BUG: close duplicated file descriptor if fdopen fails - #32386
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| monkeypatch.setattr(os, "dup", dup) | ||
| assert_raises(exc, np.fromfile, f) | ||
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| def test_fromfile_failed_fdopen_closes_dup( |
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wasm and musl don't validate the file descriptor, so this test will fail there:
https://github.com/numpy/numpy/actions/runs/32527587113/job/97469436653?pr=32386#step:8:3325
The other CI failures are unrelated and will be fixed by #32407.
Suggested change
| def test_fromfile_failed_fdopen_closes_dup( | |
| @pytest.mark.skipif(IS_WASM or IS_MUSL, | |
| reason="musl and emscripten libc fdopen do not validate the fd") | |
| def test_fromfile_failed_fdopen_closes_dup( |
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Thanks, added the WASM/musl skip and rebased onto current main, which includes #32407. The full test module and fresh CircleCI run pass.
ngoldbaum
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| ret = PyObject_CallMethod(os, "close", "i", fd2); | ||
| Py_XDECREF(ret); | ||
| Py_DECREF(os); |
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ret = PyObject_CallMethod(os, "close", "i", fd2);
Py_DECREF(os);
if (ret == NULL) {
PyErr_WriteUnraisable(NULL);
}
Py_XDECREF(ret);
PyErr_SetString(PyExc_IOError,
"Getting a FILE* from a Python file object via "
"_fdopen failed. If you built NumPy, you probably "
"linked with the wrong debug/release runtime");
return NULL;
The PyObject_CallMethod call could fail. Since you're trying to raise an exception anyway, I don't think there's a good way to handle that, so better to make that explicit instead of overwriting an active exception.
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Agreed, I now report a failed os.close call with PyErr_WriteUnraisable before setting the intended OSError. I also exercised this failure path locally.
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Both review suggestions are addressed in bb1d945, and the fresh CircleCI run is green. Could you please take another look when convenient? |
ngoldbaum
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Thanks @sgoel2be24-cyber! |
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Co-authored-by: Shikhar Goel <223222024+sgoel2be24-cyber@users.noreply.github.com>
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BUG: close duplicated file descriptor if fdopen fails (#32386)
736-c41-2c1-e464fc974
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This MR contains the following updates: | Package | Type | Update | Change | OpenSSF | |---|---|---|---|---| | [numpy](https://github.com/numpy/numpy) ([changelog](https://numpy.org/doc/stable/release)) | dependencies | patch | `2.5.2` → `2.5.3` | [](https://securityscorecards.dev/viewer/?uri=github.com/numpy/numpy) | | [openai](https://github.com/openai/openai-python) | dependencies | patch | `2.52.0` → `2.52.1` | [](https://securityscorecards.dev/viewer/?uri=github.com/openai/openai-python) | | [pydantic](https://github.com/pydantic/pydantic) ([changelog](https://docs.pydantic.dev/latest/changelog/)) | dependencies | patch | `2.13.4` → `2.13.5` | [](https://securityscorecards.dev/viewer/?uri=github.com/pydantic/pydantic) | | [pydantic-ai](https://github.com/pydantic/pydantic-ai) ([changelog](https://github.com/pydantic/pydantic-ai/releases)) | dependencies | patch | `2.27.0` → `2.27.1` | [](https://securityscorecards.dev/viewer/?uri=github.com/pydantic/pydantic-ai) | | [types-requests](https://github.com/python/typeshed) ([changelog](https://github.com/typeshed-internal/stub_uploader/blob/main/data/changelogs/requests.md)) | dependencies | patch | `2.33.0.20260712` → `2.33.0.20260906` | [](https://securityscorecards.dev/viewer/?uri=github.com/python/typeshed) | | [uvicorn](https://github.com/Kludex/uvicorn) ([changelog](https://uvicorn.dev/release-notes)) | dependencies | patch | `0.52.3` → `0.52.4` | [](https://securityscorecards.dev/viewer/?uri=github.com/Kludex/uvicorn) | --- ### Release Notes <details> <summary>numpy/numpy (numpy)</summary> ### [`v2.5.3`](https://github.com/numpy/numpy/releases/tag/v2.5.3): (Sep 6, 2026) [Compare Source](numpy/numpy@v2.5.2...v2.5.3) ### NumPy 2.5.3 Release Notes The NumPy 2.5.3 is a patch release that fixes bugs discovered after the 2.5.2 release. Apart from the usual bug and maintenance work, there are a number of StringDType related fixes for problems discovered during the ongoing string work in the main branch. This release supports Python versions 3.12-3.15 #### Changes - Casting a fixed-width byte string array (`np.bytes_`) to `StringDType` now raises `TypeError` when the bytes are not valid UTF-8. Previously the invalid bytes were stored as-is and later caused undefined behavior in string operations. ([gh-32296](numpy/numpy#32296)) - `MaskedArray._fill_value` would become stale when ufuncs that change dtype left the result holding a fill\_value typed for the old dtype. The mismatch was silent until something later called `_check_fill_value`, such as `.view()`, and then a `TypeError` would be raised. Now, when the copied fill\_value is no longer valid for the new dtype, fall back to the default fill\_value for that dtype instead of propagating the stale value. This may raise a `ComplexWarning` if the fill\_value is complex and the new dtype is real. ([gh-32423](numpy/numpy#32423)) #### Contributors A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Charles Harris - Iason Krommydas - James Davies + - Joren Hammudoglu - Maanas Arora - Matti Picus - Nathan Goldbaum - Shikhar Goel + - Yeonho Kim + #### Pull requests merged A total of 27 pull requests were merged for this release. - [#​32235](numpy/numpy#32235): MAINT: Prepare 2.5.x for further development - [#​32289](numpy/numpy#32289): BUG: raise ValueError when reading into record array with references... - [#​32290](numpy/numpy#32290): BUG: avoid uninitialized memory access / NULL-pointer deref in... - [#​32291](numpy/numpy#32291): TYP: fix `np.random.{get,set}_bit_generator` implicit re-exports... - [#​32292](numpy/numpy#32292): BUG: don't assume strides are a multiple of itemsize in stringdtype... - [#​32293](numpy/numpy#32293): CI: fix ccache CC override, add CXX in mac Conda CI ([#​32285](numpy/numpy#32285)) - [#​32303](numpy/numpy#32303): BUG: Fix ref leak in \[convert\_from\_type]{#convert\_from\_type} for custom scalar types... - [#​32304](numpy/numpy#32304): BUG: fix a number of issues around iterators and StringDType... - [#​32326](numpy/numpy#32326): TST: avoid allocating huge tuple of arrays in concatenate test... - [#​32338](numpy/numpy#32338): BUG: avoid possible UB in 'safe' multiplication helpers ([#​32294](numpy/numpy#32294)) - [#​32339](numpy/numpy#32339): MAINT: use `PyObject_` functions instead of raw `PyArray_ ones` ([#​32331](numpy/numpy#32331)) - [#​32378](numpy/numpy#32378): BUG: validate UTF-8 and harden StringDType bounds handling ([#​32296](numpy/numpy#32296)) - [#​32380](numpy/numpy#32380): BUG: fix two error handling mistakes in stringdtype replace loop... - [#​32381](numpy/numpy#32381): BUG: fix visibility annotations for functions in StringDType... - [#​32384](numpy/numpy#32384): MAINT: Update ml\_dtypes pin to 8/21/2026. - [#​32385](numpy/numpy#32385): MAINT: Update numpy/\_core/src/umath/svml - [#​32410](numpy/numpy#32410): MAINT: skip failing cython limited API tests on Cython 3.3.0... - [#​32427](numpy/numpy#32427): BUG: close duplicated file descriptor if fdopen fails ([#​32386](numpy/numpy#32386)) - [#​32428](numpy/numpy#32428): MAINT: add missing space in warning and error messages ([#​32405](numpy/numpy#32405)) - [#​32430](numpy/numpy#32430): BUG: fix error handling in StringDType to fixed-width bytes case... - [#​32441](numpy/numpy#32441): MAINT: Only run nightly BLAS tests on main. - [#​32471](numpy/numpy#32471): BUG: fix memory leak in StringDType creation error path ([#​32470](numpy/numpy#32470)) - [#​32477](numpy/numpy#32477): BUG: fix stale fill\_value after ufuncs change MaskedArray dtype... - [#​32478](numpy/numpy#32478): MAINT: exit deadlock tests quickly on slow hardware ([#​32466](numpy/numpy#32466)) - [#​32481](numpy/numpy#32481): BUG: Backport StringDType byteorder fixes - [#​32506](numpy/numpy#32506): DOC: use static scipy doc site for intershpinx ([#​32503](numpy/numpy#32503)) - [#​32509](numpy/numpy#32509): BUG: fix crash in ufunc.resolve\_dtypes with a Python scalar type... </details> <details> <summary>openai/openai-python (openai)</summary> ### [`v2.52.1`](https://github.com/openai/openai-python/blob/HEAD/CHANGELOG.md#2521-2026-07-31) [Compare Source](openai/openai-python@v2.52.0...v2.52.1) Full Changelog: [v2.52.0...v2.52.1](openai/openai-python@v2.52.0...v2.52.1) ##### Chores - **ci:** pin setup-uv v5 to its underlying commit ([#​3560](openai/openai-python#3560)) ([cbdc98b](openai/openai-python@cbdc98b)) </details> <details> <summary>pydantic/pydantic (pydantic)</summary> ### [`v2.13.5`](https://github.com/pydantic/pydantic/releases/tag/v2.13.5) [Compare Source](pydantic/pydantic@v2.13.4...v2.13.5) #### v2.13.5 (2026-08-28) ##### What's Changed ##### Fixes - Allow reuse of validators when plugins are set by [@​Viicos](https://github.com/Viicos) in [#​13535](pydantic/pydantic#13535) - Fix missing GC traversal on some `pydantic-core` struct fields by [@​Viicos](https://github.com/Viicos) in [#​13624](pydantic/pydantic#13624) - Fix missing GC traversal in `pydantic-core` for `GeneralFieldsSerializer` by [@​Viicos](https://github.com/Viicos) in [#​13629](pydantic/pydantic#13629) - Count validated model fields once in smart unions by [@​tamird](https://github.com/tamird) in [#​13731](pydantic/pydantic#13731) </details> <details> <summary>pydantic/pydantic-ai (pydantic-ai)</summary> ### [`v2.27.1`](https://github.com/pydantic/pydantic-ai/releases/tag/v2.27.1): (2026-08-10) [Compare Source](pydantic/pydantic-ai@v2.27.0...v2.27.1) ##### 🛡️ Security This release fixed an information-disclosure issue: retry-prompt content (validation feedback sent back to the model, which can quote invalid values from its output) was not redacted by `InstrumentationSettings(include_content=False)` when the retry was not tied to a tool call. Now disclosed as [GHSA-3gh4-cghq-f8v4](GHSA-3gh4-cghq-f8v4) (low). Fixed here in `2.27.1` ([#​7357](pydantic/pydantic-ai#7357)); v1 users should upgrade to `1.107.4` or later. <!-- Release notes generated using configuration in .github/release.yml at main --> #### What's Changed ##### 🐛 Bug Fixes - Restore tool spans for failed argument validation by [@​adtyavrdhn](https://github.com/adtyavrdhn) in [#​6601](pydantic/pydantic-ai#6601) - Fix `XaiStreamedResponse` finish\_reason mapping for streaming responses by [@​pydanty](https://github.com/pydanty)\[bot] in [#​6814](pydantic/pydantic-ai#6814) - Point offline web UI hosting at the self-contained chat UI build by [@​dsfaccini](https://github.com/dsfaccini) in [#​7349](pydantic/pydantic-ai#7349) - Allow adaptive thinking with Tool Output and forced tool choice on Anthropic by [@​pydanty](https://github.com/pydanty)\[bot] in [#​7200](pydantic/pydantic-ai#7200) - Gate `RetryPromptPart` OpenTelemetry content on `include_content` by [@​sean-kim05](https://github.com/sean-kim05) in [#​7357](pydantic/pydantic-ai#7357) **Full Changelog**: <pydantic/pydantic-ai@v2.27.0...v2.27.1> </details> <details> <summary>Kludex/uvicorn (uvicorn)</summary> ### [`v0.52.4`](https://github.com/Kludex/uvicorn/releases/tag/0.52.4): Version 0.52.4 [Compare Source](Kludex/uvicorn@0.52.3...0.52.4) ##### Fixed - Remove duplicate `Date` headers from accepted WebSocket handshakes with `websockets-sansio` ([#​3078](Kludex/uvicorn#3078)) **Full Changelog**: <Kludex/uvicorn@0.52.3...0.52.4> </details> --- - [ ] <!-- rebase-check -->If you want to rebase/retry this MR, check this box --- This MR has been generated by [Mend Renovate CLI](https://github.com/renovatebot/renovate). <!--renovate-debug:eyJjcmVhdGVkSW5WZXIiOiI0NC4zOS4yIiwidXBkYXRlZEluVmVyIjoiNDQuOTAuMiIsInRhcmdldEJyYW5jaCI6Im1haW4iLCJsYWJlbHMiOlsiZGVwZW5kZW5jaWVzIiwicmVub3ZhdGUiXX0=--> See merge request swiss-armed-forces/cyber-command/cea/loom!769 Co-authored-by: Loom MR Pipeline Trigger <group_103951964_bot_9504bb8dead6d4e406ad817a607f24be@noreply.gitlab.com> Co-authored-by: shrewd-laidback palace <shrewd-laidback-palace-736-c41-2c1-e464fc974@swiss-armed-forces-open-source.ch>
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Fixes #32373
PR summary
The duplicated file descriptor `fd2` was leaked which was created through Python’s `os.dup`.The fix was done by making the
osmodule reference retained until the conversion is finished. If 'fdopen' fails, the code callsos.close(fd2)before returning the existing error. Pairingos.closewithos.dupis also safer for Windows runtime ownership.The regression test makes
os.dupreturn an invalid descriptor (-2) sofdopenfails, records calls toos.close, confirmsnp.fromfileraises OSError, and verifies that the descriptor was passed to os.close.First time committer introduction
I use NumPy in machine-learning projects for numerical computations and data preprocessing, and this is my first contribution to NumPy.
AI Disclosure
I used Codex 5.6 Sol High for assistance with issue selection ,preparing the C fix, regression test, and verification and understanding the code.I have personally reviewed and understand the changes.