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Require Pillow >=13.0.0 (raises minimum Python to 3.11) - #112
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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>
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>
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* Disable fail-fast in CI test matrix Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Fix CI install and test failures - 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 (raises minimum Python to 3.11) (#112) * 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> --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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Requires
pillow >=13.0.0. Pillow was only a transitive dependency before, locked at 10.2.0.Stacked on #111 so CI runs with the fixed workflow, since
main's CI is broken until #110/#111 merge. Merge #111 (then #110) first, or retarget this PR tomainafterwards.Breaking: Python 3.11 only
Pillow 13.0.0 requires Python >=3.11, so the supported Python range moves from
>=3.9,<3.11to>=3.11,<3.12. The upper bound stays below 3.12 because the locked torch 2.1.2 only supports up to 3.11.pillow10.2.0 → 13.0.0. It also dropsasync-timeout,exceptiongroupandimportlib-resources, which were only needed on Python <3.11.target-version, the README conda example and the CI matrix (now["3.11"]).Breaking:
torchdrugremovedtorchdrug's last release (0.2.1, July 2023) requires Python <3.11, sopoe install-torchdrugcan't work any more. GearNet was its only user:utils.sparse_coo_tensoris torchdrug's unchecked wrapper aroundtorch.sparse_coo_tensor, so it's replaced with the torch call directly. I checked locally against a dense reference with duplicate (uncoalesced) indices on torch 2.1.2.data.Graph.from_tensorswas only used inMessagePassingBase._message_and_aggregate, which nothing calls. The method is removed.install-torchdrugpoe task and the CI step that ran it.Testing
CI
Build CPU (3.11)✅: 20 passed, 6 skipped (run). The GearNet forward-pass test is among the skipped tests ("too slow for GitHub Actions"), so it's worth running GearNet locally before merging.🤖 Generated with Claude Code