # assert result.to_bytes() == expected + # + # @pytest.mark.parametrize( + # ("start", "patch", "expected"), + # [ + # (0, b"XX", b"XXAAAAAAAA"), + # (3, b"XX", b"AAAXXAAAAA"), + # (8, b"XX", b"AAAAAAAAXX"), + # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), + # (5, b"B", b"AAAAABAAAA"), + # (0, b"BCDE", b"BCDEAAAAAA"), + # ], + # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], + # ) + # def test_set_range_sync( + # self, store: MemoryStore, start: int, patch: bytes, expected: bytes + # ) -> None: + # """set_range_sync should overwrite bytes at the given offset.""" + # store._is_open = True + # store._store_dict["test/key"] = cpu.Buffer.from_bytes(b"AAAAAAAAAA") + # store.set_range_sync("test/key", cpu.Buffer.from_bytes(patch), start=start) + # result = store.get_sync(key="test/key", prototype=cpu.buffer_prototype) + # assert result is not None + # assert result.to_bytes() == expected + # TODO: fix this warning @pytest.mark.filterwarnings("ignore:Unclosed client session:ResourceWarning") From a75add93e2114c9e4fdc732702178ee33537ed8a Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Mon, 13 Jul 2026 21:14:32 +0200 Subject: [PATCH 399/468] test: ignore Python 3.15 fork-with-threads DeprecationWarning in test_multiprocessing (#4143) Python 3.15 makes os.fork() emit a DeprecationWarning when the process has multiple threads (python/cpython#84559). zarr's sync event-loop thread is always running by the time test_multiprocessing forks, and the suite runs with filterwarnings = ["error"], so the fork parametrizations fail on 3.15. Fork-safety despite those threads is exactly what this test pins down (zarr registers an os.register_at_fork handler), so keep the coverage and ignore the warning with a targeted per-param filter. Fixes #4086 Assisted-by: ClaudeCode:claude-fable-5 --- changes/4086.misc.md | 1 + tests/test_array.py | 15 ++++++++++++--- 2 files changed, 13 insertions(+), 3 deletions(-) create mode 100644 changes/4086.misc.md diff --git a/changes/4086.misc.md b/changes/4086.misc.md new file mode 100644 index 0000000000..2564cf9ea1 --- /dev/null +++ b/changes/4086.misc.md @@ -0,0 +1 @@ +Fix `test_multiprocessing[fork]` failing on Python 3.15, where `os.fork()` in a multi-threaded process emits a `DeprecationWarning` that the test suite promotes to an error. diff --git a/tests/test_array.py b/tests/test_array.py index 4faf99eb9e..d2f324439d 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -1903,9 +1903,18 @@ def _index_array(arr: AnyArray, index: Any) -> Any: [ pytest.param( "fork", - marks=pytest.mark.skipif( - sys.platform in ("win32", "darwin"), reason="fork not supported on Windows or OSX" - ), + marks=[ + pytest.mark.skipif( + sys.platform in ("win32", "darwin"), + reason="fork not supported on Windows or OSX", + ), + # Python 3.15 deprecates fork() in multi-threaded processes, and zarr's + # sync event-loop thread is always running here. Fork-safety despite + # those threads is exactly what this test pins down, so keep running it. + pytest.mark.filterwarnings( + r"ignore:This process \(pid=\d+\) is multi-threaded, use of fork\(\):DeprecationWarning" + ), + ], ), "spawn", pytest.param( From de2cce1adc41a4d38721bf62b25eb312a52066dd Mon Sep 17 00:00:00 2001 From: Amadeus Brandes <79119643+AMBRA7592@users.noreply.github.com> Date: Tue, 14 Jul 2026 11:48:16 +0200 Subject: [PATCH 400/468] fix: skip object store prefix markers in list_dir (#4117) * fix: skip object store prefix markers in list_dir Signed-off-by: ABrandes <79119643+AMBRA7592@users.noreply.github.com> * Address list_dir prefix marker review Signed-off-by: ABrandes <79119643+AMBRA7592@users.noreply.github.com> * Format prefix marker follow-up Signed-off-by: ABrandes <79119643+AMBRA7592@users.noreply.github.com> * Test S3 prefix marker handling Signed-off-by: ABrandes <79119643+AMBRA7592@users.noreply.github.com> * Filter boto3 deprecation in S3 test Signed-off-by: ABrandes <79119643+AMBRA7592@users.noreply.github.com> * Address final prefix marker review Signed-off-by: ABrandes <79119643+AMBRA7592@users.noreply.github.com> --------- Signed-off-by: ABrandes <79119643+AMBRA7592@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- changes/4032.bugfix.md | 1 + src/zarr/core/array.py | 6 +++++- src/zarr/storage/_memory.py | 2 +- src/zarr/storage/_obstore.py | 6 +++++- tests/test_array.py | 4 +++- tests/test_store/test_object.py | 37 ++++++++++++++++++++++++++++++++- 6 files changed, 51 insertions(+), 5 deletions(-) create mode 100644 changes/4032.bugfix.md diff --git a/changes/4032.bugfix.md b/changes/4032.bugfix.md new file mode 100644 index 0000000000..4c9476f583 --- /dev/null +++ b/changes/4032.bugfix.md @@ -0,0 +1 @@ +Fixed `ObjectStore.list_dir` for object-store listings that include a directory-marker object matching the requested non-root prefix. diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 2bf761bd3d..f75ef72415 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -4018,7 +4018,11 @@ async def _shards_initialized( x async for x in array.store_path.store.list_prefix(prefix=array.store_path.path) ] store_contents_relative = [ - _relativize_path(path=key, prefix=array.store_path.path) for key in store_contents + _relativize_path(path=key, prefix=array.store_path.path) + for key in store_contents + # obstore can include a directory marker whose key matches the listed prefix; + # it is not an initialized shard and must be excluded before relativizing. + if array.store_path.path == "" or key != array.store_path.path ] return tuple( chunk_key for chunk_key in array._iter_shard_keys() if chunk_key in store_contents_relative diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index e867706155..5f5b632d4a 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -219,7 +219,7 @@ async def list_dir(self, prefix: str) -> AsyncIterator[str]: keys_unique = { key.removeprefix(f"{prefix}/").split("/")[0] for key in self._store_dict - if key.startswith(f"{prefix}/") and key != prefix + if key.startswith(f"{prefix}/") and key not in {prefix, f"{prefix}/"} } for key in keys_unique: diff --git a/src/zarr/storage/_obstore.py b/src/zarr/storage/_obstore.py index ffea523f9f..b34a5f624d 100644 --- a/src/zarr/storage/_obstore.py +++ b/src/zarr/storage/_obstore.py @@ -267,7 +267,11 @@ async def _transform_list_dir( for path in chain( list_result["common_prefixes"], map(itemgetter("path"), list_result["objects"]) ): - yield _relativize_path(path=path, prefix=prefix) + if prefix != "" and path == prefix: + continue + relpath = _relativize_path(path=path, prefix=prefix) + if relpath: + yield relpath class _BoundedRequest(TypedDict): diff --git a/tests/test_array.py b/tests/test_array.py index d2f324439d..b1a7a3c0f2 100644 --- a/tests/test_array.py +++ b/tests/test_array.py @@ -45,7 +45,7 @@ default_serializer_v3, ) from zarr.core.array_spec import ArrayConfig, ArrayConfigParams -from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, default_buffer_prototype +from zarr.core.buffer import NDArrayLike, NDArrayLikeOrScalar, cpu, default_buffer_prototype from zarr.core.chunk_grids import ( SHARDED_INNER_CHUNK_MAX_BYTES, guess_chunks, @@ -447,6 +447,8 @@ async def test_chunks_initialized( arr = zarr.create_array( store, name=path, shape=shape, shards=shard_shape, chunks=chunk_shape, dtype="i1" ) + if path: + await store.set(path, cpu.Buffer.from_bytes(b"")) chunks_accumulated = tuple( accumulate(tuple(tuple(v.split(" ")) for v in arr._iter_shard_keys())) diff --git a/tests/test_store/test_object.py b/tests/test_store/test_object.py index 6a4b796639..cd85a48eb8 100644 --- a/tests/test_store/test_object.py +++ b/tests/test_store/test_object.py @@ -1,4 +1,5 @@ # ruff: noqa: E402 +import re from pathlib import Path from typing import TypedDict @@ -9,9 +10,10 @@ from hypothesis.stateful import ( run_state_machine_as_test, ) -from obstore.store import LocalStore, MemoryStore +from obstore.store import LocalStore, MemoryStore, S3Store from zarr.core.buffer import Buffer, cpu +from zarr.core.sync import _collect_aiterator from zarr.storage import ObjectStore from zarr.testing.stateful import ZarrHierarchyStateMachine from zarr.testing.store import StoreTests @@ -97,6 +99,39 @@ async def test_store_getsize_prefix(self, store: ObjectStore[LocalStore]) -> Non assert total_size == len(buf) * 2 +@pytest.mark.filterwarnings( + re.escape("ignore:datetime.datetime.utcnow() is deprecated:DeprecationWarning") +) +async def test_list_dir_ignores_s3_prefix_marker(moto_server: str) -> None: + """Ensure obstore's exact-prefix S3 directory marker is not listed as a child.""" + boto3 = pytest.importorskip("boto3") + bucket = "object-store-prefix-marker" + client = boto3.client( + "s3", + endpoint_url=moto_server, + region_name="us-east-1", + aws_access_key_id="x", + aws_secret_access_key="x", + ) + client.create_bucket(Bucket=bucket) + client.put_object(Bucket=bucket, Key="g/", Body=b"") + + store = ObjectStore( + S3Store( + bucket=bucket, + endpoint=moto_server, + region="us-east-1", + access_key_id="x", + secret_access_key="x", + client_options={"allow_http": True}, + virtual_hosted_style_request=False, + ) + ) + + assert await _collect_aiterator(store.list_dir("g")) == () + assert await _collect_aiterator(store.list_dir("g/")) == () + + @pytest.mark.slow_hypothesis def test_zarr_hierarchy() -> None: sync_store = ObjectStore(MemoryStore()) From bbe27d7ce9713d50e34df2cda5108f4dcf410b92 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Tue, 14 Jul 2026 13:39:53 +0200 Subject: [PATCH 401/468] fix: byte-order handling for structured dtypes in the bytes codec (#4142) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 --- changes/4141.bugfix.md | 1 + src/zarr/codecs/bytes.py | 33 +++++++++++----- tests/test_codecs/test_bytes.py | 69 ++++++++++++++++++++++++++------- 3 files changed, 80 insertions(+), 23 deletions(-) create mode 100644 changes/4141.bugfix.md diff --git a/changes/4141.bugfix.md b/changes/4141.bugfix.md new file mode 100644 index 0000000000..6a132da3f5 --- /dev/null +++ b/changes/4141.bugfix.md @@ -0,0 +1 @@ +Fix silent byte-order corruption for structured dtypes with the `bytes` codec: multi-byte fields are now byte-swapped to the codec's configured `endian` on write and decoded honoring it on read, so non-native-endian structured data (e.g. big-endian fields, as produced by virtual references to external data) round-trips correctly. diff --git a/src/zarr/codecs/bytes.py b/src/zarr/codecs/bytes.py index 240c077627..fae762fd08 100644 --- a/src/zarr/codecs/bytes.py +++ b/src/zarr/codecs/bytes.py @@ -100,14 +100,28 @@ def _decode_sync( chunk_spec: ArraySpec, ) -> NDBuffer: endian_str = self.endian + dtype = chunk_spec.dtype.to_native_dtype() + # The byte order of the stored data is set by this codec's `endian` + # configuration; the byte order of the decoded array is set by the array's + # data type. The two are independent: the raw bytes are viewed with a dtype + # in the stored byte order, then converted to the declared dtype if needed. if isinstance(chunk_spec.dtype, HasEndianness): - dtype = replace(chunk_spec.dtype, endianness=endian_str).to_native_dtype() # type: ignore[call-arg] + view_dtype = replace(chunk_spec.dtype, endianness=endian_str).to_native_dtype() # type: ignore[call-arg] + elif isinstance(chunk_spec.dtype, Struct) and endian_str is not None: + # Per the struct data type spec, all multi-byte fields are stored in the + # byte order configured on this codec. + view_dtype = dtype.newbyteorder(endian_str) else: - dtype = chunk_spec.dtype.to_native_dtype() + view_dtype = dtype as_array_like = chunk_bytes.as_array_like() chunk_array = chunk_spec.prototype.nd_buffer.from_ndarray_like( - as_array_like.view(dtype=dtype) # type: ignore[attr-defined] + as_array_like.view(dtype=view_dtype) # type: ignore[attr-defined] ) + if view_dtype != dtype: + # This byte-swapping conversion copies the chunk. The dtype inequality + # guard keeps the common case, where the stored and declared byte orders + # already match, on the zero-copy view path above. + chunk_array = chunk_array.astype(dtype) # ensure correct chunk shape if chunk_array.shape != chunk_spec.shape: @@ -129,13 +143,14 @@ def _encode_sync( chunk_spec: ArraySpec, ) -> Buffer | None: assert isinstance(chunk_array, NDBuffer) - if ( - chunk_array.dtype.itemsize > 1 - and self.endian is not None - and self.endian != chunk_array.byteorder - ): + if chunk_array.dtype.itemsize > 1 and self.endian is not None: + # Compare full dtypes rather than the top-level byteorder: numpy reports + # byteorder '|' for structured dtypes even when their fields are + # byte-order-sensitive, so newbyteorder is the only reliable way to + # detect (and normalize) a byte-order mismatch. new_dtype = chunk_array.dtype.newbyteorder(self.endian) - chunk_array = chunk_array.astype(new_dtype) + if new_dtype != chunk_array.dtype: + chunk_array = chunk_array.astype(new_dtype) nd_array = chunk_array.as_ndarray_like() # Flatten the nd-array (only copy if needed) and reinterpret as bytes diff --git a/tests/test_codecs/test_bytes.py b/tests/test_codecs/test_bytes.py index 03dd0b40c6..ead778f526 100644 --- a/tests/test_codecs/test_bytes.py +++ b/tests/test_codecs/test_bytes.py @@ -33,29 +33,50 @@ @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) -@pytest.mark.parametrize("input_dtype", [">u2", "<u2"]) +@pytest.mark.parametrize( + "input_dtype", + [ + ">u2", + "<u2", + [("flux", ">f4"), ("mask", ">i4")], + [("flux", "<f4"), ("mask", "<i4")], + ], + ids=["big-scalar", "little-scalar", "big-struct", "little-struct"], +) @pytest.mark.parametrize("store_endian", ["big", "little"]) async def test_endian( store: Store, - input_dtype: Literal[">u2", "<u2"], + input_dtype: str | list[tuple[str, str]], store_endian: Literal["big", "little"], ) -> None: """ The `bytes` codec stores multi-byte data in the byte order configured on the codec, regardless of the input array's byte order, and reads it back to the - original values. The input-dtype/store-endian cross-product exercises the - encode-side byteswap (input byte order != store byte order) and the no-op - case alike. Compression is disabled so the stored chunk is the codec's raw - output and its byte layout can be asserted directly. + original values. For structured dtypes this applies to every multi-byte + field, per the `struct` data type spec; the struct cases guard against the + endianness bugs from + https://github.com/zarr-developers/zarr-python/issues/4141, where the + encode path never byte-swapped struct fields (numpy reports byteorder '|' + for void dtypes) and the decode path ignored the codec's endian entirely. + The input-dtype/store-endian cross-product exercises the encode-side + byteswap (input byte order != store byte order) and the no-op case alike. + Compression is disabled so the stored chunk is the codec's raw output and + its byte layout can be asserted directly. """ - data = np.arange(0, 256, dtype=input_dtype).reshape((16, 16)) + dtype = np.dtype(input_dtype) + if dtype.fields is None: + data = np.arange(0, 256, dtype=dtype).reshape((16, 16)) + else: + data = np.zeros((16, 16), dtype=dtype) + data["flux"] = np.arange(0, 256).reshape((16, 16)) + data["mask"] = np.arange(256, 512).reshape((16, 16)) path = "endian" spath = StorePath(store, path) a = await zarr.api.asynchronous.create_array( spath, shape=data.shape, chunks=(16, 16), - dtype="uint16", + dtype=dtype, fill_value=0, compressors=None, serializer=BytesCodec(endian=store_endian), @@ -66,8 +87,7 @@ async def test_endian( # The stored chunk is laid out in the byte order configured on the codec. stored = await store.get(f"{path}/c/0/0", prototype=default_buffer_prototype()) assert stored is not None - expected_dtype = ">u2" if store_endian == "big" else "<u2" - assert stored.to_bytes() == data.astype(expected_dtype).tobytes() + assert stored.to_bytes() == data.astype(dtype.newbyteorder(store_endian)).tobytes() # ... and the data reads back to the original values. readback_data = await _AsyncArrayProxy(a)[:, :].get() @@ -78,9 +98,27 @@ def test_bytes_codec_supports_sync() -> None: assert isinstance(BytesCodec(), SupportsSyncCodec) -def test_bytes_codec_sync_roundtrip() -> None: - codec = BytesCodec() - arr = np.arange(100, dtype="float64") +@pytest.mark.parametrize("endian", ENDIAN) +@pytest.mark.parametrize( + "native_dtype", + [np.dtype("float64"), np.dtype(">u2"), np.dtype([("a", ">f4"), ("b", "<i4")])], + ids=["native-scalar", "big-scalar", "mixed-endian-struct"], +) +def test_bytes_codec_sync_roundtrip(endian: EndianLiteral, native_dtype: np.dtype[Any]) -> None: + """ + The synchronous encode/decode path round-trips data, and the two byte + orders involved are independent: the codec's `endian` configuration governs + only the stored byte layout (every multi-byte value, including struct + fields, is laid out in the codec's byte order regardless of the input + array's byte order), while the decoded buffer's byte order is governed by + the array's data type regardless of the codec's. The mixed-endian struct + case pins that per-field byte order of the in-memory dtype survives a + roundtrip through a single stored byte order. + """ + if native_dtype.fields is None: + arr = np.arange(100, dtype=native_dtype) + else: + arr = np.array([(1.5, 2), (3.5, 4), (5.5, 6), (7.5, 8)], dtype=native_dtype) zdtype = get_data_type_from_native_dtype(arr.dtype) spec = ArraySpec( shape=arr.shape, @@ -91,11 +129,14 @@ def test_bytes_codec_sync_roundtrip() -> None: ) nd_buf: NDBuffer = default_buffer_prototype().nd_buffer.from_numpy_array(arr) - codec = codec.evolve_from_array_spec(spec) + codec = BytesCodec(endian=endian).evolve_from_array_spec(spec) encoded = codec._encode_sync(nd_buf, spec) assert encoded is not None + assert encoded.to_bytes() == arr.astype(native_dtype.newbyteorder(endian)).tobytes() + decoded = codec._decode_sync(encoded, spec) + assert decoded.dtype == zdtype.to_native_dtype() np.testing.assert_array_equal(arr, decoded.as_numpy_array()) From d916f759dca7ee41bfa56f51a2295b8b0e90a81a Mon Sep 17 00:00:00 2001 From: Ilan Gold <ilanbassgold@gmail.com> Date: Tue, 14 Jul 2026 17:13:03 +0200 Subject: [PATCH 402/468] chore: add Ilan Gold to the team list (#4145) --- TEAM.md | 1 + 1 file changed, 1 insertion(+) diff --git a/TEAM.md b/TEAM.md index dc22a1ee87..ce9de1d486 100644 --- a/TEAM.md +++ b/TEAM.md @@ -11,6 +11,7 @@ - @dcherian (Deepak Cherian) - @TomAugspurger (Tom Augspurger) - @maxrjones (Max Jones) +- @ilan-gold (Ilan Gold) ## Emeritus core-developers - @alimanfoo (Alistair Miles) From 91a8ec06dc4d475fe40691e0ab668dd655d3751a Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 16 Jul 2026 16:34:50 +0200 Subject: [PATCH 403/468] docs: 3.3.0 release notes (#4148) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * docs: 3.3.0 release notes Add missing changelog fragments for #3955 (datetime64/timedelta64 V3 metadata types), #3966 (writes to 0-dimensional sharded arrays), and the public alias renames that accompanied the #3963/#3968 enum deprecations, then build the 3.3.0 release notes with towncrier, consuming all fragments accumulated since v3.2.1. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> --- changes/202.bugfix.md | 1 - changes/214.misc.md | 1 - changes/215.misc.md | 1 - changes/2929.bugfix.md | 3 - changes/3004.feature.md | 4 - changes/3009.doc.md | 1 - changes/3417.bugfix.md | 4 - changes/3469.bugfix.md | 1 - changes/3826.feature.md | 1 - changes/3885.bugfix.md | 1 - changes/3885.feature.1.md | 1 - changes/3885.feature.md | 1 - changes/3899.bugfix.md | 7 -- changes/3908.misc.md | 1 - changes/3925.feature.md | 1 - changes/3954.bugfix.md | 1 - changes/3963.removal.md | 6 -- changes/3968.removal.md | 17 ----- changes/3972.misc.md | 1 - changes/3973.removal.md | 1 - changes/3975.misc.md | 1 - changes/3977.bugfix.md | 1 - changes/3979.misc.md | 1 - changes/3984.doc.md | 4 - changes/3987.feature.md | 1 - changes/3990.misc.md | 5 -- changes/3998.misc.md | 1 - changes/4000.misc.md | 1 - changes/4001.misc.md | 6 -- changes/4003.bugfix.md | 19 ----- changes/4016.bugfix.md | 1 - changes/4032.bugfix.md | 1 - changes/4046.misc.md | 1 - changes/4052.doc.md | 21 ----- changes/4053.doc.md | 1 - changes/4054.misc.md | 1 - changes/4059.bugfix.md | 1 - changes/4073.misc.md | 1 - changes/4074.bugfix.md | 7 -- changes/4086.misc.md | 1 - changes/4116.bugfix.md | 1 - changes/4132.doc.md | 6 -- changes/4133.doc.md | 1 - changes/4138.misc.md | 1 - changes/4141.bugfix.md | 1 - docs/release-notes.md | 156 ++++++++++++++++++++++++++++++++++++++ 46 files changed, 156 insertions(+), 141 deletions(-) delete mode 100644 changes/202.bugfix.md delete mode 100644 changes/214.misc.md delete mode 100644 changes/215.misc.md delete mode 100644 changes/2929.bugfix.md delete mode 100644 changes/3004.feature.md delete mode 100644 changes/3009.doc.md delete mode 100644 changes/3417.bugfix.md delete mode 100644 changes/3469.bugfix.md delete mode 100644 changes/3826.feature.md delete mode 100644 changes/3885.bugfix.md delete mode 100644 changes/3885.feature.1.md delete mode 100644 changes/3885.feature.md delete mode 100644 changes/3899.bugfix.md delete mode 100644 changes/3908.misc.md delete mode 100644 changes/3925.feature.md delete mode 100644 changes/3954.bugfix.md delete mode 100644 changes/3963.removal.md delete mode 100644 changes/3968.removal.md delete mode 100644 changes/3972.misc.md delete mode 100644 changes/3973.removal.md delete mode 100644 changes/3975.misc.md delete mode 100644 changes/3977.bugfix.md delete mode 100644 changes/3979.misc.md delete mode 100644 changes/3984.doc.md delete mode 100644 changes/3987.feature.md delete mode 100644 changes/3990.misc.md delete mode 100644 changes/3998.misc.md delete mode 100644 changes/4000.misc.md delete mode 100644 changes/4001.misc.md delete mode 100644 changes/4003.bugfix.md delete mode 100644 changes/4016.bugfix.md delete mode 100644 changes/4032.bugfix.md delete mode 100644 changes/4046.misc.md delete mode 100644 changes/4052.doc.md delete mode 100644 changes/4053.doc.md delete mode 100644 changes/4054.misc.md delete mode 100644 changes/4059.bugfix.md delete mode 100644 changes/4073.misc.md delete mode 100644 changes/4074.bugfix.md delete mode 100644 changes/4086.misc.md delete mode 100644 changes/4116.bugfix.md delete mode 100644 changes/4132.doc.md delete mode 100644 changes/4133.doc.md delete mode 100644 changes/4138.misc.md delete mode 100644 changes/4141.bugfix.md diff --git a/changes/202.bugfix.md b/changes/202.bugfix.md deleted file mode 100644 index 9c9bd40f21..0000000000 --- a/changes/202.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Stop emitting an `UnstableSpecificationWarning` when serializing the `struct` data type to Zarr V3 metadata. The `struct` data type now has a stable Zarr V3 specification. The legacy `structured` alias and the unspecified `null_terminated_bytes`, `raw_bytes`, and `variable_length_bytes` data types continue to warn. diff --git a/changes/214.misc.md b/changes/214.misc.md deleted file mode 100644 index 8611362e84..0000000000 --- a/changes/214.misc.md +++ /dev/null @@ -1 +0,0 @@ -Bind the shared moto S3 test server to an ephemeral port instead of a fixed one. The fixed port deadlocked `pytest -n auto`: session-scoped fixtures run once per xdist worker, so concurrent workers raced to bind the same port and the losers blocked forever in `ThreadedMotoServer.start()`. diff --git a/changes/215.misc.md b/changes/215.misc.md deleted file mode 100644 index f8df7cc632..0000000000 --- a/changes/215.misc.md +++ /dev/null @@ -1 +0,0 @@ -Enable pytest's `strict = true` config option (strict config, markers, xfail, and parametrization ids), replacing the `--strict-config`/`--strict-markers` addopts flags that pytest silently ignored before 9.1, and fix the seven duplicate parametrization ids it surfaced — including restoring float-JSON roundtrip cases that were meant to cover numpy scalars but ran plain-float cases twice instead. Also arm pytest's faulthandler watchdog (`faulthandler_timeout = 600` with `faulthandler_exit_on_timeout`) so a deadlocked test dumps every thread's traceback and fails the run instead of hanging indefinitely. diff --git a/changes/2929.bugfix.md b/changes/2929.bugfix.md deleted file mode 100644 index 533a5f86c1..0000000000 --- a/changes/2929.bugfix.md +++ /dev/null @@ -1,3 +0,0 @@ -Fix equality comparison of `ArrayV2Metadata` and `ArrayV3Metadata` objects with a -`NaN` fill value. Such objects are now compared by their JSON-serialized form, so two -otherwise-identical metadata objects with a `NaN` (or infinite) fill value compare equal. diff --git a/changes/3004.feature.md b/changes/3004.feature.md deleted file mode 100644 index 9d3816a50c..0000000000 --- a/changes/3004.feature.md +++ /dev/null @@ -1,4 +0,0 @@ -Optimizes reading multiple chunks from a shard. Serial calls to `Store.get()` -in the sharding codec have been replaced with a single call to -`Store.get_ranges()`, which coalesces nearby byte ranges and fetches them -concurrently. diff --git a/changes/3009.doc.md b/changes/3009.doc.md deleted file mode 100644 index 777672b77b..0000000000 --- a/changes/3009.doc.md +++ /dev/null @@ -1 +0,0 @@ -Document the changes to `zarr.errors` in the 3.0 migration guide, including the removal of v2 exception classes and the introduction of `NodeNotFoundError`. diff --git a/changes/3417.bugfix.md b/changes/3417.bugfix.md deleted file mode 100644 index be5b44f3e9..0000000000 --- a/changes/3417.bugfix.md +++ /dev/null @@ -1,4 +0,0 @@ -Fixed `BytesCodec.from_dict` so that `BytesCodec` instances roundtrip to / from -their dict representation. `BytesCodec.from_dict` now interprets a missing -`endian` configuration as `endian=None` (matching what `BytesCodec.to_dict` -emits), instead of falling back to the system's native byte order. diff --git a/changes/3469.bugfix.md b/changes/3469.bugfix.md deleted file mode 100644 index eb56e87476..0000000000 --- a/changes/3469.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed `save_array`, `Group.__setitem__`, and `load` for 0-dimensional arrays. diff --git a/changes/3826.feature.md b/changes/3826.feature.md deleted file mode 100644 index 8909e777c5..0000000000 --- a/changes/3826.feature.md +++ /dev/null @@ -1 +0,0 @@ -Added a `subchunk_write_order` option to `ShardingCodec` to control the physical order of subchunks within a shard. Supported values are `morton`, `unordered`, `lexicographic`, and `colexicographic`. `unordered` makes no guarantee about subchunk layout. This setting affects only on-disk layout, not the data read back, and is not persisted in array metadata: it applies per codec instance and is not recovered when reopening a sharded array. diff --git a/changes/3885.bugfix.md b/changes/3885.bugfix.md deleted file mode 100644 index d4c1dd5c03..0000000000 --- a/changes/3885.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed inner-codec spec evolution for sharded arrays. The sharding codec now threads the array spec through its inner codec chain when evolving codecs, so a codec that changes the dtype upstream of `BytesCodec` no longer leaves the inner chain evolved against the wrong spec (which previously failed at decode time). This runs on the default `BatchedCodecPipeline` as well. Standard inner chains (`[BytesCodec]`, `[BytesCodec, ZstdCodec]`, transpose + bytes) are byte-identical to before. Restores the behavior of #2179. diff --git a/changes/3885.feature.1.md b/changes/3885.feature.1.md deleted file mode 100644 index 0a51ba6844..0000000000 --- a/changes/3885.feature.1.md +++ /dev/null @@ -1 +0,0 @@ -Added `SyncByteGetter` and `SyncByteSetter` runtime-checkable protocols and a `get_ranges_sync` method on the `Store` ABC. These let custom byte getters/setters opt into the synchronous codec pipeline's fast path for in-memory IO, which the sharding codec uses for its inner chunks. diff --git a/changes/3885.feature.md b/changes/3885.feature.md deleted file mode 100644 index 13010f521e..0000000000 --- a/changes/3885.feature.md +++ /dev/null @@ -1 +0,0 @@ -Added `FusedCodecPipeline`, an opt-in codec pipeline that runs codec compute synchronously and in bulk (avoiding the per-chunk async scheduling overhead of the default `BatchedCodecPipeline`), giving large speedups for sharded arrays (up to ~24x writes / ~14x reads on many-chunks-per-shard layouts, more with compression) and no regressions on compute-bound workloads. The default `BatchedCodecPipeline` is unchanged for standard configurations, so existing code keeps working unless you opt in; enable the new pipeline with `zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"})`. diff --git a/changes/3899.bugfix.md b/changes/3899.bugfix.md deleted file mode 100644 index e2b2177a39..0000000000 --- a/changes/3899.bugfix.md +++ /dev/null @@ -1,7 +0,0 @@ -Make chunk normalization properly handle `-1` as a compact representation of the -length of an entire axis. Reject several previously-accepted but ill-defined -chunk specifications: `chunks=True` (previously silently produced size-1 chunks), -chunk tuples shorter than the array's number of dimensions (previously padded to -the array's shape), and `None` as a per-dimension chunk size. These all now -raise informative errors. Also fix chunk handling for 0-length array dimensions, -and add explicit rejection of 0-length chunks. diff --git a/changes/3908.misc.md b/changes/3908.misc.md deleted file mode 100644 index 66717e8444..0000000000 --- a/changes/3908.misc.md +++ /dev/null @@ -1 +0,0 @@ -Reuse a constant `ArraySpec` during indexing when possible. \ No newline at end of file diff --git a/changes/3925.feature.md b/changes/3925.feature.md deleted file mode 100644 index ed07be309c..0000000000 --- a/changes/3925.feature.md +++ /dev/null @@ -1 +0,0 @@ -Add `zarr.abc.store.Store.get_ranges` for concurrent, coalesced multi-range reads from a single key. The method is defined on the `Store` ABC with a default implementation built on `Store.get`, so every store inherits a working version; stores with native multi-range backends (e.g. `FsspecStore`) can override for efficiency. Coalescing knobs (`max_concurrency`, `max_gap_bytes`, `max_coalesced_bytes`) are passed as keyword arguments to `get_ranges`. Failures from underlying fetches surface as a `BaseExceptionGroup` (PEP 654); callers should use `except*` to filter for specific exception types such as `FileNotFoundError`. diff --git a/changes/3954.bugfix.md b/changes/3954.bugfix.md deleted file mode 100644 index 1a6c93a8ac..0000000000 --- a/changes/3954.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Handle missing consolidated metadata in leaf Group nodes. diff --git a/changes/3963.removal.md b/changes/3963.removal.md deleted file mode 100644 index a83fd53853..0000000000 --- a/changes/3963.removal.md +++ /dev/null @@ -1,6 +0,0 @@ -The ``BloscShuffle`` and ``BloscCname`` enums (``zarr.codecs.BloscShuffle``, -``zarr.codecs.BloscCname``) are now deprecated. Pass the equivalent literal -string (e.g. ``"zstd"``, ``"bitshuffle"``) when constructing a ``BloscCodec``. -The enum classes remain importable but emit ``DeprecationWarning`` on member -access, and will be removed in a future release. ``BloscCodec.cname`` and -``BloscCodec.shuffle`` are now plain strings rather than enum members. diff --git a/changes/3968.removal.md b/changes/3968.removal.md deleted file mode 100644 index 075e4a15a9..0000000000 --- a/changes/3968.removal.md +++ /dev/null @@ -1,17 +0,0 @@ -The ``Endian`` (``zarr.codecs.bytes.Endian``) and ``ShardingCodecIndexLocation`` -(``zarr.codecs.ShardingCodecIndexLocation``) enums are now deprecated. Pass the -equivalent literal string instead (e.g. ``"little"`` / ``"big"``, ``"start"`` / -``"end"``). The enum classes remain importable but emit ``DeprecationWarning`` -on member access, and will be removed in a future release. ``BytesCodec.endian`` -and ``ShardingCodec.index_location`` are now plain strings rather than enum -members. - -Two follow-on changes from this deprecation: - -- ``NDBuffer.byteorder`` now returns a literal string (``"little"`` or - ``"big"``) rather than an ``Endian`` member. Subclasses overriding this - property should update their return type. -- The module-level binding ``zarr.codecs.bytes.default_system_endian`` was - removed. ``BytesCodec()`` continues to default to ``sys.byteorder``; - external callers that imported ``default_system_endian`` should use - ``sys.byteorder`` directly. diff --git a/changes/3972.misc.md b/changes/3972.misc.md deleted file mode 100644 index 60e5f75cca..0000000000 --- a/changes/3972.misc.md +++ /dev/null @@ -1 +0,0 @@ -Run `mypy` via `uv run mypy` instead of `pre-commit`'s isolated venv. The `dev` dependency group in `pyproject.toml`, locked by `uv.lock`, is now the single source of truth for `mypy`'s dependency set, eliminating the duplicate dependency list previously maintained in `.pre-commit-config.yaml` and giving every contributor and CI an identical, reproducible type-checking environment. diff --git a/changes/3973.removal.md b/changes/3973.removal.md deleted file mode 100644 index c25ac967a2..0000000000 --- a/changes/3973.removal.md +++ /dev/null @@ -1 +0,0 @@ -Removed the NumPy 1.x implementation of the `VariableLengthUTF8` data type because NumPy 1.x is no longer supported under [SPEC0](https://scientific-python.org/specs/spec-0000/). \ No newline at end of file diff --git a/changes/3975.misc.md b/changes/3975.misc.md deleted file mode 100644 index b90147988a..0000000000 --- a/changes/3975.misc.md +++ /dev/null @@ -1 +0,0 @@ -Store `chunks_per_shard` explicitly as a field on `_ShardIndex` instead of inferring it from `offsets_and_lengths.shape[:-1]`. The previous derivation collapsed to rank-1 for 0-D arrays, requiring a numpy-compat cast workaround that is now removed. Also removes the unused `_ShardIndex.is_dense` method, which was ported from an earlier prototype and never had any call sites or tests. diff --git a/changes/3977.bugfix.md b/changes/3977.bugfix.md deleted file mode 100644 index 6a8d9b4244..0000000000 --- a/changes/3977.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix flaky stateful test bookkeeping when `delete_dir` matches string prefixes instead of true directory descendants. Previously a path such as `6/faNT…` could be incorrectly removed when deleting `6/f`. (See [issue #3977](https://github.com/zarr-developers/zarr-python/issues/3977).) diff --git a/changes/3979.misc.md b/changes/3979.misc.md deleted file mode 100644 index 3d49547148..0000000000 --- a/changes/3979.misc.md +++ /dev/null @@ -1 +0,0 @@ -Remove the `UnstableSpecificationWarning` emitted when serializing a `FixedLengthUTF32` data type instance, as a spec for this data type has been published to zarr-extensions. \ No newline at end of file diff --git a/changes/3984.doc.md b/changes/3984.doc.md deleted file mode 100644 index 1b92fb8e74..0000000000 --- a/changes/3984.doc.md +++ /dev/null @@ -1,4 +0,0 @@ -Clarify the difference between `zarr.load` and `zarr.open` in their docstrings. -`load` eagerly reads data into an in-memory array, while `open` returns a -lazy `Array` or `Group` backed by the store, with `See Also` cross-references -linking the two. diff --git a/changes/3987.feature.md b/changes/3987.feature.md deleted file mode 100644 index 2492b4d7dd..0000000000 --- a/changes/3987.feature.md +++ /dev/null @@ -1 +0,0 @@ -Two new fields on `ArrayConfig` control how the sharding codec coalesces partial-shard reads: `sharding_coalesce_max_gap_bytes` (default 1 MiB) and `sharding_coalesce_max_bytes` (default 16 MiB). When reading multiple chunks from the same shard, nearby byte ranges are merged into a single request to the store if separated by no more than `sharding_coalesce_max_gap_bytes` and the merged read stays within `sharding_coalesce_max_bytes`. Defaults are seeded from the matching `array.sharding_coalesce_max_gap_bytes` / `array.sharding_coalesce_max_bytes` keys in [`zarr.config`][] at array-creation time, and can be overridden per array by passing `config={...}` to [`zarr.create_array`][]. diff --git a/changes/3990.misc.md b/changes/3990.misc.md deleted file mode 100644 index ff3fcf4cf2..0000000000 --- a/changes/3990.misc.md +++ /dev/null @@ -1,5 +0,0 @@ -Widen `ChunksLike` type alias to use `Iterable` instead of `Sequence`, and also -remove `None` from the type union. This supports a broader range of types, -removing the necessity to "materialize" iterable values simply to satisfy type -annotations. It also allows use of `ChunksLike` in cases where `None` should -not be permitted. diff --git a/changes/3998.misc.md b/changes/3998.misc.md deleted file mode 100644 index bacfa93a8b..0000000000 --- a/changes/3998.misc.md +++ /dev/null @@ -1 +0,0 @@ -Centralized JSON document I/O behind free functions in `zarr.core._json` and removed the unused private `Store._get_bytes`/`_get_json` methods and their per-store overrides. diff --git a/changes/4000.misc.md b/changes/4000.misc.md deleted file mode 100644 index 17d48d3016..0000000000 --- a/changes/4000.misc.md +++ /dev/null @@ -1 +0,0 @@ -Run all doctests via pytest and fix all broken doctests. diff --git a/changes/4001.misc.md b/changes/4001.misc.md deleted file mode 100644 index adbba988d9..0000000000 --- a/changes/4001.misc.md +++ /dev/null @@ -1,6 +0,0 @@ -Restore sharding write performance for shards with many inner chunks. The -`subchunk_write_order` feature inadvertently rebuilt the per-shard chunk -coordinate grid (up to tens of thousands of coordinate tuples) on every shard -write. These coordinates are now computed once per shard shape and cached, so -repeated writes to same-shaped shards reuse them, restoring write throughput to -its previous level. diff --git a/changes/4003.bugfix.md b/changes/4003.bugfix.md deleted file mode 100644 index 36327b55df..0000000000 --- a/changes/4003.bugfix.md +++ /dev/null @@ -1,19 +0,0 @@ -`FsspecStore.from_url()` and `from_mapper()` now close the async filesystem -they create when `store.close()` is called. Previously the underlying aiohttp -`ClientSession` was left open until garbage collection, producing -`"Unclosed client session"` `ResourceWarning`s from aiohttp. - -The fix introduces `FsspecStore._owns_fs`, a boolean that is ``True`` only when -`FsspecStore` itself created the filesystem (via `from_url` or `from_mapper` -when a sync→async conversion was performed). When `_owns_fs` is ``True``, -`store.close()` calls the new `_close_fs()` helper, which invokes -`fs.set_session()` and closes the returned client. Callers who supply their own -filesystem instance to `FsspecStore()` directly remain responsible for its -lifecycle; `_owns_fs` is ``False`` for those stores. - -**Scope note**: This fix closes the S3 client session that is active at the time -`store.close()` is called. Some S3-backed filesystem implementations (e.g. -s3fs with ``cache_regions=True``) may internally refresh and replace their -client during I/O operations, abandoning prior sessions before ``store.close()`` -is invoked. Those intermediate sessions are outside the scope of this fix and -are an issue in the upstream filesystem library. diff --git a/changes/4016.bugfix.md b/changes/4016.bugfix.md deleted file mode 100644 index 01984110f7..0000000000 --- a/changes/4016.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed an invalid `zarr.create_array` example in the quick-start documentation (it passed an unsupported `mode` argument) and made the cloud-storage example execute against a mock S3 backend in CI. Added a test ensuring every Python code block in the documentation is either executed or explicitly opted out with a documented reason, so an invalid example can no longer go untested. diff --git a/changes/4032.bugfix.md b/changes/4032.bugfix.md deleted file mode 100644 index 4c9476f583..0000000000 --- a/changes/4032.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed `ObjectStore.list_dir` for object-store listings that include a directory-marker object matching the requested non-root prefix. diff --git a/changes/4046.misc.md b/changes/4046.misc.md deleted file mode 100644 index 96c0c7d78a..0000000000 --- a/changes/4046.misc.md +++ /dev/null @@ -1 +0,0 @@ -Replace the internal `DefaultFillValue` sentinel class with a `typing_extensions.Sentinel`, and raise the minimum `typing_extensions` version to 4.14. diff --git a/changes/4052.doc.md b/changes/4052.doc.md deleted file mode 100644 index 90b4679db5..0000000000 --- a/changes/4052.doc.md +++ /dev/null @@ -1,21 +0,0 @@ -Updated the custom dtype example in `examples/custom_dtype/custom_dtype.py` to -use only the public API, eliminating all non-public imports, illustrating what -users should do. - -To better support this, the following types and functions were made available -from public modules: - -| Type/Function | Non-public module | Public module | -| ------------------------- | ------------------------ | ------------- | -| `DataTypeValidationError` | `zarr.core.dtype.common` | `zarr.errors` | -| `JSON` | `zarr.core.common` | `zarr.types` | -| `ZarrFormat` | `zarr.core.common` | `zarr.types` | -| `DTypeConfig_V2` | `zarr.core.dtype.common` | `zarr.types` | -| `DTypeJSON` | `zarr.core.dtype.common` | `zarr.types` | -| `DTypeSpec_V2` | `zarr.core.dtype.common` | `zarr.dtype` | -| `check_dtype_spec_v2` | `zarr.core.dtype.common` | `zarr.dtype` | - -`DataTypeValidationError` was *moved* to `zarr.errors`. Importing it from -`zarr.core.dtype.common` (its original location), `zarr.core.dtype`, or -`zarr.dtype` still works but now raises a `ZarrDeprecationWarning`. The remaining -types and functions are simply re-exported from the listed public module. diff --git a/changes/4053.doc.md b/changes/4053.doc.md deleted file mode 100644 index 3220b2b4ec..0000000000 --- a/changes/4053.doc.md +++ /dev/null @@ -1 +0,0 @@ -Document a self-merge policy in the contributor guide, describing when a core developer may merge their own pull request without a second reviewer and which changes warrant more caution. diff --git a/changes/4054.misc.md b/changes/4054.misc.md deleted file mode 100644 index 4aa9435b84..0000000000 --- a/changes/4054.misc.md +++ /dev/null @@ -1 +0,0 @@ -Add Hypothesis property tests for block and mask indexing (`test_block_indexing`, `test_mask_indexing`), along with a `block_indices` strategy in `zarr.testing.strategies`. These extend the existing randomized indexing coverage (basic, orthogonal, and vectorized) to the block and mask selection methods. diff --git a/changes/4059.bugfix.md b/changes/4059.bugfix.md deleted file mode 100644 index 16fb582f65..0000000000 --- a/changes/4059.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Prevents mutation of the attributes dict provided by the user by copying them instead of keeping the reference diff --git a/changes/4073.misc.md b/changes/4073.misc.md deleted file mode 100644 index bcc6b8281e..0000000000 --- a/changes/4073.misc.md +++ /dev/null @@ -1 +0,0 @@ -Extend the `test_block_indexing` Hypothesis property test to cover rectilinear chunk grids and sharded regular grids, and generalize the `block_indices` strategy in `zarr.testing.strategies` to build its array-space oracle from cumulative chunk offsets (`chunk_sizes` parameter) instead of a uniform chunk size. diff --git a/changes/4074.bugfix.md b/changes/4074.bugfix.md deleted file mode 100644 index d55a52b887..0000000000 --- a/changes/4074.bugfix.md +++ /dev/null @@ -1,7 +0,0 @@ -Fixed several storage and codec bugs: - -- Reading a value with a `SuffixByteRequest` larger than the value now correctly returns the whole value (matching HTTP `bytes=-N` suffix-range semantics), instead of silently returning incorrect data for `MemoryStore`. -- `LoggingStore.get_partial_values` and `FsspecStore.get_partial_values` no longer return empty results when `key_ranges` is passed as a one-shot iterable (e.g. a generator). -- `Store.getsize_prefix` no longer over-counts sibling keys that merely share a string prefix (e.g. `getsize_prefix("foo")` no longer includes keys under `foobar/`). -- `ZipStore.close()` no longer raises `AttributeError` when the store was created but never opened (including when used as a context manager without any I/O). -- `codecs_from_list` now raises a descriptive `TypeError` when a `BytesBytesCodec` immediately follows an `ArrayArrayCodec`, instead of a misleading "Required ArrayBytesCodec was not found" `ValueError`. diff --git a/changes/4086.misc.md b/changes/4086.misc.md deleted file mode 100644 index 2564cf9ea1..0000000000 --- a/changes/4086.misc.md +++ /dev/null @@ -1 +0,0 @@ -Fix `test_multiprocessing[fork]` failing on Python 3.15, where `os.fork()` in a multi-threaded process emits a `DeprecationWarning` that the test suite promotes to an error. diff --git a/changes/4116.bugfix.md b/changes/4116.bugfix.md deleted file mode 100644 index e99eac8c95..0000000000 --- a/changes/4116.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed writing Fortran-ordered (F-contiguous) arrays through the variable-length string and bytes codecs and through numcodecs array-array filters such as `Delta`, `FixedScaleOffset` and `PackBits`. Chunks are now passed to numcodecs as C-contiguous arrays, so elements are no longer stored in transposed order. diff --git a/changes/4132.doc.md b/changes/4132.doc.md deleted file mode 100644 index 3325c82f43..0000000000 --- a/changes/4132.doc.md +++ /dev/null @@ -1,6 +0,0 @@ -Fixed many documentation errors found in a full review of the user guide, including -prose contradicted by rendered example output on the performance page, invisible -code blocks, an incorrect S3 example, stale "not yet implemented" claims in the -v3 migration guide, and undocumented optional dependency groups. Also improved -navigation order, cross-linking between pages, and coverage of group member -enumeration, bulk attribute updates, and the `use_consolidated` keyword. diff --git a/changes/4133.doc.md b/changes/4133.doc.md deleted file mode 100644 index 9690318b46..0000000000 --- a/changes/4133.doc.md +++ /dev/null @@ -1 +0,0 @@ -Fixed the documented default of ``max_age_seconds`` in the ``CacheStore`` docstring: the default is ``"infinity"`` (no expiration), not ``None``, which is rejected. Also noted that ``cache_store`` must support deletes. diff --git a/changes/4138.misc.md b/changes/4138.misc.md deleted file mode 100644 index 2cf0365bb9..0000000000 --- a/changes/4138.misc.md +++ /dev/null @@ -1 +0,0 @@ -Pass a list rather than a generator to `pytest.mark.parametrize` in `tests/test_docs.py`, so the test suite collects cleanly under pytest 9.1 (which deprecates non-Collection iterables and, under `filterwarnings = error`, turns that into a collection error). diff --git a/changes/4141.bugfix.md b/changes/4141.bugfix.md deleted file mode 100644 index 6a132da3f5..0000000000 --- a/changes/4141.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fix silent byte-order corruption for structured dtypes with the `bytes` codec: multi-byte fields are now byte-swapped to the codec's configured `endian` on write and decoded honoring it on read, so non-native-endian structured data (e.g. big-endian fields, as produced by virtual references to external data) round-trips correctly. diff --git a/docs/release-notes.md b/docs/release-notes.md index 3ba870ac92..e85137f2b6 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -2,6 +2,162 @@ <!-- towncrier release notes start --> +## 3.3.0 (2026-07-15) + +### Features + +- Optimizes reading multiple chunks from a shard. Serial calls to `Store.get()` + in the sharding codec have been replaced with a single call to + `Store.get_ranges()`, which coalesces nearby byte ranges and fetches them + concurrently. ([#3004](https://github.com/zarr-developers/zarr-python/issues/3004)) +- Added a `subchunk_write_order` option to `ShardingCodec` to control the physical order of subchunks within a shard. Supported values are `morton`, `unordered`, `lexicographic`, and `colexicographic`. `unordered` makes no guarantee about subchunk layout. This setting affects only on-disk layout, not the data read back, and is not persisted in array metadata: it applies per codec instance and is not recovered when reopening a sharded array. ([#3826](https://github.com/zarr-developers/zarr-python/issues/3826)) +- Added `SyncByteGetter` and `SyncByteSetter` runtime-checkable protocols and a `get_ranges_sync` method on the `Store` ABC. These let custom byte getters/setters opt into the synchronous codec pipeline's fast path for in-memory IO, which the sharding codec uses for its inner chunks. ([#3885](https://github.com/zarr-developers/zarr-python/issues/3885)) +- Added `FusedCodecPipeline`, an opt-in codec pipeline that runs codec compute synchronously and in bulk (avoiding the per-chunk async scheduling overhead of the default `BatchedCodecPipeline`), giving large speedups for sharded arrays (up to ~24x writes / ~14x reads on many-chunks-per-shard layouts, more with compression) and no regressions on compute-bound workloads. The default `BatchedCodecPipeline` is unchanged for standard configurations, so existing code keeps working unless you opt in; enable the new pipeline with `zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"})`. ([#3885](https://github.com/zarr-developers/zarr-python/issues/3885)) +- Add `zarr.abc.store.Store.get_ranges` for concurrent, coalesced multi-range reads from a single key. The method is defined on the `Store` ABC with a default implementation built on `Store.get`, so every store inherits a working version; stores with native multi-range backends (e.g. `FsspecStore`) can override for efficiency. Coalescing knobs (`max_concurrency`, `max_gap_bytes`, `max_coalesced_bytes`) are passed as keyword arguments to `get_ranges`. Failures from underlying fetches surface as a `BaseExceptionGroup` (PEP 654); callers should use `except*` to filter for specific exception types such as `FileNotFoundError`. ([#3925](https://github.com/zarr-developers/zarr-python/issues/3925)) +- Two new fields on `ArrayConfig` control how the sharding codec coalesces partial-shard reads: `sharding_coalesce_max_gap_bytes` (default 1 MiB) and `sharding_coalesce_max_bytes` (default 16 MiB). When reading multiple chunks from the same shard, nearby byte ranges are merged into a single request to the store if separated by no more than `sharding_coalesce_max_gap_bytes` and the merged read stays within `sharding_coalesce_max_bytes`. Defaults are seeded from the matching `array.sharding_coalesce_max_gap_bytes` / `array.sharding_coalesce_max_bytes` keys in [`zarr.config`][] at array-creation time, and can be overridden per array by passing `config={...}` to [`zarr.create_array`][]. ([#3987](https://github.com/zarr-developers/zarr-python/issues/3987)) + +### Bugfixes + +- Stop emitting an `UnstableSpecificationWarning` when serializing the `struct` data type to Zarr V3 metadata. The `struct` data type now has a stable Zarr V3 specification. The legacy `structured` alias and the unspecified `null_terminated_bytes`, `raw_bytes`, and `variable_length_bytes` data types continue to warn. ([#202](https://github.com/zarr-developers/zarr-python/issues/202)) +- Fix equality comparison of `ArrayV2Metadata` and `ArrayV3Metadata` objects with a + `NaN` fill value. Such objects are now compared by their JSON-serialized form, so two + otherwise-identical metadata objects with a `NaN` (or infinite) fill value compare equal. ([#2929](https://github.com/zarr-developers/zarr-python/issues/2929)) +- Fixed `BytesCodec.from_dict` so that `BytesCodec` instances roundtrip to / from + their dict representation. `BytesCodec.from_dict` now interprets a missing + `endian` configuration as `endian=None` (matching what `BytesCodec.to_dict` + emits), instead of falling back to the system's native byte order. ([#3417](https://github.com/zarr-developers/zarr-python/issues/3417)) +- Fixed `save_array`, `Group.__setitem__`, and `load` for 0-dimensional arrays. ([#3469](https://github.com/zarr-developers/zarr-python/issues/3469)) +- Fixed inner-codec spec evolution for sharded arrays. The sharding codec now threads the array spec through its inner codec chain when evolving codecs, so a codec that changes the dtype upstream of `BytesCodec` no longer leaves the inner chain evolved against the wrong spec (which previously failed at decode time). This runs on the default `BatchedCodecPipeline` as well. Standard inner chains (`[BytesCodec]`, `[BytesCodec, ZstdCodec]`, transpose + bytes) are byte-identical to before. Restores the behavior of #2179. ([#3885](https://github.com/zarr-developers/zarr-python/issues/3885)) +- Make chunk normalization properly handle `-1` as a compact representation of the + length of an entire axis. Reject several previously-accepted but ill-defined + chunk specifications: `chunks=True` (previously silently produced size-1 chunks), + chunk tuples shorter than the array's number of dimensions (previously padded to + the array's shape), and `None` as a per-dimension chunk size. These all now + raise informative errors. Also fix chunk handling for 0-length array dimensions, + and add explicit rejection of 0-length chunks. ([#3899](https://github.com/zarr-developers/zarr-python/issues/3899)) +- Handle missing consolidated metadata in leaf Group nodes. ([#3954](https://github.com/zarr-developers/zarr-python/issues/3954)) +- Corrected the JSON type definitions for the `numpy.datetime64` and + `numpy.timedelta64` data types in Zarr V3 metadata: the `configuration` object + (holding `unit` and `scale_factor`) is now required, matching the published + specifications for these data types. Also updated the specification links in + the docstrings to point to the zarr-extensions repository. ([#3955](https://github.com/zarr-developers/zarr-python/issues/3955)) +- Fixed writing to 0-dimensional arrays that use the sharding codec. Previously + assigning to a 0-dimensional sharded array raised an error. ([#3966](https://github.com/zarr-developers/zarr-python/issues/3966)) +- Fix flaky stateful test bookkeeping when `delete_dir` matches string prefixes instead of true directory descendants. Previously a path such as `6/faNT…` could be incorrectly removed when deleting `6/f`. (See [issue #3977](https://github.com/zarr-developers/zarr-python/issues/3977).) ([#3977](https://github.com/zarr-developers/zarr-python/issues/3977)) +- `FsspecStore.from_url()` and `from_mapper()` now close the async filesystem + they create when `store.close()` is called. Previously the underlying aiohttp + `ClientSession` was left open until garbage collection, producing + `"Unclosed client session"` `ResourceWarning`s from aiohttp. + + The fix introduces `FsspecStore._owns_fs`, a boolean that is ``True`` only when + `FsspecStore` itself created the filesystem (via `from_url` or `from_mapper` + when a sync→async conversion was performed). When `_owns_fs` is ``True``, + `store.close()` calls the new `_close_fs()` helper, which invokes + `fs.set_session()` and closes the returned client. Callers who supply their own + filesystem instance to `FsspecStore()` directly remain responsible for its + lifecycle; `_owns_fs` is ``False`` for those stores. + + **Scope note**: This fix closes the S3 client session that is active at the time + `store.close()` is called. Some S3-backed filesystem implementations (e.g. + s3fs with ``cache_regions=True``) may internally refresh and replace their + client during I/O operations, abandoning prior sessions before ``store.close()`` + is invoked. Those intermediate sessions are outside the scope of this fix and + are an issue in the upstream filesystem library. ([#4003](https://github.com/zarr-developers/zarr-python/issues/4003)) +- Fixed an invalid `zarr.create_array` example in the quick-start documentation (it passed an unsupported `mode` argument) and made the cloud-storage example execute against a mock S3 backend in CI. Added a test ensuring every Python code block in the documentation is either executed or explicitly opted out with a documented reason, so an invalid example can no longer go untested. ([#4016](https://github.com/zarr-developers/zarr-python/issues/4016)) +- Fixed `ObjectStore.list_dir` for object-store listings that include a directory-marker object matching the requested non-root prefix. ([#4032](https://github.com/zarr-developers/zarr-python/issues/4032)) +- Prevents mutation of the attributes dict provided by the user by copying them instead of keeping the reference ([#4059](https://github.com/zarr-developers/zarr-python/issues/4059)) +- Fixed several storage and codec bugs: + + - Reading a value with a `SuffixByteRequest` larger than the value now correctly returns the whole value (matching HTTP `bytes=-N` suffix-range semantics), instead of silently returning incorrect data for `MemoryStore`. + - `LoggingStore.get_partial_values` and `FsspecStore.get_partial_values` no longer return empty results when `key_ranges` is passed as a one-shot iterable (e.g. a generator). + - `Store.getsize_prefix` no longer over-counts sibling keys that merely share a string prefix (e.g. `getsize_prefix("foo")` no longer includes keys under `foobar/`). + - `ZipStore.close()` no longer raises `AttributeError` when the store was created but never opened (including when used as a context manager without any I/O). + - `codecs_from_list` now raises a descriptive `TypeError` when a `BytesBytesCodec` immediately follows an `ArrayArrayCodec`, instead of a misleading "Required ArrayBytesCodec was not found" `ValueError`. + + ([#4074](https://github.com/zarr-developers/zarr-python/issues/4074)) +- Fixed writing Fortran-ordered (F-contiguous) arrays through the variable-length string and bytes codecs and through numcodecs array-array filters such as `Delta`, `FixedScaleOffset` and `PackBits`. Chunks are now passed to numcodecs as C-contiguous arrays, so elements are no longer stored in transposed order. ([#4116](https://github.com/zarr-developers/zarr-python/issues/4116)) +- Fix silent byte-order corruption for structured dtypes with the `bytes` codec: multi-byte fields are now byte-swapped to the codec's configured `endian` on write and decoded honoring it on read, so non-native-endian structured data (e.g. big-endian fields, as produced by virtual references to external data) round-trips correctly. ([#4141](https://github.com/zarr-developers/zarr-python/issues/4141)) + +### Improved Documentation + +- Document the changes to `zarr.errors` in the 3.0 migration guide, including the removal of v2 exception classes and the introduction of `NodeNotFoundError`. ([#3009](https://github.com/zarr-developers/zarr-python/issues/3009)) +- Clarify the difference between `zarr.load` and `zarr.open` in their docstrings. + `load` eagerly reads data into an in-memory array, while `open` returns a + lazy `Array` or `Group` backed by the store, with `See Also` cross-references + linking the two. ([#3984](https://github.com/zarr-developers/zarr-python/issues/3984)) +- Updated the custom dtype example in `examples/custom_dtype/custom_dtype.py` to + use only the public API, eliminating all non-public imports, illustrating what + users should do. + + To better support this, the following types and functions were made available + from public modules: + + | Type/Function | Non-public module | Public module | + | ------------------------- | ------------------------ | ------------- | + | `DataTypeValidationError` | `zarr.core.dtype.common` | `zarr.errors` | + | `JSON` | `zarr.core.common` | `zarr.types` | + | `ZarrFormat` | `zarr.core.common` | `zarr.types` | + | `DTypeConfig_V2` | `zarr.core.dtype.common` | `zarr.types` | + | `DTypeJSON` | `zarr.core.dtype.common` | `zarr.types` | + | `DTypeSpec_V2` | `zarr.core.dtype.common` | `zarr.dtype` | + | `check_dtype_spec_v2` | `zarr.core.dtype.common` | `zarr.dtype` | + + `DataTypeValidationError` was *moved* to `zarr.errors`. Importing it from + `zarr.core.dtype.common` (its original location), `zarr.core.dtype`, or + `zarr.dtype` still works but now raises a `ZarrDeprecationWarning`. The remaining + types and functions are simply re-exported from the listed public module. ([#4052](https://github.com/zarr-developers/zarr-python/issues/4052)) +- Document a self-merge policy in the contributor guide, describing when a core developer may merge their own pull request without a second reviewer and which changes warrant more caution. ([#4053](https://github.com/zarr-developers/zarr-python/issues/4053)) +- Fixed many documentation errors found in a full review of the user guide, including + prose contradicted by rendered example output on the performance page, invisible + code blocks, an incorrect S3 example, stale "not yet implemented" claims in the + v3 migration guide, and undocumented optional dependency groups. Also improved + navigation order, cross-linking between pages, and coverage of group member + enumeration, bulk attribute updates, and the `use_consolidated` keyword. ([#4132](https://github.com/zarr-developers/zarr-python/issues/4132)) +- Fixed the documented default of ``max_age_seconds`` in the ``CacheStore`` docstring: the default is ``"infinity"`` (no expiration), not ``None``, which is rejected. Also noted that ``cache_store`` must support deletes. ([#4133](https://github.com/zarr-developers/zarr-python/issues/4133)) + +### Deprecations and Removals + +- The ``BloscShuffle`` and ``BloscCname`` enums (``zarr.codecs.BloscShuffle``, + ``zarr.codecs.BloscCname``) are now deprecated. Pass the equivalent literal + string (e.g. ``"zstd"``, ``"bitshuffle"``) when constructing a ``BloscCodec``. + The enum classes remain importable but emit ``DeprecationWarning`` on member + access, and will be removed in a future release. ``BloscCodec.cname`` and + ``BloscCodec.shuffle`` are now plain strings rather than enum members. + + Additional renames in ``zarr.codecs.blosc`` from the same change: the type + aliases ``Shuffle`` and ``CName`` are now ``BloscShuffleLiteral`` and + ``BloscCnameLiteral``, the constant ``SHUFFLE`` is now ``BLOSC_SHUFFLE`` + (with a new ``BLOSC_CNAME`` alongside it), and ``BloscShuffle.from_int`` + now returns a literal string rather than an enum member. ([#3963](https://github.com/zarr-developers/zarr-python/issues/3963)) +- The ``Endian`` (``zarr.codecs.bytes.Endian``) and ``ShardingCodecIndexLocation`` + (``zarr.codecs.ShardingCodecIndexLocation``) enums are now deprecated. Pass the + equivalent literal string instead (e.g. ``"little"`` / ``"big"``, ``"start"`` / + ``"end"``). The enum classes remain importable but emit ``DeprecationWarning`` + on member access, and will be removed in a future release. ``BytesCodec.endian`` + and ``ShardingCodec.index_location`` are now plain strings rather than enum + members. + + Two follow-on changes from this deprecation: + + - ``NDBuffer.byteorder`` now returns a literal string (``"little"`` or + ``"big"``) rather than an ``Endian`` member. Subclasses overriding this + property should update their return type. + - The module-level binding ``zarr.codecs.bytes.default_system_endian`` was + removed. ``BytesCodec()`` continues to default to ``sys.byteorder``; + external callers that imported ``default_system_endian`` should use + ``sys.byteorder`` directly. + + Additionally, the module-level function ``zarr.codecs.sharding.parse_index_location`` + was made private as part of this change. + + ([#3968](https://github.com/zarr-developers/zarr-python/issues/3968)) +- Removed the NumPy 1.x implementation of the `VariableLengthUTF8` data type because NumPy 1.x is no longer supported under [SPEC0](https://scientific-python.org/specs/spec-0000/). ([#3973](https://github.com/zarr-developers/zarr-python/issues/3973)) + +### Misc + +- [#214](https://github.com/zarr-developers/zarr-python/issues/214), [#215](https://github.com/zarr-developers/zarr-python/issues/215), [#3908](https://github.com/zarr-developers/zarr-python/issues/3908), [#3972](https://github.com/zarr-developers/zarr-python/issues/3972), [#3975](https://github.com/zarr-developers/zarr-python/issues/3975), [#3979](https://github.com/zarr-developers/zarr-python/issues/3979), [#3990](https://github.com/zarr-developers/zarr-python/issues/3990), [#3998](https://github.com/zarr-developers/zarr-python/issues/3998), [#4000](https://github.com/zarr-developers/zarr-python/issues/4000), [#4001](https://github.com/zarr-developers/zarr-python/issues/4001), [#4046](https://github.com/zarr-developers/zarr-python/issues/4046), [#4054](https://github.com/zarr-developers/zarr-python/issues/4054), [#4073](https://github.com/zarr-developers/zarr-python/issues/4073), [#4086](https://github.com/zarr-developers/zarr-python/issues/4086), [#4138](https://github.com/zarr-developers/zarr-python/issues/4138) + + ## 3.2.1 (2026-05-05) ### Bugfixes From 23d96d38ae1cb1b722681f16eec7af171890b367 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 16 Jul 2026 11:30:12 -0400 Subject: [PATCH 404/468] chore: CI worfklows for linting docs (#4076) * chore: CI worfklows for missing docs and RST docstrings * Add linter for docs * Add link checking workflow * fix links * fix: apply suggestions from code review * refactor: readability improvements * chore: switch lychee action to opening issue on failure --------- Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- .github/workflows/docs.yml | 5 + .github/workflows/links.yml | 32 +++ .markdownlint-cli2.jsonc | 54 +++++ .pre-commit-config.yaml | 10 + ci/check_documented_exports.py | 161 +++++++++++++ ci/lint_docs.py | 284 +++++++++++++++++++++++ docs/contributing.md | 23 +- docs/index.md | 14 +- docs/quick-start.md | 2 - docs/release-notes.md | 2 + docs/user-guide/attributes.md | 1 + docs/user-guide/consolidated_metadata.md | 1 - docs/user-guide/data_types.md | 7 + docs/user-guide/experimental.md | 1 - docs/user-guide/extending.md | 1 + docs/user-guide/groups.md | 1 - docs/user-guide/performance.md | 6 +- docs/user-guide/storage.md | 8 +- lychee.toml | 20 ++ src/zarr/core/metadata/v2.py | 2 +- src/zarr/testing/store.py | 6 +- 21 files changed, 608 insertions(+), 33 deletions(-) create mode 100644 .github/workflows/links.yml create mode 100644 .markdownlint-cli2.jsonc create mode 100644 ci/check_documented_exports.py create mode 100644 ci/lint_docs.py create mode 100644 lychee.toml diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 59eca8d9b9..c72b493b12 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -24,6 +24,11 @@ jobs: persist-credentials: false - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - run: uv sync --group docs + # Fast source-level guards that need no built site, so they run before the (slower) + # build for a quick failure: every public export is in the API reference, and no + # docstring/Markdown carries reStructuredText markup that MkDocs won't render. + - run: uv run python ci/check_documented_exports.py docs/api + - run: uv run python ci/lint_docs.py # --strict turns warnings into errors, so a docs code block that fails to execute # at build time (e.g. a non-exec python fence disrupting a later exec="true" block) # fails CI instead of merging as a silent warning. diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml new file mode 100644 index 0000000000..a53de8da83 --- /dev/null +++ b/.github/workflows/links.yml @@ -0,0 +1,32 @@ +name: Check links + +on: + repository_dispatch: + workflow_dispatch: + # pull_request: + schedule: + - cron: "00 18 * * *" + +jobs: + linkChecker: + runs-on: ubuntu-latest + permissions: + issues: write # required for peter-evans/create-issue-from-file + steps: + - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + with: + persist-credentials: false + + - name: Link Checker + id: lychee + uses: lycheeverse/lychee-action@8646ba30535128ac92d33dfc9133794bfdd9b411 # v2.8.0 + with: + fail: false + + - name: Create Issue From File + if: steps.lychee.outputs.exit_code != 0 + uses: peter-evans/create-issue-from-file@fca9117c27cdc29c6c4db3b86c48e4115a786710 # v6.0.0 + with: + title: Link Checker Report + content-filepath: ./lychee/out.md + labels: report, automated issue diff --git a/.markdownlint-cli2.jsonc b/.markdownlint-cli2.jsonc new file mode 100644 index 0000000000..3dfdf96856 --- /dev/null +++ b/.markdownlint-cli2.jsonc @@ -0,0 +1,54 @@ +// markdownlint-cli2 configuration for zarr-python docs. +// +// We keep the rules that catch real rendering/structure problems and disable those that +// are pure style, conflict with house conventions, or fire false positives against our +// MkDocs/mkdocstrings + pymdownx toolchain. Complementary, not overlapping, with +// ci/lint_docs.py (RST residue + list-breaking fences) and `mkdocs build --strict`. +{ + "config": { + "default": true, + + // House style: Markdown paragraphs are single unwrapped lines, so line length is not + // a meaningful constraint. + "MD013": false, + + // Purely stylistic marker/emphasis choices -- not worth the churn across existing docs. + "MD004": false, // ul bullet style (-, *, +) + "MD007": false, // ul indentation width + "MD050": false, // strong (bold) style + "MD035": false, // hr style + + // False positives from our toolchain: + // mkdocstrings cross-refs `[`X`][zarr.X]` read as undefined reference links (MD052); + // pymdownx.magiclink auto-links bare URLs (MD034); + // md_in_html lets us embed intentional raw HTML (MD033); + // generated/included files (api stubs, snippets) need not open with an H1 (MD041). + "MD052": false, + "MD034": false, + "MD033": false, + "MD041": false, + + // Duplicate headings are legitimate under different sections (e.g. repeated + // "Documentation"); only flag true sibling duplicates. + "MD024": { "siblings_only": true }, + + // Opinionated table/link/command rules with low value for these docs. + "MD055": false, // table pipe style + "MD060": false, // table column style + "MD059": false, // "descriptive" link text (no "click here") + "MD014": false, // $ before commands without shown output + + // markdownlint does not understand MkDocs `!!!` admonitions, so it reads their + // 4-space-indented bodies as indented code blocks and flags them (and, via inferred + // file style, flags real fenced blocks too). Cannot coexist with our admonitions. + "MD046": false // code block style (fenced vs indented) + // Kept on (structural / real rendering bugs): MD012 (multiple blanks), MD022/MD031/MD032 + // (blanks around headings/fences/lists), MD025 (single H1), MD029 (ordered-list prefix), + // MD040 (fenced code language), MD042 (empty links), + // MD047 (trailing newline), MD056 (table column count), among others. + }, + "globs": ["docs/**/*.md"], + "ignores": [ + "docs/api/**" // mkdocstrings stubs (`::: zarr.X`) + ] +} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e08c98abca..57a1d0d4f7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -31,6 +31,16 @@ repos: - id: check-yaml exclude: mkdocs.yml - id: trailing-whitespace + - repo: https://github.com/DavidAnson/markdownlint-cli2 + rev: v0.22.1 + hooks: + # Markdown structure/hygiene. Rule selection and ignores are in + # .markdownlint-cli2.jsonc; complements ci/lint_docs.py (RST residue, + # list-breaking fences) and `mkdocs build --strict`. Scoped to docs/ to + # match the config's globs (pre-commit passes filenames, which would + # otherwise override that scoping and lint all repo Markdown). + - id: markdownlint-cli2 + files: ^docs/ - repo: local hooks: - id: mypy diff --git a/ci/check_documented_exports.py b/ci/check_documented_exports.py new file mode 100644 index 0000000000..0772954399 --- /dev/null +++ b/ci/check_documented_exports.py @@ -0,0 +1,161 @@ +"""Check that every public top-level export is in the API reference. + +The API reference is authored as explicit mkdocstrings directives (``::: target``) +under ``docs/api/`` -- one per documented symbol -- rather than autodoc, so a newly +added ``zarr.__all__`` entry will not appear in the docs until someone writes a page +for it (or it becomes a rendered member of an already-documented module). This script +catches that gap: it resolves every ``:::`` target, expands module directives into the +members they render (honoring ``members: false``), and asserts each name in +``zarr.__all__`` resolves to a documented object. + +Usage: + python ci/check_documented_exports.py [API_DOCS_DIR] + +API_DOCS_DIR defaults to the repo-root ``docs/api``. Exits non-zero (and prints the +undocumented exports to stderr) if any public export is missing from the reference. +""" + +from __future__ import annotations + +import importlib +import re +import sys +from pathlib import Path +from types import ModuleType +from typing import TYPE_CHECKING, Any + +import zarr + +if TYPE_CHECKING: + from collections.abc import Iterator + +REPO_ROOT = Path(__file__).parent.parent.resolve() +DEFAULT_API_DOCS_ROOT = REPO_ROOT / "docs" / "api" + +# Names in zarr.__all__ that are intentionally absent from the API reference. +# Keep this list short and justified -- it is the only escape hatch from the guard. +EXEMPT_EXPORTS = { + "__version__", # version string, not an API symbol + "print_debug_info", # debugging helper, deliberately not in the reference +} + +# A mkdocstrings autodoc directive: `::: some.dotted.target` at the start of a line. +DIRECTIVE_RE = re.compile(r"^:::[ \t]+(?P<target>\S+)") +# `members: false` (or `members: []`) within a directive's option block disables +# rendering of a module's members. +MEMBERS_DISABLED_RE = re.compile(r"^\s+members:\s*(false|\[\s*\])\s*$") + + +def resolve(target: str) -> Any: + """Resolve a `:::` target (a dotted path) to the Python object it documents.""" + try: + return importlib.import_module(target) + except ImportError: + pass + module_path, _, attr = target.rpartition(".") + try: + return getattr(importlib.import_module(module_path), attr) + except (ImportError, AttributeError): + return None + + +def iter_directives(text: str) -> Iterator[tuple[str, bool]]: + """Yield ``(target, members_enabled)`` for each ``:::`` directive in ``text``. + + The file is split into lines once; for each directive we scan its indented option + block -- stopping at the first non-indented line, which ends the block -- so options + belonging to a later directive are never consulted. ``members_enabled`` is False when + that block sets ``members: false`` (or ``members: []``).""" + lines = text.splitlines() + i = 0 + while i < len(lines): + match = DIRECTIVE_RE.match(lines[i]) + if match is None: + i += 1 + continue + members_enabled = True + i += 1 + while i < len(lines): + line = lines[i] + if line.strip() == "": + i += 1 + continue + if not line.startswith((" ", "\t")): + break # non-indented line: end of this directive's option block + if MEMBERS_DISABLED_RE.match(line): + members_enabled = False + i += 1 + yield match.group("target"), members_enabled + + +def module_member_ids(module: ModuleType) -> Iterator[int]: + """Yield the id() of each public member a module directive renders. + + The rendered members are the module's ``__all__`` if defined, else its public + (non-underscore) attributes.""" + member_names = getattr(module, "__all__", None) or [ + name for name in dir(module) if not name.startswith("_") + ] + for name in member_names: + member = getattr(module, name, None) + if member is not None: + yield id(member) + + +def documented_object_ids(api_docs_root: Path) -> set[int]: + """Collect the id()s of every object rendered by a `:::` directive under api_docs_root. + + A directive pointing at an object documents that object. A directive pointing at a + module documents the module's public members unless the directive sets + ``members: false``.""" + documented: set[int] = set() + for md_file in sorted(api_docs_root.rglob("*.md")): + for target, members_enabled in iter_directives(md_file.read_text(encoding="utf-8")): + obj = resolve(target) + if obj is None: + continue + documented.add(id(obj)) + if isinstance(obj, ModuleType) and members_enabled: + documented.update(module_member_ids(obj)) + return documented + + +def find_undocumented_exports(api_docs_root: Path) -> list[str]: + documented = documented_object_ids(api_docs_root) + return sorted( + name + for name in zarr.__all__ + if name not in EXEMPT_EXPORTS and id(getattr(zarr, name)) not in documented + ) + + +def main() -> int: + args = sys.argv[1:] + api_docs_root = Path(args[0]).resolve() if args else DEFAULT_API_DOCS_ROOT + if not api_docs_root.exists(): + print(f"{api_docs_root} does not exist.", file=sys.stderr) + return 1 + + missing = find_undocumented_exports(api_docs_root) + if not missing: + print(f"All {len(zarr.__all__)} public exports are documented.") + return 0 + + print( + f"Found {len(missing)} public export(s) in zarr.__all__ missing from the API " + "reference (docs/api/):\n", + file=sys.stderr, + ) + for name in missing: + print(f" - zarr.{name}", file=sys.stderr) + print( + "\nAdd a `::: zarr.<name>` page under docs/api/zarr/ (and register it in " + "mkdocs.yml and docs/api/zarr/index.md), or -- if the export is intentionally " + "undocumented -- add it to EXEMPT_EXPORTS in this script with a reason.", + file=sys.stderr, + ) + return 1 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/ci/lint_docs.py b/ci/lint_docs.py new file mode 100644 index 0000000000..ff7b56649b --- /dev/null +++ b/ci/lint_docs.py @@ -0,0 +1,284 @@ +"""Lint docstrings and Markdown for reStructuredText markup that won't render. + +This project renders API docs with mkdocstrings (``docstring_style: numpy``) and prose +with MkDocs + Markdown -- not Sphinx/reStructuredText. RST constructs that survive from +older docstrings (or muscle memory) are not interpreted: a Sphinx role passes through as +literal text instead of becoming a link, an ``.. note::`` directive renders as a stray +line, and a ``:param:`` field list never becomes a documented parameter. + +Crucially, none of this is caught by the rest of the docs CI. ``mkdocs build --strict`` +sees the residue as ordinary prose (no warning), and ``ci/check_unlinked_types.py`` only +finds cross-references mkdocstrings *attempted* to resolve -- a raw ``:class:`` role is +never attempted, so it leaves no unlinked-type span. This linter fills that gap with a +fast, source-level check that needs no docs build. + +Checks fall into two groups -- RST markup that silently fails under MkDocs/mkdocstrings, +and a Markdown structural problem that renders as valid-but-wrong HTML (so `mkdocs build` +emits no warning): + + sphinx-role :class:`X`, :func:`X`, :py:meth:`X` -> [`X`][zarr.X] + rst-directive .. note:: / .. code-block:: python -> MkDocs admonition / fenced code + rst-field :param x:, :returns:, :rtype: -> numpydoc Parameters/Returns/Raises + rst-link `text <https://example>`_ -> [text](https://example) + list-break unindented code fence between list items -> indent the fence under its item + +The ``list-break`` check catches a fenced code block at column 0 placed *between* two list +items: because the fence is not indented into the preceding item, Markdown ends the list at +the fence and the following item starts a fresh list -- renumbering an ordered list (1, 1, 2 +instead of 1, 2, 3) or breaking the grouping/spacing of any list. markdownlint's MD029 only +notices this for sequentially-numbered ordered lists; lazily-numbered (1., 1.) and unordered +lists slip past it, so this structural check covers the gap. + +Usage: + python ci/lint_docs.py [PATH ...] + +PATH defaults to the repo-root ``src/zarr`` and ``docs``. Each PATH may be a file or a +directory (directories are searched for ``*.py`` and ``*.md``). Exits non-zero if any +issues are found. +""" + +from __future__ import annotations + +import ast +import re +import sys +from dataclasses import dataclass +from pathlib import Path +from typing import NamedTuple + +REPO_ROOT = Path(__file__).parent.parent.resolve() +DEFAULT_PATHS = (REPO_ROOT / "src" / "zarr", REPO_ROOT / "docs") + +# A Sphinx interpreted-text role: an optional domain, a role name, then a backtick +# target -- e.g. :class:`Foo` or :py:meth:`Foo.bar`. Requires the trailing backtick so +# plain "::" (RST literal markers, time strings, mkdocs-material :icon: shortcodes) and +# URLs ("https://") never match. +SPHINX_ROLE = re.compile(r":[a-zA-Z_]\w*(?::[a-zA-Z_]\w*)?:`[^`\n]+`") + +# An RST directive line: ".. name::" (with or without an argument after it). RST hyperlink +# targets (".. _label:") and comments (".. text") lack the "::" and are not flagged. +RST_DIRECTIVE = re.compile(r"^\s*\.\.[ \t]+[\w-]+::") + +# An RST field-list entry used for docstring fields. The role names above (class, func, +# ...) are deliberately excluded so a role is reported as a role, not a field. +RST_FIELD = re.compile( + r"^\s*:(param|parameter|arg|argument|key|keyword|kwarg|type|returns?|rtype" + r"|raises?|except|exception|yields?|ytype|var|cvar|ivar)\b[^:]*:" +) + +# An RST external hyperlink: `text <url>`_ +RST_LINK = re.compile(r"`[^`\n]+<https?://[^>\n]+>`_") + +# A list item at column 0: an ordered marker (1. / 1)) or a bullet (-, *, +) followed by +# whitespace and content. Leading-whitespace (nested/continuation) lines are intentionally +# not matched -- the list-break check only fires on top-level items. +LIST_ITEM = re.compile(r"^(?:\d+[.)]|[-*+])\s+\S") + + +class Check(NamedTuple): + """One docs-residue check: its category, the line pattern that flags it (None for a + structural check matched outside ``_scan_line``), and the user-facing remediation + shown by ``main()``. Keeping ``example``/``fix`` here makes this the single source for + the help text, so adding a check can't leave the help out of date.""" + + category: str + pattern: re.Pattern[str] | None + example: str + fix: str + + +# ``list-break`` carries no pattern -- it is detected structurally in find_list_breaking_fences, +# not by scanning a single line -- but it appears here so it shares the remediation help. +CHECKS = ( + Check("sphinx-role", SPHINX_ROLE, ":class:`X`", "[`X`][zarr.X]"), + Check("rst-directive", RST_DIRECTIVE, ".. note::", "MkDocs admonition (!!! note)"), + Check("rst-field", RST_FIELD, ":param x:", "numpydoc Parameters/Returns/Raises section"), + Check("rst-link", RST_LINK, "`text <url>`_", "[text](url)"), + Check("list-break", None, "fence between items", "indent the fence 4 spaces to nest it"), +) + + +@dataclass(frozen=True) +class Finding: + path: Path + line: int + category: str + snippet: str + + def format(self) -> str: + try: + location: Path | str = self.path.relative_to(REPO_ROOT) + except ValueError: + location = self.path + return f" {location}:{self.line}: [{self.category}] {self.snippet.strip()}" + + +def _scan_line(text: str) -> list[str]: + """Return every RST-residue category found in a single line (a line can carry more + than one, e.g. a role and an external link).""" + return [c.category for c in CHECKS if c.pattern is not None and c.pattern.search(text)] + + +def lint_python(path: Path) -> list[Finding]: + """Scan the docstrings (module, classes, functions) of a Python file. + + Only docstrings are checked -- they are what mkdocstrings renders -- so RST-looking + text inside ordinary code or string literals is never misreported.""" + source = path.read_text(encoding="utf-8") + try: + tree = ast.parse(source) + except SyntaxError as exc: # pragma: no cover - surfaced, not silently skipped + return [Finding(path, exc.lineno or 0, "syntax-error", str(exc.msg))] + + doc_nodes = (ast.Module, ast.ClassDef, ast.FunctionDef, ast.AsyncFunctionDef) + # node.body[0].value is the docstring literal; its lineno is the line the string opens + # on, so content line i maps to source line (start + i). + docstrings = [ + (docstring, node.body[0].value.lineno) # type: ignore[attr-defined] + for node in ast.walk(tree) + if isinstance(node, doc_nodes) + if (docstring := ast.get_docstring(node, clean=False)) + ] + return [ + Finding(path, start + offset, category, line) + for docstring, start in docstrings + for offset, line in enumerate(docstring.splitlines()) + for category in _scan_line(line) + ] + + +class Fence(NamedTuple): + """A fenced code block, by 0-based line index. ``terminated`` is False when the fence + has no closing delimiter before EOF, in which case ``close`` is the last line.""" + + open: int + close: int + terminated: bool + + +def fenced_blocks(lines: list[str]) -> list[Fence]: + """Index every fenced code block in ``lines``. + + An unterminated fence is malformed Markdown that `mkdocs build` surfaces anyway; it is + still returned (with ``terminated=False``, ``close`` at the last line) so callers that + skip code can skip to EOF.""" + blocks: list[Fence] = [] + fence: str | None = None + open_idx = -1 + for i, line in enumerate(lines): + stripped = line.lstrip() + if fence is None: + if stripped.startswith(("```", "~~~")): + fence, open_idx = stripped[:3], i + elif stripped.startswith(fence): + blocks.append(Fence(open_idx, i, terminated=True)) + fence = None + if fence is not None: + blocks.append(Fence(open_idx, len(lines) - 1, terminated=False)) + return blocks + + +def find_list_breaking_fences(lines: list[str], blocks: list[Fence]) -> list[tuple[int, str]]: + """Return ``(lineno, snippet)`` for each fenced code block at column 0 that splits a + list -- i.e. one whose nearest non-blank neighbours on both sides are top-level list + items. Such a fence is not indented into the preceding item, so Markdown closes the + list at the fence and the following item starts a new one. The fix is to indent the + fence (4 spaces) so it nests inside its list item. See the module docstring. + + Conservative on purpose: it requires a list item *directly* before and after (a + continuation line or paragraph in between is not matched), keeping false positives low + for a check that fails CI. Unterminated fences are ignored.""" + + def neighbour(start: int, step: int) -> str | None: + j = start + step + while 0 <= j < len(lines): + if lines[j].strip(): + return lines[j] + j += step + return None + + def splits_a_list(open_i: int, close_i: int) -> bool: + if lines[open_i][:1].isspace(): + return False # indented fence: already nested in the list item, not a break + before = neighbour(open_i, -1) + after = neighbour(close_i, +1) + return bool(before and after and LIST_ITEM.match(before) and LIST_ITEM.match(after)) + + return [ + (fence.open + 1, lines[fence.open]) + for fence in blocks + if fence.terminated and splits_a_list(fence.open, fence.close) + ] + + +def lint_markdown(path: Path) -> list[Finding]: + """Scan a Markdown file: RST residue in prose (skipping fenced code blocks), plus + fenced code blocks that break a list (see find_list_breaking_fences).""" + lines = path.read_text(encoding="utf-8").splitlines() + blocks = fenced_blocks(lines) + in_code = {i for fence in blocks for i in range(fence.open, fence.close + 1)} + + prose = [ + Finding(path, lineno, category, line) + for lineno, line in enumerate(lines, start=1) + if lineno - 1 not in in_code + for category in _scan_line(line) + ] + breaks = [ + Finding(path, lineno, "list-break", snippet) + for lineno, snippet in find_list_breaking_fences(lines, blocks) + ] + return prose + breaks + + +def iter_files(paths: tuple[Path, ...]) -> list[Path]: + files: list[Path] = [] + for path in paths: + if path.is_file(): + files.append(path) + elif path.is_dir(): + files.extend(sorted(path.rglob("*.py"))) + files.extend(sorted(path.rglob("*.md"))) + else: + raise FileNotFoundError(f"{path} does not exist") + return files + + +LINTERS = {".py": lint_python, ".md": lint_markdown} + + +def lint(paths: tuple[Path, ...]) -> list[Finding]: + return [ + finding + for file in iter_files(paths) + if file.suffix in LINTERS + for finding in LINTERS[file.suffix](file) + ] + + +def main() -> int: + args = sys.argv[1:] + paths = tuple(Path(a).resolve() for a in args) if args else DEFAULT_PATHS + findings = lint(paths) + + if not findings: + print("No reStructuredText residue or list-breaking fences found in docs.") + return 0 + + print( + f"Found {len(findings)} docs issue(s) -- RST markup that will not render under " + "MkDocs/mkdocstrings, or Markdown that renders as valid-but-wrong HTML:\n", + file=sys.stderr, + ) + for finding in findings: + print(finding.format(), file=sys.stderr) + remediation = "\n".join(f" {c.category:<13} {c.example:<19} -> {c.fix}" for c in CHECKS) + print( + f"\nFix each issue (see ci/lint_docs.py header):\n{remediation}", + file=sys.stderr, + ) + return 1 + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/docs/contributing.md b/docs/contributing.md index eaab26fbc7..df46f381de 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -12,23 +12,23 @@ If you find a bug, please raise a [GitHub issue](https://github.com/zarr-develop 1. A minimal, self-contained snippet of Python code reproducing the problem. You can format the code nicely using markdown, e.g.: -```python exec="false" reason="illustrative pseudocode with a '# etc.' placeholder, not runnable" -import zarr -g = zarr.group() -# etc. -``` + ```python exec="false" reason="illustrative pseudocode with a '# etc.' placeholder, not runnable" + import zarr + g = zarr.group() + # etc. + ``` 2. An explanation of why the current behavior is wrong/not desired, and what you expect instead. 3. Information about the version of Zarr, along with versions of dependencies and the Python interpreter, and installation information. The version of Zarr can be obtained from the `zarr.__version__` attribute. Please also state how Zarr was installed, e.g., "installed via pip into a virtual environment", or "installed using conda". Information about other packages installed can be obtained by executing `pip freeze` (if using pip to install packages) or `conda env export` (if using conda to install packages) from the operating system command prompt. The version of the Python interpreter can be obtained by running a Python interactive session, e.g.: -```console -python -``` + ```console + python + ``` -```ansi -Python 3.12.7 | packaged by conda-forge | (main, Oct 4 2024, 15:57:01) [Clang 17.0.6 ] on darwin -``` + ```ansi + Python 3.12.7 | packaged by conda-forge | (main, Oct 4 2024, 15:57:01) [Clang 17.0.6 ] on darwin + ``` ## Enhancement proposals @@ -401,7 +401,6 @@ The Zarr library is an implementation of a file format standard defined external If an existing Zarr format version changes, or a new version of the Zarr format is released, then the Zarr library will generally require changes. It is very likely that a new Zarr format will require extensive breaking changes to the Zarr library, and so support for a new Zarr format in the Zarr library will almost certainly come in a new `major` release. When the Zarr library adds support for a new Zarr format, there may be a period of accelerated changes as developers refine newly added APIs and deprecate old APIs. In such a transitional phase breaking changes may be more frequent than usual. - ## Experimental API policy The `zarr.experimental` namespace contains features that are under active development and may change without notice. When contributing to or depending on experimental features, please keep the following in mind: diff --git a/docs/index.md b/docs/index.md index 1ec5e93c75..ee4098a8ea 100644 --- a/docs/index.md +++ b/docs/index.md @@ -6,7 +6,6 @@ [Developer Chat](https://ossci.zulipchat.com/) | [Zarr specifications](https://zarr-specs.readthedocs.io) - Zarr is a powerful library for storage of n-dimensional arrays, supporting chunking, compression, and various backends, making it a versatile choice for scientific and large-scale data. @@ -37,22 +36,20 @@ conda install -c conda-forge zarr <div class="grid cards" markdown> -- [:material-clock-fast:{ .lg .middle } __Quick start__](quick-start.md) +- [:material-clock-fast:{ .lg .middle } __Quick start__](quick-start.md) --- New to Zarr? Check out the quick start guide. It contains a brief introduction to Zarr's main concepts and links to additional tutorials. - -- [:material-book-open:{ .lg .middle } __User guide__](user-guide/index.md) +- [:material-book-open:{ .lg .middle } __User guide__](user-guide/index.md) --- A detailed guide for how to use Zarr-Python. - -- [:material-api:{ .lg .middle } __API Reference__](api/zarr/index.md) +- [:material-api:{ .lg .middle } __API Reference__](api/zarr/index.md) --- @@ -61,8 +58,7 @@ conda install -c conda-forge zarr which parameters can be used. It assumes that you have an understanding of the key concepts. - -- [:material-account-group:{ .lg .middle } __Contributor's Guide__](contributing.md) +- [:material-account-group:{ .lg .middle } __Contributor's Guide__](contributing.md) --- @@ -72,7 +68,6 @@ conda install -c conda-forge zarr </div> - ## Project Status More information about the Zarr format can be found on the [main website](https://zarr.dev). @@ -80,6 +75,7 @@ More information about the Zarr format can be found on the [main website](https: If you are using Zarr-Python, we would [love to hear about it](https://github.com/zarr-developers/community/issues/19). ### Funding and Support + The project is fiscally sponsored by [NumFOCUS](https://numfocus.org/), a US 501(c)(3) public charity, and development has been supported by the [MRC Centre for Genomics and Global Health](https://github.com/cggh/) diff --git a/docs/quick-start.md b/docs/quick-start.md index 29232d2a04..17cb1c599a 100644 --- a/docs/quick-start.md +++ b/docs/quick-start.md @@ -50,7 +50,6 @@ written to a `LocalStore` in the `data/example-1.zarr` directory. Zarr supports data compression and filters. For example, to use Blosc compression: - ```python exec="true" session="quickstart" source="above" result="ansi" # Create a 2D Zarr array with Blosc compression @@ -73,7 +72,6 @@ print(z.info) This compresses the data using the Blosc codec with shuffle enabled for better compression. - ## Hierarchical Groups Zarr allows you to create hierarchical groups, similar to directories: diff --git a/docs/release-notes.md b/docs/release-notes.md index e85137f2b6..7a5b12f59f 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -1,5 +1,7 @@ # Release notes +<!-- markdownlint-disable MD012 -- towncrier intentionally emits a blank line between releases --> + <!-- towncrier release notes start --> ## 3.3.0 (2026-07-15) diff --git a/docs/user-guide/attributes.md b/docs/user-guide/attributes.md index 96a5d67584..8c11c853f1 100644 --- a/docs/user-guide/attributes.md +++ b/docs/user-guide/attributes.md @@ -20,6 +20,7 @@ print('foo' in root.attrs) ```python exec="true" session="attributes" source="above" result="ansi" print(root.attrs['foo']) ``` + ```python exec="true" session="attributes" source="above" result="ansi" print(sorted(z.attrs)) ``` diff --git a/docs/user-guide/consolidated_metadata.md b/docs/user-guide/consolidated_metadata.md index 7030ed6cbc..9cb4d87c89 100644 --- a/docs/user-guide/consolidated_metadata.md +++ b/docs/user-guide/consolidated_metadata.md @@ -119,7 +119,6 @@ removed, or modified, consolidated metadata may not be desirable. `use_consolidated=False` to [`zarr.open_group`][] to always read child metadata directly from the store. - ## Stores Without Support for Consolidated Metadata Some stores may want to opt out of the consolidated metadata mechanism. This diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md index 642a09d714..ac966f885f 100644 --- a/docs/user-guide/data_types.md +++ b/docs/user-guide/data_types.md @@ -194,9 +194,11 @@ Python supports nearly all of the data types in NumPy. If you need a data type t here, it's possible to create it yourself: see [Adding new data types](#adding-new-data-types). #### Boolean + - [Boolean][zarr.dtype.Bool] #### Integral + - [Signed 8-bit integer][zarr.dtype.Int8] - [Signed 16-bit integer][zarr.dtype.Int16] - [Signed 32-bit integer][zarr.dtype.Int32] @@ -207,6 +209,7 @@ here, it's possible to create it yourself: see [Adding new data types](#adding-n - [Unsigned 64-bit integer][zarr.dtype.UInt64] #### Floating-point + - [16-bit floating-point][zarr.dtype.Float16] - [32-bit floating-point][zarr.dtype.Float32] - [64-bit floating-point][zarr.dtype.Float64] @@ -214,19 +217,23 @@ here, it's possible to create it yourself: see [Adding new data types](#adding-n - [128-bit complex floating-point][zarr.dtype.Complex128] #### String + - [Fixed-length UTF-32 string][zarr.dtype.FixedLengthUTF32] - [Variable-length UTF-8 string][zarr.dtype.VariableLengthUTF8] #### Bytes + - [Fixed-length null-terminated bytes][zarr.dtype.NullTerminatedBytes] - [Fixed-length raw bytes][zarr.dtype.RawBytes] - [Variable-length bytes][zarr.dtype.VariableLengthBytes] #### Temporal + - [DateTime64][zarr.dtype.DateTime64] - [TimeDelta64][zarr.dtype.TimeDelta64] #### Struct-like + - [Structured][zarr.dtype.Structured] !!! note "Zarr V3 Structured Data Types" diff --git a/docs/user-guide/experimental.md b/docs/user-guide/experimental.md index a70ee923fe..e14146610c 100644 --- a/docs/user-guide/experimental.md +++ b/docs/user-guide/experimental.md @@ -168,7 +168,6 @@ print(f"Speedup is {speedup}") Cache effectiveness is particularly pronounced with repeated access to the same data chunks. - ### Cache Configuration The CacheStore can be configured with several parameters: diff --git a/docs/user-guide/extending.md b/docs/user-guide/extending.md index 8602ec8c3b..f852f9105e 100644 --- a/docs/user-guide/extending.md +++ b/docs/user-guide/extending.md @@ -14,6 +14,7 @@ in the following ways: [numcodecs.registry.register_codec](https://numcodecs.readthedocs.io/en/stable/registry.html#numcodecs.registry.register_codec). There are three types of codecs in Zarr: + - array-to-array - array-to-bytes - bytes-to-bytes diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index a2b40dfe8a..337ad39554 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -174,4 +174,3 @@ Groups also have the [`zarr.Group.tree`][] method, e.g.: ```python exec="true" session="groups" source="above" result="ansi" print(root.tree()) ``` - diff --git a/docs/user-guide/performance.md b/docs/user-guide/performance.md index 818386578c..52c1cf0d71 100644 --- a/docs/user-guide/performance.md +++ b/docs/user-guide/performance.md @@ -120,7 +120,6 @@ The order of chunks **within each shard** can be changed via the `subchunk_write By default [`morton`](https://en.wikipedia.org/wiki/Z-order_curve) order provides good spatial locality. [`lexicographic` (i.e., row-major)](https://en.wikipedia.org/wiki/Row-_and_column-major_order), for example, may be better suited to "batched" workflows where some form of sequential reading through a fixed number of outer dimensions is desired, and `colexicographic` is its reverse. `unordered` makes no guarantee about the order in which subchunks are laid out within a shard. - ### Empty chunks It is possible to configure how Zarr handles the storage of chunks that are "empty" @@ -221,11 +220,13 @@ zarr.config.set({'async.concurrency': 128}) ``` Higher concurrency values can improve throughput when: + - Working with remote storage (e.g., S3, GCS) where network latency is high - Reading/writing many small chunks in parallel - The storage backend can handle many concurrent requests Lower concurrency values may be beneficial when: + - Working with local storage with limited I/O bandwidth - Memory is constrained (each concurrent operation requires buffer space) - Using Zarr within a parallel computing framework (see below) @@ -258,7 +259,7 @@ concurrently. **Important**: When using many Dask threads, you may need to reduce both Zarr's `async.concurrency` and `threading.max_workers` settings to avoid creating too many concurrent operations. The total number of concurrent I/O operations can be roughly estimated as: -``` +```text total_concurrency ≈ dask_threads × zarr_async_concurrency ``` @@ -298,6 +299,7 @@ You may need to experiment with different values to find the optimal balance for Zarr arrays are designed to be thread-safe for concurrent reads and writes from multiple threads within the same process. However, proper synchronization is required when writing to overlapping regions from multiple threads. For multi-process parallelism, Zarr provides safe concurrent writes as long as: + - Different processes write to different chunks - The storage backend supports atomic writes (most do) diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index d32fe217c9..7e0154b2a0 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -41,17 +41,21 @@ group = zarr.create_group(store=data) print(group) ``` +<!-- markdownlint-disable-next-line MD042 -- empty link is an intentional MkDocs anchor target --> [](){#user-guide-store-like} + ### StoreLike `StoreLike` values can be: - a `Path` or string indicating a location on the local file system. This will create a [local store](#local-store): + ```python exec="true" session="storage" source="above" result="ansi" group = zarr.open_group(store='data/foo/bar') print(group) ``` + ```python exec="true" session="storage" source="above" result="ansi" from pathlib import Path group = zarr.open_group(store=Path('data/foo/bar')) @@ -59,6 +63,7 @@ print(group) ``` - an FSSpec URI string, indicating a [remote store](#remote-store) location: + ```python exec="true" session="storage" source="above" result="ansi" # Note: requires s3fs to be installed group = zarr.open_group( @@ -70,10 +75,12 @@ print(group) ``` - an empty dictionary or None, which will create a new [memory store](#memory-store): + ```python exec="true" session="storage" source="above" result="ansi" group = zarr.create_group(store={}) print(group) ``` + ```python exec="true" session="storage" source="above" result="ansi" group = zarr.create_group(store=None) print(group) @@ -152,7 +159,6 @@ print(store) When using an S3-compatible service other than AWS, pass the service endpoint to the filesystem via `client_kwargs={'endpoint_url': 'https://...'}`. - ### Memory Store The [`zarr.storage.MemoryStore`][] stores Zarr data (metadata and chunks) in an diff --git a/lychee.toml b/lychee.toml new file mode 100644 index 0000000000..38b2b8ab7a --- /dev/null +++ b/lychee.toml @@ -0,0 +1,20 @@ +# Configuration for the lychee link checker (https://lychee.cli.rs/). +# Auto-discovered as ./lychee.toml by the lychee GitHub Action. + +# Files lychee should not scan for links. +exclude_path = [ + # mkdocs-material theme overrides: hrefs are Jinja expressions like + # `{{ '../' ~ base_url }}`, not real URLs, so lychee cannot resolve them. + "docs/overrides", + # Design notes: working records that point at transient artifacts (commits, + # fork branches, compare URLs) which are expected to disappear over time. + "design", +] + +# URL patterns to ignore (regex, matched against the full URL). +exclude = [ + # Local docs preview server shown in the contributing guide ("hatch run serve"), + # documentation of a command rather than a reachable link. + '^https?://0\.0\.0\.0', + '^https?://(localhost|127\.0\.0\.1)(:\d+)?', +] diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index ac32521239..91515d87b9 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -120,7 +120,7 @@ def ndim(self) -> int: def chunk_grid(self) -> ChunkGrid: """Backwards-compatible chunk grid property. - .. deprecated:: + !!! warning "Deprecated" Access the chunk grid via the array layer instead. This property will be removed in a future release. """ diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index 80a0996ca6..46287ccffb 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -40,21 +40,21 @@ class StoreTests[S: Store, B: Buffer]: @staticmethod def _require_get_sync(store: S) -> SupportsGetSync: - """Skip unless *store* implements :class:`SupportsGetSync`.""" + """Skip unless *store* implements [`SupportsGetSync`][zarr.abc.store.SupportsGetSync].""" if not isinstance(store, SupportsGetSync): pytest.skip("store does not implement SupportsGetSync") return store # type: ignore[unreachable] @staticmethod def _require_set_sync(store: S) -> SupportsSetSync: - """Skip unless *store* implements :class:`SupportsSetSync`.""" + """Skip unless *store* implements [`SupportsSetSync`][zarr.abc.store.SupportsSetSync].""" if not isinstance(store, SupportsSetSync): pytest.skip("store does not implement SupportsSetSync") return store # type: ignore[unreachable] @staticmethod def _require_delete_sync(store: S) -> SupportsDeleteSync: - """Skip unless *store* implements :class:`SupportsDeleteSync`.""" + """Skip unless *store* implements [`SupportsDeleteSync`][zarr.abc.store.SupportsDeleteSync].""" if not isinstance(store, SupportsDeleteSync): pytest.skip("store does not implement SupportsDeleteSync") return store # type: ignore[unreachable] From 7f8834ab14d607d1ec03209d9509a153fe81b173 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 16 Jul 2026 13:42:21 -0400 Subject: [PATCH 405/468] chore: cleanup indentation and guidance for release (#4153) * chore: cleanup indentation and guidance for release * Make explanation a comment --- .github/ISSUE_TEMPLATE/release-checklist.md | 7 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/prepare_release.yml | 74 ------ ci/lint_docs.py | 67 ++++- docs/contributing.md | 21 +- docs/release-notes.md | 258 ++++++++++---------- docs/user-guide/data_types.md | 20 +- docs/user-guide/v3_migration.md | 73 +++--- 8 files changed, 251 insertions(+), 271 deletions(-) delete mode 100644 .github/workflows/prepare_release.yml diff --git a/.github/ISSUE_TEMPLATE/release-checklist.md b/.github/ISSUE_TEMPLATE/release-checklist.md index 5e073cb59f..309c76b4dc 100644 --- a/.github/ISSUE_TEMPLATE/release-checklist.md +++ b/.github/ISSUE_TEMPLATE/release-checklist.md @@ -18,8 +18,8 @@ assignees: '' - [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/#support-window) to see if the minimum supported version of Python or NumPy needs bumping. - [ ] Verify that the latest CI workflows on `main` are passing: [Tests](https://github.com/zarr-developers/zarr-python/actions/workflows/test.yml), [GPU Tests](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml), [Hypothesis](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml), [Docs](https://github.com/zarr-developers/zarr-python/actions/workflows/docs.yml), [Lint](https://github.com/zarr-developers/zarr-python/actions/workflows/lint.yml), [Wheels](https://github.com/zarr-developers/zarr-python/actions/workflows/releases.yml). -- [ ] Run the ["Prepare release" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) with the target version. This will build the changelog and open a release PR with the `run-downstream` label. -- [ ] Verify that the [downstream tests](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) (triggered automatically by the `run-downstream` label) pass on the release PR. +- [ ] Run the [downstream tests](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) against `main`: go to the workflow page, click "Run workflow", and select the `main` branch. Verify that the Xarray and numcodecs integration tests pass. +- [ ] Open a release PR with the changelog entries for the upcoming release, generated with `uv run --only-group release towncrier build --version x.y.z`. - [ ] Review the release PR and verify the changelog in `docs/release-notes.md` looks correct. - [ ] Merge the release PR. @@ -45,7 +45,8 @@ In rare cases (e.g. patch releases for an older minor version), you may need to - Create the release branch from the appropriate tag if it doesn't already exist. - Cherry-pick or backport the necessary commits onto the branch. -- Run `towncrier build --version x.y.z` and commit the result to the release branch instead of `main`. +- Run `towncrier build --version x.y.z` and open the release PR against the release branch instead of `main`. +- Run the downstream tests against the release branch instead of `main`. - When drafting the GitHub Release, set the target to the release branch instead of `main`. - After the release, ensure any relevant changelog updates are also reflected on `main`. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 1d12aa02eb..47adb4b19e 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,7 +15,7 @@ - [ ] I am a human, these are my changes, and I have reviewed and understood every change and can explain why each is correct. -AI coding assistance is welcome, but a human must be the author and is responsible for the contents of the PR. The description and any review responses must be in your own words. Please read [AI-assisted contributions](https://zarr.readthedocs.io/en/stable/contributing/#ai-assisted-contributions) before opening. +<!-- AI coding assistance is welcome, but a human must be the author and is responsible for the contents of the PR. The description and any review responses must be in your own words. Please read [AI-assisted contributions](https://zarr.readthedocs.io/en/stable/contributing/#ai-assisted-contributions) before opening. --> ## TODO diff --git a/.github/workflows/prepare_release.yml b/.github/workflows/prepare_release.yml deleted file mode 100644 index d558779bf2..0000000000 --- a/.github/workflows/prepare_release.yml +++ /dev/null @@ -1,74 +0,0 @@ -name: Prepare release notes - -on: - workflow_dispatch: - inputs: - version: - description: 'Release version notes (e.g. 3.2.0)' - required: true - type: string - target_branch: - description: 'Branch to target' - required: false - default: 'main' - type: string - -permissions: - contents: write - pull-requests: write - -jobs: - prepare: - name: Build changelog and open PR - runs-on: ubuntu-latest - steps: - - name: Validate inputs - run: | - if [[ ! "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+([-\.][a-zA-Z0-9]+)*$ ]]; then - echo "::error::Invalid version format: '$VERSION'" - exit 1 - fi - if [[ ! "$TARGET_BRANCH" =~ ^[a-zA-Z0-9._/-]+$ ]]; then - echo "::error::Invalid branch name: '$TARGET_BRANCH'" - exit 1 - fi - env: - VERSION: ${{ inputs.version }} - TARGET_BRANCH: ${{ inputs.target_branch }} - - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 - with: - ref: ${{ inputs.target_branch }} - fetch-depth: 0 - persist-credentials: false - - - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 - - - name: Build changelog - # Use the pinned towncrier from the `release` dependency group (single - # source of truth) rather than an unpinned standalone install. - run: uv run --only-group release towncrier build --version "$VERSION" --yes - env: - VERSION: ${{ inputs.version }} - - - name: Create pull request - uses: peter-evans/create-pull-request@5f6978faf089d4d20b00c7766989d076bb2fc7f1 # v8.1.1 - with: - branch: release/v${{ inputs.version }} - base: ${{ inputs.target_branch }} - title: "Release v${{ inputs.version }}" - body: | - Automated release preparation for v${{ inputs.version }}. - - This PR was generated by the "Prepare release" workflow. It includes: - - Rendered changelog via `towncrier build --version ${{ inputs.version }}` - - Removal of consumed changelog fragments from `changes/` - - ## Checklist - - - [ ] Review the rendered changelog in `docs/release-notes.md` - - [ ] Downstream tests pass (see [downstream workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml)) - - [ ] Merge this PR, then [draft a GitHub Release](https://github.com/zarr-developers/zarr-python/releases/new) targeting `${{ inputs.target_branch }}` with tag `v${{ inputs.version }}` - commit-message: "chore: build changelog for v${{ inputs.version }}" - labels: run-downstream - delete-branch: true diff --git a/ci/lint_docs.py b/ci/lint_docs.py index ff7b56649b..a847e8aa9d 100644 --- a/ci/lint_docs.py +++ b/ci/lint_docs.py @@ -13,7 +13,7 @@ fast, source-level check that needs no docs build. Checks fall into two groups -- RST markup that silently fails under MkDocs/mkdocstrings, -and a Markdown structural problem that renders as valid-but-wrong HTML (so `mkdocs build` +and Markdown structural problems that render as valid-but-wrong HTML (so `mkdocs build` emits no warning): sphinx-role :class:`X`, :func:`X`, :py:meth:`X` -> [`X`][zarr.X] @@ -21,6 +21,8 @@ rst-field :param x:, :returns:, :rtype: -> numpydoc Parameters/Returns/Raises rst-link `text <https://example>`_ -> [text](https://example) list-break unindented code fence between list items -> indent the fence under its item + list-indent continuation block indented < 4 spaces -> indent it 4 spaces + list-blank list item directly after indented block -> blank line before the item The ``list-break`` check catches a fenced code block at column 0 placed *between* two list items: because the fence is not indented into the preceding item, Markdown ends the list at @@ -29,6 +31,15 @@ notices this for sequentially-numbered ordered lists; lazily-numbered (1., 1.) and unordered lists slip past it, so this structural check covers the gap. +The ``list-indent`` and ``list-blank`` checks catch the two halves of Python-Markdown's +strict list-continuation rules, which differ from CommonMark. A blank-line-separated +block (paragraph, nested list, table) belongs to a list item only when indented at least +4 spaces; at the 2-space indent other renderers accept, Python-Markdown ends the list and +the block escapes to the top level (``list-indent``). And a new list item can not start +directly after an indented continuation block: without a blank line first, the ``- `` line +is lazily absorbed into the preceding paragraph as literal text (``list-blank``). Both +produced silently-broken changelog rendering in ``docs/release-notes.md``. + Usage: python ci/lint_docs.py [PATH ...] @@ -87,14 +98,16 @@ class Check(NamedTuple): fix: str -# ``list-break`` carries no pattern -- it is detected structurally in find_list_breaking_fences, -# not by scanning a single line -- but it appears here so it shares the remediation help. +# The ``list-*`` checks carry no pattern -- they are detected structurally, not by scanning +# a single line -- but they appear here so they share the remediation help. CHECKS = ( Check("sphinx-role", SPHINX_ROLE, ":class:`X`", "[`X`][zarr.X]"), Check("rst-directive", RST_DIRECTIVE, ".. note::", "MkDocs admonition (!!! note)"), Check("rst-field", RST_FIELD, ":param x:", "numpydoc Parameters/Returns/Raises section"), Check("rst-link", RST_LINK, "`text <url>`_", "[text](url)"), Check("list-break", None, "fence between items", "indent the fence 4 spaces to nest it"), + Check("list-indent", None, "2-space continuation", "indent the block 4 spaces under its item"), + Check("list-blank", None, "item after indented block", "add a blank line before the item"), ) @@ -211,9 +224,49 @@ def splits_a_list(open_i: int, close_i: int) -> bool: ] +def find_list_continuation_issues( + lines: list[str], in_code: set[int] +) -> list[tuple[int, str, str]]: + """Return ``(lineno, category, snippet)`` for list continuations Python-Markdown will + mis-render (see the module docstring): + + - ``list-indent``: a blank-line-separated block inside a list item indented 1-3 + spaces. Python-Markdown requires 4; at less, the block escapes the list. + - ``list-blank``: a top-level list item directly after a line indented 4+ spaces. + Without a blank line in between, the item is absorbed into the preceding paragraph + as literal ``- `` text. + + Lazy continuations (an indented line with no blank line before it) are valid at any + indent and are not flagged. Fenced-code lines are opaque: never flagged themselves, + but they keep the item scope open and their indent feeds the ``list-blank`` check so + an item directly after an indented fence is still caught.""" + findings: list[tuple[int, str, str]] = [] + in_item = False # inside a top-level list item's scope + prev_blank = True + prev_indent = 0 + for i, line in enumerate(lines): + stripped = line.strip() + if not stripped: + prev_blank = True + continue + indent = len(line) - len(line.lstrip(" ")) + if i not in in_code: + if indent == 0: + is_item = bool(LIST_ITEM.match(line)) + if is_item and in_item and not prev_blank and prev_indent >= 4: + findings.append((i + 1, "list-blank", line)) + in_item = is_item + elif in_item and prev_blank and indent < 4: + findings.append((i + 1, "list-indent", line)) + prev_blank = False + prev_indent = indent + return findings + + def lint_markdown(path: Path) -> list[Finding]: """Scan a Markdown file: RST residue in prose (skipping fenced code blocks), plus - fenced code blocks that break a list (see find_list_breaking_fences).""" + list-structure problems (see find_list_breaking_fences and + find_list_continuation_issues).""" lines = path.read_text(encoding="utf-8").splitlines() blocks = fenced_blocks(lines) in_code = {i for fence in blocks for i in range(fence.open, fence.close + 1)} @@ -228,7 +281,11 @@ def lint_markdown(path: Path) -> list[Finding]: Finding(path, lineno, "list-break", snippet) for lineno, snippet in find_list_breaking_fences(lines, blocks) ] - return prose + breaks + continuations = [ + Finding(path, lineno, category, snippet) + for lineno, category, snippet in find_list_continuation_issues(lines, in_code) + ] + return prose + breaks + continuations def iter_files(paths: tuple[Path, ...]) -> list[Path]: diff --git a/docs/contributing.md b/docs/contributing.md index df46f381de..aeb88e6ce1 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -354,18 +354,7 @@ This policy exists to lower the cost of routine work and to help newer core deve ### Release procedure -Open an issue on GitHub announcing the release using the release checklist template: -[https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md). The release checklist includes all steps necessary for the release. - -#### Preparing a release - -Releases are prepared using the ["Prepare release notes"](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) workflow. To run it: - -1. Go to the [workflow page](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) and click "Run workflow". -2. Enter the release version (e.g. `3.2.0`) and the target branch (defaults to `main`). -3. The workflow will run `towncrier build` to render the changelog, remove consumed fragments from `changes/`, and open a pull request on the `release/v<version>` branch. -4. The release PR is automatically labeled `run-downstream`, which triggers the [downstream test workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) to run Xarray and numcodecs integration tests against the release branch. -5. Review the rendered changelog in `docs/release-notes.md` and verify downstream tests pass before merging. +To give the release visibility and a single place to track progress, open an issue on GitHub announcing the release using the [release checklist template](https://github.com/zarr-developers/zarr-python/issues/new?template=release-checklist.md). The release checklist includes all steps necessary for the release. ## Compatibility and versioning policies @@ -377,17 +366,17 @@ Releases are classified by the library changes contained in that release. This c * **major** releases (for example, `2.18.0` -> `3.0.0`) are for changes that will require extensive adaptation efforts from many users and downstream projects. For example, breaking changes to widely-used user-facing APIs should only be applied in a major release. - Users and downstream projects should carefully consider the impact of a major release before adopting it. In advance of a major release, developers should communicate the scope of the upcoming changes, and help users prepare for them. + Users and downstream projects should carefully consider the impact of a major release before adopting it. In advance of a major release, developers should communicate the scope of the upcoming changes, and help users prepare for them. * **minor** releases (for example, `3.0.0` -> `3.1.0`) are for changes that do not require significant effort from most users or downstream projects to respond to. API changes are possible in minor releases if the burden on users imposed by those changes is sufficiently small. - For example, a recently released API may need fixes or refinements that are breaking, but low impact due to the recency of the feature. Such API changes are permitted in a minor release. + For example, a recently released API may need fixes or refinements that are breaking, but low impact due to the recency of the feature. Such API changes are permitted in a minor release. - Minor releases are safe for most users and downstream projects to adopt. + Minor releases are safe for most users and downstream projects to adopt. * **patch** releases (for example, `3.1.0` -> `3.1.1`) are for changes that contain no breaking or behavior changes for downstream projects or users. Examples of changes suitable for a patch release are bugfixes and documentation improvements. - Users should always feel safe upgrading to the latest patch release. + Users should always feel safe upgrading to the latest patch release. Note that this versioning scheme is not consistent with [Semantic Versioning](https://semver.org/). Contrary to SemVer, the Zarr library may release breaking changes in `minor` releases, or even `patch` releases under exceptional circumstances. But we should strive to avoid doing so. diff --git a/docs/release-notes.md b/docs/release-notes.md index 7a5b12f59f..3fd8a5f360 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -51,32 +51,34 @@ `ClientSession` was left open until garbage collection, producing `"Unclosed client session"` `ResourceWarning`s from aiohttp. - The fix introduces `FsspecStore._owns_fs`, a boolean that is ``True`` only when - `FsspecStore` itself created the filesystem (via `from_url` or `from_mapper` - when a sync→async conversion was performed). When `_owns_fs` is ``True``, - `store.close()` calls the new `_close_fs()` helper, which invokes - `fs.set_session()` and closes the returned client. Callers who supply their own - filesystem instance to `FsspecStore()` directly remain responsible for its - lifecycle; `_owns_fs` is ``False`` for those stores. - - **Scope note**: This fix closes the S3 client session that is active at the time - `store.close()` is called. Some S3-backed filesystem implementations (e.g. - s3fs with ``cache_regions=True``) may internally refresh and replace their - client during I/O operations, abandoning prior sessions before ``store.close()`` - is invoked. Those intermediate sessions are outside the scope of this fix and - are an issue in the upstream filesystem library. ([#4003](https://github.com/zarr-developers/zarr-python/issues/4003)) + The fix introduces `FsspecStore._owns_fs`, a boolean that is ``True`` only when + `FsspecStore` itself created the filesystem (via `from_url` or `from_mapper` + when a sync→async conversion was performed). When `_owns_fs` is ``True``, + `store.close()` calls the new `_close_fs()` helper, which invokes + `fs.set_session()` and closes the returned client. Callers who supply their own + filesystem instance to `FsspecStore()` directly remain responsible for its + lifecycle; `_owns_fs` is ``False`` for those stores. + + **Scope note**: This fix closes the S3 client session that is active at the time + `store.close()` is called. Some S3-backed filesystem implementations (e.g. + s3fs with ``cache_regions=True``) may internally refresh and replace their + client during I/O operations, abandoning prior sessions before ``store.close()`` + is invoked. Those intermediate sessions are outside the scope of this fix and + are an issue in the upstream filesystem library. ([#4003](https://github.com/zarr-developers/zarr-python/issues/4003)) + - Fixed an invalid `zarr.create_array` example in the quick-start documentation (it passed an unsupported `mode` argument) and made the cloud-storage example execute against a mock S3 backend in CI. Added a test ensuring every Python code block in the documentation is either executed or explicitly opted out with a documented reason, so an invalid example can no longer go untested. ([#4016](https://github.com/zarr-developers/zarr-python/issues/4016)) - Fixed `ObjectStore.list_dir` for object-store listings that include a directory-marker object matching the requested non-root prefix. ([#4032](https://github.com/zarr-developers/zarr-python/issues/4032)) - Prevents mutation of the attributes dict provided by the user by copying them instead of keeping the reference ([#4059](https://github.com/zarr-developers/zarr-python/issues/4059)) - Fixed several storage and codec bugs: - - Reading a value with a `SuffixByteRequest` larger than the value now correctly returns the whole value (matching HTTP `bytes=-N` suffix-range semantics), instead of silently returning incorrect data for `MemoryStore`. - - `LoggingStore.get_partial_values` and `FsspecStore.get_partial_values` no longer return empty results when `key_ranges` is passed as a one-shot iterable (e.g. a generator). - - `Store.getsize_prefix` no longer over-counts sibling keys that merely share a string prefix (e.g. `getsize_prefix("foo")` no longer includes keys under `foobar/`). - - `ZipStore.close()` no longer raises `AttributeError` when the store was created but never opened (including when used as a context manager without any I/O). - - `codecs_from_list` now raises a descriptive `TypeError` when a `BytesBytesCodec` immediately follows an `ArrayArrayCodec`, instead of a misleading "Required ArrayBytesCodec was not found" `ValueError`. + - Reading a value with a `SuffixByteRequest` larger than the value now correctly returns the whole value (matching HTTP `bytes=-N` suffix-range semantics), instead of silently returning incorrect data for `MemoryStore`. + - `LoggingStore.get_partial_values` and `FsspecStore.get_partial_values` no longer return empty results when `key_ranges` is passed as a one-shot iterable (e.g. a generator). + - `Store.getsize_prefix` no longer over-counts sibling keys that merely share a string prefix (e.g. `getsize_prefix("foo")` no longer includes keys under `foobar/`). + - `ZipStore.close()` no longer raises `AttributeError` when the store was created but never opened (including when used as a context manager without any I/O). + - `codecs_from_list` now raises a descriptive `TypeError` when a `BytesBytesCodec` immediately follows an `ArrayArrayCodec`, instead of a misleading "Required ArrayBytesCodec was not found" `ValueError`. + + ([#4074](https://github.com/zarr-developers/zarr-python/issues/4074)) - ([#4074](https://github.com/zarr-developers/zarr-python/issues/4074)) - Fixed writing Fortran-ordered (F-contiguous) arrays through the variable-length string and bytes codecs and through numcodecs array-array filters such as `Delta`, `FixedScaleOffset` and `PackBits`. Chunks are now passed to numcodecs as C-contiguous arrays, so elements are no longer stored in transposed order. ([#4116](https://github.com/zarr-developers/zarr-python/issues/4116)) - Fix silent byte-order corruption for structured dtypes with the `bytes` codec: multi-byte fields are now byte-swapped to the codec's configured `endian` on write and decoded honoring it on read, so non-native-endian structured data (e.g. big-endian fields, as produced by virtual references to external data) round-trips correctly. ([#4141](https://github.com/zarr-developers/zarr-python/issues/4141)) @@ -91,23 +93,24 @@ use only the public API, eliminating all non-public imports, illustrating what users should do. - To better support this, the following types and functions were made available - from public modules: - - | Type/Function | Non-public module | Public module | - | ------------------------- | ------------------------ | ------------- | - | `DataTypeValidationError` | `zarr.core.dtype.common` | `zarr.errors` | - | `JSON` | `zarr.core.common` | `zarr.types` | - | `ZarrFormat` | `zarr.core.common` | `zarr.types` | - | `DTypeConfig_V2` | `zarr.core.dtype.common` | `zarr.types` | - | `DTypeJSON` | `zarr.core.dtype.common` | `zarr.types` | - | `DTypeSpec_V2` | `zarr.core.dtype.common` | `zarr.dtype` | - | `check_dtype_spec_v2` | `zarr.core.dtype.common` | `zarr.dtype` | - - `DataTypeValidationError` was *moved* to `zarr.errors`. Importing it from - `zarr.core.dtype.common` (its original location), `zarr.core.dtype`, or - `zarr.dtype` still works but now raises a `ZarrDeprecationWarning`. The remaining - types and functions are simply re-exported from the listed public module. ([#4052](https://github.com/zarr-developers/zarr-python/issues/4052)) + To better support this, the following types and functions were made available + from public modules: + + | Type/Function | Non-public module | Public module | + | ------------------------- | ------------------------ | ------------- | + | `DataTypeValidationError` | `zarr.core.dtype.common` | `zarr.errors` | + | `JSON` | `zarr.core.common` | `zarr.types` | + | `ZarrFormat` | `zarr.core.common` | `zarr.types` | + | `DTypeConfig_V2` | `zarr.core.dtype.common` | `zarr.types` | + | `DTypeJSON` | `zarr.core.dtype.common` | `zarr.types` | + | `DTypeSpec_V2` | `zarr.core.dtype.common` | `zarr.dtype` | + | `check_dtype_spec_v2` | `zarr.core.dtype.common` | `zarr.dtype` | + + `DataTypeValidationError` was *moved* to `zarr.errors`. Importing it from + `zarr.core.dtype.common` (its original location), `zarr.core.dtype`, or + `zarr.dtype` still works but now raises a `ZarrDeprecationWarning`. The remaining + types and functions are simply re-exported from the listed public module. ([#4052](https://github.com/zarr-developers/zarr-python/issues/4052)) + - Document a self-merge policy in the contributor guide, describing when a core developer may merge their own pull request without a second reviewer and which changes warrant more caution. ([#4053](https://github.com/zarr-developers/zarr-python/issues/4053)) - Fixed many documentation errors found in a full review of the user guide, including prose contradicted by rendered example output on the performance page, invisible @@ -126,11 +129,12 @@ access, and will be removed in a future release. ``BloscCodec.cname`` and ``BloscCodec.shuffle`` are now plain strings rather than enum members. - Additional renames in ``zarr.codecs.blosc`` from the same change: the type - aliases ``Shuffle`` and ``CName`` are now ``BloscShuffleLiteral`` and - ``BloscCnameLiteral``, the constant ``SHUFFLE`` is now ``BLOSC_SHUFFLE`` - (with a new ``BLOSC_CNAME`` alongside it), and ``BloscShuffle.from_int`` - now returns a literal string rather than an enum member. ([#3963](https://github.com/zarr-developers/zarr-python/issues/3963)) + Additional renames in ``zarr.codecs.blosc`` from the same change: the type + aliases ``Shuffle`` and ``CName`` are now ``BloscShuffleLiteral`` and + ``BloscCnameLiteral``, the constant ``SHUFFLE`` is now ``BLOSC_SHUFFLE`` + (with a new ``BLOSC_CNAME`` alongside it), and ``BloscShuffle.from_int`` + now returns a literal string rather than an enum member. ([#3963](https://github.com/zarr-developers/zarr-python/issues/3963)) + - The ``Endian`` (``zarr.codecs.bytes.Endian``) and ``ShardingCodecIndexLocation`` (``zarr.codecs.ShardingCodecIndexLocation``) enums are now deprecated. Pass the equivalent literal string instead (e.g. ``"little"`` / ``"big"``, ``"start"`` / @@ -139,20 +143,21 @@ and ``ShardingCodec.index_location`` are now plain strings rather than enum members. - Two follow-on changes from this deprecation: + Two follow-on changes from this deprecation: - - ``NDBuffer.byteorder`` now returns a literal string (``"little"`` or - ``"big"``) rather than an ``Endian`` member. Subclasses overriding this - property should update their return type. - - The module-level binding ``zarr.codecs.bytes.default_system_endian`` was - removed. ``BytesCodec()`` continues to default to ``sys.byteorder``; - external callers that imported ``default_system_endian`` should use - ``sys.byteorder`` directly. + - ``NDBuffer.byteorder`` now returns a literal string (``"little"`` or + ``"big"``) rather than an ``Endian`` member. Subclasses overriding this + property should update their return type. + - The module-level binding ``zarr.codecs.bytes.default_system_endian`` was + removed. ``BytesCodec()`` continues to default to ``sys.byteorder``; + external callers that imported ``default_system_endian`` should use + ``sys.byteorder`` directly. - Additionally, the module-level function ``zarr.codecs.sharding.parse_index_location`` - was made private as part of this change. + Additionally, the module-level function ``zarr.codecs.sharding.parse_index_location`` + was made private as part of this change. + + ([#3968](https://github.com/zarr-developers/zarr-python/issues/3968)) - ([#3968](https://github.com/zarr-developers/zarr-python/issues/3968)) - Removed the NumPy 1.x implementation of the `VariableLengthUTF8` data type because NumPy 1.x is no longer supported under [SPEC0](https://scientific-python.org/specs/spec-0000/). ([#3973](https://github.com/zarr-developers/zarr-python/issues/3973)) ### Misc @@ -191,19 +196,19 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Add support for rectilinear (variable-sized) chunk grids. This feature is experimental and must be explicitly enabled via `zarr.config.set({'array.rectilinear_chunks': True})`. - Rectilinear chunks can be used through: + Rectilinear chunks can be used through: - - **Creating arrays**: Pass nested sequences (e.g., `[[10, 20, 30], [50, 50]]`) to `chunks` - in `zarr.create_array`, `zarr.from_array`, `zarr.zeros`, `zarr.ones`, `zarr.full`, - `zarr.open`, and related functions, or to `chunk_shape` in `zarr.create`. - - **Opening existing arrays**: Arrays stored with the `rectilinear` chunk grid are read - transparently via `zarr.open` and `zarr.open_array`. - - **Rectilinear sharding**: Shard boundaries can be rectilinear while inner chunks remain regular. + - **Creating arrays**: Pass nested sequences (e.g., `[[10, 20, 30], [50, 50]]`) to `chunks` + in `zarr.create_array`, `zarr.from_array`, `zarr.zeros`, `zarr.ones`, `zarr.full`, + `zarr.open`, and related functions, or to `chunk_shape` in `zarr.create`. + - **Opening existing arrays**: Arrays stored with the `rectilinear` chunk grid are read + transparently via `zarr.open` and `zarr.open_array`. + - **Rectilinear sharding**: Shard boundaries can be rectilinear while inner chunks remain regular. - **Breaking change**: The `validate` method on `BaseCodec` and `CodecPipeline` now receives - a `ChunkGridMetadata` instance instead of a `ChunkGrid` instance for the `chunk_grid` - parameter. Third-party codecs that override `validate` and inspect the chunk grid will need to - update their type annotations. No known downstream packages were using this parameter. ([#3802](https://github.com/zarr-developers/zarr-python/issues/3802)) + **Breaking change**: The `validate` method on `BaseCodec` and `CodecPipeline` now receives + a `ChunkGridMetadata` instance instead of a `ChunkGrid` instance for the `chunk_grid` + parameter. Third-party codecs that override `validate` and inspect the chunk grid will need to + update their type annotations. No known downstream packages were using this parameter. ([#3802](https://github.com/zarr-developers/zarr-python/issues/3802)) - Add `cast_value` and `scale_offset` codecs. ([#3874](https://github.com/zarr-developers/zarr-python/issues/3874)) @@ -394,52 +399,52 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Ensure that invocations of `create_array` use consistent keyword arguments, with consistent defaults. - [`zarr.api.synchronous.create_array`][] now takes a `write_data` keyword argument - The `Group.create_array` method takes `data` and `write_data` keyword arguments. - The functions [`zarr.api.asynchronous.create`][], [`zarr.api.asynchronous.create_array`] - and the methods `Group.create_array`, `Group.array`, had the default - `fill_value` changed from `0` to the `DEFAULT_FILL_VALUE` value, which instructs Zarr to - use the default scalar value associated with the array's data type as the fill value. These are - all functions or methods for array creation that mirror, wrap or are wrapped by, another function - that already has a default `fill_value` set to `DEFAULT_FILL_VALUE`. This change is necessary - to make these functions consistent across the entire codebase, but as this changes default values, - new data might have a different fill value than expected after this change. - - For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this - change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode - strings, the default fill value might be different after this change. Users who were relying on how - Zarr interpreted `0` as a non-numeric scalar value should set their desired fill value explicitly - after this change. + [`zarr.api.synchronous.create_array`][] now takes a `write_data` keyword argument + The `Group.create_array` method takes `data` and `write_data` keyword arguments. + The functions [`zarr.api.asynchronous.create`][], [`zarr.api.asynchronous.create_array`] + and the methods `Group.create_array`, `Group.array`, had the default + `fill_value` changed from `0` to the `DEFAULT_FILL_VALUE` value, which instructs Zarr to + use the default scalar value associated with the array's data type as the fill value. These are + all functions or methods for array creation that mirror, wrap or are wrapped by, another function + that already has a default `fill_value` set to `DEFAULT_FILL_VALUE`. This change is necessary + to make these functions consistent across the entire codebase, but as this changes default values, + new data might have a different fill value than expected after this change. + + For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this + change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode + strings, the default fill value might be different after this change. Users who were relying on how + Zarr interpreted `0` as a non-numeric scalar value should set their desired fill value explicitly + after this change. - Added public API for Buffer ABCs and implementations. - Use `zarr.buffer` to access buffer implementations, and - `zarr.abc.buffer` for the interface to implement new buffer types. + Use `zarr.buffer` to access buffer implementations, and + `zarr.abc.buffer` for the interface to implement new buffer types. - Users previously importing buffer from `zarr.core.buffer` should update their - imports to use `zarr.buffer`. As a reminder, all of `zarr.core` is - considered a private API that's not covered by zarr-python's versioning policy. ([#2871](https://github.com/zarr-developers/zarr-python/issues/2871)) + Users previously importing buffer from `zarr.core.buffer` should update their + imports to use `zarr.buffer`. As a reminder, all of `zarr.core` is + considered a private API that's not covered by zarr-python's versioning policy. ([#2871](https://github.com/zarr-developers/zarr-python/issues/2871)) - Adds zarr-specific data type classes. - This change adds a `ZDType` base class for Zarr V2 and Zarr V3 data types. Child classes are - defined for each NumPy data type. Each child class defines routines for `JSON` serialization. - New data types can be created and registered dynamically. + This change adds a `ZDType` base class for Zarr V2 and Zarr V3 data types. Child classes are + defined for each NumPy data type. Each child class defines routines for `JSON` serialization. + New data types can be created and registered dynamically. - Prior to this change, Zarr Python had two streams for handling data types. For Zarr V2 arrays, - we used NumPy data type identifiers. For Zarr V3 arrays, we used a fixed set of string enums. Both - of these systems proved hard to extend. + Prior to this change, Zarr Python had two streams for handling data types. For Zarr V2 arrays, + we used NumPy data type identifiers. For Zarr V3 arrays, we used a fixed set of string enums. Both + of these systems proved hard to extend. - This change is largely internal, but it does change the type of the `dtype` and `data_type` - fields on the `ArrayV2Metadata` and `ArrayV3Metadata` classes. Previously, `ArrayV2Metadata.dtype` - was a NumPy `dtype` object, and `ArrayV3Metadata.data_type` was an internally-defined `enum`. - After this change, both `ArrayV2Metadata.dtype` and `ArrayV3Metadata.data_type` are instances of - `ZDType`. A NumPy data type can be generated from a `ZDType` via the `ZDType.to_native_dtype()` - method. The internally-defined Zarr V3 `enum` class is gone entirely, but the `ZDType.to_json(zarr_format=3)` - method can be used to generate either a string, or dictionary that has a string `name` field, that - represents the string value previously associated with that `enum`. + This change is largely internal, but it does change the type of the `dtype` and `data_type` + fields on the `ArrayV2Metadata` and `ArrayV3Metadata` classes. Previously, `ArrayV2Metadata.dtype` + was a NumPy `dtype` object, and `ArrayV3Metadata.data_type` was an internally-defined `enum`. + After this change, both `ArrayV2Metadata.dtype` and `ArrayV3Metadata.data_type` are instances of + `ZDType`. A NumPy data type can be generated from a `ZDType` via the `ZDType.to_native_dtype()` + method. The internally-defined Zarr V3 `enum` class is gone entirely, but the `ZDType.to_json(zarr_format=3)` + method can be used to generate either a string, or dictionary that has a string `name` field, that + represents the string value previously associated with that `enum`. - For more on this new feature, see the [documentation](user-guide/data_types.md) ([#2874](https://github.com/zarr-developers/zarr-python/issues/2874)) + For more on this new feature, see the [documentation](user-guide/data_types.md) ([#2874](https://github.com/zarr-developers/zarr-python/issues/2874)) - Added `NDBuffer.empty` method for faster ndbuffer initialization. ([#3191](https://github.com/zarr-developers/zarr-python/issues/3191)) @@ -451,10 +456,10 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Fixes a variety of issues related to string data types. - - Brings the `VariableLengthUTF8` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8 - - Disallows creation of 0-length fixed-length data types - - Adds a regression test for the `VariableLengthUTF8` data type that checks against version 3.0.8 - - Allows users to request the `VariableLengthUTF8` data type with `str`, `"str"`, or `"string"`. ([#3170](https://github.com/zarr-developers/zarr-python/issues/3170)) + - Brings the `VariableLengthUTF8` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8 + - Disallows creation of 0-length fixed-length data types + - Adds a regression test for the `VariableLengthUTF8` data type that checks against version 3.0.8 + - Allows users to request the `VariableLengthUTF8` data type with `str`, `"str"`, or `"string"`. ([#3170](https://github.com/zarr-developers/zarr-python/issues/3170)) - Add human readable size for No. bytes stored to `info_complete` ([#3190](https://github.com/zarr-developers/zarr-python/issues/3190)) @@ -475,26 +480,26 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Add a description on how to create a RemoteStore of a specific filesystem to the `Remote Store` section in `docs/user-guide/storage.md`. State in the docstring of `FsspecStore.from_url` that the filesystem type is inferred from the URL scheme. - It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. ([#3212](https://github.com/zarr-developers/zarr-python/issues/3212)) + It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. ([#3212](https://github.com/zarr-developers/zarr-python/issues/3212)) ### Deprecations and Removals - Removes default chunk encoding settings (filters, serializer, compressors) from the global configuration object. - This removal is justified on the basis that storing chunk encoding settings in the config required - a brittle, confusing, and inaccurate categorization of array data types, which was particularly - unsuitable after the recent addition of new data types that didn't fit naturally into the - pre-existing categories. + This removal is justified on the basis that storing chunk encoding settings in the config required + a brittle, confusing, and inaccurate categorization of array data types, which was particularly + unsuitable after the recent addition of new data types that didn't fit naturally into the + pre-existing categories. - The default chunk encoding is the same (Zstandard compression, and the required object codecs for - variable length data types), but the chunk encoding is now generated by functions that cannot be - reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should - instead specify the desired chunk encoding explicitly when creating an array. + The default chunk encoding is the same (Zstandard compression, and the required object codecs for + variable length data types), but the chunk encoding is now generated by functions that cannot be + reconfigured at runtime. Users who relied on setting the default chunk encoding via the global configuration object should + instead specify the desired chunk encoding explicitly when creating an array. - This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that - arrays with a `VariableLengthUTF8` or `VariableLengthBytes` data type cannot be created without the - correct "object codec". ([#3228](https://github.com/zarr-developers/zarr-python/issues/3228)) + This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that + arrays with a `VariableLengthUTF8` or `VariableLengthBytes` data type cannot be created without the + correct "object codec". ([#3228](https://github.com/zarr-developers/zarr-python/issues/3228)) - Removes support for passing keyword-only arguments positionally to the following functions and methods: `save_array`, `open`, `group`, `open_group`, `create`, `get_basic_selection`, `set_basic_selection`, @@ -546,8 +551,8 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr For large arrays this will result in smaller default chunk sizes. To retain previous behaviour, explicitly set the chunk shape to the data shape. - This fix matches the existing chunking behaviour of - `zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. ([#3103](https://github.com/zarr-developers/zarr-python/issues/3103)) + This fix matches the existing chunking behaviour of + `zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. ([#3103](https://github.com/zarr-developers/zarr-python/issues/3103)) - When `zarr.save` has an argument `path=some/path/` and multiple arrays in `args`, the path resulted in `some/path/some/path` due to using the `path` argument twice while building the array path. This is now fixed. ([#3127](https://github.com/zarr-developers/zarr-python/issues/3127)) @@ -556,12 +561,12 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Suppress `FileNotFoundError` when deleting non-existent keys in the `obstore` adapter. - When writing empty chunks (i.e. chunks where all values are equal to the array's fill value) to a zarr array, zarr - will delete those chunks from the underlying store. For zarr arrays backed by the `obstore` adapter, this will potentially - raise a `FileNotFoundError` if the chunk doesn't already exist. - Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store, - suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect - from the store. ([#3140](https://github.com/zarr-developers/zarr-python/issues/3140)) + When writing empty chunks (i.e. chunks where all values are equal to the array's fill value) to a zarr array, zarr + will delete those chunks from the underlying store. For zarr arrays backed by the `obstore` adapter, this will potentially + raise a `FileNotFoundError` if the chunk doesn't already exist. + Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store, + suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect + from the store. ([#3140](https://github.com/zarr-developers/zarr-python/issues/3140)) - Trying to open a StorePath/Array with `mode='r'` when the store is not read-only creates a read-only copy of the store. ([#3156](https://github.com/zarr-developers/zarr-python/issues/3156)) @@ -583,8 +588,9 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - It is now possible to specify no compressor when creating a zarr format 2 array. This can be done by passing `compressor=None` to the various array creation routines. - The default behaviour of automatically choosing a suitable default compressor remains if the compressor argument is not given. - To reproduce the behaviour in previous zarr-python versions when `compressor=None` was passed, pass `compressor='auto'` instead. ([#3039](https://github.com/zarr-developers/zarr-python/issues/3039)) + The default behaviour of automatically choosing a suitable default compressor remains if the compressor argument is not given. + To reproduce the behaviour in previous zarr-python versions when `compressor=None` was passed, pass `compressor='auto'` instead. ([#3039](https://github.com/zarr-developers/zarr-python/issues/3039)) + - Fixed the typing of `dimension_names` arguments throughout so that it now accepts iterables that contain `None` alongside `str`. ([#3045](https://github.com/zarr-developers/zarr-python/issues/3045)) - Using various functions to open data with `mode='a'` no longer deletes existing data in the store. ([#3062](https://github.com/zarr-developers/zarr-python/issues/3062)) - Internally use `typesize` constructor parameter for `numcodecs.blosc.Blosc` to improve compression ratios back to the v2-package levels. ([#2962](https://github.com/zarr-developers/zarr-python/issues/2962)) diff --git a/docs/user-guide/data_types.md b/docs/user-guide/data_types.md index ac966f885f..91f828a738 100644 --- a/docs/user-guide/data_types.md +++ b/docs/user-guide/data_types.md @@ -139,17 +139,17 @@ Zarr V3 introduced several key changes to how data types are represented: The basic data types are identified by strings like `"int8"`, `"int16"`, etc., and data types that require a configuration can be identified by a JSON object. - For example, this JSON object declares a datetime data type: - - ```json - { - "name": "numpy.datetime64", - "configuration": { - "unit": "s", - "scale_factor": 10 + For example, this JSON object declares a datetime data type: + + ```json + { + "name": "numpy.datetime64", + "configuration": { + "unit": "s", + "scale_factor": 10 + } } - } - ``` + ``` - Zarr V3 data types do not have endianness. This is a departure from Zarr V2, where multi-byte data types are defined with endianness information. Instead, Zarr V3 requires that the endianness diff --git a/docs/user-guide/v3_migration.md b/docs/user-guide/v3_migration.md index 6d9d516ebe..4d97963be2 100644 --- a/docs/user-guide/v3_migration.md +++ b/docs/user-guide/v3_migration.md @@ -42,40 +42,40 @@ the following actions in order: will be compatible in Zarr-Python 3. However, the following breaking API changes are planned: - - `numcodecs.*` will no longer be available in `zarr.*`. To migrate, import codecs - directly from `numcodecs`: - - ```python exec="false" reason="intentionally shows the old/incorrect import for contrast" - from numcodecs import Blosc - # instead of: - # from zarr import Blosc - ``` - - - The `zarr.v3_api_available` feature flag is being removed. In Zarr-Python 3 - the v3 API is always available, so you shouldn't need to use this flag. - - `zarr.errors` has been consolidated. Several exception classes from - Zarr-Python 2 (such as `zarr.errors.PathNotFoundError`) have been removed - or replaced. For example, missing nodes now raise `zarr.errors.NodeNotFoundError` - (which subclasses both `BaseZarrError` and `FileNotFoundError`) instead of - `zarr.errors.PathNotFoundError`. Review any code that catches exceptions - from `zarr.errors` after migrating. - - The following internal modules are being removed or significantly changed. If - your application relies on imports from any of the below modules, you will need - to either a) modify your application to no longer rely on these imports or b) - vendor the parts of the specific modules that you need. - - * `zarr.attrs` has gone, with no replacement - * `zarr.codecs` has changed, see "Codecs" section below for more information - * `zarr.context` has gone, with no replacement - * `zarr.core` remains but should be considered private API - * `zarr.hierarchy` has gone, with no replacement (use `zarr.Group` in place of `zarr.hierarchy.Group`) - * `zarr.indexing` has gone, with no replacement - * `zarr.meta` has gone, with no replacement - * `zarr.meta_v1` has gone, with no replacement - * `zarr.sync` has gone, with no replacement - * `zarr.types` has gone, with no replacement - * `zarr.util` has gone, with no replacement - * `zarr.n5` has gone, see below for an alternative N5 option + - `numcodecs.*` will no longer be available in `zarr.*`. To migrate, import codecs + directly from `numcodecs`: + + ```python exec="false" reason="intentionally shows the old/incorrect import for contrast" + from numcodecs import Blosc + # instead of: + # from zarr import Blosc + ``` + + - The `zarr.v3_api_available` feature flag is being removed. In Zarr-Python 3 + the v3 API is always available, so you shouldn't need to use this flag. + - `zarr.errors` has been consolidated. Several exception classes from + Zarr-Python 2 (such as `zarr.errors.PathNotFoundError`) have been removed + or replaced. For example, missing nodes now raise `zarr.errors.NodeNotFoundError` + (which subclasses both `BaseZarrError` and `FileNotFoundError`) instead of + `zarr.errors.PathNotFoundError`. Review any code that catches exceptions + from `zarr.errors` after migrating. + - The following internal modules are being removed or significantly changed. If + your application relies on imports from any of the below modules, you will need + to either a) modify your application to no longer rely on these imports or b) + vendor the parts of the specific modules that you need. + + * `zarr.attrs` has gone, with no replacement + * `zarr.codecs` has changed, see "Codecs" section below for more information + * `zarr.context` has gone, with no replacement + * `zarr.core` remains but should be considered private API + * `zarr.hierarchy` has gone, with no replacement (use `zarr.Group` in place of `zarr.hierarchy.Group`) + * `zarr.indexing` has gone, with no replacement + * `zarr.meta` has gone, with no replacement + * `zarr.meta_v1` has gone, with no replacement + * `zarr.sync` has gone, with no replacement + * `zarr.types` has gone, with no replacement + * `zarr.util` has gone, with no replacement + * `zarr.n5` has gone, see below for an alternative N5 option 3. Test that your package works with version 3. 4. Update the pin to include `zarr>=3,<4`. @@ -123,8 +123,9 @@ The following sections provide details on breaking changes in Zarr-Python 3. 2. The h5py compatibility methods `create_dataset` and `require_dataset` have been removed. Use the following replacements: - - [`zarr.Group.create_array`][] in place of `Group.create_dataset` - - [`zarr.Group.require_array`][] in place of `Group.require_dataset` + - [`zarr.Group.create_array`][] in place of `Group.create_dataset` + - [`zarr.Group.require_array`][] in place of `Group.require_dataset` + 3. Disallow "." syntax for getting group members. To get a member of a group named `foo`, use `group["foo"]` in place of `group.foo`. 4. The `zarr.storage.init_group` low-level helper function has been removed. Use From 326545217ffe60112b2da1175a7423ff4acb7219 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 17 Jul 2026 13:18:56 +0200 Subject: [PATCH 406/468] chore(deps): bump the actions group across 1 directory with 6 updates (#4152) Bumps the actions group with 6 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/checkout](https://github.com/actions/checkout) | `6.0.3` | `7.0.0` | | [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) | `8.2.0` | `8.3.2` | | [CodSpeedHQ/action](https://github.com/codspeedhq/action) | `4.18.1` | `4.18.5` | | [github-community-projects/issue-metrics](https://github.com/github-community-projects/issue-metrics) | `4.2.8` | `5.0.0` | | [lycheeverse/lychee-action](https://github.com/lycheeverse/lychee-action) | `2.8.0` | `2.9.0` | | [actions/labeler](https://github.com/actions/labeler) | `6.1.0` | `6.2.0` | Updates `actions/checkout` from 6.0.3 to 7.0.0 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v6.0.3...9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0) Updates `astral-sh/setup-uv` from 8.2.0 to 8.3.2 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/fac544c07dec837d0ccb6301d7b5580bf5edae39...11f9893b081a58869d3b5fccaea48c9e9e46f990) Updates `CodSpeedHQ/action` from 4.18.1 to 4.18.5 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/a4a36bb07c0638b0b4ca52bf1f3dad1b4289e52f...f99becdce5e5d51fd556489ebef684f4ecfd6286) Updates `github-community-projects/issue-metrics` from 4.2.8 to 5.0.0 - [Release notes](https://github.com/github-community-projects/issue-metrics/releases) - [Commits](https://github.com/github-community-projects/issue-metrics/compare/44173f9e0a3b2144a777a10a340e4c09a25ac9f8...df8c49d20958f9345281fa2124858bd0ad227e1f) Updates `lycheeverse/lychee-action` from 2.8.0 to 2.9.0 - [Release notes](https://github.com/lycheeverse/lychee-action/releases) - [Commits](https://github.com/lycheeverse/lychee-action/compare/8646ba30535128ac92d33dfc9133794bfdd9b411...e7477775783ea5526144ba13e8db5eec57747ce8) Updates `actions/labeler` from 6.1.0 to 6.2.0 - [Release notes](https://github.com/actions/labeler/releases) - [Commits](https://github.com/actions/labeler/compare/f27b608878404679385c85cfa523b85ccb86e213...b8dd2d9be0f68b860e7dae5dae7d772984eacd6d) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/labeler dependency-version: 6.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 8.3.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 4.18.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github-community-projects/issue-metrics dependency-version: 5.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: lycheeverse/lychee-action dependency-version: 2.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 2 +- .github/workflows/codspeed.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/downstream.yml | 4 ++-- .github/workflows/gpu_test.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/issue-metrics.yml | 2 +- .github/workflows/links.yml | 4 ++-- .github/workflows/lint.yml | 2 +- .github/workflows/needs_release_notes.yml | 2 +- .github/workflows/test.yml | 8 ++++---- .github/workflows/zarr-metadata-release.yml | 2 +- .github/workflows/zarr-metadata.yml | 6 +++--- 13 files changed, 20 insertions(+), 20 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 25034b868d..0033b43db2 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -22,7 +22,7 @@ jobs: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Check zarr-python changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 1d8e847ec5..39cd8eb261 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@a4a36bb07c0638b0b4ca52bf1f3dad1b4289e52f # v4.18.1 + uses: CodSpeedHQ/action@f99becdce5e5d51fd556489ebef684f4ecfd6286 # v4.18.5 with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index c72b493b12..baf9233fc7 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -22,7 +22,7 @@ jobs: - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - run: uv sync --group docs # Fast source-level guards that need no built site, so they run before the (slower) # build for a quick failure: every public export is in the API reference, and no diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index d8aa2907be..f65f8d47e3 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -45,7 +45,7 @@ jobs: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install xarray and test dependencies working-directory: xarray @@ -102,7 +102,7 @@ jobs: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install numcodecs with test-zarr-main group working-directory: numcodecs diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index f2bf4907fa..bbbb3e5133 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -62,7 +62,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index 01212dfb56..e836f30a5b 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -57,7 +57,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml index 53860d21c8..adbd2748a0 100644 --- a/.github/workflows/issue-metrics.yml +++ b/.github/workflows/issue-metrics.yml @@ -33,7 +33,7 @@ jobs: echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV" - name: Run issue-metrics tool - uses: github-community-projects/issue-metrics@44173f9e0a3b2144a777a10a340e4c09a25ac9f8 # v4.2.8 + uses: github-community-projects/issue-metrics@df8c49d20958f9345281fa2124858bd0ad227e1f # v5.0.0 env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"' diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml index a53de8da83..f606f12a3e 100644 --- a/.github/workflows/links.yml +++ b/.github/workflows/links.yml @@ -13,13 +13,13 @@ jobs: permissions: issues: write # required for peter-evans/create-issue-from-file steps: - - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3 + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - name: Link Checker id: lychee - uses: lycheeverse/lychee-action@8646ba30535128ac92d33dfc9133794bfdd9b411 # v2.8.0 + uses: lycheeverse/lychee-action@e7477775783ea5526144ba13e8db5eec57747ce8 # v2.9.0 with: fail: false diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 8190b1e061..dacba6648f 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -27,7 +27,7 @@ jobs: with: python-version: "3.12" - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 with: enable-cache: true - uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2.0.5 diff --git a/.github/workflows/needs_release_notes.yml b/.github/workflows/needs_release_notes.yml index 1f79725b86..fa555d1478 100644 --- a/.github/workflows/needs_release_notes.yml +++ b/.github/workflows/needs_release_notes.yml @@ -21,7 +21,7 @@ jobs: pull-requests: write # Required to add labels to PRs runs-on: ubuntu-latest steps: - - uses: actions/labeler@f27b608878404679385c85cfa523b85ccb86e213 # v6.1.0 + - uses: actions/labeler@b8dd2d9be0f68b860e7dae5dae7d772984eacd6d # v6.2.0 with: repo-token: ${{ secrets.GITHUB_TOKEN }} sync-labels: true diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 7bc43512b5..ab78cfbe2b 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -66,7 +66,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -115,7 +115,7 @@ jobs: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -150,7 +150,7 @@ jobs: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -174,7 +174,7 @@ jobs: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Run Benchmarks diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index db05489798..5021f79d2e 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -51,7 +51,7 @@ jobs: path: dist - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 with: enable-cache: false diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml index 95e8251227..4e5bb0fb1a 100644 --- a/.github/workflows/zarr-metadata.yml +++ b/.github/workflows/zarr-metadata.yml @@ -36,7 +36,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 with: enable-cache: true - name: Set up Python ${{ matrix.python-version }} @@ -58,7 +58,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 - name: Run ruff run: uvx ruff check . @@ -74,7 +74,7 @@ jobs: with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0 + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 with: enable-cache: true - name: Set up Python From 50b7e016590d76011382771fd52843949782c9c0 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Fri, 17 Jul 2026 15:34:21 +0200 Subject: [PATCH 407/468] Fix/memorystore buffer aliasing (#4157) * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * fix(store): copy buffers on write in MemoryStore Encoding an uncompressed chunk hands the store a zero-copy view of the caller's array, and MemoryStore keeps whatever it is given alive in a dict rather than serializing it. Mutating the source array after a write therefore rewrote chunks already committed to the store, silently. Stores that serialize on write (LocalStore, ZipStore, remote stores) are unaffected, so they keep the full benefit of #3885. Only MemoryStore pays the copy, and only where it was aliasing to begin with: an uncompressed 34 MB write goes from ~23 ms to ~39 ms, while compressed writes are unchanged. Copying at the store boundary rather than narrowing the fast path in _merge_chunk_array also fixes the single-chunk case, which aliased in v3.2.1 too. Assisted-by: ClaudeCode:claude-opus-4.8 * docs: add changelog entry for MemoryStore buffer copy Assisted-by: ClaudeCode:claude-opus-4.8 * docs: correct changelog --- changes/4157.bugfix.md | 11 +++++++ src/zarr/core/buffer/core.py | 2 ++ src/zarr/storage/_memory.py | 24 ++++++++++++++-- tests/test_store/test_memory.py | 51 ++++++++++++++++++++++++++++++++- 4 files changed, 84 insertions(+), 4 deletions(-) create mode 100644 changes/4157.bugfix.md diff --git a/changes/4157.bugfix.md b/changes/4157.bugfix.md new file mode 100644 index 0000000000..6b0d0fcc67 --- /dev/null +++ b/changes/4157.bugfix.md @@ -0,0 +1,11 @@ +`MemoryStore` now copies buffers as they are written, so it never retains the +caller's memory. Previously an uncompressed write handed the store a zero-copy +view of the user's array, and mutating that array afterwards would silently +rewrite chunks already committed to the store. + +Only `MemoryStore` is affected: stores that serialize on write, such as +`LocalStore` and `ZipStore`, never aliased the caller's memory. Uncompressed +writes to a `MemoryStore` are correspondingly slower, since the copy that makes +the stored data independent is now actually performed; compressed writes are +unchanged. Buffers supplied through the `store_dict` argument remain the +caller's responsibility and are stored as-is. diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py index 497543f88f..b8f7f11cd4 100644 --- a/src/zarr/core/buffer/core.py +++ b/src/zarr/core/buffer/core.py @@ -45,6 +45,8 @@ def __getitem__(self, key: slice) -> Self: ... def __setitem__(self, key: slice, value: Any) -> None: ... + def copy(self) -> Self: ... + @runtime_checkable class NDArrayLike(Protocol): diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index 5f5b632d4a..97dd355515 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -26,6 +26,18 @@ logger = getLogger(__name__) +def _copy_buffer(value: Buffer) -> Buffer: + """Copy `value` so the store does not retain the caller's memory. + + Encoding a chunk can hand the store a zero-copy view of the user's array + (an uncompressed write is the common case), and unlike stores that + serialize on write, this one keeps whatever it is given alive in a dict. + Without this copy a later mutation of the user's array would rewrite + chunks already committed to the store. + """ + return type(value).from_array_like(value.as_array_like().copy()) + + class MemoryStore(Store): """ Store for local memory. @@ -42,6 +54,12 @@ class MemoryStore(Store): supports_writes supports_deletes supports_listing + + Notes + ----- + Writes copy the buffer they are given, so the store never aliases the + caller's memory. Buffers passed via `store_dict` are the caller's + responsibility and are stored as-is. """ supports_writes: bool = True @@ -117,7 +135,7 @@ def set_sync(self, key: str, value: Buffer) -> None: raise TypeError( f"MemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead." ) - self._store_dict[key] = value + self._store_dict[key] = _copy_buffer(value) def delete_sync(self, key: str) -> None: self._check_writable() @@ -178,13 +196,13 @@ async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None buf[byte_range[0] : byte_range[1]] = value self._store_dict[key] = buf else: - self._store_dict[key] = value + self._store_dict[key] = _copy_buffer(value) async def set_if_not_exists(self, key: str, value: Buffer) -> None: # docstring inherited self._check_writable() await self._ensure_open() - self._store_dict.setdefault(key, value) + self._store_dict.setdefault(key, _copy_buffer(value)) async def delete(self, key: str) -> None: # docstring inherited diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 35504718a7..36265423e6 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -8,7 +8,7 @@ import pytest import zarr -from zarr.core.buffer import Buffer, cpu, gpu +from zarr.core.buffer import Buffer, cpu, default_buffer_prototype, gpu from zarr.errors import ZarrUserWarning from zarr.storage import GpuMemoryStore, ManagedMemoryStore, MemoryStore from zarr.testing.store import StoreTests @@ -76,6 +76,55 @@ async def test_deterministic_size( np.testing.assert_array_equal(a[:3], 1) np.testing.assert_array_equal(a[3:], 0) + @pytest.mark.parametrize("method", ["set", "set_sync", "set_if_not_exists"]) + async def test_set_does_not_retain_caller_buffer(self, store: MemoryStore, method: str) -> None: + """Writing a buffer must not alias the caller's memory. + + MemoryStore keeps whatever it is handed alive in a dict, so retaining + the caller's buffer lets a later mutation of that buffer rewrite data + already committed to the store. + """ + source = np.frombuffer(bytearray(b"\x01\x02\x03\x04"), dtype="B") + value = cpu.Buffer.from_array_like(source) + + if method == "set_sync": + store.set_sync("k", value) + else: + await getattr(store, method)("k", value) + + source[:] = 0xF # mutate the caller's memory after the write + stored = await store.get("k", prototype=default_buffer_prototype()) + assert stored is not None + assert stored.to_bytes() == b"\x01\x02\x03\x04" + + @pytest.mark.parametrize( + "pipeline", + [ + "zarr.core.codec_pipeline.BatchedCodecPipeline", + "zarr.core.codec_pipeline.FusedCodecPipeline", + ], + ) + @pytest.mark.parametrize(("shape", "chunks"), [((30,), (10,)), ((8,), (4,)), ((4,), (4,))]) + def test_write_does_not_alias_source_array( + self, pipeline: str, shape: tuple[int], chunks: tuple[int] + ) -> None: + """Mutating the source array after a write must not corrupt stored chunks. + + Without compression the encoded buffer is a zero-copy view of the + caller's array all the way down to the store, so this covers both the + single-chunk and multi-chunk write paths. + """ + with zarr.config.set({"codec_pipeline.path": pipeline}): + array = zarr.create_array( + store=MemoryStore(), shape=shape, chunks=chunks, dtype="i4", compressors=None + ) + source = np.arange(shape[0], dtype="i4") + expected = source.copy() + array[:] = source + source[:] = -1 + + np.testing.assert_array_equal(array[:], expected) + # --- byte-range-write tests: disabled --- # Byte-range-write support (set_range / set_range_sync / SupportsSetRange) # was removed from this PR pending a decision on the store interface. These From ab769985d7aa0279e9f628ab4148660bbf4921a5 Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Sun, 19 Jul 2026 14:19:48 -0400 Subject: [PATCH 408/468] chore: refine link checker configuration (#4158) --- lychee.toml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/lychee.toml b/lychee.toml index 38b2b8ab7a..54a5b49b8d 100644 --- a/lychee.toml +++ b/lychee.toml @@ -1,6 +1,9 @@ # Configuration for the lychee link checker (https://lychee.cli.rs/). # Auto-discovered as ./lychee.toml by the lychee GitHub Action. +# Treat redirect status codes as success rather than failures. +accept = ["200..=299"] + # Files lychee should not scan for links. exclude_path = [ # mkdocs-material theme overrides: hrefs are Jinja expressions like @@ -17,4 +20,6 @@ exclude = [ # documentation of a command rather than a reachable link. '^https?://0\.0\.0\.0', '^https?://(localhost|127\.0\.0\.1)(:\d+)?', + # SPEC 0 page times out but is valid. + '^https://scientific-python\.org/specs/spec-0000', ] From ecc2d77718dbc4343da052347c4377945246d4fa Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Mon, 20 Jul 2026 16:39:17 +0200 Subject: [PATCH 409/468] fix(store): don't close a shared filesystem in FsspecStore.close() (#4165) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * fix(store): FsspecStore.close() no longer closes the filesystem FsspecStore.close() closed the underlying filesystem's session, on the premise that a store built by from_url "owns" the filesystem it created. That premise does not hold: fsspec caches and shares filesystem instances across callers (its instance cache keys on storage options, not path), and users can hand one filesystem to many stores directly. Closing one store therefore killed the session that sibling stores were still using, and left the dead filesystem in fsspec's cache for later callers. Determining whether a filesystem is actually shared requires reaching into fsspec's private instance cache (_cache, _fs_token, cachable) and walking wrapper chains for caching/proxy filesystems — an implementation detail that leaks upward and that we would have to keep in sync with fsspec forever, getting it subtly wrong in between. The wrapper case alone (simplecache::/dir://) already slipped through a cache-membership check. The filesystem's lifecycle is simply not the store's to manage. This removes the ownership model added in the unreleased gh-4003: no _owns_fs, no _close_fs, no ownership transfer in with_read_only, and close() just marks the store not-open. The only thing given up is suppressing an "Unclosed client session" ResourceWarning, which was true anyway — the session belongs to a cached filesystem that outlives the store. Since gh-4003 never shipped (latest release is v3.2.1), its changelog fragment is removed rather than superseded. Assisted-by: ClaudeCode:claude-opus-4.8 * test: skip with_read_only fs test when AsyncFileSystemWrapper is absent test_with_read_only_shares_filesystem replaced an ownership test that carried a guard for fsspec < 2024.12.0, and the guard was dropped in the rewrite. The test still opens a file:// URL, which needs AsyncFileSystemWrapper, so it failed the min_deps job. Assisted-by: ClaudeCode:claude-opus-4.8 * docs: correct changelog claim about gh-4003 release status The fragment said gh-4003 was unreleased with no net change for released versions. Its text is already in the staged 3.3.0 release notes, so the revert is a real behavior change for anyone relying on close() releasing the session. Assisted-by: ClaudeCode:claude-opus-4.8 * docs: remove changelog entry for unreleased versions --- src/zarr/storage/_fsspec.py | 70 ++++------------- tests/test_store/test_fsspec.py | 134 ++++++++------------------------ 2 files changed, 47 insertions(+), 157 deletions(-) diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 617980ac19..37d134dd95 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -3,7 +3,6 @@ import json import warnings from contextlib import suppress -from logging import getLogger from typing import TYPE_CHECKING, Any from packaging.version import parse as parse_version @@ -19,8 +18,6 @@ from zarr.errors import ZarrUserWarning from zarr.storage._utils import _dereference_path -logger = getLogger(__name__) - if TYPE_CHECKING: from collections.abc import AsyncIterator, Iterable @@ -38,26 +35,6 @@ ) -async def _close_fs(fs: AsyncFileSystem) -> None: - """ - Best-effort async close of an fsspec async filesystem owned by FsspecStore. - - For filesystems that expose `set_session()` (e.g. s3fs) the underlying - aiohttp `ClientSession` is closed explicitly, which prevents - "Unclosed client session" `ResourceWarning`s from aiohttp. For all - other filesystem types the call is a no-op (not every implementation - manages an HTTP session directly). - - Note that `set_session()` lazily creates a session if none exists yet, so - closing a store that never performed any I/O may instantiate a session - purely to close it. This is accepted best-effort behavior; fsspec does not - expose a stable, cross-implementation way to test for an existing session. - """ - if hasattr(fs, "set_session"): - session = await fs.set_session() - await session.close() - - def _make_async(fs: AbstractFileSystem) -> AsyncFileSystem: """Convert a sync FSSpec filesystem to an async FFSpec filesystem @@ -126,6 +103,15 @@ class FsspecStore(Store): ZarrUserWarning If the file system (fs) was not created with `asynchronous=True`. + Notes + ----- + Closing the store does not close the underlying filesystem or its network + session. fsspec caches and shares filesystem instances across callers, so + the store cannot know whether it is the only user, and closing a shared + session would break other stores. The filesystem's lifecycle belongs to + whoever created it; use fsspec's own tools (e.g. `clear_instance_cache`) + to release it. + See Also -------- FsspecStore.from_upath @@ -152,9 +138,6 @@ def __init__( self.fs = fs self.path = path self.allowed_exceptions = allowed_exceptions - # True only when this store created fs itself (from_url / from_mapper with new instance). - # Callers who supply their own fs remain responsible for its lifecycle. - self._owns_fs: bool = False if not self.fs.async_impl: raise TypeError("Filesystem needs to support async operations.") @@ -220,17 +203,13 @@ def from_mapper( ------- FsspecStore """ - original_fs = fs_map.fs - fs = _make_async(original_fs) - store = cls( + fs = _make_async(fs_map.fs) + return cls( fs=fs, path=fs_map.root, read_only=read_only, allowed_exceptions=allowed_exceptions, ) - # _make_async returns a new instance when converting sync→async; own it. - store._owns_fs = fs is not original_fs - return store @classmethod def from_url( @@ -272,39 +251,16 @@ def from_url( if not fs.async_impl: fs = _make_async(fs) - store = cls(fs=fs, path=path, read_only=read_only, allowed_exceptions=allowed_exceptions) - store._owns_fs = True - return store + return cls(fs=fs, path=path, read_only=read_only, allowed_exceptions=allowed_exceptions) def with_read_only(self, read_only: bool = False) -> FsspecStore: # docstring inherited - new_store = type(self)( + return type(self)( fs=self.fs, path=self.path, allowed_exceptions=self.allowed_exceptions, read_only=read_only, ) - # The derived store shares the same fs. Transfer ownership so the - # surviving store closes it, and clear ours to avoid a double-close. - # Otherwise the common `from_url(...).with_read_only()` chain would - # drop the only owner (the unreferenced source) and leak the session. - new_store._owns_fs = self._owns_fs - self._owns_fs = False - return new_store - - def close(self) -> None: - # docstring inherited - if self._owns_fs: - from zarr.core.sync import sync as zarr_sync - - # Best-effort: a failure to release the session must not block close(), - # but log it so a genuine regression in the close path stays observable - # rather than silently reverting to the leaking behavior. - try: - zarr_sync(_close_fs(self.fs)) - except Exception: - logger.debug("Failed to close owned filesystem %r", self.fs, exc_info=True) - super().close() async def clear(self) -> None: # docstring inherited diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 898d49ec08..515e1526b6 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -276,75 +276,20 @@ async def test_delete_dir_unsupported_deletes(self, store: FsspecStore) -> None: ): await store.delete_dir("test_prefix") - # ── Filesystem lifecycle (ownership) ────────────────────────────────────── + # ── Filesystem lifecycle ────────────────────────────────────────────────── - def test_from_url_owns_filesystem(self, endpoint_url: str) -> None: - """FsspecStore.from_url() creates the async fs; it must own it.""" + async def test_close_marks_store_closed(self, endpoint_url: str) -> None: + """close() must succeed and mark the store not-open.""" store = FsspecStore.from_url( f"s3://{test_bucket_name}/lifecycle/", storage_options={"endpoint_url": endpoint_url, "anon": False}, ) - assert store._owns_fs - store.close() - - async def test_from_url_close_releases_store(self, endpoint_url: str) -> None: - """ - close() on a from_url() store must succeed without error and mark the - store as closed. For the owned filesystem, _close_fs() is invoked to - release the underlying S3 client / aiohttp connection pool. - """ - store = FsspecStore.from_url( - f"s3://{test_bucket_name}/lifecycle/", - storage_options={"endpoint_url": endpoint_url, "anon": False}, - ) - # Materialise the S3 client and connection pool. await store.set("probe", cpu.Buffer.from_bytes(b"x")) store.close() assert not store._is_open - def test_direct_construction_does_not_own_filesystem(self, endpoint_url: str) -> None: - """Direct FsspecStore() must not claim ownership — the caller owns the fs.""" - try: - from fsspec import url_to_fs - except ImportError: - from fsspec.core import url_to_fs - fs, path = url_to_fs( - f"s3://{test_bucket_name}", endpoint_url=endpoint_url, anon=False, asynchronous=True - ) - store = FsspecStore(fs=fs, path=path) - assert not store._owns_fs - - @pytest.mark.skipif( - parse_version(fsspec.__version__) < parse_version("2024.03.01"), - reason="Prior bug in from_upath", - ) - def test_from_upath_does_not_own_filesystem(self, endpoint_url: str) -> None: - """from_upath() uses the UPath's existing fs; the store must not own it.""" - upath = pytest.importorskip("upath") - path = upath.UPath( - f"s3://{test_bucket_name}/foo/bar/", - endpoint_url=endpoint_url, - anon=False, - asynchronous=True, - ) - store = FsspecStore.from_upath(path) - assert not store._owns_fs - - def test_from_mapper_does_not_own_already_async_filesystem(self, endpoint_url: str) -> None: - """from_mapper() with an already-async fs must not claim ownership.""" - s3_filesystem = s3fs.S3FileSystem( - asynchronous=True, - endpoint_url=endpoint_url, - anon=False, - skip_instance_cache=True, - ) - mapper = s3_filesystem.get_mapper(f"s3://{test_bucket_name}/") - store = FsspecStore.from_mapper(mapper) - # _make_async returns the same instance for an already-async fs. - assert not store._owns_fs - def array_roundtrip(store: FsspecStore) -> None: """ @@ -574,47 +519,47 @@ def test_open_s3map_raises(endpoint_url: str) -> None: zarr.open(store=mapper, storage_options={"anon": True}, mode="w", shape=(3, 3)) -async def test_close_fs_closes_s3_client() -> None: - """ - _close_fs() must call set_session() and then close() on the returned - S3 client. This is verified with mocks to avoid a real S3 connection. - """ - from unittest.mock import AsyncMock +async def test_close_does_not_close_filesystem_session() -> None: + """close() must not touch the filesystem's session. - from zarr.storage._fsspec import _close_fs + fsspec caches and shares filesystem instances across callers, so the + session is not the store's to close. HTTP is used because its aiohttp + session is observably closed for good; s3fs transparently reconnects, which + would hide a regression. No request is issued — set_session() only + constructs the session. + """ + pytest.importorskip("aiohttp") + store = FsspecStore.from_url("http://example.com/a") + session = await store.fs.set_session() - mock_client = AsyncMock() - mock_fs = AsyncMock() - mock_fs.set_session = AsyncMock(return_value=mock_client) + store.close() - await _close_fs(mock_fs) + assert not session.closed - mock_fs.set_session.assert_called_once() - mock_client.close.assert_called_once() +async def test_close_does_not_break_a_sibling_store() -> None: + """Closing one store must not close a session another store is using. -async def test_close_fs_no_op_for_fs_without_set_session() -> None: - """_close_fs() must be a no-op for filesystems that don't expose set_session().""" - from unittest.mock import AsyncMock + Two stores from different URLs on one host are handed the same cached + filesystem; a store that closed it on close() would take the sibling's + session down too. This is the regression guard for that bug. + """ + pytest.importorskip("aiohttp") + s1 = FsspecStore.from_url("http://example.com/a") + s2 = FsspecStore.from_url("http://example.com/b") + session = await s2.fs.set_session() - from zarr.storage._fsspec import _close_fs + s1.close() - mock_fs = AsyncMock(spec=[]) # empty spec — no set_session attribute - await _close_fs(mock_fs) # must not raise + assert not session.closed @pytest.mark.skipif( parse_version(fsspec.__version__) < parse_version("2024.12.0"), reason="No AsyncFileSystemWrapper", ) -def test_from_mapper_owns_wrapped_sync_filesystem(tmp_path: pathlib.Path) -> None: - """ - from_mapper() with a sync fs must wrap it in AsyncFileSystemWrapper and - claim ownership so that close() cleans it up. - - The local filesystem is synchronous; _make_async() produces a new - AsyncFileSystemWrapper instance — a different object from the original fs. - """ +def test_from_mapper_wraps_sync_filesystem(tmp_path: pathlib.Path) -> None: + """from_mapper() with a sync fs wraps it in an AsyncFileSystemWrapper.""" import fsspec as _fsspec from fsspec.implementations.asyn_wrapper import AsyncFileSystemWrapper @@ -622,32 +567,21 @@ def test_from_mapper_owns_wrapped_sync_filesystem(tmp_path: pathlib.Path) -> Non mapper = fs.get_mapper(str(tmp_path)) store = FsspecStore.from_mapper(mapper) assert isinstance(store.fs, AsyncFileSystemWrapper) - assert store._owns_fs @pytest.mark.skipif( parse_version(fsspec.__version__) < parse_version("2024.12.0"), reason="No AsyncFileSystemWrapper", ) -def test_with_read_only_transfers_filesystem_ownership(tmp_path: pathlib.Path) -> None: - """ - with_read_only() must transfer fs ownership to the derived store and clear - it on the source, so the surviving store closes the shared fs exactly once. - - In the common ``from_url(...).with_read_only()`` chain the source store is - immediately unreferenced; if ownership were not transferred, the only owner - would be garbage-collected without close() and the session would leak. - """ +def test_with_read_only_shares_filesystem(tmp_path: pathlib.Path) -> None: + """with_read_only() returns a store sharing the source's filesystem.""" source = FsspecStore.from_url(f"file://{tmp_path}", storage_options={"auto_mkdir": False}) - assert source._owns_fs derived = source.with_read_only(read_only=True) - # Ownership moved to the survivor; the source no longer owns it (no double-close). - assert derived._owns_fs - assert not source._owns_fs - # The derived store shares the same underlying fs. assert derived.fs is source.fs + assert derived.read_only + assert not source.read_only @pytest.mark.parametrize("asynchronous", [True, False]) From faba4bc8f2cdf379879179778cc3c9b202136be8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 22 Jul 2026 23:42:13 +0200 Subject: [PATCH 410/468] chore(deps): bump setuptools from 82.0.1 to 83.0.0 (#4176) Bumps [setuptools](https://github.com/pypa/setuptools) from 82.0.1 to 83.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](https://github.com/pypa/setuptools/compare/v82.0.1...v83.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-version: 83.0.0 dependency-type: indirect ... 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[actions/attest](https://github.com/actions/attest) and [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action). Updates `actions/labeler` from 6.2.0 to 7.0.0 - [Release notes](https://github.com/actions/labeler/releases) - [Commits](https://github.com/actions/labeler/compare/b8dd2d9be0f68b860e7dae5dae7d772984eacd6d...bf12e9b00b37c5c0ca2b87b79b2daf7891dbda13) Updates `actions/attest` from 4.1.1 to 4.2.0 - [Release notes](https://github.com/actions/attest/releases) - [Changelog](https://github.com/actions/attest/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest/compare/a1948c3f048ba23858d222213b7c278aabede763...f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6) Updates `zizmorcore/zizmor-action` from 0.5.7 to 0.6.0 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/192e21d79ab29983730a13d1382995c2307fbcaa...6599ee8b7a49aef6a770f63d261d214911a7ce02) --- updated-dependencies: - dependency-name: actions/labeler dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/attest dependency-version: 4.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.6.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/needs_release_notes.yml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/zarr-metadata-release.yml | 4 ++-- .github/workflows/zizmor.yml | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/needs_release_notes.yml b/.github/workflows/needs_release_notes.yml index fa555d1478..e001e8cd43 100644 --- a/.github/workflows/needs_release_notes.yml +++ b/.github/workflows/needs_release_notes.yml @@ -21,7 +21,7 @@ jobs: pull-requests: write # Required to add labels to PRs runs-on: ubuntu-latest steps: - - uses: actions/labeler@b8dd2d9be0f68b860e7dae5dae7d772984eacd6d # v6.2.0 + - uses: actions/labeler@bf12e9b00b37c5c0ca2b87b79b2daf7891dbda13 # v7.0.0 with: repo-token: ${{ secrets.GITHUB_TOKEN }} sync-labels: true diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 4d460f4a56..fe0d09f300 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -81,7 +81,7 @@ jobs: name: releases path: dist - name: Generate artifact attestation - uses: actions/attest@a1948c3f048ba23858d222213b7c278aabede763 # v4.1.1 + uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 with: subject-path: dist/* - name: Publish package to PyPI diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index 5021f79d2e..bc9ecf9871 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -82,7 +82,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@a1948c3f048ba23858d222213b7c278aabede763 # v4.1.1 + uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 with: subject-path: dist/* @@ -107,7 +107,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@a1948c3f048ba23858d222213b7c278aabede763 # v4.1.1 + uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 with: subject-path: dist/* diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 6250426bae..1567bea713 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -32,4 +32,4 @@ jobs: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@192e21d79ab29983730a13d1382995c2307fbcaa # v0.5.7 + uses: zizmorcore/zizmor-action@6599ee8b7a49aef6a770f63d261d214911a7ce02 # v0.6.0 From 0b727571268c8962717ab5c23965c4642fe6bd36 Mon Sep 17 00:00:00 2001 From: Joe Hamman <joe@earthmover.io> Date: Mon, 27 Jul 2026 19:31:14 -0700 Subject: [PATCH 413/468] feat: ZipStore accepts open binary file-like objects (#4187) Allows constructing a ZipStore from any seekable binary reader, enabling zip archives on remote storage: - io objects (BytesIO, fsspec file objects) are used directly - minimal readers that are not io.IOBase instances and whose read() may return buffer-protocol objects rather than bytes (e.g. obstore.ReadableFile) are adapted via a small io.RawIOBase wrapper when opened for reading clear()/move() raise NotImplementedError for file-object-backed stores. Co-authored-by: Claude Fable 5 <noreply@anthropic.com> --- changes/4187.feature.md | 4 + docs/user-guide/storage.md | 13 +++ src/zarr/storage/_zip.py | 114 +++++++++++++++++++++++-- tests/test_store/test_zip.py | 159 +++++++++++++++++++++++++++++++++++ 4 files changed, 281 insertions(+), 9 deletions(-) create mode 100644 changes/4187.feature.md diff --git a/changes/4187.feature.md b/changes/4187.feature.md new file mode 100644 index 0000000000..87133e2034 --- /dev/null +++ b/changes/4187.feature.md @@ -0,0 +1,4 @@ +`ZipStore` now accepts an open binary file-like object in place of a path, enabling +zip archives on remote storage (e.g. a file opened with `fsspec` or an +`obstore.ReadableFile`). Operations that require a filesystem location +(`clear`, `move`) raise `NotImplementedError` for file-object-backed stores. diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index 7e0154b2a0..0ba6202c76 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -124,6 +124,19 @@ array = zarr.create_array(store=store, shape=(2,), dtype='float64') print(array) ``` +In place of a path, `ZipStore` also accepts an open binary file object (for +example a file opened with `fsspec`, or an `obstore` reader), enabling zip +archives on remote storage. The file must stay open for as long as the store +is in use: + +```python exec="true" session="storage" source="above" result="ansi" +store.close() +f = open('data.zip', mode='rb') # must stay open while the store is used +array = zarr.open_array(store=zarr.storage.ZipStore(f), mode='r') +print(array[:]) +f.close() +``` + ### Remote Store The [`zarr.storage.FsspecStore`][] stores the contents of a Zarr hierarchy following the same diff --git a/src/zarr/storage/_zip.py b/src/zarr/storage/_zip.py index 430b0c3e2a..69ae18bc2c 100644 --- a/src/zarr/storage/_zip.py +++ b/src/zarr/storage/_zip.py @@ -1,12 +1,13 @@ from __future__ import annotations +import io import os import shutil import threading import time import zipfile from pathlib import Path -from typing import TYPE_CHECKING, Any, Literal +from typing import IO, TYPE_CHECKING, Any, Literal from zarr.abc.store import ( ByteRequest, @@ -23,14 +24,67 @@ ZipStoreAccessModeLiteral = Literal["r", "w", "a"] +class _RawReaderAdapter(io.RawIOBase): + """ + Adapt a minimal seekable reader to the `io` interface `zipfile` needs. + + Some file-like objects (e.g. `obstore.ReadableFile`) implement + `read`/`seek`/`tell` but are not `io.IOBase` instances, and their + `read` may return a buffer-protocol object rather than `bytes`. + Wrapping in this adapter plus `io.BufferedReader` yields real `bytes`. + + Reads are clamped to the bytes remaining before EOF: some readers + (obstore < 0.6) raise on short reads rather than returning fewer bytes. + The size is cached, which is safe because the adapter is only used for + read-only access. + """ + + def __init__(self, fileobj: IO[bytes]) -> None: + self._fileobj = fileobj + self._size: int | None = None + + def _get_size(self) -> int: + if self._size is None: + pos = self._fileobj.tell() + self._size = self._fileobj.seek(0, os.SEEK_END) + self._fileobj.seek(pos) + return self._size + + def readable(self) -> bool: + return True + + def seekable(self) -> bool: + return True + + def seek(self, pos: int, whence: int = 0) -> int: + return self._fileobj.seek(pos, whence) + + def tell(self) -> int: + return self._fileobj.tell() + + def readinto(self, b: Any) -> int: + n_requested = min(len(b), self._get_size() - self._fileobj.tell()) + if n_requested <= 0: + return 0 + data = self._fileobj.read(n_requested) + n = len(data) + b[:n] = memoryview(data) + return n + + class ZipStore(Store): """ Store using a ZIP file. Parameters ---------- - path : str - Location of file. + path : str, Path, or IO[bytes] + Location of file, or an open binary file object. A file object must + support `read`, `seek`, and `tell`; objects that are not `io.IOBase` + instances (e.g. an `obstore` reader) are adapted automatically but + can only be used for reading (`mode="r"`). The file object must stay + open for the lifetime of the store, and operations that require a + filesystem location (`clear`, `move`, pickling) are not supported. mode : str, optional One of 'r' to read an existing file, 'w' to truncate and write a new file, 'a' to append to an existing file, or 'x' to exclusively create @@ -58,16 +112,17 @@ class ZipStore(Store): supports_deletes: bool = False supports_listing: bool = True - path: Path + path: Path | None compression: int allowZip64: bool _zf: zipfile.ZipFile _lock: threading.RLock + _fileobj: IO[bytes] | None def __init__( self, - path: Path | str, + path: Path | str | IO[bytes], *, mode: ZipStoreAccessModeLiteral = "r", read_only: bool | None = None, @@ -81,8 +136,28 @@ def __init__( if isinstance(path, str): path = Path(path) - assert isinstance(path, Path) - self.path = path # root? + if isinstance(path, Path): + self.path = path # root? + self._fileobj = None + else: + self.path = None + if not isinstance(path, io.IOBase): + if not all( + callable(getattr(path, attr, None)) for attr in ("read", "seek", "tell") + ): + raise TypeError( + f"expected a path or an open binary file object supporting " + f"read/seek/tell, got {type(path).__name__}" + ) + if mode != "r": + raise TypeError( + f"a file object that is not an io.IOBase instance can only be " + f"opened for reading (mode='r', got mode={mode!r})" + ) + # e.g. an obstore ReadableFile: readable and seekable, but + # not an io object and reads may not return bytes + path = io.BufferedReader(_RawReaderAdapter(path)) + self._fileobj = path self._zmode = mode self.compression = compression @@ -95,7 +170,7 @@ def _sync_open(self) -> None: self._lock = threading.RLock() self._zf = zipfile.ZipFile( - self.path, + self.path if self.path is not None else self._fileobj, # type: ignore[arg-type] mode=self._zmode, compression=self.compression, allowZip64=self.allowZip64, @@ -107,6 +182,13 @@ async def _open(self) -> None: self._sync_open() def __getstate__(self) -> dict[str, Any]: + if self.path is None: + # A path-backed store pickles its path and reopens the file on + # unpickling; an open file object cannot be serialized that way. + raise TypeError( + "cannot pickle a ZipStore backed by a file-like object; " + "construct the store from a path instead" + ) # We need a copy to not modify the state of the original store state = self.__dict__.copy() for attr in ["_zf", "_lock"]: @@ -130,6 +212,10 @@ async def clear(self) -> None: # docstring inherited with self._lock: self._check_writable() + if self.path is None: + raise NotImplementedError( + "clear() is not supported for a ZipStore backed by a file-like object" + ) self._zf.close() os.remove(self.path) self._zf = zipfile.ZipFile( @@ -137,13 +223,19 @@ async def clear(self) -> None: ) def __str__(self) -> str: + if self.path is None: + return f"zip://{self._fileobj!r}" return f"zip://{self.path}" def __repr__(self) -> str: return f"ZipStore('{self}')" def __eq__(self, other: object) -> bool: - return isinstance(other, type(self)) and self.path == other.path + return ( + isinstance(other, type(self)) + and self.path == other.path + and self._fileobj is other._fileobj + ) def _get( self, @@ -297,6 +389,10 @@ async def move(self, path: Path | str) -> None: """ Move the store to another path. """ + if self.path is None: + raise NotImplementedError( + "move() is not supported for a ZipStore backed by a file-like object" + ) if isinstance(path, str): path = Path(path) self.close() diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py index ed69114b51..0d8dadd18a 100644 --- a/tests/test_store/test_zip.py +++ b/tests/test_store/test_zip.py @@ -1,6 +1,8 @@ from __future__ import annotations +import io import os +import pickle import shutil import tempfile import zipfile @@ -188,6 +190,163 @@ async def test_move(self, tmp_path: Path) -> None: assert np.array_equal(array[...], np.arange(10)) +class TestZipStoreFileObj: + """ZipStore backed by an open binary file-like object instead of a path.""" + + @pytest.fixture + def zip_bytes(self, tmp_path: Path) -> bytes: + path = tmp_path / "data.zip" + store = ZipStore(path, mode="w") + zarr.create_array(store, data=np.arange(10), chunks=(5,)) + store.close() + return path.read_bytes() + + def test_read_from_fileobj(self, zip_bytes: bytes) -> None: + # an existing archive can be read through any seekable binary reader + store = ZipStore(io.BytesIO(zip_bytes), mode="r") + array = zarr.open_array(store, mode="r") + assert np.array_equal(array[...], np.arange(10)) + assert store.path is None + + def test_write_to_fileobj(self) -> None: + # a writable file object receives the archive; the bytes it holds + # after close() are a complete, reopenable zip + buffer = io.BytesIO() + store = ZipStore(buffer, mode="w", read_only=False) + zarr.create_array(store, data=np.arange(4)) + store.close() + + roundtrip = ZipStore(io.BytesIO(buffer.getvalue()), mode="r") + array = zarr.open_array(roundtrip, mode="r") + assert np.array_equal(array[...], np.arange(4)) + + async def test_clear_unsupported(self, zip_bytes: bytes) -> None: + # clear() requires a filesystem location, so it raises a clear error + # for file-object-backed stores + store = ZipStore(io.BytesIO(zip_bytes), mode="a", read_only=False) + store._sync_open() + with pytest.raises(NotImplementedError, match="clear.*file-like"): + await store.clear() + + async def test_move_unsupported(self, zip_bytes: bytes) -> None: + # move() requires a filesystem location, so it raises a clear error + # for file-object-backed stores + store = ZipStore(io.BytesIO(zip_bytes), mode="a", read_only=False) + store._sync_open() + with pytest.raises(NotImplementedError, match="move.*file-like"): + await store.move("elsewhere.zip") + + def test_invalid_file_object_rejected(self) -> None: + # objects without read/seek/tell are rejected at construction, not + # deep inside zipfile + with pytest.raises(TypeError, match="read/seek/tell"): + ZipStore(42, mode="r") # type: ignore[arg-type] + + @pytest.mark.parametrize("mode", ["w", "a", "x"]) + def test_non_iobase_reader_write_modes_rejected(self, zip_bytes: bytes, mode: str) -> None: + # readers that are not io.IOBase instances are adapted for reading + # only; write modes are rejected at construction with a clear error + class MinimalReader: + def __init__(self, data: bytes) -> None: + self._buffer = io.BytesIO(data) + + def read(self, size: int, /) -> bytes: + return self._buffer.read(size) + + def seek(self, pos: int, whence: int = 0, /) -> int: + return self._buffer.seek(pos, whence) + + def tell(self) -> int: + return self._buffer.tell() + + with pytest.raises(TypeError, match="opened for reading"): + ZipStore(MinimalReader(zip_bytes), mode=mode, read_only=False) # type: ignore[arg-type] + + def test_fsspec_file(self, tmp_path: Path, zip_bytes: bytes) -> None: + # a file opened through fsspec (already an io.IOBase) is used directly; + # fsspec's local filesystem stands in for a remote one + fsspec = pytest.importorskip("fsspec") + + path = tmp_path / "fsspec.zip" + path.write_bytes(zip_bytes) + with fsspec.open(f"local://{path}", "rb") as fileobj: + store = ZipStore(fileobj, mode="r") + array = zarr.open_array(store, mode="r") + assert np.array_equal(array[...], np.arange(10)) + assert store.path is None + + def test_obstore_reader(self, tmp_path: Path, zip_bytes: bytes) -> None: + # obstore's ReadableFile is not an io.IOBase and its read() returns a + # buffer-protocol object; ZipStore adapts it via _RawReaderAdapter + obstore = pytest.importorskip("obstore") + from obstore.store import LocalStore as ObstoreLocalStore + + (tmp_path / "obstore.zip").write_bytes(zip_bytes) + reader = obstore.open_reader(ObstoreLocalStore(str(tmp_path)), "obstore.zip") + store = ZipStore(reader, mode="r") + array = zarr.open_array(store, mode="r") + assert np.array_equal(array[...], np.arange(10)) + + def test_raw_reader_adapter_eof(self) -> None: + from zarr.storage._zip import _RawReaderAdapter + + class MinimalReader: + """Non-io.IOBase reader exposing only read/seek/tell, like obstore.""" + + def __init__(self, data: bytes) -> None: + self._buffer = io.BytesIO(data) + + def read(self, size: int, /) -> bytes: + return self._buffer.read(size) + + def seek(self, pos: int, whence: int = 0, /) -> int: + return self._buffer.seek(pos, whence) + + def tell(self) -> int: + return self._buffer.tell() + + # the adapter must clamp reads to EOF: some readers (obstore < 0.6) + # raise on short reads instead of returning fewer bytes + data = b"0123456789" + adapter = _RawReaderAdapter(MinimalReader(data)) # type: ignore[arg-type] + + # A read straddling EOF returns only the remaining bytes. + adapter.seek(len(data) - 3) + buf = bytearray(8) + assert adapter.readinto(buf) == 3 + assert bytes(buf[:3]) == data[-3:] + + # A read at EOF returns 0. + assert adapter.tell() == len(data) + assert adapter.readinto(bytearray(8)) == 0 + + def test_pickle_fileobj_raises(self, zip_bytes: bytes) -> None: + # an open file object cannot be reliably serialized, so pickling a + # file-object-backed store raises with a pointer at the alternative + store = ZipStore(io.BytesIO(zip_bytes), mode="r") + with pytest.raises(TypeError, match="cannot pickle a ZipStore backed by a file-like"): + pickle.dumps(store) + + def test_pickle_path_backed_roundtrip(self, tmp_path: Path, zip_bytes: bytes) -> None: + # path-backed stores remain picklable: the path is serialized and the + # archive is reopened on unpickling + path = tmp_path / "pickled.zip" + path.write_bytes(zip_bytes) + store = ZipStore(path, mode="r") + unpickled = pickle.loads(pickle.dumps(store)) + array = zarr.open_array(unpickled, mode="r") + assert np.array_equal(array[...], np.arange(10)) + + def test_str_and_eq(self, zip_bytes: bytes) -> None: + # file-object-backed stores stringify with the object repr and + # compare equal only when backed by the very same file object + fileobj = io.BytesIO(zip_bytes) + store = ZipStore(fileobj, mode="r") + assert str(store).startswith("zip://<") + assert store == ZipStore(fileobj, mode="r") + assert store != ZipStore(io.BytesIO(zip_bytes), mode="r") + + class ZipStoreLifecycleMachine(RuleBasedStateMachine): """Drive a ZipStore through construct / open / write / close transitions. From cb93ef80f3d825446fe4fa97499d0787b410f0a9 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Tue, 28 Jul 2026 16:56:48 +0200 Subject: [PATCH 414/468] feat: add type-safe `get_array` and `get_group` methods to `AsyncGroup` and `Group` (#4128) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat: add type-safe get_array and get_group methods to AsyncGroup and Group Add `get_array` and `get_group` methods that return the child node at a given path or raise: `ArrayNotFoundError`/`GroupNotFoundError` when no node exists, and `ContainsGroupError`/`ContainsArrayError` when the node is the wrong kind. Paths mirror `getitem` semantics, so nested paths like "subgroup/subarray" work on both the plain and consolidated-metadata lookup routes. Existing tests that fetched a child via `getitem` and then manually narrowed the type with `isinstance` asserts or a walrus expression now use the new methods instead. Assisted-by: ClaudeCode:claude-fable-5 * fix: pass pre-formatted messages to error constructors in get_array/get_group The multi-argument template form of BaseZarrError.__init__ is documented as deprecated; build the message string at the raise site instead, matching every other call site in the codebase. Assisted-by: ClaudeCode:claude-fable-5 * docs: add changelog entry for get_array/get_group Assisted-by: ClaudeCode:claude-fable-5 * docs: demonstrate get_array/get_group in the groups user guide Assisted-by: ClaudeCode:claude-fable-5 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- changes/4128.feature.md | 1 + docs/user-guide/groups.md | 23 ++++ src/zarr/core/group.py | 133 +++++++++++++++++++++++ tests/test_group.py | 81 +++++++++++++- tests/test_metadata/test_consolidated.py | 9 +- tests/test_store/test_zip.py | 5 +- 6 files changed, 239 insertions(+), 13 deletions(-) create mode 100644 changes/4128.feature.md diff --git a/changes/4128.feature.md b/changes/4128.feature.md new file mode 100644 index 0000000000..c62a615ac2 --- /dev/null +++ b/changes/4128.feature.md @@ -0,0 +1 @@ +Added `Group.get_array`, `Group.get_group`, `AsyncGroup.get_array`, and `AsyncGroup.get_group`: type-safe accessors that return the child array or group at a given path, raising `ArrayNotFoundError` / `GroupNotFoundError` if no node exists there, and `ContainsGroupError` / `ContainsArrayError` if the node is not of the requested kind. Unlike `Group.__getitem__`, which returns `Array | Group`, these methods have precise return types. Nested paths like `"subgroup/subarray"` are supported. diff --git a/docs/user-guide/groups.md b/docs/user-guide/groups.md index 337ad39554..7429a03847 100644 --- a/docs/user-guide/groups.md +++ b/docs/user-guide/groups.md @@ -51,6 +51,29 @@ print(root['foo/bar']) print(root['foo/bar/baz']) ``` +Accessing a member with `[]` returns either an [`zarr.Array`][] or a [`zarr.Group`][], depending on +what is stored at the given path. When you expect a node of a particular kind, use +[`zarr.Group.get_array`][] or [`zarr.Group.get_group`][] instead. These methods accept the same +paths as `[]`, but they have precise return types and raise an error if no node exists at the +given path, or if the node is not of the expected kind: + +```python exec="true" session="groups" source="above" result="ansi" +print(root.get_group('foo')) +``` + +```python exec="true" session="groups" source="above" result="ansi" +print(root.get_array('foo/bar/baz')) +``` + +```python exec="true" session="groups" source="above" result="ansi" +from zarr.errors import ContainsGroupError + +try: + root.get_array('foo') +except ContainsGroupError as e: + print(e) +``` + The [`zarr.Group.tree`][] method can be used to print a tree representation of the hierarchy, e.g.: diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 0aaf89234e..922eaf1498 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -51,6 +51,7 @@ from zarr.core.metadata.io import save_metadata from zarr.core.sync import SyncMixin, sync from zarr.errors import ( + ArrayNotFoundError, ContainsArrayError, ContainsGroupError, GroupNotFoundError, @@ -820,6 +821,70 @@ async def get[DefaultT]( except KeyError: return default + async def get_array(self, path: str) -> AnyAsyncArray: + """Obtain an array member of this group, raising if it is absent or not an array. + + Parameters + ---------- + path : str + Path of the array relative to this group. May contain `/` to reference + a member of a subgroup, e.g. `subgroup/subarray`. + + Returns + ------- + AsyncArray + The array at the given path. + + Raises + ------ + ArrayNotFoundError + If no node exists at the given path. + ContainsGroupError + If the node at the given path is a group rather than an array. + """ + store_path = self.store_path / path + try: + node = await self.getitem(path) + except KeyError as e: + msg = f"No array found in store {store_path.store!r} at path {store_path.path!r}" + raise ArrayNotFoundError(msg) from e + if isinstance(node, AsyncGroup): + msg = f"A group exists in store {store_path.store!r} at path {store_path.path!r}." + raise ContainsGroupError(msg) + return node + + async def get_group(self, path: str) -> AsyncGroup: + """Obtain a group member of this group, raising if it is absent or not a group. + + Parameters + ---------- + path : str + Path of the group relative to this group. May contain `/` to reference + a member of a subgroup, e.g. `subgroup/subsubgroup`. + + Returns + ------- + AsyncGroup + The group at the given path. + + Raises + ------ + GroupNotFoundError + If no node exists at the given path. + ContainsArrayError + If the node at the given path is an array rather than a group. + """ + store_path = self.store_path / path + try: + node = await self.getitem(path) + except KeyError as e: + msg = f"No group found in store {store_path.store!r} at path {store_path.path!r}" + raise GroupNotFoundError(msg) from e + if isinstance(node, AsyncArray): + msg = f"An array exists in store {store_path.store!r} at path {store_path.path!r}." + raise ContainsArrayError(msg) + return node + async def _save_metadata(self, ensure_parents: bool = False) -> None: await save_metadata(self.store_path, self.metadata, ensure_parents=ensure_parents) @@ -1880,6 +1945,74 @@ def get[DefaultT]( except KeyError: return default + def get_array(self, path: str) -> AnyArray: + """Obtain an array member of this group, raising if it is absent or not an array. + + Parameters + ---------- + path : str + Path of the array relative to this group. May contain `/` to reference + a member of a subgroup, e.g. `subgroup/subarray`. + + Returns + ------- + Array + The array at the given path. + + Raises + ------ + ArrayNotFoundError + If no node exists at the given path. + ContainsGroupError + If the node at the given path is a group rather than an array. + + Examples + -------- + ```python + import zarr + from zarr.core.group import Group + group = Group.from_store(zarr.storage.MemoryStore()) + group.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="float64") + group.get_array("subarray") + # <Array memory://... shape=(10,) dtype=float64> + ``` + """ + return Array(self._sync(self._async_group.get_array(path))) + + def get_group(self, path: str) -> Group: + """Obtain a group member of this group, raising if it is absent or not a group. + + Parameters + ---------- + path : str + Path of the group relative to this group. May contain `/` to reference + a member of a subgroup, e.g. `subgroup/subsubgroup`. + + Returns + ------- + Group + The group at the given path. + + Raises + ------ + GroupNotFoundError + If no node exists at the given path. + ContainsArrayError + If the node at the given path is an array rather than a group. + + Examples + -------- + ```python + import zarr + from zarr.core.group import Group + group = Group.from_store(zarr.storage.MemoryStore()) + group.create_group(name="subgroup") + group.get_group("subgroup") + # <Group memory://...> + ``` + """ + return Group(self._sync(self._async_group.get_group(path))) + def __delitem__(self, key: str) -> None: """Delete a group member. diff --git a/tests/test_group.py b/tests/test_group.py index 1acd5551ca..29377a5392 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -41,8 +41,10 @@ from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.core.sync import _collect_aiterator, sync from zarr.errors import ( + ArrayNotFoundError, ContainsArrayError, ContainsGroupError, + GroupNotFoundError, MetadataValidationError, ZarrUserWarning, ) @@ -101,7 +103,7 @@ async def test_create_creates_parents(store: Store, zarr_format: ZarrFormat) -> root = await zarr.api.asynchronous.open_group( store=store, ) - agroup = await root.getitem("a") + agroup = await root.get_group("a") assert agroup.attrs == {"key": "value"} # create a child node with a couple intermediates @@ -446,6 +448,77 @@ def test_group_get_with_default(store: Store, zarr_format: ZarrFormat) -> None: assert result.attrs["foo"] == "bar" +def test_group_get_array(store: Store, zarr_format: ZarrFormat) -> None: + """ + `Group.get_array` returns the array at the given path, for both direct child names + and nested paths, and the result is statically typed as an Array. + """ + group = Group.from_store(store, zarr_format=zarr_format) + subgroup = group.create_group(name="subgroup") + subarray = group.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="uint8") + subsubarray = subgroup.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="uint8") + + observed = group.get_array("subarray") + assert isinstance(observed, Array) + assert observed == subarray + assert group.get_array("subgroup/subarray") == subsubarray + + +def test_group_get_array_missing(store: Store, zarr_format: ZarrFormat) -> None: + """ + `Group.get_array` raises `ArrayNotFoundError` when no node exists at the given path. + """ + group = Group.from_store(store, zarr_format=zarr_format) + with pytest.raises(ArrayNotFoundError, match="No array found in store"): + group.get_array("missing") + + +def test_group_get_array_wrong_node_type(store: Store, zarr_format: ZarrFormat) -> None: + """ + `Group.get_array` raises `ContainsGroupError` when the node at the given path is a + group rather than an array. + """ + group = Group.from_store(store, zarr_format=zarr_format) + group.create_group(name="subgroup") + with pytest.raises(ContainsGroupError, match="A group exists in store"): + group.get_array("subgroup") + + +def test_group_get_group(store: Store, zarr_format: ZarrFormat) -> None: + """ + `Group.get_group` returns the group at the given path, for both direct child names + and nested paths, and the result is statically typed as a Group. + """ + group = Group.from_store(store, zarr_format=zarr_format) + subgroup = group.create_group(name="subgroup") + subsubgroup = subgroup.create_group(name="subsubgroup") + + observed = group.get_group("subgroup") + assert isinstance(observed, Group) + assert observed == subgroup + assert group.get_group("subgroup/subsubgroup") == subsubgroup + + +def test_group_get_group_missing(store: Store, zarr_format: ZarrFormat) -> None: + """ + `Group.get_group` raises `GroupNotFoundError` when no node exists at the given path. + """ + group = Group.from_store(store, zarr_format=zarr_format) + with pytest.raises(GroupNotFoundError, match="No group found in store"): + group.get_group("missing") + + +def test_group_get_group_wrong_node_type(store: Store, zarr_format: ZarrFormat) -> None: + """ + `Group.get_group` raises `ContainsArrayError` when the node at the given path is an + array rather than a group. + """ + group = Group.from_store(store, zarr_format=zarr_format) + group.create_array(name="subarray", shape=(10,), chunks=(10,), dtype="uint8") + with pytest.raises(ContainsArrayError, match="An array exists in store"): + group.get_group("subarray") + + @pytest.mark.parametrize("consolidated", [True, False]) def test_group_delitem(store: Store, zarr_format: ZarrFormat, consolidated: bool) -> None: """ @@ -1469,7 +1542,7 @@ async def test_group_getitem_consolidated(self, store: Store) -> None: # On disk, we've consolidated all the metadata in the root zarr.json group = await zarr.api.asynchronous.open(store=store) - rg0 = await group.getitem("g0") + rg0 = await group.get_group("g0") expected = ConsolidatedMetadata( metadata={ @@ -1490,10 +1563,10 @@ async def test_group_getitem_consolidated(self, store: Store) -> None: ) assert rg0.metadata.consolidated_metadata == expected - rg1 = await rg0.getitem("g1") + rg1 = await rg0.get_group("g1") assert rg1.metadata.consolidated_metadata == expected.metadata["g1"].consolidated_metadata - rg2 = await rg1.getitem("g2") + rg2 = await rg1.get_group("g2") assert rg2.metadata.consolidated_metadata == ConsolidatedMetadata(metadata={}) async def test_group_delitem_consolidated(self, store: Store) -> None: diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index 3596d2bcaa..e6087435fe 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -111,12 +111,10 @@ async def test_getitem_consolidated_empty_leaf_group( group = await zarr.api.asynchronous.open_consolidated( store=memory_store, zarr_format=zarr_format ) - raw = await group.getitem("raw") - assert isinstance(raw, zarr.AsyncGroup) + raw = await group.get_group("raw") assert raw.metadata.consolidated_metadata is not None - varm = await raw.getitem("varm") - assert isinstance(varm, zarr.AsyncGroup) + varm = await raw.get_group("varm") assert varm.metadata.consolidated_metadata == ConsolidatedMetadata(metadata={}) async def test_open_consolidated_false_raises(self) -> None: @@ -770,8 +768,7 @@ async def test_absolute_path_for_subgroup(self, memory_store: zarr.storage.Memor await zarr.api.asynchronous.consolidate_metadata(memory_store) group = await zarr.api.asynchronous.open_group(store=memory_store) - subgroup = await group.getitem("/a") - assert isinstance(subgroup, AsyncGroup) + subgroup = await group.get_group("/a") members = [x async for x in subgroup.keys()] # noqa: SIM118 assert members == ["b"] diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py index 0d8dadd18a..32b18c5273 100644 --- a/tests/test_store/test_zip.py +++ b/tests/test_store/test_zip.py @@ -22,7 +22,6 @@ import zarr from zarr import create_array from zarr.core.buffer import Buffer, cpu, default_buffer_prototype -from zarr.core.group import Group from zarr.core.sync import sync from zarr.storage import ZipStore from zarr.testing.store import StoreTests @@ -141,13 +140,13 @@ def test_externally_zipped_store(self, tmp_path: Path) -> None: zarr_path = tmp_path / "foo.zarr" root = zarr.open_group(store=zarr_path, mode="w") root.require_group("foo") - assert isinstance(foo := root["foo"], Group) # noqa: RUF018 + foo = root.get_group("foo") foo["bar"] = np.array([1]) shutil.make_archive(str(zarr_path), "zip", zarr_path) zip_path = tmp_path / "foo.zarr.zip" zipped = zarr.open_group(ZipStore(zip_path, mode="r"), mode="r") assert list(zipped.keys()) == list(root.keys()) - assert isinstance(group := zipped["foo"], Group) + group = zipped.get_group("foo") assert list(group.keys()) == list(group.keys()) async def test_list_without_explicit_open(self, tmp_path: Path) -> None: From 015732f58cc67888f7f638e09ca447c9349c85eb Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Tue, 28 Jul 2026 22:06:03 +0200 Subject: [PATCH 415/468] feat(zarr-metadata): Zarr metadata model layer (#4119) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat(zarr-metadata): add model._validation — structural validators Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): add model._array — array metadata models Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): port array model test suite Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): add group metadata models Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): add consolidated metadata model tests Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): export model layer from package front door Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): changelog entry for the model layer Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): harden model validation and error reporting Findings from an API-ergonomics exercise (a fresh agent consuming defective metadata documents): - ValidationProblem gains a machine-readable kind (missing_key / invalid_type / invalid_value / invalid_json), ending message string-matching in consumers. - The v2 array validator now enforces what its types declare (dtype, order, compressor, filters, dimension_separator), and all four document validators check the fixed zarr_format / node_type literals. - All ingestion failures surface as MetadataValidationError: missing store keys and undecodable bytes in from_key_value (previously KeyError / JSONDecodeError) and constructor invariants (previously bare ValueError). - ZarrMetadataV3 is renamed NamedConfigModelV3: it models a name + configuration pair, and the old name read as a whole-document type. - Discoverability: the validate_*/is_*/parse_* contract is documented on zarr_metadata.model itself; update() documents that it does not re-validate; the v2 to_json/to_key_value attributes split is documented on both. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): annotate metadata fields with role alias MetadataFieldModelV3 Model fields and consumer signatures should convey the logical meaning of the type (a metadata-document field), not the form it takes when JSON-serialized (a named configuration). MetadataFieldModelV3 is today exactly NamedConfigModelV3; if a future spec revision adds a field form that cannot normalize to name + configuration, the alias widens to a union and annotation sites do not move. Mirrors the raw-layer split between NamedConfigV3 (shape) and MetadataV3 (field union). Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): assert required-key coverage via the typed constant test_v3_to_json_includes_required_fields hand-enumerated keys with chained asserts, restating what ARRAY_METADATA_REQUIRED_KEYS_V3 already defines. Now: one coverage assert driven by the constant (tracks the TypedDict automatically) and one whole-document equality for the values. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): single whole-document comparison for v3 to_json The subset assert against ARRAY_METADATA_REQUIRED_KEYS_V3 was redundant: equality with a literal that spells out the full document already covers every required key. One dict, one assert. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): close validation holes found by adversarial review Invalid documents that previously passed validation: - shape/chunks containing JSON booleans (bool is an int subclass in Python but not an integer in a metadata document) or negative values - dimension_names whose length does not match shape - attributes and configuration values that are not JSON-serializable — now checked recursively like fill_value, so an int-keyed dict cannot be silently rewritten by json.dumps on round-trip and a set() cannot escape as a TypeError from to_key_value - consolidated_metadata envelopes: the group validator now deep-validates the envelope and its entries via the shared validate_consolidated_metadata_v3, which ConsolidatedMetadataModelV3 .from_json also uses, so is_group_metadata_v3 never vouches for a document the model constructor would reject Three pre-existing test fixtures paired dimension_names=('x',) with the default scalar shape () and were themselves spec-invalid; they now use a matching 1-d shape. Deliberately unchanged, pending a design decision: unknown extension fields with must_understand: true still pass (which layer owns the spec's refusal duty), and empty v2 dtype records / empty codec names still pass (domain territory). Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): expose must_understand_fields on the v3 models The v3 core spec: 'An implementation MUST fail to open Zarr groups or arrays if any metadata fields are present which (a) the implementation does not recognize and (b) are not explicitly set to "must_understand": false' — and fields are implicitly must-understand unless waived. The model layer cannot discharge this itself: recognition is reader-specific (consolidated_metadata is itself an extension field one reader understands and another does not), and a document carrying a must-understand extension is still a valid document. So the models partition by obligation: must_understand_fields is the subset of extra_fields not explicitly waived, and a compliant reader fails to open when must_understand_fields.keys() - recognized is non-empty. The design spec pins that duty on the part-2 resolve layer, matching what zarr-python's parse_extra_fields enforces today. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): executable example of pydantic integration Delegate wholesale rather than letting pydantic introspect the dataclass: InstanceOf (is-instance core schema) + BeforeValidator(from_json) + PlainSerializer(to_json, return_type=dict). Field-by-field validation is impossible anyway (the models' annotation-only imports live behind TYPE_CHECKING, so pydantic raises class-not-fully-defined) and would diverge from the library's structural validation via coercion if it weren't. MetadataValidationError subclasses ValueError, so failed parses surface as pydantic ValidationError with the loc-annotated messages. pydantic is already in the package's test dependency group. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): document pydantic's native dataclass path and why not Correcting the previous commit's too-strong claim: pydantic CAN introspect the model dataclass — TypeAdapter(...).rebuild() with the TYPE_CHECKING-only names supplied as _types_namespace resolves the schema, and __post_init__ invariants still run. A new test exercises that path and pins why it is not the recommended integration: it validates the model shape, not the document (bare-string data_type rejected — no from_json normalization), and pydantic's lax coercion silently re-opens holes the library validators close (shape=[True, -5] coerces to (1, -5); a wrong dimension_names count passes). Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): engine-backed pydantic BaseModel example (pydantic-zarr pattern) For consumers that want a first-class BaseModel — JSON schema generation and generics for typed attributes, as in pydantic-zarr's ArraySpec — the example adds a third pattern: pydantic-native fields as the user-facing surface, with the library as the engine. A mode='before' validator canonicalizes every input via from_json(...).to_json(), so structural validation and normalization run before pydantic parses fields (the [True, -5] coercion divergence cannot occur), and to_metadata_model / to_document bridge both ways through the document form. One translation noted at the bridge: the document spells 'no dimension names' as key absence, the pydantic side as None. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): pin that a null dimension_names field is invalid Spec: 'If specified, must be an array of strings or null objects... If dimension_names is not specified, all dimensions are unnamed.' The null object is a permitted element (an unnamed dimension), never the field value; key absence is the only spelling of 'not specified'. Pins the validator's existing rejection so it is not later 'fixed' to accept null-as-absence, and documents that in-memory None maps to key absence on serialization. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): optional pydantic integration as zarr_metadata.pydantic Gamed out three shapes with prototypes before choosing: - dunders on the core classes (works, verified pydantic 2.0-2.13, but puts a framework protocol in the dependency-free layer); - pydantic-aware SUBCLASSES in a namespace (rejected on empirical failures: identity split breaks equality, core instances are rejected by subclass-typed fields, and nested construction produces core-class children unless every cross-reference is overridden); - Annotated field types over the CORE classes in an opt-in module (chosen): instances are the core classes so interop is free, pydantic imports eagerly at the module (loud failure when absent), core stays framework-free, and pydantic-protocol risk is quarantined to one clearly-labeled module. The module exports one field type per model. Validation delegates to from_json (structural validation and normalization cannot be bypassed by pydantic coercion), instances pass through, serialization emits the canonical document, and WithJsonSchema describes the accepted document form so model_json_schema works. Tests cover all seven field types, core-instance interop, error quality, JSON schema, roundtrip, and that importing zarr_metadata does not import pydantic. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): create_default derives the chunk grid from shape create_default(shape=(100, 100)) silently kept the scalar default's 0-d chunk grid (chunk_shape: ()), producing a structurally-valid but semantically inconsistent document — a footgun for every test fixture built on it. When shape is overridden and the grid is not, the default is now one regular chunk covering the array (v3 chunk_shape == shape, v2 chunks == shape); an explicit chunk_grid/chunks override still wins. update() stays a dumb dataclasses.replace, per its documented contract. One existing whole-document test literal carried exactly this inconsistency (shape (10,) with chunk_shape ()) and was updated. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-metadata): pin zero-length-dimension case of the derived chunk grid The spec's constraint is conditional ('non-zero when the corresponding dimensions of the arrays have non-zero length'), so chunk_shape == shape is sound for every shape, including empty dimensions. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): document that create_default's derivation is one-way Overriding shape without a grid derives the grid; the reverse does not hold. A user-supplied chunk_grid is an extension point taken verbatim — deriving shape from it would require interpreting grid configurations, which the model layer never does and cannot do for unrecognized grid names. Pinned by test so the asymmetry reads as a decision, not an oversight; the v2 model documents the same one-way rule for chunks for cross-version consistency. Assisted-by: ClaudeCode:claude-fable-5 * refactor(zarr-metadata): eliminate every type-ignore comment Audited all 24 (15 src, 9 tests); each was either obsolete, replaceable by a sound cast, or avoidable by better-typed code: - Two fill_value arg-type ignores were factually obsolete: their justifying comment said 'fill_value: object in upstream TypedDict', but 0.3.0 narrowed it to JSONValue. - Eight pre-existing call-arg/reportInvalidTypeForm ignores on the PEP 728 TypedDicts and the recursive JSONValue alias were mypy-dialect suppressions that the checker of record (pyright strict with enableExperimentalFeatures) never needed; mypy has never checked this package. - The two extra_fields comprehensions are a genuine checker limitation (a key filter cannot narrow a PEP 728 TypedDict's item-value union), now expressed as casts whose comments state the soundness claim instead of suppressing the diagnostic. - pydantic.py's generic coercer factory takes the parse callable explicitly instead of calling from_json through type[_M]. - NamedConfigModelV3.from_json casts the validated configuration (sound since configuration values are now deep-validated as JSON). - Tests: _build_v2/_build_v3 gained real Unpack[...Partial] signatures; raw-document pydantic inputs go through model_validate (the idiomatic entry point for untyped data) instead of ignoring constructor signatures; the frozen-dataclass test uses setattr for its intentional runtime error. src and tests/model now carry zero type-ignore comments. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): absent v2 dimension_separator means '.', not '/' roborev job 426 (branch review) found that ArrayMetadataModelV2 normalized an ABSENT dimension_separator key to '/', inherited verbatim from the zng prototype. The v2 convention's default is '.': a consumer deriving chunk keys from the model against a real-world v2 array written with the default separator would have looked for '0/0' instead of '0.0'. No test caught it because every fixture started from create_default(), which always carries an explicit separator. Absence is normalized to an explicit '.' -- a semantics-preserving spelling normalization consistent with the model's existing canonical forms (bare-string metadata fields, missing configuration). The field is deliberately NOT modeled as Optional: the document grammar has no null spelling for this key, and a None in the model invites writing 'dimension_separator': null into documents. Pinned by three tests, including explicit-null rejection. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): UNSET sentinel for absent optional document keys Establishes the models' None/absence invariant: None in a model always corresponds to a JSON null in the document (a v2 compressor/filters value, an unnamed dimension inside dimension_names), and UNSET always means the key is absent. The two are never interchangeable. Applied to the two fields that used None as an absence marker: dimension_names (ArrayMetadataModelV3) and consolidated_metadata (GroupMetadataModelV3). For dimension_names this also preserves a semantic distinction d-v-b identified: an absent field ("there are no dimension names") and an explicit all-null array ("every dimension has a name, which is null") are different documents; both spellings now round-trip faithfully and compare unequal. Normalizing absence to the all-null form was considered and rejected: the spellings' interpretations coincide but interpretation-equivalence is the resolve layer's business, and collapsing document-level distinctions on that basis is the layer violation this package exists to avoid. Verified that current zarr-python never writes "consolidated_metadata": null (GroupMetadata.to_dict pops the key), so None there was purely an absence marker, not a document spelling. UnsetType is a single-member enum (identity-checkable, repr "UNSET", deliberately truthy so `if not x` cannot silently treat it as absent); UNSET and UnsetType are exported from zarr_metadata.model and the package front door. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): accept and preserve the wild consolidated_metadata null Historical zarr-python versions wrote "consolidated_metadata": null into group documents for groups without consolidated metadata, so real stores contain the spelling; the validator was rejecting those documents ("expected a mapping"). Per the None/UNSET invariant, the field is now honestly three-state: UNSET (key absent), None (the document's literal null, preserved on round-trip), or a ConsolidatedMetadataModelV3. Interpreting null as absence is the consumer's call, not a document rewrite by this layer. Also records an implementation constraint on the sentinel itself: typing_extensions.Sentinel (PEP 661) is the intended spelling, but pyright 1.1.411 degrades a Sentinel to Unknown in dataclass FIELD annotations (function signatures work), verified by probe both with and without enableExperimentalFeatures. Using it would reintroduce suppressions at every use site under the strict gate, so UNSET stays a single-member enum, with the Sentinel switch documented in _sentinel.py for when pyright catches up. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): repair consolidated_metadata null to absence, not preserve it d-v-b: the bugged spelling should not be preserved or honored. The three-state field reverts to two states (model | UNSET): a document carrying "consolidated_metadata": null — written by a historical zarr-python bug — remains readable (the validator accepts it so real stores open), but the spelling gets no model representation: it is read as absence and never written back. This is the one deliberate exception to faithful round-tripping, pinned as such: from_json(null_doc) equals from_json(absent_doc), and to_json omits the key. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): pin the Sentinel blocker to pyright regression #11115 Investigated: the Unknown-degradation of typing_extensions.Sentinel is a confirmed upstream pyright regression, not by-design. Introduced in 1.1.405 (verified: 1.1.404 is clean on the same probe, 1.1.411 fails), affects reads of any class-body attribute annotation (dataclass or plain class), does not affect function signatures or module variables, and Final on the sentinel does not help. Tracked as microsoft/pyright#11115 (open, bug+regression); #11467 closed as its duplicate. The enum sentinel stays until the fix lands. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): sentinel switch is blocked by mypy too, not just pyright Pinning a working pyright (<= 1.1.404) in CI was considered and does not suffice: the pin controls one of four checker surfaces. Contributor IDEs (Pylance bundles current pyright) and downstream consumers' pyright read the py.typed inline annotations with their own versions, and decisively, mypy 2.1.0 has no PEP 661 support at all — a sentinel in type position is a hard [valid-type] error, which would degrade these fields to Any for mypy consumers, including zarr-python itself. The enum is currently the only spelling with exact types on every surface; switch when pyright#11115 is fixed AND mypy implements PEP 661. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): PEP 661 is Final (Python 3.15), not a draft Corrects the sentinel implementation note: PEP 661 was accepted 2026-04-23 and ships as stdlib sentinel in Python 3.15. The two checker gaps blocking the Sentinel spelling (pyright regression #11115, mypy not yet implementing the PEP) are therefore temporary gaps against a Final standard, and the enum is a stopgap with a defined end state. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): ty fully supports typed sentinels; pyright/mypy are the laggards ty 0.0.56 types the Sentinel spelling perfectly in dataclass fields: exact T | UNSET unions, both-direction is/is-not narrowing, and wrong-typed constructor arguments rejected (verified with reveal_type, so it is real inference, not silent Any). The checker matrix for sentinel-in-type-position is therefore ty full / pyright regressed (#11115) / mypy not implemented — recorded so the switch decision has current calibration. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): adopt the PEP 661 sentinel for UNSET d-v-b's call: PEP 661 is Final, ty already types the sentinel spelling exactly, mypy support is in review (python/mypy#21647) and treated as imminent, and pyright has a known-good version — so use the standard sentinel today rather than carrying the enum stopgap. - UNSET is now typing_extensions.Sentinel("UNSET"), used directly in type expressions (tuple[str | None, ...] | UNSET); the UnsetType companion enum is gone from the API. - typing_extensions floor bumped to 4.14 (where Sentinel arrived). - CI pins pyright==1.1.404, the last version before the class-attribute sentinel regression (microsoft/pyright#11115); pyproject documents the same pin for local runs. 0 errors on the pin; ty checks the sentinel fields clean (its 2 remaining diagnostics are its incomplete PEP 728 extra_items write support, unrelated). - Known short-term cost, accepted deliberately: mypy-checked consumers need cast/type-ignore at narrowing sites until mypy#21647 merges, and contributors' Pylance may show phantom Unknowns until the pyright fix ships. Recorded in _sentinel.py and the changelog. - The pydantic native-introspection test reverts to documenting that introspection is unsupported (pydantic 2.13 cannot schema a Sentinel); the delegation patterns are unaffected. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): .zattrs presence is part of the store, not an artifact Resolves the last flagged round-trip question from the initial port: to_key_value on the v2 models always emitted a .zattrs key, so a store that never had one gained a file on round-trip. Per d-v-b's ruling, attributes on ArrayMetadataModelV2/GroupMetadataModelV2 is now `dict[str, JSONValue] | UNSET`: UNSET means no .zattrs file (and no attributes key in the merged document form) and emits nothing, while any dict — including an explicit empty {} — means the file exists and is emitted. The two spellings stay distinct through round-trips, per the None/UNSET invariant; create_default defaults to UNSET (a fresh minimal node has no .zattrs). Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): require typing_extensions>=4.16 so UNSET pickles by reference Models hold the UNSET sentinel as field values (dimension_names, attributes), so any object graph containing a model must survive pickling and deep-copying. A sentinel's contract is identity — state-based pickling would produce impostor objects that fail every `is UNSET` check — which is why typing_extensions <= 4.15 refused to pickle sentinels at all. typing_extensions 4.16 implements Sentinel.__reduce__ as pickling by reference (a lookup of the sentinel's name on its defining module), the same mechanism enum members use, so the singleton identity survives the round trip. Bump the floor and pin the behavior with tests: identity across pickle/copy/deepcopy, models holding UNSET round-tripping, and a guard that a non-importable sentinel still fails loudly rather than pickling by state. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * refactor(zarr-metadata): format-version-first naming; dataclasses primary, JSON suffix for documents Applies the naming decisions from the PR discussion: ZarrV2/ZarrV3 moves to the front of every type name so a format version cannot be misread as a class revision, and the model dataclasses take the bare entity names (ZarrV3ArrayMetadata, ZarrV3GroupMetadata, ZarrV3ConsolidatedMetadata, ZarrV3NamedConfig, role alias ZarrV3MetadataField) while the TypedDict document forms carry a JSON suffix (ZarrV3ArrayMetadataJSON, ..., ZarrV3MetadataFieldJSON, ZarrV3NamedConfigJSON). The zarr_metadata.pydantic field types take the bare entity names, matching the model classes they validate into; the module now references the model module qualified to keep those names free. Raw-layer names released in 0.3.0 are renamed without aliases (pre-1.0), documented in changes/4119.removal.md. Validation problem messages name documents in plain English instead of type names. snake_case function names (validate_array_metadata_v3, ...) and SCREAMING_SNAKE constants are deliberately untouched: the revision ambiguity the rename fixes does not arise for them, and renaming them is a separate decision. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * fix(zarr-metadata): harden model validation Assisted-by: Codex:gpt-5 * docs(zarr-metadata): define v3 conformance boundary Assisted-by: Codex:gpt-5 * fix(zarr-metadata): preserve v3 extension obligations Assisted-by: Codex:gpt-5 * fix(zarr-metadata): enforce v3 core extension rules Assisted-by: Codex:gpt-5 * fix(zarr-metadata): align v3 additional field types Assisted-by: Codex:gpt-5 * chore(zarr-metadata): finalize v3 model conformance Assisted-by: Codex:gpt-5 * docs: remove llm docs * chore(zarr-metadata): correct changelog PR number Assisted-by: Codex:gpt-5 * fix(metadata): enforce canonical document boundaries Assisted-by: Codex:GPT-5 * docs(metadata): record review fix design Assisted-by: Codex:gpt-5 * fix(metadata): align validation and schemas Assisted-by: Codex:gpt-5 * fix(metadata): tighten validation boundaries Assisted-by: Codex:gpt-5 * fix(metadata): repair package CI Assisted-by: Codex:gpt-5 * chore: remove stray design notes from docs Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-metadata): deep-copy mutable state in to_json output to_json previously returned documents holding direct references to the model's internal dicts (attributes, named-config configurations, extra fields, v2 compressor/filters, consolidated entries), so mutating a serialized document silently mutated the frozen model. Every value that can hold a mutable container is now deep-copied on the way out, with parametrized tests proving mutation independence for all seven models. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): describe the widened package scope The README tagline, intro, and scope section (and the PyPI description) still presented the package as type definitions only. Restructure them around the two layers plus optional integration, extend the contribution scope to models and structural validation, and state the runtime-behavior boundary explicitly. Assisted-by: ClaudeCode:claude-fable-5 * style(zarr-metadata): move None to the end of the JSONValue union The unpinned ruff in CI now enforces RUF036. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-metadata): export store-key aliases and type to_key_value with them The six store-key Literal aliases were private and unused: only reachable via underscore modules, and absent from every signature. Export them from zarr_metadata.model beside their constants (matching the package's name/constant pairing everywhere else), and key each to_key_value return mapping by them so the store keys a model can emit are visible in its signature. from_key_value keeps Mapping[str, bytes] input on purpose — it accepts whole store mappings. A pair test guards export and value drift, and the removal note now states the version-placement and JSON-suffix conventions explicitly. Assisted-by: ClaudeCode:claude-fable-5 * refactor(zarr-metadata): make every public type name parse against a naming grammar Three grammars now cover the public surface, enforced by a conformance test that walks every public module's __all__: - core document/model names: ZarrV{2,3} + entity + optional role suffix (JSON / JSONPartial / Partial / StoreKey) - extension-entity names: registered entity + exactly one role suffix (CodecMetadata, DataTypeName, FillValue, ...) - a closed standalone-vocabulary allowlist for role-less scalar and diagnostic types, with a staleness guard The three .z-file document types were the only names that fit no grammar and are renamed: ZArrayMetadata -> ZarrV2ZArrayJSON, ZGroupMetadata -> ZarrV2ZGroupJSON, ZAttrsMetadata -> ZarrV2ZAttrsJSON. The leading V2 of V2ChunkKeyEncodingMetadata is that encoding's registered entity name, not a format version; its module docstring now says so. Assisted-by: ClaudeCode:claude-fable-5 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com> --- .github/workflows/zarr-metadata.yml | 5 +- packages/zarr-metadata/README.md | 81 +- .../zarr-metadata/changes/4119.feature.md | 92 + .../zarr-metadata/changes/4119.removal.md | 41 + packages/zarr-metadata/pyproject.toml | 19 +- .../src/zarr_metadata/__init__.py | 114 +- .../src/zarr_metadata/_common.py | 16 +- .../src/zarr_metadata/_pydantic_schema.py | 114 ++ .../src/zarr_metadata/model/__init__.py | 132 ++ .../src/zarr_metadata/model/_array.py | 498 +++++ .../src/zarr_metadata/model/_group.py | 442 +++++ .../src/zarr_metadata/model/_sentinel.py | 37 + .../src/zarr_metadata/model/_validation.py | 875 +++++++++ .../src/zarr_metadata/pydantic.py | 176 ++ .../src/zarr_metadata/v2/__init__.py | 38 +- .../src/zarr_metadata/v2/array.py | 83 +- .../src/zarr_metadata/v2/attributes.py | 6 +- .../src/zarr_metadata/v2/codec.py | 4 +- .../src/zarr_metadata/v2/consolidated.py | 18 +- .../src/zarr_metadata/v2/group.py | 26 +- .../src/zarr_metadata/v3/__init__.py | 18 +- .../src/zarr_metadata/v3/_common.py | 10 +- .../src/zarr_metadata/v3/array.py | 80 +- .../zarr_metadata/v3/chunk_key_encoding/v2.py | 6 + .../src/zarr_metadata/v3/codec/__init__.py | 2 +- .../src/zarr_metadata/v3/codec/cast_value.py | 4 +- .../src/zarr_metadata/v3/codec/crc32c.py | 2 +- .../v3/codec/sharding_indexed.py | 6 +- .../src/zarr_metadata/v3/consolidated.py | 28 +- .../src/zarr_metadata/v3/data_type/struct.py | 4 +- .../src/zarr_metadata/v3/group.py | 20 +- .../zarr-metadata/tests/model/__init__.py | 0 packages/zarr-metadata/tests/model/_cases.py | 65 + .../zarr-metadata/tests/model/test_array.py | 1738 +++++++++++++++++ .../zarr-metadata/tests/model/test_group.py | 572 ++++++ .../tests/model/test_pydantic.py | 302 +++ .../tests/model/test_pydantic_module.py | 264 +++ .../tests/model/test_sentinel.py | 89 + .../tests/test_partial_equivalence.py | 16 +- .../zarr-metadata/tests/test_public_api.py | 164 +- .../tests/v2/array/test_fixtures.py | 6 +- .../tests/v2/consolidated/test_fixtures.py | 4 +- .../tests/v2/group/test_fixtures.py | 6 +- .../tests/v3/array/test_fixtures.py | 6 +- .../tests/v3/array/with_extra_field.json | 2 +- .../tests/v3/consolidated/test_fixtures.py | 4 +- .../tests/v3/group/test_fixtures.py | 4 +- 47 files changed, 5940 insertions(+), 299 deletions(-) create mode 100644 packages/zarr-metadata/changes/4119.feature.md create mode 100644 packages/zarr-metadata/changes/4119.removal.md create mode 100644 packages/zarr-metadata/src/zarr_metadata/_pydantic_schema.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/model/__init__.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/model/_array.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/model/_group.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/model/_sentinel.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/model/_validation.py create mode 100644 packages/zarr-metadata/src/zarr_metadata/pydantic.py create mode 100644 packages/zarr-metadata/tests/model/__init__.py create mode 100644 packages/zarr-metadata/tests/model/_cases.py create mode 100644 packages/zarr-metadata/tests/model/test_array.py create mode 100644 packages/zarr-metadata/tests/model/test_group.py create mode 100644 packages/zarr-metadata/tests/model/test_pydantic.py create mode 100644 packages/zarr-metadata/tests/model/test_pydantic_module.py create mode 100644 packages/zarr-metadata/tests/model/test_sentinel.py diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml index 4e5bb0fb1a..df7d96cc1c 100644 --- a/.github/workflows/zarr-metadata.yml +++ b/.github/workflows/zarr-metadata.yml @@ -82,7 +82,10 @@ jobs: - name: Sync test dependency group run: uv sync --group test --python 3.11 - name: Run pyright - run: uv run --group test --with pyright pyright src + # Pinned to the last version that types PEP 661 sentinels in class + # attributes correctly; 1.1.405+ regressed (microsoft/pyright#11115). + # Unpin when the fix lands. + run: uv run --group test --with 'pyright==1.1.404' pyright src zarr-metadata-complete: name: zarr-metadata complete diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md index a842e07886..69b80d7332 100644 --- a/packages/zarr-metadata/README.md +++ b/packages/zarr-metadata/README.md @@ -1,51 +1,86 @@ # zarr-metadata -Python type definitions for Zarr v2 and v3 metadata. +Python types, models, and validators for Zarr v2 and v3 metadata. ## What this is -A typed-data package: `TypedDict` definitions and `Literal` aliases for the -JSON shapes specified by the [Zarr v2](https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html) -and [Zarr v3](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) -specifications, plus types for [`zarr-extensions`](https://github.com/zarr-developers/zarr-extensions/) -and a few widely-used-but-unspecified entities (e.g. consolidated metadata). +Two layers and an optional integration: + +- **Typed JSON shapes**: `TypedDict` definitions and `Literal` aliases for the + JSON documents specified by the [Zarr v2](https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html) + and [Zarr v3](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) + specifications, plus types for [`zarr-extensions`](https://github.com/zarr-developers/zarr-extensions/) + and a few widely-used-but-unspecified entities (e.g. consolidated metadata). +- **Document models** (`zarr_metadata.model`): canonical frozen-dataclass + models of whole metadata documents, with structural validators, loc-aware + parsers, and store-key (de)serialization. A document produced by `to_json` + shares no mutable state with the model that produced it. +- **Optional Pydantic integration** (`zarr_metadata.pydantic`, requires + Pydantic 2.13 or newer): each model as a Pydantic field type that validates + raw documents through the same strict parser. ## What this is for -These types describe the JSON shape of Zarr metadata. They are -intended for libraries that **read, write, validate, or transform** -Zarr metadata. Pair them with a runtime validator like -[pydantic](https://docs.pydantic.dev/) to check JSON loaded from disk: +The public `TypedDict` definitions describe the static JSON shape of Zarr +metadata. For strict, loc-aware validation of JSON loaded from disk, use the +model parser: ```python import json -from pydantic import TypeAdapter -from zarr_metadata.v3.array import ArrayMetadataV3 +from zarr_metadata.model import ZarrV3ArrayMetadata with open("zarr.json", "rb") as f: raw = json.load(f) -metadata = TypeAdapter(ArrayMetadataV3).validate_python(raw) +metadata = ZarrV3ArrayMetadata.from_json(raw) +``` + +The optional Pydantic integration delegates raw input to the same strict +parser and returns the same normalized model class: + +```python +from pydantic import TypeAdapter +import zarr_metadata.pydantic as zmp + +metadata = TypeAdapter(zmp.ZarrV3ArrayMetadata).validate_python(raw) +encoded = metadata.to_key_value()["zarr.json"] ``` -## What this is *not* +A bare `TypeAdapter` over a public document `TypedDict` is a coercive shape +adapter, not a Zarr conformance validator; it may coerce values or discard +members that the strict model parser rejects. + +## Validation boundary -- Not a parser or builder. There are no `make_array_metadata(...)` factories — - that surface belongs to consumer libraries. -- Not a runtime validator on its own. Pair with `pydantic`, `msgspec`, or - similar to enforce shapes at decode time. +The model validators enforce the declared document structure and a small set +of context-free consistency rules, including fixed format literals, finite +JSON numbers, non-negative dimensions, non-empty v3 codec pipelines, and one +`dimension_names` entry per array dimension. They do not interpret extension +names or configurations, resolve codec pipelines, or decide whether a data +type, chunk grid, codec, or storage transformer is supported. Those decisions +belong to consumer implementations. -Even with a runtime validator, these types only describe **structural** -shape — they will not flag *semantically* invalid metadata, like a 3D v3 -array whose `dimension_names` has 4 entries instead of 3. That's a job -for downstream validator routines. +The Pydantic integration's generated JSON Schemas express independently +checkable document structure and field constraints, but they are not a +replacement for runtime model validation. Standard JSON Schema treats a +mathematically integral number such as `1.0` as an integer, while the runtime +boundary requires Python `int` values, and it cannot express arbitrary +same-length relations such as `dimension_names` versus `shape` or v2 `chunks` +versus `shape`. Consumers should run the model parser after schema validation. ## Scope At minimum, this library supports what Zarr-Python needs: the complete Zarr v2 and v3 specs, consolidated metadata, and a subset of the metadata defined in `zarr-extensions`. We are generally open to contributions that -add types for Zarr metadata with a published spec. +add types, models, or structural validation for Zarr metadata with a +published spec. + +Runtime array behavior is out of scope: nothing here encodes or decodes +chunks, resolves codec or data type names to implementations, or performs +store I/O. The models begin and end at the metadata documents themselves — +`from_key_value` / `to_key_value` map documents to store keys and bytes, +and everything past that belongs to consumer libraries. ## Releasing diff --git a/packages/zarr-metadata/changes/4119.feature.md b/packages/zarr-metadata/changes/4119.feature.md new file mode 100644 index 0000000000..b9d0bb508c --- /dev/null +++ b/packages/zarr-metadata/changes/4119.feature.md @@ -0,0 +1,92 @@ +Added `zarr_metadata.model`: frozen-dataclass models (`ZarrV2ArrayMetadata`, +`ZarrV3ArrayMetadata`, `ZarrV2GroupMetadata`, `ZarrV3GroupMetadata`, +`ZarrV2ConsolidatedMetadata`, `ZarrV3ConsolidatedMetadata`, `ZarrV3NamedConfig`) +that are canonical, semantically lossless representations of Zarr metadata +documents, plus structural validators (`validate_*` / `is_*` / `parse_*`). +Every v3 extension point (data type, chunk grid, chunk key encoding, codecs, +storage transformers) is held as `ZarrV3NamedConfig`: a name, configuration, +and `must_understand` obligation; nothing is interpreted. On the wire, an +empty configuration with the default obligation uses the spec's plain-string +shorthand. Model fields are annotated with the role alias +`ZarrV3MetadataField` (today exactly `ZarrV3NamedConfig`), so annotations +convey the logical meaning and stay put if the spec adds another field form. + +Validation is strict about what the types declare: v2 `dtype` / `order` / +`compressor` / `filters` / `dimension_separator` shapes and the fixed +`zarr_format` / `node_type` literals are all enforced. Every +`ValidationProblem` carries a machine-readable `kind` +(`missing_key` / `invalid_type` / `invalid_value` / `invalid_json`) so +consumers can dispatch on the failure mode without matching message strings, +and every ingestion failure — including missing store keys and undecodable +bytes in `from_key_value` — surfaces as `MetadataValidationError`. An +adversarial review added further structural checks: JSON booleans are not +accepted as dimension lengths, dimensions are non-negative, +`dimension_names` must have one entry per dimension of `shape`, `attributes` +and `configuration` values are JSON-checked recursively (like `fill_value`), +non-finite floats and non-standard JSON constants are rejected, abstract +mappings and sequences normalize to encoder-safe canonical containers, +v2 `shape` and `chunks` must have the same rank, non-null v2 filter pipelines +contain at least one filter, document `TypeIs` guards only narrow values that +already use the declared canonical containers, +and the inline consolidated-metadata envelope and entries are deep-validated +so the group validator's verdict always agrees with the model constructor. + +The v3 models expose `must_understand_fields`: the subset of `extra_fields` +not explicitly waived with `must_understand: false` (fields are implicitly +must-understand per the spec). Readers discharge the spec's fail-to-open +duty by subtracting the extension names they recognize; the model only +partitions by obligation, since recognition is reader-specific. + +Optional pydantic integration ships as `zarr_metadata.pydantic` (importing it +requires pydantic 2.13 or newer; the core package does not depend on it): one +`Annotated` +field type per model, validating raw documents through `from_json`, passing +core-model instances through unchanged, serializing via `to_json`, and +publishing JSON Schemas derived from private constrained document types that +mirror the independently expressible runtime rules. Cross-field cardinality +relations still require runtime validation. The instances are the core model +classes, so values interoperate freely with non-pydantic code. + +`create_default` keeps its output self-consistent: overriding `shape` without +a chunk grid derives one regular chunk covering the array (v3 +`chunk_shape == shape`; v2 `chunks == shape`) instead of silently keeping the +scalar default's 0-d grid. + +A v2 `.zarray` that omits `dimension_separator` is interpreted with the v2 +convention's default `"."` (the model previously normalized absence to `"/"`, +which would misaddress the chunks of real-world default-separator arrays). +The value is never null: absent, `"."`, or `"/"` are the only spellings. + +Optional document keys use `UNSET` — a PEP 661 sentinel +(`typing_extensions.Sentinel`), usable directly in type expressions — never +`None`: in a model, `None` always corresponds to a JSON `null` in the +document (a v2 `compressor`, an unnamed dimension inside `dimension_names`), +and `UNSET` always means the key is absent. Checker note: ty types the +sentinel exactly; pyright needs `<= 1.1.404` until microsoft/pyright#11115 +is fixed (this package's CI pins it); mypy users need a `cast` or +`type: ignore` at narrowing sites until python/mypy#21647 merges. This keeps semantically distinct spellings +distinct — an absent `dimension_names` ("there are no dimension names") and +an explicit `[null, null]` ("every dimension has a name, which is null") are +different documents and round-trip as such. The `consolidated_metadata: null` +written by a historical zarr-python bug is the one deliberate exception to +faithful round-tripping: those stores remain readable, but the bug spelling +is repaired to absence on read and never written back. + +The v2 models treat the `.zattrs` file's presence as part of the store: +`attributes` is `UNSET` when no `.zattrs` file exists (and `to_key_value` +emits none), while an explicit empty `.zattrs` is `{}` and round-trips as a +file. Previously `to_key_value` always emitted `.zattrs`, silently adding a +file to stores that never had one. + +The store-key `Literal` aliases (`ZarrV2ArrayMetadataStoreKey`, +`ZarrV2AttributesStoreKey`, ...) are exported from `zarr_metadata.model` +alongside their constants, and each `to_key_value` return type is keyed by +them, so the set of store keys a model can emit is visible in its signature. +`from_key_value` deliberately keeps `Mapping[str, bytes]` input: it accepts +any string-keyed store mapping and ignores unrelated keys. + +`to_json` returns a document that shares no mutable state with the model: +every value that can hold a mutable container (attributes, configurations, +extra fields, v2 codec configurations, fill values, consolidated entries) is +deep-copied on the way out, so editing a serialized document can never +silently mutate the frozen model that produced it. diff --git a/packages/zarr-metadata/changes/4119.removal.md b/packages/zarr-metadata/changes/4119.removal.md new file mode 100644 index 0000000000..2a9a6f84c4 --- /dev/null +++ b/packages/zarr-metadata/changes/4119.removal.md @@ -0,0 +1,41 @@ +The document (TypedDict) types are renamed to put the format version at the +front of the name and to mark the JSON-document form with a `JSON` suffix, +so a format version can never be misread as a class revision and the bare +entity names are reserved for the `zarr_metadata.model` dataclasses: + +- `ArrayMetadataV2` → `ZarrV2ArrayMetadataJSON` (and `...Partial` accordingly) +- `ArrayMetadataV3` → `ZarrV3ArrayMetadataJSON` (and `...Partial` accordingly) +- `GroupMetadataV2` → `ZarrV2GroupMetadataJSON` (and `...Partial` accordingly) +- `GroupMetadataV3` → `ZarrV3GroupMetadataJSON` (and `...Partial` accordingly) +- `ConsolidatedMetadataV2` → `ZarrV2ConsolidatedMetadataJSON` +- `ConsolidatedMetadataV3` → `ZarrV3ConsolidatedMetadataJSON` +- `NamedConfigV3` → `ZarrV3NamedConfigJSON` +- `MetadataV3` → `ZarrV3MetadataFieldJSON` (the union of the bare-name and + named-configuration spellings of one metadata field) +- `ExtensionFieldV3` → `ZarrV3ExtensionField` +- `CodecMetadataV2` → `ZarrV2CodecMetadata` +- `DataTypeMetadataV2` → `ZarrV2DataTypeMetadata` +- `ArrayOrderV2` → `ZarrV2ArrayOrder` +- `ArrayDimensionSeparatorV2` → `ZarrV2ArrayDimensionSeparator` +- `ZArrayMetadata` → `ZarrV2ZArrayJSON` (the strict on-disk `.zarray` document) +- `ZGroupMetadata` → `ZarrV2ZGroupJSON` (the strict on-disk `.zgroup` document) +- `ZAttrsMetadata` → `ZarrV2ZAttrsJSON` (the `.zattrs` document) + +The old names are removed, not aliased. The `zarr_metadata.pydantic` field +types take the bare entity names (`ZarrV3ArrayMetadata`, ...), matching the +model classes they validate into. + +The conventions, stated once for future additions: CamelCase type names put +the format version first (`ZarrV2ArrayMetadataJSON`, +`ZarrV3ArrayMetadataStoreKey`), while SCREAMING_SNAKE constants and +snake_case functions put it last (`ARRAY_METADATA_STORE_KEY_V2`, +`validate_array_metadata_v3`). The `JSON` suffix marks a raw-document type +whose bare name is taken by (or reserved for) a `zarr_metadata.model` +dataclass; raw field-level types the models hold verbatim +(`ZarrV2CodecMetadata`, `ZarrV3ExtensionField`) keep their bare names. +Extension-entity types put the registered entity name first and end in +exactly one role suffix (`BloscCodecMetadata`, `Uint8DataTypeName`) — the +`V2` in `V2ChunkKeyEncodingMetadata` is that encoding's entity name, not a +format version, which is always spelled `ZarrV2`/`ZarrV3`. Every public +type name is checked against this grammar by +`tests/test_public_api.py::test_public_type_names_comply_with_naming_grammar`. diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 05667d59e3..edc4b696a6 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -5,7 +5,7 @@ build-backend = "hatchling.build" [project] name = "zarr-metadata" dynamic = ["version"] -description = "Spec-defined metadata types for Zarr v2 and v3." +description = "Spec-defined metadata types, models, and validators for Zarr v2 and v3." readme = "README.md" requires-python = ">=3.11" license = "MIT" @@ -32,7 +32,11 @@ classifiers = [ ] keywords = ["zarr"] dependencies = [ - "typing_extensions>=4.13", + # >=4.16: first release where `Sentinel` pickles by reference + # (`__reduce__` returns the sentinel's name), so `UNSET` — and any model + # holding it — can cross process boundaries and be deep-copied with its + # singleton identity intact. 4.15 and earlier refuse to pickle sentinels. + "typing_extensions>=4.16", ] [project.urls] @@ -43,7 +47,7 @@ Changelog = "https://github.com/zarr-developers/zarr-python/blob/main/packages/z Documentation = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/README.md" [dependency-groups] -test = ["pytest", "pydantic>=2"] +test = ["pytest", "pydantic>=2.13", "jsonschema"] [tool.hatch.version] source = "vcs" @@ -67,9 +71,9 @@ xfail_strict = true addopts = ["-ra", "--strict-config", "--strict-markers"] filterwarnings = [ "error", - # pydantic warns about ReadOnly TypedDict items not being enforced at runtime. - # That's expected here — we rely on type-checker enforcement, not pydantic mutation guards. - "ignore::UserWarning:pydantic._internal._generate_schema", + # Pydantic validates these public immutable-shape TypedDicts correctly but + # cannot enforce the type checker's ReadOnly mutation restriction. + "ignore:Items? .* using the `ReadOnly` qualifier.*:UserWarning:pydantic._internal._generate_schema", ] [tool.numpydoc_validation] @@ -82,6 +86,9 @@ checks = [ "PR06", ] +# CI pins pyright==1.1.404: later versions regress PEP 661 sentinel typing in +# class attributes (microsoft/pyright#11115), which zarr_metadata.model._sentinel +# relies on. Use the same pin locally; unpin when the fix lands. [tool.pyright] include = ["src"] enableExperimentalFeatures = true diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index 46949570a2..b5e52e976d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -1,22 +1,48 @@ from importlib.metadata import version -from zarr_metadata._common import JSONValue, NamedConfigV3 +from zarr_metadata._common import JSONValue, ZarrV3NamedConfigJSON +from zarr_metadata.model import ( + UNSET, + MetadataValidationError, + ProblemKind, + ValidationProblem, + ZarrV2ArrayMetadata, + ZarrV2ArrayMetadataPartial, + ZarrV2ConsolidatedMetadata, + ZarrV2GroupMetadata, + ZarrV2GroupMetadataPartial, + ZarrV3ArrayMetadata, + ZarrV3ArrayMetadataPartial, + ZarrV3ConsolidatedMetadata, + ZarrV3GroupMetadata, + ZarrV3GroupMetadataPartial, + ZarrV3MetadataField, + ZarrV3NamedConfig, +) from zarr_metadata.v2.array import ( ARRAY_DIMENSION_SEPARATOR_V2, ARRAY_ORDER_V2, - ArrayDimensionSeparatorV2, - ArrayMetadataV2, - ArrayMetadataV2Partial, - ArrayOrderV2, - DataTypeMetadataV2, - ZArrayMetadata, -) -from zarr_metadata.v2.attributes import ZAttrsMetadata -from zarr_metadata.v2.codec import CodecMetadataV2 -from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 -from zarr_metadata.v2.group import GroupMetadataV2, GroupMetadataV2Partial, ZGroupMetadata -from zarr_metadata.v3._common import MetadataV3 -from zarr_metadata.v3.array import ArrayMetadataV3, ArrayMetadataV3Partial, ExtensionFieldV3 + ZarrV2ArrayDimensionSeparator, + ZarrV2ArrayMetadataJSON, + ZarrV2ArrayMetadataJSONPartial, + ZarrV2ArrayOrder, + ZarrV2DataTypeMetadata, + ZarrV2ZArrayJSON, +) +from zarr_metadata.v2.attributes import ZarrV2ZAttrsJSON +from zarr_metadata.v2.codec import ZarrV2CodecMetadata +from zarr_metadata.v2.consolidated import ZarrV2ConsolidatedMetadataJSON +from zarr_metadata.v2.group import ( + ZarrV2GroupMetadataJSON, + ZarrV2GroupMetadataJSONPartial, + ZarrV2ZGroupJSON, +) +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON +from zarr_metadata.v3.array import ( + ZarrV3ArrayMetadataJSON, + ZarrV3ArrayMetadataJSONPartial, + ZarrV3ExtensionField, +) from zarr_metadata.v3.chunk_grid.rectilinear import ( RECTILINEAR_CHUNK_GRID_NAME, RectilinearChunkGridMetadata, @@ -86,7 +112,7 @@ TransposeCodecName, ) from zarr_metadata.v3.codec.zstd import ZSTD_CODEC_NAME, ZstdCodecMetadata, ZstdCodecName -from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 +from zarr_metadata.v3.consolidated import ZarrV3ConsolidatedMetadataJSON from zarr_metadata.v3.data_type.bool import ( BOOL_DATA_TYPE_NAME, BoolDataTypeName, @@ -185,7 +211,7 @@ Uint64DataTypeName, Uint64FillValue, ) -from zarr_metadata.v3.group import GroupMetadataV3, GroupMetadataV3Partial +from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON, ZarrV3GroupMetadataJSONPartial __version__ = version("zarr-metadata") @@ -231,15 +257,10 @@ "UINT16_DATA_TYPE_NAME", "UINT32_DATA_TYPE_NAME", "UINT64_DATA_TYPE_NAME", + "UNSET", "V2_CHUNK_KEY_ENCODING_NAME", "V2_CHUNK_KEY_ENCODING_SEPARATOR", "ZSTD_CODEC_NAME", - "ArrayDimensionSeparatorV2", - "ArrayMetadataV2", - "ArrayMetadataV2Partial", - "ArrayMetadataV3", - "ArrayMetadataV3Partial", - "ArrayOrderV2", "BloscCName", "BloscCodecMetadata", "BloscCodecName", @@ -254,31 +275,22 @@ "CastRoundingMode", "CastValueCodecMetadata", "CastValueCodecName", - "CodecMetadataV2", "Complex64DataTypeName", "Complex64FillValue", "Complex128DataTypeName", "Complex128FillValue", - "ConsolidatedMetadataV2", - "ConsolidatedMetadataV3", "Crc32cCodecMetadata", "Crc32cCodecName", - "DataTypeMetadataV2", "DefaultChunkKeyEncodingMetadata", "DefaultChunkKeyEncodingName", "DefaultChunkKeyEncodingSeparator", "Endianness", - "ExtensionFieldV3", "Float16DataTypeName", "Float16FillValue", "Float32DataTypeName", "Float32FillValue", "Float64DataTypeName", "Float64FillValue", - "GroupMetadataV2", - "GroupMetadataV2Partial", - "GroupMetadataV3", - "GroupMetadataV3Partial", "GzipCodecMetadata", "GzipCodecName", "Int8DataTypeName", @@ -290,13 +302,13 @@ "Int64DataTypeName", "Int64FillValue", "JSONValue", - "MetadataV3", - "NamedConfigV3", + "MetadataValidationError", "NumpyDatetime64DataTypeName", "NumpyDatetime64FillValue", "NumpyTimeUnit", "NumpyTimedelta64DataTypeName", "NumpyTimedelta64FillValue", + "ProblemKind", "RawBytesDataTypeName", "RawBytesFillValue", "RectilinearChunkGridMetadata", @@ -325,9 +337,39 @@ "V2ChunkKeyEncodingMetadata", "V2ChunkKeyEncodingName", "V2ChunkKeyEncodingSeparator", - "ZArrayMetadata", - "ZAttrsMetadata", - "ZGroupMetadata", + "ValidationProblem", + "ZarrV2ArrayDimensionSeparator", + "ZarrV2ArrayMetadata", + "ZarrV2ArrayMetadataJSON", + "ZarrV2ArrayMetadataJSONPartial", + "ZarrV2ArrayMetadataPartial", + "ZarrV2ArrayOrder", + "ZarrV2CodecMetadata", + "ZarrV2ConsolidatedMetadata", + "ZarrV2ConsolidatedMetadataJSON", + "ZarrV2DataTypeMetadata", + "ZarrV2GroupMetadata", + "ZarrV2GroupMetadataJSON", + "ZarrV2GroupMetadataJSONPartial", + "ZarrV2GroupMetadataPartial", + "ZarrV2ZArrayJSON", + "ZarrV2ZAttrsJSON", + "ZarrV2ZGroupJSON", + "ZarrV3ArrayMetadata", + "ZarrV3ArrayMetadataJSON", + "ZarrV3ArrayMetadataJSONPartial", + "ZarrV3ArrayMetadataPartial", + "ZarrV3ConsolidatedMetadata", + "ZarrV3ConsolidatedMetadataJSON", + "ZarrV3ExtensionField", + "ZarrV3GroupMetadata", + "ZarrV3GroupMetadataJSON", + "ZarrV3GroupMetadataJSONPartial", + "ZarrV3GroupMetadataPartial", + "ZarrV3MetadataField", + "ZarrV3MetadataFieldJSON", + "ZarrV3NamedConfig", + "ZarrV3NamedConfigJSON", "ZstdCodecMetadata", "ZstdCodecName", "__version__", diff --git a/packages/zarr-metadata/src/zarr_metadata/_common.py b/packages/zarr-metadata/src/zarr_metadata/_common.py index 598a12e80c..f3259f7b73 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_common.py +++ b/packages/zarr-metadata/src/zarr_metadata/_common.py @@ -13,7 +13,14 @@ JSONValue = TypeAliasType( "JSONValue", - "int | float | bool | None | str | list[JSONValue] | tuple[JSONValue, ...] | Mapping[str, JSONValue]", # type: ignore[reportInvalidTypeForm] + int + | float + | bool + | str + | list["JSONValue"] + | tuple["JSONValue", ...] + | Mapping[str, "JSONValue"] + | None, ) """A recursive type alias for JSON-encodable values. @@ -24,13 +31,14 @@ """ -class NamedConfigV3(TypedDict): +class ZarrV3NamedConfigJSON(TypedDict): """ Externally-tagged union member for a metadata field. - The `configuration` mapping holds arbitrary JSON-encodable values; - it is typed as `Mapping[str, JSONValue]`. + The optional `configuration` mapping holds arbitrary JSON-encodable + values. `must_understand` is implicitly true when absent. """ name: str configuration: NotRequired[Mapping[str, JSONValue]] + must_understand: NotRequired[bool] diff --git a/packages/zarr-metadata/src/zarr_metadata/_pydantic_schema.py b/packages/zarr-metadata/src/zarr_metadata/_pydantic_schema.py new file mode 100644 index 0000000000..e9792d6931 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/_pydantic_schema.py @@ -0,0 +1,114 @@ +"""Private input types used only to generate accurate Pydantic JSON schemas.""" + +from __future__ import annotations + +from collections.abc import Mapping # noqa: TC003 # resolved by Pydantic at runtime +from typing import Annotated, Literal, NotRequired + +from pydantic import Field +from typing_extensions import TypedDict + +from zarr_metadata._common import JSONValue +from zarr_metadata.v2.array import ( # noqa: TC001 # resolved by Pydantic at runtime + ZarrV2DataTypeMetadata, +) +from zarr_metadata.v2.codec import ( # resolved by Pydantic at runtime + ZarrV2CodecMetadata, +) + +NonNegativeInt = Annotated[int, Field(ge=0)] + + +class ZarrV3NamedConfigJSON(TypedDict, closed=True): + """Closed v3 named configuration accepted at optional extension points.""" + + name: str + configuration: NotRequired[Mapping[str, JSONValue]] + must_understand: NotRequired[bool] + + +class ZarrV3MandatoryNamedConfigJSON(TypedDict, closed=True): + """Closed named configuration accepted where understanding is mandatory.""" + + name: str + configuration: NotRequired[Mapping[str, JSONValue]] + must_understand: NotRequired[Literal[True]] + + +ZarrV3MetadataFieldJSON = str | ZarrV3NamedConfigJSON +ZarrV3MandatoryMetadataFieldJSON = str | ZarrV3MandatoryNamedConfigJSON +ZarrV3CodecPipelineJSON = Annotated[tuple[ZarrV3MetadataFieldJSON, ...], Field(min_length=1)] +ZarrV2FilterPipelineJSON = Annotated[tuple[ZarrV2CodecMetadata, ...], Field(min_length=1)] + + +class ZarrV3ArrayMetadataJSON(TypedDict, extra_items=JSONValue): + """Schema input for a v3 array document, including arbitrary extensions.""" + + zarr_format: Literal[3] + node_type: Literal["array"] + data_type: ZarrV3MandatoryMetadataFieldJSON + shape: tuple[NonNegativeInt, ...] + chunk_grid: ZarrV3MandatoryMetadataFieldJSON + chunk_key_encoding: ZarrV3MandatoryMetadataFieldJSON + fill_value: JSONValue + codecs: ZarrV3CodecPipelineJSON + attributes: NotRequired[Mapping[str, JSONValue]] + storage_transformers: NotRequired[tuple[ZarrV3MetadataFieldJSON, ...]] + dimension_names: NotRequired[tuple[str | None, ...]] + + +class ZarrV3ConsolidatedMetadataJSON(TypedDict, closed=True): + """Schema input for the closed inline consolidated-metadata envelope.""" + + kind: Literal["inline"] + must_understand: Literal[False] + metadata: Mapping[str, ZarrV3ArrayMetadataJSON | ZarrV3GroupMetadataJSON] + + +class ZarrV3GroupMetadataJSON(TypedDict, extra_items=JSONValue): + """Schema input for a v3 group document, including arbitrary extensions.""" + + zarr_format: Literal[3] + node_type: Literal["group"] + attributes: NotRequired[Mapping[str, JSONValue]] + consolidated_metadata: NotRequired[ZarrV3ConsolidatedMetadataJSON | None] + + +class ZarrV2ArrayMetadataJSON(TypedDict, closed=True): + """Schema input for the closed, merged v2 array representation.""" + + zarr_format: Literal[2] + shape: tuple[NonNegativeInt, ...] + chunks: tuple[NonNegativeInt, ...] + dtype: ZarrV2DataTypeMetadata + compressor: ZarrV2CodecMetadata | None + fill_value: JSONValue + order: Literal["C", "F"] + filters: ZarrV2FilterPipelineJSON | None + dimension_separator: NotRequired[Literal[".", "/"]] + attributes: NotRequired[Mapping[str, JSONValue]] + + +class ZarrV2GroupMetadataJSON(TypedDict, closed=True): + """Schema input for the closed, merged v2 group representation.""" + + zarr_format: Literal[2] + attributes: NotRequired[Mapping[str, JSONValue]] + + +class ZarrV2ConsolidatedMetadataJSON(TypedDict, closed=True): + """Schema input matching the v2 consolidated model's structural parser.""" + + zarr_consolidated_format: Literal[1] + metadata: Mapping[str, JSONValue] + + +__all__ = [ + "ZarrV2ArrayMetadataJSON", + "ZarrV2ConsolidatedMetadataJSON", + "ZarrV2GroupMetadataJSON", + "ZarrV3ArrayMetadataJSON", + "ZarrV3ConsolidatedMetadataJSON", + "ZarrV3GroupMetadataJSON", + "ZarrV3MetadataFieldJSON", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/model/__init__.py b/packages/zarr-metadata/src/zarr_metadata/model/__init__.py new file mode 100644 index 0000000000..e726c54d3e --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/model/__init__.py @@ -0,0 +1,132 @@ +"""In-memory models for Zarr metadata documents. + +Models are frozen dataclasses that hold a canonical, semantically lossless +representation of the JSON documents; they never interpret extension points +(codecs, chunk grids, data types). Validators check JSON structure, not domain validity. +Each document concept gets a `validate_*` function returning every problem +found (a `list[ValidationProblem]`, each with a machine-readable `kind`), an +`is_*` type guard, and a `parse_*` function that narrows or raises +`MetadataValidationError`. Model `from_json` / `from_key_value` constructors +raise `MetadataValidationError` for every ingestion failure, including +missing store keys and undecodable bytes. +""" + +from zarr_metadata.model._array import ( + ARRAY_METADATA_STORE_KEY_V2, + ARRAY_METADATA_STORE_KEY_V3, + ATTRIBUTES_STORE_KEY_V2, + ZarrV2ArrayMetadata, + ZarrV2ArrayMetadataPartial, + ZarrV2ArrayMetadataStoreKey, + ZarrV2AttributesStoreKey, + ZarrV3ArrayMetadata, + ZarrV3ArrayMetadataPartial, + ZarrV3ArrayMetadataStoreKey, + ZarrV3MetadataField, + ZarrV3NamedConfig, +) +from zarr_metadata.model._group import ( + CONSOLIDATED_METADATA_KEY_V3, + CONSOLIDATED_METADATA_STORE_KEY_V2, + GROUP_METADATA_STORE_KEY_V2, + GROUP_METADATA_STORE_KEY_V3, + ZarrV2ConsolidatedMetadata, + ZarrV2ConsolidatedMetadataStoreKey, + ZarrV2GroupMetadata, + ZarrV2GroupMetadataPartial, + ZarrV2GroupMetadataStoreKey, + ZarrV3ConsolidatedMetadata, + ZarrV3GroupMetadata, + ZarrV3GroupMetadataPartial, + ZarrV3GroupMetadataStoreKey, +) +from zarr_metadata.model._sentinel import UNSET +from zarr_metadata.model._validation import ( + ARRAY_METADATA_OPTIONAL_KEYS_V3, + ARRAY_METADATA_REQUIRED_KEYS_V2, + ARRAY_METADATA_REQUIRED_KEYS_V3, + ARRAY_METADATA_STANDARD_KEYS_V3, + GROUP_METADATA_OPTIONAL_KEYS_V3, + GROUP_METADATA_REQUIRED_KEYS_V2, + GROUP_METADATA_REQUIRED_KEYS_V3, + GROUP_METADATA_STANDARD_KEYS_V3, + MetadataValidationError, + ProblemKind, + ValidationProblem, + is_array_metadata_v2, + is_array_metadata_v3, + is_group_metadata_v2, + is_group_metadata_v3, + is_json, + is_metadata_field_v3, + parse_array_metadata_v2, + parse_array_metadata_v3, + parse_group_metadata_v2, + parse_group_metadata_v3, + parse_json, + parse_metadata_field_v3, + validate_array_metadata_v2, + validate_array_metadata_v3, + validate_group_metadata_v2, + validate_group_metadata_v3, + validate_json, + validate_metadata_field_v3, +) + +__all__ = [ + "ARRAY_METADATA_OPTIONAL_KEYS_V3", + "ARRAY_METADATA_REQUIRED_KEYS_V2", + "ARRAY_METADATA_REQUIRED_KEYS_V3", + "ARRAY_METADATA_STANDARD_KEYS_V3", + "ARRAY_METADATA_STORE_KEY_V2", + "ARRAY_METADATA_STORE_KEY_V3", + "ATTRIBUTES_STORE_KEY_V2", + "CONSOLIDATED_METADATA_KEY_V3", + "CONSOLIDATED_METADATA_STORE_KEY_V2", + "GROUP_METADATA_OPTIONAL_KEYS_V3", + "GROUP_METADATA_REQUIRED_KEYS_V2", + "GROUP_METADATA_REQUIRED_KEYS_V3", + "GROUP_METADATA_STANDARD_KEYS_V3", + "GROUP_METADATA_STORE_KEY_V2", + "GROUP_METADATA_STORE_KEY_V3", + "UNSET", + "MetadataValidationError", + "ProblemKind", + "ValidationProblem", + "ZarrV2ArrayMetadata", + "ZarrV2ArrayMetadataPartial", + "ZarrV2ArrayMetadataStoreKey", + "ZarrV2AttributesStoreKey", + "ZarrV2ConsolidatedMetadata", + "ZarrV2ConsolidatedMetadataStoreKey", + "ZarrV2GroupMetadata", + "ZarrV2GroupMetadataPartial", + "ZarrV2GroupMetadataStoreKey", + "ZarrV3ArrayMetadata", + "ZarrV3ArrayMetadataPartial", + "ZarrV3ArrayMetadataStoreKey", + "ZarrV3ConsolidatedMetadata", + "ZarrV3GroupMetadata", + "ZarrV3GroupMetadataPartial", + "ZarrV3GroupMetadataStoreKey", + "ZarrV3MetadataField", + "ZarrV3NamedConfig", + "is_array_metadata_v2", + "is_array_metadata_v3", + "is_group_metadata_v2", + "is_group_metadata_v3", + "is_json", + "is_metadata_field_v3", + "parse_array_metadata_v2", + "parse_array_metadata_v3", + "parse_group_metadata_v2", + "parse_group_metadata_v3", + "parse_json", + "parse_metadata_field_v3", + "validate_array_metadata_v2", + "validate_array_metadata_v3", + "validate_group_metadata_v2", + "validate_group_metadata_v3", + "validate_json", + "validate_metadata_field_v3", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_array.py b/packages/zarr-metadata/src/zarr_metadata/model/_array.py new file mode 100644 index 0000000000..c4c967f891 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/model/_array.py @@ -0,0 +1,498 @@ +"""In-memory models for Zarr array metadata documents.""" + +from __future__ import annotations + +import copy +import dataclasses +from collections.abc import Mapping +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, Final, Literal, TypeAlias, cast + +from typing_extensions import TypedDict, Unpack + +from zarr_metadata.model._sentinel import UNSET +from zarr_metadata.model._validation import ( + ARRAY_METADATA_STANDARD_KEYS_V3, + MetadataValidationError, + ValidationProblem, + arrays_to_tuples, + dump_store_json, + load_store_json, + parse_array_metadata_v2, + parse_array_metadata_v3, + parse_metadata_field_v3, +) + +if TYPE_CHECKING: + from zarr_metadata._common import JSONValue, ZarrV3NamedConfigJSON + from zarr_metadata.v2.array import ( + ZarrV2ArrayDimensionSeparator, + ZarrV2ArrayMetadataJSON, + ZarrV2ArrayOrder, + ZarrV2DataTypeMetadata, + ) + from zarr_metadata.v2.codec import ZarrV2CodecMetadata + from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON + from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON, ZarrV3ExtensionField + +ZarrV3ArrayMetadataStoreKey = Literal["zarr.json"] +ARRAY_METADATA_STORE_KEY_V3: Final[ZarrV3ArrayMetadataStoreKey] = "zarr.json" + +ZarrV2ArrayMetadataStoreKey = Literal[".zarray"] +ARRAY_METADATA_STORE_KEY_V2: Final[ZarrV2ArrayMetadataStoreKey] = ".zarray" + +ZarrV2AttributesStoreKey = Literal[".zattrs"] +ATTRIBUTES_STORE_KEY_V2: Final[ZarrV2AttributesStoreKey] = ".zattrs" + + +@dataclass(frozen=True, slots=True, kw_only=True) +class ZarrV3NamedConfig: + """A normalized v3 metadata field with its reader obligation. + + Bare names and missing configurations normalize to an empty configuration. + Bare names and missing `must_understand` members normalize to the spec's + implicit `True` value. + """ + + name: str + configuration: dict[str, JSONValue] + must_understand: bool = True + + def to_json(self) -> ZarrV3MetadataFieldJSON: + if not self.configuration and self.must_understand: + return self.name + out: ZarrV3NamedConfigJSON = {"name": self.name} + if self.configuration: + # to_json output shares no mutable state with the model. + out["configuration"] = copy.deepcopy(self.configuration) + if not self.must_understand: + out["must_understand"] = False + return out + + @classmethod + def from_json(cls, data: object) -> ZarrV3NamedConfig: + field = parse_metadata_field_v3(data) + if isinstance(field, str): + return cls(name=field, configuration={}, must_understand=True) + # Sound cast: parse_metadata_field_v3 checked the configuration is a + # string-keyed mapping of JSON values; arrays_to_tuples only converts + # lists to tuples within that shape. + configuration = cast( + "dict[str, JSONValue]", arrays_to_tuples(dict(field.get("configuration", {}))) + ) + return cls( + name=field["name"], + configuration=configuration, + must_understand=field.get("must_understand", True), + ) + + +ZarrV3MetadataField: TypeAlias = ZarrV3NamedConfig +"""The in-memory model of one field of a v3 metadata document. + +This is the role-named alias for annotation positions: model fields and +consumer signatures should say `ZarrV3MetadataField` (the logical meaning) +rather than `ZarrV3NamedConfig` (the serialized form the field currently +takes). Today every metadata field normalizes to a named configuration plus +its reader obligation, so the alias is exactly `ZarrV3NamedConfig`; if a future +spec revision adds a field form that cannot be normalized to those values, +this alias widens to a union and annotation sites do not change. Mirrors the +raw-layer split between `ZarrV3NamedConfigJSON` (shape) and +`ZarrV3MetadataFieldJSON` (field union). +""" + + +def must_understand_subset( + extra_fields: Mapping[str, ZarrV3ExtensionField], +) -> dict[str, ZarrV3ExtensionField]: + """The subset of `extra_fields` the reader is obligated to understand. + + Per the v3 spec, an extension field is implicitly `must_understand: True` + unless it explicitly says otherwise, and an implementation MUST fail to + open a group or array carrying fields it does not recognize that are not + explicitly `must_understand: false`. A non-mapping field value cannot + carry the explicit waiver, so it always requires understanding (the + runtime isinstance check defends against values looser than the declared + `ZarrV3ExtensionField`). + """ + fields = cast("Mapping[str, object]", extra_fields) + return cast( + "dict[str, ZarrV3ExtensionField]", + { + name: value + for name, value in fields.items() + if not ( + isinstance(value, Mapping) + and cast("Mapping[str, object]", value).get("must_understand") is False + ) + }, + ) + + +class ZarrV3ArrayMetadataPartial(TypedDict, total=False): + """ + Partial form of the constructor-settable fields of `ZarrV3ArrayMetadata`. + + Every key is optional and typed with the model's own (not serialized) + value types, so it describes valid keyword arguments to + `ZarrV3ArrayMetadata.update`. The `init=False` fields `zarr_format` and + `node_type` are intentionally excluded, since they cannot be passed to + `dataclasses.replace`. + + Drift between this type and the model's settable fields is prevented by + `tests/model/test_array.py::test_partial_keys_match_settable_model_fields`. + """ + + shape: tuple[int, ...] + fill_value: JSONValue + data_type: ZarrV3MetadataField + chunk_grid: ZarrV3MetadataField + codecs: tuple[ZarrV3MetadataField, ...] + chunk_key_encoding: ZarrV3MetadataField + dimension_names: tuple[str | None, ...] | UNSET + attributes: dict[str, JSONValue] + storage_transformers: tuple[ZarrV3MetadataField, ...] + extra_fields: dict[str, ZarrV3ExtensionField] + + +@dataclass(frozen=True, slots=True, kw_only=True) +class ZarrV3ArrayMetadata: + """In-memory model of a v3 array metadata document. + + A canonical, semantically lossless representation of the `zarr.json` + content for an array. Extension points (`data_type`, `chunk_grid`, + `chunk_key_encoding`, `codecs`, `storage_transformers`) are held as + `ZarrV3MetadataField` values (currently `ZarrV3NamedConfig` name, + configuration, and obligation records) and are never interpreted; + `fill_value` is held verbatim in its JSON form. Equivalent extension + spellings normalize to shorthand strings when configuration is empty and + understanding is required. + """ + + zarr_format: Literal[3] = field(default=3, init=False) + node_type: Literal["array"] = field(default="array", init=False) + shape: tuple[int, ...] + fill_value: JSONValue + data_type: ZarrV3MetadataField + chunk_grid: ZarrV3MetadataField + codecs: tuple[ZarrV3MetadataField, ...] + chunk_key_encoding: ZarrV3MetadataField + dimension_names: tuple[str | None, ...] | UNSET + attributes: dict[str, JSONValue] + storage_transformers: tuple[ZarrV3MetadataField, ...] + extra_fields: dict[str, ZarrV3ExtensionField] + + @classmethod + def create_default(cls, **overrides: Unpack[ZarrV3ArrayMetadataPartial]) -> ZarrV3ArrayMetadata: + """ + Create a default (empty) v3 array metadata model, with optional overrides. + + The default is a structurally-valid scalar `uint8` array — the array + analog of `list()` returning `[]`. Any field can be overridden by keyword + (the same fields accepted by `update`). Overriding `shape` without + `chunk_grid` derives a consistent default grid: one regular chunk + covering the array (`chunk_shape` equal to `shape`). + + The derivation is deliberately one-way. A user-supplied `chunk_grid` + is an extension point and is taken verbatim — deriving `shape` from + it would require interpreting the grid's configuration, which this + layer never does (and cannot do for unrecognized grid names). So + overriding `chunk_grid` without `shape` keeps the scalar default + `shape=()`, and consistency between the two is the caller's + responsibility. + """ + if "shape" in overrides and "chunk_grid" not in overrides: + overrides["chunk_grid"] = ZarrV3NamedConfig( + name="regular", configuration={"chunk_shape": tuple(overrides["shape"])} + ) + default = cls( + shape=(), + fill_value=0, + data_type=ZarrV3NamedConfig(name="uint8", configuration={}), + chunk_grid=ZarrV3NamedConfig(name="regular", configuration={"chunk_shape": ()}), + codecs=(ZarrV3NamedConfig(name="bytes", configuration={}),), + chunk_key_encoding=ZarrV3NamedConfig(name="default", configuration={}), + dimension_names=UNSET, + attributes={}, + storage_transformers=(), + extra_fields={}, + ) + return default.update(**overrides) + + def update(self, **kwargs: Unpack[ZarrV3ArrayMetadataPartial]) -> ZarrV3ArrayMetadata: + """ + Return a new `ZarrV3ArrayMetadata` with the given fields updated. + + Only the constructor-settable fields listed in + `ZarrV3ArrayMetadataPartial` can be updated; any attempt to update + other fields (including the fixed `zarr_format` / `node_type`) is + rejected at the type level. Each given field fully replaces its + previous value, including `extra_fields`. + + This is useful for test fixtures that want to override a few fields of a + base template without having to re-specify the entire document. + + No re-validation is performed (`update` is `dataclasses.replace`), so + a repair or edit can produce an invalid document; validity is checked + on `from_json`, not on field replacement. + """ + return dataclasses.replace(self, **kwargs) + + def __post_init__(self) -> None: + overlap = set(self.extra_fields.keys()).intersection(ARRAY_METADATA_STANDARD_KEYS_V3) + if overlap: + raise MetadataValidationError( + [ + ValidationProblem( + ("extra_fields",), + "Extra fields cannot overlap with standard Zarr V3 array metadata fields", + "invalid_value", + ) + ] + ) + + def to_json(self) -> ZarrV3ArrayMetadataJSON: + # to_json output shares no mutable state with the model: every value + # that can hold a mutable container is deep-copied. + out: ZarrV3ArrayMetadataJSON = { + "zarr_format": self.zarr_format, + "node_type": self.node_type, + "shape": self.shape, + "fill_value": copy.deepcopy(self.fill_value), + "data_type": self.data_type.to_json(), + "chunk_grid": self.chunk_grid.to_json(), + "codecs": tuple(codec.to_json() for codec in self.codecs), + "chunk_key_encoding": self.chunk_key_encoding.to_json(), + } + if self.dimension_names is not UNSET: + out["dimension_names"] = self.dimension_names + if len(self.attributes) > 0: + out["attributes"] = copy.deepcopy(self.attributes) + if len(self.storage_transformers) > 0: + out["storage_transformers"] = tuple( + transformer.to_json() for transformer in self.storage_transformers + ) + # Extra fields are the TypedDict's `extra_items` (PEP 728). Assign them + # by key rather than `out.update(**...)`: type checkers understand the + # indexed-write path against `extra_items`, but not the `update(**...)` + # overload. + for key, value in self.extra_fields.items(): + out[key] = copy.deepcopy(value) + return out + + @classmethod + def from_json(cls, data: object) -> ZarrV3ArrayMetadata: + parsed = parse_array_metadata_v3(arrays_to_tuples(data)) + # Sound cast: the TypedDict types all non-standard keys as its + # `extra_items` (`ZarrV3ExtensionField`); the comprehension's inferred value + # type is the union over ALL keys because the key filter cannot narrow it. + extra_fields = cast( + "dict[str, ZarrV3ExtensionField]", + {k: v for k, v in parsed.items() if k not in ARRAY_METADATA_STANDARD_KEYS_V3}, + ) + return cls( + shape=parsed["shape"], + fill_value=parsed["fill_value"], + data_type=ZarrV3NamedConfig.from_json(parsed["data_type"]), + chunk_grid=ZarrV3NamedConfig.from_json(parsed["chunk_grid"]), + codecs=tuple(ZarrV3NamedConfig.from_json(c) for c in parsed["codecs"]), + chunk_key_encoding=ZarrV3NamedConfig.from_json(parsed["chunk_key_encoding"]), + dimension_names=parsed.get("dimension_names", UNSET), + attributes=dict(parsed.get("attributes", {})), + storage_transformers=tuple( + ZarrV3NamedConfig.from_json(t) for t in parsed.get("storage_transformers", ()) + ), + extra_fields=extra_fields, + ) + + @property + def must_understand_fields(self) -> dict[str, ZarrV3ExtensionField]: + """Extra fields the reader is obligated to understand. + + Everything in `extra_fields` not explicitly waived with + `must_understand: false` (the spec's implicit-true rule). A compliant + reader MUST fail to open the array if this contains any field it does + not recognize; the model layer only partitions by obligation, since + recognition is reader-specific. + """ + return must_understand_subset(self.extra_fields) + + @classmethod + def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV3ArrayMetadata: + return cls.from_json(load_store_json(mapping, ARRAY_METADATA_STORE_KEY_V3)) + + def to_key_value( + self, *, indent: int | str | None = None + ) -> Mapping[ZarrV3ArrayMetadataStoreKey, bytes]: + return {ARRAY_METADATA_STORE_KEY_V3: dump_store_json(self.to_json(), indent=indent)} + + +class ZarrV2ArrayMetadataPartial(TypedDict, total=False): + """ + Partial form of the constructor-settable fields of `ZarrV2ArrayMetadata`. + + Every key is optional and typed with the model's own value types, so it + describes valid keyword arguments to `ZarrV2ArrayMetadata.update` and + `create_default`. The `init=False` field `zarr_format` is intentionally + excluded, since it cannot be passed to `dataclasses.replace`. + + Drift between this type and the model's settable fields is prevented by + `tests/model/test_array.py::test_v2_partial_keys_match_settable_model_fields`. + """ + + shape: tuple[int, ...] + dtype: ZarrV2DataTypeMetadata + chunks: tuple[int, ...] + fill_value: JSONValue + order: ZarrV2ArrayOrder + compressor: ZarrV2CodecMetadata | None + filters: tuple[ZarrV2CodecMetadata, ...] | None + dimension_separator: ZarrV2ArrayDimensionSeparator + attributes: dict[str, JSONValue] | UNSET + + +@dataclass(frozen=True, slots=True, kw_only=True) +class ZarrV2ArrayMetadata: + """In-memory model of a v2 array metadata document. + + A canonical, lossless representation of the `.zarray` content plus the + sibling `.zattrs` attributes. `dtype`, `compressor`, and `filters` are + held in their raw JSON forms and are never interpreted; `fill_value` is + held verbatim in its JSON form. `attributes` is `UNSET` when no + `.zattrs` file (or merged `attributes` key) exists — distinct from an + explicit empty `.zattrs`, which is `{}` and round-trips as a file. One + spelling normalization: a `.zarray` that omits `dimension_separator` + means `"."` by the v2 convention, and the model holds and re-emits that + value explicitly. + """ + + zarr_format: Literal[2] = field(default=2, init=False) + shape: tuple[int, ...] + dtype: ZarrV2DataTypeMetadata + chunks: tuple[int, ...] + fill_value: JSONValue + order: ZarrV2ArrayOrder + compressor: ZarrV2CodecMetadata | None + filters: tuple[ZarrV2CodecMetadata, ...] | None + # "." is the v2 convention's default for an ABSENT dimension_separator key; + # from_json normalizes absence to it (a semantics-preserving spelling + # normalization, like the v3 bare-string metadata-field form). The value + # is never None: the document grammar has no null spelling for this field. + dimension_separator: ZarrV2ArrayDimensionSeparator = field(default=".") + attributes: dict[str, JSONValue] | UNSET + + def update(self, **kwargs: Unpack[ZarrV2ArrayMetadataPartial]) -> ZarrV2ArrayMetadata: + """ + Return a new `ZarrV2ArrayMetadata` with the given fields updated. + + Only the constructor-settable fields listed in + `ZarrV2ArrayMetadataPartial` can be updated; the fixed `zarr_format` is + rejected at the type level. Each given field fully replaces its previous + value. + """ + return dataclasses.replace(self, **kwargs) + + @classmethod + def create_default(cls, **overrides: Unpack[ZarrV2ArrayMetadataPartial]) -> ZarrV2ArrayMetadata: + """ + Create a default (empty) v2 array metadata model, with optional overrides. + + The default is a structurally-valid scalar `uint8` (`"|u1"`) array — the + array analog of `list()` returning `[]`. Any field can be overridden by + keyword (the same fields accepted by `update`). Overriding `shape` + without `chunks` derives `chunks` equal to `shape` (one chunk covering + the array). + + The derivation is deliberately one-way, matching the v3 model: + overriding `chunks` without `shape` keeps the scalar default + `shape=()`, and consistency between the two is the caller's + responsibility. + """ + if "shape" in overrides and "chunks" not in overrides: + overrides["chunks"] = tuple(overrides["shape"]) + default = cls( + shape=(), + dtype="|u1", + chunks=(), + fill_value=0, + order="C", + compressor=None, + filters=None, + attributes=UNSET, + ) + return default.update(**overrides) + + def to_json(self) -> ZarrV2ArrayMetadataJSON: + """Return the merged in-memory document form. + + `attributes` is included when set (even empty). This is not the + on-disk `.zarray` content: a conforming `.zarray` must exclude + `attributes` (they live in the sibling `.zattrs` file). Use + `to_key_value` to produce the spec-conforming split for storage. + """ + # to_json output shares no mutable state with the model: every value + # that can hold a mutable container is deep-copied. + out: ZarrV2ArrayMetadataJSON = { + "zarr_format": self.zarr_format, + "shape": self.shape, + "dtype": self.dtype, + "order": self.order, + "chunks": self.chunks, + "fill_value": copy.deepcopy(self.fill_value), + "dimension_separator": self.dimension_separator, + "compressor": copy.deepcopy(self.compressor), + "filters": copy.deepcopy(self.filters), + } + if self.attributes is not UNSET: + out["attributes"] = copy.deepcopy(self.attributes) + return out + + @classmethod + def from_json(cls, data: object) -> ZarrV2ArrayMetadata: + parsed = parse_array_metadata_v2(arrays_to_tuples(data)) + return cls( + shape=parsed["shape"], + dtype=parsed["dtype"], + chunks=parsed["chunks"], + fill_value=parsed["fill_value"], + order=parsed["order"], + compressor=parsed["compressor"], + filters=parsed["filters"], + dimension_separator=parsed.get("dimension_separator", "."), + attributes=(dict(parsed["attributes"]) if "attributes" in parsed else UNSET), + ) + + @classmethod + def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2ArrayMetadata: + zarray_raw = cast("object", load_store_json(mapping, ARRAY_METADATA_STORE_KEY_V2)) + if not isinstance(zarray_raw, Mapping): + return cls.from_json(zarray_raw) + zarray = cast("Mapping[str, object]", zarray_raw) + if "attributes" in zarray: + raise MetadataValidationError( + [ + ValidationProblem( + ("attributes",), + "unexpected document member", + "invalid_value", + ) + ] + ) + if ATTRIBUTES_STORE_KEY_V2 in mapping: + zattrs = cast("object", load_store_json(mapping, ATTRIBUTES_STORE_KEY_V2)) + return cls.from_json({**zarray, "attributes": zattrs}) + return cls.from_json(zarray) + + def to_key_value( + self, *, indent: int | str | None = None + ) -> Mapping[ZarrV2ArrayMetadataStoreKey | ZarrV2AttributesStoreKey, bytes]: + # Attributes live only in the sibling `.zattrs` file; the `.zarray` + # document must exclude them. The `.zattrs` key is present exactly + # when attributes are set (even empty) — UNSET emits no file. + zarray = {k: v for k, v in self.to_json().items() if k != "attributes"} + out: dict[ZarrV2ArrayMetadataStoreKey | ZarrV2AttributesStoreKey, bytes] = { + ARRAY_METADATA_STORE_KEY_V2: dump_store_json(zarray, indent=indent) + } + if self.attributes is not UNSET: + out[ATTRIBUTES_STORE_KEY_V2] = dump_store_json(self.attributes, indent=indent) + return out diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_group.py b/packages/zarr-metadata/src/zarr_metadata/model/_group.py new file mode 100644 index 0000000000..d576833c26 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/model/_group.py @@ -0,0 +1,442 @@ +"""In-memory models for Zarr group and consolidated metadata documents.""" + +from __future__ import annotations + +import copy +import dataclasses +from collections.abc import Mapping +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, Final, Literal, cast + +from typing_extensions import TypedDict, Unpack + +from zarr_metadata.model._array import ( + ATTRIBUTES_STORE_KEY_V2, + ZarrV3ArrayMetadata, + must_understand_subset, +) +from zarr_metadata.model._sentinel import UNSET +from zarr_metadata.model._validation import ( + GROUP_METADATA_STANDARD_KEYS_V3, + MetadataValidationError, + ValidationProblem, + arrays_to_tuples, + dump_store_json, + load_store_json, + parse_group_metadata_v2, + parse_group_metadata_v3, + validate_consolidated_metadata_v3, + validate_json, +) + +if TYPE_CHECKING: + from zarr_metadata._common import JSONValue + from zarr_metadata.model._array import ZarrV2AttributesStoreKey + from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON + from zarr_metadata.v3.array import ZarrV3ExtensionField + from zarr_metadata.v3.consolidated import ZarrV3ConsolidatedMetadataJSON + from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON + +ZarrV3GroupMetadataStoreKey = Literal["zarr.json"] +GROUP_METADATA_STORE_KEY_V3: Final[ZarrV3GroupMetadataStoreKey] = "zarr.json" + +ZarrV2GroupMetadataStoreKey = Literal[".zgroup"] +GROUP_METADATA_STORE_KEY_V2: Final[ZarrV2GroupMetadataStoreKey] = ".zgroup" + +ZarrV2ConsolidatedMetadataStoreKey = Literal[".zmetadata"] +CONSOLIDATED_METADATA_STORE_KEY_V2: Final[ZarrV2ConsolidatedMetadataStoreKey] = ".zmetadata" + +# The key under which consolidated metadata is embedded in a v3 group document. +# This is a reference-implementation convention (not a spec artifact), stored +# as an extension field on the group's `zarr.json`. +CONSOLIDATED_METADATA_KEY_V3: Final = "consolidated_metadata" + + +class ZarrV3GroupMetadataPartial(TypedDict, total=False): + """ + Partial form of the constructor-settable fields of `ZarrV3GroupMetadata`. + + Every key is optional and typed with the model's own value types, so it + describes valid keyword arguments to `ZarrV3GroupMetadata.update` and + `create_default`. The `init=False` fields `zarr_format` and `node_type` + are intentionally excluded, since they cannot be passed to + `dataclasses.replace`. + + Drift between this type and the model's settable fields is prevented by + `tests/model/test_group.py::test_group_partial_keys_match_settable_model_fields`. + """ + + attributes: dict[str, JSONValue] + consolidated_metadata: ZarrV3ConsolidatedMetadata | UNSET + extra_fields: dict[str, ZarrV3ExtensionField] + + +@dataclass(frozen=True, slots=True, kw_only=True) +class ZarrV3GroupMetadata: + """In-memory model of a v3 group metadata document. + + A canonical, semantically lossless representation of the `zarr.json` + content for a group. The `consolidated_metadata` reference-implementation + convention is modeled as a typed field holding thin child models; every + other unknown top-level key lands in `extra_fields` verbatim. + """ + + zarr_format: Literal[3] = field(default=3, init=False) + node_type: Literal["group"] = field(default="group", init=False) + attributes: dict[str, JSONValue] + consolidated_metadata: ZarrV3ConsolidatedMetadata | UNSET + extra_fields: dict[str, ZarrV3ExtensionField] + + def __post_init__(self) -> None: + reserved = GROUP_METADATA_STANDARD_KEYS_V3 | {CONSOLIDATED_METADATA_KEY_V3} + if set(self.extra_fields.keys()).intersection(reserved): + raise MetadataValidationError( + [ + ValidationProblem( + ("extra_fields",), + "Extra fields cannot overlap with standard Zarr V3 group metadata fields", + "invalid_value", + ) + ] + ) + + @classmethod + def create_default(cls, **overrides: Unpack[ZarrV3GroupMetadataPartial]) -> ZarrV3GroupMetadata: + """ + Create a default (empty) v3 group metadata model, with optional overrides. + + The default is a structurally-valid group with no attributes — the group + analog of `list()` returning `[]`. Any field can be overridden by keyword + (the same fields accepted by `update`). + """ + default = cls(attributes={}, consolidated_metadata=UNSET, extra_fields={}) + return default.update(**overrides) + + def update(self, **kwargs: Unpack[ZarrV3GroupMetadataPartial]) -> ZarrV3GroupMetadata: + """ + Return a new `ZarrV3GroupMetadata` with the given fields updated. + + Only the constructor-settable fields listed in + `ZarrV3GroupMetadataPartial` can be updated; the fixed `zarr_format` / + `node_type` are rejected at the type level. Each given field fully + replaces its previous value, including `extra_fields`. + """ + return dataclasses.replace(self, **kwargs) + + def to_json(self) -> ZarrV3GroupMetadataJSON: + # to_json output shares no mutable state with the model: every value + # that can hold a mutable container is deep-copied. + out: ZarrV3GroupMetadataJSON = { + "zarr_format": self.zarr_format, + "node_type": self.node_type, + } + if len(self.attributes) > 0: + out["attributes"] = copy.deepcopy(self.attributes) + if self.consolidated_metadata is not UNSET: + # Consolidated metadata is a known non-core top-level JSON field. + out[CONSOLIDATED_METADATA_KEY_V3] = cast( + "ZarrV3ExtensionField", self.consolidated_metadata.to_json() + ) + for key, value in self.extra_fields.items(): + out[key] = copy.deepcopy(value) + return out + + @classmethod + def from_json(cls, data: object) -> ZarrV3GroupMetadata: + parsed = parse_group_metadata_v3(arrays_to_tuples(data)) + # Cast for narrowing across standard and arbitrary extra TypedDict items. + consolidated_raw = cast("object", parsed.get(CONSOLIDATED_METADATA_KEY_V3, UNSET)) + consolidated: ZarrV3ConsolidatedMetadata | UNSET + if consolidated_raw is UNSET or consolidated_raw is None: + # consolidated_metadata: null was written by a historical + # zarr-python bug; it gets no model representation. It is read as + # absence and never written back — repaired, not preserved. + consolidated = UNSET + else: + consolidated = ZarrV3ConsolidatedMetadata.from_json(consolidated_raw) + # Sound cast: the TypedDict types all non-standard keys as its + # `extra_items` (`ZarrV3ExtensionField`); the comprehension's inferred value + # type is the union over ALL keys because the key filter cannot narrow it. + extra_fields = cast( + "dict[str, ZarrV3ExtensionField]", + { + k: v + for k, v in parsed.items() + if k not in GROUP_METADATA_STANDARD_KEYS_V3 and k != CONSOLIDATED_METADATA_KEY_V3 + }, + ) + return cls( + attributes=dict(parsed.get("attributes", {})), + consolidated_metadata=consolidated, + extra_fields=extra_fields, + ) + + @property + def must_understand_fields(self) -> dict[str, ZarrV3ExtensionField]: + """Extra fields the reader is obligated to understand. + + Everything in `extra_fields` not explicitly waived with + `must_understand: false` (the spec's implicit-true rule). A compliant + reader MUST fail to open the group if this contains any field it does + not recognize; the model layer only partitions by obligation, since + recognition is reader-specific. + """ + return must_understand_subset(self.extra_fields) + + @classmethod + def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV3GroupMetadata: + return cls.from_json(load_store_json(mapping, GROUP_METADATA_STORE_KEY_V3)) + + def to_key_value( + self, *, indent: int | str | None = None + ) -> Mapping[ZarrV3GroupMetadataStoreKey, bytes]: + return {GROUP_METADATA_STORE_KEY_V3: dump_store_json(self.to_json(), indent=indent)} + + +@dataclass(frozen=True, slots=True, kw_only=True) +class ZarrV3ConsolidatedMetadata: + """In-memory model of v3 inline consolidated metadata. + + Models the reference-implementation convention where consolidated metadata + is embedded as an extension field on a group's `zarr.json`. Each entry in + `metadata` is a complete child document, held as a thin array or group + model. `must_understand` is typed permissively as `bool` to mirror the + document shape, but only `False` is valid; this is enforced at runtime. + """ + + kind: Literal["inline"] = field(default="inline", init=False) + must_understand: bool = False + metadata: dict[str, ZarrV3ArrayMetadata | ZarrV3GroupMetadata] + + def __post_init__(self) -> None: + if self.must_understand is not False: + raise MetadataValidationError( + [ + ValidationProblem( + ("must_understand",), + f"Invalid value for 'must_understand'. Expected False. " + f"Got {self.must_understand!r}.", + "invalid_value", + ) + ] + ) + + def to_json(self) -> ZarrV3ConsolidatedMetadataJSON: + # `must_understand` is emitted as the literal False: the field is typed + # permissively as `bool`, but `__post_init__` guarantees the value. + return { + "kind": self.kind, + "must_understand": False, + "metadata": {key: node.to_json() for key, node in self.metadata.items()}, + } + + @classmethod + def from_json(cls, data: object) -> ZarrV3ConsolidatedMetadata: + normalized = arrays_to_tuples(data) + problems = validate_consolidated_metadata_v3(normalized) + if problems: + raise MetadataValidationError(problems) + env = cast("Mapping[str, object]", normalized) + entries: dict[str, ZarrV3ArrayMetadata | ZarrV3GroupMetadata] = {} + for key, entry in cast("Mapping[str, object]", env["metadata"]).items(): + node_type = cast("Mapping[str, object]", entry).get("node_type") + if node_type == "array": + entries[key] = ZarrV3ArrayMetadata.from_json(entry) + else: + entries[key] = ZarrV3GroupMetadata.from_json(entry) + return cls(metadata=entries) + + +class ZarrV2GroupMetadataPartial(TypedDict, total=False): + """ + Partial form of the constructor-settable fields of `ZarrV2GroupMetadata`. + + Every key is optional and typed with the model's own value types, so it + describes valid keyword arguments to `ZarrV2GroupMetadata.update` and + `create_default`. The `init=False` field `zarr_format` is intentionally + excluded, since it cannot be passed to `dataclasses.replace`. + + Drift between this type and the model's settable fields is prevented by + `tests/model/test_group.py::test_group_partial_keys_match_settable_model_fields`. + """ + + attributes: dict[str, JSONValue] | UNSET + + +@dataclass(frozen=True, slots=True, kw_only=True) +class ZarrV2GroupMetadata: + """In-memory model of a v2 group metadata document. + + A canonical, lossless representation of the `.zgroup` content plus the + sibling `.zattrs` attributes, folded into a single in-memory value + (mirroring the merged `ZarrV2GroupMetadataJSON` document form). `attributes` is + `UNSET` when no `.zattrs` file (or merged `attributes` key) exists — + distinct from an explicit empty `.zattrs`, which is `{}` and round-trips + as a file. + """ + + zarr_format: Literal[2] = field(default=2, init=False) + attributes: dict[str, JSONValue] | UNSET + + @classmethod + def create_default(cls, **overrides: Unpack[ZarrV2GroupMetadataPartial]) -> ZarrV2GroupMetadata: + """ + Create a default (empty) v2 group metadata model, with optional overrides. + + The default is a structurally-valid group with no attributes — the group + analog of `list()` returning `[]`. Any field can be overridden by keyword + (the same fields accepted by `update`). + """ + default = cls(attributes=UNSET) + return default.update(**overrides) + + def update(self, **kwargs: Unpack[ZarrV2GroupMetadataPartial]) -> ZarrV2GroupMetadata: + """ + Return a new `ZarrV2GroupMetadata` with the given fields updated. + + Only the constructor-settable fields listed in + `ZarrV2GroupMetadataPartial` can be updated; the fixed `zarr_format` + is rejected at the type level. Each given field fully replaces its + previous value. + """ + return dataclasses.replace(self, **kwargs) + + def to_json(self) -> ZarrV2GroupMetadataJSON: + """Return the merged in-memory document form. + + `attributes` is included when set (even empty). This is not the + on-disk `.zgroup` content: a conforming `.zgroup` must exclude + `attributes` (they live in the sibling `.zattrs` file). Use + `to_key_value` to produce the spec-conforming split for storage. + """ + # to_json output shares no mutable state with the model. + out: ZarrV2GroupMetadataJSON = {"zarr_format": self.zarr_format} + if self.attributes is not UNSET: + out["attributes"] = copy.deepcopy(self.attributes) + return out + + @classmethod + def from_json(cls, data: object) -> ZarrV2GroupMetadata: + parsed = parse_group_metadata_v2(arrays_to_tuples(data)) + return cls(attributes=(dict(parsed["attributes"]) if "attributes" in parsed else UNSET)) + + @classmethod + def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2GroupMetadata: + zgroup_raw = cast("object", load_store_json(mapping, GROUP_METADATA_STORE_KEY_V2)) + if not isinstance(zgroup_raw, Mapping): + return cls.from_json(zgroup_raw) + zgroup = cast("Mapping[str, object]", zgroup_raw) + if "attributes" in zgroup: + raise MetadataValidationError( + [ + ValidationProblem( + ("attributes",), + "unexpected document member", + "invalid_value", + ) + ] + ) + if ATTRIBUTES_STORE_KEY_V2 in mapping: + zattrs = cast("object", load_store_json(mapping, ATTRIBUTES_STORE_KEY_V2)) + return cls.from_json({**zgroup, "attributes": zattrs}) + return cls.from_json(zgroup) + + def to_key_value( + self, *, indent: int | str | None = None + ) -> Mapping[ZarrV2GroupMetadataStoreKey | ZarrV2AttributesStoreKey, bytes]: + # Attributes live only in the sibling `.zattrs` file; the `.zgroup` + # document must exclude them. The `.zattrs` key is present exactly + # when attributes are set (even empty) — UNSET emits no file. + zgroup = {k: v for k, v in self.to_json().items() if k != "attributes"} + out: dict[ZarrV2GroupMetadataStoreKey | ZarrV2AttributesStoreKey, bytes] = { + GROUP_METADATA_STORE_KEY_V2: dump_store_json(zgroup, indent=indent) + } + if self.attributes is not UNSET: + out[ATTRIBUTES_STORE_KEY_V2] = dump_store_json(self.attributes, indent=indent) + return out + + +@dataclass(frozen=True, slots=True, kw_only=True) +class ZarrV2ConsolidatedMetadata: + """In-memory model of a v2 `.zmetadata` document. + + The `metadata` map holds the flat file-keyed entries (`"path/.zarray"`, + `"path/.zattrs"`, ...) verbatim, preserving the normalized JSON tree. + Entries are deliberately NOT merged into per-node models: which nodes had + a `.zattrs` file at all is information the canonical representation must + keep. Interpreting entries into node models is consumer work. + """ + + zarr_consolidated_format: Literal[1] = field(default=1, init=False) + metadata: dict[str, JSONValue] + + def to_json(self) -> dict[str, JSONValue]: + # to_json output shares no mutable state with the model. + return { + "zarr_consolidated_format": self.zarr_consolidated_format, + "metadata": copy.deepcopy(self.metadata), + } + + @classmethod + def from_json(cls, data: object) -> ZarrV2ConsolidatedMetadata: + normalized = arrays_to_tuples(data) + if not isinstance(normalized, Mapping): + raise MetadataValidationError( + [ValidationProblem((), "expected a mapping", "invalid_type")] + ) + doc = cast("Mapping[str, object]", normalized) + problems: list[ValidationProblem] = [ + ValidationProblem((key,), "missing required key", "missing_key") + for key in ("zarr_consolidated_format", "metadata") + if key not in doc + ] + problems.extend( + ValidationProblem((key,), "unexpected document member", "invalid_value") + for key in doc.keys() - {"zarr_consolidated_format", "metadata"} + ) + if "zarr_consolidated_format" in doc and ( + not isinstance(doc["zarr_consolidated_format"], int) + or isinstance(doc["zarr_consolidated_format"], bool) + or doc["zarr_consolidated_format"] != 1 + ): + problems.append( + ValidationProblem( + ("zarr_consolidated_format",), + f"expected 1, got {doc['zarr_consolidated_format']!r}", + "invalid_value", + ) + ) + if "metadata" in doc: + entries = doc["metadata"] + if not isinstance(entries, Mapping) or not all( + isinstance(k, str) for k in cast("Mapping[object, object]", entries) + ): + problems.append( + ValidationProblem( + ("metadata",), "expected a mapping with string keys", "invalid_type" + ) + ) + else: + for key, value in cast("Mapping[str, object]", entries).items(): + problems.extend( + ValidationProblem( + ("metadata", key, *problem.loc), problem.message, problem.kind + ) + for problem in validate_json(value) + ) + if problems: + raise MetadataValidationError(problems) + entries_tupled = cast( + "dict[str, JSONValue]", + arrays_to_tuples(dict(cast("Mapping[str, object]", doc["metadata"]))), + ) + return cls(metadata=entries_tupled) + + @classmethod + def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2ConsolidatedMetadata: + return cls.from_json(load_store_json(mapping, CONSOLIDATED_METADATA_STORE_KEY_V2)) + + def to_key_value( + self, *, indent: int | str | None = None + ) -> Mapping[ZarrV2ConsolidatedMetadataStoreKey, bytes]: + return {CONSOLIDATED_METADATA_STORE_KEY_V2: dump_store_json(self.to_json(), indent=indent)} diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_sentinel.py b/packages/zarr-metadata/src/zarr_metadata/model/_sentinel.py new file mode 100644 index 0000000000..ad71e216fa --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/model/_sentinel.py @@ -0,0 +1,37 @@ +"""The absence sentinel for optional metadata-document keys. + +The models observe one invariant: `None` in a model always corresponds to a +JSON `null` in the document (a v2 `compressor`/`filters` value, an unnamed +dimension inside `dimension_names`), and `UNSET` always means the document +key is absent. The two are never interchangeable, so a model value can never +leak into a document as a spelling the writer did not intend. + +Check with identity: `if model.dimension_names is UNSET: ...`. + +Because the contract is identity, the sentinel must never be reconstructed +from state: pickling and copying work by *reference* (typing_extensions >= +4.16 implements `Sentinel.__reduce__` as a lookup of the sentinel's name on +its defining module), so `pickle.loads(pickle.dumps(UNSET)) is UNSET` holds +across process boundaries, and models holding `UNSET` pickle and deep-copy +freely. Earlier typing_extensions releases refused to pickle sentinels +outright — hence the `>=4.16` floor in this package's dependencies. + +Checker support (PEP 661 is Final; stdlib `sentinel` arrives in Python +3.15): ty types this spelling exactly, including `is`/`is not` narrowing. +Pyright supports it but a regression (1.1.405+, tracked as +https://github.com/microsoft/pyright/issues/11115) degrades class-attribute +reads to `Unknown`, so this package pins pyright to the last good version +until the fix lands. Mypy support is in review +(https://github.com/python/mypy/pull/21647); until it merges, mypy-checked +consumers of these fields need a `cast` or `type: ignore` at narrowing +sites. This is a deliberate short-term cost: the sentinel is the standard, +and the checkers are converging on it. +""" + +from __future__ import annotations + +from typing_extensions import Sentinel + +UNSET = Sentinel("UNSET") +"""Marks a metadata-document key as absent (PEP 661 sentinel; usable directly +in type expressions, e.g. `tuple[str, ...] | UNSET`). Test with `is UNSET`.""" diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_validation.py b/packages/zarr-metadata/src/zarr_metadata/model/_validation.py new file mode 100644 index 0000000000..a12e1911b1 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/model/_validation.py @@ -0,0 +1,875 @@ +"""Structural validation for Zarr metadata documents. + +Validators check JSON structure (key presence, value shapes, and fixed +literals like `zarr_format`), not domain validity. Each concept gets a +`validate_*` function returning every problem found, an `is_*` type guard, +and a `parse_*` function that narrows or raises `MetadataValidationError`. + +Every `ValidationProblem` carries a machine-readable `kind` alongside its +human-readable `message`, so consumers can dispatch on the failure mode +(`missing_key`, `invalid_type`, `invalid_value`, `invalid_json`) without +string-matching messages. +""" + +from __future__ import annotations + +import json +import math +from collections.abc import Mapping, Sequence +from dataclasses import dataclass +from typing import Any, Final, Literal, NoReturn, cast + +from typing_extensions import TypeIs + +from zarr_metadata._common import JSONValue +from zarr_metadata.v2.array import ZarrV2ArrayMetadataJSON +from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON +from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON +from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON + +ProblemKind = Literal["missing_key", "invalid_type", "invalid_value", "invalid_json"] +"""Machine-readable classification of a `ValidationProblem`. + +- `missing_key`: a required key (document key or store key) is absent. +- `invalid_type`: a value has the wrong structural type (e.g. a string where + a mapping is required, a non-JSON-serializable object). +- `invalid_value`: a value has an acceptable type but an invalid content + (e.g. `zarr_format: 2` in a v3 document, `order: "Q"`). +- `invalid_json`: bytes that do not decode as JSON. +""" + + +@dataclass(frozen=True, slots=True) +class ValidationProblem: + """A single structural problem found while validating a metadata document. + + `loc` is the path from the document root to the offending value, e.g. + `("codecs", 0, "name")`. An empty `loc` refers to the document as a whole. + `kind` classifies the failure mode for programmatic dispatch; `message` + is the human-readable description. + """ + + loc: tuple[str | int, ...] + message: str + kind: ProblemKind + + def __str__(self) -> str: + location = ".".join(str(part) for part in self.loc) if self.loc else "<root>" + return f"{location}: {self.message}" + + +class MetadataValidationError(ValueError): + """Raised when a value fails structural metadata validation. + + Carries every problem found (not just the first) in `.problems`. + """ + + def __init__(self, problems: list[ValidationProblem]) -> None: + self.problems = problems + super().__init__("\n".join(str(problem) for problem in problems)) + + +def _prefix(loc_head: str | int, problems: list[ValidationProblem]) -> list[ValidationProblem]: + """Prepend `loc_head` to the `loc` of every problem (for nested validators).""" + return [ValidationProblem((loc_head, *p.loc), p.message, p.kind) for p in problems] + + +def validate_json(value: object) -> list[ValidationProblem]: + """Return every reason `value` is not JSON-serializable (recursively).""" + if isinstance(value, float): + if math.isfinite(value): + return [] + return [ValidationProblem((), f"non-finite float {value!r} is not JSON", "invalid_value")] + if isinstance(value, (str, int, bool)) or value is None: + return [] + problems: list[ValidationProblem] = [] + if isinstance(value, Mapping): + for key, item in cast("Mapping[object, object]", value).items(): + if not isinstance(key, str): + problems.append( + ValidationProblem((), f"non-string key {key!r} in JSON object", "invalid_type") + ) + continue + problems.extend(_prefix(key, validate_json(item))) + return problems + if isinstance(value, Sequence) and not isinstance(value, (bytes, bytearray)): + for index, item in enumerate(cast("Sequence[object]", value)): + problems.extend(_prefix(index, validate_json(item))) + return problems + return [ValidationProblem((), f"not a JSON-serializable value: {value!r}", "invalid_type")] + + +def _is_canonical_json(value: object) -> TypeIs[JSONValue]: + """Whether `value` already uses the concrete containers in `JSONValue`.""" + if isinstance(value, float): + return math.isfinite(value) + if isinstance(value, (str, int, bool)) or value is None: + return True + if isinstance(value, (list, tuple)): + sequence = cast("list[object] | tuple[object, ...]", value) + return all(_is_canonical_json(item) for item in sequence) + if isinstance(value, dict): + mapping = cast("dict[object, object]", value) + return all( + isinstance(key, str) and _is_canonical_json(item) for key, item in mapping.items() + ) + return False + + +def is_json(value: object) -> TypeIs[JSONValue]: + """Whether `value` is a canonical JSON structure (recursively).""" + return _is_canonical_json(value) + + +def parse_json(value: object) -> JSONValue: + """Return a canonical `JSONValue`, or raise `MetadataValidationError`.""" + normalized = arrays_to_tuples(value) + problems = validate_json(normalized) + if problems: + raise MetadataValidationError(problems) + return cast(JSONValue, normalized) + + +# The standard top-level keys of a v3 array metadata document. Anything outside +# this set is an extension field. Built from the TypedDict's required/optional +# key sets (which resolve inherited keys, unlike `__annotations__`). +ARRAY_METADATA_REQUIRED_KEYS_V3: Final[frozenset[str]] = frozenset( + ZarrV3ArrayMetadataJSON.__required_keys__ +) +ARRAY_METADATA_OPTIONAL_KEYS_V3: Final[frozenset[str]] = frozenset( + ZarrV3ArrayMetadataJSON.__optional_keys__ +) +ARRAY_METADATA_STANDARD_KEYS_V3: Final[frozenset[str]] = ( + ARRAY_METADATA_REQUIRED_KEYS_V3 | ARRAY_METADATA_OPTIONAL_KEYS_V3 +) + +ARRAY_METADATA_REQUIRED_KEYS_V2: Final[frozenset[str]] = frozenset( + ZarrV2ArrayMetadataJSON.__required_keys__ +) +ARRAY_METADATA_OPTIONAL_KEYS_V2: Final[frozenset[str]] = frozenset( + ZarrV2ArrayMetadataJSON.__optional_keys__ +) +ARRAY_METADATA_STANDARD_KEYS_V2: Final[frozenset[str]] = ( + ARRAY_METADATA_REQUIRED_KEYS_V2 | ARRAY_METADATA_OPTIONAL_KEYS_V2 +) + +# The standard top-level keys of a v3 group metadata document. Anything outside +# this set is an extension field. +GROUP_METADATA_REQUIRED_KEYS_V3: Final[frozenset[str]] = frozenset( + ZarrV3GroupMetadataJSON.__required_keys__ +) +GROUP_METADATA_OPTIONAL_KEYS_V3: Final[frozenset[str]] = frozenset( + ZarrV3GroupMetadataJSON.__optional_keys__ +) +GROUP_METADATA_STANDARD_KEYS_V3: Final[frozenset[str]] = ( + GROUP_METADATA_REQUIRED_KEYS_V3 | GROUP_METADATA_OPTIONAL_KEYS_V3 +) + +GROUP_METADATA_REQUIRED_KEYS_V2: Final[frozenset[str]] = frozenset( + ZarrV2GroupMetadataJSON.__required_keys__ +) +GROUP_METADATA_OPTIONAL_KEYS_V2: Final[frozenset[str]] = frozenset( + ZarrV2GroupMetadataJSON.__optional_keys__ +) +GROUP_METADATA_STANDARD_KEYS_V2: Final[frozenset[str]] = ( + GROUP_METADATA_REQUIRED_KEYS_V2 | GROUP_METADATA_OPTIONAL_KEYS_V2 +) + + +def _missing_keys(required: frozenset[str], doc: Mapping[str, object]) -> list[ValidationProblem]: + """One `missing_key` problem per required key absent from `doc`.""" + return [ + ValidationProblem((key,), "missing required key", "missing_key") + for key in sorted(required - doc.keys()) + ] + + +def _unexpected_keys( + allowed: frozenset[str], doc: Mapping[object, object] +) -> list[ValidationProblem]: + """One problem per member outside a closed document's declared shape.""" + problems: list[ValidationProblem] = [] + for key in doc: + if not isinstance(key, str): + problems.append( + ValidationProblem((), f"non-string document key {key!r}", "invalid_type") + ) + elif key not in allowed: + problems.append( + ValidationProblem((key,), "unexpected document member", "invalid_value") + ) + return problems + + +def _check_literal( + doc: Mapping[str, object], key: str, expected: object +) -> list[ValidationProblem]: + """One `invalid_value` problem if `doc[key]` is present but not `expected`.""" + if key in doc and (type(doc[key]) is not type(expected) or doc[key] != expected): + return [ + ValidationProblem((key,), f"expected {expected!r}, got {doc[key]!r}", "invalid_value") + ] + return [] + + +def _validate_extension_fields_v3( + doc: Mapping[object, object], + standard_keys: frozenset[str], + *, + additional_reserved_keys: frozenset[str] = frozenset(), +) -> list[ValidationProblem]: + """Validate v3 top-level key types and unknown-field JSON payloads.""" + problems: list[ValidationProblem] = [] + reserved_keys = standard_keys | additional_reserved_keys + for key, value in doc.items(): + if not isinstance(key, str): + problems.append( + ValidationProblem((), f"non-string top-level key {key!r}", "invalid_type") + ) + continue + if key in reserved_keys: + continue + problems.extend(_prefix(key, validate_json(value))) + return problems + + +def validate_metadata_field_v3( + value: object, *, allow_must_understand_false: bool = True +) -> list[ValidationProblem]: + """Return every reason `value` is not a v3 metadata field. + + A metadata field is a bare name string or a mapping containing `name` and + optional `configuration` and `must_understand` members. + """ + if isinstance(value, str): + return [] + if not isinstance(value, Mapping): + return [ + ValidationProblem( + (), + "expected a metadata field (string or extension object)", + "invalid_type", + ) + ] + field = cast("Mapping[object, object]", value) + problems: list[ValidationProblem] = [] + allowed_keys = frozenset({"name", "configuration", "must_understand"}) + for key in field: + if not isinstance(key, str): + problems.append( + ValidationProblem((), f"non-string metadata field key {key!r}", "invalid_type") + ) + elif key not in allowed_keys: + problems.append( + ValidationProblem((key,), "unexpected metadata field member", "invalid_value") + ) + if not isinstance(field.get("name"), str): + problems.append(ValidationProblem(("name",), "expected a string name", "invalid_type")) + if "configuration" in field: + configuration = field["configuration"] + if not isinstance(configuration, Mapping): + problems.append( + ValidationProblem(("configuration",), "expected a mapping", "invalid_type") + ) + elif not all(isinstance(k, str) for k in cast("Mapping[object, object]", configuration)): + problems.append( + ValidationProblem(("configuration",), "expected string keys", "invalid_type") + ) + else: + for key, item in cast("Mapping[str, object]", configuration).items(): + problems.extend(_prefix("configuration", _prefix(key, validate_json(item)))) + if "must_understand" in field: + must_understand = field["must_understand"] + if not isinstance(must_understand, bool): + problems.append( + ValidationProblem(("must_understand",), "expected a boolean", "invalid_type") + ) + elif not allow_must_understand_false and not must_understand: + problems.append( + ValidationProblem( + ("must_understand",), + "false is not supported at this extension point", + "invalid_value", + ) + ) + return problems + + +def is_metadata_field_v3(value: object) -> TypeIs[ZarrV3MetadataFieldJSON]: + """Whether `value` is a v3 metadata field: a bare name or a named config.""" + if isinstance(value, str): + return True + if not isinstance(value, dict): + return False + field = cast("dict[object, object]", value) + return _is_canonical_json(field) and not validate_metadata_field_v3(field) + + +def parse_metadata_field_v3(value: object) -> ZarrV3MetadataFieldJSON: + """Return `value` narrowed to `ZarrV3MetadataFieldJSON`, or raise `MetadataValidationError`.""" + normalized = arrays_to_tuples(value) + problems = validate_metadata_field_v3(normalized) + if problems: + raise MetadataValidationError(problems) + return cast(ZarrV3MetadataFieldJSON, normalized) + + +def _is_int_sequence(value: object) -> bool: + """Whether `value` is a non-string sequence of integers. + + JSON booleans decode to `bool`, which is an `int` subclass in Python but + is not an integer in a metadata document, so booleans are excluded. + """ + return ( + not isinstance(value, (str, bytes, bytearray)) + and isinstance(value, Sequence) + and all( + isinstance(item, int) and not isinstance(item, bool) + for item in cast("Sequence[object]", value) + ) + ) + + +def _validate_dim_sequence(doc: Mapping[str, object], key: str) -> list[ValidationProblem]: + """Validate a dimension sequence (`shape` / `chunks`) if present in `doc`. + + Dimension lengths are non-negative integers. + """ + if key not in doc: + return [] + value = doc[key] + if not _is_int_sequence(value): + return [ValidationProblem((key,), "expected a sequence of int", "invalid_type")] + if any(item < 0 for item in cast("Sequence[int]", value)): + return [ValidationProblem((key,), "expected non-negative integers", "invalid_value")] + return [] + + +def _is_dtype_v2(value: object) -> bool: + """Whether `value` is shaped like a v2 dtype: a string or field records. + + A field record is a `(name, dtype)` or `(name, dtype, shape)` sequence, + where `dtype` is itself a string or nested field records and `shape` is a + sequence of int. The string content is NOT interpreted — whether the + string names a real dtype is domain validity, not structure. + """ + if isinstance(value, str): + return True + if not isinstance(value, Sequence): + return False + for record in cast("Sequence[object]", value): + if isinstance(record, str) or not isinstance(record, Sequence): + return False + fields = cast("Sequence[object]", record) + if len(fields) not in (2, 3): + return False + if not isinstance(fields[0], str): + return False + if not _is_dtype_v2(fields[1]): + return False + if len(fields) == 3 and not _is_int_sequence(fields[2]): + return False + return True + + +def _is_canonical_dtype_v2(value: object) -> bool: + """Whether a validated v2 dtype uses the tuple-backed public representation.""" + if isinstance(value, str): + return True + if not isinstance(value, tuple): + return False + for record in cast("tuple[object, ...]", value): + if not isinstance(record, tuple): + return False + fields = cast("tuple[object, ...]", record) + if not _is_canonical_dtype_v2(fields[1]): + return False + if len(fields) == 3 and not isinstance(fields[2], tuple): + return False + return True + + +def _is_canonical_metadata_field_v3(value: object) -> bool: + """Whether a validated v3 metadata field has its declared runtime container type.""" + return isinstance(value, (str, dict)) + + +def _is_canonical_array_metadata_v3(value: object) -> bool: + """Whether a validated v3 array document matches `ZarrV3ArrayMetadataJSON` at runtime.""" + if not isinstance(value, dict): + return False + doc = cast("dict[str, object]", value) + if not isinstance(doc["shape"], tuple) or not isinstance(doc["codecs"], tuple): + return False + if "storage_transformers" in doc and not isinstance(doc["storage_transformers"], tuple): + return False + if "dimension_names" in doc and not isinstance(doc["dimension_names"], tuple): + return False + if not all( + _is_canonical_metadata_field_v3(doc[key]) + for key in ("data_type", "chunk_grid", "chunk_key_encoding") + ): + return False + if not all( + _is_canonical_metadata_field_v3(item) for item in cast("tuple[object, ...]", doc["codecs"]) + ): + return False + return "storage_transformers" not in doc or all( + _is_canonical_metadata_field_v3(item) + for item in cast("tuple[object, ...]", doc["storage_transformers"]) + ) + + +def _is_canonical_array_metadata_v2(value: object) -> bool: + """Whether a validated v2 array document matches `ZarrV2ArrayMetadataJSON` at runtime.""" + if not isinstance(value, dict): + return False + doc = cast("dict[str, object]", value) + if not isinstance(doc["shape"], tuple) or not isinstance(doc["chunks"], tuple): + return False + if not _is_canonical_dtype_v2(doc["dtype"]): + return False + compressor = doc["compressor"] + if compressor is not None and not isinstance(compressor, dict): + return False + filters = doc["filters"] + return filters is None or ( + isinstance(filters, tuple) + and all(isinstance(item, dict) for item in cast("tuple[object, ...]", filters)) + ) + + +def _is_codec_v2(value: object) -> bool: + """Whether `value` is shaped like a v2 codec config: a mapping with a string `id`.""" + return isinstance(value, Mapping) and isinstance( + cast("Mapping[object, object]", value).get("id"), str + ) + + +def _validate_codec_v2(value: object) -> list[ValidationProblem]: + """Validate a v2 codec's required shape and JSON-valued configuration.""" + if not _is_codec_v2(value): + return [ + ValidationProblem( + (), "expected a codec configuration with a string 'id'", "invalid_type" + ) + ] + return validate_json(value) + + +def _validate_attributes(value: object) -> list[ValidationProblem]: + """Validate an `attributes` value: a mapping with string keys. + + Returns a problem at `("attributes",)` if it is not, else `[]`. Shared by the + v2 and v3 validators. Unlike the other `validate_*` functions (which + return value-relative locs for the caller to `_prefix`), this emits the + already-parent-relative `("attributes",)` loc, since it is only ever called + with a document's `attributes` value. + """ + if not isinstance(value, Mapping) or not all( + isinstance(k, str) for k in cast("Mapping[object, object]", value) + ): + return [ + ValidationProblem( + ("attributes",), "expected a mapping with string keys", "invalid_type" + ) + ] + problems: list[ValidationProblem] = [] + for key, item in cast("Mapping[str, object]", value).items(): + problems.extend(_prefix("attributes", _prefix(key, validate_json(item)))) + return problems + + +def validate_array_metadata_v3(value: object) -> list[ValidationProblem]: + """Return every reason `value` is not a structurally-valid v3 array doc. + + Checks structure, not domain validity. Unknown top-level keys are allowed + (they map to `extra_fields`). + """ + if not isinstance(value, Mapping): + return [ValidationProblem((), "expected a mapping", "invalid_type")] + doc = cast("Mapping[str, object]", value) + problems: list[ValidationProblem] = _missing_keys(ARRAY_METADATA_REQUIRED_KEYS_V3, doc) + problems.extend( + _validate_extension_fields_v3( + cast("Mapping[object, object]", value), ARRAY_METADATA_STANDARD_KEYS_V3 + ) + ) + problems.extend(_check_literal(doc, "zarr_format", 3)) + problems.extend(_check_literal(doc, "node_type", "array")) + problems.extend(_validate_dim_sequence(doc, "shape")) + if "fill_value" in doc: + problems.extend(_prefix("fill_value", validate_json(doc["fill_value"]))) + for key in ("data_type", "chunk_grid", "chunk_key_encoding"): + if key in doc: + problems.extend( + _prefix( + key, + validate_metadata_field_v3(doc[key], allow_must_understand_false=False), + ) + ) + for key in ("codecs", "storage_transformers"): + if key in doc: + entries = doc[key] + if isinstance(entries, str) or not isinstance(entries, Sequence): + problems.append(ValidationProblem((key,), "expected a sequence", "invalid_type")) + else: + if key == "codecs" and len(cast("Sequence[object]", entries)) == 0: + problems.append( + ValidationProblem( + ("codecs",), "expected at least one codec", "invalid_value" + ) + ) + for index, entry in enumerate(cast("Sequence[object]", entries)): + problems.extend(_prefix(key, _prefix(index, validate_metadata_field_v3(entry)))) + if "attributes" in doc: + problems.extend(_validate_attributes(doc["attributes"])) + if "dimension_names" in doc: + # Simple typed sequences (dimension_names, shape, chunks) report a single + # field-level loc, not per-bad-item locs; per-index locs are reserved for + # the metadata-field lists (codecs, storage_transformers). + names = doc["dimension_names"] + if isinstance(names, str) or not isinstance(names, Sequence): + problems.append( + ValidationProblem(("dimension_names",), "expected a sequence", "invalid_type") + ) + elif not all( + item is None or isinstance(item, str) for item in cast("Sequence[object]", names) + ): + problems.append( + ValidationProblem( + ("dimension_names",), "expected items of str or None", "invalid_type" + ) + ) + elif _is_int_sequence(doc.get("shape")) and len(cast("Sequence[object]", names)) != len( + cast("Sequence[int]", doc["shape"]) + ): + problems.append( + ValidationProblem( + ("dimension_names",), + "expected one name per dimension of shape", + "invalid_value", + ) + ) + return problems + + +def is_array_metadata_v3(value: object) -> TypeIs[ZarrV3ArrayMetadataJSON]: + """Whether `value` is a structurally-valid v3 array metadata document.""" + return ( + _is_canonical_json(value) + and not validate_array_metadata_v3(value) + and _is_canonical_array_metadata_v3(value) + ) + + +def parse_array_metadata_v3(value: object) -> ZarrV3ArrayMetadataJSON: + """Return `value` as `ZarrV3ArrayMetadataJSON`, or raise `MetadataValidationError`.""" + normalized = arrays_to_tuples(value) + problems = validate_array_metadata_v3(normalized) + if problems: + raise MetadataValidationError(problems) + return cast("ZarrV3ArrayMetadataJSON", normalized) + + +def validate_array_metadata_v2(value: object) -> list[ValidationProblem]: + """Return every reason `value` is not a structurally-valid v2 array doc. + + Checks structure, not domain validity: `dtype` must be a string or field + records, but the string content is not interpreted; `compressor` and + `filters` are required keys that may be `None`, and otherwise must be + codec configurations (mappings with a string `id`). + """ + if not isinstance(value, Mapping): + return [ValidationProblem((), "expected a mapping", "invalid_type")] + doc = cast("Mapping[str, object]", value) + problems: list[ValidationProblem] = _missing_keys(ARRAY_METADATA_REQUIRED_KEYS_V2, doc) + problems.extend( + _unexpected_keys(ARRAY_METADATA_STANDARD_KEYS_V2, cast("Mapping[object, object]", value)) + ) + problems.extend(_check_literal(doc, "zarr_format", 2)) + shape_problems = _validate_dim_sequence(doc, "shape") + chunks_problems = _validate_dim_sequence(doc, "chunks") + problems.extend(shape_problems) + problems.extend(chunks_problems) + if ( + not shape_problems + and not chunks_problems + and _is_int_sequence(doc.get("shape")) + and _is_int_sequence(doc.get("chunks")) + ): + shape = cast("Sequence[int]", doc["shape"]) + chunks = cast("Sequence[int]", doc["chunks"]) + if len(shape) != len(chunks): + problems.append( + ValidationProblem( + ("chunks",), + "expected the same number of dimensions as shape", + "invalid_value", + ) + ) + if "dtype" in doc and not _is_dtype_v2(doc["dtype"]): + problems.append( + ValidationProblem( + ("dtype",), + "expected a v2 dtype string or a sequence of field records", + "invalid_type", + ) + ) + if "order" in doc and doc["order"] not in ("C", "F"): + problems.append( + ValidationProblem( + ("order",), f"expected 'C' or 'F', got {doc['order']!r}", "invalid_value" + ) + ) + if "compressor" in doc: + compressor = doc["compressor"] + if compressor is not None: + problems.extend(_prefix("compressor", _validate_codec_v2(compressor))) + if "filters" in doc: + filters = doc["filters"] + if filters is not None and ( + isinstance(filters, str) + or not isinstance(filters, Sequence) + or not all(_is_codec_v2(item) for item in cast("Sequence[object]", filters)) + ): + problems.append( + ValidationProblem( + ("filters",), + "expected null or a sequence of codec configurations with string 'id's", + "invalid_type", + ) + ) + elif filters is not None: + if len(cast("Sequence[object]", filters)) == 0: + problems.append( + ValidationProblem(("filters",), "expected at least one filter", "invalid_value") + ) + for index, item in enumerate(cast("Sequence[object]", filters)): + problems.extend(_prefix("filters", _prefix(index, validate_json(item)))) + if "dimension_separator" in doc and doc["dimension_separator"] not in (".", "/"): + problems.append( + ValidationProblem( + ("dimension_separator",), + f"expected '.' or '/', got {doc['dimension_separator']!r}", + "invalid_value", + ) + ) + if "fill_value" in doc: + problems.extend(_prefix("fill_value", validate_json(doc["fill_value"]))) + if "attributes" in doc: + problems.extend(_validate_attributes(doc["attributes"])) + return problems + + +def is_array_metadata_v2(value: object) -> TypeIs[ZarrV2ArrayMetadataJSON]: + """Whether `value` is a structurally-valid v2 array metadata document.""" + return ( + _is_canonical_json(value) + and not validate_array_metadata_v2(value) + and _is_canonical_array_metadata_v2(value) + ) + + +def parse_array_metadata_v2(value: object) -> ZarrV2ArrayMetadataJSON: + """Return `value` as `ZarrV2ArrayMetadataJSON`, or raise `MetadataValidationError`.""" + normalized = arrays_to_tuples(value) + problems = validate_array_metadata_v2(normalized) + if problems: + raise MetadataValidationError(problems) + return cast("ZarrV2ArrayMetadataJSON", normalized) + + +def validate_consolidated_metadata_v3(value: object) -> list[ValidationProblem]: + """Return every reason `value` is not a valid inline consolidated envelope. + + Locs are value-relative (the caller prefixes with `consolidated_metadata` + where appropriate). Entries recurse into the array and group document + validators, so a validator verdict always agrees with what + `ZarrV3ConsolidatedMetadata.from_json` accepts. + """ + if not isinstance(value, Mapping): + return [ValidationProblem((), "expected a mapping", "invalid_type")] + env = cast("Mapping[str, object]", value) + problems: list[ValidationProblem] = [ + ValidationProblem((key,), "missing required key", "missing_key") + for key in ("kind", "must_understand", "metadata") + if key not in env + ] + problems.extend( + _unexpected_keys( + frozenset({"kind", "must_understand", "metadata"}), + cast("Mapping[object, object]", value), + ) + ) + problems.extend(_check_literal(env, "kind", "inline")) + if "must_understand" in env and env["must_understand"] is not False: + problems.append(ValidationProblem(("must_understand",), "expected False", "invalid_value")) + if "metadata" in env: + entries = env["metadata"] + if not isinstance(entries, Mapping): + problems.append(ValidationProblem(("metadata",), "expected a mapping", "invalid_type")) + else: + for key, entry in cast("Mapping[object, object]", entries).items(): + if not isinstance(key, str): + problems.append( + ValidationProblem(("metadata",), f"non-string key {key!r}", "invalid_type") + ) + continue + entry_obj: object = entry + node_type: object = None + if isinstance(entry, Mapping): + node_type = cast("Mapping[str, object]", entry).get("node_type") + if node_type == "array": + problems.extend( + _prefix("metadata", _prefix(key, validate_array_metadata_v3(entry_obj))) + ) + elif node_type == "group": + problems.extend( + _prefix("metadata", _prefix(key, validate_group_metadata_v3(entry_obj))) + ) + else: + problems.append( + ValidationProblem( + ("metadata", key, "node_type"), + "expected 'array' or 'group'", + "invalid_value", + ) + ) + return problems + + +def validate_group_metadata_v3(value: object) -> list[ValidationProblem]: + """Return every reason `value` is not a structurally-valid v3 group doc. + + Checks structure, not domain validity. Unknown top-level keys are allowed + (they map to `extra_fields`); a `consolidated_metadata` key, if present, + is deep-validated (envelope and entries) via + `validate_consolidated_metadata_v3`. + """ + if not isinstance(value, Mapping): + return [ValidationProblem((), "expected a mapping", "invalid_type")] + doc = cast("Mapping[str, object]", value) + problems: list[ValidationProblem] = _missing_keys(GROUP_METADATA_REQUIRED_KEYS_V3, doc) + problems.extend( + _validate_extension_fields_v3( + cast("Mapping[object, object]", value), + GROUP_METADATA_STANDARD_KEYS_V3, + additional_reserved_keys=frozenset({"consolidated_metadata"}), + ) + ) + problems.extend(_check_literal(doc, "zarr_format", 3)) + problems.extend(_check_literal(doc, "node_type", "group")) + if "attributes" in doc: + problems.extend(_validate_attributes(doc["attributes"])) + if "consolidated_metadata" in doc and doc["consolidated_metadata"] is not None: + # consolidated_metadata: null (a historical zarr-python bug) is + # structurally accepted so those stores remain readable, but the model + # repairs it to absence on read and never writes it back. + problems.extend( + _prefix( + "consolidated_metadata", + validate_consolidated_metadata_v3(doc["consolidated_metadata"]), + ) + ) + return problems + + +def is_group_metadata_v3(value: object) -> TypeIs[ZarrV3GroupMetadataJSON]: + """Whether `value` is a structurally-valid v3 group metadata document.""" + return _is_canonical_json(value) and not validate_group_metadata_v3(value) + + +def parse_group_metadata_v3(value: object) -> ZarrV3GroupMetadataJSON: + """Return `value` narrowed to `ZarrV3GroupMetadataJSON`, or raise `MetadataValidationError`.""" + normalized = arrays_to_tuples(value) + problems = validate_group_metadata_v3(normalized) + if problems: + raise MetadataValidationError(problems) + return cast(ZarrV3GroupMetadataJSON, normalized) + + +def validate_group_metadata_v2(value: object) -> list[ValidationProblem]: + """Return every reason `value` is not a structurally-valid v2 group doc. + + Validates the in-memory merged form: the `.zgroup` fields plus an + optional `attributes` mapping folded in from `.zattrs`. + """ + if not isinstance(value, Mapping): + return [ValidationProblem((), "expected a mapping", "invalid_type")] + doc = cast("Mapping[str, object]", value) + problems: list[ValidationProblem] = _missing_keys(GROUP_METADATA_REQUIRED_KEYS_V2, doc) + problems.extend( + _unexpected_keys(GROUP_METADATA_STANDARD_KEYS_V2, cast("Mapping[object, object]", value)) + ) + problems.extend(_check_literal(doc, "zarr_format", 2)) + if "attributes" in doc: + problems.extend(_validate_attributes(doc["attributes"])) + return problems + + +def is_group_metadata_v2(value: object) -> TypeIs[ZarrV2GroupMetadataJSON]: + """Whether `value` is a structurally-valid v2 group metadata document.""" + return _is_canonical_json(value) and not validate_group_metadata_v2(value) + + +def parse_group_metadata_v2(value: object) -> ZarrV2GroupMetadataJSON: + """Return `value` narrowed to `ZarrV2GroupMetadataJSON`, or raise `MetadataValidationError`.""" + normalized = arrays_to_tuples(value) + problems = validate_group_metadata_v2(normalized) + if problems: + raise MetadataValidationError(problems) + return cast(ZarrV2GroupMetadataJSON, normalized) + + +def _reject_json_constant(constant: str) -> NoReturn: + """Reject the JavaScript constants accepted by Python's JSON decoder.""" + raise ValueError(f"non-standard JSON constant {constant!r}") + + +def load_store_json(mapping: Mapping[str, bytes], key: str) -> Any: + """Decode the JSON document stored at `key` in `mapping`. + + Every ingestion failure surfaces as `MetadataValidationError`: a missing + store key is a `missing_key` problem and undecodable bytes are an + `invalid_json` problem, rather than leaking `KeyError` / + `json.JSONDecodeError` to callers. + """ + if key not in mapping: + raise MetadataValidationError( + [ValidationProblem((key,), "missing store key", "missing_key")] + ) + try: + return json.loads(mapping[key], parse_constant=_reject_json_constant) + except (UnicodeDecodeError, ValueError) as exc: + raise MetadataValidationError( + [ValidationProblem((key,), f"invalid JSON: {exc}", "invalid_json")] + ) from exc + + +def dump_store_json(value: object, *, indent: int | str | None = None) -> bytes: + """Encode a metadata document as strict RFC 8259 JSON bytes.""" + return json.dumps(value, indent=indent, allow_nan=False).encode("utf-8") + + +def arrays_to_tuples(obj: object) -> object: + """Recursively materialize mappings and convert array-like values to tuples.""" + if isinstance(obj, Sequence) and not isinstance(obj, (str, bytes, bytearray)): + sequence = cast("Sequence[object]", obj) + converted_sequence = tuple(arrays_to_tuples(item) for item in sequence) + if isinstance(obj, tuple) and all( + converted is original + for converted, original in zip(converted_sequence, sequence, strict=True) + ): + return cast("tuple[object, ...]", obj) + return converted_sequence + if isinstance(obj, Mapping): + mapping = cast("Mapping[object, object]", obj) + converted: dict[object, object] = { + key: arrays_to_tuples(value) for key, value in mapping.items() + } + if isinstance(obj, dict) and all(converted[key] is value for key, value in mapping.items()): + return cast("object", obj) + return converted + return obj diff --git a/packages/zarr-metadata/src/zarr_metadata/pydantic.py b/packages/zarr-metadata/src/zarr_metadata/pydantic.py new file mode 100644 index 0000000000..8584efa570 --- /dev/null +++ b/packages/zarr-metadata/src/zarr_metadata/pydantic.py @@ -0,0 +1,176 @@ +"""Optional pydantic (v2) integration: field types over the core models. + +Importing this module requires pydantic; the core package deliberately does +not depend on it, so this module is never imported by `zarr_metadata` itself. + +Each exported name is an `Annotated` field type over the corresponding core +model class — the instances ARE the core classes, so values interoperate +freely with non-pydantic code (equality, isinstance, nesting). Validation +delegates to the library: a raw document routes through `from_json` (the +single source of truth for structural validation and normalization, so +pydantic's field-level coercion can never bypass it), an existing model +instance passes through unchanged, and serialization emits the canonical +document via `to_json`. `MetadataValidationError` subclasses `ValueError`, +so a failed parse surfaces as a pydantic `ValidationError` carrying the +loc-annotated problem messages. + +Usage: + + import zarr_metadata.pydantic as zmp + + class ArrayManifest(BaseModel): + path: str + metadata: zmp.ZarrV3ArrayMetadata + +Static type checkers see each field type as its core model class, so +`manifest.metadata` is a `zarr_metadata.model.ZarrV3ArrayMetadata`. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Annotated, TypeVar + +from pydantic import BeforeValidator, InstanceOf, PlainSerializer + +from zarr_metadata import model as _model +from zarr_metadata._pydantic_schema import ( + ZarrV2ArrayMetadataJSON as _ZarrV2ArrayMetadataSchema, +) +from zarr_metadata._pydantic_schema import ( + ZarrV2ConsolidatedMetadataJSON as _ZarrV2ConsolidatedMetadataSchema, +) +from zarr_metadata._pydantic_schema import ( + ZarrV2GroupMetadataJSON as _ZarrV2GroupMetadataSchema, +) +from zarr_metadata._pydantic_schema import ( + ZarrV3ArrayMetadataJSON as _ZarrV3ArrayMetadataSchema, +) +from zarr_metadata._pydantic_schema import ( + ZarrV3ConsolidatedMetadataJSON as _ZarrV3ConsolidatedMetadataSchema, +) +from zarr_metadata._pydantic_schema import ( + ZarrV3GroupMetadataJSON as _ZarrV3GroupMetadataSchema, +) +from zarr_metadata._pydantic_schema import ( + ZarrV3MetadataFieldJSON as _ZarrV3MetadataFieldSchema, +) +from zarr_metadata.v2.array import ZarrV2ArrayMetadataJSON as _ZarrV2ArrayMetadataJSON +from zarr_metadata.v2.consolidated import ( + ZarrV2ConsolidatedMetadataJSON as _ZarrV2ConsolidatedMetadataJSON, +) +from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON as _ZarrV2GroupMetadataJSON +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON as _ZarrV3MetadataFieldJSON +from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON as _ZarrV3ArrayMetadataJSON +from zarr_metadata.v3.consolidated import ( + ZarrV3ConsolidatedMetadataJSON as _ZarrV3ConsolidatedMetadataJSON, +) +from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON as _ZarrV3GroupMetadataJSON + +if TYPE_CHECKING: + from collections.abc import Callable + +_M = TypeVar("_M") + + +def _coerce_to(cls: type[_M], parse: Callable[[object], _M]) -> Callable[[object], _M]: + """A validator that passes instances of `cls` through and parses anything else.""" + + def coerce(value: object) -> _M: + if isinstance(value, cls): + return value + return parse(value) + + return coerce + + +ZarrV3ArrayMetadata = Annotated[ + InstanceOf[_model.ZarrV3ArrayMetadata], + BeforeValidator( + _coerce_to(_model.ZarrV3ArrayMetadata, _model.ZarrV3ArrayMetadata.from_json), + json_schema_input_type=_ZarrV3ArrayMetadataSchema, + ), + PlainSerializer(_model.ZarrV3ArrayMetadata.to_json, return_type=_ZarrV3ArrayMetadataJSON), +] +"""Field type for a v3 array metadata document (`zarr.json` content).""" + +ZarrV2ArrayMetadata = Annotated[ + InstanceOf[_model.ZarrV2ArrayMetadata], + BeforeValidator( + _coerce_to(_model.ZarrV2ArrayMetadata, _model.ZarrV2ArrayMetadata.from_json), + json_schema_input_type=_ZarrV2ArrayMetadataSchema, + ), + PlainSerializer(_model.ZarrV2ArrayMetadata.to_json, return_type=_ZarrV2ArrayMetadataJSON), +] +"""Field type for a v2 array metadata document (merged `.zarray` + `.zattrs` form).""" + +ZarrV3GroupMetadata = Annotated[ + InstanceOf[_model.ZarrV3GroupMetadata], + BeforeValidator( + _coerce_to(_model.ZarrV3GroupMetadata, _model.ZarrV3GroupMetadata.from_json), + json_schema_input_type=_ZarrV3GroupMetadataSchema, + ), + PlainSerializer(_model.ZarrV3GroupMetadata.to_json, return_type=_ZarrV3GroupMetadataJSON), +] +"""Field type for a v3 group metadata document (`zarr.json` content).""" + +ZarrV2GroupMetadata = Annotated[ + InstanceOf[_model.ZarrV2GroupMetadata], + BeforeValidator( + _coerce_to(_model.ZarrV2GroupMetadata, _model.ZarrV2GroupMetadata.from_json), + json_schema_input_type=_ZarrV2GroupMetadataSchema, + ), + PlainSerializer(_model.ZarrV2GroupMetadata.to_json, return_type=_ZarrV2GroupMetadataJSON), +] +"""Field type for a v2 group metadata document (merged `.zgroup` + `.zattrs` form).""" + +ZarrV3ConsolidatedMetadata = Annotated[ + InstanceOf[_model.ZarrV3ConsolidatedMetadata], + BeforeValidator( + _coerce_to( + _model.ZarrV3ConsolidatedMetadata, + _model.ZarrV3ConsolidatedMetadata.from_json, + ), + json_schema_input_type=_ZarrV3ConsolidatedMetadataSchema, + ), + PlainSerializer( + _model.ZarrV3ConsolidatedMetadata.to_json, + return_type=_ZarrV3ConsolidatedMetadataJSON, + ), +] +"""Field type for v3 inline consolidated metadata.""" + +ZarrV2ConsolidatedMetadata = Annotated[ + InstanceOf[_model.ZarrV2ConsolidatedMetadata], + BeforeValidator( + _coerce_to( + _model.ZarrV2ConsolidatedMetadata, + _model.ZarrV2ConsolidatedMetadata.from_json, + ), + json_schema_input_type=_ZarrV2ConsolidatedMetadataSchema, + ), + PlainSerializer( + _model.ZarrV2ConsolidatedMetadata.to_json, + return_type=_ZarrV2ConsolidatedMetadataJSON, + ), +] +"""Field type for a v2 `.zmetadata` document.""" + +ZarrV3MetadataField = Annotated[ + InstanceOf[_model.ZarrV3NamedConfig], + BeforeValidator( + _coerce_to(_model.ZarrV3NamedConfig, _model.ZarrV3NamedConfig.from_json), + json_schema_input_type=_ZarrV3MetadataFieldSchema, + ), + PlainSerializer(_model.ZarrV3NamedConfig.to_json, return_type=_ZarrV3MetadataFieldJSON), +] +"""Field type for one normalized v3 metadata extension envelope.""" + +__all__ = [ + "ZarrV2ArrayMetadata", + "ZarrV2ConsolidatedMetadata", + "ZarrV2GroupMetadata", + "ZarrV3ArrayMetadata", + "ZarrV3ConsolidatedMetadata", + "ZarrV3GroupMetadata", + "ZarrV3MetadataField", +] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py index 4e9a76125b..b9001d168e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/__init__.py @@ -1,26 +1,26 @@ """Zarr v2 metadata types.""" from zarr_metadata.v2.array import ( - ArrayDimensionSeparatorV2, - ArrayMetadataV2, - ArrayOrderV2, - DataTypeMetadataV2, - ZArrayMetadata, + ZarrV2ArrayDimensionSeparator, + ZarrV2ArrayMetadataJSON, + ZarrV2ArrayOrder, + ZarrV2DataTypeMetadata, + ZarrV2ZArrayJSON, ) -from zarr_metadata.v2.attributes import ZAttrsMetadata -from zarr_metadata.v2.codec import CodecMetadataV2 -from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 -from zarr_metadata.v2.group import GroupMetadataV2, ZGroupMetadata +from zarr_metadata.v2.attributes import ZarrV2ZAttrsJSON +from zarr_metadata.v2.codec import ZarrV2CodecMetadata +from zarr_metadata.v2.consolidated import ZarrV2ConsolidatedMetadataJSON +from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON, ZarrV2ZGroupJSON __all__ = [ - "ArrayDimensionSeparatorV2", - "ArrayMetadataV2", - "ArrayOrderV2", - "CodecMetadataV2", - "ConsolidatedMetadataV2", - "DataTypeMetadataV2", - "GroupMetadataV2", - "ZArrayMetadata", - "ZAttrsMetadata", - "ZGroupMetadata", + "ZarrV2ArrayDimensionSeparator", + "ZarrV2ArrayMetadataJSON", + "ZarrV2ArrayOrder", + "ZarrV2CodecMetadata", + "ZarrV2ConsolidatedMetadataJSON", + "ZarrV2DataTypeMetadata", + "ZarrV2GroupMetadataJSON", + "ZarrV2ZArrayJSON", + "ZarrV2ZAttrsJSON", + "ZarrV2ZGroupJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 999c341dc7..84b6446bcb 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -3,18 +3,27 @@ from collections.abc import Mapping from typing import Final, Literal, NotRequired -from typing_extensions import TypedDict +from typing_extensions import TypeAliasType, TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v2.codec import CodecMetadataV2 - -DataTypeMetadataV2 = str | tuple[tuple[str, str] | tuple[str, str, tuple[int, ...]], ...] +from zarr_metadata.v2.codec import ZarrV2CodecMetadata + +ZarrV2DataTypeMetadata = TypeAliasType( + "ZarrV2DataTypeMetadata", + str + | tuple[ + tuple[str, "ZarrV2DataTypeMetadata"] + | tuple[str, "ZarrV2DataTypeMetadata", tuple[int, ...]], + ..., + ], +) """The v2 dtype representation. Either a numpy-style dtype string (e.g. `"<f8"`, `"|S10"`) or a tuple of field records describing a structured dtype. Each field record is either a 2-tuple `(name, datatype)` or a 3-tuple `(name, datatype, shape)` -(the 3-tuple form indicates a subarray field). +(the 3-tuple form indicates a subarray field). A field datatype may itself +be another structured dtype. Endianness is encoded in the prefix character of the dtype string; parsing it out is a caller concern, not part of this type. @@ -22,7 +31,7 @@ See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html#data-type-encoding """ -ArrayOrderV2 = Literal["C", "F"] +ZarrV2ArrayOrder = Literal["C", "F"] """Literal type of permitted values for the `order` field of v2 array metadata. `"C"` (row-major) or `"F"` (column-major) — the in-chunk byte layout. @@ -33,7 +42,7 @@ ARRAY_ORDER_V2: Final = ("C", "F") """Tuple of permitted values for the `order` field of v2 array metadata.""" -ArrayDimensionSeparatorV2 = Literal[".", "/"] +ZarrV2ArrayDimensionSeparator = Literal[".", "/"] """Literal type of permitted values for the `dimension_separator` field of v2 array metadata. `"."` (legacy default) joins chunk grid coordinates as `0.0`, `0.1`, ... @@ -46,13 +55,13 @@ """Tuple of permitted values for the `dimension_separator` field of v2 array metadata.""" -class ZArrayMetadata(TypedDict): +class ZarrV2ZArrayJSON(TypedDict): """ On-disk `.zarray` file content. Strict shape of the JSON document persisted at `<path>/.zarray` for a v2 array. User attributes live in a sibling `.zattrs` file and are - NOT part of this type; see `ZAttrsMetadata`. + NOT part of this type; see `ZarrV2ZAttrsJSON`. See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ @@ -60,15 +69,15 @@ class ZArrayMetadata(TypedDict): zarr_format: Literal[2] shape: tuple[int, ...] chunks: tuple[int, ...] - dtype: DataTypeMetadataV2 - compressor: CodecMetadataV2 | None + dtype: ZarrV2DataTypeMetadata + compressor: ZarrV2CodecMetadata | None fill_value: JSONValue - order: ArrayOrderV2 - filters: tuple[CodecMetadataV2, ...] | None - dimension_separator: NotRequired[ArrayDimensionSeparatorV2] + order: ZarrV2ArrayOrder + filters: tuple[ZarrV2CodecMetadata, ...] | None + dimension_separator: NotRequired[ZarrV2ArrayDimensionSeparator] -class ArrayMetadataV2(TypedDict): +class ZarrV2ArrayMetadataJSON(TypedDict): """ Zarr v2 array metadata document, in-memory merged form. @@ -78,7 +87,7 @@ class ArrayMetadataV2(TypedDict): `attributes` field so a single TypedDict represents the complete in-memory state of a v2 array node. Consumers that read or write a real `.zarray` file should split / merge `attributes` accordingly, - or use `ZArrayMetadata` (strict on-disk) plus `ZAttrsMetadata` directly. + or use `ZarrV2ZArrayJSON` (strict on-disk) plus `ZarrV2ZAttrsJSON` directly. See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ @@ -86,12 +95,12 @@ class ArrayMetadataV2(TypedDict): zarr_format: Literal[2] shape: tuple[int, ...] chunks: tuple[int, ...] - dtype: DataTypeMetadataV2 - compressor: CodecMetadataV2 | None + dtype: ZarrV2DataTypeMetadata + compressor: ZarrV2CodecMetadata | None fill_value: JSONValue - order: ArrayOrderV2 - filters: tuple[CodecMetadataV2, ...] | None - dimension_separator: NotRequired[ArrayDimensionSeparatorV2] + order: ZarrV2ArrayOrder + filters: tuple[ZarrV2CodecMetadata, ...] | None + dimension_separator: NotRequired[ZarrV2ArrayDimensionSeparator] attributes: NotRequired[Mapping[str, JSONValue]] """User attributes from the sibling `.zattrs` file (not part of `.zarray`). @@ -99,11 +108,11 @@ class ArrayMetadataV2(TypedDict): """ -class ArrayMetadataV2Partial(TypedDict, total=False): +class ZarrV2ArrayMetadataJSONPartial(TypedDict, total=False): """ - Partial form of `ArrayMetadataV2`: every field is `NotRequired`. + Partial form of `ZarrV2ArrayMetadataJSON`: every field is `NotRequired`. - Field annotations mirror `ArrayMetadataV2` exactly. The only difference is + Field annotations mirror `ZarrV2ArrayMetadataJSON` exactly. The only difference is `total=False`, which makes every key optional at the type level. Use this when typing dicts that intentionally hold a subset of a complete @@ -113,26 +122,26 @@ class ArrayMetadataV2Partial(TypedDict, total=False): The `NotRequired[...]` wrappers on `dimension_separator` and `attributes` are intentional: keeping them preserves byte-identical `__annotations__` - with `ArrayMetadataV2` so the `==` check in + with `ZarrV2ArrayMetadataJSON` so the `==` check in `tests/test_partial_equivalence.py` passes without special-casing those fields (PEP 655 explicitly permits `NotRequired` inside `total=False`). Note: v2 array metadata has no `extra_items` setting (the v2 spec has no extension-field concept), so this partial inherits the same closed shape. - Drift between this type and `ArrayMetadataV2` is prevented by + Drift between this type and `ZarrV2ArrayMetadataJSON` is prevented by `tests/test_partial_equivalence.py`. """ zarr_format: Literal[2] shape: tuple[int, ...] chunks: tuple[int, ...] - dtype: DataTypeMetadataV2 - compressor: CodecMetadataV2 | None + dtype: ZarrV2DataTypeMetadata + compressor: ZarrV2CodecMetadata | None fill_value: JSONValue - order: ArrayOrderV2 - filters: tuple[CodecMetadataV2, ...] | None - dimension_separator: NotRequired[ArrayDimensionSeparatorV2] + order: ZarrV2ArrayOrder + filters: tuple[ZarrV2CodecMetadata, ...] | None + dimension_separator: NotRequired[ZarrV2ArrayDimensionSeparator] attributes: NotRequired[Mapping[str, JSONValue]] """User attributes from the sibling `.zattrs` file (not part of `.zarray`). @@ -143,10 +152,10 @@ class ArrayMetadataV2Partial(TypedDict, total=False): __all__ = [ "ARRAY_DIMENSION_SEPARATOR_V2", "ARRAY_ORDER_V2", - "ArrayDimensionSeparatorV2", - "ArrayMetadataV2", - "ArrayMetadataV2Partial", - "ArrayOrderV2", - "DataTypeMetadataV2", - "ZArrayMetadata", + "ZarrV2ArrayDimensionSeparator", + "ZarrV2ArrayMetadataJSON", + "ZarrV2ArrayMetadataJSONPartial", + "ZarrV2ArrayOrder", + "ZarrV2DataTypeMetadata", + "ZarrV2ZArrayJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py index 18b8ded9da..f7cc31babe 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py @@ -7,16 +7,16 @@ from zarr_metadata._common import JSONValue -ZAttrsMetadata = Mapping[str, JSONValue] +ZarrV2ZAttrsJSON = Mapping[str, JSONValue] """On-disk `.zattrs` file content. A JSON object holding user-defined attributes for a v2 array or group. Spec-defined keys for arrays / groups live in sibling `.zarray` / `.zgroup` -files (modeled by `ZArrayMetadata` / `ZGroupMetadata`). This type does not +files (modeled by `ZarrV2ZArrayJSON` / `ZarrV2ZGroupJSON`). This type does not constrain the keys or values of the attributes mapping. """ __all__ = [ - "ZAttrsMetadata", + "ZarrV2ZAttrsJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/codec.py b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py index 6d194b7e29..69125544e6 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/codec.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/codec.py @@ -10,7 +10,7 @@ from zarr_metadata._common import JSONValue -class CodecMetadataV2(TypedDict, extra_items=JSONValue): # type: ignore[call-arg] +class ZarrV2CodecMetadata(TypedDict, extra_items=JSONValue): """ A numcodecs configuration dict, used as a v2 compressor or filter. @@ -25,5 +25,5 @@ class CodecMetadataV2(TypedDict, extra_items=JSONValue): # type: ignore[call-ar __all__ = [ - "CodecMetadataV2", + "ZarrV2CodecMetadata", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py index 61a5527085..6b586bb92e 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py @@ -10,12 +10,12 @@ from typing_extensions import TypedDict -from zarr_metadata.v2.array import ZArrayMetadata -from zarr_metadata.v2.attributes import ZAttrsMetadata -from zarr_metadata.v2.group import ZGroupMetadata +from zarr_metadata.v2.array import ZarrV2ZArrayJSON +from zarr_metadata.v2.attributes import ZarrV2ZAttrsJSON +from zarr_metadata.v2.group import ZarrV2ZGroupJSON -class ConsolidatedMetadataV2(TypedDict): +class ZarrV2ConsolidatedMetadataJSON(TypedDict): """ `.zmetadata` file contents. @@ -24,9 +24,9 @@ class ConsolidatedMetadataV2(TypedDict): that path. The keys include the filename suffix, not just the node path; the value's shape is determined by which file the key points at: - - `<path>/.zarray` -> `ZArrayMetadata` - - `<path>/.zgroup` -> `ZGroupMetadata` - - `<path>/.zattrs` -> `ZAttrsMetadata` + - `<path>/.zarray` -> `ZarrV2ZArrayJSON` + - `<path>/.zgroup` -> `ZarrV2ZGroupJSON` + - `<path>/.zattrs` -> `ZarrV2ZAttrsJSON` The TypedDict cannot discriminate the value shape on the key suffix at the type level; consumers should narrow at runtime by inspecting @@ -34,9 +34,9 @@ class ConsolidatedMetadataV2(TypedDict): """ zarr_consolidated_format: int - metadata: Mapping[str, ZArrayMetadata | ZGroupMetadata | ZAttrsMetadata] + metadata: Mapping[str, ZarrV2ZArrayJSON | ZarrV2ZGroupJSON | ZarrV2ZAttrsJSON] __all__ = [ - "ConsolidatedMetadataV2", + "ZarrV2ConsolidatedMetadataJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/group.py b/packages/zarr-metadata/src/zarr_metadata/v2/group.py index 5f456fe8d3..50f2482e6f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/group.py @@ -11,14 +11,14 @@ from zarr_metadata._common import JSONValue -class ZGroupMetadata(TypedDict): +class ZarrV2ZGroupJSON(TypedDict): """ On-disk `.zgroup` file content. Strict shape of the JSON document persisted at `<path>/.zgroup` for a v2 group. The spec defines exactly one field. User attributes live in a sibling `.zattrs` file and are NOT part of this type; see - `ZAttrsMetadata`. + `ZarrV2ZAttrsJSON`. See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ @@ -26,7 +26,7 @@ class ZGroupMetadata(TypedDict): zarr_format: Literal[2] -class GroupMetadataV2(TypedDict): +class ZarrV2GroupMetadataJSON(TypedDict): """ Zarr v2 group metadata document, in-memory merged form. @@ -34,8 +34,8 @@ class GroupMetadataV2(TypedDict): and `.zattrs` (user attributes). On disk these are persisted as two separate files; this type folds them so a single TypedDict represents the complete in-memory state of a v2 group node. Consumers that read - or write the real on-disk files should use `ZGroupMetadata` (strict - `.zgroup`) plus `ZAttrsMetadata` directly. + or write the real on-disk files should use `ZarrV2ZGroupJSON` (strict + `.zgroup`) plus `ZarrV2ZAttrsJSON` directly. See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ @@ -44,11 +44,11 @@ class GroupMetadataV2(TypedDict): attributes: NotRequired[Mapping[str, JSONValue]] -class GroupMetadataV2Partial(TypedDict, total=False): +class ZarrV2GroupMetadataJSONPartial(TypedDict, total=False): """ - Partial form of `GroupMetadataV2`: every field is `NotRequired`. + Partial form of `ZarrV2GroupMetadataJSON`: every field is `NotRequired`. - Field annotations mirror `GroupMetadataV2` exactly. The only difference is + Field annotations mirror `ZarrV2GroupMetadataJSON` exactly. The only difference is `total=False`, which makes every key optional at the type level. Use this when typing dicts that intentionally hold a subset of a complete @@ -58,7 +58,7 @@ class GroupMetadataV2Partial(TypedDict, total=False): `*Partial` types; the practical effect is that `zarr_format` becomes optional. The `NotRequired[...]` wrapper on `attributes` is intentional: keeping it - preserves byte-identical `__annotations__` with `GroupMetadataV2` so the + preserves byte-identical `__annotations__` with `ZarrV2GroupMetadataJSON` so the `==` check in `tests/test_partial_equivalence.py` passes without special-casing that field (PEP 655 explicitly permits `NotRequired` inside `total=False`). @@ -66,7 +66,7 @@ class GroupMetadataV2Partial(TypedDict, total=False): Note: v2 group metadata has no `extra_items` setting (the v2 spec has no extension-field concept), so this partial inherits the same closed shape. - Drift between this type and `GroupMetadataV2` is prevented by + Drift between this type and `ZarrV2GroupMetadataJSON` is prevented by `tests/test_partial_equivalence.py`. """ @@ -75,7 +75,7 @@ class GroupMetadataV2Partial(TypedDict, total=False): __all__ = [ - "GroupMetadataV2", - "GroupMetadataV2Partial", - "ZGroupMetadata", + "ZarrV2GroupMetadataJSON", + "ZarrV2GroupMetadataJSONPartial", + "ZarrV2ZGroupJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py index c897f20d52..4e335f9573 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/__init__.py @@ -1,14 +1,14 @@ """Zarr v3 metadata types.""" -from zarr_metadata.v3._common import MetadataV3 -from zarr_metadata.v3.array import ArrayMetadataV3, ExtensionFieldV3 -from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 -from zarr_metadata.v3.group import GroupMetadataV3 +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON +from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON, ZarrV3ExtensionField +from zarr_metadata.v3.consolidated import ZarrV3ConsolidatedMetadataJSON +from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON __all__ = [ - "ArrayMetadataV3", - "ConsolidatedMetadataV3", - "ExtensionFieldV3", - "GroupMetadataV3", - "MetadataV3", + "ZarrV3ArrayMetadataJSON", + "ZarrV3ConsolidatedMetadataJSON", + "ZarrV3ExtensionField", + "ZarrV3GroupMetadataJSON", + "ZarrV3MetadataFieldJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/_common.py b/packages/zarr-metadata/src/zarr_metadata/v3/_common.py index 3424587a43..406b76b723 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/_common.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/_common.py @@ -2,14 +2,14 @@ This module is private (underscore-prefixed) and exists to avoid circular imports between leaf modules and sub-package `__init__.py` re-exports. -Public consumers should import `MetadataV3` from `zarr_metadata.v3`. +Public consumers should import `ZarrV3MetadataFieldJSON` from `zarr_metadata.v3`. """ -from zarr_metadata._common import NamedConfigV3 +from zarr_metadata._common import ZarrV3NamedConfigJSON -MetadataV3 = str | NamedConfigV3 +ZarrV3MetadataFieldJSON = str | ZarrV3NamedConfigJSON """The JSON shape of any v3 metadata extension-point entry: either a bare -short-hand name string or a `{name, configuration}` envelope. +short-hand name string or a `{name, configuration, must_understand}` envelope. Used for `data_type`, `chunk_grid`, `chunk_key_encoding`, individual codec entries, and `storage_transformers` in v3 array metadata, and for @@ -19,5 +19,5 @@ __all__ = [ - "MetadataV3", + "ZarrV3MetadataFieldJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index a8b0fa3358..96341f73ca 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -1,73 +1,49 @@ """Zarr v3 array metadata types.""" from collections.abc import Mapping -from typing import Literal, NotRequired +from typing import Literal, NotRequired, TypeAlias from typing_extensions import TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v3._common import MetadataV3 +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON +ZarrV3ExtensionField: TypeAlias = JSONValue +"""The JSON value of an unknown top-level v3 metadata field. -class ExtensionFieldV3(TypedDict, extra_items=JSONValue): # type: ignore[call-arg] - """ - Required shape of any extension field on a v3 metadata document. - - The Zarr v3 spec permits extra keys on array and group metadata - documents, provided each value is an object with a `must_understand` - boolean key. This TypedDict captures that constraint and is used as - the `extra_items=` parameter on `ArrayMetadataV3` and `GroupMetadataV3`. - - `must_understand` is typed as `bool` rather than `Literal[False]` so - that applications which understand a particular extension can produce - or consume it with `must_understand: true` (signalling that readers - that don't recognize the extension MUST refuse to open the document). - The common case is still `false`, signalling that unknown readers may - safely ignore the field. - - Spec interpretation: this type follows the original Zarr v3.0 reading - of the spec, under which any object with a `must_understand` key is a - valid extension field. The v3.1 spec rewrite added language requiring - extension fields to also include a `name: str` key (the "Extension - definition" form). Under the strict v3.1 reading, real-world extension - fields written by zarr-python and zarrs (notably `consolidated_metadata`, - which has no `name` field) are out of spec. The community consensus at - the time of writing is that this is a regression to be reverted; this - package models the v3.0 / pre-revert interpretation. See - https://github.com/zarr-developers/zarr-specs/issues/371 for the - ongoing discussion. - """ - - must_understand: bool +An object carrying the literal member `must_understand: false` may be ignored. +Every other JSON shape implicitly requires understanding; recognition itself +belongs to the reader rather than this structural type. +""" -class ArrayMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[call-arg] +class ZarrV3ArrayMetadataJSON(TypedDict, extra_items=ZarrV3ExtensionField): """ Zarr v3 array metadata document (the `zarr.json` content for an array). - Extra keys are permitted if they conform to `ExtensionFieldV3`. + Extra keys may contain arbitrary JSON values. See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#array-metadata """ zarr_format: Literal[3] node_type: Literal["array"] - data_type: MetadataV3 + data_type: ZarrV3MetadataFieldJSON shape: tuple[int, ...] - chunk_grid: MetadataV3 - chunk_key_encoding: MetadataV3 + chunk_grid: ZarrV3MetadataFieldJSON + chunk_key_encoding: ZarrV3MetadataFieldJSON fill_value: JSONValue - codecs: tuple[MetadataV3, ...] + codecs: tuple[ZarrV3MetadataFieldJSON, ...] attributes: NotRequired[Mapping[str, JSONValue]] - storage_transformers: NotRequired[tuple[MetadataV3, ...]] + storage_transformers: NotRequired[tuple[ZarrV3MetadataFieldJSON, ...]] dimension_names: NotRequired[tuple[str | None, ...]] -class ArrayMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV3): # type: ignore[call-arg] +class ZarrV3ArrayMetadataJSONPartial(TypedDict, total=False, extra_items=ZarrV3ExtensionField): """ - Partial form of `ArrayMetadataV3`: every field is `NotRequired`. + Partial form of `ZarrV3ArrayMetadataJSON`: every field is `NotRequired`. - Field annotations and `extra_items=` mirror `ArrayMetadataV3` exactly. + Field annotations and `extra_items=` mirror `ZarrV3ArrayMetadataJSON` exactly. The only difference is `total=False`, which makes every key optional at the type level. @@ -78,29 +54,29 @@ class ArrayMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV The `NotRequired[...]` wrappers on `attributes`, `storage_transformers`, and `dimension_names` are intentional: keeping them preserves byte-identical - `__annotations__` with `ArrayMetadataV3` so the `==` check in + `__annotations__` with `ZarrV3ArrayMetadataJSON` so the `==` check in `tests/test_partial_equivalence.py` passes without special-casing those fields (PEP 655 explicitly permits `NotRequired` inside `total=False`). - Drift between this type and `ArrayMetadataV3` is prevented by + Drift between this type and `ZarrV3ArrayMetadataJSON` is prevented by `tests/test_partial_equivalence.py`. """ zarr_format: Literal[3] node_type: Literal["array"] - data_type: MetadataV3 + data_type: ZarrV3MetadataFieldJSON shape: tuple[int, ...] - chunk_grid: MetadataV3 - chunk_key_encoding: MetadataV3 + chunk_grid: ZarrV3MetadataFieldJSON + chunk_key_encoding: ZarrV3MetadataFieldJSON fill_value: JSONValue - codecs: tuple[MetadataV3, ...] + codecs: tuple[ZarrV3MetadataFieldJSON, ...] attributes: NotRequired[Mapping[str, JSONValue]] - storage_transformers: NotRequired[tuple[MetadataV3, ...]] + storage_transformers: NotRequired[tuple[ZarrV3MetadataFieldJSON, ...]] dimension_names: NotRequired[tuple[str | None, ...]] __all__ = [ - "ArrayMetadataV3", - "ArrayMetadataV3Partial", - "ExtensionFieldV3", + "ZarrV3ArrayMetadataJSON", + "ZarrV3ArrayMetadataJSONPartial", + "ZarrV3ExtensionField", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py index fef5793626..e2783d296d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/chunk_key_encoding/v2.py @@ -4,6 +4,12 @@ Intended only to allow existing v2 arrays to be converted to v3 without having to rename chunks. Not recommended for new arrays. +Naming note: these are Zarr **v3** types. The leading `V2` in +`V2ChunkKeyEncodingMetadata` (and friends) is the encoding's registered +*entity name* (`"v2"`), not the format-version marker that `ZarrV2...` +names carry — this package's version-prefixed names always spell it +`ZarrV2` / `ZarrV3`. + See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#chunk-key-encoding """ diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py index b4f357117f..c8a9a150fc 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/__init__.py @@ -11,7 +11,7 @@ `<X>CodecConfiguration`, etc., import directly from the leaf submodule. For the field-level "any codec entry" alias (used in array metadata's -`codecs` list and in sharding's inner pipelines), import `MetadataV3` +`codecs` list and in sharding's inner pipelines), import `ZarrV3MetadataFieldJSON` from `zarr_metadata.v3`. See https://zarr-specs.readthedocs.io/en/latest/v3/codecs/index.html diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py index 7e9b071669..96c39e5916 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/cast_value.py @@ -9,7 +9,7 @@ from typing_extensions import TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v3._common import MetadataV3 +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON CAST_VALUE_CODEC_NAME: Final = "cast_value" """The `name` field value of the `cast_value` codec.""" @@ -71,7 +71,7 @@ class CastValueCodecConfiguration(TypedDict): bare-string primitive name or a `{name, configuration}` envelope. """ - data_type: MetadataV3 + data_type: ZarrV3MetadataFieldJSON rounding: NotRequired[CastRoundingMode] out_of_range: NotRequired[CastOutOfRangeMode] scalar_map: NotRequired[ScalarMap] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py index ea35ae5f1d..6b9b46c43d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/crc32c.py @@ -18,7 +18,7 @@ """Literal type of the `name` field of the `crc32c` codec.""" -class Empty(TypedDict, closed=True): # type: ignore[call-arg] +class Empty(TypedDict, closed=True): """An empty mapping""" diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py index a1488f7c30..a8c9247ec4 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/codec/sharding_indexed.py @@ -8,7 +8,7 @@ from typing_extensions import TypedDict -from zarr_metadata.v3._common import MetadataV3 +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON SHARDING_INDEXED_CODEC_NAME: Final = "sharding_indexed" """The `name` field value of the `sharding_indexed` codec.""" @@ -40,8 +40,8 @@ class ShardingIndexedCodecConfiguration(TypedDict): """ chunk_shape: tuple[int, ...] - codecs: tuple[MetadataV3, ...] - index_codecs: tuple[MetadataV3, ...] + codecs: tuple[ZarrV3MetadataFieldJSON, ...] + index_codecs: tuple[ZarrV3MetadataFieldJSON, ...] index_location: NotRequired[ShardingIndexLocation] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py index 486a0897a5..bcbe675947 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py @@ -5,14 +5,10 @@ implementation (and zarrs), where consolidated metadata is embedded as an extension field on a group's `zarr.json`. -The shape modeled here (`{kind, must_understand, metadata}` with no `name` -field) reflects the original Zarr v3.0 reading of the extension-field -rules. Under the strict Zarr v3.1 reading, every extension field must -also include a `name: str` key, which would make this shape — and every -real-world consolidated metadata document in the wild — out of spec. -See `ExtensionFieldV3` and -https://github.com/zarr-developers/zarr-specs/issues/371 for the -ongoing discussion. +This is a known non-core interoperability extension. Its +`{kind, must_understand, metadata}` payload is an unknown top-level JSON value +to the core document model; implementations that recognize the convention may +interpret it through this dedicated type. """ from collections.abc import Mapping @@ -20,24 +16,24 @@ from typing_extensions import TypedDict -from zarr_metadata.v3.array import ArrayMetadataV3 -from zarr_metadata.v3.group import GroupMetadataV3 +from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON +from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON -class ConsolidatedMetadataV3(TypedDict): +class ZarrV3ConsolidatedMetadataJSON(TypedDict): """ Inline consolidated metadata embedded in a v3 group. - The `metadata` map contains only v3 array and group entries - v2 - entries are excluded by design. Mixing v2 entries into a v3 - consolidated metadata document is invalid per spec. + The `metadata` map contains only v3 array and group entries. V2 entries + are excluded from this interoperability convention by design; the v3 core + specification does not define consolidated metadata. """ kind: Literal["inline"] must_understand: Literal[False] - metadata: Mapping[str, ArrayMetadataV3 | GroupMetadataV3] + metadata: Mapping[str, ZarrV3ArrayMetadataJSON | ZarrV3GroupMetadataJSON] __all__ = [ - "ConsolidatedMetadataV3", + "ZarrV3ConsolidatedMetadataJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py index 5291e5c309..b1b6b50308 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/data_type/struct.py @@ -10,7 +10,7 @@ from typing_extensions import ReadOnly, TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v3._common import MetadataV3 +from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON STRUCT_DATA_TYPE_NAME: Final = "struct" """The `name` field value of the `struct` data type.""" @@ -33,7 +33,7 @@ class StructField(TypedDict): """ name: ReadOnly[str] - data_type: ReadOnly[MetadataV3] + data_type: ReadOnly[ZarrV3MetadataFieldJSON] class StructConfiguration(TypedDict): diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py index 27186b6059..033e91ff8c 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -9,14 +9,14 @@ from typing_extensions import TypedDict from zarr_metadata._common import JSONValue -from zarr_metadata.v3.array import ExtensionFieldV3 +from zarr_metadata.v3.array import ZarrV3ExtensionField -class GroupMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[call-arg] +class ZarrV3GroupMetadataJSON(TypedDict, extra_items=ZarrV3ExtensionField): """ Zarr v3 group metadata document (the `zarr.json` content for a group). - Extra keys are permitted if they conform to `ExtensionFieldV3`. + Extra keys may contain arbitrary JSON values. See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#group-metadata """ @@ -26,11 +26,11 @@ class GroupMetadataV3(TypedDict, extra_items=ExtensionFieldV3): # type: ignore[ attributes: NotRequired[Mapping[str, JSONValue]] -class GroupMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV3): # type: ignore[call-arg] +class ZarrV3GroupMetadataJSONPartial(TypedDict, total=False, extra_items=ZarrV3ExtensionField): """ - Partial form of `GroupMetadataV3`: every field is `NotRequired`. + Partial form of `ZarrV3GroupMetadataJSON`: every field is `NotRequired`. - Field annotations and `extra_items=` mirror `GroupMetadataV3` exactly. + Field annotations and `extra_items=` mirror `ZarrV3GroupMetadataJSON` exactly. The only difference is `total=False`, which makes every key optional at the type level. @@ -40,12 +40,12 @@ class GroupMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV into a complete document elsewhere. The `NotRequired[...]` wrapper on `attributes` is intentional: keeping it - preserves byte-identical `__annotations__` with `GroupMetadataV3` so the + preserves byte-identical `__annotations__` with `ZarrV3GroupMetadataJSON` so the `==` check in `tests/test_partial_equivalence.py` passes without special-casing that field (PEP 655 explicitly permits `NotRequired` inside `total=False`). - Drift between this type and `GroupMetadataV3` is prevented by + Drift between this type and `ZarrV3GroupMetadataJSON` is prevented by `tests/test_partial_equivalence.py`. """ @@ -55,6 +55,6 @@ class GroupMetadataV3Partial(TypedDict, total=False, extra_items=ExtensionFieldV __all__ = [ - "GroupMetadataV3", - "GroupMetadataV3Partial", + "ZarrV3GroupMetadataJSON", + "ZarrV3GroupMetadataJSONPartial", ] diff --git a/packages/zarr-metadata/tests/model/__init__.py b/packages/zarr-metadata/tests/model/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-metadata/tests/model/_cases.py b/packages/zarr-metadata/tests/model/_cases.py new file mode 100644 index 0000000000..15faa65539 --- /dev/null +++ b/packages/zarr-metadata/tests/model/_cases.py @@ -0,0 +1,65 @@ +from __future__ import annotations + +import re +from dataclasses import dataclass +from typing import TYPE_CHECKING, Generic, TypeVar + +import pytest + +if TYPE_CHECKING: + from contextlib import AbstractContextManager + +TIn = TypeVar("TIn") +TOut = TypeVar("TOut") + + +@dataclass(frozen=True) +class Expect(Generic[TIn, TOut]): + """A test case with explicit input, expected output, and a human-readable id.""" + + input: TIn + output: TOut + id: str + + +@dataclass(frozen=True) +class ExpectFail(Generic[TIn]): + """A test case that should raise an exception. + + `msg` is a regex matched against the exception text (pytest's native + `match=` semantics). Leave it `None` to assert only the exception type. Set + `escape=True` when `msg` is a literal that contains regex metacharacters + such as `(`, `[`, or `.`; `escape` has no effect when `msg` is `None`. + """ + + input: TIn + exception: type[Exception] + id: str + msg: str | None = None + escape: bool = False + + def raises(self) -> AbstractContextManager[pytest.ExceptionInfo[Exception]]: + if self.msg is None: + return pytest.raises(self.exception) + pattern = re.escape(self.msg) if self.escape else self.msg + return pytest.raises(self.exception, match=pattern) + + +def mutate_nested_containers(value: object) -> None: + """Recursively mutate every mutable container reachable inside `value`. + + Adds a marker key to every dict and appends a marker to every list, + descending through tuples. Used to prove a `to_json` document shares no + mutable state with the model that produced it. + """ + if isinstance(value, dict): + for item in value.values(): + mutate_nested_containers(item) + value["__mutated__"] = "__mutated__" + elif isinstance(value, list): + for item in value: + mutate_nested_containers(item) + value.append("__mutated__") + elif isinstance(value, tuple): + for item in value: + mutate_nested_containers(item) diff --git a/packages/zarr-metadata/tests/model/test_array.py b/packages/zarr-metadata/tests/model/test_array.py new file mode 100644 index 0000000000..467ef1e2ad --- /dev/null +++ b/packages/zarr-metadata/tests/model/test_array.py @@ -0,0 +1,1738 @@ +"""Tests for the metadata models in ``zarr_metadata.model``.""" + +import copy +import dataclasses +import json +from collections import UserDict +from collections.abc import Callable +from typing import TYPE_CHECKING, get_args + +import pytest +from typing_extensions import Unpack + +from tests.model._cases import Expect, ExpectFail, mutate_nested_containers +from zarr_metadata.model import ( + ARRAY_METADATA_OPTIONAL_KEYS_V3, + ARRAY_METADATA_REQUIRED_KEYS_V3, + ARRAY_METADATA_STANDARD_KEYS_V3, + UNSET, + MetadataValidationError, + ValidationProblem, + ZarrV2ArrayMetadata, + ZarrV2ArrayMetadataPartial, + ZarrV3ArrayMetadata, + ZarrV3ArrayMetadataPartial, + ZarrV3MetadataField, + ZarrV3NamedConfig, + is_array_metadata_v2, + is_array_metadata_v3, + is_json, + is_metadata_field_v3, + parse_array_metadata_v2, + parse_array_metadata_v3, + parse_json, + parse_metadata_field_v3, + validate_array_metadata_v2, + validate_array_metadata_v3, + validate_json, + validate_metadata_field_v3, +) +from zarr_metadata.model._validation import _prefix, arrays_to_tuples + +if TYPE_CHECKING: + from zarr_metadata._common import JSONValue + from zarr_metadata.v2 import ZarrV2CodecMetadata + +# --- public exports -------------------------------------------------------- + + +def test_guards_exported_from_package() -> None: + """The wire-type guard/parser functions are exported from the package.""" + import zarr_metadata.model + + for name in ( + "is_json", + "parse_json", + "is_metadata_field_v3", + "parse_metadata_field_v3", + "is_array_metadata_v3", + "parse_array_metadata_v3", + "is_array_metadata_v2", + "parse_array_metadata_v2", + ): + assert name in zarr_metadata.model.__all__ + assert hasattr(zarr_metadata.model, name) + + +def test_store_key_pairs_exported_from_package() -> None: + """Each store-key constant is exported together with its Literal type + alias, and the pair cannot drift apart.""" + import zarr_metadata.model as m + + pairs = [ + ("ARRAY_METADATA_STORE_KEY_V2", "ZarrV2ArrayMetadataStoreKey"), + ("ARRAY_METADATA_STORE_KEY_V3", "ZarrV3ArrayMetadataStoreKey"), + ("ATTRIBUTES_STORE_KEY_V2", "ZarrV2AttributesStoreKey"), + ("GROUP_METADATA_STORE_KEY_V2", "ZarrV2GroupMetadataStoreKey"), + ("GROUP_METADATA_STORE_KEY_V3", "ZarrV3GroupMetadataStoreKey"), + ("CONSOLIDATED_METADATA_STORE_KEY_V2", "ZarrV2ConsolidatedMetadataStoreKey"), + ] + for const_name, alias_name in pairs: + assert const_name in m.__all__ + assert alias_name in m.__all__ + assert (getattr(m, const_name),) == get_args(getattr(m, alias_name)) + + +def test_validation_diagnostics_exported_from_package() -> None: + """The validation-diagnostic types and validators are exported from the package.""" + import zarr_metadata.model + + for name in ( + "ValidationProblem", + "MetadataValidationError", + "validate_json", + "validate_metadata_field_v3", + "validate_array_metadata_v3", + "validate_array_metadata_v2", + ): + assert name in zarr_metadata.model.__all__ + assert hasattr(zarr_metadata.model, name) + + +def test_expect_expectfail_smoke() -> None: + """The Expect/ExpectFail test-case dataclasses behave as expected.""" + e = Expect(input=1, output=2, id="x") + assert (e.input, e.output, e.id) == (1, 2, "x") + f = ExpectFail(input=1, exception=ValueError, id="y", msg="boom") + with f.raises(): + raise ValueError("boom") + + +def test_v3_from_json_error_lists_all_problems() -> None: + """A malformed v3 document surfaces every problem via MetadataValidationError.problems.""" + doc: dict[str, object] = dict(ZarrV3ArrayMetadata.create_default().to_json()) + del doc["shape"] + doc["data_type"] = 5 + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV3ArrayMetadata.from_json(doc) + locs = {p.loc for p in exc_info.value.problems} + assert ("shape",) in locs + assert ("data_type",) in locs + + +# --- JSON type / fill_value contract --------------------------------------- + + +def test_json_value_type_accepts_json_shapes() -> None: + # JSONValue is the package's public JSON type alias; assigning JSON-shaped + # values to it is valid. + """The JSONValue type alias accepts JSON-shaped values.""" + value: JSONValue = {"a": [1, 2.0, "x", True, None]} + assert value == {"a": [1, 2.0, "x", True, None]} + + +def test_string_nan_fill_value_roundtrips() -> None: + # Non-finite floats are represented as the spec strings ("NaN", "Infinity", + # "-Infinity") by the caller — the metadata layer does not interpret dtypes. + # The string form round-trips cleanly under default dataclass equality, + # unlike a raw float('nan') (which is an invalid fill_value the caller must + # not pass). + """A string 'NaN' fill_value round-trips cleanly (non-finite floats are the caller's responsibility).""" + m = ZarrV3ArrayMetadata.create_default(fill_value="NaN") + assert ZarrV3ArrayMetadata.from_json(m.to_json()) == m + assert ZarrV3ArrayMetadata.from_json(m.to_json()).fill_value == "NaN" + + +# --- ZarrV3NamedConfig.to_json ------------------------------------------------ + +ZARR_TO_JSON_CASES = [ + Expect( + ZarrV3NamedConfig(name="regular", configuration={"chunk_shape": [1]}), + {"name": "regular", "configuration": {"chunk_shape": [1]}}, + id="with-configuration", + ), + Expect( + ZarrV3NamedConfig(name="bytes", configuration={}), + "bytes", + id="empty-configuration-shorthand", + ), +] + + +@pytest.mark.parametrize("case", ZARR_TO_JSON_CASES, ids=lambda c: c.id) +def test_zarr_metadata_v3_to_json(case: Expect[ZarrV3NamedConfig, object]) -> None: + """ZarrV3NamedConfig.to_json emits the canonical extension form.""" + assert case.input.to_json() == case.output + + +def test_zarr_metadata_v3_to_json_preserves_false_obligation() -> None: + """An empty optional extension stays an object so false is not lost.""" + model = ZarrV3NamedConfig(name="optional", configuration={}, must_understand=False) + assert model.to_json() == {"name": "optional", "must_understand": False} + + +# --- ZarrV3NamedConfig.from_json ----------------------------------------------- + +ZARR_FROM_JSON_CASES = [ + Expect("bytes", ZarrV3NamedConfig(name="bytes", configuration={}), id="bare-string"), + Expect( + {"name": "regular", "configuration": {"chunk_shape": [1]}}, + ZarrV3NamedConfig(name="regular", configuration={"chunk_shape": (1,)}), + id="object-with-config", + ), + Expect( + {"name": "bytes"}, + ZarrV3NamedConfig(name="bytes", configuration={}), + id="object-without-config", + ), +] + + +@pytest.mark.parametrize("case", ZARR_FROM_JSON_CASES, ids=lambda c: c.id) +def test_zarr_metadata_v3_from_json(case: Expect[object, ZarrV3NamedConfig]) -> None: + """ZarrV3NamedConfig.from_json parses both the bare-string and object forms.""" + assert ZarrV3NamedConfig.from_json(case.input) == case.output + + +def test_zarr_metadata_v3_from_json_preserves_false_obligation() -> None: + """Explicit false is represented on the normalized model.""" + model = ZarrV3NamedConfig.from_json({"name": "optional", "must_understand": False}) + assert model.must_understand is False + + +# --- V3 baseline ----------------------------------------------------------- + + +def test_v3_to_json_emits_canonical_document() -> None: + """V3 to_json emits exactly the expected document (which covers every + spec-required key by construction).""" + out = ZarrV3ArrayMetadata.create_default( + shape=(10,), data_type=ZarrV3NamedConfig(name="int32", configuration={}) + ).to_json() + assert out == { + "zarr_format": 3, + "node_type": "array", + "shape": (10,), + "fill_value": 0, + "data_type": "int32", + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": (10,)}}, + "codecs": ("bytes",), + "chunk_key_encoding": "default", + } + + +def test_v3_dimension_names_included_when_present() -> None: + """V3 to_json includes dimension_names when they are set.""" + out: dict[str, object] = dict( + ZarrV3ArrayMetadata.create_default(dimension_names=("x",)).to_json() + ) + assert out["dimension_names"] == ("x",) + + +def test_v3_dimension_names_omitted_when_none() -> None: + """V3 to_json omits dimension_names when they are UNSET.""" + out = ZarrV3ArrayMetadata.create_default(dimension_names=UNSET).to_json() + assert "dimension_names" not in out + + +# --- BUG 1: attributes gated on dimension_names ---------------------------- + + +def test_v3_attributes_included_when_dimension_names_is_none() -> None: + """Attributes must be emitted regardless of dimension_names. + + Regression: attributes were gated on ``dimension_names is not None``, + so non-empty attributes were silently dropped when there were no + dimension names. + """ + out: dict[str, object] = dict( + ZarrV3ArrayMetadata.create_default( + dimension_names=UNSET, attributes={"foo": "bar"} + ).to_json() + ) + assert out["attributes"] == {"foo": "bar"} + + +# --- BUG 2: single storage transformer dropped ----------------------------- + + +def test_v3_single_storage_transformer_included() -> None: + """A single storage transformer must be emitted. + + Regression: the guard used ``> 1`` instead of ``> 0``, dropping a + lone storage transformer. + """ + st = ZarrV3NamedConfig(name="some_transformer", configuration={}) + out: dict[str, object] = dict( + ZarrV3ArrayMetadata.create_default(storage_transformers=(st,)).to_json() + ) + assert out["storage_transformers"] == ("some_transformer",) + + +def test_v3_no_storage_transformers_omitted() -> None: + """V3 to_json omits storage_transformers when empty.""" + out = ZarrV3ArrayMetadata.create_default(storage_transformers=()).to_json() + assert "storage_transformers" not in out + + +# --- V3 extra fields ------------------------------------------------------- + + +def test_v3_extra_fields_merged() -> None: + """V3 to_json merges extra_fields into the top-level document.""" + out = ZarrV3ArrayMetadata.create_default( + extra_fields={"my_ext": {"must_understand": False}} + ).to_json() + assert out["my_ext"] == {"must_understand": False} + + +def test_v3_extra_fields_overlapping_standard_field_rejected() -> None: + """Constructing a V3 model with an extra field that collides with a standard key is rejected.""" + with pytest.raises(ValueError): + ZarrV3ArrayMetadata.create_default(extra_fields={"shape": {"must_understand": False}}) + + +# --- V3 key/value ---------------------------------------------------------- + + +def test_v3_to_key_value_is_valid_json_under_zarr_json() -> None: + """V3 to_key_value produces valid JSON bytes under the zarr.json key.""" + kv = ZarrV3ArrayMetadata.create_default(attributes={"a": 1}).to_key_value() + assert set(kv) == {"zarr.json"} + parsed = json.loads(kv["zarr.json"].decode("utf-8")) + assert parsed["zarr_format"] == 3 + assert parsed["attributes"] == {"a": 1} + + +# --- V3 standard-key sets -------------------------------------------------- + + +def test_standard_keys_is_union_of_required_and_optional() -> None: + """The standard-key set is the union of the required and optional key sets.""" + assert ( + ARRAY_METADATA_STANDARD_KEYS_V3 + == ARRAY_METADATA_REQUIRED_KEYS_V3 | ARRAY_METADATA_OPTIONAL_KEYS_V3 + ) + + +def test_standard_keys_contains_known_fields_and_excludes_extensions() -> None: + """The standard-key set contains known fields and excludes extension keys.""" + assert { + "zarr_format", + "node_type", + "shape", + "codecs", + } <= ARRAY_METADATA_STANDARD_KEYS_V3 + assert "my_ext" not in ARRAY_METADATA_STANDARD_KEYS_V3 + + +# --- create_default -------------------------------------------------------- + + +def test_v3_create_default_is_valid_empty_array() -> None: + """V3 create_default builds a structurally valid empty array that round-trips.""" + m = ZarrV3ArrayMetadata.create_default() + assert m.shape == () + assert m.data_type == ZarrV3NamedConfig(name="uint8", configuration={}) + assert m.fill_value == 0 + assert m.attributes == {} + assert m.extra_fields == {} + # the default document is structurally valid and round-trips + assert validate_array_metadata_v3(m.to_json()) == [] + assert ZarrV3ArrayMetadata.from_json(m.to_json()) == m + + +def test_v3_create_default_applies_overrides() -> None: + """V3 create_default applies keyword overrides over the defaults.""" + m = ZarrV3ArrayMetadata.create_default(shape=(4, 4), attributes={"a": 1}) + assert m.shape == (4, 4) + assert m.attributes == {"a": 1} + # un-overridden fields keep their defaults + assert m.data_type == ZarrV3NamedConfig(name="uint8", configuration={}) + + +def test_v2_create_default_is_valid_empty_array() -> None: + """V2 create_default builds a structurally valid empty array that round-trips.""" + m = ZarrV2ArrayMetadata.create_default() + assert m.shape == () + assert m.chunks == () + assert m.fill_value == 0 + assert m.compressor is None + assert m.filters is None + assert m.attributes is UNSET + assert validate_array_metadata_v2(m.to_json()) == [] + assert ZarrV2ArrayMetadata.from_json(m.to_json()) == m + + +def test_v2_create_default_applies_overrides() -> None: + """V2 create_default applies keyword overrides over the defaults.""" + m = ZarrV2ArrayMetadata.create_default(shape=(8,), attributes={"k": "v"}) + assert m.shape == (8,) + assert m.attributes == {"k": "v"} + assert m.dtype == "|u1" # default dtype unchanged + + +# --- V3 update ------------------------------------------------------------- + +# Cluster 3: update same-shape pairs across versions — parametrized + +UPDATE_NEW_INSTANCE_PARAMS = [ + pytest.param(ZarrV3ArrayMetadata, id="v3"), + pytest.param(ZarrV2ArrayMetadata, id="v2"), +] + + +@pytest.mark.parametrize("model_cls", UPDATE_NEW_INSTANCE_PARAMS) +def test_update_returns_new_instance( + model_cls: type[ZarrV3ArrayMetadata | ZarrV2ArrayMetadata], +) -> None: + """update returns a new instance with the field replaced, leaving the original unchanged.""" + base = model_cls.create_default(shape=(10,)) + updated = base.update(shape=(20,)) + assert updated.shape == (20,) + assert base.shape == (10,) # original unchanged + assert isinstance(updated, model_cls) + + +UPDATE_NO_ARGS_PARAMS = [ + pytest.param(ZarrV3ArrayMetadata, id="v3"), + pytest.param(ZarrV2ArrayMetadata, id="v2"), +] + + +@pytest.mark.parametrize("model_cls", UPDATE_NO_ARGS_PARAMS) +def test_update_no_args_returns_equal_model( + model_cls: type[ZarrV3ArrayMetadata | ZarrV2ArrayMetadata], +) -> None: + """update with no arguments returns a model equal to the original.""" + base = model_cls.create_default() + assert base.update() == base + + +# V3-only update tests — kept direct (extra_fields is v3-specific) + + +def test_update_can_replace_extra_fields() -> None: + """update can replace the extra_fields mapping.""" + base = ZarrV3ArrayMetadata.create_default(extra_fields={}) + updated = base.update(extra_fields={"my_ext": {"must_understand": False}}) + assert updated.extra_fields == {"my_ext": {"must_understand": False}} + + +def test_update_replaces_extra_fields_rather_than_merging() -> None: + """update replaces extra_fields wholesale rather than merging.""" + base = ZarrV3ArrayMetadata.create_default(extra_fields={"a": {"must_understand": False}}) + updated = base.update(extra_fields={"b": {"must_understand": True}}) + assert updated.extra_fields == {"b": {"must_understand": True}} + + +def test_partial_keys_match_settable_model_fields() -> None: + """The partial TypedDict must list exactly the constructor-settable fields. + + Guards against drift: adding/removing a settable field on the model + without updating ``ZarrV3ArrayMetadataPartial`` fails here. + """ + settable = {f.name for f in dataclasses.fields(ZarrV3ArrayMetadata) if f.init} + assert set(ZarrV3ArrayMetadataPartial.__annotations__) == settable + + +# --- V2 model -------------------------------------------------------------- + + +def test_v2_partial_keys_match_settable_model_fields() -> None: + """The v2 partial TypedDict must list exactly the settable fields.""" + settable = {f.name for f in dataclasses.fields(ZarrV2ArrayMetadata) if f.init} + assert set(ZarrV2ArrayMetadataPartial.__annotations__) == settable + + +def test_v2_to_key_value_splits_zarray_and_zattrs() -> None: + """V2 to_key_value splits the document into .zarray and .zattrs.""" + kv = ZarrV2ArrayMetadata.create_default(attributes={"a": 1}).to_key_value() + assert set(kv) == {".zarray", ".zattrs"} + zarray = json.loads(kv[".zarray"].decode("utf-8")) + zattrs = json.loads(kv[".zattrs"].decode("utf-8")) + assert zarray["zarr_format"] == 2 + assert zattrs == {"a": 1} + + +def test_v2_zarray_excludes_attributes() -> None: + """The on-disk ``.zarray`` document must not contain user attributes. + + In v2, attributes live only in the sibling ``.zattrs`` file. The bundled + ``ZarrV2ArrayMetadataJSON`` / ``to_json()`` carry attributes for convenience, but + ``to_key_value()`` must split them out. + """ + kv = ZarrV2ArrayMetadata.create_default(attributes={"a": 1}).to_key_value() + zarray = json.loads(kv[".zarray"].decode("utf-8")) + assert "attributes" not in zarray + + +def test_v2_to_json_still_includes_attributes() -> None: + """``to_json()`` is the bundled in-memory form and keeps attributes.""" + out: dict[str, object] = dict(ZarrV2ArrayMetadata.create_default(attributes={"a": 1}).to_json()) + assert out["attributes"] == {"a": 1} + + +# --- arrays_to_tuples helper ---------------------------------------------- + +ARRAYS_TO_TUPLES_CASES = [ + Expect([1, 2, 3], (1, 2, 3), id="top-level-list"), + Expect({"a": [1, [2, 3]], "b": "x"}, {"a": (1, (2, 3)), "b": "x"}, id="nested-in-dict"), + Expect(5, 5, id="scalar-int"), + Expect("s", "s", id="scalar-str"), + Expect(None, None, id="scalar-none"), + Expect( + {"name": "bytes", "configuration": {"nums": [1, 2]}}, + {"name": "bytes", "configuration": {"nums": (1, 2)}}, + id="dict-keys-preserved", + ), +] + + +@pytest.mark.parametrize("case", ARRAYS_TO_TUPLES_CASES, ids=lambda c: c.id) +def test_arrays_to_tuples(case: Expect[object, object]) -> None: + """arrays_to_tuples recursively converts JSON arrays to tuples.""" + assert arrays_to_tuples(case.input) == case.output + + +# --- ZarrV3ArrayMetadata.from_json ---------------------------------------- + + +def test_v3_from_json_reconstructs_required_fields() -> None: + """V3 from_json reconstructs the required fields from a document.""" + doc = ZarrV3ArrayMetadata.create_default( + shape=(7,), + attributes={"a": 1}, + data_type=ZarrV3NamedConfig(name="int32", configuration={}), + ).to_json() + model = ZarrV3ArrayMetadata.from_json(doc) + assert model.shape == (7,) + assert model.data_type == ZarrV3NamedConfig(name="int32", configuration={}) + assert model.attributes == {"a": 1} + + +def test_v3_from_json_defaults_for_omitted_optionals() -> None: + """V3 from_json supplies defaults for omitted optional fields.""" + doc = ZarrV3ArrayMetadata.create_default( + attributes={}, storage_transformers=(), dimension_names=UNSET + ).to_json() + # to_json omits these entirely; from_json must restore defaults + model = ZarrV3ArrayMetadata.from_json(doc) + assert model.attributes == {} + assert model.storage_transformers == () + assert model.dimension_names is UNSET + + +def test_v3_from_json_routes_unknown_keys_to_extra_fields() -> None: + """V3 from_json routes unknown top-level keys into extra_fields.""" + doc = ZarrV3ArrayMetadata.create_default( + extra_fields={"my_ext": {"must_understand": False}} + ).to_json() + model = ZarrV3ArrayMetadata.from_json(doc) + assert model.extra_fields == {"my_ext": {"must_understand": False}} + + +def test_v3_from_json_standard_keys_not_in_extra_fields() -> None: + """V3 from_json keeps standard keys out of extra_fields.""" + doc = ZarrV3ArrayMetadata.create_default( + shape=(10,), attributes={"a": 1}, dimension_names=("x",) + ).to_json() + model = ZarrV3ArrayMetadata.from_json(doc) + assert model.extra_fields == {} + + +def test_v3_from_json_nested_arrays_in_attributes_become_tuples() -> None: + """V3 from_json converts nested arrays in attributes into tuples.""" + doc = ZarrV3ArrayMetadata.create_default(attributes={"scale": [[1, 2], [3, 4]]}).to_json() + model = ZarrV3ArrayMetadata.from_json(doc) + assert model.attributes == {"scale": ((1, 2), (3, 4))} + + +# --- ZarrV3ArrayMetadata.from_key_value ---------------------------------- + + +def test_v3_from_key_value_parses_zarr_json() -> None: + """V3 from_key_value parses the zarr.json entry into a model.""" + kv = ZarrV3ArrayMetadata.create_default(shape=(3,)).to_key_value() + model = ZarrV3ArrayMetadata.from_key_value(kv) + assert model.shape == (3,) + + +# --- Cluster 2: from_key_value missing-key raises (parametrized) ----------- + +FROM_KEY_VALUE_MISSING_PARAMS = [ + pytest.param( + ZarrV3ArrayMetadata, + ExpectFail({}, MetadataValidationError, id="v3-missing-zarr-json", msg="missing store key"), + id="v3-missing-zarr-json", + ), + pytest.param( + ZarrV2ArrayMetadata, + ExpectFail({}, MetadataValidationError, id="v2-missing-zarray", msg="missing store key"), + id="v2-missing-zarray", + ), +] + + +@pytest.mark.parametrize(("model_cls", "case"), FROM_KEY_VALUE_MISSING_PARAMS) +def test_from_key_value_missing_key_raises( + model_cls: type[ZarrV3ArrayMetadata | ZarrV2ArrayMetadata], + case: ExpectFail[dict[str, bytes]], +) -> None: + """from_key_value raises MetadataValidationError when the required store key is absent.""" + with case.raises(): + model_cls.from_key_value(case.input) + + +# --- Cluster 1: round-trips (model → json → model, parametrized) ----------- + +ROUNDTRIP_MODEL_JSON_PARAMS = [ + pytest.param( + ZarrV3ArrayMetadata, + ZarrV3ArrayMetadata.create_default( + shape=(10,), + attributes={"a": 1}, + dimension_names=("x",), + storage_transformers=(ZarrV3NamedConfig(name="t", configuration={}),), + extra_fields={"ext": {"must_understand": False}}, + ), + id="v3-full", + ), + pytest.param( + ZarrV3ArrayMetadata, + ZarrV3ArrayMetadata.create_default( + attributes={}, + dimension_names=UNSET, + storage_transformers=(), + extra_fields={}, + ), + id="v3-empty-optionals", + ), + pytest.param( + ZarrV2ArrayMetadata, + ZarrV2ArrayMetadata.create_default(attributes={"a": 1}, filters=None, compressor=None), + id="v2-basic", + ), +] + + +@pytest.mark.parametrize(("model_cls", "model"), ROUNDTRIP_MODEL_JSON_PARAMS) +def test_roundtrip_model_json_model( + model_cls: type[ZarrV3ArrayMetadata | ZarrV2ArrayMetadata], + model: ZarrV3ArrayMetadata | ZarrV2ArrayMetadata, +) -> None: + """A model round-trips through to_json/from_json back to an equal model.""" + assert model_cls.from_json(model.to_json()) == model + + +# --- Round-trips (model → key_value → model, parametrized) ----------------- + +ROUNDTRIP_KEY_VALUE_PARAMS = [ + pytest.param( + ZarrV3ArrayMetadata, + ZarrV3ArrayMetadata.create_default(attributes={"a": 1}), + id="v3", + ), + pytest.param( + ZarrV2ArrayMetadata, + ZarrV2ArrayMetadata.create_default(attributes={"a": 1}), + id="v2", + ), +] + + +@pytest.mark.parametrize(("model_cls", "model"), ROUNDTRIP_KEY_VALUE_PARAMS) +def test_roundtrip_via_key_value( + model_cls: type[ZarrV3ArrayMetadata | ZarrV2ArrayMetadata], + model: ZarrV3ArrayMetadata | ZarrV2ArrayMetadata, +) -> None: + """A model round-trips through to_key_value/from_key_value back to an equal model.""" + assert model_cls.from_key_value(model.to_key_value()) == model + + +# --- Round-trips (json → model → json, direction distinct — kept direct) --- + + +def test_v3_roundtrip_json_model_json() -> None: + """A v3 document round-trips through from_json/to_json back to an equal document.""" + doc = ZarrV3ArrayMetadata.create_default( + shape=(10,), attributes={"a": 1}, dimension_names=("x",) + ).to_json() + assert ZarrV3ArrayMetadata.from_json(doc).to_json() == doc + + +def test_v2_roundtrip_json_model_json() -> None: + """A v2 document round-trips through from_json/to_json back to an equal document.""" + doc = ZarrV2ArrayMetadata.create_default(attributes={"a": 1}).to_json() + assert ZarrV2ArrayMetadata.from_json(doc).to_json() == doc + + +# --- to_json shares no mutable state with the model ------------------------ + +TO_JSON_NO_ALIASING_PARAMS = [ + pytest.param( + ZarrV3ArrayMetadata.create_default( + shape=(2,), + attributes={"a": {"b": [1]}}, + codecs=(ZarrV3NamedConfig(name="blosc", configuration={"opts": {"level": 1}}),), + extra_fields={"ext": {"must_understand": False, "cfg": {"x": [1]}}}, + ), + id="v3", + ), + pytest.param( + ZarrV2ArrayMetadata.create_default( + attributes={"a": {"b": [1]}}, + compressor={"id": "zstd", "opts": {"level": 1}}, + filters=({"id": "delta", "cfg": [1]},), + fill_value=[0, 0], + ), + id="v2", + ), +] + + +@pytest.mark.parametrize("model", TO_JSON_NO_ALIASING_PARAMS) +def test_to_json_shares_no_mutable_state_with_model( + model: ZarrV3ArrayMetadata | ZarrV2ArrayMetadata, +) -> None: + """Mutating a document returned by to_json leaves the model unchanged.""" + baseline = copy.deepcopy(model.to_json()) + mutate_nested_containers(model.to_json()) + assert model.to_json() == baseline + + +def test_v3_parser_accepts_bare_string_data_type() -> None: + """V3 from_json accepts a bare-string data_type and re-serializes it canonically.""" + doc = ZarrV3ArrayMetadata.create_default().to_json() + doc["data_type"] = "int32" + model = ZarrV3ArrayMetadata.from_json(doc) + assert model.data_type == ZarrV3NamedConfig(name="int32", configuration={}) + assert model.to_json()["data_type"] == "int32" + + +@pytest.mark.parametrize("name", ["bytes", "ANY string", "urn:example:codec"]) +def test_metadata_field_accepts_any_string_name(name: str) -> None: + """The structural layer checks the name type, not syntax or registration.""" + assert validate_metadata_field_v3({"name": name}) == [] + + +@pytest.mark.parametrize("value", [0, 1, "false", None]) +def test_metadata_field_must_understand_must_be_boolean(value: object) -> None: + """must_understand is a JSON boolean, not a truthy scalar.""" + problems = validate_metadata_field_v3({"name": "x", "must_understand": value}) + assert [(problem.loc, problem.kind) for problem in problems] == [ + (("must_understand",), "invalid_type") + ] + + +def test_metadata_field_rejects_unknown_envelope_member() -> None: + """Unknown envelope keys cannot be silently discarded during normalization.""" + problems = validate_metadata_field_v3({"name": "x", "typo": 1}) + assert [(problem.loc, problem.kind) for problem in problems] == [(("typo",), "invalid_value")] + + +@pytest.mark.parametrize("field", ["codecs", "storage_transformers"]) +def test_optional_extension_points_allow_must_understand_false(field: str) -> None: + """Codecs and storage transformers may be explicitly ignorable.""" + doc: dict[str, object] = dict(ZarrV3ArrayMetadata.create_default().to_json()) + doc[field] = ({"name": "optional", "must_understand": False},) + assert validate_array_metadata_v3(doc) == [] + + +@pytest.mark.parametrize("field", ["data_type", "chunk_grid", "chunk_key_encoding"]) +def test_required_extension_points_reject_must_understand_false(field: str) -> None: + """Core extension points needed to locate or decode chunks cannot be ignored.""" + doc: dict[str, object] = dict(ZarrV3ArrayMetadata.create_default().to_json()) + doc[field] = {"name": "optional", "must_understand": False} + assert [(problem.loc, problem.kind) for problem in validate_array_metadata_v3(doc)] == [ + ((field, "must_understand"), "invalid_value") + ] + + +def test_v3_codecs_cannot_be_empty() -> None: + """The core document requires at least one array-to-bytes codec.""" + doc: dict[str, object] = dict(ZarrV3ArrayMetadata.create_default().to_json()) + doc["codecs"] = () + assert [(problem.loc, problem.kind) for problem in validate_array_metadata_v3(doc)] == [ + (("codecs",), "invalid_value") + ] + + +def test_v2_roundtrip_with_compressor_and_filters() -> None: + # Non-None compressor/filters must round-trip; extra assertion on .compressor. + """A v2 model with non-None compressor and filters round-trips.""" + compressor: ZarrV2CodecMetadata = {"id": "blosc", "clevel": 5} + filters: tuple[ZarrV2CodecMetadata, ...] = ({"id": "delta"},) + m = ZarrV2ArrayMetadata.create_default(compressor=compressor, filters=filters) + restored = ZarrV2ArrayMetadata.from_json(m.to_json()) + assert restored == m + assert restored.compressor == {"id": "blosc", "clevel": 5} + + +# --- ZarrV2ArrayMetadata.from_json ---------------------------------------- + + +def test_v2_from_json_reconstructs_fields() -> None: + """V2 from_json reconstructs the fields from a document.""" + doc = ZarrV2ArrayMetadata.create_default(shape=(4,), attributes={"a": 1}, dtype="<i4").to_json() + model = ZarrV2ArrayMetadata.from_json(doc) + assert model.shape == (4,) + assert model.dtype == "<i4" + assert model.attributes == {"a": 1} + + +def test_v2_from_json_attributes_absent_is_unset() -> None: + """V2 from_json reads an absent attributes key as UNSET, distinct from an + explicit empty mapping.""" + absent = ZarrV2ArrayMetadata.from_json(ZarrV2ArrayMetadata.create_default().to_json()) + explicit = ZarrV2ArrayMetadata.from_json( + ZarrV2ArrayMetadata.create_default(attributes={}).to_json() + ) + assert absent.attributes is UNSET + assert explicit.attributes == {} + assert absent != explicit + + +# --- ZarrV2ArrayMetadata.from_key_value -------------------------------- + + +def test_v2_from_key_value_remerges_zattrs() -> None: + """V2 from_key_value re-merges .zattrs back into attributes.""" + kv = ZarrV2ArrayMetadata.create_default(attributes={"a": 1}, shape=(10,)).to_key_value() + model = ZarrV2ArrayMetadata.from_key_value(kv) + assert model.attributes == {"a": 1} + assert model.shape == (10,) + + +@pytest.mark.parametrize("extra_key", ["attributes", "vendor_extension"]) +def test_v2_from_key_value_rejects_zarray_extra_members(extra_key: str) -> None: + """Raw `.zarray` documents reject every non-spec member.""" + doc: dict[str, object] = dict(ZarrV2ArrayMetadata.create_default().to_json()) + doc.pop("attributes", None) + doc[extra_key] = {} + + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV2ArrayMetadata.from_key_value({".zarray": json.dumps(doc).encode()}) + + assert [(problem.loc, problem.kind) for problem in exc_info.value.problems] == [ + ((extra_key,), "invalid_value") + ] + + +def test_v2_zattrs_presence_round_trips() -> None: + """The .zattrs file's presence is part of the store: an absent file reads + as UNSET and emits no .zattrs; an explicit empty file reads as {} and + emits .zattrs — the two stores stay distinct through a round-trip.""" + explicit_kv = dict(ZarrV2ArrayMetadata.create_default(attributes={}).to_key_value()) + assert ".zattrs" in explicit_kv + absent_kv = dict(explicit_kv) + del absent_kv[".zattrs"] + + absent = ZarrV2ArrayMetadata.from_key_value(absent_kv) + explicit = ZarrV2ArrayMetadata.from_key_value(explicit_kv) + assert absent.attributes is UNSET + assert explicit.attributes == {} + assert ".zattrs" not in absent.to_key_value() + assert ".zattrs" in explicit.to_key_value() + + +def test_v2_from_json_nested_arrays_in_attributes_become_tuples() -> None: + """V2 from_json converts nested arrays in attributes into tuples.""" + doc = ZarrV2ArrayMetadata.create_default(attributes={"axes": [[0, 1], [2, 3]]}).to_json() + model = ZarrV2ArrayMetadata.from_json(doc) + assert model.attributes == {"axes": ((0, 1), (2, 3))} + + +# --- scalar wire-type guards (is_/validate_/parse_) ------------------------ +# +# Each value is modelled once as Expect[object, frozenset[tuple[str | int, ...]]] +# where `output` is the set of expected problem locs validate_* must report — +# frozenset() means VALID. Valid iff output == frozenset(). + +JSON_VALIDATE_CASES: list[Expect[object, frozenset[tuple[str | int, ...]]]] = [ + Expect("s", frozenset(), id="str"), + Expect(1, frozenset(), id="int"), + Expect(1.5, frozenset(), id="float"), + Expect(True, frozenset(), id="bool"), + Expect(None, frozenset(), id="none"), + Expect({"a": [1, {"b": None}], "c": "x"}, frozenset(), id="nested-containers"), + Expect((1, 2, 3), frozenset(), id="tuple-array"), + Expect(float("nan"), frozenset({()}), id="nan"), + Expect(float("inf"), frozenset({()}), id="inf"), + Expect(float("-inf"), frozenset({()}), id="negative-inf"), + Expect(object(), frozenset({()}), id="object"), + Expect(b"abc", frozenset({()}), id="bytes"), + Expect(bytearray(b"abc"), frozenset({()}), id="bytearray"), + Expect({1: "x"}, frozenset({()}), id="non-str-key"), + Expect([1, object()], frozenset({(1,)}), id="non-json-list-item"), + Expect({"ok": object()}, frozenset({("ok",)}), id="non-json-value"), +] + + +@pytest.mark.parametrize("case", JSON_VALIDATE_CASES, ids=lambda c: c.id) +def test_is_json(case: Expect[object, frozenset[tuple[str | int, ...]]]) -> None: + """is_json reports whether a value is JSON-serializable.""" + assert is_json(case.input) is (case.output == frozenset()) + + +@pytest.mark.parametrize("case", JSON_VALIDATE_CASES, ids=lambda c: c.id) +def test_validate_json(case: Expect[object, frozenset[tuple[str | int, ...]]]) -> None: + """validate_json reports the problems (and their locs) for a value.""" + problems = validate_json(case.input) + assert (problems == []) is (case.output == frozenset()) + assert {p.loc for p in problems} >= case.output + + +@pytest.mark.parametrize("case", JSON_VALIDATE_CASES, ids=lambda c: c.id) +def test_parse_json(case: Expect[object, frozenset[tuple[str | int, ...]]]) -> None: + """parse_json returns valid JSON values and raises on invalid ones.""" + if case.output == frozenset(): + parsed = parse_json(case.input) + assert arrays_to_tuples(parsed) == arrays_to_tuples(case.input) + else: + with pytest.raises(MetadataValidationError): + parse_json(case.input) + + +def test_parse_json_materializes_abstract_containers() -> None: + """Accepted Mapping and Sequence values normalize to JSON encoder containers.""" + value = UserDict({"values": range(3)}) + + parsed = parse_json(value) + + assert parsed == {"values": (0, 1, 2)} + assert type(parsed) is dict + assert type(parsed["values"]) is tuple + json.dumps(parsed, allow_nan=False) + + +def test_json_type_guard_rejects_abstract_sequence() -> None: + """A guard cannot narrow an abstract sequence that only the parser materializes.""" + assert not is_json(range(3)) + assert parse_json(range(3)) == (0, 1, 2) + + +def test_parse_metadata_field_materializes_abstract_containers() -> None: + """Named-config parsing produces canonical containers at every nesting level.""" + value = UserDict({"name": "example", "configuration": UserDict({"values": range(2)})}) + + parsed = parse_metadata_field_v3(value) + + assert isinstance(parsed, dict) + assert parsed == {"name": "example", "configuration": {"values": (0, 1)}} + assert type(parsed["configuration"]) is dict + + +def test_metadata_field_type_guard_rejects_abstract_mapping() -> None: + """A metadata-field guard only narrows concrete TypedDict-shaped objects.""" + value = UserDict({"name": "bytes"}) + + assert not is_metadata_field_v3(value) + assert parse_metadata_field_v3(value) == {"name": "bytes"} + + +def test_validate_json_reports_json_in_message() -> None: + """validate_json's message for a non-JSON value mentions JSON.""" + problems = validate_json(object()) + assert problems[0].loc == () + assert "JSON" in problems[0].message + + +METADATA_FIELD_VALIDATE_CASES: list[Expect[object, frozenset[tuple[str | int, ...]]]] = [ + Expect("bytes", frozenset(), id="bare-string"), + Expect({"name": "x", "configuration": {"a": 1}}, frozenset(), id="named-config"), + Expect({"name": "bytes"}, frozenset(), id="name-only"), + Expect(5, frozenset({()}), id="not-str-or-mapping"), + Expect({"configuration": {}}, frozenset({("name",)}), id="missing-name"), + Expect({"name": 3}, frozenset({("name",)}), id="non-str-name"), + Expect( + {"name": "x", "configuration": [1]}, + frozenset({("configuration",)}), + id="config-not-mapping", + ), + Expect( + {"name": "x", "configuration": {1: "y"}}, + frozenset({("configuration",)}), + id="config-non-str-key", + ), +] + + +@pytest.mark.parametrize("case", METADATA_FIELD_VALIDATE_CASES, ids=lambda c: c.id) +def test_is_metadata_field_v3(case: Expect[object, frozenset[tuple[str | int, ...]]]) -> None: + """is_metadata_field_v3 reports whether a value is a v3 metadata field.""" + assert is_metadata_field_v3(case.input) is (case.output == frozenset()) + + +@pytest.mark.parametrize("case", METADATA_FIELD_VALIDATE_CASES, ids=lambda c: c.id) +def test_validate_metadata_field_v3( + case: Expect[object, frozenset[tuple[str | int, ...]]], +) -> None: + """validate_metadata_field_v3 reports the problems for a metadata-field value.""" + problems = validate_metadata_field_v3(case.input) + assert (problems == []) is (case.output == frozenset()) + assert {p.loc for p in problems} >= case.output + + +@pytest.mark.parametrize("case", METADATA_FIELD_VALIDATE_CASES, ids=lambda c: c.id) +def test_parse_metadata_field_v3( + case: Expect[object, frozenset[tuple[str | int, ...]]], +) -> None: + """parse_metadata_field_v3 returns valid fields and raises on invalid ones.""" + if case.output == frozenset(): + assert parse_metadata_field_v3(case.input) is case.input + else: + with pytest.raises(MetadataValidationError): + parse_metadata_field_v3(case.input) + + +# --- array-document wire-type guards (is_/validate_/parse_) ---------------- +# +# Each case starts from a valid document (built by `make`) and applies a +# mutation. `expected_locs` are loc paths `validate_*` must report for the +# invalid cases (a subset check, so accumulation of OTHER problems is allowed). + + +def _build_v3(**overrides: Unpack[ZarrV3ArrayMetadataPartial]) -> dict[str, object]: + return dict(ZarrV3ArrayMetadata.create_default(**overrides).to_json()) + + +def _build_v2(**overrides: Unpack[ZarrV2ArrayMetadataPartial]) -> dict[str, object]: + return dict(ZarrV2ArrayMetadata.create_default(**overrides).to_json()) + + +def _mutate(build: Callable[[], dict], mutate: Callable[[dict], object]) -> Callable[[], dict]: + def _factory() -> dict: + doc = build() + mutate(doc) + return doc + + return _factory + + +def _del(key: str) -> Callable[[dict], object]: + return lambda doc: doc.pop(key) + + +def _set(key: str, value: object) -> Callable[[dict], object]: + return lambda doc: doc.__setitem__(key, value) + + +V3_DOC_CASES: list[Expect[Callable[[], object], frozenset[tuple[str | int, ...]]]] = [ + Expect(_build_v3, frozenset(), id="valid"), + Expect( + lambda: _build_v3(shape=(10,), attributes={"a": 1}, dimension_names=("x",)), + frozenset(), + id="valid-with-attributes-and-dim-names", + ), + Expect( + lambda: _build_v3(extra_fields={"my_ext": {"must_understand": False}}), + frozenset(), + id="valid-with-extra-fields", + ), + Expect(_mutate(_build_v3, _del("shape")), frozenset({("shape",)}), id="missing-shape"), + Expect( + _mutate(_build_v3, _set("data_type", 5)), + frozenset({("data_type",)}), + id="bad-data-type", + ), + Expect( + _mutate(_build_v3, _set("shape", "not-a-shape")), + frozenset({("shape",)}), + id="shape-not-sequence", + ), + Expect( + _mutate(_build_v3, _set("shape", [1, "x"])), + frozenset({("shape",)}), + id="shape-non-int-item", + ), + Expect( + _mutate(_build_v3, _set("codecs", (5,))), + frozenset({("codecs", 0)}), + id="bad-codec-entry", + ), + Expect(lambda: [1, 2, 3], frozenset({()}), id="non-mapping-list"), + Expect(lambda: "nope", frozenset({()}), id="non-mapping-str"), + Expect( + _mutate(_mutate(_build_v3, _del("shape")), _set("data_type", 5)), + frozenset({("shape",), ("data_type",)}), + id="missing-shape-and-bad-data-type", + ), +] + +V2_DOC_CASES: list[Expect[Callable[[], object], frozenset[tuple[str | int, ...]]]] = [ + Expect(_build_v2, frozenset(), id="valid"), + Expect(lambda: _build_v2(attributes={"a": 1}), frozenset(), id="valid-with-attributes"), + Expect( + lambda: _build_v2(compressor=None, filters=None), + frozenset(), + id="valid-none-compressor-filters", + ), + Expect( + _mutate(_build_v2, _del("chunks")), + frozenset({("chunks",)}), + id="missing-chunks", + ), + Expect( + _mutate(_build_v2, _set("shape", [1, "x"])), + frozenset({("shape",)}), + id="bad-shape", + ), + Expect( + _mutate(_mutate(_build_v2, _del("chunks")), _set("shape", [1, "x"])), + frozenset({("chunks",), ("shape",)}), + id="missing-chunks-and-bad-shape", + ), +] + +ALL_DOC_CASES = [ + *( + pytest.param( + is_array_metadata_v3, + validate_array_metadata_v3, + parse_array_metadata_v3, + c, + id=f"v3-{c.id}", + ) + for c in V3_DOC_CASES + ), + *( + pytest.param( + is_array_metadata_v2, + validate_array_metadata_v2, + parse_array_metadata_v2, + c, + id=f"v2-{c.id}", + ) + for c in V2_DOC_CASES + ), +] + + +@pytest.mark.parametrize(("is_fn", "validate_fn", "parse_fn", "case"), ALL_DOC_CASES) +def test_array_metadata_guards( + is_fn: Callable[[object], bool], + validate_fn: Callable[[object], list[ValidationProblem]], + parse_fn: Callable[[object], object], + case: Expect[Callable[[], object], frozenset[tuple[str | int, ...]]], +) -> None: + """is_/validate_/parse_ array-metadata guards agree on validity and locs for each case.""" + doc = case.input() + valid = case.output == frozenset() + assert is_fn(doc) is valid + problems = validate_fn(doc) + assert (problems == []) is valid + assert {p.loc for p in problems} >= case.output + if valid: + assert parse_fn(doc) is doc + else: + with pytest.raises(MetadataValidationError): + parse_fn(doc) + + +# --- strict from_json validation ------------------------------------------- + + +FROM_JSON_REJECT_PARAMS = [ + pytest.param( + ZarrV3ArrayMetadata, + ExpectFail(lambda: {"zarr_format": 3}, MetadataValidationError, id="x"), + id="v3-missing-required", + ), + pytest.param( + ZarrV3ArrayMetadata, + ExpectFail(_mutate(_build_v3, _set("data_type", 5)), MetadataValidationError, id="x"), + id="v3-bad-field-type", + ), + pytest.param( + ZarrV2ArrayMetadata, + ExpectFail(lambda: {"zarr_format": 2}, MetadataValidationError, id="x"), + id="v2-missing-required", + ), + pytest.param( + ZarrV3NamedConfig, + ExpectFail(lambda: 5, MetadataValidationError, id="x"), + id="zarr-metadata-bad-input", + ), +] + + +@pytest.mark.parametrize(("model", "case"), FROM_JSON_REJECT_PARAMS) +def test_from_json_rejects_malformed( + model: type[ZarrV3ArrayMetadata | ZarrV2ArrayMetadata | ZarrV3NamedConfig], + case: ExpectFail[Callable[[], object]], +) -> None: + """from_json raises MetadataValidationError on a malformed document.""" + with case.raises(): + model.from_json(case.input()) + + +# --- ValidationProblem / MetadataValidationError / _prefix ----------------- +# Small structural tests — not "parametrize over inputs" shaped, kept direct. + + +def test_validation_problem_str_with_loc() -> None: + """ValidationProblem.__str__ renders a non-empty loc as a dotted path.""" + p = ValidationProblem(loc=("codecs", 0, "name"), message="expected str", kind="invalid_type") + assert str(p) == "codecs.0.name: expected str" + + +def test_validation_problem_str_empty_loc() -> None: + """ValidationProblem.__str__ renders an empty loc as <root>.""" + p = ValidationProblem(loc=(), message="not a mapping", kind="invalid_type") + assert str(p) == "<root>: not a mapping" + + +def test_validation_problem_is_frozen() -> None: + """ValidationProblem is immutable (frozen dataclass).""" + p = ValidationProblem(loc=("shape",), message="x", kind="invalid_type") + with pytest.raises(dataclasses.FrozenInstanceError): + # setattr: assigning to a frozen field is an intentional runtime error, + # spelled dynamically so it is not also a static type error. + setattr(p, "message", "y") # noqa: B010 + + +def test_metadata_validation_error_holds_problems() -> None: + """MetadataValidationError carries its problem list and renders them in its message.""" + problems = [ + ValidationProblem(loc=("shape",), message="missing required key", kind="missing_key"), + ValidationProblem( + loc=("data_type",), message="expected a metadata field", kind="invalid_type" + ), + ] + err = MetadataValidationError(problems) + assert err.problems == problems + assert "shape: missing required key" in str(err) + assert "data_type: expected a metadata field" in str(err) + + +def test_prefix_prepends_loc_head() -> None: + """_prefix prepends a loc head to each problem's loc.""" + problems = [ValidationProblem(loc=("name",), message="expected str", kind="invalid_type")] + prefixed = _prefix(0, problems) + assert prefixed == [ + ValidationProblem(loc=(0, "name"), message="expected str", kind="invalid_type") + ] + + +# --- Stricter v2/v3 field validation and error kinds ------------------------- + + +def test_v2_dtype_must_be_string_or_records() -> None: + """A non-string, non-records v2 dtype is rejected with an invalid_type problem.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"dtype": 42} + problems = validate_array_metadata_v2(doc) + assert [(p.loc, p.kind) for p in problems] == [(("dtype",), "invalid_type")] + + +def test_v2_structured_dtype_records_accepted() -> None: + """A structured v2 dtype (field records, optionally nested/shaped) validates.""" + dtype = (("a", "<i4"), ("b", (("c", "|u1"),)), ("d", "<f8", (2, 2))) + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"dtype": dtype} + assert validate_array_metadata_v2(doc) == [] + + +def test_v2_structured_dtype_malformed_record_rejected() -> None: + """A field record with the wrong arity is rejected.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"dtype": (("a",),)} + problems = validate_array_metadata_v2(doc) + assert [p.loc for p in problems] == [("dtype",)] + + +def test_v2_order_literal_enforced() -> None: + """An order other than 'C' or 'F' is rejected with an invalid_value problem.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"order": "Q"} + problems = validate_array_metadata_v2(doc) + assert [(p.loc, p.kind) for p in problems] == [(("order",), "invalid_value")] + + +def test_v2_compressor_must_be_codec_or_none() -> None: + """A compressor that is not null or a codec config mapping is rejected.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"compressor": "zlib"} + problems = validate_array_metadata_v2(doc) + assert [(p.loc, p.kind) for p in problems] == [(("compressor",), "invalid_type")] + + +def test_v2_compressor_requires_string_id() -> None: + """A compressor mapping without a string id is rejected.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"compressor": {"level": 3}} + problems = validate_array_metadata_v2(doc) + assert [p.loc for p in problems] == [("compressor",)] + + +def test_v2_filters_must_be_codec_sequence_or_none() -> None: + """Filters that are not null or a sequence of codec configs are rejected.""" + for bad in (7, (5,), "gzip"): + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"filters": bad} + problems = validate_array_metadata_v2(doc) + assert [(p.loc, p.kind) for p in problems] == [(("filters",), "invalid_type")], bad + + +def test_v2_shape_and_chunks_must_have_equal_rank() -> None: + """Raw v2 metadata requires one chunk length per array dimension.""" + doc = dict(ZarrV2ArrayMetadata.create_default(shape=(2, 3)).to_json()) + doc["chunks"] = (1,) + + assert [(p.loc, p.kind) for p in validate_array_metadata_v2(doc)] == [ + (("chunks",), "invalid_value") + ] + with pytest.raises(MetadataValidationError, match="same number of dimensions"): + ZarrV2ArrayMetadata.from_key_value({".zarray": json.dumps(doc).encode()}) + + +def test_v2_filters_must_be_nonempty_when_present() -> None: + """A non-null v2 filter sequence contains one or more codec configurations.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) + doc["filters"] = () + + assert [(p.loc, p.kind) for p in validate_array_metadata_v2(doc)] == [ + (("filters",), "invalid_value") + ] + with pytest.raises(MetadataValidationError, match="at least one filter"): + ZarrV2ArrayMetadata.from_key_value({".zarray": json.dumps(doc).encode()}) + + +def test_v2_dimension_separator_literal_enforced() -> None: + """A dimension_separator other than '.' or '/' is rejected.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"dimension_separator": "-"} + problems = validate_array_metadata_v2(doc) + assert [(p.loc, p.kind) for p in problems] == [(("dimension_separator",), "invalid_value")] + + +def test_v2_zarr_format_literal_enforced() -> None: + """A v2 document claiming zarr_format 3 is rejected with an invalid_value problem.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"zarr_format": 3} + problems = validate_array_metadata_v2(doc) + assert [(p.loc, p.kind) for p in problems] == [(("zarr_format",), "invalid_value")] + + +def test_v3_zarr_format_literal_enforced() -> None: + """A v3 document claiming zarr_format 2 is rejected with an invalid_value problem.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"zarr_format": 2} + problems = validate_array_metadata_v3(doc) + assert [(p.loc, p.kind) for p in problems] == [(("zarr_format",), "invalid_value")] + + +@pytest.mark.parametrize( + ("document", "validate"), + [ + pytest.param( + dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"zarr_format": 2.0}, + validate_array_metadata_v2, + id="v2", + ), + pytest.param( + dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"zarr_format": 3.0}, + validate_array_metadata_v3, + id="v3", + ), + ], +) +def test_array_zarr_format_rejects_float( + document: object, validate: Callable[[object], list[ValidationProblem]] +) -> None: + """Integer-valued floats do not satisfy integer format literals.""" + assert [(p.loc, p.kind) for p in validate(document)] == [(("zarr_format",), "invalid_value")] + + +def test_array_v2_rejects_unknown_document_member() -> None: + """The closed v2 merged-document shape rejects undeclared members.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"unexpected": 1} + + assert [(p.loc, p.kind) for p in validate_array_metadata_v2(doc)] == [ + (("unexpected",), "invalid_value") + ] + + +def test_array_v3_from_json_materializes_abstract_containers() -> None: + """A flexible input mapping becomes the canonical dict/tuple model shape.""" + doc = UserDict(dict(ZarrV3ArrayMetadata.create_default(shape=(2,)).to_json())) + doc["shape"] = range(2) + + model = ZarrV3ArrayMetadata.from_json(doc) + + assert model.shape == (0, 1) + assert type(model.shape) is tuple + + +def test_from_key_value_rejects_non_standard_json_constant() -> None: + """Store JSON decoding rejects JavaScript NaN/Infinity constants.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) + doc["fill_value"] = float("nan") + raw = json.dumps(doc) + + with pytest.raises(MetadataValidationError, match="invalid JSON"): + ZarrV3ArrayMetadata.from_key_value({"zarr.json": raw.encode()}) + + +def test_to_key_value_rejects_non_finite_model_value() -> None: + """Strict encoding prevents directly-constructed models from writing invalid JSON.""" + model = ZarrV3ArrayMetadata.create_default(fill_value=float("nan")) + + with pytest.raises(ValueError, match="JSON compliant"): + model.to_key_value() + + +def test_v3_node_type_literal_enforced() -> None: + """A v3 array document claiming node_type 'group' is rejected.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"node_type": "group"} + problems = validate_array_metadata_v3(doc) + assert [(p.loc, p.kind) for p in problems] == [(("node_type",), "invalid_value")] + + +def test_missing_key_kind_is_machine_readable() -> None: + """A missing required key is distinguishable by kind, without message matching.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) + del doc["chunk_key_encoding"] + problems = validate_array_metadata_v3(doc) + assert problems == [ + ValidationProblem(("chunk_key_encoding",), "missing required key", "missing_key") + ] + + +# --- Unified error channels --------------------------------------------------- + + +def test_from_key_value_invalid_json_raises_metadata_error() -> None: + """Undecodable store bytes raise MetadataValidationError (kind invalid_json), not JSONDecodeError.""" + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV3ArrayMetadata.from_key_value({"zarr.json": b"{not json"}) + assert [p.kind for p in exc_info.value.problems] == ["invalid_json"] + + +def test_from_key_value_invalid_utf8_raises_metadata_error() -> None: + """Invalid UTF-8 store bytes use the same invalid_json error channel.""" + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV3ArrayMetadata.from_key_value({"zarr.json": b"\x80"}) + assert [p.kind for p in exc_info.value.problems] == ["invalid_json"] + + +def test_v2_from_key_value_scalar_root_raises_metadata_error() -> None: + """A scalar .zarray document fails through the unified metadata error channel.""" + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV2ArrayMetadata.from_key_value({".zarray": b"null"}) + assert [(problem.loc, problem.kind) for problem in exc_info.value.problems] == [ + ((), "invalid_type") + ] + + +def test_from_key_value_missing_key_kind() -> None: + """A missing store key surfaces as a missing_key problem at the store-key loc.""" + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV2ArrayMetadata.from_key_value({}) + assert exc_info.value.problems == [ + ValidationProblem((".zarray",), "missing store key", "missing_key") + ] + + +def test_extra_fields_overlap_raises_metadata_error() -> None: + """The extra-fields overlap invariant raises MetadataValidationError (a ValueError).""" + with pytest.raises(MetadataValidationError, match="Extra fields") as exc_info: + ZarrV3ArrayMetadata.create_default(extra_fields={"shape": {"must_understand": False}}) + assert [p.kind for p in exc_info.value.problems] == ["invalid_value"] + + +def test_extension_point_fields_annotated_with_role_alias() -> None: + """Extension-point fields are annotated with ZarrV3MetadataField (the + logical role), not ZarrV3NamedConfig (the current serialized form), so a + future widening of the field union does not move annotation sites.""" + assert ZarrV3MetadataField is ZarrV3NamedConfig + annotations = ZarrV3ArrayMetadata.__annotations__ + for field_name in ("data_type", "chunk_grid", "chunk_key_encoding"): + assert annotations[field_name] == "ZarrV3MetadataField" + for field_name in ("codecs", "storage_transformers"): + assert annotations[field_name] == "tuple[ZarrV3MetadataField, ...]" + + +# --- Adversarial-probe fixes: documents that used to pass validation --------- + + +def test_shape_rejects_json_booleans() -> None: + """JSON booleans are not integers: shape/chunks containing true/false are + rejected (bool is an int subclass in Python, so isinstance alone passes).""" + v3 = dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"shape": (True, True)} + assert [p.loc for p in validate_array_metadata_v3(v3)] == [("shape",)] + v2 = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"chunks": (True,)} + assert [p.loc for p in validate_array_metadata_v2(v2)] == [("chunks",)] + + +def test_shape_rejects_negative_dimensions() -> None: + """Dimension lengths must be non-negative; a negative entry is invalid_value.""" + v3 = dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"shape": (-1,)} + assert [(p.loc, p.kind) for p in validate_array_metadata_v3(v3)] == [ + (("shape",), "invalid_value") + ] + v2 = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"chunks": (-5,)} + assert [(p.loc, p.kind) for p in validate_array_metadata_v2(v2)] == [ + (("chunks",), "invalid_value") + ] + + +def test_dimension_names_length_must_match_shape() -> None: + """dimension_names must have one entry per dimension of shape.""" + doc = dict(ZarrV3ArrayMetadata.create_default(shape=(10,)).to_json()) | { + "dimension_names": ("x", "y", "z") + } + assert [(p.loc, p.kind) for p in validate_array_metadata_v3(doc)] == [ + (("dimension_names",), "invalid_value") + ] + + +def test_attributes_values_must_be_json() -> None: + """Attribute values are JSON-checked recursively (like fill_value), so a + non-serializable value is a validation problem, not a later TypeError.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"attributes": {"a": {1, 2}}} + problems = validate_array_metadata_v3(doc) + assert [(p.loc, p.kind) for p in problems] == [(("attributes", "a"), "invalid_type")] + + +def test_configuration_values_must_be_json() -> None: + """Configuration values are JSON-checked recursively, so an int-keyed dict + cannot pass validation and be silently rewritten by json.dumps.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) | { + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": {1: 2}}} + } + problems = validate_array_metadata_v3(doc) + assert [(p.loc, p.kind) for p in problems] == [ + (("chunk_grid", "configuration", "chunk_shape"), "invalid_type") + ] + + +def test_v3_extension_keys_must_be_strings() -> None: + """A non-string top-level key cannot be represented by a v3 document type.""" + doc: dict[object, object] = dict(ZarrV3ArrayMetadata.create_default().to_json()) + doc[1] = {"must_understand": False} + assert [(problem.loc, problem.kind) for problem in validate_array_metadata_v3(doc)] == [ + ((), "invalid_type") + ] + + +def test_v3_extension_values_must_be_json() -> None: + """Extension payloads are JSON-checked before a model is constructed.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) + doc["ext"] = {"must_understand": False, "payload": object()} + assert [(problem.loc, problem.kind) for problem in validate_array_metadata_v3(doc)] == [ + (("ext", "payload"), "invalid_type") + ] + + +def test_v3_json_extension_without_waiver_is_preserved_as_must_understand() -> None: + """A JSON extension without an explicit false waiver remains must-understand.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) + doc["ext"] = 1 + parsed = parse_array_metadata_v3(doc) + assert is_array_metadata_v3(parsed) + model = ZarrV3ArrayMetadata.from_json(doc) + assert model.extra_fields["ext"] == 1 + assert model.must_understand_fields == {"ext": 1} + + +def test_v2_codec_configuration_values_must_be_json() -> None: + """Non-JSON codec parameters are rejected for compressors and filters.""" + for field, value, expected_loc in ( + ("compressor", {"id": "x", "payload": object()}, ("compressor", "payload")), + ("filters", ({"id": "x", "payload": object()},), ("filters", 0, "payload")), + ): + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) + doc[field] = value + assert [(problem.loc, problem.kind) for problem in validate_array_metadata_v2(doc)] == [ + (expected_loc, "invalid_type") + ] + + +def test_dimension_sequences_reject_binary_values() -> None: + """Binary buffers are not JSON arrays even though they are integer sequences.""" + v3 = dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"shape": b"\x02"} + v2 = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"chunks": b"\x02"} + assert [(problem.loc, problem.kind) for problem in validate_array_metadata_v3(v3)] == [ + (("shape",), "invalid_type") + ] + assert [(problem.loc, problem.kind) for problem in validate_array_metadata_v2(v2)] == [ + (("chunks",), "invalid_type") + ] + + +def test_array_parsers_normalize_json_lists_before_narrowing() -> None: + """Parsers return tuple-backed document types while guards reject raw list forms.""" + v3_raw = json.loads(json.dumps(ZarrV3ArrayMetadata.create_default(shape=(2,)).to_json())) + v2_raw = json.loads(json.dumps(ZarrV2ArrayMetadata.create_default(shape=(2,)).to_json())) + + assert validate_array_metadata_v3(v3_raw) == [] + assert validate_array_metadata_v2(v2_raw) == [] + assert not is_array_metadata_v3(v3_raw) + assert not is_array_metadata_v2(v2_raw) + + v3_parsed = parse_array_metadata_v3(v3_raw) + v2_parsed = parse_array_metadata_v2(v2_raw) + assert isinstance(v3_parsed["shape"], tuple) + assert isinstance(v3_parsed["codecs"], tuple) + assert isinstance(v2_parsed["shape"], tuple) + assert isinstance(v2_parsed["chunks"], tuple) + + +def test_array_guards_reject_noncanonical_nested_json() -> None: + """Document guards cannot narrow values that only parsers can materialize.""" + v3 = dict(ZarrV3ArrayMetadata.create_default().to_json()) + v3["fill_value"] = range(2) + v2 = dict(ZarrV2ArrayMetadata.create_default().to_json()) + v2["fill_value"] = range(2) + + assert not is_array_metadata_v3(v3) + assert not is_array_metadata_v2(v2) + assert parse_array_metadata_v3(v3)["fill_value"] == (0, 1) + assert parse_array_metadata_v2(v2)["fill_value"] == (0, 1) + + +# --- must_understand partition (spec: MUST fail to open unrecognized fields) -- + + +def test_must_understand_fields_partition() -> None: + """must_understand_fields contains every extra field not explicitly waived + with must_understand: false, including implicitly-true and non-mapping + fields, so a reader can discharge the spec's fail-to-open duty by + subtracting the extensions it recognizes.""" + model = ZarrV3ArrayMetadata.create_default( + extra_fields={ + "ext_a": {"name": "a", "must_understand": False}, + "ext_b": {"name": "b"}, + "ext_c": {"name": "c", "must_understand": True}, + "ext_d": 123, + } + ) + assert set(model.must_understand_fields) == {"ext_b", "ext_c", "ext_d"} + recognized = {"ext_b"} + assert model.must_understand_fields.keys() - recognized == {"ext_c", "ext_d"} + + +def test_must_understand_fields_empty_when_all_waived() -> None: + """must_understand_fields is empty when every extra field is explicitly waived.""" + model = ZarrV3ArrayMetadata.create_default( + extra_fields={"ext_a": {"name": "a", "must_understand": False}} + ) + assert model.must_understand_fields == {} + + +def test_dimension_names_null_field_rejected() -> None: + """A dimension_names field whose VALUE is null is invalid: the spec permits + null as an element (an unnamed dimension), never as the field value — "not + specified" is spelled by omitting the key. Consumers bridging from an + in-memory None sentinel must drop the key, not write null.""" + doc = dict(ZarrV3ArrayMetadata.create_default().to_json()) | {"dimension_names": None} + problems = validate_array_metadata_v3(doc) + assert [(p.loc, p.kind) for p in problems] == [(("dimension_names",), "invalid_type")] + # and the model's own None spelling correctly maps to key absence + assert ( + "dimension_names" not in ZarrV3ArrayMetadata.create_default(dimension_names=UNSET).to_json() + ) + + +# --- create_default derives the chunk grid from shape ------------------------ + + +def test_v3_create_default_chunk_grid_follows_shape() -> None: + """Overriding shape without chunk_grid derives a consistent default grid: + one chunk covering the array (chunk_shape == shape), instead of silently + keeping the scalar default's 0-d grid.""" + model = ZarrV3ArrayMetadata.create_default(shape=(100, 100)) + assert model.chunk_grid == ZarrV3NamedConfig( + name="regular", configuration={"chunk_shape": (100, 100)} + ) + + +def test_v3_create_default_explicit_chunk_grid_respected() -> None: + """An explicit chunk_grid override wins over the shape-derived default.""" + grid = ZarrV3NamedConfig(name="regular", configuration={"chunk_shape": (10, 10)}) + model = ZarrV3ArrayMetadata.create_default(shape=(100, 100), chunk_grid=grid) + assert model.chunk_grid == grid + + +def test_v2_create_default_chunks_follow_shape() -> None: + """Overriding shape without chunks derives chunks == shape.""" + model = ZarrV2ArrayMetadata.create_default(shape=(100, 100)) + assert model.chunks == (100, 100) + + +def test_v2_create_default_explicit_chunks_respected() -> None: + """An explicit chunks override wins over the shape-derived default.""" + model = ZarrV2ArrayMetadata.create_default(shape=(100, 100), chunks=(10, 10)) + assert model.chunks == (10, 10) + + +def test_v3_create_default_zero_length_dimensions() -> None: + """chunk_shape == shape is spec-sound even with zero-length dimensions: + 'The chunk shape elements are non-zero when the corresponding dimensions + of the arrays have non-zero length' — the constraint is conditional, so a + zero chunk length is permitted exactly where the dimension is empty.""" + model = ZarrV3ArrayMetadata.create_default(shape=(0, 3)) + assert model.chunk_grid.configuration["chunk_shape"] == (0, 3) + + +def test_create_default_derivation_is_one_way() -> None: + """Overriding the chunk grid (v3) or chunks (v2) without shape leaves the + scalar default shape=() untouched: a user-supplied chunk_grid is an + extension point taken verbatim, and deriving shape from it would require + interpreting grid configurations, which the model layer never does.""" + grid = ZarrV3NamedConfig(name="regular", configuration={"chunk_shape": (10, 10)}) + v3 = ZarrV3ArrayMetadata.create_default(chunk_grid=grid) + assert v3.shape == () + assert v3.chunk_grid == grid + v2 = ZarrV2ArrayMetadata.create_default(chunks=(10, 10)) + assert v2.shape == () + assert v2.chunks == (10, 10) + + +# --- v2 dimension_separator default (roborev job 426) ------------------------- + + +def test_v2_absent_dimension_separator_means_dot() -> None: + """A .zarray that omits dimension_separator uses the v2 convention default + '.', not '/': chunk keys of real-world default-separator v2 arrays look + like '0.0'. The model normalizes the absent key to an explicit '.' — a + semantics-preserving spelling normalization.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) + del doc["dimension_separator"] + model = ZarrV2ArrayMetadata.from_json(doc) + assert model.dimension_separator == "." + assert model.to_json()["dimension_separator"] == "." + + +def test_v2_from_key_value_without_separator_means_dot() -> None: + """The .zarray store-file path applies the same '.' default for an absent + dimension_separator key.""" + doc = { + k: v + for k, v in ZarrV2ArrayMetadata.create_default().to_json().items() + if k not in ("dimension_separator", "attributes") + } + import json as _json + + model = ZarrV2ArrayMetadata.from_key_value({".zarray": _json.dumps(doc).encode()}) + assert model.dimension_separator == "." + + +def test_v2_null_dimension_separator_rejected() -> None: + """dimension_separator may be absent, '.', or '/' — never null: the + document grammar has no null spelling for this field.""" + doc = dict(ZarrV2ArrayMetadata.create_default().to_json()) | {"dimension_separator": None} + problems = validate_array_metadata_v2(doc) + assert [(p.loc, p.kind) for p in problems] == [(("dimension_separator",), "invalid_value")] + + +def test_dimension_names_absent_and_all_null_are_distinct() -> None: + """An absent dimension_names field and an explicit all-null one are + semantically different documents: the explicit form says every dimension + has a name, which is null; absence says there are no dimension names. + The model preserves the distinction (UNSET vs a tuple of Nones), and both + spellings round-trip faithfully.""" + absent_doc = dict(ZarrV3ArrayMetadata.create_default(shape=(2, 3)).to_json()) + explicit_doc = absent_doc | {"dimension_names": (None, None)} + + absent = ZarrV3ArrayMetadata.from_json(absent_doc) + explicit = ZarrV3ArrayMetadata.from_json(explicit_doc) + + assert absent.dimension_names is UNSET + assert explicit.dimension_names == (None, None) + assert absent != explicit + assert "dimension_names" not in absent.to_json() + assert absent.to_json() == absent_doc + assert explicit.to_json() == explicit_doc diff --git a/packages/zarr-metadata/tests/model/test_group.py b/packages/zarr-metadata/tests/model/test_group.py new file mode 100644 index 0000000000..4b8c22b84d --- /dev/null +++ b/packages/zarr-metadata/tests/model/test_group.py @@ -0,0 +1,572 @@ +"""Tests for the group and consolidated metadata models in `zarr_metadata.model`.""" + +import copy +import dataclasses +import json +from collections import UserDict +from collections.abc import Callable + +import pytest + +from tests.model._cases import mutate_nested_containers +from zarr_metadata.model import UNSET +from zarr_metadata.model._array import ZarrV3ArrayMetadata +from zarr_metadata.model._group import ( + ZarrV2ConsolidatedMetadata, + ZarrV2GroupMetadata, + ZarrV2GroupMetadataPartial, + ZarrV3ConsolidatedMetadata, + ZarrV3GroupMetadata, + ZarrV3GroupMetadataPartial, +) +from zarr_metadata.model._validation import ( + MetadataValidationError, + ValidationProblem, + is_group_metadata_v2, + is_group_metadata_v3, + parse_group_metadata_v2, + parse_group_metadata_v3, + validate_group_metadata_v2, + validate_group_metadata_v3, +) + +# --- ZarrV3GroupMetadata --------------------------------------------------- + + +def test_group_v3_roundtrip() -> None: + """A v3 group document round-trips through the model unchanged.""" + doc = {"zarr_format": 3, "node_type": "group", "attributes": {"a": (1, 2)}} + model = ZarrV3GroupMetadata.from_json(doc) + assert model.to_json() == doc + + +def test_group_v3_omits_empty_attributes() -> None: + """to_json omits the attributes key when attributes is empty.""" + model = ZarrV3GroupMetadata.create_default() + assert "attributes" not in model.to_json() + + +def test_group_v3_lists_become_tuples() -> None: + """from_json converts JSON arrays in attributes to tuples.""" + doc = {"zarr_format": 3, "node_type": "group", "attributes": {"a": [1, 2]}} + model = ZarrV3GroupMetadata.from_json(doc) + assert model.attributes == {"a": (1, 2)} + + +def test_group_v3_extra_fields_roundtrip() -> None: + """Unknown top-level keys land in extra_fields and reappear in to_json.""" + doc = { + "zarr_format": 3, + "node_type": "group", + "my_extension": {"name": "thing", "must_understand": False}, + } + model = ZarrV3GroupMetadata.from_json(doc) + assert model.extra_fields == {"my_extension": {"name": "thing", "must_understand": False}} + assert model.to_json() == doc + + +def test_group_v3_json_extra_field_roundtrips_as_must_understand() -> None: + """A non-object extra field is preserved and implicitly requires understanding.""" + doc = {"zarr_format": 3, "node_type": "group", "ext": [1, 2]} + model = ZarrV3GroupMetadata.from_json(doc) + assert model.to_json()["ext"] == (1, 2) + assert model.must_understand_fields == {"ext": (1, 2)} + + +def test_group_v3_extra_fields_overlap_rejected() -> None: + """Constructing a v3 group model with extra_fields shadowing a standard key raises.""" + with pytest.raises(ValueError, match="Extra fields"): + ZarrV3GroupMetadata( + attributes={}, + consolidated_metadata=UNSET, + extra_fields={"node_type": {"name": "x", "must_understand": False}}, + ) + + +def test_group_v3_consolidated_extra_field_rejected() -> None: + """extra_fields may not shadow the consolidated_metadata convention key.""" + with pytest.raises(ValueError, match="Extra fields"): + ZarrV3GroupMetadata( + attributes={}, + consolidated_metadata=UNSET, + extra_fields={"consolidated_metadata": {"name": "x", "must_understand": False}}, + ) + + +def test_group_v3_missing_required_key() -> None: + """parse_group_metadata_v3 reports each missing required key.""" + with pytest.raises(MetadataValidationError, match="node_type"): + parse_group_metadata_v3({"zarr_format": 3}) + + +def test_group_v3_bad_attributes() -> None: + """parse_group_metadata_v3 rejects a non-mapping attributes value.""" + with pytest.raises(MetadataValidationError, match="attributes"): + parse_group_metadata_v3({"zarr_format": 3, "node_type": "group", "attributes": 5}) + + +@pytest.mark.parametrize( + ("document", "validate"), + [ + pytest.param( + {"zarr_format": 2.0}, + validate_group_metadata_v2, + id="v2", + ), + pytest.param( + {"zarr_format": 3.0, "node_type": "group"}, + validate_group_metadata_v3, + id="v3", + ), + ], +) +def test_group_zarr_format_rejects_float( + document: object, validate: Callable[[object], list[ValidationProblem]] +) -> None: + """Integer-valued floats do not satisfy integer format literals.""" + assert [(p.loc, p.kind) for p in validate(document)] == [(("zarr_format",), "invalid_value")] + + +def test_group_v2_rejects_unknown_document_member() -> None: + """The closed v2 merged-document shape rejects undeclared members.""" + assert [(p.loc, p.kind) for p in validate_group_metadata_v2({"zarr_format": 2, "x": 1})] == [ + (("x",), "invalid_value") + ] + + +@pytest.mark.parametrize( + ("parse", "document"), + [ + pytest.param(parse_group_metadata_v2, {"zarr_format": 2}, id="v2"), + pytest.param( + parse_group_metadata_v3, + {"zarr_format": 3, "node_type": "group"}, + id="v3", + ), + ], +) +def test_group_parser_materializes_abstract_mapping( + parse: Callable[[object], object], document: dict[str, object] +) -> None: + """A successful group parser always returns the declared concrete TypedDict shape.""" + parsed = parse(UserDict(document)) + + assert type(parsed) is dict + assert parsed == document + + +def test_group_guards_reject_noncanonical_nested_json() -> None: + """Document guards cannot narrow values that only parsers can materialize.""" + v3 = {"zarr_format": 3, "node_type": "group", "extension": range(2)} + v2 = {"zarr_format": 2, "attributes": {"values": range(2)}} + + assert not is_group_metadata_v3(v3) + assert not is_group_metadata_v2(v2) + assert parse_group_metadata_v3(v3)["extension"] == (0, 1) + assert parse_group_metadata_v2(v2)["attributes"] == {"values": (0, 1)} + + +def test_group_v3_extension_fields_are_validated() -> None: + """Group extension payloads must be JSON values with a must-understand flag.""" + doc = { + "zarr_format": 3, + "node_type": "group", + "ext": {"must_understand": False, "payload": object()}, + } + assert [(problem.loc, problem.kind) for problem in validate_group_metadata_v3(doc)] == [ + (("ext", "payload"), "invalid_type") + ] + + +def test_group_v3_key_value_roundtrip() -> None: + """from_key_value(to_key_value()) is the identity for v3 groups.""" + model = ZarrV3GroupMetadata.create_default(attributes={"a": 1}) + assert ZarrV3GroupMetadata.from_key_value(model.to_key_value()) == model + + +def test_group_v3_update() -> None: + """update replaces the given fields and returns a new instance.""" + base = ZarrV3GroupMetadata.create_default() + updated = base.update(attributes={"a": 1}) + assert updated.attributes == {"a": 1} + assert base.attributes == {} + + +# --- ZarrV2GroupMetadata --------------------------------------------------- + + +def test_group_v2_key_value_split() -> None: + """v2 to_key_value writes .zgroup and .zattrs; from_key_value merges them.""" + model = ZarrV2GroupMetadata.create_default(attributes={"a": 1}) + kv = model.to_key_value() + assert set(kv) == {".zgroup", ".zattrs"} + assert json.loads(kv[".zgroup"]) == {"zarr_format": 2} + assert ZarrV2GroupMetadata.from_key_value(kv) == model + + +@pytest.mark.parametrize("extra_key", ["attributes", "vendor_extension"]) +def test_v2_group_from_key_value_rejects_zgroup_extra_members(extra_key: str) -> None: + """Raw `.zgroup` documents reject every non-spec member.""" + doc: dict[str, object] = {"zarr_format": 2, extra_key: {}} + + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV2GroupMetadata.from_key_value({".zgroup": json.dumps(doc).encode()}) + + assert [(problem.loc, problem.kind) for problem in exc_info.value.problems] == [ + ((extra_key,), "invalid_value") + ] + + +def test_group_v2_zattrs_presence_round_trips() -> None: + """A v2 group with no .zattrs file parses with UNSET attributes and emits + no .zattrs; an explicit empty .zattrs stays a file — the stores remain + distinct through a round-trip.""" + absent = ZarrV2GroupMetadata.from_key_value({".zgroup": b'{"zarr_format": 2}'}) + assert absent.attributes is UNSET + assert ".zattrs" not in absent.to_key_value() + explicit = ZarrV2GroupMetadata.from_key_value( + {".zgroup": b'{"zarr_format": 2}', ".zattrs": b"{}"} + ) + assert explicit.attributes == {} + assert ".zattrs" in explicit.to_key_value() + assert absent != explicit + + +def test_group_v2_json_roundtrip() -> None: + """A merged-form v2 group document round-trips through the model unchanged.""" + doc = {"zarr_format": 2, "attributes": {"a": 1}} + model = ZarrV2GroupMetadata.from_json(doc) + assert model.to_json() == doc + + +def test_group_v2_omits_empty_attributes() -> None: + """to_json omits the attributes key when attributes is empty.""" + assert "attributes" not in ZarrV2GroupMetadata.create_default().to_json() + + +def test_group_v2_not_a_mapping() -> None: + """parse_group_metadata_v2 rejects a non-mapping document.""" + with pytest.raises(MetadataValidationError, match="expected a mapping"): + parse_group_metadata_v2([1, 2, 3]) + + +def test_group_v2_missing_required_key() -> None: + """parse_group_metadata_v2 reports a missing zarr_format key.""" + with pytest.raises(MetadataValidationError, match="zarr_format"): + parse_group_metadata_v2({}) + + +# --- Partial TypedDict drift guards ----------------------------------------- + + +def test_group_partial_keys_match_settable_model_fields() -> None: + """Each group partial TypedDict must list exactly the settable model fields. + + Guards against drift: adding/removing a settable field on a group model + without updating its `*Partial` TypedDict fails here. + """ + for model_cls, partial_cls in ( + (ZarrV3GroupMetadata, ZarrV3GroupMetadataPartial), + (ZarrV2GroupMetadata, ZarrV2GroupMetadataPartial), + ): + settable = {f.name for f in dataclasses.fields(model_cls) if f.init} + assert set(partial_cls.__annotations__) == settable + + +# --- ZarrV3ConsolidatedMetadata -------------------------------------------- + + +def test_consolidated_v3_roundtrip() -> None: + """A v3 group with inline consolidated metadata round-trips, with child + entries parsed into array/group models.""" + child = ZarrV3ArrayMetadata.create_default(shape=(2,)).to_json() + doc = { + "zarr_format": 3, + "node_type": "group", + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": {"a": child, "g": {"zarr_format": 3, "node_type": "group"}}, + }, + } + model = ZarrV3GroupMetadata.from_json(doc) + assert isinstance(model.consolidated_metadata, ZarrV3ConsolidatedMetadata) + assert isinstance(model.consolidated_metadata.metadata["a"], ZarrV3ArrayMetadata) + assert isinstance(model.consolidated_metadata.metadata["g"], ZarrV3GroupMetadata) + assert model.to_json() == doc + + +def test_consolidated_v3_must_understand_true_rejected() -> None: + """ZarrV3ConsolidatedMetadata enforces must_understand=False at runtime.""" + with pytest.raises(ValueError, match="must_understand"): + ZarrV3ConsolidatedMetadata(must_understand=True, metadata={}) + + +def test_consolidated_v3_from_json_must_understand_true_rejected() -> None: + """from_json rejects a consolidated document carrying must_understand=true.""" + with pytest.raises(MetadataValidationError, match="must_understand"): + ZarrV3ConsolidatedMetadata.from_json( + {"kind": "inline", "must_understand": True, "metadata": {}} + ) + + +def test_consolidated_v3_entry_without_node_type_rejected() -> None: + """from_json rejects a consolidated entry lacking a recognizable node_type.""" + with pytest.raises(MetadataValidationError, match="node_type"): + ZarrV3ConsolidatedMetadata.from_json( + {"kind": "inline", "must_understand": False, "metadata": {"a": {"zarr_format": 3}}} + ) + + +def test_consolidated_v3_not_a_mapping() -> None: + """from_json rejects a non-mapping consolidated document.""" + with pytest.raises(MetadataValidationError, match="expected a mapping"): + ZarrV3ConsolidatedMetadata.from_json(5) + + +# --- ZarrV2ConsolidatedMetadata -------------------------------------------- + + +def test_consolidated_v2_verbatim_roundtrip() -> None: + """The v2 .zmetadata model holds the flat file-keyed map verbatim, + including nodes that have no .zattrs entry.""" + doc = { + "zarr_consolidated_format": 1, + "metadata": { + ".zgroup": {"zarr_format": 2}, + "a/.zarray": { + "zarr_format": 2, + "shape": (2,), + "chunks": (2,), + "dtype": "|u1", + "fill_value": 0, + "order": "C", + "compressor": None, + "filters": None, + }, + }, + } + model = ZarrV2ConsolidatedMetadata.from_json(doc) + assert model.to_json() == doc + + +def test_consolidated_v2_key_value_roundtrip() -> None: + """from_key_value(to_key_value()) is the identity for .zmetadata documents.""" + model = ZarrV2ConsolidatedMetadata.from_json( + {"zarr_consolidated_format": 1, "metadata": {".zgroup": {"zarr_format": 2}}} + ) + assert ZarrV2ConsolidatedMetadata.from_key_value(model.to_key_value()) == model + + +def test_consolidated_v2_lists_become_tuples() -> None: + """from_json converts JSON arrays inside entries to tuples.""" + doc = { + "zarr_consolidated_format": 1, + "metadata": {"a/.zarray": {"shape": [2, 3]}}, + } + model = ZarrV2ConsolidatedMetadata.from_json(doc) + assert model.metadata == {"a/.zarray": {"shape": (2, 3)}} + + +def test_consolidated_v2_envelope_validation() -> None: + """from_json rejects a .zmetadata document missing the metadata key.""" + with pytest.raises(MetadataValidationError, match="metadata"): + ZarrV2ConsolidatedMetadata.from_json({"zarr_consolidated_format": 1}) + + +def test_consolidated_v2_not_a_mapping() -> None: + """from_json rejects a non-mapping .zmetadata document.""" + with pytest.raises(MetadataValidationError, match="expected a mapping"): + ZarrV2ConsolidatedMetadata.from_json([1]) + + +def test_consolidated_v2_format_literal_enforced() -> None: + """A .zmetadata document must declare consolidated format 1.""" + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV2ConsolidatedMetadata.from_json({"zarr_consolidated_format": 2, "metadata": {}}) + assert [(problem.loc, problem.kind) for problem in exc_info.value.problems] == [ + (("zarr_consolidated_format",), "invalid_value") + ] + + +def test_consolidated_v2_metadata_values_must_be_json() -> None: + """Non-JSON values in the flat metadata map are rejected during ingestion.""" + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV2ConsolidatedMetadata.from_json( + {"zarr_consolidated_format": 1, "metadata": {".zgroup": object()}} + ) + assert [(problem.loc, problem.kind) for problem in exc_info.value.problems] == [ + (("metadata", ".zgroup"), "invalid_type") + ] + + +def test_group_v2_from_key_value_scalar_root_raises_metadata_error() -> None: + """A scalar .zgroup document fails through the unified metadata error channel.""" + with pytest.raises(MetadataValidationError) as exc_info: + ZarrV2GroupMetadata.from_key_value({".zgroup": b"null"}) + assert [(problem.loc, problem.kind) for problem in exc_info.value.problems] == [ + ((), "invalid_type") + ] + + +# --- Literal-value enforcement ----------------------------------------------- + + +def test_group_v3_literals_enforced() -> None: + """A v3 group doc with wrong zarr_format or node_type is rejected with invalid_value.""" + base = ZarrV3GroupMetadata.create_default().to_json() + for key, bad in (("zarr_format", 2), ("node_type", "array")): + problems = validate_group_metadata_v3(dict(base) | {key: bad}) + assert [(p.loc, p.kind) for p in problems] == [((key,), "invalid_value")], key + + +def test_group_v2_zarr_format_literal_enforced() -> None: + """A v2 group doc claiming zarr_format 3 is rejected with invalid_value.""" + problems = validate_group_metadata_v2({"zarr_format": 3}) + assert [(p.loc, p.kind) for p in problems] == [(("zarr_format",), "invalid_value")] + + +# --- Consolidated envelope validated by the group validator ------------------ + + +def test_group_v3_validator_agrees_with_from_json_on_consolidated() -> None: + """The group validator validates the consolidated envelope and entries, so + is_group_metadata_v3 never vouches for a document from_json would reject.""" + bad_docs = ( + # empty envelope: missing kind/must_understand/metadata + {"zarr_format": 3, "node_type": "group", "consolidated_metadata": {}}, + # entry without a recognizable node_type + { + "zarr_format": 3, + "node_type": "group", + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": {"a": {"zarr_format": 3}}, + }, + }, + # must_understand: true + { + "zarr_format": 3, + "node_type": "group", + "consolidated_metadata": { + "kind": "inline", + "must_understand": True, + "metadata": {}, + }, + }, + ) + for doc in bad_docs: + assert validate_group_metadata_v3(doc) != [], doc + with pytest.raises(MetadataValidationError): + ZarrV3GroupMetadata.from_json(doc) + + +def test_group_v3_valid_consolidated_passes_validator() -> None: + """A well-formed consolidated group validates cleanly (control case).""" + child = ZarrV3ArrayMetadata.create_default(shape=(2,)).to_json() + doc = { + "zarr_format": 3, + "node_type": "group", + "consolidated_metadata": { + "kind": "inline", + "must_understand": False, + "metadata": {"a": child, "g": {"zarr_format": 3, "node_type": "group"}}, + }, + } + assert validate_group_metadata_v3(doc) == [] + + +def test_v3_consolidated_rejects_unknown_envelope_member() -> None: + """The inline consolidated envelope is closed and never drops accepted members.""" + doc = { + "kind": "inline", + "must_understand": False, + "metadata": {}, + "unexpected": 1, + } + + with pytest.raises(MetadataValidationError, match="unexpected"): + ZarrV3ConsolidatedMetadata.from_json(doc) + + +def test_v2_consolidated_rejects_unknown_document_member() -> None: + """The v2 consolidated document is closed and never drops accepted members.""" + doc = {"zarr_consolidated_format": 1, "metadata": {}, "unexpected": 1} + + with pytest.raises(MetadataValidationError, match="unexpected"): + ZarrV2ConsolidatedMetadata.from_json(doc) + + +# --- must_understand partition ------------------------------------------------ + + +def test_group_must_understand_fields_partition() -> None: + """The group model partitions extra fields by the spec's implicit-true rule, + like the array model.""" + model = ZarrV3GroupMetadata.create_default( + extra_fields={ + "waived": {"name": "w", "must_understand": False}, + "implicit": {"name": "i"}, + } + ) + assert set(model.must_understand_fields) == {"implicit"} + + +def test_group_v3_null_consolidated_metadata_repaired_to_absence() -> None: + """consolidated_metadata: null was written by a historical zarr-python bug. + Those stores must remain readable, but the bug spelling is not honored: + it is read as absence (UNSET) and never written back — the round-trip + deliberately repairs the document rather than preserving the bug.""" + null_doc = {"zarr_format": 3, "node_type": "group", "consolidated_metadata": None} + assert validate_group_metadata_v3(null_doc) == [] + model = ZarrV3GroupMetadata.from_json(null_doc) + assert model.consolidated_metadata is UNSET + assert "consolidated_metadata" not in model.to_json() + assert model == ZarrV3GroupMetadata.from_json({"zarr_format": 3, "node_type": "group"}) + + +# --- to_json shares no mutable state with the model ------------------------ + +TO_JSON_NO_ALIASING_PARAMS = [ + pytest.param( + ZarrV3GroupMetadata.create_default( + attributes={"a": {"b": [1]}}, + consolidated_metadata=ZarrV3ConsolidatedMetadata( + metadata={ + "child": ZarrV3ArrayMetadata.create_default(attributes={"x": {"y": 1}}), + "grp": ZarrV3GroupMetadata.create_default(attributes={"x": {"y": 1}}), + } + ), + extra_fields={"ext": {"must_understand": False, "cfg": {"x": [1]}}}, + ), + id="v3-group", + ), + pytest.param( + ZarrV2GroupMetadata.create_default(attributes={"a": {"b": [1]}}), + id="v2-group", + ), + pytest.param( + ZarrV3ConsolidatedMetadata( + metadata={"child": ZarrV3ArrayMetadata.create_default(attributes={"x": {"y": 1}})} + ), + id="v3-consolidated", + ), + pytest.param( + ZarrV2ConsolidatedMetadata(metadata={"a/.zarray": {"nested": {"x": [1]}}}), + id="v2-consolidated", + ), +] + + +@pytest.mark.parametrize("model", TO_JSON_NO_ALIASING_PARAMS) +def test_to_json_shares_no_mutable_state_with_model( + model: ZarrV3GroupMetadata + | ZarrV2GroupMetadata + | ZarrV3ConsolidatedMetadata + | ZarrV2ConsolidatedMetadata, +) -> None: + """Mutating a document returned by to_json leaves the model unchanged.""" + baseline = copy.deepcopy(model.to_json()) + mutate_nested_containers(model.to_json()) + assert model.to_json() == baseline diff --git a/packages/zarr-metadata/tests/model/test_pydantic.py b/packages/zarr-metadata/tests/model/test_pydantic.py new file mode 100644 index 0000000000..e5714bb8fb --- /dev/null +++ b/packages/zarr-metadata/tests/model/test_pydantic.py @@ -0,0 +1,302 @@ +"""Executable example: integrating the metadata models with pydantic (v2). + +Pydantic's native dataclass introspection CAN be made to work (see +`test_native_dataclass_introspection_is_possible_but_diverges`): the models +keep their annotation-only imports behind `TYPE_CHECKING`, so a bare +`TypeAdapter(ZarrV3ArrayMetadata)` raises `class-not-fully-defined`, but +`rebuild(_types_namespace=...)` with the names supplied resolves the schema. +It is still the wrong tool: it validates the MODEL SHAPE, not the DOCUMENT — +no `from_json` normalization (a bare-string `data_type` is rejected), and +pydantic's lax coercion silently re-opens holes the library's validators +close (`shape=[True, -5]` coerces to `(1, -5)`; a wrong `dimension_names` +count passes). The recommended integration delegates wholesale — treat the +model as an opaque value: + +- `InstanceOf` makes pydantic's core schema an is-instance check (no field + introspection), +- validation goes through `from_json` (the single source of truth for what + a well-formed document is, including normalization: bare-string metadata + fields, arrays-to-tuples), +- serialization goes through `to_json` (the canonical document form). + +`MetadataValidationError` subclasses `ValueError`, so pydantic converts a +failed parse into its own `ValidationError` with the loc-annotated problem +messages intact. +""" + +from collections.abc import Mapping +from typing import Annotated, Generic, TypeVar + +import pytest +from pydantic import ( + BaseModel, + BeforeValidator, + ConfigDict, + InstanceOf, + PlainSerializer, + PydanticSchemaGenerationError, + PydanticUserError, + TypeAdapter, + ValidationError, + model_validator, +) + +from zarr_metadata import JSONValue +from zarr_metadata.model import ZarrV3ArrayMetadata, ZarrV3NamedConfig + +# --- the integration (this is the example) ----------------------------------- + + +def _as_array_metadata_v3(value: object) -> ZarrV3ArrayMetadata: + """Accept an existing model instance or a raw metadata document.""" + if isinstance(value, ZarrV3ArrayMetadata): + return value + return ZarrV3ArrayMetadata.from_json(value) + + +# return_type is explicit because to_json's own annotation (`ZarrV3ArrayMetadataJSON`) +# is a TYPE_CHECKING-only name pydantic cannot resolve at runtime. +ArrayMetadataV3Field = Annotated[ + InstanceOf[ZarrV3ArrayMetadata], + BeforeValidator(_as_array_metadata_v3), + PlainSerializer(ZarrV3ArrayMetadata.to_json, return_type=dict), +] +"""A pydantic-ready field type for v3 array metadata. + +Validates raw documents via `from_json`, passes model instances through, +and serializes to the canonical document form via `to_json`. +""" + + +class ArrayManifest(BaseModel): + """Example consumer model: a named array with its metadata document.""" + + path: str + metadata: ArrayMetadataV3Field + + +# --- tests pinning the example ------------------------------------------------ + +VALID_DOC = { + "zarr_format": 3, + "node_type": "array", + "shape": [10], + "data_type": "uint8", + "fill_value": 0, + "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": [5]}}, + "chunk_key_encoding": {"name": "default"}, + "codecs": [{"name": "bytes"}], +} + + +def test_raw_document_is_validated_into_a_model() -> None: + """A raw metadata document on a pydantic field is parsed by from_json, + with the library's normalization applied (tuples, canonical field form).""" + manifest = ArrayManifest.model_validate({"path": "a/b", "metadata": VALID_DOC}) + assert isinstance(manifest.metadata, ZarrV3ArrayMetadata) + assert manifest.metadata.shape == (10,) + assert manifest.metadata.data_type.name == "uint8" + + +def test_model_instance_passes_through() -> None: + """An already-constructed model instance is accepted unchanged.""" + model = ZarrV3ArrayMetadata.from_json(VALID_DOC) + manifest = ArrayManifest(path="a/b", metadata=model) + assert manifest.metadata is model + + +def test_invalid_document_surfaces_problems_in_validation_error() -> None: + """A structurally-invalid document fails pydantic validation, carrying the + loc-annotated problem messages from MetadataValidationError.""" + doc = dict(VALID_DOC) + del doc["chunk_key_encoding"] + with pytest.raises(ValidationError) as exc_info: + ArrayManifest.model_validate({"path": "a/b", "metadata": doc}) + assert "chunk_key_encoding: missing required key" in str(exc_info.value) + + +def test_dump_emits_canonical_document() -> None: + """model_dump serializes the field via to_json — the canonical document, + not pydantic's field-by-field view of the dataclass.""" + manifest = ArrayManifest.model_validate({"path": "a/b", "metadata": VALID_DOC}) + dumped = manifest.model_dump() + assert dumped["metadata"] == manifest.metadata.to_json() + # Empty configurations use the extension-definition shorthand form. + assert dumped["metadata"]["data_type"] == "uint8" + + +def test_json_roundtrip_through_pydantic() -> None: + """model_dump_json output re-validates to an equal manifest (JSON emits + tuples as arrays; from_json converts them back).""" + manifest = ArrayManifest.model_validate({"path": "a/b", "metadata": VALID_DOC}) + revived = ArrayManifest.model_validate_json(manifest.model_dump_json()) + assert revived == manifest + + +def test_type_adapter_standalone() -> None: + """The annotated alias also works without a BaseModel, via TypeAdapter.""" + adapter = TypeAdapter(ArrayMetadataV3Field) + model = adapter.validate_python(VALID_DOC) + assert isinstance(model, ZarrV3ArrayMetadata) + assert adapter.dump_python(model) == model.to_json() + + +# --- the road not taken: native dataclass introspection ---------------------- + + +def test_native_dataclass_introspection_is_not_supported() -> None: + """Pydantic cannot field-introspect the model dataclasses: the UNSET + sentinel (PEP 661, typing_extensions.Sentinel) in the optional-field + annotations has no pydantic schema (as of pydantic 2.13), so even the + rebuild-with-namespace recipe fails. Introspection was already the wrong + tool before the sentinel existed — it validated the model shape rather + than the document, and its lax coercion re-opened validator holes (e.g. + shape=[True, -5] coerced to (1, -5)) — so the delegation patterns above + are the only supported integrations. If this test ever fails because + pydantic learned to handle sentinels, revisit whether the introspection + path needs its divergences documented again.""" + from zarr_metadata._common import JSONValue + from zarr_metadata.model import UNSET + from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON + from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON, ZarrV3ExtensionField + + def build_and_use() -> None: + adapter = TypeAdapter(ZarrV3ArrayMetadata) + adapter.rebuild( + force=True, + _types_namespace={ + "JSONValue": JSONValue, + "ZarrV3ExtensionField": ZarrV3ExtensionField, + "ZarrV3MetadataFieldJSON": ZarrV3MetadataFieldJSON, + "ZarrV3ArrayMetadataJSON": ZarrV3ArrayMetadataJSON, + "ZarrV3NamedConfig": ZarrV3NamedConfig, + "ZarrV3MetadataField": ZarrV3NamedConfig, + "UNSET": UNSET, + }, + ) + adapter.validate_python({}) + + with pytest.raises((AttributeError, PydanticSchemaGenerationError, PydanticUserError)): + build_and_use() + + +# --- a first-class pydantic model, engine-backed (the pydantic-zarr pattern) -- +# +# When a consumer wants a real BaseModel — JSON schema generation, and +# generics for typed attributes, as in pydantic-zarr's ArraySpec — the model +# fields are pydantic-native, but validation and serialization still route +# through the library: a mode="before" validator canonicalizes every input +# document with from_json(...).to_json(), so the structural validators and +# normalization run BEFORE pydantic parses fields (no coercion divergence), +# and the document form is the bridge in both directions. + +AttrsT = TypeVar("AttrsT") + + +class NamedConfig(BaseModel): + """Pydantic mirror of a normalized metadata extension envelope.""" + + name: str + configuration: dict[str, JSONValue] = {} + must_understand: bool = True + + +class ArrayMetadataV3Spec(BaseModel, Generic[AttrsT]): + """A pydantic-native, attribute-typed view of a v3 array metadata document. + + The library is the engine: every input is canonicalized and structurally + validated by `ZarrV3ArrayMetadata.from_json` before pydantic sees the + fields, and `to_document` / `to_metadata_model` emit through the library. + """ + + model_config = ConfigDict(frozen=True) + + zarr_format: int = 3 + node_type: str = "array" + shape: tuple[int, ...] + data_type: NamedConfig + chunk_grid: NamedConfig + chunk_key_encoding: NamedConfig + fill_value: JSONValue + codecs: tuple[NamedConfig, ...] + attributes: AttrsT + dimension_names: tuple[str | None, ...] | None = None + storage_transformers: tuple[NamedConfig, ...] = () + + @model_validator(mode="before") + @classmethod + def _canonicalize(cls, data: object) -> object: + """Route every input document through the library's validation and + normalization; pydantic then parses only canonical documents.""" + if isinstance(data, Mapping): + doc = dict(ZarrV3ArrayMetadata.from_json(data).to_json()) + for key in ("data_type", "chunk_grid", "chunk_key_encoding"): + if isinstance(doc[key], str): + doc[key] = {"name": doc[key]} + for key in ("codecs", "storage_transformers"): + doc[key] = tuple( + {"name": item} if isinstance(item, str) else item for item in doc.get(key, ()) + ) + doc.setdefault("attributes", {}) + return doc + return data + + def to_metadata_model(self) -> ZarrV3ArrayMetadata: + """Bridge back to the canonical model, via the document form. + + In the document, "no dimension names" is key-absence, not null; the + pydantic-side None translates to dropping the key. + """ + doc = self.model_dump() + if doc["dimension_names"] is None: + del doc["dimension_names"] + return ZarrV3ArrayMetadata.from_json(doc) + + def to_document(self) -> dict[str, object]: + """The canonical document (omit-empty conventions applied).""" + return dict(self.to_metadata_model().to_json()) + + +class MicroscopyAttrs(BaseModel): + """Example of consumer-typed attributes, pydantic-zarr style.""" + + resolution_um: float + + +def test_spec_typed_attributes() -> None: + """The generic parameter types the attributes, so consumers get validated, + attribute-level access — the pydantic-zarr ArraySpec pattern.""" + doc = dict(VALID_DOC) | {"attributes": {"resolution_um": 0.5}} + spec = ArrayMetadataV3Spec[MicroscopyAttrs].model_validate(doc) + assert spec.attributes.resolution_um == 0.5 + assert spec.data_type == NamedConfig(name="uint8") + + +def test_spec_engine_validates_before_pydantic() -> None: + """The library's structural validation runs before pydantic's parsing, so + coercion cannot re-open validator holes (contrast with the native + introspection test above, where [True, -5] coerced to (1, -5)).""" + with pytest.raises(ValidationError, match="shape"): + ArrayMetadataV3Spec[MicroscopyAttrs].model_validate( + dict(VALID_DOC) | {"shape": [True, -5], "attributes": {"resolution_um": 0.5}} + ) + + +def test_spec_bridges_to_canonical_model_and_document() -> None: + """to_metadata_model / to_document round-trip through the document form, + and the emitted document matches what the library itself would emit.""" + doc = dict(VALID_DOC) | {"attributes": {"resolution_um": 0.5}} + spec = ArrayMetadataV3Spec[MicroscopyAttrs].model_validate(doc) + model = spec.to_metadata_model() + assert isinstance(model, ZarrV3ArrayMetadata) + assert spec.to_document() == dict(model.to_json()) + # and back: the document revalidates to an equal spec + assert ArrayMetadataV3Spec[MicroscopyAttrs].model_validate(spec.to_document()) == spec + + +def test_spec_json_schema_generation() -> None: + """A real BaseModel means model_json_schema works — the capability the + opaque InstanceOf pattern cannot provide.""" + schema = ArrayMetadataV3Spec[MicroscopyAttrs].model_json_schema() + assert schema["properties"]["shape"]["type"] == "array" + assert "MicroscopyAttrs" in schema["$defs"] diff --git a/packages/zarr-metadata/tests/model/test_pydantic_module.py b/packages/zarr-metadata/tests/model/test_pydantic_module.py new file mode 100644 index 0000000000..d15b3f118c --- /dev/null +++ b/packages/zarr-metadata/tests/model/test_pydantic_module.py @@ -0,0 +1,264 @@ +"""Tests for `zarr_metadata.pydantic`, the optional pydantic field-type module. + +The hand-rolled recipes in `test_pydantic.py` document how the integration +works; this module ships it. Instances are the CORE model classes (no +parallel hierarchy), so values interoperate freely with non-pydantic code. +""" + +import json +import warnings + +import pytest +from jsonschema import Draft202012Validator +from pydantic import BaseModel, TypeAdapter, ValidationError + +import zarr_metadata.pydantic as zmp +from zarr_metadata.model import ( + ZarrV2ArrayMetadata, + ZarrV2ConsolidatedMetadata, + ZarrV2GroupMetadata, + ZarrV3ArrayMetadata, + ZarrV3ConsolidatedMetadata, + ZarrV3GroupMetadata, + ZarrV3NamedConfig, +) + +V3_ARRAY_DOC = dict(ZarrV3ArrayMetadata.create_default(shape=(4,)).to_json()) +V2_ARRAY_DOC = dict(ZarrV2ArrayMetadata.create_default(shape=(4,), chunks=(2,)).to_json()) +V3_GROUP_DOC = {"zarr_format": 3, "node_type": "group", "attributes": {"a": 1}} +V2_GROUP_DOC = {"zarr_format": 2, "attributes": {"a": 1}} +V3_CONSOLIDATED_DOC = { + "kind": "inline", + "must_understand": False, + "metadata": {"a": dict(V3_ARRAY_DOC)}, +} +V2_CONSOLIDATED_DOC = { + "zarr_consolidated_format": 1, + "metadata": {".zgroup": {"zarr_format": 2}}, +} + +FIELD_CASES = [ + pytest.param(zmp.ZarrV3ArrayMetadata, ZarrV3ArrayMetadata, V3_ARRAY_DOC, id="array-v3"), + pytest.param(zmp.ZarrV2ArrayMetadata, ZarrV2ArrayMetadata, V2_ARRAY_DOC, id="array-v2"), + pytest.param(zmp.ZarrV3GroupMetadata, ZarrV3GroupMetadata, V3_GROUP_DOC, id="group-v3"), + pytest.param(zmp.ZarrV2GroupMetadata, ZarrV2GroupMetadata, V2_GROUP_DOC, id="group-v2"), + pytest.param( + zmp.ZarrV3ConsolidatedMetadata, + ZarrV3ConsolidatedMetadata, + V3_CONSOLIDATED_DOC, + id="consolidated-v3", + ), + pytest.param( + zmp.ZarrV2ConsolidatedMetadata, + ZarrV2ConsolidatedMetadata, + V2_CONSOLIDATED_DOC, + id="consolidated-v2", + ), + pytest.param(zmp.ZarrV3MetadataField, ZarrV3NamedConfig, {"name": "bytes"}, id="field-v3"), +] + + +@pytest.mark.parametrize(("field_type", "model_cls", "doc"), FIELD_CASES) +def test_field_type_validates_and_dumps_canonically( + field_type: object, model_cls: type, doc: dict[str, object] +) -> None: + """Each field type parses its raw document into the CORE model class, + passes existing instances through unchanged, and dumps the canonical + document via to_json.""" + adapter = TypeAdapter(field_type) + model = adapter.validate_python(doc) + assert type(model) is model_cls + assert adapter.validate_python(model) is model + assert adapter.dump_python(model) == model.to_json() + + +def test_core_instances_interoperate() -> None: + """A core model instance (e.g. handed out by zarr-python) drops straight + into a pydantic field — the reason the module ships Annotated aliases over + the core classes rather than pydantic-aware subclasses.""" + + class Manifest(BaseModel): + metadata: zmp.ZarrV3ArrayMetadata + + core = ZarrV3ArrayMetadata.from_json(V3_ARRAY_DOC) + manifest = Manifest(metadata=core) + assert manifest.metadata is core + + +def test_validation_error_carries_problems() -> None: + """A defective document fails with the library's loc-annotated messages.""" + + class Manifest(BaseModel): + metadata: zmp.ZarrV3ArrayMetadata + + doc = dict(V3_ARRAY_DOC) + del doc["chunk_key_encoding"] + with pytest.raises(ValidationError, match="chunk_key_encoding: missing required key"): + Manifest.model_validate({"metadata": doc}) + + +def test_json_schema_generation() -> None: + """model_json_schema works, describing the document form each field accepts.""" + + class Manifest(BaseModel): + metadata: zmp.ZarrV3ArrayMetadata + codec: zmp.ZarrV3MetadataField + + schema = Manifest.model_json_schema() + metadata_schema = schema["$defs"]["ZarrV3ArrayMetadataJSON"] + assert schema["properties"]["metadata"]["$ref"] == "#/$defs/ZarrV3ArrayMetadataJSON" + assert metadata_schema["required"] == [ + "zarr_format", + "node_type", + "data_type", + "shape", + "chunk_grid", + "chunk_key_encoding", + "fill_value", + "codecs", + ] + assert metadata_schema["properties"]["zarr_format"] == { + "const": 3, + "title": "Zarr Format", + "type": "integer", + } + assert schema["properties"]["codec"]["anyOf"] == [ + {"type": "string"}, + {"$ref": "#/$defs/ZarrV3NamedConfigJSON"}, + ] + + +def test_json_schema_generation_emits_no_warnings() -> None: + """Consumers can generate every public integration schema without warning filters.""" + field_types = ( + zmp.ZarrV3ArrayMetadata, + zmp.ZarrV2ArrayMetadata, + zmp.ZarrV3GroupMetadata, + zmp.ZarrV2GroupMetadata, + zmp.ZarrV3ConsolidatedMetadata, + zmp.ZarrV2ConsolidatedMetadata, + zmp.ZarrV3MetadataField, + ) + + with warnings.catch_warnings(): + warnings.simplefilter("error") + for field_type in field_types: + TypeAdapter(field_type).json_schema() + + +def test_v2_recursive_structured_dtype_is_in_pydantic_schema() -> None: + """The schema accepts nested structured dtypes supported by the v2 specification.""" + doc = json.loads(json.dumps(V2_ARRAY_DOC)) + doc["dtype"] = [["outer", [["inner", "<i4"]]]] + adapter = TypeAdapter(zmp.ZarrV2ArrayMetadata) + + assert adapter.validate_python(doc).dtype == (("outer", (("inner", "<i4"),)),) + assert Draft202012Validator(adapter.json_schema()).is_valid(doc) + + +def _assert_runtime_and_schema_reject(field_type: object, document: dict[str, object]) -> None: + adapter = TypeAdapter(field_type) + with pytest.raises(ValidationError): + adapter.validate_python(document) + assert list(Draft202012Validator(adapter.json_schema()).iter_errors(document)) + + +def test_v3_array_schema_rejects_empty_codecs() -> None: + """The generated schema mirrors the runtime non-empty codec pipeline rule.""" + doc = json.loads(json.dumps(V3_ARRAY_DOC)) + doc["codecs"] = [] + + _assert_runtime_and_schema_reject(zmp.ZarrV3ArrayMetadata, doc) + + +def test_array_schemas_reject_negative_dimensions() -> None: + """Both array schemas mirror the runtime non-negative dimension rule.""" + for field_type, source in ( + (zmp.ZarrV3ArrayMetadata, V3_ARRAY_DOC), + (zmp.ZarrV2ArrayMetadata, V2_ARRAY_DOC), + ): + doc = json.loads(json.dumps(source)) + doc["shape"] = [-1] + _assert_runtime_and_schema_reject(field_type, doc) + + +def test_v2_array_schema_rejects_empty_filters() -> None: + """The v2 schema mirrors the runtime one-or-more filter rule.""" + doc = json.loads(json.dumps(V2_ARRAY_DOC)) + doc["filters"] = [] + + _assert_runtime_and_schema_reject(zmp.ZarrV2ArrayMetadata, doc) + + +@pytest.mark.parametrize("field", ["data_type", "chunk_grid", "chunk_key_encoding"]) +def test_v3_array_schema_rejects_false_at_mandatory_extension_points(field: str) -> None: + """Mandatory v3 extension points cannot opt out of understanding.""" + doc = json.loads(json.dumps(V3_ARRAY_DOC)) + doc[field] = {"name": "example", "must_understand": False} + + _assert_runtime_and_schema_reject(zmp.ZarrV3ArrayMetadata, doc) + + +def test_metadata_field_schema_rejects_unknown_members() -> None: + """Named-configuration envelopes are closed in both runtime and schema validation.""" + _assert_runtime_and_schema_reject( + zmp.ZarrV3MetadataField, + {"name": "example", "unexpected": 1}, + ) + + +@pytest.mark.parametrize( + ("field_type", "source"), + [ + (zmp.ZarrV2ArrayMetadata, V2_ARRAY_DOC), + (zmp.ZarrV2GroupMetadata, V2_GROUP_DOC), + (zmp.ZarrV2ConsolidatedMetadata, V2_CONSOLIDATED_DOC), + ], +) +def test_v2_schema_rejects_unknown_document_members( + field_type: object, source: dict[str, object] +) -> None: + """Closed v2 merged documents expose their runtime boundary in JSON Schema.""" + doc = json.loads(json.dumps(source)) + doc["unexpected"] = 1 + + _assert_runtime_and_schema_reject(field_type, doc) + + +def test_v3_array_schema_allows_unknown_extension_fields() -> None: + """Schema constraints do not close the v3 top-level extension namespace.""" + doc = json.loads(json.dumps(V3_ARRAY_DOC)) + doc["vendor_extension"] = {"anything": [1, 2]} + adapter = TypeAdapter(zmp.ZarrV3ArrayMetadata) + + assert adapter.validate_python(doc).extra_fields == {"vendor_extension": {"anything": (1, 2)}} + assert Draft202012Validator(adapter.json_schema()).is_valid(doc) + + +def test_json_roundtrip() -> None: + """model_dump_json output re-validates to an equal pydantic model.""" + + class Manifest(BaseModel): + metadata: zmp.ZarrV3ArrayMetadata + + manifest = Manifest.model_validate({"metadata": V3_ARRAY_DOC}) + assert Manifest.model_validate_json(manifest.model_dump_json()) == manifest + + +def test_metadata_field_serializes_shorthand_and_false_object() -> None: + """The optional integration exposes the core model's canonical extension form.""" + adapter = TypeAdapter(zmp.ZarrV3MetadataField) + assert adapter.dump_python(adapter.validate_python({"name": "bytes"})) == "bytes" + assert adapter.dump_python( + adapter.validate_python({"name": "optional", "must_understand": False}) + ) == {"name": "optional", "must_understand": False} + + +def test_core_package_does_not_import_pydantic() -> None: + """Importing zarr_metadata (in a fresh interpreter) must not import + pydantic: the integration is opt-in via zarr_metadata.pydantic.""" + import subprocess + import sys + + code = "import sys, zarr_metadata; assert 'pydantic' not in sys.modules, 'leaked'" + subprocess.run([sys.executable, "-c", code], check=True) diff --git a/packages/zarr-metadata/tests/model/test_sentinel.py b/packages/zarr-metadata/tests/model/test_sentinel.py new file mode 100644 index 0000000000..252a4cdd30 --- /dev/null +++ b/packages/zarr-metadata/tests/model/test_sentinel.py @@ -0,0 +1,89 @@ +"""Tests for the pickling and copying behavior of the `UNSET` sentinel. + +The sentinel's contract is identity, so it must never be reconstructed from +state. typing_extensions >= 4.16 pickles sentinels by reference (a lookup of +the sentinel's name on its defining module), which preserves the singleton +across process boundaries; these tests pin that behavior, since models hold +`UNSET` as field values and must survive pickling and deep-copying. + +The model round-trip tests compare whole structures: dataclass equality +compares every field, and `UNSET` compares by identity, so an impostor +sentinel produced by state-based pickling would fail the equality check. +""" + +from __future__ import annotations + +import copy +import pickle + +import pytest +from typing_extensions import Sentinel + +from zarr_metadata.model import ( + UNSET, + ZarrV2ArrayMetadata, + ZarrV2GroupMetadata, + ZarrV3ArrayMetadata, + ZarrV3ConsolidatedMetadata, + ZarrV3GroupMetadata, +) + +# Whole-model cases covering the states we know are problematic for +# serialization: every optional-key field in the UNSET (absent) state, the +# same fields in the present state (including present-but-empty, which must +# stay distinct from absent), and UNSET nested inside consolidated metadata. +MODEL_CASES = { + "array-v3-dimension-names-unset": ZarrV3ArrayMetadata.create_default(shape=(4,)), + "array-v3-dimension-names-set": ZarrV3ArrayMetadata.create_default(shape=(2, 2)).update( + dimension_names=("x", None) + ), + "array-v2-attributes-unset": ZarrV2ArrayMetadata.create_default(shape=(4,)), + "array-v2-attributes-empty": ZarrV2ArrayMetadata.create_default(shape=(4,), attributes={}), + "group-v2-attributes-unset": ZarrV2GroupMetadata.create_default(), + "group-v2-attributes-set": ZarrV2GroupMetadata.create_default(attributes={"a": 1}), + "group-v3-consolidated-unset": ZarrV3GroupMetadata.create_default(), + "group-v3-consolidated-with-unset-inside": ZarrV3GroupMetadata.create_default( + consolidated_metadata=ZarrV3ConsolidatedMetadata( + metadata={ + "child": ZarrV3ArrayMetadata.create_default(shape=(4,)), + "subgroup": ZarrV3GroupMetadata.create_default(), + } + ) + ), +} + + +def test_unset_pickle_round_trip_preserves_identity() -> None: + restored = pickle.loads(pickle.dumps(UNSET)) + assert restored is UNSET + + +def test_unset_copy_preserves_identity() -> None: + assert copy.copy(UNSET) is UNSET + assert copy.deepcopy(UNSET) is UNSET + + +@pytest.mark.parametrize("model", MODEL_CASES.values(), ids=MODEL_CASES.keys()) +def test_model_pickle_round_trip( + model: ZarrV2ArrayMetadata | ZarrV3ArrayMetadata | ZarrV2GroupMetadata | ZarrV3GroupMetadata, +) -> None: + restored = pickle.loads(pickle.dumps(model)) + assert restored == model + + +@pytest.mark.parametrize("model", MODEL_CASES.values(), ids=MODEL_CASES.keys()) +def test_model_deepcopy( + model: ZarrV2ArrayMetadata | ZarrV3ArrayMetadata | ZarrV2GroupMetadata | ZarrV3GroupMetadata, +) -> None: + assert copy.deepcopy(model) == model + + +def test_non_importable_sentinel_fails_to_pickle() -> None: + """Sentinels pickle by reference, never by state. A sentinel that is not + an importable attribute of its module has no reference to pickle, so + dumping it must fail loudly — a successful dump here would mean the + implementation regressed to state-based pickling, which would produce + identity-breaking impostor objects on the receiving side.""" + local_sentinel = Sentinel("local_sentinel") + with pytest.raises((pickle.PicklingError, TypeError)): + pickle.dumps(local_sentinel) diff --git a/packages/zarr-metadata/tests/test_partial_equivalence.py b/packages/zarr-metadata/tests/test_partial_equivalence.py index 995a6a21e1..33492b2356 100644 --- a/packages/zarr-metadata/tests/test_partial_equivalence.py +++ b/packages/zarr-metadata/tests/test_partial_equivalence.py @@ -14,17 +14,17 @@ import pytest -from zarr_metadata.v2.array import ArrayMetadataV2, ArrayMetadataV2Partial -from zarr_metadata.v2.group import GroupMetadataV2, GroupMetadataV2Partial -from zarr_metadata.v3.array import ArrayMetadataV3, ArrayMetadataV3Partial -from zarr_metadata.v3.group import GroupMetadataV3, GroupMetadataV3Partial +from zarr_metadata.v2.array import ZarrV2ArrayMetadataJSON, ZarrV2ArrayMetadataJSONPartial +from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON, ZarrV2GroupMetadataJSONPartial +from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON, ZarrV3ArrayMetadataJSONPartial +from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON, ZarrV3GroupMetadataJSONPartial # (full, partial) pairs to check. Add new pairs here as more are introduced. PAIRS: list[tuple[type, type]] = [ - (ArrayMetadataV3, ArrayMetadataV3Partial), - (GroupMetadataV3, GroupMetadataV3Partial), - (ArrayMetadataV2, ArrayMetadataV2Partial), - (GroupMetadataV2, GroupMetadataV2Partial), + (ZarrV3ArrayMetadataJSON, ZarrV3ArrayMetadataJSONPartial), + (ZarrV3GroupMetadataJSON, ZarrV3GroupMetadataJSONPartial), + (ZarrV2ArrayMetadataJSON, ZarrV2ArrayMetadataJSONPartial), + (ZarrV2GroupMetadataJSON, ZarrV2GroupMetadataJSONPartial), ] diff --git a/packages/zarr-metadata/tests/test_public_api.py b/packages/zarr-metadata/tests/test_public_api.py index d3270579c3..e65c680fd1 100644 --- a/packages/zarr-metadata/tests/test_public_api.py +++ b/packages/zarr-metadata/tests/test_public_api.py @@ -1,5 +1,7 @@ """Test that the curated front-door names are accessible from the top-level zarr_metadata package.""" +import importlib +import pkgutil import re from typing import get_args @@ -21,26 +23,43 @@ def _group_rank(s: str) -> int: EXPECTED = [ # Category A — metadata-document types - "ArrayMetadataV2", - "ArrayMetadataV2Partial", - "ZArrayMetadata", - "GroupMetadataV2", - "GroupMetadataV2Partial", - "ZGroupMetadata", - "ConsolidatedMetadataV2", - "ZAttrsMetadata", - "CodecMetadataV2", - "ArrayMetadataV3", - "ArrayMetadataV3Partial", - "ExtensionFieldV3", - "GroupMetadataV3", - "GroupMetadataV3Partial", - "ConsolidatedMetadataV3", - "NamedConfigV3", - "MetadataV3", + "ZarrV2ArrayMetadataJSON", + "ZarrV2ArrayMetadataJSONPartial", + "ZarrV2ZArrayJSON", + "ZarrV2GroupMetadataJSON", + "ZarrV2GroupMetadataJSONPartial", + "ZarrV2ZGroupJSON", + "ZarrV2ConsolidatedMetadataJSON", + "ZarrV2ZAttrsJSON", + "ZarrV2CodecMetadata", + "ZarrV3ArrayMetadataJSON", + "ZarrV3ArrayMetadataJSONPartial", + "ZarrV3ExtensionField", + "ZarrV3GroupMetadataJSON", + "ZarrV3GroupMetadataJSONPartial", + "ZarrV3ConsolidatedMetadataJSON", + "ZarrV3NamedConfigJSON", + "ZarrV3MetadataFieldJSON", "JSONValue", + # Category A' — metadata models (in-memory dataclasses over the documents) + "ZarrV2ArrayMetadata", + "ZarrV2ArrayMetadataPartial", + "ZarrV3ArrayMetadata", + "ZarrV3ArrayMetadataPartial", + "ZarrV2GroupMetadata", + "ZarrV2GroupMetadataPartial", + "ZarrV3GroupMetadata", + "ZarrV3GroupMetadataPartial", + "ZarrV2ConsolidatedMetadata", + "ZarrV3ConsolidatedMetadata", + "ZarrV3NamedConfig", + "ZarrV3MetadataField", + "ValidationProblem", + "MetadataValidationError", + "ProblemKind", + "UNSET", # v2 data-type encoding union - "DataTypeMetadataV2", + "ZarrV2DataTypeMetadata", # Category B — codec canonical unions "BloscCodecMetadata", "BytesCodecMetadata", @@ -129,9 +148,9 @@ def _group_rank(s: str) -> int: "RawBytesFillValue", # Category E — constant+Literal pairs "ARRAY_ORDER_V2", - "ArrayOrderV2", + "ZarrV2ArrayOrder", "ARRAY_DIMENSION_SEPARATOR_V2", - "ArrayDimensionSeparatorV2", + "ZarrV2ArrayDimensionSeparator", "ENDIANNESS", "Endianness", "BYTES_CODEC_NAME", @@ -200,6 +219,109 @@ def test_all_is_grouped_and_unique() -> None: assert len(zm.__all__) == len(set(zm.__all__)) +# --- naming grammar --------------------------------------------------------- + +# Core document/model names: the format version comes first (`ZarrV2` / +# `ZarrV3`), then the CamelCase entity, then an optional role suffix +# (`JSON`, `JSONPartial`, `Partial`, `StoreKey`) — validated loosely here +# because `JSON` decomposes into single-letter words under any strict +# word-splitting regex. +_CORE_NAME = re.compile(r"^ZarrV[23](?:[A-Z][a-z0-9]*)+$") + +# Zarr v3 extension-entity names: the registered entity comes first (`Blosc`, +# `Uint8`, ... — `V2` here is the *entity name* of the v2-compatibility chunk +# key encoding, not a format-version marker, which is always spelled +# `ZarrV2`/`ZarrV3`), followed by exactly one role suffix. +_EXTENSION_ROLES = ( + "CodecConfiguration", + "CodecMetadata", + "CodecName", + "CodecObject", + "ChunkGridConfiguration", + "ChunkGridMetadata", + "ChunkGridName", + "ChunkGridObject", + "ChunkKeyEncodingConfiguration", + "ChunkKeyEncodingMetadata", + "ChunkKeyEncodingName", + "ChunkKeyEncodingObject", + "ChunkKeyEncodingSeparator", + "DataTypeName", + "FillValue", + "Configuration", + "Component", +) +_EXTENSION_NAME = re.compile(r"^(?:[A-Z][a-z0-9]*)+?(?:" + "|".join(_EXTENSION_ROLES) + r")$") + +# Standalone vocabulary: scalar Literal aliases, structural helper shapes, and +# the validation diagnostics. Closed by hand — a new name belongs here only if +# it is genuinely role-less; anything document- or entity-shaped must fit the +# grammars above instead. +_STANDALONE_VOCAB = frozenset( + { + "Base64Bytes", + "BloscCName", + "BloscShuffle", + "CastOutOfRangeMode", + "CastRoundingMode", + "Endianness", + "HexFloat16", + "HexFloat32", + "HexFloat64", + "JSONValue", + "MetadataValidationError", + "NumpyDatetime64", + "NumpyTimeUnit", + "NumpyTimedelta64", + "ProblemKind", + "RectilinearDimSpec", + "ScalarMap", + "ScalarMapEntry", + "ShardingIndexLocation", + "Struct", + "StructField", + "ValidationProblem", + } +) + + +def _public_type_names() -> set[tuple[str, str]]: + """Every (module, CamelCase name) pair exported via a public `__all__`.""" + module_names = {"zarr_metadata"} + for info in pkgutil.walk_packages(zm.__path__, prefix="zarr_metadata."): + if not any(part.startswith("_") for part in info.name.split(".")[1:]): + module_names.add(info.name) + out: set[tuple[str, str]] = set() + for module_name in module_names: + module = importlib.import_module(module_name) + for name in getattr(module, "__all__", ()): + if name.startswith("_") or name.isupper() or name.islower(): + continue + out.add((module_name, name)) + return out + + +def test_public_type_names_comply_with_naming_grammar() -> None: + """Every public type name parses against the package naming grammar: + version-first core names, entity-plus-role extension names, or the closed + standalone vocabulary.""" + exported = _public_type_names() + violations = [ + f"{module}.{name}" + for module, name in sorted(exported) + if name not in _STANDALONE_VOCAB + and not _CORE_NAME.match(name) + and not _EXTENSION_NAME.match(name) + ] + assert not violations, f"names outside the naming grammar: {violations}" + + +def test_standalone_vocab_is_not_stale() -> None: + """Every allowlisted vocabulary name is still actually exported.""" + exported_names = {name for _, name in _public_type_names()} + assert exported_names >= _STANDALONE_VOCAB + + def test_promoted_pairs_drift() -> None: pairs = [ (zm.ENDIANNESS, zm.Endianness), @@ -209,7 +331,7 @@ def test_promoted_pairs_drift() -> None: (zm.NUMPY_TIME_UNIT, zm.NumpyTimeUnit), (zm.CAST_ROUNDING_MODE, zm.CastRoundingMode), (zm.CAST_OUT_OF_RANGE_MODE, zm.CastOutOfRangeMode), - (zm.ARRAY_ORDER_V2, zm.ArrayOrderV2), + (zm.ARRAY_ORDER_V2, zm.ZarrV2ArrayOrder), ] for const, lit in pairs: assert set(const) == set(get_args(lit)) diff --git a/packages/zarr-metadata/tests/v2/array/test_fixtures.py b/packages/zarr-metadata/tests/v2/array/test_fixtures.py index 1576aae8db..578d3647ab 100644 --- a/packages/zarr-metadata/tests/v2/array/test_fixtures.py +++ b/packages/zarr-metadata/tests/v2/array/test_fixtures.py @@ -1,7 +1,7 @@ """Decode v2 array metadata fixtures via pydantic. Each `*.json` file in this directory is a representative on-disk -`.zarray` that should validate cleanly as `ZArrayMetadata` (the strict +`.zarray` that should validate cleanly as `ZarrV2ZArrayJSON` (the strict on-disk shape). User attributes live in sibling `.zattrs` files and are not part of these fixtures. @@ -17,11 +17,11 @@ import pytest from pydantic import TypeAdapter -from zarr_metadata.v2.array import ZArrayMetadata +from zarr_metadata.v2.array import ZarrV2ZArrayJSON FIXTURES_DIR = Path(__file__).parent FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) -ADAPTER = TypeAdapter(ZArrayMetadata) +ADAPTER = TypeAdapter(ZarrV2ZArrayJSON) @pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) diff --git a/packages/zarr-metadata/tests/v2/consolidated/test_fixtures.py b/packages/zarr-metadata/tests/v2/consolidated/test_fixtures.py index 9dad66d074..e802c5bef8 100644 --- a/packages/zarr-metadata/tests/v2/consolidated/test_fixtures.py +++ b/packages/zarr-metadata/tests/v2/consolidated/test_fixtures.py @@ -8,11 +8,11 @@ import pytest from pydantic import TypeAdapter -from zarr_metadata.v2.consolidated import ConsolidatedMetadataV2 +from zarr_metadata.v2.consolidated import ZarrV2ConsolidatedMetadataJSON FIXTURES_DIR = Path(__file__).parent FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) -ADAPTER = TypeAdapter(ConsolidatedMetadataV2) +ADAPTER = TypeAdapter(ZarrV2ConsolidatedMetadataJSON) @pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) diff --git a/packages/zarr-metadata/tests/v2/group/test_fixtures.py b/packages/zarr-metadata/tests/v2/group/test_fixtures.py index 1ad88a577b..29652185b2 100644 --- a/packages/zarr-metadata/tests/v2/group/test_fixtures.py +++ b/packages/zarr-metadata/tests/v2/group/test_fixtures.py @@ -1,7 +1,7 @@ """Decode v2 group metadata fixtures via pydantic. Each `*.json` file in this directory is a representative on-disk -`.zgroup` that should validate cleanly as `ZGroupMetadata` (the strict +`.zgroup` that should validate cleanly as `ZarrV2ZGroupJSON` (the strict on-disk shape). User attributes live in sibling `.zattrs` files and are not part of these fixtures. """ @@ -14,11 +14,11 @@ import pytest from pydantic import TypeAdapter -from zarr_metadata.v2.group import ZGroupMetadata +from zarr_metadata.v2.group import ZarrV2ZGroupJSON FIXTURES_DIR = Path(__file__).parent FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) -ADAPTER = TypeAdapter(ZGroupMetadata) +ADAPTER = TypeAdapter(ZarrV2ZGroupJSON) @pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) diff --git a/packages/zarr-metadata/tests/v3/array/test_fixtures.py b/packages/zarr-metadata/tests/v3/array/test_fixtures.py index fccd00d481..c84cc4042b 100644 --- a/packages/zarr-metadata/tests/v3/array/test_fixtures.py +++ b/packages/zarr-metadata/tests/v3/array/test_fixtures.py @@ -1,7 +1,7 @@ """Decode v3 array metadata fixtures via pydantic. Each `*.json` file in this directory is a representative on-disk -`zarr.json` that should validate cleanly as `ArrayMetadataV3`. +`zarr.json` that should validate cleanly as `ZarrV3ArrayMetadataJSON`. Fixtures are named for the variant they exercise (regular vs rectilinear grid, blosc/gzip/zstd/sharding_indexed codecs, named-config dtypes, optional fields, extra fields). @@ -15,11 +15,11 @@ import pytest from pydantic import TypeAdapter -from zarr_metadata.v3.array import ArrayMetadataV3 +from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON FIXTURES_DIR = Path(__file__).parent FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) -ADAPTER = TypeAdapter(ArrayMetadataV3) +ADAPTER = TypeAdapter(ZarrV3ArrayMetadataJSON) @pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) diff --git a/packages/zarr-metadata/tests/v3/array/with_extra_field.json b/packages/zarr-metadata/tests/v3/array/with_extra_field.json index 46a7f0f235..bd7a9f5b45 100644 --- a/packages/zarr-metadata/tests/v3/array/with_extra_field.json +++ b/packages/zarr-metadata/tests/v3/array/with_extra_field.json @@ -16,6 +16,6 @@ ], "my_custom_extension": { "must_understand": false, - "purpose": "exercise the extra_items=ExtensionFieldV3 path" + "purpose": "exercise the extra_items=ZarrV3ExtensionField path" } } diff --git a/packages/zarr-metadata/tests/v3/consolidated/test_fixtures.py b/packages/zarr-metadata/tests/v3/consolidated/test_fixtures.py index 4d9e300bae..d052b16986 100644 --- a/packages/zarr-metadata/tests/v3/consolidated/test_fixtures.py +++ b/packages/zarr-metadata/tests/v3/consolidated/test_fixtures.py @@ -8,11 +8,11 @@ import pytest from pydantic import TypeAdapter -from zarr_metadata.v3.consolidated import ConsolidatedMetadataV3 +from zarr_metadata.v3.consolidated import ZarrV3ConsolidatedMetadataJSON FIXTURES_DIR = Path(__file__).parent FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) -ADAPTER = TypeAdapter(ConsolidatedMetadataV3) +ADAPTER = TypeAdapter(ZarrV3ConsolidatedMetadataJSON) @pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) diff --git a/packages/zarr-metadata/tests/v3/group/test_fixtures.py b/packages/zarr-metadata/tests/v3/group/test_fixtures.py index 2015d5ce96..ffcdedef2b 100644 --- a/packages/zarr-metadata/tests/v3/group/test_fixtures.py +++ b/packages/zarr-metadata/tests/v3/group/test_fixtures.py @@ -8,11 +8,11 @@ import pytest from pydantic import TypeAdapter -from zarr_metadata.v3.group import GroupMetadataV3 +from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON FIXTURES_DIR = Path(__file__).parent FIXTURES = sorted(FIXTURES_DIR.glob("*.json")) -ADAPTER = TypeAdapter(GroupMetadataV3) +ADAPTER = TypeAdapter(ZarrV3GroupMetadataJSON) @pytest.mark.parametrize("fixture", FIXTURES, ids=lambda p: p.stem) From 0c07bf5ed6619b7e5c0b01aece7a93fc88de07b6 Mon Sep 17 00:00:00 2001 From: Goutam Adwant <8672451+goutamadwant@users.noreply.github.com> Date: Tue, 28 Jul 2026 22:24:08 +0200 Subject: [PATCH 416/468] fix: let open_like create arrays by default (#4146) * fix: let open_like create arrays by default * test: cover open_like read-only mode --------- Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- changes/3352.bugfix.md | 3 +++ src/zarr/api/asynchronous.py | 6 ++++- src/zarr/api/synchronous.py | 6 +++-- tests/test_api.py | 47 ++++++++++++++++++++++++++++++++++++ 4 files changed, 59 insertions(+), 3 deletions(-) create mode 100644 changes/3352.bugfix.md diff --git a/changes/3352.bugfix.md b/changes/3352.bugfix.md new file mode 100644 index 0000000000..7461486776 --- /dev/null +++ b/changes/3352.bugfix.md @@ -0,0 +1,3 @@ +Fix `zarr.api.asynchronous.open_like` so it can create a new array by default when the +target path does not already exist. It now defaults to `mode="a"`; when using a read-only +store to open an existing array, pass `mode="r"` explicitly. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index c751d6a31c..f5e614a051 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -1292,7 +1292,9 @@ async def open_like(a: ArrayLike, path: str, **kwargs: Any) -> AnyAsyncArray: path : str The path to the new array. **kwargs - Any keyword arguments to pass to the array constructor. + Additional keyword arguments passed to `open_array`. + If `mode` is omitted or `None`, it defaults to `"a"`. Pass `mode="r"` when + opening an existing array from a read-only store. Returns ------- @@ -1300,6 +1302,8 @@ async def open_like(a: ArrayLike, path: str, **kwargs: Any) -> AnyAsyncArray: The opened array. """ like_kwargs = _like_args(a) | kwargs + if like_kwargs.get("mode") is None: + like_kwargs["mode"] = "a" return await open_array(path=path, **like_kwargs) # type: ignore[arg-type] diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index 3231837a04..dc12d5f7af 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -1399,11 +1399,13 @@ def open_like(a: ArrayLike, path: str, **kwargs: Any) -> AnyArray: path : str The path to the new array. **kwargs - Any keyword arguments to pass to the array constructor. + Additional keyword arguments passed to `open_array`. + If `mode` is omitted or `None`, it defaults to `"a"`. Pass `mode="r"` when + opening an existing array from a read-only store. Returns ------- - AsyncArray + Array The opened array. """ return Array(sync(async_api.open_like(a, path=path, **kwargs))) diff --git a/tests/test_api.py b/tests/test_api.py index 1b4414ae63..cbe8ea3b44 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -168,6 +168,53 @@ async def test_array_like_creation( assert np.all(Array(new_arr)[:] == expect_fill) +@pytest.mark.parametrize("mode_kwargs", [{}, {"mode": None}]) +async def test_open_like_creates_array_by_default( + zarr_format: ZarrFormat, mode_kwargs: dict[str, None] +) -> None: + ref_arr = zarr.create_array( + store={}, + shape=(11, 12), + dtype="uint8", + chunks=(11, 12), + zarr_format=zarr_format, + fill_value=100, + ) + + new_arr = await zarr.api.asynchronous.open_like( + ref_arr, + path="foo", + store={}, + zarr_format=zarr_format, + **mode_kwargs, + ) + + assert new_arr.shape == ref_arr.shape + assert new_arr.chunks == ref_arr.chunks + assert new_arr.dtype == ref_arr.dtype + assert np.all(Array(new_arr)[:] == ref_arr.fill_value) + + +async def test_open_like_default_mode_rejects_read_only_store( + zarr_format: ZarrFormat, +) -> None: + ref_arr = zarr.create_array( + store={}, + shape=(11, 12), + dtype="uint8", + chunks=(11, 12), + zarr_format=zarr_format, + ) + + with pytest.raises(ValueError, match="Store is read-only but mode is 'a'"): + await zarr.api.asynchronous.open_like( + ref_arr, + path="foo", + store=MemoryStore(read_only=True), + zarr_format=zarr_format, + ) + + # TODO: parametrize over everything this function takes @pytest.mark.parametrize("store", ["memory"], indirect=True) def test_create_array(store: Store, zarr_format: ZarrFormat) -> None: From bd24f4f4a28212bcceb52edf07fb4b10a738651d Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 12:53:53 +0200 Subject: [PATCH 417/468] fix: keep FusedCodecPipeline compute off the event-loop thread (#4194) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * fix(codec_pipeline): keep FusedCodecPipeline compute off the event-loop thread FusedCodecPipeline.read/write ran their synchronous fast path inline on the coroutine servicing the request — i.e. on the global zarr_io event loop thread. Single-chunk batches decoded inline on the loop and multi-chunk batches blocked the loop in pool.map, so every sync-API call from every user thread serialized behind each other's codec compute. The blocked window scales with codec cost, which is why users reported the fused pipeline as "slower for zstd-compressed data" under multi-threaded (dask-style, one chunk per call) access: at 8 reader threads on 4 MiB zstd chunks it was 3.4x slower than BatchedCodecPipeline, and throughput did not scale with threads at all (336 -> 439 ms from 1 to 8 threads, versus 669 -> 121 ms for batched). Offload the synchronous batch to a worker thread with asyncio.to_thread: one hop per batch, not per chunk, preserving the fused pipeline's win over per-chunk async scheduling while keeping the loop free. After the fix the same workload scales 625 -> 109 ms from 1 to 8 threads, beating batched at every thread count; single-threaded performance is unchanged (the hop costs ~75 us per batch). The regression test asserts deterministically (no timing) that codec compute never runs on a thread with a running event loop, covering single- and multi-chunk reads and writes through the sync API. A new benchmark covers the many-threads/one-chunk-per-call access pattern. Assisted-by: ClaudeCode:claude-fable-5 * docs: rename change note to upstream PR number (4194) towncrier's issue_format links to zarr-developers/zarr-python issues, so 247 (the fork PR number) would render a link to an unrelated old issue. Assisted-by: ClaudeCode:claude-fable-5 * test: guard event-loop test against vacuity if the sync fast path stops triggering The test asserts a negative (compute never ran on the loop thread). If a refactor made the sync fast path stop triggering, the traced ChunkTransform methods would never be called (the async fallback uses AsyncChunkTransform) and the test would pass while guarding nothing. Assert the traced hooks actually ran. Assisted-by: ClaudeCode:claude-fable-5 --- changes/4194.bugfix.md | 10 ++++++ src/zarr/core/codec_pipeline.py | 16 +++++++-- tests/benchmarks/test_e2e.py | 48 ++++++++++++++++++++++++++ tests/test_fused_pipeline.py | 61 +++++++++++++++++++++++++++++++++ 4 files changed, 133 insertions(+), 2 deletions(-) create mode 100644 changes/4194.bugfix.md diff --git a/changes/4194.bugfix.md b/changes/4194.bugfix.md new file mode 100644 index 0000000000..21a4924664 --- /dev/null +++ b/changes/4194.bugfix.md @@ -0,0 +1,10 @@ +`FusedCodecPipeline` no longer runs chunk IO and codec compute on the thread +driving zarr's internal event loop. Previously each read/write executed its +synchronous fast path inline on that loop thread, and because every sync-API +call from every user thread is serviced by the same loop, concurrent +operations serialized behind each other's codec work — reported as the fused +pipeline being slower than `BatchedCodecPipeline` for zstd-compressed data +under multi-threaded (e.g. dask) access. The synchronous batch now runs on a +worker thread (one hop per batch, not per chunk), keeping the loop free. +Multi-threaded single-chunk reads of zstd data are ~4.5x faster than before +and now scale with reader threads; single-threaded performance is unchanged. diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 2e3f1ed122..4b8831bc7b 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -1182,7 +1182,15 @@ async def read( (isinstance(first_bg, StorePath) and isinstance(first_bg.store, SupportsGetSync)) or (not isinstance(first_bg, StorePath) and isinstance(first_bg, SyncByteGetter)) ): - return self.read_sync(batch, out, drop_axes, max_workers=_resolve_max_workers()) + # One thread hop for the WHOLE batch — not per chunk, so the fused + # design's win over per-chunk async scheduling is preserved. Running + # read_sync inline here would block the event loop for the duration + # of the batch's IO+compute; every sync-API call from every user + # thread shares this one loop, so inline execution serializes + # concurrent callers behind each other's codec compute. + return await asyncio.to_thread( + self.read_sync, batch, out, drop_axes, max_workers=_resolve_max_workers() + ) # Non-sync store (e.g. ZipStore): can't use the sync fast path. But if the # array-bytes codec supports partial decoding (sharding), still route @@ -1235,7 +1243,11 @@ async def write( (isinstance(first_bs, StorePath) and isinstance(first_bs.store, SupportsSetSync)) or (not isinstance(first_bs, StorePath) and isinstance(first_bs, SyncByteSetter)) ): - self.write_sync(batch, value, drop_axes, max_workers=_resolve_max_workers()) + # One thread hop for the whole batch; see the matching comment in + # `read` for why write_sync must not run inline on the event loop. + await asyncio.to_thread( + self.write_sync, batch, value, drop_axes, max_workers=_resolve_max_workers() + ) return await _async_write_fallback(self, batch, value, drop_axes) diff --git a/tests/benchmarks/test_e2e.py b/tests/benchmarks/test_e2e.py index 9d60d9a2fb..487485e262 100644 --- a/tests/benchmarks/test_e2e.py +++ b/tests/benchmarks/test_e2e.py @@ -190,3 +190,51 @@ def setup() -> tuple[tuple[zarr.Array, EllipsisType], dict]: # type: ignore[typ return (arr, Ellipsis), {} benchmark.pedantic(getitem, setup=setup, rounds=3) # type: ignore[no-untyped-call] + + +_CONCURRENT_READ_THREADS = 8 +_concurrent_layout = Layout(shape=(64_000_000,), chunks=(4_000_000,), shards=None) + + +@pytest.mark.parametrize("pipeline", ["batched", "fused_full_threaded"], indirect=True) +@pytest.mark.parametrize("compression_name", ["zstd", None]) +@pytest.mark.parametrize("store", ["local"], indirect=["store"]) +def test_read_array_concurrent( + bench_store: Store, + compression_name: CompressorName, + pipeline: str, + benchmark: BenchmarkFixture, +) -> None: + """Dask-style access: several user threads each reading one chunk per call. + + All sync-API calls are serviced by the one global event loop, so this + measures how much of each read's IO+compute the pipeline runs while + holding the loop: anything inline serializes the readers. + """ + from concurrent.futures import ThreadPoolExecutor + + layout = _concurrent_layout + arr = create_array( + bench_store, + dtype="uint8", + shape=layout.shape, + chunks=layout.chunks, + shards=layout.shards, + compressors=compressors[compression_name], # type: ignore[arg-type] + fill_value=0, + ) + arr[:] = _data(layout.shape) + selections = [ + slice(start, start + layout.chunks[0]) + for start in range(0, layout.shape[0], layout.chunks[0]) + ] + + def read_all_chunks_concurrently() -> None: + with ThreadPoolExecutor(max_workers=_CONCURRENT_READ_THREADS) as executor: + list(executor.map(lambda sel: arr[sel], selections)) + + def setup() -> tuple[tuple[()], dict]: # type: ignore[type-arg] + clear_cache() + return (), {} + + benchmark.pedantic(read_all_chunks_concurrently, setup=setup, rounds=3) # type: ignore[no-untyped-call] diff --git a/tests/test_fused_pipeline.py b/tests/test_fused_pipeline.py index 73c2c6e1c3..09e9241c07 100644 --- a/tests/test_fused_pipeline.py +++ b/tests/test_fused_pipeline.py @@ -34,6 +34,67 @@ def test_construction(codecs: tuple[Any, ...]) -> None: assert pipeline.codecs == codecs +def test_sync_api_compute_off_event_loop(monkeypatch: pytest.MonkeyPatch) -> None: + """Codec compute must never run on the thread driving the event loop. + + Every sync-API call, from every user thread, is serviced by the one global + `zarr_io` event loop. Running decode/encode inline on that loop's thread + turns it into a mutex around codec compute: concurrent readers serialize, + and the penalty grows with codec cost (observed as "fused pipeline is + slower for zstd data" under dask-style multi-threaded single-chunk reads). + """ + import asyncio + + from zarr.core.chunk_utils import ChunkTransform + + compute_on_loop = {"decode": False, "encode": False} + calls = {"decode": 0, "encode": 0} + real_decode = ChunkTransform.decode_chunk + real_encode = ChunkTransform.encode_chunk + + def _running_loop() -> bool: + try: + asyncio.get_running_loop() + except RuntimeError: + return False + return True + + def traced_decode(self: ChunkTransform, chunk_bytes: Any, chunk_spec: Any) -> Any: + calls["decode"] += 1 + compute_on_loop["decode"] = compute_on_loop["decode"] or _running_loop() + return real_decode(self, chunk_bytes, chunk_spec) + + def traced_encode(self: ChunkTransform, chunk_array: Any, chunk_spec: Any) -> Any: + calls["encode"] += 1 + compute_on_loop["encode"] = compute_on_loop["encode"] or _running_loop() + return real_encode(self, chunk_array, chunk_spec) + + monkeypatch.setattr(ChunkTransform, "decode_chunk", traced_decode) + monkeypatch.setattr(ChunkTransform, "encode_chunk", traced_encode) + + with zarr_config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): + arr = zarr.create_array( + MemoryStore(), + shape=(8, 8), + chunks=(4, 4), + dtype="float64", + compressors=ZstdCodec(level=1), + ) + data = np.arange(64, dtype="float64").reshape(8, 8) + arr[:4, :4] = data[:4, :4] # single-chunk write (batch of 1) + arr[:] = data # multi-chunk write + # Guard against vacuity: if the sync fast path stops triggering, the + # traced ChunkTransform methods are never called (the async fallback + # uses AsyncChunkTransform) and the on-loop flags stay trivially False. + assert calls["encode"] > 0 + assert compute_on_loop["encode"] is False + + np.testing.assert_array_equal(arr[:4, :4], data[:4, :4]) # single-chunk read + np.testing.assert_array_equal(arr[:], data) # multi-chunk read + assert calls["decode"] > 0 + assert compute_on_loop["decode"] is False + + def test_evolve_from_array_spec() -> None: """evolve_from_array_spec creates a sync transform.""" from zarr.core.array_spec import ArrayConfig, ArraySpec From aa2b8e298e0b8c245737b1240a5c56c8957998b9 Mon Sep 17 00:00:00 2001 From: Sebastian Hoffmann <shoffmann.git@gmail.com> Date: Wed, 29 Jul 2026 13:43:06 +0200 Subject: [PATCH 418/468] fix(ArraySpec): proper and robust equality semantics for ArraySpec by checking fill_value for byte-identicality, fixes #3054. (#4183) * fix(ArraySpec): proper and robust equality semantics for ArraySpec by checking fill_value for byte-identicality, fixes #3054. * fix: added extra case for unequal types * Update tests/test_array_spec.py * addressed reviewers comments * test: add end-to-end regression test for structured-dtype fills in sharded arrays, and changelog entry The new test exercises the sharding codec's chunk-spec caches with an unhashable np.void fill value (#3054), which the ArraySpec test suite only covers at the unit level. Assisted-by: ClaudeCode:claude-fable-5 --------- Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> Co-authored-by: Davis Bennett <davis.v.bennett.git@gmail.com> --- changes/4183.bugfix.md | 3 + src/zarr/codecs/sharding.py | 8 +- src/zarr/core/array_spec.py | 22 +++- tests/test_array_spec.py | 179 +++++++++++++++++++++++++++++ tests/test_codecs/test_sharding.py | 23 ++++ 5 files changed, 228 insertions(+), 7 deletions(-) create mode 100644 changes/4183.bugfix.md create mode 100644 tests/test_array_spec.py diff --git a/changes/4183.bugfix.md b/changes/4183.bugfix.md new file mode 100644 index 0000000000..809708f596 --- /dev/null +++ b/changes/4183.bugfix.md @@ -0,0 +1,3 @@ +Fixed `TypeError: unhashable type: 'writeable void-scalar'` when writing to sharded arrays whose fill value is a `np.void` scalar, e.g. arrays with a structured dtype. + +`ArraySpec` equality and hashing now compare the fill value by its byte representation rather than numeric equality. As a result, two specs with a `NaN` (or `NaT`) fill value now compare equal, while fill values of `-0.0` and `0.0` now compare unequal. This also restores the sharding codec's per-chunk spec cache, which had been disabled because of this bug. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 2d4d63d400..f20979066d 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -411,11 +411,7 @@ def __init__( object.__setattr__(self, "subchunk_write_order", subchunk_write_order) # Use instance-local lru_cache to avoid memory leaks - - # numpy void scalars are not hashable, which means an array spec with a fill value that is - # a numpy void scalar will break the lru_cache. This is commented for now but should be - # fixed. See https://github.com/zarr-developers/zarr-python/issues/3054 - # object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) + object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) object.__setattr__(self, "_get_index_chunk_spec", lru_cache()(self._get_index_chunk_spec)) object.__setattr__(self, "_get_chunks_per_shard", lru_cache()(self._get_chunks_per_shard)) object.__setattr__(self, "_shard_index_size", lru_cache()(self._shard_index_size)) @@ -441,7 +437,7 @@ def __setstate__(self, state: dict[str, Any]) -> None: object.__setattr__(self, "subchunk_write_order", state["subchunk_write_order"]) # Use instance-local lru_cache to avoid memory leaks - # object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) + object.__setattr__(self, "_get_chunk_spec", lru_cache()(self._get_chunk_spec)) object.__setattr__(self, "_get_index_chunk_spec", lru_cache()(self._get_index_chunk_spec)) object.__setattr__(self, "_get_chunks_per_shard", lru_cache()(self._get_chunks_per_shard)) object.__setattr__(self, "_shard_index_size", lru_cache()(self._shard_index_size)) diff --git a/src/zarr/core/array_spec.py b/src/zarr/core/array_spec.py index 89163f7d83..1f4ffd6f09 100644 --- a/src/zarr/core/array_spec.py +++ b/src/zarr/core/array_spec.py @@ -3,6 +3,8 @@ from dataclasses import dataclass, fields from typing import TYPE_CHECKING, Any, Literal, Self, TypedDict, cast +import numpy as np + from zarr.core.common import ( MemoryOrder, parse_bool, @@ -132,7 +134,7 @@ def parse_array_config(data: ArrayConfigLike | None) -> ArrayConfig: return ArrayConfig.from_dict(data) -@dataclass(frozen=True) +@dataclass(frozen=True, eq=False) class ArraySpec: shape: tuple[int, ...] dtype: ZDType[TBaseDType, TBaseScalar] @@ -157,6 +159,24 @@ def __init__( object.__setattr__(self, "config", config) object.__setattr__(self, "prototype", prototype) + def _key(self) -> tuple[object, ...]: + """Returns the tuple used for equality/hash identity.""" + fill_value = self.fill_value + if isinstance(fill_value, np.generic): + # fill_values should be byte-identical, otherwise they correspond to different values in memory / on disk. + # Importantly, this ensures np.nan == np.nan, NaT == NaT, and -0.0 != 0.0. + # It also fixes np.void fill_values being unhashable (#3054). + fill_value = fill_value.tobytes() + return (self.shape, self.dtype, fill_value, self.config, self.prototype) + + def __eq__(self, other: object) -> bool: + if not isinstance(other, ArraySpec): + return NotImplemented + return self._key() == other._key() + + def __hash__(self) -> int: + return hash(self._key()) + @property def ndim(self) -> int: return len(self.shape) diff --git a/tests/test_array_spec.py b/tests/test_array_spec.py new file mode 100644 index 0000000000..4fbc0b1205 --- /dev/null +++ b/tests/test_array_spec.py @@ -0,0 +1,179 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +import numpy as np +import pytest + +from zarr.core.array_spec import ArrayConfig, ArraySpec +from zarr.core.buffer import BufferPrototype, default_buffer_prototype +from zarr.core.buffer.cpu import NDBuffer +from zarr.core.dtype import get_data_type_from_native_dtype + +if TYPE_CHECKING: + from collections.abc import Callable + + from zarr.core.common import MemoryOrder + + +def _make_spec( + *, + shape: tuple[int, ...] = (4, 4), + native_dtype: Any = "int16", + fill_value: Any = 0, + order: MemoryOrder = "C", + write_empty_chunks: bool = False, + prototype: BufferPrototype | None = None, +) -> ArraySpec: + """Creates an ArraySpec with common defaults""" + zdtype = get_data_type_from_native_dtype(np.dtype(native_dtype)) + fill_value = zdtype.cast_scalar(fill_value) # mirrors ArrayV3Metadata's fill_value + return ArraySpec( + shape=shape, + dtype=zdtype, + fill_value=fill_value, + config=ArrayConfig(order=order, write_empty_chunks=write_empty_chunks), + prototype=prototype if prototype is not None else default_buffer_prototype(), + ) + + +class _AltNDBuffer(NDBuffer): + """A distinct NDBuffer subclass""" + + +_ALT_PROTOTYPE = BufferPrototype( + buffer=default_buffer_prototype().buffer, + nd_buffer=_AltNDBuffer, +) # a distinct BufferPrototype with a different nd_buffer subclass + + +# Difficult / important cases: +# issue #3054: np.void is unhashable when writeable +# nan/NaT aren't self-equal yet must compare equal for a ArraySpec +SPECS = [ + pytest.param({"native_dtype": "int16", "fill_value": 7}, id="int16"), + pytest.param({"native_dtype": "float64", "fill_value": 1.5}, id="float64"), + pytest.param({"native_dtype": "float64", "fill_value": float("nan")}, id="float64-nan"), + pytest.param({"native_dtype": "float64", "fill_value": -0.0}, id="float64-negzero"), + pytest.param({"native_dtype": "complex128", "fill_value": 1 + 2j}, id="complex128"), + pytest.param( + {"native_dtype": "complex128", "fill_value": complex(-0.0, -0.0)}, + id="complex128-negzero", + ), + pytest.param({"native_dtype": "bool", "fill_value": True}, id="bool"), + pytest.param( + {"native_dtype": "datetime64[s]", "fill_value": np.datetime64("2020-01-01")}, + id="datetime64", + ), + pytest.param( + {"native_dtype": "datetime64[s]", "fill_value": np.datetime64("NaT", "s")}, + id="datetime64-NaT", + ), + pytest.param( + {"native_dtype": [("a", "f8"), ("b", "i8")], "fill_value": (1.0, 2)}, + id="structured-void", + ), + pytest.param({"native_dtype": "U5", "fill_value": "hello"}, id="fixed-string"), + pytest.param({"shape": ()}, id="scalar-shape"), + pytest.param({"shape": (0,)}, id="zero-size"), + pytest.param({"order": "F"}, id="order-F"), +] + + +# Mutations: each mutate kwargs to an unequal version +def _grow_shape(kw: dict[str, Any]) -> dict[str, Any]: + return {"shape": (*kw.get("shape", (4, 4)), 1)} + + +def _flip_order(kw: dict[str, Any]) -> dict[str, Any]: + return {"order": "F" if kw.get("order", "C") == "C" else "C"} + + +def _swap_prototype(_kw: dict[str, Any]) -> dict[str, Any]: + return {"prototype": _ALT_PROTOTYPE} + + +MUTATIONS = [ + pytest.param(_grow_shape, id="shape"), + pytest.param(_flip_order, id="order"), + pytest.param(_swap_prototype, id="prototype"), +] + + +@pytest.mark.parametrize("kwargs", SPECS) +def test_hashable(kwargs: dict[str, Any]) -> None: + """Every ArraySpec is hashable, including structured (np.void) fill values.""" + assert isinstance(hash(_make_spec(**kwargs)), int) + + +@pytest.mark.parametrize("kwargs", SPECS) +def test_equal_specs_hash_equal(kwargs: dict[str, Any]) -> None: + """Independently built specs with identical fields are equal and hash equal.""" + a = _make_spec(**kwargs) + b = _make_spec(**kwargs) + assert a == b + assert hash(a) == hash(b) + + +@pytest.mark.parametrize("kwargs", SPECS) +@pytest.mark.parametrize("mutate", MUTATIONS) +def test_distinct_specs_unequal( + mutate: Callable[[dict[str, Any]], dict[str, Any]], + kwargs: dict[str, Any], +) -> None: + """Changing one dtype-independent field makes a spec unequal to its base.""" + base = _make_spec(**kwargs) + variant = _make_spec(**{**kwargs, **mutate(kwargs)}) + assert base != variant + + +@pytest.mark.parametrize( + ("base", "variant"), + [ + pytest.param({"fill_value": 0}, {"fill_value": 1}, id="fill_value"), + pytest.param({"native_dtype": "int16"}, {"native_dtype": "int32"}, id="dtype"), + pytest.param( + {"native_dtype": "float32", "fill_value": 1.0}, + {"native_dtype": "float64", "fill_value": 1.0}, + id="dtype-float-promote", + ), + ], +) +def test_dtype_and_fill_value_matter(base: dict[str, Any], variant: dict[str, Any]) -> None: + """dtype and fill_value participate in equality; they can't join the cross + product because fill_value is coupled to dtype.""" + assert _make_spec(**base) != _make_spec(**variant) + + +@pytest.mark.parametrize( + ("native_dtype", "neg_fill", "pos_fill"), + [ + pytest.param("float16", -0.0, 0.0, id="float16"), + pytest.param("float32", -0.0, 0.0, id="float32"), + pytest.param("float64", -0.0, 0.0, id="float64"), + pytest.param("complex128", complex(-0.0, -0.0), 0j, id="complex128-both"), + pytest.param("complex128", complex(0.0, -0.0), 0j, id="complex128-imag"), + pytest.param("complex128", complex(-0.0, 0.0), 0j, id="complex128-real"), + pytest.param([("a", "f8")], (-0.0,), (0.0,), id="structured"), + ], +) +def test_signed_zero_fills_are_distinct(native_dtype: Any, neg_fill: Any, pos_fill: Any) -> None: + """A -0.0 fill writes different bytes than +0.0, so the specs are not equal.""" + neg = _make_spec(native_dtype=native_dtype, fill_value=neg_fill) + pos = _make_spec(native_dtype=native_dtype, fill_value=pos_fill) + assert neg != pos + + +@pytest.mark.parametrize( + ("obj"), + [ + pytest.param(None, id="None"), + pytest.param(42, id="int"), + pytest.param("hello", id="str"), + pytest.param([1, 2, 3], id="list"), + pytest.param({"a": 1}, id="dict"), + ], +) +def test_unequal_with_invalid_type(obj: Any) -> None: + assert (_make_spec() == obj) is False + assert _make_spec() != obj diff --git a/tests/test_codecs/test_sharding.py b/tests/test_codecs/test_sharding.py index 9e6bebd8df..de576dbef5 100644 --- a/tests/test_codecs/test_sharding.py +++ b/tests/test_codecs/test_sharding.py @@ -734,6 +734,29 @@ async def test_delete_empty_shards(store: Store) -> None: assert len(chunk_bytes) == 16 * 2 + 8 * 8 * 2 + 4 +def test_structured_dtype_fill_value() -> None: + """Sharded arrays with a structured dtype are writable and readable even though + the fill value is an (unhashable) ``np.void`` scalar: the sharding codec's + chunk-spec caches key on ``ArraySpec``, whose hash must handle void fills + (see https://github.com/zarr-developers/zarr-python/issues/3054).""" + dtype = np.dtype([("a", "i4"), ("b", "f4")]) + arr = zarr.create_array( + MemoryStore(), + shape=(8,), + chunks=(2,), + shards=(4,), + dtype=dtype, + fill_value=(1, 2.0), + ) + data = np.array([(i, i / 2) for i in range(8)], dtype=dtype) + arr[:4] = data[:4] + + expected = np.zeros(8, dtype=dtype) + expected[:4] = data[:4] + expected[4:] = (1, 2.0) # untouched shard reads back as the fill value + assert np.array_equal(arr[:], expected) + + def test_pickle() -> None: """ShardingCodec round-trips through pickle, including the non-serialized ``subchunk_write_order`` (which ``to_dict`` omits and which must not silently From b213b548d2ecc8ab060a5fa5c22e97856c708361 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 13:43:37 +0200 Subject: [PATCH 419/468] fix: make benchmark page-cache clearing opt-in, never prompt for sudo (#4200) * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * fix: make benchmark page-cache clearing opt-in, never prompt for sudo clear_cache() in tests/benchmarks/test_e2e.py ran sudo unconditionally in every benchmark's setup, so a plain `pytest` run blocked on a password prompt (#4199). It is now a no-op unless ZARR_BENCHMARK_CLEAR_CACHE is set, uses `sudo -n` so it can never block interactively, and the broken Darwin invocation ("&&" passed as an argument to sync) is fixed. The benchmark CI jobs set the variable to keep clearing caches. Closes #4199 Assisted-by: ClaudeCode:claude-fable-5 --- .github/workflows/codspeed.yml | 2 ++ .github/workflows/test.yml | 2 ++ changes/4199.bugfix.md | 1 + tests/benchmarks/test_e2e.py | 23 ++++++++++++++++++++--- 4 files changed, 25 insertions(+), 3 deletions(-) create mode 100644 changes/4199.bugfix.md diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 39cd8eb261..427262d598 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -33,6 +33,8 @@ jobs: version: '1.16.5' - name: Run the benchmarks uses: CodSpeedHQ/action@f99becdce5e5d51fd556489ebef684f4ecfd6286 # v4.18.5 + env: + ZARR_BENCHMARK_CLEAR_CACHE: '1' with: mode: walltime run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index ab78cfbe2b..ce6b7e3eba 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -178,6 +178,8 @@ jobs: - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Run Benchmarks + env: + ZARR_BENCHMARK_CLEAR_CACHE: '1' run: | hatch env run --env "test.py3.13-minimal" run-benchmark diff --git a/changes/4199.bugfix.md b/changes/4199.bugfix.md new file mode 100644 index 0000000000..d0c522cd7e --- /dev/null +++ b/changes/4199.bugfix.md @@ -0,0 +1 @@ +The end-to-end benchmarks no longer invoke `sudo` to drop the OS page cache during a regular `pytest` run. Cache clearing is now opt-in via the `ZARR_BENCHMARK_CLEAR_CACHE` environment variable, which the benchmark CI jobs set. diff --git a/tests/benchmarks/test_e2e.py b/tests/benchmarks/test_e2e.py index 487485e262..de69fca59b 100644 --- a/tests/benchmarks/test_e2e.py +++ b/tests/benchmarks/test_e2e.py @@ -4,8 +4,10 @@ from __future__ import annotations +import os import platform import subprocess +import warnings from functools import lru_cache from operator import getitem, setitem from typing import TYPE_CHECKING, Any, Literal @@ -21,12 +23,27 @@ def clear_cache() -> None: + """Drop the OS page cache between benchmark rounds. + + Requires passwordless sudo, so it is opt-in: set `ZARR_BENCHMARK_CLEAR_CACHE=1` + to enable it (as the benchmark CI jobs do). By default this is a no-op, so a + plain `pytest` run never prompts for a sudo password (see issue #4199). + `sudo -n` guarantees we fail instead of blocking on a password prompt even + when the variable is set. + """ + if os.environ.get("ZARR_BENCHMARK_CLEAR_CACHE", "") not in ("1", "true"): + return if platform.system() == "Darwin": - subprocess.call(["sync", "&&", "sudo", "purge"]) + subprocess.call(["sync"]) + subprocess.call(["sudo", "-n", "purge"]) elif platform.system() == "Linux": - subprocess.call(["sudo", "sh", "-c", "sync; echo 3 > /proc/sys/vm/drop_caches"]) + subprocess.call(["sudo", "-n", "sh", "-c", "sync; echo 3 > /proc/sys/vm/drop_caches"]) else: - raise Exception("Unsupported platform") # noqa: TRY002 + warnings.warn( + f"ZARR_BENCHMARK_CLEAR_CACHE is set but cache clearing is not supported on " + f"{platform.system()}; skipping.", + stacklevel=2, + ) if TYPE_CHECKING: From 401e597bed1e6bfd43be75adabbbf92a3ddf2e43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Selman=20=C3=96zleyen?= <32667648+selmanozleyen@users.noreply.github.com> Date: Wed, 29 Jul 2026 15:13:47 +0200 Subject: [PATCH 420/468] perf(indexing): speed up sorted 1-D coordinate selections (#4172) * perf(indexing): sorted 1-D fast path * clean up comments * name changelog file * rename changes file * add guard for uint and add test case for it * apply suggestions * add test_coordinate_indexer_1d_last_chunk_boundary_does_not_overflow and it's fix * add path whenever the requests are sparse * first == last edge case and do the cost check inside the active path not before (duh) * update the changelog file * rewording --------- Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- changes/4172.misc.md | 7 +++ src/zarr/core/indexing.py | 54 +++++++++++++++++++ tests/test_indexing.py | 110 ++++++++++++++++++++++++++++++++++++++ 3 files changed, 171 insertions(+) create mode 100644 changes/4172.misc.md diff --git a/changes/4172.misc.md b/changes/4172.misc.md new file mode 100644 index 0000000000..0be7226476 --- /dev/null +++ b/changes/4172.misc.md @@ -0,0 +1,7 @@ +Improved `CoordinateIndexer` construction for large, sorted, in-bounds, one-dimensional integer +coordinate selections over regular chunk grids (e.g. `arr.get_coordinate_selection(sorted_idx)`, +`arr.vindex[sorted_idx]`, and the gather behind sparse/CSR row selections). When boundary searching +is estimated to be cheaper than processing every coordinate, per-chunk projections are now built +with `searchsorted`, making index construction ~15x faster for large gathers. Sparse sorted +selections spanning many chunks relative to their coordinate count, as well as unsorted, negative, +multi-dimensional, and irregular-grid selections, continue to use the existing implementation. diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index f6eb495cd9..875c22fbd3 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -22,6 +22,7 @@ import numpy as np import numpy.typing as npt +from zarr.core.chunk_grids import FixedDimension from zarr.core.common import ceildiv, product from zarr.core.metadata.v2 import ArrayV2Metadata from zarr.core.metadata.v3 import ArrayV3Metadata @@ -1206,6 +1207,59 @@ def __init__( f"got {selection!r}" ) + # Optimization for a single sorted, in-bounds, 1-D integer coordinate array over a + # regular (fixed-size) chunk grid. The general path below makes several full passes over + # the flat selection. For sufficiently dense selections, locating the internal chunk + # boundaries with searchsorted is cheaper. + if len(selection_normalized) == 1: + (coords,) = selection_normalized + g0 = dim_grids[0] + # coords is an integer ndarray here: is_coordinate_selection() validated above, and + # the normalization turned ints/lists into arrays. Only the sorted-1D-over-regular-grid + # shape is special-cased; everything else falls through to the general path below. + if ( + isinstance(g0, FixedDimension) + and g0.size > 0 # guard the divide below + and coords.ndim == 1 + and coords.size > 0 + and coords[0] >= 0 + and coords[-1] < shape[0] + and coords[0] <= coords[-1] + ): + size = g0.size + first = int(coords[0]) // size + last = int(coords[-1]) // size + chunk_span = last - first + 1 + # searchsorted does O(log n) work per chunk in the spanned range. Fall through + # when directly processing the coordinates is expected to be cheaper. + if ( + chunk_span * coords.size.bit_length() < coords.size + and bool((coords[:-1] <= coords[1:]).all()) # sorted -> grouped by chunk + ): + # Search only internal boundaries. Derive the first and last counts from the + # selection bounds so that the boundary after the last chunk cannot overflow. + if first == last: + counts = np.array([coords.size], dtype=np.intp) + else: + edges = np.arange(first + 1, last + 1, dtype=coords.dtype) * size + cuts = np.searchsorted(coords, edges) + counts = np.diff(cuts, prepend=0, append=coords.size) + chunk_rixs = (first + np.nonzero(counts)[0]).astype(np.intp) + chunk_nitems = np.zeros(nchunks, dtype=np.intp) + chunk_nitems[first : last + 1] = counts + chunk_nitems_cumsum = np.cumsum(chunk_nitems) + + object.__setattr__(self, "sel_shape", coords.shape) + object.__setattr__(self, "selection", (coords,)) + object.__setattr__(self, "sel_sort", None) + object.__setattr__(self, "chunk_nitems_cumsum", chunk_nitems_cumsum) + object.__setattr__(self, "chunk_rixs", chunk_rixs) + object.__setattr__(self, "chunk_mixs", (chunk_rixs,)) + object.__setattr__(self, "dim_grids", dim_grids) + object.__setattr__(self, "shape", coords.shape) + object.__setattr__(self, "drop_axes", ()) + return + # handle wraparound, boundscheck for dim_sel, dim_len in zip(selection_normalized, shape, strict=True): # handle wraparound diff --git a/tests/test_indexing.py b/tests/test_indexing.py index 3d80f6364c..04fbdad8c6 100644 --- a/tests/test_indexing.py +++ b/tests/test_indexing.py @@ -14,8 +14,10 @@ from tests.conftest import Expect, ExpectFail from zarr import Array from zarr.core.buffer import default_buffer_prototype +from zarr.core.chunk_grids import ChunkGrid from zarr.core.indexing import ( BasicSelection, + CoordinateIndexer, CoordinateSelection, OrthogonalSelection, Selection, @@ -1047,8 +1049,15 @@ def _test_get_coordinate_selection( Expect(input=[3, 25, 8, 17], output=None, id="out-of-order"), Expect(input=[1, 8, 15, 29], output=None, id="sorted"), Expect(input=[29, 15, 8, 1], output=None, id="reversed"), + Expect(input=np.array([29, 15, 8, 1], dtype=np.uint32), output=None, id="reversed-uint"), Expect(input=[2, 2, 8, 8], output=None, id="duplicates"), Expect(input=np.array([[2, 4], [6, 8]]), output=None, id="multi-dim"), + # sorted-1D fast path (chunk_shape=(7,)): boundaries, contiguous runs, single chunk, full + Expect(input=[0, 6, 7, 13, 14, 28, 29], output=None, id="sorted-chunk-boundaries"), + Expect(input=[0, 1, 2, 8, 9, 10, 21, 22, 23], output=None, id="sorted-contiguous-runs"), + Expect(input=[1, 2, 3, 4, 5, 6], output=None, id="sorted-single-chunk"), + Expect(input=list(range(30)), output=None, id="sorted-full"), + Expect(input=[0, 0, 7, 7, 7, 29], output=None, id="sorted-duplicates-boundaries"), ] # get_coordinate_selection and vindex word their errors differently for these @@ -1141,6 +1150,107 @@ def test_get_coordinate_selection_1d( _test_get_coordinate_selection(a, z, case.input) +@pytest.mark.parametrize( + ("chunks", "shards"), + [((7,), None), ((7,), (21,))], + ids=["chunked", "sharded"], +) +def test_get_coordinate_selection_1d_fast_path( + store: StorePath, chunks: tuple[int, ...], shards: tuple[int, ...] | None +) -> None: + """The sorted-1D-runs fast path in CoordinateIndexer matches numpy on chunked and sharded arrays. + + Exercises the boundary/run/single-chunk/full-array cases that the fast path optimizes, plus + the sharded case where the top-level (shard) grid drives chunk assignment. + """ + a = np.arange(210, dtype=int) + z = zarr.create_array( + store=store / str(uuid4()), + shape=a.shape, + dtype=a.dtype, + chunks=chunks, + shards=shards, + ) + z[:] = a + rng = np.random.default_rng(0) + selections = [ + np.sort(rng.choice(210, 60, replace=False)), # scattered sorted + np.array([0, 6, 7, 20, 21, 209]), # chunk/shard boundaries + np.concatenate([np.arange(s, s + 5) for s in (0, 33, 100, 180)]), # contiguous runs + np.array([0, 0, 7, 7, 209]), # sorted with duplicates + np.arange(210), # whole array + np.array([5]), # single element + ] + for sel in selections: + assert_array_equal(a[sel], z.get_coordinate_selection(sel)) + assert_array_equal(a[sel], z.vindex[sel]) + + +def test_coordinate_indexer_1d_last_chunk_boundary_does_not_overflow() -> None: + max_intp = np.iinfo(np.intp).max + chunk_size = max_intp // 2 + 1 + coords = np.arange(max_intp - 4, max_intp, dtype=np.intp) + chunk_grid = ChunkGrid.from_sizes((max_intp,), (chunk_size,)) + + (projection,) = tuple(CoordinateIndexer((coords,), (max_intp,), chunk_grid)) + + assert projection.chunk_coords == (1,) + assert_array_equal(projection.chunk_selection[0], coords - chunk_size) + assert projection.out_selection == slice(0, 4) + + +@pytest.mark.parametrize("coord_dtype", [np.int8, np.uint8, np.uint32]) +def test_coordinate_selection_1d_narrow_dtype_large_chunk( + store: StorePath, coord_dtype: type[np.integer[Any]] +) -> None: + source = np.arange(1_000) + coords = np.arange(10, dtype=coord_dtype) + z = zarr_array_from_numpy_array(store, source, chunk_shape=(1_000,)) + + assert_array_equal(z.get_coordinate_selection(coords), source[coords]) + assert_array_equal(z.vindex[coords], source[coords]) + assert_array_equal(z[coords], source[coords]) + + expected = source.copy() + expected[coords] = -1 + z.set_coordinate_selection(coords, -1) + assert_array_equal(z[:], expected) + z[:] = source + z.vindex[coords] = -1 + assert_array_equal(z[:], expected) + + +def test_coordinate_indexer_1d_sparse_selection_uses_general_path( + monkeypatch: pytest.MonkeyPatch, +) -> None: + coords = np.array([0, 99]) + chunk_grid = ChunkGrid.from_sizes((100,), (1,)) + + def unexpected_searchsorted(*args: Any, **kwargs: Any) -> None: + pytest.fail("sparse coordinate selection should not call searchsorted") + + monkeypatch.setattr(np, "searchsorted", unexpected_searchsorted) + projections = tuple(CoordinateIndexer((coords,), (100,), chunk_grid)) + + assert tuple(projection.chunk_coords for projection in projections) == ((0,), (99,)) + + +def test_get_coordinate_selection_1d_irregular_grid(store: StorePath) -> None: + """Coordinate selections on an irregular (rectilinear) chunk grid bypass the sorted-1D fast + path (which requires a regular grid) and still match numpy via the general path.""" + a = np.arange(30, dtype=int) + with zarr.config.set({"array.rectilinear_chunks": True}): + z = zarr.create_array( + store=store / str(uuid4()), + shape=a.shape, + dtype=a.dtype, + chunks=((3, 3, 4, 5, 5, 5, 5),), + ) + z[:] = a + for sel in (np.array([1, 8, 15, 29]), np.array([0, 3, 3, 29]), np.arange(30)): + assert_array_equal(a[sel], z.get_coordinate_selection(sel)) + + @pytest.mark.parametrize("case", _COORD_1D_BAD_CASES, ids=lambda c: c.id) def test_get_coordinate_selection_1d_raises(store: StorePath, case: ExpectFail[Any]) -> None: """get_coordinate_selection and vindex both raise IndexError for invalid 1D selections.""" From 123268a7e467945c7d6a88e8d67d96c4ebb26809 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 15:20:39 +0200 Subject: [PATCH 421/468] fix: FusedCodecPipeline falls back to async path for sharded arrays with async-only inner codecs (#4179) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ShardingCodec structurally satisfies SupportsSyncCodec, but its sync methods delegate to the configured inner and index codec chains — so a shard whose inner or index chain contains a codec implementing only the async codec interface passed the fused pipeline's sync gate and then raised TypeError mid-IO in ChunkTransform construction. Sync capability is now answered by _codec_supports_sync, which combines the structural protocol check with a per-instance _sync_capable opt-out (absent means capable). ShardingCodec reports False when any codec in its inner or index chain is not sync-capable (recursively, so a nested shard propagates its opt-out outward), which makes ChunkTransform construction raise at pipeline evolve time and the pipeline decline the sync fast path — such arrays route through the async paths, matching BatchedCodecPipeline. Fully sync-capable chains keep the fast path. Closes #4178 Assisted-by: ClaudeCode:claude-fable-5 --- changes/4179.bugfix.md | 1 + src/zarr/abc/codec.py | 14 ++++++ src/zarr/codecs/sharding.py | 26 ++++++++++- src/zarr/core/chunk_utils.py | 10 +++- tests/test_fused_pipeline.py | 88 ++++++++++++++++++++++++++++++++++++ 5 files changed, 135 insertions(+), 4 deletions(-) create mode 100644 changes/4179.bugfix.md diff --git a/changes/4179.bugfix.md b/changes/4179.bugfix.md new file mode 100644 index 0000000000..e02523114c --- /dev/null +++ b/changes/4179.bugfix.md @@ -0,0 +1 @@ +Fixed the opt-in `FusedCodecPipeline` for sharded arrays whose inner or index codec chain contains a codec implementing only the async codec interface (no `SupportsSyncCodec`). Such arrays previously raised `TypeError: All codecs must implement SupportsSyncCodec` on both read and write; the pipeline now declines its synchronous fast path for them and falls back to the async path, matching the behavior of the default `BatchedCodecPipeline`. Fully sync-capable codec chains keep the fast path unchanged. diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py index 61c5dc9948..34d349e6d1 100644 --- a/src/zarr/abc/codec.py +++ b/src/zarr/abc/codec.py @@ -82,6 +82,20 @@ def _decode_sync(self, chunk_data: CO, chunk_spec: ArraySpec) -> CI: ... def _encode_sync(self, chunk_data: CI, chunk_spec: ArraySpec) -> CO | None: ... +def _codec_supports_sync(codec: object) -> bool: + """Whether `codec` can actually run on a synchronous (no event loop) path. + + Structural membership in `SupportsSyncCodec` is necessary but not always + sufficient: a codec can provide `_decode_sync`/`_encode_sync` whose ability + to run depends on runtime configuration the type system cannot see. + `ShardingCodec` is the canonical case — its sync methods delegate to its + configured inner and index codec chains, so they only work when every codec + in those chains is itself sync-capable. Such codecs opt out dynamically via + a `_sync_capable` attribute/property (absent means capable). + """ + return isinstance(codec, SupportsSyncCodec) and getattr(codec, "_sync_capable", True) + + class BaseCodec[CI: CodecInput, CO: CodecOutput](Metadata): """Generic base class for codecs. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index f20979066d..8f23606011 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -14,7 +14,7 @@ ArrayBytesCodecPartialEncodeMixin, Codec, CodecPipeline, - SupportsSyncCodec, + _codec_supports_sync, ) from zarr.abc.store import ( ByteGetter, @@ -1402,8 +1402,30 @@ def _is_complete_shard_write( is_complete_chunk for *_, is_complete_chunk in indexed_chunks ) + @property + def _sync_capable(self) -> bool: + """Dynamic opt-out consulted by `_codec_supports_sync` / `ChunkTransform`. + + This codec structurally satisfies `SupportsSyncCodec`, but every sync + method (`_decode_sync`, `_encode_sync`, `_decode_partial_sync`, + `_encode_partial_sync`) delegates to the inner and index codec chains + through `ChunkTransform`, so it can only run synchronously when every + codec in BOTH chains is itself sync-capable. Reporting False here makes + `ChunkTransform` construction raise, which in turn makes + `FusedCodecPipeline.evolve_from_array_spec` set `sync_transform=None` — + the whole pipeline then declines the sync fast path and routes through + the async paths (partial shard decode / async fallback write), exactly + as it does for an async-only TOP-level codec or a non-sync store. + """ + return self._inner_codecs_sync_capable() and self._index_codecs_sync_capable() + + def _inner_codecs_sync_capable(self) -> bool: + # _codec_supports_sync (not bare isinstance) so a nested sharding codec + # with an async-only inner chain propagates its opt-out outward. + return all(_codec_supports_sync(c) for c in self.codecs) + def _index_codecs_sync_capable(self) -> bool: - return all(isinstance(c, SupportsSyncCodec) for c in self.index_codecs) + return all(_codec_supports_sync(c) for c in self.index_codecs) async def _decode_shard_index( self, index_bytes: Buffer, chunks_per_shard: tuple[int, ...] diff --git a/src/zarr/core/chunk_utils.py b/src/zarr/core/chunk_utils.py index ee42e60cce..d93793f853 100644 --- a/src/zarr/core/chunk_utils.py +++ b/src/zarr/core/chunk_utils.py @@ -3,7 +3,7 @@ from dataclasses import dataclass, field from typing import TYPE_CHECKING, Any, cast -from zarr.abc.codec import GetResult, SupportsSyncCodec +from zarr.abc.codec import GetResult, SupportsSyncCodec, _codec_supports_sync from zarr.core.indexing import is_scalar if TYPE_CHECKING: @@ -240,7 +240,13 @@ class ChunkTransform: def __post_init__(self) -> None: from zarr.core.codec_pipeline import codecs_from_list - non_sync = [c for c in self.codecs if not isinstance(c, SupportsSyncCodec)] + # _codec_supports_sync, not a bare isinstance check: a codec can satisfy + # the SupportsSyncCodec protocol structurally yet be unable to run + # synchronously (ShardingCodec whose inner/index chain contains an + # async-only codec). Such codecs opt out via `_sync_capable`, and the + # TypeError here is what makes FusedCodecPipeline.evolve_from_array_spec + # decline the sync fast path and fall back to the async pipeline. + non_sync = [c for c in self.codecs if not _codec_supports_sync(c)] if non_sync: names = ", ".join(type(c).__name__ for c in non_sync) raise TypeError( diff --git a/tests/test_fused_pipeline.py b/tests/test_fused_pipeline.py index 09e9241c07..02b4026fd9 100644 --- a/tests/test_fused_pipeline.py +++ b/tests/test_fused_pipeline.py @@ -8,6 +8,7 @@ import pytest import zarr +from zarr.abc.codec import BytesBytesCodec from zarr.codecs.bytes import BytesCodec from zarr.codecs.gzip import GzipCodec from zarr.codecs.transpose import TransposeCodec @@ -643,6 +644,93 @@ def spy_write_sync(self: Any, *args: Any, **kwargs: Any) -> Any: ) +# --------------------------------------------------------------------------- +# Async-only codecs inside a shard's inner codec chain +# --------------------------------------------------------------------------- + + +class _AsyncOnlyNoopCodec(BytesBytesCodec): # type: ignore[misc,unused-ignore] + """A no-op BB codec implementing ONLY the async codec interface. + + Deliberately does NOT satisfy `SupportsSyncCodec` (no `_decode_sync` / + `_encode_sync`), modelling a third-party codec that predates the sync + protocol. Class-level counters prove the codec actually ran. + """ + + is_fixed_size = True + encode_calls = 0 + decode_calls = 0 + + def to_dict(self) -> dict[str, Any]: + return {"name": "test-async-only-noop", "configuration": {}} + + @classmethod + def from_dict(cls, data: dict[str, Any]) -> _AsyncOnlyNoopCodec: + return cls() + + def compute_encoded_size(self, input_byte_length: int, _spec: Any) -> int: + return input_byte_length + + async def _encode_single(self, chunk_bytes: Any, chunk_spec: Any) -> Any: + type(self).encode_calls += 1 + return chunk_bytes + + async def _decode_single(self, chunk_bytes: Any, chunk_spec: Any) -> Any: + type(self).decode_calls += 1 + return chunk_bytes + + +def test_sharded_roundtrip_with_async_only_inner_codec() -> None: + """A sharded array whose INNER codec chain contains an async-only codec + round-trips under FusedCodecPipeline (full write, partial write, full read, + partial read). + + Regression: the pipeline's top-level guard (evolve_from_array_spec -> + sync_transform=None) only inspected the top-level chain. ShardingCodec + structurally satisfies SupportsSyncCodec, so a sync transform was built and + the sync fast path dove into ShardingCodec's sync shard paths, which raised + TypeError from the inner ChunkTransform. The pipeline must instead decline + the sync fast path and fall back to the async inner pipeline, like + BatchedCodecPipeline. + """ + _AsyncOnlyNoopCodec.encode_calls = 0 + _AsyncOnlyNoopCodec.decode_calls = 0 + + with zarr_config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): + store = MemoryStore() + arr = zarr.create_array( + store=store, + shape=(16, 16), + shards=(8, 8), + chunks=(4, 4), + dtype="int32", + compressors=[_AsyncOnlyNoopCodec()], + fill_value=-1, + ) + assert isinstance(arr._async_array.codec_pipeline, FusedCodecPipeline) + + data = np.arange(256, dtype="int32").reshape(16, 16) + arr[:] = data # full write + np.testing.assert_array_equal(arr[:], data) # full read + np.testing.assert_array_equal(arr[2:11, 3:14], data[2:11, 3:14]) # partial read + + arr[5:7, 5:13] = 0 # partial write (read-merge-write of existing shards) + data[5:7, 5:13] = 0 + np.testing.assert_array_equal(arr[:], data) + + assert _AsyncOnlyNoopCodec.encode_calls > 0, "async-only inner codec never encoded" + assert _AsyncOnlyNoopCodec.decode_calls > 0, "async-only inner codec never decoded" + + # The stored bytes are valid for the default pipeline too: read them back + # under BatchedCodecPipeline (default codec_pipeline.path). Opening from + # metadata needs the codec name in the registry. + from zarr.registry import register_codec + + register_codec("test-async-only-noop", _AsyncOnlyNoopCodec) + reread = zarr.open_array(store=store, mode="r") + np.testing.assert_array_equal(reread[:], data) + + # --------------------------------------------------------------------------- # AsyncChunkTransform: the async per-chunk codec chain used on the async # fallback path. It is the async mirror of ChunkTransform, so it must produce From 80880a0425243406e145a69b722d7411c1dc6563 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 17:54:21 +0200 Subject: [PATCH 422/468] fix: fused pipeline falls back for partial-mixin codecs without sync partial methods (#4201) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The partial dispatch in FusedCodecPipeline.read_sync/write_sync asserted the private _decode_partial_sync/_encode_partial_sync methods, which only ShardingCodec implements. A codec advertising the public partial mixins (ArrayBytesCodecPartialDecodeMixin/-EncodeMixin) with only the documented async partial methods died with a bare AssertionError — or, under python -O, an AttributeError mid-IO. The asserts are now capability gates: codecs without the sync partial methods take the full-chunk sync path instead. The related crash for sharded arrays with async-only inner codecs is fixed separately in zarr-developers/zarr-python#4179. Assisted-by: ClaudeCode:claude-fable-5 --- changes/4201.bugfix.md | 1 + src/zarr/core/codec_pipeline.py | 24 ++++-- tests/test_fused_pipeline.py | 141 +++++++++++++++++++++++++++++++- 3 files changed, 155 insertions(+), 11 deletions(-) create mode 100644 changes/4201.bugfix.md diff --git a/changes/4201.bugfix.md b/changes/4201.bugfix.md new file mode 100644 index 0000000000..d837a8a9e2 --- /dev/null +++ b/changes/4201.bugfix.md @@ -0,0 +1 @@ +Fixed the opt-in `FusedCodecPipeline` for serializers that advertise the partial-decode/encode mixins with only the documented async partial methods: the partial dispatch previously asserted on the private `_decode_partial_sync`/`_encode_partial_sync` hooks (an `AssertionError`, or an `AttributeError` mid-IO under `python -O`); such codecs now take the full-chunk sync path. diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 4b8831bc7b..56a06b906c 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -1039,10 +1039,14 @@ def read_sync( # Partial-decode fast path: the AB codec owns IO (read only the # byte ranges needed for the requested selection). Same condition - # and dispatch as BatchedCodecPipeline.read_batch. - if self.supports_partial_decode: - codec = self.array_bytes_codec - assert hasattr(codec, "_decode_partial_sync") + # and dispatch as BatchedCodecPipeline.read_batch, plus a gate on the + # sync partial method: the public partial-decode contract + # (`ArrayBytesCodecPartialDecodeMixin`) only requires the async + # `_decode_partial_single`, so a codec may support partial decode + # without `_decode_partial_sync` — such codecs take the full-chunk + # path below instead. + codec = self.array_bytes_codec + if self.supports_partial_decode and hasattr(codec, "_decode_partial_sync"): def _read_one( item: tuple[Any, ArraySpec, SelectorTuple, SelectorTuple, bool], @@ -1111,10 +1115,14 @@ def write_sync( # Partial-encode path: the AB codec owns IO (read, merge, encode, # write). Same condition and calling convention as - # BatchedCodecPipeline.write_batch. - if self.supports_partial_encode: - codec = self.array_bytes_codec - assert hasattr(codec, "_encode_partial_sync") + # BatchedCodecPipeline.write_batch, plus a gate on the sync partial + # method: the public partial-encode contract + # (`ArrayBytesCodecPartialEncodeMixin`) only requires the async + # `_encode_partial_single`, so a codec may support partial encode + # without `_encode_partial_sync` — such codecs take the full-chunk + # path below instead. + codec = self.array_bytes_codec + if self.supports_partial_encode and hasattr(codec, "_encode_partial_sync"): scalar = len(value.shape) == 0 def _write_one( diff --git a/tests/test_fused_pipeline.py b/tests/test_fused_pipeline.py index 02b4026fd9..fd86936853 100644 --- a/tests/test_fused_pipeline.py +++ b/tests/test_fused_pipeline.py @@ -2,21 +2,32 @@ from __future__ import annotations -from typing import Any +from dataclasses import dataclass, field, replace +from typing import TYPE_CHECKING, Any import numpy as np import pytest import zarr -from zarr.abc.codec import BytesBytesCodec +from zarr.abc.codec import ( + ArrayBytesCodec, + ArrayBytesCodecPartialDecodeMixin, + ArrayBytesCodecPartialEncodeMixin, + BytesBytesCodec, +) from zarr.codecs.bytes import BytesCodec from zarr.codecs.gzip import GzipCodec from zarr.codecs.transpose import TransposeCodec from zarr.codecs.zstd import ZstdCodec from zarr.core.codec_pipeline import FusedCodecPipeline from zarr.core.config import config as zarr_config +from zarr.registry import register_codec from zarr.storage import MemoryStore, StorePath +if TYPE_CHECKING: + from zarr.core.array_spec import ArraySpec + from zarr.core.buffer import Buffer, NDBuffer + @pytest.mark.parametrize( "codecs", @@ -261,7 +272,7 @@ def test_chunk_transform_uses_runtime_prototype() -> None: """ from zarr.abc.codec import BytesBytesCodec from zarr.core.array_spec import ArrayConfig, ArraySpec - from zarr.core.buffer import Buffer, BufferPrototype, default_buffer_prototype + from zarr.core.buffer import BufferPrototype, default_buffer_prototype from zarr.core.chunk_utils import ChunkTransform from zarr.core.dtype import get_data_type_from_native_dtype @@ -831,3 +842,127 @@ def test_async_decode_encode_passes_through_none_chunks() -> None: assert decoded[1] is None assert decoded[0] is not None np.testing.assert_array_equal(decoded[0].as_numpy_array(), data) + + +# --------------------------------------------------------------------------- +# Graceful fallback for partial-mixin codecs without private sync-partial hooks +# +# The public partial-decode/encode contract (`ArrayBytesCodecPartialDecodeMixin` +# / `ArrayBytesCodecPartialEncodeMixin`) only requires the async +# `_decode_partial_single` / `_encode_partial_single`. The fused pipeline must +# route such codecs through its full-chunk sync path instead of asserting on +# the private `_decode_partial_sync` / `_encode_partial_sync` hooks. The double +# below is a minimal conforming implementer of that contract; it guards the +# public extension API, so it must not grow the private sync-partial methods. +# --------------------------------------------------------------------------- + + +@dataclass(frozen=True) +class PartialMixinCodec( + ArrayBytesCodec, ArrayBytesCodecPartialDecodeMixin, ArrayBytesCodecPartialEncodeMixin +): + """Serializer with sync whole-chunk methods plus ONLY async partial methods. + + This is the pre-fused public contract for partial-capable codecs: the + mixins' `_decode_partial_single` / `_encode_partial_single`. It must not + implement `_decode_partial_sync` / `_encode_partial_sync`. + """ + + inner: BytesCodec = field(default_factory=BytesCodec) + + @classmethod + def from_dict(cls, data: dict[str, Any]) -> PartialMixinCodec: + return cls() + + def to_dict(self) -> dict[str, Any]: + return {"name": "test-partial-mixin"} + + def evolve_from_array_spec(self, array_spec: ArraySpec) -> PartialMixinCodec: + return replace(self, inner=self.inner.evolve_from_array_spec(array_spec)) + + def compute_encoded_size(self, input_byte_length: int, chunk_spec: ArraySpec) -> int: + return self.inner.compute_encoded_size(input_byte_length, chunk_spec) + + def _decode_sync(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + return self.inner._decode_sync(chunk_bytes, chunk_spec) + + def _encode_sync(self, chunk_array: NDBuffer, chunk_spec: ArraySpec) -> Buffer | None: + return self.inner._encode_sync(chunk_array, chunk_spec) + + async def _decode_single(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> NDBuffer: + return self._decode_sync(chunk_bytes, chunk_spec) + + async def _encode_single(self, chunk_array: NDBuffer, chunk_spec: ArraySpec) -> Buffer | None: + return self._encode_sync(chunk_array, chunk_spec) + + async def _decode_partial_single( + self, byte_getter: Any, selection: Any, chunk_spec: ArraySpec + ) -> NDBuffer | None: + chunk_bytes = await byte_getter.get(prototype=chunk_spec.prototype) + if chunk_bytes is None: + return None + return self._decode_sync(chunk_bytes, chunk_spec)[selection] + + async def _encode_partial_single( + self, byte_setter: Any, chunk_array: NDBuffer, selection: Any, chunk_spec: ArraySpec + ) -> None: + existing = await byte_setter.get(prototype=chunk_spec.prototype) + if existing is None: + full = chunk_spec.prototype.nd_buffer.create( + shape=chunk_spec.shape, + dtype=chunk_spec.dtype.to_native_dtype(), + fill_value=chunk_spec.fill_value, + ) + else: + full = self._decode_sync(existing, chunk_spec) + full[selection] = chunk_array + encoded = self._encode_sync(full, chunk_spec) + assert encoded is not None + await byte_setter.set(encoded) + + +register_codec("test-partial-mixin", PartialMixinCodec) + +_FUSED = {"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"} +_BATCHED = {"codec_pipeline.path": "zarr.core.codec_pipeline.BatchedCodecPipeline"} + + +@pytest.mark.filterwarnings("ignore::zarr.errors.UnstableSpecificationWarning") +@pytest.mark.parametrize("dtype", ["uint8", "float64"]) +def test_partial_mixin_codec_async_partial_only_round_trip(dtype: str) -> None: + """A serializer advertising the partial mixins with only async partial + methods must round-trip under the fused pipeline: full write, full read, + partial read, partial write, plus cross-pipeline parity with + BatchedCodecPipeline.""" + data = np.arange(64, dtype=dtype).reshape(8, 8) + + with zarr_config.set(_FUSED): + store = MemoryStore() + arr = zarr.create_array( + store, + shape=(8, 8), + chunks=(4, 4), + dtype=dtype, + serializer=PartialMixinCodec(), + compressors=None, + filters=None, + fill_value=0, + ) + + pipeline = arr._async_array.codec_pipeline + assert isinstance(pipeline, FusedCodecPipeline) + assert pipeline.supports_partial_decode + assert pipeline.supports_partial_encode + assert pipeline.sync_transform is not None + + arr[:] = data + np.testing.assert_array_equal(arr[:], data) + np.testing.assert_array_equal(arr[1:5, 2:7], data[1:5, 2:7]) + + expected = data.copy() + expected[2:6, 1:3] = 7 + arr[2:6, 1:3] = expected[2:6, 1:3] + np.testing.assert_array_equal(arr[:], expected) + + with zarr_config.set(_BATCHED): + np.testing.assert_array_equal(zarr.open_array(store, mode="r")[:], expected) From ba832363cd8b517a4545528c54230c43a2c5f95e Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 17:55:26 +0200 Subject: [PATCH 423/468] fix: FusedCodecPipeline must apply outer AA/BB codecs on partial paths (#4202) FusedCodecPipeline.supports_partial_decode/supports_partial_encode passed require_no_aa_bb=False, unlike BatchedCodecPipeline (True). With an outer array-array or bytes-bytes codec around a sharding serializer (e.g. compressors=[GzipCodec()], or filters=[TransposeCodec()]), the fused pipeline's partial read/write branches called ShardingCodec's partial sync methods directly on the raw stored value, skipping those outer codecs entirely. That wrote non-conforming bytes for an outer BB codec (unreadable by BatchedCodecPipeline or any conforming reader) and silently produced wrong data for an outer AA codec. Pass require_no_aa_bb=True in both fused properties so these chains fall through to the full-chunk fused path instead, matching batched behavior. Adds cross-pipeline parity coverage (full and partial read/write) for sharding with an outer compressor and with an outer transpose filter, and removes the "known limitation" exclusion that previously kept the sharding+compressor case out of the nested-sharding parity matrix. Assisted-by: ClaudeCode:claude-sonnet-5 --- changes/4202.bugfix.md | 10 +++ src/zarr/core/codec_pipeline.py | 18 ++--- tests/test_pipeline_parity.py | 133 ++++++++++++++++++++++++++++---- 3 files changed, 135 insertions(+), 26 deletions(-) create mode 100644 changes/4202.bugfix.md diff --git a/changes/4202.bugfix.md b/changes/4202.bugfix.md new file mode 100644 index 0000000000..6130fc5b33 --- /dev/null +++ b/changes/4202.bugfix.md @@ -0,0 +1,10 @@ +Fixed `FusedCodecPipeline` (the opt-in synchronous pipeline) silently skipping +array-array/bytes-bytes codecs placed outside a sharding serializer on its +partial-decode/partial-encode fast paths. With an outer compressor (e.g. +`compressors=[GzipCodec()]` around a `ShardingCodec` serializer), the fused +pipeline wrote non-conforming stored bytes that `BatchedCodecPipeline` (and any +other conforming reader) could not read, and could fail to read data that +`BatchedCodecPipeline` had written. With an outer array-array codec (e.g. +`TransposeCodec`), it silently returned wrong data in both directions with no +error. Only the opt-in `FusedCodecPipeline` was affected; the default +`BatchedCodecPipeline` was never impacted. diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 56a06b906c..ca760ece59 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -143,10 +143,10 @@ def pipeline_supports_partial_decode( selection non-contiguous, a BB codec can rewrite the bytes), making partial decode infeasible. - NOTE: the two pipelines currently pass different ``require_no_aa_bb`` values - (Batched: True; Fused: False). That divergence is intentional-for-now and - tracked separately; this function centralizes the predicate without changing - either pipeline's behavior. + Both pipelines pass `require_no_aa_bb=True`: an outer AA/BB codec (e.g. a + compressor wrapping a sharding serializer) must see every byte of the + chunk, so a partial branch that only re-decodes/re-encodes the inner + sharding codec would silently bypass it. """ if require_no_aa_bb and (len(array_array_codecs) + len(bytes_bytes_codecs)) != 0: return False @@ -162,8 +162,7 @@ def pipeline_supports_partial_encode( ) -> bool: """Whether a codec pipeline can encode a partial selection without a full rewrite. - Mirror of ``pipeline_supports_partial_decode`` for encoding. See its note re: - the per-pipeline ``require_no_aa_bb`` divergence. + Mirror of `pipeline_supports_partial_decode` for encoding. """ if require_no_aa_bb and (len(array_array_codecs) + len(bytes_bytes_codecs)) != 0: return False @@ -934,14 +933,11 @@ def __iter__(self) -> Iterator[Codec]: @property def supports_partial_decode(self) -> bool: - # NOTE: unlike BatchedCodecPipeline this does NOT require the AA/BB codec - # lists to be empty (require_no_aa_bb=False). That divergence is tracked - # separately; see pipeline_supports_partial_decode. return pipeline_supports_partial_decode( self.array_bytes_codec, array_array_codecs=self.array_array_codecs, bytes_bytes_codecs=self.bytes_bytes_codecs, - require_no_aa_bb=False, + require_no_aa_bb=True, ) @property @@ -950,7 +946,7 @@ def supports_partial_encode(self) -> bool: self.array_bytes_codec, array_array_codecs=self.array_array_codecs, bytes_bytes_codecs=self.bytes_bytes_codecs, - require_no_aa_bb=False, + require_no_aa_bb=True, ) def validate( diff --git a/tests/test_pipeline_parity.py b/tests/test_pipeline_parity.py index 717f0f48f1..94d95c4c24 100644 --- a/tests/test_pipeline_parity.py +++ b/tests/test_pipeline_parity.py @@ -33,6 +33,8 @@ from __future__ import annotations +import warnings +from contextlib import contextmanager from typing import TYPE_CHECKING, Any import numpy as np @@ -48,7 +50,9 @@ ShardingCodec, SubchunkWriteOrder, ) +from zarr.codecs.transpose import TransposeCodec from zarr.core.config import config as zarr_config +from zarr.errors import ZarrUserWarning from zarr.storage import MemoryStore if TYPE_CHECKING: @@ -107,11 +111,15 @@ def _store_snapshot(store: MemoryStore) -> dict[str, bytes]: ("2d-unsharded", {"shape": (20, 20), "chunks": (5, 5), "shards": None}), ("2d-sharded", {"shape": (20, 20), "chunks": (5, 5), "shards": (10, 10)}), # Nested sharding: outer chunk (10,10) sharded into inner chunks (5,5). - # Restricted to bytes-only codec because combining an outer ShardingCodec - # with a compressor (gzip) triggers a ZarrUserWarning and results in a - # checksum mismatch inside the inner shard index — a known limitation, not - # a pipeline-parity bug. The bytes-only path still exercises the full - # two-level shard encoding/decoding in both pipelines. + # Restricted to the codec configs that don't set their own `serializer` + # (bytes-only, gzip): this layout supplies an explicit nested-ShardingCodec + # `serializer`, and a codec config that also sets `serializer` (e.g. + # bytes-big-endian) would silently clobber it via dict merge, dropping + # sharding from the test entirely rather than exercising it. The gzip + # config applies as an outer bytes-bytes codec around the outer + # ShardingCodec -- this is the regression coverage for the fused pipeline + # applying outer AA/BB codecs around sharding (see + # `pipeline_supports_partial_decode`/`pipeline_supports_partial_encode`). ( "2d-nested-sharded", { @@ -122,9 +130,7 @@ def _store_snapshot(store: MemoryStore) -> dict[str, bytes]: chunk_shape=(10, 10), codecs=[ShardingCodec(chunk_shape=(5, 5))], ), - # Only run with the bytes-only codec config; gzip is incompatible - # with nested sharding (see comment above). - "_codec_ids": {"bytes-only"}, + "_codec_ids": {"bytes-only", "gzip"}, }, ), ] @@ -226,6 +232,23 @@ def _matrix() -> Iterator[Any]: # --------------------------------------------------------------------------- +@contextmanager +def _ignore_sharding_combo_warning() -> Iterator[None]: + """Suppress the "combining sharding_indexed disables partial reads" warning. + + Only the nested-sharded-plus-outer-codec matrix cell emits this; scoping the + ignore filter to just its message/category (rather than blanket-disabling + warnings) keeps every other warning in the run promoted to an error as usual. + """ + with warnings.catch_warnings(): + warnings.filterwarnings( + "ignore", + message=r"Combining a `sharding_indexed` codec.*", + category=ZarrUserWarning, + ) + yield + + def _write_under_pipeline( pipeline_path: str, codec_kwargs: CodecConfig, @@ -244,12 +267,13 @@ def _write_under_pipeline( create_kwargs = {"dtype": "float64", **array_layout, **codec_kwargs} store = MemoryStore() with zarr_config.set({"codec_pipeline.path": pipeline_path}): - arr = zarr.create_array( - store=store, - fill_value=0, - config={"write_empty_chunks": write_empty_chunks}, - **create_kwargs, - ) + with _ignore_sharding_combo_warning(): + arr = zarr.create_array( + store=store, + fill_value=0, + config={"write_empty_chunks": write_empty_chunks}, + **create_kwargs, + ) for sel, val in sequence: arr[sel] = val contents = arr[...] @@ -259,7 +283,8 @@ def _write_under_pipeline( def _read_under_pipeline(pipeline_path: str, store: MemoryStore) -> Any: """Re-open an existing store under the chosen pipeline and read it whole.""" with zarr_config.set({"codec_pipeline.path": pipeline_path}): - arr = zarr.open_array(store=store, mode="r") + with _ignore_sharding_combo_warning(): + arr = zarr.open_array(store=store, mode="r") return arr[...] @@ -418,3 +443,81 @@ def run(pipeline_path: str) -> tuple[dict[str, bytes], Any]: f"(index_location={index_location!r}) — byte-range write fast path likely assumed " f"the wrong physical chunk order" ) + + +# --------------------------------------------------------------------------- +# Outer array-array / bytes-bytes codecs around a sharding serializer +# --------------------------------------------------------------------------- +# +# Regression coverage for FusedCodecPipeline.supports_partial_decode/encode: +# it used to allow AA/BB codecs outside the sharding codec, so its partial +# branches called ShardingCodec._decode_partial_sync/_encode_partial_sync +# directly on the raw stored value, skipping any outer filter/compressor. +# That corrupted on-disk bytes for an outer bytes-bytes codec (unreadable by +# the other pipeline) and silently produced wrong data for an outer +# array-array codec. Both configs below force the partial branches: a +# region write and a region read are included alongside the full ones. + +_OUTER_AA_BB_CONFIGS: list[tuple[str, CodecConfig]] = [ + ( + "outer-gzip-around-sharding", + { + "serializer": ShardingCodec(chunk_shape=(2, 2)), + "compressors": [GzipCodec(level=1)], + }, + ), + ( + "outer-transpose-around-sharding", + { + "filters": [TransposeCodec(order=(1, 0))], + "serializer": ShardingCodec(chunk_shape=(2, 2)), + "compressors": None, + }, + ), +] + + +@pytest.mark.parametrize(("config_id", "codec_kwargs"), _OUTER_AA_BB_CONFIGS) +@pytest.mark.parametrize( + ("writer", "reader"), + [(_BATCHED, _FUSED), (_FUSED, _BATCHED)], + ids=["batched-write-fused-read", "fused-write-batched-read"], +) +def test_pipeline_parity_outer_aa_bb_codecs( + config_id: str, + codec_kwargs: CodecConfig, + writer: str, + reader: str, +) -> None: + """Data written under one pipeline with outer AA/BB codecs must read back + correctly under the other, including through a partial write and a + partial read. + """ + shape = (8, 8) + data = (np.arange(int(np.prod(shape))).reshape(shape) + 1).astype("uint16") + store = MemoryStore() + + with zarr_config.set({"codec_pipeline.path": writer}): + with _ignore_sharding_combo_warning(): + arr = zarr.create_array( + store=store, + shape=shape, + chunks=(4, 4), + dtype=data.dtype, + fill_value=0, + **codec_kwargs, + ) + arr[...] = data + arr[2:5, 1:3] = 99 # region write -- exercises the partial-encode branch + + expected = data.copy() + expected[2:5, 1:3] = 99 + + with zarr_config.set({"codec_pipeline.path": reader}): + with _ignore_sharding_combo_warning(): + arr2 = zarr.open_array(store=store, mode="r") + full = arr2[...] + partial = arr2[1:3, 2:7] # region read -- exercises the partial-decode branch + + np.testing.assert_array_equal(full, expected) + np.testing.assert_array_equal(partial, expected[1:3, 2:7]) From bf818318d25c216721d8078d8a585dc734192be6 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 19:27:52 +0200 Subject: [PATCH 424/468] fix: gate bulk full-shard decode on identity reads; harden shard-index density check (#4203) The FusedCodecPipeline's vectorized whole-shard decode accepted any indexer without `sel_shape` whose output shape matched the shard shape. An OrthogonalIndexer from `arr[perm, :]` / `arr.oindex[...]` satisfies that, so reordering or duplicating fancy-index reads on uncompressed, crc-free sharded arrays silently returned the shard in natural order. The bulk path now requires an identity full read: one whole-dimension, step-1 slice per dimension (structural, not a BasicIndexer type check, since `arr[:]` arrives as an OrthogonalIndexer). Also: - decline structured dtypes in the bulk path, which lacks the Struct byte-order branch of BytesCodec._decode_sync (latent until #3054 is fixed); - `_ShardIndex.is_dense` now requires offsets to exactly tile the data section instead of merely being unique, so corrupt indexes with overlapping or out-of-range offsets (e.g. pointing into an index_location='start' index region) cannot be served as array data. Assisted-by: ClaudeCode:claude-fable-5 --- changes/4203.bugfix.md | 1 + src/zarr/codecs/sharding.py | 96 +++++++--- tests/test_codecs/test_sharding_unit.py | 234 +++++++++++++++++++++++- tests/test_fastpath_equivalence.py | 90 +++++---- 4 files changed, 358 insertions(+), 63 deletions(-) create mode 100644 changes/4203.bugfix.md diff --git a/changes/4203.bugfix.md b/changes/4203.bugfix.md new file mode 100644 index 0000000000..42ca977193 --- /dev/null +++ b/changes/4203.bugfix.md @@ -0,0 +1 @@ +Fixed silent data corruption in the experimental `FusedCodecPipeline`: reordering or duplicating fancy-index reads (e.g. `arr[perm, :]`, `arr.oindex[[0, 0, 1], :]`) on uncompressed, crc-free sharded arrays could return the shard in natural order because the vectorized whole-shard decode accepted any selection whose output shape matched the shard shape. The bulk decode now fires only for identity full-shard reads, declines structured dtypes (whose byte-order handling it lacks), and requires shard-index offsets to exactly tile the data section, so corrupt indexes with overlapping or out-of-range offsets can no longer be served as array data. diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index 8f23606011..cdfdae6c89 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -53,10 +53,12 @@ from zarr.core.config import config as zarr_config from zarr.core.dtype.common import HasEndianness from zarr.core.dtype.npy.int import UInt64 +from zarr.core.dtype.npy.structured import Struct from zarr.core.indexing import ( BasicIndexer, ChunkProjection, SelectorTuple, + SliceDimIndexer, _lexicographic_order, colexicographic_order_coords, get_indexer, @@ -109,6 +111,32 @@ class ShardingCodecIndexLocation(metaclass=_DeprecatedStrEnumMeta): ) +def _is_identity_full_read(indexer: Any, shard_shape: tuple[int, ...]) -> bool: + """True when `indexer` selects every element of a `shard_shape` array in + natural order: one whole-dimension, step-1 `SliceDimIndexer` per dimension. + + Structural on purpose, not `isinstance(indexer, BasicIndexer)`: a full + `arr[:]` read reaches the shard as an `OrthogonalIndexer`, so a type gate + would silently disable the bulk fast path for the most common case. Any + gather (integer-array / boolean / coordinate selection), subset, strided, + or integer-scalar selection fails the per-dimension check — output shape + alone is not enough, because a reordering or duplicating selection can have + the same shape as the shard while requiring `chunk_selection` / + `out_selection` to be honored. + """ + dim_indexers = getattr(indexer, "dim_indexers", None) + if dim_indexers is None or len(dim_indexers) != len(shard_shape): + return False + return all( + isinstance(dim_indexer, SliceDimIndexer) + and dim_indexer.dim_len == dim_len + and dim_indexer.start == 0 + and dim_indexer.stop == dim_len + and dim_indexer.step == 1 + for dim_indexer, dim_len in zip(dim_indexers, shard_shape, strict=True) + ) + + def _parse_index_location(data: object) -> IndexLocation: if isinstance(data, str) and data in INDEX_LOCATION: return data # type: ignore[return-value] @@ -192,12 +220,17 @@ def is_all_empty(self) -> bool: def get_full_chunk_map(self) -> npt.NDArray[np.bool_]: return np.not_equal(self.offsets_and_lengths[..., 0], MAX_UINT_64) - def is_dense(self, chunk_byte_length: int) -> bool: - """True when every chunk is present, fixed-length, and uniquely placed. - - Used to gate the vectorized whole-shard decode: a dense fixed-size shard - is a regular grid of equal-length payloads, so it can be reshaped/scattered - in bulk rather than decoded chunk-by-chunk. + def is_dense(self, chunk_byte_length: int, *, data_section_start: int) -> bool: + """True when the chunk payloads exactly tile the shard's data section. + + Every chunk must be present with length `chunk_byte_length`, and the + sorted offsets must be exactly `data_section_start + i * chunk_byte_length` + for `i` in `0..n_chunks-1`: no gaps, no overlaps, and nothing outside the + data section (a corrupt index could otherwise point chunks into the + index region or out of the blob). Used to gate the vectorized + whole-shard decode: a dense fixed-size shard is a regular grid of + equal-length payloads, so it can be reshaped/scattered in bulk rather + than decoded chunk-by-chunk. """ offsets = self.offsets_and_lengths[..., 0].reshape(-1) lengths = self.offsets_and_lengths[..., 1].reshape(-1) @@ -207,8 +240,10 @@ def is_dense(self, chunk_byte_length: int) -> bool: # all the same fixed length if not bool(np.all(lengths == chunk_byte_length)): return False - # offsets unique (no two chunks share a slot) - return int(np.unique(offsets).size) == int(offsets.size) + expected = np.uint64(data_section_start) + np.arange( + offsets.size, dtype=np.uint64 + ) * np.uint64(chunk_byte_length) + return bool(np.array_equal(np.sort(offsets), expected)) def get_chunk_slice(self, chunk_coords: tuple[int, ...]) -> tuple[int, int] | None: localized_chunk = self._localize_chunk(chunk_coords) @@ -1086,8 +1121,12 @@ def _decode_full_shard_bulk_if_uncompressed( dtype/endian view with no reordering. A trailing crc32c is NOT accepted (the bulk path can't verify per-chunk checksums, so crc shards keep the per-chunk path's corruption detection); + - the data type is not structured (the byte-order handling below has no + `Struct` branch); + - `indexer` is an identity full-shard read (`_is_identity_full_read`); - the stored index is dense (every chunk present, equal fixed length, - contiguous) so the data section is a regular grid of chunk payloads. + exactly tiling the data section) so the data section is a regular + grid of chunk payloads. Chunk positions are read from the stored index, so this is correct for any `subchunk_write_order` (morton / lexicographic / colexicographic / @@ -1107,27 +1146,29 @@ def _decode_full_shard_bulk_if_uncompressed( return None ab_codec = self.codecs[0] + # The byte-order handling below lacks the structured-dtype branch of + # `BytesCodec._decode_sync` (which applies `newbyteorder` to multi-byte + # struct fields), so structured dtypes must take the per-chunk path. + if isinstance(shard_spec.dtype, Struct): + return None + chunks_per_shard = self._get_chunks_per_shard(shard_spec) chunk_spec = self._get_chunk_spec(shard_spec) n_chunks = product(chunks_per_shard) if n_chunks == 0: return None - # Only valid for a plain contiguous full-shard read, where each chunk - # lands at its natural grid position. The `sel_shape` check is - # load-bearing: a gather indexer (CoordinateIndexer, from vindex / an - # oindex with an integer-array selection) reorders points and exposes - # `sel_shape`, but its `.shape` is the FLATTENED point count, which can - # equal the shard shape by coincidence (trivially in 1-D). Gating on - # shape alone lets such a selection through, and the bulk path then - # returns the shard in natural order, silently dropping the reordering. - # A contiguous full read (BasicIndexer, or a non-gathering - # OrthogonalIndexer from `arr[:]`) has no `sel_shape` and is served here. - # Anything that gathers must fall through to the per-chunk path so + # Only valid for an identity full-shard read, where each chunk lands at + # its natural grid position. The per-dimension check is load-bearing: + # a gather selection (an `OrthogonalIndexer` with an integer-array or + # boolean dimension, from `arr[perm, :]` / `arr.oindex[...]`, or a + # `CoordinateIndexer` from vindex) can have an output `.shape` equal to + # the shard shape while reordering or duplicating points — serving it + # from the bulk path would return the shard in natural order, silently + # dropping the reordering. Anything that is not a full-slice-per- + # dimension read falls through to the per-chunk path so # chunk_selection / out_selection are honored. - if getattr(indexer, "sel_shape", None) is not None: - return None - if tuple(indexer.shape) != tuple(shard_spec.shape): + if not _is_identity_full_read(indexer, shard_spec.shape): return None chunk_byte_length = self._inner_chunk_byte_length(chunk_spec) @@ -1141,7 +1182,8 @@ def _decode_full_shard_bulk_if_uncompressed( else: index_bytes = shard_bytes[-shard_index_size:] index = self._decode_shard_index_sync(index_bytes, chunks_per_shard) - if not index.is_dense(chunk_byte_length): + data_section_start = shard_index_size if self.index_location == "start" else 0 + if not index.is_dense(chunk_byte_length, data_section_start=data_section_start): return None # --- bulk reconstruct --- @@ -1227,9 +1269,9 @@ def _decode_partial_sync( return None bulk = self._decode_full_shard_bulk_if_uncompressed(shard_bytes, shard_spec, indexer) if bulk is not None: - # The bulk path only fires for a contiguous full-shard read (it - # returns None for any gather indexer that exposes `sel_shape`), - # so the result is already shard-shaped — no reshape needed. + # The bulk path only fires for an identity full-shard read + # (`_is_identity_full_read`), so the result is already + # shard-shaped and in natural order — no reshape needed. return bulk shard_reader = self._shard_reader_from_bytes_sync(shard_bytes, chunks_per_shard) shard_dict: ShardMapping = shard_reader diff --git a/tests/test_codecs/test_sharding_unit.py b/tests/test_codecs/test_sharding_unit.py index 34d468fa05..d8b8242a28 100644 --- a/tests/test_codecs/test_sharding_unit.py +++ b/tests/test_codecs/test_sharding_unit.py @@ -2,12 +2,14 @@ import asyncio from dataclasses import dataclass, replace -from typing import TYPE_CHECKING, Any, cast +from typing import TYPE_CHECKING, Any, Literal, cast from unittest.mock import AsyncMock import numpy as np +import numpy.typing as npt import pytest +import zarr from zarr.abc.codec import ArrayArrayCodec, ArrayBytesCodec from zarr.codecs.bytes import BytesCodec from zarr.codecs.crc32c_ import Crc32cCodec @@ -24,8 +26,10 @@ from zarr.core.buffer import NDBuffer, default_buffer_prototype from zarr.core.buffer.cpu import Buffer from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer +from zarr.core.chunk_grids import ChunkGrid from zarr.core.config import config from zarr.core.dtype import get_data_type_from_native_dtype +from zarr.core.indexing import BasicIndexer from zarr.storage._common import StorePath from zarr.storage._memory import MemoryStore @@ -910,3 +914,231 @@ async def mock_load_index( kwargs = store_mock.get_ranges.call_args.kwargs assert kwargs["max_gap_bytes"] == 12345 assert kwargs["max_coalesced_bytes"] == 67890 + + +# ============================================================================ +# Bulk full-shard decode: identity-read gating and dtype gating +# ============================================================================ + +_FUSED_PIPELINE = "zarr.core.codec_pipeline.FusedCodecPipeline" + + +def _fused_uncompressed_array( + index_location: Literal["start", "end"], +) -> tuple[Any, npt.NDArray[np.int32]]: + """Sharded `(8, 8)` array whose inner chain is a bare BytesCodec (no crc), + one shard covering the whole array, filled with `arange` data. Callers must + be inside a config context selecting the fused pipeline.""" + shards: ShardsConfigParam = {"shape": (8, 8), "index_location": index_location} + arr = zarr.create_array( + store=MemoryStore(), + shape=(8, 8), + chunks=(2, 2), + shards=shards, + dtype="int32", + compressors=None, + filters=None, + fill_value=0, + config={"write_empty_chunks": True}, + ) + ref = np.arange(64, dtype="int32").reshape(8, 8) + arr[:] = ref + return arr, ref + + +def _spy_on_bulk_decode(monkeypatch: pytest.MonkeyPatch) -> list[bool]: + """Record, per call, whether `_decode_full_shard_bulk_if_uncompressed` + engaged (returned non-None).""" + engaged: list[bool] = [] + orig = ShardingCodec._decode_full_shard_bulk_if_uncompressed + + def spy(self: ShardingCodec, shard_bytes: Any, shard_spec: Any, indexer: Any) -> Any: + result = orig(self, shard_bytes, shard_spec, indexer) + engaged.append(result is not None) + return result + + monkeypatch.setattr(ShardingCodec, "_decode_full_shard_bulk_if_uncompressed", spy) + return engaged + + +_PERM_8 = np.array([7, 2, 5, 0, 3, 6, 1, 4]) +_DUP_8 = np.array([0, 0, 1, 2, 3, 4, 5, 6]) + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +@pytest.mark.parametrize( + ("read", "expected", "expect_bulk"), + [ + pytest.param(lambda a: a[:], lambda r: r, True, id="full-slice"), + pytest.param(lambda a: a[...], lambda r: r, True, id="ellipsis"), + pytest.param( + lambda a: a[_PERM_8, :], lambda r: r[_PERM_8, :], False, id="fancy-permutation" + ), + pytest.param(lambda a: a[_DUP_8, :], lambda r: r[_DUP_8, :], False, id="fancy-duplicates"), + pytest.param( + lambda a: a.oindex[_PERM_8, :], + lambda r: r[_PERM_8, :], + False, + id="oindex-permutation", + ), + pytest.param( + lambda a: a.oindex[_DUP_8, :], lambda r: r[_DUP_8, :], False, id="oindex-duplicates" + ), + pytest.param(lambda a: a[1:7, :], lambda r: r[1:7, :], False, id="subset-slice"), + ], +) +def test_bulk_decode_engagement_and_correctness( + monkeypatch: pytest.MonkeyPatch, + index_location: Literal["start", "end"], + read: Any, + expected: Any, + expect_bulk: bool, +) -> None: + """Under the fused pipeline on an uncompressed crc-free shard, the bulk + whole-shard decode fires exactly for identity full reads — and every read + returns what numpy returns. The engagement assertions keep the correctness + half non-vacuous: a gate that simply disabled the fast path would pass the + value checks but fail here.""" + engaged = _spy_on_bulk_decode(monkeypatch) + with config.set({"codec_pipeline.path": _FUSED_PIPELINE}): + arr, ref = _fused_uncompressed_array(index_location) + engaged.clear() + np.testing.assert_array_equal(read(arr), expected(ref)) + if expect_bulk: + assert len(engaged) > 0, "bulk fast path was never reached for a full read" + assert all(engaged), "bulk fast path did not engage for a full read" + else: + assert not any(engaged), "bulk fast path engaged for a non-identity selection" + + +@pytest.mark.parametrize("index_location", ["start", "end"]) +def test_multi_shard_permutation_read(index_location: Literal["start", "end"]) -> None: + """A row permutation crossing shard boundaries must return permuted data + under the fused pipeline (each shard sees a gather selection whose shape + coincides with the shard shape).""" + shards: ShardsConfigParam = {"shape": (8, 8), "index_location": index_location} + with config.set({"codec_pipeline.path": _FUSED_PIPELINE}): + arr = zarr.create_array( + store=MemoryStore(), + shape=(16, 16), + chunks=(2, 2), + shards=shards, + dtype="int32", + compressors=None, + filters=None, + fill_value=0, + config={"write_empty_chunks": True}, + ) + ref = np.arange(256, dtype="int32").reshape(16, 16) + arr[:] = ref + perm = np.array([9, 3, 12, 0, 15, 6, 10, 1, 14, 5, 8, 2, 13, 7, 11, 4]) + np.testing.assert_array_equal(arr[perm, :8], ref[perm, :8]) + np.testing.assert_array_equal(arr.oindex[perm, :8], ref[perm, :8]) + + +def _dense_shard_blob( + codec: ShardingCodec, data: np.ndarray[Any, np.dtype[Any]], chunk_len: int +) -> Buffer: + """Hand-assemble a dense `index_location="end"` shard blob for 1-D `data`: + natural-order chunk payloads followed by the encoded index.""" + n_chunks = data.shape[0] // chunk_len + chunk_nbytes = chunk_len * data.dtype.itemsize + index = _ShardIndex.create_empty((n_chunks,)) + for i in range(n_chunks): + index.set_chunk_slice((i,), slice(i * chunk_nbytes, (i + 1) * chunk_nbytes)) + index_bytes = codec._encode_shard_index_sync(index) + return Buffer.from_bytes(data.tobytes() + index_bytes.to_bytes()) + + +def _identity_indexer(shape: tuple[int, ...], chunk_shape: tuple[int, ...]) -> BasicIndexer: + return BasicIndexer( + tuple(slice(0, s) for s in shape), + shape=shape, + chunk_grid=ChunkGrid.from_sizes(shape, chunk_shape), + ) + + +def _spec_for(data: np.ndarray[Any, np.dtype[Any]]) -> ArraySpec: + zdt = get_data_type_from_native_dtype(data.dtype) + return ArraySpec( + shape=data.shape, + dtype=zdt, + fill_value=zdt.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + + +def test_bulk_decode_declines_structured_dtype() -> None: + """The bulk path has no structured-dtype byte-order handling (the `Struct` + branch of `BytesCodec._decode_sync`), so it must decline structured specs. + The plain-dtype control on an identically constructed blob proves the + decline comes from the dtype gate, not from a malformed blob.""" + codec = ShardingCodec(chunk_shape=(2,), codecs=[BytesCodec(endian="little")]) + + # control: same construction with a plain dtype engages the bulk path + plain = np.arange(4, dtype="<i4") + bulk = codec._decode_full_shard_bulk_if_uncompressed( + _dense_shard_blob(codec, plain, 2), _spec_for(plain), _identity_indexer((4,), (2,)) + ) + assert bulk is not None + np.testing.assert_array_equal(bulk.as_numpy_array(), plain) + + struct_data = np.zeros(4, dtype=np.dtype([("a", "<i4"), ("b", "<f8")])) + struct_data["a"] = np.arange(4) + result = codec._decode_full_shard_bulk_if_uncompressed( + _dense_shard_blob(codec, struct_data, 2), + _spec_for(struct_data), + _identity_indexer((4,), (2,)), + ) + assert result is None + + +# ============================================================================ +# _ShardIndex.is_dense: offsets must tile the data section exactly +# ============================================================================ + + +@pytest.mark.parametrize("chunks_per_shard", [(4,), (2, 2)]) +@pytest.mark.parametrize("data_section_start", [0, 32]) +@pytest.mark.parametrize("layout_order", ["natural", "reversed"]) +def test_shard_index_is_dense_accepts_tiling_layouts( + chunks_per_shard: tuple[int, ...], data_section_start: int, layout_order: str +) -> None: + """`is_dense` accepts every layout whose fixed-size payloads exactly tile + the data section, wherever that section starts and in whatever order the + chunks were laid out.""" + chunk_len = 24 + n = int(np.prod(chunks_per_shard)) + slots = np.arange(n) + if layout_order == "reversed": + slots = slots[::-1] + offsets = data_section_start + slots * chunk_len + index = _ShardIndex.create_empty(chunks_per_shard) + for coord, off in zip(np.ndindex(chunks_per_shard), offsets, strict=True): + index.set_chunk_slice(tuple(coord), slice(int(off), int(off) + chunk_len)) + assert index.is_dense(chunk_len, data_section_start=data_section_start) is True + + +def test_shard_index_is_dense_rejects_overlapping_offsets() -> None: + """Unique but overlapping offsets (second payload starts inside the first) + are not dense.""" + chunk_len = 24 + index = _ShardIndex.create_empty((2,)) + index.set_chunk_slice((0,), slice(0, chunk_len)) + index.set_chunk_slice((1,), slice(12, 12 + chunk_len)) + assert index.is_dense(chunk_len, data_section_start=0) is False + + +def test_shard_index_is_dense_rejects_out_of_range_offsets() -> None: + """An offset outside the data section (here: chunk 0 pointing into an + `index_location="start"` index region) is not dense, even though offsets + are unique and non-overlapping.""" + chunk_len = 24 + data_section_start = 16 + index = _ShardIndex.create_empty((2,)) + index.set_chunk_slice((0,), slice(0, chunk_len)) + index.set_chunk_slice( + (1,), slice(data_section_start + chunk_len, data_section_start + 2 * chunk_len) + ) + assert index.is_dense(chunk_len, data_section_start=data_section_start) is False diff --git a/tests/test_fastpath_equivalence.py b/tests/test_fastpath_equivalence.py index 317b8742f1..9a2f782d13 100644 --- a/tests/test_fastpath_equivalence.py +++ b/tests/test_fastpath_equivalence.py @@ -196,34 +196,43 @@ def test_merge_complete_chunk_returns_view_and_write_does_not_mutate_source() -> # --------------------------------------------------------------------------- # Whole-shard bulk decode under arbitrary indexing: the bulk decode only fires -# for a *contiguous full-shard* read, but it is reached through the partial-read -# path (`_decode_partial_sync`), whose only gate is `indexer.shape == -# shard_spec.shape`. A reordering coordinate/orthogonal selection that happens -# to touch every chunk (so the flattened point count equals the shard shape) -# must NOT be served by the bulk path in natural order — it must honor the -# selection. This pins the END-TO-END read (the gate lives in the array read -# path, not in `_decode_full_shard_bulk_if_uncompressed` itself), which -# `test_bulk_shard_decode_equals_general_decode` (BasicIndexer only) cannot -# reach. See the vindex-on-uncompressed-shard corruption bug. +# for an *identity full-shard* read (every dimension a whole-dim step-1 slice), +# but it is reached through the partial-read path (`_decode_partial_sync`) for +# any indexer. A reordering or duplicating coordinate/orthogonal selection can +# have an output shape equal to the shard shape — trivially in 1-D (any +# selection of `shard_len` points), and in >=2-D whenever an axis-0 index array +# has exactly `shard_shape[0]` entries — and must NOT be served by the bulk +# path in natural order; it must honor the selection. This pins the END-TO-END +# read, which `test_bulk_shard_decode_equals_general_decode` (identity +# BasicIndexer only) cannot reach. See the vindex- and +# oindex-on-uncompressed-shard corruption bugs. # --------------------------------------------------------------------------- @st.composite def _uncompressed_shard_index_cases(draw: st.DrawFn) -> dict[str, Any]: - # 1-D is where the trigger is easiest: a CoordinateIndexer's `.shape` is the - # flattened point count, which equals a 1-D shard shape exactly when the - # selection visits `shard_len` points. - chunk = draw(st.integers(1, 4)) - grid = draw(st.integers(1, 4)) - shard_len = chunk * grid + ndim = draw(st.integers(1, 2)) + chunk_shape = tuple(draw(st.integers(1, 4)) for _ in range(ndim)) + grid = tuple(draw(st.integers(1, 4)) for _ in range(ndim)) + shard_shape = tuple(c * g for c, g in zip(chunk_shape, grid, strict=True)) dtype = draw(_DTYPES) - data = draw(npst.arrays(dtype=np.dtype(dtype), shape=(shard_len,))) - perm = draw(st.permutations(list(range(shard_len)))) + data = draw(npst.arrays(dtype=np.dtype(dtype), shape=shard_shape)) + dim0 = shard_shape[0] + # axis-0 index array sized to the dimension: either a permutation + # (reordering, no duplicates) or an arbitrary list (duplicates likely) — + # both keep the output shape equal to the shard shape. + if draw(st.booleans()): + idx = np.array(draw(st.permutations(list(range(dim0)))), dtype=np.intp) + else: + idx = np.array( + draw(st.lists(st.integers(0, dim0 - 1), min_size=dim0, max_size=dim0)), + dtype=np.intp, + ) return { - "chunk": chunk, - "shard_len": shard_len, + "chunk_shape": chunk_shape, + "shard_shape": shard_shape, "data": data, - "perm": np.array(perm), + "idx": idx, "endian": draw(st.sampled_from(["little", "big"])), "index_location": draw(st.sampled_from(["start", "end"])), "subchunk_write_order": draw( @@ -235,33 +244,44 @@ def _uncompressed_shard_index_cases(draw: st.DrawFn) -> dict[str, Any]: @settings(max_examples=200, deadline=None) @given(case=_uncompressed_shard_index_cases()) def test_reordering_read_on_uncompressed_shard_honors_selection(case: dict[str, Any]) -> None: - """A reordering vindex/oindex over a full uncompressed shard must return the - permuted data, not the shard in natural order — under the Fused pipeline - (where the bulk-decode fast path engages) exactly as under numpy.""" - perm = case["perm"] + """A reordering or duplicating fancy/vindex/oindex read over a full + uncompressed shard must return the selected data, not the shard in natural + order — under the Fused pipeline (where the bulk-decode fast path engages) + exactly as under numpy.""" + idx = case["idx"] data = case["data"] + ndim = data.ndim serializer = BytesCodec(endian=case["endian"]) with zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): arr = zarr.create_array( store=MemoryStore(), - shape=(case["shard_len"],), - chunks=(case["chunk"],), - shards=(case["shard_len"],), + shape=case["shard_shape"], + chunks=case["chunk_shape"], + shards={"shape": case["shard_shape"], "index_location": case["index_location"]}, dtype=data.dtype, serializer=serializer, compressors=None, filters=None, fill_value=0, ) - arr[:] = data - - # vindex with a full-coverage permutation: flattened point count == - # shard shape, so the buggy gate would mis-classify this as a contiguous - # full-shard read and return data unpermuted. - np.testing.assert_array_equal(arr.vindex[perm], data[perm]) - # oindex with a single reordering index list along the only axis. - np.testing.assert_array_equal(arr.oindex[perm], data[perm]) + arr[...] = data + + # axis-0 index array (rest full slices): an OrthogonalIndexer whose + # output shape equals the shard shape but which reorders/duplicates rows. + rest = (slice(None),) * (ndim - 1) + np.testing.assert_array_equal(arr[(idx, *rest)], data[idx]) + np.testing.assert_array_equal(arr.oindex[(idx, *rest)], data[idx]) + if ndim == 1: + # coordinate selection: flattened point count == shard shape. + np.testing.assert_array_equal(arr.vindex[idx], data[idx]) + else: + # 2-D broadcast index arrays: full-coverage coordinate selection + # whose shape equals the shard shape. + cols = np.arange(case["shard_shape"][1]) + np.testing.assert_array_equal( + arr.vindex[idx[:, None], cols[None, :]], data[idx[:, None], cols[None, :]] + ) # --------------------------------------------------------------------------- From b2ece6f82c5281d02a8a4408fb13f791870c65bd Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 19:40:02 +0200 Subject: [PATCH 425/468] docs(zarr-metadata): standalone documentation site; add package justfile (#4208) * docs(zarr-metadata): add API reference to the docs site Add mkdocstrings pages for every public zarr_metadata module (model, pydantic, v2, and v3 with its chunk_grid, chunk_key_encoding, codec, and data_type subpackages) under a new zarr-metadata group in the API Reference nav. griffe documents the package statically from packages/zarr-metadata/src, so the docs build environment does not need the package installed. Point the package's Documentation URL at the rendered reference instead of the README. Assisted-by: ClaudeCode:claude-fable-5 * chore(zarr-metadata): add justfile with package-scoped dev recipes Recipes mirror the zarr-metadata CI jobs (pytest, ruff, pyright pinned to the version CI uses, on CI's python) plus changelog-draft and docs-serve conveniences. Recipes run from the package directory regardless of where just is invoked, and remain reachable from the repo root as 'just packages/zarr-metadata/<recipe>'; a future root justfile can namespace them with a 'mod' declaration. Assisted-by: ClaudeCode:claude-fable-5 * chore(zarr-metadata): make docs-serve robust to a busy port With no argument, docs-serve now binds port 8000 if free and otherwise falls back to an ephemeral free port. An explicitly requested port is used as-is so a conflict fails loudly. Assisted-by: ClaudeCode:claude-fable-5 * chore(zarr-metadata): point docs-serve at the package docs, fix cleanup Print the zarr-metadata API reference URL once the server accepts connections, since mkdocs's own 'Serving on' line points at the zarr-python site root. Run the server in its own process group so stopping the recipe kills the whole uv->mkdocs tree instead of leaving an orphaned server holding the port. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): make the package docs a standalone site Move the zarr-metadata API reference out of the zarr-python site into a self-contained mkdocs site under packages/zarr-metadata (own mkdocs.yml, landing page, and .readthedocs.yaml for a dedicated RTD project), so the package presents as a separate project with docs versioned by its own zarr_metadata-v* release tags rather than zarr-python's. The zarr-python API Reference nav now links out to the standalone site instead of embedding the pages. The package gains a pinned docs dependency group, a docs build job in its CI workflow, and docs-check / docs-serve justfile recipes targeting the package site. Assisted-by: ClaudeCode:claude-fable-5 * update index.md * ci(zarr-metadata): delegate workflow steps to the justfile The workflow duplicated every command the justfile defines; jobs now run 'just test/lint/typecheck/docs-check' so the justfile is the single source of truth for the package's verbs. CI keeps only its own concerns: the python matrix sync for pytest, and uv caching. The pyright job's python/sync steps are dropped because the typecheck recipe pins the interpreter and pyright version itself. Assisted-by: ClaudeCode:claude-fable-5 --- .github/workflows/zarr-metadata.yml | 45 ++++++-- mkdocs.yml | 1 + packages/zarr-metadata/.readthedocs.yaml | 20 ++++ packages/zarr-metadata/README.md | 19 ++++ packages/zarr-metadata/docs/api/index.md | 31 ++++++ packages/zarr-metadata/docs/api/model.md | 5 + packages/zarr-metadata/docs/api/pydantic.md | 5 + packages/zarr-metadata/docs/api/v2.md | 17 +++ .../zarr-metadata/docs/api/v3/chunk_grid.md | 11 ++ .../docs/api/v3/chunk_key_encoding.md | 11 ++ packages/zarr-metadata/docs/api/v3/codec.md | 25 +++++ .../zarr-metadata/docs/api/v3/data_type.md | 45 ++++++++ packages/zarr-metadata/docs/api/v3/index.md | 15 +++ packages/zarr-metadata/docs/index.md | 102 +++++++++++++++++ packages/zarr-metadata/justfile | 58 ++++++++++ packages/zarr-metadata/mkdocs.yml | 103 ++++++++++++++++++ packages/zarr-metadata/pyproject.toml | 13 ++- 17 files changed, 514 insertions(+), 12 deletions(-) create mode 100644 packages/zarr-metadata/.readthedocs.yaml create mode 100644 packages/zarr-metadata/docs/api/index.md create mode 100644 packages/zarr-metadata/docs/api/model.md create mode 100644 packages/zarr-metadata/docs/api/pydantic.md create mode 100644 packages/zarr-metadata/docs/api/v2.md create mode 100644 packages/zarr-metadata/docs/api/v3/chunk_grid.md create mode 100644 packages/zarr-metadata/docs/api/v3/chunk_key_encoding.md create mode 100644 packages/zarr-metadata/docs/api/v3/codec.md create mode 100644 packages/zarr-metadata/docs/api/v3/data_type.md create mode 100644 packages/zarr-metadata/docs/api/v3/index.md create mode 100644 packages/zarr-metadata/docs/index.md create mode 100644 packages/zarr-metadata/justfile create mode 100644 packages/zarr-metadata/mkdocs.yml diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml index df7d96cc1c..b5f56dd508 100644 --- a/.github/workflows/zarr-metadata.yml +++ b/.github/workflows/zarr-metadata.yml @@ -1,5 +1,8 @@ name: zarr-metadata +# Job steps delegate to packages/zarr-metadata/justfile, the single source of +# truth for this package's verbs; CI owns only the python matrix and caching. + on: push: branches: [main] @@ -39,12 +42,14 @@ jobs: uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 with: enable-cache: true + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 - name: Set up Python ${{ matrix.python-version }} run: uv python install ${{ matrix.python-version }} - name: Sync test dependency group run: uv sync --group test --python ${{ matrix.python-version }} - name: Run pytest - run: uv run --group test pytest tests + run: just test ruff: name: ruff @@ -59,8 +64,10 @@ jobs: persist-credentials: false - name: Install uv uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 - name: Run ruff - run: uvx ruff check . + run: just lint pyright: name: pyright @@ -77,19 +84,35 @@ jobs: uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 with: enable-cache: true - - name: Set up Python - run: uv python install 3.11 - - name: Sync test dependency group - run: uv sync --group test --python 3.11 + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 - name: Run pyright - # Pinned to the last version that types PEP 661 sentinels in class - # attributes correctly; 1.1.405+ regressed (microsoft/pyright#11115). - # Unpin when the fix lands. - run: uv run --group test --with 'pyright==1.1.404' pyright src + # The pyright version and interpreter pins live in the justfile. + run: just typecheck + + docs: + name: docs + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-metadata + steps: + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + with: + enable-cache: true + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 + - name: Build docs + run: just docs-check zarr-metadata-complete: name: zarr-metadata complete - needs: [test, ruff, pyright] + needs: [test, ruff, pyright, docs] if: always() runs-on: ubuntu-latest steps: diff --git a/mkdocs.yml b/mkdocs.yml index 46bfc1764c..87aaf23430 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -92,6 +92,7 @@ nav: - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.testing.utils</code>': api/zarr/testing/utils.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros</code>': api/zarr/functions/zeros.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros_like</code>': api/zarr/functions/zeros_like.md + - 'zarr-metadata ↪': https://zarr-metadata.readthedocs.io/ - release-notes.md - contributing.md hooks: diff --git a/packages/zarr-metadata/.readthedocs.yaml b/packages/zarr-metadata/.readthedocs.yaml new file mode 100644 index 0000000000..b89846f570 --- /dev/null +++ b/packages/zarr-metadata/.readthedocs.yaml @@ -0,0 +1,20 @@ +# Read the Docs configuration for the zarr-metadata docs site, separate from +# the zarr-python site configured by the repo-root .readthedocs.yaml. The RTD +# project for zarr-metadata must set its configuration-file path to +# packages/zarr-metadata/.readthedocs.yaml. +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.12" + jobs: + install: + - pip install --upgrade pip + - pip install ./packages/zarr-metadata --group packages/zarr-metadata/pyproject.toml:docs + build: + html: + - mkdocs build --strict -f packages/zarr-metadata/mkdocs.yml --site-dir $READTHEDOCS_OUTPUT/html + +mkdocs: + configuration: packages/zarr-metadata/mkdocs.yml diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md index 69b80d7332..6b6b172aec 100644 --- a/packages/zarr-metadata/README.md +++ b/packages/zarr-metadata/README.md @@ -2,6 +2,8 @@ Python types, models, and validators for Zarr v2 and v3 metadata. +Documentation: <https://zarr-metadata.readthedocs.io/> + ## What this is Two layers and an optional integration: @@ -82,6 +84,23 @@ store I/O. The models begin and end at the metadata documents themselves — `from_key_value` / `to_key_value` map documents to store keys and bytes, and everything past that belongs to consumer libraries. +## Developing + +Package-scoped development commands live in the [`justfile`](./justfile) +(requires [just](https://github.com/casey/just)): + +``` +just test # run the test suite (extra args go to pytest) +just lint # ruff, same invocation as CI +just typecheck # pyright, pinned to the version CI uses +just docs-check # strict build of the docs site +just check # all of the above +just docs-serve # serve the docs site locally +``` + +Run them from this directory, or from anywhere in the repository as +`just packages/zarr-metadata/<recipe>`. + ## Releasing The package version is derived from git tags by `hatch-vcs`. Tags must diff --git a/packages/zarr-metadata/docs/api/index.md b/packages/zarr-metadata/docs/api/index.md new file mode 100644 index 0000000000..2aa39ab161 --- /dev/null +++ b/packages/zarr-metadata/docs/api/index.md @@ -0,0 +1,31 @@ +--- +title: API reference +--- + +# API reference + +The package is organized to mirror the structure of the Zarr specifications: + +- [`zarr_metadata.model`](model.md) — frozen-dataclass document models, + structural validators, loc-aware parsers, and the `UNSET` sentinel +- [`zarr_metadata.pydantic`](pydantic.md) — optional Pydantic field types + over the models +- [`zarr_metadata.v2`](v2.md) — `TypedDict` shapes for Zarr v2 documents + (`.zarray`, `.zgroup`, `.zattrs`, `.zmetadata`) +- [`zarr_metadata.v3`](v3/index.md) — `TypedDict` shapes for Zarr v3 + documents, with subpackages for [chunk grids](v3/chunk_grid.md), + [chunk key encodings](v3/chunk_key_encoding.md), [codecs](v3/codec.md), + and [data types](v3/data_type.md) + +Every public name is also re-exported at the top level, so +`from zarr_metadata import ZarrV3ArrayMetadataJSON` and +`from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON` are equivalent. + +## Common types + +A few cross-cutting aliases are exported only from the top-level +`zarr_metadata` namespace: + +::: zarr_metadata.JSONValue + +::: zarr_metadata.ZarrV3NamedConfigJSON diff --git a/packages/zarr-metadata/docs/api/model.md b/packages/zarr-metadata/docs/api/model.md new file mode 100644 index 0000000000..c82ba98f2d --- /dev/null +++ b/packages/zarr-metadata/docs/api/model.md @@ -0,0 +1,5 @@ +--- +title: model +--- + +::: zarr_metadata.model diff --git a/packages/zarr-metadata/docs/api/pydantic.md b/packages/zarr-metadata/docs/api/pydantic.md new file mode 100644 index 0000000000..edecb416a7 --- /dev/null +++ b/packages/zarr-metadata/docs/api/pydantic.md @@ -0,0 +1,5 @@ +--- +title: pydantic +--- + +::: zarr_metadata.pydantic diff --git a/packages/zarr-metadata/docs/api/v2.md b/packages/zarr-metadata/docs/api/v2.md new file mode 100644 index 0000000000..2fe5b6ec56 --- /dev/null +++ b/packages/zarr-metadata/docs/api/v2.md @@ -0,0 +1,17 @@ +--- +title: v2 +--- + +::: zarr_metadata.v2 + options: + members: false + +::: zarr_metadata.v2.array + +::: zarr_metadata.v2.group + +::: zarr_metadata.v2.attributes + +::: zarr_metadata.v2.codec + +::: zarr_metadata.v2.consolidated diff --git a/packages/zarr-metadata/docs/api/v3/chunk_grid.md b/packages/zarr-metadata/docs/api/v3/chunk_grid.md new file mode 100644 index 0000000000..724b1c9d8d --- /dev/null +++ b/packages/zarr-metadata/docs/api/v3/chunk_grid.md @@ -0,0 +1,11 @@ +--- +title: chunk_grid +--- + +::: zarr_metadata.v3.chunk_grid + options: + members: false + +::: zarr_metadata.v3.chunk_grid.regular + +::: zarr_metadata.v3.chunk_grid.rectilinear diff --git a/packages/zarr-metadata/docs/api/v3/chunk_key_encoding.md b/packages/zarr-metadata/docs/api/v3/chunk_key_encoding.md new file mode 100644 index 0000000000..bb063deb25 --- /dev/null +++ b/packages/zarr-metadata/docs/api/v3/chunk_key_encoding.md @@ -0,0 +1,11 @@ +--- +title: chunk_key_encoding +--- + +::: zarr_metadata.v3.chunk_key_encoding + options: + members: false + +::: zarr_metadata.v3.chunk_key_encoding.default + +::: zarr_metadata.v3.chunk_key_encoding.v2 diff --git a/packages/zarr-metadata/docs/api/v3/codec.md b/packages/zarr-metadata/docs/api/v3/codec.md new file mode 100644 index 0000000000..cb96d2c7d5 --- /dev/null +++ b/packages/zarr-metadata/docs/api/v3/codec.md @@ -0,0 +1,25 @@ +--- +title: codec +--- + +::: zarr_metadata.v3.codec + options: + members: false + +::: zarr_metadata.v3.codec.blosc + +::: zarr_metadata.v3.codec.bytes + +::: zarr_metadata.v3.codec.cast_value + +::: zarr_metadata.v3.codec.crc32c + +::: zarr_metadata.v3.codec.gzip + +::: zarr_metadata.v3.codec.scale_offset + +::: zarr_metadata.v3.codec.sharding_indexed + +::: zarr_metadata.v3.codec.transpose + +::: zarr_metadata.v3.codec.zstd diff --git a/packages/zarr-metadata/docs/api/v3/data_type.md b/packages/zarr-metadata/docs/api/v3/data_type.md new file mode 100644 index 0000000000..f482c33201 --- /dev/null +++ b/packages/zarr-metadata/docs/api/v3/data_type.md @@ -0,0 +1,45 @@ +--- +title: data_type +--- + +::: zarr_metadata.v3.data_type + options: + members: false + +::: zarr_metadata.v3.data_type.bool + +::: zarr_metadata.v3.data_type.int8 + +::: zarr_metadata.v3.data_type.int16 + +::: zarr_metadata.v3.data_type.int32 + +::: zarr_metadata.v3.data_type.int64 + +::: zarr_metadata.v3.data_type.uint8 + +::: zarr_metadata.v3.data_type.uint16 + +::: zarr_metadata.v3.data_type.uint32 + +::: zarr_metadata.v3.data_type.uint64 + +::: zarr_metadata.v3.data_type.float16 + +::: zarr_metadata.v3.data_type.float32 + +::: zarr_metadata.v3.data_type.float64 + +::: zarr_metadata.v3.data_type.complex64 + +::: zarr_metadata.v3.data_type.complex128 + +::: zarr_metadata.v3.data_type.raw + +::: zarr_metadata.v3.data_type.bytes + +::: zarr_metadata.v3.data_type.string + +::: zarr_metadata.v3.data_type.numpy_datetime64 + +::: zarr_metadata.v3.data_type.numpy_timedelta64 diff --git a/packages/zarr-metadata/docs/api/v3/index.md b/packages/zarr-metadata/docs/api/v3/index.md new file mode 100644 index 0000000000..f20267d372 --- /dev/null +++ b/packages/zarr-metadata/docs/api/v3/index.md @@ -0,0 +1,15 @@ +--- +title: v3 +--- + +::: zarr_metadata.v3 + options: + members: false + +::: zarr_metadata.v3.ZarrV3MetadataFieldJSON + +::: zarr_metadata.v3.array + +::: zarr_metadata.v3.group + +::: zarr_metadata.v3.consolidated diff --git a/packages/zarr-metadata/docs/index.md b/packages/zarr-metadata/docs/index.md new file mode 100644 index 0000000000..2004f2dc54 --- /dev/null +++ b/packages/zarr-metadata/docs/index.md @@ -0,0 +1,102 @@ +--- +title: zarr-metadata +--- + +# zarr-metadata + +Basic tools for modelling Zarr metadata, with minimal dependencies. + +`zarr-metadata` is developed in the +[zarr-python repository](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-metadata) +and released independently of `zarr` itself. Install it with: + +``` +pip install zarr-metadata +``` + +## Who needs this + +This library might be useful to you if your software interacts with Zarr metadata documents. + +## What this is + +This library is *not* a full Zarr implementation. Instead, it's a collection of data structures and routines that +closely model the content of the Zarr specifications, such as: + +- **Typed JSON shapes** ([`zarr_metadata.v2`](api/v2.md) and + [`zarr_metadata.v3`](api/v3/index.md)): `TypedDict` definitions and + `Literal` aliases for the JSON documents specified by the + [Zarr v2](https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html) and + [Zarr v3](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) + specifications, plus types for + [zarr-extensions](https://github.com/zarr-developers/zarr-extensions/) and a + few widely-used-but-unspecified entities (e.g. consolidated metadata). +- **Document models** ([`zarr_metadata.model`](api/model.md)): canonical + frozen-dataclass models of whole metadata documents, with structural + validators, loc-aware parsers, and store-key (de)serialization. A document + produced by `to_json` shares no mutable state with the model that produced + it. +- **Optional Pydantic integration** ([`zarr_metadata.pydantic`](api/pydantic.md), + requires Pydantic 2.13 or newer): each model as a Pydantic field type that + validates raw documents through the same strict parser. + +## What this is for + +The public `TypedDict` definitions describe the static JSON shape of Zarr +metadata. For strict, loc-aware validation of JSON loaded from disk, use the +model parser: + +```python +import json +from zarr_metadata.model import ZarrV3ArrayMetadata + +with open("zarr.json", "rb") as f: + raw = json.load(f) + +metadata = ZarrV3ArrayMetadata.from_json(raw) +``` + +The optional Pydantic integration delegates raw input to the same strict +parser and returns the same normalized model class: + +```python +from pydantic import TypeAdapter +import zarr_metadata.pydantic as zmp + +metadata = TypeAdapter(zmp.ZarrV3ArrayMetadata).validate_python(raw) +encoded = metadata.to_key_value()["zarr.json"] +``` + +A bare `TypeAdapter` over a public document `TypedDict` is a coercive shape +adapter, not a Zarr conformance validator; it may coerce values or discard +members that the strict model parser rejects. + +## Validation boundary + +The model validators enforce the declared document structure and a small set +of context-free consistency rules, including fixed format literals, finite +JSON numbers, non-negative dimensions, non-empty v3 codec pipelines, and one +`dimension_names` entry per array dimension. They do not interpret extension +names or configurations, resolve codec pipelines, or decide whether a data +type, chunk grid, codec, or storage transformer is supported. Those decisions +belong to consumer implementations. + +## Scope + +At minimum, this library supports what Zarr-Python needs: the complete +Zarr v2 and v3 specs, consolidated metadata, and a subset of the metadata +defined in `zarr-extensions`. We are generally open to contributions that +add types, models, or structural validation for Zarr metadata with a +published spec. + +Runtime array behavior is out of scope: nothing here encodes or decodes +chunks, resolves codec or data type names to implementations, or performs +store I/O. The models begin and end at the metadata documents themselves — +`from_key_value` / `to_key_value` map documents to store keys and bytes, +and everything past that belongs to consumer libraries. + +## Reference + +- [API reference](api/index.md) +- [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/CHANGELOG.md) +- [License (MIT)](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/LICENSE.txt) diff --git a/packages/zarr-metadata/justfile b/packages/zarr-metadata/justfile new file mode 100644 index 0000000000..0f1861ed7d --- /dev/null +++ b/packages/zarr-metadata/justfile @@ -0,0 +1,58 @@ +# Development verbs for the zarr-metadata package. Recipes run with this +# directory as the working directory regardless of where `just` is invoked. + +# List available recipes +default: + @just --list + +# Run the test suite; extra args are passed to pytest +test *args: + uv run --group test pytest tests {{ args }} + +# Lint with the same invocation CI uses +lint: + uvx ruff check . + +# Pinned to the last pyright that types PEP 661 sentinels in class attributes +# correctly; 1.1.405+ regressed (microsoft/pyright#11115). Unpin when fixed. +pyright_version := "1.1.404" + +# CI runs pyright on python 3.11; the pinned pyright predates 3.14, whose +# stdlib it cannot parse, so pin the interpreter to match CI. +# Type-check the package sources +typecheck: + uv run --python 3.11 --group test --with 'pyright=={{ pyright_version }}' pyright src + +# Run everything CI runs for this package +check: lint typecheck test docs-check + +# Preview the changelog that the next release would generate +changelog-draft: + uvx towncrier build --draft --version Unreleased + +# Build this package's documentation site, warnings as errors +docs-check: + env DISABLE_MKDOCS_2_WARNING=true uv run --group docs mkdocs build --strict + +# With no argument, uses port 8000 if free, otherwise an ephemeral free port; +# an explicitly requested port is used as-is so a conflict fails loudly. +# Serve this package's documentation site +docs-serve port="": + #!/usr/bin/env bash + set -euo pipefail + port="{{ port }}" + if [ -z "$port" ]; then + port=$(uv run --group docs python -c ' + import socket + s = socket.socket() + try: + s.bind(("127.0.0.1", 8000)) + except OSError: + s.close() + s = socket.socket() + s.bind(("127.0.0.1", 0)) + print(s.getsockname()[1]) + s.close() + ') + fi + exec env DISABLE_MKDOCS_2_WARNING=true uv run --group docs mkdocs serve -a "localhost:$port" diff --git a/packages/zarr-metadata/mkdocs.yml b/packages/zarr-metadata/mkdocs.yml new file mode 100644 index 0000000000..40912d6251 --- /dev/null +++ b/packages/zarr-metadata/mkdocs.yml @@ -0,0 +1,103 @@ +site_name: zarr-metadata +repo_name: zarr-developers/zarr-python +repo_url: https://github.com/zarr-developers/zarr-python +edit_uri: edit/main/packages/zarr-metadata/docs/ +site_description: Spec-defined metadata types, models, and validators for Zarr v2 and v3. +site_author: Davis Bennett +site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://zarr-metadata.readthedocs.io/'] +docs_dir: docs +use_directory_urls: true + +nav: + - index.md + - API Reference: + - api/index.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.model</code>': api/model.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.pydantic</code>': api/pydantic.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v2</code>': api/v2.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v3</code>': + - api/v3/index.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v3.chunk_grid</code>': api/v3/chunk_grid.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v3.chunk_key_encoding</code>': api/v3/chunk_key_encoding.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v3.codec</code>': api/v3/codec.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v3.data_type</code>': api/v3/data_type.md + - Changelog: https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/CHANGELOG.md + +watch: + - src + +theme: + language: en + name: material + + palette: + # Light mode + - media: "(prefers-color-scheme: light)" + scheme: default + toggle: + icon: material/brightness-7 + name: Switch to dark mode + + # Dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + toggle: + icon: material/brightness-4 + name: Switch to light mode + + font: + text: Roboto + code: Roboto Mono + + features: + - content.code.annotate + - content.code.copy + - navigation.indexes + - navigation.instant + - navigation.tracking + - search.suggest + - search.share + +plugins: + - autorefs + - search + - mkdocstrings: + enable_inventory: true + handlers: + python: + paths: [src] + options: + allow_inspection: true + docstring_section_style: list + docstring_style: numpy + inherited_members: true + line_length: 60 + separate_signature: true + show_root_heading: true + show_signature_annotations: true + show_source: true + show_symbol_type_toc: true + signature_crossrefs: true + show_if_no_docstring: true + extensions: + - griffe_inherited_docstrings + + inventories: + - https://docs.python.org/3/objects.inv + - https://zarr.readthedocs.io/en/stable/objects.inv + +markdown_extensions: + - admonition + - attr_list + - def_list + - footnotes + - md_in_html + - pymdownx.details + - pymdownx.superfences + - toc: + permalink: true + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index edc4b696a6..6e97d26409 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -44,10 +44,21 @@ Homepage = "https://github.com/zarr-developers/zarr-python" Source = "https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-metadata" Issues = "https://github.com/zarr-developers/zarr-python/issues" Changelog = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/CHANGELOG.md" -Documentation = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/README.md" +Documentation = "https://zarr-metadata.readthedocs.io/" [dependency-groups] test = ["pytest", "pydantic>=2.13", "jsonschema"] +docs = [ + # Pins match the zarr-python docs environment in the repo-root + # pyproject.toml so the two sites render with the same toolchain. + "mkdocs-material==9.7.6", + "mkdocs==1.6.1", + "mkdocstrings==1.0.4", + "mkdocstrings-python==2.0.5", + "griffe-inherited-docstrings==1.1.3", + # mkdocstrings uses ruff to format rendered signatures + "ruff==0.15.20", +] [tool.hatch.version] source = "vcs" From 69ca264664bd74ba55c594490acdd49cd70b7fe8 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 21:36:59 +0200 Subject: [PATCH 426/468] docs(zarr-metadata): docs-site polish: repo link, titles, RTD build skips, branding (#4210) * docs(zarr-metadata): point the site's repo link at the package directory The material header source widget linked to the zarr-python repository root, presenting the site as zarr-python's. Link the package directory and label it zarr-python/packages/zarr-metadata instead. edit_uri becomes absolute because mkdocs would append it to repo_url's subpath. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): drop redundant frontmatter title on the homepage Material appends the site name to explicit frontmatter titles, so the homepage browser title rendered as 'zarr-metadata - zarr-metadata'. Without the frontmatter it falls back to the site name alone. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-metadata): skip unrelated RTD PR builds; add site logo and favicon Both Read the Docs projects rebuilt on every pull request regardless of what changed. Each config now cancels PR builds via exit code 183 when the diff against origin/main does not touch its half of the repo: the zarr-metadata project skips PRs that leave packages/zarr-metadata untouched, and the zarr-python project skips PRs confined to it. Scoped to external versions because origin/main is only a meaningful diff base for PR builds. The package site also gets the zarr logo and favicon, copied from the zarr-python docs, instead of stock Material icons. Assisted-by: ClaudeCode:claude-fable-5 * fix(docs): quote-free exclude pathspec in RTD build-skip rule Read the Docs strips shell quoting from build commands, so the quoted ':(exclude)packages/zarr-metadata' pathspec reached /bin/sh unquoted and the bare parenthesis was a syntax error, failing every zarr PR build. Use git's quote-free :! exclude form, which survives the stripping; reproduced the mangling and verified both forms against dash locally. Assisted-by: ClaudeCode:claude-fable-5 --- .readthedocs.yaml | 13 +++++++++++++ packages/zarr-metadata/.readthedocs.yaml | 10 ++++++++++ .../docs/_static/favicon-96x96.png | Bin 0 -> 12714 bytes packages/zarr-metadata/docs/_static/logo_bw.png | Bin 0 -> 45208 bytes packages/zarr-metadata/docs/index.md | 4 ---- packages/zarr-metadata/mkdocs.yml | 11 ++++++++--- 6 files changed, 31 insertions(+), 7 deletions(-) create mode 100644 packages/zarr-metadata/docs/_static/favicon-96x96.png create mode 100644 packages/zarr-metadata/docs/_static/logo_bw.png diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 1edd099ebd..55b5d6fed0 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,6 +5,19 @@ build: tools: python: "3.12" jobs: + post_checkout: + # Cancel pull request builds whose changes are confined to the + # zarr-metadata package, which has its own Read the Docs project. Exit + # code 183 cancels the build and reports success to the Git provider. + # Scoped to PR builds ("external" versions) because origin/main is only + # a meaningful diff base there. Read the Docs strips shell quoting from + # commands, so the exclude pathspec must use the quote-free :! form, + # not ':(exclude)'. + - | + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- :!packages/zarr-metadata; + then + exit 183; + fi install: - pip install --upgrade pip - pip install .[remote] --group docs diff --git a/packages/zarr-metadata/.readthedocs.yaml b/packages/zarr-metadata/.readthedocs.yaml index b89846f570..ace6ccddfd 100644 --- a/packages/zarr-metadata/.readthedocs.yaml +++ b/packages/zarr-metadata/.readthedocs.yaml @@ -9,6 +9,16 @@ build: tools: python: "3.12" jobs: + post_checkout: + # Cancel pull request builds that do not touch this package. Exit code + # 183 cancels the build and reports success to the Git provider. 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index 2004f2dc54..58e4f290c6 100644 --- a/packages/zarr-metadata/docs/index.md +++ b/packages/zarr-metadata/docs/index.md @@ -1,7 +1,3 @@ ---- -title: zarr-metadata ---- - # zarr-metadata Basic tools for modelling Zarr metadata, with minimal dependencies. diff --git a/packages/zarr-metadata/mkdocs.yml b/packages/zarr-metadata/mkdocs.yml index 40912d6251..6c4a590b3c 100644 --- a/packages/zarr-metadata/mkdocs.yml +++ b/packages/zarr-metadata/mkdocs.yml @@ -1,7 +1,10 @@ site_name: zarr-metadata -repo_name: zarr-developers/zarr-python -repo_url: https://github.com/zarr-developers/zarr-python -edit_uri: edit/main/packages/zarr-metadata/docs/ +# The package lives in the zarr-python monorepo; point the header source +# widget at the package directory rather than the repository root. +repo_name: zarr-python/packages/zarr-metadata +repo_url: https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-metadata +# Absolute because mkdocs would otherwise append this to repo_url's subpath. +edit_uri: https://github.com/zarr-developers/zarr-python/edit/main/packages/zarr-metadata/docs/ site_description: Spec-defined metadata types, models, and validators for Zarr v2 and v3. site_author: Davis Bennett site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://zarr-metadata.readthedocs.io/'] @@ -29,6 +32,8 @@ watch: theme: language: en name: material + logo: _static/logo_bw.png + favicon: _static/favicon-96x96.png palette: # Light mode From 63fc294bec25c41983c1a45f7f03bd6f801a7ff9 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 29 Jul 2026 22:16:48 +0200 Subject: [PATCH 427/468] chore(zarr-metadata): build 0.4.0 changelog (#4211) Consume the pending news fragments (the #4119 model layer's feature and removal notes, plus a new doc fragment for the standalone documentation site and justfile from #4208/#4210) into CHANGELOG.md via towncrier for the zarr_metadata-v0.4.0 release. Assisted-by: ClaudeCode:claude-fable-5 --- packages/zarr-metadata/CHANGELOG.md | 153 ++++++++++++++++++ .../zarr-metadata/changes/4119.feature.md | 92 ----------- .../zarr-metadata/changes/4119.removal.md | 41 ----- 3 files changed, 153 insertions(+), 133 deletions(-) delete mode 100644 packages/zarr-metadata/changes/4119.feature.md delete mode 100644 packages/zarr-metadata/changes/4119.removal.md diff --git a/packages/zarr-metadata/CHANGELOG.md b/packages/zarr-metadata/CHANGELOG.md index a3ff1177a0..981c7706bf 100644 --- a/packages/zarr-metadata/CHANGELOG.md +++ b/packages/zarr-metadata/CHANGELOG.md @@ -2,6 +2,159 @@ <!-- towncrier release notes start --> +## 0.4.0 (2026-07-29) + +### Features + +- Added `zarr_metadata.model`: frozen-dataclass models (`ZarrV2ArrayMetadata`, + `ZarrV3ArrayMetadata`, `ZarrV2GroupMetadata`, `ZarrV3GroupMetadata`, + `ZarrV2ConsolidatedMetadata`, `ZarrV3ConsolidatedMetadata`, `ZarrV3NamedConfig`) + that are canonical, semantically lossless representations of Zarr metadata + documents, plus structural validators (`validate_*` / `is_*` / `parse_*`). + Every v3 extension point (data type, chunk grid, chunk key encoding, codecs, + storage transformers) is held as `ZarrV3NamedConfig`: a name, configuration, + and `must_understand` obligation; nothing is interpreted. On the wire, an + empty configuration with the default obligation uses the spec's plain-string + shorthand. Model fields are annotated with the role alias + `ZarrV3MetadataField` (today exactly `ZarrV3NamedConfig`), so annotations + convey the logical meaning and stay put if the spec adds another field form. + + Validation is strict about what the types declare: v2 `dtype` / `order` / + `compressor` / `filters` / `dimension_separator` shapes and the fixed + `zarr_format` / `node_type` literals are all enforced. Every + `ValidationProblem` carries a machine-readable `kind` + (`missing_key` / `invalid_type` / `invalid_value` / `invalid_json`) so + consumers can dispatch on the failure mode without matching message strings, + and every ingestion failure — including missing store keys and undecodable + bytes in `from_key_value` — surfaces as `MetadataValidationError`. An + adversarial review added further structural checks: JSON booleans are not + accepted as dimension lengths, dimensions are non-negative, + `dimension_names` must have one entry per dimension of `shape`, `attributes` + and `configuration` values are JSON-checked recursively (like `fill_value`), + non-finite floats and non-standard JSON constants are rejected, abstract + mappings and sequences normalize to encoder-safe canonical containers, + v2 `shape` and `chunks` must have the same rank, non-null v2 filter pipelines + contain at least one filter, document `TypeIs` guards only narrow values that + already use the declared canonical containers, + and the inline consolidated-metadata envelope and entries are deep-validated + so the group validator's verdict always agrees with the model constructor. + + The v3 models expose `must_understand_fields`: the subset of `extra_fields` + not explicitly waived with `must_understand: false` (fields are implicitly + must-understand per the spec). Readers discharge the spec's fail-to-open + duty by subtracting the extension names they recognize; the model only + partitions by obligation, since recognition is reader-specific. + + Optional pydantic integration ships as `zarr_metadata.pydantic` (importing it + requires pydantic 2.13 or newer; the core package does not depend on it): one + `Annotated` + field type per model, validating raw documents through `from_json`, passing + core-model instances through unchanged, serializing via `to_json`, and + publishing JSON Schemas derived from private constrained document types that + mirror the independently expressible runtime rules. Cross-field cardinality + relations still require runtime validation. The instances are the core model + classes, so values interoperate freely with non-pydantic code. + + `create_default` keeps its output self-consistent: overriding `shape` without + a chunk grid derives one regular chunk covering the array (v3 + `chunk_shape == shape`; v2 `chunks == shape`) instead of silently keeping the + scalar default's 0-d grid. + + A v2 `.zarray` that omits `dimension_separator` is interpreted with the v2 + convention's default `"."` (the model previously normalized absence to `"/"`, + which would misaddress the chunks of real-world default-separator arrays). + The value is never null: absent, `"."`, or `"/"` are the only spellings. + + Optional document keys use `UNSET` — a PEP 661 sentinel + (`typing_extensions.Sentinel`), usable directly in type expressions — never + `None`: in a model, `None` always corresponds to a JSON `null` in the + document (a v2 `compressor`, an unnamed dimension inside `dimension_names`), + and `UNSET` always means the key is absent. Checker note: ty types the + sentinel exactly; pyright needs `<= 1.1.404` until microsoft/pyright#11115 + is fixed (this package's CI pins it); mypy users need a `cast` or + `type: ignore` at narrowing sites until python/mypy#21647 merges. This keeps semantically distinct spellings + distinct — an absent `dimension_names` ("there are no dimension names") and + an explicit `[null, null]` ("every dimension has a name, which is null") are + different documents and round-trip as such. The `consolidated_metadata: null` + written by a historical zarr-python bug is the one deliberate exception to + faithful round-tripping: those stores remain readable, but the bug spelling + is repaired to absence on read and never written back. + + The v2 models treat the `.zattrs` file's presence as part of the store: + `attributes` is `UNSET` when no `.zattrs` file exists (and `to_key_value` + emits none), while an explicit empty `.zattrs` is `{}` and round-trips as a + file. Previously `to_key_value` always emitted `.zattrs`, silently adding a + file to stores that never had one. + + The store-key `Literal` aliases (`ZarrV2ArrayMetadataStoreKey`, + `ZarrV2AttributesStoreKey`, ...) are exported from `zarr_metadata.model` + alongside their constants, and each `to_key_value` return type is keyed by + them, so the set of store keys a model can emit is visible in its signature. + `from_key_value` deliberately keeps `Mapping[str, bytes]` input: it accepts + any string-keyed store mapping and ignores unrelated keys. + + `to_json` returns a document that shares no mutable state with the model: + every value that can hold a mutable container (attributes, configurations, + extra fields, v2 codec configurations, fill values, consolidated entries) is + deep-copied on the way out, so editing a serialized document can never + silently mutate the frozen model that produced it. ([#4119](https://github.com/zarr-developers/zarr-python/issues/4119)) + +### Improved Documentation + +- `zarr-metadata` now has a standalone documentation site at + <https://zarr-metadata.readthedocs.io/>, with a comprehensive API reference + covering every public module, versioned by this package's release tags. The + package also gained a `justfile` collecting its development commands + (`test`, `lint`, `typecheck`, `docs-check`, `docs-serve`, `changelog-draft`), + which the package CI workflow now delegates to. ([#4208](https://github.com/zarr-developers/zarr-python/issues/4208)) + +### Deprecations and Removals + +- The document (TypedDict) types are renamed to put the format version at the + front of the name and to mark the JSON-document form with a `JSON` suffix, + so a format version can never be misread as a class revision and the bare + entity names are reserved for the `zarr_metadata.model` dataclasses: + + - `ArrayMetadataV2` → `ZarrV2ArrayMetadataJSON` (and `...Partial` accordingly) + - `ArrayMetadataV3` → `ZarrV3ArrayMetadataJSON` (and `...Partial` accordingly) + - `GroupMetadataV2` → `ZarrV2GroupMetadataJSON` (and `...Partial` accordingly) + - `GroupMetadataV3` → `ZarrV3GroupMetadataJSON` (and `...Partial` accordingly) + - `ConsolidatedMetadataV2` → `ZarrV2ConsolidatedMetadataJSON` + - `ConsolidatedMetadataV3` → `ZarrV3ConsolidatedMetadataJSON` + - `NamedConfigV3` → `ZarrV3NamedConfigJSON` + - `MetadataV3` → `ZarrV3MetadataFieldJSON` (the union of the bare-name and + named-configuration spellings of one metadata field) + - `ExtensionFieldV3` → `ZarrV3ExtensionField` + - `CodecMetadataV2` → `ZarrV2CodecMetadata` + - `DataTypeMetadataV2` → `ZarrV2DataTypeMetadata` + - `ArrayOrderV2` → `ZarrV2ArrayOrder` + - `ArrayDimensionSeparatorV2` → `ZarrV2ArrayDimensionSeparator` + - `ZArrayMetadata` → `ZarrV2ZArrayJSON` (the strict on-disk `.zarray` document) + - `ZGroupMetadata` → `ZarrV2ZGroupJSON` (the strict on-disk `.zgroup` document) + - `ZAttrsMetadata` → `ZarrV2ZAttrsJSON` (the `.zattrs` document) + + The old names are removed, not aliased. The `zarr_metadata.pydantic` field + types take the bare entity names (`ZarrV3ArrayMetadata`, ...), matching the + model classes they validate into. + + The conventions, stated once for future additions: CamelCase type names put + the format version first (`ZarrV2ArrayMetadataJSON`, + `ZarrV3ArrayMetadataStoreKey`), while SCREAMING_SNAKE constants and + snake_case functions put it last (`ARRAY_METADATA_STORE_KEY_V2`, + `validate_array_metadata_v3`). The `JSON` suffix marks a raw-document type + whose bare name is taken by (or reserved for) a `zarr_metadata.model` + dataclass; raw field-level types the models hold verbatim + (`ZarrV2CodecMetadata`, `ZarrV3ExtensionField`) keep their bare names. + Extension-entity types put the registered entity name first and end in + exactly one role suffix (`BloscCodecMetadata`, `Uint8DataTypeName`) — the + `V2` in `V2ChunkKeyEncodingMetadata` is that encoding's entity name, not a + format version, which is always spelled `ZarrV2`/`ZarrV3`. Every public + type name is checked against this grammar by + `tests/test_public_api.py::test_public_type_names_comply_with_naming_grammar`. + + ([#4119](https://github.com/zarr-developers/zarr-python/issues/4119)) + + ## 0.3.0 (2026-06-19) ### Deprecations and Removals diff --git a/packages/zarr-metadata/changes/4119.feature.md b/packages/zarr-metadata/changes/4119.feature.md deleted file mode 100644 index b9d0bb508c..0000000000 --- a/packages/zarr-metadata/changes/4119.feature.md +++ /dev/null @@ -1,92 +0,0 @@ -Added `zarr_metadata.model`: frozen-dataclass models (`ZarrV2ArrayMetadata`, -`ZarrV3ArrayMetadata`, `ZarrV2GroupMetadata`, `ZarrV3GroupMetadata`, -`ZarrV2ConsolidatedMetadata`, `ZarrV3ConsolidatedMetadata`, `ZarrV3NamedConfig`) -that are canonical, semantically lossless representations of Zarr metadata -documents, plus structural validators (`validate_*` / `is_*` / `parse_*`). -Every v3 extension point (data type, chunk grid, chunk key encoding, codecs, -storage transformers) is held as `ZarrV3NamedConfig`: a name, configuration, -and `must_understand` obligation; nothing is interpreted. On the wire, an -empty configuration with the default obligation uses the spec's plain-string -shorthand. Model fields are annotated with the role alias -`ZarrV3MetadataField` (today exactly `ZarrV3NamedConfig`), so annotations -convey the logical meaning and stay put if the spec adds another field form. - -Validation is strict about what the types declare: v2 `dtype` / `order` / -`compressor` / `filters` / `dimension_separator` shapes and the fixed -`zarr_format` / `node_type` literals are all enforced. Every -`ValidationProblem` carries a machine-readable `kind` -(`missing_key` / `invalid_type` / `invalid_value` / `invalid_json`) so -consumers can dispatch on the failure mode without matching message strings, -and every ingestion failure — including missing store keys and undecodable -bytes in `from_key_value` — surfaces as `MetadataValidationError`. An -adversarial review added further structural checks: JSON booleans are not -accepted as dimension lengths, dimensions are non-negative, -`dimension_names` must have one entry per dimension of `shape`, `attributes` -and `configuration` values are JSON-checked recursively (like `fill_value`), -non-finite floats and non-standard JSON constants are rejected, abstract -mappings and sequences normalize to encoder-safe canonical containers, -v2 `shape` and `chunks` must have the same rank, non-null v2 filter pipelines -contain at least one filter, document `TypeIs` guards only narrow values that -already use the declared canonical containers, -and the inline consolidated-metadata envelope and entries are deep-validated -so the group validator's verdict always agrees with the model constructor. - -The v3 models expose `must_understand_fields`: the subset of `extra_fields` -not explicitly waived with `must_understand: false` (fields are implicitly -must-understand per the spec). Readers discharge the spec's fail-to-open -duty by subtracting the extension names they recognize; the model only -partitions by obligation, since recognition is reader-specific. - -Optional pydantic integration ships as `zarr_metadata.pydantic` (importing it -requires pydantic 2.13 or newer; the core package does not depend on it): one -`Annotated` -field type per model, validating raw documents through `from_json`, passing -core-model instances through unchanged, serializing via `to_json`, and -publishing JSON Schemas derived from private constrained document types that -mirror the independently expressible runtime rules. Cross-field cardinality -relations still require runtime validation. The instances are the core model -classes, so values interoperate freely with non-pydantic code. - -`create_default` keeps its output self-consistent: overriding `shape` without -a chunk grid derives one regular chunk covering the array (v3 -`chunk_shape == shape`; v2 `chunks == shape`) instead of silently keeping the -scalar default's 0-d grid. - -A v2 `.zarray` that omits `dimension_separator` is interpreted with the v2 -convention's default `"."` (the model previously normalized absence to `"/"`, -which would misaddress the chunks of real-world default-separator arrays). -The value is never null: absent, `"."`, or `"/"` are the only spellings. - -Optional document keys use `UNSET` — a PEP 661 sentinel -(`typing_extensions.Sentinel`), usable directly in type expressions — never -`None`: in a model, `None` always corresponds to a JSON `null` in the -document (a v2 `compressor`, an unnamed dimension inside `dimension_names`), -and `UNSET` always means the key is absent. Checker note: ty types the -sentinel exactly; pyright needs `<= 1.1.404` until microsoft/pyright#11115 -is fixed (this package's CI pins it); mypy users need a `cast` or -`type: ignore` at narrowing sites until python/mypy#21647 merges. This keeps semantically distinct spellings -distinct — an absent `dimension_names` ("there are no dimension names") and -an explicit `[null, null]` ("every dimension has a name, which is null") are -different documents and round-trip as such. The `consolidated_metadata: null` -written by a historical zarr-python bug is the one deliberate exception to -faithful round-tripping: those stores remain readable, but the bug spelling -is repaired to absence on read and never written back. - -The v2 models treat the `.zattrs` file's presence as part of the store: -`attributes` is `UNSET` when no `.zattrs` file exists (and `to_key_value` -emits none), while an explicit empty `.zattrs` is `{}` and round-trips as a -file. Previously `to_key_value` always emitted `.zattrs`, silently adding a -file to stores that never had one. - -The store-key `Literal` aliases (`ZarrV2ArrayMetadataStoreKey`, -`ZarrV2AttributesStoreKey`, ...) are exported from `zarr_metadata.model` -alongside their constants, and each `to_key_value` return type is keyed by -them, so the set of store keys a model can emit is visible in its signature. -`from_key_value` deliberately keeps `Mapping[str, bytes]` input: it accepts -any string-keyed store mapping and ignores unrelated keys. - -`to_json` returns a document that shares no mutable state with the model: -every value that can hold a mutable container (attributes, configurations, -extra fields, v2 codec configurations, fill values, consolidated entries) is -deep-copied on the way out, so editing a serialized document can never -silently mutate the frozen model that produced it. diff --git a/packages/zarr-metadata/changes/4119.removal.md b/packages/zarr-metadata/changes/4119.removal.md deleted file mode 100644 index 2a9a6f84c4..0000000000 --- a/packages/zarr-metadata/changes/4119.removal.md +++ /dev/null @@ -1,41 +0,0 @@ -The document (TypedDict) types are renamed to put the format version at the -front of the name and to mark the JSON-document form with a `JSON` suffix, -so a format version can never be misread as a class revision and the bare -entity names are reserved for the `zarr_metadata.model` dataclasses: - -- `ArrayMetadataV2` → `ZarrV2ArrayMetadataJSON` (and `...Partial` accordingly) -- `ArrayMetadataV3` → `ZarrV3ArrayMetadataJSON` (and `...Partial` accordingly) -- `GroupMetadataV2` → `ZarrV2GroupMetadataJSON` (and `...Partial` accordingly) -- `GroupMetadataV3` → `ZarrV3GroupMetadataJSON` (and `...Partial` accordingly) -- `ConsolidatedMetadataV2` → `ZarrV2ConsolidatedMetadataJSON` -- `ConsolidatedMetadataV3` → `ZarrV3ConsolidatedMetadataJSON` -- `NamedConfigV3` → `ZarrV3NamedConfigJSON` -- `MetadataV3` → `ZarrV3MetadataFieldJSON` (the union of the bare-name and - named-configuration spellings of one metadata field) -- `ExtensionFieldV3` → `ZarrV3ExtensionField` -- `CodecMetadataV2` → `ZarrV2CodecMetadata` -- `DataTypeMetadataV2` → `ZarrV2DataTypeMetadata` -- `ArrayOrderV2` → `ZarrV2ArrayOrder` -- `ArrayDimensionSeparatorV2` → `ZarrV2ArrayDimensionSeparator` -- `ZArrayMetadata` → `ZarrV2ZArrayJSON` (the strict on-disk `.zarray` document) -- `ZGroupMetadata` → `ZarrV2ZGroupJSON` (the strict on-disk `.zgroup` document) -- `ZAttrsMetadata` → `ZarrV2ZAttrsJSON` (the `.zattrs` document) - -The old names are removed, not aliased. The `zarr_metadata.pydantic` field -types take the bare entity names (`ZarrV3ArrayMetadata`, ...), matching the -model classes they validate into. - -The conventions, stated once for future additions: CamelCase type names put -the format version first (`ZarrV2ArrayMetadataJSON`, -`ZarrV3ArrayMetadataStoreKey`), while SCREAMING_SNAKE constants and -snake_case functions put it last (`ARRAY_METADATA_STORE_KEY_V2`, -`validate_array_metadata_v3`). The `JSON` suffix marks a raw-document type -whose bare name is taken by (or reserved for) a `zarr_metadata.model` -dataclass; raw field-level types the models hold verbatim -(`ZarrV2CodecMetadata`, `ZarrV3ExtensionField`) keep their bare names. -Extension-entity types put the registered entity name first and end in -exactly one role suffix (`BloscCodecMetadata`, `Uint8DataTypeName`) — the -`V2` in `V2ChunkKeyEncodingMetadata` is that encoding's entity name, not a -format version, which is always spelled `ZarrV2`/`ZarrV3`. Every public -type name is checked against this grammar by -`tests/test_public_api.py::test_public_type_names_comply_with_naming_grammar`. From 020e5c3494c7bb794da1a94b970c326ddbdbca7a Mon Sep 17 00:00:00 2001 From: Max Jones <14077947+maxrjones@users.noreply.github.com> Date: Thu, 30 Jul 2026 00:45:46 -0400 Subject: [PATCH 428/468] docs: fix link checker error and update redirected links; run checker weekly (#4214) --- .github/workflows/links.yml | 2 +- README.md | 22 +- docs/contributing.md | 2 +- docs/quick-start.md | 4 +- docs/release-notes.md | 406 +++++++++++++------------- docs/user-guide/arrays.md | 6 +- docs/user-guide/installation.md | 8 +- docs/user-guide/storage.md | 11 +- packages/zarr-metadata/CHANGELOG.md | 20 +- packages/zarr-metadata/README.md | 2 +- packages/zarr-metadata/pyproject.toml | 2 +- pyproject.toml | 2 +- 12 files changed, 242 insertions(+), 245 deletions(-) diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml index f606f12a3e..0af76deece 100644 --- a/.github/workflows/links.yml +++ b/.github/workflows/links.yml @@ -5,7 +5,7 @@ on: workflow_dispatch: # pull_request: schedule: - - cron: "00 18 * * *" + - cron: "00 18 * * 1" # weekly, Mondays at 18:00 UTC jobs: linkChecker: diff --git a/README.md b/README.md index fb0890d18c..7557936b6f 100644 --- a/README.md +++ b/README.md @@ -8,24 +8,24 @@ [![CondaForge](https://anaconda.org/conda-forge/zarr/badges/version.svg)](https://anaconda.org/anaconda/zarr/) [![Package Status](https://img.shields.io/pypi/status/zarr.svg)](https://pypi.org/project/zarr/) [![License](https://img.shields.io/pypi/l/zarr.svg)](https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt) -[![Coverage](https://codecov.io/gh/zarr-developers/zarr-python/branch/main/graph/badge.svg)](https://codecov.io/gh/zarr-developers/zarr-python) -[![Downloads](https://pepy.tech/badge/zarr)](https://zarr.readthedocs.io) +[![Coverage](https://codecov.io/gh/zarr-developers/zarr-python/branch/main/graph/badge.svg)](https://app.codecov.io/gh/zarr-developers/zarr-python) +[![Downloads](https://static.pepy.tech/badge/zarr)](https://zarr.readthedocs.io/en/stable/) [![Developer Chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://ossci.zulipchat.com/#narrow/channel/423692-Zarr-Python) [![Citation](https://zenodo.org/badge/DOI/10.5281/zenodo.3773450.svg)](https://doi.org/10.5281/zenodo.3773450) ## What is it? -Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. See the [documentation](https://zarr.readthedocs.io) for more information. +Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. See the [documentation](https://zarr.readthedocs.io/en/stable/) for more information. ## Main Features -- [**Create**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#creating-an-array) N-dimensional arrays with any NumPy `dtype`. -- [**Chunk arrays**](https://zarr.readthedocs.io/en/stable/user-guide/performance.html#chunk-optimizations) along any dimension. -- [**Compress**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#compressors) and/or filter chunks using any NumCodecs codec. -- [**Store arrays**](https://zarr.readthedocs.io/en/stable/user-guide/storage.html) in memory, on disk, inside a zip file, on S3, etc... -- [**Read**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#reading-and-writing-data) an array [**concurrently**](https://zarr.readthedocs.io/en/stable/user-guide/performance.html#parallel-computing-and-synchronization) from multiple threads or processes. -- [**Write**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#reading-and-writing-data) to an array concurrently from multiple threads or processes. -- Organize arrays into hierarchies via [**groups**](https://zarr.readthedocs.io/en/stable/quickstart.html#hierarchical-groups). +- [**Create**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#creating-an-array) N-dimensional arrays with any NumPy `dtype`. +- [**Chunk arrays**](https://zarr.readthedocs.io/en/stable/user-guide/performance/#chunk-optimizations) along any dimension. +- [**Compress**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#compressors) and/or filter chunks using any NumCodecs codec. +- [**Store arrays**](https://zarr.readthedocs.io/en/stable/user-guide/storage/) in memory, on disk, inside a zip file, on S3, etc... +- [**Read**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#reading-and-writing-data) an array [**concurrently**](https://zarr.readthedocs.io/en/stable/user-guide/performance/#parallel-computing-and-synchronization) from multiple threads or processes. +- [**Write**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#reading-and-writing-data) to an array concurrently from multiple threads or processes. +- Organize arrays into hierarchies via [**groups**](https://zarr.readthedocs.io/en/stable/quick-start/#hierarchical-groups). ## Where to get it @@ -41,4 +41,4 @@ or via `conda`: conda install -c conda-forge zarr ``` -For more details, including how to install from source, see the [installation documentation](https://zarr.readthedocs.io/en/stable/index.html#installation). +For more details, including how to install from source, see the [installation documentation](https://zarr.readthedocs.io/en/stable/#installation). diff --git a/docs/contributing.md b/docs/contributing.md index aeb88e6ce1..dea7256c36 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -419,4 +419,4 @@ performance benchmarks as part of our test suite. The benchmarks are found in `t By default pytest is configured to run these benchmarks as plain tests (i.e., no benchmarking). To run a benchmark with timing measurements, use the `--benchmark-enable` when invoking `pytest`. -The benchmarks are run as part of the continuous integration suite through [codspeed](https://codspeed.io/zarr-developers/zarr-python). +The benchmarks are run as part of the continuous integration suite through [codspeed](https://app.codspeed.io/zarr-developers/zarr-python). diff --git a/docs/quick-start.md b/docs/quick-start.md index 17cb1c599a..123f05d5e9 100644 --- a/docs/quick-start.md +++ b/docs/quick-start.md @@ -164,8 +164,8 @@ print(z[:]) ``` Zarr also integrates seamlessly with cloud object storage such as Amazon S3 and Google -Cloud Storage using external libraries like [s3fs](https://s3fs.readthedocs.io) or -[gcsfs](https://gcsfs.readthedocs.io). Remote storage support requires the `remote` +Cloud Storage using external libraries like [s3fs](https://s3fs.readthedocs.io/en/latest/) or +[gcsfs](https://gcsfs.readthedocs.io/en/latest/). Remote storage support requires the `remote` optional dependencies (`pip install "zarr[remote]"`) as well as a filesystem library for your storage service, such as `s3fs` for S3: diff --git a/docs/release-notes.md b/docs/release-notes.md index 3fd8a5f360..7b147a30bd 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -11,12 +11,12 @@ - Optimizes reading multiple chunks from a shard. Serial calls to `Store.get()` in the sharding codec have been replaced with a single call to `Store.get_ranges()`, which coalesces nearby byte ranges and fetches them - concurrently. ([#3004](https://github.com/zarr-developers/zarr-python/issues/3004)) -- Added a `subchunk_write_order` option to `ShardingCodec` to control the physical order of subchunks within a shard. Supported values are `morton`, `unordered`, `lexicographic`, and `colexicographic`. `unordered` makes no guarantee about subchunk layout. This setting affects only on-disk layout, not the data read back, and is not persisted in array metadata: it applies per codec instance and is not recovered when reopening a sharded array. ([#3826](https://github.com/zarr-developers/zarr-python/issues/3826)) -- Added `SyncByteGetter` and `SyncByteSetter` runtime-checkable protocols and a `get_ranges_sync` method on the `Store` ABC. These let custom byte getters/setters opt into the synchronous codec pipeline's fast path for in-memory IO, which the sharding codec uses for its inner chunks. ([#3885](https://github.com/zarr-developers/zarr-python/issues/3885)) -- Added `FusedCodecPipeline`, an opt-in codec pipeline that runs codec compute synchronously and in bulk (avoiding the per-chunk async scheduling overhead of the default `BatchedCodecPipeline`), giving large speedups for sharded arrays (up to ~24x writes / ~14x reads on many-chunks-per-shard layouts, more with compression) and no regressions on compute-bound workloads. The default `BatchedCodecPipeline` is unchanged for standard configurations, so existing code keeps working unless you opt in; enable the new pipeline with `zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"})`. ([#3885](https://github.com/zarr-developers/zarr-python/issues/3885)) -- Add `zarr.abc.store.Store.get_ranges` for concurrent, coalesced multi-range reads from a single key. The method is defined on the `Store` ABC with a default implementation built on `Store.get`, so every store inherits a working version; stores with native multi-range backends (e.g. `FsspecStore`) can override for efficiency. Coalescing knobs (`max_concurrency`, `max_gap_bytes`, `max_coalesced_bytes`) are passed as keyword arguments to `get_ranges`. Failures from underlying fetches surface as a `BaseExceptionGroup` (PEP 654); callers should use `except*` to filter for specific exception types such as `FileNotFoundError`. ([#3925](https://github.com/zarr-developers/zarr-python/issues/3925)) -- Two new fields on `ArrayConfig` control how the sharding codec coalesces partial-shard reads: `sharding_coalesce_max_gap_bytes` (default 1 MiB) and `sharding_coalesce_max_bytes` (default 16 MiB). When reading multiple chunks from the same shard, nearby byte ranges are merged into a single request to the store if separated by no more than `sharding_coalesce_max_gap_bytes` and the merged read stays within `sharding_coalesce_max_bytes`. Defaults are seeded from the matching `array.sharding_coalesce_max_gap_bytes` / `array.sharding_coalesce_max_bytes` keys in [`zarr.config`][] at array-creation time, and can be overridden per array by passing `config={...}` to [`zarr.create_array`][]. ([#3987](https://github.com/zarr-developers/zarr-python/issues/3987)) + concurrently. ([#3004](https://github.com/zarr-developers/zarr-python/pull/3004)) +- Added a `subchunk_write_order` option to `ShardingCodec` to control the physical order of subchunks within a shard. Supported values are `morton`, `unordered`, `lexicographic`, and `colexicographic`. `unordered` makes no guarantee about subchunk layout. This setting affects only on-disk layout, not the data read back, and is not persisted in array metadata: it applies per codec instance and is not recovered when reopening a sharded array. ([#3826](https://github.com/zarr-developers/zarr-python/pull/3826)) +- Added `SyncByteGetter` and `SyncByteSetter` runtime-checkable protocols and a `get_ranges_sync` method on the `Store` ABC. These let custom byte getters/setters opt into the synchronous codec pipeline's fast path for in-memory IO, which the sharding codec uses for its inner chunks. ([#3885](https://github.com/zarr-developers/zarr-python/pull/3885)) +- Added `FusedCodecPipeline`, an opt-in codec pipeline that runs codec compute synchronously and in bulk (avoiding the per-chunk async scheduling overhead of the default `BatchedCodecPipeline`), giving large speedups for sharded arrays (up to ~24x writes / ~14x reads on many-chunks-per-shard layouts, more with compression) and no regressions on compute-bound workloads. The default `BatchedCodecPipeline` is unchanged for standard configurations, so existing code keeps working unless you opt in; enable the new pipeline with `zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"})`. ([#3885](https://github.com/zarr-developers/zarr-python/pull/3885)) +- Add `zarr.abc.store.Store.get_ranges` for concurrent, coalesced multi-range reads from a single key. The method is defined on the `Store` ABC with a default implementation built on `Store.get`, so every store inherits a working version; stores with native multi-range backends (e.g. `FsspecStore`) can override for efficiency. Coalescing knobs (`max_concurrency`, `max_gap_bytes`, `max_coalesced_bytes`) are passed as keyword arguments to `get_ranges`. Failures from underlying fetches surface as a `BaseExceptionGroup` (PEP 654); callers should use `except*` to filter for specific exception types such as `FileNotFoundError`. ([#3925](https://github.com/zarr-developers/zarr-python/pull/3925)) +- Two new fields on `ArrayConfig` control how the sharding codec coalesces partial-shard reads: `sharding_coalesce_max_gap_bytes` (default 1 MiB) and `sharding_coalesce_max_bytes` (default 16 MiB). When reading multiple chunks from the same shard, nearby byte ranges are merged into a single request to the store if separated by no more than `sharding_coalesce_max_gap_bytes` and the merged read stays within `sharding_coalesce_max_bytes`. Defaults are seeded from the matching `array.sharding_coalesce_max_gap_bytes` / `array.sharding_coalesce_max_bytes` keys in [`zarr.config`][] at array-creation time, and can be overridden per array by passing `config={...}` to [`zarr.create_array`][]. ([#3987](https://github.com/zarr-developers/zarr-python/pull/3987)) ### Bugfixes @@ -27,24 +27,24 @@ - Fixed `BytesCodec.from_dict` so that `BytesCodec` instances roundtrip to / from their dict representation. `BytesCodec.from_dict` now interprets a missing `endian` configuration as `endian=None` (matching what `BytesCodec.to_dict` - emits), instead of falling back to the system's native byte order. ([#3417](https://github.com/zarr-developers/zarr-python/issues/3417)) + emits), instead of falling back to the system's native byte order. ([#3417](https://github.com/zarr-developers/zarr-python/pull/3417)) - Fixed `save_array`, `Group.__setitem__`, and `load` for 0-dimensional arrays. ([#3469](https://github.com/zarr-developers/zarr-python/issues/3469)) -- Fixed inner-codec spec evolution for sharded arrays. The sharding codec now threads the array spec through its inner codec chain when evolving codecs, so a codec that changes the dtype upstream of `BytesCodec` no longer leaves the inner chain evolved against the wrong spec (which previously failed at decode time). This runs on the default `BatchedCodecPipeline` as well. Standard inner chains (`[BytesCodec]`, `[BytesCodec, ZstdCodec]`, transpose + bytes) are byte-identical to before. Restores the behavior of #2179. ([#3885](https://github.com/zarr-developers/zarr-python/issues/3885)) +- Fixed inner-codec spec evolution for sharded arrays. The sharding codec now threads the array spec through its inner codec chain when evolving codecs, so a codec that changes the dtype upstream of `BytesCodec` no longer leaves the inner chain evolved against the wrong spec (which previously failed at decode time). This runs on the default `BatchedCodecPipeline` as well. Standard inner chains (`[BytesCodec]`, `[BytesCodec, ZstdCodec]`, transpose + bytes) are byte-identical to before. Restores the behavior of #2179. ([#3885](https://github.com/zarr-developers/zarr-python/pull/3885)) - Make chunk normalization properly handle `-1` as a compact representation of the length of an entire axis. Reject several previously-accepted but ill-defined chunk specifications: `chunks=True` (previously silently produced size-1 chunks), chunk tuples shorter than the array's number of dimensions (previously padded to the array's shape), and `None` as a per-dimension chunk size. These all now raise informative errors. Also fix chunk handling for 0-length array dimensions, - and add explicit rejection of 0-length chunks. ([#3899](https://github.com/zarr-developers/zarr-python/issues/3899)) + and add explicit rejection of 0-length chunks. ([#3899](https://github.com/zarr-developers/zarr-python/pull/3899)) - Handle missing consolidated metadata in leaf Group nodes. ([#3954](https://github.com/zarr-developers/zarr-python/issues/3954)) - Corrected the JSON type definitions for the `numpy.datetime64` and `numpy.timedelta64` data types in Zarr V3 metadata: the `configuration` object (holding `unit` and `scale_factor`) is now required, matching the published specifications for these data types. Also updated the specification links in - the docstrings to point to the zarr-extensions repository. ([#3955](https://github.com/zarr-developers/zarr-python/issues/3955)) + the docstrings to point to the zarr-extensions repository. ([#3955](https://github.com/zarr-developers/zarr-python/pull/3955)) - Fixed writing to 0-dimensional arrays that use the sharding codec. Previously - assigning to a 0-dimensional sharded array raised an error. ([#3966](https://github.com/zarr-developers/zarr-python/issues/3966)) + assigning to a 0-dimensional sharded array raised an error. ([#3966](https://github.com/zarr-developers/zarr-python/pull/3966)) - Fix flaky stateful test bookkeeping when `delete_dir` matches string prefixes instead of true directory descendants. Previously a path such as `6/faNT…` could be incorrectly removed when deleting `6/f`. (See [issue #3977](https://github.com/zarr-developers/zarr-python/issues/3977).) ([#3977](https://github.com/zarr-developers/zarr-python/issues/3977)) - `FsspecStore.from_url()` and `from_mapper()` now close the async filesystem they create when `store.close()` is called. Previously the underlying aiohttp @@ -64,7 +64,7 @@ s3fs with ``cache_regions=True``) may internally refresh and replace their client during I/O operations, abandoning prior sessions before ``store.close()`` is invoked. Those intermediate sessions are outside the scope of this fix and - are an issue in the upstream filesystem library. ([#4003](https://github.com/zarr-developers/zarr-python/issues/4003)) + are an issue in the upstream filesystem library. ([#4003](https://github.com/zarr-developers/zarr-python/pull/4003)) - Fixed an invalid `zarr.create_array` example in the quick-start documentation (it passed an unsupported `mode` argument) and made the cloud-storage example execute against a mock S3 backend in CI. Added a test ensuring every Python code block in the documentation is either executed or explicitly opted out with a documented reason, so an invalid example can no longer go untested. ([#4016](https://github.com/zarr-developers/zarr-python/issues/4016)) - Fixed `ObjectStore.list_dir` for object-store listings that include a directory-marker object matching the requested non-root prefix. ([#4032](https://github.com/zarr-developers/zarr-python/issues/4032)) @@ -77,9 +77,9 @@ - `ZipStore.close()` no longer raises `AttributeError` when the store was created but never opened (including when used as a context manager without any I/O). - `codecs_from_list` now raises a descriptive `TypeError` when a `BytesBytesCodec` immediately follows an `ArrayArrayCodec`, instead of a misleading "Required ArrayBytesCodec was not found" `ValueError`. - ([#4074](https://github.com/zarr-developers/zarr-python/issues/4074)) + ([#4074](https://github.com/zarr-developers/zarr-python/pull/4074)) -- Fixed writing Fortran-ordered (F-contiguous) arrays through the variable-length string and bytes codecs and through numcodecs array-array filters such as `Delta`, `FixedScaleOffset` and `PackBits`. Chunks are now passed to numcodecs as C-contiguous arrays, so elements are no longer stored in transposed order. ([#4116](https://github.com/zarr-developers/zarr-python/issues/4116)) +- Fixed writing Fortran-ordered (F-contiguous) arrays through the variable-length string and bytes codecs and through numcodecs array-array filters such as `Delta`, `FixedScaleOffset` and `PackBits`. Chunks are now passed to numcodecs as C-contiguous arrays, so elements are no longer stored in transposed order. ([#4116](https://github.com/zarr-developers/zarr-python/pull/4116)) - Fix silent byte-order corruption for structured dtypes with the `bytes` codec: multi-byte fields are now byte-swapped to the codec's configured `endian` on write and decoded honoring it on read, so non-native-endian structured data (e.g. big-endian fields, as produced by virtual references to external data) round-trips correctly. ([#4141](https://github.com/zarr-developers/zarr-python/issues/4141)) ### Improved Documentation @@ -88,7 +88,7 @@ - Clarify the difference between `zarr.load` and `zarr.open` in their docstrings. `load` eagerly reads data into an in-memory array, while `open` returns a lazy `Array` or `Group` backed by the store, with `See Also` cross-references - linking the two. ([#3984](https://github.com/zarr-developers/zarr-python/issues/3984)) + linking the two. ([#3984](https://github.com/zarr-developers/zarr-python/pull/3984)) - Updated the custom dtype example in `examples/custom_dtype/custom_dtype.py` to use only the public API, eliminating all non-public imports, illustrating what users should do. @@ -109,16 +109,16 @@ `DataTypeValidationError` was *moved* to `zarr.errors`. Importing it from `zarr.core.dtype.common` (its original location), `zarr.core.dtype`, or `zarr.dtype` still works but now raises a `ZarrDeprecationWarning`. The remaining - types and functions are simply re-exported from the listed public module. ([#4052](https://github.com/zarr-developers/zarr-python/issues/4052)) + types and functions are simply re-exported from the listed public module. ([#4052](https://github.com/zarr-developers/zarr-python/pull/4052)) -- Document a self-merge policy in the contributor guide, describing when a core developer may merge their own pull request without a second reviewer and which changes warrant more caution. ([#4053](https://github.com/zarr-developers/zarr-python/issues/4053)) +- Document a self-merge policy in the contributor guide, describing when a core developer may merge their own pull request without a second reviewer and which changes warrant more caution. ([#4053](https://github.com/zarr-developers/zarr-python/pull/4053)) - Fixed many documentation errors found in a full review of the user guide, including prose contradicted by rendered example output on the performance page, invisible code blocks, an incorrect S3 example, stale "not yet implemented" claims in the v3 migration guide, and undocumented optional dependency groups. Also improved navigation order, cross-linking between pages, and coverage of group member - enumeration, bulk attribute updates, and the `use_consolidated` keyword. ([#4132](https://github.com/zarr-developers/zarr-python/issues/4132)) -- Fixed the documented default of ``max_age_seconds`` in the ``CacheStore`` docstring: the default is ``"infinity"`` (no expiration), not ``None``, which is rejected. Also noted that ``cache_store`` must support deletes. ([#4133](https://github.com/zarr-developers/zarr-python/issues/4133)) + enumeration, bulk attribute updates, and the `use_consolidated` keyword. ([#4132](https://github.com/zarr-developers/zarr-python/pull/4132)) +- Fixed the documented default of ``max_age_seconds`` in the ``CacheStore`` docstring: the default is ``"infinity"`` (no expiration), not ``None``, which is rejected. Also noted that ``cache_store`` must support deletes. ([#4133](https://github.com/zarr-developers/zarr-python/pull/4133)) ### Deprecations and Removals @@ -133,7 +133,7 @@ aliases ``Shuffle`` and ``CName`` are now ``BloscShuffleLiteral`` and ``BloscCnameLiteral``, the constant ``SHUFFLE`` is now ``BLOSC_SHUFFLE`` (with a new ``BLOSC_CNAME`` alongside it), and ``BloscShuffle.from_int`` - now returns a literal string rather than an enum member. ([#3963](https://github.com/zarr-developers/zarr-python/issues/3963)) + now returns a literal string rather than an enum member. ([#3963](https://github.com/zarr-developers/zarr-python/pull/3963)) - The ``Endian`` (``zarr.codecs.bytes.Endian``) and ``ShardingCodecIndexLocation`` (``zarr.codecs.ShardingCodecIndexLocation``) enums are now deprecated. Pass the @@ -156,13 +156,13 @@ Additionally, the module-level function ``zarr.codecs.sharding.parse_index_location`` was made private as part of this change. - ([#3968](https://github.com/zarr-developers/zarr-python/issues/3968)) + ([#3968](https://github.com/zarr-developers/zarr-python/pull/3968)) -- Removed the NumPy 1.x implementation of the `VariableLengthUTF8` data type because NumPy 1.x is no longer supported under [SPEC0](https://scientific-python.org/specs/spec-0000/). ([#3973](https://github.com/zarr-developers/zarr-python/issues/3973)) +- Removed the NumPy 1.x implementation of the `VariableLengthUTF8` data type because NumPy 1.x is no longer supported under [SPEC0](https://scientific-python.org/specs/spec-0000/). ([#3973](https://github.com/zarr-developers/zarr-python/pull/3973)) ### Misc -- [#214](https://github.com/zarr-developers/zarr-python/issues/214), [#215](https://github.com/zarr-developers/zarr-python/issues/215), [#3908](https://github.com/zarr-developers/zarr-python/issues/3908), [#3972](https://github.com/zarr-developers/zarr-python/issues/3972), [#3975](https://github.com/zarr-developers/zarr-python/issues/3975), [#3979](https://github.com/zarr-developers/zarr-python/issues/3979), [#3990](https://github.com/zarr-developers/zarr-python/issues/3990), [#3998](https://github.com/zarr-developers/zarr-python/issues/3998), [#4000](https://github.com/zarr-developers/zarr-python/issues/4000), [#4001](https://github.com/zarr-developers/zarr-python/issues/4001), [#4046](https://github.com/zarr-developers/zarr-python/issues/4046), [#4054](https://github.com/zarr-developers/zarr-python/issues/4054), [#4073](https://github.com/zarr-developers/zarr-python/issues/4073), [#4086](https://github.com/zarr-developers/zarr-python/issues/4086), [#4138](https://github.com/zarr-developers/zarr-python/issues/4138) +- [#214](https://github.com/zarr-developers/zarr-python/issues/214), [#215](https://github.com/zarr-developers/zarr-python/pull/215), [#3908](https://github.com/zarr-developers/zarr-python/pull/3908), [#3972](https://github.com/zarr-developers/zarr-python/pull/3972), [#3975](https://github.com/zarr-developers/zarr-python/pull/3975), [#3979](https://github.com/zarr-developers/zarr-python/pull/3979), [#3990](https://github.com/zarr-developers/zarr-python/pull/3990), [#3998](https://github.com/zarr-developers/zarr-python/pull/3998), [#4000](https://github.com/zarr-developers/zarr-python/pull/4000), [#4001](https://github.com/zarr-developers/zarr-python/pull/4001), [#4046](https://github.com/zarr-developers/zarr-python/pull/4046), [#4054](https://github.com/zarr-developers/zarr-python/pull/4054), [#4073](https://github.com/zarr-developers/zarr-python/issues/4073), [#4086](https://github.com/zarr-developers/zarr-python/issues/4086), [#4138](https://github.com/zarr-developers/zarr-python/pull/4138) ## 3.2.1 (2026-05-05) @@ -172,17 +172,17 @@ - Fixed a `CastValue` validation bug where the "can we use an out-of-range mode" check inspected the source dtype instead of the target dtype. This meant arrays with a float source dtype and an integer target dtype incorrectly raised a `ValueError` - when configured with a `wrap` out-of-range mode. ([#3938](https://github.com/zarr-developers/zarr-python/issues/3938)) + when configured with a `wrap` out-of-range mode. ([#3938](https://github.com/zarr-developers/zarr-python/pull/3938)) - Fixed a bug where the codec pipeline evolved each codec against the original array spec instead of the spec produced by upstream array-to-array codecs. This caused failures whenever an upstream codec changed the dtype between codec boundaries — e.g. arrays using `CastValue` to convert a single-byte source dtype (`int8`) to a multi-byte target dtype (`int16`) raised a `ValueError` from - `BytesCodec` about a missing `endian` configuration. ([#3941](https://github.com/zarr-developers/zarr-python/issues/3941)) + `BytesCodec` about a missing `endian` configuration. ([#3941](https://github.com/zarr-developers/zarr-python/pull/3941)) - Fixed breakage in existing fsspec-dependent workflows caused by associating the "memory" URL scheme with instances of `ManagedMemoryStore` instead of fsspec's memory-backed store. After this change, store URLs with a "memory" scheme are handled differently when `fsspec` is installed: with `fsspec`, a `FsspecStore` backed by a `MemoryFileSystem` is used. Without `fsspec`, -a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr-python/issues/3944)) +a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr-python/pull/3944)) ## 3.2.0 (2026-04-30) @@ -190,9 +190,9 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Adds a new in-memory storage backend called `ManagedMemoryStore`. Instances of `ManagedMemoryStore` function similarly to `MemoryStore`, but instances of `ManagedMemoryStore` can be constructed from - a URL like `memory://store`. ([#3679](https://github.com/zarr-developers/zarr-python/issues/3679)) -- Added `array.read_missing_chunks` configuration option. When set to `False`, reading missing chunks raises a `ChunkNotFoundError` instead of filling them with the array's fill value. ([#3748](https://github.com/zarr-developers/zarr-python/issues/3748)) -- Added `Struct` class (subclass of `Structured`) implementing the zarr-extensions `struct` dtype spec. Uses object-style field format and dict fill values. Legacy `Structured` remains available for backward compatibility. ([#3781](https://github.com/zarr-developers/zarr-python/issues/3781)) + a URL like `memory://store`. ([#3679](https://github.com/zarr-developers/zarr-python/pull/3679)) +- Added `array.read_missing_chunks` configuration option. When set to `False`, reading missing chunks raises a `ChunkNotFoundError` instead of filling them with the array's fill value. ([#3748](https://github.com/zarr-developers/zarr-python/pull/3748)) +- Added `Struct` class (subclass of `Structured`) implementing the zarr-extensions `struct` dtype spec. Uses object-style field format and dict fill values. Legacy `Structured` remains available for backward compatibility. ([#3781](https://github.com/zarr-developers/zarr-python/pull/3781)) - Add support for rectilinear (variable-sized) chunk grids. This feature is experimental and must be explicitly enabled via `zarr.config.set({'array.rectilinear_chunks': True})`. @@ -208,37 +208,37 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr **Breaking change**: The `validate` method on `BaseCodec` and `CodecPipeline` now receives a `ChunkGridMetadata` instance instead of a `ChunkGrid` instance for the `chunk_grid` parameter. Third-party codecs that override `validate` and inspect the chunk grid will need to - update their type annotations. No known downstream packages were using this parameter. ([#3802](https://github.com/zarr-developers/zarr-python/issues/3802)) + update their type annotations. No known downstream packages were using this parameter. ([#3802](https://github.com/zarr-developers/zarr-python/pull/3802)) -- Add `cast_value` and `scale_offset` codecs. ([#3874](https://github.com/zarr-developers/zarr-python/issues/3874)) +- Add `cast_value` and `scale_offset` codecs. ([#3874](https://github.com/zarr-developers/zarr-python/pull/3874)) ### Bugfixes - Fix `SyncError` raised when assigning a `zarr.Array` as the value in a `__setitem__` call (e.g. `dst[:] = src` where `src` is a zarr array). The source array is now converted to a NumPy array before entering the async codec pipeline. ([#3611](https://github.com/zarr-developers/zarr-python/issues/3611)) - Fix an issue that prevents the correct parsing of special NumPy `uint32` dtypes resulting e.g. - from bit wise operations on `uint32` arrays on Windows. ([#3797](https://github.com/zarr-developers/zarr-python/issues/3797)) + from bit wise operations on `uint32` arrays on Windows. ([#3797](https://github.com/zarr-developers/zarr-python/pull/3797)) - Fix `ZipStore.list()`, `list_dir()`, and `exists()` to auto-open the zip file when called before `open()`, consistent with the existing behavior of `get()` and `set()`. ([#3846](https://github.com/zarr-developers/zarr-python/issues/3846)) -- Fix handling of `NaT` default fill values for `datetime64` and `timedelta64` data types. Equality checks now use `numpy.isnat` so that the default fill value compares correctly against `NaT`. ([#3863](https://github.com/zarr-developers/zarr-python/issues/3863)) -- Use the unit associated with the `Datetime64` data type when creating the default `Nat` scalar value. ([#3920](https://github.com/zarr-developers/zarr-python/issues/3920)) +- Fix handling of `NaT` default fill values for `datetime64` and `timedelta64` data types. Equality checks now use `numpy.isnat` so that the default fill value compares correctly against `NaT`. ([#3863](https://github.com/zarr-developers/zarr-python/pull/3863)) +- Use the unit associated with the `Datetime64` data type when creating the default `Nat` scalar value. ([#3920](https://github.com/zarr-developers/zarr-python/pull/3920)) ### Improved Documentation - Document removal of `zarr.storage.init_group` in v3 migration guide, with replacement using `zarr.open_group`/`zarr.create_group`. ([#2720](https://github.com/zarr-developers/zarr-python/issues/2720)) - Document the `threading.max_workers` configuration option in the performance guide. ([#3492](https://github.com/zarr-developers/zarr-python/issues/3492)) - Corrects the type annotation reported for the `batch_info` parameter in the `CodecPipeline.write` - method docstring. ([#3836](https://github.com/zarr-developers/zarr-python/issues/3836)) -- Remove result="ansi" from code blocks in the user guide that were causing empty output cells in the rendered documentation. ([#3845](https://github.com/zarr-developers/zarr-python/issues/3845)) + method docstring. ([#3836](https://github.com/zarr-developers/zarr-python/pull/3836)) +- Remove result="ansi" from code blocks in the user guide that were causing empty output cells in the rendered documentation. ([#3845](https://github.com/zarr-developers/zarr-python/pull/3845)) ### Deprecations and Removals -- Remove deprecated `zarr.convenience` and `zarr.creation` modules. ([#3900](https://github.com/zarr-developers/zarr-python/issues/3900)) -- Remove the deprecated `zarr_version` parameter from several functions and methods. That parameter is replaced with `zarr_format`. ([#3901](https://github.com/zarr-developers/zarr-python/issues/3901)) -- Remove deprecated `Group` methods `array`, `require_dataset`, and `create_dataset`. ([#3902](https://github.com/zarr-developers/zarr-python/issues/3902)) -- Remove deprecated `AsyncArray.create` and `Array.create` methods. ([#3903](https://github.com/zarr-developers/zarr-python/issues/3903)) +- Remove deprecated `zarr.convenience` and `zarr.creation` modules. ([#3900](https://github.com/zarr-developers/zarr-python/pull/3900)) +- Remove the deprecated `zarr_version` parameter from several functions and methods. That parameter is replaced with `zarr_format`. ([#3901](https://github.com/zarr-developers/zarr-python/pull/3901)) +- Remove deprecated `Group` methods `array`, `require_dataset`, and `create_dataset`. ([#3902](https://github.com/zarr-developers/zarr-python/pull/3902)) +- Remove deprecated `AsyncArray.create` and `Array.create` methods. ([#3903](https://github.com/zarr-developers/zarr-python/pull/3903)) ### Misc -- [#3546](https://github.com/zarr-developers/zarr-python/issues/3546), [#3793](https://github.com/zarr-developers/zarr-python/issues/3793), [#3800](https://github.com/zarr-developers/zarr-python/issues/3800), [#3828](https://github.com/zarr-developers/zarr-python/issues/3828), [#3830](https://github.com/zarr-developers/zarr-python/issues/3830), [#3833](https://github.com/zarr-developers/zarr-python/issues/3833), [#3837](https://github.com/zarr-developers/zarr-python/issues/3837), [#3897](https://github.com/zarr-developers/zarr-python/issues/3897) +- [#3546](https://github.com/zarr-developers/zarr-python/issues/3546), [#3793](https://github.com/zarr-developers/zarr-python/pull/3793), [#3800](https://github.com/zarr-developers/zarr-python/pull/3800), [#3828](https://github.com/zarr-developers/zarr-python/pull/3828), [#3830](https://github.com/zarr-developers/zarr-python/pull/3830), [#3833](https://github.com/zarr-developers/zarr-python/pull/3833), [#3837](https://github.com/zarr-developers/zarr-python/pull/3837), [#3897](https://github.com/zarr-developers/zarr-python/pull/3897) ## 3.1.6 (2026-03-19) @@ -246,42 +246,42 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr ### Features - Exposes the array runtime configuration as an attribute called `config` on the `Array` and - `AsyncArray` classes. The previous `AsyncArray._config` attribute is now a deprecated alias for `AsyncArray.config`. ([#3668](https://github.com/zarr-developers/zarr-python/issues/3668)) -- Adds a method for creating a new `Array` / `AsyncArray` instance with a new runtime configuration, and fixes inaccurate documentation about the `write_empty_chunks` configuration parameter. ([#3668](https://github.com/zarr-developers/zarr-python/issues/3668)) + `AsyncArray` classes. The previous `AsyncArray._config` attribute is now a deprecated alias for `AsyncArray.config`. ([#3668](https://github.com/zarr-developers/zarr-python/pull/3668)) +- Adds a method for creating a new `Array` / `AsyncArray` instance with a new runtime configuration, and fixes inaccurate documentation about the `write_empty_chunks` configuration parameter. ([#3668](https://github.com/zarr-developers/zarr-python/pull/3668)) - Adds synchronous methods to stores that do not benefit from an async event loop. The shape of these methods is defined by protocol classes to support structural subtyping. ([#3725](https://github.com/zarr-developers/zarr-python/pull/3725)) - Fix near-miss penalty in `_morton_order` with hybrid ceiling+argsort strategy. ([#3718](https://github.com/zarr-developers/zarr-python/pull/3718)) ### Bugfixes -- Correct the target bytes number for auto-chunking when auto-sharding. ([#3603](https://github.com/zarr-developers/zarr-python/issues/3603)) -- Fixed a bug in the sharding codec that prevented nested shard reads in certain cases. ([#3655](https://github.com/zarr-developers/zarr-python/issues/3655)) -- Fix obstore `_transform_list_dir` implementation to correctly relativize paths (removing `lstrip` usage). ([#3657](https://github.com/zarr-developers/zarr-python/issues/3657)) -- Raise error when trying to encode `numpy.dtypes.StringDType` with `na_object` set. ([#3695](https://github.com/zarr-developers/zarr-python/issues/3695)) -- `CacheStore`, `LoggingStore` and `LatencyStore` now support with_read_only. ([#3700](https://github.com/zarr-developers/zarr-python/issues/3700)) -- Skip chunk coordinate enumeration in resize when the array is only growing, avoiding unbounded memory usage for large arrays. ([#3702](https://github.com/zarr-developers/zarr-python/issues/3702)) -- Fix a performance bug in morton curve generation. ([#3705](https://github.com/zarr-developers/zarr-python/issues/3705)) -- Add a dedicated in-memory cache for byte-range requests to the experimental `CacheStore`. ([#3710](https://github.com/zarr-developers/zarr-python/issues/3710)) +- Correct the target bytes number for auto-chunking when auto-sharding. ([#3603](https://github.com/zarr-developers/zarr-python/pull/3603)) +- Fixed a bug in the sharding codec that prevented nested shard reads in certain cases. ([#3655](https://github.com/zarr-developers/zarr-python/pull/3655)) +- Fix obstore `_transform_list_dir` implementation to correctly relativize paths (removing `lstrip` usage). ([#3657](https://github.com/zarr-developers/zarr-python/pull/3657)) +- Raise error when trying to encode `numpy.dtypes.StringDType` with `na_object` set. ([#3695](https://github.com/zarr-developers/zarr-python/pull/3695)) +- `CacheStore`, `LoggingStore` and `LatencyStore` now support with_read_only. ([#3700](https://github.com/zarr-developers/zarr-python/pull/3700)) +- Skip chunk coordinate enumeration in resize when the array is only growing, avoiding unbounded memory usage for large arrays. ([#3702](https://github.com/zarr-developers/zarr-python/pull/3702)) +- Fix a performance bug in morton curve generation. ([#3705](https://github.com/zarr-developers/zarr-python/pull/3705)) +- Add a dedicated in-memory cache for byte-range requests to the experimental `CacheStore`. ([#3710](https://github.com/zarr-developers/zarr-python/pull/3710)) - `BaseFloat._check_scalar` rejects invalid string values. ([#3586](https://github.com/zarr-developers/zarr-python/issues/3586)) -- Apply drop_axes squeeze in partial decode path for sharding. ([#3763](https://github.com/zarr-developers/zarr-python/issues/3763)) -- Set `copy=False` in reshape operation. ([#3649](https://github.com/zarr-developers/zarr-python/issues/3649)) -- Validate that dask-style chunks have regular shapes. ([#3779](https://github.com/zarr-developers/zarr-python/issues/3779)) +- Apply drop_axes squeeze in partial decode path for sharding. ([#3763](https://github.com/zarr-developers/zarr-python/pull/3763)) +- Set `copy=False` in reshape operation. ([#3649](https://github.com/zarr-developers/zarr-python/pull/3649)) +- Validate that dask-style chunks have regular shapes. ([#3779](https://github.com/zarr-developers/zarr-python/pull/3779)) ### Improved Documentation - Add documentation example for creating uncompressed arrays in the Compression section of the user guide. ([#3464](https://github.com/zarr-developers/zarr-python/issues/3464)) -- Add AI-assisted code policy to the contributing guide. ([#3769](https://github.com/zarr-developers/zarr-python/issues/3769)) -- Added a glossary. ([#3767](https://github.com/zarr-developers/zarr-python/issues/3767)) +- Add AI-assisted code policy to the contributing guide. ([#3769](https://github.com/zarr-developers/zarr-python/pull/3769)) +- Added a glossary. ([#3767](https://github.com/zarr-developers/zarr-python/pull/3767)) ### Misc -- [#3562](https://github.com/zarr-developers/zarr-python/issues/3562), [#3605](https://github.com/zarr-developers/zarr-python/issues/3605), [#3619](https://github.com/zarr-developers/zarr-python/issues/3619), [#3623](https://github.com/zarr-developers/zarr-python/issues/3623), [#3636](https://github.com/zarr-developers/zarr-python/issues/3636), [#3648](https://github.com/zarr-developers/zarr-python/issues/3648), [#3656](https://github.com/zarr-developers/zarr-python/issues/3656), [#3658](https://github.com/zarr-developers/zarr-python/issues/3658), [#3673](https://github.com/zarr-developers/zarr-python/issues/3673), [#3704](https://github.com/zarr-developers/zarr-python/issues/3704), [#3706](https://github.com/zarr-developers/zarr-python/issues/3706), [#3708](https://github.com/zarr-developers/zarr-python/issues/3708), [#3712](https://github.com/zarr-developers/zarr-python/issues/3712), [#3713](https://github.com/zarr-developers/zarr-python/issues/3713), [#3717](https://github.com/zarr-developers/zarr-python/issues/3717), [#3721](https://github.com/zarr-developers/zarr-python/issues/3721), [#3728](https://github.com/zarr-developers/zarr-python/issues/3728), [#3778](https://github.com/zarr-developers/zarr-python/issues/3778) +- [#3562](https://github.com/zarr-developers/zarr-python/pull/3562), [#3605](https://github.com/zarr-developers/zarr-python/pull/3605), [#3619](https://github.com/zarr-developers/zarr-python/pull/3619), [#3623](https://github.com/zarr-developers/zarr-python/pull/3623), [#3636](https://github.com/zarr-developers/zarr-python/pull/3636), [#3648](https://github.com/zarr-developers/zarr-python/pull/3648), [#3656](https://github.com/zarr-developers/zarr-python/pull/3656), [#3658](https://github.com/zarr-developers/zarr-python/pull/3658), [#3673](https://github.com/zarr-developers/zarr-python/pull/3673), [#3704](https://github.com/zarr-developers/zarr-python/pull/3704), [#3706](https://github.com/zarr-developers/zarr-python/pull/3706), [#3708](https://github.com/zarr-developers/zarr-python/pull/3708), [#3712](https://github.com/zarr-developers/zarr-python/pull/3712), [#3713](https://github.com/zarr-developers/zarr-python/pull/3713), [#3717](https://github.com/zarr-developers/zarr-python/pull/3717), [#3721](https://github.com/zarr-developers/zarr-python/pull/3721), [#3728](https://github.com/zarr-developers/zarr-python/pull/3728), [#3778](https://github.com/zarr-developers/zarr-python/pull/3778) ## 3.1.5 (2025-11-21) ### Bugfixes -- Fix formatting errors in the release notes section of the docs. ([#3594](https://github.com/zarr-developers/zarr-python/issues/3594)) +- Fix formatting errors in the release notes section of the docs. ([#3594](https://github.com/zarr-developers/zarr-python/pull/3594)) ## 3.1.4 (2025-11-20) @@ -289,31 +289,31 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr ### Features - The `Array` class can now also be parametrized in the same manner as the `AsyncArray` class, allowing Zarr format v2 and v3 `Array`s to be distinguished. - New types have been added to `zarr.types` to help with this. ([#3304](https://github.com/zarr-developers/zarr-python/issues/3304)) -- Adds `zarr.experimental.cache_store.CacheStore`, a `Store` that implements caching by combining two other `Store` instances. See the [docs page](https://zarr.readthedocs.io/en/latest/user-guide/experimental#cachestore) for more information about this feature. ([#3366](https://github.com/zarr-developers/zarr-python/issues/3366)) -- Adds a `zarr.experimental` module for unstable user-facing features. ([#3490](https://github.com/zarr-developers/zarr-python/issues/3490)) -- Add a `array.target_shard_size_bytes` to [`zarr.config`][] to allow users to set a maximum number of bytes per-shard when `shards="auto"` in, for example, [`zarr.create_array`][]. ([#3547](https://github.com/zarr-developers/zarr-python/issues/3547)) -- Make `async_array` on the [`zarr.Array`][] class public (`_async_array` will remain untouched, but its stability is not guaranteed). ([#3556](https://github.com/zarr-developers/zarr-python/issues/3556)) + New types have been added to `zarr.types` to help with this. ([#3304](https://github.com/zarr-developers/zarr-python/pull/3304)) +- Adds `zarr.experimental.cache_store.CacheStore`, a `Store` that implements caching by combining two other `Store` instances. See the [docs page](https://zarr.readthedocs.io/en/latest/user-guide/experimental#cachestore) for more information about this feature. ([#3366](https://github.com/zarr-developers/zarr-python/pull/3366)) +- Adds a `zarr.experimental` module for unstable user-facing features. ([#3490](https://github.com/zarr-developers/zarr-python/pull/3490)) +- Add a `array.target_shard_size_bytes` to [`zarr.config`][] to allow users to set a maximum number of bytes per-shard when `shards="auto"` in, for example, [`zarr.create_array`][]. ([#3547](https://github.com/zarr-developers/zarr-python/pull/3547)) +- Make `async_array` on the [`zarr.Array`][] class public (`_async_array` will remain untouched, but its stability is not guaranteed). ([#3556](https://github.com/zarr-developers/zarr-python/pull/3556)) ### Bugfixes -- Fix a bug that prevented `PCodec` from being properly resolved when loading arrays using that compressor. ([#3483](https://github.com/zarr-developers/zarr-python/issues/3483)) +- Fix a bug that prevented `PCodec` from being properly resolved when loading arrays using that compressor. ([#3483](https://github.com/zarr-developers/zarr-python/pull/3483)) - Fixed a bug that prevented Zarr Python from opening Zarr V3 array metadata documents that contained - extra keys with permissible values (dicts with a `"must_understand"` key set to `"false"`). ([#3530](https://github.com/zarr-developers/zarr-python/issues/3530)) + extra keys with permissible values (dicts with a `"must_understand"` key set to `"false"`). ([#3530](https://github.com/zarr-developers/zarr-python/pull/3530)) - Fixed a bug where the `"consolidated_metadata"` key was written to metadata documents even when - consolidated metadata was not used, resulting in invalid metadata documents. ([#3535](https://github.com/zarr-developers/zarr-python/issues/3535)) + consolidated metadata was not used, resulting in invalid metadata documents. ([#3535](https://github.com/zarr-developers/zarr-python/pull/3535)) - Improve write performance to large shards by up to 10x. ([#3560](https://github.com/zarr-developers/zarr-python/issues/3560)) ### Improved Documentation -- Use mkdocs-material for Zarr-Python documentation ([#3118](https://github.com/zarr-developers/zarr-python/issues/3118)) +- Use mkdocs-material for Zarr-Python documentation ([#3118](https://github.com/zarr-developers/zarr-python/pull/3118)) - Document different values of StoreLike with examples in the user guide. ([#3303](https://github.com/zarr-developers/zarr-python/issues/3303)) -- Reorganize the top-level `examples` directory to give each example its own sub-directory. Adds content to the docs for each example. ([#3502](https://github.com/zarr-developers/zarr-python/issues/3502)) +- Reorganize the top-level `examples` directory to give each example its own sub-directory. Adds content to the docs for each example. ([#3502](https://github.com/zarr-developers/zarr-python/pull/3502)) - Updated 3.0 Migration Guide to include function signature change to zarr.Array.resize function. ([#3536](https://github.com/zarr-developers/zarr-python/issues/3536)) ### Misc -- [#3515](https://github.com/zarr-developers/zarr-python/issues/3515), [#3532](https://github.com/zarr-developers/zarr-python/issues/3532), [#3533](https://github.com/zarr-developers/zarr-python/issues/3533), [#3553](https://github.com/zarr-developers/zarr-python/issues/3553) +- [#3515](https://github.com/zarr-developers/zarr-python/pull/3515), [#3532](https://github.com/zarr-developers/zarr-python/pull/3532), [#3533](https://github.com/zarr-developers/zarr-python/pull/3533), [#3553](https://github.com/zarr-developers/zarr-python/pull/3553) ## 3.1.3 (2025-09-18) @@ -321,20 +321,20 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr ### Features - Add a command-line interface to migrate v2 Zarr metadata to v3. Corresponding functions are also provided under zarr.metadata. ([#1798](https://github.com/zarr-developers/zarr-python/issues/1798)) -- Add obstore implementation of delete_dir. ([#3310](https://github.com/zarr-developers/zarr-python/issues/3310)) -- Adds a registry for chunk key encodings for extensibility. This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. ([#3436](https://github.com/zarr-developers/zarr-python/issues/3436)) -- Trying to open a group at a path where an array already exists now raises a helpful error. ([#3444](https://github.com/zarr-developers/zarr-python/issues/3444)) +- Add obstore implementation of delete_dir. ([#3310](https://github.com/zarr-developers/zarr-python/pull/3310)) +- Adds a registry for chunk key encodings for extensibility. This allows users to implement a custom `ChunkKeyEncoding`, which can be registered via `register_chunk_key_encoding` or as an entry point under `zarr.chunk_key_encoding`. ([#3436](https://github.com/zarr-developers/zarr-python/pull/3436)) +- Trying to open a group at a path where an array already exists now raises a helpful error. ([#3444](https://github.com/zarr-developers/zarr-python/pull/3444)) ### Bugfixes - Prevents creation of groups (.create_group) or arrays (.create_array) as children of an existing array. ([#2582](https://github.com/zarr-developers/zarr-python/issues/2582)) -- Fix a bug preventing `ones_like`, `full_like`, `empty_like`, `zeros_like` and `open_like` functions from accepting an explicit specification of array attributes like shape, dtype, chunks etc. The functions `full_like`, `empty_like`, and `open_like` now also more consistently infer a `fill_value` parameter from the provided array. ([#2992](https://github.com/zarr-developers/zarr-python/issues/2992)) +- Fix a bug preventing `ones_like`, `full_like`, `empty_like`, `zeros_like` and `open_like` functions from accepting an explicit specification of array attributes like shape, dtype, chunks etc. The functions `full_like`, `empty_like`, and `open_like` now also more consistently infer a `fill_value` parameter from the provided array. ([#2992](https://github.com/zarr-developers/zarr-python/pull/2992)) - LocalStore now uses atomic writes, which should prevent some cases of corrupted data. ([#3411](https://github.com/zarr-developers/zarr-python/issues/3411)) -- Fix a potential race condition when using `zarr.create_array` with the `data` parameter set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for that array. ([#3422](https://github.com/zarr-developers/zarr-python/issues/3422)) -- Fix ChunkGrid definition (broken in 3.1.2) ([#3425](https://github.com/zarr-developers/zarr-python/issues/3425)) -- Ensure syntax like `root['/subgroup']` works equivalently to `root['subgroup']` when using consolidated metadata. ([#3428](https://github.com/zarr-developers/zarr-python/issues/3428)) -- Creating a new group with `zarr.group` no longer errors. This fixes a regression introduced in version 3.1.2. ([#3431](https://github.com/zarr-developers/zarr-python/issues/3431)) -- Setting `fill_value` to a float like `0.0` when the data type of the array is an integer is a common mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python will not create such arrays. ([#3448](https://github.com/zarr-developers/zarr-python/issues/3448)) +- Fix a potential race condition when using `zarr.create_array` with the `data` parameter set to a NumPy array. Previously Zarr was iterating over the newly created array with a granularity that was too low. Now Zarr chooses a granularity that matches the size of the stored objects for that array. ([#3422](https://github.com/zarr-developers/zarr-python/pull/3422)) +- Fix ChunkGrid definition (broken in 3.1.2) ([#3425](https://github.com/zarr-developers/zarr-python/pull/3425)) +- Ensure syntax like `root['/subgroup']` works equivalently to `root['subgroup']` when using consolidated metadata. ([#3428](https://github.com/zarr-developers/zarr-python/pull/3428)) +- Creating a new group with `zarr.group` no longer errors. This fixes a regression introduced in version 3.1.2. ([#3431](https://github.com/zarr-developers/zarr-python/pull/3431)) +- Setting `fill_value` to a float like `0.0` when the data type of the array is an integer is a common mistake. This change lets Zarr Python read arrays with this erroneous metadata, although Zarr Python will not create such arrays. ([#3448](https://github.com/zarr-developers/zarr-python/pull/3448)) ### Deprecations and Removals @@ -342,56 +342,56 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr ### Misc -- [#3376](https://github.com/zarr-developers/zarr-python/issues/3376), [#3390](https://github.com/zarr-developers/zarr-python/issues/3390), [#3403](https://github.com/zarr-developers/zarr-python/issues/3403), [#3449](https://github.com/zarr-developers/zarr-python/issues/3449) +- [#3376](https://github.com/zarr-developers/zarr-python/pull/3376), [#3390](https://github.com/zarr-developers/zarr-python/pull/3390), [#3403](https://github.com/zarr-developers/zarr-python/pull/3403), [#3449](https://github.com/zarr-developers/zarr-python/pull/3449) ## 3.1.2 (2025-08-25) ### Features -- Added support for async vectorized and orthogonal indexing. ([#3083](https://github.com/zarr-developers/zarr-python/issues/3083)) -- Make config param optional in init_array ([#3391](https://github.com/zarr-developers/zarr-python/issues/3391)) +- Added support for async vectorized and orthogonal indexing. ([#3083](https://github.com/zarr-developers/zarr-python/pull/3083)) +- Make config param optional in init_array ([#3391](https://github.com/zarr-developers/zarr-python/pull/3391)) ### Bugfixes - Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value. ([#3144](https://github.com/zarr-developers/zarr-python/issues/3144)) -- Fix a bug in `create_array` caused by iterating over chunk-aligned regions instead of shard-aligned regions when writing data. Additionally, the behavior of `nchunks_initialized` has been adjusted. This function consistently reports the number of chunks present in stored objects, even when the array uses the sharding codec. ([#3299](https://github.com/zarr-developers/zarr-python/issues/3299)) -- Opening an array or group with `mode="r+"` will no longer create new arrays or groups. ([#3307](https://github.com/zarr-developers/zarr-python/issues/3307)) -- Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected. ([#3367](https://github.com/zarr-developers/zarr-python/issues/3367)) -- Ensure passing `config` is handled properly when `open`ing an existing array. ([#3378](https://github.com/zarr-developers/zarr-python/issues/3378)) -- Raise a Zarr-specific error class when a codec can't be found by name when deserializing the given codecs. This avoids hiding this error behind a "not part of a zarr hierarchy" warning. ([#3395](https://github.com/zarr-developers/zarr-python/issues/3395)) +- Fix a bug in `create_array` caused by iterating over chunk-aligned regions instead of shard-aligned regions when writing data. Additionally, the behavior of `nchunks_initialized` has been adjusted. This function consistently reports the number of chunks present in stored objects, even when the array uses the sharding codec. ([#3299](https://github.com/zarr-developers/zarr-python/pull/3299)) +- Opening an array or group with `mode="r+"` will no longer create new arrays or groups. ([#3307](https://github.com/zarr-developers/zarr-python/pull/3307)) +- Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected. ([#3367](https://github.com/zarr-developers/zarr-python/pull/3367)) +- Ensure passing `config` is handled properly when `open`ing an existing array. ([#3378](https://github.com/zarr-developers/zarr-python/pull/3378)) +- Raise a Zarr-specific error class when a codec can't be found by name when deserializing the given codecs. This avoids hiding this error behind a "not part of a zarr hierarchy" warning. ([#3395](https://github.com/zarr-developers/zarr-python/pull/3395)) ### Misc -- [#3098](https://github.com/zarr-developers/zarr-python/issues/3098), [#3288](https://github.com/zarr-developers/zarr-python/issues/3288), [#3318](https://github.com/zarr-developers/zarr-python/issues/3318), [#3368](https://github.com/zarr-developers/zarr-python/issues/3368), [#3371](https://github.com/zarr-developers/zarr-python/issues/3371), [#3372](https://github.com/zarr-developers/zarr-python/issues/3372), [#3374](https://github.com/zarr-developers/zarr-python/issues/3374) +- [#3098](https://github.com/zarr-developers/zarr-python/pull/3098), [#3288](https://github.com/zarr-developers/zarr-python/pull/3288), [#3318](https://github.com/zarr-developers/zarr-python/pull/3318), [#3368](https://github.com/zarr-developers/zarr-python/issues/3368), [#3371](https://github.com/zarr-developers/zarr-python/pull/3371), [#3372](https://github.com/zarr-developers/zarr-python/pull/3372), [#3374](https://github.com/zarr-developers/zarr-python/pull/3374) ## 3.1.1 (2025-07-28) ### Features -- Add lightweight implementations of `.getsize()` and `.getsize_prefix()` for ObjectStore. ([#3227](https://github.com/zarr-developers/zarr-python/issues/3227)) +- Add lightweight implementations of `.getsize()` and `.getsize_prefix()` for ObjectStore. ([#3227](https://github.com/zarr-developers/zarr-python/pull/3227)) ### Bugfixes -- Creating a Zarr format 2 array with the `order` keyword argument no longer raises a warning. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) -- Fixed the error message when passing both `config` and `write_empty_chunks` arguments to reflect the current behaviour (`write_empty_chunks` takes precedence). ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) -- Creating a Zarr format 3 array with the `order` argument now consistently ignores this argument and raises a warning. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) -- When using [`from_array`][zarr.api.asynchronous.from_array] to copy a Zarr format 2 array to a Zarr format 3 array, if the memory order of the input array is `"F"` a warning is raised and the order ignored. This is because Zarr format 3 arrays are always stored in "C" order. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) -- The `config` argument to [`zarr.create`][zarr.create] (and functions that create arrays) is now used - previously it had no effect. ([#3112](https://github.com/zarr-developers/zarr-python/issues/3112)) -- Ensure that all abstract methods of [`ZDType`][zarr.core.dtype.ZDType] raise a `NotImplementedError` when invoked. ([#3251](https://github.com/zarr-developers/zarr-python/issues/3251)) -- Register 'gpu' marker with pytest for downstream StoreTests. ([#3258](https://github.com/zarr-developers/zarr-python/issues/3258)) +- Creating a Zarr format 2 array with the `order` keyword argument no longer raises a warning. ([#3112](https://github.com/zarr-developers/zarr-python/pull/3112)) +- Fixed the error message when passing both `config` and `write_empty_chunks` arguments to reflect the current behaviour (`write_empty_chunks` takes precedence). ([#3112](https://github.com/zarr-developers/zarr-python/pull/3112)) +- Creating a Zarr format 3 array with the `order` argument now consistently ignores this argument and raises a warning. ([#3112](https://github.com/zarr-developers/zarr-python/pull/3112)) +- When using [`from_array`][zarr.api.asynchronous.from_array] to copy a Zarr format 2 array to a Zarr format 3 array, if the memory order of the input array is `"F"` a warning is raised and the order ignored. This is because Zarr format 3 arrays are always stored in "C" order. ([#3112](https://github.com/zarr-developers/zarr-python/pull/3112)) +- The `config` argument to [`zarr.create`][zarr.create] (and functions that create arrays) is now used - previously it had no effect. ([#3112](https://github.com/zarr-developers/zarr-python/pull/3112)) +- Ensure that all abstract methods of [`ZDType`][zarr.core.dtype.ZDType] raise a `NotImplementedError` when invoked. ([#3251](https://github.com/zarr-developers/zarr-python/pull/3251)) +- Register 'gpu' marker with pytest for downstream StoreTests. ([#3258](https://github.com/zarr-developers/zarr-python/pull/3258)) - Expand the range of types accepted by `parse_data_type` to include strings and Sequences. -- Move the functionality of `zarr.core.dtype.parse_data_type` to a new function called `zarr.dtype.parse_dtype`. This change ensures that nomenclature is consistent across the codebase. `zarr.core.dtype.parse_data_type` remains, so this change is not breaking. ([#3264](https://github.com/zarr-developers/zarr-python/issues/3264)) -- Fix a regression introduced in 3.1.0 that prevented `inf`, `-inf`, and `nan` values from being stored in `attributes`. ([#3280](https://github.com/zarr-developers/zarr-python/issues/3280)) -- Fixes [`Group.nmembers()`][zarr.Group.nmembers] ignoring depth when using consolidated metadata. ([#3287](https://github.com/zarr-developers/zarr-python/issues/3287)) +- Move the functionality of `zarr.core.dtype.parse_data_type` to a new function called `zarr.dtype.parse_dtype`. This change ensures that nomenclature is consistent across the codebase. `zarr.core.dtype.parse_data_type` remains, so this change is not breaking. ([#3264](https://github.com/zarr-developers/zarr-python/pull/3264)) +- Fix a regression introduced in 3.1.0 that prevented `inf`, `-inf`, and `nan` values from being stored in `attributes`. ([#3280](https://github.com/zarr-developers/zarr-python/pull/3280)) +- Fixes [`Group.nmembers()`][zarr.Group.nmembers] ignoring depth when using consolidated metadata. ([#3287](https://github.com/zarr-developers/zarr-python/pull/3287)) ### Improved Documentation -- Expand the data type docs to include a demonstration of the `parse_data_type` function. Expand the docstring for the `parse_data_type` function. ([#3249](https://github.com/zarr-developers/zarr-python/issues/3249)) -- Add a section on codecs to the migration guide. ([#3273](https://github.com/zarr-developers/zarr-python/issues/3273)) +- Expand the data type docs to include a demonstration of the `parse_data_type` function. Expand the docstring for the `parse_data_type` function. ([#3249](https://github.com/zarr-developers/zarr-python/pull/3249)) +- Add a section on codecs to the migration guide. ([#3273](https://github.com/zarr-developers/zarr-python/pull/3273)) ### Misc -- Remove warnings about vlen-utf8 and vlen-bytes codecs ([#3268](https://github.com/zarr-developers/zarr-python/issues/3268)) +- Remove warnings about vlen-utf8 and vlen-bytes codecs ([#3268](https://github.com/zarr-developers/zarr-python/pull/3268)) ## 3.1.0 (2025-07-14) @@ -444,13 +444,13 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr method can be used to generate either a string, or dictionary that has a string `name` field, that represents the string value previously associated with that `enum`. - For more on this new feature, see the [documentation](user-guide/data_types.md) ([#2874](https://github.com/zarr-developers/zarr-python/issues/2874)) + For more on this new feature, see the [documentation](user-guide/data_types.md) ([#2874](https://github.com/zarr-developers/zarr-python/pull/2874)) -- Added `NDBuffer.empty` method for faster ndbuffer initialization. ([#3191](https://github.com/zarr-developers/zarr-python/issues/3191)) +- Added `NDBuffer.empty` method for faster ndbuffer initialization. ([#3191](https://github.com/zarr-developers/zarr-python/pull/3191)) -- The minimum version of NumPy has increased to 1.26. ([#3226](https://github.com/zarr-developers/zarr-python/issues/3226)) +- The minimum version of NumPy has increased to 1.26. ([#3226](https://github.com/zarr-developers/zarr-python/pull/3226)) -- Add an alternate `from_array_metadata_and_store` constructor to `CodecPipeline`. ([#3233](https://github.com/zarr-developers/zarr-python/issues/3233)) +- Add an alternate `from_array_metadata_and_store` constructor to `CodecPipeline`. ([#3233](https://github.com/zarr-developers/zarr-python/pull/3233)) ### Bugfixes @@ -459,28 +459,28 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - Brings the `VariableLengthUTF8` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8 - Disallows creation of 0-length fixed-length data types - Adds a regression test for the `VariableLengthUTF8` data type that checks against version 3.0.8 - - Allows users to request the `VariableLengthUTF8` data type with `str`, `"str"`, or `"string"`. ([#3170](https://github.com/zarr-developers/zarr-python/issues/3170)) + - Allows users to request the `VariableLengthUTF8` data type with `str`, `"str"`, or `"string"`. ([#3170](https://github.com/zarr-developers/zarr-python/pull/3170)) -- Add human readable size for No. bytes stored to `info_complete` ([#3190](https://github.com/zarr-developers/zarr-python/issues/3190)) +- Add human readable size for No. bytes stored to `info_complete` ([#3190](https://github.com/zarr-developers/zarr-python/pull/3190)) - Restores the ability to create a Zarr V2 array with a `null` fill value by introducing a new class `DefaultFillValue`, and setting the default value of the `fill_value` parameter in array creation routines to an instance of `DefaultFillValue`. For Zarr V3 arrays, `None` will act as an - alias for a `DefaultFillValue` instance, thus preserving compatibility with existing code. ([#3198](https://github.com/zarr-developers/zarr-python/issues/3198)) + alias for a `DefaultFillValue` instance, thus preserving compatibility with existing code. ([#3198](https://github.com/zarr-developers/zarr-python/pull/3198)) - Fix the type of `ArrayV2Metadata.codec` to constrain it to `numcodecs.abc.Codec | None`. Previously the type was more permissive, allowing objects that can be parsed into Codecs (e.g., the codec name). - The constructor of `ArrayV2Metadata` still allows the permissive input when creating new objects. ([#3232](https://github.com/zarr-developers/zarr-python/issues/3232)) + The constructor of `ArrayV2Metadata` still allows the permissive input when creating new objects. ([#3232](https://github.com/zarr-developers/zarr-python/pull/3232)) ### Improved Documentation - Add a self-contained example of data type extension to the `examples` directory, and expanded - the documentation for data types. ([#3157](https://github.com/zarr-developers/zarr-python/issues/3157)) + the documentation for data types. ([#3157](https://github.com/zarr-developers/zarr-python/pull/3157)) - Add a description on how to create a RemoteStore of a specific filesystem to the `Remote Store` section in `docs/user-guide/storage.md`. State in the docstring of `FsspecStore.from_url` that the filesystem type is inferred from the URL scheme. - It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. ([#3212](https://github.com/zarr-developers/zarr-python/issues/3212)) + It should help a user handling the case when the type of FsspecStore doesn't match the URL scheme. ([#3212](https://github.com/zarr-developers/zarr-python/pull/3212)) ### Deprecations and Removals @@ -499,7 +499,7 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr This change also adds an extra validation step to the creation of Zarr V2 arrays, which ensures that arrays with a `VariableLengthUTF8` or `VariableLengthBytes` data type cannot be created without the - correct "object codec". ([#3228](https://github.com/zarr-developers/zarr-python/issues/3228)) + correct "object codec". ([#3228](https://github.com/zarr-developers/zarr-python/pull/3228)) - Removes support for passing keyword-only arguments positionally to the following functions and methods: `save_array`, `open`, `group`, `open_group`, `create`, `get_basic_selection`, `set_basic_selection`, @@ -516,27 +516,27 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr ### Bugfixes - Removed an unnecessary check from `_fsspec._make_async` that would raise an exception when - creating a read-only store backed by a local file system with `auto_mkdir` set to `False`. ([#3193](https://github.com/zarr-developers/zarr-python/issues/3193)) + creating a read-only store backed by a local file system with `auto_mkdir` set to `False`. ([#3193](https://github.com/zarr-developers/zarr-python/pull/3193)) -- Add missing import for AsyncFileSystemWrapper for _make_async in _fsspec.py ([#3195](https://github.com/zarr-developers/zarr-python/issues/3195)) +- Add missing import for AsyncFileSystemWrapper for _make_async in _fsspec.py ([#3195](https://github.com/zarr-developers/zarr-python/pull/3195)) ## 3.0.9 (2025-06-30) ### Features -- Add `zarr.storage.FsspecStore.from_mapper()` so that `zarr.open()` supports stores of type `fsspec.mapping.FSMap`. ([#2774](https://github.com/zarr-developers/zarr-python/issues/2774)) +- Add `zarr.storage.FsspecStore.from_mapper()` so that `zarr.open()` supports stores of type `fsspec.mapping.FSMap`. ([#2774](https://github.com/zarr-developers/zarr-python/pull/2774)) -- Implemented `move` for `LocalStore` and `ZipStore`. This allows users to move the store to a different root path. ([#3021](https://github.com/zarr-developers/zarr-python/issues/3021)) +- Implemented `move` for `LocalStore` and `ZipStore`. This allows users to move the store to a different root path. ([#3021](https://github.com/zarr-developers/zarr-python/pull/3021)) -- Added `zarr.errors.GroupNotFoundError`, which is raised when attempting to open a group that does not exist. ([#3066](https://github.com/zarr-developers/zarr-python/issues/3066)) +- Added `zarr.errors.GroupNotFoundError`, which is raised when attempting to open a group that does not exist. ([#3066](https://github.com/zarr-developers/zarr-python/pull/3066)) -- Adds `fill_value` to the list of attributes displayed in the output of the `AsyncArray.info()` method. ([#3081](https://github.com/zarr-developers/zarr-python/issues/3081)) +- Adds `fill_value` to the list of attributes displayed in the output of the `AsyncArray.info()` method. ([#3081](https://github.com/zarr-developers/zarr-python/pull/3081)) -- Use `numpy.zeros` instead of `np.full` for a performance speedup when creating a `zarr.core.buffer.NDBuffer` with `fill_value=0`. ([#3082](https://github.com/zarr-developers/zarr-python/issues/3082)) +- Use `numpy.zeros` instead of `np.full` for a performance speedup when creating a `zarr.core.buffer.NDBuffer` with `fill_value=0`. ([#3082](https://github.com/zarr-developers/zarr-python/pull/3082)) -- Port more stateful testing actions from [Icechunk](https://icechunk.io). ([#3130](https://github.com/zarr-developers/zarr-python/issues/3130)) +- Port more stateful testing actions from [Icechunk](https://icechunk.io/en/stable/). ([#3130](https://github.com/zarr-developers/zarr-python/pull/3130)) -- Adds a `with_read_only` convenience method to the `Store` abstract base class (raises `NotImplementedError`) and implementations to the `MemoryStore`, `ObjectStore`, `LocalStore`, and `FsspecStore` classes. ([#3138](https://github.com/zarr-developers/zarr-python/issues/3138)) +- Adds a `with_read_only` convenience method to the `Store` abstract base class (raises `NotImplementedError`) and implementations to the `MemoryStore`, `ObjectStore`, `LocalStore`, and `FsspecStore` classes. ([#3138](https://github.com/zarr-developers/zarr-python/pull/3138)) ### Bugfixes @@ -544,7 +544,7 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr - For Zarr format 2, allow fixed-length string arrays to be created without automatically inserting a `Vlen-UT8` codec in the array of filters. Fixed-length string arrays do not need this codec. This - change fixes a regression where fixed-length string arrays created with Zarr Python 3 could not be read with Zarr Python 2.18. ([#3100](https://github.com/zarr-developers/zarr-python/issues/3100)) + change fixes a regression where fixed-length string arrays created with Zarr Python 3 could not be read with Zarr Python 2.18. ([#3100](https://github.com/zarr-developers/zarr-python/pull/3100)) - When creating arrays without explicitly specifying a chunk size using `zarr.create` and other array creation routines, the chunk size will now set automatically instead of defaulting to the data shape. @@ -552,12 +552,12 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr To retain previous behaviour, explicitly set the chunk shape to the data shape. This fix matches the existing chunking behaviour of - `zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. ([#3103](https://github.com/zarr-developers/zarr-python/issues/3103)) + `zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`. ([#3103](https://github.com/zarr-developers/zarr-python/pull/3103)) - When `zarr.save` has an argument `path=some/path/` and multiple arrays in `args`, the path resulted in `some/path/some/path` due to using the `path` - argument twice while building the array path. This is now fixed. ([#3127](https://github.com/zarr-developers/zarr-python/issues/3127)) + argument twice while building the array path. This is now fixed. ([#3127](https://github.com/zarr-developers/zarr-python/pull/3127)) -- Fix `zarr.open` default for argument `mode` when `store` is `read_only` ([#3128](https://github.com/zarr-developers/zarr-python/issues/3128)) +- Fix `zarr.open` default for argument `mode` when `store` is `read_only` ([#3128](https://github.com/zarr-developers/zarr-python/pull/3128)) - Suppress `FileNotFoundError` when deleting non-existent keys in the `obstore` adapter. @@ -566,9 +566,9 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr raise a `FileNotFoundError` if the chunk doesn't already exist. Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store, suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect - from the store. ([#3140](https://github.com/zarr-developers/zarr-python/issues/3140)) + from the store. ([#3140](https://github.com/zarr-developers/zarr-python/pull/3140)) -- Trying to open a StorePath/Array with `mode='r'` when the store is not read-only creates a read-only copy of the store. ([#3156](https://github.com/zarr-developers/zarr-python/issues/3156)) +- Trying to open a StorePath/Array with `mode='r'` when the store is not read-only creates a read-only copy of the store. ([#3156](https://github.com/zarr-developers/zarr-python/pull/3156)) ## 3.0.8 (2025-05-19) @@ -578,195 +578,195 @@ a `ManagedMemoryStore` is used. ([#3944](https://github.com/zarr-developers/zarr ### Features -- Added a `print_debug_info` function for bug reports. ([#2913](https://github.com/zarr-developers/zarr-python/issues/2913)) +- Added a `print_debug_info` function for bug reports. ([#2913](https://github.com/zarr-developers/zarr-python/pull/2913)) ### Bugfixes -- Fix a bug that prevented the number of initialized chunks being counted properly. ([#2862](https://github.com/zarr-developers/zarr-python/issues/2862)) -- Fixed sharding with GPU buffers. ([#2978](https://github.com/zarr-developers/zarr-python/issues/2978)) +- Fix a bug that prevented the number of initialized chunks being counted properly. ([#2862](https://github.com/zarr-developers/zarr-python/pull/2862)) +- Fixed sharding with GPU buffers. ([#2978](https://github.com/zarr-developers/zarr-python/pull/2978)) - Fix structured `dtype` fill value serialization for consolidated metadata ([#2998](https://github.com/zarr-developers/zarr-python/issues/2998)) - It is now possible to specify no compressor when creating a zarr format 2 array. This can be done by passing `compressor=None` to the various array creation routines. The default behaviour of automatically choosing a suitable default compressor remains if the compressor argument is not given. - To reproduce the behaviour in previous zarr-python versions when `compressor=None` was passed, pass `compressor='auto'` instead. ([#3039](https://github.com/zarr-developers/zarr-python/issues/3039)) + To reproduce the behaviour in previous zarr-python versions when `compressor=None` was passed, pass `compressor='auto'` instead. ([#3039](https://github.com/zarr-developers/zarr-python/pull/3039)) -- Fixed the typing of `dimension_names` arguments throughout so that it now accepts iterables that contain `None` alongside `str`. ([#3045](https://github.com/zarr-developers/zarr-python/issues/3045)) -- Using various functions to open data with `mode='a'` no longer deletes existing data in the store. ([#3062](https://github.com/zarr-developers/zarr-python/issues/3062)) -- Internally use `typesize` constructor parameter for `numcodecs.blosc.Blosc` to improve compression ratios back to the v2-package levels. ([#2962](https://github.com/zarr-developers/zarr-python/issues/2962)) +- Fixed the typing of `dimension_names` arguments throughout so that it now accepts iterables that contain `None` alongside `str`. ([#3045](https://github.com/zarr-developers/zarr-python/pull/3045)) +- Using various functions to open data with `mode='a'` no longer deletes existing data in the store. ([#3062](https://github.com/zarr-developers/zarr-python/pull/3062)) +- Internally use `typesize` constructor parameter for `numcodecs.blosc.Blosc` to improve compression ratios back to the v2-package levels. ([#2962](https://github.com/zarr-developers/zarr-python/pull/2962)) - Specifying the memory order of Zarr format 2 arrays using the `order` keyword argument has been fixed. ([#2950](https://github.com/zarr-developers/zarr-python/issues/2950)) ### Misc -- [#2972](https://github.com/zarr-developers/zarr-python/issues/2972), [#3027](https://github.com/zarr-developers/zarr-python/issues/3027), [#3049](https://github.com/zarr-developers/zarr-python/issues/3049) +- [#2972](https://github.com/zarr-developers/zarr-python/pull/2972), [#3027](https://github.com/zarr-developers/zarr-python/pull/3027), [#3049](https://github.com/zarr-developers/zarr-python/pull/3049) ## 3.0.7 (2025-04-22) ### Features -- Add experimental ObjectStore storage class based on obstore. ([#1661](https://github.com/zarr-developers/zarr-python/issues/1661)) -- Add `zarr.from_array` using concurrent streaming of source data ([#2622](https://github.com/zarr-developers/zarr-python/issues/2622)) +- Add experimental ObjectStore storage class based on obstore. ([#1661](https://github.com/zarr-developers/zarr-python/pull/1661)) +- Add `zarr.from_array` using concurrent streaming of source data ([#2622](https://github.com/zarr-developers/zarr-python/pull/2622)) ### Bugfixes - 0-dimensional arrays are now returning a scalar. Therefore, the return type of `__getitem__` changed to NDArrayLikeOrScalar. This change is to make the behavior of 0-dimensional arrays consistent with - `numpy` scalars. ([#2718](https://github.com/zarr-developers/zarr-python/issues/2718)) -- Fix `fill_value` serialization for `NaN` in `ArrayV2Metadata` and add property-based testing of round-trip serialization ([#2802](https://github.com/zarr-developers/zarr-python/issues/2802)) + `numpy` scalars. ([#2718](https://github.com/zarr-developers/zarr-python/pull/2718)) +- Fix `fill_value` serialization for `NaN` in `ArrayV2Metadata` and add property-based testing of round-trip serialization ([#2802](https://github.com/zarr-developers/zarr-python/pull/2802)) - Fixes `ConsolidatedMetadata` serialization of `nan`, `inf`, and `-inf` to be - consistent with the behavior of `ArrayMetadata`. ([#2996](https://github.com/zarr-developers/zarr-python/issues/2996)) + consistent with the behavior of `ArrayMetadata`. ([#2996](https://github.com/zarr-developers/zarr-python/pull/2996)) ### Improved Documentation -- Updated the 3.0 migration guide to include the removal of "." syntax for getting group members. ([#2991](https://github.com/zarr-developers/zarr-python/issues/2991), [#2997](https://github.com/zarr-developers/zarr-python/issues/2997)) +- Updated the 3.0 migration guide to include the removal of "." syntax for getting group members. ([#2991](https://github.com/zarr-developers/zarr-python/issues/2991), [#2997](https://github.com/zarr-developers/zarr-python/pull/2997)) ### Misc - Define a new versioning policy based on Effective Effort Versioning. This replaces the old Semantic - Versioning-based policy. ([#2924](https://github.com/zarr-developers/zarr-python/issues/2924), [#2910](https://github.com/zarr-developers/zarr-python/issues/2910)) + Versioning-based policy. ([#2924](https://github.com/zarr-developers/zarr-python/issues/2924), [#2910](https://github.com/zarr-developers/zarr-python/pull/2910)) - Make warning filters in the tests more specific, so warnings emitted by tests added in the future - are more likely to be caught instead of ignored. ([#2714](https://github.com/zarr-developers/zarr-python/issues/2714)) -- Avoid an unnecessary memory copy when writing Zarr to a local file ([#2944](https://github.com/zarr-developers/zarr-python/issues/2944)) + are more likely to be caught instead of ignored. ([#2714](https://github.com/zarr-developers/zarr-python/pull/2714)) +- Avoid an unnecessary memory copy when writing Zarr to a local file ([#2944](https://github.com/zarr-developers/zarr-python/pull/2944)) ## 3.0.6 (2025-03-20) ### Bugfixes -- Restore functionality of `del z.attrs['key']` to actually delete the key. ([#2908](https://github.com/zarr-developers/zarr-python/issues/2908)) +- Restore functionality of `del z.attrs['key']` to actually delete the key. ([#2908](https://github.com/zarr-developers/zarr-python/pull/2908)) ## 3.0.5 (2025-03-07) ### Bugfixes - Fixed a bug where `StorePath` creation would not apply standard path normalization to the `path` parameter, - which led to the creation of arrays and groups with invalid keys. ([#2850](https://github.com/zarr-developers/zarr-python/issues/2850)) -- Prevent update_attributes calls from deleting old attributes ([#2870](https://github.com/zarr-developers/zarr-python/issues/2870)) + which led to the creation of arrays and groups with invalid keys. ([#2850](https://github.com/zarr-developers/zarr-python/pull/2850)) +- Prevent update_attributes calls from deleting old attributes ([#2870](https://github.com/zarr-developers/zarr-python/pull/2870)) ### Misc -- [#2796](https://github.com/zarr-developers/zarr-python/issues/2796) +- [#2796](https://github.com/zarr-developers/zarr-python/pull/2796) ## 3.0.4 (2025-02-23) ### Features -- Adds functions for concurrently creating multiple arrays and groups. ([#2665](https://github.com/zarr-developers/zarr-python/issues/2665)) +- Adds functions for concurrently creating multiple arrays and groups. ([#2665](https://github.com/zarr-developers/zarr-python/pull/2665)) ### Bugfixes -- Fixed a bug where `ArrayV2Metadata` could save `filters` as an empty array. ([#2847](https://github.com/zarr-developers/zarr-python/issues/2847)) -- Fix a bug when setting values of a smaller last chunk. ([#2851](https://github.com/zarr-developers/zarr-python/issues/2851)) +- Fixed a bug where `ArrayV2Metadata` could save `filters` as an empty array. ([#2847](https://github.com/zarr-developers/zarr-python/pull/2847)) +- Fix a bug when setting values of a smaller last chunk. ([#2851](https://github.com/zarr-developers/zarr-python/pull/2851)) ### Misc -- [#2828](https://github.com/zarr-developers/zarr-python/issues/2828) +- [#2828](https://github.com/zarr-developers/zarr-python/pull/2828) ## 3.0.3 (2025-02-14) ### Features -- Improves performance of FsspecStore.delete_dir for remote filesystems supporting concurrent/batched deletes, e.g., s3fs. ([#2661](https://github.com/zarr-developers/zarr-python/issues/2661)) -- Added `zarr.config.enable_gpu` to update Zarr's configuration to use GPUs. ([#2751](https://github.com/zarr-developers/zarr-python/issues/2751)) -- Avoid reading chunks during writes where possible. [#757](https://github.com/zarr-developers/zarr-python/issues/757) ([#2784](https://github.com/zarr-developers/zarr-python/issues/2784)) -- `LocalStore` learned to `delete_dir`. This makes array and group deletes more efficient. ([#2804](https://github.com/zarr-developers/zarr-python/issues/2804)) -- Add `zarr.testing.strategies.array_metadata` to generate ArrayV2Metadata and ArrayV3Metadata instances. ([#2813](https://github.com/zarr-developers/zarr-python/issues/2813)) -- Add arbitrary `shards` to Hypothesis strategy for generating arrays. ([#2822](https://github.com/zarr-developers/zarr-python/issues/2822)) +- Improves performance of FsspecStore.delete_dir for remote filesystems supporting concurrent/batched deletes, e.g., s3fs. ([#2661](https://github.com/zarr-developers/zarr-python/pull/2661)) +- Added `zarr.config.enable_gpu` to update Zarr's configuration to use GPUs. ([#2751](https://github.com/zarr-developers/zarr-python/pull/2751)) +- Avoid reading chunks during writes where possible. [#757](https://github.com/zarr-developers/zarr-python/issues/757) ([#2784](https://github.com/zarr-developers/zarr-python/pull/2784)) +- `LocalStore` learned to `delete_dir`. This makes array and group deletes more efficient. ([#2804](https://github.com/zarr-developers/zarr-python/pull/2804)) +- Add `zarr.testing.strategies.array_metadata` to generate ArrayV2Metadata and ArrayV3Metadata instances. ([#2813](https://github.com/zarr-developers/zarr-python/pull/2813)) +- Add arbitrary `shards` to Hypothesis strategy for generating arrays. ([#2822](https://github.com/zarr-developers/zarr-python/pull/2822)) ### Bugfixes -- Fixed bug with Zarr using device memory, instead of host memory, for storing metadata when using GPUs. ([#2751](https://github.com/zarr-developers/zarr-python/issues/2751)) +- Fixed bug with Zarr using device memory, instead of host memory, for storing metadata when using GPUs. ([#2751](https://github.com/zarr-developers/zarr-python/pull/2751)) - The array returned by `zarr.empty` and an empty `zarr.core.buffer.cpu.NDBuffer` will now be filled with the specified fill value, or with zeros if no fill value is provided. - This fixes a bug where Zarr format 2 data with no fill value was written with un-predictable chunk sizes. ([#2755](https://github.com/zarr-developers/zarr-python/issues/2755)) -- Fix zip-store path checking for stores with directories listed as files. ([#2758](https://github.com/zarr-developers/zarr-python/issues/2758)) -- Use removeprefix rather than replace when removing filename prefixes in `FsspecStore.list` ([#2778](https://github.com/zarr-developers/zarr-python/issues/2778)) -- Enable automatic removal of `needs release notes` with labeler action ([#2781](https://github.com/zarr-developers/zarr-python/issues/2781)) -- Use the proper label config ([#2785](https://github.com/zarr-developers/zarr-python/issues/2785)) -- Alters the behavior of `create_array` to ensure that any groups implied by the array's name are created if they do not already exist. Also simplifies the type signature for any function that takes an ArrayConfig-like object. ([#2795](https://github.com/zarr-developers/zarr-python/issues/2795)) -- Enitialise empty chunks to the default fill value during writing and add default fill values for datetime, timedelta, structured, and other (void* fixed size) data types ([#2799](https://github.com/zarr-developers/zarr-python/issues/2799)) -- Ensure utf8 compliant strings are used to construct numpy arrays in property-based tests ([#2801](https://github.com/zarr-developers/zarr-python/issues/2801)) -- Fix pickling for ZipStore ([#2807](https://github.com/zarr-developers/zarr-python/issues/2807)) -- Update numcodecs to not overwrite codec configuration ever. Closes [#2800](https://github.com/zarr-developers/zarr-python/issues/2800). ([#2811](https://github.com/zarr-developers/zarr-python/issues/2811)) -- Fix fancy indexing (e.g. arr[5, [0, 1]]) with the sharding codec ([#2817](https://github.com/zarr-developers/zarr-python/issues/2817)) + This fixes a bug where Zarr format 2 data with no fill value was written with un-predictable chunk sizes. ([#2755](https://github.com/zarr-developers/zarr-python/pull/2755)) +- Fix zip-store path checking for stores with directories listed as files. ([#2758](https://github.com/zarr-developers/zarr-python/pull/2758)) +- Use removeprefix rather than replace when removing filename prefixes in `FsspecStore.list` ([#2778](https://github.com/zarr-developers/zarr-python/pull/2778)) +- Enable automatic removal of `needs release notes` with labeler action ([#2781](https://github.com/zarr-developers/zarr-python/pull/2781)) +- Use the proper label config ([#2785](https://github.com/zarr-developers/zarr-python/pull/2785)) +- Alters the behavior of `create_array` to ensure that any groups implied by the array's name are created if they do not already exist. Also simplifies the type signature for any function that takes an ArrayConfig-like object. ([#2795](https://github.com/zarr-developers/zarr-python/pull/2795)) +- Enitialise empty chunks to the default fill value during writing and add default fill values for datetime, timedelta, structured, and other (void* fixed size) data types ([#2799](https://github.com/zarr-developers/zarr-python/pull/2799)) +- Ensure utf8 compliant strings are used to construct numpy arrays in property-based tests ([#2801](https://github.com/zarr-developers/zarr-python/pull/2801)) +- Fix pickling for ZipStore ([#2807](https://github.com/zarr-developers/zarr-python/pull/2807)) +- Update numcodecs to not overwrite codec configuration ever. Closes [#2800](https://github.com/zarr-developers/zarr-python/issues/2800). ([#2811](https://github.com/zarr-developers/zarr-python/pull/2811)) +- Fix fancy indexing (e.g. arr[5, [0, 1]]) with the sharding codec ([#2817](https://github.com/zarr-developers/zarr-python/pull/2817)) ### Improved Documentation -- Added new user guide on GPU. ([#2751](https://github.com/zarr-developers/zarr-python/issues/2751)) +- Added new user guide on GPU. ([#2751](https://github.com/zarr-developers/zarr-python/pull/2751)) ## 3.0.2 (2025-01-31) ### Features -- Test `getsize()` and `getsize_prefix()` in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Test that a `ValueError` is raised for invalid byte range syntax in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Separate instantiating and opening a store in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Add a test for using Stores as context managers in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Implemented `LoggingStore.open()`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- `LoggingStore` is now a generic class. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Test `getsize()` and `getsize_prefix()` in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Test that a `ValueError` is raised for invalid byte range syntax in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Separate instantiating and opening a store in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Add a test for using Stores as context managers in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Implemented `LoggingStore.open()`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- `LoggingStore` is now a generic class. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) - Change StoreTest's `test_store_repr`, `test_store_supports_writes`, `test_store_supports_partial_writes`, and `test_store_supports_listing` - to be implemented using `@abstractmethod`, rather than raising `NotImplementedError`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Test the error raised for invalid buffer arguments in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Test that data can be written to a store that's not yet open using the store.set method in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) + to be implemented using `@abstractmethod`, rather than raising `NotImplementedError`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Test the error raised for invalid buffer arguments in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Test that data can be written to a store that's not yet open using the store.set method in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) - Adds a new function `init_array` for initializing an array in storage, and refactors `create_array` to use `init_array`. `create_array` takes two new parameters: `data`, an optional array-like object, and `write_data`, a bool which defaults to `True`. If `data` is given to `create_array`, then the `dtype` and `shape` attributes of `data` are used to define the corresponding attributes of the resulting Zarr array. Additionally, if `data` is given and `write_data` is `True`, - then the values in `data` will be written to the newly created array. ([#2761](https://github.com/zarr-developers/zarr-python/issues/2761)) + then the values in `data` will be written to the newly created array. ([#2761](https://github.com/zarr-developers/zarr-python/pull/2761)) ### Bugfixes -- Wrap sync fsspec filesystems with `AsyncFileSystemWrapper`. ([#2533](https://github.com/zarr-developers/zarr-python/issues/2533)) -- Added backwards compatibility for Zarr format 2 structured arrays. ([#2681](https://github.com/zarr-developers/zarr-python/issues/2681)) -- Update equality for `LoggingStore` and `WrapperStore` such that 'other' must also be a `LoggingStore` or `WrapperStore` respectively, rather than only checking the types of the stores they wrap. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Ensure that `ZipStore` is open before getting or setting any values. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Use stdout rather than stderr as the default stream for `LoggingStore`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) -- Match the errors raised by read only stores in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/issues/2693)) +- Wrap sync fsspec filesystems with `AsyncFileSystemWrapper`. ([#2533](https://github.com/zarr-developers/zarr-python/pull/2533)) +- Added backwards compatibility for Zarr format 2 structured arrays. ([#2681](https://github.com/zarr-developers/zarr-python/pull/2681)) +- Update equality for `LoggingStore` and `WrapperStore` such that 'other' must also be a `LoggingStore` or `WrapperStore` respectively, rather than only checking the types of the stores they wrap. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Ensure that `ZipStore` is open before getting or setting any values. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Use stdout rather than stderr as the default stream for `LoggingStore`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) +- Match the errors raised by read only stores in `StoreTests`. ([#2693](https://github.com/zarr-developers/zarr-python/pull/2693)) - Fixed `ZipStore` to make sure the correct attributes are saved when instances are pickled. - This fixes a previous bug that prevented using `ZipStore` with a `ProcessPoolExecutor`. ([#2762](https://github.com/zarr-developers/zarr-python/issues/2762)) -- Updated the optional test dependencies to include `botocore` and `fsspec`. ([#2768](https://github.com/zarr-developers/zarr-python/issues/2768)) + This fixes a previous bug that prevented using `ZipStore` with a `ProcessPoolExecutor`. ([#2762](https://github.com/zarr-developers/zarr-python/pull/2762)) +- Updated the optional test dependencies to include `botocore` and `fsspec`. ([#2768](https://github.com/zarr-developers/zarr-python/pull/2768)) - Fixed the fsspec tests to skip if `botocore` is not installed. - Previously they would have failed with an import error. ([#2768](https://github.com/zarr-developers/zarr-python/issues/2768)) -- Optimize full chunk writes. ([#2782](https://github.com/zarr-developers/zarr-python/issues/2782)) + Previously they would have failed with an import error. ([#2768](https://github.com/zarr-developers/zarr-python/pull/2768)) +- Optimize full chunk writes. ([#2782](https://github.com/zarr-developers/zarr-python/pull/2782)) ### Improved Documentation - Changed the machinery for creating changelog entries. - Now individual entries should be added as files to the `changes` directory in the `zarr-python` repository, instead of directly to the changelog file. ([#2736](https://github.com/zarr-developers/zarr-python/issues/2736)) + Now individual entries should be added as files to the `changes` directory in the `zarr-python` repository, instead of directly to the changelog file. ([#2736](https://github.com/zarr-developers/zarr-python/pull/2736)) ### Other - Created a type alias `ChunkKeyEncodingLike` to model the union of `ChunkKeyEncoding` instances and the dict form of the parameters of those instances. `ChunkKeyEncodingLike` should be used by high-level functions to provide a convenient - way for creating `ChunkKeyEncoding` objects. ([#2763](https://github.com/zarr-developers/zarr-python/issues/2763)) + way for creating `ChunkKeyEncoding` objects. ([#2763](https://github.com/zarr-developers/zarr-python/pull/2763)) ## 3.0.1 (2025-01-17) -* Implement `zarr.from_array` using concurrent streaming ([#2622](https://github.com/zarr-developers/zarr-python/issues/2622)). +* Implement `zarr.from_array` using concurrent streaming ([#2622](https://github.com/zarr-developers/zarr-python/pull/2622)). ### Bug fixes -* Fixes `order` argument for Zarr format 2 arrays ([#2679](https://github.com/zarr-developers/zarr-python/issues/2679)). +* Fixes `order` argument for Zarr format 2 arrays ([#2679](https://github.com/zarr-developers/zarr-python/pull/2679)). * Fixes a bug that prevented reading Zarr format 2 data with consolidated metadata written using `zarr-python` version 2 ([#2694](https://github.com/zarr-developers/zarr-python/issues/2694)). * Ensure that compressor=None results in no compression when writing Zarr format 2 data ([#2708](https://github.com/zarr-developers/zarr-python/issues/2708)). * Fix for empty consolidated metadata dataset: backwards compatibility with - Zarr-Python 2 ([#2695](https://github.com/zarr-developers/zarr-python/issues/2695)). + Zarr-Python 2 ([#2695](https://github.com/zarr-developers/zarr-python/pull/2695)). ### Documentation -* Add v3.0.0 release announcement banner ([#2677](https://github.com/zarr-developers/zarr-python/issues/2677)). -* Quickstart guide alignment with V3 API ([#2697](https://github.com/zarr-developers/zarr-python/issues/2697)). -* Fix doctest failures related to numcodecs 0.15 ([#2727](https://github.com/zarr-developers/zarr-python/issues/2727)). +* Add v3.0.0 release announcement banner ([#2677](https://github.com/zarr-developers/zarr-python/pull/2677)). +* Quickstart guide alignment with V3 API ([#2697](https://github.com/zarr-developers/zarr-python/pull/2697)). +* Fix doctest failures related to numcodecs 0.15 ([#2727](https://github.com/zarr-developers/zarr-python/pull/2727)). ### Other * Removed some unnecessary files from the source distribution - to reduce its size. ([#2686](https://github.com/zarr-developers/zarr-python/issues/2686)). -* Enable codecov in GitHub actions ([#2682](https://github.com/zarr-developers/zarr-python/issues/2682)). -* Speed up hypothesis tests ([#2650](https://github.com/zarr-developers/zarr-python/issues/2650)). -* Remove multiple imports for an import name ([#2723](https://github.com/zarr-developers/zarr-python/issues/2723)). + to reduce its size. ([#2686](https://github.com/zarr-developers/zarr-python/pull/2686)). +* Enable codecov in GitHub actions ([#2682](https://github.com/zarr-developers/zarr-python/pull/2682)). +* Speed up hypothesis tests ([#2650](https://github.com/zarr-developers/zarr-python/pull/2650)). +* Remove multiple imports for an import name ([#2723](https://github.com/zarr-developers/zarr-python/pull/2723)). ## 3.0.0 (2025-01-09) diff --git a/docs/user-guide/arrays.md b/docs/user-guide/arrays.md index 51b2fa1a17..a192845f9e 100644 --- a/docs/user-guide/arrays.md +++ b/docs/user-guide/arrays.md @@ -199,7 +199,7 @@ print(arr_f.config) A number of different compressors can be used with Zarr. Zarr includes Blosc, Zstandard and Gzip compressors. Additional compressors are available through -a separate package called [NumCodecs](https://numcodecs.readthedocs.io/) which provides various +a separate package called [NumCodecs](https://numcodecs.readthedocs.io/en/stable/) which provides various compressor libraries including LZ4, Zlib, BZ2 and LZMA. Different compressors can be provided via the `compressors` keyword argument accepted by all array creation functions. For example: @@ -256,7 +256,7 @@ z[:] = data print(f"Compressors: {z.compressors}") ``` -Here is an example using LZMA from [NumCodecs](https://numcodecs.readthedocs.io/) with a custom filter pipeline including LZMA's +Here is an example using LZMA from [NumCodecs](https://numcodecs.readthedocs.io/en/stable/) with a custom filter pipeline including LZMA's built-in delta filter: ```python exec="true" session="arrays" source="above" result="ansi" @@ -295,7 +295,7 @@ z = zarr.create_array(store='data/example-9.zarr', shape=data.shape, dtype=data. print(z.info_complete()) ``` -For more information about available filter codecs, see the [Numcodecs](https://numcodecs.readthedocs.io/) documentation. +For more information about available filter codecs, see the [Numcodecs](https://numcodecs.readthedocs.io/en/stable/) documentation. ## Advanced indexing diff --git a/docs/user-guide/installation.md b/docs/user-guide/installation.md index 4af7667a44..a7487e83c8 100644 --- a/docs/user-guide/installation.md +++ b/docs/user-guide/installation.md @@ -5,12 +5,12 @@ Required dependencies include: - [Python](https://docs.python.org/3/) (3.12 or later) -- [packaging](https://packaging.pypa.io) (22.0 or later) +- [packaging](https://packaging.pypa.io/en/stable/) (22.0 or later) - [numpy](https://numpy.org) (2.0 or later) -- [numcodecs](https://numcodecs.readthedocs.io) (0.14 or later) +- [numcodecs](https://numcodecs.readthedocs.io/en/stable/) (0.14 or later) - [google-crc32c](https://github.com/googleapis/python-crc32c) (1.5 or later) -- [typing_extensions](https://typing-extensions.readthedocs.io) (4.14 or later) -- [donfig](https://donfig.readthedocs.io) (0.8 or later) +- [typing_extensions](https://typing-extensions.readthedocs.io/en/latest/) (4.14 or later) +- [donfig](https://donfig.readthedocs.io/en/latest/) (0.8 or later) ## pip diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index 0ba6202c76..b288c9976d 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -1,7 +1,7 @@ # Storage guide Zarr-Python supports multiple storage backends, including: local file systems, -Zip files, remote stores via [fsspec](https://filesystem-spec.readthedocs.io) (S3, HTTP, etc.), and in-memory stores. In +Zip files, remote stores via [fsspec](https://filesystem-spec.readthedocs.io/en/latest/) (S3, HTTP, etc.), and in-memory stores. In Zarr-Python 3, stores must implement the abstract store API from [`zarr.abc.store.Store`][]. @@ -12,7 +12,7 @@ Zarr-Python 3, stores must implement the abstract store API from ## Implicit Store Creation In most cases, it is not required to create a `Store` object explicitly. Passing a string -(or other [StoreLike value](#storelike)) to Zarr's top level API will result in the store +(or other [StoreLike value](#user-guide-store-like)) to Zarr's top level API will result in the store being created automatically: ```python exec="true" session="storage" source="above" result="ansi" @@ -41,10 +41,7 @@ group = zarr.create_group(store=data) print(group) ``` -<!-- markdownlint-disable-next-line MD042 -- empty link is an intentional MkDocs anchor target --> -[](){#user-guide-store-like} - -### StoreLike +### StoreLike {#user-guide-store-like} `StoreLike` values can be: @@ -142,7 +139,7 @@ f.close() The [`zarr.storage.FsspecStore`][] stores the contents of a Zarr hierarchy following the same logical layout as the [`LocalStore`][zarr.storage.LocalStore], except the store is assumed to be on a remote storage system such as cloud object storage (e.g. AWS S3, Google Cloud Storage, Azure Blob Store). The -[`zarr.storage.FsspecStore`][] is backed by [fsspec](https://filesystem-spec.readthedocs.io) and can support any backend +[`zarr.storage.FsspecStore`][] is backed by [fsspec](https://filesystem-spec.readthedocs.io/en/latest/) and can support any backend that implements the [AbstractFileSystem](https://filesystem-spec.readthedocs.io/en/stable/api.html#fsspec.spec.AbstractFileSystem) API. `storage_options` can be used to configure the fsspec backend: diff --git a/packages/zarr-metadata/CHANGELOG.md b/packages/zarr-metadata/CHANGELOG.md index 981c7706bf..ac4ad3535a 100644 --- a/packages/zarr-metadata/CHANGELOG.md +++ b/packages/zarr-metadata/CHANGELOG.md @@ -159,7 +159,7 @@ ### Deprecations and Removals -- Introduces a new `JSONValue` type that models python objects that serialize directly to JSON. This type is used to annotate the contents of `attributes` and `fill_value` fields, replacing the use of the overly wide `object` type. This is technically a breaking change. ([#4037](https://github.com/zarr-developers/zarr-python/issues/4037)) +- Introduces a new `JSONValue` type that models python objects that serialize directly to JSON. This type is used to annotate the contents of `attributes` and `fill_value` fields, replacing the use of the overly wide `object` type. This is technically a breaking change. ([#4037](https://github.com/zarr-developers/zarr-python/pull/4037)) - Promoted a curated "front door" of names to the top-level `zarr_metadata` namespace, so consumers can write e.g. `from zarr_metadata import ArrayMetadataV3, ShardingIndexLocation, BLOSC_CNAME` instead of importing from @@ -180,7 +180,7 @@ `name`-or-`{name, configuration}` shape). Also added the `NUMPY_TIME_UNIT` runtime constant (a `Final` tuple paired with - the `NumpyTimeUnit` Literal) in `zarr_metadata.v3.data_type.numpy_timedelta64`. ([#4083](https://github.com/zarr-developers/zarr-python/issues/4083)) + the `NumpyTimeUnit` Literal) in `zarr_metadata.v3.data_type.numpy_timedelta64`. ([#4083](https://github.com/zarr-developers/zarr-python/pull/4083)) ## 0.2.0 (2026-05-19) @@ -193,13 +193,13 @@ identify the chunk bytes produced by a writer. **Breaking** for consumers that previously typed gzip codec metadata as the bare string or constructed a `GzipCodecConfiguration` without `level`. - ([#3978](https://github.com/zarr-developers/zarr-python/issues/3978)) + ([#3978](https://github.com/zarr-developers/zarr-python/pull/3978)) - `BytesCodecObject.configuration` is now `NotRequired`. The configuration has no required keys (`endian` is conditionally required at runtime based on data type), so the object form may omit it entirely — matching the bare-string short-hand. **Soft-breaking** for consumers that previously relied on `configuration` always being present. - ([#3978](https://github.com/zarr-developers/zarr-python/issues/3978)) + ([#3978](https://github.com/zarr-developers/zarr-python/pull/3978)) - Better modelling of Zarr v2 stored metadata. Zarr v2 splits a node's metadata across two JSON documents (`.zarray`/`.zgroup` and `.zattrs`), but `GroupMetadataV2` had no `attributes` field while `ArrayMetadataV2` @@ -207,7 +207,7 @@ `attributes` field, and `ArrayMetadataV2.attributes` is now `NotRequired` for symmetry. **Soft-breaking** for consumers that relied on `ArrayMetadataV2.attributes` always being present. - ([#3962](https://github.com/zarr-developers/zarr-python/issues/3962)) + ([#3962](https://github.com/zarr-developers/zarr-python/pull/3962)) ### Features @@ -219,7 +219,7 @@ (test fixtures, fragment templates, in-progress builders). An equivalence test pins each `Partial` to the keys and value types of its full sibling so the two cannot drift. - ([#3982](https://github.com/zarr-developers/zarr-python/issues/3982)) + ([#3982](https://github.com/zarr-developers/zarr-python/pull/3982)) - Added three new top-level types modelling the **strict on-disk** shape of Zarr v2 metadata documents: `ZArrayMetadata` (the `.zarray` file), `ZGroupMetadata` (the `.zgroup` file), and `ZAttrsMetadata` (the @@ -227,13 +227,13 @@ what's stored on disk; use the merged `ArrayMetadataV2`/`GroupMetadataV2` when you want the in-memory representation a Python program typically works with. - ([#3962](https://github.com/zarr-developers/zarr-python/issues/3962)) + ([#3962](https://github.com/zarr-developers/zarr-python/pull/3962)) - Added typed constants exposing the spec-permitted values of constrained Literal fields, importable at the per-codec module level. For example, `from zarr_metadata.v3.codec.bytes import ENDIAN` provides `("little", "big")` as a tuple, enabling runtime iteration or validator generation without re-stating the Literal values by hand. - ([#3978](https://github.com/zarr-developers/zarr-python/issues/3978)) + ([#3978](https://github.com/zarr-developers/zarr-python/pull/3978)) ## 0.1.1 (2026-05-06) @@ -242,7 +242,7 @@ - First usable release on PyPI. Version 0.1.0 was uploaded then deleted to reserve the project name; this version is the first one PyPI will install. No source changes from 0.1.0. - ([#3949](https://github.com/zarr-developers/zarr-python/issues/3949)) + ([#3949](https://github.com/zarr-developers/zarr-python/pull/3949)) ## 0.1.0 (2026-05-01) @@ -253,4 +253,4 @@ of `zarr-extensions` types and the un-specified-but-widely-used consolidated metadata documents. Pair with a runtime validator like `pydantic` to check JSON loaded from disk. - ([#3919](https://github.com/zarr-developers/zarr-python/issues/3919)) + ([#3919](https://github.com/zarr-developers/zarr-python/pull/3919)) diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md index 6b6b172aec..34c53988db 100644 --- a/packages/zarr-metadata/README.md +++ b/packages/zarr-metadata/README.md @@ -2,7 +2,7 @@ Python types, models, and validators for Zarr v2 and v3 metadata. -Documentation: <https://zarr-metadata.readthedocs.io/> +Documentation: <https://zarr-metadata.readthedocs.io/en/stable/> ## What this is diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 6e97d26409..1ef1c31624 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -115,5 +115,5 @@ filename = "CHANGELOG.md" package = "zarr_metadata" underlines = ["", "", ""] title_format = "## {version} ({project_date})" -issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues/{issue})" +issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/pull/{issue})" start_string = "<!-- towncrier release notes start -->\n" diff --git a/pyproject.toml b/pyproject.toml index 727071b5a3..1927ce4d7c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -514,7 +514,7 @@ directory = 'changes' filename = "docs/release-notes.md" underlines = ["", "", ""] title_format = "## {version} ({project_date})" -issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues/{issue})" +issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/pull/{issue})" start_string = "<!-- towncrier release notes start -->\n" [tool.codespell] From a88f88951e7b1bc19f19adad2fb364158851076a Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 30 Jul 2026 07:10:15 +0200 Subject: [PATCH 429/468] fix: make ManagedMemoryStore/GpuMemoryStore sync methods parity-safe (#4204) ManagedMemoryStore inherited get_sync/set_sync/delete_sync from MemoryStore, which use the raw key, while every async method prefixed keys with self.path. Any code taking the sync fast path (e.g. FusedCodecPipeline) wrote/read chunks outside the store's path prefix, so a fresh handle re-reading through the prefix silently got fill values. Override the three sync methods to prefix like their async counterparts. GpuMemoryStore.set_sync gets the same treatment: it now converts its value to a gpu.Buffer like set does, preserving the store's all-values-are-gpu invariant for the sync API. Also fix ManagedMemoryStore.get_partial_values, which applied self.path twice whenever path was non-empty (it pre-prefixed keys, then delegated to MemoryStore.get_partial_values, which itself dispatches through the already-overridden self.get) -- this made it return None for every key. Discovered via the strengthened test fixture below. Add sync/async parity laws to the shared StoreTests suite so every store subclass exercises this invariant: set through one API and read through the other (including byte_range variants), and confirm delete_sync is visible to async get. These are the tests that would have caught the ManagedMemoryStore bug. TestManagedMemoryStore's raw set/get test helpers now respect self.path, and store_kwargs uses a non-empty path, so prefix handling is actually exercised instead of passing vacuously. Add an end-to-end regression with FusedCodecPipeline writing to a ManagedMemoryStore(path=...) sharing a dict with a fresh handle. Add a LocalStore.delete_sync directory-branch test. Assisted-by: ClaudeCode:claude-sonnet-5 --- changes/4204.bugfix.md | 16 +++++++ src/zarr/storage/_memory.py | 44 +++++++++++++++---- src/zarr/testing/store.py | 65 ++++++++++++++++++++++++++++ tests/test_store/test_local.py | 14 ++++++ tests/test_store/test_memory.py | 76 ++++++++++++++++++++++++++++++--- 5 files changed, 202 insertions(+), 13 deletions(-) create mode 100644 changes/4204.bugfix.md diff --git a/changes/4204.bugfix.md b/changes/4204.bugfix.md new file mode 100644 index 0000000000..90101d1059 --- /dev/null +++ b/changes/4204.bugfix.md @@ -0,0 +1,16 @@ +`ManagedMemoryStore.get_sync`/`set_sync`/`delete_sync` now apply the store's +`path` prefix, matching the async `get`/`set`/`delete` methods. Previously the +sync methods were inherited unchanged from `MemoryStore` and used the raw key, +so code that takes the sync fast path (e.g. `FusedCodecPipeline`) would read +and write chunks outside the store's `path` prefix, silently returning fill +values when the data was re-read through a fresh handle. `GpuMemoryStore.set_sync` +now converts its value to a `gpu.Buffer`, matching `set`, so writes through the +sync API keep the store's all-values-are-GPU invariant. Also fixed +`ManagedMemoryStore.get_partial_values` applying its `path` prefix twice +whenever `path` is non-empty, which made it always return `None` for every +requested key. + +The shared store test suite (`zarr.testing.store.StoreTests`) gained +sync/async parity checks — comparing sync and async observations of the same +key on the same store instance, including with a `byte_range` — so every +store subclass now exercises this invariant. diff --git a/src/zarr/storage/_memory.py b/src/zarr/storage/_memory.py index 97dd355515..f42c38df69 100644 --- a/src/zarr/storage/_memory.py +++ b/src/zarr/storage/_memory.py @@ -314,6 +314,19 @@ async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None gpu_value = value if isinstance(value, gpu.Buffer) else gpu.Buffer.from_buffer(value) await super().set(key, gpu_value, byte_range=byte_range) + def set_sync(self, key: str, value: Buffer) -> None: + # docstring inherited + self._check_writable() + assert isinstance(key, str) + if not isinstance(value, Buffer): + raise TypeError( + f"GpuMemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead." + ) + # Convert to gpu.Buffer, mirroring `set` above: every value in this store's + # backing dict must be a gpu.Buffer, regardless of which API wrote it. + gpu_value = value if isinstance(value, gpu.Buffer) else gpu.Buffer.from_buffer(value) + super().set_sync(key, gpu_value) + # ----------------------------------------------------------------------------- # ManagedMemoryStore and its registry @@ -572,25 +585,40 @@ def from_url(cls, url: str, *, read_only: bool = False) -> ManagedMemoryStore: # Override MemoryStore methods to use path prefix and check process - async def get( + def get_sync( self, key: str, + *, prototype: BufferPrototype | None = None, byte_range: ByteRequest | None = None, ) -> Buffer | None: # docstring inherited - return await super().get( + return super().get_sync( _join_paths([self.path, key]), prototype=prototype, byte_range=byte_range ) - async def get_partial_values( + def set_sync(self, key: str, value: Buffer) -> None: + # docstring inherited + super().set_sync(_join_paths([self.path, key]), value) + + def delete_sync(self, key: str) -> None: + # docstring inherited + super().delete_sync(_join_paths([self.path, key])) + + async def get( self, - prototype: BufferPrototype, - key_ranges: Iterable[tuple[str, ByteRequest | None]], - ) -> list[Buffer | None]: + key: str, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: # docstring inherited - key_ranges = [(_join_paths([self.path, key]), byte_range) for key, byte_range in key_ranges] - return await super().get_partial_values(prototype, key_ranges) + return await super().get( + _join_paths([self.path, key]), prototype=prototype, byte_range=byte_range + ) + + # get_partial_values is intentionally NOT overridden here: MemoryStore.get_partial_values + # dispatches per-key through `self.get`, which already resolves to the override above. + # Re-prefixing the keys here as well would apply `self.path` twice. async def exists(self, key: str) -> bool: # docstring inherited diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index 46287ccffb..d7011440e0 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -618,6 +618,71 @@ def test_delete_sync_missing(self, store: S) -> None: # should not raise deleter.delete_sync("nonexistent_sync") + # ------------------------------------------------------------------- + # Sync/async parity laws + # ------------------------------------------------------------------- + # A store's sync and async methods must observe the same key the same + # way. This is stronger than the individual test_get_sync/test_set_sync/ + # test_delete_sync tests above: those write and read back through the + # *same* API (sync-only or, via `self.set`/`self.get`, bypassing the + # store entirely), so a sync method that skips logic the async method + # applies (e.g. a path prefix) can still pass them. These laws write + # through one API and observe through the other. + + @pytest.mark.parametrize("direction", ["set_async_get_sync", "set_sync_get_async"]) + async def test_sync_async_set_get_parity(self, store: S, direction: str) -> None: + setter = self._require_set_sync(store) + getter = self._require_get_sync(store) + data_buf = self.buffer_cls.from_bytes(b"\x01\x02\x03\x04") + key = "parity_set_get" + if direction == "set_async_get_sync": + await store.set(key, data_buf) + result = getter.get_sync(key) + else: + setter.set_sync(key, data_buf) + result = await store.get(key, prototype=default_buffer_prototype()) + assert result is not None + assert_bytes_equal(result, data_buf) + + async def test_delete_sync_visible_to_async_get(self, store: S) -> None: + deleter = self._require_delete_sync(store) + if not store.supports_deletes: + pytest.skip("store does not support deletes") + data_buf = self.buffer_cls.from_bytes(b"\x01\x02\x03\x04") + key = "parity_delete" + await store.set(key, data_buf) + deleter.delete_sync(key) + result = await store.get(key, prototype=default_buffer_prototype()) + assert result is None + + @pytest.mark.parametrize( + "byte_range", + [ + None, + RangeByteRequest(1, 4), + OffsetByteRequest(1), + SuffixByteRequest(1), + RangeByteRequest(10, 20), + ], + ids=["none", "range", "offset", "suffix", "range-past-eof"], + ) + async def test_get_sync_byte_range_parity( + self, store: S, byte_range: ByteRequest | None + ) -> None: + getter = self._require_get_sync(store) + data_buf = self.buffer_cls.from_bytes(b"\x01\x02\x03\x04") + key = "parity_byte_range" + await store.set(key, data_buf) + sync_result = getter.get_sync(key, byte_range=byte_range) + async_result = await store.get( + key, prototype=default_buffer_prototype(), byte_range=byte_range + ) + if async_result is None: + assert sync_result is None + else: + assert sync_result is not None + assert_bytes_equal(sync_result, async_result) + class LatencyStore(WrapperStore[Store]): """ diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index f65f618d65..61e48a269f 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -46,6 +46,20 @@ async def test_empty_with_empty_subdir(self, store: LocalStore) -> None: (store.root / "foo/bar").mkdir(parents=True) assert await store.is_empty("") + def test_delete_sync_directory(self, store: LocalStore) -> None: + """`delete_sync` on a key that is a directory must remove the whole tree. + + Mirrors the async `delete_dir` behavior: deleting `"foo"` where + `"foo"` is a directory containing further nested paths should remove + everything under it, not just fail or delete a single file. + """ + (store.root / "foo" / "bar").mkdir(parents=True) + (store.root / "foo" / "bar" / "baz").write_bytes(b"data") + + store.delete_sync("foo") + + assert not (store.root / "foo").exists() + def test_creates_new_directory(self, tmp_path: pathlib.Path) -> None: target = tmp_path.joinpath("a", "b", "c") assert not target.exists() diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index 36265423e6..a976f3738e 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -11,6 +11,7 @@ from zarr.core.buffer import Buffer, cpu, default_buffer_prototype, gpu from zarr.errors import ZarrUserWarning from zarr.storage import GpuMemoryStore, ManagedMemoryStore, MemoryStore +from zarr.storage._utils import _join_paths from zarr.testing.store import StoreTests from zarr.testing.utils import gpu_test @@ -233,31 +234,48 @@ def test_from_dict(self) -> None: for v in result._store_dict.values(): assert type(v) is gpu.Buffer + def test_set_sync_converts_to_gpu_buffer(self, store: GpuMemoryStore) -> None: + """`set_sync` must convert its value to a `gpu.Buffer`, mirroring `set`. + + `GpuMemoryStore`'s invariant is that every stored value is a + `gpu.Buffer`. Without this override, the inherited `MemoryStore.set_sync` + would store the CPU buffer it was given as-is, breaking that invariant + for whichever code path (e.g. the fused pipeline) uses the sync API. + """ + cpu_value = cpu.Buffer.from_bytes(b"aaaa") + msg = "Creating a zarr.buffer.gpu.Buffer with an array that does not support the __cuda_array_interface__ for zero-copy transfers, falling back to slow copy based path" + with pytest.warns(ZarrUserWarning, match=msg): + store.set_sync("k", cpu_value) + assert type(store._store_dict["k"]) is gpu.Buffer + class TestManagedMemoryStore(StoreTests[ManagedMemoryStore, cpu.Buffer]): store_cls = ManagedMemoryStore buffer_cls = cpu.Buffer async def set(self, store: ManagedMemoryStore, key: str, value: Buffer) -> None: - store._store_dict[key] = value + store._store_dict[_join_paths([store.path, key])] = value async def get(self, store: ManagedMemoryStore, key: str) -> Buffer: - return store._store_dict[key] + return store._store_dict[_join_paths([store.path, key])] @pytest.fixture def store_kwargs(self, request: pytest.FixtureRequest) -> dict[str, Any]: # Use a unique name per test to avoid sharing state between tests # but ensure the name is deterministic for equality tests # Replace '/' with '-' since store names cannot contain '/' + # A non-empty path exercises prefix handling; a store with an + # unprefixed key in its backing dict would pass these tests + # vacuously with path="". sanitized_name = request.node.name.replace("/", "-") - return {"name": f"test-{sanitized_name}"} + return {"name": f"test-{sanitized_name}", "path": "prefix"} @pytest.fixture async def store(self, store_kwargs: dict[str, Any]) -> ManagedMemoryStore: return self.store_cls(**store_kwargs) def test_store_repr(self, store: ManagedMemoryStore) -> None: - assert str(store) == f"memory://{store.name}" + assert str(store) == _join_paths([f"memory://{store.name}", store.path]) async def test_serializable_store(self, store: ManagedMemoryStore) -> None: """ @@ -383,7 +401,10 @@ def test_from_url(self, store: ManagedMemoryStore) -> None: def test_from_url_with_path(self, store: ManagedMemoryStore) -> None: """Test that from_url extracts path component from URL.""" - url = f"{store}/some/path" + # Reconnect to the fixture's dict via its name, but with an empty + # path, so appending "/some/path" below yields exactly that path. + base = ManagedMemoryStore(name=store.name) + url = f"{base}/some/path" store2 = ManagedMemoryStore.from_url(url) assert store2._store_dict is store._store_dict assert store2.path == "some/path" @@ -512,3 +533,48 @@ def test_garbage_collection(self) -> None: # URL should no longer resolve with pytest.raises(ValueError, match="garbage collected"): ManagedMemoryStore.from_url(url) + + def test_sync_methods_respect_path_prefix(self) -> None: + """`get_sync`/`set_sync`/`delete_sync` must prefix keys with `self.path`, + exactly like the async `get`/`set`/`delete` methods. + + `ManagedMemoryStore` used to inherit these from `MemoryStore`, which + writes/reads the raw key. Two stores sharing a dict with different + `path` values would then cross-talk through the sync API. + """ + store = ManagedMemoryStore(name="sync-prefix-test", path="subdir") + data_buf = self.buffer_cls.from_bytes(b"value") + + store.set_sync("key", data_buf) + assert "subdir/key" in store._store_dict + assert "key" not in store._store_dict + + result = store.get_sync("key") + assert result is not None + assert result.to_bytes() == b"value" + + store.delete_sync("key") + assert "subdir/key" not in store._store_dict + + def test_fused_pipeline_respects_path_prefix(self) -> None: + """End-to-end regression: the fused pipeline's sync store fast path must + write chunks under the store's path prefix. + + `FusedCodecPipeline` uses `set_sync`/`get_sync` when a store implements + the sync protocols. If those methods skip the prefix that the async + methods apply, chunk data lands outside `self.path` and a fresh handle + re-reading through the prefix silently sees fill values instead. + """ + with zarr.config.set( + {"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"} + ): + store = ManagedMemoryStore(name="fused-prefix-test", path="subdir") + arr = zarr.create_array(store, shape=(4,), chunks=(4,), dtype="uint8", zarr_format=3) + arr[:] = np.arange(4, dtype="uint8") + + bad_keys = [k for k in store._store_dict if not k.startswith("subdir/")] + assert bad_keys == [], f"keys written outside the store's path prefix: {bad_keys}" + + store2 = ManagedMemoryStore.from_url("memory://fused-prefix-test/subdir") + arr2 = zarr.open_array(store2, mode="r") + np.testing.assert_array_equal(arr2[:], np.arange(4, dtype="uint8")) From 6f9724cb14686e0737ed144be5d945fe1fbde578 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 30 Jul 2026 11:08:29 +0200 Subject: [PATCH 430/468] fix: minor correctness and hygiene fixes from the sync-pipeline audit (#4205) - Codec construction warnings (e.g. sharding's "disables partial reads") fired twice per array open, and on every decode/encode through the fused pipeline's async fallback. Re-constructions of an already-validated codec chain now go through codecs_from_list_unchecked, which validates structure without repeating first-construction advisory warnings; each warning fires exactly once per open under both pipelines. - concurrent_iter returned a lazy generator while its docstring promised eagerly scheduled tasks; it now materializes the task list so awaiting one at a time cannot serialize the batch. - A garbage codec_pipeline.max_workers value (e.g. from the environment) raised ValueError mid-read; it now warns and falls back to the default, consistent with tolerant handling of config input. - The as-completed pipeline helpers abandoned in-flight tasks when one failed, leaving stray background writes and "Task exception was never retrieved" warnings; failures now cancel and drain outstanding tasks. - Benchmarks: seed the data generator for reproducibility; fix a copy-pasted docstring. - Remove dead commented-out test blocks referencing the removed set_range API. Assisted-by: ClaudeCode:claude-sonnet-5 --- changes/4205.bugfix.md | 9 ++ src/zarr/core/array.py | 6 ++ src/zarr/core/chunk_utils.py | 8 +- src/zarr/core/codec_pipeline.py | 145 +++++++++++++++++++++++++------ src/zarr/core/common.py | 20 ++--- tests/benchmarks/test_e2e.py | 5 +- tests/test_codecs/test_codecs.py | 46 +++++++++- tests/test_common.py | 28 ++++++ tests/test_fused_pipeline.py | 101 ++++++++++++++++++++- tests/test_store/test_local.py | 52 ----------- tests/test_store/test_memory.py | 53 ----------- 11 files changed, 325 insertions(+), 148 deletions(-) create mode 100644 changes/4205.bugfix.md diff --git a/changes/4205.bugfix.md b/changes/4205.bugfix.md new file mode 100644 index 0000000000..0492febb7d --- /dev/null +++ b/changes/4205.bugfix.md @@ -0,0 +1,9 @@ +Fixed several small correctness issues from the codec-pipeline performance work: construction-time +codec warnings (e.g. sharding's "disables partial reads" warning) no longer fire twice per array +open — including for `FusedCodecPipeline`, which previously re-warned via its own codec-chain +reconstruction and, on the async fallback path, on every decode/encode call; `concurrent_iter` now +schedules its tasks eagerly, matching its documented contract; an invalid +`codec_pipeline.max_workers` config/environment value now warns and falls back to the default +instead of raising mid-read; and `FusedCodecPipeline`'s async fallback helpers now cancel +already-spawned fetch/decode/write tasks instead of abandoning them in the background when one +fails. diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index f75ef72415..cd51dad50c 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -228,6 +228,12 @@ def create_codec_pipeline(metadata: ArrayMetadata, *, store: Store | None = None pass if isinstance(metadata, ArrayV3Metadata): + # The pipeline built here is a throwaway: `evolve_from_array_spec` below + # reconstructs codecs against the evolved spec. `from_codecs` is the + # chain's first construction, so its advisory warnings (e.g. sharding's + # "disables partial reads" warning) fire here; `evolve_from_array_spec` + # re-splits the same already-warned-about chain via + # `codecs_from_list_unchecked`, so it does not re-emit them. pipeline = get_pipeline_class().from_codecs(metadata.codecs) from zarr.core.metadata.v3 import RegularChunkGridMetadata diff --git a/src/zarr/core/chunk_utils.py b/src/zarr/core/chunk_utils.py index d93793f853..b26d5478b2 100644 --- a/src/zarr/core/chunk_utils.py +++ b/src/zarr/core/chunk_utils.py @@ -238,7 +238,7 @@ class ChunkTransform: ) def __post_init__(self) -> None: - from zarr.core.codec_pipeline import codecs_from_list + from zarr.core.codec_pipeline import codecs_from_list_unchecked # _codec_supports_sync, not a bare isinstance check: a codec can satisfy # the SupportsSyncCodec protocol structurally yet be unable to run @@ -253,7 +253,11 @@ def __post_init__(self) -> None: f"All codecs must implement SupportsSyncCodec. The following do not: {names}" ) - aa, ab, bb = codecs_from_list(list(self.codecs)) + # `ChunkTransform` is built from a codec chain that already went + # through `codecs_from_list` when the owning pipeline was constructed + # (see `FusedCodecPipeline.evolve_from_array_spec`), so re-splitting it + # here must not re-emit that chain's advisory warnings. + aa, ab, bb = codecs_from_list_unchecked(list(self.codecs)) # SupportsSyncCodec was verified above; the cast is purely for mypy. self._aa_codecs = cast("tuple[SupportsSyncCodec[NDBuffer, NDBuffer], ...]", tuple(aa)) self._ab_codec = cast("SupportsSyncCodec[NDBuffer, Buffer]", ab) diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index ca760ece59..92fd0970fe 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -4,7 +4,7 @@ import threading from concurrent.futures import ThreadPoolExecutor from dataclasses import dataclass, field -from itertools import batched, pairwise +from itertools import batched, chain, pairwise from typing import TYPE_CHECKING, Any, cast from warnings import warn @@ -54,10 +54,23 @@ def _resolve_max_workers() -> int: """Helper for getting the maximum number of workers available to the `FusedCodecPipeline`""" import os as _os + default = _os.cpu_count() or 1 cfg = config.get("codec_pipeline.max_workers", default=None) if cfg is None: - return _os.cpu_count() or 1 - return max(1, int(cfg)) + return default + try: + return max(1, int(cfg)) + except (TypeError, ValueError): + # This value arrives via the config/env layer (e.g. + # `ZARR_CODEC_PIPELINE__MAX_WORKERS`), so tolerate bad input here + # instead of raising mid-read. + warn( + f"Ignoring invalid `codec_pipeline.max_workers` config value {cfg!r}; " + f"falling back to {default}.", + category=ZarrUserWarning, + stacklevel=2, + ) + return default def _get_pool(max_workers: int) -> ThreadPoolExecutor: @@ -169,6 +182,23 @@ def pipeline_supports_partial_encode( return isinstance(array_bytes_codec, ArrayBytesCodecPartialEncodeMixin) +async def _cancel_and_drain(futures: Iterable[asyncio.Future[Any]]) -> None: + """Cancel every not-yet-done future/task and await its outcome. + + Used to clean up work spawned by a drain loop (`asyncio.as_completed` + + `await`) when the loop exits early via exception. Without this, tasks + already spawned keep running unattended after the caller has moved on, + and an eventual failure surfaces as an unraisable "exception was never + retrieved" warning instead of being observed here. + """ + pending = [f for f in futures if not f.done()] + if len(pending) == 0: + return + for f in pending: + f.cancel() + await asyncio.gather(*pending, return_exceptions=True) + + async def _fetch_and_decode_as_completed( batch: Sequence[tuple[ByteGetter | None, ArraySpec]], transform: ChunkTransform, @@ -201,20 +231,29 @@ def _decode(buffer: Buffer | None, chunk_spec: ArraySpec) -> NDBuffer | None: _fetch, config.get("async.concurrency"), ) - for fetch_coro in asyncio.as_completed(fetch_tasks): - idx, buffer = await fetch_coro - chunk_spec = batch[idx][1] - # Bridge both paths to asyncio.Future so the final collection loop - # can `await` uniformly without blocking the event loop. For the - # pool path that means `wrap_future` (not `pool.submit(...).result()`, - # which would block the loop thread for the duration of every decode - # — freezing any unrelated coroutines sharing this loop). - if pool is None: - decode_futures[idx].set_result(_decode(buffer, chunk_spec)) - else: - decode_futures[idx] = asyncio.wrap_future(pool.submit(_decode, buffer, chunk_spec)) + try: + for fetch_coro in asyncio.as_completed(fetch_tasks): + idx, buffer = await fetch_coro + chunk_spec = batch[idx][1] + # Bridge both paths to asyncio.Future so the final collection loop + # can `await` uniformly without blocking the event loop. For the + # pool path that means `wrap_future` (not `pool.submit(...).result()`, + # which would block the loop thread for the duration of every decode + # — freezing any unrelated coroutines sharing this loop). + if pool is None: + decode_futures[idx].set_result(_decode(buffer, chunk_spec)) + else: + decode_futures[idx] = asyncio.wrap_future(pool.submit(_decode, buffer, chunk_spec)) - return await asyncio.gather(*decode_futures) + return await asyncio.gather(*decode_futures) + finally: + # On the happy path every future here is already done, so this is a + # no-op; on failure it stops abandoned fetches/decodes from + # continuing to run unattended after this function has raised. A + # single call over both iterables (not two sequential calls) so that + # outer-task cancellation during the first drain can't skip the + # second, leaving its futures/tasks unobserved. + await _cancel_and_drain(chain(fetch_tasks, decode_futures)) async def _encode_and_write_as_completed( @@ -263,10 +302,20 @@ async def _write(idx: int, chunk_bytes: Buffer | None) -> None: # Kick off each chunk's write the instant its encode lands, so writes of # already-compressed chunks proceed while the rest are still encoding. write_tasks: list[asyncio.Task[None]] = [] - for encode_coro in asyncio.as_completed(encode_futures): - idx, chunk_bytes = await encode_coro - write_tasks.append(asyncio.ensure_future(_write(idx, chunk_bytes))) - await asyncio.gather(*write_tasks) + try: + for encode_coro in asyncio.as_completed(encode_futures): + idx, chunk_bytes = await encode_coro + write_tasks.append(asyncio.ensure_future(_write(idx, chunk_bytes))) + await asyncio.gather(*write_tasks) + finally: + # On the happy path every future here is already done, so this is a + # no-op; on failure (an encode or a write raising) it stops + # already-spawned writes from continuing in the background after + # this function has raised. A single call over both iterables (not + # two sequential calls) so that outer-task cancellation during the + # first drain can't skip the second, leaving its futures/tasks + # unobserved. + await _cancel_and_drain(chain(write_tasks, encode_futures)) async def _async_read_fallback( @@ -468,7 +517,11 @@ class AsyncChunkTransform: _bb_codecs: tuple[BytesBytesCodec, ...] = field(init=False, repr=False, compare=False) def __post_init__(self) -> None: - aa, ab, bb = codecs_from_list(list(self.codecs)) + # `AsyncChunkTransform` is (re)constructed per decode/encode call from a + # codec chain that already went through `codecs_from_list` when the + # pipeline itself was built, so re-splitting it here must not re-emit + # that chain's advisory warnings on every call. + aa, ab, bb = codecs_from_list_unchecked(list(self.codecs)) self._aa_codecs = aa self._ab_codec = ab self._bb_codecs = bb @@ -532,7 +585,19 @@ class BatchedCodecPipeline(CodecPipeline): batch_size: int def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: - return type(self).from_codecs(evolve_codecs(self, array_spec)) + # Re-splits an already-`codecs_from_list`-validated (and warned-about) + # chain against the evolved spec, so this uses the quiet variant rather + # than routing through `from_codecs` (which would re-warn). + evolved_codecs = evolve_codecs(self, array_spec) + array_array_codecs, array_bytes_codec, bytes_bytes_codecs = codecs_from_list_unchecked( + evolved_codecs + ) + return type(self)( + array_array_codecs=array_array_codecs, + array_bytes_codec=array_bytes_codec, + bytes_bytes_codecs=bytes_bytes_codecs, + batch_size=self.batch_size, + ) @classmethod def from_codecs(cls, codecs: Iterable[Codec], *, batch_size: int | None = None) -> Self: @@ -794,14 +859,20 @@ async def write( def codecs_from_list( codecs: Iterable[Codec], ) -> tuple[tuple[ArrayArrayCodec, ...], ArrayBytesCodec, tuple[BytesBytesCodec, ...]]: + """Split `codecs` into `(array_array, array_bytes, bytes_bytes)`, validating order. + + Emits user-facing advisory warnings about the codec chain (e.g. sharding's + "disables partial reads" warning). Use this for the FIRST construction of a + codec chain from user-supplied codecs. Use `codecs_from_list_unchecked` when + re-splitting a chain that was already validated and warned about by a prior + `codecs_from_list` call (e.g. `evolve_from_array_spec` re-splitting the same + codecs against an evolved spec) — re-warning there would fire the same + advisory once per reconstruction instead of once per user-facing chain. + """ from zarr.codecs.sharding import ShardingCodec codecs = tuple(codecs) # materialize to avoid generator consumption issues - array_array: tuple[ArrayArrayCodec, ...] = () - array_bytes_maybe: ArrayBytesCodec | None = None - bytes_bytes: tuple[BytesBytesCodec, ...] = () - if any(isinstance(codec, ShardingCodec) for codec in codecs) and len(codecs) > 1: warn( "Combining a `sharding_indexed` codec disables partial reads and " @@ -809,6 +880,23 @@ def codecs_from_list( category=ZarrUserWarning, stacklevel=3, ) + return codecs_from_list_unchecked(codecs) + + +def codecs_from_list_unchecked( + codecs: Iterable[Codec], +) -> tuple[tuple[ArrayArrayCodec, ...], ArrayBytesCodec, tuple[BytesBytesCodec, ...]]: + """Split `codecs` into `(array_array, array_bytes, bytes_bytes)`, validating order. + + Same structural validation as `codecs_from_list` (raises on bad codec + ordering or a missing/duplicate array-bytes codec) but does NOT emit + user-facing advisory warnings. See `codecs_from_list` for when to use each. + """ + codecs = tuple(codecs) # materialize to avoid generator consumption issues + + array_array: tuple[ArrayArrayCodec, ...] = () + array_bytes_maybe: ArrayBytesCodec | None = None + bytes_bytes: tuple[BytesBytesCodec, ...] = () for prev_codec, cur_codec in pairwise((None, *codecs)): if isinstance(cur_codec, ArrayArrayCodec): @@ -911,8 +999,11 @@ def from_codecs(cls, codecs: Iterable[Codec], *, batch_size: int | None = None) ) def evolve_from_array_spec(self, array_spec: ArraySpec) -> Self: + # Re-splits an already-`codecs_from_list`-validated (and warned-about) + # chain against the evolved spec, so this uses the quiet variant to + # avoid re-emitting the same advisory warning on every array open. evolved_codecs = evolve_codecs(self.codecs, array_spec) - aa, ab, bb = codecs_from_list(evolved_codecs) + aa, ab, bb = codecs_from_list_unchecked(evolved_codecs) try: sync_transform: ChunkTransform | None = ChunkTransform(codecs=evolved_codecs) diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 4114cb7645..1541683b09 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -93,26 +93,26 @@ def concurrent_iter[T: tuple[Any, ...], V]( items: Iterable[T], func: Callable[..., Awaitable[V]], limit: int | None = None, -) -> Iterator[asyncio.Task[V]]: +) -> list[asyncio.Task[V]]: """Launch `func(*item)` for each item concurrently, returning the tasks. When `limit` is set, no more than `limit` calls are in flight at once. Tasks are returned in input order; callers that want completion order should wrap the result in `asyncio.as_completed`. - Note on `ensure_future`: when the result is passed to `asyncio.gather` or - `asyncio.as_completed`, those already wrap awaitables into tasks, so the - `ensure_future` here is redundant. It matters for callers that iterate and - await tasks one at a time — without eager scheduling, each coroutine would - only start when individually awaited, serializing the work and defeating - the semaphore. It also makes the return type honest (real `Task`s support - `.cancel()`, `.done()`, callbacks) rather than bare coroutines. + Every task is scheduled (via `ensure_future`) before this function + returns, not on first iteration of the result. That matters for callers + that await the returned tasks one at a time — without eager scheduling, + each coroutine would only start when individually awaited, serializing + the work and defeating the semaphore. It also makes the return type + honest (real `Task`s support `.cancel()`, `.done()`, callbacks) rather + than bare coroutines. See https://docs.python.org/3/library/asyncio-task.html#coroutines: "Note that simply calling a coroutine will not schedule it to be executed:" """ if limit is None: - return (asyncio.ensure_future(func(*item)) for item in items) + return [asyncio.ensure_future(func(*item)) for item in items] sem = asyncio.Semaphore(limit) @@ -120,7 +120,7 @@ async def run(item: T) -> V: async with sem: return await func(*item) - return (asyncio.ensure_future(run(item)) for item in items) + return [asyncio.ensure_future(run(item)) for item in items] async def concurrent_map[T: tuple[Any, ...], V]( diff --git a/tests/benchmarks/test_e2e.py b/tests/benchmarks/test_e2e.py index de69fca59b..9720778d8f 100644 --- a/tests/benchmarks/test_e2e.py +++ b/tests/benchmarks/test_e2e.py @@ -63,7 +63,8 @@ def _data(shape: tuple[int]) -> np.ndarray: noise_level = 1 pattern = (np.sin(np.linspace(0, 2 * np.pi, period)) * 50 + 128).round().astype(np.uint8) data = np.tile(pattern, int(np.ceil(n / period)))[:n].astype(np.int16) - data += np.random.randint(-noise_level, noise_level + 1, size=n, dtype=np.int16) + rng = np.random.default_rng(0) + data += rng.integers(-noise_level, noise_level + 1, size=n, dtype=np.int16) return np.clip(data, 0, 255).astype(np.uint8) @@ -189,7 +190,7 @@ def test_read_array( get_data: Callable[[tuple[int]], np.ndarray | int], ) -> None: """ - Test the time required to fill an array with a single value + Test the time required to read the entirety of an array """ arr = create_array( bench_store, diff --git a/tests/test_codecs/test_codecs.py b/tests/test_codecs/test_codecs.py index 01ac02920f..8b4585503c 100644 --- a/tests/test_codecs/test_codecs.py +++ b/tests/test_codecs/test_codecs.py @@ -1,6 +1,7 @@ from __future__ import annotations import json +import warnings from dataclasses import dataclass from typing import TYPE_CHECKING, Any @@ -22,7 +23,7 @@ from zarr.core.metadata.v3 import ArrayV3Metadata from zarr.dtype import UInt8 from zarr.errors import ZarrUserWarning -from zarr.storage import StorePath +from zarr.storage import MemoryStore, StorePath if TYPE_CHECKING: from zarr.abc.codec import Codec @@ -375,6 +376,49 @@ def test_invalid_metadata_create_array() -> None: ) +@pytest.mark.parametrize( + "pipeline_path", + [ + "zarr.core.codec_pipeline.BatchedCodecPipeline", + "zarr.core.codec_pipeline.FusedCodecPipeline", + ], +) +def test_sharding_warning_fires_once_per_open(pipeline_path: str) -> None: + """Construction-time codec warnings (e.g. sharding's partial-reads warning) + must fire exactly once per array open, not once per internal codec-chain + reconstruction. + + `create_codec_pipeline` builds a throwaway pipeline via `from_codecs` (which + warns) and then calls `evolve_from_array_spec` on it, which re-splits the + (already-warned-about) codec chain against the evolved spec. That re-split + goes through `codecs_from_list_unchecked` rather than `codecs_from_list`, so + it does not re-emit the warning. `FusedCodecPipeline` additionally builds a + `ChunkTransform` (and, on the async fallback path, an `AsyncChunkTransform` + per call) from the same evolved codec chain, which must use the same quiet + variant. + """ + with config.set({"codec_pipeline.path": pipeline_path}): + store = MemoryStore() + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + zarr.create_array( + store, + shape=(16, 16), + chunks=(16, 16), + dtype=np.dtype("uint8"), + fill_value=0, + serializer=ShardingCodec(chunk_shape=(8, 8)), + compressors=[GzipCodec()], + ) + + with warnings.catch_warnings(record=True) as caught: + warnings.simplefilter("always") + zarr.open_array(store, mode="r") + + matches = [w for w in caught if "disables partial reads" in str(w.message)] + assert len(matches) == 1 + + @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"]) async def test_resize(store: Store) -> None: data = np.zeros((16, 18), dtype="uint16") diff --git a/tests/test_common.py b/tests/test_common.py index 2fe0743e14..5d8df326da 100644 --- a/tests/test_common.py +++ b/tests/test_common.py @@ -1,5 +1,6 @@ from __future__ import annotations +import asyncio from collections.abc import Iterable from typing import TYPE_CHECKING, get_args @@ -9,6 +10,7 @@ from zarr.core.common import ( ANY_ACCESS_MODE, AccessModeLiteral, + concurrent_iter, parse_int, parse_name, parse_shapelike, @@ -32,6 +34,32 @@ def test_access_modes() -> None: assert set(ANY_ACCESS_MODE) == set(get_args(AccessModeLiteral)) +async def test_concurrent_iter_schedules_eagerly() -> None: + """`concurrent_iter` must return already-scheduled tasks, not a lazy generator. + + Its docstring promises `func(*item)` is launched concurrently for every + item up front; a caller that awaits the returned tasks one at a time + (rather than via `gather`/`as_completed`, which force iteration) relies + on that eager scheduling to get any overlap at all. + """ + started = [False, False, False] + + async def mark(i: int) -> int: + started[i] = True + return i + + tasks = concurrent_iter([(0,), (1,), (2,)], mark) + + # Give the event loop one chance to run before awaiting anything + # individually. If `concurrent_iter` were lazy, nothing would have been + # scheduled yet and `started` would still be all-False here. + await asyncio.sleep(0) + assert started == [True, True, True] + + results = [await t for t in tasks] + assert results == [0, 1, 2] + + # todo: test def test_concurrent_map() -> None: ... diff --git a/tests/test_fused_pipeline.py b/tests/test_fused_pipeline.py index fd86936853..7fa3ef2277 100644 --- a/tests/test_fused_pipeline.py +++ b/tests/test_fused_pipeline.py @@ -2,6 +2,7 @@ from __future__ import annotations +import asyncio from dataclasses import dataclass, field, replace from typing import TYPE_CHECKING, Any @@ -25,8 +26,9 @@ from zarr.storage import MemoryStore, StorePath if TYPE_CHECKING: + from zarr.abc.store import ByteRequest from zarr.core.array_spec import ArraySpec - from zarr.core.buffer import Buffer, NDBuffer + from zarr.core.buffer import Buffer, BufferPrototype, NDBuffer @pytest.mark.parametrize( @@ -439,6 +441,103 @@ def test_thread_pool_read_worker_exception_propagates() -> None: arr[:] +def test_resolve_max_workers_warns_and_falls_back_on_invalid_config() -> None: + """`codec_pipeline.max_workers` arrives via the config/env layer (e.g. + `ZARR_CODEC_PIPELINE__MAX_WORKERS`), so garbage input should warn and fall + back to the default rather than raising mid-read. + """ + import os + + import zarr.core.codec_pipeline as cp_mod + from zarr.errors import ZarrUserWarning + + default = os.cpu_count() or 1 + with zarr_config.set({"codec_pipeline.max_workers": "fast"}): + with pytest.warns(ZarrUserWarning, match="max_workers"): + result = cp_mod._resolve_max_workers() + assert result == default + + +async def test_encode_and_write_as_completed_cancels_stray_writes_on_failure() -> None: + """A failing write must not leave sibling writes running in the background. + + `_encode_and_write_as_completed` fires one write task per chunk as soon as + its encode completes, then `gather`s them. Plain `gather` (without + `return_exceptions=True`) re-raises the first exception without cancelling + the other in-flight tasks, so a still-running write would keep going after + the caller has already seen the exception -- and its eventual outcome is + never retrieved (an unraisable "Task exception was never retrieved" + warning if it later fails). + """ + from zarr.core.array_spec import ArrayConfig, ArraySpec + from zarr.core.buffer import default_buffer_prototype + from zarr.core.buffer.cpu import NDBuffer as CPUNDBuffer + from zarr.core.chunk_utils import ChunkTransform + from zarr.core.codec_pipeline import _encode_and_write_as_completed + from zarr.core.dtype import get_data_type_from_native_dtype + + write_started = asyncio.Event() + write_finished = False + + class _SlowByteSetter: + async def get( + self, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Buffer | None: + return None + + async def set(self, value: Buffer) -> None: + nonlocal write_finished + write_started.set() + await asyncio.sleep(0.2) + write_finished = True + + async def delete(self) -> None: + pass + + async def set_if_not_exists(self, default: Buffer) -> None: + pass + + class _FailingByteSetter: + async def get( + self, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Buffer | None: + return None + + async def set(self, value: Buffer) -> None: + raise RuntimeError("simulated write failure") + + async def delete(self) -> None: + pass + + async def set_if_not_exists(self, default: Buffer) -> None: + pass + + zdtype = get_data_type_from_native_dtype(np.dtype("uint8")) + chunk_spec = ArraySpec( + shape=(1,), + dtype=zdtype, + fill_value=zdtype.cast_scalar(0), + config=ArrayConfig(order="C", write_empty_chunks=True), + prototype=default_buffer_prototype(), + ) + chunk_array = CPUNDBuffer.from_numpy_array(np.zeros(1, dtype="uint8")) + transform = ChunkTransform(codecs=(BytesCodec(),)) + + batch = [ + (_SlowByteSetter(), chunk_array, chunk_spec), + (_FailingByteSetter(), chunk_array, chunk_spec), + ] + + with pytest.raises(RuntimeError, match="simulated write failure"): + await _encode_and_write_as_completed(batch, transform) # type: ignore[arg-type] + + assert write_started.is_set() + # Give the slow write's sleep long enough to finish if it were left + # running unattended in the background instead of being cancelled. + await asyncio.sleep(0.3) + assert not write_finished, "the slow write should have been cancelled, not left running" + + def test_concurrent_reads_shared_transform_with_pool() -> None: """Concurrent decode through the shared ChunkTransform produces correct data. diff --git a/tests/test_store/test_local.py b/tests/test_store/test_local.py index 61e48a269f..90d214ee2c 100644 --- a/tests/test_store/test_local.py +++ b/tests/test_store/test_local.py @@ -122,58 +122,6 @@ async def test_move( ): await store2.move(destination) - # --- byte-range-write tests: disabled --- - # Byte-range-write support (set_range / set_range_sync / SupportsSetRange) - # was removed from this PR pending a decision on the store interface. These - # tests are known-good and kept commented out to restore once that lands. - # def test_supports_set_range(self, store: LocalStore) -> None: - # """LocalStore should implement SupportsSetRange.""" - # assert isinstance(store, SupportsSetRange) - # - # @pytest.mark.parametrize( - # ("start", "patch", "expected"), - # [ - # (0, b"XX", b"XXAAAAAAAA"), - # (3, b"XX", b"AAAXXAAAAA"), - # (8, b"XX", b"AAAAAAAAXX"), - # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), - # (5, b"B", b"AAAAABAAAA"), - # (0, b"BCDE", b"BCDEAAAAAA"), - # ], - # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], - # ) - # async def test_set_range( - # self, store: LocalStore, start: int, patch: bytes, expected: bytes - # ) -> None: - # """set_range should overwrite bytes at the given offset.""" - # await store.set("test/key", cpu.Buffer.from_bytes(b"AAAAAAAAAA")) - # await store.set_range("test/key", cpu.Buffer.from_bytes(patch), start=start) - # result = await store.get("test/key", prototype=cpu.buffer_prototype) - # assert result is not None - # assert result.to_bytes() == expected - # - # @pytest.mark.parametrize( - # ("start", "patch", "expected"), - # [ - # (0, b"XX", b"XXAAAAAAAA"), - # (3, b"XX", b"AAAXXAAAAA"), - # (8, b"XX", b"AAAAAAAAXX"), - # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), - # (5, b"B", b"AAAAABAAAA"), - # (0, b"BCDE", b"BCDEAAAAAA"), - # ], - # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], - # ) - # def test_set_range_sync( - # self, store: LocalStore, start: int, patch: bytes, expected: bytes - # ) -> None: - # """set_range_sync should overwrite bytes at the given offset.""" - # sync(store.set("test/key", cpu.Buffer.from_bytes(b"AAAAAAAAAA"))) - # store.set_range_sync("test/key", cpu.Buffer.from_bytes(patch), start=start) - # result = store.get_sync(key="test/key", prototype=cpu.buffer_prototype) - # assert result is not None - # assert result.to_bytes() == expected - @pytest.mark.parametrize("exclusive", [True, False]) def test_atomic_write_successful(tmp_path: pathlib.Path, exclusive: bool) -> None: diff --git a/tests/test_store/test_memory.py b/tests/test_store/test_memory.py index a976f3738e..013dae7044 100644 --- a/tests/test_store/test_memory.py +++ b/tests/test_store/test_memory.py @@ -126,59 +126,6 @@ def test_write_does_not_alias_source_array( np.testing.assert_array_equal(array[:], expected) - # --- byte-range-write tests: disabled --- - # Byte-range-write support (set_range / set_range_sync / SupportsSetRange) - # was removed from this PR pending a decision on the store interface. These - # tests are known-good and kept commented out to restore once that lands. - # def test_supports_set_range(self, store: MemoryStore) -> None: - # """MemoryStore should implement SupportsSetRange.""" - # assert isinstance(store, SupportsSetRange) - # - # @pytest.mark.parametrize( - # ("start", "patch", "expected"), - # [ - # (0, b"XX", b"XXAAAAAAAA"), - # (3, b"XX", b"AAAXXAAAAA"), - # (8, b"XX", b"AAAAAAAAXX"), - # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), - # (5, b"B", b"AAAAABAAAA"), - # (0, b"BCDE", b"BCDEAAAAAA"), - # ], - # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], - # ) - # async def test_set_range( - # self, store: MemoryStore, start: int, patch: bytes, expected: bytes - # ) -> None: - # """set_range should overwrite bytes at the given offset.""" - # await store.set("test/key", cpu.Buffer.from_bytes(b"AAAAAAAAAA")) - # await store.set_range("test/key", cpu.Buffer.from_bytes(patch), start=start) - # result = await store.get("test/key", prototype=cpu.buffer_prototype) - # assert result is not None - # assert result.to_bytes() == expected - # - # @pytest.mark.parametrize( - # ("start", "patch", "expected"), - # [ - # (0, b"XX", b"XXAAAAAAAA"), - # (3, b"XX", b"AAAXXAAAAA"), - # (8, b"XX", b"AAAAAAAAXX"), - # (0, b"ZZZZZZZZZZ", b"ZZZZZZZZZZ"), - # (5, b"B", b"AAAAABAAAA"), - # (0, b"BCDE", b"BCDEAAAAAA"), - # ], - # ids=["start", "middle", "end", "full-overwrite", "single-byte", "multi-byte-start"], - # ) - # def test_set_range_sync( - # self, store: MemoryStore, start: int, patch: bytes, expected: bytes - # ) -> None: - # """set_range_sync should overwrite bytes at the given offset.""" - # store._is_open = True - # store._store_dict["test/key"] = cpu.Buffer.from_bytes(b"AAAAAAAAAA") - # store.set_range_sync("test/key", cpu.Buffer.from_bytes(patch), start=start) - # result = store.get_sync(key="test/key", prototype=cpu.buffer_prototype) - # assert result is not None - # assert result.to_bytes() == expected - # TODO: fix this warning @pytest.mark.filterwarnings("ignore:Unclosed client session:ResourceWarning") From ec8e70ad86990e4c1bf57478fe13769885e31882 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 30 Jul 2026 12:00:36 +0000 Subject: [PATCH 431/468] chore(deps): bump the python-dependencies group across 1 directory with 11 updates (#4216) * chore(deps): bump the python-dependencies group across 1 directory with 11 updates Bumps the python-dependencies group with 11 updates in the / directory: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.5.0` | `2.5.1` | | [typer](https://github.com/fastapi/typer) | `0.26.8` | `0.27.0` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.14.3` | `7.15.2` | | [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.155.7` | `6.160.0` | | [tomlkit](https://github.com/python-poetry/tomlkit) | `0.15.0` | `0.15.1` | | [uv](https://github.com/astral-sh/uv) | `0.11.26` | `0.11.31` | | [mkdocs-material[imaging]](https://github.com/squidfunk/mkdocs-material) | `9.7.6` | `9.7.7` | | [mkdocstrings](https://github.com/mkdocstrings/mkdocstrings) | `1.0.4` | `1.0.6` | | [markdown-exec[ansi]](https://github.com/pawamoy/markdown-exec) | `1.12.1` | `1.12.3` | | [ruff](https://github.com/astral-sh/ruff) | `0.15.20` | `0.15.22` | | [mypy](https://github.com/python/mypy) | `2.1.0` | `2.3.0` | Updates `numpy` from 2.5.0 to 2.5.1 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.5.0...v2.5.1) Updates `typer` from 0.26.8 to 0.27.0 - [Release notes](https://github.com/fastapi/typer/releases) - [Changelog](https://github.com/fastapi/typer/blob/master/docs/release-notes.md) - [Commits](https://github.com/fastapi/typer/compare/0.26.8...0.27.0) Updates `coverage` from 7.14.3 to 7.15.2 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](https://github.com/coveragepy/coveragepy/compare/7.14.3...7.15.2) Updates `hypothesis` from 6.155.7 to 6.160.0 - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/v6.155.7...v6.160.0) Updates `tomlkit` from 0.15.0 to 0.15.1 - [Release notes](https://github.com/python-poetry/tomlkit/releases) - [Changelog](https://github.com/python-poetry/tomlkit/blob/master/CHANGELOG.md) - [Commits](https://github.com/python-poetry/tomlkit/compare/0.15.0...0.15.1) Updates `uv` from 0.11.26 to 0.11.31 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/0.11.31/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.11.26...0.11.31) Updates `mkdocs-material[imaging]` from 9.7.6 to 9.7.7 - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](https://github.com/squidfunk/mkdocs-material/compare/9.7.6...9.7.7) Updates `mkdocstrings` from 1.0.4 to 1.0.6 - [Release notes](https://github.com/mkdocstrings/mkdocstrings/releases) - [Changelog](https://github.com/mkdocstrings/mkdocstrings/blob/main/CHANGELOG.md) - [Commits](https://github.com/mkdocstrings/mkdocstrings/compare/1.0.4...1.0.6) Updates `markdown-exec[ansi]` from 1.12.1 to 1.12.3 - [Release notes](https://github.com/pawamoy/markdown-exec/releases) - [Changelog](https://github.com/pawamoy/markdown-exec/blob/main/CHANGELOG.md) - [Commits](https://github.com/pawamoy/markdown-exec/compare/1.12.1...1.12.3) Updates `ruff` from 0.15.20 to 0.15.22 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/0.15.22/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.15.20...0.15.22) Updates `mypy` from 2.1.0 to 2.3.0 - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](https://github.com/python/mypy/compare/v2.1.0...v2.3.0) --- updated-dependencies: - dependency-name: coverage dependency-version: 7.15.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: hypothesis dependency-version: 6.160.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: markdown-exec[ansi] dependency-version: 1.12.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: mkdocs-material[imaging] dependency-version: 9.7.7 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: mkdocstrings dependency-version: 1.0.6 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: mypy dependency-version: 2.3.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: numpy dependency-version: 2.5.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.15.22 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: tomlkit dependency-version: 0.15.1 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: typer dependency-version: 0.27.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: uv dependency-version: 0.11.31 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <support@github.com> * fix: satisfy numpy 2.5.1 type stubs in indexing selection normalization numpy 2.5.1 stubs infer np.asarray(<list>) as a float64 array, so mypy now rejects the untyped asarray calls in replace_lists and CoordinateIndexer. Pass dtype=np.intp where the integer dtype is guaranteed, and cast to ArrayOfIntOrBool where the list contents are only known at runtime. Assisted-by: ClaudeCode:claude-fable-5 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- pyproject.toml | 18 +- src/zarr/core/indexing.py | 5 +- uv.lock | 675 ++++++++++++++++++++------------------ 3 files changed, 371 insertions(+), 327 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1927ce4d7c..684ac80b77 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -94,18 +94,18 @@ homepage = "https://github.com/zarr-developers/zarr-python" # pins deliberately, e.g. via dependabot or `uv lock --upgrade`. [dependency-groups] test = [ - "coverage==7.14.3", + "coverage==7.15.2", "pytest==9.1.1", "pytest-asyncio==1.4.0", "pytest-cov==7.1.0", "pytest-accept==0.3.0", "numpydoc==1.10.0", - "hypothesis==6.155.7", + "hypothesis==6.160.0", "pytest-xdist==3.8.0", "pytest-benchmark==5.2.3", "pytest-codspeed==5.0.3", - "tomlkit==0.15.0", - "uv==0.11.26", + "tomlkit==0.15.1", + "uv==0.11.31", ] remote-tests = [ {include-group = "test"}, @@ -121,15 +121,15 @@ release = [ ] docs = [ # Doc building - "mkdocs-material[imaging]==9.7.6", + "mkdocs-material[imaging]==9.7.7", "mkdocs==1.6.1", - "mkdocstrings==1.0.4", + "mkdocstrings==1.0.6", "mkdocstrings-python==2.0.5", "mike==2.2.0", "mkdocs-redirects==1.2.3", - "markdown-exec[ansi]==1.12.1", + "markdown-exec[ansi]==1.12.3", "griffe-inherited-docstrings==1.1.3", - "ruff==0.15.20", + "ruff==0.15.22", # Changelog generation {include-group = "release"}, # Optional dependencies to run examples @@ -143,7 +143,7 @@ dev = [ {include-group = "remote-tests"}, {include-group = "docs"}, "universal-pathlib", - "mypy==2.1.0", + "mypy==2.3.0", ] [tool.coverage.report] diff --git a/src/zarr/core/indexing.py b/src/zarr/core/indexing.py index 875c22fbd3..a1b050cb7b 100644 --- a/src/zarr/core/indexing.py +++ b/src/zarr/core/indexing.py @@ -512,7 +512,8 @@ def replace_ellipsis(selection: Any, shape: tuple[int, ...]) -> SelectionNormali def replace_lists(selection: SelectionNormalized) -> SelectionNormalized: return tuple( - np.asarray(dim_sel) if isinstance(dim_sel, list) else dim_sel for dim_sel in selection + cast("ArrayOfIntOrBool", np.asarray(dim_sel)) if isinstance(dim_sel, list) else dim_sel + for dim_sel in selection ) @@ -1193,7 +1194,7 @@ def __init__( # some initial normalization selection_normalized = cast("CoordinateSelectionNormalized", ensure_tuple(selection)) selection_normalized = tuple( - np.asarray([i]) if is_integer(i) else i for i in selection_normalized + np.asarray([i], dtype=np.intp) if is_integer(i) else i for i in 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name = "astroid", specifier = "==4.1.2" }, { name = "botocore" }, - { name = "coverage", specifier = "==7.14.3" }, + { name = "coverage", specifier = "==7.15.2" }, { name = "fsspec", specifier = ">=2023.10.0" }, { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, - { name = "hypothesis", specifier = "==6.155.7" }, - { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.1" }, + { name = "hypothesis", specifier = "==6.160.0" }, + { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.3" }, { name = "mike", specifier = "==2.2.0" }, { name = "mkdocs", specifier = "==1.6.1" }, - { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.6" }, + { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.7" }, { name = "mkdocs-redirects", specifier = "==1.2.3" }, - { name = "mkdocstrings", specifier = "==1.0.4" }, + { name = "mkdocstrings", specifier = "==1.0.6" }, { name = "mkdocstrings-python", specifier = "==2.0.5" }, { name = "moto", extras = ["s3", "server"], specifier = "==5.2.2" }, - { name = "mypy", specifier = "==2.1.0" }, + { name = "mypy", specifier = "==2.3.0" }, { name = "numcodecs", extras = ["msgpack"] }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "obstore", specifier = ">=0.5.1" }, @@ -3546,35 +3589,35 @@ dev = [ { name = "pytest-cov", specifier = "==7.1.0" }, { name = "pytest-xdist", specifier = "==3.8.0" }, { name = "requests", specifier = "==2.34.2" }, - { name = "ruff", specifier = "==0.15.20" }, + { name = "ruff", specifier = "==0.15.22" }, { name = "s3fs", specifier = ">=2023.10.0" }, - { name = "tomlkit", specifier = "==0.15.0" }, + { name = "tomlkit", specifier = "==0.15.1" }, { name = "towncrier", specifier = "==25.8.0" }, { name = "universal-pathlib" }, - { name = "uv", specifier = "==0.11.26" }, + { name = "uv", specifier = "==0.11.31" }, ] docs = [ { name = "astroid", specifier = "==4.1.2" }, { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, - { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.1" }, + { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.3" }, { name = "mike", specifier = "==2.2.0" }, { name = "mkdocs", specifier = "==1.6.1" }, - { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.6" }, + { name = "mkdocs-material", extras = ["imaging"], specifier = "==9.7.7" }, { name = "mkdocs-redirects", specifier = "==1.2.3" }, - { name = "mkdocstrings", specifier = "==1.0.4" }, + { name = "mkdocstrings", specifier = "==1.0.6" }, { name = "mkdocstrings-python", specifier = "==2.0.5" }, { name = "numcodecs", extras = ["msgpack"] }, { name = "pytest", specifier = "==9.1.1" }, - { name = "ruff", specifier = "==0.15.20" }, + { name = "ruff", specifier = "==0.15.22" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "towncrier", specifier = "==25.8.0" }, ] release = [{ name = "towncrier", specifier = "==25.8.0" }] remote-tests = [ { name = "botocore" }, - { name = "coverage", specifier = "==7.14.3" }, + { name = "coverage", specifier = "==7.15.2" }, { name = "fsspec", specifier = ">=2023.10.0" }, - { name = "hypothesis", specifier = "==6.155.7" }, + { name = "hypothesis", specifier = "==6.160.0" }, { name = "moto", extras = ["s3", "server"], specifier = "==5.2.2" }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "obstore", specifier = ">=0.5.1" }, @@ -3587,12 +3630,12 @@ remote-tests = [ { name = "pytest-xdist", specifier = "==3.8.0" }, { name = "requests", specifier = "==2.34.2" }, { name = "s3fs", specifier = ">=2023.10.0" }, - { name = "tomlkit", specifier = "==0.15.0" }, - { name = "uv", specifier = "==0.11.26" }, + { name = "tomlkit", specifier = "==0.15.1" }, + { name = "uv", specifier = "==0.11.31" }, ] test = [ - { name = "coverage", specifier = "==7.14.3" }, - { name = "hypothesis", specifier = "==6.155.7" }, + { name = "coverage", specifier = "==7.15.2" }, + { name = "hypothesis", specifier = "==6.160.0" }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "pytest", specifier = "==9.1.1" }, { name = "pytest-accept", specifier = "==0.3.0" }, @@ -3601,6 +3644,6 @@ test = [ { name = "pytest-codspeed", specifier = "==5.0.3" }, { name = "pytest-cov", specifier = "==7.1.0" }, { name = "pytest-xdist", specifier = "==3.8.0" }, - { name = "tomlkit", specifier = "==0.15.0" }, - { name = "uv", specifier = "==0.11.26" }, + { name = "tomlkit", specifier = "==0.15.1" }, + { name = "uv", specifier = "==0.11.31" }, ] From 57e66d92ed26eb02ca3931f253de052c0a890042 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 30 Jul 2026 14:28:22 +0200 Subject: [PATCH 432/468] fix: reject malformed chunk keys in DefaultChunkKeyEncoding (#4219) * fix: reject malformed chunk keys in DefaultChunkKeyEncoding decode_chunk_key stripped a single leading character and split the rest, so any key at all decoded to something. "0/1" silently became (1,) -- the "0" was eaten as if it were the "c" prefix -- and a key written with one separator decoded wrongly under an encoding configured with the other. Validate the "c<separator>" prefix and raise ValueError when it is absent, so a key that is not a chunk key for this encoding is reported rather than silently misread. Adds the tests this method never had, covering the round trip for both separators and each way a key can fail to carry the prefix. Assisted-by: ClaudeCode:claude-fable-5 * Rename 250.bugfix.md to 4219.bugfix.md --- changes/4219.bugfix.md | 3 ++ src/zarr/core/chunk_key_encodings.py | 6 ++- tests/test_chunk_key_encodings.py | 65 ++++++++++++++++++++++++++++ 3 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 changes/4219.bugfix.md create mode 100644 tests/test_chunk_key_encodings.py diff --git a/changes/4219.bugfix.md b/changes/4219.bugfix.md new file mode 100644 index 0000000000..728e8a7e3a --- /dev/null +++ b/changes/4219.bugfix.md @@ -0,0 +1,3 @@ +`DefaultChunkKeyEncoding.decode_chunk_key` now validates that a chunk key +starts with the configured `c<separator>` prefix and raises `ValueError` for +malformed keys, instead of silently decoding them incorrectly. diff --git a/src/zarr/core/chunk_key_encodings.py b/src/zarr/core/chunk_key_encodings.py index 098f2c8981..fb2fd95dee 100644 --- a/src/zarr/core/chunk_key_encodings.py +++ b/src/zarr/core/chunk_key_encodings.py @@ -79,7 +79,11 @@ def __post_init__(self) -> None: def decode_chunk_key(self, chunk_key: str) -> tuple[int, ...]: if chunk_key == "c": return () - return tuple(map(int, chunk_key[1:].split(self.separator))) + # Strip the "c<sep>" prefix (e.g. "c/" or "c.") before splitting. + prefix = "c" + self.separator + if chunk_key.startswith(prefix): + return tuple(map(int, chunk_key[len(prefix) :].split(self.separator))) + raise ValueError(f"Invalid chunk key for default encoding: {chunk_key!r}") def encode_chunk_key(self, chunk_coords: tuple[int, ...]) -> str: return self.separator.join(map(str, ("c",) + chunk_coords)) diff --git a/tests/test_chunk_key_encodings.py b/tests/test_chunk_key_encodings.py new file mode 100644 index 0000000000..dcc93b9249 --- /dev/null +++ b/tests/test_chunk_key_encodings.py @@ -0,0 +1,65 @@ +from __future__ import annotations + +import pytest + +from zarr.core.chunk_key_encodings import DefaultChunkKeyEncoding, V2ChunkKeyEncoding + + +@pytest.mark.parametrize("separator", ["/", "."]) +@pytest.mark.parametrize( + "coords", + [(), (0,), (1, 2), (10, 0, 3)], +) +def test_default_encoding_round_trips(separator: str, coords: tuple[int, ...]) -> None: + """Encoding coordinates and decoding the result returns the coordinates.""" + encoding = DefaultChunkKeyEncoding(separator=separator) # type: ignore[arg-type] + + key = encoding.encode_chunk_key(coords) + assert encoding.decode_chunk_key(key) == coords + + +@pytest.mark.parametrize("separator", ["/", "."]) +@pytest.mark.parametrize("coords", [(0,), (1, 2), (10, 0, 3)]) +def test_v2_encoding_round_trips(separator: str, coords: tuple[int, ...]) -> None: + """The v2 encoding round-trips coordinates for either separator.""" + encoding = V2ChunkKeyEncoding(separator=separator) # type: ignore[arg-type] + + key = encoding.encode_chunk_key(coords) + assert encoding.decode_chunk_key(key) == coords + + +@pytest.mark.parametrize("separator", ["/", "."]) +def test_v2_zero_dimensional_key_is_ambiguous(separator: str) -> None: + """A 0-d v2 array stores its sole chunk under `"0"`, the same key a 1-d + array uses for chunk 0, so decoding cannot recover the empty tuple on its + own -- the array's dimensionality is what disambiguates it.""" + encoding = V2ChunkKeyEncoding(separator=separator) # type: ignore[arg-type] + + assert encoding.encode_chunk_key(()) == "0" + assert encoding.decode_chunk_key("0") == (0,) + + +@pytest.mark.parametrize( + "chunk_key", + [ + "0/1", # no "c" prefix at all + "c0/1", # "c" not followed by the separator + "x/0/1", # wrong prefix character + "", + ], +) +def test_default_encoding_rejects_key_without_prefix(chunk_key: str) -> None: + """A key that does not carry the `c<separator>` prefix is not a chunk key + for this encoding, and must be rejected rather than silently decoded.""" + encoding = DefaultChunkKeyEncoding(separator="/") + + with pytest.raises(ValueError, match="Invalid chunk key"): + encoding.decode_chunk_key(chunk_key) + + +def test_default_encoding_rejects_key_using_the_other_separator() -> None: + """A key encoded with `.` is not valid for a `/`-separated encoding.""" + encoding = DefaultChunkKeyEncoding(separator="/") + + with pytest.raises(ValueError, match="Invalid chunk key"): + encoding.decode_chunk_key("c.0.1") From 6f52da5b8ce4e28031f4ad6c3287795fec971105 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 30 Jul 2026 17:44:37 +0200 Subject: [PATCH 433/468] fix: gate fused sync fast paths on full store sync capability; wrappers forward it (#4206) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The fused write gate checked only SupportsSetSync, but write_sync also needs get_sync (partial-chunk read-modify-write) and delete_sync (all-fill chunk cleanup): a set-sync-only store passed the gate, wrote some chunks, then died mid-batch with TypeError. And WrapperStore forwarded no *_sync method, so every wrapped store (e.g. LatencyStore) silently lost the sync fast path — latency benchmarks measured the async fallback while claiming to measure the fused sync path. Both gates now consult _store_supports_sync_io: structural membership in SupportsSyncStore (the full get/set/delete sync surface) combined with a per-instance _supports_sync_io opt-out (absent means capable). This is a private, interim convention pending a formal sync/async store architecture — the store-side twin of the codec-side _sync_capable convention from #4179 — deliberately not new public API. WrapperStore delegates the three sync methods and forwards the wrapped store's capability, so wrapping a sync store keeps the fast path and wrapping an async-only store falls back cleanly; LoggingStore logs the delegated sync calls. LatencyStore fixes: sync reads/writes now sleep the configured latency on the worker thread; get_ranges/get_partial_values route through the latency-injecting get instead of bypassing the wrapper; _with_store passes the raw (loc, scale) latency config instead of a single sampled float, so derived stores keep the distribution. Assisted-by: ClaudeCode:claude-fable-5 --- changes/4206.bugfix.md | 1 + src/zarr/abc/store.py | 47 +++++- src/zarr/codecs/sharding.py | 4 +- src/zarr/core/codec_pipeline.py | 32 ++-- src/zarr/experimental/cache_store.py | 10 ++ src/zarr/storage/_logging.py | 21 +++ src/zarr/storage/_wrapper.py | 42 ++++- src/zarr/testing/store.py | 80 ++++++++- tests/test_codec_pipeline_suite.py | 18 ++- tests/test_experimental/test_cache_store.py | 37 +++++ tests/test_fused_pipeline.py | 170 +++++++++++++++++++- tests/test_store/test_get_ranges.py | 8 +- tests/test_store/test_latency.py | 108 +++++++++++++ tests/test_store/test_wrapper.py | 50 +++++- 14 files changed, 596 insertions(+), 32 deletions(-) create mode 100644 changes/4206.bugfix.md diff --git a/changes/4206.bugfix.md b/changes/4206.bugfix.md new file mode 100644 index 0000000000..a01c969449 --- /dev/null +++ b/changes/4206.bugfix.md @@ -0,0 +1 @@ +Fixed `FusedCodecPipeline`'s gating of its synchronous fast paths: stores exposing only part of the sync surface (e.g. `set_sync` without `get_sync`) now fall back cleanly to the async path instead of failing mid-write, and `WrapperStore` now forwards `get_sync`/`set_sync`/`delete_sync` to the wrapped store so wrapped sync-capable stores keep the fast path. The capability decision uses a private, interim convention (`zarr.abc.store._store_supports_sync_io`) rather than new public API, pending a formal sync/async store architecture. Also fixed `LatencyStore`: synchronous reads and writes now pay the configured latency, `get_ranges`/`get_partial_values` no longer bypass latency injection, and derived stores (e.g. from `with_read_only`) keep a stochastic `(loc, scale)` latency configuration instead of freezing a single sample. diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py index c60d2468c5..af528ec533 100644 --- a/src/zarr/abc/store.py +++ b/src/zarr/abc/store.py @@ -662,6 +662,15 @@ def delete_sync(self) -> None: ... @runtime_checkable class SupportsGetSync(Protocol): + """Store protocol for synchronous reads (`get_sync`). + + The store sync surface is all-or-nothing: a store implementing any of the + `*_sync` methods must implement all of them (`SupportsSyncStore`), because + consumers mix sync reads, writes, and deletes within one operation. + Capability-gated callers consult `_store_supports_sync_io` rather than the + individual protocols. + """ + def get_sync( self, key: str, @@ -673,16 +682,52 @@ def get_sync( @runtime_checkable class SupportsSetSync(Protocol): + """Store protocol for synchronous writes (`set_sync`). + + See `SupportsGetSync` for the all-or-nothing contract on the store sync + surface. + """ + def set_sync(self, key: str, value: Buffer) -> None: ... @runtime_checkable class SupportsDeleteSync(Protocol): + """Store protocol for synchronous deletes (`delete_sync`). + + See `SupportsGetSync` for the all-or-nothing contract on the store sync + surface. + """ + def delete_sync(self, key: str) -> None: ... @runtime_checkable -class SupportsSyncStore(SupportsGetSync, SupportsSetSync, SupportsDeleteSync, Protocol): ... +class SupportsSyncStore(SupportsGetSync, SupportsSetSync, SupportsDeleteSync, Protocol): + """The full store sync surface: `get_sync`, `set_sync`, and `delete_sync`.""" + + +def _store_supports_sync_io(store: object) -> bool: + """Whether `store` can serve the full synchronous IO surface right now. + + Structural membership in `SupportsSyncStore` is necessary but not always + sufficient: a store can present the `*_sync` methods while its ability to + run them depends on runtime state the type system cannot see. Wrapper + stores are the canonical case — `WrapperStore` delegates the sync methods + to the store it wraps, so they only work when the wrapped store is itself + sync-capable. Such stores opt out dynamically via a `_supports_sync_io` + attribute/property (absent means capable). + + This is an interim, private convention pending a formal sync/async store + architecture — the store-side twin of the codec-side `_sync_capable` + convention consulted by `zarr.abc.codec._codec_supports_sync`. + + Synchronous IO is all-or-nothing: consumers such as the fused codec + pipeline mix synchronous reads, writes, and deletes within one batch + (e.g. a partial-chunk write reads existing bytes and an all-fill chunk is + deleted), so a partial sync surface never satisfies this predicate. + """ + return isinstance(store, SupportsSyncStore) and getattr(store, "_supports_sync_io", True) async def set_or_delete(byte_setter: ByteSetter, value: Buffer | None) -> None: diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index cdfdae6c89..d8ca8bdf62 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -23,7 +23,7 @@ RangeByteRequest, Store, SuffixByteRequest, - SupportsGetSync, + _store_supports_sync_io, ) from zarr.codecs._deprecated_enum import _coerce_enum_input, _DeprecatedStrEnumMeta from zarr.codecs.bytes import BytesCodec @@ -1721,7 +1721,7 @@ def _load_partial_shard_maybe_sync( shard_dict: ShardMutableMapping = {} store = byte_getter.store if hasattr(byte_getter, "store") else None - if isinstance(store, Store) and isinstance(store, SupportsGetSync): + if isinstance(store, Store) and _store_supports_sync_io(store): # External store: coalesce via get_ranges_sync (mirrors get_ranges). byte_ranges = [byte_range for _, byte_range in chunk_coord_byte_ranges] try: diff --git a/src/zarr/core/codec_pipeline.py b/src/zarr/core/codec_pipeline.py index 92fd0970fe..597f338c42 100644 --- a/src/zarr/core/codec_pipeline.py +++ b/src/zarr/core/codec_pipeline.py @@ -331,8 +331,8 @@ async def _async_read_fallback( then scatters each decoded chunk into `out` at its `out_selection`. Used by both `BatchedCodecPipeline.read_batch` (non-partial-decode - branch) and `FusedCodecPipeline.read` (when the store is not a - `SupportsGetSync` / sync transform is unavailable). + branch) and `FusedCodecPipeline.read` (when the store does not advertise + sync IO / sync transform is unavailable). """ chunk_array_batch: list[NDBuffer | None] @@ -393,8 +393,8 @@ async def _async_write_fallback( if encoding produced `None` or the chunk dropped). Used by both `BatchedCodecPipeline.write_batch` (non-partial-encode - branch) and `FusedCodecPipeline.write` (when the store is not a - `SupportsSetSync` / sync transform is unavailable). + branch) and `FusedCodecPipeline.write` (when the store does not advertise + sync IO / sync transform is unavailable). """ if use_sync := ( @@ -1265,16 +1265,17 @@ async def read( return () # Fast path: sync transform plus synchronous IO. For StorePath the gate - # is on the STORE's sync support (StorePath always has a get_sync - # method, but it only works when its store does); for other byte - # getters (e.g. the sharding codec's in-memory _ShardingByteGetter) the - # SyncByteGetter protocol is the gate. - from zarr.abc.store import SupportsGetSync, SyncByteGetter + # is the STORE's sync-IO capability (`_store_supports_sync_io`) (StorePath always has a + # get_sync method, but it only works when its store implements the full + # sync surface); for other byte getters (e.g. the sharding codec's + # in-memory _ShardingByteGetter) the SyncByteGetter protocol is the + # gate. + from zarr.abc.store import SyncByteGetter, _store_supports_sync_io from zarr.storage._common import StorePath first_bg = batch[0][0] if self.sync_transform is not None and ( - (isinstance(first_bg, StorePath) and isinstance(first_bg.store, SupportsGetSync)) + (isinstance(first_bg, StorePath) and _store_supports_sync_io(first_bg.store)) or (not isinstance(first_bg, StorePath) and isinstance(first_bg, SyncByteGetter)) ): # One thread hop for the WHOLE batch — not per chunk, so the fused @@ -1328,14 +1329,17 @@ async def write( return # Fast path: sync transform plus synchronous IO. Mirrors `read`: gate - # StorePath on the store's sync support, other byte setters (e.g. the - # sharding codec's in-memory _ShardingByteSetter) on SyncByteSetter. - from zarr.abc.store import SupportsSetSync, SyncByteSetter + # StorePath on the store's sync-IO capability (`_store_supports_sync_io`) — write_sync + # needs the FULL sync surface (get_sync for partial-chunk + # read-modify-write, delete_sync for all-fill chunks), not just + # set_sync — and other byte setters (e.g. the sharding codec's + # in-memory _ShardingByteSetter) on SyncByteSetter. + from zarr.abc.store import SyncByteSetter, _store_supports_sync_io from zarr.storage._common import StorePath first_bs = batch[0][0] if self.sync_transform is not None and ( - (isinstance(first_bs, StorePath) and isinstance(first_bs.store, SupportsSetSync)) + (isinstance(first_bs, StorePath) and _store_supports_sync_io(first_bs.store)) or (not isinstance(first_bs, StorePath) and isinstance(first_bs, SyncByteSetter)) ): # One thread hop for the whole batch; see the matching comment in diff --git a/src/zarr/experimental/cache_store.py b/src/zarr/experimental/cache_store.py index dd50693ad9..20cb4d4c0f 100644 --- a/src/zarr/experimental/cache_store.py +++ b/src/zarr/experimental/cache_store.py @@ -329,6 +329,16 @@ async def _get_no_cache( await self._cache_miss(key, byte_range, result) return result + @property + def _supports_sync_io(self) -> bool: + # The caching logic lives only in the async get/set/delete overrides; + # the sync methods inherited from `WrapperStore` delegate straight to + # the source store, so a sync-capable consumer (the fused codec + # pipeline) would write and delete around the cache, leaving stale + # entries that later async reads serve as current data. Opt out of + # sync IO until the sync surface is cache-aware. + return False + async def get( self, key: str, diff --git a/src/zarr/storage/_logging.py b/src/zarr/storage/_logging.py index c6f58ccd61..cdf0731430 100644 --- a/src/zarr/storage/_logging.py +++ b/src/zarr/storage/_logging.py @@ -204,6 +204,27 @@ async def delete(self, key: str) -> None: with self.log(key): return await self._store.delete(key=key) + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + # docstring inherited + with self.log(key): + return super().get_sync(key, prototype=prototype, byte_range=byte_range) + + def set_sync(self, key: str, value: Buffer) -> None: + # docstring inherited + with self.log(key): + return super().set_sync(key, value) + + def delete_sync(self, key: str) -> None: + # docstring inherited + with self.log(key): + return super().delete_sync(key) + async def list(self) -> AsyncGenerator[str, None]: # docstring inherited with self.log(): diff --git a/src/zarr/storage/_wrapper.py b/src/zarr/storage/_wrapper.py index 37aeb8166f..6f498a655d 100644 --- a/src/zarr/storage/_wrapper.py +++ b/src/zarr/storage/_wrapper.py @@ -11,7 +11,13 @@ from zarr.abc.store import ByteRequest from zarr.core.buffer import BufferPrototype -from zarr.abc.store import Store +from zarr.abc.store import ( + Store, + SupportsDeleteSync, + SupportsGetSync, + SupportsSetSync, + _store_supports_sync_io, +) class WrapperStore[T_Store: Store](Store): @@ -149,6 +155,40 @@ def supports_writes(self) -> bool: def supports_deletes(self) -> bool: return self._store.supports_deletes + @property + def _supports_sync_io(self) -> bool: + # The delegating `*_sync` methods below make every wrapper structurally + # satisfy `SupportsSyncStore`; whether they can actually run depends on + # the wrapped store, so forward its capability (see + # `zarr.abc.store._store_supports_sync_io`). + return _store_supports_sync_io(self._store) + + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + """Forward `get_sync` to the wrapped store.""" + if not isinstance(self._store, SupportsGetSync): + raise TypeError(f"Store {type(self._store).__name__} does not support synchronous get.") + return self._store.get_sync(key, prototype=prototype, byte_range=byte_range) # type: ignore[unreachable] + + def set_sync(self, key: str, value: Buffer) -> None: + """Forward `set_sync` to the wrapped store.""" + if not isinstance(self._store, SupportsSetSync): + raise TypeError(f"Store {type(self._store).__name__} does not support synchronous set.") + self._store.set_sync(key, value) # type: ignore[unreachable] + + def delete_sync(self, key: str) -> None: + """Forward `delete_sync` to the wrapped store.""" + if not isinstance(self._store, SupportsDeleteSync): + raise TypeError( + f"Store {type(self._store).__name__} does not support synchronous delete." + ) + self._store.delete_sync(key) # type: ignore[unreachable] + async def delete(self, key: str) -> None: await self._store.delete(key) diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index d7011440e0..f64d8e9364 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -2,6 +2,7 @@ import asyncio import pickle +import time from abc import abstractmethod from typing import TYPE_CHECKING, Self @@ -10,6 +11,7 @@ from zarr.storage import WrapperStore if TYPE_CHECKING: + from collections.abc import AsyncIterator, Iterable, Sequence from typing import Any from zarr.core.buffer.core import BufferPrototype @@ -718,7 +720,10 @@ def set_latency(self) -> float: return max(0.0, np.random.normal(loc=self._set_latency[0], scale=self._set_latency[1])) def _with_store(self, store: Store) -> Self: - return type(self)(store, get_latency=self.get_latency, set_latency=self.set_latency) + # Pass the raw latency config, not the sampled `get_latency`/`set_latency` + # properties — sampling would freeze a `(loc, scale)` distribution into + # one fixed float on derived stores (e.g. via `with_read_only`). + return type(self)(store, get_latency=self._get_latency, set_latency=self._set_latency) async def set(self, key: str, value: Buffer) -> None: """ @@ -763,3 +768,76 @@ async def get( """ await asyncio.sleep(self.get_latency) return await self._store.get(key, prototype=prototype, byte_range=byte_range) + + def get_sync( + self, + key: str, + *, + prototype: BufferPrototype | None = None, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + """Add latency to `get_sync`. + + Sleeps `self.get_latency` on the calling thread (the sync path runs on + worker threads, not the event loop) before delegating to the wrapped + store. + """ + time.sleep(self.get_latency) + return super().get_sync(key, prototype=prototype, byte_range=byte_range) + + def set_sync(self, key: str, value: Buffer) -> None: + """Add latency to `set_sync`. + + Sleeps `self.set_latency` on the calling thread (the sync path runs on + worker threads, not the event loop) before delegating to the wrapped + store. + """ + time.sleep(self.set_latency) + super().set_sync(key, value) + + async def get_ranges( + self, + key: str, + byte_ranges: Sequence[ByteRequest | None], + *, + prototype: BufferPrototype, + max_concurrency: int | None = None, + max_gap_bytes: int | None = None, + max_coalesced_bytes: int | None = None, + ) -> AsyncIterator[Sequence[tuple[int, Buffer | None]]]: + """Byte-range reads built on `self.get`, so each fetch pays latency. + + Routes through the coalescing `Store.get_ranges` default instead of the + `WrapperStore` delegation, which would bypass this wrapper's `get` and + therefore the synthetic latency. `None` for a coalescing kwarg means + "use the `Store` default". + """ + kwargs: dict[str, int] = {} + if max_concurrency is not None: + kwargs["max_concurrency"] = max_concurrency + if max_gap_bytes is not None: + kwargs["max_gap_bytes"] = max_gap_bytes + if max_coalesced_bytes is not None: + kwargs["max_coalesced_bytes"] = max_coalesced_bytes + async for group in Store.get_ranges(self, key, byte_ranges, prototype=prototype, **kwargs): + yield group + + async def get_partial_values( + self, + prototype: BufferPrototype, + key_ranges: Iterable[tuple[str, ByteRequest | None]], + ) -> list[Buffer | None]: + """Partial-value reads built on `self.get`, so each fetch pays latency. + + Issues one `self.get` per `(key, byte_range)` pair instead of the + `WrapperStore` delegation, which would bypass this wrapper's `get` and + therefore the synthetic latency. + """ + return list( + await asyncio.gather( + *( + self.get(key, prototype=prototype, byte_range=byte_range) + for key, byte_range in key_ranges + ) + ) + ) diff --git a/tests/test_codec_pipeline_suite.py b/tests/test_codec_pipeline_suite.py index 07e1aa2ec4..f0376d185a 100644 --- a/tests/test_codec_pipeline_suite.py +++ b/tests/test_codec_pipeline_suite.py @@ -9,8 +9,8 @@ Each test also runs over a *store axis* that exercises both code paths the synchronous pipelines branch on: -* ``sync`` -> ``MemoryStore`` (supports ``get_sync``/``set_sync``: fast path) -* ``async`` -> ``LatencyStore(MemoryStore())`` (NOT sync-capable: async fallback) +* ``sync`` -> ``MemoryStore`` (full sync surface: fast path) +* ``async`` -> ``_NoSyncIOStore(MemoryStore())`` (NOT sync-capable: async fallback) The async axis is deliberate: a regression that only affects the async fallback of the default pipeline (e.g. a codec-spec-evolution bug that surfaces only on @@ -50,14 +50,22 @@ STORE_KINDS = ["sync", "async"] +class _NoSyncIOStore(LatencyStore): + """An in-memory store that advertises no sync IO capability, so a + synchronous pipeline must fall back to its async path. (A plain wrapper + won't do: `WrapperStore` forwards the wrapped store's sync capability.)""" + + @property + def _supports_sync_io(self) -> bool: + return False + + def _make_store(kind: str) -> Store: if kind == "sync": # MemoryStore supports get_sync/set_sync -> synchronous fast path. return MemoryStore() if kind == "async": - # LatencyStore is NOT SupportsGetSync/SupportsSetSync, so a synchronous - # pipeline must fall back to its async path. Zero latency keeps it fast. - return LatencyStore(MemoryStore(), get_latency=0.0, set_latency=0.0) + return _NoSyncIOStore(MemoryStore(), get_latency=0.0, set_latency=0.0) raise AssertionError(kind) diff --git a/tests/test_experimental/test_cache_store.py b/tests/test_experimental/test_cache_store.py index 5ad56a4335..f688a6ca02 100644 --- a/tests/test_experimental/test_cache_store.py +++ b/tests/test_experimental/test_cache_store.py @@ -1036,3 +1036,40 @@ async def test_delete_invalidates_cached_byte_ranges(self) -> None: # Key is gone from source result = await cached_store.get("key", proto) assert result is None + + +def test_cache_store_opts_out_of_sync_io() -> None: + """`CacheStore` must not advertise sync IO capability. + + Its caching logic lives only in the async `get`/`set`/`delete` overrides, + while the inherited `WrapperStore` sync methods delegate straight to the + source store. If the fused codec pipeline took the sync fast path, writes + and deletes would bypass the cache and later async reads would serve stale + entries. The opt-out forces sync-capable consumers onto the async path, + which keeps the cache coherent. + """ + from zarr.abc.store import _store_supports_sync_io + from zarr.storage import MemoryStore + + cached = CacheStore(MemoryStore(), cache_store=MemoryStore()) + assert _store_supports_sync_io(cached) is False + + +async def test_cache_coherent_after_fused_pipeline_write() -> None: + """Writing through the fused pipeline must not leave stale cache entries.""" + import numpy as np + + import zarr + from zarr.core.config import config as zarr_config + from zarr.storage import MemoryStore + + source = MemoryStore() + cached = CacheStore(source, cache_store=MemoryStore()) + with zarr_config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): + arr = zarr.create_array(cached, shape=(8,), chunks=(8,), dtype="int32", fill_value=0) + arr[:] = np.arange(8, dtype="int32") + np.testing.assert_array_equal(arr[:], np.arange(8)) + # Overwrite, then read back through the same cached handle: the read + # must observe the overwrite, not a cached copy of the first write. + arr[:] = np.arange(100, 108, dtype="int32") + np.testing.assert_array_equal(arr[:], np.arange(100, 108)) diff --git a/tests/test_fused_pipeline.py b/tests/test_fused_pipeline.py index 7fa3ef2277..5c712fa97a 100644 --- a/tests/test_fused_pipeline.py +++ b/tests/test_fused_pipeline.py @@ -16,6 +16,7 @@ ArrayBytesCodecPartialEncodeMixin, BytesBytesCodec, ) +from zarr.abc.store import Store, _store_supports_sync_io from zarr.codecs.bytes import BytesCodec from zarr.codecs.gzip import GzipCodec from zarr.codecs.transpose import TransposeCodec @@ -23,9 +24,13 @@ from zarr.core.codec_pipeline import FusedCodecPipeline from zarr.core.config import config as zarr_config from zarr.registry import register_codec -from zarr.storage import MemoryStore, StorePath +from zarr.storage import MemoryStore, StorePath, WrapperStore +from zarr.storage._utils import _normalize_byte_range_index +from zarr.testing.store import LatencyStore if TYPE_CHECKING: + from collections.abc import AsyncIterator, Callable, Iterable + from zarr.abc.store import ByteRequest from zarr.core.array_spec import ArraySpec from zarr.core.buffer import Buffer, BufferPrototype, NDBuffer @@ -1065,3 +1070,166 @@ def test_partial_mixin_codec_async_partial_only_round_trip(dtype: str) -> None: with zarr_config.set(_BATCHED): np.testing.assert_array_equal(zarr.open_array(store, mode="r")[:], expected) + + +# Sync-IO capability gating (`zarr.abc.store._store_supports_sync_io`) +# +# The fused read/write fast paths must engage iff the store advertises the +# FULL synchronous IO surface (get_sync + set_sync + delete_sync): write_sync +# needs get_sync for partial-chunk read-modify-write and delete_sync for +# all-fill chunk cleanup, so gating on any single protocol can crash +# mid-batch. Wrappers must forward the capability of the wrapped store. +# --------------------------------------------------------------------------- + + +class AsyncOnlyStore(Store): + """Dict-backed store implementing only the async `Store` surface (no `*_sync`).""" + + def __init__(self) -> None: + super().__init__(read_only=False) + self._data: dict[str, Buffer] = {} + + def __eq__(self, other: object) -> bool: + return other is self + + @property + def supports_writes(self) -> bool: + return True + + @property + def supports_deletes(self) -> bool: + return True + + @property + def supports_listing(self) -> bool: + return True + + async def get( + self, key: str, prototype: BufferPrototype, byte_range: ByteRequest | None = None + ) -> Buffer | None: + try: + value = self._data[key] + except KeyError: + return None + start, stop = _normalize_byte_range_index(value, byte_range) + return prototype.buffer.from_buffer(value[start:stop]) + + async def get_partial_values( + self, + prototype: BufferPrototype, + key_ranges: Iterable[tuple[str, ByteRequest | None]], + ) -> list[Buffer | None]: + return [await self.get(key, prototype, byte_range) for key, byte_range in key_ranges] + + async def exists(self, key: str) -> bool: + return key in self._data + + async def set(self, key: str, value: Buffer) -> None: + self._check_writable() + self._data[key] = value + + async def delete(self, key: str) -> None: + self._check_writable() + self._data.pop(key, None) + + async def list(self) -> AsyncIterator[str]: + for key in list(self._data): + yield key + + async def list_prefix(self, prefix: str) -> AsyncIterator[str]: + for key in list(self._data): + if key.startswith(prefix): + yield key + + async def list_dir(self, prefix: str) -> AsyncIterator[str]: + if prefix and not prefix.endswith("/"): + prefix += "/" + seen: set[str] = set() + for key in list(self._data): + if key.startswith(prefix): + head = key.removeprefix(prefix).split("/")[0] + if head not in seen: + seen.add(head) + yield head + + +class SetOnlySyncStore(AsyncOnlyStore): + """Implements `set_sync` but not `get_sync`/`delete_sync` (partial sync surface).""" + + def set_sync(self, key: str, value: Buffer) -> None: + self._check_writable() + self._data[key] = value + + +@pytest.mark.parametrize( + ("store_factory", "expect_sync_path"), + [ + (MemoryStore, True), + (lambda: WrapperStore(MemoryStore()), True), + (lambda: LatencyStore(MemoryStore()), True), + (SetOnlySyncStore, False), + (lambda: WrapperStore(AsyncOnlyStore()), False), + ], + ids=[ + "full-sync", + "wrapper-of-sync", + "latency-wrapper-of-sync", + "set-sync-only", + "wrapper-of-async-only", + ], +) +def test_sync_io_capability_gates_fused_paths( + store_factory: Callable[[], Store], expect_sync_path: bool +) -> None: + """The fused pipeline takes the sync fast path iff the store satisfies + `_store_supports_sync_io`, + and every store round-trips correctly through full writes, partial + (read-modify-write) writes, and all-fill (delete) writes — a store with a + partial sync surface must get a clean async fallback, never a mid-batch + error.""" + from unittest.mock import patch + + store = store_factory() + assert _store_supports_sync_io(store) is expect_sync_path + + calls = {"read_sync": 0, "write_sync": 0} + orig_read_sync = FusedCodecPipeline.read_sync + orig_write_sync = FusedCodecPipeline.write_sync + + def spy_read_sync(self: FusedCodecPipeline, *args: Any, **kwargs: Any) -> Any: + calls["read_sync"] += 1 + return orig_read_sync(self, *args, **kwargs) + + def spy_write_sync(self: FusedCodecPipeline, *args: Any, **kwargs: Any) -> Any: + calls["write_sync"] += 1 + return orig_write_sync(self, *args, **kwargs) + + with zarr_config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): + arr = zarr.create_array( + store=store, + shape=(8,), + chunks=(4,), + dtype="uint8", + compressors=None, + fill_value=0, + ) + assert isinstance(arr._async_array.codec_pipeline, FusedCodecPipeline) + with ( + patch.object(FusedCodecPipeline, "read_sync", spy_read_sync), + patch.object(FusedCodecPipeline, "write_sync", spy_write_sync), + ): + data = np.arange(8, dtype="uint8") + arr[:] = data # complete-chunk writes + arr[:3] = 7 # partial write -> read-modify-write needs get + data[:3] = 7 + np.testing.assert_array_equal(arr[:], data) + arr[4:8] = 0 # all-fill chunk -> delete needed + data[4:8] = 0 + np.testing.assert_array_equal(arr[:], data) + + if expect_sync_path: + assert calls["write_sync"] > 0, "sync-capable store did not take the sync write path" + assert calls["read_sync"] > 0, "sync-capable store did not take the sync read path" + else: + assert calls["write_sync"] == 0, "non-sync store took the sync write path" + assert calls["read_sync"] == 0, "non-sync store took the sync read path" diff --git a/tests/test_store/test_get_ranges.py b/tests/test_store/test_get_ranges.py index f04251adf4..522d6565aa 100644 --- a/tests/test_store/test_get_ranges.py +++ b/tests/test_store/test_get_ranges.py @@ -16,12 +16,12 @@ from zarr.abc.store import RangeByteRequest from zarr.core.buffer import default_buffer_prototype -from zarr.storage import MemoryStore +from zarr.storage import MemoryStore, ZipStore from zarr.storage._wrapper import WrapperStore -from zarr.testing.store import LatencyStore if TYPE_CHECKING: from collections.abc import AsyncIterator, Sequence + from pathlib import Path from zarr.abc.store import ByteRequest from zarr.core.buffer import Buffer, BufferPrototype @@ -89,11 +89,11 @@ def test_get_ranges_sync_missing_key_raises() -> None: store.get_ranges_sync("does-not-exist", [RangeByteRequest(0, 10)], prototype=proto) -def test_get_ranges_sync_on_non_sync_store_raises_type_error() -> None: +def test_get_ranges_sync_on_non_sync_store_raises_type_error(tmp_path: Path) -> None: """`get_ranges_sync` requires the store to support synchronous reads (`SupportsGetSync`); a non-sync store raises TypeError rather than silently falling back.""" - store = LatencyStore(MemoryStore(), get_latency=0.0, set_latency=0.0) + store = ZipStore(tmp_path / "store.zip", mode="w") proto = default_buffer_prototype() with pytest.raises(TypeError, match="does not support synchronous reads"): store.get_ranges_sync("k", [RangeByteRequest(0, 10)], prototype=proto) diff --git a/tests/test_store/test_latency.py b/tests/test_store/test_latency.py index 38ffb17dd6..9cb71fd6a0 100644 --- a/tests/test_store/test_latency.py +++ b/tests/test_store/test_latency.py @@ -1,8 +1,16 @@ from __future__ import annotations +import time +from unittest.mock import patch + +import numpy as np import pytest +import zarr +from zarr.abc.store import RangeByteRequest from zarr.core.buffer import default_buffer_prototype +from zarr.core.codec_pipeline import FusedCodecPipeline +from zarr.core.config import config as zarr_config from zarr.storage import MemoryStore from zarr.testing.store import LatencyStore @@ -55,3 +63,103 @@ async def test_latency_store_with_read_only_round_trip() -> None: # The original read-only wrapper remains read-only assert latency_ro.read_only + + +@pytest.mark.parametrize( + ("get_latency", "set_latency"), + [ + (0.01, 0.02), + ((0.1, 0.05), (0.2, 0.01)), + ], + ids=["scalar", "distribution"], +) +def test_with_store_preserves_latency_config( + get_latency: float | tuple[float, float], set_latency: float | tuple[float, float] +) -> None: + """Derived stores (e.g. via `with_read_only`) keep the raw latency config — + a `(loc, scale)` distribution must not collapse to one sampled float.""" + store = LatencyStore(MemoryStore(), get_latency=get_latency, set_latency=set_latency) + derived = store.with_read_only(True) + assert derived._get_latency == store._get_latency + assert derived._set_latency == store._set_latency + + +def test_sync_methods_inject_latency(monkeypatch: pytest.MonkeyPatch) -> None: + """`get_sync`/`set_sync` sleep the configured latency on the calling thread + before delegating to the wrapped store.""" + sleeps: list[float] = [] + monkeypatch.setattr(time, "sleep", sleeps.append) + + store = LatencyStore(MemoryStore(), get_latency=0.123, set_latency=0.456) + buf = default_buffer_prototype().buffer.from_bytes(b"abcd") + store.set_sync("key", buf) + assert sleeps == [pytest.approx(0.456)] + out = store.get_sync("key", prototype=default_buffer_prototype()) + assert out is not None + assert out.to_bytes() == b"abcd" + assert sleeps == [pytest.approx(0.456), pytest.approx(0.123)] + + +async def test_get_ranges_pays_latency_per_fetch() -> None: + """`get_ranges` routes through the coalescing default built on `self.get`, + so each merged fetch pays the configured latency instead of bypassing it + via WrapperStore delegation. Two ranges further apart than `max_gap_bytes` + cannot coalesce -> exactly two `get` calls.""" + proto = default_buffer_prototype() + inner = MemoryStore() + await inner.set("blob", proto.buffer.from_bytes(bytes(4 << 20))) + store = LatencyStore(inner, get_latency=0.0) + + requests = [RangeByteRequest(0, 10), RangeByteRequest(2 << 20, (2 << 20) + 10)] + results: list[tuple[int, object]] = [] + with patch.object(store, "get", wraps=store.get) as get_spy: + async for group in store.get_ranges("blob", requests, prototype=proto): + results.extend(group) + assert get_spy.await_count == 2 + assert sorted(idx for idx, _ in results) == [0, 1] + for _, buf in results: + assert buf is not None + assert len(buf) == 10 # type: ignore[arg-type] + + +async def test_get_partial_values_routes_through_get() -> None: + """`get_partial_values` issues one `self.get` per key-range so each fetch + pays the configured latency instead of bypassing it via WrapperStore + delegation.""" + proto = default_buffer_prototype() + inner = MemoryStore() + await inner.set("blob", proto.buffer.from_bytes(b"0123456789")) + store = LatencyStore(inner, get_latency=0.0) + + with patch.object(store, "get", wraps=store.get) as get_spy: + results = await store.get_partial_values( + proto, [("blob", RangeByteRequest(0, 4)), ("blob", None)] + ) + assert get_spy.await_count == 2 + assert results[0] is not None + assert results[0].to_bytes() == b"0123" + assert results[1] is not None + assert results[1].to_bytes() == b"0123456789" + + +def test_latency_store_engages_fused_sync_path() -> None: + """A LatencyStore wrapping a sync-capable store must take the fused sync + fast path: reads go through the inner store's `get_sync`, not the async + fallback.""" + inner = MemoryStore() + store = LatencyStore(inner, get_latency=0.0, set_latency=0.0) + with zarr_config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"}): + arr = zarr.create_array( + store=store, + shape=(8,), + chunks=(4,), + dtype="uint8", + compressors=None, + fill_value=0, + ) + assert isinstance(arr._async_array.codec_pipeline, FusedCodecPipeline) + data = np.arange(8, dtype="uint8") + arr[:] = data + with patch.object(inner, "get_sync", wraps=inner.get_sync) as get_sync_spy: + np.testing.assert_array_equal(arr[:], data) + assert get_sync_spy.call_count == 2 # one per chunk diff --git a/tests/test_store/test_wrapper.py b/tests/test_store/test_wrapper.py index b34a63d5d0..e556a108c5 100644 --- a/tests/test_store/test_wrapper.py +++ b/tests/test_store/test_wrapper.py @@ -4,12 +4,12 @@ import pytest -from zarr.abc.store import ByteRequest, Store +from zarr.abc.store import ByteRequest, Store, _store_supports_sync_io from zarr.core.buffer import Buffer from zarr.core.buffer.cpu import Buffer as CPUBuffer from zarr.core.buffer.cpu import buffer_prototype -from zarr.storage import LocalStore, WrapperStore -from zarr.testing.store import StoreTests +from zarr.storage import LocalStore, MemoryStore, WrapperStore, ZipStore +from zarr.testing.store import LatencyStore, StoreTests if TYPE_CHECKING: from pathlib import Path @@ -123,3 +123,47 @@ async def get( await store_wrapped.get(key, buffer_prototype) captured = capsys.readouterr() assert f"getting {key}" in captured.out + + +@pytest.mark.parametrize( + ("store_factory", "expected"), + [ + (lambda tmp: MemoryStore(), True), + (lambda tmp: LocalStore(str(tmp)), True), + (lambda tmp: WrapperStore(MemoryStore()), True), + (lambda tmp: LatencyStore(MemoryStore()), True), + (lambda tmp: ZipStore(tmp / "store.zip", mode="w"), False), + (lambda tmp: WrapperStore(ZipStore(tmp / "store.zip", mode="w")), False), + ], + ids=[ + "memory", + "local", + "wrapper-of-memory", + "latency-wrapper-of-memory", + "zip", + "wrapper-of-zip", + ], +) +def test_supports_sync_io(store_factory: Any, expected: bool, tmp_path: Path | Any) -> None: + """`_store_supports_sync_io` is True only for stores implementing the full + sync surface (get_sync + set_sync + delete_sync); wrappers forward the + wrapped store's capability via `_supports_sync_io`.""" + assert _store_supports_sync_io(store_factory(tmp_path)) is expected + + +def test_wrapper_get_sync_without_inner_sync_raises(tmp_path: Any) -> None: + store = WrapperStore(ZipStore(tmp_path / "store.zip", mode="w")) + with pytest.raises(TypeError, match="does not support synchronous get"): + store.get_sync("key") + + +def test_wrapper_set_sync_without_inner_sync_raises(tmp_path: Any) -> None: + store = WrapperStore(ZipStore(tmp_path / "store.zip", mode="w")) + with pytest.raises(TypeError, match="does not support synchronous set"): + store.set_sync("key", CPUBuffer.from_bytes(b"data")) + + +def test_wrapper_delete_sync_without_inner_sync_raises(tmp_path: Any) -> None: + store = WrapperStore(ZipStore(tmp_path / "store.zip", mode="w")) + with pytest.raises(TypeError, match="does not support synchronous delete"): + store.delete_sync("key") From 53e6dc66b834988912194985a1051ad4db4f0141 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 30 Jul 2026 18:32:00 +0200 Subject: [PATCH 434/468] docs: dev blog, performance examples, and compiled 3.3.0 release notes (#4191) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adds a development blog to the documentation site with a 3.3.0 release post covering the FusedCodecPipeline and sharded partial-read coalescing, plus two runnable examples referenced by the post (examples/codec_pipeline_performance, examples/sharding_coalescing). Compiles every pending changelog fragment into a single 3.3.0 release notes section dated 2026-07-30, merging it with the section compiled earlier in #4148, and empties changes/ — making this commit suitable to tag as v3.3.0. Assisted-by: ClaudeCode:claude-fable-5 --- changes/3352.bugfix.md | 3 - changes/4128.feature.md | 1 - changes/4157.bugfix.md | 11 - changes/4172.misc.md | 7 - changes/4179.bugfix.md | 1 - changes/4183.bugfix.md | 3 - changes/4187.feature.md | 4 - changes/4194.bugfix.md | 10 - changes/4199.bugfix.md | 1 - changes/4201.bugfix.md | 1 - changes/4202.bugfix.md | 10 - changes/4203.bugfix.md | 1 - changes/4204.bugfix.md | 16 -- changes/4205.bugfix.md | 9 - changes/4206.bugfix.md | 1 - changes/4219.bugfix.md | 3 - docs/blog/.authors.yml | 6 + docs/blog/index.md | 3 + docs/blog/posts/3.3.0-release.md | 169 +++++++++++++ docs/release-notes.md | 134 +++++++++-- .../examples/codec_pipeline_performance.md | 7 + .../examples/sharding_coalescing.md | 7 + examples/codec_pipeline_performance/README.md | 59 +++++ .../codec_pipeline_performance.py | 214 +++++++++++++++++ examples/sharding_coalescing/README.md | 63 +++++ .../sharding_coalescing.py | 226 ++++++++++++++++++ mkdocs.yml | 12 + 27 files changed, 876 insertions(+), 106 deletions(-) delete mode 100644 changes/3352.bugfix.md delete mode 100644 changes/4128.feature.md delete mode 100644 changes/4157.bugfix.md delete mode 100644 changes/4172.misc.md delete mode 100644 changes/4179.bugfix.md delete mode 100644 changes/4183.bugfix.md delete mode 100644 changes/4187.feature.md delete mode 100644 changes/4194.bugfix.md delete mode 100644 changes/4199.bugfix.md delete mode 100644 changes/4201.bugfix.md delete mode 100644 changes/4202.bugfix.md delete mode 100644 changes/4203.bugfix.md delete mode 100644 changes/4204.bugfix.md delete mode 100644 changes/4205.bugfix.md delete mode 100644 changes/4206.bugfix.md delete mode 100644 changes/4219.bugfix.md create mode 100644 docs/blog/.authors.yml create mode 100644 docs/blog/index.md create mode 100644 docs/blog/posts/3.3.0-release.md create mode 100644 docs/user-guide/examples/codec_pipeline_performance.md create mode 100644 docs/user-guide/examples/sharding_coalescing.md create mode 100644 examples/codec_pipeline_performance/README.md create mode 100644 examples/codec_pipeline_performance/codec_pipeline_performance.py create mode 100644 examples/sharding_coalescing/README.md create mode 100644 examples/sharding_coalescing/sharding_coalescing.py diff --git a/changes/3352.bugfix.md b/changes/3352.bugfix.md deleted file mode 100644 index 7461486776..0000000000 --- a/changes/3352.bugfix.md +++ /dev/null @@ -1,3 +0,0 @@ -Fix `zarr.api.asynchronous.open_like` so it can create a new array by default when the -target path does not already exist. It now defaults to `mode="a"`; when using a read-only -store to open an existing array, pass `mode="r"` explicitly. diff --git a/changes/4128.feature.md b/changes/4128.feature.md deleted file mode 100644 index c62a615ac2..0000000000 --- a/changes/4128.feature.md +++ /dev/null @@ -1 +0,0 @@ -Added `Group.get_array`, `Group.get_group`, `AsyncGroup.get_array`, and `AsyncGroup.get_group`: type-safe accessors that return the child array or group at a given path, raising `ArrayNotFoundError` / `GroupNotFoundError` if no node exists there, and `ContainsGroupError` / `ContainsArrayError` if the node is not of the requested kind. Unlike `Group.__getitem__`, which returns `Array | Group`, these methods have precise return types. Nested paths like `"subgroup/subarray"` are supported. diff --git a/changes/4157.bugfix.md b/changes/4157.bugfix.md deleted file mode 100644 index 6b0d0fcc67..0000000000 --- a/changes/4157.bugfix.md +++ /dev/null @@ -1,11 +0,0 @@ -`MemoryStore` now copies buffers as they are written, so it never retains the -caller's memory. Previously an uncompressed write handed the store a zero-copy -view of the user's array, and mutating that array afterwards would silently -rewrite chunks already committed to the store. - -Only `MemoryStore` is affected: stores that serialize on write, such as -`LocalStore` and `ZipStore`, never aliased the caller's memory. Uncompressed -writes to a `MemoryStore` are correspondingly slower, since the copy that makes -the stored data independent is now actually performed; compressed writes are -unchanged. Buffers supplied through the `store_dict` argument remain the -caller's responsibility and are stored as-is. diff --git a/changes/4172.misc.md b/changes/4172.misc.md deleted file mode 100644 index 0be7226476..0000000000 --- a/changes/4172.misc.md +++ /dev/null @@ -1,7 +0,0 @@ -Improved `CoordinateIndexer` construction for large, sorted, in-bounds, one-dimensional integer -coordinate selections over regular chunk grids (e.g. `arr.get_coordinate_selection(sorted_idx)`, -`arr.vindex[sorted_idx]`, and the gather behind sparse/CSR row selections). When boundary searching -is estimated to be cheaper than processing every coordinate, per-chunk projections are now built -with `searchsorted`, making index construction ~15x faster for large gathers. Sparse sorted -selections spanning many chunks relative to their coordinate count, as well as unsorted, negative, -multi-dimensional, and irregular-grid selections, continue to use the existing implementation. diff --git a/changes/4179.bugfix.md b/changes/4179.bugfix.md deleted file mode 100644 index e02523114c..0000000000 --- a/changes/4179.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed the opt-in `FusedCodecPipeline` for sharded arrays whose inner or index codec chain contains a codec implementing only the async codec interface (no `SupportsSyncCodec`). Such arrays previously raised `TypeError: All codecs must implement SupportsSyncCodec` on both read and write; the pipeline now declines its synchronous fast path for them and falls back to the async path, matching the behavior of the default `BatchedCodecPipeline`. Fully sync-capable codec chains keep the fast path unchanged. diff --git a/changes/4183.bugfix.md b/changes/4183.bugfix.md deleted file mode 100644 index 809708f596..0000000000 --- a/changes/4183.bugfix.md +++ /dev/null @@ -1,3 +0,0 @@ -Fixed `TypeError: unhashable type: 'writeable void-scalar'` when writing to sharded arrays whose fill value is a `np.void` scalar, e.g. arrays with a structured dtype. - -`ArraySpec` equality and hashing now compare the fill value by its byte representation rather than numeric equality. As a result, two specs with a `NaN` (or `NaT`) fill value now compare equal, while fill values of `-0.0` and `0.0` now compare unequal. This also restores the sharding codec's per-chunk spec cache, which had been disabled because of this bug. diff --git a/changes/4187.feature.md b/changes/4187.feature.md deleted file mode 100644 index 87133e2034..0000000000 --- a/changes/4187.feature.md +++ /dev/null @@ -1,4 +0,0 @@ -`ZipStore` now accepts an open binary file-like object in place of a path, enabling -zip archives on remote storage (e.g. a file opened with `fsspec` or an -`obstore.ReadableFile`). Operations that require a filesystem location -(`clear`, `move`) raise `NotImplementedError` for file-object-backed stores. diff --git a/changes/4194.bugfix.md b/changes/4194.bugfix.md deleted file mode 100644 index 21a4924664..0000000000 --- a/changes/4194.bugfix.md +++ /dev/null @@ -1,10 +0,0 @@ -`FusedCodecPipeline` no longer runs chunk IO and codec compute on the thread -driving zarr's internal event loop. Previously each read/write executed its -synchronous fast path inline on that loop thread, and because every sync-API -call from every user thread is serviced by the same loop, concurrent -operations serialized behind each other's codec work — reported as the fused -pipeline being slower than `BatchedCodecPipeline` for zstd-compressed data -under multi-threaded (e.g. dask) access. The synchronous batch now runs on a -worker thread (one hop per batch, not per chunk), keeping the loop free. -Multi-threaded single-chunk reads of zstd data are ~4.5x faster than before -and now scale with reader threads; single-threaded performance is unchanged. diff --git a/changes/4199.bugfix.md b/changes/4199.bugfix.md deleted file mode 100644 index d0c522cd7e..0000000000 --- a/changes/4199.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -The end-to-end benchmarks no longer invoke `sudo` to drop the OS page cache during a regular `pytest` run. Cache clearing is now opt-in via the `ZARR_BENCHMARK_CLEAR_CACHE` environment variable, which the benchmark CI jobs set. diff --git a/changes/4201.bugfix.md b/changes/4201.bugfix.md deleted file mode 100644 index d837a8a9e2..0000000000 --- a/changes/4201.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed the opt-in `FusedCodecPipeline` for serializers that advertise the partial-decode/encode mixins with only the documented async partial methods: the partial dispatch previously asserted on the private `_decode_partial_sync`/`_encode_partial_sync` hooks (an `AssertionError`, or an `AttributeError` mid-IO under `python -O`); such codecs now take the full-chunk sync path. diff --git a/changes/4202.bugfix.md b/changes/4202.bugfix.md deleted file mode 100644 index 6130fc5b33..0000000000 --- a/changes/4202.bugfix.md +++ /dev/null @@ -1,10 +0,0 @@ -Fixed `FusedCodecPipeline` (the opt-in synchronous pipeline) silently skipping -array-array/bytes-bytes codecs placed outside a sharding serializer on its -partial-decode/partial-encode fast paths. With an outer compressor (e.g. -`compressors=[GzipCodec()]` around a `ShardingCodec` serializer), the fused -pipeline wrote non-conforming stored bytes that `BatchedCodecPipeline` (and any -other conforming reader) could not read, and could fail to read data that -`BatchedCodecPipeline` had written. With an outer array-array codec (e.g. -`TransposeCodec`), it silently returned wrong data in both directions with no -error. Only the opt-in `FusedCodecPipeline` was affected; the default -`BatchedCodecPipeline` was never impacted. diff --git a/changes/4203.bugfix.md b/changes/4203.bugfix.md deleted file mode 100644 index 42ca977193..0000000000 --- a/changes/4203.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed silent data corruption in the experimental `FusedCodecPipeline`: reordering or duplicating fancy-index reads (e.g. `arr[perm, :]`, `arr.oindex[[0, 0, 1], :]`) on uncompressed, crc-free sharded arrays could return the shard in natural order because the vectorized whole-shard decode accepted any selection whose output shape matched the shard shape. The bulk decode now fires only for identity full-shard reads, declines structured dtypes (whose byte-order handling it lacks), and requires shard-index offsets to exactly tile the data section, so corrupt indexes with overlapping or out-of-range offsets can no longer be served as array data. diff --git a/changes/4204.bugfix.md b/changes/4204.bugfix.md deleted file mode 100644 index 90101d1059..0000000000 --- a/changes/4204.bugfix.md +++ /dev/null @@ -1,16 +0,0 @@ -`ManagedMemoryStore.get_sync`/`set_sync`/`delete_sync` now apply the store's -`path` prefix, matching the async `get`/`set`/`delete` methods. Previously the -sync methods were inherited unchanged from `MemoryStore` and used the raw key, -so code that takes the sync fast path (e.g. `FusedCodecPipeline`) would read -and write chunks outside the store's `path` prefix, silently returning fill -values when the data was re-read through a fresh handle. `GpuMemoryStore.set_sync` -now converts its value to a `gpu.Buffer`, matching `set`, so writes through the -sync API keep the store's all-values-are-GPU invariant. Also fixed -`ManagedMemoryStore.get_partial_values` applying its `path` prefix twice -whenever `path` is non-empty, which made it always return `None` for every -requested key. - -The shared store test suite (`zarr.testing.store.StoreTests`) gained -sync/async parity checks — comparing sync and async observations of the same -key on the same store instance, including with a `byte_range` — so every -store subclass now exercises this invariant. diff --git a/changes/4205.bugfix.md b/changes/4205.bugfix.md deleted file mode 100644 index 0492febb7d..0000000000 --- a/changes/4205.bugfix.md +++ /dev/null @@ -1,9 +0,0 @@ -Fixed several small correctness issues from the codec-pipeline performance work: construction-time -codec warnings (e.g. sharding's "disables partial reads" warning) no longer fire twice per array -open — including for `FusedCodecPipeline`, which previously re-warned via its own codec-chain -reconstruction and, on the async fallback path, on every decode/encode call; `concurrent_iter` now -schedules its tasks eagerly, matching its documented contract; an invalid -`codec_pipeline.max_workers` config/environment value now warns and falls back to the default -instead of raising mid-read; and `FusedCodecPipeline`'s async fallback helpers now cancel -already-spawned fetch/decode/write tasks instead of abandoning them in the background when one -fails. diff --git a/changes/4206.bugfix.md b/changes/4206.bugfix.md deleted file mode 100644 index a01c969449..0000000000 --- a/changes/4206.bugfix.md +++ /dev/null @@ -1 +0,0 @@ -Fixed `FusedCodecPipeline`'s gating of its synchronous fast paths: stores exposing only part of the sync surface (e.g. `set_sync` without `get_sync`) now fall back cleanly to the async path instead of failing mid-write, and `WrapperStore` now forwards `get_sync`/`set_sync`/`delete_sync` to the wrapped store so wrapped sync-capable stores keep the fast path. The capability decision uses a private, interim convention (`zarr.abc.store._store_supports_sync_io`) rather than new public API, pending a formal sync/async store architecture. Also fixed `LatencyStore`: synchronous reads and writes now pay the configured latency, `get_ranges`/`get_partial_values` no longer bypass latency injection, and derived stores (e.g. from `with_read_only`) keep a stochastic `(loc, scale)` latency configuration instead of freezing a single sample. diff --git a/changes/4219.bugfix.md b/changes/4219.bugfix.md deleted file mode 100644 index 728e8a7e3a..0000000000 --- a/changes/4219.bugfix.md +++ /dev/null @@ -1,3 +0,0 @@ -`DefaultChunkKeyEncoding.decode_chunk_key` now validates that a chunk key -starts with the configured `c<separator>` prefix and raises `ValueError` for -malformed keys, instead of silently decoding them incorrectly. diff --git a/docs/blog/.authors.yml b/docs/blog/.authors.yml new file mode 100644 index 0000000000..10ce423cfc --- /dev/null +++ b/docs/blog/.authors.yml @@ -0,0 +1,6 @@ +authors: + d-v-b: + name: Davis Bennett + description: Core developer + avatar: https://github.com/d-v-b.png + url: https://github.com/d-v-b diff --git a/docs/blog/index.md b/docs/blog/index.md new file mode 100644 index 0000000000..fca29e2578 --- /dev/null +++ b/docs/blog/index.md @@ -0,0 +1,3 @@ +# Blog + +News, release highlights, and design notes from the Zarr-Python developers. diff --git a/docs/blog/posts/3.3.0-release.md b/docs/blog/posts/3.3.0-release.md new file mode 100644 index 0000000000..13368848ae --- /dev/null +++ b/docs/blog/posts/3.3.0-release.md @@ -0,0 +1,169 @@ +--- +date: 2026-07-30 +authors: + - d-v-b +categories: + - Release +--- + +# Zarr-Python 3.3.0 + +We're happy to announce the release of version 3.3.0 of Zarr-Python. It's been a while since our last release ([3.2.1](https://github.com/zarr-developers/zarr-python/releases/tag/v3.2.1) dropped in May of this year), +and we're bringing some exciting additions to the latest version. For the full release notes, see the [3.3.0 release notes](../../release-notes.md), otherwise stick around for an overview of two performance-centric highlights of this release. + +<!-- more --> + +## Faster low-latency storage + +Relevant issues and pull requests: + +- [#3524](https://github.com/zarr-developers/zarr-python/issues/3524) -- the performance report that started this work +- [#3885](https://github.com/zarr-developers/zarr-python/pull/3885) -- synchronous codec APIs and the `FusedCodecPipeline` + +### The cost of async overhead + +Zarr-Python 3.x uses async routines for fetching data and decoding chunks. In terms of code, this means our store (data fetching) and codec (chunk decoding) APIs are both async. This makes +I/O against high-latency storage backends like cloud object storage efficient. But for *low-latency* storage, like in-process memory or the file system, async routines add measurable overhead and offer no benefit. Async only adds value when there's work to be done while waiting for I/O to complete, but when I/O latency is low, it completes too quickly to run anything while waiting, and we are left paying the performance bill for obligatory async task scheduling that offered no value. + +This performance problem became acute when Zarr-Python users reported that in-memory array indexing workloads ran *slower* in Zarr-Python 3.1.3 relative to Zarr-Python 2.18.7 ([#3524](https://github.com/zarr-developers/zarr-python/issues/3524)). Fortunately this performance regression had a straightforward fix (I don't say "easy" because it was a lot of work). + +### Synchronous execution restores performance + +If async overhead makes low-latency storage slow, does *removing* that overhead restore performance? Yes, it does! + +In [#3885](https://github.com/zarr-developers/zarr-python/pull/3885) we defined synchronous versions of our storage and codec APIs -- the `SyncByteGetter` and `SyncByteSetter` protocols, plus a `get_ranges_sync` method on the `Store` ABC -- and then combined them in a new codec orchestration class called `FusedCodecPipeline`. The `FusedCodecPipeline` is an opt-in alternative to the default (the `BatchedCodecPipeline`) that gives large speedups for low-latency storage. It is currently marked [experimental](../../user-guide/experimental.md), so we may change it as we learn more; the default pipeline is untouched, and existing code keeps working unless you opt in. + +The win here is *not* a faster compressor. It is the removal of async scheduling overhead (including some [nasty `asyncio.to_thread` overhead](https://github.com/python/cpython/issues/136084)), plus a few vectorized fast paths for dense, uncompressed shards. And we only expect this new pipeline to accelerate workloads targeting a subset of storage backends, namely any store with methods that advertise low latency. + +On this author's 10-core Apple M4 laptop, the `FusedCodecPipeline` delivers the following results against memory-backed arrays: + +- uncompressed writes are *~4 times faster* +- uncompressed reads are *~5 times faster* +- compressed writes are *~2 times faster* +- compressed reads are *~2 times faster* + +These numbers came from a [runnable example](../../user-guide/examples/codec_pipeline_performance.md) that ships with the documentation. Run it yourself to get a sense of how the `FusedCodecPipeline` behaves on your system -- when and how you use it depends on your hardware, your array layout, and how your chunks are compressed. What's certain is that for in-memory arrays, and arrays saved to the local file system, the `FusedCodecPipeline` is worth a try. + +Getting good numbers requires choosing the right level of thread-based parallelism for your workload, which is part of the configuration of the `FusedCodecPipeline`. For uncompressed chunks there's no CPU-bound work to do after fetching a chunk and so +thread-based parallelism is worse than useless and slows things down. But for compressed chunks, threading offers a substantial payoff. + +### How to use it + +Select the pipeline through the [runtime configuration](../../user-guide/config.md) by setting `codec_pipeline.path`. Set it globally to affect every array created or opened afterwards: + +```python exec="true" session="blog-330" source="above" +import zarr + +zarr.config.set( + {"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"} +) +``` + +Or scope it to a block of code by using `zarr.config.set` as a context manager, which is the safer choice if you only want the new pipeline for part of your program: + +```python exec="true" session="blog-330" source="above" result="ansi" +import numpy as np +import zarr +from zarr.storage import MemoryStore + +with zarr.config.set( + {"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"} +): + arr = zarr.create_array( + store=MemoryStore(), + shape=(1000, 1000), + chunks=(100, 100), + shards=(1000, 1000), + dtype="float32", + ) + arr[:] = np.random.random((1000, 1000)).astype("float32") + result = arr[:] + +print(result.shape) +``` + +Thread-based parallelism is configured separately, via `codec_pipeline.max_workers`. It defaults to `None`, meaning a pool sized to `os.cpu_count()`. Note that this setting is read *only* by the `FusedCodecPipeline` -- the default `BatchedCodecPipeline` ignores it, so tuning it without opting in above does nothing. + +As noted, memory-backed and uncompressed workloads often do better with a single worker, which runs everything inline on the calling thread: + +```python exec="true" session="blog-330" source="above" +import zarr + +# No thread pool: run codec compute inline. Often best for uncompressed, +# memory-backed arrays, where there's no CPU-bound work to overlap. +zarr.config.set({"codec_pipeline.max_workers": 1}) + +# A fixed-size thread pool, which pays off once compression is in play. +zarr.config.set({"codec_pipeline.max_workers": 8}) + +# Or back to the default, sized to the number of CPUs. +zarr.config.set({"codec_pipeline.max_workers": None}) +``` + +To return to the default pipeline, set `codec_pipeline.path` back to the batched implementation: + +```python exec="true" session="blog-330" source="above" +import zarr + +zarr.config.set( + {"codec_pipeline.path": "zarr.core.codec_pipeline.BatchedCodecPipeline"} +) +``` + +## Faster sharded reads + +Relevant issues and pull requests: + +- [#3004](https://github.com/zarr-developers/zarr-python/pull/3004) -- optimize partial shard reads +- [#3925](https://github.com/zarr-developers/zarr-python/pull/3925) -- `Store.get_ranges` for concurrent, coalesced multi-range reads +- [#3987](https://github.com/zarr-developers/zarr-python/pull/3987) -- control coalescing through `ArrayConfig` and the runtime config + +### How sharding works + +Chunks encoded with the `sharding_indexed` codec contain a secondary level of chunking, called subchunks. For example, if the `chunk_grid` field of the array metadata declares an "outer chunk" size of, say `(10, 10)`, a `sharding_indexed` codec in the `codecs` field could declare an "inner chunk" size of `(5, 5)`. Readers accessing such a chunk will observe a stored object (a stream of bytes) that decodes to an array with size `(10, 10)` (the "outer chunk"), which is comprised of four separate, contiguous byte ranges that each decode to a `(5, 5)` inner chunk. Each inner chunk occupies its own byte range in the outer chunk. + +A reader can satisfy a request for all four inner chunks by issuing four separate byte-range requests, or by making a *single* request for a byte range that spans all four inner chunks. The latter option is nice because it cuts down on the number of requests we need. Historically Zarr-Python used this optimization when reading entire outer chunks; in 3.3.0, we use this optimization in more cases, resulting in more efficient I/O patterns for sharded reads. + +### Interval equivalence + +Byte ranges, being intervals, obey some combination rules: the values in two half-open intervals `[a, b), [b, c)` can be captured by the single interval `[a, c)`. That means a reader can get multiple inner chunks with *one* byte-range request by requesting a range of bytes starting with the first byte of the first subchunk and ending with the last byte of the last subchunk. When individual requests are expensive, this kind of optimization is worth a lot. + +The requested inner chunks are not necessarily contiguous -- there might be a byte range gap between them. As long as that gap is not too big, its often efficient to fetch the entire byte range, gap included, and pick out the inner chunk byte ranges after I/O is done. + +### Byte range coalescing + +We call this procedure -- merging adjacent byte ranges -- "byte range coalescing", and it's a new performance optimization shipping in Zarr-Python 3.3.0. Unlike the `FusedCodecPipeline`, this one is on by default with base settings we think are good, so most users won't need to tune anything. + +Two knobs control it, both documented in the [runtime configuration guide](../../user-guide/config.md). Nearby byte ranges in the same shard are merged into a single request when the gap between them is no larger than `array.sharding_coalesce_max_gap_bytes` (default 1 MiB) and the merged read stays within `array.sharding_coalesce_max_bytes` (default 16 MiB). The gap threshold is what trades wasted bytes against saved requests: raising it reads more data you didn't ask for, in exchange for fewer requests. + +For a runnable demonstration -- counting the store requests saved and timing them against a store with simulated latency -- see the [sharded read coalescing example](../../user-guide/examples/sharding_coalescing.md). + +You can set them globally, or per array by passing `config={...}` to [`zarr.create_array`][]: + +```python exec="true" session="blog-330" source="above" result="ansi" +import zarr +from zarr.storage import MemoryStore + +arr = zarr.create_array( + store=MemoryStore(), + shape=(1000, 1000), + chunks=(100, 100), + shards=(1000, 1000), + dtype="float32", + config={ + "sharding_coalesce_max_gap_bytes": 4 * 1024**2, # 4 MiB + "sharding_coalesce_max_bytes": 64 * 1024**2, # 64 MiB + }, +) +print(arr.shape) +``` + +## Tell us what you think + +We hope these new features are helpful, and we would appreciate any feedback that helps us improve them, or any other aspect of Zarr-Python. + +## Going faster + +The updates in this release are just the first step of a larger performance-oriented direction for Zarr-Python. Landing these two enhancements taught us a *lot* about the performance-sensitive areas of the library. We can and will invest more time in performance tuning, e.g. by adding or changing abstractions, writing code for special cases, etc. + +We plan to consider including compiled code that should enable significant performance improvements. The [`zarrs`](https://zarrs.dev/) project is an ecosystem of Zarr tools written in Rust, with [extremely high performance](https://book.zarrs.dev/#-zarrs-is-fast-). Is there a `zarrs` binding in Zarr-Python's future? I hope so! We are keenly observing development of [`zarrista`](https://developmentseed.org/zarrista/latest/) as a proof-of-concept for what a Python-`zarrs` binding layer might look like. Stay tuned! diff --git a/docs/release-notes.md b/docs/release-notes.md index 7b147a30bd..3b54ea993a 100644 --- a/docs/release-notes.md +++ b/docs/release-notes.md @@ -4,7 +4,7 @@ <!-- towncrier release notes start --> -## 3.3.0 (2026-07-15) +## 3.3.0 (2026-07-30) ### Features @@ -14,13 +14,19 @@ concurrently. ([#3004](https://github.com/zarr-developers/zarr-python/pull/3004)) - Added a `subchunk_write_order` option to `ShardingCodec` to control the physical order of subchunks within a shard. Supported values are `morton`, `unordered`, `lexicographic`, and `colexicographic`. `unordered` makes no guarantee about subchunk layout. This setting affects only on-disk layout, not the data read back, and is not persisted in array metadata: it applies per codec instance and is not recovered when reopening a sharded array. ([#3826](https://github.com/zarr-developers/zarr-python/pull/3826)) - Added `SyncByteGetter` and `SyncByteSetter` runtime-checkable protocols and a `get_ranges_sync` method on the `Store` ABC. These let custom byte getters/setters opt into the synchronous codec pipeline's fast path for in-memory IO, which the sharding codec uses for its inner chunks. ([#3885](https://github.com/zarr-developers/zarr-python/pull/3885)) -- Added `FusedCodecPipeline`, an opt-in codec pipeline that runs codec compute synchronously and in bulk (avoiding the per-chunk async scheduling overhead of the default `BatchedCodecPipeline`), giving large speedups for sharded arrays (up to ~24x writes / ~14x reads on many-chunks-per-shard layouts, more with compression) and no regressions on compute-bound workloads. The default `BatchedCodecPipeline` is unchanged for standard configurations, so existing code keeps working unless you opt in; enable the new pipeline with `zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"})`. ([#3885](https://github.com/zarr-developers/zarr-python/pull/3885)) +- Added `FusedCodecPipeline`, an opt-in codec pipeline that runs codec compute synchronously and in bulk (avoiding the per-chunk async scheduling overhead of the default `BatchedCodecPipeline`), giving large speedups for sharded arrays. The default `BatchedCodecPipeline` is unchanged for standard configurations, so existing code keeps working unless you opt in; enable the new pipeline with `zarr.config.set({"codec_pipeline.path": "zarr.core.codec_pipeline.FusedCodecPipeline"})`. ([#3885](https://github.com/zarr-developers/zarr-python/pull/3885)) - Add `zarr.abc.store.Store.get_ranges` for concurrent, coalesced multi-range reads from a single key. The method is defined on the `Store` ABC with a default implementation built on `Store.get`, so every store inherits a working version; stores with native multi-range backends (e.g. `FsspecStore`) can override for efficiency. Coalescing knobs (`max_concurrency`, `max_gap_bytes`, `max_coalesced_bytes`) are passed as keyword arguments to `get_ranges`. Failures from underlying fetches surface as a `BaseExceptionGroup` (PEP 654); callers should use `except*` to filter for specific exception types such as `FileNotFoundError`. ([#3925](https://github.com/zarr-developers/zarr-python/pull/3925)) - Two new fields on `ArrayConfig` control how the sharding codec coalesces partial-shard reads: `sharding_coalesce_max_gap_bytes` (default 1 MiB) and `sharding_coalesce_max_bytes` (default 16 MiB). When reading multiple chunks from the same shard, nearby byte ranges are merged into a single request to the store if separated by no more than `sharding_coalesce_max_gap_bytes` and the merged read stays within `sharding_coalesce_max_bytes`. Defaults are seeded from the matching `array.sharding_coalesce_max_gap_bytes` / `array.sharding_coalesce_max_bytes` keys in [`zarr.config`][] at array-creation time, and can be overridden per array by passing `config={...}` to [`zarr.create_array`][]. ([#3987](https://github.com/zarr-developers/zarr-python/pull/3987)) +- Added `Group.get_array`, `Group.get_group`, `AsyncGroup.get_array`, and `AsyncGroup.get_group`: type-safe accessors that return the child array or group at a given path, raising `ArrayNotFoundError` / `GroupNotFoundError` if no node exists there, and `ContainsGroupError` / `ContainsArrayError` if the node is not of the requested kind. Unlike `Group.__getitem__`, which returns `Array | Group`, these methods have precise return types. Nested paths like `"subgroup/subarray"` are supported. ([#4128](https://github.com/zarr-developers/zarr-python/pull/4128)) +- `ZipStore` now accepts an open binary file-like object in place of a path, enabling + zip archives on remote storage (e.g. a file opened with `fsspec` or an + `obstore.ReadableFile`). Operations that require a filesystem location + (`clear`, `move`) raise `NotImplementedError` for file-object-backed stores. ([#4187](https://github.com/zarr-developers/zarr-python/pull/4187)) + ### Bugfixes -- Stop emitting an `UnstableSpecificationWarning` when serializing the `struct` data type to Zarr V3 metadata. The `struct` data type now has a stable Zarr V3 specification. The legacy `structured` alias and the unspecified `null_terminated_bytes`, `raw_bytes`, and `variable_length_bytes` data types continue to warn. ([#202](https://github.com/zarr-developers/zarr-python/issues/202)) +- Stop emitting an `UnstableSpecificationWarning` when serializing the `struct` data type to Zarr V3 metadata. The `struct` data type now has a stable Zarr V3 specification. The legacy `structured` alias and the unspecified `null_terminated_bytes`, `raw_bytes`, and `variable_length_bytes` data types continue to warn. ([#4100](https://github.com/zarr-developers/zarr-python/pull/4100)) - Fix equality comparison of `ArrayV2Metadata` and `ArrayV3Metadata` objects with a `NaN` fill value. Such objects are now compared by their JSON-serialized form, so two otherwise-identical metadata objects with a `NaN` (or infinite) fill value compare equal. ([#2929](https://github.com/zarr-developers/zarr-python/issues/2929)) @@ -46,25 +52,11 @@ - Fixed writing to 0-dimensional arrays that use the sharding codec. Previously assigning to a 0-dimensional sharded array raised an error. ([#3966](https://github.com/zarr-developers/zarr-python/pull/3966)) - Fix flaky stateful test bookkeeping when `delete_dir` matches string prefixes instead of true directory descendants. Previously a path such as `6/faNT…` could be incorrectly removed when deleting `6/f`. (See [issue #3977](https://github.com/zarr-developers/zarr-python/issues/3977).) ([#3977](https://github.com/zarr-developers/zarr-python/issues/3977)) -- `FsspecStore.from_url()` and `from_mapper()` now close the async filesystem - they create when `store.close()` is called. Previously the underlying aiohttp - `ClientSession` was left open until garbage collection, producing - `"Unclosed client session"` `ResourceWarning`s from aiohttp. - - The fix introduces `FsspecStore._owns_fs`, a boolean that is ``True`` only when - `FsspecStore` itself created the filesystem (via `from_url` or `from_mapper` - when a sync→async conversion was performed). When `_owns_fs` is ``True``, - `store.close()` calls the new `_close_fs()` helper, which invokes - `fs.set_session()` and closes the returned client. Callers who supply their own - filesystem instance to `FsspecStore()` directly remain responsible for its - lifecycle; `_owns_fs` is ``False`` for those stores. - - **Scope note**: This fix closes the S3 client session that is active at the time - `store.close()` is called. Some S3-backed filesystem implementations (e.g. - s3fs with ``cache_regions=True``) may internally refresh and replace their - client during I/O operations, abandoning prior sessions before ``store.close()`` - is invoked. Those intermediate sessions are outside the scope of this fix and - are an issue in the upstream filesystem library. ([#4003](https://github.com/zarr-developers/zarr-python/pull/4003)) +- `FsspecStore.close()` no longer closes the underlying fsspec filesystem or its + network session. fsspec caches and shares filesystem instances across callers, + so the store cannot know whether it is the only user, and closing a shared + session would break other stores; the filesystem's lifecycle belongs to + whoever created it. ([#4165](https://github.com/zarr-developers/zarr-python/pull/4165)) - Fixed an invalid `zarr.create_array` example in the quick-start documentation (it passed an unsupported `mode` argument) and made the cloud-storage example execute against a mock S3 backend in CI. Added a test ensuring every Python code block in the documentation is either executed or explicitly opted out with a documented reason, so an invalid example can no longer go untested. ([#4016](https://github.com/zarr-developers/zarr-python/issues/4016)) - Fixed `ObjectStore.list_dir` for object-store listings that include a directory-marker object matching the requested non-root prefix. ([#4032](https://github.com/zarr-developers/zarr-python/issues/4032)) @@ -82,6 +74,82 @@ - Fixed writing Fortran-ordered (F-contiguous) arrays through the variable-length string and bytes codecs and through numcodecs array-array filters such as `Delta`, `FixedScaleOffset` and `PackBits`. Chunks are now passed to numcodecs as C-contiguous arrays, so elements are no longer stored in transposed order. ([#4116](https://github.com/zarr-developers/zarr-python/pull/4116)) - Fix silent byte-order corruption for structured dtypes with the `bytes` codec: multi-byte fields are now byte-swapped to the codec's configured `endian` on write and decoded honoring it on read, so non-native-endian structured data (e.g. big-endian fields, as produced by virtual references to external data) round-trips correctly. ([#4141](https://github.com/zarr-developers/zarr-python/issues/4141)) +- Fix `zarr.api.asynchronous.open_like` so it can create a new array by default when the + target path does not already exist. It now defaults to `mode="a"`; when using a read-only + store to open an existing array, pass `mode="r"` explicitly. ([#3352](https://github.com/zarr-developers/zarr-python/pull/3352)) +- `MemoryStore` now copies buffers as they are written, so it never retains the + caller's memory. Previously an uncompressed write handed the store a zero-copy + view of the user's array, and mutating that array afterwards would silently + rewrite chunks already committed to the store. + + Only `MemoryStore` is affected: stores that serialize on write, such as + `LocalStore` and `ZipStore`, never aliased the caller's memory. Uncompressed + writes to a `MemoryStore` are correspondingly slower, since the copy that makes + the stored data independent is now actually performed; compressed writes are + unchanged. Buffers supplied through the `store_dict` argument remain the + caller's responsibility and are stored as-is. ([#4157](https://github.com/zarr-developers/zarr-python/pull/4157)) + +- Fixed the opt-in `FusedCodecPipeline` for sharded arrays whose inner or index codec chain contains a codec implementing only the async codec interface (no `SupportsSyncCodec`). Such arrays previously raised `TypeError: All codecs must implement SupportsSyncCodec` on both read and write; the pipeline now declines its synchronous fast path for them and falls back to the async path, matching the behavior of the default `BatchedCodecPipeline`. Fully sync-capable codec chains keep the fast path unchanged. ([#4179](https://github.com/zarr-developers/zarr-python/pull/4179)) +- Fixed `TypeError: unhashable type: 'writeable void-scalar'` when writing to sharded arrays whose fill value is a `np.void` scalar, e.g. arrays with a structured dtype. + + `ArraySpec` equality and hashing now compare the fill value by its byte representation rather than numeric equality. As a result, two specs with a `NaN` (or `NaT`) fill value now compare equal, while fill values of `-0.0` and `0.0` now compare unequal. This also restores the sharding codec's per-chunk spec cache, which had been disabled because of this bug. ([#4183](https://github.com/zarr-developers/zarr-python/pull/4183)) + +- `FusedCodecPipeline` no longer runs chunk IO and codec compute on the thread + driving zarr's internal event loop. Previously each read/write executed its + synchronous fast path inline on that loop thread, and because every sync-API + call from every user thread is serviced by the same loop, concurrent + operations serialized behind each other's codec work — reported as the fused + pipeline being slower than `BatchedCodecPipeline` for zstd-compressed data + under multi-threaded (e.g. dask) access. The synchronous batch now runs on a + worker thread (one hop per batch, not per chunk), keeping the loop free. + Multi-threaded single-chunk reads of compressed data now scale with reader + threads; single-threaded performance is unchanged. ([#4194](https://github.com/zarr-developers/zarr-python/pull/4194)) +- The end-to-end benchmarks no longer invoke `sudo` to drop the OS page cache during a regular `pytest` run. Cache clearing is now opt-in via the `ZARR_BENCHMARK_CLEAR_CACHE` environment variable, which the benchmark CI jobs set. ([#4199](https://github.com/zarr-developers/zarr-python/pull/4199)) +- Fixed the opt-in `FusedCodecPipeline` for serializers that advertise the partial-decode/encode mixins with only the documented async partial methods: the partial dispatch previously asserted on the private `_decode_partial_sync`/`_encode_partial_sync` hooks (an `AssertionError`, or an `AttributeError` mid-IO under `python -O`); such codecs now take the full-chunk sync path. ([#4201](https://github.com/zarr-developers/zarr-python/pull/4201)) +- Fixed `FusedCodecPipeline` (the opt-in synchronous pipeline) silently skipping + array-array/bytes-bytes codecs placed outside a sharding serializer on its + partial-decode/partial-encode fast paths. With an outer compressor (e.g. + `compressors=[GzipCodec()]` around a `ShardingCodec` serializer), the fused + pipeline wrote non-conforming stored bytes that `BatchedCodecPipeline` (and any + other conforming reader) could not read, and could fail to read data that + `BatchedCodecPipeline` had written. With an outer array-array codec (e.g. + `TransposeCodec`), it silently returned wrong data in both directions with no + error. Only the opt-in `FusedCodecPipeline` was affected; the default + `BatchedCodecPipeline` was never impacted. ([#4202](https://github.com/zarr-developers/zarr-python/pull/4202)) +- Fixed silent data corruption in the experimental `FusedCodecPipeline`: reordering or duplicating fancy-index reads (e.g. `arr[perm, :]`, `arr.oindex[[0, 0, 1], :]`) on uncompressed, crc-free sharded arrays could return the shard in natural order because the vectorized whole-shard decode accepted any selection whose output shape matched the shard shape. The bulk decode now fires only for identity full-shard reads, declines structured dtypes (whose byte-order handling it lacks), and requires shard-index offsets to exactly tile the data section, so corrupt indexes with overlapping or out-of-range offsets can no longer be served as array data. ([#4203](https://github.com/zarr-developers/zarr-python/pull/4203)) +- `ManagedMemoryStore.get_sync`/`set_sync`/`delete_sync` now apply the store's + `path` prefix, matching the async `get`/`set`/`delete` methods. Previously the + sync methods were inherited unchanged from `MemoryStore` and used the raw key, + so code that takes the sync fast path (e.g. `FusedCodecPipeline`) would read + and write chunks outside the store's `path` prefix, silently returning fill + values when the data was re-read through a fresh handle. `GpuMemoryStore.set_sync` + now converts its value to a `gpu.Buffer`, matching `set`, so writes through the + sync API keep the store's all-values-are-GPU invariant. Also fixed + `ManagedMemoryStore.get_partial_values` applying its `path` prefix twice + whenever `path` is non-empty, which made it always return `None` for every + requested key. + + The shared store test suite (`zarr.testing.store.StoreTests`) gained + sync/async parity checks — comparing sync and async observations of the same + key on the same store instance, including with a `byte_range` — so every + store subclass now exercises this invariant. The suite's former + `test_get_bytes`/`test_get_json` methods (and their `_sync` variants) were + folded into these parity tests and no longer exist as separate methods. ([#4204](https://github.com/zarr-developers/zarr-python/pull/4204)) + +- Fixed several small correctness issues from the codec-pipeline performance work: construction-time + codec warnings (e.g. sharding's "disables partial reads" warning) no longer fire twice per array + open — including for `FusedCodecPipeline`, which previously re-warned via its own codec-chain + reconstruction and, on the async fallback path, on every decode/encode call; `concurrent_iter` now + schedules its tasks eagerly, matching its documented contract; an invalid + `codec_pipeline.max_workers` config/environment value now warns and falls back to the default + instead of raising mid-read; and `FusedCodecPipeline`'s async fallback helpers now cancel + already-spawned fetch/decode/write tasks instead of abandoning them in the background when one + fails. ([#4205](https://github.com/zarr-developers/zarr-python/pull/4205)) +- Fixed `FusedCodecPipeline`'s gating of its synchronous fast paths: stores exposing only part of the sync surface (e.g. `set_sync` without `get_sync`) now fall back cleanly to the async path instead of failing mid-write, and `WrapperStore` now forwards `get_sync`/`set_sync`/`delete_sync` to the wrapped store so wrapped sync-capable stores keep the fast path. The capability decision uses a private, interim convention (`zarr.abc.store._store_supports_sync_io`) rather than new public API, pending a formal sync/async store architecture. Also fixed `LatencyStore`: synchronous reads and writes now pay the configured latency, `get_ranges`/`get_partial_values` no longer bypass latency injection, and derived stores (e.g. from `with_read_only`) keep a stochastic `(loc, scale)` latency configuration instead of freezing a single sample. ([#4206](https://github.com/zarr-developers/zarr-python/pull/4206)) +- `DefaultChunkKeyEncoding.decode_chunk_key` now validates that a chunk key + starts with the configured `c<separator>` prefix and raises `ValueError` for + malformed keys, instead of silently decoding them incorrectly. ([#4219](https://github.com/zarr-developers/zarr-python/pull/4219)) + ### Improved Documentation - Document the changes to `zarr.errors` in the 3.0 migration guide, including the removal of v2 exception classes and the introduction of `NodeNotFoundError`. ([#3009](https://github.com/zarr-developers/zarr-python/issues/3009)) @@ -120,13 +188,30 @@ enumeration, bulk attribute updates, and the `use_consolidated` keyword. ([#4132](https://github.com/zarr-developers/zarr-python/pull/4132)) - Fixed the documented default of ``max_age_seconds`` in the ``CacheStore`` docstring: the default is ``"infinity"`` (no expiration), not ``None``, which is rejected. Also noted that ``cache_store`` must support deletes. ([#4133](https://github.com/zarr-developers/zarr-python/pull/4133)) +- Added a blog section to the documentation, with a post covering two performance + highlights of the 3.3.0 release: the opt-in `FusedCodecPipeline` and byte-range + coalescing for partial reads of sharded arrays. + + Added two runnable examples that accompany the post: + `examples/codec_pipeline_performance` compares the `BatchedCodecPipeline` and + `FusedCodecPipeline` on a sharded array across two stores and two codec + regimes, showing when the fused pipeline's thread pool helps and when it does + not, and `examples/sharding_coalescing` demonstrates how read coalescing + reduces the number of store requests when reading subregions of a sharded + array. + + Also removed the hardware-specific speedup figures from the `FusedCodecPipeline` + release note, since they depend on the array layout, codec, and machine. ([#4191](https://github.com/zarr-developers/zarr-python/pull/4191)) + ### Deprecations and Removals - The ``BloscShuffle`` and ``BloscCname`` enums (``zarr.codecs.BloscShuffle``, ``zarr.codecs.BloscCname``) are now deprecated. Pass the equivalent literal string (e.g. ``"zstd"``, ``"bitshuffle"``) when constructing a ``BloscCodec``. The enum classes remain importable but emit ``DeprecationWarning`` on member - access, and will be removed in a future release. ``BloscCodec.cname`` and + access, and will be removed in a future release. They are no longer ``Enum`` + subclasses: constructor calls (e.g. ``BloscCname("zstd")``), iteration, and + ``.value`` access no longer work. ``BloscCodec.cname`` and ``BloscCodec.shuffle`` are now plain strings rather than enum members. Additional renames in ``zarr.codecs.blosc`` from the same change: the type @@ -162,8 +247,9 @@ ### Misc -- [#214](https://github.com/zarr-developers/zarr-python/issues/214), [#215](https://github.com/zarr-developers/zarr-python/pull/215), [#3908](https://github.com/zarr-developers/zarr-python/pull/3908), [#3972](https://github.com/zarr-developers/zarr-python/pull/3972), [#3975](https://github.com/zarr-developers/zarr-python/pull/3975), [#3979](https://github.com/zarr-developers/zarr-python/pull/3979), [#3990](https://github.com/zarr-developers/zarr-python/pull/3990), [#3998](https://github.com/zarr-developers/zarr-python/pull/3998), [#4000](https://github.com/zarr-developers/zarr-python/pull/4000), [#4001](https://github.com/zarr-developers/zarr-python/pull/4001), [#4046](https://github.com/zarr-developers/zarr-python/pull/4046), [#4054](https://github.com/zarr-developers/zarr-python/pull/4054), [#4073](https://github.com/zarr-developers/zarr-python/issues/4073), [#4086](https://github.com/zarr-developers/zarr-python/issues/4086), [#4138](https://github.com/zarr-developers/zarr-python/pull/4138) +- [#4139](https://github.com/zarr-developers/zarr-python/pull/4139), [#4140](https://github.com/zarr-developers/zarr-python/pull/4140), [#3908](https://github.com/zarr-developers/zarr-python/pull/3908), [#3972](https://github.com/zarr-developers/zarr-python/pull/3972), [#3975](https://github.com/zarr-developers/zarr-python/pull/3975), [#3979](https://github.com/zarr-developers/zarr-python/pull/3979), [#3990](https://github.com/zarr-developers/zarr-python/pull/3990), [#3998](https://github.com/zarr-developers/zarr-python/pull/3998), [#4000](https://github.com/zarr-developers/zarr-python/pull/4000), [#4001](https://github.com/zarr-developers/zarr-python/pull/4001), [#4012](https://github.com/zarr-developers/zarr-python/pull/4012), [#4046](https://github.com/zarr-developers/zarr-python/pull/4046), [#4054](https://github.com/zarr-developers/zarr-python/pull/4054), [#4073](https://github.com/zarr-developers/zarr-python/issues/4073), [#4086](https://github.com/zarr-developers/zarr-python/issues/4086), [#4138](https://github.com/zarr-developers/zarr-python/pull/4138) +- [#4172](https://github.com/zarr-developers/zarr-python/pull/4172) ## 3.2.1 (2026-05-05) diff --git a/docs/user-guide/examples/codec_pipeline_performance.md b/docs/user-guide/examples/codec_pipeline_performance.md new file mode 100644 index 0000000000..f21e31636e --- /dev/null +++ b/docs/user-guide/examples/codec_pipeline_performance.md @@ -0,0 +1,7 @@ +--8<-- "examples/codec_pipeline_performance/README.md" + +## Source Code + +```python exec="false" reason="pymdownx snippet include directive, not python source" +--8<-- "examples/codec_pipeline_performance/codec_pipeline_performance.py" +``` diff --git a/docs/user-guide/examples/sharding_coalescing.md b/docs/user-guide/examples/sharding_coalescing.md new file mode 100644 index 0000000000..8b2e054af5 --- /dev/null +++ b/docs/user-guide/examples/sharding_coalescing.md @@ -0,0 +1,7 @@ +--8<-- "examples/sharding_coalescing/README.md" + +## Source Code + +```python exec="false" reason="pymdownx snippet include directive, not python source" +--8<-- "examples/sharding_coalescing/sharding_coalescing.py" +``` diff --git a/examples/codec_pipeline_performance/README.md b/examples/codec_pipeline_performance/README.md new file mode 100644 index 0000000000..5d85412c29 --- /dev/null +++ b/examples/codec_pipeline_performance/README.md @@ -0,0 +1,59 @@ +# Codec Pipeline Performance + +This example compares the default `BatchedCodecPipeline` against the opt-in +`FusedCodecPipeline` on a sharded array, across two stores (memory and local) +and two codec regimes (uncompressed and gzip), at one worker and at `cpu_count`. + +A *codec pipeline* turns chunks of array data into stored bytes and back, running +the configured codecs and performing the storage IO. The default +`BatchedCodecPipeline` schedules both asynchronously -- roughly one coroutine per +chunk operation. That model pays off for high-latency stores, where there is +useful work to do while waiting on IO. For low-latency stores (in-process memory, +the local filesystem) the IO completes too quickly for the overlap to be worth +its cost, and the async scheduling becomes pure overhead. + +`FusedCodecPipeline` runs codec compute and synchronous IO synchronously, +removing that overhead. It is +[experimental](https://zarr.readthedocs.io/en/stable/user-guide/experimental/) +and opt-in; the default pipeline is unchanged. + +## What it shows + +- How to select a pipeline with `zarr.config.set`, and why the array must be + *created* inside the config block: the pipeline class is resolved at array + construction time and then travels with the array. +- That the benefit depends strongly on layout and on whether compression is in + play. Some configurations are slower under the fused pipeline -- the script + reports speedups below 1.00x rather than hiding them. +- That `codec_pipeline.max_workers` is read only by `FusedCodecPipeline`; the + default pipeline ignores it entirely. + +## Running + +```bash +uv run codec_pipeline_performance.py +``` + +The script has no arguments and writes only to an in-memory store. + +## Interpreting the output + +The numbers are specific to your CPU, your Python build, and the workload chosen +here. They are a measurement of your machine, not a published benchmark -- treat +a single run as indicative and re-measure against your own data and store before +switching pipelines in production. + +Two effects are worth watching for: + +- **The two codec regimes tell opposite stories about `max_workers`.** + Uncompressed IO is dominated by per-chunk *scheduling*, so `Fused (1 worker)` + is already fastest and a thread pool only adds overhead. gzip is genuinely + CPU-bound: a single worker compresses chunk after chunk sequentially and can + be *slower than the default*, while a thread pool spreads that compression + over cores and reclaims the win. That flip is why the fused pipeline is + threaded by default, and why pinning `max_workers=1` is worth it for + memory-backed uncompressed data. +- **Chunk size decides whether threading can help at all.** The 64×64 inner + chunks here are small enough that per-chunk scheduling dominates uncompressed + IO, yet large enough that per-chunk gzip is real work to parallelize. Much + coarser chunks leave the pool with too few items to spread. diff --git a/examples/codec_pipeline_performance/codec_pipeline_performance.py b/examples/codec_pipeline_performance/codec_pipeline_performance.py new file mode 100644 index 0000000000..b821f3e6a7 --- /dev/null +++ b/examples/codec_pipeline_performance/codec_pipeline_performance.py @@ -0,0 +1,214 @@ +# /// script +# requires-python = ">=3.11" +# dependencies = [ +# "zarr @ git+https://github.com/zarr-developers/zarr-python.git@main", +# "numpy", +# ] +# /// + +""" +Compare the `BatchedCodecPipeline` and the `FusedCodecPipeline`. + +The default `BatchedCodecPipeline` schedules storage IO and codec compute +asynchronously -- roughly one coroutine per chunk operation. For a *sharded* +array that means one coroutine per inner chunk inside every shard. That is the +right model for high-latency stores, where there is useful work to do while +waiting for IO. For low-latency stores (in-process memory, the local +filesystem) the IO completes too quickly for the overlap to pay for itself, and +the scheduling becomes pure overhead. + +The `FusedCodecPipeline` runs codec compute and synchronous IO synchronously, +removing that overhead. Whether it wins, and whether its thread pool helps, +depends on which resource is actually scarce: + + * Uncompressed IO is dominated by per-chunk *scheduling*, not compute. There + is nothing for a thread pool to parallelize, so a single worker is already + fastest and extra workers only add overhead. + * gzip is genuinely CPU-bound. A single worker compresses every chunk + sequentially and can be *slower than the default*, while a thread pool + spreads that compression across cores and reclaims the win. This is when + `max_workers > 1` earns its keep. + +Run it with: + + uv run codec_pipeline_performance.py + +Numbers are hardware-, layout-, and codec-dependent. Treat the output as a +measurement of *your* machine, not as a published benchmark. +""" + +from __future__ import annotations + +import operator +import os +import statistics +import tempfile +import timeit +from pathlib import Path +from typing import TYPE_CHECKING + +import numpy as np + +import zarr +from zarr.storage import LocalStore, MemoryStore + +if TYPE_CHECKING: + from collections.abc import Callable + + from zarr.abc.store import Store + +BATCHED = "zarr.core.codec_pipeline.BatchedCodecPipeline" +FUSED = "zarr.core.codec_pipeline.FusedCodecPipeline" + +# gzip is CPU-bound to encode, which is exactly the regime where the thread +# pool matters. Level 6 is gzip's own default. +GZIP = {"name": "gzip", "configuration": {"level": 6}} + +# 4096x4096 int32 = 64 MiB, split into 16 shards of 1024x1024, each holding +# 16x16 = 256 inner chunks of 64x64 -> 4096 inner chunks in total. The chunks +# are small enough that per-chunk coroutine scheduling dominates uncompressed +# IO, yet large enough that per-chunk gzip is real work to spread over cores. +SHAPE = (4096, 4096) +SHARDS = (1024, 1024) +CHUNKS = (64, 64) +DTYPE = "int32" + +CONFIGS: tuple[tuple[str, dict[str, object]], ...] = ( + ("Batched (default)", {"codec_pipeline.path": BATCHED}), + ("Fused (1 worker)", {"codec_pipeline.path": FUSED, "codec_pipeline.max_workers": 1}), + ("Fused (cpu_count)", {"codec_pipeline.path": FUSED, "codec_pipeline.max_workers": None}), +) + + +def time_call(fn: Callable[[], object], repeat: int = 3) -> float: + """Median wall-clock seconds for one call to `fn`. + + `timeit.Timer` supplies `perf_counter` and disables the cyclic garbage + collector during each run, so a collection triggered by earlier work cannot + land inside a measurement. `number=1` because a single call here already + moves 64 MiB -- the per-call overhead `timeit` amortizes is irrelevant at + this scale. + """ + return statistics.median(timeit.Timer(fn).repeat(repeat=repeat, number=1)) + + +def measure( + settings: dict[str, object], + store: Store, + data: np.ndarray, + compressors: object, +) -> tuple[float, float]: + """Time one full write and one full read of `data` under `settings`. + + The whole operation runs inside `zarr.config.set`, not just the array + construction. The pipeline class is resolved when the array is built, but + `codec_pipeline.max_workers` is read *per operation*, so a timed call made + outside the config block would silently use whatever worker count was + globally in effect -- which makes every configuration look identical. + """ + everything = slice(None) + + def write_once() -> None: + with zarr.config.set(settings): + array = zarr.create_array( + store=store, + shape=SHAPE, + chunks=CHUNKS, + shards=SHARDS, + dtype=DTYPE, + compressors=compressors, + fill_value=0, + overwrite=True, + ) + operator.setitem(array, everything, data) + + write = time_call(write_once) + + # The bytes on disk are identical whichever pipeline wrote them, so reading + # back what we just wrote isolates read performance on the same data. + def read_once() -> object: + with zarr.config.set(settings): + return zarr.open_array(store=store, mode="r")[everything] + + read = time_call(read_once) + + if not np.array_equal(read_once(), data): + raise AssertionError("round trip mismatch") + return write, read + + +def make_store(kind: str, tmp: Path) -> Store: + if kind == "memory": + return MemoryStore() + return LocalStore(tmp / f"demo_{kind}_{os.getpid()}.zarr") + + +def main() -> None: + n_cpu = os.cpu_count() or 1 + + # Each regime gets the data that actually exercises it. `arange` is + # trivially compressible, which is fine when nothing compresses it, but it + # would make gzip finish almost instantly and hide the CPU-bound behavior + # this example is about. The noisy array keeps gzip genuinely busy. + n = int(np.prod(SHAPE)) + plain_data = np.arange(n, dtype=DTYPE).reshape(SHAPE) + noisy_data = np.random.default_rng(0).integers(0, 2**24, size=SHAPE, dtype=DTYPE) + + n_shards = int(np.prod([s // c for s, c in zip(SHAPE, SHARDS, strict=True)])) + per_shard = int(np.prod([s // c for s, c in zip(SHARDS, CHUNKS, strict=True)])) + print(f"zarr {zarr.__version__} | {n_cpu} CPUs") + print( + f"array {SHAPE} {DTYPE} = {plain_data.nbytes / 2**20:.0f} MiB | " + f"{n_shards} shards x {per_shard} inner chunks = {n_shards * per_shard} chunks\n" + ) + + with tempfile.TemporaryDirectory() as tmp: + for store_kind in ("memory", "local"): + for codec_label, compressors, data in ( + ("uncompressed", None, plain_data), + ("gzip-6 (CPU-bound)", GZIP, noisy_data), + ): + print(f"=== {store_kind} store / {codec_label} ===") + print( + f"{'pipeline':<22}{'write (s)':>11}{'vs base':>10}" + f"{'read (s)':>12}{'vs base':>10}" + ) + results: dict[str, tuple[float, float]] = {} + for label, settings in CONFIGS: + store = make_store(store_kind, Path(tmp)) + results[label] = measure(settings, store, data, compressors) + + base_write, base_read = results[CONFIGS[0][0]] + for label, (write, read) in results.items(): + print( + f"{label:<22}{write:>10.3f}{base_write / write:>9.1f}x" + f"{read:>11.3f}{base_read / read:>9.1f}x" + ) + + # The headline comparison: does the thread pool earn its keep? + single_write, single_read = results["Fused (1 worker)"] + pool_write, pool_read = results["Fused (cpu_count)"] + print( + f" workers (cpu_count vs 1 worker): " + f"write {single_write / pool_write:.1f}x " + f"read {single_read / pool_read:.1f}x" + ) + print() + + print( + "Reading it:\n" + " * Uncompressed IO is scheduling-bound, so Fused (1 worker) is already\n" + " fastest -- a thread pool has nothing to parallelize and only adds\n" + " overhead.\n" + " * gzip is CPU-bound, so Fused (1 worker) can be *slower* than the\n" + " default, while Fused (cpu_count) spreads compression across cores\n" + " and reclaims the win. That flip is why the fused pipeline is\n" + " threaded by default, and why pinning max_workers=1 is worth it for\n" + " memory-backed uncompressed data.\n" + " * `codec_pipeline.max_workers` is read only by the FusedCodecPipeline;\n" + " the default BatchedCodecPipeline ignores it." + ) + + +if __name__ == "__main__": + main() diff --git a/examples/sharding_coalescing/README.md b/examples/sharding_coalescing/README.md new file mode 100644 index 0000000000..29ba08c9ce --- /dev/null +++ b/examples/sharding_coalescing/README.md @@ -0,0 +1,63 @@ +# Sharded Read Coalescing + +This example demonstrates byte-range coalescing for partial reads of sharded +arrays, a performance optimization added in Zarr-Python 3.3.0 and enabled by +default. + +A shard is one stored object containing many inner chunks, each occupying its own +byte range. Reading N inner chunks could mean N separate byte-range requests. +Because byte ranges are intervals, nearby ranges can be merged: `[a, b)` and +`[b, c)` together cover `[a, c)`, so a single request can serve both. Merging +trades reading some bytes you did not ask for against issuing fewer requests -- +worthwhile whenever a request is expensive, as with object storage. + +## What it shows + +- Reading scattered inner chunks from one shard with coalescing **off** issues + one store request per inner chunk; with the **default** settings the same read + collapses to a single request. +- The resulting wall-clock difference against a store with simulated latency. +- That coalescing changes only *how* data is fetched, never *what* is returned -- + the script asserts both configurations produce identical arrays. +- A case where coalescing changes nothing: a contiguous selection already has + adjacent byte ranges, so it merges under any setting. + +## Running + +```bash +uv run sharding_coalescing.py +``` + +## How the comparison is set up + +Two details make the effect observable, and both are worth understanding if you +adapt this script: + +- **The selection must have gaps.** A contiguous read produces adjacent byte + ranges that merge regardless of configuration. The strided selections skip + inner chunks, creating the gaps that the `sharding_coalesce_max_gap_bytes` + budget decides whether to bridge. +- **Latency must be charged per merged fetch.** The example defines a small + `WrapperStore` subclass that sleeps in `get`. It deliberately does *not* keep + `WrapperStore.get_ranges`, which forwards straight to the wrapped store and + would bypass the latency entirely; inheriting the `Store` ABC's `get_ranges` + instead runs the coalescer over its own `get`, so each merged fetch pays once. + + `zarr.testing.store` ships a ready-made `LatencyStore`, but importing it pulls + in `pytest`. Defining the wrapper inline keeps the example runnable with only + `zarr` and `numpy` installed. + +## Configuration + +Two settings control the behavior, both settable globally via `zarr.config` or +per array via `config=` on `zarr.create_array` / `Array.with_config`: + +| Setting | Default | Meaning | +| --- | --- | --- | +| `sharding_coalesce_max_gap_bytes` | 1 MiB | Merge two ranges only if the gap between them is no larger than this | +| `sharding_coalesce_max_bytes` | 16 MiB | Never let a merged read exceed this size | + +Setting the gap to `0` merges only exactly-adjacent ranges, which approximates +the pre-3.3.0 behavior; that is how the example emulates the old path. Raising +the gap reads more unwanted bytes in exchange for fewer round trips -- the right +value depends on how expensive a request is against how fast your link is. diff --git a/examples/sharding_coalescing/sharding_coalescing.py b/examples/sharding_coalescing/sharding_coalescing.py new file mode 100644 index 0000000000..5da62ed806 --- /dev/null +++ b/examples/sharding_coalescing/sharding_coalescing.py @@ -0,0 +1,226 @@ +# /// script +# requires-python = ">=3.11" +# dependencies = [ +# "zarr @ git+https://github.com/zarr-developers/zarr-python.git@main", +# "numpy", +# ] +# /// + +""" +Demonstrate byte-range coalescing for partial reads of sharded arrays. + +A shard is a single stored object holding many inner chunks, each occupying +its own byte range. Reading N inner chunks could mean issuing N separate +byte-range requests to the store. Because byte ranges are intervals, a reader +can instead merge nearby ranges: `[a, b)` and `[b, c)` together cover +`[a, c)`, so one request can serve both. Merging trades reading some bytes you +did not ask for against issuing fewer requests -- a good trade whenever a +request is expensive, which is the normal case for object storage. + +Zarr-Python 3.3.0 does this automatically. Two settings control it: + + * `sharding_coalesce_max_gap_bytes` (default 1 MiB) -- merge two ranges only + if the gap between them is no larger than this. + * `sharding_coalesce_max_bytes` (default 16 MiB) -- never let a merged read + exceed this size. + +Setting the gap to 0 disables merging of non-adjacent ranges, which +approximates the pre-3.3.0 behavior. This script compares the two, counting +store requests and measuring wall-clock time against a store with simulated +latency. + +Run it with: + + uv run sharding_coalescing.py +""" + +from __future__ import annotations + +import asyncio +import operator +import statistics +import timeit +from contextlib import contextmanager +from functools import partial +from typing import TYPE_CHECKING + +import numpy as np + +import zarr +import zarr.core._coalesce as coalesce_module +from zarr.abc.store import ByteRequest, RangeByteRequest, Store +from zarr.storage import MemoryStore, WrapperStore + +if TYPE_CHECKING: + from collections.abc import Callable, Iterator, Sequence + + from zarr.core.buffer import Buffer, BufferPrototype + +# Emulates the pre-3.3.0 behavior: with a zero gap budget, only ranges that are +# exactly adjacent get merged, so scattered inner chunks are fetched one by one. +NO_COALESCING = {"sharding_coalesce_max_gap_bytes": 0} + +# The shipped defaults. Spelled out here so the comparison is explicit rather +# than relying on whatever the global config happens to be. +DEFAULT_COALESCING = { + "sharding_coalesce_max_gap_bytes": 1 << 20, # 1 MiB + "sharding_coalesce_max_bytes": 16 << 20, # 16 MiB +} + +GET_LATENCY_S = 0.005 # 5 ms per request, a modest stand-in for object storage + + +class PerRequestLatencyStore(WrapperStore[Store]): + """Wraps a store, charging a fixed latency per byte-range fetch. + + `zarr.testing.store` ships a `LatencyStore`, but importing it pulls in + `pytest`; defining the wrapper here keeps this example runnable with only + zarr and numpy installed. + + Two details matter for the measurement: + + * The latency is applied in `get`, which is what an individual fetch costs. + * `get_ranges` is explicitly *not* overridden to forward to the wrapped + store. `WrapperStore.get_ranges` does forward, which would skip this + class's `get` entirely and make every configuration look identical. + Inheriting the `Store` ABC's implementation instead runs the coalescer + over `self.get`, so each *merged* fetch pays the latency once -- which is + exactly the cost coalescing exists to reduce. + """ + + get_ranges = Store.get_ranges + + def __init__(self, store: Store, *, get_latency: float) -> None: + super().__init__(store) + self.get_latency = get_latency + + def _with_store(self, store: Store) -> PerRequestLatencyStore: + # `WrapperStore` rebuilds the wrapper when opening read-only, so the + # latency setting has to be carried across. + return type(self)(store, get_latency=self.get_latency) + + async def get( + self, + key: str, + prototype: BufferPrototype, + byte_range: ByteRequest | None = None, + ) -> Buffer | None: + await asyncio.sleep(self.get_latency) + return await self._store.get(key, prototype, byte_range) + + +@contextmanager +def counting_requests() -> Iterator[Callable[[], int]]: + """Count the store fetches issued inside the block. + + Wraps the coalescing planner rather than the store: every merged group it + returns, plus every range it declined to merge, becomes exactly one fetch. + Counting here rather than at the store means the number reported is the + planner's decision, which is precisely what the settings control. + """ + original = coalesce_module.coalesce_ranges + total = 0 + + def counting_coalesce_ranges( + byte_ranges: Sequence[ByteRequest | None], + *, + max_gap_bytes: int, + max_coalesced_bytes: int, + ) -> tuple[ + list[list[tuple[int, RangeByteRequest]]], + list[tuple[int, ByteRequest | None]], + ]: + nonlocal total + groups, uncoalescable = original( + byte_ranges, + max_gap_bytes=max_gap_bytes, + max_coalesced_bytes=max_coalesced_bytes, + ) + total += len(groups) + len(uncoalescable) + return groups, uncoalescable + + coalesce_module.coalesce_ranges = counting_coalesce_ranges + try: + yield lambda: total + finally: + coalesce_module.coalesce_ranges = original + + +def measure_read(array: zarr.Array, selection: slice) -> tuple[int, float]: + """Return (store fetches, median seconds) for reading `selection`.""" + read = partial(operator.getitem, array, selection) + + with counting_requests() as fetches: + result = read() + requests = fetches() + + # `timeit.Timer` supplies the loop, `perf_counter`, and GC handling. The + # median of several runs keeps one unlucky run from dominating. + elapsed = statistics.median(timeit.Timer(read).repeat(repeat=5, number=1)) + + assert result.size > 0 # a read that returned nothing would time as "fast" + return requests, elapsed + + +def main() -> None: + n = 8192 + chunk = 64 + inner_chunks = n // chunk + + base = MemoryStore() + source = (np.arange(n, dtype="uint64") % 251).astype("uint8") + + # One shard holding every inner chunk, uncompressed so inner-chunk byte + # offsets stay predictable and the demonstration is easy to reason about. + writable = zarr.create_array( + store=base, shape=(n,), chunks=(chunk,), shards=(n,), dtype="uint8", compressors=None + ) + writable[:] = source + + store = PerRequestLatencyStore(base, get_latency=GET_LATENCY_S) + + print(f"zarr {zarr.__version__}") + print(f"array: {n} uint8 values, {inner_chunks} inner chunks of {chunk} in a single shard") + print(f"store: MemoryStore wrapped with {GET_LATENCY_S * 1000:.0f} ms of latency per request\n") + + # A strided selection touches inner chunks with unread chunks in between, + # so there are real gaps for the coalescer to bridge. A contiguous + # selection would merge under any setting, since its ranges are adjacent. + selections = { + "every 2nd inner chunk": slice(None, None, chunk * 2), + "every 4th inner chunk": slice(None, None, chunk * 4), + "contiguous quarter": slice(0, n // 4), + } + + header = f"{'selection':<24} {'coalescing':<12} {'requests':>9} {'time':>10}" + print(header) + print("-" * len(header)) + + for label, selection in selections.items(): + results = {} + for mode, config in (("off", NO_COALESCING), ("default", DEFAULT_COALESCING)): + array = zarr.open_array(store=store, mode="r").with_config(config) + requests, elapsed = measure_read(array, selection) + results[mode] = (requests, elapsed) + print(f"{label:<24} {mode:<12} {requests:>9} {elapsed * 1000:>9.1f}ms") + + off_requests, off_time = results["off"] + on_requests, on_time = results["default"] + if on_requests < off_requests: + print( + f"{'':<24} {'->':<12} " + f"{off_requests // on_requests:>8}x fewer {off_time / on_time:>9.1f}x faster" + ) + else: + print(f"{'':<24} {'->':<12} {'no change (ranges already adjacent)':>30}") + print() + + # Correctness is the point: coalescing must not change what you read back. + for mode, config in (("off", NO_COALESCING), ("default", DEFAULT_COALESCING)): + array = zarr.open_array(store=store, mode="r").with_config(config) + assert np.array_equal(array[::128], source[::128]), mode + print("Both configurations return identical data; coalescing only changes how it is fetched.") + + +if __name__ == "__main__": + main() diff --git a/mkdocs.yml b/mkdocs.yml index 87aaf23430..b414c73196 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -31,6 +31,8 @@ nav: - Examples: - user-guide/examples/custom_dtype.md - user-guide/examples/rectilinear_chunks.md + - user-guide/examples/codec_pipeline_performance.md + - user-guide/examples/sharding_coalescing.md - API Reference: - api/zarr/index.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc</code>': @@ -95,6 +97,8 @@ nav: - 'zarr-metadata ↪': https://zarr-metadata.readthedocs.io/ - release-notes.md - contributing.md + - Blog: + - blog/index.md hooks: - mkdocs_hooks.py @@ -153,6 +157,14 @@ extra_css: plugins: - autorefs + - blog: + blog_dir: blog + post_dir: "{blog}/posts" + post_url_format: "{slug}" + # The blog is a simple reverse-chronological list of posts; the archive + # and category indexes add navigation we don't have the volume to justify. + archive: false + categories: false - search - markdown-exec - mkdocstrings: From a994a4fc972fed428eab6a26d4f14bb95d22c144 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Fri, 31 Jul 2026 11:23:10 +0200 Subject: [PATCH 435/468] feat: add the zarr-indexing package (TensorStore-style index transforms, ndsel wire format) (#4196) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * feat: add the zarr-indexing package (TensorStore-style index transforms) Standalone workspace package extracted from the lazy-indexing branch (zarr-developers#3906): composable, lazy coordinate transforms (IndexTransform / IndexDomain / output maps), dependency-aware chunk resolution against a DimensionGridLike protocol, and an ndsel-conformant JSON wire format validated against the vendored conformance corpus. zarr itself does not depend on zarr-indexing yet — the runtime wiring lands separately once 0.1.0 is published. The package is numpy-only; its tests exercise chunk resolution against zarr's concrete ChunkGrid, so they run from the workspace root (uv sync --all-packages). Assisted-by: ClaudeCode:claude-fable-5 * style: conventional submodule import in the chunk-resolution tests Assisted-by: ClaudeCode:claude-fable-5 * perf(zarr-indexing): joint chunk enumeration for correlated vindex maps Candidate-chunk enumeration took the cartesian product of each correlated ArrayMap's per-dimension distinct chunk ids and relied on intersect() to filter untouched combinations. For a diagonal selection of P scattered points that is P**2 intersect calls — quadratic in the number of selected points, the same workload shape as zarr-developers#4174 (400 points: ~2.6s; 10k points: ~30min). Group correlated maps jointly instead: broadcast their per-point chunk ids, take the distinct rows (np.unique(axis=0), O(P log P)), and enumerate exactly the touched combinations. Candidate slots now carry chunk-coordinate tuples covering one or more output dimensions; orthogonal/constant/slice dimensions keep their existing per-dimension candidates. 400-point diagonal resolution drops from 2628ms to 14ms and scales linearly. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): standalone documentation site; add package justfile Mirror the treatment zarr-metadata received in #4208/#4210 onto zarr-indexing: a self-contained mkdocs site under the package (own mkdocs.yml, landing page, ndsel wire-format guide, mkdocstrings page per module, and .readthedocs.yaml for a dedicated RTD project), so the package presents as a separate project with docs versioned by its own zarr_indexing-v* release tags rather than zarr-python's. The zarr-python site's API Reference nav links out to it, and each RTD project now skips PR builds that do not touch its half of the repo. The package gains a pinned docs dependency group, a docs build job in its CI workflow, and a justfile with package-scoped dev recipes. Two recipes deviate from the zarr-metadata original by design: - `test` runs against the workspace-root environment (`uv run --project ../.. --all-packages --group test`), because the chunk-resolution tests exercise this package against zarr's chunk grids and `zarr` is deliberately not a dependency of this package. - `typecheck` uses plain `pyright`, unpinned and on the default interpreter, mirroring this package's own CI invocation. The zarr-metadata pin exists for a PEP 661 sentinel regression that zarr-indexing's sources do not hit. composition.py gains the module docstring the other modules already have, since mkdocstrings renders it as the page introduction. Assisted-by: ClaudeCode:claude-fable-5 * chore: drop the already-released 4141 changelog fragment The bytes-codec byte-order fix this fragment describes shipped upstream and its entry is already in docs/release-notes.md; the fragment survived on this branch only as a rebase remnant, and would emit a duplicate entry in the next release. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): canonicalize ndsel references to zarr-developers/ndsel Also aligns the zarr-indexing workflow's setup-uv pin (v8.3.2) with the rest of the repo. The vendored-corpus sha is present upstream; the historical d-v-b/ndsel#1 PR reference stays as provenance. Assisted-by: ClaudeCode:claude-fable-5 * chore: drop the root uv-workspace wiring for zarr-indexing Per review: the root pyproject.toml should not change in this PR. The package now operates fully standalone (like zarr-metadata); the test invocations layer the package into the repo-root environment as an editable overlay instead (python -m pytest, since a base-env console script would not see the overlay). Assisted-by: ClaudeCode:claude-fable-5 --- .github/workflows/check_changelogs.yml | 3 + .github/workflows/zarr-indexing-release.yml | 117 ++ .github/workflows/zarr-indexing.yml | 123 ++ .readthedocs.yaml | 15 +- mkdocs.yml | 1 + packages/zarr-indexing/.readthedocs.yaml | 30 + packages/zarr-indexing/CHANGELOG.md | 3 + packages/zarr-indexing/LICENSE.txt | 21 + packages/zarr-indexing/README.md | 53 + .../zarr-indexing/changes/3906.feature.md | 1 + packages/zarr-indexing/changes/README.md | 25 + .../docs/_static/favicon-96x96.png | Bin 0 -> 12714 bytes .../zarr-indexing/docs/_static/logo_bw.png | Bin 0 -> 45208 bytes .../docs/api/chunk_resolution.md | 5 + .../zarr-indexing/docs/api/composition.md | 5 + packages/zarr-indexing/docs/api/domain.md | 5 + packages/zarr-indexing/docs/api/errors.md | 5 + packages/zarr-indexing/docs/api/grid.md | 5 + packages/zarr-indexing/docs/api/index.md | 47 + packages/zarr-indexing/docs/api/json.md | 5 + packages/zarr-indexing/docs/api/messages.md | 5 + packages/zarr-indexing/docs/api/output_map.md | 5 + packages/zarr-indexing/docs/api/transform.md | 5 + packages/zarr-indexing/docs/index.md | 150 ++ packages/zarr-indexing/docs/ndsel.md | 156 ++ packages/zarr-indexing/justfile | 58 + packages/zarr-indexing/mkdocs.yml | 110 ++ packages/zarr-indexing/pyproject.toml | 124 ++ .../src/zarr_indexing/__init__.py | 74 + .../src/zarr_indexing/chunk_resolution.py | 380 +++++ .../src/zarr_indexing/composition.py | 133 ++ .../zarr-indexing/src/zarr_indexing/domain.py | 189 +++ .../zarr-indexing/src/zarr_indexing/errors.py | 21 + .../zarr-indexing/src/zarr_indexing/grid.py | 25 + .../zarr-indexing/src/zarr_indexing/json.py | 325 ++++ .../src/zarr_indexing/messages.py | 657 +++++++++ .../src/zarr_indexing/output_map.py | 105 ++ .../zarr-indexing/src/zarr_indexing/py.typed | 0 .../src/zarr_indexing/transform.py | 1311 +++++++++++++++++ .../tests/conformance/PROVENANCE.md | 20 + .../zarr-indexing/tests/conformance/README.md | 16 + .../zarr-indexing/tests/conformance/box.json | 50 + .../tests/conformance/errors.json | 23 + .../tests/conformance/point.json | 30 + .../tests/conformance/points.json | 34 + .../tests/conformance/slice.json | 61 + .../tests/conformance/transform.json | 57 + .../tests/test_chunk_resolution.py | 521 +++++++ .../zarr-indexing/tests/test_composition.py | 166 +++ .../zarr-indexing/tests/test_conformance.py | 55 + packages/zarr-indexing/tests/test_domain.py | 202 +++ packages/zarr-indexing/tests/test_json.py | 336 +++++ packages/zarr-indexing/tests/test_messages.py | 91 ++ .../tests/test_ndsel_tensorstore.py | 52 + .../zarr-indexing/tests/test_output_map.py | 56 + .../tests/test_tensorstore_parity.py | 263 ++++ .../zarr-indexing/tests/test_transform.py | 628 ++++++++ 57 files changed, 6955 insertions(+), 8 deletions(-) create mode 100644 .github/workflows/zarr-indexing-release.yml create mode 100644 .github/workflows/zarr-indexing.yml create mode 100644 packages/zarr-indexing/.readthedocs.yaml create mode 100644 packages/zarr-indexing/CHANGELOG.md create mode 100644 packages/zarr-indexing/LICENSE.txt create mode 100644 packages/zarr-indexing/README.md create mode 100644 packages/zarr-indexing/changes/3906.feature.md create mode 100644 packages/zarr-indexing/changes/README.md create mode 100644 packages/zarr-indexing/docs/_static/favicon-96x96.png create mode 100644 packages/zarr-indexing/docs/_static/logo_bw.png create mode 100644 packages/zarr-indexing/docs/api/chunk_resolution.md create mode 100644 packages/zarr-indexing/docs/api/composition.md create mode 100644 packages/zarr-indexing/docs/api/domain.md create mode 100644 packages/zarr-indexing/docs/api/errors.md create mode 100644 packages/zarr-indexing/docs/api/grid.md create mode 100644 packages/zarr-indexing/docs/api/index.md create mode 100644 packages/zarr-indexing/docs/api/json.md create mode 100644 packages/zarr-indexing/docs/api/messages.md create mode 100644 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packages/zarr-indexing/tests/test_domain.py create mode 100644 packages/zarr-indexing/tests/test_json.py create mode 100644 packages/zarr-indexing/tests/test_messages.py create mode 100644 packages/zarr-indexing/tests/test_ndsel_tensorstore.py create mode 100644 packages/zarr-indexing/tests/test_output_map.py create mode 100644 packages/zarr-indexing/tests/test_tensorstore_parity.py create mode 100644 packages/zarr-indexing/tests/test_transform.py diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index 0033b43db2..d7a54fc2c4 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -29,3 +29,6 @@ jobs: - name: Check zarr-metadata changelog entries run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-metadata/changes + + - name: Check zarr-indexing changelog entries + run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-indexing/changes diff --git a/.github/workflows/zarr-indexing-release.yml b/.github/workflows/zarr-indexing-release.yml new file mode 100644 index 0000000000..7cfd571eae --- /dev/null +++ b/.github/workflows/zarr-indexing-release.yml @@ -0,0 +1,117 @@ +name: zarr-indexing release + +on: + workflow_dispatch: + push: + tags: + - 'zarr_indexing-v*' + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: false + +jobs: + build: + name: Build wheel and sdist + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-indexing + steps: + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + with: + persist-credentials: false + fetch-depth: 0 # hatch-vcs needs full history + tags + + - name: Install Hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' + + - name: Build + run: hatch build + + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + with: + name: zarr-indexing-dist + path: packages/zarr-indexing/dist + + test_artifacts: + name: Test built artifacts + needs: [build] + runs-on: ubuntu-latest + steps: + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + with: + name: zarr-indexing-dist + path: dist + + - name: Install uv + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + with: + enable-cache: false + + - name: Set up Python + run: uv python install 3.12 + + - name: Install built wheel and run import smoke test + run: | + wheel=$(ls dist/*.whl) + uv run --with "${wheel}" --python 3.12 --no-project \ + python -c "import zarr_indexing; print('zarr_indexing', zarr_indexing.__version__)" + + upload_pypi: + name: Upload to PyPI + needs: [build, test_artifacts] + if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/zarr_indexing-v') + runs-on: ubuntu-latest + environment: + name: zarr-indexing-releases + url: https://pypi.org/p/zarr-indexing + permissions: + id-token: write # required for OIDC trusted publishing + attestations: write # required for artifact attestations + steps: + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + with: + name: zarr-indexing-dist + path: dist + + - name: Generate artifact attestation + uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 + with: + subject-path: dist/* + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 + + upload_testpypi: + name: Upload to TestPyPI + needs: [build, test_artifacts] + if: github.event_name == 'workflow_dispatch' + runs-on: ubuntu-latest + environment: + name: zarr-indexing-releases-test + url: https://test.pypi.org/p/zarr-indexing + permissions: + id-token: write + attestations: write + steps: + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + with: + name: zarr-indexing-dist + path: dist + + - name: Generate artifact attestation + uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 + with: + subject-path: dist/* + + - name: Publish package to TestPyPI + uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 + with: + repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/zarr-indexing.yml b/.github/workflows/zarr-indexing.yml new file mode 100644 index 0000000000..2106b10916 --- /dev/null +++ b/.github/workflows/zarr-indexing.yml @@ -0,0 +1,123 @@ +name: zarr-indexing + +on: + push: + branches: [main] + paths: + - 'packages/zarr-indexing/**' + - '.github/workflows/zarr-indexing.yml' + pull_request: + paths: + - 'packages/zarr-indexing/**' + - '.github/workflows/zarr-indexing.yml' + workflow_dispatch: + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + test: + name: pytest py=${{ matrix.python-version }} + runs-on: ubuntu-latest + defaults: + run: + shell: bash + strategy: + fail-fast: false + matrix: + python-version: ['3.12', '3.13', '3.14'] + steps: + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + with: + enable-cache: true + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + # The transform tests exercise chunk resolution against zarr's ChunkGrid, + # so they run from the repo root against the root environment (which + # provides `zarr`) with this package as an editable overlay rather than in + # package isolation. + - name: Sync test dependency group + run: uv sync --group test --python ${{ matrix.python-version }} + - name: Run pytest + run: uv run --no-sync --group test --with-editable ./packages/zarr-indexing python -m pytest packages/zarr-indexing/tests + + ruff: + name: ruff + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-indexing + steps: + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + - name: Run ruff + run: uvx ruff check . + + pyright: + name: pyright + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-indexing + steps: + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + with: + enable-cache: true + - name: Set up Python + run: uv python install 3.12 + - name: Sync test dependency group + run: uv sync --group test --python 3.12 + - name: Run pyright + run: uv run --group test --with pyright pyright src + + docs: + name: docs + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-indexing + steps: + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + with: + enable-cache: true + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 + - name: Build docs + # The strict mkdocs build lives in packages/zarr-indexing/justfile. + run: just docs-check + + zarr-indexing-complete: + name: zarr-indexing complete + needs: [test, ruff, pyright, docs] + if: always() + runs-on: ubuntu-latest + steps: + - name: Check failure + if: | + contains(needs.*.result, 'failure') || + contains(needs.*.result, 'cancelled') + run: exit 1 + - name: Success + run: echo Success! diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 55b5d6fed0..dddf8449a4 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -6,15 +6,14 @@ build: python: "3.12" jobs: post_checkout: - # Cancel pull request builds whose changes are confined to the - # zarr-metadata package, which has its own Read the Docs project. Exit - # code 183 cancels the build and reports success to the Git provider. - # Scoped to PR builds ("external" versions) because origin/main is only - # a meaningful diff base there. Read the Docs strips shell quoting from - # commands, so the exclude pathspec must use the quote-free :! form, - # not ':(exclude)'. + # Cancel pull request builds whose changes are confined to the packages + # that have their own Read the Docs projects. Exit code 183 cancels the + # build and reports success to the Git provider. Scoped to PR builds + # ("external" versions) because origin/main is only a meaningful diff + # base there. Read the Docs strips shell quoting from commands, so the + # exclude pathspecs must use the quote-free :! form, not ':(exclude)'. - | - if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- :!packages/zarr-metadata; + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- :!packages/zarr-metadata :!packages/zarr-indexing; then exit 183; fi diff --git a/mkdocs.yml b/mkdocs.yml index b414c73196..6a0d94052e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -95,6 +95,7 @@ nav: - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros</code>': api/zarr/functions/zeros.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros_like</code>': api/zarr/functions/zeros_like.md - 'zarr-metadata ↪': https://zarr-metadata.readthedocs.io/ + - 'zarr-indexing ↪': https://zarr-indexing.readthedocs.io/ - release-notes.md - contributing.md - Blog: diff --git a/packages/zarr-indexing/.readthedocs.yaml b/packages/zarr-indexing/.readthedocs.yaml new file mode 100644 index 0000000000..b8c7b76e2b --- /dev/null +++ b/packages/zarr-indexing/.readthedocs.yaml @@ -0,0 +1,30 @@ +# Read the Docs configuration for the zarr-indexing docs site, separate from +# the zarr-python site configured by the repo-root .readthedocs.yaml. The RTD +# project for zarr-indexing must set its configuration-file path to +# packages/zarr-indexing/.readthedocs.yaml. +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.12" + jobs: + post_checkout: + # Cancel pull request builds that do not touch this package. Exit code + # 183 cancels the build and reports success to the Git provider. Scoped + # to PR builds ("external" versions) because origin/main is only a + # meaningful diff base there. + - | + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- packages/zarr-indexing; + then + exit 183; + fi + install: + - pip install --upgrade pip + - pip install ./packages/zarr-indexing --group packages/zarr-indexing/pyproject.toml:docs + build: + html: + - mkdocs build --strict -f packages/zarr-indexing/mkdocs.yml --site-dir $READTHEDOCS_OUTPUT/html + +mkdocs: + configuration: packages/zarr-indexing/mkdocs.yml diff --git a/packages/zarr-indexing/CHANGELOG.md b/packages/zarr-indexing/CHANGELOG.md new file mode 100644 index 0000000000..7c4bc92cad --- /dev/null +++ b/packages/zarr-indexing/CHANGELOG.md @@ -0,0 +1,3 @@ +# Release notes + +<!-- towncrier release notes start --> diff --git a/packages/zarr-indexing/LICENSE.txt b/packages/zarr-indexing/LICENSE.txt new file mode 100644 index 0000000000..1e8da4d242 --- /dev/null +++ b/packages/zarr-indexing/LICENSE.txt @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2015-2025 Zarr Developers <https://github.com/zarr-developers> + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/packages/zarr-indexing/README.md b/packages/zarr-indexing/README.md new file mode 100644 index 0000000000..ccdfe595a5 --- /dev/null +++ b/packages/zarr-indexing/README.md @@ -0,0 +1,53 @@ +# zarr-indexing + +Composable, lazy coordinate transforms for Zarr array indexing. + +Documentation: <https://zarr-indexing.readthedocs.io/> + +This package implements TensorStore-inspired index transforms. The core idea: +every indexing operation (slicing, fancy indexing, etc.) produces a coordinate +mapping from user space to storage space. These mappings compose lazily — no +I/O until you explicitly read or write. + +Key types: + +- `IndexDomain` — a rectangular region of integer coordinates +- `IndexTransform` — maps input coordinates to storage coordinates +- `ConstantMap`, `DimensionMap`, `ArrayMap` — the three ways a single output + dimension can depend on the input +- `compose` — chain two transforms into one + +The package depends only on NumPy and the standard library; it does not import +`zarr`. It is developed in the [zarr-python](https://github.com/zarr-developers/zarr-python) +repository and consumed by `zarr` to resolve array indexing operations. + +## Installation + +```bash +pip install zarr-indexing +``` + +## Developing + +Package-scoped development commands live in the [`justfile`](./justfile) +(requires [just](https://github.com/casey/just)): + +``` +just test # run the test suite (extra args go to pytest) +just lint # ruff, same invocation as CI +just typecheck # pyright, same invocation as CI +just docs-check # strict build of the docs site +just check # all of the above +just docs-serve # serve the docs site locally +``` + +Run them from this directory, or from anywhere in the repository as +`just packages/zarr-indexing/<recipe>`. + +The test recipe runs against the workspace-root environment, because the +chunk-resolution tests exercise this package against `zarr`'s chunk grids and +`zarr` is deliberately not a dependency of this package. + +## License + +MIT diff --git a/packages/zarr-indexing/changes/3906.feature.md b/packages/zarr-indexing/changes/3906.feature.md new file mode 100644 index 0000000000..fa51b4438e --- /dev/null +++ b/packages/zarr-indexing/changes/3906.feature.md @@ -0,0 +1 @@ +Reworked the JSON layer to conform to the [ndsel](https://github.com/zarr-developers/ndsel) draft wire format, which adapts TensorStore's `IndexTransform`. A new `zarr_indexing.messages` module (`parse_ndsel`, `normalize_ndsel`, `NdselError`) is a pure JSON-to-JSON layer that accepts all five message kinds (`point`/`box`/`slice`/`points`/`transform`) and normalizes them to the canonical transform body, enforcing the full ndsel error taxonomy. The package is checked against the vendored, language-agnostic ndsel conformance corpus. `index_transform_to_json`/`index_transform_from_json` (and the domain variants) now produce and consume the canonical body. On serialization, orthogonal (`oindex`) `index_array` maps no longer emit `input_dimension` alongside `index_array` (a combination both ndsel and TensorStore reject), and degenerate all-singleton index arrays collapse to constant maps; the in-memory `input_dimension` is reconstructed from the array's dependency axes on load. diff --git a/packages/zarr-indexing/changes/README.md b/packages/zarr-indexing/changes/README.md new file mode 100644 index 0000000000..feb3f8674e --- /dev/null +++ b/packages/zarr-indexing/changes/README.md @@ -0,0 +1,25 @@ +Writing a changelog entry for `zarr-indexing` +----------------------------------------------- + +Fragments in **this** directory are release notes for the `zarr-indexing` +package only — kept separate from the parent zarr-python `changes/` +directory so a PR touching only `packages/zarr-indexing/` produces a +release note for this package only. + +Please put a new file in this directory named `xxxx.<type>.md`, where + +- `xxxx` is the pull request number associated with this entry +- `<type>` is one of: + - feature + - bugfix + - doc + - removal + - misc + +Inside the file, please write a short description of what you have +changed, and how it impacts users of `zarr-indexing`. + +A `zarr-indexing` release runs `towncrier build` in `packages/zarr-indexing/`, +which consumes the fragments here and updates `CHANGELOG.md`. 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+ +::: zarr_indexing.chunk_resolution diff --git a/packages/zarr-indexing/docs/api/composition.md b/packages/zarr-indexing/docs/api/composition.md new file mode 100644 index 0000000000..59affe016c --- /dev/null +++ b/packages/zarr-indexing/docs/api/composition.md @@ -0,0 +1,5 @@ +--- +title: composition +--- + +::: zarr_indexing.composition diff --git a/packages/zarr-indexing/docs/api/domain.md b/packages/zarr-indexing/docs/api/domain.md new file mode 100644 index 0000000000..b039d3a7f4 --- /dev/null +++ b/packages/zarr-indexing/docs/api/domain.md @@ -0,0 +1,5 @@ +--- +title: domain +--- + +::: zarr_indexing.domain diff --git a/packages/zarr-indexing/docs/api/errors.md b/packages/zarr-indexing/docs/api/errors.md new file mode 100644 index 0000000000..994a74248a --- /dev/null +++ b/packages/zarr-indexing/docs/api/errors.md @@ -0,0 +1,5 @@ +--- +title: errors +--- + +::: zarr_indexing.errors diff --git a/packages/zarr-indexing/docs/api/grid.md b/packages/zarr-indexing/docs/api/grid.md new file mode 100644 index 0000000000..c4c9cadb4f --- /dev/null +++ b/packages/zarr-indexing/docs/api/grid.md @@ -0,0 +1,5 @@ +--- +title: grid +--- + +::: zarr_indexing.grid diff --git a/packages/zarr-indexing/docs/api/index.md b/packages/zarr-indexing/docs/api/index.md new file mode 100644 index 0000000000..b9a58b70fa --- /dev/null +++ b/packages/zarr-indexing/docs/api/index.md @@ -0,0 +1,47 @@ +--- +title: API reference +--- + +# API reference + +The modules are layered: the transform algebra at the bottom, chunk resolution +and the wire format built on top of it. + +**The transform algebra** + +- [`zarr_indexing.domain`](domain.md) — `IndexDomain`, a rectangular region of + integer coordinates with an explicit (possibly non-zero) origin +- [`zarr_indexing.output_map`](output_map.md) — `ConstantMap`, `DimensionMap`, + and `ArrayMap`: three representations of a set of integer coordinates, one + per storage dimension +- [`zarr_indexing.transform`](transform.md) — `IndexTransform`, which pairs a + domain with output maps, plus the indexing (`[...]`, `.oindex`, `.vindex`), + `intersect`, and `translate` operations, and `selection_to_transform` +- [`zarr_indexing.composition`](composition.md) — `compose`, which chains two + transforms into one + +**Chunk resolution** + +- [`zarr_indexing.chunk_resolution`](chunk_resolution.md) — + `iter_chunk_transforms` (transform + chunk grid → per-chunk transforms) and + `sub_transform_to_selections` (the bridge back to the selection tuples the + current codec pipeline expects) +- [`zarr_indexing.grid`](grid.md) — `DimensionGridLike`, the Protocol + describing the narrow chunk-grid surface chunk resolution consumes, so that + nothing here imports `zarr` + +**The ndsel wire format** (see [the guide](../ndsel.md)) + +- [`zarr_indexing.messages`](messages.md) — `parse_ndsel` / `normalize_ndsel`, + the pure JSON→JSON message layer, and `NdselError` +- [`zarr_indexing.json`](json.md) — lowering between canonical ndsel bodies and + in-memory transforms + +**Errors** + +- [`zarr_indexing.errors`](errors.md) — the canonical index-error types, which + `zarr.errors` re-exports by identity + +Every name listed in `zarr_indexing.__all__` is re-exported at the top level, +so `from zarr_indexing import IndexTransform` and +`from zarr_indexing.transform import IndexTransform` are equivalent. diff --git a/packages/zarr-indexing/docs/api/json.md b/packages/zarr-indexing/docs/api/json.md new file mode 100644 index 0000000000..0183ab30e7 --- /dev/null +++ b/packages/zarr-indexing/docs/api/json.md @@ -0,0 +1,5 @@ +--- +title: json +--- + +::: zarr_indexing.json diff --git a/packages/zarr-indexing/docs/api/messages.md b/packages/zarr-indexing/docs/api/messages.md new file mode 100644 index 0000000000..6c2a434540 --- /dev/null +++ b/packages/zarr-indexing/docs/api/messages.md @@ -0,0 +1,5 @@ +--- +title: messages +--- + +::: zarr_indexing.messages diff --git a/packages/zarr-indexing/docs/api/output_map.md b/packages/zarr-indexing/docs/api/output_map.md new file mode 100644 index 0000000000..55114a6997 --- /dev/null +++ b/packages/zarr-indexing/docs/api/output_map.md @@ -0,0 +1,5 @@ +--- +title: output_map +--- + +::: zarr_indexing.output_map diff --git a/packages/zarr-indexing/docs/api/transform.md b/packages/zarr-indexing/docs/api/transform.md new file mode 100644 index 0000000000..bd754f5ec5 --- /dev/null +++ b/packages/zarr-indexing/docs/api/transform.md @@ -0,0 +1,5 @@ +--- +title: transform +--- + +::: zarr_indexing.transform diff --git a/packages/zarr-indexing/docs/index.md b/packages/zarr-indexing/docs/index.md new file mode 100644 index 0000000000..d123cbd32b --- /dev/null +++ b/packages/zarr-indexing/docs/index.md @@ -0,0 +1,150 @@ +# zarr-indexing + +Composable, lazy coordinate transforms for Zarr array indexing. + +`zarr-indexing` is developed in the +[zarr-python repository](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing) +and released independently of `zarr` itself. Install it with: + +``` +pip install zarr-indexing +``` + +## What this is + +An indexing operation — a slice, an integer, a fancy index array — is a +*mapping* from the coordinates a user asks for to the coordinates that live in +storage. This library makes that mapping a first-class value: an +[`IndexTransform`](api/transform.md). Transforms compose, so a view of a view +of an array is still a single transform, and nothing is read until someone +asks for data. + +Three pieces do the work: + +- **The transform algebra** ([`zarr_indexing.transform`](api/transform.md), + [`zarr_indexing.domain`](api/domain.md), + [`zarr_indexing.output_map`](api/output_map.md), + [`zarr_indexing.composition`](api/composition.md)): an `IndexTransform` + pairs an input [`IndexDomain`](api/domain.md) — a rectangular region of + integer coordinates, which unlike NumPy may have a non-zero origin — with + one output map per storage dimension. `ConstantMap`, `DimensionMap`, and + `ArrayMap` are three representations of the same thing, a set of integer + coordinates, traded off against each other for efficiency. +- **Chunk resolution** ([`zarr_indexing.chunk_resolution`](api/chunk_resolution.md)): + given a transform and a chunk grid, which chunks does this selection touch, + which coordinates does it touch *inside* each chunk, and where do the values + land in the output buffer? The resolver is dependency-aware: correlated + (`vindex`) array maps are enumerated jointly rather than as a cartesian + product, and orthogonal (`oindex`) array maps contribute only the chunks + their index arrays actually land in, so resolution scales with the number of + selected coordinates instead of with the size of the grid. +- **A wire format** ([`zarr_indexing.messages`](api/messages.md), + [`zarr_indexing.json`](api/json.md)): selections serialize to and from + [ndsel](https://github.com/zarr-developers/ndsel), a JSON representation of + NumPy-style n-dimensional selections. See [the ndsel wire format](ndsel.md). + +The package depends only on NumPy and the standard library. In particular it +does not import `zarr`: the chunk-grid surface chunk resolution needs is +described by the [`DimensionGridLike`](api/grid.md) Protocol, which zarr's +per-dimension grids satisfy structurally. + +## Relationship to TensorStore + +The model is [TensorStore's](https://google.github.io/tensorstore/index_space.html) +index transform, reimplemented in Python against NumPy: index domains with +explicit origins, output index maps of constant / single-input-dimension / +index-array flavour, and composition as the single operation that stacks +views. Names and semantics follow TensorStore where they overlap — notably, +negative indices are literal coordinates, not Python-style offsets from the +end, and it is the caller's job to normalize them. + +The differences are the ones NumPy compatibility forces. `ArrayMap` records +the input dimension an *orthogonal* (`oindex`) index array varies over, which +TensorStore's format has no field for; the +[serializer collapses or reconstructs that field](api/json.md) so the wire +format stays TensorStore-loadable. Chunk resolution and the `oindex`/`vindex` +helpers exist to serve NumPy-shaped selection semantics, which TensorStore +does not have to model. + +## Quickstart + +Indexing a transform produces a new transform. No I/O happens, and no +coordinates are materialized: + +```python +from zarr_indexing import IndexTransform + +transform = IndexTransform.from_shape((100, 100)) + +view = transform[10:50, 5] +view.domain # IndexDomain(inclusive_min=(10,), exclusive_max=(50,)) +view.selection_repr # '{ [10, 50), 5 }' +``` + +The domain describes what the *user* sees (here a single dimension, 40 long, +with origin 10); the output maps describe what *storage* sees (a stride-1 +`DimensionMap` and the `ConstantMap` for the dropped dimension). + +Fancy indexing works the same way, in both flavours, and still materializes +nothing but the index arrays themselves: + +```python +import numpy as np + +transform.oindex[np.array([3, 1, 90]), 0:4] # '{ {3, 1, 90}, [0, 4) }', shape (3, 4) +transform.vindex[np.array([0, 40, 99]), np.array([1, 2, 3])] # shape (3,) +``` + +Transforms built independently stack with +[`compose`](api/composition.md), which is what `transform[...]` uses +internally when you index an already-indexed view: + +```python +from zarr_indexing import compose + +inner = IndexTransform.from_shape((100,))[::2] # storage 0, 2, 4, ... over domain [0, 50) +outer = IndexTransform.from_shape((50,))[10:20] + +compose(outer, inner).selection_repr # '{ [20, 40) step 2 }' +``` + +Resolution against a chunk grid is where a transform finally meets storage. +Chunk resolution asks the grid only for the per-dimension index-to-chunk +mapping described by [`DimensionGridLike`](api/grid.md), so any object with +those four methods will do: + +```python +from dataclasses import dataclass + +from zarr_indexing import iter_chunk_transforms + + +@dataclass(frozen=True) +class RegularDimensionGrid: + chunk: int + + def index_to_chunk(self, idx): return idx // self.chunk + def chunk_offset(self, chunk_ix): return chunk_ix * self.chunk + def chunk_size(self, chunk_ix): return self.chunk + def indices_to_chunks(self, indices): return indices // self.chunk + + +grids = [RegularDimensionGrid(32), RegularDimensionGrid(32)] + +for chunk_coords, sub_transform, out_indices in iter_chunk_transforms(view, grids): + print(chunk_coords, sub_transform.selection_repr) +# (0, 0) { [10, 32), 5 } +# (1, 0) { [0, 18), 5 } +``` + +Each yielded `sub_transform` is the original transform restricted to one chunk +and translated into chunk-local coordinates — exactly what a codec pipeline +needs to decode that chunk and scatter the result. `out_indices` carries the +output scatter indices for array selections, and is `None` for basic indexing. + +## Reference + +- [The ndsel wire format](ndsel.md) +- [API reference](api/index.md) +- [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/CHANGELOG.md) +- [License (MIT)](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/LICENSE.txt) diff --git a/packages/zarr-indexing/docs/ndsel.md b/packages/zarr-indexing/docs/ndsel.md new file mode 100644 index 0000000000..74f394b758 --- /dev/null +++ b/packages/zarr-indexing/docs/ndsel.md @@ -0,0 +1,156 @@ +--- +title: The ndsel wire format +--- + +# The ndsel wire format + +[ndsel](https://github.com/zarr-developers/ndsel) is a draft JSON +representation of NumPy-style n-dimensional selections, adapted from +TensorStore's `IndexTransform` model. `zarr-indexing` implements it in two +layers, and the split between them is the thing worth understanding: + +| Layer | Module | Depends on | Job | +| --- | --- | --- | --- | +| Message | [`zarr_indexing.messages`](api/messages.md) | stdlib only | JSON in, canonical JSON out. Validates and desugars. Never rounds, clamps, or drops information. | +| Engine | [`zarr_indexing.json`](api/json.md) | NumPy | Lowers a *canonical* body into an in-memory [`IndexTransform`](api/transform.md), and back. | + +Constraints that only make sense for a real array — finite bounds, index +arrays as `ndarray`s — live in the engine layer and nowhere else. That is why +`messages` can happily normalize a message with `"-inf"` bounds that +`json.transform_from_canonical` will refuse to lower. + +## Two entry points + +[`parse_ndsel`](api/messages.md#zarr_indexing.messages.parse_ndsel) +structurally validates a message of any kind and returns it **unchanged** — +use it when you want to keep a message in its compact shorthand form but +confirm it is well formed. + +[`normalize_ndsel`](api/messages.md#zarr_indexing.messages.normalize_ndsel) +desugars a message into the single deterministic **canonical transform body** +of the spec (section 4.3): a bare `IndexTransform` body without the `kind` +discriminator. + +```python +from zarr_indexing import normalize_ndsel + +normalize_ndsel({"kind": "box", "inclusive_min": [10, 5], "shape": [40, 1]}) +# {'input_rank': 2, +# 'input_inclusive_min': [10, 5], +# 'input_exclusive_max': [50, 6], +# 'input_labels': ['', ''], +# 'output': [{'offset': 0, 'stride': 1, 'input_dimension': 0}, +# {'offset': 0, 'stride': 1, 'input_dimension': 1}]} +``` + +Normalization is idempotent: re-tag the output with `kind: "transform"` and +normalizing it again returns the same body. Because the canonical body is +field-for-field a TensorStore `IndexTransform` minus `kind`, a normalized +message loads directly into `tensorstore.IndexTransform(json=...)`. + +Both entry points raise +[`NdselError`](api/messages.md#zarr_indexing.messages.NdselError), which +carries the spec `reason` code (`unknown_kind`, `rank_mismatch`, `step_zero`, +`output_map_conflict`, …) alongside a human-readable detail, so callers can +branch on the code rather than on message text. + +## The five message kinds + +Four are shorthands; the fifth is the canonical form itself. + +| `kind` | Fields | Selects | +| --- | --- | --- | +| `point` | `coords` | A single element. Normalizes to rank 0 with one `constant` output map per dimension. | +| `box` | `inclusive_min`, one of `exclusive_max` / `inclusive_max` / `shape`, `labels` | A rectangular region. Exactly one upper-bound spelling may appear. | +| `slice` | `start`, `stop`, `step`, `labels` | A strided region, one Python-style slice per dimension. | +| `points` | `coords` (a list of coordinate rows) | An explicit list of points — the `vindex` case. Normalizes to one `index_array` output map per dimension over a shared rank-1 input domain. | +| `transform` | `input_rank`, `input_inclusive_min`, one of the three `input_*` upper bounds, `input_labels`, `output` | The full canonical form. | + +Value rules the message layer enforces throughout: every integer is a 64-bit +signed value; JSON booleans are **not** integers (Python's +`isinstance(True, int)` is guarded against explicitly); the `"-inf"` / `"+inf"` +sentinels are legal only in bound positions; and an implicit bound is the +one-element `[n]`-bracket form, whose implicit/explicit flag survives +normalization intact. + +## Lowering to a transform + +The engine layer converts between canonical bodies and `IndexTransform`s: + +```python +from zarr_indexing import transform_from_canonical, transform_to_canonical + +t = transform_from_canonical(canonical) +transform_to_canonical(t) == canonical +``` + +`index_transform_to_json` / `index_transform_from_json` (and the +`index_domain_*` variants) are these same converters under their historical +names. + +Two engine constraints apply here and only here. A canonical body carrying a +`"-inf"` or `"+inf"` bound cannot be lowered — an `IndexDomain` addresses a +finite array — so `transform_from_canonical` raises. And implicit bounds lower +*by value*: the `[n]`-bracket flag is a message-layer concern, and the engine +keeps only the integer. + +### The `index_array` round trip + +ndsel and TensorStore both **reject** an output map that carries both +`input_dimension` and `index_array`. The in-memory +[`ArrayMap`](api/output_map.md#zarr_indexing.output_map.ArrayMap), though, +records an `input_dimension` to pin the axis an orthogonal (`oindex`) array +varies over. The serializer bridges that gap in both directions: + +- **On serialize**, a non-degenerate `index_array` map is emitted *without* + `input_dimension`. +- **On load**, the in-memory `input_dimension` is reconstructed from the + full-rank array's dependency axes — its non-singleton axes. An array that + solely owns a single non-singleton axis is orthogonal; arrays that share + non-singleton axes, or vary over several, are correlated (`vindex`), and get + `input_dimension = None`. A single 1-D array over a rank-1 domain is + inherently ambiguous between the two flavours and reconstructs as + orthogonal, which is behaviorally identical in that case. + +There is one deliberate exception, worth calling out because it is the one +place a round trip changes representation rather than preserving it. An +all-singleton `index_array` — size 1 — selects the same coordinate no matter +what the input is, so it is **collapsed to a `constant` map** on serialize: + +```python +from zarr_indexing import IndexTransform, transform_to_canonical + +transform_to_canonical(IndexTransform.from_shape((100, 100)).oindex[[5], 0:2]) +# {'input_rank': 2, +# 'input_inclusive_min': [0, 0], +# 'input_exclusive_max': [1, 2], +# 'input_labels': ['', ''], +# 'output': [{'offset': 5}, +# {'offset': 0, 'stride': 1, 'input_dimension': 1}]} +``` + +The size-1 input dimension stays in the domain, unconsumed by any output map — +still a valid transform, and still the right output shape. A length-1 `oindex` +selection therefore round-trips *behaviorally* (an `ArrayMap` comes back as a +`ConstantMap`) rather than by object identity. + +## Conformance + +The package is checked against the language-agnostic ndsel conformance corpus, +vendored unmodified under +[`tests/conformance/`](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing/tests/conformance) +— one JSON file per message kind plus `errors.json`, with the source commit +recorded in `PROVENANCE.md`. Each fixture is either a *success* case +(`input` + expected `normalized` body) or an *error* case (`input` + expected +reason code), and an implementation is conformant iff `normalize` reproduces +every one. `tests/test_conformance.py` runs the whole corpus as one +parametrized test per fixture, so a corpus update reports failures fixture by +fixture rather than as a single opaque assertion. + +Do not edit the vendored files; to pick up spec changes, re-vendor from a newer +ndsel commit and update the recorded SHA. + +A second, optional test (`tests/test_ndsel_tensorstore.py`, skipped unless +`tensorstore` is installed) closes the loop against a real TensorStore by +loading canonical bodies into `tensorstore.IndexTransform` and re-loading +TensorStore's own `to_json()` output back through the engine layer. diff --git a/packages/zarr-indexing/justfile b/packages/zarr-indexing/justfile new file mode 100644 index 0000000000..20e1b2b837 --- /dev/null +++ b/packages/zarr-indexing/justfile @@ -0,0 +1,58 @@ +# Development verbs for the zarr-indexing package. Recipes run with this +# directory as the working directory regardless of where `just` is invoked. + +# List available recipes +default: + @just --list + +# The chunk-resolution tests exercise this package against zarr's ChunkGrid, so +# they need an environment that has both `zarr` and this package installed. +# `zarr` is deliberately not a dependency of this package, and the repo is not +# a uv workspace, so run against the repo-root environment (which provides +# `zarr`) with this package layered in as an editable overlay — the same +# invocation CI uses. +# Run the test suite; extra args are passed to pytest +test *args: + uv run --project ../.. --group test --with-editable . python -m pytest tests {{ args }} + +# Lint with the same invocation CI uses +lint: + uvx ruff check . + +# Type-check the package sources +typecheck: + uv run --group test --with pyright pyright src + +# Run everything CI runs for this package +check: lint typecheck test docs-check + +# Preview the changelog that the next release would generate +changelog-draft: + uvx towncrier build --draft --version Unreleased + +# Build this package's documentation site, warnings as errors +docs-check: + env DISABLE_MKDOCS_2_WARNING=true uv run --group docs mkdocs build --strict + +# With no argument, uses port 8000 if free, otherwise an ephemeral free port; +# an explicitly requested port is used as-is so a conflict fails loudly. +# Serve this package's documentation site +docs-serve port="": + #!/usr/bin/env bash + set -euo pipefail + port="{{ port }}" + if [ -z "$port" ]; then + port=$(uv run --group docs python -c ' + import socket + s = socket.socket() + try: + s.bind(("127.0.0.1", 8000)) + except OSError: + s.close() + s = socket.socket() + s.bind(("127.0.0.1", 0)) + print(s.getsockname()[1]) + s.close() + ') + fi + exec env DISABLE_MKDOCS_2_WARNING=true uv run --group docs mkdocs serve -a "localhost:$port" diff --git a/packages/zarr-indexing/mkdocs.yml b/packages/zarr-indexing/mkdocs.yml new file mode 100644 index 0000000000..d7261f32e1 --- /dev/null +++ b/packages/zarr-indexing/mkdocs.yml @@ -0,0 +1,110 @@ +site_name: zarr-indexing +# The package lives in the zarr-python monorepo; point the header source +# widget at the package directory rather than the repository root. +repo_name: zarr-python/packages/zarr-indexing +repo_url: https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing +# Absolute because mkdocs would otherwise append this to repo_url's subpath. +edit_uri: https://github.com/zarr-developers/zarr-python/edit/main/packages/zarr-indexing/docs/ +site_description: Composable, lazy coordinate transforms for Zarr array indexing. +site_author: Davis Bennett +site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://zarr-indexing.readthedocs.io/'] +docs_dir: docs +use_directory_urls: true + +nav: + - index.md + - ndsel.md + - API Reference: + - api/index.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.transform</code>': api/transform.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.domain</code>': api/domain.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.output_map</code>': api/output_map.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.composition</code>': api/composition.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.chunk_resolution</code>': api/chunk_resolution.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.grid</code>': api/grid.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.json</code>': api/json.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.messages</code>': api/messages.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.errors</code>': api/errors.md + - Changelog: https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/CHANGELOG.md + +watch: + - src + +theme: + language: en + name: material + logo: _static/logo_bw.png + favicon: _static/favicon-96x96.png + + palette: + # Light mode + - media: "(prefers-color-scheme: light)" + scheme: default + toggle: + icon: material/brightness-7 + name: Switch to dark mode + + # Dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + toggle: + icon: material/brightness-4 + name: Switch to light mode + + font: + text: Roboto + code: Roboto Mono + + features: + - content.code.annotate + - content.code.copy + - navigation.indexes + - navigation.instant + - navigation.tracking + - search.suggest + - search.share + +plugins: + - autorefs + - search + - mkdocstrings: + enable_inventory: true + handlers: + python: + paths: [src] + options: + allow_inspection: true + docstring_section_style: list + docstring_style: numpy + inherited_members: true + line_length: 60 + separate_signature: true + show_root_heading: true + show_signature_annotations: true + show_source: true + show_symbol_type_toc: true + signature_crossrefs: true + show_if_no_docstring: true + extensions: + - griffe_inherited_docstrings + + inventories: + - https://docs.python.org/3/objects.inv + - https://numpy.org/doc/stable/objects.inv + - https://zarr.readthedocs.io/en/stable/objects.inv + +markdown_extensions: + - admonition + - attr_list + - def_list + - footnotes + - md_in_html + - pymdownx.details + - pymdownx.superfences + - toc: + permalink: true + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite diff --git a/packages/zarr-indexing/pyproject.toml b/packages/zarr-indexing/pyproject.toml new file mode 100644 index 0000000000..21ba4ef7e7 --- /dev/null +++ b/packages/zarr-indexing/pyproject.toml @@ -0,0 +1,124 @@ +[build-system] +requires = ["hatchling>=1.29.0", "hatch-vcs"] +build-backend = "hatchling.build" + +[project] +name = "zarr-indexing" +dynamic = ["version"] +description = "Composable, lazy coordinate transforms for Zarr array indexing." +readme = "README.md" +requires-python = ">=3.12" +license = "MIT" +license-files = ["LICENSE.txt"] +authors = [ + { name = "Davis Bennett", email = "davis.v.bennett@gmail.com" }, +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "Intended Audience :: Information Technology", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Topic :: Scientific/Engineering", + "Topic :: Software Development :: Libraries :: Python Modules", + "Typing :: Typed", +] +keywords = ["zarr"] +dependencies = [ + "numpy>=2", +] + +[project.urls] +Homepage = "https://github.com/zarr-developers/zarr-python" +Source = "https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing" +Issues = "https://github.com/zarr-developers/zarr-python/issues" +Changelog = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/CHANGELOG.md" +Documentation = "https://zarr-indexing.readthedocs.io/" + +[dependency-groups] +# The transform tests exercise chunk resolution against zarr's ChunkGrid +# (tests/test_chunk_resolution.py) and are collected by the parent zarr-python +# test suite, which already has zarr installed. `zarr` is intentionally NOT +# listed here to avoid a workspace dependency cycle; run these tests from the +# repo root (`uv run pytest packages/zarr-indexing/tests`), not in isolation. +test = ["pytest"] +docs = [ + # Pins match the zarr-python docs environment in the repo-root + # pyproject.toml so the two sites render with the same toolchain. + "mkdocs-material==9.7.6", + "mkdocs==1.6.1", + "mkdocstrings==1.0.4", + "mkdocstrings-python==2.0.5", + "griffe-inherited-docstrings==1.1.3", + # mkdocstrings uses ruff to format rendered signatures + "ruff==0.15.20", +] + +[tool.hatch.version] +source = "vcs" +tag-pattern = '^zarr_indexing-v(?P<version>.+)$' +# `git_describe_command` ensures we get the zarr_indexing tags instead of latest. +# `local_scheme` strips the git commit info so the appending info is just a counter from latest tag. +# test-pypi doesn't accept git commit info in tags, and the count should be enough to distinguish unique runs. +raw-options = { root = "../..", git_describe_command = "git describe --dirty --tags --long --match zarr_indexing-v*", local_scheme = "no-local-version" } + +[tool.hatch.build.targets.wheel] +packages = ["src/zarr_indexing"] + +[tool.ruff] +extend = "../../pyproject.toml" +target-version = "py312" + +[tool.pytest.ini_options] +minversion = "7" +testpaths = ["tests"] +xfail_strict = true +addopts = ["-ra", "--strict-config", "--strict-markers"] +filterwarnings = [ + "error", +] + +[tool.pyright] +include = ["src"] +enableExperimentalFeatures = true +typeCheckingMode = "strict" +pythonVersion = "3.12" +# This strict config was written for zarr-metadata's JSON/dataclass-shaped +# code. zarr-indexing is numpy-heavy, and numpy's stubs return partially +# unknown types (e.g. `ndarray[Unknown, Unknown]`, `dtype[Unknown]`) even for +# fully-typed call sites, so the reportUnknown* family below cannot reasonably +# be satisfied here. Downgraded to warnings (not silenced) rather than +# disabled outright, and CI (which only fails the pyright job on errors, not +# warnings) still surfaces them for visibility. +reportUnknownVariableType = "warning" +reportUnknownArgumentType = "warning" +reportUnknownMemberType = "warning" +reportUnknownParameterType = "warning" + +[tool.numpydoc_validation] +checks = [ + "GL10", + "SS04", + "PR02", + "PR03", + "PR05", + "PR06", +] + +[tool.towncrier] +# Fragments for this package live alongside the package source, separate +# from the parent zarr-python `changes/` directory, so a PR touching only +# `packages/zarr-indexing/` produces a release note for this package only. +directory = "changes" +filename = "CHANGELOG.md" +package = "zarr_indexing" +underlines = ["", "", ""] +title_format = "## {version} ({project_date})" +issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues/{issue})" +start_string = "<!-- towncrier release notes start -->\n" diff --git a/packages/zarr-indexing/src/zarr_indexing/__init__.py b/packages/zarr-indexing/src/zarr_indexing/__init__.py new file mode 100644 index 0000000000..effe38ca88 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/__init__.py @@ -0,0 +1,74 @@ +"""Composable, lazy coordinate transforms for zarr array indexing. + +This package implements TensorStore-inspired index transforms. The core idea: +every indexing operation (slicing, fancy indexing, etc.) produces a coordinate +mapping from user space to storage space. These mappings compose lazily — no +I/O until you explicitly read or write. + +Key types: + +- `IndexDomain` — a rectangular region of integer coordinates +- `IndexTransform` — maps input coordinates to storage coordinates +- `ConstantMap`, `DimensionMap`, `ArrayMap` — the three ways a single + output dimension can depend on the input (see `output_map.py`) +- `compose` — chain two transforms into one + +The chunk-resolution helpers (`iter_chunk_transforms`, +`sub_transform_to_selections`) and `selection_to_transform` are also exported +here: they form the surface the zarr integration layer (array indexing) depends +on. The `*Like` grid Protocols describe the chunk-grid surface chunk resolution +consumes without importing zarr. +""" + +from importlib.metadata import version + +from zarr_indexing.chunk_resolution import ( + iter_chunk_transforms, + sub_transform_to_selections, +) +from zarr_indexing.composition import compose +from zarr_indexing.domain import IndexDomain +from zarr_indexing.grid import DimensionGridLike +from zarr_indexing.json import ( + IndexDomainJSON, + IndexTransformJSON, + OutputIndexMapJSON, + index_domain_from_json, + index_domain_to_json, + index_transform_from_json, + index_transform_to_json, + transform_from_canonical, + transform_to_canonical, +) +from zarr_indexing.messages import NdselError, normalize_ndsel, parse_ndsel +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap +from zarr_indexing.transform import IndexTransform, selection_to_transform + +__version__ = version("zarr-indexing") + +__all__ = [ + "ArrayMap", + "ConstantMap", + "DimensionGridLike", + "DimensionMap", + "IndexDomain", + "IndexDomainJSON", + "IndexTransform", + "IndexTransformJSON", + "NdselError", + "OutputIndexMap", + "OutputIndexMapJSON", + "__version__", + "compose", + "index_domain_from_json", + "index_domain_to_json", + "index_transform_from_json", + "index_transform_to_json", + "iter_chunk_transforms", + "normalize_ndsel", + "parse_ndsel", + "selection_to_transform", + "sub_transform_to_selections", + "transform_from_canonical", + "transform_to_canonical", +] diff --git a/packages/zarr-indexing/src/zarr_indexing/chunk_resolution.py b/packages/zarr-indexing/src/zarr_indexing/chunk_resolution.py new file mode 100644 index 0000000000..7aea86ad02 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/chunk_resolution.py @@ -0,0 +1,380 @@ +"""Chunk resolution — mapping transforms to chunk-level I/O. + +Given an `IndexTransform` (which coordinates a user wants to access) and a +`ChunkGrid` (how storage is divided into chunks), chunk resolution answers: + + For each chunk, which storage coordinates does this transform touch, + and where do those values land in the output buffer? + +The algorithm is: + +1. **Enumerate candidate chunks** — determine which chunks could possibly + be touched by the transform's output coordinate ranges. + +2. **Intersect** — for each candidate chunk, call + `transform.intersect(chunk_domain)` to restrict the transform to + coordinates within that chunk. If the intersection is empty, skip it. + +3. **Translate** — shift the restricted transform to chunk-local coordinates + via `transform.translate(-chunk_origin)`. + +4. **Yield** — produce `(chunk_coords, local_transform, surviving_indices)` + triples that the codec pipeline consumes. + +Sorted one-dimensional correlated array maps can be partitioned directly +because every touched chunk owns a contiguous slice of the index array. That +case bypasses candidate enumeration and repeated intersection. + +`sub_transform_to_selections` bridges from the transform representation +back to the raw `(chunk_selection, out_selection, drop_axes)` tuples that +the current codec pipeline expects. This bridge will go away when the codec +pipeline accepts transforms natively. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +import numpy as np + +from zarr_indexing.domain import IndexDomain +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap +from zarr_indexing.transform import IndexTransform + +if TYPE_CHECKING: + from collections.abc import Iterator, Sequence + + from zarr_indexing.grid import DimensionGridLike + +OutIndices = ( + dict[int, np.ndarray[Any, np.dtype[np.intp]]] | np.ndarray[Any, np.dtype[np.intp]] | None +) + +ChunkTransformResult = tuple[ + tuple[int, ...], + IndexTransform, + OutIndices, +] + + +def _one_dimensional_correlated_array_map( + transform: IndexTransform, +) -> tuple[ArrayMap, np.ndarray[Any, np.dtype[np.intp]]] | None: + """Return a nonempty correlated 1-D ArrayMap and its storage coordinates. + + A one-dimensional array selection has no cross-dimensional correlation to + preserve. The computed storage coordinates are also reused by general + resolution when they are unsorted. + """ + if transform.input_rank != 1 or transform.output_rank != 1: + return None + + m = transform.output[0] + if ( + not isinstance(m, ArrayMap) + or m.input_dimension is not None + or m.index_array.ndim != 1 + or m.index_array.size == 0 + ): + return None + + return m, m.offset + m.stride * m.index_array + + +def _iter_sorted_1d_array_map( + m: ArrayMap, + storage: np.ndarray[Any, np.dtype[np.intp]], + dim_grid: DimensionGridLike, +) -> Iterator[ChunkTransformResult]: + """Resolve a sorted 1-D ArrayMap one touched chunk at a time.""" + start = 0 + while start < storage.size: + chunk = dim_grid.index_to_chunk(int(storage[start])) + chunk_start = dim_grid.chunk_offset(chunk) + chunk_stop = chunk_start + dim_grid.chunk_size(chunk) + stop = int(np.searchsorted(storage, chunk_stop, side="left")) + + restricted = IndexTransform( + domain=IndexDomain(inclusive_min=(0,), exclusive_max=(stop - start,)), + output=( + ArrayMap( + index_array=m.index_array[start:stop], + offset=m.offset, + stride=m.stride, + input_dimension=m.input_dimension, + ), + ), + ) + local = restricted.translate((-chunk_start,)) + surviving = np.arange(start, stop, dtype=np.intp) + + yield (chunk,), local, surviving + start = stop + + +def iter_chunk_transforms( + transform: IndexTransform, + dim_grids: Sequence[DimensionGridLike], +) -> Iterator[ChunkTransformResult]: + """Resolve a composed IndexTransform against per-dimension chunk grids. + + `dim_grids` holds one `DimensionGridLike` per output (storage) dimension — + for zarr this is the chunk grid's per-dimension sequence. Yields + `(chunk_coords, sub_transform, out_indices)` triples: + + - `chunk_coords`: which chunk to access. + - `sub_transform`: maps output buffer coords to chunk-local coords. + - `out_indices`: for vectorized/array indexing, the output scatter + indices (integer array). `None` for basic/slice indexing. + """ + + array_map_1d = _one_dimensional_correlated_array_map(transform) + if array_map_1d is not None: + sorted_map, storage = array_map_1d + if storage[0] <= storage[-1] and bool(np.all(storage[1:] >= storage[:-1])): + dim_grid = dim_grids[0] + first_chunk = dim_grid.index_to_chunk(int(storage[0])) + if dim_grid.chunk_size(first_chunk) > 0: + yield from _iter_sorted_1d_array_map(sorted_map, storage, dim_grid) + return + + # Enumerate candidate chunks via the cartesian product of per-slot candidate + # chunk ids, then for each candidate intersect the transform with the chunk + # domain (`transform.intersect` handles orthogonal and vectorized cases + # alike, filtering out combinations it does not actually touch). + # + # A slot covers one or more output dimensions and contributes exactly the + # chunk-coordinate tuples those dimensions can touch: + # + # - `ConstantMap`/`DimensionMap` dims each form their own slot with a + # contiguous range — a single chunk for a constant, and the span between + # the first and last chunk for a slice. These are already tight (or + # nearly so). + # - Orthogonal `ArrayMap` (fancy) dims each form their own slot with only + # the *distinct* chunk ids the index array actually lands in + # (`np.unique`), never the dense `range(min_chunk, max_chunk + 1)` + # between them. A sparse fancy selection (e.g. two far-apart coordinates) + # would otherwise enumerate every chunk in the bounding box, making + # resolution scale with grid size instead of with the number of selected + # coordinates. + # - Correlated (vindex) `ArrayMap` dims share one *joint* slot holding the + # distinct chunk-coordinate tuples the points actually land in. The + # cartesian product of their per-dimension distinct sets would include + # combinations no point touches — quadratic in the number of selected + # points for a diagonal selection — while the joint distinct set is + # bounded by the point count (see zarr-python gh-4174). + correlated_dims: list[int] = [] + correlated_chunk_ids: list[np.ndarray[Any, np.dtype[np.intp]]] = [] + slot_dims: list[tuple[int, ...]] = [] + slot_candidates: list[Sequence[tuple[int, ...]]] = [] + for out_dim, m in enumerate(transform.output): + dg = dim_grids[out_dim] + if isinstance(m, ConstantMap): + # Single chunk + c = dg.index_to_chunk(m.offset) + slot_dims.append((out_dim,)) + slot_candidates.append(((c,),)) + elif isinstance(m, DimensionMap): + d = m.input_dimension + dim_lo = transform.domain.inclusive_min[d] + dim_hi = transform.domain.exclusive_max[d] + if dim_lo >= dim_hi: + return # empty domain + if m.stride > 0: + s_min = m.offset + m.stride * dim_lo + s_max = m.offset + m.stride * (dim_hi - 1) + else: + s_min = m.offset + m.stride * (dim_hi - 1) + s_max = m.offset + m.stride * dim_lo + first = dg.index_to_chunk(s_min) + last = dg.index_to_chunk(s_max) + slot_dims.append((out_dim,)) + slot_candidates.append([(c,) for c in range(first, last + 1)]) + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap). + # Storage coordinates were already computed for a correlated 1-D map. + storage = ( + array_map_1d[1] if array_map_1d is not None else m.offset + m.stride * m.index_array + ) + if storage.size == 0: + # Empty fancy selection: no coordinates, so no chunks are touched. + return + # Keep the index-array shape: correlated maps broadcast against each + # other below, and raveling first would lose the singleton axes. + chunk_ids = dg.indices_to_chunks(storage.astype(np.intp)) + if m.input_dimension is None: + correlated_dims.append(out_dim) + correlated_chunk_ids.append(chunk_ids) + else: + slot_dims.append((out_dim,)) + slot_candidates.append([(int(c),) for c in np.unique(chunk_ids)]) + + if len(correlated_dims) == 1: + slot_dims.append((correlated_dims[0],)) + slot_candidates.append([(int(c),) for c in np.unique(correlated_chunk_ids[0])]) + elif len(correlated_dims) >= 2: + # Group the points jointly: distinct rows of the per-point chunk + # coordinates, O(points log points) regardless of grid size. + broadcast = np.broadcast_arrays(*correlated_chunk_ids) + stacked = np.stack([b.ravel() for b in broadcast], axis=1) + joint = np.unique(stacked, axis=0) + slot_dims.append(tuple(correlated_dims)) + slot_candidates.append([tuple(int(c) for c in row) for row in joint]) + + import itertools + + output_rank = len(transform.output) + for combo in itertools.product(*slot_candidates): + chunk_coords_list = [0] * output_rank + for dims, part in zip(slot_dims, combo, strict=True): + for d, c in zip(dims, part, strict=True): + chunk_coords_list[d] = c + chunk_coords = tuple(chunk_coords_list) + + # Build the chunk domain in storage space + chunk_min: list[int] = [] + chunk_max: list[int] = [] + chunk_shift: list[int] = [] + for out_dim, c in enumerate(chunk_coords): + dg = dim_grids[out_dim] + c_start = dg.chunk_offset(c) + c_size = dg.chunk_size(c) + chunk_min.append(c_start) + chunk_max.append(c_start + c_size) + chunk_shift.append(-c_start) + + chunk_domain = IndexDomain( + inclusive_min=tuple(chunk_min), + exclusive_max=tuple(chunk_max), + ) + + # Intersect transform with chunk domain + result = transform.intersect(chunk_domain) + if result is None: + continue + + restricted, surviving = result + + # Translate to chunk-local coordinates + local = restricted.translate(tuple(chunk_shift)) + + yield (chunk_coords, local, surviving) + + +def sub_transform_to_selections( + sub_transform: IndexTransform, + out_indices: OutIndices = None, +) -> tuple[ + tuple[int | slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]], ...], + tuple[slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]], ...], + tuple[int, ...], +]: + """Convert a chunk-local sub-transform to raw selections for the codec pipeline. + + Parameters + ---------- + sub_transform + A chunk-local IndexTransform (output maps already translated to + chunk-local coordinates). + out_indices + For vectorized indexing: the output scatter indices for this chunk. + None for orthogonal/basic indexing. + + Returns + ------- + tuple + `(chunk_selection, out_selection, drop_axes)` + """ + inclusive_min = sub_transform.domain.inclusive_min + exclusive_max = sub_transform.domain.exclusive_max + + # Orthogonal outer product: >= 2 ArrayMaps each bound to a distinct input + # dimension. out_indices is a per-output-dim dict of surviving positions. The + # codec applies chunk_array[chunk_sel] / out[out_sel] with NumPy semantics, so + # build np.ix_-style selections (mirroring the legacy OrthogonalIndexer): one + # 1-D selector per dimension, expanded to an open mesh. ConstantMap dims are + # size-1 in chunk space and squeezed out via drop_axes. + if isinstance(out_indices, dict): + chunk_arrays: list[np.ndarray[Any, np.dtype[np.intp]]] = [] + out_arrays: list[np.ndarray[Any, np.dtype[np.intp]]] = [] + drop_axes: list[int] = [] + for out_dim, m in enumerate(sub_transform.output): + if isinstance(m, ConstantMap): + chunk_arrays.append(np.array([m.offset], dtype=np.intp)) + drop_axes.append(out_dim) + elif isinstance(m, DimensionMap): + rng = np.arange(inclusive_min[m.input_dimension], exclusive_max[m.input_dimension]) + chunk_arrays.append((m.offset + m.stride * rng).astype(np.intp)) + out_arrays.append(rng.astype(np.intp)) + else: # ArrayMap + idx = m.index_array.ravel() + chunk_arrays.append((m.offset + m.stride * idx).astype(np.intp)) + out_arrays.append(out_indices[out_dim]) + return np.ix_(*chunk_arrays), np.ix_(*out_arrays), tuple(drop_axes) + + # Correlated (vindex) sub-transforms carry ArrayMaps with `input_dimension` + # None. They scatter through a single flat index (`out_indices`) into the + # row-major-flattened output buffer; the chunk selection reads a + # (points, residual-slice) block via the raveled coordinate arrays and any + # residual DimensionMap slices. + correlated = any( + isinstance(m, ArrayMap) and m.input_dimension is None for m in sub_transform.output + ) + if correlated: + chunk_sel: list[int | slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]]] = [] + for m in sub_transform.output: + if isinstance(m, ConstantMap): + chunk_sel.append(m.offset) + elif isinstance(m, DimensionMap): + d = m.input_dimension + start = m.offset + m.stride * inclusive_min[d] + stop = m.offset + m.stride * exclusive_max[d] + if m.stride < 0: + start, stop = stop + 1, start + 1 + chunk_sel.append(slice(start, stop, m.stride)) + else: # ArrayMap + idx = m.index_array.reshape(-1) + chunk_sel.append((m.offset + m.stride * idx).astype(np.intp)) + # Chunk resolution always supplies the flat scatter index for a + # correlated transform. Absent one (a bare sub-transform), fall back to an + # identity scatter over the whole flattened output buffer. + # `out_indices` is narrowed to a flat scatter array or None here (the + # per-dimension dict is an orthogonal outer product, handled above). + out_scatter: slice | np.ndarray[Any, np.dtype[np.intp]] + if out_indices is None: + n = 1 + for s in sub_transform.domain.shape: + n *= s + out_scatter = slice(0, n) + else: + out_scatter = out_indices + return tuple(chunk_sel), (out_scatter,), () + + chunk_sel = [] # annotated in the correlated branch above (same function scope) + out_sel: list[slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]]] = [] + + # Single-pass build for the basic / single-orthogonal-array cases. + # ConstantMap dims are dropped (no out_sel entry). + for m in sub_transform.output: + if isinstance(m, ConstantMap): + chunk_sel.append(m.offset) + elif isinstance(m, DimensionMap): + d = m.input_dimension + dim_lo = inclusive_min[d] + dim_hi = exclusive_max[d] + start = m.offset + m.stride * dim_lo + stop = m.offset + m.stride * dim_hi + if m.stride < 0: + start, stop = stop + 1, start + 1 + chunk_sel.append(slice(start, stop, m.stride)) + out_sel.append(slice(dim_lo, dim_hi)) + else: # ArrayMap (orthogonal: full-rank, raveled to its 1-D fancy coords) + idx = m.index_array.reshape(-1) + if m.offset == 0 and m.stride == 1: + chunk_sel.append(idx) + else: + chunk_sel.append((m.offset + m.stride * idx).astype(np.intp)) + # Orthogonal ArrayMap: out_indices holds the surviving positions. + out_sel.append(out_indices if out_indices is not None else slice(0, idx.size)) + + return tuple(chunk_sel), tuple(out_sel), () diff --git a/packages/zarr-indexing/src/zarr_indexing/composition.py b/packages/zarr-indexing/src/zarr_indexing/composition.py new file mode 100644 index 0000000000..f5cc82599c --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/composition.py @@ -0,0 +1,133 @@ +"""Composition — chaining two transforms into one. + +`compose(outer, inner)` is the operation that makes views stack. `outer` maps +user coordinates to intermediate coordinates, `inner` maps those intermediate +coordinates to storage, and the result maps user coordinates straight to +storage — so a view of a view of an array is still a single +`IndexTransform`, and indexing never accumulates layers to walk at read time. + +Composition works one output map at a time, and each case reduces to +substituting the outer map into the inner one: + +- A `ConstantMap` inner map ignores its input, so it survives unchanged. +- A `DimensionMap` inner map is affine, so composing it with an outer + `ConstantMap` or `DimensionMap` folds into new `offset`/`stride` values; + composing it with an outer `ArrayMap` leaves the index array alone and + rescales around it. +- An `ArrayMap` inner map must be *evaluated* at the coordinates the outer + transform produces, which is the only case that touches array data. +""" + +from __future__ import annotations + +import numpy as np + +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap +from zarr_indexing.transform import IndexTransform + + +def compose(outer: IndexTransform, inner: IndexTransform) -> IndexTransform: + """Compose two IndexTransforms. + + `outer` maps user coords (rank m) to intermediate coords (rank n). + `inner` maps intermediate coords (rank n) to storage coords (rank p). + The result maps user coords (rank m) to storage coords (rank p). + + Precondition: `outer.output_rank == inner.domain.ndim`. + """ + if outer.output_rank != inner.domain.ndim: + raise ValueError( + f"outer output rank ({outer.output_rank}) must match inner input rank " + f"({inner.domain.ndim})" + ) + + result_output = [_compose_single(outer, inner_map) for inner_map in inner.output] + + return IndexTransform(domain=outer.domain, output=tuple(result_output)) + + +def _compose_single(outer: IndexTransform, inner_map: OutputIndexMap) -> OutputIndexMap: + """Compose a single inner output map with the full outer transform.""" + if isinstance(inner_map, ConstantMap): + return ConstantMap(offset=inner_map.offset) + + if isinstance(inner_map, DimensionMap): + return _compose_dimension(outer, inner_map) + + # inner_map: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + return _compose_array(outer, inner_map) + + +def _compose_dimension(outer: IndexTransform, inner_map: DimensionMap) -> OutputIndexMap: + """Compose when inner is a DimensionMap. + + storage = offset_i + stride_i * intermediate[dim_i] + where intermediate[dim_i] = outer.output[dim_i](user_input) + """ + dim_i = inner_map.input_dimension + offset_i = inner_map.offset + stride_i = inner_map.stride + outer_map = outer.output[dim_i] + + if isinstance(outer_map, ConstantMap): + return ConstantMap(offset=offset_i + stride_i * outer_map.offset) + + if isinstance(outer_map, DimensionMap): + return DimensionMap( + input_dimension=outer_map.input_dimension, + offset=offset_i + stride_i * outer_map.offset, + stride=stride_i * outer_map.stride, + ) + + # outer_map: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + # Affine post-composition leaves the index array (and hence its full + # input rank and dependency axes) untouched; carry the orthogonal + # binding through unchanged. + return ArrayMap( + index_array=outer_map.index_array, + offset=offset_i + stride_i * outer_map.offset, + stride=stride_i * outer_map.stride, + input_dimension=outer_map.input_dimension, + ) + + +def _compose_array(outer: IndexTransform, inner_map: ArrayMap) -> OutputIndexMap: + """Compose when inner is an ArrayMap. + + storage = offset_i + stride_i * arr_i[intermediate] + We need to evaluate arr_i at the intermediate coordinates produced by outer. + """ + arr_i = inner_map.index_array + offset_i = inner_map.offset + stride_i = inner_map.stride + + # Check if all outer outputs are constant + all_constant = all(isinstance(m, ConstantMap) for m in outer.output) + + if all_constant: + # Evaluate arr_i at the single constant point + idx = tuple(m.offset for m in outer.output if isinstance(m, ConstantMap)) + value = int(arr_i[idx]) + return ConstantMap(offset=offset_i + stride_i * value) + + # For 1D inner array with a single outer output (simple case) + if arr_i.ndim == 1 and len(outer.output) == 1: + outer_map = outer.output[0] + + if isinstance(outer_map, DimensionMap): + dim_size = outer.domain.shape[outer_map.input_dimension] + user_indices = np.arange(dim_size, dtype=np.intp) + intermediate_vals = outer_map.offset + outer_map.stride * user_indices + new_arr = arr_i[intermediate_vals] + return ArrayMap(index_array=new_arr, offset=offset_i, stride=stride_i) + + if isinstance(outer_map, ArrayMap): + intermediate_vals = outer_map.offset + outer_map.stride * outer_map.index_array + new_arr = arr_i[intermediate_vals] + return ArrayMap(index_array=new_arr, offset=offset_i, stride=stride_i) + + # General multi-dim case: not yet implemented + raise NotImplementedError( + "Composing a multi-dimensional inner array map with non-constant outer maps " + "is not yet supported." + ) diff --git a/packages/zarr-indexing/src/zarr_indexing/domain.py b/packages/zarr-indexing/src/zarr_indexing/domain.py new file mode 100644 index 0000000000..f20d5bf7bd --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/domain.py @@ -0,0 +1,189 @@ +"""Index domains — rectangular regions in N-dimensional integer space. + +An `IndexDomain` represents the set of valid coordinates for an array or +array view. It is the cartesian product of per-dimension integer ranges:: + + IndexDomain(inclusive_min=(2, 5), exclusive_max=(10, 20)) + # represents {(i, j) : 2 <= i < 10, 5 <= j < 20} + +Unlike NumPy, domains can have **non-zero origins**. After slicing +`arr[5:10]`, the result has origin 5 and shape 5 — coordinates 5 through +9 are valid. This follows the TensorStore convention. +""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import Any + + +@dataclass(frozen=True, slots=True) +class IndexDomain: + """A rectangular region in N-dimensional index space. + + The valid coordinates are the integers in + `[inclusive_min[d], exclusive_max[d])` for each dimension `d`. + """ + + inclusive_min: tuple[int, ...] + exclusive_max: tuple[int, ...] + labels: tuple[str, ...] | None = None + # Lazily-memoized shape. Excluded from init/repr/eq/hash: it is derived + # state, not part of the domain's identity. The domain is frozen, so the + # value is computed at most once (see `shape`). `None` is the unset + # sentinel; an empty shape caches as `()`. + _shape: tuple[int, ...] | None = field(default=None, init=False, repr=False, compare=False) + + def __post_init__(self) -> None: + if len(self.inclusive_min) != len(self.exclusive_max): + raise ValueError( + f"inclusive_min and exclusive_max must have the same length. " + f"Got {len(self.inclusive_min)} and {len(self.exclusive_max)}." + ) + for i, (lo, hi) in enumerate(zip(self.inclusive_min, self.exclusive_max, strict=True)): + if lo > hi: + raise ValueError( + f"inclusive_min must be <= exclusive_max for all dimensions. " + f"Dimension {i}: {lo} > {hi}" + ) + if self.labels is not None and len(self.labels) != len(self.inclusive_min): + raise ValueError( + f"labels must have the same length as dimensions. " + f"Got {len(self.labels)} labels for {len(self.inclusive_min)} dimensions." + ) + + @classmethod + def from_shape(cls, shape: tuple[int, ...]) -> IndexDomain: + """Create a domain with origin at zero.""" + return cls( + inclusive_min=(0,) * len(shape), + exclusive_max=shape, + ) + + @property + def ndim(self) -> int: + return len(self.inclusive_min) + + @property + def origin(self) -> tuple[int, ...]: + return self.inclusive_min + + @property + def shape(self) -> tuple[int, ...]: + cached = self._shape + if cached is None: + cached = tuple( + hi - lo for lo, hi in zip(self.inclusive_min, self.exclusive_max, strict=True) + ) + object.__setattr__(self, "_shape", cached) + return cached + + def contains(self, index: tuple[int, ...]) -> bool: + if len(index) != self.ndim: + return False + return all( + lo <= idx < hi + for lo, hi, idx in zip(self.inclusive_min, self.exclusive_max, index, strict=True) + ) + + def contains_domain(self, other: IndexDomain) -> bool: + if other.ndim != self.ndim: + return False + return all( + self_lo <= other_lo and other_hi <= self_hi + for self_lo, self_hi, other_lo, other_hi in zip( + self.inclusive_min, + self.exclusive_max, + other.inclusive_min, + other.exclusive_max, + strict=True, + ) + ) + + def intersect(self, other: IndexDomain) -> IndexDomain | None: + if other.ndim != self.ndim: + raise ValueError( + f"Cannot intersect domains with different ranks: {self.ndim} vs {other.ndim}" + ) + new_min = tuple( + max(a, b) for a, b in zip(self.inclusive_min, other.inclusive_min, strict=True) + ) + new_max = tuple( + min(a, b) for a, b in zip(self.exclusive_max, other.exclusive_max, strict=True) + ) + if any(lo >= hi for lo, hi in zip(new_min, new_max, strict=True)): + return None + return IndexDomain(inclusive_min=new_min, exclusive_max=new_max) + + def translate(self, offset: tuple[int, ...]) -> IndexDomain: + if len(offset) != self.ndim: + raise ValueError( + f"Offset must have same length as domain dimensions. " + f"Domain has {self.ndim} dimensions, offset has {len(offset)}." + ) + new_min = tuple(lo + off for lo, off in zip(self.inclusive_min, offset, strict=True)) + new_max = tuple(hi + off for hi, off in zip(self.exclusive_max, offset, strict=True)) + return IndexDomain(inclusive_min=new_min, exclusive_max=new_max) + + def narrow(self, selection: Any) -> IndexDomain: + """Apply a basic selection and return a narrowed domain. + Indices are absolute coordinates. Integer indices produce length-1 extent. + Strided slices are not supported — use IndexTransform for strides. + """ + normalized = _normalize_selection(selection, self.ndim) + new_inclusive_min: list[int] = [] + new_exclusive_max: list[int] = [] + for dim_idx, (sel, dim_lo, dim_hi) in enumerate( + zip(normalized, self.inclusive_min, self.exclusive_max, strict=True) + ): + if isinstance(sel, int): + if sel < dim_lo or sel >= dim_hi: + raise IndexError( + f"index {sel} is out of bounds for dimension {dim_idx} " + f"with domain [{dim_lo}, {dim_hi})" + ) + new_inclusive_min.append(sel) + new_exclusive_max.append(sel + 1) + else: + start, stop, step = sel.start, sel.stop, sel.step + if step is not None and step != 1: + raise IndexError( + "IndexDomain.narrow only supports step=1 slices. " + f"Got step={step}. Use IndexTransform for strided access." + ) + abs_start = dim_lo if start is None else start + abs_stop = dim_hi if stop is None else stop + abs_start = max(abs_start, dim_lo) + abs_stop = min(abs_stop, dim_hi) + abs_stop = max(abs_stop, abs_start) + new_inclusive_min.append(abs_start) + new_exclusive_max.append(abs_stop) + return IndexDomain( + inclusive_min=tuple(new_inclusive_min), + exclusive_max=tuple(new_exclusive_max), + ) + + +def _normalize_selection(selection: Any, ndim: int) -> tuple[int | slice, ...]: + """Normalize a basic selection to a tuple of ints/slices with length ndim.""" + if not isinstance(selection, tuple): + selection = (selection,) + result: list[int | slice] = [] + ellipsis_seen = False + for sel in selection: + if sel is Ellipsis: + if ellipsis_seen: + raise IndexError("an index can only have a single ellipsis ('...')") + ellipsis_seen = True + num_missing = ndim - (len(selection) - 1) + result.extend([slice(None)] * num_missing) + else: + result.append(sel) + while len(result) < ndim: + result.append(slice(None)) + if len(result) > ndim: + raise IndexError( + f"too many indices for array: array has {ndim} dimensions, " + f"but {len(result)} were indexed" + ) + return tuple(result) diff --git a/packages/zarr-indexing/src/zarr_indexing/errors.py b/packages/zarr-indexing/src/zarr_indexing/errors.py new file mode 100644 index 0000000000..fa2f6fc5d3 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/errors.py @@ -0,0 +1,21 @@ +"""Canonical index-error types raised by the transform algebra. + +These are the authoritative class definitions. `zarr.errors` re-exports the +same objects (`from zarr_indexing.errors import ...`) so that, e.g., +`zarr.errors.BoundsCheckError is zarr_indexing.errors.BoundsCheckError`. +Both subclass the built-in `IndexError`, so existing `except IndexError` (or +`except zarr.errors.BoundsCheckError`) catch sites keep working unchanged. +""" + +from __future__ import annotations + +__all__ = [ + "BoundsCheckError", + "VindexInvalidSelectionError", +] + + +class VindexInvalidSelectionError(IndexError): ... + + +class BoundsCheckError(IndexError): ... diff --git a/packages/zarr-indexing/src/zarr_indexing/grid.py b/packages/zarr-indexing/src/zarr_indexing/grid.py new file mode 100644 index 0000000000..de1dae2dfc --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/grid.py @@ -0,0 +1,25 @@ +"""Structural typing for the chunk-grid surface used by chunk resolution. + +`chunk_resolution` needs only a narrow slice of a chunk grid: the per-dimension +mapping between storage indices and chunk coordinates, passed as one +`DimensionGridLike` per storage dimension. Rather than import zarr's concrete +grid types, we type against this Protocol; zarr's per-dimension grids satisfy +it structurally, so no zarr import is needed here. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Protocol + +if TYPE_CHECKING: + import numpy as np + import numpy.typing as npt + + +class DimensionGridLike(Protocol): + """The per-dimension chunk-mapping surface consumed by chunk resolution.""" + + def index_to_chunk(self, idx: int) -> int: ... + def chunk_offset(self, chunk_ix: int) -> int: ... + def chunk_size(self, chunk_ix: int) -> int: ... + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: ... diff --git a/packages/zarr-indexing/src/zarr_indexing/json.py b/packages/zarr-indexing/src/zarr_indexing/json.py new file mode 100644 index 0000000000..c95696f309 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/json.py @@ -0,0 +1,325 @@ +"""Lowering between canonical ndsel bodies and in-memory `IndexTransform`s. + +This is the **engine layer**. Where `messages.py` is pure JSON→JSON and imposes +no array constraints, this module converts a *canonical* ndsel transform body +(spec section 4.3, as produced by `zarr_indexing.messages.normalize_ndsel`) +into the numpy-backed `IndexTransform` the chunk engine runs on, and back. + +Two engine constraints live **here and only here**: + +- **Finite bounds.** An `IndexDomain` addresses a finite array, so a canonical + body carrying a `"-inf"`/`"+inf"` bound cannot be lowered; `from_json` raises. +- **Implicit bounds lower by value.** The `[n]`-bracket implicit/explicit flag + is a message-layer concern; the engine keeps only the integer value. + +## The `index_array` wire format (and the degenerate-collapse it documents) + +ndsel and TensorStore both **reject** an output map that carries *both* +`input_dimension` and `index_array`. The in-memory `ArrayMap`, however, records +an `input_dimension` to pin the axis an orthogonal (`oindex`) array varies over. +This module bridges the gap: + +- **On serialize** (`transform_to_canonical`): + 1. An all-singleton `index_array` (size 1) selects a single coordinate + regardless of input, so it is **collapsed to a `constant` map** + `{offset: offset + stride*value}`. The size-1 input dimension stays in the + domain, unconsumed — a valid transform. This makes a length-1 `oindex` + selection round-trip *behaviorally* (an `ArrayMap` becomes a `ConstantMap`) + rather than by object identity. + 2. Non-degenerate `index_array` maps are emitted **without** `input_dimension`. + +- **On load** (`transform_from_canonical`): the in-memory `input_dimension` is + reconstructed from the full-rank array's dependency axes (its non-singleton + axes, see `transform._array_map_dependency_axes`). An array that solely owns a + single non-singleton axis is orthogonal (`input_dimension = that axis`); arrays + that share non-singleton axes, or vary over several, are correlated (`vindex`, + `input_dimension = None`). A single 1-D array over a rank-1 domain is + inherently ambiguous between the two flavours; it reconstructs as orthogonal, + which is behaviorally identical for the single-array case. + +`index_transform_to_json` / `index_transform_from_json` (and the `*_domain_*` +variants) are these canonical converters under their historical names. +""" + +from __future__ import annotations + +from collections import Counter +from typing import Any, Required, TypedDict + +import numpy as np + +from zarr_indexing.domain import IndexDomain +from zarr_indexing.messages import normalize_ndsel +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap +from zarr_indexing.transform import ( + IndexTransform, + _array_map_dependency_axes, # pyright: ignore[reportPrivateUsage] +) + +# `_array_map_dependency_axes` is a leading-underscore helper in `transform.py`, +# but it is deliberately shared with this module (the engine-level JSON <-> +# `IndexTransform` lowering below needs the same dependency-axis logic that +# `transform.py`'s own array-reindexing helpers use). It is not part of the +# package's public API; pyright's `reportPrivateUsage` flags the cross-module +# import anyway. See `chunk_resolution.py`'s `_dimensions` suppression for the +# analogous rationale — whether to promote either symbol out of "private" is +# an open pre-publish API decision, not resolved here. + +# --------------------------------------------------------------------------- +# TypedDict definitions (canonical JSON shapes) +# --------------------------------------------------------------------------- + +# An `index_array` serializes via `ndarray.tolist()`, so it is a nested list of +# ints whose nesting depth equals the array rank. +NestedIntList = list[Any] + +# A canonical *lowered* body carries only finite integer bounds, but the JSON +# shape admits the full ndsel `bound` grammar: an explicit int / sentinel, or a +# one-element implicit `[value]` array. +IndexValueJSON = int | str +BoundJSON = int | str | list[IndexValueJSON] + + +class IndexDomainJSON(TypedDict, total=False): + """Canonical JSON representation of an IndexDomain.""" + + input_inclusive_min: Required[list[BoundJSON]] + input_exclusive_max: Required[list[BoundJSON]] + input_labels: Required[list[str]] + + +class OutputIndexMapJSON(TypedDict, total=False): + """Canonical JSON representation of a single output index map. + + Exactly one of three forms (distinguished by which fields are present): + + - `{"offset": 5}` — constant + - `{"offset": 0, "stride": 1, "input_dimension": 0}` — single_input_dimension + - `{"offset": 0, "stride": 1, "index_array": [...], + "index_array_bounds": ["-inf", "+inf"]}` — index_array + """ + + offset: int + stride: int + input_dimension: int + index_array: NestedIntList + index_array_bounds: list[IndexValueJSON] + + +class IndexTransformJSON(TypedDict, total=False): + """Canonical JSON representation of an IndexTransform (spec section 4.3).""" + + input_rank: Required[int] + input_inclusive_min: Required[list[BoundJSON]] + input_exclusive_max: Required[list[BoundJSON]] + input_labels: Required[list[str]] + output: Required[list[OutputIndexMapJSON]] + + +# --------------------------------------------------------------------------- +# Bound / label lowering (engine constraints) +# --------------------------------------------------------------------------- + + +def _lower_bound(bound: BoundJSON, where: str) -> int: + """Lower a canonical bound to a finite integer, rejecting infinities.""" + value = bound[0] if isinstance(bound, list) else bound + if value == "-inf" or value == "+inf": + raise ValueError( + f"{where} is infinite ({value!r}); an IndexDomain addresses a finite " + f"array and cannot lower an infinite bound" + ) + return int(value) + + +def _lower_labels(labels: list[str]) -> tuple[str, ...] | None: + """All-empty labels collapse to `None` so a label-free domain round-trips.""" + return None if all(label == "" for label in labels) else tuple(labels) + + +def _emit_labels(labels: tuple[str, ...] | None, rank: int) -> list[str]: + """Emit canonical labels: `[""]*rank` when the domain is unlabeled.""" + return [""] * rank if labels is None else list(labels) + + +# --------------------------------------------------------------------------- +# IndexDomain serialization +# --------------------------------------------------------------------------- + + +def index_domain_to_json(domain: IndexDomain) -> IndexDomainJSON: + """Convert an IndexDomain to its canonical JSON representation.""" + return { + "input_inclusive_min": list(domain.inclusive_min), + "input_exclusive_max": list(domain.exclusive_max), + "input_labels": _emit_labels(domain.labels, domain.ndim), + } + + +def index_domain_from_json(data: IndexDomainJSON) -> IndexDomain: + """Construct an IndexDomain from its canonical JSON representation.""" + inclusive_min = tuple( + _lower_bound(b, f"input_inclusive_min[{i}]") + for i, b in enumerate(data["input_inclusive_min"]) + ) + exclusive_max = tuple( + _lower_bound(b, f"input_exclusive_max[{i}]") + for i, b in enumerate(data["input_exclusive_max"]) + ) + labels = _lower_labels(list(data["input_labels"])) + return IndexDomain(inclusive_min=inclusive_min, exclusive_max=exclusive_max, labels=labels) + + +# --------------------------------------------------------------------------- +# OutputIndexMap serialization +# --------------------------------------------------------------------------- + + +def output_index_map_to_json(m: OutputIndexMap) -> OutputIndexMapJSON: + """Convert an output index map to its canonical JSON representation. + + A degenerate all-singleton `ArrayMap` collapses to a `constant` map; a + non-degenerate one is emitted without `input_dimension` (see the module + docstring on the wire format). + """ + if isinstance(m, ConstantMap): + return {"offset": m.offset} + + if isinstance(m, DimensionMap): + return {"offset": m.offset, "stride": m.stride, "input_dimension": m.input_dimension} + + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + if m.index_array.size == 1: + value = int(m.index_array.reshape(-1)[0]) + return {"offset": m.offset + m.stride * value} + return { + "offset": m.offset, + "stride": m.stride, + "index_array": m.index_array.tolist(), + "index_array_bounds": ["-inf", "+inf"], + } + + +def output_index_map_from_json(data: OutputIndexMapJSON) -> OutputIndexMap: + """Construct an output index map from its canonical JSON representation. + + An `index_array` map's `input_dimension` is reconstructed from the array's + dependency axes in isolation (single non-singleton axis → orthogonal). The + transform-level loader classifies globally; use it when several maps may + share axes. + """ + if "index_array" in data: + arr = np.asarray(data["index_array"], dtype=np.intp) + return ArrayMap( + index_array=arr, + offset=data.get("offset", 0), + stride=data.get("stride", 1), + input_dimension=_solo_dependency_axis(arr), + ) + + if "input_dimension" in data: + return DimensionMap( + input_dimension=data["input_dimension"], + offset=data.get("offset", 0), + stride=data.get("stride", 1), + ) + + return ConstantMap(offset=data.get("offset", 0)) + + +def _solo_dependency_axis(arr: np.ndarray[Any, Any]) -> int | None: + """The single axis a lone `index_array` varies over, or `None` if not exactly one.""" + dep = _array_map_dependency_axes(arr) + return dep[0] if len(dep) == 1 else None + + +# --------------------------------------------------------------------------- +# IndexTransform serialization +# --------------------------------------------------------------------------- + + +def transform_to_canonical(transform: IndexTransform) -> IndexTransformJSON: + """Convert an IndexTransform to its canonical ndsel transform body. + + The result is fully explicit (spec section 4.3): `input_rank`, fully written + bounds and labels, and an explicit `output` with `offset`/`stride` present + on every affine and array map. + """ + return { + "input_rank": transform.domain.ndim, + "input_inclusive_min": list(transform.domain.inclusive_min), + "input_exclusive_max": list(transform.domain.exclusive_max), + "input_labels": _emit_labels(transform.domain.labels, transform.domain.ndim), + "output": [output_index_map_to_json(m) for m in transform.output], + } + + +def transform_from_canonical(data: IndexTransformJSON) -> IndexTransform: + """Construct an IndexTransform from a canonical (or canonicalizable) body. + + The body is first run through the message layer (`normalize_ndsel`) so that + omitted fields — identity `output`, default bounds/labels — are filled and + validated, then lowered to the engine representation. `index_array` maps' + `input_dimension` values are reconstructed by global dependency-axis + ownership (see the module docstring). + """ + body = normalize_ndsel({"kind": "transform", **data}) + + inclusive_min = tuple( + _lower_bound(b, f"input_inclusive_min[{i}]") + for i, b in enumerate(body["input_inclusive_min"]) + ) + exclusive_max = tuple( + _lower_bound(b, f"input_exclusive_max[{i}]") + for i, b in enumerate(body["input_exclusive_max"]) + ) + domain = IndexDomain( + inclusive_min=inclusive_min, + exclusive_max=exclusive_max, + labels=_lower_labels(body["input_labels"]), + ) + + output_raw: list[dict[str, Any]] = body["output"] + + # Classify index_array maps globally: an axis owned by exactly one array map + # (and the map's sole non-singleton axis) marks that map orthogonal; shared + # or multiple non-singleton axes mark the maps correlated (vindex). + array_axes: dict[int, tuple[int, ...]] = {} + axis_owners: Counter[int] = Counter() + for i, om in enumerate(output_raw): + if "index_array" in om: + arr = np.asarray(om["index_array"], dtype=np.intp) + dep = _array_map_dependency_axes(arr) + array_axes[i] = dep + axis_owners.update(dep) + + output: list[OutputIndexMap] = [] + for i, om in enumerate(output_raw): + if "index_array" in om: + dep = array_axes[i] + input_dim = dep[0] if len(dep) == 1 and axis_owners[dep[0]] == 1 else None + output.append( + ArrayMap( + index_array=np.asarray(om["index_array"], dtype=np.intp), + offset=om.get("offset", 0), + stride=om.get("stride", 1), + input_dimension=input_dim, + ) + ) + elif "input_dimension" in om: + output.append( + DimensionMap( + input_dimension=om["input_dimension"], + offset=om.get("offset", 0), + stride=om.get("stride", 1), + ) + ) + else: + output.append(ConstantMap(offset=om.get("offset", 0))) + + return IndexTransform(domain=domain, output=tuple(output)) + + +# Historical names, now pointing at the canonical converters. +index_transform_to_json = transform_to_canonical +index_transform_from_json = transform_from_canonical diff --git a/packages/zarr-indexing/src/zarr_indexing/messages.py b/packages/zarr-indexing/src/zarr_indexing/messages.py new file mode 100644 index 0000000000..d5761d1a38 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/messages.py @@ -0,0 +1,657 @@ +"""The ndsel message layer — pure JSON in, canonical JSON out. + +This module implements the [ndsel](https://github.com/zarr-developers/ndsel) draft wire +format: a JSON-serializable representation of NumPy-style n-dimensional +selections that adapts TensorStore's `IndexTransform` model. It is a **pure +JSON→JSON** layer: it depends on nothing but the standard library, imposes no +engine (numpy/array) constraints, and never rounds, clamps, or drops +information. Engine constraints (finite bounds, in-memory `IndexTransform` +construction) live one layer up, in `json.py`. + +Two entry points: + +- `parse_ndsel(obj)` — structurally validate an ndsel message of any of the + five kinds (`point`/`box`/`slice`/`points`/`transform`), returning it + unchanged. Raises `NdselError` (carrying a spec reason code) on any defect. +- `normalize_ndsel(obj)` — desugar and canonicalize a message to the single + deterministic **canonical transform body** of the spec (section 4.3): a bare + `IndexTransform` JSON body, without the `kind` discriminator. `normalize` is + idempotent when its output is re-tagged with `kind: "transform"`. + +The canonical body is, field-for-field, a TensorStore `IndexTransform` (minus +`kind`), so a normalized `transform` loads directly into TensorStore once +`kind` is stripped. + +Value rules enforced here: every integer is a 64-bit signed value; JSON +booleans are **not** integers (Python's `isinstance(True, int)` is guarded +against explicitly); the `"-inf"`/`"+inf"` sentinels are legal only in bound +positions; an implicit bound is the one-element `[n]`-bracket form, and its +implicit/explicit flag is preserved through normalization. +""" + +from __future__ import annotations + +from typing import Any + +__all__ = [ + "NdselError", + "normalize_ndsel", + "parse_ndsel", +] + +# --------------------------------------------------------------------------- +# Error taxonomy +# --------------------------------------------------------------------------- + +#: The complete set of ndsel reason codes (spec section 6). +REASON_CODES = frozenset( + { + "invalid_json", + "unknown_kind", + "unknown_field", + "multiple_upper_bounds", + "bounds_out_of_order", + "output_map_conflict", + "rank_mismatch", + "step_zero", + "negative_step_unsupported", + } +) + + +class NdselError(ValueError): + """An ndsel message failed validation. + + Carries the spec `reason` code (one of `REASON_CODES`) so callers and the + conformance harness can assert on it directly, plus a human-readable + `detail`. + """ + + def __init__(self, reason: str, detail: str = "") -> None: + self.reason = reason + self.detail = detail + super().__init__(f"{reason}: {detail}" if detail else reason) + + +# --------------------------------------------------------------------------- +# 64-bit signed integer range (spec section 3.5) +# --------------------------------------------------------------------------- + +_I64_MIN = -(2**63) +_I64_MAX = 2**63 - 1 + +_KNOWN_KINDS = frozenset({"point", "box", "slice", "points", "transform"}) + +# The two upper-bound spellings, keyed by message prefix. Only one of the three +# per group may appear (spec section 4.1 / 5.2). +_BOX_UPPER = ("exclusive_max", "inclusive_max", "shape") +_TRANSFORM_UPPER = ("input_exclusive_max", "input_inclusive_max", "input_shape") + +_OUTPUT_MAP_FIELDS = frozenset( + {"offset", "stride", "input_dimension", "index_array", "index_array_bounds"} +) + + +# --------------------------------------------------------------------------- +# Leaf value validators +# --------------------------------------------------------------------------- + + +def _is_int(value: Any) -> bool: + """True iff `value` is a JSON integer — an `int` that is not a `bool`. + + JSON has no boolean-as-integer: `True`/`False` are rejected even though + Python makes `bool` a subclass of `int` (spec section 3.6). + """ + return isinstance(value, int) and not isinstance(value, bool) + + +def _check_int(value: Any, where: str) -> int: + """Validate a plain-integer position: an in-range i64, never a sentinel.""" + if not _is_int(value): + raise NdselError("invalid_json", f"{where} must be an integer, got {value!r}") + if value < _I64_MIN or value > _I64_MAX: + raise NdselError("invalid_json", f"{where} is outside the 64-bit signed range: {value}") + return int(value) + + +def _is_sentinel(value: Any) -> bool: + return value in ("-inf", "+inf") + + +def _check_index_value(value: Any, where: str) -> int | str: + """Validate an `index-value`: an in-range i64 or a `"-inf"`/`"+inf"` sentinel.""" + if _is_sentinel(value): + return str(value) + return _check_int(value, where) + + +def _check_bound(value: Any, where: str) -> int | str | list[int | str]: + """Validate a `bound`: an explicit `index-value`, or a one-element implicit `[index-value]`.""" + if isinstance(value, list): + if len(value) != 1: + raise NdselError( + "invalid_json", + f"{where} implicit bound must be a one-element array, got {value!r}", + ) + return [_check_index_value(value[0], where)] + return _check_index_value(value, where) + + +def _check_int_list(value: Any, where: str) -> list[int]: + if not isinstance(value, list): + raise NdselError("invalid_json", f"{where} must be an array, got {value!r}") + return [_check_int(v, f"{where}[{i}]") for i, v in enumerate(value)] + + +def _check_bound_list(value: Any, where: str) -> list[Any]: + if not isinstance(value, list): + raise NdselError("invalid_json", f"{where} must be an array, got {value!r}") + return [_check_bound(v, f"{where}[{i}]") for i, v in enumerate(value)] + + +def _check_label_list(value: Any, where: str) -> list[str]: + if not isinstance(value, list): + raise NdselError("invalid_json", f"{where} must be an array, got {value!r}") + for i, v in enumerate(value): + if not isinstance(v, str): + raise NdselError("invalid_json", f"{where}[{i}] must be a string, got {v!r}") + return list(value) + + +# --------------------------------------------------------------------------- +# Extended-integer order for bounds (spec section 4.1) +# --------------------------------------------------------------------------- + + +def _bound_value(bound: int | str | list[int | str]) -> int | str: + """The underlying `index-value` of a bound, dropping the implicit bracket.""" + return bound[0] if isinstance(bound, list) else bound + + +def _bound_is_implicit(bound: int | str | list[int | str]) -> bool: + return isinstance(bound, list) + + +def _ext_key(value: int | str) -> tuple[int, int]: + """A sort key giving the extended-integer order `-inf < n < +inf` exactly. + + Uses an integer tier plus the value, so no float rounding of near-`2**63` + integers can misorder the `inclusive_min <= exclusive_max` check. + """ + if value == "-inf": + return (0, 0) + if value == "+inf": + return (2, 0) + assert isinstance(value, int) + return (1, value) + + +def _rewrap(value: int | str, *, implicit: bool) -> int | str | list[int | str]: + return [value] if implicit else value + + +# --------------------------------------------------------------------------- +# Message-level helpers +# --------------------------------------------------------------------------- + + +def _require_object(obj: Any) -> dict[str, Any]: + if not isinstance(obj, dict): + raise NdselError("invalid_json", f"message must be a JSON object, got {type(obj).__name__}") + return obj + + +def _message_kind(obj: dict[str, Any]) -> str: + kind = obj.get("kind") + if not isinstance(kind, str): + raise NdselError("invalid_json", "message must have a string 'kind' field") + if kind not in _KNOWN_KINDS: + raise NdselError("unknown_kind", f"unknown kind {kind!r}") + return kind + + +def _check_membership(obj: dict[str, Any], allowed: frozenset[str], what: str) -> None: + """Strict membership (spec section 3.7): reject any undefined member.""" + for key in obj: + if key not in allowed: + raise NdselError("unknown_field", f"{what} has undefined member {key!r}") + + +def _single_upper_bound(obj: dict[str, Any], fields: tuple[str, str, str]) -> str | None: + present = [f for f in fields if f in obj] + if len(present) > 1: + raise NdselError( + "multiple_upper_bounds", + f"at most one of {fields} may be present; got {present}", + ) + return present[0] if present else None + + +def _resolve_upper_bound( + upper_field: str | None, + upper_raw: list[Any] | None, + inclusive_min: list[Any], + rank: int, + *, + kind_of: str, +) -> list[int | str | list[int | str]]: + """Produce `exclusive_max` from whichever upper-bound spelling was supplied. + + - `exclusive_max`/`input_exclusive_max` → used directly. + - `inclusive_max`/`input_inclusive_max` → each element `+1`. + - `shape`/`input_shape` → `inclusive_min + shape` per element. + - none → an **implicit `+inf`** in every dimension. + + The implicit/explicit bracket travels with the extent-bearing field (the + upper bound, or `shape`), matching the spec's `[n]`-bracket convention. + """ + if upper_field is None: + return [["+inf"] for _ in range(rank)] + + assert upper_raw is not None + if kind_of == "exclusive": + return list(upper_raw) + + result: list[int | str | list[int | str]] = [] + for k in range(rank): + raw = upper_raw[k] + implicit = _bound_is_implicit(raw) + value = _bound_value(raw) + if kind_of == "inclusive": + new = _inclusive_to_exclusive(value) + else: # shape + new = _shape_to_exclusive(_bound_value(inclusive_min[k]), value) + result.append(_rewrap(new, implicit=implicit)) + return result + + +def _inclusive_to_exclusive(value: int | str) -> int | str: + if value == "+inf" or value == "-inf": + return value + assert isinstance(value, int) + return value + 1 + + +def _shape_to_exclusive(min_value: int | str, shape_value: int | str) -> int | str: + if shape_value == "+inf" or min_value == "+inf": + return "+inf" + if min_value == "-inf": + return "-inf" + assert isinstance(min_value, int) + assert isinstance(shape_value, int) + return min_value + shape_value + + +def _validate_domain(inclusive_min: list[Any], exclusive_max: list[Any], *, prefix: str) -> None: + """Every dimension must satisfy `inclusive_min <= exclusive_max` (empty is valid).""" + for k, (lo, hi) in enumerate(zip(inclusive_min, exclusive_max, strict=True)): + if _ext_key(_bound_value(lo)) > _ext_key(_bound_value(hi)): + raise NdselError( + "bounds_out_of_order", + f"{prefix}[{k}]: inclusive_min {_bound_value(lo)!r} > " + f"exclusive_max {_bound_value(hi)!r}", + ) + + +def _identity_output(rank: int) -> list[dict[str, Any]]: + return [{"offset": 0, "stride": 1, "input_dimension": k} for k in range(rank)] + + +# --------------------------------------------------------------------------- +# Per-kind desugaring +# --------------------------------------------------------------------------- + + +def _normalize_point(obj: dict[str, Any]) -> dict[str, Any]: + _check_membership(obj, frozenset({"kind", "coords"}), "point") + if "coords" not in obj: + raise NdselError("invalid_json", "point requires 'coords'") + coords = _check_int_list(obj["coords"], "coords") + return { + "input_rank": 0, + "input_inclusive_min": [], + "input_exclusive_max": [], + "input_labels": [], + "output": [{"offset": c} for c in coords], + } + + +def _infer_rank( + obj: dict[str, Any], + named_lengths: list[tuple[str, int]], + *, + declared: int | None, +) -> int: + """Reconcile a declared rank (if any) with every present array's length.""" + rank = declared + for name, length in named_lengths: + if rank is None: + rank = length + elif rank != length: + raise NdselError( + "rank_mismatch", + f"{name} has length {length}, inconsistent with rank {rank}", + ) + return rank if rank is not None else 0 + + +def _normalize_box(obj: dict[str, Any]) -> dict[str, Any]: + allowed = frozenset( + {"kind", "inclusive_min", "exclusive_max", "inclusive_max", "shape", "labels"} + ) + _check_membership(obj, allowed, "box") + + inclusive_min_raw = ( + _check_bound_list(obj["inclusive_min"], "inclusive_min") if "inclusive_min" in obj else None + ) + upper_field = _single_upper_bound(obj, _BOX_UPPER) + upper_raw = _check_bound_list(obj[upper_field], upper_field) if upper_field else None + labels_raw = _check_label_list(obj["labels"], "labels") if "labels" in obj else None + + named_lengths: list[tuple[str, int]] = [] + if inclusive_min_raw is not None: + named_lengths.append(("inclusive_min", len(inclusive_min_raw))) + if upper_raw is not None: + named_lengths.append((upper_field or "", len(upper_raw))) + if labels_raw is not None: + named_lengths.append(("labels", len(labels_raw))) + rank = _infer_rank(obj, named_lengths, declared=None) + + inclusive_min = inclusive_min_raw if inclusive_min_raw is not None else [0] * rank + exclusive_max = _resolve_upper_bound( + upper_field, upper_raw, inclusive_min, rank, kind_of=_upper_kind(upper_field, _BOX_UPPER) + ) + labels = labels_raw if labels_raw is not None else [""] * rank + _validate_domain(inclusive_min, exclusive_max, prefix="box") + + return { + "input_rank": rank, + "input_inclusive_min": inclusive_min, + "input_exclusive_max": exclusive_max, + "input_labels": labels, + "output": _identity_output(rank), + } + + +def _upper_kind(upper_field: str | None, fields: tuple[str, str, str]) -> str: + if upper_field is None or upper_field == fields[0]: + return "exclusive" + if upper_field == fields[1]: + return "inclusive" + return "shape" + + +def _normalize_slice(obj: dict[str, Any]) -> dict[str, Any]: + allowed = frozenset({"kind", "start", "stop", "step", "labels"}) + _check_membership(obj, allowed, "slice") + if "start" not in obj: + raise NdselError("invalid_json", "slice requires 'start'") + if "stop" not in obj: + raise NdselError("invalid_json", "slice requires 'stop'") + start = _check_int_list(obj["start"], "start") + stop = _check_int_list(obj["stop"], "stop") + step = _check_int_list(obj["step"], "step") if "step" in obj else [1] * len(start) + labels_raw = _check_label_list(obj["labels"], "labels") if "labels" in obj else None + + n = len(start) + for name, arr in (("stop", stop), ("step", step)): + if len(arr) != n: + raise NdselError( + "rank_mismatch", f"{name} has length {len(arr)}, expected {n} (from start)" + ) + if labels_raw is not None and len(labels_raw) != n: + raise NdselError( + "rank_mismatch", f"labels has length {len(labels_raw)}, expected {n} (from start)" + ) + + for k, s in enumerate(step): + if s == 0: + raise NdselError("step_zero", f"step[{k}] is zero") + if s < 0: + raise NdselError("negative_step_unsupported", f"step[{k}] is negative ({s})") + + inclusive_min: list[Any] = [] + exclusive_max: list[Any] = [] + output: list[dict[str, Any]] = [] + for k in range(n): + a, b, s = start[k], stop[k], step[k] + m = max(0, -(-(b - a) // s)) # ceil((b - a) / s) + o = _trunc_div(a, s) # trunc(a / s), toward zero + offset = a - s * o # lattice phase, in (-s, s) + inclusive_min.append(o) + exclusive_max.append(o + m) + output.append({"offset": offset, "stride": s, "input_dimension": k}) + + labels = labels_raw if labels_raw is not None else [""] * n + return { + "input_rank": n, + "input_inclusive_min": inclusive_min, + "input_exclusive_max": exclusive_max, + "input_labels": labels, + "output": output, + } + + +def _normalize_points(obj: dict[str, Any]) -> dict[str, Any]: + _check_membership(obj, frozenset({"kind", "coords"}), "points") + if "coords" not in obj: + raise NdselError("invalid_json", "points requires 'coords'") + coords = obj["coords"] + if not isinstance(coords, list): + raise NdselError("invalid_json", f"points coords must be an array, got {coords!r}") + + rows: list[list[int]] = [] + n: int | None = None + for i, row in enumerate(coords): + if not isinstance(row, list): + raise NdselError("invalid_json", f"points coords[{i}] must be an array, got {row!r}") + row_ints = [_check_int(v, f"coords[{i}][{j}]") for j, v in enumerate(row)] + if n is None: + n = len(row_ints) + elif len(row_ints) != n: + raise NdselError( + "rank_mismatch", + f"points coords[{i}] has length {len(row_ints)}, expected {n} (ragged)", + ) + rows.append(row_ints) + + m = len(rows) + n = n if n is not None else 0 + output = [ + { + "offset": 0, + "stride": 1, + "index_array": [rows[i][k] for i in range(m)], + "index_array_bounds": ["-inf", "+inf"], + } + for k in range(n) + ] + return { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [m], + "input_labels": [""], + "output": output, + } + + +def _normalize_output_map(raw: Any, where: str) -> dict[str, Any]: + if not isinstance(raw, dict): + raise NdselError("invalid_json", f"{where} must be a JSON object, got {raw!r}") + _check_membership(raw, _OUTPUT_MAP_FIELDS, where) + + has_index_array = "index_array" in raw + has_input_dim = "input_dimension" in raw + if has_index_array and has_input_dim: + raise NdselError( + "output_map_conflict", + f"{where} carries both 'input_dimension' and 'index_array'", + ) + + offset = _check_int(raw["offset"], f"{where}.offset") if "offset" in raw else 0 + + if has_index_array: + stride = _check_int(raw["stride"], f"{where}.stride") if "stride" in raw else 1 + bounds = ( + _check_index_array_bounds(raw["index_array_bounds"], where) + if "index_array_bounds" in raw + else ["-inf", "+inf"] + ) + # index_array is carried verbatim (spec section 7 defers shape validation). + return { + "offset": offset, + "stride": stride, + "index_array": raw["index_array"], + "index_array_bounds": bounds, + } + + if has_input_dim: + input_dim = _check_int(raw["input_dimension"], f"{where}.input_dimension") + if input_dim < 0: + raise NdselError( + "invalid_json", f"{where}.input_dimension must be >= 0, got {input_dim}" + ) + stride = _check_int(raw["stride"], f"{where}.stride") if "stride" in raw else 1 + return {"offset": offset, "stride": stride, "input_dimension": input_dim} + + # Constant map: only offset survives. A stray `stride`/`index_array_bounds` + # is schema-valid (the output-map schema permits those members on any map), + # so it is silently dropped rather than rejected — a constant carries only + # `offset` in canonical form (spec section 4.3). + return {"offset": offset} + + +def _check_index_array_bounds(value: Any, where: str) -> list[int | str]: + if not isinstance(value, list) or len(value) != 2: + raise NdselError( + "invalid_json", + f"{where}.index_array_bounds must be a two-element array, got {value!r}", + ) + return [ + _check_index_value(value[0], f"{where}.index_array_bounds[0]"), + _check_index_value(value[1], f"{where}.index_array_bounds[1]"), + ] + + +def _normalize_transform(obj: dict[str, Any]) -> dict[str, Any]: + allowed = frozenset( + { + "kind", + "input_rank", + "input_inclusive_min", + "input_exclusive_max", + "input_inclusive_max", + "input_shape", + "input_labels", + "output", + } + ) + _check_membership(obj, allowed, "transform") + + declared_rank: int | None = None + if "input_rank" in obj: + declared_rank = _check_int(obj["input_rank"], "input_rank") + if declared_rank < 0: + raise NdselError("invalid_json", f"input_rank must be >= 0, got {declared_rank}") + + inclusive_min_raw = ( + _check_bound_list(obj["input_inclusive_min"], "input_inclusive_min") + if "input_inclusive_min" in obj + else None + ) + upper_field = _single_upper_bound(obj, _TRANSFORM_UPPER) + upper_raw = _check_bound_list(obj[upper_field], upper_field) if upper_field else None + labels_raw = ( + _check_label_list(obj["input_labels"], "input_labels") if "input_labels" in obj else None + ) + + named_lengths: list[tuple[str, int]] = [] + if inclusive_min_raw is not None: + named_lengths.append(("input_inclusive_min", len(inclusive_min_raw))) + if upper_raw is not None: + named_lengths.append((upper_field or "", len(upper_raw))) + if labels_raw is not None: + named_lengths.append(("input_labels", len(labels_raw))) + rank = _infer_rank(obj, named_lengths, declared=declared_rank) + + inclusive_min = inclusive_min_raw if inclusive_min_raw is not None else [0] * rank + exclusive_max = _resolve_upper_bound( + upper_field, + upper_raw, + inclusive_min, + rank, + kind_of=_upper_kind(upper_field, _TRANSFORM_UPPER), + ) + labels = labels_raw if labels_raw is not None else [""] * rank + _validate_domain(inclusive_min, exclusive_max, prefix="input") + + if "output" in obj: + if not isinstance(obj["output"], list): + raise NdselError("invalid_json", f"output must be an array, got {obj['output']!r}") + output = [_normalize_output_map(m, f"output[{i}]") for i, m in enumerate(obj["output"])] + else: + output = _identity_output(rank) + + return { + "input_rank": rank, + "input_inclusive_min": inclusive_min, + "input_exclusive_max": exclusive_max, + "input_labels": labels, + "output": output, + } + + +_NORMALIZERS = { + "point": _normalize_point, + "box": _normalize_box, + "slice": _normalize_slice, + "points": _normalize_points, + "transform": _normalize_transform, +} + + +# --------------------------------------------------------------------------- +# trunc division (spec section 5.3 correction, matches _trunc_div in transform.py) +# --------------------------------------------------------------------------- + + +def _trunc_div(a: int, b: int) -> int: + """Integer division rounded toward zero (C semantics).""" + q = a // b + if q < 0 and q * b != a: + q += 1 + return q + + +# --------------------------------------------------------------------------- +# Public entry points +# --------------------------------------------------------------------------- + + +def normalize_ndsel(obj: Any) -> dict[str, Any]: + """Desugar and canonicalize an ndsel message to its canonical transform body. + + Accepts any of the five message kinds and returns the bare canonical + `IndexTransform` body of spec section 4.3 — no `kind` field. Raises + `NdselError` (carrying a reason code) for any invalid input. + """ + message = _require_object(obj) + kind = _message_kind(message) + return _NORMALIZERS[kind](message) + + +def parse_ndsel(obj: Any) -> dict[str, Any]: + """Structurally validate an ndsel message, returning it unchanged. + + A lighter gate than `normalize_ndsel`: it confirms the message is a + well-formed ndsel message of a recognized kind (correct field membership, + JSON types, upper-bound exclusivity, domain ordering, step signs) and + raises `NdselError` otherwise, but does not desugar it. Useful for + validating a message you intend to keep in its compact shorthand form. + """ + message = _require_object(obj) + _message_kind(message) + # Validation and desugaring share one pass; run it and discard the body. + normalize_ndsel(message) + return message diff --git a/packages/zarr-indexing/src/zarr_indexing/output_map.py b/packages/zarr-indexing/src/zarr_indexing/output_map.py new file mode 100644 index 0000000000..581229bd22 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/output_map.py @@ -0,0 +1,105 @@ +"""Output index maps — three representations of a set of integer coordinates. + +An output index map describes, for one dimension of storage, which coordinates +an array access will touch. Conceptually it is a **set of integers**. Three +representations cover the cases that arise in practice: + +- `ConstantMap(offset=5)` — a singleton set: `{5}` +- `DimensionMap(input_dimension=0, offset=3, stride=2)` over input `[0, 5)` + — an arithmetic progression: `{3, 5, 7, 9, 11}` +- `ArrayMap(index_array=[1, 5, 9])` — an explicit enumeration: `{1, 5, 9}` + +Every output map supports two set-theoretic operations (defined on +`IndexTransform`, which provides the input domain context these maps lack): + +- **intersect** — restrict to coordinates within a range (e.g., a chunk). + `{3, 5, 7, 9, 11} ∩ [4, 8) = {5, 7}` +- **translate** — shift every coordinate by a constant (e.g., make chunk-local). + `{5, 7} - 4 = {1, 3}` + +These two operations are the foundation of chunk resolution: for each chunk, +intersect the map with the chunk's range, then translate to chunk-local +coordinates. + +The three types exist because they trade off generality for efficiency: + +- `ConstantMap`: O(1) storage, O(1) intersection +- `DimensionMap`: O(1) storage, O(1) intersection (analytical) +- `ArrayMap`: O(n) storage, O(n) intersection (must scan the array) + +Collapsing everything to `ArrayMap` would be correct but wasteful — a +billion-element slice would materialize a billion coordinates just to group +them by chunk, when `DimensionMap` does it with three integers. +""" + +from __future__ import annotations + +from dataclasses import dataclass +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + import numpy as np + import numpy.typing as npt + + +@dataclass(frozen=True, slots=True) +class ConstantMap: + """A singleton set: one storage coordinate. + + Represents `{offset}`. Arises from integer indexing (e.g., `arr[5]` + fixes one dimension to coordinate 5). + """ + + offset: int = 0 + + +@dataclass(frozen=True, slots=True) +class DimensionMap: + """An arithmetic progression of storage coordinates. + + Represents `{offset + stride * i : i in input_range}`, where the input + range comes from the enclosing `IndexTransform`'s domain. Arises from + slice indexing (e.g., `arr[2:10:3]` gives offset=2, stride=3). + """ + + input_dimension: int + offset: int = 0 + stride: int = 1 + + +@dataclass(frozen=True, slots=True) +class ArrayMap: + """An explicit enumeration of storage coordinates. + + Represents `{offset + stride * index_array[i] : i in input_range}`. + Arises from fancy indexing (e.g., `arr[[1, 5, 9]]` or boolean masks). + + Freshly constructed maps are normalized to the **full input rank** of their + enclosing transform: `index_array` has the enclosing domain's rank, sized + fully on the axes it varies over and singleton (size 1) elsewhere. The + dependency axes are therefore derivable from the shape (see + `transform._array_map_dependency_axes`), which distinguishes the two flavours + of multi-array fancy indexing: + + - **orthogonal** (`oindex`): each array varies along a single, *distinct* + axis (all others singleton); the result is their outer product. + - **vectorized** (`vindex`): the arrays are correlated and share the same + non-singleton (broadcast) axes; the result is a pointwise scatter. + + `input_dimension` records the single axis an orthogonal array varies over + (`None` for vectorized), binding it the way `DimensionMap` is bound. It is + usually redundant with the shape-derived classifier, but stays authoritative + for the shapes the classifier cannot distinguish: a length-1 orthogonal + selection normalizes to an all-singleton array (no non-singleton axis), and + length-1 vectorized arrays are equally degenerate. `None` therefore marks a + map as correlated, and an integer pins the dependency axis of a degenerate + orthogonal map (see `transform._array_map_dependent_axis`). + """ + + index_array: npt.NDArray[np.intp] + offset: int = 0 + stride: int = 1 + input_dimension: int | None = None + + +OutputIndexMap = ConstantMap | DimensionMap | ArrayMap diff --git a/packages/zarr-indexing/src/zarr_indexing/py.typed b/packages/zarr-indexing/src/zarr_indexing/py.typed new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-indexing/src/zarr_indexing/transform.py b/packages/zarr-indexing/src/zarr_indexing/transform.py new file mode 100644 index 0000000000..e1a3898b1d --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/transform.py @@ -0,0 +1,1311 @@ +"""Index transforms — composable, lazy coordinate mappings. + +An `IndexTransform` pairs an **input domain** (the coordinates a user sees) +with a tuple of **output maps** (the storage coordinates those inputs map to). +One output map per storage dimension. See `output_map.py` for the three +output map types. + +Key operations: + +- **Indexing** (`transform[2:8]`, `.oindex[idx]`, `.vindex[idx]`) — + produces a new transform with a narrower input domain and adjusted output + maps. No I/O occurs. This is how lazy slicing works. + +- **intersect(output_domain)** — restrict to storage coordinates within a + region. This is chunk resolution: "which of my coordinates fall in this + chunk?" + +- **translate(shift)** — shift all output coordinates. This makes coordinates + chunk-local: "express my coordinates relative to the chunk origin." + +- **compose(outer, inner)** — chain two transforms. See `composition.py`. + +The transform is the atomic unit that connects user-facing indexing to +chunk-level I/O. Every `Array` holds a transform (identity by default). +`Array.lazy[...]` composes a new transform lazily. Reading resolves the +transform against the chunk grid via intersect + translate. +""" + +from __future__ import annotations + +import math +from dataclasses import dataclass +from typing import Any, Literal, cast + +import numpy as np + +from zarr_indexing.domain import IndexDomain +from zarr_indexing.errors import BoundsCheckError, VindexInvalidSelectionError +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap + + +@dataclass(frozen=True, slots=True) +class IndexTransform: + """A composable mapping from input coordinates to storage coordinates. + + An `IndexTransform` has: + + - `domain`: an `IndexDomain` describing the valid input coordinates + (the user-facing shape, possibly with non-zero origin). + - `output`: a tuple of output maps (one per storage dimension), each + describing which storage coordinates the inputs touch. + + For a freshly opened array, the transform is the identity: input + coordinate `i` maps to storage coordinate `i`. Indexing operations + compose new transforms without I/O. + """ + + domain: IndexDomain + output: tuple[OutputIndexMap, ...] + + def __post_init__(self) -> None: + for i, m in enumerate(self.output): + if isinstance(m, DimensionMap): + if m.input_dimension < 0 or m.input_dimension >= self.domain.ndim: + raise ValueError( + f"output[{i}].input_dimension = {m.input_dimension} " + f"is out of range for input rank {self.domain.ndim}" + ) + elif isinstance(m, ArrayMap) and m.index_array.ndim > self.domain.ndim: + # ArrayMap index arrays produced by indexing and chunk resolution + # are normalized to the full input rank (an axis the array varies + # over is full-sized, every other axis a singleton). A rank + # *exceeding* the domain is always a bug. A rank *below* it is + # tolerated: TensorStore-format JSON (external input) may supply a + # lower-rank index array that broadcasts against the input domain, + # and `_array_map_dependency_axes` treats any missing leading axes + # as singleton dependencies. + raise ValueError( + f"output[{i}].index_array has {m.index_array.ndim} dims " + f"but input domain has {self.domain.ndim} dims" + ) + + @property + def input_rank(self) -> int: + return self.domain.ndim + + @property + def output_rank(self) -> int: + return len(self.output) + + @classmethod + def identity(cls, domain: IndexDomain) -> IndexTransform: + output = tuple(DimensionMap(input_dimension=i) for i in range(domain.ndim)) + return cls(domain=domain, output=output) + + @classmethod + def from_shape(cls, shape: tuple[int, ...]) -> IndexTransform: + return cls.identity(IndexDomain.from_shape(shape)) + + @property + def selection_repr(self) -> str: + """Compact domain string, e.g. `'{ [2, 8), [0, 10) }'`. + + Follows TensorStore's IndexDomain notation: each dimension shown + as `[inclusive_min, exclusive_max)` with stride annotation if not 1. + Constant (integer-indexed) dimensions show as a single value. + Array-indexed dimensions show the set of selected coordinates. + """ + parts: list[str] = [] + for m in self.output: + if isinstance(m, ConstantMap): + parts.append(str(m.offset)) + elif isinstance(m, DimensionMap): + d = m.input_dimension + lo = self.domain.inclusive_min[d] + hi = self.domain.exclusive_max[d] + start = m.offset + m.stride * lo + stop = m.offset + m.stride * hi + if m.stride == 1: + parts.append(f"[{start}, {stop})") + else: + parts.append(f"[{start}, {stop}) step {m.stride}") + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + storage = m.offset + m.stride * m.index_array + n = int(storage.size) # .size, not len(): index_array may be 0-d + if n <= 5: + vals = ", ".join(str(int(v)) for v in storage.ravel()) + parts.append("{" + vals + "}") + else: + parts.append("{" + f"array({n})" + "}") + return "{ " + ", ".join(parts) + " }" + + def __repr__(self) -> str: + maps: list[str] = [] + for i, m in enumerate(self.output): + if isinstance(m, ConstantMap): + maps.append(f"out[{i}] = {m.offset}") + elif isinstance(m, DimensionMap): + maps.append(f"out[{i}] = {m.offset} + {m.stride} * in[{m.input_dimension}]") + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + maps.append(f"out[{i}] = {m.offset} + {m.stride} * arr{m.index_array.shape}[in]") + maps_str = ", ".join(maps) + return f"IndexTransform(domain={self.domain}, {maps_str})" + + def intersect( + self, output_domain: IndexDomain + ) -> ( + tuple[ + IndexTransform, + dict[int, np.ndarray[Any, np.dtype[np.intp]]] + | np.ndarray[Any, np.dtype[np.intp]] + | None, + ] + | None + ): + """Restrict this transform to storage coordinates within output_domain. + + Returns `(restricted_transform, out_indices)` or None if empty. + + `out_indices` carries the surviving output positions: `None` when all + positions survive (ConstantMap/DimensionMap only), a single integer array + for one ArrayMap (or correlated/vectorized ArrayMaps), or a dict keyed by + output dimension for >= 2 orthogonal ArrayMaps (an outer product). + """ + return _intersect(self, output_domain) + + def translate(self, shift: tuple[int, ...]) -> IndexTransform: + """Shift all output coordinates by `shift`.""" + if len(shift) != self.output_rank: + raise ValueError(f"shift must have length {self.output_rank}, got {len(shift)}") + new_output: list[OutputIndexMap] = [] + for m, s in zip(self.output, shift, strict=True): + if isinstance(m, ConstantMap): + new_output.append(ConstantMap(offset=m.offset + s)) + elif isinstance(m, DimensionMap): + new_output.append( + DimensionMap( + input_dimension=m.input_dimension, + offset=m.offset + s, + stride=m.stride, + ) + ) + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + new_output.append( + ArrayMap( + index_array=m.index_array, + offset=m.offset + s, + stride=m.stride, + input_dimension=m.input_dimension, + ) + ) + return IndexTransform(domain=self.domain, output=tuple(new_output)) + + def __getitem__(self, selection: Any) -> IndexTransform: + return _apply_basic_indexing(self, selection) + + def translate_domain_by(self, shift: tuple[int, ...]) -> IndexTransform: + """Shift the *input* domain by `shift`, preserving which cells are addressed. + + TensorStore's `translate_by`: the domain moves, and every output map is + re-offset so that new coordinate `c` addresses the cell that `c - shift` + addressed before. ArrayMaps are indexed positionally over the domain, so + their index arrays are unchanged. + """ + if len(shift) != self.input_rank: + raise ValueError(f"shift must have length {self.input_rank}, got {len(shift)}") + new_domain = self.domain.translate(shift) + new_output: list[OutputIndexMap] = [] + for m in self.output: + if isinstance(m, DimensionMap): + s = shift[m.input_dimension] + new_output.append( + DimensionMap( + input_dimension=m.input_dimension, + offset=m.offset - m.stride * s, + stride=m.stride, + ) + ) + else: + # ConstantMap: no input dependence. ArrayMap: positional over + # the domain, invariant under domain translation. + new_output.append(m) + return IndexTransform(domain=new_domain, output=tuple(new_output)) + + def translate_domain_to(self, origins: tuple[int, ...]) -> IndexTransform: + """Move the input domain so its per-dimension origins equal `origins`. + + TensorStore's `translate_to`; `translate_domain_to((0,) * rank)` + re-zeros a view's coordinate system without changing which cells it + addresses. + """ + if len(origins) != self.input_rank: + raise ValueError(f"origins must have length {self.input_rank}, got {len(origins)}") + shift = tuple(o - m for o, m in zip(origins, self.domain.inclusive_min, strict=True)) + return self.translate_domain_by(shift) + + @property + def oindex(self) -> _OIndexHelper: + return _OIndexHelper(self) + + @property + def vindex(self) -> _VIndexHelper: + return _VIndexHelper(self) + + +def _intersect( + transform: IndexTransform, output_domain: IndexDomain +) -> ( + tuple[ + IndexTransform, + dict[int, np.ndarray[Any, np.dtype[np.intp]]] | np.ndarray[Any, np.dtype[np.intp]] | None, + ] + | None +): + """Intersect a transform with an output domain (e.g., a chunk's bounds). + + For each output dimension, restrict to storage coordinates within + `[output_domain.inclusive_min[d], output_domain.exclusive_max[d])`. + + Two flavours of fancy indexing require different treatment, distinguished by + the ArrayMaps' dependency axes (see `_array_map_dependency_axes`): + + - **orthogonal** (`oindex`): each ArrayMap varies over a single, distinct + input axis, forming an outer product. Every output dimension is intersected + independently and the input domain narrowed per axis. + - **correlated** (`vindex`): the ArrayMaps share their (broadcast) dependency + axes and scatter through a single flat index. A point survives only if ALL + its storage coordinates fall within the output domain; residual slice + dimensions are intersected independently, as in the orthogonal case. + + A `None` `input_dimension` marks a correlated map, so any such map routes the + whole transform through the correlated intersection. + + Returns `None` if the intersection is empty. + """ + if output_domain.ndim != transform.output_rank: + raise ValueError( + f"output_domain rank ({output_domain.ndim}) != " + f"transform output rank ({transform.output_rank})" + ) + + correlated_dims = [ + i + for i, m in enumerate(transform.output) + if isinstance(m, ArrayMap) and m.input_dimension is None + ] + if len(correlated_dims) > 0: + return _intersect_correlated(transform, output_domain, correlated_dims) + return _intersect_orthogonal(transform, output_domain) + + +def _intersect_dimension_map( + m: DimensionMap, input_lo: int, input_hi: int, lo: int, hi: int +) -> tuple[int, int] | None: + """Narrow a DimensionMap's input range to storage coordinates in `[lo, hi)`. + + `input_lo`/`input_hi` are the current (possibly already narrowed) input + range for the map's axis. Returns the new `(input_lo, input_hi)` or `None` + if no input produces an in-bounds storage coordinate. + """ + if input_lo >= input_hi: + return None + if m.stride > 0: + new_input_lo = max(input_lo, math.ceil((lo - m.offset) / m.stride)) + new_input_hi = min(input_hi, math.ceil((hi - m.offset) / m.stride)) + elif m.stride < 0: + new_input_lo = max(input_lo, math.ceil((hi - 1 - m.offset) / m.stride)) + new_input_hi = min(input_hi, math.ceil((lo - 1 - m.offset) / m.stride)) + else: + if lo <= m.offset < hi: + new_input_lo, new_input_hi = input_lo, input_hi + else: + return None + if new_input_lo >= new_input_hi: + return None + return new_input_lo, new_input_hi + + +def _intersect_orthogonal( + transform: IndexTransform, output_domain: IndexDomain +) -> ( + tuple[ + IndexTransform, + dict[int, np.ndarray[Any, np.dtype[np.intp]]] | np.ndarray[Any, np.dtype[np.intp]] | None, + ] + | None +): + """Intersect a transform with no correlated ArrayMaps. + + Every output dimension is intersected independently. Multiple ArrayMaps bound + to distinct input dimensions form an outer product, so each array's surviving + *output* positions are tracked separately. + """ + new_min = list(transform.domain.inclusive_min) + new_max = list(transform.domain.exclusive_max) + new_output: list[OutputIndexMap] = [] + out_positions: dict[int, np.ndarray[Any, np.dtype[np.intp]]] = {} + + for out_dim, m in enumerate(transform.output): + lo = output_domain.inclusive_min[out_dim] + hi = output_domain.exclusive_max[out_dim] + + if isinstance(m, ConstantMap): + if lo <= m.offset < hi: + new_output.append(m) + else: + return None + + elif isinstance(m, DimensionMap): + d = m.input_dimension + narrowed = _intersect_dimension_map(m, new_min[d], new_max[d], lo, hi) + if narrowed is None: + return None + new_min[d], new_max[d] = narrowed + new_output.append(m) + + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + # Orthogonal: the array varies over a single axis (its dependency + # axis, or `input_dimension` for a degenerate length-1 array). Filter + # along that axis and keep the array at full input rank so the + # singleton axes it broadcasts over are preserved. + d = _array_map_dependent_axis(m) + storage = m.offset + m.stride * m.index_array + mask = (storage >= lo) & (storage < hi) + # The array is singleton on every axis but `d`, so its mask reduces + # to a 1-D vector along `d`. + survivors = np.nonzero(mask.reshape(-1))[0].astype(np.intp) + if survivors.size == 0: + return None + filtered = np.take(m.index_array, survivors, axis=d) + new_output.append( + ArrayMap( + index_array=np.asarray(filtered, dtype=np.intp), + offset=m.offset, + stride=m.stride, + input_dimension=m.input_dimension, + ) + ) + new_max[d] = new_min[d] + int(survivors.size) + out_positions[out_dim] = survivors + + new_domain = IndexDomain( + inclusive_min=tuple(new_min), + exclusive_max=tuple(new_max), + ) + result = IndexTransform(domain=new_domain, output=tuple(new_output)) + + # Hand back the surviving output positions in the shape the bridge expects: + # None (no arrays), a single vector (one array), or a per-output-dim dict + # (>= 2 orthogonal arrays → outer product). + out_indices: ( + dict[int, np.ndarray[Any, np.dtype[np.intp]]] | np.ndarray[Any, np.dtype[np.intp]] | None + ) + if len(out_positions) == 0: + out_indices = None + elif len(out_positions) == 1: + out_indices = next(iter(out_positions.values())) + else: + out_indices = out_positions + return (result, out_indices) + + +def _intersect_correlated( + transform: IndexTransform, + output_domain: IndexDomain, + correlated_dims: list[int], +) -> tuple[IndexTransform, np.ndarray[Any, np.dtype[np.intp]]] | None: + """Intersect a correlated (vindex) transform with an output domain. + + The correlated ArrayMaps share their broadcast (dependency) axes; a broadcast + point survives only if ALL its storage coordinates fall within the output + domain. Residual DimensionMap dimensions are intersected independently (as in + the orthogonal case) and preserved, so a partial vindex — e.g. two coordinate + arrays over a 3-D array, leaving one slice dimension — resolves correctly. + + The surviving broadcast axes collapse to a single axis; the returned + `out_indices` is the flat scatter index into the (row-major flattened) + output buffer, of shape `(surviving_points,) + (residual slice sizes)`. + """ + corr_maps = [cast("ArrayMap", transform.output[i]) for i in correlated_dims] + + # Mixing correlated and orthogonal ArrayMaps in one transform is not produced + # by any single selection and is not supported here. + orthogonal_array_dims = [ + i + for i, m in enumerate(transform.output) + if isinstance(m, ArrayMap) and m.input_dimension is not None + ] + if len(orthogonal_array_dims) > 0: + raise NotImplementedError( + "intersecting a transform with both correlated and orthogonal " + "ArrayMaps is not supported" + ) + + # The broadcast (dependency) axes are shared by every correlated map; they are + # the leading axes of the domain, followed by the residual slice axes. + broadcast_axes = _array_map_dependency_axes(corr_maps[0].index_array) + broadcast_shape = tuple(corr_maps[0].index_array.shape[a] for a in broadcast_axes) + + # Joint bounds mask over the broadcast block. + combined: np.ndarray[Any, np.dtype[np.bool_]] | None = None + for out_dim in correlated_dims: + cm = cast("ArrayMap", transform.output[out_dim]) + storage = cm.offset + cm.stride * cm.index_array + lo = output_domain.inclusive_min[out_dim] + hi = output_domain.exclusive_max[out_dim] + mask = (storage >= lo) & (storage < hi) + combined = mask if combined is None else (combined & mask) + assert combined is not None + # The correlated maps are singleton on every non-broadcast axis, so the mask + # collapses (C-order) to the broadcast block. + combined_bcast = combined.reshape(broadcast_shape) + surviving = np.nonzero(combined_bcast.reshape(-1))[0].astype(np.intp) + if surviving.size == 0: + return None + + # Intersect residual (slice / constant) dimensions independently. Slice dims + # are ordered by input dimension so their flat-buffer strides are row-major. + slice_dims: list[tuple[int, int, int, int, DimensionMap]] = [] # (in_dim, lo, hi, full, m) + for out_dim, m in enumerate(transform.output): + if out_dim in correlated_dims: + continue + lo = output_domain.inclusive_min[out_dim] + hi = output_domain.exclusive_max[out_dim] + if isinstance(m, ConstantMap): + if not (lo <= m.offset < hi): + return None + elif isinstance(m, DimensionMap): + d = m.input_dimension + input_lo = transform.domain.inclusive_min[d] + input_hi = transform.domain.exclusive_max[d] + narrowed = _intersect_dimension_map(m, input_lo, input_hi, lo, hi) + if narrowed is None: + return None + slice_dims.append((d, narrowed[0], narrowed[1], input_hi - input_lo, m)) + slice_dims.sort(key=lambda item: item[0]) + + n_points = int(surviving.size) + n_slice = len(slice_dims) + corr_values = { + out_dim: cast("ArrayMap", transform.output[out_dim]) + .index_array.reshape(broadcast_shape) + .reshape(-1)[surviving] + for out_dim in correlated_dims + } + + # New domain: the collapsed broadcast axis, then one axis per residual slice. + new_min = [0] + new_max = [n_points] + new_input_dim_of = {} + for new_axis, (d, nlo, nhi, _full, _m) in enumerate(slice_dims, start=1): + new_min.append(nlo) + new_max.append(nhi) + new_input_dim_of[d] = new_axis + new_domain = IndexDomain(inclusive_min=tuple(new_min), exclusive_max=tuple(new_max)) + + corr_shape = (n_points,) + (1,) * n_slice + new_output: list[OutputIndexMap] = [] + for out_dim, m in enumerate(transform.output): + if out_dim in correlated_dims: + corr = cast("ArrayMap", m) + new_output.append( + ArrayMap( + index_array=corr_values[out_dim].reshape(corr_shape).astype(np.intp), + offset=corr.offset, + stride=corr.stride, + ) + ) + elif isinstance(m, ConstantMap): + new_output.append(m) + else: + assert isinstance(m, DimensionMap) + new_output.append( + DimensionMap( + input_dimension=new_input_dim_of[m.input_dimension], + offset=m.offset, + stride=m.stride, + ) + ) + result = IndexTransform(domain=new_domain, output=tuple(new_output)) + + # Flat scatter index into the row-major output buffer of shape + # (broadcast points, residual slice sizes...): flat = point * prod(slice) + + # (row-major offset within the slice block). + prod_slice = 1 + for _d, _lo, _hi, full, _m in slice_dims: + prod_slice *= full + out_indices: np.ndarray[Any, np.dtype[np.intp]] = (surviving * prod_slice).reshape( + (n_points,) + (1,) * n_slice + ) + running = 1 + for j in range(n_slice - 1, -1, -1): + _d, nlo, nhi, full, _m = slice_dims[j] + coords = np.arange(nlo, nhi, dtype=np.intp) * running + shape = [1] * (1 + n_slice) + shape[1 + j] = coords.size + out_indices = out_indices + coords.reshape(shape) + running *= full + return (result, out_indices.astype(np.intp)) + + +def _normalize_basic_selection(selection: Any, ndim: int) -> tuple[int | slice | None, ...]: + """Normalize a selection to a tuple of int, slice, or None (newaxis), + expanding ellipsis and padding with slice(None) as needed. + """ + if not isinstance(selection, tuple): + selection = (selection,) + + # Count non-newaxis, non-ellipsis entries to determine how many real dims are addressed + n_newaxis = sum(1 for s in selection if s is None) + has_ellipsis = any(s is Ellipsis for s in selection) + n_real = len(selection) - n_newaxis - (1 if has_ellipsis else 0) + + if n_real > ndim: + raise IndexError( + f"too many indices for array: array has {ndim} dimensions, but {n_real} were indexed" + ) + + result: list[int | slice | None] = [] + ellipsis_seen = False + for sel in selection: + if sel is Ellipsis: + if ellipsis_seen: + raise IndexError("an index can only have a single ellipsis ('...')") + ellipsis_seen = True + num_missing = ndim - n_real + result.extend([slice(None)] * num_missing) + elif isinstance(sel, (int, np.integer)): + result.append(int(sel)) + elif isinstance(sel, slice) or sel is None: + result.append(sel) + else: + raise IndexError(f"unsupported selection type for basic indexing: {type(sel)!r}") + + # Pad remaining dimensions with slice(None) + while sum(1 for s in result if s is not None) < ndim: + result.append(slice(None)) + + return tuple(result) + + +def _reindex_array( + m: ArrayMap, + normalized: tuple[int | slice | None, ...], + domain: IndexDomain, +) -> np.ndarray[Any, np.dtype[np.intp]]: + """Apply basic indexing operations to an ArrayMap's index_array. + + The array's axes correspond to the transform's input dimensions (0-indexed + over the domain shape). Each axis is either a **dependency axis** — the array + genuinely varies with that input dimension — or a **singleton** axis it + broadcasts over. Integer indexing, slicing, or newaxis is applied to the + array only along its dependency axes; a selection on a singleton axis does not + touch the array's values (it just narrows or drops that broadcast axis). + """ + dependent = set(_array_map_dependency_axes(m.index_array)) + if m.input_dimension is not None: + # Degenerate length-1 orthogonal selection: the recorded axis is a + # dependency even though its size (1) makes it look singleton. + dependent.add(m.input_dimension) + arr = m.index_array + + # Build a numpy indexing tuple: one entry per old input dimension + idx: list[Any] = [] + old_dim = 0 + newaxis_positions: list[int] = [] + result_axis = 0 + + for sel in normalized: + if sel is None: + newaxis_positions.append(result_axis) + result_axis += 1 + elif isinstance(sel, int): + if old_dim < arr.ndim: + if old_dim in dependent: + # Convert absolute domain coordinate to 0-based array index + idx.append(sel - domain.inclusive_min[old_dim]) + else: + # Broadcast axis: keep the single element and drop the axis. + idx.append(0) + old_dim += 1 + else: + # sel: slice (normalized: tuple[int | slice | None, ...]) + if old_dim < arr.ndim: + if old_dim in dependent: + lo = domain.inclusive_min[old_dim] + hi = domain.exclusive_max[old_dim] + # Bounds are literal domain coordinates; the stored array is + # indexed positionally, so shift by the domain origin. + start, step, _origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) + pos = start - lo + idx.append(slice(pos, pos + size * step, step)) + else: + # Broadcast axis: preserve the singleton (it still broadcasts + # over the narrowed domain), regardless of the slice bounds. + idx.append(slice(None)) + old_dim += 1 + result_axis += 1 + + result = arr[tuple(idx)] if idx else arr + + for pos in newaxis_positions: + result = np.expand_dims(result, axis=pos) + + return np.asarray(result, dtype=np.intp) + + +_FANCY_AFTER_FANCY_MSG = ( + "applying a fancy (orthogonal/vectorized) selection to a view that already " + "has a fancy-indexed axis is not supported (fancy-after-fancy composition): " + "the new coordinates would index a broadcast axis of the existing selection. " + "Materialize the view first with `.result()` and index the array, or reorder " + "the selections so the fancy step is applied last." +) + + +def _guard_fancy_after_fancy(m: ArrayMap, fancy_dims: set[int] | list[int]) -> None: + """Reject a fancy step that lands on a broadcast axis of an existing ArrayMap. + + A new orthogonal/vectorized selection can only be absorbed into an existing + ArrayMap along the axes that map genuinely varies over (its dependency axes, + plus the recorded `input_dimension` for a degenerate length-1 orthogonal + selection). A fancy index targeting any other axis — a singleton axis the map + merely broadcasts over — cannot be reindexed and used to leak a raw NumPy + `IndexError` at resolve time. Raise a clear `NotImplementedError` instead. + """ + dependent = set(_array_map_dependency_axes(m.index_array)) + if m.input_dimension is not None: + dependent.add(m.input_dimension) + for d in fancy_dims: + if d < m.index_array.ndim and d not in dependent: + raise NotImplementedError(_FANCY_AFTER_FANCY_MSG) + + +def _reindex_array_oindex( + arr: np.ndarray[Any, np.dtype[np.intp]], + normalized: tuple[Any, ...] | list[Any], + domain: IndexDomain, +) -> np.ndarray[Any, np.dtype[np.intp]]: + """Apply oindex/vindex selection to an existing ArrayMap's index_array. + + Each old input dimension gets either an array (fancy index that axis) + or a slice applied to the corresponding array axis. + """ + idx: list[Any] = [] + for old_dim, sel in enumerate(normalized): + if old_dim >= arr.ndim: + break + lo = domain.inclusive_min[old_dim] + if isinstance(sel, np.ndarray): + # Values are literal domain coordinates; the stored array is + # indexed positionally, so shift by the domain origin. + idx.append(sel - lo) + elif isinstance(sel, slice): + hi = domain.exclusive_max[old_dim] + start, step, _origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) + pos = start - lo + idx.append(slice(pos, pos + size * step, step)) + else: + idx.append(slice(None)) + + result = arr[tuple(idx)] if idx else arr + return np.asarray(result, dtype=np.intp) + + +def _apply_basic_indexing(transform: IndexTransform, selection: Any) -> IndexTransform: + """Apply basic indexing (int, slice, ellipsis, newaxis) to an IndexTransform.""" + normalized = _normalize_basic_selection(selection, transform.domain.ndim) + + new_inclusive_min: list[int] = [] + new_exclusive_max: list[int] = [] + old_dim = 0 + new_dim_idx = 0 + old_to_new_dim: dict[int, int] = {} + dropped_dims: set[int] = set() + + # Per old-dim: the slice parameters (for computing new output maps) + dim_slice_params: dict[int, tuple[int, int, int]] = {} # old_dim -> (start, stop, step) + dim_int_val: dict[int, int] = {} # old_dim -> integer index value + + for sel in normalized: + if sel is None: + # newaxis: add a size-1 dimension + new_inclusive_min.append(0) + new_exclusive_max.append(1) + new_dim_idx += 1 + elif isinstance(sel, int): + # Integer index: drop this input dimension. + # Negative indices are literal coordinates (TensorStore convention), + # NOT "from the end" like NumPy. The Array layer handles conversion. + lo = transform.domain.inclusive_min[old_dim] + hi = transform.domain.exclusive_max[old_dim] + idx = sel + if idx < lo or idx >= hi: + hint = _LITERAL_HINT if sel < 0 else "" + raise BoundsCheckError( + f"index {sel} is out of bounds for dimension {old_dim} " + f"(valid indices [{lo}, {hi})){hint}" + ) + dropped_dims.add(old_dim) + dim_int_val[old_dim] = idx + old_dim += 1 + else: + # sel: slice (normalized: tuple[int | slice | None, ...]) + lo = transform.domain.inclusive_min[old_dim] + hi = transform.domain.exclusive_max[old_dim] + + # TensorStore semantics: bounds are literal coordinates; a step-1 + # slice keeps them as the new domain, a strided slice's domain is + # [trunc(start/step), trunc(start/step) + size). + start, step, origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) + new_inclusive_min.append(origin) + new_exclusive_max.append(origin + size) + dim_slice_params[old_dim] = (start, step, origin) + old_to_new_dim[old_dim] = new_dim_idx + new_dim_idx += 1 + old_dim += 1 + + new_domain = IndexDomain( + inclusive_min=tuple(new_inclusive_min), + exclusive_max=tuple(new_exclusive_max), + ) + + # Now update output maps + new_output: list[OutputIndexMap] = [] + for m in transform.output: + if isinstance(m, ConstantMap): + new_output.append(m) + elif isinstance(m, DimensionMap): + d = m.input_dimension + if d in dropped_dims: + # Integer index: this output becomes constant + new_offset = m.offset + m.stride * dim_int_val[d] + new_output.append(ConstantMap(offset=new_offset)) + elif d in old_to_new_dim: + # Slice: new coordinate `origin + k` maps to old coordinate + # `start + k*step`, i.e. old = start - step*origin + step*new. + start, step, origin = dim_slice_params[d] + new_offset = m.offset + m.stride * (start - step * origin) + new_stride = m.stride * step + new_input_dim = old_to_new_dim[d] + new_output.append( + DimensionMap( + input_dimension=new_input_dim, offset=new_offset, stride=new_stride + ) + ) + else: + raise RuntimeError(f"unexpected: dimension {d} not handled") + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + new_arr = _reindex_array(m, normalized, transform.domain) + array_input_dim: int | None = None + if m.input_dimension is not None: + array_input_dim = old_to_new_dim.get(m.input_dimension, m.input_dimension) + new_output.append( + ArrayMap( + index_array=new_arr, + offset=m.offset, + stride=m.stride, + input_dimension=array_input_dim, + ) + ) + + return IndexTransform(domain=new_domain, output=tuple(new_output)) + + +def _array_map_dependency_axes(index_array: np.ndarray[Any, Any]) -> tuple[int, ...]: + """Return the input axes on which a normalized index array varies. + + Normalized `ArrayMap` index arrays carry the full input rank of their + enclosing transform: an axis the array varies over has its full size, while + an axis the array is independent of is a singleton (size 1). The dependency + axes are therefore exactly the non-singleton axes. An orthogonal (`oindex`) + array depends on a single axis; a vectorized (`vindex`) array depends on all + of the (shared) broadcast axes. + """ + return tuple(axis for axis, size in enumerate(index_array.shape) if size != 1) + + +def _array_map_dependent_axis(m: ArrayMap) -> int: + """Return the single input axis an orthogonal `ArrayMap` varies over. + + Normally this is the array's one non-singleton axis. A degenerate length-1 + orthogonal selection normalizes to an all-singleton shape (its dependency + axes are empty and indistinguishable by shape from a scalar), so + `input_dimension` breaks the tie — it records the axis the map binds. + """ + dep = _array_map_dependency_axes(m.index_array) + if len(dep) == 1: + return dep[0] + if m.input_dimension is not None: + return m.input_dimension + raise ValueError( + f"orthogonal ArrayMap must vary over exactly one axis; got dependency " + f"axes {dep} with input_dimension={m.input_dimension}" + ) + + +def _reshape_to_axis( + values: np.ndarray[Any, np.dtype[np.intp]], axis: int, ndim: int +) -> np.ndarray[Any, np.dtype[np.intp]]: + """Reshape a 1-D selection to full rank `ndim` varying only along `axis`. + + The result has `values` laid out along `axis` and singleton (size-1) axes + everywhere else, so its dependency axis is derivable from its shape. + """ + flat = np.asarray(values, dtype=np.intp).ravel() + shape = [1] * ndim + shape[axis] = flat.shape[0] + return flat.reshape(shape) + + +class _OIndexHelper: + """Helper that provides orthogonal (outer) indexing via `transform.oindex[...]`.""" + + def __init__(self, transform: IndexTransform) -> None: + self._transform = transform + + def __getitem__(self, selection: Any) -> IndexTransform: + return _apply_oindex(self._transform, selection) + + +def _normalize_oindex_selection( + selection: Any, ndim: int +) -> tuple[np.ndarray[Any, np.dtype[np.intp]] | slice, ...]: + """Normalize an oindex selection: arrays, slices, booleans, integers.""" + if not isinstance(selection, tuple): + selection = (selection,) + + # Expand ellipsis + has_ellipsis = any(s is Ellipsis for s in selection) + n_ellipsis = 1 if has_ellipsis else 0 + n_real = len(selection) - n_ellipsis + + result: list[np.ndarray[Any, np.dtype[np.intp]] | slice] = [] + for sel in selection: + if sel is Ellipsis: + num_missing = ndim - n_real + result.extend([slice(None)] * num_missing) + elif isinstance(sel, np.ndarray) and sel.dtype == np.bool_: + # Boolean array -> integer indices + (indices,) = np.nonzero(sel) + result.append(indices.astype(np.intp)) + elif isinstance(sel, np.ndarray): + result.append(sel.astype(np.intp)) + elif isinstance(sel, slice): + result.append(sel) + elif isinstance(sel, (int, np.integer)): + # Convert integer scalars to 1-element arrays for orthogonal indexing + result.append(np.array([int(sel)], dtype=np.intp)) + elif isinstance(sel, (list, tuple)): + result.append(np.asarray(sel, dtype=np.intp)) + else: + result.append(sel) + + # Pad with slice(None) + while len(result) < ndim: + result.append(slice(None)) + + return tuple(result) + + +def _apply_oindex(transform: IndexTransform, selection: Any) -> IndexTransform: + """Apply orthogonal indexing to an IndexTransform. + + Each index array is applied independently per dimension (outer product). + """ + normalized = _normalize_oindex_selection(selection, transform.domain.ndim) + + new_inclusive_min: list[int] = [] + new_exclusive_max: list[int] = [] + new_dim_idx = 0 + old_to_new_dim: dict[int, int] = {} + + # Info per old dim + dim_array: dict[int, np.ndarray[Any, np.dtype[np.intp]]] = {} + dim_slice_params: dict[int, tuple[int, int, int]] = {} + + for old_dim, sel in enumerate(normalized): + if isinstance(sel, np.ndarray): + lo = transform.domain.inclusive_min[old_dim] + hi = transform.domain.exclusive_max[old_dim] + # Index-array values are literal domain coordinates; the fancy dim + # they create gets a fresh zero-origin [0, n) domain (TensorStore). + _check_array_in_bounds(sel, lo, hi) + dim_array[old_dim] = sel + new_inclusive_min.append(0) + new_exclusive_max.append(len(sel)) + old_to_new_dim[old_dim] = new_dim_idx + new_dim_idx += 1 + else: + # sel: slice (_normalize_oindex_selection returns + # tuple[np.ndarray | slice, ...]) + lo = transform.domain.inclusive_min[old_dim] + hi = transform.domain.exclusive_max[old_dim] + start, step, origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) + new_inclusive_min.append(origin) + new_exclusive_max.append(origin + size) + dim_slice_params[old_dim] = (start, step, origin) + old_to_new_dim[old_dim] = new_dim_idx + new_dim_idx += 1 + + new_domain = IndexDomain( + inclusive_min=tuple(new_inclusive_min), + exclusive_max=tuple(new_exclusive_max), + ) + + new_output: list[OutputIndexMap] = [] + for m in transform.output: + if isinstance(m, ConstantMap): + new_output.append(m) + elif isinstance(m, DimensionMap): + d = m.input_dimension + if d in dim_array: + new_axis = old_to_new_dim[d] + # Normalize to full input rank: the selection varies along its own + # new axis and is singleton on every other axis. The dependency + # axis is then derivable from the shape (a single non-singleton + # axis marks the selection orthogonal / outer-product rather than + # vectorized). `input_dimension` is kept populated as a + # compatibility shim for consumers not yet migrated to the + # shape-derived classifier. + full_arr = _reshape_to_axis(dim_array[d], new_axis, new_dim_idx) + new_output.append( + ArrayMap( + index_array=full_arr, + offset=m.offset, + stride=m.stride, + input_dimension=new_axis, + ) + ) + elif d in dim_slice_params: + start, step, origin = dim_slice_params[d] + new_offset = m.offset + m.stride * (start - step * origin) + new_stride = m.stride * step + new_input_dim = old_to_new_dim[d] + new_output.append( + DimensionMap( + input_dimension=new_input_dim, offset=new_offset, stride=new_stride + ) + ) + else: + raise RuntimeError(f"unexpected: dimension {d} not handled") + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + _guard_fancy_after_fancy(m, list(dim_array.keys())) + new_arr = _reindex_array_oindex(m.index_array, normalized, transform.domain) + array_input_dim: int | None = None + if m.input_dimension is not None: + array_input_dim = old_to_new_dim.get(m.input_dimension, m.input_dimension) + new_output.append( + ArrayMap( + index_array=new_arr, + offset=m.offset, + stride=m.stride, + input_dimension=array_input_dim, + ) + ) + + return IndexTransform(domain=new_domain, output=tuple(new_output)) + + +class _VIndexHelper: + """Helper that provides vectorized (fancy) indexing via `transform.vindex[...]`.""" + + def __init__(self, transform: IndexTransform) -> None: + self._transform = transform + + def __getitem__(self, selection: Any) -> IndexTransform: + return _apply_vindex(self._transform, selection) + + +def _apply_vindex(transform: IndexTransform, selection: Any) -> IndexTransform: + """Apply vectorized indexing to an IndexTransform. + + All array indices are broadcast together. Broadcast dimensions are prepended, + followed by non-array (slice) dimensions. + """ + if not isinstance(selection, tuple): + selection = (selection,) + + # Expand ellipsis and count consumed dimensions + # Boolean arrays with ndim > 1 consume ndim dims + n_consumed = 0 + for s in selection: + if s is Ellipsis: + continue + if isinstance(s, np.ndarray) and s.dtype == np.bool_ and s.ndim > 1: + n_consumed += s.ndim + else: + n_consumed += 1 + ndim = transform.domain.ndim + + expanded: list[Any] = [] + for sel in selection: + if sel is Ellipsis: + num_missing = ndim - n_consumed + expanded.extend([slice(None)] * num_missing) + else: + expanded.append(sel) + # Count dimensions already consumed by expanded entries + n_expanded_dims = 0 + for sel in expanded: + if isinstance(sel, np.ndarray) and sel.dtype == np.bool_ and sel.ndim > 1: + n_expanded_dims += sel.ndim + else: + n_expanded_dims += 1 + while n_expanded_dims < ndim: + expanded.append(slice(None)) + n_expanded_dims += 1 + + # Convert booleans, lists, ints to integer arrays + processed: list[np.ndarray[Any, np.dtype[np.intp]] | slice] = [] + for sel in expanded: + if isinstance(sel, np.ndarray) and sel.dtype == np.bool_: + indices_tuple = np.nonzero(sel) + processed.extend(indices.astype(np.intp) for indices in indices_tuple) + elif isinstance(sel, np.ndarray): + processed.append(sel.astype(np.intp)) + elif isinstance(sel, (list, tuple)): + processed.append(np.asarray(sel, dtype=np.intp)) + elif isinstance(sel, (int, np.integer)): + processed.append(np.array([int(sel)], dtype=np.intp)) + else: + processed.append(sel) + + # Separate array dims and slice dims + array_dims: list[int] = [] + slice_dims: list[int] = [] + arrays: list[np.ndarray[Any, np.dtype[np.intp]]] = [] + + for i, sel in enumerate(processed): + if isinstance(sel, np.ndarray): + lo = transform.domain.inclusive_min[i] + hi = transform.domain.exclusive_max[i] + _check_array_in_bounds(sel, lo, hi) + array_dims.append(i) + arrays.append(sel) + else: + slice_dims.append(i) + + # Broadcast all arrays together + broadcast_arrays: list[np.ndarray[Any, np.dtype[np.intp]]] + if len(arrays) > 0: + broadcast_arrays = list(np.broadcast_arrays(*arrays)) + broadcast_shape = broadcast_arrays[0].shape + else: + broadcast_arrays = [] + broadcast_shape = () + + # Build new domain: broadcast dims first, then slice dims + new_inclusive_min: list[int] = [] + new_exclusive_max: list[int] = [] + + # Broadcast dimensions + for s in broadcast_shape: + new_inclusive_min.append(0) + new_exclusive_max.append(s) + + # Slice dimensions (preserved-domain literal semantics, like basic indexing) + slice_dim_params: dict[int, tuple[int, int, int]] = {} + for old_dim in slice_dims: + sel = processed[old_dim] + assert isinstance(sel, slice) + lo = transform.domain.inclusive_min[old_dim] + hi = transform.domain.exclusive_max[old_dim] + start, step, origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) + new_inclusive_min.append(origin) + new_exclusive_max.append(origin + size) + slice_dim_params[old_dim] = (start, step, origin) + + new_domain = IndexDomain( + inclusive_min=tuple(new_inclusive_min), + exclusive_max=tuple(new_exclusive_max), + ) + + # Build output maps + array_dim_to_broadcast: dict[int, np.ndarray[Any, np.dtype[np.intp]]] = {} + for i, d in enumerate(array_dims): + array_dim_to_broadcast[d] = broadcast_arrays[i] + + # New dim index for slice dims starts after broadcast dims + n_broadcast_dims = len(broadcast_shape) + + new_output: list[OutputIndexMap] = [] + for m in transform.output: + if isinstance(m, ConstantMap): + new_output.append(m) + elif isinstance(m, DimensionMap): + d = m.input_dimension + if d in array_dim_to_broadcast: + # Normalize to full input rank: the broadcast (correlated) axes + # come first, followed by a singleton axis per slice dimension. + # Every vectorized array shares the same broadcast axes, so the + # dependency axes derived from the shape coincide — the signature + # of a pointwise scatter rather than an outer product. + broadcast_arr = array_dim_to_broadcast[d] + full_arr = broadcast_arr.reshape(broadcast_shape + (1,) * len(slice_dims)) + new_output.append( + ArrayMap( + index_array=full_arr, + offset=m.offset, + stride=m.stride, + ) + ) + else: + # Slice dim: new coord `origin + k` maps to old `start + k*step` + start, step, origin = slice_dim_params[d] + new_offset = m.offset + m.stride * (start - step * origin) + new_stride = m.stride * step + new_input_dim = n_broadcast_dims + slice_dims.index(d) + new_output.append( + DimensionMap( + input_dimension=new_input_dim, offset=new_offset, stride=new_stride + ) + ) + else: + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + _guard_fancy_after_fancy(m, array_dims) + new_arr = _reindex_array_oindex(m.index_array, processed, transform.domain) + new_output.append( + ArrayMap( + index_array=new_arr, + offset=m.offset, + stride=m.stride, + input_dimension=m.input_dimension, + ) + ) + + return IndexTransform(domain=new_domain, output=tuple(new_output)) + + +_LITERAL_HINT = ( + "; within this transform layer, indices are literal domain coordinates (the " + "public Array boundary wraps NumPy-style negatives before they reach here)" +) + + +def _trunc_div(a: int, b: int) -> int: + """Integer division rounded toward zero (C semantics), as TensorStore uses + for strided-slice domain origins — distinct from Python's floor division + for negative operands (`trunc(-9/2) == -4` where `-9 // 2 == -5`).""" + q = a // b + if q < 0 and q * b != a: + q += 1 + return q + + +def _resolve_slice_ts(sel: slice, dim: int, lo: int, hi: int) -> tuple[int, int, int, int]: + """Resolve a slice against domain `[lo, hi)` with TensorStore semantics. + + Slice bounds are **literal domain coordinates** — never from-the-end, never + clamped. Rules (each verified against tensorstore 0.1.84): + + - defaults: `start = lo`, `stop = hi`; + - a non-empty interval must be contained in the domain (no clamping — a + NumPy-style out-of-range or negative bound is an error, not a shorter or + wrapped result); + - an **empty** interval (`start == stop`) is valid anywhere; + - reversed bounds (`start > stop` with positive step) are an error, not + an empty result; + - the result's domain origin is `trunc(start/step)` (rounded toward + zero) and coordinate `origin + k` maps to input `start + k*step`. + + Returns `(start, step, origin, size)` in domain coordinates. + """ + step = 1 if sel.step is None else sel.step + if step <= 0: + # Negative steps are valid in TensorStore but not yet supported here; + # step 0 is invalid everywhere. + raise IndexError("slice step must be positive") + start = lo if sel.start is None else sel.start + stop = hi if sel.stop is None else sel.stop + if stop < start: + raise IndexError( + f"slice interval [{start}, {stop}) with step {step} does not specify " + f"a valid interval for dimension {dim} (start > stop)" + ) + size = -(-(stop - start) // step) # ceil((stop - start) / step) + if size > 0 and (start < lo or stop > hi): + hint = _LITERAL_HINT if (start < 0 or stop < 0) and lo >= 0 else "" + raise BoundsCheckError( + f"slice interval [{start}, {stop}) is not contained within domain " + f"[{lo}, {hi}) for dimension {dim}{hint}" + ) + origin = _trunc_div(start, step) + return start, step, origin, size + + +def _check_array_in_bounds(arr: np.ndarray[Any, np.dtype[np.intp]], lo: int, hi: int) -> None: + """Reject index-array values outside the domain `[lo, hi)`. + + Index-array values are literal domain coordinates (TensorStore semantics): + a value below `inclusive_min` is out of bounds rather than counting from + the end. Out-of-range values raise instead of silently wrapping. + """ + if arr.size == 0: + return + lo_val, hi_val = int(arr.min()), int(arr.max()) + if lo_val < lo: + hint = _LITERAL_HINT if lo_val < 0 and lo >= 0 else "" + raise BoundsCheckError( + f"index {lo_val} is out of bounds (valid indices [{lo}, {hi})){hint}" + ) + if hi_val >= hi: + raise BoundsCheckError(f"index {hi_val} is out of bounds (valid indices [{lo}, {hi}))") + + +def _validate_array_selection(selection: Any, shape: tuple[int, ...], mode: str) -> None: + """Validate array-based selections (orthogonal, vectorized). + + Rejects types that are not valid for coordinate/vectorized indexing. + Does not check bounds — the transform operations handle that. + """ + items = selection if isinstance(selection, tuple) else (selection,) + for sel in items: + if isinstance(sel, slice): + # vindex is coordinate-only (matches eager zarr): every axis needs an + # integer/boolean array, never a slice. Orthogonal (oindex) allows slices. + if mode == "vectorized": + raise VindexInvalidSelectionError( + "unsupported selection type for vectorized indexing; only " + "coordinate selection (tuple of integer arrays) and mask selection " + f"(single Boolean array) are supported; got {selection!r}" + ) + continue + if sel is Ellipsis or isinstance(sel, (int, np.integer)): + continue + if isinstance(sel, (list, np.ndarray)): + continue + raise IndexError(f"unsupported selection type for {mode} indexing: {type(sel)!r}") + + +def _validate_basic_selection(selection: Any) -> None: + """Validate that a selection only contains basic indexing types (int, slice, Ellipsis). + + Rejects None (newaxis), arrays, lists, floats, strings, etc. + """ + items = selection if isinstance(selection, tuple) else (selection,) + for s in items: + if s is Ellipsis or isinstance(s, (int, np.integer, slice)): + continue + raise IndexError(f"unsupported selection type for basic indexing: {type(s)!r}") + + +def selection_to_transform( + selection: Any, + transform: IndexTransform, + mode: Literal["basic", "orthogonal", "vectorized"], +) -> IndexTransform: + """Convert a user selection into a composed IndexTransform. + + Negative indices are treated as literal coordinates (TensorStore convention). + The caller (Array layer) is responsible for converting numpy-style negative + indices before calling this function. + """ + if mode == "basic": + _validate_basic_selection(selection) + return transform[selection] + elif mode == "orthogonal": + _validate_array_selection(selection, transform.domain.shape, mode) + return transform.oindex[selection] + elif mode == "vectorized": + _validate_array_selection(selection, transform.domain.shape, mode) + return transform.vindex[selection] + else: + raise ValueError(f"Unknown mode: {mode!r}") diff --git a/packages/zarr-indexing/tests/conformance/PROVENANCE.md b/packages/zarr-indexing/tests/conformance/PROVENANCE.md new file mode 100644 index 0000000000..0a6faef60b --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/PROVENANCE.md @@ -0,0 +1,20 @@ +# Provenance of the ndsel conformance corpus + +The JSON fixtures in this directory (`point.json`, `box.json`, `slice.json`, +`points.json`, `transform.json`, `errors.json`) and `README.md` are **vendored, +unmodified**, from the ndsel reference repository. + +- **Source:** <https://github.com/zarr-developers/ndsel> +- **Branch:** `main` (merge of d-v-b/ndsel#1, `fix/slice-origin-trunc`) +- **Commit:** `c59bc556c` (fixtures byte-identical to the previously vendored + `c132b4c1caa3205830ce35a42502363171f650a7`) +- **Path in source:** `conformance/` + +**Do not edit these files.** They are vendored as-is so that +`zarr_indexing`' ndsel message layer can be checked against the same +language-agnostic corpus every other ndsel implementation runs. To update the +corpus, re-vendor from a newer ndsel commit and update the commit SHA above. + +ndsel PR #1 (merged) corrected the `slice` desugaring origin from +`floor(a/s)` to `trunc(a/s)` (rounding toward zero), which matches +`zarr_indexing`' existing `_trunc_div` semantics. diff --git a/packages/zarr-indexing/tests/conformance/README.md b/packages/zarr-indexing/tests/conformance/README.md new file mode 100644 index 0000000000..ecb0c57ca2 --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/README.md @@ -0,0 +1,16 @@ +# ndsel conformance corpus + +Language-agnostic fixtures. Each file is a JSON array of cases. + +A **success** case: + { "name": "...", "input": <message>, "normalized": <canonical transform without `kind`> } + +An **error** case: + { "name": "...", "input": <message>, "error": "<reason_code>" } + +An implementation is conformant iff, for every success case, +`normalize(input)` equals `normalized` by structural JSON equality, and for +every error case, `normalize(input)` is rejected with the given reason code. + +The `normalized` value is a canonical `transform` body (the `kind` field is +omitted; implementations compare the transform structure). diff --git a/packages/zarr-indexing/tests/conformance/box.json b/packages/zarr-indexing/tests/conformance/box.json new file mode 100644 index 0000000000..e847872f86 --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/box.json @@ -0,0 +1,50 @@ +[ + { + "name": "box/2d-min-max", + "input": { "kind": "box", "inclusive_min": [0, 0], "exclusive_max": [3, 4] }, + "normalized": { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [3, 4], + "input_labels": ["", ""], + "output": [ + { "offset": 0, "stride": 1, "input_dimension": 0 }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + } + }, + { + "name": "box/shape-only-origin-zero", + "input": { "kind": "box", "shape": [5] }, + "normalized": { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [5], + "input_labels": [""], + "output": [ { "offset": 0, "stride": 1, "input_dimension": 0 } ] + } + }, + { + "name": "box/inclusive-max", + "input": { "kind": "box", "inclusive_min": [2], "inclusive_max": [9] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [2], "input_exclusive_max": [10], + "input_labels": [""], + "output": [ { "offset": 0, "stride": 1, "input_dimension": 0 } ] + } + }, + { + "name": "box/implicit-and-infinite-bounds", + "input": { "kind": "box", "inclusive_min": [["-inf"], 0], "exclusive_max": [["+inf"], 4], "labels": ["t", ""] }, + "normalized": { + "input_rank": 2, + "input_inclusive_min": [["-inf"], 0], + "input_exclusive_max": [["+inf"], 4], + "input_labels": ["t", ""], + "output": [ + { "offset": 0, "stride": 1, "input_dimension": 0 }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + } + } +] diff --git a/packages/zarr-indexing/tests/conformance/errors.json b/packages/zarr-indexing/tests/conformance/errors.json new file mode 100644 index 0000000000..e5e08bab3c --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/errors.json @@ -0,0 +1,23 @@ +[ + { "name": "error/step-zero", "input": { "kind": "slice", "start": [0], "stop": [4], "step": [0] }, "error": "step_zero" }, + { "name": "error/negative-step", "input": { "kind": "slice", "start": [9], "stop": [0], "step": [-2] }, "error": "negative_step_unsupported" }, + { "name": "error/multiple-upper-bounds", "input": { "kind": "box", "shape": [3], "exclusive_max": [3] }, "error": "multiple_upper_bounds" }, + { "name": "error/rank-mismatch", "input": { "kind": "slice", "start": [0, 0], "stop": [4] }, "error": "rank_mismatch" }, + { "name": "error/unknown-kind", "input": { "kind": "bogus" }, "error": "unknown_kind" }, + { "name": "error/transform-multiple-upper-bounds", "input": { "kind": "transform", "input_shape": [3], "input_exclusive_max": [3] }, "error": "multiple_upper_bounds" }, + { "name": "error/transform-rank-mismatch", "input": { "kind": "transform", "input_rank": 2, "input_inclusive_min": [0] }, "error": "rank_mismatch" }, + { "name": "error/missing-kind", "input": { "coords": [1, 2] }, "error": "invalid_json" }, + { "name": "error/point-missing-coords", "input": { "kind": "point" }, "error": "invalid_json" }, + { "name": "error/point-bool-coord", "input": { "kind": "point", "coords": [true] }, "error": "invalid_json" }, + { "name": "error/slice-missing-stop", "input": { "kind": "slice", "start": [0] }, "error": "invalid_json" }, + { "name": "error/box-non-list-bound", "input": { "kind": "box", "inclusive_min": 5 }, "error": "invalid_json" }, + { "name": "error/points-bool-coord", "input": { "kind": "points", "coords": [[true]] }, "error": "invalid_json" }, + { "name": "error/integer-out-of-i64-range", "input": { "kind": "point", "coords": [99999999999999999999] }, "error": "invalid_json" }, + { "name": "error/box-inverted-bounds", "input": { "kind": "box", "inclusive_min": [5], "exclusive_max": [3] }, "error": "bounds_out_of_order" }, + { "name": "error/box-negative-shape", "input": { "kind": "box", "shape": [-3] }, "error": "bounds_out_of_order" }, + { "name": "error/transform-inverted-bounds", "input": { "kind": "transform", "input_inclusive_min": [0], "input_exclusive_max": [-1] }, "error": "bounds_out_of_order" }, + { "name": "error/output-map-conflict", "input": { "kind": "transform", "output": [{ "input_dimension": 0, "index_array": [1, 2] }] }, "error": "output_map_conflict" }, + { "name": "error/box-unknown-field", "input": { "kind": "box", "shapee": [3] }, "error": "unknown_field" }, + { "name": "error/point-unknown-field", "input": { "kind": "point", "coords": [1], "extra": true }, "error": "unknown_field" }, + { "name": "error/output-map-unknown-field", "input": { "kind": "transform", "output": [{ "offset": 0, "bogus": 1 }] }, "error": "unknown_field" } +] diff --git a/packages/zarr-indexing/tests/conformance/point.json b/packages/zarr-indexing/tests/conformance/point.json new file mode 100644 index 0000000000..99a5ea16d8 --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/point.json @@ -0,0 +1,30 @@ +[ + { + "name": "point/2d", + "input": { "kind": "point", "coords": [4, 7] }, + "normalized": { + "input_rank": 0, + "input_inclusive_min": [], + "input_exclusive_max": [], + "input_labels": [], + "output": [ { "offset": 4 }, { "offset": 7 } ] + } + }, + { + "name": "point/scalar-0d", + "input": { "kind": "point", "coords": [] }, + "normalized": { + "input_rank": 0, "input_inclusive_min": [], "input_exclusive_max": [], + "input_labels": [], "output": [] + } + }, + { + "name": "point/large-i64", + "input": { "kind": "point", "coords": [1152921504606846976] }, + "normalized": { + "input_rank": 0, "input_inclusive_min": [], "input_exclusive_max": [], + "input_labels": [], + "output": [ { "offset": 1152921504606846976 } ] + } + } +] diff --git a/packages/zarr-indexing/tests/conformance/points.json b/packages/zarr-indexing/tests/conformance/points.json new file mode 100644 index 0000000000..1ad92e12b1 --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/points.json @@ -0,0 +1,34 @@ +[ + { + "name": "points/three-2d", + "input": { "kind": "points", "coords": [[1, 10], [2, 20], [3, 30]] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [0], "input_exclusive_max": [3], + "input_labels": [""], + "output": [ + { "offset": 0, "stride": 1, "index_array": [1, 2, 3], "index_array_bounds": ["-inf", "+inf"] }, + { "offset": 0, "stride": 1, "index_array": [10, 20, 30], "index_array_bounds": ["-inf", "+inf"] } + ] + } + }, + { + "name": "points/1d", + "input": { "kind": "points", "coords": [[5], [9], [2]] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [0], "input_exclusive_max": [3], + "input_labels": [""], + "output": [ + { "offset": 0, "stride": 1, "index_array": [5, 9, 2], "index_array_bounds": ["-inf", "+inf"] } + ] + } + }, + { + "name": "points/empty", + "input": { "kind": "points", "coords": [] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [0], "input_exclusive_max": [0], + "input_labels": [""], + "output": [] + } + } +] diff --git a/packages/zarr-indexing/tests/conformance/slice.json b/packages/zarr-indexing/tests/conformance/slice.json new file mode 100644 index 0000000000..2f1a0694ce --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/slice.json @@ -0,0 +1,61 @@ +[ + { + "name": "slice/unit-step-preserves-frame", + "input": { "kind": "slice", "start": [5], "stop": [10] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [5], "input_exclusive_max": [10], + "input_labels": [""], + "output": [ { "offset": 0, "stride": 1, "input_dimension": 0 } ] + } + }, + { + "name": "slice/divisible-stride", + "input": { "kind": "slice", "start": [4], "stop": [10], "step": [2] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [2], "input_exclusive_max": [5], + "input_labels": [""], + "output": [ { "offset": 0, "stride": 2, "input_dimension": 0 } ] + } + }, + { + "name": "slice/nondivisible-stride-phase-offset", + "input": { "kind": "slice", "start": [5], "stop": [10], "step": [2] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [2], "input_exclusive_max": [5], + "input_labels": [""], + "output": [ { "offset": 1, "stride": 2, "input_dimension": 0 } ] + } + }, + { + "name": "slice/2d-mixed-step", + "input": { "kind": "slice", "start": [0, 5], "stop": [10, 10], "step": [2, 1] }, + "normalized": { + "input_rank": 2, + "input_inclusive_min": [0, 5], + "input_exclusive_max": [5, 10], + "input_labels": ["", ""], + "output": [ + { "offset": 0, "stride": 2, "input_dimension": 0 }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + } + }, + { + "name": "slice/negative-start-trunc-origin", + "input": { "kind": "slice", "start": [-9], "stop": [5], "step": [2] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-4], "input_exclusive_max": [3], + "input_labels": [""], + "output": [ { "offset": -1, "stride": 2, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-start-trunc-origin-step3", + "input": { "kind": "slice", "start": [-8], "stop": [6], "step": [3] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-2], "input_exclusive_max": [3], + "input_labels": [""], + "output": [ { "offset": -2, "stride": 3, "input_dimension": 0 } ] + } + } +] diff --git a/packages/zarr-indexing/tests/conformance/transform.json b/packages/zarr-indexing/tests/conformance/transform.json new file mode 100644 index 0000000000..f26157aaab --- /dev/null +++ b/packages/zarr-indexing/tests/conformance/transform.json @@ -0,0 +1,57 @@ +[ + { + "name": "transform/omitted-output-identity", + "input": { "kind": "transform", "input_inclusive_min": [0, 0], "input_exclusive_max": [3, 4] }, + "normalized": { + "input_rank": 2, "input_inclusive_min": [0, 0], "input_exclusive_max": [3, 4], + "input_labels": ["", ""], + "output": [ + { "offset": 0, "stride": 1, "input_dimension": 0 }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + } + }, + { + "name": "transform/implicit-bounds-and-labels", + "input": { + "kind": "transform", + "input_inclusive_min": [["-inf"], 7], + "input_exclusive_max": [["+inf"], 11], + "input_labels": ["x", "y"] + }, + "normalized": { + "input_rank": 2, + "input_inclusive_min": [["-inf"], 7], + "input_exclusive_max": [["+inf"], 11], + "input_labels": ["x", "y"], + "output": [ + { "offset": 0, "stride": 1, "input_dimension": 0 }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + } + }, + { + "name": "transform/explicit-output-all-three-map-kinds", + "input": { + "kind": "transform", + "input_inclusive_min": [0], + "input_exclusive_max": [3], + "output": [ + { "offset": 7 }, + { "input_dimension": 0, "stride": 2 }, + { "index_array": [1, 2, 3] } + ] + }, + "normalized": { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [3], + "input_labels": [""], + "output": [ + { "offset": 7 }, + { "offset": 0, "stride": 2, "input_dimension": 0 }, + { "offset": 0, "stride": 1, "index_array": [1, 2, 3], "index_array_bounds": ["-inf", "+inf"] } + ] + } + } +] diff --git a/packages/zarr-indexing/tests/test_chunk_resolution.py b/packages/zarr-indexing/tests/test_chunk_resolution.py new file mode 100644 index 0000000000..0738384e2b --- /dev/null +++ b/packages/zarr-indexing/tests/test_chunk_resolution.py @@ -0,0 +1,521 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING + +import numpy as np +from zarr.core.chunk_grids import ChunkGrid, FixedDimension, VaryingDimension + +from zarr_indexing import chunk_resolution +from zarr_indexing.chunk_resolution import iter_chunk_transforms, sub_transform_to_selections +from zarr_indexing.domain import IndexDomain +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap +from zarr_indexing.transform import IndexTransform + +if TYPE_CHECKING: + import pytest + + +class TestChunkResolutionIdentity: + def test_single_chunk(self) -> None: + """Array fits in one chunk.""" + t = IndexTransform.from_shape((10,)) + grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=10),)) + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 1 + coords, sub_t, _ = results[0] + assert coords == (0,) + assert sub_t.domain.shape == (10,) + + def test_multiple_chunks_1d(self) -> None: + """1D array spanning 3 chunks.""" + t = IndexTransform.from_shape((30,)) + grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=30),)) + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 3 + coords_list = [r[0] for r in results] + assert (0,) in coords_list + assert (1,) in coords_list + assert (2,) in coords_list + + def test_multiple_chunks_2d(self) -> None: + """2D array spanning 2x3 chunks.""" + t = IndexTransform.from_shape((20, 30)) + grid = ChunkGrid( + dimensions=( + FixedDimension(size=10, extent=20), + FixedDimension(size=10, extent=30), + ) + ) + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 6 + coords_list = [r[0] for r in results] + assert (0, 0) in coords_list + assert (1, 2) in coords_list + + +class TestChunkResolutionSliced: + def test_slice_within_chunk(self) -> None: + """Slice that falls within a single chunk.""" + # Chunk resolution consumes zero-origin transforms: the I/O layer + # normalizes preserved (user-facing) domains via translate_domain_to + # before resolving, so mirror that contract here. + t = IndexTransform.from_shape((100,))[5:8].translate_domain_to((0,)) + grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=100),)) + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 1 + coords, sub_t, _ = results[0] + assert coords == (0,) + assert isinstance(sub_t.output[0], DimensionMap) + assert sub_t.output[0].offset == 5 + + def test_slice_across_chunks(self) -> None: + """Slice that spans two chunks.""" + t = IndexTransform.from_shape((100,))[8:15] + grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=100),)) + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 2 + coords_list = [r[0] for r in results] + assert (0,) in coords_list + assert (1,) in coords_list + + +class TestChunkResolutionConstant: + def test_integer_index(self) -> None: + """Integer index produces constant map — single chunk per constant dim.""" + t = IndexTransform.from_shape((100, 100))[25, :] + grid = ChunkGrid( + dimensions=( + FixedDimension(size=10, extent=100), + FixedDimension(size=10, extent=100), + ) + ) + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 10 + for coords, _, _ in results: + assert coords[0] == 2 + + +class TestChunkResolutionArray: + def test_array_index(self) -> None: + """Array index map — chunks determined by array values.""" + idx = np.array([5, 15, 25], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=idx),), + ) + grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=30),)) + results = list(iter_chunk_transforms(t, grid._dimensions)) + coords_list = [r[0] for r in results] + assert (0,) in coords_list + assert (1,) in coords_list + assert (2,) in coords_list + + +class TestChunkResolutionSorted1D: + def test_matches_general_resolution_for_randomized_sorted_selections( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """Direct partitioning matches the original resolver across varied inputs.""" + rng = np.random.default_rng(0) + grids = ( + ChunkGrid(dimensions=(FixedDimension(size=7, extent=30),)), + ChunkGrid(dimensions=(VaryingDimension(edges=(3, 4, 8, 5, 10), extent=30),)), + ) + + for grid in grids: + for _ in range(50): + idx = np.sort(rng.integers(0, 30, size=int(rng.integers(1, 80)))).astype(np.intp) + transform = IndexTransform.from_shape((30,)).vindex[idx] + direct = list(iter_chunk_transforms(transform, grid._dimensions)) + + with monkeypatch.context() as context: + context.setattr( + chunk_resolution, + "_one_dimensional_correlated_array_map", + lambda _transform: None, + ) + general = list(iter_chunk_transforms(transform, grid._dimensions)) + + assert [result[0] for result in direct] == [result[0] for result in general] + for direct_result, general_result in zip(direct, general, strict=True): + _, direct_t, direct_out = direct_result + _, general_t, general_out = general_result + assert direct_t.domain == general_t.domain + + direct_chunk_sel, direct_out_sel, direct_drop = sub_transform_to_selections( + direct_t, direct_out + ) + general_chunk_sel, general_out_sel, general_drop = sub_transform_to_selections( + general_t, general_out + ) + assert direct_drop == general_drop + np.testing.assert_array_equal(direct_chunk_sel[0], general_chunk_sel[0]) + np.testing.assert_array_equal(direct_out_sel[0], general_out_sel[0]) + + def test_sorted_vindex_partitions_chunks_without_intersection( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """Sorted vectorized coordinates are sliced directly per touched chunk.""" + idx = np.array([0, 3, 4, 4, 9, 11], dtype=np.intp) + t = IndexTransform.from_shape((12,)).vindex[idx] + grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=12),)) + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + assert [result[0] for result in results] == [(0,), (1,), (2,)] + assert calls["n"] == 0 + + expected_chunk_indices = ([0, 3], [0, 0], [1, 3]) + expected_out_indices = ([0, 1], [2, 3], [4, 5]) + for result, expected_chunk, expected_out in zip( + results, expected_chunk_indices, expected_out_indices, strict=True + ): + _, sub_t, out_indices = result + chunk_sel, out_sel, drop_axes = sub_transform_to_selections(sub_t, out_indices) + np.testing.assert_array_equal(chunk_sel[0], expected_chunk) + np.testing.assert_array_equal(out_sel[0], expected_out) + assert drop_axes == () + + def test_sorted_array_map_preserves_offset_and_stride(self) -> None: + """Storage partitioning retains the ArrayMap's offset and stride.""" + t = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=( + ArrayMap( + index_array=np.array([0, 1, 2], dtype=np.intp), + offset=1, + stride=3, + ), + ), + ) + grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=8),)) + + results = list(iter_chunk_transforms(t, grid._dimensions)) + + assert [result[0] for result in results] == [(0,), (1,)] + expected_chunk_indices = ([1], [0, 3]) + expected_out_indices = ([0], [1, 2]) + for result, expected_chunk, expected_out in zip( + results, expected_chunk_indices, expected_out_indices, strict=True + ): + _, sub_t, out_indices = result + chunk_sel, out_sel, _ = sub_transform_to_selections(sub_t, out_indices) + np.testing.assert_array_equal(chunk_sel[0], expected_chunk) + np.testing.assert_array_equal(out_sel[0], expected_out) + + def test_sorted_vindex_with_varying_chunks(self) -> None: + """Touched-boundary searches also support a non-uniform 1-D grid.""" + idx = np.array([0, 1, 2, 3, 5, 9], dtype=np.intp) + t = IndexTransform.from_shape((10,)).vindex[idx] + grid = ChunkGrid(dimensions=(VaryingDimension(edges=(2, 3, 5), extent=10),)) + + results = list(iter_chunk_transforms(t, grid._dimensions)) + + assert [result[0] for result in results] == [(0,), (1,), (2,)] + expected_chunk_indices = ([0, 1], [0, 1], [0, 4]) + for result, expected_chunk in zip(results, expected_chunk_indices, strict=True): + _, sub_t, out_indices = result + chunk_sel, _, _ = sub_transform_to_selections(sub_t, out_indices) + np.testing.assert_array_equal(chunk_sel[0], expected_chunk) + + def test_sorted_vindex_with_zero_sized_dimension_uses_general_resolution( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """A zero-sized grid cannot be partitioned by touched boundaries.""" + t = IndexTransform.from_shape((10,)).vindex[np.array([1], dtype=np.intp)] + grid = ChunkGrid(dimensions=(FixedDimension(size=0, extent=10),)) + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + assert results == [] + assert calls["n"] == 1 + + def test_unsorted_vindex_uses_general_resolution(self, monkeypatch: pytest.MonkeyPatch) -> None: + """Unsorted coordinates continue through the general intersection logic.""" + t = IndexTransform.from_shape((12,)).vindex[np.array([9, 0, 4], dtype=np.intp)] + grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=12),)) + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + assert [result[0] for result in results] == [(0,), (1,), (2,)] + assert calls["n"] == 3 + + def test_sorted_oindex_uses_general_resolution(self, monkeypatch: pytest.MonkeyPatch) -> None: + """Orthogonal ArrayMaps retain their existing domain-aware resolution.""" + t = IndexTransform.from_shape((12,)).oindex[np.array([0, 4, 9], dtype=np.intp)] + grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=12),)) + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + assert [result[0] for result in results] == [(0,), (1,), (2,)] + assert calls["n"] == 3 + + +def _count_intersect_calls(monkeypatch: pytest.MonkeyPatch) -> dict[str, int]: + """Wrap `IndexTransform.intersect` with a call counter. + + Returns a mutable dict whose `"n"` entry is the number of times + `intersect` is invoked. Used to assert that candidate-chunk enumeration is + proportional to the *touched* chunks, not the dense bounding box between the + min and max touched chunk. + """ + calls = {"n": 0} + original = IndexTransform.intersect + + def counting(self: IndexTransform, output_domain: IndexDomain) -> object: + calls["n"] += 1 + return original(self, output_domain) + + monkeypatch.setattr(IndexTransform, "intersect", counting) + return calls + + +class TestChunkResolutionTouchedOnly: + """`iter_chunk_transforms` must enumerate only the chunks a fancy selection + actually touches — never the dense `range(min_chunk, max_chunk + 1)` bounding + box. These guard against a regression to bounding-box enumeration, whose cost + scales with grid size rather than with the number of selected coordinates. + """ + + def test_1d_sparse_vindex_enumerates_only_touched_chunks( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """Two far-apart coordinates on a 1000-chunk grid touch exactly 2 chunks. + + A dense bounding-box enumeration would intersect ~1000 candidate chunks; + touched-only enumeration intersects exactly 2. + """ + # 4000 elements, chunk size 4 -> 1000 chunks. coords 1 and 3997 land in + # chunk 0 and chunk 999 respectively (998 empty chunks between them). + grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=4000),)) + t = IndexTransform.from_shape((4000,)).vindex[np.array([1, 3997], dtype=np.intp)] + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + coords = sorted(r[0] for r in results) + assert coords == [(0,), (999,)] + # Sorted 1-D coordinates are partitioned directly, without intersecting + # either the touched chunks or the 998 empty chunks between them. + assert calls["n"] == 0 + + def test_2d_orthogonal_enumerates_only_touched_chunks( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """Orthogonal outer product of two 2-coordinate arrays touches 2x2 chunks. + + Per-dimension distinct touched chunks: {0, 999} on each axis. The outer + product is 2*2 = 4 candidate chunks (all survive), versus ~1e6 for a + dense 1000x1000 bounding box. + """ + grid = ChunkGrid( + dimensions=( + FixedDimension(size=4, extent=4000), + FixedDimension(size=4, extent=4000), + ) + ) + t = IndexTransform.from_shape((4000, 4000)).oindex[ + np.array([1, 3997], dtype=np.intp), np.array([2, 3998], dtype=np.intp) + ] + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + coords = sorted(r[0] for r in results) + assert coords == [(0, 0), (0, 999), (999, 0), (999, 999)] + assert calls["n"] == 4 + + def test_2d_correlated_vindex_enumerates_joint_touched_chunks( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """Two correlated (vindex) coordinate arrays scatter to 2 diagonal chunks. + + The two points (1, 2) and (3997, 3998) touch chunks (0, 0) and + (999, 999). Correlated coordinate arrays are grouped *jointly*, so + enumeration intersects exactly the 2 touched chunks — never the 2x2 + cartesian product of per-dimension distinct chunks, and never the dense + 1e6 grid. + """ + grid = ChunkGrid( + dimensions=( + FixedDimension(size=4, extent=4000), + FixedDimension(size=4, extent=4000), + ) + ) + t = IndexTransform.from_shape((4000, 4000)).vindex[ + np.array([1, 3997], dtype=np.intp), np.array([2, 3998], dtype=np.intp) + ] + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + coords = sorted(r[0] for r in results) + assert coords == [(0, 0), (999, 999)] + assert calls["n"] == 2 + + def test_2d_correlated_vindex_diagonal_is_linear_in_points( + self, monkeypatch: pytest.MonkeyPatch + ) -> None: + """A diagonal of P correlated points touches P chunks with O(P) intersections. + + Enumerating the cartesian product of per-dimension distinct chunk sets + would cost P**2 intersections (2500 here) — quadratic in the number of + selected points for the scattered selections of zarr-python gh-4174. + Joint grouping keeps resolution work proportional to the touched chunks. + """ + p = 50 + grid = ChunkGrid( + dimensions=( + FixedDimension(size=4, extent=4000), + FixedDimension(size=4, extent=4000), + ) + ) + # point i lands in chunk (2i, 2i): all per-dimension chunks distinct + coords_1d = np.arange(p, dtype=np.intp) * 8 + t = IndexTransform.from_shape((4000, 4000)).vindex[coords_1d, coords_1d] + + calls = _count_intersect_calls(monkeypatch) + results = list(iter_chunk_transforms(t, grid._dimensions)) + + assert sorted(r[0] for r in results) == [(2 * i, 2 * i) for i in range(p)] + assert calls["n"] == p + + +class TestSubTransformToSelections: + def test_constant_map(self) -> None: + """ConstantMap produces int selection + drop axis.""" + t = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(ConstantMap(offset=5),), + ) + chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) + assert chunk_sel == (5,) + assert out_sel == () + assert drop_axes == () + + def test_dimension_map_stride_1(self) -> None: + """DimensionMap with stride=1 produces contiguous slice.""" + t = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(DimensionMap(input_dimension=0, offset=3, stride=1),), + ) + chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) + assert chunk_sel == (slice(3, 13, 1),) + assert out_sel == (slice(0, 10),) + assert drop_axes == () + + def test_dimension_map_strided(self) -> None: + """DimensionMap with stride>1 produces strided slice.""" + t = IndexTransform( + domain=IndexDomain.from_shape((5,)), + output=(DimensionMap(input_dimension=0, offset=2, stride=3),), + ) + chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) + assert chunk_sel == (slice(2, 17, 3),) + assert out_sel == (slice(0, 5),) + assert drop_axes == () + + def test_array_map(self) -> None: + """ArrayMap produces integer array selection.""" + arr = np.array([1, 5, 9], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=arr, offset=0, stride=1),), + ) + chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) + assert isinstance(chunk_sel[0], np.ndarray) + np.testing.assert_array_equal(chunk_sel[0], arr) + # Without chunk_mask, out_sel falls back to domain-based slices + assert out_sel == (slice(0, 3),) + assert drop_axes == () + + def test_array_map_with_offset_stride(self) -> None: + """ArrayMap with offset and stride computes storage coords.""" + arr = np.array([0, 1, 2], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=arr, offset=10, stride=5),), + ) + chunk_sel, _out_sel, drop_axes = sub_transform_to_selections(t) + assert isinstance(chunk_sel[0], np.ndarray) + np.testing.assert_array_equal(chunk_sel[0], np.array([10, 15, 20])) + assert drop_axes == () + + def test_mixed_maps_2d(self) -> None: + """Mix of ConstantMap and DimensionMap.""" + t = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=( + ConstantMap(offset=5), + DimensionMap(input_dimension=0, offset=0, stride=1), + ), + ) + chunk_sel, _out_sel, drop_axes = sub_transform_to_selections(t) + assert chunk_sel[0] == 5 + assert chunk_sel[1] == slice(0, 10, 1) + # drop_axes is empty — integer in chunk_sel naturally drops the dim via numpy + assert drop_axes == () + + +class TestChunkResolutionArrayMapFlavours: + """Chunk resolution must yield outer-product (np.ix_) selectors for + orthogonal ArrayMaps and shared flat-scatter selectors for correlated ones, + and must return early for empty fancy selections.""" + + def test_empty_array_selection_yields_nothing(self) -> None: + """An empty ArrayMap selection produces no chunk transforms (no crash).""" + t = IndexTransform( + domain=IndexDomain.from_shape((0,)), + output=(ArrayMap(index_array=np.array([], dtype=np.intp)),), + ) + grid = ChunkGrid(dimensions=(FixedDimension(size=3, extent=10),)) + assert list(iter_chunk_transforms(t, grid._dimensions)) == [] + + def test_orthogonal_outer_product_selectors(self) -> None: + """Two independent arrays produce np.ix_-style (mesh) chunk/out selectors.""" + t = IndexTransform.from_shape((10, 10)).oindex[np.array([1, 3]), np.array([2, 4, 6])] + grid = ChunkGrid( + dimensions=(FixedDimension(size=10, extent=10), FixedDimension(size=10, extent=10)) + ) + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 1 + _coords, sub_t, out_indices = results[0] + chunk_sel, out_sel, drop_axes = sub_transform_to_selections(sub_t, out_indices) + # np.ix_ produces one 2-D open-mesh selector per axis, for both sides. + assert len(chunk_sel) == 2 + assert len(out_sel) == 2 + assert isinstance(chunk_sel[0], np.ndarray) + assert isinstance(chunk_sel[1], np.ndarray) + assert chunk_sel[0].shape == (2, 1) + assert chunk_sel[1].shape == (1, 3) + assert drop_axes == () + + def test_correlated_scatter_with_residual_slice(self) -> None: + """Correlated arrays + a residual slice dim scatter through a single flat + index whose shape matches the (points, slice) block read from the chunk.""" + t = IndexTransform.from_shape((4, 3, 5)).vindex[np.array([1, 3]), np.array([2, 0])] + grid = ChunkGrid( + dimensions=( + FixedDimension(size=4, extent=4), + FixedDimension(size=3, extent=3), + FixedDimension(size=5, extent=5), + ) + ) + # One chunk holds everything: both points survive, slice dim spans [0,5). + results = list(iter_chunk_transforms(t, grid._dimensions)) + assert len(results) == 1 + _coords, sub_t, out_indices = results[0] + chunk_sel, out_sel, _drop = sub_transform_to_selections(sub_t, out_indices) + # Chunk side: flat coordinate arrays for the two correlated dims plus a + # slice for the residual dim. + assert len(chunk_sel) == 3 + np.testing.assert_array_equal(np.asarray(chunk_sel[0]), [1, 3]) + np.testing.assert_array_equal(np.asarray(chunk_sel[1]), [2, 0]) + assert chunk_sel[2] == slice(0, 5, 1) + # Output side: a single flat scatter index of shape (points, slice) = (2, 5). + assert len(out_sel) == 1 + assert np.asarray(out_sel[0]).shape == (2, 5) diff --git a/packages/zarr-indexing/tests/test_composition.py b/packages/zarr-indexing/tests/test_composition.py new file mode 100644 index 0000000000..dd92f59b80 --- /dev/null +++ b/packages/zarr-indexing/tests/test_composition.py @@ -0,0 +1,166 @@ +from __future__ import annotations + +import numpy as np +import pytest + +from zarr_indexing.composition import compose +from zarr_indexing.domain import IndexDomain +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap +from zarr_indexing.transform import IndexTransform + + +class TestComposeConstantInner: + """Inner = constant. Result is always constant.""" + + def test_constant_inner_any_outer(self) -> None: + outer = IndexTransform.from_shape((5,)) + inner = IndexTransform( + domain=IndexDomain.from_shape((5,)), + output=(ConstantMap(offset=42),), + ) + result = compose(outer, inner) + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == 42 + + +class TestComposeDimensionInner: + """Inner = DimensionMap.""" + + def test_dimension_inner_constant_outer(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(ConstantMap(offset=5),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(DimensionMap(input_dimension=0, offset=10, stride=3),), + ) + result = compose(outer, inner) + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == 25 + + def test_dimension_inner_dimension_outer(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(DimensionMap(input_dimension=0, offset=5, stride=2),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(DimensionMap(input_dimension=0, offset=10, stride=3),), + ) + result = compose(outer, inner) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == 25 + assert result.output[0].stride == 6 + assert result.output[0].input_dimension == 0 + + def test_dimension_inner_array_outer(self) -> None: + arr = np.array([0, 2, 4], dtype=np.intp) + outer = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=arr, offset=5, stride=2),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(DimensionMap(input_dimension=0, offset=10, stride=3),), + ) + result = compose(outer, inner) + assert isinstance(result.output[0], ArrayMap) + assert result.output[0].offset == 25 + assert result.output[0].stride == 6 + np.testing.assert_array_equal(result.output[0].index_array, arr) + + +class TestComposeArrayInner: + """Inner = ArrayMap.""" + + def test_array_inner_constant_outer(self) -> None: + inner_arr = np.array([10, 20, 30], dtype=np.intp) + outer = IndexTransform( + domain=IndexDomain.from_shape((5,)), + output=(ConstantMap(offset=1),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=inner_arr, offset=0, stride=1),), + ) + result = compose(outer, inner) + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == 20 + + def test_array_inner_array_outer(self) -> None: + outer_arr = np.array([0, 2, 1], dtype=np.intp) + inner_arr = np.array([10, 20, 30], dtype=np.intp) + outer = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=outer_arr, offset=0, stride=1),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=inner_arr, offset=0, stride=1),), + ) + result = compose(outer, inner) + assert isinstance(result.output[0], ArrayMap) + expected = np.array([10, 30, 20], dtype=np.intp) + np.testing.assert_array_equal(result.output[0].index_array, expected) + + +class TestComposeMultiDim: + def test_2d_identity_compose(self) -> None: + a = IndexTransform.from_shape((10, 20)) + b = IndexTransform.from_shape((10, 20)) + result = compose(a, b) + assert result.domain.shape == (10, 20) + for i in range(2): + m = result.output[i] + assert isinstance(m, DimensionMap) + assert m.input_dimension == i + assert m.offset == 0 + assert m.stride == 1 + + def test_mixed_map_types(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=( + ConstantMap(offset=5), + DimensionMap(input_dimension=0, offset=0, stride=1), + ), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((10, 10)), + output=( + DimensionMap(input_dimension=0, offset=2, stride=3), + DimensionMap(input_dimension=1, offset=0, stride=1), + ), + ) + result = compose(outer, inner) + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == 17 + assert isinstance(result.output[1], DimensionMap) + assert result.output[1].input_dimension == 0 + assert result.output[1].offset == 0 + assert result.output[1].stride == 1 + + def test_rank_mismatch_raises(self) -> None: + outer = IndexTransform.from_shape((10,)) + inner = IndexTransform.from_shape((10, 20)) + with pytest.raises(ValueError, match="rank"): + compose(outer, inner) + + +class TestComposeChain: + def test_three_transforms(self) -> None: + a = IndexTransform.from_shape((100,)) + b = IndexTransform( + domain=IndexDomain.from_shape((100,)), + output=(DimensionMap(input_dimension=0, offset=10, stride=1),), + ) + c = IndexTransform( + domain=IndexDomain.from_shape((100,)), + output=(DimensionMap(input_dimension=0, offset=5, stride=2),), + ) + bc = compose(b, c) + abc = compose(a, bc) + assert isinstance(abc.output[0], DimensionMap) + assert abc.output[0].offset == 25 + assert abc.output[0].stride == 2 diff --git a/packages/zarr-indexing/tests/test_conformance.py b/packages/zarr-indexing/tests/test_conformance.py new file mode 100644 index 0000000000..207a9d8236 --- /dev/null +++ b/packages/zarr-indexing/tests/test_conformance.py @@ -0,0 +1,55 @@ +"""ndsel conformance corpus harness. + +Runs the vendored, language-agnostic ndsel fixtures (see +`tests/conformance/PROVENANCE.md`) against this package's message layer +(`zarr_indexing.messages`). An implementation is conformant iff: + +- for every *success* fixture, `normalize_ndsel(input)` equals the fixture's + `normalized` value by structural JSON equality; +- for every *error* fixture, `normalize_ndsel(input)` is rejected with an + `NdselError` carrying the fixture's `error` reason code. +""" + +from __future__ import annotations + +import json +from pathlib import Path +from typing import Any + +import pytest + +from zarr_indexing.messages import NdselError, normalize_ndsel + +_CONFORMANCE_DIR = Path(__file__).parent / "conformance" + + +def _load_cases() -> list[tuple[str, dict[str, Any]]]: + cases: list[tuple[str, dict[str, Any]]] = [] + for path in sorted(_CONFORMANCE_DIR.glob("*.json")): + data = json.loads(path.read_text()) + cases.extend((f"{path.stem}::{case['name']}", case) for case in data) + return cases + + +_CASES = _load_cases() +_SUCCESS = [(name, c) for name, c in _CASES if "normalized" in c] +_ERROR = [(name, c) for name, c in _CASES if "error" in c] + + +def test_corpus_is_present() -> None: + # Guard against an empty/missing vendored corpus silently passing. + assert len(_SUCCESS) > 0 + assert len(_ERROR) > 0 + + +@pytest.mark.parametrize(("name", "case"), _SUCCESS, ids=[name for name, _ in _SUCCESS]) +def test_success_fixture(name: str, case: dict[str, Any]) -> None: + result = normalize_ndsel(case["input"]) + assert result == case["normalized"] + + +@pytest.mark.parametrize(("name", "case"), _ERROR, ids=[name for name, _ in _ERROR]) +def test_error_fixture(name: str, case: dict[str, Any]) -> None: + with pytest.raises(NdselError) as excinfo: + normalize_ndsel(case["input"]) + assert excinfo.value.reason == case["error"] diff --git a/packages/zarr-indexing/tests/test_domain.py b/packages/zarr-indexing/tests/test_domain.py new file mode 100644 index 0000000000..9664a0b08a --- /dev/null +++ b/packages/zarr-indexing/tests/test_domain.py @@ -0,0 +1,202 @@ +from __future__ import annotations + +import pytest + +from zarr_indexing.domain import IndexDomain + + +class TestIndexDomainConstruction: + def test_from_shape(self) -> None: + d = IndexDomain.from_shape((10, 20)) + assert d.inclusive_min == (0, 0) + assert d.exclusive_max == (10, 20) + assert d.ndim == 2 + assert d.origin == (0, 0) + assert d.shape == (10, 20) + + def test_from_shape_0d(self) -> None: + d = IndexDomain.from_shape(()) + assert d.ndim == 0 + assert d.shape == () + + def test_non_zero_origin(self) -> None: + d = IndexDomain(inclusive_min=(5, 10), exclusive_max=(15, 30)) + assert d.origin == (5, 10) + assert d.shape == (10, 20) + assert d.ndim == 2 + + def test_validation_mismatched_lengths(self) -> None: + with pytest.raises(ValueError, match="same length"): + IndexDomain(inclusive_min=(0,), exclusive_max=(10, 20)) + + def test_validation_min_greater_than_max(self) -> None: + with pytest.raises(ValueError, match="inclusive_min must be <="): + IndexDomain(inclusive_min=(10,), exclusive_max=(5,)) + + def test_empty_domain(self) -> None: + d = IndexDomain(inclusive_min=(5,), exclusive_max=(5,)) + assert d.shape == (0,) + + def test_labels(self) -> None: + d = IndexDomain(inclusive_min=(0, 0), exclusive_max=(10, 20), labels=("x", "y")) + assert d.labels == ("x", "y") + + def test_labels_none(self) -> None: + d = IndexDomain.from_shape((10,)) + assert d.labels is None + + +class TestIndexDomainContains: + def test_contains_inside(self) -> None: + d = IndexDomain.from_shape((10, 20)) + assert d.contains((0, 0)) is True + assert d.contains((9, 19)) is True + assert d.contains((5, 10)) is True + + def test_contains_outside(self) -> None: + d = IndexDomain.from_shape((10, 20)) + assert d.contains((10, 0)) is False + assert d.contains((-1, 0)) is False + assert d.contains((0, 20)) is False + + def test_contains_non_zero_origin(self) -> None: + d = IndexDomain(inclusive_min=(5,), exclusive_max=(10,)) + assert d.contains((5,)) is True + assert d.contains((9,)) is True + assert d.contains((4,)) is False + assert d.contains((10,)) is False + + def test_contains_wrong_ndim(self) -> None: + d = IndexDomain.from_shape((10, 20)) + assert d.contains((5,)) is False + + def test_contains_domain_inside(self) -> None: + outer = IndexDomain.from_shape((10, 20)) + inner = IndexDomain(inclusive_min=(2, 3), exclusive_max=(8, 15)) + assert outer.contains_domain(inner) is True + + def test_contains_domain_outside(self) -> None: + outer = IndexDomain.from_shape((10, 20)) + inner = IndexDomain(inclusive_min=(2, 3), exclusive_max=(11, 15)) + assert outer.contains_domain(inner) is False + + def test_contains_domain_wrong_ndim(self) -> None: + outer = IndexDomain.from_shape((10, 20)) + inner = IndexDomain.from_shape((5,)) + assert outer.contains_domain(inner) is False + + +class TestIndexDomainIntersect: + def test_overlapping(self) -> None: + a = IndexDomain(inclusive_min=(0, 0), exclusive_max=(10, 10)) + b = IndexDomain(inclusive_min=(5, 5), exclusive_max=(15, 15)) + result = a.intersect(b) + assert result is not None + assert result.inclusive_min == (5, 5) + assert result.exclusive_max == (10, 10) + + def test_disjoint(self) -> None: + a = IndexDomain(inclusive_min=(0,), exclusive_max=(5,)) + b = IndexDomain(inclusive_min=(10,), exclusive_max=(15,)) + assert a.intersect(b) is None + + def test_touching_boundary(self) -> None: + a = IndexDomain(inclusive_min=(0,), exclusive_max=(5,)) + b = IndexDomain(inclusive_min=(5,), exclusive_max=(10,)) + assert a.intersect(b) is None + + def test_contained(self) -> None: + a = IndexDomain.from_shape((20,)) + b = IndexDomain(inclusive_min=(5,), exclusive_max=(10,)) + result = a.intersect(b) + assert result is not None + assert result.inclusive_min == (5,) + assert result.exclusive_max == (10,) + + def test_wrong_ndim(self) -> None: + a = IndexDomain.from_shape((10,)) + b = IndexDomain.from_shape((10, 20)) + with pytest.raises(ValueError, match="different ranks"): + a.intersect(b) + + +class TestIndexDomainTranslate: + def test_translate_positive(self) -> None: + d = IndexDomain.from_shape((10, 20)) + result = d.translate((5, 10)) + assert result.inclusive_min == (5, 10) + assert result.exclusive_max == (15, 30) + + def test_translate_negative(self) -> None: + d = IndexDomain(inclusive_min=(10, 20), exclusive_max=(30, 40)) + result = d.translate((-10, -20)) + assert result.inclusive_min == (0, 0) + assert result.exclusive_max == (20, 20) + + def test_translate_wrong_length(self) -> None: + d = IndexDomain.from_shape((10,)) + with pytest.raises(ValueError, match="same length"): + d.translate((1, 2)) + + +class TestIndexDomainNarrow: + def test_narrow_slice(self) -> None: + d = IndexDomain.from_shape((10, 20)) + result = d.narrow((slice(2, 8), slice(5, 15))) + assert result.inclusive_min == (2, 5) + assert result.exclusive_max == (8, 15) + + def test_narrow_int(self) -> None: + d = IndexDomain.from_shape((10, 20)) + result = d.narrow((3, slice(None))) + assert result.inclusive_min == (3, 0) + assert result.exclusive_max == (4, 20) + + def test_narrow_ellipsis(self) -> None: + d = IndexDomain.from_shape((10, 20, 30)) + result = d.narrow((slice(1, 5), ...)) + assert result.inclusive_min == (1, 0, 0) + assert result.exclusive_max == (5, 20, 30) + + def test_narrow_slice_none(self) -> None: + d = IndexDomain.from_shape((10,)) + result = d.narrow((slice(None),)) + assert result == d + + def test_narrow_non_zero_origin(self) -> None: + d = IndexDomain(inclusive_min=(10,), exclusive_max=(20,)) + result = d.narrow((slice(12, 18),)) + assert result.inclusive_min == (12,) + assert result.exclusive_max == (18,) + + def test_narrow_int_out_of_bounds(self) -> None: + d = IndexDomain.from_shape((10,)) + with pytest.raises(IndexError, match="out of bounds"): + d.narrow((10,)) + + def test_narrow_int_below_origin(self) -> None: + d = IndexDomain(inclusive_min=(5,), exclusive_max=(10,)) + with pytest.raises(IndexError, match="out of bounds"): + d.narrow((4,)) + + def test_narrow_clamps_to_domain(self) -> None: + d = IndexDomain.from_shape((10,)) + result = d.narrow((slice(-5, 100),)) + assert result.inclusive_min == (0,) + assert result.exclusive_max == (10,) + + def test_narrow_bare_slice(self) -> None: + d = IndexDomain.from_shape((10,)) + result = d.narrow(slice(2, 8)) + assert result.inclusive_min == (2,) + assert result.exclusive_max == (8,) + + def test_narrow_too_many_indices(self) -> None: + d = IndexDomain.from_shape((10,)) + with pytest.raises(IndexError, match="too many indices"): + d.narrow((1, 2)) + + def test_narrow_step_not_one(self) -> None: + d = IndexDomain.from_shape((10,)) + with pytest.raises(IndexError, match="step=1"): + d.narrow((slice(0, 10, 2),)) diff --git a/packages/zarr-indexing/tests/test_json.py b/packages/zarr-indexing/tests/test_json.py new file mode 100644 index 0000000000..42b59b2c30 --- /dev/null +++ b/packages/zarr-indexing/tests/test_json.py @@ -0,0 +1,336 @@ +from __future__ import annotations + +import numpy as np +import pytest + +from zarr_indexing.domain import IndexDomain +from zarr_indexing.json import ( + IndexTransformJSON, + index_domain_from_json, + index_domain_to_json, + index_transform_from_json, + index_transform_to_json, + output_index_map_from_json, + output_index_map_to_json, +) +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap +from zarr_indexing.transform import IndexTransform + + +def _maps_equal(a: object, b: object) -> bool: + if type(a) is not type(b): + return False + if isinstance(a, ConstantMap): + assert isinstance(b, ConstantMap) + return a.offset == b.offset + if isinstance(a, DimensionMap): + assert isinstance(b, DimensionMap) + return (a.input_dimension, a.offset, a.stride) == (b.input_dimension, b.offset, b.stride) + assert isinstance(a, ArrayMap) + assert isinstance(b, ArrayMap) + return ( + a.offset == b.offset + and a.stride == b.stride + and a.input_dimension == b.input_dimension + and np.array_equal(a.index_array, b.index_array) + ) + + +def _transforms_equal(a: IndexTransform, b: IndexTransform) -> bool: + """Structural equality that compares `ArrayMap` index arrays element-wise + (`IndexTransform`'s dataclass `__eq__` cannot, as numpy `==` is ambiguous).""" + return ( + a.domain == b.domain + and len(a.output) == len(b.output) + and all(_maps_equal(x, y) for x, y in zip(a.output, b.output, strict=True)) + ) + + +class TestIndexDomainJSON: + def test_roundtrip(self) -> None: + domain = IndexDomain(inclusive_min=(2, 5), exclusive_max=(10, 20)) + json = index_domain_to_json(domain) + assert json == { + "input_inclusive_min": [2, 5], + "input_exclusive_max": [10, 20], + "input_labels": ["", ""], + } + restored = index_domain_from_json(json) + assert restored == domain + + def test_with_labels(self) -> None: + domain = IndexDomain(inclusive_min=(0, 0), exclusive_max=(10, 20), labels=("x", "y")) + json = index_domain_to_json(domain) + assert json["input_labels"] == ["x", "y"] + restored = index_domain_from_json(json) + assert restored.labels == ("x", "y") + + def test_without_labels_emits_empty_and_round_trips_to_none(self) -> None: + domain = IndexDomain.from_shape((5,)) + json = index_domain_to_json(domain) + # Canonical form always writes labels; an unlabeled domain gets [""]*rank. + assert json["input_labels"] == [""] + restored = index_domain_from_json(json) + assert restored.labels is None + + def test_zero_origin(self) -> None: + domain = IndexDomain.from_shape((10, 20, 30)) + json = index_domain_to_json(domain) + assert json == { + "input_inclusive_min": [0, 0, 0], + "input_exclusive_max": [10, 20, 30], + "input_labels": ["", "", ""], + } + assert index_domain_from_json(json) == domain + + +class TestOutputIndexMapJSON: + def test_constant(self) -> None: + m = ConstantMap(offset=42) + json = output_index_map_to_json(m) + assert json == {"offset": 42} + restored = output_index_map_from_json(json) + assert isinstance(restored, ConstantMap) + assert restored.offset == 42 + + def test_constant_zero(self) -> None: + m = ConstantMap(offset=0) + json = output_index_map_to_json(m) + assert json == {"offset": 0} + restored = output_index_map_from_json(json) + assert isinstance(restored, ConstantMap) + assert restored.offset == 0 + + def test_dimension(self) -> None: + m = DimensionMap(input_dimension=1, offset=10, stride=3) + json = output_index_map_to_json(m) + assert json == {"offset": 10, "stride": 3, "input_dimension": 1} + restored = output_index_map_from_json(json) + assert isinstance(restored, DimensionMap) + assert restored.input_dimension == 1 + assert restored.offset == 10 + assert restored.stride == 3 + + def test_dimension_stride_1_written(self) -> None: + """Canonical form writes stride even at its default of 1.""" + m = DimensionMap(input_dimension=0) + json = output_index_map_to_json(m) + assert json == {"offset": 0, "stride": 1, "input_dimension": 0} + restored = output_index_map_from_json(json) + assert isinstance(restored, DimensionMap) + assert restored.stride == 1 + + def test_array(self) -> None: + arr = np.array([1, 5, 9], dtype=np.intp) + m = ArrayMap(index_array=arr, offset=2, stride=3) + json = output_index_map_to_json(m) + # Canonical: stride/offset present, index_array_bounds present, and + # no input_dimension (ndsel/TensorStore reject it beside index_array). + assert json == { + "offset": 2, + "stride": 3, + "index_array": [1, 5, 9], + "index_array_bounds": ["-inf", "+inf"], + } + restored = output_index_map_from_json(json) + assert isinstance(restored, ArrayMap) + np.testing.assert_array_equal(restored.index_array, arr) + assert restored.offset == 2 + assert restored.stride == 3 + + def test_array_stride_1_written(self) -> None: + arr = np.array([0, 1, 2], dtype=np.intp) + m = ArrayMap(index_array=arr) + json = output_index_map_to_json(m) + assert json["stride"] == 1 + restored = output_index_map_from_json(json) + assert isinstance(restored, ArrayMap) + assert restored.stride == 1 + + def test_array_2d(self) -> None: + arr = np.array([[1, 2], [3, 4]], dtype=np.intp) + m = ArrayMap(index_array=arr) + json = output_index_map_to_json(m) + assert json["index_array"] == [[1, 2], [3, 4]] + restored = output_index_map_from_json(json) + assert isinstance(restored, ArrayMap) + np.testing.assert_array_equal(restored.index_array, arr) + + def test_degenerate_singleton_array_collapses_to_constant(self) -> None: + """An all-singleton index_array selects one coordinate -> constant map.""" + m = ArrayMap(index_array=np.array([[4]], dtype=np.intp), offset=1, stride=2) + json = output_index_map_to_json(m) + assert json == {"offset": 1 + 2 * 4} + restored = output_index_map_from_json(json) + assert isinstance(restored, ConstantMap) + assert restored.offset == 9 + + +class TestIndexTransformJSON: + def test_identity(self) -> None: + t = IndexTransform.from_shape((10, 20)) + json = index_transform_to_json(t) + assert json == { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [10, 20], + "input_labels": ["", ""], + "output": [ + {"offset": 0, "stride": 1, "input_dimension": 0}, + {"offset": 0, "stride": 1, "input_dimension": 1}, + ], + } + restored = index_transform_from_json(json) + assert restored.domain == t.domain + assert len(restored.output) == 2 + for orig, rest in zip(t.output, restored.output, strict=True): + assert type(orig) is type(rest) + + def test_sliced(self) -> None: + t = IndexTransform.from_shape((100,))[10:50:2] + json = index_transform_to_json(t) + restored = index_transform_from_json(json) + assert restored.domain.shape == t.domain.shape + assert isinstance(restored.output[0], DimensionMap) + orig = t.output[0] + assert isinstance(orig, DimensionMap) + assert restored.output[0].offset == orig.offset + assert restored.output[0].stride == orig.stride + + def test_with_constant(self) -> None: + t = IndexTransform.from_shape((10, 20))[3] + json = index_transform_to_json(t) + restored = index_transform_from_json(json) + assert isinstance(restored.output[0], ConstantMap) + assert restored.output[0].offset == 3 + assert isinstance(restored.output[1], DimensionMap) + + def test_with_array(self) -> None: + idx = np.array([1, 5, 9], dtype=np.intp) + t = IndexTransform.from_shape((10, 20)).oindex[idx, :] + json = index_transform_to_json(t) + # The oindex array must not carry input_dimension on the wire. + assert "input_dimension" not in json["output"][0] + restored = index_transform_from_json(json) + assert isinstance(restored.output[0], ArrayMap) + # Orthogonal arrays are normalized to full input rank with a singleton + # axis on the dimension they do not vary over. + assert restored.output[0].index_array.shape == (3, 1) + np.testing.assert_array_equal(restored.output[0].index_array, idx.reshape(3, 1)) + # input_dimension is reconstructed from the sole non-singleton axis. + assert restored.output[0].input_dimension == 0 + assert isinstance(restored.output[1], DimensionMap) + + def test_roundtrip_preserves_singleton_axes(self) -> None: + """Full-rank orthogonal arrays keep their singleton axes across JSON.""" + t = IndexTransform.from_shape((10, 20)).oindex[np.array([1, 3]), np.array([2, 4, 6])] + restored = index_transform_from_json(index_transform_to_json(t)) + orig0, orig1 = t.output[0], t.output[1] + rest0, rest1 = restored.output[0], restored.output[1] + assert isinstance(orig0, ArrayMap) + assert isinstance(orig1, ArrayMap) + assert isinstance(rest0, ArrayMap) + assert isinstance(rest1, ArrayMap) + assert rest0.index_array.shape == (2, 1) + assert rest1.index_array.shape == (1, 3) + np.testing.assert_array_equal(rest0.index_array, orig0.index_array) + np.testing.assert_array_equal(rest1.index_array, orig1.index_array) + # Distinct, exclusively-owned axes -> reconstructed as orthogonal. + assert rest0.input_dimension == 0 + assert rest1.input_dimension == 1 + + def test_with_labels(self) -> None: + domain = IndexDomain(inclusive_min=(0, 0), exclusive_max=(10, 20), labels=("x", "y")) + t = IndexTransform.identity(domain) + json = index_transform_to_json(t) + assert json["input_labels"] == ["x", "y"] + restored = index_transform_from_json(json) + assert restored.domain.labels == ("x", "y") + + def test_tensorstore_compatible_format(self) -> None: + """A canonical body loads and round-trips through the engine layer.""" + json: IndexTransformJSON = { + "input_rank": 3, + "input_inclusive_min": [0, 0, 0], + "input_exclusive_max": [100, 200, 3], + "input_labels": ["x", "y", "channel"], + "output": [ + {"offset": 5}, + {"offset": 10, "stride": 2, "input_dimension": 1}, + {"offset": 0, "stride": 1, "index_array": [1, 2, 0]}, + ], + } + t = index_transform_from_json(json) + assert t.domain.shape == (100, 200, 3) + assert t.domain.labels == ("x", "y", "channel") + assert isinstance(t.output[0], ConstantMap) + assert t.output[0].offset == 5 + assert isinstance(t.output[1], DimensionMap) + assert t.output[1].offset == 10 + assert t.output[1].stride == 2 + assert t.output[1].input_dimension == 1 + assert isinstance(t.output[2], ArrayMap) + np.testing.assert_array_equal(t.output[2].index_array, [1, 2, 0]) + + # Roundtrip + json_rt = index_transform_to_json(t) + t_rt = index_transform_from_json(json_rt) + assert t_rt.domain == t.domain + + +class TestCanonicalRoundTrips: + """Round-trip `transform == from(to(transform))`, up to the documented + degenerate-collapse (all-singleton ArrayMap -> ConstantMap).""" + + def test_oindex_multi_axis(self) -> None: + t = IndexTransform.from_shape((10, 20, 30)).oindex[np.array([1, 3]), :, np.array([2, 4, 6])] + rt = index_transform_from_json(index_transform_to_json(t)) + assert _transforms_equal(rt, t) + + def test_oindex_with_slice(self) -> None: + t = IndexTransform.from_shape((10, 20))[2:8].oindex[np.array([3, 5, 7]), :] + rt = index_transform_from_json(index_transform_to_json(t)) + assert _transforms_equal(rt, t) + + def test_vindex(self) -> None: + t = IndexTransform.from_shape((10, 20)).vindex[np.array([1, 3, 5]), np.array([2, 4, 6])] + rt = index_transform_from_json(index_transform_to_json(t)) + assert _transforms_equal(rt, t) + + def test_vindex_with_residual_slice(self) -> None: + t = IndexTransform.from_shape((10, 20, 30)).vindex[np.array([1, 3]), np.array([2, 4]), :] + rt = index_transform_from_json(index_transform_to_json(t)) + assert _transforms_equal(rt, t) + + def test_length1_degenerate_oindex_collapses(self) -> None: + """A length-1 oindex array becomes an all-singleton ArrayMap; the JSON + round-trip collapses it to a ConstantMap (behaviorally identical).""" + t = IndexTransform.from_shape((10, 20)).oindex[np.array([7]), :] + m = t.output[0] + assert isinstance(m, ArrayMap) + assert m.index_array.size == 1 + + rt = index_transform_from_json(index_transform_to_json(t)) + # The degenerate array collapsed to a constant selecting the same cell. + rm = rt.output[0] + assert isinstance(rm, ConstantMap) + assert rm.offset == 7 + # The size-1 input dimension survives, unconsumed, in the domain. + assert rt.domain == t.domain + + def test_slices_and_constants(self) -> None: + t = IndexTransform.from_shape((10, 20, 30))[2:8:2, 5, :] + rt = index_transform_from_json(index_transform_to_json(t)) + assert _transforms_equal(rt, t) + + +def test_infinite_bound_rejected_on_lowering() -> None: + body: IndexTransformJSON = { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [["+inf"]], + "input_labels": [""], + "output": [{"offset": 0, "stride": 1, "input_dimension": 0}], + } + with pytest.raises(ValueError, match="infinite"): + index_transform_from_json(body) diff --git a/packages/zarr-indexing/tests/test_messages.py b/packages/zarr-indexing/tests/test_messages.py new file mode 100644 index 0000000000..14bed66448 --- /dev/null +++ b/packages/zarr-indexing/tests/test_messages.py @@ -0,0 +1,91 @@ +"""Message-layer tests beyond the vendored conformance corpus. + +The corpus (see `test_conformance.py`) covers the desugaring matrix and error +codes. These tests pin behaviors the corpus does not: `normalize` idempotence, +`parse_ndsel`, 64-bit boundary handling, and schema-valid-but-redundant maps. +""" + +from __future__ import annotations + +from typing import Any + +import pytest + +from zarr_indexing.messages import NdselError, normalize_ndsel, parse_ndsel + +_MESSAGES = [ + {"kind": "point", "coords": [4, 7]}, + {"kind": "box", "inclusive_min": [0, 0], "exclusive_max": [3, 4]}, + {"kind": "box", "inclusive_min": [["-inf"], 0], "exclusive_max": [["+inf"], 4]}, + {"kind": "slice", "start": [5], "stop": [10], "step": [2]}, + {"kind": "points", "coords": [[1, 10], [2, 20]]}, + { + "kind": "transform", + "input_inclusive_min": [0], + "input_exclusive_max": [3], + "output": [{"offset": 7}, {"input_dimension": 0, "stride": 2}, {"index_array": [1, 2, 3]}], + }, +] + + +@pytest.mark.parametrize("message", _MESSAGES) +def test_normalize_is_idempotent(message: dict[str, Any]) -> None: + once = normalize_ndsel(message) + twice = normalize_ndsel({"kind": "transform", **once}) + assert twice == once + + +@pytest.mark.parametrize("message", _MESSAGES) +def test_parse_returns_message_unchanged(message: dict[str, Any]) -> None: + assert parse_ndsel(message) == message + + +def test_parse_rejects_invalid() -> None: + with pytest.raises(NdselError) as excinfo: + parse_ndsel({"kind": "slice", "start": [0]}) + assert excinfo.value.reason == "invalid_json" + + +def test_constant_map_drops_redundant_stride() -> None: + # A constant map (no input_dimension, no index_array) is schema-valid even + # with a stray stride; it canonicalizes to offset-only. + result = normalize_ndsel( + {"kind": "transform", "input_rank": 0, "output": [{"offset": 5, "stride": 9}]} + ) + assert result["output"] == [{"offset": 5}] + + +def test_i64_min_and_max_round_trip() -> None: + i64_min, i64_max = -(2**63), 2**63 - 1 + result = normalize_ndsel({"kind": "point", "coords": [i64_min, i64_max]}) + assert result["output"] == [{"offset": i64_min}, {"offset": i64_max}] + + +def test_i64_overflow_rejected() -> None: + with pytest.raises(NdselError) as excinfo: + normalize_ndsel({"kind": "point", "coords": [2**63]}) + assert excinfo.value.reason == "invalid_json" + + +def test_bool_in_output_offset_rejected() -> None: + with pytest.raises(NdselError) as excinfo: + normalize_ndsel({"kind": "transform", "input_rank": 0, "output": [{"offset": True}]}) + assert excinfo.value.reason == "invalid_json" + + +def test_sentinel_not_allowed_in_plain_integer_position() -> None: + with pytest.raises(NdselError) as excinfo: + normalize_ndsel({"kind": "point", "coords": ["+inf"]}) + assert excinfo.value.reason == "invalid_json" + + +def test_not_an_object_rejected() -> None: + with pytest.raises(NdselError) as excinfo: + normalize_ndsel([1, 2, 3]) + assert excinfo.value.reason == "invalid_json" + + +def test_empty_string_kind_is_unknown_kind() -> None: + with pytest.raises(NdselError) as excinfo: + normalize_ndsel({"kind": ""}) + assert excinfo.value.reason == "unknown_kind" diff --git a/packages/zarr-indexing/tests/test_ndsel_tensorstore.py b/packages/zarr-indexing/tests/test_ndsel_tensorstore.py new file mode 100644 index 0000000000..794ac5f3d5 --- /dev/null +++ b/packages/zarr-indexing/tests/test_ndsel_tensorstore.py @@ -0,0 +1,52 @@ +"""Cross-check canonical ndsel bodies against a real TensorStore. + +A normalized ndsel `transform` body is, field-for-field, a TensorStore +`IndexTransform` (minus the `kind` discriminator, which the canonical body never +carries). This test loads a handful of finite-bound canonical bodies into +`tensorstore.IndexTransform(json=...)` and confirms that TensorStore's own +`to_json()` re-loads, through our engine layer, into an equivalent transform. + +Skipped when tensorstore is not installed. Run it explicitly with: + + uv run --with tensorstore pytest \ + packages/zarr-indexing/tests/test_ndsel_tensorstore.py -q +""" + +from __future__ import annotations + +import numpy as np +import pytest + +from zarr_indexing.json import transform_from_canonical, transform_to_canonical +from zarr_indexing.transform import IndexTransform + +ts = pytest.importorskip("tensorstore") + + +def _canonical_transforms() -> list[IndexTransform]: + base = IndexTransform.from_shape((10, 20)) + return [ + base, # identity + base[2:8:2, :], # strided DimensionMap + identity + base[3, :], # integer index -> ConstantMap + DimensionMap + base.oindex[np.array([1, 5, 9]), :], # orthogonal index_array + IndexTransform.from_shape((10, 20, 30)).vindex[ + np.array([1, 3]), np.array([2, 4]), : + ], # correlated index_arrays + residual slice + ] + + +@pytest.mark.parametrize("transform", _canonical_transforms()) +def test_body_loads_in_tensorstore_and_round_trips(transform: IndexTransform) -> None: + body = transform_to_canonical(transform) + + # (1) The canonical body loads directly as a TensorStore IndexTransform. + ts_transform = ts.IndexTransform(json=body) + + # (2) TensorStore's own JSON re-loads, through our engine, to an equivalent + # transform. Comparing via our canonical form normalizes away + # representational choices (index_array_bounds, default omissions) that + # both sides make differently but that denote the same selection. + ts_json = ts_transform.to_json() + reloaded = transform_from_canonical(ts_json) + assert transform_to_canonical(reloaded) == transform_to_canonical(transform) diff --git a/packages/zarr-indexing/tests/test_output_map.py b/packages/zarr-indexing/tests/test_output_map.py new file mode 100644 index 0000000000..498101444e --- /dev/null +++ b/packages/zarr-indexing/tests/test_output_map.py @@ -0,0 +1,56 @@ +from __future__ import annotations + +import numpy as np + +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap + + +class TestConstantMap: + def test_construction(self) -> None: + m = ConstantMap(offset=42) + assert m.offset == 42 + + def test_default_offset(self) -> None: + m = ConstantMap() + assert m.offset == 0 + + def test_frozen(self) -> None: + m = ConstantMap(offset=5) + assert isinstance(m, ConstantMap) + + +class TestDimensionMap: + def test_construction(self) -> None: + m = DimensionMap(input_dimension=3, offset=5, stride=2) + assert m.input_dimension == 3 + assert m.offset == 5 + assert m.stride == 2 + + def test_defaults(self) -> None: + m = DimensionMap(input_dimension=0) + assert m.offset == 0 + assert m.stride == 1 + + def test_frozen(self) -> None: + m = DimensionMap(input_dimension=0) + assert isinstance(m, DimensionMap) + + +class TestArrayMap: + def test_construction(self) -> None: + arr = np.array([1, 3, 5], dtype=np.intp) + m = ArrayMap(index_array=arr, offset=10, stride=2) + assert m.offset == 10 + assert m.stride == 2 + np.testing.assert_array_equal(m.index_array, arr) + + def test_defaults(self) -> None: + arr = np.array([0, 1], dtype=np.intp) + m = ArrayMap(index_array=arr) + assert m.offset == 0 + assert m.stride == 1 + + def test_frozen(self) -> None: + arr = np.array([0], dtype=np.intp) + m = ArrayMap(index_array=arr) + assert isinstance(m, ArrayMap) diff --git a/packages/zarr-indexing/tests/test_tensorstore_parity.py b/packages/zarr-indexing/tests/test_tensorstore_parity.py new file mode 100644 index 0000000000..1ed99046e9 --- /dev/null +++ b/packages/zarr-indexing/tests/test_tensorstore_parity.py @@ -0,0 +1,263 @@ +"""TensorStore-parity oracle tests for IndexTransform semantics. + +Every case in this module was executed against tensorstore 0.1.84 (see the +lazy-indexing design notes): the expected domains, values, and error conditions +are TensorStore's observed behavior, which zarr's lazy indexing matches by +design. Core rules pinned here: + +- **Domain preservation**: a step-1 slice keeps the literal coordinates of the + selected interval (`a[2:10]` has domain `[2, 10)`); nothing re-zeros + implicitly. Re-zeroing is explicit via `translate_to`. +- **Strided-domain rule**: for step ``k``, ``origin = trunc(start/k)`` (rounded + toward zero), ``shape = ceil((stop - start)/k)``, and coordinate + ``origin + i`` maps to base cell ``start + i*k``. +- **Strict containment**: non-empty slice intervals must lie within the domain + — no clamping, no negative-wrapping; empty intervals are valid anywhere; + reversed non-empty bounds are an error, not an empty result. +- **Fancy-dim rule**: index-array dims get fresh explicit ``[0, n)`` domains; + index-array values are absolute domain coordinates. +- **Translate rules**: ``translate_by``/``translate_to`` shift the input domain + while preserving which cells are addressed. +""" + +from __future__ import annotations + +from typing import ClassVar + +import numpy as np +import pytest + +from zarr_indexing.domain import IndexDomain +from zarr_indexing.errors import BoundsCheckError +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap +from zarr_indexing.transform import IndexTransform + + +def _identity(lo: int, hi: int) -> IndexTransform: + """Identity transform over the 1-D domain [lo, hi).""" + return IndexTransform.identity(IndexDomain(inclusive_min=(lo,), exclusive_max=(hi,))) + + +def _a() -> IndexTransform: + """The oracle's base fixture: identity over [0, 12).""" + return _identity(0, 12) + + +def _w() -> IndexTransform: + """The oracle's translated fixture: identity over [-10, 2), cell c -> base c + 10.""" + return _a().translate_domain_by((-10,)) + + +def _dim(t: IndexTransform) -> DimensionMap: + m = t.output[0] + assert isinstance(m, DimensionMap) + return m + + +def _base_cells(t: IndexTransform) -> list[int]: + """The base cells a 1-D single-DimensionMap transform addresses, in order.""" + m = _dim(t) + lo, hi = t.domain.inclusive_min[0], t.domain.exclusive_max[0] + return [m.offset + m.stride * c for c in range(lo, hi)] + + +class TestDomainPreservation: + """Oracle section 1-2: step-1 slices keep literal coordinates.""" + + def test_slice_preserves_domain(self) -> None: + t = _a()[2:10] + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((2,), (10,)) + assert _base_cells(t) == list(range(2, 10)) + + def test_integer_on_preserved_domain_is_a_coordinate(self) -> None: + v = _a()[2:10] + assert isinstance(v[3].output[0], ConstantMap) + assert v[3].output[0].offset == 3 # coordinate 3 = base cell 3 + assert v[2].output[0].offset == 2 + assert v[9].output[0].offset == 9 + + @pytest.mark.parametrize("bad", [0, -1, 10]) + def test_out_of_domain_integer_raises(self, bad: int) -> None: + with pytest.raises(BoundsCheckError, match=r"valid indices \[2, 10\)"): + _a()[2:10][bad] + + def test_slice_of_slice_is_literal(self) -> None: + v = _a()[2:10] + t = v[3:7] + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((3,), (7,)) + assert _base_cells(t) == [3, 4, 5, 6] + + def test_ellipsis_preserves_domain(self) -> None: + v = _a()[2:10] + t = v[...] + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((2,), (10,)) + + +class TestNegativeOriginDomain: + """Oracle section 3: on domain [-10, 2), -1 is just another index.""" + + def test_translated_domain(self) -> None: + w = _w() + assert (w.domain.inclusive_min, w.domain.exclusive_max) == ((-10,), (2,)) + assert _base_cells(w) == list(range(12)) + + @pytest.mark.parametrize(("coord", "base"), [(-5, 5), (-10, 0), (-1, 9), (1, 11)]) + def test_negative_coordinates_address_cells(self, coord: int, base: int) -> None: + t = _w()[coord] + assert isinstance(t.output[0], ConstantMap) + assert t.output[0].offset == base + + @pytest.mark.parametrize("bad", [-11, 2]) + def test_out_of_domain_raises(self, bad: int) -> None: + with pytest.raises(BoundsCheckError, match=r"valid indices \[-10, 2\)"): + _w()[bad] + + def test_negative_slice_bounds_are_coordinates(self) -> None: + t = _w()[-5:] + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((-5,), (2,)) + assert _base_cells(t) == [5, 6, 7, 8, 9, 10, 11] + t2 = _w()[-5:-2] + assert (t2.domain.inclusive_min, t2.domain.exclusive_max) == ((-5,), (-2,)) + assert _base_cells(t2) == [5, 6, 7] + + +class TestStridedDomains: + """Oracle section 5: origin = trunc(start/step), coord origin+i -> start + i*step.""" + + # (slice, expected (lo, hi), expected base cells) — verbatim oracle rows. + CASES: ClassVar[list[tuple[slice, tuple[int, int], list[int]]]] = [ + (slice(1, 10, 3), (0, 3), [1, 4, 7]), + (slice(None, None, 2), (0, 6), [0, 2, 4, 6, 8, 10]), + (slice(2, 11, 3), (0, 3), [2, 5, 8]), + (slice(0, 12, 4), (0, 3), [0, 4, 8]), + (slice(5, 12, 2), (2, 6), [5, 7, 9, 11]), + (slice(6, 12, 2), (3, 6), [6, 8, 10]), + (slice(7, 12, 3), (2, 4), [7, 10]), + ] + + @pytest.mark.parametrize(("sel", "dom", "cells"), CASES) + def test_strided_domain_and_cells( + self, sel: slice, dom: tuple[int, int], cells: list[int] + ) -> None: + t = _a()[sel] + assert (t.domain.inclusive_min[0], t.domain.exclusive_max[0]) == dom + assert _base_cells(t) == cells + + def test_strided_on_negative_origin(self) -> None: + # w[-9:2:2] -> domain [-4, 2), base cells 1,3,5,7,9,11 + t = _w()[-9:2:2] + assert (t.domain.inclusive_min[0], t.domain.exclusive_max[0]) == (-4, 2) + assert _base_cells(t) == [1, 3, 5, 7, 9, 11] + # w[::2] -> domain [-5, 1), base cells 0,2,4,6,8,10 + t2 = _w()[::2] + assert (t2.domain.inclusive_min[0], t2.domain.exclusive_max[0]) == (-5, 1) + assert _base_cells(t2) == [0, 2, 4, 6, 8, 10] + + def test_strided_composition(self) -> None: + s = _a()[1:10:3] # domain [0, 3), cells 1,4,7 + assert [s[k].output[0].offset for k in range(3)] == [1, 4, 7] + t = s[1:3] + assert (t.domain.inclusive_min[0], t.domain.exclusive_max[0]) == (1, 3) + assert _base_cells(t) == [4, 7] + t2 = _a()[::2][1:4] + assert (t2.domain.inclusive_min[0], t2.domain.exclusive_max[0]) == (1, 4) + assert _base_cells(t2) == [2, 4, 6] + t3 = _a()[::2][::2] + assert (t3.domain.inclusive_min[0], t3.domain.exclusive_max[0]) == (0, 3) + assert _base_cells(t3) == [0, 4, 8] + + @pytest.mark.parametrize("bad", [-2, -1, 3, 4]) + def test_strided_bounds(self, bad: int) -> None: + with pytest.raises(BoundsCheckError, match=r"valid indices \[0, 3\)"): + _a()[1:10:3][bad] + + +class TestStrictContainment: + """Oracle section 11: no clamping, no wrapping; empty intervals valid anywhere.""" + + @pytest.mark.parametrize( + "sel", + [ + slice(5, 100), + slice(-3, None), + slice(-3, -1), + slice(0, 13), + slice(12, 14), + slice(100, 200), + ], + ) + def test_uncontained_interval_raises(self, sel: slice) -> None: + with pytest.raises(BoundsCheckError, match="not contained"): + _a()[sel] + + def test_uncontained_on_negative_origin(self) -> None: + with pytest.raises(BoundsCheckError, match="not contained"): + _w()[-20:] + + @pytest.mark.parametrize( + ("sel", "pos"), [(slice(5, 5), 5), (slice(0, 0), 0), (slice(13, 13), 13)] + ) + def test_empty_interval_valid_anywhere(self, sel: slice, pos: int) -> None: + t = _a()[sel] + assert t.domain.shape == (0,) + assert t.domain.inclusive_min[0] == pos + + @pytest.mark.parametrize("sel", [slice(5, 2), slice(100, 50)]) + def test_reversed_bounds_raise(self, sel: slice) -> None: + with pytest.raises(IndexError, match="valid.*interval|interval"): + _a()[sel] + + +class TestTranslate: + """Oracle sections 4 and 12: translate_by / translate_to preserve the cell mapping.""" + + def test_translate_to_zero(self) -> None: + t = _a()[2:10].translate_domain_to((0,)) + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((0,), (8,)) + assert _base_cells(t) == list(range(2, 10)) + + def test_translate_to_offset(self) -> None: + t = _a().translate_domain_to((5,)) + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((5,), (17,)) + assert _base_cells(t) == list(range(12)) + + def test_translate_by_composes_with_stride(self) -> None: + # a[::2].translate_by[5] -> domain [5, 11), base = 2*(coord-5) + t = _a()[::2].translate_domain_by((5,)) + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((5,), (11,)) + assert _base_cells(t) == [0, 2, 4, 6, 8, 10] + assert t[5].output[0].offset == 0 + assert t[10].output[0].offset == 10 + with pytest.raises(BoundsCheckError, match=r"valid indices \[5, 11\)"): + t[0] + + def test_translate_strided_to(self) -> None: + t = _a()[1:10:3].translate_domain_to((100,)) + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((100,), (103,)) + assert _base_cells(t) == [1, 4, 7] + + +class TestFancyDims: + """Oracle section 7: fancy dims get fresh [0, n); values are absolute coordinates.""" + + def test_index_array_values_are_coordinates(self) -> None: + v = _a()[2:10] + t = v.oindex[(np.array([3, 5], dtype=np.intp),)] + assert (t.domain.inclusive_min, t.domain.exclusive_max) == ((0,), (2,)) + m = t.output[0] + assert isinstance(m, ArrayMap) + storage = m.offset + m.stride * m.index_array + np.testing.assert_array_equal(np.asarray(storage).ravel(), [3, 5]) + + def test_index_array_on_negative_origin(self) -> None: + t = _w().oindex[(np.array([-10, -1], dtype=np.intp),)] + m = t.output[0] + assert isinstance(m, ArrayMap) + storage = m.offset + m.stride * m.index_array + np.testing.assert_array_equal(np.asarray(storage).ravel(), [0, 9]) + + def test_index_array_out_of_domain_raises(self) -> None: + v = _a()[2:10] + for bad in ([0, 3], [-1, 3], [3, 10]): + with pytest.raises(BoundsCheckError): + v.oindex[(np.array(bad, dtype=np.intp),)] diff --git a/packages/zarr-indexing/tests/test_transform.py b/packages/zarr-indexing/tests/test_transform.py new file mode 100644 index 0000000000..baecd9ada2 --- /dev/null +++ b/packages/zarr-indexing/tests/test_transform.py @@ -0,0 +1,628 @@ +from __future__ import annotations + +import numpy as np +import pytest + +from zarr_indexing.domain import IndexDomain +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap +from zarr_indexing.transform import IndexTransform, selection_to_transform + + +class TestIndexTransformConstruction: + def test_from_shape(self) -> None: + t = IndexTransform.from_shape((10, 20)) + assert t.input_rank == 2 + assert t.output_rank == 2 + assert t.domain.shape == (10, 20) + assert t.domain.origin == (0, 0) + for i, m in enumerate(t.output): + assert isinstance(m, DimensionMap) + assert m.input_dimension == i + assert m.offset == 0 + assert m.stride == 1 + + def test_identity(self) -> None: + domain = IndexDomain(inclusive_min=(5,), exclusive_max=(15,)) + t = IndexTransform.identity(domain) + assert t.input_rank == 1 + assert t.output_rank == 1 + assert t.domain == domain + assert isinstance(t.output[0], DimensionMap) + assert t.output[0].input_dimension == 0 + + def test_from_shape_0d(self) -> None: + t = IndexTransform.from_shape(()) + assert t.input_rank == 0 + assert t.output_rank == 0 + assert t.domain.shape == () + + def test_custom_output_maps(self) -> None: + domain = IndexDomain.from_shape((10,)) + maps = (ConstantMap(offset=42), DimensionMap(input_dimension=0, offset=5, stride=2)) + t = IndexTransform(domain=domain, output=maps) + assert t.input_rank == 1 + assert t.output_rank == 2 + + def test_validation_input_dimension_out_of_range(self) -> None: + domain = IndexDomain.from_shape((10,)) + maps = (DimensionMap(input_dimension=5),) + with pytest.raises(ValueError, match="input_dimension"): + IndexTransform(domain=domain, output=maps) + + +class TestIndexTransformBasicIndexing: + def test_slice_identity(self) -> None: + """slice(None) on identity transform is a no-op.""" + t = IndexTransform.from_shape((10, 20)) + result = t[slice(None), slice(None)] + assert result.domain.shape == (10, 20) + assert result.input_rank == 2 + assert result.output_rank == 2 + + def test_slice_narrows(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = t[2:8, 5:15] + # Domains are preserved (TensorStore): the slice keeps its literal + # coordinates, so the map stays the identity (out = in). + assert result.domain.shape == (6, 10) + assert result.domain.origin == (2, 5) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == 0 + assert result.output[0].stride == 1 + assert result.output[0].input_dimension == 0 + assert isinstance(result.output[1], DimensionMap) + assert result.output[1].offset == 0 + assert result.output[1].input_dimension == 1 + + def test_strided_slice(self) -> None: + t = IndexTransform.from_shape((10,)) + result = t[::2] + assert result.domain.shape == (5,) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == 0 + assert result.output[0].stride == 2 + + def test_strided_slice_with_start(self) -> None: + t = IndexTransform.from_shape((10,)) + result = t[1:9:3] + # indices: 1, 4, 7 -> 3 elements + assert result.domain.shape == (3,) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == 1 + assert result.output[0].stride == 3 + + def test_int_drops_dimension(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = t[3] + assert result.input_rank == 1 + assert result.output_rank == 2 + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == 3 + assert isinstance(result.output[1], DimensionMap) + assert result.output[1].input_dimension == 0 + + def test_int_middle_dimension(self) -> None: + t = IndexTransform.from_shape((10, 20, 30)) + result = t[:, 5, :] + assert result.input_rank == 2 + assert result.output_rank == 3 + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].input_dimension == 0 + assert isinstance(result.output[1], ConstantMap) + assert result.output[1].offset == 5 + assert isinstance(result.output[2], DimensionMap) + assert result.output[2].input_dimension == 1 + + def test_ellipsis(self) -> None: + t = IndexTransform.from_shape((10, 20, 30)) + result = t[2:8, ...] + assert result.input_rank == 3 + assert result.domain.shape == (6, 20, 30) + + def test_newaxis(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = t[np.newaxis, :, :] + assert result.input_rank == 3 + assert result.domain.shape == (1, 10, 20) + assert result.output_rank == 2 + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].input_dimension == 1 + assert isinstance(result.output[1], DimensionMap) + assert result.output[1].input_dimension == 2 + + def test_int_out_of_bounds(self) -> None: + t = IndexTransform.from_shape((10,)) + with pytest.raises(IndexError): + t[10] + + def test_negative_int_is_literal(self) -> None: + """Negative indices are literal coordinates (TensorStore convention), + not 'from the end' like NumPy.""" + t = IndexTransform.from_shape((10,)) + with pytest.raises(IndexError): + t[-1] # -1 is out of bounds for domain [0, 10) + + def test_negative_int_valid_with_negative_origin(self) -> None: + """Negative index is valid if the domain includes negative coordinates.""" + domain = IndexDomain(inclusive_min=(-5,), exclusive_max=(5,)) + t = IndexTransform.identity(domain) + result = t[-3] + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == -3 + + def test_composition_of_slices(self) -> None: + """Slicing a sliced transform re-selects in literal domain coordinates.""" + t = IndexTransform.from_shape((100,)) + result = t[10:50][15:30] + assert result.domain.shape == (15,) + assert result.domain.origin == (15,) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == 0 + assert result.output[0].stride == 1 + + def test_composition_of_strides(self) -> None: + t = IndexTransform.from_shape((100,)) + result = t[::2][::3] + # t[::2] -> shape (50,), offset=0, stride=2 + # [::3] -> shape ceil(50/3)=17, offset=0, stride=2*3=6 + assert result.domain.shape == (17,) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].stride == 6 + + def test_bare_int(self) -> None: + """Non-tuple selection.""" + t = IndexTransform.from_shape((10, 20)) + result = t[3] + assert result.input_rank == 1 + + def test_bare_slice(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = t[2:8] + assert result.domain.shape == (6, 20) + + +class TestBasicIndexingOnArrayMaps: + """When a transform already has ArrayMap outputs, basic indexing must + apply the corresponding operation to the index_array's axes.""" + + def test_int_on_array_map_drops_axis(self) -> None: + """Integer index on a dimension referenced by an ArrayMap should + index into the array on that axis.""" + arr = np.array([[10, 20], [30, 40], [50, 60]], dtype=np.intp) + # 2D input domain (3, 2), one ArrayMap output + t = IndexTransform( + domain=IndexDomain.from_shape((3, 2)), + output=(ArrayMap(index_array=arr),), + ) + # Index with int on dim 0 -> pick row 1 -> arr[1, :] = [30, 40] + result = t[1] + assert result.input_rank == 1 + assert result.domain.shape == (2,) + assert isinstance(result.output[0], ArrayMap) + np.testing.assert_array_equal(result.output[0].index_array, np.array([30, 40])) + + def test_slice_on_array_map(self) -> None: + """Slice on a dimension referenced by an ArrayMap should slice the array.""" + arr = np.array([10, 20, 30, 40, 50], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((5,)), + output=(ArrayMap(index_array=arr),), + ) + result = t[1:4] + assert result.domain.shape == (3,) + assert isinstance(result.output[0], ArrayMap) + np.testing.assert_array_equal(result.output[0].index_array, np.array([20, 30, 40])) + + def test_strided_slice_on_array_map(self) -> None: + """Strided slice on ArrayMap should stride the array.""" + arr = np.array([10, 20, 30, 40, 50], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((5,)), + output=(ArrayMap(index_array=arr),), + ) + result = t[::2] + assert result.domain.shape == (3,) + assert isinstance(result.output[0], ArrayMap) + np.testing.assert_array_equal(result.output[0].index_array, np.array([10, 30, 50])) + + def test_newaxis_on_array_map(self) -> None: + """Newaxis should insert an axis in the index_array.""" + arr = np.array([10, 20, 30], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=arr),), + ) + result = t[np.newaxis, :] + assert result.input_rank == 2 + assert result.domain.shape == (1, 3) + assert isinstance(result.output[0], ArrayMap) + assert result.output[0].index_array.shape == (1, 3) + np.testing.assert_array_equal(result.output[0].index_array, np.array([[10, 20, 30]])) + + def test_int_drops_one_of_two_array_dims(self) -> None: + """2D array map, int on dim 0, slice on dim 1.""" + arr = np.array([[10, 20, 30], [40, 50, 60]], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((2, 3)), + output=(ArrayMap(index_array=arr),), + ) + result = t[0, 1:3] + assert result.input_rank == 1 + assert result.domain.shape == (2,) + assert isinstance(result.output[0], ArrayMap) + # arr[0, 1:3] = [20, 30] + np.testing.assert_array_equal(result.output[0].index_array, np.array([20, 30])) + + +class TestIndexTransformOindex: + def test_oindex_int_array(self) -> None: + t = IndexTransform.from_shape((10, 20)) + idx = np.array([1, 3, 5], dtype=np.intp) + result = t.oindex[idx, :] + assert result.input_rank == 2 + assert result.domain.shape == (3, 20) + assert isinstance(result.output[0], ArrayMap) + # Full input rank: the array varies along its own axis (0), singleton on 1. + assert result.output[0].index_array.shape == (3, 1) + np.testing.assert_array_equal(result.output[0].index_array, idx.reshape(3, 1)) + assert result.output[0].offset == 0 + assert result.output[0].stride == 1 + assert isinstance(result.output[1], DimensionMap) + assert result.output[1].input_dimension == 1 + + def test_oindex_bool_array(self) -> None: + t = IndexTransform.from_shape((5,)) + mask = np.array([True, False, True, False, True]) + result = t.oindex[mask] + assert result.domain.shape == (3,) + assert isinstance(result.output[0], ArrayMap) + np.testing.assert_array_equal( + result.output[0].index_array, np.array([0, 2, 4], dtype=np.intp) + ) + + def test_oindex_mixed(self) -> None: + t = IndexTransform.from_shape((10, 20)) + idx = np.array([2, 4], dtype=np.intp) + result = t.oindex[idx, 5:15] + assert result.input_rank == 2 + assert result.domain.shape == (2, 10) + # fancy dim: fresh zero-origin; slice dim: preserved literal coords + assert result.domain.origin == (0, 5) + assert isinstance(result.output[0], ArrayMap) + assert isinstance(result.output[1], DimensionMap) + assert result.output[1].offset == 0 + + def test_oindex_multiple_arrays(self) -> None: + t = IndexTransform.from_shape((10, 20, 30)) + idx0 = np.array([1, 3], dtype=np.intp) + idx1 = np.array([5, 10, 15], dtype=np.intp) + result = t.oindex[idx0, :, idx1] + assert result.input_rank == 3 + assert result.domain.shape == (2, 20, 3) + assert isinstance(result.output[0], ArrayMap) + assert isinstance(result.output[1], DimensionMap) + assert isinstance(result.output[2], ArrayMap) + + def test_oindex_multiple_arrays_preserves_independent_axes(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = t.oindex[np.array([1, 3]), np.array([2, 4, 6])] + assert result.domain.shape == (2, 3) + assert isinstance(result.output[0], ArrayMap) + assert isinstance(result.output[1], ArrayMap) + assert result.output[0].index_array.shape == (2, 1) + assert result.output[1].index_array.shape == (1, 3) + + +class TestIndexTransformVindex: + def test_vindex_single_array(self) -> None: + t = IndexTransform.from_shape((10,)) + idx = np.array([1, 3, 5], dtype=np.intp) + result = t.vindex[idx] + assert result.input_rank == 1 + assert result.domain.shape == (3,) + assert isinstance(result.output[0], ArrayMap) + np.testing.assert_array_equal(result.output[0].index_array, idx) + + def test_vindex_broadcast(self) -> None: + t = IndexTransform.from_shape((10, 20)) + idx0 = np.array([[1, 2], [3, 4]], dtype=np.intp) + idx1 = np.array([[10, 11], [12, 13]], dtype=np.intp) + result = t.vindex[idx0, idx1] + assert result.input_rank == 2 + assert result.domain.shape == (2, 2) + assert isinstance(result.output[0], ArrayMap) + assert isinstance(result.output[1], ArrayMap) + np.testing.assert_array_equal(result.output[0].index_array, idx0) + np.testing.assert_array_equal(result.output[1].index_array, idx1) + + def test_vindex_with_slice(self) -> None: + t = IndexTransform.from_shape((10, 20, 30)) + idx = np.array([1, 3, 5], dtype=np.intp) + result = t.vindex[idx, :, :] + assert result.input_rank == 3 + assert result.domain.shape == (3, 20, 30) + assert isinstance(result.output[0], ArrayMap) + + def test_vindex_bool_mask(self) -> None: + t = IndexTransform.from_shape((5,)) + mask = np.array([True, False, True, False, True]) + result = t.vindex[mask] + assert result.domain.shape == (3,) + assert isinstance(result.output[0], ArrayMap) + + def test_vindex_broadcast_different_shapes(self) -> None: + t = IndexTransform.from_shape((10, 20)) + idx0 = np.array([1, 2, 3], dtype=np.intp) + idx1 = np.array([[10], [11]], dtype=np.intp) + result = t.vindex[idx0, idx1] + assert result.input_rank == 2 + assert result.domain.shape == (2, 3) + + def test_vindex_multiple_arrays_preserves_shared_axes(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = t.vindex[np.array([1, 3]), np.array([2, 4])] + assert result.domain.shape == (2,) + assert isinstance(result.output[0], ArrayMap) + assert isinstance(result.output[1], ArrayMap) + assert result.output[0].index_array.shape == (2,) + assert result.output[1].index_array.shape == (2,) + + +class TestSelectionToTransform: + def test_basic_slice(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = selection_to_transform((slice(2, 8), slice(5, 15)), t, "basic") + assert result.domain.shape == (6, 10) + assert result.domain.origin == (2, 5) # preserved literal coordinates + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == 0 + + def test_basic_int(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = selection_to_transform((3, slice(None)), t, "basic") + assert result.input_rank == 1 + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == 3 + + def test_basic_ellipsis(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = selection_to_transform(Ellipsis, t, "basic") + assert result.domain.shape == (10, 20) + + def test_orthogonal(self) -> None: + t = IndexTransform.from_shape((10, 20)) + idx = np.array([1, 3, 5], dtype=np.intp) + result = selection_to_transform((idx, slice(None)), t, "orthogonal") + assert result.domain.shape == (3, 20) + assert isinstance(result.output[0], ArrayMap) + + def test_vectorized(self) -> None: + t = IndexTransform.from_shape((10, 20)) + idx0 = np.array([1, 3], dtype=np.intp) + idx1 = np.array([5, 7], dtype=np.intp) + result = selection_to_transform((idx0, idx1), t, "vectorized") + assert result.domain.shape == (2,) + assert isinstance(result.output[0], ArrayMap) + assert isinstance(result.output[1], ArrayMap) + + def test_composition_with_non_identity(self) -> None: + """Indexing a sliced transform uses literal domain coordinates. + + The slice [10:50] preserves its domain, so a follow-up [15:30] + re-selects coordinates 15..29 of the base (TensorStore semantics), and + the composed map stays the identity (out = in). + """ + t = IndexTransform.from_shape((100,))[10:50] + result = selection_to_transform(slice(15, 30), t, "basic") + assert (result.domain.inclusive_min, result.domain.exclusive_max) == ((15,), (30,)) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == 0 + assert result.output[0].stride == 1 + + +class TestIndexTransformIntersect: + def test_constant_inside(self) -> None: + t = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(ConstantMap(offset=5),), + ) + result = t.intersect(IndexDomain(inclusive_min=(0,), exclusive_max=(10,))) + assert result is not None + restricted, surviving = result + assert isinstance(restricted.output[0], ConstantMap) + assert restricted.output[0].offset == 5 + assert surviving is None + + def test_constant_outside(self) -> None: + t = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(ConstantMap(offset=5),), + ) + result = t.intersect(IndexDomain(inclusive_min=(10,), exclusive_max=(20,))) + assert result is None + + def test_dimension_partial(self) -> None: + """DimensionMap over [0,10) intersected with [5,15) narrows input to [5,10).""" + t = IndexTransform.from_shape((10,)) + result = t.intersect(IndexDomain(inclusive_min=(5,), exclusive_max=(15,))) + assert result is not None + restricted, surviving = result + assert restricted.domain.inclusive_min == (5,) + assert restricted.domain.exclusive_max == (10,) + assert surviving is None + + def test_dimension_no_overlap(self) -> None: + t = IndexTransform.from_shape((10,)) + result = t.intersect(IndexDomain(inclusive_min=(20,), exclusive_max=(30,))) + assert result is None + + def test_dimension_strided(self) -> None: + """stride=2, offset=1 over [0,5): storage 1,3,5,7,9. Chunk [4,8).""" + t = IndexTransform( + domain=IndexDomain.from_shape((5,)), + output=(DimensionMap(input_dimension=0, offset=1, stride=2),), + ) + result = t.intersect(IndexDomain(inclusive_min=(4,), exclusive_max=(8,))) + assert result is not None + restricted, _surviving = result + # input 2->5, input 3->7. Both in [4,8). + assert restricted.domain.inclusive_min == (2,) + assert restricted.domain.exclusive_max == (4,) + + def test_array_partial(self) -> None: + arr = np.array([3, 8, 15, 22], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((4,)), + output=(ArrayMap(index_array=arr),), + ) + result = t.intersect(IndexDomain(inclusive_min=(5,), exclusive_max=(20,))) + assert result is not None + restricted, surviving = result + assert isinstance(restricted.output[0], ArrayMap) + np.testing.assert_array_equal(restricted.output[0].index_array, np.array([8, 15])) + assert surviving is not None + np.testing.assert_array_equal(surviving, np.array([1, 2])) + + def test_array_none_inside(self) -> None: + arr = np.array([1, 2, 3], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=arr),), + ) + assert t.intersect(IndexDomain(inclusive_min=(10,), exclusive_max=(20,))) is None + + def test_2d_mixed(self) -> None: + """2D: ConstantMap on dim 0, DimensionMap on dim 1.""" + t = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=( + ConstantMap(offset=5), + DimensionMap(input_dimension=0, offset=0, stride=1), + ), + ) + chunk = IndexDomain(inclusive_min=(0, 5), exclusive_max=(10, 15)) + result = t.intersect(chunk) + assert result is not None + restricted, _ = result + assert isinstance(restricted.output[0], ConstantMap) + assert restricted.output[0].offset == 5 + assert isinstance(restricted.output[1], DimensionMap) + assert restricted.domain.inclusive_min == (5,) + assert restricted.domain.exclusive_max == (10,) + + +class TestIndexTransformTranslate: + def test_translate_constant(self) -> None: + t = IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(ConstantMap(offset=5),), + ) + result = t.translate((-5,)) + assert isinstance(result.output[0], ConstantMap) + assert result.output[0].offset == 0 + + def test_translate_dimension(self) -> None: + t = IndexTransform.from_shape((10,)) + result = t.translate((-3,)) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == -3 + assert result.output[0].stride == 1 + + def test_translate_array(self) -> None: + arr = np.array([5, 10], dtype=np.intp) + t = IndexTransform( + domain=IndexDomain.from_shape((2,)), + output=(ArrayMap(index_array=arr, offset=3),), + ) + result = t.translate((-3,)) + assert isinstance(result.output[0], ArrayMap) + assert result.output[0].offset == 0 + np.testing.assert_array_equal(result.output[0].index_array, arr) + + def test_translate_2d(self) -> None: + t = IndexTransform.from_shape((10, 20)) + result = t.translate((-5, -10)) + assert isinstance(result.output[0], DimensionMap) + assert result.output[0].offset == -5 + assert isinstance(result.output[1], DimensionMap) + assert result.output[1].offset == -10 + + +class TestArrayMapDependencyAxes: + """`_array_map_dependency_axes` derives the input axes an array varies on + from its (full-rank) shape: non-singleton axes vary, singleton axes do not.""" + + def test_orthogonal_single_axis(self) -> None: + from zarr_indexing.transform import _array_map_dependency_axes + + t = IndexTransform.from_shape((10, 20)).oindex[np.array([1, 3]), np.array([2, 4, 6])] + m0, m1 = t.output[0], t.output[1] + assert isinstance(m0, ArrayMap) + assert isinstance(m1, ArrayMap) + assert _array_map_dependency_axes(m0.index_array) == (0,) + assert _array_map_dependency_axes(m1.index_array) == (1,) + + def test_vectorized_shares_axes(self) -> None: + from zarr_indexing.transform import _array_map_dependency_axes + + t = IndexTransform.from_shape((10, 20)).vindex[np.array([1, 3]), np.array([2, 4])] + m0, m1 = t.output[0], t.output[1] + assert isinstance(m0, ArrayMap) + assert isinstance(m1, ArrayMap) + assert _array_map_dependency_axes(m0.index_array) == (0,) + assert _array_map_dependency_axes(m1.index_array) == (0,) + + def test_scalar_array_has_no_dependency(self) -> None: + from zarr_indexing.transform import _array_map_dependency_axes + + assert _array_map_dependency_axes(np.ones((1, 1), dtype=np.intp)) == () + + +class TestIntersectArrayMapClassification: + """`_intersect` must distinguish orthogonal (outer-product) ArrayMaps from + correlated (vectorized) ones by their dependency axes, keep surviving arrays + at full input rank, and preserve residual (slice) dimensions.""" + + def test_orthogonal_outer_product_keeps_full_rank(self) -> None: + """Two arrays on distinct axes narrow independently and stay full rank; + out_indices is a per-output-dim dict of surviving positions.""" + t = IndexTransform.from_shape((10, 10)).oindex[np.array([1, 3, 8]), np.array([2, 6, 9])] + # Chunk covering storage [0,5) x [0,5): rows 1,3 survive (out pos 0,1), + # cols 2 survives (out pos 0). + chunk = IndexDomain(inclusive_min=(0, 0), exclusive_max=(5, 5)) + result = t.intersect(chunk) + assert result is not None + restricted, out_indices = result + assert isinstance(restricted.output[0], ArrayMap) + assert isinstance(restricted.output[1], ArrayMap) + # Full input rank preserved (not raveled to 1-D). + assert restricted.output[0].index_array.ndim == 2 + assert restricted.output[1].index_array.ndim == 2 + assert restricted.domain.ndim == 2 + assert isinstance(out_indices, dict) + np.testing.assert_array_equal(out_indices[0], np.array([0, 1])) + np.testing.assert_array_equal(out_indices[1], np.array([0])) + + def test_correlated_with_residual_slice_preserves_slice_dim(self) -> None: + """A vindex transform with two correlated arrays plus a residual slice + dim intersects without a rank error and keeps the DimensionMap.""" + t = IndexTransform.from_shape((4, 3, 5)).vindex[np.array([1, 3]), np.array([2, 0])] + # Chunk covering storage [0,2) x [2,3) x [0,5): only point (1,2,*) is in + # bounds on both array dims -> one surviving broadcast point. + chunk = IndexDomain(inclusive_min=(0, 2, 0), exclusive_max=(2, 3, 5)) + result = t.intersect(chunk) + assert result is not None + restricted, out_indices = result + # A DimensionMap for the residual slice dim survives (no post-init error). + assert any(isinstance(m, DimensionMap) for m in restricted.output) + assert out_indices is not None + + def test_length1_orthogonal_not_treated_as_correlated(self) -> None: + """A length-1 orthogonal array (all-singleton shape) is still an outer + product with the length-3 axis: out_indices is a dict, not a flat array.""" + t = IndexTransform.from_shape((6, 6)).oindex[np.array([2]), np.array([1, 3, 5])] + chunk = IndexDomain(inclusive_min=(0, 0), exclusive_max=(6, 6)) + result = t.intersect(chunk) + assert result is not None + _restricted, out_indices = result + assert isinstance(out_indices, dict) From 24f9ad19430dc88bc1d92b5e1936ac6b3e20f4fe Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Sun, 2 Aug 2026 15:09:12 +0200 Subject: [PATCH 436/468] fix: make consolidated metadata nesting independent of persisted key order (#4227) * fix: make consolidated metadata nesting independent of persisted key order `ConsolidatedMetadata._flat_to_nested` grouped the flat keys with `itertools.groupby` over keys sorted by depth alone. `groupby` only groups *consecutive* runs, so when a parent's children were not adjacent it emitted several runs for the same parent and the surrounding dict comprehension kept only the last one. Every child in the earlier runs was silently never re-parented, and lingered as a bogus slash-containing key at the top level, making it unreachable through the consolidated metadata. The persisted key order is arbitrary, so nesting must not depend on it. Group by parent with an accumulating mapping instead. This is reachable from zarr-python itself: `to_dict` sorts keys by `(depth, NFKC-casefold(key))`, so sibling subtrees whose names differ only by case interleave and trigger exactly this pattern. Fixes #4226 Assisted-by: ClaudeCode:claude-opus-5 * docs: add changelog entry for 273 Assisted-by: ClaudeCode:claude-opus-5 * docs: renumber changelog fragment to the upstream PR number Assisted-by: ClaudeCode:claude-opus-5 --- changes/4227.bugfix.md | 1 + src/zarr/core/group.py | 11 +++-- tests/test_metadata/test_consolidated.py | 62 ++++++++++++++++++++++++ 3 files changed, 69 insertions(+), 5 deletions(-) create mode 100644 changes/4227.bugfix.md diff --git a/changes/4227.bugfix.md b/changes/4227.bugfix.md new file mode 100644 index 0000000000..18293178bd --- /dev/null +++ b/changes/4227.bugfix.md @@ -0,0 +1 @@ +Consolidated metadata is now reconstructed independently of the order the keys appear in on disk. Previously, sibling subtrees whose keys were not adjacent in the persisted mapping lost their children, which made nodes unreachable through consolidated metadata -- most visibly for sibling groups whose names differ only by case. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 922eaf1498..65f7767a29 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -1,7 +1,6 @@ from __future__ import annotations import asyncio -import itertools import logging import unicodedata import warnings @@ -237,10 +236,12 @@ def _flat_to_nested( # In the example, the group at `/a/b` will have consolidated metadata # for its children `array-0` and `array-1`. - keys = sorted(metadata, key=lambda k: k.count("/")) - grouped = { - k: list(v) for k, v in itertools.groupby(keys, key=lambda k: k.rsplit("/", 1)[0]) - } + # Group keys by their parent path. This must not rely on same-parent keys + # being adjacent: the persisted key order is arbitrary, so accumulate + # instead of using itertools.groupby, which only groups consecutive runs. + grouped: dict[str, list[str]] = defaultdict(list) + for k in sorted(metadata, key=lambda k: k.count("/")): + grouped[k.rsplit("/", 1)[0]].append(k) # we go top down and directly manipulate metadata. for key, children_keys in grouped.items(): diff --git a/tests/test_metadata/test_consolidated.py b/tests/test_metadata/test_consolidated.py index e6087435fe..cd0fd92d74 100644 --- a/tests/test_metadata/test_consolidated.py +++ b/tests/test_metadata/test_consolidated.py @@ -839,3 +839,65 @@ async def test_open_group_in_non_consolidating_stores() -> None: # Opening a group with use_consolidated=True should fail with pytest.raises(ValueError, match="doesn't support consolidated metadata"): await AsyncGroup.open(memory_store, use_consolidated=True) + + +@pytest.mark.parametrize( + "order", + [ + # keys grouped by parent, the order zarr-python used to write before it + # started sorting the persisted keys + ["a", "b", "a/x", "a/y", "b/x", "b/y"], + # sibling subtrees interleaved, which is what the (depth, casefold) sort + # produces for names differing only by case + ["a", "b", "a/x", "b/x", "a/y", "b/y"], + # reversed, to cover a parent appearing after its children in the mapping + ["b/y", "b/x", "a/y", "a/x", "b", "a"], + ], +) +def test_flat_to_nested_is_order_independent(order: list[str]) -> None: + """The persisted key order is arbitrary, so nesting must not depend on it.""" + group_metadata: dict[str, JSON] = {"zarr_format": 3, "node_type": "group", "attributes": {}} + consolidated = ConsolidatedMetadata.from_dict( + { + "kind": "inline", + "must_understand": False, + "metadata": dict.fromkeys(order, group_metadata), + } + ) + + assert sorted(consolidated.metadata) == ["a", "b"] + for name in ("a", "b"): + child = consolidated.metadata[name] + assert isinstance(child, GroupMetadata) + assert child.consolidated_metadata is not None + assert sorted(child.consolidated_metadata.metadata) == ["x", "y"] + + +async def test_consolidated_metadata_case_differing_siblings(memory_store: Store) -> None: + """Sibling nodes whose names differ only by case each keep their own children. + + Regression test for https://github.com/zarr-developers/zarr-python/issues/4226 + """ + root = await zarr.api.asynchronous.create_group(store=memory_store) + for name in ("Study", "study"): + child = await root.create_group(f"obs/{name}") + await child.create_array(name="categories", shape=(2,), dtype="uint8") + await child.create_array(name="codes", shape=(2,), dtype="uint8") + + with pytest.warns( + ZarrUserWarning, + match="Consolidated metadata is currently not part in the Zarr format 3 specification.", + ): + await consolidate_metadata(memory_store) + + consolidated = await open_consolidated(store=memory_store) + result = sorted([key async for key, _ in consolidated.members(max_depth=None)]) + assert result == [ + "obs", + "obs/Study", + "obs/Study/categories", + "obs/Study/codes", + "obs/study", + "obs/study/categories", + "obs/study/codes", + ] From 976be695a843dd2e5ebea5157f4cc7c22d9adef2 Mon Sep 17 00:00:00 2001 From: Joe Hamman <joe@earthmover.io> Date: Mon, 3 Aug 2026 10:15:17 -0700 Subject: [PATCH 437/468] Convert rst double-backtick docstring markup to markdown (#4193) Docstring-only change: replace ``code`` (reStructuredText) with `code` (Markdown) in zarr.api.asynchronous, zarr.registry, and zarr.storage._common, matching the repo's mkdocs-based docs. Co-authored-by: Claude Fable 5 <noreply@anthropic.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- changes/4193.doc.md | 4 + src/zarr/api/asynchronous.py | 72 +++++++++--------- src/zarr/api/synchronous.py | 140 +++++++++++++++++----------------- src/zarr/core/array.py | 142 +++++++++++++++++------------------ src/zarr/registry.py | 18 ++--- src/zarr/storage/_common.py | 18 ++--- 6 files changed, 199 insertions(+), 195 deletions(-) create mode 100644 changes/4193.doc.md diff --git a/changes/4193.doc.md b/changes/4193.doc.md new file mode 100644 index 0000000000..0972e8be2c --- /dev/null +++ b/changes/4193.doc.md @@ -0,0 +1,4 @@ +Converted remaining reStructuredText-style double-backtick markup to Markdown +single backticks in the docstrings of `zarr.api.asynchronous`, +`zarr.api.synchronous`, `zarr.core.array`, `zarr.registry`, and +`zarr.storage._common`. No functional changes. diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py index f5e614a051..3bdc254ea5 100644 --- a/src/zarr/api/asynchronous.py +++ b/src/zarr/api/asynchronous.py @@ -103,7 +103,7 @@ def _infer_overwrite(mode: AccessModeLiteral) -> bool: """ - Check that an ``AccessModeLiteral`` is compatible with overwriting an existing Zarr node. + Check that an `AccessModeLiteral` is compatible with overwriting an existing Zarr node. """ return mode in _OVERWRITE_MODES @@ -112,9 +112,9 @@ def _warn_unimplemented_kwargs(kwargs: dict[str, Any]) -> None: """ Emit a "not yet implemented" warning for each provided keyword argument that is not None. - ``kwargs`` maps a keyword argument name to its supplied value. The ``stacklevel`` is chosen + `kwargs` maps a keyword argument name to its supplied value. The `stacklevel` is chosen so the warning points at the caller of the public API function (the same location as an - inline ``warnings.warn(..., stacklevel=2)`` would). + inline `warnings.warn(..., stacklevel=2)` would). """ for name, value in kwargs.items(): if value is not None: @@ -194,7 +194,7 @@ async def consolidate_metadata( Upon completion, the metadata of the root node in the Zarr hierarchy will be updated to include all the metadata of child nodes. For Stores that do - not support consolidated metadata, this operation raises a ``TypeError``. + not support consolidated metadata, this operation raises a `TypeError`. Parameters ---------- @@ -215,10 +215,10 @@ async def consolidate_metadata( Returns ------- group: AsyncGroup - The group, with the ``consolidated_metadata`` field set to include + The group, with the `consolidated_metadata` field set to include the metadata of each child node. If the Store doesn't support consolidated metadata, this function raises a `TypeError`. - See ``Store.supports_consolidated_metadata``. + See `Store.supports_consolidated_metadata`. """ store_path = await make_store_path(store, path=path) @@ -420,7 +420,7 @@ async def open_consolidated( *args: Any, use_consolidated: Literal[True] = True, **kwargs: Any ) -> AsyncGroup: """ - Alias for [`open_group`][zarr.api.asynchronous.open_group] with ``use_consolidated=True``. + Alias for [`open_group`][zarr.api.asynchronous.open_group] with `use_consolidated=True`. """ if use_consolidated is not True: raise TypeError( @@ -484,7 +484,7 @@ async def save_array( arr : ndarray NumPy array with data to save. zarr_format : {2, 3, None}, optional - The zarr format to use when saving. The default is ``None``, which will + The zarr format to use when saving. The default is `None`, which will use the default Zarr format defined in the global configuration object. path : str or None, optional The path within the store where the array will be saved. @@ -745,12 +745,12 @@ async def create_group( path : str, optional Group path within store. overwrite : bool, optional - If True, pre-existing data at ``path`` will be deleted before + If True, pre-existing data at `path` will be deleted before creating the group. zarr_format : {2, 3, None}, optional The zarr format to use when saving. - If no ``zarr_format`` is provided, the default format will be used. - This default can be changed by modifying the value of ``default_zarr_format`` + If no `zarr_format` is provided, the default format will be used. + This default can be changed by modifying the value of `default_zarr_format` in [`zarr.config`][zarr.config]. storage_options : dict If using an fsspec URL to create the store, these will be passed to @@ -828,17 +828,17 @@ async def open_group( Whether to use consolidated metadata. By default, consolidated metadata is used if it's present in the - store (in the ``zarr.json`` for Zarr format 3 and in the ``.zmetadata`` file + store (in the `zarr.json` for Zarr format 3 and in the `.zmetadata` file for Zarr format 2). - To explicitly require consolidated metadata, set ``use_consolidated=True``, + To explicitly require consolidated metadata, set `use_consolidated=True`, which will raise an exception if consolidated metadata is not found. - To explicitly *not* use consolidated metadata, set ``use_consolidated=False``, + To explicitly *not* use consolidated metadata, set `use_consolidated=False`, which will fall back to using the regular, non consolidated metadata. Zarr format 2 allowed configuring the key storing the consolidated metadata - (``.zmetadata`` by default). Specify the custom key as ``use_consolidated`` + (`.zmetadata` by default). Specify the custom key as `use_consolidated` to load consolidated metadata from a non-default key. Returns @@ -924,27 +924,27 @@ async def create( shape : int or tuple of ints Array shape. chunks : int or tuple of ints, optional - Chunk shape. If True, will be guessed from ``shape`` and ``dtype``. If - False, will be set to ``shape``, i.e., single chunk for the whole array. + Chunk shape. If True, will be guessed from `shape` and `dtype`. If + False, will be set to `shape`, i.e., single chunk for the whole array. If an int, the chunk size in each dimension will be given by the value - of ``chunks``. Default is True. + of `chunks`. Default is True. dtype : str or dtype, optional NumPy dtype. compressor : Codec, optional Primary compressor to compress chunk data. - Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. + Zarr format 2 only. Zarr format 3 arrays should use `codecs` instead. - If neither ``compressor`` nor ``filters`` are provided, the default compressor + If neither `compressor` nor `filters` are provided, the default compressor [`zarr.codecs.ZstdCodec`][] is used. - If ``compressor`` is set to ``None``, no compression is used. + If `compressor` is set to `None`, no compression is used. fill_value : Any, optional Fill value for the array. order : {'C', 'F'}, optional - Deprecated in favor of the ``config`` keyword argument. - Pass ``{'order': <value>}`` to ``create`` instead of using this parameter. + Deprecated in favor of the `config` keyword argument. + Pass `{'order': <value>}` to `create` instead of using this parameter. Memory layout to be used within each chunk. - If not specified, the ``array.order`` parameter in the global config will be used. + If not specified, the `array.order` parameter in the global config will be used. store : StoreLike or None, default=None StoreLike object to open. See the [storage documentation in the user guide][user-guide-store-like] @@ -952,12 +952,12 @@ async def create( synchronizer : object, optional Array synchronizer. overwrite : bool, optional - If True, delete all pre-existing data in ``store`` at ``path`` before + If True, delete all pre-existing data in `store` at `path` before creating the array. path : str, optional Path under which array is stored. chunk_store : StoreLike or None, default=None - Separate storage for chunks. If not provided, ``store`` will be used + Separate storage for chunks. If not provided, `store` will be used for storage of both chunks and metadata. filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that @@ -970,14 +970,14 @@ async def create( For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default based on the data + The default value of `"auto"` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. - To create an array with no filters, provide an empty iterable or the value ``None``. + To create an array with no filters, provide an empty iterable or the value `None`. cache_metadata : bool, optional If True, array configuration metadata will be cached for the lifetime of the object. If False, array metadata will be reloaded @@ -993,17 +993,17 @@ async def create( A codec to encode object arrays, only needed if dtype=object. dimension_separator : {'.', '/'}, optional Separator placed between the dimensions of a chunk. - Zarr format 2 only. Zarr format 3 arrays should use ``chunk_key_encoding`` instead. + Zarr format 2 only. Zarr format 3 arrays should use `chunk_key_encoding` instead. write_empty_chunks : bool, optional - Deprecated in favor of the ``config`` keyword argument. - Pass ``{'write_empty_chunks': <value>}`` to ``create`` instead of using this parameter. + Deprecated in favor of the `config` keyword argument. + Pass `{'write_empty_chunks': <value>}` to `create` instead of using this parameter. If True, all chunks will be stored regardless of their contents. If False, each chunk is compared to the array's fill value prior to storing. If a chunk is uniformly equal to the fill value, then that chunk is not be stored, and the store entry for that chunk's key is deleted. zarr_format : {2, 3, None}, optional - The Zarr format to use when creating an array. The default is ``None``, + The Zarr format to use when creating an array. The default is `None`, which instructs Zarr to choose the default Zarr format value defined in the runtime configuration. meta_array : array-like, optional @@ -1016,15 +1016,15 @@ async def create( chunk_key_encoding : ChunkKeyEncoding, optional A specification of how the chunk keys are represented in storage. Zarr format 3 only. Zarr format 2 arrays should use `dimension_separator` instead. - Default is ``("default", "/")``. + Default is `("default", "/")`. codecs : Sequence of Codecs or dicts, optional An iterable of Codec or dict serializations of Codecs. Zarr V3 only. - The elements of ``codecs`` specify the transformation from array values to stored bytes. - Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. + The elements of `codecs` specify the transformation from array values to stored bytes. + Zarr format 3 only. Zarr format 2 arrays should use `filters` and `compressor` instead. If no codecs are provided, default codecs will be used based on the data type of the array. - For most data types, the default codecs are the tuple ``(BytesCodec(), ZstdCodec())``; + For most data types, the default codecs are the tuple `(BytesCodec(), ZstdCodec())`; data types that require a special [`zarr.abc.codec.ArrayBytesCodec`][], like variable-length strings or bytes, will use the [`zarr.abc.codec.ArrayBytesCodec`][] required for the data type instead of [`zarr.codecs.BytesCodec`][]. dimension_names : Iterable[str | None] | None = None diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index dc12d5f7af..ebf42dca37 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -106,10 +106,10 @@ def consolidate_metadata( Returns ------- group: Group - The group, with the ``consolidated_metadata`` field set to include + The group, with the `consolidated_metadata` field set to include the metadata of each child node. If the Store doesn't support consolidated metadata, this function raises a `TypeError`. - See ``Store.supports_consolidated_metadata``. + See `Store.supports_consolidated_metadata`. """ return Group(sync(async_api.consolidate_metadata(store, path=path, zarr_format=zarr_format))) @@ -247,7 +247,7 @@ def open( def open_consolidated(*args: Any, use_consolidated: Literal[True] = True, **kwargs: Any) -> Group: """ - Alias for [`open_group`][zarr.api.synchronous.open_group] with ``use_consolidated=True``. + Alias for [`open_group`][zarr.api.synchronous.open_group] with `use_consolidated=True`. """ return Group( sync(async_api.open_consolidated(*args, use_consolidated=use_consolidated, **kwargs)) @@ -303,7 +303,7 @@ def save_array( arr : ndarray NumPy array with data to save. zarr_format : {2, 3, None}, optional - The zarr format to use when saving. The default is ``None``, which will + The zarr format to use when saving. The default is `None`, which will use the default Zarr format defined in the global configuration object. path : str or None, optional The path within the store where the array will be saved. @@ -530,17 +530,17 @@ def open_group( Whether to use consolidated metadata. By default, consolidated metadata is used if it's present in the - store (in the ``zarr.json`` for Zarr format 3 and in the ``.zmetadata`` file + store (in the `zarr.json` for Zarr format 3 and in the `.zmetadata` file for Zarr format 2). - To explicitly require consolidated metadata, set ``use_consolidated=True``, + To explicitly require consolidated metadata, set `use_consolidated=True`, which will raise an exception if consolidated metadata is not found. - To explicitly *not* use consolidated metadata, set ``use_consolidated=False``, + To explicitly *not* use consolidated metadata, set `use_consolidated=False`, which will fall back to using the regular, non consolidated metadata. Zarr format 2 allowed configuring the key storing the consolidated metadata - (``.zmetadata`` by default). Specify the custom key as ``use_consolidated`` + (`.zmetadata` by default). Specify the custom key as `use_consolidated` to load consolidated metadata from a non-default key. Returns @@ -587,12 +587,12 @@ def create_group( path : str, optional Group path within store. overwrite : bool, optional - If True, pre-existing data at ``path`` will be deleted before + If True, pre-existing data at `path` will be deleted before creating the group. zarr_format : {2, 3, None}, optional The zarr format to use when saving. - If no ``zarr_format`` is provided, the default format will be used. - This default can be changed by modifying the value of ``default_zarr_format`` + If no `zarr_format` is provided, the default format will be used. + This default can be changed by modifying the value of `default_zarr_format` in [`zarr.config`][zarr.config]. storage_options : dict If using an fsspec URL to create the store, these will be passed to @@ -662,27 +662,27 @@ def create( shape : int or tuple of ints Array shape. chunks : int or tuple of ints, optional - Chunk shape. If True, will be guessed from ``shape`` and ``dtype``. If - False, will be set to ``shape``, i.e., single chunk for the whole array. + Chunk shape. If True, will be guessed from `shape` and `dtype`. If + False, will be set to `shape`, i.e., single chunk for the whole array. If an int, the chunk size in each dimension will be given by the value - of ``chunks``. Default is True. + of `chunks`. Default is True. dtype : str or dtype, optional NumPy dtype. compressor : Codec, optional Primary compressor to compress chunk data. - Zarr format 2 only. Zarr format 3 arrays should use ``codecs`` instead. + Zarr format 2 only. Zarr format 3 arrays should use `codecs` instead. - If neither ``compressor`` nor ``filters`` are provided, the default compressor + If neither `compressor` nor `filters` are provided, the default compressor [`zarr.codecs.ZstdCodec`][] is used. - If ``compressor`` is set to ``None``, no compression is used. + If `compressor` is set to `None`, no compression is used. fill_value : Any, optional Fill value for the array. order : {'C', 'F'}, optional - Deprecated in favor of the ``config`` keyword argument. - Pass ``{'order': <value>}`` to ``create`` instead of using this parameter. + Deprecated in favor of the `config` keyword argument. + Pass `{'order': <value>}` to `create` instead of using this parameter. Memory layout to be used within each chunk. - If not specified, the ``array.order`` parameter in the global config will be used. + If not specified, the `array.order` parameter in the global config will be used. store : StoreLike or None, default=None StoreLike object to open. See the [storage documentation in the user guide][user-guide-store-like] @@ -690,12 +690,12 @@ def create( synchronizer : object, optional Array synchronizer. overwrite : bool, optional - If True, delete all pre-existing data in ``store`` at ``path`` before + If True, delete all pre-existing data in `store` at `path` before creating the array. path : str, optional Path under which array is stored. chunk_store : StoreLike or None, default=None - Separate storage for chunks. If not provided, ``store`` will be used + Separate storage for chunks. If not provided, `store` will be used for storage of both chunks and metadata. filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that @@ -708,14 +708,14 @@ def create( For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default based on the data + The default value of `"auto"` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. - To create an array with no filters, provide an empty iterable or the value ``None``. + To create an array with no filters, provide an empty iterable or the value `None`. cache_metadata : bool, optional If True, array configuration metadata will be cached for the lifetime of the object. If False, array metadata will be reloaded @@ -731,17 +731,17 @@ def create( A codec to encode object arrays, only needed if dtype=object. dimension_separator : {'.', '/'}, optional Separator placed between the dimensions of a chunk. - Zarr format 2 only. Zarr format 3 arrays should use ``chunk_key_encoding`` instead. + Zarr format 2 only. Zarr format 3 arrays should use `chunk_key_encoding` instead. write_empty_chunks : bool, optional - Deprecated in favor of the ``config`` keyword argument. - Pass ``{'write_empty_chunks': <value>}`` to ``create`` instead of using this parameter. + Deprecated in favor of the `config` keyword argument. + Pass `{'write_empty_chunks': <value>}` to `create` instead of using this parameter. If True, all chunks will be stored regardless of their contents. If False, each chunk is compared to the array's fill value prior to storing. If a chunk is uniformly equal to the fill value, then that chunk is not be stored, and the store entry for that chunk's key is deleted. zarr_format : {2, 3, None}, optional - The Zarr format to use when creating an array. The default is ``None``, + The Zarr format to use when creating an array. The default is `None`, which instructs Zarr to choose the default Zarr format value defined in the runtime configuration. meta_array : array-like, optional @@ -754,15 +754,15 @@ def create( chunk_key_encoding : ChunkKeyEncoding, optional A specification of how the chunk keys are represented in storage. Zarr format 3 only. Zarr format 2 arrays should use `dimension_separator` instead. - Default is ``("default", "/")``. + Default is `("default", "/")`. codecs : Sequence of Codecs or dicts, optional An iterable of Codec or dict serializations of Codecs. Zarr V3 only. - The elements of ``codecs`` specify the transformation from array values to stored bytes. - Zarr format 3 only. Zarr format 2 arrays should use ``filters`` and ``compressor`` instead. + The elements of `codecs` specify the transformation from array values to stored bytes. + Zarr format 3 only. Zarr format 2 arrays should use `filters` and `compressor` instead. If no codecs are provided, default codecs will be used based on the data type of the array. - For most data types, the default codecs are the tuple ``(BytesCodec(), ZstdCodec())``; + For most data types, the default codecs are the tuple `(BytesCodec(), ZstdCodec())`; data types that require a special [`zarr.abc.codec.ArrayBytesCodec`][], like variable-length strings or bytes, will use the [`zarr.abc.codec.ArrayBytesCodec`][] required for the data type instead of [`zarr.codecs.BytesCodec`][]. dimension_names : Iterable[str | None] | None = None @@ -849,24 +849,24 @@ def create_array( [storage documentation in the user guide][user-guide-store-like] for a description of all valid StoreLike values. name : str or None, optional - The name of the array within the store. If ``name`` is ``None``, the array will be located + The name of the array within the store. If `name` is `None`, the array will be located at the root of the store. shape : ShapeLike, optional - Shape of the array. Must be ``None`` if ``data`` is provided. + Shape of the array. Must be `None` if `data` is provided. dtype : ZDTypeLike | None - Data type of the array. Must be ``None`` if ``data`` is provided. + Data type of the array. Must be `None` if `data` is provided. data : np.ndarray, optional Array-like data to use for initializing the array. If this parameter is provided, the - ``shape`` and ``dtype`` parameters must be ``None``. + `shape` and `dtype` parameters must be `None`. chunks : tuple[int, ...] | Sequence[Sequence[int]] | Literal["auto"], default="auto" Chunk shape of the array. If chunks is "auto", a chunk shape is guessed based on the shape of the array and the dtype. A nested list of per-dimension edge sizes creates a rectilinear grid. Rectilinear chunk grids are experimental and must be explicitly enabled - with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + with `zarr.config.set({'array.rectilinear_chunks': True})` while the feature is stabilizing. shards : tuple[int, ...], optional - Shard shape of the array. The default value of ``None`` results in no sharding at all. + Shard shape of the array. The default value of `None` results in no sharding at all. filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. @@ -879,35 +879,35 @@ def create_array( For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default based on the data + The default value of `"auto"` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. - To create an array with no filters, provide an empty iterable or the value ``None``. + To create an array with no filters, provide an empty iterable or the value `None`. compressors : Iterable[Codec], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and returns another bytestream. Multiple compressors may be provided for Zarr format 3. - If no ``compressors`` are provided, a default set of compressors will be used. - These defaults can be changed by modifying the value of ``array.v3_default_compressors`` + If no `compressors` are provided, a default set of compressors will be used. + These defaults can be changed by modifying the value of `array.v3_default_compressors` in [`zarr.config`][zarr.config]. - Use ``None`` to omit default compressors. + Use `None` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. - If no ``compressor`` is provided, a default compressor will be used. + If no `compressor` is provided, a default compressor will be used. in [`zarr.config`][zarr.config]. - Use ``None`` to omit the default compressor. + Use `None` to omit the default compressor. serializer : dict[str, JSON] | ArrayBytesCodec, optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. - If no ``serializer`` is provided, a default serializer will be used. - These defaults can be changed by modifying the value of ``array.v3_default_serializer`` + If no `serializer` is provided, a default serializer will be used. + These defaults can be changed by modifying the value of `array.v3_default_serializer` in [`zarr.config`][zarr.config]. fill_value : Any, optional Fill value for the array. @@ -916,17 +916,17 @@ def create_array( For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory - order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. - If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. + order for Zarr format 3 arrays is via the `config` parameter, e.g. `{'config': 'C'}`. + If no `order` is provided, a default order will be used. + This default can be changed by modifying the value of `array.order` in [`zarr.config`][zarr.config]. zarr_format : {2, 3}, optional The zarr format to use when saving. attributes : dict, optional Attributes for the array. chunk_key_encoding : ChunkKeyEncodingLike, optional A specification of how the chunk keys are represented in storage. - For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. - For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. + For Zarr format 3, the default is `{"name": "default", "separator": "/"}}`. + For Zarr format 2, the default is `{"name": "v2", "separator": "."}}`. dimension_names : Iterable[str], optional The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. @@ -935,13 +935,13 @@ def create_array( Ignored otherwise. overwrite : bool, default False Whether to overwrite an array with the same name in the store, if one exists. - If ``True``, all existing paths in the store will be deleted. + If `True`, all existing paths in the store will be deleted. config : ArrayConfigLike, optional Runtime configuration for the array. write_data : bool - If a pre-existing array-like object was provided to this function via the ``data`` parameter - then ``write_data`` determines whether the values in that array-like object should be - written to the Zarr array created by this function. If ``write_data`` is ``False``, then the + If a pre-existing array-like object was provided to this function via the `data` parameter + then `write_data` determines whether the values in that array-like object should be + written to the Zarr array created by this function. If `write_data` is `False`, then the array will be left empty. Returns @@ -1024,10 +1024,10 @@ def from_array( The array to copy. write_data : bool, default True Whether to copy the data from the input array to the new array. - If ``write_data`` is ``False``, the new array will be created with the same metadata as the + If `write_data` is `False`, the new array will be created with the same metadata as the input array, but without any data. name : str or None, optional - The name of the array within the store. If ``name`` is ``None``, the array will be located + The name of the array within the store. If `name` is `None`, the array will be located at the root of the store. chunks : tuple[int, ...] or Sequence[Sequence[int]] or "auto" or "keep", optional Chunk shape of the array. @@ -1038,7 +1038,7 @@ def from_array( - tuple[int, ...]: A tuple of integers representing the chunk shape (regular grid). - Sequence[Sequence[int]]: Per-dimension chunk edge lists (rectilinear grid). Rectilinear chunk grids are experimental and must be explicitly enabled - with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + with `zarr.config.set({'array.rectilinear_chunks': True})` while the feature is stabilizing. If not specified, defaults to "keep" if data is a zarr Array, otherwise "auto". @@ -1063,16 +1063,16 @@ def from_array( For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the order of your filters is consistent with the behavior of each filter. - The default value of ``"keep"`` instructs Zarr to infer ``filters`` from ``data``. - If that inference is not possible, Zarr will fall back to the behavior specified by ``"auto"``, + The default value of `"keep"` instructs Zarr to infer `filters` from `data`. + If that inference is not possible, Zarr will fall back to the behavior specified by `"auto"`, which is to choose default filters based on the data type of the array and the Zarr format specified. - For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple ``()``. + For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple `()`. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters is a tuple with a single element which is a codec specific to that particular data type. - To create an array with no filters, provide an empty iterable or the value ``None``. + To create an array with no filters, provide an empty iterable or the value `None`. compressors : Iterable[Codec] or "auto" or "keep", optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -1089,17 +1089,17 @@ def from_array( - "auto": Automatically determine the compressors based on the array's dtype. - "keep": Retain the compressors of the input array if it is a zarr Array. - If no ``compressors`` are provided, defaults to "keep" if data is a zarr Array, otherwise "auto". + If no `compressors` are provided, defaults to "keep" if data is a zarr Array, otherwise "auto". serializer : dict[str, JSON] | ArrayBytesCodec or "auto" or "keep", optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. Following values are supported: - - dict[str, JSON]: A dict representation of an ``ArrayBytesCodec``. - - ArrayBytesCodec: An instance of ``ArrayBytesCodec``. + - dict[str, JSON]: A dict representation of an `ArrayBytesCodec`. + - ArrayBytesCodec: An instance of `ArrayBytesCodec`. - "auto": a default serializer will be used. These defaults can be changed by modifying the value of - ``array.v3_default_serializer`` in [`zarr.config`][zarr.config]. + `array.v3_default_serializer` in [`zarr.config`][zarr.config]. - "keep": Retain the serializer of the input array if it is a zarr Array. fill_value : Any, optional @@ -1110,7 +1110,7 @@ def from_array( For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory - order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. + order for Zarr format 3 arrays is via the `config` parameter, e.g. `{'config': 'C'}`. If not specified, defaults to the memory order of the data array. zarr_format : {2, 3}, optional The zarr format to use when saving. @@ -1120,8 +1120,8 @@ def from_array( If not specified, defaults to the attributes of the data array. chunk_key_encoding : ChunkKeyEncoding, optional A specification of how the chunk keys are represented in storage. - For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. - For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. + For Zarr format 3, the default is `{"name": "default", "separator": "/"}}`. + For Zarr format 2, the default is `{"name": "v2", "separator": "."}}`. If not specified and the data array has the same zarr format as the target array, the chunk key encoding of the data array is used. dimension_names : Iterable[str | None] | None diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index cd51dad50c..2b31eefcd4 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -160,7 +160,7 @@ from zarr.types import AnyArray, AnyAsyncArray, ArrayV2, ArrayV3, AsyncArrayV2, AsyncArrayV3 -# Array and AsyncArray are defined in the base ``zarr`` namespace +# Array and AsyncArray are defined in the base `zarr` namespace __all__ = [ "DEFAULT_FILL_VALUE", "create_codec_pipeline", @@ -336,8 +336,8 @@ async def _prepare_overwrite( """ Prepare a store path for writing a new node. - If ``overwrite`` is true and the store supports deletes, any existing node at - ``store_path`` is deleted. Otherwise, the absence of an existing node is enforced + If `overwrite` is true and the store supports deletes, any existing node at + `store_path` is deleted. Otherwise, the absence of an existing node is enforced (raising if one is present). """ if overwrite and store_path.store.supports_deletes: @@ -867,10 +867,10 @@ def read_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Boundary chunks that extend past the array shape are clipped, so the last size along a dimension may be smaller than the declared - chunk size. This matches the dask ``Array.chunks`` convention. + chunk size. This matches the dask `Array.chunks` convention. When sharding is used, returns the inner chunk sizes. - Otherwise, returns the outer chunk sizes (same as ``write_chunk_sizes``). + Otherwise, returns the outer chunk sizes (same as `write_chunk_sizes`). Returns ------- @@ -900,7 +900,7 @@ def write_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Always returns the outer chunk sizes, regardless of sharding. Boundary chunks that extend past the array shape are clipped, so the last size along a dimension may be smaller than the declared - chunk size. This matches the dask ``Array.chunks`` convention. + chunk size. This matches the dask `Array.chunks` convention. Returns ------- @@ -1439,7 +1439,7 @@ def nbytes(self) -> int: ----- This value is calculated by multiplying the number of elements in the array and the size of each element, the latter of which is determined by the dtype of the array. - For this reason, ``nbytes`` will likely be inaccurate for arrays with variable-length + For this reason, `nbytes` will likely be inaccurate for arrays with variable-length dtypes. It is not possible to determine the size of an array with variable-length elements from the shape and dtype alone. """ @@ -2041,10 +2041,10 @@ def read_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Boundary chunks that extend past the array shape are clipped, so the last size along a dimension may be smaller than the declared - chunk size. This matches the dask ``Array.chunks`` convention. + chunk size. This matches the dask `Array.chunks` convention. When sharding is used, returns the inner chunk sizes. - Otherwise, returns the outer chunk sizes (same as ``write_chunk_sizes``). + Otherwise, returns the outer chunk sizes (same as `write_chunk_sizes`). Returns ------- @@ -2068,7 +2068,7 @@ def write_chunk_sizes(self) -> tuple[tuple[int, ...], ...]: Always returns the outer chunk sizes, regardless of sharding. Boundary chunks that extend past the array shape are clipped, so the last size along a dimension may be smaller than the declared - chunk size. This matches the dask ``Array.chunks`` convention. + chunk size. This matches the dask `Array.chunks` convention. Returns ------- @@ -2286,7 +2286,7 @@ def nbytes(self) -> int: ----- This value is calculated by multiplying the number of elements in the array and the size of each element, the latter of which is determined by the dtype of the array. - For this reason, ``nbytes`` will likely be inaccurate for arrays with variable-length + For this reason, `nbytes` will likely be inaccurate for arrays with variable-length dtypes. It is not possible to determine the size of an array with variable-length elements from the shape and dtype alone. """ @@ -2300,7 +2300,7 @@ def nchunks_initialized(self) -> int: This value is calculated as the product of the number of initialized shards and the number of chunks per shard. For arrays that do not use sharding, the number of chunks per shard is effectively 1, and in that case the number of chunks initialized is the same as the number of stored objects associated with an - array. For a direct count of the number of initialized stored objects, see ``nshards_initialized``. + array. For a direct count of the number of initialized stored objects, see `nshards_initialized`. Returns ------- @@ -3980,7 +3980,7 @@ def info_complete(self) -> Any: """ Returns all the information about an array, including information from the Store. - In addition to the statically known information like ``name`` and ``zarr_format``, + In addition to the statically known information like `name` and `zarr_format`, this includes additional information like the size of the array in bytes and the number of chunks written. @@ -4098,10 +4098,10 @@ async def from_array( The array to copy. write_data : bool, default True Whether to copy the data from the input array to the new array. - If ``write_data`` is ``False``, the new array will be created with the same metadata as the + If `write_data` is `False`, the new array will be created with the same metadata as the input array, but without any data. name : str or None, optional - The name of the array within the store. If ``name`` is ``None``, the array will be located + The name of the array within the store. If `name` is `None`, the array will be located at the root of the store. chunks : tuple[int, ...] or Sequence[Sequence[int]] or "auto" or "keep", optional Chunk shape of the array. @@ -4112,7 +4112,7 @@ async def from_array( - tuple[int, ...]: A tuple of integers representing the chunk shape (regular grid). - Sequence[Sequence[int]]: Per-dimension chunk edge lists (rectilinear grid). Rectilinear chunk grids are experimental and must be explicitly enabled - with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + with `zarr.config.set({'array.rectilinear_chunks': True})` while the feature is stabilizing. If not specified, defaults to "keep" if data is a zarr Array, otherwise "auto". @@ -4137,16 +4137,16 @@ async def from_array( For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the order of your filters is consistent with the behavior of each filter. - The default value of ``"keep"`` instructs Zarr to infer ``filters`` from ``data``. - If that inference is not possible, Zarr will fall back to the behavior specified by ``"auto"``, + The default value of `"keep"` instructs Zarr to infer `filters` from `data`. + If that inference is not possible, Zarr will fall back to the behavior specified by `"auto"`, which is to choose default filters based on the data type of the array and the Zarr format specified. - For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple ``()``. + For all data types in Zarr V3, and most data types in Zarr V2, the default filters are the empty tuple `()`. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters is a tuple with a single element which is a codec specific to that particular data type. - To create an array with no filters, provide an empty iterable or the value ``None``. + To create an array with no filters, provide an empty iterable or the value `None`. compressors : Iterable[Codec] or "auto" or "keep", optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. @@ -4163,17 +4163,17 @@ async def from_array( - "auto": Automatically determine the compressors based on the array's dtype. - "keep": Retain the compressors of the input array if it is a zarr Array. - If no ``compressors`` are provided, defaults to "keep" if data is a zarr Array, otherwise "auto". + If no `compressors` are provided, defaults to "keep" if data is a zarr Array, otherwise "auto". serializer : dict[str, JSON] | ArrayBytesCodec or "auto" or "keep", optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. Following values are supported: - - dict[str, JSON]: A dict representation of an ``ArrayBytesCodec``. - - ArrayBytesCodec: An instance of ``ArrayBytesCodec``. + - dict[str, JSON]: A dict representation of an `ArrayBytesCodec`. + - ArrayBytesCodec: An instance of `ArrayBytesCodec`. - "auto": a default serializer will be used. These defaults can be changed by modifying the value of - ``array.v3_default_serializer`` in [`zarr.config`][zarr.config]. + `array.v3_default_serializer` in [`zarr.config`][zarr.config]. - "keep": Retain the serializer of the input array if it is a zarr Array. fill_value : Any, optional @@ -4184,7 +4184,7 @@ async def from_array( For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory - order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. + order for Zarr format 3 arrays is via the `config` parameter, e.g. `{'config': 'C'}`. If not specified, defaults to the memory order of the data array. zarr_format : {2, 3}, optional The zarr format to use when saving. @@ -4194,8 +4194,8 @@ async def from_array( If not specified, defaults to the attributes of the data array. chunk_key_encoding : ChunkKeyEncoding, optional A specification of how the chunk keys are represented in storage. - For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. - For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. + For Zarr format 3, the default is `{"name": "default", "separator": "/"}}`. + For Zarr format 2, the default is `{"name": "v2", "separator": "."}}`. If not specified and the data array has the same zarr format as the target array, the chunk key encoding of the data array is used. dimension_names : Iterable[str | None] | None @@ -4373,7 +4373,7 @@ async def init_array( Chunk shape of the array. If not specified, default are guessed based on the shape and dtype. shards : tuple[int, ...], optional - Shard shape of the array. The default value of ``None`` results in no sharding at all. + Shard shape of the array. The default value of `None` results in no sharding at all. filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. @@ -4385,26 +4385,26 @@ async def init_array( For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default based on the data + The default value of `"auto"` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. - To create an array with no filters, provide an empty iterable or the value ``None``. + To create an array with no filters, provide an empty iterable or the value `None`. compressors : Iterable[Codec] | Literal["auto"], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. - The default value of ``"auto"`` instructs Zarr to use a default of [`zarr.codecs.ZstdCodec`][]. + The default value of `"auto"` instructs Zarr to use a default of [`zarr.codecs.ZstdCodec`][]. - To create an array with no compressors, provide an empty iterable or the value ``None``. + To create an array with no compressors, provide an empty iterable or the value `None`. serializer : dict[str, JSON] | ArrayBytesCodec | Literal["auto"], optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. - The default value of ``"auto"`` instructs Zarr to use a default codec based on the data type of the array. + The default value of `"auto"` instructs Zarr to use a default codec based on the data type of the array. For most data types this default codec is [`zarr.codecs.BytesCodec`][]. For [`zarr.dtype.VariableLengthUTF8`][], the default codec is [`zarr.codecs.VlenUTF8Codec`][]. For [`zarr.dtype.VariableLengthBytes`][], the default codec is [`zarr.codecs.VlenBytesCodec`][]. @@ -4415,17 +4415,17 @@ async def init_array( For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory - order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. - If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. + order for Zarr format 3 arrays is via the `config` parameter, e.g. `{'config': 'C'}`. + If no `order` is provided, a default order will be used. + This default can be changed by modifying the value of `array.order` in [`zarr.config`][zarr.config]. zarr_format : {2, 3}, optional The zarr format to use when saving. attributes : dict, optional Attributes for the array. chunk_key_encoding : ChunkKeyEncodingLike, optional A specification of how the chunk keys are represented in storage. - For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. - For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. + For Zarr format 3, the default is `{"name": "default", "separator": "/"}}`. + For Zarr format 2, the default is `{"name": "v2", "separator": "."}}`. dimension_names : Iterable[str], optional The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. @@ -4433,7 +4433,7 @@ async def init_array( Whether to overwrite an array with the same name in the store, if one exists. config : ArrayConfigLike or None, default=None Configuration for this array. - If ``None``, the default array runtime configuration will be used. This default + If `None`, the default array runtime configuration will be used. This default is stored in the global configuration object. Returns @@ -4595,24 +4595,24 @@ async def create_array( [storage documentation in the user guide][user-guide-store-like] for a description of all valid StoreLike values. name : str or None, optional - The name of the array within the store. If ``name`` is ``None``, the array will be located + The name of the array within the store. If `name` is `None`, the array will be located at the root of the store. shape : ShapeLike, optional - Shape of the array. Must be ``None`` if ``data`` is provided. + Shape of the array. Must be `None` if `data` is provided. dtype : ZDTypeLike | None - Data type of the array. Must be ``None`` if ``data`` is provided. + Data type of the array. Must be `None` if `data` is provided. data : np.ndarray, optional Array-like data to use for initializing the array. If this parameter is provided, the - ``shape`` and ``dtype`` parameters must be ``None``. + `shape` and `dtype` parameters must be `None`. chunks : tuple[int, ...] | Sequence[Sequence[int]] | Literal["auto"], default="auto" Chunk shape of the array. If chunks is "auto", a chunk shape is guessed based on the shape of the array and the dtype. A nested list of per-dimension edge sizes creates a rectilinear grid. Rectilinear chunk grids are experimental and must be explicitly enabled - with ``zarr.config.set({'array.rectilinear_chunks': True})`` while the + with `zarr.config.set({'array.rectilinear_chunks': True})` while the feature is stabilizing. shards : tuple[int, ...], optional - Shard shape of the array. The default value of ``None`` results in no sharding at all. + Shard shape of the array. The default value of `None` results in no sharding at all. filters : Iterable[Codec] | Literal["auto"], optional Iterable of filters to apply to each chunk of the array, in order, before serializing that chunk to bytes. @@ -4625,35 +4625,35 @@ async def create_array( For Zarr format 2, a "filter" can be any numcodecs codec; you should ensure that the order of your filters is consistent with the behavior of each filter. - The default value of ``"auto"`` instructs Zarr to use a default based on the data + The default value of `"auto"` instructs Zarr to use a default based on the data type of the array and the Zarr format specified. For all data types in Zarr V3, and most data types in Zarr V2, the default filters are empty. The only cases where default filters are not empty is when the Zarr format is 2, and the data type is a variable-length data type like [`zarr.dtype.VariableLengthUTF8`][] or [`zarr.dtype.VariableLengthUTF8`][]. In these cases, the default filters contains a single element which is a codec specific to that particular data type. - To create an array with no filters, provide an empty iterable or the value ``None``. + To create an array with no filters, provide an empty iterable or the value `None`. compressors : Iterable[Codec], optional List of compressors to apply to the array. Compressors are applied in order, and after any filters are applied (if any are specified) and the data is serialized into bytes. For Zarr format 3, a "compressor" is a codec that takes a bytestream, and returns another bytestream. Multiple compressors may be provided for Zarr format 3. - If no ``compressors`` are provided, a default set of compressors will be used. - These defaults can be changed by modifying the value of ``array.v3_default_compressors`` + If no `compressors` are provided, a default set of compressors will be used. + These defaults can be changed by modifying the value of `array.v3_default_compressors` in [`zarr.config`][zarr.config]. - Use ``None`` to omit default compressors. + Use `None` to omit default compressors. For Zarr format 2, a "compressor" can be any numcodecs codec. Only a single compressor may be provided for Zarr format 2. - If no ``compressor`` is provided, a default compressor will be used. + If no `compressor` is provided, a default compressor will be used. in [`zarr.config`][zarr.config]. - Use ``None`` to omit the default compressor. + Use `None` to omit the default compressor. serializer : dict[str, JSON] | ArrayBytesCodec, optional Array-to-bytes codec to use for encoding the array data. Zarr format 3 only. Zarr format 2 arrays use implicit array-to-bytes conversion. - If no ``serializer`` is provided, a default serializer will be used. - These defaults can be changed by modifying the value of ``array.v3_default_serializer`` + If no `serializer` is provided, a default serializer will be used. + These defaults can be changed by modifying the value of `array.v3_default_serializer` in [`zarr.config`][zarr.config]. fill_value : Any, optional Fill value for the array. @@ -4662,17 +4662,17 @@ async def create_array( For Zarr format 2, this parameter sets the memory order of the array. For Zarr format 3, this parameter is deprecated, because memory order is a runtime parameter for Zarr format 3 arrays. The recommended way to specify the memory - order for Zarr format 3 arrays is via the ``config`` parameter, e.g. ``{'config': 'C'}``. - If no ``order`` is provided, a default order will be used. - This default can be changed by modifying the value of ``array.order`` in [`zarr.config`][zarr.config]. + order for Zarr format 3 arrays is via the `config` parameter, e.g. `{'config': 'C'}`. + If no `order` is provided, a default order will be used. + This default can be changed by modifying the value of `array.order` in [`zarr.config`][zarr.config]. zarr_format : {2, 3}, optional The zarr format to use when saving. attributes : dict, optional Attributes for the array. chunk_key_encoding : ChunkKeyEncodingLike, optional A specification of how the chunk keys are represented in storage. - For Zarr format 3, the default is ``{"name": "default", "separator": "/"}}``. - For Zarr format 2, the default is ``{"name": "v2", "separator": "."}}``. + For Zarr format 3, the default is `{"name": "default", "separator": "/"}}`. + For Zarr format 2, the default is `{"name": "v2", "separator": "."}}`. dimension_names : Iterable[str], optional The names of the dimensions (default is None). Zarr format 3 only. Zarr format 2 arrays should not use this parameter. @@ -4681,13 +4681,13 @@ async def create_array( Ignored otherwise. overwrite : bool, default False Whether to overwrite an array with the same name in the store, if one exists. - If ``True``, all existing paths in the store will be deleted. + If `True`, all existing paths in the store will be deleted. config : ArrayConfigLike, optional Runtime configuration for the array. write_data : bool - If a pre-existing array-like object was provided to this function via the ``data`` parameter - then ``write_data`` determines whether the values in that array-like object should be - written to the Zarr array created by this function. If ``write_data`` is ``False``, then the + If a pre-existing array-like object was provided to this function via the `data` parameter + then `write_data` determines whether the values in that array-like object should be + written to the Zarr array created by this function. If `write_data` is `False`, then the array will be left empty. Returns @@ -4885,7 +4885,7 @@ def default_compressors_v3(dtype: ZDType[Any, Any]) -> tuple[BytesBytesCodec, .. """ Given a data type, return the default compressors for that data type. - This is just a tuple containing ``ZstdCodec`` + This is just a tuple containing `ZstdCodec` """ return (ZstdCodec(),) @@ -4894,12 +4894,12 @@ def default_serializer_v3(dtype: ZDType[Any, Any]) -> ArrayBytesCodec: """ Given a data type, return the default serializer for that data type. - The default serializer for most data types is the ``BytesCodec``, which may or may not be + The default serializer for most data types is the `BytesCodec`, which may or may not be parameterized with an endianness, depending on whether the data type has endianness. Variable - length strings and variable length bytes have hard-coded serializers -- ``VLenUTF8Codec`` and - ``VLenBytesCodec``, respectively. + length strings and variable length bytes have hard-coded serializers -- `VLenUTF8Codec` and + `VLenBytesCodec`, respectively. - Structured data types with multi-byte fields use ``BytesCodec`` with little-endian encoding. + Structured data types with multi-byte fields use `BytesCodec` with little-endian encoding. """ serializer: ArrayBytesCodec = BytesCodec(endian=None) @@ -4923,7 +4923,7 @@ def default_filters_v2(dtype: ZDType[Any, Any]) -> tuple[Numcodec] | None: Given a data type, return the default filters for that data type. For data types that require an object codec, namely variable length data types, - this is a tuple containing the object codec. Otherwise it's ``None``. + this is a tuple containing the object codec. Otherwise it's `None`. """ if isinstance(dtype, HasObjectCodec): if dtype.object_codec_id == "vlen-bytes": @@ -4944,7 +4944,7 @@ def default_compressor_v2(dtype: ZDType[Any, Any]) -> Numcodec: """ Given a data type, return the default compressors for that data type. - This is just the numcodecs ``Zstd`` codec. + This is just the numcodecs `Zstd` codec. """ from numcodecs import Zstd @@ -5101,7 +5101,7 @@ def _parse_data_params( dtype: ZDTypeLike | None, ) -> tuple[np.ndarray[Any, np.dtype[Any]] | None, ShapeLike, ZDTypeLike]: """ - Ensure an array-like ``data`` parameter is consistent with the ``dtype`` and ``shape`` + Ensure an array-like `data` parameter is consistent with the `dtype` and `shape` parameters. """ if data is None: diff --git a/src/zarr/registry.py b/src/zarr/registry.py index 48f60fabd7..c2c0eb2921 100644 --- a/src/zarr/registry.py +++ b/src/zarr/registry.py @@ -196,9 +196,9 @@ def _resolve_codec(data: dict[str, JSON]) -> Codec: def _parse_bytes_bytes_codec(data: dict[str, JSON] | Codec) -> BytesBytesCodec: """ - Normalize the input to a ``BytesBytesCodec`` instance. - If the input is already a ``BytesBytesCodec``, it is returned as is. If the input is a dict, it - is converted to a ``BytesBytesCodec`` instance via the ``_resolve_codec`` function. + Normalize the input to a `BytesBytesCodec` instance. + If the input is already a `BytesBytesCodec`, it is returned as is. If the input is a dict, it + is converted to a `BytesBytesCodec` instance via the `_resolve_codec` function. """ from zarr.abc.codec import BytesBytesCodec @@ -216,9 +216,9 @@ def _parse_bytes_bytes_codec(data: dict[str, JSON] | Codec) -> BytesBytesCodec: def _parse_array_bytes_codec(data: dict[str, JSON] | Codec) -> ArrayBytesCodec: """ - Normalize the input to a ``ArrayBytesCodec`` instance. - If the input is already a ``ArrayBytesCodec``, it is returned as is. If the input is a dict, it - is converted to a ``ArrayBytesCodec`` instance via the ``_resolve_codec`` function. + Normalize the input to a `ArrayBytesCodec` instance. + If the input is already a `ArrayBytesCodec`, it is returned as is. If the input is a dict, it + is converted to a `ArrayBytesCodec` instance via the `_resolve_codec` function. """ from zarr.abc.codec import ArrayBytesCodec @@ -236,9 +236,9 @@ def _parse_array_bytes_codec(data: dict[str, JSON] | Codec) -> ArrayBytesCodec: def _parse_array_array_codec(data: dict[str, JSON] | Codec) -> ArrayArrayCodec: """ - Normalize the input to a ``ArrayArrayCodec`` instance. - If the input is already a ``ArrayArrayCodec``, it is returned as is. If the input is a dict, it - is converted to a ``ArrayArrayCodec`` instance via the ``_resolve_codec`` function. + Normalize the input to a `ArrayArrayCodec` instance. + If the input is already a `ArrayArrayCodec`, it is returned as is. If the input is a dict, it + is converted to a `ArrayArrayCodec` instance via the `_resolve_codec` function. """ from zarr.abc.codec import ArrayArrayCodec diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 7e9c035c69..ed554327cd 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -84,11 +84,11 @@ async def open(cls, store: Store, path: str, mode: AccessModeLiteral | None = No The accepted values are: - - ``'r'``: read only (must exist) - - ``'r+'``: read/write (must exist) - - ``'a'``: read/write (create if doesn't exist) - - ``'w'``: read/write (overwrite if exists) - - ``'w-'``: read/write (create if doesn't exist). + - `'r'`: read only (must exist) + - `'r+'`: read/write (must exist) + - `'a'`: read/write (create if doesn't exist) + - `'w'`: read/write (overwrite if exists) + - `'w-'`: read/write (create if doesn't exist). Raises ------ @@ -209,7 +209,7 @@ async def delete_dir(self) -> None: async def set_if_not_exists(self, default: Buffer) -> None: """ - Store a key to ``value`` if the key is not already present. + Store a key to `value` if the key is not already present. Parameters ---------- @@ -250,7 +250,7 @@ def get_sync( prototype: BufferPrototype | None = None, byte_range: ByteRequest | None = None, ) -> Buffer | None: - """Synchronous read — delegates to ``self.store.get_sync(self.path, ...)``.""" + """Synchronous read — delegates to `self.store.get_sync(self.path, ...)`.""" if not isinstance(self.store, SupportsGetSync): raise TypeError(f"Store {type(self.store).__name__} does not support synchronous get.") if prototype is None: @@ -258,13 +258,13 @@ def get_sync( return self.store.get_sync(self.path, prototype=prototype, byte_range=byte_range) def set_sync(self, value: Buffer) -> None: - """Synchronous write — delegates to ``self.store.set_sync(self.path, value)``.""" + """Synchronous write — delegates to `self.store.set_sync(self.path, value)`.""" if not isinstance(self.store, SupportsSetSync): raise TypeError(f"Store {type(self.store).__name__} does not support synchronous set.") self.store.set_sync(self.path, value) def delete_sync(self) -> None: - """Synchronous delete — delegates to ``self.store.delete_sync(self.path)``.""" + """Synchronous delete — delegates to `self.store.delete_sync(self.path)`.""" if not isinstance(self.store, SupportsDeleteSync): raise TypeError( f"Store {type(self.store).__name__} does not support synchronous delete." From 5a4767b9c4e6fcf5e4d60a7db0d08dc506935e45 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 5 Aug 2026 10:38:09 +0200 Subject: [PATCH 438/468] refactor(zarr-metadata)!: unify constant naming grammar with type names (#4232) A constant's name is now a purely syntactic transformation of the name of the `Literal` type it manifests, so the format version comes first and is spelled `ZARR_V2`/`ZARR_V3`, matching the `ZarrV2`/`ZarrV3` prefix already used by type names. This replaces the 0.4.0 split under which types put the version first and constants put it last; there is now one rule instead of two. Nine constants are renamed without aliases (pre-1.0). Digit runs stay glued to the token they follow, which keeps the spec vocabulary intact: `Uint8DataTypeName` pairs with `UINT8_DATA_TYPE_NAME`, not `UINT_8_...`, and `Crc32cCodecName` with `CRC32C_CODEC_NAME`. No dtype, codec, chunk-grid, or chunk-key-encoding constant changed name. A strict letter/digit split would have renamed 18 of them for the worse. Store keys also move to the modules describing the documents they name. They are facts about the on-disk specs, so they belong beside the types they key: `ZARR_V2_ATTRIBUTES_STORE_KEY` now lives in `v2/attributes.py` next to `ZarrV2ZAttrsJSON`, rather than in the array model. This keeps the `v2`/`v3` packages as leaf spec-description modules that never import from `model`, and drops the `_group.py` -> `_array.py` import of a key that was never array-specific. `zarr_metadata.model` re-exports all of them, and they are now also exported from the top-level namespace alongside the rest of the spec vocabulary. `CONSOLIDATED_METADATA_KEY_V3` is renamed and moved likewise, but is not a store key: v3 consolidated metadata is embedded as an extension field in the group's own `zarr.json`, so it has no paired `Literal` alias and is not passed to the store-json helpers. Three tests pin what the refactor made implicit: constant names are derived from their types mechanically, the two v3 node store keys still name the same file now that they live in different modules, and the set of value-ambiguous constants the derivation check cannot see is counted so its coverage cannot shrink unnoticed. Assisted-by: ClaudeCode:claude-opus-4.8 --- .../zarr-metadata/changes/4232.removal.md | 63 +++++++ packages/zarr-metadata/docs/api/index.md | 5 +- .../src/zarr_metadata/__init__.py | 34 +++- .../src/zarr_metadata/model/__init__.py | 56 +++--- .../src/zarr_metadata/model/_array.py | 36 ++-- .../src/zarr_metadata/model/_group.py | 58 +++--- .../src/zarr_metadata/v2/array.py | 17 +- .../src/zarr_metadata/v2/attributes.py | 14 ++ .../src/zarr_metadata/v2/consolidated.py | 14 ++ .../src/zarr_metadata/v2/group.py | 11 +- .../src/zarr_metadata/v3/array.py | 15 +- .../src/zarr_metadata/v3/consolidated.py | 12 +- .../src/zarr_metadata/v3/group.py | 15 +- .../zarr-metadata/tests/model/test_array.py | 64 ++++++- .../zarr-metadata/tests/test_public_api.py | 165 +++++++++++++++++- 15 files changed, 480 insertions(+), 99 deletions(-) create mode 100644 packages/zarr-metadata/changes/4232.removal.md diff --git a/packages/zarr-metadata/changes/4232.removal.md b/packages/zarr-metadata/changes/4232.removal.md new file mode 100644 index 0000000000..73b2a18666 --- /dev/null +++ b/packages/zarr-metadata/changes/4232.removal.md @@ -0,0 +1,63 @@ +Unified the naming grammar for SCREAMING_SNAKE constants with the one used for +type names. A constant's name is now a purely syntactic transformation of the +name of the `Literal` type it manifests, so the format version is spelled +`ZARR_V2`/`ZARR_V3` and comes first, matching the `ZarrV2`/`ZarrV3` prefix on +the corresponding type: + +- `ARRAY_METADATA_STORE_KEY_V2` → `ZARR_V2_ARRAY_METADATA_STORE_KEY` +- `ARRAY_METADATA_STORE_KEY_V3` → `ZARR_V3_ARRAY_METADATA_STORE_KEY` +- `ATTRIBUTES_STORE_KEY_V2` → `ZARR_V2_ATTRIBUTES_STORE_KEY` +- `GROUP_METADATA_STORE_KEY_V2` → `ZARR_V2_GROUP_METADATA_STORE_KEY` +- `GROUP_METADATA_STORE_KEY_V3` → `ZARR_V3_GROUP_METADATA_STORE_KEY` +- `CONSOLIDATED_METADATA_STORE_KEY_V2` → `ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY` +- `ARRAY_ORDER_V2` → `ZARR_V2_ARRAY_ORDER` +- `ARRAY_DIMENSION_SEPARATOR_V2` → `ZARR_V2_ARRAY_DIMENSION_SEPARATOR` +- `CONSOLIDATED_METADATA_KEY_V3` → `ZARR_V3_CONSOLIDATED_METADATA_KEY` + +The old names are removed, not aliased. This supersedes the 0.4.0 convention +under which type names put the format version first while constants put it +last: every constant that manifests a `Literal` type now follows the same rule +as that type. + +The last of those is the one rename the syntactic rule does not force: +`ZARR_V3_CONSOLIDATED_METADATA_KEY` manifests no `Literal` type, so it is +outside the rule and was renamed for consistency with its siblings. + +Digit runs stay glued to the token they follow, so spec vocabulary is +preserved: `Uint8DataTypeName` pairs with `UINT8_DATA_TYPE_NAME` (not +`UINT_8_...`) and `Crc32cCodecName` with `CRC32C_CODEC_NAME`. No dtype, codec, +chunk-grid, or chunk-key-encoding constant changed name. + +Constants that do not manifest a `Literal` type are outside the rule and are +unchanged: the `*_METADATA_*_KEYS_V2`/`_V3` key sets, the +`CANONICAL_*_HEX_FLOAT*` bit patterns, and `UNSET`. The key sets keep the +version-last spelling, so `zarr_metadata.model` exports both +`ARRAY_METADATA_REQUIRED_KEYS_V2` and `ZARR_V2_ARRAY_METADATA_STORE_KEY`. They +name validation policy rather than a spec document, have no paired type to +derive from, and renaming them would be a second breaking change buying only +cosmetic consistency — so it is deliberately deferred. + +`tests/test_public_api.py::test_constant_names_derive_from_their_type_names` +derives every constant name from the type it manifests and asserts they match, +so the two grammars cannot diverge again. + +Store keys also moved to the modules that describe the documents they name, +matching the package's layering (the `v2`/`v3` modules describe the specs; the +`model` layer is built on top of them). `ZARR_V2_ATTRIBUTES_STORE_KEY` now +lives in `zarr_metadata.v2.attributes` beside the `.zattrs` type it names, +rather than in the array model; the other five moved likewise, and +`ZarrV2AttributesStoreKey` is no longer an array-specific concept. +`zarr_metadata.model` re-exports all six, so +`from zarr_metadata.model import ZARR_V2_ARRAY_METADATA_STORE_KEY` is +unaffected. + +`CONSOLIDATED_METADATA_KEY_V3` moved to `zarr_metadata.v3.consolidated` and was +renamed to `ZARR_V3_CONSOLIDATED_METADATA_KEY` for consistency. It is not a +store key: unlike v2's `.zmetadata` file, v3 consolidated metadata is embedded +as an extension field inside the group's own `zarr.json`. + +All seven keys and the six store-key `Literal` aliases are now also exported +from the top-level `zarr_metadata` namespace, alongside the document types and +the rest of the spec vocabulary, so `from zarr_metadata import +ZARR_V2_ARRAY_METADATA_STORE_KEY` works. The model layer's validators, parsers, +type guards, and metadata key sets remain `zarr_metadata.model` imports. diff --git a/packages/zarr-metadata/docs/api/index.md b/packages/zarr-metadata/docs/api/index.md index 2aa39ab161..5e230c7aa2 100644 --- a/packages/zarr-metadata/docs/api/index.md +++ b/packages/zarr-metadata/docs/api/index.md @@ -17,9 +17,12 @@ The package is organized to mirror the structure of the Zarr specifications: [chunk key encodings](v3/chunk_key_encoding.md), [codecs](v3/codec.md), and [data types](v3/data_type.md) -Every public name is also re-exported at the top level, so +The document types, models, and spec vocabulary — including the store keys — +are re-exported at the top level, so `from zarr_metadata import ZarrV3ArrayMetadataJSON` and `from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON` are equivalent. +The model layer's validators, parsers, type guards, and metadata key sets are +imported from [`zarr_metadata.model`](model.md) directly. ## Common types diff --git a/packages/zarr-metadata/src/zarr_metadata/__init__.py b/packages/zarr-metadata/src/zarr_metadata/__init__.py index b5e52e976d..1a6b39f04d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/__init__.py @@ -3,25 +3,38 @@ from zarr_metadata._common import JSONValue, ZarrV3NamedConfigJSON from zarr_metadata.model import ( UNSET, + ZARR_V2_ARRAY_METADATA_STORE_KEY, + ZARR_V2_ATTRIBUTES_STORE_KEY, + ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY, + ZARR_V2_GROUP_METADATA_STORE_KEY, + ZARR_V3_ARRAY_METADATA_STORE_KEY, + ZARR_V3_CONSOLIDATED_METADATA_KEY, + ZARR_V3_GROUP_METADATA_STORE_KEY, MetadataValidationError, ProblemKind, ValidationProblem, ZarrV2ArrayMetadata, ZarrV2ArrayMetadataPartial, + ZarrV2ArrayMetadataStoreKey, + ZarrV2AttributesStoreKey, ZarrV2ConsolidatedMetadata, + ZarrV2ConsolidatedMetadataStoreKey, ZarrV2GroupMetadata, ZarrV2GroupMetadataPartial, + ZarrV2GroupMetadataStoreKey, ZarrV3ArrayMetadata, ZarrV3ArrayMetadataPartial, + ZarrV3ArrayMetadataStoreKey, ZarrV3ConsolidatedMetadata, ZarrV3GroupMetadata, ZarrV3GroupMetadataPartial, + ZarrV3GroupMetadataStoreKey, ZarrV3MetadataField, ZarrV3NamedConfig, ) from zarr_metadata.v2.array import ( - ARRAY_DIMENSION_SEPARATOR_V2, - ARRAY_ORDER_V2, + ZARR_V2_ARRAY_DIMENSION_SEPARATOR, + ZARR_V2_ARRAY_ORDER, ZarrV2ArrayDimensionSeparator, ZarrV2ArrayMetadataJSON, ZarrV2ArrayMetadataJSONPartial, @@ -217,8 +230,6 @@ __all__ = [ - "ARRAY_DIMENSION_SEPARATOR_V2", - "ARRAY_ORDER_V2", "BLOSC_CNAME", "BLOSC_CODEC_NAME", "BLOSC_SHUFFLE", @@ -260,6 +271,15 @@ "UNSET", "V2_CHUNK_KEY_ENCODING_NAME", "V2_CHUNK_KEY_ENCODING_SEPARATOR", + "ZARR_V2_ARRAY_DIMENSION_SEPARATOR", + "ZARR_V2_ARRAY_METADATA_STORE_KEY", + "ZARR_V2_ARRAY_ORDER", + "ZARR_V2_ATTRIBUTES_STORE_KEY", + "ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY", + "ZARR_V2_GROUP_METADATA_STORE_KEY", + "ZARR_V3_ARRAY_METADATA_STORE_KEY", + "ZARR_V3_CONSOLIDATED_METADATA_KEY", + "ZARR_V3_GROUP_METADATA_STORE_KEY", "ZSTD_CODEC_NAME", "BloscCName", "BloscCodecMetadata", @@ -343,15 +363,19 @@ "ZarrV2ArrayMetadataJSON", "ZarrV2ArrayMetadataJSONPartial", "ZarrV2ArrayMetadataPartial", + "ZarrV2ArrayMetadataStoreKey", "ZarrV2ArrayOrder", + "ZarrV2AttributesStoreKey", "ZarrV2CodecMetadata", "ZarrV2ConsolidatedMetadata", "ZarrV2ConsolidatedMetadataJSON", + "ZarrV2ConsolidatedMetadataStoreKey", "ZarrV2DataTypeMetadata", "ZarrV2GroupMetadata", "ZarrV2GroupMetadataJSON", "ZarrV2GroupMetadataJSONPartial", "ZarrV2GroupMetadataPartial", + "ZarrV2GroupMetadataStoreKey", "ZarrV2ZArrayJSON", "ZarrV2ZAttrsJSON", "ZarrV2ZGroupJSON", @@ -359,6 +383,7 @@ "ZarrV3ArrayMetadataJSON", "ZarrV3ArrayMetadataJSONPartial", "ZarrV3ArrayMetadataPartial", + "ZarrV3ArrayMetadataStoreKey", "ZarrV3ConsolidatedMetadata", "ZarrV3ConsolidatedMetadataJSON", "ZarrV3ExtensionField", @@ -366,6 +391,7 @@ "ZarrV3GroupMetadataJSON", "ZarrV3GroupMetadataJSONPartial", "ZarrV3GroupMetadataPartial", + "ZarrV3GroupMetadataStoreKey", "ZarrV3MetadataField", "ZarrV3MetadataFieldJSON", "ZarrV3NamedConfig", diff --git a/packages/zarr-metadata/src/zarr_metadata/model/__init__.py b/packages/zarr-metadata/src/zarr_metadata/model/__init__.py index e726c54d3e..edf3561d1d 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/__init__.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/__init__.py @@ -12,33 +12,20 @@ """ from zarr_metadata.model._array import ( - ARRAY_METADATA_STORE_KEY_V2, - ARRAY_METADATA_STORE_KEY_V3, - ATTRIBUTES_STORE_KEY_V2, ZarrV2ArrayMetadata, ZarrV2ArrayMetadataPartial, - ZarrV2ArrayMetadataStoreKey, - ZarrV2AttributesStoreKey, ZarrV3ArrayMetadata, ZarrV3ArrayMetadataPartial, - ZarrV3ArrayMetadataStoreKey, ZarrV3MetadataField, ZarrV3NamedConfig, ) from zarr_metadata.model._group import ( - CONSOLIDATED_METADATA_KEY_V3, - CONSOLIDATED_METADATA_STORE_KEY_V2, - GROUP_METADATA_STORE_KEY_V2, - GROUP_METADATA_STORE_KEY_V3, ZarrV2ConsolidatedMetadata, - ZarrV2ConsolidatedMetadataStoreKey, ZarrV2GroupMetadata, ZarrV2GroupMetadataPartial, - ZarrV2GroupMetadataStoreKey, ZarrV3ConsolidatedMetadata, ZarrV3GroupMetadata, ZarrV3GroupMetadataPartial, - ZarrV3GroupMetadataStoreKey, ) from zarr_metadata.model._sentinel import UNSET from zarr_metadata.model._validation import ( @@ -73,23 +60,52 @@ validate_metadata_field_v3, ) +# Store keys are facts about the on-disk specs, so they are defined in the +# `v2`/`v3` modules that describe those documents. They are re-exported here +# because the model layer is where consumers reach for them. +from zarr_metadata.v2.array import ( + ZARR_V2_ARRAY_METADATA_STORE_KEY, + ZarrV2ArrayMetadataStoreKey, +) +from zarr_metadata.v2.attributes import ( + ZARR_V2_ATTRIBUTES_STORE_KEY, + ZarrV2AttributesStoreKey, +) +from zarr_metadata.v2.consolidated import ( + ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY, + ZarrV2ConsolidatedMetadataStoreKey, +) +from zarr_metadata.v2.group import ( + ZARR_V2_GROUP_METADATA_STORE_KEY, + ZarrV2GroupMetadataStoreKey, +) +from zarr_metadata.v3.array import ( + ZARR_V3_ARRAY_METADATA_STORE_KEY, + ZarrV3ArrayMetadataStoreKey, +) +from zarr_metadata.v3.consolidated import ZARR_V3_CONSOLIDATED_METADATA_KEY +from zarr_metadata.v3.group import ( + ZARR_V3_GROUP_METADATA_STORE_KEY, + ZarrV3GroupMetadataStoreKey, +) + __all__ = [ "ARRAY_METADATA_OPTIONAL_KEYS_V3", "ARRAY_METADATA_REQUIRED_KEYS_V2", "ARRAY_METADATA_REQUIRED_KEYS_V3", "ARRAY_METADATA_STANDARD_KEYS_V3", - "ARRAY_METADATA_STORE_KEY_V2", - "ARRAY_METADATA_STORE_KEY_V3", - "ATTRIBUTES_STORE_KEY_V2", - "CONSOLIDATED_METADATA_KEY_V3", - "CONSOLIDATED_METADATA_STORE_KEY_V2", "GROUP_METADATA_OPTIONAL_KEYS_V3", "GROUP_METADATA_REQUIRED_KEYS_V2", "GROUP_METADATA_REQUIRED_KEYS_V3", "GROUP_METADATA_STANDARD_KEYS_V3", - "GROUP_METADATA_STORE_KEY_V2", - "GROUP_METADATA_STORE_KEY_V3", "UNSET", + "ZARR_V2_ARRAY_METADATA_STORE_KEY", + "ZARR_V2_ATTRIBUTES_STORE_KEY", + "ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY", + "ZARR_V2_GROUP_METADATA_STORE_KEY", + "ZARR_V3_ARRAY_METADATA_STORE_KEY", + "ZARR_V3_CONSOLIDATED_METADATA_KEY", + "ZARR_V3_GROUP_METADATA_STORE_KEY", "MetadataValidationError", "ProblemKind", "ValidationProblem", diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_array.py b/packages/zarr-metadata/src/zarr_metadata/model/_array.py index c4c967f891..0b562bc188 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_array.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_array.py @@ -6,7 +6,7 @@ import dataclasses from collections.abc import Mapping from dataclasses import dataclass, field -from typing import TYPE_CHECKING, Final, Literal, TypeAlias, cast +from typing import TYPE_CHECKING, Literal, TypeAlias, cast from typing_extensions import TypedDict, Unpack @@ -22,27 +22,27 @@ parse_array_metadata_v3, parse_metadata_field_v3, ) +from zarr_metadata.v2.array import ZARR_V2_ARRAY_METADATA_STORE_KEY +from zarr_metadata.v2.attributes import ZARR_V2_ATTRIBUTES_STORE_KEY +from zarr_metadata.v3.array import ZARR_V3_ARRAY_METADATA_STORE_KEY if TYPE_CHECKING: from zarr_metadata._common import JSONValue, ZarrV3NamedConfigJSON from zarr_metadata.v2.array import ( ZarrV2ArrayDimensionSeparator, ZarrV2ArrayMetadataJSON, + ZarrV2ArrayMetadataStoreKey, ZarrV2ArrayOrder, ZarrV2DataTypeMetadata, ) + from zarr_metadata.v2.attributes import ZarrV2AttributesStoreKey from zarr_metadata.v2.codec import ZarrV2CodecMetadata from zarr_metadata.v3._common import ZarrV3MetadataFieldJSON - from zarr_metadata.v3.array import ZarrV3ArrayMetadataJSON, ZarrV3ExtensionField - -ZarrV3ArrayMetadataStoreKey = Literal["zarr.json"] -ARRAY_METADATA_STORE_KEY_V3: Final[ZarrV3ArrayMetadataStoreKey] = "zarr.json" - -ZarrV2ArrayMetadataStoreKey = Literal[".zarray"] -ARRAY_METADATA_STORE_KEY_V2: Final[ZarrV2ArrayMetadataStoreKey] = ".zarray" - -ZarrV2AttributesStoreKey = Literal[".zattrs"] -ATTRIBUTES_STORE_KEY_V2: Final[ZarrV2AttributesStoreKey] = ".zattrs" + from zarr_metadata.v3.array import ( + ZarrV3ArrayMetadataJSON, + ZarrV3ArrayMetadataStoreKey, + ZarrV3ExtensionField, + ) @dataclass(frozen=True, slots=True, kw_only=True) @@ -319,12 +319,12 @@ def must_understand_fields(self) -> dict[str, ZarrV3ExtensionField]: @classmethod def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV3ArrayMetadata: - return cls.from_json(load_store_json(mapping, ARRAY_METADATA_STORE_KEY_V3)) + return cls.from_json(load_store_json(mapping, ZARR_V3_ARRAY_METADATA_STORE_KEY)) def to_key_value( self, *, indent: int | str | None = None ) -> Mapping[ZarrV3ArrayMetadataStoreKey, bytes]: - return {ARRAY_METADATA_STORE_KEY_V3: dump_store_json(self.to_json(), indent=indent)} + return {ZARR_V3_ARRAY_METADATA_STORE_KEY: dump_store_json(self.to_json(), indent=indent)} class ZarrV2ArrayMetadataPartial(TypedDict, total=False): @@ -464,7 +464,7 @@ def from_json(cls, data: object) -> ZarrV2ArrayMetadata: @classmethod def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2ArrayMetadata: - zarray_raw = cast("object", load_store_json(mapping, ARRAY_METADATA_STORE_KEY_V2)) + zarray_raw = cast("object", load_store_json(mapping, ZARR_V2_ARRAY_METADATA_STORE_KEY)) if not isinstance(zarray_raw, Mapping): return cls.from_json(zarray_raw) zarray = cast("Mapping[str, object]", zarray_raw) @@ -478,8 +478,8 @@ def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2ArrayMetadata: ) ] ) - if ATTRIBUTES_STORE_KEY_V2 in mapping: - zattrs = cast("object", load_store_json(mapping, ATTRIBUTES_STORE_KEY_V2)) + if ZARR_V2_ATTRIBUTES_STORE_KEY in mapping: + zattrs = cast("object", load_store_json(mapping, ZARR_V2_ATTRIBUTES_STORE_KEY)) return cls.from_json({**zarray, "attributes": zattrs}) return cls.from_json(zarray) @@ -491,8 +491,8 @@ def to_key_value( # when attributes are set (even empty) — UNSET emits no file. zarray = {k: v for k, v in self.to_json().items() if k != "attributes"} out: dict[ZarrV2ArrayMetadataStoreKey | ZarrV2AttributesStoreKey, bytes] = { - ARRAY_METADATA_STORE_KEY_V2: dump_store_json(zarray, indent=indent) + ZARR_V2_ARRAY_METADATA_STORE_KEY: dump_store_json(zarray, indent=indent) } if self.attributes is not UNSET: - out[ATTRIBUTES_STORE_KEY_V2] = dump_store_json(self.attributes, indent=indent) + out[ZARR_V2_ATTRIBUTES_STORE_KEY] = dump_store_json(self.attributes, indent=indent) return out diff --git a/packages/zarr-metadata/src/zarr_metadata/model/_group.py b/packages/zarr-metadata/src/zarr_metadata/model/_group.py index d576833c26..63dfe5611f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/model/_group.py +++ b/packages/zarr-metadata/src/zarr_metadata/model/_group.py @@ -6,12 +6,11 @@ import dataclasses from collections.abc import Mapping from dataclasses import dataclass, field -from typing import TYPE_CHECKING, Final, Literal, cast +from typing import TYPE_CHECKING, Literal, cast from typing_extensions import TypedDict, Unpack from zarr_metadata.model._array import ( - ATTRIBUTES_STORE_KEY_V2, ZarrV3ArrayMetadata, must_understand_subset, ) @@ -28,28 +27,20 @@ validate_consolidated_metadata_v3, validate_json, ) +from zarr_metadata.v2.attributes import ZARR_V2_ATTRIBUTES_STORE_KEY +from zarr_metadata.v2.consolidated import ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY +from zarr_metadata.v2.group import ZARR_V2_GROUP_METADATA_STORE_KEY +from zarr_metadata.v3.consolidated import ZARR_V3_CONSOLIDATED_METADATA_KEY +from zarr_metadata.v3.group import ZARR_V3_GROUP_METADATA_STORE_KEY if TYPE_CHECKING: from zarr_metadata._common import JSONValue - from zarr_metadata.model._array import ZarrV2AttributesStoreKey - from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON + from zarr_metadata.v2.attributes import ZarrV2AttributesStoreKey + from zarr_metadata.v2.consolidated import ZarrV2ConsolidatedMetadataStoreKey + from zarr_metadata.v2.group import ZarrV2GroupMetadataJSON, ZarrV2GroupMetadataStoreKey from zarr_metadata.v3.array import ZarrV3ExtensionField from zarr_metadata.v3.consolidated import ZarrV3ConsolidatedMetadataJSON - from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON - -ZarrV3GroupMetadataStoreKey = Literal["zarr.json"] -GROUP_METADATA_STORE_KEY_V3: Final[ZarrV3GroupMetadataStoreKey] = "zarr.json" - -ZarrV2GroupMetadataStoreKey = Literal[".zgroup"] -GROUP_METADATA_STORE_KEY_V2: Final[ZarrV2GroupMetadataStoreKey] = ".zgroup" - -ZarrV2ConsolidatedMetadataStoreKey = Literal[".zmetadata"] -CONSOLIDATED_METADATA_STORE_KEY_V2: Final[ZarrV2ConsolidatedMetadataStoreKey] = ".zmetadata" - -# The key under which consolidated metadata is embedded in a v3 group document. -# This is a reference-implementation convention (not a spec artifact), stored -# as an extension field on the group's `zarr.json`. -CONSOLIDATED_METADATA_KEY_V3: Final = "consolidated_metadata" + from zarr_metadata.v3.group import ZarrV3GroupMetadataJSON, ZarrV3GroupMetadataStoreKey class ZarrV3GroupMetadataPartial(TypedDict, total=False): @@ -88,7 +79,7 @@ class ZarrV3GroupMetadata: extra_fields: dict[str, ZarrV3ExtensionField] def __post_init__(self) -> None: - reserved = GROUP_METADATA_STANDARD_KEYS_V3 | {CONSOLIDATED_METADATA_KEY_V3} + reserved = GROUP_METADATA_STANDARD_KEYS_V3 | {ZARR_V3_CONSOLIDATED_METADATA_KEY} if set(self.extra_fields.keys()).intersection(reserved): raise MetadataValidationError( [ @@ -134,7 +125,7 @@ def to_json(self) -> ZarrV3GroupMetadataJSON: out["attributes"] = copy.deepcopy(self.attributes) if self.consolidated_metadata is not UNSET: # Consolidated metadata is a known non-core top-level JSON field. - out[CONSOLIDATED_METADATA_KEY_V3] = cast( + out[ZARR_V3_CONSOLIDATED_METADATA_KEY] = cast( "ZarrV3ExtensionField", self.consolidated_metadata.to_json() ) for key, value in self.extra_fields.items(): @@ -145,7 +136,7 @@ def to_json(self) -> ZarrV3GroupMetadataJSON: def from_json(cls, data: object) -> ZarrV3GroupMetadata: parsed = parse_group_metadata_v3(arrays_to_tuples(data)) # Cast for narrowing across standard and arbitrary extra TypedDict items. - consolidated_raw = cast("object", parsed.get(CONSOLIDATED_METADATA_KEY_V3, UNSET)) + consolidated_raw = cast("object", parsed.get(ZARR_V3_CONSOLIDATED_METADATA_KEY, UNSET)) consolidated: ZarrV3ConsolidatedMetadata | UNSET if consolidated_raw is UNSET or consolidated_raw is None: # consolidated_metadata: null was written by a historical @@ -162,7 +153,8 @@ def from_json(cls, data: object) -> ZarrV3GroupMetadata: { k: v for k, v in parsed.items() - if k not in GROUP_METADATA_STANDARD_KEYS_V3 and k != CONSOLIDATED_METADATA_KEY_V3 + if k not in GROUP_METADATA_STANDARD_KEYS_V3 + and k != ZARR_V3_CONSOLIDATED_METADATA_KEY }, ) return cls( @@ -185,12 +177,12 @@ def must_understand_fields(self) -> dict[str, ZarrV3ExtensionField]: @classmethod def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV3GroupMetadata: - return cls.from_json(load_store_json(mapping, GROUP_METADATA_STORE_KEY_V3)) + return cls.from_json(load_store_json(mapping, ZARR_V3_GROUP_METADATA_STORE_KEY)) def to_key_value( self, *, indent: int | str | None = None ) -> Mapping[ZarrV3GroupMetadataStoreKey, bytes]: - return {GROUP_METADATA_STORE_KEY_V3: dump_store_json(self.to_json(), indent=indent)} + return {ZARR_V3_GROUP_METADATA_STORE_KEY: dump_store_json(self.to_json(), indent=indent)} @dataclass(frozen=True, slots=True, kw_only=True) @@ -322,7 +314,7 @@ def from_json(cls, data: object) -> ZarrV2GroupMetadata: @classmethod def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2GroupMetadata: - zgroup_raw = cast("object", load_store_json(mapping, GROUP_METADATA_STORE_KEY_V2)) + zgroup_raw = cast("object", load_store_json(mapping, ZARR_V2_GROUP_METADATA_STORE_KEY)) if not isinstance(zgroup_raw, Mapping): return cls.from_json(zgroup_raw) zgroup = cast("Mapping[str, object]", zgroup_raw) @@ -336,8 +328,8 @@ def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2GroupMetadata: ) ] ) - if ATTRIBUTES_STORE_KEY_V2 in mapping: - zattrs = cast("object", load_store_json(mapping, ATTRIBUTES_STORE_KEY_V2)) + if ZARR_V2_ATTRIBUTES_STORE_KEY in mapping: + zattrs = cast("object", load_store_json(mapping, ZARR_V2_ATTRIBUTES_STORE_KEY)) return cls.from_json({**zgroup, "attributes": zattrs}) return cls.from_json(zgroup) @@ -349,10 +341,10 @@ def to_key_value( # when attributes are set (even empty) — UNSET emits no file. zgroup = {k: v for k, v in self.to_json().items() if k != "attributes"} out: dict[ZarrV2GroupMetadataStoreKey | ZarrV2AttributesStoreKey, bytes] = { - GROUP_METADATA_STORE_KEY_V2: dump_store_json(zgroup, indent=indent) + ZARR_V2_GROUP_METADATA_STORE_KEY: dump_store_json(zgroup, indent=indent) } if self.attributes is not UNSET: - out[ATTRIBUTES_STORE_KEY_V2] = dump_store_json(self.attributes, indent=indent) + out[ZARR_V2_ATTRIBUTES_STORE_KEY] = dump_store_json(self.attributes, indent=indent) return out @@ -434,9 +426,11 @@ def from_json(cls, data: object) -> ZarrV2ConsolidatedMetadata: @classmethod def from_key_value(cls, mapping: Mapping[str, bytes]) -> ZarrV2ConsolidatedMetadata: - return cls.from_json(load_store_json(mapping, CONSOLIDATED_METADATA_STORE_KEY_V2)) + return cls.from_json(load_store_json(mapping, ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY)) def to_key_value( self, *, indent: int | str | None = None ) -> Mapping[ZarrV2ConsolidatedMetadataStoreKey, bytes]: - return {CONSOLIDATED_METADATA_STORE_KEY_V2: dump_store_json(self.to_json(), indent=indent)} + return { + ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY: dump_store_json(self.to_json(), indent=indent) + } diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/array.py b/packages/zarr-metadata/src/zarr_metadata/v2/array.py index 84b6446bcb..e026e5c655 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/array.py @@ -39,7 +39,7 @@ See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ -ARRAY_ORDER_V2: Final = ("C", "F") +ZARR_V2_ARRAY_ORDER: Final = ("C", "F") """Tuple of permitted values for the `order` field of v2 array metadata.""" ZarrV2ArrayDimensionSeparator = Literal[".", "/"] @@ -51,7 +51,7 @@ See https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html """ -ARRAY_DIMENSION_SEPARATOR_V2: Final = (".", "/") +ZARR_V2_ARRAY_DIMENSION_SEPARATOR: Final = (".", "/") """Tuple of permitted values for the `dimension_separator` field of v2 array metadata.""" @@ -149,12 +149,21 @@ class ZarrV2ArrayMetadataJSONPartial(TypedDict, total=False): """ +ZarrV2ArrayMetadataStoreKey = Literal[".zarray"] +"""Literal type of the store key holding a v2 array's metadata document.""" + +ZARR_V2_ARRAY_METADATA_STORE_KEY: Final[ZarrV2ArrayMetadataStoreKey] = ".zarray" +"""The store key a v2 array's metadata document is persisted under.""" + + __all__ = [ - "ARRAY_DIMENSION_SEPARATOR_V2", - "ARRAY_ORDER_V2", + "ZARR_V2_ARRAY_DIMENSION_SEPARATOR", + "ZARR_V2_ARRAY_METADATA_STORE_KEY", + "ZARR_V2_ARRAY_ORDER", "ZarrV2ArrayDimensionSeparator", "ZarrV2ArrayMetadataJSON", "ZarrV2ArrayMetadataJSONPartial", + "ZarrV2ArrayMetadataStoreKey", "ZarrV2ArrayOrder", "ZarrV2DataTypeMetadata", "ZarrV2ZArrayJSON", diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py index f7cc31babe..68785d1660 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/attributes.py @@ -4,6 +4,7 @@ """ from collections.abc import Mapping +from typing import Final, Literal from zarr_metadata._common import JSONValue @@ -17,6 +18,19 @@ """ +ZarrV2AttributesStoreKey = Literal[".zattrs"] +"""Literal type of the store key holding a v2 node's user attributes.""" + +ZARR_V2_ATTRIBUTES_STORE_KEY: Final[ZarrV2AttributesStoreKey] = ".zattrs" +"""The store key a v2 node's user attributes are persisted under. + +Shared by arrays and groups: both node types keep their attributes in a +sibling `.zattrs` file. +""" + + __all__ = [ + "ZARR_V2_ATTRIBUTES_STORE_KEY", + "ZarrV2AttributesStoreKey", "ZarrV2ZAttrsJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py index 6b586bb92e..999c9131da 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/consolidated.py @@ -7,6 +7,7 @@ """ from collections.abc import Mapping +from typing import Final, Literal from typing_extensions import TypedDict @@ -37,6 +38,19 @@ class ZarrV2ConsolidatedMetadataJSON(TypedDict): metadata: Mapping[str, ZarrV2ZArrayJSON | ZarrV2ZGroupJSON | ZarrV2ZAttrsJSON] +ZarrV2ConsolidatedMetadataStoreKey = Literal[".zmetadata"] +"""Literal type of the store key holding a v2 hierarchy's consolidated metadata.""" + +ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY: Final[ZarrV2ConsolidatedMetadataStoreKey] = ".zmetadata" +"""The store key a v2 hierarchy's consolidated metadata is persisted under. + +Like the document it names, this is a reference-implementation convention +rather than a spec artifact; see the module docstring. +""" + + __all__ = [ + "ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY", "ZarrV2ConsolidatedMetadataJSON", + "ZarrV2ConsolidatedMetadataStoreKey", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v2/group.py b/packages/zarr-metadata/src/zarr_metadata/v2/group.py index 50f2482e6f..34d72742c2 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v2/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v2/group.py @@ -4,7 +4,7 @@ """ from collections.abc import Mapping -from typing import Literal, NotRequired +from typing import Final, Literal, NotRequired from typing_extensions import TypedDict @@ -74,8 +74,17 @@ class ZarrV2GroupMetadataJSONPartial(TypedDict, total=False): attributes: NotRequired[Mapping[str, JSONValue]] +ZarrV2GroupMetadataStoreKey = Literal[".zgroup"] +"""Literal type of the store key holding a v2 group's metadata document.""" + +ZARR_V2_GROUP_METADATA_STORE_KEY: Final[ZarrV2GroupMetadataStoreKey] = ".zgroup" +"""The store key a v2 group's metadata document is persisted under.""" + + __all__ = [ + "ZARR_V2_GROUP_METADATA_STORE_KEY", "ZarrV2GroupMetadataJSON", "ZarrV2GroupMetadataJSONPartial", + "ZarrV2GroupMetadataStoreKey", "ZarrV2ZGroupJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/array.py b/packages/zarr-metadata/src/zarr_metadata/v3/array.py index 96341f73ca..31a5f6b755 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/array.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/array.py @@ -1,7 +1,7 @@ """Zarr v3 array metadata types.""" from collections.abc import Mapping -from typing import Literal, NotRequired, TypeAlias +from typing import Final, Literal, NotRequired, TypeAlias from typing_extensions import TypedDict @@ -75,8 +75,21 @@ class ZarrV3ArrayMetadataJSONPartial(TypedDict, total=False, extra_items=ZarrV3E dimension_names: NotRequired[tuple[str | None, ...]] +ZarrV3ArrayMetadataStoreKey = Literal["zarr.json"] +"""Literal type of the store key holding a v3 array's metadata document.""" + +ZARR_V3_ARRAY_METADATA_STORE_KEY: Final[ZarrV3ArrayMetadataStoreKey] = "zarr.json" +"""The store key a v3 array's metadata document is persisted under. + +v3 uses one key for both node types; the document's `node_type` field +distinguishes an array from a group. +""" + + __all__ = [ + "ZARR_V3_ARRAY_METADATA_STORE_KEY", "ZarrV3ArrayMetadataJSON", "ZarrV3ArrayMetadataJSONPartial", + "ZarrV3ArrayMetadataStoreKey", "ZarrV3ExtensionField", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py index bcbe675947..a9fe0c1f8f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/consolidated.py @@ -12,7 +12,7 @@ """ from collections.abc import Mapping -from typing import Literal +from typing import Final, Literal from typing_extensions import TypedDict @@ -34,6 +34,16 @@ class ZarrV3ConsolidatedMetadataJSON(TypedDict): metadata: Mapping[str, ZarrV3ArrayMetadataJSON | ZarrV3GroupMetadataJSON] +ZARR_V3_CONSOLIDATED_METADATA_KEY: Final = "consolidated_metadata" +"""The key under which consolidated metadata is embedded in a v3 group document. + +Unlike the v2 `.zmetadata` file, this is not a store key: consolidated metadata +is carried as an extension field inside the group's own `zarr.json`. Like its v2 +counterpart it is a reference-implementation convention, not a spec artifact. +""" + + __all__ = [ + "ZARR_V3_CONSOLIDATED_METADATA_KEY", "ZarrV3ConsolidatedMetadataJSON", ] diff --git a/packages/zarr-metadata/src/zarr_metadata/v3/group.py b/packages/zarr-metadata/src/zarr_metadata/v3/group.py index 033e91ff8c..37bfdd6934 100644 --- a/packages/zarr-metadata/src/zarr_metadata/v3/group.py +++ b/packages/zarr-metadata/src/zarr_metadata/v3/group.py @@ -4,7 +4,7 @@ """ from collections.abc import Mapping -from typing import Literal, NotRequired +from typing import Final, Literal, NotRequired from typing_extensions import TypedDict @@ -54,7 +54,20 @@ class ZarrV3GroupMetadataJSONPartial(TypedDict, total=False, extra_items=ZarrV3E attributes: NotRequired[Mapping[str, JSONValue]] +ZarrV3GroupMetadataStoreKey = Literal["zarr.json"] +"""Literal type of the store key holding a v3 group's metadata document.""" + +ZARR_V3_GROUP_METADATA_STORE_KEY: Final[ZarrV3GroupMetadataStoreKey] = "zarr.json" +"""The store key a v3 group's metadata document is persisted under. + +v3 uses one key for both node types; the document's `node_type` field +distinguishes a group from an array. +""" + + __all__ = [ + "ZARR_V3_GROUP_METADATA_STORE_KEY", "ZarrV3GroupMetadataJSON", "ZarrV3GroupMetadataJSONPartial", + "ZarrV3GroupMetadataStoreKey", ] diff --git a/packages/zarr-metadata/tests/model/test_array.py b/packages/zarr-metadata/tests/model/test_array.py index 467ef1e2ad..95dc7aea3a 100644 --- a/packages/zarr-metadata/tests/model/test_array.py +++ b/packages/zarr-metadata/tests/model/test_array.py @@ -64,25 +64,71 @@ def test_guards_exported_from_package() -> None: assert hasattr(zarr_metadata.model, name) +# `ZARR_V3_CONSOLIDATED_METADATA_KEY` is deliberately absent: it names a key +# *inside* a v3 group document, not a store key, so it has no paired `Literal` +# and no `to_key_value` signature to appear in. See `test_v3_consolidated_key_ +# is_not_a_store_key`, which pins that distinction. +STORE_KEY_PAIRS = [ + ("ZARR_V2_ARRAY_METADATA_STORE_KEY", "ZarrV2ArrayMetadataStoreKey", "zarr_metadata.v2.array"), + ("ZARR_V3_ARRAY_METADATA_STORE_KEY", "ZarrV3ArrayMetadataStoreKey", "zarr_metadata.v3.array"), + ("ZARR_V2_ATTRIBUTES_STORE_KEY", "ZarrV2AttributesStoreKey", "zarr_metadata.v2.attributes"), + ("ZARR_V2_GROUP_METADATA_STORE_KEY", "ZarrV2GroupMetadataStoreKey", "zarr_metadata.v2.group"), + ("ZARR_V3_GROUP_METADATA_STORE_KEY", "ZarrV3GroupMetadataStoreKey", "zarr_metadata.v3.group"), + ( + "ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY", + "ZarrV2ConsolidatedMetadataStoreKey", + "zarr_metadata.v2.consolidated", + ), +] + + def test_store_key_pairs_exported_from_package() -> None: """Each store-key constant is exported together with its Literal type alias, and the pair cannot drift apart.""" import zarr_metadata.model as m - pairs = [ - ("ARRAY_METADATA_STORE_KEY_V2", "ZarrV2ArrayMetadataStoreKey"), - ("ARRAY_METADATA_STORE_KEY_V3", "ZarrV3ArrayMetadataStoreKey"), - ("ATTRIBUTES_STORE_KEY_V2", "ZarrV2AttributesStoreKey"), - ("GROUP_METADATA_STORE_KEY_V2", "ZarrV2GroupMetadataStoreKey"), - ("GROUP_METADATA_STORE_KEY_V3", "ZarrV3GroupMetadataStoreKey"), - ("CONSOLIDATED_METADATA_STORE_KEY_V2", "ZarrV2ConsolidatedMetadataStoreKey"), - ] - for const_name, alias_name in pairs: + for const_name, alias_name, _ in STORE_KEY_PAIRS: assert const_name in m.__all__ assert alias_name in m.__all__ assert (getattr(m, const_name),) == get_args(getattr(m, alias_name)) +def test_store_keys_are_defined_in_their_spec_modules() -> None: + """Store keys are facts about the on-disk specs, so each is defined in the + `v2`/`v3` module describing that document — not in the model layer, which + only re-exports them.""" + import importlib + + for const_name, alias_name, module_name in STORE_KEY_PAIRS: + module = importlib.import_module(module_name) + for name in (const_name, alias_name): + assert name in module.__all__, f"{name} should be exported by {module_name}" + + +def test_v3_consolidated_key_is_not_a_store_key() -> None: + """v3 consolidated metadata is embedded as a field inside the group's own + `zarr.json`, not persisted under its own store key. It therefore has no + paired `Literal` alias, unlike every true store key — which is why it is + excluded from `STORE_KEY_PAIRS` rather than merely forgotten.""" + import zarr_metadata.model as m + + assert "ZARR_V3_CONSOLIDATED_METADATA_KEY" in m.__all__ + assert not hasattr(m, "ZarrV3ConsolidatedMetadataKey") + assert m.ZARR_V3_CONSOLIDATED_METADATA_KEY not in { + getattr(m, const_name) for const_name, _, _ in STORE_KEY_PAIRS + } + + +def test_v3_node_store_keys_agree() -> None: + """v3 keys both node types' metadata under one store key, distinguished by + the document's `node_type`. The array and group constants are separately + typed but must name the same file; adjacency used to make that obvious, and + they now live in different modules.""" + import zarr_metadata.model as m + + assert m.ZARR_V3_ARRAY_METADATA_STORE_KEY == m.ZARR_V3_GROUP_METADATA_STORE_KEY + + def test_validation_diagnostics_exported_from_package() -> None: """The validation-diagnostic types and validators are exported from the package.""" import zarr_metadata.model diff --git a/packages/zarr-metadata/tests/test_public_api.py b/packages/zarr-metadata/tests/test_public_api.py index e65c680fd1..6613aa394b 100644 --- a/packages/zarr-metadata/tests/test_public_api.py +++ b/packages/zarr-metadata/tests/test_public_api.py @@ -3,7 +3,7 @@ import importlib import pkgutil import re -from typing import get_args +from typing import Literal, get_args, get_origin import zarr_metadata as zm @@ -58,6 +58,23 @@ def _group_rank(s: str) -> int: "MetadataValidationError", "ProblemKind", "UNSET", + # Store keys — the names the documents are persisted under. Defined in the + # v2/v3 spec modules, re-exported through `zarr_metadata.model`. + "ZARR_V2_ARRAY_METADATA_STORE_KEY", + "ZarrV2ArrayMetadataStoreKey", + "ZARR_V2_GROUP_METADATA_STORE_KEY", + "ZarrV2GroupMetadataStoreKey", + "ZARR_V2_ATTRIBUTES_STORE_KEY", + "ZarrV2AttributesStoreKey", + "ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY", + "ZarrV2ConsolidatedMetadataStoreKey", + "ZARR_V3_ARRAY_METADATA_STORE_KEY", + "ZarrV3ArrayMetadataStoreKey", + "ZARR_V3_GROUP_METADATA_STORE_KEY", + "ZarrV3GroupMetadataStoreKey", + # Not a store key: v3 consolidated metadata is embedded in the group's own + # `zarr.json`, so it has no paired Literal alias. + "ZARR_V3_CONSOLIDATED_METADATA_KEY", # v2 data-type encoding union "ZarrV2DataTypeMetadata", # Category B — codec canonical unions @@ -147,9 +164,9 @@ def _group_rank(s: str) -> int: "RawBytesDataTypeName", "RawBytesFillValue", # Category E — constant+Literal pairs - "ARRAY_ORDER_V2", + "ZARR_V2_ARRAY_ORDER", "ZarrV2ArrayOrder", - "ARRAY_DIMENSION_SEPARATOR_V2", + "ZARR_V2_ARRAY_DIMENSION_SEPARATOR", "ZarrV2ArrayDimensionSeparator", "ENDIANNESS", "Endianness", @@ -285,14 +302,19 @@ def test_all_is_grouped_and_unique() -> None: ) -def _public_type_names() -> set[tuple[str, str]]: - """Every (module, CamelCase name) pair exported via a public `__all__`.""" +def _iter_module_names() -> set[str]: + """Every public module in the package, including the top-level namespace.""" module_names = {"zarr_metadata"} for info in pkgutil.walk_packages(zm.__path__, prefix="zarr_metadata."): if not any(part.startswith("_") for part in info.name.split(".")[1:]): module_names.add(info.name) + return module_names + + +def _public_type_names() -> set[tuple[str, str]]: + """Every (module, CamelCase name) pair exported via a public `__all__`.""" out: set[tuple[str, str]] = set() - for module_name in module_names: + for module_name in _iter_module_names(): module = importlib.import_module(module_name) for name in getattr(module, "__all__", ()): if name.startswith("_") or name.isupper() or name.islower(): @@ -323,6 +345,8 @@ def test_standalone_vocab_is_not_stale() -> None: def test_promoted_pairs_drift() -> None: + """Each promoted runtime constant holds exactly the values of the `Literal` + type it manifests, so the two cannot drift apart.""" pairs = [ (zm.ENDIANNESS, zm.Endianness), (zm.BLOSC_CNAME, zm.BloscCName), @@ -331,7 +355,134 @@ def test_promoted_pairs_drift() -> None: (zm.NUMPY_TIME_UNIT, zm.NumpyTimeUnit), (zm.CAST_ROUNDING_MODE, zm.CastRoundingMode), (zm.CAST_OUT_OF_RANGE_MODE, zm.CastOutOfRangeMode), - (zm.ARRAY_ORDER_V2, zm.ZarrV2ArrayOrder), + (zm.ZARR_V2_ARRAY_ORDER, zm.ZarrV2ArrayOrder), + (zm.ZARR_V2_ARRAY_DIMENSION_SEPARATOR, zm.ZarrV2ArrayDimensionSeparator), + (zm.DEFAULT_CHUNK_KEY_ENCODING_SEPARATOR, zm.DefaultChunkKeyEncodingSeparator), + (zm.V2_CHUNK_KEY_ENCODING_SEPARATOR, zm.V2ChunkKeyEncodingSeparator), ] for const, lit in pairs: assert set(const) == set(get_args(lit)) + + +def constant_name_for(type_name: str) -> str: + """Derive a constant's name from the name of the type it manifests. + + The transformation is purely syntactic: split at each lowercase-to-uppercase + boundary and before an uppercase run that starts a new word, then uppercase. + Digit runs stay glued to the token they follow (`Uint8` -> `UINT8`, + `Crc32c` -> `CRC32C`), because a digit boundary in CamelCase does not mark a + word boundary in the spec vocabulary these names model. + + Consecutive capitals do not split, so acronym-adjacent names derive badly: + `ZarrV2ZArrayJSON` -> `ZARR_V2ZARRAY_JSON` and `...JSONPartial` -> + `...JSONPARTIAL`. Every such name in the package today is a `TypedDict` or + `TypeAliasType` that backs no constant, so none reaches this function — but + a future `Literal` spelled that way would silently be held to a bad name. + Splitting acronyms correctly needs a vocabulary, not a regex, so the rule + stays syntactic and this stays a known limit. + """ + return re.sub(r"(?<=[a-z0-9])(?=[A-Z][a-z])|(?<=[a-z])(?=[A-Z])", "_", type_name).upper() + + +def _literal_backed_constants() -> list[tuple[str, str, str]]: + """Every (module, constant, type) triple where a module-level SCREAMING_SNAKE + constant holds exactly the values of a `Literal` type in the same module. + + Pairing is by value, not by proximity: a constant manifests the type whose + members it enumerates. Constants with no such type (extension-field keys, + key sets, canonical bit patterns) are exempt from the naming rule and are + simply absent from the result. + """ + out: list[tuple[str, str, str]] = [] + for module_name in _iter_module_names(): + module = importlib.import_module(module_name) + literals = { + name: frozenset(get_args(obj)) + for name, obj in vars(module).items() + if not name.startswith("_") + and not name.isupper() + and get_origin(obj) is Literal + and get_args(obj) + } + if not literals: + continue + for const_name, value in vars(module).items(): + if const_name.startswith("_") or not const_name.isupper(): + continue + members = frozenset(value) if isinstance(value, tuple) else frozenset({value}) + if not all(isinstance(m, str) for m in members): + continue + matches = [t for t, args in literals.items() if args == members] + # A single unambiguous type means this constant manifests it. Ties + # (two Literals with identical members) carry no signal about which + # name the constant should take, so they are skipped. + if len(matches) == 1: + out.append((module_name, const_name, matches[0])) + return out + + +def _value_tied_constants() -> set[str]: + """Constants whose manifested type is ambiguous because two or more `Literal` + types in the same module share its exact members. + + These are invisible to the derivation check, so they are surfaced here and + counted, rather than silently dropped inside the pairing helper.""" + tied: set[str] = set() + for module_name in _iter_module_names(): + module = importlib.import_module(module_name) + literals = [ + frozenset(get_args(obj)) + for name, obj in vars(module).items() + if not name.startswith("_") + and not name.isupper() + and get_origin(obj) is Literal + and get_args(obj) + ] + for const_name, value in vars(module).items(): + if const_name.startswith("_") or not const_name.isupper(): + continue + members = frozenset(value) if isinstance(value, tuple) else frozenset({value}) + if not all(isinstance(m, str) for m in members): + continue + if sum(1 for args in literals if args == members) > 1: + tied.add(f"{module_name}.{const_name}") + return tied + + +# Constants whose `Literal` type cannot be identified by value because another +# `Literal` in the same module has identical members. Pairing is by value, so a +# tie carries no signal about which name the constant should take. These are +# checked by eye; the count below fails if the tied set grows silently. +KNOWN_VALUE_TIES = 9 + + +def test_constant_names_derive_from_their_type_names() -> None: + """Every `Literal`-backed constant whose type can be identified by value has + a name that is the mechanical transform of that type's name. + + Constants tied to more than one identically-valued `Literal` are exempt (see + `KNOWN_VALUE_TIES`), as are constants in private modules and those backing + no `Literal` at all — so this pins the rule for most of the package, not all + of it.""" + pairs = _literal_backed_constants() + assert pairs, "found no Literal-backed constants to check" + violations = [ + f"{module}: {const} should be {constant_name_for(type_name)} (manifests {type_name})" + for module, const, type_name in pairs + if const != constant_name_for(type_name) + ] + assert not violations, "constants whose names do not derive from their type:\n" + "\n".join( + violations + ) + + +def test_value_tied_constants_are_a_known_set() -> None: + """The derivation check cannot see constants whose type is ambiguous by + value. Pin how many there are, so the exempt set cannot grow unnoticed and + quietly shrink the rule's coverage.""" + tied = _value_tied_constants() + assert len(tied) == KNOWN_VALUE_TIES, ( + f"value-tied constants changed (expected {KNOWN_VALUE_TIES}, got {len(tied)}); " + f"these are unchecked by the derivation rule and must be named by hand:\n" + + "\n".join(sorted(tied)) + ) From 4e13cf577d5be18b8e5312fa254d1a3034a3d321 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 5 Aug 2026 16:34:26 +0200 Subject: [PATCH 439/468] fix: preserve non-JSON-serializable storage options in _make_async (#4239) * fix: preserve non-JSON-serializable storage options in _make_async Converting a sync instance of an async-capable filesystem to an async instance went through fs.to_json()/from_json(), which raises TypeError when storage options hold objects like azure.identity credentials. Reconstruct the filesystem from storage_args/storage_options instead. Closes #4220 Assisted-by: ClaudeCode:claude-fable-5 * Rename 4220.bugfix.md to 4239.bugfix.md --- changes/4239.bugfix.md | 1 + src/zarr/storage/_fsspec.py | 9 ++++----- tests/test_store/test_fsspec.py | 18 ++++++++++++++++++ 3 files changed, 23 insertions(+), 5 deletions(-) create mode 100644 changes/4239.bugfix.md diff --git a/changes/4239.bugfix.md b/changes/4239.bugfix.md new file mode 100644 index 0000000000..b5bc92f18b --- /dev/null +++ b/changes/4239.bugfix.md @@ -0,0 +1 @@ +`FsspecStore.from_mapper` and `FsspecStore.from_url` no longer fail when converting a synchronous instance of an async-capable filesystem whose storage options contain objects that cannot be serialized to JSON (e.g. an `azure.identity.DefaultAzureCredential`). The async instance is now constructed from the original filesystem arguments instead of a JSON round-trip. diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index 37d134dd95..b109f80935 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -1,6 +1,5 @@ from __future__ import annotations -import json import warnings from contextlib import suppress from typing import TYPE_CHECKING, Any @@ -51,10 +50,10 @@ def _make_async(fs: AbstractFileSystem) -> AsyncFileSystem: # Already an async instance of an async filesystem, nothing to do return fs if fs.async_impl: - # Convert sync instance of an async fs to an async instance - fs_dict = json.loads(fs.to_json()) - fs_dict["asynchronous"] = True - return fsspec.AbstractFileSystem.from_json(json.dumps(fs_dict)) + # Convert sync instance of an async fs to an async instance. Reuse the original + # constructor arguments rather than round-tripping through JSON, since storage + # options may hold objects that are not JSON-serializable (e.g. credentials). + return type(fs)(*fs.storage_args, **{**fs.storage_options, "asynchronous": True}) if fsspec_version < parse_version("2024.12.0"): raise ImportError( diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index 515e1526b6..c367b908c5 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -584,6 +584,24 @@ def test_with_read_only_shares_filesystem(tmp_path: pathlib.Path) -> None: assert not source.read_only +def test_make_async_preserves_unserializable_storage_options() -> None: + """A sync instance of an async filesystem whose storage options hold objects that + cannot round-trip through JSON (e.g. an Azure credential) must still convert. + + See https://github.com/zarr-developers/zarr-python/issues/4220 + """ + pytest.importorskip("aiohttp") + credential = object() # stand-in for e.g. azure.identity.DefaultAzureCredential + sync_fs = fsspec.filesystem("http", client_kwargs={"auth": credential}) + assert sync_fs.async_impl + assert not sync_fs.asynchronous + + async_fs = _make_async(sync_fs) + + assert async_fs.asynchronous + assert async_fs.client_kwargs["auth"] is credential + + @pytest.mark.parametrize("asynchronous", [True, False]) def test_make_async(asynchronous: bool, endpoint_url: str) -> None: s3_filesystem = s3fs.S3FileSystem( From e382be8907f71729cd106d2ccf0b38eb016dc3c6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 6 Aug 2026 15:03:30 -0400 Subject: [PATCH 440/468] chore(deps): bump cryptography from 48.0.1 to 50.0.0 (#4240) Bumps [cryptography](https://github.com/pyca/cryptography) from 48.0.1 to 50.0.0. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pyca/cryptography/compare/48.0.1...50.0.0) --- updated-dependencies: - dependency-name: cryptography dependency-version: 50.0.0 dependency-type: indirect ... 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Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- uv.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/uv.lock b/uv.lock index b7f8ae9b3c..048816cf02 100644 --- a/uv.lock +++ b/uv.lock @@ -2409,15 +2409,15 @@ wheels = [ [[package]] name = "pymdown-extensions" -version = "10.21.3" +version = "11.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "markdown" }, { name = "pyyaml" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/9e/26/d1015444da4d952a1ca487a236b522eb979766f0295a0bd0c5fc089989a9/pymdown_extensions-10.21.3.tar.gz", hash = "sha256:72cfcf55f07aea0d4af2c4f11dd4e52466ddfb1bb819673146398e0bd3a77354", size = 854140, upload-time = "2026-05-13T12:57:32.267Z" } +sdist = { url = "https://files.pythonhosted.org/packages/47/67/f1e79672a5f91985577c7984c9709ca110e4fd37fe7fd167b60422e6ccc2/pymdown_extensions-11.0.tar.gz", hash = "sha256:8269cef0247f9e2d0a62fcea10860aba05c1cbab5470fd4b63230b96434dc589", size = 857049, upload-time = "2026-06-23T02:27:45.146Z" } wheels = [ - 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[Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0...3d3c42e5aac5ba805825da76410c181273ba90b1) Updates `astral-sh/setup-uv` from 8.3.2 to 9.0.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/11f9893b081a58869d3b5fccaea48c9e9e46f990...c771a70e6277c0a99b617c7a806ffedaca235ff9) Updates `CodSpeedHQ/action` from 4.18.5 to 5.0.1 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/f99becdce5e5d51fd556489ebef684f4ecfd6286...88472375d0a4572cf70a9f1fe3a4e0ab8da1b924) Updates `actions/setup-python` from 6.3.0 to 7.0.0 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/ece7cb06caefa5fff74198d8649806c4678c61a1...5fda3b95a4ea91299a34e894583c3862153e4b97) Updates `scientific-python/issue-from-pytest-log-action` from 1.6.0 to 1.6.1 - [Release notes](https://github.com/scientific-python/issue-from-pytest-log-action/releases) - [Commits](https://github.com/scientific-python/issue-from-pytest-log-action/compare/87351a8f864e969567cda22a25a2f214cbe2340f...054799b34bd75a5fd6c86277a4a8a575224e60c6) Updates `j178/prek-action` from 2.0.5 to 3.0.0 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/e98a699c41eb69ab013a45817a0406469a748f8d...4e14d07f9231acabce116ccfca13b13dd9755ece) Updates `actions/attest` from 4.2.0 to 4.2.1 - [Release notes](https://github.com/actions/attest/releases) - [Changelog](https://github.com/actions/attest/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest/compare/f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6...508db95dd578ae2727ebd6217d5ba78e4fbda05d) Updates `pypa/gh-action-pypi-publish` from 1.14.0 to 1.14.2 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/cef221092ed1bacb1cc03d23a2d87d1d172e277b...dc37677b2e1c63e2034f94d8a5b11f265b73ba33) Updates `zizmorcore/zizmor-action` from 0.6.0 to 0.6.1 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/6599ee8b7a49aef6a770f63d261d214911a7ce02...6fc4b006235f201fdab3722e17240ab420d580e5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 9.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: CodSpeedHQ/action dependency-version: 5.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/setup-python dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: scientific-python/issue-from-pytest-log-action dependency-version: 1.6.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 3.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/attest dependency-version: 4.2.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.6.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- .github/workflows/check_changelogs.yml | 4 ++-- .github/workflows/codspeed.yml | 4 ++-- .github/workflows/docs.yml | 4 ++-- .github/workflows/downstream.yml | 16 +++++++------- .github/workflows/gpu_test.yml | 6 +++--- .github/workflows/hypothesis.yaml | 8 +++---- .github/workflows/links.yml | 2 +- .github/workflows/lint.yml | 8 +++---- .github/workflows/nightly_wheels.yml | 4 ++-- .github/workflows/releases.yml | 8 +++---- .github/workflows/test.yml | 24 ++++++++++----------- .github/workflows/zarr-indexing-release.yml | 12 +++++------ .github/workflows/zarr-indexing.yml | 16 +++++++------- .github/workflows/zarr-metadata-release.yml | 12 +++++------ .github/workflows/zarr-metadata.yml | 16 +++++++------- .github/workflows/zizmor.yml | 4 ++-- 16 files changed, 74 insertions(+), 74 deletions(-) diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index d7a54fc2c4..b6c01e70fc 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -17,12 +17,12 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Check zarr-python changelog entries run: uv run --no-sync python ci/check_changelog_entries.py diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 427262d598..17e9de89ba 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -23,7 +23,7 @@ jobs: github.event_name == 'workflow_dispatch' || (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark')) steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 persist-credentials: false @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@f99becdce5e5d51fd556489ebef684f4ecfd6286 # v4.18.5 + uses: CodSpeedHQ/action@88472375d0a4572cf70a9f1fe3a4e0ab8da1b924 # v5.0.1 env: ZARR_BENCHMARK_CLEAR_CACHE: '1' with: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index baf9233fc7..792ee431ab 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -19,10 +19,10 @@ jobs: name: Check docs runs-on: ubuntu-latest steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + - uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - run: uv sync --group docs # Fast source-level guards that need no built site, so they run before the (slower) # build for a quick failure: every public export is in the API reference, and no diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml index f65f8d47e3..98cd0fee3f 100644 --- a/.github/workflows/downstream.yml +++ b/.github/workflows/downstream.yml @@ -21,13 +21,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out zarr-python - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 persist-credentials: false - name: Check out xarray - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: repository: pydata/xarray path: xarray @@ -40,12 +40,12 @@ jobs: # `meson-python: error: Unknown option "pixi-conda-environment"`, breaking # the job before any test runs. Tests that need a backend we don't install # are skipped via xarray's `requires_*` markers, not failed. - - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install xarray and test dependencies working-directory: xarray @@ -83,13 +83,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out zarr-python - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 persist-credentials: false - name: Check out numcodecs - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: repository: zarr-developers/numcodecs fetch-depth: 0 @@ -97,12 +97,12 @@ jobs: submodules: recursive persist-credentials: false - - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: '3.13' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install numcodecs with test-zarr-main group working-directory: numcodecs diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml index bbbb3e5133..bf8700400e 100644 --- a/.github/workflows/gpu_test.yml +++ b/.github/workflows/gpu_test.yml @@ -34,7 +34,7 @@ jobs: python-version: ['3.12'] steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 # grab all branches and tags persist-credentials: false @@ -57,12 +57,12 @@ jobs: echo $LD_LIBRARY_PATH nvcc -V - name: Set up Python - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index e836f30a5b..cfe4477e52 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -39,7 +39,7 @@ jobs: dependency-set: ["optional"] steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Set HYPOTHESIS_PROFILE based on trigger @@ -52,12 +52,12 @@ jobs: echo "HYPOTHESIS_PROFILE=ci" >> $GITHUB_ENV fi - name: Set up Python - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install Hatch uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc with: @@ -109,7 +109,7 @@ jobs: && steps.status.outcome == 'failure' && github.event_name == 'schedule' && github.repository_owner == 'zarr-developers' - uses: scientific-python/issue-from-pytest-log-action@87351a8f864e969567cda22a25a2f214cbe2340f # v1.6.0 + uses: scientific-python/issue-from-pytest-log-action@054799b34bd75a5fd6c86277a4a8a575224e60c6 # v1.6.1 with: log-path: output-${{ matrix.python-version }}-log.jsonl issue-title: "Nightly Hypothesis tests failed" diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml index 0af76deece..d52639a708 100644 --- a/.github/workflows/links.yml +++ b/.github/workflows/links.yml @@ -13,7 +13,7 @@ jobs: permissions: issues: write # required for peter-evans/create-issue-from-file steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index dacba6648f..83cc0a1b3e 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -19,15 +19,15 @@ jobs: name: Lint runs-on: ubuntu-latest steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Set up Python - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: "3.12" - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true - - uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2.0.5 + - uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0 diff --git a/.github/workflows/nightly_wheels.yml b/.github/workflows/nightly_wheels.yml index 0a0cafd425..5b99c523a1 100644 --- a/.github/workflows/nightly_wheels.yml +++ b/.github/workflows/nightly_wheels.yml @@ -22,13 +22,13 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: submodules: true fetch-depth: 0 persist-credentials: false - - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 name: Install Python with: python-version: '3.14' diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index fe0d09f300..759c443dd5 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -26,13 +26,13 @@ jobs: fail-fast: false steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: submodules: true fetch-depth: 0 persist-credentials: false - - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 name: Install Python with: python-version: '3.12' @@ -81,8 +81,8 @@ jobs: name: releases path: dist - name: Generate artifact attestation - uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 + uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 with: subject-path: dist/* - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index ce6b7e3eba..50bb85ff5c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -56,17 +56,17 @@ jobs: runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 # grab all branches and tags persist-credentials: false - name: Set up Python - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -105,17 +105,17 @@ jobs: - python-version: "3.12" dependency-set: upstream steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 persist-credentials: false - name: Set up Python - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: ${{ matrix.python-version }} cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -140,17 +140,17 @@ jobs: name: doctests runs-on: ubuntu-latest steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3 persist-credentials: false - name: Set up Python - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Set Up Hatch Env @@ -164,17 +164,17 @@ jobs: name: Benchmark smoke test runs-on: ubuntu-latest steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: fetch-depth: 0 persist-credentials: false - name: Set up Python - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0 with: python-version: '3.13' cache: 'pip' - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install Hatch run: python -m pip install hatch==1.16.5 - name: Run Benchmarks diff --git a/.github/workflows/zarr-indexing-release.yml b/.github/workflows/zarr-indexing-release.yml index 7cfd571eae..de57594d2b 100644 --- a/.github/workflows/zarr-indexing-release.yml +++ b/.github/workflows/zarr-indexing-release.yml @@ -22,7 +22,7 @@ jobs: shell: bash working-directory: packages/zarr-indexing steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false fetch-depth: 0 # hatch-vcs needs full history + tags @@ -51,7 +51,7 @@ jobs: path: dist - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: false @@ -82,12 +82,12 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 + uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 with: subject-path: dist/* - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 upload_testpypi: name: Upload to TestPyPI @@ -107,11 +107,11 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 + uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 with: subject-path: dist/* - name: Publish package to TestPyPI - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 with: repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/zarr-indexing.yml b/.github/workflows/zarr-indexing.yml index 2106b10916..afaa9e6db7 100644 --- a/.github/workflows/zarr-indexing.yml +++ b/.github/workflows/zarr-indexing.yml @@ -31,11 +31,11 @@ jobs: matrix: python-version: ['3.12', '3.13', '3.14'] steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true - name: Set up Python ${{ matrix.python-version }} @@ -57,11 +57,11 @@ jobs: shell: bash working-directory: packages/zarr-indexing steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Run ruff run: uvx ruff check . @@ -73,11 +73,11 @@ jobs: shell: bash working-directory: packages/zarr-indexing steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true - name: Set up Python @@ -95,11 +95,11 @@ jobs: shell: bash working-directory: packages/zarr-indexing steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true - name: Install just diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index bc9ecf9871..f9516ead71 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -22,7 +22,7 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false fetch-depth: 0 # hatch-vcs needs full history + tags @@ -51,7 +51,7 @@ jobs: path: dist - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: false @@ -82,12 +82,12 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 + uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 with: subject-path: dist/* - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 upload_testpypi: name: Upload to TestPyPI @@ -107,11 +107,11 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0 + uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 with: subject-path: dist/* - name: Publish package to TestPyPI - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0 + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 with: repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/zarr-metadata.yml b/.github/workflows/zarr-metadata.yml index b5f56dd508..5b3b83b0e0 100644 --- a/.github/workflows/zarr-metadata.yml +++ b/.github/workflows/zarr-metadata.yml @@ -35,11 +35,11 @@ jobs: matrix: python-version: ['3.11', '3.12', '3.13', '3.14'] steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true - name: Install just @@ -59,11 +59,11 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: Install just uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 - name: Run ruff @@ -77,11 +77,11 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true - name: Install just @@ -98,11 +98,11 @@ jobs: shell: bash working-directory: packages/zarr-metadata steps: - - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true - name: Install just diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 1567bea713..9022c56455 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -27,9 +27,9 @@ jobs: security-events: write # Required by zizmor-action to upload SARIF files steps: - name: Checkout repository - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@6599ee8b7a49aef6a770f63d261d214911a7ce02 # v0.6.0 + uses: zizmorcore/zizmor-action@6fc4b006235f201fdab3722e17240ab420d580e5 # v0.6.1 From 96a54615b108d6d37b6f9722ad8d6165a0e7b185 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Tue, 11 Aug 2026 17:32:42 +0200 Subject: [PATCH 444/468] chore: bump ruff to 0.16.0 and fix new default-rule violations (#4213) Ruff 0.16.0 enables a much larger default rule set (flake8-bugbear, blind-except, bandit subset, pylint subset, etc.) and formats Python code blocks inside Markdown files. This bumps the pin in pyproject.toml and pre-commit, applies the automatic fixes (RUF036 None-at-end-of-union, RUF100 unused noqa, PLR1716 chained comparison), and resolves the rest by hand: - StorePath.__eq__ narrows a blind 'except Exception: pass' to 'except AttributeError: return False' (BLE001/S110) - reset_resources_after_fork drops 'loop' and 'iothread' from the global statement; they are mutated in place, not rebound (PLW0602) - subprocess.run calls in tests pass check=False explicitly since they assert on returncode themselves (PLW1510) - intentional patterns (returning the caught exception in sync._runner, self-equality assertion in the store test suite) get targeted noqa comments (BLE001/PLR0124) Assisted-by: ClaudeCode:claude-fable-5 Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- changes/4213.misc.md | 1 + design/chunk-grid.md | 67 +++++++++++-------- pyproject.toml | 2 +- src/zarr/api/synchronous.py | 2 +- src/zarr/codecs/sharding.py | 2 +- src/zarr/core/array.py | 6 +- src/zarr/core/dtype/common.py | 2 +- src/zarr/core/sync.py | 6 +- src/zarr/storage/_common.py | 5 +- src/zarr/testing/store.py | 2 +- src/zarr/testing/strategies.py | 6 +- tests/test_api.py | 2 +- tests/test_codecs/test_blosc.py | 4 +- tests/test_dtype_registry.py | 2 +- tests/test_examples.py | 2 +- .../test_v2_dtype_regression.py | 2 + tests/test_store/test_core.py | 2 +- tests/test_store/test_object.py | 1 - tests/test_unified_chunk_grid.py | 4 +- tests/test_v2.py | 2 +- uv.lock | 46 ++++++------- 22 files changed, 91 insertions(+), 79 deletions(-) create mode 100644 changes/4213.misc.md diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 57a1d0d4f7..7f49f47187 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ default_language_version: repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.20 + rev: v0.16.0 hooks: - id: ruff-check args: ["--fix", "--show-fixes"] diff --git a/changes/4213.misc.md b/changes/4213.misc.md new file mode 100644 index 0000000000..150e60b57b --- /dev/null +++ b/changes/4213.misc.md @@ -0,0 +1 @@ +Updated ruff to 0.16.0 and fixed the violations surfaced by its expanded default rule set: narrowed a blind `except Exception` in `StorePath.__eq__` to `AttributeError`, removed unnecessary `global` declarations in `zarr.core.sync`, made `subprocess.run` calls in tests pass `check=False` explicitly, and applied automatic fixes (`None` moved to the end of type unions, unused `noqa` directives removed). diff --git a/design/chunk-grid.md b/design/chunk-grid.md index eaa5fffad5..0f12e35c4b 100644 --- a/design/chunk-grid.md +++ b/design/chunk-grid.md @@ -162,9 +162,9 @@ class DimensionGrid(Protocol): @property def extent(self) -> int: ... def index_to_chunk(self, idx: int) -> int: ... - def chunk_offset(self, chunk_ix: int) -> int: ... # raises IndexError if OOB - def chunk_size(self, chunk_ix: int) -> int: ... # raises IndexError if OOB - def data_size(self, chunk_ix: int) -> int: ... # raises IndexError if OOB + def chunk_offset(self, chunk_ix: int) -> int: ... # raises IndexError if OOB + def chunk_size(self, chunk_ix: int) -> int: ... # raises IndexError if OOB + def data_size(self, chunk_ix: int) -> int: ... # raises IndexError if OOB def indices_to_chunks(self, indices: NDArray[np.intp]) -> NDArray[np.intp]: ... @property def unique_edge_lengths(self) -> Iterable[int]: ... @@ -181,8 +181,8 @@ The protocol is `@runtime_checkable`, enabling polymorphic handling of both dime ```python @dataclass(frozen=True) class ChunkSpec: - slices: tuple[slice, ...] # valid data region in array coordinates - codec_shape: tuple[int, ...] # buffer shape for codec processing + slices: tuple[slice, ...] # valid data region in array coordinates + codec_shape: tuple[int, ...] # buffer shape for codec processing @property def shape(self) -> tuple[int, ...]: @@ -199,34 +199,34 @@ For interior chunks, `shape == codec_shape`. For boundary chunks of a regular gr ```python # Creating arrays -arr = zarr.create_array(shape=(100, 200), chunks=(10, 20)) # regular -arr = zarr.create_array(shape=(60, 100), chunks=[[10, 20, 30], [25, 25, 25, 25]]) # rectilinear +arr = zarr.create_array(shape=(100, 200), chunks=(10, 20)) # regular +arr = zarr.create_array(shape=(60, 100), chunks=[[10, 20, 30], [25, 25, 25, 25]]) # rectilinear # ChunkGrid as a collection -grid = arr._chunk_grid # ChunkGrid (bound to array shape) -grid.grid_shape # (10, 10) — number of chunks per dimension -grid.ndim # 2 -grid.is_regular # True if all dimensions are Fixed +grid = arr._chunk_grid # ChunkGrid (bound to array shape) +grid.grid_shape # (10, 10) — number of chunks per dimension +grid.ndim # 2 +grid.is_regular # True if all dimensions are Fixed -spec = grid[0, 1] # ChunkSpec for chunk at grid position (0, 1) -spec.slices # (slice(0, 10), slice(20, 40)) -spec.shape # (10, 20) — data shape -spec.codec_shape # (10, 20) — same for interior chunks +spec = grid[0, 1] # ChunkSpec for chunk at grid position (0, 1) +spec.slices # (slice(0, 10), slice(20, 40)) +spec.shape # (10, 20) — data shape +spec.codec_shape # (10, 20) — same for interior chunks -boundary = grid[9, 0] # boundary chunk (extent=100, size=10) -boundary.shape # (10, 20) — data shape -boundary.codec_shape # (10, 20) — codec sees full buffer +boundary = grid[9, 0] # boundary chunk (extent=100, size=10) +boundary.shape # (10, 20) — data shape +boundary.codec_shape # (10, 20) — codec sees full buffer -grid[99, 99] # None — out of bounds +grid[99, 99] # None — out of bounds -for spec in grid: # iterate all chunks +for spec in grid: # iterate all chunks ... # .chunks property: retained for regular grids, raises NotImplementedError for rectilinear -arr.chunks # (10, 20) +arr.chunks # (10, 20) # .read_chunk_sizes / .write_chunk_sizes: works for all grids (dask-style) -arr.write_chunk_sizes # ((10, 10, ..., 10), (20, 20, ..., 20)) +arr.write_chunk_sizes # ((10, 10, ..., 10), (20, 20, ..., 20)) ``` `ChunkGrid.__getitem__` constructs `ChunkSpec` using `chunk_size` for `codec_shape` and `data_size` for `slices`: @@ -274,7 +274,10 @@ When `extent < sum(edges)`, the dimension is always stored as `VaryingDimension` {"name": "regular", "configuration": {"chunk_shape": [10, 20]}} # Rectilinear grid (with RLE compression and "kind" field): -{"name": "rectilinear", "configuration": {"kind": "inline", "chunk_shapes": [[10, 20, 30], [[25, 4]]]}} +{ + "name": "rectilinear", + "configuration": {"kind": "inline", "chunk_shapes": [[10, 20, 30], [[25, 4]]]}, +} ``` Both names deserialize to the same `ChunkGrid` class. The serialized form does not include the array extent — that comes from `shape` in array metadata and is combined with the chunk grid when constructing a `ChunkGrid` via `ChunkGrid.from_metadata()`. @@ -324,9 +327,9 @@ The underlying `ChunkGrid.chunk_sizes` property (on the grid, not the array) ret #### Resize ```python -arr.resize((80, 100)) # re-binds extent; FixedDimension stays fixed -arr.resize((200, 100)) # VaryingDimension grows by appending a new chunk -arr.resize((30, 100)) # VaryingDimension shrinks: preserves all edges, re-binds extent +arr.resize((80, 100)) # re-binds extent; FixedDimension stays fixed +arr.resize((200, 100)) # VaryingDimension grows by appending a new chunk +arr.resize((30, 100)) # VaryingDimension shrinks: preserves all edges, re-binds extent ``` Resize uses `ChunkGrid.update_shape(new_shape)`, which delegates to each dimension's `.resize()` method: @@ -363,8 +366,8 @@ When `chunks="keep"`, the logic checks `data._chunk_grid.is_regular`: The indexing pipeline is coupled to regular grid assumptions — every per-dimension indexer takes a scalar `dim_chunk_len: int` and uses `//` and `*`: ```python -dim_chunk_ix = self.dim_sel // self.dim_chunk_len # IntDimIndexer -dim_offset = dim_chunk_ix * self.dim_chunk_len # SliceDimIndexer +dim_chunk_ix = self.dim_sel // self.dim_chunk_len # IntDimIndexer +dim_offset = dim_chunk_ix * self.dim_chunk_len # SliceDimIndexer ``` Replace `dim_chunk_len: int` with the dimension object (`FixedDimension | VaryingDimension`). The shared interface means the indexer code structure stays the same — `dim_sel // dim_chunk_len` becomes `dim_grid.index_to_chunk(dim_sel)`. O(1) for regular, binary search for varying. @@ -590,14 +593,18 @@ If cubed needs to support both old and new zarr-python: def _create_zarr_indexer(selection, shape, chunks): if zarr.__version__[0] == "3": from zarr.core.indexing import OrthogonalIndexer + try: from zarr.core.chunk_grids import ChunkGrid + return OrthogonalIndexer(selection, shape, ChunkGrid.from_sizes(shape, chunks)) except ImportError: from zarr.core.chunk_grids import RegularChunkGrid + return OrthogonalIndexer(selection, shape, RegularChunkGrid(chunk_shape=chunks)) else: from zarr.indexing import OrthogonalIndexer + return OrthogonalIndexer(selection, ZarrArrayIndexingAdaptor(shape, chunks)) ``` @@ -625,13 +632,15 @@ def _resolve_chunk_grid(chunk_grid, shape): """Coerce ChunkGridMetadata to runtime ChunkGrid if needed.""" from zarr.core.chunk_grids import ChunkGrid as _ChunkGrid from zarr.core.metadata.v3 import ChunkGridMetadata + if isinstance(chunk_grid, _ChunkGrid): return chunk_grid if isinstance(chunk_grid, ChunkGridMetadata): warnings.warn( "Passing ChunkGridMetadata to indexers is deprecated. " "Use ChunkGrid.from_sizes() instead.", - DeprecationWarning, stacklevel=2, + DeprecationWarning, + stacklevel=2, ) if hasattr(chunk_grid, "chunk_shape"): return _ChunkGrid.from_sizes(shape, tuple(chunk_grid.chunk_shape)) diff --git a/pyproject.toml b/pyproject.toml index 684ac80b77..663a1ea286 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -129,7 +129,7 @@ docs = [ "mkdocs-redirects==1.2.3", "markdown-exec[ansi]==1.12.3", "griffe-inherited-docstrings==1.1.3", - "ruff==0.15.22", + "ruff==0.16.0", # Changelog generation {include-group = "release"}, # Optional dependencies to run examples diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py index ebf42dca37..30ddf9ce6a 100644 --- a/src/zarr/api/synchronous.py +++ b/src/zarr/api/synchronous.py @@ -998,7 +998,7 @@ def from_array( write_data: bool = True, name: str | None = None, chunks: ChunksLike | Literal["auto", "keep"] = "keep", - shards: ShardsLike | None | Literal["keep"] = "keep", + shards: ShardsLike | Literal["keep"] | None = "keep", filters: FiltersLike | Literal["keep"] = "keep", compressors: CompressorsLike | Literal["keep"] = "keep", serializer: SerializerLike | Literal["keep"] = "keep", diff --git a/src/zarr/codecs/sharding.py b/src/zarr/codecs/sharding.py index d8ca8bdf62..41780e45b4 100644 --- a/src/zarr/codecs/sharding.py +++ b/src/zarr/codecs/sharding.py @@ -841,7 +841,7 @@ def _encode_partial_sync( # `_sentinel` distinguishes "not computed yet" from a memoized `None` # (an empty chunk). _sentinel = object() - scalar_complete_result: Buffer | None | object = _sentinel + scalar_complete_result: Buffer | object | None = _sentinel for chunk_coords, chunk_sel, out_sel, is_complete_chunk in indexer: if is_scalar and is_complete_chunk: diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py index 2b31eefcd4..9cb66f339e 100644 --- a/src/zarr/core/array.py +++ b/src/zarr/core/array.py @@ -2181,7 +2181,7 @@ def filters(self) -> tuple[Numcodec, ...] | tuple[ArrayArrayCodec, ...]: return self.async_array.filters @property - def serializer(self) -> None | ArrayBytesCodec: + def serializer(self) -> ArrayBytesCodec | None: """ Array-to-bytes codec to use for serializing the chunks into bytes. """ @@ -4072,7 +4072,7 @@ async def from_array( write_data: bool = True, name: str | None = None, chunks: ChunksLike | Literal["auto", "keep"] = "keep", - shards: ShardsLike | None | Literal["keep"] = "keep", + shards: ShardsLike | Literal["keep"] | None = "keep", filters: FiltersLike | Literal["keep"] = "keep", compressors: CompressorsLike | Literal["keep"] = "keep", serializer: SerializerLike | Literal["keep"] = "keep", @@ -4763,7 +4763,7 @@ async def create_array( def _parse_keep_array_attr( data: AnyArray | npt.ArrayLike, chunks: ChunksLike | Literal["auto", "keep"], - shards: ShardsLike | None | Literal["keep"], + shards: ShardsLike | Literal["keep"] | None, filters: FiltersLike | Literal["keep"], compressors: CompressorsLike | Literal["keep"], serializer: SerializerLike | Literal["keep"], diff --git a/src/zarr/core/dtype/common.py b/src/zarr/core/dtype/common.py index 76d763d267..61cbfe0360 100644 --- a/src/zarr/core/dtype/common.py +++ b/src/zarr/core/dtype/common.py @@ -52,7 +52,7 @@ DTypeName_V2 = StructuredName_V2 | str -class DTypeConfig_V2[TDTypeNameV2: DTypeName_V2, TObjectCodecID: None | str](TypedDict): +class DTypeConfig_V2[TDTypeNameV2: DTypeName_V2, TObjectCodecID: str | None](TypedDict): name: ReadOnly[TDTypeNameV2] object_codec_id: ReadOnly[TObjectCodecID] diff --git a/src/zarr/core/sync.py b/src/zarr/core/sync.py index 160950ba64..724b31a464 100644 --- a/src/zarr/core/sync.py +++ b/src/zarr/core/sync.py @@ -90,7 +90,9 @@ def reset_resources_after_fork() -> None: Ensure that global resources are reset after a fork. Without this function, forked processes will retain invalid references to the parent process's resources. """ - global loop, iothread, _executor + # `loop` and `iothread` are mutated in place rather than rebound, so only + # `_executor` needs the global declaration. + global _executor # These lines are excluded from coverage because this function only runs in a child process, # which is not observed by the test coverage instrumentation. Despite the apparent lack of # test coverage, this function should be adequately tested by any test that uses Zarr IO with @@ -112,7 +114,7 @@ async def _runner[T](coro: Coroutine[Any, Any, T]) -> T | BaseException: """ try: return await coro - except Exception as ex: + except Exception as ex: # noqa: BLE001 -- the caller re-raises the returned exception return ex diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index ed554327cd..64dc486e01 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -297,9 +297,8 @@ def __eq__(self, other: object) -> bool: """ try: return self.store == other.store and self.path == other.path # type: ignore[attr-defined, no-any-return] - except Exception: - pass - return False + except AttributeError: + return False type StoreLike = Store | StorePath | FSMap | Path | str | dict[str, Buffer] diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py index f64d8e9364..4c948a783c 100644 --- a/src/zarr/testing/store.py +++ b/src/zarr/testing/store.py @@ -115,7 +115,7 @@ def test_store_type(self, store: S) -> None: def test_store_eq(self, store: S, store_kwargs: dict[str, Any]) -> None: # check self equality - assert store == store + assert store == store # noqa: PLR0124 -- self-equality is the property under test # check store equality with same inputs # asserting this is important for being able to compare (de)serialized stores diff --git a/src/zarr/testing/strategies.py b/src/zarr/testing/strategies.py index 99e81b0389..6679dbcee4 100644 --- a/src/zarr/testing/strategies.py +++ b/src/zarr/testing/strategies.py @@ -132,7 +132,7 @@ def clear_store(x: Store) -> Store: @st.composite -def dimension_names(draw: st.DrawFn, *, ndim: int | None = None) -> list[None | str] | None: +def dimension_names(draw: st.DrawFn, *, ndim: int | None = None) -> list[str | None] | None: simple_text = st.text(zarr_key_chars, min_size=0) return draw(st.none() | st.lists(st.none() | simple_text, min_size=ndim, max_size=ndim)) # type: ignore[arg-type] @@ -292,7 +292,7 @@ def arrays( if arrays is None: arrays = numpy_arrays(shapes=shapes) nparray = draw(arrays, label="array data") - dim_names: None | list[str | None] = None + dim_names: list[str | None] | None = None serializer: SerializerLike = "auto" compressors_unsearched: CompressorsLike = "auto" @@ -328,7 +328,7 @@ def arrays( else: chunks_param = draw(chunk_shapes(shape=nparray.shape), label="chunk shape") - if all(s > c and c > 1 for s, c in zip(nparray.shape, chunks_param, strict=True)): + if all(s > c > 1 for s, c in zip(nparray.shape, chunks_param, strict=True)): shard_shape = draw( st.none() | shard_shapes(shape=nparray.shape, chunk_shape=chunks_param), label="shard shape", diff --git a/tests/test_api.py b/tests/test_api.py index cbe8ea3b44..2b831e942d 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -419,7 +419,7 @@ async def test_open_group_unspecified_version(tmp_path: Path, zarr_format: ZarrF @pytest.mark.parametrize("n_args", [10, 1, 0]) @pytest.mark.parametrize("n_kwargs", [10, 1, 0]) @pytest.mark.parametrize("path", [None, "some_path"]) -def test_save(store: Store, n_args: int, n_kwargs: int, path: None | str) -> None: +def test_save(store: Store, n_args: int, n_kwargs: int, path: str | None) -> None: data = np.arange(10) args = [np.arange(10) for _ in range(n_args)] kwargs = {f"arg_{i}": data for i in range(n_kwargs)} diff --git a/tests/test_codecs/test_blosc.py b/tests/test_codecs/test_blosc.py index f5f13f4d05..e342dba8bb 100644 --- a/tests/test_codecs/test_blosc.py +++ b/tests/test_codecs/test_blosc.py @@ -74,7 +74,7 @@ async def test_blosc_evolve(dtype: str) -> None: @pytest.mark.parametrize("shuffle", [None, "bitshuffle", "legacy-enum"]) @pytest.mark.parametrize("typesize", [None, 1, 2]) def test_tunable_attrs_param( - shuffle: None | BloscShuffleLiteral | str, typesize: None | int + shuffle: BloscShuffleLiteral | str | None, typesize: int | None ) -> None: """ Test that the tunable_attrs parameter is set as expected when creating a BloscCodec. @@ -83,7 +83,7 @@ def test_tunable_attrs_param( # contaminating the BloscCodec construction below with that warning. if shuffle == "legacy-enum": with pytest.warns(DeprecationWarning, match="BloscShuffle.shuffle"): - shuffle_arg: None | BloscShuffleLiteral | str = BloscShuffle.shuffle + shuffle_arg: BloscShuffleLiteral | str | None = BloscShuffle.shuffle else: shuffle_arg = shuffle diff --git a/tests/test_dtype_registry.py b/tests/test_dtype_registry.py index f0946014fc..40239c1132 100644 --- a/tests/test_dtype_registry.py +++ b/tests/test_dtype_registry.py @@ -170,7 +170,7 @@ def test_entrypoint_dtype(zarr_format: ZarrFormat) -> None: ) def test_parse_data_type( data_type: ZDType[Any, Any], - json_style: tuple[ZarrFormat, None | Literal["internal", "metadata"]], + json_style: tuple[ZarrFormat, Literal["internal", "metadata"] | None], dtype_parser_func: Any, ) -> None: """ diff --git a/tests/test_examples.py b/tests/test_examples.py index 9f8085e8c2..a6634e8cc6 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -80,7 +80,7 @@ def test_scripts_can_run(script_path: Path, tmp_path: Path) -> None: # This allows the example to be useful to users who don't have Zarr installed, but also testable. resave_script(script_path, dest_path) result = subprocess.run( - ["uv", "run", "--refresh", str(dest_path)], capture_output=True, text=True + ["uv", "run", "--refresh", str(dest_path)], capture_output=True, text=True, check=False ) assert result.returncode == 0, ( f"Script at {script_path} failed to run. Output: {result.stdout} Error: {result.stderr}" diff --git a/tests/test_regression/test_v2_dtype_regression.py b/tests/test_regression/test_v2_dtype_regression.py index c7b4a53a52..faba087e32 100644 --- a/tests/test_regression/test_v2_dtype_regression.py +++ b/tests/test_regression/test_v2_dtype_regression.py @@ -215,6 +215,7 @@ def test_roundtrip_v2(source_array_v2: ArrayV2, tmp_path: Path, script_path: Pat ], capture_output=True, text=True, + check=False, ) assert copy_op.returncode == 0, f"stdout {copy_op.stdout}\n stderr{copy_op.stderr}" out_array = zarr.open_array(store=out_path, mode="r", zarr_format=2) @@ -240,6 +241,7 @@ def test_roundtrip_v3(source_array_v3: ArrayV3, tmp_path: Path) -> None: ], capture_output=True, text=True, + check=False, ) assert copy_op.returncode == 0 out_array = zarr.open_array(store=out_path, mode="r", zarr_format=3) diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index d2784e1b4b..4138eebe6a 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -33,7 +33,7 @@ ) def store_like( request: pytest.FixtureRequest, -) -> Generator[None | str | Path | StorePath | MemoryStore | dict[Any, Any], None, None]: +) -> Generator[str | Path | StorePath | MemoryStore | dict[Any, Any] | None, None, None]: if request.param == "none": yield None elif request.param == "temp_dir_str": diff --git a/tests/test_store/test_object.py b/tests/test_store/test_object.py index cd85a48eb8..1ea148b3c3 100644 --- a/tests/test_store/test_object.py +++ b/tests/test_store/test_object.py @@ -1,4 +1,3 @@ -# ruff: noqa: E402 import re from pathlib import Path from typing import TypedDict diff --git a/tests/test_unified_chunk_grid.py b/tests/test_unified_chunk_grid.py index 0df5a5d9fd..f0b54519ab 100644 --- a/tests/test_unified_chunk_grid.py +++ b/tests/test_unified_chunk_grid.py @@ -2784,8 +2784,8 @@ def test_rectilinear_roundtrip(json_input: RectilinearChunkGridMetadataJSON) -> 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python-dependencies group with 4 updates in the / directory: [fsspec](https://github.com/fsspec/filesystem_spec), [hypothesis](https://github.com/HypothesisWorks/hypothesis), [uv](https://github.com/astral-sh/uv) and [ruff](https://github.com/astral-sh/ruff). Updates `fsspec` from 2026.6.0 to 2026.7.0 - [Commits](https://github.com/fsspec/filesystem_spec/compare/2026.6.0...2026.7.0) Updates `hypothesis` from 6.160.0 to 6.164.0 - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/v6.160.0...v6.164.0) Updates `uv` from 0.11.31 to 0.12.0 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.11.31...0.12.0) Updates `s3fs` from 2026.6.0 to 2026.7.0 - [Changelog](https://github.com/fsspec/s3fs/blob/main/release-procedure.md) - [Commits](https://github.com/fsspec/s3fs/commits/2026.7.0) Updates `ruff` from 0.15.22 to 0.16.0 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.15.22...0.16.0) --- updated-dependencies: - dependency-name: fsspec dependency-version: 2026.7.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: hypothesis dependency-version: 6.163.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.16.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: s3fs dependency-version: 2026.7.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: uv dependency-version: 0.12.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- pyproject.toml | 4 +- uv.lock | 154 +++++++++++++++++++++++++------------------------ 2 files changed, 81 insertions(+), 77 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 663a1ea286..8b8534cb65 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -100,12 +100,12 @@ test = [ "pytest-cov==7.1.0", "pytest-accept==0.3.0", "numpydoc==1.10.0", - "hypothesis==6.160.0", + "hypothesis==6.164.0", "pytest-xdist==3.8.0", "pytest-benchmark==5.2.3", "pytest-codspeed==5.0.3", "tomlkit==0.15.1", - "uv==0.11.31", + "uv==0.12.0", ] remote-tests = [ {include-group = "test"}, diff --git a/uv.lock b/uv.lock index e1d469fd84..5e3e33aefe 100644 --- a/uv.lock +++ b/uv.lock @@ -955,11 +955,11 @@ wheels = [ [[package]] name = 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">=2023.10.0" }, { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, - { name = "hypothesis", specifier = "==6.160.0" }, + { name = "hypothesis", specifier = "==6.164.0" }, { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.3" }, { name = "mike", specifier = "==2.2.0" }, { name = "mkdocs", specifier = "==1.6.1" }, @@ -3591,7 +3595,7 @@ dev = [ { name = "tomlkit", specifier = "==0.15.1" }, { name = "towncrier", specifier = "==25.8.0" }, { name = "universal-pathlib" }, - { name = "uv", specifier = "==0.11.31" }, + { name = "uv", specifier = "==0.12.0" }, ] docs = [ { name = "astroid", specifier = "==4.1.2" }, @@ -3614,7 +3618,7 @@ remote-tests = [ { name = "botocore" }, { name = "coverage", specifier = "==7.15.2" }, { name = "fsspec", specifier = ">=2023.10.0" }, - { name = "hypothesis", specifier = "==6.160.0" }, + { name = "hypothesis", specifier = "==6.164.0" }, { name = "moto", extras = ["s3", "server"], specifier = "==5.2.2" }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "obstore", specifier = ">=0.5.1" }, @@ -3628,11 +3632,11 @@ remote-tests = [ { name = "requests", specifier = "==2.34.2" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "tomlkit", specifier = "==0.15.1" }, - { name = "uv", specifier = "==0.11.31" }, + { name = "uv", specifier = "==0.12.0" }, ] test = [ { name = "coverage", specifier = "==7.15.2" }, - { name = "hypothesis", specifier = "==6.160.0" }, + { name = "hypothesis", specifier = "==6.164.0" }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "pytest", specifier = "==9.1.1" }, { name = "pytest-accept", specifier = "==0.3.0" }, @@ -3642,5 +3646,5 @@ test = [ { name = "pytest-cov", specifier = "==7.1.0" }, { name = "pytest-xdist", specifier = "==3.8.0" }, { name = "tomlkit", specifier = "==0.15.1" }, - { name = "uv", specifier = "==0.11.31" }, + { name = "uv", specifier = "==0.12.0" }, ] From f63e61d982df914032522ccee5e0b1492af1f7ab Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 11:02:02 +0200 Subject: [PATCH 446/468] docs: add a page linking to the companion packages (#4247) * docs: add a page linking to the companion packages The zarr-metadata and zarr-indexing docs are already Read the Docs subprojects of zarr-python and resolve under /projects/, but nothing in the main docs pointed at them except two entries buried at the bottom of the API Reference nav, which linked to the standalone *.readthedocs.io domains rather than the /projects/ paths Read the Docs advertises as canonical. Add a top-level "Related Projects" page listing each companion package, surface it as a card on the landing page, repoint the API Reference nav entries at the canonical subproject URLs, and give each subproject a nav link back to the parent docs. The changelog fragment is named for the issue rather than the PR because the upstream PR number is not known yet; rename it to that number when this is opened upstream. Closes #4246 Assisted-by: ClaudeCode:claude-opus-5 * Rename 4246.doc.md to 4247.doc.md * docs: projects -> subprojects * docs: rewire docs references correctly --- changes/4247.doc.md | 5 +++++ docs/index.md | 8 +++++++ docs/subprojects.md | 35 +++++++++++++++++++++++++++++++ mkdocs.yml | 9 ++++++-- packages/zarr-indexing/mkdocs.yml | 3 +++ packages/zarr-metadata/mkdocs.yml | 3 +++ 6 files changed, 61 insertions(+), 2 deletions(-) create mode 100644 changes/4247.doc.md create mode 100644 docs/subprojects.md diff --git a/changes/4247.doc.md b/changes/4247.doc.md new file mode 100644 index 0000000000..6dbca1d3d6 --- /dev/null +++ b/changes/4247.doc.md @@ -0,0 +1,5 @@ +Added a "Related Projects" page to the documentation listing the companion +packages developed in this repository — `zarr-metadata` and `zarr-indexing` — +and linked it from the landing page. Links to those packages now use the +canonical `https://zarr.readthedocs.io/projects/...` URLs, and each companion +package's documentation links back to the `zarr-python` docs. diff --git a/docs/index.md b/docs/index.md index ee4098a8ea..eb3b6a5000 100644 --- a/docs/index.md +++ b/docs/index.md @@ -58,6 +58,14 @@ conda install -c conda-forge zarr which parameters can be used. It assumes that you have an understanding of the key concepts. +- [:material-package-variant:{ .lg .middle } __Related projects__](subprojects.md) + + --- + + Companion packages developed in the zarr-python repository and released + independently, such as `zarr-metadata` and `zarr-indexing`, plus pointers to + the wider Zarr ecosystem. + - [:material-account-group:{ .lg .middle } __Contributor's Guide__](contributing.md) --- diff --git a/docs/subprojects.md b/docs/subprojects.md new file mode 100644 index 0000000000..1903f759d2 --- /dev/null +++ b/docs/subprojects.md @@ -0,0 +1,35 @@ +# Subprojects + +Alongside `zarr` itself, the +[zarr-python repository](https://github.com/zarr-developers/zarr-python) hosts a +small number of companion packages. Each one is developed in the same repository +but versioned, released, and documented independently, so you can depend on it +without taking on `zarr` as a dependency. + +<div class="grid cards" markdown> + +- [:material-code-json:{ .lg .middle } __zarr-metadata__](https://zarr.readthedocs.io/projects/zarr-metadata/) + + --- + + Spec-defined metadata types, models, and validators for Zarr v2 and v3, with + minimal dependencies. Useful if your software reads or writes Zarr metadata + documents but does not need a full Zarr implementation. + + ```bash + pip install zarr-metadata + ``` + +- [:material-vector-polyline:{ .lg .middle } __zarr-indexing__](https://zarr.readthedocs.io/projects/zarr-indexing/) + + --- + + Composable, lazy coordinate transforms for Zarr array indexing. Makes the + mapping from requested coordinates to stored coordinates a first-class, + composable value, and resolves which chunks a selection touches. + + ```bash + pip install zarr-indexing + ``` + +</div> diff --git a/mkdocs.yml b/mkdocs.yml index 6a0d94052e..ca8165af4c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -33,6 +33,7 @@ nav: - user-guide/examples/rectilinear_chunks.md - user-guide/examples/codec_pipeline_performance.md - user-guide/examples/sharding_coalescing.md + - subprojects.md - API Reference: - api/zarr/index.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.abc</code>': @@ -94,8 +95,12 @@ nav: - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr.testing.utils</code>': api/zarr/testing/utils.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros</code>': api/zarr/functions/zeros.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-function"></code> <code>zarr.zeros_like</code>': api/zarr/functions/zeros_like.md - - 'zarr-metadata ↪': https://zarr-metadata.readthedocs.io/ - - 'zarr-indexing ↪': https://zarr-indexing.readthedocs.io/ + # The companion packages are Read the Docs subprojects of this one; link + # to the /projects/ paths Read the Docs advertises as canonical rather + # than to their standalone *.readthedocs.io domains, so following one + # keeps the reader on this site's domain. + - 'zarr-metadata ↪': https://zarr.readthedocs.io/projects/zarr-metadata/ + - 'zarr-indexing ↪': https://zarr.readthedocs.io/projects/zarr-indexing/ - release-notes.md - contributing.md - Blog: diff --git a/packages/zarr-indexing/mkdocs.yml b/packages/zarr-indexing/mkdocs.yml index d7261f32e1..43a5ea5b4c 100644 --- a/packages/zarr-indexing/mkdocs.yml +++ b/packages/zarr-indexing/mkdocs.yml @@ -26,6 +26,9 @@ nav: - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.messages</code>': api/messages.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.errors</code>': api/errors.md - Changelog: https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/CHANGELOG.md + # This site is a Read the Docs subproject of zarr-python; give readers a way + # back to the parent docs, which list every companion package. + - 'zarr-python ↪': https://zarr.readthedocs.io/ watch: - src diff --git a/packages/zarr-metadata/mkdocs.yml b/packages/zarr-metadata/mkdocs.yml index 6c4a590b3c..18e1fc8c35 100644 --- a/packages/zarr-metadata/mkdocs.yml +++ b/packages/zarr-metadata/mkdocs.yml @@ -25,6 +25,9 @@ nav: - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v3.codec</code>': api/v3/codec.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_metadata.v3.data_type</code>': api/v3/data_type.md - Changelog: https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-metadata/CHANGELOG.md + # This site is a Read the Docs subproject of zarr-python; give readers a way + # back to the parent docs, which list every companion package. + - 'zarr-python ↪': https://zarr.readthedocs.io/ watch: - src From 5abdee22028cabe14da5c192a3d11d494a061451 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 11:34:51 +0200 Subject: [PATCH 447/468] build(zarr-metadata): the sdist ships an allowlist, not whatever is lying around (#4248) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit hatchling had no sdist configuration here either, so a source distribution carried everything in the package directory. Building from a working tree with scratch files in it put `.env.local`, a notebook and a `__scratch/` dump in the tarball. A tagged release builds from a fresh CI checkout and so was never actually at risk, but nothing made that a property of the package rather than of the runner. The list is derived from this package rather than copied from zarr-indexing, which needed `docs/snippets` and `examples/` because its suite executes them. Nothing here does: every fixture is a JSON file next to the test module that reads it, so `/tests` is the whole test dependency. `/docs` and `/mkdocs.yml` ride along because they are self-contained — mkdocstrings reads `src` and the config reaches nowhere outside the package — so the sdist documents itself as well as tests itself. `changes/` and `.readthedocs.yaml` are left out: towncrier fragments are repo bookkeeping, and the RTD config addresses paths from the repo root, where an unpacked sdist is not. Verified by unpacking the built sdist into a bare venv and working from there: 595 tests pass and `mkdocs build --strict` succeeds. Assisted-by: ClaudeCode:claude-opus-5 --- packages/zarr-metadata/pyproject.toml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 1ef1c31624..0df3385dc7 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -71,6 +71,26 @@ raw-options = { root = "../..", git_describe_command = "git describe --dirty --t [tool.hatch.build.targets.wheel] packages = ["src/zarr_metadata"] +# An allowlist, so nothing that merely happens to sit in the package directory +# — a scratch script, a stray notebook — can ride along in a release. The list +# keeps an sdist self-testing and self-documenting: every fixture this suite +# reads is a JSON file sitting next to the test module that loads it, so +# `/tests` is the whole test dependency, and `/docs` plus `/mkdocs.yml` are a +# self-contained site (mkdocstrings reads `src`, nothing reaches outside the +# package) so `just docs-check` runs from an unpacked sdist too. `changes/` +# and `.readthedocs.yaml` are deliberately absent: towncrier fragments are +# repo bookkeeping, and the RTD config addresses paths from the repo root. +# `pyproject.toml`, `README.md` and `LICENSE.txt` are added by hatchling itself. +[tool.hatch.build.targets.sdist] +include = [ + "/src", + "/tests", + "/docs", + "/mkdocs.yml", + "/justfile", + "/CHANGELOG.md", +] + [tool.ruff] extend = "../../pyproject.toml" target-version = "py311" From 0f7c883ad2509d017e54097874ce4d62609157eb Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 12:11:13 +0200 Subject: [PATCH 448/468] HTTP server that exposes stores, arrays, groups (#3732) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * implement store server and node server * update tests and add v2 -> v3 example * add __all__ and clean up tests * add docs and changelog * add proper server * rework examples (simplify) and make server a context manager * minor tweaks to server * fix: byte-order handling for structured dtypes in the bytes codec (#220) * fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes #4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5 * fix: adapt server branch to current starlette/uvicorn starlette 1.3 deprecated using httpx with its TestClient, which the warnings-as-errors filter turns into a collection error; add httpx2 to the test dependency group. uvicorn 0.51 removed Server.install_signal_handlers and now skips signal-handler setup off the main thread natively, so drop the monkey-patch workaround. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-server): scaffold packages/zarr-server Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-server): move server code, tests, and example into the package The moved code now uses only public zarr API: zarr.buffer.cpu replaces zarr.core.buffer.cpu, spec-defined key names are inlined, chunk-key encodings are duck-typed on their spec names, and the shard grid shape is computed locally from public Array attributes. Also mirrors the root repo's [tool.numpydoc_validation] override in the package's pyproject.toml, since numpydoc-validation resolves config from the nearest pyproject.toml and would otherwise apply its stricter default checks to the moved docstrings. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-server): package README; retarget root changelog fragment at the core fix Assisted-by: ClaudeCode:claude-fable-5 * refactor!: remove the HTTP server from zarr core The server now lives in packages/zarr-server (published as zarr-server). The feature never shipped in a zarr release, so there is no deprecation shim. The decode_chunk_key strictness fix stays in zarr core. Assisted-by: ClaudeCode:claude-fable-5 * ci(zarr-server): add package test and release workflows Assisted-by: ClaudeCode:claude-fable-5 * chore(zarr-server): refresh package lockfile after root server-extra removal The package lock embeds the workspace-root zarr project's metadata; Task 4 removed the root server extra and httpx2 test dep after this lock was first generated. Assisted-by: ClaudeCode:claude-fable-5 * fix: reject path-traversal segments in zarr-server request handling store_app (and thus serve_store) passed the request path straight to the store without validation, since the is_valid_node_key gate only ran for node_app. Starlette percent-decodes path params, so a request like GET /..%2fsecret.txt arrived as literal ".." and LocalStore resolved it outside the store root, allowing arbitrary file read via GET and arbitrary file write via PUT. Closes this path-traversal vulnerability by rejecting any "." or ".." path segment in _handle_request before the store is touched, for both store_app and node_app. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-server): close absolute-key path-traversal bypass in request guard The path-traversal guard in _handle_request only rejected "." and ".." segments. A percent-encoded leading slash (e.g. "/%2fetc%2fhostname") decodes to an absolute path param ("/etc/hostname"), whose split() produces an empty leading segment with no "." or ".." segment, so the guard let it through. LocalStore resolves an absolute key by discarding its configured root, allowing arbitrary filesystem read/write outside the store. Reject empty segments too, closing the bypass. Assisted-by: ClaudeCode:claude-fable-5 * ci(zarr-server): bump actions/attest to v4.2.0 to match sibling workflow Keeps the zarr-server release workflow's pinned action SHAs in sync with the dependabot bump that landed in zarr-metadata-release.yml via the merge. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-server): fold backslash separators and reject drive-qualified keys The traversal guard in _handle_request split only on "/", so backslash- separated segments like "..\\..\\win.ini" and drive-qualified or UNC-rooted keys like "C:/Windows/win.ini" or "\\host\share\x" passed through untouched. On Windows, LocalStore joins keys onto its root via pathlib, which discards the root entirely for a drive-qualified or rooted key -- turning percent-encoded backslash paths into arbitrary file read/write. Fold backslashes to "/" before the segment check (mirroring zarr's own normalize_path) and add an ntpath.splitdrive check to catch drive letters and UNC prefixes that don't produce empty/"."/".." segments. Added TDD coverage that fails against the old guard (via a store double that raises if get/set is ever called) and passes against the fix. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-server): fix vacuous two-level traversal test The `/..%2f..%2fsecret.txt` case in test_encoded_traversal_variants_ return_404 climbed two levels from tmp_path/store_root to tmp_path/.., but the secret was written at tmp_path/secret.txt (one level up) -- so the case passed for the wrong reason (no such file, not "guard blocked it") even with the traversal guard deleted entirely. Nest the store root exactly `climb_depth` directories below tmp_path per case, so every case's ".." segments resolve to tmp_path/secret.txt. Verified by mutation: copied _serve.py to a scratch dir (never the repo), deleted the guard body, and ran TestPathTraversalProtection against it via PYTHONPATH. Before this fix, 12/13 traversal tests failed against the mutant (1 false pass -- this vacuous case). After this fix, 13/13 fail against the mutant, and all still pass against the real guard. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-server): bound BackgroundServer shutdown instead of blocking forever shutdown() joined the server thread with no timeout, and uvicorn's graceful wait is itself unbounded: force_exit is only set by a signal handler uvicorn deliberately skips off the main thread. A client mid request could wedge __exit__ unrecoverably. Bound uvicorn's graceful wait with timeout_graceful_shutdown and fall back to force_exit if the thread outlives it, both driven by a new shutdown_timeout parameter on serve_store/serve_node. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-server)!: only accept HTTP methods the handler implements _handle_request special-cased PUT and let every other verb fall through to the read path, so a server built with DELETE/POST/PATCH answered them with the key's contents and changed nothing. HTTPMethod advertised all of them. Narrow HTTPMethod to GET/PUT/HEAD and reject anything else when the app is built. Doing this before the first release avoids narrowing a published type later. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-server): document client deps; lint the package's changelog in CI The README's round-trip example reads back through FsspecStore, which needs an HTTP-capable fsspec that zarr-server does not depend on, so a clean install failed on the PyPI landing page's headline snippet. Same for examples/serve.py under a plain interpreter, which needs httpx. check_changelogs.yml also never visited packages/zarr-server/changes, so a malformed fragment would have passed PR CI and failed at release time. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-server): add docs dependency group and cover the README round-trip Reading a served array back with zarr.open_array(url) routes through FsspecStore -- zarr's only URL-string backend -- so the README's headline example needs an HTTP-capable fsspec that the package itself has no reason to depend on. Carry that in a docs group, mirroring the root project's group for running examples, and use it to test the round-trip in CI so the example cannot rot. Assisted-by: ClaudeCode:claude-fable-5 * refactor(zarr-http-server)!: rename zarr-server to zarr-http-server The package is HTTP-specific end to end -- Starlette/ASGI, byte-range headers, CORS, HTTP verbs -- so the unqualified name overclaimed its scope and squatted the generic name that a future transport (an S3-compatible or WebDAV frontend) would want. Renames the distribution, the zarr_http_server module, the package directory, the zarr_http_server-v* release tags, both workflows and their artifact and PyPI environment names. Nothing is published yet, so this costs nothing now and would be permanent after the first upload. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-http-server): reject an empty methods set instead of failing open Starlette's Route treats a falsy `methods` as "match every method", and an empty set passes the unsupported-verb check trivially, so store_app(store, methods=set()) served GET, DELETE, POST, PATCH and TRACE alike and accepted PUT writes -- the opposite of what the caller asked for, and the same fail-open the method narrowing set out to close. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-http-server): report the bound port, unblock the loop, 404 unopenable children Three defects the adversarial re-review reproduced: BackgroundServer reported the requested port, so port=0 produced http://host:0 while the socket was bound elsewhere -- clients following the documented url reached an unrelated service. Group key validation opened children through zarr's synchronous API directly on the event loop, serializing every concurrent request behind it (20 concurrent requests: 10.5s, now 1.1s) and outlasting the shutdown timeout. Move it to a worker thread. Child lookup caught only KeyError, so a corrupt metadata document or a codec from an uninstalled plugin surfaced as 500 and made a whole subtree unservable during ordinary operation. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-http-server): close the S5-S13 follow-ups from the adversarial review Hostile keys the store cannot express (embedded NUL, over-long names) now answer 404 instead of surfacing ValueError/OSError as a 500. PUT bodies are capped at DEFAULT_MAX_BODY_SIZE and answer 413 past it; Store.set takes a whole Buffer, so a body cannot be streamed and one request would otherwise size the server's memory. 206 responses carry Content-Range, and a range beyond the end or an inverted one answers 416 rather than an empty 206. A 0-d v2 array's sole chunk, stored under "0", is now servable: the key decodes to a 1-tuple no 0-d grid could match, so it needs the array's dimensionality to disambiguate. Array and group metadata key sets are split, so a v2 group no longer claims .zarray as its own; bind failures report the likely cause instead of a bare timeout; and serve_* gain a background: bool overload. The two out-of-bounds chunk tests planted no data, so they passed for the wrong reason -- mutating the bounds check to return True left the suite green. They now plant data at the out-of-grid key, and that mutation fails 3 tests. Adds the missing coverage for this branch's one core change, and widens the workflow's path filter to src/zarr, since the package resolves zarr from the repo root and a core change can break it. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-http-server): stop reporting I/O failures as misses; enforce the body cap while reading The round-3 review found the previous round's error handling was too broad and its body cap too narrow. except (ValueError, OSError) around store.get and store.set caught the whole errno family, so EACCES, EROFS and ENOSPC all answered 404. Under the v3 spec an absent chunk is an uninitialized one and a reader is right to substitute the array's fill value, so 404 asserts something about the store's contents: an unreadable chunk answered that way has a correct client silently materialize fill values over data that exists, and a failed write looks like a pointless one rather than a failure. Only ENAMETOOLONG and EINVAL now mean "this key names nothing"; everything else surfaces. NUL bytes are rejected in the guard instead, so the store's own errors always mean real I/O trouble. max_body_size only consulted Content-Length, which a chunked request does not send, so request.body() buffered the whole thing before the check: 256 MiB passed a 1 KiB cap at 572 MiB peak RSS. The body is now read incrementally and abandoned at the cap -- the same attack peaks at 59 MiB. Also: a range too wide to allocate answers 416 rather than raising MemoryError; the force_exit fallback join is bounded, so shutdown cannot outlast its timeout; DEFAULT_MAX_BODY_SIZE is importable, since it is the documented default of three public functions; and _make_starlette_app loses a parameter it never read. Adds the coverage the review found missing: shard-grid bounds (the mutant served an out-of-grid shard key against a green suite), wrong-arity chunk keys, the chunked body path, I/O failures as 5xx, and a parser-level assertion for inverted ranges, which the status code alone could not distinguish on a MemoryStore. The drive-letter check stays unconditional. It over-rejects a first-segment node name like a:b, which is legal on POSIX -- but ntpath treats any single character before a colon as a drive, so there is no safe subset, and the guard is a string gate in front of an arbitrary Store whose path semantics this package cannot know. Assisted-by: ClaudeCode:claude-fable-5 * fix(ci): silence BLE001 on two intentional broad excepts ruff 0.16 selects BLE001 under the root config's `B` prefix, so the package's `uvx ruff check .` job failed on two deliberate blind excepts. Both are intentional and already documented, so they get targeted noqa comments, matching how #4213 handled the same rule in the core tree. Assisted-by: ClaudeCode:claude-opus-5 * chore: drop stale changelog fragment for the chunk key fix The DefaultChunkKeyEncoding.decode_chunk_key fix this fragment described was split out into #4219 and has already shipped -- its text is in docs/release-notes.md verbatim. Leaving the fragment here would emit the same paragraph a second time under a #3732 link, for a change this branch no longer contains. Assisted-by: ClaudeCode:claude-opus-5 * ci: check zarr-http-server changelogs and align action pins check_changelogs.yml validated the root, zarr-metadata and zarr-indexing changes/ directories but not zarr-http-server's, so the new package's fragments were the only ones whose filenames went unchecked. The two new workflows were also written before #4241 bumped the actions group, so they pinned older checkout/setup-uv/attest/pypi-publish SHAs than their siblings. Bump them to the versions main already uses; the release workflow is now identical to zarr-metadata's modulo the package name. Assisted-by: ClaudeCode:claude-opus-5 * docs(http-server): add justfile and Read the Docs scaffold Brings the package in line with zarr-metadata and zarr-indexing, which each own a justfile and a separate Read the Docs site. The docs content is a scaffold -- an overview page and an API reference over the public namespace -- meant to be filled in later; the point is to get the site wired up and building under --strict now. The `docs` dependency group previously held the runtime deps for the README examples, but Read the Docs and `just docs-check` both expect it to carry the mkdocs toolchain, as it does in the sibling packages. Those example deps move to a new `examples` group and the test job follows. CI gains a `docs` job matching the siblings', so a scaffold that stops building fails the gate. The repo-root .readthedocs.yaml skips PR builds confined to this package now that it has its own site, and the root docs nav links out to it. Creating the Read the Docs project itself is a manual step: point its configuration-file path at packages/zarr-http-server/.readthedocs.yaml. Assisted-by: ClaudeCode:claude-opus-5 * fix(http-server): correct silent-corruption and HTTP-conformance defects Two of these answered a request successfully while leaving the client with data that does not exist. Chunk keys were validated by decoding coordinates and bounds-checking them, never by re-encoding. `int` is lenient in ways a store key is not -- leading zeros, a leading `+`/`-`, surrounding whitespace, underscore separators, non-ASCII decimal digits -- so `c/00/00` decoded to (0, 0) and validated, then went to the store verbatim. A PUT answered 204 and stored the body under a key no reader looks up: success reported, data invisible. Validation now requires the key to equal `metadata.encode_chunk_key(coords)`, which makes the accepted set exactly the set zarr can read. Decoding delegates to the encoding's own decoder rather than reimplementing the default/v2 grammars, so a new or third-party chunk key encoding works without changes here. Resolving a group child caught bare `Exception` and returned False, which turned an unreadable child -- EACCES, EIO, a corrupt metadata document, a missing codec plugin -- into 404. Under the v3 spec an absent chunk is an uninitialized one, so a correct reader answers that 404 by substituting the fill value over data that exists. Only KeyError is caught now; a key that could not be judged surfaces as 5xx rather than being reported absent. The rest are conformance fixes on the same request path: - A Range header the server cannot use is now ignored with a 200 rather than refused with a 416, per RFC 9110 §14.2. This covers an unrecognized unit and a multi-range request, both legal to send. - A suffix range resolves against the object's size, so a 206 always carries the Content-Range that RFC 9110 §15.3.7 requires. Sharding reads a shard index this way, so the header was missing on a hot path. - A last-byte-pos wider than the store can materialize is clamped to the end of the object per §14.1.2 instead of raising out of the store as a 500. - A byte position is parsed as 1*DIGIT rather than by `int`, which accepted `+0`, ` 0` and `0_0`. - PUT to a read-only store answers 403 instead of letting the store's ValueError surface as a 500. Assisted-by: ClaudeCode:claude-opus-5 * test(http-server): property tests over a real endpoint Adds hypothesis properties that drive a real uvicorn server over a socket, so the assertions cover what only exists on the wire: header parsing, method dispatch, status codes. Each property checks the response *and* the backing store. That pairing is what the previous suite could not do: a PUT to a non-canonical chunk key answered 204 and wrote a key no reader consults, which a response-only assertion cannot see. Refused requests assert the store is byte-for-byte unchanged; accepted writes assert the bytes landed under the key the client named and that a zarr client reads back the values. Keys are generated in two families -- in-band (the node's metadata and the canonical spelling of each chunk key in its grid) and out-of-band (non-canonical spellings, out-of-grid coordinates, traversal probes, a sibling node's keys). Two details worth keeping: - Traversal probes are percent-encoded. An HTTP client resolves dot-segments before sending, so httpx turns "../secret" into "/secret" and a literal probe asserts nothing; encoded, it reaches the server and Starlette decodes it back into a real ".." segment. - The matrix includes LocalStore, not just MemoryStore. MemoryStore slices a `bytes` and accepts any range bound, so it cannot distinguish a clamped over-wide range from a refused one -- mutation-testing the suite showed that property passing against deliberately broken code until a filesystem-backed server was added. Verified by reverting each fix in turn and confirming the corresponding property fails. Assisted-by: ClaudeCode:claude-opus-5 * fix(http-server): stop reading EINVAL from a store as a missing key `_names_nothing` reclassified two errnos as absence so a client could not turn a freely chosen key into a 5xx. `ENAMETOOLONG` earns that: it is the store answering about the name -- nothing can be stored under a name it cannot express -- and `encode_chunk_key` never produces a segment near a filesystem's length limit, so it is unreachable for real data. `EINVAL` does not. It is POSIX's catch-all, reachable on a perfectly ordinary short key through a bad seek or an unsupported filesystem feature, and under the v3 spec an absent chunk is an uninitialized one -- so answering 404 has a correct reader write fill values over a chunk that exists but could not be read. That is the same defect already fixed in the group-child lookup and in chunk key validation: reporting "something went wrong" as "it is not there". Nothing exercised EINVAL in practice. A NUL in a key raises ValueError and is rejected before the store anyway, and an over-long key raises ENAMETOOLONG, so this narrows the guard to the case that was doing the work. The traversal, absolute-key and drive-letter guards deliberately stay where they are rather than deferring to the store. LocalStore.get/set are `self.root / key` with no validation -- zarr's normalize_path applies at the StorePath layer, not to raw store keys -- so `../sibling.txt` and an absolute key both write outside the store root. This server is the component that feeds a Store unvalidated strings from the network, so it is the component that has to reject them. Assisted-by: ClaudeCode:claude-opus-5 * feat(http-server): stop sealing over CORSMiddleware and uvicorn.Config Wrapping an API means taking responsibility for its parameters, not hiding the ones we did not think to name. Two wrappers were doing the latter. `CorsOptions` carried 2 of `CORSMiddleware`'s 8 parameters, so `allow_headers`, `allow_credentials`, `allow_origin_regex`, `allow_private_network`, `expose_headers` and `max_age` were unreachable without bypassing this package. It now mirrors the full signature, with every key optional. Two of the defaults are ours rather than Starlette's, because the server knows what its caller should not have to. It emits `Content-Range` on every ranged response, which is not a CORS-safelisted response header, so `expose_headers` defaults to `["Content-Range"]` -- without it a browser client could read the bytes but not learn which bytes it got, which made the suffix-range Content-Range fix invisible to exactly the clients CORS exists for. It accepts a `Range` request header, so `allow_headers` defaults to `["Range"]`; Starlette's empty default answered a preflight naming Range with 400. Defaults apply only to absent keys, so an explicit `expose_headers: []` means "expose nothing". `_start_server` passed 4 of `uvicorn.Config`'s 52 parameters, which put TLS, `proxy_headers`/`forwarded_allow_ips`, `root_path`, `log_level`, `limit_concurrency` and unix-socket binds out of reach entirely. A `uvicorn_options: Mapping[str, object] | None` is merged over the three options set here, so a caller key wins. uvicorn ships no TypedDict for Config -- its only TypedDicts are ASGI protocol events -- so the mapping is hand-typed and the cast is confined to the call site. Un-sealing uvicorn makes two BackgroundServer attributes reachable that could previously only be one thing. `url` now reports the scheme actually in use, so configuring TLS yields https, and `host`/`port`/`url` are None for a uds or fd bind rather than naming an address nothing is listening on. Assisted-by: ClaudeCode:claude-opus-5 * fix(http-server): lifecycle, HEAD cost, and CORS/route method agreement Clears the findings left open from the review. Lifecycle. `_start_server` raised on its startup timeout without ever signalling the server, so the thread went on to bind the port and serve forever as a daemon with no handle to stop it -- and a retry on the same port then failed with the other error. It now sets should_exit and force_exit and joins before raising. `shutdown()` returned normally when the thread survived both joins, reporting success for a server still bound and still serving; it now raises. The first join also matched uvicorn's own `timeout_graceful_shutdown` exactly, and uvicorn spends ~0.2s tearing down before that wait even begins, so the join always expired first and escalated to force_exit on the orderly path -- which makes uvicorn skip ASGI lifespan shutdown. The join now outlasts the graceful bound by a margin, and reads that bound from the config so it stays correct when a caller sets it through uvicorn_options. HEAD. A HEAD body is discarded at the wire, but HEAD fell through to the GET handler, so answering one transferred the whole value: measured at 10 MB read to report a length. It is now answered from `Store.getsize` -- a stat on a filesystem store, an info call on a remote one -- and reads zero bytes. HEAD is served whenever GET is, which is what Starlette does and what RFC 9110 asks of an origin server; the README and docstrings said otherwise and now say so. CORS. `cors_options["allow_methods"]` was passed through unchecked, so an app could advertise methods its route rejects: a browser caches that preflight and every later cross-origin call fails with 405 after a successful handshake. Advertising an unserved method is now a ValueError at construction, consistent with how unsupported `methods` are already rejected, and `"*"` expands to what is actually served rather than to every verb Starlette knows. An absent `allow_methods` is left alone -- widening it to everything served would newly advertise PUT cross-origin on a write-enabled app that never asked for it. Media type. The JSON content type was keyed off a third hardcoded "zarr.json", so a v2 array's `.zarray` was served as octet-stream. It is now derived from the same tables that decide which keys a node owns. Also documents that `store_app` does not validate keys: it proxies the raw key space and has no array semantics to check against, so a client that misspells a chunk key gets a successful write to a key no reader consults. `node_app` rejects that with 404. Assisted-by: ClaudeCode:claude-opus-5 * ci(http-server): run the justfile's recipes instead of copies of them The workflow repeated the commands the justfile already defines -- `uvx ruff check .` and the mypy invocation were byte-identical copies, and the pytest step differed only by the sync that precedes it. Two definitions of the same verb drift silently: renaming the `docs` dependency group to `examples` required the same edit in both places, and updating only one would have left `just check` and CI testing different things with nothing failing. CI now calls `just test`, `just lint` and `just typecheck` (it already called `just docs-check`), keeping the python matrix and caching, which are genuinely CI's concern. This matches zarr-metadata, whose workflow already states the arrangement; zarr-indexing remains half-converted. Delegating also meant fixing what the shared recipe would otherwise spread: `just lint` ran an unpinned `uvx ruff`, which is precisely how this job broke before -- ruff 0.16 began selecting BLE001 under the root config's `B` prefix and failed on rules the pre-commit-pinned ruff never enforced, with no code change to blame. The recipe now pins the same version .pre-commit-config.yaml does, so the local gate, the pre-commit gate and CI enforce one standard. Assisted-by: ClaudeCode:claude-opus-5 * ci: build the zarr-http-server docs on pre-push A dead cross-reference or a nav entry pointing at a removed file only fails at `mkdocs build --strict`, which until now happened first in CI. This catches it before the code leaves the machine. Scoped deliberately. `stages: [pre-push]` overrides the repo default of running on every commit: this builds the whole site, which is too slow to pay per commit and is only actionable before pushing. `files:` limits it to changes that touch the package, and `pass_filenames: false` because mkdocs builds a site rather than a list of files. It delegates to `just docs-check` so the build has one definition shared with CI, and is added to `ci.skip` alongside mypy for the same reason that one is skipped: pre-commit.ci's runners have neither `uv` nor the repo checkout needed to resolve the environment. The zarr-http-server workflow covers it there. Note this hook and CI still declare their toolchains separately -- the hook shells out to the local `just`/`uv`, CI installs them itself. That is inherent to pre-commit.ci not being able to run them, and is the same trade already accepted for mypy. Also refreshes packages/zarr-http-server/uv.lock, which references the root project's dependency groups, for the hypothesis and uv bumps that arrived with the main merge. Assisted-by: ClaudeCode:claude-opus-5 * feat(http-server): make the read-only guarantee explicit and enforced Read-only was already the default -- `store_app(store)` answers 405 to PUT, POST, DELETE and PATCH, and POST is unconfigurable because there is no handler behavior for it -- but nothing said so and little pinned it. Only PUT was covered against the default app; POST, DELETE and PATCH were covered only against a fixture built with writes enabled, so "the default app is read-only" was not actually a tested claim. Adds a test class covering both layers the guarantee rests on: `methods`, which decides what the route answers, and the store, which decides whether a write could succeed at all. Each refusal also asserts the value is unchanged, matching the property tests -- a 405 that still wrote would otherwise pass. Serving PUT from a read-only store is now a ValueError at construction. A store's `read_only` is fixed when it is built, so that combination can never succeed; it previously surfaced as a 403 to whichever client tried to write first, long after whoever misconfigured it had moved on. The handler's 403 stays as a backstop for a store whose read_only is not fixed, and the test for it builds the app through the private builder since the public entry points now reject the combination. Documents `store.with_read_only(True)` as the categorical recipe: it is the stronger of the two layers because it holds even if the HTTP layer is misconfigured. Assisted-by: ClaudeCode:claude-opus-5 * feat(http-server): name the read-only and read-write method sets `READ_ONLY_METHODS` and `READ_WRITE_METHODS` let a call site say which it is, rather than leaving that to the presence or absence of an argument. The read-only one is exactly the default, so passing it changes nothing except that the intent is written down. The value is the other direction: a writable app must name a method set, so `grep -r 'methods='` finds every place that opts into writes -- which is what makes a deployment auditable without a separate read-only entry point. Both are frozensets, so one caller cannot widen the default for every other, and both name HEAD explicitly: Starlette serves it wherever GET goes, and a constant that omitted it would misdescribe the route. `methods` now accepts any `AbstractSet`, which is what lets a frozenset constant be passed where a `set` was previously required. Assisted-by: ClaudeCode:claude-opus-5 * feat(http-server): model read-only methods in the type domain Renames the constants to READ_ONLY_HTTP_METHODS / READ_WRITE_HTTP_METHODS so they say what kind of method they hold, matching the HTTPMethod type they are drawn from. Adds `ReadOnlyHTTPMethod = Literal["GET", "HEAD"]`, which moves the distinction from a runtime convention to something a checker enforces: a `frozenset[ReadOnlyHTTPMethod]` cannot contain "PUT", so a read-only interface can be declared rather than merely configured. Verified against mypy --strict -- assigning either a set containing "PUT" or READ_WRITE_HTTP_METHODS to that annotation is an error, while READ_ONLY_HTTP_METHODS is accepted. HTTPMethod is now the union of that and a private `_WriteHTTPMethod` rather than a third hand-written list of the same strings, and both constants plus _SUPPORTED_METHODS are derived from the Literals via get_args. The runtime sets and the static types therefore cannot disagree about what this server serves: widening a Literal is the only edit needed, and a test pins the contents so that widening is deliberate. Assisted-by: ClaudeCode:claude-opus-5 * docs(http-server): add a notebook example, and run both examples in tests The only example used `with serve_node(...)`, which is the one form that cannot work in a notebook: it shuts the server down when the cell ends, so anyone copying it gets a dead server by the next cell. Nothing in the package mentioned notebooks at all. Adds examples/serve_notebook.ipynb covering the lifecycle a kernel needs -- start with background=True and keep the handle, use it across cells, then shutdown() -- plus metadata and chunk reads, a byte range, and a refused PUT. Two arguments carry it: background=True runs uvicorn in a daemon thread with its own loop so the kernel's loop is untouched, and port=0 means re-running a start cell picks a new port instead of failing with "address already in use". A README section says the same in prose. The notebook is executed by the suite through nbclient, in a real kernel, and asserts its own expectations, so a behavior change fails there rather than in someone's notebook. Verified by mutation: making writes the default breaks the notebook's `assert refused.status_code == 405` and surfaces as a CellExecutionError naming the cell. examples/serve.py is now executed too, which required fixing the same fixed-port footgun the notebook section warns about -- it bound 8000, so it failed if anything else held that port. It runs in-process rather than under `uv run`, because its inline script metadata resolves zarr-http-server from git and would test main instead of the working tree. Assisted-by: ClaudeCode:claude-opus-5 * feat(http-server): expose serve() for arbitrary ASGI apps Serving two nodes did not need two servers, but the only way to run several was to reach past this package: `serve_store`/`serve_node` each take exactly one store or node, so a composed app had no route to the background-server ergonomics -- `port=0` into `server.url`, and `shutdown()` -- only a blocking `uvicorn.run`. `_start_server` already did this for any Starlette app; it was just private. `serve(app, ...)` makes it public, with the same background/blocking overloads the shorthands have. `serve_store` and `serve_node` now delegate to it and stay, because they are the common case and are what the docs and examples use; retiring them is still available later. The split the pair muddles is now visible: what an app *serves* (`methods`, `cors_options`, `max_body_size`) is settled when the app is built, and `serve` only decides how it runs. Documents the three ways to serve several nodes -- serve their common parent group, serve the whole store, or mount separate apps and run the result -- with tests covering mounted nodes in *separate* stores, that each mount serves only its own data, and that `serve` runs the composed app in the background. Also derives the bounded-shutdown test's threshold from the timeouts that produce it. It hard-coded 3.0s, which was generous when shutdown could take at most 2x shutdown_timeout and marginal once the join margin was added -- it began failing under load rather than at the moment the constant changed. Assisted-by: ClaudeCode:claude-opus-5 * refactor(http-server)!: split blocking and background into two functions `background: bool` decided whether a call returns immediately with a handle or never returns at all -- the largest difference a call site can have, hidden in a keyword. The return type depended on it too, which is why every runner carried three @overload stanzas: nine in total, all of them working around that one flag, and `background=False` returned None, a value meaningless half the time. `serve(app)` now blocks and `serve_background(app)` returns a BackgroundServer. Neither needs an overload. Splitting forced the shorthand question, since the axes multiply: keeping serve_store/serve_node alongside two modes means six runner functions. The public surface is instead two builders and two runners -- `serve_background(store_app(store))` replaces `serve_store(store, background=True)`. That is one more call, and it puts the two halves where they belong: what an app serves is settled when it is built, and the runner only decides how it runs. _serve.py drops from 1301 to ~1100 lines with the duplicated signatures and docstrings gone. `serve_background` defaults to `port=0` where `serve` defaults to 8000. Deliberate: a background server is reached through `server.url`, and a fixed default makes starting a second one -- or re-running a notebook cell -- fail on a collision, while a blocking server usually wants a port others already know. BREAKING CHANGE: serve_store and serve_node are removed. The package is unreleased, so nothing depends on them yet. Assisted-by: ClaudeCode:claude-opus-5 * feat(http-server): default both runners to port="auto" `serve` defaulted to 8000 and `serve_background` to 0, which read as an arbitrary disagreement between two sibling functions about a shared parameter. Both now default to `"auto"`: prefer 8000, fall back to any free port if it is taken, and report the result through `server.url` and uvicorn's own startup line. What makes the fallback safe is that it applies only to the default. An explicit port still binds exactly that or fails, because a caller who names one usually has a proxy or a container port mapping expecting the server there -- silently moving would break it while looking healthy. `port=0` keeps its OS meaning of "any free port, no preference". The port is bound here and the socket handed to `Server.run(sockets=...)` rather than probing for a free port and passing uvicorn the number: probing releases the port before uvicorn claims it, which is the bind-then-close race that makes "find a free port" helpers flaky. Holding the socket means nothing can take it in between. `Config.port` is set to what was actually bound, so uvicorn's "running on ..." line does not name a port it is not serving. Two cases the mechanism has to respect: a `uds` or `fd` bind in uvicorn_options skips the TCP bind entirely, and the address family comes from `getaddrinfo` rather than a hard-coded AF_INET, which would bind the wrong family for an IPv6 host. Both are covered by tests, as is that an explicit taken port still raises. Assisted-by: ClaudeCode:claude-opus-5 * revert: drop changes to files this package does not own The PR should not reach outside packages/zarr-http-server and .github, and four files did. Two were unrelated churn: docs/api/zarr/experimental.md renamed a heading in the *core* zarr docs about zarr.experimental.cache_store, left over from when this server lived at zarr.experimental.serve, and uv.lock carried an idna bump nothing here asked for. Reverted; `uv lock --check` is clean. Two were premature rather than wrong. mkdocs.yml added a nav link to zarr-http-server.readthedocs.io and .readthedocs.yaml skipped the repo-root docs build for changes confined to this package. Both belong with a Read the Docs project that does not exist yet -- until it does, the nav link 404s and the build skip means neither site builds the package's docs. mkdocs.yml is also what GitHub reported a conflict on, which is what surfaced this. They should land in the follow-up that creates the RTD project. What remains outside the package is two root files that have nowhere else to live: the pre-push docs hook, since a pre-commit hook is necessarily repo-level, and a comment-only change to pyproject.toml noting that the release workflow's `zarr_http_server-v*` tags are among those the `git describe --match v*` filter exists to exclude. Assisted-by: ClaudeCode:claude-opus-5 --- .github/workflows/check_changelogs.yml | 3 + .../workflows/zarr-http-server-release.yml | 117 + .github/workflows/zarr-http-server.yml | 139 ++ .pre-commit-config.yaml | 31 +- packages/zarr-http-server/.readthedocs.yaml | 30 + packages/zarr-http-server/CHANGELOG.md | 3 + packages/zarr-http-server/LICENSE.txt | 21 + packages/zarr-http-server/README.md | 405 +++ .../zarr-http-server/changes/3732.feature.md | 3 + packages/zarr-http-server/changes/README.md | 25 + .../docs/_static/favicon-96x96.png | Bin 0 -> 12714 bytes .../zarr-http-server/docs/_static/logo_bw.png | Bin 0 -> 45208 bytes packages/zarr-http-server/docs/api/index.md | 31 + packages/zarr-http-server/docs/index.md | 58 + packages/zarr-http-server/examples/serve.py | 45 + .../examples/serve_notebook.ipynb | 213 ++ packages/zarr-http-server/justfile | 68 + packages/zarr-http-server/mkdocs.yml | 99 + packages/zarr-http-server/pyproject.toml | 141 ++ .../src/zarr_http_server/__init__.py | 38 + .../src/zarr_http_server/_keys.py | 218 ++ .../src/zarr_http_server/_serve.py | 1170 +++++++++ .../src/zarr_http_server/py.typed | 0 packages/zarr-http-server/tests/conftest.py | 30 + .../zarr-http-server/tests/test_examples.py | 60 + .../zarr-http-server/tests/test_properties.py | 580 +++++ packages/zarr-http-server/tests/test_serve.py | 1831 ++++++++++++++ packages/zarr-http-server/uv.lock | 2212 +++++++++++++++++ pyproject.toml | 6 +- 29 files changed, 7569 insertions(+), 8 deletions(-) create mode 100644 .github/workflows/zarr-http-server-release.yml create mode 100644 .github/workflows/zarr-http-server.yml create mode 100644 packages/zarr-http-server/.readthedocs.yaml create mode 100644 packages/zarr-http-server/CHANGELOG.md create mode 100644 packages/zarr-http-server/LICENSE.txt create mode 100644 packages/zarr-http-server/README.md create mode 100644 packages/zarr-http-server/changes/3732.feature.md create mode 100644 packages/zarr-http-server/changes/README.md create mode 100644 packages/zarr-http-server/docs/_static/favicon-96x96.png create mode 100644 packages/zarr-http-server/docs/_static/logo_bw.png create mode 100644 packages/zarr-http-server/docs/api/index.md create mode 100644 packages/zarr-http-server/docs/index.md create mode 100644 packages/zarr-http-server/examples/serve.py create mode 100644 packages/zarr-http-server/examples/serve_notebook.ipynb create mode 100644 packages/zarr-http-server/justfile create mode 100644 packages/zarr-http-server/mkdocs.yml create mode 100644 packages/zarr-http-server/pyproject.toml create mode 100644 packages/zarr-http-server/src/zarr_http_server/__init__.py create mode 100644 packages/zarr-http-server/src/zarr_http_server/_keys.py create mode 100644 packages/zarr-http-server/src/zarr_http_server/_serve.py create mode 100644 packages/zarr-http-server/src/zarr_http_server/py.typed create mode 100644 packages/zarr-http-server/tests/conftest.py create mode 100644 packages/zarr-http-server/tests/test_examples.py create mode 100644 packages/zarr-http-server/tests/test_properties.py create mode 100644 packages/zarr-http-server/tests/test_serve.py create mode 100644 packages/zarr-http-server/uv.lock diff --git a/.github/workflows/check_changelogs.yml b/.github/workflows/check_changelogs.yml index b6c01e70fc..c391f63738 100644 --- a/.github/workflows/check_changelogs.yml +++ b/.github/workflows/check_changelogs.yml @@ -32,3 +32,6 @@ jobs: - name: Check zarr-indexing changelog entries run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-indexing/changes + + - name: Check zarr-http-server changelog entries + run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-http-server/changes diff --git a/.github/workflows/zarr-http-server-release.yml b/.github/workflows/zarr-http-server-release.yml new file mode 100644 index 0000000000..b8940f7560 --- /dev/null +++ b/.github/workflows/zarr-http-server-release.yml @@ -0,0 +1,117 @@ +name: zarr-http-server release + +on: + workflow_dispatch: + push: + tags: + - 'zarr_http_server-v*' + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: false + +jobs: + build: + name: Build wheel and sdist + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-http-server + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + persist-credentials: false + fetch-depth: 0 # hatch-vcs needs full history + tags + + - name: Install Hatch + uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc + with: + version: '1.16.5' + + - name: Build + run: hatch build + + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + with: + name: zarr-http-server-dist + path: packages/zarr-http-server/dist + + test_artifacts: + name: Test built artifacts + needs: [build] + runs-on: ubuntu-latest + steps: + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + with: + name: zarr-http-server-dist + path: dist + + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + with: + enable-cache: false + + - name: Set up Python + run: uv python install 3.12 + + - name: Install built wheel and run import smoke test + run: | + wheel=$(ls dist/*.whl) + uv run --with "${wheel}" --python 3.12 --no-project \ + python -c "import zarr_http_server; print('zarr_http_server', zarr_http_server.__version__)" + + upload_pypi: + name: Upload to PyPI + needs: [build, test_artifacts] + if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/zarr_http_server-v') + runs-on: ubuntu-latest + environment: + name: zarr-http-server-releases + url: https://pypi.org/p/zarr-http-server + permissions: + id-token: write # required for OIDC trusted publishing + attestations: write # required for artifact attestations + steps: + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + with: + name: zarr-http-server-dist + path: dist + + - name: Generate artifact attestation + uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + with: + subject-path: dist/* + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 + + upload_testpypi: + name: Upload to TestPyPI + needs: [build, test_artifacts] + if: github.event_name == 'workflow_dispatch' + runs-on: ubuntu-latest + environment: + name: zarr-http-server-releases-test + url: https://test.pypi.org/p/zarr-http-server + permissions: + id-token: write + attestations: write + steps: + - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + with: + name: zarr-http-server-dist + path: dist + + - name: Generate artifact attestation + uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + with: + subject-path: dist/* + + - name: Publish package to TestPyPI + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 + with: + repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/zarr-http-server.yml b/.github/workflows/zarr-http-server.yml new file mode 100644 index 0000000000..16589f0d7d --- /dev/null +++ b/.github/workflows/zarr-http-server.yml @@ -0,0 +1,139 @@ +name: zarr-http-server + +# Job steps delegate to packages/zarr-http-server/justfile, the single source +# of truth for this package's verbs; CI owns only the python matrix and +# caching. Keeping the commands in one place is what makes `just check` +# locally mean the same thing as a green run here. + +on: + push: + branches: [main] + paths: + - 'packages/zarr-http-server/**' + - '.github/workflows/zarr-http-server.yml' + # The package resolves zarr from the repo root for its own tests, so a + # core change can break it. Run this suite when core changes too. + - 'src/zarr/**' + pull_request: + paths: + - 'packages/zarr-http-server/**' + - '.github/workflows/zarr-http-server.yml' + # The package resolves zarr from the repo root for its own tests, so a + # core change can break it. Run this suite when core changes too. + - 'src/zarr/**' + workflow_dispatch: + +permissions: + contents: read + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + test: + name: pytest py=${{ matrix.python-version }} + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-http-server + strategy: + fail-fast: false + matrix: + python-version: ['3.12', '3.13', '3.14'] + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + with: + enable-cache: true + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 + - name: Sync test dependency groups + # The examples group carries the deps the README examples need, so the + # test that reads a served array back with a zarr client runs here + # instead of silently skipping. + run: uv sync --group test --group examples --python ${{ matrix.python-version }} + - name: Run pytest + run: just test + + ruff: + name: ruff + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-http-server + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 + - name: Run ruff + run: just lint + + mypy: + name: mypy + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-http-server + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + with: + enable-cache: true + - name: Set up Python + run: uv python install 3.12 + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 + - name: Sync test dependency group + run: uv sync --group test --python 3.12 + - name: Run mypy + run: just typecheck + + docs: + name: docs + runs-on: ubuntu-latest + defaults: + run: + shell: bash + working-directory: packages/zarr-http-server + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 + with: + persist-credentials: false + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + with: + enable-cache: true + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 + - name: Build docs + run: just docs-check + + zarr-http-server-complete: + name: zarr-http-server complete + needs: [test, ruff, mypy, docs] + if: always() + runs-on: ubuntu-latest + steps: + - name: Check failure + if: | + contains(needs.*.result, 'failure') || + contains(needs.*.result, 'cancelled') + run: exit 1 + - name: Success + run: echo Success! diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7f49f47187..54345c819e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,11 +2,13 @@ ci: autoupdate_commit_msg: "chore: update pre-commit hooks" autoupdate_schedule: "monthly" autofix_prs: false - # mypy runs as a `language: system` hook via `uv run mypy`, which needs `uv` - # and the repo checkout to resolve the dev environment from `uv.lock` — - # unavailable on pre-commit.ci's runners. It is covered instead by the Lint - # GitHub Actions workflow and by local prek runs. - skip: [mypy] + # Both of these are `language: system` hooks that shell out to the local + # toolchain — `uv` for mypy, `uv` and `just` for the docs build — and need + # the repo checkout to resolve their environments from `uv.lock`. Neither is + # available on pre-commit.ci's runners. Each is covered instead by a GitHub + # Actions job (Lint for mypy, zarr-http-server for the docs build) and by + # local prek runs. + skip: [mypy, zarr-http-server-docs] default_stages: [pre-commit, pre-push] @@ -50,6 +52,25 @@ repos: pass_filenames: false always_run: true types_or: [python, pyi] + # Builds the zarr-http-server docs site with warnings as errors, which + # catches a dead cross-reference or a nav entry pointing at a file that + # no longer exists before it reaches CI. + # + # `stages: [pre-push]` overrides the default of running on every commit: + # this is a whole-site build, too slow to pay per commit and only + # actionable before the code leaves the machine. `files:` limits it to + # changes that touch the package, and `pass_filenames: false` because + # mkdocs builds the site, not a list of files. Delegating to the + # justfile keeps one definition of the build shared with CI. + - id: zarr-http-server-docs + name: zarr-http-server docs build + language: system + entry: >- + just --justfile packages/zarr-http-server/justfile + --working-directory packages/zarr-http-server docs-check + pass_filenames: false + files: ^packages/zarr-http-server/ + stages: [pre-push] - repo: https://github.com/scientific-python/cookie rev: 2026.06.18 hooks: diff --git a/packages/zarr-http-server/.readthedocs.yaml b/packages/zarr-http-server/.readthedocs.yaml new file mode 100644 index 0000000000..62a1e82b77 --- /dev/null +++ b/packages/zarr-http-server/.readthedocs.yaml @@ -0,0 +1,30 @@ +# Read the Docs configuration for the zarr-http-server docs site, separate from +# the zarr-python site configured by the repo-root .readthedocs.yaml. The RTD +# project for zarr-http-server must set its configuration-file path to +# packages/zarr-http-server/.readthedocs.yaml. +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.12" + jobs: + post_checkout: + # Cancel pull request builds that do not touch this package. Exit code + # 183 cancels the build and reports success to the Git provider. Scoped + # to PR builds ("external" versions) because origin/main is only a + # meaningful diff base there. + - | + if [ "$READTHEDOCS_VERSION_TYPE" = "external" ] && git diff --quiet origin/main -- packages/zarr-http-server; + then + exit 183; + fi + install: + - pip install --upgrade pip + - pip install ./packages/zarr-http-server --group packages/zarr-http-server/pyproject.toml:docs + build: + html: + - mkdocs build --strict -f packages/zarr-http-server/mkdocs.yml --site-dir $READTHEDOCS_OUTPUT/html + +mkdocs: + configuration: packages/zarr-http-server/mkdocs.yml diff --git a/packages/zarr-http-server/CHANGELOG.md b/packages/zarr-http-server/CHANGELOG.md new file mode 100644 index 0000000000..7c4bc92cad --- /dev/null +++ b/packages/zarr-http-server/CHANGELOG.md @@ -0,0 +1,3 @@ +# Release notes + +<!-- towncrier release notes start --> diff --git a/packages/zarr-http-server/LICENSE.txt b/packages/zarr-http-server/LICENSE.txt new file mode 100644 index 0000000000..1e8da4d242 --- /dev/null +++ b/packages/zarr-http-server/LICENSE.txt @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2015-2025 Zarr Developers <https://github.com/zarr-developers> + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/packages/zarr-http-server/README.md b/packages/zarr-http-server/README.md new file mode 100644 index 0000000000..069b33abf8 --- /dev/null +++ b/packages/zarr-http-server/README.md @@ -0,0 +1,405 @@ +# zarr-http-server + +HTTP server for Zarr stores, arrays, and groups. + +`zarr-http-server` exposes a Zarr `Store`, `Array`, or `Group` over HTTP via an +ASGI app, so any HTTP-capable client (including zarr-python itself, via +`FsspecStore` or `ObjectStore`) can read the data. The app is built on +[Starlette](https://www.starlette.io/) and can be run with any ASGI server; +the `serve` / `serve_background` helpers run it with +[Uvicorn](https://www.uvicorn.org/). + +## Installation + +```bash +pip install zarr-http-server +``` + +### Building an ASGI App + +`store_app` creates an ASGI app that exposes every key +in a store. Only point it at a store whose full contents are safe to serve +publicly — it grants read (and, if `PUT` is enabled, write) access to +everything the store contains, with no per-key filtering: + +```python +import zarr +from zarr_http_server import store_app + +store = zarr.storage.MemoryStore() +zarr.create_array(store, shape=(100, 100), chunks=(10, 10), dtype="float64") + +app = store_app(store) + +# Run with any ASGI server, e.g. Uvicorn: +# uvicorn my_module:app --host 0.0.0.0 --port 8000 +``` + +`node_app` creates an ASGI app that only serves keys +belonging to a specific `Array` or `Group`. Requests for keys outside the node +receive a 404, even if those keys exist in the underlying store: + +```python +import zarr +from zarr_http_server import node_app + +store = zarr.storage.MemoryStore() +root = zarr.open_group(store) +root.create_array("a", shape=(10,), dtype="int32") +root.create_array("b", shape=(20,), dtype="float64") + +# Only serve the array at "a" — requests for "b" will return 404. +arr = root["a"] +app = node_app(arr) +``` + +### Running the Server + +Build an app with `store_app` or `node_app`, then run it. `serve` blocks +until the server is stopped, which is the shape for a script or a container +entrypoint: + +```python +from zarr_http_server import serve, store_app + +serve(store_app(store), host="127.0.0.1", port=8000) +``` + +`serve_background` instead starts the server in a daemon thread and returns a +`BackgroundServer` as soon as the socket is listening, so the caller can carry +on. These are two functions rather than one with a flag, because they differ +in the only thing that matters at a call site: whether control comes back. The +handle is also a context manager: + +Both default to `port="auto"`, which prefers port 8000 but falls back to any +free port if it is taken, reporting the result through `server.url` and +uvicorn's startup line. An **explicit** port means the opposite — bind exactly +that or fail — because a caller who names one usually has a proxy or a +container port mapping expecting the server there, and silently moving would +break it while looking healthy. `port=0` keeps its usual meaning of "any free +port, no preference". + +The example below also *reads back* over HTTP, which is a client-side +concern: `zarr.open_array(server.url)` goes through `FsspecStore`, which needs +an HTTP-capable fsspec that `zarr-http-server` does not pull in. + +```bash +pip install "fsspec[http]" +``` + + +```python +import numpy as np + +import zarr +from zarr_http_server import node_app, serve_background +from zarr.storage import MemoryStore + +store = MemoryStore() +arr = zarr.create_array(store, shape=(100,), chunks=(10,), dtype="float64") +arr[:] = np.arange(100, dtype="float64") + +with serve_background(node_app(arr), host="127.0.0.1") as server: + # Now open the served array from another zarr client. + remote = zarr.open_array(server.url, mode="r") + np.testing.assert_array_equal(remote[:], arr[:]) +# Server is shut down automatically when the block exits. +``` + +### Serving Several Nodes + +Serving two arrays does not mean running two servers. Which approach fits +depends on where the arrays live. + +If they share a parent group, serve the parent — `node_app` recurses through +its members, so both are reachable under one port and node scoping still +applies to everything outside it: + +```python +server = serve_background(node_app(root)) +# -> /a/zarr.json, /a/c/0, /b/zarr.json, ... +``` + +If everything in the store is safe to expose, `store_app(store)` does the +same for the whole key space. + +Otherwise — arrays in *different* stores, or nodes that are not siblings — +`store_app` and `node_app` return plain Starlette apps, so mount them and run +the result: + +```python +from starlette.applications import Starlette +from starlette.routing import Mount + +from zarr_http_server import node_app, serve_background + +app = Starlette(routes=[ + Mount("/first", app=node_app(one)), + Mount("/second", app=node_app(other)), +]) +server = serve_background(app) +``` + +Each mount keeps its own validation, so a request under one cannot reach +another's data — `/first/../second/zarr.json` and its percent-encoded +spellings all return 404. + +Both runners take any ASGI app, so the split is clean: what an app *serves* +(`methods`, `cors_options`, `max_body_size`) is settled when the app is built, +while `serve` / `serve_background` only decide how it runs (`host`, `port`, +`shutdown_timeout`, `uvicorn_options`). + +### Serving from a Notebook + +A notebook needs a server that outlives the cell that started it, so the +`with serve_background(...)` form above is the wrong shape — it shuts the server down +as soon as the block ends. Start it, keep the handle, and stop it later: + +```python +# cell 1 — start +server = serve_background(node_app(array), host="127.0.0.1") +print(server.url) # e.g. http://127.0.0.1:54635 + +# cell 2..n — use it, across as many cells as you like +httpx.get(f"{server.url}/zarr.json") + +# last cell — stop +server.shutdown() +``` + +Two things make this comfortable in a kernel you re-run. `serve_background` +runs Uvicorn in a daemon thread with its own event loop, so it never touches +the kernel's loop and cannot block it. And its default `port="auto"` falls +back to a free port when 8000 is taken — re-running a start cell without +stopping the previous server is the classic notebook mistake, and a fixed port +fails there with *address already in use*. `server.url` reports the port +actually bound. + +If you forget to stop one, the thread is a daemon, so restarting the kernel +always clears it — and since each start takes a fresh port, a forgotten server +does not block the next one. + +[`examples/serve_notebook.ipynb`](examples/serve_notebook.ipynb) is a runnable +version of this, covering metadata and chunk reads, byte ranges, and that +writes are refused by default. It is executed by the test suite, so it cannot +drift from the code. + +### Uvicorn Configuration + +`serve` and `serve_background` name the options most callers need — `host`, +`port`, `shutdown_timeout` — and forward anything else to +`uvicorn.Config` through `uvicorn_options`, so nothing uvicorn can do is out +of reach: + +```python +server = serve_background( + store_app(store), + host="0.0.0.0", + port=8443, + uvicorn_options={ + "ssl_keyfile": "key.pem", + "ssl_certfile": "cert.pem", + "proxy_headers": True, + "forwarded_allow_ips": "10.0.0.0/8", + "log_level": "warning", + }, +) +``` + +Keys you pass are merged over the ones set for you, so they win. `server.url` +reflects the scheme actually in use (`https` when TLS is configured) and is +`None` when the server is not bound to a TCP host and port — a `uds` or `fd` +bind has no URL to report. + +### CORS Support + +Both `store_app` and `node_app` accept a `CorsOptions` parameter to enable +[CORS](https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS) middleware for +browser-based clients: + +```python +from zarr_http_server import CorsOptions, store_app + +app = store_app( + store, + cors_options=CorsOptions( + allow_origins=["*"], + allow_methods=["GET"], + ), +) +``` + +`CorsOptions` carries every parameter Starlette's `CORSMiddleware` accepts — +`allow_headers`, `allow_credentials`, `allow_origin_regex`, +`allow_private_network`, `expose_headers` and `max_age` as well as the two +above — so configuring CORS never means reaching around this package. All keys +are optional. + +Two defaults differ from Starlette's, because the server knows things the +caller should not have to. It emits `Content-Range` on every ranged response, +which is *not* a CORS-safelisted response header, so `expose_headers` defaults +to `["Content-Range"]` — otherwise a browser client can read the bytes but not +learn which bytes it got. And it accepts a `Range` request header, so +`allow_headers` defaults to `["Range"]` — otherwise a preflight naming `Range` +is rejected. A key you supply replaces the default outright, so +`expose_headers=[]` means "expose nothing". + +### HTTP Range Requests + +The server supports the standard `Range` header for partial reads. The three +forms defined by [RFC 7233](https://httpwg.org/specs/rfc7233.html) are supported: + +| Header | Meaning | +| -------------------- | ------------------------------ | +| `bytes=0-99` | First 100 bytes | +| `bytes=100-` | Everything from byte 100 | +| `bytes=-50` | Last 50 bytes | + +A successful range request returns HTTP 206 (Partial Content) with a +`Content-Range` header, including for suffix ranges — the server resolves +`bytes=-50` against the object's size so the response says which bytes it +carries. + +A range that is well-formed but names nothing readable — one lying wholly +beyond the end of the object, an inverted one such as `bytes=5-2`, or +`bytes=-0` — returns 416 (Range Not Satisfiable). A last-byte-position past +the end of the object is *not* in that category: per RFC 9110 §14.1.2 it is +clamped, so `bytes=0-999999` on a short object returns the whole thing. + +A `Range` header the server cannot use is **ignored** rather than refused, per +RFC 9110 §14.2: an unrecognized unit (`chars=0-7`), a multi-range request +(`bytes=0-7, 10-20`, which this server does not build multipart responses +for), or malformed syntax all return 200 with the full representation. + +### Read-only Serving + +Read-only is the default. `store_app(store)` and `node_app(node)` accept +`GET` and `HEAD` and answer **405** to `PUT`, `POST`, `DELETE` and `PATCH` — +no argument is needed to get there. + +`POST` is not merely unrouted, it is unconfigurable: the accepted methods are +`GET`, `HEAD` and `PUT`, and asking for anything else raises `ValueError` when +the app is built. There is no handler behavior for `POST`, so no configuration +can produce one. + +Two named sets let a call site state which it is, instead of leaving it to the +presence or absence of an argument: + +```python +from zarr_http_server import READ_ONLY_HTTP_METHODS, READ_WRITE_HTTP_METHODS, store_app + +app = store_app(store, methods=READ_ONLY_HTTP_METHODS) # GET, HEAD +app = store_app(store, methods=READ_WRITE_HTTP_METHODS) # GET, HEAD, PUT +``` + +The distinction also exists in the type domain. `ReadOnlyHTTPMethod` is a +`Literal["GET", "HEAD"]`, so a read-only set can be *declared* rather than +merely configured — a `frozenset[ReadOnlyHTTPMethod]` containing `"PUT"` is a +type error, not a runtime surprise: + +```python +from zarr_http_server import ReadOnlyHTTPMethod + +reads: frozenset[ReadOnlyHTTPMethod] = frozenset({"GET", "HEAD"}) # ok +reads = frozenset({"GET", "PUT"}) # type error +``` + +Both constants are derived from these Literals, so the runtime sets and the +static types cannot disagree about what the server serves. + +`READ_ONLY_HTTP_METHODS` is exactly the default, so passing it changes nothing +except that the intent is now written down. The practical value is the other +direction: a writable app *must* name a method set, so +`grep -r 'methods=' ` finds every place that opts into writes. + +For a guarantee that does not depend on getting `methods` right, make the +*store* read-only. The store refuses writes itself, so no routing mistake — +now or in a later edit — can produce one: + +```python +app = store_app(store.with_read_only(True)) + +# For a node, open it read-only and node_app inherits that store: +app = node_app(zarr.open_array(store, mode="r")) +``` + +These two layers are independent, and the store is the stronger one: it holds +even if the HTTP layer is misconfigured. Asking for both at once — +`methods={"GET", "PUT"}` on a read-only store — is a contradiction that can +never succeed, so it raises `ValueError` at construction rather than turning +into a 403 for whichever client tries to write first. + +### Write Support + +By default only reads are accepted: `GET`, and `HEAD` alongside it. Starlette +routes `HEAD` wherever `GET` goes, as RFC 9110 §9.3.2 asks of every origin +server, so naming `GET` gets you both — a `HEAD` is answered from the value's +size without transferring it. To enable writes, pass `methods={"GET", "PUT"}`: + +```python +app = store_app(store, methods={"GET", "PUT"}) +``` + +Accepted methods are `GET`, `HEAD`, and `PUT`; anything else raises +`ValueError` when the app is built, since the handler has no behavior for it. + +A `PUT` request stores the request body at the given path and returns 204 (No +Content). Bodies are capped at `DEFAULT_MAX_BODY_SIZE` (256 MiB) and a larger +one returns 413 (Content Too Large) -- `Store.set` takes a whole buffer, so an +accepted body is held in memory in full. Raise or remove the cap with +`max_body_size`: + +```python +from zarr_http_server import DEFAULT_MAX_BODY_SIZE, store_app + +app = store_app(store, methods={"GET", "PUT"}, max_body_size=None) +``` + +Note that `store_app` exposes every key in the store, so `PUT` grants +unrestricted write access to all of it. `node_app` confines writes to keys +belonging to the node -- though a client that can write a node's metadata can +change what that node contains, and so what it will serve. + +`store_app` also does not *validate* keys, because it proxies the store's raw +key space and has no array semantics to check against. A client that misspells +a chunk key — `c/00/00` where zarr writes `c/0/0` — gets a successful write to +a key no reader will ever consult, so the data is stored but invisible to +anyone opening the array. `node_app` rejects such a key with 404, since it +knows which node it is serving and therefore which keys are real. If you are +serving a zarr hierarchy to clients you do not control and writes are enabled, +prefer `node_app`. + +### Shutting Down + +`BackgroundServer.shutdown()` (and leaving the `with` block) waits up to +`shutdown_timeout` seconds -- 5 by default -- for in-flight requests to finish +before forcing the server closed: + +```python +with serve_background(node_app(arr), shutdown_timeout=30) as server: + ... +``` + +## Example + +`examples/serve.py` creates an in-memory Zarr array, serves it over HTTP with +`serve_background`, and fetches the `zarr.json` metadata document and a raw chunk +using `httpx`. + +`examples/serve_notebook.ipynb` is the notebook equivalent, showing how to +start a server in one cell and stop it in another. Both are executed by the +test suite. + +Running it with uv is the simplest route — the script declares its own +dependencies inline, so uv installs them for you: + +```bash +uv run examples/serve.py +``` + +To run it with a plain interpreter, install its `httpx` dependency first: + +```bash +pip install httpx +python examples/serve.py +``` diff --git a/packages/zarr-http-server/changes/3732.feature.md b/packages/zarr-http-server/changes/3732.feature.md new file mode 100644 index 0000000000..accd91ab81 --- /dev/null +++ b/packages/zarr-http-server/changes/3732.feature.md @@ -0,0 +1,3 @@ +Initial release of `zarr-http-server`: an HTTP server exposing Zarr stores, +arrays, and groups over an ASGI app, extracted from the +`zarr.experimental.serve` prototype in zarr-python. diff --git a/packages/zarr-http-server/changes/README.md b/packages/zarr-http-server/changes/README.md new file mode 100644 index 0000000000..80f0be782c --- /dev/null +++ b/packages/zarr-http-server/changes/README.md @@ -0,0 +1,25 @@ +Writing a changelog entry for `zarr-http-server` +--------------------------------------------- + +Fragments in **this** directory are released notes for the `zarr-http-server` +package only — kept separate from the parent zarr-python `changes/` +directory so a PR touching only `packages/zarr-http-server/` produces a +release note for this package only. + +Please put a new file in this directory named `xxxx.<type>.md`, where + +- `xxxx` is the pull request number associated with this entry +- `<type>` is one of: + - feature + - bugfix + - doc + - removal + - misc + +Inside the file, please write a short description of what you have +changed, and how it impacts users of `zarr-http-server`. + +A `zarr-http-server` release runs `towncrier build` in `packages/zarr-http-server/`, +which consumes the fragments here and updates `CHANGELOG.md`. 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+Everything public is re-exported from the top-level `zarr_http_server` +namespace; the private `_serve` and `_keys` modules are implementation detail +and carry no compatibility guarantee. + +## Building an app + +::: zarr_http_server.store_app + +::: zarr_http_server.node_app + +## Running a server + +::: zarr_http_server.serve + +::: zarr_http_server.serve_background + +::: zarr_http_server.BackgroundServer + +## Configuration + +::: zarr_http_server.CorsOptions + +::: zarr_http_server.HTTPMethod + +::: zarr_http_server.DEFAULT_MAX_BODY_SIZE diff --git a/packages/zarr-http-server/docs/index.md b/packages/zarr-http-server/docs/index.md new file mode 100644 index 0000000000..5671c12d00 --- /dev/null +++ b/packages/zarr-http-server/docs/index.md @@ -0,0 +1,58 @@ +# zarr-http-server + +HTTP server for Zarr stores, arrays, and groups. + +`zarr-http-server` is developed in the +[zarr-python repository](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-http-server) +and released independently of `zarr` itself. Install it with: + +``` +pip install zarr-http-server +``` + +!!! warning "Experimental" + + This package is experimental. Its API may change or be removed at any + point. + +## What this is + +`zarr-http-server` exposes a Zarr `Store`, `Array`, or `Group` over HTTP via an +ASGI app, so any HTTP-capable client — including zarr-python itself, via +`FsspecStore` or `ObjectStore` — can read the data. The app is built on +[Starlette](https://www.starlette.io/) and can be run with any ASGI server; +the `serve` / `serve_background` helpers run it with +[Uvicorn](https://www.uvicorn.org/). + +Two levels of exposure are available: + +- **Whole store** ([`store_app`][zarr_http_server.store_app], + run with [`serve`][zarr_http_server.serve]) — serves every key in a + store, exposing its entire key/value space. +- **Single node** ([`node_app`][zarr_http_server.node_app], + run with [`serve_background`][zarr_http_server.serve_background]) — serves only the keys + belonging to one `Array` or `Group`. Requests for keys outside that node + return 404 even when those keys exist in the underlying store. + +Byte-range reads, configurable CORS headers, and a configurable set of allowed +HTTP methods are handled by the app. + +!!! danger "Serving a whole store grants access to all of it" + + `store_app` applies no per-key filtering. Only point it + at a store whose full contents are safe to serve, and note that enabling + `PUT` grants write access to everything the store contains. + +## Getting started + +The [README](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/README.md) +carries worked examples for building an ASGI app, running a blocking or +background server, and configuring CORS and allowed methods. Runnable +versions live in +[`examples/`](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-http-server/examples). + +## Reference + +- [API reference](api/index.md) +- [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/CHANGELOG.md) +- [License (MIT)](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/LICENSE.txt) diff --git a/packages/zarr-http-server/examples/serve.py b/packages/zarr-http-server/examples/serve.py new file mode 100644 index 0000000000..45caa9ea67 --- /dev/null +++ b/packages/zarr-http-server/examples/serve.py @@ -0,0 +1,45 @@ +# /// script +# requires-python = ">=3.12" +# dependencies = [ +# "zarr-http-server @ git+https://github.com/zarr-developers/zarr-python.git@main#subdirectory=packages/zarr-http-server", +# "httpx", +# ] +# /// +""" +Serve a Zarr array over HTTP and fetch its metadata and chunks. + +This example creates an in-memory array, serves it in a background thread, +then uses ``httpx`` to request the ``zarr.json`` metadata document and a raw +chunk. +""" + +import json + +import httpx +import numpy as np +import zarr +from zarr.storage import MemoryStore + +from zarr_http_server import node_app, serve_background + +# -- create an array -------------------------------------------------------- +store = MemoryStore() +data = np.arange(1000, dtype="uint8").reshape(10, 10, 10) +# no compression +arr = zarr.create_array(store, data=data, chunks=(5, 5, 5), write_data=True, compressors=None) + +# -- serve it in the background --------------------------------------------- +# port=0 asks the OS for a free port, so running this twice -- or running it +# while something else holds 8000 -- works. `server.url` reports what it bound. +with serve_background(node_app(arr), host="127.0.0.1") as server: + # -- fetch metadata ------------------------------------------------------ + resp = httpx.get(f"{server.url}/zarr.json") + assert resp.status_code == 200 + meta = resp.json() + print("zarr.json:") + print(json.dumps(meta, indent=2)) + + # -- fetch a raw chunk --------------------------------------------------- + resp = httpx.get(f"{server.url}/c/0/0/0") + assert resp.status_code == 200 + print(f"\nchunk c/0/0/0: {len(resp.content)} bytes") diff --git a/packages/zarr-http-server/examples/serve_notebook.ipynb b/packages/zarr-http-server/examples/serve_notebook.ipynb new file mode 100644 index 0000000000..e751a526c1 --- /dev/null +++ b/packages/zarr-http-server/examples/serve_notebook.ipynb @@ -0,0 +1,213 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "6cb56289", + "metadata": {}, + "source": [ + "# Serving a Zarr array from a notebook\n", + "\n", + "A notebook needs a server that outlives the cell that started it, which is the\n", + "one thing the `with serve_background(...)` form in the README cannot give\n", + "that shuts the server down as soon as the block ends.\n", + "\n", + "The notebook pattern is instead:\n", + "\n", + "1. start with `serve_background` and keep the handle,\n", + "2. use the server across as many cells as you like,\n", + "3. `shutdown()` when you are done.\n", + "\n", + "Two details make this comfortable in a kernel you re-run:\n", + "\n", + "- **`serve_background`** runs uvicorn in a daemon thread with its own event\n", + " loop, so it never touches the kernel's loop and cannot block it.\n", + "- **`port=\"auto\"`**, its default, prefers port 8000 but takes a free one if\n", + " it is busy. Re-running a start cell without stopping the previous server is\n", + " the classic notebook mistake, and a fixed port fails there with *address\n", + " already in use*. `server.url` reports the port actually bound." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e2e217fa", + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import zarr\n", + "from zarr.storage import MemoryStore\n", + "\n", + "from zarr_http_server import node_app, serve_background\n", + "\n", + "store = MemoryStore()\n", + "array = zarr.create_array(\n", + " store,\n", + " data=np.arange(1000, dtype=\"uint8\").reshape(10, 10, 10),\n", + " chunks=(5, 5, 5),\n", + " compressors=None,\n", + " write_data=True,\n", + ")\n", + "array.info" + ] + }, + { + "cell_type": "markdown", + "id": "35752272", + "metadata": {}, + "source": [ + "## Start\n", + "\n", + "`serve_background` returns a `BackgroundServer` as soon as the socket is\n", + "so the next cell can use it immediately." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b5010cdb", + "metadata": {}, + "outputs": [], + "source": [ + "server = serve_background(node_app(array), host=\"127.0.0.1\")\n", + "\n", + "print(f\"serving at {server.url}\")\n", + "assert server.url is not None" + ] + }, + { + "cell_type": "markdown", + "id": "d4e1f8d6", + "metadata": {}, + "source": [ + "## Use it\n", + "\n", + "The server is alive across cells now. Anything that speaks HTTP can read from\n", + "it -- here `httpx`, but a browser or another zarr client works the same way.\n", + "\n", + "(With `fsspec[http]` installed you can also do\n", + "`zarr.open_array(server.url, mode=\"r\")` to read the array back through zarr\n", + "itself.)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5ac501fa", + "metadata": {}, + "outputs": [], + "source": [ + "import httpx\n", + "\n", + "metadata = httpx.get(f\"{server.url}/zarr.json\", timeout=30)\n", + "print(metadata.status_code, metadata.headers[\"content-type\"])\n", + "assert metadata.status_code == 200\n", + "assert metadata.json()[\"shape\"] == [10, 10, 10]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c7a94eff", + "metadata": {}, + "outputs": [], + "source": [ + "chunk = httpx.get(f\"{server.url}/c/0/0/0\", timeout=30)\n", + "print(f\"chunk c/0/0/0: {len(chunk.content)} bytes\")\n", + "assert chunk.status_code == 200\n", + "\n", + "# Byte ranges work too, and say which bytes came back.\n", + "part = httpx.get(f\"{server.url}/c/0/0/0\", headers={\"Range\": \"bytes=0-9\"}, timeout=30)\n", + "print(part.status_code, part.headers[\"content-range\"], part.content)\n", + "assert part.status_code == 206\n", + "assert part.content == chunk.content[:10]" + ] + }, + { + "cell_type": "markdown", + "id": "c8fd3ea2", + "metadata": {}, + "source": [ + "## Writes are off unless you ask\n", + "\n", + "The default is read-only, so a stray `PUT` from a notebook cell -- or from\n", + "anyone else who can reach the port -- is refused." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2f6bee45", + "metadata": {}, + "outputs": [], + "source": [ + "refused = httpx.put(f\"{server.url}/c/0/0/0\", content=b\"nope\", timeout=30)\n", + "print(\"PUT ->\", refused.status_code)\n", + "assert refused.status_code == 405" + ] + }, + { + "cell_type": "markdown", + "id": "74f4bebc", + "metadata": {}, + "source": [ + "## Stop\n", + "\n", + "`shutdown()` waits for in-flight requests, then forces the server closed. It\n", + "raises if the thread will not stop, so a silent failure cannot leave you\n", + "believing the port is free when it is not." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "53a3e8d4", + "metadata": {}, + "outputs": [], + "source": [ + "server.shutdown()\n", + "\n", + "# The port really is closed now.\n", + "try:\n", + " httpx.get(f\"{server.url}/zarr.json\", timeout=5)\n", + "except httpx.HTTPError as exc:\n", + " print(f\"as expected, no longer serving: {type(exc).__name__}\")\n", + "else:\n", + " raise AssertionError(\"server still responding after shutdown\")" + ] + }, + { + "cell_type": "markdown", + "id": "8a7742e0", + "metadata": {}, + "source": [ + "## If you forget to stop one\n", + "\n", + "The server thread is a daemon, so it dies with the kernel -- restarting the\n", + "kernel always clears it. Because `port=0` picks a fresh port each time, a\n", + "forgotten server does not block the next one either; it just holds a port\n", + "until the kernel exits.\n", + "\n", + "If you want the shutdown tied to a block rather than a cell, the context\n", + "manager form still works inside a single cell:\n", + "\n", + "```python\n", + "with serve_background(node_app(array)) as server:\n", + " ... # everything must happen in this cell\n", + "```" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/packages/zarr-http-server/justfile b/packages/zarr-http-server/justfile new file mode 100644 index 0000000000..d65b1b53b7 --- /dev/null +++ b/packages/zarr-http-server/justfile @@ -0,0 +1,68 @@ +# Development verbs for the zarr-http-server package. Recipes run with this +# directory as the working directory regardless of where `just` is invoked. +# +# CI calls these recipes rather than repeating their commands, so a green run +# in .github/workflows/zarr-http-server.yml means the same thing as a green +# `just check` here. + +# Pinned to the ruff that .pre-commit-config.yaml uses, so this and the +# pre-commit gate enforce one standard. An unpinned `uvx ruff` floats to the +# newest release: when ruff 0.16 began selecting BLE001 under the root +# config's `B` prefix, this job failed on rules the pinned ruff never enforced, +# with no code change to blame. Bump alongside the pre-commit rev. +ruff_version := "0.16.0" + +# List available recipes +default: + @just --list + +# The `examples` group carries the deps the README examples need, so the test +# that reads a served array back with a zarr client runs here instead of +# silently skipping. +# Run the test suite; extra args are passed to pytest +test *args: + uv run --group test --group examples pytest tests {{ args }} + +# Lint the package sources and tests +lint: + uvx ruff@{{ ruff_version }} check . + +# This package type-checks with mypy (see [tool.mypy] in pyproject.toml) +# rather than the pyright used by the other packages under packages/. +# Type-check the package sources +typecheck: + uv run --group test --with mypy mypy src + +# Run everything CI runs for this package +check: lint typecheck test docs-check + +# Preview the changelog that the next release would generate +changelog-draft: + uvx towncrier build --draft --version Unreleased + +# Build this package's documentation site, warnings as errors +docs-check: + env DISABLE_MKDOCS_2_WARNING=true uv run --group docs mkdocs build --strict + +# With no argument, uses port 8000 if free, otherwise an ephemeral free port; +# an explicitly requested port is used as-is so a conflict fails loudly. +# Serve this package's documentation site +docs-serve port="": + #!/usr/bin/env bash + set -euo pipefail + port="{{ port }}" + if [ -z "$port" ]; then + port=$(uv run --group docs python -c ' + import socket + s = socket.socket() + try: + s.bind(("127.0.0.1", 8000)) + except OSError: + s.close() + s = socket.socket() + s.bind(("127.0.0.1", 0)) + print(s.getsockname()[1]) + s.close() + ') + fi + exec env DISABLE_MKDOCS_2_WARNING=true uv run --group docs mkdocs serve -a "localhost:$port" diff --git a/packages/zarr-http-server/mkdocs.yml b/packages/zarr-http-server/mkdocs.yml new file mode 100644 index 0000000000..4e7843f36d --- /dev/null +++ b/packages/zarr-http-server/mkdocs.yml @@ -0,0 +1,99 @@ +site_name: zarr-http-server +# The package lives in the zarr-python monorepo; point the header source +# widget at the package directory rather than the repository root. +repo_name: zarr-python/packages/zarr-http-server +repo_url: https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-http-server +# Absolute because mkdocs would otherwise append this to repo_url's subpath. +edit_uri: https://github.com/zarr-developers/zarr-python/edit/main/packages/zarr-http-server/docs/ +site_description: HTTP server for Zarr stores, arrays, and groups. +site_author: Davis Bennett +site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://zarr-http-server.readthedocs.io/'] +docs_dir: docs +use_directory_urls: true + +nav: + - index.md + - API Reference: + - api/index.md + - Changelog: https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/CHANGELOG.md + +watch: + - src + +theme: + language: en + name: material + logo: _static/logo_bw.png + favicon: _static/favicon-96x96.png + + palette: + # Light mode + - media: "(prefers-color-scheme: light)" + scheme: default + toggle: + icon: material/brightness-7 + name: Switch to dark mode + + # Dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + toggle: + icon: material/brightness-4 + name: Switch to light mode + + font: + text: Roboto + code: Roboto Mono + + features: + - content.code.annotate + - content.code.copy + - navigation.indexes + - navigation.instant + - navigation.tracking + - search.suggest + - search.share + +plugins: + - autorefs + - search + - mkdocstrings: + enable_inventory: true + handlers: + python: + paths: [src] + options: + allow_inspection: true + docstring_section_style: list + docstring_style: numpy + inherited_members: true + line_length: 60 + separate_signature: true + show_root_heading: true + show_signature_annotations: true + show_source: true + show_symbol_type_toc: true + signature_crossrefs: true + show_if_no_docstring: true + extensions: + - griffe_inherited_docstrings + + inventories: + - https://docs.python.org/3/objects.inv + - https://zarr.readthedocs.io/en/stable/objects.inv + +markdown_extensions: + - admonition + - attr_list + - def_list + - footnotes + - md_in_html + - pymdownx.details + - pymdownx.superfences + - toc: + permalink: true + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite diff --git a/packages/zarr-http-server/pyproject.toml b/packages/zarr-http-server/pyproject.toml new file mode 100644 index 0000000000..ef38d67e49 --- /dev/null +++ b/packages/zarr-http-server/pyproject.toml @@ -0,0 +1,141 @@ +[build-system] +requires = ["hatchling>=1.29.0", "hatch-vcs"] +build-backend = "hatchling.build" + +[project] +name = "zarr-http-server" +dynamic = ["version"] +description = "HTTP server for Zarr stores, arrays, and groups." +readme = "README.md" +requires-python = ">=3.12" +license = "MIT" +license-files = ["LICENSE.txt"] +authors = [ + { name = "Davis Bennett", email = "davis.v.bennett@gmail.com" }, +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "Intended Audience :: Information Technology", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Topic :: Scientific/Engineering", + "Topic :: Internet :: WWW/HTTP :: HTTP Servers", + "Typing :: Typed", +] +keywords = ["zarr", "http", "server", "asgi"] +dependencies = [ + "zarr>=3.1", + "starlette>=1.0", + "uvicorn>=0.29", +] + +[project.urls] +Homepage = "https://github.com/zarr-developers/zarr-python" +Source = "https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-http-server" +Issues = "https://github.com/zarr-developers/zarr-python/issues" +Changelog = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/CHANGELOG.md" +Documentation = "https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/README.md" + +[dependency-groups] +test = [ + "pytest", + "httpx", + "httpx2", + "hypothesis", + # Executing examples/serve_notebook.ipynb in the suite: nbformat reads it, + # nbclient runs it, ipykernel is the kernel it runs in. + "nbformat", + "nbclient", + "ipykernel", +] +examples = [ + # Optional dependencies to run the README examples. Reading a served + # array back with `zarr.open_array(url)` goes through FsspecStore, which + # needs an HTTP-capable fsspec; `examples/serve.py` uses httpx. + "fsspec[http]", + "httpx", +] +docs = [ + # Pins match the zarr-python docs environment in the repo-root + # pyproject.toml so the two sites render with the same toolchain. + "mkdocs-material==9.7.7", + "mkdocs==1.6.1", + "mkdocstrings==1.0.6", + "mkdocstrings-python==2.0.5", + "griffe-inherited-docstrings==1.1.3", + # mkdocstrings uses ruff to format rendered signatures + "ruff==0.16.0", +] + +# Dev-only: resolve zarr from the repo root so package tests run against +# in-repo zarr. Affects uv resolution only, not published metadata. +[tool.uv.sources] +zarr = { path = "../..", editable = true } + +[tool.hatch.version] +source = "vcs" +tag-pattern = '^zarr_http_server-v(?P<version>.+)$' +# `git_describe_command` ensures we get the zarr_http_server tags instead of latest. +# `local_scheme` strips the git commit info so the appending info is just a counter from latest tag. +# test-pypi doesn't accept git commit info in tags, and the count should be enough to distinguish unique runs. +raw-options = { root = "../..", git_describe_command = "git describe --dirty --tags --long --match zarr_http_server-v*", local_scheme = "no-local-version" } + +[tool.hatch.build.targets.wheel] +packages = ["src/zarr_http_server"] + +[tool.ruff] +extend = "../../pyproject.toml" +target-version = "py312" + +[tool.pytest.ini_options] +minversion = "7" +testpaths = ["tests"] +xfail_strict = true +addopts = ["-ra", "--strict-config", "--strict-markers"] +filterwarnings = [ + "error", +] + +[tool.mypy] +files = ["src"] +python_version = "3.12" +ignore_missing_imports = true +namespace_packages = false +pretty = true +show_error_code_links = true +show_error_context = true +strict = true +warn_unreachable = true +enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool", "truthy-iterable"] + +[tool.numpydoc_validation] +# Mirrors the root zarr-python config so moved docstrings (written for that +# config) don't trip stricter defaults just because this package has its own +# pyproject.toml. See https://numpydoc.readthedocs.io/en/latest/validation.html#built-in-validation-checks +checks = [ + "GL10", + "SS04", + "PR02", + "PR03", + "PR05", + "PR06", +] + +[tool.towncrier] +# Fragments for this package live alongside the package source, separate +# from the parent zarr-python `changes/` directory, so a PR touching only +# `packages/zarr-http-server/` produces a release note for this package only. +directory = "changes" +filename = "CHANGELOG.md" +package = "zarr_http_server" +underlines = ["", "", ""] +title_format = "## {version} ({project_date})" +issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/issues/{issue})" +start_string = "<!-- towncrier release notes start -->\n" diff --git a/packages/zarr-http-server/src/zarr_http_server/__init__.py b/packages/zarr-http-server/src/zarr_http_server/__init__.py new file mode 100644 index 0000000000..4f4fbd22f8 --- /dev/null +++ b/packages/zarr-http-server/src/zarr_http_server/__init__.py @@ -0,0 +1,38 @@ +"""Zarr-http-server: HTTP server for Zarr stores, arrays, and groups.""" + +from importlib.metadata import version + +from zarr_http_server._serve import ( + AUTO_PORT, + DEFAULT_MAX_BODY_SIZE, + DEFAULT_PORT, + READ_ONLY_HTTP_METHODS, + READ_WRITE_HTTP_METHODS, + BackgroundServer, + CorsOptions, + HTTPMethod, + ReadOnlyHTTPMethod, + node_app, + serve, + serve_background, + store_app, +) + +__version__ = version("zarr-http-server") + +__all__ = [ + "AUTO_PORT", + "DEFAULT_MAX_BODY_SIZE", + "DEFAULT_PORT", + "READ_ONLY_HTTP_METHODS", + "READ_WRITE_HTTP_METHODS", + "BackgroundServer", + "CorsOptions", + "HTTPMethod", + "ReadOnlyHTTPMethod", + "__version__", + "node_app", + "serve", + "serve_background", + "store_app", +] diff --git a/packages/zarr-http-server/src/zarr_http_server/_keys.py b/packages/zarr-http-server/src/zarr_http_server/_keys.py new file mode 100644 index 0000000000..e468cd066d --- /dev/null +++ b/packages/zarr-http-server/src/zarr_http_server/_keys.py @@ -0,0 +1,218 @@ +"""Utilities for determining the set of valid store keys for zarr nodes. + +A zarr node (array or group) implicitly defines a subset of keys in the +underlying store. For an **array** the valid keys are: + +* metadata documents (``zarr.json`` for v3, ``.zarray`` / ``.zattrs`` for v2) +* chunk (or shard) keys whose decoded coordinates fall within the storage grid + +For a **group** the valid keys are: + +* its own metadata documents +* any path ``<child>/<subkey>`` where ``<child>`` is a direct member and + ``<subkey>`` is recursively valid for that child +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +ZARR_JSON = "zarr.json" +ZARRAY_JSON = ".zarray" +ZGROUP_JSON = ".zgroup" +ZATTRS_JSON = ".zattrs" +ZMETADATA_V2_JSON = ".zmetadata" + +if TYPE_CHECKING: + from zarr import Array, Group + +_ARRAY_METADATA_KEYS_V3 = frozenset({ZARR_JSON}) +_ARRAY_METADATA_KEYS_V2 = frozenset({ZARRAY_JSON, ZATTRS_JSON}) +_GROUP_METADATA_KEYS_V3 = frozenset({ZARR_JSON}) +_GROUP_METADATA_KEYS_V2 = frozenset({ZGROUP_JSON, ZATTRS_JSON, ZMETADATA_V2_JSON}) + + +def array_metadata_keys(zarr_format: int) -> frozenset[str]: + """Return the metadata key basenames an array owns, for a zarr format. + + Parameters + ---------- + zarr_format : int + The zarr format version (2 or 3). + + Returns + ------- + frozenset of str + """ + if zarr_format == 3: + return _ARRAY_METADATA_KEYS_V3 + return _ARRAY_METADATA_KEYS_V2 + + +def group_metadata_keys(zarr_format: int) -> frozenset[str]: + """Return the metadata key basenames a group owns, for a zarr format. + + Parameters + ---------- + zarr_format : int + The zarr format version (2 or 3). + + Returns + ------- + frozenset of str + """ + if zarr_format == 3: + return _GROUP_METADATA_KEYS_V3 + return _GROUP_METADATA_KEYS_V2 + + +def decode_chunk_key(array: Array[Any], key: str) -> tuple[int, ...] | None: + """Try to decode *key* into chunk coordinates for *array*. + + Parameters + ---------- + array : Array + The array whose chunk key encoding should be used. + key : str + The candidate chunk key string. + + Returns + ------- + tuple of int, or None + The decoded coordinates, or ``None`` if *key* is not a valid chunk key. + """ + try: + if array.metadata.zarr_format == 2: + coords = tuple(int(p) for p in key.split(array.metadata.dimension_separator)) + # A 0-d v2 array holds its single chunk under "0", which decodes + # to a 1-tuple that no 0-d grid could match. + if len(array.shape) == 0: + return () if coords == (0,) else None + return coords + + # Ask zarr rather than predicting it: the encoding owns its own + # grammar, so a new or third-party chunk key encoding decodes here + # without this package knowing anything about it. + return array.metadata.chunk_key_encoding.decode_chunk_key(key) + except (ValueError, TypeError, NotImplementedError): + return None + + +def _shard_grid_shape(array: Array[Any]) -> tuple[int, ...]: + """Shape of the shard grid, falling back to the chunk grid when unsharded.""" + shard_shape = array.shards if array.shards is not None else array.chunks + return tuple(-(-s // c) for s, c in zip(array.shape, shard_shape, strict=True)) + + +def is_valid_chunk_key(array: Array[Any], key: str) -> bool: + """Check whether *key* is a valid chunk key for *array*. + + Decodes the key, checks that the resulting coordinates fall within the + storage grid (shard grid if sharding is used, chunk grid otherwise), and + requires the key to be spelled exactly as zarr itself would spell it. + + That last check is what makes the accepted key set equal to the set of + keys zarr can actually read. Decoding alone is lenient -- `int` accepts + leading zeros, a leading `+`/`-`, surrounding whitespace, underscore + separators, and non-ASCII decimal digits -- so `c/00/00` and `c/0/0` + decode to the same coordinates while naming *different* store keys. A + write to the non-canonical spelling would be stored under a key no reader + ever looks up: the client sees success and the data is invisible. + + Parameters + ---------- + array : Array + The array to validate against. + key : str + The candidate chunk key string. + + Returns + ------- + bool + """ + coords = decode_chunk_key(array, key) + if coords is None: + return False + grid = _shard_grid_shape(array) + if len(coords) != len(grid): + return False + if not all(0 <= c < g for c, g in zip(coords, grid, strict=True)): + return False + return array.metadata.encode_chunk_key(coords) == key + + +def is_valid_array_key(array: Array[Any], key: str) -> bool: + """Check whether *key* is a valid store key for *array*. + + Valid keys are metadata documents and chunk keys. + + Parameters + ---------- + array : Array + The array to validate against. + key : str + The candidate key, relative to the array's root. + + Returns + ------- + bool + """ + if key in array_metadata_keys(array.metadata.zarr_format): + return True + return is_valid_chunk_key(array, key) + + +def is_valid_node_key(node: Array[Any] | Group, key: str) -> bool: + """Check whether *key* is a valid store key relative to *node*. + + For an ``Array``, valid keys are metadata documents and chunk keys. + + For a ``Group``, valid keys are the group's own metadata documents, or + a path of the form ``<child>/<subkey>`` where ``<child>`` is a direct + member and ``<subkey>`` is recursively valid for that child. + + Parameters + ---------- + node : Array or Group + The zarr node to validate against. + key : str + The candidate key, relative to the node's root. + + Returns + ------- + bool + """ + from zarr import Array + + if isinstance(node, Array): + return is_valid_array_key(node, key) + + # Group + if key in group_metadata_keys(node.metadata.zarr_format): + return True + + # Try to match the first path component against a child member. + if "/" in key: + child_name, remainder = key.split("/", 1) + else: + # A bare name with no slash can't be a valid group-level key — + # groups contain children (which have subkeys), not bare keys. + return False + + try: + child = node[child_name] + except KeyError: + # There is no such member, so no key beneath it can be valid. + # + # Only a missing name is caught here. Anything else -- an I/O error + # reading the child's metadata, unparsable JSON, a codec from a + # plugin this process lacks -- means the key could not be *judged*, + # which is not the same as judging it absent. Reporting those as 404 + # would be a lie with teeth: under the v3 spec an absent chunk is an + # uninitialized one, so a correct reader answers a 404 by silently + # substituting the array's fill value over data that exists. Letting + # them propagate surfaces a 500, which is the honest answer and the + # one a client cannot mistake for data. + return False + + return is_valid_node_key(child, remainder) diff --git a/packages/zarr-http-server/src/zarr_http_server/_serve.py b/packages/zarr-http-server/src/zarr_http_server/_serve.py new file mode 100644 index 0000000000..dce1df6b12 --- /dev/null +++ b/packages/zarr-http-server/src/zarr_http_server/_serve.py @@ -0,0 +1,1170 @@ +from __future__ import annotations + +import asyncio +import errno +import logging +import ntpath +import socket +import sys +import threading +import time +from enum import Enum, auto +from functools import partial +from typing import TYPE_CHECKING, Any, Literal, Self, TypedDict, cast, get_args + +from zarr.abc.store import OffsetByteRequest, RangeByteRequest, SuffixByteRequest +from zarr.buffer import cpu + +from zarr_http_server._keys import array_metadata_keys, group_metadata_keys, is_valid_node_key + +if TYPE_CHECKING: + from collections.abc import Mapping + from collections.abc import Set as AbstractSet + + import uvicorn + from starlette.applications import Starlette + from starlette.requests import Request + from starlette.responses import Response + from zarr import Array, Group + from zarr.abc.store import ByteRequest, Store + +__all__ = [ + "AUTO_PORT", + "DEFAULT_MAX_BODY_SIZE", + "DEFAULT_PORT", + "READ_ONLY_HTTP_METHODS", + "READ_WRITE_HTTP_METHODS", + "BackgroundServer", + "CorsOptions", + "HTTPMethod", + "ReadOnlyHTTPMethod", + "node_app", + "serve", + "serve_background", + "store_app", +] + + +class CorsOptions(TypedDict, total=False): + """Options forwarded to Starlette's `CORSMiddleware`. + + Every parameter the middleware accepts appears here, so configuring CORS + never requires reaching around this package. Keys left out fall back to + the defaults described below; a key that is present is used verbatim, + including an empty list. + + Two defaults differ from Starlette's own, because this server knows + something its caller should not have to. It emits `Content-Range` on + every ranged response, which is *not* a CORS-safelisted response header -- + with Starlette's empty `expose_headers` a browser client can read the + bytes but not learn which bytes it got. And it accepts a `Range` request + header, which Starlette's empty `allow_headers` would reject at preflight. + + * `expose_headers` defaults to `["Content-Range"]` + * `allow_headers` defaults to `["Range"]` + + Everything else defaults to the middleware's own value: no origins, `GET` + only, no credentials, no origin regex, no private-network access, and a + 600-second preflight cache. + """ + + allow_origins: list[str] + allow_methods: list[str] + allow_headers: list[str] + allow_credentials: bool + allow_origin_regex: str | None + allow_private_network: bool + expose_headers: list[str] + max_age: int + + +_CORS_DEFAULTS: CorsOptions = { + "expose_headers": ["Content-Range"], + "allow_headers": ["Range"], +} + + +ReadOnlyHTTPMethod = Literal["GET", "HEAD"] +"""An HTTP method that cannot modify the store. + +Distinguished from `HTTPMethod` in the type domain, not only at runtime, so a +read-only interface can be *declared* rather than merely configured: a +parameter annotated `AbstractSet[ReadOnlyHTTPMethod]` cannot be handed `"PUT"` +without a type error, whatever the value turns out to be at runtime. + +`HEAD` belongs here because Starlette routes it wherever `GET` goes, which is +what RFC 9110 §9.3.2 asks of an origin server. It is answered from the value's +size rather than by building and discarding a body. +""" + +_WriteHTTPMethod = Literal["PUT"] +"""An HTTP method that modifies the store. + +Private because nothing needs to name "the write methods" on its own -- it +exists so `HTTPMethod` can be defined as the union rather than as a third +hand-written list of the same strings. +""" + +HTTPMethod = ReadOnlyHTTPMethod | _WriteHTTPMethod +"""An HTTP method this server implements. + +`GET` and `HEAD` read a key; `PUT` writes one. Other verbs are not accepted: +the handler has no behavior for them, so serving them would silently answer +as if they were `GET`. +""" + +# Derived from the types above rather than restated, so the runtime sets and +# the static types cannot disagree about what this server serves. Adding a +# method to a Literal is then the only edit needed. +READ_ONLY_HTTP_METHODS: frozenset[ReadOnlyHTTPMethod] = frozenset(get_args(ReadOnlyHTTPMethod)) +"""Methods that only read. The default for every app in this package. + +Naming the set makes a read-only deployment say so at the call site, rather +than being the absence of an argument: + + store_app(store, methods=READ_ONLY_HTTP_METHODS) + +Typed as a set of `ReadOnlyHTTPMethod`, so a caller building on it keeps the +static guarantee: adding `"PUT"` to a `frozenset[ReadOnlyHTTPMethod]` is a +type error, not a runtime surprise. + +The stronger guarantee is a read-only store, which holds however `methods` is +configured -- see `store.with_read_only(True)`. +""" + +READ_WRITE_HTTP_METHODS: frozenset[HTTPMethod] = frozenset( + get_args(ReadOnlyHTTPMethod) + get_args(_WriteHTTPMethod) +) +"""Methods that read and write. Serving these grants clients write access. + +Every writable app must name a method set, so this constant is also what makes +writable deployments findable: grepping for `READ_WRITE_HTTP_METHODS` (or for +`methods=` generally) turns up every place that opts in. +""" + +_SUPPORTED_METHODS: frozenset[str] = READ_WRITE_HTTP_METHODS + +_LOGGER = logging.getLogger("uvicorn.error") +"""uvicorn's own logger, so a port fallback appears alongside its startup lines.""" + +DEFAULT_PORT = 8000 +"""Port tried first when `port="auto"`.""" + +AUTO_PORT: Literal["auto"] = "auto" +"""Sentinel for `port`: prefer `DEFAULT_PORT`, but settle for any free port. + +An explicit port is a requirement -- it binds that port or fails -- because a +caller who names one usually has something else expecting the server there. +`"auto"` says the opposite: no particular port is needed, so a collision +should not stop the server from starting. `port=0` keeps its usual meaning of +"any free port", with no preference. +""" + +_STARTUP_TIMEOUT = 5.0 +"""Seconds to wait for a background server to report that it is listening.""" + +_STARTUP_ABANDON_TIMEOUT = 5.0 +"""Seconds to wait for a server that failed to start to stop again.""" + +_SHUTDOWN_JOIN_MARGIN = 1.0 +"""Seconds to wait beyond uvicorn's graceful bound before forcing shutdown. + +uvicorn spends a fixed ~0.2s tearing down (a 0.1s loop tick plus a 0.1s +sleep) before its own `timeout_graceful_shutdown` wait begins, so a join that +merely equals that bound is guaranteed to expire first and escalate to +`force_exit` -- which makes uvicorn skip ASGI lifespan shutdown. +""" + +DEFAULT_MAX_BODY_SIZE = 256 * 1024 * 1024 +"""Default cap on a `PUT` body, in bytes. + +`Store.set` takes a whole `Buffer`, so an accepted body is held in memory in +full; the body is read incrementally and abandoned once it passes this cap, +so one request cannot size the server's memory use. Pass +`max_body_size=None` to lift the cap and read the body whole. +""" + + +class BackgroundServer: + """A running background HTTP server that can be used as a context manager. + + Wraps a ``uvicorn.Server`` running in a daemon thread. When used as a + context manager the server is shut down automatically on exit. + + Parameters + ---------- + server : uvicorn.Server + The running uvicorn server instance. + thread : threading.Thread + The daemon thread running the server. + host : str or None + The host the server was asked to bind, or ``None`` when it is not + listening on a TCP socket. + port : int or None + The port actually bound, or ``None`` when the server is not listening + on a TCP socket. + scheme : str, optional + URL scheme the server is reachable over. Defaults to ``"http"``. + shutdown_timeout : int, optional + Seconds to wait for in-flight requests to finish gracefully during + :meth:`shutdown` before forcing the server closed. Defaults to ``5``. + + Examples + -------- + >>> with serve_background(node_app(arr)) as server: # doctest: +SKIP + ... print(f"Listening on {server.host}:{server.port}") + ... # server is shut down when the block exits + """ + + def __init__( + self, + server: uvicorn.Server, + thread: threading.Thread, + *, + host: str | None, + port: int | None, + scheme: str = "http", + shutdown_timeout: int = 5, + ) -> None: + self._server = server + self._thread = thread + self.host = host + self.port = port + self.scheme = scheme + self._shutdown_timeout = shutdown_timeout + + @property + def url(self) -> str | None: + """The base URL of the running server. + + ``None`` when the server is not listening on a TCP socket -- a unix + socket or an inherited file descriptor has no host and port, and + inventing one would be a URL that connects to nothing. + """ + if self.host is None or self.port is None: + return None + return f"{self.scheme}://{self.host}:{self.port}" + + def shutdown(self) -> None: + """Signal the server to shut down and wait for it to stop. + + Waits for the server thread to exit on its own, then escalates to + ``force_exit`` if it has not, so a request wedged outside uvicorn's + loop cannot block here forever. + + Raises + ------ + RuntimeError + If the thread is still running after both waits. Returning + normally would report success for a server that is still bound to + its port and still serving, which the caller cannot detect any + other way. + """ + self._server.should_exit = True + # Outlast uvicorn's own graceful wait rather than matching it. uvicorn + # spends roughly 0.2s on teardown (a 0.1s loop tick plus a 0.1s sleep) + # *before* its `timeout_graceful_shutdown` wait even begins, so an + # equal bound here always expires first -- escalating to force_exit on + # the path that is supposed to be the orderly one, which makes uvicorn + # skip ASGI lifespan shutdown entirely. + self._thread.join(timeout=self._graceful_timeout + _SHUTDOWN_JOIN_MARGIN) + if self._thread.is_alive(): + self._server.force_exit = True + self._thread.join(timeout=self._shutdown_timeout) + + if self._thread.is_alive(): + raise RuntimeError( + "Server thread did not stop within " + f"{self._graceful_timeout + _SHUTDOWN_JOIN_MARGIN + self._shutdown_timeout:.1f}s, " + "even after force_exit. The server may still be serving and " + "holding its port; a request blocked in a store call cannot be " + "cancelled from here." + ) + + @property + def _graceful_timeout(self) -> float: + """uvicorn's own graceful-shutdown bound, whoever configured it.""" + configured = self._server.config.timeout_graceful_shutdown + return float(configured) if configured is not None else float(self._shutdown_timeout) + + def __enter__(self) -> Self: + return self + + def __exit__(self, *args: object) -> None: + self.shutdown() + + +class _RangeVerdict(Enum): + """The outcome of a Range header that does not name a readable range.""" + + IGNORE = auto() + """Serve the full representation with 200, as if no Range had been sent.""" + + UNSATISFIABLE = auto() + """Answer 416: the range is well-formed but names nothing readable.""" + + +_MAX_BYTE_POS = sys.maxsize +"""Largest byte position this server will pass to a store. + +Range bounds arrive as arbitrary-precision Python integers, but a store +ultimately turns them into an index-sized `seek`/`read`. Feeding an oversized +value through raises `OverflowError`/`ValueError` from deep inside the store +rather than producing a response, so bounds are clamped or rejected here. +""" + + +def _parse_int(text: str) -> int | None: + """Parse a byte position, accepting only the canonical spelling of one. + + `int` is lenient in ways an HTTP byte position is not -- it accepts + surrounding whitespace, a leading `+`/`-`, underscore separators, and + non-ASCII decimal digits -- so `bytes=+0-1` and `bytes=0_0-1` would parse. + RFC 9110 defines a byte position as 1*DIGIT. + """ + if not text.isascii() or not text.isdigit(): + return None + return int(text) + + +def _parse_range_header(range_header: str) -> ByteRequest | _RangeVerdict: + """Parse an HTTP Range header into a ByteRequest. + + A header this server cannot turn into a single read is *ignored* rather + than rejected. RFC 9110 §14.2 requires a server to ignore a Range whose + unit it does not recognize, and permits ignoring one it cannot parse; in + both cases the correct answer is the full representation, not 416. + Answering 416 would tell a client the object is unreadable when it is + merely the request that was unsupported -- and a client coalescing two + chunk reads into one multi-range request would take that at face value. + + 416 is reserved for a well-formed range that genuinely names nothing. + + Parameters + ---------- + range_header : str + The value of the Range header, e.g. ``"bytes=0-99"`` or ``"bytes=-100"``. + + Returns + ------- + ByteRequest or _RangeVerdict + A ``RangeByteRequest``, ``OffsetByteRequest``, or ``SuffixByteRequest`` + for a readable range, otherwise the verdict to apply. + """ + if not range_header.startswith("bytes="): + # An unrecognized range unit; RFC 9110 §14.2 says MUST ignore. + return _RangeVerdict.IGNORE + range_spec = range_header[len("bytes=") :] + if "," in range_spec: + # A multipart range. Legal to send, and legal to answer with the whole + # representation; this server does not build multipart/byteranges. + return _RangeVerdict.IGNORE + + if range_spec.startswith("-"): + # suffix request: bytes=-N + suffix = _parse_int(range_spec[1:]) + if suffix is None: + return _RangeVerdict.IGNORE + if suffix == 0: + # "the last zero bytes" names nothing. + return _RangeVerdict.UNSATISFIABLE + return SuffixByteRequest(suffix=min(suffix, _MAX_BYTE_POS)) + + parts = range_spec.split("-", 1) + if len(parts) != 2: + return _RangeVerdict.IGNORE + start_str, end_str = parts + start = _parse_int(start_str) + if start is None: + return _RangeVerdict.IGNORE + if start > _MAX_BYTE_POS: + # No object can be this long, so the range starts past every end. + return _RangeVerdict.UNSATISFIABLE + if end_str == "": + # offset request: bytes=N- + return OffsetByteRequest(offset=start) + end_pos = _parse_int(end_str) + if end_pos is None: + return _RangeVerdict.IGNORE + # HTTP end is inclusive, ByteRequest end is exclusive. A last-byte-pos at + # or past the end of the object is satisfiable -- RFC 9110 §14.1.2 says to + # clamp it -- so an oversized bound is capped rather than refused. + end = min(end_pos, _MAX_BYTE_POS - 1) + 1 + if start >= end: + # An inverted range like "bytes=5-2" is unsatisfiable, not a read + # of negative length. + return _RangeVerdict.UNSATISFIABLE + return RangeByteRequest(start=start, end=end) + + +def _is_drive_qualified(path: str) -> bool: + """Whether *path* carries a drive or UNC prefix that would discard a store root. + + A drive-qualified key such as `C:/Windows`, or the drive-relative `a:b`, + replaces the root it is joined to rather than extending it. This is + rejected on every platform, not just Windows: the check is a string-level + gate in front of an arbitrary `Store`, and this package cannot know how a + given implementation resolves keys. + + The cost is that a node whose *first* path segment looks like `<x>:...` + is unreachable -- `ntpath` treats any single character before a colon as + a drive, so there is no safe subset to admit. Such names are legal but + rare, and later segments are unaffected (`sub/a:b` is served normally). + + Parameters + ---------- + path : str + The candidate key, with separators already folded to `/`. + + Returns + ------- + bool + """ + return ntpath.splitdrive(path)[0] != "" + + +def _names_nothing(exc: OSError) -> bool: + """Whether an `OSError` answers about the *name*, rather than reporting failure. + + `ENAMETOOLONG` is the store saying no such name is expressible here. That + is an answer about the key -- nothing can be stored under it, so a miss is + honest -- and it is unreachable for real data, because `encode_chunk_key` + never produces a segment near a filesystem's length limit. Answering 404 + therefore cannot make a reader substitute fill values over a chunk that + exists, and it keeps a client from turning a freely chosen key into a 5xx. + + Every other `errno` describes a failure to complete the operation and must + surface as one. `EINVAL` was accepted here and was the dangerous case: it + is POSIX's catch-all, reachable on a perfectly ordinary short key through + a bad seek or an unsupported filesystem feature. Under the v3 spec an + absent chunk is an uninitialized one, so reporting such a failure as 404 + has a correct reader write fill values over data that is merely + unreadable. When in doubt the store's own signal is the one to trust: + `None` means absent, a raised error means the request could not be + answered. + + Parameters + ---------- + exc : OSError + The error raised by the store. + + Returns + ------- + bool + """ + return exc.errno == errno.ENAMETOOLONG + + +def _content_range(byte_range: RangeByteRequest | OffsetByteRequest, length: int) -> str: + """Build a `Content-Range` value for a 206 response. + + Parameters + ---------- + byte_range : RangeByteRequest or OffsetByteRequest + The range that was served. A suffix request is resolved to an absolute + range before reaching here, because RFC 9110 §15.3.7 requires every + single-part 206 to carry a `Content-Range` and a suffix's first-byte + position is not knowable without the object's size. + length : int + The number of bytes actually returned. + + Returns + ------- + str + A `bytes <first>-<last>/*` value. + """ + start = byte_range.start if isinstance(byte_range, RangeByteRequest) else byte_range.offset + # The total length is unknown here; RFC 9110 permits "*" in its place. + return f"bytes {start}-{start + length - 1}/*" + + +async def _resolve_suffix( + store: Store, path: str, byte_range: SuffixByteRequest +) -> RangeByteRequest | _RangeVerdict: + """Turn a suffix request into an absolute range using the object's size. + + A suffix range names its bytes relative to an end this server does not + otherwise need to know. Resolving it here is what lets the 206 carry a + `Content-Range`, which RFC 9110 requires and which a caller reading a + shard index needs in order to locate what it was given. + """ + try: + size = await store.getsize(path) + except FileNotFoundError: + return _RangeVerdict.UNSATISFIABLE + if size == 0: + return _RangeVerdict.UNSATISFIABLE + # A suffix longer than the object is satisfiable and yields the whole + # object, per RFC 9110 §14.1.2. + return RangeByteRequest(start=max(0, size - byte_range.suffix), end=size) + + +_JSON_BASENAMES = ( + array_metadata_keys(2) + | array_metadata_keys(3) + | group_metadata_keys(2) + | group_metadata_keys(3) +) +"""Metadata documents that are JSON, for every zarr format. + +Derived from the same tables that decide which keys a node owns, so a v2 +array's `.zarray` is typed as JSON rather than as opaque bytes -- and adding a +document in one place cannot leave the media type behind in the other. +""" + + +def content_type_for(path: str) -> str: + """Media type for a store key, chosen by its basename.""" + if path.rsplit("/", 1)[-1] in _JSON_BASENAMES: + return "application/json" + return "application/octet-stream" + + +async def _head_response(store: Store, path: str, content_type: str) -> Response: + """Answer a HEAD without transferring the value. + + A HEAD body is discarded at the wire, so routing HEAD through the GET + handler reads the whole object -- megabytes of chunk or shard -- to report + a length. `Store.getsize` is a `stat` on a filesystem store and an + info/HEAD call on a remote one. + """ + from starlette.responses import Response + + try: + size = await store.getsize(path) + except FileNotFoundError: + return Response(status_code=404) + except OSError as exc: + if not _names_nothing(exc): + raise + return Response(status_code=404) + return Response(status_code=200, media_type=content_type, headers={"Content-Length": str(size)}) + + +async def _get_response( + store: Store, + path: str, + byte_range: RangeByteRequest | OffsetByteRequest | None = None, +) -> Response: + """Fetch a key from the store and return an HTTP response.""" + from starlette.responses import Response + + proto = cpu.buffer_prototype + content_type = content_type_for(path) + + try: + buf = await store.get(path, proto, byte_range=byte_range) + except (MemoryError, OverflowError): + # The client's last-byte-pos is wider than the store can materialize + # -- it sizes its read from the range, not from the object. RFC 9110 + # §14.1.2 makes a last-byte-pos at or past the end of the object + # satisfiable and clamps it to the end, so re-read from the same start + # to EOF, which is what the clamped range denotes. Refusing with 416 + # would deny a request that is merely over-wide, and a client asking + # for "from here to well past the end" is asking a normal question. + if not isinstance(byte_range, RangeByteRequest): + raise + byte_range = OffsetByteRequest(offset=byte_range.start) + buf = await store.get(path, proto, byte_range=byte_range) + except OSError as exc: + if not _names_nothing(exc): + # A real I/O failure, which must not be reported as a miss. Under + # the v3 spec an absent chunk is an uninitialized one, and a + # reader is right to substitute the array's fill value for it -- + # so 404 asserts something about the store's contents. An + # unreadable chunk is not an uninitialized chunk, and answering + # 404 would have a correct client silently materialize fill + # values over data that exists. + raise + return Response(status_code=404) + if buf is None: + return Response(status_code=404) + + if byte_range is None: + return Response(content=buf.to_bytes(), status_code=200, media_type=content_type) + + body = buf.to_bytes() + if len(body) == 0: + # The range lies wholly beyond the end of the object. + return Response(status_code=416) + + headers = {"Content-Range": _content_range(byte_range, len(body))} + return Response(content=body, status_code=206, media_type=content_type, headers=headers) + + +async def _handle_request(request: Request) -> Response: + """Handle a request, optionally filtering by node validity.""" + from starlette.responses import Response + + store: Store = request.app.state.store + node: Array[Any] | Group | None = request.app.state.node + prefix: str = request.app.state.prefix + path = request.path_params.get("path", "") + + # Reject non-canonical / traversal-prone keys before touching the store. + # Starlette percent-decodes path params, so "..%2f" arrives as a literal + # ".." segment and "%2f"-encoded leading slashes arrive as an empty leading + # segment (making the key absolute, which escapes a filesystem store root). + # Backslashes are separators on Windows and drive-qualified or + # root-relative keys discard a filesystem store's root entirely, so fold + # separators before checking segments -- mirroring zarr's normalize_path + # (src/zarr/storage/_utils.py) plus a drive check it doesn't need. Legitimate + # zarr keys never contain empty, ".", or ".." segments, or a drive letter. + segments = path.replace("\\", "/").split("/") + if any(segment in ("", ".", "..") for segment in segments) or _is_drive_qualified(path): + return Response(status_code=404) + + # A NUL can never appear in a store key, and reaches the filesystem layer + # as a raised error rather than a miss. Rejecting it here keeps that out + # of the store, so the store's own errors always mean real I/O trouble. + if "\x00" in path: + return Response(status_code=404) + + # If serving a node, validate the key before touching the store. Group + # validation opens children through zarr's synchronous API, which drives + # the store to completion and would otherwise block the event loop for + # the duration -- serializing every concurrent request behind it, and + # outlasting the shutdown timeout. + if node is not None and not await asyncio.to_thread(is_valid_node_key, node, path): + return Response(status_code=404) + + # Resolve the full store key by prepending the node's prefix. + store_key = f"{prefix}/{path}" if prefix else path + + if request.method == "PUT": + if store.read_only: + # The store will refuse this with a ValueError from deep inside + # `set`, which is a 500 -- a server fault. Refusing to write to a + # read-only store is not a fault, it is the answer. + return Response(status_code=403) + + max_body_size: int | None = request.app.state.max_body_size + if max_body_size is None: + body = await request.body() + else: + declared = request.headers.get("content-length") + if declared is not None and declared.isdigit() and int(declared) > max_body_size: + return Response(status_code=413) + + # Read incrementally and stop at the cap. `request.body()` would + # buffer the whole body first, which a chunked request can use to + # exceed the cap by any amount before it is ever checked. + chunks: list[bytes] = [] + received = 0 + async for chunk in request.stream(): + received += len(chunk) + if received > max_body_size: + return Response(status_code=413) + chunks.append(chunk) + body = b"".join(chunks) + + buf = cpu.buffer_prototype.buffer.from_bytes(body) + try: + await store.set(store_key, buf) + except OSError as exc: + if not _names_nothing(exc): + # A real write failure -- a full disk, a read-only mount, a + # permissions problem. Reporting it as 404 would tell the + # client the write is pointless rather than failed. + raise + return Response(status_code=404) + return Response(status_code=204) + + if request.method == "HEAD": + # A HEAD body is discarded at the wire, so reading the value to build + # one transfers the whole object to answer a question about its size. + # `getsize` is a stat on a filesystem store and a HEAD/info call on a + # remote one. + return await _head_response(store, store_key, content_type_for(path)) + + range_header = request.headers.get("range") + byte_range: RangeByteRequest | OffsetByteRequest | None = None + if range_header is not None: + parsed = _parse_range_header(range_header) + if parsed is _RangeVerdict.UNSATISFIABLE: + return Response(status_code=416) + if isinstance(parsed, SuffixByteRequest): + parsed = await _resolve_suffix(store, store_key, parsed) + if parsed is _RangeVerdict.UNSATISFIABLE: + return Response(status_code=416) + # _RangeVerdict.IGNORE falls through with byte_range still None, which + # serves the full representation with 200. + if not isinstance(parsed, _RangeVerdict): + byte_range = parsed + + return await _get_response(store, store_key, byte_range) + + +def _make_starlette_app( + *, + methods: AbstractSet[HTTPMethod] | None = None, + cors_options: CorsOptions | None = None, +) -> Starlette: + """Create a Starlette app with the request handler. + + Raises + ------ + ValueError + If `methods` contains anything outside `GET`, `PUT`, and `HEAD`. + """ + from starlette.applications import Starlette + from starlette.middleware.cors import CORSMiddleware + from starlette.routing import Route + + if methods is None: + methods = READ_ONLY_HTTP_METHODS + + # An empty set must not reach Starlette: `Route` treats a falsy `methods` + # as "match every method", so asking for no methods would serve them all. + if not methods: + raise ValueError( + "methods must name at least one HTTP method; " + f"accepted methods are {', '.join(sorted(_SUPPORTED_METHODS))}." + ) + + unsupported = sorted(set(methods) - _SUPPORTED_METHODS) + if unsupported: + raise ValueError( + f"Unsupported HTTP method(s): {', '.join(unsupported)}. " + f"Accepted methods are {', '.join(sorted(_SUPPORTED_METHODS))}." + ) + + app = Starlette( + routes=[Route("/{path:path}", _handle_request, methods=list(methods))], + ) + + if cors_options is not None: + # Typed loosely on purpose: unpacking a merged TypedDict loses the + # per-key types, so the looseness is contained to this block rather + # than spread across casts at each use. + merged: dict[str, Any] = {**_CORS_DEFAULTS, **cors_options} + if "allow_methods" in merged: + # Only when the caller said something. Absent, Starlette's own + # `GET`-only default stands: widening it to everything served + # would newly advertise `PUT` cross-origin on a write-enabled app + # that never asked for it. + merged["allow_methods"] = _reconcile_allow_methods( + merged["allow_methods"], served=_served_methods(methods) + ) + app.add_middleware( + CORSMiddleware, + # Our defaults first, so a key the caller supplied wins outright + # rather than being merged into -- an explicit `expose_headers: []` + # means "expose nothing", not "expose our default". + **merged, + ) + return app + + +def _reject_writes_to_a_read_only_store( + store: Store, methods: AbstractSet[HTTPMethod] | None +) -> None: + """Refuse a configuration whose writes can never succeed. + + A store's `read_only` is fixed when it is built, so asking to serve `PUT` + from one is a contradiction that would only reveal itself as a 403 on the + first write a client attempts -- possibly long after deployment, and to + the client rather than to whoever misconfigured it. Saying so at + construction matches how unsupported `methods` and contradictory + `cors_options` are already handled. + + Raises + ------ + ValueError + If `methods` asks for `PUT` on a read-only store. + """ + if methods is not None and "PUT" in methods and store.read_only: + raise ValueError( + "methods asks for PUT, but the store is read-only, so no write " + "could ever succeed. Drop PUT to serve reads, or pass a writable " + "store (`store.with_read_only(False)`)." + ) + + +def _served_methods(methods: AbstractSet[HTTPMethod]) -> frozenset[str]: + """The methods the route will actually answer. + + Starlette adds `HEAD` to any route that serves `GET`, which RFC 9110 + §9.3.2 asks of every origin server, so `HEAD` is served whenever `GET` is + whether or not it was named. + """ + served = set(methods) + if "GET" in served: + served.add("HEAD") + return frozenset(served) + + +def _reconcile_allow_methods(allow_methods: list[str], *, served: frozenset[str]) -> list[str]: + """Check `cors_options["allow_methods"]` against what the route serves. + + An advertised method the route rejects is a promise the server cannot + keep: a browser caches the preflight and every later cross-origin call + fails with 405 after a successful handshake. The reverse is worse -- the + same silence lets `allow_methods=["*"]` on a write-enabled app hand every + origin on the internet write access, which is exactly the footgun the + `methods` validation above exists to prevent. + + `"*"` expands to what is actually served rather than being rejected: it + is the idiomatic spelling of "everything this app does", and the app + cannot do more than it serves. + """ + if "*" in allow_methods: + return sorted(served) + + unserved = sorted(set(allow_methods) - served) + if unserved: + raise ValueError( + f"cors_options['allow_methods'] advertises {', '.join(unserved)}, " + f"which this app does not serve (it serves {', '.join(sorted(served))}). " + "A browser would cache that preflight and every such request would " + "then fail with 405." + ) + return list(allow_methods) + + +def _build_server( + app: Starlette, + *, + host: str, + port: int | Literal["auto"], + shutdown_timeout: int, + uvicorn_options: Mapping[str, object] | None, +) -> tuple[uvicorn.Server, dict[str, object], socket.socket | None]: + """Configure a `uvicorn.Server` for *app*, and report how it will bind. + + Returns the options actually used -- a key from `uvicorn_options` may have + replaced one passed here -- and, for `port="auto"`, the socket already + bound on the caller's behalf, which must be handed to `Server.run`. + """ + import uvicorn + + options: dict[str, object] = { + "host": host, + "port": port, + "timeout_graceful_shutdown": shutdown_timeout, + } + if uvicorn_options is not None: + options.update(uvicorn_options) + + sock: socket.socket | None = None + if options.get("port") == AUTO_PORT: + if _binds_without_a_port(options): + # A uds or fd bind ignores host and port; leave a valid int in + # place of the sentinel so `Config` still type-checks. + options["port"] = DEFAULT_PORT + else: + # Bind here rather than probing and handing uvicorn a port number: + # probing would release the port before uvicorn claimed it, which + # is the bind-then-close race that makes "find a free port" helpers + # flaky. Holding the socket means nothing can take it in between. + sock = _bind_preferred_or_free(str(options["host"]), DEFAULT_PORT) + # Keep Config agreeing with reality, so uvicorn's own "running on + # ..." line names the port it is really serving. + options["port"] = sock.getsockname()[1] + + # uvicorn.Config's parameters are individually typed and there are ~50 of + # them; `Mapping[str, object]` is the honest type for the public argument, + # so the cast is confined to the call itself. + return uvicorn.Server(uvicorn.Config(app, **cast("dict[str, Any]", options))), options, sock + + +def _binds_without_a_port(options: Mapping[str, object]) -> bool: + """Whether these options bind something other than a TCP host and port.""" + return options.get("uds") is not None or options.get("fd") is not None + + +def _bind_preferred_or_free(host: str, preferred: int) -> socket.socket: + """Bind *preferred* on *host* if it is free, otherwise any free port. + + The address family comes from `getaddrinfo` rather than being assumed: + hard-coding `AF_INET` would fail for an IPv6 host such as ``"::1"``. + """ + for candidate in (preferred, 0): + family, socktype, proto, _, sockaddr = socket.getaddrinfo( + host, candidate, type=socket.SOCK_STREAM + )[0] + sock = socket.socket(family, socktype, proto) + sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) + try: + sock.bind(sockaddr) + except OSError: + sock.close() + if candidate == 0: + # Nothing is free, which is a real failure rather than a + # reason to keep looking. + raise + _LOGGER.info( + "port %d is in use; binding a free port instead. Pass an " + "explicit port to require a particular one.", + preferred, + ) + continue + return sock + raise AssertionError("unreachable") # pragma: no cover + + +def serve( + app: Starlette, + *, + host: str = "127.0.0.1", + port: int | Literal["auto"] = AUTO_PORT, + shutdown_timeout: int = 5, + uvicorn_options: Mapping[str, object] | None = None, +) -> None: + """Run an ASGI app under Uvicorn, blocking until it is stopped. + + Returns only when the server stops, so this is the shape for a process + whose job is to serve -- a script, a container entrypoint. Use + :func:`serve_background` when the caller has more to do. + + Build the app first with :func:`store_app` or :func:`node_app`, or compose + several of them; what an app serves is settled when it is built, and this + only decides how it runs. + + .. code-block:: python + + serve(store_app(store), host="0.0.0.0", port=8000) + + Parameters + ---------- + app : Starlette + The ASGI app to run. + host : str, optional + The host to bind to. Defaults to ``"127.0.0.1"``. + port : int, optional + The port to bind to. Defaults to ``8000``. + shutdown_timeout : int, optional + Seconds to wait for in-flight requests to finish gracefully when the + server is shut down, via uvicorn's ``timeout_graceful_shutdown``. + Defaults to ``5``. + uvicorn_options : Mapping[str, object], optional + Extra options passed straight to `uvicorn.Config`, merged over the + ones set here (`host`, `port`, `timeout_graceful_shutdown`), so a + caller key wins. This is the escape hatch for anything uvicorn can do + that this signature does not name -- TLS via `ssl_keyfile` / + `ssl_certfile`, `proxy_headers` and `forwarded_allow_ips` behind a + reverse proxy, `root_path` when mounted under a prefix, `log_level`, + `limit_concurrency`, or a `uds` / `fd` bind. + """ + server, _, sock = _build_server( + app, + host=host, + port=port, + shutdown_timeout=shutdown_timeout, + uvicorn_options=uvicorn_options, + ) + server.run(sockets=[sock] if sock is not None else None) + + +def serve_background( + app: Starlette, + *, + host: str = "127.0.0.1", + port: int | Literal["auto"] = AUTO_PORT, + shutdown_timeout: int = 5, + uvicorn_options: Mapping[str, object] | None = None, +) -> BackgroundServer: + """Start an ASGI app under Uvicorn in a daemon thread and return at once. + + Returns once the socket is listening, so the next statement can use the + server. The returned handle is also a context manager: + + .. code-block:: python + + with serve_background(node_app(array)) as server: + httpx.get(f"{server.url}/zarr.json") + + In a notebook, where the server must outlive the cell that started it, + keep the handle instead and call :meth:`BackgroundServer.shutdown` later. + + Parameters + ---------- + app : Starlette + The ASGI app to run. + host : str, optional + The host to bind to. Defaults to ``"127.0.0.1"``. + port : int, optional + The port to bind to. Defaults to ``0``, which asks the OS for a free + one -- unlike :func:`serve`, whose caller usually needs a port others + already know. A background server is normally reached through + :attr:`BackgroundServer.url`, and a fixed default would make starting + a second one, or re-running a notebook cell, fail on a port collision. + shutdown_timeout : int, optional + Seconds to wait for in-flight requests to finish gracefully, both for + uvicorn's ``timeout_graceful_shutdown`` and for the wait + :meth:`BackgroundServer.shutdown` uses before forcing the thread + closed. Defaults to ``5``. + uvicorn_options : Mapping[str, object], optional + Extra options passed straight to `uvicorn.Config`, merged over the + ones set here so a caller key wins. See :func:`serve`. Binding + somewhere other than a TCP host and port leaves + :attr:`BackgroundServer.url` as ``None``. + + Returns + ------- + BackgroundServer + A handle for the running server. + + Raises + ------ + RuntimeError + If the server does not start -- most often because the port is + already in use. + """ + server, options, sock = _build_server( + app, + host=host, + port=port, + shutdown_timeout=shutdown_timeout, + uvicorn_options=uvicorn_options, + ) + + # uvicorn skips signal-handler installation off the main thread + # (Server.capture_signals), so no workaround is needed here. + thread = threading.Thread( + target=partial(server.run, sockets=[sock] if sock is not None else None), daemon=True + ) + thread.start() + + deadline = time.monotonic() + _STARTUP_TIMEOUT + while not server.started: + if not thread.is_alive(): + # uvicorn logs the underlying error and calls sys.exit, which in a + # thread ends it without surfacing anything to the caller. The + # overwhelmingly common cause is a port already in use. + raise RuntimeError( + f"Server thread exited before startup completed; {host}:{port} " + "may already be in use. See the server log for the cause." + ) + if time.monotonic() > deadline: + # The thread is still alive here, unlike the branch above, and it + # is about to finish starting. Raising without stopping it would + # leave a server bound to the port with no handle to shut it down + # -- a daemon thread serving for the rest of the process, and a + # retry on the same port failing with the other error above. + server.should_exit = True + server.force_exit = True + thread.join(timeout=_STARTUP_ABANDON_TIMEOUT) + raise RuntimeError( + f"Server failed to start within {_STARTUP_TIMEOUT:g} seconds; " + "it has been signalled to stop." + ) + time.sleep(0.01) + + # Report the port the socket actually bound rather than the one asked for, + # so `port=0` ("pick a free port") yields a usable `url`. A unix-socket or + # file-descriptor bind has no host and port at all, so both stay None and + # `url` reports None rather than naming an address nothing is listening on. + bound_port: int | None = None + for bound in server.servers: + for sock in bound.sockets: + sockname = sock.getsockname() + if isinstance(sockname, tuple) and len(sockname) >= 2: + bound_port = int(sockname[1]) + break + break + + # The host is taken from the request rather than the socket: a wildcard + # bind reports "0.0.0.0", which is not an address a client can connect to. + requested_host = options.get("host") + bound_host = ( + str(requested_host) if bound_port is not None and requested_host is not None else None + ) + + return BackgroundServer( + server, + thread, + host=bound_host, + port=bound_port, + scheme="https" if server.config.is_ssl else "http", + shutdown_timeout=shutdown_timeout, + ) + + +def store_app( + store: Store, + *, + methods: AbstractSet[HTTPMethod] | None = None, + cors_options: CorsOptions | None = None, + max_body_size: int | None = DEFAULT_MAX_BODY_SIZE, +) -> Starlette: + """Create a Starlette ASGI app that serves every key in a zarr ``Store``. + + Parameters + ---------- + store : Store + The zarr store to serve. + methods : set of HTTPMethod, optional + The HTTP methods to accept: any of `"GET"`, `"HEAD"`, and `"PUT"`. + Defaults to `{"GET"}`, which also serves `HEAD`. Passing any other + method raises `ValueError`. + cors_options : CorsOptions, optional + If provided, CORS middleware will be added with the given options. + max_body_size : int or None, optional + Largest `PUT` body to accept, in bytes; larger requests get a 413. + `Store.set` takes a whole `Buffer`, so bodies cannot be streamed and + are held in memory in full. Defaults to `DEFAULT_MAX_BODY_SIZE`; + pass `None` to lift the cap. + + Returns + ------- + Starlette + An ASGI application. + """ + _reject_writes_to_a_read_only_store(store, methods) + app = _make_starlette_app(methods=methods, cors_options=cors_options) + app.state.store = store + app.state.node = None + app.state.prefix = "" + app.state.max_body_size = max_body_size + return app + + +def node_app( + node: Array[Any] | Group, + *, + methods: AbstractSet[HTTPMethod] | None = None, + cors_options: CorsOptions | None = None, + max_body_size: int | None = DEFAULT_MAX_BODY_SIZE, +) -> Starlette: + """Create a Starlette ASGI app that serves only the keys belonging to a + zarr ``Array`` or ``Group``. + + For an ``Array``, the served keys are the metadata document(s) and all + chunk (or shard) keys whose coordinates fall within the array's grid. + + For a ``Group``, the served keys are the group's own metadata plus any + path that resolves through the group's members to a valid array metadata + document or chunk key. + + Requests for keys outside this set receive a 404 response, even if the + underlying store contains data at that path. + + Parameters + ---------- + node : Array or Group + The zarr array or group to serve. + methods : set of HTTPMethod, optional + The HTTP methods to accept: any of `"GET"`, `"HEAD"`, and `"PUT"`. + Defaults to `{"GET"}`, which also serves `HEAD`. Passing any other + method raises `ValueError`. + cors_options : CorsOptions, optional + If provided, CORS middleware will be added with the given options. + max_body_size : int or None, optional + Largest `PUT` body to accept, in bytes; larger requests get a 413. + `Store.set` takes a whole `Buffer`, so bodies cannot be streamed and + are held in memory in full. Defaults to `DEFAULT_MAX_BODY_SIZE`; + pass `None` to lift the cap. + + Returns + ------- + Starlette + An ASGI application. + """ + _reject_writes_to_a_read_only_store(node.store_path.store, methods) + app = _make_starlette_app(methods=methods, cors_options=cors_options) + app.state.store = node.store_path.store + app.state.node = node + app.state.prefix = node.store_path.path + app.state.max_body_size = max_body_size + return app diff --git a/packages/zarr-http-server/src/zarr_http_server/py.typed b/packages/zarr-http-server/src/zarr_http_server/py.typed new file mode 100644 index 0000000000..e69de29bb2 diff --git a/packages/zarr-http-server/tests/conftest.py b/packages/zarr-http-server/tests/conftest.py new file mode 100644 index 0000000000..84694b42ba --- /dev/null +++ b/packages/zarr-http-server/tests/conftest.py @@ -0,0 +1,30 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING, Literal + +import pytest +from zarr.storage import MemoryStore + +if TYPE_CHECKING: + from zarr.abc.store import Store + +ZarrFormat = Literal[2, 3] + + +@pytest.fixture +def store(request: pytest.FixtureRequest) -> Store: + """Store fixture resolved via indirect parametrization.""" + if request.param != "memory": + raise ValueError(f"unsupported store param: {request.param!r}") + return MemoryStore() + + +@pytest.fixture(params=(2, 3), ids=["zarr2", "zarr3"]) +def zarr_format(request: pytest.FixtureRequest) -> ZarrFormat: + """Zarr format version fixture, parametrized over v2 and v3.""" + if request.param == 2: + return 2 + elif request.param == 3: + return 3 + msg = f"Invalid zarr format requested. Got {request.param}, expected one of (2, 3)." + raise ValueError(msg) diff --git a/packages/zarr-http-server/tests/test_examples.py b/packages/zarr-http-server/tests/test_examples.py new file mode 100644 index 0000000000..20a5d5b1b0 --- /dev/null +++ b/packages/zarr-http-server/tests/test_examples.py @@ -0,0 +1,60 @@ +"""The shipped examples must keep working. + +An example that has quietly rotted is worse than no example: it is the first +thing a new user copies. These run the real files rather than a paraphrase of +them, so a signature change or a behavior change fails here rather than in +someone's notebook. +""" + +from __future__ import annotations + +import pathlib +import runpy + +import pytest + +EXAMPLES = pathlib.Path(__file__).resolve().parent.parent / "examples" +NOTEBOOK = EXAMPLES / "serve_notebook.ipynb" +SCRIPT = EXAMPLES / "serve.py" + + +@pytest.mark.parametrize("path", [NOTEBOOK, SCRIPT], ids=["notebook", "script"]) +def test_example_exists(path: pathlib.Path) -> None: + """Guards the paths above: a renamed or moved example would otherwise turn + its execution test into a skip, or a no-op, that nobody notices.""" + assert path.is_file(), f"missing example at {path}" + + +def test_serve_script_runs() -> None: + """Run examples/serve.py top to bottom. + + In-process rather than as a subprocess: the script's inline uv metadata + resolves `zarr-http-server` from git, so `uv run` on it would test whatever + is on main instead of the working tree. + """ + runpy.run_path(str(SCRIPT), run_name="__main__") + + +def test_serve_notebook_executes() -> None: + """Run every cell in a real kernel. + + The notebook asserts its own expectations -- status codes, byte ranges, + that a PUT is refused, that the port is closed after `shutdown()` -- so + this is not merely a check that nothing raised. `NotebookClient.execute` + defaults to ``allow_errors=False``, so any failed cell raises + `CellExecutionError` and fails this test with that cell's traceback. + """ + nbformat = pytest.importorskip("nbformat") + nbclient = pytest.importorskip("nbclient") + pytest.importorskip("ipykernel", reason="a kernel is needed to execute the notebook") + + notebook = nbformat.read(NOTEBOOK, as_version=4) + + # Run with the notebook's own directory as cwd, so any relative path it + # uses means the same thing as when a reader opens it. + nbclient.NotebookClient( + notebook, + timeout=300, + kernel_name="python3", + resources={"metadata": {"path": str(EXAMPLES)}}, + ).execute() diff --git a/packages/zarr-http-server/tests/test_properties.py b/packages/zarr-http-server/tests/test_properties.py new file mode 100644 index 0000000000..ff54392dfc --- /dev/null +++ b/packages/zarr-http-server/tests/test_properties.py @@ -0,0 +1,580 @@ +"""Property-based tests driven against a real HTTP endpoint. + +Every test here talks to an actual uvicorn server over a socket, not to an +in-process ASGI client, so the properties cover the parts of the stack that +only exist on the wire: header parsing, method dispatch, and status codes. + +Each property checks **two** things after a request -- the response, and the +state of the backing store. That pairing is the point. A server can answer +correctly and corrupt the store, or refuse a request and write anyway, and a +response-only assertion sees neither. The bug that motivated this module did +exactly that: a `PUT` to a non-canonically spelled chunk key ("c/00/00" +instead of "c/0/0") answered `204 No Content` and stored the body under a key +no reader ever looks up, so the client saw success and the data was invisible. + +The vocabulary below splits keys into two families: + +* **in-band** -- keys the served node genuinely owns: its metadata documents + and the canonical spelling of each chunk key in its grid. These must be + served, and writes to them must be visible to a zarr reader. +* **out-of-band** -- everything else: non-canonical spellings of a valid + chunk key, coordinates outside the grid, traversal attempts, and keys + belonging to a sibling node. These must be refused *and* must leave the + store byte-for-byte unchanged. +""" + +from __future__ import annotations + +import re +from dataclasses import dataclass +from typing import TYPE_CHECKING, Any, Literal +from urllib.parse import quote + +import httpx +import numpy as np +import pytest +import zarr +from hypothesis import assume, given, settings +from hypothesis import strategies as st +from zarr.buffer import cpu +from zarr.core.sync import sync + +from zarr_http_server import node_app, serve_background, store_app +from zarr_http_server._keys import _shard_grid_shape + +if TYPE_CHECKING: + from collections.abc import Iterator + + from zarr import Array + from zarr.abc.store import Store + +# Real HTTP round trips are slower and jumpier than hypothesis' default +# deadline allows, and a CI runner under load makes that worse. +_HTTP = settings(deadline=None, max_examples=50) + +# An uncompressed array so a chunk's bytes are exactly its raw values: a PUT +# body of the right length is a legitimate chunk, which lets these tests +# assert that a write is readable through a zarr client rather than merely +# present in the store. +_SHAPE = (6, 4) +_CHUNKS = (2, 2) +_DTYPE = "int32" + + +@dataclass(frozen=True) +class Served: + """A running server plus the handles needed to reason about its keys.""" + + url: str + store: Store + array: Array[Any] + kind: Literal["store", "node"] + + http_prefix: str + """Prepended to an array-relative key to form the request path.""" + + store_prefix: str + """Prepended to an array-relative key to form the backing store key.""" + + def path(self, array_relative_key: str) -> str: + return f"{self.http_prefix}{array_relative_key}" + + def store_key(self, array_relative_key: str) -> str: + return f"{self.store_prefix}{array_relative_key}" + + +def _snapshot(store: Store) -> dict[str, bytes]: + """Every key in *store* mapped to its bytes. + + Comparing two snapshots is how these tests assert that a rejected request + changed nothing -- not just that it added no key, but that it modified + none either. + """ + + async def _read() -> dict[str, bytes]: + out: dict[str, bytes] = {} + async for key in store.list(): + buf = await store.get(key, cpu.buffer_prototype) + if buf is not None: + out[key] = buf.to_bytes() + return out + + return sync(_read()) + + +@pytest.fixture( + scope="module", + params=[ + ("store", 2, "memory"), + ("store", 3, "memory"), + ("node", 2, "memory"), + ("node", 3, "memory"), + # LocalStore reads through the filesystem, which sizes its read from + # the range rather than from the object and so raises on an over-wide + # one. MemoryStore just slices a `bytes` and is happy with any bound, + # so a memory-only matrix cannot tell a clamped range from a refused + # one -- the store backend is part of what these properties test. + ("store", 3, "local"), + ("node", 3, "local"), + ], + ids=["store-v2", "store-v3", "node-v2", "node-v3", "store-v3-local", "node-v3-local"], +) +def served( + request: pytest.FixtureRequest, tmp_path_factory: pytest.TempPathFactory +) -> Iterator[Served]: + """One real server per (app kind, zarr format, store backend). + + Module-scoped because hypothesis drives hundreds of requests per test and + a server per example would dominate the runtime. `port=0` lets the OS + choose the port and `server.url` reports what it actually bound, which + avoids the bind-then-close race of picking a port up front. + """ + kind, zarr_format, backend = request.param + + store: Store + if backend == "local": + root_dir = tmp_path_factory.mktemp(f"{kind}-v{zarr_format}") + store = zarr.storage.LocalStore(root_dir) + else: + store = zarr.storage.MemoryStore() + root = zarr.open_group(store, mode="w", zarr_format=zarr_format) + array = root.create_array( + "inside", shape=_SHAPE, chunks=_CHUNKS, dtype=_DTYPE, compressors=None + ) + array[:] = np.arange(int(np.prod(_SHAPE)), dtype=_DTYPE).reshape(_SHAPE) + # A sibling the node_app must never serve, and whose keys therefore make + # good out-of-band probes. + sibling = root.create_array( + "outside", shape=_CHUNKS, chunks=_CHUNKS, dtype=_DTYPE, compressors=None + ) + sibling[:] = 1 + + if kind == "node": + server = serve_background(node_app(array, methods={"GET", "PUT"}), host="127.0.0.1", port=0) + http_prefix = "" + else: + server = serve_background( + store_app(store, methods={"GET", "PUT"}), host="127.0.0.1", port=0 + ) + http_prefix = "inside/" + assert server is not None + + try: + yield Served( + url=server.url, + store=store, + array=array, + kind=kind, + http_prefix=http_prefix, + store_prefix="inside/", + ) + finally: + server.shutdown() + + +def _grid(array: Array[Any]) -> tuple[int, ...]: + return _shard_grid_shape(array) + + +@st.composite +def chunk_coords(draw: st.DrawFn, array: Array[Any]) -> tuple[int, ...]: + """Coordinates of a chunk that exists in *array*'s storage grid.""" + return tuple(draw(st.integers(min_value=0, max_value=g - 1)) for g in _grid(array)) + + +@st.composite +def out_of_grid_coords(draw: st.DrawFn, array: Array[Any]) -> tuple[int, ...]: + """Coordinates outside the grid, so the key is well-formed but names nothing.""" + grid = _grid(array) + axis = draw(st.integers(min_value=0, max_value=len(grid) - 1)) + coords = list(draw(chunk_coords(array))) + coords[axis] = draw(st.integers(min_value=grid[axis], max_value=grid[axis] + 50)) + return tuple(coords) + + +# The confusability with ASCII digits is the point: `int()` accepts these as +# decimal digits, so they name a different store key while decoding to the +# same coordinate. That is the defect these strategies probe for. +_ARABIC_INDIC = "٠١٢٣٤٥٦٧٨٩" +_FULLWIDTH = "０１２３４５６７８９" # noqa: RUF001 + + +def _respellings(digits: str) -> list[str]: + """Strings `int()` maps to the same value as *digits*, spelled differently. + + These are exactly the spellings that make decode-only validation unsafe: + each names a *different* store key while decoding to the same coordinate. + """ + value = int(digits) + return [ + f"0{digits}", + f"00{digits}", + f"+{digits}", + f" {digits}", + f"{digits} ", + f"\t{digits}", + "".join(_ARABIC_INDIC[int(d)] for d in digits), + "".join(_FULLWIDTH[int(d)] for d in digits), + *([f"-{digits}"] if value == 0 else []), + ] + + +@st.composite +def non_canonical_chunk_keys(draw: st.DrawFn, array: Array[Any]) -> str: + """A chunk key that decodes into the grid but is not zarr's own spelling. + + Built by taking the canonical key and re-spelling one of its digit runs, + which keeps this strategy independent of the chunk key encoding's grammar. + """ + coords = draw(chunk_coords(array)) + canonical = array.metadata.encode_chunk_key(coords) + runs = list(re.finditer(r"\d+", canonical)) + assume(runs) + run = draw(st.sampled_from(runs)) + replacement = draw(st.sampled_from(_respellings(run.group()))) + key = canonical[: run.start()] + replacement + canonical[run.end() :] + assume(key != canonical) + return key + + +TRAVERSAL_KEYS = [ + # Percent-encoded on purpose. An HTTP client resolves dot-segments before + # it sends -- httpx turns "../secret" into "/secret" and ".." into "/" per + # RFC 3986 §5.2.4 -- so a literal "../" probe never reaches the server as + # traversal and asserts nothing. Encoded, it survives the client intact + # and Starlette decodes it back into a real ".." segment on arrival, which + # is the form the server's own guard has to catch. + "..%2Fsecret", + "%2e%2e%2Fsecret", + "%2e%2e%2F%2e%2e%2Fetc%2Fpasswd", + "%2e%2e", + "%2e", + "%2e%2Fzarr.json", + "a%2F..%2F..%2Fb", + "%2Fabsolute", + "sub%2F%2Fempty", + "C%3A%2Fwindows", + "..%5Cwindows", + "a%5C..%5C..%5Cb", + "%00nul", +] + + +def _chunk_payload(array: Array[Any]) -> bytes: + """Bytes of a full, uncompressed chunk for *array*.""" + return np.zeros(_CHUNKS, dtype=array.dtype).tobytes() + + +def _url(served: Served, array_relative_key: str) -> str: + """Request URL for a key, percent-encoded so it survives the wire verbatim. + + Generated keys contain characters a URL cannot carry literally -- a tab + makes httpx raise `InvalidURL`, and a space or a non-ASCII digit would be + re-encoded on the way out anyway. Encoding here means Starlette decodes + the path param back to exactly the key the strategy produced, so the + property really is "for any key K, a request for K is refused" rather than + "for any key the URL parser happened to leave alone". + """ + return f"{served.url}/{quote(served.path(array_relative_key), safe='/')}" + + +def _require_node_scope(served: Served) -> None: + """Skip a property that only a node-scoped app can satisfy. + + `store_app` proxies the store's raw key space and has no array semantics + to validate against, so every syntactically acceptable key is in-band for + it by contract -- including a non-canonical chunk spelling. Only + `node_app` claims to serve exactly one node's keys, so only `node_app` can + be held to what that set contains. + """ + if served.kind != "node": + pytest.skip("store_app serves the raw key space; node scoping does not apply") + + +class TestInBandRequests: + """Keys the node owns are served, and writes to them are visible.""" + + @given(data=st.data()) + @_HTTP + def test_get_of_a_canonical_key_returns_the_stored_bytes( + self, served: Served, data: st.DataObject + ) -> None: + """A GET of an in-band key returns exactly what the store holds, and + reading never changes the store.""" + coords = data.draw(chunk_coords(served.array)) + relative = served.array.metadata.encode_chunk_key(coords) + + before = _snapshot(served.store) + response = httpx.get(_url(served, relative), timeout=30) + + expected = before.get(served.store_key(relative)) + if expected is None: + assert response.status_code == 404 + else: + assert response.status_code == 200 + assert response.content == expected + assert _snapshot(served.store) == before + + @given(data=st.data()) + @_HTTP + def test_put_of_a_canonical_key_is_stored_and_readable( + self, served: Served, data: st.DataObject + ) -> None: + """The headline property: a PUT that reports success must be visible. + + Success means three things at once -- a 2xx, the bytes landing under + the key the client named, and a zarr client subsequently reading back + the values that were written. The original defect satisfied the first + and failed the other two. + """ + coords = data.draw(chunk_coords(served.array)) + fill = data.draw(st.integers(min_value=-(2**31), max_value=2**31 - 1)) + relative = served.array.metadata.encode_chunk_key(coords) + payload = np.full(_CHUNKS, fill, dtype=served.array.dtype).tobytes() + + before = _snapshot(served.store) + response = httpx.put(_url(served, relative), content=payload, timeout=30) + assert response.status_code == 204 + + after = _snapshot(served.store) + key = served.store_key(relative) + assert after[key] == payload, "the body did not land under the key the client named" + assert set(after) - set(before) <= {key}, "the write touched a key the client did not name" + + # The write is not merely present, it is legible: reopen the array and + # read the chunk the coordinates address. + reread = zarr.open_array(served.store, path="inside") + block = tuple(slice(c * s, (c + 1) * s) for c, s in zip(coords, _CHUNKS, strict=True)) + assert np.array_equal(reread[block], np.full(_CHUNKS, fill, dtype=served.array.dtype)) + + @given(data=st.data()) + @_HTTP + def test_range_of_a_stored_key_returns_the_matching_slice( + self, served: Served, data: st.DataObject + ) -> None: + """A satisfiable range returns exactly the bytes it names, and says so + in Content-Range.""" + relative = served.array.metadata.encode_chunk_key(tuple(0 for _ in _grid(served.array))) + key = served.store_key(relative) + before = _snapshot(served.store) + assume(key in before) + body = before[key] + + start = data.draw(st.integers(min_value=0, max_value=len(body) - 1)) + end = data.draw(st.integers(min_value=start, max_value=len(body) - 1)) + + response = httpx.get( + _url(served, relative), headers={"Range": f"bytes={start}-{end}"}, timeout=30 + ) + + assert response.status_code == 206 + assert response.content == body[start : end + 1] + # RFC 9110 §15.3.7: a single-part 206 must carry Content-Range, and it + # must describe the bytes actually returned. + content_range = response.headers["content-range"] + assert content_range.startswith(f"bytes {start}-{start + len(response.content) - 1}/") + assert _snapshot(served.store) == before + + @given(suffix=st.integers(min_value=1, max_value=200)) + @_HTTP + def test_suffix_range_returns_the_tail_and_locates_it( + self, served: Served, suffix: int + ) -> None: + """A suffix range must report where in the object its bytes came from. + + Zarr's sharding codec reads a shard index this way, so a 206 without + Content-Range leaves the reader unable to tell a clamped whole-object + read from the tail it asked for. + """ + relative = served.array.metadata.encode_chunk_key(tuple(0 for _ in _grid(served.array))) + key = served.store_key(relative) + before = _snapshot(served.store) + assume(key in before) + body = before[key] + + response = httpx.get( + _url(served, relative), headers={"Range": f"bytes=-{suffix}"}, timeout=30 + ) + + assert response.status_code == 206 + expected = body[-suffix:] if suffix <= len(body) else body + assert response.content == expected + first = len(body) - len(expected) + assert response.headers["content-range"].startswith(f"bytes {first}-{len(body) - 1}/") + assert _snapshot(served.store) == before + + +class TestOutOfBandRequests: + """Keys the node does not own are refused, and change nothing.""" + + @given(data=st.data()) + @_HTTP + def test_non_canonical_chunk_key_is_refused_and_writes_nothing( + self, served: Served, data: st.DataObject + ) -> None: + """The regression that motivated this module. + + A key that decodes into the grid but is spelled differently from + zarr's own rendering names a store key no reader consults. Accepting a + write to it reports success and loses the data, so it must be refused + and the store must be untouched. + """ + _require_node_scope(served) + relative = data.draw(non_canonical_chunk_keys(served.array)) + payload = _chunk_payload(served.array) + + before = _snapshot(served.store) + put = httpx.put(_url(served, relative), content=payload, timeout=30) + assert put.status_code == 404 + assert _snapshot(served.store) == before, "a refused write still modified the store" + + get = httpx.get(_url(served, relative), timeout=30) + assert get.status_code == 404 + assert _snapshot(served.store) == before + + @given(data=st.data()) + @_HTTP + def test_out_of_grid_chunk_key_is_refused_and_writes_nothing( + self, served: Served, data: st.DataObject + ) -> None: + """Coordinates past the end of the grid address no chunk of this array.""" + _require_node_scope(served) + coords = data.draw(out_of_grid_coords(served.array)) + relative = served.array.metadata.encode_chunk_key(coords) + + before = _snapshot(served.store) + put = httpx.put(_url(served, relative), content=_chunk_payload(served.array), timeout=30) + get = httpx.get(_url(served, relative), timeout=30) + + assert put.status_code == 404 + assert get.status_code == 404 + assert _snapshot(served.store) == before + + @given(key=st.sampled_from(TRAVERSAL_KEYS)) + @_HTTP + def test_traversal_key_is_refused_and_writes_nothing(self, served: Served, key: str) -> None: + """Nothing that tries to leave the served scope may be served or written.""" + before = _snapshot(served.store) + put = httpx.put(f"{served.url}/{key}", content=b"payload", timeout=30) + get = httpx.get(f"{served.url}/{key}", timeout=30) + + assert put.status_code in (403, 404, 405), f"{key!r} was accepted for writing" + assert get.status_code in (403, 404, 405), f"{key!r} was served" + assert _snapshot(served.store) == before + + @given(data=st.data()) + @_HTTP + def test_node_app_never_serves_a_sibling(self, served: Served, data: st.DataObject) -> None: + """A node_app is scoped to one node, so a sibling's keys are invisible + even though they exist in the same store.""" + if served.kind != "node": + pytest.skip("store_app deliberately serves the whole store") + + coords = data.draw(chunk_coords(served.array)) + chunk = served.array.metadata.encode_chunk_key(coords) + relative = data.draw( + st.sampled_from( + [ + f"outside/{chunk}", + "outside/zarr.json", + "outside/.zarray", + f"../outside/{chunk}", + ] + ) + ) + + before = _snapshot(served.store) + get = httpx.get(f"{served.url}/{relative}", timeout=30) + put = httpx.put(f"{served.url}/{relative}", content=b"payload", timeout=30) + + assert get.status_code == 404 + assert put.status_code == 404 + assert _snapshot(served.store) == before + + +class TestMethodsAndRanges: + """Transport-level invariants that hold for every key.""" + + @given( + method=st.sampled_from(["DELETE", "POST", "PATCH", "OPTIONS"]), + data=st.data(), + ) + @_HTTP + def test_unconfigured_method_is_refused_and_writes_nothing( + self, served: Served, method: str, data: st.DataObject + ) -> None: + """Only the methods the app was configured with may reach the store.""" + coords = data.draw(chunk_coords(served.array)) + relative = served.array.metadata.encode_chunk_key(coords) + + before = _snapshot(served.store) + response = httpx.request(method, _url(served, relative), content=b"payload", timeout=30) + + assert response.status_code == 405 + assert _snapshot(served.store) == before + + @given( + header=st.sampled_from( + [ + "bytes=abc-def", + "bytes=0-1,4-5", + "chars=0-7", + "bytes=", + "nonsense", + "bytes=+0-1", + ] + ) + ) + @_HTTP + def test_unusable_range_serves_the_whole_object(self, served: Served, header: str) -> None: + """RFC 9110 §14.2: a Range the server cannot use is ignored, not refused.""" + relative = served.array.metadata.encode_chunk_key(tuple(0 for _ in _grid(served.array))) + before = _snapshot(served.store) + key = served.store_key(relative) + assume(key in before) + + response = httpx.get(_url(served, relative), headers={"Range": header}, timeout=30) + + assert response.status_code == 200 + assert response.content == before[key] + assert "content-range" not in response.headers + + @given( + header=st.sampled_from( + [ + "bytes=5-2", + "bytes=-0", + "bytes=99999999999999999999-", + "bytes=100000-100001", + ] + ) + ) + @_HTTP + def test_unsatisfiable_range_is_refused(self, served: Served, header: str) -> None: + """A well-formed range that names nothing readable is a 416.""" + relative = served.array.metadata.encode_chunk_key(tuple(0 for _ in _grid(served.array))) + before = _snapshot(served.store) + assume(served.store_key(relative) in before) + + response = httpx.get(_url(served, relative), headers={"Range": header}, timeout=30) + + assert response.status_code == 416 + assert _snapshot(served.store) == before + + @given(end=st.integers(min_value=10**19, max_value=10**30)) + @_HTTP + def test_absurdly_wide_range_is_clamped_not_refused(self, served: Served, end: int) -> None: + """RFC 9110 §14.1.2 clamps a last-byte-pos past the end of the object, + so an over-wide range reads to EOF rather than erroring.""" + relative = served.array.metadata.encode_chunk_key(tuple(0 for _ in _grid(served.array))) + key = served.store_key(relative) + before = _snapshot(served.store) + assume(key in before) + + response = httpx.get( + _url(served, relative), headers={"Range": f"bytes=0-{end}"}, timeout=30 + ) + + assert response.status_code == 206 + assert response.content == before[key] + assert _snapshot(served.store) == before diff --git a/packages/zarr-http-server/tests/test_serve.py b/packages/zarr-http-server/tests/test_serve.py new file mode 100644 index 0000000000..8db6752ba1 --- /dev/null +++ b/packages/zarr-http-server/tests/test_serve.py @@ -0,0 +1,1831 @@ +from __future__ import annotations + +import asyncio +import errno +import os +import socket +from typing import TYPE_CHECKING, Any, Literal, get_args + +import numpy as np +import pytest +import zarr +from starlette.applications import Starlette +from starlette.routing import Mount +from starlette.testclient import TestClient +from zarr.buffer import cpu +from zarr.storage import LocalStore, MemoryStore + +from zarr_http_server._serve import ( + _SHUTDOWN_JOIN_MARGIN, + READ_ONLY_HTTP_METHODS, + READ_WRITE_HTTP_METHODS, + CorsOptions, + ReadOnlyHTTPMethod, + _bind_preferred_or_free, + _parse_range_header, + _RangeVerdict, + node_app, + serve_background, + store_app, +) + +if TYPE_CHECKING: + import pathlib + from collections.abc import Coroutine, Iterator + + from zarr.abc.store import Store + +ZarrFormat = Literal[2, 3] + +SHUTDOWN_TIMEOUT = 1 +"""shutdown_timeout used by the bounded-shutdown test.""" + +SLOW_HANDLER_SECONDS = 5 +"""How long that test's handler sleeps -- far longer than the shutdown bound, +so an unbounded join would be obvious.""" + + +def sync[T](coro: Coroutine[Any, Any, T]) -> T: + """Run a store coroutine to completion (tests use MemoryStore only).""" + return asyncio.run(coro) + + +@pytest.fixture +def group_with_arrays(store: Store) -> zarr.Group: + """Create a group containing a regular array and a sharded array.""" + root = zarr.open_group(store, mode="w") + zarr.create_array(root.store_path / "regular", shape=(4, 4), chunks=(2, 2), dtype="f8") + zarr.create_array( + root.store_path / "sharded", + shape=(8, 8), + chunks=(2, 2), + shards=(4, 4), + dtype="i4", + ) + return root + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestNodeAppDoesNotExposeNonZarrKeys: + """node_app must never expose keys that are not part of the zarr hierarchy.""" + + def test_non_zarr_key_returns_404(self, store: Store, group_with_arrays: zarr.Group) -> None: + """A key that is not valid zarr metadata or a valid chunk key should return 404, + even if the underlying store contains data at that path.""" + non_zarr_buf = cpu.buffer_prototype.buffer.from_bytes(b"secret data") + sync(store.set("secret.txt", non_zarr_buf)) + + app = node_app(group_with_arrays) + client = TestClient(app) + + # The non-zarr key must not be accessible. + response = client.get("/secret.txt") + assert response.status_code == 404 + + def test_non_zarr_key_nested_returns_404( + self, store: Store, group_with_arrays: zarr.Group + ) -> None: + """A non-zarr key nested under a real array's path should return 404, + even though the path prefix matches a valid zarr node.""" + non_zarr_buf = cpu.buffer_prototype.buffer.from_bytes(b"not a chunk") + sync(store.set("regular/notes.txt", non_zarr_buf)) + + app = node_app(group_with_arrays) + client = TestClient(app) + + response = client.get("/regular/notes.txt") + assert response.status_code == 404 + + def test_valid_metadata_is_accessible(self, group_with_arrays: zarr.Group) -> None: + """Zarr metadata keys (zarr.json) for both the root group and child arrays + should be served with a 200 status.""" + app = node_app(group_with_arrays) + client = TestClient(app) + + # Root group metadata + response = client.get("/zarr.json") + assert response.status_code == 200 + + # Array metadata + response = client.get("/regular/zarr.json") + assert response.status_code == 200 + + def test_valid_chunk_is_accessible(self, group_with_arrays: zarr.Group) -> None: + """A valid, in-bounds chunk key for an array with written data should + be served with a 200 status.""" + arr = group_with_arrays["regular"] + assert isinstance(arr, zarr.Array) + arr[:] = np.ones((4, 4)) + + app = node_app(group_with_arrays) + client = TestClient(app) + + # c/0/0 is a valid chunk key for a (4,4) array with (2,2) chunks. + response = client.get("/regular/c/0/0") + assert response.status_code == 200 + + def test_out_of_bounds_chunk_key_returns_404( + self, store: Store, group_with_arrays: zarr.Group + ) -> None: + """A chunk key that is syntactically valid but references indices beyond + the array's chunk grid should return 404.""" + arr = group_with_arrays["regular"] + assert isinstance(arr, zarr.Array) + arr[:] = np.ones((4, 4)) + + # Put real data at the out-of-grid key, so that a 404 can only come + # from the bounds check -- not from the key merely being absent. + planted = cpu.buffer_prototype.buffer.from_bytes(b"out of grid") + sync(store.set("regular/c/99/99", planted)) + assert sync(store.get("regular/c/99/99", cpu.buffer_prototype)) is not None + + app = node_app(group_with_arrays) + client = TestClient(app) + + # (4,4) array with (2,2) chunks has grid shape (2,2), so c/99/99 is + # syntactically valid but out of bounds. + response = client.get("/regular/c/99/99") + assert response.status_code == 404 + + def test_empty_path_returns_404(self, group_with_arrays: zarr.Group) -> None: + """A request to the root path '/' should return 404 because an empty + string is not a valid zarr key.""" + app = node_app(group_with_arrays) + client = TestClient(app) + + response = client.get("/") + assert response.status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestShardedArrayByteRangeReads: + """Byte-range reads against a sharded array served via node_app.""" + + def test_range_read_returns_206(self, group_with_arrays: zarr.Group) -> None: + """A Range header requesting a specific byte range (e.g. bytes=0-7) should + return 206 Partial Content with exactly those bytes.""" + arr = group_with_arrays["sharded"] + assert isinstance(arr, zarr.Array) + arr[:] = np.arange(64, dtype="i4").reshape((8, 8)) + + app = node_app(group_with_arrays) + client = TestClient(app) + + # c/0/0 is the first shard key for an (8,8) array with (4,4) shards. + full_response = client.get("/sharded/c/0/0") + assert full_response.status_code == 200 + full_body = full_response.content + + # Request the first 8 bytes. + range_response = client.get("/sharded/c/0/0", headers={"Range": "bytes=0-7"}) + assert range_response.status_code == 206 + assert range_response.content == full_body[:8] + + def test_suffix_range_read(self, group_with_arrays: zarr.Group) -> None: + """A suffix byte range (e.g. bytes=-4) should return the last N bytes + of the resource with a 206 status.""" + arr = group_with_arrays["sharded"] + assert isinstance(arr, zarr.Array) + arr[:] = np.arange(64, dtype="i4").reshape((8, 8)) + + app = node_app(group_with_arrays) + client = TestClient(app) + + full_response = client.get("/sharded/c/0/0") + full_body = full_response.content + + # Request the last 4 bytes. + range_response = client.get("/sharded/c/0/0", headers={"Range": "bytes=-4"}) + assert range_response.status_code == 206 + assert range_response.content == full_body[-4:] + + def test_offset_range_read(self, group_with_arrays: zarr.Group) -> None: + """An offset byte range (e.g. bytes=4-) should return all bytes from + the given offset to the end, with a 206 status.""" + arr = group_with_arrays["sharded"] + assert isinstance(arr, zarr.Array) + arr[:] = np.arange(64, dtype="i4").reshape((8, 8)) + + app = node_app(group_with_arrays) + client = TestClient(app) + + full_response = client.get("/sharded/c/0/0") + full_body = full_response.content + + # Request everything from byte 4 onward. + range_response = client.get("/sharded/c/0/0", headers={"Range": "bytes=4-"}) + assert range_response.status_code == 206 + assert range_response.content == full_body[4:] + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestUnusableRangeHeadersAreIgnored: + """A Range this server cannot turn into a read is ignored, not refused. + + RFC 9110 §14.2 requires ignoring a Range whose unit is unrecognized and + permits ignoring one that will not parse; either way the answer is 200 + with the full representation. Refusing with 416 would tell a client the + object is unreadable when only the request shape was unsupported -- and + a multi-range request, which is legal to send and which proxies and + download accelerators do send, would take that at face value. + """ + + @pytest.mark.parametrize( + "header", + [ + "bytes=abc-def", + "bytes=-abc", + "bytes=abc-", + "bytes=0-7,10-20", + "chars=0-7", + "bytes=", + "bytes=+0-1", + ], + ) + def test_unusable_range_serves_full_representation(self, store: Store, header: str) -> None: + """Non-numeric bounds, multi-range, a non-'bytes' unit, an empty spec + and a non-canonical byte position all fall back to a plain 200.""" + body = b"some data here" + sync(store.set("key", cpu.buffer_prototype.buffer.from_bytes(body))) + + client = TestClient(store_app(store), raise_server_exceptions=False) + + response = client.get("/key", headers={"Range": header}) + assert response.status_code == 200 + assert response.content == body + assert "content-range" not in response.headers + + +class TestParseRangeHeader: + """Unit tests for _parse_range_header.""" + + def test_parser_rejects_an_inverted_range(self) -> None: + """Pin the parser itself: on a MemoryStore an unguarded inverted range + happens to return b"" and still yields 416, so the status code alone + cannot tell whether the guard is present.""" + assert _parse_range_header("bytes=5-2") is _RangeVerdict.UNSATISFIABLE + assert _parse_range_header("bytes=0-0") is not _RangeVerdict.UNSATISFIABLE + + def test_valid_range(self) -> None: + """'bytes=0-99' should parse into a RangeByteRequest with start=0 and + end=100 (end is exclusive, so the inclusive HTTP end is incremented).""" + from zarr.abc.store import RangeByteRequest + + result = _parse_range_header("bytes=0-99") + assert result == RangeByteRequest(start=0, end=100) + + def test_valid_suffix(self) -> None: + """'bytes=-50' should parse into a SuffixByteRequest requesting the + last 50 bytes of the resource.""" + from zarr.abc.store import SuffixByteRequest + + result = _parse_range_header("bytes=-50") + assert result == SuffixByteRequest(suffix=50) + + def test_valid_offset(self) -> None: + """'bytes=10-' should parse into an OffsetByteRequest starting at + byte 10 and reading to the end of the resource.""" + from zarr.abc.store import OffsetByteRequest + + result = _parse_range_header("bytes=10-") + assert result == OffsetByteRequest(offset=10) + + def test_non_bytes_unit(self) -> None: + """An unrecognized range unit must be ignored, per RFC 9110 §14.2.""" + assert _parse_range_header("chars=0-7") is _RangeVerdict.IGNORE + + def test_garbage_values(self) -> None: + """Non-numeric bounds are ignored rather than raising a ValueError.""" + assert _parse_range_header("bytes=abc-def") is _RangeVerdict.IGNORE + + def test_multi_range(self) -> None: + """Multi-range requests (e.g. bytes=0-7,10-20) are legal to send; this + server does not build multipart/byteranges, so it serves the whole + representation instead of refusing.""" + assert _parse_range_header("bytes=0-7,10-20") is _RangeVerdict.IGNORE + + def test_empty_spec(self) -> None: + """A Range header with no range specifier after 'bytes=' is ignored.""" + assert _parse_range_header("bytes=") is _RangeVerdict.IGNORE + + def test_non_canonical_byte_position(self) -> None: + """`int` would accept these; RFC 9110 defines a byte position as + 1*DIGIT, so they are not ranges and the header is ignored.""" + assert _parse_range_header("bytes=+0-1") is _RangeVerdict.IGNORE + assert _parse_range_header("bytes= 0-1") is _RangeVerdict.IGNORE + assert _parse_range_header("bytes=0_0-1") is _RangeVerdict.IGNORE + + def test_oversized_start_is_unsatisfiable(self) -> None: + """A first-byte-pos past any possible object names nothing.""" + assert _parse_range_header("bytes=99999999999999999999-") is _RangeVerdict.UNSATISFIABLE + + def test_zero_length_suffix_is_unsatisfiable(self) -> None: + """ "The last zero bytes" names nothing.""" + assert _parse_range_header("bytes=-0") is _RangeVerdict.UNSATISFIABLE + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestWriteViaPut: + """store_app and node_app can be configured to accept PUT writes.""" + + def test_put_writes_to_store(self, store: Store) -> None: + """A PUT request to store_app with PUT enabled should write the + request body into the store at the given key.""" + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + payload = b"hello zarr" + response = client.put("/some/key", content=payload) + assert response.status_code == 204 + + # Verify the data landed in the store. + buf = sync(store.get("some/key", cpu.buffer_prototype)) + assert buf is not None + assert buf.to_bytes() == payload + + def test_put_then_get_roundtrip(self, store: Store) -> None: + """Data written via PUT should be retrievable via a subsequent GET + at the same key.""" + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + payload = b"\x00\x01\x02\x03" + client.put("/data/blob", content=payload) + + response = client.get("/data/blob") + assert response.status_code == 200 + assert response.content == payload + + def test_put_rejected_when_not_configured(self, store: Store) -> None: + """PUT requests should return 405 Method Not Allowed when the server + is created with the default methods (GET only).""" + app = store_app(store) + client = TestClient(app) + + response = client.put("/some/key", content=b"data") + assert response.status_code == 405 + + def test_put_on_node_validates_key(self, store: Store, group_with_arrays: zarr.Group) -> None: + """PUT requests via node_app should be rejected with 404 when the + target key is not a valid zarr key (metadata or chunk).""" + app = node_app(group_with_arrays, methods={"GET", "PUT"}) + client = TestClient(app) + + response = client.put("/not_a_zarr_key.bin", content=b"data") + assert response.status_code == 404 + + def test_put_to_valid_chunk_key_succeeds(self, group_with_arrays: zarr.Group) -> None: + """PUT requests via node_app to a valid chunk key should succeed + with 204, and the written data should be retrievable via GET.""" + app = node_app(group_with_arrays, methods={"GET", "PUT"}) + client = TestClient(app) + + payload = b"\x00" * 32 + response = client.put("/regular/c/0/0", content=payload) + assert response.status_code == 204 + + # Confirm it round-trips. + get_response = client.get("/regular/c/0/0") + assert get_response.status_code == 200 + assert get_response.content == payload + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestMethodValidation: + """Only the methods the handler implements may be served.""" + + def test_supported_methods_are_served(self, store: Store) -> None: + """GET, PUT and HEAD each behave as their verb implies.""" + app = store_app(store, methods={"GET", "PUT", "HEAD"}) + client = TestClient(app) + + assert client.put("/zarr.json", content=b'{"a":1}').status_code == 204 + assert client.get("/zarr.json").content == b'{"a":1}' + + # HEAD reports the same status as GET but carries no body. + head = client.head("/zarr.json") + assert head.status_code == 200 + assert head.content == b"" + + def test_empty_method_set_raises(self, store: Store) -> None: + """Asking for no methods must be rejected rather than producing a + server that answers every verb, including writes: Starlette treats a + falsy `methods` on a Route as "match anything".""" + for build in ( + lambda: store_app(store, methods=set()), + lambda: node_app(zarr.open_group(store, mode="a"), methods=set()), + ): + with pytest.raises(ValueError, match="at least one"): + build() + + @pytest.mark.parametrize("method", ["DELETE", "POST", "PATCH", "OPTIONS", "TRACE"]) + def test_unsupported_method_raises(self, store: Store, method: str) -> None: + """A verb the handler cannot implement is rejected when the app is + built, rather than silently answering as if it were a GET.""" + for build in ( + lambda: store_app(store, methods={"GET", method}), # type: ignore[arg-type] + lambda: node_app(zarr.open_group(store, mode="a"), methods={"GET", method}), # type: ignore[arg-type] + ): + with pytest.raises(ValueError, match=method): + build() + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestStoreAppEdgeCases: + """Edge cases for store_app.""" + + def test_get_nonexistent_key_returns_404(self, store: Store) -> None: + """GET for a key that does not exist in the store should return 404.""" + app = store_app(store) + client = TestClient(app) + + response = client.get("/no/such/key") + assert response.status_code == 404 + + def test_empty_path_returns_404(self, store: Store) -> None: + """GET to the root path '/' (empty key) should return 404 because + an empty string is not a valid store key.""" + app = store_app(store) + client = TestClient(app) + + response = client.get("/") + assert response.status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestNodeAppDirectArray: + """Serve a single array directly (not through a group).""" + + def test_serve_nested_array_directly(self, store: Store) -> None: + """When node_app is given a nested array (not a group), requests + should use keys relative to that array's path. Metadata and in-bounds + chunks should return 200, and out-of-bounds chunks should return 404.""" + root = zarr.open_group(store, mode="w") + arr = zarr.create_array( + root.store_path / "sub/nested", + shape=(4,), + chunks=(2,), + dtype="f8", + ) + arr[:] = np.arange(4, dtype="f8") + + # Serve the array directly — its prefix is "sub/nested". + app = node_app(arr) + client = TestClient(app) + + # Metadata should be accessible at the array root. + response = client.get("/zarr.json") + assert response.status_code == 200 + + # Chunk keys are relative to the array. + response = client.get("/c/0") + assert response.status_code == 200 + + response = client.get("/c/1") + assert response.status_code == 200 + + # Out of bounds. + response = client.get("/c/99") + assert response.status_code == 404 + + def test_serve_root_array(self, store: Store) -> None: + """When node_app is given an array stored at the root of a store + (empty prefix), metadata and chunk keys should be accessible at + their natural paths.""" + arr = zarr.create_array( + store, + shape=(6,), + chunks=(3,), + dtype="i4", + ) + arr[:] = np.arange(6, dtype="i4") + + # Root-level array has prefix = "". + app = node_app(arr) + client = TestClient(app) + + response = client.get("/zarr.json") + assert response.status_code == 200 + + response = client.get("/c/0") + assert response.status_code == 200 + + response = client.get("/c/1") + assert response.status_code == 200 + + response = client.get("/c/2") + assert response.status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestContentType: + """Responses should have the correct Content-Type.""" + + def test_metadata_has_json_content_type(self, group_with_arrays: zarr.Group) -> None: + """Zarr metadata files (zarr.json) should be served with + Content-Type: application/json.""" + app = node_app(group_with_arrays) + client = TestClient(app) + + response = client.get("/zarr.json") + assert response.status_code == 200 + assert response.headers["content-type"] == "application/json" + + def test_chunk_has_octet_stream_content_type(self, group_with_arrays: zarr.Group) -> None: + """Chunk data should be served with Content-Type: application/octet-stream + since it is binary data.""" + arr = group_with_arrays["regular"] + assert isinstance(arr, zarr.Array) + arr[:] = np.ones((4, 4)) + + app = node_app(group_with_arrays) + client = TestClient(app) + + response = client.get("/regular/c/0/0") + assert response.status_code == 200 + assert response.headers["content-type"] == "application/octet-stream" + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestCorsMiddleware: + """CORS middleware should add the expected headers.""" + + def test_cors_headers_present(self, store: Store) -> None: + """When cors_options are provided, responses should include the + Access-Control-Allow-Origin header matching the request origin.""" + buf = cpu.buffer_prototype.buffer.from_bytes(b"data") + sync(store.set("key", buf)) + + cors = CorsOptions(allow_origins=["https://example.com"], allow_methods=["GET"]) + app = store_app(store, cors_options=cors) + client = TestClient(app) + + response = client.get("/key", headers={"Origin": "https://example.com"}) + assert response.status_code == 200 + assert response.headers["access-control-allow-origin"] == "https://example.com" + + def test_cors_preflight(self, store: Store) -> None: + """CORS preflight OPTIONS requests should return 200 with the + Access-Control-Allow-Origin header when CORS is configured.""" + cors = CorsOptions(allow_origins=["*"], allow_methods=["GET", "PUT"]) + app = store_app(store, methods={"GET", "PUT"}, cors_options=cors) + client = TestClient(app) + + response = client.options( + "/any/path", + headers={ + "Origin": "https://example.com", + "Access-Control-Request-Method": "PUT", + }, + ) + assert response.status_code == 200 + assert "access-control-allow-origin" in response.headers + + def test_no_cors_headers_without_option(self, store: Store) -> None: + """When no cors_options are provided, responses should not include + any CORS headers, even if the request includes an Origin header.""" + buf = cpu.buffer_prototype.buffer.from_bytes(b"data") + sync(store.set("key", buf)) + + app = store_app(store) + client = TestClient(app) + + response = client.get("/key", headers={"Origin": "https://example.com"}) + assert response.status_code == 200 + assert "access-control-allow-origin" not in response.headers + + +def _metadata_key(zarr_format: ZarrFormat) -> str: + """Return the metadata key for the given zarr format.""" + return "zarr.json" if zarr_format == 3 else ".zarray" + + +def _chunk_key(zarr_format: ZarrFormat, coords: str) -> str: + """Return a chunk key for the given format. + + *coords* is a dot-separated string like ``"0.0"``. For v3 this becomes + ``"c/0/0"``; for v2 it is returned unchanged. + """ + if zarr_format == 3: + return "c/" + coords.replace(".", "/") + return coords + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestNodeAppV2AndV3: + """Test node_app with both v2 and v3 arrays side by side.""" + + def test_metadata_accessible(self, store: Store, zarr_format: ZarrFormat) -> None: + """The format-appropriate metadata key should be served with 200.""" + arr = zarr.create_array(store, shape=(4,), chunks=(2,), dtype="f8", zarr_format=zarr_format) + app = node_app(arr) + client = TestClient(app) + + response = client.get(f"/{_metadata_key(zarr_format)}") + assert response.status_code == 200 + + def test_chunk_accessible(self, store: Store, zarr_format: ZarrFormat) -> None: + """An in-bounds chunk key should be served with 200 for both formats.""" + arr = zarr.create_array(store, shape=(4,), chunks=(2,), dtype="f8", zarr_format=zarr_format) + arr[:] = np.ones(4) + + app = node_app(arr) + client = TestClient(app) + + response = client.get(f"/{_chunk_key(zarr_format, '0')}") + assert response.status_code == 200 + + def test_out_of_bounds_chunk_returns_404(self, store: Store, zarr_format: ZarrFormat) -> None: + """An out-of-bounds chunk key should return 404 for both formats.""" + arr = zarr.create_array(store, shape=(4,), chunks=(2,), dtype="f8", zarr_format=zarr_format) + arr[:] = np.ones(4) + + # Plant data at the out-of-grid key so the 404 must come from the + # bounds check rather than from the key being absent. + key = _chunk_key(zarr_format, "99") + sync(store.set(key, cpu.buffer_prototype.buffer.from_bytes(b"out of grid"))) + assert sync(store.get(key, cpu.buffer_prototype)) is not None + + app = node_app(arr) + client = TestClient(app) + + response = client.get(f"/{key}") + assert response.status_code == 404 + + def test_non_zarr_key_returns_404(self, store: Store, zarr_format: ZarrFormat) -> None: + """A non-zarr key should return 404 regardless of format.""" + arr = zarr.create_array(store, shape=(4,), chunks=(2,), dtype="f8", zarr_format=zarr_format) + non_zarr_buf = cpu.buffer_prototype.buffer.from_bytes(b"secret") + sync(store.set("secret.txt", non_zarr_buf)) + + app = node_app(arr) + client = TestClient(app) + + response = client.get("/secret.txt") + assert response.status_code == 404 + + def test_data_roundtrip(self, store: Store, zarr_format: ZarrFormat) -> None: + """Data written to an array should be readable via store_app for + both formats.""" + arr = zarr.create_array(store, shape=(4,), chunks=(2,), dtype="f8", zarr_format=zarr_format) + arr[:] = np.arange(4, dtype="f8") + + app = store_app(store) + client = TestClient(app) + + # Metadata should be accessible. + response = client.get(f"/{_metadata_key(zarr_format)}") + assert response.status_code == 200 + + # First chunk should be accessible. + response = client.get(f"/{_chunk_key(zarr_format, '0')}") + assert response.status_code == 200 + assert len(response.content) > 0 + + +class TestPathTraversalProtection: + """store_app and node_app must reject path-traversal attempts before + touching the store, regardless of URL-encoding tricks.""" + + def test_get_traversal_outside_store_root_returns_404(self, tmp_path: Any) -> None: + """A GET for a percent-encoded '../secret.txt' must not escape the + store root and read a file outside it.""" + from zarr.storage import LocalStore + + root = tmp_path / "store_root" + root.mkdir() + secret = tmp_path / "secret.txt" + secret.write_text("top secret contents") + + store = LocalStore(root) + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + response = client.get("/..%2fsecret.txt") + assert response.status_code == 404 + assert b"top secret" not in response.content + + def test_put_traversal_outside_store_root_returns_404(self, tmp_path: Any) -> None: + """A PUT to a percent-encoded '../pwned.txt' must not escape the + store root and write a file outside it.""" + from zarr.storage import LocalStore + + root = tmp_path / "store_root" + root.mkdir() + pwned = tmp_path / "pwned.txt" + + store = LocalStore(root) + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + response = client.put("/..%2fpwned.txt", content=b"pwned") + assert response.status_code == 404 + assert not pwned.exists() + + @pytest.mark.parametrize( + ("encoded_path", "climb_depth"), + [ + ("/..%2fsecret.txt", 1), + ("/%2e%2e/secret.txt", 1), + ("/..%2f..%2fsecret.txt", 2), + ], + ) + def test_encoded_traversal_variants_return_404( + self, tmp_path: Any, encoded_path: str, climb_depth: int + ) -> None: + """Various percent-encoded traversal spellings must all be rejected. + + The store root is nested exactly ``climb_depth`` directories below + ``tmp_path`` and the secret lives at ``tmp_path/secret.txt`` -- the + exact location each traversal's ".." segments resolve to -- so a + case with a missing or deleted guard would actually reach the + secret instead of just returning 404 for an unrelated reason (e.g. + a two-level climb landing on a directory that happens to be empty). + """ + from zarr.storage import LocalStore + + parts = [f"level{i}" for i in range(climb_depth - 1)] + ["store_root"] + root = tmp_path.joinpath(*parts) + root.mkdir(parents=True) + secret = tmp_path / "secret.txt" + secret.write_text("top secret contents") + + store = LocalStore(root) + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + response = client.get(encoded_path) + assert response.status_code == 404 + assert b"top secret" not in response.content + + def test_get_absolute_key_bypass_returns_404(self, tmp_path: Any) -> None: + """A percent-encoded leading slash decodes to an ABSOLUTE path param + (e.g. request '/%2fetc%2fhostname' -> path param '/etc/hostname'). + '/etc/hostname'.split('/') -> ['', 'etc', 'hostname'] has no '.' or + '..' segment, so the two-element guard misses it, but LocalStore + resolves an absolute key by discarding its root entirely -- an + arbitrary-file read. The empty leading segment must be rejected.""" + from zarr.storage import LocalStore + + root = tmp_path / "store_root" + root.mkdir() + secret = tmp_path / "secret_abs.txt" + secret.write_text("top secret absolute contents") + + store = LocalStore(root) + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + # Mirror the exploit: percent-encode every "/" (including the + # leading one) in the absolute secret path as "%2f". + encoded_path = "/" + str(secret).replace("/", "%2f") + + response = client.get(encoded_path) + assert response.status_code == 404 + assert b"top secret absolute" not in response.content + assert secret.read_text() == "top secret absolute contents" + + def test_put_absolute_key_bypass_returns_404(self, tmp_path: Any) -> None: + """Same absolute-key vector as above, but for PUT: a percent-encoded + leading slash must not allow writing a file outside the store root.""" + from zarr.storage import LocalStore + + root = tmp_path / "store_root" + root.mkdir() + pwned = tmp_path / "pwned_abs.txt" + + store = LocalStore(root) + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + encoded_path = "/" + str(pwned).replace("/", "%2f") + + response = client.put(encoded_path, content=b"pwned") + assert response.status_code == 404 + assert not pwned.exists() + + @pytest.mark.parametrize( + "encoded_path", + [ + "/..%5C..%5Cwin.ini", + "/%5CWindows%5Cwin.ini", + "/C:/Windows/win.ini", + "/C:%5CWindows", + "/%5C%5Chost%5Cshare%5Cx", + ], + ) + def test_backslash_and_drive_traversal_variants_return_404(self, encoded_path: str) -> None: + """Backslash is a path separator on Windows, and a drive-qualified or + root-relative key discards a filesystem store's root entirely on + Windows, even though POSIX only ever treats '/' as a separator. The + guard must reject these purely from the string, before the store is + ever touched -- verified here by making the store raise if called.""" + from unittest.mock import AsyncMock + + from zarr.storage import MemoryStore + + store = MemoryStore() + store.get = AsyncMock(side_effect=AssertionError("store.get should not be called")) # type: ignore[method-assign] + store.set = AsyncMock(side_effect=AssertionError("store.set should not be called")) # type: ignore[method-assign] + + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + response = client.get(encoded_path) + assert response.status_code == 404 + + def test_put_backslash_traversal_returns_404(self) -> None: + """A PUT to a backslash-encoded '..\\..\\pwned.txt' must be rejected + before the store is touched, mirroring the GET case above.""" + from unittest.mock import AsyncMock + + from zarr.storage import MemoryStore + + store = MemoryStore() + store.set = AsyncMock(side_effect=AssertionError("store.set should not be called")) # type: ignore[method-assign] + + app = store_app(store, methods={"GET", "PUT"}) + client = TestClient(app) + + response = client.put("/..%5C..%5Cpwned.txt", content=b"pwned") + assert response.status_code == 404 + + +def _get_free_port() -> int: + """Return an unused TCP port on localhost.""" + import socket + + with socket.socket() as s: + s.bind(("127.0.0.1", 0)) + port: int = s.getsockname()[1] + return port + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestServeBackground: + """Test serve_background with store- and node-scoped apps.""" + + def test_background_server_over_a_store_app(self, store: Store) -> None: + """serve_background over a store app should return a BackgroundServer + that responds to HTTP requests and can be used as a context manager.""" + import httpx + + from zarr_http_server import serve_background + + buf = cpu.buffer_prototype.buffer.from_bytes(b"hello") + sync(store.set("key", buf)) + + port = _get_free_port() + with serve_background(store_app(store), host="127.0.0.1", port=port) as server: + assert server.host == "127.0.0.1" + assert server.port == port + assert server.url == f"http://127.0.0.1:{port}" + + response = httpx.get(f"{server.url}/key") + assert response.status_code == 200 + assert response.content == b"hello" + + def test_background_server_over_a_node_app(self, store: Store) -> None: + """serve_background over a node app should return a BackgroundServer + that responds to HTTP requests and can be used as a context manager.""" + import httpx + + from zarr_http_server import serve_background + + arr = zarr.create_array(store, shape=(4,), chunks=(2,), dtype="f8") + arr[:] = np.arange(4, dtype="f8") + + port = _get_free_port() + with serve_background(node_app(arr), host="127.0.0.1", port=port) as server: + response = httpx.get(f"{server.url}/zarr.json") + assert response.status_code == 200 + + +class TestStoreFailuresAreNotReportedAsMisses: + """Under the v3 spec an absent chunk is an uninitialized one, and a reader + is right to substitute the array's fill value for it. A 404 therefore + asserts something about the store's contents, and an I/O failure must not + borrow it -- that would have a correct client materialize fill values over + data that exists.""" + + @pytest.mark.skipif(os.geteuid() == 0, reason="root bypasses the permission bits under test") + def test_unreadable_key_is_a_server_error(self, tmp_path: pathlib.Path) -> None: + root = tmp_path / "root" + root.mkdir() + (root / "key").write_bytes(b"real data") + os.chmod(root / "key", 0o000) + + client = TestClient(store_app(LocalStore(str(root))), raise_server_exceptions=False) + try: + assert client.get("/key").status_code >= 500 + finally: + os.chmod(root / "key", 0o600) + + @pytest.mark.skipif(os.geteuid() == 0, reason="root bypasses the permission bits under test") + def test_unwritable_store_is_a_server_error(self, tmp_path: pathlib.Path) -> None: + root = tmp_path / "ro" + root.mkdir() + os.chmod(root, 0o500) + + client = TestClient( + store_app(LocalStore(str(root)), methods={"GET", "PUT"}), + raise_server_exceptions=False, + ) + try: + assert client.put("/key", content=b"data").status_code >= 500 + finally: + os.chmod(root, 0o700) + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestShardGridBounds: + """A sharded array's storage grid is its shard grid, not its chunk grid.""" + + def test_out_of_shard_grid_key_returns_404(self, store: Store) -> None: + arr = zarr.create_array(store, shape=(8, 8), chunks=(2, 2), shards=(4, 4), dtype="i4") + arr[:] = np.arange(64, dtype="i4").reshape(8, 8) + + # (8,8) with (4,4) shards has a 2x2 shard grid, so c/3/3 is out of it. + # Plant data there so the 404 must come from the bounds check. + sync(store.set("c/3/3", cpu.buffer_prototype.buffer.from_bytes(b"PLANTED"))) + assert sync(store.get("c/3/3", cpu.buffer_prototype)) is not None + + client = TestClient(node_app(arr)) + assert client.get("/c/0/0").status_code == 200 + assert client.get("/c/3/3").status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestWrongArityChunkKeys: + """A chunk key with the wrong number of coordinates is invalid, and must + not reach the grid comparison -- zip(strict=True) would raise there.""" + + @pytest.mark.parametrize("key", ["c/0", "c/0/0/0", "c/0/0/0/0"]) + def test_wrong_arity_returns_404(self, store: Store, key: str) -> None: + arr = zarr.create_array(store, shape=(4, 4), chunks=(2, 2), dtype="f8") + arr[:] = np.ones((4, 4)) + + sync(store.set(key, cpu.buffer_prototype.buffer.from_bytes(b"PLANTED"))) + + client = TestClient(node_app(arr), raise_server_exceptions=False) + assert client.get(f"/{key}").status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestNodeNamesContainingAColon: + """A leading `<x>:` is a drive reference to `ntpath`, so the guard rejects + it on every platform to keep it a pure string gate in front of any store. + The documented cost is that such a name is unreachable in the first + segment -- but only there.""" + + def test_colon_named_node_in_a_later_segment_is_served(self, store: Store) -> None: + root = zarr.open_group(store, mode="w") + sub = root.create_group("sub") + sub.create_array("a:b", shape=(2,), chunks=(2,), dtype="f8") + + client = TestClient(node_app(root)) + assert client.get("/sub/a:b/zarr.json").status_code == 200 + + def test_colon_named_node_in_the_first_segment_is_rejected(self, store: Store) -> None: + root = zarr.open_group(store, mode="w") + root.create_array("a:b", shape=(2,), chunks=(2,), dtype="f8") + + client = TestClient(node_app(root)) + assert client.get("/a:b/zarr.json").status_code == 404 + + +class TestChunkedBodyIsCapped: + """A chunked request carries no Content-Length, so the cap has to hold + while the body is being read rather than after it is buffered.""" + + def test_chunked_body_over_cap_is_rejected(self, tmp_path: pathlib.Path) -> None: + store = LocalStore(str(tmp_path / "root")) + client = TestClient( + store_app(store, methods={"GET", "PUT"}, max_body_size=64), + raise_server_exceptions=False, + ) + + def body() -> Iterator[bytes]: + for _ in range(20): + yield b"x" * 32 + + # httpx sends an iterator body with Transfer-Encoding: chunked. + assert client.put("/key", content=body()).status_code == 413 + assert not (tmp_path / "root" / "key").exists() + + +class TestHostileKeysAreNotServerErrors: + """A key the store cannot express is a miss, not a server fault: the + server must never answer 5xx for input a client can choose freely. + + This needs a filesystem-backed store -- a `MemoryStore` accepts any key + as a dict key, so only `LocalStore` surfaces the underlying errors (an + embedded NUL, a name longer than the filesystem allows). + """ + + @pytest.mark.parametrize( + "path", ["/x%00y", "/ok.txt%00", "/" + "a" * 3000, "/" + "b" * 3000 + "/zarr.json"] + ) + def test_unexpressable_key_returns_404_not_500(self, tmp_path: pathlib.Path, path: str) -> None: + store = LocalStore(str(tmp_path / "root")) + client = TestClient(store_app(store, methods={"GET", "PUT"})) + + assert client.get(path).status_code == 404 + assert client.put(path, content=b"x").status_code == 404 + + +class TestGenericStoreFailuresAreNotMisses: + """Only an error that answers about the *name* may become a 404. + + `ENAMETOOLONG` says no such name is expressible, which is an answer about + the key. `EINVAL` is POSIX's catch-all and is reachable on a perfectly + ordinary short key -- a bad seek, an unsupported filesystem feature -- so + reporting it as absence would have a v3 reader write fill values over a + chunk that exists but could not be read. + """ + + @staticmethod + def _store_failing_with(code: int) -> Store: + class Failing(MemoryStore): + async def get(self, key: str, prototype: Any, byte_range: Any = None) -> Any: + raise OSError(code, os.strerror(code)) + + async def set(self, key: str, value: Any) -> None: + raise OSError(code, os.strerror(code)) + + return Failing() + + def test_einval_is_not_reported_as_absent(self) -> None: + """The regression this class exists for.""" + client = TestClient( + store_app(self._store_failing_with(errno.EINVAL), methods={"GET", "PUT"}), + raise_server_exceptions=False, + ) + + assert client.get("/c/0/0").status_code >= 500 + assert client.put("/c/0/0", content=b"data").status_code >= 500 + + def test_enametoolong_is_still_a_miss(self) -> None: + """A name the store cannot express holds nothing, so 404 is honest.""" + client = TestClient( + store_app(self._store_failing_with(errno.ENAMETOOLONG), methods={"GET", "PUT"}), + raise_server_exceptions=False, + ) + + assert client.get("/c/0/0").status_code == 404 + assert client.put("/c/0/0", content=b"data").status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestPutBodyLimit: + """`Store.set` takes a whole buffer, so an unbounded body would let one + request size the server's memory use.""" + + def test_body_over_the_limit_is_rejected(self, store: Store) -> None: + client = TestClient(store_app(store, methods={"GET", "PUT"}, max_body_size=64)) + + assert client.put("/key", content=b"x" * 65).status_code == 413 + # Nothing was written. + assert sync(store.get("key", cpu.buffer_prototype)) is None + # A body within the limit still succeeds. + assert client.put("/key", content=b"x" * 64).status_code == 204 + + def test_limit_can_be_lifted(self, store: Store) -> None: + client = TestClient(store_app(store, methods={"GET", "PUT"}, max_body_size=None)) + assert client.put("/key", content=b"x" * 5000).status_code == 204 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestRangeResponseCorrectness: + """A 206 must describe which bytes it carries, and a range that cannot be + satisfied must say so rather than returning an empty 206.""" + + def test_206_carries_content_range(self, store: Store) -> None: + sync(store.set("key", cpu.buffer_prototype.buffer.from_bytes(b"0123456789"))) + client = TestClient(store_app(store)) + + response = client.get("/key", headers={"Range": "bytes=2-5"}) + assert response.status_code == 206 + assert response.content == b"2345" + assert response.headers["Content-Range"] == "bytes 2-5/*" + + def test_range_beyond_end_is_416(self, store: Store) -> None: + sync(store.set("key", cpu.buffer_prototype.buffer.from_bytes(b"0123456789"))) + client = TestClient(store_app(store)) + + assert client.get("/key", headers={"Range": "bytes=1000-2000"}).status_code == 416 + + def test_inverted_range_is_416(self, store: Store) -> None: + sync(store.set("key", cpu.buffer_prototype.buffer.from_bytes(b"0123456789"))) + client = TestClient(store_app(store)) + + assert client.get("/key", headers={"Range": "bytes=5-2"}).status_code == 416 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestZeroDimensionalArray: + """A 0-d array has exactly one chunk, spelled `0` in v2 and `c` in v3.""" + + @pytest.mark.parametrize("zarr_format", [2, 3]) + def test_sole_chunk_is_served(self, store: Store, zarr_format: ZarrFormat) -> None: + arr = zarr.create_array(store, shape=(), dtype="i4", zarr_format=zarr_format) + arr[...] = 7 + + client = TestClient(node_app(arr)) + chunk_key = "0" if zarr_format == 2 else "c" + + assert client.get(f"/{chunk_key}").status_code == 200 + # A 1-d coordinate is not valid for a 0-d grid. + assert client.get("/0/0").status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestGroupAndArrayMetadataKeysAreDistinct: + """A v2 group owns `.zgroup`; `.zarray` belongs to arrays, and vice versa.""" + + def test_node_does_not_claim_the_other_kind_of_metadata(self, store: Store) -> None: + root = zarr.open_group(store, mode="w", zarr_format=2) + arr = root.create_array("a", shape=(2,), chunks=(2,), dtype="f8") + + # Plant both documents so a 404 reflects the key set, not absence. + sync(store.set(".zarray", cpu.buffer_prototype.buffer.from_bytes(b"{}"))) + sync(store.set("a/.zgroup", cpu.buffer_prototype.buffer.from_bytes(b"{}"))) + + assert TestClient(node_app(root)).get("/.zarray").status_code == 404 + assert TestClient(node_app(arr)).get("/.zgroup").status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestBackgroundServerReportsBoundPort: + """`port=0` asks the OS for a free port, so the server must report the + port it actually bound rather than the zero it was asked for.""" + + def test_port_zero_reports_the_bound_port(self, store: Store) -> None: + import httpx + + from zarr_http_server import serve_background + + sync(store.set("key", cpu.buffer_prototype.buffer.from_bytes(b"hello"))) + + with serve_background(store_app(store), host="127.0.0.1", port=0) as server: + assert server.port != 0 + assert server.url == f"http://127.0.0.1:{server.port}" + # The reported URL is the one that actually serves the data. + assert httpx.get(f"{server.url}/key").content == b"hello" + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestUnopenableChildIsAnError: + """A child that cannot be *judged* must not be reported as absent. + + 404 is a claim about the store's contents, and under the v3 spec an + absent chunk is an uninitialized one -- so a correct reader answers 404 + by silently substituting the array's fill value. Returning it for a child + whose metadata could not be read would materialize zeros over data that + exists. Only a genuinely missing member is a 404; corrupt metadata, an + I/O error, or a codec this process lacks all surface as 5xx. + """ + + def test_child_with_unparseable_metadata_is_not_reported_as_missing(self, store: Store) -> None: + """A corrupt child metadata document must not yield 404.""" + root = zarr.open_group(store, mode="w") + root.create_array("good", shape=(2,), chunks=(2,), dtype="f8") + sync(store.set("junk/zarr.json", cpu.buffer_prototype.buffer.from_bytes(b"not json"))) + + client = TestClient(node_app(root), raise_server_exceptions=False) + + assert client.get("/good/zarr.json").status_code == 200 + assert client.get("/junk/zarr.json").status_code >= 500 + assert client.get("/junk/c/0").status_code >= 500 + + def test_absent_child_is_reported_as_missing(self, store: Store) -> None: + """A member that simply is not there is still a plain 404.""" + root = zarr.open_group(store, mode="w") + root.create_array("good", shape=(2,), chunks=(2,), dtype="f8") + + client = TestClient(node_app(root), raise_server_exceptions=False) + + assert client.get("/nope/zarr.json").status_code == 404 + assert client.get("/junk/c/0").status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestReadBackWithZarrClient: + """The round-trip the README leads with: serve an array, then open it + with a zarr client over HTTP. + + This needs an HTTP-capable fsspec, which is a client-side concern that + `zarr-http-server` deliberately does not depend on -- it lives in the `docs` + dependency group, alongside the other deps the README examples need. + """ + + def test_served_array_reads_back_identically(self, store: Store) -> None: + """`zarr.open_array(server.url)` should return the same data that was + served, so the README's headline example stays true.""" + pytest.importorskip("fsspec") + pytest.importorskip("aiohttp") + + from zarr_http_server import serve_background + + expected = np.arange(100, dtype="uint8").reshape(10, 10) + arr = zarr.create_array(store, data=expected, chunks=(5, 5), write_data=True) + + port = _get_free_port() + with serve_background(node_app(arr), host="127.0.0.1", port=port) as server: + remote = zarr.open_array(server.url, mode="r") + np.testing.assert_array_equal(remote[:], expected) + + +class TestBackgroundServerBoundedShutdown: + """BackgroundServer.shutdown() must not hang forever on a slow or stuck + in-flight request.""" + + def test_shutdown_returns_promptly_with_slow_inflight_request(self) -> None: + """A request that takes far longer than shutdown_timeout must not + prevent shutdown() from returning within roughly shutdown_timeout, + via uvicorn's force_exit rather than an unbounded thread join.""" + import asyncio + import threading + import time + + import httpx + from starlette.applications import Starlette + from starlette.responses import Response + from starlette.routing import Route + + async def slow(request: Any) -> Response: + # Sleeps far longer than shutdown_timeout below, so a correct + # implementation must force the connection closed rather than + # wait for this to finish. + await asyncio.sleep(SLOW_HANDLER_SECONDS) + return Response(status_code=204) + + app = Starlette(routes=[Route("/slow", slow, methods=["GET"])]) + port = _get_free_port() + server = serve_background( + app, host="127.0.0.1", port=port, shutdown_timeout=SHUTDOWN_TIMEOUT + ) + assert server is not None + + request_errors: list[BaseException] = [] + + def make_slow_request() -> None: + try: + httpx.get(f"http://127.0.0.1:{port}/slow", timeout=10) + except Exception as exc: # noqa: BLE001 -- connection drop when the server force-closes is expected + request_errors.append(exc) + + request_thread = threading.Thread(target=make_slow_request, daemon=True) + request_thread.start() + time.sleep(0.2) # give the request time to actually start + + start = time.monotonic() + server.shutdown() + elapsed = time.monotonic() - start + + # The property is that shutdown is *bounded*, not that it hits a + # particular wall-clock number. Derive the bound from the timeouts + # that produce it rather than hard-coding one: shutdown() waits + # `shutdown_timeout + _SHUTDOWN_JOIN_MARGIN` for a graceful stop, then + # `shutdown_timeout` more after force_exit. A literal here silently + # loses its headroom whenever one of those constants changes -- which + # is what happened when the margin was introduced. + bound = (SHUTDOWN_TIMEOUT + _SHUTDOWN_JOIN_MARGIN) + SHUTDOWN_TIMEOUT + 1.0 + assert elapsed < bound, f"shutdown() took {elapsed:.2f}s, expected under {bound:.1f}s" + # ...and the point of it all: far less than the handler's own sleep, + # which an unbounded join would have waited out in full. + assert elapsed < SLOW_HANDLER_SECONDS + + request_thread.join(timeout=10) + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestCorsOptionsCoverTheMiddleware: + """`CorsOptions` exposes every `CORSMiddleware` parameter, with our own + defaults only for the two the server knows about.""" + + _ORIGIN = "https://viewer.example" + + def _client(self, store: Store, cors: CorsOptions) -> TestClient: + return TestClient(store_app(store, methods={"GET"}, cors_options=cors)) + + def test_ranged_response_is_readable_cross_origin(self, store: Store) -> None: + """`Content-Range` is not CORS-safelisted, so without `expose_headers` + a browser reads the bytes but cannot learn which bytes it got.""" + sync(store.set("k", cpu.buffer_prototype.buffer.from_bytes(b"0123456789"))) + client = self._client(store, {"allow_origins": [self._ORIGIN], "allow_methods": ["GET"]}) + + response = client.get("/k", headers={"Origin": self._ORIGIN, "Range": "bytes=0-3"}) + + assert response.status_code == 206 + assert response.headers["access-control-expose-headers"] == "Content-Range" + + def test_range_survives_a_preflight(self, store: Store) -> None: + """A preflight naming `Range` must be allowed, not answered 400.""" + client = self._client(store, {"allow_origins": [self._ORIGIN], "allow_methods": ["GET"]}) + + preflight = client.options( + "/k", + headers={ + "Origin": self._ORIGIN, + "Access-Control-Request-Method": "GET", + "Access-Control-Request-Headers": "range", + }, + ) + + assert preflight.status_code == 200 + assert "Range" in preflight.headers["access-control-allow-headers"] + + def test_caller_value_replaces_the_default(self, store: Store) -> None: + """Our defaults apply only to absent keys; a supplied key wins outright + so `expose_headers: []` means "expose nothing", not "expose ours".""" + sync(store.set("k", cpu.buffer_prototype.buffer.from_bytes(b"data"))) + base: CorsOptions = {"allow_origins": [self._ORIGIN], "allow_methods": ["GET"]} + + empty = self._client(store, {**base, "expose_headers": []}) + assert ( + "access-control-expose-headers" + not in empty.get("/k", headers={"Origin": self._ORIGIN}).headers + ) + + custom = self._client(store, {**base, "expose_headers": ["X-Custom"]}) + assert ( + custom.get("/k", headers={"Origin": self._ORIGIN}).headers[ + "access-control-expose-headers" + ] + == "X-Custom" + ) + + def test_parameters_beyond_the_original_two_are_reachable(self, store: Store) -> None: + """The regression this class exists for: `CorsOptions` used to carry + only `allow_origins` and `allow_methods`, sealing the rest away.""" + sync(store.set("k", cpu.buffer_prototype.buffer.from_bytes(b"data"))) + client = self._client( + store, + { + "allow_origin_regex": r"https://.*\.example", + "allow_credentials": True, + "max_age": 30, + }, + ) + origin = "https://sub.example" + + response = client.get("/k", headers={"Origin": origin}) + assert response.headers["access-control-allow-origin"] == origin + assert response.headers["access-control-allow-credentials"] == "true" + + preflight = client.options( + "/k", headers={"Origin": origin, "Access-Control-Request-Method": "GET"} + ) + assert preflight.headers["access-control-max-age"] == "30" + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestUvicornOptionsAreNotSealedOff: + """`uvicorn.Config` takes ~50 parameters; naming four of them and dropping + the rest would put TLS, proxy headers, `root_path` and log level out of + reach entirely.""" + + def test_options_reach_uvicorn_config(self, store: Store) -> None: + """A key this signature does not name still lands on the Config.""" + from zarr_http_server import serve_background + + server = serve_background( + store_app(store), + host="127.0.0.1", + port=0, + uvicorn_options={"root_path": "/api", "log_level": "warning"}, + ) + assert server is not None + try: + config = server._server.config + assert config.root_path == "/api" + assert config.log_level == "warning" + # Ours still apply where the caller did not override them. + assert config.timeout_graceful_shutdown == 5 + finally: + server.shutdown() + + def test_caller_options_win_over_ours(self, store: Store) -> None: + """The merge order is ours-then-theirs, so a caller can override even + an option this signature sets itself.""" + from zarr_http_server import serve_background + + server = serve_background( + store_app(store), + host="127.0.0.1", + port=0, + shutdown_timeout=5, + uvicorn_options={"timeout_graceful_shutdown": 11}, + ) + assert server is not None + try: + assert server._server.config.timeout_graceful_shutdown == 11 + finally: + server.shutdown() + + @pytest.mark.skipif(not hasattr(socket, "AF_UNIX"), reason="needs unix domain sockets") + def test_non_tcp_bind_reports_no_url(self, store: Store, tmp_path: pathlib.Path) -> None: + """A unix-socket bind has no host and port, so `url` must say so rather + than naming an address nothing is listening on.""" + import httpx + + from zarr_http_server import serve_background + + sock = str(tmp_path / "s.sock") + server = serve_background(store_app(store), uvicorn_options={"uds": sock}) + assert server is not None + try: + assert server.url is None + assert server.host is None + assert server.port is None + # ...and it really is serving, just not over TCP. + with httpx.Client(transport=httpx.HTTPTransport(uds=sock)) as client: + response = client.get("http://localhost/zarr.json", timeout=10) + assert response.status_code in (200, 404) + finally: + server.shutdown() + + +class TestHeadDoesNotTransferTheBody: + """A HEAD body is discarded at the wire, so building one is pure waste.""" + + def test_head_does_not_read_the_value(self, tmp_path: pathlib.Path) -> None: + """The regression this class exists for: HEAD used to fall through to + the GET handler and pull the whole object to report its length.""" + read = {"bytes": 0} + + class CountingLocal(LocalStore): + async def get(self, key: str, prototype: Any, byte_range: Any = None) -> Any: + buf = await super().get(key, prototype, byte_range) + if buf is not None: + read["bytes"] += len(buf) + return buf + + store = CountingLocal(str(tmp_path / "root")) + payload = b"x" * 100_000 + sync(store.set("big", cpu.buffer_prototype.buffer.from_bytes(payload))) + client = TestClient(store_app(store)) + + read["bytes"] = 0 + response = client.head("/big") + + assert response.status_code == 200 + assert response.headers["content-length"] == str(len(payload)) + assert read["bytes"] == 0, "HEAD read the value to report its length" + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + def test_head_of_a_missing_key_is_404(self, store: Store) -> None: + client = TestClient(store_app(store)) + assert client.head("/nope").status_code == 404 + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestMetadataContentType: + """Metadata documents are JSON in every zarr format, not just v3.""" + + @pytest.mark.parametrize( + ("zarr_format", "key"), [(3, "zarr.json"), (2, ".zarray"), (2, ".zattrs")] + ) + def test_metadata_is_served_as_json( + self, store: Store, zarr_format: ZarrFormat, key: str + ) -> None: + zarr.create_array( + store, name="a", shape=(4,), chunks=(2,), dtype="i4", zarr_format=zarr_format + ) + sync(store.set(f"a/{key}", cpu.buffer_prototype.buffer.from_bytes(b"{}"))) + + response = TestClient(store_app(store)).get(f"/a/{key}") + + assert response.status_code == 200 + assert response.headers["content-type"].startswith("application/json") + + +@pytest.mark.parametrize("store", ["memory"], indirect=True) +class TestCorsAllowMethodsMatchTheRoute: + """Advertising a method the route rejects is a promise the server cannot + keep: the browser caches the preflight and every later call 405s.""" + + def test_wildcard_expands_to_what_is_served(self, store: Store) -> None: + """`"*"` is the idiomatic "everything this app does", so it expands to + exactly that rather than to every verb Starlette knows.""" + app = store_app( + store, methods={"GET"}, cors_options={"allow_origins": ["*"], "allow_methods": ["*"]} + ) + + preflight = TestClient(app).options( + "/k", headers={"Origin": "https://e.test", "Access-Control-Request-Method": "GET"} + ) + + advertised = preflight.headers["access-control-allow-methods"] + assert set(advertised.replace(" ", "").split(",")) == {"GET", "HEAD"} + + def test_advertising_an_unserved_method_is_rejected(self, store: Store) -> None: + with pytest.raises(ValueError, match="does not serve"): + store_app( + store, + methods={"GET"}, + cors_options={"allow_origins": ["*"], "allow_methods": ["GET", "DELETE"]}, + ) + + def test_head_counts_as_served_when_get_is(self, store: Store) -> None: + """Starlette routes HEAD wherever GET goes, so naming it is not an error.""" + store_app( + store, + methods={"GET"}, + cors_options={"allow_origins": ["*"], "allow_methods": ["GET", "HEAD"]}, + ) + + def test_absent_allow_methods_is_left_alone(self, store: Store) -> None: + """Starlette's GET-only default stands; widening it to everything + served would newly advertise PUT on a write-enabled app.""" + app = store_app(store, methods={"GET", "PUT"}, cors_options={"allow_origins": ["*"]}) + + preflight = TestClient(app).options( + "/k", headers={"Origin": "https://e.test", "Access-Control-Request-Method": "GET"} + ) + + assert "PUT" not in preflight.headers["access-control-allow-methods"] + + +class TestReadOnlyServing: + """The guarantees a read-only deployment rests on. + + Two independent layers: `methods` decides what the route answers, and the + store decides whether a write could succeed at all. The second is the one + that survives a misconfiguration of the first, so both are pinned here. + """ + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + @pytest.mark.parametrize("method", ["PUT", "POST", "DELETE", "PATCH"]) + def test_default_app_refuses_every_mutating_method(self, store: Store, method: str) -> None: + """The default is read-only: no argument is needed to get there, and + nothing a client sends can write.""" + sync(store.set("k", cpu.buffer_prototype.buffer.from_bytes(b"data"))) + before = sync(store.get("k", cpu.buffer_prototype)).to_bytes() + client = TestClient(store_app(store), raise_server_exceptions=False) + + response = client.request(method, "/k", content=b"overwritten") + + assert response.status_code == 405 + assert sync(store.get("k", cpu.buffer_prototype)).to_bytes() == before + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + def test_post_can_never_be_enabled(self, store: Store) -> None: + """POST is not merely unrouted, it is unconfigurable: there is no + handler behavior for it, so asking is an error rather than a no-op.""" + with pytest.raises(ValueError, match="Unsupported HTTP method"): + store_app(store, methods={"GET", "POST"}) # type: ignore[arg-type] + + def test_read_only_store_refuses_writes_independently_of_methods( + self, tmp_path: pathlib.Path + ) -> None: + """The layer that survives getting `methods` wrong. + + Constructed through the private builder because the public entry + points now reject this combination outright; the handler check stays + as the backstop for a store whose `read_only` is not fixed. + """ + from zarr_http_server._serve import _make_starlette_app + + writable = LocalStore(str(tmp_path / "root")) + sync(writable.set("k", cpu.buffer_prototype.buffer.from_bytes(b"data"))) + + app = _make_starlette_app(methods={"GET", "PUT"}) + app.state.store = writable.with_read_only(True) + app.state.node = None + app.state.prefix = "" + app.state.max_body_size = None + + response = TestClient(app, raise_server_exceptions=False).put("/k", content=b"x") + + assert response.status_code == 403 + assert sync(writable.get("k", cpu.buffer_prototype)).to_bytes() == b"data" + + def test_put_on_a_read_only_store_is_rejected_at_construction( + self, tmp_path: pathlib.Path + ) -> None: + """A write that could never succeed is a configuration error, not a + runtime 403 delivered to whoever happens to try first.""" + store = LocalStore(str(tmp_path / "root")).with_read_only(True) + + with pytest.raises(ValueError, match="store is read-only"): + store_app(store, methods={"GET", "PUT"}) + + def test_read_only_node_is_rejected_at_construction(self, tmp_path: pathlib.Path) -> None: + """The same check applies to a node, whose store it inherits.""" + store = LocalStore(str(tmp_path / "root")) + zarr.create_array(store, shape=(4,), chunks=(2,), dtype="i4", compressors=None) + read_only_array = zarr.open_array(store, mode="r") + + with pytest.raises(ValueError, match="store is read-only"): + node_app(read_only_array, methods={"GET", "PUT"}) + + +class TestMethodSetConstants: + """Named method sets let a call site state its intent, and make writable + deployments findable: every writable app must name one.""" + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + def test_read_only_constant_matches_the_default(self, store: Store) -> None: + """Passing it explicitly and omitting `methods` are the same server, so + saying so out loud costs nothing.""" + sync(store.set("k", cpu.buffer_prototype.buffer.from_bytes(b"data"))) + + default = TestClient(store_app(store), raise_server_exceptions=False) + named = TestClient( + store_app(store, methods=READ_ONLY_HTTP_METHODS), raise_server_exceptions=False + ) + + for method in ["GET", "HEAD", "PUT", "POST", "DELETE", "PATCH"]: + assert default.request(method, "/k").status_code == ( + named.request(method, "/k").status_code + ) + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + @pytest.mark.parametrize("method", ["PUT", "POST", "DELETE", "PATCH"]) + def test_read_only_constant_refuses_writes(self, store: Store, method: str) -> None: + sync(store.set("k", cpu.buffer_prototype.buffer.from_bytes(b"data"))) + client = TestClient( + store_app(store, methods=READ_ONLY_HTTP_METHODS), raise_server_exceptions=False + ) + + assert client.request(method, "/k", content=b"x").status_code == 405 + assert sync(store.get("k", cpu.buffer_prototype)).to_bytes() == b"data" + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + def test_read_write_constant_permits_exactly_put(self, store: Store) -> None: + """It grants writes -- and still not POST, which has no handler.""" + client = TestClient( + store_app(store, methods=READ_WRITE_HTTP_METHODS), raise_server_exceptions=False + ) + + assert client.put("/k", content=b"data").status_code == 204 + assert client.post("/k", content=b"data").status_code == 405 + assert sync(store.get("k", cpu.buffer_prototype)).to_bytes() == b"data" + + def test_constants_cannot_be_mutated_by_a_caller(self) -> None: + """Frozen, so one caller cannot widen the default for every other.""" + assert isinstance(READ_ONLY_HTTP_METHODS, frozenset) + assert isinstance(READ_WRITE_HTTP_METHODS, frozenset) + assert "PUT" not in READ_ONLY_HTTP_METHODS + + def test_constants_match_the_types_they_model(self) -> None: + """The sets are derived from the Literals, so they cannot disagree + about what this server serves. Pinning the contents here makes + widening either type a deliberate, visible edit.""" + assert frozenset(get_args(ReadOnlyHTTPMethod)) == READ_ONLY_HTTP_METHODS + assert set(READ_ONLY_HTTP_METHODS) == {"GET", "HEAD"} + assert set(READ_WRITE_HTTP_METHODS) == {"GET", "HEAD", "PUT"} + # Read-only is a strict subset: the only difference is the write verb. + assert READ_ONLY_HTTP_METHODS < READ_WRITE_HTTP_METHODS + assert {"PUT"} == READ_WRITE_HTTP_METHODS - READ_ONLY_HTTP_METHODS + + +class TestServeAnyApp: + """`serve` runs whatever ASGI app it is handed, which is what makes + several nodes on one port possible.""" + + @staticmethod + def _two_mounted_arrays() -> tuple[Starlette, bytes, bytes]: + """Two arrays in *separate* stores, so no common parent exists and + mounting is the only way to serve both from one server.""" + first, second = MemoryStore(), MemoryStore() + one = zarr.create_array(first, shape=(4,), chunks=(2,), dtype="i4", compressors=None) + other = zarr.create_array(second, shape=(4,), chunks=(2,), dtype="i4", compressors=None) + one[:] = 7 + other[:] = 9 + + app = Starlette( + routes=[Mount("/first", app=node_app(one)), Mount("/second", app=node_app(other))] + ) + return app, np.full(2, 7, dtype="i4").tobytes(), np.full(2, 9, dtype="i4").tobytes() + + def test_mounted_apps_each_serve_their_own_node(self) -> None: + app, first_chunk, second_chunk = self._two_mounted_arrays() + client = TestClient(app, raise_server_exceptions=False) + + assert client.get("/first/zarr.json").status_code == 200 + assert client.get("/second/zarr.json").status_code == 200 + assert client.get("/first/c/0").content == first_chunk + assert client.get("/second/c/0").content == second_chunk + + @pytest.mark.parametrize( + "path", + [ + "/first/%2e%2e/second/zarr.json", + "/first/..%2f..%2fsecond/zarr.json", + "/first/%2e%2e%2fsecond/c/0", + "/first/%2fsecond/zarr.json", + ], + ) + def test_one_mount_cannot_reach_another(self, path: str) -> None: + """Per-node validation runs inside each mount, so composing apps does + not widen what any of them serves.""" + app, _, _ = self._two_mounted_arrays() + + assert TestClient(app, raise_server_exceptions=False).get(path).status_code == 404 + + def test_serve_runs_a_composed_app_in_the_background(self) -> None: + """The gap `serve` closes: a composed app previously had no way to use + the background-server ergonomics, only a blocking `uvicorn.run`.""" + import httpx + + app, first_chunk, second_chunk = self._two_mounted_arrays() + + server = serve_background(app, host="127.0.0.1", port=0) + try: + assert server.url is not None + assert httpx.get(f"{server.url}/first/c/0", timeout=30).content == first_chunk + assert httpx.get(f"{server.url}/second/c/0", timeout=30).content == second_chunk + finally: + server.shutdown() + + +class TestPortSelection: + """`port="auto"` prefers a predictable port but never fails over one. + + An explicit port means the opposite -- bind exactly that or fail -- because + a caller who names one usually has something else expecting the server + there, and silently moving would break it while looking healthy. + """ + + @staticmethod + def _free_port() -> int: + """A port that was free a moment ago. Only ever used as the *preferred* + port, never bound afterwards, so the usual bind-then-close race does + not apply: if something takes it, that is the case under test.""" + with socket.socket() as sock: + sock.bind(("127.0.0.1", 0)) + return int(sock.getsockname()[1]) + + def test_preferred_port_is_used_when_free(self) -> None: + preferred = self._free_port() + + sock = _bind_preferred_or_free("127.0.0.1", preferred) + try: + assert sock.getsockname()[1] == preferred + finally: + sock.close() + + def test_falls_back_when_the_preferred_port_is_taken(self) -> None: + with socket.socket() as squatter: + squatter.bind(("127.0.0.1", 0)) + squatter.listen() + taken = int(squatter.getsockname()[1]) + + sock = _bind_preferred_or_free("127.0.0.1", taken) + try: + assert sock.getsockname()[1] != taken + finally: + sock.close() + + def test_address_family_follows_the_host(self) -> None: + """Hard-coding AF_INET would bind the wrong family for an IPv6 host.""" + try: + sock = _bind_preferred_or_free("::1", 0) + except OSError: # pragma: no cover - depends on the host's networking + pytest.skip("no IPv6 loopback available") + try: + assert sock.family == socket.AF_INET6 + finally: + sock.close() + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + def test_auto_produces_a_working_server(self, store: Store) -> None: + """Whichever port it lands on, `url` names it and the server answers.""" + import httpx + + server = serve_background(store_app(store)) + try: + assert server.url is not None + assert server.port is not None + assert httpx.get(f"{server.url}/nope", timeout=30).status_code == 404 + finally: + server.shutdown() + + # uvicorn answers a failed bind with `sys.exit` on its own thread, which + # pytest reports as an unhandled thread exception -- and this package turns + # warnings into errors. That exit is exactly what the RuntimeError below + # reports to the caller, so it is expected here rather than a defect. + @pytest.mark.filterwarnings("ignore::pytest.PytestUnhandledThreadExceptionWarning") + @pytest.mark.parametrize("store", ["memory"], indirect=True) + def test_an_explicit_port_that_is_taken_fails(self, store: Store) -> None: + """The regression this class exists for: `auto` must not leak into the + explicit case, where a collision has to be loud.""" + with socket.socket() as squatter: + squatter.bind(("127.0.0.1", 0)) + squatter.listen() + taken = int(squatter.getsockname()[1]) + + with pytest.raises(RuntimeError, match="may already be in use"): + serve_background(store_app(store), port=taken) + + @pytest.mark.parametrize("store", ["memory"], indirect=True) + def test_port_zero_still_means_any_free_port(self, store: Store) -> None: + """`0` keeps its OS meaning rather than being folded into `auto`.""" + server = serve_background(store_app(store), port=0) + try: + 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}, +] + +[package.metadata.requires-dev] +docs = [ + { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, + { name = "mkdocs", specifier = "==1.6.1" }, + { name = "mkdocs-material", specifier = "==9.7.7" }, + { name = "mkdocstrings", specifier = "==1.0.6" }, + { name = "mkdocstrings-python", specifier = "==2.0.5" }, + { name = "ruff", specifier = "==0.16.0" }, +] +examples = [ + { name = "fsspec", extras = ["http"] }, + { name = "httpx" }, +] +test = [ + { name = "httpx" }, + { name = "httpx2" }, + { name = "hypothesis" }, + { name = "ipykernel" }, + { name = "nbclient" }, + { name = "nbformat" }, + { name = "pytest" }, +] diff --git a/pyproject.toml b/pyproject.toml index 8b8534cb65..6626f8f0bc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -160,9 +160,9 @@ omit = [ version.source = "vcs" # Only consider zarr-python's own `v*` tags when deriving the version. Without # this filter `git describe` matches the most recent tag of any shape, -# including the `zarr_metadata-v*` tags used to release the zarr-metadata -# subpackage — which would make a from-source build report a `0.2.x` version -# instead of `3.x`. +# including the `zarr_metadata-v*` and `zarr_http_server-v*` tags used to +# release the subpackages under `packages/` — which would make a from-source +# build report e.g. a `0.2.x` version instead of `3.x`. version.raw-options = { git_describe_command = "git describe --dirty --tags --long --match v*" } [tool.hatch.build] From 579ffb55f374443c3ec5b4bfb02869ed117fe7a2 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 15:30:42 +0200 Subject: [PATCH 449/468] docs: update readme (#4251) * docs: update readme * Update README.md Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update README.md Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update README.md Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> * Update README.md Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --------- Co-authored-by: Max Jones <14077947+maxrjones@users.noreply.github.com> --- README.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 7557936b6f..330c1da5ea 100644 --- a/README.md +++ b/README.md @@ -15,13 +15,13 @@ ## What is it? -Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. See the [documentation](https://zarr.readthedocs.io/en/stable/) for more information. +The `zarr` library is a Python implementation of the [Zarr storage format](https://zarr.dev/). `zarr` delivers compressed, chunked, N-dimensional arrays that work well for parallel computing and object storage. See the [documentation](https://zarr.readthedocs.io/en/stable/) for more information. ## Main Features -- [**Create**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#creating-an-array) N-dimensional arrays with any NumPy `dtype`. +- [**Create**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#creating-an-array) N-dimensional arrays with NumPy-compatible `dtype`s. - [**Chunk arrays**](https://zarr.readthedocs.io/en/stable/user-guide/performance/#chunk-optimizations) along any dimension. -- [**Compress**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#compressors) and/or filter chunks using any NumCodecs codec. +- [**Encode**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#compressors) chunks using a variety of useful encodings (e.g., compression). - [**Store arrays**](https://zarr.readthedocs.io/en/stable/user-guide/storage/) in memory, on disk, inside a zip file, on S3, etc... - [**Read**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#reading-and-writing-data) an array [**concurrently**](https://zarr.readthedocs.io/en/stable/user-guide/performance/#parallel-computing-and-synchronization) from multiple threads or processes. - [**Write**](https://zarr.readthedocs.io/en/stable/user-guide/arrays/#reading-and-writing-data) to an array concurrently from multiple threads or processes. @@ -42,3 +42,11 @@ conda install -c conda-forge zarr ``` For more details, including how to install from source, see the [installation documentation](https://zarr.readthedocs.io/en/stable/#installation). + +## Repository sub-packages + +In addition to the primary `zarr` implementation, this repository contains other packages that provide specialized functionality with minimal dependencies: + +- [`zarr-metadata`](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-metadata): Tools for Zarr metadata. Install with `pip install zarr-metadata`. +- [`zarr-indexing`](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing): Tools for lazily indexing chunked arrays. Install with `pip install zarr-indexing`. +- [`zarr-http-server`](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-http-server): An HTTP server implementation targeting Zarr data. Install with `pip install zarr-http-server`. From d9af955f29c05f9c4065e8b190e35d1ec2a25463 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 15:47:24 +0200 Subject: [PATCH 450/468] =?UTF-8?q?feat(zarr-indexing):=20LazyArray=20?= =?UTF-8?q?=E2=80=94=20generic=20lazy=20indexing=20over=20array-API=20arra?= =?UTF-8?q?ys=20(#4222)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat(zarr-indexing): LazyArray — generic lazy indexing over array-API arrays A generic wrapper for any array-API-like source (numpy, zarr, cupy, ...) adding TensorStore-style lazy indexing with a positional NumPy dialect: eager __getitem__, .lazy/.oindex/.vindex composing transforms without data access, result()/__array__ materializing. Resolution is partition-based: parts() iterates the base array's partitions projected through the view as resolvable sub-LazyArrays (Partition carries global box coordinates, out placement, and completeness); with_parts() re-partitions the same base explicitly; a single lowering engine serves both partitioned and whole-array sources. Partitioning is discovered from the source (read_chunk_sizes, .chunks) or declared, and never surfaced as a chunks vocabulary. Box selections (no index arrays; affine, interval-representable) are first-class: is_box, bounding_box() (exact hull up to stride), and strides() complete the slab-read story; the design-notes page records the box-vs-query taxonomy and the relationship to TensorStore. Dunders: __dask_tokenize__ (deterministic, canonical-ndsel-body-based), __len__, __iter__, 0-d conversions, pickling. Degenerate all-singleton index-array maps now collapse to constant maps in the transform algebra, and NumPy advanced-index placement rules are implemented faithfully. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-indexing): negative-step slices, per merged ndsel 1.0-draft.2 `arr[::-1]` reverses. One desugaring rule covers both signs, as TensorStore 0.1.84 does and as ndsel PR #2 now specifies: omitted bounds resolve on the side the traversal starts and stops (`hi-1` and `lo-1` going down), the source interval is [start, stop) going up and [stop+1, start+1) going down, an empty interval is legal at any coordinate, an interval running the wrong way is an error rather than a silent empty, and the origin is trunc(start/step) for either sign. The corpus is re-vendored from ndsel 92d6a32 in this same commit, because it is the definition of correct here: `slice.json` gains ten negative-step fixtures, `errors.json` retires `negative_step_unsupported` for three `bounds_out_of_order` fixtures, and the message layer is changed to satisfy them. The retired reason code is documented as such rather than removed. A latent bug that only negative steps could reach: `_reindex_array` built `slice(pos, pos + size*step, step)`, and a downward walk reaching the front of the array computes a negative stop, which NumPy reads as counting from the end — `slice(6, -1, -1)` selects nothing where `slice(6, None, -1)` selects seven elements reversed. Both reindex helpers now go through `_positional_slice`. The stride<0 branches of `_intersect_dimension_map` and `iter_chunk_transforms` were written defensively and had never been reachable. They are now, and they were right: the parts-coverage test gains two reversing views, and the seeded sweep generates downward slices (4,352 of 7,200 chains carry one) across every partitioning. At the wrapper boundary the dialect stays NumPy's, which differs in one place: a reversed *positional* interval like `lazy[2:5:-1]` is empty, not an error, because that is what `x[2:5:-1]` means. Only literal coordinates call it a direction error. Tests: the study's recorded TensorStore corpus lands in `test_tensorstore_parity.py` — fifteen desugarings with their domains, offsets and strides, the three rows that discriminate trunc from floor and ceil, both error families, empty-outside-the-domain, five recorded compositions, and the recorded index-array reversal (a negative step over a gathered axis reverses the array rather than attaching a stride). Assisted-by: ClaudeCode:claude-fable-5 * polish(zarr-indexing): re-review minors — step-zero ValueError, kw-only Partition, strides docs - slice step zero now raises ValueError, matching NumPy in the wrapper's positional dialect (was IndexError) - Partition is keyword-only: box was inserted mid-field-list, so positional construction would silently misbind - strides() documents the empty-box case (bounding_box None, strides still defined) Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): plain technical language throughout Rewrite the package's documentation surfaces — docs/index.md, docs/design-notes.md, docs/ndsel.md, docs/api/index.md, the LazyArray, boundary, and transform docstrings, and the 267 changelog fragment — in plain declarative English. Metaphor, personification, rhetorical framing, and emphasis used for effect are replaced with statements of the same technical content. No technical claim, API name, example, or example output changes. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): American spelling (flavour -> flavor) Assisted-by: ClaudeCode:claude-fable-5 * ci(zarr-indexing): scoped lint ignores for the deliberate blind excepts A new ruff release (the CI job floats via uvx) flags BLE001/S110 at the chunk-discovery tolerance and tokenize-fallback sites. Both catches are intentional contracts: discovery must degrade to no-information on any foreign-object failure, and a token call must never raise. Configured as per-file-ignores rather than noqa comments because the pinned pre-commit ruff strips the comments as unused (RUF100) while the floating CI ruff requires them. Assisted-by: ClaudeCode:claude-fable-5 * ci(zarr-indexing): pin ruff in the lint job and justfile Mirrors the main-branch pin (d-v-b#271) so this PR's workflow runs the same ruff version; bump together with the pyproject pin. Assisted-by: ClaudeCode:claude-fable-5 * docs: add lazy-indexing examples for NumPy and Dask Two runnable examples in the house style: wrapping a NumPy array in LazyArray (attribute forwarding, composing selections, box vs query selections, partitions), and using a LazyArray with Dask (from_array, one task per partition, deterministic tokens). Assisted-by: ClaudeCode:claude-fable-5 * docs: compare dask task graphs with fused transforms in the dask example Adds a timed comparison of chained selections through dask.array against the same selections composed into one transform, and a section on when each is the right tool: dask's graph earns its cost when there is computation across chunks, and is overhead when it only defers indexing. Assisted-by: ClaudeCode:claude-fable-5 * test: run examples against this repository's local packages The example runner rewrote only the `zarr` dependency to the local checkout, so an example depending on an in-repo package resolved it from git main instead — and the lazy-indexing examples failed in CI, since LazyArray is not on main yet. Rewrite every package this repository ships, leaving dependencies an example does not declare alone. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-indexing): negotiate what indexing a source supports `LazyArray` assumed every wrapped array could do basic slicing and did all fancy work itself, reading a block and post-indexing it with NumPy. That over-reads when the source could gather natively, and it walks a source axis by axis with `take` where one request would do. Each wrapper now carries an `IndexingSupport` level — BASIC, OUTER, OUTER_1VECTOR, VECTORIZED, the taxonomy and member names of xarray's `IndexingSupport` — and every read is split into the largest part of the selection that level can express, asked of the source in one call through `oindex`/`vindex` when it has them, and a residual transform applied to the block that comes back. The split is applied per partition as well as per whole-array read, so a part costs one request. The level is resolved at construction: an explicit `with_indexing_support` wins, then the source's own `__zarr_indexing_support__` (read defensively), then conservative inference — a NumPy array or zarr's `oindex`/`vindex` pair reads as VECTORIZED, everything else as BASIC, the only assumption that is always correct. A multi-array outer request only ever goes to an `oindex` accessor, because a bare `__getitem__` key with two arrays means an outer product to HDF5 and a correlated gather to NumPy. The level decides how much data crosses the boundary, never what `result()` returns. Tests hold that invariant directly: every selection case, at all four levels, against NumPy and zarr sources, partitioned and not; plus test doubles that raise when handed a key their declared level forbids, so exceeding a declaration fails loudly rather than working by accident. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): token the data, not how it is read The token included the partitioning while deliberately excluding the indexing-support level, though both are read strategies that leave the values unchanged. Excluding both means two wrappers that describe the same data token alike, so a consumer caching on tokens reuses one result across partitionings and support levels. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): an empty downward walk selects nothing A slice with a negative step whose start lies before the front of the axis selects nothing, but the positional slice was written as `slice(start, stop, step)` with a negative stop, which NumPy reads as counting from the end: an empty selection of a fancy axis returned the whole axis reversed, and the correlated form raised a broadcast error. Write an empty selection out explicitly. The randomized basic-selection generator drew negative-step starts from `[0, size)` only, so a start before the front of the axis was unreachable and the suite could not see this. It now draws from below `-size` as well, and three cases pin the behavior directly. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): a selection of slices is not a fancy selection An `oindex`/`vindex` step whose entries are all slices carries no coordinates: it narrows the view's own axes and must compose like basic indexing. `_reindex_array_oindex` instead applied each entry positionally to the corresponding axis of the existing index array, without asking whether that axis is one the array varies over or a singleton it merely broadcasts along — the distinction its basic-indexing sibling `_reindex_array` has always made. A slice starting past 0 therefore indexed a size-1 broadcast axis out of range and truncated the whole index array to size 0. A view with no coordinates left resolves to no parts, and `result()` handed back its unwritten `np.empty` buffer: live, on the default path, for any source that advertises chunks. `_reindex_array_oindex` now takes the `ArrayMap` and applies an entry only along its dependency axes (plus the `input_dimension` that breaks the tie for a degenerate length-1 orthogonal selection), preserving a broadcast singleton whatever the slice says. Coordinates never reach a broadcast axis — `_guard_fancy_after_fancy` still rejects genuine fancy-after-fancy with `NotImplementedError`, now under test. Four defects from the same review ride along: - `_array_map_dependency_axes` counted a length-**0** axis as an axis the array varies over, so an empty orthogonal selection classified as correlated and `array_map_dependent_axis` rejected it — a raise on the unpartitioned path where every partitioned path returned the right empty answer. An axis of size 0 carries no dependency any more than a singleton does. - `parts()` raised on a view emptied by a slice over an axis of extent 1. A correlated selection of one point normalizes to an all-singleton index array, so emptying the domain leaves the array at size 1 and the resolver went looking for a chunk. An empty input domain now yields no parts and meets no output domain, matching `result()`. - `sub_transform_to_selections` built `slice(stop + 1, start + 1, stride)` for a negative stride — endpoints swapped, step still negative, so it selected nothing where the reversed axis was meant. Both branches now lower through `_positional_slice`, the same walk an `ArrayMap` axis is reindexed by, which knows a downward walk reaching the front must stop at `None`. - `compose()` evaluated an inner index array over `range(size)` rather than over the outer domain's own range, and addressed it from 0 rather than from the inner domain's origin. Every coordinate resolved to the wrong cell whenever a domain did not start at 0 — which a step-1 slice and a negative-step slice both produce routinely here. - `transform_from_canonical` now rejects a non-integer `index_array` with an `NdselError` carrying `invalid_json`, instead of silently truncating `[0.9, 1.9]` to cells 0 and 1, coercing booleans, or leaking NumPy's own conversion error for strings. The fuzzer missed the first two because `_random_chain` drew at most one fancy step and had no way to spell a step that goes through a fancy accessor while carrying only slices. It now draws such a step separately, and the seeded sweep gained a `parts()` counterpart: `result()` can absorb a defect that the iteration contract cannot, since an empty view assembles correctly from no parts at all. Both sweeps fail on the pre-fix source, as does the new exhaustive stride/extent sweep over the chunk-selection bridge. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): count a domain axis no output map depends on A `vindex` coordinate array with a singleton broadcast axis contributes an axis it does not vary over. A later basic index that consumes the axis it *does* vary over collapses the map to a `ConstantMap` and leaves the broadcast axis in the domain, referenced by nothing. Three places assumed that could not happen: - `sub_transform_to_selections` built `out_selection` with one entry per output map, so a view with such an axis got an index tuple of lower rank than the buffer. `out[out_selection] = value` then placed the part against the leading axes and broadcast the rest — silently wrong data on a partitioned read, and a `parts()` walk that left cells unwritten. - `_restore_domain_axis_order` put an unreferenced axis back as a singleton whatever the domain said. At extent 0 that fabricated a row for a selection whose own `shape` reported it empty. - `_lower_correlated` built its flat gather index from the domain's broadcast shape but added coordinates straight off the stored index array, which is singleton on the axes it does not vary over. The two disagree exactly when a correlated map is constant along a shared broadcast axis. `out_selection` is now built per domain dimension throughout, an unreferenced axis is restored at its own extent, and a correlated map's coordinates are broadcast to the block before being combined. The randomized chain sweep never generated the shape at fault: `_random_vindex` only produced `(length,)` and `(length, 1)` coordinate arrays, neither of which leaves a singleton axis for a later step to strand. It now draws a broadcast rank and places each array's varying axis within it, which reproduces all three failures on the unfixed code. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): a materialized view never hands back the source Five fixes to the wrapper's edges, none of which changes what a selection means. `result()` and `__array__` no longer alias the wrapped array. An unpartitioned read of a basic selection lowers to plain slicing, so it came back as a *view* of the source; NumPy 2 hands whatever `__array__` returns straight to the caller, so `numpy.array(view, copy=True)` aliased it and a write reached through. Under any partitioning the same read allocates, so this also made the answer depend on how the read was divided. The result is now detached whenever it may share memory with the wrapped array, and the `copy=False` refusal no longer justifies itself with a claim the other branch violated. `result()` verifies that the partition walk covered the output before returning it. The buffer is deliberately uninitialized, so any defect in the walk was reported as plausible-looking numbers rather than as an error. The cells each part addresses are counted from the selectors' own shapes — nothing is read — and a walk that does not add up to the view's size raises. Measured on a 16 MiB read: 51 us of accounting against 6.5 ms of read for 64 parts, within noise end to end, and +1.7% at 512 parts. The `BASIC` floor is a promise about the *source*, not about the blocks it returns. The residual is finished with `take`, `reshape` and `transpose`, which were applied to the block unconverted — so a source meeting exactly the documented floor crashed on `oindex[[4, 0, 0], :, :]`. A block that is neither a NumPy array nor an array-API namespace of its own is now coerced, which leaves a device array where it is. `numpy.matrix` is refused at construction: it never reduces rank, so a view's shape and its result disagree on every rank-reducing selection. A `numpy.ma` source keeps its mask through a partitioned read, which allocates a masked buffer. A declaration holding a *foreign* enum member that names one of these four levels — xarray's `IndexingSupport`, whose members these are borrowed from — is honored rather than discarded, since discarding it fell through to inference and answered with a *more* permissive level than the source asked for. `is_complete` is true for a reversing view, which reads every cell of its box back to front; the stride-1 test it failed was about direction, not coverage. `with_parts` accepts `(0,)` and `(0, 0)` for a zero-length axis, which said the same thing as the `()` and uniform spellings it already took, and the positivity error names the working form. Above the token digest limit and without dask, `__dask_tokenize__` returns a value that matches nothing rather than a shape-and-dtype description that two different 4 MiB arrays shared. A cache keyed on it misses instead of lying. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): correct claims a reviewer found false Every statement below was executed before being rewritten, and the replacement was executed too. - "`view + 1`" / "arithmetic materializes through `__array__`" is false. `LazyArray` defines no arithmetic dunders, so `view + 1` raises `TypeError`. What does work is a NumPy *function* — `numpy.add(view, 1)`, `numpy.sum(view)`, `numpy.stack([view, view])` — and an ndarray on the left of the operator. Corrected in the module docstring, `docs/index.md` and the changelog fragment. - "An empty selection returns `None` from both" is false: an empty *box* reports `strides()` and only `bounding_box()` is `None`. The `strides()` docstring already said so; the design notes now agree with it. - "A box touches a contiguous run of parts" is false for a strided box — `[::4]` over 2-wide parts visits every other part. The true property, and the one a partition-walk optimizer would want, is a regularly-spaced run in increasing order, each part at most once. - "TensorStore permits a lower-rank index array" is backwards. Checked against tensorstore 0.1.84: its JSON parser rejects a rank-1 array over a rank-2 domain and accepts full rank with singletons, which is what we emit. *Our* loader is the permissive one. The passage now says both models want full rank, keeps the real rationale (the singletons are what makes the orthogonal/vectorized distinction derivable), and describes our lower-rank acceptance as the compatibility affordance it is. - "Two limits remain" omitted fancy-after-fancy, which is a live `NotImplementedError` reachable from the documented surface, while `index.md` invited chaining fancy steps "anywhere in the chain". Current scope now lists five limits, including the diagonal-view and mixed correlated/orthogonal ones, and both prose pages point at it. - "A single whole-array part stays in the wrapped array's namespace" is only true with *no* partitioning: `result()` branches on whether a partitioning is in force, not on how many boxes it has, so `with_parts((4, 6))` on a 4x6 array returns a plain ndarray. - The changelog stated the support-detection precedence backwards (declaration wins, not inference); `index.md` had a sentence missing its noun; the module docstring's one-line `bounding_box()` summary dropped the stride caveat the three other locations keep; and the package README, the PyPI long description, never mentioned `LazyArray`. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): hold the full-rank invariant inside the engine The index-array rank was checked only from above, so a lower-rank array could exist inside the engine and be read for dependency axes it did not have. Nothing produced one: the tolerance was there for a test asserting compatibility with a body TensorStore itself rejects (verified against 0.1.84 — a rank-1 array over a rank-3 domain is an error in its JSON parser). Require the full input rank in the type, widen a lower-rank array at the JSON boundary where external input arrives, and give the test the shape TensorStore accepts. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): an index array spans the domain it is read over An index array axis must be the domain's extent or a singleton it broadcasts over. Any other size leaves input coordinates with no entry, which read as a smaller selection rather than as the error it is: the truncated array behind one of this review's silent-corruption bugs was a (3, 0) array over a (3, 2) domain, which this rejects at construction. Two fixtures carried the inconsistency they were meant to exercise — an empty array over a domain with room for two coordinates, and a widening case whose array covered three of four positions — and now describe domains their arrays span. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-indexing): a state machine for chained indexing, and the rank-0 part it found Adds `zarr_indexing.testing`, behind a `testing` extra: a Hypothesis state machine that composes indexing steps onto a LazyArray and checks each step's shape, `result()`, and `parts()` assembly against NumPy, plus the selection strategies on their own. A project can point it at its own array by overriding one method. The machine asserts the documented assembly literally — a part's values must arrive at the shape its out_selection addresses — which is how it found the defect it also fixes: intersecting a correlated transform with a part's bounds collapsed the surviving broadcast block into one axis even when the block was already rank 0, so a view narrowed to a single point produced parts of rank 1. A rank-0 block now stays rank 0, and `result()` drops the reshape that was absorbing the mismatch. Merged from the branch that produced it, which predates the coverage guard in `result()`; the guard stays and the reshape it compensated with goes. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): the defects an adversarial review found at the boundaries Six reviewers went at the package, each proving findings by execution. The algebra held: ~85k chained selections against NumPy, ~24k part assemblies with poisoned buffers, 3.8k transform round-trips evaluated as coordinate maps, all clean. Everything below was at a boundary. `result()` and `__array__(copy=True)` could hand back a live view of the source. `_detach` asked whether the *source* was an ndarray, but a duck array that merely stores its data in NumPy returns NumPy views, and those went straight to the caller — while three docstrings promised the opposite unconditionally. It now asks whether the *result* owns its buffer, so memory is released only when sharing is disproved rather than when it cannot be established. The wire format could not reload its own output. `tolist()` renders every empty array as `[]` once the leading axis is the zero-length one, so an ordinary empty selection lost the axis it varied over, and the loader put it back on a different one by prepending singletons. Nested lists cannot express the shape either, so the body carries it. `index_domain_from_json` was a second undefended way into the same objects: a bare `int()` that truncated 3.9, coerced "3" and True, and let a non-string label into a tuple[str, ...]. It goes through the message layer now, as a transform body always did. With it: a rank ceiling, i64 checks on desugared bounds so normalization stays idempotent, ordered index_array_bounds, and typed errors where raw ones leaked. `sub_transform_to_selections` transposed its blocks two ways. A ConstantMap was emitted as a bare integer, which NumPy counts among the *advanced* indices whenever an index array is present, moving the broadcast axis to the front when a slice separates them — while `out_selection` is built positionally. And the correlated branch documented a points-major block but assembled the chunk selection in output order, so a residual slice before the coordinates arrived slice-major. Constants are length-one slices now, named in drop_axes, and the correlated scatter is permuted to the block NumPy actually returns. Nothing caught either one because `LazyArray` resolves a part through its own lowering and never reads `chunk_selection`; one of the two was even asserted as correct in a passing test's comment. Three further failures were one stale field: `_apply_vindex` carried `input_dimension` onto a map the vindex had just made correlated. The value outlived the shape that justified it and was believed later by a scatter that filed positions under the wrong axis — which is why one view's answer depended on how it was partitioned. The dependency is read back off the array now, and `__post_init__` checks the field it was wrong about: ArrayMap was the one map whose `input_dimension` nothing validated. Also: `oindex` over a correlated view applied its index tuple positionally, NumPy's vectorized rule, collapsing two arrays into one axis; `compose()` indexed an inner array's broadcast singletons by the raw coordinate and sized its one-dimensional shortcut by the input rank while gating on the output rank; and neither checked that the outer transform's output lands inside the inner domain, where a negative would have wrapped. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-indexing): generate the selections that were never generated A mutation audit ran 31 mutations and 10 survived. They were not scattered: the invariants check thoroughly what a view *returns* and never what it *claims about itself*, and the strategies could not draw whole classes of selection. The generators now draw them. Orthogonal slices carry a step and may stop early, so a strided or reversed slice reaches `oindex` at all. Coordinate lists and masks can be empty, so a fancy selection that selects nothing exists — the shape that lost its axis on the way through JSON. Vectorized coordinate arrays can be multi-dimensional, so a rank-raising `vindex` is generated. Measured over 4000 draws each, every one of those counts was previously 0. The first run of the widened generators found a live defect: an empty Python list carries no element type and NumPy defaults it to float64, so `oindex[[]]` was refused as a non-integer index array. `json.py` already had that case; the boundary did not. NumPy takes `a[np.ix_([])]`, and so does this now. `Partition.is_complete` gets an invariant. It is what a consumer reads to decide it may take a whole-box read, so a wrongly-`True` one is silent corruption — and three separate mutations to `_covers_whole_part` survived the entire suite, including ones reporting `is_complete` for a part carrying two of its three cells. Asserted one way only: the flag is documented as conservative and only the claim to cover everything has to be earned. Two more state machines. The sorted one-dimensional fancy path needs both ranks to be 1, and the output rank is the *source's*, so the rank-3 default source walled it off entirely — 0 hits from the machine against 105 from the unit tests, in the path where reordering and duplicate coordinates are partitioned. A rank-1 source now reaches it 322 times per run. A source with an extent-1 axis covers the other side of a distinction the code draws from the domain rather than the array. Finally the two remaining mutants, both checked by mutating and confirming the failure: the index-array bound checks are probed one past the boundary rather than comfortably outside it, and `_out_selection_cell_count`'s guard is tested directly, since a partition walk only ever produces the forward in-bounds intervals that never reach it. Assisted-by: ClaudeCode:claude-fable-5 * refactor(zarr-indexing)!: settle the API decisions that get dearer after 1.0 `with_parts` decided what it had been given by inspecting the type of it: a sequence of integers meant uniform boxes, a sequence of sequences meant per-axis sizes, and `None` meant no partitioning at all — which also sent `result()` down an entirely different code path. Three semantics behind one parameter, and no way to ask for one of them and be told when you had spelled it wrong. They are now `with_parts`, `with_parts_per_axis` and `unpartitioned`. A harness that draws from a list of mixed partitionings still needs the dispatch, so it exists once, as `zarr_indexing.testing.repartition`. The sizes those methods take are relative to the array being read, not to the view reading it, and a narrowed view partitions the base extents — which could only be discovered from an error message. `base_shape` says it. `ArrayMap`, `IndexTransform` and `Partition` are `frozen=True`, which reads as a promise that a value can be compared and hashed. Both raised: `==` on the index arrays returned an array and then `ValueError: the truth value of an array is ambiguous`, and `hash()` refused an ndarray outright. So no transform could enter a set or key a cache, and the package had already grown an internal `_is_identity_transform` because of it. An `ArrayMap` was frozen but the array inside it was not, so reaching through a view's transform to `index_array[0] = 9` silently changed what the view returned. It is held through a read-only view now — a view rather than a flag on the caller's array, since constructing a map should not take away the right to write to an array you still own. `IndexDomain.narrow` clamped a slice bound to the domain, in a package whose stated invariant is no clamping and no negative wrapping. `narrow(slice(-3, None))` on `[0, 10)` therefore returned the whole axis — reading as the NumPy spelling of "the last three" and answering with something else — and a stop past the end returned a domain its own parent did not contain. Both raise `BoundsCheckError` now, and a stride raises `ValueError` like every other unimplemented request rather than `IndexError`. `Partition.array` was a view of the array while `LazyArray.array` was the raw source: adjacent types, one name, inverted meanings. The part's is `view`. Smaller: `BoundsCheckError` and `VindexInvalidSelectionError` are exported at the top level, being what exported functions raise; `errors.py` no longer claims `zarr.errors` re-exports them by identity, which is false and would have been believed; `parts()` says it is single-use; and `sub_transform_to_selections` says it is provisional rather than implying the rest of the API's stability. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): correct the claims a reviewer could check, and two dialect gaps `boundary.py` justified applying scalars before the advanced indices by asserting NumPy does the same, citing `a[0, [1, 2], :]`. NumPy groups a scalar *with* the advanced indices for placement, so the two disagree the moment a slice separates them: `a[0, ..., [1, 2]]` is `(2, 3)` where `a[0][..., [1, 2]]` is `(3, 2)`. Scalar-first is this package's documented dialect and stays; the reasoning was wrong, and a wrong reason invites someone to "fix" the correct end later. Two places where the dialect really did diverge, both now matching NumPy. A zero-dimensional integer array is a scalar — `a[np.array(2), :]` drops its axis — but only Python and NumPy integers counted, so a 0-d array was widened into a length-1 index array and kept an axis; that was a third answer, agreeing with neither NumPy nor eager zarr. And a multi-dimensional array in an orthogonal selection is refused where the rule lives, instead of surfacing two layers down as a rank complaint about an `index_array` the caller never wrote. `iter_chunk_transforms` documented two shapes for `out_indices` and returns three: the `dict[int, ndarray]` an orthogonal selection with several index arrays produces was missing, from the function downstream integrators use most. Packaging: the README is the PyPI long description, so the monorepo-only development section moved to CONTRIBUTING.md and the dead relative link to the justfile went with it. The examples pinned `zarr-indexing` to a moving `main` rather than to a release they document. Three of the six docs pins claimed to match the repo root and did not, and the justfile's ruff comment contradicted the package's own pin. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): collapse an empty index array instead of extending the format The previous commit fixed the empty-selection round trip by carrying an `index_array_shape` field, on the reasoning that JSON nested lists cannot express the shape of an array with a leading zero axis — `[]` is the only spelling of every empty shape, and `[[]]` is (1, 0) with nothing for (0, 1). That much is true, but the conclusion was wrong: it invented a field ndsel does not define, so the documents this package wrote stopped being ndsel documents. The reference implementation does not have the problem, because it never emits an empty index array. `t[ts.d[0][[]]]` in TensorStore is `out[0] = 0`, emitted as `{}` — a constant map. An empty index array names no cell, and it can only be empty because an input dimension is, since the full-rank invariant makes every axis either 1 or the domain's extent. Nothing is ever read through it, the emptiness is carried by the domain, and the map is degenerate in exactly the way a size-1 array is — which this format already collapses. So it collapses the same way, and the extension is gone. The loader still recovers the axis from the domain for an empty array arriving from a producer that does emit one, since ndsel does not forbid it; that path just no longer has a first-party caller. Checked against tensorstore 0.1.84: every canonical body from 4000 randomized transforms loads into `ts.IndexTransform`, and every one re-emits itself unchanged. No spec change needed. Assisted-by: ClaudeCode:claude-fable-5 * fix(indexing): address lazy array review findings Assisted-by: Codex:gpt-5 * fix(zarr-indexing): keep an empty masked result masked whichever parts are in force An empty view is now answered without reading the source, and the shortcut reached for the array namespace's own `empty`, which knows nothing about masks. An unpartitioned empty view over a masked source therefore came back a plain array while the same view partitioned came back masked — no cells either way, so no value changed, but the caller's type depended on how the read had been divided, which `result()` promises it never does. A masked source goes through `_output_buffer`, which is the branch that knows. Assisted-by: ClaudeCode:claude-fable-5 * docs(indexing): design chunk projection API Assisted-by: Codex:gpt-5.6 * feat(indexing): add reusable chunk plans Assisted-by: Codex:gpt-5.6 * feat(indexing): project chunks through paired transforms Assisted-by: Codex:gpt-5.6 * refactor(indexing): build lazy parts from projections Assisted-by: Codex:gpt-5.6 * refactor(indexing): expose projection-only chunk planning Assisted-by: Codex:gpt-5.6 * docs(indexing): design visual indexing guide Assisted-by: Codex:gpt-5.6 * docs(indexing): explain coordinate origins Assisted-by: Codex:gpt-5.6 * docs(indexing): motivate negative chunk coordinates Assisted-by: Codex:gpt-5.6 * feat(indexing-docs): add SVG diagram renderer Assisted-by: Codex:gpt-5.6 * fix(indexing-docs): harden diagram rendering Assisted-by: Codex:gpt-5.6 * feat(indexing-docs): add accessible guide diagrams Assisted-by: Codex:gpt-5.6 * fix(indexing-docs): correct guide figure semantics Assisted-by: Codex:gpt-5.6 * fix(indexing-docs): prevent selection label overlap Assisted-by: Codex:gpt-5.6 * fix(indexing-docs): validate arrow label offsets Assisted-by: Codex:gpt-5.6 * test(indexing-docs): add executable guide examples Assisted-by: Codex:gpt-5.6 * docs(indexing): add NumPy-first visual tour Assisted-by: Codex:gpt-5.6 * docs(indexing): explain chunk projections visually Assisted-by: Codex:gpt-5.6 * docs(indexing): add indexing and integration references Assisted-by: Codex:gpt-5.6 * fix(indexing-docs): satisfy strict example typing Assisted-by: Codex:gpt-5.6 * docs(indexing): connect visual guide to reference docs Assisted-by: Codex:gpt-5.6 * fix(indexing-docs): source landing quickstart from example Assisted-by: Codex:gpt-5.6 * ci(indexing): verify executable visual docs Assisted-by: Codex:gpt-5.6 * fix(indexing): address visual guide review Assisted-by: Codex:gpt-5.6 * fix(indexing): improve chunk overlay on phones Assisted-by: Codex:gpt-5.6 * docs(indexing): design system-memory chunk cache example Assisted-by: Codex:gpt-5.6 * docs(indexing): introduce half-open intervals Assisted-by: Codex:gpt-5.6 * test(indexing): narrow diagram label elements Assisted-by: Codex:gpt-5.6 * docs(indexing): demonstrate a system-memory chunk cache Assisted-by: Codex:gpt-5.6 * chore(indexing): stop tracking design specs Assisted-by: Codex:gpt-5.6 * feat(indexing): apply and invert transforms Assisted-by: Codex:gpt-5.6 * fix(indexing): handle scalar and wide transform coordinates Assisted-by: Codex:gpt-5.6 * docs(indexing): explain the chunk-cache lifecycle Assisted-by: Codex:gpt-5.6 * fix(indexing): keep lifecycle diagram readable Assisted-by: Codex:gpt-5.6 * fix(indexing): keep lifecycle caption stationary Assisted-by: Codex:gpt-5.6 * fix(indexing): keep guide diagrams readable Assisted-by: Codex:gpt-5.6 * test(indexing): enforce unique guide figure wrappers Assisted-by: Codex:gpt-5.6 * test(indexing): scan all guide sources for figure duplicates Assisted-by: Codex:gpt-5.6 * docs(indexing): distinguish cache indexing modes Assisted-by: Codex:gpt-5.6 * docs(indexing): scope lazy examples to package Assisted-by: Codex:gpt-5.6 * fix(indexing): expose docs modules to root tests Assisted-by: Codex:gpt-5.6 * docs(indexing): omit text from diagram legends Assisted-by: Codex:gpt-5.6 * docs(indexing): strengthen chunk outlines Assisted-by: Codex:gpt-5.6 * docs(indexing): label unselected chunk cells Assisted-by: Codex:gpt-5.6 * fix(indexing): show coordinates in basic selection Assisted-by: Codex:gpt-5.6 * docs(indexing): clarify coordinate-value mapping Assisted-by: Codex:gpt-5.6 * docs(indexing): simplify half-open intervals Assisted-by: Codex:gpt-5.6 * docs(indexing): explain ordered concatenation Assisted-by: Codex:gpt-5.6 * docs(indexing): consolidate visual guide Assisted-by: Codex:gpt-5.6 * docs(indexing): clarify basic selection figure Assisted-by: Codex:gpt-5.6 * docs(indexing): simplify coordinate introduction Assisted-by: Codex:gpt-5.6 * docs(indexing): explain result axis construction Assisted-by: Codex:gpt-5.6 * docs(indexing): enclose slice result axis Assisted-by: Codex:gpt-5.6 * fix(indexing): clarify result array comparison Assisted-by: Codex:gpt-5.6 * fix(indexing): preserve tutorial result ranks Assisted-by: Codex:gpt-5.6 * docs(indexing): promote chunk cache example Assisted-by: Codex:gpt-5.6 * docs(indexing): render chunk cache source Assisted-by: Codex:gpt-5.6 * fix(indexing): close final correctness gaps Assisted-by: Codex:gpt-5.6 * docs(indexing): replace diagrams with ascii Assisted-by: Codex:gpt-5.6 * chore(indexing): remove svg diagram pipeline Assisted-by: Codex:gpt-5.6 * docs(indexing): simplify guide navigation Assisted-by: Codex:gpt-5.6 * fix(indexing): align selection diagram columns Assisted-by: Codex:gpt-5.6 * feat(indexing): add explicit array readers Assisted-by: Codex:gpt-5.6 * refactor(indexing): resolve lazy arrays through readers Assisted-by: Codex:gpt-5.6 * docs(indexing): exercise readers in chunk cache example Assisted-by: Codex:gpt-5.6 * fix(indexing): preserve cache request event ordering Assisted-by: Codex:gpt-5.6 * refactor(indexing): remove indexing capability taxonomy Assisted-by: Codex:gpt-5.6 * docs(indexing): explain explicit reader execution Assisted-by: Codex:gpt-5.6 * test(indexing): avoid constructor spelling assertion Assisted-by: Codex:gpt-5.6 * fix(indexing): complete reader migration Assisted-by: Codex:gpt-5.6 * fix(indexing): keep reader helpers private Assisted-by: Codex:gpt-5.6 * docs(indexing): finalize reader safety contract Assisted-by: Codex:gpt-5.6 * feat(indexing): add compact chunk grids Assisted-by: Codex:gpt-5.6 * fix(indexing): check affine coordinate arithmetic Assisted-by: Codex:gpt-5.6 * fix(indexing): validate composed constants Assisted-by: Codex:gpt-5.6 * fix(indexing): expose grid size representation Assisted-by: Codex:gpt-5.6 * fix(indexing): validate direct advanced selections Assisted-by: Codex:gpt-5.6 * fix(indexing): handle boolean list masks Assisted-by: Codex:gpt-5.6 * fix(indexing): project sparse affine selections directly Assisted-by: Codex:gpt-5.6 * fix(indexing): normalize chunk planner positions Assisted-by: Codex:gpt-5.6 * fix(indexing): lower reader transforms through bounded slabs Assisted-by: Codex:gpt-5.6 * refactor(indexing): expose global partition read context Assisted-by: Codex:gpt-5.6 * fix(indexing): resolve read context annotations Assisted-by: Codex:gpt-5.6 * feat(indexing): reuse prepared partition plans Assisted-by: Codex:gpt-5.6 * fix(indexing): validate prepared partition coverage Assisted-by: Codex:gpt-5.6 * test(indexing): enforce transform materialization laws Assisted-by: Codex:gpt-5.6 * docs(indexing): clarify chunk projection locality Assisted-by: Codex:gpt-5.6 * fix(indexing): harden transform and partition validation Assisted-by: Codex:gpt-5.6 * docs(indexing): separate examples from snippets Assisted-by: Codex:gpt-5.6 * feat(indexing): support index protocol selectors Assisted-by: Codex:gpt-5.6 * feat(indexing): compose fancy selections without restriction A second oindex/vindex/mask step may now land on any axis of an already-fancy view, including axes an existing index array merely broadcasts along. Array-carrying transforms route through compose() instead of being rewritten in place: the selection is applied to an identity transform over the current domain (same dialect by construction) and chained on, which evaluates the existing index arrays at the new coordinates. The in-place reindex machinery and its fancy-after-fancy guard are deleted. Resolution classifies transforms by structure (the new public index_array_structure): pure per-axis outer products keep the orthogonal resolvers; correlated maps, mixtures, and index arrays sharing an input axis (diagonal gathers) all take the pointwise path, whose intersect and lower stages now broadcast per-map blocks instead of assuming full-block index arrays. Only hand-built affine diagonals (an index array and a slice map bound to the same axis) remain unsupported. This removes the crash where a slice-only vindex step (view.lazy.vindex[...] or vindex[..., scalar]) after a correlated gather misclassified the gather as orthogonal and failed at result(), and fixes a stale input_dimension surviving integer indexing of an empty map's pinned axis. Also, from the same review: result(parts=...) raises ValueError instead of AssertionError when supplied parts do not tile the view; with_parts and with_parts_per_axis raise the documented ValueError for non-iterable input; prepared-part validation uses plain assignment for box parts; and __dask_tokenize__ digests the canonical transform body instead of embedding it, keeping tokens small for large fancy selections. The testing state machine now draws any number of fancy steps per chain. Assisted-by: ClaudeCode:claude-fable-5 * refactor(indexing)!: retire ArrayMap.input_dimension What an index-array map depends on is now read from one place: its full-rank array's shape, whose non-singleton axes are the dependency axes. The retired field pinned the orthogonal axis redundantly and could contradict the array it rode on; every bug found in two adversarial review rounds traced back to its bookkeeping (stale values surviving reindexing, misclassification of correlated maps, dangling axes after integer indexing). The one shape the field disambiguated - a single-coordinate, all-singleton array - is normalized away instead: the selection and composition layers build it as the ConstantMap it equals (output_map.array_map_or_constant), exactly as the JSON serializer has always collapsed it on the wire. A consequence is that a length-1 fancy selection now classifies as a box (is_box, bounding_box, strides), which is the semantically sharper answer. Hand-built all-singleton, empty, or shared-axis ArrayMaps remain valid values and resolve through the pointwise path. Fallout removed with the field: the post-init consistency validation, the basic-indexing renumbering of pinned axes, the JSON loader's global dependency-axis reconstruction, and composition's binding carry-through. The sorted 1-D chunk-planning fast path now applies to either fancy spelling, since the flavors coincide in one dimension. The wire format is unaffected - it never carried the field. BREAKING: ArrayMap.__init__ no longer accepts input_dimension, and the attribute is gone; array_map_dependent_axis now answers from the shape alone. Assisted-by: ClaudeCode:claude-fable-5 * feat(zarr-indexing): a reader for sources that only accept unit-step slices BasicReader reads the minimum by pushing strided and descending selections down as positive-step slices, which assumes the source accepts any step. Integrating a zarrs-backed array showed how common the narrower contract is: FFI bindings and HTTP range endpoints support nothing but slice(start, stop, 1), leaving every such backend to rewrite the same cover-and-restride lowering in its facade. UnitStepReader moves that lowering behind the Reader boundary. The decomposition covers each DimensionMap with the smallest ascending unit-step slab and replays the original stride in the residual — the same move the basic decomposition already makes for direction, extended to magnitude. The residual lowering needed no change: positive strides slice the block, descending ones were always gathered. The cost is explicit in the docstring: a strided selection over-reads its cover by the stride factor, bounded by partitioning the wrapping LazyArray. The existing reader contract cases and the affine-overflow parity test now run across all three built-in readers, through a source that rejects anything but ascending unit-step slices inside its bounds. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the dense-box re-partition idiom is_box and strides() exist so a consumer can choose a read strategy, but the three lines that act on them were only discoverable by deriving them. The integrations guide now states the policy: a dense box resolves best as one backend slab read — re-partition to the base shape and let the backend dispatch, decode in parallel, and partial-decode shards on its own side — while strided boxes and gathers keep the partitioning, which bounds every cover by one part and makes hull-sized reads of sparse selections structurally impossible. The snippet is executable and pins both regimes by observed reads: the corner gather touches four single cells, never the hull; the dense box is exactly one call. A closing subsection points sources that only accept unit-step slices at unit_step_reader. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-indexing): re-vendor ndsel conformance corpus at 49b9e1db Re-vendor from zarr-developers/ndsel main (49b9e1db1ca93c55f320b025a666367de87a9014, merge of ndsel PR #3). Only transform.json changed vs the previously vendored 92d6a32d: two new fixtures pin empty index_array serialization — normalize carries an empty index_array verbatim rather than rewriting it to a constant map, while a producer SHOULD collapse it to a constant output map, which zarr_indexing.json already does. All other corpus files are byte-identical. Assisted-by: ClaudeCode:claude-fable-5 * ci(zarr-indexing): run the tensorstore parity tests test_ndsel_tensorstore.py skipped everywhere because tensorstore was in no dependency group or workflow. Add a dedicated step to the test job that overlays tensorstore (>=0.1.84, wheels cover the whole 3.12-3.14 matrix) and runs the two parity modules; the main pytest run stays byte-identical to the local canonical invocation. Verified locally against tensorstore 0.1.85 on CPython 3.14: 88 passed, 0 skipped. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-indexing): derive the docs include graph instead of registering it The doc-example tests accreted during the documentation build-out as one-off guardrails: hand-maintained registries of snippet regions, exact heading and navigation strings, substring pins on teaching prose, and tombstones for migrations that already happened. Each new snippet had to be registered by hand, and editing a sentence could fail CI. The registries also missed the one failure they existed to prevent: a page including a region nobody registered was invisible to them. The suite now states two kinds of contract and nothing else. Structural: every '--8<--' include in the rendered markdown — discovered by scanning, so new snippets are covered the day they are written — resolves to exactly one file with a balanced, non-empty region, and every snippet executes, its inline assertions serving as the value check where expected values were previously duplicated into test tables. Behavioral: the pattern matrix, the wrapped-source contract, and the chunk-cache lifecycle keep their tests, because an example cannot assert its own error paths. pymdownx.snippets gains check_paths: true, so the strict docs build now fails on an unresolvable include instead of silently rendering nothing. Verified both directions: a deliberately broken region name fails the scan test (naming page, file, and region) and the docs build. Editorial choices — section order, wording, nav — return to review, where they belong. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): lead every page with the simple idea The guide opened with two meta-paragraphs and an annotated table of contents; the one-sentence mental model — lazy indexing builds a view, planning partitions it, result() materializes it — sat below them. It opens with that sentence now, and says plainly that the first four sections serve anyone indexing arrays while the last two serve integrators, so most readers know they can stop early. Advanced material moves out of the beginner path. Negative-origin domains, grid prepending, and the EdgeDimensionGrid/DimensionGridLike comparison sat in section two, before the reader had met a transform; they now live in the design notes as 'Negative-origin domains and prependable grids', linked from the two places that want them. The paired-projection section introduces the cell domain concretely — a table with one row per selected cell, chunk-local address on one side, result position on the other — before naming it. The landing page gains the missing why: many arrays support only plain slicing, and this package grafts the full NumPy dialect onto them. The pattern reference leads with the selection matrix readers come for and moves the positions-vs-literal-coordinates table after it. The materialization warning becomes a list, and captions that narrated their own code are cut. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): document every public method of the public API Every public class, method, and property reachable from the package root now carries a docstring stating its contract: the coordinate frame it speaks (global source, chunk-grid, or zero-origin chunk-local), whether a chunk length is the declared codec size or the boundary-clipped data extent, what is bounds-checked and what extrapolates, and which inputs raise which errors. Protocol members (DimensionGridLike, DimensionGrid) are written as implementer obligations, since the docstring is the contract a third-party grid must satisfy. Dataclass-generated __init__ methods are left to their class docstrings; adding a docstring there would mean hand-writing the constructor for no behavioral reason. Docstrings only — no code, signature, or existing-docstring changes. Verified: an introspection audit over __all__ reports zero public members without docstrings; the full suite and pyright are unchanged. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): attribute docstrings for every public field The previous pass documented methods and properties; dataclass and TypedDict fields — IndexDomain.exclusive_max and 41 siblings across fifteen classes — carried no per-attribute documentation, only prose in their class docstrings. Each public field now has an attribute docstring stating what the value means, its coordinate frame or units, and the invariant it carries (literal bounds may be negative, edges are declared codec sizes unclipped by extent, derived fields say what they are derived from, wire bounds admit the infinities the engine refuses to lower). Found by an AST audit, since attribute docstrings are invisible to runtime introspection; that audit now reports zero undocumented public fields. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the input/output-to-request/source dictionary, and each map kind in NumPy terms An IndexTransform is a function between coordinate spaces, and its fields speak function vocabulary (input, output) while every array-minded reader speaks request and source. The confusion this causes is concentrated in one word: 'output' looks like data, but names the output side of the coordinate function — which is where values are read FROM, since data flows against the arrow. The transform section of the guide and the transform API page now state the dictionary outright, in a two-row table, at the moment a reader first meets the fields, along with why the neutral names exist: composition, where an interior transform has neither a request nor a source side. The three output map kinds are now demonstrated executably against their NumPy counterparts: DimensionMap against basic and negative-step slices, ArrayMap against fancy indexing with order and duplicates preserved, and ConstantMap against numpy.broadcast_to — stated as the value-faithful counterpart precisely because no NumPy selection spells a retained constant axis; an integer index drops it, and a repeated fancy index matches the values while degrading the description to a coordinate list. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): flat landing page — motivation, example, links The grid cards misrendered (misaligned card bodies) and earned their keep poorly: two navigation targets dressed as a layout feature. The landing page now follows the shape convention of projects like pydantic — motivation paragraph, install, one quickstart with a sentence stating the lazy/eager boundary, then a single annotated link list. The two cards' start-here targets survive as the visual guide entry, which names both audiences and their entry points in one line each. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): a single-point bounds error never mentions a batch apply() delegates to the vectorized kernel shared with apply_many() — the right direction, since the batch path is the hot one — but the kernel's diagnostic leaked through it: apply((11,)) on a [-10, 10) domain reported 'point at batch position ()', naming a batch the caller never formed, from a private frame the caller never called. The kernel now raises an internal structured signal (dimension, value, bounds, batch position) and each public entry formats it in its own vocabulary, 'from None' so the traceback ends at the API layer: apply says 'coordinate 11 on input dimension 0 is outside the domain [-10, 10)'; apply_many keeps the batch-position form, where that context is exactly right. Message-only change; BoundsCheckError remains the type on both paths. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): annotation syntax in docstring type slots Parameters and Returns entries now state types as annotations — Sequence[int], tuple[int, ...], numpy.typing.NDArray[numpy.intp] — instead of prose like 'sequence of int' or bare 'tuple'. The annotation is the type's one precise spelling, matches the signature beside it, and names the exact shape where prose left it to the description (both boundary functions' bare 'tuple' entries now state their element structure). Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the chunk cache example is named for what it is The example was born napari_chunk_cache, and the docs spent two bold disclaimers insisting it is a napari-like consumer, not a napari integration — while the nav entry, section headings, and class names had already settled on 'system-memory chunk cache'. A name that needs disclaimers is the wrong name. The directory, script, and docs page are now system_memory_chunk_cache, matching everything else; napari remains where it belongs, in prose, as the motivating access pattern. Path-only rename: no code, region names, or prose claims change. The derived include-graph test and the strict docs build (check_paths) verify every include and link followed the move. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): an empty domain reads as empty through every reader Composing a fancy selection onto an empty-domain view emits an ArrayMap that is legitimately empty along the vanished axis — a shape the package promises resolves like any other. The resolvers broke that promise: _correlated_map_coords tried to reshape the 0-size array to its non-zero singleton block axes and raised ValueError from all three built-in readers on a direct read_into, a sequence the pre-composition engine handled. LazyArray.result() masked it only through its own size-0 short-circuit. _lower now answers an empty domain first — nothing is selected, so no resolver needs to evaluate maps that may be empty along vanished axes — and the correlated path independently returns no coordinates for an empty broadcast block. Found by an adversarial review fuzzing composed selection chains (3 of 400 random chains hit it); the regression test pins the exact public-API reproduction across all three readers. Assisted-by: ClaudeCode:claude-fable-5 * test(zarr-indexing): execute the CLI examples; strict builds guard anchors and nav Two claims from the doc-test restructure were false, and an adversarial review proved both empirically. First, the lazy_indexing_* examples were said to run under the repository-root example runner; that runner globs only the root examples directory, so the two CLI examples ran under no test at all. They now run as subprocesses here, the dask one skipping where dask is absent. Second, the module docstring claimed mkdocs --strict covered the deleted anchor and nav guards; a strict build passed with a deliberately broken cross-page anchor and with a page omitted from nav, because both are INFO-level by default. mkdocs.yml now sets those validations to warn, which strict promotes to errors — verified failing on a broken anchor and passing clean. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the vindex error's real contract, and neutral map vocabulary VindexInvalidSelectionError's docstring claimed it covered every non-coordinate vindex form; in fact only the wrapper's validation raises it, only for slices — other invalid entries raise plain IndexError, and the engine-level IndexTransform.vindex accepts residual slice dimensions without raising. The docstring now states the actual raise site. The transform-algebra docstrings (transform, output_map, composition, json) also drop 'storage' for neutral input/output vocabulary: a transform's output side is just output coordinates — in a composition chain an interior transform has no storage side at all. The request/source/storage translation stays where it belongs, in the guide's vocabulary table and the endpoint layers (readers, grids) that really do face arrays. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): an executable Examples section on every public object Every public class and function in the package root now carries a numpydoc Examples section in doctest form: 37 new examples, each a small intuition-builder in the shape the IndexTransform walk-through set — the domain is the result's coordinates, the output maps are the rule, and where an object corresponds to a NumPy indexing concept the example demonstrates the equivalence (DimensionMap against a slice, ArrayMap against fancy indexing with duplicates surviving, ConstantMap against numpy.broadcast_to, compose against chained slicing). The error classes demonstrate their actual raise; the wire types round-trip real bodies. The examples are enforced, not decorative — and closing that loop exposed that the package's existing doctests were never collected anywhere: the package pyproject shadows the repository root's pytest configuration, and no invocation named src. The package config now enables --doctest-modules with the root's option flags, testpaths includes src/zarr_indexing, and the justfile recipe and CI workflow collect it explicitly. 1280 tests pass, 45 of them doctests. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): apply and apply_many say what they locate, not their signature 'Map one input coordinate to an output coordinate' restates the type signature in prose — any function maps inputs to outputs. The summaries now speak the class docstring's array-indexing frame: apply maps a coordinate of the domain (a result cell) to the source coordinate its value is read from, by evaluating each output map; apply_many is the batch form. Both gain a doctest locating cells of the [::2] transform, and both state that no data is touched — this is the coordinate arrow, running result to source. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): method summaries never lean on the ambiguous naked input/output 'input' and 'output' are reserved algebra terms in this package, and in a method summary they collide with ordinary function-speak: identity's 'input coordinate i maps to output coordinate i' reads equally as the algebra statement and as a vacuous description of any function — the same trap apply's summary fell into. identity, intersect, and translate now speak the array frame instead: every result cell reads the source at its own address; keep only the cells whose source coordinates fall inside the box; shift the source coordinates every cell reads. Field docstrings and class summaries keep the naked terms where no call is in sight and the technical reading is the only one available. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): drop non-behavior statements that disambiguate nothing 'No data is touched' in apply/apply_many and 'without I/O' on the oindex/vindex accessors stated what the functions do not do without clarifying what they do: nothing about a coordinate lookup, or about an accessor documented to return a new transform, suggests data movement. Removed. The statements that earn their negation stay: the module thesis, the class contract, and __getitem__ — where subscription syntax genuinely suggests an eager read to anyone arriving from zarr. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): a flat sidebar — sections must earn their existence 'Use lazy indexing' held one page: a disclosure triangle and a competing label with no organization gained. 'Practical reference' classified nothing and grouped two pages serving different audiences — the exact split the guide's opening and the landing page's annotated links already route explicitly. Both dissolve into top-level entries. Examples and API Reference keep their sections, being the only real collections at this site's size; the ndsel wire format and design notes gain explicit labels and sit in the for-builders tail before the API. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the three guide pages are one Guide section Visual guide, indexing patterns, and integration boundaries sat at top level with the same rank as the fifteen-page API Reference — three pages wearing category clothes. They are one collection, and the docs/guide/ directory said so all along: learn it, look it up, apply it at the boundary. Pydantic's sidebar confirms the pattern (its narrative layer is one Concepts section) while cautioning against copying its tab bar and zero-loose-pages norm, which pay off at fifty pages and cost discovery at eight. navigation.indexes makes the Guide entry itself land on the visual guide, so the common click is free; standalone artifacts (landing, ndsel spec, design notes, changelog) keep their top-level standing. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the pattern matrix models selections as transforms The indexing-pattern reference framed every row through LazyArray, as if the wrapper defined the semantics. It does not: every dialect compiles to an IndexTransform, and the wrapper is a regular array-like API whose only distinction is that operations on .lazy return views. The matrix now speaks the algebra — t[1:5, ::2], t.oindex[rows, columns] on IndexTransform.from_shape((6, 8)) — and the executable snippet compiles each selection through the transform accessors, reads the box/query category structurally off the output maps, and resolves values through the public reader. The wrapper is demoted to a closing note, and the test suite keeps it honest by running the same matrix through LazyArray: the snippet proves the algebra, the test proves the wrapper agrees. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the pattern matrix hand-builds each idiom's transform Showing t[1:5, ::2] demonstrated only that IndexTransform supports __getitem__ — syntax, not the object. Each idiom is now modeled by hand: domain plus output maps, with the anatomy stated per case (the dropped axis surviving as a ConstantMap, reversal as nothing but a negative stride, emptiness living in the domain, a mask being its nonzero coordinates, and fancy flavor spelled entirely by index-array shape — distinct axes for the outer product, a shared axis for pointwise). The table shows each idiom's maps; the executable matrix checks every model's shape, category, and NumPy values, then proves the selection compiler derives the same transform — after translate_domain_to, since compiled basic selections keep literal domains, a wrinkle the page now names. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): close the guide's thirteen confirmed explanation gaps An adversarial pedagogy review (five reader personas, three skeptics per finding) confirmed thirteen distinct gaps; all are closed. Rendered excerpts no longer reference invisible code: the map-kind examples' resolve helper is now shown and introduced — doubling as the guide's first statement of how a bare transform meets data — and the axis-manipulation excerpts carry their own setup. The sharpest finding, a genuine contradiction, is corrected: the guide claimed an integer index is not a ConstantMap while the pattern matrix models image[2, :] with exactly one; the responsibility now sits where the model puts it — the domain decides axes, the map only fixes a coordinate, and a broadcast is a domain axis no map consumes. The wrapper's partitioning vocabulary is introduced before use: with_parts leaves the composition snippet (it taught nothing there), 'parts' is defined in the chunk-plan section, Partition/.view/.projection/ .out_selection get an introducing sentence before the frame warning, and the integrations page states the chunks-attribute discovery its read counts silently relied on. plan_chunks' argument is described truthfully (one per-dimension grid, four-method contract, dimension_grids_from_chunks as the built-in), oindex is defined at first use, 'cover' and 'bounding hull' are defined where the dense-box policy leans on them, the reads-through-the-chunk-local-side claim now matches the code, the pattern table uses the executable's real variable names, and the guide's footer no longer skips the rest of its own collection. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the idiom matrix shows both constructor halves Each row of the idiom-to-model matrix now carries the domain beside the output maps — the complete IndexTransform model, not half of it. The redundant result-shape column folds into the domain spelling, with one sentence stating why that is no loss: the domain is the result's coordinates, so its shape is the result shape. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the idiom matrix shows complete transforms in wire form A table cell reading from_shape((4, 4)) was a receiverless method call — syntax debris, not a model. Each idiom now appears as its complete transform in the ndsel canonical body: explicit domain bounds, one output map per source dimension, nothing to squint at. The wire form also teaches for free — the dropped axis of image[2, :] is visibly the bare {"offset": 2} constant form, emptiness is visibly a zero-width bound, and outer-product versus pointwise is visibly nesting versus flat arrays. The nine bodies cannot rot: a new test pins each JSON block to transform_to_canonical of the corresponding executable model, in order. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): pattern matrix entries pair Python and JSON in tabs Each idiom now shows both spellings of its model in linked content tabs: the Python construction and the ndsel canonical body. content.tabs.link keeps every pair switched together, so a reader can walk the whole matrix in either language. The pinning test grows teeth on both sides: the JSON tab must equal the model's canonical form, and the Python tab must evaluate — in the executable matrix's own namespace — to the model itself, so neither tab can drift from the code. Assisted-by: ClaudeCode:claude-fable-5 * docs: update index * docs(zarr-indexing): state the read-only contract LazyArray never declared The wrapper defines no __setitem__, but nothing said so: the class docstring, the module docstring, the guide, and the landing page were all silent, leaving a real contract to be discovered by TypeError. The class docstring and the guide's materialization warning now state it, together with where writing does belong — a consumer plans the selection with plan_chunks and owns the read-modify-write, because chunk atomicity and concurrent-writer policy are the backend's to decide. The flip side is stated where a source is described: a wrapped array needs shape, dtype, and __getitem__ and nothing more, so a read-only source (an HTTP endpoint, a snapshot, a decoded-chunk cache) wraps as well as a writable one. Naming was considered and rejected. LazyArrayView would mislead, since a NumPy view shares memory and writes through — the opposite of the truth — and LazyReadOnlyArray names a non-capability and implies a writable sibling. Read-only-ness follows from the object being a deferred description of a read; a documented contract closes the gap that a loud, immediate TypeError already made non-silent. Assisted-by: ClaudeCode:claude-fable-5 * docs: clarify intended use * refactor(zarr-indexing)!: the types own their one serialization The canonical converters were free functions in json.py, and the reason given for that — keeping the algebra core ignorant of the wire format — did not survive inspection: importing the package already loads json.py and messages.py through __init__, so nothing was decoupled for anyone. And the usual reason to keep a type ignorant of its serialization is to avoid privileging one of several; this repo admits exactly one, spec- defined and TensorStore-compatible, whose own IndexTransform carries to_json(). So the conversions are methods now: IndexTransform.to_json/from_json, IndexDomain.to_json/from_json, and to_json on each output map kind. output_index_map_from_json stays a function, moved to output_map.py, because the wire form is a tagged union — loading it dispatches rather than belonging to any one kind. The surface shrinks rather than grows. Each conversion had two public spellings (the canonical name plus a historical *_to_json alias); both are gone, leaving one. json.py keeps the wire vocabulary — the TypedDicts and JSON type aliases — and the lowering rules the types share move to a package-private _wire.py, which is what they always were: pyright caught underscore-private helpers being read from three other modules. Assisted-by: ClaudeCode:claude-fable-5 * refactor(zarr-indexing)!: operations belong to their types, algorithms go private Applying the lesson from the serialization move to the rest of the package, and checked against TensorStore, whose split is unusually clear: its public index_space headers are the types, while every transform operation — compose_transforms, inverse_transform, transpose, translate, the slice ops — lives in internal/ and surfaces as a method. Its Python IndexTransform is all methods and no free functions. composition.py was the same defect json.py had: 242 lines, zero types, one public function over a type defined elsewhere, with its own API page as if it were a subsystem. The algorithm is now private in _composition.py and the public spelling is outer.compose(inner). selection_to_transform becomes transform.select(selection, mode), index_array_structure becomes a property, and array_map_dependent_axis becomes ArrayMap.dependent_axis — it described an ArrayMap while living in transform.py. Two smaller repairs fall out. affine.py, never exported and never documented, takes the underscore it had earned. And the dependency-axes helper that three modules read across a private boundary becomes ArrayMap.dependency_axes, which is what it always was: something a map knows about itself. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): release notes point at this PR, and describe the shipped API Three fragments carried fork PR numbers (267, 272, 273), which towncrier renders as links to zarr-developers/zarr-python issues of those numbers — unrelated upstream issues. They are this PR's work and now say so. Their contents had also aged past the code. The LazyArray note described array_map_dependent_axis, compose() and transform_from_canonical, none of which survive; the composition note named index_array_structure as a function. All now name the shipped spelling. The merged ndsel fragment already on main said index_transform_to_json and its siblings 'now produce and consume the canonical body' — true when written, but this PR removes them, and both fragments render in the same unreleased changelog, so it would have introduced and withdrawn one API in a single release. One recategorization: the note covering with_parts becoming three named methods, Partition.array becoming Partition.view, and the new equality and hashing sat under misc, whose towncrier default shows the link and discards the text — user-visible breaking changes, invisible in the changelog. Moved to removals, which also drops a duplicated #4222 link from the misc line. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): the LazyArray note is a release entry, not a manual One fragment had grown to 1844 words — two thirds of all release-note text, rendering as a single bullet. It was the PR's commit log: the feature, then nine paragraphs of defects found and fixed along the way. Those defects belong to the pull request, not the changelog. This package has never released — CHANGELOG.md holds nothing but the towncrier marker — so every one of them was a bug in code no reader could have run, and a first release that recounts them describes a journey nobody took. What remains is what the package offers, split by capability rather than by the order the work happened: LazyArray and its partitioning, source-independent chunk planning, the reader boundary, the testing subpackage, and negative-step slices. Each is scannable, and the detail they used to carry is in the guide and design notes, which they now link. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): a first release describes the package, not its development With no release before this PR merges, the Bugfixes and Deprecations sections were describing work no reader could have experienced: defects in code that never shipped, and the withdrawal of functions nobody could have imported. Both sections are gone. Their surviving content is stated as what the package offers. The algebra's types carry their own operations — composition, selection, application, classification and serialization on IndexTransform, dependency axes on ArrayMap, value semantics on all three — which is a capability, not a migration. base_shape joins the partitioning entry. The remaining entries drop the last of their before-and-after framing: a first release has no 'now', and nothing in it was 'fixed'. Assisted-by: ClaudeCode:claude-fable-5 * fix(zarr-indexing): satisfy lint rules CI enables and the pinned ruff does not CI's ruff runs a broader rule set than the version pinned in .pre-commit-config.yaml, so three violations passed locally and failed there. All three are worth fixing on their own terms rather than suppressing. The BadIndex fixtures return 2.5 from __index__ deliberately — the point is an object that violates the protocol, so the package can be shown rejecting it. PLE0305 reads that as a mistake. `cast("int", 2.5)` keeps the runtime lie the test needs while saying the lie is intentional, and drops the `# type: ignore` it needed for mypy. The stateful test imported `zarr_indexing.testing.stateful as stateful`; `from zarr_indexing.testing import stateful` is the form the rest of the suite uses, and the import block re-sorts around it. Assisted-by: ClaudeCode:claude-fable-5 * test: the root example runner forgets about zarr-indexing again It was taught to substitute a local `zarr-indexing` checkout into a PEP 723 header, but no example at the repository root declares that dependency — the three there are zarr-only — and `set_dep` leaves an undeclared one alone, so the entry never fired. The runner also globs `examples/` only, so it could never have reached the package's own examples in `packages/zarr-indexing/examples/`; the package's suite asserted as much, checking they were absent from the root. Those examples do now run, as subprocesses in the package's own `test_doc_examples.py`, which is where a package's examples belong. This restores `tests/test_examples.py` to what main has: root examples, the one local package they actually use, and no knowledge of `packages/`. Assisted-by: ClaudeCode:claude-fable-5 * docs(zarr-indexing): restore the release notes 0.1.0 users actually need zarr-indexing 0.1.0 is on PyPI, tagged at a994a4fc. Its CHANGELOG.md holds nothing but the towncrier marker — the release was cut without ever building its notes — and I read that emptiness as "never released", then deleted the Bugfixes and Deprecations sections on the grounds that nobody could have experienced them. They could. Comparing the installed 0.1.0 against this branch, ten public names disappear: compose, selection_to_transform, transform_to_canonical, transform_from_canonical, index_transform_to_json, index_transform_from_json, index_domain_to_json, index_domain_from_json, iter_chunk_transforms and sub_transform_to_selections. Every one is an import that breaks on upgrade, and the notes said nothing about any of them. The four removal fragments and the bugfix fragment are restored, and the last two removals — the provisional tuple resolver and selector bridge, which only a feature fragment had mentioned in passing — are named. The fixes that were buried in the LazyArray feature entry move to Bugfixes where they belong, as a list rather than the nine paragraphs they were. The duplicate feature entry I had written to carry the surviving API names goes, its content being what the removal entries already say from the migrating reader's side. Assisted-by: ClaudeCode:claude-fable-5 * build(zarr-indexing): the sdist ships an allowlist, not whatever is lying around hatchling had no sdist configuration, so a source distribution carried everything in the package directory. Building from a working tree with scratch files in it put eight of them in the tarball. A tagged release builds from a fresh CI checkout and so was never actually at risk, but nothing made that a property of the package rather than of the runner. The allowlist is chosen to keep an sdist able to test itself: tests/ carries the vendored ndsel conformance corpus, and test_doc_examples.py executes docs/snippets/*.py and examples/*/*.py, so those directories are part of the suite rather than documentation shipped for its own sake. Verified by unpacking the built sdist into a bare venv and running its tests there — 1058 pass, the rest skipping on optional dependencies. Assisted-by: ClaudeCode:claude-fable-5 * ci(zarr-indexing): the justfile is the single definition of each check The docs job already called `just docs-check`, and zarr-metadata's workflow runs entirely on `just`, but zarr-indexing's test, ruff and pyright jobs spelled their commands out again. Every recipe existed twice, so adding the src/ doctest collection meant editing both places, and forgetting either would have let them drift silently. They drift already. The justfile pinned ruff 0.15.22 while the repo moved to 0.16.0 in #4213 — the divergence behind this branch's lint failure — and its own comment says the two are meant to be bumped together. The pin is now 0.16.0, and because CI reads it from the justfile there is one place to bump next time. The tensorstore parity run gains the recipe it never had, so `just check` finally means what its comment claims: everything CI runs. The test job moves into the package directory to give the recipes their expected working directory, and syncs `--project ../..` so it still resolves against the repo-root environment that provides `zarr`. Verified by running every recipe CI now calls: test (1290 passed), test-tensorstore (88), lint, typecheck, docs-check. 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a/.github/workflows/zarr-indexing.yml +++ b/.github/workflows/zarr-indexing.yml @@ -26,6 +26,7 @@ jobs: defaults: run: shell: bash + working-directory: packages/zarr-indexing strategy: fail-fast: false matrix: @@ -38,16 +39,22 @@ jobs: uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 with: enable-cache: true + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 - name: Set up Python ${{ matrix.python-version }} run: uv python install ${{ matrix.python-version }} # The transform tests exercise chunk resolution against zarr's ChunkGrid, - # so they run from the repo root against the root environment (which - # provides `zarr`) with this package as an editable overlay rather than in - # package isolation. + # so they run against the repo-root environment (which provides `zarr`) + # with this package as an editable overlay rather than in package + # isolation. The recipes carry that invocation; this step only fixes the + # interpreter the matrix asked for. - name: Sync test dependency group - run: uv sync --group test --python ${{ matrix.python-version }} + run: uv sync --project ../.. --group test --python ${{ matrix.python-version }} - name: Run pytest - run: uv run --no-sync --group test --with-editable ./packages/zarr-indexing python -m pytest packages/zarr-indexing/tests + # Suites and invocation live in packages/zarr-indexing/justfile. + run: just test + - name: Run pytest (tensorstore parity) + run: just test-tensorstore ruff: name: ruff @@ -62,8 +69,11 @@ jobs: persist-credentials: false - name: Install uv uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 - name: Run ruff - run: uvx ruff check . + # The ruff version pin lives in packages/zarr-indexing/justfile. + run: just lint pyright: name: pyright @@ -84,8 +94,11 @@ jobs: run: uv python install 3.12 - name: Sync test dependency group run: uv sync --group test --python 3.12 + - name: Install just + uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v4 - name: Run pyright - run: uv run --group test --with pyright pyright src + # The pyright invocation lives in packages/zarr-indexing/justfile. + run: just typecheck docs: name: docs diff --git a/packages/zarr-indexing/CONTRIBUTING.md b/packages/zarr-indexing/CONTRIBUTING.md new file mode 100644 index 0000000000..632e24929f --- /dev/null +++ b/packages/zarr-indexing/CONTRIBUTING.md @@ -0,0 +1,27 @@ +# Contributing to zarr-indexing + +Package-scoped development commands live in the [`justfile`](./justfile) +(requires [just](https://github.com/casey/just)): + +``` +just test # run the test suite (extra args go to pytest) +just lint # ruff, same invocation as CI +just typecheck # pyright, same invocation as CI +just docs-check # strict build of the docs site +just check # all of the above +just docs-serve # serve the docs site locally +``` + +Run them from this directory, or from anywhere in the repository as +`just packages/zarr-indexing/<recipe>`. + +The test recipe runs against the workspace-root environment, because the +chunk-resolution tests exercise this package against `zarr`'s chunk grids and +`zarr` is deliberately not a dependency of this package. + +## License + +MIT + +The package lives at `packages/zarr-indexing` inside the +[zarr-python](https://github.com/zarr-developers/zarr-python) repository. diff --git a/packages/zarr-indexing/README.md b/packages/zarr-indexing/README.md index ccdfe595a5..7e2cec10dd 100644 --- a/packages/zarr-indexing/README.md +++ b/packages/zarr-indexing/README.md @@ -11,8 +11,20 @@ I/O until you explicitly read or write. Key types: +- `LazyArray` — wraps a system-memory/basic-indexing source and adds a `.lazy` + accessor: `LazyArray.from_numpy(numpy_array).lazy[10:50, ::2].lazy.oindex[[3, 1, 1], :]` + composes a transform and returns a new view without reading data, and + `result()` materializes it into owned system memory. `LazyArray(source)` uses + the conservative basic reader; `from_numpy` explicitly selects NumPy's + optimized reader. Device arrays require an explicit custom reader responsible + for transferring values into the supplied system-memory output buffer. +- `Reader` — the explicit backend execution boundary: transforms say which + values belong in the result, while readers say how a backend obtains them - `IndexDomain` — a rectangular region of integer coordinates - `IndexTransform` — maps input coordinates to storage coordinates +- `ChunkPlan` and `ChunkProjection` — lazily partition a selection over a + caller-selected grid and pair each chunk-local transform with its placement in + the request, without binding a storage backend or scheduler - `ConstantMap`, `DimensionMap`, `ArrayMap` — the three ways a single output dimension can depend on the input - `compose` — chain two transforms into one @@ -27,27 +39,14 @@ repository and consumed by `zarr` to resolve array indexing operations. pip install zarr-indexing ``` -## Developing +## Examples -Package-scoped development commands live in the [`justfile`](./justfile) -(requires [just](https://github.com/casey/just)): +- [Lazy indexing a NumPy array](examples/lazy_indexing_numpy/README.md) +- [Lazy indexing with Dask](examples/lazy_indexing_dask/README.md) -``` -just test # run the test suite (extra args go to pytest) -just lint # ruff, same invocation as CI -just typecheck # pyright, same invocation as CI -just docs-check # strict build of the docs site -just check # all of the above -just docs-serve # serve the docs site locally -``` - -Run them from this directory, or from anywhere in the repository as -`just packages/zarr-indexing/<recipe>`. - -The test recipe runs against the workspace-root environment, because the -chunk-resolution tests exercise this package against `zarr`'s chunk grids and -`zarr` is deliberately not a dependency of this package. - -## License +## Contributing -MIT +Development commands, the test suite and the docs build are described in +[CONTRIBUTING.md](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/CONTRIBUTING.md) +in the repository. Issues and pull requests go to +[zarr-developers/zarr-python](https://github.com/zarr-developers/zarr-python). diff --git a/packages/zarr-indexing/changes/3906.feature.md b/packages/zarr-indexing/changes/3906.feature.md index fa51b4438e..4a4b754bd8 100644 --- a/packages/zarr-indexing/changes/3906.feature.md +++ b/packages/zarr-indexing/changes/3906.feature.md @@ -1 +1 @@ -Reworked the JSON layer to conform to the [ndsel](https://github.com/zarr-developers/ndsel) draft wire format, which adapts TensorStore's `IndexTransform`. A new `zarr_indexing.messages` module (`parse_ndsel`, `normalize_ndsel`, `NdselError`) is a pure JSON-to-JSON layer that accepts all five message kinds (`point`/`box`/`slice`/`points`/`transform`) and normalizes them to the canonical transform body, enforcing the full ndsel error taxonomy. The package is checked against the vendored, language-agnostic ndsel conformance corpus. `index_transform_to_json`/`index_transform_from_json` (and the domain variants) now produce and consume the canonical body. On serialization, orthogonal (`oindex`) `index_array` maps no longer emit `input_dimension` alongside `index_array` (a combination both ndsel and TensorStore reject), and degenerate all-singleton index arrays collapse to constant maps; the in-memory `input_dimension` is reconstructed from the array's dependency axes on load. +Reworked the JSON layer to conform to the [ndsel](https://github.com/zarr-developers/ndsel) draft wire format, which adapts TensorStore's `IndexTransform`. A new `zarr_indexing.messages` module (`parse_ndsel`, `normalize_ndsel`, `NdselError`) is a pure JSON-to-JSON layer that accepts all five message kinds (`point`/`box`/`slice`/`points`/`transform`) and normalizes them to the canonical transform body, enforcing the full ndsel error taxonomy. The package is checked against the vendored, language-agnostic ndsel conformance corpus. Serialization produces and consumes the canonical body (`IndexTransform.to_json`/`from_json`, and the `IndexDomain` pair). On serialization, orthogonal (`oindex`) `index_array` maps no longer emit `input_dimension` alongside `index_array` (a combination both ndsel and TensorStore reject), and degenerate all-singleton index arrays collapse to constant maps; the in-memory `input_dimension` is reconstructed from the array's dependency axes on load. diff --git a/packages/zarr-indexing/changes/4222.bugfix.1.md b/packages/zarr-indexing/changes/4222.bugfix.1.md new file mode 100644 index 0000000000..8cff5be6e4 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.bugfix.1.md @@ -0,0 +1,39 @@ +Correctness fixes to indexing and resolution, all reachable from 0.1.0: + +- An integer index applied to an axis a previous `oindex`/`vindex` step had + already indexed left an all-singleton `ArrayMap` still naming the axis the + integer removed, which after renumbering aliased a different one. Such a map + now collapses to a `ConstantMap` at composition time. +- A `vindex` selection whose coordinate arrays are not on the leading axes + (`vindex[..., i, j]`, `vindex[..., mask]`) laid out its result incorrectly and + raised a shape mismatch on a partitioned read. Gathered dimensions now follow + NumPy's placement rule, and the per-part gather is realigned to the scatter. +- An `oindex`/`vindex` step whose entries are all slices, applied to a view with + a fancy-indexed axis, applied those slices positionally to every axis of the + existing index array — including broadcast singletons — truncating it to size + 0, so `result()` returned an unwritten buffer. Reindexing is now + dependency-aware. +- `parts()` raised on a view emptied by a slice over an axis of extent 1; an + empty domain now yields no parts, matching `result()`. +- Negative-stride chunk projection swapped the endpoints while keeping the step + negative, selecting nothing where the reversed axis was meant. Composition + evaluated an inner index array over `range(size)` rather than the outer + domain's own range, resolving every coordinate wrongly whenever that domain + did not start at 0 — which both step-1 and negative-step slices produce. +- A domain dimension no output map depends on, left behind when a later basic + index consumes the axis a `vindex` array varied over, was miscounted in three + places: the partition walk's out-selection rank, the lowering engine's axis + restoration, and the correlated gather's broadcast. +- The parts of a correlated view narrowed to a single point came back rank 1 + where the view was rank 0, so the documented + `out[part.out_selection] = part.view.result()` assembly raised `ValueError`. +- `result()` could return memory shared with the wrapped array: an unpartitioned + read of a basic selection lowered to plain slicing and handed back a view of + the source, and `numpy.array(view, copy=True)` inherited the alias. It now + always allocates, and verifies the parts covered the output before returning. +- `IndexTransform.from_json` rejects a non-integer `index_array` with an + `NdselError` carrying `invalid_json`, rather than truncating a float array, + coercing booleans, or leaking NumPy's conversion error for strings. +- `result(parts=...)` raises `ValueError` rather than `AssertionError` when the + supplied parts do not tile the view, and `with_parts` / `with_parts_per_axis` + raise the documented `ValueError` for non-iterable input. diff --git a/packages/zarr-indexing/changes/4222.bugfix.md b/packages/zarr-indexing/changes/4222.bugfix.md new file mode 100644 index 0000000000..0717e1e384 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.bugfix.md @@ -0,0 +1,9 @@ +An adversarial review of the whole package found, and this fixes, several +defects at its boundaries: `result()` and `__array__(copy=True)` could hand back +a live view of a source that merely stored its data in NumPy; the wire format +emitted a document nothing could load for a selection that selects nothing, and +its domain loader validated nothing; chunk-selection lowering described a +transposed block in two separate cases; a map derived from a vectorized +selection carried a stale `input_dimension`, which made one view's answer depend +on how it was partitioned; and `oindex` over a correlated view applied NumPy's +vectorized rule instead of the outer product. diff --git a/packages/zarr-indexing/changes/4222.feature.1.md b/packages/zarr-indexing/changes/4222.feature.1.md new file mode 100644 index 0000000000..bc62baf357 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.feature.1.md @@ -0,0 +1,7 @@ +Added `UnitStepReader` / `unit_step_reader`: a backend adapter for sources +whose basic indexing accepts only ascending step-1 slices (FFI bindings, HTTP +range endpoints). Every key it presents is `slice(start, stop, 1)` per axis; +strides, reversals, and gathers are applied to the in-memory block by the +residual lowering. The integrations guide documents the companion dense-box +re-partition idiom — resolving a unit-stride rectangular view as one backend +slab read while keeping partitioned reads for strided and fancy selections. diff --git a/packages/zarr-indexing/changes/4222.feature.2.md b/packages/zarr-indexing/changes/4222.feature.2.md new file mode 100644 index 0000000000..722f56db99 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.feature.2.md @@ -0,0 +1,24 @@ +Added `LazyArray`, which grafts the full NumPy indexing dialect onto any source +exposing `shape`, `dtype`, and basic integer/slice `__getitem__` — a chunked +store, an FFI binding, an HTTP endpoint. `view.lazy[...]`, `.lazy.oindex[...]` +and `.lazy.vindex[...]` each compose an `IndexTransform` and return a new view +without reading anything; `result()` materializes. Selections use positional +NumPy semantics (negatives wrap, scalars drop their axis, coordinate arrays keep +order and duplicates), which the new `zarr_indexing.boundary` module translates +into the algebra's literal coordinates. The wrapper describes reads only, and +behaves as a duck array: eager `__getitem__` and `__array__` make it a +`dask.array.from_array` source. + +A read is divided along a **partitioning** — discovered from the wrapped array, +or chosen with `with_parts` / `with_parts_per_axis` / `unpartitioned`. +`parts()` yields one `Partition` per box, pairing a resolvable sub-view with +where its cells belong in the result; `result()` is the assembly of that walk, +and re-partitioning never changes what it returns. `base_shape` says which shape a partitioning is expressed in. `is_box`, `bounding_box()` +and `strides()` report whether a selection is rectangular, so a consumer can +dispatch a slab read against a gather. + +See the [guide](https://zarr-indexing.readthedocs.io/en/latest/guide/) for the +model and the +[design notes](https://zarr-indexing.readthedocs.io/en/latest/design-notes/) +for the box/query distinction, the relationship to TensorStore, and current +scope limits. diff --git a/packages/zarr-indexing/changes/4222.feature.3.md b/packages/zarr-indexing/changes/4222.feature.3.md new file mode 100644 index 0000000000..ef0e1512c2 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.feature.3.md @@ -0,0 +1,9 @@ +Added source-independent chunk planning. `plan_chunks(transform, grids)` returns +a lazy, reusable `ChunkPlan` whose `ChunkProjection`s each pair a chunk-local +transform with a transform back to the request, over one shared cell domain, so +a consumer can read a chunk and place its values without re-deriving either. The +same representation covers basic, orthogonal and vectorized indexing, and +carries global chunk bounds plus conservative full/partial/unknown coverage. +I/O, buffering and scheduling stay with the consumer. `zarr_indexing.grid` gained +`EdgeDimensionGrid` and `dimension_grids_from_chunks` for building the per-axis +grids it takes. diff --git a/packages/zarr-indexing/changes/4222.feature.4.md b/packages/zarr-indexing/changes/4222.feature.4.md new file mode 100644 index 0000000000..623d381083 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.feature.4.md @@ -0,0 +1,8 @@ +`LazyArray` has an explicit reader boundary: an `IndexTransform` decides which +values belong in a result, and a `Reader` decides how one backend obtains them, +preserving the transform exactly. `LazyArray(source)` is conservative and assumes +only basic indexing; `LazyArray.from_numpy(array)` selects the optimized NumPy +reader; `with_reader` selects any other. Readers do not define indexing +semantics, partitioning, scheduling, or result ownership. Both built-in readers +lower through NumPy system memory, so a device array needs a custom reader that +transfers into the supplied output buffer. diff --git a/packages/zarr-indexing/changes/4222.feature.5.md b/packages/zarr-indexing/changes/4222.feature.5.md new file mode 100644 index 0000000000..859667775f --- /dev/null +++ b/packages/zarr-indexing/changes/4222.feature.5.md @@ -0,0 +1,8 @@ +Added the `zarr_indexing.testing` subpackage, behind a `testing` extra +(`pip install zarr-indexing[testing]`), carrying the Hypothesis machinery this +package tests itself with. `ChainedIndexingStateMachine` composes basic, +orthogonal and vectorized selections onto a `LazyArray` wrapping an array you +supply, then checks every view's shape, `result()`, and assembled `parts()` +against NumPy; `zarr_indexing.testing.strategies` exports the selection +strategies alone, for a project with its own harness. Nothing outside the +subpackage imports Hypothesis. diff --git a/packages/zarr-indexing/changes/4222.feature.6.md b/packages/zarr-indexing/changes/4222.feature.6.md new file mode 100644 index 0000000000..8c65f947e6 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.feature.6.md @@ -0,0 +1,9 @@ +Negative-step slices are supported, following merged ndsel 1.0-draft.2 and +TensorStore 0.1.84: `arr[::-1]`, `arr[5:1:-2]`, and reversal composed over an +already-strided or already-gathered view. One desugaring rule covers both signs — +omitted bounds resolve on the side the traversal starts and stops, and the origin +is `trunc(start / step)` — while a reversed interval is an error rather than a +silently empty selection. A reversing slice normally yields a negative domain +origin, since the result stays anchored to the source coordinate frame; +`LazyArray` re-bases every view to origin 0, so its positional dialect is +unaffected. diff --git a/packages/zarr-indexing/changes/4222.feature.md b/packages/zarr-indexing/changes/4222.feature.md new file mode 100644 index 0000000000..c02ab54edb --- /dev/null +++ b/packages/zarr-indexing/changes/4222.feature.md @@ -0,0 +1,11 @@ +Fancy selections compose without restriction, on both `LazyArray` and +`IndexTransform`: a second `oindex`/`vindex`/mask step may land on any axis of +an already-fancy view, including axes an existing index array merely broadcasts +along. Array-carrying transforms are chained through `compose`, and resolution +handles the resulting mixed, correlated and diagonal index-array structures on +one shared pointwise path, classified by `IndexTransform.index_array_structure`. +Only hand-built affine diagonals — an index array and a slice map bound to the +same axis — remain unsupported. + +`__dask_tokenize__` digests a view's canonical transform body rather than +embedding it, so tokens stay small for large fancy selections. diff --git a/packages/zarr-indexing/changes/4222.misc.md b/packages/zarr-indexing/changes/4222.misc.md new file mode 100644 index 0000000000..1bd73e1c80 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.misc.md @@ -0,0 +1,5 @@ +Restructured the documentation-contract tests: the snippet include graph is +now discovered by scanning the rendered markdown instead of hand-maintained +registries, prose and navigation assertions moved out of CI, and +`pymdownx.snippets` now sets `check_paths: true` so an unresolvable include +fails `mkdocs build --strict` instead of silently rendering nothing. diff --git a/packages/zarr-indexing/changes/4222.removal.1.md b/packages/zarr-indexing/changes/4222.removal.1.md new file mode 100644 index 0000000000..33ff9cb423 --- /dev/null +++ b/packages/zarr-indexing/changes/4222.removal.1.md @@ -0,0 +1,12 @@ +The canonical JSON converters are now methods on the types that own the +serialization: `IndexTransform.to_json()` / `IndexTransform.from_json()`, +`IndexDomain.to_json()` / `IndexDomain.from_json()`, and `to_json()` on each +output map kind. `output_index_map_from_json` remains a function, in +`zarr_indexing.output_map`, because the wire form is a tagged union and +loading it dispatches rather than belonging to any one kind. + +The free functions they replace — `transform_to_canonical`, +`transform_from_canonical`, `index_domain_to_json`, `index_domain_from_json`, +`output_index_map_to_json`, and the historical aliases +`index_transform_to_json` / `index_transform_from_json` — are removed. There +had been two spellings of each conversion; there is now one. diff --git a/packages/zarr-indexing/changes/4222.removal.2.md b/packages/zarr-indexing/changes/4222.removal.2.md new file mode 100644 index 0000000000..d3321ea81c --- /dev/null +++ b/packages/zarr-indexing/changes/4222.removal.2.md @@ -0,0 +1,15 @@ +Operations moved onto the types that own them, following the arrangement +TensorStore uses (public headers are the types; every transform operation +lives in `internal/` and surfaces as a method): + +- `compose(outer, inner)` is now `outer.compose(inner)`, and the algorithm + moved to the private `zarr_indexing._composition`. +- `selection_to_transform(selection, transform, mode)` is now + `transform.select(selection, mode)`. +- `index_array_structure(transform)` is now the `transform.index_array_structure` + property. +- `array_map_dependent_axis(m)` is now the `ArrayMap.dependent_axis` property, + alongside a new `ArrayMap.dependency_axes` giving every axis a map varies over. + +`zarr_indexing.affine` is now the private `zarr_indexing._affine`; it was +never exported or documented. diff --git a/packages/zarr-indexing/changes/4222.removal.3.md b/packages/zarr-indexing/changes/4222.removal.3.md new file mode 100644 index 0000000000..d5210f4c8d --- /dev/null +++ b/packages/zarr-indexing/changes/4222.removal.3.md @@ -0,0 +1,6 @@ +`with_parts` is now three named methods — `with_parts`, `with_parts_per_axis` +and `unpartitioned` — instead of one parameter whose meaning was decided by the +type of what it was given. `Partition.array` is `Partition.view`, no longer the +inverse of `LazyArray.array`. `ArrayMap`, `IndexTransform` and `Partition` can +be compared and hashed, which `frozen=True` had implied and neither could do. +`LazyArray.base_shape` says which shape a partitioning is expressed in. diff --git a/packages/zarr-indexing/changes/4222.removal.md b/packages/zarr-indexing/changes/4222.removal.md new file mode 100644 index 0000000000..5782c9ab4d --- /dev/null +++ b/packages/zarr-indexing/changes/4222.removal.md @@ -0,0 +1,11 @@ +`ArrayMap` no longer has an `input_dimension` field: what a map depends on is +read from its full-rank index array's shape (its non-singleton axes), the +single source of truth. A selection narrowed to a single coordinate is now +built as the `ConstantMap` it equals (`array_map_or_constant`), so a length-1 +fancy selection classifies as a box; hand-built all-singleton or shared-axis +`ArrayMap`s resolve through the pointwise path. The wire format is unaffected — +it never carried the field. + +The provisional tuple resolver and selector bridge are gone with it: +`iter_chunk_transforms` and `sub_transform_to_selections` are removed, their +role taken by `plan_chunks` and the paired projections it returns. diff --git a/packages/zarr-indexing/docs/api/boundary.md b/packages/zarr-indexing/docs/api/boundary.md new file mode 100644 index 0000000000..4f9fa99531 --- /dev/null +++ b/packages/zarr-indexing/docs/api/boundary.md @@ -0,0 +1,5 @@ +--- +title: boundary +--- + +::: zarr_indexing.boundary diff --git a/packages/zarr-indexing/docs/api/composition.md b/packages/zarr-indexing/docs/api/composition.md deleted file mode 100644 index 59affe016c..0000000000 --- a/packages/zarr-indexing/docs/api/composition.md +++ /dev/null @@ -1,5 +0,0 @@ ---- -title: composition ---- - -::: zarr_indexing.composition diff --git a/packages/zarr-indexing/docs/api/grid.md b/packages/zarr-indexing/docs/api/grid.md index c4c9cadb4f..b7c376eb85 100644 --- a/packages/zarr-indexing/docs/api/grid.md +++ b/packages/zarr-indexing/docs/api/grid.md @@ -2,4 +2,21 @@ title: grid --- +`zarr_indexing.grid` owns compact chunk-grid metadata so indexing plans can be +constructed without importing Zarr. `FixedDimension(size, extent)` represents +regular chunks in constant memory, including a clipped final data region; +`VaryingDimension(edges, extent)` represents explicit rectilinear chunk edges. +`ChunkGrid(dimensions=...)` combines these dimensions and returns `ChunkSpec` +objects whose `shape` is the valid data size and whose `codec_shape` preserves +the full codec-buffer size at a regular-grid boundary. + +`dimension_grids_from_chunks` returns these compact dimensions: integer chunk +shapes become `FixedDimension` instances and explicit per-axis edge sequences +become `VaryingDimension` instances. `DimensionGridLike` remains the narrow +protocol used by the chunk planner, while `EdgeDimensionGrid` is kept for +explicit edge-based and coordinate-origin examples. + +Zarr's array implementation can later import these compact grid types from +`zarr_indexing`; this package intentionally has no import dependency on Zarr. + ::: zarr_indexing.grid diff --git a/packages/zarr-indexing/docs/api/index.md b/packages/zarr-indexing/docs/api/index.md index b9a58b70fa..674c701a0f 100644 --- a/packages/zarr-indexing/docs/api/index.md +++ b/packages/zarr-indexing/docs/api/index.md @@ -4,6 +4,19 @@ title: API reference # API reference +Choose the guide stopping point that matches your job before following module +links: + +- **Use lazy indexing:** finish + [Lazy views compose](../guide/index.md#lazy-views-compose), + then open [`zarr_indexing.lazy_array`](lazy_array.md) for `LazyArray`. +- **Integrate a chunked source:** finish + [One cell domain, two projections](../guide/index.md#one-cell-domain-two-projections), + then open [`zarr_indexing.chunk_resolution`](chunk_resolution.md) for + `plan_chunks`. Start with + [Coordinates are addresses](../guide/index.md#coordinates-are-addresses) if + literal coordinates are unfamiliar. + The modules are layered: the transform algebra at the bottom, chunk resolution and the wire format built on top of it. @@ -17,18 +30,33 @@ and the wire format built on top of it. - [`zarr_indexing.transform`](transform.md) — `IndexTransform`, which pairs a domain with output maps, plus the indexing (`[...]`, `.oindex`, `.vindex`), `intersect`, and `translate` operations, and `selection_to_transform` -- [`zarr_indexing.composition`](composition.md) — `compose`, which chains two transforms into one **Chunk resolution** - [`zarr_indexing.chunk_resolution`](chunk_resolution.md) — - `iter_chunk_transforms` (transform + chunk grid → per-chunk transforms) and - `sub_transform_to_selections` (the bridge back to the selection tuples the - current codec pipeline expects) + `plan_chunks`, which lazily projects a request through a caller-selected grid, + plus the reusable `ChunkPlan` and paired-transform `ChunkProjection` values - [`zarr_indexing.grid`](grid.md) — `DimensionGridLike`, the Protocol describing the narrow chunk-grid surface chunk resolution consumes, so that - nothing here imports `zarr` + nothing here imports `zarr`, plus `EdgeDimensionGrid` and + `dimension_grids_from_chunks`, a concrete per-axis grid for callers with no + zarr grid to hand + +**Lazy arrays** + +- [`zarr_indexing.lazy_array`](lazy_array.md) — `LazyArray`, a wrapper for + system-memory/basic-indexing sources that adds a `.lazy` accessor for + TensorStore-style deferred indexing, plus `Partition` and `parts()` / + `with_parts()`, which determine the boxes a read is broken into. Device + sources require an explicit custom reader that transfers into the supplied + system-memory output +- [`zarr_indexing.reader`](reader.md) — `Reader`, the backend execution boundary + that obtains the values described by a complete transform; `basic_reader` + serves conservative duck arrays and `numpy_reader` is selected explicitly by + `LazyArray.from_numpy` +- [`zarr_indexing.boundary`](boundary.md) — the translation between NumPy's + positional dialect and the transform algebra's literal coordinates **The ndsel wire format** (see [the guide](../ndsel.md)) @@ -39,9 +67,21 @@ and the wire format built on top of it. **Errors** -- [`zarr_indexing.errors`](errors.md) — the canonical index-error types, which - `zarr.errors` re-exports by identity +- [`zarr_indexing.errors`](errors.md) — the index-error types this package + raises, also exported at the top level. `zarr.errors` defines classes of the + same names, which are different objects; both subclass `IndexError` + +**Test support** (needs the `testing` extra) + +- [`zarr_indexing.testing.stateful`](testing_stateful.md) — + `ChainedIndexingStateMachine`, a Hypothesis state machine that composes + indexing steps onto a `LazyArray` wrapping your array and checks every step + against NumPy, plus `apply_selection`, the NumPy model it checks against +- [`zarr_indexing.testing.strategies`](testing_strategies.md) — the selection + strategies the machine draws from, for a project that has its own harness Every name listed in `zarr_indexing.__all__` is re-exported at the top level, so `from zarr_indexing import IndexTransform` and `from zarr_indexing.transform import IndexTransform` are equivalent. +`zarr_indexing.testing` is deliberately not among them: it imports +`hypothesis`, which the rest of the package does not. diff --git a/packages/zarr-indexing/docs/api/lazy_array.md b/packages/zarr-indexing/docs/api/lazy_array.md new file mode 100644 index 0000000000..f855511d46 --- /dev/null +++ b/packages/zarr-indexing/docs/api/lazy_array.md @@ -0,0 +1,27 @@ +--- +title: lazy_array +--- + +`LazyArray.lazy[...]` is metadata-only: every derived view keeps the same +reader and composes its transform without reading data. `result()` allocates +owned system memory, then calls that reader once for each projected part. +Rectangular parts write directly into their final slices; advanced placement +may first use an owned dense temporary. `LazyArray(source)` assumes only basic +indexing, while `LazyArray.from_numpy(array)` explicitly selects NumPy's +optimized reader. + +The built-in readers lower through NumPy system memory and support sources +whose basic reads can be converted there. They do not implicitly transfer +device arrays; a device source needs an explicit custom reader that transfers +into the supplied system-memory output. Derived views and parts share their +reader and part views may be materialized concurrently, so stateful readers +must synchronize their own mutable state. + +Every public `Partition.view.transform` directly maps that view's zero-origin +coordinates into its raw `Partition.view.array`, including for non-first +partitions. `Partition.projection.chunk_transform` intentionally stays local to +the selected chunk. During materialization the reader receives both frames in +one `ReadContext`: the public global transform in `context.transform` and the +same local plan in `context.projection`. + +::: zarr_indexing.lazy_array diff --git a/packages/zarr-indexing/docs/api/reader.md b/packages/zarr-indexing/docs/api/reader.md new file mode 100644 index 0000000000..39129c4d47 --- /dev/null +++ b/packages/zarr-indexing/docs/api/reader.md @@ -0,0 +1,51 @@ +--- +title: Readers +--- + +# Readers + +An `IndexTransform` defines which source value belongs at every result +position. A `Reader` defines how a particular backend obtains those values. +Readers do not define indexing semantics, partitioning, scheduling, or result +ownership. + +`Reader.read_into(source, context, out)` receives a `ReadContext` whose +`transform` maps zero-origin output-buffer coordinates to global coordinates in +`source`, with `context.transform.domain.shape == out.shape`. Its optional +`projection` is the existing plan for a partitioned read. The projection's +`chunk_transform` remains chunk-local, its `cell_transform` describes result +placement, and its `chunk_domain` describes the grid cell. The global read +transform and the projection's chunk transform deliberately use different +coordinate frames. + +An implementation must fill every cell of `out` in place, preserve the global +transform's exact values, order, and dtype, and return `None`. It must neither +replace nor retain `out`, which may be a strided writable view. Backend +exceptions propagate unchanged. Derived part views share their reader and may +be resolved concurrently, so a stateful reader owns its own synchronization. + +Reader wrappers compose by intercepting this one operation and forwarding the +same source, context, and output buffer to an inner reader: + +```python +class RecordingReader: + def __init__(self, inner): + self.inner = inner + self.calls = [] + + def read_into(self, source, context, out, /): + self.calls.append((source, context, out)) + self.inner.read_into(source, context, out) + + +inner = RecordingReader(numpy_reader) +outer = RecordingReader(inner) +view = LazyArray.from_numpy(array).with_reader(outer) +values = view.result() +``` + +Both wrappers observe the same three objects, in outer-to-inner order. This +delegation pattern supports policies such as logging and caching without +library-defined wrapper primitives. + +::: zarr_indexing.reader diff --git a/packages/zarr-indexing/docs/api/testing_stateful.md b/packages/zarr-indexing/docs/api/testing_stateful.md new file mode 100644 index 0000000000..0aeb57df29 --- /dev/null +++ b/packages/zarr-indexing/docs/api/testing_stateful.md @@ -0,0 +1,5 @@ +--- +title: testing.stateful +--- + +::: zarr_indexing.testing.stateful diff --git a/packages/zarr-indexing/docs/api/testing_strategies.md b/packages/zarr-indexing/docs/api/testing_strategies.md new file mode 100644 index 0000000000..1dd7d59457 --- /dev/null +++ b/packages/zarr-indexing/docs/api/testing_strategies.md @@ -0,0 +1,5 @@ +--- +title: testing.strategies +--- + +::: zarr_indexing.testing.strategies diff --git a/packages/zarr-indexing/docs/api/transform.md b/packages/zarr-indexing/docs/api/transform.md index bd754f5ec5..8e67a162c1 100644 --- a/packages/zarr-indexing/docs/api/transform.md +++ b/packages/zarr-indexing/docs/api/transform.md @@ -2,4 +2,17 @@ title: transform --- +An `IndexTransform` is a function between coordinate spaces, and its field +names follow the function, not the data: + +| the API says | in array terms | +| --- | --- | +| input space (`domain`, `input_rank`) | request coordinates — the result being built | +| output space (`output`, one map per dimension) | source coordinates — where values are read | + +`output` is not data: it is the rule, per source dimension, for producing +coordinates. Values flow source → request, against the arrow. The +[guide](../guide/index.md#a-transform-points-from-the-request-to-the-source) +demonstrates each output map form against its NumPy counterpart. + ::: zarr_indexing.transform diff --git a/packages/zarr-indexing/docs/design-notes.md b/packages/zarr-indexing/docs/design-notes.md new file mode 100644 index 0000000000..78b352d376 --- /dev/null +++ b/packages/zarr-indexing/docs/design-notes.md @@ -0,0 +1,296 @@ +--- +title: Design notes +--- + +# Design notes + +This page records advanced rationale that the API does not state directly: how +this library relates to TensorStore, why rectangular selections are a category +rather than a fast path, and what is deliberately not implemented yet. The +visual guide owns the mechanics of +[literal coordinates](guide/index.md#coordinates-are-addresses), +[view composition](guide/index.md#lazy-views-compose), +[chunk plans](guide/index.md#a-request-becomes-a-chunk-plan), and +[their paired projections](guide/index.md#one-cell-domain-two-projections). + +## Relationship to TensorStore + +The core is [TensorStore's](https://google.github.io/tensorstore/index_space.html) +index-transform model, reimplemented in Python against NumPy. The visual guide +introduces the shared model in +[Coordinates are addresses](guide/index.md#coordinates-are-addresses) and +[Lazy views compose](guide/index.md#lazy-views-compose); the comparison here is +about the deliberately matching semantics: + +- **The model.** Both use an `IndexTransform` made of an input domain and one + output index map per storage dimension, in constant, affine, and index-array + forms. +- **Slice semantics.** Slice bounds are literal domain coordinates: no + clamping, no negative wrapping, non-empty intervals must be contained in the + domain, and a strided slice's domain origin is `trunc(start/step)` rounded + toward zero. Every one of those rules was executed against tensorstore 0.1.84 + and is pinned in `tests/test_tensorstore_parity.py`. +- **The wire format.** A canonical [ndsel](ndsel.md) transform body is, + field-for-field, a TensorStore `IndexTransform` minus the `kind` + discriminator, and `tests/test_ndsel_tensorstore.py` loads our bodies into + `tensorstore.IndexTransform(json=...)` and round-trips them back through our + engine layer. + +The representations differ in one place: index arrays. Both models want an index +array at the transform's full input rank, with singleton axes for the dimensions +a map does not vary over. TensorStore enforces it — its JSON parser rejects a +rank-1 array over a rank-2 domain outright, with `Index array for output +dimension 0 has rank 1 but must have rank 2` (checked against tensorstore +0.1.84) — while our loader is the more permissive of the two and also accepts a +lower-rank array that broadcasts against the input domain. That is a +compatibility affordance, not a difference in the model: ndsel leaves index-array +rank to [the engine layer](ndsel.md#lowering-to-a-transform), and everything the +algebra builds itself is at full rank. + +The reason full rank matters here is that we *derive* meaning from those +singletons rather than merely tolerating them: an array full-sized on one axis +and singleton elsewhere is orthogonal, and one varying over several shared axes +is vectorized, so the distinction is readable off the shape — and the shape is +the *only* place it lives. An earlier `ArrayMap.input_dimension` field pinned +the orthogonal axis redundantly and was retired: the one shape it disambiguated +(a single-coordinate array, all axes singleton) is now normalized away at +construction, collapsed to the `ConstantMap` it equals, exactly as +[the serializer](api/json.md) has always collapsed it on the wire. + +Four deliberate differences: + +| | TensorStore | `zarr-indexing` | +| --- | --- | --- | +| Dialect | One strict dialect everywhere: literal coordinates, no negative wrapping | The algebra keeps that dialect; each public boundary picks its own. [`LazyArray`](api/lazy_array.md) speaks positional NumPy, `zarr.Array.lazy` speaks literal. [`zarr_indexing.boundary`](api/boundary.md) is the translation | +| Scheduling | An internal C++ scheduler owns concurrency and chunk ordering | [`parts()`](api/lazy_array.md) exposes the partition structure so the caller's own scheduler — dask, a thread pool, a task queue — drives it | +| Wire format | Implementation-defined JSON, specified by what the implementation accepts | [ndsel](ndsel.md) is spec-first, with a vendored language-agnostic conformance corpus every implementation runs | +| Backends | A driver ecosystem (zarr, N5, neuroglancer, GCS, …) built into the library | No drivers. The default reader needs `shape`, `dtype`, basic integer/slice indexing, and selected slabs convertible to NumPy system memory; other backends use explicit custom readers. A device reader owns transfer into the supplied system-memory output | + +The mechanics of a +[chunk plan](guide/index.md#a-request-becomes-a-chunk-plan) and its +[paired projections](guide/index.md#one-cell-domain-two-projections) belong to +the visual guide. +The relevant comparison is that both libraries use the paired-transform +boundary rather than a read key plus scatter indices, so slices, outer products, +and correlated gathers remain ordinary transforms that a consumer can lower to +its own execution vocabulary. + +The ownership boundary differs. `plan_chunks` retains only the logical request +and caller-supplied grid; it does not own reads, writes, buffers, locks, or +scheduling. Zarr can therefore plan reads against an inner codec-chunk grid and +writes against an atomic shard grid; napari or dask can turn the same +projections into tasks without putting a dask dependency in this package. +`coverage` is relative to that selected grid: `full` proves a blind replacement +safe, `partial` proves it is not, and `unknown` conservatively covers fancy +selections whose duplicates would require additional work to classify. + +The comparison also runs the other way. TensorStore is a mature, heavily +optimized C++ system whose performance this library cannot approach: resolution +here is Python-level bookkeeping over NumPy, and the per-part overhead is +significant. This library is small and depends on nothing beyond NumPy, so the +algebra can be adopted by a Python project that wants the model without the C++ +runtime. + +## Bounding-box selections vs query selections + +Every selection this library can express falls into exactly one of two +categories. The boundary between them is structural, not a heuristic: + +**A box** is a transform whose output maps are all `ConstantMap` or +`DimensionMap` — no `ArrayMap`. Such a map is affine and monotone: storage +coordinate `offset + stride * i` for `i` running over an interval. The whole +selection is therefore described by `O(ndim)` integers — an interval and a +stride per dimension — composition and intersection are interval arithmetic, +and the coordinates it touches form a regular lattice. Basic indexing produces +one, and composing basic indexing with basic indexing keeps one. + +**A query** is a transform with at least one `ArrayMap` — an explicit lookup +table of coordinates. It costs `O(n)` to store, it has no locality (the +coordinates may repeat, reverse, or scatter arbitrarily), and intersecting it +with a region means scanning it. `oindex`, `vindex`, and boolean masks all +produce one, and once an axis is a query, subsequent basic indexing cannot make +it a box again. A second query composes onto any axis of an existing one — +including the axes it merely broadcasts along — by evaluating the existing +lookup tables at the new coordinates. + +Those coordinate arrays are ordered sequences, never mathematical sets. Their +order and duplicate entries are part of the indexing semantics and must survive +planning and materialization. + +[ndsel](ndsel.md) encodes the same split in its message kinds: `point`, `box`, +and `slice` desugar to constant and affine output maps and are always boxes; +`points` desugars to `index_array` maps, and a `transform` body is a box +exactly when none of its output maps carries an `index_array`. A consumer can +therefore classify a selection off the wire without materializing anything: + +```python +from zarr_indexing import IndexTransform + +IndexTransform.from_shape((100, 80))[10:50, ::4].to_json()["output"] +# [{'offset': 0, 'stride': 1, 'input_dimension': 0}, +# {'offset': 0, 'stride': 4, 'input_dimension': 1}] + +import numpy as np +gather = IndexTransform.from_shape((100, 80)).oindex[np.array([90, 3, 3]), slice(None)] +gather.to_json()["output"][0] +# {'offset': 0, 'stride': 1, 'index_array': [[90], [3], [3]], +# 'index_array_bounds': ['-inf', '+inf']} +``` + +The distinction matters to consumers of a selection. A box can be tiled into +rectangular dask chunks or passed to a viewer or tile server that only accepts +rectangles; a query cannot, and has to be resolved into a gather. A box can also +be served as a single strided slab read, but the read has to be strided: reading +its bounding box and discarding the rest transfers proportionally more data as +soon as any stride exceeds 1. The two also behave differently under +partitioning: a box touches a regularly-spaced run of parts, in increasing +order, each at most once — a stride larger than a part's extent skips parts +outright, so the run is not contiguous — while a query can touch any subset of +them, in any order, more than once. + +[`LazyArray`](api/lazy_array.md) exposes the category directly: + +```python +import numpy as np +import zarr + +from zarr_indexing import LazyArray + +arr = zarr.create_array({}, shape=(100, 80), chunks=(30, 40), dtype="int32") +arr[:] = np.arange(8000).reshape(100, 80) +lazy = LazyArray(arr) + +slab = lazy.lazy[10:50, ::4] +slab.is_box # True +slab.bounding_box() # ((10, 50), (0, 77)) +slab.strides() # (1, 4) +slab.shape # (40, 20) + +gather = lazy.lazy.oindex[[90, 3, 3], :] +gather.is_box # False +gather.bounding_box() # ((3, 91), (0, 80)) +gather.strides() # None +gather.shape # (3, 80) +``` + +`bounding_box()` is defined for both: it is the hull, the smallest interval per +storage dimension containing every coordinate the selection reaches. +`strides()` is defined only for a box and gives the step per dimension. +Together the two describe a box selection completely. + +Both are needed, because a box is dense in its hull only when every stride is +1. The slab above spans a 40x77 hull over the 40x20 cells it selects, so a +consumer that issued one rectangular read of the hull and discarded the rest +would transfer 3.85x the data. A query's hull is looser still and carries no +stride at all: 88 rows of hull over three selected rows. An empty *box* touches +no coordinate to report an interval around, so `bounding_box()` is `None` while +`strides()` still answers — the step is a property of the selection's shape, not +of the region it reaches. Only a query returns `None` from both. + +There is deliberately no separate `BoxView` type today. A statically-typed +rectangular-only view is a plausible next step, but it should be introduced by +a consumer that needs the guarantee in its signatures rather than +speculatively; `is_box` is the runtime check until then. + +## Negative-origin domains and prependable grids + +Literal coordinates let a domain grow at its lower end without changing the +identity of anything already present. Prepending three cells extends `[0, 6)` +to `[-3, 6)`: the new cells receive addresses `-3`, `-2`, and `-1`, while the +old cells keep addresses `0` through `5`. Coordinate `0` does not become +coordinate `3`. + +The adjacent intervals `[-3, 0)`, `[0, 3)`, and `[3, 6)` follow the half-open +adjacency rule: each stopping boundary is included exactly once as the next +interval's starting boundary. + +```text +before [0, 6): + + | 0 1 2 | 3 4 5 | +chunk coordinate | 0 | 1 | + +after [-3, 6): + +| -3 -2 -1 | 0 1 2 | 3 4 5 | +| -1 | 0 | 1 | chunk coordinate +``` + +The same holds for chunk grids. `EdgeDimensionGrid` is the convenient +concrete grid for a zero-origin array: its chunk offsets are prefix sums +starting at zero. `DimensionGridLike` is the more general protocol consumed +by chunk planning, so it admits grids with negative chunk and cell +coordinates, including this prependable example: + +```python +--8<-- "snippets/coordinate_origins.py:prepend-grid" +``` + +Here the literal cell domain `[-3, 0)` belongs to chunk `-1`. Both public +projection transforms share the same synthetic input cell domain `[0, 3)`. +Evaluating its three points shows the two distinct outputs: +`chunk_transform` produces zero-origin chunk-local coordinates `0, 1, 2`, +while `cell_transform` produces the literal request coordinates `-3, -2, -1`. +The shared input domain is not itself the chunk-local coordinate frame. + +## Related work + +TensorStore is the prior art for the transform algebra, as described above. At +the execution boundary, this package instead gives each backend a `ReadContext` +through a `Reader`. Its global transform answers **which values?**; the reader +answers **how does this backend obtain them?** A partition view's transform +directly addresses the raw source in global coordinates. Its optional +projection retains the paired planning transforms, of which only +`chunk_transform` addresses zero-origin chunk-local coordinates. The reader +must preserve the global transform exactly, but it does not participate in +indexing semantics, partitioning, scheduling, or result ownership. + +Earlier versions used a capability taxonomy modeled on historical indexing +dialects. That model required deciding which fragment of a request a backend +could accept and finishing the rest elsewhere. A reader lowers the complete +transform and can compose through delegation instead. This resembles +[zarrita.js store extensions](https://zarrita.dev/packages/zarrita.html), where +storage-specific behavior is an explicit extension point rather than an +inferred array capability. The implementation remains independently authored: +no code is shared with TensorStore, xarray, or zarrita.js. + +## Current scope + +Negative steps are supported as of ndsel 1.0-draft.2: `a[::-1]` reverses, one +desugaring rule covers both signs, and a reversed interval is an error rather +than a silently empty selection. One consequence: a negative step normally +produces a negative domain origin. Reversing a length-20 zero-origin axis gives +the domain `[-19, 1)`, because the result stays anchored to the source +coordinate frame and a reversing map traverses that frame backwards. `LazyArray` +re-bases every view to origin 0, so the positional dialect never exposes it; a +caller working with `IndexTransform` directly will see it, and re-bases +explicitly with `translate_domain_to` for NumPy-shaped coordinates. + +Fancy selections compose without restriction: a second `oindex`/`vindex`/mask +step may land on any axis of an already-fancy view, including axes an existing +index array merely broadcasts along, so +`lazy.oindex[[2, 0], :].lazy.oindex[:, [1, 3]]` selects the outer product it +spells. An array-carrying transform is composed — the new selection is applied +to an identity transform over the current domain and chained on with `compose`, +which evaluates the existing lookup tables at the new coordinates — rather than +rewritten in place. Resolution classifies the result by structure +(`index_array_structure`): pure per-axis outer products keep the orthogonal +resolvers, and everything else — correlated maps, mixtures, index arrays +sharing an input axis (a diagonal gather, reachable only by hand-building a +transform) — takes the pointwise path that collapses the joint block. + +Three limits remain, all intentional and all expected to be lifted: + +- **Affine diagonals.** A hand-built transform in which an *index array* and a + *slice map* bind the same input dimension, or two slice maps share one, is + rejected at resolution with `NotImplementedError`. No selection dialect + produces one; supporting them means lowering the slice maps into the joint + block too. *Planned.* +- **Finite explicit bounds only.** `IndexDomain` has no implicit or unbounded + dimensions; the message layer will normalize a body with `"-inf"`/`"+inf"` + bounds, but the engine layer refuses to lower one into a transform. + TensorStore supports both. *Planned.* +- **Labels are carried, not propagated.** `IndexDomain` holds optional + dimension labels and the wire format round-trips them, but indexing + operations build new domains without them, so a label does not survive a + slice. *Planned.* diff --git a/packages/zarr-indexing/docs/examples/lazy_indexing_dask.md b/packages/zarr-indexing/docs/examples/lazy_indexing_dask.md new file mode 100644 index 0000000000..5c722fe355 --- /dev/null +++ b/packages/zarr-indexing/docs/examples/lazy_indexing_dask.md @@ -0,0 +1,7 @@ +--8<-- "lazy_indexing_dask/README.md" + +## Source Code + +```python +--8<-- "lazy_indexing_dask/lazy_indexing_dask.py" +``` diff --git a/packages/zarr-indexing/docs/examples/lazy_indexing_numpy.md b/packages/zarr-indexing/docs/examples/lazy_indexing_numpy.md new file mode 100644 index 0000000000..8a09ce4d01 --- /dev/null +++ b/packages/zarr-indexing/docs/examples/lazy_indexing_numpy.md @@ -0,0 +1,15 @@ +--8<-- "lazy_indexing_numpy/README.md" + +`LazyArray(source)` uses the conservative built-in reader: `source` must expose +`shape`, `dtype`, and basic integer/slice indexing, and every selected slab must +be convertible to NumPy system memory. Coordinate arrays passed through +`oindex` or `vindex` are ordered and duplicate-preserving; they are not sets. +When a view is partitioned, each `Partition.view.transform` addresses the raw +source globally while `Partition.projection.chunk_transform` stays +zero-origin and chunk-local. + +## Source Code + +```python +--8<-- "lazy_indexing_numpy/lazy_indexing_numpy.py" +``` diff --git a/packages/zarr-indexing/docs/examples/system_memory_chunk_cache.md b/packages/zarr-indexing/docs/examples/system_memory_chunk_cache.md new file mode 100644 index 0000000000..e4d92ba2b6 --- /dev/null +++ b/packages/zarr-indexing/docs/examples/system_memory_chunk_cache.md @@ -0,0 +1,11 @@ +--8<-- "system_memory_chunk_cache/README.md" + +`LazyArray` owns the indexing-derived result shape and assembly, while the +example's `SystemMemoryChunkReader` owns synchronous system-memory cache state +and chunk reads for each materialized part. + +## Source Code + +```python +--8<-- "system_memory_chunk_cache/system_memory_chunk_cache.py" +``` diff --git a/packages/zarr-indexing/docs/guide/index.md b/packages/zarr-indexing/docs/guide/index.md new file mode 100644 index 0000000000..780cfd7e56 --- /dev/null +++ b/packages/zarr-indexing/docs/guide/index.md @@ -0,0 +1,444 @@ +# Visual guide + +The whole model in one sentence: indexing through `LazyArray.lazy` builds a +view, chunk planning partitions its coordinates, and `result()` materializes +the view. This page follows one familiar NumPy selection, `source[2:5]`, +through those stages. + +The first four sections are for anyone indexing arrays: coordinates, +transforms, composition, and result axes. **If you are using lazy indexing +rather than building a storage backend, you can stop after section four.** +The last two sections are for integrators: they turn a request into a chunk +plan and pair each chunk read with its place in the result. + +Throughout, one division of labor holds: the transform answers **which +values?** and is independent of the backend; the reader answers **how do I +obtain them?** and must preserve the transform exactly. + +## An index selects coordinates {#an-index-selects-coordinates} + +Begin with an ordinary NumPy array. `source` contains the values 10 through 15. +The selection `source[2:5]` takes source coordinates 2, 3, and 4, containing +the values 12, 13, and 14. + +```text +source coordinate | 0 1 2 3 4 5 +source value | 10 11 12 13 14 15 +selection | [12 13 14] + source[2:5] + +result coordinate | 0 1 2 +source coordinate | 2 3 4 +result value | 12 13 14 +``` + +The result defines its own coordinates: `0`, `1`, and `2`. The aligned rows +make the correspondence explicit: those result coordinates receive values +`12`, `13`, and `14` from source coordinates `2`, `3`, and `4`. + +The wrapper below gives the same familiar selection a lazy spelling. Indexing +through `.lazy` creates `view`; the last line asks for its values and checks the +observable NumPy result. + +```python +--8<-- "snippets/canonical_slice.py:canonical-slice" +``` + +The important first step is simply that an index describes which source values +fill a result in a particular order. The next section gives the numbers on both +sides of that description a precise meaning. + +## Coordinates are addresses {#coordinates-are-addresses} + +### How to read a half-open interval + +`[0, 1)` is a **half-open interval**: start at 0, inclusive, and stop at 1, exclusive. +The `[` includes the lower boundary, while the `)` excludes the upper boundary. +For integer coordinates, `[0, 1)` therefore enumerates the ordered sequence +`[0]`. + +Half-openness lets adjacent slices and chunks meet without a gap or overlap. +Concatenation is ordered: the first interval is followed by the second. When +the first interval's exclusive stop matches the second interval's inclusive +start, the shared boundary coordinate appears exactly once. + +- `[0, 1) -> [0]` — Start at 0 and stop before 1, so the sequence contains only 0. +- `[1, 3) -> [1, 2]` — Start at 1 and stop before 3, so the sequence contains 1 and 2. +- `concat([0, 1), [1, 3)) = [0, 3)` — Append the second interval after the + first. Their matching exclusive/inclusive boundary produces one continuous + interval without a gap or duplicated coordinate. + +Explicit coordinates, including coordinate arrays, are always ordered +sequences rather than mathematical sets. Their order is semantic, and repeated +coordinates remain repeated in the result. + +In the transform algebra, **coordinates are just integers**. A negative +coordinate is a real address in a domain, with the same status as zero or a +positive coordinate; it is not automatically shorthand for counting backward +from an array's end. + +```text +domain [-2, 3) + +coordinate | -2 -1 0 1 2 +status | address address address address address +``` + +`IndexDomain` makes those bounds explicit. In the example below, narrowing the +domain at `-1` selects the literal address `-1`; the wrapper at the end treats +`-1` the way NumPy does — as the last position. + +```python +--8<-- "snippets/coordinate_origins.py:coordinate-origin" +``` + +Why carry literal coordinates at all? They let independently described +regions keep stable addresses — a domain can even grow at its lower end +without renumbering what is already there. The [design +notes](../design-notes.md#negative-origin-domains-and-prependable-grids) work +through that prepending example; nothing else in this guide depends on it. + +The literal model and NumPy's positional model are both useful, but they answer +different questions: + +| Surface | Meaning of an integer index | Meaning of `-1` | +| --- | --- | --- | +| `IndexDomain` and `IndexTransform` | A literal coordinate in the current domain | The actual address `-1`, if the domain contains it | +| `LazyArray.lazy` | A NumPy-style position in the current view | The last position, normalized before it reaches the transform algebra | + +`LazyArray` uses positions because it is an array-like wrapper: each derived +view starts at position zero and negative indices wrap exactly as they do in +NumPy. The lower-level domain and transform types keep literal coordinates. + +### A transform points from the request to the source + +An `IndexTransform` records how every coordinate in a request finds its source +coordinate. For the slice from the first section, request coordinate `i` maps +to source coordinate `i + 2`. This direction is deliberate: request to source, +not source to request. + +```text +request coordinate | 0 1 2 + | | | | + i + 2 | v v v +source coordinate | 2 3 4 +source value | 12 13 14 +``` + +A transform speaks function vocabulary while this guide speaks array +vocabulary. The two line up like this: + +| the API says | this guide says | +| --- | --- | +| input space (`domain`, `input_rank`) | request coordinates — the result being built | +| output space (`output`, one map per dimension) | source coordinates — where values are read | + +`output` names the output side of the coordinate *function*, not the data: +values flow source → request, against the arrow. The neutral names exist +because transforms compose — in a chain, an interior transform's output space +is just the next transform's input space, neither a request nor a source. + +### The three map kinds, in NumPy terms + +Every output dimension is produced by one of three map forms. Each has a +NumPy counterpart, shown executably below. The examples share one helper — +and it doubles as the answer to how a bare transform meets data at all: a +reader materializes it into a buffer. + +```python +--8<-- "snippets/output_maps.py:resolve-helper" +``` + +`DimensionMap` is an arithmetic rule — the slice above is one, mapping +request `i` to source coordinate `i + 2`: + +```python +--8<-- "snippets/output_maps.py:dimension-map" +``` + +`ArrayMap` stores explicit source coordinates for irregular or fancy +indexing; order and repeats survive into the result: + +```python +--8<-- "snippets/output_maps.py:array-map" +``` + +`ConstantMap` fixes one source coordinate for every request cell. Whether an +axis appears in the result is decided by the **domain**, never by the map: +`image[2, :]` compiles to a `ConstantMap(2)` with no corresponding domain +axis (the axis is dropped), while pairing a constant map with a length-`n` +domain axis that no map consumes yields `n` cells all reading one +coordinate — a broadcast, the one arrangement with no NumPy index +counterpart: + +```python +--8<-- "snippets/output_maps.py:constant-map" +``` + +Together, the request domain and these per-source-dimension maps are the +complete reusable description of an index. + +## Lazy views compose {#lazy-views-compose} + +A lazy view can be indexed again. Each step changes the request-to-source +description, but it does not read an intermediate array. The chain is reduced +to one direct transform from the newest request to the original source. + +```text +source[2:5][::-1][1:] + +new request | intermediate view | original source +------------+-------------------+---------------- + 0 | 1 | 3 + 1 | 2 | 2 + +direct map: request i -> source (3 - i) +``` + +The executable example first selects `source[2:5]`, then reverses that view +and trims its first element: + +```python +--8<-- "snippets/lazy_composition.py:lazy-composition" +``` + +Immediately after `composed` is created—and before the final `result()` call—its +metadata is ready to inspect: + +| Available without reading | Value in this example | +| --- | --- | +| `composed.shape` | `(2,)` | +| `composed.transform` | One transform mapping request `i` to source `3 - i` | + +Neither property needs source values. Composition works only on the coordinate +description; the assertion's call to `result()` is the first operation in the +example that materializes the selected data. + +!!! warning "Stop here: the materialization boundary" + Indexing through `.lazy[...]` never reads. These do: + + - `result()` + - eager indexing of the wrapper: `view[...]` + - `numpy.asarray(view)`, or passing the view to any NumPy function + (`numpy.add(view, 1)` converts, and therefore materializes, the view) + + Python arithmetic such as `view + 1` raises `TypeError` instead: this + wrapper defers indexing, not a general compute graph. + + Nor does it write. There is no `__setitem__`, so `view[...] = values` + raises `TypeError` too, and a wrapped source needs no `__setitem__` of + its own. A consumer that writes plans the selection with `plan_chunks` + and performs its own read-modify-write, keeping chunk atomicity and + concurrent-writer policy on the backend's side of the boundary. + +## An index defines a result array {#an-index-defines-a-result-array} + +An index chooses source points and also defines how those points are arranged in +the result. In the 3-by-4 image below, `image[1, :]` and `image[1:2, :]` choose +the same four source points: values `4`, `5`, `6`, and `7`. + +```text +same selected source cells + +source coordinate | (1, 0) (1, 1) (1, 2) (1, 3) +value | 4 5 6 7 + +image[1, :] + +result coordinate | 0 1 2 3 +value | 4 5 6 7 +shape | (4,); source axis 0 is omitted + +image[1:2, :] + +result coordinate | (0, 0) (0, 1) (0, 2) (0, 3) +value | 4 5 6 7 +shape | (1, 4); source axis 0 is retained with length 1 +``` + +The integer in `image[1, :]` fixes source axis 0. No result coordinate varies +along that axis, so it is omitted and the result shape is `(4,)`. The slice in +`image[1:2, :]` preserves source axis 0 as a length-one result axis, so the +result shape is `(1, 4)`. + +```python +--8<-- "snippets/axis_manipulation.py:axis-shape-comparison" +``` + +`None` inserts a new length-one axis without selecting different source points. +Here it produces the shape `(4, 1)`: + +```python +--8<-- "snippets/axis_manipulation.py:axis-insertion" +``` + +## A request becomes a chunk plan {#a-request-becomes-a-chunk-plan} + +Continue with the 3-by-4 image and `image[1, :]` introduced above. Giving the +image a 2-by-2 chunk shape does not change the four selected values or their +order. It changes only how the work is divided: columns 0 and 1 come from chunk +`(0, 0)`, while columns 2 and 3 come from chunk `(0, 1)`. + +```text + column + 0 1 | 2 3 + ----------+---------- +row 0 0 1 | 2 3 +row 1 [4] [5]| [6] [7] <- image[1, :] + ----------+---------- +row 2 8 9 | 10 11 + + left part right part +chunk_coords (0, 0) (0, 1) +global chunk_domain [0,2) x [0,2) [0,2) x [2,4) +selected global cells (1,0), (1,1) (1,2), (1,3) +chunk-local cells (1,0), (1,1) (1,0), (1,1) +request coordinates 0, 1 2, 3 +``` + +Every planned chunk keeps three coordinate frames distinct: + +- `chunk_coords` identifies a cell in the chunk grid. Chunk coordinates are + literal integers, so a grid that grows at its lower end can hold a chunk + whose coordinate really is `-1` — not an alias for the final chunk (see the + [design notes](../design-notes.md#negative-origin-domains-and-prependable-grids)). +- `chunk_domain` gives that chunk's bounds in **global source coordinates**. + Here the two domains are `[0, 2) × [0, 2)` and `[0, 2) × [2, 4)`. +- Chunk-local positions start from zero inside each chunk. Global column 2 is + therefore local column 0 in chunk `(0, 1)`. This zero-origin local frame is + separate from both the global `chunk_domain` and the possibly negative + chunk coordinate. + +`plan_chunks` needs only a transform and the chunk layout: one grid object +per source dimension. A per-dimension grid answers four questions — which +chunk contains a source index, where a chunk starts, how long it is, and +the vectorized form of the first (`index_to_chunk`, `chunk_offset`, +`chunk_size`, `indices_to_chunks`). The library builds these from chunk +sizes via `dimension_grids_from_chunks`; the executable example hand-rolls +one instead, to show that the whole contract is those four answers. It +plans the canonical request over 2-by-2 chunks, and iterates the same plan +again to show that planning is reusable. (The two transforms it inspects on +each projection are the next section's subject.) + +```python +--8<-- "snippets/chunk_projection.py:chunk-projection" +``` + +The plan describes work but does not perform it. It contains no array source, +storage backend, codec pipeline, buffer, or scheduler. A Zarr reader, a task +queue, or a viewport can consume the same logical plan and decide independently +how and when to fetch its two chunks. + +On the wrapper, this partitioning is called **parts**: `with_parts(shape)` +gives a `LazyArray` a grid of uniform boxes to divide its reads along +(re-partitioning is a pure setter — it changes how a read is divided, never +what `result()` returns), and a wrapped array advertising its own `chunks` +is partitioned that way automatically. + +A zero-length source axis has no chunks. `LazyArray` accepts a positive uniform +part shape for that axis, or explicit per-axis spellings `()`, `(0,)`, and +`(0, 0)`; each produces no parts and the same empty result. Zero-sized parts +remain invalid on a nonempty axis. + +## One cell domain, two projections {#one-cell-domain-two-projections} + +A chunk read has to answer two questions at once: which cells belong to this +chunk, and where does each of those cells belong in the requested result? + +Think of a projection as a small table with one row per selected cell. For +each row, `chunk_transform` gives the cell's zero-origin address inside the +chunk, and `cell_transform` gives the position in the requested result that +receives its value. The row numbers of that table are the shared **cell +domain** — a synthetic input space both transforms accept, which is why one +input point can be evaluated on both sides. + +```text +left chunk (0, 0) + +shared cell coordinate | 0 1 +cell_transform | v v +request coordinate | 0 1 + +shared cell coordinate | 0 1 +chunk_transform | v v +chunk-local coordinate | (1, 0) (1, 1) + +right chunk (0, 1) + +shared cell coordinate | 0 1 +request coordinate | 2 3 +chunk-local coordinate | (1, 0) (1, 1) +``` + +The directions are exact: **shared synthetic input cell domain → request via +`cell_transform`**, and **shared cell domain → chunk-local via +`chunk_transform`**. Neither arrow starts at the request or maps one output +space into the other. + +On the wrapper, `view.parts()` returns one `Partition` per planned chunk; +each bundles a sub-view of the request (`.view`), that chunk's projection +(`.projection`), and the NumPy selection placing its values in the result +(`.out_selection`). + +Within one `Partition`, the frames divide: `Partition.view.transform` is a +different, global transform — it maps the part view directly into the raw +wrapped source — while only `Partition.projection.chunk_transform` uses +zero-origin chunk-local coordinates. Readers receive both so the global +source address and the local planning frame cannot be confused. + +| Projection field | What its output coordinates mean | +| --- | --- | +| `cell_transform` | Literal coordinates in the original request; its output rank is the request rank | +| `chunk_transform` | Zero-origin coordinates in the selected chunk's local frame; its output rank is the source rank | + +The cell domain enumerates corresponding cells; it is not itself either +output coordinate space. The canonical row selection has a one-dimensional +request and a two-dimensional source, so its paired projections have request +rank one and source rank two. + +### Order and duplicates need the request-side projection + +Orthogonal indexing (`.lazy.oindex`) applies each axis's indexer +independently, like `numpy.ix_` — an outer product; the +[pattern reference](patterns.md) develops the dialects. It can visit source +cells in an order that does not match chunk order, and it can visit one +source cell more than once. In the request below, row 4 comes first and +row 1 appears twice. + +```text +request position | 0 1 2 +source row | 4 1 1 +result row | row 4 row 1 row 1 +``` + +A source bounding box cannot reconstruct this result. The box spanning rows 1 +through 4 also includes unrequested rows 2 and 3, and its increasing coordinate +order does not record that row 4 comes first. Narrowing the read to just rows 1 +and 4 still does not record the second use of row 1. For the same reason, a +chunk-local selector alone says which cells to read inside a chunk but cannot +say which request positions receive them, especially when the chunks are +processed in a different order. + +The executable example assembles the 3-by-4 request from a 6-by-8 source with +3-by-4 chunks. Each `Partition` resolves its own sub-view — the global +transform addressing the raw source — and `out_selection` places those +values at their request-side positions; the paired projection stays +available on `part.projection` for consumers that read chunks directly. +The assertion checks the reordered, duplicated result against direct NumPy +indexing. + +```python +--8<-- "snippets/chunk_projection.py:advanced-projection" +``` + +The paired representation preserves information that a bounding box or local +selector discards: exact request order, duplicate destinations, and the +correspondence between every request position and its chunk-local source cell. + +--- + +<nav aria-label="Guide navigation"> + <strong>Previous:</strong> <a href="../">zarr-indexing</a> + · + <strong>Next:</strong> <a href="patterns/">Indexing patterns</a> +</nav> diff --git a/packages/zarr-indexing/docs/guide/integrations.md b/packages/zarr-indexing/docs/guide/integrations.md new file mode 100644 index 0000000000..03661ed43c --- /dev/null +++ b/packages/zarr-indexing/docs/guide/integrations.md @@ -0,0 +1,214 @@ +# Integration boundaries + +This package supplies indexing plans. It does **not** supply scheduling, +caching, codecs, or async orchestration. A consumer decides when projections +run, how decoded chunks are obtained, and where completed values are retained. +An `IndexTransform` says which source values belong in a result; a `Reader` +lowers that complete transform for one backend. The reader does not choose +indexing semantics or result ownership. + +## Zarr chunk dispatch + +A Zarr-oriented reader can consume each public `ChunkProjection` and use its +`chunk_coords` to obtain one decoded chunk from its own storage and codec +layers. This tiny source keeps four in-memory chunks keyed by their global +chunk coordinates and records the exact reads. For each projection, the +consumer enumerates the shared synthetic input cell domain, evaluates +`chunk_transform` to read zero-origin chunk-local coordinates, and evaluates +`cell_transform` to place each value at its literal request coordinate. + +```python +--8<-- "snippets/integrations.py:zarr-consumer" +``` + +The two reads are exactly `(0, 0)` and `(0, 1)`; untouched chunks `(1, 0)` and +`(1, 1)` are never read. The assembled request is `[4, 5, 6, 7]`. The +example intentionally begins with already decoded in-memory chunks: storage +keys, codecs, scheduling, caching, and asynchronous orchestration remain the +consumer's policy rather than responsibilities of the plan. + +## One slab read or many part reads + +A backend with its own native subset read — a Rust or C zarr implementation, +a database, an HTTP range endpoint — resolves a **dense box** (`is_box` with +every stride 1) best as a single read: hand it the whole selection and let it +dispatch to chunks, decode in parallel, and partial-decode shards on its own +side of the boundary. Splitting that read along this library's partitioning +only adds round-trips. Every **other** selection — a strided box, an `oindex` +or `vindex` gather — is where the partitioning earns its keep. The **cover** +of a read is the smallest step-1 slab enclosing every coordinate it needs; +partitioned, each part's cover is bounded by that part's box, so a sparse +selection can never force one read of its whole bounding hull (the smallest +rectangle containing every selected coordinate — a thousand rows for the two +of `oindex[[0, 999]]`). + +The composed view carries enough to make that call at materialization time, +and re-partitioning is a pure setter, so the policy is three lines: + +```python +--8<-- "snippets/integrations.py:dense-box-repartition" +``` + +The corner gather reads four single cells instead of the 10-by-10 hull, and +the dense box becomes exactly one backend call. Both regimes go through +`result()`; only the partitioning in force differs. + +### Sources that accept only unit-step slices + +The default `basic_reader` pushes strided and descending selections down as +positive-step slices, which reads the minimum but assumes the source accepts +any step. Many backends do not: FFI bindings and range requests often +support nothing but `slice(start, stop, 1)`. Select +[`unit_step_reader`][zarr_indexing.reader.UnitStepReader] for such a source +and every key it receives is an ascending unit-step slice per axis, with +strides, reversals, and gathers applied to the in-memory block instead: + +```python +view = LazyArray(source).with_reader(unit_step_reader) +``` + +A strided selection then over-reads its cover by the stride factor, which the +partitioning above bounds by one part. + +## napari-like consumer + +This is a **napari-like consumer**, not a napari integration. It models the +boundary a viewport could use without importing or claiming support for +napari. `RecordingArray` exposes a chunked, basic-indexing source — and its +`chunks` attribute is why the reads below split along `(2, 2)` boxes: +`LazyArray` discovers a partitioning from the wrapped array at construction +(`read_chunk_sizes`, then `chunks`), with `with_parts` as the explicit +override. Composing the +visible slice records no reads. Only `result()` materializes it, with the exact +source selectors `1:2, 0:2` and `1:2, 2:4`; neither selector crosses into an +untouched neighboring chunk. + +```python +--8<-- "snippets/integrations.py:viewport-consumer" +``` + +The viewport owns its interaction loop and any cancellation, caching, or +background execution. `LazyArray` contributes the composable selection and +the partition plan, then resolves only when the consumer asks for the result. + +### A system-memory chunk cache + +Napari accepts NumPy-like array objects and can defer materialization until an +image region is displayed. The indexing plan still deliberately owns no cache +or scheduler. A viewport adapter can place that policy around the plan, as the +executable reference below demonstrates. + +This remains a **napari-like consumer, not a napari integration**. It models +only decoded chunks resident in system memory, synchronously. + +For setup instructions and the complete executable, see the +[system-memory chunk cache example](../examples/system_memory_chunk_cache.md). + +```text + read succeeds +NEW -> QUEUED -> LOADING -------------> READY -> EVICTED + ^ | + | | read fails + | v + +--------- FAILED + retry + +EVICTED -> QUEUED + reload +``` + +The example keeps the lifecycle records and transitions explicit: + +```python +--8<-- "system_memory_chunk_cache/system_memory_chunk_cache.py:chunk-cache-types" +``` + +Its source represents already decoded chunks and records each read: + +```python +--8<-- "system_memory_chunk_cache/system_memory_chunk_cache.py:chunk-cache-source" +``` + +`LazyArray` converts a cache selection into transforms and partitions, then +allocates and assembles the result. The facade constructs exactly one tuple +from `view.parts()`: it derives the chunk coordinates to pin from that tuple, +then passes the same owned parts to `view.result(parts=parts)`. Planning is +therefore performed once for the request rather than repeated during +materialization. Neither pinning nor the result call rebuilds the plan; both +reuse those prepared `Partition` objects. + +`SystemMemoryChunkReader` receives one `ReadContext` for each materialized +part. Its global `context.transform` directly addresses the raw source, while +`context.projection.chunk_transform` addresses the already identified chunk +locally. The reader consumes that supplied projection directly; it never calls +the chunk planner. `LazyArray` retains responsibility for the projection's +result placement and final assembly. The reader owns only cache state and +source reads, while `SystemMemoryChunkCache` remains the thin NumPy-style facade +that prepares and pins the one plan: + +Its indexing dialects remain explicit: `cache[key]` accepts basic indexing +(integers, slices, ellipsis, and new axes), while `cache.oindex[key]` combines +per-axis index arrays as an outer product. Array keys are not silently treated +as orthogonal by plain square brackets; callers choose that behavior through +the named accessor. + +```python +--8<-- "system_memory_chunk_cache/system_memory_chunk_cache.py:chunk-cache-wrapper" +``` + +### Follow one viewport through the cache + +```python +--8<-- "system_memory_chunk_cache/system_memory_chunk_cache.py:chunk-cache-worked-example" +``` + +The worked example uses a 6-by-8 image, 3-by-4 chunks, and capacity for two +decoded chunks. Every read delta follows directly from the viewport request: + +| Step | Viewport | New reads | Resident afterward | Why | +| --- | --- | --- | --- | --- | +| 1 | `image[1:5, 2]` | `(0, 0)`, `(1, 0)` | `(0, 0)`, `(1, 0)` | Both projected chunks are loaded and assembled as `[10, 18, 26, 34]`. | +| 2 | `image[3:5, 2]` | None | `(0, 0)`, `(1, 0)` | The ready buffer for `(1, 0)` is reused and becomes most recently used. | +| 3 | `image[0:2, 5]` | `(0, 1)` | `(0, 1)`, `(1, 0)` | Placement returns `[5, 13]`, then LRU pressure evicts `(0, 0)`. | +| 4 | `image[1:5, 2]` | `(0, 0)` | `(0, 0)`, `(1, 0)` | The evicted chunk is reloaded while the required ready chunk is retained. | +| 5 | `image[3:5, 4:6]` | `(1, 1)` fails; no repeated read; `(1, 1)` succeeds after retry | `(0, 0)`, `(1, 1)` | Failure is retained until explicit retry; the repaired source then returns `[[28, 29], [36, 37]]`. | + +Chunks required by an active request are pinned through assembly, so a request +may temporarily span more chunks than the steady-state capacity. Capacity is +counted in decoded chunks—not records or bytes—and eviction occurs only after +all requested values have been placed. Because pinning and materialization use +the same prepared tuple, those lifecycle decisions cannot drift from the parts +that are actually read, and the cache never has to infer or reconstruct a +projection. + +The event log makes the failure boundary equally explicit: + +| Chunk | Transition | Reason | +| --- | --- | --- | +| `(1, 1)` | `NEW -> QUEUED` | requested | +| `(1, 1)` | `QUEUED -> LOADING` | queue drained | +| `(1, 1)` | `LOADING -> FAILED` | source read failed | +| `(1, 1)` | `FAILED -> QUEUED` | explicit retry | +| `(1, 1)` | `QUEUED -> LOADING` | queue drained | +| `(1, 1)` | `LOADING -> READY` | source read completed | + +A repeated request while the record is `FAILED` creates no event and performs +no source read. The retained failure forces the caller to choose when retry is +appropriate. A real viewport adapter could drain the queue in workers and +invalidate its canvas when chunks become ready without changing the selection +or projection semantics shown here. + +[Napari's image-layer documentation](https://napari.org/dev/howtos/layers/image.html) +describes its NumPy-like array boundary. Neuroglancer's +[`ChunkState`](https://github.com/google/neuroglancer/blob/master/src/chunk_manager/base.ts) +is conceptual prior art for making residency explicit. This example is a +smaller, independently authored, synchronous teaching model; it does not copy +that implementation or reproduce its full worker/GPU lifecycle. + +--- + +<nav aria-label="Reference page navigation"> + <strong>Previous:</strong> <a href="../patterns/">Indexing pattern reference</a> + · + <strong>API:</strong> <a href="../../api/">API reference</a> +</nav> diff --git a/packages/zarr-indexing/docs/guide/patterns.md b/packages/zarr-indexing/docs/guide/patterns.md new file mode 100644 index 0000000000..9c3501da8a --- /dev/null +++ b/packages/zarr-indexing/docs/guide/patterns.md @@ -0,0 +1,327 @@ +# Indexing pattern reference + +Every NumPy indexing idiom is modeled by an `IndexTransform`: a domain (the +result's coordinates) and one output map per source dimension. This page +builds that model **by hand for each idiom**, so the anatomy is explicit — +which map kind an idiom needs, where the offset and stride go, and how an +index array's shape spells outer-product versus pointwise. Each model is +then proven equal to what the selection compiler derives, and its values +are checked against NumPy. + +## The idiom-to-model matrix + +Each idiom over a 6-by-8 `image`, shown two ways: the Python construction, +and the same transform in **wire form** — the [ndsel](../ndsel.md) +canonical body `to_json` produces. Both spell the whole +object: a domain whose extent is the result shape, then one output map per +source dimension. The index-array variables (`rows`, `columns`, +`mask_rows, mask_columns = np.nonzero(mask)`, and friends) are defined in +the executable matrix at the end of the page. + +**`image[1:5, ::2]`** — box. The offset picks where cell 0 reads; the +stride skips: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((4, 4)), + output=( + DimensionMap(input_dimension=0, offset=1), + DimensionMap(input_dimension=1, stride=2), + ), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [4, 4], + "input_labels": ["", ""], + "output": [ + {"offset": 1, "stride": 1, "input_dimension": 0}, + {"offset": 0, "stride": 2, "input_dimension": 1} + ] + } + ``` + +**`image[2, :]`** — box. A rank-1 domain with two output maps: the dropped +axis survives as the wire's constant form, a bare `{"offset": 2}`: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((8,)), + output=(ConstantMap(2), DimensionMap(input_dimension=0)), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [8], + "input_labels": [""], + "output": [ + {"offset": 2}, + {"offset": 0, "stride": 1, "input_dimension": 0} + ] + } + ``` + +**`image[::-2, :]`** — box. Reversal is nothing but a negative stride, and +the offset is where cell 0 reads (row 5): + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((3, 8)), + output=( + DimensionMap(input_dimension=0, offset=5, stride=-2), + DimensionMap(input_dimension=1), + ), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [3, 8], + "input_labels": ["", ""], + "output": [ + {"offset": 5, "stride": -2, "input_dimension": 0}, + {"offset": 0, "stride": 1, "input_dimension": 1} + ] + } + ``` + +**`image[2:2, :]`** — box. Emptiness lives in the domain +(`input_exclusive_max[0]` equals the minimum); the maps are ordinary: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((0, 8)), + output=( + DimensionMap(input_dimension=0, offset=2), + DimensionMap(input_dimension=1), + ), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [0, 8], + "input_labels": ["", ""], + "output": [ + {"offset": 2, "stride": 1, "input_dimension": 0}, + {"offset": 0, "stride": 1, "input_dimension": 1} + ] + } + ``` + +**`image[mask]`** — query. A mask is its nonzero coordinates: two +correlated index arrays over one flat axis, entry `i` of each pairing into +one cell: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(ArrayMap(mask_rows), ArrayMap(mask_columns)), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [10], + "input_labels": [""], + "output": [ + {"offset": 0, "stride": 1, "index_array": [0, 0, 1, 1, 2, 3, 3, 4, 5, 5], "index_array_bounds": ["-inf", "+inf"]}, + {"offset": 0, "stride": 1, "index_array": [0, 5, 2, 7, 4, 1, 6, 3, 0, 5], "index_array_bounds": ["-inf", "+inf"]} + ] + } + ``` + +**`image[np.ix_(rows, columns)]`** — query. The outer product is spelled by +nesting: `[[4], [1], [1]]` varies down the first axis, `[[2, 5]]` across +the second, each singleton along the other: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((3, 2)), + output=(ArrayMap(rows.reshape(3, 1)), ArrayMap(columns.reshape(1, 2))), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [3, 2], + "input_labels": ["", ""], + "output": [ + {"offset": 0, "stride": 1, "index_array": [[4], [1], [1]], "index_array_bounds": ["-inf", "+inf"]}, + {"offset": 0, "stride": 1, "index_array": [[2, 5]], "index_array_bounds": ["-inf", "+inf"]} + ] + } + ``` + +**`image[vector_rows, vector_columns]`** — query. Pointwise: two flat +arrays over one shared axis: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(vector_rows), ArrayMap(vector_columns)), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [3], + "input_labels": [""], + "output": [ + {"offset": 0, "stride": 1, "index_array": [4, 1, 1], "index_array_bounds": ["-inf", "+inf"]}, + {"offset": 0, "stride": 1, "index_array": [2, 5, 2], "index_array_bounds": ["-inf", "+inf"]} + ] + } + ``` + +**`image[broadcast_rows, broadcast_columns]`** — query. NumPy broadcasting, +materialized: each map carries the full `(2, 3)` block: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((2, 3)), + output=( + ArrayMap(np.broadcast_to(broadcast_rows, (2, 3))), + ArrayMap(np.broadcast_to(broadcast_columns, (2, 3))), + ), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [2, 3], + "input_labels": ["", ""], + "output": [ + {"offset": 0, "stride": 1, "index_array": [[0, 0, 0], [3, 3, 3]], "index_array_bounds": ["-inf", "+inf"]}, + {"offset": 0, "stride": 1, "index_array": [[1, 4, 6], [1, 4, 6]], "index_array_bounds": ["-inf", "+inf"]} + ] + } + ``` + +**`image[rows, 2:6]`** — query. One lookup table (order and repeats kept) +beside one ordinary affine map — one index array makes the whole selection +a query: + +=== "Python" + + ```python + IndexTransform( + domain=IndexDomain.from_shape((3, 4)), + output=( + ArrayMap(rows.reshape(3, 1)), + DimensionMap(input_dimension=1, offset=2), + ), + ) + ``` + +=== "JSON" + + ```json + { + "input_rank": 2, + "input_inclusive_min": [0, 0], + "input_exclusive_max": [3, 4], + "input_labels": ["", ""], + "output": [ + {"offset": 0, "stride": 1, "index_array": [[4], [1], [1]], "index_array_bounds": ["-inf", "+inf"]}, + {"offset": 2, "stride": 1, "input_dimension": 1} + ] + } + ``` + +Two structural rules do all the work: + +- **Category**: `ConstantMap` and `DimensionMap` entries keep a selection a + box at any composition depth; one `ArrayMap` makes it a query permanently. + See the [design notes](../design-notes.md#bounding-box-selections-vs-query-selections) + for why consumers dispatch on this. +- **Fancy flavor is spelled by shape**: index arrays varying over distinct + axes (singleton elsewhere) form an outer product; arrays sharing their + non-singleton axes pair pointwise. + +## The executable matrix + +Each case hand-builds the model, checks shape, category, and NumPy values +(resolved through the public reader), then proves the selection compiler +derives the same transform. One wrinkle the last assert documents: compiled +*basic* selections keep literal domains (`t[1:5, ...]` starts at +coordinate 1 — see [Positions vs literal coordinates](#positions-vs-literal-coordinates)), +so they equal the zero-origin models after `translate_domain_to`: + +```python +--8<-- "snippets/indexing_patterns.py:indexing-patterns" +``` + +`LazyArray` adds nothing to these semantics: it is a regular array-like API +whose `.lazy`, `.lazy.oindex`, and `.lazy.vindex` accessors compile the same +dialects to the same transforms — the only difference is the return type, a +view instead of an array. The test suite holds the wrapper to this matrix. + +## Positions vs literal coordinates + +| Surface | Meaning of an integer index | Meaning of `-1` | +| --- | --- | --- | +| `IndexDomain` and `IndexTransform` | A literal coordinate in the current domain | The address `-1`, when the domain contains it | +| `LazyArray.lazy` | A NumPy-style position in the current view | The last position, normalized before transform composition | + +The wrapper's three indexing modes all use positions in the current view. Each +derived view begins at position zero, while the transform algebra underneath +retains literal coordinates. The +[Coordinates are addresses](index.md#coordinates-are-addresses) section develops +that distinction with non-zero and negative-origin domains. + +--- + +<nav aria-label="Reference page navigation"> + <strong>Next:</strong> <a href="../integrations/">Integration boundaries</a> +</nav> diff --git a/packages/zarr-indexing/docs/index.md b/packages/zarr-indexing/docs/index.md index d123cbd32b..1dd151d8ca 100644 --- a/packages/zarr-indexing/docs/index.md +++ b/packages/zarr-indexing/docs/index.md @@ -1,150 +1,53 @@ # zarr-indexing -Composable, lazy coordinate transforms for Zarr array indexing. +This library is for modelling and transforming NumPy-style array indexing expressions. It separates +the *declaration* of an array indexing expression from the result of that expression. -`zarr-indexing` is developed in the -[zarr-python repository](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing) -and released independently of `zarr` itself. Install it with: - -``` -pip install zarr-indexing -``` - -## What this is - -An indexing operation — a slice, an integer, a fancy index array — is a -*mapping* from the coordinates a user asks for to the coordinates that live in -storage. This library makes that mapping a first-class value: an -[`IndexTransform`](api/transform.md). Transforms compose, so a view of a view -of an array is still a single transform, and nothing is read until someone -asks for data. - -Three pieces do the work: - -- **The transform algebra** ([`zarr_indexing.transform`](api/transform.md), - [`zarr_indexing.domain`](api/domain.md), - [`zarr_indexing.output_map`](api/output_map.md), - [`zarr_indexing.composition`](api/composition.md)): an `IndexTransform` - pairs an input [`IndexDomain`](api/domain.md) — a rectangular region of - integer coordinates, which unlike NumPy may have a non-zero origin — with - one output map per storage dimension. `ConstantMap`, `DimensionMap`, and - `ArrayMap` are three representations of the same thing, a set of integer - coordinates, traded off against each other for efficiency. -- **Chunk resolution** ([`zarr_indexing.chunk_resolution`](api/chunk_resolution.md)): - given a transform and a chunk grid, which chunks does this selection touch, - which coordinates does it touch *inside* each chunk, and where do the values - land in the output buffer? The resolver is dependency-aware: correlated - (`vindex`) array maps are enumerated jointly rather than as a cartesian - product, and orthogonal (`oindex`) array maps contribute only the chunks - their index arrays actually land in, so resolution scales with the number of - selected coordinates instead of with the size of the grid. -- **A wire format** ([`zarr_indexing.messages`](api/messages.md), - [`zarr_indexing.json`](api/json.md)): selections serialize to and from - [ndsel](https://github.com/zarr-developers/ndsel), a JSON representation of - NumPy-style n-dimensional selections. See [the ndsel wire format](ndsel.md). +Developed for use in [`zarr`](https://zarr.readthedocs.io). -The package depends only on NumPy and the standard library. In particular it -does not import `zarr`: the chunk-grid surface chunk resolution needs is -described by the [`DimensionGridLike`](api/grid.md) Protocol, which zarr's -per-dimension grids satisfy structurally. +Inspired by [TensorStore](https://google.github.io/tensorstore/), which pioneered +the approach used here. -## Relationship to TensorStore -The model is [TensorStore's](https://google.github.io/tensorstore/index_space.html) -index transform, reimplemented in Python against NumPy: index domains with -explicit origins, output index maps of constant / single-input-dimension / -index-array flavour, and composition as the single operation that stacks -views. Names and semantics follow TensorStore where they overlap — notably, -negative indices are literal coordinates, not Python-style offsets from the -end, and it is the caller's job to normalize them. +## Install -The differences are the ones NumPy compatibility forces. `ArrayMap` records -the input dimension an *orthogonal* (`oindex`) index array varies over, which -TensorStore's format has no field for; the -[serializer collapses or reconstructs that field](api/json.md) so the wire -format stays TensorStore-loadable. Chunk resolution and the `oindex`/`vindex` -helpers exist to serve NumPy-shaped selection semantics, which TensorStore -does not have to model. - -## Quickstart - -Indexing a transform produces a new transform. No I/O happens, and no -coordinates are materialized: - -```python -from zarr_indexing import IndexTransform - -transform = IndexTransform.from_shape((100, 100)) +`zarr-indexing` is developed in the +[zarr-python repository](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing) +and released independently of `zarr` itself: -view = transform[10:50, 5] -view.domain # IndexDomain(inclusive_min=(10,), exclusive_max=(50,)) -view.selection_repr # '{ [10, 50), 5 }' ``` - -The domain describes what the *user* sees (here a single dimension, 40 long, -with origin 10); the output maps describe what *storage* sees (a stride-1 -`DimensionMap` and the `ConstantMap` for the dropped dimension). - -Fancy indexing works the same way, in both flavours, and still materializes -nothing but the index arrays themselves: - -```python -import numpy as np - -transform.oindex[np.array([3, 1, 90]), 0:4] # '{ {3, 1, 90}, [0, 4) }', shape (3, 4) -transform.vindex[np.array([0, 40, 99]), np.array([1, 2, 3])] # shape (3,) +pip install zarr-indexing ``` -Transforms built independently stack with -[`compose`](api/composition.md), which is what `transform[...]` uses -internally when you index an already-indexed view: - -```python -from zarr_indexing import compose - -inner = IndexTransform.from_shape((100,))[::2] # storage 0, 2, 4, ... over domain [0, 50) -outer = IndexTransform.from_shape((50,))[10:20] - -compose(outer, inner).selection_repr # '{ [20, 40) step 2 }' -``` +## Quickstart -Resolution against a chunk grid is where a transform finally meets storage. -Chunk resolution asks the grid only for the per-dimension index-to-chunk -mapping described by [`DimensionGridLike`](api/grid.md), so any object with -those four methods will do: +Wrap an array, compose a lazy view through `.lazy`, and call `result()` when +you want its values: ```python -from dataclasses import dataclass - -from zarr_indexing import iter_chunk_transforms - - -@dataclass(frozen=True) -class RegularDimensionGrid: - chunk: int - - def index_to_chunk(self, idx): return idx // self.chunk - def chunk_offset(self, chunk_ix): return chunk_ix * self.chunk - def chunk_size(self, chunk_ix): return self.chunk - def indices_to_chunks(self, indices): return indices // self.chunk - - -grids = [RegularDimensionGrid(32), RegularDimensionGrid(32)] - -for chunk_coords, sub_transform, out_indices in iter_chunk_transforms(view, grids): - print(chunk_coords, sub_transform.selection_repr) -# (0, 0) { [10, 32), 5 } -# (1, 0) { [0, 18), 5 } +--8<-- "snippets/canonical_slice.py:landing-quickstart" ``` -Each yielded `sub_transform` is the original transform restricted to one chunk -and translated into chunk-local coordinates — exactly what a codec pipeline -needs to decode that chunk and scatter the result. `out_indices` carries the -output scatter indices for array selections, and is `None` for basic indexing. - -## Reference - -- [The ndsel wire format](ndsel.md) +Nothing is read until the `result()` call, however many selections are +composed. [Lazy views compose](guide/index.md#lazy-views-compose) shows how +the chain stays one description, and where the materialization boundary is. + +## Learn more + +- [Visual guide](guide/index.md) — one selection followed from coordinates to + chunk plan. Using lazy indexing, start at + [An index selects coordinates](guide/index.md#an-index-selects-coordinates); + integrating a chunked backend, start at + [A request becomes a chunk plan](guide/index.md#a-request-becomes-a-chunk-plan). +- [Indexing pattern reference](guide/patterns.md) — every selection form with + its NumPy-verified result. +- [Integration boundaries](guide/integrations.md) — what a reader, writer, or + scheduler owns, and what the plan owns. +- [Lazy indexing a NumPy array](examples/lazy_indexing_numpy.md) and + [with Dask](examples/lazy_indexing_dask.md) — runnable examples. +- [The ndsel wire format](ndsel.md) — the JSON form of a selection. +- [Design notes](design-notes.md) — TensorStore lineage, box vs query, and + deliberate limits. - [API reference](api/index.md) - [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/CHANGELOG.md) -- [License (MIT)](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/LICENSE.txt) + · [License (MIT)](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/LICENSE.txt) diff --git a/packages/zarr-indexing/docs/ndsel.md b/packages/zarr-indexing/docs/ndsel.md index 74f394b758..94971d49bf 100644 --- a/packages/zarr-indexing/docs/ndsel.md +++ b/packages/zarr-indexing/docs/ndsel.md @@ -6,8 +6,11 @@ title: The ndsel wire format [ndsel](https://github.com/zarr-developers/ndsel) is a draft JSON representation of NumPy-style n-dimensional selections, adapted from -TensorStore's `IndexTransform` model. `zarr-indexing` implements it in two -layers, and the split between them is the thing worth understanding: +TensorStore's `IndexTransform` model. This page documents the wire format, not +the coordinate model: [Coordinates are addresses](guide/index.md#coordinates-are-addresses) +introduces literal coordinates, and +[Lazy views compose](guide/index.md#lazy-views-compose) shows how views combine +before a transform is serialized. `zarr-indexing` implements ndsel in two layers: | Layer | Module | Depends on | Job | | --- | --- | --- | --- | @@ -15,16 +18,16 @@ layers, and the split between them is the thing worth understanding: | Engine | [`zarr_indexing.json`](api/json.md) | NumPy | Lowers a *canonical* body into an in-memory [`IndexTransform`](api/transform.md), and back. | Constraints that only make sense for a real array — finite bounds, index -arrays as `ndarray`s — live in the engine layer and nowhere else. That is why -`messages` can happily normalize a message with `"-inf"` bounds that -`json.transform_from_canonical` will refuse to lower. +arrays as `ndarray`s — live in the engine layer and nowhere else. As a result, +`messages` normalizes a message with `"-inf"` bounds that +`IndexTransform.from_json` refuses to lower. ## Two entry points [`parse_ndsel`](api/messages.md#zarr_indexing.messages.parse_ndsel) -structurally validates a message of any kind and returns it **unchanged** — -use it when you want to keep a message in its compact shorthand form but -confirm it is well formed. +structurally validates a message of any kind and returns it unchanged. Use it +to confirm that a message is well formed while keeping it in its compact +shorthand form. [`normalize_ndsel`](api/messages.md#zarr_indexing.messages.normalize_ndsel) desugars a message into the single deterministic **canonical transform body** @@ -78,19 +81,19 @@ normalization intact. The engine layer converts between canonical bodies and `IndexTransform`s: ```python -from zarr_indexing import transform_from_canonical, transform_to_canonical +from zarr_indexing import IndexTransform -t = transform_from_canonical(canonical) -transform_to_canonical(t) == canonical +t = IndexTransform.from_json(canonical) +t.to_json() == canonical ``` -`index_transform_to_json` / `index_transform_from_json` (and the -`index_domain_*` variants) are these same converters under their historical -names. +`IndexDomain` carries the same pair for a bare domain body, and each output +map kind has a `to_json`; `output_index_map_from_json` dispatches the wire's +tagged union back to the right kind. Two engine constraints apply here and only here. A canonical body carrying a `"-inf"` or `"+inf"` bound cannot be lowered — an `IndexDomain` addresses a -finite array — so `transform_from_canonical` raises. And implicit bounds lower +finite array — so `IndexTransform.from_json` raises. And implicit bounds lower *by value*: the `[n]`-bracket flag is a message-layer concern, and the engine keeps only the integer. @@ -109,18 +112,18 @@ varies over. The serializer bridges that gap in both directions: solely owns a single non-singleton axis is orthogonal; arrays that share non-singleton axes, or vary over several, are correlated (`vindex`), and get `input_dimension = None`. A single 1-D array over a rank-1 domain is - inherently ambiguous between the two flavours and reconstructs as + inherently ambiguous between the two flavors and reconstructs as orthogonal, which is behaviorally identical in that case. -There is one deliberate exception, worth calling out because it is the one -place a round trip changes representation rather than preserving it. An -all-singleton `index_array` — size 1 — selects the same coordinate no matter -what the input is, so it is **collapsed to a `constant` map** on serialize: +There is one deliberate exception, and it is the only place a round trip changes +representation rather than preserving it. An all-singleton `index_array` — size +1 — selects the same coordinate regardless of the input, so it is collapsed to +a `constant` map on serialize: ```python -from zarr_indexing import IndexTransform, transform_to_canonical +from zarr_indexing import IndexTransform -transform_to_canonical(IndexTransform.from_shape((100, 100)).oindex[[5], 0:2]) +IndexTransform.from_shape((100, 100)).oindex[[5], 0:2].to_json() # {'input_rank': 2, # 'input_inclusive_min': [0, 0], # 'input_exclusive_max': [1, 2], @@ -129,10 +132,10 @@ transform_to_canonical(IndexTransform.from_shape((100, 100)).oindex[[5], 0:2]) # {'offset': 0, 'stride': 1, 'input_dimension': 1}]} ``` -The size-1 input dimension stays in the domain, unconsumed by any output map — -still a valid transform, and still the right output shape. A length-1 `oindex` -selection therefore round-trips *behaviorally* (an `ArrayMap` comes back as a -`ConstantMap`) rather than by object identity. +The size-1 input dimension stays in the domain, unconsumed by any output map. +The transform is still valid and the output shape is unchanged. A length-1 +`oindex` selection therefore round-trips behaviorally (an `ArrayMap` comes back +as a `ConstantMap`) rather than by object identity. ## Conformance @@ -151,6 +154,6 @@ Do not edit the vendored files; to pick up spec changes, re-vendor from a newer ndsel commit and update the recorded SHA. A second, optional test (`tests/test_ndsel_tensorstore.py`, skipped unless -`tensorstore` is installed) closes the loop against a real TensorStore by -loading canonical bodies into `tensorstore.IndexTransform` and re-loading -TensorStore's own `to_json()` output back through the engine layer. +`tensorstore` is installed) checks against TensorStore itself by loading +canonical bodies into `tensorstore.IndexTransform` and re-loading TensorStore's +own `to_json()` output back through the engine layer. diff --git a/packages/zarr-indexing/docs/snippets/axis_manipulation.py b/packages/zarr-indexing/docs/snippets/axis_manipulation.py new file mode 100644 index 0000000000..1d1369fd87 --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/axis_manipulation.py @@ -0,0 +1,29 @@ +"""Indexing defines result axes as well as selected source points.""" + +import numpy as np + +from zarr_indexing import LazyArray + +# --8<-- [start:axis-shape-comparison] +image = np.arange(12).reshape(3, 4) +lazy = LazyArray.from_numpy(image) + +integer_view = lazy.lazy[1, :] +slice_view = lazy.lazy[1:2, :] + +INTEGER_RESULT = integer_view.result() +SLICE_RESULT = slice_view.result() + +assert INTEGER_RESULT.tolist() == [4, 5, 6, 7] +assert INTEGER_RESULT.shape == (4,) +assert SLICE_RESULT.tolist() == [[4, 5, 6, 7]] +assert SLICE_RESULT.shape == (1, 4) +# --8<-- [end:axis-shape-comparison] + +# --8<-- [start:axis-insertion] +inserted_view = lazy.lazy[1, :, None] +INSERTED_RESULT = inserted_view.result() + +assert INSERTED_RESULT.tolist() == [[4], [5], [6], [7]] +assert INSERTED_RESULT.shape == (4, 1) +# --8<-- [end:axis-insertion] diff --git a/packages/zarr-indexing/docs/snippets/canonical_slice.py b/packages/zarr-indexing/docs/snippets/canonical_slice.py new file mode 100644 index 0000000000..fc4417f641 --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/canonical_slice.py @@ -0,0 +1,30 @@ +"""The canonical basic-selection example used throughout the guide.""" + +import numpy as np + +from zarr_indexing import LazyArray + + +# --8<-- [start:landing-quickstart] +import numpy as np + +from zarr_indexing import LazyArray + +source = np.array([10, 11, 12, 13, 14, 15]) +view = LazyArray.from_numpy(source).lazy[2:5] + +view.result() +# array([12, 13, 14]) +# --8<-- [end:landing-quickstart] + +LANDING_QUICKSTART_RESULT = view.result() +assert LANDING_QUICKSTART_RESULT.tolist() == [12, 13, 14] + + +# --8<-- [start:canonical-slice] +source = np.array([10, 11, 12, 13, 14, 15]) +lazy = LazyArray.from_numpy(source) +view = lazy.lazy[2:5] + +assert view.result().tolist() == [12, 13, 14] +# --8<-- [end:canonical-slice] diff --git a/packages/zarr-indexing/docs/snippets/chunk_projection.py b/packages/zarr-indexing/docs/snippets/chunk_projection.py new file mode 100644 index 0000000000..5c56aafbbd --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/chunk_projection.py @@ -0,0 +1,57 @@ +"""Use public chunk projections without choosing a storage backend.""" + +import numpy as np +from numpy.typing import NDArray +from typing import cast + +from zarr_indexing import DimensionGridLike, IndexTransform, LazyArray, plan_chunks + + +# --8<-- [start:chunk-projection] +class RegularGrid: + """A small parameterized implementation of the public grid protocol.""" + + def __init__(self, size: int) -> None: + self.size = size + + def index_to_chunk(self, index: int) -> int: + return index // self.size + + def chunk_offset(self, chunk: int) -> int: + return chunk * self.size + + def chunk_size(self, chunk: int) -> int: + return self.size + + def indices_to_chunks(self, indices: NDArray[np.intp]) -> NDArray[np.intp]: + return np.floor_divide(indices, self.size).astype(np.intp) + + +transform = IndexTransform.from_shape((3, 4))[1, 0:4] +grids = cast( + tuple[DimensionGridLike, DimensionGridLike], + (RegularGrid(2), RegularGrid(2)), +) +plan = plan_chunks(transform, grids) +PROJECTIONS = tuple(plan) +assert tuple(projection.chunk_coords for projection in plan) == ((0, 0), (0, 1)) + +PAIRED_DOMAINS = tuple( + (projection.chunk_transform.domain, projection.cell_transform.domain) + for projection in PROJECTIONS +) +assert all(chunk_domain == cell_domain for chunk_domain, cell_domain in PAIRED_DOMAINS) +# --8<-- [end:chunk-projection] + + +# --8<-- [start:advanced-projection] +image = np.arange(48).reshape(6, 8) +advanced = LazyArray.from_numpy(image).with_parts((3, 4)).lazy.oindex[[4, 1, 1], 2:6] + +ADVANCED_EXPECTED = image[[4, 1, 1]][:, 2:6] +ADVANCED_RESULT = np.empty_like(ADVANCED_EXPECTED) +for part in advanced.parts(): + ADVANCED_RESULT[part.out_selection] = part.view.result() + +np.testing.assert_array_equal(ADVANCED_RESULT, ADVANCED_EXPECTED) +# --8<-- [end:advanced-projection] diff --git a/packages/zarr-indexing/docs/snippets/coordinate_origins.py b/packages/zarr-indexing/docs/snippets/coordinate_origins.py new file mode 100644 index 0000000000..724312e5e8 --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/coordinate_origins.py @@ -0,0 +1,65 @@ +"""Literal coordinate domains and a grid that supports prepending.""" + +import numpy as np +from numpy.typing import NDArray +from typing import cast + +from zarr_indexing import ( + DimensionGridLike, + IndexDomain, + IndexTransform, + LazyArray, + plan_chunks, +) + + +# --8<-- [start:coordinate-origin] +domain = IndexDomain(inclusive_min=(-2,), exclusive_max=(3,)) +assert domain.contains((-1,)) +assert domain.narrow(-1).inclusive_min == (-1,) + +values = np.array([10, 20, 30, 40, 50]) +assert LazyArray.from_numpy(values).lazy[-1:].result().tolist() == [50] +# --8<-- [end:coordinate-origin] + + +# --8<-- [start:prepend-grid] +class PrependableGrid: + """A regular grid whose coordinates may extend below zero.""" + + def index_to_chunk(self, index: int) -> int: + return index // 3 + + def chunk_offset(self, chunk: int) -> int: + return chunk * 3 + + def chunk_size(self, chunk: int) -> int: + return 3 + + def indices_to_chunks(self, indices: NDArray[np.intp]) -> NDArray[np.intp]: + return np.floor_divide(indices, 3).astype(np.intp) + + +projection, = plan_chunks( + IndexTransform.identity(IndexDomain((-3,), (0,))), + cast(tuple[DimensionGridLike], (PrependableGrid(),)), +) +assert projection.chunk_coords == (-1,) +assert projection.chunk_domain == IndexDomain((-3,), (0,)) +assert projection.chunk_transform.domain == IndexDomain((0,), (3,)) + + +assert projection.chunk_transform.domain == projection.cell_transform.domain +PREPEND_SHARED_CELL_COORDS = ((0,), (1,), (2,)) +prepend_shared_cell_points = np.asarray(PREPEND_SHARED_CELL_COORDS, dtype=np.intp) +PREPEND_CHUNK_LOCAL_COORDS = tuple( + tuple(point) + for point in projection.chunk_transform.apply_many(prepend_shared_cell_points).tolist() +) +PREPEND_REQUEST_COORDS = tuple( + tuple(point) + for point in projection.cell_transform.apply_many(prepend_shared_cell_points).tolist() +) +assert PREPEND_CHUNK_LOCAL_COORDS == ((0,), (1,), (2,)) +assert PREPEND_REQUEST_COORDS == ((-3,), (-2,), (-1,)) +# --8<-- [end:prepend-grid] diff --git a/packages/zarr-indexing/docs/snippets/indexing_patterns.py b/packages/zarr-indexing/docs/snippets/indexing_patterns.py new file mode 100644 index 0000000000..86ec75e4bc --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/indexing_patterns.py @@ -0,0 +1,210 @@ +"""Every indexing idiom hand-built as an IndexTransform, proven against the compiler.""" + +from typing import Any, Literal, TypedDict + +import numpy as np + +from zarr_indexing import ( + ArrayMap, + ConstantMap, + DimensionMap, + IndexDomain, + IndexTransform, + ReadContext, + numpy_reader, +) + + +# --8<-- [start:indexing-patterns] +class PatternCase(TypedDict): + """One indexing idiom: its hand-built transform model and its NumPy result.""" + + name: str + mode: Literal["basic", "oindex", "vindex"] + selection: Any + transform: IndexTransform + expected: Any + shape: tuple[int, ...] + category: Literal["box", "query"] + + +image = np.arange(48).reshape(6, 8) +rows = np.array([4, 1, 1], dtype=np.intp) +columns = np.array([2, 5], dtype=np.intp) +mask = image % 5 == 0 +mask_rows, mask_columns = np.nonzero(mask) +vector_rows = np.array([4, 1, 1], dtype=np.intp) +vector_columns = np.array([2, 5, 2], dtype=np.intp) +broadcast_rows = np.array([[0], [3]], dtype=np.intp) +broadcast_columns = np.array([[1, 4, 6]], dtype=np.intp) + +PATTERN_CASES: tuple[PatternCase, ...] = ( + { + # image[1:5, ::2] — an offset picks where cell 0 reads; a stride skips. + "name": "basic-slice", + "mode": "basic", + "selection": (slice(1, 5), slice(None, None, 2)), + "transform": IndexTransform( + domain=IndexDomain.from_shape((4, 4)), + output=( + DimensionMap(input_dimension=0, offset=1), + DimensionMap(input_dimension=1, stride=2), + ), + ), + "expected": image[1:5, ::2], + "shape": (4, 4), + "category": "box", + }, + { + # image[2, :] — the dropped axis survives as a ConstantMap: the result + # is rank 1, but there is still one output map per source dimension. + "name": "integer-axis-removal", + "mode": "basic", + "selection": (2, slice(None)), + "transform": IndexTransform( + domain=IndexDomain.from_shape((8,)), + output=(ConstantMap(2), DimensionMap(input_dimension=0)), + ), + "expected": image[2, :], + "shape": (8,), + "category": "box", + }, + { + # image[::-2, :] — reversal is only a negative stride; the offset is + # where result cell 0 reads (the last selected row, 5). + "name": "negative-stride", + "mode": "basic", + "selection": (slice(None, None, -2), slice(None)), + "transform": IndexTransform( + domain=IndexDomain.from_shape((3, 8)), + output=( + DimensionMap(input_dimension=0, offset=5, stride=-2), + DimensionMap(input_dimension=1), + ), + ), + "expected": image[::-2, :], + "shape": (3, 8), + "category": "box", + }, + { + # image[2:2, :] — emptiness lives in the domain; the maps are ordinary. + "name": "empty-selection", + "mode": "basic", + "selection": (slice(2, 2), slice(None)), + "transform": IndexTransform( + domain=IndexDomain.from_shape((0, 8)), + output=( + DimensionMap(input_dimension=0, offset=2), + DimensionMap(input_dimension=1), + ), + ), + "expected": image[2:2, :], + "shape": (0, 8), + "category": "box", + }, + { + # image[mask] — a mask is its nonzero coordinates: two correlated + # ArrayMaps over one flat result axis, row i paired with column i. + "name": "boolean-mask", + "mode": "vindex", + "selection": mask, + "transform": IndexTransform( + domain=IndexDomain.from_shape((10,)), + output=(ArrayMap(mask_rows), ArrayMap(mask_columns)), + ), + "expected": image[mask], + "shape": (10,), + "category": "query", + }, + { + # image[np.ix_(rows, columns)] — the outer product is spelled by shape: + # each array varies over its own distinct axis, singleton on the other. + "name": "orthogonal", + "mode": "oindex", + "selection": (rows, columns), + "transform": IndexTransform( + domain=IndexDomain.from_shape((3, 2)), + output=(ArrayMap(rows.reshape(3, 1)), ArrayMap(columns.reshape(1, 2))), + ), + "expected": image[np.ix_(rows, columns)], + "shape": (3, 2), + "category": "query", + }, + { + # image[vector_rows, vector_columns] — pointwise: both arrays share + # the same axis, so entry i of each pairs into one coordinate. + "name": "vectorized", + "mode": "vindex", + "selection": (vector_rows, vector_columns), + "transform": IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(vector_rows), ArrayMap(vector_columns)), + ), + "expected": image[vector_rows, vector_columns], + "shape": (3,), + "category": "query", + }, + { + # image[broadcast_rows, broadcast_columns] — NumPy broadcasting, + # materialized: each map carries the full (2, 3) broadcast block. + "name": "broadcasting", + "mode": "vindex", + "selection": (broadcast_rows, broadcast_columns), + "transform": IndexTransform( + domain=IndexDomain.from_shape((2, 3)), + output=( + ArrayMap(np.broadcast_to(broadcast_rows, (2, 3))), + ArrayMap(np.broadcast_to(broadcast_columns, (2, 3))), + ), + ), + "expected": image[broadcast_rows, broadcast_columns], + "shape": (2, 3), + "category": "query", + }, + { + # image[rows, 2:6] — one lookup-table axis (repeats and order kept) + # beside one ordinary affine axis: one ArrayMap makes the whole + # selection a query. + "name": "repeated-out-of-order", + "mode": "oindex", + "selection": (rows, slice(2, 6)), + "transform": IndexTransform( + domain=IndexDomain.from_shape((3, 4)), + output=( + ArrayMap(rows.reshape(3, 1)), + DimensionMap(input_dimension=1, offset=2), + ), + ), + "expected": image[rows, 2:6], + "shape": (3, 4), + "category": "query", + }, +) + +base = IndexTransform.from_shape(image.shape) + + +def resolve(transform: IndexTransform) -> np.ndarray[Any, Any]: + """Materialize a transform against `image` through the public reader.""" + out = np.empty(transform.domain.shape, dtype=image.dtype) + numpy_reader.read_into(image, ReadContext(transform), out) + return out + + +for case in PATTERN_CASES: + transform = case["transform"] + + # The model is the idiom: shape, values, and category all follow from it. + assert transform.domain.shape == case["shape"] + np.testing.assert_array_equal(resolve(transform), case["expected"]) + is_query = any(isinstance(m, ArrayMap) for m in transform.output) + assert ("query" if is_query else "box") == case["category"] + + # The selection compiler derives the same transform. Compiled basic + # selections keep literal domains (t[1:5, ...] starts at 1, not 0); + # re-zeroing exposes the equality with the NumPy-shaped model. + compiled = base[case["selection"]] if case["mode"] == "basic" else ( + getattr(base, case["mode"])[case["selection"]] + ) + assert compiled.translate_domain_to((0,) * compiled.input_rank) == transform +# --8<-- [end:indexing-patterns] diff --git a/packages/zarr-indexing/docs/snippets/integrations.py b/packages/zarr-indexing/docs/snippets/integrations.py new file mode 100644 index 0000000000..5699c0d319 --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/integrations.py @@ -0,0 +1,167 @@ +"""Boundaries for chunked-source and viewport consumers.""" + +from typing import Any + +import numpy as np + +from zarr_indexing import IndexDomain, LazyArray + + +# --8<-- [start:zarr-consumer] +class RecordingChunkSource: + """A decoded-chunk source keyed by public chunk coordinates.""" + + def __init__(self, chunks: dict[tuple[int, ...], np.ndarray[Any, Any]]) -> None: + self.chunks = chunks + self.reads: list[tuple[int, ...]] = [] + + def read(self, chunk_coords: tuple[int, ...]) -> np.ndarray[Any, Any]: + self.reads.append(chunk_coords) + return self.chunks[chunk_coords] + + +def _domain_points(domain: IndexDomain) -> np.ndarray[Any, np.dtype[np.intp]]: + """Enumerate a rectangular domain with a trailing coordinate axis.""" + if domain.ndim == 0: + return np.empty((1, 0), dtype=np.intp) + points = np.moveaxis(np.indices(domain.shape, dtype=np.intp), 0, -1).reshape( + -1, domain.ndim + ) + points += np.asarray(domain.inclusive_min, dtype=np.intp) + return points + + +def _gather_and_scatter( + destination: np.ndarray[Any, Any], + source: np.ndarray[Any, Any], + source_points: np.ndarray[Any, np.dtype[np.intp]], + destination_points: np.ndarray[Any, np.dtype[np.intp]], +) -> np.ndarray[Any, Any]: + """Gather and scatter a flattened point batch, including rank zero.""" + values = np.asarray(source[tuple(source_points.T)]).reshape(-1) + if destination_points.shape[-1] == 0: + destination[()] = values.reshape(destination.shape)[()] + else: + destination[tuple(destination_points.T)] = values + return values + + +zarr_image = np.arange(12).reshape(3, 4) +zarr_chunks = { + (chunk_row, chunk_column): zarr_image[ + chunk_row * 2 : (chunk_row + 1) * 2, + chunk_column * 2 : (chunk_column + 1) * 2, + ] + for chunk_row in range(2) + for chunk_column in range(2) +} +zarr_source = RecordingChunkSource(zarr_chunks) +zarr_view = LazyArray.from_numpy(zarr_image).with_parts((2, 2)).lazy[1, 0:4] +ZARR_RESULT = np.empty(zarr_view.shape, dtype=zarr_image.dtype) +shared_domains: list[tuple[IndexDomain, IndexDomain]] = [] +chunk_local_coords: list[tuple[tuple[int, ...], ...]] = [] +request_coords: list[tuple[tuple[int, ...], ...]] = [] +read_values: list[tuple[int, ...]] = [] + +for part in zarr_view.parts(): + projection = part.projection + assert projection.chunk_transform.domain == projection.cell_transform.domain + shared_domains.append( + (projection.chunk_transform.domain, projection.cell_transform.domain) + ) + domain = projection.chunk_transform.domain + cell_points = _domain_points(domain) + local_points_array = projection.chunk_transform.apply_many(cell_points) + result_points_array = projection.cell_transform.apply_many(cell_points) + chunk = zarr_source.read(projection.chunk_coords) + values_array = _gather_and_scatter( + ZARR_RESULT, chunk, local_points_array, result_points_array + ) + local_points = tuple(tuple(point) for point in local_points_array.tolist()) + result_points = tuple(tuple(point) for point in result_points_array.tolist()) + values = tuple(int(value) for value in values_array) + chunk_local_coords.append(local_points) + request_coords.append(result_points) + read_values.append(values) + +ZARR_SOURCE_KEYS = tuple(zarr_source.chunks) +ZARR_SOURCE_READS = tuple(zarr_source.reads) +ZARR_DISPATCHED_CHUNKS = ZARR_SOURCE_READS +ZARR_SHARED_DOMAINS = tuple(shared_domains) +ZARR_CHUNK_LOCAL_COORDS = tuple(chunk_local_coords) +ZARR_REQUEST_COORDS = tuple(request_coords) +ZARR_READ_VALUES = tuple(read_values) +assert ZARR_SOURCE_KEYS == ((0, 0), (0, 1), (1, 0), (1, 1)) +assert ZARR_SOURCE_READS == ((0, 0), (0, 1)) +assert ZARR_CHUNK_LOCAL_COORDS == (((1, 0), (1, 1)), ((1, 0), (1, 1))) +assert ZARR_REQUEST_COORDS == (((0,), (1,)), ((2,), (3,))) +assert ZARR_READ_VALUES == ((4, 5), (6, 7)) +assert ZARR_RESULT.tolist() == [4, 5, 6, 7] +# --8<-- [end:zarr-consumer] + + +# --8<-- [start:viewport-consumer] +class RecordingArray: + """An array-like source that records the basic reads it receives.""" + + def __init__(self, data: np.ndarray[Any, Any], chunks: tuple[int, ...]) -> None: + self._data = data + self.chunks = chunks + self.keys: list[tuple[slice, ...]] = [] + + @property + def shape(self) -> tuple[int, ...]: + return self._data.shape + + @property + def dtype(self) -> np.dtype[Any]: + return self._data.dtype + + def __getitem__(self, key: tuple[slice, ...]) -> np.ndarray[Any, Any]: + self.keys.append(key) + return self._data[key] + + +viewport_source = RecordingArray(np.arange(12).reshape(3, 4), chunks=(2, 2)) +viewport = LazyArray(viewport_source).lazy[1, 0:4] +VIEWPORT_READS_BEFORE_RESULT = tuple(viewport_source.keys) +assert VIEWPORT_READS_BEFORE_RESULT == () +assert viewport.result().tolist() == [4, 5, 6, 7] + +VIEWPORT_SOURCE_KEYS = tuple(viewport_source.keys) +VIEWPORT_SOURCE_CHUNKS = tuple( + (key[0].start // 2, key[1].start // 2) for key in VIEWPORT_SOURCE_KEYS +) +assert VIEWPORT_SOURCE_KEYS == ( + (slice(1, 2, 1), slice(0, 2, 1)), + (slice(1, 2, 1), slice(2, 4, 1)), +) +assert VIEWPORT_SOURCE_CHUNKS == ((0, 0), (0, 1)) +# --8<-- [end:viewport-consumer] + + +# --8<-- [start:dense-box-repartition] +def materialize(view: LazyArray) -> Any: + """Read a dense box as one slab; resolve everything else per part.""" + strides = view.strides() + if view.is_box and strides is not None and all(s == 1 for s in strides): + view = view.with_parts(view.base_shape) + return view.result() + + +slab_source = RecordingArray(np.arange(100).reshape(10, 10), chunks=(4, 4)) +slab = LazyArray(slab_source) + +dense = slab.lazy[2:9, 1:8] # a dense box: every stride 1 +assert materialize(dense).shape == (7, 7) +assert len(slab_source.keys) == 1 # one slab read; the source dispatches + +slab_source.keys.clear() +gather = slab.lazy.oindex[[0, 9], [0, 9]] # a query: keep the chunk parts +assert materialize(gather).tolist() == [[0, 9], [90, 99]] +assert len(slab_source.keys) == 4 # four covers, each inside one chunk +assert all( + (key[0].stop - key[0].start) * (key[1].stop - key[1].start) == 1 + for key in slab_source.keys +) +# --8<-- [end:dense-box-repartition] diff --git a/packages/zarr-indexing/docs/snippets/lazy_composition.py b/packages/zarr-indexing/docs/snippets/lazy_composition.py new file mode 100644 index 0000000000..a4d9884b2b --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/lazy_composition.py @@ -0,0 +1,14 @@ +"""Composing views keeps indexing lazy until the final result call.""" + +import numpy as np + +from zarr_indexing import LazyArray + + +# --8<-- [start:lazy-composition] +source = np.array([10, 11, 12, 13, 14, 15]) +view = LazyArray.from_numpy(source).lazy[2:5] +composed = view.lazy[::-1].lazy[1:] + +assert composed.result().tolist() == source[2:5][::-1][1:].tolist() +# --8<-- [end:lazy-composition] diff --git a/packages/zarr-indexing/docs/snippets/output_maps.py b/packages/zarr-indexing/docs/snippets/output_maps.py new file mode 100644 index 0000000000..a78fc73b50 --- /dev/null +++ b/packages/zarr-indexing/docs/snippets/output_maps.py @@ -0,0 +1,67 @@ +"""The three output map kinds, each demonstrated against its NumPy counterpart.""" + +from typing import Any + +import numpy as np + +from zarr_indexing import ( + ArrayMap, + ConstantMap, + DimensionMap, + IndexDomain, + IndexTransform, + ReadContext, + numpy_reader, +) + +# --8<-- [start:resolve-helper] +source = np.array([10, 11, 12, 13, 14, 15]) + + +def resolve(transform: IndexTransform, values: np.ndarray[Any, Any]) -> np.ndarray[Any, Any]: + """Materialize `transform` against `values` through the public reader.""" + out = np.empty(transform.domain.shape, dtype=values.dtype) + numpy_reader.read_into(values, ReadContext(transform), out) + return out +# --8<-- [end:resolve-helper] + + +# --8<-- [start:dimension-map] +# DimensionMap is an affine rule: request i reads source offset + stride * i. +# Its NumPy counterpart is a basic slice. +sliced = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(DimensionMap(input_dimension=0, offset=2, stride=1),), +) +assert resolve(sliced, source).tolist() == source[2:5].tolist() + +# A negative stride walks the source backward, like a negative-step slice. +reversed_view = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(DimensionMap(input_dimension=0, offset=4, stride=-2),), +) +assert resolve(reversed_view, source).tolist() == source[4::-2].tolist() +# --8<-- [end:dimension-map] + +# --8<-- [start:array-map] +# ArrayMap is an explicit list of source coordinates; order and duplicates +# are semantic. Its NumPy counterpart is fancy indexing. +gather = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(ArrayMap(index_array=np.array([4, 1, 1])),), +) +assert resolve(gather, source).tolist() == source[[4, 1, 1]].tolist() +# --8<-- [end:array-map] + +# --8<-- [start:constant-map] +# ConstantMap reads one source coordinate for every request cell. No NumPy +# selection spells this operation: source[0] drops the axis, and a repeated +# fancy index source[[0, 0, 0, 0]] matches the values but degrades the +# description to a coordinate list. The value-faithful counterpart is a +# broadcast. +repeat = IndexTransform( + domain=IndexDomain.from_shape((4,)), + output=(ConstantMap(offset=0),), +) +assert resolve(repeat, source).tolist() == np.broadcast_to(source[0:1], (4,)).tolist() +# --8<-- [end:constant-map] diff --git a/packages/zarr-indexing/examples/lazy_indexing_dask/README.md b/packages/zarr-indexing/examples/lazy_indexing_dask/README.md new file mode 100644 index 0000000000..c9edb903ef --- /dev/null +++ b/packages/zarr-indexing/examples/lazy_indexing_dask/README.md @@ -0,0 +1,55 @@ +# Lazy Indexing with Dask + +This example demonstrates how to use `zarr_indexing.LazyArray` with Dask, both as +an array Dask can wrap and as a source of independent tasks, and compares the two +ways of deferring an indexing operation. + +The example shows how to: + +- Pass a `LazyArray` — over a Zarr array or over a view of one — to + `dask.array.from_array` +- Build one Dask task per partition from `parts()`, compute them in parallel, and + place each result with the partition's `out_selection` +- Read `is_complete` to tell which partitions cover a stored chunk completely +- Rely on `__dask_tokenize__`, so that equal selections produce equal tokens and + Dask can cache and deduplicate the work +- Measure what a task graph costs for indexing-only work, against composing the + same selections into one transform + +A `LazyArray` exposes no `chunks` attribute, so `dask.array.from_array` chooses +its own block size unless one is given. The partitioning that `parts()` reports +is discovered from the wrapped array and is independent of Dask's blocks. + +## Choosing Between Them + +If Dask is doing arithmetic across chunks, reductions, rechunking, or distributed +execution, it is the right tool, and its task graph is what makes that work. + +If Dask is used *only* to defer indexing — take a view now, read it later, with +no computation in between — then the graph is overhead. Dask slices the chunk +grid on every indexing operation and records another layer, so composing +selections costs time proportional to both the depth of the chain and the number +of chunks in the array, and reading walks what was accumulated. `LazyArray` +composes each selection into the single transform it already holds, so composing +is independent of the depth of the chain, and reading enumerates only the +partitions the selection touches. The last test in this example prints both, and +the gap widens with the number of chunks and the number of selections. + +## Running the Example + +The script declares its dependencies inline +([PEP 723](https://peps.python.org/pep-0723/)), so the easiest way to run it is +with [uv](https://docs.astral.sh/uv/), which installs them automatically: + +```bash +cd packages/zarr-indexing +uv run --with-editable . examples/lazy_indexing_dask/lazy_indexing_dask.py +``` + +Alternatively, run it with plain Python, in which case you must first install +`zarr`, `zarr-indexing`, `dask[array]`, `numpy`, and `pytest` yourself: + +```bash +cd packages/zarr-indexing +python examples/lazy_indexing_dask/lazy_indexing_dask.py +``` diff --git a/packages/zarr-indexing/examples/lazy_indexing_dask/lazy_indexing_dask.py b/packages/zarr-indexing/examples/lazy_indexing_dask/lazy_indexing_dask.py new file mode 100644 index 0000000000..d6ed43f322 --- /dev/null +++ b/packages/zarr-indexing/examples/lazy_indexing_dask/lazy_indexing_dask.py @@ -0,0 +1,181 @@ +# /// script +# requires-python = ">=3.12" +# dependencies = [ +# "zarr @ git+https://github.com/zarr-developers/zarr-python.git@main", +# "zarr-indexing>=0.1", +# "dask[array]==2025.3.0", +# "numpy==2.4.3", +# "pytest==9.0.2" +# ] +# /// +# + +""" +Demonstrate using zarr_indexing.LazyArray with Dask +""" + +import sys +import time + +import dask +import dask.array as da +import numpy as np +import pytest +import zarr +from dask.base import tokenize + +from zarr_indexing import LazyArray + + +@pytest.fixture +def source() -> zarr.Array: + """A chunked Zarr array to wrap.""" + array = zarr.create_array(store={}, shape=(40, 30), chunks=(10, 10), dtype="i4") + array[:] = np.arange(40 * 30).reshape(40, 30) + return array + + +def test_from_array(source: zarr.Array) -> None: + """Hand a LazyArray to `dask.array.from_array`.""" + lazy = LazyArray(source) + + # `from_array` needs `shape`, `dtype`, and `__getitem__`, which the wrapper + # provides. Each Dask block reads its own region through the wrapper. + array = da.from_array(lazy, chunks=(10, 10)) + print(array) + assert np.array_equal(array.compute(scheduler="threads"), source[:]) + + # A view works the same way, and its shape is the shape of the selection. + view = LazyArray(source).lazy[5:35, 3:27] + array = da.from_array(view, chunks=(10, 10)) + assert array.shape == (30, 24) + assert np.array_equal(array.compute(scheduler="threads"), source[5:35, 3:27]) + + +def test_parts_as_tasks(source: zarr.Array) -> None: + """Build one task per partition and compute them in parallel.""" + view = LazyArray(source).lazy[5:35, 3:27] + + # The partitioning is discovered from the wrapped array's chunks, so each + # partition of the view lies within one stored chunk. + parts = list(view.parts()) + print(f"{len(parts)} parts for a {view.shape} view of a {source.shape} array") + + # A partition carries a sub-view to resolve and where its result belongs, so + # the reads are independent and the placement needs no coordination. + @dask.delayed + def read(part: object) -> np.ndarray: + return part.view.result() + + blocks = dask.compute(*[read(part) for part in parts], scheduler="threads") + + result = np.empty(view.shape, dtype=view.dtype) + for part, block in zip(parts, blocks, strict=True): + result[part.out_selection] = block + assert np.array_equal(result, source[5:35, 3:27]) + + # `is_complete` reports whether a partition covers its whole partition of + # the base array, which a writer uses to choose between overwriting a chunk + # and reading it first. + complete = [part.box for part in parts if part.is_complete] + print(f"{len(complete)} of {len(parts)} parts cover their chunk completely") + + +def test_tokenize(source: zarr.Array) -> None: + """Deterministic tokens let Dask cache and deduplicate work.""" + lazy = LazyArray(source) + + # Two wrappers over the same array and the same selection are the same task + # to Dask, whether or not they are the same Python object. + assert tokenize(lazy) == tokenize(LazyArray(source)) + assert tokenize(lazy.lazy[0:10]) == tokenize(LazyArray(source).lazy[0:10]) + + # Different selections are different tasks. + assert tokenize(lazy.lazy[0:10]) != tokenize(lazy.lazy[10:20]) + + # Selections that describe the same region are the same task, however they + # were composed. + assert tokenize(lazy.lazy[0:20].lazy[5:10]) == tokenize(lazy.lazy[5:10]) + + +def test_indexing_only_workload() -> None: + """Compare an accumulating task graph with a fused transform. + + Dask records each indexing operation as another graph layer, and slices the + chunk grid to build it, so composing selections costs time proportional to + the number of selections and the number of chunks. `LazyArray` composes each + selection into the single transform it already holds, so the cost of + composing does not grow with the depth of the chain, and reading resolves + that one transform rather than walking a graph. + + Timings are printed rather than asserted, since they depend on the machine. + """ + data = np.zeros((2000, 4), dtype="i4") # 2000 chunks, one row each + + def dask_chain(depth: int) -> da.Array: + array = da.from_array(data, chunks=(1, 4)) + for _ in range(depth): + array = array[1:] + return array + + def lazy_chain(depth: int) -> LazyArray: + view = LazyArray.from_numpy(data) + for _ in range(depth): + view = view.lazy[1:] + return view + + # Read once through each path first, so the timings below exclude the cost + # of importing and initializing the machinery. + dask_chain(1)[:2].compute(scheduler="synchronous") + lazy_chain(1).lazy[:2].result() + + header = ( + f"{'selections':>10} {'dask compose':>13} {'dask read':>10} {'layers':>7}" + f" {'LazyArray compose':>18} {'LazyArray read':>15}" + ) + print(header) + for depth in (1, 5, 20): + start = time.perf_counter() + chained = dask_chain(depth) + dask_compose = time.perf_counter() - start + + start = time.perf_counter() + from_dask = chained[:2].compute(scheduler="synchronous") + dask_read = time.perf_counter() - start + + start = time.perf_counter() + view = lazy_chain(depth) + lazy_compose = time.perf_counter() - start + + start = time.perf_counter() + from_lazy = view.lazy[:2].result() + lazy_read = time.perf_counter() - start + + # Both paths describe the same selection, so they read the same data. + assert np.array_equal(from_dask, from_lazy) + + layers = len(chained.__dask_graph__().layers) + print( + f"{depth:>10} {dask_compose * 1e3:>12.2f}ms {dask_read * 1e3:>9.2f}ms {layers:>7}" + f" {lazy_compose * 1e3:>17.3f}ms {lazy_read * 1e3:>14.3f}ms" + ) + + +if __name__ == "__main__": + # Run the example with printed output, and a dummy pytest configuration file specified. + # Without the dummy configuration file, at test time pytest will attempt to use the + # configuration file in the project root, which will error because Zarr is using some + # plugins that are not installed in this example. + sys.exit( + pytest.main( + [ + "-s", + __file__, + f"-c {__file__}", + # Suppress: "PytestAssertRewriteWarning: Module already imported so + # cannot be rewritten; zarr" + "-W", + "ignore::pytest.PytestAssertRewriteWarning", + ] + ) + ) diff --git a/packages/zarr-indexing/examples/lazy_indexing_numpy/README.md b/packages/zarr-indexing/examples/lazy_indexing_numpy/README.md new file mode 100644 index 0000000000..e76e065047 --- /dev/null +++ b/packages/zarr-indexing/examples/lazy_indexing_numpy/README.md @@ -0,0 +1,38 @@ +# Lazy Indexing a NumPy Array + +This example demonstrates how to wrap an array in `zarr_indexing.LazyArray` and +index it without reading data. + +The example shows how to: + +- Wrap a NumPy array and read the forwarded `shape`, `dtype`, and `ndim` +- Compose selections through `.lazy[...]`, `.lazy.oindex[...]`, and + `.lazy.vindex[...]`, and materialize the composed view once with `result()` +- Tell a box selection (slices and integers, described by an interval and a step + per dimension) from a query selection (points gathered through an index array) + using `is_box`, `bounding_box()`, and `strides()` +- Declare a partitioning with `with_parts()`, iterate it with `parts()`, and + assemble a result from the partitions + +`LazyArray` wraps any object exposing `shape`, `dtype`, and `__getitem__`, so the +same API applies to a Zarr array, and the partitioning is then discovered from +the array's chunks. The Dask example covers that case. + +## Running the Example + +The script declares its dependencies inline +([PEP 723](https://peps.python.org/pep-0723/)), so the easiest way to run it is +with [uv](https://docs.astral.sh/uv/), which installs them automatically: + +```bash +cd packages/zarr-indexing +uv run --with-editable . examples/lazy_indexing_numpy/lazy_indexing_numpy.py +``` + +Alternatively, run it with plain Python, in which case you must first install +`zarr-indexing`, `numpy`, and `pytest` yourself: + +```bash +cd packages/zarr-indexing +python examples/lazy_indexing_numpy/lazy_indexing_numpy.py +``` diff --git a/packages/zarr-indexing/examples/lazy_indexing_numpy/lazy_indexing_numpy.py b/packages/zarr-indexing/examples/lazy_indexing_numpy/lazy_indexing_numpy.py new file mode 100644 index 0000000000..ae29a7fc51 --- /dev/null +++ b/packages/zarr-indexing/examples/lazy_indexing_numpy/lazy_indexing_numpy.py @@ -0,0 +1,133 @@ +# /// script +# requires-python = ">=3.12" +# dependencies = [ +# "zarr-indexing>=0.1", +# "numpy==2.4.3", +# "pytest==9.0.2" +# ] +# /// +# + +""" +Demonstrate lazy indexing over a plain NumPy array with zarr_indexing.LazyArray +""" + +import sys + +import numpy as np +import pytest + +from zarr_indexing import LazyArray + + +def test_wrap_and_compose() -> None: + """Wrap an array, compose selections without reading, then materialize once.""" + data = np.arange(12 * 8).reshape(12, 8) + lazy = LazyArray.from_numpy(data) + + # The wrapper forwards the attributes an array consumer expects. + assert lazy.shape == (12, 8) + assert lazy.dtype == data.dtype + assert lazy.ndim == 2 + + # `.lazy[...]` returns another LazyArray. No element of `data` is read. + view = lazy.lazy[2:10, ::2] + print(view) + assert view.shape == (8, 4) + + # Selections compose. Each step narrows the view; still nothing is read. + smaller = view.lazy[1:5, 1:3] + + # `result()` performs the read. NumPy is the reference for the whole chain. + assert np.array_equal(smaller.result(), data[2:10, ::2][1:5, 1:3]) + + # Selections use positional NumPy semantics: indices count from zero within + # the current view, and negative indices count from the end. + assert np.array_equal(lazy.lazy[-1].result(), data[-1]) + assert np.array_equal(lazy.lazy[::-1].result(), data[::-1]) + + # Orthogonal and vectorized indexing are available under the same accessor. + rows = np.array([9, 1, 4]) + assert np.array_equal(lazy.lazy.oindex[rows, :].result(), data[rows, :]) + cols = np.array([0, 3, 7]) + assert np.array_equal(lazy.lazy.vindex[rows, cols].result(), data[rows, cols]) + + # A LazyArray is also an ordinary duck array: __getitem__ reads immediately, + # and np.asarray materializes the view. + assert np.array_equal(lazy[2:4, 0], data[2:4, 0]) + assert np.array_equal(np.asarray(view), data[2:10, ::2]) + + +def test_box_and_query_selections() -> None: + """Distinguish selections that describe a region from selections that gather points.""" + data = np.arange(12 * 8).reshape(12, 8) + lazy = LazyArray.from_numpy(data) + + # A box selection is built from slices and integers alone. It is described + # completely by an interval and a step per dimension, so a consumer can + # serve it as one strided read. + box = lazy.lazy[2:10, ::2] + print(f"box: is_box={box.is_box} bounding_box={box.bounding_box()} strides={box.strides()}") + assert box.is_box + assert box.bounding_box() == ((2, 10), (0, 7)) + assert box.strides() == (1, 2) + + # A query selection gathers points through an index array. Its coordinates + # are a lookup table, so `strides()` is undefined and `bounding_box()` is + # the hull of the points rather than an exact description. + query = lazy.lazy.oindex[np.array([9, 1, 4]), :] + print(f"query: is_box={query.is_box} bounding_box={query.bounding_box()}") + assert not query.is_box + assert query.strides() is None + assert query.bounding_box() == ((1, 10), (0, 8)) + + # Composing a box onto a query keeps it a query. + assert not query.lazy[0:2, 0:2].is_box + + +def test_parts() -> None: + """Iterate the partitions a view covers, and assemble the result from them.""" + data = np.arange(12 * 8).reshape(12, 8) + + # A plain NumPy array declares no partitioning, so `with_parts` states one. + # Partitioning changes the granularity of reads, never the result. + lazy = LazyArray.from_numpy(data).with_parts((4, 4)) + view = lazy.lazy[2:10, ::2] + + parts = list(view.parts()) + print(f"{len(parts)} parts") + for part in parts[:2]: + print(f" base_coords={part.base_coords} box={part.box} complete={part.is_complete}") + + # Each part carries a sub-view of its own, where that sub-view lands in the + # result, and whether it covers its partition completely. Resolving the + # parts and placing them is what `result()` does. + assembled = np.empty(view.shape, dtype=view.dtype) + for part in parts: + assembled[part.out_selection] = part.view.result() + assert np.array_equal(assembled, view.result()) + + # The partitioning is a read strategy, so a different one gives the same data. + assert np.array_equal( + LazyArray.from_numpy(data).with_parts((5, 3)).lazy[2:10, ::2].result(), assembled + ) + + +if __name__ == "__main__": + # Run the example with printed output, and a dummy pytest configuration file specified. + # Without the dummy configuration file, at test time pytest will attempt to use the + # configuration file in the project root, which will error because Zarr is using some + # plugins that are not installed in this example. + sys.exit( + pytest.main( + [ + "-s", + __file__, + f"-c {__file__}", + # Suppress: "PytestAssertRewriteWarning: Module already imported so + # cannot be rewritten; zarr" + "-W", + "ignore::pytest.PytestAssertRewriteWarning", + ] + ) + ) diff --git a/packages/zarr-indexing/examples/system_memory_chunk_cache/README.md b/packages/zarr-indexing/examples/system_memory_chunk_cache/README.md new file mode 100644 index 0000000000..d6271f9401 --- /dev/null +++ b/packages/zarr-indexing/examples/system_memory_chunk_cache/README.md @@ -0,0 +1,46 @@ +# System-memory chunk cache + +This executable reference architecture demonstrates a small, synchronous +system-memory chunk cache for a NumPy-like image consumer. It is inspired by +Neuroglancer's explicit chunk lifecycle: + +```text +NEW -> QUEUED -> LOADING -> READY + | + v + FAILED + +READY -> EVICTED +FAILED -> QUEUED (explicit retry) +``` + +`RecordingChunkSource` owns decoded source-chunk reads and records them for the +example. `LazyArray` converts NumPy-style indexing into transforms and +partitions, then assembles the final result. `SystemMemoryChunkReader` +intercepts each materialized part and owns the lifecycle records, queue +draining, resident ready buffers, LRU eviction, retained load failures, and +explicit retry. The reader owns cache state and source reads, but not result +shape or assembly. + +Each request calls `view.parts()` once and keeps the resulting tuple. The cache +pins the tuple's chunk coordinates, then materializes with +`view.result(parts=parts)`, so scheduling and assembly reuse one plan. Every +reader call consumes the exact projection attached to its `ReadContext`; the +reader does not invoke the chunk planner again. + +The requests demonstrate lazy selections, paired chunk projections, overlapping +viewport requests that reuse resident chunks, eviction under capacity pressure, +a retained failure that does not retry implicitly, and an explicit retry after +the source is repaired. The integration guide contains the detailed request +table. + +This is synchronous system-memory reference architecture, not a +production-ready cache, scheduler, renderer, or complete napari integration. +Its types are intentionally not exported by `zarr_indexing`. + +## Running the example + +```bash +cd packages/zarr-indexing +uv run --with-editable . examples/system_memory_chunk_cache/system_memory_chunk_cache.py +``` diff --git a/packages/zarr-indexing/examples/system_memory_chunk_cache/system_memory_chunk_cache.py b/packages/zarr-indexing/examples/system_memory_chunk_cache/system_memory_chunk_cache.py new file mode 100644 index 0000000000..1645d89b2c --- /dev/null +++ b/packages/zarr-indexing/examples/system_memory_chunk_cache/system_memory_chunk_cache.py @@ -0,0 +1,432 @@ +# /// script +# requires-python = ">=3.12" +# dependencies = [ +# "zarr-indexing>=0.1", +# "numpy==2.4.3", +# ] +# /// +# +from __future__ import annotations + +from contextlib import contextmanager +from dataclasses import dataclass +from enum import StrEnum +from typing import TYPE_CHECKING, Any + +import numpy as np + +from zarr_indexing import ( + IndexDomain, + LazyArray, + ReadContext, +) + +if TYPE_CHECKING: + from collections.abc import Callable, Iterator + + +type ChunkCoords = tuple[int, ...] + + +# --8<-- [start:chunk-cache-types] +class ChunkState(StrEnum): + NEW = "new" + QUEUED = "queued" + LOADING = "loading" + READY = "ready" + FAILED = "failed" + EVICTED = "evicted" + + +@dataclass(slots=True) +class ChunkRecord: + state: ChunkState = ChunkState.NEW + buffer: np.ndarray[Any, Any] | None = None + error: Exception | None = None + last_access: int = -1 + + +@dataclass(frozen=True, slots=True) +class ChunkEvent: + chunk_coords: ChunkCoords + previous: ChunkState + current: ChunkState + reason: str + + +class ChunkLoadError(RuntimeError): + pass + + +# --8<-- [end:chunk-cache-types] + + +# --8<-- [start:chunk-cache-source] +class RecordingChunkSource: + def __init__(self, data: np.ndarray[Any, Any], chunks: tuple[int, ...]) -> None: + self._data = data + self.chunks = chunks + self.reads: list[ChunkCoords] = [] + self.failures: set[ChunkCoords] = set() + + @property + def shape(self) -> tuple[int, ...]: + return self._data.shape + + @property + def dtype(self) -> np.dtype[Any]: + return self._data.dtype + + def __getitem__(self, key: Any) -> np.ndarray[Any, Any]: + raise AssertionError("the cache must read complete chunks through read_chunk") + + def read_chunk(self, chunk_coords: ChunkCoords) -> np.ndarray[Any, Any]: + self.reads.append(chunk_coords) + if chunk_coords in self.failures: + raise OSError(f"source read failed for chunk {chunk_coords}") + key = tuple( + slice(coord * size, min((coord + 1) * size, extent)) + for coord, size, extent in zip(chunk_coords, self.chunks, self.shape, strict=True) + ) + return self._data[key].copy() + + +def _domain_points(domain: IndexDomain) -> np.ndarray[Any, np.dtype[np.intp]]: + """Enumerate a rectangular domain with a trailing coordinate axis.""" + if domain.ndim == 0: + return np.empty((1, 0), dtype=np.intp) + points = np.moveaxis(np.indices(domain.shape, dtype=np.intp), 0, -1).reshape(-1, domain.ndim) + points += np.asarray(domain.inclusive_min, dtype=np.intp) + return points + + +def _gather_and_scatter( + destination: np.ndarray[Any, Any], + source: np.ndarray[Any, Any], + source_points: np.ndarray[Any, np.dtype[np.intp]], + destination_points: np.ndarray[Any, np.dtype[np.intp]], +) -> np.ndarray[Any, Any]: + """Gather and scatter a flattened point batch, including rank zero.""" + values = np.asarray(source[tuple(source_points.T)]).reshape(-1) + if destination_points.shape[-1] == 0: + destination[()] = values.reshape(destination.shape)[()] + else: + destination[tuple(destination_points.T)] = values + return values + + +# --8<-- [end:chunk-cache-source] + + +# --8<-- [start:chunk-cache-wrapper] +LEGAL_TRANSITIONS: dict[ChunkState, frozenset[ChunkState]] = { + ChunkState.NEW: frozenset({ChunkState.QUEUED}), + ChunkState.QUEUED: frozenset({ChunkState.LOADING}), + ChunkState.LOADING: frozenset({ChunkState.READY, ChunkState.FAILED}), + ChunkState.READY: frozenset({ChunkState.EVICTED}), + ChunkState.FAILED: frozenset({ChunkState.QUEUED}), + ChunkState.EVICTED: frozenset({ChunkState.QUEUED}), +} + + +class _OrthogonalIndexer: + """Expose outer-product indexing without changing ``cache[key]`` semantics.""" + + def __init__(self, getitem: Callable[[Any], np.ndarray[Any, Any]]) -> None: + self._getitem = getitem + + def __getitem__(self, key: Any) -> np.ndarray[Any, Any]: + return self._getitem(key) + + +class SystemMemoryChunkReader: + def __init__(self, *, capacity: int) -> None: + self.capacity = capacity + self._records: dict[ChunkCoords, ChunkRecord] = {} + self._queue: list[ChunkCoords] = [] + self._clock = 0 + self._requests = 0 + self.events: list[ChunkEvent] = [] + self.projection_uses: list[tuple[str, str]] = [] + + def state(self, chunk_coords: ChunkCoords) -> ChunkState: + return self._record(chunk_coords).state + + def resident(self) -> tuple[ChunkCoords, ...]: + return tuple( + sorted( + coords + for coords, record in self._records.items() + if record.state is ChunkState.READY + ) + ) + + def _record(self, chunk_coords: ChunkCoords) -> ChunkRecord: + return self._records.setdefault(chunk_coords, ChunkRecord()) + + def _transition(self, chunk_coords: ChunkCoords, current: ChunkState, reason: str) -> None: + record = self._record(chunk_coords) + if current not in LEGAL_TRANSITIONS[record.state]: + raise ValueError(f"illegal chunk transition {record.state} -> {current}") + previous = record.state + record.state = current + self.events.append(ChunkEvent(chunk_coords, previous, current, reason)) + + def retry(self, chunk_coords: ChunkCoords) -> None: + record = self._record(chunk_coords) + if record.state is not ChunkState.FAILED: + raise ValueError(f"retry requires failed chunk {chunk_coords}, got {record.state}") + record.error = None + self._transition(chunk_coords, ChunkState.QUEUED, "explicit retry") + self._queue.append(chunk_coords) + + @contextmanager + def request(self, required: tuple[ChunkCoords, ...]) -> Iterator[None]: + """Prepare every part and defer eviction until one request completes.""" + self._prepare(required) + self._requests += 1 + try: + yield + except Exception: + self._requests -= 1 + raise + else: + self._requests -= 1 + if self._requests == 0: + self._evict(pinned=frozenset()) + + def _touch(self, record: ChunkRecord) -> None: + self._clock += 1 + record.last_access = self._clock + + def _queue_once(self, chunk_coords: ChunkCoords) -> None: + record = self._record(chunk_coords) + if record.state in {ChunkState.QUEUED, ChunkState.LOADING, ChunkState.READY}: + return + if record.state is ChunkState.FAILED: + raise ValueError(f"failed chunk {chunk_coords} requires explicit retry") + self._transition(chunk_coords, ChunkState.QUEUED, "requested") + self._queue.append(chunk_coords) + + def _prepare(self, required: tuple[ChunkCoords, ...]) -> None: + for chunk_coords in required: + record = self._record(chunk_coords) + if record.state is ChunkState.FAILED: + assert record.error is not None + raise ChunkLoadError( + f"chunk {chunk_coords} is failed; call retry first" + ) from record.error + + for chunk_coords in required: + record = self._record(chunk_coords) + if record.state is ChunkState.READY: + self._touch(record) + else: + self._queue_once(chunk_coords) + + def _ensure_ready( + self, + source: RecordingChunkSource, + required: tuple[ChunkCoords, ...], + ) -> None: + if self._requests == 0: + self._prepare(required) + self._drain(source, frozenset(required)) + + def _drain(self, source: RecordingChunkSource, required: frozenset[ChunkCoords]) -> None: + pending = self._queue + self._queue = [] + for index, chunk_coords in enumerate(pending): + if chunk_coords not in required: + self._queue.append(chunk_coords) + continue + record = self._record(chunk_coords) + self._transition(chunk_coords, ChunkState.LOADING, "queue drained") + try: + record.buffer = source.read_chunk(chunk_coords) + except OSError as error: + record.buffer = None + record.error = error + self._transition(chunk_coords, ChunkState.FAILED, "source read failed") + self._queue.extend(pending[index + 1 :]) + raise ChunkLoadError(f"could not load chunk {chunk_coords}") from error + record.error = None + self._transition(chunk_coords, ChunkState.READY, "source read completed") + self._touch(record) + + def _evict(self, *, pinned: frozenset[ChunkCoords]) -> None: + while len(self.resident()) > self.capacity: + candidates = ( + (record.last_access, chunk_coords) + for chunk_coords, record in self._records.items() + if record.state is ChunkState.READY and chunk_coords not in pinned + ) + _, chunk_coords = min(candidates) + record = self._record(chunk_coords) + record.buffer = None + self._transition(chunk_coords, ChunkState.EVICTED, "LRU capacity") + + def read_into( + self, + source: RecordingChunkSource, + context: ReadContext, + out: np.ndarray[Any, Any], + /, + ) -> None: + projection = context.projection + if projection is None: + raise ValueError("SystemMemoryChunkReader requires context.projection") + required = (projection.chunk_coords,) + self._ensure_ready(source, required) + record = self._record(projection.chunk_coords) + assert record.buffer is not None + cell_points = _domain_points(projection.chunk_transform.domain) + chunk_points = projection.chunk_transform.apply_many(cell_points) + destination_points = _domain_points(context.transform.domain) + _gather_and_scatter(out, record.buffer, chunk_points, destination_points) + self.projection_uses.append(("chunk_transform", "context.transform")) + if self._requests == 0: + self._evict(pinned=frozenset()) + + +class SystemMemoryChunkCache: + def __init__(self, source: RecordingChunkSource, *, capacity: int) -> None: + self.source = source + self.reader = SystemMemoryChunkReader(capacity=capacity) + self._lazy = LazyArray(source).with_reader(self.reader) + + @property + def shape(self) -> tuple[int, ...]: + return self.source.shape + + @property + def dtype(self) -> np.dtype[Any]: + return self.source.dtype + + @property + def oindex(self) -> _OrthogonalIndexer: + return _OrthogonalIndexer(lambda key: self._read(key, orthogonal=True)) + + @property + def events(self) -> list[ChunkEvent]: + return self.reader.events + + @property + def projection_uses(self) -> tuple[tuple[str, str], ...]: + return tuple(self.reader.projection_uses) + + def state(self, chunk_coords: ChunkCoords) -> ChunkState: + return self.reader.state(chunk_coords) + + def resident(self) -> tuple[ChunkCoords, ...]: + return self.reader.resident() + + def retry(self, chunk_coords: ChunkCoords) -> None: + self.reader.retry(chunk_coords) + + def __getitem__(self, key: Any) -> np.ndarray[Any, Any]: + return self._read(key, orthogonal=False) + + def _read(self, key: Any, *, orthogonal: bool) -> np.ndarray[Any, Any]: + self.reader.projection_uses.clear() + lazy = self._lazy.lazy + view = lazy.oindex[key] if orthogonal else lazy[key] + # One prepared tuple is the request plan: pin from it, then hand the + # same owned parts back to LazyArray for assembly without replanning. + parts = tuple(view.parts()) + required = tuple(dict.fromkeys(part.base_coords for part in parts)) + with self.reader.request(required): + return np.asarray(view.result(parts=parts)) + + +# --8<-- [end:chunk-cache-wrapper] + + +# --8<-- [start:chunk-cache-worked-example] +image = np.arange(48).reshape(6, 8) +source = RecordingChunkSource(image, chunks=(3, 4)) +cache = SystemMemoryChunkCache(source, capacity=2) + +READS_BEFORE_SELECTION = tuple(source.reads) +INITIAL_RESULT = cache[1:5, 2] +INITIAL_READS = tuple(source.reads) + +before_overlap = len(source.reads) +OVERLAP_RESULT = cache[3:5, 2] +OVERLAP_NEW_READS = tuple(source.reads[before_overlap:]) + +before_eviction = len(source.reads) +EVICTION_RESULT = cache[0:2, 5] +EVICTION_NEW_READS = tuple(source.reads[before_eviction:]) +AFTER_EVICTION_RESIDENT = cache.resident() + +before_reload = len(source.reads) +RELOAD_RESULT = cache[1:5, 2] +RELOAD_NEW_READS = tuple(source.reads[before_reload:]) +AFTER_RELOAD_RESIDENT = cache.resident() + +source.failures.add((1, 1)) +failed_once = False +try: + cache[3:5, 4:6] +except ChunkLoadError: + failed_once = True +assert failed_once +FAILED_READ_COUNT = source.reads.count((1, 1)) +failed_twice = False +try: + cache[3:5, 4:6] +except ChunkLoadError: + failed_twice = True +assert failed_twice +FAILED_REPEAT_READ_COUNT = source.reads.count((1, 1)) +FAILURE_READ_COUNTS = (FAILED_READ_COUNT, FAILED_REPEAT_READ_COUNT) + +source.failures.remove((1, 1)) +cache.retry((1, 1)) +before_retry = len(source.reads) +RETRY_RESULT = cache[3:5, 4:6] +RETRY_NEW_READS = tuple(source.reads[before_retry:]) +RETRY_STATE = cache.state((1, 1)).value +WORKED_EVENTS = tuple(cache.events) +FAILED_TRANSITIONS = tuple( + event.current.value for event in WORKED_EVENTS if event.chunk_coords == (1, 1) +) +FAILED_EVENT_ROWS = tuple( + (event.previous.value, event.current.value, event.reason) + for event in WORKED_EVENTS + if event.chunk_coords == (1, 1) +) +# --8<-- [end:chunk-cache-worked-example] + +assert READS_BEFORE_SELECTION == () +assert INITIAL_RESULT.tolist() == [10, 18, 26, 34] +assert INITIAL_READS == ((0, 0), (1, 0)) +assert OVERLAP_RESULT.tolist() == [26, 34] +assert OVERLAP_NEW_READS == () +assert EVICTION_RESULT.tolist() == [5, 13] +assert EVICTION_NEW_READS == ((0, 1),) +assert AFTER_EVICTION_RESIDENT == ((0, 1), (1, 0)) +assert RELOAD_RESULT.tolist() == [10, 18, 26, 34] +assert RELOAD_NEW_READS == ((0, 0),) +assert AFTER_RELOAD_RESIDENT == ((0, 0), (1, 0)) +assert FAILURE_READ_COUNTS == (1, 1) +assert RETRY_RESULT.tolist() == [[28, 29], [36, 37]] +assert RETRY_NEW_READS == ((1, 1),) +assert RETRY_STATE == "ready" +assert FAILED_TRANSITIONS == ( + "queued", + "loading", + "failed", + "queued", + "loading", + "ready", +) +assert FAILED_EVENT_ROWS == ( + ("new", "queued", "requested"), + ("queued", "loading", "queue drained"), + ("loading", "failed", "source read failed"), + ("failed", "queued", "explicit retry"), + ("queued", "loading", "queue drained"), + ("loading", "ready", "source read completed"), +) diff --git a/packages/zarr-indexing/justfile b/packages/zarr-indexing/justfile index 20e1b2b837..1b7164f647 100644 --- a/packages/zarr-indexing/justfile +++ b/packages/zarr-indexing/justfile @@ -13,18 +13,27 @@ default: # invocation CI uses. # Run the test suite; extra args are passed to pytest test *args: - uv run --project ../.. --group test --with-editable . python -m pytest tests {{ args }} + uv run --project ../.. --group test --with-editable . python -m pytest tests src/zarr_indexing {{ args }} -# Lint with the same invocation CI uses +# TensorStore is the oracle for the parity suites, which skip without it. It +# ships binary wheels only, so it rides in as a run-time overlay rather than +# joining a dependency group; if a future Python lacks a tensorstore wheel, +# gate the CI job that calls this on the matrix version. +# Run the tensorstore parity suites; extra args are passed to pytest +test-tensorstore *args: + uv run --project ../.. --group test --with-editable . --with 'tensorstore>=0.1.84' python -m pytest tests/test_ndsel_tensorstore.py tests/test_tensorstore_parity.py {{ args }} + +# Lint with the same invocation CI uses. Ruff is pinned to the repo-wide +# version (see pyproject.toml [dependency-groups] docs); bump together. lint: - uvx ruff check . + uvx ruff@0.16.0 check . -# Type-check the package sources +# Type-check the package sources, documentation Python, and their contract tests typecheck: - uv run --group test --with pyright pyright src + uv run --group test --with pyright pyright # Run everything CI runs for this package -check: lint typecheck test docs-check +check: lint typecheck test test-tensorstore docs-check # Preview the changelog that the next release would generate changelog-draft: diff --git a/packages/zarr-indexing/mkdocs.yml b/packages/zarr-indexing/mkdocs.yml index 43a5ea5b4c..d97e63b150 100644 --- a/packages/zarr-indexing/mkdocs.yml +++ b/packages/zarr-indexing/mkdocs.yml @@ -10,21 +10,52 @@ site_author: Davis Bennett site_url: !ENV [READTHEDOCS_CANONICAL_URL, 'https://zarr-indexing.readthedocs.io/'] docs_dir: docs use_directory_urls: true +exclude_docs: | + snippets/*.py +# --strict promotes warnings to errors, but broken link anchors and pages +# missing from nav are only INFO by default — a strict build passed with +# both breakages. Warn so strict actually fails on them. +validation: + links: + anchors: warn + nav: + omitted_files: warn + +# Top-level rank is consistent: collections (Guide, Examples, API Reference) +# and standalone artifacts (landing, ndsel spec, design notes, changelog). +# Guide mirrors the docs/guide/ directory — its three pages are one +# collection (learn / look up / integrate), pydantic's Concepts pattern at +# small scale; navigation.indexes makes the Guide entry itself land on the +# visual guide. No tabs: at eight content pages, hiding sections costs more +# than it organizes. nav: - index.md - - ndsel.md + - Guide: + - guide/index.md + - Indexing patterns: guide/patterns.md + - Integration boundaries: guide/integrations.md + - Examples: + - Lazy indexing a NumPy array: examples/lazy_indexing_numpy.md + - Lazy indexing with Dask: examples/lazy_indexing_dask.md + - System-memory chunk cache: examples/system_memory_chunk_cache.md + - The ndsel wire format: ndsel.md + - Design notes: design-notes.md - API Reference: - api/index.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.transform</code>': api/transform.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.domain</code>': api/domain.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.output_map</code>': api/output_map.md - - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.composition</code>': api/composition.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.chunk_resolution</code>': api/chunk_resolution.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.grid</code>': api/grid.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.lazy_array</code>': api/lazy_array.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.reader</code>': api/reader.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.boundary</code>': api/boundary.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.json</code>': api/json.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.messages</code>': api/messages.md - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.errors</code>': api/errors.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.testing.stateful</code>': api/testing_stateful.md + - '<code class="doc-symbol doc-symbol-toc doc-symbol-module"></code> <code>zarr_indexing.testing.strategies</code>': api/testing_strategies.md - Changelog: https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-indexing/CHANGELOG.md # This site is a Read the Docs subproject of zarr-python; give readers a way # back to the parent docs, which list every companion package. @@ -61,6 +92,7 @@ theme: features: - content.code.annotate - content.code.copy + - content.tabs.link - navigation.indexes - navigation.instant - navigation.tracking @@ -111,3 +143,13 @@ markdown_extensions: line_spans: __span pygments_lang_class: true - pymdownx.inlinehilite + # Content tabs (Python/JSON pairs in the pattern matrix); content.tabs.link + # in the theme features keeps every pair switched together. + - pymdownx.tabbed: + alternate_style: true + - pymdownx.snippets: + base_path: [docs, examples] + # Fail the build on an unresolvable include or missing region instead + # of silently rendering nothing. tests/test_doc_examples.py mirrors + # base_path when it verifies the include graph. + check_paths: true diff --git a/packages/zarr-indexing/pyproject.toml b/packages/zarr-indexing/pyproject.toml index 21ba4ef7e7..60f69a1dbb 100644 --- a/packages/zarr-indexing/pyproject.toml +++ b/packages/zarr-indexing/pyproject.toml @@ -34,6 +34,12 @@ dependencies = [ "numpy>=2", ] +[project.optional-dependencies] +# `zarr_indexing.testing` — a Hypothesis state machine and selection strategies +# for projects checking their own array against this package. Nothing else in +# the package imports hypothesis. +testing = ["hypothesis>=6.160.0"] + [project.urls] Homepage = "https://github.com/zarr-developers/zarr-python" Source = "https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-indexing" @@ -47,17 +53,20 @@ Documentation = "https://zarr-indexing.readthedocs.io/" # test suite, which already has zarr installed. `zarr` is intentionally NOT # listed here to avoid a workspace dependency cycle; run these tests from the # repo root (`uv run pytest packages/zarr-indexing/tests`), not in isolation. -test = ["pytest"] +# `hypothesis` arrives via the `testing` extra, which is what +# `zarr_indexing.testing` needs; the repo-root `test` group pins the exact +# version CI runs against. Bump the two together. +test = ["pytest", "hypothesis>=6.160.0"] docs = [ # Pins match the zarr-python docs environment in the repo-root # pyproject.toml so the two sites render with the same toolchain. - "mkdocs-material==9.7.6", + "mkdocs-material==9.7.7", "mkdocs==1.6.1", - "mkdocstrings==1.0.4", + "mkdocstrings==1.0.6", "mkdocstrings-python==2.0.5", "griffe-inherited-docstrings==1.1.3", # mkdocstrings uses ruff to format rendered signatures - "ruff==0.15.20", + "ruff==0.15.22", ] [tool.hatch.version] @@ -71,21 +80,59 @@ raw-options = { root = "../..", git_describe_command = "git describe --dirty --t [tool.hatch.build.targets.wheel] packages = ["src/zarr_indexing"] +# An allowlist, so nothing that merely happens to sit in the package directory +# — a scratch script, a stray notebook — can ride along in a release. The list +# keeps an sdist self-testing: `tests/` carries the vendored ndsel conformance +# corpus, and `tests/test_doc_examples.py` executes `docs/snippets/*.py` and +# `examples/*/*.py`, so those are part of the suite rather than decoration. +# `pyproject.toml`, `README.md` and `LICENSE.txt` are added by hatchling itself. +[tool.hatch.build.targets.sdist] +include = [ + "/src", + "/tests", + "/docs", + "/examples", + "/mkdocs.yml", + "/justfile", + "/CHANGELOG.md", + "/CONTRIBUTING.md", +] + [tool.ruff] extend = "../../pyproject.toml" target-version = "py312" +[tool.ruff.lint.per-file-ignores] +# Chunk discovery and __dask_tokenize__ deliberately catch Exception: a +# foreign source's attributes may fail arbitrarily and discovery must degrade +# to "no information"; a token call must never raise. Configured here (not as +# noqa comments) because the pinned pre-commit ruff and the floating CI ruff +# disagree on whether these rules fire, and RUF100 strips the comments. +"src/zarr_indexing/lazy_array.py" = ["BLE001", "S110"] + [tool.pytest.ini_options] minversion = "7" -testpaths = ["tests"] +# src is collected for its doctests: every public object's Examples section +# executes under --doctest-modules, so the documented examples cannot rot. +testpaths = ["tests", "src/zarr_indexing"] +pythonpath = ["."] xfail_strict = true -addopts = ["-ra", "--strict-config", "--strict-markers"] +addopts = ["-ra", "--strict-config", "--strict-markers", "--doctest-modules"] +doctest_optionflags = [ + "NORMALIZE_WHITESPACE", + "ELLIPSIS", + "IGNORE_EXCEPTION_DETAIL", +] filterwarnings = [ "error", ] [tool.pyright] -include = ["src"] +include = [ + "src", + "docs/snippets", + "tests/test_doc_examples.py", +] enableExperimentalFeatures = true typeCheckingMode = "strict" pythonVersion = "3.12" diff --git a/packages/zarr-indexing/src/zarr_indexing/__init__.py b/packages/zarr-indexing/src/zarr_indexing/__init__.py index effe38ca88..9acfd28a21 100644 --- a/packages/zarr-indexing/src/zarr_indexing/__init__.py +++ b/packages/zarr-indexing/src/zarr_indexing/__init__.py @@ -11,64 +11,106 @@ - `IndexTransform` — maps input coordinates to storage coordinates - `ConstantMap`, `DimensionMap`, `ArrayMap` — the three ways a single output dimension can depend on the input (see `output_map.py`) -- `compose` — chain two transforms into one +- `IndexTransform.compose` — chain two transforms into one -The chunk-resolution helpers (`iter_chunk_transforms`, -`sub_transform_to_selections`) and `selection_to_transform` are also exported -here: they form the surface the zarr integration layer (array indexing) depends -on. The `*Like` grid Protocols describe the chunk-grid surface chunk resolution +`LazyArray` wraps a system-memory/basic-indexing source and gives it deferred +indexing through `.lazy[...]`, yielding its reads as `Partition`s. Other +backends use an explicit `Reader` adapter. + +`plan_chunks` projects a transform through a caller-selected chunk grid without +coupling the result to a storage backend or scheduler. `selection_to_transform` +is also exported for consumers starting with a NumPy-style selection. The +`DimensionGridLike` Protocol describes the narrow grid surface chunk resolution consumes without importing zarr. """ from importlib.metadata import version from zarr_indexing.chunk_resolution import ( - iter_chunk_transforms, - sub_transform_to_selections, + ChunkCoverage, + ChunkPlan, + ChunkProjection, + plan_chunks, ) -from zarr_indexing.composition import compose from zarr_indexing.domain import IndexDomain -from zarr_indexing.grid import DimensionGridLike +from zarr_indexing.errors import BoundsCheckError, VindexInvalidSelectionError +from zarr_indexing.grid import ( + ChunkGrid, + ChunkSpec, + DimensionGrid, + DimensionGridLike, + EdgeDimensionGrid, + FixedDimension, + VaryingDimension, + dimension_grids_from_chunks, +) from zarr_indexing.json import ( IndexDomainJSON, IndexTransformJSON, OutputIndexMapJSON, - index_domain_from_json, - index_domain_to_json, - index_transform_from_json, - index_transform_to_json, - transform_from_canonical, - transform_to_canonical, ) +from zarr_indexing.lazy_array import LazyArray, Partition from zarr_indexing.messages import NdselError, normalize_ndsel, parse_ndsel -from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap -from zarr_indexing.transform import IndexTransform, selection_to_transform +from zarr_indexing.output_map import ( + ArrayMap, + ConstantMap, + DimensionMap, + OutputIndexMap, + output_index_map_from_json, +) +from zarr_indexing.reader import ( + BasicReader, + NumPyReader, + ReadContext, + Reader, + UnitStepReader, + basic_reader, + numpy_reader, + unit_step_reader, +) +from zarr_indexing.transform import ( + IndexTransform, +) __version__ = version("zarr-indexing") __all__ = [ "ArrayMap", + "BasicReader", + "BoundsCheckError", + "ChunkCoverage", + "ChunkGrid", + "ChunkPlan", + "ChunkProjection", + "ChunkSpec", "ConstantMap", + "DimensionGrid", "DimensionGridLike", "DimensionMap", + "EdgeDimensionGrid", + "FixedDimension", "IndexDomain", "IndexDomainJSON", "IndexTransform", "IndexTransformJSON", + "LazyArray", "NdselError", + "NumPyReader", "OutputIndexMap", "OutputIndexMapJSON", + "Partition", + "ReadContext", + "Reader", + "UnitStepReader", + "VaryingDimension", + "VindexInvalidSelectionError", "__version__", - "compose", - "index_domain_from_json", - "index_domain_to_json", - "index_transform_from_json", - "index_transform_to_json", - "iter_chunk_transforms", + "basic_reader", + "dimension_grids_from_chunks", "normalize_ndsel", + "numpy_reader", + "output_index_map_from_json", "parse_ndsel", - "selection_to_transform", - "sub_transform_to_selections", - "transform_from_canonical", - "transform_to_canonical", + "plan_chunks", + "unit_step_reader", ] diff --git a/packages/zarr-indexing/src/zarr_indexing/_affine.py b/packages/zarr-indexing/src/zarr_indexing/_affine.py new file mode 100644 index 0000000000..d1846ffe2d --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/_affine.py @@ -0,0 +1,77 @@ +"""Checked affine coordinate arithmetic.""" + +from __future__ import annotations + +from typing import Any, overload + +import numpy as np +import numpy.typing as npt + +_INTP_INFO = np.iinfo(np.intp) + + +def _fits_intp(value: int) -> bool: + return _INTP_INFO.min <= value <= _INTP_INFO.max + + +@overload +def checked_affine(offset: int, stride: int, coordinates: int) -> int: ... + + +@overload +def checked_affine( + offset: int, + stride: int, + coordinates: npt.NDArray[np.integer[Any]], +) -> npt.NDArray[np.intp]: ... + + +def checked_affine( + offset: int, + stride: int, + coordinates: int | npt.NDArray[np.integer[Any]], +) -> int | npt.NDArray[np.intp]: + """Evaluate ``offset + stride * coordinates`` without integer overflow. + + Bounds are established with Python integers before coordinates are cast or + NumPy performs fixed-width arithmetic. The common representable case then + uses an ``np.intp`` fast path whose multiplication and addition were proven + safe; cancellation cases use exact object arithmetic. + """ + offset = int(offset) + stride = int(stride) + if not isinstance(coordinates, np.ndarray): + mapped = offset + stride * int(coordinates) + if not _fits_intp(mapped): + raise OverflowError(f"output coordinate {mapped} is outside np.intp range") + return mapped + + if coordinates.size == 0: + return np.empty(coordinates.shape, dtype=np.intp) + + coordinate_min = int(np.min(coordinates)) + coordinate_max = int(np.max(coordinates)) + product_at_min = stride * coordinate_min + product_at_max = stride * coordinate_max + mapped_at_min = offset + product_at_min + mapped_at_max = offset + product_at_max + mapped_min = min(mapped_at_min, mapped_at_max) + mapped_max = max(mapped_at_min, mapped_at_max) + if not _fits_intp(mapped_min) or not _fits_intp(mapped_max): + invalid = mapped_min if not _fits_intp(mapped_min) else mapped_max + raise OverflowError(f"output coordinate {invalid} is outside np.intp range") + + safe_fixed_width = ( + _fits_intp(coordinate_min) + and _fits_intp(coordinate_max) + and _fits_intp(offset) + and _fits_intp(stride) + and _fits_intp(product_at_min) + and _fits_intp(product_at_max) + ) + if safe_fixed_width: + intp_coordinates = coordinates.astype(np.intp, copy=False) + return np.asarray(offset + stride * intp_coordinates, dtype=np.intp) + + exact = offset + stride * coordinates.astype(object) + return np.asarray(exact, dtype=np.intp) diff --git a/packages/zarr-indexing/src/zarr_indexing/_composition.py b/packages/zarr-indexing/src/zarr_indexing/_composition.py new file mode 100644 index 0000000000..f90ea26fa7 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/_composition.py @@ -0,0 +1,242 @@ +"""Composition — chaining two transforms into one. + +`compose(outer, inner)` is the operation that makes views stack. `outer` maps +user coordinates to intermediate coordinates, `inner` maps those intermediate +coordinates to output coordinates, and the result maps user coordinates +straight through — so a view of a view of an array is still a single +`IndexTransform`, and indexing never accumulates layers to walk at read time. + +Composition works one output map at a time, and each case reduces to +substituting the outer map into the inner one: + +- A `ConstantMap` inner map ignores its input, so it survives unchanged. +- A `DimensionMap` inner map is affine, so composing it with an outer + `ConstantMap` or `DimensionMap` folds into new `offset`/`stride` values; + composing it with an outer `ArrayMap` leaves the index array alone and + rescales around it. +- An `ArrayMap` inner map must be *evaluated* at the coordinates the outer + transform produces, which is the only case that touches array data. +""" + +from __future__ import annotations + +from typing import Any + +import numpy as np + +from zarr_indexing._affine import checked_affine +from zarr_indexing.errors import BoundsCheckError +from zarr_indexing.output_map import ( + ArrayMap, + ConstantMap, + DimensionMap, + OutputIndexMap, + array_map_or_constant, +) +from zarr_indexing.transform import IndexTransform + + +def compose(outer: IndexTransform, inner: IndexTransform) -> IndexTransform: + """Compose two IndexTransforms. + + `outer` maps user coords (rank m) to intermediate coords (rank n). + `inner` maps intermediate coords (rank n) to output coords (rank p). + The result maps user coords (rank m) to output coords (rank p). + + Precondition: `outer.output_rank == inner.domain.ndim`. + + Examples + -------- + Chained indexing — `source[2:5]`, then `[::-1]` on the result — collapses + to a single transform (a reversed axis keeps literal coordinates, so the + composed domain is `[-4, -1)`): + + >>> inner = IndexTransform.from_shape((10,))[2:5] + >>> outer = IndexTransform.identity(inner.domain)[::-1] + >>> chained = compose(outer, inner) + >>> chained == inner[::-1] + True + >>> [chained.apply((i,)) for i in (-4, -3, -2)] + [(4,), (3,), (2,)] + >>> np.arange(10)[2:5][::-1].tolist() + [4, 3, 2] + """ + if outer.output_rank != inner.domain.ndim: + raise ValueError( + f"outer output rank ({outer.output_rank}) must match inner input rank " + f"({inner.domain.ndim})" + ) + + _validate_outer_outputs(outer, inner) + + result_output = [ + _compose_single(outer, inner_map, inner.domain.inclusive_min) for inner_map in inner.output + ] + + return IndexTransform(domain=outer.domain, output=tuple(result_output)) + + +def _validate_outer_outputs(outer: IndexTransform, inner: IndexTransform) -> None: + """Prove that every intermediate coordinate is in the inner domain. + + An empty outer domain has no points, so containment is vacuously true. For + a nonempty domain, each map form has an exact, constant-space range proof: + constants are singletons, dimension maps are affine intervals, and array + maps need only their extrema. + """ + if any(extent == 0 for extent in outer.domain.shape): + return + + for axis, (outer_map, inner_lo, inner_hi) in enumerate( + zip( + outer.output, + inner.domain.inclusive_min, + inner.domain.exclusive_max, + strict=True, + ) + ): + output_lo, output_hi = _output_bounds(outer, outer_map) + if output_lo < inner_lo or output_hi >= inner_hi: + raise BoundsCheckError( + f"outer output dimension {axis} produces coordinates " + f"[{output_lo}, {output_hi}] outside the inner input domain " + f"[{inner_lo}, {inner_hi})" + ) + + +def _output_bounds(outer: IndexTransform, output_map: OutputIndexMap) -> tuple[int, int]: + """Return the exact inclusive bounds of one output map on a nonempty domain.""" + if isinstance(output_map, ConstantMap): + return output_map.offset, output_map.offset + + if isinstance(output_map, DimensionMap): + input_lo = outer.domain.inclusive_min[output_map.input_dimension] + input_hi = outer.domain.exclusive_max[output_map.input_dimension] + first = output_map.offset + output_map.stride * input_lo + last = output_map.offset + output_map.stride * (input_hi - 1) + return min(first, last), max(first, last) + + index_lo = int(output_map.index_array.min()) + index_hi = int(output_map.index_array.max()) + first = output_map.offset + output_map.stride * index_lo + last = output_map.offset + output_map.stride * index_hi + return min(first, last), max(first, last) + + +def _compose_single( + outer: IndexTransform, inner_map: OutputIndexMap, inner_origin: tuple[int, ...] +) -> OutputIndexMap: + """Compose a single inner output map with the full outer transform.""" + if isinstance(inner_map, ConstantMap): + return ConstantMap(offset=inner_map.offset) + + if isinstance(inner_map, DimensionMap): + return _compose_dimension(outer, inner_map) + + # inner_map: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + return _compose_array(outer, inner_map, inner_origin) + + +def _compose_dimension(outer: IndexTransform, inner_map: DimensionMap) -> OutputIndexMap: + """Compose when inner is a DimensionMap. + + storage = offset_i + stride_i * intermediate[dim_i] + where intermediate[dim_i] = outer.output[dim_i](user_input) + """ + dim_i = inner_map.input_dimension + offset_i = inner_map.offset + stride_i = inner_map.stride + outer_map = outer.output[dim_i] + + if isinstance(outer_map, ConstantMap): + return ConstantMap(offset=checked_affine(offset_i, stride_i, outer_map.offset)) + + if isinstance(outer_map, DimensionMap): + return DimensionMap( + input_dimension=outer_map.input_dimension, + offset=offset_i + stride_i * outer_map.offset, + stride=stride_i * outer_map.stride, + ) + + # outer_map: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + # Affine post-composition leaves the index array (and hence its full + # input rank and dependency axes) untouched. + return ArrayMap( + index_array=outer_map.index_array, + offset=offset_i + stride_i * outer_map.offset, + stride=stride_i * outer_map.stride, + ) + + +def _dimension_positions( + outer: IndexTransform, outer_map: DimensionMap, inner_origin: int +) -> np.ndarray[Any, np.dtype[np.intp]]: + """Build exact positional indices for an affine outer map.""" + dimension = outer_map.input_dimension + extent = outer.domain.shape[dimension] + start = checked_affine( + outer_map.offset - inner_origin, + outer_map.stride, + outer.domain.inclusive_min[dimension], + ) + shape = (1,) * dimension + (extent,) + (1,) * (outer.input_rank - dimension - 1) + if extent == 0: + return np.empty(shape, dtype=np.intp) + if extent == 1: + return np.full(shape, start, dtype=np.intp) + steps = np.arange(extent, dtype=np.intp) + return checked_affine(start, outer_map.stride, steps).reshape(shape) + + +def _array_positions(outer_map: ArrayMap, inner_origin: int) -> np.ndarray[Any, np.dtype[np.intp]]: + """Build exact positional indices without fixed-width affine overflow.""" + return checked_affine(outer_map.offset - inner_origin, outer_map.stride, outer_map.index_array) + + +def _positions_for_axis( + outer: IndexTransform, outer_map: OutputIndexMap, inner_origin: int +) -> int | np.ndarray[Any, np.dtype[np.intp]]: + """Convert one intermediate coordinate map to inner-array positions.""" + if isinstance(outer_map, ConstantMap): + return outer_map.offset - inner_origin + if isinstance(outer_map, DimensionMap): + return _dimension_positions(outer, outer_map, inner_origin) + return _array_positions(outer_map, inner_origin) + + +def _compose_array( + outer: IndexTransform, inner_map: ArrayMap, inner_origin: tuple[int, ...] +) -> OutputIndexMap: + """Compose when inner is an ArrayMap. + + storage = offset_i + stride_i * arr_i[intermediate] + We need to evaluate arr_i at the intermediate coordinates produced by outer. + + Both domains carry their own origin, and neither is necessarily 0 — a step-1 + slice keeps its literal bounds and a negative step produces a negative + origin, so non-zero origins are the ordinary case here rather than the exotic + one. The intermediate coordinates are read over the *outer* domain's own + range, and the inner array is addressed positionally from the *inner* + domain's origin. + """ + arr_i = inner_map.index_array + if any(extent == 0 for extent in outer.domain.shape): + # The empty map is singleton on every non-empty axis: it varies over no + # axis at all, and the emptiness lives in the domain emitted alongside. + empty_shape = tuple(0 if extent == 0 else 1 for extent in outer.domain.shape) + return ArrayMap( + index_array=np.empty(empty_shape, dtype=arr_i.dtype), + offset=inner_map.offset, + stride=inner_map.stride, + ) + + positions = tuple( + 0 if size == 1 else _positions_for_axis(outer, outer_map, origin) + for outer_map, origin, size in zip(outer.output, inner_origin, arr_i.shape, strict=True) + ) + # A gather narrowed to one coordinate — scalar or all-singleton — is the + # ConstantMap it equals; `array_map_or_constant` normalizes both. + gathered = np.asarray(arr_i[positions]) + if gathered.ndim == 0: + return ConstantMap(offset=checked_affine(inner_map.offset, inner_map.stride, int(gathered))) + return array_map_or_constant(gathered, offset=inner_map.offset, stride=inner_map.stride) diff --git a/packages/zarr-indexing/src/zarr_indexing/_selector.py b/packages/zarr-indexing/src/zarr_indexing/_selector.py new file mode 100644 index 0000000000..3a632ec886 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/_selector.py @@ -0,0 +1,41 @@ +"""Internal scalar-selector coercion shared by indexing dialects.""" + +from __future__ import annotations + +import operator +from typing import Any, SupportsIndex, cast + +import numpy as np + + +def is_bool_scalar(value: Any) -> bool: + """Return whether ``value`` is a Python or NumPy boolean scalar.""" + return isinstance(value, (bool, np.bool_)) + + +def as_scalar_index(value: Any) -> int | None: + """Return a non-boolean scalar selector as an exact Python integer. + + Selector coercion follows Python's ``__index__`` protocol, rather than + accepting only the concrete integer classes we happen to know about. In + particular, ``operator.index`` rejects lossy ``__int__``-only objects and + validates that ``__index__`` really returned an integer. + """ + if is_bool_scalar(value): + return None + # ndarray defines ``__index__`` for its scalar-integer case, but the + # attribute also makes non-scalar and non-integer arrays look like + # ``SupportsIndex`` at runtime. Those are array selectors, not malformed + # scalar selectors, and must continue through array dtype validation. + if isinstance(value, np.ndarray): + array = cast("np.ndarray[Any, np.dtype[Any]]", value) + if array.ndim != 0 or array.dtype.kind not in "iu": + return None + if not isinstance(value, SupportsIndex): + return None + return operator.index(cast(SupportsIndex, value)) + + +def require_index(value: Any) -> int: + """Coerce a required slice component through ``__index__``.""" + return operator.index(value) diff --git a/packages/zarr-indexing/src/zarr_indexing/_wire.py b/packages/zarr-indexing/src/zarr_indexing/_wire.py new file mode 100644 index 0000000000..c3e6fd82b6 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/_wire.py @@ -0,0 +1,119 @@ +"""Shared lowering rules between the canonical ndsel wire form and the engine. + +Package-private: the types that serialize themselves (`IndexDomain`, +`IndexTransform`, the output map kinds) all need these, so they cannot live in +any one of them, and they are not API. The three engine constraints named in +[`zarr_indexing.json`][zarr_indexing.json] — finite bounds, implicit bounds +lowering by value, integer `index_array` content — are enforced here. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +import numpy as np + +from zarr_indexing.messages import NdselError + +if TYPE_CHECKING: + from zarr_indexing.domain import IndexDomain + from zarr_indexing.json import BoundJSON + + +def lower_bound(bound: BoundJSON, where: str) -> int: + """Lower a canonical bound to a finite integer, rejecting infinities. + + Reached only with a bound the message layer has already validated as an + `index-value`, so the one thing left to rule out is a sentinel: an + `IndexDomain` addresses a finite array. + """ + value = bound[0] if isinstance(bound, list) else bound + if value == "-inf" or value == "+inf": + raise NdselError( + "invalid_json", + f"{where} is infinite ({value!r}); an IndexDomain addresses a finite " + f"array and cannot lower an infinite bound", + ) + return int(value) + + +def lower_index_array(raw: Any, where: str) -> np.ndarray[Any, np.dtype[np.intp]]: + """Lower a canonical `index_array` to `intp`, rejecting non-integer content. + + The message layer carries `index_array` verbatim — the spec defers its shape + and type to the engine — so this is where the content is checked. An index + array names output coordinates, and nothing but an integer names one: converting + `[0.9, 1.9]` would silently read cells 0 and 1, and `[true, false]` cells 1 + and 0. Strings raise here rather than leaking NumPy's own conversion error. + """ + if not isinstance(raw, list): + # A bare integer would become a rank-0 array and then be widened into a + # length-1 map, so a document that names no cells would select one. + raise NdselError( + "invalid_json", + f"{where} must be an array of integers, got {raw!r}", + ) + try: + arr = np.asarray(raw) + except (TypeError, ValueError) as exc: + raise NdselError("invalid_json", f"{where} is not an array: {exc}") from exc + if arr.size == 0 and arr.dtype.kind == "f": + # An empty JSON list carries no element type and NumPy defaults it to + # float64. An empty selection is legal, so take it as an empty index array. + return np.zeros(arr.shape, dtype=np.intp) + if arr.dtype.kind not in "iu": + raise NdselError( + "invalid_json", + f"{where} must hold integers, got an array of {arr.dtype.name}; an " + f"index array names output coordinates, which floats, booleans and " + f"strings do not", + ) + return np.asarray(arr, dtype=np.intp) + + +def lower_labels(labels: list[str]) -> tuple[str, ...] | None: + """All-empty labels collapse to `None` so a label-free domain round-trips.""" + return None if all(label == "" for label in labels) else tuple(labels) + + +def emit_labels(labels: tuple[str, ...] | None, rank: int) -> list[str]: + """Emit canonical labels: `[""]*rank` when the domain is unlabeled.""" + return [""] * rank if labels is None else list(labels) + + +def full_rank_index_array( + arr: np.ndarray[Any, np.dtype[np.intp]], + domain: IndexDomain, + where: str, +) -> np.ndarray[Any, np.dtype[np.intp]]: + """Give an incoming `index_array` the input rank the engine requires. + + ndsel leaves index-array rank unvalidated, so a conformant producer may send + an array of lower rank that broadcasts against the domain. A non-empty one + is aligned to the *trailing* input dimensions, which is how NumPy broadcasts + and how a producer omitting leading singletons means it to be read. + + An empty array is a different matter: `[]` is the only spelling of every + empty shape once the leading axis is the zero-length one, so the axis it + varies over cannot be read off it. It is recovered from the domain, which + can only be empty on the axis in question — and rejected when the domain + leaves that ambiguous. This package never emits such a document (an empty + map is degenerate and collapses to a constant, as TensorStore's does), so + this path exists for external producers alone. + """ + if arr.size == 0 and arr.ndim != domain.ndim: + empty_axes = [k for k, extent in enumerate(domain.shape) if extent == 0] + if len(empty_axes) != 1: + raise NdselError( + "invalid_json", + f"{where}.index_array is empty, but the input domain has " + f"{len(empty_axes)} zero-length dimensions, so the axis it varies " + f"over cannot be recovered", + ) + shape = [1] * domain.ndim + shape[empty_axes[0]] = 0 + return arr.reshape(tuple(shape)) + + if arr.ndim < domain.ndim: + return arr.reshape((1,) * (domain.ndim - arr.ndim) + arr.shape) + return arr diff --git a/packages/zarr-indexing/src/zarr_indexing/boundary.py b/packages/zarr-indexing/src/zarr_indexing/boundary.py new file mode 100644 index 0000000000..e7f1b1c4bd --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/boundary.py @@ -0,0 +1,374 @@ +"""The positional (NumPy) selection dialect, lowered onto the transform algebra. + +The transform algebra uses **literal domain coordinates**: an index is a point +in the view's own coordinate system, which after `view = arr[10:50]` runs from +10 to 49, and a negative index is a negative coordinate rather than an offset +from the end (TensorStore's convention — see `zarr_indexing.transform`). + +NumPy uses **positions**: index 0 always means the first element of the object +being indexed, and `-1` means the last. This module translates between the two. +It validates a selection against the view's shape with NumPy semantics, then +shifts every coordinate by the domain's origin so the transform layer sees +literal coordinates. + +Note +---- +`zarr.Array` currently carries its own copy of this normalization, tuned to a +different boundary contract (`Array.lazy[...]` deliberately exposes the literal +dialect, so a view's coordinates keep their meaning across composition). This +module is the generic, zarr-free version used by `LazyArray`; consolidating +zarr's copy onto it is left to a follow-up. +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any, Literal + +import numpy as np + +from zarr_indexing._selector import as_scalar_index, is_bool_scalar, require_index + +if TYPE_CHECKING: + from zarr_indexing.domain import IndexDomain + +SelectionMode = Literal["basic", "orthogonal", "vectorized"] + + +def _as_index_array(sel: Any) -> np.ndarray[Any, np.dtype[Any]] | None: + """Return `sel` as an ndarray if it is array-like, else None.""" + if isinstance(sel, np.ndarray): + return sel + if isinstance(sel, (list, tuple)): + arr = np.asarray(sel) + if arr.size == 0 and arr.dtype.kind == "f": + # An empty Python list carries no element type and NumPy defaults it + # to float64. Selecting nothing is legal — NumPy takes `a[np.ix_([])]` + # — so read it as the empty integer selection it spells, rather than + # rejecting it for a dtype it never had a chance to have. + return np.zeros(arr.shape, dtype=np.intp) + if arr.dtype.kind in "biu": + return arr + raise IndexError( + f"arrays used as indices must be of integer or boolean type; got dtype {arr.dtype}" + ) + return None + + +def _axes_consumed(sel: Any, mode: SelectionMode) -> int: + """How many axes of the view a single selection entry consumes.""" + if sel is None: + return 0 + arr = _as_index_array(sel) + # A multidimensional boolean mask consumes one axis per mask dimension. + # Orthogonal indexing is per-axis by construction, so a mask there is 1-D + # and consumes exactly one axis. + if mode == "vectorized" and arr is not None and arr.dtype == np.bool_: + return arr.ndim + return 1 + + +def _normalize_int(value: int, size: int, axis: int) -> int: + """Bounds-check a positional integer index, wrapping negatives NumPy-style.""" + idx = value + if idx < 0: + idx += size + if idx < 0 or idx >= size: + raise IndexError(f"index {value} is out of bounds for axis {axis} with size {size}") + return idx + + +def _normalize_slice(sel: slice, size: int, axis: int) -> tuple[int, int, int]: + """Resolve a positional slice to `(start, stop, step)`, either direction. + + `slice.indices` already applies NumPy's rules — negative bounds count from + the end, out-of-range bounds clamp, and a reversed slice runs downward with + `stop` one *below* the last selected position. The one thing it does not do + is canonicalize an empty result: it can hand back a stop on the far side of + the start (`5:2` going up, `2:5` going down), which the transform layer + reads as a direction error rather than an empty selection. Collapsing it to + `stop == start` keeps NumPy's "empty, not an error" answer. + """ + start_bound = None if sel.start is None else require_index(sel.start) + stop_bound = None if sel.stop is None else require_index(sel.stop) + step = 1 if sel.step is None else require_index(sel.step) + if step == 0: + raise ValueError(f"slice step cannot be zero (axis {axis})") # ValueError: NumPy parity + start, stop, step = slice(start_bound, stop_bound, step).indices(size) + stop = max(stop, start) if step > 0 else min(stop, start) + return start, stop, step + + +def _normalize_int_array( + arr: np.ndarray[Any, np.dtype[Any]], size: int, axis: int +) -> np.ndarray[Any, np.dtype[np.intp]]: + """Bounds-check a positional integer index array, wrapping negatives.""" + if arr.dtype.kind not in "iu": + raise IndexError( + f"arrays used as indices must be of integer or boolean type; got dtype {arr.dtype}" + ) + # Cast before wrapping: an unsigned array cannot represent the intermediate + # negative values, and `intp` covers every index NumPy can address. + out = arr.astype(np.intp, copy=True) + if out.size > 0: + negative = out < 0 + if bool(negative.any()): + out = np.where(negative, out + size, out) + lo, hi = int(out.min()), int(out.max()) + if lo < 0 or hi >= size: + bad = lo if lo < 0 else hi + raise IndexError(f"index {bad} is out of bounds for axis {axis} with size {size}") + return out + + +def _expanded_axis_walk(entries: tuple[Any, ...], ndim: int, mode: SelectionMode) -> list[int]: + """The starting axis each entry addresses, with an ellipsis expanded. + + The returned list has one entry per element of `entries`; the value for an + `Ellipsis` (or a `newaxis`) is the axis it starts at, which is also the axis + the following entry resumes from once the skipped axes are accounted for. + """ + for sel in entries: + if is_bool_scalar(sel): + raise IndexError( + "boolean scalars are not valid indices; use a boolean array " + "matching the shape of the axes it selects" + ) + if sum(1 for sel in entries if sel is Ellipsis) > 1: + raise IndexError("an index can only have a single ellipsis ('...')") + consumed = sum(_axes_consumed(sel, mode) for sel in entries if sel is not Ellipsis) + if consumed > ndim: + raise IndexError( + f"too many indices for array: array has {ndim} dimensions, but {consumed} were indexed" + ) + + axes: list[int] = [] + axis = 0 + for sel in entries: + axes.append(axis) + axis += (ndim - consumed) if sel is Ellipsis else _axes_consumed(sel, mode) + return axes + + +def validate_advanced_selection( + selection: Any, + domain: IndexDomain, + mode: Literal["orthogonal", "vectorized"], +) -> None: + """Validate advanced-index selector dtypes and boolean mask extents. + + This is the validation shared by positional callers such as `LazyArray` + and direct `IndexTransform.oindex` / `.vindex` callers. It deliberately + does not normalize coordinates: direct transforms use literal coordinates, + whereas positional callers shift and wrap them separately. + """ + entries: tuple[Any, ...] = selection if isinstance(selection, tuple) else (selection,) + axes = _expanded_axis_walk(entries, domain.ndim, mode) + + for sel, axis in zip(entries, axes, strict=True): + arr = _as_index_array(sel) + if arr is None: + continue + if arr.dtype == np.bool_: + n_axes = _axes_consumed(sel, mode) + expected = domain.shape[axis : axis + n_axes] + if arr.shape != tuple(expected): + extent = ( + f"dimension {expected[0]}" + if len(expected) == 1 + else f"dimensions {tuple(expected)}" + ) + raise IndexError( + f"boolean index has shape {arr.shape} but {extent} has shape {tuple(expected)}" + ) + elif arr.dtype.kind not in "iu": + raise IndexError( + f"arrays used as indices must be of integer or boolean type; got dtype {arr.dtype}" + ) + + +def split_scalar_axes( + selection: Any, + domain: IndexDomain, + mode: SelectionMode, +) -> tuple[tuple[Any, ...] | None, Any]: + """Peel scalar integer indices out of a fancy selection. + + A scalar integer drops its axis, and neither the orthogonal nor the + vectorized path of the transform algebra models that — both widen a scalar + into a length-1 index array, which keeps the axis — so the scalars are split + off here and applied as a separate basic step first. + + Applying them *first* is this package's rule, not NumPy's. NumPy groups a + scalar with the advanced indices for the purpose of placing the broadcast + result, so the two disagree when a scalar and an index array are separated: + `a[0, ..., [1, 2]]` has shape `(2, 3)` for a `(2, 3, 4)` array, where + `a[0][..., [1, 2]]` has shape `(3, 2)`. The earlier claim here that they + always agree rested on `a[0, [1, 2], :]`, where the indices are adjacent and + they happen to. Scalar-first is the documented dialect (see the `lazy_array` + module docstring) — the divergence is deliberate, and this note exists so + that the correct end is not "fixed" later. + + Parameters + ---------- + selection + A positional orthogonal or vectorized selection. + domain + The domain of the view being indexed. + mode + `"orthogonal"` or `"vectorized"`; controls how many axes each entry + covers, which decides where the scalars sit. + + Returns + ------- + tuple[tuple[Any, ...] | None, Any] + `(basic_selection, remaining_selection)`. `basic_selection` is a + full-rank basic selection in **literal** domain coordinates that drops + the scalar axes, or `None` when the selection has no scalar entries (in + which case `remaining_selection` is `selection` unchanged). + + Raises + ------ + IndexError + If a boolean scalar is used as an index, an index is out of bounds, or + too many indices are supplied. + """ + entries = selection if isinstance(selection, tuple) else (selection,) + axes = _expanded_axis_walk(entries, domain.ndim, mode) + + scalar_axes: dict[int, int] = {} + remaining: list[Any] = [] + for sel, axis in zip(entries, axes, strict=True): + scalar = as_scalar_index(sel) + if scalar is not None: + scalar_axes[axis] = _normalize_int(scalar, domain.shape[axis], axis) + else: + remaining.append(sel) + + if len(scalar_axes) == 0: + return None, selection + + basic: list[Any] = [] + for axis in range(domain.ndim): + lo = domain.inclusive_min[axis] + if axis in scalar_axes: + basic.append(lo + scalar_axes[axis]) + else: + basic.append(slice(lo, domain.exclusive_max[axis])) + return tuple(basic), tuple(remaining) + + +def normalize_positional_selection( + selection: Any, + domain: IndexDomain, + mode: SelectionMode, +) -> Any: + """Translate a positional (NumPy-dialect) selection into literal coordinates. + + Positions are zero-based offsets into the current view; negatives wrap + from the end. The returned selection addresses the same cells in the + literal coordinate system `domain` uses, ready for + `zarr_indexing.transform.selection_to_transform`. + + Parameters + ---------- + selection + A NumPy-style selection: integers, slices, `Ellipsis`, integer arrays or + lists, or boolean arrays. + domain + The domain of the view being indexed. Its shape defines the positional + bounds and its origin the coordinate shift. + mode + Which selection dialect the entries follow: `"basic"` (integers and + slices), `"orthogonal"` (per-axis arrays, outer product), or + `"vectorized"` (correlated coordinate arrays or a single mask). + + Returns + ------- + tuple[Any, ...] + The selection with every coordinate expressed in literal domain + coordinates. + + Raises + ------ + IndexError + If a boolean scalar is used as an index, a boolean mask does not match + the shape of the axes it covers, an index is out of bounds, or too many + indices are supplied. + """ + entries = selection if isinstance(selection, tuple) else (selection,) + shape = domain.shape + origin = domain.inclusive_min + ndim = domain.ndim + + if mode in ("orthogonal", "vectorized"): + validate_advanced_selection(selection, domain, mode) + else: + for sel in entries: + if is_bool_scalar(sel): + raise IndexError( + "boolean scalars are not valid indices; use a boolean array " + "matching the shape of the axes it selects" + ) + + n_ellipsis = sum(1 for sel in entries if sel is Ellipsis) + if n_ellipsis > 1: + raise IndexError("an index can only have a single ellipsis ('...')") + consumed = sum(_axes_consumed(sel, mode) for sel in entries if sel is not Ellipsis) + if consumed > ndim: + raise IndexError( + f"too many indices for array: array has {ndim} dimensions, but {consumed} were indexed" + ) + + result: list[Any] = [] + axis = 0 + for sel in entries: + if sel is Ellipsis: + # Passed through rather than expanded: every mode of + # `selection_to_transform` expands an ellipsis (and pads short + # selections) to whole-axis slices itself, and `vectorized` mode + # rejects an explicit slice, so expanding here would turn a legal + # partial coordinate selection into an error. + result.append(Ellipsis) + axis += ndim - consumed + continue + if sel is None: + # newaxis: no axis of the view is consumed, and there is no + # coordinate to shift. The transform layer decides whether the mode + # accepts it. + result.append(None) + continue + + arr = _as_index_array(sel) + if arr is not None and arr.dtype == np.bool_: + n_axes = _axes_consumed(sel, mode) + expected = shape[axis : axis + n_axes] + if arr.shape != tuple(expected): + raise IndexError( + f"boolean index has shape {arr.shape} but the axes it " + f"covers have shape {tuple(expected)}" + ) + for offset, positions in enumerate(np.nonzero(arr)): + result.append(positions.astype(np.intp) + origin[axis + offset]) + axis += n_axes + continue + + if axis >= ndim: + raise IndexError( + f"too many indices for array: array has {ndim} dimensions, " + f"but {consumed} were indexed" + ) + size = shape[axis] + if arr is not None: + result.append(_normalize_int_array(arr, size, axis) + origin[axis]) + elif isinstance(sel, slice): + start, stop, step = _normalize_slice(sel, size, axis) + result.append(slice(start + origin[axis], stop + origin[axis], step)) + elif (scalar := as_scalar_index(sel)) is not None: + result.append(_normalize_int(scalar, size, axis) + origin[axis]) + else: + raise IndexError(f"unsupported selection type: {type(sel)!r}") + axis += 1 + + # Axes the selection did not mention are left to `selection_to_transform`, + # which pads them with whole-axis slices in every mode. + return tuple(result) diff --git a/packages/zarr-indexing/src/zarr_indexing/chunk_resolution.py b/packages/zarr-indexing/src/zarr_indexing/chunk_resolution.py index 7aea86ad02..af148685a0 100644 --- a/packages/zarr-indexing/src/zarr_indexing/chunk_resolution.py +++ b/packages/zarr-indexing/src/zarr_indexing/chunk_resolution.py @@ -18,80 +18,222 @@ 3. **Translate** — shift the restricted transform to chunk-local coordinates via `transform.translate(-chunk_origin)`. -4. **Yield** — produce `(chunk_coords, local_transform, surviving_indices)` - triples that the codec pipeline consumes. +4. **Project** — pair the chunk-local storage transform with a transform back + to the request's cells. Both use the same compact, zero-origin domain. Sorted one-dimensional correlated array maps can be partitioned directly because every touched chunk owns a contiguous slice of the index array. That case bypasses candidate enumeration and repeated intersection. -`sub_transform_to_selections` bridges from the transform representation -back to the raw `(chunk_selection, out_selection, drop_axes)` tuples that -the current codec pipeline expects. This bridge will go away when the codec -pipeline accepts transforms natively. +The public result is a lazy, reusable `ChunkPlan`. Each `ChunkProjection` is +source-independent: it identifies the chunk and expresses both sides of the +gather without assuming NumPy selectors, a codec pipeline, or an execution +scheduler. """ from __future__ import annotations -from typing import TYPE_CHECKING, Any +from dataclasses import dataclass +from typing import TYPE_CHECKING, Any, Literal import numpy as np +from zarr_indexing._affine import checked_affine from zarr_indexing.domain import IndexDomain from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap -from zarr_indexing.transform import IndexTransform +from zarr_indexing.transform import ( + IndexTransform, +) if TYPE_CHECKING: from collections.abc import Iterator, Sequence from zarr_indexing.grid import DimensionGridLike -OutIndices = ( +_OutIndices = ( dict[int, np.ndarray[Any, np.dtype[np.intp]]] | np.ndarray[Any, np.dtype[np.intp]] | None ) -ChunkTransformResult = tuple[ +_ChunkTransformResult = tuple[ tuple[int, ...], IndexTransform, - OutIndices, + _OutIndices, ] +type ChunkCoverage = Literal["full", "partial", "unknown"] + + +def _data_size(dim_grid: DimensionGridLike, chunk_ix: int) -> int: + """Return a chunk's data extent, falling back for narrow-protocol grids.""" + data_size = getattr(dim_grid, "data_size", None) + if data_size is None: + return dim_grid.chunk_size(chunk_ix) + return int(data_size(chunk_ix)) + + +@dataclass(frozen=True, slots=True) +class ChunkProjection: + """One source-independent projection of a request through a chunk. + + Both transforms share a synthetic input domain. ``chunk_transform`` maps + that domain to chunk-local storage coordinates; ``cell_transform`` maps it + to the original request domain. + + Attributes + ---------- + chunk_coords + Coordinates of the selected cell in the caller's grid. + chunk_domain + Bounds of that grid cell in global storage coordinates. + chunk_transform + Mapping from the shared synthetic domain to chunk-local storage. + cell_transform + Mapping from the shared synthetic domain to request coordinates. + coverage + Whether the request is proven to cover the whole grid cell exactly + once. Fancy selections are conservatively ``"unknown"``. + + Examples + -------- + Row 1 of a `(3, 4)` array with `(2, 2)` chunks touches only part of the + first chunk, whose domain spans rows `[0, 2)` and columns `[0, 2)`: + + >>> from zarr_indexing import IndexTransform + >>> from zarr_indexing.grid import dimension_grids_from_chunks + >>> grids = dimension_grids_from_chunks((2, 2), shape=(3, 4)) + >>> plan = plan_chunks(IndexTransform.from_shape((3, 4))[1, :], grids) + >>> first = next(iter(plan)) + >>> first.chunk_coords + (0, 0) + >>> first.chunk_domain.shape + (2, 2) + >>> first.coverage + 'partial' + """ + + chunk_coords: tuple[int, ...] + chunk_domain: IndexDomain + chunk_transform: IndexTransform + cell_transform: IndexTransform + coverage: ChunkCoverage + + def __post_init__(self) -> None: + if self.chunk_transform.domain != self.cell_transform.domain: + raise ValueError( + "chunk_transform and cell_transform must share an input domain; " + f"got {self.chunk_transform.domain!r} and {self.cell_transform.domain!r}" + ) + + +@dataclass(frozen=True, slots=True) +class ChunkPlan: + """A reusable, lazy partition of an index transform over a chunk grid. + + Construct plans with `plan_chunks`; iterating either the plan or + `projections()` performs a fresh chunk walk. + + Examples + -------- + Row 1 of a `(3, 4)` array with `(2, 2)` chunks crosses two chunks, and + the plan can be walked again after it is exhausted: + + >>> from zarr_indexing import IndexTransform + >>> from zarr_indexing.grid import dimension_grids_from_chunks + >>> grids = dimension_grids_from_chunks((2, 2), shape=(3, 4)) + >>> plan = plan_chunks(IndexTransform.from_shape((3, 4))[1, :], grids) + >>> [p.chunk_coords for p in plan] + [(0, 0), (0, 1)] + >>> [p.chunk_coords for p in plan.projections()] + [(0, 0), (0, 1)] + """ + + transform: IndexTransform + """The composed request this plan partitions.""" + + dimension_grids: tuple[DimensionGridLike, ...] + """One grid per storage dimension, defining the chunk layout the plan walks.""" -def _one_dimensional_correlated_array_map( + def projections(self) -> Iterator[ChunkProjection]: + """Return a fresh iterator over the chunks touched by this plan.""" + return _iter_chunk_projections(self.transform, self.dimension_grids) + + def __iter__(self) -> Iterator[ChunkProjection]: + """Equivalent to `projections()`: each iteration performs a fresh chunk walk.""" + return self.projections() + + +def plan_chunks( + transform: IndexTransform, + dimension_grids: Sequence[DimensionGridLike], +) -> ChunkPlan: + """Plan a transform against a caller-selected chunk grid. + + Parameters + ---------- + transform + Mapping from the request domain to storage coordinates. + dimension_grids + One storage grid per transform output dimension. + + Returns + ------- + ChunkPlan + A reusable plan whose projections are computed lazily. + + Examples + -------- + Row 1 of a `(3, 4)` array with `(2, 2)` chunks touches the two chunks in + the top grid row, each contributing a `(2, 2)` chunk domain: + + >>> from zarr_indexing import IndexTransform + >>> from zarr_indexing.grid import dimension_grids_from_chunks + >>> grids = dimension_grids_from_chunks((2, 2), shape=(3, 4)) + >>> plan = plan_chunks(IndexTransform.from_shape((3, 4))[1, :], grids) + >>> [p.chunk_coords for p in plan] + [(0, 0), (0, 1)] + >>> [p.chunk_domain.shape for p in plan] + [(2, 2), (2, 2)] + """ + grids = tuple(dimension_grids) + if len(grids) != transform.output_rank: + raise ValueError( + "dimension_grids must have one entry per transform output dimension; " + f"got {len(grids)} grids for output rank {transform.output_rank}" + ) + return ChunkPlan(transform=transform, dimension_grids=grids) + + +def _one_dimensional_array_map( transform: IndexTransform, ) -> tuple[ArrayMap, np.ndarray[Any, np.dtype[np.intp]]] | None: - """Return a nonempty correlated 1-D ArrayMap and its storage coordinates. + """Return a nonempty 1-D single-ArrayMap transform's map and storage coords. A one-dimensional array selection has no cross-dimensional correlation to - preserve. The computed storage coordinates are also reused by general - resolution when they are unsorted. + preserve — the orthogonal and vectorized flavors coincide there — so the + sorted fast path applies to either spelling. The computed storage + coordinates are also reused by general resolution when they are unsorted. """ if transform.input_rank != 1 or transform.output_rank != 1: return None m = transform.output[0] - if ( - not isinstance(m, ArrayMap) - or m.input_dimension is not None - or m.index_array.ndim != 1 - or m.index_array.size == 0 - ): + if not isinstance(m, ArrayMap) or m.index_array.ndim != 1 or m.index_array.size == 0: return None - return m, m.offset + m.stride * m.index_array + return m, checked_affine(m.offset, m.stride, m.index_array) def _iter_sorted_1d_array_map( m: ArrayMap, storage: np.ndarray[Any, np.dtype[np.intp]], dim_grid: DimensionGridLike, -) -> Iterator[ChunkTransformResult]: +) -> Iterator[_ChunkTransformResult]: """Resolve a sorted 1-D ArrayMap one touched chunk at a time.""" start = 0 while start < storage.size: chunk = dim_grid.index_to_chunk(int(storage[start])) chunk_start = dim_grid.chunk_offset(chunk) - chunk_stop = chunk_start + dim_grid.chunk_size(chunk) + chunk_stop = chunk_start + _data_size(dim_grid, chunk) stop = int(np.searchsorted(storage, chunk_stop, side="left")) restricted = IndexTransform( @@ -101,7 +243,6 @@ def _iter_sorted_1d_array_map( index_array=m.index_array[start:stop], offset=m.offset, stride=m.stride, - input_dimension=m.input_dimension, ), ), ) @@ -112,23 +253,24 @@ def _iter_sorted_1d_array_map( start = stop -def iter_chunk_transforms( +def _iter_chunk_transform_results( transform: IndexTransform, dim_grids: Sequence[DimensionGridLike], -) -> Iterator[ChunkTransformResult]: - """Resolve a composed IndexTransform against per-dimension chunk grids. +) -> Iterator[_ChunkTransformResult]: + """Resolve a transform into private intersection bookkeeping. - `dim_grids` holds one `DimensionGridLike` per output (storage) dimension — - for zarr this is the chunk grid's per-dimension sequence. Yields - `(chunk_coords, sub_transform, out_indices)` triples: - - - `chunk_coords`: which chunk to access. - - `sub_transform`: maps output buffer coords to chunk-local coords. - - `out_indices`: for vectorized/array indexing, the output scatter - indices (integer array). `None` for basic/slice indexing. + The survivor arrays are an implementation detail immediately converted to + a public `cell_transform` by `_iter_chunk_projections`. """ - array_map_1d = _one_dimensional_correlated_array_map(transform) + if any(size == 0 for size in transform.domain.shape): + # An empty view touches no chunk. Checked on the domain rather than on + # the index arrays: an axis of genuine extent 1 is stored as a broadcast + # singleton, so a slice that empties the domain does not shrink the + # array, and the emptiness shows only here. + return + + array_map_1d = _one_dimensional_array_map(transform) if array_map_1d is not None: sorted_map, storage = array_map_1d if storage[0] <= storage[-1] and bool(np.all(storage[1:] >= storage[:-1])): @@ -163,6 +305,7 @@ def iter_chunk_transforms( # combinations no point touches — quadratic in the number of selected # points for a diagonal selection — while the joint distinct set is # bounded by the point count (see zarr-python gh-4174). + structure = transform.index_array_structure correlated_dims: list[int] = [] correlated_chunk_ids: list[np.ndarray[Any, np.dtype[np.intp]]] = [] slot_dims: list[tuple[int, ...]] = [] @@ -171,7 +314,8 @@ def iter_chunk_transforms( dg = dim_grids[out_dim] if isinstance(m, ConstantMap): # Single chunk - c = dg.index_to_chunk(m.offset) + coordinate = checked_affine(m.offset, 0, 0) + c = dg.index_to_chunk(coordinate) slot_dims.append((out_dim,)) slot_candidates.append(((c,),)) elif isinstance(m, DimensionMap): @@ -180,34 +324,51 @@ def iter_chunk_transforms( dim_hi = transform.domain.exclusive_max[d] if dim_lo >= dim_hi: return # empty domain + first_storage = checked_affine(m.offset, m.stride, dim_lo) if m.stride > 0: - s_min = m.offset + m.stride * dim_lo - s_max = m.offset + m.stride * (dim_hi - 1) + s_min = first_storage + s_max = checked_affine(m.offset, m.stride, dim_hi - 1) + elif m.stride < 0: + s_min = checked_affine(m.offset, m.stride, dim_hi - 1) + s_max = first_storage else: - s_min = m.offset + m.stride * (dim_hi - 1) - s_max = m.offset + m.stride * dim_lo + s_min = s_max = first_storage first = dg.index_to_chunk(s_min) last = dg.index_to_chunk(s_max) slot_dims.append((out_dim,)) - slot_candidates.append([(c,) for c in range(first, last + 1)]) + point_count = dim_hi - dim_lo + chunk_count = last - first + 1 + if point_count < chunk_count: + steps = np.arange(point_count, dtype=np.intp) + storage = checked_affine(first_storage, m.stride, steps) + chunk_ids = dg.indices_to_chunks(storage) + slot_candidates.append([(int(c),) for c in np.unique(chunk_ids)]) + else: + slot_candidates.append([(c,) for c in range(first, last + 1)]) else: # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap). # Storage coordinates were already computed for a correlated 1-D map. storage = ( - array_map_1d[1] if array_map_1d is not None else m.offset + m.stride * m.index_array + array_map_1d[1] + if array_map_1d is not None + else checked_affine(m.offset, m.stride, m.index_array) ) if storage.size == 0: # Empty fancy selection: no coordinates, so no chunks are touched. return # Keep the index-array shape: correlated maps broadcast against each # other below, and raveling first would lose the singleton axes. - chunk_ids = dg.indices_to_chunks(storage.astype(np.intp)) - if m.input_dimension is None: - correlated_dims.append(out_dim) - correlated_chunk_ids.append(chunk_ids) - else: + chunk_ids = dg.indices_to_chunks(storage) + if structure == "orthogonal": slot_dims.append((out_dim,)) slot_candidates.append([(int(c),) for c in np.unique(chunk_ids)]) + else: + # Every index array of a general transform joins one joint + # slot: their chunk ids broadcast over the shared block, so the + # distinct tuples enumerate only combinations some point + # actually touches. + correlated_dims.append(out_dim) + correlated_chunk_ids.append(chunk_ids) if len(correlated_dims) == 1: slot_dims.append((correlated_dims[0],)) @@ -238,7 +399,7 @@ def iter_chunk_transforms( for out_dim, c in enumerate(chunk_coords): dg = dim_grids[out_dim] c_start = dg.chunk_offset(c) - c_size = dg.chunk_size(c) + c_size = _data_size(dg, c) chunk_min.append(c_start) chunk_max.append(c_start + c_size) chunk_shift.append(-c_start) @@ -261,120 +422,174 @@ def iter_chunk_transforms( yield (chunk_coords, local, surviving) -def sub_transform_to_selections( - sub_transform: IndexTransform, - out_indices: OutIndices = None, -) -> tuple[ - tuple[int | slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]], ...], - tuple[slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]], ...], - tuple[int, ...], -]: - """Convert a chunk-local sub-transform to raw selections for the codec pipeline. - - Parameters - ---------- - sub_transform - A chunk-local IndexTransform (output maps already translated to - chunk-local coordinates). - out_indices - For vectorized indexing: the output scatter indices for this chunk. - None for orthogonal/basic indexing. +def _covers_whole_chunk(transform: IndexTransform, chunk_shape: tuple[int, ...]) -> bool: + """Whether an affine chunk-local transform bijects onto every chunk cell.""" + domain = transform.domain + used_nontrivial_inputs: set[int] = set() + for out_dim, m in enumerate(transform.output): + extent = chunk_shape[out_dim] + if isinstance(m, ConstantMap): + if extent != 1 or m.offset != 0: + return False + elif isinstance(m, DimensionMap): + if abs(m.stride) != 1: + return False + lo = domain.inclusive_min[m.input_dimension] + hi = domain.exclusive_max[m.input_dimension] + if hi <= lo: + if extent != 0: + return False + continue + first = m.offset + m.stride * lo + last = m.offset + m.stride * (hi - 1) + if min(first, last) != 0 or max(first, last) != extent - 1: + return False + if extent > 1: + if m.input_dimension in used_nontrivial_inputs: + return False + used_nontrivial_inputs.add(m.input_dimension) + else: + return False + nontrivial_inputs = {dimension for dimension, extent in enumerate(domain.shape) if extent > 1} + return used_nontrivial_inputs == nontrivial_inputs + + +def _orthogonal_cell_transform( + original: IndexTransform, + restricted: IndexTransform, + survivors: dict[int, np.ndarray[Any, np.dtype[np.intp]]] | np.ndarray[Any, np.dtype[np.intp]], +) -> IndexTransform: + """Map a compacted orthogonal intersection back to request coordinates.""" + by_input_dimension: dict[int, np.ndarray[Any, np.dtype[np.intp]]] = {} + if isinstance(survivors, dict): + survivor_items = survivors.items() + else: + array_output_dimensions = [ + output_dimension + for output_dimension, output_map in enumerate(original.output) + if isinstance(output_map, ArrayMap) + ] + if len(array_output_dimensions) != 1: + raise ValueError( + "one survivor array requires exactly one orthogonal ArrayMap; " + f"found output dimensions {array_output_dimensions}" + ) + survivor_items = ((array_output_dimensions[0], survivors),) - Returns - ------- - tuple - `(chunk_selection, out_selection, drop_axes)` - """ - inclusive_min = sub_transform.domain.inclusive_min - exclusive_max = sub_transform.domain.exclusive_max - - # Orthogonal outer product: >= 2 ArrayMaps each bound to a distinct input - # dimension. out_indices is a per-output-dim dict of surviving positions. The - # codec applies chunk_array[chunk_sel] / out[out_sel] with NumPy semantics, so - # build np.ix_-style selections (mirroring the legacy OrthogonalIndexer): one - # 1-D selector per dimension, expanded to an open mesh. ConstantMap dims are - # size-1 in chunk space and squeezed out via drop_axes. - if isinstance(out_indices, dict): - chunk_arrays: list[np.ndarray[Any, np.dtype[np.intp]]] = [] - out_arrays: list[np.ndarray[Any, np.dtype[np.intp]]] = [] - drop_axes: list[int] = [] - for out_dim, m in enumerate(sub_transform.output): - if isinstance(m, ConstantMap): - chunk_arrays.append(np.array([m.offset], dtype=np.intp)) - drop_axes.append(out_dim) - elif isinstance(m, DimensionMap): - rng = np.arange(inclusive_min[m.input_dimension], exclusive_max[m.input_dimension]) - chunk_arrays.append((m.offset + m.stride * rng).astype(np.intp)) - out_arrays.append(rng.astype(np.intp)) - else: # ArrayMap - idx = m.index_array.ravel() - chunk_arrays.append((m.offset + m.stride * idx).astype(np.intp)) - out_arrays.append(out_indices[out_dim]) - return np.ix_(*chunk_arrays), np.ix_(*out_arrays), tuple(drop_axes) - - # Correlated (vindex) sub-transforms carry ArrayMaps with `input_dimension` - # None. They scatter through a single flat index (`out_indices`) into the - # row-major-flattened output buffer; the chunk selection reads a - # (points, residual-slice) block via the raveled coordinate arrays and any - # residual DimensionMap slices. - correlated = any( - isinstance(m, ArrayMap) and m.input_dimension is None for m in sub_transform.output + for output_dimension, positions in survivor_items: + output_map = original.output[output_dimension] + if not isinstance(output_map, ArrayMap): + raise TypeError( + f"survivors for output dimension {output_dimension} do not describe an ArrayMap" + ) + input_dimension = output_map.dependent_axis + if input_dimension is None: + raise ValueError( + f"output dimension {output_dimension} has no orthogonal input dimension" + ) + by_input_dimension[input_dimension] = np.asarray(positions, dtype=np.intp) + + output: list[ConstantMap | DimensionMap | ArrayMap] = [] + rank = original.input_rank + for input_dimension in range(rank): + positions = by_input_dimension.get(input_dimension) + if positions is None: + output.append(DimensionMap(input_dimension=input_dimension)) + continue + shape = (1,) * input_dimension + (positions.size,) + (1,) * (rank - input_dimension - 1) + output.append( + ArrayMap( + index_array=positions.reshape(shape), + offset=original.domain.inclusive_min[input_dimension], + ) + ) + return IndexTransform(domain=restricted.domain, output=tuple(output)) + + +def _correlated_cell_transform( + original: IndexTransform, + restricted: IndexTransform, + survivors: np.ndarray[Any, np.dtype[np.intp]], +) -> IndexTransform: + """Map compacted correlated points back through the request's row-major domain.""" + positions = np.asarray(survivors, dtype=np.intp) + # Correlated broadcast axes already contribute positional survivor offsets; + # residual affine axes still contribute literal coordinates. Remove only + # the latter origins before unraveling the fully positional flat offsets. + literal_axes = { + output_map.input_dimension + for output_map in original.output + if isinstance(output_map, DimensionMap) + } + origin_offset = 0 + flat_stride = 1 + for input_dimension in range(original.input_rank - 1, -1, -1): + if input_dimension in literal_axes: + origin_offset += original.domain.inclusive_min[input_dimension] * flat_stride + extent = original.domain.shape[input_dimension] + flat_stride *= extent + coordinates = np.unravel_index( + checked_affine(-origin_offset, 1, positions), original.domain.shape ) - if correlated: - chunk_sel: list[int | slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]]] = [] - for m in sub_transform.output: - if isinstance(m, ConstantMap): - chunk_sel.append(m.offset) - elif isinstance(m, DimensionMap): - d = m.input_dimension - start = m.offset + m.stride * inclusive_min[d] - stop = m.offset + m.stride * exclusive_max[d] - if m.stride < 0: - start, stop = stop + 1, start + 1 - chunk_sel.append(slice(start, stop, m.stride)) - else: # ArrayMap - idx = m.index_array.reshape(-1) - chunk_sel.append((m.offset + m.stride * idx).astype(np.intp)) - # Chunk resolution always supplies the flat scatter index for a - # correlated transform. Absent one (a bare sub-transform), fall back to an - # identity scatter over the whole flattened output buffer. - # `out_indices` is narrowed to a flat scatter array or None here (the - # per-dimension dict is an orthogonal outer product, handled above). - out_scatter: slice | np.ndarray[Any, np.dtype[np.intp]] - if out_indices is None: - n = 1 - for s in sub_transform.domain.shape: - n *= s - out_scatter = slice(0, n) - else: - out_scatter = out_indices - return tuple(chunk_sel), (out_scatter,), () + output = tuple( + ArrayMap( + index_array=np.asarray(coordinate, dtype=np.intp), + offset=origin, + ) + for coordinate, origin in zip(coordinates, original.domain.inclusive_min, strict=True) + ) + return IndexTransform(domain=restricted.domain, output=output) - chunk_sel = [] # annotated in the correlated branch above (same function scope) - out_sel: list[slice | np.ndarray[tuple[int, ...], np.dtype[np.intp]]] = [] - # Single-pass build for the basic / single-orthogonal-array cases. - # ConstantMap dims are dropped (no out_sel entry). - for m in sub_transform.output: - if isinstance(m, ConstantMap): - chunk_sel.append(m.offset) - elif isinstance(m, DimensionMap): - d = m.input_dimension - dim_lo = inclusive_min[d] - dim_hi = exclusive_max[d] - start = m.offset + m.stride * dim_lo - stop = m.offset + m.stride * dim_hi - if m.stride < 0: - start, stop = stop + 1, start + 1 - chunk_sel.append(slice(start, stop, m.stride)) - out_sel.append(slice(dim_lo, dim_hi)) - else: # ArrayMap (orthogonal: full-rank, raveled to its 1-D fancy coords) - idx = m.index_array.reshape(-1) - if m.offset == 0 and m.stride == 1: - chunk_sel.append(idx) - else: - chunk_sel.append((m.offset + m.stride * idx).astype(np.intp)) - # Orthogonal ArrayMap: out_indices holds the surviving positions. - out_sel.append(out_indices if out_indices is not None else slice(0, idx.size)) +def _cell_transform( + original: IndexTransform, + restricted: IndexTransform, + survivors: _OutIndices, +) -> IndexTransform: + """Convert private survivor bookkeeping into a direction-neutral transform.""" + if survivors is None: + return IndexTransform.identity(restricted.domain) + if original.index_array_structure == "general": + if isinstance(survivors, dict): + raise ValueError("general intersections require one shared survivor array") + return _correlated_cell_transform(original, restricted, survivors) + return _orthogonal_cell_transform(original, restricted, survivors) + - return tuple(chunk_sel), tuple(out_sel), () +def _iter_chunk_projections( + transform: IndexTransform, + dim_grids: Sequence[DimensionGridLike], +) -> Iterator[ChunkProjection]: + """Convert private intersection results into public paired projections.""" + for chunk_coords, chunk_transform, survivors in _iter_chunk_transform_results( + transform, dim_grids + ): + chunk_min = tuple( + grid.chunk_offset(coord) for grid, coord in zip(dim_grids, chunk_coords, strict=True) + ) + chunk_shape = tuple( + _data_size(grid, coord) for grid, coord in zip(dim_grids, chunk_coords, strict=True) + ) + chunk_domain = IndexDomain( + inclusive_min=chunk_min, + exclusive_max=tuple( + origin + extent for origin, extent in zip(chunk_min, chunk_shape, strict=True) + ), + ) + cell_transform = _cell_transform(transform, chunk_transform, survivors) + synthetic_origin = (0,) * chunk_transform.input_rank + chunk_transform = chunk_transform.translate_domain_to(synthetic_origin) + cell_transform = cell_transform.translate_domain_to(synthetic_origin) + if survivors is not None or any(isinstance(m, ArrayMap) for m in chunk_transform.output): + coverage: ChunkCoverage = "unknown" + elif _covers_whole_chunk(chunk_transform, chunk_shape): + coverage = "full" + else: + coverage = "partial" + yield ChunkProjection( + chunk_coords=chunk_coords, + chunk_domain=chunk_domain, + chunk_transform=chunk_transform, + cell_transform=cell_transform, + coverage=coverage, + ) diff --git a/packages/zarr-indexing/src/zarr_indexing/composition.py b/packages/zarr-indexing/src/zarr_indexing/composition.py deleted file mode 100644 index f5cc82599c..0000000000 --- a/packages/zarr-indexing/src/zarr_indexing/composition.py +++ /dev/null @@ -1,133 +0,0 @@ -"""Composition — chaining two transforms into one. - -`compose(outer, inner)` is the operation that makes views stack. `outer` maps -user coordinates to intermediate coordinates, `inner` maps those intermediate -coordinates to storage, and the result maps user coordinates straight to -storage — so a view of a view of an array is still a single -`IndexTransform`, and indexing never accumulates layers to walk at read time. - -Composition works one output map at a time, and each case reduces to -substituting the outer map into the inner one: - -- A `ConstantMap` inner map ignores its input, so it survives unchanged. -- A `DimensionMap` inner map is affine, so composing it with an outer - `ConstantMap` or `DimensionMap` folds into new `offset`/`stride` values; - composing it with an outer `ArrayMap` leaves the index array alone and - rescales around it. -- An `ArrayMap` inner map must be *evaluated* at the coordinates the outer - transform produces, which is the only case that touches array data. -""" - -from __future__ import annotations - -import numpy as np - -from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap -from zarr_indexing.transform import IndexTransform - - -def compose(outer: IndexTransform, inner: IndexTransform) -> IndexTransform: - """Compose two IndexTransforms. - - `outer` maps user coords (rank m) to intermediate coords (rank n). - `inner` maps intermediate coords (rank n) to storage coords (rank p). - The result maps user coords (rank m) to storage coords (rank p). - - Precondition: `outer.output_rank == inner.domain.ndim`. - """ - if outer.output_rank != inner.domain.ndim: - raise ValueError( - f"outer output rank ({outer.output_rank}) must match inner input rank " - f"({inner.domain.ndim})" - ) - - result_output = [_compose_single(outer, inner_map) for inner_map in inner.output] - - return IndexTransform(domain=outer.domain, output=tuple(result_output)) - - -def _compose_single(outer: IndexTransform, inner_map: OutputIndexMap) -> OutputIndexMap: - """Compose a single inner output map with the full outer transform.""" - if isinstance(inner_map, ConstantMap): - return ConstantMap(offset=inner_map.offset) - - if isinstance(inner_map, DimensionMap): - return _compose_dimension(outer, inner_map) - - # inner_map: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) - return _compose_array(outer, inner_map) - - -def _compose_dimension(outer: IndexTransform, inner_map: DimensionMap) -> OutputIndexMap: - """Compose when inner is a DimensionMap. - - storage = offset_i + stride_i * intermediate[dim_i] - where intermediate[dim_i] = outer.output[dim_i](user_input) - """ - dim_i = inner_map.input_dimension - offset_i = inner_map.offset - stride_i = inner_map.stride - outer_map = outer.output[dim_i] - - if isinstance(outer_map, ConstantMap): - return ConstantMap(offset=offset_i + stride_i * outer_map.offset) - - if isinstance(outer_map, DimensionMap): - return DimensionMap( - input_dimension=outer_map.input_dimension, - offset=offset_i + stride_i * outer_map.offset, - stride=stride_i * outer_map.stride, - ) - - # outer_map: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) - # Affine post-composition leaves the index array (and hence its full - # input rank and dependency axes) untouched; carry the orthogonal - # binding through unchanged. - return ArrayMap( - index_array=outer_map.index_array, - offset=offset_i + stride_i * outer_map.offset, - stride=stride_i * outer_map.stride, - input_dimension=outer_map.input_dimension, - ) - - -def _compose_array(outer: IndexTransform, inner_map: ArrayMap) -> OutputIndexMap: - """Compose when inner is an ArrayMap. - - storage = offset_i + stride_i * arr_i[intermediate] - We need to evaluate arr_i at the intermediate coordinates produced by outer. - """ - arr_i = inner_map.index_array - offset_i = inner_map.offset - stride_i = inner_map.stride - - # Check if all outer outputs are constant - all_constant = all(isinstance(m, ConstantMap) for m in outer.output) - - if all_constant: - # Evaluate arr_i at the single constant point - idx = tuple(m.offset for m in outer.output if isinstance(m, ConstantMap)) - value = int(arr_i[idx]) - return ConstantMap(offset=offset_i + stride_i * value) - - # For 1D inner array with a single outer output (simple case) - if arr_i.ndim == 1 and len(outer.output) == 1: - outer_map = outer.output[0] - - if isinstance(outer_map, DimensionMap): - dim_size = outer.domain.shape[outer_map.input_dimension] - user_indices = np.arange(dim_size, dtype=np.intp) - intermediate_vals = outer_map.offset + outer_map.stride * user_indices - new_arr = arr_i[intermediate_vals] - return ArrayMap(index_array=new_arr, offset=offset_i, stride=stride_i) - - if isinstance(outer_map, ArrayMap): - intermediate_vals = outer_map.offset + outer_map.stride * outer_map.index_array - new_arr = arr_i[intermediate_vals] - return ArrayMap(index_array=new_arr, offset=offset_i, stride=stride_i) - - # General multi-dim case: not yet implemented - raise NotImplementedError( - "Composing a multi-dimensional inner array map with non-constant outer maps " - "is not yet supported." - ) diff --git a/packages/zarr-indexing/src/zarr_indexing/domain.py b/packages/zarr-indexing/src/zarr_indexing/domain.py index f20d5bf7bd..a353b81254 100644 --- a/packages/zarr-indexing/src/zarr_indexing/domain.py +++ b/packages/zarr-indexing/src/zarr_indexing/domain.py @@ -14,7 +14,12 @@ from __future__ import annotations from dataclasses import dataclass, field -from typing import Any +from typing import TYPE_CHECKING, Any + +from zarr_indexing.errors import BoundsCheckError + +if TYPE_CHECKING: + from zarr_indexing.json import IndexDomainJSON @dataclass(frozen=True, slots=True) @@ -23,11 +28,32 @@ class IndexDomain: The valid coordinates are the integers in `[inclusive_min[d], exclusive_max[d])` for each dimension `d`. + + Examples + -------- + >>> domain = IndexDomain(inclusive_min=(2, 5), exclusive_max=(10, 20)) + >>> domain.shape + (8, 15) + + Unlike a NumPy shape, a domain keeps literal coordinates: narrowing to + `[5, 10)` gives a region whose valid coordinates are 5 through 9, not + re-zeroed: + + >>> view = IndexDomain.from_shape((10,)).narrow(slice(5, 10)) + >>> view.origin, view.shape + ((5,), (5,)) + >>> view.contains((5,)), view.contains((0,)) + (True, False) """ inclusive_min: tuple[int, ...] + """The lower corner: each dimension's smallest literal coordinate. May be negative.""" + exclusive_max: tuple[int, ...] + """Each dimension's upper bound, excluded: valid coordinates end at `exclusive_max - 1`.""" + labels: tuple[str, ...] | None = None + """Optional per-dimension names; carried through the wire format, never consulted by indexing.""" # Lazily-memoized shape. Excluded from init/repr/eq/hash: it is derived # state, not part of the domain's identity. The domain is frozen, so the # value is computed at most once (see `shape`). `None` is the unset @@ -62,14 +88,17 @@ def from_shape(cls, shape: tuple[int, ...]) -> IndexDomain: @property def ndim(self) -> int: + """Number of dimensions.""" return len(self.inclusive_min) @property def origin(self) -> tuple[int, ...]: + """The lower corner of the domain — an alias for `inclusive_min`, and may be negative.""" return self.inclusive_min @property def shape(self) -> tuple[int, ...]: + """Per-dimension extents: `exclusive_max - inclusive_min` for each dimension.""" cached = self._shape if cached is None: cached = tuple( @@ -79,6 +108,12 @@ def shape(self) -> tuple[int, ...]: return cached def contains(self, index: tuple[int, ...]) -> bool: + """Whether the literal coordinate `index` lies inside this domain. + + Coordinates are literal, not NumPy-style offsets: a negative value is + the coordinate itself, valid only if the domain's bounds include it. + A tuple of the wrong length is simply not contained (returns `False`). + """ if len(index) != self.ndim: return False return all( @@ -87,6 +122,11 @@ def contains(self, index: tuple[int, ...]) -> bool: ) def contains_domain(self, other: IndexDomain) -> bool: + """Whether every coordinate of `other` lies inside this domain. + + An empty `other` within this domain's bounds is contained. A rank + mismatch returns `False` rather than raising. + """ if other.ndim != self.ndim: return False return all( @@ -101,6 +141,13 @@ def contains_domain(self, other: IndexDomain) -> bool: ) def intersect(self, other: IndexDomain) -> IndexDomain | None: + """Return the overlap of this domain with `other`, or `None` if they are disjoint. + + Raises + ------ + ValueError + If the two domains have different ranks. + """ if other.ndim != self.ndim: raise ValueError( f"Cannot intersect domains with different ranks: {self.ndim} vs {other.ndim}" @@ -116,6 +163,15 @@ def intersect(self, other: IndexDomain) -> IndexDomain | None: return IndexDomain(inclusive_min=new_min, exclusive_max=new_max) def translate(self, offset: tuple[int, ...]) -> IndexDomain: + """Return this domain shifted by `offset` per dimension; the shape is unchanged. + + Offsets may be negative, and the result may have a negative origin. + + Raises + ------ + ValueError + If `offset` does not have one entry per dimension. + """ if len(offset) != self.ndim: raise ValueError( f"Offset must have same length as domain dimensions. " @@ -127,8 +183,22 @@ def translate(self, offset: tuple[int, ...]) -> IndexDomain: def narrow(self, selection: Any) -> IndexDomain: """Apply a basic selection and return a narrowed domain. - Indices are absolute coordinates. Integer indices produce length-1 extent. - Strided slices are not supported — use IndexTransform for strides. + + Indices are absolute coordinates, not NumPy-style offsets: `-3` names + the coordinate `-3`, and is out of bounds unless the domain contains it. + Integer indices produce a length-1 extent. Strided slices are not + supported — use `IndexTransform` for strides. + + Raises + ------ + BoundsCheckError + If a bound lies outside this domain. A slice bound used to be + clamped instead, so `narrow(slice(-3, None))` on `[0, 10)` quietly + returned the whole axis — reading as the NumPy spelling of "the last + three" and answering with something else — and `narrow(slice(20, + 30))` returned a domain its own parent did not contain. The rest of + the algebra states no clamping and no negative wrapping as an + invariant and enforces it; this is the one place that did not. """ normalized = _normalize_selection(selection, self.ndim) new_inclusive_min: list[int] = [] @@ -138,7 +208,7 @@ def narrow(self, selection: Any) -> IndexDomain: ): if isinstance(sel, int): if sel < dim_lo or sel >= dim_hi: - raise IndexError( + raise BoundsCheckError( f"index {sel} is out of bounds for dimension {dim_idx} " f"with domain [{dim_lo}, {dim_hi})" ) @@ -147,22 +217,88 @@ def narrow(self, selection: Any) -> IndexDomain: else: start, stop, step = sel.start, sel.stop, sel.step if step is not None and step != 1: - raise IndexError( + raise ValueError( "IndexDomain.narrow only supports step=1 slices. " f"Got step={step}. Use IndexTransform for strided access." ) abs_start = dim_lo if start is None else start abs_stop = dim_hi if stop is None else stop - abs_start = max(abs_start, dim_lo) - abs_stop = min(abs_stop, dim_hi) - abs_stop = max(abs_stop, abs_start) + for bound, name in ((abs_start, "start"), (abs_stop, "stop")): + if bound < dim_lo or bound > dim_hi: + raise BoundsCheckError( + f"slice {name} {bound} is out of bounds for dimension " + f"{dim_idx} with domain [{dim_lo}, {dim_hi}); indices " + f"here are absolute coordinates, so they are neither " + f"clamped to the domain nor counted from its end" + ) + # An empty interval is legal; a reversed one is the same request + # spelled backwards, and reads as empty rather than as an error. new_inclusive_min.append(abs_start) - new_exclusive_max.append(abs_stop) + new_exclusive_max.append(max(abs_stop, abs_start)) return IndexDomain( inclusive_min=tuple(new_inclusive_min), exclusive_max=tuple(new_exclusive_max), ) + # -- serialization ------------------------------------------------------ + + def to_json(self) -> IndexDomainJSON: + """Convert to the canonical ndsel JSON representation. + + Examples + -------- + >>> IndexDomain(inclusive_min=(0,), exclusive_max=(3,)).to_json() + {'input_inclusive_min': [0], 'input_exclusive_max': [3], 'input_labels': ['']} + """ + from zarr_indexing._wire import emit_labels + + return { + "input_inclusive_min": list(self.inclusive_min), + "input_exclusive_max": list(self.exclusive_max), + "input_labels": emit_labels(self.labels, self.ndim), + } + + @classmethod + def from_json(cls, data: IndexDomainJSON) -> IndexDomain: + """Construct from the canonical ndsel JSON representation. + + The document is validated by the message layer first, exactly as a + transform body is. Reading the keys directly would be a second, + undefended way into the same objects: `int(value)` alone accepts + `3.9`, `"3"` and `True`, and each of those builds a domain that is + not the document's. + + Examples + -------- + >>> domain = IndexDomain.from_json( + ... {"input_inclusive_min": [1], "input_exclusive_max": [4], "input_labels": [""]} + ... ) + >>> (domain.inclusive_min, domain.exclusive_max, domain.shape) + ((1,), (4,), (3,)) + >>> IndexDomain.from_json(domain.to_json()) == domain + True + """ + from zarr_indexing._wire import lower_bound, lower_labels + from zarr_indexing.messages import NdselError, normalize_ndsel + + # The annotation says what a well-formed caller passes; this is a parser + # of documents that arrive from elsewhere, so the shape is checked + # rather than assumed. + if not isinstance(data, dict): # pyright: ignore[reportUnnecessaryIsInstance] + raise NdselError("invalid_json", f"an index domain must be a JSON object, got {data!r}") + body = normalize_ndsel({**data, "kind": "transform"}) + return cls( + inclusive_min=tuple( + lower_bound(b, f"input_inclusive_min[{i}]") + for i, b in enumerate(body["input_inclusive_min"]) + ), + exclusive_max=tuple( + lower_bound(b, f"input_exclusive_max[{i}]") + for i, b in enumerate(body["input_exclusive_max"]) + ), + labels=lower_labels(body["input_labels"]), + ) + def _normalize_selection(selection: Any, ndim: int) -> tuple[int | slice, ...]: """Normalize a basic selection to a tuple of ints/slices with length ndim.""" diff --git a/packages/zarr-indexing/src/zarr_indexing/errors.py b/packages/zarr-indexing/src/zarr_indexing/errors.py index fa2f6fc5d3..efd3b1ecd6 100644 --- a/packages/zarr-indexing/src/zarr_indexing/errors.py +++ b/packages/zarr-indexing/src/zarr_indexing/errors.py @@ -1,10 +1,12 @@ """Canonical index-error types raised by the transform algebra. -These are the authoritative class definitions. `zarr.errors` re-exports the -same objects (`from zarr_indexing.errors import ...`) so that, e.g., -`zarr.errors.BoundsCheckError is zarr_indexing.errors.BoundsCheckError`. -Both subclass the built-in `IndexError`, so existing `except IndexError` (or -`except zarr.errors.BoundsCheckError`) catch sites keep working unchanged. +Both subclass the built-in `IndexError`, so an `except IndexError` catch site +keeps working unchanged whichever library raised. + +`zarr.errors` defines classes of the same names, and they are *not* these +objects: `zarr.errors.BoundsCheckError is BoundsCheckError` is false. Catching +zarr's around a call into this package therefore catches nothing but their +shared `IndexError` base. Import these from here. """ from __future__ import annotations @@ -15,7 +17,51 @@ ] -class VindexInvalidSelectionError(IndexError): ... +class VindexInvalidSelectionError(IndexError): + """A wrapper `vindex` selection contained a slice. + + Raised by `LazyArray`'s selection validation: the wrapper's vectorized + dialect accepts coordinate selections (integer arrays, with scalars and + an ellipsis) or a single boolean mask, and rejects slices with this + error. Other invalid entries raise plain `IndexError`, and the + engine-level `IndexTransform.vindex` is wider — it accepts residual + slice dimensions without raising. + + Examples + -------- + Raised by the wrapper, not the engine — a slice inside `vindex`: + + >>> import numpy as np + >>> from zarr_indexing import LazyArray + >>> view = LazyArray.from_numpy(np.arange(12).reshape(3, 4)) + >>> view.lazy.vindex[np.array([0, 2]), :] + Traceback (most recent call last): + ... + zarr_indexing.errors.VindexInvalidSelectionError: ... + """ + + +class BoundsCheckError(IndexError): + """A selection addressed coordinates outside the domain being indexed. + + Raised for out-of-domain integer indices, slice bounds, index-array + values, and points passed to `IndexTransform.apply`. Coordinates in this + algebra are literal: they are never clamped, and a negative value below + the domain's `inclusive_min` is out of bounds rather than counted from + the end. + + Examples + -------- + >>> from zarr_indexing import IndexTransform + >>> IndexTransform.from_shape((8,)).apply((9,)) + Traceback (most recent call last): + ... + zarr_indexing.errors.BoundsCheckError: ... + A negative index is a literal coordinate, not "from the end": -class BoundsCheckError(IndexError): ... + >>> IndexTransform.from_shape((8,))[-1] + Traceback (most recent call last): + ... + zarr_indexing.errors.BoundsCheckError: ... + """ diff --git a/packages/zarr-indexing/src/zarr_indexing/grid.py b/packages/zarr-indexing/src/zarr_indexing/grid.py index de1dae2dfc..20ad3f95c2 100644 --- a/packages/zarr-indexing/src/zarr_indexing/grid.py +++ b/packages/zarr-indexing/src/zarr_indexing/grid.py @@ -1,25 +1,826 @@ -"""Structural typing for the chunk-grid surface used by chunk resolution. +"""Compact chunk grids and the narrow planner protocol. -`chunk_resolution` needs only a narrow slice of a chunk grid: the per-dimension -mapping between storage indices and chunk coordinates, passed as one -`DimensionGridLike` per storage dimension. Rather than import zarr's concrete -grid types, we type against this Protocol; zarr's per-dimension grids satisfy -it structurally, so no zarr import is needed here. +``DimensionGridLike`` describes only the per-axis operations required by +``plan_chunks``. The concrete compact grids below also retain enough metadata +to describe chunk data regions and codec buffer regions without importing +Zarr's array implementation. """ from __future__ import annotations -from typing import TYPE_CHECKING, Protocol +import bisect +import itertools +import operator +from dataclasses import dataclass, field +from functools import reduce +from typing import TYPE_CHECKING, Any, Protocol, cast, runtime_checkable + +import numpy as np if TYPE_CHECKING: - import numpy as np + from collections.abc import Iterable, Iterator, Sequence + import numpy.typing as npt class DimensionGridLike(Protocol): - """The per-dimension chunk-mapping surface consumed by chunk resolution.""" + """The per-dimension chunk-mapping surface consumed by chunk resolution. + + Examples + -------- + `EdgeDimensionGrid` provides this surface. Chunk sizes `(2, 3)` tile + source coordinates `[0, 5)`, so index 4 lands in the second chunk: + + >>> grid = EdgeDimensionGrid([2, 3]) + >>> grid.index_to_chunk(4) + 1 + >>> grid.chunk_offset(1), grid.chunk_size(1) + (2, 3) + """ + + def index_to_chunk(self, idx: int) -> int: + """Map a global source index to the index of the chunk that contains it. + + Implementers must raise `IndexError` when `idx` lies outside `[0, extent)`. + """ + ... + + def chunk_offset(self, chunk_ix: int) -> int: + """The global source coordinate at which chunk `chunk_ix` begins.""" + ... + + def chunk_size(self, chunk_ix: int) -> int: + """The declared length of chunk `chunk_ix`, i.e. its codec buffer size along this axis.""" + ... + + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: + """Vectorized `index_to_chunk`: map global source indices to chunk indices. + + Implementers must raise `IndexError` if any index lies outside `[0, extent)`. + """ + ... + + +def _bounded_indices(indices: npt.NDArray[np.intp], extent: int) -> npt.NDArray[np.intp]: + """Normalize a vector lookup and enforce the scalar grid bounds.""" + arr = np.asarray(indices, dtype=np.intp) + if arr.size > 0 and (int(arr.min()) < 0 or int(arr.max()) >= extent): + raise IndexError( + f"indices must lie in [0, {extent}); got [{int(arr.min())}, {int(arr.max())}]" + ) + return arr + + +@dataclass(frozen=True) +class FixedDimension: + """Uniform chunk size with a boundary chunk clipped to the axis extent. + + Examples + -------- + Chunks of size 3 on an axis of extent 10 give 4 chunks. The last chunk + still declares a codec buffer of 3 but holds only 1 valid element: + + >>> dim = FixedDimension(size=3, extent=10) + >>> dim.nchunks + 4 + >>> dim.index_to_chunk(7) + 2 + >>> dim.chunk_size(3), dim.data_size(3) + (3, 1) + """ + + size: int + """The declared chunk length along this axis; every chunk's codec buffer size.""" + + extent: int + """The axis length in global source coordinates.""" + + nchunks: int = field(init=False, repr=False) + """Derived: the number of chunks holding data within `extent`.""" + + ngridcells: int = field(init=False, repr=False) + """Derived: the number of declared grid cells; equals `nchunks` for a fixed dimension.""" + + def __post_init__(self) -> None: + if self.size < 0: + raise ValueError(f"FixedDimension size must be >= 0, got {self.size}") + if self.extent < 0: + raise ValueError(f"FixedDimension extent must be >= 0, got {self.extent}") + if self.size == 0 and self.extent > 0: + raise ValueError( + "FixedDimension size must be > 0 when extent is nonzero; " + f"got size {self.size} and extent {self.extent}" + ) + nchunks = 0 if self.size == 0 else (self.extent + self.size - 1) // self.size + object.__setattr__(self, "nchunks", nchunks) + object.__setattr__(self, "ngridcells", nchunks) + + def index_to_chunk(self, idx: int) -> int: + """Map a global source index to its chunk index (`idx // size`). + + Raises `IndexError` when `idx` lies outside `[0, extent)`. + """ + if idx < 0 or idx >= self.extent: + raise IndexError(f"index {idx} is out of bounds for extent {self.extent}") + return 0 if self.size == 0 else idx // self.size + + def chunk_offset(self, chunk_ix: int) -> int: + """The global source coordinate where chunk `chunk_ix` begins (`chunk_ix * size`). + + Not bounds-checked: chunk indices past the last chunk extrapolate linearly. + """ + return chunk_ix * self.size + + def chunk_size(self, chunk_ix: int) -> int: + """The declared chunk length, `size` for every chunk. + + The boundary chunk is not clipped here; use `data_size` for the valid data length. + """ + return self.size + + def data_size(self, chunk_ix: int) -> int: + """The number of valid data elements in chunk `chunk_ix`, clipped to `extent`. + + Interior chunks report `size`; the boundary chunk reports the remainder, and chunk + indices at or past `nchunks` report 0. + """ + if self.size == 0: + return 0 + return max(0, min(self.size, self.extent - chunk_ix * self.size)) + + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: + """Vectorized `index_to_chunk` over an array of global source indices. + + Raises `IndexError` if any index lies outside `[0, extent)`. + """ + arr = _bounded_indices(indices, self.extent) + if self.size == 0: + return np.zeros_like(arr) + return arr // self.size + + def with_extent(self, new_extent: int) -> FixedDimension: + """Return a copy with the same chunk size and the axis extent set to `new_extent`.""" + return FixedDimension(size=self.size, extent=new_extent) + + def resize(self, new_extent: int) -> FixedDimension: + """Return a copy resized to `new_extent`; the fixed chunk size covers any new extent.""" + return FixedDimension(size=self.size, extent=new_extent) + + @property + def size_repr(self) -> str: + """The chunk size rendered as a scalar for `ChunkGrid.__repr__`.""" + return str(self.size) + + +@dataclass(frozen=True, init=False) +class VaryingDimension: + """Explicit chunk edge lengths, with trailing data clipped to ``extent``. + + Examples + -------- + Edges `(2, 3, 5)` clipped to extent 9: the last chunk declares 5 but + holds only 4 valid elements, and index 4 lands in the second chunk: + + >>> dim = VaryingDimension(edges=(2, 3, 5), extent=9) + >>> dim.nchunks + 3 + >>> dim.index_to_chunk(4) + 1 + >>> dim.chunk_offset(2) + 5 + >>> dim.chunk_size(2), dim.data_size(2) + (5, 4) + """ + + edges: tuple[int, ...] + """The declared per-chunk edge lengths, in order; codec buffer sizes, unclipped.""" + + cumulative: tuple[int, ...] + """Prefix sums of `edges`; derived, and what index lookups binary-search.""" + + extent: int + """The axis length in global source coordinates; at most the sum of `edges`.""" + nchunks: int = field(init=False, repr=False) + """Derived: the number of chunks holding data within `extent`.""" + + ngridcells: int = field(init=False, repr=False) + """Derived: the number of declared edges; exceeds `nchunks` when trailing cells are empty.""" + + def __init__(self, edges: Sequence[int], extent: int) -> None: + edges_tuple = tuple(edges) + if not edges_tuple: + raise ValueError("VaryingDimension edges must not be empty") + if any(edge <= 0 for edge in edges_tuple): + raise ValueError(f"All edge lengths must be > 0, got {edges_tuple}") + cumulative = tuple(itertools.accumulate(edges_tuple)) + if extent < 0: + raise ValueError(f"VaryingDimension extent must be >= 0, got {extent}") + if extent > cumulative[-1]: + raise ValueError( + f"VaryingDimension extent {extent} exceeds sum of edges {cumulative[-1]}" + ) + object.__setattr__(self, "edges", edges_tuple) + object.__setattr__(self, "cumulative", cumulative) + object.__setattr__(self, "extent", extent) + nchunks = 0 if extent == 0 else bisect.bisect_left(cumulative, extent) + 1 + object.__setattr__(self, "nchunks", nchunks) + object.__setattr__(self, "ngridcells", len(edges_tuple)) + + def index_to_chunk(self, idx: int) -> int: + """Map a global source index to the chunk whose edge interval contains it. + + Raises `IndexError` when `idx` lies outside `[0, extent)`. + """ + if idx < 0 or idx >= self.extent: + raise IndexError(f"index {idx} is out of bounds for extent {self.extent}") + return bisect.bisect_right(self.cumulative, idx) + + def chunk_offset(self, chunk_ix: int) -> int: + """The global source coordinate where chunk `chunk_ix` begins (sum of prior edges).""" + return self.cumulative[chunk_ix - 1] if chunk_ix > 0 else 0 + + def chunk_size(self, chunk_ix: int) -> int: + """The declared edge length of chunk `chunk_ix`. + + Trailing chunks are not clipped to `extent` here; use `data_size` for that. + """ + return self.edges[chunk_ix] + + def data_size(self, chunk_ix: int) -> int: + """The number of valid data elements in chunk `chunk_ix`, clipped to `extent`. + + Grid cells that lie entirely at or past `extent` report 0. + """ + offset = self.chunk_offset(chunk_ix) + return max(0, min(self.edges[chunk_ix], self.extent - offset)) + + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: + """Vectorized `index_to_chunk` over an array of global source indices. + + Raises `IndexError` if any index lies outside `[0, extent)`. + """ + arr = _bounded_indices(indices, self.extent) + return np.searchsorted(self.cumulative, arr, side="right") + + def with_extent(self, new_extent: int) -> VaryingDimension: + """Return a copy with the same edges re-clipped to `new_extent`. + + The existing edges must already cover the new extent; raises `ValueError` when + `new_extent` exceeds the sum of edges. Use `resize` to grow past the edges. + """ + if self.cumulative[-1] < new_extent: + raise ValueError( + f"VaryingDimension edge sum {self.cumulative[-1]} is less than new extent " + f"{new_extent}" + ) + return VaryingDimension(self.edges, extent=new_extent) + + def resize(self, new_extent: int) -> VaryingDimension: + """Return a copy resized to `new_extent`. + + Shrinking (or growing within the existing edges) keeps the edges and re-clips them; + growing past the sum of edges appends one new trailing edge covering the remainder. + """ + if new_extent == self.extent: + return self + if new_extent > self.cumulative[-1]: + return VaryingDimension((*self.edges, new_extent - self.cumulative[-1]), new_extent) + return VaryingDimension(self.edges, extent=new_extent) + + @property + def size_repr(self) -> str: + """The edge lengths rendered as a tuple for `ChunkGrid.__repr__`.""" + return repr(self.edges) + + +@runtime_checkable +class DimensionGrid(Protocol): + """Structural interface shared by the compact dimension grids. + + Examples + -------- + `FixedDimension` satisfies the protocol structurally: + + >>> dim = FixedDimension(size=2, extent=5) + >>> isinstance(dim, DimensionGrid) + True + >>> dim.nchunks, dim.extent + (3, 5) + >>> dim.with_extent(4).nchunks + 2 + """ + + @property + def nchunks(self) -> int: + """The number of chunks holding data within `extent`.""" + ... + + @property + def ngridcells(self) -> int: + """The number of declared grid cells; may exceed `nchunks` when trailing cells are empty.""" + ... + + @property + def extent(self) -> int: + """The axis length in global source coordinates.""" + ... + + def index_to_chunk(self, idx: int) -> int: + """Map a global source index to the chunk index that contains it. + + Implementers must raise `IndexError` when `idx` lies outside `[0, extent)`. + """ + ... + + def chunk_offset(self, chunk_ix: int) -> int: + """The global source coordinate at which chunk `chunk_ix` begins.""" + ... + + def chunk_size(self, chunk_ix: int) -> int: + """The declared (codec buffer) length of chunk `chunk_ix`, never clipped to `extent`.""" + ... + + def data_size(self, chunk_ix: int) -> int: + """The valid data length of chunk `chunk_ix`, clipped to `extent` at the boundary.""" + ... + + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: + """Vectorized `index_to_chunk`; must raise `IndexError` for indices outside `[0, extent)`.""" + ... + + def with_extent(self, new_extent: int) -> DimensionGrid: + """Return a grid with the existing chunk layout re-clipped to `new_extent`. + + Implementers must not invent new grid cells: raise `ValueError` when the declared + layout cannot cover `new_extent`. + """ + ... + + def resize(self, new_extent: int) -> DimensionGrid: + """Return a grid covering `new_extent`, extending the chunk layout when it must grow.""" + ... + + @property + def size_repr(self) -> str: + """A compact rendering of the chunk sizes, used by `ChunkGrid.__repr__`.""" + ... + + +@dataclass(frozen=True) +class ChunkSpec: + """A chunk's valid data region and its full codec buffer shape. + + Examples + -------- + The last chunk of a size-10 axis chunked by 3 holds one valid element + (`slices`), while its codec buffer still spans 3: + + >>> spec = ChunkGrid.from_sizes((10,), (3,))[3] + >>> spec.slices + (slice(9, 10, 1),) + >>> spec.shape, spec.codec_shape + ((1,), (3,)) + >>> spec.is_boundary + True + """ + + slices: tuple[slice, ...] + """Per-dimension bounds of the valid data region, in global source coordinates.""" + + codec_shape: tuple[int, ...] + """The declared (codec buffer) chunk shape, unclipped by the array extent.""" + + @property + def shape(self) -> tuple[int, ...]: + """The shape of the valid data region described by `slices`. + + Smaller than `codec_shape` on boundary chunks, where the array extent clips the chunk. + """ + return tuple(chunk_slice.stop - chunk_slice.start for chunk_slice in self.slices) + + @property + def is_boundary(self) -> bool: + """Whether the valid data region is smaller than the full codec buffer on any axis.""" + return self.shape != self.codec_shape + + +@dataclass(frozen=True) +class ChunkGrid: + """A concrete regular or rectilinear arrangement of chunks for one array. + + Examples + -------- + A `(3, 4)` array with `(2, 2)` chunks has a `(2, 2)` grid whose bottom + row of chunks is clipped to one valid row of data: + + >>> grid = ChunkGrid.from_sizes((3, 4), (2, 2)) + >>> grid.grid_shape + (2, 2) + >>> grid.chunk_sizes + ((2, 1), (2, 2)) + >>> spec = grid[1, 0] + >>> spec.shape, spec.codec_shape, spec.is_boundary + ((1, 2), (2, 2), True) + """ + + dimensions: tuple[DimensionGrid, ...] + """One per-axis grid, each mapping that axis's source indices to chunks.""" + + _is_regular: bool = field(init=False, repr=False) + + def __post_init__(self) -> None: + object.__setattr__( + self, + "_is_regular", + all(isinstance(dimension, FixedDimension) for dimension in self.dimensions), + ) + + def __repr__(self) -> str: + sizes = ", ".join(dimension.size_repr for dimension in self.dimensions) + shape = tuple(dimension.extent for dimension in self.dimensions) + return f"ChunkGrid(chunk_sizes=({sizes}), array_shape={shape})" + + @classmethod + def from_sizes( + cls, array_shape: Sequence[int], chunk_sizes: Sequence[int | Sequence[int]] + ) -> ChunkGrid: + """Build a grid from an array shape and one chunk-size spec per dimension. + + An `int` entry gives a fixed chunk size along that axis; a sequence of ints gives + explicit per-chunk edge lengths. A uniform sequence consistent with the axis extent + collapses to a fixed dimension, so the result may report `is_regular`. + + Parameters + ---------- + array_shape : Sequence[int] + The array extent along each dimension, in global source coordinates. + chunk_sizes : Sequence[int | Sequence[int]] + Per-dimension chunk layout: a single size or explicit edge lengths. + """ + extents = _shape_tuple(array_shape) + if len(extents) != len(chunk_sizes): + raise ValueError( + f"array_shape has {len(extents)} dimensions but chunk_sizes has " + f"{len(chunk_sizes)} dimensions" + ) + dimensions: list[DimensionGrid] = [] + for dimension_spec, extent in zip(chunk_sizes, extents, strict=True): + if isinstance(dimension_spec, int): + dimensions.append(FixedDimension(size=dimension_spec, extent=extent)) + else: + edges = tuple(dimension_spec) + if not edges: + raise ValueError("Each dimension must have at least one chunk") + if ( + edges[0] > 0 + and all(edge == edges[0] for edge in edges) + and (extent == sum(edges) or len(edges) == (extent + edges[0] - 1) // edges[0]) + ): + dimensions.append(FixedDimension(size=edges[0], extent=extent)) + else: + dimensions.append(VaryingDimension(edges, extent=extent)) + return cls(dimensions=tuple(dimensions)) + + @property + def ndim(self) -> int: + """The number of dimensions.""" + return len(self.dimensions) + + @property + def is_regular(self) -> bool: + """Whether every dimension uses a single fixed chunk size. + + False when any axis carries explicit (rectilinear) per-chunk edge lengths. + """ + return self._is_regular + + @property + def grid_shape(self) -> tuple[int, ...]: + """The number of data-bearing chunks along each dimension.""" + return tuple(dimension.nchunks for dimension in self.dimensions) + + @property + def chunk_shape(self) -> tuple[int, ...]: + """The uniform declared chunk shape of a regular grid. + + Raises `ValueError` for rectilinear grids, which have no single chunk shape; + use `grid[coords]` for per-chunk sizes instead. + """ + if not self.is_regular: + raise ValueError( + "chunk_shape is only available for regular chunk grids. " + "Use grid[coords] for per-chunk sizes." + ) + return tuple( + dimension.size for dimension in self.dimensions if isinstance(dimension, FixedDimension) + ) + + @property + def chunk_sizes(self) -> tuple[tuple[int, ...], ...]: + """Per-dimension tuples of each chunk's valid data length. + + Boundary chunks report their clipped extent, not the declared codec size. + """ + return tuple( + tuple(dimension.data_size(index) for index in range(dimension.nchunks)) + for dimension in self.dimensions + ) + + def __getitem__(self, coords: int | tuple[int, ...]) -> ChunkSpec | None: + """Look up the `ChunkSpec` at the given chunk coordinates (grid cells, not indices). + + Returns `None` when any coordinate falls outside the grid; raises `ValueError` + when the number of coordinates does not match `ndim`. The spec's slices are in + global source coordinates. + """ + if isinstance(coords, int): + coords = (coords,) + if len(coords) != self.ndim: + raise ValueError( + f"Expected {self.ndim} coordinate(s) for a {self.ndim}-d chunk grid, " + f"got {len(coords)}." + ) + slices: list[slice] = [] + codec_shape: list[int] = [] + for dimension, index in zip(self.dimensions, coords, strict=True): + if index < 0 or index >= dimension.nchunks: + return None + offset = dimension.chunk_offset(index) + slices.append(slice(offset, offset + dimension.data_size(index), 1)) + codec_shape.append(dimension.chunk_size(index)) + return ChunkSpec(tuple(slices), tuple(codec_shape)) + + def __iter__(self) -> Iterator[ChunkSpec]: + """Yield a `ChunkSpec` for every data-bearing chunk in row-major (C) order.""" + for coords in itertools.product( + *(range(dimension.nchunks) for dimension in self.dimensions) + ): + spec = self[coords] + if spec is not None: + yield spec + + def all_chunk_coords( + self, + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, + ) -> Iterator[tuple[int, ...]]: + """Iterate chunk coordinates over a rectangular grid region in row-major (C) order. + + `origin` defaults to the grid origin and `selection_shape` to the rest of the grid. + The region is not bounds-checked: an oversized region yields coordinates outside + the grid, which `__getitem__` resolves to `None`. + """ + origin_parsed = (0,) * self.ndim if origin is None else tuple(origin) + selection_shape_parsed = ( + tuple( + grid_size - coordinate + for coordinate, grid_size in zip(origin_parsed, self.grid_shape, strict=True) + ) + if selection_shape is None + else tuple(selection_shape) + ) + return itertools.product( + *( + range(coordinate, coordinate + size) + for coordinate, size in zip(origin_parsed, selection_shape_parsed, strict=True) + ) + ) + + def iter_chunk_regions( + self, + *, + origin: Sequence[int] | None = None, + selection_shape: Sequence[int] | None = None, + ) -> Iterator[tuple[slice, ...]]: + """Yield each chunk's valid-data slices, in global source coordinates. + + Covers the same region as `all_chunk_coords`, silently skipping coordinates + that fall outside the grid. + """ + for coords in self.all_chunk_coords(origin=origin, selection_shape=selection_shape): + spec = self[coords] + if spec is not None: + yield spec.slices + + def get_nchunks(self) -> int: + """The total number of data-bearing chunks: the product of `grid_shape` (1 if 0-d).""" + return reduce(operator.mul, (dimension.nchunks for dimension in self.dimensions), 1) + + def update_shape(self, new_shape: tuple[int, ...]) -> ChunkGrid: + """Return a grid resized to `new_shape` by resizing each dimension. + + Fixed axes keep their chunk size; rectilinear axes gain one trailing edge when + grown past their declared edges. Raises `ValueError` when `new_shape` does not + have `ndim` entries. + """ + if len(new_shape) != self.ndim: + raise ValueError( + f"new_shape has {len(new_shape)} dimensions but chunk grid has {self.ndim} dimensions" + ) + return ChunkGrid( + dimensions=tuple( + dimension.resize(new_extent) + for dimension, new_extent in zip(self.dimensions, new_shape, strict=True) + ) + ) + + +class EdgeDimensionGrid: + """An explicitly edge-based grid for coordinate-origin examples and planners. + + Examples + -------- + Chunk sizes `(2, 3)` tile source coordinates `[0, 5)`; lookups outside + that range raise: + + >>> grid = EdgeDimensionGrid([2, 3]) + >>> grid.num_chunks, grid.extent + (2, 5) + >>> grid.index_to_chunk(2) + 1 + >>> grid.index_to_chunk(5) + Traceback (most recent call last): + ... + IndexError: index 5 is out of bounds for an axis of extent 5 + """ + + __slots__ = ("_offsets", "sizes") + + sizes: tuple[int, ...] + """The length of each chunk along the axis, in order; every entry is positive.""" + + def __init__(self, sizes: Sequence[int]) -> None: + """Build a one-axis grid from explicit per-chunk sizes. + + Every size must be positive; raises `ValueError` otherwise. A zero-length axis + is spelled as an empty sequence (no chunks), not as a zero size. + + Parameters + ---------- + sizes : Sequence[int] + The length of each chunk along the axis, in order. + """ + normalized = tuple(int(size) for size in sizes) + for index, size in enumerate(normalized): + if size <= 0: + raise ValueError( + f"chunk sizes must be positive; got {size} at position {index} of {normalized}. " + "A zero-length axis is spelled as no chunks at all: EdgeDimensionGrid(())" + ) + self.sizes = normalized + offsets: np.ndarray[Any, np.dtype[np.intp]] = np.zeros(len(normalized) + 1, dtype=np.intp) + if normalized: + np.cumsum(np.asarray(normalized, dtype=np.intp), out=offsets[1:]) + self._offsets = offsets + + @property + def num_chunks(self) -> int: + """The number of chunks along the axis.""" + return len(self.sizes) + + @property + def extent(self) -> int: + """The axis length in global source coordinates: the sum of all chunk sizes.""" + return int(self._offsets[-1]) + + def __repr__(self) -> str: + return f"EdgeDimensionGrid(sizes={self.sizes})" + + def __eq__(self, other: object) -> bool: + if not isinstance(other, EdgeDimensionGrid): + return NotImplemented + return self.sizes == other.sizes + + def __hash__(self) -> int: + return hash((type(self).__name__, self.sizes)) + + def index_to_chunk(self, idx: int) -> int: + """Map a global source index to the chunk whose interval contains it. + + Raises `IndexError` when `idx` lies outside `[0, extent)`. + """ + if idx < 0 or idx >= self.extent: + raise IndexError(f"index {idx} is out of bounds for an axis of extent {self.extent}") + return int(np.searchsorted(self._offsets, idx, side="right")) - 1 + + def chunk_offset(self, chunk_ix: int) -> int: + """The global source coordinate where chunk `chunk_ix` begins. + + Raises `IndexError` when `chunk_ix` lies outside `[0, num_chunks)`. + """ + if chunk_ix < 0 or chunk_ix >= len(self.sizes): + raise IndexError( + f"chunk index {chunk_ix} is out of bounds for {len(self.sizes)} chunks" + ) + return int(self._offsets[chunk_ix]) + + def chunk_size(self, chunk_ix: int) -> int: + """The length of chunk `chunk_ix`; every chunk holds data, so no boundary clipping applies. + + Raises `IndexError` when `chunk_ix` lies outside `[0, num_chunks)`. + """ + if chunk_ix < 0 or chunk_ix >= len(self.sizes): + raise IndexError( + f"chunk index {chunk_ix} is out of bounds for {len(self.sizes)} chunks" + ) + return self.sizes[chunk_ix] + + def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: + """Vectorized `index_to_chunk` over an array of global source indices. + + Raises `IndexError` if any index lies outside `[0, extent)`. + """ + arr = _bounded_indices(indices, self.extent) + return (np.searchsorted(self._offsets, arr, side="right") - 1).astype(np.intp) + + +def _shape_tuple(shape: Sequence[int]) -> tuple[int, ...]: + result = tuple(int(size) for size in shape) + if any(size < 0 for size in result): + raise ValueError(f"shape entries must be non-negative; got {result}") + return result + + +def _entry_kind(entry: Any) -> str: + if isinstance(entry, (int, np.integer)) and not isinstance(entry, bool): + return "int" + if isinstance(entry, (str, bytes)): + return "neither" + try: + iter(cast("Iterable[Any]", entry)) + except TypeError: + return "neither" + return "sequence" + + +def dimension_grids_from_chunks( + chunks: Sequence[int] | Sequence[Sequence[int]], shape: Sequence[int] +) -> tuple[DimensionGrid, ...]: + """Build compact dimensions from regular sizes or explicit per-axis edges. + + Examples + -------- + One integer per dimension builds fixed grids, ready for `plan_chunks`: + + >>> from zarr_indexing import IndexTransform, plan_chunks + >>> grids = dimension_grids_from_chunks((2, 2), shape=(3, 4)) + >>> [type(grid).__name__ for grid in grids] + ['FixedDimension', 'FixedDimension'] + >>> plan = plan_chunks(IndexTransform.from_shape((3, 4))[1, :], grids) + >>> [p.chunk_coords for p in plan] + [(0, 0), (0, 1)] + """ + shape_t = _shape_tuple(shape) + entries: tuple[Any, ...] = tuple(chunks) + if len(entries) != len(shape_t): + raise ValueError( + f"chunks must have one entry per dimension; got {len(entries)} entries for shape {shape_t}" + ) + + conventions = ( + "chunks must be either a uniform chunk shape (one integer per dimension) " + "or per-axis chunk sizes (one sequence of integers per dimension)" + ) + kinds = [_entry_kind(entry) for entry in entries] + neither = [(axis, entries[axis]) for axis, kind in enumerate(kinds) if kind == "neither"] + if neither: + described = ", ".join(f"{entry!r} at dimension {axis}" for axis, entry in neither) + verb = "is" if len(neither) == 1 else "are" + raise ValueError(f"{conventions}; {described} {verb} neither") + + integer_count = sum(kind == "int" for kind in kinds) + if entries and integer_count == len(entries): + dimensions: list[DimensionGrid] = [] + for entry, extent in zip(entries, shape_t, strict=True): + size = int(entry) + if size <= 0: + raise ValueError(f"chunk shape entries must be positive; got {size}") + dimensions.append(FixedDimension(size=size, extent=extent)) + return tuple(dimensions) + if integer_count: + raise ValueError(f"{conventions}, not a mixture; got {entries!r}") - def index_to_chunk(self, idx: int) -> int: ... - def chunk_offset(self, chunk_ix: int) -> int: ... - def chunk_size(self, chunk_ix: int) -> int: ... - def indices_to_chunks(self, indices: npt.NDArray[np.intp]) -> npt.NDArray[np.intp]: ... + dimensions = [] + for axis, (entry, extent) in enumerate(zip(entries, shape_t, strict=True)): + elements: tuple[Any, ...] = tuple(cast("Iterable[Any]", entry)) + if any( + not isinstance(element, (int, np.integer)) or isinstance(element, bool) + for element in elements + ): + raise ValueError( + f"per-axis chunk sizes must be integers; dimension {axis} has {entry!r}" + ) + edges = tuple(int(element) for element in elements) + total = sum(edges) + if total != extent: + raise ValueError( + f"per-axis chunk sizes for dimension {axis} sum to {total}, but the array extent is {extent}" + ) + if extent == 0 and all(edge == 0 for edge in edges): + dimensions.append(FixedDimension(size=0, extent=0)) + continue + if any(edge <= 0 for edge in edges): + raise ValueError(f"chunk sizes must be positive; got {edges}") + dimensions.append(VaryingDimension(edges=edges, extent=extent)) + return tuple(dimensions) diff --git a/packages/zarr-indexing/src/zarr_indexing/json.py b/packages/zarr-indexing/src/zarr_indexing/json.py index c95696f309..8bf42c74a5 100644 --- a/packages/zarr-indexing/src/zarr_indexing/json.py +++ b/packages/zarr-indexing/src/zarr_indexing/json.py @@ -1,70 +1,61 @@ -"""Lowering between canonical ndsel bodies and in-memory `IndexTransform`s. +"""The canonical ndsel wire vocabulary, and the rules for lowering it. This is the **engine layer**. Where `messages.py` is pure JSON→JSON and imposes -no array constraints, this module converts a *canonical* ndsel transform body -(spec section 4.3, as produced by `zarr_indexing.messages.normalize_ndsel`) -into the numpy-backed `IndexTransform` the chunk engine runs on, and back. +no array constraints, this module holds the JSON shapes a canonical ndsel body +takes (spec section 4.3, as produced by `zarr_indexing.messages.normalize_ndsel`) +together with the lowering rules that turn one into the numpy-backed engine +representation. -Two engine constraints live **here and only here**: +The conversions themselves are **methods on the types**, since each type owns +its one serialization: `IndexTransform.to_json` / `from_json`, +`IndexDomain.to_json` / `from_json`, and `to_json` on each output map kind, +with `output_index_map_from_json` in `zarr_indexing.output_map` dispatching the +wire's tagged union back to the right kind. This module is what they share. + +Three engine constraints live **here and only here**: - **Finite bounds.** An `IndexDomain` addresses a finite array, so a canonical body carrying a `"-inf"`/`"+inf"` bound cannot be lowered; `from_json` raises. - **Implicit bounds lower by value.** The `[n]`-bracket implicit/explicit flag is a message-layer concern; the engine keeps only the integer value. +- **Integer `index_array` content.** The message layer carries `index_array` + verbatim (the spec defers its shape and type), so lowering is where a float, + boolean or string array is rejected — as an `NdselError`, rather than + truncating `[0.9, 1.9]` to cells 0 and 1 or leaking a raw NumPy error. ## The `index_array` wire format (and the degenerate-collapse it documents) ndsel and TensorStore both **reject** an output map that carries *both* -`input_dimension` and `index_array`. The in-memory `ArrayMap`, however, records -an `input_dimension` to pin the axis an orthogonal (`oindex`) array varies over. -This module bridges the gap: - -- **On serialize** (`transform_to_canonical`): - 1. An all-singleton `index_array` (size 1) selects a single coordinate - regardless of input, so it is **collapsed to a `constant` map** - `{offset: offset + stride*value}`. The size-1 input dimension stays in the - domain, unconsumed — a valid transform. This makes a length-1 `oindex` - selection round-trip *behaviorally* (an `ArrayMap` becomes a `ConstantMap`) - rather than by object identity. - 2. Non-degenerate `index_array` maps are emitted **without** `input_dimension`. - -- **On load** (`transform_from_canonical`): the in-memory `input_dimension` is - reconstructed from the full-rank array's dependency axes (its non-singleton - axes, see `transform._array_map_dependency_axes`). An array that solely owns a - single non-singleton axis is orthogonal (`input_dimension = that axis`); arrays - that share non-singleton axes, or vary over several, are correlated (`vindex`, - `input_dimension = None`). A single 1-D array over a rank-1 domain is - inherently ambiguous between the two flavours; it reconstructs as orthogonal, - which is behaviorally identical for the single-array case. - -`index_transform_to_json` / `index_transform_from_json` (and the `*_domain_*` -variants) are these canonical converters under their historical names. +`input_dimension` and `index_array`; `input_dimension` belongs to affine +(`single_input_dimension`) maps. The in-memory `ArrayMap` matches: what a map +depends on is read from its full-rank array's shape (its non-singleton axes), +so there is nothing to reconstruct on load. On serialize (`to_json`): + +1. An all-singleton `index_array` (size 1) selects a single coordinate + regardless of input, so it is **collapsed to a `constant` map** + `{offset: offset + stride*value}`. The size-1 input dimension stays in the + domain, unconsumed — a valid transform. The selection layer already builds + such maps as `ConstantMap` (`output_map.array_map_or_constant`); this covers + hand-built transforms. +2. An **empty** `index_array` (size 0) collapses the same way, to + `{offset: 0}`. It names no cell, and it can only be empty because an input + dimension is — the full-rank invariant makes every axis either 1 or the + domain's extent — so nothing is ever read through it and the emptiness is + carried by the domain, which is emitted separately. TensorStore does the + same: `t[ts.d[0][[]]]` is `out[0] = 0`, emitted as `{}`. Emitting the array + instead would produce a document neither implementation could load, because + `ndarray.tolist()` renders every empty array as `[]` once the leading axis + is the zero-length one, and nested lists cannot spell the shape back — + `[[]]` is `(1, 0)` and nothing spells `(0, 1)`. +3. Non-degenerate `index_array` maps are emitted with their array and bounds + only. + """ from __future__ import annotations -from collections import Counter from typing import Any, Required, TypedDict -import numpy as np - -from zarr_indexing.domain import IndexDomain -from zarr_indexing.messages import normalize_ndsel -from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap -from zarr_indexing.transform import ( - IndexTransform, - _array_map_dependency_axes, # pyright: ignore[reportPrivateUsage] -) - -# `_array_map_dependency_axes` is a leading-underscore helper in `transform.py`, -# but it is deliberately shared with this module (the engine-level JSON <-> -# `IndexTransform` lowering below needs the same dependency-axis logic that -# `transform.py`'s own array-reindexing helpers use). It is not part of the -# package's public API; pyright's `reportPrivateUsage` flags the cross-module -# import anyway. See `chunk_resolution.py`'s `_dimensions` suppression for the -# analogous rationale — whether to promote either symbol out of "private" is -# an open pre-publish API decision, not resolved here. - # --------------------------------------------------------------------------- # TypedDict definitions (canonical JSON shapes) # --------------------------------------------------------------------------- @@ -81,11 +72,28 @@ class IndexDomainJSON(TypedDict, total=False): - """Canonical JSON representation of an IndexDomain.""" + """Canonical JSON representation of an IndexDomain. + + Examples + -------- + >>> doc: IndexDomainJSON = { + ... "input_inclusive_min": [0], + ... "input_exclusive_max": [4], + ... "input_labels": ["x"], + ... } + >>> from zarr_indexing import IndexDomain + >>> IndexDomain.from_json(doc).shape + (4,) + """ input_inclusive_min: Required[list[BoundJSON]] + """Per-dimension lower bounds; `"-inf"` is legal on the wire but cannot be lowered.""" + input_exclusive_max: Required[list[BoundJSON]] + """Per-dimension exclusive upper bounds; `"+inf"` is legal on the wire but cannot be lowered.""" + input_labels: Required[list[str]] + """Per-dimension names; the empty string marks an unlabeled dimension.""" class OutputIndexMapJSON(TypedDict, total=False): @@ -97,229 +105,62 @@ class OutputIndexMapJSON(TypedDict, total=False): - `{"offset": 0, "stride": 1, "input_dimension": 0}` — single_input_dimension - `{"offset": 0, "stride": 1, "index_array": [...], "index_array_bounds": ["-inf", "+inf"]}` — index_array + + Examples + -------- + >>> from zarr_indexing import output_index_map_from_json + >>> constant: OutputIndexMapJSON = {"offset": 5} + >>> output_index_map_from_json(constant) + ConstantMap(offset=5) + >>> affine: OutputIndexMapJSON = {"offset": 0, "stride": 2, "input_dimension": 1} + >>> output_index_map_from_json(affine) + DimensionMap(input_dimension=1, offset=0, stride=2) """ offset: int + """Constant term; alone it is the whole constant form.""" + stride: int + """Multiplier applied to the input coordinate or to each `index_array` value.""" + input_dimension: int + """The input dimension the single_input_dimension form reads.""" + index_array: NestedIntList + """Nested lists of output coordinates, one nesting level per input dimension.""" + index_array_bounds: list[IndexValueJSON] + """Bounds the `index_array` values are promised to lie in; `["-inf", "+inf"]` if unconstrained.""" class IndexTransformJSON(TypedDict, total=False): - """Canonical JSON representation of an IndexTransform (spec section 4.3).""" - - input_rank: Required[int] - input_inclusive_min: Required[list[BoundJSON]] - input_exclusive_max: Required[list[BoundJSON]] - input_labels: Required[list[str]] - output: Required[list[OutputIndexMapJSON]] - - -# --------------------------------------------------------------------------- -# Bound / label lowering (engine constraints) -# --------------------------------------------------------------------------- - - -def _lower_bound(bound: BoundJSON, where: str) -> int: - """Lower a canonical bound to a finite integer, rejecting infinities.""" - value = bound[0] if isinstance(bound, list) else bound - if value == "-inf" or value == "+inf": - raise ValueError( - f"{where} is infinite ({value!r}); an IndexDomain addresses a finite " - f"array and cannot lower an infinite bound" - ) - return int(value) - - -def _lower_labels(labels: list[str]) -> tuple[str, ...] | None: - """All-empty labels collapse to `None` so a label-free domain round-trips.""" - return None if all(label == "" for label in labels) else tuple(labels) - - -def _emit_labels(labels: tuple[str, ...] | None, rank: int) -> list[str]: - """Emit canonical labels: `[""]*rank` when the domain is unlabeled.""" - return [""] * rank if labels is None else list(labels) - - -# --------------------------------------------------------------------------- -# IndexDomain serialization -# --------------------------------------------------------------------------- - - -def index_domain_to_json(domain: IndexDomain) -> IndexDomainJSON: - """Convert an IndexDomain to its canonical JSON representation.""" - return { - "input_inclusive_min": list(domain.inclusive_min), - "input_exclusive_max": list(domain.exclusive_max), - "input_labels": _emit_labels(domain.labels, domain.ndim), - } - - -def index_domain_from_json(data: IndexDomainJSON) -> IndexDomain: - """Construct an IndexDomain from its canonical JSON representation.""" - inclusive_min = tuple( - _lower_bound(b, f"input_inclusive_min[{i}]") - for i, b in enumerate(data["input_inclusive_min"]) - ) - exclusive_max = tuple( - _lower_bound(b, f"input_exclusive_max[{i}]") - for i, b in enumerate(data["input_exclusive_max"]) - ) - labels = _lower_labels(list(data["input_labels"])) - return IndexDomain(inclusive_min=inclusive_min, exclusive_max=exclusive_max, labels=labels) - - -# --------------------------------------------------------------------------- -# OutputIndexMap serialization -# --------------------------------------------------------------------------- - - -def output_index_map_to_json(m: OutputIndexMap) -> OutputIndexMapJSON: - """Convert an output index map to its canonical JSON representation. - - A degenerate all-singleton `ArrayMap` collapses to a `constant` map; a - non-degenerate one is emitted without `input_dimension` (see the module - docstring on the wire format). + """Canonical JSON representation of an IndexTransform (spec section 4.3). + + Examples + -------- + >>> doc: IndexTransformJSON = { + ... "input_rank": 1, + ... "input_inclusive_min": [0], + ... "input_exclusive_max": [2], + ... "input_labels": [""], + ... "output": [{"offset": 1, "stride": 2, "input_dimension": 0}], + ... } + >>> from zarr_indexing import IndexTransform + >>> IndexTransform.from_json(doc).domain.shape + (2,) """ - if isinstance(m, ConstantMap): - return {"offset": m.offset} - - if isinstance(m, DimensionMap): - return {"offset": m.offset, "stride": m.stride, "input_dimension": m.input_dimension} - - # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) - if m.index_array.size == 1: - value = int(m.index_array.reshape(-1)[0]) - return {"offset": m.offset + m.stride * value} - return { - "offset": m.offset, - "stride": m.stride, - "index_array": m.index_array.tolist(), - "index_array_bounds": ["-inf", "+inf"], - } - - -def output_index_map_from_json(data: OutputIndexMapJSON) -> OutputIndexMap: - """Construct an output index map from its canonical JSON representation. - - An `index_array` map's `input_dimension` is reconstructed from the array's - dependency axes in isolation (single non-singleton axis → orthogonal). The - transform-level loader classifies globally; use it when several maps may - share axes. - """ - if "index_array" in data: - arr = np.asarray(data["index_array"], dtype=np.intp) - return ArrayMap( - index_array=arr, - offset=data.get("offset", 0), - stride=data.get("stride", 1), - input_dimension=_solo_dependency_axis(arr), - ) - - if "input_dimension" in data: - return DimensionMap( - input_dimension=data["input_dimension"], - offset=data.get("offset", 0), - stride=data.get("stride", 1), - ) - - return ConstantMap(offset=data.get("offset", 0)) - - -def _solo_dependency_axis(arr: np.ndarray[Any, Any]) -> int | None: - """The single axis a lone `index_array` varies over, or `None` if not exactly one.""" - dep = _array_map_dependency_axes(arr) - return dep[0] if len(dep) == 1 else None + input_rank: Required[int] + """The number of input dimensions; the bounds and labels lists match it in length.""" -# --------------------------------------------------------------------------- -# IndexTransform serialization -# --------------------------------------------------------------------------- + input_inclusive_min: Required[list[BoundJSON]] + """Per-dimension lower bounds; `"-inf"` is legal on the wire but cannot be lowered.""" + input_exclusive_max: Required[list[BoundJSON]] + """Per-dimension exclusive upper bounds; `"+inf"` is legal on the wire but cannot be lowered.""" -def transform_to_canonical(transform: IndexTransform) -> IndexTransformJSON: - """Convert an IndexTransform to its canonical ndsel transform body. + input_labels: Required[list[str]] + """Per-dimension names; the empty string marks an unlabeled dimension.""" - The result is fully explicit (spec section 4.3): `input_rank`, fully written - bounds and labels, and an explicit `output` with `offset`/`stride` present - on every affine and array map. - """ - return { - "input_rank": transform.domain.ndim, - "input_inclusive_min": list(transform.domain.inclusive_min), - "input_exclusive_max": list(transform.domain.exclusive_max), - "input_labels": _emit_labels(transform.domain.labels, transform.domain.ndim), - "output": [output_index_map_to_json(m) for m in transform.output], - } - - -def transform_from_canonical(data: IndexTransformJSON) -> IndexTransform: - """Construct an IndexTransform from a canonical (or canonicalizable) body. - - The body is first run through the message layer (`normalize_ndsel`) so that - omitted fields — identity `output`, default bounds/labels — are filled and - validated, then lowered to the engine representation. `index_array` maps' - `input_dimension` values are reconstructed by global dependency-axis - ownership (see the module docstring). - """ - body = normalize_ndsel({"kind": "transform", **data}) - - inclusive_min = tuple( - _lower_bound(b, f"input_inclusive_min[{i}]") - for i, b in enumerate(body["input_inclusive_min"]) - ) - exclusive_max = tuple( - _lower_bound(b, f"input_exclusive_max[{i}]") - for i, b in enumerate(body["input_exclusive_max"]) - ) - domain = IndexDomain( - inclusive_min=inclusive_min, - exclusive_max=exclusive_max, - labels=_lower_labels(body["input_labels"]), - ) - - output_raw: list[dict[str, Any]] = body["output"] - - # Classify index_array maps globally: an axis owned by exactly one array map - # (and the map's sole non-singleton axis) marks that map orthogonal; shared - # or multiple non-singleton axes mark the maps correlated (vindex). - array_axes: dict[int, tuple[int, ...]] = {} - axis_owners: Counter[int] = Counter() - for i, om in enumerate(output_raw): - if "index_array" in om: - arr = np.asarray(om["index_array"], dtype=np.intp) - dep = _array_map_dependency_axes(arr) - array_axes[i] = dep - axis_owners.update(dep) - - output: list[OutputIndexMap] = [] - for i, om in enumerate(output_raw): - if "index_array" in om: - dep = array_axes[i] - input_dim = dep[0] if len(dep) == 1 and axis_owners[dep[0]] == 1 else None - output.append( - ArrayMap( - index_array=np.asarray(om["index_array"], dtype=np.intp), - offset=om.get("offset", 0), - stride=om.get("stride", 1), - input_dimension=input_dim, - ) - ) - elif "input_dimension" in om: - output.append( - DimensionMap( - input_dimension=om["input_dimension"], - offset=om.get("offset", 0), - stride=om.get("stride", 1), - ) - ) - else: - output.append(ConstantMap(offset=om.get("offset", 0))) - - return IndexTransform(domain=domain, output=tuple(output)) - - -# Historical names, now pointing at the canonical converters. -index_transform_to_json = transform_to_canonical -index_transform_from_json = transform_from_canonical + output: Required[list[OutputIndexMapJSON]] + """One output map per output dimension.""" diff --git a/packages/zarr-indexing/src/zarr_indexing/lazy_array.py b/packages/zarr-indexing/src/zarr_indexing/lazy_array.py new file mode 100644 index 0000000000..950a97b25e --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/lazy_array.py @@ -0,0 +1,1365 @@ +"""`LazyArray` — TensorStore-style lazy indexing over array-like sources. + +`LazyArray` wraps a source with `shape`, `dtype`, and basic integer/slice +`__getitem__`, whose reads can be lowered through NumPy system memory. It adds +a `.lazy` accessor whose indexing operations build up an +[`IndexTransform`](transform.md) instead of reading data: + +```python +view = LazyArray(source).lazy[10:50, ::2].lazy.oindex[[3, 1, 1], :] +view.shape # known without touching the data +values = view.result() +``` + +Nothing is read until `result()` (or `__array__`, or an eager `__getitem__`). +Every `.lazy` operation is metadata-only. Composition does not accumulate +layers: a view of a view is still a single transform and retains its reader. + +Parts +----- +A `LazyArray` carries a **partitioning** of the array it wraps: a grid of boxes +that a read is broken into. `parts()` walks those boxes as they fall through the +view, yielding a [`Partition`](#zarr_indexing.lazy_array.Partition) per box. Its +paired projection describes the chunk-local read and where its cells land in the +request; `view` carries that partition's transform. `result()` allocates one +fresh output buffer, then reads each partition once through the selected reader +into the final buffer or an owned temporary for fancy placement. + +The part view's transform directly addresses its raw wrapped array. The paired +projection deliberately retains the chunk-local frame; both travel together in +the `ReadContext` passed to the reader. + +The partitioning is discovered from the wrapped array at construction — first +`read_chunk_sizes` (zarr's clipped per-axis sizes, sharding-aware), then +`chunks`, read as per-axis sizes if its entries are sequences and as a uniform +box shape if they are integers. Those attribute names belong to the wrapped +array; this API refers only to parts. An array that advertises neither gets a +single whole-array part, and resolving it reads the whole view through its +selected reader in one pass. + +`with_parts` replaces the partitioning without touching the data or the view: + +```python +view.with_parts((64, 64)) # uniform boxes, tail clipped +view.with_parts_per_axis(((3, 3, 1),)) # explicit per-axis sizes +view.unpartitioned() # one whole-array part; resolve in one shot +``` + +Repartitioning changes how the read is divided, not what `result()` returns. +Parts that do not align with the source's own boxes are permitted and can be +useful (to bound peak memory, or to batch small reads); they cost extra I/O but +do not affect correctness. + +Readers +------- +Every wrapper carries a reader that owns the backend-specific request. The +transform answers **which values?** and is independent of the backend; the +reader answers **how does this backend obtain them?** and must preserve the +complete transform exactly. Readers do not define indexing semantics, +partitioning, scheduling, or result ownership. The conservative +`LazyArray(source)` uses `basic_reader`, which needs only basic slicing. +`LazyArray.from_numpy(array)` explicitly opts into `numpy_reader` for direct +NumPy indexing. `with_reader()` replaces the reader without reading or changing +the view metadata. The reader object is shared by all derived views and their +parts. Consumers may materialize part views concurrently; `LazyArray` does not +serialize calls, so a stateful reader must synchronize its own mutable state. + +Both built-in readers lower through NumPy system memory. They do not implicitly +transfer device arrays. A device source requires an explicit custom reader that +performs any needed transfer into the supplied system-memory output buffer. + +Boxes and queries +----------------- +A selection is either **rectangular** — an interval and a stride per dimension, +which is what basic indexing composes to at any depth — or a **query**, an +explicit list of coordinates, which is what `oindex`, `vindex`, and masks +produce and which subsequent basic indexing cannot undo. `is_box` reports the +category and `bounding_box()` reports the storage region touched: the exact +interval per dimension for a box, a hull for a query. A box is only *dense* in +that interval when every entry of `strides()` is 1. The distinction is +structural rather than an optimization; [the design +notes](../design-notes.md) describe why it matters to consumers of a selection. + +The positional dialect +---------------------- +Selections on `LazyArray` are **positional, NumPy-style**: index 0 is the first +element of the current view, `-1` is the last, boolean masks must match the +view's shape, and every index is bounds-checked against the view. + +This differs deliberately from `zarr.Array.lazy[...]`, which exposes the +**literal** TensorStore dialect: a zarr view keeps the coordinate system of the +array it came from, so after `v = arr.lazy[10:50]` the first element of `v` is +`v[10]` and a negative index is out of bounds rather than counted from the end. +That dialect suits zarr, where a view's coordinates stay comparable with the +parent array's. `LazyArray` is a duck array and has to behave like the array it +wraps to be usable as a NumPy drop-in or as a dask source, so it re-zeroes its +coordinates on every view and uses positions. `zarr_indexing.boundary` performs +the translation between the two. + +Two more NumPy rules the dialect keeps, in every mode: + +- A scalar integer drops its axis. Any non-boolean object implementing Python's + `SupportsIndex` protocol is accepted as one, including in slice bounds and + steps; an `__int__` method alone is deliberately not enough. A scalar is a + basic index wherever it appears, applied before any advanced index rather + than broadcast against one. So + `lazy.oindex[0]` has the shape of `x[0]`, `lazy.oindex[0, [1, 2], :]` means + `x[0][numpy.ix_([1, 2], ...)]`, and `lazy.oindex[0, 1, 2]` and + `lazy.vindex[0, 1, 2]` are both zero-rank. Use a length-1 list to keep an + axis. +- Advanced indices are placed as NumPy places them. For a `vindex` selection + that leaves some axes unindexed, the gathered dimensions sit where the + coordinate arrays sat when those arrays are adjacent, and lead when a slice + separates them — so `lazy.vindex[..., i, j]` has shape + `(x.shape[0], *broadcast)`, matching `x[..., i, j]`. + +Materializing on fallback +------------------------- +`LazyArray` implements `__array__` but deliberately implements neither +`__array_ufunc__` nor `__array_function__`. A NumPy *function* given a view +therefore materializes the whole thing through +`__array__` and works on the resulting array: `numpy.sum(view)`, +`numpy.add(view, 1)` and `numpy.stack([view, view])` all do, and so does +`numpy.ones(view.shape) + view`, where the ndarray on the left dispatches. + +Python's arithmetic *operators* do not: `view + 1` raises `TypeError`, because +the wrapper defines no arithmetic dunders and an `int` has nothing to dispatch +to. Both facts follow from the same intent — laziness here applies to indexing, +not to building a deferred compute graph — and a `LazyArray` is not a drop-in +for arithmetic on a large array either way. Use `.lazy[...]` to narrow the view +first, or pass the wrapper to `dask.array.from_array` so that dask owns the +compute graph. + +Ownership +--------- +`result()` always allocates fresh system memory before reading through the +selected reader. A `numpy.ma` source keeps its mask by receiving a masked +output buffer; other source-specific array types do not survive materializing. +""" + +from __future__ import annotations + +import hashlib +import json +import math +import operator +import uuid +from collections.abc import Sequence +from dataclasses import dataclass, field +from typing import TYPE_CHECKING, Any, Protocol, cast + +import numpy as np + +from zarr_indexing.boundary import ( + SelectionMode, + normalize_positional_selection, + split_scalar_axes, +) +from zarr_indexing.chunk_resolution import ( + ChunkProjection, + plan_chunks, +) +from zarr_indexing.grid import DimensionGrid, FixedDimension, dimension_grids_from_chunks +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap +from zarr_indexing.reader import ( + ReadContext, + Reader, + basic_reader, + numpy_reader, +) +from zarr_indexing.transform import ( + IndexTransform, +) + +if TYPE_CHECKING: + from collections.abc import Callable, Iterator + + SelectFn = Callable[[Any, SelectionMode], "LazyArray"] + +__all__ = ["LazyArray", "Partition"] + +# Above this many bytes, the no-dask token fallback describes an array +# structurally instead of digesting its contents. See `_wrapped_token`. +_TOKEN_DIGEST_LIMIT = 1 << 20 + + +def _invoke_reader( + reader: Reader, + source: Any, + context: ReadContext, + out: np.ndarray[Any, Any], +) -> None: + """Invoke a reader and enforce its in-place return contract.""" + returned = reader.read_into(source, context, out) + if returned is not None: + raise TypeError(f"reader.read_into must return None, got {type(returned).__name__}") + + +def _is_correlated(transform: IndexTransform) -> bool: + """True when the transform gathers a list of points rather than an outer product.""" + return transform.index_array_structure == "general" + + +class ArrayLike(Protocol): + """The surface `LazyArray` needs from the array it wraps.""" + + @property + def shape(self) -> tuple[int, ...]: ... + @property + def dtype(self) -> Any: ... + def __getitem__(self, key: Any) -> Any: ... + + +# NumPy's dtype-specialized ``__getitem__`` overloads do not structurally match +# the deliberately broad protocol above under strict type checking. Accept an +# ndarray explicitly so users do not have to erase its type with ``cast(Any, …)``. +_WrappedArray = ArrayLike | np.ndarray[Any, Any] + + +# --------------------------------------------------------------------------- # +# Partition discovery +# --------------------------------------------------------------------------- # + + +def _read_source_attribute(array: Any, name: str) -> Any: + """Read a partition-describing attribute, treating any failure as "absent". + + Discovery inspects an object we did not write. A missing attribute is the + common case, but zarr raises an `AttributeError` subclass from + `read_chunk_sizes` on a lazy view, and other backends compute the attribute + lazily and may fail for their own reasons. Any failure here means "this + array does not advertise a partitioning", never a hard error. + """ + try: + return getattr(array, name, None) + # Guarded properties (e.g. zarr's LazyViewError) and broken foreign + # attributes may raise anything; discovery must degrade to None. + except Exception: + return None + + +def _discover_parts(array: Any, shape: tuple[int, ...]) -> tuple[DimensionGrid, ...] | None: + """Resolve the partitioning advertised by `array`, or None for one whole part. + + Discovery parses external input: an attribute that does not describe a + partitioning of `shape` means "this object does not advertise one I + understand", and the array is treated as unpartitioned rather than rejected. + A partitioning is an I/O strategy, so reading the whole array is always a + correct fallback. `with_parts` is a public API and validates strictly. + """ + declared = _read_source_attribute(array, "read_chunk_sizes") + if declared is None: + declared = _read_source_attribute(array, "chunks") + if declared is None: + return None + try: + return dimension_grids_from_chunks(declared, shape) + except (ValueError, TypeError): + return None + + +def _whole_array_grids(shape: tuple[int, ...]) -> tuple[DimensionGrid, ...]: + """A partitioning with a single part covering the whole array.""" + return tuple(FixedDimension(size=extent, extent=extent) for extent in shape) + + +# --------------------------------------------------------------------------- # +# The lowering engine +# --------------------------------------------------------------------------- # + + +def _is_identity_transform(transform: IndexTransform, shape: tuple[int, ...]) -> bool: + """True when `transform` maps every coordinate of `shape` to itself. + + Structural rather than an `==` against `IndexTransform.from_shape`: an + `ArrayMap` holds an ndarray, so equality on two transforms that both carry + one would try to take the truth value of an array. + """ + domain = transform.domain + if domain.inclusive_min != (0,) * len(shape) or domain.exclusive_max != shape: + return False + if len(transform.output) != len(shape): + return False + return all( + isinstance(m, DimensionMap) and m.input_dimension == i and m.offset == 0 and m.stride == 1 + for i, m in enumerate(transform.output) + ) + + +# --------------------------------------------------------------------------- # +# Partitions +# --------------------------------------------------------------------------- # + + +@dataclass(frozen=True, slots=True, eq=False) +class _PartOwner: + """Opaque identity shared only by one view and the parts it prepared.""" + + +def _partition_out_selection( + cell_transform: IndexTransform, +) -> tuple[Any, ...]: + """Lower ``cell_transform`` to NumPy selectors on the request buffer.""" + domain = cell_transform.domain + if _is_correlated(cell_transform): + correlated_selectors: list[np.ndarray[Any, np.dtype[np.intp]]] = [] + for output_map in cell_transform.output: + if isinstance(output_map, ConstantMap): + coordinates = np.full(domain.shape, output_map.offset, dtype=np.intp) + elif isinstance(output_map, DimensionMap): + input_dimension = output_map.input_dimension + axis = np.arange( + domain.inclusive_min[input_dimension], + domain.exclusive_max[input_dimension], + dtype=np.intp, + ) + shape = ( + (1,) * input_dimension + + (axis.size,) + + ((1,) * (domain.ndim - input_dimension - 1)) + ) + coordinates = np.broadcast_to(axis.reshape(shape), domain.shape) + coordinates = output_map.offset + output_map.stride * coordinates + else: + coordinates = output_map.offset + output_map.stride * np.broadcast_to( + output_map.index_array, domain.shape + ) + correlated_selectors.append(np.asarray(coordinates, dtype=np.intp)) + return tuple(correlated_selectors) + + selectors: list[int | slice | np.ndarray[Any, np.dtype[np.intp]]] = [] + n_array_maps = sum(isinstance(output_map, ArrayMap) for output_map in cell_transform.output) + for output_map in cell_transform.output: + if isinstance(output_map, ConstantMap): + selectors.append(output_map.offset) + elif isinstance(output_map, DimensionMap): + input_dimension = output_map.input_dimension + lo = domain.inclusive_min[input_dimension] + hi = domain.exclusive_max[input_dimension] + selectors.append( + slice( + output_map.offset + output_map.stride * lo, + output_map.offset + output_map.stride * hi, + output_map.stride, + ) + ) + else: + selectors.append( + (output_map.offset + output_map.stride * output_map.index_array.ravel()).astype( + np.intp + ) + ) + if n_array_maps > 1: + axes = [ + np.asarray([selector], dtype=np.intp) + if isinstance(selector, int) + else ( + np.arange(selector.start, selector.stop, selector.step, dtype=np.intp) + if isinstance(selector, slice) + else selector + ) + for selector in selectors + ] + return np.ix_(*axes) + return tuple(selectors) + + +def _out_selection_cell_count(selection: tuple[Any, ...], out_shape: tuple[int, ...]) -> int: + """How many cells of an array of shape `out_shape` a `Partition.out_selection` writes. + + Counted from the selectors' own shapes, so nothing is read and no index + array is materialized. The selectors are slices and integer arrays: the + slices contribute their lengths, and the arrays broadcast against each other + exactly as NumPy's advanced indexing broadcasts them, whether they arrive as + an open mesh (`numpy.ix_`) or as parallel coordinates (`unravel_index`). + """ + total = 1 + array_shapes: list[tuple[int, ...]] = [] + if len(selection) != len(out_shape): + raise AssertionError( + f"a partition addressed {len(selection)} of the view's {len(out_shape)} " + "dimensions; this is a bug in zarr-indexing's partition walk" + ) + for selector, extent in zip(selection, out_shape, strict=True): + if isinstance(selector, slice): + start: Any = selector.start + stop: Any = selector.stop + step: Any = selector.step + if step is None and start is not None and stop is not None and 0 <= start <= stop: + # The shape a partition walk actually produces: a concrete, + # forward, in-bounds interval. Sized directly, so the common + # path allocates neither a tuple nor a range. + total *= int(stop) - int(start) + else: + total *= len(range(*selector.indices(extent))) + else: + array_shapes.append(tuple(int(s) for s in np.shape(selector))) + if len(array_shapes) > 0: + total *= math.prod(np.broadcast_shapes(*array_shapes)) + return total + + +@dataclass(frozen=True, kw_only=True) +class Partition: + """One box of a `LazyArray`'s partitioning, as it falls through the view. + + Yielded by [`LazyArray.parts`][zarr_indexing.lazy_array.LazyArray.parts]. + The parts of a view tile it exactly and disjointly: assembling every + `view.result()` at its `out_selection` reproduces the whole view's + `result()`, and each part can be resolved independently and concurrently. + Derived parts retain the same reader object; a shared stateful reader owns + synchronization for concurrent calls. + + A consumer that needs the plan before materialization can prepare it once + and reuse the same immutable parts for both scheduling and assembly: + + ```python + parts = tuple(view.parts()) + schedule(part.base_coords for part in parts) + values = view.result(parts=parts) + ``` + + Prepared parts are owned by the exact view that created them and must tile + it completely. Passing parts from another view, even an equivalent one, is + rejected without reading; omitting a part is likewise rejected rather than + returning a partly initialized result. + + Attributes + ---------- + projection + The source-independent description of this part. Its paired + `chunk_transform` and `cell_transform` share one compact synthetic + domain, mapping each selected cell to chunk-local storage and request + coordinates respectively. This is the authoritative placement model; + `base_coords` and `is_complete` are conveniences derived from it. + base_coords + Which box of the base partitioning this is, one coordinate per dimension + of the wrapped array. + box + The box itself, in the global storage coordinates of the wrapped + array: one `[inclusive_min, exclusive_max)` interval per dimension. It + describes the whole partition cell, while `view.bounding_box()` is the + global hull of only the selected values in that cell. For a nested or + repartitioned view this box may be narrower than + `projection.chunk_domain`. + view + A `LazyArray` covering exactly the cells of the view that live in this + box. Its transform directly addresses its raw wrapped `array`; only the + projection's `chunk_transform` is chunk-local. Resolving the view reads + the box once through its selected reader. Named `view` rather than + `array` because `LazyArray.array` is the opposite thing — the raw + wrapped source — and the two sat next to each other meaning inverses. + out_selection + Where `view.result()` belongs in an array of the whole view's shape — a + NumPy index tuple with one entry per dimension of the view, usable + directly as `out[part.out_selection] = ...`. + is_complete + Whether the view covers the whole box. Useful to a writer deciding + between a blind overwrite and a read-modify-write. Fancy projections + report `False` because their coverage is deliberately `unknown` until + duplicate-aware proof is added. + + Examples + -------- + Assembling every part's result at its `out_selection` reproduces the view: + + >>> import numpy as np + >>> source = np.arange(12).reshape(3, 4) + >>> view = LazyArray.from_numpy(source).with_parts((2, 2)) + >>> out = np.empty(view.shape, dtype=view.dtype) + >>> for part in view.parts(): + ... out[part.out_selection] = part.view.result() + >>> bool((out == source).all()) + True + """ + + projection: ChunkProjection + box: tuple[tuple[int, int], ...] + view: LazyArray + out_selection: tuple[Any, ...] + _owner: _PartOwner | None = field(default=None, repr=False, compare=False) + + @property + def base_coords(self) -> tuple[int, ...]: + """Coordinates of this partition in the selected base grid.""" + return self.projection.chunk_coords + + @property + def is_complete(self) -> bool: + """Whether the projection proves it covers the entire selected cell.""" + return self.projection.coverage == "full" + + +def _validate_prepared_parts(parts: Sequence[Partition], out_shape: tuple[int, ...]) -> None: + """Require `parts` to address every output cell exactly once. + + Prepared parts are caller-supplied input, so a plan that does not tile the + view is a `ValueError`, not an assertion about this library's own walk. + """ + coverage = np.zeros(out_shape, dtype=np.bool_) + addressed = 0 + try: + for part in parts: + # Name a rank mismatch explicitly instead of letting NumPy treat + # omitted selectors as implicit full slices. + addressed += _out_selection_cell_count(part.out_selection, out_shape) + if all(isinstance(selector, slice) for selector in part.out_selection): + # The common box part: plain assignment, no pointwise walk. + coverage[part.out_selection] = True + else: + # `logical_or.at` applies duplicate advanced coordinates one by + # one instead of buffering them as ordinary advanced indexing + # would. + np.logical_or.at(coverage, part.out_selection, True) + except (AssertionError, IndexError, TypeError, ValueError) as error: + raise ValueError("prepared parts do not tile the view exactly") from error + if addressed != math.prod(out_shape) or not np.all(coverage): + raise ValueError("prepared parts do not tile the view exactly") + + +# --------------------------------------------------------------------------- # +# Tokenization +# --------------------------------------------------------------------------- # + + +def _wrapped_token(array: Any) -> Any: + """A token for the wrapped array. + + In order of preference: the array's own `__dask_tokenize__`; + `dask.base.tokenize` when dask is importable (imported lazily — this package + never requires it); otherwise a local fallback that digests the contents of + a small array. + + The two environments do not agree, and neither is a translation of the + other: a token taken with dask installed is meaningless to a process without + it, and the reverse. A token is an identifier within one process, not a + portable name. + + Above `_TOKEN_DIGEST_LIMIT` the local fallback has nothing left to identify + the contents with — reading them is exactly what a token call must not do — + so it declines to claim equality at all and returns a value that matches + nothing, including itself. A cache keyed on it misses; the alternative, a + structural description, is a cache that hands one array's result to a + different array of the same shape and dtype. + """ + hook = getattr(array, "__dask_tokenize__", None) + if hook is not None: + try: + return hook() + # A token must never raise; fall through to the structural fallback. + except Exception: # pragma: no cover - a hook that refuses to run + pass + try: + # dask is an optional peer, never a dependency of this package, so it is + # imported here and its absence is ordinary. + from dask.base import tokenize # pyright: ignore[reportMissingImports] + except ImportError: + pass + else: + return tokenize(array) + + shape = tuple(int(s) for s in getattr(array, "shape", ())) + dtype = getattr(array, "dtype", None) + structural = (type(array).__qualname__, shape, str(dtype)) + # A token nothing can equal, for when the contents cannot be identified. It + # is the shape and dtype that would otherwise be mistaken for an identity, + # so they are kept alongside it for a reader looking at a graph. + unidentified = (*structural, "unidentified", uuid.uuid4().hex) + + # Decide whether to digest the contents from the *declared* size. Measuring + # it by converting first would read the whole array — a multi-gigabyte store + # pulled into memory by a token call, which is the opposite of the point. + itemsize = getattr(dtype, "itemsize", None) + if not isinstance(itemsize, int) or itemsize * math.prod(shape) > _TOKEN_DIGEST_LIMIT: + return unidentified + try: + contents = np.ascontiguousarray(array) + # A token must never raise; an unreadable source is simply unidentified. + except Exception: + return unidentified + return (*structural, hashlib.sha256(contents.tobytes()).hexdigest()) + + +# --------------------------------------------------------------------------- # +# The wrapper +# --------------------------------------------------------------------------- # + + +class LazyArray: + """A lazily-indexable view over a system-memory/basic-indexing source. + + Wrapping neither copies nor reads the wrapped array at construction time. + Indexing through `.lazy` composes an `IndexTransform` and returns another + `LazyArray`; `result()` materializes. + + Selections use the **positional NumPy dialect** and reads are broken up + along a **partitioning** discovered from the wrapped array. Every derived + view retains its reader; that reader receives the complete projected + transform once per part. See the module docstring, which also covers how the + dialect differs from `zarr.Array.lazy` and why every non-indexing NumPy + operation materializes the view. + + This wrapper describes **reads**. It defines no `__setitem__`, so + assigning into a view raises `TypeError`. Writing belongs to the + consumer: plan the selection with + [`plan_chunks`][zarr_indexing.chunk_resolution.plan_chunks] and own the + read-modify-write, since chunk atomicity and concurrent-writer policy are + the backend's to decide, not an indexing plan's. + + Parameters + ---------- + array + The array to wrap. It must expose `shape`, `dtype`, and `__getitem__` + with basic (integer/slice) indexing; `__setitem__` is not required, so + a read-only source wraps as well as a writable one. Its partitioning, + if it advertises one, is discovered here; use `with_parts` to choose + a different one. + This conservative constructor selects `basic_reader`; use `from_numpy` + for a NumPy array or `with_reader` to select another backend adapter. + + Examples + -------- + >>> import numpy as np + >>> source = np.arange(12).reshape(3, 4) + >>> view = LazyArray.from_numpy(source).with_parts((2, 2)).lazy[1:, ::2] + >>> view.shape + (2, 2) + >>> view.result() + array([[ 4, 6], + [ 8, 10]]) + """ + + __slots__ = ("_array", "_part_owner", "_parts", "_reader", "_transform", "_window") + + def __init__(self, array: _WrappedArray) -> None: + """Wrap `array` without reading it; parameters are documented on the class. + + The only validation here is the `numpy.matrix` rejection (`TypeError`). + """ + if isinstance(array, np.matrix): + # `np.matrix` keeps every result two-dimensional, so `m[1]` has shape + # `(1, n)` where every other array-like gives `(n,)`. A view's shape + # comes from the transform, which follows NumPy's rule, so the two + # disagree on every rank-reducing selection. Refused at the door + # rather than resolved into a shape the view did not promise. + raise TypeError( + "numpy.matrix cannot be wrapped: it never reduces rank, so a " + "view's shape and its result would disagree. Convert it first, " + "with numpy.asarray(m)." + ) + shape = tuple(int(s) for s in array.shape) + self._array = array + self._window: tuple[slice, ...] | None = None + self._transform = IndexTransform.from_shape(shape) + self._parts = _discover_parts(array, shape) + self._reader = basic_reader + self._part_owner = _PartOwner() + + @classmethod + def from_numpy(cls, array: np.ndarray[Any, Any]) -> LazyArray: + """Wrap a NumPy array with its explicitly selected optimized reader.""" + if not isinstance(cast(object, array), np.ndarray): + raise TypeError( + f"LazyArray.from_numpy requires a numpy.ndarray, got {type(array).__name__}" + ) + return cls(array).with_reader(numpy_reader) + + @classmethod + def _derive( + cls, + array: _WrappedArray, + transform: IndexTransform, + parts: tuple[DimensionGrid, ...] | None, + window: tuple[slice, ...] | None, + reader: Reader, + ) -> LazyArray: + """Build a wrapper sharing `array` but carrying a new transform or partitioning.""" + view = cls.__new__(cls) + view._array = array + # Views re-zero their coordinate system: the positional dialect means a + # view's first element is at position 0 whatever it was sliced from. + view._transform = transform.translate_domain_to((0,) * transform.input_rank) + view._parts = parts + view._window = window + view._reader = reader + view._part_owner = _PartOwner() + return view + + @property + def _base_shape(self) -> tuple[int, ...]: + """The shape of what this wrapper treats as its base array.""" + if self._window is None: + return tuple(int(s) for s in self._array.shape) + return tuple(s.stop - s.start for s in self._window) + + # -- array-like surface ------------------------------------------------- + + @property + def array(self) -> _WrappedArray: + """The wrapped array.""" + return self._array + + @property + def base_shape(self) -> tuple[int, ...]: + """The shape the partitioning is expressed in — not this view's shape. + + `with_parts` and `with_parts_per_axis` describe boxes of the array being + read, not of the view reading it, so a narrowed view still partitions + the extents named here. For a part's own `array`, this is the part's + box, which is why the same call means different sizes there. Without + somewhere to read it, the frame in force could only be inferred from an + error message. + """ + return self._base_shape + + @property + def transform(self) -> IndexTransform: + """The composed transform from this view's coordinates to storage.""" + return self._transform + + @property + def shape(self) -> tuple[int, ...]: + """The shape of this view — the transform's input domain, not the source's.""" + return self._transform.domain.shape + + @property + def ndim(self) -> int: + """Number of dimensions of this view — the transform's input rank.""" + return self._transform.input_rank + + @property + def size(self) -> int: + """Total number of elements in this view (the product of `shape`).""" + return math.prod(self.shape) + + @property + def dtype(self) -> Any: + """The wrapped array's dtype; views never change it.""" + return self._array.dtype + + @property + def reader(self) -> Reader: + """The backend adapter used when this view materializes.""" + return self._reader + + def with_reader(self, reader: Reader) -> LazyArray: + """Return the same metadata view resolved through `reader`.""" + if not callable(getattr(reader, "read_into", None)): + raise TypeError(f"reader.read_into must be callable, got {type(reader).__name__}") + return LazyArray._derive( + self._array, + self._transform, + self._parts, + self._window, + reader, + ) + + # -- shape of the selection --------------------------------------------- + + @property + def is_box(self) -> bool: + """Whether this view selects a rectangular region rather than a point list. + + True exactly when the composed transform's output maps are all + `ConstantMap` or `DimensionMap` — no `ArrayMap`. Such a selection is + affine and monotone along every axis, so it is described completely by + an interval and a stride per dimension: + [`bounding_box`][zarr_indexing.lazy_array.LazyArray.bounding_box] + together with + [`strides`][zarr_indexing.lazy_array.LazyArray.strides]. Basic indexing, + at any depth of composition, stays a box; one `oindex`, `vindex`, or + mask anywhere in the chain makes the selection a query permanently. + + A box is dense — every cell of its bounding box selected — only when + every stride is 1. A strided box covers its hull sparsely: + `lazy[10:50, ::4]` selects 40x20 cells out of a 40x77 hull, so a + consumer that reads the whole hull and discards the rest transfers 3.85x + the data it needs. Check `strides` before treating a box as a single + slab read. + + The distinction lets a consumer decide between a slab read and a + gather; see [the design notes](../design-notes.md) for why it is a + category rather than an optimization. + + Examples + -------- + >>> import numpy as np + >>> array = LazyArray.from_numpy(np.arange(12).reshape(3, 4)) + >>> (array.lazy[1:, ::2].is_box, array.lazy.oindex[[2, 0], :].is_box) + (True, False) + """ + return not any(isinstance(m, ArrayMap) for m in self._transform.output) + + def bounding_box(self) -> tuple[tuple[int, int], ...] | None: + """The storage region this view touches, one interval per storage dimension. + + Defined for any selection, box or not, as the hull: the smallest + `[inclusive_min, exclusive_max)` interval per dimension of the array + this view reads from that contains every coordinate the selection + reaches. + + The hull is dense — every cell in it selected — only for a box whose + every stride is 1. A strided box selects a sublattice of its hull (pair + this with [`strides`][zarr_indexing.lazy_array.LazyArray.strides] to + describe it fully), and a query's hull is a superset that can be + arbitrarily loose: `oindex[[0, 999]]` has a 1000-wide hull over two + rows. + + Returns + ------- + tuple of (int, int), or None + One interval per storage dimension, or `None` when the view is + empty (`size == 0`) and so touches no coordinate at all, leaving no + interval to report. + + Notes + ----- + The coordinates directly address the raw `array` this view exposes. + Consequently, partition views report source-global hulls; + [`Partition.box`][zarr_indexing.lazy_array.Partition] separately gives + the whole global partition cell rather than only the selected hull. + + Examples + -------- + >>> import numpy as np + >>> array = LazyArray.from_numpy(np.arange(12).reshape(3, 4)) + >>> array.lazy[1:, ::2].bounding_box() + ((1, 3), (0, 3)) + >>> array.lazy.oindex[[2, 0], :].bounding_box() + ((0, 3), (0, 4)) + >>> array.lazy[1:1].bounding_box() is None + True + """ + if self.size == 0: + return None + domain = self._transform.domain + bounds: list[tuple[int, int]] = [] + for m in self._transform.output: + if isinstance(m, ConstantMap): + bounds.append((m.offset, m.offset + 1)) + elif isinstance(m, DimensionMap): + d = m.input_dimension + first = m.offset + m.stride * domain.inclusive_min[d] + last = m.offset + m.stride * (domain.exclusive_max[d] - 1) + bounds.append((min(first, last), max(first, last) + 1)) + else: + coords = m.offset + m.stride * m.index_array + bounds.append((int(coords.min()), int(coords.max()) + 1)) + return tuple(bounds) + + def strides(self) -> tuple[int, ...] | None: + """The step between selected coordinates, one per storage dimension. + + Together with `bounding_box()`, this fully describes a box selection: + `bounding_box()` gives the interval per dimension, `strides()` gives the + step per dimension. A stride of 1 means every cell of the hull along + that dimension is selected; `k` means every `k`-th. Dimensions fixed by + an integer index report 1 — they span a single coordinate. + + Returns + ------- + tuple of int, or None + One positive stride per storage dimension, or `None` when + [`is_box`][zarr_indexing.lazy_array.LazyArray.is_box] is false: a + query's coordinates are a lookup table and have no step. An empty + box still reports its strides even though + [`bounding_box`][zarr_indexing.lazy_array.LazyArray.bounding_box] + returns `None`, because the step is a property of the selection's + shape, not of the (empty) region it touches. + + Notes + ----- + Magnitudes only. A reversing view (`lazy[::-1]`) selects the same set of + coordinates as the equivalent forward view, so it reports the same + bounding box and the same strides. The traversal direction is recorded + in the transform, not in this description of the region touched. A + consumer that needs the order reads the transform, or reverses the block + it gets back. + + Examples + -------- + >>> import numpy as np + >>> array = LazyArray.from_numpy(np.arange(24).reshape(4, 6)) + >>> (array.lazy[1:, ::2].bounding_box(), array.lazy[1:, ::2].strides()) + (((1, 4), (0, 5)), (1, 2)) + >>> array.lazy[2, ::3].strides() + (1, 3) + >>> array.lazy.oindex[[2, 0], :].strides() is None + True + """ + if not self.is_box: + return None + return tuple( + 1 if isinstance(m, ConstantMap) else abs(m.stride) for m in self._transform.output + ) + + # -- partitioning ------------------------------------------------------- + + def with_parts(self, parts: Sequence[int]) -> LazyArray: + """Return the same view, read in uniform boxes of shape `parts`. + + One integer per dimension of `base_shape`, with the trailing box in each + dimension clipped to the extent. The transform, the wrapped array, and + therefore `result()` are all unchanged; only the boxes the read is + broken into differ. Nothing is copied and nothing is read. + + For per-axis sizes see + [`with_parts_per_axis`][zarr_indexing.lazy_array.LazyArray.with_parts_per_axis], + and to read in one pass see + [`unpartitioned`][zarr_indexing.lazy_array.LazyArray.unpartitioned]. + The three were one parameter whose meaning was decided by inspecting the + type of what it was given, which left no way to ask for one of them and + be told when you had spelled it wrong. + + Parameters + ---------- + parts + The box shape, one integer per dimension of `base_shape`. + + Returns + ------- + LazyArray + The same view with a new partitioning. + + Raises + ------ + ValueError + If `parts` has the wrong length or contains a non-positive extent. + Uniform part sizes must remain positive even for a zero-length + axis; use `with_parts_per_axis` for the accepted explicit zero-axis + spellings. + + Examples + -------- + >>> import numpy as np + >>> view = LazyArray.from_numpy(np.arange(12).reshape(3, 4)) + >>> [part.base_coords for part in view.with_parts((2, 3)).parts()] + [(0, 0), (0, 1), (1, 0), (1, 1)] + """ + entries = self._part_entries(parts, "with_parts") + if any(isinstance(entry, Sequence) for entry in entries): + raise ValueError( + "with_parts takes one integer per dimension; for per-axis box " + "sizes use with_parts_per_axis" + ) + return self._with_grids(dimension_grids_from_chunks(entries, self._base_shape)) + + def with_parts_per_axis(self, sizes: Sequence[Sequence[int]]) -> LazyArray: + """Return the same view, read in boxes of explicitly listed sizes. + + The dask convention: one sequence of box extents per dimension of + `base_shape`, each summing to that dimension's extent. Use it when the + boxes are not uniform — a partitioning discovered from a store, or one + whose last box differs by more than clipping. + + Parameters + ---------- + sizes + One sequence of box extents per dimension of `base_shape`. + + Returns + ------- + LazyArray + The same view with a new partitioning. + + Raises + ------ + ValueError + If `sizes` has the wrong length, contains a negative extent, uses a + zero extent on a nonempty axis, or declares sizes that do not sum + to `base_shape`. On a zero-length axis, `()`, `(0,)`, and repeated + zeros all describe no chunks. + + Examples + -------- + >>> import numpy as np + >>> view = LazyArray.from_numpy(np.arange(12).reshape(3, 4)) + >>> [part.box for part in view.with_parts_per_axis(((1, 2), (4,))).parts()] + [((0, 1), (0, 4)), ((1, 3), (0, 4))] + """ + entries = self._part_entries(sizes, "with_parts_per_axis") + return self._with_grids(dimension_grids_from_chunks(entries, self._base_shape)) + + @staticmethod + def _part_entries(parts: Sequence[Any], method: str) -> tuple[Any, ...]: + """Materialize a partitioning argument, naming a non-iterable a ValueError. + + Both partitioning methods document ValueError for malformed input; a + bare integer would otherwise surface as a TypeError from iteration. + """ + try: + return tuple(parts) + except TypeError as error: + raise ValueError( + f"{method} takes one entry per dimension of base_shape; got {parts!r}" + ) from error + + def unpartitioned(self) -> LazyArray: + """Return the same view, read in one pass. + + `result()` still allocates its owned output buffer first, then calls the + reader once with the whole projected transform. `parts()` still yields a + single part covering everything. + + Returns + ------- + LazyArray + The same view with no partitioning. + """ + return self._with_grids(None) + + def _with_grids(self, grids: tuple[DimensionGrid, ...] | None) -> LazyArray: + return LazyArray._derive(self._array, self._transform, grids, self._window, self._reader) + + def parts(self) -> Iterator[Partition]: + """Iterate the base partitioning, projected through this view. + + Single-use: this is a generator, so it is consumed by the first walk and + a second `for` over the same object yields nothing. Call `parts()` again + for a fresh walk, or keep a `list` of it if you need to revisit. + + Yields one [`Partition`][zarr_indexing.lazy_array.Partition] per box the + view actually touches. The parts tile the view exactly and disjointly, + and each carries a `LazyArray` that can be resolved on its own: in + another thread, in another order, or not at all. Those views share this + view's reader, and `LazyArray` does not serialize calls, so a stateful + reader must synchronize its own mutable state. + + A wrapper with no partitioning (see `with_parts`) yields a single part + covering the whole array. + + Yields + ------ + Partition + One per touched box, in the resolver's own order. + + Examples + -------- + >>> import numpy as np + >>> view = LazyArray.from_numpy(np.arange(12).reshape(3, 4)).with_parts((2, 2)) + >>> part = next(view.lazy[:, 1:].parts()) + >>> (part.base_coords, part.view.shape, part.is_complete) + ((0, 0), (2, 1), False) + """ + base_shape = self._base_shape + grids = self._parts if self._parts is not None else _whole_array_grids(base_shape) + rank = len(base_shape) + + if self._window is None: + plan_transform = self._transform + else: + plan_transform = self._transform.translate(tuple(-item.start for item in self._window)) + + for projection in plan_chunks(plan_transform, grids): + base_coords = projection.chunk_coords + local = projection.chunk_transform + origin = tuple(grid.chunk_offset(c) for grid, c in zip(grids, base_coords, strict=True)) + extent = tuple(grid.data_size(c) for grid, c in zip(grids, base_coords, strict=True)) + if origin == (0,) * rank and extent == base_shape: + # The part is the whole base: lowering directly against the + # source beats materializing a block that is the source. + window = self._window + elif self._window is None: + window = tuple(slice(o, o + e) for o, e in zip(origin, extent, strict=True)) + else: + window = tuple( + slice(w.start + o, w.start + o + e) + for w, o, e in zip(self._window, origin, extent, strict=True) + ) + # The global box, computed from the origin directly rather than from + # `window`: a part covering the whole base carries no window (so + # nothing is pre-materialized) but still sits somewhere concrete. + if self._window is None: + global_origin = origin + else: + global_origin = tuple( + w.start + o for w, o in zip(self._window, origin, strict=True) + ) + yield Partition( + projection=projection, + box=tuple((o, o + e) for o, e in zip(global_origin, extent, strict=True)), + view=LazyArray._derive( + self._array, + local.translate(global_origin), + None, + window, + self._reader, + ), + out_selection=_partition_out_selection(projection.cell_transform), + _owner=self._part_owner, + ) + + # -- indexing ----------------------------------------------------------- + + @property + def lazy(self) -> _LazyIndexer: + """Lazy indexing: `lazy[...]`, `lazy.oindex[...]`, `lazy.vindex[...]`. + + Each returns a new `LazyArray` view; no data is read. + """ + return _LazyIndexer(self._select) + + def _select(self, selection: Any, mode: SelectionMode) -> LazyArray: + transform = self._transform + if mode != "basic": + # NumPy applies scalar integers as basic indices before the advanced + # ones, dropping their axes. Split them into their own step. + scalar_selection, selection = split_scalar_axes(selection, transform.domain, mode) + if scalar_selection is not None: + transform = transform.select(scalar_selection, "basic") + transform = transform.translate_domain_to((0,) * transform.input_rank) + literal = normalize_positional_selection(selection, transform.domain, mode) + if mode == "basic": + # IndexTransform's basic path includes NumPy's `None`/newaxis. + # `selection_to_transform` intentionally exposes a narrower basic + # selection contract and rejects it. + composed = transform[literal] + else: + composed = transform.select(literal, mode) + return LazyArray._derive(self._array, composed, self._parts, self._window, self._reader) + + def __getitem__(self, selection: Any) -> Any: + """Read a basic selection eagerly, like `numpy.ndarray.__getitem__`. + + Reads here are eager, not lazy, so that a `LazyArray` works as a duck + array for consumers (dask's `from_array`, `numpy.asarray`) that expect + indexing to produce data. Use `.lazy[...]` for the lazy form. + """ + return self._select(selection, "basic").result() + + def result(self, *, parts: Sequence[Partition] | None = None) -> Any: + """Materialize this view. + + Every result starts as a fresh system-memory buffer. Each touched + partition is read through the selected reader directly into its + rectangular destination, or into an owned dense temporary before fancy + placement. Empty views allocate without reading the source. + + Parameters + ---------- + parts + A reusable sequence previously returned by this exact view's + `parts()` method. Supplying it reuses that partition plan instead + of constructing another one. The parts must tile the view exactly. + + Returns + ------- + numpy.ndarray + An array of shape `self.shape`, identical whatever partitioning is + in force, always in fresh system memory. A view with a zero-rank + domain returns a zero-dimensional array, not a scalar. + + Raises + ------ + ValueError + If supplied parts were prepared by another view, or do not tile + this view exactly. The output buffer is uninitialized where nothing + was written, so a bad plan is reported rather than returned. + AssertionError + If this library's own partition walk fails to cover the view — a + bug in zarr-indexing, never a consequence of the caller's input. + """ + prepared_parts = None if parts is None else tuple(parts) + if prepared_parts is not None and any( + # Module-private provenance deliberately crosses the two public + # wrapper types without becoming part of either public surface. + part._owner is not self._part_owner # pyright: ignore[reportPrivateUsage] + for part in prepared_parts + ): + raise ValueError("prepared parts do not belong to this view") + + out_shape = self.shape + if prepared_parts is not None: + _validate_prepared_parts(prepared_parts, out_shape) + out = self._output_buffer(out_shape) + size = math.prod(out_shape) + if size == 0: + return out + + if prepared_parts is None and self._parts is None: + _invoke_reader(self._reader, self._array, ReadContext(self._transform), out) + return out + + written = 0 + selected_parts = self.parts() if prepared_parts is None else prepared_parts + for part in selected_parts: + # Counted before the scatter, so a part addressing the wrong + # number of axes is named rather than reported as a broadcast + # failure against the buffer. + written += _out_selection_cell_count(part.out_selection, out_shape) + direct = all(isinstance(selector, slice) for selector in part.out_selection) + if direct: + destination = out if len(part.out_selection) == 0 else out[part.out_selection] + else: + destination = part.view._output_buffer(part.view.shape) + _invoke_reader( + self._reader, + self._array, + ReadContext(part.view.transform, part.projection), + destination, + ) + if not direct: + out[part.out_selection] = destination + if written != size: + # The buffer is uninitialized where no part wrote, so a partition + # walk that does not tile the view exactly would otherwise hand + # back process memory dressed as data. The parts are disjoint by + # contract, so counting the cells each addresses is enough: + # a gap undercounts and an overlap overcounts. + if prepared_parts is not None: + raise ValueError( + "prepared parts do not tile the view exactly: " + f"they addressed {written} of the view's {size} cells" + ) + raise AssertionError( + f"the partition walk addressed {written} of the view's {size} " + "cells; this is a bug in zarr-indexing's partition walk" + ) + return out + + def _output_buffer(self, out_shape: tuple[int, ...]) -> Any: + """The buffer `result()` scatters parts into. + + Deliberately uninitialized: every cell is written by exactly one part, + and `result()` verifies that before returning. A masked source gets a + masked buffer so that reader writes preserve the mask; other source- + specific array types do not survive materializing. + """ + dtype = np.dtype(self.dtype) + if isinstance(self._array, np.ma.MaskedArray): + return np.ma.masked_all(out_shape, dtype=dtype) + return np.empty(out_shape, dtype=dtype) + + # -- protocols ---------------------------------------------------------- + + def __array__(self, dtype: Any = None, copy: bool | None = None) -> Any: + """Materialize the view as a NumPy array. + + The result never shares memory with the wrapped array, whatever `copy` + asks for: `result()` already allocates, so `copy=True` gets an array the + caller owns and `copy=None` gets the same one rather than a second + allocation. `copy=False` is refused, because materializing means reading + — the values do not exist as a NumPy array until this call makes them. + """ + if copy is False: + raise ValueError( + "a LazyArray cannot be converted to a NumPy array without a " + "copy: a view is a description of a read, and the values only " + "exist once the read is made" + ) + return np.asarray(self.result(), dtype=dtype) + + def __dask_tokenize__(self) -> Any: + """A deterministic token: the wrapped array and the view. + + Two wrappers produce equal tokens when they wrap the same data and + address the same cells. The view contributes a digest of its canonical + ndsel body, so transforms that differ only in representation produce + the same token, and a fancy selection with a large index array does not + embed that array's JSON in the token. See `_wrapped_token` for the + determinism scope of the wrapped array's contribution; dask is imported + lazily and is never a requirement of this package. + + The partitioning and reader are deliberately absent. Both decide how + the data is read — in which boxes, and through which request strategy — + and neither changes the values that come back, so two wrappers differing + only in those describe the same data. A token identifies data, so they + token alike and a consumer that caches on tokens reuses one result for + both. + """ + canonical = json.dumps(self._transform.to_json(), sort_keys=True) + return ( + type(self).__qualname__, + _wrapped_token(self._array), + hashlib.sha256(canonical.encode()).hexdigest(), + ) + + def __len__(self) -> int: + """The length of the first axis, as for a NumPy array; `TypeError` on a 0-d view.""" + if self.ndim == 0: + raise TypeError("len() of unsized object") + return self.shape[0] + + def __iter__(self) -> Iterator[Any]: + """Iterate eagerly over the first axis, like a NumPy array. + + The rank check happens in `__iter__` itself rather than in the + generator, so `iter(view)` on a zero-rank view raises immediately as + NumPy's does, instead of waiting for the first `next`. + """ + if self.ndim == 0: + raise TypeError("iteration over a 0-d array") + return (self[position] for position in range(self.shape[0])) + + # NumPy's own conversions decide what a size-1 (or wrong-sized) view means, + # including which exception it raises, so these delegate rather than + # reimplement. Each materializes the view first. + def __bool__(self) -> bool: + return bool(self.result()) + + def __int__(self) -> int: + return int(self.result()) + + def __float__(self) -> float: + return float(self.result()) + + def __index__(self) -> int: + return operator.index(self.result()) + + def __repr__(self) -> str: + wrapped = type(self._array).__name__ + described = [f"{wrapped} shape={self.shape} dtype={self.dtype}"] + if not _is_identity_transform(self._transform, self._base_shape): + described.append(f"view={self._transform.selection_repr}") + return f"<LazyArray {' '.join(described)}>" + + +class _LazyIndexer: + """The `.lazy` accessor: builds views instead of reading data. + + Holds the owning view's bound `_select` rather than the view itself, so the + accessor classes never reach into another object's internals. + """ + + __slots__ = ("_select",) + + def __init__(self, select: SelectFn) -> None: + self._select = select + + def __getitem__(self, selection: Any) -> LazyArray: + """Basic (integer / slice / ellipsis) indexing, lazily.""" + return self._select(selection, "basic") + + @property + def oindex(self) -> _LazyOIndex: + """Orthogonal (outer-product) indexing, lazily.""" + return _LazyOIndex(self._select) + + @property + def vindex(self) -> _LazyVIndex: + """Vectorized (coordinate / mask) indexing, lazily.""" + return _LazyVIndex(self._select) + + +class _LazyOIndex: + """`lazy.oindex[...]` — one selection per axis, combined as an outer product.""" + + __slots__ = ("_select",) + + def __init__(self, select: SelectFn) -> None: + self._select = select + + def __getitem__(self, selection: Any) -> LazyArray: + return self._select(selection, "orthogonal") + + +class _LazyVIndex: + """`lazy.vindex[...]` — correlated coordinate arrays, or a single mask.""" + + __slots__ = ("_select",) + + def __init__(self, select: SelectFn) -> None: + self._select = select + + def __getitem__(self, selection: Any) -> LazyArray: + return self._select(selection, "vectorized") diff --git a/packages/zarr-indexing/src/zarr_indexing/messages.py b/packages/zarr-indexing/src/zarr_indexing/messages.py index d5761d1a38..df0e0c87eb 100644 --- a/packages/zarr-indexing/src/zarr_indexing/messages.py +++ b/packages/zarr-indexing/src/zarr_indexing/messages.py @@ -54,6 +54,9 @@ "output_map_conflict", "rank_mismatch", "step_zero", + # Retired in 1.0-draft.2, when negative `step` became specified. Kept in + # the set so a message carrying the code is still recognized, but no + # condition in this implementation emits it. "negative_step_unsupported", } ) @@ -65,9 +68,23 @@ class NdselError(ValueError): Carries the spec `reason` code (one of `REASON_CODES`) so callers and the conformance harness can assert on it directly, plus a human-readable `detail`. + + Examples + -------- + >>> try: + ... normalize_ndsel({"kind": "bogus"}) + ... except NdselError as error: + ... (error.reason, str(error)) + ('unknown_kind', "unknown_kind: unknown kind 'bogus'") """ def __init__(self, reason: str, detail: str = "") -> None: + """Store `reason` and `detail` and compose the message as `"reason: detail"`. + + `reason` is a spec reason code (one of `REASON_CODES`); `detail` is + optional human-readable context, and when empty the message is the + bare `reason`. + """ self.reason = reason self.detail = detail super().__init__(f"{reason}: {detail}" if detail else reason) @@ -88,9 +105,21 @@ def __init__(self, reason: str, detail: str = "") -> None: _TRANSFORM_UPPER = ("input_exclusive_max", "input_inclusive_max", "input_shape") _OUTPUT_MAP_FIELDS = frozenset( - {"offset", "stride", "input_dimension", "index_array", "index_array_bounds"} + { + "offset", + "stride", + "input_dimension", + "index_array", + "index_array_bounds", + } ) +# An upper bound on `input_rank`, because normalization allocates proportionally +# to it — an identity `output`, a bound per dimension, a label per dimension — +# from a document that carries no data behind the number. Matches the rank +# TensorStore accepts, which is well above any real array. +_MAX_RANK = 32 + # --------------------------------------------------------------------------- # Leaf value validators @@ -259,28 +288,50 @@ def _resolve_upper_bound( implicit = _bound_is_implicit(raw) value = _bound_value(raw) if kind_of == "inclusive": - new = _inclusive_to_exclusive(value) + new = _inclusive_to_exclusive(value, f"{upper_field}[{k}]") else: # shape - new = _shape_to_exclusive(_bound_value(inclusive_min[k]), value) + new = _shape_to_exclusive(_bound_value(inclusive_min[k]), value, f"{upper_field}[{k}]") result.append(_rewrap(new, implicit=implicit)) return result -def _inclusive_to_exclusive(value: int | str) -> int | str: +def _checked_i64(value: int, where: str) -> int: + """An arithmetic result that must still be a 64-bit signed integer. + + Normalization is idempotent (spec section 4.3): whatever it emits must pass + the same validation on the way back in. Desugaring adds — `inclusive_max + 1`, + `inclusive_min + shape` — so a bound at the top of the range would otherwise + be emitted one past it and rejected by the next call on our own output. + """ + if value < _I64_MIN or value > _I64_MAX: + raise NdselError( + "invalid_json", + f"{where} is {value}, which is outside the 64-bit signed range; the " + f"normalized form cannot represent it", + ) + return value + + +def _inclusive_to_exclusive(value: int | str, where: str) -> int | str: if value == "+inf" or value == "-inf": return value assert isinstance(value, int) - return value + 1 + return _checked_i64(value + 1, f"{where} converted to an exclusive bound") -def _shape_to_exclusive(min_value: int | str, shape_value: int | str) -> int | str: +def _shape_to_exclusive(min_value: int | str, shape_value: int | str, where: str) -> int | str: + if shape_value == "-inf": + raise NdselError( + "invalid_json", + f"{where} is '-inf'; a shape counts cells and cannot be negatively infinite", + ) if shape_value == "+inf" or min_value == "+inf": return "+inf" if min_value == "-inf": return "-inf" assert isinstance(min_value, int) assert isinstance(shape_value, int) - return min_value + shape_value + return _checked_i64(min_value + shape_value, f"{where} added to its inclusive_min") def _validate_domain(inclusive_min: list[Any], exclusive_max: list[Any], *, prefix: str) -> None: @@ -408,17 +459,27 @@ def _normalize_slice(obj: dict[str, Any]) -> dict[str, Any]: for k, s in enumerate(step): if s == 0: raise NdselError("step_zero", f"step[{k}] is zero") - if s < 0: - raise NdselError("negative_step_unsupported", f"step[{k}] is negative ({s})") inclusive_min: list[Any] = [] exclusive_max: list[Any] = [] output: list[dict[str, Any]] = [] for k in range(n): a, b, s = start[k], stop[k], step[k] - m = max(0, -(-(b - a) // s)) # ceil((b - a) / s) - o = _trunc_div(a, s) # trunc(a / s), toward zero - offset = a - s * o # lattice phase, in (-s, s) + # One rule for both signs (spec 5.3): the traversal runs from `a` + # toward `b`, so the source interval's length is `b - a` going up and + # `a - b` going down. + length = (b - a) if s > 0 else (a - b) + if length < 0: + # A reversed interval is a mistake about the direction of travel, + # not an empty selection. `b == a` is the way to select nothing. + raise NdselError( + "bounds_out_of_order", + f"start[{k}]={a} and stop[{k}]={b} with step {s} run the wrong " + "way; an empty selection is spelled stop == start", + ) + m = -(-length // abs(s)) # ceil(length / |s|) + o = _trunc_div(a, s) # trunc(a / s), toward zero, both signs + offset = a - s * o # lattice phase, |offset| < |s| inclusive_min.append(o) exclusive_max.append(o + m) output.append({"offset": offset, "stride": s, "input_dimension": k}) @@ -499,12 +560,13 @@ def _normalize_output_map(raw: Any, where: str) -> dict[str, Any]: else ["-inf", "+inf"] ) # index_array is carried verbatim (spec section 7 defers shape validation). - return { + normalized: dict[str, Any] = { "offset": offset, "stride": stride, "index_array": raw["index_array"], "index_array_bounds": bounds, } + return normalized if has_input_dim: input_dim = _check_int(raw["input_dimension"], f"{where}.input_dimension") @@ -528,10 +590,14 @@ def _check_index_array_bounds(value: Any, where: str) -> list[int | str]: "invalid_json", f"{where}.index_array_bounds must be a two-element array, got {value!r}", ) - return [ - _check_index_value(value[0], f"{where}.index_array_bounds[0]"), - _check_index_value(value[1], f"{where}.index_array_bounds[1]"), - ] + lo = _check_index_value(value[0], f"{where}.index_array_bounds[0]") + hi = _check_index_value(value[1], f"{where}.index_array_bounds[1]") + if _ext_key(lo) > _ext_key(hi): + raise NdselError( + "bounds_out_of_order", + f"{where}.index_array_bounds: lower bound {lo!r} > upper bound {hi!r}", + ) + return [lo, hi] def _normalize_transform(obj: dict[str, Any]) -> dict[str, Any]: @@ -554,6 +620,14 @@ def _normalize_transform(obj: dict[str, Any]) -> dict[str, Any]: declared_rank = _check_int(obj["input_rank"], "input_rank") if declared_rank < 0: raise NdselError("invalid_json", f"input_rank must be >= 0, got {declared_rank}") + if declared_rank > _MAX_RANK: + # Normalization fills a bound, a label and an identity output map per + # dimension, so an unbacked rank is a request to allocate from a + # document that carries nothing. + raise NdselError( + "invalid_json", + f"input_rank must be <= {_MAX_RANK}, got {declared_rank}", + ) inclusive_min_raw = ( _check_bound_list(obj["input_inclusive_min"], "input_inclusive_min") @@ -590,6 +664,16 @@ def _normalize_transform(obj: dict[str, Any]) -> dict[str, Any]: if not isinstance(obj["output"], list): raise NdselError("invalid_json", f"output must be an array, got {obj['output']!r}") output = [_normalize_output_map(m, f"output[{i}]") for i, m in enumerate(obj["output"])] + for i, m in enumerate(output): + # An `input_dimension` names one of *this* transform's input + # dimensions, so the rank is what bounds it. Checked here rather than + # in `_normalize_output_map`, which sees one map and not the rank. + if "input_dimension" in m and m["input_dimension"] >= rank: + raise NdselError( + "rank_mismatch", + f"output[{i}].input_dimension is {m['input_dimension']}, " + f"outside the valid range [0, {rank}) for input_rank {rank}", + ) else: output = _identity_output(rank) @@ -635,6 +719,14 @@ def normalize_ndsel(obj: Any) -> dict[str, Any]: Accepts any of the five message kinds and returns the bare canonical `IndexTransform` body of spec section 4.3 — no `kind` field. Raises `NdselError` (carrying a reason code) for any invalid input. + + Examples + -------- + >>> body = normalize_ndsel({"kind": "box", "shape": [2, 3]}) + >>> (body["input_rank"], body["input_inclusive_min"], body["input_exclusive_max"]) + (2, [0, 0], [2, 3]) + >>> body["output"][0] + {'offset': 0, 'stride': 1, 'input_dimension': 0} """ message = _require_object(obj) kind = _message_kind(message) @@ -649,6 +741,14 @@ def parse_ndsel(obj: Any) -> dict[str, Any]: JSON types, upper-bound exclusivity, domain ordering, step signs) and raises `NdselError` otherwise, but does not desugar it. Useful for validating a message you intend to keep in its compact shorthand form. + + Examples + -------- + >>> message = {"kind": "point", "coords": [3, 4]} + >>> parse_ndsel(message) is message + True + >>> normalize_ndsel(message)["output"] + [{'offset': 3}, {'offset': 4}] """ message = _require_object(obj) _message_kind(message) diff --git a/packages/zarr-indexing/src/zarr_indexing/output_map.py b/packages/zarr-indexing/src/zarr_indexing/output_map.py index 581229bd22..3ee7250efa 100644 --- a/packages/zarr-indexing/src/zarr_indexing/output_map.py +++ b/packages/zarr-indexing/src/zarr_indexing/output_map.py @@ -1,21 +1,24 @@ -"""Output index maps — three representations of a set of integer coordinates. +"""Output index maps — three ordered mappings to integer coordinates. -An output index map describes, for one dimension of storage, which coordinates -an array access will touch. Conceptually it is a **set of integers**. Three -representations cover the cases that arise in practice: +An output index map describes how input cells address one dimension of +the output space. Its coordinates form an **ordered, duplicate-preserving sequence** +aligned with the input domain, never a mathematical set. Three representations +cover the cases that arise in practice: -- `ConstantMap(offset=5)` — a singleton set: `{5}` +- `ConstantMap(offset=5)` — every request cell maps to coordinate `5` - `DimensionMap(input_dimension=0, offset=3, stride=2)` over input `[0, 5)` - — an arithmetic progression: `{3, 5, 7, 9, 11}` -- `ArrayMap(index_array=[1, 5, 9])` — an explicit enumeration: `{1, 5, 9}` + — the ordered arithmetic progression `[3, 5, 7, 9, 11]` +- `ArrayMap(index_array=[5, 1, 1])` — the explicit sequence `[5, 1, 1]`, + preserving both order and the repeated coordinate -Every output map supports two set-theoretic operations (defined on -`IndexTransform`, which provides the input domain context these maps lack): +Every output map participates in two operations defined on `IndexTransform`, +which provides the input-domain context these maps lack: -- **intersect** — restrict to coordinates within a range (e.g., a chunk). - `{3, 5, 7, 9, 11} ∩ [4, 8) = {5, 7}` +- **intersect** — retain mapped cells whose coordinates lie within a range + (e.g., a chunk), without changing their order or multiplicity. + Restricting `[3, 5, 5, 9]` to `[4, 8)` produces `[5, 5]`. - **translate** — shift every coordinate by a constant (e.g., make chunk-local). - `{5, 7} - 4 = {1, 3}` + Translating `[5, 5, 7]` by `-4` produces `[1, 1, 3]`. These two operations are the foundation of chunk resolution: for each chunk, intersect the map with the chunk's range, then translate to chunk-local @@ -35,71 +38,366 @@ from __future__ import annotations from dataclasses import dataclass -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Any + +import numpy as np + +from zarr_indexing._affine import checked_affine if TYPE_CHECKING: - import numpy as np import numpy.typing as npt + from zarr_indexing.json import OutputIndexMapJSON + + +def _array_map_dependency_axes(index_array: np.ndarray[Any, Any]) -> tuple[int, ...]: + """Return the input axes on which a normalized index array varies. + + Normalized `ArrayMap` index arrays carry the full input rank of their + enclosing transform: an axis the array varies over has its full size, while + an axis the array is independent of is a singleton (size 1). The dependency + axes are therefore exactly the axes of size 2 or more. An orthogonal + (`oindex`) array depends on a single axis; a vectorized (`vindex`) array + depends on all of the (shared) broadcast axes. + + A size-**0** axis carries no dependency either: the array has no values to + vary, so an empty selection stays the flavor it was made as rather than + reading as correlated with every other axis. + """ + return tuple(axis for axis, size in enumerate(index_array.shape) if size > 1) + @dataclass(frozen=True, slots=True) class ConstantMap: - """A singleton set: one storage coordinate. + """A constant output-coordinate mapping. + + Every input cell maps to `offset`. Arises from integer indexing (e.g., + `arr[5]` fixes one dimension to coordinate 5). + + Examples + -------- + Every input cell maps to the same output coordinate — the NumPy analogy + is a broadcast (`np.broadcast_to(5, (3,))`), not an index: - Represents `{offset}`. Arises from integer indexing (e.g., `arr[5]` - fixes one dimension to coordinate 5). + >>> from zarr_indexing.domain import IndexDomain + >>> from zarr_indexing.transform import IndexTransform + >>> domain = IndexDomain.from_shape((3,)) + >>> t = IndexTransform(domain=domain, output=(ConstantMap(offset=5),)) + >>> t.apply((0,)), t.apply((1,)), t.apply((2,)) + ((5,), (5,), (5,)) """ offset: int = 0 + """The fixed output coordinate every input cell maps to.""" + + def to_json(self) -> OutputIndexMapJSON: + """Convert to the canonical wire form: the bare `constant` map. + + Examples + -------- + >>> ConstantMap(5).to_json() + {'offset': 5} + """ + return {"offset": self.offset} @dataclass(frozen=True, slots=True) class DimensionMap: - """An arithmetic progression of storage coordinates. + """An ordered affine mapping to output coordinates. + + Maps each input coordinate `i` to `offset + stride * i`, where the input + range comes from the enclosing `IndexTransform`'s domain. Arises from slice + indexing (e.g., `arr[2:10:3]` gives offset=2, stride=3). - Represents `{offset + stride * i : i in input_range}`, where the input - range comes from the enclosing `IndexTransform`'s domain. Arises from - slice indexing (e.g., `arr[2:10:3]` gives offset=2, stride=3). + Examples + -------- + The slice `arr[2:11:3]` reads coordinates `2, 5, 8` — the rule + `offset + stride * i` with `offset=2`, `stride=3`: + + >>> m = DimensionMap(input_dimension=0, offset=2, stride=3) + >>> [m.offset + m.stride * i for i in range(3)] + [2, 5, 8] + >>> np.arange(11)[2:11:3].tolist() + [2, 5, 8] """ input_dimension: int + """The input (domain) dimension whose coordinate this map reads.""" + offset: int = 0 + """The output coordinate that input coordinate `0` maps to.""" + stride: int = 1 + """The output-coordinate step per unit input step; negative walks backward, zero repeats `offset`.""" + + def to_json(self) -> OutputIndexMapJSON: + """Convert to the canonical wire form: the `single_input_dimension` map. + + Examples + -------- + >>> DimensionMap(input_dimension=1, offset=0, stride=2).to_json() + {'offset': 0, 'stride': 2, 'input_dimension': 1} + """ + return { + "offset": self.offset, + "stride": self.stride, + "input_dimension": self.input_dimension, + } @dataclass(frozen=True, slots=True) class ArrayMap: - """An explicit enumeration of storage coordinates. + """An explicit ordered, duplicate-preserving coordinate mapping. - Represents `{offset + stride * index_array[i] : i in input_range}`. - Arises from fancy indexing (e.g., `arr[[1, 5, 9]]` or boolean masks). + Maps each input position `i` to `offset + stride * index_array[i]`. + Index-array order and repeated entries are semantic and remain present in + the result. Arises from fancy indexing (e.g., `arr[[5, 1, 1]]` or boolean + masks). Freshly constructed maps are normalized to the **full input rank** of their enclosing transform: `index_array` has the enclosing domain's rank, sized fully on the axes it varies over and singleton (size 1) elsewhere. The - dependency axes are therefore derivable from the shape (see - `transform._array_map_dependency_axes`), which distinguishes the two flavours - of multi-array fancy indexing: + shape is the single source of truth for what the map depends on — its + **dependency axes** are exactly its non-singleton axes (see + `_array_map_dependency_axes`) — and it distinguishes the two + flavors of multi-array fancy indexing: - **orthogonal** (`oindex`): each array varies along a single, *distinct* axis (all others singleton); the result is their outer product. - **vectorized** (`vindex`): the arrays are correlated and share the same non-singleton (broadcast) axes; the result is a pointwise scatter. - `input_dimension` records the single axis an orthogonal array varies over - (`None` for vectorized), binding it the way `DimensionMap` is bound. It is - usually redundant with the shape-derived classifier, but stays authoritative - for the shapes the classifier cannot distinguish: a length-1 orthogonal - selection normalizes to an all-singleton array (no non-singleton axis), and - length-1 vectorized arrays are equally degenerate. `None` therefore marks a - map as correlated, and an integer pins the dependency axis of a degenerate - orthogonal map (see `transform._array_map_dependent_axis`). + A map holding exactly one coordinate carries no shape to read a dependency + from, and none is needed: it is the `ConstantMap` it equals, and the + selection layer builds that instead (see `array_map_or_constant`). A + hand-built all-singleton `ArrayMap` is still a valid value; resolution + classifies it with the correlated maps and reads it pointwise. + + Examples + -------- + The fancy selection `arr[[5, 1, 1]]` reads coordinate 5, then 1, then 1 + — order and the duplicate preserved, exactly as NumPy fancy indexing: + + >>> m = ArrayMap(index_array=np.array([5, 1, 1])) + >>> [m.offset + m.stride * c for c in m.index_array.tolist()] + [5, 1, 1] + >>> np.arange(10)[[5, 1, 1]].tolist() + [5, 1, 1] """ - index_array: npt.NDArray[np.intp] + index_array: npt.NDArray[np.integer[Any]] + """Explicit coordinates at the enclosing transform's full input rank; order and + duplicates are semantic. Its non-singleton axes are the map's dependency axes.""" + offset: int = 0 + """Constant term of the affine adjustment: the output coordinate is `offset + stride * index_array[i]`.""" + stride: int = 1 - input_dimension: int | None = None + """Multiplier applied to each `index_array` value before `offset` is added.""" + + def __post_init__(self) -> None: + """Own the index array and expose it read-only. + + A map is frozen, but the array inside it was not: reaching through a + view's transform to `index_array[0] = 9` silently changed what the view + returned, in a package whose whole contract is that a view is a + description of a read and resolving it twice answers alike. Owning the + array also prevents the caller from changing the contents behind the + read-only view, which would invalidate this value object's hash. + """ + # Immutable bytes are the ultimate owner so callers cannot re-enable + # the WRITEABLE flag, as they can on a read-only array that owns its + # allocation. `asarray` also accepts the NumPy scalars that reach here + # after indexing an array down to one element. + array = np.asarray(self.index_array) + if not np.issubdtype(array.dtype, np.integer): + raise TypeError(f"index_array must have an integer dtype, got {array.dtype}") + normalized = checked_affine(0, 1, array) + frozen = np.frombuffer(normalized.tobytes(), dtype=np.intp).reshape(normalized.shape) + object.__setattr__(self, "index_array", frozen) + + def __reduce__(self) -> tuple[object, tuple[object, int, int]]: + """Reconstruct through `__init__`, preserving the ownership invariant.""" + return ( + type(self), + (self.index_array, self.offset, self.stride), + ) + + def __eq__(self, other: object) -> bool: + """Value equality, comparing index arrays element-wise. + + The generated `__eq__` compares them with `==`, whose result for two + arrays is an array — so asking whether two maps are equal raised + `ValueError: the truth value of an array ... is ambiguous`. `frozen=True` + reads as a promise that a value can be compared and hashed, and this is + what makes good on it. + """ + if not isinstance(other, ArrayMap): + return NotImplemented + return ( + self.offset == other.offset + and self.stride == other.stride + and self.index_array.shape == other.index_array.shape + and bool(np.array_equal(self.index_array, other.index_array)) + ) + + def __hash__(self) -> int: + """Hashed by the array's contents, so equal maps hash alike. + + The generated `__hash__` hashed the ndarray itself, which is unhashable; + a map could therefore not go in a set, or key a cache. + """ + return hash( + ( + self.offset, + self.stride, + self.index_array.shape, + self.index_array.tobytes(), + ) + ) + + @property + def dependency_axes(self) -> tuple[int, ...]: + """Every input axis this map varies over: its non-singleton axes. + + One axis means orthogonal, several mean correlated, and none means + the map is degenerate — the shape is the single source of truth for + all three. + + Examples + -------- + >>> ArrayMap(index_array=np.array([[4, 0, 2]])).dependency_axes + (1,) + >>> ArrayMap(index_array=np.array([[1, 2], [3, 4]])).dependency_axes + (0, 1) + """ + return _array_map_dependency_axes(self.index_array) + + @property + def dependent_axis(self) -> int | None: + """Return the single input axis an orthogonal `ArrayMap` varies over. + + This is the array's one non-singleton axis, read from the shape — the + single source of truth for what a map depends on. The selection layer + collapses a single-coordinate map to a `ConstantMap` + (`array_map_or_constant`), so a non-empty map built by this package always + has at least one dependency axis. + + Returns + ------- + int or None + The axis the map varies over, or `None` when it varies over no input + axis at all — an empty map, or a hand-built all-singleton one. `None` + is a valid result, not an error; such maps resolve through the + pointwise (general) path. + + Raises + ------ + ValueError + If the map varies over more than one axis, which makes it correlated + rather than orthogonal. + + Examples + -------- + An `oindex` selection on axis 1 of a rank-2 transform stores its + coordinates full-sized on axis 1 and singleton on axis 0, so the + dependency axis is read straight off the shape: + + >>> m = ArrayMap(index_array=np.array([[4, 0, 2]])) + >>> m.index_array.shape + (1, 3) + >>> m.dependent_axis + 1 + """ + dep = self.dependency_axes + if len(dep) == 1: + return dep[0] + if len(dep) == 0: + return None + raise ValueError( + f"orthogonal ArrayMap must vary over exactly one axis; got dependency axes {dep}" + ) + + def to_json(self) -> OutputIndexMapJSON: + """Convert to the canonical wire form, collapsing a degenerate map. + + A map holding exactly one coordinate, or none at all, is emitted as a + `constant` map — see the module note on the wire format in + [`zarr_indexing.json`][zarr_indexing.json]. Both are degenerate: the + first selects one coordinate whatever the input, and the second names + no cell and can only be empty because an input dimension is, so the + emptiness travels in the domain instead. + + Examples + -------- + >>> ArrayMap(np.array([[4], [1], [1]])).to_json()["index_array"] + [[4], [1], [1]] + >>> ArrayMap(np.array([7])).to_json() # degenerate: one coordinate + {'offset': 7} + """ + if self.index_array.size == 1: + value = int(self.index_array.reshape(-1)[0]) + return {"offset": self.offset + self.stride * value} + if self.index_array.size == 0: + return {"offset": 0} + return { + "offset": self.offset, + "stride": self.stride, + "index_array": self.index_array.tolist(), + "index_array_bounds": ["-inf", "+inf"], + } + + +def output_index_map_from_json(data: OutputIndexMapJSON) -> OutputIndexMap: + """Construct the output map a canonical wire form names. + + The wire form is a tagged union — `index_array`, then `input_dimension`, + else constant — so loading it dispatches to the right kind here rather + than on any one of them. + + Examples + -------- + >>> output_index_map_from_json({"offset": 5}) + ConstantMap(offset=5) + >>> output_index_map_from_json({"offset": 0, "stride": 2, "input_dimension": 1}) + DimensionMap(input_dimension=1, offset=0, stride=2) + """ + from zarr_indexing._wire import lower_index_array + + if "index_array" in data: + return ArrayMap( + index_array=lower_index_array(data["index_array"], "index_array"), + offset=data.get("offset", 0), + stride=data.get("stride", 1), + ) + if "input_dimension" in data: + return DimensionMap( + input_dimension=data["input_dimension"], + offset=data.get("offset", 0), + stride=data.get("stride", 1), + ) + return ConstantMap(offset=data.get("offset", 0)) + + +def array_map_or_constant( + index_array: npt.NDArray[np.integer[Any]], + offset: int = 0, + stride: int = 1, +) -> ArrayMap | ConstantMap: + """An `ArrayMap`, collapsed to the `ConstantMap` it equals when it can be. + + An index array holding exactly one coordinate maps every input cell to the + same place; representing it as a lookup table would leave a map whose shape + names no dependency axis, the one form the shape-derived classifier cannot + read. The selection and composition layers build their array maps through + this helper so that a non-empty `ArrayMap` always varies over at least one + axis. An empty array stays an `ArrayMap`: it maps no cell at all, and the + emptiness lives in the domain that accompanies it. + """ + arr = np.asarray(index_array) + if arr.size == 1: + return ConstantMap(offset=checked_affine(offset, stride, int(arr.reshape(-1)[0]))) + return ArrayMap(index_array=arr, offset=offset, stride=stride) OutputIndexMap = ConstantMap | DimensionMap | ArrayMap diff --git a/packages/zarr-indexing/src/zarr_indexing/reader.py b/packages/zarr-indexing/src/zarr_indexing/reader.py new file mode 100644 index 0000000000..8d47d51d21 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/reader.py @@ -0,0 +1,585 @@ +"""Backend reader protocol and built-in system-memory implementations.""" + +from __future__ import annotations + +import math +from dataclasses import dataclass +from typing import TYPE_CHECKING, Any, Final, Protocol + +if TYPE_CHECKING: + from collections.abc import Callable + +import numpy as np + +from zarr_indexing._affine import checked_affine +from zarr_indexing.chunk_resolution import ChunkProjection # noqa: TC001 (runtime annotation) +from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap +from zarr_indexing.transform import ( + IndexTransform, +) + +__all__ = [ + "BasicReader", + "NumPyReader", + "ReadContext", + "Reader", + "UnitStepReader", + "basic_reader", + "numpy_reader", + "unit_step_reader", +] + + +@dataclass(frozen=True, slots=True) +class ReadContext: + """A source-global transform and optional projection for a partitioned read. + + Examples + -------- + >>> transform = IndexTransform.from_shape((6,))[1:5:2] + >>> context = ReadContext(transform) + >>> context.transform.domain.shape + (2,) + >>> context.projection is None + True + """ + + transform: IndexTransform + """Maps zero-origin output-buffer coordinates to global coordinates in the source.""" + + projection: ChunkProjection | None = None + """The partition plan when this read is one part of a partitioned view, else `None`.""" + + +class Reader(Protocol): + """Backend adapter that fills supplied system-memory result buffers. + + A reader may be shared by every view and part derived from one + [`LazyArray`][zarr_indexing.lazy_array.LazyArray]. Part reads may run + concurrently, so a stateful implementation must synchronize its own + mutable state. `LazyArray` deliberately adds no serialization. + + Examples + -------- + The protocol is not `runtime_checkable`; an object satisfies it by + exposing a conforming `read_into`, as `basic_reader` does: + + >>> transform = IndexTransform.from_shape((6,))[1:5:2] + >>> source = np.arange(6) + >>> out = np.empty(transform.domain.shape, dtype=source.dtype) + >>> basic_reader.read_into(source, ReadContext(transform), out) + >>> out.tolist() + [1, 3] + """ + + def read_into( + self, + source: Any, + context: ReadContext, + out: np.ndarray[Any, Any], + /, + ) -> None: + """Fill `out` with the exact source values selected by `context`. + + `context.transform` maps zero-origin coordinates in the output buffer + to global coordinates in `source`, and its domain shape equals + `out.shape`. `context.projection`, when present, is the corresponding + partition plan: its `chunk_transform` is chunk-local, its + `cell_transform` describes result placement, and its `chunk_domain` + describes the grid cell. Fill every cell in place, preserving the + transform's exact values, order, and dtype, then return `None`. Do not + replace or retain `out`; it may be a strided writable view rather than + an owning array. + + Backend exceptions propagate unchanged. Because callers may resolve + parts concurrently through the same reader object, stateful readers + are responsible for synchronizing their own state. + """ + ... + + +class BasicReader: + """Reader for system-memory sources exposing basic integer/slice indexing. + + Each transform is decomposed into the smallest enclosing positive-slice + slab and a residual transform. The slab is read once with basic indexing, + so fancy or negative-step selections may over-read, and the residual is + then lowered through NumPy system-memory operations into the supplied + buffer. + + Slice results must permit conversion to NumPy system memory. Device arrays + that reject implicit conversion require a custom reader responsible for + transferring values into the supplied system-memory output buffer. + + Examples + -------- + >>> transform = IndexTransform.from_shape((6,))[1:5:2] + >>> source = np.arange(6) + >>> out = np.empty(transform.domain.shape, dtype=source.dtype) + >>> BasicReader().read_into(source, ReadContext(transform), out) + >>> out.tolist() == source[1:5:2].tolist() + True + """ + + __slots__ = () + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + """Read one transform through a positive-slice slab and residual lowering.""" + transform = context.transform + key, residual = _decompose_basic(transform) + block = np.asanyarray(source[key]) + out[...] = _lower(block, residual) + + +class NumPyReader: + """Reader optimized for NumPy system-memory arrays. + + This is the reader selected by + [`LazyArray.from_numpy`][zarr_indexing.lazy_array.LazyArray.from_numpy]. It + applies the complete transform with NumPy operations and is applicable to + `numpy.ndarray` sources, including `numpy.ma.MaskedArray`. + + Examples + -------- + >>> transform = IndexTransform.from_shape((3, 4))[::2, 1:3] + >>> source = np.arange(12).reshape(3, 4) + >>> out = np.empty(transform.domain.shape, dtype=source.dtype) + >>> NumPyReader().read_into(source, ReadContext(transform), out) + >>> out.tolist() + [[1, 2], [9, 10]] + """ + + __slots__ = () + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + """Read one transform through a narrowed slab into `out`.""" + transform = context.transform + key, residual = _decompose_basic(transform) + block = np.asanyarray(source[key]) + out[...] = _lower(block, residual) + + +class UnitStepReader: + """Reader for sources whose basic indexing accepts only step-1 slices. + + Each transform is decomposed into the smallest enclosing ascending + unit-step slab and a residual transform, so the source only ever receives + `slice(start, stop, 1)` on every axis — the one form an API without + general strided reads (an FFI binding, an HTTP range endpoint) supports. + `BasicReader` instead pushes strided and reversed slices down, which + reads less but asks more of the source. + + The residual lowering applies strides, reversals, and gathers to the + in-memory block, so a strided selection over-reads its cover by the + stride factor. Partitioning the wrapping + [`LazyArray`][zarr_indexing.lazy_array.LazyArray] (`with_parts`) bounds + each cover by a part. + + Slice results must permit conversion to NumPy system memory, exactly as + for `BasicReader`. + + Examples + -------- + The source below is only ever asked for step-1 slices — here the cover + `slice(1, 4, 1)` — and the stride is replayed against the block: + + >>> transform = IndexTransform.from_shape((6,))[1:5:2] + >>> source = np.arange(6) + >>> out = np.empty(transform.domain.shape, dtype=source.dtype) + >>> UnitStepReader().read_into(source, ReadContext(transform), out) + >>> out.tolist() + [1, 3] + """ + + __slots__ = () + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + """Read one transform through an ascending unit-step slab into `out`.""" + transform = context.transform + key, residual = _decompose_unit_step(transform) + block = np.asanyarray(source[key]) + out[...] = _lower(block, residual) + + +basic_reader: Final = BasicReader() +numpy_reader: Final = NumPyReader() +unit_step_reader: Final = UnitStepReader() + + +def _take(array: Any, indices: np.ndarray[Any, np.dtype[np.intp]], axis: int) -> Any: + return np.take(array, indices, axis=axis) + + +def _reshape(array: Any, shape: tuple[int, ...]) -> Any: + return np.reshape(array, shape) + + +def _transpose(array: Any, permutation: tuple[int, ...]) -> Any: + return np.transpose(array, permutation) + + +def _expand_dims(array: Any, axis: int) -> Any: + return np.expand_dims(array, axis) + + +def _dimension_map_coords( + m: DimensionMap, transform: IndexTransform +) -> np.ndarray[Any, np.dtype[np.intp]]: + """The storage coordinates a DimensionMap enumerates, in view order.""" + d = m.input_dimension + lo = transform.domain.inclusive_min[d] + hi = transform.domain.exclusive_max[d] + extent = hi - lo + if extent == 0: + return np.empty((0,), dtype=np.intp) + first = checked_affine(m.offset, m.stride, lo) + return checked_affine(first, m.stride, np.arange(extent, dtype=np.intp)) + + +def _array_map_coords(m: ArrayMap) -> np.ndarray[Any, np.dtype[np.intp]]: + """The storage coordinates an ArrayMap enumerates, flattened.""" + return checked_affine(m.offset, m.stride, m.index_array).reshape(-1) + + +def _correlated_map_coords( + m: ArrayMap, broadcast_axes: list[int], broadcast_shape: tuple[int, ...], input_rank: int +) -> np.ndarray[Any, np.dtype[np.intp]]: + """One storage coordinate per point of the correlated block, flattened. + + A correlated `ArrayMap`'s index array carries the transform's full input + rank, with a singleton on every axis it does not vary over — including + broadcast axes it shares with the *other* correlated maps but is itself + constant along. Flattening it directly would then yield fewer coordinates + than there are points, so it is reduced to the broadcast block and + broadcast up to it explicitly. + """ + coords = checked_affine(m.offset, m.stride, m.index_array) + if math.prod(broadcast_shape) == 0: + # A zero-extent broadcast axis makes the correlated block empty — for + # example an ArrayMap composed over an empty domain, which the package + # promises resolves like any other. The per-axis reshape below cannot + # express that block (a 0-size array does not reshape to the non-zero + # singleton axes), and there is no coordinate to produce anyway. + return np.empty(0, dtype=np.intp) + if coords.ndim == input_rank: + # Drop the axes bound by a slice, which the map is singleton along. + # Removing size-1 axes by reshape preserves element order wherever they + # sit, so no transpose is needed. + coords = coords.reshape(tuple(coords.shape[axis] for axis in broadcast_axes)) + return np.ascontiguousarray(np.broadcast_to(coords, broadcast_shape)).reshape(-1) + + +def _restore_domain_axis_order( + result: Any, axis_input_dims: list[int], domain_shape: tuple[int, ...] +) -> Any: + """Permute `result`'s axes into input-domain order, restoring dropped axes. + + `axis_input_dims[k]` is the input (domain) dimension that axis `k` of + `result` corresponds to. Axes are permuted so that they appear in increasing + domain-dimension order, and any domain dimension no output map depends on is + reinserted at **its own extent**. + + An unreferenced dimension is not always a singleton. A `vindex` coordinate + array with a broadcast axis it does not vary over leaves that axis in the + domain; a later basic index that consumes the axis the array *does* vary + over collapses the map to a `ConstantMap` and leaves the broadcast axis + behind, with whatever extent the basic index gave it — including 0. Every + position along such an axis holds the same values, so it is restored by + repeating the block, and an extent of 0 restores an empty result rather than + fabricating a row. + + This is also where NumPy's advanced-index placement rules are absorbed: + whatever order the gather produced, the lowered result always comes back in + the view's own axis order. + """ + if len(set(axis_input_dims)) != len(axis_input_dims): + raise NotImplementedError( + "resolving a transform whose output maps share an input dimension " + "(a diagonal view) is not supported" + ) + order = sorted(range(len(axis_input_dims)), key=lambda k: axis_input_dims[k]) + if order != list(range(len(order))): + result = _transpose(result, tuple(order)) + covered = set(axis_input_dims) + for dim, extent in enumerate(domain_shape): + if dim in covered: + continue + result = _expand_dims(result, dim) + if extent != 1: + result = _take(result, np.zeros(extent, dtype=np.intp), axis=dim) + return result + + +def _lower(array: Any, transform: IndexTransform) -> Any: + """Lower a transform to one pass of array operations over `array`. + + Every read, partitioned or not, goes through this function. The result is + always in the transform's own domain axis order and of exactly its domain + shape. + """ + if math.prod(transform.domain.shape) == 0: + # An empty domain selects nothing, and its maps may legitimately be + # empty along the vanished axes (an ArrayMap composed over an empty + # domain, which the package promises resolves like any other). The + # resolvers below cannot evaluate such maps — and have no reason to. + return np.empty(transform.domain.shape, dtype=np.asanyarray(array).dtype) + if transform.index_array_structure == "general": + result = _lower_general(array, transform) + else: + result = _lower_orthogonal(array, transform) + if isinstance(result, np.generic): + # Basic indexing every axis of a NumPy array yields a scalar; `result()` + # documents a zero-dimensional array. + return np.asarray(result) + return result + + +def _lower_orthogonal(array: Any, transform: IndexTransform) -> Any: + """Basic slicing plus one `take` per fancy-indexed axis (an outer product). + + Orthogonal `ArrayMap`s vary over distinct input axes, so gathering them one + axis at a time is exact — a `take` along one storage axis leaves every other + axis's coordinates untouched. + """ + outputs = transform.output + gathered: dict[int, np.ndarray[Any, np.dtype[np.intp]]] = {} + for out_dim, m in enumerate(outputs): + if isinstance(m, ArrayMap): + gathered[out_dim] = _array_map_coords(m) + elif isinstance(m, DimensionMap) and m.stride <= 0: + # Reversing and repeating maps have no positive-step slice; gather them. + gathered[out_dim] = _dimension_map_coords(m, transform) + + result = array + for out_dim, coords in gathered.items(): + result = _take(result, coords, axis=out_dim) + + selection: list[Any] = [] + axis_input_dims: list[int] = [] + for out_dim, m in enumerate(outputs): + if isinstance(m, ConstantMap): + selection.append(m.offset) + continue + if out_dim in gathered: + selection.append(slice(None)) + else: + assert isinstance(m, DimensionMap) + d = m.input_dimension + lo = transform.domain.inclusive_min[d] + hi = transform.domain.exclusive_max[d] + selection.append(slice(m.offset + m.stride * lo, m.offset + m.stride * hi, m.stride)) + if isinstance(m, ArrayMap): + axis = m.dependent_axis + if axis is None: + raise NotImplementedError( + "resolving an orthogonal ArrayMap that varies over no input " + "dimension is not supported; such a map should have been " + "collapsed to a ConstantMap" + ) + axis_input_dims.append(axis) + else: + axis_input_dims.append(m.input_dimension) + result = result[tuple(selection)] + return _restore_domain_axis_order(result, axis_input_dims, transform.domain.shape) + + +def _lower_general(array: Any, transform: IndexTransform) -> Any: + """Flatten the index-array axes, gather the points once, reshape back. + + The general path for every index-array structure the orthogonal resolver + cannot take: correlated (`vindex`) maps, maps sharing an input axis (a + diagonal gather), and mixtures of correlated and orthogonal maps. All + index arrays are treated as lookup tables over the joint block of + non-slice axes: the corresponding storage axes are moved to the front and + flattened, the per-point coordinates are converted to offsets into that + flat axis with row-major strides, and a single `take` collects them. + """ + outputs = transform.output + correlated_dims = [d for d, m in enumerate(outputs) if isinstance(m, ArrayMap)] + + slice_input_dims = {m.input_dimension for m in outputs if isinstance(m, DimensionMap)} + broadcast_axes = [d for d in range(transform.input_rank) if d not in slice_input_dims] + broadcast_shape = tuple(transform.domain.shape[d] for d in broadcast_axes) + + for d in correlated_dims: + arr_map = outputs[d] + assert isinstance(arr_map, ArrayMap) + # The axes the array varies over (its non-singleton axes; see + # transform._array_map_dependency_axes) must all live in the block. + dependency = (axis for axis, size in enumerate(arr_map.index_array.shape) if size > 1) + if any(a not in broadcast_axes for a in dependency): + # Reachable only by hand-building a transform: no selection binds + # the same input axis to both a slice map and an index array. + raise NotImplementedError( + "resolving a transform whose index array varies over an input " + "dimension also bound by a slice map is not supported" + ) + + # Gather any reversing or repeating slice axis first, then take the basic-slice + # cut. The correlated axes keep their full extent: their coordinates are absolute. + gathered: dict[int, np.ndarray[Any, np.dtype[np.intp]]] = { + d: _dimension_map_coords(m, transform) + for d, m in enumerate(outputs) + if isinstance(m, DimensionMap) and m.stride <= 0 + } + result = array + for out_dim, coords in gathered.items(): + result = _take(result, coords, axis=out_dim) + + selection: list[Any] = [] + residual_axis_dims: list[int] = [] + correlated_positions: list[int] = [] + residual_positions: list[int] = [] + axis = 0 + for out_dim, m in enumerate(outputs): + if isinstance(m, ConstantMap): + selection.append(m.offset) + continue + if out_dim in correlated_dims: + selection.append(slice(None)) + correlated_positions.append(axis) + elif out_dim in gathered: + selection.append(slice(None)) + residual_positions.append(axis) + assert isinstance(m, DimensionMap) + residual_axis_dims.append(m.input_dimension) + else: + assert isinstance(m, DimensionMap) + d = m.input_dimension + lo = transform.domain.inclusive_min[d] + hi = transform.domain.exclusive_max[d] + selection.append(slice(m.offset + m.stride * lo, m.offset + m.stride * hi, m.stride)) + residual_positions.append(axis) + residual_axis_dims.append(d) + axis += 1 + result = result[tuple(selection)] + + # Correlated axes to the front, in output order, so the flattening strides + # below match the order the coordinates are combined in. + perm = tuple(correlated_positions) + tuple(residual_positions) + if perm != tuple(range(len(perm))): + result = _transpose(result, perm) + + n_corr = len(correlated_dims) + corr_sizes = tuple(int(s) for s in result.shape[:n_corr]) + tail_shape = tuple(int(s) for s in result.shape[n_corr:]) + result = _reshape(result, (math.prod(corr_sizes), *tail_shape)) + + flat_index = np.zeros(math.prod(broadcast_shape), dtype=np.intp) + stride = 1 + for position in range(n_corr - 1, -1, -1): + m = outputs[correlated_dims[position]] + assert isinstance(m, ArrayMap) + flat_index = flat_index + ( + _correlated_map_coords(m, broadcast_axes, broadcast_shape, transform.input_rank) + * stride + ) + stride *= corr_sizes[position] + + result = _take(result, flat_index, axis=0) + result = _reshape(result, broadcast_shape + tail_shape) + return _restore_domain_axis_order( + result, list(broadcast_axes) + residual_axis_dims, transform.domain.shape + ) + + +def _push_slice_for_dimension_map( + m: DimensionMap, transform: IndexTransform +) -> tuple[slice, DimensionMap]: + """The positive-step slice covering a `DimensionMap`, and its block-local map. + + A negative step is read forwards and reversed by the residual: a source is + only ever asked for a slice that walks upwards, which is the one form every + array-like agrees on. + """ + d = m.input_dimension + lo = transform.domain.inclusive_min[d] + hi = max(transform.domain.exclusive_max[d], lo) + if hi == lo: + return slice(0, 0, 1), DimensionMap(input_dimension=d, offset=-lo, stride=1) + first = checked_affine(m.offset, m.stride, lo) + last = checked_affine(m.offset, m.stride, hi - 1) + if m.stride > 0: + return ( + slice(first, last + 1, m.stride), + DimensionMap(input_dimension=d, offset=-lo, stride=1), + ) + if m.stride == 0: + return ( + slice(first, first + 1, 1), + DimensionMap(input_dimension=d, offset=0, stride=0), + ) + # Descending: the block holds the same coordinates in ascending order, so + # the residual walks it backwards from the last block position. + return ( + slice(last, first + 1, -m.stride), + DimensionMap(input_dimension=d, offset=hi - 1, stride=-1), + ) + + +def _push_unit_slice_for_dimension_map( + m: DimensionMap, transform: IndexTransform +) -> tuple[slice, DimensionMap]: + """The unit-step slice covering a `DimensionMap`, and its block-local map. + + Strides and reversals stay in the residual: the source is only ever asked + for a contiguous ascending slice, and the original stride is replayed + against the in-memory block. The cover therefore over-reads a strided + selection by its stride factor, which is the price of a source that + accepts nothing but `slice(start, stop, 1)`. + """ + d = m.input_dimension + lo = transform.domain.inclusive_min[d] + hi = max(transform.domain.exclusive_max[d], lo) + if hi == lo: + return slice(0, 0, 1), DimensionMap(input_dimension=d, offset=-lo, stride=1) + first = checked_affine(m.offset, m.stride, lo) + if m.stride == 0: + return ( + slice(first, first + 1, 1), + DimensionMap(input_dimension=d, offset=0, stride=0), + ) + last = checked_affine(m.offset, m.stride, hi - 1) + origin = min(first, last) + return ( + slice(origin, max(first, last) + 1, 1), + DimensionMap(input_dimension=d, offset=m.offset - origin, stride=m.stride), + ) + + +def _decompose_basic(transform: IndexTransform) -> tuple[tuple[slice, ...], IndexTransform]: + return _decompose(transform, _push_slice_for_dimension_map) + + +def _decompose_unit_step(transform: IndexTransform) -> tuple[tuple[slice, ...], IndexTransform]: + return _decompose(transform, _push_unit_slice_for_dimension_map) + + +def _decompose( + transform: IndexTransform, + push_dimension_map: Callable[[DimensionMap, IndexTransform], tuple[slice, DimensionMap]], +) -> tuple[tuple[slice, ...], IndexTransform]: + key: list[slice] = [] + residual: list[OutputIndexMap] = [] + for output_map in transform.output: + if isinstance(output_map, ConstantMap): + coordinate = checked_affine(output_map.offset, 0, 0) + key.append(slice(coordinate, coordinate + 1, 1)) + residual.append(ConstantMap(offset=0)) + elif isinstance(output_map, DimensionMap): + pushed, local = push_dimension_map(output_map, transform) + key.append(pushed) + residual.append(local) + else: + coordinates = checked_affine( + output_map.offset, output_map.stride, output_map.index_array + ) + if coordinates.size == 0: + key.append(slice(0, 0, 1)) + local_index = coordinates + else: + origin = int(coordinates.min()) + key.append(slice(origin, int(coordinates.max()) + 1, 1)) + local_index = checked_affine(-origin, 1, coordinates) + residual.append(ArrayMap(index_array=local_index)) + return tuple(key), IndexTransform(domain=transform.domain, output=tuple(residual)) diff --git a/packages/zarr-indexing/src/zarr_indexing/testing/__init__.py b/packages/zarr-indexing/src/zarr_indexing/testing/__init__.py new file mode 100644 index 0000000000..e98d051900 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/testing/__init__.py @@ -0,0 +1,57 @@ +"""Test support for projects whose arrays are read through `LazyArray`. + +A Hypothesis state machine that composes indexing steps onto a `LazyArray` +wrapping your array and checks every step against NumPy +([`stateful`][zarr_indexing.testing.stateful]), and the selection strategies it +draws from, exported on their own for a project that has its own harness +([`strategies`][zarr_indexing.testing.strategies]). + +```python +from zarr_indexing.testing import ChainedIndexingStateMachine, state_machine_test + +class MyArrayIndexing(ChainedIndexingStateMachine): + def make_source(self, data): + array = my_format.create(shape=data.shape, dtype=data.dtype) + array[:] = data + return array + +TestMyArrayIndexing = state_machine_test(MyArrayIndexing) +``` + +This subpackage needs `hypothesis`, which the rest of `zarr_indexing` does not: +install it with the `testing` extra (`pip install zarr-indexing[testing]`). +""" + +from zarr_indexing.testing.stateful import ( + DEFAULT_DATA, + DEFAULT_PARTITIONINGS, + DEFAULT_SETTINGS, + ChainedIndexingStateMachine, + apply_selection, + outer_selection, + repartition, + state_machine_test, +) +from zarr_indexing.testing.strategies import ( + basic_selections, + masks, + orthogonal_selections, + slice_selections, + vectorized_selections, +) + +__all__ = [ + "DEFAULT_DATA", + "DEFAULT_PARTITIONINGS", + "DEFAULT_SETTINGS", + "ChainedIndexingStateMachine", + "apply_selection", + "basic_selections", + "masks", + "orthogonal_selections", + "outer_selection", + "repartition", + "slice_selections", + "state_machine_test", + "vectorized_selections", +] diff --git a/packages/zarr-indexing/src/zarr_indexing/testing/stateful.py b/packages/zarr-indexing/src/zarr_indexing/testing/stateful.py new file mode 100644 index 0000000000..4458d7922a --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/testing/stateful.py @@ -0,0 +1,380 @@ +"""A stateful property test for indexing an array through `LazyArray`. + +`ChainedIndexingStateMachine` composes indexing steps onto a `LazyArray` +wrapping *your* array — `lazy[...]`, `lazy.oindex[...]`, `lazy.vindex[...]`, +each step applied to the view the last one produced — while applying the same +steps to a NumPy array holding the same values. After every step the view must +still agree with that model three ways: its shape, its `result()`, and the +assembly of its `parts()`. + +Point it at an array by subclassing and overriding `make_source`: + +```python +from zarr_indexing.testing import ChainedIndexingStateMachine, state_machine_test + +class MyArrayIndexing(ChainedIndexingStateMachine): + def make_source(self, data): + array = my_format.create(shape=data.shape, dtype=data.dtype) + array[:] = data + return array + +TestMyArrayIndexing = state_machine_test(MyArrayIndexing) +``` + +`data`, `partitionings`, and `readers` are class attributes; override any of +them to widen or narrow what is drawn. The base class needs no `make_source` at +all — left alone it wraps the NumPy array itself, which is a useful smoke test +of this package but says nothing about yours. + +What it is checking +------------------- +The parts invariant is the one with teeth. +[`Partition`][zarr_indexing.lazy_array.Partition] documents +`out[part.out_selection] = part.view.result()` as the assembly procedure, so +this checks that literally: a part's values must arrive at exactly the shape its +`out_selection` addresses — not merely a shape that broadcasts into it — land +there, and cover the view once. Checking through `result()` alone would prove +only that `result()` is self-consistent. + +The `choose_reader` rule draws a reader and applies it to the view, so the +execution strategy becomes part of the chain. Every reader listed by a subclass +must preserve the NumPy model for its source. The universal `basic_reader` is +always exercised, even when a subclass lists only specialized readers; with no +declared readers it is the sole strategy drawn. + +Requires the `testing` extra (`pip install zarr-indexing[testing]`). +""" + +from __future__ import annotations + +import math +from collections.abc import Sequence +from typing import TYPE_CHECKING, Any, ClassVar + +import numpy as np +from hypothesis import HealthCheck, settings +from hypothesis import strategies as st +from hypothesis.stateful import RuleBasedStateMachine, initialize, invariant, precondition, rule + +from zarr_indexing.lazy_array import LazyArray +from zarr_indexing.reader import Reader, basic_reader +from zarr_indexing.testing.strategies import ( + basic_selections, + orthogonal_selections, + slice_selections, + vectorized_selections, +) + +if TYPE_CHECKING: + from zarr_indexing.boundary import SelectionMode + +__all__ = [ + "DEFAULT_DATA", + "DEFAULT_PARTITIONINGS", + "DEFAULT_SETTINGS", + "ChainedIndexingStateMachine", + "apply_selection", + "outer_selection", + "repartition", + "state_machine_test", +] + +DEFAULT_DATA = np.arange(7 * 5 * 4, dtype=np.int64).reshape(7, 5, 4) +"""The values the source holds by default: distinct, so a misplaced cell shows.""" + +DEFAULT_PARTITIONINGS: tuple[Any, ...] = ( + None, + (2, 2, 2), + (7, 5, 4), + (3, 2, 3), + ((3, 3, 1), (2, 2, 1), (3, 1)), + (4, 3, 3), +) +"""Partitionings to read under: a single whole-array part, uniform boxes of +several shapes (some of which do not divide the extent), and explicit per-axis +sizes. Boxes that straddle whatever the source declares are deliberate — they +cost extra I/O but must not change an answer.""" + +DEFAULT_SETTINGS = settings( + max_examples=250, + stateful_step_count=10, + deadline=None, + suppress_health_check=[ + HealthCheck.data_too_large, + HealthCheck.filter_too_much, + HealthCheck.too_slow, + ], +) +"""Enough examples to find a defect reachable only through a narrow chain, at a +few seconds per run when there is nothing to find. Every step is followed by +checks that each materialize the whole view, so the budget buys examples rather +than long chains — a chain runs out of axes to index within a few steps anyway. + +`filter_too_much` is suppressed because a chain that reaches a rank-0 view +leaves only `repartition` enabled, so a run that opens there is discarded.""" + + +# --------------------------------------------------------------------------- # +# The NumPy model +# --------------------------------------------------------------------------- # + + +def outer_selection(array: Any, selection: Sequence[Any]) -> Any: + """Apply an orthogonal selection to a NumPy array: the outer product of its axes. + + NumPy has no operator for this, so the model is built from `numpy.ix_`. + Scalar integers are basic indices — NumPy applies them first and drops the + axis — so they are peeled off before the outer product is formed. + """ + + def is_scalar(sel: Any) -> bool: + return isinstance(sel, (int, np.integer)) and not isinstance(sel, bool) + + scalars = tuple(sel if is_scalar(sel) else slice(None) for sel in selection) + reduced = array[scalars] + axes = [ + np.arange(size)[sel] + for size, sel in zip(reduced.shape, [s for s in selection if not is_scalar(s)], strict=True) + ] + if len(axes) == 0: + return reduced + return reduced[np.ix_(*axes)] + + +def apply_selection(array: Any, selection: tuple[Any, ...], mode: SelectionMode) -> Any: + """Apply a selection to a NumPy array in the given mode — the model a view is checked against. + + NumPy's own semantics *are* basic and vectorized indexing, so only the + orthogonal mode needs building (see `outer_selection`). + """ + if mode == "orthogonal": + return outer_selection(array, selection) + return array[selection] + + +def state_machine_test( + machine: type[RuleBasedStateMachine], *, config: settings = DEFAULT_SETTINGS +) -> Any: + """The pytest-collectable `TestCase` for a machine, with settings applied. + + Hypothesis builds a fresh `TestCase` per state-machine class, so settings + set on a base class do not reach a subclass's; this applies them where they + land. Assign the result to a module-level name beginning with `Test`. + """ + case = machine.TestCase + case.settings = config + return case + + +def repartition(view: LazyArray, parts: Any) -> LazyArray: + """Apply one of `partitionings` to a view. + + The three partitioning spellings are three named methods, so a list holding + a mix of them needs a dispatch somewhere. Choosing among them is what a test + harness drawing from that list is doing, so it lives here rather than being + pushed back into the public API as a type-inspecting parameter. + """ + if parts is None: + return view.unpartitioned() + if any(isinstance(entry, Sequence) for entry in parts): + return view.with_parts_per_axis(parts) + return view.with_parts(parts) + + +# --------------------------------------------------------------------------- # +# The machine +# --------------------------------------------------------------------------- # + +_SOURCE = "_zarr_indexing_cached_source" + + +class ChainedIndexingStateMachine(RuleBasedStateMachine): + """Indexing steps composed onto one `LazyArray`, against NumPy as the model. + + Subclass and override `make_source` to point it at your own array. See the + module docstring for the shape of that subclass and for what the invariants + check. + + Attributes + ---------- + data + The values the source holds, and the model every step is checked + against. Any shape and dtype NumPy supports; every axis must be + non-empty. + partitionings + Drawn once per run, before any indexing: `with_parts` is a pure setter + that carries through composition untouched and is read only when a view + resolves, so choosing it up front reaches the same states choosing it + mid-chain does, and spends the whole step budget on indexing. + readers + Execution strategies `choose_reader` may draw. Every listed reader must + preserve the model for the source. `basic_reader` is always included; + `None` means the reader already carried by the constructed view. + """ + + data: ClassVar[Any] = DEFAULT_DATA + partitionings: ClassVar[Sequence[Any]] = DEFAULT_PARTITIONINGS + readers: ClassVar[Sequence[Reader] | None] = None + + def make_source(self, data: Any) -> Any: + """Build the array under test, holding `data`. + + Called once per machine class and cached, not once per example: an + example is cheap and a source may not be. The machine only ever reads, + so the same object serves every run — but it must therefore not be + mutated by anything else while the test runs. + + The default returns `data` itself, so an unsubclassed machine exercises + this package against NumPy. + """ + return data + + def __init__(self) -> None: + super().__init__() + cls = type(self) + self.model: Any = np.asarray(cls.data) + source = cls.__dict__.get(_SOURCE) + if source is None: + source = self.make_source(self.model) + setattr(cls, _SOURCE, source) + self.view = LazyArray(source) + self.reader_choices = _reader_set(self.view, cls.readers) + self.chain: list[tuple[str, Any]] = [] + + def _indexable(self) -> bool: + """Whether there is anything left to index. + + A rank-0 or empty view takes no further step — NumPy would reject one + too — so the chain ends there, and the invariants keep checking. + """ + return self.model.ndim > 0 and self.model.size > 0 + + def _step(self, mode: SelectionMode, selection: tuple[Any, ...]) -> None: + self.chain.append((mode, selection)) + self.model = apply_selection(self.model, selection, mode) + if mode == "basic": + self.view = self.view.lazy[selection] + elif mode == "orthogonal": + self.view = self.view.lazy.oindex[selection] + else: + self.view = self.view.lazy.vindex[selection] + + # -- rules -------------------------------------------------------------- + + @initialize(data=st.data()) + def choose_partitioning(self, data: st.DataObject) -> None: + """Fix how the read is broken up, before any indexing.""" + parts = data.draw(st.sampled_from(list(type(self).partitionings))) + self.view = repartition(self.view, parts) + self.chain.append(("parts", parts)) + + @precondition(lambda self: self._indexable()) + @rule(data=st.data()) + def basic(self, data: st.DataObject) -> None: + self._step("basic", data.draw(basic_selections(self.model.shape))) + + @precondition(lambda self: self._indexable()) + @rule(data=st.data()) + def orthogonal(self, data: st.DataObject) -> None: + self._step("orthogonal", data.draw(orthogonal_selections(self.model.shape))) + + @precondition(lambda self: self._indexable()) + @rule(data=st.data()) + def vectorized(self, data: st.DataObject) -> None: + self._step("vectorized", data.draw(vectorized_selections(self.model.shape))) + + @precondition(lambda self: self._indexable()) + @rule(data=st.data()) + def slices_only(self, data: st.DataObject) -> None: + """An `oindex` step carrying only slices is not a fancy selection. + + It narrows the view's own axes and composes like basic indexing. Drawn + as its own rule so that narrowing an existing index array by slices — + a distinct code path from narrowing it with coordinates — stays + exercised at full weight. + """ + self._step("orthogonal", data.draw(slice_selections(self.model.shape))) + + @rule(data=st.data()) + def choose_reader(self, data: st.DataObject) -> None: + """Read the rest of the chain through another conforming strategy.""" + reader = data.draw(st.sampled_from(list(self.reader_choices))) + self.view = self.view.with_reader(reader) + self.chain.append(("reader", type(reader).__qualname__)) + + @precondition(lambda self: not self._indexable()) + @rule(data=st.data()) + def repartition(self, data: st.DataObject) -> None: + """Re-box a chain that has run out of axes to index. + + Something must stay enabled once the view is rank-0 or empty, or + Hypothesis has no move to make and abandons the run. Re-boxing is the + useful thing to do there: it changes nothing the invariants may see, and + a rank-0 view read through every partitioning is exactly the state a + collapsed correlated selection reaches. + """ + parts = data.draw(st.sampled_from(list(type(self).partitionings))) + self.view = repartition(self.view, parts) + self.chain.append(("parts", parts)) + + # -- invariants --------------------------------------------------------- + + @invariant() + def the_view_has_the_models_shape(self) -> None: + assert self.view.shape == self.model.shape, self.chain + + @invariant() + def result_matches_the_model(self) -> None: + np.testing.assert_array_equal( + np.asarray(self.view.result()), self.model, err_msg=str(self.chain) + ) + + @invariant() + def parts_tile_the_view(self) -> None: + """The documented assembly, run literally. + + Every part's values arrive at exactly the shape its `out_selection` + addresses — not merely a shape that broadcasts into it — and together + the parts cover the view once. + """ + assembled = np.zeros(self.view.shape, dtype=self.view.dtype) + hits = np.zeros(self.view.shape, dtype=np.int64) + for part in self.view.parts(): + value = np.asarray(part.view.result()) + assert value.shape == assembled[part.out_selection].shape, ( + f"part {part.base_coords} carries {value.shape} for an out_selection " + f"addressing {assembled[part.out_selection].shape}: {self.chain}" + ) + # `is_complete` is what a consumer reads to decide it may take a + # whole-box read and skip assembling anything, so a wrongly-`True` + # one is the silent-corruption case. Asserted one way only: the flag + # is documented as conservative, free to say `False` about a part it + # does cover (a strided walk over a one-cell box, a fancy axis that + # happens to enumerate everything), and only the claim to cover + # everything has to be earned. Both quantities are already in hand + # here, and nothing else in the suite compares them. + if part.is_complete: + box_cells = math.prod(stop - start for start, stop in part.box) + assert value.size == box_cells, ( + f"part {part.base_coords} reports is_complete but carries " + f"{value.size} of its box's {box_cells} cells: {self.chain}" + ) + assembled[part.out_selection] = value + np.add.at(hits, part.out_selection, 1) + + np.testing.assert_array_equal(assembled, self.model, err_msg=str(self.chain)) + np.testing.assert_array_equal( + hits, np.ones(self.view.shape, dtype=np.int64), err_msg=str(self.chain) + ) + + +def _reader_set(view: LazyArray, declared: Sequence[Reader] | None) -> tuple[Reader, ...]: + """The readers `choose_reader` draws from, `basic_reader` always among them.""" + readers = list(declared) if declared is not None else [view.reader] + if all(reader is not basic_reader for reader in readers): + readers.insert(0, basic_reader) + unique: list[Reader] = [] + for reader in readers: + if all(reader is not existing for existing in unique): + unique.append(reader) + return tuple(unique) diff --git a/packages/zarr-indexing/src/zarr_indexing/testing/strategies.py b/packages/zarr-indexing/src/zarr_indexing/testing/strategies.py new file mode 100644 index 0000000000..63a3d351a9 --- /dev/null +++ b/packages/zarr-indexing/src/zarr_indexing/testing/strategies.py @@ -0,0 +1,207 @@ +"""Hypothesis strategies for the selections `LazyArray` accepts. + +Each strategy takes the shape of the array being indexed and generates one +selection for it — an index tuple with one entry per axis, in the spelling its +mode expects. They are the generators behind +[`ChainedIndexingStateMachine`][zarr_indexing.testing.stateful.ChainedIndexingStateMachine] +and are exported on their own for a project that has its own test harness and +wants only the hard part. + +```python +from hypothesis import given, strategies as st +from zarr_indexing.testing.strategies import basic_selections + +@given(selection=basic_selections((7, 5, 4))) +def test_my_array_slices_like_numpy(selection): + assert_array_equal(my_array[selection], reference[selection]) +``` + +Every axis of `shape` must be non-empty: a selection over an axis of extent 0 +has no coordinates to draw. Filter or narrow the shape before calling. + +Requires the `testing` extra (`pip install zarr-indexing[testing]`). +""" + +from __future__ import annotations + +import operator +from typing import TYPE_CHECKING, Any + +import numpy as np +from hypothesis import strategies as st + +if TYPE_CHECKING: + from collections.abc import Callable + +__all__ = [ + "basic_selections", + "empty_masks", + "masks", + "orthogonal_selections", + "slice_selections", + "vectorized_selections", +] + + +def _entries(shape: tuple[int, ...], entry: Callable[[int], st.SearchStrategy[Any]]) -> Any: + """One `entry` strategy per axis, as an index tuple.""" + return st.tuples(*[entry(size) for size in shape]) + + +def _basic_entry(size: int) -> st.SearchStrategy[Any]: + steps = st.integers(1, 3) + return st.one_of( + # A scalar integer drops its axis, in every mode, exactly as NumPy does. + st.integers(-size, size - 1), + st.builds(slice, st.integers(0, size), st.integers(0, size), steps), + # Downward. The start is drawn from below `-size` as well, where the walk + # begins off the front and selects nothing — a case that reads as an + # ordinary negative index but is empty — and a stop that falls off the + # front is spelled `None`. + st.builds( + slice, + st.integers(-2 * size - 1, size - 1), + st.none() | st.integers(0, size), + steps.map(operator.neg), + ), + st.just(slice(None)), + ) + + +def _orthogonal_entry(size: int) -> st.SearchStrategy[Any]: + """One axis of an `oindex` selection. + + The slices carry a step and are free to stop early. Drawing them as + `slice(start, size)` alone meant no strided or reversed slice ever reached + `oindex`, and no orthogonal selection ever stopped short of the axis end. + + An empty coordinate list is drawn too. It selects nothing, which is legal + and is exactly the shape that lost its axis on the way through JSON — but + with `min_size=1` no fancy selection was ever empty. + """ + coordinate = st.integers(-size, size - 1) + return st.one_of( + coordinate, + st.lists(coordinate, min_size=1, max_size=4), + st.just([]), + masks((size,)), + empty_masks((size,)), + st.builds( + slice, + st.integers(0, size - 1), + st.integers(0, size) | st.none(), + st.integers(1, 3) | st.integers(-3, -1), + ), + ) + + +def _slice_entry(size: int) -> st.SearchStrategy[slice]: + return st.one_of( + st.builds(slice, st.integers(0, size - 1), st.just(size), st.integers(1, 2)), + st.just(slice(None, None, -1)), + st.just(slice(None)), + ) + + +@st.composite +def masks(draw: st.DrawFn, shape: tuple[int, ...]) -> np.ndarray[Any, np.dtype[np.bool_]]: + """Boolean masks over `shape`, each selecting at least one cell. + + An all-False mask is legal but is a separate concern — it empties the view, + and a chain of selections is more interesting when every step leaves + something to index — so one cell is always forced True. + """ + size = int(np.prod(shape)) + flags = np.array(draw(st.lists(st.booleans(), min_size=size, max_size=size))) + flags[draw(st.integers(0, size - 1))] = True + return flags.reshape(shape) + + +def empty_masks(shape: tuple[int, ...]) -> st.SearchStrategy[np.ndarray[Any, np.dtype[np.bool_]]]: + """The all-False mask over `shape` — a fancy selection that empties the view. + + Split out from `masks`, which forces a cell True so a chain has something + left to index at the next step. Drawn on its own because an empty fancy + selection is a shape the code paths treat separately, and nothing generated + one. + """ + return st.just(np.zeros(shape, dtype=np.bool_)) + + +def basic_selections(shape: tuple[int, ...]) -> st.SearchStrategy[tuple[Any, ...]]: + """Basic selections: one scalar integer or slice per axis. + + Slices run in both directions, including the two empty spellings — a + forward slice whose stop precedes its start, and a backward one whose start + is off the front of the axis. + """ + return _entries(shape, _basic_entry) + + +def orthogonal_selections(shape: tuple[int, ...]) -> st.SearchStrategy[tuple[Any, ...]]: + """Orthogonal (`oindex`) selections: an outer product of per-axis choices. + + Each axis draws a scalar, a coordinate list (unsorted, with duplicates), a + boolean mask, or a slice. + """ + return _entries(shape, _orthogonal_entry) + + +def slice_selections(shape: tuple[int, ...]) -> st.SearchStrategy[tuple[Any, ...]]: + """Selections of slices alone, for the `oindex` spelling that carries no coordinates. + + Such a step is not a fancy selection — it narrows the view's own axes and + composes like basic indexing — so it is legal after a fancy step, where + genuine coordinates are not. The starts reach past the origin, which is what + distinguishes a step that walks an existing index array's dependency axes + from one that walks its broadcast singletons. + """ + return _entries(shape, _slice_entry) + + +@st.composite +def vectorized_selections(draw: st.DrawFn, shape: tuple[int, ...]) -> tuple[Any, ...]: + """Vectorized (`vindex`) selections over a leading or trailing block of axes. + + `vindex` is coordinate-only — it rejects a slice outright — so a partial + selection names its axes by position: a leading block, or a trailing one + reached through an ellipsis. Either a single boolean mask spanning the whole + covered block, or one entry per axis, each a coordinate array or a scalar + (a scalar being a basic index NumPy applies before the coordinates). + """ + ndim = len(shape) + trailing = draw(st.booleans()) + count = draw(st.integers(1, ndim)) + axes = range(ndim - count, ndim) if trailing else range(count) + sizes = [shape[axis] for axis in axes] + + entries: list[Any] + if draw(st.booleans()): + entries = [draw(masks(tuple(sizes)))] + else: + # The coordinate arrays share one shape, which is what makes the + # selection correlated. That shape is not always one-dimensional: a + # vectorized read of a (2, 3) block of points is an ordinary thing to + # ask for and produces a result of that rank. Drawing only 1-D arrays + # meant no rank-raising vindex was ever generated — and a length of 0 + # covers the empty case the same way `_orthogonal_entry` does. + coordinate_shape = draw( + st.one_of( + st.integers(0, 4).map(lambda length: (length,)), + st.tuples(st.integers(1, 2), st.integers(1, 3)), + ) + ) + entries = [ + draw( + st.one_of( + st.integers(-size, size - 1), + st.lists( + st.integers(-size, size - 1), + min_size=int(np.prod(coordinate_shape)), + max_size=int(np.prod(coordinate_shape)), + ).map(lambda values: np.array(values, dtype=np.intp).reshape(coordinate_shape)), + ) + ) + for size in sizes + ] + return (Ellipsis, *entries) if trailing else tuple(entries) diff --git a/packages/zarr-indexing/src/zarr_indexing/transform.py b/packages/zarr-indexing/src/zarr_indexing/transform.py index e1a3898b1d..a8a5963a26 100644 --- a/packages/zarr-indexing/src/zarr_indexing/transform.py +++ b/packages/zarr-indexing/src/zarr_indexing/transform.py @@ -1,8 +1,8 @@ """Index transforms — composable, lazy coordinate mappings. An `IndexTransform` pairs an **input domain** (the coordinates a user sees) -with a tuple of **output maps** (the storage coordinates those inputs map to). -One output map per storage dimension. See `output_map.py` for the three +with a tuple of **output maps** (the output coordinates those inputs map to). +One output map per output dimension. See `output_map.py` for the three output map types. Key operations: @@ -11,52 +11,108 @@ produces a new transform with a narrower input domain and adjusted output maps. No I/O occurs. This is how lazy slicing works. -- **intersect(output_domain)** — restrict to storage coordinates within a +- **intersect(output_domain)** — restrict to output coordinates within a region. This is chunk resolution: "which of my coordinates fall in this chunk?" - **translate(shift)** — shift all output coordinates. This makes coordinates chunk-local: "express my coordinates relative to the chunk origin." -- **compose(outer, inner)** — chain two transforms. See `composition.py`. +- **`transform.compose(inner)`** — chain two transforms into one. The transform is the atomic unit that connects user-facing indexing to -chunk-level I/O. Every `Array` holds a transform (identity by default). -`Array.lazy[...]` composes a new transform lazily. Reading resolves the -transform against the chunk grid via intersect + translate. +chunk-level I/O. A wrapper holds one — `LazyArray` starts from the identity — +and `.lazy[...]` composes a new transform lazily rather than reading. Reading +resolves the transform against the chunk grid via intersect + translate. """ from __future__ import annotations -import math from dataclasses import dataclass -from typing import Any, Literal, cast +from typing import TYPE_CHECKING, Any, Literal, cast import numpy as np +from zarr_indexing._affine import checked_affine +from zarr_indexing._selector import as_scalar_index, require_index +from zarr_indexing.boundary import validate_advanced_selection from zarr_indexing.domain import IndexDomain from zarr_indexing.errors import BoundsCheckError, VindexInvalidSelectionError -from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap, OutputIndexMap +from zarr_indexing.output_map import ( + ArrayMap, + ConstantMap, + DimensionMap, + OutputIndexMap, + array_map_or_constant, +) + +if TYPE_CHECKING: + from collections.abc import Sequence + + import numpy.typing as npt + + from zarr_indexing.json import IndexTransformJSON + + +@dataclass(frozen=True, slots=True) +class _PointOutOfBounds(Exception): + """Internal signal from the shared point kernel: one coordinate left the domain. + + Never escapes this module. `apply` and `apply_many` format it as the + public `BoundsCheckError`, each in its own vocabulary — the kernel knows + batches, but a single-point caller must never hear about them. + """ + + dimension: int + value: int + lower: int + upper: int + batch_position: tuple[int, ...] @dataclass(frozen=True, slots=True) class IndexTransform: - """A composable mapping from input coordinates to storage coordinates. + """A composable mapping from input coordinates to output coordinates. An `IndexTransform` has: - `domain`: an `IndexDomain` describing the valid input coordinates - (the user-facing shape, possibly with non-zero origin). - - `output`: a tuple of output maps (one per storage dimension), each - describing which storage coordinates the inputs touch. - - For a freshly opened array, the transform is the identity: input - coordinate `i` maps to storage coordinate `i`. Indexing operations - compose new transforms without I/O. + (the result's coordinate range, possibly with non-zero origin). + - `output`: a tuple of output maps (one per output dimension), each + describing which output coordinates the inputs touch. + + In array-indexing terms: `domain` describes the coordinates of the result + array an indexing operation produces, and `output` is the rule relating + each result coordinate to a coordinate in the source. Note the direction — + the transform's input side is the result, its output side addresses the + source; the coordinate mapping runs opposite to the data flow. + + Indexing an existing transform composes a new one without I/O. + + Examples + -------- + The operation "every other element of a 100-element array, starting at + index 0" — `array[::2]` — is a 50-cell domain whose cell `i` reads + output coordinate `2 * i`: + + >>> domain = IndexDomain.from_shape((50,)) + >>> output = (DimensionMap(input_dimension=0, offset=0, stride=2),) + >>> transform = IndexTransform(domain=domain, output=output) + >>> transform.apply((0,)), transform.apply((1,)), transform.apply((49,)) + ((0,), (2,), (98,)) + + The selection compiler derives the identical transform from the source's + shape and the slice: + + >>> transform == IndexTransform.from_shape((100,))[::2] + True """ domain: IndexDomain + """The input domain: the request coordinates this transform accepts.""" + output: tuple[OutputIndexMap, ...] + """One output map per output dimension, each producing that dimension's coordinate.""" def __post_init__(self) -> None: for i, m in enumerate(self.output): @@ -66,37 +122,332 @@ def __post_init__(self) -> None: f"output[{i}].input_dimension = {m.input_dimension} " f"is out of range for input rank {self.domain.ndim}" ) - elif isinstance(m, ArrayMap) and m.index_array.ndim > self.domain.ndim: - # ArrayMap index arrays produced by indexing and chunk resolution - # are normalized to the full input rank (an axis the array varies - # over is full-sized, every other axis a singleton). A rank - # *exceeding* the domain is always a bug. A rank *below* it is - # tolerated: TensorStore-format JSON (external input) may supply a - # lower-rank index array that broadcasts against the input domain, - # and `_array_map_dependency_axes` treats any missing leading axes - # as singleton dependencies. - raise ValueError( - f"output[{i}].index_array has {m.index_array.ndim} dims " - f"but input domain has {self.domain.ndim} dims" - ) + elif isinstance(m, ArrayMap): + # An index array carries the transform's full input rank: the axis + # a map varies over is full-sized, every other axis a singleton. + # The rank is what makes the dependency axes readable from the + # shape, so a mismatch is a bug rather than a spelling. External + # JSON may use a lower-rank array that broadcasts against the + # domain; `from_json` widens those on the way in, + # so the invariant holds for every transform that exists. + if m.index_array.ndim != self.domain.ndim: + raise ValueError( + f"output[{i}].index_array has {m.index_array.ndim} dims " + f"but input domain has {self.domain.ndim} dims" + ) + # Every axis is either the domain's extent or a singleton it + # broadcasts over. Any other size addresses input coordinates the + # array has no entry for, which reads as a smaller selection + # rather than as the error it is. + bad = [ + (axis, size, extent) + for axis, (size, extent) in enumerate( + zip(m.index_array.shape, self.domain.shape, strict=True) + ) + if size not in (1, extent) + ] + if len(bad) > 0: + axis, size, extent = bad[0] + raise ValueError( + f"output[{i}].index_array has {size} entries on axis {axis}, " + f"which is neither 1 nor the domain's extent of {extent} " + f"(index_array shape {m.index_array.shape}, " + f"domain shape {self.domain.shape})" + ) + + def __eq__(self, other: object) -> bool: + """Value equality. `ArrayMap` compares its index array element-wise, so + a transform holding one can be compared at all — the generated `__eq__` + raised `ValueError: the truth value of an array ... is ambiguous`.""" + if not isinstance(other, IndexTransform): + return NotImplemented + return self.domain == other.domain and self.output == other.output + + def __hash__(self) -> int: + """Hashed by value, so a transform can key a cache or enter a set.""" + return hash((self.domain, self.output)) @property def input_rank(self) -> int: + """Number of input dimensions — the rank of `domain`.""" return self.domain.ndim @property def output_rank(self) -> int: + """Number of output dimensions — one per output map.""" return len(self.output) @classmethod def identity(cls, domain: IndexDomain) -> IndexTransform: + """The identity transform over `domain`: every result cell reads the source at its own address.""" output = tuple(DimensionMap(input_dimension=i) for i in range(domain.ndim)) return cls(domain=domain, output=output) @classmethod def from_shape(cls, shape: tuple[int, ...]) -> IndexTransform: + """The identity transform over a zero-origin domain of the given `shape`.""" return cls.identity(IndexDomain.from_shape(shape)) + def apply(self, point: Sequence[int]) -> tuple[int, ...]: + """Map one coordinate of `domain` to the source coordinate that fills it. + + In array-indexing terms: `point` names a cell of the result array, and + the returned tuple — each `output` map evaluated at `point` — names the + source-array cell its value is read from: the coordinate arrow, + running result to source. + + Parameters + ---------- + point : Sequence[int] + One literal coordinate for each input dimension. + + Returns + ------- + tuple[int, ...] + One coordinate for each output map. + + Raises + ------ + ValueError + If ``point`` does not have exactly one coordinate per input + dimension. + TypeError + If the coordinates do not have an integer dtype. + BoundsCheckError + If a coordinate lies outside the input domain. + OverflowError + If a mapped output coordinate cannot be represented by + ``np.intp``. + + Examples + -------- + The `[::2]` transform reads result cell `i` from source coordinate + `2 * i`, so cell 3 of the result holds `source[6]`: + + >>> transform = IndexTransform.from_shape((100,))[::2] + >>> transform.apply((3,)) + (6,) + """ + coordinates = np.asarray(point) + expected_shape = (self.input_rank,) + if coordinates.shape != expected_shape: + raise ValueError(f"point must have shape {expected_shape}, got {coordinates.shape}") + # An empty Python sequence has no elements from which NumPy can infer + # an integer dtype, but it is the unique point in a rank-zero domain. + if self.input_rank == 0 and isinstance(point, (list, tuple)): + coordinates = coordinates.astype(np.intp) + try: + result = self._apply_points(coordinates) + except _PointOutOfBounds as error: + raise BoundsCheckError( + f"coordinate {error.value} on input dimension {error.dimension} " + f"is outside the domain [{error.lower}, {error.upper})" + ) from None + return tuple(int(value) for value in result) + + def apply_many(self, points: npt.ArrayLike) -> npt.NDArray[np.intp]: + """Map a batch of `domain` coordinates to the source coordinates that fill them. + + The vectorized form of `apply`: each row of `points` names a result + cell, and the corresponding output row names the source-array cell + its value is read from. + + Parameters + ---------- + points : numpy.typing.ArrayLike + Integer coordinates with shape ``batch_shape + (input_rank,)``. + + Returns + ------- + numpy.typing.NDArray[numpy.intp] + An owned array with shape ``batch_shape + (output_rank,)``. + + Raises + ------ + ValueError + If ``points`` has no trailing coordinate axis or that axis does + not contain exactly one coordinate per input dimension. + TypeError + If the coordinates do not have an integer dtype. + BoundsCheckError + If a coordinate lies outside the input domain. + OverflowError + If a mapped output coordinate cannot be represented by + ``np.intp``. + + Examples + -------- + Three result cells of the `[::2]` transform, located in one call: + + >>> transform = IndexTransform.from_shape((100,))[::2] + >>> transform.apply_many(np.array([[0], [1], [49]])).tolist() + [[0], [2], [98]] + """ + coordinates = np.asarray(points) + if coordinates.ndim == 0 or coordinates.shape[-1] != self.input_rank: + raise ValueError( + "points must have a trailing coordinate axis of size " + f"{self.input_rank}, got shape {coordinates.shape}" + ) + try: + return self._apply_points(coordinates) + except _PointOutOfBounds as error: + raise BoundsCheckError( + f"point at batch position {error.batch_position} has input dimension " + f"{error.dimension} coordinate {error.value} outside " + f"[{error.lower}, {error.upper})" + ) from None + + def _apply_points(self, points: np.ndarray[Any, Any]) -> npt.NDArray[np.intp]: + """Vectorized implementation shared by ``apply`` and ``apply_many``. + + Out-of-domain coordinates raise the internal `_PointOutOfBounds` + signal; each public entry point formats it in its own vocabulary — + `apply` never mentions a batch, `apply_many` names the batch position.""" + if not np.issubdtype(points.dtype, np.integer): + raise TypeError(f"points must have an integer dtype, got {points.dtype}") + + invalid = np.zeros(points.shape, dtype=np.bool_) + for dimension, (lower, upper) in enumerate( + zip(self.domain.inclusive_min, self.domain.exclusive_max, strict=True) + ): + invalid[..., dimension] = (points[..., dimension] < lower) | ( + points[..., dimension] >= upper + ) + invalid_positions = np.argwhere(invalid) + if invalid_positions.size > 0: + first = invalid_positions[0] + dimension = int(first[-1]) + batch_position = tuple(int(position) for position in first[:-1]) + point_index = tuple(int(position) for position in first) + value = int(points[point_index]) + lower = self.domain.inclusive_min[dimension] + upper = self.domain.exclusive_max[dimension] + raise _PointOutOfBounds(dimension, value, lower, upper, batch_position) + + batch_shape = points.shape[:-1] + result = np.empty(batch_shape + (self.output_rank,), dtype=np.intp) + for output_dimension, output_map in enumerate(self.output): + if isinstance(output_map, ConstantMap): + if result[..., output_dimension].size == 0: + continue + result[..., output_dimension] = checked_affine(output_map.offset, 0, 0) + elif isinstance(output_map, DimensionMap): + result[..., output_dimension] = checked_affine( + output_map.offset, + output_map.stride, + points[..., output_map.input_dimension], + ) + else: + index = tuple( + np.zeros(batch_shape, dtype=np.intp) + if output_map.index_array.shape[axis] == 1 + else _positions_from_origin(points[..., axis], self.domain.inclusive_min[axis]) + for axis in range(self.input_rank) + ) + result[..., output_dimension] = checked_affine( + output_map.offset, + output_map.stride, + np.asarray(output_map.index_array[index]), + ) + return result + + def inverted(self) -> IndexTransform: + """Return the restricted, exactly representable inverse transform. + + Inversion is defined for square transforms containing only constants + and unique unit-stride dimension maps. Any input dimension not named by + a dimension map must have singleton extent, so its coordinate can be + recovered as a constant. + + Returns + ------- + IndexTransform + A new transform mapping output coordinates back to input + coordinates. + + Raises + ------ + ValueError + If this transform does not have a representable inverse, including + when input labels cannot be transferred to unlabeled output + dimensions. + """ + if self.domain.labels is not None: + raise ValueError( + "cannot invert transform: input labels cannot be represented " + "because output dimensions do not carry labels" + ) + if self.input_rank != self.output_rank: + raise ValueError( + "cannot invert transform: input rank must equal output rank, got " + f"{self.input_rank} and {self.output_rank}" + ) + + referenced: set[int] = set() + for output_dimension, output_map in enumerate(self.output): + if isinstance(output_map, ArrayMap): + raise ValueError( # noqa: TRY004 - valid map, invalid inverse + f"cannot invert transform: output[{output_dimension}] is an ArrayMap" + ) + if isinstance(output_map, DimensionMap): + if output_map.stride not in (-1, 1): + raise ValueError( + "cannot invert transform: DimensionMap stride must be +1 or -1, " + f"got {output_map.stride} for output[{output_dimension}]" + ) + if output_map.input_dimension in referenced: + raise ValueError( + "cannot invert transform: input dimension " + f"{output_map.input_dimension} is referenced more than once" + ) + referenced.add(output_map.input_dimension) + + for input_dimension, extent in enumerate(self.domain.shape): + if input_dimension not in referenced and extent != 1: + raise ValueError( + "cannot invert transform: unreferenced input dimension " + f"{input_dimension} has extent {extent}, not 1" + ) + + inverse_min: list[int] = [] + inverse_max: list[int] = [] + inverse_output: dict[int, OutputIndexMap] = {} + for output_dimension, output_map in enumerate(self.output): + if isinstance(output_map, ConstantMap): + inverse_min.append(output_map.offset) + inverse_max.append(output_map.offset + 1) + continue + + assert isinstance(output_map, DimensionMap) + input_dimension = output_map.input_dimension + lower = self.domain.inclusive_min[input_dimension] + upper = self.domain.exclusive_max[input_dimension] + if output_map.stride == 1: + inverse_min.append(output_map.offset + lower) + inverse_max.append(output_map.offset + upper) + inverse_output[input_dimension] = DimensionMap( + output_dimension, + offset=-output_map.offset, + ) + else: + inverse_min.append(output_map.offset - upper + 1) + inverse_max.append(output_map.offset - lower + 1) + inverse_output[input_dimension] = DimensionMap( + output_dimension, + offset=output_map.offset, + stride=-1, + ) + + for input_dimension, lower in enumerate(self.domain.inclusive_min): + if input_dimension not in referenced: + inverse_output[input_dimension] = ConstantMap(lower) + + return IndexTransform( + domain=IndexDomain(tuple(inverse_min), tuple(inverse_max)), + output=tuple(inverse_output[dimension] for dimension in range(self.input_rank)), + ) + @property def selection_repr(self) -> str: """Compact domain string, e.g. `'{ [2, 8), [0, 10) }'`. @@ -155,7 +506,10 @@ def intersect( ] | None ): - """Restrict this transform to storage coordinates within output_domain. + """Keep only the cells whose source coordinates fall inside `output_domain`. + + Chunk resolution is the canonical caller: intersecting a request with + one chunk's box keeps the cells that chunk can serve. Returns `(restricted_transform, out_indices)` or None if empty. @@ -167,7 +521,13 @@ def intersect( return _intersect(self, output_domain) def translate(self, shift: tuple[int, ...]) -> IndexTransform: - """Shift all output coordinates by `shift`.""" + """Shift the source coordinates every cell reads by `shift`, per dimension. + + The domain is untouched: the result keeps its cells, and each one + reads from a shifted source address — for example, making a chunk's + global addresses chunk-local by translating by the chunk's negated + origin. + """ if len(shift) != self.output_rank: raise ValueError(f"shift must have length {self.output_rank}, got {len(shift)}") new_output: list[OutputIndexMap] = [] @@ -189,12 +549,18 @@ def translate(self, shift: tuple[int, ...]) -> IndexTransform: index_array=m.index_array, offset=m.offset + s, stride=m.stride, - input_dimension=m.input_dimension, ) ) return IndexTransform(domain=self.domain, output=tuple(new_output)) def __getitem__(self, selection: Any) -> IndexTransform: + """Compose a basic selection (int, slice, ellipsis, newaxis) into a new transform. + + No I/O occurs. Integers and slice bounds are literal domain coordinates + (TensorStore convention): negative values are not counted from the end, + and out-of-domain values raise `BoundsCheckError`. Integer indices drop + their input dimension; `None` inserts a size-1 dimension. + """ return _apply_basic_indexing(self, selection) def translate_domain_by(self, shift: tuple[int, ...]) -> IndexTransform: @@ -239,12 +605,255 @@ def translate_domain_to(self, origins: tuple[int, ...]) -> IndexTransform: @property def oindex(self) -> _OIndexHelper: + """Accessor for the orthogonal (outer-product) indexing dialect. + + `transform.oindex[sel]` applies each index array independently per + dimension and returns a new transform. + """ return _OIndexHelper(self) @property def vindex(self) -> _VIndexHelper: + """Accessor for the vectorized (coordinate/mask) indexing dialect. + + `transform.vindex[sel]` broadcasts all index arrays together, NumPy + fancy-indexing style, and returns a new transform. + """ return _VIndexHelper(self) + @property + def index_array_structure(self) -> Literal["none", "orthogonal", "general"]: + """Classify how a transform's index arrays relate to its input axes. + + Returns + ------- + `"none"` when no output map is an `ArrayMap`; `"orthogonal"` when every + `ArrayMap` varies over exactly one input axis, each its own (an outer + product, one independent gather per axis); `"general"` otherwise — + correlated (`vindex`) maps sharing their non-singleton axes, maps produced + by composing fancy steps, maps sharing an input axis (a diagonal gather), + and empty or hand-built all-singleton maps whose shape names no axis. The + orthogonal resolvers narrow one axis at a time and are only sound for + `"orthogonal"`; everything else takes the pointwise path that collapses + the joint block. Everything is read off the index arrays' shapes. + + Examples + -------- + >>> t = IndexTransform.from_shape((4, 5)) + >>> t.index_array_structure + 'none' + + `oindex` arrays each vary over their own axis (an outer product): + + >>> t.oindex[[0, 2], [1, 3]].index_array_structure + 'orthogonal' + + `vindex` arrays are correlated — they share the broadcast axis: + + >>> t.vindex[np.array([0, 2]), np.array([1, 3])].index_array_structure + 'general' + """ + seen: set[int] = set() + has_array = False + for m in self.output: + if not isinstance(m, ArrayMap): + continue + has_array = True + dep = m.dependency_axes + if len(dep) != 1 or dep[0] in seen: + return "general" + seen.add(dep[0]) + return "orthogonal" if has_array else "none" + + def select( + self, + selection: Any, + mode: Literal["basic", "orthogonal", "vectorized"] = "basic", + ) -> IndexTransform: + """Convert a user selection into a composed IndexTransform. + + Negative indices are treated as literal coordinates (TensorStore convention). + The caller (Array layer) is responsible for converting numpy-style negative + indices before calling this function. + + Examples + -------- + The `mode` picks the dialect; the result is the composed self the + corresponding accessor builds: + + >>> t = IndexTransform.from_shape((10,)) + >>> t.select(slice(2, 8)) == t[2:8] + True + >>> s = t.select(([9, 0, 0],), mode="orthogonal") + >>> s.apply((0,)), s.apply((1,)), s.apply((2,)) + ((9,), (0,), (0,)) + """ + if mode == "basic": + _validate_basic_selection(selection) + return self[selection] + elif mode == "orthogonal": + _validate_array_selection(selection, self.domain.shape, mode) + return self.oindex[selection] + elif mode == "vectorized": + _validate_array_selection(selection, self.domain.shape, mode) + return self.vindex[selection] + else: + raise ValueError(f"Unknown mode: {mode!r}") + + def compose(self, inner: IndexTransform) -> IndexTransform: + """Chain `inner` onto this transform, yielding one direct transform. + + This transform maps its own input coordinates to `inner`'s input + coordinates, and `inner` maps those onward; the result maps this + transform's input coordinates straight to `inner`'s output + coordinates. Composition is what keeps a view of a view a single + description rather than a stack of layers, and it is exact: index + arrays are evaluated at the new coordinates rather than accumulated. + + The precondition is that this transform's output rank equals `inner`'s + input rank; a mismatch, or coordinates leaving `inner`'s domain, raises. + + Examples + -------- + Chained indexing — `source[2:5]`, then `[::-1]` on the result — + collapses to one transform (a reversed axis keeps literal coordinates, + so the composed domain is `[-4, -1)`): + + >>> inner = IndexTransform.from_shape((10,))[2:5] + >>> outer = IndexTransform.identity(inner.domain)[::-1] + >>> chained = outer.compose(inner) + >>> chained == inner[::-1] + True + >>> [chained.apply((i,)) for i in (-4, -3, -2)] + [(4,), (3,), (2,)] + """ + from zarr_indexing._composition import compose + + return compose(self, inner) + + # -- serialization ------------------------------------------------------ + + def to_json(self) -> IndexTransformJSON: + """Convert to the canonical ndsel transform body (spec section 4.3). + + The result is fully explicit: `input_rank`, fully written bounds and + labels, and an `output` carrying `offset`/`stride` on every affine and + array map. It is field-for-field a TensorStore `IndexTransform` minus + the `kind` discriminator, so it loads directly into + `tensorstore.IndexTransform(json=...)`. + + Examples + -------- + >>> body = IndexTransform.from_shape((6,))[1:5:2].to_json() + >>> (body["input_inclusive_min"], body["input_exclusive_max"]) + ([0], [2]) + >>> body["output"] + [{'offset': 1, 'stride': 2, 'input_dimension': 0}] + """ + from zarr_indexing._wire import emit_labels + + return { + "input_rank": self.domain.ndim, + "input_inclusive_min": list(self.domain.inclusive_min), + "input_exclusive_max": list(self.domain.exclusive_max), + "input_labels": emit_labels(self.domain.labels, self.domain.ndim), + "output": [m.to_json() for m in self.output], + } + + @classmethod + def from_json(cls, data: IndexTransformJSON) -> IndexTransform: + """Construct from a canonical (or canonicalizable) ndsel transform body. + + The body is first run through the message layer (`normalize_ndsel`) so + that omitted fields — identity `output`, default bounds and labels — + are filled and validated, then lowered to the engine representation. + Lower-rank `index_array`s are widened to the full input rank on the way + in. + + Examples + -------- + >>> body = IndexTransform.from_shape((6,))[1:5:2].to_json() + >>> transform = IndexTransform.from_json(body) + >>> transform.domain.shape + (2,) + >>> transform.to_json() == body # the round trip is exact + True + """ + from zarr_indexing._wire import ( + full_rank_index_array, + lower_bound, + lower_index_array, + lower_labels, + ) + from zarr_indexing.messages import NdselError, normalize_ndsel + + if not isinstance(data, dict): # pyright: ignore[reportUnnecessaryIsInstance] + raise NdselError( + "invalid_json", f"a transform body must be a JSON object, got {data!r}" + ) + kind = data.get("kind", "transform") + if kind != "transform": + # Spelled before normalization so a body carrying its own `kind` + # cannot reinterpret the document as some other message and return + # a selection this constructor never promised. + raise NdselError("invalid_json", f"a transform body cannot carry kind {kind!r}") + body = normalize_ndsel({**data, "kind": "transform"}) + + domain = IndexDomain( + inclusive_min=tuple( + lower_bound(b, f"input_inclusive_min[{i}]") + for i, b in enumerate(body["input_inclusive_min"]) + ), + exclusive_max=tuple( + lower_bound(b, f"input_exclusive_max[{i}]") + for i, b in enumerate(body["input_exclusive_max"]) + ), + labels=lower_labels(body["input_labels"]), + ) + + output: list[OutputIndexMap] = [] + for i, om in enumerate(body["output"]): + if "index_array" in om: + where = f"output[{i}]" + arr = lower_index_array(om["index_array"], f"{where}.index_array") + # ndsel leaves index-array rank unvalidated, so an external + # producer may send an array of lower rank that broadcasts + # against the domain. Widen it here, on the way in, so every + # transform that exists holds the full-rank invariant the + # engine reads dependency axes from. + output.append( + ArrayMap( + index_array=full_rank_index_array(arr, domain, where), + offset=om.get("offset", 0), + stride=om.get("stride", 1), + ) + ) + elif "input_dimension" in om: + output.append( + DimensionMap( + input_dimension=om["input_dimension"], + offset=om.get("offset", 0), + stride=om.get("stride", 1), + ) + ) + else: + output.append(ConstantMap(offset=om.get("offset", 0))) + + try: + return cls(domain=domain, output=tuple(output)) + except ValueError as exc: + # The engine's invariants are the last gate a document passes, and + # they speak in the engine's vocabulary. A document that fails them + # is invalid input, so it leaves here as one — with the engine's + # account of what was wrong kept, since it names the offending + # output map and axis. + raise NdselError("rank_mismatch", str(exc)) from exc + + +def _positions_from_origin(coordinates: np.ndarray[Any, Any], origin: int) -> npt.NDArray[np.intp]: + """Convert literal coordinates to positional indices without wrapping.""" + return checked_affine(-int(origin), 1, coordinates) + def _intersect( transform: IndexTransform, output_domain: IndexDomain @@ -257,22 +866,22 @@ def _intersect( ): """Intersect a transform with an output domain (e.g., a chunk's bounds). - For each output dimension, restrict to storage coordinates within + For each output dimension, restrict to output coordinates within `[output_domain.inclusive_min[d], output_domain.exclusive_max[d])`. - Two flavours of fancy indexing require different treatment, distinguished by - the ArrayMaps' dependency axes (see `_array_map_dependency_axes`): + Two flavors of fancy indexing require different treatment, distinguished by + the ArrayMaps' dependency axes (see `ArrayMap.dependency_axes`): - **orthogonal** (`oindex`): each ArrayMap varies over a single, distinct input axis, forming an outer product. Every output dimension is intersected independently and the input domain narrowed per axis. - **correlated** (`vindex`): the ArrayMaps share their (broadcast) dependency axes and scatter through a single flat index. A point survives only if ALL - its storage coordinates fall within the output domain; residual slice + its output coordinates fall within the output domain; residual slice dimensions are intersected independently, as in the orthogonal case. - A `None` `input_dimension` marks a correlated map, so any such map routes the - whole transform through the correlated intersection. + The routing is `index_array_structure`: only a pure per-axis outer product + takes the orthogonal path. Returns `None` if the intersection is empty. """ @@ -282,33 +891,36 @@ def _intersect( f"transform output rank ({transform.output_rank})" ) - correlated_dims = [ - i - for i, m in enumerate(transform.output) - if isinstance(m, ArrayMap) and m.input_dimension is None - ] - if len(correlated_dims) > 0: - return _intersect_correlated(transform, output_domain, correlated_dims) + if any(size == 0 for size in transform.domain.shape): + # An empty input domain addresses no coordinates at all, so it meets no + # output domain. Deciding it here keeps the per-flavor intersections from + # having to reconcile an empty domain with an index array that is *not* + # empty: a genuine extent-1 axis is stored as a broadcast singleton, so + # emptying its domain leaves the array at size 1. + return None + + if transform.index_array_structure == "general": + return _intersect_general(transform, output_domain) return _intersect_orthogonal(transform, output_domain) def _intersect_dimension_map( m: DimensionMap, input_lo: int, input_hi: int, lo: int, hi: int ) -> tuple[int, int] | None: - """Narrow a DimensionMap's input range to storage coordinates in `[lo, hi)`. + """Narrow a DimensionMap's input range to output coordinates in `[lo, hi)`. `input_lo`/`input_hi` are the current (possibly already narrowed) input range for the map's axis. Returns the new `(input_lo, input_hi)` or `None` - if no input produces an in-bounds storage coordinate. + if no input produces an in-bounds output coordinate. """ if input_lo >= input_hi: return None if m.stride > 0: - new_input_lo = max(input_lo, math.ceil((lo - m.offset) / m.stride)) - new_input_hi = min(input_hi, math.ceil((hi - m.offset) / m.stride)) + new_input_lo = max(input_lo, _ceil_div(lo - m.offset, m.stride)) + new_input_hi = min(input_hi, _ceil_div(hi - m.offset, m.stride)) elif m.stride < 0: - new_input_lo = max(input_lo, math.ceil((hi - 1 - m.offset) / m.stride)) - new_input_hi = min(input_hi, math.ceil((lo - 1 - m.offset) / m.stride)) + new_input_lo = max(input_lo, _ceil_div(hi - 1 - m.offset, m.stride)) + new_input_hi = min(input_hi, _ceil_div(lo - 1 - m.offset, m.stride)) else: if lo <= m.offset < hi: new_input_lo, new_input_hi = input_lo, input_hi @@ -319,6 +931,11 @@ def _intersect_dimension_map( return new_input_lo, new_input_hi +def _ceil_div(numerator: int, denominator: int) -> int: + """Return ``ceil(numerator / denominator)`` using exact integer arithmetic.""" + return -((-numerator) // denominator) + + def _intersect_orthogonal( transform: IndexTransform, output_domain: IndexDomain ) -> ( @@ -359,12 +976,18 @@ def _intersect_orthogonal( else: # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) - # Orthogonal: the array varies over a single axis (its dependency - # axis, or `input_dimension` for a degenerate length-1 array). Filter - # along that axis and keep the array at full input rank so the - # singleton axes it broadcasts over are preserved. - d = _array_map_dependent_axis(m) - storage = m.offset + m.stride * m.index_array + # Orthogonal: the array varies over a single axis. Filter along that + # axis and keep the array at full input rank so the singleton axes + # it broadcasts over are preserved. + axis = m.dependent_axis + if axis is None: + raise ValueError( + f"output[{out_dim}] is an ArrayMap that varies over no input " + "dimension; a map with no dependency axis should have been " + "collapsed to a ConstantMap" + ) + d = axis + storage = checked_affine(m.offset, m.stride, m.index_array) mask = (storage >= lo) & (storage < hi) # The array is singleton on every axis but `d`, so its mask reduces # to a 1-D vector along `d`. @@ -377,7 +1000,6 @@ def _intersect_orthogonal( index_array=np.asarray(filtered, dtype=np.intp), offset=m.offset, stride=m.stride, - input_dimension=m.input_dimension, ) ) new_max[d] = new_min[d] + int(survivors.size) @@ -404,56 +1026,71 @@ def _intersect_orthogonal( return (result, out_indices) -def _intersect_correlated( +def _intersect_general( transform: IndexTransform, output_domain: IndexDomain, - correlated_dims: list[int], ) -> tuple[IndexTransform, np.ndarray[Any, np.dtype[np.intp]]] | None: - """Intersect a correlated (vindex) transform with an output domain. + """Intersect a transform with any index-array structure, pointwise. - The correlated ArrayMaps share their broadcast (dependency) axes; a broadcast - point survives only if ALL its storage coordinates fall within the output + Every `ArrayMap` — correlated, orthogonal, or several sharing an axis — is + treated as a lookup table over the joint block of non-slice axes: a block + point survives only if ALL its output coordinates fall within the output domain. Residual DimensionMap dimensions are intersected independently (as in the orthogonal case) and preserved, so a partial vindex — e.g. two coordinate arrays over a 3-D array, leaving one slice dimension — resolves correctly. + Treating an orthogonal map this way forfeits its per-axis independence (the + block enumerates the outer product), which is why the pure-orthogonal case + keeps its own resolver. The surviving broadcast axes collapse to a single axis; the returned `out_indices` is the flat scatter index into the (row-major flattened) output buffer, of shape `(surviving_points,) + (residual slice sizes)`. + + A rank-0 broadcast block — every coordinate array a scalar, as after + `vindex[...]` narrowed to a single point — has no axis to collapse and stays + rank 0: the block either survives whole or the intersection is empty. The + result keeps only the residual slice axes and `out_indices` loses its leading + points axis, so the sub-transform's rank still matches the view's. """ - corr_maps = [cast("ArrayMap", transform.output[i]) for i in correlated_dims] - - # Mixing correlated and orthogonal ArrayMaps in one transform is not produced - # by any single selection and is not supported here. - orthogonal_array_dims = [ - i - for i, m in enumerate(transform.output) - if isinstance(m, ArrayMap) and m.input_dimension is not None - ] - if len(orthogonal_array_dims) > 0: - raise NotImplementedError( - "intersecting a transform with both correlated and orthogonal " - "ArrayMaps is not supported" - ) + correlated_dims = [i for i, m in enumerate(transform.output) if isinstance(m, ArrayMap)] + + # The broadcast axes are exactly the input axes no `DimensionMap` binds: a + # correlated transform's input domain is its residual slice axes plus the + # collapsed broadcast block. Deriving them by complement rather than from the + # index array's non-singleton axes keeps this correct when a broadcast axis + # is itself size 1, and when NumPy's placement rule puts the broadcast block + # somewhere other than the front (see `_broadcast_insertion_point`). + bound_axes = {m.input_dimension for m in transform.output if isinstance(m, DimensionMap)} + broadcast_axes = tuple(a for a in range(transform.input_rank) if a not in bound_axes) + broadcast_shape = tuple(transform.domain.shape[a] for a in broadcast_axes) - # The broadcast (dependency) axes are shared by every correlated map; they are - # the leading axes of the domain, followed by the residual slice axes. - broadcast_axes = _array_map_dependency_axes(corr_maps[0].index_array) - broadcast_shape = tuple(corr_maps[0].index_array.shape[a] for a in broadcast_axes) + for out_dim in correlated_dims: + arr_map = cast("ArrayMap", transform.output[out_dim]) + if any(a not in broadcast_axes for a in arr_map.dependency_axes): + # Reachable only by hand-building a transform: no selection binds + # the same input axis to both a slice map and an index array. + raise NotImplementedError( + "intersecting a transform whose index array varies over an " + "input dimension also bound by a slice map is not supported" + ) # Joint bounds mask over the broadcast block. combined: np.ndarray[Any, np.dtype[np.bool_]] | None = None for out_dim in correlated_dims: cm = cast("ArrayMap", transform.output[out_dim]) - storage = cm.offset + cm.stride * cm.index_array + storage = checked_affine(cm.offset, cm.stride, cm.index_array) lo = output_domain.inclusive_min[out_dim] hi = output_domain.exclusive_max[out_dim] mask = (storage >= lo) & (storage < hi) combined = mask if combined is None else (combined & mask) assert combined is not None - # The correlated maps are singleton on every non-broadcast axis, so the mask - # collapses (C-order) to the broadcast block. - combined_bcast = combined.reshape(broadcast_shape) + # Index arrays are singleton on every non-broadcast axis, so the mask + # collapses (C-order) to the broadcast block. A map may also be singleton + # along a block axis it does not vary over (an orthogonal member, or a + # leftover broadcast axis), so the collapsed mask is broadcast up to the + # full block rather than reshaped. + combined_block = combined.reshape(tuple(combined.shape[a] for a in broadcast_axes)) + combined_bcast = np.broadcast_to(combined_block, broadcast_shape) surviving = np.nonzero(combined_bcast.reshape(-1))[0].astype(np.intp) if surviving.size == 0: return None @@ -481,24 +1118,32 @@ def _intersect_correlated( n_points = int(surviving.size) n_slice = len(slice_dims) - corr_values = { - out_dim: cast("ArrayMap", transform.output[out_dim]) - .index_array.reshape(broadcast_shape) - .reshape(-1)[surviving] - for out_dim in correlated_dims - } - - # New domain: the collapsed broadcast axis, then one axis per residual slice. - new_min = [0] - new_max = [n_points] + corr_values: dict[int, np.ndarray[Any, np.dtype[np.intp]]] = {} + for out_dim in correlated_dims: + arr = cast("ArrayMap", transform.output[out_dim]).index_array + block = arr.reshape(tuple(arr.shape[a] for a in broadcast_axes)) + corr_values[out_dim] = np.asarray( + np.ascontiguousarray(np.broadcast_to(block, broadcast_shape)).reshape(-1)[surviving], + dtype=np.intp, + ) + + # A rank-0 broadcast block contributes no axis: the leading `(n_points,)` of + # the domain, of every index array, and of `out_indices` is present only when + # there was a block to collapse. + points_shape = (n_points,) if len(broadcast_shape) > 0 else () + + # New domain: the collapsed broadcast axis if there is one, then one axis per + # residual slice. + new_min = [0] * len(points_shape) + new_max = list(points_shape) new_input_dim_of = {} - for new_axis, (d, nlo, nhi, _full, _m) in enumerate(slice_dims, start=1): + for new_axis, (d, nlo, nhi, _full, _m) in enumerate(slice_dims, start=len(points_shape)): new_min.append(nlo) new_max.append(nhi) new_input_dim_of[d] = new_axis new_domain = IndexDomain(inclusive_min=tuple(new_min), exclusive_max=tuple(new_max)) - corr_shape = (n_points,) + (1,) * n_slice + corr_shape = points_shape + (1,) * n_slice new_output: list[OutputIndexMap] = [] for out_dim, m in enumerate(transform.output): if out_dim in correlated_dims: @@ -523,23 +1168,36 @@ def _intersect_correlated( ) result = IndexTransform(domain=new_domain, output=tuple(new_output)) - # Flat scatter index into the row-major output buffer of shape - # (broadcast points, residual slice sizes...): flat = point * prod(slice) + - # (row-major offset within the slice block). - prod_slice = 1 - for _d, _lo, _hi, full, _m in slice_dims: - prod_slice *= full - out_indices: np.ndarray[Any, np.dtype[np.intp]] = (surviving * prod_slice).reshape( - (n_points,) + (1,) * n_slice + # Flat scatter index into the caller's row-major output buffer, whose shape + # is the *input* domain's shape. The buffer is addressed positionally, so + # this assumes a zero-origin domain — the resolvers normalize with + # `translate_domain_to` before resolving. + # + # Each surviving point is a flat index into the broadcast block; unravel it + # to per-axis coordinates so the buffer stride of each broadcast axis is + # applied at its real position, wherever NumPy's placement rule put it. + domain_shape = transform.domain.shape + buffer_strides = [1] * len(domain_shape) + for axis in range(len(domain_shape) - 2, -1, -1): + buffer_strides[axis] = buffer_strides[axis + 1] * domain_shape[axis + 1] + + point_offsets = np.zeros(n_points, dtype=np.intp) + if len(broadcast_shape) > 0: + for axis, coords_along_axis in zip( + broadcast_axes, np.unravel_index(surviving, broadcast_shape), strict=True + ): + point_offsets = point_offsets + coords_along_axis.astype(np.intp) * buffer_strides[axis] + + n_lead = len(points_shape) + out_indices: np.ndarray[Any, np.dtype[np.intp]] = point_offsets.reshape( + points_shape + (1,) * n_slice ) - running = 1 - for j in range(n_slice - 1, -1, -1): - _d, nlo, nhi, full, _m = slice_dims[j] - coords = np.arange(nlo, nhi, dtype=np.intp) * running - shape = [1] * (1 + n_slice) - shape[1 + j] = coords.size + for j in range(n_slice): + d, nlo, nhi, _full, _m = slice_dims[j] + coords = np.arange(nlo, nhi, dtype=np.intp) * buffer_strides[d] + shape = [1] * (n_lead + n_slice) + shape[n_lead + j] = coords.size out_indices = out_indices + coords.reshape(shape) - running *= full return (result, out_indices.astype(np.intp)) @@ -569,8 +1227,8 @@ def _normalize_basic_selection(selection: Any, ndim: int) -> tuple[int | slice | ellipsis_seen = True num_missing = ndim - n_real result.extend([slice(None)] * num_missing) - elif isinstance(sel, (int, np.integer)): - result.append(int(sel)) + elif (scalar := as_scalar_index(sel)) is not None: + result.append(scalar) elif isinstance(sel, slice) or sel is None: result.append(sel) else: @@ -583,6 +1241,24 @@ def _normalize_basic_selection(selection: Any, ndim: int) -> tuple[int | slice | return tuple(result) +def _positional_slice(pos: int, size: int, step: int) -> slice: + """A NumPy slice selecting `size` elements from `pos`, walking by `step`. + + The stop is `pos + size*step`, except in two cases. An empty selection is + written out explicitly, because the arithmetic form can be a negative stop + that NumPy would read as counting from the end. And a downward walk + reaching the start of the array must stop at `None`, for the same reason: + `slice(6, -1, -1)` selects nothing where `slice(6, None, -1)` selects the + first seven elements in reverse. + """ + if size <= 0: + return slice(0, 0, 1) + stop = pos + size * step + if step < 0 and stop < 0: + return slice(pos, None, step) + return slice(pos, stop, step) + + def _reindex_array( m: ArrayMap, normalized: tuple[int | slice | None, ...], @@ -592,16 +1268,12 @@ def _reindex_array( The array's axes correspond to the transform's input dimensions (0-indexed over the domain shape). Each axis is either a **dependency axis** — the array - genuinely varies with that input dimension — or a **singleton** axis it + varies with that input dimension — or a **singleton** axis it broadcasts over. Integer indexing, slicing, or newaxis is applied to the array only along its dependency axes; a selection on a singleton axis does not touch the array's values (it just narrows or drops that broadcast axis). """ - dependent = set(_array_map_dependency_axes(m.index_array)) - if m.input_dimension is not None: - # Degenerate length-1 orthogonal selection: the recorded axis is a - # dependency even though its size (1) makes it look singleton. - dependent.add(m.input_dimension) + dependent = set(m.dependency_axes) arr = m.index_array # Build a numpy indexing tuple: one entry per old input dimension @@ -633,7 +1305,7 @@ def _reindex_array( # indexed positionally, so shift by the domain origin. start, step, _origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) pos = start - lo - idx.append(slice(pos, pos + size * step, step)) + idx.append(_positional_slice(pos, size, step)) else: # Broadcast axis: preserve the singleton (it still broadcasts # over the narrowed domain), regardless of the slice bounds. @@ -649,62 +1321,29 @@ def _reindex_array( return np.asarray(result, dtype=np.intp) -_FANCY_AFTER_FANCY_MSG = ( - "applying a fancy (orthogonal/vectorized) selection to a view that already " - "has a fancy-indexed axis is not supported (fancy-after-fancy composition): " - "the new coordinates would index a broadcast axis of the existing selection. " - "Materialize the view first with `.result()` and index the array, or reorder " - "the selections so the fancy step is applied last." -) - - -def _guard_fancy_after_fancy(m: ArrayMap, fancy_dims: set[int] | list[int]) -> None: - """Reject a fancy step that lands on a broadcast axis of an existing ArrayMap. - - A new orthogonal/vectorized selection can only be absorbed into an existing - ArrayMap along the axes that map genuinely varies over (its dependency axes, - plus the recorded `input_dimension` for a degenerate length-1 orthogonal - selection). A fancy index targeting any other axis — a singleton axis the map - merely broadcasts over — cannot be reindexed and used to leak a raw NumPy - `IndexError` at resolve time. Raise a clear `NotImplementedError` instead. +def _compose_selection( + transform: IndexTransform, + selection: Any, + mode: Literal["orthogonal", "vectorized"], +) -> IndexTransform: + """Apply an advanced selection to an array-carrying transform by composition. + + The selection is applied to an identity transform over the current domain — + the same code path a fresh transform takes, so the dialect (placement, + bounds, domains) is identical by construction — and the result is chained + onto `transform` with `compose`, which evaluates the existing index arrays + at the new coordinates. This is how a second fancy step lands on *any* axis + of an already-fancy view: axes an existing array varies over, axes it merely + broadcasts along, or a mixture. """ - dependent = set(_array_map_dependency_axes(m.index_array)) - if m.input_dimension is not None: - dependent.add(m.input_dimension) - for d in fancy_dims: - if d < m.index_array.ndim and d not in dependent: - raise NotImplementedError(_FANCY_AFTER_FANCY_MSG) - - -def _reindex_array_oindex( - arr: np.ndarray[Any, np.dtype[np.intp]], - normalized: tuple[Any, ...] | list[Any], - domain: IndexDomain, -) -> np.ndarray[Any, np.dtype[np.intp]]: - """Apply oindex/vindex selection to an existing ArrayMap's index_array. + # Deferred import: `composition` imports this module at import time. - Each old input dimension gets either an array (fancy index that axis) - or a slice applied to the corresponding array axis. - """ - idx: list[Any] = [] - for old_dim, sel in enumerate(normalized): - if old_dim >= arr.ndim: - break - lo = domain.inclusive_min[old_dim] - if isinstance(sel, np.ndarray): - # Values are literal domain coordinates; the stored array is - # indexed positionally, so shift by the domain origin. - idx.append(sel - lo) - elif isinstance(sel, slice): - hi = domain.exclusive_max[old_dim] - start, step, _origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) - pos = start - lo - idx.append(slice(pos, pos + size * step, step)) - else: - idx.append(slice(None)) - - result = arr[tuple(idx)] if idx else arr - return np.asarray(result, dtype=np.intp) + identity = IndexTransform.identity(transform.domain) + if mode == "orthogonal": + outer = _apply_oindex(identity, selection) + else: + outer = _apply_vindex(identity, selection) + return outer.compose(transform) def _apply_basic_indexing(transform: IndexTransform, selection: Any) -> IndexTransform: @@ -791,55 +1430,18 @@ def _apply_basic_indexing(transform: IndexTransform, selection: Any) -> IndexTra else: raise RuntimeError(f"unexpected: dimension {d} not handled") else: - # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) + # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap). + # A result narrowed to a single coordinate collapses to the + # ConstantMap it equals — whether an integer consumed the dependency + # axis or a slice narrowed it to one entry — so a non-empty ArrayMap + # always varies over at least one axis. Nothing here renumbers: the + # array's axes are the new domain's axes by construction. new_arr = _reindex_array(m, normalized, transform.domain) - array_input_dim: int | None = None - if m.input_dimension is not None: - array_input_dim = old_to_new_dim.get(m.input_dimension, m.input_dimension) - new_output.append( - ArrayMap( - index_array=new_arr, - offset=m.offset, - stride=m.stride, - input_dimension=array_input_dim, - ) - ) + new_output.append(array_map_or_constant(new_arr, offset=m.offset, stride=m.stride)) return IndexTransform(domain=new_domain, output=tuple(new_output)) -def _array_map_dependency_axes(index_array: np.ndarray[Any, Any]) -> tuple[int, ...]: - """Return the input axes on which a normalized index array varies. - - Normalized `ArrayMap` index arrays carry the full input rank of their - enclosing transform: an axis the array varies over has its full size, while - an axis the array is independent of is a singleton (size 1). The dependency - axes are therefore exactly the non-singleton axes. An orthogonal (`oindex`) - array depends on a single axis; a vectorized (`vindex`) array depends on all - of the (shared) broadcast axes. - """ - return tuple(axis for axis, size in enumerate(index_array.shape) if size != 1) - - -def _array_map_dependent_axis(m: ArrayMap) -> int: - """Return the single input axis an orthogonal `ArrayMap` varies over. - - Normally this is the array's one non-singleton axis. A degenerate length-1 - orthogonal selection normalizes to an all-singleton shape (its dependency - axes are empty and indistinguishable by shape from a scalar), so - `input_dimension` breaks the tie — it records the axis the map binds. - """ - dep = _array_map_dependency_axes(m.index_array) - if len(dep) == 1: - return dep[0] - if m.input_dimension is not None: - return m.input_dimension - raise ValueError( - f"orthogonal ArrayMap must vary over exactly one axis; got dependency " - f"axes {dep} with input_dimension={m.input_dimension}" - ) - - def _reshape_to_axis( values: np.ndarray[Any, np.dtype[np.intp]], axis: int, ndim: int ) -> np.ndarray[Any, np.dtype[np.intp]]: @@ -889,11 +1491,16 @@ def _normalize_oindex_selection( result.append(sel.astype(np.intp)) elif isinstance(sel, slice): result.append(sel) - elif isinstance(sel, (int, np.integer)): + elif (scalar := as_scalar_index(sel)) is not None: # Convert integer scalars to 1-element arrays for orthogonal indexing - result.append(np.array([int(sel)], dtype=np.intp)) + result.append(np.array([scalar], dtype=np.intp)) elif isinstance(sel, (list, tuple)): - result.append(np.asarray(sel, dtype=np.intp)) + array = np.asarray(sel) + if array.dtype == np.bool_: + (indices,) = np.nonzero(array) + result.append(indices.astype(np.intp)) + else: + result.append(np.asarray(sel, dtype=np.intp)) else: result.append(sel) @@ -908,7 +1515,15 @@ def _apply_oindex(transform: IndexTransform, selection: Any) -> IndexTransform: """Apply orthogonal indexing to an IndexTransform. Each index array is applied independently per dimension (outer product). + + A transform that already carries index arrays takes the composition path + (`_compose_selection`) instead of being rewritten in place, so the new + selection may land on any axis — including axes an existing array merely + broadcasts along. """ + validate_advanced_selection(selection, transform.domain, "orthogonal") + if any(isinstance(m, ArrayMap) for m in transform.output): + return _compose_selection(transform, selection, "orthogonal") normalized = _normalize_oindex_selection(selection, transform.domain.ndim) new_inclusive_min: list[int] = [] @@ -957,22 +1572,13 @@ def _apply_oindex(transform: IndexTransform, selection: Any) -> IndexTransform: d = m.input_dimension if d in dim_array: new_axis = old_to_new_dim[d] - # Normalize to full input rank: the selection varies along its own - # new axis and is singleton on every other axis. The dependency - # axis is then derivable from the shape (a single non-singleton - # axis marks the selection orthogonal / outer-product rather than - # vectorized). `input_dimension` is kept populated as a - # compatibility shim for consumers not yet migrated to the - # shape-derived classifier. + # Normalize to full input rank: the selection varies along its + # own new axis and is singleton on every other axis, so the + # dependency axis is readable from the shape. A single-entry + # selection holds one coordinate and collapses to the + # ConstantMap it equals; its length-1 axis stays in the domain. full_arr = _reshape_to_axis(dim_array[d], new_axis, new_dim_idx) - new_output.append( - ArrayMap( - index_array=full_arr, - offset=m.offset, - stride=m.stride, - input_dimension=new_axis, - ) - ) + new_output.append(array_map_or_constant(full_arr, offset=m.offset, stride=m.stride)) elif d in dim_slice_params: start, step, origin = dim_slice_params[d] new_offset = m.offset + m.stride * (start - step * origin) @@ -986,19 +1592,10 @@ def _apply_oindex(transform: IndexTransform, selection: Any) -> IndexTransform: else: raise RuntimeError(f"unexpected: dimension {d} not handled") else: - # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) - _guard_fancy_after_fancy(m, list(dim_array.keys())) - new_arr = _reindex_array_oindex(m.index_array, normalized, transform.domain) - array_input_dim: int | None = None - if m.input_dimension is not None: - array_input_dim = old_to_new_dim.get(m.input_dimension, m.input_dimension) - new_output.append( - ArrayMap( - index_array=new_arr, - offset=m.offset, - stride=m.stride, - input_dimension=array_input_dim, - ) + # m: ArrayMap — unreachable: array-carrying transforms took the + # composition path at the top of this function. + raise AssertionError( # noqa: TRY004 - unreachable, not a dispatch + "unreachable: ArrayMap transforms are composed" ) return IndexTransform(domain=new_domain, output=tuple(new_output)) @@ -1014,25 +1611,62 @@ def __getitem__(self, selection: Any) -> IndexTransform: return _apply_vindex(self._transform, selection) +def _broadcast_insertion_point(array_dims: Sequence[int], slice_dims: Sequence[int]) -> int: + """Where the broadcast dimensions land, as a count of leading slice dimensions. + + NumPy's advanced-indexing placement rule: when the advanced indices are all + next to each other in the index tuple, the broadcast dimensions are inserted + at the spot they occupied; when a slice separates them, they lead. So + `a[:, i, j]` has shape `(len(a), *broadcast)` while `a[i, :, j]` has shape + `(*broadcast, a.shape[1])`. + + Returns the number of slice dimensions that precede the broadcast block; `0` + means the broadcast dimensions lead. + """ + if len(array_dims) == 0: + return 0 + first, last = array_dims[0], array_dims[-1] + separated = any(first < d < last for d in slice_dims) + if separated: + return 0 + return sum(1 for d in slice_dims if d < first) + + +def _as_boolean_index_array(selection: Any) -> np.ndarray[Any, np.dtype[np.bool_]] | None: + """Return an array-like boolean index as an ndarray, else None.""" + if not isinstance(selection, (np.ndarray, list, tuple)): + return None + array = np.asarray(selection) + if array.dtype != np.bool_: + return None + return array + + +def _selection_axis_count(selection: Any) -> int: + """Return how many input axes one vectorized selection entry consumes.""" + boolean_array = _as_boolean_index_array(selection) + return boolean_array.ndim if boolean_array is not None else 1 + + def _apply_vindex(transform: IndexTransform, selection: Any) -> IndexTransform: """Apply vectorized indexing to an IndexTransform. All array indices are broadcast together. Broadcast dimensions are prepended, followed by non-array (slice) dimensions. + + A transform that already carries index arrays takes the composition path + (`_compose_selection`) instead of being rewritten in place; see + `_apply_oindex`. """ + validate_advanced_selection(selection, transform.domain, "vectorized") + if any(isinstance(m, ArrayMap) for m in transform.output): + return _compose_selection(transform, selection, "vectorized") if not isinstance(selection, tuple): selection = (selection,) - # Expand ellipsis and count consumed dimensions - # Boolean arrays with ndim > 1 consume ndim dims - n_consumed = 0 - for s in selection: - if s is Ellipsis: - continue - if isinstance(s, np.ndarray) and s.dtype == np.bool_ and s.ndim > 1: - n_consumed += s.ndim - else: - n_consumed += 1 + # Expand ellipsis and count consumed dimensions. Boolean masks consume one + # input axis per mask dimension, whether spelled as an ndarray or a list. + n_consumed = sum(_selection_axis_count(s) for s in selection if s is not Ellipsis) ndim = transform.domain.ndim expanded: list[Any] = [] @@ -1043,12 +1677,7 @@ def _apply_vindex(transform: IndexTransform, selection: Any) -> IndexTransform: else: expanded.append(sel) # Count dimensions already consumed by expanded entries - n_expanded_dims = 0 - for sel in expanded: - if isinstance(sel, np.ndarray) and sel.dtype == np.bool_ and sel.ndim > 1: - n_expanded_dims += sel.ndim - else: - n_expanded_dims += 1 + n_expanded_dims = sum(_selection_axis_count(sel) for sel in expanded) while n_expanded_dims < ndim: expanded.append(slice(None)) n_expanded_dims += 1 @@ -1056,15 +1685,16 @@ def _apply_vindex(transform: IndexTransform, selection: Any) -> IndexTransform: # Convert booleans, lists, ints to integer arrays processed: list[np.ndarray[Any, np.dtype[np.intp]] | slice] = [] for sel in expanded: - if isinstance(sel, np.ndarray) and sel.dtype == np.bool_: - indices_tuple = np.nonzero(sel) + boolean_array = _as_boolean_index_array(sel) + if boolean_array is not None: + indices_tuple = np.nonzero(boolean_array) processed.extend(indices.astype(np.intp) for indices in indices_tuple) elif isinstance(sel, np.ndarray): processed.append(sel.astype(np.intp)) elif isinstance(sel, (list, tuple)): processed.append(np.asarray(sel, dtype=np.intp)) - elif isinstance(sel, (int, np.integer)): - processed.append(np.array([int(sel)], dtype=np.intp)) + elif (scalar := as_scalar_index(sel)) is not None: + processed.append(np.array([scalar], dtype=np.intp)) else: processed.append(sel) @@ -1092,27 +1722,30 @@ def _apply_vindex(transform: IndexTransform, selection: Any) -> IndexTransform: broadcast_arrays = [] broadcast_shape = () - # Build new domain: broadcast dims first, then slice dims - new_inclusive_min: list[int] = [] - new_exclusive_max: list[int] = [] - - # Broadcast dimensions - for s in broadcast_shape: - new_inclusive_min.append(0) - new_exclusive_max.append(s) - # Slice dimensions (preserved-domain literal semantics, like basic indexing) slice_dim_params: dict[int, tuple[int, int, int]] = {} + slice_bounds: list[tuple[int, int]] = [] for old_dim in slice_dims: sel = processed[old_dim] assert isinstance(sel, slice) lo = transform.domain.inclusive_min[old_dim] hi = transform.domain.exclusive_max[old_dim] start, step, origin, size = _resolve_slice_ts(sel, old_dim, lo, hi) - new_inclusive_min.append(origin) - new_exclusive_max.append(origin + size) + slice_bounds.append((origin, origin + size)) slice_dim_params[old_dim] = (start, step, origin) + n_before = _broadcast_insertion_point(array_dims, slice_dims) + + # Build the new domain with NumPy's placement rule: the broadcast + # (correlated) dimensions sit where the advanced indices sat when those are + # adjacent, and lead when a slice separates them. + new_inclusive_min = [lo for lo, _ in slice_bounds[:n_before]] + new_exclusive_max = [hi for _, hi in slice_bounds[:n_before]] + new_inclusive_min.extend([0] * len(broadcast_shape)) + new_exclusive_max.extend(broadcast_shape) + new_inclusive_min.extend(lo for lo, _ in slice_bounds[n_before:]) + new_exclusive_max.extend(hi for _, hi in slice_bounds[n_before:]) + new_domain = IndexDomain( inclusive_min=tuple(new_inclusive_min), exclusive_max=tuple(new_exclusive_max), @@ -1139,36 +1772,27 @@ def _apply_vindex(transform: IndexTransform, selection: Any) -> IndexTransform: # dependency axes derived from the shape coincide — the signature # of a pointwise scatter rather than an outer product. broadcast_arr = array_dim_to_broadcast[d] - full_arr = broadcast_arr.reshape(broadcast_shape + (1,) * len(slice_dims)) - new_output.append( - ArrayMap( - index_array=full_arr, - offset=m.offset, - stride=m.stride, - ) + full_arr = broadcast_arr.reshape( + (1,) * n_before + broadcast_shape + (1,) * (len(slice_dims) - n_before) ) + new_output.append(array_map_or_constant(full_arr, offset=m.offset, stride=m.stride)) else: # Slice dim: new coord `origin + k` maps to old `start + k*step` start, step, origin = slice_dim_params[d] new_offset = m.offset + m.stride * (start - step * origin) new_stride = m.stride * step - new_input_dim = n_broadcast_dims + slice_dims.index(d) + position = slice_dims.index(d) + new_input_dim = position if position < n_before else position + n_broadcast_dims new_output.append( DimensionMap( input_dimension=new_input_dim, offset=new_offset, stride=new_stride ) ) else: - # m: ArrayMap (OutputIndexMap = ConstantMap | DimensionMap | ArrayMap) - _guard_fancy_after_fancy(m, array_dims) - new_arr = _reindex_array_oindex(m.index_array, processed, transform.domain) - new_output.append( - ArrayMap( - index_array=new_arr, - offset=m.offset, - stride=m.stride, - input_dimension=m.input_dimension, - ) + # m: ArrayMap — unreachable: array-carrying transforms took the + # composition path at the top of this function. + raise AssertionError( # noqa: TRY004 - unreachable, not a dispatch + "unreachable: ArrayMap transforms are composed" ) return IndexTransform(domain=new_domain, output=tuple(new_output)) @@ -1194,39 +1818,58 @@ def _resolve_slice_ts(sel: slice, dim: int, lo: int, hi: int) -> tuple[int, int, """Resolve a slice against domain `[lo, hi)` with TensorStore semantics. Slice bounds are **literal domain coordinates** — never from-the-end, never - clamped. Rules (each verified against tensorstore 0.1.84): - - - defaults: `start = lo`, `stop = hi`; + clamped. One rule covers both signs of the step (each part verified against + tensorstore 0.1.84, and matching ndsel 1.0-draft.2 section 5.3): + + - defaults follow the direction of travel: `start = lo`, `stop = hi` going + up; `start = hi - 1`, `stop = lo - 1` going down; + - the traversal runs from `start` toward `stop`, which is excluded, so the + source interval is `[start, stop)` going up and `[stop + 1, start + 1)` + going down; - a non-empty interval must be contained in the domain (no clamping — a NumPy-style out-of-range or negative bound is an error, not a shorter or wrapped result); - - an **empty** interval (`start == stop`) is valid anywhere; - - reversed bounds (`start > stop` with positive step) are an error, not - an empty result; - - the result's domain origin is `trunc(start/step)` (rounded toward - zero) and coordinate `origin + k` maps to input `start + k*step`. + - an empty interval is valid anywhere, for either sign; + - an interval running the wrong way (`stop` on the far side of `start` from + the direction of travel) is an error, not an empty result; + - the result's domain origin is `trunc(start/step)` — toward zero, for both + signs — and coordinate `origin + k` maps to input `start + k*step`. + + A negative step normally produces a negative origin: reversing a + zero-origin axis of length 20 gives the domain `[-19, 1)`. The coordinate + frame stays anchored to the source; a caller that needs non-negative + coordinates re-bases explicitly with `translate_domain_to`. Returns `(start, step, origin, size)` in domain coordinates. """ - step = 1 if sel.step is None else sel.step - if step <= 0: - # Negative steps are valid in TensorStore but not yet supported here; - # step 0 is invalid everywhere. - raise IndexError("slice step must be positive") - start = lo if sel.start is None else sel.start - stop = hi if sel.stop is None else sel.stop - if stop < start: + start_bound = None if sel.start is None else require_index(sel.start) + stop_bound = None if sel.stop is None else require_index(sel.stop) + step = 1 if sel.step is None else require_index(sel.step) + if step == 0: + raise IndexError("slice step must not be zero") + if step > 0: + start = lo if start_bound is None else start_bound + stop = hi if stop_bound is None else stop_bound + interval_lo, interval_hi = start, stop + else: + start = hi - 1 if start_bound is None else start_bound + stop = lo - 1 if stop_bound is None else stop_bound + interval_lo, interval_hi = stop + 1, start + 1 + length = interval_hi - interval_lo + if length < 0: raise IndexError( - f"slice interval [{start}, {stop}) with step {step} does not specify " - f"a valid interval for dimension {dim} (start > stop)" + f"slice from {start} to {stop} with step {step} does not specify a " + f"valid interval for dimension {dim}: the derived interval " + f"[{interval_lo}, {interval_hi}) runs the wrong way. An empty " + "selection is spelled stop == start." ) - size = -(-(stop - start) // step) # ceil((stop - start) / step) - if size > 0 and (start < lo or stop > hi): + if length > 0 and (interval_lo < lo or interval_hi > hi): hint = _LITERAL_HINT if (start < 0 or stop < 0) and lo >= 0 else "" raise BoundsCheckError( - f"slice interval [{start}, {stop}) is not contained within domain " - f"[{lo}, {hi}) for dimension {dim}{hint}" + f"slice interval [{interval_lo}, {interval_hi}) is not contained " + f"within domain [{lo}, {hi}) for dimension {dim}{hint}" ) + size = -(-length // abs(step)) # ceil(length / |step|) origin = _trunc_div(start, step) return start, step, origin, size @@ -1268,9 +1911,20 @@ def _validate_array_selection(selection: Any, shape: tuple[int, ...], mode: str) f"(single Boolean array) are supported; got {selection!r}" ) continue - if sel is Ellipsis or isinstance(sel, (int, np.integer)): + if sel is Ellipsis or as_scalar_index(sel) is not None: continue if isinstance(sel, (list, np.ndarray)): + if mode == "orthogonal": + array = np.asarray(sel) + # An orthogonal selection is per-axis, so an integer array names + # coordinates along one axis and can only be one-dimensional. + # Left to the engine, this surfaced much later as a rank + # complaint about an `index_array` the caller never wrote. + if array.dtype.kind in "iu" and array.ndim > 1: + raise IndexError( + f"integer arrays in an orthogonal selection must be " + f"1-dimensional only; got one with {array.ndim} dimensions" + ) continue raise IndexError(f"unsupported selection type for {mode} indexing: {type(sel)!r}") @@ -1282,30 +1936,6 @@ def _validate_basic_selection(selection: Any) -> None: """ items = selection if isinstance(selection, tuple) else (selection,) for s in items: - if s is Ellipsis or isinstance(s, (int, np.integer, slice)): + if s is Ellipsis or isinstance(s, slice) or as_scalar_index(s) is not None: continue raise IndexError(f"unsupported selection type for basic indexing: {type(s)!r}") - - -def selection_to_transform( - selection: Any, - transform: IndexTransform, - mode: Literal["basic", "orthogonal", "vectorized"], -) -> IndexTransform: - """Convert a user selection into a composed IndexTransform. - - Negative indices are treated as literal coordinates (TensorStore convention). - The caller (Array layer) is responsible for converting numpy-style negative - indices before calling this function. - """ - if mode == "basic": - _validate_basic_selection(selection) - return transform[selection] - elif mode == "orthogonal": - _validate_array_selection(selection, transform.domain.shape, mode) - return transform.oindex[selection] - elif mode == "vectorized": - _validate_array_selection(selection, transform.domain.shape, mode) - return transform.vindex[selection] - else: - raise ValueError(f"Unknown mode: {mode!r}") diff --git a/packages/zarr-indexing/tests/conformance/PROVENANCE.md b/packages/zarr-indexing/tests/conformance/PROVENANCE.md index 0a6faef60b..749a2810e7 100644 --- a/packages/zarr-indexing/tests/conformance/PROVENANCE.md +++ b/packages/zarr-indexing/tests/conformance/PROVENANCE.md @@ -5,9 +5,10 @@ The JSON fixtures in this directory (`point.json`, `box.json`, `slice.json`, unmodified**, from the ndsel reference repository. - **Source:** <https://github.com/zarr-developers/ndsel> -- **Branch:** `main` (merge of d-v-b/ndsel#1, `fix/slice-origin-trunc`) -- **Commit:** `c59bc556c` (fixtures byte-identical to the previously vendored - `c132b4c1caa3205830ce35a42502363171f650a7`) +- **Branch:** `main` (merge of d-v-b/ndsel#3, empty `index_array` serialization) +- **Commit:** `49b9e1db1ca93c55f320b025a666367de87a9014` (previously vendored: + `92d6a32df0cd1ac47d548f14f42909a95997cf19`, before that `c59bc556c`, itself + byte-identical to `c132b4c1caa3205830ce35a42502363171f650a7`) - **Path in source:** `conformance/` **Do not edit these files.** They are vendored as-is so that @@ -18,3 +19,21 @@ corpus, re-vendor from a newer ndsel commit and update the commit SHA above. ndsel PR #1 (merged) corrected the `slice` desugaring origin from `floor(a/s)` to `trunc(a/s)` (rounding toward zero), which matches `zarr_indexing`' existing `_trunc_div` semantics. + +ndsel PR #2 (merged) specified negative `step`, which changed two fixtures: + +- `slice.json` gained the negative-step cases (full reverse, `|s| > 1` + non-divisible, negative-coordinate intervals, empty-at-any-coordinate). +- `errors.json` retired `error/negative-step` — the reason code + `negative_step_unsupported` is retired with it — and replaced it with three + `bounds_out_of_order` fixtures pinning that a reversed interval is an error + for either sign of the step, rather than being clamped to empty. + +Re-vendoring those two files and teaching `zarr_indexing.messages` the new +desugaring are one change: the corpus is the definition of correct here, so it +lands in the same commit as the code that satisfies it. + +ndsel PR #3 (merged) specified empty `index_array` serialization, adding two +fixtures to `transform.json`: `normalize` carries an empty `index_array` +verbatim (it is not rewritten to a constant map), while a producer SHOULD +collapse it to a constant output map — which `zarr_indexing.json` already does. diff --git a/packages/zarr-indexing/tests/conformance/errors.json b/packages/zarr-indexing/tests/conformance/errors.json index e5e08bab3c..072acd0af5 100644 --- a/packages/zarr-indexing/tests/conformance/errors.json +++ b/packages/zarr-indexing/tests/conformance/errors.json @@ -1,6 +1,8 @@ [ { "name": "error/step-zero", "input": { "kind": "slice", "start": [0], "stop": [4], "step": [0] }, "error": "step_zero" }, - { "name": "error/negative-step", "input": { "kind": "slice", "start": [9], "stop": [0], "step": [-2] }, "error": "negative_step_unsupported" }, + { "name": "error/slice-reversed-interval-unit-step", "input": { "kind": "slice", "start": [9], "stop": [0] }, "error": "bounds_out_of_order" }, + { "name": "error/slice-reversed-interval-positive-step", "input": { "kind": "slice", "start": [9], "stop": [0], "step": [2] }, "error": "bounds_out_of_order" }, + { "name": "error/slice-reversed-interval-negative-step", "input": { "kind": "slice", "start": [5], "stop": [6], "step": [-1] }, "error": "bounds_out_of_order" }, { "name": "error/multiple-upper-bounds", "input": { "kind": "box", "shape": [3], "exclusive_max": [3] }, "error": "multiple_upper_bounds" }, { "name": "error/rank-mismatch", "input": { "kind": "slice", "start": [0, 0], "stop": [4] }, "error": "rank_mismatch" }, { "name": "error/unknown-kind", "input": { "kind": "bogus" }, "error": "unknown_kind" }, diff --git a/packages/zarr-indexing/tests/conformance/slice.json b/packages/zarr-indexing/tests/conformance/slice.json index 2f1a0694ce..959ebc6247 100644 --- a/packages/zarr-indexing/tests/conformance/slice.json +++ b/packages/zarr-indexing/tests/conformance/slice.json @@ -57,5 +57,100 @@ "input_labels": [""], "output": [ { "offset": -2, "stride": 3, "input_dimension": 0 } ] } + }, + { + "name": "slice/negative-step-full-reverse", + "input": { "kind": "slice", "start": [19], "stop": [-1], "step": [-1] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-19], "input_exclusive_max": [1], + "input_labels": [""], + "output": [ { "offset": 0, "stride": -1, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-divisible-span", + "input": { "kind": "slice", "start": [15], "stop": [5], "step": [-2] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-7], "input_exclusive_max": [-2], + "input_labels": [""], + "output": [ { "offset": 1, "stride": -2, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-nondivisible-span", + "input": { "kind": "slice", "start": [15], "stop": [5], "step": [-4] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-3], "input_exclusive_max": [0], + "input_labels": [""], + "output": [ { "offset": 3, "stride": -4, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-down-to-zero", + "input": { "kind": "slice", "start": [9], "stop": [0], "step": [-2] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-4], "input_exclusive_max": [1], + "input_labels": [""], + "output": [ { "offset": 1, "stride": -2, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-negative-interval", + "input": { "kind": "slice", "start": [-1], "stop": [-6], "step": [-2] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [0], "input_exclusive_max": [3], + "input_labels": [""], + "output": [ { "offset": -1, "stride": -2, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-negative-interval-step3", + "input": { "kind": "slice", "start": [-2], "stop": [-9], "step": [-3] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [0], "input_exclusive_max": [3], + "input_labels": [""], + "output": [ { "offset": -2, "stride": -3, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-single-point", + "input": { "kind": "slice", "start": [5], "stop": [4], "step": [-3] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-1], "input_exclusive_max": [0], + "input_labels": [""], + "output": [ { "offset": 2, "stride": -3, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-empty", + "input": { "kind": "slice", "start": [5], "stop": [5], "step": [-1] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-5], "input_exclusive_max": [-5], + "input_labels": [""], + "output": [ { "offset": 0, "stride": -1, "input_dimension": 0 } ] + } + }, + { + "name": "slice/negative-step-keeps-labels", + "input": { "kind": "slice", "start": [19], "stop": [-1], "step": [-1], "labels": ["x"] }, + "normalized": { + "input_rank": 1, "input_inclusive_min": [-19], "input_exclusive_max": [1], + "input_labels": ["x"], + "output": [ { "offset": 0, "stride": -1, "input_dimension": 0 } ] + } + }, + { + "name": "slice/2d-mixed-sign-step", + "input": { "kind": "slice", "start": [19, 0], "stop": [-1, 10], "step": [-1, 2] }, + "normalized": { + "input_rank": 2, + "input_inclusive_min": [-19, 0], + "input_exclusive_max": [1, 5], + "input_labels": ["", ""], + "output": [ + { "offset": 0, "stride": -1, "input_dimension": 0 }, + { "offset": 0, "stride": 2, "input_dimension": 1 } + ] + } } ] diff --git a/packages/zarr-indexing/tests/conformance/transform.json b/packages/zarr-indexing/tests/conformance/transform.json index f26157aaab..3d12fe3352 100644 --- a/packages/zarr-indexing/tests/conformance/transform.json +++ b/packages/zarr-indexing/tests/conformance/transform.json @@ -53,5 +53,42 @@ { "offset": 0, "stride": 1, "index_array": [1, 2, 3], "index_array_bounds": ["-inf", "+inf"] } ] } + }, + { + "name": "transform/empty-index-array-carried-verbatim", + "input": { + "kind": "transform", + "input_inclusive_min": [0, 0], + "input_exclusive_max": [0, 3], + "output": [{ "index_array": [] }, { "input_dimension": 1 }] + }, + "normalized": { + "input_rank": 2, "input_inclusive_min": [0, 0], "input_exclusive_max": [0, 3], + "input_labels": ["", ""], + "output": [ + { "offset": 0, "stride": 1, "index_array": [], "index_array_bounds": ["-inf", "+inf"] }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + } + }, + { + "name": "transform/empty-index-array-is-idempotent", + "input": { + "input_rank": 2, "input_inclusive_min": [0, 0], "input_exclusive_max": [0, 3], + "input_labels": ["", ""], + "kind": "transform", + "output": [ + { "offset": 0, "stride": 1, "index_array": [], "index_array_bounds": ["-inf", "+inf"] }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + }, + "normalized": { + "input_rank": 2, "input_inclusive_min": [0, 0], "input_exclusive_max": [0, 3], + "input_labels": ["", ""], + "output": [ + { "offset": 0, "stride": 1, "index_array": [], "index_array_bounds": ["-inf", "+inf"] }, + { "offset": 0, "stride": 1, "input_dimension": 1 } + ] + } } ] diff --git a/packages/zarr-indexing/tests/test_chunk_resolution.py b/packages/zarr-indexing/tests/test_chunk_resolution.py index 0738384e2b..fbd779f463 100644 --- a/packages/zarr-indexing/tests/test_chunk_resolution.py +++ b/packages/zarr-indexing/tests/test_chunk_resolution.py @@ -1,521 +1,598 @@ from __future__ import annotations -from typing import TYPE_CHECKING +from typing import Any import numpy as np -from zarr.core.chunk_grids import ChunkGrid, FixedDimension, VaryingDimension - -from zarr_indexing import chunk_resolution -from zarr_indexing.chunk_resolution import iter_chunk_transforms, sub_transform_to_selections +import pytest +from hypothesis import assume, given +from hypothesis import strategies as st + +import zarr_indexing +from zarr_indexing import ( + ChunkGrid, + ChunkPlan, + ChunkProjection, + FixedDimension, + VaryingDimension, + chunk_resolution, + plan_chunks, +) from zarr_indexing.domain import IndexDomain +from zarr_indexing.grid import dimension_grids_from_chunks from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap from zarr_indexing.transform import IndexTransform -if TYPE_CHECKING: - import pytest - - -class TestChunkResolutionIdentity: - def test_single_chunk(self) -> None: - """Array fits in one chunk.""" - t = IndexTransform.from_shape((10,)) - grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=10),)) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 1 - coords, sub_t, _ = results[0] - assert coords == (0,) - assert sub_t.domain.shape == (10,) - - def test_multiple_chunks_1d(self) -> None: - """1D array spanning 3 chunks.""" - t = IndexTransform.from_shape((30,)) - grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=30),)) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 3 - coords_list = [r[0] for r in results] - assert (0,) in coords_list - assert (1,) in coords_list - assert (2,) in coords_list - - def test_multiple_chunks_2d(self) -> None: - """2D array spanning 2x3 chunks.""" - t = IndexTransform.from_shape((20, 30)) - grid = ChunkGrid( - dimensions=( - FixedDimension(size=10, extent=20), - FixedDimension(size=10, extent=30), + +def _storage_of(transform: IndexTransform, point: tuple[int, ...]) -> tuple[int, ...]: + """Evaluate the three map forms at one point, independently of planning.""" + result: list[int] = [] + for output_map in transform.output: + if isinstance(output_map, ConstantMap): + result.append(output_map.offset) + elif isinstance(output_map, DimensionMap): + result.append(output_map.offset + output_map.stride * point[output_map.input_dimension]) + else: + index = tuple( + 0 + if output_map.index_array.shape[axis] == 1 + else point[axis] - transform.domain.inclusive_min[axis] + for axis in range(output_map.index_array.ndim) ) - ) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 6 - coords_list = [r[0] for r in results] - assert (0, 0) in coords_list - assert (1, 2) in coords_list - - -class TestChunkResolutionSliced: - def test_slice_within_chunk(self) -> None: - """Slice that falls within a single chunk.""" - # Chunk resolution consumes zero-origin transforms: the I/O layer - # normalizes preserved (user-facing) domains via translate_domain_to - # before resolving, so mirror that contract here. - t = IndexTransform.from_shape((100,))[5:8].translate_domain_to((0,)) - grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=100),)) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 1 - coords, sub_t, _ = results[0] - assert coords == (0,) - assert isinstance(sub_t.output[0], DimensionMap) - assert sub_t.output[0].offset == 5 - - def test_slice_across_chunks(self) -> None: - """Slice that spans two chunks.""" - t = IndexTransform.from_shape((100,))[8:15] - grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=100),)) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 2 - coords_list = [r[0] for r in results] - assert (0,) in coords_list - assert (1,) in coords_list - - -class TestChunkResolutionConstant: - def test_integer_index(self) -> None: - """Integer index produces constant map — single chunk per constant dim.""" - t = IndexTransform.from_shape((100, 100))[25, :] - grid = ChunkGrid( - dimensions=( - FixedDimension(size=10, extent=100), - FixedDimension(size=10, extent=100), + result.append( + output_map.offset + output_map.stride * int(output_map.index_array[index]) ) + return tuple(result) + + +def _points(domain: IndexDomain) -> list[tuple[int, ...]]: + """Enumerate a small finite domain in its own coordinates.""" + return [ + tuple( + coordinate + origin + for coordinate, origin in zip(position, domain.inclusive_min, strict=True) ) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 10 - for coords, _, _ in results: - assert coords[0] == 2 - - -class TestChunkResolutionArray: - def test_array_index(self) -> None: - """Array index map — chunks determined by array values.""" - idx = np.array([5, 15, 25], dtype=np.intp) - t = IndexTransform( - domain=IndexDomain.from_shape((3,)), - output=(ArrayMap(index_array=idx),), + for position in np.ndindex(*domain.shape) + ] + + +def _count_intersect_calls(monkeypatch: pytest.MonkeyPatch) -> dict[str, int]: + """Count real intersections to protect touched-only candidate enumeration.""" + calls = {"n": 0} + original = IndexTransform.intersect + + def counting(self: IndexTransform, output_domain: IndexDomain) -> object: + calls["n"] += 1 + return original(self, output_domain) + + monkeypatch.setattr(IndexTransform, "intersect", counting) + return calls + + +def test_basic_plan_is_reiterable_and_projects_both_spaces() -> None: + """A plan can be revisited without losing either side of each projection.""" + transform = IndexTransform.from_shape((6,))[1:6] + grids = dimension_grids_from_chunks((3,), (6,)) + + plan = plan_chunks(transform, grids) + first = list(plan) + second = list(plan.projections()) + + assert isinstance(plan, ChunkPlan) + assert all(isinstance(projection, ChunkProjection) for projection in first) + assert [projection.chunk_coords for projection in first] == [(0,), (1,)] + assert [projection.chunk_domain for projection in first] == [ + IndexDomain((0,), (3,)), + IndexDomain((3,), (6,)), + ] + assert [projection.coverage for projection in first] == ["partial", "full"] + assert first == second + assert all( + projection.chunk_transform.domain == projection.cell_transform.domain + for projection in first + ) + assert all(projection.chunk_transform.domain.origin == (0,) for projection in first) + + +def test_projection_requires_one_shared_synthetic_domain() -> None: + """Paired transforms with different cell domains are rejected as incoherent.""" + with pytest.raises(ValueError, match="must share an input domain"): + ChunkProjection( + chunk_coords=(0,), + chunk_domain=IndexDomain.from_shape((3,)), + chunk_transform=IndexTransform.identity(IndexDomain.from_shape((2,))), + cell_transform=IndexTransform.identity(IndexDomain.from_shape((1,))), + coverage="partial", + ) + + +def test_projection_plan_is_the_only_public_chunk_resolution_surface() -> None: + """The greenfield API does not retain tuple or NumPy-selector bridges.""" + assert {"ChunkCoverage", "ChunkPlan", "ChunkProjection", "plan_chunks"} <= set( + zarr_indexing.__all__ + ) + assert "iter_chunk_transforms" not in zarr_indexing.__all__ + assert "sub_transform_to_selections" not in zarr_indexing.__all__ + + +def test_plan_rejects_grid_rank_different_from_transform_output_rank() -> None: + """A missing storage grid dimension is rejected before iteration.""" + transform = IndexTransform.from_shape((2, 3)) + + with pytest.raises(ValueError, match="1 grids for output rank 2"): + plan_chunks(transform, dimension_grids_from_chunks((2,), (2,))) + + +@pytest.mark.parametrize( + ("transform", "expected"), + [ + (IndexTransform.from_shape((5,)), ["full", "full"]), + (IndexTransform.from_shape((5,))[::-1], ["full", "full"]), + (IndexTransform.from_shape((5,))[::2], ["partial", "partial"]), + (IndexTransform.from_shape((5,))[2], ["partial"]), + ( + IndexTransform.from_shape((5,)).oindex[np.array([0, 1, 2, 3, 4])], + ["unknown", "unknown"], + ), + ], + ids=["clipped-edge", "reverse", "strided", "scalar", "fancy-is-conservative"], +) +def test_coverage_classification(transform: IndexTransform, expected: list[str]) -> None: + """Coverage is exact for affine requests and conservative for gathers.""" + grids = dimension_grids_from_chunks((3,), (5,)) + + assert [projection.coverage for projection in plan_chunks(transform, grids)] == expected + + +def test_repeated_input_dependency_is_not_full_coverage() -> None: + transform = IndexTransform( + domain=IndexDomain.from_shape((2,)), + output=(DimensionMap(input_dimension=0), DimensionMap(input_dimension=0)), + ) + grids = dimension_grids_from_chunks((2, 2), (2, 2)) + + assert [projection.coverage for projection in plan_chunks(transform, grids)] == ["partial"] + + +def test_unused_input_axis_is_not_full_coverage() -> None: + transform = IndexTransform( + domain=IndexDomain.from_shape((2, 2)), + output=(DimensionMap(input_dimension=0),), + ) + grids = dimension_grids_from_chunks((2,), (2,)) + + assert [projection.coverage for projection in plan_chunks(transform, grids)] == ["partial"] + + +@pytest.mark.parametrize( + ("transform", "grids"), + [ + ( + IndexTransform.from_shape((2, 3)), + dimension_grids_from_chunks((2, 3), (2, 3)), + ), + ( + IndexTransform( + domain=IndexDomain.from_shape((2, 3)), + output=(DimensionMap(input_dimension=1), DimensionMap(input_dimension=0)), + ), + dimension_grids_from_chunks((3, 2), (3, 2)), + ), + ( + IndexTransform.from_shape((2, 3))[::-1, ::-1], + dimension_grids_from_chunks((2, 3), (2, 3)), + ), + ( + IndexTransform( + domain=IndexDomain((4, 7), (6, 10)), + output=( + DimensionMap(input_dimension=0, offset=-4), + DimensionMap(input_dimension=1, offset=-7), + ), + ), + dimension_grids_from_chunks((2, 3), (2, 3)), + ), + ], + ids=["identity", "axis-permutation", "reversal", "translated-unit-affine"], +) +def test_bijective_unit_affine_transforms_retain_full_coverage( + transform: IndexTransform, grids: tuple[Any, ...] +) -> None: + assert [projection.coverage for projection in plan_chunks(transform, grids)] == ["full"] + + +def test_rank_zero_transform_has_full_coverage() -> None: + transform = IndexTransform.identity(IndexDomain((), ())) + + assert [projection.coverage for projection in plan_chunks(transform, ())] == ["full"] + + +@pytest.mark.parametrize( + ("transform", "grids", "expected_coords"), + [ + ( + IndexTransform.from_shape((30,)), + dimension_grids_from_chunks((10,), (30,)), + [(0,), (1,), (2,)], + ), + ( + IndexTransform.from_shape((20, 30)), + dimension_grids_from_chunks((10, 10), (20, 30)), + [(i, j) for i in range(2) for j in range(3)], + ), + ( + IndexTransform.from_shape((100, 100))[25, :], + dimension_grids_from_chunks((10, 10), (100, 100)), + [(2, j) for j in range(10)], + ), + ( + IndexTransform.from_shape((100,))[8:15], + dimension_grids_from_chunks((10,), (100,)), + [(0,), (1,)], + ), + ], + ids=["one-dimensional", "two-dimensional", "constant-map", "slice"], +) +def test_affine_plans_touch_the_expected_chunks( + transform: IndexTransform, + grids: tuple[Any, ...], + expected_coords: list[tuple[int, ...]], +) -> None: + """Identity, constant, and sliced transforms enumerate literal grid cells.""" + assert [projection.chunk_coords for projection in plan_chunks(transform, grids)] == ( + expected_coords + ) + + +@pytest.mark.parametrize( + ("transform", "grids"), + [ + ( + IndexTransform.from_shape((6,)).oindex[np.array([4, 0, 4, 2])], + dimension_grids_from_chunks((3,), (6,)), + ), + ( + IndexTransform.from_shape((4, 5)).oindex[np.array([3, 0]), np.array([4, 1, 1])], + dimension_grids_from_chunks(((1, 3), (2, 3)), (4, 5)), + ), + ( + IndexTransform.from_shape((2, 4, 5)).vindex[ + ..., np.array([3, 0, 3]), np.array([4, 1, 1]) + ], + dimension_grids_from_chunks((1, 2, 3), (2, 4, 5)), + ), + ], + ids=["repeated-oindex", "irregular-oindex", "vindex-with-residual"], +) +def test_projection_invariants_for_fancy_selections( + transform: IndexTransform, grids: tuple[Any, ...] +) -> None: + """Both transforms agree pointwise and cell ranges tile request space once.""" + plan = plan_chunks(transform, grids) + request_points: list[tuple[int, ...]] = [] + + for projection in plan: + assert projection.coverage == "unknown" + assert projection.chunk_transform.domain == projection.cell_transform.domain + for cell_point in _points(projection.cell_transform.domain): + request_point = _storage_of(projection.cell_transform, cell_point) + chunk_point = _storage_of(projection.chunk_transform, cell_point) + storage_point = _storage_of(plan.transform, request_point) + chunk_origin = projection.chunk_domain.inclusive_min + assert chunk_point == tuple( + value - origin for value, origin in zip(storage_point, chunk_origin, strict=True) + ) + assert all( + 0 <= value < extent + for value, extent in zip(chunk_point, projection.chunk_domain.shape, strict=True) + ) + request_points.append(request_point) + + assert sorted(request_points) == sorted(_points(transform.domain)) + + +@pytest.mark.parametrize( + "grid", + [ + pytest.param(FixedDimension(size=2, extent=4), id="fixed"), + pytest.param(VaryingDimension(edges=(1, 3), extent=4), id="varying"), + ], +) +def test_orthogonal_array_map_plan_rejects_coordinate_below_grid(grid: Any) -> None: + transform = IndexTransform( + domain=IndexDomain.from_shape((2,)), + output=(ArrayMap(np.array([-1, 1], dtype=np.intp)),), + ) + + # The sorted 1-D fast path reports the first offending coordinate. + with pytest.raises(IndexError, match=r"index -1 is out of bounds"): + list(plan_chunks(transform, (grid,))) + + +@pytest.mark.parametrize( + "grid", + [ + pytest.param(FixedDimension(size=2, extent=4), id="fixed"), + pytest.param(VaryingDimension(edges=(1, 3), extent=4), id="varying"), + ], +) +def test_orthogonal_array_map_plan_rejects_coordinate_above_grid(grid: Any) -> None: + transform = IndexTransform( + domain=IndexDomain.from_shape((2,)), + output=(ArrayMap(np.array([1, 4], dtype=np.intp)),), + ) + + # The sorted 1-D fast path reports the first offending coordinate. + with pytest.raises(IndexError, match=r"index 4 is out of bounds"): + list(plan_chunks(transform, (grid,))) + + +def test_nonempty_identity_plan_rejects_zero_size_fixed_dimension() -> None: + transform = IndexTransform.from_shape((4,)) + + with pytest.raises(ValueError, match="size must be > 0 when extent is nonzero"): + list(plan_chunks(transform, (FixedDimension(size=0, extent=4),))) + + +@given( + origin=st.integers(min_value=-4, max_value=4), + extent=st.integers(min_value=0, max_value=8), + stride=st.integers(min_value=-3, max_value=3), +) +def test_affine_projection_pairs_reconstruct_independent_source_coordinates( + origin: int, extent: int, stride: int +) -> None: + """Bounded literal-domain examples preserve every request/storage pair.""" + anchor = extent - 1 if stride < 0 else 0 + offset = anchor - stride * origin + expected_pairs = [ + ((coordinate,), (source_coordinate,)) + for coordinate in range(origin, origin + extent) + if 0 <= (source_coordinate := offset + stride * coordinate) < extent + ] + assume(expected_pairs) + + unrestricted = IndexTransform( + domain=IndexDomain((origin,), (origin + extent,)), + output=(DimensionMap(input_dimension=0, offset=offset, stride=stride),), + ) + intersection = unrestricted.intersect(IndexDomain.from_shape((extent,))) + assume(intersection is not None) + transform, _ = intersection + grids = dimension_grids_from_chunks((min(3, extent),), (extent,)) + + reconstructed_pairs = [ + ( + _storage_of(projection.cell_transform, cell_coordinate), + tuple( + local_coordinate + chunk_origin + for local_coordinate, chunk_origin in zip( + _storage_of(projection.chunk_transform, cell_coordinate), + projection.chunk_domain.inclusive_min, + strict=True, + ) + ), ) - grid = ChunkGrid(dimensions=(FixedDimension(size=10, extent=30),)) - results = list(iter_chunk_transforms(t, grid._dimensions)) - coords_list = [r[0] for r in results] - assert (0,) in coords_list - assert (1,) in coords_list - assert (2,) in coords_list + for projection in plan_chunks(transform, grids) + for cell_coordinate in _points(projection.cell_transform.domain) + ] + + assert sorted(reconstructed_pairs) == sorted(expected_pairs) + + +def test_correlated_projection_preserves_nonzero_request_coordinates() -> None: + base = IndexTransform.identity(IndexDomain((2, 5), (4, 8))) + transform = base.vindex[np.array([2, 3], dtype=np.intp), :] + grids = dimension_grids_from_chunks((2, 4), (4, 8)) + + points = [ + transform.apply(projection.cell_transform.apply(cell)) + for projection in plan_chunks(transform, grids) + for cell in _points(projection.cell_transform.domain) + ] + + assert sorted(points) == [(2, 5), (2, 6), (2, 7), (3, 5), (3, 6), (3, 7)] + + +def test_correlated_projection_preserves_translated_advanced_axis_coordinates() -> None: + transform = ( + IndexTransform.from_shape((4,)) + .vindex[np.array([0, 3], dtype=np.intp)] + .translate_domain_by((5,)) + ) + grids = dimension_grids_from_chunks((2,), (4,)) + + request_points = [ + projection.cell_transform.apply(cell) + for projection in plan_chunks(transform, grids) + for cell in _points(projection.cell_transform.domain) + ] + + assert sorted(request_points) == [(5,), (6,)] + + +def test_empty_request_has_no_projections() -> None: + """An empty fancy selection does not fabricate a touched chunk.""" + transform = IndexTransform.from_shape((10,)).oindex[np.array([], dtype=np.intp)] + grids = dimension_grids_from_chunks((3,), (10,)) + + assert list(plan_chunks(transform, grids)) == [] -class TestChunkResolutionSorted1D: - def test_matches_general_resolution_for_randomized_sorted_selections( +class TestSortedOneDimensionalPlan: + def test_matches_general_resolution_for_randomized_selections( self, monkeypatch: pytest.MonkeyPatch ) -> None: - """Direct partitioning matches the original resolver across varied inputs.""" + """The direct sorted path has the same paired transforms as intersection.""" rng = np.random.default_rng(0) grids = ( ChunkGrid(dimensions=(FixedDimension(size=7, extent=30),)), ChunkGrid(dimensions=(VaryingDimension(edges=(3, 4, 8, 5, 10), extent=30),)), ) - for grid in grids: for _ in range(50): - idx = np.sort(rng.integers(0, 30, size=int(rng.integers(1, 80)))).astype(np.intp) - transform = IndexTransform.from_shape((30,)).vindex[idx] - direct = list(iter_chunk_transforms(transform, grid._dimensions)) - + indices = np.sort(rng.integers(0, 30, size=int(rng.integers(1, 80)))).astype( + np.intp + ) + transform = IndexTransform.from_shape((30,)).vindex[indices] + direct = list(plan_chunks(transform, grid.dimensions)) with monkeypatch.context() as context: context.setattr( chunk_resolution, - "_one_dimensional_correlated_array_map", + "_one_dimensional_array_map", lambda _transform: None, ) - general = list(iter_chunk_transforms(transform, grid._dimensions)) + general = list(plan_chunks(transform, grid.dimensions)) + assert direct == general - assert [result[0] for result in direct] == [result[0] for result in general] - for direct_result, general_result in zip(direct, general, strict=True): - _, direct_t, direct_out = direct_result - _, general_t, general_out = general_result - assert direct_t.domain == general_t.domain - - direct_chunk_sel, direct_out_sel, direct_drop = sub_transform_to_selections( - direct_t, direct_out - ) - general_chunk_sel, general_out_sel, general_drop = sub_transform_to_selections( - general_t, general_out - ) - assert direct_drop == general_drop - np.testing.assert_array_equal(direct_chunk_sel[0], general_chunk_sel[0]) - np.testing.assert_array_equal(direct_out_sel[0], general_out_sel[0]) - - def test_sorted_vindex_partitions_chunks_without_intersection( - self, monkeypatch: pytest.MonkeyPatch - ) -> None: - """Sorted vectorized coordinates are sliced directly per touched chunk.""" - idx = np.array([0, 3, 4, 4, 9, 11], dtype=np.intp) - t = IndexTransform.from_shape((12,)).vindex[idx] + def test_sorted_coordinates_bypass_intersection(self, monkeypatch: pytest.MonkeyPatch) -> None: + """Sorted coordinates partition directly at touched chunk boundaries.""" + transform = IndexTransform.from_shape((12,)).vindex[ + np.array([0, 3, 4, 4, 9, 11], dtype=np.intp) + ] grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=12),)) - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert [result[0] for result in results] == [(0,), (1,), (2,)] + projections = list(plan_chunks(transform, grid.dimensions)) + + assert [projection.chunk_coords for projection in projections] == [(0,), (1,), (2,)] assert calls["n"] == 0 + assert [ + [ + _storage_of(projection.cell_transform, point)[0] + for point in _points(projection.cell_transform.domain) + ] + for projection in projections + ] == [[0, 1], [2, 3], [4, 5]] + + def test_unsorted_coordinates_use_intersection(self, monkeypatch: pytest.MonkeyPatch) -> None: + """Unsorted coordinates retain the general intersection path.""" + transform = IndexTransform.from_shape((12,)).vindex[np.array([9, 0, 4], dtype=np.intp)] + grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=12),)) + calls = _count_intersect_calls(monkeypatch) - expected_chunk_indices = ([0, 3], [0, 0], [1, 3]) - expected_out_indices = ([0, 1], [2, 3], [4, 5]) - for result, expected_chunk, expected_out in zip( - results, expected_chunk_indices, expected_out_indices, strict=True - ): - _, sub_t, out_indices = result - chunk_sel, out_sel, drop_axes = sub_transform_to_selections(sub_t, out_indices) - np.testing.assert_array_equal(chunk_sel[0], expected_chunk) - np.testing.assert_array_equal(out_sel[0], expected_out) - assert drop_axes == () - - def test_sorted_array_map_preserves_offset_and_stride(self) -> None: - """Storage partitioning retains the ArrayMap's offset and stride.""" - t = IndexTransform( - domain=IndexDomain.from_shape((3,)), - output=( - ArrayMap( - index_array=np.array([0, 1, 2], dtype=np.intp), - offset=1, - stride=3, - ), - ), - ) - grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=8),)) - - results = list(iter_chunk_transforms(t, grid._dimensions)) - - assert [result[0] for result in results] == [(0,), (1,)] - expected_chunk_indices = ([1], [0, 3]) - expected_out_indices = ([0], [1, 2]) - for result, expected_chunk, expected_out in zip( - results, expected_chunk_indices, expected_out_indices, strict=True - ): - _, sub_t, out_indices = result - chunk_sel, out_sel, _ = sub_transform_to_selections(sub_t, out_indices) - np.testing.assert_array_equal(chunk_sel[0], expected_chunk) - np.testing.assert_array_equal(out_sel[0], expected_out) - - def test_sorted_vindex_with_varying_chunks(self) -> None: - """Touched-boundary searches also support a non-uniform 1-D grid.""" - idx = np.array([0, 1, 2, 3, 5, 9], dtype=np.intp) - t = IndexTransform.from_shape((10,)).vindex[idx] - grid = ChunkGrid(dimensions=(VaryingDimension(edges=(2, 3, 5), extent=10),)) - - results = list(iter_chunk_transforms(t, grid._dimensions)) - - assert [result[0] for result in results] == [(0,), (1,), (2,)] - expected_chunk_indices = ([0, 1], [0, 1], [0, 4]) - for result, expected_chunk in zip(results, expected_chunk_indices, strict=True): - _, sub_t, out_indices = result - chunk_sel, _, _ = sub_transform_to_selections(sub_t, out_indices) - np.testing.assert_array_equal(chunk_sel[0], expected_chunk) - - def test_sorted_vindex_with_zero_sized_dimension_uses_general_resolution( - self, monkeypatch: pytest.MonkeyPatch - ) -> None: - """A zero-sized grid cannot be partitioned by touched boundaries.""" - t = IndexTransform.from_shape((10,)).vindex[np.array([1], dtype=np.intp)] - grid = ChunkGrid(dimensions=(FixedDimension(size=0, extent=10),)) + projections = list(plan_chunks(transform, grid.dimensions)) - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) + assert [projection.chunk_coords for projection in projections] == [(0,), (1,), (2,)] + assert calls["n"] == 3 - assert results == [] - assert calls["n"] == 1 - def test_unsorted_vindex_uses_general_resolution(self, monkeypatch: pytest.MonkeyPatch) -> None: - """Unsorted coordinates continue through the general intersection logic.""" - t = IndexTransform.from_shape((12,)).vindex[np.array([9, 0, 4], dtype=np.intp)] - grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=12),)) +class CountingUnitGrid: + """A real unit grid that counts every planner-grid operation.""" - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) + def __init__(self, extent: int) -> None: + self._grid = FixedDimension(size=1, extent=extent) + self.calls = 0 - assert [result[0] for result in results] == [(0,), (1,), (2,)] - assert calls["n"] == 3 + def index_to_chunk(self, idx: int) -> int: + self.calls += 1 + return self._grid.index_to_chunk(idx) - def test_sorted_oindex_uses_general_resolution(self, monkeypatch: pytest.MonkeyPatch) -> None: - """Orthogonal ArrayMaps retain their existing domain-aware resolution.""" - t = IndexTransform.from_shape((12,)).oindex[np.array([0, 4, 9], dtype=np.intp)] - grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=12),)) + def chunk_offset(self, chunk_ix: int) -> int: + self.calls += 1 + return self._grid.chunk_offset(chunk_ix) - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) + def chunk_size(self, chunk_ix: int) -> int: + self.calls += 1 + return self._grid.chunk_size(chunk_ix) - assert [result[0] for result in results] == [(0,), (1,), (2,)] - assert calls["n"] == 3 + def indices_to_chunks( + self, indices: np.ndarray[Any, np.dtype[np.intp]] + ) -> np.ndarray[Any, np.dtype[np.intp]]: + self.calls += 1 + return self._grid.indices_to_chunks(indices) -def _count_intersect_calls(monkeypatch: pytest.MonkeyPatch) -> dict[str, int]: - """Wrap `IndexTransform.intersect` with a call counter. +def test_sparse_affine_plan_does_not_visit_intervening_chunks() -> None: + grid = CountingUnitGrid(extent=100_001) + transform = IndexTransform.from_shape((100_001,))[::100_000] - Returns a mutable dict whose `"n"` entry is the number of times - `intersect` is invoked. Used to assert that candidate-chunk enumeration is - proportional to the *touched* chunks, not the dense bounding box between the - min and max touched chunk. - """ - calls = {"n": 0} - original = IndexTransform.intersect + assert [projection.chunk_coords for projection in plan_chunks(transform, (grid,))] == [ + (0,), + (100_000,), + ] + assert grid.calls <= 12 - def counting(self: IndexTransform, output_domain: IndexDomain) -> object: - calls["n"] += 1 - return original(self, output_domain) - monkeypatch.setattr(IndexTransform, "intersect", counting) - return calls +def test_sparse_affine_plan_handles_large_origin_cancellation() -> None: + origin = int(np.iinfo(np.intp).max) + transform = IndexTransform( + domain=IndexDomain((origin,), (origin + 2,)), + output=(DimensionMap(input_dimension=0, offset=-2 * origin, stride=2),), + ) + grids = dimension_grids_from_chunks((1,), (3,)) + assert [projection.chunk_coords for projection in plan_chunks(transform, grids)] == [ + (0,), + (2,), + ] -class TestChunkResolutionTouchedOnly: - """`iter_chunk_transforms` must enumerate only the chunks a fancy selection - actually touches — never the dense `range(min_chunk, max_chunk + 1)` bounding - box. These guard against a regression to bounding-box enumeration, whose cost - scales with grid size rather than with the number of selected coordinates. - """ - def test_1d_sparse_vindex_enumerates_only_touched_chunks( +class TestTouchedOnlyCandidateEnumeration: + def test_sparse_one_dimensional_selection_skips_the_dense_span( self, monkeypatch: pytest.MonkeyPatch ) -> None: - """Two far-apart coordinates on a 1000-chunk grid touch exactly 2 chunks. - - A dense bounding-box enumeration would intersect ~1000 candidate chunks; - touched-only enumeration intersects exactly 2. - """ - # 4000 elements, chunk size 4 -> 1000 chunks. coords 1 and 3997 land in - # chunk 0 and chunk 999 respectively (998 empty chunks between them). + """Two sorted points on a 1000-cell grid require no intersections.""" + transform = IndexTransform.from_shape((4000,)).vindex[np.array([1, 3997], dtype=np.intp)] grid = ChunkGrid(dimensions=(FixedDimension(size=4, extent=4000),)) - t = IndexTransform.from_shape((4000,)).vindex[np.array([1, 3997], dtype=np.intp)] - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) - coords = sorted(r[0] for r in results) - assert coords == [(0,), (999,)] - # Sorted 1-D coordinates are partitioned directly, without intersecting - # either the touched chunks or the 998 empty chunks between them. + projections = list(plan_chunks(transform, grid.dimensions)) + + assert [projection.chunk_coords for projection in projections] == [(0,), (999,)] assert calls["n"] == 0 - def test_2d_orthogonal_enumerates_only_touched_chunks( - self, monkeypatch: pytest.MonkeyPatch + @pytest.mark.parametrize( + ("mode", "expected_coords", "expected_calls"), + [ + ("orthogonal", [(0, 0), (0, 999), (999, 0), (999, 999)], 4), + ("correlated", [(0, 0), (999, 999)], 2), + ], + ) + def test_sparse_two_dimensional_selection_uses_only_touched_combinations( + self, + monkeypatch: pytest.MonkeyPatch, + mode: str, + expected_coords: list[tuple[int, int]], + expected_calls: int, ) -> None: - """Orthogonal outer product of two 2-coordinate arrays touches 2x2 chunks. - - Per-dimension distinct touched chunks: {0, 999} on each axis. The outer - product is 2*2 = 4 candidate chunks (all survive), versus ~1e6 for a - dense 1000x1000 bounding box. - """ - grid = ChunkGrid( - dimensions=( - FixedDimension(size=4, extent=4000), - FixedDimension(size=4, extent=4000), - ) + """Orthogonal points use their outer product; correlated points remain paired.""" + base = IndexTransform.from_shape((4000, 4000)) + first = np.array([1, 3997], dtype=np.intp) + second = np.array([2, 3998], dtype=np.intp) + transform = ( + base.oindex[first, second] if mode == "orthogonal" else base.vindex[first, second] ) - t = IndexTransform.from_shape((4000, 4000)).oindex[ - np.array([1, 3997], dtype=np.intp), np.array([2, 3998], dtype=np.intp) - ] - - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) - - coords = sorted(r[0] for r in results) - assert coords == [(0, 0), (0, 999), (999, 0), (999, 999)] - assert calls["n"] == 4 - - def test_2d_correlated_vindex_enumerates_joint_touched_chunks( - self, monkeypatch: pytest.MonkeyPatch - ) -> None: - """Two correlated (vindex) coordinate arrays scatter to 2 diagonal chunks. - - The two points (1, 2) and (3997, 3998) touch chunks (0, 0) and - (999, 999). Correlated coordinate arrays are grouped *jointly*, so - enumeration intersects exactly the 2 touched chunks — never the 2x2 - cartesian product of per-dimension distinct chunks, and never the dense - 1e6 grid. - """ grid = ChunkGrid( dimensions=( FixedDimension(size=4, extent=4000), FixedDimension(size=4, extent=4000), ) ) - t = IndexTransform.from_shape((4000, 4000)).vindex[ - np.array([1, 3997], dtype=np.intp), np.array([2, 3998], dtype=np.intp) - ] - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) - coords = sorted(r[0] for r in results) - assert coords == [(0, 0), (999, 999)] - assert calls["n"] == 2 + projections = list(plan_chunks(transform, grid.dimensions)) - def test_2d_correlated_vindex_diagonal_is_linear_in_points( + assert sorted(projection.chunk_coords for projection in projections) == expected_coords + assert calls["n"] == expected_calls + + def test_correlated_diagonal_scales_with_points_not_their_product( self, monkeypatch: pytest.MonkeyPatch ) -> None: - """A diagonal of P correlated points touches P chunks with O(P) intersections. - - Enumerating the cartesian product of per-dimension distinct chunk sets - would cost P**2 intersections (2500 here) — quadratic in the number of - selected points for the scattered selections of zarr-python gh-4174. - Joint grouping keeps resolution work proportional to the touched chunks. - """ - p = 50 + """Fifty diagonal points require fifty, rather than 2500, intersections.""" + n_points = 50 + coordinates = np.arange(n_points, dtype=np.intp) * 8 + transform = IndexTransform.from_shape((4000, 4000)).vindex[coordinates, coordinates] grid = ChunkGrid( dimensions=( FixedDimension(size=4, extent=4000), FixedDimension(size=4, extent=4000), ) ) - # point i lands in chunk (2i, 2i): all per-dimension chunks distinct - coords_1d = np.arange(p, dtype=np.intp) * 8 - t = IndexTransform.from_shape((4000, 4000)).vindex[coords_1d, coords_1d] - calls = _count_intersect_calls(monkeypatch) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert sorted(r[0] for r in results) == [(2 * i, 2 * i) for i in range(p)] - assert calls["n"] == p + projections = list(plan_chunks(transform, grid.dimensions)) - -class TestSubTransformToSelections: - def test_constant_map(self) -> None: - """ConstantMap produces int selection + drop axis.""" - t = IndexTransform( - domain=IndexDomain.from_shape((10,)), - output=(ConstantMap(offset=5),), - ) - chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) - assert chunk_sel == (5,) - assert out_sel == () - assert drop_axes == () - - def test_dimension_map_stride_1(self) -> None: - """DimensionMap with stride=1 produces contiguous slice.""" - t = IndexTransform( - domain=IndexDomain.from_shape((10,)), - output=(DimensionMap(input_dimension=0, offset=3, stride=1),), - ) - chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) - assert chunk_sel == (slice(3, 13, 1),) - assert out_sel == (slice(0, 10),) - assert drop_axes == () - - def test_dimension_map_strided(self) -> None: - """DimensionMap with stride>1 produces strided slice.""" - t = IndexTransform( - domain=IndexDomain.from_shape((5,)), - output=(DimensionMap(input_dimension=0, offset=2, stride=3),), - ) - chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) - assert chunk_sel == (slice(2, 17, 3),) - assert out_sel == (slice(0, 5),) - assert drop_axes == () - - def test_array_map(self) -> None: - """ArrayMap produces integer array selection.""" - arr = np.array([1, 5, 9], dtype=np.intp) - t = IndexTransform( - domain=IndexDomain.from_shape((3,)), - output=(ArrayMap(index_array=arr, offset=0, stride=1),), - ) - chunk_sel, out_sel, drop_axes = sub_transform_to_selections(t) - assert isinstance(chunk_sel[0], np.ndarray) - np.testing.assert_array_equal(chunk_sel[0], arr) - # Without chunk_mask, out_sel falls back to domain-based slices - assert out_sel == (slice(0, 3),) - assert drop_axes == () - - def test_array_map_with_offset_stride(self) -> None: - """ArrayMap with offset and stride computes storage coords.""" - arr = np.array([0, 1, 2], dtype=np.intp) - t = IndexTransform( - domain=IndexDomain.from_shape((3,)), - output=(ArrayMap(index_array=arr, offset=10, stride=5),), - ) - chunk_sel, _out_sel, drop_axes = sub_transform_to_selections(t) - assert isinstance(chunk_sel[0], np.ndarray) - np.testing.assert_array_equal(chunk_sel[0], np.array([10, 15, 20])) - assert drop_axes == () - - def test_mixed_maps_2d(self) -> None: - """Mix of ConstantMap and DimensionMap.""" - t = IndexTransform( - domain=IndexDomain.from_shape((10,)), - output=( - ConstantMap(offset=5), - DimensionMap(input_dimension=0, offset=0, stride=1), - ), - ) - chunk_sel, _out_sel, drop_axes = sub_transform_to_selections(t) - assert chunk_sel[0] == 5 - assert chunk_sel[1] == slice(0, 10, 1) - # drop_axes is empty — integer in chunk_sel naturally drops the dim via numpy - assert drop_axes == () - - -class TestChunkResolutionArrayMapFlavours: - """Chunk resolution must yield outer-product (np.ix_) selectors for - orthogonal ArrayMaps and shared flat-scatter selectors for correlated ones, - and must return early for empty fancy selections.""" - - def test_empty_array_selection_yields_nothing(self) -> None: - """An empty ArrayMap selection produces no chunk transforms (no crash).""" - t = IndexTransform( - domain=IndexDomain.from_shape((0,)), - output=(ArrayMap(index_array=np.array([], dtype=np.intp)),), - ) - grid = ChunkGrid(dimensions=(FixedDimension(size=3, extent=10),)) - assert list(iter_chunk_transforms(t, grid._dimensions)) == [] - - def test_orthogonal_outer_product_selectors(self) -> None: - """Two independent arrays produce np.ix_-style (mesh) chunk/out selectors.""" - t = IndexTransform.from_shape((10, 10)).oindex[np.array([1, 3]), np.array([2, 4, 6])] - grid = ChunkGrid( - dimensions=(FixedDimension(size=10, extent=10), FixedDimension(size=10, extent=10)) - ) - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 1 - _coords, sub_t, out_indices = results[0] - chunk_sel, out_sel, drop_axes = sub_transform_to_selections(sub_t, out_indices) - # np.ix_ produces one 2-D open-mesh selector per axis, for both sides. - assert len(chunk_sel) == 2 - assert len(out_sel) == 2 - assert isinstance(chunk_sel[0], np.ndarray) - assert isinstance(chunk_sel[1], np.ndarray) - assert chunk_sel[0].shape == (2, 1) - assert chunk_sel[1].shape == (1, 3) - assert drop_axes == () - - def test_correlated_scatter_with_residual_slice(self) -> None: - """Correlated arrays + a residual slice dim scatter through a single flat - index whose shape matches the (points, slice) block read from the chunk.""" - t = IndexTransform.from_shape((4, 3, 5)).vindex[np.array([1, 3]), np.array([2, 0])] - grid = ChunkGrid( - dimensions=( - FixedDimension(size=4, extent=4), - FixedDimension(size=3, extent=3), - FixedDimension(size=5, extent=5), - ) - ) - # One chunk holds everything: both points survive, slice dim spans [0,5). - results = list(iter_chunk_transforms(t, grid._dimensions)) - assert len(results) == 1 - _coords, sub_t, out_indices = results[0] - chunk_sel, out_sel, _drop = sub_transform_to_selections(sub_t, out_indices) - # Chunk side: flat coordinate arrays for the two correlated dims plus a - # slice for the residual dim. - assert len(chunk_sel) == 3 - np.testing.assert_array_equal(np.asarray(chunk_sel[0]), [1, 3]) - np.testing.assert_array_equal(np.asarray(chunk_sel[1]), [2, 0]) - assert chunk_sel[2] == slice(0, 5, 1) - # Output side: a single flat scatter index of shape (points, slice) = (2, 5). - assert len(out_sel) == 1 - assert np.asarray(out_sel[0]).shape == (2, 5) + assert sorted(projection.chunk_coords for projection in projections) == [ + (2 * index, 2 * index) for index in range(n_points) + ] + assert calls["n"] == n_points diff --git a/packages/zarr-indexing/tests/test_composition.py b/packages/zarr-indexing/tests/test_composition.py index dd92f59b80..0cb6155344 100644 --- a/packages/zarr-indexing/tests/test_composition.py +++ b/packages/zarr-indexing/tests/test_composition.py @@ -3,8 +3,8 @@ import numpy as np import pytest -from zarr_indexing.composition import compose from zarr_indexing.domain import IndexDomain +from zarr_indexing.errors import BoundsCheckError from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap from zarr_indexing.transform import IndexTransform @@ -18,7 +18,7 @@ def test_constant_inner_any_outer(self) -> None: domain=IndexDomain.from_shape((5,)), output=(ConstantMap(offset=42),), ) - result = compose(outer, inner) + result = outer.compose(inner) assert isinstance(result.output[0], ConstantMap) assert result.output[0].offset == 42 @@ -35,27 +35,40 @@ def test_dimension_inner_constant_outer(self) -> None: domain=IndexDomain.from_shape((10,)), output=(DimensionMap(input_dimension=0, offset=10, stride=3),), ) - result = compose(outer, inner) + result = outer.compose(inner) assert isinstance(result.output[0], ConstantMap) assert result.output[0].offset == 25 + def test_dimension_inner_constant_outer_rejects_affine_overflow(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ConstantMap(offset=2**62),), + ) + inner = IndexTransform( + domain=IndexDomain((2**62,), (2**62 + 1,)), + output=(DimensionMap(input_dimension=0, stride=4),), + ) + + with pytest.raises(OverflowError, match="outside np.intp"): + outer.compose(inner) + def test_dimension_inner_dimension_outer(self) -> None: outer = IndexTransform( - domain=IndexDomain.from_shape((10,)), + domain=IndexDomain.from_shape((3,)), output=(DimensionMap(input_dimension=0, offset=5, stride=2),), ) inner = IndexTransform( domain=IndexDomain.from_shape((10,)), output=(DimensionMap(input_dimension=0, offset=10, stride=3),), ) - result = compose(outer, inner) + result = outer.compose(inner) assert isinstance(result.output[0], DimensionMap) assert result.output[0].offset == 25 assert result.output[0].stride == 6 assert result.output[0].input_dimension == 0 def test_dimension_inner_array_outer(self) -> None: - arr = np.array([0, 2, 4], dtype=np.intp) + arr = np.array([0, 1, 2], dtype=np.intp) outer = IndexTransform( domain=IndexDomain.from_shape((3,)), output=(ArrayMap(index_array=arr, offset=5, stride=2),), @@ -64,7 +77,7 @@ def test_dimension_inner_array_outer(self) -> None: domain=IndexDomain.from_shape((10,)), output=(DimensionMap(input_dimension=0, offset=10, stride=3),), ) - result = compose(outer, inner) + result = outer.compose(inner) assert isinstance(result.output[0], ArrayMap) assert result.output[0].offset == 25 assert result.output[0].stride == 6 @@ -84,10 +97,23 @@ def test_array_inner_constant_outer(self) -> None: domain=IndexDomain.from_shape((3,)), output=(ArrayMap(index_array=inner_arr, offset=0, stride=1),), ) - result = compose(outer, inner) + result = outer.compose(inner) assert isinstance(result.output[0], ConstantMap) assert result.output[0].offset == 20 + def test_array_inner_constant_outer_rejects_affine_overflow(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ConstantMap(offset=0),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ArrayMap(np.array([2**62], dtype=np.intp), stride=4),), + ) + + with pytest.raises(OverflowError, match="outside np.intp"): + outer.compose(inner) + def test_array_inner_array_outer(self) -> None: outer_arr = np.array([0, 2, 1], dtype=np.intp) inner_arr = np.array([10, 20, 30], dtype=np.intp) @@ -99,17 +125,104 @@ def test_array_inner_array_outer(self) -> None: domain=IndexDomain.from_shape((3,)), output=(ArrayMap(index_array=inner_arr, offset=0, stride=1),), ) - result = compose(outer, inner) + result = outer.compose(inner) assert isinstance(result.output[0], ArrayMap) expected = np.array([10, 30, 20], dtype=np.intp) np.testing.assert_array_equal(result.output[0].index_array, expected) +def _storage_of(transform: IndexTransform, point: tuple[int, ...]) -> tuple[int, ...]: + """The storage coordinates a transform assigns to one input point. + + The point is given in the transform's own domain coordinates; an index array + carries the full input rank, singleton on the axes it does not vary over, and + is addressed positionally from the domain origin. + """ + coords: list[int] = [] + for m in transform.output: + if isinstance(m, ConstantMap): + coords.append(m.offset) + elif isinstance(m, DimensionMap): + coords.append(m.offset + m.stride * point[m.input_dimension]) + else: + origin = transform.domain.inclusive_min + idx = tuple( + 0 if m.index_array.shape[axis] == 1 else point[axis] - origin[axis] + for axis in range(m.index_array.ndim) + ) + coords.append(m.offset + m.stride * int(m.index_array[idx])) + return tuple(coords) + + +def _assert_composes_pointwise(outer: IndexTransform, inner: IndexTransform) -> None: + """`outer.compose(inner)` must agree with running the two in sequence.""" + composed = outer.compose(inner) + assert composed.domain == outer.domain + lo = outer.domain.inclusive_min + hi = outer.domain.exclusive_max + for coord in np.ndindex(*outer.domain.shape): + point = tuple(int(c) + int(o) for c, o in zip(coord, lo, strict=True)) + assert all(point[d] < hi[d] for d in range(len(hi))) + intermediate = _storage_of(outer, point) + assert _storage_of(composed, point) == _storage_of(inner, intermediate) + + +class TestComposeOverANonZeroOriginDomain: + """The outer domain need not start at 0 — a step-1 slice preserves its + literal bounds and a negative step produces a negative origin — so the inner + map has to be evaluated over the outer domain's real range.""" + + def test_array_inner_sliced_outer(self) -> None: + inner = IndexTransform.from_shape((10,)).oindex[np.array([3, 1, 4, 1, 5])] + outer = IndexTransform.identity(IndexDomain.from_shape((5,)))[1:4] + assert outer.domain.inclusive_min == (1,) + result = outer.compose(inner) + assert isinstance(result.output[0], ArrayMap) + np.testing.assert_array_equal( + result.output[0].index_array, np.array([1, 4, 1], dtype=np.intp) + ) + _assert_composes_pointwise(outer, inner) + + def test_array_inner_reversed_outer(self) -> None: + inner = IndexTransform.from_shape((10,)).oindex[np.array([3, 1, 4, 1, 5])] + outer = IndexTransform.identity(IndexDomain.from_shape((5,)))[::-1] + assert outer.domain.inclusive_min == (-4,) + result = outer.compose(inner) + assert isinstance(result.output[0], ArrayMap) + np.testing.assert_array_equal( + result.output[0].index_array, np.array([5, 1, 4, 1, 3], dtype=np.intp) + ) + _assert_composes_pointwise(outer, inner) + + def test_array_inner_strided_outer(self) -> None: + inner = IndexTransform.from_shape((10,)).oindex[np.array([3, 1, 4, 1, 5, 9])] + outer = IndexTransform.identity(IndexDomain.from_shape((6,)))[1::2] + _assert_composes_pointwise(outer, inner) + + def test_array_inner_translated_outer(self) -> None: + inner = IndexTransform.from_shape((10,)).oindex[np.array([3, 1, 4, 1, 5])] + outer = IndexTransform.identity(IndexDomain.from_shape((5,))).translate_domain_to((-2,)) + _assert_composes_pointwise(outer, inner) + + def test_array_inner_array_outer_over_a_shifted_domain(self) -> None: + inner = IndexTransform.from_shape((10,)).oindex[np.array([3, 1, 4, 1, 5])] + outer = IndexTransform.from_shape((5,)).oindex[np.array([4, 0, 2])] + _assert_composes_pointwise(outer, inner) + + def test_array_inner_constant_outer_over_a_shifted_domain(self) -> None: + inner = IndexTransform.from_shape((10,)).oindex[np.array([3, 1, 4, 1, 5])] + outer = IndexTransform( + domain=IndexDomain.from_shape((4,)), + output=(ConstantMap(offset=3),), + ) + _assert_composes_pointwise(outer, inner) + + class TestComposeMultiDim: def test_2d_identity_compose(self) -> None: a = IndexTransform.from_shape((10, 20)) b = IndexTransform.from_shape((10, 20)) - result = compose(a, b) + result = a.compose(b) assert result.domain.shape == (10, 20) for i in range(2): m = result.output[i] @@ -133,7 +246,7 @@ def test_mixed_map_types(self) -> None: DimensionMap(input_dimension=1, offset=0, stride=1), ), ) - result = compose(outer, inner) + result = outer.compose(inner) assert isinstance(result.output[0], ConstantMap) assert result.output[0].offset == 17 assert isinstance(result.output[1], DimensionMap) @@ -145,7 +258,149 @@ def test_rank_mismatch_raises(self) -> None: outer = IndexTransform.from_shape((10,)) inner = IndexTransform.from_shape((10, 20)) with pytest.raises(ValueError, match="rank"): - compose(outer, inner) + outer.compose(inner) + + +class TestComposeInnerDomainValidation: + @pytest.mark.parametrize( + ("outer_map", "inner_lower"), + [ + (ConstantMap(offset=10), 10), + (ConstantMap(offset=14), 10), + (DimensionMap(input_dimension=0, offset=10, stride=1), 10), + (DimensionMap(input_dimension=0, offset=14, stride=-1), 10), + (DimensionMap(input_dimension=0, offset=10**100, stride=1), 10**100), + ], + ids=["lower-bound", "upper-bound", "forward", "reverse", "arbitrary-integer"], + ) + def test_valid_constant_and_affine_boundaries( + self, outer_map: ConstantMap | DimensionMap, inner_lower: int + ) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((5,)), + output=(outer_map,), + ) + inner = IndexTransform( + domain=IndexDomain((inner_lower,), (inner_lower + 5,)), + output=(DimensionMap(input_dimension=0),), + ) + + result = outer.compose(inner) + + assert result.domain == outer.domain + _assert_composes_pointwise(outer, inner) + + def test_rejects_constant_outer_coordinate_outside_inner_domain(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ConstantMap(offset=2),), + ) + inner = IndexTransform.identity(IndexDomain((0,), (2,))) + + with pytest.raises(BoundsCheckError, match="outside.*inner.*domain"): + outer.compose(inner) + + def test_rejects_affine_outer_range_crossing_inner_domain(self) -> None: + outer = IndexTransform( + domain=IndexDomain((10**100,), (10**100 + 3,)), + output=(DimensionMap(input_dimension=0),), + ) + inner = IndexTransform.identity(IndexDomain((10**100,), (10**100 + 2,))) + + with pytest.raises(BoundsCheckError, match="outside.*inner.*domain"): + outer.compose(inner) + + def test_empty_outer_domain_does_not_evaluate_nonexistent_points(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((0,)), + output=(ConstantMap(offset=99),), + ) + inner = IndexTransform.identity(IndexDomain((0,), (2,))) + + result = outer.compose(inner) + + assert result.domain.shape == (0,) + assert result.output == (ConstantMap(offset=99),) + + +class TestComposeMultidimensionalArrayInner: + def test_identity_gathers_a_two_dimensional_array_map(self) -> None: + inner = IndexTransform( + domain=IndexDomain.from_shape((2, 3)), + output=( + ArrayMap( + index_array=np.array([[11, 13, 17], [19, 23, 29]], dtype=np.intp), + offset=5, + stride=2, + ), + ), + ) + outer = IndexTransform.identity(inner.domain) + + result = outer.compose(inner) + + assert result == inner + _assert_composes_pointwise(outer, inner) + + def test_mixed_affine_and_constant_outputs_gather_with_metadata(self) -> None: + inner = IndexTransform( + domain=IndexDomain((4, 8), (7, 10)), + output=( + ArrayMap( + index_array=np.array([[2, 3], [5, 7], [11, 13]], dtype=np.intp), + offset=-3, + stride=4, + ), + ), + ) + outer = IndexTransform( + domain=IndexDomain((-2,), (0,)), + output=( + DimensionMap(input_dimension=0, offset=7, stride=1), + ConstantMap(offset=9), + ), + ) + + result = outer.compose(inner) + + assert result.domain == outer.domain + assert len(result.output) == 1 + array_map = result.output[0] + assert isinstance(array_map, ArrayMap) + assert array_map.index_array.shape == (2,) + assert array_map.offset == -3 + assert array_map.stride == 4 + np.testing.assert_array_equal(array_map.index_array, np.array([7, 13], dtype=np.intp)) + _assert_composes_pointwise(outer, inner) + + def test_out_of_bounds_affine_output_is_rejected_before_gather(self) -> None: + outer = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=( + DimensionMap(input_dimension=0, offset=1, stride=1), + ConstantMap(offset=0), + ), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((3, 2)), + output=(ArrayMap(np.arange(6, dtype=np.intp).reshape(3, 2)),), + ) + + with pytest.raises(BoundsCheckError, match="outside.*inner.*domain"): + outer.compose(inner) + + def test_rank_zero_array_map_composition(self) -> None: + domain = IndexDomain((), ()) + outer = IndexTransform.identity(domain) + inner = IndexTransform( + domain=domain, + output=(ArrayMap(np.array(7, dtype=np.intp), offset=2, stride=3),), + ) + + result = outer.compose(inner) + + assert result.domain == domain + assert result.output == (ConstantMap(offset=23),) class TestComposeChain: @@ -156,11 +411,64 @@ def test_three_transforms(self) -> None: output=(DimensionMap(input_dimension=0, offset=10, stride=1),), ) c = IndexTransform( - domain=IndexDomain.from_shape((100,)), + domain=IndexDomain.from_shape((110,)), output=(DimensionMap(input_dimension=0, offset=5, stride=2),), ) - bc = compose(b, c) - abc = compose(a, bc) + bc = b.compose(c) + abc = a.compose(bc) assert isinstance(abc.output[0], DimensionMap) assert abc.output[0].offset == 25 assert abc.output[0].stride == 2 + + +def test_composing_an_inner_array_with_a_broadcast_axis_wider_than_one_cell() -> None: + """A non-dependency axis is a singleton that broadcasts, so its coordinate is 0. + + Indexing it by the raw intermediate coordinate walked off the end of an axis + the array only has one entry for. + """ + outer = IndexTransform( + domain=IndexDomain(inclusive_min=(-2,), exclusive_max=(0,)), + output=(ConstantMap(offset=1), ConstantMap(offset=0)), + ) + inner = IndexTransform( + domain=IndexDomain(inclusive_min=(0, 0), exclusive_max=(2, 1)), + output=(ArrayMap(index_array=np.array([[13]], dtype=np.intp), offset=-2, stride=2),), + ) + composed = outer.compose(inner) + assert composed.output[0] == ConstantMap(offset=24) + + +def test_composing_a_one_dimensional_inner_array_under_a_higher_rank_outer() -> None: + """The shortcut gated on the output rank but sized by the input rank. + + A rank-2 outer therefore built a rank-1 array for a rank-2 domain, which the + engine's own invariant then rejected. + """ + outer = IndexTransform( + domain=IndexDomain.from_shape((2, 3)), + output=(DimensionMap(input_dimension=0, offset=1, stride=1),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((4,)), + output=(ArrayMap(index_array=np.array([7, 3, 5, 1], dtype=np.intp)),), + ) + composed = outer.compose(inner) + array_map = composed.output[0] + assert isinstance(array_map, ArrayMap) + assert array_map.index_array.shape == (2, 1) + np.testing.assert_array_equal(array_map.index_array, np.array([[3], [5]])) + + +def test_composing_out_of_the_inner_domain_is_refused() -> None: + """An intermediate outside the inner domain wrapped NumPy-style and read a cell.""" + outer = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ConstantMap(offset=-3),), + ) + inner = IndexTransform( + domain=IndexDomain.from_shape((2,)), + output=(ArrayMap(index_array=np.array([7, 3], dtype=np.intp)),), + ) + with pytest.raises(BoundsCheckError, match="outside.*inner.*domain"): + outer.compose(inner) diff --git a/packages/zarr-indexing/tests/test_doc_examples.py b/packages/zarr-indexing/tests/test_doc_examples.py new file mode 100644 index 0000000000..240bd48531 --- /dev/null +++ b/packages/zarr-indexing/tests/test_doc_examples.py @@ -0,0 +1,488 @@ +"""Executable documentation contracts. + +Two kinds of test live here, and nothing else: + +1. **Structural.** Every snippet include in the rendered docs resolves to a + real file and a balanced, non-empty region — discovered by scanning the + markdown, never hand-registered — and every example file executes. The + examples carry their own inline assertions, so executing one *is* the + value check; expected values are stated once, in the example, beside the + prose that narrates them. +2. **Behavioral.** Documented classes are exercised where the example cannot + assert the behavior itself: error paths, cache lifecycle invariants, and + contracts stated in prose about types the docs define. + +Editorial choices — section order, exact wording, teaching progression — are +deliberately not pinned here; they belong to review. Structural breakage +belongs to `mkdocs build --strict`, whose configuration makes it actually +fail on the relevant classes: `check_paths: true` for unresolvable includes, +and `validation` set to warn (strict turns warnings into errors) for broken +link anchors and nav-omitted pages. +""" + +from __future__ import annotations + +import re +import runpy +import subprocess +import sys +from pathlib import Path +from typing import Any + +import numpy as np +import pytest + +import zarr_indexing +import zarr_indexing.lazy_array as lazy_array_module +from zarr_indexing import IndexTransform, LazyArray, ReadContext + +DOCS = Path(__file__).parents[1] / "docs" +PACKAGE_ROOT = DOCS.parent +STANDALONE_EXAMPLES = PACKAGE_ROOT / "examples" +DOC_SNIPPETS_DIR = DOCS / "snippets" +CACHE_EXAMPLE = STANDALONE_EXAMPLES / "system_memory_chunk_cache" / "system_memory_chunk_cache.py" + +# Mirrors `pymdownx.snippets: base_path` in mkdocs.yml. If that list changes, +# change this one in the same commit. +SNIPPET_BASE_PATHS = (DOCS, STANDALONE_EXAMPLES) + +_INCLUDE = re.compile(r'--8<--\s+"(?P<target>[^":\n]+?)(?::(?P<region>[^"\n]+))?"') + + +def _markdown_includes() -> tuple[tuple[str, str, str | None], ...]: + """Every snippet include in the rendered docs: (page, target, region).""" + return tuple( + (str(page.relative_to(DOCS)), match["target"], match["region"]) + for page in sorted(DOCS.rglob("*.md")) + for match in _INCLUDE.finditer(page.read_text()) + ) + + +INCLUDES = _markdown_includes() +# In-process executables: every snippet, plus the one standalone example that +# is importable as a module. The lazy_indexing_* examples are CLI scripts +# (they parse argv and call sys.exit), so they run as subprocesses below — +# no other test in the repository executes them. +EXECUTABLES = (*sorted(DOC_SNIPPETS_DIR.glob("*.py")), CACHE_EXAMPLE) +CLI_EXAMPLES = tuple( + script for script in sorted(STANDALONE_EXAMPLES.glob("*/*.py")) if script not in EXECUTABLES +) + +PATTERN_NAMESPACE: dict[str, Any] = runpy.run_path(str(DOC_SNIPPETS_DIR / "indexing_patterns.py")) +PATTERN_CASES: tuple[dict[str, Any], ...] = PATTERN_NAMESPACE["PATTERN_CASES"] +CACHE_NAMESPACE: dict[str, Any] = runpy.run_path(str(CACHE_EXAMPLE)) + +# The documented pattern matrix must keep covering every selection family. +REQUIRED_PATTERNS = { + "basic-slice", + "integer-axis-removal", + "negative-stride", + "empty-selection", + "boolean-mask", + "orthogonal", + "vectorized", + "broadcasting", + "repeated-out-of-order", +} + + +# --------------------------------------------------------------------------- # +# Structural: the include graph and the executable examples +# --------------------------------------------------------------------------- # + + +def test_docs_reference_snippets_at_all() -> None: + """An empty scan means the include regex rotted, not that the docs did.""" + assert len(INCLUDES) >= 10 + assert any(region for _, _, region in INCLUDES) + + +@pytest.mark.parametrize( + ("page", "target", "region"), + INCLUDES, + ids=[ + f"{page}->{target}" + (f":{region}" if region else "") for page, target, region in INCLUDES + ], +) +def test_markdown_include_resolves(page: str, target: str, region: str | None) -> None: + """Each include names exactly one real file; each region is balanced and non-empty.""" + resolved = [base / target for base in SNIPPET_BASE_PATHS if (base / target).is_file()] + assert len(resolved) == 1, f"{page} includes {target!r}: resolved to {resolved or 'nothing'}" + if region is None: + return + source = resolved[0].read_text() + starts = re.findall(rf"^\s*# --8<-- \[start:{re.escape(region)}\]$", source, re.MULTILINE) + ends = re.findall(rf"^\s*# --8<-- \[end:{re.escape(region)}\]$", source, re.MULTILINE) + assert len(starts) == 1, f"{target}:{region} needs exactly one start marker, has {len(starts)}" + assert len(ends) == 1, f"{target}:{region} needs exactly one end marker, has {len(ends)}" + body = source.split(starts[0], maxsplit=1)[1].split(ends[0], maxsplit=1)[0] + assert body.strip(), f"{target}:{region} is empty" + + +def test_snippet_directories_hold_only_their_kind() -> None: + """Rendered pages are markdown; executable snippets are Python.""" + assert all(p.suffix == ".md" for p in (DOCS / "examples").iterdir() if p.is_file()) + assert all(p.suffix == ".py" for p in DOC_SNIPPETS_DIR.iterdir() if p.is_file()) + + +@pytest.mark.parametrize("example", EXECUTABLES, ids=lambda path: path.stem) +def test_documentation_example_executes(example: Path) -> None: + """Examples are executable contracts; their inline asserts are the values check.""" + runpy.run_path(str(example), run_name="__main__") + + +@pytest.mark.parametrize("script", CLI_EXAMPLES, ids=lambda path: path.stem) +def test_cli_example_runs_as_a_subprocess(script: Path) -> None: + """The CLI examples exit 0 when run the way their READMEs instruct.""" + if "dask" in script.stem: + pytest.importorskip("dask.array") + completed = subprocess.run( + [sys.executable, str(script)], + capture_output=True, + text=True, + cwd=script.parent, + check=False, + ) + assert completed.returncode == 0, completed.stderr[-2000:] + + +@pytest.mark.parametrize( + "example_dir", + sorted(p for p in STANDALONE_EXAMPLES.iterdir() if p.is_dir()), + ids=lambda path: path.name, +) +def test_standalone_example_is_a_documented_script(example_dir: Path) -> None: + """Each standalone example ships a README and a same-named runnable script.""" + script = example_dir / f"{example_dir.name}.py" + assert script.is_file() + assert (example_dir / "README.md").is_file() + assert (DOCS / "examples" / f"{example_dir.name}.md").is_file() + assert script.read_text().startswith("# /// script\n"), "examples stay PEP 723 runnable" + + +# --------------------------------------------------------------------------- # +# Behavioral: the documented pattern matrix +# --------------------------------------------------------------------------- # + + +def test_indexing_pattern_matrix_is_complete() -> None: + assert {case["name"] for case in PATTERN_CASES} == REQUIRED_PATTERNS + + +def test_pattern_page_tabs_are_the_models() -> None: + """Both tabs of every matrix entry are the executable model, in order. + + The JSON tab must be the model's canonical wire form; the Python tab + must evaluate (in the executable matrix's namespace) to the model + itself. Either tab drifting from the snippet fails here. + """ + import json + import textwrap + + page = (DOCS / "guide" / "patterns.md").read_text() + + json_blocks = re.findall(r"```json\n(.*?)```", page, re.DOTALL) + assert len(json_blocks) == len(PATTERN_CASES) + for block, case in zip(json_blocks, PATTERN_CASES, strict=True): + assert json.loads(block) == case["transform"].to_json(), case["name"] + + python_blocks = [ + textwrap.dedent(block) + for block in re.findall(r"```python\n(.*?)```", page, re.DOTALL) + if "--8<--" not in block + ] + assert len(python_blocks) == len(PATTERN_CASES) + for block, case in zip(python_blocks, PATTERN_CASES, strict=True): + constructed = eval(block, dict(PATTERN_NAMESPACE)) + assert constructed == case["transform"], case["name"] + + +@pytest.mark.parametrize("case", PATTERN_CASES, ids=lambda case: case["name"]) +def test_indexing_pattern_matrix_matches_numpy(case: dict[str, Any]) -> None: + """The wrapper agrees with the matrix the snippet proves at the transform level.""" + image = PATTERN_NAMESPACE["image"] + lazy = LazyArray.from_numpy(image) + accessor = { + "basic": lazy.lazy, + "oindex": lazy.lazy.oindex, + "vindex": lazy.lazy.vindex, + }[case["mode"]] + view = accessor[case["selection"]] + result = view.result() + + np.testing.assert_array_equal(result, case["expected"]) + assert result.shape == case["shape"] + assert ("box" if view.is_box else "query") == case["category"] + + +# --------------------------------------------------------------------------- # +# Behavioral: contracts the guide states about wrapped sources and parts +# --------------------------------------------------------------------------- # + + +def test_default_source_contract_converts_basic_selected_slabs_to_system_memory() -> None: + """A source may return Python slabs as long as NumPy can convert each selected slab.""" + + class ListSlabSource: + def __init__(self) -> None: + self.data = np.arange(20).reshape(4, 5) + self.keys: list[tuple[Any, ...]] = [] + + @property + def shape(self) -> tuple[int, ...]: + return self.data.shape + + @property + def dtype(self) -> np.dtype[Any]: + return self.data.dtype + + def __getitem__(self, key: tuple[Any, ...]) -> object: + assert all(isinstance(item, (int, slice)) for item in key) + self.keys.append(key) + return self.data[key].tolist() + + source = ListSlabSource() + result = LazyArray(source).with_parts((2, 3)).lazy.oindex[[3, 1, 1], 1:5:2].result() + + np.testing.assert_array_equal(result, np.array([[16, 18], [6, 8], [6, 8]])) + assert len(source.keys) > 0 + assert all(all(isinstance(item, (int, slice)) for item in key) for key in source.keys) + + +def test_coordinate_array_example_preserves_order_and_duplicates() -> None: + """Coordinate arrays are ordered sequences, not mathematical sets.""" + view = LazyArray.from_numpy(np.arange(6)).with_parts((2,)).lazy.oindex[[4, 1, 1, 3]] + + np.testing.assert_array_equal(view.result(), np.array([4, 1, 1, 3])) + assembled = np.empty(view.shape, dtype=view.dtype) + for part in view.parts(): + assembled[part.out_selection] = part.view.result() + np.testing.assert_array_equal(assembled, np.array([4, 1, 1, 3])) + + +def test_documented_partition_transform_is_global_and_projection_is_chunk_local() -> None: + source = np.arange(8) + part = tuple(LazyArray.from_numpy(source).with_parts((4,)).parts())[1] + + assert part.view.transform.apply((0,)) == (4,) + assert part.view.array[part.view.transform.apply((0,))] == 4 + assert part.projection.chunk_transform.apply((0,)) == (0,) + + +@pytest.mark.parametrize( + ("mode", "parts"), + [ + ("per-axis", ((0,), (3,))), + ("per-axis", ((), (3,))), + ("uniform", (1, 1)), + ("per-axis", ((0, 0), (3,))), + ], + ids=["single-zero", "empty-sequence", "positive-uniform", "repeated-zero"], +) +def test_documented_zero_length_axis_partition_spellings_execute(mode: str, parts: Any) -> None: + data = np.zeros((0, 3)) + base = LazyArray.from_numpy(data) + view = base.with_parts(parts) if mode == "uniform" else base.with_parts_per_axis(parts) + + assert view.result().shape == (0, 3) + assert tuple(view.parts()) == () + + +def test_projection_example_exposes_paired_directions() -> None: + """Both transforms of every projection keep their documented output ranks.""" + namespace = runpy.run_path(str(DOC_SNIPPETS_DIR / "chunk_projection.py")) + np.testing.assert_array_equal(namespace["ADVANCED_RESULT"], namespace["ADVANCED_EXPECTED"]) + assert all(p.chunk_transform.output_rank == 2 for p in namespace["PROJECTIONS"]) + assert all(p.cell_transform.output_rank == 1 for p in namespace["PROJECTIONS"]) + + +@pytest.mark.parametrize( + "example", + [DOC_SNIPPETS_DIR / "integrations.py", CACHE_EXAMPLE], + ids=lambda path: path.stem, +) +def test_projection_examples_assemble_rank_zero_domains(example: Path) -> None: + """The examples' shared assembly helpers handle a zero-rank cell domain.""" + namespace = runpy.run_path(str(example)) + domain = zarr_indexing.IndexDomain((), ()) + cell_points = namespace["_domain_points"](domain) + destination = np.empty((), dtype=np.intp) + + values = namespace["_gather_and_scatter"]( + destination, + np.array(7, dtype=np.intp), + cell_points, + cell_points, + ) + + assert cell_points.shape == (1, 0) + assert values.shape == (1,) + assert destination[()] == 7 + + +# --------------------------------------------------------------------------- # +# Behavioral: the documented chunk cache (error paths the example cannot show) +# --------------------------------------------------------------------------- # + + +def make_documented_cache() -> tuple[Any, Any]: + source_type = CACHE_NAMESPACE["RecordingChunkSource"] + cache_type = CACHE_NAMESPACE["SystemMemoryChunkCache"] + source = source_type(np.arange(48).reshape(6, 8), chunks=(3, 4)) + return source, cache_type(source, capacity=2) + + +def test_system_memory_cache_assembles_and_deduplicates_public_projections() -> None: + source, cache = make_documented_cache() + + np.testing.assert_array_equal(cache.oindex[[1, 1], 2], np.array([10, 10])) + assert tuple(source.reads) == ((0, 0),) + assert cache.projection_uses == (("chunk_transform", "context.transform"),) + + +def test_chunk_cache_queues_all_parts_before_loading( + monkeypatch: pytest.MonkeyPatch, +) -> None: + source, cache = make_documented_cache() + planning_count = 0 + original_plan_chunks = lazy_array_module.plan_chunks + + def counted_plan_chunks(*args: Any, **kwargs: Any) -> Any: + nonlocal planning_count + planning_count += 1 + return original_plan_chunks(*args, **kwargs) + + with monkeypatch.context() as request_patch: + request_patch.setattr(lazy_array_module, "plan_chunks", counted_plan_chunks) + result = cache[1:5, 2] + + np.testing.assert_array_equal(result, np.array([10, 18, 26, 34])) + assert planning_count == 1 + assert source.reads == [(0, 0), (1, 0)] + + assert [ + (event.chunk_coords, event.previous.value, event.current.value) for event in cache.events + ] == [ + ((0, 0), "new", "queued"), + ((1, 0), "new", "queued"), + ((0, 0), "queued", "loading"), + ((0, 0), "loading", "ready"), + ((1, 0), "queued", "loading"), + ((1, 0), "loading", "ready"), + ] + + +def test_chunk_cache_reader_resolves_a_transform_from_cached_chunks() -> None: + """The reader boundary consumes the prepared projections of real parts.""" + source_type = CACHE_NAMESPACE["RecordingChunkSource"] + reader_type = CACHE_NAMESPACE["SystemMemoryChunkReader"] + source = source_type(np.arange(48).reshape(6, 8), chunks=(3, 4)) + reader = reader_type(capacity=2) + view = LazyArray(source).with_reader(reader).lazy[1:5, 2] + parts = tuple(view.parts()) + out = np.empty(view.shape, dtype=source.dtype) + for part in parts: + destination = out[part.out_selection] + assert ( + reader.read_into( + source, + ReadContext(part.view.transform, part.projection), + destination, + ) + is None + ) + + np.testing.assert_array_equal(out, np.array([10, 18, 26, 34])) + assert source.reads == [(0, 0), (1, 0)] + assert reader.projection_uses == [ + ("chunk_transform", "context.transform"), + ("chunk_transform", "context.transform"), + ] + + +def test_chunk_cache_reader_requires_a_prepared_projection() -> None: + source_type = CACHE_NAMESPACE["RecordingChunkSource"] + reader_type = CACHE_NAMESPACE["SystemMemoryChunkReader"] + source = source_type(np.arange(48).reshape(6, 8), chunks=(3, 4)) + transform = IndexTransform.from_shape(source.shape)[1:3, 2].translate_domain_to((0,)) + out = np.empty(transform.domain.shape, dtype=source.dtype) + + with pytest.raises(ValueError, match="requires context.projection"): + reader_type(capacity=2).read_into(source, ReadContext(transform), out) + + +def test_system_memory_cache_separates_basic_and_orthogonal_indexing() -> None: + source_type = CACHE_NAMESPACE["RecordingChunkSource"] + cache_type = CACHE_NAMESPACE["SystemMemoryChunkCache"] + data = np.arange(48).reshape(6, 8) + cache = cache_type(source_type(data, chunks=(3, 4)), capacity=4) + row = np.array([0, 2]) + column = np.array([1, 3]) + + np.testing.assert_array_equal(cache[0:3, 1:4], data[0:3, 1:4]) + np.testing.assert_array_equal( + cache.oindex[row, column], + data[np.ix_(row, column)], + ) + + +def test_system_memory_cache_does_not_treat_array_keys_as_orthogonal() -> None: + source, cache = make_documented_cache() + row = np.array([0, 2]) + column = np.array([1, 3]) + + with pytest.raises(IndexError, match="unsupported selection type for basic indexing"): + cache[row, column] + + assert tuple(source.reads) == () + + +def test_system_memory_cache_assembles_a_scalar_selection() -> None: + source, cache = make_documented_cache() + + result = cache[1, 2] + + assert result.shape == () + assert result[()] == 10 + assert tuple(source.reads) == ((0, 0),) + assert cache.projection_uses == (("chunk_transform", "context.transform"),) + + +def test_system_memory_cache_is_documentation_only() -> None: + assert not hasattr(zarr_indexing, "SystemMemoryChunkCache") + assert not hasattr(zarr_indexing, "ChunkState") + + +def test_chunk_source_failure_is_retained_as_failed_with_its_cause() -> None: + source, cache = make_documented_cache() + source.failures.add((1, 1)) + + with pytest.raises(CACHE_NAMESPACE["ChunkLoadError"]) as error: + cache[3:5, 4:6] + + assert isinstance(error.value.__cause__, OSError) + assert cache.state((1, 1)).value == "failed" + assert tuple(source.reads) == ((1, 1),) + + +def test_failed_chunk_is_not_retried_implicitly() -> None: + source, cache = make_documented_cache() + source.failures.add((1, 1)) + with pytest.raises(CACHE_NAMESPACE["ChunkLoadError"]): + cache[3:5, 4:6] + with pytest.raises(CACHE_NAMESPACE["ChunkLoadError"]): + cache[3:5, 4:6] + + assert tuple(source.reads) == ((1, 1),) + + +def test_retry_requires_a_failed_chunk() -> None: + _, cache = make_documented_cache() + with pytest.raises(ValueError, match="retry requires failed chunk .*new"): + cache.retry((0, 0)) + + +def test_illegal_chunk_transition_is_rejected() -> None: + _, cache = make_documented_cache() + with pytest.raises(ValueError, match="illegal chunk transition new -> ready"): + cache.reader._transition((0, 0), CACHE_NAMESPACE["ChunkState"].READY, "test") diff --git a/packages/zarr-indexing/tests/test_domain.py b/packages/zarr-indexing/tests/test_domain.py index 9664a0b08a..0278ecd714 100644 --- a/packages/zarr-indexing/tests/test_domain.py +++ b/packages/zarr-indexing/tests/test_domain.py @@ -3,6 +3,7 @@ import pytest from zarr_indexing.domain import IndexDomain +from zarr_indexing.errors import BoundsCheckError class TestIndexDomainConstruction: @@ -171,19 +172,32 @@ def test_narrow_non_zero_origin(self) -> None: def test_narrow_int_out_of_bounds(self) -> None: d = IndexDomain.from_shape((10,)) - with pytest.raises(IndexError, match="out of bounds"): + with pytest.raises(BoundsCheckError, match="out of bounds"): d.narrow((10,)) def test_narrow_int_below_origin(self) -> None: d = IndexDomain(inclusive_min=(5,), exclusive_max=(10,)) - with pytest.raises(IndexError, match="out of bounds"): + with pytest.raises(BoundsCheckError, match="out of bounds"): d.narrow((4,)) - def test_narrow_clamps_to_domain(self) -> None: + def test_narrow_refuses_a_bound_outside_the_domain(self) -> None: + """Clamping made two different requests answer alike, and neither well. + + Indices here are absolute coordinates, so `-5` is a coordinate this + domain does not contain rather than NumPy's "five from the end" — and + clamping returned the whole axis for it, which is what a caller writing + the NumPy spelling would least expect. A stop past the end produced a + domain the parent did not contain. + """ d = IndexDomain.from_shape((10,)) - result = d.narrow((slice(-5, 100),)) - assert result.inclusive_min == (0,) - assert result.exclusive_max == (10,) + with pytest.raises(BoundsCheckError, match="absolute coordinates"): + d.narrow((slice(-5, 100),)) + with pytest.raises(BoundsCheckError, match="out of bounds"): + d.narrow((slice(20, 30),)) + + def test_narrow_accepts_the_bounds_of_the_domain_itself(self) -> None: + d = IndexDomain.from_shape((10,)) + assert d.narrow((slice(0, 10),)) == d def test_narrow_bare_slice(self) -> None: d = IndexDomain.from_shape((10,)) @@ -197,6 +211,8 @@ def test_narrow_too_many_indices(self) -> None: d.narrow((1, 2)) def test_narrow_step_not_one(self) -> None: + """A stride is not a bounds failure — the rest of the algebra raises + `ValueError` for a request it does not implement, and so does this.""" d = IndexDomain.from_shape((10,)) - with pytest.raises(IndexError, match="step=1"): + with pytest.raises(ValueError, match="step=1"): d.narrow((slice(0, 10, 2),)) diff --git a/packages/zarr-indexing/tests/test_json.py b/packages/zarr-indexing/tests/test_json.py index 42b59b2c30..9848c6801f 100644 --- a/packages/zarr-indexing/tests/test_json.py +++ b/packages/zarr-indexing/tests/test_json.py @@ -1,21 +1,23 @@ from __future__ import annotations +from typing import TYPE_CHECKING, Any + import numpy as np import pytest from zarr_indexing.domain import IndexDomain -from zarr_indexing.json import ( - IndexTransformJSON, - index_domain_from_json, - index_domain_to_json, - index_transform_from_json, - index_transform_to_json, +from zarr_indexing.messages import NdselError +from zarr_indexing.output_map import ( + ArrayMap, + ConstantMap, + DimensionMap, output_index_map_from_json, - output_index_map_to_json, ) -from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap from zarr_indexing.transform import IndexTransform +if TYPE_CHECKING: + from zarr_indexing.json import IndexTransformJSON + def _maps_equal(a: object, b: object) -> bool: if type(a) is not type(b): @@ -31,7 +33,6 @@ def _maps_equal(a: object, b: object) -> bool: return ( a.offset == b.offset and a.stride == b.stride - and a.input_dimension == b.input_dimension and np.array_equal(a.index_array, b.index_array) ) @@ -49,45 +50,45 @@ def _transforms_equal(a: IndexTransform, b: IndexTransform) -> bool: class TestIndexDomainJSON: def test_roundtrip(self) -> None: domain = IndexDomain(inclusive_min=(2, 5), exclusive_max=(10, 20)) - json = index_domain_to_json(domain) + json = domain.to_json() assert json == { "input_inclusive_min": [2, 5], "input_exclusive_max": [10, 20], "input_labels": ["", ""], } - restored = index_domain_from_json(json) + restored = IndexDomain.from_json(json) assert restored == domain def test_with_labels(self) -> None: domain = IndexDomain(inclusive_min=(0, 0), exclusive_max=(10, 20), labels=("x", "y")) - json = index_domain_to_json(domain) + json = domain.to_json() assert json["input_labels"] == ["x", "y"] - restored = index_domain_from_json(json) + restored = IndexDomain.from_json(json) assert restored.labels == ("x", "y") def test_without_labels_emits_empty_and_round_trips_to_none(self) -> None: domain = IndexDomain.from_shape((5,)) - json = index_domain_to_json(domain) + json = domain.to_json() # Canonical form always writes labels; an unlabeled domain gets [""]*rank. assert json["input_labels"] == [""] - restored = index_domain_from_json(json) + restored = IndexDomain.from_json(json) assert restored.labels is None def test_zero_origin(self) -> None: domain = IndexDomain.from_shape((10, 20, 30)) - json = index_domain_to_json(domain) + json = domain.to_json() assert json == { "input_inclusive_min": [0, 0, 0], "input_exclusive_max": [10, 20, 30], "input_labels": ["", "", ""], } - assert index_domain_from_json(json) == domain + assert IndexDomain.from_json(json) == domain class TestOutputIndexMapJSON: def test_constant(self) -> None: m = ConstantMap(offset=42) - json = output_index_map_to_json(m) + json = m.to_json() assert json == {"offset": 42} restored = output_index_map_from_json(json) assert isinstance(restored, ConstantMap) @@ -95,7 +96,7 @@ def test_constant(self) -> None: def test_constant_zero(self) -> None: m = ConstantMap(offset=0) - json = output_index_map_to_json(m) + json = m.to_json() assert json == {"offset": 0} restored = output_index_map_from_json(json) assert isinstance(restored, ConstantMap) @@ -103,7 +104,7 @@ def test_constant_zero(self) -> None: def test_dimension(self) -> None: m = DimensionMap(input_dimension=1, offset=10, stride=3) - json = output_index_map_to_json(m) + json = m.to_json() assert json == {"offset": 10, "stride": 3, "input_dimension": 1} restored = output_index_map_from_json(json) assert isinstance(restored, DimensionMap) @@ -114,7 +115,7 @@ def test_dimension(self) -> None: def test_dimension_stride_1_written(self) -> None: """Canonical form writes stride even at its default of 1.""" m = DimensionMap(input_dimension=0) - json = output_index_map_to_json(m) + json = m.to_json() assert json == {"offset": 0, "stride": 1, "input_dimension": 0} restored = output_index_map_from_json(json) assert isinstance(restored, DimensionMap) @@ -123,7 +124,7 @@ def test_dimension_stride_1_written(self) -> None: def test_array(self) -> None: arr = np.array([1, 5, 9], dtype=np.intp) m = ArrayMap(index_array=arr, offset=2, stride=3) - json = output_index_map_to_json(m) + json = m.to_json() # Canonical: stride/offset present, index_array_bounds present, and # no input_dimension (ndsel/TensorStore reject it beside index_array). assert json == { @@ -141,7 +142,7 @@ def test_array(self) -> None: def test_array_stride_1_written(self) -> None: arr = np.array([0, 1, 2], dtype=np.intp) m = ArrayMap(index_array=arr) - json = output_index_map_to_json(m) + json = m.to_json() assert json["stride"] == 1 restored = output_index_map_from_json(json) assert isinstance(restored, ArrayMap) @@ -150,7 +151,7 @@ def test_array_stride_1_written(self) -> None: def test_array_2d(self) -> None: arr = np.array([[1, 2], [3, 4]], dtype=np.intp) m = ArrayMap(index_array=arr) - json = output_index_map_to_json(m) + json = m.to_json() assert json["index_array"] == [[1, 2], [3, 4]] restored = output_index_map_from_json(json) assert isinstance(restored, ArrayMap) @@ -159,7 +160,7 @@ def test_array_2d(self) -> None: def test_degenerate_singleton_array_collapses_to_constant(self) -> None: """An all-singleton index_array selects one coordinate -> constant map.""" m = ArrayMap(index_array=np.array([[4]], dtype=np.intp), offset=1, stride=2) - json = output_index_map_to_json(m) + json = m.to_json() assert json == {"offset": 1 + 2 * 4} restored = output_index_map_from_json(json) assert isinstance(restored, ConstantMap) @@ -169,7 +170,7 @@ def test_degenerate_singleton_array_collapses_to_constant(self) -> None: class TestIndexTransformJSON: def test_identity(self) -> None: t = IndexTransform.from_shape((10, 20)) - json = index_transform_to_json(t) + json = t.to_json() assert json == { "input_rank": 2, "input_inclusive_min": [0, 0], @@ -180,7 +181,7 @@ def test_identity(self) -> None: {"offset": 0, "stride": 1, "input_dimension": 1}, ], } - restored = index_transform_from_json(json) + restored = IndexTransform.from_json(json) assert restored.domain == t.domain assert len(restored.output) == 2 for orig, rest in zip(t.output, restored.output, strict=True): @@ -188,8 +189,8 @@ def test_identity(self) -> None: def test_sliced(self) -> None: t = IndexTransform.from_shape((100,))[10:50:2] - json = index_transform_to_json(t) - restored = index_transform_from_json(json) + json = t.to_json() + restored = IndexTransform.from_json(json) assert restored.domain.shape == t.domain.shape assert isinstance(restored.output[0], DimensionMap) orig = t.output[0] @@ -199,8 +200,8 @@ def test_sliced(self) -> None: def test_with_constant(self) -> None: t = IndexTransform.from_shape((10, 20))[3] - json = index_transform_to_json(t) - restored = index_transform_from_json(json) + json = t.to_json() + restored = IndexTransform.from_json(json) assert isinstance(restored.output[0], ConstantMap) assert restored.output[0].offset == 3 assert isinstance(restored.output[1], DimensionMap) @@ -208,23 +209,21 @@ def test_with_constant(self) -> None: def test_with_array(self) -> None: idx = np.array([1, 5, 9], dtype=np.intp) t = IndexTransform.from_shape((10, 20)).oindex[idx, :] - json = index_transform_to_json(t) + json = t.to_json() # The oindex array must not carry input_dimension on the wire. assert "input_dimension" not in json["output"][0] - restored = index_transform_from_json(json) + restored = IndexTransform.from_json(json) assert isinstance(restored.output[0], ArrayMap) # Orthogonal arrays are normalized to full input rank with a singleton # axis on the dimension they do not vary over. assert restored.output[0].index_array.shape == (3, 1) np.testing.assert_array_equal(restored.output[0].index_array, idx.reshape(3, 1)) - # input_dimension is reconstructed from the sole non-singleton axis. - assert restored.output[0].input_dimension == 0 assert isinstance(restored.output[1], DimensionMap) def test_roundtrip_preserves_singleton_axes(self) -> None: """Full-rank orthogonal arrays keep their singleton axes across JSON.""" t = IndexTransform.from_shape((10, 20)).oindex[np.array([1, 3]), np.array([2, 4, 6])] - restored = index_transform_from_json(index_transform_to_json(t)) + restored = IndexTransform.from_json(t.to_json()) orig0, orig1 = t.output[0], t.output[1] rest0, rest1 = restored.output[0], restored.output[1] assert isinstance(orig0, ArrayMap) @@ -235,16 +234,13 @@ def test_roundtrip_preserves_singleton_axes(self) -> None: assert rest1.index_array.shape == (1, 3) np.testing.assert_array_equal(rest0.index_array, orig0.index_array) np.testing.assert_array_equal(rest1.index_array, orig1.index_array) - # Distinct, exclusively-owned axes -> reconstructed as orthogonal. - assert rest0.input_dimension == 0 - assert rest1.input_dimension == 1 def test_with_labels(self) -> None: domain = IndexDomain(inclusive_min=(0, 0), exclusive_max=(10, 20), labels=("x", "y")) t = IndexTransform.identity(domain) - json = index_transform_to_json(t) + json = t.to_json() assert json["input_labels"] == ["x", "y"] - restored = index_transform_from_json(json) + restored = IndexTransform.from_json(json) assert restored.domain.labels == ("x", "y") def test_tensorstore_compatible_format(self) -> None: @@ -257,10 +253,12 @@ def test_tensorstore_compatible_format(self) -> None: "output": [ {"offset": 5}, {"offset": 10, "stride": 2, "input_dimension": 1}, - {"offset": 0, "stride": 1, "index_array": [1, 2, 0]}, + # Full input rank, which is what TensorStore itself requires: + # it rejects a rank-1 array over a rank-3 domain outright. + {"offset": 0, "stride": 1, "index_array": [[[1, 2, 0]]]}, ], } - t = index_transform_from_json(json) + t = IndexTransform.from_json(json) assert t.domain.shape == (100, 200, 3) assert t.domain.labels == ("x", "y", "channel") assert isinstance(t.output[0], ConstantMap) @@ -270,11 +268,11 @@ def test_tensorstore_compatible_format(self) -> None: assert t.output[1].stride == 2 assert t.output[1].input_dimension == 1 assert isinstance(t.output[2], ArrayMap) - np.testing.assert_array_equal(t.output[2].index_array, [1, 2, 0]) + np.testing.assert_array_equal(t.output[2].index_array, [[[1, 2, 0]]]) # Roundtrip - json_rt = index_transform_to_json(t) - t_rt = index_transform_from_json(json_rt) + json_rt = t.to_json() + t_rt = IndexTransform.from_json(json_rt) assert t_rt.domain == t.domain @@ -284,34 +282,41 @@ class TestCanonicalRoundTrips: def test_oindex_multi_axis(self) -> None: t = IndexTransform.from_shape((10, 20, 30)).oindex[np.array([1, 3]), :, np.array([2, 4, 6])] - rt = index_transform_from_json(index_transform_to_json(t)) + rt = IndexTransform.from_json(t.to_json()) assert _transforms_equal(rt, t) def test_oindex_with_slice(self) -> None: t = IndexTransform.from_shape((10, 20))[2:8].oindex[np.array([3, 5, 7]), :] - rt = index_transform_from_json(index_transform_to_json(t)) + rt = IndexTransform.from_json(t.to_json()) assert _transforms_equal(rt, t) def test_vindex(self) -> None: t = IndexTransform.from_shape((10, 20)).vindex[np.array([1, 3, 5]), np.array([2, 4, 6])] - rt = index_transform_from_json(index_transform_to_json(t)) + rt = IndexTransform.from_json(t.to_json()) assert _transforms_equal(rt, t) def test_vindex_with_residual_slice(self) -> None: t = IndexTransform.from_shape((10, 20, 30)).vindex[np.array([1, 3]), np.array([2, 4]), :] - rt = index_transform_from_json(index_transform_to_json(t)) + rt = IndexTransform.from_json(t.to_json()) assert _transforms_equal(rt, t) def test_length1_degenerate_oindex_collapses(self) -> None: - """A length-1 oindex array becomes an all-singleton ArrayMap; the JSON - round-trip collapses it to a ConstantMap (behaviorally identical).""" + """A length-1 oindex selection is the ConstantMap it equals. + + The selection layer collapses it at construction; a hand-built + all-singleton ArrayMap still collapses on serialize, so the canonical + wire form is a `constant` map either way. + """ t = IndexTransform.from_shape((10, 20)).oindex[np.array([7]), :] m = t.output[0] - assert isinstance(m, ArrayMap) - assert m.index_array.size == 1 - - rt = index_transform_from_json(index_transform_to_json(t)) - # The degenerate array collapsed to a constant selecting the same cell. + assert isinstance(m, ConstantMap) + assert m.offset == 7 + + hand_built = IndexTransform( + domain=t.domain, + output=(ArrayMap(index_array=np.array([[7]], dtype=np.intp)), t.output[1]), + ) + rt = IndexTransform.from_json(hand_built.to_json()) rm = rt.output[0] assert isinstance(rm, ConstantMap) assert rm.offset == 7 @@ -320,10 +325,83 @@ def test_length1_degenerate_oindex_collapses(self) -> None: def test_slices_and_constants(self) -> None: t = IndexTransform.from_shape((10, 20, 30))[2:8:2, 5, :] - rt = index_transform_from_json(index_transform_to_json(t)) + rt = IndexTransform.from_json(t.to_json()) assert _transforms_equal(rt, t) +def _index_array_body(index_array: Any, rank: int = 1, extent: int = 2) -> IndexTransformJSON: + return { + "input_rank": rank, + "input_inclusive_min": [0] * rank, + "input_exclusive_max": [extent] * rank, + "input_labels": [""] * rank, + "output": [{"offset": 0, "stride": 1, "index_array": index_array}], + } + + +@pytest.mark.parametrize( + ("index_array", "detail"), + [ + ([0.9, 1.9], "float64"), + ([0, 1.5], "float64"), + ([True, False], "bool"), + (["a", "b"], "str"), + # Not lists at all, so they are turned away before their content is + # looked at: a bare string would be iterated into characters, and a bare + # integer would become a rank-0 array and then a length-1 map, so a + # document naming no cells would select one. + ("abc", "must be an array of integers"), + (5, "must be an array of integers"), + ([None, None], "object"), + ], + ids=["floats", "mixed", "bools", "strings", "string", "scalar", "nulls"], +) +def test_a_non_integer_index_array_is_rejected(index_array: Any, detail: str) -> None: + """An `index_array` addresses output coordinates, so it must be integral. + + Lowering a float array silently truncated it (`[0.9, 1.9]` selected cells 0 + and 1), a bool array coerced to 0/1, and a string array leaked a raw NumPy + `ValueError` from the middle of the conversion. + """ + with pytest.raises(NdselError) as excinfo: + IndexTransform.from_json(_index_array_body(index_array)) + assert excinfo.value.reason == "invalid_json" + assert "index_array" in str(excinfo.value) + assert detail in str(excinfo.value) + + +def test_a_ragged_index_array_is_rejected() -> None: + """A nested list that is not rectangular is not an array at all.""" + with pytest.raises(NdselError) as excinfo: + IndexTransform.from_json(_index_array_body([[0, 1], [2]])) + assert excinfo.value.reason == "invalid_json" + + +@pytest.mark.parametrize( + ("index_array", "rank", "extent"), + [([0, 1], 1, 2), ([[0], [1]], 2, 2), ([], 1, 0)], + ids=["1d", "2d", "empty"], +) +def test_an_integer_index_array_is_accepted(index_array: Any, rank: int, extent: int) -> None: + """Integers of any nesting still lower, including an empty selection. + + An empty array selects nothing, so the domain it is read over is empty too; + a domain with room for coordinates the array does not supply is rejected + (see `test_an_index_array_that_does_not_span_its_domain_is_rejected`). + """ + t = IndexTransform.from_json(_index_array_body(index_array, rank, extent)) + m = t.output[0] + assert isinstance(m, ArrayMap) + assert m.index_array.dtype == np.intp + + +def test_a_non_integer_index_array_is_rejected_by_the_map_loader() -> None: + """The single-map loader enforces the same constraint as the transform one.""" + with pytest.raises(NdselError) as excinfo: + output_index_map_from_json({"index_array": [0.5, 1.5]}) + assert excinfo.value.reason == "invalid_json" + + def test_infinite_bound_rejected_on_lowering() -> None: body: IndexTransformJSON = { "input_rank": 1, @@ -333,4 +411,176 @@ def test_infinite_bound_rejected_on_lowering() -> None: "output": [{"offset": 0, "stride": 1, "input_dimension": 0}], } with pytest.raises(ValueError, match="infinite"): - index_transform_from_json(body) + IndexTransform.from_json(body) + + +def test_a_lower_rank_index_array_is_widened_on_the_way_in() -> None: + """External JSON may broadcast a lower-rank array; the engine never holds one. + + ndsel leaves index-array rank unvalidated, so a conformant producer may send + an array of lower rank. It is widened at the boundary, which keeps the + full-rank invariant true of every transform the engine builds. + """ + # A rank-1 array widens into the trailing axis, so it spans that axis's + # extent of four. + body: IndexTransformJSON = { + "input_inclusive_min": [0, 0], + "input_exclusive_max": [3, 4], + "output": [{"index_array": [1, 2, 0, 2]}, {"input_dimension": 1}], + } + transform = IndexTransform.from_json(body) + array_map = transform.output[0] + assert isinstance(array_map, ArrayMap) + assert array_map.index_array.shape == (1, 4) + assert array_map.index_array.ndim == transform.domain.ndim + + +def test_an_index_array_of_the_wrong_rank_is_rejected() -> None: + """Inside the engine, a rank that does not match the domain is a bug.""" + with pytest.raises(ValueError, match="index_array has 1 dims"): + IndexTransform( + domain=IndexDomain.from_shape((3, 4)), + output=(ArrayMap(index_array=np.array([1, 2, 0], dtype=np.intp)),), + ) + + +def test_an_index_array_that_does_not_span_its_domain_is_rejected() -> None: + """An array with entries for only part of an axis is not a smaller selection. + + Reading it that way is how a truncated index array turned into a partially + written result rather than an error. + """ + with pytest.raises(ValueError, match="neither 1 nor the domain's extent"): + IndexTransform( + domain=IndexDomain.from_shape((3, 2)), + output=( + ArrayMap(index_array=np.zeros((3, 0), dtype=np.intp)), + DimensionMap(input_dimension=1), + ), + ) + + +def test_an_empty_index_array_collapses_to_a_constant() -> None: + """Selecting nothing must survive a trip through JSON. + + An empty index array names no cell, and can only be empty because an input + dimension is, so nothing is ever read through it. It is degenerate in + exactly the way a size-1 array is, and collapses the same way — which is + also what TensorStore emits for `t[ts.d[0][[]]]`. + + Emitting the array instead produced a document nothing could load: + `tolist()` renders every empty array as `[]` once the leading axis is the + zero-length one, so the rank went with it, and the loader put the dependency + back on a different axis by prepending singletons. + """ + for shape, selection in ( + ((5, 3), (np.array([], dtype=np.intp), slice(None))), + ((5, 5), (np.array([], dtype=np.intp), np.array([], dtype=np.intp))), + ): + transform = IndexTransform.from_shape(shape).oindex[selection] + body = transform.to_json() + + assert all("index_array" not in m for m in body["output"]) + reloaded = IndexTransform.from_json(body) + assert reloaded.domain == transform.domain + assert reloaded.to_json() == body + + +def test_an_empty_index_array_from_elsewhere_is_recovered_from_the_domain() -> None: + """A producer that does emit one is still readable when the domain settles it. + + This package never writes such a document, but ndsel does not forbid it, and + the domain names the axis unambiguously when exactly one dimension is empty. + """ + body: IndexTransformJSON = { + "input_inclusive_min": [0, 0], + "input_exclusive_max": [0, 4], + "output": [{"index_array": []}, {"input_dimension": 1}], + } + array_map = IndexTransform.from_json(body).output[0] + assert isinstance(array_map, ArrayMap) + assert array_map.index_array.shape == (0, 1) + + +def test_an_ambiguous_empty_index_array_is_rejected() -> None: + """Two zero-length dimensions leave nothing to recover the axis from.""" + body: IndexTransformJSON = { + "input_inclusive_min": [0, 0], + "input_exclusive_max": [0, 0], + "output": [{"index_array": []}, {"input_dimension": 1}], + } + with pytest.raises(NdselError) as excinfo: + IndexTransform.from_json(body) + assert excinfo.value.reason == "invalid_json" + assert "zero-length" in str(excinfo.value) + + +@pytest.mark.parametrize( + ("document", "reason", "detail"), + [ + ( + {"input_inclusive_min": [0.0], "input_exclusive_max": [3], "input_labels": [""]}, + "invalid_json", + "must be an integer", + ), + ( + {"input_inclusive_min": [0], "input_exclusive_max": ["3"], "input_labels": [""]}, + "invalid_json", + "must be an integer", + ), + ( + {"input_inclusive_min": [False], "input_exclusive_max": [True], "input_labels": [""]}, + "invalid_json", + "must be an integer", + ), + ( + {"input_inclusive_min": [0], "input_exclusive_max": [3], "input_labels": [5]}, + "invalid_json", + "must be a string", + ), + ( + {"input_inclusive_min": [0], "input_exclusive_max": [2**200], "input_labels": [""]}, + "invalid_json", + "64-bit signed range", + ), + ], + ids=["float", "string", "bool", "non-string-label", "out-of-range"], +) +def test_a_malformed_domain_document_is_rejected(document: Any, reason: str, detail: str) -> None: + """The domain loader validates what the message layer validates. + + Reading the keys directly was a second, undefended way into the same + objects: a bare `int()` truncated `3.9` to 3, coerced `"3"` and `True`, and + let a non-string label into a `tuple[str, ...]` — each building a domain + that was not the document's, and re-dumping as a different document. + """ + with pytest.raises(NdselError) as excinfo: + IndexDomain.from_json(document) + assert excinfo.value.reason == reason + assert detail in str(excinfo.value) + + +def test_a_transform_body_cannot_reinterpret_itself_as_another_message() -> None: + """A `kind` inside the body must not change which message is being read.""" + with pytest.raises(NdselError) as excinfo: + IndexTransform.from_json({"kind": "points", "coords": [[1, 2], [3, 4]]}) + assert excinfo.value.reason == "invalid_json" + assert "kind" in str(excinfo.value) + + +def test_an_engine_invariant_failure_leaves_the_loader_as_a_typed_error() -> None: + """A document is invalid input however deep the check that catches it lives. + + The engine's rank and span invariants are the last gate a document passes, + and they raised a bare `ValueError` written in the engine's vocabulary. + """ + body: IndexTransformJSON = { + "input_rank": 1, + "input_inclusive_min": [0], + "input_exclusive_max": [5], + "input_labels": [""], + "output": [{"index_array": [[1, 2], [3, 4]]}], + } + with pytest.raises(NdselError) as excinfo: + IndexTransform.from_json(body) + assert excinfo.value.reason == "rank_mismatch" diff --git a/packages/zarr-indexing/tests/test_lazy_array.py b/packages/zarr-indexing/tests/test_lazy_array.py new file mode 100644 index 0000000000..ab94be1ae5 --- /dev/null +++ b/packages/zarr-indexing/tests/test_lazy_array.py @@ -0,0 +1,2618 @@ +"""Tests for `zarr_indexing.grid` grids and the `LazyArray` wrapper. + +The happy-path suite is a single oracle test: every selection case is applied +both to a `LazyArray` and to the NumPy array it wraps, and the results must +match. The case list is crossed with four source flavors — an unchunked NumPy +array, NumPy with each of the two declared chunk conventions, and a zarr array +whose chunking is auto-discovered — so the chunked and unchunked resolution +strategies are held to the same answers. +""" + +from __future__ import annotations + +import operator +import pickle +from concurrent.futures import ThreadPoolExecutor +from dataclasses import replace +from typing import TYPE_CHECKING, Any, cast + +import numpy as np +import pytest + +import zarr_indexing.lazy_array as lazy_array_module +from zarr_indexing import ( + ArrayMap, + ChunkGrid, + ChunkProjection, + ConstantMap, + DimensionMap, + EdgeDimensionGrid, + FixedDimension, + IndexTransform, + LazyArray, + ReadContext, + VaryingDimension, + dimension_grids_from_chunks, +) +from zarr_indexing.lazy_array import _out_selection_cell_count, _validate_prepared_parts +from zarr_indexing.reader import Reader, basic_reader, numpy_reader +from zarr_indexing.testing import repartition + +if TYPE_CHECKING: + from collections.abc import Callable, Sequence + +SHAPE = (7, 5, 4) +PART_SHAPE = (3, 2, 3) +EXPLICIT_PARTS = ((3, 3, 1), (2, 2, 1), (3, 1)) + + +class IndexLike: + """A scalar integer selector implemented only through `__index__`.""" + + def __init__(self, value: int) -> None: + self.value = value + + def __index__(self) -> int: + return self.value + + +class IntOnly: + def __int__(self) -> int: + return 2 + + +class BadIndex: + """An `__index__` that lies: the protocol requires an integer.""" + + def __index__(self) -> int: + return cast("int", 2.5) + + +def reference() -> np.ndarray[Any, np.dtype[np.int64]]: + """The array every source flavor holds, and the oracle for every case.""" + return np.arange(int(np.prod(SHAPE)), dtype=np.int64).reshape(SHAPE) + + +class DelegatingReader: + def __init__(self, inner: Reader) -> None: + self.inner = inner + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + self.inner.read_into(source, context, out) + + +def outer(ref: np.ndarray[Any, Any], selections: Sequence[Any]) -> np.ndarray[Any, Any]: + """NumPy oracle for orthogonal indexing: the outer product of per-axis selections. + + Scalar integers are basic indices — NumPy applies them first and drops the + axis — so they are peeled off before the outer product is formed. + """ + scalars = tuple( + sel if isinstance(sel, (int, np.integer)) and not isinstance(sel, bool) else slice(None) + for sel in selections + ) + reduced = ref[scalars] + axes = [ + np.arange(size)[sel] + for size, sel in zip( + reduced.shape, + [ + s + for s in selections + if not (isinstance(s, (int, np.integer)) and not isinstance(s, bool)) + ], + strict=True, + ) + ] + if len(axes) == 0: + return reduced + return reduced[np.ix_(*axes)] + + +# --------------------------------------------------------------------------- +# EdgeDimensionGrid +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + ("sizes", "expected_index_to_chunk", "expected_offsets", "expected_sizes"), + [ + # A clipped edge chunk. + ((3, 3, 1), [0, 0, 0, 1, 1, 1, 2], [0, 3, 6], [3, 3, 1]), + # A single chunk covering the whole axis. + ((4,), [0, 0, 0, 0], [0], [4]), + # A size-1 axis. + ((1,), [0], [0], [1]), + # Irregular sizes: the grid does not have to be regular. + ((1, 2, 1), [0, 1, 1, 2], [0, 1, 3], [1, 2, 1]), + ], +) +def test_edge_dimension_grid( + sizes: tuple[int, ...], + expected_index_to_chunk: list[int], + expected_offsets: list[int], + expected_sizes: list[int], +) -> None: + """All four `DimensionGridLike` methods agree with hand-computed values.""" + grid = EdgeDimensionGrid(sizes) + extent = sum(sizes) + + assert grid.num_chunks == len(sizes) + assert grid.extent == extent + assert [grid.index_to_chunk(i) for i in range(extent)] == expected_index_to_chunk + assert [grid.chunk_offset(c) for c in range(len(sizes))] == expected_offsets + assert [grid.chunk_size(c) for c in range(len(sizes))] == expected_sizes + np.testing.assert_array_equal( + grid.indices_to_chunks(np.arange(extent, dtype=np.intp)), + np.asarray(expected_index_to_chunk, dtype=np.intp), + ) + + +def test_edge_dimension_grid_rejects_nonpositive_size() -> None: + with pytest.raises(ValueError, match="chunk sizes must be positive"): + EdgeDimensionGrid((3, 0, 2)) + + +def test_edge_dimension_grid_rejects_out_of_bounds_index() -> None: + with pytest.raises(IndexError, match="out of bounds for an axis of extent 4"): + EdgeDimensionGrid((3, 1)).index_to_chunk(4) + + +def test_edge_dimension_grid_rejects_out_of_bounds_chunk() -> None: + with pytest.raises(IndexError, match="chunk index 2 is out of bounds"): + EdgeDimensionGrid((3, 1)).chunk_offset(2) + + +@pytest.mark.parametrize( + "grid", + [ + pytest.param(FixedDimension(size=2, extent=4), id="fixed"), + pytest.param(VaryingDimension(edges=(1, 3), extent=4), id="varying"), + ], +) +def test_compact_dimension_grid_rejects_vector_below_extent(grid: Any) -> None: + with pytest.raises(IndexError, match=r"indices must lie in \[0, 4\); got \[-1, 1\]"): + grid.indices_to_chunks(np.array([-1, 1], dtype=np.intp)) + + +@pytest.mark.parametrize( + "grid", + [ + pytest.param(FixedDimension(size=2, extent=4), id="fixed"), + pytest.param(VaryingDimension(edges=(1, 3), extent=4), id="varying"), + ], +) +def test_compact_dimension_grid_rejects_vector_above_extent(grid: Any) -> None: + with pytest.raises(IndexError, match=r"indices must lie in \[0, 4\); got \[1, 4\]"): + grid.indices_to_chunks(np.array([1, 4], dtype=np.intp)) + + +def test_fixed_dimension_rejects_zero_size_for_nonempty_extent() -> None: + with pytest.raises(ValueError, match="size must be > 0 when extent is nonzero"): + FixedDimension(size=0, extent=4) + + +def test_fixed_dimension_retains_zero_size_for_zero_extent() -> None: + grid = FixedDimension(size=0, extent=0) + + assert grid.nchunks == 0 + assert grid.ngridcells == 0 + + +@pytest.mark.parametrize( + ("chunks", "shape", "expected"), + [ + # Uniform chunk shape, tail clipped. + ((3, 4), (7, 4), (FixedDimension(size=3, extent=7), FixedDimension(size=4, extent=4))), + # Dask-convention per-axis sizes, passed through. + ( + ((3, 3, 1), (2, 2)), + (7, 4), + (VaryingDimension(edges=(3, 3, 1), extent=7), VaryingDimension(edges=(2, 2), extent=4)), + ), + # A chunk longer than the axis collapses to one clipped chunk. + ((10,), (4,), (FixedDimension(size=10, extent=4),)), + # A zero-length axis has no chunks at all. + ((3,), (0,), (FixedDimension(size=3, extent=0),)), + ], +) +def test_dimension_grids_from_chunks( + chunks: Any, shape: tuple[int, ...], expected: tuple[Any, ...] +) -> None: + grids = dimension_grids_from_chunks(chunks, shape) + assert grids == expected + + +def test_regular_dimension_metadata_is_constant_in_chunk_count() -> None: + dimensions = dimension_grids_from_chunks((1,), (1_000_000,)) + + assert dimensions == (FixedDimension(size=1, extent=1_000_000),) + assert dimensions[0].nchunks == 1_000_000 + assert dimensions[0].index_to_chunk(999_999) == 999_999 + + +def test_chunk_grid_distinguishes_codec_and_data_shape_at_the_edge() -> None: + grid = ChunkGrid(dimensions=(FixedDimension(size=3, extent=7),)) + + edge = grid[(2,)] + + assert edge is not None + assert edge.slices == (slice(6, 7, 1),) + assert edge.shape == (1,) + assert edge.codec_shape == (3,) + + +def test_dimension_grids_reject_negative_shape() -> None: + with pytest.raises(ValueError, match="shape entries must be non-negative"): + dimension_grids_from_chunks((3,), (-1,)) + + +def test_dimension_grids_from_chunks_rejects_wrong_length() -> None: + with pytest.raises(ValueError, match="one entry per dimension"): + dimension_grids_from_chunks((3,), (7, 4)) + + +def test_dimension_grids_from_chunks_rejects_mixed_conventions() -> None: + with pytest.raises(ValueError, match="not a mixture"): + dimension_grids_from_chunks((3, (2, 2)), (7, 4)) + + +def test_dimension_grids_from_chunks_rejects_wrong_total() -> None: + with pytest.raises(ValueError, match="sum to 5, but the array extent is 7"): + dimension_grids_from_chunks(((3, 2), (4,)), (7, 4)) + + +def test_dimension_grids_from_chunks_rejects_non_sequence_entry() -> None: + """A float entry is neither convention, and says so instead of raising TypeError.""" + with pytest.raises(ValueError, match=r"3\.5 at dimension 0 is neither"): + dimension_grids_from_chunks((3.5, (4,)), (7, 4)) + + +def test_array_map_dependent_axis_reports_no_axis() -> None: + """A map varying over nothing answers None rather than a stale binding.""" + correlated = ArrayMap(index_array=np.array([[1], [2]], dtype=np.intp)) + assert correlated.dependent_axis == 0 + assert ArrayMap(index_array=np.array([[3]], dtype=np.intp)).dependent_axis is None + + +def test_scalar_on_a_fancy_axis_collapses_to_a_constant() -> None: + """The degenerate-collapse rule: an all-singleton ArrayMap becomes a ConstantMap. + + Without it the map keeps an `input_dimension` naming an axis the integer + index just removed, which after renumbering aliases a different axis. + """ + view = IndexTransform.from_shape((7, 5)).oindex[np.array([3, 1]), slice(None)][0] + assert view.output[0] == ConstantMap(offset=3) + assert isinstance(view.output[1], DimensionMap) + assert view.domain.shape == (5,) + + +# --------------------------------------------------------------------------- +# Sources +# --------------------------------------------------------------------------- + + +def make_zarr_source() -> Any: + """A zarr array holding `reference()`, whose parts are auto-discovered.""" + zarr = pytest.importorskip("zarr") + array = zarr.create_array({}, shape=SHAPE, chunks=PART_SHAPE, dtype="int64") + array[:] = reference() + return array + + +def make_source(flavor: str) -> LazyArray: + """Build a `LazyArray` over `reference()` with the requested partitioning.""" + data = reference() + if flavor == "numpy-whole": + return LazyArray(data) + if flavor == "numpy-explicit-parts": + return LazyArray(data).with_parts_per_axis(EXPLICIT_PARTS) + if flavor == "numpy-uniform-parts": + return LazyArray(data).with_parts(PART_SHAPE) + if flavor == "zarr": + return LazyArray(make_zarr_source()) + if flavor == "zarr-misaligned": + # Parts that deliberately straddle the zarr array's own chunks. + return LazyArray(make_zarr_source()).with_parts((4, 3, 3)) + raise TypeError(f"unknown source flavor {flavor!r}") + + +FLAVORS = [ + "numpy-whole", + "numpy-explicit-parts", + "numpy-uniform-parts", + "zarr", + "zarr-misaligned", +] + + +@pytest.fixture(params=FLAVORS) +def source(request: pytest.FixtureRequest) -> LazyArray: + return make_source(request.param) + + +# --------------------------------------------------------------------------- +# The oracle +# --------------------------------------------------------------------------- + +MASK = (reference() % 11) == 0 +# A mask over the two trailing axes, for the `vindex[..., mask]` idiom. +TRAILING_MASK = (reference()[0] % 3) == 0 + +# (id, lazy view builder, NumPy oracle). Integer scalars are deliberately absent +# from the orthogonal cases: the transform algebra keeps an int-selected axis as +# a length-1 axis under `oindex`, which `np.ix_` cannot express. +CASES: list[tuple[str, Callable[[LazyArray], LazyArray], Callable[[Any], Any]]] = [ + ( + "basic-strided-and-int-drop", + lambda a: a.lazy[1:6:2, :, -1], + lambda r: r[1:6:2, :, -1], + ), + ("basic-ellipsis", lambda a: a.lazy[..., -2], lambda r: r[..., -2]), + ("basic-negative-scalar", lambda a: a.lazy[-3], lambda r: r[-3]), + ("basic-newaxis", lambda a: a.lazy[None, :, :, None], lambda r: r[None, :, :, None]), + ("basic-empty", lambda a: a.lazy[:, 2:2, :], lambda r: r[:, 2:2, :]), + ("basic-all-scalars", lambda a: a.lazy[-1, 0, 2], lambda r: r[-1, 0, 2]), + ( + "oindex-unsorted-duplicates-multi-axis", + lambda a: a.lazy.oindex[[4, 0, 0, 2], :, [3, 1]], + lambda r: outer(r, ([4, 0, 0, 2], slice(None), [3, 1])), + ), + ( + "oindex-negative-and-slice", + lambda a: a.lazy.oindex[:, [-1, 0], 1:4], + lambda r: outer(r, (slice(None), [-1, 0], slice(1, 4))), + ), + ( + "oindex-boolean-axis", + lambda a: a.lazy.oindex[np.array([True, False, True, False, False, False, True]), :, :], + lambda r: outer( + r, + (np.array([True, False, True, False, False, False, True]), slice(None), slice(None)), + ), + ), + ( + "vindex-coordinates", + lambda a: a.lazy.vindex[np.array([0, 6, 3]), np.array([1, 4, 0]), np.array([2, 0, 1])], + lambda r: r[np.array([0, 6, 3]), np.array([1, 4, 0]), np.array([2, 0, 1])], + ), + ( + "vindex-broadcast-pair", + lambda a: a.lazy.vindex[np.array([[0], [6]]), np.array([1, 4]), np.array([2, 0])], + lambda r: r[np.array([[0], [6]]), np.array([1, 4]), np.array([2, 0])], + ), + ( + "vindex-negative-coordinates", + lambda a: a.lazy.vindex[np.array([-1, -7]), np.array([-2, 0]), np.array([0, -1])], + lambda r: r[np.array([-1, -7]), np.array([-2, 0]), np.array([0, -1])], + ), + ("vindex-mask", lambda a: a.lazy.vindex[MASK], lambda r: r[MASK]), + ( + "compose-basic-then-oindex", + lambda a: a.lazy[1:6].lazy.oindex[[3, 0, 0], [4, 1], :], + lambda r: outer(r[1:6], ([3, 0, 0], [4, 1], slice(None))), + ), + ( + "compose-oindex-then-basic-other-axis", + lambda a: a.lazy.oindex[[4, 0, 2], :, :].lazy[:, 1:4, ::2], + lambda r: outer(r, ([4, 0, 2], slice(None), slice(None)))[:, 1:4, ::2], + ), + ( + "compose-basic-then-basic", + lambda a: a.lazy[2:, 1:].lazy[::2, -1], + lambda r: r[2:, 1:][::2, -1], + ), + ( + "compose-basic-then-vindex", + lambda a: a.lazy[1:6, :, 1:].lazy.vindex[ + np.array([0, 4]), np.array([2, 0]), np.array([1, 2]) + ], + lambda r: r[1:6, :, 1:][np.array([0, 4]), np.array([2, 0]), np.array([1, 2])], + ), + # Scalar integers are basic indices in the positional dialect: they drop the + # axis, in every mode, exactly as NumPy does. + ("oindex-scalar-drops-axis", lambda a: a.lazy.oindex[0], lambda r: r[0]), + ( + "oindex-scalar-with-arrays", + lambda a: a.lazy.oindex[0, [1, 2], :], + lambda r: outer(r, (0, [1, 2], slice(None))), + ), + ( + "oindex-scalar-middle-axis", + lambda a: a.lazy.oindex[[3, 1], -1, :], + lambda r: outer(r, ([3, 1], -1, slice(None))), + ), + ("oindex-all-scalars", lambda a: a.lazy.oindex[0, 1, 2], lambda r: r[0, 1, 2]), + ("vindex-all-scalars", lambda a: a.lazy.vindex[0, 1, 2], lambda r: r[0, 1, 2]), + ( + "vindex-scalar-with-arrays", + lambda a: a.lazy.vindex[0, [1, 2], [3, 0]], + lambda r: r[0, [1, 2], [3, 0]], + ), + ( + "vindex-scalar-on-middle-axis", + lambda a: a.lazy.vindex[[1, 2], 0, [3, 0]], + lambda r: r[[1, 2], 0, [3, 0]], + ), + # Scalar applied to a previously fancy-indexed axis, both orders. + ( + "compose-oindex-then-scalar", + lambda a: a.lazy.oindex[[3, 1], :, :].lazy[0], + lambda r: outer(r, ([3, 1], slice(None), slice(None)))[0], + ), + ( + "compose-oindex-then-scalar-negative", + lambda a: a.lazy.oindex[[3, 1, 1], :, :].lazy[-1, 2], + lambda r: outer(r, ([3, 1, 1], slice(None), slice(None)))[-1, 2], + ), + ( + "compose-scalar-then-oindex", + lambda a: a.lazy[0].lazy.oindex[[3, 1], :], + lambda r: outer(r[0], ([3, 1], slice(None))), + ), + ( + "compose-vindex-then-scalar", + lambda a: a.lazy.vindex[np.array([0, 6, 3]), np.array([1, 4, 0]), np.array([2, 0, 1])].lazy[ + 1 + ], + lambda r: r[np.array([0, 6, 3]), np.array([1, 4, 0]), np.array([2, 0, 1])][1], + ), + # Partial vindex whose coordinate arrays are NOT on the leading axes: NumPy + # inserts the gathered axis where the (adjacent) advanced indices sat. + ( + "vindex-trailing-arrays", + lambda a: a.lazy.vindex[..., np.array([1, 4, 0]), np.array([2, 0, 1])], + lambda r: r[..., np.array([1, 4, 0]), np.array([2, 0, 1])], + ), + ( + "vindex-single-trailing-array", + lambda a: a.lazy.vindex[..., np.array([3, 0, 1])], + lambda r: r[..., np.array([3, 0, 1])], + ), + ( + "vindex-trailing-mask", + lambda a: a.lazy.vindex[..., TRAILING_MASK], + lambda r: r[..., TRAILING_MASK], + ), + ( + "vindex-leading-partial", + lambda a: a.lazy.vindex[np.array([1, 2, 2])], + lambda r: r[np.array([1, 2, 2])], + ), + ( + "compose-basic-then-vindex-trailing", + lambda a: a.lazy[2:, 1:].lazy.vindex[..., np.array([1, 3, 0])], + lambda r: r[2:, 1:][..., np.array([1, 3, 0])], + ), + # A ConstantMap sitting between a slice and the coordinate arrays: NumPy + # counts the integer as an advanced index, so the gathered axis moves to the + # front of the chunk block even though the arrays are trailing. + ( + "compose-vindex-trailing-then-scalar", + lambda a: a.lazy.vindex[..., np.array([3, 0])].lazy[2], + lambda r: r[..., np.array([3, 0])][2], + ), + # Two fancy axes, then a scalar on the first: the surviving ArrayMap ends up + # behind a ConstantMap and a slice, which is where NumPy's integer-counts-as- + # advanced rule bites. + ( + "compose-oindex-two-axes-then-scalar", + lambda a: a.lazy.oindex[[3, 1, 0], 3:5, [2, 0, 2]].lazy[0], + lambda r: outer(r, ([3, 1, 0], slice(3, 5), [2, 0, 2]))[0], + ), + # Negative steps: the positional dialect is NumPy's, including the empty + # cases NumPy allows where the transform algebra alone would object. + ("reverse", lambda a: a.lazy[::-1], lambda r: r[::-1]), + ("reverse-every-axis", lambda a: a.lazy[::-1, ::-1, ::-1], lambda r: r[::-1, ::-1, ::-1]), + ("reverse-strided", lambda a: a.lazy[::-2], lambda r: r[::-2]), + ("reverse-nondivisible", lambda a: a.lazy[::-3], lambda r: r[::-3]), + ("reverse-bounded", lambda a: a.lazy[5:1:-1], lambda r: r[5:1:-1]), + ("reverse-negative-start", lambda a: a.lazy[-1:None:-1], lambda r: r[-1:None:-1]), + ("reverse-past-the-start", lambda a: a.lazy[:-8:-1], lambda r: r[:-8:-1]), + ("reverse-empty", lambda a: a.lazy[2:2:-1], lambda r: r[2:2:-1]), + # NumPy reads a reversed *positional* interval as empty; only the literal + # layer calls it a direction error. + ("reverse-inverted-is-empty", lambda a: a.lazy[2:5:-1], lambda r: r[2:5:-1]), + ("reverse-with-int-drop", lambda a: a.lazy[::-2, 2, ::-1], lambda r: r[::-2, 2, ::-1]), + ("reverse-trailing-axis", lambda a: a.lazy[..., ::-1], lambda r: r[..., ::-1]), + ( + "compose-reverse-then-reverse", + lambda a: a.lazy[::-1].lazy[::-1], + lambda r: r[::-1][::-1], + ), + ( + "compose-strided-then-reverse", + lambda a: a.lazy[::2].lazy[::-1], + lambda r: r[::2][::-1], + ), + ( + "compose-reverse-then-strided", + lambda a: a.lazy[::-1].lazy[::2], + lambda r: r[::-1][::2], + ), + ( + "compose-reverse-then-oindex", + lambda a: a.lazy[::-1].lazy.oindex[[3, 0, 0], :, :], + lambda r: outer(r[::-1], ([3, 0, 0], slice(None), slice(None))), + ), + ( + "compose-oindex-then-reverse", + lambda a: a.lazy.oindex[[3, 1, 2], :, :].lazy[::-1], + lambda r: outer(r, ([3, 1, 2], slice(None), slice(None)))[::-1], + ), + ( + "compose-reverse-then-vindex", + lambda a: a.lazy[::-1].lazy.vindex[..., np.array([1, 3, 0])], + lambda r: r[::-1][..., np.array([1, 3, 0])], + ), + ( + "compose-vindex-trailing-then-scalar-and-slice", + lambda a: a.lazy.vindex[..., np.array([3, 0, 1])].lazy[-1, 1:4], + lambda r: r[..., np.array([3, 0, 1])][-1, 1:4], + ), + # A downward walk that begins off the front of the axis selects nothing. + # Written against an oindex axis and a vindex axis, where the selection is + # carried by an index array rather than by the domain. + ( + "compose-oindex-then-empty-downward-walk", + lambda a: a.lazy.oindex[np.array([3, 1, 4]), :, :].lazy[-8::-1], + lambda r: r[np.array([3, 1, 4])][-8::-1], + ), + ( + "compose-vindex-then-empty-downward-walk", + lambda a: a.lazy.vindex[np.array([3, 1]), np.array([2, 0])].lazy[-9::-2], + lambda r: r[np.array([3, 1]), np.array([2, 0])][-9::-2], + ), + ( + "empty-downward-walk-on-a-plain-axis", + lambda a: a.lazy[-11::-1], + lambda r: r[-11::-1], + ), + # A fancy *spelling* whose entries are all slices is not a fancy selection: + # it narrows the view's own axes and must compose exactly like basic + # indexing. The slices start past 0, so a step that applied them to the + # broadcast (singleton) axes of the existing index array would truncate it. + ( + "compose-oindex-then-oindex-slices-only", + lambda a: a.lazy.oindex[[4, 0, 0], :, :].lazy.oindex[:, 2:5, 1:], + lambda r: outer(r, ([4, 0, 0], slice(None), slice(None)))[:, 2:5, 1:], + ), + ( + "compose-oindex-then-oindex-slices-only-strided", + lambda a: a.lazy.oindex[:, [3, 1, 1], :].lazy.oindex[1::2, :, ::-1], + lambda r: outer(r, (slice(None), [3, 1, 1], slice(None)))[1::2, :, ::-1], + ), + ( + "compose-vindex-then-oindex-slices-only", + lambda a: a.lazy.vindex[np.array([4, 0, 2]), np.array([1, 3, 0])].lazy.oindex[1:, 2:], + lambda r: r[np.array([4, 0, 2]), np.array([1, 3, 0])][1:, 2:], + ), + ( + "compose-oindex-then-oindex-array-on-its-own-axis", + lambda a: a.lazy.oindex[[4, 0, 0], :, :].lazy.oindex[[2, 0], 3:, :], + lambda r: outer( + outer(r, ([4, 0, 0], slice(None), slice(None))), + ([2, 0], slice(3, None), slice(None)), + ), + ), +] + + +@pytest.mark.parametrize(("build", "oracle"), [c[1:] for c in CASES], ids=[c[0] for c in CASES]) +def test_selection_matches_numpy( + source: LazyArray, + build: Callable[[LazyArray], LazyArray], + oracle: Callable[[Any], Any], +) -> None: + """Every selection resolves to what NumPy computes positionally on the same data.""" + view = build(source) + expected = np.asarray(oracle(reference())) + + assert view.shape == expected.shape + assert view.ndim == expected.ndim + np.testing.assert_array_equal(np.asarray(view.result()), expected) + # `__getitem__` is eager, and `__array__` routes through `result()`. + np.testing.assert_array_equal(np.asarray(view), expected) + + +# --------------------------------------------------------------------------- +# Randomized chain sweep +# --------------------------------------------------------------------------- + + +def _random_basic(rng: np.random.Generator, shape: tuple[int, ...]) -> tuple[Any, ...]: + selection: list[Any] = [] + for size in shape: + roll = rng.random() + if roll < 0.3: + selection.append(int(rng.integers(-size, size))) + elif roll < 0.55: + start = int(rng.integers(0, size)) + stop = int(rng.integers(start, size + 1)) + selection.append(slice(start, stop, int(rng.integers(1, 4)))) + elif roll < 0.8: + # Downward: `start >= stop` and the stop may fall off the front, + # which is spelled `None`. The start is drawn from below `-size` as + # well, where the walk begins off the front and selects nothing — + # a case that reads as an ordinary negative index but is empty. + start = int(rng.integers(-2 * size - 1, size)) if size else 0 + stop_choice = int(rng.integers(-1, max(start, 0) + 1)) + stop = None if stop_choice < 0 else stop_choice + selection.append(slice(start, stop, -int(rng.integers(1, 4)))) + else: + selection.append(slice(None)) + return tuple(selection) + + +def _random_oindex(rng: np.random.Generator, shape: tuple[int, ...]) -> tuple[Any, ...]: + selection: list[Any] = [] + for size in shape: + roll = rng.random() + if roll < 0.25: + selection.append(int(rng.integers(-size, size))) + elif roll < 0.65: + count = int(rng.integers(1, 5)) + selection.append(rng.integers(-size, size, size=count).tolist()) + elif roll < 0.8: + mask = rng.random(size) < 0.5 + mask[int(rng.integers(0, size))] = True + selection.append(mask) + else: + start = int(rng.integers(0, size)) + selection.append(slice(start, size)) + return tuple(selection) + + +def _broadcast_singleton_axes( + rng: np.random.Generator, entries: list[Any], length: int +) -> list[Any]: + """Reshape 1-D coordinate arrays so the selection carries singleton axes. + + A coordinate array of shape `(1, n)` or `(n, 1)` contributes a broadcast axis + it does not vary over. That axis stays in the view's domain, and a later + basic index that consumes its partner leaves it referenced by no output map + at all — the shape that makes a broadcast axis and a genuine extent-1 axis + indistinguishable from the index array alone. + """ + rank = int(rng.integers(2, 4)) + reshaped: list[Any] = [] + for entry in entries: + if not isinstance(entry, np.ndarray): + reshaped.append(entry) + continue + varying = int(rng.integers(0, rank)) + reshaped.append( + entry.reshape(tuple(length if axis == varying else 1 for axis in range(rank))) + ) + return reshaped + + +def _random_vindex(rng: np.random.Generator, shape: tuple[int, ...]) -> tuple[Any, ...]: + ndim = len(shape) + count = int(rng.integers(1, ndim + 1)) + trailing = bool(rng.random() < 0.5) + axes = range(ndim - count, ndim) if trailing else range(count) + sizes = [shape[axis] for axis in axes] + + entries: list[Any] + if rng.random() < 0.2: + # A single boolean mask spanning the whole covered block. + mask = rng.random(tuple(sizes)) < 0.5 + mask.flat[int(rng.integers(0, mask.size))] = True + entries = [mask] + else: + length = int(rng.integers(1, 5)) + entries = [ + int(rng.integers(-size, size)) + if rng.random() < 0.25 + else rng.integers(-size, size, size=length) + for size in sizes + ] + if rng.random() < 0.35: + entries = _broadcast_singleton_axes(rng, entries, length) + return (Ellipsis, *entries) if trailing else tuple(entries) + + +def _apply_oracle( + ref: np.ndarray[Any, Any], mode: str, selection: tuple[Any, ...] +) -> np.ndarray[Any, Any]: + if mode == "orthogonal": + return outer(ref, selection) + # NumPy's own semantics *are* basic and vectorized indexing. + return ref[selection] + + +def _apply_view(view: LazyArray, mode: str, selection: tuple[Any, ...]) -> LazyArray: + if mode == "basic": + return view.lazy[selection] + if mode == "orthogonal": + return view.lazy.oindex[selection] + return view.lazy.vindex[selection] + + +def _random_slices_only(rng: np.random.Generator, shape: tuple[int, ...]) -> tuple[Any, ...]: + """A selection of slices alone, spelled through `oindex`. + + `oindex` entries that are all slices are not a fancy selection — they narrow + the view's own axes and must compose like basic indexing. A start past 0 is + what distinguishes a step that walks the index array's dependency axes from + one that walks its broadcast singletons, so slices are drawn to reach past + the origin. (`vindex` is coordinate-only and rejects a slice outright, so + this spelling has no vectorized counterpart.) + """ + selection: list[Any] = [] + for size in shape: + roll = rng.random() + if roll < 0.4: + start = int(rng.integers(0, size)) if size else 0 + selection.append(slice(start, size)) + elif roll < 0.7: + start = int(rng.integers(0, size)) if size else 0 + selection.append(slice(start, size, int(rng.integers(1, 3)))) + elif roll < 0.85: + selection.append(slice(None, None, -1)) + else: + selection.append(slice(None)) + return tuple(selection) + + +def _random_chain(rng: np.random.Generator) -> list[tuple[str, tuple[Any, ...]]]: + """A chain of 2-4 steps, any of which may be fancy. + + A step spelled through `oindex` but carrying only slices is drawn separately + (`slices-only`): it narrows an existing index array by a *slice* rather than + by coordinates, a distinct code path kept at full weight. + """ + n_steps = int(rng.integers(2, 5)) + fancy_steps = {int(rng.integers(0, n_steps)) for _ in range(2)} + slices_only_at = int(rng.integers(0, n_steps)) if rng.random() < 0.4 else -1 + + chain: list[tuple[str, tuple[Any, ...]]] = [] + running = reference() + for step in range(n_steps): + if running.ndim == 0 or running.size == 0: + break + if step in fancy_steps: + mode = "orthogonal" if rng.random() < 0.5 else "vectorized" + else: + mode = "basic" + if step == slices_only_at and step not in fancy_steps: + mode = "orthogonal" + selection = _random_slices_only(rng, running.shape) + elif mode == "basic": + selection = _random_basic(rng, running.shape) + elif mode == "orthogonal": + selection = _random_oindex(rng, running.shape) + else: + selection = _random_vindex(rng, running.shape) + chain.append((mode, selection)) + running = _apply_oracle(running, mode, selection) + return chain + + +@pytest.mark.parametrize("flavor", FLAVORS) +def test_random_chains_match_numpy(flavor: str) -> None: + """A seeded sweep of composed chains, under every partitioning. + + The partitioning invariant as a property: `result()` is identical whatever + boxes the read is broken into, including boxes deliberately misaligned with + the source's own. + """ + rng = np.random.default_rng(20260730) + source = make_source(flavor) + partitionings: list[Any] = [None, (2, 2, 2), (7, 5, 4), ((4, 3), (1, 3, 1), (3, 1))] + # Reads against a real store cost more per chain; the NumPy flavors carry + # the bulk of the sweep and exercise the identical code path. + n_chains = 120 if flavor.startswith("zarr") else 400 + + for _ in range(n_chains): + chain = _random_chain(rng) + expected = reference() + for mode, selection in chain: + expected = _apply_oracle(expected, mode, selection) + + view = source + for mode, selection in chain: + view = _apply_view(view, mode, selection) + + assert view.shape == expected.shape, f"{flavor}: {chain}" + np.testing.assert_array_equal( + np.asarray(view.result()), np.asarray(expected), err_msg=f"{flavor}: {chain}" + ) + for parts in partitionings: + np.testing.assert_array_equal( + np.asarray(repartition(view, parts).result()), + np.asarray(expected), + err_msg=f"{flavor} parts={parts}: {chain}", + ) + + +# `result()` can absorb a defect that `parts()` cannot — an empty view assembles +# correctly from no parts at all, and a rank-0 one can be reshaped into place — +# so the iteration contract needs its own sweep, asserting the documented +# assembly literally rather than through `result()`. That sweep is the +# `ChainedIndexing` state machine in `test_lazy_array_stateful.py`, which drives +# the same operations and shrinks a failure to the chain that caused it. + + +PARTITIONINGS_1D: list[Any] = [None, (1,), (2,), (5,)] + + +def test_a_slice_only_fancy_step_after_a_fancy_step_reads_real_data() -> None: + """`oindex[:, 2:8]` after an `oindex` narrows the view, it does not re-index it. + + The second step carries no coordinates, so it is not fancy-after-fancy: it + must compose like basic indexing. Applying its slices to the *broadcast* + axes of the first step's index array instead truncates that array to size 0, + which leaves the resolver with no parts to read and `result()` handing back + an unwritten buffer. + """ + base = np.arange(24).reshape(3, 8) + expected = base[np.ix_([0, 2], range(8))][:, 2:8] + + for parts in (None, (2, 4), (1, 8), (3, 3)): + view = ( + repartition(LazyArray(base), parts).lazy.oindex[np.array([0, 2]), :].lazy.oindex[:, 2:8] + ) + assert view.shape == expected.shape, f"parts={parts}" + np.testing.assert_array_equal(np.asarray(view.result()), expected, err_msg=f"{parts}") + + +def test_a_fancy_step_composes_onto_any_axis_of_a_fancy_view() -> None: + """A second fancy step may land on axes the first one merely broadcasts along. + + Composition evaluates the existing index arrays at the new coordinates, so + `oindex` after `oindex`, `vindex` after `oindex`, and both orders around a + correlated gather all resolve — under every partitioning. + """ + base = np.arange(24).reshape(3, 8) + rows, cols = np.array([0, 2]), np.array([1, 3, 3]) + + for parts in (None, (2, 4), (1, 8), (3, 3)): + view = repartition(LazyArray(base), parts).lazy.oindex[rows, :] + + composed = view.lazy.oindex[:, cols] + expected = base[np.ix_(rows, cols)] + assert composed.shape == expected.shape, f"parts={parts}" + np.testing.assert_array_equal(np.asarray(composed.result()), expected, err_msg=f"{parts}") + + gathered = view.lazy.vindex[np.array([0, 1]), np.array([7, 0])] + np.testing.assert_array_equal( + np.asarray(gathered.result()), + base[np.ix_(rows, range(8))][[0, 1], [7, 0]], + err_msg=f"{parts}", + ) + + pointwise = repartition(LazyArray(base), parts).lazy.vindex[[0, 1, 2], [0, 2, 3]] + np.testing.assert_array_equal( + np.asarray(pointwise.lazy.oindex[[2, 0]].result()), + base[[0, 1, 2], [0, 2, 3]][[2, 0]], + err_msg=f"{parts}", + ) + np.testing.assert_array_equal( + np.asarray(pointwise.lazy.vindex[[1, 1, 0]].result()), + base[[0, 1, 2], [0, 2, 3]][[1, 1, 0]], + err_msg=f"{parts}", + ) + + +def test_a_partial_vindex_after_an_oindex_resolves_the_mixed_transform() -> None: + """A composed transform can mix correlated and orthogonal index arrays. + + `oindex` on the last axis then `vindex` on the first two leaves the + orthogonal gather in place while the new coordinate arrays are correlated; + resolution takes the pointwise path. + """ + base = np.arange(60).reshape(3, 4, 5) + expected = base[:, :, [4, 0]][[0, 2], [1, 3]] + + for parts in (None, (2, 2, 2), (3, 4, 5), (1, 1, 1)): + view = repartition(LazyArray(base), parts).lazy.oindex[:, :, [4, 0]] + composed = view.lazy.vindex[np.array([0, 2]), np.array([1, 3])] + assert composed.shape == expected.shape, f"parts={parts}" + np.testing.assert_array_equal(np.asarray(composed.result()), expected, err_msg=f"{parts}") + + +def test_a_boolean_mask_composes_onto_a_fancy_view() -> None: + base = np.arange(60).reshape(3, 4, 5) + mask = np.array([True, False, True]) + expected = base[[0, 1, 2]][mask] + + for parts in (None, (2, 2, 2), (1, 4, 5)): + view = repartition(LazyArray(base), parts).lazy.oindex[[0, 1, 2], :, :] + np.testing.assert_array_equal( + np.asarray(view.lazy.oindex[mask].result()), expected, err_msg=f"{parts}" + ) + + +def test_an_ellipsis_only_vindex_step_preserves_a_correlated_gather() -> None: + """Regression: a slice-only vindex step misread correlated maps as orthogonal. + + `vindex[...]` (and `vindex[..., scalar]`, whose remainder after the scalar + is split off is ellipsis-only) used to stamp each correlated map with its + block axis as an orthogonal binding. Two "orthogonal" maps then shared one + input axis, and the partition walk rejected its own transform mid-read. + """ + base = np.arange(16).reshape(4, 4) + + for parts in (None, (2, 2), (4, 4), (1, 3)): + pointwise = repartition(LazyArray(base), parts).lazy.vindex[[0, 1, 2], [0, 2, 3]] + np.testing.assert_array_equal( + np.asarray(pointwise.lazy.vindex[...].result()), + base[[0, 1, 2], [0, 2, 3]], + err_msg=f"{parts}", + ) + + planar = repartition(LazyArray(base), parts).lazy.vindex[ + np.array([[0], [1]]), np.array([[1], [3]]) + ] + np.testing.assert_array_equal( + np.asarray(planar.lazy.vindex[..., np.array(0)].result()), + base[[0, 1], [1, 3]], + err_msg=f"{parts}", + ) + + +# --------------------------------------------------------------------------- +# Domain dimensions no output map depends on +# --------------------------------------------------------------------------- +# +# A `vindex` coordinate array with a *singleton* broadcast axis leaves that axis +# in the view's domain while the map varies only over its partner. A later basic +# index that consumes the partner collapses the map to a `ConstantMap`, and the +# singleton axis survives with nothing referencing it. Every stage of resolution +# has to keep counting it: the lowered block needs the axis back at its true +# extent, and a part has to say where its values belong along it. + +UNREFERENCED_AXIS_PARTITIONINGS: list[Any] = [None, (1, 1, 1), (2, 2, 2), (3, 4, 5), (3, 1, 2)] + +# (id, view builder, NumPy oracle) over `np.arange(60).reshape(3, 4, 5)`. +UNREFERENCED_AXIS_CASES: list[ + tuple[str, Callable[[LazyArray], LazyArray], Callable[[Any], Any]] +] = [ + ( + "leading-singleton-row", + lambda a: a.lazy.vindex[np.array([[2, 0]])].lazy[:, 0], + lambda r: r[np.array([[2, 0]])][:, 0], + ), + ( + "trailing-singleton-column", + lambda a: a.lazy.vindex[np.array([[2], [0]])].lazy[0], + lambda r: r[np.array([[2], [0]])][0], + ), + ( + "repeated-coordinates-over-a-singleton", + lambda a: a.lazy.vindex[np.array([[1, 1]]), np.array([[3, 3]])].lazy[:, 0], + lambda r: r[np.array([[1, 1]]), np.array([[3, 3]])][:, 0], + ), + ( + "unreferenced-axis-emptied", + lambda a: a.lazy.vindex[np.array([[2, 0]])].lazy[0:0, 0], + lambda r: r[np.array([[2, 0]])][0:0, 0], + ), + ( + "partial-vindex-with-a-residual-slice", + lambda a: a.lazy.vindex[np.array([[2, 0]]), np.array([[1, 3]])].lazy[:, 0, 1:4], + lambda r: r[np.array([[2, 0]]), np.array([[1, 3]])][:, 0, 1:4], + ), +] + + +def unreferenced_axis_reference() -> np.ndarray[Any, np.dtype[np.int64]]: + return np.arange(60, dtype=np.int64).reshape(3, 4, 5) + + +@pytest.mark.parametrize( + ("build", "oracle"), + [case[1:] for case in UNREFERENCED_AXIS_CASES], + ids=[case[0] for case in UNREFERENCED_AXIS_CASES], +) +@pytest.mark.parametrize("parts", UNREFERENCED_AXIS_PARTITIONINGS) +def test_a_domain_axis_no_output_map_depends_on_still_resolves( + build: Callable[[LazyArray], LazyArray], + oracle: Callable[[Any], Any], + parts: Any, +) -> None: + """The value, the shape and the tiling all hold when an axis is unreferenced.""" + data = unreferenced_axis_reference() + expected = np.asarray(oracle(data)) + view = build(repartition(LazyArray(data), parts)) + + assert view.shape == expected.shape + np.testing.assert_array_equal(np.asarray(view.result()), expected) + + hits = np.zeros(view.shape, dtype=np.int64) + assembled = np.zeros(view.shape, dtype=view.dtype) + for part in view.parts(): + assembled[part.out_selection] = np.asarray(part.view.result()) + np.add.at(hits, part.out_selection, 1) + np.testing.assert_array_equal(assembled, expected) + np.testing.assert_array_equal(hits, np.ones(view.shape, dtype=np.int64)) + + +def test_an_unreferenced_domain_axis_of_extent_zero_stays_empty() -> None: + """An emptied broadcast axis must not be restored as a fabricated row. + + The lowered block has no axis for a dimension nothing depends on, so the + resolver puts one back. Putting it back at extent 1 invents a row of data + for a selection whose own `shape` says it is empty. + """ + data = np.arange(140, dtype=np.int64).reshape(7, 5, 4) + coords = np.array([[6], [3], [0]]) + for parts in (None, (1, 1, 1), (3, 2, 3), (7, 5, 4)): + view = repartition(LazyArray(data), parts).lazy.vindex[coords, -4].lazy[0, 0:0] + expected = data[coords, -4][0, 0:0] + assert view.shape == expected.shape == (0, 4), f"parts={parts}" + np.testing.assert_array_equal(np.asarray(view.result()), expected, err_msg=f"{parts}") + assert list(view.parts()) == [] + + +def test_a_zero_length_axis_resolves_the_same_way_under_every_partitioning() -> None: + """A size-0 axis carries no dependency, so it cannot make a map correlated.""" + base = np.zeros((3, 0)) + expected = base[np.ix_([1, 0, 0], np.arange(0, dtype=int))] + + for parts in (None, ((1, 1, 1), ()), ((3,), ())): + view = ( + repartition(LazyArray(base), parts) + .lazy.oindex[np.array([1, -3, -3]), :] + .lazy.oindex[:, :] + ) + assert view.shape == expected.shape, f"parts={parts}" + np.testing.assert_array_equal(np.asarray(view.result()), expected, err_msg=f"{parts}") + assert list(view.parts()) == [] + + +def test_an_empty_slice_of_a_length_one_correlated_axis_has_no_parts() -> None: + """`parts()` agrees with `result()` that an emptied view selects nothing. + + A correlated selection of exactly one point normalizes to an all-singleton + index array, indistinguishable by shape from an axis the map broadcasts + over — so a later slice that empties the domain leaves the array at size 1. + """ + base = np.arange(5) + mask = np.array([False, True, False, False, False]) + + for parts in PARTITIONINGS_1D: + view = repartition(LazyArray(base), parts).lazy.vindex[mask].lazy[1:-2] + assert view.shape == (0,), f"parts={parts}" + assert list(view.parts()) == [], f"parts={parts}" + np.testing.assert_array_equal(np.asarray(view.result()), base[mask][1:-2]) + + +def test_an_empty_slice_of_a_length_one_vindex_pair_has_no_parts() -> None: + """The same emptied view, spelled with explicit coordinates over two axes.""" + base = np.arange(35).reshape(7, 5) + + for parts in (None, (2, 2), (7, 5)): + view = ( + repartition(LazyArray(base), parts).lazy.vindex[np.array([6]), np.array([0])].lazy[0:0] + ) + assert view.shape == (0,), f"parts={parts}" + assert list(view.parts()) == [], f"parts={parts}" + np.testing.assert_array_equal( + np.asarray(view.result()), base[np.array([6]), np.array([0])][0:0] + ) + + +def test_a_correlated_view_narrowed_to_one_point_has_parts_of_the_views_rank() -> None: + """A rank-0 broadcast block survives intersection without gaining an axis. + + `Partition` documents `out[part.out_selection] = part.view.result()` as the + assembly, so a part's values must arrive at the rank the view has — including + the rank 0 a correlated selection reaches once every coordinate is a scalar. + """ + base = np.arange(140).reshape(7, 5, 4) + cases = [ + # No residual slice: the whole view is the one gathered point. + ((np.array([-1]), np.array([-1]), np.array([2])), 0), + # One residual slice dimension survives alongside the collapsed block. + ((np.array([6, 1]), np.array([4, 0])), 1), + ] + + for parts in (None, (2, 2, 2), (3, 3, 3), (7, 5, 4)): + for selection, tail in cases: + expected = base[selection][tail] + view = repartition(LazyArray(base), parts).lazy.vindex[selection].lazy[tail] + assert view.shape == expected.shape, f"parts={parts}, {selection}" + + assembled = np.zeros(view.shape, dtype=view.dtype) + hits = np.zeros(view.shape, dtype=np.int64) + for part in view.parts(): + assembled[part.out_selection] = np.asarray(part.view.result()) + np.add.at(hits, part.out_selection, 1) + + err = f"parts={parts}, {selection}" + np.testing.assert_array_equal(assembled, expected, err_msg=err) + np.testing.assert_array_equal(hits, np.ones(view.shape, dtype=np.int64), err_msg=err) + np.testing.assert_array_equal(np.asarray(view.result()), expected, err_msg=err) + + +def test_eager_getitem_returns_data(source: LazyArray) -> None: + """`arr[...]` reads immediately, like `numpy.ndarray.__getitem__`.""" + np.testing.assert_array_equal(np.asarray(source[1:3, ::2, -1]), reference()[1:3, ::2, -1]) + + +# --------------------------------------------------------------------------- +# Attribute forwarding +# --------------------------------------------------------------------------- + + +def test_forwards_array_attributes(source: LazyArray) -> None: + assert source.shape == SHAPE + assert source.ndim == len(SHAPE) + assert source.size == int(np.prod(SHAPE)) + assert source.dtype == np.dtype("int64") + assert len(source) == SHAPE[0] + assert "LazyArray" in repr(source) + + +def test_view_shape_comes_from_the_transform(source: LazyArray) -> None: + """A view reports its own shape, not the wrapped array's.""" + view = source.lazy[1:6:2, :, -1] + assert view.shape == (3, 5) + assert view.ndim == 2 + assert view.size == 15 + assert view.dtype == source.dtype + assert "view=" in repr(view) + + +def test_the_wrapper_has_no_chunks_vocabulary() -> None: + """`chunks` is the *source's* word, never the wrapper's.""" + assert not hasattr(make_source("numpy-whole"), "chunks") + assert not hasattr(make_source("zarr"), "chunks") + with pytest.raises(TypeError): + LazyArray(reference(), chunks=PART_SHAPE) # type: ignore[call-arg] + + +def test_scalar_is_basic_even_when_a_slice_separates_it_from_the_arrays() -> None: + """A documented, deliberate departure from one NumPy corner. + + NumPy counts an integer as an *advanced* index for its placement rule, so + `x[0, :, i]` has shape `(len(i), x.shape[1])` — the arrays lead because the + slice separates the integer from them. The positional dialect instead treats + every scalar as a basic index applied first, which is the rule the rest of + the surface follows and the only one `oindex` can express, so the same + selection reads as `x[0][:, i]`. + """ + data = reference() + view = make_source("numpy-uniform-parts").lazy.vindex[0, ..., np.array([3, 0])] + np.testing.assert_array_equal(np.asarray(view.result()), data[0][..., np.array([3, 0])]) + assert view.shape == data[0][..., np.array([3, 0])].shape + assert view.shape != data[0, ..., np.array([3, 0])].shape + + +def test_zero_dimensional_result_is_an_array(source: LazyArray) -> None: + """Both resolvers agree on the kind of a zero-rank result.""" + result = source.lazy[0, 1, 2].result() + assert isinstance(result, np.ndarray) + assert result.ndim == 0 + assert result[()] == reference()[0, 1, 2] + + +def test_construction_selects_readers_explicitly() -> None: + data = reference() + assert LazyArray(data).reader is basic_reader + assert LazyArray.from_numpy(data).reader is numpy_reader + + +def test_reader_wrappers_forward_the_read_contract_unchanged() -> None: + events: list[tuple[str, Any, ReadContext, Any]] = [] + + class RecordingDelegatingReader: + def __init__(self, name: str, inner: Reader) -> None: + self.name = name + self.inner = inner + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + events.append((self.name, source, context, out)) + self.inner.read_into(source, context, out) + + data = reference() + inner = RecordingDelegatingReader("inner", numpy_reader) + outer = RecordingDelegatingReader("outer", inner) + view = LazyArray(data).with_reader(outer).lazy[1:6:2, ::-1, 1].unpartitioned() + + result = view.result() + + assert [name for name, _, _, _ in events] == ["outer", "inner"] + outer_call, inner_call = events + assert outer_call[1] is inner_call[1] is data + assert outer_call[2] is inner_call[2] + assert outer_call[3] is inner_call[3] is result + np.testing.assert_array_equal(result, data[1:6:2, ::-1, 1]) + + +@pytest.mark.parametrize("value", [object(), [1, 2, 3], "array"]) +def test_from_numpy_rejects_non_ndarrays(value: Any) -> None: + with pytest.raises(TypeError, match="from_numpy requires a numpy.ndarray"): + LazyArray.from_numpy(value) + + +class RecordingReader: + def __init__(self) -> None: + self.calls: list[tuple[Any, ReadContext, Any]] = [] + self.contexts: list[ReadContext] = [] + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + self.calls.append((source, context, out)) + self.contexts.append(context) + basic_reader.read_into(source, context, out) + + +def test_view_operations_preserve_the_reader_without_reading() -> None: + data = reference() + reader = RecordingReader() + base = LazyArray(data).with_reader(reader) + views = ( + base.lazy[1:5], + base.with_parts((2, 2, 2)), + base.with_parts_per_axis(((3, 3, 1), (2, 3), (1, 3))), + base.unpartitioned(), + ) + assert reader.calls == [] + assert all(view.reader is reader for view in views) + assert all(part.view.reader is reader for part in views[1].parts()) + + +@pytest.mark.parametrize("value", [object(), None, lambda: None]) +def test_with_reader_requires_callable_read_into(value: Any) -> None: + with pytest.raises(TypeError, match="reader.read_into must be callable"): + LazyArray(reference()).with_reader(value) + + +class ReturningReader: + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> Any: + return np.empty(context.transform.domain.shape, dtype=source.dtype) + + +def test_result_rejects_a_reader_that_returns_a_value() -> None: + view = LazyArray(reference()).with_reader(ReturningReader()) + with pytest.raises(TypeError, match="must return None"): + view.result() + + +class BufferRecordingReader(RecordingReader): + def __init__(self) -> None: + super().__init__() + self.owns_data: list[bool] = [] + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + self.owns_data.append(bool(out.flags.owndata)) + super().read_into(source, context, out) + + +def test_reader_is_called_once_per_touched_part() -> None: + data = np.arange(48).reshape(6, 8) + reader = RecordingReader() + view = LazyArray(data).with_reader(reader).with_parts((3, 4)).lazy[1:5, 2] + np.testing.assert_array_equal(view.result(), data[1:5, 2]) + assert len(reader.calls) == len(tuple(view.parts())) == 2 + assert all( + call[1].transform.domain.inclusive_min == (0,) * call[1].transform.input_rank + for call in reader.calls + ) + + +def test_partition_reader_receives_global_transform_and_existing_projection() -> None: + reader = RecordingReader() + view = LazyArray(np.arange(8)).with_reader(reader).with_parts((4,)) + expected = [part.projection for part in view.parts()] + + np.testing.assert_array_equal(view.result(), np.arange(8)) + + assert [context.projection for context in reader.contexts] == expected + assert [context.transform.apply((0,)) for context in reader.contexts] == [(0,), (4,)] + + +def test_an_empty_result_does_not_call_the_reader() -> None: + reader = RecordingReader() + result = LazyArray(reference()).with_reader(reader).lazy[:, 0:0, :].result() + assert result.shape == (7, 0, 4) + assert reader.calls == [] + + +def test_rectangular_parts_write_into_result_views() -> None: + reader = BufferRecordingReader() + view = LazyArray(reference()).with_reader(reader).with_parts((2, 2, 2)).lazy[1:6, 1:4] + view.result() + assert reader.owns_data + assert not any(reader.owns_data) + + +def test_fancy_part_placement_uses_owned_dense_temporaries() -> None: + reader = BufferRecordingReader() + view = ( + LazyArray(reference()) + .with_reader(reader) + .with_parts((2, 2, 2)) + .lazy.oindex[[6, 1, 1], :, :] + ) + np.testing.assert_array_equal(view.result(), reference()[np.ix_([6, 1, 1], range(5), range(4))]) + assert any(reader.owns_data) + + +def test_reader_exception_propagates_unchanged() -> None: + error = RuntimeError("backend failed") + + class FailingReader: + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + raise error + + with pytest.raises(RuntimeError) as caught: + LazyArray(reference()).with_reader(FailingReader()).result() + assert caught.value is error + + +class ForeignArray: + """A minimal array-like whose advertised `chunks` we do not control.""" + + def __init__(self, data: np.ndarray[Any, Any], chunks: Any) -> None: + self._data = data + self.chunks = chunks + + @property + def shape(self) -> tuple[int, ...]: + return self._data.shape + + @property + def dtype(self) -> Any: + return self._data.dtype + + def __getitem__(self, key: Any) -> Any: + return self._data[key] + + +def test_malformed_discovered_parts_are_ignored() -> None: + """A foreign object's unusable `chunks` falls back to one whole-array part. + + Discovery parses external input, so an attribute that does not describe a + partitioning of the shape means "none I understand", not an error. + """ + data = reference() + for bogus in (((3, 3), (5,), (4,)), (3, 2), "nope", (3.5, 2, 2)): + wrapped = LazyArray(ForeignArray(data, bogus)) + assert len(list(wrapped.parts())) == 1 + np.testing.assert_array_equal(np.asarray(wrapped.lazy[1:3].result()), data[1:3]) + + +def test_discovered_parts_come_from_the_source_vocabulary() -> None: + """`read_chunk_sizes` wins over `chunks`, and both are read as parts.""" + data = reference() + wrapped = LazyArray(ForeignArray(data, PART_SHAPE)) + assert [part.base_coords for part in wrapped.parts()][:3] == [(0, 0, 0), (0, 0, 1), (0, 1, 0)] + assert len(list(wrapped.parts())) == 3 * 3 * 2 + + +# --------------------------------------------------------------------------- +# Boxes +# --------------------------------------------------------------------------- + +# (id, build, expected is_box, expected bounding_box). The bounds are storage +# intervals of the wrapped (7, 5, 4) array, computed by hand. +BOX_CASES: list[tuple[str, Callable[[LazyArray], LazyArray], bool, Any]] = [ + ("identity", lambda a: a, True, ((0, 7), (0, 5), (0, 4))), + ("basic-slice", lambda a: a.lazy[1:6, :, 1:3], True, ((1, 6), (0, 5), (1, 3))), + # Stride 2 over axis 1 touches 0, 2, 4; the hull is the closed span. + ("strided", lambda a: a.lazy[::3, ::2, :], True, ((0, 7), (0, 5), (0, 4))), + ("int-drop", lambda a: a.lazy[2, :, -1], True, ((2, 3), (0, 5), (3, 4))), + ("all-scalars", lambda a: a.lazy[0, 1, 2], True, ((0, 1), (1, 2), (2, 3))), + ("negative-and-open", lambda a: a.lazy[-2:], True, ((5, 7), (0, 5), (0, 4))), + ( + "oindex", + lambda a: a.lazy.oindex[[4, 0, 0], :, [3, 1]], + False, + ((0, 5), (0, 5), (1, 4)), + ), + ( + "vindex", + lambda a: a.lazy.vindex[np.array([0, 6, 3]), np.array([1, 4, 0]), np.array([2, 0, 1])], + False, + ((0, 7), (0, 5), (0, 3)), + ), + ("mask", lambda a: a.lazy.vindex[MASK], False, ((0, 7), (0, 5), (0, 4))), + # Composition preserves the category in both directions. + ("box-of-box", lambda a: a.lazy[1:6].lazy[:, 1:3], True, ((1, 6), (1, 3), (0, 4))), + ( + "box-after-fancy", + lambda a: a.lazy.oindex[[4, 0, 2], :, :].lazy[0:2], + False, + ((0, 5), (0, 5), (0, 4)), + ), + ("empty", lambda a: a.lazy[2:2], True, None), + ( + "empty-fancy", + lambda a: a.lazy.oindex[np.array([], dtype=np.intp), :, :], + False, + None, + ), +] + + +@pytest.mark.parametrize( + ("build", "expected_is_box", "expected_bounds"), + [case[1:] for case in BOX_CASES], + ids=[case[0] for case in BOX_CASES], +) +def test_is_box_and_bounding_box( + source: LazyArray, + build: Callable[[LazyArray], LazyArray], + expected_is_box: bool, + expected_bounds: Any, +) -> None: + """The box/query taxonomy, and the hull every selection has either way.""" + view = build(source) + assert view.is_box is expected_is_box + assert view.bounding_box() == expected_bounds + + +def test_a_unit_stride_box_is_dense_in_its_bounding_box() -> None: + """Stride 1 everywhere: the hull is exactly what the view selects.""" + data = reference() + view = make_source("numpy-uniform-parts").lazy[1:6, :, 1:3] + assert view.is_box + assert view.strides() == (1, 1, 1) + bounds = view.bounding_box() + assert bounds is not None + np.testing.assert_array_equal( + np.asarray(view.result()), + data[tuple(slice(lo, hi) for lo, hi in bounds)], + ) + + +def test_a_strided_box_is_sparse_in_its_bounding_box() -> None: + """Stride > 1: the hull is a superset, and `strides()` is what says by how much.""" + data = reference() + view = make_source("numpy-uniform-parts").lazy[1:6, ::2, :] + assert view.is_box + assert view.strides() == (1, 2, 1) + bounds = view.bounding_box() + assert bounds is not None + assert bounds == ((1, 6), (0, 5), (0, 4)) + + hull = data[tuple(slice(lo, hi) for lo, hi in bounds)] + assert hull.size == 5 * 5 * 4 + assert view.size == 5 * 3 * 4 + # A consumer that slabbed the hull and threw the rest away would over-read. + assert hull.size > view.size + # Applying the strides to the hull recovers the selection exactly. + np.testing.assert_array_equal( + np.asarray(view.result()), + hull[tuple(slice(None, None, step) for step in view.strides() or ())], + ) + + +def test_strides_are_none_for_a_query() -> None: + view = make_source("numpy-uniform-parts").lazy.oindex[[5, 1], :, :] + assert not view.is_box + assert view.strides() is None + + +def test_an_integer_indexed_dimension_has_stride_one() -> None: + view = make_source("numpy-uniform-parts").lazy[2, ::3, :] + assert view.strides() == (1, 3, 1) + assert view.bounding_box() == ((2, 3), (0, 4), (0, 4)) + + +def test_a_query_bounding_box_is_only_a_hull() -> None: + """For a fancy selection the box is a superset, and `is_box` says so.""" + view = make_source("numpy-uniform-parts").lazy.oindex[[5, 1], :, :] + assert not view.is_box + assert view.bounding_box() == ((1, 6), (0, 5), (0, 4)) + # The hull spans 5 rows; the selection touches 2 of them. + assert view.shape[0] == 2 + + +# --------------------------------------------------------------------------- +# Parts +# --------------------------------------------------------------------------- + + +class _ReadMustNotRun: + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + raise AssertionError("prepared-plan validation must happen before any read") + + +def test_prepared_part_validation_allocates_boolean_coverage_bitmap( + monkeypatch: pytest.MonkeyPatch, +) -> None: + view = LazyArray.from_numpy(reference()).with_parts(PART_SHAPE).lazy[1:6, ::2, 1:] + parts = tuple(view.parts()) + allocations: list[tuple[tuple[int, ...], np.dtype[Any]]] = [] + real_zeros = np.zeros + + def recording_zeros(shape: Any, *args: Any, **kwargs: Any) -> np.ndarray[Any, Any]: + result = real_zeros(shape, *args, **kwargs) + allocations.append((tuple(shape), result.dtype)) + return result + + monkeypatch.setattr(lazy_array_module.np, "zeros", recording_zeros) + + _validate_prepared_parts(parts, view.shape) + + assert allocations == [(view.shape, np.dtype(np.bool_))] + + +@pytest.mark.parametrize( + ("data", "part_shape", "build", "expected"), + [ + pytest.param( + np.arange(8), + (3,), + lambda array: array.lazy[1:7:2], + np.array([1, 3, 5]), + id="basic-reordered-parts", + ), + pytest.param( + np.arange(8), + (3,), + lambda array: array.lazy[3], + np.array(3), + id="scalar", + ), + pytest.param( + np.arange(20).reshape(4, 5), + (2, 3), + lambda array: array.lazy.oindex[[3, 1, 1], [4, 0]], + np.array([[19, 15], [9, 5], [9, 5]]), + id="orthogonal-fancy", + ), + pytest.param( + np.arange(20).reshape(4, 5), + (2, 3), + lambda array: array.lazy.vindex[[3, 1, 1], [4, 0, 4]], + np.array([19, 5, 9]), + id="correlated-fancy", + ), + pytest.param( + np.arange(8), + (3,), + lambda array: array.lazy[2:2], + np.array([], dtype=np.int64), + id="empty", + ), + ], +) +def test_result_accepts_prepared_parts_from_the_same_view( + monkeypatch: pytest.MonkeyPatch, + data: np.ndarray[Any, Any], + part_shape: tuple[int, ...], + build: Callable[[LazyArray], LazyArray], + expected: np.ndarray[Any, Any], +) -> None: + view = build(LazyArray.from_numpy(data).with_parts(part_shape)) + parts = tuple(reversed(tuple(view.parts()))) + + def unexpected_replan(self: LazyArray) -> Any: + raise AssertionError("result(parts=...) must not construct another partition plan") + + monkeypatch.setattr(LazyArray, "parts", unexpected_replan) + + np.testing.assert_array_equal(view.result(parts=parts), expected) + + +def test_result_rejects_prepared_parts_owned_by_another_view() -> None: + data = reference() + base = LazyArray.from_numpy(data).with_reader(_ReadMustNotRun()).with_parts(PART_SHAPE) + view = base.lazy[1:6, ::2, 1:] + owned_parts = tuple(view.parts()) + foreign_parts = tuple(base.lazy[1:6, ::2, 1:].parts()) + mixed_parts = (owned_parts[0], *foreign_parts[1:]) + + with pytest.raises(ValueError, match="prepared parts do not belong to this view"): + view.result(parts=mixed_parts) + + +def test_result_rejects_prepared_parts_that_do_not_tile_the_view() -> None: + data = reference() + view = ( + LazyArray.from_numpy(data) + .with_reader(_ReadMustNotRun()) + .with_parts(PART_SHAPE) + .lazy[1:6, ::2, 1:] + ) + parts = tuple(view.parts()) + + with pytest.raises(ValueError, match="prepared parts do not tile the view exactly"): + view.result(parts=parts[:-1]) + + +def test_result_rejects_prepared_parts_with_a_duplicate_and_omission() -> None: + view = LazyArray.from_numpy(np.arange(8)).with_reader(_ReadMustNotRun()).with_parts((4,)) + first, _second = tuple(view.parts()) + + with pytest.raises(ValueError, match="prepared parts do not tile the view exactly"): + view.result(parts=(first, first)) + + +def test_result_rejects_complete_prepared_parts_plus_a_duplicate() -> None: + view = LazyArray.from_numpy(np.arange(8)).with_reader(_ReadMustNotRun()).with_parts((4,)) + first, second = tuple(view.parts()) + + with pytest.raises(ValueError, match="prepared parts do not tile the view exactly"): + view.result(parts=(first, second, first)) + + +def test_result_rejects_overlapping_prepared_parts() -> None: + view = LazyArray.from_numpy(np.arange(8)).with_reader(_ReadMustNotRun()).with_parts((4,)) + first, second = tuple(view.parts()) + overlapping = replace(second, out_selection=(slice(2, 6),)) + + with pytest.raises(ValueError, match="prepared parts do not tile the view exactly"): + view.result(parts=(first, overlapping)) + + +def test_result_rejects_wrong_rank_prepared_parts() -> None: + view = LazyArray.from_numpy(np.arange(8)).with_reader(_ReadMustNotRun()).with_parts((4,)) + first, second = tuple(view.parts()) + wrong_rank = replace(first, out_selection=()) + + with pytest.raises(ValueError, match="prepared parts do not tile the view exactly"): + view.result(parts=(wrong_rank, second)) + + +def test_result_rejects_empty_prepared_parts_for_a_nonempty_view() -> None: + view = LazyArray.from_numpy(np.arange(8)).with_reader(_ReadMustNotRun()).with_parts((4,)) + + with pytest.raises(ValueError, match="prepared parts do not tile the view exactly"): + view.result(parts=()) + + +def test_result_accepts_empty_prepared_parts_for_an_empty_view() -> None: + view = ( + LazyArray.from_numpy(np.arange(8)).with_reader(_ReadMustNotRun()).with_parts((4,)).lazy[0:0] + ) + + np.testing.assert_array_equal(view.result(parts=()), np.array([], dtype=np.int64)) + + +@pytest.mark.parametrize("flavor", FLAVORS) +@pytest.mark.parametrize( + "build", + [ + lambda a: a, + lambda a: a.lazy[1:6, :, 1:], + lambda a: a.lazy.oindex[[4, 0, 0], :, [3, 1]], + lambda a: a.lazy.vindex[..., np.array([1, 4, 0]), np.array([2, 0, 1])], + # A reversing view drives the negative-stride branches of + # `_intersect_dimension_map` and chunk projection, which were + # written defensively long before anything could reach them. + lambda a: a.lazy[::-1, ::-2, :], + lambda a: a.lazy[5:1:-1, :, ::-1], + ], + ids=["identity", "basic", "oindex", "vindex", "reversed", "reversed-bounded"], +) +def test_parts_tile_the_view_exactly_and_disjointly( + flavor: str, build: Callable[[LazyArray], LazyArray] +) -> None: + """Assembling the parts reproduces `result()`; the placements cover with no overlap.""" + view = build(make_source(flavor)) + expected = np.asarray(view.result()) + + assembled = np.zeros(view.shape, dtype=view.dtype) + hits = np.zeros(view.shape, dtype=np.int64) + for part in view.parts(): + assembled[part.out_selection] = np.asarray(part.view.result()) + # `np.add.at` accumulates per element; `+= 1` on a fancy index would + # count a repeated position once and hide a real overlap. + np.add.at(hits, part.out_selection, 1) + + np.testing.assert_array_equal(assembled, expected) + np.testing.assert_array_equal(hits, np.ones(view.shape, dtype=np.int64)) + + +def _transform_point(transform: IndexTransform, point: tuple[int, ...]) -> tuple[int, ...]: + """Evaluate a transform pointwise for projection placement assertions.""" + result: list[int] = [] + for output_map in transform.output: + if isinstance(output_map, ConstantMap): + result.append(output_map.offset) + elif isinstance(output_map, DimensionMap): + result.append(output_map.offset + output_map.stride * point[output_map.input_dimension]) + else: + index = tuple( + 0 + if output_map.index_array.shape[axis] == 1 + else point[axis] - transform.domain.inclusive_min[axis] + for axis in range(output_map.index_array.ndim) + ) + result.append( + output_map.offset + output_map.stride * int(output_map.index_array[index]) + ) + return tuple(result) + + +@pytest.mark.parametrize( + "build", + [ + lambda array: array.lazy.oindex[[6, 0, 2], :, [3, 1]], + lambda array: array.lazy.vindex[..., np.array([4, 0, 4]), np.array([3, 1, 1])], + ], + ids=["orthogonal", "vectorized"], +) +def test_partition_exposes_projection_as_its_placement_authority( + build: Callable[[LazyArray], LazyArray], +) -> None: + """A part's NumPy placement addresses exactly its cell-transform range.""" + view = build(LazyArray(reference()).with_parts(PART_SHAPE)) + assembled = np.zeros(view.shape, dtype=view.dtype) + + for part in view.parts(): + projection = part.projection + assert isinstance(projection, ChunkProjection) + assert part.view.transform == projection.chunk_transform.translate( + tuple(lo for lo, _ in part.box) + ) + assert part.base_coords == projection.chunk_coords + assert part.box == tuple( + zip( + projection.chunk_domain.inclusive_min, + projection.chunk_domain.exclusive_max, + strict=True, + ) + ) + + expected_hits = np.zeros(view.shape, dtype=np.int8) + cell_domain = projection.cell_transform.domain + for positional_point in np.ndindex(*cell_domain.shape): + cell_point = tuple( + coordinate + origin + for coordinate, origin in zip( + positional_point, cell_domain.inclusive_min, strict=True + ) + ) + expected_hits[_transform_point(projection.cell_transform, cell_point)] = 1 + actual_hits = np.zeros(view.shape, dtype=np.int8) + actual_hits[part.out_selection] = 1 + np.testing.assert_array_equal(actual_hits, expected_hits) + + assembled[part.out_selection] = np.asarray(part.view.result()) + + np.testing.assert_array_equal(assembled, np.asarray(view.result())) + + +def test_nonfirst_partition_transform_directly_addresses_its_array() -> None: + source = np.arange(8) + part = list(LazyArray.from_numpy(source).with_parts((4,)).parts())[1] + + assert part.box == ((4, 8),) + assert part.view.transform.apply((0,)) == (4,) + assert part.view.array[part.view.transform.apply((0,))] == 4 + assert part.view.result()[0] == 4 + assert part.projection.chunk_transform.apply((0,)) == (0,) + + +def test_partition_token_encodes_its_public_global_transform() -> None: + source = np.arange(8) + base = LazyArray.from_numpy(source) + partition_view = list(base.with_parts((4,)).parts())[1].view + direct_view = base.lazy[4:8] + + assert partition_view.__dask_tokenize__() == direct_view.__dask_tokenize__() + + +def test_parts_resolve_independently_and_concurrently() -> None: + """Each part's `array` is a standalone `LazyArray` with no shared mutable state.""" + view = make_source("zarr").lazy[1:7, :, 1:].with_parts((2, 2, 2)) + parts = list(view.parts()) + assert len(parts) > 1 + + with ThreadPoolExecutor(max_workers=4) as pool: + values = list(pool.map(lambda part: np.asarray(part.view.result()), parts)) + + assembled = np.zeros(view.shape, dtype=view.dtype) + for part, value in zip(parts, values, strict=True): + assembled[part.out_selection] = value + np.testing.assert_array_equal(assembled, np.asarray(view.result())) + + +def test_parts_report_completeness() -> None: + """`is_complete` distinguishes a fully-covered box from a partial one.""" + array = make_source("numpy-uniform-parts") + assert all(part.is_complete for part in array.parts()) + # Boxes along axis 2 are [0, 3) and [3, 4); dropping column 0 leaves the + # first partially covered and the second whole. + trimmed = {part.base_coords[2]: part.is_complete for part in array.lazy[:, :, 1:].parts()} + assert trimmed == {0: False, 1: True} + # A fancy axis is always reported incomplete. + assert not any(part.is_complete for part in array.lazy.oindex[[4, 0, 0], :, :].parts()) + + +def test_partition_boxes_are_global_and_tile_the_base() -> None: + """Both the selected hull and the whole partition box use global coordinates.""" + view = make_source("numpy-uniform-parts").lazy[1:6, :, 1:] + parts = {part.base_coords: part for part in view.parts()} + + # The reviewer's repro: two parts of the same view now expose distinct + # source-global selected hulls as well as distinct whole partition boxes. + first, second = parts[0, 0, 0], parts[0, 1, 0] + assert first.view.bounding_box() == ((1, 3), (0, 2), (1, 3)) + assert second.view.bounding_box() == ((1, 3), (2, 4), (1, 3)) + assert first.box != second.box + assert first.box == ((0, 3), (0, 2), (0, 3)) + assert second.box == ((0, 3), (2, 4), (0, 3)) + + # Every box is the base partitioning's own box for those coordinates, and + # the touched boxes tile the region the view reads without overlapping. + grids = dimension_grids_from_chunks(PART_SHAPE, SHAPE) + for coords, part in parts.items(): + expected = tuple( + (grid.chunk_offset(c), grid.chunk_offset(c) + grid.data_size(c)) + for grid, c in zip(grids, coords, strict=True) + ) + assert part.box == expected + covered = np.zeros(SHAPE, dtype=np.int64) + for part in parts.values(): + covered[tuple(slice(lo, hi) for lo, hi in part.box)] += 1 + assert covered.max() == 1 + # The view reads rows 1..5 and columns 1.., so every box it touches + # intersects that region and no box outside it is visited. + assert covered[1:6, :, 1:].sum() > 0 + assert covered[6:, :, :].sum() == 0 + + +def test_partition_box_of_a_whole_array_part() -> None: + part = next(iter(make_source("numpy-whole").parts())) + assert part.box == tuple((0, extent) for extent in SHAPE) + + +def test_an_unpartitioned_wrapper_has_a_single_whole_array_part() -> None: + view = make_source("numpy-whole") + parts = list(view.parts()) + assert len(parts) == 1 + assert parts[0].base_coords == (0, 0, 0) + assert parts[0].view.shape == SHAPE + assert parts[0].is_complete + np.testing.assert_array_equal(np.asarray(parts[0].view.result()), reference()) + + +def test_with_parts_keeps_the_view_and_the_base() -> None: + view = make_source("zarr").lazy[1:6, ::2] + repartitioned = view.with_parts((2, 1, 4)) + assert repartitioned.shape == view.shape + assert repartitioned.array is view.array + assert repartitioned.transform == view.transform + # A different partitioning really is a different set of boxes. + assert [part.base_coords for part in repartitioned.parts()] != [ + part.base_coords for part in view.parts() + ] + np.testing.assert_array_equal(np.asarray(repartitioned.result()), np.asarray(view.result())) + + +def test_with_parts_none_forces_one_shot_resolution() -> None: + view = make_source("zarr").lazy.oindex[[4, 0, 0], :, :] + whole = view.unpartitioned() + assert len(list(whole.parts())) == 1 + np.testing.assert_array_equal(np.asarray(whole.result()), np.asarray(view.result())) + + +@pytest.mark.parametrize( + ("parts", "match"), + [ + ((3,), "one entry per dimension"), + ((3, (2, 2), 4), "not a mixture"), + (((3, 3), (2, 2, 1), (3, 1)), "sum to 6, but the array extent is 7"), + ((3, 0, 3), "chunk shape entries must be positive"), + # A float or a None belongs to neither convention; saying "not a + # mixture" would send the reader looking for the wrong mistake. + ((3.5, 2, 2), r"3\.5 at dimension 0 is neither"), + ((None, 5, 4), "None at dimension 0 is neither"), + ((3.5, 2.5, 2.5), r"3\.5 at dimension 0, 2\.5 at dimension 1, .* are neither"), + (((1.5, 5.5), (5,), (4,)), "per-axis chunk sizes must be integers; dimension 0"), + ], +) +def test_with_parts_validates_strictly(parts: Any, match: str) -> None: + """`with_parts` is our own API, so a malformed partitioning raises.""" + with pytest.raises(ValueError, match=match): + repartition(make_source("numpy-whole"), parts) + + +# --------------------------------------------------------------------------- +# Protocols +# --------------------------------------------------------------------------- + + +def test_dask_token_is_deterministic_and_discriminating() -> None: + """Same data and same view token alike; a different selection differs.""" + data = reference() + base = LazyArray(data) + assert base.__dask_tokenize__() == LazyArray(reference()).__dask_tokenize__() + + tokens = { + "base": base.__dask_tokenize__(), + "view": base.lazy[1:3].__dask_tokenize__(), + "other view": base.lazy[2:4].__dask_tokenize__(), + "other data": LazyArray(data + 1).__dask_tokenize__(), + } + assert len({repr(token) for token in tokens.values()}) == len(tokens) + # Equivalent transforms reached different ways still token alike. + assert base.lazy[1:5].lazy[0:2].__dask_tokenize__() == base.lazy[1:3].__dask_tokenize__() + + +def test_reader_and_partitioning_do_not_change_dask_identity() -> None: + base = LazyArray(reference()) + token = base.__dask_tokenize__() + assert base.with_reader(numpy_reader).__dask_tokenize__() == token + assert base.with_reader(basic_reader).__dask_tokenize__() == token + assert base.with_parts((2, 2, 2)).__dask_tokenize__() == token + + +@pytest.mark.parametrize("reader", [basic_reader, numpy_reader, DelegatingReader(numpy_reader)]) +def test_reader_survives_pickle(reader: Reader) -> None: + view = LazyArray(reference()).with_reader(reader).lazy[1:5, ::2] + restored = pickle.loads(pickle.dumps(view)) + assert type(restored.reader) is type(reader) + np.testing.assert_array_equal(restored.result(), view.result()) + + +def test_iteration_yields_eager_slices(source: LazyArray) -> None: + rows = list(source.lazy[2:5]) + assert len(rows) == 3 + for row, expected in zip(rows, reference()[2:5], strict=True): + np.testing.assert_array_equal(np.asarray(row), expected) + + +def test_iteration_over_a_zero_dimensional_view_is_rejected() -> None: + with pytest.raises(TypeError, match="iteration over a 0-d array"): + iter(make_source("numpy-uniform-parts").lazy[0, 0, 0]) + + +def test_len_of_a_zero_dimensional_view_is_rejected() -> None: + with pytest.raises(TypeError, match="len\\(\\) of unsized object"): + len(make_source("numpy-uniform-parts").lazy[0, 0, 0]) + + +@pytest.mark.parametrize( + ("convert", "selection"), + [ + (bool, (1, 1, 1)), + (int, (1, 1, 1)), + (float, (1, 1, 1)), + (operator.index, (1, 1, 1)), + (bool, (1, 1, slice(0, 1))), + ], + ids=["bool-0d", "int-0d", "float-0d", "index-0d", "bool-size-1"], +) +def test_scalar_conversions_match_numpy(convert: Any, selection: Any) -> None: + """Size-1 conversions delegate to NumPy, values and all.""" + data = reference() + view = make_source("numpy-uniform-parts").lazy[selection] + assert convert(view) == convert(data[selection]) + + +@pytest.mark.parametrize( + ("convert", "selection", "error"), + [ + (bool, (slice(0, 2), 0, 0), ValueError), + (bool, (slice(0, 0), 0, 0), ValueError), + (int, (slice(0, 1), 0, 0), TypeError), + (float, (slice(0, 2), 0, 0), TypeError), + (operator.index, (slice(0, 1), 0, 0), TypeError), + ], + ids=["bool-many", "bool-empty", "int-1d", "float-many", "index-1d"], +) +def test_scalar_conversions_raise_what_numpy_raises( + convert: Any, selection: Any, error: type[Exception] +) -> None: + data = reference() + view = make_source("numpy-uniform-parts").lazy[selection] + with pytest.raises(error): + convert(view) + with pytest.raises(error): + convert(data[selection]) + + +def test_pickle_round_trip() -> None: + """A wrapper over a picklable base survives a round trip, view and parts intact.""" + view = LazyArray(reference()).with_parts((2, 2, 2)).lazy[1:6, ::2].lazy.oindex[[3, 0, 0], :, :] + restored = pickle.loads(pickle.dumps(view)) + assert restored.shape == view.shape + assert restored.__dask_tokenize__() == view.__dask_tokenize__() + np.testing.assert_array_equal(np.asarray(restored.result()), np.asarray(view.result())) + + +# --------------------------------------------------------------------------- +# dask interop +# --------------------------------------------------------------------------- + + +def test_dask_from_array_roundtrip() -> None: + """A `LazyArray` is a drop-in dask source — no translation ceremony.""" + da = pytest.importorskip("dask.array") + source = make_source("zarr") + + lazy = da.from_array(source) + np.testing.assert_array_equal(lazy.compute(), reference()) + + # dask chooses its own blocks; the wrapper reads each of them through its + # own parts, so the two partitionings need not agree. + blocked = da.from_array(source, chunks=(4, 3, 3)) + assert blocked.chunks == ((4, 3), (3, 2), (3, 1)) + np.testing.assert_array_equal(blocked[2:, ::2].compute(), reference()[2:, ::2]) + + +# --------------------------------------------------------------------------- +# Errors +# --------------------------------------------------------------------------- + + +def test_boolean_scalar_is_rejected() -> None: + with pytest.raises(IndexError, match="boolean scalars are not valid indices"): + make_source("numpy-uniform-parts").lazy[True] + + +@pytest.mark.parametrize( + ("mode", "selection", "expected"), + [ + pytest.param("basic", IndexLike(2), np.array(2), id="basic-scalar"), + pytest.param( + "basic", + slice(IndexLike(1), IndexLike(7), IndexLike(2)), + np.array([1, 3, 5]), + id="basic-slice-components", + ), + pytest.param("orthogonal", IndexLike(2), np.array(2), id="orthogonal-scalar"), + pytest.param("vectorized", IndexLike(2), np.array(2), id="vectorized-scalar"), + ], +) +def test_positional_selectors_support_the_index_protocol( + mode: str, selection: Any, expected: np.ndarray[Any, Any] +) -> None: + source = LazyArray.from_numpy(np.arange(8)) + if mode == "basic": + view = source.lazy[selection] + else: + view = getattr(source.lazy, "oindex" if mode == "orthogonal" else "vindex")[selection] + + result = np.asarray(view.result()) + assert result.shape == expected.shape + np.testing.assert_array_equal(result, expected) + + +def test_positional_selector_rejects_int_only_objects() -> None: + with pytest.raises(IndexError, match="unsupported selection type"): + LazyArray.from_numpy(np.arange(8)).lazy[IntOnly()] + + +def test_positional_selector_propagates_malformed_index_protocol() -> None: + with pytest.raises(TypeError, match="__index__ returned non-int"): + LazyArray.from_numpy(np.arange(8)).lazy[BadIndex()] + + +def test_positional_slice_propagates_malformed_index_protocol() -> None: + with pytest.raises(TypeError, match="__index__ returned non-int"): + LazyArray.from_numpy(np.arange(8)).lazy[:: BadIndex()] + + +def test_protocol_objects_inside_an_index_array_remain_invalid() -> None: + selection = np.array([IndexLike(2)], dtype=object) + with pytest.raises(IndexError, match="integer or boolean"): + LazyArray.from_numpy(np.arange(8)).lazy.oindex[selection] + + +def test_mask_shape_must_match_the_view() -> None: + array = make_source("numpy-uniform-parts") + with pytest.raises(IndexError, match="boolean index has shape"): + array.lazy.vindex[np.ones((2, 2, 2), dtype=bool)] + + +def test_scalar_index_out_of_bounds() -> None: + with pytest.raises(IndexError, match="index 7 is out of bounds for axis 0 with size 7"): + make_source("numpy-uniform-parts").lazy[7] + + +def test_scalar_index_out_of_bounds_in_a_view() -> None: + """Bounds are the *view's*, not the wrapped array's.""" + array = make_source("numpy-uniform-parts").lazy[1:4] + with pytest.raises(IndexError, match="index 3 is out of bounds for axis 0 with size 3"): + array.lazy[3] + + +def test_index_array_out_of_bounds() -> None: + array = make_source("numpy-uniform-parts") + with pytest.raises(IndexError, match="index 99 is out of bounds for axis 0 with size 7"): + array.lazy.oindex[[0, 99], :, :] + + +def test_too_many_indices() -> None: + with pytest.raises(IndexError, match="too many indices"): + make_source("numpy-uniform-parts").lazy[0, 0, 0, 0] + + +def test_copy_false_conversion_is_rejected() -> None: + array = make_source("numpy-uniform-parts") + with pytest.raises(ValueError, match="cannot be converted to a NumPy array without a copy"): + np.array(array, copy=False) + + +# --------------------------------------------------------------------------- +# Negative steps +# --------------------------------------------------------------------------- + + +def test_reversed_box_reports_a_positive_stride(source: LazyArray) -> None: + """A reversal is still a box; `strides()` is magnitudes, so it matches the forward twin.""" + reversed_view = source.lazy[::-2] + forward = source.lazy[::2] + assert reversed_view.is_box + assert reversed_view.strides() == forward.strides() == (2, 1, 1) + assert reversed_view.bounding_box() == ((0, 7), (0, 5), (0, 4)) + + +def test_a_reversed_view_is_re_based_to_origin_zero() -> None: + """The literal domain of a reversal is negative; the positional dialect hides it.""" + view = make_source("numpy-whole").lazy[::-1] + # The algebra's own answer keeps the source frame. + assert IndexTransform.from_shape(SHAPE)[::-1].domain.inclusive_min[0] == -6 + # The wrapper re-bases, so positions start at 0 as NumPy expects. + assert view.transform.domain.inclusive_min == (0, 0, 0) + assert view.shape == SHAPE + np.testing.assert_array_equal(np.asarray(view.result()), reference()[::-1]) + + +def test_zero_step_is_rejected() -> None: + with pytest.raises(ValueError, match="step cannot be zero"): + make_source("numpy-whole").lazy[::0] + + +def test_reversed_positional_interval_is_empty_not_an_error() -> None: + """NumPy's rule at the boundary; the literal layer keeps TensorStore's.""" + view = make_source("numpy-uniform-parts").lazy[2:5:-1] + assert view.shape == (0, 5, 4) + np.testing.assert_array_equal(np.asarray(view.result()), reference()[2:5:-1]) + # Literal coordinates, on the other hand, call it a direction error. + with pytest.raises(IndexError, match="valid interval"): + IndexTransform.from_shape(SHAPE)[2:5:-1] + + +def test_negative_step_over_a_fancy_axis_reverses_the_coordinates(source: LazyArray) -> None: + """Reversing a gathered axis materializes, rather than attaching a stride.""" + view = source.lazy.oindex[[3, 1, 2], :, :].lazy[::-1] + expected = outer(reference(), ([3, 1, 2], slice(None), slice(None)))[::-1] + np.testing.assert_array_equal(np.asarray(view.result()), expected) + m = view.transform.output[0] + assert isinstance(m, ArrayMap) + np.testing.assert_array_equal(m.index_array.reshape(-1), np.array([2, 1, 3])) + + +# --------------------------------------------------------------------------- +# Minimal sources +# --------------------------------------------------------------------------- + + +class MinimalSource: + """The floor of the wrapped-array protocol: `shape`, `dtype`, `__getitem__`.""" + + def __init__(self, data: np.ndarray[Any, Any]) -> None: + self._data = data + + @property + def shape(self) -> tuple[int, ...]: + return self._data.shape + + @property + def dtype(self) -> Any: + return self._data.dtype + + def __getitem__(self, key: Any) -> Any: + return self._data[key] + + +class RecordingSource(MinimalSource): + """A minimal source that records every attempted data read.""" + + def __init__(self, data: np.ndarray[Any, Any]) -> None: + super().__init__(data) + self.reads: list[Any] = [] + + def __getitem__(self, key: Any) -> Any: + self.reads.append(key) + return super().__getitem__(key) + + +@pytest.mark.parametrize( + "build", + [ + lambda a: a.lazy[:, 2:2, :], + lambda a: a.lazy.vindex[np.array([[6], [3], [0]]), -4].lazy[0, 0:0], + ], + ids=["ordinary", "unreferenced-axis"], +) +def test_an_empty_view_does_not_read_its_source( + build: Callable[[LazyArray], LazyArray], +) -> None: + source = RecordingSource(reference()) + result = build(LazyArray(source)).result() + + assert result.size == 0 + assert source.reads == [] + + +# --------------------------------------------------------------------------- +# Materializing +# --------------------------------------------------------------------------- + + +class NumpyBackedSource: + """A duck array that stores its data in NumPy and returns views from reads. + + Not an `np.ndarray`, so nothing about the source can be compared against the + result's memory — but its blocks are NumPy views of storage the caller must + not be handed. The `BASIC` source this package invites people to wrap. + """ + + def __init__(self, data: np.ndarray[Any, Any]) -> None: + self.data = data + + @property + def shape(self) -> tuple[int, ...]: + return self.data.shape + + @property + def dtype(self) -> Any: + return self.data.dtype + + def __getitem__(self, selection: Any) -> Any: + return self.data[selection] + + +@pytest.mark.parametrize("parts", [None, (2, 2, 2), SHAPE]) +@pytest.mark.parametrize("wrap", [lambda d: d, NumpyBackedSource], ids=["ndarray", "duck"]) +@pytest.mark.parametrize( + ("build", "description"), + [ + (lambda a: a.lazy[1:3, :, :], "a basic slice"), + (lambda a: a.lazy[:, :, :], "the whole array"), + (lambda a: a.lazy[::-1, :, :], "a reversal"), + (lambda a: a.lazy.oindex[[2, 0], :, :], "a gather"), + ], +) +def test_materializing_never_hands_back_the_wrapped_array( + parts: Any, + wrap: Callable[[np.ndarray[Any, Any]], Any], + build: Callable[[LazyArray], LazyArray], + description: str, +) -> None: + """Writing to a materialized result must never reach the source. + + An unpartitioned read of a basic selection can be answered with a *view* of + the wrapped array, and NumPy 2 hands whatever `__array__` returns straight to + the caller. Every route out of the wrapper detaches, so the answer does not + depend on how the read happened to be divided. + + Run over both a raw `ndarray` and a duck array that merely stores its data in + NumPy: the second is the case where the source cannot be compared against the + result, so detaching has to decide from the result's own buffer instead. + """ + data = reference() + view = build(repartition(LazyArray(wrap(data)), parts)) + + for materialize in ( + lambda v: v.result(), + lambda v: np.array(v, copy=True), + lambda v: np.asarray(v), + lambda v: np.array(v), + ): + before = data.copy() + materialized = np.asarray(materialize(view)) + assert not np.shares_memory(materialized, data), description + materialized[...] = -1 + np.testing.assert_array_equal(data, before, err_msg=description) + + +def test_an_eager_getitem_never_hands_back_the_wrapped_array() -> None: + data = reference() + block = LazyArray(data)[1:3] + block[...] = -1 + np.testing.assert_array_equal(data, reference()) + + +def test_result_refuses_to_return_a_partly_written_buffer( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """A partition walk that leaves a gap must raise, not return process memory. + + `result()` scatters into an uninitialized buffer, which is only safe because + the parts tile the view. This is the guard that turns any future break of + that contract into a failure instead of into plausible-looking numbers. + """ + view = LazyArray(reference()).with_parts(PART_SHAPE).lazy[:, 1:, :] + complete = LazyArray.parts + + def drop_one(self: LazyArray) -> Any: + return list(complete(self))[:-1] + + monkeypatch.setattr(LazyArray, "parts", drop_one) + with pytest.raises(AssertionError, match="partition walk addressed"): + view.result() + + +def test_result_refuses_a_partition_of_the_wrong_rank(monkeypatch: pytest.MonkeyPatch) -> None: + """A part addressing fewer axes than the view has is caught by name.""" + view = LazyArray(reference()).with_parts(PART_SHAPE).lazy[:, 1:, :] + complete = LazyArray.parts + + def truncate(self: LazyArray) -> Any: + return [replace(part, out_selection=part.out_selection[:-1]) for part in complete(self)] + + monkeypatch.setattr(LazyArray, "parts", truncate) + with pytest.raises(AssertionError, match="of the view's 3 dimensions"): + view.result() + + +class DuckBlock: + """An array-like meeting exactly the documented `BASIC` floor and no more. + + `shape`, `dtype`, and a `__getitem__` that understands integers and slices. + Anything else — an integer array, `take`, `reshape` — raises, and indexing it + yields another one of itself, so a block that comes back from it is as + limited as the source was. + """ + + def __init__(self, data: np.ndarray[Any, Any]) -> None: + self._data = data + + @property + def shape(self) -> tuple[int, ...]: + return self._data.shape + + @property + def dtype(self) -> Any: + return self._data.dtype + + def __array__(self, dtype: Any = None, copy: bool | None = None) -> Any: + return np.array(self._data, dtype=dtype, copy=True if copy is None else copy) + + def __getitem__(self, key: Any) -> DuckBlock: + selectors = key if isinstance(key, tuple) else (key,) + for selector in selectors: + if not isinstance(selector, (int, np.integer, slice)): + raise TypeError(f"basic indexing only, got {selector!r}") + return DuckBlock(self._data[key]) + + +@pytest.mark.parametrize( + ("build", "oracle"), + [ + (lambda a: a.lazy[1:5, ::2, :], lambda r: r[1:5, ::2, :]), + ( + lambda a: a.lazy.oindex[[4, 0, 0], :, :], + lambda r: r[np.ix_([4, 0, 0], range(5), range(4))], + ), + (lambda a: a.lazy.vindex[[4, 0], [1, 1]], lambda r: r[[4, 0], [1, 1]]), + (lambda a: a.lazy[::-1, :, :], lambda r: r[::-1, :, :]), + ], + ids=["basic", "oindex", "vindex", "reversal"], +) +@pytest.mark.parametrize("parts", [None, PART_SHAPE]) +def test_a_source_meeting_only_the_basic_floor_resolves_any_selection( + build: Callable[[LazyArray], LazyArray], oracle: Callable[[Any], Any], parts: Any +) -> None: + """The floor is a promise about the source; its blocks are coerced, not trusted.""" + expected = np.asarray(oracle(reference())) + view = build(repartition(LazyArray(DuckBlock(reference())), parts)) + assert view.shape == expected.shape + np.testing.assert_array_equal(np.asarray(view.result()), expected) + + +def test_the_duck_block_double_refuses_a_fancy_key() -> None: + """A negative control: the floor test only means something if the double bites.""" + with pytest.raises(TypeError, match="basic indexing only"): + DuckBlock(reference())[np.array([1, 0])] + + +# --------------------------------------------------------------------------- +# Sources with their own opinions +# --------------------------------------------------------------------------- + + +@pytest.mark.filterwarnings("ignore::PendingDeprecationWarning") +def test_numpy_matrix_is_refused() -> None: + """`np.matrix` never reduces rank, so a view's shape could not be honored.""" + with pytest.raises(TypeError, match="numpy.matrix cannot be wrapped"): + LazyArray(np.matrix(np.arange(12).reshape(3, 4))) + + +@pytest.mark.parametrize("parts", [None, (2, 2), (1, 4), (3, 4)]) +def test_a_masked_source_keeps_its_mask_under_every_partitioning(parts: Any) -> None: + data = np.ma.masked_greater(np.arange(12).reshape(3, 4), 7) + got = repartition(LazyArray(data), parts).lazy[:, 1:].result() + expected = data[:, 1:] + assert isinstance(got, np.ma.MaskedArray), parts + np.testing.assert_array_equal(np.ma.getmaskarray(got), np.ma.getmaskarray(expected)) + np.testing.assert_array_equal(np.ma.filled(got, 0), np.ma.filled(expected, 0)) + + +@pytest.mark.parametrize("parts", [None, (2, 2), (3, 4)]) +def test_a_masked_source_keeps_its_mask_when_the_view_is_empty(parts: Any) -> None: + """An empty result is still a result, and its type must not depend on the parts. + + An empty view is answered without reading the source at all, and that + shortcut reached for the array namespace's own `empty` — which knows nothing + about masks — so an unpartitioned empty view came back a plain array while + the same view partitioned came back masked. No cells either way, so nothing + about the values changed; the caller just got a different type depending on + how the read had been divided. + """ + data = np.ma.masked_greater(np.arange(12).reshape(3, 4), 7) + got = repartition(LazyArray(data), parts).lazy[:, 2:2].result() + assert isinstance(got, np.ma.MaskedArray), parts + assert np.asarray(got).shape == (3, 0), parts + + +def test_a_large_array_without_dask_refuses_to_claim_equality( + monkeypatch: pytest.MonkeyPatch, +) -> None: + """Above the digest limit the fallback must miss a cache rather than lie. + + Two arrays differing in one element used to token identically, because the + fallback described the shape and dtype and gave up on the contents. + """ + import sys + + monkeypatch.setitem(sys.modules, "dask.base", None) + big = np.zeros(1 << 19, dtype=np.int64) + other = big.copy() + other[0] = 1 + + assert LazyArray(big).__dask_tokenize__() != LazyArray(other).__dask_tokenize__() + assert LazyArray(big).__dask_tokenize__() != LazyArray(big).__dask_tokenize__() + + # Below the limit the contents are digested, so equal data still tokens alike. + small = np.zeros(8, dtype=np.int64) + assert LazyArray(small).__dask_tokenize__() == LazyArray(small.copy()).__dask_tokenize__() + + +# --------------------------------------------------------------------------- +# Completeness and partition spellings +# --------------------------------------------------------------------------- + + +def test_a_reversing_view_covers_its_parts() -> None: + """A reversal reads every cell of every box, back to front.""" + data = np.arange(48).reshape(8, 6) + forward = LazyArray(data).with_parts((2, 2)).lazy[:, :] + reversed_view = LazyArray(data).with_parts((2, 2)).lazy[::-1, ::-1] + assert [part.is_complete for part in reversed_view.parts()] == [ + part.is_complete for part in forward.parts() + ] + assert all(part.is_complete for part in reversed_view.parts()) + + +def test_a_strided_reversal_is_still_incomplete() -> None: + data = np.arange(48).reshape(8, 6) + view = LazyArray(data).with_parts((2, 2)).lazy[::-2, :] + assert not any(part.is_complete for part in view.parts()) + + +@pytest.mark.parametrize("parts", [((0,), (3,)), ((), (3,)), (1, 1), ((0, 0), (3,))]) +def test_a_zero_length_axis_accepts_every_spelling_of_no_chunks(parts: Any) -> None: + """`(0,)`, `(0, 0)`, `()` and a uniform shape all describe an axis with no cells.""" + data = np.zeros((0, 3)) + view = repartition(LazyArray(data), parts) + assert view.result().shape == (0, 3) + assert list(view.parts()) == [] + + +def test_a_zero_chunk_on_a_nonempty_axis_is_still_rejected() -> None: + with pytest.raises(ValueError, match="chunk sizes must be positive"): + LazyArray(np.zeros((4, 3))).with_parts_per_axis(((0, 4), (3,))) + + +@pytest.mark.parametrize( + "selection", + [ + (slice(None, None, -1), slice(None), slice(None)), + (slice(3, 1, -1), slice(None), slice(None)), + (slice(None, None, -2), slice(None, None, -1), slice(None)), + ], + ids=["reversed", "reversed-partial", "reversed-strided"], +) +def test_the_coverage_count_agrees_with_numpy_for_reversed_selections( + selection: tuple[Any, ...], +) -> None: + """The safety net behind `result()`'s coverage assertion, checked on its own. + + `_out_selection_cell_count` sizes a partition's `out_selection` without + materializing it, and `result()` trusts that count to decide whether the + walk covered the view. Nothing pinned it for a reversed slice, so dropping + its `start <= stop` guard — or wrapping the subtraction in `abs()` — left + the suite green. A net nobody tests only matters once something else breaks, + which is exactly when it needs to be right. + """ + data = reference() + view = LazyArray(data).with_parts((2, 2, 2)).lazy[selection] + out_shape = view.shape + for part in view.parts(): + counted = _out_selection_cell_count(part.out_selection, out_shape) + assert counted == np.empty(out_shape)[part.out_selection].size + + +@pytest.mark.parametrize( + ("selection", "out_shape", "expected"), + [ + (((slice(2, 5)),), (10,), 3), + # A backwards interval selects nothing. The fast path subtracts, which + # would make this negative and let an incomplete walk sum to the view's + # own size — so the count falls back to `range` whenever the interval is + # not a forward, in-bounds one. + (((slice(5, 2)),), (10,), 0), + # Counts from the end, to index 8 — past the stop, so nothing. + (((slice(-2, 5)),), (10,), 0), + ((slice(5, 2), slice(0, 3)), (10, 10), 0), + ], + ids=["forward", "backwards", "negative-start", "backwards-in-a-pair"], +) +def test_the_coverage_count_matches_numpy_for_intervals_the_fast_path_declines( + selection: tuple[Any, ...], out_shape: tuple[int, ...], expected: int +) -> None: + """The guard on `result()`'s safety net, exercised where the walk cannot reach it. + + A partition walk only ever produces concrete forward in-bounds intervals, so + the guard that keeps everything else off the subtraction fast path is not + reachable through `parts()` at all — which is why removing it left the whole + suite green. It is the net's own contract, so it is checked directly. + """ + counted = _out_selection_cell_count(selection, out_shape) + assert counted == np.empty(out_shape)[selection].size + assert counted == expected + + +def test_a_zero_dimensional_index_array_drops_its_axis_like_a_scalar() -> None: + """`a[np.array(2), :]` is `a[2, :]` in NumPy, and now here too. + + Only Python and NumPy integers counted as scalars, so a 0-d array fell + through to the fancy path and was widened into a length-1 index array — + keeping an axis NumPy drops. That was a third answer, agreeing with neither + NumPy nor eager zarr, which rejects it. + """ + data = np.arange(20).reshape(4, 5) + for mode, expected in ( + ("oindex", data[np.array(2), :]), + ("vindex", data[np.array(2), np.array(3)]), + ): + view = ( + LazyArray(data).lazy.oindex[np.array(2), slice(None)] + if mode == "oindex" + else LazyArray(data).lazy.vindex[np.array(2), np.array(3)] + ) + assert view.shape == expected.shape, mode + np.testing.assert_array_equal(np.asarray(view.result()), expected, err_msg=mode) + + +def test_a_multidimensional_array_in_an_orthogonal_selection_is_refused() -> None: + """The rule belongs to the selection, so the message speaks its vocabulary. + + Left to the engine, this surfaced as a rank complaint about an `index_array` + the caller never wrote — the transform layer's words for a mistake made two + layers above it. + """ + with pytest.raises(IndexError, match="must be 1-dimensional"): + LazyArray(np.arange(20).reshape(4, 5)).lazy.oindex[[[0, 1], [2, 3]], slice(None)] + + +def test_with_parts_rejects_a_bare_integer() -> None: + """Both partitioning methods document ValueError for malformed input.""" + view = LazyArray.from_numpy(np.arange(12).reshape(3, 4)) + with pytest.raises(ValueError, match="one entry per dimension"): + view.with_parts(3) # type: ignore[arg-type] + with pytest.raises(ValueError, match="one entry per dimension"): + view.with_parts_per_axis(3) # type: ignore[arg-type] + + +def test_fancy_composition_over_an_empty_axis() -> None: + """Regression: composing fancy steps over an empty axis stays unpinned. + + The empty-domain branch of `compose` produces index arrays that are + singleton on every non-empty axis; pinning one to an axis it merely + broadcasts along made a later basic step index a size-1 axis positionally + and raise, deep inside a legal chain. + """ + base = np.empty((3, 0, 6), dtype=np.int64) + view = LazyArray(base).lazy.oindex[[2, 1], :, [5, 0, 3]] + assert view.shape == (2, 0, 3) + composed = view.lazy.oindex[[1, 0], :, [2, 2]] + assert composed.shape == (2, 0, 2) + scalar = composed.lazy.vindex[..., np.array(1)] + assert scalar.shape == (2, 0) + assert np.asarray(scalar.result()).shape == (2, 0) diff --git a/packages/zarr-indexing/tests/test_lazy_array_stateful.py b/packages/zarr-indexing/tests/test_lazy_array_stateful.py new file mode 100644 index 0000000000..4f5dadc1e4 --- /dev/null +++ b/packages/zarr-indexing/tests/test_lazy_array_stateful.py @@ -0,0 +1,114 @@ +"""This package's own use of the state machine it exports. + +`ChainedIndexingStateMachine` composes indexing steps onto a `LazyArray` and +checks each step against NumPy — see +`zarr_indexing.testing.stateful` for what the invariants assert and why. + +Two sources: a NumPy array, which exercises both built-in readers, and a real +zarr array, whose partitioning is discovered from the store rather than +declared. The zarr case runs a smaller budget: it reads through a store, and it +exercises the same code paths. + +This replaces a seeded `_random_chain` sweep in `test_lazy_array` that read +chained selections through `parts()`. That sweep did reach the states it was +meant to, but a rank-0 correlated view was absorbed by a reshape in `result()` +and mirrored into the sweep rather than read as a failure; asserting the +documented assembly literally makes that impossible to paper over. +`test_lazy_array` keeps its `result()`-based sweep, which is the deterministic +cross-flavor coverage this does not attempt. +""" + +from __future__ import annotations + +from typing import Any, ClassVar + +import numpy as np +import pytest +from hypothesis import settings + +from zarr_indexing import LazyArray, ReadContext +from zarr_indexing.reader import basic_reader, numpy_reader +from zarr_indexing.testing import ( + DEFAULT_SETTINGS, + ChainedIndexingStateMachine, + state_machine_test, + stateful, +) + + +class NumpyIndexing(ChainedIndexingStateMachine): + readers = (numpy_reader,) + + +TestNumpyIndexing = state_machine_test(NumpyIndexing) + + +class UnhashableReader: + __hash__ = None + + def read_into(self, source: Any, context: ReadContext, out: Any, /) -> None: + basic_reader.read_into(source, context, out) + + def __eq__(self, other: object) -> bool: + return isinstance(other, UnhashableReader) + + +def test_reader_set_deduplicates_by_identity_without_hashing() -> None: + first = UnhashableReader() + second = UnhashableReader() + + readers = stateful._reader_set(LazyArray(np.arange(3)), (first, first, second)) + + assert readers[0] is basic_reader + assert readers[1] is first + assert readers[2] is second + assert len(readers) == 3 + + +class OneDimensionalIndexing(ChainedIndexingStateMachine): + """The same chains over a rank-1 source. + + The sorted one-dimensional fancy path in `chunk_resolution` is entered only + when both the input and output ranks are 1, and the output rank is the + *source's* — so the rank-3 default walls that path off from the machine + entirely, and from every downstream project told to subclass it. That path + is where reordering and duplicate coordinates are partitioned, which is the + corruption class this whole harness exists to catch. + """ + + data = np.arange(30, dtype=np.int64) + partitionings: ClassVar[tuple[Any, ...]] = (None, (4,), (30,), ((7, 8, 15),)) + + +TestOneDimensionalIndexing = state_machine_test(OneDimensionalIndexing) + + +class SingletonAxisIndexing(ChainedIndexingStateMachine): + """A source with an extent-1 axis, which the code must not read as a broadcast one. + + An index array's axis is a singleton either because the map broadcasts over + it or because the domain is genuinely one cell wide there, and the two are + told apart by the domain rather than the array. Nothing generated the second + kind. + """ + + data = np.arange(2 * 1 * 3, dtype=np.int64).reshape(2, 1, 3) + partitionings: ClassVar[tuple[Any, ...]] = (None, (1, 1, 1), (2, 1, 2)) + + +TestSingletonAxisIndexing = state_machine_test(SingletonAxisIndexing) + + +class ZarrIndexing(ChainedIndexingStateMachine): + """The same chains against a zarr array through the universal basic reader.""" + + def make_source(self, data: Any) -> Any: + zarr = pytest.importorskip("zarr") + array = zarr.create_array({}, shape=data.shape, chunks=(3, 2, 3), dtype=data.dtype) + array[:] = data + return array + + +TestZarrIndexing = state_machine_test( + ZarrIndexing, config=settings(DEFAULT_SETTINGS, max_examples=50) +) diff --git a/packages/zarr-indexing/tests/test_messages.py b/packages/zarr-indexing/tests/test_messages.py index 14bed66448..2ebd41a263 100644 --- a/packages/zarr-indexing/tests/test_messages.py +++ b/packages/zarr-indexing/tests/test_messages.py @@ -89,3 +89,45 @@ def test_empty_string_kind_is_unknown_kind() -> None: with pytest.raises(NdselError) as excinfo: normalize_ndsel({"kind": ""}) assert excinfo.value.reason == "unknown_kind" + + +class TestNegativeStep: + """ndsel 1.0-draft.2 section 5.3: one desugaring rule, both signs.""" + + def test_full_reverse(self) -> None: + """The spec's own worked example: reversing a length-20 axis.""" + body = normalize_ndsel({"kind": "slice", "start": [19], "stop": [-1], "step": [-1]}) + assert body["input_inclusive_min"] == [-19] + assert body["input_exclusive_max"] == [1] + assert body["output"] == [{"offset": 0, "stride": -1, "input_dimension": 0}] + + def test_trunc_origin_for_a_negative_step(self) -> None: + """`trunc(15 / -2) == -7`; `floor` would give -8.""" + body = normalize_ndsel({"kind": "slice", "start": [15], "stop": [5], "step": [-2]}) + assert body["input_inclusive_min"] == [-7] + assert body["input_exclusive_max"] == [-2] + assert body["output"] == [{"offset": 1, "stride": -2, "input_dimension": 0}] + + def test_empty_is_legal_at_any_coordinate(self) -> None: + body = normalize_ndsel({"kind": "slice", "start": [5], "stop": [5], "step": [-1]}) + assert body["input_inclusive_min"] == body["input_exclusive_max"] == [-5] + + @pytest.mark.parametrize( + "message", + [ + {"kind": "slice", "start": [9], "stop": [0]}, + {"kind": "slice", "start": [9], "stop": [0], "step": [2]}, + {"kind": "slice", "start": [5], "stop": [6], "step": [-1]}, + ], + ids=["unit-step", "positive-step", "negative-step"], + ) + def test_a_reversed_interval_is_an_error(self, message: dict[str, object]) -> None: + """Not clamped to empty: travelling the wrong way is a mistake, either sign.""" + with pytest.raises(NdselError) as excinfo: + normalize_ndsel(message) + assert excinfo.value.reason == "bounds_out_of_order" + + def test_zero_step_still_errors(self) -> None: + with pytest.raises(NdselError) as excinfo: + normalize_ndsel({"kind": "slice", "start": [0], "stop": [4], "step": [0]}) + assert excinfo.value.reason == "step_zero" diff --git a/packages/zarr-indexing/tests/test_ndsel_tensorstore.py b/packages/zarr-indexing/tests/test_ndsel_tensorstore.py index 794ac5f3d5..ab9465c8d1 100644 --- a/packages/zarr-indexing/tests/test_ndsel_tensorstore.py +++ b/packages/zarr-indexing/tests/test_ndsel_tensorstore.py @@ -17,7 +17,6 @@ import numpy as np import pytest -from zarr_indexing.json import transform_from_canonical, transform_to_canonical from zarr_indexing.transform import IndexTransform ts = pytest.importorskip("tensorstore") @@ -38,7 +37,7 @@ def _canonical_transforms() -> list[IndexTransform]: @pytest.mark.parametrize("transform", _canonical_transforms()) def test_body_loads_in_tensorstore_and_round_trips(transform: IndexTransform) -> None: - body = transform_to_canonical(transform) + body = transform.to_json() # (1) The canonical body loads directly as a TensorStore IndexTransform. ts_transform = ts.IndexTransform(json=body) @@ -48,5 +47,5 @@ def test_body_loads_in_tensorstore_and_round_trips(transform: IndexTransform) -> # representational choices (index_array_bounds, default omissions) that # both sides make differently but that denote the same selection. ts_json = ts_transform.to_json() - reloaded = transform_from_canonical(ts_json) - assert transform_to_canonical(reloaded) == transform_to_canonical(transform) + reloaded = IndexTransform.from_json(ts_json) + assert reloaded.to_json() == transform.to_json() diff --git a/packages/zarr-indexing/tests/test_output_map.py b/packages/zarr-indexing/tests/test_output_map.py index 498101444e..d1e21efaa7 100644 --- a/packages/zarr-indexing/tests/test_output_map.py +++ b/packages/zarr-indexing/tests/test_output_map.py @@ -1,6 +1,9 @@ from __future__ import annotations +import pickle + import numpy as np +import pytest from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap @@ -54,3 +57,43 @@ def test_frozen(self) -> None: arr = np.array([0], dtype=np.intp) m = ArrayMap(index_array=arr) assert isinstance(m, ArrayMap) + + def test_owns_index_array_and_keeps_hash_stable(self) -> None: + arr = np.array([1, 3, 5], dtype=np.intp) + m = ArrayMap(index_array=arr) + lookup = {m: "value"} + + arr[:] = 9 + + np.testing.assert_array_equal(m.index_array, [1, 3, 5]) + assert lookup[m] == "value" + + def test_pickle_round_trip_keeps_index_array_read_only(self) -> None: + restored = pickle.loads(pickle.dumps(ArrayMap(index_array=np.array([1, 3, 5])))) + + assert not restored.index_array.flags.writeable + with pytest.raises(ValueError, match="read-only"): + restored.index_array[0] = 9 + + def test_index_array_cannot_be_made_writeable(self) -> None: + m = ArrayMap(index_array=np.array([1, 3, 5])) + + with pytest.raises(ValueError): + m.index_array.flags.writeable = True + + def test_equal_array_maps_have_equal_hashes_across_integer_dtypes(self) -> None: + left = ArrayMap(np.array([1, 2], dtype=np.int32)) + right = ArrayMap(np.array([1, 2], dtype=np.int64)) + assert left == right + assert hash(left) == hash(right) + assert left.index_array.dtype == np.dtype(np.intp) + + def test_rejects_non_integer_index_array(self) -> None: + with pytest.raises(TypeError, match="index_array must have an integer dtype"): + ArrayMap(np.array([1.5, 2.0], dtype=np.float64)) + + def test_rejects_unsigned_index_array_value_outside_intp(self) -> None: + outside_intp = np.array([np.iinfo(np.uint64).max], dtype=np.uint64) + + with pytest.raises(OverflowError, match="outside np.intp range"): + ArrayMap(outside_intp) diff --git a/packages/zarr-indexing/tests/test_reader.py b/packages/zarr-indexing/tests/test_reader.py new file mode 100644 index 0000000000..11241a316c --- /dev/null +++ b/packages/zarr-indexing/tests/test_reader.py @@ -0,0 +1,514 @@ +from __future__ import annotations + +import math +from typing import TYPE_CHECKING, Any, get_type_hints + +import numpy as np +import numpy.typing as npt +import pytest + +import zarr_indexing.reader as reader_module +from zarr_indexing import ( + ArrayMap, + ChunkProjection, + ConstantMap, + DimensionMap, + IndexDomain, + IndexTransform, + LazyArray, + ReadContext, + plan_chunks, +) +from zarr_indexing.grid import dimension_grids_from_chunks +from zarr_indexing.reader import basic_reader, numpy_reader, unit_step_reader + +if TYPE_CHECKING: + from collections.abc import Callable + + +class BasicOnlySource: + def __init__(self, data: np.ndarray[Any, Any]) -> None: + self.data = data + self.keys: list[tuple[Any, ...]] = [] + + @property + def shape(self) -> tuple[int, ...]: + return self.data.shape + + @property + def dtype(self) -> np.dtype[Any]: + return self.data.dtype + + def __getitem__(self, key: tuple[Any, ...]) -> np.ndarray[Any, Any]: + assert all(isinstance(item, slice) and (item.step or 1) > 0 for item in key) + self.keys.append(key) + return self.data[key] + + +class UnitStepOnlySource(BasicOnlySource): + """A source that rejects everything but ascending unit-step slices.""" + + def __getitem__(self, key: tuple[Any, ...]) -> np.ndarray[Any, Any]: + assert all( + isinstance(item, slice) and item.step == 1 and 0 <= item.start <= item.stop <= size + for item, size in zip(key, self.data.shape, strict=True) + ) + self.keys.append(key) + return self.data[key] + + +SOURCE = np.arange(6 * 7 * 8).reshape(6, 7, 8) +BASE = IndexTransform.from_shape(SOURCE.shape) + + +SUCCESSFUL_CONTRACT_CASES = ( + pytest.param( + np.arange(8), + IndexTransform.from_shape((8,))[3], + (3,), + np.zeros((1, 0), dtype=np.intp), + np.array([[3]], dtype=np.intp), + np.array(3), + lambda array: array.lazy[3], + id="constant", + ), + pytest.param( + np.arange(8), + IndexTransform.from_shape((8,))[1:8:2], + (3,), + np.array([[0], [1], [2], [3]], dtype=np.intp), + np.array([[1], [3], [5], [7]], dtype=np.intp), + np.array([1, 3, 5, 7]), + lambda array: array.lazy[1:8:2], + id="positive-affine", + ), + pytest.param( + np.arange(8), + IndexTransform.from_shape((8,))[::-2], + (3,), + np.array([[-3], [-2], [-1], [0]], dtype=np.intp), + np.array([[7], [5], [3], [1]], dtype=np.intp), + np.array([7, 5, 3, 1]), + lambda array: array.lazy[::-2], + id="negative-affine", + ), + pytest.param( + np.arange(8), + IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=(DimensionMap(input_dimension=0, offset=2, stride=0),), + ), + (3,), + np.array([[0], [1], [2]], dtype=np.intp), + np.array([[2], [2], [2]], dtype=np.intp), + np.array([2, 2, 2]), + lambda array: array.lazy.oindex[[2, 2, 2]], + id="zero-affine", + ), + pytest.param( + np.arange(20).reshape(4, 5), + IndexTransform.from_shape((4, 5)).oindex[[3, 1, 1], [4, 0]], + (2, 3), + np.array([[0, 0], [0, 1], [1, 0], [1, 1], [2, 0], [2, 1]], dtype=np.intp), + np.array([[3, 4], [3, 0], [1, 4], [1, 0], [1, 4], [1, 0]], dtype=np.intp), + np.array([[19, 15], [9, 5], [9, 5]]), + lambda array: array.lazy.oindex[[3, 1, 1], [4, 0]], + id="orthogonal-array", + ), + pytest.param( + np.arange(20).reshape(4, 5), + IndexTransform.from_shape((4, 5)).vindex[[3, 1, 1], [4, 0, 4]], + (2, 3), + np.array([[0], [1], [2]], dtype=np.intp), + np.array([[3, 4], [1, 0], [1, 4]], dtype=np.intp), + np.array([19, 5, 9]), + lambda array: array.lazy.vindex[[3, 1, 1], [4, 0, 4]], + id="correlated-array", + ), + pytest.param( + np.arange(8), + IndexTransform( + domain=IndexDomain((4,), (7,)), + output=(DimensionMap(input_dimension=0, offset=-3, stride=1),), + ), + (3,), + np.array([[4], [5], [6]], dtype=np.intp), + np.array([[1], [2], [3]], dtype=np.intp), + np.array([1, 2, 3]), + None, + id="non-zero-origin", + ), + pytest.param( + np.arange(8), + IndexTransform.from_shape((8,))[2:2], + (3,), + np.empty((0, 1), dtype=np.intp), + np.empty((0, 1), dtype=np.intp), + np.array([], dtype=np.intp), + lambda array: array.lazy[2:2], + id="empty", + ), +) + + +@pytest.mark.parametrize( + ( + "source_data", + "transform", + "chunk_shape", + "request_coordinates", + "storage_coordinates", + "expected_values", + "lazy_selection", + ), + SUCCESSFUL_CONTRACT_CASES, +) +def test_successful_transform_contract_across_planning_readers_and_lazy_array( + source_data: np.ndarray[Any, Any], + transform: IndexTransform, + chunk_shape: tuple[int, ...], + request_coordinates: npt.NDArray[np.intp], + storage_coordinates: npt.NDArray[np.intp], + expected_values: np.ndarray[Any, Any], + lazy_selection: Callable[[LazyArray], LazyArray] | None, +) -> None: + """One literal matrix keeps transform, planning, readers, and wrappers aligned.""" + np.testing.assert_array_equal(transform.apply_many(request_coordinates), storage_coordinates) + + grids = dimension_grids_from_chunks(chunk_shape, source_data.shape) + reconstructed_pairs = [ + ( + tuple(projection.cell_transform.apply(cell_coordinate)), + tuple( + local_coordinate + chunk_origin + for local_coordinate, chunk_origin in zip( + projection.chunk_transform.apply(cell_coordinate), + projection.chunk_domain.inclusive_min, + strict=True, + ) + ), + ) + for projection in plan_chunks(transform, grids) + for cell_coordinate in _domain_coordinates(projection.cell_transform.domain) + ] + expected_pairs = list( + zip( + map(tuple, request_coordinates.tolist()), + map(tuple, storage_coordinates.tolist()), + strict=True, + ) + ) + assert sorted(reconstructed_pairs) == sorted(expected_pairs) + + for reader, source in ( + (basic_reader, BasicOnlySource(source_data)), + (numpy_reader, source_data), + (unit_step_reader, UnitStepOnlySource(source_data)), + ): + out = np.empty(transform.domain.shape, dtype=source_data.dtype) + assert reader.read_into(source, ReadContext(transform), out) is None + np.testing.assert_array_equal(out, expected_values) + + if lazy_selection is not None: + view = lazy_selection(LazyArray.from_numpy(source_data).with_parts(chunk_shape)) + np.testing.assert_array_equal(view.result(), expected_values) + + +def _domain_coordinates(domain: IndexDomain) -> list[tuple[int, ...]]: + return [ + tuple( + position + origin for position, origin in zip(index, domain.inclusive_min, strict=True) + ) + for index in np.ndindex(*domain.shape) + ] + + +def test_read_context_public_annotations_resolve() -> None: + assert get_type_hints(ReadContext)["projection"] == ChunkProjection | None + + +READER_CASES = ( + pytest.param( + SOURCE, + BASE[1:6:2, 2, ::-2], + np.array( + [ + [79, 77, 75, 73], + [191, 189, 187, 185], + [303, 301, 299, 297], + ] + ), + id="strided-reversed-nonzero-origin", + ), + pytest.param( + SOURCE, + BASE.oindex[[5, 1, 1], slice(1, 6), [7, 2]], + np.array( + [ + [[295, 290], [303, 298], [311, 306], [319, 314], [327, 322]], + [[71, 66], [79, 74], [87, 82], [95, 90], [103, 98]], + [[71, 66], [79, 74], [87, 82], [95, 90], [103, 98]], + ] + ), + id="orthogonal-nonzero-origin", + ), + pytest.param( + SOURCE, + BASE.vindex[np.array([[5], [1]]), np.array([[2, 4, 0]])], + np.array( + [ + [ + [296, 297, 298, 299, 300, 301, 302, 303], + [312, 313, 314, 315, 316, 317, 318, 319], + [280, 281, 282, 283, 284, 285, 286, 287], + ], + [ + [72, 73, 74, 75, 76, 77, 78, 79], + [88, 89, 90, 91, 92, 93, 94, 95], + [56, 57, 58, 59, 60, 61, 62, 63], + ], + ] + ), + id="correlated-broadcast", + ), + pytest.param( + SOURCE, + BASE.vindex[[5, 1], [2, 2]], + np.array( + [ + [296, 297, 298, 299, 300, 301, 302, 303], + [72, 73, 74, 75, 76, 77, 78, 79], + ] + ), + id="correlated-vector", + ), + pytest.param( + SOURCE, + BASE[:, 0:0, :], + np.empty((6, 0, 8), dtype=SOURCE.dtype), + id="empty", + ), + pytest.param(SOURCE, BASE[2, 3, 4], np.array(140), id="scalar"), + pytest.param( + np.arange(8), + IndexTransform( + domain=IndexDomain((4,), (7,)), + output=(DimensionMap(input_dimension=0, offset=2, stride=0),), + ), + np.array([2, 2, 2]), + id="zero-stride-nonzero-origin", + ), +) + + +@pytest.mark.parametrize(("source_data", "transform", "expected"), READER_CASES) +@pytest.mark.parametrize("reader_name", ["basic", "numpy", "unit-step"]) +def test_builtin_readers_match_the_transform( + source_data: np.ndarray[Any, Any], + transform: IndexTransform, + expected: np.ndarray[Any, Any], + reader_name: str, +) -> None: + out = np.empty(transform.domain.shape, dtype=source_data.dtype) + if reader_name == "basic": + source = BasicOnlySource(source_data) + result = basic_reader.read_into(source, ReadContext(transform), out) + assert len(source.keys) == 1 + elif reader_name == "unit-step": + source = UnitStepOnlySource(source_data) + result = unit_step_reader.read_into(source, ReadContext(transform), out) + assert len(source.keys) == 1 + else: + result = numpy_reader.read_into(source_data, ReadContext(transform), out) + assert result is None + np.testing.assert_array_equal(out, expected) + + +@pytest.mark.parametrize("reader_name", ["basic", "numpy", "unit-step"]) +def test_builtin_readers_share_transform_affine_overflow(reader_name: str) -> None: + transform = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ArrayMap(np.array([2**62], dtype=np.intp), stride=4),), + ) + + with pytest.raises(OverflowError, match="outside np.intp"): + transform.apply_many(np.array([[0]], dtype=np.intp)) + + out = np.empty(transform.domain.shape, dtype=np.intp) + if reader_name == "basic": + with pytest.raises(OverflowError, match="outside np.intp"): + basic_reader.read_into(BasicOnlySource(np.arange(1)), ReadContext(transform), out) + elif reader_name == "unit-step": + with pytest.raises(OverflowError, match="outside np.intp"): + unit_step_reader.read_into( + UnitStepOnlySource(np.arange(1)), ReadContext(transform), out + ) + else: + with pytest.raises(OverflowError, match="outside np.intp"): + numpy_reader.read_into(np.arange(1), ReadContext(transform), out) + + +def test_empty_domain_composed_fancy_transform_reads_as_empty() -> None: + """An ArrayMap composed over an empty domain resolves like any other map. + + The composed map is legitimately empty along the vanished axis; the + resolvers used to fail reshaping it instead of noticing that an empty + domain selects nothing. + """ + source_data = np.arange(6).reshape(2, 3) + view = LazyArray.from_numpy(source_data).lazy.oindex[slice(0, 0), np.array([2, 1, 2, 0])] + transform = view.lazy.oindex[slice(None), np.array([1, 3, 1])].transform + assert transform.domain.shape == (0, 3) + + for reader, source in ( + (basic_reader, BasicOnlySource(source_data)), + (numpy_reader, source_data), + (unit_step_reader, UnitStepOnlySource(source_data)), + ): + out = np.empty(transform.domain.shape, dtype=source_data.dtype) + assert reader.read_into(source, ReadContext(transform), out) is None + + +def test_unit_step_reader_reads_through_lazy_array() -> None: + """The full dialect resolves through a source that only accepts unit-step slices. + + `UnitStepOnlySource` asserts the shape of every key it receives, so each + selection here also proves no strided, descending, or non-slice key + reached the source — partitioned and unpartitioned alike. + """ + selections: tuple[Callable[[LazyArray], LazyArray], ...] = ( + lambda v: v.lazy[1:5, ::2, ::-1], + lambda v: v.lazy[5:1:-2, None, 3, ::3], + lambda v: v.lazy.oindex[[3, 0, 3], ::-2, [7, 7]], + lambda v: v.lazy.vindex[np.array([[0, 5]]), np.array([[6], [0]]), 2], + lambda v: v.lazy[2:2, :, ::-1], + lambda v: v.lazy[::5, 6, 1:8:4], + ) + for select in selections: + for parts in (None, (2, 3, 8), (6, 7, 1)): + source = UnitStepOnlySource(SOURCE) + view = LazyArray(source).with_reader(unit_step_reader) + if parts is not None: + view = view.with_parts(parts) + expected = select(LazyArray.from_numpy(SOURCE)).result() + np.testing.assert_array_equal(select(view).result(), expected) + # An empty view allocates without reading; every other one must read. + assert (len(source.keys) > 0) == (expected.size > 0) + + +def test_constant_outside_intp_has_transform_planner_reader_error_parity() -> None: + outside_intp = int(np.iinfo(np.intp).max) + 1 + transform = IndexTransform( + domain=IndexDomain((), ()), + output=(ConstantMap(offset=outside_intp),), + ) + + with pytest.raises(OverflowError, match="outside np.intp range"): + transform.apply_many(np.zeros((1, 0), dtype=np.intp)) + + grids = dimension_grids_from_chunks((1,), (1,)) + with pytest.raises(OverflowError, match="outside np.intp range"): + list(plan_chunks(transform, grids)) + + for reader, source in ( + (basic_reader, BasicOnlySource(np.arange(1))), + (numpy_reader, np.arange(1)), + ): + with pytest.raises(OverflowError, match="outside np.intp range"): + reader.read_into(source, ReadContext(transform), np.empty((), dtype=np.intp)) + + +def test_numpy_reader_narrows_basic_slab_before_gather( + monkeypatch: pytest.MonkeyPatch, +) -> None: + source = np.arange(1_000_000).reshape(1000, 1000) + transform = IndexTransform.from_shape(source.shape).oindex[:10, [0, 999]] + seen: list[tuple[int, ...]] = [] + real_take = reader_module._take # pyright: ignore[reportPrivateUsage] + + def recording_take(array: Any, indices: npt.NDArray[np.intp], axis: int) -> Any: + seen.append(tuple(int(value) for value in array.shape)) + return real_take(array, indices, axis) + + monkeypatch.setattr(reader_module, "_take", recording_take) + out = np.empty(transform.domain.shape, dtype=source.dtype) + assert numpy_reader.read_into(source, ReadContext(transform), out) is None + assert out.shape == (10, 2) + np.testing.assert_array_equal( + out, + np.array( + [ + [0, 999], + [1000, 1999], + [2000, 2999], + [3000, 3999], + [4000, 4999], + [5000, 5999], + [6000, 6999], + [7000, 7999], + [8000, 8999], + [9000, 9999], + ] + ), + ) + assert seen + assert all(math.prod(shape) <= 20_000 for shape in seen), seen + + +def test_numpy_reader_preserves_a_mask_in_the_supplied_buffer() -> None: + source = np.ma.masked_greater(np.arange(12).reshape(3, 4), 7) + transform = IndexTransform.from_shape(source.shape)[:, 1:] + out = np.ma.masked_all(transform.domain.shape, dtype=source.dtype) + assert numpy_reader.read_into(source, ReadContext(transform), out) is None + np.testing.assert_array_equal(np.ma.getmaskarray(out), np.ma.getmaskarray(source[:, 1:])) + np.testing.assert_array_equal(np.ma.filled(out, 0), np.ma.filled(source[:, 1:], 0)) + + +# --------------------------------------------------------------------------- +# Diagonal gathers — output maps sharing an input axis +# --------------------------------------------------------------------------- + + +def test_reading_a_diagonal_gather_transform() -> None: + """Two index arrays bound to the same input axis resolve pointwise. + + No selection dialect produces this transform — it is the hand-built + diagonal-extraction form — but the reader resolves it through the same + pointwise path as a correlated gather. + """ + data = np.arange(30).reshape(5, 6) + rows = np.array([4, 0, 2]) + cols = np.array([1, 5, 2]) + transform = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=( + ArrayMap(index_array=rows), + ArrayMap(index_array=cols), + ), + ) + + out = np.empty((3,), dtype=data.dtype) + basic_reader.read_into(data, ReadContext(transform), out) + np.testing.assert_array_equal(out, data[rows, cols]) + + out = np.empty((3,), dtype=data.dtype) + numpy_reader.read_into(data, ReadContext(transform), out) + np.testing.assert_array_equal(out, data[rows, cols]) + + +def test_reading_a_diagonal_gather_with_a_residual_slice_axis() -> None: + data = np.arange(60).reshape(5, 6, 2) + rows = np.array([[4], [0], [2]]) + cols = np.array([[1], [5], [2]]) + transform = IndexTransform( + domain=IndexDomain.from_shape((3, 2)), + output=( + ArrayMap(index_array=rows), + ArrayMap(index_array=cols), + DimensionMap(input_dimension=1), + ), + ) + + out = np.empty((3, 2), dtype=data.dtype) + basic_reader.read_into(data, ReadContext(transform), out) + np.testing.assert_array_equal(out, data[rows[:, 0], cols[:, 0], :]) diff --git a/packages/zarr-indexing/tests/test_tensorstore_parity.py b/packages/zarr-indexing/tests/test_tensorstore_parity.py index 1ed99046e9..9f4123fc02 100644 --- a/packages/zarr-indexing/tests/test_tensorstore_parity.py +++ b/packages/zarr-indexing/tests/test_tensorstore_parity.py @@ -208,6 +208,178 @@ def test_reversed_bounds_raise(self, sel: slice) -> None: _a()[sel] +class TestNegativeStep: + """Section 1 of the negative-step study: one desugaring rule, both signs. + + Every expectation below is TensorStore 0.1.84's recorded output (study + sections 1.3-1.5), which an exhaustive 32,980-case sweep found zero + disagreements with. + """ + + # (domain, slice, expected domain, expected offset, expected stride, cells) + RECORDED: ClassVar[list[tuple[tuple[int, int], slice, tuple[int, int], int, int]]] = [ + ((0, 20), slice(15, 5, -1), (-15, -5), 0, -1), + ((0, 20), slice(15, 5, -2), (-7, -2), 1, -2), + ((0, 20), slice(15, 4, -2), (-7, -1), 1, -2), + ((0, 20), slice(None, None, -1), (-19, 1), 0, -1), + ((0, 20), slice(None, None, -2), (-9, 1), 1, -2), + ((0, 20), slice(5, None, -1), (-5, 1), 0, -1), + ((0, 20), slice(None, 5, -1), (-19, -5), 0, -1), + ((0, 20), slice(5, 5, -1), (-5, -5), 0, -1), + ((0, 20), slice(5, 4, -1), (-5, -4), 0, -1), + ((0, 20), slice(5, 4, -3), (-1, 0), 2, -3), + ((0, 20), slice(15, 5, -4), (-3, 0), 3, -4), + ((0, 20), slice(15, 5, -7), (-2, 0), 1, -7), + ((5, 25), slice(None, None, -2), (-12, -2), 0, -2), + ((-10, 10), slice(-1, -6, -2), (0, 3), -1, -2), + ((-10, 10), slice(-2, -9, -3), (0, 3), -2, -3), + ] + + @pytest.mark.parametrize( + ("domain", "sel", "expected_domain", "offset", "stride"), + RECORDED, + ids=[f"{d}{s}" for d, s, _, _, _ in RECORDED], + ) + def test_recorded_desugaring( + self, + domain: tuple[int, int], + sel: slice, + expected_domain: tuple[int, int], + offset: int, + stride: int, + ) -> None: + t = _identity(*domain)[sel] + assert (t.domain.inclusive_min[0], t.domain.exclusive_max[0]) == expected_domain + m = _dim(t) + assert (m.offset, m.stride) == (offset, stride) + + @pytest.mark.parametrize( + ("domain", "sel", "cells"), + [ + ((0, 20), slice(15, 5, -1), list(range(15, 5, -1))), + ((0, 20), slice(15, 5, -2), [15, 13, 11, 9, 7]), + ((0, 20), slice(None, None, -1), list(range(19, -1, -1))), + ((0, 20), slice(15, 5, -7), [15, 8]), + ((5, 25), slice(None, None, -2), list(range(24, 4, -2))), + ((-10, 10), slice(-1, -6, -2), [-1, -3, -5]), + ((-10, 10), slice(-2, -9, -3), [-2, -5, -8]), + ], + ) + def test_recorded_cells(self, domain: tuple[int, int], sel: slice, cells: list[int]) -> None: + assert _base_cells(_identity(*domain)[sel]) == cells + + def test_trunc_not_floor_or_ceil(self) -> None: + """The three rows of study section 1.2 that discriminate the rounding.""" + # floor would give -8 here, trunc gives -7. + assert _identity(0, 20)[15:5:-2].domain.inclusive_min[0] == -7 + # ceil would give 1 for both of these; trunc gives 0. + assert _identity(-10, 10)[-1:-6:-2].domain.inclusive_min[0] == 0 + assert _identity(-10, 10)[-2:-9:-3].domain.inclusive_min[0] == 0 + + @pytest.mark.parametrize("sel", [slice(5, 15, -1), slice(5, 6, -1)]) + def test_inverted_interval_raises(self, sel: slice) -> None: + with pytest.raises(IndexError, match="valid.*interval"): + _identity(0, 20)[sel] + + @pytest.mark.parametrize("sel", [slice(20, 0, -1), slice(20, 19, -1), slice(15, -5, -1)]) + def test_uncontained_interval_raises(self, sel: slice) -> None: + with pytest.raises(BoundsCheckError, match="not contained"): + _identity(0, 20)[sel] + + def test_zero_step_raises(self) -> None: + with pytest.raises(IndexError, match="step must not be zero"): + _identity(0, 20)[15:5:0] + + def test_empty_interval_legal_outside_the_domain(self) -> None: + t = _identity(0, 20)[25:25:-1] + assert t.domain.shape == (0,) + assert t.domain.inclusive_min[0] == -25 + + @pytest.mark.parametrize( + ("domain", "first", "second", "expected_domain", "offset", "stride", "cells"), + [ + # Study section 1.5, recorded verbatim. Each row applies `second` + # to the view `first` produced — strides multiply, and a double + # reverse recovers the identity. + ( + (0, 20), + slice(0, 20, 2), + slice(None, None, -1), + (-9, 1), + 0, + -2, + list(range(18, -2, -2)), + ), + ((0, 20), slice(0, 20, 2), slice(None, None, -2), (-4, 1), 2, -4, [18, 14, 10, 6, 2]), + ( + (0, 20), + slice(None, None, -1), + slice(None, None, -1), + (0, 20), + 0, + 1, + list(range(20)), + ), + ( + (0, 20), + slice(None, None, -1), + slice(None, None, 2), + (-9, 1), + 1, + -2, + list(range(19, -1, -2)), + ), + ( + (-10, 10), + slice(None, None, -1), + slice(None, None, -3), + (-3, 4), + -1, + 3, + [-10, -7, -4, -1, 2, 5, 8], + ), + ], + ids=[ + "strided-then-reverse", + "strided-then-reverse-by-two", + "double-reverse-is-identity", + "reverse-then-strided", + "reverse-then-strided-on-negative-origin", + ], + ) + def test_recorded_composition( + self, + domain: tuple[int, int], + first: slice, + second: slice, + expected_domain: tuple[int, int], + offset: int, + stride: int, + cells: list[int], + ) -> None: + t = _identity(*domain)[first][second] + assert (t.domain.inclusive_min[0], t.domain.exclusive_max[0]) == expected_domain + m = _dim(t) + assert (m.offset, m.stride) == (offset, stride) + assert _base_cells(t) == cells + + def test_negative_step_over_an_index_array_reverses_it(self) -> None: + """Study section 1.5: a reversing step materializes, it does not stride. + + Recorded: `oindex[[3, 1, 2]]` then `[2:-1:-1]` gives index array + `[[2], [1], [3]]` over domain `[-2, 1)`. + """ + base = IndexTransform.identity(IndexDomain(inclusive_min=(0, 0), exclusive_max=(4, 5))) + gathered = base.oindex[np.array([3, 1, 2]), slice(None)] + reversed_view = gathered[2:-1:-1, :] + + assert reversed_view.domain.inclusive_min[0] == -2 + assert reversed_view.domain.exclusive_max[0] == 1 + m = reversed_view.output[0] + assert isinstance(m, ArrayMap) + np.testing.assert_array_equal(m.index_array.reshape(-1), np.array([2, 1, 3])) + + class TestTranslate: """Oracle sections 4 and 12: translate_by / translate_to preserve the cell mapping.""" diff --git a/packages/zarr-indexing/tests/test_transform.py b/packages/zarr-indexing/tests/test_transform.py index baecd9ada2..a13eaf6e28 100644 --- a/packages/zarr-indexing/tests/test_transform.py +++ b/packages/zarr-indexing/tests/test_transform.py @@ -1,11 +1,39 @@ from __future__ import annotations +from typing import cast + import numpy as np import pytest from zarr_indexing.domain import IndexDomain +from zarr_indexing.errors import BoundsCheckError +from zarr_indexing.lazy_array import LazyArray from zarr_indexing.output_map import ArrayMap, ConstantMap, DimensionMap -from zarr_indexing.transform import IndexTransform, selection_to_transform +from zarr_indexing.transform import ( + IndexTransform, +) + + +class IndexLike: + """A scalar integer selector implemented only through `__index__`.""" + + def __init__(self, value: int) -> None: + self.value = value + + def __index__(self) -> int: + return self.value + + +class IntOnly: + def __int__(self) -> int: + return 2 + + +class BadIndex: + """An `__index__` that lies: the protocol requires an integer.""" + + def __index__(self) -> int: + return cast("int", 2.5) class TestIndexTransformConstruction: @@ -50,6 +78,323 @@ def test_validation_input_dimension_out_of_range(self) -> None: IndexTransform(domain=domain, output=maps) +class TestIndexTransformApply: + @pytest.mark.parametrize( + ("transform", "points", "expected"), + [ + pytest.param( + IndexTransform.identity(IndexDomain((-2, 5), (1, 8))), + np.array([-2, 7], dtype=np.int64), + np.array([-2, 7], dtype=np.intp), + id="identity-negative-and-nonzero-origins", + ), + pytest.param( + IndexTransform( + domain=IndexDomain((3,), (6,)), + output=( + ConstantMap(41), + DimensionMap(0, offset=10, stride=-2), + ), + ), + np.array([[3], [5]], dtype=np.int16), + np.array([[41, 4], [41, 0]], dtype=np.intp), + id="constant-and-negative-stride", + ), + pytest.param( + IndexTransform( + domain=IndexDomain((-2, 5), (1, 8)), + output=( + ArrayMap( + np.array([[7], [11], [13]], dtype=np.intp), + offset=-1, + stride=2, + ), + ), + ), + np.array( + [ + [[-2, 5], [-1, 7]], + [[0, 6], [-2, 6]], + ], + dtype=np.intp, + ), + np.array([[[13], [21]], [[25], [13]]], dtype=np.intp), + id="array-map-singleton-broadcast-multidimensional-batch", + ), + pytest.param( + IndexTransform(IndexDomain((), ()), (ConstantMap(42),)), + np.empty((2, 0), dtype=np.intp), + np.array([[42], [42]], dtype=np.intp), + id="rank-zero-input", + ), + pytest.param( + IndexTransform(IndexDomain((-1,), (2,)), ()), + np.array([[-1], [1]], dtype=np.intp), + np.empty((2, 0), dtype=np.intp), + id="rank-zero-output", + ), + pytest.param( + IndexTransform.identity(IndexDomain.from_shape((2,))), + np.empty((0, 1), dtype=np.intp), + np.empty((0, 1), dtype=np.intp), + id="empty-batch", + ), + ], + ) + def test_apply_many_maps_integer_point_batches( + self, + transform: IndexTransform, + points: np.ndarray, + expected: np.ndarray, + ) -> None: + result = transform.apply_many(points) + + np.testing.assert_array_equal(result, expected) + assert result.dtype == np.dtype(np.intp) + assert result.flags.owndata + + def test_apply_maps_one_point(self) -> None: + transform = IndexTransform( + IndexDomain((-2, 4), (1, 7)), + ( + DimensionMap(1, offset=3, stride=-1), + DimensionMap(0, offset=2, stride=2), + ), + ) + + assert transform.apply((-1, 6)) == (-3, 0) + + def test_apply_rejects_a_point_with_the_wrong_rank(self) -> None: + with pytest.raises(ValueError, match=r"point must have shape \(2,\), got \(1,\)"): + IndexTransform.from_shape((2, 3)).apply((1,)) + + def test_apply_rejects_an_explicitly_floating_rank_zero_point(self) -> None: + transform = IndexTransform(IndexDomain((), ()), ()) + with pytest.raises(TypeError, match="integer dtype"): + transform.apply(np.array([], dtype=np.float64)) + + @pytest.mark.parametrize( + "points", + [ + pytest.param(np.array(1, dtype=np.intp), id="no-coordinate-axis"), + pytest.param(np.zeros((4, 3), dtype=np.intp), id="wrong-trailing-size"), + ], + ) + def test_apply_many_rejects_an_invalid_coordinate_axis(self, points: np.ndarray) -> None: + with pytest.raises(ValueError, match="trailing coordinate axis"): + IndexTransform.from_shape((2, 3)).apply_many(points) + + @pytest.mark.parametrize( + "points", + [ + pytest.param(np.array([[True]], dtype=np.bool_), id="bool"), + pytest.param(np.array([[1.0]], dtype=np.float64), id="float"), + pytest.param(np.array([["1"]], dtype=np.str_), id="string"), + pytest.param(np.array([[1]], dtype=object), id="object"), + ], + ) + def test_apply_many_rejects_non_integer_coordinates(self, points: np.ndarray) -> None: + with pytest.raises(TypeError, match="integer dtype"): + IndexTransform.from_shape((2,)).apply_many(points) + + def test_apply_many_reports_the_first_out_of_bounds_coordinate(self) -> None: + transform = IndexTransform.identity(IndexDomain((-2, 10), (2, 13))) + points = np.array( + [ + [[-2, 10], [-1, 20]], + [[9, 11], [0, 12]], + ], + dtype=np.intp, + ) + + with pytest.raises(BoundsCheckError) as error: + transform.apply_many(points) + + assert str(error.value) == ( + "point at batch position (0, 1) has input dimension 1 coordinate 20 outside [10, 13)" + ) + + def test_apply_reports_a_single_point_error_without_batch_vocabulary(self) -> None: + transform = IndexTransform.identity(IndexDomain((-10,), (10,))) + + with pytest.raises(BoundsCheckError) as error: + transform.apply((11,)) + + assert str(error.value) == ( + "coordinate 11 on input dimension 0 is outside the domain [-10, 10)" + ) + assert error.value.__cause__ is None + assert error.value.__suppress_context__ + + @pytest.mark.parametrize( + "beyond_intp", + [ + pytest.param(int(np.iinfo(np.intp).max) + 1, id="first-uint64-coordinate"), + pytest.param(int(np.iinfo(np.uint64).max), id="maximum-uint64-coordinate"), + ], + ) + def test_apply_many_maps_large_literal_coordinates_exactly(self, beyond_intp: int) -> None: + transform = IndexTransform( + IndexDomain((beyond_intp,), (beyond_intp + 1,)), + (DimensionMap(0, offset=-beyond_intp),), + ) + + result = transform.apply_many(np.array([[beyond_intp]], dtype=np.uint64)) + + np.testing.assert_array_equal(result, np.array([[0]], dtype=np.intp)) + assert result.dtype == np.dtype(np.intp) + assert result.flags.owndata + + @pytest.mark.parametrize( + ("transform", "points"), + [ + pytest.param( + IndexTransform( + IndexDomain.from_shape((1,)), + (ConstantMap(np.iinfo(np.intp).max + 1),), + ), + [[0]], + id="constant", + ), + pytest.param( + IndexTransform( + IndexDomain.from_shape((2,)), + (DimensionMap(0, offset=np.iinfo(np.intp).max),), + ), + [[1]], + id="dimension", + ), + pytest.param( + IndexTransform( + IndexDomain.from_shape((1,)), + ( + ArrayMap( + np.array([1], dtype=np.intp), + offset=np.iinfo(np.intp).max, + ), + ), + ), + [[0]], + id="array", + ), + pytest.param( + IndexTransform.identity( + IndexDomain( + (int(np.iinfo(np.intp).max) + 1,), + (int(np.iinfo(np.intp).max) + 2,), + ) + ), + np.array([[int(np.iinfo(np.intp).max) + 1]], dtype=np.uint64), + id="large-input-identity", + ), + ], + ) + def test_apply_many_rejects_mapped_coordinates_outside_intp( + self, transform: IndexTransform, points: list[list[int]] | np.ndarray + ) -> None: + with pytest.raises(OverflowError, match="output coordinate.*np.intp"): + transform.apply_many(points) + + def test_apply_many_rejects_affine_coordinate_overflow(self) -> None: + transform = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ArrayMap(np.array([2**62], dtype=np.intp), stride=4),), + ) + with pytest.raises(OverflowError, match="outside np.intp"): + transform.apply_many(np.array([[0]], dtype=np.intp)) + + def test_apply_rejects_affine_coordinate_overflow(self) -> None: + transform = IndexTransform( + domain=IndexDomain.from_shape((1,)), + output=(ArrayMap(np.array([2**62], dtype=np.intp), stride=4),), + ) + with pytest.raises(OverflowError, match="outside np.intp"): + transform.apply((0,)) + + +class TestIndexTransformInverted: + @pytest.mark.parametrize( + ("transform", "points"), + [ + pytest.param( + IndexTransform( + IndexDomain((-3, 4), (1, 7)), + ( + DimensionMap(1, offset=10), + DimensionMap(0, offset=2, stride=-1), + ), + ), + np.array([[-3, 4], [0, 6]], dtype=np.intp), + id="permutation-translation-reversal-nonzero-origin", + ), + pytest.param( + IndexTransform( + IndexDomain((5, -2), (8, -1)), + (DimensionMap(0, offset=3), ConstantMap(99)), + ), + np.array([[5, -2], [7, -2]], dtype=np.intp), + id="constant-and-unreferenced-singleton", + ), + pytest.param( + IndexTransform(IndexDomain((), ()), ()), + np.empty((1, 0), dtype=np.intp), + id="rank-zero", + ), + ], + ) + def test_inverted_round_trips_points( + self, transform: IndexTransform, points: np.ndarray + ) -> None: + inverse = transform.inverted() + mapped = transform.apply_many(points) + + np.testing.assert_array_equal(inverse.apply_many(mapped), points) + assert inverse.apply(transform.apply(tuple(points[0]))) == tuple(points[0]) + assert inverse.inverted() == transform + + def test_inverted_rejects_unequal_ranks(self) -> None: + transform = IndexTransform(IndexDomain.from_shape((2,)), (ConstantMap(1), ConstantMap(2))) + with pytest.raises(ValueError, match="input rank must equal output rank"): + transform.inverted() + + def test_inverted_rejects_an_array_map(self) -> None: + transform = IndexTransform( + IndexDomain.from_shape((2,)), + (ArrayMap(np.array([1, 0], dtype=np.intp)),), + ) + with pytest.raises(ValueError, match="ArrayMap"): + transform.inverted() + + def test_inverted_rejects_a_non_unit_stride(self) -> None: + transform = IndexTransform( + IndexDomain.from_shape((2,)), + (DimensionMap(0, stride=2),), + ) + with pytest.raises(ValueError, match=r"stride must be \+1 or -1"): + transform.inverted() + + def test_inverted_rejects_a_repeated_input_dimension(self) -> None: + transform = IndexTransform( + IndexDomain.from_shape((2, 1)), + (DimensionMap(0), DimensionMap(0, offset=5)), + ) + with pytest.raises(ValueError, match="referenced more than once"): + transform.inverted() + + def test_inverted_rejects_an_unreferenced_non_singleton_dimension(self) -> None: + transform = IndexTransform( + IndexDomain.from_shape((2, 2)), + (DimensionMap(0), ConstantMap(7)), + ) + with pytest.raises(ValueError, match="unreferenced input dimension 1.*extent 2"): + transform.inverted() + + def test_inverted_rejects_input_labels_that_cannot_be_preserved(self) -> None: + transform = IndexTransform.identity(IndexDomain((0,), (2,), labels=("row",))) + with pytest.raises(ValueError, match="input labels cannot be represented"): + transform.inverted() + + class TestIndexTransformBasicIndexing: def test_slice_identity(self) -> None: """slice(None) on identity transform is a no-op.""" @@ -180,6 +525,45 @@ def test_bare_slice(self) -> None: result = t[2:8] assert result.domain.shape == (6, 20) + @pytest.mark.parametrize( + ("mode", "selection", "expected_selection"), + [ + pytest.param("basic", IndexLike(2), 2, id="basic-scalar"), + pytest.param( + "basic", + slice(IndexLike(1), IndexLike(7), IndexLike(2)), + slice(1, 7, 2), + id="basic-slice-components", + ), + pytest.param("oindex", IndexLike(2), 2, id="orthogonal-scalar"), + pytest.param("vindex", IndexLike(2), 2, id="vectorized-scalar"), + ], + ) + def test_literal_selectors_support_the_index_protocol( + self, mode: str, selection: object, expected_selection: object + ) -> None: + transform = IndexTransform.from_shape((8,)) + if mode == "basic": + result = transform[selection] + expected = transform[expected_selection] + else: + result = getattr(transform, mode)[selection] + expected = getattr(transform, mode)[expected_selection] + + assert result == expected + + def test_literal_selector_rejects_int_only_objects(self) -> None: + with pytest.raises(IndexError, match="unsupported selection type"): + IndexTransform.from_shape((8,))[IntOnly()] + + def test_literal_selector_propagates_malformed_index_protocol(self) -> None: + with pytest.raises(TypeError, match="__index__ returned non-int"): + IndexTransform.from_shape((8,))[BadIndex()] + + def test_literal_slice_propagates_malformed_index_protocol(self) -> None: + with pytest.raises(TypeError, match="__index__ returned non-int"): + IndexTransform.from_shape((8,))[:: BadIndex()] + class TestBasicIndexingOnArrayMaps: """When a transform already has ArrayMap outputs, basic indexing must @@ -350,6 +734,17 @@ def test_vindex_bool_mask(self) -> None: assert result.domain.shape == (3,) assert isinstance(result.output[0], ArrayMap) + def test_vindex_multidimensional_boolean_list_mask(self) -> None: + result = IndexTransform.from_shape((2, 3)).vindex[ + [[True, False, True], [False, True, False]] + ] + + assert result.domain.shape == (3,) + np.testing.assert_array_equal( + result.apply_many(np.array([[0], [1], [2]], dtype=np.intp)), + np.array([[0, 0], [0, 2], [1, 1]], dtype=np.intp), + ) + def test_vindex_broadcast_different_shapes(self) -> None: t = IndexTransform.from_shape((10, 20)) idx0 = np.array([1, 2, 3], dtype=np.intp) @@ -368,10 +763,24 @@ def test_vindex_multiple_arrays_preserves_shared_axes(self) -> None: assert result.output[1].index_array.shape == (2,) +@pytest.mark.parametrize("mode", ["oindex", "vindex"]) +def test_direct_advanced_index_rejects_float_arrays(mode: str) -> None: + helper = getattr(IndexTransform.from_shape((5,)), mode) + with pytest.raises(IndexError, match="integer or boolean"): + helper[np.array([1.9, 3.2])] + + +@pytest.mark.parametrize("mode", ["oindex", "vindex"]) +def test_direct_advanced_index_rejects_wrong_length_boolean_mask(mode: str) -> None: + helper = getattr(IndexTransform.from_shape((5,)), mode) + with pytest.raises(IndexError, match="boolean index.*dimension 5"): + helper[np.array([True, False])] + + class TestSelectionToTransform: def test_basic_slice(self) -> None: t = IndexTransform.from_shape((10, 20)) - result = selection_to_transform((slice(2, 8), slice(5, 15)), t, "basic") + result = t.select((slice(2, 8), slice(5, 15)), "basic") assert result.domain.shape == (6, 10) assert result.domain.origin == (2, 5) # preserved literal coordinates assert isinstance(result.output[0], DimensionMap) @@ -379,20 +788,20 @@ def test_basic_slice(self) -> None: def test_basic_int(self) -> None: t = IndexTransform.from_shape((10, 20)) - result = selection_to_transform((3, slice(None)), t, "basic") + result = t.select((3, slice(None)), "basic") assert result.input_rank == 1 assert isinstance(result.output[0], ConstantMap) assert result.output[0].offset == 3 def test_basic_ellipsis(self) -> None: t = IndexTransform.from_shape((10, 20)) - result = selection_to_transform(Ellipsis, t, "basic") + result = t.select(Ellipsis, "basic") assert result.domain.shape == (10, 20) def test_orthogonal(self) -> None: t = IndexTransform.from_shape((10, 20)) idx = np.array([1, 3, 5], dtype=np.intp) - result = selection_to_transform((idx, slice(None)), t, "orthogonal") + result = t.select((idx, slice(None)), "orthogonal") assert result.domain.shape == (3, 20) assert isinstance(result.output[0], ArrayMap) @@ -400,7 +809,7 @@ def test_vectorized(self) -> None: t = IndexTransform.from_shape((10, 20)) idx0 = np.array([1, 3], dtype=np.intp) idx1 = np.array([5, 7], dtype=np.intp) - result = selection_to_transform((idx0, idx1), t, "vectorized") + result = t.select((idx0, idx1), "vectorized") assert result.domain.shape == (2,) assert isinstance(result.output[0], ArrayMap) assert isinstance(result.output[1], ArrayMap) @@ -413,7 +822,7 @@ def test_composition_with_non_identity(self) -> None: the composed map stays the identity (out = in). """ t = IndexTransform.from_shape((100,))[10:50] - result = selection_to_transform(slice(15, 30), t, "basic") + result = t.select(slice(15, 30), "basic") assert (result.domain.inclusive_min, result.domain.exclusive_max) == ((15,), (30,)) assert isinstance(result.output[0], DimensionMap) assert result.output[0].offset == 0 @@ -469,6 +878,72 @@ def test_dimension_strided(self) -> None: assert restricted.domain.inclusive_min == (2,) assert restricted.domain.exclusive_max == (4,) + @pytest.mark.parametrize( + ("input_domain", "output_domain", "output_map", "expected"), + [ + ( + (2**53, 2**53 + 3), + (2**53 + 1, 2**53 + 2), + DimensionMap(input_dimension=0), + (2**53 + 1, 2**53 + 2), + ), + ( + (-(2**53) - 2, -(2**53) + 1), + (-(2**53) - 1, -(2**53)), + DimensionMap(input_dimension=0), + (-(2**53) - 1, -(2**53)), + ), + ( + (-(2**53) - 2, -(2**53) + 1), + (2**53 + 1, 2**53 + 2), + DimensionMap(input_dimension=0, stride=-1), + (-(2**53) - 1, -(2**53)), + ), + ( + (2**53, 2**53 + 3), + (-(2**53) - 2, -(2**53) - 1), + DimensionMap(input_dimension=0, stride=-1), + (2**53 + 2, 2**53 + 3), + ), + ], + ids=[ + "positive-coordinates-positive-stride", + "negative-coordinates-positive-stride", + "positive-coordinates-negative-stride", + "negative-coordinates-negative-stride", + ], + ) + def test_dimension_intersection_is_exact_above_float_precision( + self, + input_domain: tuple[int, int], + output_domain: tuple[int, int], + output_map: DimensionMap, + expected: tuple[int, int], + ) -> None: + transform = IndexTransform( + domain=IndexDomain((input_domain[0],), (input_domain[1],)), + output=(output_map,), + ) + + result = transform.intersect(IndexDomain((output_domain[0],), (output_domain[1],))) + + assert result is not None + restricted, _surviving = result + assert restricted.domain == IndexDomain((expected[0],), (expected[1],)) + + def test_dimension_intersection_accepts_unbounded_python_integer_precision(self) -> None: + huge = 10**400 + transform = IndexTransform( + domain=IndexDomain((huge,), (huge + 2,)), + output=(DimensionMap(input_dimension=0),), + ) + + result = transform.intersect(IndexDomain((huge + 1,), (huge + 2,))) + + assert result is not None + restricted, _surviving = result + assert restricted.domain == IndexDomain((huge + 1,), (huge + 2,)) + def test_array_partial(self) -> None: arr = np.array([3, 8, 15, 22], dtype=np.intp) t = IndexTransform( @@ -549,33 +1024,39 @@ def test_translate_2d(self) -> None: class TestArrayMapDependencyAxes: - """`_array_map_dependency_axes` derives the input axes an array varies on + """`ArrayMap.dependency_axes` derives the input axes an array varies on from its (full-rank) shape: non-singleton axes vary, singleton axes do not.""" def test_orthogonal_single_axis(self) -> None: - from zarr_indexing.transform import _array_map_dependency_axes - t = IndexTransform.from_shape((10, 20)).oindex[np.array([1, 3]), np.array([2, 4, 6])] m0, m1 = t.output[0], t.output[1] assert isinstance(m0, ArrayMap) assert isinstance(m1, ArrayMap) - assert _array_map_dependency_axes(m0.index_array) == (0,) - assert _array_map_dependency_axes(m1.index_array) == (1,) + assert m0.dependency_axes == (0,) + assert m1.dependency_axes == (1,) def test_vectorized_shares_axes(self) -> None: - from zarr_indexing.transform import _array_map_dependency_axes - t = IndexTransform.from_shape((10, 20)).vindex[np.array([1, 3]), np.array([2, 4])] m0, m1 = t.output[0], t.output[1] assert isinstance(m0, ArrayMap) assert isinstance(m1, ArrayMap) - assert _array_map_dependency_axes(m0.index_array) == (0,) - assert _array_map_dependency_axes(m1.index_array) == (0,) + assert m0.dependency_axes == (0,) + assert m1.dependency_axes == (0,) def test_scalar_array_has_no_dependency(self) -> None: - from zarr_indexing.transform import _array_map_dependency_axes + assert ArrayMap(np.ones((1, 1), dtype=np.intp)).dependency_axes == () - assert _array_map_dependency_axes(np.ones((1, 1), dtype=np.intp)) == () + def test_zero_length_axis_has_no_dependency(self) -> None: + """An axis of size 0 carries no dependency either: it selects nothing, so + the array does not vary along it any more than along a singleton.""" + assert ArrayMap(np.zeros((0, 4), dtype=np.intp)).dependency_axes == (1,) + assert ArrayMap(np.zeros((3, 0), dtype=np.intp)).dependency_axes == (0,) + assert ArrayMap(np.zeros((0, 1), dtype=np.intp)).dependency_axes == () + + def test_zero_length_axis_does_not_make_a_map_correlated(self) -> None: + """An empty orthogonal selection is legal, so it must classify as one.""" + m = ArrayMap(index_array=np.zeros((0, 4), dtype=np.intp)) + assert m.dependent_axis == 1 class TestIntersectArrayMapClassification: @@ -617,12 +1098,153 @@ def test_correlated_with_residual_slice_preserves_slice_dim(self) -> None: assert any(isinstance(m, DimensionMap) for m in restricted.output) assert out_indices is not None - def test_length1_orthogonal_not_treated_as_correlated(self) -> None: - """A length-1 orthogonal array (all-singleton shape) is still an outer - product with the length-3 axis: out_indices is a dict, not a flat array.""" + def test_length1_orthogonal_collapses_to_a_constant(self) -> None: + """A length-1 orthogonal array holds one coordinate: it is a ConstantMap. + + The length-1 axis stays in the domain, and the remaining genuine array + intersects orthogonally — a single survivor vector, not a joint gather. + """ t = IndexTransform.from_shape((6, 6)).oindex[np.array([2]), np.array([1, 3, 5])] + assert isinstance(t.output[0], ConstantMap) + assert t.domain.shape == (1, 3) chunk = IndexDomain(inclusive_min=(0, 0), exclusive_max=(6, 6)) result = t.intersect(chunk) assert result is not None _restricted, out_indices = result - assert isinstance(out_indices, dict) + assert isinstance(out_indices, np.ndarray) + np.testing.assert_array_equal(out_indices, [0, 1, 2]) + + +class TestDerivedMapDependency: + """A map's `input_dimension` must describe the array it is built with. + + Three separate failures came from one stale value: a vectorized index applied + to an orthogonal map makes it correlated, but the old dependency was carried + onto the new array anyway. Readers fall back to that field when the shape + alone cannot say, so the wrong axis was believed much later — by a scatter + that filed positions under it, which is why the answer depended on how the + read was partitioned. + """ + + def test_a_vindex_over_a_fancy_view_is_marked_correlated(self) -> None: + base = np.arange(6) + view = ( + LazyArray(base) + .lazy.oindex[np.array([0, 1])] + .lazy.vindex[np.array([[0, 1, 0], [1, 0, 1]])] + ) + np.testing.assert_array_equal( + np.asarray(view.result()), base[[0, 1]][[[0, 1, 0], [1, 0, 1]]] + ) + + def test_the_same_view_resolves_alike_however_it_is_partitioned(self) -> None: + base = np.arange(36).reshape(6, 6) + + def build(array: LazyArray) -> LazyArray: + return array.lazy.oindex[np.array([-3, -6, -4]), -4].lazy.vindex[np.array([[-2, -3]])] + + unpartitioned = np.asarray(build(LazyArray(base)).result()) + partitioned = np.asarray(build(LazyArray(base).with_parts((3, 3))).result()) + np.testing.assert_array_equal(partitioned, unpartitioned) + np.testing.assert_array_equal(unpartitioned, np.array([[2, 20]])) + + def test_dependency_axes_are_read_from_the_shape(self) -> None: + """What a map varies over is its non-singleton axes — nothing else. + + The retired `input_dimension` field could contradict the array it rode + on; the shape cannot. + """ + t = IndexTransform( + domain=IndexDomain.from_shape((2, 3)), + output=( + ArrayMap(index_array=np.array([[0, 1, 2]], dtype=np.intp)), + ArrayMap(index_array=np.array([[0], [1]], dtype=np.intp)), + ), + ) + assert t.index_array_structure == "orthogonal" + + +def test_an_orthogonal_step_over_a_correlated_view_is_an_outer_product() -> None: + """`oindex` after `vindex` means the outer product, not a joint gather. + + The reindexing applied its index tuple positionally, which is NumPy's + *vectorized* rule, so two arrays collapsed into one axis and the result came + back a rank short of what was asked for. + """ + base = np.arange(14).reshape(7, 2) + view = LazyArray(base).lazy.vindex[ + np.array([[5, 5], [1, 2], [0, 4]]), np.array([[1, 1], [1, 0], [1, 0]]) + ] + result = np.asarray(view.lazy.oindex[np.array([1, 1, 0]), np.array([1, 1, 0, 1])].result()) + assert result.shape == (3, 4) + np.testing.assert_array_equal(result, np.array([[4, 4, 3, 4], [4, 4, 3, 4], [11, 11, 11, 11]])) + + +@pytest.mark.parametrize( + ("value", "description"), + [(1, "one below the lower bound"), (10, "the exclusive upper bound itself")], +) +def test_an_index_array_value_just_outside_the_domain_is_refused( + value: int, description: str +) -> None: + """The bound checks are probed at the boundary, not comfortably past it. + + Both were only ever exercised from well outside the domain, so relaxing + either by one — `lo - 1` instead of `lo` — went unnoticed while letting a + view read a cell it does not address. + """ + transform = IndexTransform.from_shape((12,))[2:10] + with pytest.raises(BoundsCheckError, match="out of bounds"): + transform.oindex[np.array([value, 3])] + + +def test_an_index_array_value_at_each_end_of_the_domain_is_accepted() -> None: + """The other side of the same boundary: the extremes themselves are in range.""" + transform = IndexTransform.from_shape((12,))[2:10] + array_map = transform.oindex[np.array([2, 9])].output[0] + assert isinstance(array_map, ArrayMap) + np.testing.assert_array_equal(array_map.index_array, np.array([2, 9])) + + +# --------------------------------------------------------------------------- +# Intersecting diagonal gathers +# --------------------------------------------------------------------------- + + +def test_intersecting_a_diagonal_gather_keeps_points_inside_the_domain() -> None: + """Index arrays sharing an input axis intersect pointwise, like vindex.""" + rows = np.array([4, 0, 2]) + cols = np.array([1, 5, 2]) + transform = IndexTransform( + domain=IndexDomain.from_shape((3,)), + output=( + ArrayMap(index_array=rows), + ArrayMap(index_array=cols), + ), + ) + + result = transform.intersect(IndexDomain(inclusive_min=(0, 0), exclusive_max=(3, 3))) + assert result is not None + restricted, survivors = result + # Only the point (2, 2) has both coordinates inside [0, 3) x [0, 3). + assert restricted.domain.shape == (1,) + assert isinstance(survivors, np.ndarray) + np.testing.assert_array_equal(survivors, [2]) + np.testing.assert_array_equal(restricted.apply((0,)), (2, 2)) + + assert transform.intersect(IndexDomain(inclusive_min=(0, 0), exclusive_max=(1, 1))) is None + + +def test_index_array_structure_classifies_the_three_shapes() -> None: + base = IndexTransform.from_shape((4, 6)) + assert (base[1:, ::2]).index_array_structure == "none" + assert (base.oindex[np.array([0, 2]), slice(None)]).index_array_structure == "orthogonal" + assert (base.vindex[np.array([0, 2]), np.array([1, 3])]).index_array_structure == "general" + diagonal = IndexTransform( + domain=IndexDomain.from_shape((2,)), + output=( + ArrayMap(index_array=np.array([0, 1])), + 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+[package.metadata.requires-dev] +docs = [ + { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, + { name = "mkdocs", specifier = "==1.6.1" }, + { name = "mkdocs-material", specifier = "==9.7.7" }, + { name = "mkdocstrings", specifier = "==1.0.6" }, + { name = "mkdocstrings-python", specifier = "==2.0.5" }, + { name = "ruff", specifier = "==0.15.22" }, +] +test = [ + { name = "hypothesis", specifier = ">=6.160.0" }, + { name = "pytest" }, +] From 47f09b1b9fd10052bae28d2eefb43211ba2484c2 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 15:49:15 +0200 Subject: [PATCH 451/468] docs: add card for zarr-http-server (#4249) --- docs/subprojects.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/subprojects.md b/docs/subprojects.md index 1903f759d2..9f7951e836 100644 --- a/docs/subprojects.md +++ b/docs/subprojects.md @@ -32,4 +32,14 @@ without taking on `zarr` as a dependency. pip install zarr-indexing ``` +- [:material-server:{ .lg .middle } __zarr-http-server__](https://zarr.readthedocs.io/projects/zarr-http-server/) + + --- + + HTTP server for Zarr stores, arrays, and groups. + + ```bash + pip install zarr-http-server + ``` + </div> From 5b9c09fcaa9359bc3eaa68c48eea7d31deb3dcd7 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 16:30:21 +0200 Subject: [PATCH 452/468] fix(docs): build subpackage docs from the package directory (#4252) Read the Docs pointed `-f` at each package's mkdocs.yml from the repo root. mkdocs resolves some settings relative to the current working directory rather than to the config file, so building from elsewhere looks for them in the wrong place -- and silently, because the paths are valid, just wrong. zarr-indexing hit this at v0.2.0: `pymdownx.snippets` has a relative `base_path` of `[docs, examples]`, so `--8<-- "snippets/canonical_slice.py"` resolved against the repo root and searched zarr-python's own docs/ rather than the package's. The build failed with SnippetMissingError while `just docs-check` passed, because that runs from the package directory. Building from the package directory makes the Read the Docs invocation identical to the local and CI ones, so a green build there means a green build here. $READTHEDOCS_OUTPUT is absolute, so the cd does not affect where the site lands. Applied to all three packages. Only zarr-indexing is failing today; zarr-metadata and zarr-http-server do not use snippets, so for them this is preventive -- the hazard is any config resolved against the working directory, and it would show up only on Read the Docs. Assisted-by: ClaudeCode:claude-opus-5 --- packages/zarr-http-server/.readthedocs.yaml | 15 ++++++++++++++- packages/zarr-indexing/.readthedocs.yaml | 15 ++++++++++++++- packages/zarr-metadata/.readthedocs.yaml | 15 ++++++++++++++- 3 files changed, 42 insertions(+), 3 deletions(-) diff --git a/packages/zarr-http-server/.readthedocs.yaml b/packages/zarr-http-server/.readthedocs.yaml index 62a1e82b77..efbda6852d 100644 --- a/packages/zarr-http-server/.readthedocs.yaml +++ b/packages/zarr-http-server/.readthedocs.yaml @@ -24,7 +24,20 @@ build: - pip install ./packages/zarr-http-server --group packages/zarr-http-server/pyproject.toml:docs build: html: - - mkdocs build --strict -f packages/zarr-http-server/mkdocs.yml --site-dir $READTHEDOCS_OUTPUT/html + # Build from inside the package rather than pointing `-f` at its config + # from the repo root. mkdocs resolves some settings relative to the + # current working directory rather than to the config file, so building + # from elsewhere looks for them in the wrong place -- and silently, since + # the paths are valid, just wrong. zarr-indexing hit this: with + # `pymdownx.snippets` and a relative `base_path`, its snippets were + # searched for under the repo-root docs/ and the build failed with + # SnippetMissingError, while `just docs-check` passed because it runs + # from here. Building from the package directory makes this identical to + # the local and CI invocations, so a green build there means a green + # build here. + # + # $READTHEDOCS_OUTPUT is absolute, so the cd does not affect it. + - cd packages/zarr-http-server && mkdocs build --strict --site-dir $READTHEDOCS_OUTPUT/html mkdocs: configuration: packages/zarr-http-server/mkdocs.yml diff --git a/packages/zarr-indexing/.readthedocs.yaml b/packages/zarr-indexing/.readthedocs.yaml index b8c7b76e2b..c1925182f7 100644 --- a/packages/zarr-indexing/.readthedocs.yaml +++ b/packages/zarr-indexing/.readthedocs.yaml @@ -24,7 +24,20 @@ build: - pip install ./packages/zarr-indexing --group packages/zarr-indexing/pyproject.toml:docs build: html: - - mkdocs build --strict -f packages/zarr-indexing/mkdocs.yml --site-dir $READTHEDOCS_OUTPUT/html + # Build from inside the package rather than pointing `-f` at its config + # from the repo root. mkdocs resolves some settings relative to the + # current working directory rather than to the config file, so building + # from elsewhere looks for them in the wrong place -- and silently, since + # the paths are valid, just wrong. zarr-indexing hit this: with + # `pymdownx.snippets` and a relative `base_path`, its snippets were + # searched for under the repo-root docs/ and the build failed with + # SnippetMissingError, while `just docs-check` passed because it runs + # from here. Building from the package directory makes this identical to + # the local and CI invocations, so a green build there means a green + # build here. + # + # $READTHEDOCS_OUTPUT is absolute, so the cd does not affect it. + - cd packages/zarr-indexing && mkdocs build --strict --site-dir $READTHEDOCS_OUTPUT/html mkdocs: configuration: packages/zarr-indexing/mkdocs.yml diff --git a/packages/zarr-metadata/.readthedocs.yaml b/packages/zarr-metadata/.readthedocs.yaml index ace6ccddfd..828773818c 100644 --- a/packages/zarr-metadata/.readthedocs.yaml +++ b/packages/zarr-metadata/.readthedocs.yaml @@ -24,7 +24,20 @@ build: - pip install ./packages/zarr-metadata --group packages/zarr-metadata/pyproject.toml:docs build: html: - - mkdocs build --strict -f packages/zarr-metadata/mkdocs.yml --site-dir $READTHEDOCS_OUTPUT/html + # Build from inside the package rather than pointing `-f` at its config + # from the repo root. mkdocs resolves some settings relative to the + # current working directory rather than to the config file, so building + # from elsewhere looks for them in the wrong place -- and silently, since + # the paths are valid, just wrong. zarr-indexing hit this: with + # `pymdownx.snippets` and a relative `base_path`, its snippets were + # searched for under the repo-root docs/ and the build failed with + # SnippetMissingError, while `just docs-check` passed because it runs + # from here. Building from the package directory makes this identical to + # the local and CI invocations, so a green build there means a green + # build here. + # + # $READTHEDOCS_OUTPUT is absolute, so the cd does not affect it. + - cd packages/zarr-metadata && mkdocs build --strict --site-dir $READTHEDOCS_OUTPUT/html mkdocs: configuration: packages/zarr-metadata/mkdocs.yml From bd3e3986bb4acc3d06220a2285b1165f8e7b488b Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 18:28:39 +0200 Subject: [PATCH 453/468] docs: link the zarr-http-server docs site, and fix dead links across subpackage READMEs - #287 (#4253) * docs(http-server): link the docs site and move the detail into it The README was 405 lines while the docs site was a 58-line scaffold -- inverted relative to the sibling packages, whose READMEs run 52-134 lines with the substance on Read the Docs. It also had no link to the site, which now exists. Adds `Documentation: <https://zarr-http-server.readthedocs.io/>` at the top, matching where zarr-metadata and zarr-indexing put theirs, and moves the detailed sections into a new docs/guide.md: building apps, running them, several nodes, notebooks, Uvicorn configuration, CORS, byte ranges, read-only serving, writes and shutdown. The README keeps what a reader skimming PyPI needs -- what it is, install, a quick start, the build/run split, and the warning that store_app filters nothing. Fixes found while reviewing rather than moved verbatim: - docs/index.md paired store_app with serve and node_app with serve_background as though they were coupled. They are independent; either app runs under either runner. - docs/index.md sent readers to the README for worked examples, which is backwards now and would have been a loop. - The range section cited RFC 7233, obsoleted by RFC 9110, while the rest of the same section cited 9110. - Write examples used a bare `methods={"GET", "PUT"}` although the read-only section a few paragraphs earlier introduced READ_WRITE_HTTP_METHODS for exactly that. - "Read-only serving" and "Write support" restated each other; merged. - The API reference documented 8 of the 13 public names. Added ReadOnlyHTTPMethod, READ_ONLY_HTTP_METHODS, READ_WRITE_HTTP_METHODS, AUTO_PORT and DEFAULT_PORT -- the missing ReadOnlyHTTPMethod was also breaking a cross-reference from the new guide. Deep links use /en/latest/ rather than /en/stable/: verified to resolve, and it picks up this change as soon as the site rebuilds. (zarr-metadata's README links /en/stable/, which currently 404s.) Assisted-by: ClaudeCode:claude-opus-5 * docs: fix dead links in the subpackage READMEs Two broken links found by checking every URL in all three packages' READMEs and docs rather than only the one being edited. zarr-metadata's `Documentation:` link pointed at readthedocs.io/en/stable/, which 404s -- neither it nor zarr-indexing has a `stable` version. Dropped the version segment so it matches the other two and lets Read the Docs redirect to whatever the default is. `www.uvicorn.org` no longer resolves at all: the domain is gone, not merely moved, so it fails DNS rather than returning a 404. Uvicorn's own PyPI metadata now gives `https://uvicorn.dev/` as its homepage. Fixed in the zarr-http-server README and docs index, the only two places it appeared. Every other link in the three READMEs and their docs trees resolves. The two remaining 404s are this PR's own links to the not-yet-published guide page, which resolve once the site rebuilds. Assisted-by: ClaudeCode:claude-opus-5 --- packages/zarr-http-server/README.md | 408 ++------------------ packages/zarr-http-server/docs/api/index.md | 10 + packages/zarr-http-server/docs/guide.md | 393 +++++++++++++++++++ packages/zarr-http-server/docs/index.md | 51 ++- packages/zarr-http-server/mkdocs.yml | 1 + packages/zarr-metadata/README.md | 2 +- 6 files changed, 474 insertions(+), 391 deletions(-) create mode 100644 packages/zarr-http-server/docs/guide.md diff --git a/packages/zarr-http-server/README.md b/packages/zarr-http-server/README.md index 069b33abf8..53df0d2f50 100644 --- a/packages/zarr-http-server/README.md +++ b/packages/zarr-http-server/README.md @@ -2,12 +2,17 @@ HTTP server for Zarr stores, arrays, and groups. +Documentation: <https://zarr-http-server.readthedocs.io/> + `zarr-http-server` exposes a Zarr `Store`, `Array`, or `Group` over HTTP via an -ASGI app, so any HTTP-capable client (including zarr-python itself, via -`FsspecStore` or `ObjectStore`) can read the data. The app is built on +ASGI app, so any HTTP-capable client — including zarr-python itself, via +`FsspecStore` or `ObjectStore` — can read the data. The app is built on [Starlette](https://www.starlette.io/) and can be run with any ASGI server; the `serve` / `serve_background` helpers run it with -[Uvicorn](https://www.uvicorn.org/). +[Uvicorn](https://uvicorn.dev/). + +> [!WARNING] +> This package is experimental. Its API may change or be removed at any point. ## Installation @@ -15,391 +20,52 @@ the `serve` / `serve_background` helpers run it with pip install zarr-http-server ``` -### Building an ASGI App - -`store_app` creates an ASGI app that exposes every key -in a store. Only point it at a store whose full contents are safe to serve -publicly — it grants read (and, if `PUT` is enabled, write) access to -everything the store contains, with no per-key filtering: +## Quick start ```python -import zarr -from zarr_http_server import store_app - -store = zarr.storage.MemoryStore() -zarr.create_array(store, shape=(100, 100), chunks=(10, 10), dtype="float64") - -app = store_app(store) - -# Run with any ASGI server, e.g. Uvicorn: -# uvicorn my_module:app --host 0.0.0.0 --port 8000 -``` - -`node_app` creates an ASGI app that only serves keys -belonging to a specific `Array` or `Group`. Requests for keys outside the node -receive a 404, even if those keys exist in the underlying store: - -```python -import zarr -from zarr_http_server import node_app - -store = zarr.storage.MemoryStore() -root = zarr.open_group(store) -root.create_array("a", shape=(10,), dtype="int32") -root.create_array("b", shape=(20,), dtype="float64") - -# Only serve the array at "a" — requests for "b" will return 404. -arr = root["a"] -app = node_app(arr) -``` - -### Running the Server - -Build an app with `store_app` or `node_app`, then run it. `serve` blocks -until the server is stopped, which is the shape for a script or a container -entrypoint: - -```python -from zarr_http_server import serve, store_app - -serve(store_app(store), host="127.0.0.1", port=8000) -``` - -`serve_background` instead starts the server in a daemon thread and returns a -`BackgroundServer` as soon as the socket is listening, so the caller can carry -on. These are two functions rather than one with a flag, because they differ -in the only thing that matters at a call site: whether control comes back. The -handle is also a context manager: - -Both default to `port="auto"`, which prefers port 8000 but falls back to any -free port if it is taken, reporting the result through `server.url` and -uvicorn's startup line. An **explicit** port means the opposite — bind exactly -that or fail — because a caller who names one usually has a proxy or a -container port mapping expecting the server there, and silently moving would -break it while looking healthy. `port=0` keeps its usual meaning of "any free -port, no preference". - -The example below also *reads back* over HTTP, which is a client-side -concern: `zarr.open_array(server.url)` goes through `FsspecStore`, which needs -an HTTP-capable fsspec that `zarr-http-server` does not pull in. - -```bash -pip install "fsspec[http]" -``` - - -```python -import numpy as np - import zarr from zarr_http_server import node_app, serve_background -from zarr.storage import MemoryStore - -store = MemoryStore() -arr = zarr.create_array(store, shape=(100,), chunks=(10,), dtype="float64") -arr[:] = np.arange(100, dtype="float64") - -with serve_background(node_app(arr), host="127.0.0.1") as server: - # Now open the served array from another zarr client. - remote = zarr.open_array(server.url, mode="r") - np.testing.assert_array_equal(remote[:], arr[:]) -# Server is shut down automatically when the block exits. -``` - -### Serving Several Nodes - -Serving two arrays does not mean running two servers. Which approach fits -depends on where the arrays live. - -If they share a parent group, serve the parent — `node_app` recurses through -its members, so both are reachable under one port and node scoping still -applies to everything outside it: - -```python -server = serve_background(node_app(root)) -# -> /a/zarr.json, /a/c/0, /b/zarr.json, ... -``` - -If everything in the store is safe to expose, `store_app(store)` does the -same for the whole key space. - -Otherwise — arrays in *different* stores, or nodes that are not siblings — -`store_app` and `node_app` return plain Starlette apps, so mount them and run -the result: - -```python -from starlette.applications import Starlette -from starlette.routing import Mount - -from zarr_http_server import node_app, serve_background - -app = Starlette(routes=[ - Mount("/first", app=node_app(one)), - Mount("/second", app=node_app(other)), -]) -server = serve_background(app) -``` - -Each mount keeps its own validation, so a request under one cannot reach -another's data — `/first/../second/zarr.json` and its percent-encoded -spellings all return 404. - -Both runners take any ASGI app, so the split is clean: what an app *serves* -(`methods`, `cors_options`, `max_body_size`) is settled when the app is built, -while `serve` / `serve_background` only decide how it runs (`host`, `port`, -`shutdown_timeout`, `uvicorn_options`). - -### Serving from a Notebook - -A notebook needs a server that outlives the cell that started it, so the -`with serve_background(...)` form above is the wrong shape — it shuts the server down -as soon as the block ends. Start it, keep the handle, and stop it later: - -```python -# cell 1 — start -server = serve_background(node_app(array), host="127.0.0.1") -print(server.url) # e.g. http://127.0.0.1:54635 - -# cell 2..n — use it, across as many cells as you like -httpx.get(f"{server.url}/zarr.json") - -# last cell — stop -server.shutdown() -``` -Two things make this comfortable in a kernel you re-run. `serve_background` -runs Uvicorn in a daemon thread with its own event loop, so it never touches -the kernel's loop and cannot block it. And its default `port="auto"` falls -back to a free port when 8000 is taken — re-running a start cell without -stopping the previous server is the classic notebook mistake, and a fixed port -fails there with *address already in use*. `server.url` reports the port -actually bound. - -If you forget to stop one, the thread is a daemon, so restarting the kernel -always clears it — and since each start takes a fresh port, a forgotten server -does not block the next one. - -[`examples/serve_notebook.ipynb`](examples/serve_notebook.ipynb) is a runnable -version of this, covering metadata and chunk reads, byte ranges, and that -writes are refused by default. It is executed by the test suite, so it cannot -drift from the code. - -### Uvicorn Configuration - -`serve` and `serve_background` name the options most callers need — `host`, -`port`, `shutdown_timeout` — and forward anything else to -`uvicorn.Config` through `uvicorn_options`, so nothing uvicorn can do is out -of reach: - -```python -server = serve_background( - store_app(store), - host="0.0.0.0", - port=8443, - uvicorn_options={ - "ssl_keyfile": "key.pem", - "ssl_certfile": "cert.pem", - "proxy_headers": True, - "forwarded_allow_ips": "10.0.0.0/8", - "log_level": "warning", - }, -) -``` - -Keys you pass are merged over the ones set for you, so they win. `server.url` -reflects the scheme actually in use (`https` when TLS is configured) and is -`None` when the server is not bound to a TCP host and port — a `uds` or `fd` -bind has no URL to report. - -### CORS Support - -Both `store_app` and `node_app` accept a `CorsOptions` parameter to enable -[CORS](https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS) middleware for -browser-based clients: - -```python -from zarr_http_server import CorsOptions, store_app - -app = store_app( - store, - cors_options=CorsOptions( - allow_origins=["*"], - allow_methods=["GET"], - ), -) -``` - -`CorsOptions` carries every parameter Starlette's `CORSMiddleware` accepts — -`allow_headers`, `allow_credentials`, `allow_origin_regex`, -`allow_private_network`, `expose_headers` and `max_age` as well as the two -above — so configuring CORS never means reaching around this package. All keys -are optional. - -Two defaults differ from Starlette's, because the server knows things the -caller should not have to. It emits `Content-Range` on every ranged response, -which is *not* a CORS-safelisted response header, so `expose_headers` defaults -to `["Content-Range"]` — otherwise a browser client can read the bytes but not -learn which bytes it got. And it accepts a `Range` request header, so -`allow_headers` defaults to `["Range"]` — otherwise a preflight naming `Range` -is rejected. A key you supply replaces the default outright, so -`expose_headers=[]` means "expose nothing". - -### HTTP Range Requests - -The server supports the standard `Range` header for partial reads. The three -forms defined by [RFC 7233](https://httpwg.org/specs/rfc7233.html) are supported: - -| Header | Meaning | -| -------------------- | ------------------------------ | -| `bytes=0-99` | First 100 bytes | -| `bytes=100-` | Everything from byte 100 | -| `bytes=-50` | Last 50 bytes | - -A successful range request returns HTTP 206 (Partial Content) with a -`Content-Range` header, including for suffix ranges — the server resolves -`bytes=-50` against the object's size so the response says which bytes it -carries. - -A range that is well-formed but names nothing readable — one lying wholly -beyond the end of the object, an inverted one such as `bytes=5-2`, or -`bytes=-0` — returns 416 (Range Not Satisfiable). A last-byte-position past -the end of the object is *not* in that category: per RFC 9110 §14.1.2 it is -clamped, so `bytes=0-999999` on a short object returns the whole thing. - -A `Range` header the server cannot use is **ignored** rather than refused, per -RFC 9110 §14.2: an unrecognized unit (`chars=0-7`), a multi-range request -(`bytes=0-7, 10-20`, which this server does not build multipart responses -for), or malformed syntax all return 200 with the full representation. - -### Read-only Serving - -Read-only is the default. `store_app(store)` and `node_app(node)` accept -`GET` and `HEAD` and answer **405** to `PUT`, `POST`, `DELETE` and `PATCH` — -no argument is needed to get there. - -`POST` is not merely unrouted, it is unconfigurable: the accepted methods are -`GET`, `HEAD` and `PUT`, and asking for anything else raises `ValueError` when -the app is built. There is no handler behavior for `POST`, so no configuration -can produce one. - -Two named sets let a call site state which it is, instead of leaving it to the -presence or absence of an argument: - -```python -from zarr_http_server import READ_ONLY_HTTP_METHODS, READ_WRITE_HTTP_METHODS, store_app - -app = store_app(store, methods=READ_ONLY_HTTP_METHODS) # GET, HEAD -app = store_app(store, methods=READ_WRITE_HTTP_METHODS) # GET, HEAD, PUT -``` - -The distinction also exists in the type domain. `ReadOnlyHTTPMethod` is a -`Literal["GET", "HEAD"]`, so a read-only set can be *declared* rather than -merely configured — a `frozenset[ReadOnlyHTTPMethod]` containing `"PUT"` is a -type error, not a runtime surprise: - -```python -from zarr_http_server import ReadOnlyHTTPMethod - -reads: frozenset[ReadOnlyHTTPMethod] = frozenset({"GET", "HEAD"}) # ok -reads = frozenset({"GET", "PUT"}) # type error -``` - -Both constants are derived from these Literals, so the runtime sets and the -static types cannot disagree about what the server serves. - -`READ_ONLY_HTTP_METHODS` is exactly the default, so passing it changes nothing -except that the intent is now written down. The practical value is the other -direction: a writable app *must* name a method set, so -`grep -r 'methods=' ` finds every place that opts into writes. - -For a guarantee that does not depend on getting `methods` right, make the -*store* read-only. The store refuses writes itself, so no routing mistake — -now or in a later edit — can produce one: - -```python -app = store_app(store.with_read_only(True)) - -# For a node, open it read-only and node_app inherits that store: -app = node_app(zarr.open_array(store, mode="r")) -``` - -These two layers are independent, and the store is the stronger one: it holds -even if the HTTP layer is misconfigured. Asking for both at once — -`methods={"GET", "PUT"}` on a read-only store — is a contradiction that can -never succeed, so it raises `ValueError` at construction rather than turning -into a 403 for whichever client tries to write first. - -### Write Support - -By default only reads are accepted: `GET`, and `HEAD` alongside it. Starlette -routes `HEAD` wherever `GET` goes, as RFC 9110 §9.3.2 asks of every origin -server, so naming `GET` gets you both — a `HEAD` is answered from the value's -size without transferring it. To enable writes, pass `methods={"GET", "PUT"}`: - -```python -app = store_app(store, methods={"GET", "PUT"}) -``` - -Accepted methods are `GET`, `HEAD`, and `PUT`; anything else raises -`ValueError` when the app is built, since the handler has no behavior for it. - -A `PUT` request stores the request body at the given path and returns 204 (No -Content). Bodies are capped at `DEFAULT_MAX_BODY_SIZE` (256 MiB) and a larger -one returns 413 (Content Too Large) -- `Store.set` takes a whole buffer, so an -accepted body is held in memory in full. Raise or remove the cap with -`max_body_size`: - -```python -from zarr_http_server import DEFAULT_MAX_BODY_SIZE, store_app +store = zarr.storage.MemoryStore() +array = zarr.create_array(store, shape=(100,), chunks=(10,), dtype="float64") -app = store_app(store, methods={"GET", "PUT"}, max_body_size=None) +with serve_background(node_app(array)) as server: + print(server.url) # e.g. http://127.0.0.1:8000 ``` -Note that `store_app` exposes every key in the store, so `PUT` grants -unrestricted write access to all of it. `node_app` confines writes to keys -belonging to the node -- though a client that can write a node's metadata can -change what that node contains, and so what it will serve. - -`store_app` also does not *validate* keys, because it proxies the store's raw -key space and has no array semantics to check against. A client that misspells -a chunk key — `c/00/00` where zarr writes `c/0/0` — gets a successful write to -a key no reader will ever consult, so the data is stored but invisible to -anyone opening the array. `node_app` rejects such a key with 404, since it -knows which node it is serving and therefore which keys are real. If you are -serving a zarr hierarchy to clients you do not control and writes are enabled, -prefer `node_app`. +Building an app and running it are separate steps, and either app works with +either runner: -### Shutting Down +- **Build** with `store_app` to serve every key in a store, or `node_app` to + serve only the keys belonging to one `Array` or `Group` — requests for keys + outside that node return 404 even when those keys exist in the underlying + store. +- **Run** with `serve`, which blocks, or `serve_background`, which returns a + handle you can shut down later. -`BackgroundServer.shutdown()` (and leaving the `with` block) waits up to -`shutdown_timeout` seconds -- 5 by default -- for in-flight requests to finish -before forcing the server closed: +Reads are all that is enabled by default: `GET` and `HEAD` are served, and +`PUT`, `POST`, `DELETE` and `PATCH` are answered with 405. -```python -with serve_background(node_app(arr), shutdown_timeout=30) as server: - ... -``` +> [!CAUTION] +> `store_app` applies no per-key filtering. Only point it at a store whose full +> contents are safe to serve, and note that enabling `PUT` grants write access +> to everything the store contains. The +> [user guide](https://zarr-http-server.readthedocs.io/en/latest/guide/#read-only-serving) +> covers the read-only guarantees available. -## Example +The [user guide](https://zarr-http-server.readthedocs.io/en/latest/guide/) +covers byte ranges, CORS, writes, serving several nodes, running from a +notebook, and Uvicorn configuration. -`examples/serve.py` creates an in-memory Zarr array, serves it over HTTP with -`serve_background`, and fetches the `zarr.json` metadata document and a raw chunk -using `httpx`. +## Examples -`examples/serve_notebook.ipynb` is the notebook equivalent, showing how to -start a server in one cell and stop it in another. Both are executed by the -test suite. - -Running it with uv is the simplest route — the script declares its own -dependencies inline, so uv installs them for you: +[`examples/`](examples/) holds a runnable script and a notebook, both executed +by the test suite so neither can drift from the code: ```bash uv run examples/serve.py ``` -To run it with a plain interpreter, install its `httpx` dependency first: +## License -```bash -pip install httpx -python examples/serve.py -``` +MIT — see [LICENSE.txt](LICENSE.txt). diff --git a/packages/zarr-http-server/docs/api/index.md b/packages/zarr-http-server/docs/api/index.md index 749e11b964..ce5d748b26 100644 --- a/packages/zarr-http-server/docs/api/index.md +++ b/packages/zarr-http-server/docs/api/index.md @@ -28,4 +28,14 @@ and carry no compatibility guarantee. ::: zarr_http_server.HTTPMethod +::: zarr_http_server.ReadOnlyHTTPMethod + +::: zarr_http_server.READ_ONLY_HTTP_METHODS + +::: zarr_http_server.READ_WRITE_HTTP_METHODS + +::: zarr_http_server.AUTO_PORT + +::: zarr_http_server.DEFAULT_PORT + ::: zarr_http_server.DEFAULT_MAX_BODY_SIZE diff --git a/packages/zarr-http-server/docs/guide.md b/packages/zarr-http-server/docs/guide.md new file mode 100644 index 0000000000..d52d5b882d --- /dev/null +++ b/packages/zarr-http-server/docs/guide.md @@ -0,0 +1,393 @@ +--- +title: User guide +--- + +# User guide + +## Building an ASGI app + +[`store_app`][zarr_http_server.store_app] creates an ASGI app that exposes +every key in a store. Only point it at a store whose full contents are safe to +serve publicly — it grants read (and, if `PUT` is enabled, write) access to +everything the store contains, with no per-key filtering: + +```python +import zarr +from zarr_http_server import store_app + +store = zarr.storage.MemoryStore() +zarr.create_array(store, shape=(100, 100), chunks=(10, 10), dtype="float64") + +app = store_app(store) + +# Run with any ASGI server, e.g. Uvicorn: +# uvicorn my_module:app --host 0.0.0.0 --port 8000 +``` + +[`node_app`][zarr_http_server.node_app] creates an ASGI app that only serves +keys belonging to a specific `Array` or `Group`. Requests for keys outside the +node receive a 404, even if those keys exist in the underlying store: + +```python +import zarr +from zarr_http_server import node_app + +store = zarr.storage.MemoryStore() +root = zarr.open_group(store) +root.create_array("a", shape=(10,), dtype="int32") +root.create_array("b", shape=(20,), dtype="float64") + +# Only serve the array at "a" — requests for "b" will return 404. +app = node_app(root["a"]) +``` + +## Running the server + +Build an app, then run it. Either app works with either runner. + +[`serve`][zarr_http_server.serve] blocks until the server is stopped, which is +the shape for a script or a container entrypoint: + +```python +from zarr_http_server import serve, store_app + +serve(store_app(store), host="127.0.0.1", port=8000) +``` + +[`serve_background`][zarr_http_server.serve_background] instead starts the +server in a daemon thread and returns a +[`BackgroundServer`][zarr_http_server.BackgroundServer] as soon as the socket +is listening, so the caller can carry on. These are two functions rather than +one with a flag, because they differ in the only thing that matters at a call +site: whether control comes back. + +### Choosing a port + +Both default to `port="auto"`, which prefers port 8000 but falls back to any +free port if it is taken, reporting the result through `server.url` and +Uvicorn's startup line. An **explicit** port means the opposite — bind exactly +that or fail — because a caller who names one usually has a proxy or a +container port mapping expecting the server there, and silently moving would +break it while looking healthy. `port=0` keeps its usual meaning of "any free +port, no preference". + +### Reading back with a zarr client + +`BackgroundServer` is a context manager, so the server stops when the block +exits. The example below also *reads back* over HTTP, which is a client-side +concern: `zarr.open_array(server.url)` goes through `FsspecStore`, which needs +an HTTP-capable fsspec that `zarr-http-server` does not pull in +(`pip install "fsspec[http]"`). + +```python +import numpy as np +import zarr +from zarr.storage import MemoryStore + +from zarr_http_server import node_app, serve_background + +store = MemoryStore() +arr = zarr.create_array(store, shape=(100,), chunks=(10,), dtype="float64") +arr[:] = np.arange(100, dtype="float64") + +with serve_background(node_app(arr), host="127.0.0.1") as server: + remote = zarr.open_array(server.url, mode="r") + np.testing.assert_array_equal(remote[:], arr[:]) +# Server is shut down automatically when the block exits. +``` + +### Shutting down + +`BackgroundServer.shutdown()` — and leaving the `with` block — waits up to +`shutdown_timeout` seconds, 5 by default, for in-flight requests to finish +before forcing the server closed. It raises if the thread will not stop, so a +silent failure cannot leave you believing the port is free when it is not. + +```python +with serve_background(node_app(arr), shutdown_timeout=30) as server: + ... +``` + +## Serving several nodes + +Serving two arrays does not mean running two servers. Which approach fits +depends on where the arrays live. + +If they share a parent group, serve the parent — `node_app` recurses through +its members, so both are reachable under one port and node scoping still +applies to everything outside it: + +```python +server = serve_background(node_app(root)) +# -> /a/zarr.json, /a/c/0, /b/zarr.json, ... +``` + +If everything in the store is safe to expose, `store_app(store)` does the same +for the whole key space. + +Otherwise — arrays in *different* stores, or nodes that are not siblings — +`store_app` and `node_app` return plain Starlette apps, so mount them and run +the result: + +```python +from starlette.applications import Starlette +from starlette.routing import Mount + +from zarr_http_server import node_app, serve_background + +app = Starlette(routes=[ + Mount("/first", app=node_app(one)), + Mount("/second", app=node_app(other)), +]) +server = serve_background(app) +``` + +Each mount keeps its own validation, so a request under one cannot reach +another's data — `/first/../second/zarr.json` and its percent-encoded spellings +all return 404. + +Both runners take any ASGI app, so the split is clean: what an app *serves* +(`methods`, `cors_options`, `max_body_size`) is settled when the app is built, +while `serve` / `serve_background` only decide how it runs (`host`, `port`, +`shutdown_timeout`, `uvicorn_options`). + +## Serving from a notebook + +A notebook needs a server that outlives the cell that started it, so the `with` +form above is the wrong shape — it shuts the server down as soon as the block +ends. Start it, keep the handle, and stop it later: + +```python +# cell 1 — start +server = serve_background(node_app(array), host="127.0.0.1") +print(server.url) # e.g. http://127.0.0.1:54635 + +# cell 2..n — use it, across as many cells as you like +httpx.get(f"{server.url}/zarr.json") + +# last cell — stop +server.shutdown() +``` + +Two things make this comfortable in a kernel you re-run. `serve_background` +runs Uvicorn in a daemon thread with its own event loop, so it never touches +the kernel's loop and cannot block it. And its default `port="auto"` falls back +to a free port when 8000 is taken — re-running a start cell without stopping +the previous server is the classic notebook mistake, and a fixed port fails +there with *address already in use*. `server.url` reports the port actually +bound. + +If you forget to stop one, the thread is a daemon, so restarting the kernel +always clears it — and since each start takes a fresh port, a forgotten server +does not block the next one. + +[`examples/serve_notebook.ipynb`](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/examples/serve_notebook.ipynb) +is a runnable version of this. It is executed by the test suite, so it cannot +drift from the code. + +## Uvicorn configuration + +`serve` and `serve_background` name the options most callers need — `host`, +`port`, `shutdown_timeout` — and forward anything else to `uvicorn.Config` +through `uvicorn_options`, so nothing Uvicorn can do is out of reach: + +```python +server = serve_background( + store_app(store), + host="0.0.0.0", + port=8443, + uvicorn_options={ + "ssl_keyfile": "key.pem", + "ssl_certfile": "cert.pem", + "proxy_headers": True, + "forwarded_allow_ips": "10.0.0.0/8", + "log_level": "warning", + }, +) +``` + +Keys you pass are merged over the ones set for you, so they win. `server.url` +reflects the scheme actually in use (`https` when TLS is configured) and is +`None` when the server is not bound to a TCP host and port — a `uds` or `fd` +bind has no URL to report. + +## CORS + +Both app builders accept a [`CorsOptions`][zarr_http_server.CorsOptions] +parameter to enable +[CORS](https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS) middleware for +browser-based clients: + +```python +from zarr_http_server import CorsOptions, store_app + +app = store_app( + store, + cors_options=CorsOptions( + allow_origins=["*"], + allow_methods=["GET"], + ), +) +``` + +`CorsOptions` carries every parameter Starlette's `CORSMiddleware` accepts — +`allow_headers`, `allow_credentials`, `allow_origin_regex`, +`allow_private_network`, `expose_headers` and `max_age` as well as the two +above — so configuring CORS never means reaching around this package. All keys +are optional. + +Two defaults differ from Starlette's, because the server knows things the +caller should not have to. It emits `Content-Range` on every ranged response, +which is *not* a CORS-safelisted response header, so `expose_headers` defaults +to `["Content-Range"]` — otherwise a browser client can read the bytes but not +learn which bytes it got. And it accepts a `Range` request header, so +`allow_headers` defaults to `["Range"]` — otherwise a preflight naming `Range` +is rejected. A key you supply replaces the default outright, so +`expose_headers=[]` means "expose nothing". + +`allow_methods` is checked against what the app actually serves: advertising a +method the route rejects raises `ValueError`, and `"*"` expands to what is +served rather than to every verb Starlette knows. + +## HTTP range requests + +The server supports the standard `Range` header for partial reads. The three +forms defined by [RFC 9110](https://httpwg.org/specs/rfc9110.html#field.range) +are supported: + +| Header | Meaning | +| ------------ | ------------------------ | +| `bytes=0-99` | First 100 bytes | +| `bytes=100-` | Everything from byte 100 | +| `bytes=-50` | Last 50 bytes | + +A successful range request returns HTTP 206 (Partial Content) with a +`Content-Range` header, including for suffix ranges — the server resolves +`bytes=-50` against the object's size so the response says which bytes it +carries. + +A range that is well-formed but names nothing readable — one lying wholly +beyond the end of the object, an inverted one such as `bytes=5-2`, or +`bytes=-0` — returns 416 (Range Not Satisfiable). A last-byte-position past the +end of the object is *not* in that category: per RFC 9110 §14.1.2 it is +clamped, so `bytes=0-999999` on a short object returns the whole thing. + +A `Range` header the server cannot use is **ignored** rather than refused, per +RFC 9110 §14.2: an unrecognized unit (`chars=0-7`), a multi-range request +(`bytes=0-7, 10-20`, which this server does not build multipart responses for), +or malformed syntax all return 200 with the full representation. + +## Read-only serving + +Read-only is the default. `store_app(store)` and `node_app(node)` accept `GET` +and `HEAD` and answer **405** to `PUT`, `POST`, `DELETE` and `PATCH` — no +argument is needed to get there. `HEAD` is served wherever `GET` is, as RFC +9110 §9.3.2 asks of every origin server, and is answered from the value's size +without transferring it. + +`POST` is not merely unrouted, it is unconfigurable: the accepted methods are +`GET`, `HEAD` and `PUT`, and asking for anything else raises `ValueError` when +the app is built. + +Two named sets let a call site state which it is, instead of leaving it to the +presence or absence of an argument: + +```python +from zarr_http_server import READ_ONLY_HTTP_METHODS, READ_WRITE_HTTP_METHODS, store_app + +app = store_app(store, methods=READ_ONLY_HTTP_METHODS) # GET, HEAD +app = store_app(store, methods=READ_WRITE_HTTP_METHODS) # GET, HEAD, PUT +``` + +The distinction also exists in the type domain. +[`ReadOnlyHTTPMethod`][zarr_http_server.ReadOnlyHTTPMethod] is a +`Literal["GET", "HEAD"]`, so a read-only set can be *declared* rather than +merely configured — a `frozenset[ReadOnlyHTTPMethod]` containing `"PUT"` is a +type error, not a runtime surprise: + +```python +from zarr_http_server import ReadOnlyHTTPMethod + +reads: frozenset[ReadOnlyHTTPMethod] = frozenset({"GET", "HEAD"}) # ok +reads = frozenset({"GET", "PUT"}) # type error +``` + +Both constants are derived from those Literals, so the runtime sets and the +static types cannot disagree about what the server serves. + +`READ_ONLY_HTTP_METHODS` is exactly the default, so passing it changes nothing +except that the intent is written down. The practical value is the other +direction: a writable app *must* name a method set, so `grep -r 'methods='` +finds every place that opts into writes. + +For a guarantee that does not depend on getting `methods` right, make the +*store* read-only. The store refuses writes itself, so no routing mistake — now +or in a later edit — can produce one: + +```python +app = store_app(store.with_read_only(True)) + +# For a node, open it read-only and node_app inherits that store: +app = node_app(zarr.open_array(store, mode="r")) +``` + +These two layers are independent, and the store is the stronger one: it holds +even if the HTTP layer is misconfigured. Asking for both at once — +`READ_WRITE_HTTP_METHODS` on a read-only store — is a contradiction that can +never succeed, so it raises `ValueError` at construction rather than turning +into a 403 for whichever client tries to write first. + +## Writes + +To enable writes, name a method set that includes `PUT`: + +```python +from zarr_http_server import READ_WRITE_HTTP_METHODS, store_app + +app = store_app(store, methods=READ_WRITE_HTTP_METHODS) +``` + +A `PUT` stores the request body at the given path and returns 204 (No Content). +Bodies are capped at +[`DEFAULT_MAX_BODY_SIZE`][zarr_http_server.DEFAULT_MAX_BODY_SIZE] (256 MiB) and +a larger one returns 413 (Content Too Large) — `Store.set` takes a whole +buffer, so an accepted body is held in memory in full. Raise or remove the cap +with `max_body_size`: + +```python +app = store_app(store, methods=READ_WRITE_HTTP_METHODS, max_body_size=None) +``` + +!!! danger "Writes through `store_app` are unvalidated" + + `store_app` exposes every key in the store, so `PUT` grants unrestricted + write access to all of it. It also does not *validate* keys, because it + proxies the raw key space and has no array semantics to check against: a + client that misspells a chunk key — `c/00/00` where zarr writes `c/0/0` — + gets a successful write to a key no reader will ever consult, so the data + is stored but invisible to anyone opening the array. + + `node_app` rejects such a key with 404, since it knows which node it is + serving and therefore which keys are real. If you are serving a zarr + hierarchy to clients you do not control and writes are enabled, prefer + `node_app`. + + Note also that a client that can write a node's metadata can change what + that node contains, and so what it will serve. + +## Examples + +Both live in +[`examples/`](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-http-server/examples) +and are executed by the test suite, so neither can drift from the code. + +`serve.py` creates an in-memory Zarr array, serves it, and fetches the +`zarr.json` metadata document and a raw chunk with `httpx`. It declares its own +dependencies inline, so uv installs them for you: + +```bash +uv run examples/serve.py +``` + +`serve_notebook.ipynb` is the notebook equivalent, showing how to start a +server in one cell and stop it in another. diff --git a/packages/zarr-http-server/docs/index.md b/packages/zarr-http-server/docs/index.md index 5671c12d00..271de6445e 100644 --- a/packages/zarr-http-server/docs/index.md +++ b/packages/zarr-http-server/docs/index.md @@ -22,37 +22,50 @@ ASGI app, so any HTTP-capable client — including zarr-python itself, via `FsspecStore` or `ObjectStore` — can read the data. The app is built on [Starlette](https://www.starlette.io/) and can be run with any ASGI server; the `serve` / `serve_background` helpers run it with -[Uvicorn](https://www.uvicorn.org/). +[Uvicorn](https://uvicorn.dev/). -Two levels of exposure are available: +Building an app and running it are separate steps, and either app works with +either runner: -- **Whole store** ([`store_app`][zarr_http_server.store_app], - run with [`serve`][zarr_http_server.serve]) — serves every key in a - store, exposing its entire key/value space. -- **Single node** ([`node_app`][zarr_http_server.node_app], - run with [`serve_background`][zarr_http_server.serve_background]) — serves only the keys - belonging to one `Array` or `Group`. Requests for keys outside that node +- **Build** with [`store_app`][zarr_http_server.store_app] to serve every key + in a store, or [`node_app`][zarr_http_server.node_app] to serve only the keys + belonging to one `Array` or `Group` — requests for keys outside that node return 404 even when those keys exist in the underlying store. +- **Run** with [`serve`][zarr_http_server.serve], which blocks, or + [`serve_background`][zarr_http_server.serve_background], which returns a + handle you can shut down later. Byte-range reads, configurable CORS headers, and a configurable set of allowed HTTP methods are handled by the app. -!!! danger "Serving a whole store grants access to all of it" +## Quick start + +```python +import zarr +from zarr_http_server import node_app, serve_background + +store = zarr.storage.MemoryStore() +array = zarr.create_array(store, shape=(100,), chunks=(10,), dtype="float64") - `store_app` applies no per-key filtering. Only point it - at a store whose full contents are safe to serve, and note that enabling - `PUT` grants write access to everything the store contains. +with serve_background(node_app(array)) as server: + print(server.url) # e.g. http://127.0.0.1:8000 +``` + +Reads are all that is enabled by default: `GET` and `HEAD` are served, and +`PUT`, `POST`, `DELETE` and `PATCH` are answered with 405. -## Getting started +!!! danger "Serving a whole store grants access to all of it" -The [README](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/README.md) -carries worked examples for building an ASGI app, running a blocking or -background server, and configuring CORS and allowed methods. Runnable -versions live in -[`examples/`](https://github.com/zarr-developers/zarr-python/tree/main/packages/zarr-http-server/examples). + `store_app` applies no per-key filtering. Only point it at a store whose + full contents are safe to serve, and note that enabling `PUT` grants write + access to everything the store contains. See + [read-only serving](guide.md#read-only-serving) for the guarantees + available. -## Reference +## Next steps +- [User guide](guide.md) — building apps, running them, byte ranges, CORS, + writes, notebooks, and Uvicorn configuration - [API reference](api/index.md) - [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/CHANGELOG.md) - [License (MIT)](https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/LICENSE.txt) diff --git a/packages/zarr-http-server/mkdocs.yml b/packages/zarr-http-server/mkdocs.yml index 4e7843f36d..7ebfe8c017 100644 --- a/packages/zarr-http-server/mkdocs.yml +++ b/packages/zarr-http-server/mkdocs.yml @@ -13,6 +13,7 @@ use_directory_urls: true nav: - index.md + - guide.md - API Reference: - api/index.md - Changelog: https://github.com/zarr-developers/zarr-python/blob/main/packages/zarr-http-server/CHANGELOG.md diff --git a/packages/zarr-metadata/README.md b/packages/zarr-metadata/README.md index 34c53988db..6b6b172aec 100644 --- a/packages/zarr-metadata/README.md +++ b/packages/zarr-metadata/README.md @@ -2,7 +2,7 @@ Python types, models, and validators for Zarr v2 and v3 metadata. -Documentation: <https://zarr-metadata.readthedocs.io/en/stable/> +Documentation: <https://zarr-metadata.readthedocs.io/> ## What this is From 6ba6e891d103b42d40849de229183fea26745231 Mon Sep 17 00:00:00 2001 From: Johnson K C <Johnsonkc201@gmail.com> Date: Wed, 12 Aug 2026 12:29:12 -0700 Subject: [PATCH 454/468] fix: allow `require_array` to accept a `ZDType` (#4189) * fix: allow `require_array` to accept a `ZDType` AsyncGroup.require_array normalised its dtype with np.dtype(), which cannot consume a ZDType, so requiring an existing array with one raised a TypeError. Every sibling creation method already accepts ZDTypeLike. Widen the annotation and normalise via parse_data_type().to_native_dtype(). parse_data_type(None) resolves to float64 just as np.dtype(None) did, so the default is unchanged. This leaves numpy.typing unused, so drop it. * chore: rename changelog fragment to the PR number * fix: keep the float64 default explicit for mypy parse_data_type does not accept None, so pass "float64" directly, which is what np.dtype(None) resolved to before. * test: parametrize require_array dtype cases over (input, expected) pairs Covers the `dtype=None` path, which resolves to float64 and was previously untested, and asserts on the resulting ZDType rather than the native dtype. --------- Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- changes/4189.bugfix.md | 1 + src/zarr/core/group.py | 15 ++++++++++----- tests/test_group.py | 25 +++++++++++++++++++++++++ 3 files changed, 36 insertions(+), 5 deletions(-) create mode 100644 changes/4189.bugfix.md diff --git a/changes/4189.bugfix.md b/changes/4189.bugfix.md new file mode 100644 index 0000000000..76ef7e7a5e --- /dev/null +++ b/changes/4189.bugfix.md @@ -0,0 +1 @@ +Allow `Group.require_array` to accept a `ZDType` for `dtype`, matching the other array creation methods. Previously an existing array could only be required with a string or NumPy dtype. diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 65f7767a29..548f2141d2 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -10,7 +10,6 @@ from typing import TYPE_CHECKING, Literal, assert_never, cast, overload import numpy as np -import numpy.typing as npt import zarr.api.asynchronous as async_api from zarr.abc.metadata import Metadata @@ -46,6 +45,7 @@ parse_shapelike, ) from zarr.core.config import config +from zarr.core.dtype import parse_data_type from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata from zarr.core.metadata.io import save_metadata from zarr.core.sync import SyncMixin, sync @@ -1225,7 +1225,7 @@ async def require_array( name: str, *, shape: ShapeLike, - dtype: npt.DTypeLike | None = None, + dtype: ZDTypeLike | None = None, exact: bool = False, **kwargs: Any, ) -> AnyAsyncArray: @@ -1239,8 +1239,9 @@ async def require_array( Array name. shape : int or tuple of ints Array shape. - dtype : str or dtype, optional - NumPy dtype. + dtype : ZDTypeLike, optional + The data type of the array, given as a string, a NumPy dtype, or a + Zarr data type. exact : bool, optional If True, require `dtype` to match exactly. If false, require `dtype` can be cast from array dtype. @@ -1258,7 +1259,11 @@ async def require_array( if shape != ds.shape: raise TypeError(f"Incompatible shape ({ds.shape} vs {shape})") - dtype = np.dtype(dtype) + # `np.dtype(None)` used to resolve to float64 here; keep that default. + dtype = parse_data_type( + "float64" if dtype is None else dtype, + zarr_format=self.metadata.zarr_format, + ).to_native_dtype() if exact: if ds.dtype != dtype: raise TypeError(f"Incompatible dtype ({ds.dtype} vs {dtype})") diff --git a/tests/test_group.py b/tests/test_group.py index 29377a5392..f7f2333ef5 100644 --- a/tests/test_group.py +++ b/tests/test_group.py @@ -24,6 +24,7 @@ from zarr.core._info import GroupInfo from zarr.core.buffer import default_buffer_prototype from zarr.core.config import config as zarr_config +from zarr.core.dtype import Float64, Int32 from zarr.core.dtype.common import unpack_dtype_json from zarr.core.dtype.npy.int import UInt8 from zarr.core.group import ( @@ -61,6 +62,7 @@ from zarr.core.buffer.core import Buffer from zarr.core.common import JSON, ZarrFormat + from zarr.core.dtype import ZDType, ZDTypeLike @pytest.fixture(params=["local", "memory", "zip"]) @@ -1439,6 +1441,29 @@ async def test_require_array(store: Store, zarr_format: ZarrFormat) -> None: await root.require_array("bar", shape=(10,), dtype="int8") +@pytest.mark.parametrize( + ("dtype", "expected"), + [ + (Int32(), Int32()), + (np.dtype("int32"), Int32()), + ("int32", Int32()), + (None, Float64()), + ], + ids=["zdtype", "numpy", "str", "none"], +) +async def test_require_array_zdtype( + store: Store, zarr_format: ZarrFormat, dtype: ZDTypeLike | None, expected: ZDType[Any, Any] +) -> None: + """An existing array can be required with a ZDType, as well as a string, a NumPy dtype, + or None. See https://github.com/zarr-developers/zarr-python/issues/3377 + """ + root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format) + await root.create_array("foo", shape=(10,), dtype=expected) + + foo = await root.require_array("foo", shape=(10,), dtype=dtype, exact=True) + assert foo._zdtype == expected + + @pytest.mark.parametrize("consolidate", [True, False]) async def test_members_name(store: Store, consolidate: bool, zarr_format: ZarrFormat): group = Group.from_store(store=store, zarr_format=zarr_format) From d3dc9f527e5b4b75ca492948c820a57be50aa199 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Wed, 12 Aug 2026 21:56:29 +0200 Subject: [PATCH 455/468] fix: accept numpy integers as chunk sizes (#4257) * fix: accept numpy integers as chunk sizes `normalize_chunks_nd` dispatches the scalar convenience form on `numbers.Integral`, but `normalize_chunks_1d` narrowed on `int`. Numpy integer scalars satisfy the former and not the latter, so a per-dimension numpy integer passed the outer dispatch and then fell into the branch meant for explicit per-dimension chunk sequences, where `list(chunks)` raised `TypeError: 'numpy.int64' object is not iterable`. Numpy integers arise naturally whenever a chunk shape is computed rather than written as a literal, since numpy reductions and elementwise ops yield numpy scalars. Narrow on `numbers.Integral` and coerce with `int()`, matching the caller and the sequence branch, which already accepted `Integral` elements. Move the `-1` sentinel check inside that branch. It previously ran on the raw input, so a numpy array chunk specification made `chunks == -1` return an array and raise an ambiguous-truth-value error; rectilinear specs given as numpy arrays now work. A chunk specification that is neither an integer nor iterable now names the offending value and its type instead of surfacing an opaque "object is not iterable" from `list(chunks)`. Fixes #4255 Assisted-by: ClaudeCode:claude-opus-5 * Rename 4255.bugfix.md to 4257.bugfix.md --- changes/4257.bugfix.md | 1 + src/zarr/core/chunk_grids.py | 27 ++++++++++++++++++--------- tests/test_api.py | 2 +- tests/test_chunk_grids.py | 24 ++++++++++++++++++++++++ 4 files changed, 44 insertions(+), 10 deletions(-) create mode 100644 changes/4257.bugfix.md diff --git a/changes/4257.bugfix.md b/changes/4257.bugfix.md new file mode 100644 index 0000000000..6f2740ccb4 --- /dev/null +++ b/changes/4257.bugfix.md @@ -0,0 +1 @@ +Numpy integers are accepted as chunk sizes again. Since 3.3.0 a per-dimension chunk size that was a numpy integer (e.g. `chunks=(np.int64(2), np.int64(2))`, as produced by any computed chunk shape) raised `TypeError: 'numpy.int64' object is not iterable`, because the scalar chunk path narrowed on `int` while its caller dispatched on `numbers.Integral`. Numpy arrays are now also accepted as chunk specifications, and a chunk specification that is neither an integer nor iterable now reports the offending value instead of failing with an opaque iteration error. diff --git a/src/zarr/core/chunk_grids.py b/src/zarr/core/chunk_grids.py index 2cb9762775..584829bc6c 100644 --- a/src/zarr/core/chunk_grids.py +++ b/src/zarr/core/chunk_grids.py @@ -729,17 +729,26 @@ def normalize_chunks_1d( overhang the span. The actual data extent of each chunk is determined by the chunk grid at runtime, not by this function. """ - if chunks == -1: - return np.array([span], dtype=np.int64) - if isinstance(chunks, int): - if chunks <= 0: - raise ValueError(f"Chunk size must be positive, got {chunks}") + # `numbers.Integral` rather than `int` so that numpy integer scalars (which are not + # `int` subclasses) take the uniform-chunk path instead of being treated as a sequence. + if isinstance(chunks, numbers.Integral): + chunk_size = int(chunks) + if chunk_size == -1: + return np.array([span], dtype=np.int64) + if chunk_size <= 0: + raise ValueError(f"Chunk size must be positive, got {chunk_size}") if span == 0: - return np.array([chunks], dtype=np.int64) - n = ceildiv(span, chunks) - return np.full(n, chunks, dtype=np.int64) + return np.array([chunk_size], dtype=np.int64) + n = ceildiv(span, chunk_size) + return np.full(n, chunk_size, dtype=np.int64) else: - chunk_list = list(chunks) + try: + chunk_list = list(chunks) # type: ignore[arg-type] + except TypeError: + raise TypeError( + f"Chunk specification must be an integer or an iterable of integers; got " + f"{chunks!r} of type {type(chunks).__name__}." + ) from None if not chunk_list: raise ValueError("Chunk specification must not be empty") non_int = [ diff --git a/tests/test_api.py b/tests/test_api.py index 2b831e942d..45d0c0dee4 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -79,7 +79,7 @@ def test_create(memory_store: Store) -> None: z = create(shape=(400.5, 100), store=store, overwrite=True) # type: ignore[arg-type] # create array with float chunk shape - with pytest.raises(TypeError, match="'float' object is not iterable"): + with pytest.raises(TypeError, match="Chunk specification must be an integer or an iterable"): z = create(shape=(400, 100), chunks=(16, 16.5), store=store, overwrite=True) # type: ignore[arg-type] diff --git a/tests/test_chunk_grids.py b/tests/test_chunk_grids.py index b730a43901..4640c43d1c 100644 --- a/tests/test_chunk_grids.py +++ b/tests/test_chunk_grids.py @@ -68,6 +68,15 @@ def test_guess_chunks(shape: tuple[int, ...], itemsize: int) -> None: (10, (0,), ((10,),)), ((5, 10), (0, 100), ((5,), (10,) * 10)), ((5, 10), (20, 0), ((5, 5, 5, 5), (10,))), + # numpy integers are accepted anywhere a python int is, whether as the scalar + # convenience form, as per-dimension entries, or as the `-1` sentinel. + (np.int64(10), (100,), ((10,) * 10,)), + ((np.int64(2), np.int64(2)), (4, 4), ((2, 2), (2, 2))), + ((1, 3, np.int64(16), np.int64(16)), (1, 3, 32, 32), ((1,), (3,), (16, 16), (16, 16))), + ((np.int32(30), np.int64(-1)), (100, 20), ((30, 30, 30, 30), (20,))), + (np.array([10, 10]), (100, 100), ((10,) * 10, (10,) * 10)), + # rectilinear chunks given as numpy arrays + ((np.array([60, 40]), np.array([50, 50])), (100, 100), ((60, 40), (50, 50))), ], ) def test_normalize_chunks( @@ -142,7 +151,22 @@ def test_chunk_layout_nested() -> None: id="negative-uniform", msg="Chunk size must be positive", ), + ExpectFail( + input=(np.int64(0), 100), + exception=ValueError, + id="zero-uniform-numpy", + msg="Chunk size must be positive", + ), ExpectFail(input=([], 100), exception=ValueError, id="empty-list", msg="must not be empty"), + # Scalars that are neither integers nor iterable name themselves in the error, + # rather than surfacing an opaque "object is not iterable" from `list(chunks)`. + ExpectFail( + input=(2.5, 100), + exception=TypeError, + id="non-iterable-scalar", + msg="must be an integer or an iterable of integers; got 2.5 of type float", + escape=True, + ), ExpectFail( input=([10, -1, 10], 100), exception=ValueError, From ecb58147c4246965f15d87b8dae3cb8f6292cf7e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 13 Aug 2026 07:41:18 +0200 Subject: [PATCH 456/468] chore(deps): bump the actions group with 4 updates (#4258) Bumps the actions group with 4 updates: [CodSpeedHQ/action](https://github.com/codspeedhq/action), [scientific-python/issue-from-pytest-log-action](https://github.com/scientific-python/issue-from-pytest-log-action), [actions/attest](https://github.com/actions/attest) and [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action). Updates `CodSpeedHQ/action` from 5.0.1 to 5.0.2 - [Release notes](https://github.com/codspeedhq/action/releases) - [Changelog](https://github.com/CodSpeedHQ/action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codspeedhq/action/compare/88472375d0a4572cf70a9f1fe3a4e0ab8da1b924...0ca9cbbf4623b599a6c3ed4fc8a922942705d9f1) Updates `scientific-python/issue-from-pytest-log-action` from 1.6.1 to 1.6.2 - [Release notes](https://github.com/scientific-python/issue-from-pytest-log-action/releases) - [Commits](https://github.com/scientific-python/issue-from-pytest-log-action/compare/054799b34bd75a5fd6c86277a4a8a575224e60c6...35b4e0a9e06f8e7e261778289cf4b968b722662d) Updates `actions/attest` from 4.2.1 to 4.2.2 - [Release notes](https://github.com/actions/attest/releases) - [Changelog](https://github.com/actions/attest/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest/compare/508db95dd578ae2727ebd6217d5ba78e4fbda05d...1e69f48acb82d1966a394da916b4c1698aa569d6) Updates `zizmorcore/zizmor-action` from 0.6.1 to 0.6.2 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/6fc4b006235f201fdab3722e17240ab420d580e5...3dc1ecc9bcb9e94e9b2c709687979e1298497054) --- updated-dependencies: - dependency-name: CodSpeedHQ/action dependency-version: 5.0.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: scientific-python/issue-from-pytest-log-action dependency-version: 1.6.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/attest dependency-version: 4.2.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.6.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/codspeed.yml | 2 +- .github/workflows/hypothesis.yaml | 2 +- .github/workflows/releases.yml | 2 +- .github/workflows/zarr-http-server-release.yml | 4 ++-- .github/workflows/zarr-indexing-release.yml | 4 ++-- .github/workflows/zarr-metadata-release.yml | 4 ++-- .github/workflows/zizmor.yml | 2 +- 7 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml index 17e9de89ba..f36fbff233 100644 --- a/.github/workflows/codspeed.yml +++ b/.github/workflows/codspeed.yml @@ -32,7 +32,7 @@ jobs: with: version: '1.16.5' - name: Run the benchmarks - uses: CodSpeedHQ/action@88472375d0a4572cf70a9f1fe3a4e0ab8da1b924 # v5.0.1 + uses: CodSpeedHQ/action@0ca9cbbf4623b599a6c3ed4fc8a922942705d9f1 # v5.0.2 env: ZARR_BENCHMARK_CLEAR_CACHE: '1' with: diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index cfe4477e52..dd49578dd0 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -109,7 +109,7 @@ jobs: && steps.status.outcome == 'failure' && github.event_name == 'schedule' && github.repository_owner == 'zarr-developers' - uses: scientific-python/issue-from-pytest-log-action@054799b34bd75a5fd6c86277a4a8a575224e60c6 # v1.6.1 + uses: scientific-python/issue-from-pytest-log-action@35b4e0a9e06f8e7e261778289cf4b968b722662d # v1.6.2 with: log-path: output-${{ matrix.python-version }}-log.jsonl issue-title: "Nightly Hypothesis tests failed" diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml index 759c443dd5..a08d5a6d3f 100644 --- a/.github/workflows/releases.yml +++ b/.github/workflows/releases.yml @@ -81,7 +81,7 @@ jobs: name: releases path: dist - name: Generate artifact attestation - uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + uses: actions/attest@1e69f48acb82d1966a394da916b4c1698aa569d6 # v4.2.2 with: subject-path: dist/* - name: Publish package to PyPI diff --git a/.github/workflows/zarr-http-server-release.yml b/.github/workflows/zarr-http-server-release.yml index b8940f7560..b78fa29ab7 100644 --- a/.github/workflows/zarr-http-server-release.yml +++ b/.github/workflows/zarr-http-server-release.yml @@ -82,7 +82,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + uses: actions/attest@1e69f48acb82d1966a394da916b4c1698aa569d6 # v4.2.2 with: subject-path: dist/* @@ -107,7 +107,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + uses: actions/attest@1e69f48acb82d1966a394da916b4c1698aa569d6 # v4.2.2 with: subject-path: dist/* diff --git a/.github/workflows/zarr-indexing-release.yml b/.github/workflows/zarr-indexing-release.yml index de57594d2b..2c35abad9f 100644 --- a/.github/workflows/zarr-indexing-release.yml +++ b/.github/workflows/zarr-indexing-release.yml @@ -82,7 +82,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + uses: actions/attest@1e69f48acb82d1966a394da916b4c1698aa569d6 # v4.2.2 with: subject-path: dist/* @@ -107,7 +107,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + uses: actions/attest@1e69f48acb82d1966a394da916b4c1698aa569d6 # v4.2.2 with: subject-path: dist/* diff --git a/.github/workflows/zarr-metadata-release.yml b/.github/workflows/zarr-metadata-release.yml index f9516ead71..17c285ded6 100644 --- a/.github/workflows/zarr-metadata-release.yml +++ b/.github/workflows/zarr-metadata-release.yml @@ -82,7 +82,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + uses: actions/attest@1e69f48acb82d1966a394da916b4c1698aa569d6 # v4.2.2 with: subject-path: dist/* @@ -107,7 +107,7 @@ jobs: path: dist - name: Generate artifact attestation - uses: actions/attest@508db95dd578ae2727ebd6217d5ba78e4fbda05d # v4.2.1 + uses: actions/attest@1e69f48acb82d1966a394da916b4c1698aa569d6 # v4.2.2 with: subject-path: dist/* diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml index 9022c56455..c90ba718f6 100644 --- a/.github/workflows/zizmor.yml +++ b/.github/workflows/zizmor.yml @@ -32,4 +32,4 @@ jobs: persist-credentials: false - name: Run zizmor - uses: zizmorcore/zizmor-action@6fc4b006235f201fdab3722e17240ab420d580e5 # v0.6.1 + uses: zizmorcore/zizmor-action@3dc1ecc9bcb9e94e9b2c709687979e1298497054 # v0.6.2 From 52a63801ad04cf81876abfc324c2febddaad60f1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 13 Aug 2026 10:16:31 +0200 Subject: [PATCH 457/468] chore(deps): bump the python-dependencies group with 6 updates (#4259) Bumps the python-dependencies group with 6 updates: | Package | From | To | | --- | --- | --- | | [packaging](https://github.com/pypa/packaging) | `26.2` | `26.3` | | [typer](https://github.com/fastapi/typer) | `0.27.0` | `0.27.1` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.15.2` | `7.15.3` | | [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.164.0` | `6.165.2` | | [uv](https://github.com/astral-sh/uv) | `0.12.0` | `0.12.2` | | [ruff](https://github.com/astral-sh/ruff) | `0.16.0` | `0.16.1` | Updates `packaging` from 26.2 to 26.3 - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/26.2...26.3) Updates `typer` from 0.27.0 to 0.27.1 - [Release notes](https://github.com/fastapi/typer/releases) - [Changelog](https://github.com/fastapi/typer/blob/master/docs/release-notes.md) - [Commits](https://github.com/fastapi/typer/compare/0.27.0...0.27.1) Updates `coverage` from 7.15.2 to 7.15.3 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](https://github.com/coveragepy/coveragepy/compare/7.15.2...7.15.3) Updates `hypothesis` from 6.164.0 to 6.165.2 - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/v6.164.0...v6.165.2) Updates `uv` from 0.12.0 to 0.12.2 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.12.0...0.12.2) Updates `ruff` from 0.16.0 to 0.16.1 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.16.0...0.16.1) --- updated-dependencies: - dependency-name: packaging dependency-version: '26.3' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: typer dependency-version: 0.27.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: coverage dependency-version: 7.15.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: hypothesis dependency-version: 6.165.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: uv dependency-version: 0.12.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.16.1 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- pyproject.toml | 8 +- uv.lock | 340 ++++++++++++++++++++++++------------------------- 2 files changed, 174 insertions(+), 174 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6626f8f0bc..e0fbfc08fc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -94,18 +94,18 @@ homepage = "https://github.com/zarr-developers/zarr-python" # pins deliberately, e.g. via dependabot or `uv lock --upgrade`. [dependency-groups] test = [ - "coverage==7.15.2", + "coverage==7.15.3", "pytest==9.1.1", "pytest-asyncio==1.4.0", "pytest-cov==7.1.0", "pytest-accept==0.3.0", "numpydoc==1.10.0", - "hypothesis==6.164.0", + "hypothesis==6.165.2", "pytest-xdist==3.8.0", "pytest-benchmark==5.2.3", "pytest-codspeed==5.0.3", "tomlkit==0.15.1", - "uv==0.12.0", + "uv==0.12.2", ] remote-tests = [ {include-group = "test"}, @@ -129,7 +129,7 @@ docs = [ "mkdocs-redirects==1.2.3", "markdown-exec[ansi]==1.12.3", "griffe-inherited-docstrings==1.1.3", - "ruff==0.16.0", + "ruff==0.16.1", # Changelog generation {include-group = "release"}, # Optional dependencies to run examples diff --git a/uv.lock b/uv.lock index 5e3e33aefe..120b187e7d 100644 --- a/uv.lock +++ b/uv.lock @@ -621,71 +621,71 @@ wheels = [ [[package]] name = "coverage" -version = "7.15.2" -source = { registry = "https://pypi.org/simple" } -sdist = { url = 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"astroid", specifier = "==4.1.2" }, { name = "botocore" }, - { name = "coverage", specifier = "==7.15.2" }, + { name = "coverage", specifier = "==7.15.3" }, { name = "fsspec", specifier = ">=2023.10.0" }, { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, - { name = "hypothesis", specifier = "==6.164.0" }, + { name = "hypothesis", specifier = "==6.165.2" }, { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.3" }, { name = "mike", specifier = "==2.2.0" }, { name = "mkdocs", specifier = "==1.6.1" }, @@ -3590,12 +3590,12 @@ dev = [ { name = "pytest-cov", specifier = "==7.1.0" }, { name = "pytest-xdist", specifier = "==3.8.0" }, { name = "requests", specifier = "==2.34.2" }, - { name = "ruff", specifier = "==0.16.0" }, + { name = "ruff", specifier = "==0.16.1" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "tomlkit", specifier = "==0.15.1" }, { name = "towncrier", specifier = "==25.8.0" }, { name = "universal-pathlib" }, - { name = "uv", specifier = "==0.12.0" }, + { name = "uv", specifier = "==0.12.2" }, ] docs = [ { name = "astroid", specifier = "==4.1.2" }, @@ -3609,16 +3609,16 @@ docs = [ { name = "mkdocstrings-python", specifier = "==2.0.5" }, { name = "numcodecs", extras = ["msgpack"] }, { name = "pytest", specifier = "==9.1.1" }, - { name = "ruff", specifier = "==0.16.0" }, + { name = "ruff", specifier = "==0.16.1" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "towncrier", specifier = "==25.8.0" }, ] release = [{ name = "towncrier", specifier = "==25.8.0" }] remote-tests = [ { name = "botocore" }, - { name = "coverage", specifier = "==7.15.2" }, + { name = "coverage", specifier = "==7.15.3" }, { name = "fsspec", specifier = ">=2023.10.0" }, - { name = "hypothesis", specifier = "==6.164.0" }, + { name = "hypothesis", specifier = "==6.165.2" }, { name = "moto", extras = ["s3", "server"], specifier = "==5.2.2" }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "obstore", specifier = ">=0.5.1" }, @@ -3632,11 +3632,11 @@ remote-tests = [ { name = "requests", specifier = "==2.34.2" }, { name = "s3fs", specifier = ">=2023.10.0" }, { name = "tomlkit", specifier = "==0.15.1" }, - { name = "uv", specifier = "==0.12.0" }, + { name = "uv", specifier = "==0.12.2" }, ] test = [ - { name = "coverage", specifier = "==7.15.2" }, - { name = "hypothesis", specifier = "==6.164.0" }, + { name = "coverage", specifier = "==7.15.3" }, + { name = "hypothesis", specifier = "==6.165.2" }, { name = "numpydoc", specifier = "==1.10.0" }, { name = "pytest", specifier = "==9.1.1" }, { name = "pytest-accept", specifier = "==0.3.0" }, @@ -3646,5 +3646,5 @@ test = [ { name = "pytest-cov", specifier = "==7.1.0" }, { name = "pytest-xdist", specifier = "==3.8.0" }, { name = "tomlkit", specifier = "==0.15.1" }, - { name = "uv", specifier = "==0.12.0" }, + { name = "uv", specifier = "==0.12.2" }, ] From 4aba6911221096b297649a5239173012d5c124bf Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 13 Aug 2026 13:20:41 +0200 Subject: [PATCH 458/468] fix(build): add an sdist allowlist to zarr-http-server (#4262) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit packages/zarr-http-server had no [tool.hatch.build.targets.sdist] section at all, so hatchling defaulted to 'everything not gitignored' — a blocklist by another name, and the same shape of problem the root pyproject.toml had. Add an explicit allowlist matching the ones packages/zarr-indexing and packages/zarr-metadata already carry. This drops changes/ (towncrier fragments are consumed into CHANGELOG.md at release time), .readthedocs.yaml (only means anything in the repository) and uv.lock, and keeps /examples, which the suite genuinely needs: tests/test_examples.py runs examples/serve.py and executes every cell of examples/serve_notebook.ipynb. Verified from an unpacked sdist: 210 passed, tests/test_examples.py green. Assisted-by: ClaudeCode:claude-opus-5 --- packages/zarr-http-server/pyproject.toml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/packages/zarr-http-server/pyproject.toml b/packages/zarr-http-server/pyproject.toml index ef38d67e49..10db7ae496 100644 --- a/packages/zarr-http-server/pyproject.toml +++ b/packages/zarr-http-server/pyproject.toml @@ -90,6 +90,28 @@ raw-options = { root = "../..", git_describe_command = "git describe --dirty --t [tool.hatch.build.targets.wheel] packages = ["src/zarr_http_server"] +# An allowlist, so nothing that merely happens to sit in the package directory +# — a scratch script, a stray notebook — can ride along in a release. With no +# sdist section at all hatchling defaults to "everything not gitignored", which +# is a blocklist by another name. The list keeps an sdist self-testing: +# `tests/test_examples.py` runs `examples/serve.py` and executes every cell of +# `examples/serve_notebook.ipynb`, so those are part of the suite rather than +# decoration, and `/docs` plus `/mkdocs.yml` are a self-contained site. +# `changes/` and `.readthedocs.yaml` are deliberately absent: towncrier +# fragments are consumed into `CHANGELOG.md` at release time, and the RTD +# config only means anything in the repository. `pyproject.toml`, `README.md` +# and `LICENSE.txt` are added by hatchling itself. +[tool.hatch.build.targets.sdist] +include = [ + "/src", + "/tests", + "/docs", + "/examples", + "/mkdocs.yml", + "/justfile", + "/CHANGELOG.md", +] + [tool.ruff] extend = "../../pyproject.toml" target-version = "py312" From 9fd669fd22a414ed19e79bc6a17a42b6b44ea8b8 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 13 Aug 2026 16:31:35 +0200 Subject: [PATCH 459/468] fix(build): use an sdist allowlist so the zarr sdist stops shipping subpackages (#4261) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix(build): use an sdist allowlist so the zarr sdist stops shipping subpackages The root sdist config was a blocklist naming /.github, /bench and /docs, so every release shipped whatever else happened to sit in the repository root. That included the whole packages/ tree — the zarr-indexing, zarr-metadata and zarr-http-server sources, which are released as their own distributions — plus ci/, design/, towncrier fragments and other repo furniture. 2.9M of the 1.4M sdist was other people's packages. Replace it with an explicit allowlist, matching what packages/zarr-indexing and packages/zarr-metadata already do. Including /docs also fixes a second problem: tests/test_docs.py walks docs/ and testpaths collects docs/user-guide, so with docs/ excluded the shipped test suite died at collection with 'Not a file or directory'. tests/test_docs.py now runs green from an unpacked sdist (61 passed, 2 skipped), and full collection finds 7581 tests with no errors. Assisted-by: ClaudeCode:claude-opus-5 * docs(build): trim the sdist allowlist comment Drop the narration of the blocklist this replaced -- that history lives in git -- and keep only the durable rationale and the reason each entry is on the list. Assisted-by: ClaudeCode:claude-opus-5 --- changes/4261.misc.md | 1 + pyproject.toml | 18 +++++++++++++++--- 2 files changed, 16 insertions(+), 3 deletions(-) create mode 100644 changes/4261.misc.md diff --git a/changes/4261.misc.md b/changes/4261.misc.md new file mode 100644 index 0000000000..ca2a3fbb1e --- /dev/null +++ b/changes/4261.misc.md @@ -0,0 +1 @@ +The contents of the `zarr` source distribution are now defined by an explicit allowlist rather than a blocklist. Previously the sdist bundled the whole `packages/` tree — `zarr-indexing`, `zarr-metadata` and `zarr-http-server`, which are released as their own distributions — along with CI configuration and other repository files. The sdist also now ships `docs/`, so the test suite it carries can be collected and run from an unpacked sdist. diff --git a/pyproject.toml b/pyproject.toml index e0fbfc08fc..5e8129a6a9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,11 +2,23 @@ requires = ["hatchling>=1.29.0", "hatch-vcs"] build-backend = "hatchling.build" +# An allowlist, not a blocklist: anything new — a subpackage under `packages/`, a +# config file in the repository root — stays out of the sdist unless it is named +# here. Beyond `src` and `tests`, the entries are what keeps the shipped test +# suite and docs build runnable from an unpacked sdist: `tests/test_docs.py` +# walks `docs/` and `testpaths` collects `docs/user-guide`; the pages under +# `docs/user-guide/examples/` pull their source out of `examples/` via pymdownx +# snippet includes; `mkdocs.yml` and `mkdocs_hooks.py` let `mkdocs build` run +# too. `pyproject.toml`, `README.md`, `LICENSE.txt` and `.gitignore` are added by +# hatchling itself. [tool.hatch.build.targets.sdist] -exclude = [ - "/.github", - "/bench", +include = [ + "/src", + "/tests", "/docs", + "/examples", + "/mkdocs.yml", + "/mkdocs_hooks.py", ] [project] From e62e45bfac1f9b6e0892ce4df45d75315a302be3 Mon Sep 17 00:00:00 2001 From: Yong-Shin Jiang <86658970+vup903@users.noreply.github.com> Date: Thu, 13 Aug 2026 08:06:52 -0700 Subject: [PATCH 460/468] Add unified JSON metadata validation via msgspec (#3285) (#4063) * Add unified parse_json runtime type checker (#3285) Introduce zarr.core.json_parse.parse_json, a single type-annotation-driven validator that consolidates the scattered per-field parse_* helpers. Handles primitives, Literal, unions/Optional, fixed and variadic tuples, Sequence/list (coerced to tuple), Mapping/dict, and TypedDict, with a bool-vs-int safe primitive check. Adds tests/test_json_parse.py (94 tests) and a changelog fragment. No existing call sites migrated yet; this is the proof-of-direction module. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Migrate parse_order, parse_bool, parse_zarr_format to parse_json (#3285) Pilot migration delegating three representative helpers to the unified parse_json validator. Public signatures and return types are unchanged. parse_zarr_format re-wraps parse_json's ValueError/TypeError as MetadataValidationError with the original message to preserve observable behavior. parse_json is imported function-locally to avoid circular imports. Focused suites green: test_common/test_config/test_metadata/test_json_parse = 430 passed. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Fix lint and make TypedDict NotRequired robust under future annotations (#3285) Apply ruff check/format to satisfy the Lint CI hook. Keep typing.Union/Optional spellings in tests (with noqa) to cover that origin path alongside X | Y. Rework _parse_typeddict to derive required/optional from get_type_hints(include_extras=True) + __total__ instead of __required_keys__, so class-syntax NotRequired is detected even when 'from __future__ import annotations' stringizes the hints (as in zarr's metadata modules). test_json_parse + test_common + test_metadata = 393 passed. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Annotate origin as Any to satisfy mypy in _parse_typeddict (#3285) get_origin(hint) is Required/NotRequired tripped mypy's comparison-overlap and unreachable checks; typing origin as Any keeps the runtime check while satisfying mypy. Full 'uv run --frozen mypy' is clean (190 files); ruff check/format clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Migrate Batch 1 literal parsers to parse_json (#3285) Delegate the literal/type check of parse_indexing_order, parse_node_type, parse_node_type_array, parse_separator, two parse_zarr_format variants (group, v2), and parse_name to the unified parse_json. Public signatures and return types unchanged; each preserves its original exception type and message (wrapping parse_json's ValueError/TypeError into MetadataValidationError / NodeTypeValidationError / the original ValueError/TypeError where tests assert on them). parse_json imported function-locally to avoid circular imports. Focused suites + full mypy green (1196 passed). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Migrate Batch 2 codec primitive parsers to parse_json (#3285) Delegate the int/bool type check of parse_checksum, parse_clevel, parse_blocksize, parse_typesize, parse_gzip_level, and parse_zstd_level to parse_json, keeping each helper's range/bound check and exact error messages. Original exception types are preserved by wrapping parse_json's ValueError/TypeError. Note: parse_json rejects bool where the old isinstance(data, int) accepted it; verified no caller/test passes a bool to these, so this is a deliberate, more-correct strictening. parse_json imported function-locally. Codec suite + full mypy green (794 passed). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Replace hand-written parse_json with msgspec.convert (#3285) Delete the bespoke parse_json runtime type checker and route JSON metadata validation through msgspec.convert, which handles the type coercions zarr needs (Literal membership, int/bool strictness, list-to-tuple). A small hand-written fallback (validate_json_value) covers the recursive JSON values msgspec cannot build a schema for, and adds an explicit nesting-depth limit. The registry/dtype/numcodec parsers stay hand-written since they need runtime lookups. Also fixes a latent generator-exhaustion bug in parse_storage_transformers, adds msgspec as a dependency (pinned in the min_deps env), and preserves the exception types and messages every migrated helper raised. Net ~555 lines removed. Tests, mypy and ruff all green. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Encapsulate convert + field-context error into parse_field (#3285) Address review feedback: factor the repeated convert-then-re-raise pattern out of each per-field parser. convert now raises a field-agnostic ValueError("Expected instance of TYPE, got DATA"); the new parse_field wraps it and re-raises with field context ("Failed to parse input for FIELD") using the caller's chosen exception type, chaining the original error. Every per-field parser collapses to a one-liner. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: replace Sphinx roles in json_parse with plain literals (#3285) The new ci/lint_docs.py check flags :func:/:class: roles, which pass through as literal text under MkDocs/mkdocstrings instead of becoming links. msgspec is not in the configured inventories, so cross-references would not resolve; using inline literals matches how the codebase already writes np.nonzero. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * fix: keep literal members and the offending value in parse errors (#3285) The msgspec rewrite regressed error quality for Literal types: _type_name fell back to __name__, rendering Literal[3] as bare "Literal", and parse_field dropped the value entirely. The old per-field parsers reported both, e.g. "Invalid value for 'zarr_format'. Expected '3'. Got '3.0'." _type_name now renders parameterized types via str(), so members survive, and parse_field reports expected type and received value: Failed to parse input for 'zarr_format': expected Literal[3], got 3.0. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * refactor: hoist json_parse imports to module level (#3285) These were function-local to dodge import cycles under the old hand-written parse_json. After the msgspec rewrite json_parse's only zarr import is JSON under TYPE_CHECKING, so it has no runtime zarr dependency and cannot form a cycle. Verified each touched module still imports standalone. Hoisting exposed a latent packaging gap: msgspec was added to pyproject.toml but never locked, so uv.lock lacked it. That stayed hidden only because json_parse was imported lazily; at module level it broke `uv run --frozen` (ModuleNotFoundError in the docs job). Regenerated the lock, which adds msgspec 0.21.1 and nothing else. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * docs: note the stricter metadata parsing in the changelog (#3285) The old per-field checks compared with ==, so numerically equal values passed: zarr_format=2.0 was accepted. msgspec requires an actual int, so such inputs are now rejected. Spec-conforming metadata is unaffected. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> * docs: link msgspec symbols via its inventory (#3285) Adds msgspec's Sphinx inventory so the json_parse docstrings can reference msgspec.convert and msgspec.ValidationError as real cross-references instead of inert literals. Verified the inventory is served at msgspec.dev (the jcristharif.com path in the package metadata is stale) and that both symbols resolve in it. Same-module names stay plain literals: zarr.core.json_parse is internal and not rendered in the API reference, so a cross-reference to it would not resolve and would fail `mkdocs build --strict`. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com> --- changes/3285.feature.md | 13 +++ mkdocs.yml | 1 + pyproject.toml | 2 + src/zarr/codecs/blosc.py | 26 +++--- src/zarr/codecs/gzip.py | 10 +-- src/zarr/codecs/zstd.py | 15 ++-- src/zarr/core/chunk_key_encodings.py | 5 +- src/zarr/core/common.py | 22 +++-- src/zarr/core/config.py | 7 +- src/zarr/core/group.py | 14 ++- src/zarr/core/json_parse.py | 103 ++++++++++++++++++++++ src/zarr/core/metadata/v2.py | 7 +- src/zarr/core/metadata/v3.py | 29 ++++--- tests/test_common.py | 22 ++++- tests/test_json_parse.py | 122 +++++++++++++++++++++++++++ tests/test_metadata/test_v2.py | 2 +- uv.lock | 42 +++++++++ 17 files changed, 369 insertions(+), 73 deletions(-) create mode 100644 changes/3285.feature.md create mode 100644 src/zarr/core/json_parse.py create mode 100644 tests/test_json_parse.py diff --git a/changes/3285.feature.md b/changes/3285.feature.md new file mode 100644 index 0000000000..3809c0ab02 --- /dev/null +++ b/changes/3285.feature.md @@ -0,0 +1,13 @@ +JSON metadata validation now delegates to ``msgspec.convert`` for the type +coercions it supports (``Literal`` membership, ``int`` / ``bool`` strictness, +list-to-tuple), replacing the per-field hand-written ``parse_*`` logic. A small +fallback validates the recursive JSON values msgspec cannot, now with an +explicit nesting-depth limit, and a latent generator-exhaustion bug in +``parse_storage_transformers`` is fixed. See #3285. + +As a result some metadata inputs are now parsed more strictly. The previous +per-field checks compared values with ``==``, which accepts any numerically +equal object, so a float such as ``2.0`` was accepted as ``zarr_format``; it is +now rejected because it is not an ``int``. Booleans are likewise no longer +accepted where an ``int`` is expected, since ``bool`` is an ``int`` subclass. +Metadata that conforms to the Zarr specification is unaffected. diff --git a/mkdocs.yml b/mkdocs.yml index ca8165af4c..1fde8d9fe3 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -199,6 +199,7 @@ plugins: - https://docs.xarray.dev/en/stable/objects.inv - https://numpy.org/doc/stable/objects.inv - https://numcodecs.readthedocs.io/en/stable/objects.inv + - https://msgspec.dev/objects.inv - https://developmentseed.org/obstore/latest/objects.inv - https://filesystem-spec.readthedocs.io/en/latest/objects.inv - https://requests.readthedocs.io/en/latest/objects.inv diff --git a/pyproject.toml b/pyproject.toml index 5e8129a6a9..f341a488ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,6 +49,7 @@ dependencies = [ 'google-crc32c>=1.5', 'typing_extensions>=4.14', 'donfig>=0.8', + 'msgspec>=0.19', ] dynamic = [ @@ -281,6 +282,7 @@ extra-dependencies = [ 'typing_extensions==4.14.*', 'donfig==0.8.*', 'obstore==0.5.*', + 'msgspec==0.19.*', ] [tool.hatch.envs.default] diff --git a/src/zarr/codecs/blosc.py b/src/zarr/codecs/blosc.py index 087de716fc..ee45632153 100644 --- a/src/zarr/codecs/blosc.py +++ b/src/zarr/codecs/blosc.py @@ -14,6 +14,7 @@ from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, NamedRequiredConfig, parse_named_configuration from zarr.core.dtype.common import HasItemSize +from zarr.core.json_parse import parse_field if TYPE_CHECKING: from typing import Self @@ -104,27 +105,24 @@ class BloscCname(metaclass=_DeprecatedStrEnumMeta): def parse_typesize(data: JSON) -> int: - if isinstance(data, int): - if data > 0: - return data - else: - raise ValueError( - f"Value must be greater than 0. Got {data}, which is less or equal to 0." - ) - raise TypeError(f"Value must be an int. Got {type(data)} instead.") + parsed: int = parse_field(data, int, "typesize", error=TypeError) + if parsed > 0: + return parsed + else: + raise ValueError( + f"Value must be greater than 0. Got {parsed}, which is less or equal to 0." + ) # todo: real validation def parse_clevel(data: JSON) -> int: - if isinstance(data, int): - return data - raise TypeError(f"Value should be an int. Got {type(data)} instead.") + parsed: int = parse_field(data, int, "clevel", error=TypeError) + return parsed def parse_blocksize(data: JSON) -> int: - if isinstance(data, int): - return data - raise TypeError(f"Value should be an int. Got {type(data)} instead.") + parsed: int = parse_field(data, int, "blocksize", error=TypeError) + return parsed def _parse_cname(data: object) -> BloscCnameLiteral: diff --git a/src/zarr/codecs/gzip.py b/src/zarr/codecs/gzip.py index b8591748f7..7d86a03ba8 100644 --- a/src/zarr/codecs/gzip.py +++ b/src/zarr/codecs/gzip.py @@ -10,6 +10,7 @@ from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, parse_named_configuration +from zarr.core.json_parse import parse_field if TYPE_CHECKING: from typing import Self @@ -19,13 +20,12 @@ def parse_gzip_level(data: JSON) -> int: - if not isinstance(data, (int)): - raise TypeError(f"Expected int, got {type(data)}") - if data not in range(10): + parsed: int = parse_field(data, int, "level", error=TypeError) + if parsed not in range(10): raise ValueError( - f"Expected an integer from the inclusive range (0, 9). Got {data} instead." + f"Expected an integer from the inclusive range (0, 9). Got {parsed} instead." ) - return data + return parsed @dataclass(frozen=True) diff --git a/src/zarr/codecs/zstd.py b/src/zarr/codecs/zstd.py index f93c25a3c7..6d9f8910a7 100644 --- a/src/zarr/codecs/zstd.py +++ b/src/zarr/codecs/zstd.py @@ -12,6 +12,7 @@ from zarr.abc.codec import BytesBytesCodec from zarr.core.buffer.cpu import as_numpy_array_wrapper from zarr.core.common import JSON, parse_named_configuration +from zarr.core.json_parse import parse_field if TYPE_CHECKING: from typing import Self @@ -21,17 +22,15 @@ def parse_zstd_level(data: JSON) -> int: - if isinstance(data, int): - if data >= 23: - raise ValueError(f"Value must be less than or equal to 22. Got {data} instead.") - return data - raise TypeError(f"Got value with type {type(data)}, but expected an int.") + parsed: int = parse_field(data, int, "level", error=TypeError) + if parsed >= 23: + raise ValueError(f"Value must be less than or equal to 22. Got {parsed} instead.") + return parsed def parse_checksum(data: JSON) -> bool: - if isinstance(data, bool): - return data - raise TypeError(f"Expected bool. Got {type(data)}.") + parsed: bool = parse_field(data, bool, "checksum", error=TypeError) + return parsed @dataclass(frozen=True) diff --git a/src/zarr/core/chunk_key_encodings.py b/src/zarr/core/chunk_key_encodings.py index fb2fd95dee..d871e279d2 100644 --- a/src/zarr/core/chunk_key_encodings.py +++ b/src/zarr/core/chunk_key_encodings.py @@ -13,15 +13,14 @@ NamedConfig, parse_named_configuration, ) +from zarr.core.json_parse import parse_field from zarr.registry import get_chunk_key_encoding_class, register_chunk_key_encoding SeparatorLiteral = Literal[".", "/"] def parse_separator(data: JSON) -> SeparatorLiteral: - if data not in (".", "/"): - raise ValueError(f"Expected an '.' or '/' separator. Got {data} instead.") - return cast("SeparatorLiteral", data) + return cast("SeparatorLiteral", parse_field(data, Literal[".", "/"], "separator")) class ChunkKeyEncodingParams(TypedDict): diff --git a/src/zarr/core/common.py b/src/zarr/core/common.py index 1541683b09..3da5c108b6 100644 --- a/src/zarr/core/common.py +++ b/src/zarr/core/common.py @@ -20,6 +20,7 @@ from typing_extensions import ReadOnly from zarr.core.config import config as zarr_config +from zarr.core.json_parse import convert, parse_field from zarr.errors import ZarrRuntimeWarning if TYPE_CHECKING: @@ -147,12 +148,13 @@ def parse_enum[E: Enum](data: object, cls: type[E]) -> E: def parse_name(data: JSON, expected: str | None = None) -> str: - if isinstance(data, str): - if expected is None or data == expected: - return data - raise ValueError(f"Expected '{expected}'. Got {data} instead.") - else: - raise TypeError(f"Expected a string, got an instance of {type(data)}.") + try: + data = cast("str", convert(data, str)) + except (ValueError, TypeError) as exc: + raise TypeError(f"Expected a string, got an instance of {type(data)}.") from exc + if expected is None or data == expected: + return data + raise ValueError(f"Expected '{expected}'. Got {data} instead.") def parse_configuration(data: JSON) -> JSON: @@ -227,15 +229,11 @@ def parse_fill_value(data: Any) -> Any: def parse_order(data: Any) -> Literal["C", "F"]: - if data in ("C", "F"): - return cast("Literal['C', 'F']", data) - raise ValueError(f"Expected one of ('C', 'F'), got {data} instead.") + return cast("Literal['C', 'F']", parse_field(data, Literal["C", "F"], "order")) def parse_bool(data: Any) -> bool: - if isinstance(data, bool): - return data - raise ValueError(f"Expected bool, got {data} instead.") + return cast("bool", convert(data, bool)) def parse_int(data: Any) -> int: diff --git a/src/zarr/core/config.py b/src/zarr/core/config.py index 42c5ed3b60..c0ebb31353 100644 --- a/src/zarr/core/config.py +++ b/src/zarr/core/config.py @@ -33,6 +33,8 @@ from donfig import Config as DConfig +from zarr.core.json_parse import parse_field + if TYPE_CHECKING: from donfig.config_obj import ConfigSet @@ -159,7 +161,4 @@ def enable_gpu(self) -> ConfigSet: def parse_indexing_order(data: Any) -> Literal["C", "F"]: - if data in ("C", "F"): - return cast("Literal['C', 'F']", data) - msg = f"Expected one of ('C', 'F'), got {data} instead." - raise ValueError(msg) + return cast("Literal['C', 'F']", parse_field(data, Literal["C", "F"], "order")) diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py index 548f2141d2..d061e1a5c6 100644 --- a/src/zarr/core/group.py +++ b/src/zarr/core/group.py @@ -46,6 +46,7 @@ ) from zarr.core.config import config from zarr.core.dtype import parse_data_type +from zarr.core.json_parse import parse_field from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata from zarr.core.metadata.io import save_metadata from zarr.core.sync import SyncMixin, sync @@ -85,18 +86,15 @@ def parse_zarr_format(data: Any) -> ZarrFormat: """Parse the zarr_format field from metadata.""" - if data in (2, 3): - return cast("ZarrFormat", data) - msg = f"Invalid zarr_format. Expected one of 2 or 3. Got {data}." - raise ValueError(msg) + return cast("ZarrFormat", parse_field(data, Literal[2, 3], "zarr_format")) def parse_node_type(data: Any) -> NodeType: """Parse the node_type field from metadata.""" - if data in ("array", "group"): - return cast("Literal['array', 'group']", data) - msg = f"Invalid value for 'node_type'. Expected 'array' or 'group'. Got '{data}'." - raise MetadataValidationError(msg) + return cast( + "Literal['array', 'group']", + parse_field(data, Literal["array", "group"], "node_type", error=MetadataValidationError), + ) # todo: convert None to empty dict diff --git a/src/zarr/core/json_parse.py b/src/zarr/core/json_parse.py new file mode 100644 index 0000000000..09c5ca074e --- /dev/null +++ b/src/zarr/core/json_parse.py @@ -0,0 +1,103 @@ +"""Helpers for validating JSON-decoded metadata. + +Most JSON metadata validation is delegated to +[`msgspec.convert`][msgspec.convert], which handles the type coercions Zarr +needs (``Literal`` membership, ``int``/``bool`` strictness, list-to-tuple, +``TypedDict`` with ``NotRequired``). ``convert`` is a thin wrapper that +translates [`msgspec.ValidationError`][msgspec.ValidationError] into the +``TypeError`` the rest of the codebase already raises. + +msgspec cannot handle two things in Zarr's metadata types: + +* the recursive ``JSON`` / ``JSONValue`` aliases, which it rejects at + schema-build time, and +* PEP 728 ``extra_items=`` extension fields, which it silently drops. + +``validate_json_value`` is the small hand-written fallback for the first of +those. See https://github.com/zarr-developers/zarr-python/issues/3285. +""" + +from __future__ import annotations + +from collections.abc import Mapping +from typing import TYPE_CHECKING, Any, Final, cast, get_origin + +import msgspec + +if TYPE_CHECKING: + from zarr.core.common import JSON + +__all__ = ["MAX_JSON_DEPTH", "convert", "parse_field", "validate_json_value"] + +MAX_JSON_DEPTH: Final = 64 +"""Maximum nesting depth accepted by ``validate_json_value``.""" + + +def _type_name(type_: Any) -> str: + """Render ``type_`` for an error message. + + Parameterized types keep their arguments, so a ``Literal`` reports its + members (``Literal[2, 3]``) rather than the bare origin name. ``__name__`` + would drop them, which loses the most useful part of the message. + """ + if get_origin(type_) is not None: + return str(type_).replace("typing.", "") + return getattr(type_, "__name__", None) or str(type_).replace("typing.", "") + + +def convert(value: object, type_: Any, *, strict: bool = True) -> Any: + """Validate and coerce ``value`` against ``type_`` via [`msgspec.convert`][msgspec.convert]. + + On a mismatch msgspec raises + [`msgspec.ValidationError`][msgspec.ValidationError]; this re-raises + a plain, field-agnostic ``ValueError`` naming the expected type, so callers + can add their own field context (see ``parse_field``). + """ + try: + return msgspec.convert(value, type_, strict=strict) + except msgspec.ValidationError as exc: + raise ValueError(f"Expected instance of {_type_name(type_)}, got {value!r}.") from exc + + +def parse_field( + data: object, type_: Any, field: str, *, error: type[Exception] = ValueError +) -> Any: + """Validate ``data`` for metadata field ``field`` against ``type_``. + + Wraps ``convert`` and, on failure, re-raises ``error`` with field + context, chaining the underlying type error. This keeps the + ``convert``-then-re-raise pattern in one place rather than repeating it in + every per-field parser. + """ + try: + return convert(data, type_) + except ValueError as exc: + raise error( + f"Failed to parse input for {field!r}: expected {_type_name(type_)}, got {data!r}." + ) from exc + + +def validate_json_value(value: object, *, max_depth: int = MAX_JSON_DEPTH, _depth: int = 0) -> JSON: + """Check that ``value`` is a JSON value and return it unchanged. + + msgspec cannot build a schema for Zarr's recursive ``JSON`` / ``JSONValue`` + aliases, so this covers the fields typed that way (``attributes``, + ``fill_value``, extension-field values). Unlike the previous per-field + parsers it also enforces ``max_depth``: a pathologically nested document + could otherwise exhaust the interpreter stack. + """ + if _depth > max_depth: + raise ValueError(f"JSON value nesting exceeds the maximum depth of {max_depth}.") + if value is None or isinstance(value, (bool, int, float, str)): + return cast("JSON", value) + if isinstance(value, (list, tuple)): + for item in value: + validate_json_value(item, max_depth=max_depth, _depth=_depth + 1) + return cast("JSON", value) + if isinstance(value, Mapping): + for key, item in value.items(): + if not isinstance(key, str): + raise TypeError(f"JSON object keys must be str, got {type(key).__name__}.") + validate_json_value(item, max_depth=max_depth, _depth=_depth + 1) + return cast("JSON", value) + raise TypeError(f"Value {value!r} is not a valid JSON value.") diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py index 91515d87b9..70d4e1e59c 100644 --- a/src/zarr/core/metadata/v2.py +++ b/src/zarr/core/metadata/v2.py @@ -41,6 +41,7 @@ parse_shapelike, ) from zarr.core.config import config, parse_indexing_order +from zarr.core.json_parse import parse_field from zarr.core.metadata.common import parse_attributes @@ -278,9 +279,9 @@ def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]: def parse_zarr_format(data: object) -> Literal[2]: - if data == 2: - return 2 - raise ValueError(f"Invalid value. Expected 2. Got {data}.") + from typing import Literal + + return cast("Literal[2]", parse_field(data, Literal[2], "zarr_format")) def parse_filters(data: object) -> tuple[Numcodec, ...] | None: diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py index 9eaccc5076..fc47f8fc95 100644 --- a/src/zarr/core/metadata/v3.py +++ b/src/zarr/core/metadata/v3.py @@ -34,6 +34,7 @@ from zarr.core.config import config from zarr.core.dtype import VariableLengthUTF8, ZDType, get_data_type_from_json from zarr.core.dtype.common import check_dtype_spec_v3 +from zarr.core.json_parse import parse_field, validate_json_value from zarr.core.metadata.common import parse_attributes from zarr.errors import MetadataValidationError, NodeTypeValidationError, UnknownCodecError from zarr.registry import get_codec_class @@ -47,17 +48,16 @@ def parse_zarr_format(data: object) -> Literal[3]: - if data == 3: - return 3 - msg = f"Invalid value for 'zarr_format'. Expected '3'. Got '{data}'." - raise MetadataValidationError(msg) + return cast( + "Literal[3]", parse_field(data, Literal[3], "zarr_format", error=MetadataValidationError) + ) def parse_node_type_array(data: object) -> Literal["array"]: - if data == "array": - return "array" - msg = f"Invalid value for 'node_type'. Expected 'array'. Got '{data}'." - raise NodeTypeValidationError(msg) + return cast( + 'Literal["array"]', + parse_field(data, Literal["array"], "node_type", error=NodeTypeValidationError), + ) def parse_codecs(data: object) -> tuple[Codec, ...]: @@ -130,11 +130,12 @@ def parse_storage_transformers(data: object) -> tuple[dict[str, JSON], ...]: """ if data is None: return () - if isinstance(data, Iterable): - if len(tuple(data)) >= 1: - return data # type: ignore[return-value] - else: - return () + if isinstance(data, Iterable) and not isinstance(data, (str, bytes)): + # Materialise once. The previous implementation called ``len(tuple(data))`` + # and then returned ``data`` itself, which exhausted (and discarded) a + # one-shot iterable and could return a value typed as a tuple that was not + # actually a tuple. + return tuple(data) raise TypeError( f"Invalid storage_transformers. Expected an iterable of dicts. Got {type(data)} instead." ) @@ -656,7 +657,7 @@ def from_dict(cls, data: dict[str, JSON]) -> Self: chunk_grid=_data_typed["chunk_grid"], # type: ignore[arg-type] chunk_key_encoding=_data_typed["chunk_key_encoding"], # type: ignore[arg-type] codecs=_data_typed["codecs"], - attributes=_data_typed.get("attributes", {}), # type: ignore[arg-type] + attributes=validate_json_value(_data_typed.get("attributes", {})), # type: ignore[arg-type] dimension_names=_data_typed.get("dimension_names", None), fill_value=fill_value_parsed, data_type=data_type, diff --git a/tests/test_common.py b/tests/test_common.py index 5d8df326da..846dcbbad9 100644 --- a/tests/test_common.py +++ b/tests/test_common.py @@ -11,8 +11,10 @@ ANY_ACCESS_MODE, AccessModeLiteral, concurrent_iter, + parse_bool, parse_int, parse_name, + parse_order, parse_shapelike, product, ) @@ -97,10 +99,28 @@ def test_parse_name_valid(data: tuple[Any, Any]) -> None: @pytest.mark.parametrize("data", [0, 1, "hello", "f"]) def test_parse_indexing_order_invalid(data: Any) -> None: - with pytest.raises(ValueError, match="Expected one of"): + with pytest.raises(ValueError, match="Failed to parse input for 'order'"): parse_indexing_order(data) +@pytest.mark.parametrize("data", [0, 1, "hello", "f"]) +def test_parse_order_invalid(data: Any) -> None: + with pytest.raises(ValueError, match="Failed to parse input for 'order'"): + parse_order(data) + + +@pytest.mark.parametrize("data", [0, 1, "true", None, [True]]) +def test_parse_bool_invalid(data: Any) -> None: + """Non-bool values are rejected with a ValueError.""" + with pytest.raises(ValueError, match="Expected instance of bool"): + parse_bool(data) + + +@pytest.mark.parametrize("data", [True, False]) +def test_parse_bool_valid(data: bool) -> None: + assert parse_bool(data) is data + + @pytest.mark.parametrize("data", ["1", 1.0, True, False, None, [1], (1,)]) def test_parse_int_invalid(data: Any) -> None: """Non-int values (including bools, which are int subclasses) are rejected.""" diff --git a/tests/test_json_parse.py b/tests/test_json_parse.py new file mode 100644 index 0000000000..da723119aa --- /dev/null +++ b/tests/test_json_parse.py @@ -0,0 +1,122 @@ +"""Tests for :mod:`zarr.core.json_parse`. + +``convert`` delegates JSON type coercion to :func:`msgspec.convert` (translating +``msgspec.ValidationError`` into ``TypeError``); ``validate_json_value`` is the +hand-written fallback for the recursive ``JSON`` alias msgspec cannot build, +including a nesting-depth limit. The final group is a regression test for the +``parse_storage_transformers`` fix that motivated the depth limit work. +""" + +from __future__ import annotations + +from typing import Literal + +import pytest + +from zarr.core.json_parse import MAX_JSON_DEPTH, convert, parse_field, validate_json_value +from zarr.core.metadata.v3 import parse_storage_transformers + + +class TestConvert: + def test_literal(self) -> None: + assert convert(3, Literal[3]) == 3 + assert convert("array", Literal["array", "group"]) == "array" + + def test_literal_rejects_non_member(self) -> None: + with pytest.raises(ValueError, match="Expected instance of"): + convert(4, Literal[3]) + with pytest.raises(ValueError, match="Expected instance of"): + convert("Q", Literal["C", "F"]) + + def test_sequence_coerced_to_tuple(self) -> None: + assert convert([1, 2, 3], tuple[int, ...]) == (1, 2, 3) + assert convert([1, 2], tuple[int, int]) == (1, 2) + + def test_int(self) -> None: + assert convert(5, int) == 5 + + def test_bool_int_strictness(self) -> None: + # bool is an int subclass, but the two must not be interchangeable. + with pytest.raises(ValueError): + convert(True, int) + with pytest.raises(ValueError): + convert(1, bool) + # ... and True must not satisfy Literal[1]. + with pytest.raises(ValueError): + convert(True, Literal[1]) + + +class TestParseField: + def test_valid_passthrough(self) -> None: + assert parse_field(3, Literal[3], "zarr_format") == 3 + + def test_wraps_with_field_context(self) -> None: + with pytest.raises(ValueError, match="Failed to parse input for 'zarr_format'"): + parse_field(4, Literal[3], "zarr_format") + + def test_custom_error_type_and_chaining(self) -> None: + class MyError(ValueError): + pass + + with pytest.raises(MyError, match="Failed to parse input for 'node_type'") as exc_info: + parse_field(5, Literal["array"], "node_type", error=MyError) + # the generic type error is chained as the cause + assert isinstance(exc_info.value.__cause__, ValueError) + + +class TestValidateJsonValue: + @pytest.mark.parametrize("value", [None, True, 1, 1.5, "s"]) + def test_primitives(self, value: object) -> None: + assert validate_json_value(value) is value + + def test_nested(self) -> None: + value = {"a": [1, 2.0, "x", True, None], "b": {"c": [{}]}} + assert validate_json_value(value) is value + + def test_rejects_non_str_keys(self) -> None: + with pytest.raises(TypeError, match="keys must be str"): + validate_json_value({1: "x"}) + + def test_rejects_non_json_leaf(self) -> None: + with pytest.raises(TypeError, match="not a valid JSON value"): + validate_json_value(object()) + with pytest.raises(TypeError, match="not a valid JSON value"): + validate_json_value({"a": object()}) + + def test_depth_limit(self) -> None: + def nest(depth: int) -> object: + v: object = "leaf" + for _ in range(depth): + v = {"k": v} + return v + + # At the limit it passes; one level deeper it is rejected. This bound is + # new behavior the previous per-field parsers never had. + assert validate_json_value(nest(MAX_JSON_DEPTH)) is not None + with pytest.raises(ValueError, match="maximum depth"): + validate_json_value(nest(MAX_JSON_DEPTH + 1)) + + +class TestStorageTransformersRegression: + """`parse_storage_transformers` used to call `len(tuple(data))` and then + return `data` itself, exhausting a one-shot iterable and returning a value + typed as a tuple but not actually a tuple.""" + + def test_none(self) -> None: + assert parse_storage_transformers(None) == () + + def test_empty(self) -> None: + assert parse_storage_transformers([]) == () + + def test_list_returns_tuple(self) -> None: + result = parse_storage_transformers([{"a": 1}]) + assert result == ({"a": 1},) + assert isinstance(result, tuple) + + def test_generator_not_exhausted(self) -> None: + result = parse_storage_transformers(iter([{"a": 1}, {"b": 2}])) + assert result == ({"a": 1}, {"b": 2}) + + def test_non_iterable_rejected(self) -> None: + with pytest.raises(TypeError, match="Expected an iterable"): + parse_storage_transformers(5) diff --git a/tests/test_metadata/test_v2.py b/tests/test_metadata/test_v2.py index 0f280f0401..1358f458d6 100644 --- a/tests/test_metadata/test_v2.py +++ b/tests/test_metadata/test_v2.py @@ -32,7 +32,7 @@ def test_parse_zarr_format_valid() -> None: # The explicit id for "3" avoids colliding with the auto-generated id for the int 3. @pytest.mark.parametrize("data", [None, 1, 3, 4, 5, pytest.param("3", id="3-str")]) def test_parse_zarr_format_invalid(data: Any) -> None: - with pytest.raises(ValueError, match=f"Invalid value. Expected 2. 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">=2023.10.0" }, { name = "google-crc32c", specifier = ">=1.5" }, + { name = "msgspec", specifier = ">=0.19" }, { name = "numcodecs", specifier = ">=0.14" }, { name = "numpy", specifier = ">=2" }, { name = "obstore", marker = "extra == 'remote'", specifier = ">=0.5.1" }, From 12aa83b69b1513b6958d49fc0e3c6768c0b2e1f8 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Thu, 13 Aug 2026 21:50:07 +0200 Subject: [PATCH 461/468] deps: bump cast-value.rs to >= 0.4.2 (#4260) * deps: bump cast-value.rs to >= 0.4.2 * deps: update uv.lock for cast-value-rs >= 0.4.2 The pyproject floor alone left uv.lock pinning 0.4.0, so any lock-honoring install (uv sync --locked/--frozen) kept the version that silently transposes non-row-major input. Assisted-by: ClaudeCode:claude-fable-5 * fix(cast_value): enforce the cast-value-rs floor at runtime The pyproject floor only binds installs that go through the zarr[cast-value-rs] extra. An environment that already has an older cast-value-rs installed kept silently corrupting non-row-major input after upgrading zarr, which is the failure this floor exists to stop. Check the installed version at import and raise from _do_cast, so the error surfaces when the codec is used rather than breaking `import zarr` for everyone else. A backend without distribution metadata (a `maturin develop` build) has no version to compare and is left alone. Assisted-by: ClaudeCode:claude-fable-5 * test(cast_value): cover cast_value next to the transpose codec Regression test for #4237: a cast_value codec on either side of a transpose codec must round-trip, because transpose hands the next codec a non-row-major view. Imported unchanged from #4238, where this test was written. The np.ascontiguousarray workaround that accompanied it there is deliberately left out: cast-value-rs 0.4.2 normalizes layout itself, and the workaround promotes 0-d arrays to shape (1,), breaking 0-d arrays. Co-authored-by: Raphael Jolivet <raphael.jolivet@minesparis.psl.eu> Assisted-by: ClaudeCode:claude-fable-5 --------- Co-authored-by: Raphael Jolivet <contact@raphael-jolivet.name> Co-authored-by: Raphael Jolivet <raphael.jolivet@minesparis.psl.eu> --- changes/4260.bugfix.md | 1 + pyproject.toml | 2 +- src/zarr/codecs/cast_value.py | 45 +++++++-- tests/test_codecs/test_cast_value.py | 134 +++++++++++++++++++++++++++ uv.lock | 122 ++++++++++++------------ 5 files changed, 230 insertions(+), 74 deletions(-) create mode 100644 changes/4260.bugfix.md diff --git a/changes/4260.bugfix.md b/changes/4260.bugfix.md new file mode 100644 index 0000000000..b703c47a35 --- /dev/null +++ b/changes/4260.bugfix.md @@ -0,0 +1 @@ +The `cast_value` codec now requires `cast-value-rs>=0.4.2`. Earlier versions of that backend silently corrupted data when handed an array that was not row-major — the layout the `transpose` codec produces — so a `cast_value` codec next to a `transpose` codec would either write transposed values with no error or fail with `ValueError: Input array must be contiguous`. The minimum version is enforced at runtime as well as in the package metadata, so an environment that already has an older `cast-value-rs` installed now raises `ImportError` when the codec is used, instead of corrupting data. diff --git a/pyproject.toml b/pyproject.toml index f341a488ed..dca663277e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -81,7 +81,7 @@ remote = [ gpu = [ "cupy-cuda12x; sys_platform != 'darwin'", ] -cast-value-rs = ["cast-value-rs"] +cast-value-rs = ["cast-value-rs>=0.4.2"] cli = ["typer"] optional = ["universal-pathlib"] diff --git a/src/zarr/codecs/cast_value.py b/src/zarr/codecs/cast_value.py index eb8a4de248..b19a10c873 100644 --- a/src/zarr/codecs/cast_value.py +++ b/src/zarr/codecs/cast_value.py @@ -5,16 +5,18 @@ rounding, out-of-range handling, and explicit scalar mappings. Requires the optional ``cast-value-rs`` package for the actual casting -logic. Install it with: ``pip install cast-value-rs``. +logic. Install it with: ``pip install 'cast-value-rs>=0.4.2'``. """ from __future__ import annotations from collections.abc import Mapping from dataclasses import dataclass, replace +from importlib.metadata import PackageNotFoundError, version from typing import TYPE_CHECKING, Final, Literal, TypedDict, cast import numpy as np +from packaging.version import Version from zarr.abc.codec import ArrayArrayCodec from zarr.core.common import JSON, parse_named_configuration @@ -123,12 +125,40 @@ def parse_scalar_map(obj: ScalarMapJSON | ScalarMap) -> ScalarMap: # Backend: cast-value-rs # --------------------------------------------------------------------------- +# Versions below this silently transpose input arrays that are not row-major - +# the layout `transpose` hands to the next codec - writing corrupted data with +# no error. Keep in sync with the `cast-value-rs` extra in pyproject.toml. +CAST_VALUE_RS_MIN_VERSION: Final = "0.4.2" + +_INSTALL_HINT: Final = f"Install it with: pip install 'cast-value-rs>={CAST_VALUE_RS_MIN_VERSION}'" + + +def _check_backend_version() -> str | None: + """Return a message describing an unusable backend version, or `None` if it is usable.""" + try: + installed = version("cast-value-rs") + except PackageNotFoundError: + # Importable but without distribution metadata, e.g. a `maturin develop` + # build. There is no version to compare, so let it through. + return None + if Version(installed) < Version(CAST_VALUE_RS_MIN_VERSION): + return ( + f"The cast_value codec requires cast-value-rs >= {CAST_VALUE_RS_MIN_VERSION}, " + f"but version {installed} is installed. Earlier versions silently corrupt data " + f"when the input array is not row-major. {_INSTALL_HINT}" + ) + return None + + +# Set once at import; raised from `_do_cast`, so an unusable backend does not +# make `import zarr` fail for users who never touch this codec. +_BACKEND_ERROR: str | None try: from cast_value_rs import cast_array as cast_array_rs - - _HAS_RUST_BACKEND = True except ModuleNotFoundError: - _HAS_RUST_BACKEND = False + _BACKEND_ERROR = f"The cast_value codec requires the 'cast-value-rs' package. {_INSTALL_HINT}" +else: + _BACKEND_ERROR = _check_backend_version() def _check_representable( @@ -305,11 +335,8 @@ def _do_cast( target_dtype: np.dtype, scalar_map: Mapping[str | float | int, str | float | int] | None, ) -> np.ndarray: - if not _HAS_RUST_BACKEND: - raise ImportError( - "The cast_value codec requires the 'cast-value-rs' package. " - "Install it with: pip install cast-value-rs" - ) + if _BACKEND_ERROR is not None: + raise ImportError(_BACKEND_ERROR) scalar_map_entries: dict[float | int, float | int] | None = None if scalar_map is not None: src_dtype = arr.dtype diff --git a/tests/test_codecs/test_cast_value.py b/tests/test_codecs/test_cast_value.py index c43edb76e8..c2e78770d9 100644 --- a/tests/test_codecs/test_cast_value.py +++ b/tests/test_codecs/test_cast_value.py @@ -4,10 +4,13 @@ import numpy as np import pytest +from numpy.testing import assert_array_equal import zarr from tests.conftest import Expect, ExpectFail +from zarr.codecs import BytesCodec, TransposeCodec from zarr.codecs.cast_value import CastValue +from zarr.storage import MemoryStore try: import cast_value_rs # noqa: F401 @@ -477,3 +480,134 @@ def test_parse_scalar_map(case: Expect[Any, Any]) -> None: from zarr.codecs.cast_value import parse_scalar_map assert parse_scalar_map(case.input) == case.output + + +# --------------------------------------------------------------------------- +# Backend version guard +# --------------------------------------------------------------------------- + + +@pytest.mark.parametrize( + "case", + [ + Expect(input="0.4.2", output=None, id="exactly-minimum"), + Expect(input="0.4.3", output=None, id="newer-patch"), + Expect(input="0.5.0", output=None, id="newer-minor"), + Expect(input="1.0.0", output=None, id="newer-major"), + Expect(input="0.4.2.post1", output=None, id="post-release"), + Expect(input="0.4.0", output="0.4.0", id="known-corrupting"), + Expect(input="0.4.1", output="0.4.1", id="one-patch-below"), + Expect(input="0.3.0", output="0.3.0", id="older-minor"), + Expect(input="0.4.2.dev1", output="0.4.2.dev1", id="pre-release-of-minimum"), + ], + ids=lambda c: c.id, +) +def test_check_backend_version( + case: Expect[str, str | None], monkeypatch: pytest.MonkeyPatch +) -> None: + """Versions at or above the minimum pass; older ones report the installed version.""" + from zarr.codecs import cast_value as mod + + monkeypatch.setattr(mod, "version", lambda _: case.input) + result = mod._check_backend_version() + + if case.output is None: + assert result is None + else: + assert result is not None + assert case.output in result + assert mod.CAST_VALUE_RS_MIN_VERSION in result + + +def test_check_backend_version_allows_missing_metadata(monkeypatch: pytest.MonkeyPatch) -> None: + """A backend without distribution metadata is allowed: there is no version to compare.""" + from importlib.metadata import PackageNotFoundError + + from zarr.codecs import cast_value as mod + + def raise_not_found(_: str) -> str: + raise PackageNotFoundError + + monkeypatch.setattr(mod, "version", raise_not_found) + assert mod._check_backend_version() is None + + +def test_encode_rejects_outdated_backend(monkeypatch: pytest.MonkeyPatch) -> None: + """Using the codec with an outdated backend raises instead of corrupting data.""" + from zarr.codecs import cast_value as mod + + monkeypatch.setattr(mod, "_BACKEND_ERROR", "outdated backend") + codec = CastValue(data_type="uint16") + + with pytest.raises(ImportError, match="outdated backend"): + codec._do_cast( + np.arange(4, dtype=np.float32), target_dtype=np.dtype("uint16"), scalar_map=None + ) + + +def test_min_version_matches_pyproject() -> None: + """The runtime floor and the packaging floor must not drift apart.""" + import re + import tomllib + from pathlib import Path + + from zarr.codecs.cast_value import CAST_VALUE_RS_MIN_VERSION + + pyproject = Path(__file__).parents[2] / "pyproject.toml" + if not pyproject.is_file(): + pytest.skip("pyproject.toml is not available in an installed checkout") + + with pyproject.open("rb") as f: + extras = tomllib.load(f)["project"]["optional-dependencies"] + + (requirement,) = extras["cast-value-rs"] + match = re.fullmatch(r"cast-value-rs>=(?P<version>[\w.]+)", requirement) + assert match is not None, f"unexpected requirement form: {requirement!r}" + assert match.group("version") == CAST_VALUE_RS_MIN_VERSION + + +# --------------------------------------------------------------------------- +# Non-contiguous input (regression for #4237) +# --------------------------------------------------------------------------- + + +@requires_cast_value_rs +def test_enforce_contiguous_arrays() -> None: + """ + Transpose codec produces non-contiguous arrays. + Ensure cast_value makes them contiguous before processing. + """ + data = np.arange(20, dtype=np.float32).reshape(5, 2, 2) + + def make_array(filters: list[Any]) -> Any: + return zarr.create_array( + store=MemoryStore(), + shape=data.shape, + dtype=data.dtype, + chunks=data.shape, + filters=filters, + serializer=BytesCodec(endian="little"), + compressors=None, + zarr_format=3, + ) + + # Cast before transpose + array = make_array( + [ + CastValue(data_type="uint16"), + TransposeCodec(order=(1, 2, 0)), + ] + ) + array[:] = data + assert_array_equal(array[:], data) + + # Cast after transpose + array = 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(#4264) * fix(zarr-metadata): make JSONValue's array arm covariant `list["JSONValue"] | tuple["JSONValue", ...]` is invariant in the element type, so a value typed with any narrower element -- a `list[str]` field on a TypedDict, a `Sequence[float]` -- was not assignable to `JSONValue`, and a TypedDict carrying such fields was not assignable to `Mapping[str, JSONValue]`. pyright's diagnostic for the failure suggests the fix verbatim: "Consider switching from list to Sequence which is covariant." The array arm is now `Sequence["JSONValue"]`. The docstring records the deliberate type-level cost (`Sequence` admits `str`/`bytes`; runtime narrowing must exclude them regardless of the alias's spelling). Found while aliasing zarr-cm's JsonValue to this type: the two aliases are structurally identical except for this arm, and with it changed, pyright unifies them across the package boundary. Assisted-by: ClaudeCode:claude-opus-5 * Rename 295.bugfix.md to 4264.bugfix.md --- packages/zarr-metadata/changes/4264.bugfix.md | 9 +++++++ .../src/zarr_metadata/_common.py | 24 ++++++++++++------- 2 files changed, 24 insertions(+), 9 deletions(-) create mode 100644 packages/zarr-metadata/changes/4264.bugfix.md diff --git a/packages/zarr-metadata/changes/4264.bugfix.md b/packages/zarr-metadata/changes/4264.bugfix.md new file mode 100644 index 0000000000..466bf5941d --- /dev/null +++ b/packages/zarr-metadata/changes/4264.bugfix.md @@ -0,0 +1,9 @@ +`JSONValue`'s array arm is now the covariant `Sequence["JSONValue"]` rather +than the invariant `list["JSONValue"] | tuple["JSONValue", ...]`. Values typed +with a narrower element type — a `list[str]` field on a TypedDict, a +`Sequence[float]` — now count as JSON values, and TypedDicts whose fields +carry precise types are now assignable to `Mapping[str, JSONValue]`. +Type-level cost, accepted deliberately: `Sequence` says nothing about the +concrete container and admits `str`/`bytes`, so runtime code narrowing a JSON +array must exclude `str`/`bytes`/`bytearray` — as it already had to, since +`str` was always a union arm. diff --git a/packages/zarr-metadata/src/zarr_metadata/_common.py b/packages/zarr-metadata/src/zarr_metadata/_common.py index f3259f7b73..08c143107f 100644 --- a/packages/zarr-metadata/src/zarr_metadata/_common.py +++ b/packages/zarr-metadata/src/zarr_metadata/_common.py @@ -6,21 +6,14 @@ `zarr_metadata.v3.data_type`. """ -from collections.abc import Mapping +from collections.abc import Mapping, Sequence from typing import NotRequired from typing_extensions import TypeAliasType, TypedDict JSONValue = TypeAliasType( "JSONValue", - int - | float - | bool - | str - | list["JSONValue"] - | tuple["JSONValue", ...] - | Mapping[str, "JSONValue"] - | None, + int | float | bool | str | Sequence["JSONValue"] | Mapping[str, "JSONValue"] | None, ) """A recursive type alias for JSON-encodable values. @@ -28,6 +21,19 @@ self-reference is a named recursion point that pydantic can resolve when building a `TypeAdapter`; a bare recursive `TypeAlias` raises `PydanticUserError`/`RecursionError` at validation time. + +The array arm is the covariant `Sequence` rather than the invariant +`list["JSONValue"] | tuple["JSONValue", ...]`, so values typed with a +*narrower* element type still count as JSON values: a `list[str]` field on a +TypedDict is assignable to `JSONValue` under `Sequence` but not under +`list[JSONValue]` (`list` is invariant in its element type, and pyright's +diagnostic for that failure suggests exactly this change). This is what lets +downstream TypedDicts give their fields precise types (`Sequence[str]`, +`list[int]`, ...) while remaining assignable to `Mapping[str, JSONValue]`. +The type-level cost, accepted deliberately: `Sequence` says nothing about the +concrete container, and it admits `str`/`bytes` (`str` was already a union +arm); runtime code narrowing a JSON array must exclude `str`/`bytes`/ +`bytearray` regardless of how this alias is spelled. """ From f4a239c72e0548db5faedfbe1a36cfea6e837b25 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Fri, 14 Aug 2026 14:40:45 +0200 Subject: [PATCH 463/468] chore(zarr-metadata): build 0.5.0 changelog (#4266) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * chore(zarr-metadata): note the sdist allowlist, and let misc entries speak #4248 gave this package's sdist an explicit allowlist and merged without a news fragment, so a user-visible packaging change was about to miss the 0.5.0 notes. Add one. Filing it as `misc` exposed that towncrier's built-in `misc` type sets `showcontent = false`: the entry would render as a bare PR link, which tells a reader nothing. Restate all five types the `changes/README.md` menu offers — declaring any type replaces the built-in set — as the defaults verbatim except for `misc`, which now shows its content. A change worth a release note is worth a sentence, whatever its category. Assisted-by: ClaudeCode:claude-opus-5 * chore(zarr-metadata): build 0.5.0 changelog Consume the pending news fragments — #4232's constant-naming-grammar removal note, #4264's note widening `JSONValue`'s array arm to the covariant `Sequence`, and #4248's sdist allowlist — into CHANGELOG.md via towncrier for the zarr_metadata-v0.5.0 release. Minor, not patch: the `JSONValue` widening changes a published type's meaning for every consumer that annotates against it, and #4232 removes the old version-last constant spellings outright. Assisted-by: ClaudeCode:claude-opus-5 --- packages/zarr-metadata/CHANGELOG.md | 90 +++++++++++++++++++ .../zarr-metadata/changes/4232.removal.md | 63 ------------- packages/zarr-metadata/changes/4264.bugfix.md | 9 -- packages/zarr-metadata/pyproject.toml | 30 +++++++ 4 files changed, 120 insertions(+), 72 deletions(-) delete mode 100644 packages/zarr-metadata/changes/4232.removal.md delete mode 100644 packages/zarr-metadata/changes/4264.bugfix.md diff --git a/packages/zarr-metadata/CHANGELOG.md b/packages/zarr-metadata/CHANGELOG.md index ac4ad3535a..c1e9f81a61 100644 --- a/packages/zarr-metadata/CHANGELOG.md +++ b/packages/zarr-metadata/CHANGELOG.md @@ -2,6 +2,96 @@ <!-- towncrier release notes start --> +## 0.5.0 (2026-08-14) + +### Bugfixes + +- `JSONValue`'s array arm is now the covariant `Sequence["JSONValue"]` rather + than the invariant `list["JSONValue"] | tuple["JSONValue", ...]`. Values typed + with a narrower element type — a `list[str]` field on a TypedDict, a + `Sequence[float]` — now count as JSON values, and TypedDicts whose fields + carry precise types are now assignable to `Mapping[str, JSONValue]`. + Type-level cost, accepted deliberately: `Sequence` says nothing about the + concrete container and admits `str`/`bytes`, so runtime code narrowing a JSON + array must exclude `str`/`bytes`/`bytearray` — as it already had to, since + `str` was always a union arm. ([#4264](https://github.com/zarr-developers/zarr-python/pull/4264)) + +### Deprecations and Removals + +- Unified the naming grammar for SCREAMING_SNAKE constants with the one used for + type names. A constant's name is now a purely syntactic transformation of the + name of the `Literal` type it manifests, so the format version is spelled + `ZARR_V2`/`ZARR_V3` and comes first, matching the `ZarrV2`/`ZarrV3` prefix on + the corresponding type: + + - `ARRAY_METADATA_STORE_KEY_V2` → `ZARR_V2_ARRAY_METADATA_STORE_KEY` + - `ARRAY_METADATA_STORE_KEY_V3` → `ZARR_V3_ARRAY_METADATA_STORE_KEY` + - `ATTRIBUTES_STORE_KEY_V2` → `ZARR_V2_ATTRIBUTES_STORE_KEY` + - `GROUP_METADATA_STORE_KEY_V2` → `ZARR_V2_GROUP_METADATA_STORE_KEY` + - `GROUP_METADATA_STORE_KEY_V3` → `ZARR_V3_GROUP_METADATA_STORE_KEY` + - `CONSOLIDATED_METADATA_STORE_KEY_V2` → `ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY` + - `ARRAY_ORDER_V2` → `ZARR_V2_ARRAY_ORDER` + - `ARRAY_DIMENSION_SEPARATOR_V2` → `ZARR_V2_ARRAY_DIMENSION_SEPARATOR` + - `CONSOLIDATED_METADATA_KEY_V3` → `ZARR_V3_CONSOLIDATED_METADATA_KEY` + + The old names are removed, not aliased. This supersedes the 0.4.0 convention + under which type names put the format version first while constants put it + last: every constant that manifests a `Literal` type now follows the same rule + as that type. + + The last of those is the one rename the syntactic rule does not force: + `ZARR_V3_CONSOLIDATED_METADATA_KEY` manifests no `Literal` type, so it is + outside the rule and was renamed for consistency with its siblings. + + Digit runs stay glued to the token they follow, so spec vocabulary is + preserved: `Uint8DataTypeName` pairs with `UINT8_DATA_TYPE_NAME` (not + `UINT_8_...`) and `Crc32cCodecName` with `CRC32C_CODEC_NAME`. No dtype, codec, + chunk-grid, or chunk-key-encoding constant changed name. + + Constants that do not manifest a `Literal` type are outside the rule and are + unchanged: the `*_METADATA_*_KEYS_V2`/`_V3` key sets, the + `CANONICAL_*_HEX_FLOAT*` bit patterns, and `UNSET`. The key sets keep the + version-last spelling, so `zarr_metadata.model` exports both + `ARRAY_METADATA_REQUIRED_KEYS_V2` and `ZARR_V2_ARRAY_METADATA_STORE_KEY`. They + name validation policy rather than a spec document, have no paired type to + derive from, and renaming them would be a second breaking change buying only + cosmetic consistency — so it is deliberately deferred. + + `tests/test_public_api.py::test_constant_names_derive_from_their_type_names` + derives every constant name from the type it manifests and asserts they match, + so the two grammars cannot diverge again. + + Store keys also moved to the modules that describe the documents they name, + matching the package's layering (the `v2`/`v3` modules describe the specs; the + `model` layer is built on top of them). `ZARR_V2_ATTRIBUTES_STORE_KEY` now + lives in `zarr_metadata.v2.attributes` beside the `.zattrs` type it names, + rather than in the array model; the other five moved likewise, and + `ZarrV2AttributesStoreKey` is no longer an array-specific concept. + `zarr_metadata.model` re-exports all six, so + `from zarr_metadata.model import ZARR_V2_ARRAY_METADATA_STORE_KEY` is + unaffected. + + `CONSOLIDATED_METADATA_KEY_V3` moved to `zarr_metadata.v3.consolidated` and was + renamed to `ZARR_V3_CONSOLIDATED_METADATA_KEY` for consistency. It is not a + store key: unlike v2's `.zmetadata` file, v3 consolidated metadata is embedded + as an extension field inside the group's own `zarr.json`. + + All seven keys and the six store-key `Literal` aliases are now also exported + from the top-level `zarr_metadata` namespace, alongside the document types and + the rest of the spec vocabulary, so `from zarr_metadata import + ZARR_V2_ARRAY_METADATA_STORE_KEY` works. The model layer's validators, parsers, + type guards, and metadata key sets remain `zarr_metadata.model` imports. + + ([#4232](https://github.com/zarr-developers/zarr-python/pull/4232)) + +### Misc + +- The source distribution now ships an explicit allowlist (`/src`, `/tests`, + `/docs`, `/mkdocs.yml`, `/justfile`, `/CHANGELOG.md`) rather than whatever + happens to sit in the package directory, so an sdist both tests and documents + itself and cannot pick up scratch files from the tree it was built in. ([#4248](https://github.com/zarr-developers/zarr-python/pull/4248)) + + ## 0.4.0 (2026-07-29) ### Features diff --git a/packages/zarr-metadata/changes/4232.removal.md b/packages/zarr-metadata/changes/4232.removal.md deleted file mode 100644 index 73b2a18666..0000000000 --- a/packages/zarr-metadata/changes/4232.removal.md +++ /dev/null @@ -1,63 +0,0 @@ -Unified the naming grammar for SCREAMING_SNAKE constants with the one used for -type names. A constant's name is now a purely syntactic transformation of the -name of the `Literal` type it manifests, so the format version is spelled -`ZARR_V2`/`ZARR_V3` and comes first, matching the `ZarrV2`/`ZarrV3` prefix on -the corresponding type: - -- `ARRAY_METADATA_STORE_KEY_V2` → `ZARR_V2_ARRAY_METADATA_STORE_KEY` -- `ARRAY_METADATA_STORE_KEY_V3` → `ZARR_V3_ARRAY_METADATA_STORE_KEY` -- `ATTRIBUTES_STORE_KEY_V2` → `ZARR_V2_ATTRIBUTES_STORE_KEY` -- `GROUP_METADATA_STORE_KEY_V2` → `ZARR_V2_GROUP_METADATA_STORE_KEY` -- `GROUP_METADATA_STORE_KEY_V3` → `ZARR_V3_GROUP_METADATA_STORE_KEY` -- `CONSOLIDATED_METADATA_STORE_KEY_V2` → `ZARR_V2_CONSOLIDATED_METADATA_STORE_KEY` -- `ARRAY_ORDER_V2` → `ZARR_V2_ARRAY_ORDER` -- `ARRAY_DIMENSION_SEPARATOR_V2` → `ZARR_V2_ARRAY_DIMENSION_SEPARATOR` -- `CONSOLIDATED_METADATA_KEY_V3` → `ZARR_V3_CONSOLIDATED_METADATA_KEY` - -The old names are removed, not aliased. This supersedes the 0.4.0 convention -under which type names put the format version first while constants put it -last: every constant that manifests a `Literal` type now follows the same rule -as that type. - -The last of those is the one rename the syntactic rule does not force: -`ZARR_V3_CONSOLIDATED_METADATA_KEY` manifests no `Literal` type, so it is -outside the rule and was renamed for consistency with its siblings. - -Digit runs stay glued to the token they follow, so spec vocabulary is -preserved: `Uint8DataTypeName` pairs with `UINT8_DATA_TYPE_NAME` (not -`UINT_8_...`) and `Crc32cCodecName` with `CRC32C_CODEC_NAME`. No dtype, codec, -chunk-grid, or chunk-key-encoding constant changed name. - -Constants that do not manifest a `Literal` type are outside the rule and are -unchanged: the `*_METADATA_*_KEYS_V2`/`_V3` key sets, the -`CANONICAL_*_HEX_FLOAT*` bit patterns, and `UNSET`. The key sets keep the -version-last spelling, so `zarr_metadata.model` exports both -`ARRAY_METADATA_REQUIRED_KEYS_V2` and `ZARR_V2_ARRAY_METADATA_STORE_KEY`. They -name validation policy rather than a spec document, have no paired type to -derive from, and renaming them would be a second breaking change buying only -cosmetic consistency — so it is deliberately deferred. - -`tests/test_public_api.py::test_constant_names_derive_from_their_type_names` -derives every constant name from the type it manifests and asserts they match, -so the two grammars cannot diverge again. - -Store keys also moved to the modules that describe the documents they name, -matching the package's layering (the `v2`/`v3` modules describe the specs; the -`model` layer is built on top of them). `ZARR_V2_ATTRIBUTES_STORE_KEY` now -lives in `zarr_metadata.v2.attributes` beside the `.zattrs` type it names, -rather than in the array model; the other five moved likewise, and -`ZarrV2AttributesStoreKey` is no longer an array-specific concept. -`zarr_metadata.model` re-exports all six, so -`from zarr_metadata.model import ZARR_V2_ARRAY_METADATA_STORE_KEY` is -unaffected. - -`CONSOLIDATED_METADATA_KEY_V3` moved to `zarr_metadata.v3.consolidated` and was -renamed to `ZARR_V3_CONSOLIDATED_METADATA_KEY` for consistency. It is not a -store key: unlike v2's `.zmetadata` file, v3 consolidated metadata is embedded -as an extension field inside the group's own `zarr.json`. - -All seven keys and the six store-key `Literal` aliases are now also exported -from the top-level `zarr_metadata` namespace, alongside the document types and -the rest of the spec vocabulary, so `from zarr_metadata import -ZARR_V2_ARRAY_METADATA_STORE_KEY` works. The model layer's validators, parsers, -type guards, and metadata key sets remain `zarr_metadata.model` imports. diff --git a/packages/zarr-metadata/changes/4264.bugfix.md b/packages/zarr-metadata/changes/4264.bugfix.md deleted file mode 100644 index 466bf5941d..0000000000 --- a/packages/zarr-metadata/changes/4264.bugfix.md +++ /dev/null @@ -1,9 +0,0 @@ -`JSONValue`'s array arm is now the covariant `Sequence["JSONValue"]` rather -than the invariant `list["JSONValue"] | tuple["JSONValue", ...]`. Values typed -with a narrower element type — a `list[str]` field on a TypedDict, a -`Sequence[float]` — now count as JSON values, and TypedDicts whose fields -carry precise types are now assignable to `Mapping[str, JSONValue]`. -Type-level cost, accepted deliberately: `Sequence` says nothing about the -concrete container and admits `str`/`bytes`, so runtime code narrowing a JSON -array must exclude `str`/`bytes`/`bytearray` — as it already had to, since -`str` was always a union arm. diff --git a/packages/zarr-metadata/pyproject.toml b/packages/zarr-metadata/pyproject.toml index 0df3385dc7..a58d3579a1 100644 --- a/packages/zarr-metadata/pyproject.toml +++ b/packages/zarr-metadata/pyproject.toml @@ -137,3 +137,33 @@ underlines = ["", "", ""] title_format = "## {version} ({project_date})" issue_format = "[#{issue}](https://github.com/zarr-developers/zarr-python/pull/{issue})" start_string = "<!-- towncrier release notes start -->\n" + +# Declaring any type replaces towncrier's built-in set, so all five the +# `changes/README.md` menu offers are restated here. They are the defaults +# verbatim except for `misc`, whose `showcontent` towncrier defaults to false: +# a `misc` entry would render as a bare PR link, which tells a reader nothing. +# A change worth a release note is worth a sentence, whatever its category. +[[tool.towncrier.type]] +directory = "feature" +name = "Features" +showcontent = true + +[[tool.towncrier.type]] +directory = "bugfix" +name = "Bugfixes" +showcontent = true + +[[tool.towncrier.type]] +directory = "doc" +name = "Improved Documentation" +showcontent = true + +[[tool.towncrier.type]] +directory = "removal" +name = "Deprecations and Removals" +showcontent = true + +[[tool.towncrier.type]] +directory = "misc" +name = "Misc" +showcontent = true From 743169953b6fca7edaa08fe7ce0814989b6ea51c Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Fri, 14 Aug 2026 21:29:41 +0200 Subject: [PATCH 464/468] docs: add roadmap page outlining future plans (#4149) --- changes/4149.doc.md | 1 + docs/roadmap.md | 189 ++++++++++++++++++++++++++++++++++++++++++++ mkdocs.yml | 2 +- 3 files changed, 191 insertions(+), 1 deletion(-) create mode 100644 changes/4149.doc.md create mode 100644 docs/roadmap.md diff --git a/changes/4149.doc.md b/changes/4149.doc.md new file mode 100644 index 0000000000..8a473acac9 --- /dev/null +++ b/changes/4149.doc.md @@ -0,0 +1 @@ +Added a Roadmap page to the documentation outlining future plans and intended changes to the library. diff --git a/docs/roadmap.md b/docs/roadmap.md new file mode 100644 index 0000000000..4b5dbc4599 --- /dev/null +++ b/docs/roadmap.md @@ -0,0 +1,189 @@ +# Roadmap + +This page describes where Zarr-Python is headed: the goals for the next major +cycle of work, the changes we intend to make, and how those changes will be +released. It is a living document; discussion and counter-proposals are welcome +on the +[Zarr-Python issue tracker](https://github.com/zarr-developers/zarr-python/issues). + +*The history of this roadmap, including the detailed technical proposals it +was distilled from, can be traced in the +[zarr-python-planning](https://github.com/zarr-developers/zarr-python-planning) +repository.* + +!!! note + + This roadmap reflects the current thinking of the core developers. It is a + statement of direction, not a schedule. We don't know how long these changes + will take, only that we are committed to moving the project in the direction outlined + here. + +## Where we are + +The [3.0 release](https://github.com/zarr-developers/zarr-python/releases/tag/v3.0.0) +was a total redesign of the library's internals, with three goals: full support +for the Zarr V2 and V3 storage formats, storage APIs that are ergonomic for high-latency +storage (such as cloud storage), and backwards compatibility with Zarr-Python 2.x where +possible. Those goals were largely achieved! Going by the content of issues and pull requests +submitted to the library, few users are grappling with 2.x → 3.x migration issues. Instead, we see +users asking for things like better APIs, where "better" usually means faster. + +The 3.x redesign was carried out under hard backwards-compatibility +constraints, and it inherited many structural patterns from the 2.x +implementation it replaced. The library has never had a release cycle whose +primary goal was the *shape* of the internals. The next body of work — which we +call **"v4"** — is that overdue investment. We think iterating on the internals of +the library will make it *much* easier to bring faster, more expressive APIs to Zarr-Python +users. + +## Goals + +If the 3.0 goals could be sloganized as "migrate to Zarr V3, and improve cloud +storage support", the slogan for the v4 goals is: +**"a frictionless Zarr-based Python ecosystem for chunked arrays"**. Zarr-Python +should be *foundational* for the growing number of Python packages that work +with data in the Zarr format. Concretely, that means pushing in these +directions: + +- Deliver excellent performance, out of the box, while retaining maintainability. +- Make Zarr-Python APIs ergonomic and useful for developers. +- Expand our scope to cover vital quality-of-life routines like data copying, + rechunking, and the like. +- Ease the growth of Python tools across all levels of the Zarr stack. +- Accelerate the implementation of new codecs, chunk grids, chunk key + encodings, etc. + +An important design input: [`zarrs`](https://github.com/zarrs/zarrs) (Rust) and +[TensorStore](https://github.com/google/tensorstore) (C++) are two independent +Zarr implementations that use architectural patterns we want to learn from. +We see them as complementary rather than competitive. + +!!! note + + Many of the features in this roadmap will not require breaking public 3.x APIs. We can and will + ship those features in 3.x releases; at the same time, we consider it clarifying to frame the + coherent development direction as vectored at a 4.0 milestone. + +## The Zarr stack + +Different applications need different levels of Zarr support: a convention +validator only needs to read metadata documents; a visualization tool may only +need read-only array access; other tools need everything. We think of this as a +"Zarr stack", from most abstract to most concrete: + +1. **Conventions** — application and/or domain-specific schemas built on top of Zarr (OME-NGFF, + GeoZarr, anndata-zarr, multiscales). +2. **Groups** — Zarr hierarchies, traversal, group-level attributes. +3. **Arrays** — the user-facing array object, plus indexing and slicing. +4. **Chunk decoding** — the codec pipeline. +5. **Chunk addressing** — chunk grids and key encodings that map array + coordinates to store keys. +6. **Stores** — the key-value layer. +7. **Metadata** — pure data documents describing arrays and groups. + +Today, Zarr-Python is a monolith that serves every level: a consumer who only +needs metadata handling has to install the full dependency footprint of the +whole library, and a faster chunk-decoding implementation cannot plug in +without re-implementing the layers above it. The v4 direction is to re-shape +Zarr-Python around the stack, so that each level is something you can depend +on, conform to, or replace, without buying every other level. + +We plan to "stackify" Zarr-Python by spinning core functionality out into separate Python packages, e.g. `zarr-metadata`, `zarr-indexing`, `zarr-storage`, +`zarr-codec`, `zarr-dtype`, each with narrow scope, all composed in the `zarr` package. The Rust `zarrs` library +successfully uses a structure like this, and we are keen to share the benefits of a more modular, maintainable codebase. Two of these subpackages, +[`zarr-metadata`](https://zarr.readthedocs.io/projects/zarr-metadata/en/latest/) and [`zarr-indexing`](https://zarr.readthedocs.io/projects/zarr-indexing/en/latest/), are already +published. + +## What we intend to change + +The following section details how we want to evolve the internal logic that drives Zarr-Python. + +### Foundation: swappable backends + +We propose to refactor Zarr-Python internals around a *swappable engine* — a protocol, or protocols, +that define the core routines a Zarr implementation must support. Zarr-Python becomes one user-facing +API that can be driven by multiple backends, including externally defined backends. We think this will allow users on many different platforms to get the best performance for their particular environment while retaining a familiar API. + +#### Rust bindings + +We want a Python backend (i.e., the status quo), but also a Rust-based backend, via bindings to the +[`zarrs`](https://docs.rs/zarrs/latest/zarrs/) crate. The [zarrs-python](https://zarrs-python.readthedocs.io/en/latest/) project demonstrates that +bridging `zarrs` and Zarr-Python buys a *lot* of performance in the specific case of chunk encoding. But zarrs-python is constrained today by limited +modularity in Zarr-Python internals. Refactoring our internals around swappable backends should address this limitation. + +Any Python package that interfaces with `zarrs` will need Pythonic bindings to the Rust library. So we are *very* excited about the [zarrista](https://developmentseed.org/zarrista/latest/) package, which aims to provide complete Python bindings for `zarrs`. + +#### Sync / Async partitioning + +Internally we will branch over two kinds of backends: synchronous and asynchronous. The synchronous backend is suitable for arrays and groups persisted to low-latency storage like in-memory stores or local file systems, where async scheduling is pure friction. The asynchronous backend will use Python's `async` support and will provide concurrent APIs where it helps: for arrays and groups persisted to high-latency storage. + +### Lazy indexing + +The Zarr-Python Array API was initially designed to mirror NumPy, with eager +array indexing syntax. `Array.__getitem__` performs IO eagerly and returns a NumPy array. +That was helpful to the dominant use-case at the time of its creation, but it +means deferred IO and computation currently require an external library +such as Dask. It means there is no built-in support for representing multi-step +reads as a single deferred plan. Further, it means that every chained +selection round-trips to storage independently. + +We can fix this by introducing an API for lazy indexing. Under this model, an array indexing operation +like `array[::2]` desugars to a declarative state like `(array, selection)`. Chained selections like +`array[10:100][::2]` are fused immediately, and we defer actual IO for the time when the result of +indexing is needed. [TensorStore](https://google.github.io/tensorstore/) is an excellent role model +for Zarr-Python here, and we can deliver this functionality without breaking ordinary indexing behavior. +See this [discussion](https://github.com/zarr-developers/zarr-python/discussions/1603) for more +background. + +### Data types + +First-class support for ML-specific dtypes — `bfloat16`, the `float8` +variants, packed `int4`/`uint4` — via +[`ml_dtypes`](https://github.com/jax-ml/ml_dtypes). These data types have specifications written up in `zarr-extensions`, but there's no simple to get them integrated in Zarr-Python today. + +### Device-agnostic IO + +Make Zarr-Python's IO surfaces device-agnostic rather than adding GPU support +as a bolted-on feature: stores and codecs grow APIs for writing into a +caller-provided buffer (`read_into`, `decode_into`), and the `Array` facade +returns array-like objects in the user's chosen Array API namespace. GPU +support falls out once the assumption of CPU destinations is removed, and CPU +paths get faster too, because pre-allocated output buffers eliminate per-chunk +allocation. + +### Configuration, registries, and plugins + +Move configuration from "global mutable state read implicitly" to "typed data +passed explicitly": a typed config object replacing the untyped global `donfig` +dict, array-scoped runtime config passed at open time, a registry redesign that +addresses implementations by stable identity and resolves plugin name-conflicts +deliberately, and named profiles replacing global mutators. + +### Coordinated and distributed writes + +This area is actually an unfinished aspect of the 2.x → 3.0 migration: Zarr-Python 2.x supported +synchronization logic via file-based locks, and we have not implemented equivalent functionality in +3.x. We don't have *concrete* plans for closing this gap. Re-implementing simple object-based locking, for +backends that support it, is a direct solution we should consider. But a transactional storage model, +where a sequence of basic storage operations like reading and writing could be submitted in a batch and +executed serially, with rollbacks under failure, is also quite appealing. +As with array indexing, TensorStore is the trailblazer here, and we can learn from its example. + +We can also avoid the need for synchronization mechanisms entirely with better planning. +Many users of the 2.x synchronization tooling needed to simply write values from one chunked source +to another, without worrying about chunk alignment. This can be addressed e.g. by creating a write +plan that partitions the input chunks into batches within which writes cannot race. + +## How to get involved + +- **Discuss the plans.** Comments and counter-proposals on any of the themes + above are welcome on the + [issue tracker](https://github.com/zarr-developers/zarr-python/issues) and in + the [developer chat](https://ossci.zulipchat.com/). +- **Review in-flight work.** The `IndexTransform` algebra that lazy indexing is + built on is in review at + [#3906](https://github.com/zarr-developers/zarr-python/pull/3906). +- **Weigh in as a downstream maintainer.** If your project's use of + Zarr-Python would be affected by the codec API rewrite, the stores rewrite, + or the lazy-indexing work, the planning phase is the time to surface + workloads or patterns that don't fit. diff --git a/mkdocs.yml b/mkdocs.yml index 1fde8d9fe3..4d06701a87 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -102,6 +102,7 @@ nav: - 'zarr-metadata ↪': https://zarr.readthedocs.io/projects/zarr-metadata/ - 'zarr-indexing ↪': https://zarr.readthedocs.io/projects/zarr-indexing/ - release-notes.md + - roadmap.md - contributing.md - Blog: - blog/index.md @@ -221,7 +222,6 @@ plugins: 'search.html.md': 'index.md' 'tutorial.md': 'user-guide/installation.md' 'getting-started.md': 'quick-start.md' - 'roadmap.md': 'https://zarr.readthedocs.io/en/v3.0.8/developers/roadmap.html' 'installation.md': 'user-guide/installation.md' 'release.md': 'release-notes.md' 'about.html.md': 'index.md' From ce10c0b9ae89aa306a6ba0f4284c40c5488ec5f8 Mon Sep 17 00:00:00 2001 From: Davis Bennett <davis.v.bennett@gmail.com> Date: Mon, 17 Aug 2026 14:41:27 +0200 Subject: [PATCH 465/468] fix: accept universal-pathlib UPath as a StoreLike value (#4265) * chore(deps): bump the actions group across 1 directory with 8 updates (#176) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) | `0.9.5` | `0.9.6` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `6.0.0` | `6.0.1` | | [github/issue-metrics](https://github.com/github/issue-metrics) | `4.2.2` | `4.2.7` | | [j178/prek-action](https://github.com/j178/prek-action) | `2.0.3` | `2.0.4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `7.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | | [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) | `0.5.3` | `0.5.6` | Updates `prefix-dev/setup-pixi` from 0.9.5 to 0.9.6 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0...5185adfbffb4bd703da3010310260805d89ebb11) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) Updates `github/issue-metrics` from 4.2.2 to 4.2.7 - [Release notes](https://github.com/github/issue-metrics/releases) - [Commits](https://github.com/github/issue-metrics/compare/c9e9838147fd355dace335ba787f01b6641a400a...1e38d5e62363e14db8019ed7d106b9855bdba6cc) Updates `j178/prek-action` from 2.0.3 to 2.0.4 - [Release notes](https://github.com/j178/prek-action/releases) - [Commits](https://github.com/j178/prek-action/compare/6ad80277337ad479fe43bd70701c3f7f8aa74db3...bdca6f102f98e2b4c7029491a53dfd366469e33d) Updates `actions/upload-artifact` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v7...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v7...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.13.0...cef221092ed1bacb1cc03d23a2d87d1d172e277b) Updates `zizmorcore/zizmor-action` from 0.5.3 to 0.5.6 - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](https://github.com/zizmorcore/zizmor-action/compare/b1d7e1fb5de872772f31590499237e7cce841e8e...5f14fd08f7cf1cb1609c1e344975f152c7ee938d) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-version: 0.9.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: github/issue-metrics dependency-version: 4.2.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: j178/prek-action dependency-version: 2.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: zizmorcore/zizmor-action dependency-version: 0.5.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix: accept universal-pathlib UPath as a StoreLike value A remote UPath now creates an FsspecStore from the filesystem and storage options the UPath already carries, and a local UPath creates a LocalStore so that UPath("/data") and Path("/data") agree. This previously worked only by accident. In universal-pathlib < 0.3 every UPath subclassed pathlib.Path and implemented __fspath__, so a remote path was either converted to a URI string by the caller (xarray does this) or wrapped in a LocalStore that happened to dispatch through fsspec. Since universal-pathlib 0.3 remote paths do neither, and passing one raised TypeError: Unsupported type for store_like. The UPath branch is checked before the Path branch so that routing is identical on both universal-pathlib 0.2 and 0.3. FsspecStore.from_upath now converts the UPath's filesystem to async mode instead of raising TypeError for synchronous filesystems and warning for sync-mode instances of async ones. The memory:// routing test wraps a synchronous MemoryFileSystem, which needs fsspec's AsyncFileSystemWrapper, so it is skipped below fsspec 2024.12.0 as test_wrap_sync_filesystem already does. Closes #4244 Assisted-by: ClaudeCode:claude-fable-5 * fix: correct changelog number and pin the local root in the UPath test The changelog fragment was named for 4245, which towncrier renders as a link to an unrelated issue ("Link Checker Report"). Rename it to the PR number. test_make_store_upath only asserted the store type, so a mangled local path would still produce a LocalStore and pass. Assert the root as well. Silence PLC0414 on the UPath re-export: the alias looks redundant but is the explicit re-export mypy requires under strict mode, and ruff 0.16.0 enables the rule by default. Assisted-by: ClaudeCode:claude-opus-4.8 * docs: don't promise a storage_options error the example doesn't show The sentence ended in a colon introducing an example of passing storage_options alongside a UPath, but the snippet shows the working case and never passes storage_options. Worse, the `anon=True` on the UPath sits right after the sentence and reads as the thing being called out, when it is the recommended way to supply the option. State the rule as prose and let the example just show normal usage. Assisted-by: ClaudeCode:claude-opus-4.8 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- changes/4265.bugfix.md | 13 +++++++++ docs/user-guide/storage.md | 10 +++++++ src/zarr/storage/_common.py | 16 +++++++++-- src/zarr/storage/_fsspec.py | 6 ++++- src/zarr/storage/_utils.py | 4 ++- tests/test_store/test_core.py | 47 +++++++++++++++++++++++++++++++++ tests/test_store/test_fsspec.py | 42 +++++++++++++++++++++++++++++ 7 files changed, 134 insertions(+), 4 deletions(-) create mode 100644 changes/4265.bugfix.md diff --git a/changes/4265.bugfix.md b/changes/4265.bugfix.md new file mode 100644 index 0000000000..6daf0fc7d0 --- /dev/null +++ b/changes/4265.bugfix.md @@ -0,0 +1,13 @@ +Accept [universal-pathlib](https://github.com/fsspec/universal_pathlib) `UPath` objects wherever +zarr accepts a `StoreLike` value. A remote `UPath` now creates an `FsspecStore` using the +filesystem and storage options the `UPath` already carries, and a local `UPath` creates a +`LocalStore`, so that `UPath('/data')` and `Path('/data')` behave the same. + +Previously this worked only by accident: in universal-pathlib < 0.3 every `UPath` subclassed +`pathlib.Path` and implemented `__fspath__`, so remote paths were either converted to a URI string +by the caller or wrapped in a `LocalStore` that happened to dispatch through fsspec. Since +universal-pathlib 0.3 remote paths do neither, and passing one raised +`TypeError: Unsupported type for store_like`. + +`FsspecStore.from_upath` also now converts the `UPath`'s filesystem to async mode, instead of +raising `TypeError` for synchronous filesystems and warning for sync-mode instances of async ones. diff --git a/docs/user-guide/storage.md b/docs/user-guide/storage.md index b288c9976d..a34e2e2874 100644 --- a/docs/user-guide/storage.md +++ b/docs/user-guide/storage.md @@ -90,6 +90,16 @@ print(group) - an FSSpec [FSMap object](https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.FSMap), which will create an [FsspecStore](#remote-store). +- a [universal-pathlib](https://github.com/fsspec/universal_pathlib) `UPath`, which will create an + [FsspecStore](#remote-store), or a [local store](#local-store) if the `UPath` is local. Put your + storage options on the `UPath` itself; passing a separate `storage_options` argument alongside + one raises `TypeError`. + + ```python exec="false" reason="requires universal-pathlib, which is not in the docs environment" + from upath import UPath + group = zarr.open_group(UPath('s3://noaa-nwm-retro-v2-zarr-pds', anon=True), mode='r') + ``` + - a [`Store`][zarr.abc.store.Store] or [`StorePath`][zarr.storage.StorePath] - see explicit store creation below. diff --git a/src/zarr/storage/_common.py b/src/zarr/storage/_common.py index 64dc486e01..72b5fc8a40 100644 --- a/src/zarr/storage/_common.py +++ b/src/zarr/storage/_common.py @@ -24,7 +24,7 @@ from zarr.errors import ContainsArrayAndGroupError, ContainsArrayError, ContainsGroupError from zarr.storage._local import LocalStore from zarr.storage._memory import ManagedMemoryStore, MemoryStore -from zarr.storage._utils import _join_paths, normalize_path, parse_store_url +from zarr.storage._utils import UPath, _join_paths, normalize_path, parse_store_url _has_fsspec = importlib.util.find_spec("fsspec") if _has_fsspec: @@ -301,7 +301,7 @@ def __eq__(self, other: object) -> bool: return False -type StoreLike = Store | StorePath | FSMap | Path | str | dict[str, Buffer] +type StoreLike = Store | StorePath | FSMap | Path | UPath | str | dict[str, Buffer] async def make_store( @@ -321,6 +321,7 @@ async def make_store( - `dict[str, Buffer]` = `MemoryStore` object. - `None` = `MemoryStore` object. - `FSMap` = `FsspecStore` object. + - `UPath` = `FsspecStore` object, or `LocalStore` for a local `UPath`. Parameters ---------- @@ -381,6 +382,17 @@ async def make_store( # Create a new in-memory store return await make_store({}, mode=mode, storage_options=storage_options) + elif isinstance(store_like, UPath): + # This must be checked before Path: in universal-pathlib < 0.3 every UPath, including + # remote ones like S3Path, subclasses pathlib.Path, and would otherwise be misrouted to a + # LocalStore. Local UPaths get a LocalStore so that UPath("/data") and Path("/data") agree, + # mirroring how the equivalent strings are routed below. + if store_like.protocol in ("", "file"): + return await make_store( + Path(store_like.path), mode=mode, storage_options=storage_options + ) + return FsspecStore.from_upath(store_like, read_only=_read_only) + elif isinstance(store_like, Path): # Create a new LocalStore return await LocalStore.open(root=store_like, mode=mode, read_only=_read_only) diff --git a/src/zarr/storage/_fsspec.py b/src/zarr/storage/_fsspec.py index b109f80935..a212e95f2f 100644 --- a/src/zarr/storage/_fsspec.py +++ b/src/zarr/storage/_fsspec.py @@ -171,8 +171,12 @@ def from_upath( ------- FsspecStore """ + # A UPath hands back a filesystem in whatever mode it was constructed with, which is + # synchronous unless the caller passed asynchronous=True. Route it through _make_async so + # that sync-mode instances of async filesystems are re-created in async mode, and + # genuinely synchronous filesystems are wrapped. return cls( - fs=upath.fs, + fs=_make_async(upath.fs), path=upath.path.rstrip("/"), read_only=read_only, allowed_exceptions=allowed_exceptions, diff --git a/src/zarr/storage/_utils.py b/src/zarr/storage/_utils.py index b100f862cf..ca10b0679e 100644 --- a/src/zarr/storage/_utils.py +++ b/src/zarr/storage/_utils.py @@ -6,7 +6,9 @@ from urllib.parse import urlparse if importlib.util.find_spec("upath"): - from upath.core import UPath + # Re-exported for zarr.storage._common, which needs it to recognize UPath store_like values. + # The redundant-looking alias is the explicit re-export mypy requires under strict mode. + from upath.core import UPath as UPath # noqa: PLC0414 else: class UPath: # type: ignore[no-redef] diff --git a/tests/test_store/test_core.py b/tests/test_store/test_core.py index 4138eebe6a..7ba4344810 100644 --- a/tests/test_store/test_core.py +++ b/tests/test_store/test_core.py @@ -4,9 +4,11 @@ from typing import Any, Literal import pytest +from packaging.version import parse as parse_version import zarr from zarr import Group +from zarr.abc.store import Store from zarr.core.buffer import cpu from zarr.core.common import ZARR_JSON, AccessModeLiteral, ZarrFormat from zarr.storage import FsspecStore, LocalStore, MemoryStore, StoreLike, StorePath, ZipStore @@ -14,6 +16,7 @@ _contains_node_v3, contains_array, contains_group, + make_store, make_store_path, ) from zarr.storage._utils import ( @@ -248,6 +251,50 @@ async def test_make_store_path_storage_options_raises(store_like: StoreLike) -> await make_store_path(store_like, storage_options={"foo": "bar"}) +# universal-pathlib 0.2.x emits this from its own subclass registry when a local UPath is built. +@pytest.mark.filterwarnings( + "ignore:Detected a customized `__new__` method in subclass:DeprecationWarning" +) +@pytest.mark.parametrize( + ("url", "expected"), + [ + ("memory://bucket/foo.zarr", FsspecStore), + ("s3://bucket/foo.zarr", FsspecStore), + ("file://{tmp}/foo.zarr", LocalStore), + ("{tmp}/foo.zarr", LocalStore), + ], +) +async def test_make_store_upath(url: str, expected: type[Store], tmp_path: Path) -> None: + """ + A remote UPath becomes an FsspecStore, and a local one becomes a LocalStore, so that + UPath("/data") and Path("/data") agree. See https://github.com/zarr-developers/zarr-python/issues/4244. + """ + upath = pytest.importorskip("upath") + fsspec = pytest.importorskip("fsspec") + if url.startswith("s3://"): + pytest.importorskip("s3fs") + if url.startswith("memory://") and parse_version(fsspec.__version__) < parse_version( + "2024.12.0" + ): + # MemoryFileSystem is synchronous, so it can only be used once fsspec is new enough to + # supply AsyncFileSystemWrapper. + pytest.skip("No AsyncFileSystemWrapper") + store = await make_store(upath.UPath(url.format(tmp=tmp_path))) + assert isinstance(store, expected) + if isinstance(store, LocalStore): + # The local branch rebuilds the root from the UPath, so a mangled path would still + # produce a LocalStore. Pin the root down too, since "file://{tmp}" has no leading + # slash on Windows. + assert store.root == tmp_path / "foo.zarr" + + +async def test_make_store_upath_storage_options_raises() -> None: + """A UPath carries its own storage options, so a separate mapping is ambiguous.""" + upath = pytest.importorskip("upath") + with pytest.raises(TypeError, match="storage_options"): + await make_store(upath.UPath("memory://bucket/foo.zarr"), storage_options={"foo": "bar"}) + + async def test_unsupported() -> None: with pytest.raises(TypeError, match="Unsupported type for store_like: 'int'"): await make_store_path(1) diff --git a/tests/test_store/test_fsspec.py b/tests/test_store/test_fsspec.py index c367b908c5..bb03970d5b 100644 --- a/tests/test_store/test_fsspec.py +++ b/tests/test_store/test_fsspec.py @@ -2,6 +2,7 @@ import json import re +import warnings from typing import TYPE_CHECKING, Any import numpy as np @@ -249,6 +250,47 @@ def test_from_upath(self, endpoint_url: str) -> None: assert result.fs.asynchronous assert result.path == f"{test_bucket_name}/foo/bar" + @pytest.mark.skipif( + parse_version(fsspec.__version__) < parse_version("2024.03.01"), + reason="Prior bug in from_upath", + ) + def test_from_upath_sync_filesystem(self, endpoint_url: str) -> None: + """ + A UPath built without ``asynchronous=True`` -- the common case -- yields an async-mode + filesystem that keeps the original storage options. + """ + upath = pytest.importorskip("upath") + path = upath.UPath( + f"s3://{test_bucket_name}/foo/bar/", + endpoint_url=endpoint_url, + anon=False, + ) + assert not path.fs.asynchronous + with warnings.catch_warnings(): + warnings.simplefilter("error", ZarrUserWarning) + result = FsspecStore.from_upath(path) + assert result.fs.asynchronous + assert result.fs.endpoint_url == endpoint_url + assert result.path == f"{test_bucket_name}/foo/bar" + + async def test_open_group_from_upath(self, endpoint_url: str) -> None: + """ + Passing a remote UPath to the top-level API works. + + Regression test for https://github.com/zarr-developers/zarr-python/issues/4244. + """ + upath = pytest.importorskip("upath") + path = upath.UPath( + f"s3://{test_bucket_name}/upath-group", + endpoint_url=endpoint_url, + anon=False, + ) + group = await zarr.api.asynchronous.open_group(path, mode="w", attributes={"key": "value"}) + assert isinstance(group.store_path.store, FsspecStore) + + reopened = await zarr.api.asynchronous.open_group(path, mode="r") + assert dict(reopened.attrs) == {"key": "value"} + def test_init_warns_if_fs_asynchronous_is_false(self, endpoint_url: str) -> None: try: from fsspec import url_to_fs From 20ba31e3e1142fae83b178d6e0a29538c2b18725 Mon Sep 17 00:00:00 2001 From: glaziermag <130600081+glaziermag@users.noreply.github.com> Date: Thu, 20 Aug 2026 00:46:24 -0700 Subject: [PATCH 466/468] fix: make the nightly hypothesis failure alarm able to file issues (#4274) Co-authored-by: glaziermag <glaziermag@users.noreply.github.com> --- .github/workflows/hypothesis.yaml | 6 +++++- pyproject.toml | 1 + 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml index dd49578dd0..f463397c85 100644 --- a/.github/workflows/hypothesis.yaml +++ b/.github/workflows/hypothesis.yaml @@ -25,6 +25,9 @@ jobs: hypothesis: name: Slow Hypothesis Tests + permissions: + contents: read + issues: write environment: name: codecov-upload deployment: false @@ -83,6 +86,7 @@ jobs: id: status env: HATCH_ENV: test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} + PYTEST_ADDOPTS: "--report-log=output-${{ matrix.python-version }}-log.jsonl" run: | echo "Using Hypothesis profile: $HYPOTHESIS_PROFILE" hatch env run --env "$HATCH_ENV" run-hypothesis @@ -113,4 +117,4 @@ jobs: with: log-path: output-${{ matrix.python-version }}-log.jsonl issue-title: "Nightly Hypothesis tests failed" - issue-label: "topic-hypothesis" + issue-label: "automated issue" diff --git a/pyproject.toml b/pyproject.toml index dca663277e..ebe12bbb91 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -114,6 +114,7 @@ test = [ "pytest-accept==0.3.0", "numpydoc==1.10.0", "hypothesis==6.165.2", + "pytest-reportlog==0.4.0", "pytest-xdist==3.8.0", "pytest-benchmark==5.2.3", "pytest-codspeed==5.0.3", From bf8f8632f146449b12e0ea7e40576f8dbbde6fa1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 21 Aug 2026 10:55:20 +0200 Subject: [PATCH 467/468] chore(deps): bump the python-dependencies group across 1 directory with 7 updates (#4278) Bumps the python-dependencies group with 7 updates in the / directory: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.5.1` | `2.5.2` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.15.3` | `7.15.4` | | [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.165.2` | `6.165.5` | | [pytest-reportlog](https://github.com/pytest-dev/pytest-reportlog) | `0.4.0` | `1.0.0` | | [uv](https://github.com/astral-sh/uv) | `0.12.2` | `0.12.3` | | [ruff](https://github.com/astral-sh/ruff) | `0.16.1` | `0.16.2` | | [astroid](https://github.com/pylint-dev/astroid) | `4.1.2` | `4.3.0` | Updates `numpy` from 2.5.1 to 2.5.2 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.5.1...v2.5.2) Updates `coverage` from 7.15.3 to 7.15.4 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](https://github.com/coveragepy/coveragepy/compare/7.15.3...7.15.4) Updates `hypothesis` from 6.165.2 to 6.165.5 - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/v6.165.2...v6.165.5) Updates `pytest-reportlog` from 0.4.0 to 1.0.0 - [Release notes](https://github.com/pytest-dev/pytest-reportlog/releases) - [Changelog](https://github.com/pytest-dev/pytest-reportlog/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-reportlog/compare/v0.4.0...v1.0.0) Updates `uv` from 0.12.2 to 0.12.3 - [Release notes](https://github.com/astral-sh/uv/releases) - [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/uv/compare/0.12.2...0.12.3) Updates `ruff` from 0.16.1 to 0.16.2 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.16.1...0.16.2) Updates `astroid` from 4.1.2 to 4.3.0 - [Release notes](https://github.com/pylint-dev/astroid/releases) - [Changelog](https://github.com/pylint-dev/astroid/blob/main/ChangeLog) - [Commits](https://github.com/pylint-dev/astroid/compare/v4.1.2...v4.3.0) --- updated-dependencies: - dependency-name: numpy dependency-version: 2.5.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: coverage dependency-version: 7.15.4 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: hypothesis dependency-version: 6.165.5 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: pytest-reportlog dependency-version: 1.0.0 dependency-type: direct:development update-type: version-update:semver-major dependency-group: python-dependencies - dependency-name: uv dependency-version: 0.12.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.16.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: astroid dependency-version: 4.3.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- pyproject.toml | 12 +- uv.lock | 502 ++++++++++++++++++++++++++++--------------------- 2 files changed, 292 insertions(+), 222 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ebe12bbb91..4cfe02b0e3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -107,19 +107,19 @@ homepage = "https://github.com/zarr-developers/zarr-python" # pins deliberately, e.g. via dependabot or `uv lock --upgrade`. [dependency-groups] test = [ - "coverage==7.15.3", + "coverage==7.15.4", "pytest==9.1.1", "pytest-asyncio==1.4.0", "pytest-cov==7.1.0", "pytest-accept==0.3.0", "numpydoc==1.10.0", - "hypothesis==6.165.2", - "pytest-reportlog==0.4.0", + "hypothesis==6.165.5", + "pytest-reportlog==1.0.0", "pytest-xdist==3.8.0", "pytest-benchmark==5.2.3", "pytest-codspeed==5.0.3", "tomlkit==0.15.1", - "uv==0.12.2", + "uv==0.12.3", ] remote-tests = [ {include-group = "test"}, @@ -143,13 +143,13 @@ docs = [ "mkdocs-redirects==1.2.3", "markdown-exec[ansi]==1.12.3", "griffe-inherited-docstrings==1.1.3", - "ruff==0.16.1", + "ruff==0.16.2", # Changelog generation {include-group = "release"}, # Optional dependencies to run examples "numcodecs[msgpack]", "s3fs>=2023.10.0", - "astroid==4.1.2", + "astroid==4.3.0", "pytest==9.1.1", ] dev = [ diff --git a/uv.lock b/uv.lock index 05a746af06..327d3e0822 100644 --- a/uv.lock +++ b/uv.lock @@ -243,11 +243,11 @@ wheels = [ [[package]] name = "astroid" -version = "4.1.2" 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name = "requests" }, { name = "s3fs" }, @@ -3575,6 +3641,7 @@ test = [ { name = "pytest-benchmark" }, { name = "pytest-codspeed" }, { name = "pytest-cov" }, + { name = "pytest-reportlog" }, { name = "pytest-xdist" }, { name = "tomlkit" }, { name = "uv" }, @@ -3600,12 +3667,12 @@ provides-extras = ["cast-value-rs", "cli", "gpu", "optional", "remote"] [package.metadata.requires-dev] dev = [ - { name = "astroid", specifier = "==4.1.2" }, + { name = "astroid", specifier = "==4.3.0" }, { name = "botocore" }, - { name = "coverage", specifier = "==7.15.3" }, + { name = "coverage", specifier = "==7.15.4" }, { name = "fsspec", specifier = ">=2023.10.0" }, { name = "griffe-inherited-docstrings", specifier = "==1.1.3" }, - { name = "hypothesis", specifier = "==6.165.2" }, + { name = "hypothesis", specifier = "==6.165.5" }, { name = "markdown-exec", extras = ["ansi"], specifier = "==1.12.3" }, { name = "mike", specifier = "==2.2.0" }, { name = "mkdocs", specifier = "==1.6.1" }, @@ -3624,17 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specifier = "==3.8.0" }, { name = "tomlkit", specifier = "==0.15.1" }, - { name = "uv", specifier = "==0.12.2" }, + { name = "uv", specifier = "==0.12.3" }, ] From d44f9f92ab4f12a8008de2553a7c9988669e3910 Mon Sep 17 00:00:00 2001 From: Dylan Pulver <35541198+dylanpulver@users.noreply.github.com> Date: Sat, 22 Aug 2026 15:07:00 +0300 Subject: [PATCH 468/468] fix: reject a string-valued zero scale in the scale_offset codec (#4279) ScaleOffset.validate compared self.scale against 0 before parsing it. scale is documented and typed as int | float | str, and no string is ever == 0, so "0", "0.0" and the spec's hex form walked past the guard. On float dtypes that wrote every chunk as zero and read it back as NaN with no error; on integer dtypes it surfaced as an unhandled ZeroDivisionError. Compare the parsed scalar instead. Co-authored-by: Dylan Pulver <dylanpulver@users.noreply.github.com> --- changes/4279.bugfix.md | 1 + src/zarr/codecs/scale_offset.py | 9 ++++++--- tests/test_codecs/test_scale_offset.py | 23 +++++++++++++++++++---- 3 files changed, 26 insertions(+), 7 deletions(-) create mode 100644 changes/4279.bugfix.md diff --git a/changes/4279.bugfix.md b/changes/4279.bugfix.md new file mode 100644 index 0000000000..7d99a49ccf --- /dev/null +++ b/changes/4279.bugfix.md @@ -0,0 +1 @@ +A `scale_offset` codec configured with a string-valued zero scale is now rejected. `scale` accepts strings, and no string is ever equal to `0`, so `"0"`, `"0.0"` and the hex form `"0x0000000000000000"` skipped the "scale must be non-zero" check that the numeric `0` triggers. On float data types the array was created, every chunk was written as zero and read back as `nan` with no error, and the zero scale was persisted to the metadata so reopening the store reproduced it; on integer data types the codec raised `ZeroDivisionError` instead of `ValueError`. The check now runs on the parsed scalar rather than the value as supplied. diff --git a/src/zarr/codecs/scale_offset.py b/src/zarr/codecs/scale_offset.py index c96e177c6b..f2908da1b6 100644 --- a/src/zarr/codecs/scale_offset.py +++ b/src/zarr/codecs/scale_offset.py @@ -355,15 +355,18 @@ def validate( f"scale_offset codec only supports integer and floating-point data types. " f"Got {dtype}." ) - if self.scale == 0: - raise ValueError("scale_offset scale must be non-zero.") + parsed: dict[str, Any] = {} for name, value in [("offset", self.offset), ("scale", self.scale)]: try: - dtype.from_json_scalar(value, zarr_format=3) + parsed[name] = dtype.from_json_scalar(value, zarr_format=3) except (TypeError, ValueError, OverflowError) as e: raise ValueError( f"scale_offset {name} value {value!r} is not representable in dtype {native}." ) from e + # ``scale`` may be given as a string, and no string is ever ``== 0``, so this has to + # compare the parsed scalar rather than the value as supplied. + if parsed["scale"] == 0: + raise ValueError("scale_offset scale must be non-zero.") def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec: zdtype = chunk_spec.dtype diff --git a/tests/test_codecs/test_scale_offset.py b/tests/test_codecs/test_scale_offset.py index 513caf463a..0081bb1901 100644 --- a/tests/test_codecs/test_scale_offset.py +++ b/tests/test_codecs/test_scale_offset.py @@ -249,16 +249,31 @@ def test_uint64_encode_rejects_underflow() -> None: arr[:] = np.array([100, 50, 200], dtype="uint64") -def test_rejects_zero_scale() -> None: - """scale=0 is rejected (destroys data and breaks decode division).""" +@pytest.mark.parametrize( + ("dtype", "scale"), + [ + ("int32", 0), + ("int32", "0"), + ("float64", 0.0), + ("float64", "0.0"), + ("float64", "0x0000000000000000"), + ], + ids=["int-numeric", "int-string", "float-numeric", "float-string", "float-hex"], +) +def test_rejects_zero_scale(dtype: str, scale: object) -> None: + """scale=0 is rejected (destroys data and breaks decode division). + + A string ``scale`` is a documented input, so every spelling of zero has to be + rejected the same way as the numeric one. + """ with pytest.raises(ValueError, match="scale must be non-zero"): zarr.create_array( store={}, shape=(10,), - dtype="int32", + dtype=dtype, chunks=(10,), - filters=[ScaleOffset(offset=0, scale=0)], + filters=[ScaleOffset(offset=0, scale=scale)], compressors=None, fill_value=0, )