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Fixes linter warning: numpydoc-validation flagged mismatched underline lengths in docstring section headers.
Fixes linter warning: numpydoc-validation flagged GL08 (missing docstring) on 4 modules.
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After adding these, running `pre-commit run --all-files` indicates no existing issues.
Run `codespell --write-changes`, then manually correct.
Fix grammar using Claude Haiku 4.5, then manually correct. Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
Use `return 1` instead of `exit 1` so that sourcing the script with an invalid platform prints the error without killing the shell. Fixes geometric-intelligence#305
Verify that `source uv_env_setup.sh INVALID` does not kill the user's shell (uses return instead of exit).
Replace if/elif chain with case statement and string concatenation. No functional changes.
torch >= 2.6 defaults to weights_only=True, which breaks OGB's torch.load calls that serialize PyG data classes. Register the needed classes as safe globals so datasets load without errors. Guarded with hasattr for compatibility with torch < 2.6.
Prevents PyG's fs.torch_load from falling back to weights_only=False when loading processed datasets that contain numpy scalars and dtypes. Includes numpy.dtypes.*DType subclasses for numpy >= 1.25.
torch.tensor(existing_tensor) is deprecated; use .detach().clone(). nx.from_numpy_matrix is removed in NetworkX 3.0; use from_numpy_array.
This was referenced Apr 11, 2026
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Checklist
PR series: #303 #307 308 #309
This PR is only for commits 1b244e5..70959fc. It is number 3 in a series of staged PRs, building upon #305 by adding commits 1b244e5..70959fc; if #305 is rejected, the commits in this PR need to be reviewed.
Description
This PR fixes deprecation warnings in preparation for my subsequent PR to unpin torch. It includes commits
torch.load. This is good practice vs. allowing PyG to fall back toweights_only=False. Currently this provides no security benefit, but it will do in the future if my PyG PR is accepted.Overall, the 4 commits in this PR should be fairly benign, reduce various warning messages, and make TopoBench more amenable to upgrade beyond torch 2.3.0.
Issue
This is preparation for fixing issue #306.