[dependabot]

Bumps the python-dependencies group with 3 updates: rdkit, pytest and ruff.

Updates rdkit from 2026.3.6 to 2026.9.1

Release notes

Sourced from rdkit's releases.

2026_09_1 (Q3 2026) Release

Release_2026.09.1

(Changes relative to Release_2026.03.1)

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)

reza bagheri alashti, Rody Arantes, Marco Ballarotto, Chris Von Bargen, Kevin Boyd, Katharina Buchthal, Kerim Buyukakyuz, Arthur Chan, Michael Cho, David Cosgrove, Mike DePaulo, Eloy Félix, Peter Gedeck, Lukas Geiger, Guillaume Godin, Huw Jones, Steven Kearnes, Brian Kelley, Jakub Klinkovský, Jimmy Kromann, Niels Maeder, John Mayfield, Vedran Miletić, Dan Nealschneider, Dmytro Radchenko, Emily Rhodes, Ricardo Rodriguez, Wonseok Shin, Raul Sofia, Vaibhav Srivastava, Jon Swain, Pavel Tomanek, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello, Inwan Yoo, Nic Zonta, dd, ajeyabsf, m_holmer, zengkaipeng(SII), css, reowszer, thomp-j, vwe-ibm, ankar-dav, dpdoughe

Highlights

• This release includes a number of improvements to the RDKit's conformer generator, including beta versions of ETKDGv4 and a new strategy for selecting initial coordinates. These are not yet used by default, but we encourage people to try them out - try the rdDistGeom.ETKDGv4 parameters object and/or setting initialEmbeddingMode to rdDistGeom.INTERNAL_COORDINATE_EMBEDDING - and are looking for feedback.
• We've created a new set of Python wrappers based on nanobind instead of Boost::Python. The new wrappers, still in beta, are significantly faster. We will be doing conda-forge builds of the new wrappers and would greatly appreciate feedback from the community.
• It's now possible to do shape-based searches in synthon spaces.

Backwards incompatible changes:

• The C++ canonicalization helpers Canon::initCanonAtoms() and Canon::detail::initFragmentCanonAtoms() now require caller-owned neighbor ID storage. Canon::canon_atom::nbrIds is now a non-owning std::span<int>.
• Canon::canon_atom::bonds now uses boost::container::small_vector.
• Since #9208, atom rings are "normalized" so that the first atom in the ring definition is the one with the lowest index, and the second one is the neighbor to the first which also has the lowest index.
• 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.
• PicklerOps::QueryDetails (in GraphMol/MolPickler.h) is now a std::variant instead of a boost::variant. C++ code that inspects this type must use std::get/std::holds_alternative and .index() in place of boost::get and .which(). MolPickler.h also no longer includes

... (truncated)

Changelog

Sourced from rdkit's changelog.

Release_2027.03.1

(Changes relative to Release_2026.09.1)

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)

Highlights

Backwards incompatible changes:

• RingInfo now stores its rings in flat, contiguous arrays, and most of its C++ methods that returned references to std::vectors now return non-owning std::spans or span-based views. Specifically, RingInfo::atomRings() and RingInfo::bondRings() now return a RingInfo::RingsView instead of const VECT_INT_VECT &, and RingInfo::atomMembers() and RingInfo::bondMembers() now return std::span<const int> instead of const INT_VECT &. These views are invalidated when the RingInfo is modified. RingInfo::addRing() now takes std::span<const int> arguments. The Python, Java, and C# APIs are unchanged.

Code removed in this release:

Deprecated code (to be removed in a future release):

Release_2026.09.1

(Changes relative to Release_2026.03.1)

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)

reza bagheri alashti, Rody Arantes, Marco Ballarotto, Chris Von Bargen, Kevin Boyd, Katharina Buchthal, Kerim Buyukakyuz, Arthur Chan, Michael Cho, David Cosgrove, Mike DePaulo, Eloy Félix, Peter Gedeck, Lukas Geiger, Guillaume Godin, Huw Jones, Steven Kearnes, Brian Kelley, Jakub Klinkovský, Jimmy Kromann, Niels Maeder, John Mayfield, Vedran Miletić, Dan Nealschneider, Dmytro Radchenko, Emily Rhodes, Ricardo Rodriguez, Wonseok Shin, Raul Sofia, Vaibhav Srivastava, Jon Swain, Pavel Tomanek, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello, Inwan Yoo, Nic Zonta, dd, ajeyabsf, m_holmer, zengkaipeng(SII), css, reowszer, thomp-j, vwe-ibm, ankar-dav, dpdoughe

Highlights

• This release includes a number of improvements to the RDKit's conformer generator, including beta versions of ETKDGv4 and a new strategy for selecting initial coordinates. These are not yet used by default, but we encourage people to try them out - try the rdDistGeom.ETKDGv4 parameters object and/or

... (truncated)

Commits

• See full diff in compare view

Updates pytest from 9.1.1 to 9.2.0

Release notes

Sourced from pytest's releases.

9.2.0

pytest 9.2.0 (2026-10-27)

Removals and backward incompatible breaking changes

• #14716: -c now raises a usage error for a path that does not exist, is a directory, or is in a format pytest has no loader for. Such paths were previously either ignored or reported as an unhandled FileNotFoundError.

• #8593: The indirect, ids and scope arguments of Metafunc.parametrize() <pytest.Metafunc.parametrize> -- and therefore of @pytest.mark.parametrize <pytest.mark.parametrize ref> -- are now keyword-only.

  Passing them positionally was a common source of confusing errors, e.g. parametrize("arg1", "arg2", [(1, 2)]) made the argvalues land in indirect and failed with indirect fixture '(1, 2)' doesn't exist; such mistakes now fail with an understandable TypeError. The type annotations have always declared these arguments as keyword-only.

• #993: Plugin import failures at startup are now reported and classified instead of escaping as a raw traceback with the accidental exit code 1:

  • a plugin that cannot be found -- via -p, pytest_plugins or PYTEST_PLUGINS -- exits with pytest.ExitCode USAGE_ERROR (4), like a conftest.py that fails to import;
  • a plugin that is found but raises while importing -- including a broken pytest11 entry point or a missing plugin dependency -- exits with pytest.ExitCode INTERNAL_ERROR (3), with the traceback preserved.

  pytest.main now returns these codes instead of raising ImportError. Also fixed an IndexError from pytest's own internals when the plugin raised an exception with no arguments.

Deprecations (removal in next major release)

• #14742: The private _pytest.python.CallSpec2 name has been renamed to CallSpec. The old CallSpec2 alias remains available for now and will be removed in pytest 10 or 11.

• #14755: Schedule yield_fixture decorator for removal in pytest 10 or 11.

• #14774: Similarly to the deprecation of class-scoped fixtures defined as instance methods in pytest 9.1, all higher-scoped fixtures (module, package, and session) defined as instance methods are now deprecated.

  They suffer from the same issue the original deprecation only fixed for class-scoped fixtures, see 10819 and 14011.

• #14808: Passing a non-string value to a string-typed ini option now emits a pytest.PytestRemovedIn10Warning. This affects [tool.pytest.ini_options] in pyproject.toml. In pytest 10 this will raise a TypeError, matching the behavior of the corresponding TOML config path.

• #7323: Passing bytes to TerminalReporter.write_line() is now deprecated, pass a str instead.

New features

• #14743: Full diff: now contains a legend explaining the + & - symbols in diff output.
• #2781: When strict_markers is enabled, marker names used in -m expressions are now validated against registered markers.
• #6881: Added the parametrize_long_str_id_strategy configuration option to control how long str/bytes parameter values are handled in auto-generated test IDs. Explicit IDs set via ids=[...] or pytest.param(..., id=...) are not affected. Available strategies: short (default, values over 100 chars fall back to argname+index), sha256 (SHA-256 hex digest), legacy (keep full value), and disallow (error requesting explicit IDs).

Improvements in existing functionality

• #10745: A RecursionError whose recursion origin cannot be located now shows only the first and last 10 stack frames, matching what pytest already did when locating the origin failed outright. Previously the full traceback -- often around a thousand near-identical frames -- was rendered, which was both slow and unreadable. Pass --full-trace to see every frame.

... (truncated)

Commits

• ae1d0ff Prepare release version 9.2.0
• 143ce31 pre-commit: exclude codespell on generated release announcements
• 532dc5f tox: add attrs dependency to regen, needed in reportingdemo.rst
• a7b2446 Merge pull request #15245 from pytest-dev/claude/project-thread-9jcf91
• 679d09c [pre-commit.ci] pre-commit autoupdate (#15266)
• 41d12cd docs: clarify typing for yield fixtures
• b9022ba Merge pull request #15182 from 1871698/docs/improve-getting-started-description
• 16f87a7 docs: improve getting-started.rst test execution description
• 082ed70 Merge pull request #15255 from pytest-dev/claude/project-thread-eoi3d6
• ae37a01 Merge pull request #15227 from pytest-dev/claude/project-thread-4etye4
• Additional commits viewable in compare view

Updates ruff from 0.16.9 to 0.17.3

Release notes

Sourced from ruff's releases.

0.17.3

Release Notes

Released on 2026-10-26.

Preview features

• [suspicious] Add shared-clock-mock (#29074)

Bug fixes

• [pyupgrade] Avoid incorrect conversions to f-strings (UP032) (#25485)

Performance

• Buffer stdout in ruff format (#29631)
• Specialize ASCII identifier lexing (#29503)
• Speed up identifier and keyword lexing (#29463)

Documentation

• [flake8-bandit] Describe what the rule actually checks for httpx (S113) (#27936)

Contributors

• @​itsvedantkumar
• @​charliermarsh
• @​anishgirianish

Install ruff 0.17.3

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.17.3/ruff-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy Bypass -c "irm https://releases.astral.sh/github/ruff/releases/download/0.17.3/ruff-installer.ps1 | iex"

Download ruff 0.17.3

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

... (truncated)

Changelog

Sourced from ruff's changelog.

0.17.3

Released on 2026-10-26.

Preview features

• [suspicious] Add shared-clock-mock (#29074)

Bug fixes

• [pyupgrade] Avoid incorrect conversions to f-strings (UP032) (#25485)

Performance

• Buffer stdout in ruff format (#29631)
• Specialize ASCII identifier lexing (#29503)
• Speed up identifier and keyword lexing (#29463)

Documentation

• [flake8-bandit] Describe what the rule actually checks for httpx (S113) (#27936)

Contributors

• @​itsvedantkumar
• @​charliermarsh
• @​anishgirianish

0.17.2

Released on 2026-10-22.

Preview features

• [complexity] Add unnecessary-regular-expression-compile (#25533)

Bug fixes

• Avoid syntax errors for type variables with starred constraints (UP040, UP046, UP047, RUF053) (#28362)
• [pydocstyle] Treat backslash-escaped *args and **kwargs as documented (D417) (#29536)
• [pylint] Avoid false positive on starred elements (PLE0643) (#29483)
• [pylint] Mark fixes unsafe when deleting comments (PLR5501, PLW0120) (#29414)
• [pyupgrade] Mark fix unsafe when deleting comments (UP035) (#29413)

Performance

• Avoid intermediate names in lint name resolution (#29506)
• Prefilter bidirectional Unicode checks by UTF-8 leading bytes (#29561)
• Share postfix parsing and reduce expression copies (#29480)

... (truncated)

Commits

• ba65abf Bump version to 0.17.3 (#29745)
• fb2f921 [ty] Fix narrowing of strings and integers compared with enum members (#29743)
• d181287 [ty] Index nominal union alternatives (#29196)
• 07872ad [ty] Preserve string literals in comparisons with LiteralString (#29741)
• 95888b2 [ty] Preserve narrowing after guarded match subject captures (#29558)
• 3c8166b [ty] Fix hang when negating recursive unions of instance types (#29652)
• 3fd20e0 [ty] Preserve generic callback specializations during return refinement (#29667)
• 2f0a29e [ty] Record predicate truthiness alongside expression inference (#29706)
• 60f104a [ty] Honor @​override on overload implementations in stubs (#29470)
• 207ec3a [ty] Add diagnostic baseline support (#27636)
• Additional commits viewable in compare view

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