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build(deps): Bump the python-minor-patch group across 1 directory with 5 updates - #1677

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build(deps): Bump the python-minor-patch group across 1 directory with 5 updates#1677
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Bumps the python-minor-patch group with 5 updates in the / directory:

Package From To
koza 2.6.2 2.7.0
biolink-model 4.4.2 4.4.3
python-dotenv 1.2.3 1.2.4
ruff 0.16.8 0.17.2
boto3 1.43.100 1.43.118

Updates koza from 2.6.2 to 2.7.0

Release notes

Sourced from koza's releases.

v2.7.0

What's Changed

New Contributors

Full Changelog: monarch-initiative/koza@v2.6.2...v2.7.0

Commits
  • 1a0f254 Merge pull request #258 from monarch-initiative/chore/biolink-model-4.4.6
  • 8f19fe1 Keep biolink-model>=4.3.6 floor
  • 34613bc Merge pull request #250 from monarch-initiative/fix/249-normalize-predicate-f...
  • f431364 Require biolink-model>=4.4.6 and drop the LinkML <1.12 cap
  • f0486a0 Merge origin/main into fix/249-normalize-predicate-filter
  • b1fbe78 Merge pull request #252 from monarch-initiative/feat/prefix-canonicalization
  • 9714efe Merge pull request #245 from monarch-initiative/feature/closure-size-all-phen...
  • 8374e31 Merge pull request #187 from monarch-initiative/dependabot/github_actions/act...
  • 895412d Merge pull request #241 from monarch-initiative/dependabot/github_actions/act...
  • 156f76c canonicalize: drop edge deduplication, keep --deduplicate for nodes
  • Additional commits viewable in compare view

Updates biolink-model from 4.4.2 to 4.4.3

Release notes

Sourced from biolink-model's releases.

v4.4.3

What's Changed

New Contributors

Full Changelog: biolink/biolink-model@v4.4.2...v4.4.3

Changelog

Sourced from biolink-model's changelog.

4.4.3

What's Changed

Full Changelog: biolink/biolink-model@v4.4.2...v4.4.3

4.4.1

4.4.0

What's Changed

Full Changelog: biolink/biolink-model@v4.3.9...v4.4.0

4.3.9

What's Changed

  • migrate to uv
  • dependebot updates

4.3.8

What's Changed

... (truncated)

Commits

Updates python-dotenv from 1.2.3 to 1.2.4

Release notes

Sourced from python-dotenv's releases.

v1.2.4

Fixed

  • dotenv get no longer exits with code 1 for empty string values (KEY=) by [@​ShamikOfficial] in #700
  • An unquoted empty value followed by an inline comment (e.g. KEY= # comment) is now parsed as an empty string instead of the comment text by [@​Noethix55555] in #663
  • dotenv run --no-override now expands variable references with the same precedence as load_dotenv(override=False), so a value like ${BASE}/suffix uses the existing BASE from the environment instead of the one from the .env file by [@​ROTl24] in #698
Changelog

Sourced from python-dotenv's changelog.

[1.2.4] - 2026-10-01

Fixed

  • dotenv get no longer exits with code 1 for empty string values (KEY=) by [@​ShamikOfficial] in #700
  • An unquoted empty value followed by an inline comment (e.g. KEY= # comment) is now parsed as an empty string instead of the comment text by [@​Noethix55555] in #663
  • dotenv run --no-override now expands variable references with the same precedence as load_dotenv(override=False), so a value like ${BASE}/suffix uses the existing BASE from the environment instead of the one from the .env file by [@​ROTl24] in #698
Commits
  • a565c2c Bump version: 1.2.3 → 1.2.4
  • 4a7abd0 docs: add 1.2.4 release notes (#663, #698, #700)
  • f215c02 fix: dotenv get exits 0 for empty string values (#700)
  • 58f2d7c test: make test_run_with_command_flags portable and meaningful (#709)
  • e0310e5 fix: honor --no-override when expanding variables in dotenv run (#698)
  • a00cb2e docs: add CHANGELOG entry for #663 (fix #600)
  • f5485a6 fix: parse empty unquoted value with inline comment as empty string
  • See full diff in compare view

Updates ruff from 0.16.8 to 0.17.2

Release notes

Sourced from ruff's releases.

0.17.2

Release Notes

Released on 2026-10-22.

Preview features

  • [complexity] Add unnecessary-regular-expression-compile (#25533)

Bug fixes

  • Avoid syntax errors for type variables with starred constraints (UP040, UP046, UP047, RUF053) (#28362)
  • [pydocstyle] Treat backslash-escaped *args and **kwargs as documented (D417) (#29536)
  • [pylint] Avoid false positive on starred elements (PLE0643) (#29483)
  • [pylint] Mark fixes unsafe when deleting comments (PLR5501, PLW0120) (#29414)
  • [pyupgrade] Mark fix unsafe when deleting comments (UP035) (#29413)

Performance

  • Avoid intermediate names in lint name resolution (#29506)
  • Prefilter bidirectional Unicode checks by UTF-8 leading bytes (#29561)
  • Share postfix parsing and reduce expression copies (#29480)

Configuration

  • [pylint] Add a configurable allowlist for magic-value-comparison (PLR2004) (#18961)

Documentation

  • Clarify documentation and correct stale guidance (#29374)
  • [pyupgrade] Remove mentions of variance related to fix safety (UP040, UP047) (#29592)

Contributors

Install ruff 0.17.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.17.2/ruff-installer.sh | sh
</tr></table>

... (truncated)

Changelog

Sourced from ruff's changelog.

0.17.2

Released on 2026-10-22.

Preview features

  • [complexity] Add unnecessary-regular-expression-compile (#25533)

Bug fixes

  • Avoid syntax errors for type variables with starred constraints (UP040, UP046, UP047, RUF053) (#28362)
  • [pydocstyle] Treat backslash-escaped *args and **kwargs as documented (D417) (#29536)
  • [pylint] Avoid false positive on starred elements (PLE0643) (#29483)
  • [pylint] Mark fixes unsafe when deleting comments (PLR5501, PLW0120) (#29414)
  • [pyupgrade] Mark fix unsafe when deleting comments (UP035) (#29413)

Performance

  • Avoid intermediate names in lint name resolution (#29506)
  • Prefilter bidirectional Unicode checks by UTF-8 leading bytes (#29561)
  • Share postfix parsing and reduce expression copies (#29480)

Configuration

  • [pylint] Add a configurable allowlist for magic-value-comparison (PLR2004) (#18961)

Documentation

  • Clarify documentation and correct stale guidance (#29374)
  • [pyupgrade] Remove mentions of variance related to fix safety (UP040, UP047) (#29592)

Contributors

0.17.1

Released on 2026-10-15.

Preview features

  • [pycodestyle] Don't treat None, True, or False as keywords (E271-E274) (#29322)

... (truncated)

Commits
  • 30516b4 Bump version to 0.17.2 (#29637)
  • 59a9e85 [ty] Generalize nested types in inferred return types (#29488)
  • 0d562aa [ty] Check inherited attribute conflicts (#28559)
  • 48dcdd0 [ty] Restrict range implications from gradual equivalence (#29577)
  • 734d75a [ty] Check for unsatisfiable bodies before existentially quantifying (#29504)
  • b0f9526 [ty] Preserve checks for recursive descriptor setter types (#29148)
  • 32869b4 Avoid creating deployments for automation jobs (#29626)
  • ec891ba Link the commit in pull request report footers (#29621)
  • 8958748 [ty] Publish ecosystem reports from GitHub Actions (#29609)
  • 01f5394 [ty] Publish typing conformance reports from GitHub Actions (#29608)
  • Additional commits viewable in compare view

Updates boto3 from 1.43.100 to 1.43.118

Commits

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@dependabot
build(deps): Bump the python-minor-patch group across 1 directory wit…
9e1e7e8 
…h 5 updates

Bumps the python-minor-patch group with 5 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [koza](https://github.com/monarch-initiative/koza) | `2.6.2` | `2.7.0` |
| [biolink-model](https://github.com/biolink/biolink-model) | `4.4.2` | `4.4.3` |
| [python-dotenv](https://github.com/theskumar/python-dotenv) | `1.2.3` | `1.2.4` |
| [ruff](https://github.com/astral-sh/ruff) | `0.16.8` | `0.17.2` |
| [boto3](https://github.com/boto/boto3) | `1.43.100` | `1.43.118` |



Updates `koza` from 2.6.2 to 2.7.0
- [Release notes](https://github.com/monarch-initiative/koza/releases)
- [Commits](monarch-initiative/koza@v2.6.2...v2.7.0)

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 `python-dotenv` from 1.2.3 to 1.2.4
- [Release notes](https://github.com/theskumar/python-dotenv/releases)
- [Changelog](https://github.com/theskumar/python-dotenv/blob/main/CHANGELOG.md)
- [Commits](theskumar/python-dotenv@v1.2.3...v1.2.4)

Updates `ruff` from 0.16.8 to 0.17.2
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.16.8...0.17.2)

Updates `boto3` from 1.43.100 to 1.43.118
- [Release notes](https://github.com/boto/boto3/releases)
- [Commits](boto/boto3@1.43.100...1.43.118)

---
updated-dependencies:
- dependency-name: koza
  dependency-version: 2.7.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-minor-patch
- 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: python-dotenv
  dependency-version: 1.2.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-minor-patch
- dependency-name: ruff
  dependency-version: 0.17.2
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-minor-patch
- dependency-name: boto3
  dependency-version: 1.43.118
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-minor-patch
...

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@dependabot dependabot Bot added the dependencies Pull requests that update a dependency file label Oct 26, 2026

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