build(deps): bump the python-deps group across 1 directory with 7 updates

[dependabot]

Bumps the python-deps group with 7 updates in the / directory:

Package	From	To
pandas	3.0.3	3.0.5
tqdm	4.68.2	4.70.0
rdkit	2026.3.3	2026.3.5
packaging	26.2	26.3
torch-geometric	2.8.0	2.8.0.post1
pytest	9.0.3	9.1.1
ruff	0.15.17	0.16.2

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 4.70.0

Release notes

Sourced from tqdm's releases.

tqdm v4.70.0 stable

• contrib.concurrent: major improvements
  • support process_map(mp_context, max_tasks_per_child), thread_map(thread_name_prefix) (#1265)
  • fix total based on shortest iterable length (#1473)
  • use default max_workers (#1543 <- #1530, #1518)
  • support timeout, buffersize (#1576)
  • improve ETA (#1708 <- #1161)
  • update as_completed (#1709 <- #1565)
  • add tqdm.concurrent.intepreter_map (#1777)
• asyncio: support iterables with only __aiter__ (#1714 <- #1686)
• support reset(float("inf")) (#1783 <- #1781, #651)
• framework: test & reduce wheel size (#1782)

tqdm v4.69.1 stable

• contrib.logging: preserve filters (#1775 <- #1581)
• rich: misc fixes (#1773)
  • support generators (without len) (#1391)
  • fix potential AttributeError on exit (#1674)
• fix total=float('inf') (#1781 <- #651)
• fix potential AttributeError on exit (#1778 <- #1668, #1537, #261)
• fix minor docs typos (#1780, #1746)

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

• 96f2e60 Merge pull request #1777 from shermansiu/feat/interpreter-pool
• c27393e misc tidy
• 061c623 Disable tqdm.monitor_interval for subinterpreters because they do not have ...
• 9fc160b Update how we check for interpreter_map support in the tests
• b42463a Ensure that subinterpreters can import tqdm while unpickling the initializer
• 16d5486 Add support for nested progress bars
• 9f5890f Add initial implementation for interpreter_map
• 321f920 Merge pull request #1783 from LuShadowX/reset-inf-total
• 4664b57 minor tidy
• 426a098 Treat inf total as unknown in reset() too
• Additional commits viewable in compare view

Updates rdkit from 2026.3.3 to 2026.3.5

Release notes

Sourced from rdkit's releases.

2026_03_5 (Q1 2026) Release

Release_2026.03.5

(Changes relative to Release_2026.03.4)

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)

Katharina Buchthal, Kerim Buyukakyuz, David Cosgrove, Peter Gedeck, Tad Hurst, Egor Lyfar, Niels Maeder, Vedran Miletić, Yakov Pechersky, Emily Rhodes Jake Robson-Tull, Ricardo Rodriguez, Pavel Tomanek, Paolo Tosco, Ivan Tubert-Brohman, m_holmer

New Features and Enhancements:

• Add ROMol name accessors (github pull #9384 from i-tub)
• Handle Data SGroups with no "fieldname" (github pull #9390 from tadhurst-cdd)
• Validate coordinate map entries before distance geometry embedding (github pull #9420 from lyfar)

Documentation:

• Add stub for rdGaussianShape docs. (github pull #9440 from DavidACosgrove)

Bug Fixes:

• TautomerEnumerator.Canonicalize() raises pre-condition violation when SetRemoveBondStereo(False) on a molecule with atropisomer bond (github issue #9338 from pechersky)
• CDXML reading doesn't retain Z/E bonds (github issue #9356 from pechersky)
• RuntimeError while extracting a fragment from a molecule that cuts after an E/Z double bond (github issue #9368 from MalteHolmer)
• Fix race in MinimalLib test_substruct_library JS test (github pull #9392 from emilyrrhodes)
• Aromaticity perception in polycyclic conjugated system (github issue #9398 from nmaeder)
• Inconsistent stereochemistry of ring-bonds in BoundsMatrixBuilder (github issue #9403 from kabu00002)
• Inconsistent bounds for 1-4 distances of 6-membered rings (github issue #9404 from kabu00002)
• RDKit 2026.03.4: testDistGeomHelpers fails (github issue #9406 from pavelToman)
• Fix 64-bit fingerprint bit ID truncation in AdditionalOutput on 32-bit targets (github pull #9411 from gedeck)
• Rascal FindMCES crash when time out reached and maxFragSeparation set (github issue #9418 from jrobsontull)
• Out-of-bounds read in Mol2 bond parser due to incorrect bounds check (github issue #9421 from buyukakyuz)
• Fix maeparser warning suppression with GCC

... (truncated)

Commits

• See full diff in compare view

Updates packaging from 26.2 to 26.3

Release notes

Sourced from packaging's releases.

26.3

What's Changed

Features

• Add a public VersionRange API and SpecifierSet.to_range(), representing the versions a specifier set accepts as an interval set that supports intersection, union, difference, complement, set relations, membership tests, and filtering. VersionRange.to_specifier_set() converts a range back to a SpecifierSet where a PEP 440 form exists. (#1267, #1270, #1298)
• PEP 808: accept Metadata-Version: 2.6. (#1194)
• Add a limit argument to parse_tag() for compressed tag sets. (#1220)
• Add a prefer_sdist_predicate argument to Pylock.select() to prefer source distributions over wheels for selected packages. (#1334)
• Add pure_python_tags() to generate the pure-Python tags for a Python version without touching the running platform. (#1346)
• Add SpecifierSet.is_subset(), SpecifierSet.is_superset(), and SpecifierSet.is_disjoint(), which compare the versions two specifier sets accept. (#1313)

Behavior adaptations

• Drop support for Python 3.8; packaging now requires Python 3.9 or later. (#1157)
• Prefer native linux_* platform tags over manylinux and musllinux tags on Linux. (#160)

Fixes for versions and specifiers

• Raise InvalidVersion instead of TypeError when Version is given a non-string. (#1319)
• Raise InvalidVersion for non-string pre-release letters passed to Version.from_parts. (#1241)
• Fix an AttributeError when hashing internally trimmed versions. (#1242)
• Fix SpecifierSet.is_unsatisfiable for post-release boundary intersections. (#1257)

Fixes for requirements and markers

• Make Requirement.__hash__ consistent with __eq__ for trailing-zero-equivalent specifiers (e.g. foo==1.0.0 and foo==1.0.0.0), so equal requirements hash equal and deduplicate in sets and dicts. (#1232)
• Normalize requested extra names before comparing or hashing requirements. (#644)
• Preserve a Requirement's specifier prereleases override across a pickle round trip. (#1204)
• Raise InvalidRequirement instead of InvalidSpecifier when a requirement contains an invalid specifier. (#1332)
• Clarify the error for post-release prefix wildcards like ==1.0.post1.*. (#1299)
• Preserve quoting semantics when serializing marker values, so round-tripped markers parse back to the same marker. (#1213)
• Keep the parentheses of a nested group when serializing markers. (#1316)
• Normalize extra and dependency_groups values in nested markers at parse time. (#1246, #1310)
• Raise UndefinedComparison when a set-valued variable like extras is used outside the membership form. (#1265)
• Raise UndefinedEnvironmentName (a KeyError subclass) for missing environment keys during marker evaluation. (#1276)
• Wrap malformed string literal errors in InvalidMarker / InvalidRequirement instead of leaking a low-level error. (#1249)
• Reject requirements and markers with a trailing line break. (#1345)

Fixes for metadata and licenses

• Collect all from_email validation errors into one ExceptionGroup instead of raising the first. (#1268)
• Accept the UTF-8 charset case-insensitively in email payloads. (#1330)
• Reject malformed Description-Content-Type values. (#1329)
• Don't rewrite user values that contain {field} placeholders in error messages. (#1327)
• Route multipart email payloads to unparsed instead of asserting. (#1247)
• Make InvalidMetadata and CyclicDependencyGroup picklable. (#1328)
• Fold every line boundary str.splitlines recognizes when writing a header with RFC822Message. (#1356)

... (truncated)

Changelog

Sourced from packaging's changelog.

26.3 - 2026-08-03

Features:

Add a public :class:~packaging.ranges.VersionRange API and

:meth:SpecifierSet.to_range() <packaging.specifiers.SpecifierSet.to_range>,

representing the versions a specifier set accepts as an interval set that

supports intersection, union, difference, complement, set relations,

membership tests, and filtering.

:meth:~packaging.ranges.VersionRange.to_specifier_set converts a range back

to a :class:~packaging.specifiers.SpecifierSet where a PEP 440 form exists.

(:pull:1267, :pull:1270, :pull:1298)
PEP 808: accept Metadata-Version: 2.6. (:pull:1194)
Add a limit argument to parse_tag() for compressed tag sets.

(:issue:1220)
Add a prefer_sdist_predicate argument to Pylock.select() to prefer

source distributions over wheels for selected packages. (:pull:1334)
Add :func:~packaging.tags.pure_python_tags to generate the pure-Python

tags for a Python version without touching the running platform.

(:pull:1346)
Add :meth:SpecifierSet.is_subset() <packaging.specifiers.SpecifierSet.is_subset>, :meth:~packaging.specifiers.SpecifierSet.is_superset,

and :meth:~packaging.specifiers.SpecifierSet.is_disjoint, which compare the

versions two specifier sets accept. (:pull:1313)

Behavior adaptations:

Drop support for Python 3.8; packaging now requires Python 3.9 or later.

(:pull:1157)
Prefer native linux_* platform tags over manylinux and musllinux

tags on Linux. (:issue:160)

Fixes for versions and specifiers:

Raise InvalidVersion instead of TypeError when Version is given a

non-string. (:pull:1319)
Raise InvalidVersion for non-string pre-release letters passed to

Version.from_parts. (:pull:1241)
Fix an AttributeError when hashing internally trimmed versions.

(:pull:1242)
Fix SpecifierSet.is_unsatisfiable for post-release boundary

intersections. (:pull:1257)

Fixes for requirements and markers:

Make Requirement.__hash__ consistent with __eq__ for

trailing-zero-equivalent specifiers (e.g. foo==1.0.0 and

foo==1.0.0.0), so equal requirements hash equal and deduplicate in

sets and dicts. (:pull:1232)

</tr></table>

... (truncated)

Commits

• 929fd4b Bump for release
• f300ebf chore(deps): bump the pre-commit group with 5 updates (#1357)
• f91d975 ci(downstream): bump hatchling to 1.31.0 and fix its pytest rootdir (#1361)
• b1a7124 chore(deps): bump the github-actions group with 7 updates (#1358)
• 2d873eb fix(metadata): fold every line boundary when writing headers (#1356)
• 413d006 docs: changelog for 26.3 (#1343)
• 4eb0753 docs(metadata): explain selective field validation (#1342)
• 77e9ed4 feat(tags): add pure Python tag generator (#1346)
• 7cea5e8 ci: drop 3.13t on Windows (3.13.14t may fail to build, run takes 9 minutes) (...
• 45a8b34 docs: add missing versionadded/versionchanged directives (#1344)
• Additional commits viewable 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 0.16.2

Release notes

Sourced from ruff's releases.

0.16.2

Release Notes

Released on 2026-08-06.

Bug fixes

• [flake8-pyi] Avoid false positives on singledispatch functions (PYI041) (#27335)

Server

• Register formatting capabilities dynamically to exclude TOML files (#27332)

Contributors

• @​MeGaGiGaGon
• @​charliermarsh
• @​epage
• @​sharkdp
• @​ntBre

Install ruff 0.16.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.16.2/ruff-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy Bypass -c "irm https://releases.astral.sh/github/ruff/releases/download/0.16.2/ruff-installer.ps1 | iex"

Download ruff 0.16.2

File	Platform	Checksum
ruff-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
ruff-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
ruff-aarch64-pc-windows-msvc.zip	ARM64 Windows	checksum
ruff-i686-pc-windows-msvc.zip	x86 Windows	checksum
ruff-x86_64-pc-windows-msvc.zip	x64 Windows	checksum
ruff-aarch64-unknown-linux-gnu.tar.gz	ARM64 Linux	checksum
ruff-i686-unknown-linux-gnu.tar.gz	x86 Linux	checksum
ruff-powerpc64-unknown-linux-gnu.tar.gz	PPC64 Linux	checksum
ruff-powerpc64le-unknown-linux-gnu.tar.gz	PPC64LE Linux	checksum
ruff-riscv64gc-unknown-linux-gnu.tar.gz	RISCV Linux	checksum
ruff-s390x-unknown-linux-gnu.tar.gz	S390x Linux	checksum

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.2

Released on 2026-08-06.

Bug fixes

• [flake8-pyi] Avoid false positives on singledispatch functions (PYI041) (#27335)

Server

• Register formatting capabilities dynamically to exclude TOML files (#27332)

Contributors

• @​MeGaGiGaGon
• @​charliermarsh
• @​epage
• @​sharkdp
• @​ntBre

0.16.1

Released on 2026-07-30.

Preview features

• Add an option to opt out of human-readable names (#27160)
• [flake8-pytest-style] Make fixes safe by default and unsafe only when comments are present (PT018) (#27201)
• [pyupgrade] Skip fix when a defaulted TypeVar precedes a non-defaulted one (UP040, UP046, UP047) (#27133)
• [ruff] Fix false positive with unpacked arguments (RUF065) (#26959)

Bug fixes

• Bump gen-lsp-types to gracefully handle unknown enumeration values in LSP messages (#27230)
• [flake8-bugbear] Mark range as immutable (B008) (#27247)
• [flake8-comprehensions] NFKC-normalize keyword names in C408 fix (#26813)
• [flake8-return] Fix false positive when variable is read in finally clause (RET504) (#25441)
• [pydocstyle] Skip section detection inside RST directive bodies (D214, D405, D413) (#23635)
• [refurb] Parenthesize yield arguments in the FURB192 fix (#27192)

Rule changes

• [flake8-pytest-style] Mark PT022 fixes as unsafe (#26440)
• [refurb] Mark fixes that remove unknown separators as unsafe (FURB105) (#27200)

Server

• Fix indexing of excluded nested Ruff workspaces (#27303)
• Lint TOML files in the LSP (#26862)

... (truncated)

Commits

• 5b48a04 Bump 0.16.2 (#27555)
• 1b9e5fc Update Swatinem/rust-cache action to v2.9.2 (#27568)
• c4e86fc [ty] Add helper extension methods for half-range and equality constraints (#2...
• 17a00de [ty] Reuse primer commands in memory reports (#27553)
• 6ea296b [ty] Normalize type labels in structured docstrings (#26923)
• 2fc445f [ty] Diagnose invalid getattr calls (#27502)
• 22c7823 [ty] Enable (but downrank) auto-import completion suggestions from stub-only ...
• 05160d5 [ty] Diagnose invalid descriptor __get__ calls (#27400)
• baea3d0 [ty] Expose strict analysis options in the playground (#27543)
• c88946e [ty] Bump ecosystem-analyzer for strict project settings (#27542)
• Additional commits viewable in compare view

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