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Fix CI failures from #110 - #111
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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- Replace setup-miniconda with setup-python. Under a conda login shell poetry installed into its own environment and broke itself when the lockfile downgraded virtualenv (FileNotFoundError installing pytdc). - Test on Linux only; README states macOS/Windows are unsupported and the lockfile pins torch 2.1.2+cpu, which has no macOS arm64 wheel. - Switch the dummy dataset to PDB format: mmtf.rcsb.org has been retired and no longer resolves, failing test_train_fast_dev_run. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Require Pillow >=13.0.0 and Python 3.11 Pillow 13 requires Python >=3.11, so raise the supported range from >=3.9,<3.11 to >=3.11,<3.12 (torch 2.1.2 supports up to 3.11). Re-lock with existing pins kept: pillow 10.2.0 -> 13.0.0, and drop the async-timeout/exceptiongroup/importlib-resources backports. Update classifiers, ruff/black targets, README and the CI matrix to match. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Remove torchdrug dependency from GearNet torchdrug's last release (0.2.1, 2023) requires Python <3.11, so it cannot be installed alongside Pillow 13. GearNet only used it for utils.sparse_coo_tensor, an unchecked wrapper around torch.sparse_coo_tensor, and data.Graph.from_tensors inside _message_and_aggregate, which nothing calls. Use torch directly, drop the dead method, and remove the install-torchdrug task and CI step. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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Fixes the
Build CPUfailures on #110. Targets #110's branch so this merges into it.With fail-fast turned off, the full matrix showed three separate causes:
FileNotFoundError: ...virtualenv/activation/...while installingpytdc. Update CI workflow actions to latest versions #110 switched steps to a conda login shell, so poetry installed into the same env it runs from. The lockfile then downgradedvirtualenvunderneath it. Fix: replacesetup-minicondawithactions/setup-python@v7. Conda was only providing the Python version. Poetry now uses its in-project.venv, which is also the path the cache step saves.torch 2.1.2+cpu, which has no macOS arm64 wheel. The README says macOS and Windows aren't officially supported, so the matrix now covers Linux only: Python 3.9 and 3.10 onubuntu-latest.test_train_fast_dev_runfailed withName or service not known. RCSB retiredmmtf.rcsb.org, and thedummydataset downloads its structures in MMTF format. Fix: switchdummy.yamltoformat: "pdb".Also sets
fail-fast: falseso one Python version failing doesn't cancel the other.CI on this branch:
Build CPU (3.9)✅ andBuild CPU (3.10)✅ (run).Not addressed
14 other dataset configs (CATH, ccPDB, antibody developability, …) still use
format: "mmtf". Fresh downloads for them will fail the same way. That changes user-facing data formats, so it's left for a separate PR.🤖 Generated with Claude Code