Merge the predict_structure and featurize_structure into a single method #290
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Signed-off-by: Tsz Wai Ko <47970742+kenko911@users.noreply.github.com>
…taining and using element offsets
…ction including both
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Outside diff range, codebase verification and nitpick comments (2)
examples/Property Predictions using MEGNet or M3GNet Models.ipynb (1)
106-117: Update all instances ofpredict_structureto match the new signature.The following files contain calls to
predict_structurethat need to be reviewed and potentially updated:
tests/test_integration.pytests/utils/test_training.pytests/models/test_m3gnet.pytests/models/test_wrapper.pytests/models/test_megnet.pysrc/matgl/models/_wrappers.pysrc/matgl/models/_tensornet.pysrc/matgl/models/_m3gnet.pysrc/matgl/models/_megnet.pysrc/matgl/models/_so3net.pysrc/matgl/models/_chgnet.pysrc/matgl/cli.pyEnsure that all calls to
predict_structureinclude thereturn_features=Trueparameter where necessary.Analysis chain
LGTM! Verify the function usage in the codebase.
The code changes are approved.
However, ensure that all function calls to
predict_structurematch the new signature.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `predict_structure` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type python -A 5 $'predict_structure'Length of output: 72
Script:
#!/bin/bash # Description: Verify all function calls to `predict_structure` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type py -A 5 $'predict_structure'Length of output: 17217
src/matgl/models/_m3gnet.py (1)
Update function calls to match the new signature
The
predict_structurefunction has been updated with a new parameterreturn_features. Please ensure that all calls to this function are updated to match the new signature.Locations that need attention:
src/matgl/models/_wrappers.pysrc/matgl/models/_tensornet.pysrc/matgl/models/_so3net.pysrc/matgl/models/_megnet.pysrc/matgl/models/_chgnet.pytests/utils/test_training.pytests/test_integration.pytests/models/test_megnet.pytests/models/test_wrapper.pysrc/matgl/cli.pytests/models/test_m3gnet.pyAnalysis chain
Line range hint
297-352:
LGTM! Verify the function usage in the codebase.The code changes are approved.
However, ensure that all function calls to
predict_structurematch the new signature.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `predict_structure` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type python -A 5 $'predict_structure'Length of output: 72
Script:
#!/bin/bash # Description: Verify all function calls to `predict_structure` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg 'predict_structure' --glob '*.py' -A 5Length of output: 17221
WalkthroughThe recent changes enhance the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Notebook
participant M3GNet
User->>Notebook: Run code to extract features
Notebook->>M3GNet: Call predict_structure(struct)
M3GNet-->>Notebook: Return feature tensor or dictionary
Notebook->>User: Display features shape
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Summary
Merged the predict_structure and featurize_structure into a single method. The example is included in Property Predictions using MEGNet or M3GNet Models.ipynb.
Checklist
ruff.mypy.duecredit@due.dcitedecorators to reference relevant papers by DOI (example)Tip: Install
pre-commithooks to auto-check types and linting before every commit: