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Bumps the python-deps group with 10 updates in the / directory:

Package From To
pydantic 2.13.4 2.13.5
pandas 3.0.3 3.0.5
tqdm 4.68.2 4.70.0
rdkit 2026.3.3 2026.3.5
idna 3.18 3.19
meeko 0.7.1 0.8.0
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 0.16.5

Updates pydantic from 2.13.4 to 2.13.5

Release notes

Sourced from pydantic's releases.

v2.13.5 (2026-08-28)

What's Changed

Fixes

  • Allow reuse of validators when plugins are set by @​Viicos in #13535
  • Fix missing GC traversal on some pydantic-core struct fields by @​Viicos in #13624
  • Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer by @​Viicos in #13629
  • Count validated model fields once in smart unions by @​tamird in #13731
Changelog

Sourced from pydantic's changelog.

v2.13.5 (2026-08-28)

GitHub release

What's Changed

Fixes

  • Allow reuse of validators when plugins are set by @​Viicos in #13535
  • Fix missing GC traversal on some pydantic-core struct fields by @​Viicos in #13624
  • Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer by @​Viicos in #13629
  • Count validated model fields once in smart unions by @​tamird in #13731
Commits
  • 001dea0 Bump pypa/gh-action-pypi-publish action to v1.14.2
  • 558379f Bump twine to v7.0.0
  • 2cfd5d3 Do not check for docs build
  • a735bee Fix more Clippy lints
  • 7eed4a1 Fix Clippy 0.1.95 warnings
  • b353bbb Prepare release v2.13.5
  • 63d2ccc Count validated model fields once in smart unions
  • a53ec2e Speed up PyPy CI tests
  • d65e0f9 Workaround circular import error in Mypy
  • 47a6dbf Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer
  • Additional commits viewable in compare view

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

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

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_6 (Q1 2026) Release

Release_2026.03.6

(Changes relative to Release_2026.03.5)

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)

Kevin Boyd, Michael Cho, David Cosgrove, Mike DePaulo, Paul Emsley, Guillaume Godin, Niels Maeder, Vedran Miletić, younes ouzza, Ricardo Rodriguez, Wonseok Shin, Chris Von Bargen, Rachel Walker, Shin,

New Features and Enhancements:

  • Synthon space shape search (github pull #9279 from DavidACosgrove)
  • Speed-up BertzCT, no value changes (github pull #9447 from gratus907)
  • change source of freetype in docker builds (github pull #9448 from greglandrum)
  • Install header for SGroup data label API (github pull #9453 from cdvonbargen)
  • support ignoreAtoms in RDKitFingerprintGenerators (github pull #9459 from greglandrum)
  • ConfGen: Use a better estimate of 1-2 distances when we don't have UFF atom params (github pull #9465 from greglandrum)
  • Reduce SMILES parser bond property staging (github pull #9476 from scal444)
  • Reuse Hanoi scratch buffer in canonical ranking (github pull #9478 from scal444)
  • Use insertion sort for canonical neighbors (github pull #9492 from scal444)
  • Reduce comparisons and branches in bondholder compare (github pull #9497 from scal444)
  • Cache isAtomConjugCand in markConjAtomBonds (github pull #9498 from scal444)
  • Make checking in checked iterators stricter to avoid heap-use-after-free problems (github pull #9500 from ricrogz)

Documentation:

  • Correct comment in Point::signedAngleTo. (github pull #9445 from DavidACosgrove)

Bug Fixes:

  • make GaussianShape build without SimDivPickers on big-endian (github pull #9438 from mikedep333)
  • Fix numpy dtype handling in the InfoTheory wrappers (github pull #9443 from gratus907)
  • Three small bugs (github pull #9444 from vedranmiletic)

... (truncated)

Commits

Updates idna from 3.18 to 3.19

Release notes

Sourced from idna's releases.

v3.19

  • Restore the std3_rules option, which had no effect since changes to UTS #46 processing in Unicode 16. Note that uts46_remap() defaults to enabling STD3 rules, so direct callers will see input containing non-LDH ASCII characters rejected again.
  • Performance improvements to UTS #46 mapping, particularly for ASCII-only domains.
  • Test on free-threaded CPython with the GIL disabled and document thread safety.
  • Expose the Unicode version of the generated tables as idna.unicode_version, and show it in idna --version.
  • Add code, text, codepoint and position attributes to IDNAError so that the failed rule and the offending character can be identified without parsing the exception message.
  • The deprecated transitional argument to encode() and uts46_remap() is now completely ignored, and gives a deprecation warning for the latter.
  • Reject A-labels that are not the canonical Punycode encoding of their U-label.
  • Fix CONTEXTJ violations raising IDNAError instead of InvalidCodepointContext.
  • Consistently raise IDNAError for empty labels and non-ASCII bytes passed to label helper functions and the incremental codec.
  • Add property-based tests, extended fuzzing targets, coverage measurement, and CI checks that the data tables match the generator output.
  • Various code quality and tooling improvements.

Thanks to stefan6419846, LouieLuNZ, and Salvatore Corvaglia for contributions to this release.

Changelog

Sourced from idna's changelog.

3.19 (2026-08-18)

  • Restore the std3_rules option, which had no effect since changes to UTS #46 processing in Unicode 16. Note that uts46_remap() defaults to enabling STD3 rules, so direct callers will see input containing non-LDH ASCII characters rejected again.
  • Performance improvements to UTS #46 mapping, particularly for ASCII-only domains.
  • Test on free-threaded CPython with the GIL disabled and document thread safety.
  • Expose the Unicode version of the generated tables as idna.unicode_version, and show it in idna --version.
  • Add code, text, codepoint and position attributes to IDNAError so that the failed rule and the offending character can be identified without parsing the exception message.
  • The deprecated transitional argument to encode() and uts46_remap() is now completely ignored, and gives a deprecation warning for the latter.
  • Reject A-labels that are not the canonical Punycode encoding of their U-label.
  • Fix CONTEXTJ violations raising IDNAError instead of InvalidCodepointContext.
  • Consistently raise IDNAError for empty labels and non-ASCII bytes passed to label helper functions and the incremental codec.
  • Add property-based tests, extended fuzzing targets, coverage measurement, and CI checks that the data tables match the generator output.
  • Various code quality and tooling improvements.

Thanks to stefan6419846, LouieLuNZ, and Salvatore Corvaglia for contributions to this release.

Commits
  • 03a9a11 Release 3.19
  • 2d2a7ef Pre-release 3.19rc0
  • 5cce130 Merge pull request #268 from kjd/fix-std3-regex-alert
  • 3914b75 Split the STD3 disallowed-character range so uppercase is explicit
  • ce9fd98 Merge pull request #267 from kjd/housekeeping
  • 809240c Fail CI when the license copyright year is behind the current year
  • d9e16c5 Consolidate test fixtures, prune stale gitignore entries, and fix doc typos
  • ef30fee Remove dead code and pare back superfluous comments
  • b907913 Tighten the version support and Unicode notes in the README
  • 6204cbe Ignore local build artifacts and stop packaging stray tooling config
  • Additional commits viewable in compare view

Updates meeko from 0.7.1 to 0.8.0

Release notes

Sourced from meeko's releases.

v0.8.0

What's changed

... (truncated)

Commits
  • 41ff641 update version strings to 0.8.0
  • 6a98ea1 Merge pull request #493 from forlilab/491
  • a482043 reduce excessive verbosity of LLM generated code
  • 95ec747 Merge pull request #486 from forlilab/adjacent_padding
  • dbaf80c fix: handle mmCIF null charge markers ('?', '.') in from_cif (#491)
  • d1f5c87 feat: allow arbitrary monomers and bonds in padding
  • 2b27ca4 Merge pull request #487 from JustinKyleKirkland/fix-box-enveloping-padding
  • e4b3b42 fix: use args.padding in box_enveloping branch
  • d1ff829 test adjacent padding for disulfides
  • 7456c42 test: added a couple of tests for the adjacent padding
  • Additional commits viewable 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() &lt;packaging.specifiers.SpecifierSet.to_range&gt;,
    
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() &lt;packaging.specifiers.SpecifierSet.is_subset&gt;, :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

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 0.16.5

Release notes

Sourced from ruff's releases.

0.16.5

Release Notes

Released on 2026-08-27.

Preview features

  • Allow rules without codes (#28049)
  • Introduce category selectors (#27666)
  • Update preview default rules and categories (#27877)

Bug fixes

  • [flake8-async] Detect blocking generic HTTP requests (ASYNC210) (#28024)
  • [flake8-datetimez] Allow timezone-safe strptime chains (DTZ007) (#28023)
  • [flake8-simplify] Respect side effects in lambda defaults (SIM401) (#28000)

Server

  • Fix duplicated "of" in ClientOptions doc comment (#27978)

Documentation

  • Document rule acceptance guidelines (#27910)
  • Document the new category selectors (#27906)

Contributors

Install ruff 0.16.5

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.16.5/ruff-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy Bypass -c "irm https://releases.astral.sh/github/ruff/releases/download/0.16.5/ruff-installer.ps1 | iex"

Download ruff 0.16.5

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.5

Released on 2026-08-27.

Preview features

  • Allow rules without codes (#28049)
  • Introduce category selectors (#27666)
  • Update preview default rules and categories (#27877)

Bug fixes

  • [flake8-async] Detect blocking generic HTTP requests (ASYNC210) (

@dependabot
build(deps): bump the python-deps group across 1 directory with 10 up…
8eee28d 
…dates

Bumps the python-deps group with 10 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [pydantic](https://github.com/pydantic/pydantic) | `2.13.4` | `2.13.5` |
| [pandas](https://github.com/pandas-dev/pandas) | `3.0.3` | `3.0.5` |
| [tqdm](https://github.com/tqdm/tqdm) | `4.68.2` | `4.70.0` |
| [rdkit](https://github.com/rdkit/rdkit) | `2026.3.3` | `2026.3.5` |
| [idna](https://github.com/kjd/idna) | `3.18` | `3.19` |
| [meeko](https://github.com/forlilab/meeko) | `0.7.1` | `0.8.0` |
| [packaging](https://github.com/pypa/packaging) | `26.2` | `26.3` |
| [torch-geometric](https://github.com/pyg-team/pytorch_geometric) | `2.8.0` | `2.8.0.post1` |
| [pytest](https://github.com/pytest-dev/pytest) | `9.0.3` | `9.1.1` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.17` | `0.16.5` |



Updates `pydantic` from 2.13.4 to 2.13.5
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/v2.13.5/HISTORY.md)
- [Commits](pydantic/pydantic@v2.13.4...v2.13.5)

Updates `pandas` from 3.0.3 to 3.0.5
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v3.0.3...v3.0.5)

Updates `tqdm` from 4.68.2 to 4.70.0
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](tqdm/tqdm@v4.68.2...v4.70.0)

Updates `rdkit` from 2026.3.3 to 2026.3.5
- [Release notes](https://github.com/rdkit/rdkit/releases)
- [Changelog](https://github.com/rdkit/rdkit/blob/master/ReleaseNotes.md)
- [Commits](https://github.com/rdkit/rdkit/commits)

Updates `idna` from 3.18 to 3.19
- [Release notes](https://github.com/kjd/idna/releases)
- [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.md)
- [Commits](kjd/idna@v3.18...v3.19)

Updates `meeko` from 0.7.1 to 0.8.0
- [Release notes](https://github.com/forlilab/meeko/releases)
- [Commits](forlilab/Meeko@v0.7.1...v0.8.0)

Updates `packaging` from 26.2 to 26.3
- [Release notes](https://github.com/pypa/packaging/releases)
- [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst)
- [Commits](pypa/packaging@26.2...26.3)

Updates `torch-geometric` from 2.8.0 to 2.8.0.post1
- [Release notes](https://github.com/pyg-team/pytorch_geometric/releases)
- [Changelog](https://github.com/pyg-team/pytorch_geometric/blob/2.8.0.post1/CHANGELOG.md)
- [Commits](pyg-team/pytorch_geometric@2.8.0...2.8.0.post1)

Updates `pytest` from 9.0.3 to 9.1.1
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@9.0.3...9.1.1)

Updates `ruff` from 0.15.17 to 0.16.5
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.17...0.16.5)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-version: 2.13.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: pandas
  dependency-version: 3.0.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: tqdm
  dependency-version: 4.70.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: rdkit
  dependency-version: 2026.3.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: idna
  dependency-version: '3.19'
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: meeko
  dependency-version: 0.8.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: packaging
  dependency-version: '26.3'
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: torch-geometric
  dependency-version: 2.8.0.post1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-deps
- dependency-name: pytest
  dependency-version: 9.1.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-deps
- dependency-name: ruff
  dependency-version: 0.16.5
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-deps
...

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@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Sep 4, 2026
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