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build(deps): bump the python-packages group with 6 updates #481

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merged 2 commits into from
Dec 3, 2024

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@dependabot dependabot bot commented on behalf of github Dec 1, 2024

Bumps the python-packages group with 6 updates:

Package From To
pyarrow 18.0.0 18.1.0
cytominer-database 0.3.4 0.3.5
pytest 8.3.3 8.3.4
ruff 0.3.7 0.8.1
sphinx-autoapi 3.3.3 3.4.0
dunamai 1.22.0 1.23.0

Updates pyarrow from 18.0.0 to 18.1.0

Release notes

Sourced from pyarrow's releases.

Apache Arrow 18.1.0

Release Notes URL: https://arrow.apache.org/release/18.1.0.html

Apache Arrow 18.1.0 RC2

Release Notes: Release Candidate: 18.1.0 RC2

Apache Arrow 18.1.0 RC1

Release Notes: Release Candidate: 18.1.0 RC1

Apache Arrow 18.1.0 RC0

Release Notes: Release Candidate: 18.1.0 RC0

Commits
  • 6a0414b MINOR: [Release] Update versions for 18.1.0
  • e4aee0c MINOR: [Release] Update .deb/.rpm changelogs for 18.1.0
  • 6199e5e MINOR: [Release] Update .deb package names for 18.1.0
  • d944b8b MINOR: [Release] Update CHANGELOG.md for 18.1.0
  • ac81eed GH-44455: [C++] Update vendored date to 3.0.3 (#44482)
  • 90bfa2c GH-44432: [Swift] Use flatbuffers v24.3.7 (#44433)
  • 0d69542 MINOR: [Java] Bump org.cyclonedx:cyclonedx-maven-plugin from 2.8.2 to 2.9.0 i...
  • 602e447 MINOR: [Java] Bump logback.version from 1.5.8 to 1.5.10 in /java (#44403)
  • 67c4d5e MINOR: [Java] Bump checker.framework.version from 3.48.0 to 3.48.1 in /java (...
  • 363acb0 MINOR: [C#] Bump Grpc.Tools from 2.66.0 to 2.67.0 in /csharp (#44400)
  • Additional commits viewable in compare view

Updates cytominer-database from 0.3.4 to 0.3.5

Release notes

Sourced from cytominer-database's releases.

v0.3.5

Compatibility release for newer Python versions which may not be compatible with backports.tempfile.

Please note: This package is deprecated and will no longer be supported. Please use at your own risk!

What's Changed

Full Changelog: cytomining/cytominer-database@v0.3.4...v0.3.5

Commits

Updates pytest from 8.3.3 to 8.3.4

Release notes

Sourced from pytest's releases.

8.3.4

pytest 8.3.4 (2024-12-01)

Bug fixes

  • #12592: Fixed KeyError{.interpreted-text role="class"} crash when using --import-mode=importlib in a directory layout where a directory contains a child directory with the same name.

  • #12818: Assertion rewriting now preserves the source ranges of the original instructions, making it play well with tools that deal with the AST, like executing.

  • #12849: ANSI escape codes for colored output now handled correctly in pytest.fail{.interpreted-text role="func"} with [pytrace=False]{.title-ref}.

  • #9353: pytest.approx{.interpreted-text role="func"} now uses strict equality when given booleans.

Improved documentation

  • #10558: Fix ambiguous docstring of pytest.Config.getoption{.interpreted-text role="func"}.

  • #10829: Improve documentation on the current handling of the --basetemp option and its lack of retention functionality (temporary directory location and retention{.interpreted-text role="ref"}).

  • #12866: Improved cross-references concerning the recwarn{.interpreted-text role="fixture"} fixture.

  • #12966: Clarify filterwarnings{.interpreted-text role="ref"} docs on filter precedence/order when using multiple @pytest.mark.filterwarnings <pytest.mark.filterwarnings ref>{.interpreted-text role="ref"} marks.

Contributor-facing changes

  • #12497: Fixed two failing pdb-related tests on Python 3.13.
Commits
  • 53f8b4e Update pypa/gh-action-pypi-publish to v1.12.2
  • 98dff36 Prepare release version 8.3.4
  • 1b474e2 approx: use exact comparison for bool (#13013)
  • b541721 docs: Fix wrong statement about sys.modules with importlib import mode (#1298...
  • 16cb87b pytest.fail: fix ANSI escape codes for colored output (#12959) (#12990)
  • be6bc81 Issue #12966 Clarify filterwarnings docs on precedence when using multiple ma...
  • 7aeb72b Improve docs on basetemp and retention (#12912) (#12928)
  • c875841 Merge pull request #12917 from pytest-dev/patchback/backports/8.3.x/ded1f44e5...
  • 6502816 Merge pull request #12913 from jakkdl/dontfailonbadpath
  • 52135b0 Merge pull request #12885 from The-Compiler/pdb-py311 (#12887)
  • Additional commits viewable in compare view

Updates ruff from 0.3.7 to 0.8.1

Release notes

Sourced from ruff's releases.

0.8.1

Release Notes

Preview features

  • Formatter: Avoid invalid syntax for format-spec with quotes for all Python versions (#14625)
  • Formatter: Consider quotes inside format-specs when choosing the quotes for an f-string (#14493)
  • Formatter: Do not consider f-strings with escaped newlines as multiline (#14624)
  • Formatter: Fix f-string formatting in assignment statement (#14454)
  • Formatter: Fix unnecessary space around power operator (**) in overlong f-string expressions (#14489)
  • [airflow] Avoid implicit schedule argument to DAG and @dag (AIR301) (#14581)
  • [flake8-builtins] Exempt private built-in modules (A005) (#14505)
  • [flake8-pytest-style] Fix pytest.mark.parametrize rules to check calls instead of decorators (#14515)
  • [flake8-type-checking] Implement runtime-cast-value (TC006) (#14511)
  • [flake8-type-checking] Implement unquoted-type-alias (TC007) and quoted-type-alias (TC008) (#12927)
  • [flake8-use-pathlib] Recommend Path.iterdir() over os.listdir() (PTH208) (#14509)
  • [pylint] Extend invalid-envvar-default to detect os.environ.get (PLW1508) (#14512)
  • [pylint] Implement len-test (PLC1802) (#14309)
  • [refurb] Fix bug where methods defined using lambdas were flagged by FURB118 (#14639)
  • [ruff] Auto-add r prefix when string has no backslashes for unraw-re-pattern (RUF039) (#14536)
  • [ruff] Implement invalid-assert-message-literal-argument (RUF040) (#14488)
  • [ruff] Implement unnecessary-nested-literal (RUF041) (#14323)
  • [ruff] Implement unnecessary-regular-expression (RUF055) (#14659)

Rule changes

  • Ignore more rules for stub files (#14541)
  • [pep8-naming] Eliminate false positives for single-letter names (N811, N814) (#14584)
  • [pyflakes] Avoid false positives in @no_type_check contexts (F821, F722) (#14615)
  • [ruff] Detect redirected-noqa in file-level comments (RUF101) (#14635)
  • [ruff] Mark fixes for unsorted-dunder-all and unsorted-dunder-slots as unsafe when there are complex comments in the sequence (RUF022, RUF023) (#14560)

Bug fixes

  • Avoid fixing code to None | None for redundant-none-literal (PYI061) and never-union (RUF020) (#14583, #14589)
  • [flake8-bugbear] Fix mutable-contextvar-default to resolve annotated function calls properly (B039) (#14532)
  • [flake8-pyi, ruff] Fix traversal of nested literals and unions (PYI016, PYI051, PYI055, PYI062, RUF041) (#14641)
  • [flake8-pyi] Avoid rewriting invalid type expressions in unnecessary-type-union (PYI055) (#14660)
  • [flake8-type-checking] Avoid syntax errors and type checking problem for quoted annotations autofix (TC003, TC006) (#14634)
  • [pylint] Do not wrap function calls in parentheses in the fix for unnecessary-dunder-call (PLC2801) (#14601)
  • [ruff] Handle attrs's auto_attribs correctly (RUF009) (#14520)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.8.1

Preview features

  • Formatter: Avoid invalid syntax for format-spec with quotes for all Python versions (#14625)
  • Formatter: Consider quotes inside format-specs when choosing the quotes for an f-string (#14493)
  • Formatter: Do not consider f-strings with escaped newlines as multiline (#14624)
  • Formatter: Fix f-string formatting in assignment statement (#14454)
  • Formatter: Fix unnecessary space around power operator (**) in overlong f-string expressions (#14489)
  • [airflow] Avoid implicit schedule argument to DAG and @dag (AIR301) (#14581)
  • [flake8-builtins] Exempt private built-in modules (A005) (#14505)
  • [flake8-pytest-style] Fix pytest.mark.parametrize rules to check calls instead of decorators (#14515)
  • [flake8-type-checking] Implement runtime-cast-value (TC006) (#14511)
  • [flake8-type-checking] Implement unquoted-type-alias (TC007) and quoted-type-alias (TC008) (#12927)
  • [flake8-use-pathlib] Recommend Path.iterdir() over os.listdir() (PTH208) (#14509)
  • [pylint] Extend invalid-envvar-default to detect os.environ.get (PLW1508) (#14512)
  • [pylint] Implement len-test (PLC1802) (#14309)
  • [refurb] Fix bug where methods defined using lambdas were flagged by FURB118 (#14639)
  • [ruff] Auto-add r prefix when string has no backslashes for unraw-re-pattern (RUF039) (#14536)
  • [ruff] Implement invalid-assert-message-literal-argument (RUF040) (#14488)
  • [ruff] Implement unnecessary-nested-literal (RUF041) (#14323)
  • [ruff] Implement unnecessary-regular-expression (RUF055) (#14659)

Rule changes

  • Ignore more rules for stub files (#14541)
  • [pep8-naming] Eliminate false positives for single-letter names (N811, N814) (#14584)
  • [pyflakes] Avoid false positives in @no_type_check contexts (F821, F722) (#14615)
  • [ruff] Detect redirected-noqa in file-level comments (RUF101) (#14635)
  • [ruff] Mark fixes for unsorted-dunder-all and unsorted-dunder-slots as unsafe when there are complex comments in the sequence (RUF022, RUF023) (#14560)

Bug fixes

  • Avoid fixing code to None | None for redundant-none-literal (PYI061) and never-union (RUF020) (#14583, #14589)
  • [flake8-bugbear] Fix mutable-contextvar-default to resolve annotated function calls properly (B039) (#14532)
  • [flake8-pyi, ruff] Fix traversal of nested literals and unions (PYI016, PYI051, PYI055, PYI062, RUF041) (#14641)
  • [flake8-pyi] Avoid rewriting invalid type expressions in unnecessary-type-union (PYI055) (#14660)
  • [flake8-type-checking] Avoid syntax errors and type checking problem for quoted annotations autofix (TC003, TC006) (#14634)
  • [pylint] Do not wrap function calls in parentheses in the fix for unnecessary-dunder-call (PLC2801) (#14601)
  • [ruff] Handle attrs's auto_attribs correctly (RUF009) (#14520)

0.8.0

Check out the blog post for a migration guide and overview of the changes!

Breaking changes

See also, the "Remapped rules" section which may result in disabled rules.

  • Default to Python 3.9

... (truncated)

Commits
  • b3b2c98 Update CHANGELOG.md with the new commits for 0.8.1 (#14664)
  • abb3c6e [flake8-pyi] Avoid rewriting invalid type expressions in `unnecessary-type-...
  • 224fe75 [ruff] Implement unnecessary-regular-expression (RUF055) (#14659)
  • dc29f52 [flake8-pyi, ruff] Fix traversal of nested literals and unions (PYI016,...
  • d9cbf2f Avoids unnecessary overhead for TC004, when TC001-003 are disabled (#14657)
  • 3f6c65e [red-knot] Fix merged type after if-else without explicit else branch (#14621)
  • 976c37a Bump version to 0.8.1 (#14655)
  • a378ff3 [red-knot] Fix Boolean flags in mdtests (#14654)
  • d8bca0d Fix bug where methods defined using lambdas were flagged by FURB118 (#14639)
  • 6f1cf5b [red-knot] Minor fix in MRO tests (#14652)
  • Additional commits viewable in compare view

Updates sphinx-autoapi from 3.3.3 to 3.4.0

Release notes

Sourced from sphinx-autoapi's releases.

v3.4.0

Features

  • NamedTuples that have been created with functional syntax are documented as a class (#485)

Misc

Changelog

Sourced from sphinx-autoapi's changelog.

v3.4.0 (2024-11-29)

Features ^^^^^^^^

  • NamedTuples that have been created with functional syntax are documented as a class (#485)

Misc ^^^^

Commits
  • 9e6a70a Version 3.4.0
  • b3f768e NamedTuples are always documented as a class
  • 6f91543 Format Python code with ruff format instead of black (#498)
  • b2ff263 Keep GitHub Actions up to date with GitHub's Dependabot
  • 4e2d9ae Fix ruff compressions and performance issues (#490)
  • See full diff in compare view

Updates dunamai from 1.22.0 to 1.23.0

Release notes

Sourced from dunamai's releases.

v1.23.0 (2024-11-17)

  • Added: {major}, {minor}, and {patch} format placeholders.
Changelog

Sourced from dunamai's changelog.

v1.23.0 (2024-11-17)

  • Added: {major}, {minor}, and {patch} format placeholders.
Commits

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📚 Documentation preview 📚: https://pycytominer--481.org.readthedocs.build/en/481/

@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Dec 1, 2024
@dependabot dependabot bot force-pushed the dependabot/pip/python-packages-6bd38b2a97 branch 3 times, most recently from f09e57b to baf1be1 Compare December 2, 2024 03:11
Bumps the python-packages group with 6 updates:

| Package | From | To |
| --- | --- | --- |
| [pyarrow](https://github.com/apache/arrow) | `18.0.0` | `18.1.0` |
| [cytominer-database](https://github.com/cytomining/cytominer-database) | `0.3.4` | `0.3.5` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.3.3` | `8.3.4` |
| [ruff](https://github.com/astral-sh/ruff) | `0.3.7` | `0.8.1` |
| [sphinx-autoapi](https://github.com/readthedocs/sphinx-autoapi) | `3.3.3` | `3.4.0` |
| [dunamai](https://github.com/mtkennerly/dunamai) | `1.22.0` | `1.23.0` |


Updates `pyarrow` from 18.0.0 to 18.1.0
- [Release notes](https://github.com/apache/arrow/releases)
- [Commits](apache/arrow@apache-arrow-18.0.0...apache-arrow-18.1.0)

Updates `cytominer-database` from 0.3.4 to 0.3.5
- [Release notes](https://github.com/cytomining/cytominer-database/releases)
- [Commits](cytomining/cytominer-database@v0.3.4...v0.3.5)

Updates `pytest` from 8.3.3 to 8.3.4
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.3...8.3.4)

Updates `ruff` from 0.3.7 to 0.8.1
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@v0.3.7...0.8.1)

Updates `sphinx-autoapi` from 3.3.3 to 3.4.0
- [Release notes](https://github.com/readthedocs/sphinx-autoapi/releases)
- [Changelog](https://github.com/readthedocs/sphinx-autoapi/blob/main/CHANGELOG.rst)
- [Commits](readthedocs/sphinx-autoapi@v3.3.3...v3.4.0)

Updates `dunamai` from 1.22.0 to 1.23.0
- [Release notes](https://github.com/mtkennerly/dunamai/releases)
- [Changelog](https://github.com/mtkennerly/dunamai/blob/master/CHANGELOG.md)
- [Commits](mtkennerly/dunamai@v1.22.0...v1.23.0)

---
updated-dependencies:
- dependency-name: pyarrow
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: cytominer-database
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: sphinx-autoapi
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: dunamai
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot force-pushed the dependabot/pip/python-packages-6bd38b2a97 branch from baf1be1 to 5bbc6d3 Compare December 2, 2024 03:32
@d33bs d33bs requested review from gwaybio and kenibrewer December 3, 2024 16:48
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d33bs commented Dec 3, 2024

@gwaybio, @kenibrewer - requesting a review here as I made a small modification here to avoid the cytominer-database update (also moving forward, ignoring the updates).

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d33bs commented Dec 3, 2024

Thanks @gwaybio !

@d33bs d33bs merged commit b558b39 into main Dec 3, 2024
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@d33bs d33bs deleted the dependabot/pip/python-packages-6bd38b2a97 branch December 3, 2024 16:57
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.74%. Comparing base (e771e30) to head (4c0b5f2).
Report is 1 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #481   +/-   ##
=======================================
  Coverage   94.74%   94.74%           
=======================================
  Files          57       57           
  Lines        3156     3156           
=======================================
  Hits         2990     2990           
  Misses        166      166           
Flag Coverage Δ
unittests 94.74% <ø> (ø)

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3 participants