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Merge pull request #1142 from aalhossary/aa/bump-7.3.0-snapshot
Bump the development version to 7.3.0-SNAPSHOT
2 parents 92a7ec0 + c39c285 commit e68f60e

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‎CHANGELOG.md‎

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BioJava Changelog
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-----------------
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BioJava 7.3.0
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==============================
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### Added
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* Fetching, caching and display of electron density and cryo-EM maps #1134
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* Checksum verification (MD5, SHA-1, SHA-256) in `FileDownloadUtils`, replacing the previous
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stub. Downloads from `files.wwpdb.org` and `files.rcsb.org` are checksummed from their `ETag`
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without a second request #1133
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* `HttpStatusException`, so callers can tell "not there" from a transport failure #1133
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* `FileDownloadUtils.downloadFileWithValidation()`, which downloads and validates over a single
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connection #1133
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* `LocalPDBDirectory.getMiddleHash(String)`, computing the two-character directory from the
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right so that it is correct for both short and extended PDB IDs #1133
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* Support for the ECOD distribution format introduced at v294.1 #1141 #1139
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### Performance
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* Contact calculation is about 1.5x faster: squared distances compared against a squared cutoff,
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primitive arrays in `GridCell` instead of boxed lists, and a pre-sized `AtomContactSet` #1147
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* ASA calculation is about 1.2-1.3x faster, by the same replacement of objects with flat
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primitive arrays in the hot loops #1148
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* `EcodInstallation.getVersion()` reads the file header instead of parsing every domain. The
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current release is 653 MB and holds nearly three million records #1141
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### Fixed
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* CATH downloads use https and check the response before caching it. The previous http URL began
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redirecting, and the redirect body was cached as classification data #1133 #1138
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* CATH parsing no longer throws `ArrayIndexOutOfBoundsException` on blank or truncated lines, and
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cached files are validated before being used #1145
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* Chemical component downloads reject redirects and error responses rather than caching them #1133
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* Redirects that `HttpURLConnection` does not follow by itself - 307, 308, and any that change
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http to https - are now followed #1151 #1149
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* `FileDownloadUtils`: the `hash` argument was ignored by one overload; downloads could be
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silently truncated; temporary files leaked on failure; `validateFile` threw on a file with no
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parent directory and on an empty `.size` sidecar #1133
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* mmCIF writer emits the entry identifier as a data item, so `getPdbId()` survives a
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write-then-read round trip #1144 #1143
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* The ECOD read lock is left balanced when a download fails, so the original error is no longer
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replaced by `IllegalMonitorStateException` #1150
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* Resolution parsing warns only when the values actually differ
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### Changed
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* `createValidationFiles()` now defaults to `ETagPolicy.USE_IF_HEX_DIGEST`, so existing callers
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begin recording checksums where the server offers one #1133
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* Integration tests run nightly rather than on every pull request #1137 #1135
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* Tests migrated to JUnit 5 #1125 #1126 #1038
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* Library upgrades #1130 #1132
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### Removed
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* The `junit-addons` test dependency, no longer needed after the JUnit 5 migration #1126
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BioJava 7.2.6
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==============================
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### Fixed

‎biojava-aa-prop/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-aa-prop</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

‎biojava-alignment/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-alignment</artifactId>
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<name>biojava-alignment</name>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-core/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-core</artifactId>

‎biojava-genome/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-genome</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

‎biojava-integrationtest/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-integrationtest</artifactId>
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<packaging>jar</packaging>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>

‎biojava-modfinder/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-modfinder</artifactId>
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<name>biojava-modfinder</name>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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<type>jar</type>
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<scope>compile</scope>
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</dependency>

‎biojava-ontology/pom.xml‎

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<parent>
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<groupId>org.biojava</groupId>
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<artifactId>biojava</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-ontology</artifactId>

‎biojava-protein-comparison-tool/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-protein-comparison-tool</artifactId>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure-gui</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>net.sourceforge.jmol</groupId>

‎biojava-protein-disorder/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-protein-disorder</artifactId>
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<packaging>jar</packaging>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.2.7-SNAPSHOT</version>
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<version>7.3.0-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or
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scopes here) -->

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