build(deps): bump the python-deps group across 1 directory with 4 updates

[dependabot]

Bumps the python-deps group with 4 updates in the / directory: tqdm, rdkit, torch-geometric and ruff.

Updates tqdm from 4.67.3 to 4.68.2

Release notes

Sourced from tqdm's releases.

tqdm v4.68.2 stable

• revert accidental change to ascii default (fixes #1760)
  • UnicodeEncodeError: 'charmap' codec can't encode characters in position 6-7: character maps to <undefined> can be fixed by installing tqdm!=4.68.0,!=4.68.1
• misc docs updates
  • fix links
  • replace stray rst -> md syntax
  • consistent "progress bar" terminology (#1737)
• tests: fix coverage (fixes #1760)

tqdm v4.68.1 stable

• set name of monitor thread (#1669, #1752 <- #1435)
• fix monitor thread atexit deadlock (#1751 <- #528, #627, #1435, #1564)
• docs: minor copyediting

tqdm v4.68.0 stable

• utils: simplify terminal size detection (#1760)
• contrib
  • itertools (#1760)
    • add chain, permutations, combinations, combinations_with_replacement, batched
    • add product(repeat=1) keyword argument (#1428)
  • fix discord, telegram error handling
  • fix discord, slack, telegram format for total=None
• soft-deprecate tqdm.utils.envwrap -> envwrap
• benchmarks: fix asv
• misc linting
• misc framework updates
  • CI: migrate manual job to pre-commit.ci
  • bump workflow actions & pre-commit hooks

Commits

• 4b33952 revert accidental change to tqdm(ascii) default
• b10848f docs: fix links
• 85b62dd docs: replace stray rst -> md
• d2fb04a docs: mention OpenAI sponsorship
• 85940f9 docs: consistent progress bar terminology
• 9dbb36b tests: fix coverage
• 67cf355 Merge pull request #1751 from jaltmayerpizzorno/fix-atexit-monitor-deadlock
• cfa4a85 minor docstring updates
• f83290c Fix TMonitor deadlock at interpreter shutdown
• 59029c3 Set name for tqdm monitor thread (#1752)
• Additional commits viewable in compare view

Updates rdkit from 2026.3.2 to 2026.3.3

Release notes

Sourced from rdkit's releases.

2026_03_3 (Q1 2026) Release

Release_2026.03.3

(Changes relative to Release_2026.03.2)

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, Marco Ballarotto, Kevin Boyd, David Cosgrove, Gareth Jones, Huw Jones, Steven Kearnes, Brian Kelley, Clay Moore, Dan Nealschneider, Emily Rhodes, Ricardo Rodriguez, Raul Sofia, Chris Von Bargen

New Features and Enhancements:

• CIP labeller performance: Don't calculate auxiliary descriptors unnecessarily (github pull #9171 from d-b-w)
• Add optional default value to Mol.GetProp() in Python (github issue #9241 from emilyrrhodes)
• CIPLabeler performance: Store vector of bonds (github pull #9250 from d-b-w)
• Pandastools improvements (github pull #9251 from marcobICR)
• Add MMFF Property Getter functions to python interface (github issue #9253 from scal444)
• [bot] Update molecular templates header file (github pull #9269 from github-actions[bot])
• Adds some features to the C# SWIG wrappers (github pull #9274 from jones-gareth)
• MolDrawOptions: Option for Uniform Bond Colour with Coloured Atom Labels (github issue #9282 from hdj-elixirsoftware)
• add checked atom and bond iterators (github pull #9290 from greglandrum)
• Adds MolToCDXMLBlock to FileParsers (github pull #9291 from bp-kelley)
• add ability to block atoms/bonds from participating in tautomer zones (github pull #9297 from greglandrum)
• Improve synthon substructure search performance ~20% (github pull #9305 from d-b-w)

Documentation:

• Docs: fix CosineSimilarity formula and clarify similarity metric names in BitOps.h (github pull #9264 from rezabagher)

Bug Fixes:

• Extended fix for #9101 (github pull #9255 from RaulSofia)
• Segfault when calling MolToSmiles on submol (github issue #9270 from ricrogz)
• DrawText::setFontScale Atom Font Scaling Issue (github issue #9280 from hdj-elixirsoftware)

... (truncated)

Commits

• See full diff in compare view

Updates torch-geometric from 2.7.0 to 2.8.0

Release notes

Sourced from torch-geometric's releases.

PyG 2.8.0

We are excited to announce the release of PyG 2.8 🎉🎉🎉

• Highlights
• Breaking Changes
• Features
• Bugfixes
• Changes
• New Contributors
• Full Changelog

PyG 2.8 includes 82 commits since torch-geometric==2.7.0, with feature and bug-fix work from 16 contributors.

Highlights

Support for PyTorch 2.9-2.12

PyG 2.8 supports PyTorch 2.9, 2.10, 2.11, and 2.12, along with Python 3.10-3.14. Prebuilt wheels are available for CUDA 12.6, 12.8, 13.0, and 13.2, depending on the PyTorch version (see the table below).

PyTorch	Supported wheels
2.12.*	cpu, cu126, cu130, cu132
2.11.*	cpu, cu126, cu128, cu130
2.10.*	cpu, cu126, cu128, cu130
2.9.*	cpu, cu126, cu128, cu130

For a typical installation, PyG remains installable directly from PyPI:

pip install torch-geometric
Optional accelerated dependencies, matching your PyTorch install:
pip install pyg-lib torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html

For example, use TORCH=2.12.0 and CUDA=cu132 for PyTorch 2.12.* with CUDA 13.2.

Consolidated Acceleration on pyg-lib

PyG 2.8 trims its optional accelerated dependencies: torch-cluster and torch-spline-conv are now deprecated and ignored, with their functionality provided by pyg-lib==0.7.0. The installation and cuGraph documentation now point users toward the NVIDIA PyG container, the rapidsai/cugraph-gnn examples, and RAPIDS guidance for scalable GPU workflows (#10489, #10603, #10639, #10640).

Synthetic QA Generation for Graph RAG

The new examples/llm/txt2qa.py workflow introduces a synthetic multi-hop question-answer generation pipeline for text documents (#10559). It supports local vLLM and NVIDIA NIM API backends and is designed for creating training and evaluation data for retrieval-augmented generation systems.

Breaking Changes

• Dropped support for PyTorch 2.8. Use PyG 2.8 with PyTorch 2.9 through 2.12, or pin torch-geometric==2.7.* if you need to stay on PyTorch 2.8. Older PyTorch 2.8 wheel links remain available for existing installs (#10708).
• Removed dependencies on torch-cluster and torch-spline-conv in favor of pyg-lib==0.7.0. These packages are now deprecated and ignored if installed; the operators they previously provided now require pyg-lib==0.7.0 (#10682, #10622).

... (truncated)

Changelog

Sourced from torch-geometric's changelog.

[2.8.0] - 2026-06-05

Added

• Added from_relbench to convert RelBench databases into HeteroData (#10628)
• Added a ci: full PR label that triggers the full test suite (pytest-full) on demand instead of the regular one (#10709)
• Added PyTorch 2.11 and 2.12 support (#10708)
• Added txt2qa.py example for synthetic multi-hop QA generation from text documents, supporting vLLM (local) and NVIDIA NIM (API) backends (#10559)
• Added GraphLand benchmark via GraphLandDataset (#10458)

Changed

• Improved runtime of to_dense_batch in both eager and torch.compile (#10660)
• Dropped support for TorchScript in GATConv and GATv2Conv for correctness (#10596)

Deprecated

• Deprecated support for torch-cluster in favor of pyg-lib>=0.6.0 (#10682)
• Deprecated support for torch-spline-conv in favor of pyg-lib>=0.6.0 (#10622)

Removed

• Dropped support for PyTorch 2.8 (#10708)

Fixed

• Fixed dtype mismatch in GRetriever.inference (#10681)
• Fix MovieLens dataset incompatibility with sentence-transformers>=5.0.0 (#10668)
• Removed an unnecessary device synchronization in torch_geometric.utils.softmax (#10499)
• Fixed loading of legacy HuggingFace BERT checkpoints (#10631)
• Fixed return_attention_weights: bool being not respected in GATConv and GATv2Conv (#10596)
• Fixed download links for politifact and gossipcop datasets of UPFD (#10558)

Security

Commits

• 726310a Prepare for PyG 2.8 release (#10715)
• 3e29e61 Update README.md (#10714)
• b8495d3 [pre-commit.ci] pre-commit suggestions (#10688)
• 860c88f ci: Switch pre-commit autoupdate schedule to quarterly (#10713)
• 2189457 Add GRetriever RelBench example demo and from_relbench integration (#10681)
• caf368b Add from_relbench utility to convert RelBench databases to HeteroData (#10628)
• d0110a4 ci: Don't run tests that require dataset downloads in full test (#10710)
• 4d9bbab ci: Enable full test on PRs if labelled (#10709)
• e73fac2 Add PyTorch 2.11/2.12 support and drop PyTorch 2.8 (#10708)
• fae6596 Fix warning message in __init__.py (#10695)
• Additional commits viewable in compare view

Updates ruff from 0.15.16 to 0.15.17

Release notes

Sourced from ruff's releases.

0.15.17

Release Notes

Released on 2026-06-11.

Preview features

• Allow human-readable names in suppression comments (#25614)
• Fix handling of ignore comments within a disable/enable pair (#25845)
• Prioritize human-readable names in CLI output (#25869)
• Respect diagnostic start and parent ranges and trailing comments in ruff:ignore suppressions (#25673)
• [flake8-async] Add trio.as_safe_channel to safe decorators (ASYNC119) (#25775)
• [flake8-pytest-style] Also check pytest_asyncio fixtures (#25375)
• [ruff] Ban pytest autouse fixtures (RUF076) (#25477)
• [pyupgrade] Add from __future__ import annotations automatically (UP007, UP045) (#23259)

Bug fixes

• Fix diagnostic when ruff:enable or ruff:disable appears where ruff:ignore is expected (#25700)
• [pyupgrade] Preserve leading empty literals to avoid syntax errors (UP032) (#25491)

Rule changes

• [flake8-pytest-style] Clarify diagnostic message for single parameters (PT007) (#25592)
• [numpy] Drop autofix for np.in1d (NPY201) (#25612)
• [pylint] Exempt Python version comparisons (PLR2004) (#25743)

Performance

• Reserve AST Vecs with correct capacity for common cases (#25451)

Formatter

• Preserve whitespace for Quarto cell option comments (#25641)

CLI

• Allow rule names in ruff rule (#25640)

Other changes

• Fix playground diagnostics scrollbars (#25642)

Contributors

• @​SuryanshSS1011
• @​anishgirianish
• @​romero-deshaw
• @​karlhillx
• @​carljm

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.17

Released on 2026-06-11.

Preview features

• Allow human-readable names in suppression comments (#25614)
• Fix handling of ignore comments within a disable/enable pair (#25845)
• Prioritize human-readable names in CLI output (#25869)
• Respect diagnostic start and parent ranges and trailing comments in ruff:ignore suppressions (#25673)
• [flake8-async] Add trio.as_safe_channel to safe decorators (ASYNC119) (#25775)
• [flake8-pytest-style] Also check pytest_asyncio fixtures (#25375)
• [ruff] Ban pytest autouse fixtures (RUF076) (#25477)
• [pyupgrade] Add from __future__ import annotations automatically (UP007, UP045) (#23259)

Bug fixes

• Fix diagnostic when ruff:enable or ruff:disable appears where ruff:ignore is expected (#25700)
• [pyupgrade] Preserve leading empty literals to avoid syntax errors (UP032) (#25491)

Rule changes

• [flake8-pytest-style] Clarify diagnostic message for single parameters (PT007) (#25592)
• [numpy] Drop autofix for np.in1d (NPY201) (#25612)
• [pylint] Exempt Python version comparisons (PLR2004) (#25743)

Performance

• Reserve AST Vecs with correct capacity for common cases (#25451)

Formatter

• Preserve whitespace for Quarto cell option comments (#25641)

CLI

• Allow rule names in ruff rule (#25640)

Other changes

• Fix playground diagnostics scrollbars (#25642)

Contributors

• @​SuryanshSS1011
• @​anishgirianish
• @​romero-deshaw
• @​karlhillx
• @​carljm
• @​ntBre

... (truncated)

Commits

• 7c645a9 Bump 0.15.17 (#25872)
• f381eb1 Prioritize human-readable names in CLI output (#25869)
• b9b4546 Minor workflow simplification (#25870)
• 1e77ba0 [ty] Move PreformattedBlockScanner to format-agnostic location. (#25856)
• 6f2b772 [ty] Preserve nominal type of enum.property instances (#25849)
• be4777c [ty] Fix site-package error when multiple versions of pythons are installed i...
• 53f6ff7 Allow human-readable names in suppression comments (#25614)
• 6740325 [ty] Restrict uncached raw signature access (#25866)
• 970b1bf Auto-update snapshots when syncing typeshed (#25841)
• 0785793 Fix handling of ignore comments within a disable/enable pair (#25845)
• Additional commits viewable in compare view

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