Update CI dependencies (master) (patch)

[renovate]

This PR contains the following updates:

Package	Type	Update	Change	Age	Adoption	Passing	Confidence
astral-sh/ruff-pre-commit	repository	patch	v0.9.4 -> v0.9.9
pytest (changelog)		patch	==8.3.4 -> ==8.3.5
python-jsonschema/check-jsonschema	repository	patch	0.31.1 -> 0.31.2
ruff (source, changelog)		patch	0.9.4 -> 0.9.9
scikit-image		patch	==0.25.1 -> ==0.25.2

Note: The pre-commit manager in Renovate is not supported by the pre-commit maintainers or community. Please do not report any problems there, instead create a Discussion in the Renovate repository if you have any questions.

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Release Notes

astral-sh/ruff-pre-commit (astral-sh/ruff-pre-commit)

v0.9.9

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See: https://github.com/astral-sh/ruff/releases/tag/0.9.9

v0.9.8

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See: https://github.com/astral-sh/ruff/releases/tag/0.9.8

v0.9.7

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See: https://github.com/astral-sh/ruff/releases/tag/0.9.7

v0.9.6

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See: https://github.com/astral-sh/ruff/releases/tag/0.9.6

v0.9.5

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See: https://github.com/astral-sh/ruff/releases/tag/0.9.5

pytest-dev/pytest (pytest)

v8.3.5

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pytest 8.3.5 (2025-03-02)

Bug fixes

• #​11777: Fixed issue where sequences were still being shortened even with -vv verbosity.
• #​12888: Fixed broken input when using Python 3.13+ and a libedit build of Python, such as on macOS or with uv-managed Python binaries from the python-build-standalone project. This could manifest e.g. by a broken prompt when using Pdb, or seeing empty inputs with manual usage of input() and suspended capturing.
• #​13026: Fixed AttributeError{.interpreted-text role="class"} crash when using --import-mode=importlib when top-level directory same name as another module of the standard library.
• #​13053: Fixed a regression in pytest 8.3.4 where, when using --import-mode=importlib, a directory containing py file with the same name would cause an ImportError
• #​13083: Fixed issue where pytest could crash if one of the collected directories got removed during collection.

Improved documentation

• #​12842: Added dedicated page about using types with pytest.

  See types{.interpreted-text role="ref"} for detailed usage.

Contributor-facing changes

• #​13112: Fixed selftest failures in test_terminal.py with Pygments >= 2.19.0
• #​13256: Support for Towncier versions released in 2024 has been re-enabled
  when building Sphinx docs -- by webknjaz{.interpreted-text role="user"}.

python-jsonschema/check-jsonschema (python-jsonschema/check-jsonschema)

v0.31.2

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• Update vendored schemas: dependabot, github-workflows, gitlab-ci, mergify, renovate,
  woodpecker-ci (2025-02-19)

astral-sh/ruff (ruff)

v0.9.9

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Preview features

• Fix caching of unsupported-syntax errors (#​16425)

Bug fixes

• Only show unsupported-syntax errors in editors when preview mode is enabled (#​16429)

v0.9.8

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Preview features

• Start detecting version-related syntax errors in the parser (#​16090)

Rule changes

• [pylint] Mark fix unsafe (PLW1507) (#​16343)
• [pylint] Catch case np.nan/case math.nan in match statements (PLW0177) (#​16378)
• [ruff] Add more Pydantic models variants to the list of default copy semantics (RUF012) (#​16291)

Server

• Avoid indexing the project if configurationPreference is editorOnly (#​16381)
• Avoid unnecessary info at non-trace server log level (#​16389)
• Expand ruff.configuration to allow inline config (#​16296)
• Notify users for invalid client settings (#​16361)

Configuration

• Add per-file-target-version option (#​16257)

Bug fixes

• [refurb] Do not consider docstring(s) (FURB156) (#​16391)
• [flake8-self] Ignore attribute accesses on instance-like variables (SLF001) (#​16149)
• [pylint] Fix false positives, add missing methods, and support positional-only parameters (PLE0302) (#​16263)
• [flake8-pyi] Mark PYI030 fix unsafe when comments are deleted (#​16322)

Documentation

• Fix example for S611 (#​16316)
• Normalize inconsistent markdown headings in docstrings (#​16364)
• Document MSRV policy (#​16384)

v0.9.7

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Preview features

• Consider __new__ methods as special function type for enforcing class method or static method rules (#​13305)
• [airflow] Improve the internal logic to differentiate deprecated symbols (AIR303) (#​16013)
• [refurb] Manual timezone monkeypatching (FURB162) (#​16113)
• [ruff] Implicit class variable in dataclass (RUF045) (#​14349)
• [ruff] Skip singleton starred expressions for incorrectly-parenthesized-tuple-in-subscript (RUF031) (#​16083)
• [refurb] Check for subclasses includes subscript expressions (FURB189) (#​16155)

Rule changes

• [flake8-debugger] Also flag sys.breakpointhook and sys.__breakpointhook__ (T100) (#​16191)
• [pycodestyle] Exempt site.addsitedir(...) calls (E402) (#​16251)

Formatter

• Fix unstable formatting of trailing end-of-line comments of parenthesized attribute values (#​16187)

Server

• Fix handling of requests received after shutdown message (#​16262)
• Ignore source.organizeImports.ruff and source.fixAll.ruff code actions for a notebook cell (#​16154)
• Include document specific debug info for ruff.printDebugInformation (#​16215)
• Update server to return the debug info as string with ruff.printDebugInformation (#​16214)

CLI

• Warn on invalid noqa even when there are no diagnostics (#​16178)
• Better error messages while loading configuration extends (#​15658)

Bug fixes

• [flake8-comprehensions] Handle trailing comma in C403 fix (#​16110)
• [flake8-pyi] Avoid flagging custom-typevar-for-self on metaclass methods (PYI019) (#​16141)
• [pydocstyle] Handle arguments with the same names as sections (D417) (#​16011)
• [pylint] Correct ordering of arguments in fix for if-stmt-min-max (PLR1730) (#​16080)
• [pylint] Do not offer fix for raw strings (PLE251) (#​16132)
• [pyupgrade] Do not upgrade functional TypedDicts with private field names to the class-based syntax (UP013) (#​16219)
• [pyupgrade] Handle micro version numbers correctly (UP036) (#​16091)
• [pyupgrade] Unwrap unary expressions correctly (UP018) (#​15919)
• [refurb] Correctly handle lengths of literal strings in slice-to-remove-prefix-or-suffix (FURB188) (#​16237)
• [ruff] Skip RUF001 diagnostics when visiting string type definitions (#​16122)

Documentation

• Add FAQ entry for source.* code actions in Notebook (#​16212)
• Add SECURITY.md (#​16224)

v0.9.6

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Preview features

• [airflow] Add external_task.{ExternalTaskMarker, ExternalTaskSensor} for AIR302 (#​16014)
• [flake8-builtins] Make strict module name comparison optional (A005) (#​15951)
• [flake8-pyi] Extend fix to Python <= 3.9 for redundant-none-literal (PYI061) (#​16044)
• [pylint] Also report when the object isn't a literal (PLE1310) (#​15985)
• [ruff] Implement indented-form-feed (RUF054) (#​16049)
• [ruff] Skip type definitions for missing-f-string-syntax (RUF027) (#​16054)

Rule changes

• [flake8-annotations] Correct syntax for typing.Union in suggested return type fixes for ANN20x rules (#​16025)
• [flake8-builtins] Match upstream module name comparison (A005) (#​16006)
• [flake8-comprehensions] Detect overshadowed list/set/dict, ignore variadics and named expressions (C417) (#​15955)
• [flake8-pie] Remove following comma correctly when the unpacked dictionary is empty (PIE800) (#​16008)
• [flake8-simplify] Only trigger SIM401 on known dictionaries (#​15995)
• [pylint] Do not report calls when object type and argument type mismatch, remove custom escape handling logic (PLE1310) (#​15984)
• [pyupgrade] Comments within parenthesized value ranges should not affect applicability (UP040) (#​16027)
• [pyupgrade] Don't introduce invalid syntax when upgrading old-style type aliases with parenthesized multiline values (UP040) (#​16026)
• [pyupgrade] Ensure we do not rename two type parameters to the same name (UP049) (#​16038)
• [pyupgrade] [ruff] Don't apply renamings if the new name is shadowed in a scope of one of the references to the binding (UP049, RUF052) (#​16032)
• [ruff] Update RUF009 to behave similar to B008 and ignore attributes with immutable types (#​16048)

Server

• Root exclusions in the server to project root (#​16043)

Bug fixes

• [flake8-datetime] Ignore .replace() calls while looking for .astimezone (#​16050)
• [flake8-type-checking] Avoid TC004 false positive where the runtime definition is provided by __getattr__ (#​16052)

Documentation

• Improve ruff-lsp migration document (#​16072)
• Undeprecate ruff.nativeServer (#​16039)

v0.9.5

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Preview features

• Recognize all symbols named TYPE_CHECKING for in_type_checking_block (#​15719)
• [flake8-comprehensions] Handle builtins at top of file correctly for unnecessary-dict-comprehension-for-iterable (C420) (#​15837)
• [flake8-logging] .exception() and exc_info= outside exception handlers (LOG004, LOG014) (#​15799)
• [flake8-pyi] Fix incorrect behaviour of custom-typevar-return-type preview-mode autofix if typing was already imported (PYI019) (#​15853)
• [flake8-pyi] Fix more complex cases (PYI019) (#​15821)
• [flake8-pyi] Make PYI019 autofixable for .py files in preview mode as well as stubs (#​15889)
• [flake8-pyi] Remove type parameter correctly when it is the last (PYI019) (#​15854)
• [pylint] Fix missing parens in unsafe fix for unnecessary-dunder-call (PLC2801) (#​15762)
• [pyupgrade] Better messages and diagnostic range (UP015) (#​15872)
• [pyupgrade] Rename private type parameters in PEP 695 generics (UP049) (#​15862)
• [refurb] Also report non-name expressions (FURB169) (#​15905)
• [refurb] Mark fix as unsafe if there are comments (FURB171) (#​15832)
• [ruff] Classes with mixed type variable style (RUF053) (#​15841)
• [airflow] BashOperator has been moved to airflow.providers.standard.operators.bash.BashOperator (AIR302) (#​15922)
• [flake8-pyi] Add autofix for unused-private-type-var (PYI018) (#​15999)
• [flake8-pyi] Significantly improve accuracy of PYI019 if preview mode is enabled (#​15888)

Rule changes

• Preserve triple quotes and prefixes for strings (#​15818)
• [flake8-comprehensions] Skip when TypeError present from too many (kw)args for C410,C411, and C418 (#​15838)
• [flake8-pyi] Rename PYI019 and improve its diagnostic message (#​15885)
• [pep8-naming] Ignore @override methods (N803) (#​15954)
• [pyupgrade] Reuse replacement logic from UP046 and UP047 to preserve more comments (UP040) (#​15840)
• [ruff] Analyze deferred annotations before enforcing mutable-(data)class-default and function-call-in-dataclass-default-argument (RUF008,RUF009,RUF012) (#​15921)
• [pycodestyle] Exempt sys.path += ... calls (E402) (#​15980)

Configuration

• Config error only when flake8-import-conventions alias conflicts with isort.required-imports bound name (#​15918)
• Workaround Even Better TOML crash related to allOf (#​15992)

Bug fixes

• [flake8-comprehensions] Unnecessary list comprehension (rewrite as a set comprehension) (C403) - Handle extraneous parentheses around list comprehension (#​15877)
• [flake8-comprehensions] Handle trailing comma in fixes for unnecessary-generator-list/set (C400,C401) (#​15929)
• [flake8-pyi] Fix several correctness issues with custom-type-var-return-type (PYI019) (#​15851)
• [pep8-naming] Consider any number of leading underscore for N801 (#​15988)
• [pyflakes] Visit forward annotations in TypeAliasType as types (F401) (#​15829)
• [pylint] Correct min/max auto-fix and suggestion for (PL1730) (#​15930)
• [refurb] Handle unparenthesized tuples correctly (FURB122, FURB142) (#​15953)
• [refurb] Avoid None | None as well as better detection and fix (FURB168) (#​15779)

Documentation

• Add deprecation warning for ruff-lsp related settings (#​15850)
• Docs (linter.md): clarify that Python files are always searched for in subdirectories (#​15882)
• Fix a typo in non_pep695_generic_class.rs (#​15946)
• Improve Docs: Pylint subcategories' codes (#​15909)
• Remove non-existing lint.extendIgnore editor setting (#​15844)
• Update black deviations (#​15928)
• Mention UP049 in UP046 and UP047, add See also section to UP040 (#​15956)
• Add instance variable examples to RUF012 (#​15982)
• Explain precedence for ignore and select config (#​15883)

scikit-image/scikit-image (scikit-image)

v0.25.2

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scikit-image 0.25.2

We're happy to announce the release of scikit-image 0.25.2!

Bug Fixes

• Handle random degenerate case in skimage.graph.cut_normalized gracefully (#​7675).
• In skimage.feature.BRIEF, copy keypoints if necessary to preserve contiguity (#​7692).
• Revert a previous fix to skimage.segmentation.watershed that unintentionally changed the algorithm's behavior for markers placed at maxima in the image. We decided that the behavior originally reported as a bug (gh-6632), is not actually one (#​7702).

Documentation

• Improve docstring of skimage.restoration.rolling_ball (#​7682).

Infrastructure

• Only run the job if the PR got merged (vs merely closed) (#​7679).
• Fix typo in GH workflow (#​7681).
• Refactor GitHub's CI config and helper scripts (#​7672).
• Use pytest config in pyproject.toml in CI (#​7555).
• Lower CI build verbosity (#​7688).
• Port testing on Windows from Azure CI to GitHub's CI (#​7687).
• CI cleanup (#​7693).
• Simultaneously resolve all dependencies; add pip caching (#​7690).
• Reenable graph reproducibility test (#​7694).
• Give milestone labeler necessary permissions (#​7695).
• Milestone labeler permission not needed (#​7696).
• Fix 313t wheel build (#​7699).

Maintenance

• Include a missing image in meson.build so they are included in the wheel (#​7660).
• Add zizmor to pre-commit; address GH workflow issues raised (#​7662).

Contributors

6 authors added to this release (alphabetically):

• Jarrod Millman (@​jarrodmillman)
• Lars Grüter (@​lagru)
• Marianne Corvellec (@​mkcor)
• Matthew Brett (@​matthew-brett)
• Orion Poplawski (@​opoplawski)
• Stefan van der Walt (@​stefanv)

8 reviewers added to this release (alphabetically):

• Jarrod Millman (@​jarrodmillman)
• Juan Nunez-Iglesias (@​jni)
• Lars Grüter (@​lagru)
• Marianne Corvellec (@​mkcor)
• Mark Harfouche (@​hmaarrfk)
• Matthew Brett (@​matthew-brett)
• Ralf Gommers (@​rgommers)
• Stefan van der Walt (@​stefanv)

These lists are automatically generated, and may not be complete or may contain duplicates.

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Configuration

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