[niklashoelter]

Raises every dependency to the newest version that works with the rest of the stack. Not for merging yet: 0.9.0 pins the versions tested in Cheetah, and this stays open for a later release.

Bumped

Package	0.9.0	This PR
fairchem-core	2.24.0	2.25.0
orb-models	0.6.1	0.6.2
nvmolkit	0.5.1	0.7.0
rdkit	2026.3.1	2026.3.6 (nvmolkit 0.7.0's exact pin)
ase	3.27.0	3.29.0
scipy	1.17.1	1.18.1
hf_xet	1.2.0	1.8.0
pytest / ruff / mkdocs-material	9.1.1 / 0.17.2 / 9.7.7	9.2.0 / 0.17.4 / 9.8.1
setuptools (build backend and CI), pip, flake8 (CI)	80.10.2, 26.2.2, 7.4.1	84.2.1, 26.3, 7.5.0

Transitive dependencies moved with uv lock --upgrade, for example e3nn 0.6.0, huggingface-hub 1.33.0 and numpy 2.4.6.

Still blocked

• torch stays 2.13.0: fairchem-core 2.25.0 requires torch~=2.13.0.
• warp-lang stays 1.17.0: 1.18 and later ship CUDA 13 wheels that need driver 580 or newer (the cluster runs 535).
• orb-models 0.7.0 requires nvalchemi-toolkit-ops<0.4, but torch-sim 0.6.2 requires 0.4 or newer.
• twine 7.0.0 needs rich>=14.3.3, but orb-models' cached-path caps rich below 14.
• rdkit 2026.9 is ruled out by nvmolkit's exact pin.

Test change

pytest 9.2 rejects pytest.approx() on nested data. Five embedding tests compared lists of coordinate tuples that way; they now compare numpy arrays.

Testing

• Full suite, 2 GPUs, with HF_TOKEN: 829 passed, 5 failed before the test change; all 79 tests/test_embed.py tests pass after it.
• mkdocs build --strict passes.
• Not yet run: the workflow benchmarks. Run them before this goes into a release.