chore(deps): Bump the python-dependencies group with 5 updates

[dependabot]

Updates the requirements on ruff, pytest, pandas, matplotlib and numpy to permit the latest version.
Updates ruff to 0.16.0

Release notes

Sourced from ruff's releases.

0.16.0

Release Notes

Released on 2026-07-23.

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

Breaking changes

• Ruff now enables a much larger set of rules by default (413, up from 59). See the blog post for more details and the new Default Rules page for a full listing of the enabled rules. Note that this is primarily an expansion, but 18 of the more opinionated pycodestyle (E) and pyflakes (F) rules have been removed from the default set: E401, E402, E701, E702, E703, E711, E712, E713, E714, E721, E731, E741, E742, E743, F403, F405, F406, and F722.

• Ruff can now format Python code blocks in Markdown files and will do this by default. See the documentation for more details.

• Ruff now supports ruff: ignore comments at the ends of lines, like noqa comments, or on the line preceding a diagnostic. For example, these both suppress an unused-import (F401) diagnostic:

  import math  # ruff: ignore[F401]
  ruff: ignore[F401]
  import os

• Fixes are now shown in check and format --check output:

  ❯ ruff format --check .
  unformatted: File would be reformatted
   --> try.md:1:1
    |
  1 | ```python
    - import   math
  2 + import math
  3 | ```
    |
  1 file would be reformatted

  This example also shows off the Markdown formatting.

• format --check now supports the same output formats as the linter, including the github and gitlab outputs for rendering annotations in CI:

  ❯ ruff format --check --output-format github .
  ::error title=ruff (unformatted),file=try.md,line=2,col=8,endLine=2,endColumn=10::try.md:2:8: unformatted: File would be reformatted

  See the CLI help or documentation for the full list of supported formats.

• The filename, location, end_location, fix.edits[].location, and fix.edits[].end_location fields in the JSON output format may now be null rather than defaulting to the empty string and row 1, column 1, respectively.

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.0

Released on 2026-07-23.

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

Breaking changes

• Ruff now enables a much larger set of rules by default (413, up from 59). See the blog post for more details and the new Default Rules page for a full listing of the enabled rules. Note that this is primarily an expansion, but 18 of the more opinionated pycodestyle (E) and pyflakes (F) rules have been removed from the default set: E401, E402, E701, E702, E703, E711, E712, E713, E714, E721, E731, E741, E742, E743, F403, F405, F406, and F722.

• Ruff can now format Python code blocks in Markdown files and will do this by default. See the documentation for more details.

• Ruff now supports ruff: ignore comments at the ends of lines, like noqa comments, or on the line preceding a diagnostic. For example, these both suppress an unused-import (F401) diagnostic:

  import math  # ruff: ignore[F401]
  ruff: ignore[F401]
  import os

• Fixes are now shown in check and format --check output:

  ❯ ruff format --check .
  unformatted: File would be reformatted
   --> try.md:1:1
    |
  1 | ```python
    - import   math
  2 + import math
  3 | ```
    |
  1 file would be reformatted

  This example also shows off the Markdown formatting.

• format --check now supports the same output formats as the linter, including the github and gitlab outputs for rendering annotations in CI:

... (truncated)

Commits

• a2635fd Bump 0.16.0 (#27136)
• 3433449 [ty] Reuse full call diagnostics for implicit setter calls (#27115)
• 2240070 Reflect ruff: ignore and --add-ignore stabilization in documentation (#27...
• 17ef711 Stabilize --add-ignore (#27125)
• ef912bb Add newly stabilized rules to defaults (#27055)
• b30f040 Stabilize new default rules (#27035)
• bcd70c5 Exclude Markdown files from format-dev runs (#27052)
• 87e51e2 Fix format --check spans for syntax errors (#27045)
• afe2723 [flake8-gettext] Stabilize qualified-name and built-in binding resolution (...
• a9702d8 [flake8-bandit] Stabilize string literal binding resolution (S310) (#26944)
• Additional commits viewable in compare view

Updates pytest to 9.1.1

Release notes

Sourced from pytest's releases.

9.1.1

pytest 9.1.1 (2026-06-19)

Bug fixes

• #14220: Fixed a logic bug in pytest.RaisesGroup which would might cause it to display incorrect "It matches FooError() which was paired with BarError" messages.
• #14591: Fixed a regression in pytest 9.1.0 which caused overriding a parametrized fixture with an indirect @​pytest.mark.parametrize to fail with "duplicate parametrization of '<fixture name>'".
• #14606: Fixed list-item typing errors from mypy in @pytest.mark.parametrize <pytest.mark.parametrize ref> argvalues parameter.
• #14608: Fixed a regression in pytest 9.1.0 where conftest.py files located in <invocation dir>/test* were no longer loaded as initial conftests when invoked without arguments. This could cause certain hooks (like pytest_addoption) in these files to not fire.

Commits

• cf470ec Prepare release version 9.1.1
• e0c8ce6 Merge pull request #14625 from pytest-dev/patchback/backports/9.1.x/a07c31a97...
• 1b82d16 Merge pull request #14624 from pytest-dev/patchback/backports/9.1.x/b375b79ec...
• 501c4bc Merge pull request #14596 from bluetech/doc-classmethod
• b61f588 Merge pull request #14622 from chrisburr/fix-14608-initial-conftest-test-subdir
• 9a567e0 [automated] Update plugin list (#14617) (#14618)
• ef8b299 Merge pull request #14620 from pytest-dev/patchback/backports/9.1.x/680f9f3ed...
• 66abd07 Merge pull request #14220 from bysiber/fix-stale-iexp-raisesgroup
• 79fbf93 Merge pull request #14612 from pytest-dev/patchback/backports/9.1.x/974ed48b6...
• 0d312eb Merge pull request #14611 from bluetech/parametrize-argvalues-typing
• Additional commits viewable in compare view

Updates pandas to 3.0.5

Release notes

Sourced from pandas's releases.

pandas 3.0.5

We are pleased to announce the release of pandas 3.0.5. This is a patch release in the 3.0.x series and includes some regression fixes and bug fixes. We recommend that all users of the 3.0.x series upgrade to this version.

See the full whatsnew for a list of all the changes.

Pandas 3.0 supports Python 3.11 and higher. The release can be installed from PyPI:

python -m pip install --upgrade pandas==3.0.*

Or from conda-forge

conda install -c conda-forge pandas=3.0

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Commits

• e68db09 RLS: 3.0.5
• 0697623 Backport PR #66428: DOC: update whatsnew for 3.0.5 (#66430)
• 5d846d0 Backport PR #66090 on branch 3.0.x (BLD: exclude numpy 2.5.0 when building wh...
• bef7a2b Backport PR #66169 on branch 3.0.x (CI: Fix pyarrow-nightly job (stale nightl...
• 8188eb1 RLS: 3.0.4 (#66079)
• bd35f15 [3.0.x] BUG: fix CoW issue in eval() (#66072)
• 6195872 [backport 3.0.x] BUG: anchor whole alternation in Series.str.match for PyArro...
• 70313be Backport PR #66051 on branch 3.0.x (BUG: fix regression in DataFrame setitem ...
• 57ed3e2 [backport 3.0.x] Bump pypa/cibuildwheel from 3.4.1 to 4.1.0 (#65934) (#66026)
• f9693fc [backport 3.0.x] BUG(pandas 3.0 regression): drop(index=...) doesn't accept N...
• Additional commits viewable in compare view

Updates matplotlib to 3.11.1

Release notes

Sourced from matplotlib's releases.

REL: v3.11.1

This is the first bugfix release of the 3.11.x series.

This release contains several bug-fixes and adjustments:

• Fix tight layout of multiple subplots with sharey=True
• Fix NoNorm cursor formatting for uint8 images
• Fix occasional misalignment in reported mouse position (also fix a bug with canvas height)
• Fix clipped Axis labels on 3D plots with tight layout
• Fix inverted Axis on 3D plots
• Fix restoring 'auto' aspect in 3D axes after switching from 'equal'
• Fix missing glyphs when subsetting Type 1 fonts in PDF
• Fix oversized embedding of Type 42 fonts in PDF/PostScript files

As well as several documentation and typing improvements and corrections.

Commits

• 3c1757a REL: v3.11.1
• 792c6b5 DOC: Prepare for 3.11.1
• aaff9f6 Merge branch 'v3.11.0-doc' into v3.11.x
• d4f4527 Merge pull request #32052 from meeseeksmachine/auto-backport-of-pr-32038-on-v...
• 6ad4bcf Merge pull request #32050 from meeseeksmachine/auto-backport-of-pr-31304-on-v...
• 7fb74d3 Merge pull request #32051 from meeseeksmachine/auto-backport-of-pr-32037-on-v...
• c624aec Backport PR #32038: Fix occasional misalignment in reported mouse position (a...
• 8eda2b7 Backport PR #32037: Bump the actions group with 3 updates
• a0e7ae5 Backport PR #31304: Fix restoring 'auto' aspect in 3D axes after switching fr...
• 9001323 Merge pull request #32047 from meeseeksmachine/auto-backport-of-pr-32025-on-v...
• Additional commits viewable in compare view

Updates numpy to 2.5.1

Release notes

Sourced from numpy's releases.

v2.5.1 (July 4, 2026)

NumPy 2.5.1 Release Notes

The NumPy 2.5.1 is a patch release that fixes bugs discovered after the 2.5.0 release. The most noticeable is the fix is to the numpy datetime cython API which should allow downstream to support NumPy versions older than 2.5. Preparation for Python 3.15 continues along with typing improvements.

This release supports Python versions 3.12-3.14

Changes

• The minimum supported GCC version has been updated from 9.3.0 to 10.3.0

  (gh-31843)

Contributors

A total of 10 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Adhyan Gupta +
• Ankit Ahlawat
• Charles Harris
• Iason Krommydas
• Joren Hammudoglu
• Kumar Aditya
• Nathan Goldbaum
• Sebastian Berg
• Ties Jan Hefting +
• Vineet Kumar

Pull requests merged

A total of 20 pull requests were merged for this release.

• #31707: MAINT: Prepare 2.5.x for further development
• #31721: CI: fix new cython-lint errors (#31711)
• #31723: MAINT: Update meson to match main
• #31729: TST: use setup-sde instead of curl to get SDE binaries (#31727)
• #31829: BUG: Relax finfo to be easier accessible for all user dtypes...
• #31831: TYP: Fix flatiter.__next__ return type for object_ and...
• #31832: BUG: avoid deadlocks using NpyString API (#31682)
• #31833: BUG: fix out array leak in reduceat and accumulate when dtype...
• #31835: BUG: fix numpy datetime cython APIs to be compatible with older...
• #31836: TYP: Fix incorrect dtype inference of asarray([]) (#31732)
• #31837: TYP: Fix np.ma.masked_array 2.5.0 regression
• #31838: FIX: Refactor error handling in array_setstate to prevent typecode...
• #31839: TST: xfail multithreaded BLAS test more generously
• #31840: MAINT: Rename subroutine for crackfortran tests

... (truncated)

Changelog

Sourced from numpy's changelog.

This is a walkthrough of the NumPy 2.4.0 release on Linux, which will be the first feature release using the numpy/numpy-release <https://github.com/numpy/numpy-release>__ repository.

The commands can be copied into the command line, but be sure to replace 2.4.0 with the correct version. This should be read together with the :ref:general release guide <prepare_release>.

Facility preparation

Before beginning to make a release, use the requirements/*_requirements.txt files to ensure that you have the needed software. Most software can be installed with pip, but some will require apt-get, dnf, or whatever your system uses for software. You will also need a GitHub personal access token (PAT) to push the documentation. There are a few ways to streamline things:

• Git can be set up to use a keyring to store your GitHub personal access token. Search online for the details.

Prior to release

Add/drop Python versions

When adding or dropping Python versions, multiple config and CI files need to be edited in addition to changing the minimum version in pyproject.toml. Make these changes in an ordinary PR against main and backport if necessary. We currently release wheels for new Python versions after the first Python RC once manylinux and cibuildwheel support that new Python version.

Backport pull requests

Changes that have been marked for this release must be backported to the maintenance/2.4.x branch.

Update 2.4.0 milestones

Look at the issues/prs with 2.4.0 milestones and either push them off to a later version, or maybe remove the milestone. You may need to add a milestone.

Check the numpy-release repo

... (truncated)

Commits

• 5e1d03f Merge pull request #31863 from charris/prepare-2.5.1
• ad0b66b REL: Prepare for the NumPy 2.5.1 release.
• 9df8516 Merge pull request #31858 from charris/backport-31688
• 4dee265 Merge pull request #31857 from charris/backport-31775
• dc8d553 Merge pull request #31856 from charris/backport-31846
• 67cb4a8 fix:Signed integer overflow in datetime.c (#31688)
• baa2589 TST: Clean up imports, formatting, and assertions
• 2fe5ba4 TEST: Refactor tests to use np.testing.assert_raises_regex per review
• bb46581 MAINT: Remove deprecated Python recursion fix
• 8f34214 MAINT: Move SeedSequence recursion guard to C-layer and add tests
• Additional commits viewable in compare view

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