build(deps): bump the python-deps group across 1 directory with 6 updates

[dependabot]

Bumps the python-deps group with 6 updates in the / directory:

Package	From	To
pandas	3.0.3	3.0.5
tqdm	4.68.2	4.69.1
rdkit	2026.3.3	2026.3.4
torch-geometric	2.8.0	2.8.0.post1
pytest	9.0.3	9.1.1
ruff	0.15.17	0.16.0

Updates pandas from 3.0.3 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.

pandas 3.0.4

We are pleased to announce the release of pandas 3.0.4. 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 tqdm from 4.68.2 to 4.69.1

Release notes

Sourced from tqdm's releases.

tqdm v4.69.0 stable

• add tqdm.asyncio.gather(..., return_exceptions=False) (#1776, #1671 <- #1286)
• misc minor framework updates
  • bump workflow actions & pre-commit hooks

tqdm v4.68.4 stable

• trim to ncols even when '{bar}' not in bar_format (#1717, #1767 <- #1658)
• fix tqdm.write when stdout=None (#1768 <- #1654)

tqdm v4.68.3 stable

• utils: delay os.get_terminal_size (#1763 <- #1760)
• autonotebook: support QtConsole, Spyder, JupyterLite (#1763, #1628, #1559 <- #1283, #1098, #512)
• minor docs updates
  • fix typo (#1762)
  • use git-fame
• misc minor framework updates
  • fix & update CI build
  • pre-commit: add docs & metadata generation
  • move tox.ini -> pyproject.toml, move tox-gh-actions -> tox-gh
  • add Python 3.14, drop 3.7 support

Commits

• 93370ff bump version, merge pull requests #1781, #1773, #1778, #1775, #1780, #1746
• 238501f docs: fix redundant word typo in tests_synchronisation.py
• b78624a contrib.logging: preserve filters
• 9f92bc6 remove unnecessary comments
• 494372e Fix AttributeError in close() on failed __init__
• 796cea1 misc tidy
• 164ef73 rich: misc fixes
• f18c88e fix properly
• 90f5970 minor tidy
• ef15578 fix: handle total=inf in format_meter to avoid OverflowError
• Additional commits viewable in compare view

Updates rdkit from 2026.3.3 to 2026.3.4

Release notes

Sourced from rdkit's releases.

2026_03_4 (Q1 2026) Release

Release_2026.03.4

(Changes relative to Release_2026.03.3)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to see your contribution acknowledged with your name, please set your name in GitHub)

Rody Arantes, Katharina Buchthal, David Cosgrove, Tad Hurst, Steven Kearnes, Brian Kelley, Niels Maeder, John Mayfield, Dan Nealschneider, Yakov Pechersky, Ricardo Rodriguez, Jon Swain, Rachel Walker, Inwan Yoo, Nic Zonta, ankar-dav, ajeyabsf, thomp-j, vwe-ibm

Backwards incompatible changes:

• MolTransforms.h now includes <Eigen/Core> instead of <Eigen/Dense>. C++ code that included MolTransforms.h and relied on it to transitively pull in the Eigen dense modules (LU/QR/SVD/etc.) must now include <Eigen/Dense> directly.
• The DistGeomHelpers::EmbedParameters struct no longer has a constructor that takes arguments in C++. If you want to initialize data members to non-default values, use the designated initialization syntax. This change does not affect Python.

New Features and Enhancements:

• Add spiro flipping to 2D coord generation (github pull #9204 from ZontaNicola)
• Adds SVE to BFGSOpt (github pull #9216 from ajeyabsf)
• Multi conf gaussian shape (github pull #9265 from DavidACosgrove)
• All-In-One coordinate refinement for ETKDG (github pull #9292 from nmaeder)
• Synthon substructure search 2x performance (github pull #9307 from d-b-w)
• Configurable stereo labels in MolDraw2D (github pull #9311 from DavidACosgrove)
• Replace combineMols with RWMol::insertMol in SynthonSpaceSearch (github pull #9319 from DavidACosgrove)
• Add opt-in unity (jumbo) builds + fix latent missing include guards (github pull #9342 from skearnes)
• Make substructure search Ctrl+c interruptible (github pull #9349 from ricrogz)

Documentation:

• rdchem.pyi typing issue: non-default parameter following default parameter (github issue #9335 from ankar-dav)

Bug Fixes:

• Update RDKit_Book.rst (github pull #7946 from johnmay)

... (truncated)

Commits

• See full diff in compare view

Updates torch-geometric from 2.8.0 to 2.8.0.post1

Changelog

Sourced from torch-geometric's changelog.

[2.8.0.post1] - 2026-07-20

Fixed

• Added the missing source distribution to the PyPI release.

Commits

• d4e1c45 Prepare for 2.8.0.post1 (#10749)
• See full diff in compare view

Updates pytest from 9.0.3 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.

9.1.0

pytest 9.1.0 (2026-06-13)

Removals and backward incompatible breaking changes

• #14533: When using --doctest-modules, autouse fixtures with module, package or session scope that are defined inline in Python test modules (not plugins or conftests) will now possibly execute twice.

  If this is undesirable, move the fixture definition to a conftest.py file if possible.

  Technical explanation for those interested: When using --doctest-modules, pytest possibly collects Python modules twice, once as pytest.Module and once as a DoctestModule (depending on the configuration). Due to improvements in pytest's fixture implementation, if e.g. the DoctestModule collects a fixture, it is now visible to it only, and not to the Module. This means that both need to register the fixtures independently.

Deprecations (removal in next major release)

• #10819: Added a deprecation warning for class-scoped fixtures defined as instance methods (without @classmethod). Such fixtures set attributes on a different instance than the test methods use, leading to unexpected behavior. Use @classmethod decorator instead -- by yastcher.

  See 10819 and 14011.

• #12882: Calling request.getfixturevalue() <pytest.FixtureRequest.getfixturevalue> during teardown to request a fixture that was not already requested is now deprecated and will become an error in pytest 10.

  See dynamic-fixture-request-during-teardown for details.

• #13409: Using non-~collections.abc.Collection iterables (such as generators, iterators, or custom iterable objects) for the argvalues parameter in @pytest.mark.parametrize <pytest.mark.parametrize ref> and metafunc.parametrize <pytest.Metafunc.parametrize> is now deprecated.

  These iterables get exhausted after the first iteration, leading to tests getting unexpectedly skipped in cases such as running pytest.main() multiple times, using class-level parametrize decorators, or collecting tests multiple times.

  See parametrize-iterators for details and suggestions.

• #13946: The private config.inicfg attribute is now deprecated. Use config.getini() <pytest.Config.getini> to access configuration values instead.

  See config-inicfg for more details.

• #14004: Passing baseid to ~pytest.FixtureDef or nodeid strings to fixture registration APIs is now deprecated. These are internal pytest APIs that are used by some plugins.

... (truncated)

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 ruff from 0.15.17 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.

• 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.

• 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

... (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

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