Bump the uv-dependencies group with 6 updates

[dependabot]

Bumps the uv-dependencies group with 6 updates:

Package	From	To
click	8.3.1	8.3.3
pysam	0.23.3	0.24.0
mypy	1.20.0	1.20.2
pre-commit	4.5.1	4.6.0
ruff	0.15.8	0.15.12
pytest	9.0.2	9.0.3

Updates click from 8.3.1 to 8.3.3

Release notes

Sourced from click's releases.

8.3.3

This is the Click 8.3.3 fix release, which fixes bugs but does not otherwise change behavior and should not result in breaking changes compared to the latest feature release.

PyPI: https://pypi.org/project/click/8.3.3/ Changes: https://click.palletsprojects.com/page/changes/#version-8-3-3 Milestone: https://github.com/pallets/click/milestone/30

• Use :func:shlex.split to split pager and editor commands into argv lists for :class:subprocess.Popen, removing shell=True. #1026 #1477 #2775
• Fix TypeError when rendering help for an option whose default value is an object that doesn't support equality comparison with strings, such as semver.Version. #3298 #3299
• Fix pager test pollution under parallel execution by using pytest's tmp_path fixture instead of a shared temporary file path. #3238
• Treat Sentinel.UNSET values in a default_map as absent, so they fall through to the next default source instead of being used as the value. #3224 #3240
• Patch pdb.Pdb in CliRunner isolation so pdb.set_trace(), breakpoint(), and debuggers subclassing pdb.Pdb (ipdb, pdbpp) can interact with the real terminal instead of the captured I/O streams. #654 #824 #843 #951 #3235
• Add optional randomized parallel test execution using pytest-randomly and pytest-xdist to detect test pollution and race conditions. #3151
• Add contributor documentation for running stress tests, randomized parallel tests, and Flask smoke tests. #3151 #3177
• Show custom show_default string in prompts, matching the existing help text behavior. #2836 #2837 #3165 #3262 #3280 #3328
• Fix default=True with boolean flag_value always returning the flag_value instead of True. The default=True to flag_value substitution now only applies to non-boolean flags, where True acts as a sentinel meaning "activate this flag by default". For boolean flags, default=True is returned as a literal value. #3111 #3239
• Mark make_default_short_help as private API. #3189 #3250
• CliRunner's redirected streams now expose the original file descriptor via fileno(), so that faulthandler, subprocess, and other C-level consumers no longer crash with io.UnsupportedOperation. #2865
• Change :class:ParameterSource to an :class:~enum.IntEnum and reorder its members from most to least explicit, so values can be compared to check whether a parameter was explicitly provided. #2879 #3248

8.3.2

This is the Click 8.3.2 fix release, which fixes bugs but does not otherwise change behavior and should not result in breaking changes compared to the latest feature release.

PyPI: https://pypi.org/project/click/8.3.2/ Changes: https://click.palletsprojects.com/page/changes/#version-8-3-2 Milestone: https://github.com/pallets/click/milestone/29

... (truncated)

Changelog

Sourced from click's changelog.

Version 8.3.3

Released 2026-04-20

• Use :func:shlex.split to split pager and editor commands into argv lists for :class:subprocess.Popen, removing shell=True. :issue:1026 :pr:1477 :pr:2775
• Fix TypeError when rendering help for an option whose default value is an object that doesn't support equality comparison with strings, such as semver.Version. :issue:3298 :pr:3299
• Fix pager test pollution under parallel execution by using pytest's tmp_path fixture instead of a shared temporary file path. :pr:3238
• Treat Sentinel.UNSET values in a default_map as absent, so they fall through to the next default source instead of being used as the value. :issue:3224 :pr:3240
• Patch pdb.Pdb in CliRunner isolation so pdb.set_trace(), breakpoint(), and debuggers subclassing pdb.Pdb (ipdb, pdbpp) can interact with the real terminal instead of the captured I/O streams. :issue:654 :issue:824 :issue:843 :pr:951 :pr:3235
• Add optional randomized parallel test execution using pytest-randomly and pytest-xdist to detect test pollution and race conditions. :pr:3151
• Add contributor documentation for running stress tests, randomized parallel tests, and Flask smoke tests. :pr:3151 :pr:3177
• Show custom show_default string in prompts, matching the existing help text behavior. :issue:2836 :pr:2837 :pr:3165 :pr:3262 :pr:3280 :pr:3328
• Fix default=True with boolean flag_value always returning the flag_value instead of True. The default=True to flag_value substitution now only applies to non-boolean flags, where True acts as a sentinel meaning "activate this flag by default". For boolean flags, default=True is returned as a literal value. :issue:3111 :pr:3239
• Mark make_default_short_help as private API. :issue:3189 :pr:3250
• CliRunner's redirected streams now expose the original file descriptor via fileno(), so that faulthandler, subprocess, and other C-level consumers no longer crash with io.UnsupportedOperation. :issue:2865
• Change :class:ParameterSource to an :class:~enum.IntEnum and reorder its members from most to least explicit, so values can be compared to check whether a parameter was explicitly provided. :issue:2879 :pr:3248

Version 8.3.2

Released 2026-04-02

• Fix handling of flag_value when is_flag=False to allow such options to be used without an explicit value. :issue:3084 :pr:3152
• Hide Sentinel.UNSET values as None when using lookup_default(). :issue:3136 :pr:3199 :pr:3202 :pr:3209 :pr:3212 :pr:3224

... (truncated)

Commits

• c06d2d0 Release 8.3.3
• f1f191e Apply format guidelines to commits since latest 8.3.2 release (#3343)
• bb59ba0 Apply format guidelines to commits since latest 8.3.2 release
• 4a35225 Reduce blast-radius of UNSET in default_map (#3240)
• c07bb93 Merge branch 'stable' into unset-in-default-map
• c7e1ba8 Reorder ParameterSource (#3248)
• 76552ff Show default string in prompt (#3328)
• ac5cec5 Reorder ParameterSource from most to least explicit
• 8c452e0 Merge branch 'stable' into show-default-string-in-prompt
• 8c95c73 Reconcile default value passing and default activation (#3239)
• Additional commits viewable in compare view

Updates pysam from 0.23.3 to 0.24.0

Release notes

Sourced from pysam's releases.

v0.24.0

This pysam release wraps htslib/samtools/bcftools version 1.23.1 (PR #1343, PR #1372, and PR #1396) and now requires Cython 3.

It has been tested with Python versions 3.8 through 3.14, and wheels are available via PyPI for all of those Python versions. Wheels are built for macOS and Linux (manylinux_2_28 and musllinux_1_2) on both ARM and x86-64.

This release is the first to wrap htslib 1.22 or later, which contains significant CRAM-related operational changes inherited by pysam:

• The default output CRAM version is now 3.1 rather than 3.0. The version can be explicitly specified by using AlignmentFile(…, "wc", format_options=["version=3.0"]).

• CRAM reference data is no longer fetched from EBI's server by default. Use the REF_CACHE and REF_PATH environment variables if necessary to set up an alternative source of CRAM reference data.

The final pysam release that supported Python 3.6 and 3.7 was v0.23.0. This release is expected to be the last release supporting Python 3.8.

Bugs fixed:

• Removed AlignedSegment.modified_bases's limitation of only five modification types in MM/ML fields. (#1348, reported by @​lpryszcz)

• Fixed AlignedSegment.modified_bases crash when given a degenerate MM field that modifies no bases at all. (#1355, reported by @​JMencius)

• Fixed type hints for AlignmentFile and VariantFile constructor filename and mode parameters. (#1405, reported by @​msto)

• Fixed coverage functionality for Python 3.13 and later. Pysam's Cython code is no longer built with Python profiling enabled by default. Profiling can be re-enabled by using the PYSAM_PROFILE environment variable when building pysam from source. (#1350, reported by @​fedarko)

• Fixed capturing pysam.samtools.calmd() output, which fixed tests on 32-bit i386. Also suppressed TestBinaryCompatibility test cases on platforms where we have not calculated the expected sizes. (#1367, reported by @​emollier for Debian)

• Adjusted HTSFile.add_hts_options for Python 3: it now expects a list of str as documented, rather than needing bytes. This method's format_options argument is no longer optional. Similarly AlignmentFile(format_options=…) now accepts a list of str as documented.

New functionality:

• Updated pysam/libchtslib.pxd declarations to the HTSlib 1.23.1 API. This is the first comprehensive update that these Cython HTSlib API declarations have received. (PR #1362)

• Optimized pysam.array_to_qualitystring using Cython memoryviews, resulting in an approximately 70x-100x speed improvement in this function. (PR #1363, thanks to @​jchorl)

Documentation improvements:

• The numerous internal classes representing VariantHeader and VariantRecord fields are now documented. (#407 et al; PR #1358, PR #1359, PR #1361, PR #1394, thanks to @​TimD1)

• Clarified AlignedSegment.query_alignment_length et al behaviour for unmapped reads. (#1319, reported by @​schorlton-bugseq)

Changelog

Sourced from pysam's changelog.

Release 0.24.0

.. rubric:: 27 April 2026

This pysam release wraps htslib/samtools/bcftools version 1.23.1 (PR #1343, PR #1372, and PR #1396) and now requires Cython 3.

It has been tested with Python versions 3.8 through 3.14, and wheels are available via PyPI_ for all of those Python versions. Wheels are built for macOS and Linux (manylinux_2_28 and musllinux_1_2) on both ARM and x86-64.

This release is the first to wrap htslib 1.22 or later, which contains significant CRAM-related operational changes inherited by pysam:

• The default output CRAM version is now 3.1 rather than 3.0. The version can be explicitly specified by using :class:AlignmentFile(..., "wc", format_options=["version=3.0"]) <.AlignmentFile>.

• CRAM reference data is no longer fetched from EBI's server by default. Use the :envvar:REF_CACHE and :envvar:REF_PATH environment variables if necessary to set up an alternative source of CRAM reference data.

The final pysam release that supported Python 3.6 and 3.7 was v0.23.0. This release is expected to be the last release supporting Python 3.8.

Bugs fixed:

• Removed :attr:.AlignedSegment.modified_bases's limitation of only five modification types in MM/ML fields. (#1348, reported by Leszek Pryszcz)

• Fixed :attr:.AlignedSegment.modified_bases crash when given a degenerate MM field that modifies no bases at all. (#1355, reported by Jun Mencius)

• Fixed type hints for :class:.AlignmentFile and :class:.VariantFile constructor filename and mode parameters. (#1405, reported by Matt Stone)

• Fixed coverage functionality for Python 3.13 and later. Pysam's Cython code is no longer built with Python profiling enabled by default. :ref:Profiling <pysam-profile> can be re-enabled by using the :envvar:PYSAM_PROFILE environment variable when building pysam from source. (#1350, reported by Marcus Fedarko)

• Fixed capturing :func:pysam.samtools.calmd() <.samtools.command> output, which fixed tests on 32-bit i386. Also suppressed TestBinaryCompatibility test cases on platforms where we have not calculated the expected sizes. (#1367, reported by Étienne Mollier for Debian)

• Adjusted :attr:.HTSFile.add_hts_options for Python 3: it now expects a list of :class:str as documented, rather than needing :class:bytes.

... (truncated)

Commits

• 38b94a8 Bump version number to 0.24.0 and add release notes
• 7067acf The Profiling section should not be a subsection of PyPI installation
• 0d39f2f The htslib.org website has not been updated for this point release
• 09c3dc6 Move the VCF/BCF documentation up alongside SAM/BAM/CRAM
• 3f2aaf8 Rearrange Variant* class documentation
• 8a96ea0 Further clarify VariantRecord properties documentation
• 8a9f7f8 Correct the AlignmentFile/VariantFile filename/mode type hints
• 9aa4d1a Add documentation for all VariantHeader-related classes (PR #1394)
• 48688fc Use memoryviews to optimize array_to_qualitystring (PR #1363)
• d123986 Add VariantContig and VariantMetadata documentation (PR #1361)
• Additional commits viewable in compare view

Updates mypy from 1.20.0 to 1.20.2

Changelog

Sourced from mypy's changelog.

Mypy 1.20.2

• Use WAL with SQLite cache and fix close (Shantanu, PR 21154)
• Adjust SQLite journal mode (Ivan Levkivskyi, PR 21217)
• Correctly aggregate narrowing information on parent expressions (Shantanu, PR 21206)
• Fix regression related to generic callables (Shantanu, PR 21208)
• Fix regression by avoiding widening types in some contexts (Shantanu, PR 21242)
• Fix slicing in non-strict optional mode (Shantanu, PR 21282)
• mypyc: Fix match statement semantics for "or" pattern (Shantanu, PR 21156)
• mypyc: Fix issue with module dunder attributes (Piotr Sawicki, PR 21275)
• Initial support for Python 3.15.0a8 (Marc Mueller, PR 21255)

Acknowledgements

Thanks to all mypy contributors who contributed to this release:

• A5rocks
• Aaron Wieczorek
• Adam Turner
• Ali Hamdan
• asce
• BobTheBuidler
• Brent Westbrook
• Brian Schubert
• bzoracler
• Chris Burroughs
• Christoph Tyralla
• Colin Watson
• Donghoon Nam
• E. M. Bray
• Emma Smith
• Ethan Sarp
• George Ogden
• getzze
• grayjk
• Gregor Riepl
• Ivan Levkivskyi
• James Hilliard
• James Le Cuirot
• Jeremy Nimmer
• Joren Hammudoglu
• Kai (Kazuya Ito)
• kaushal trivedi
• Kevin Kannammalil
• Lukas Geiger
• Łukasz Langa
• Marc Mueller
• Michael R. Crusoe
• michaelm-openai
• Neil Schemenauer
• Piotr Sawicki

... (truncated)

Commits

• 145a062 Bump version to 1.20.2
• 81cd492 Fix slicing with nonstrict optional (#21282)
• 908d344 [mypyc] Set dunder attrs when adding module to sys.modules (#21275)
• ba28610 Initial support for Python 3.15.0a8 (#21255)
• 7b0e09f Fix match statement semantics for "or" pattern (#21156)
• 92b74f2 Avoid widening types in conditional_types (#21242)
• 0dcbfaa Fix is_overlapping_types for generic callables (#21208)
• 210f518 Correctly aggregate narrowing information on parent expressions (#21206)
• c34530e Only set journal mode in coordinator (#21217)
• 79a3ec6 Use WAL with SQLite cache, fix close (#21154)
• Additional commits viewable in compare view

Updates pre-commit from 4.5.1 to 4.6.0

Release notes

Sourced from pre-commit's releases.

pre-commit v4.6.0

Features

• pre-commit hook-impl: allow --hook-dir to be missing to enable easier usage with git 2.54+ git hooks.
  • #3662 PR by @​asottile.

Fixes

• pre-commit hook-impl: --hook-type is required.
  • #3661 PR by @​asottile.

Changelog

Sourced from pre-commit's changelog.

4.6.0 - 2026-04-21

Features

• pre-commit hook-impl: allow --hook-dir to be missing to enable easier usage with git 2.54+ git hooks.
  • #3662 PR by @​asottile.

Fixes

• pre-commit hook-impl: --hook-type is required.
  • #3661 PR by @​asottile.

Commits

• f35134b v4.6.0
• 2a51ffc Merge pull request #3662 from pre-commit/hook-impl-optional-hook-dir
• d7dee32 make --hook-dir optional for hook-impl
• 965aeb1 Merge pull request #3661 from pre-commit/hook-impl-required
• 2eacc06 --hook-type is required for hook-impl
• f5678bf Merge pull request #3657 from pre-commit/pre-commit-ci-update-config
• 054cc5b [pre-commit.ci] pre-commit autoupdate
• 5c0f302 Merge pull request #3652 from pre-commit/pre-commit-ci-update-config
• a5d9114 [pre-commit.ci] pre-commit autoupdate
• 129a1f5 Merge pull request #3641 from pre-commit/mxr-patch-1
• Additional commits viewable in compare view

Updates ruff from 0.15.8 to 0.15.12

Release notes

Sourced from ruff's releases.

0.15.12

Release Notes

Released on 2026-04-24.

Preview features

• Implement #ruff:file-ignore file-level suppressions (#23599)
• Implement #ruff:ignore logical-line suppressions (#23404)
• Revert preview changes to displayed diagnostic severity in LSP (#24789)
• [airflow] Implement task-branch-as-short-circuit (AIR004) (#23579)
• [flake8-bugbear] Fix break/continue handling in loop-iterator-mutation (B909) (#24440)
• [pylint] Fix PLC2701 for type parameter scopes (#24576)

Rule changes

• [pandas-vet] Suggest .array as well in PD011 (#24805)

CLI

• Respect default Unix permissions for cache files (#24794)

Documentation

• [pylint] Fix PLR0124 description not to claim self-comparison always returns the same value (#24749)
• [pyupgrade] Expand docs on reusable TypeVars and scoping (UP046) (#24153)
• Improve rules table accessibility (#24711)

Contributors

• @​dylwil3
• @​AlexWaygood
• @​woodruffw
• @​avasis-ai
• @​Dev-iL
• @​denyszhak
• @​ShipItAndPray
• @​anishgirianish
• @​augustelalande
• @​amyreese
• @​majiayu000

Install ruff 0.15.12

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.15.12/ruff-installer.sh | sh

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.12

Released on 2026-04-24.

Preview features

• Implement #ruff:file-ignore file-level suppressions (#23599)
• Implement #ruff:ignore logical-line suppressions (#23404)
• Revert preview changes to displayed diagnostic severity in LSP (#24789)
• [airflow] Implement task-branch-as-short-circuit (AIR004) (#23579)
• [flake8-bugbear] Fix break/continue handling in loop-iterator-mutation (B909) (#24440)
• [pylint] Fix PLC2701 for type parameter scopes (#24576)

Rule changes

• [pandas-vet] Suggest .array as well in PD011 (#24805)

CLI

• Respect default Unix permissions for cache files (#24794)

Documentation

• [pylint] Fix PLR0124 description not to claim self-comparison always returns the same value (#24749)
• [pyupgrade] Expand docs on reusable TypeVars and scoping (UP046) (#24153)
• Improve rules table accessibility (#24711)

Contributors

• @​dylwil3
• @​AlexWaygood
• @​woodruffw
• @​avasis-ai
• @​Dev-iL
• @​denyszhak
• @​ShipItAndPray
• @​anishgirianish
• @​augustelalande
• @​amyreese
• @​majiayu000

0.15.11

Released on 2026-04-16.

Preview features

• [ruff] Ignore RUF029 when function is decorated with asynccontextmanager (#24642)
• [airflow] Implement airflow-xcom-pull-in-template-string (AIR201) (#23583)
• [flake8-bandit] Fix S103 false positives and negatives in mask analysis (#24424)

... (truncated)

Commits

• 66f93cf Bump 0.15.12 (#24815)
• 476a4d0 [ty] Complete support for more detailed diagnostics on possibly unbound error...
• ed669ea Implement #ruff:file-ignore file-level suppressions (#23599)
• e73d952 [ty] Include inferred type in invalid-key concise diagnostic for union/inte...
• 80feb29 [ty] report only dead annotation-only locals as unused (#24811)
• 0fbf2bc Drop deprecated license classifier (#24808)
• 43b174c [ty] Infer lambda parameter types with Callable type context (#24317)
• 4f449ae [ty] Add error context for intersection types (#24772)
• 5b4e753 [ty] Add support for goto in literal enum member inlay hint (#24792)
• e7cc762 [ty] Add error context for TypedDict assignments (#24790)
• Additional commits viewable in compare view

Updates pytest from 9.0.2 to 9.0.3

Release notes

Sourced from pytest's releases.

9.0.3

pytest 9.0.3 (2026-04-07)

Bug fixes

• #12444: Fixed pytest.approx which now correctly takes into account ~collections.abc.Mapping keys order to compare them.

• #13634: Blocking a conftest.py file using the -p no: option is now explicitly disallowed.

  Previously this resulted in an internal assertion failure during plugin loading.

  Pytest now raises a clear UsageError explaining that conftest files are not plugins and cannot be disabled via -p.

• #13734: Fixed crash when a test raises an exceptiongroup with __tracebackhide__ = True.

• #14195: Fixed an issue where non-string messages passed to unittest.TestCase.subTest() were not printed.

• #14343: Fixed use of insecure temporary directory (CVE-2025-71176).

Improved documentation

• #13388: Clarified documentation for -p vs PYTEST_PLUGINS plugin loading and fixed an incorrect -p example.
• #13731: Clarified that capture fixtures (e.g. capsys and capfd) take precedence over the -s / --capture=no command-line options in Accessing captured output from a test function <accessing-captured-output>.
• #14088: Clarified that the default pytest_collection hook sets session.items before it calls pytest_collection_finish, not after.
• #14255: TOML integer log levels must be quoted: Updating reference documentation.

Contributor-facing changes

• #12689: The test reports are now published to Codecov from GitHub Actions. The test statistics is visible on the web interface.

  -- by aleguy02

Commits

• a7d58d7 Prepare release version 9.0.3
• 089d981 Merge pull request #14366 from bluetech/revert-14193-backport
• 8127eaf Revert "Fix: assertrepr_compare respects dict insertion order (#14050) (#14193)"
• 99a7e60 Merge pull request #14363 from pytest-dev/patchback/backports/9.0.x/95d8423bd...
• ddee02a Merge pull request #14343 from bluetech/cve-2025-71176-simple
• 74eac69 doc: Update training info (#14298) (#14301)
• f92dee7 Merge pull request #14267 from pytest-dev/patchback/backports/9.0.x/d6fa26c62...
• 7ee58ac Merge pull request #12378 from Pierre-Sassoulas/fix-implicit-str-concat-and-d...
• 37da870 Merge pull request #14259 from mitre88/patch-4 (#14268)
• c34bfa3 Add explanation for string context diffs (#14257) (#14266)
• Additional commits viewable in compare view

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