build(deps): bump the python-minor-patch group across 1 directory with 15 updates - #804
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…h 15 updates Bumps the python-minor-patch group with 15 updates in the / directory: | Package | From | To | | --- | --- | --- | | [kghub-downloader](https://github.com/monarch-initiative/kghub-downloader) | `0.3.11` | `0.5.0` | | [kgx](https://github.com/biolink/kgx) | `2.4.2` | `2.7.0` | | [koza](https://github.com/monarch-initiative/koza) | `2.1.1` | `2.6.2` | | [biolink-model](https://github.com/biolink/biolink-model) | `4.4.2` | `4.4.3` | | [requests-cache](https://github.com/requests-cache/requests-cache) | `1.3.2` | `1.3.3` | | [llm](https://github.com/simonw/llm) | `0.11.2` | `0.31.1` | | [curies](https://github.com/biopragmatics/curies) | `0.13.11` | `0.14.6` | | [biopython](https://github.com/biopython/biopython) | `1.87` | `1.88` | | [duckdb](https://github.com/duckdb/duckdb-python) | `1.5.3` | `1.5.5` | | [pytest](https://github.com/pytest-dev/pytest) | `9.0.3` | `9.1.1` | | [pre-commit](https://github.com/pre-commit/pre-commit) | `4.6.0` | `4.6.2` | | [parameterized](https://github.com/wolever/parameterized) | `0.8.1` | `0.9.0` | | [notebook](https://github.com/jupyter/notebook) | `7.5.6` | `7.6.2` | | [ruff](https://github.com/astral-sh/ruff) | `0.15.14` | `0.16.3` | | [boto3](https://github.com/boto/boto3) | `1.43.16` | `1.43.71` | Updates `kghub-downloader` from 0.3.11 to 0.5.0 - [Release notes](https://github.com/monarch-initiative/kghub-downloader/releases) - [Commits](monarch-initiative/kghub-downloader@v0.3.11...v0.5.0) Updates `kgx` from 2.4.2 to 2.7.0 - [Release notes](https://github.com/biolink/kgx/releases) - [Changelog](https://github.com/biolink/kgx/blob/master/CHANGELOG.md) - [Commits](biolink/kgx@v2.4.2...v2.7.0) Updates `koza` from 2.1.1 to 2.6.2 - [Release notes](https://github.com/monarch-initiative/koza/releases) - [Commits](monarch-initiative/koza@v2.1.1...v2.6.2) Updates `biolink-model` from 4.4.2 to 4.4.3 - [Release notes](https://github.com/biolink/biolink-model/releases) - [Changelog](https://github.com/biolink/biolink-model/blob/master/ChangeLog) - [Commits](biolink/biolink-model@v4.4.2...v4.4.3) Updates `requests-cache` from 1.3.2 to 1.3.3 - [Release notes](https://github.com/requests-cache/requests-cache/releases) - [Changelog](https://github.com/requests-cache/requests-cache/blob/main/HISTORY.md) - [Commits](requests-cache/requests-cache@v1.3.2...v1.3.3) Updates `llm` from 0.11.2 to 0.31.1 - [Release notes](https://github.com/simonw/llm/releases) - [Changelog](https://github.com/simonw/llm/blob/main/docs/changelog.md) - [Commits](simonw/llm@0.11.2...0.31.1) Updates `curies` from 0.13.11 to 0.14.6 - [Release notes](https://github.com/biopragmatics/curies/releases) - [Commits](biopragmatics/curies@v0.13.11...v0.14.6) Updates `biopython` from 1.87 to 1.88 - [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst) - [Commits](https://github.com/biopython/biopython/commits) Updates `duckdb` from 1.5.3 to 1.5.5 - [Release notes](https://github.com/duckdb/duckdb-python/releases) - [Commits](duckdb/duckdb-python@v1.5.3...v1.5.5) Updates `pytest` from 9.0.3 to 9.1.1 - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@9.0.3...9.1.1) Updates `pre-commit` from 4.6.0 to 4.6.2 - [Release notes](https://github.com/pre-commit/pre-commit/releases) - [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md) - [Commits](pre-commit/pre-commit@v4.6.0...v4.6.2) Updates `parameterized` from 0.8.1 to 0.9.0 - [Changelog](https://github.com/wolever/parameterized/blob/master/CHANGELOG.txt) - [Commits](wolever/parameterized@v0.8.1...v0.9.0) Updates `notebook` from 7.5.6 to 7.6.2 - [Release notes](https://github.com/jupyter/notebook/releases) - [Changelog](https://github.com/jupyter/notebook/blob/@jupyter-notebook/tree@7.6.2/CHANGELOG.md) - [Commits](https://github.com/jupyter/notebook/compare/@jupyter-notebook/tree@7.5.6...@jupyter-notebook/tree@7.6.2) Updates `ruff` from 0.15.14 to 0.16.3 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.15.14...0.16.3) Updates `boto3` from 1.43.16 to 1.43.71 - [Release notes](https://github.com/boto/boto3/releases) - [Commits](boto/boto3@1.43.16...1.43.71) --- updated-dependencies: - dependency-name: biolink-model dependency-version: 4.4.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-minor-patch - dependency-name: biopython dependency-version: '1.88' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: boto3 dependency-version: 1.43.70 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-minor-patch - dependency-name: curies dependency-version: 0.14.6 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: duckdb dependency-version: 1.5.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-minor-patch - dependency-name: kghub-downloader dependency-version: 0.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: kgx dependency-version: 2.7.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: koza dependency-version: 2.6.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: llm dependency-version: 0.31.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: notebook dependency-version: 7.6.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: parameterized dependency-version: 0.9.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: pre-commit dependency-version: 4.6.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-minor-patch - dependency-name: pytest dependency-version: 9.1.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-minor-patch - dependency-name: requests-cache dependency-version: 1.3.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-minor-patch - dependency-name: ruff dependency-version: 0.16.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-minor-patch ... 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Bumps the python-minor-patch group with 15 updates in the / directory:
0.3.110.5.02.4.22.7.02.1.12.6.24.4.24.4.31.3.21.3.30.11.20.31.10.13.110.14.61.871.881.5.31.5.59.0.39.1.14.6.04.6.20.8.10.9.07.5.67.6.20.15.140.16.31.43.161.43.71Updates
kghub-downloaderfrom 0.3.11 to 0.5.0Release notes
Sourced from kghub-downloader's releases.
... (truncated)
Commits
cb53895Merge pull request #60 from monarch-initiative/download-reportdfce22eReturn a DownloadReport from download_from_yaml and main85d4d25Merge pull request #58 from monarch-initiative/fix-gcp-vulnerability82f2c4aupdate lock file06a9633remove 3.9 check. Context: Poetry 2.3.4's installer uses newer installer/bu...546bd43remove service account and related tests that require it from CI/CD in respon...e46dbbeMerge pull request #56 from monarch-initiative/widen-typer-version-support0f16916Widen typer version support to >=0.12.38b80e8dMerge pull request #55 from monarch-initiative/verify-false-flag40c2112Add verify_ssl flag to disable SSL verification for specific sourcesUpdates
kgxfrom 2.4.2 to 2.7.0Release notes
Sourced from kgx's releases.
... (truncated)
Commits
02f56d2Merge pull request #550 from biolink/dependabot/uv/idna-3.15894b6a5Merge pull request #549 from biolink/dependabot/uv/urllib3-2.7.01ff1a68Merge pull request #545 from biolink/rdf-optimizatione9e1e56Merge pull request #548 from biolink/improve-obograph-gene-properties5e0fef9Update test_transform4 edge counts: 205 -> 206c8f15b5Bump idna from 3.11 to 3.151081032Bump urllib3 from 2.6.3 to 2.7.0e73134eFix obograph_source prefix-map destruction and predicate mappinga52606cAdd --parallel CLI option to kgx transform7120824Free part files eagerly during parallel concatUpdates
kozafrom 2.1.1 to 2.6.2Release notes
Sourced from koza's releases.
... (truncated)
Commits
dcb1b78Merge pull request #244 from monarch-initiative/fix/sort-closure-by-subjecte2f5c17closurize: materializeclosuresorted by subject_idd432922Merge pull request #238 from monarch-initiative/fix/enforce-writer-count-boundsdb5bb0aSupport count-bound enforcement in PassthroughWriter too0aedda6Enforce writer min/max node and edge count bounds99c318aMerge pull request #235 from monarch-initiative/fix-ic-multivalued-category83351d6information-content: handle multivalued (VARCHAR[]) edge category58da9e7Merge pull request #231 from monarch-initiative/feat/export-convert-verb4f30a7bMerge pull request #226 from monarch-initiative/schema-smart-profile29ac4d4Merge remote-tracking branch 'origin/main' into feat/export-convert-verbUpdates
biolink-modelfrom 4.4.2 to 4.4.3Release notes
Sourced from biolink-model's releases.
Changelog
Sourced from biolink-model's changelog.
... (truncated)
Commits
e8e8da1lint45c852bRegenerate artifacts from biolink-model.yaml4a9a999add resopnse asocitaionb14569fRegenerate artifacts from biolink-model.yamlUpdates
requests-cachefrom 1.3.2 to 1.3.3Changelog
Sourced from requests-cache's changelog.
Commits
2cdd81aUpdate dependencies and changeloga5223fcMerge pull request #1168 from requests-cache/bugfixes27d1745Run both steps of FileCache.clear() within RLock33a6a03Fix Redisttl_offsetfor items that should have no expiry965a8d8Fix DynamoDb pagination for iter and values()186a1bfUpdate dependencies and changelogd2f83ecMerge pull request #1165 from gaoflow/fix/empty-expires-indexerror917e3f9Fix IndexError when Expires header value is an empty stringccbc6afMerge pull request #1162 from requests-cache/dependabot/uv/starlette-1.3.16fe3a66Merge pull request #1161 from requests-cache/dependabot/github_actions/codeco...Updates
llmfrom 0.11.2 to 0.31.1Release notes
Sourced from llm's releases.
... (truncated)
Changelog
Sourced from llm's changelog.
... (truncated)
Commits
e4dce4cRelease 0.31.19d9ecd0Handle tool calls with empty arguments better, closes #15215ce40fdRelease 0.31706852eNew image_detail low/high/auto/original option87efea1Cleaner dynamic self.Options building, refs #1418021a29dOpenAI verbosity optionc9a3ac9New model: gpt-5.5 - refs #14180cc5a1cIgnore non-llm folders in pyproject.toml1bfb96dIgnore *.db (temporary test databases)cad03fbRegister async models for extra-openai-models.yaml, closes #1395Updates
curiesfrom 0.13.11 to 0.14.6Commits
d2893d0Bump version: 0.14.6-dev → 0.14.6a87ee6aUpdate vocabulary.py786e5d0Bump version: 0.14.5 → 0.14.6-dev3f37ec7Bump version: 0.14.5-dev → 0.14.52fde67aUpdate vocabulary.py73baf91Bump version: 0.14.4 → 0.14.5-dev85a44ebBump version: 0.14.4-dev → 0.14.4f24248dImplement XSD string parsere81bc7eAdd missing type hint9dd4a2dBump version: 0.14.3 → 0.14.4-devUpdates
biopythonfrom 1.87 to 1.88Changelog
Sourced from biopython's changelog.