abacus: add checks on pp and orb in construction of STRU #737
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes in this pull request focus on the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant make_unlabeled_stru
participant FileHandler
User->>make_unlabeled_stru: Call with parameters
make_unlabeled_stru->>FileHandler: Process pp_file
FileHandler-->>make_unlabeled_stru: Return processed pp_file
make_unlabeled_stru->>FileHandler: Process numerical_orbital
FileHandler-->>make_unlabeled_stru: Return processed numerical_orbital
make_unlabeled_stru->>User: Return output with ATOMIC_SPECIES and NUMERICAL_ORBITAL
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CodSpeed Performance ReportMerging #737 will not alter performanceComparing Summary
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #737 +/- ##
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+ Coverage 84.73% 84.80% +0.06%
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Files 81 81
Lines 7345 7336 -9
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- Hits 6224 6221 -3
+ Misses 1121 1115 -6 ☔ View full report in Codecov by Sentry. |
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- dpdata/abacus/scf.py (3 hunks)
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dpdata/abacus/scf.py
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- dpdata/abacus/scf.py (3 hunks)
- tests/test_abacus_stru_dump.py (1 hunks)
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dpdata/abacus/scf.py
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🔇 Additional comments (1)
dpdata/abacus/scf.py (1)
631-632: Docstring updated correctlyThe addition of
dest_dirparameter in the docstring is clear and follows the existing documentation style.
for more information, see https://pre-commit.ci
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (3)
dpdata/abacus/scf.py (3)
Line range hint
581-596: Function signature update: Consider backward compatibilityThe function signature has been updated to include
pp_fileas a mandatory parameter. While this change improves the function's robustness, it may break existing code that relies on the previous signature.Consider providing a default value for
pp_fileor implementing a deprecation warning to maintain backward compatibility.
660-676: Enhance error handling inprocess_file_inputThe new
process_file_inputfunction improves input handling, but it could benefit from additional error checking:
- Consider adding type checking for
file_inputbefore the isinstance checks.- Validate that the dictionary values are strings (file paths) when
file_inputis a dictionary.Example implementation:
def process_file_input(file_input, atom_names, input_name): if not isinstance(file_input, (list, tuple, dict)): raise TypeError(f"{input_name} must be a list, tuple, or dictionary") if isinstance(file_input, (list, tuple)): if len(file_input) != len(atom_names): raise ValueError(f"{input_name} length is not equal to the number of atom types") return [str(item) for item in file_input] # Ensure all items are strings elif isinstance(file_input, dict): for element in atom_names: if element not in file_input: raise KeyError(f"{input_name} does not contain {element}") if not isinstance(file_input[element], str): raise TypeError(f"Value for {element} in {input_name} must be a string") return [file_input[element] for element in atom_names]
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1-853: Overall code quality improvementsThe changes made to the
make_unlabeled_strufunction enhance its functionality and robustness. To further improve the overall code quality:
- Consider adding type hints to function signatures for better code readability and IDE support.
- Update the docstring for
make_unlabeled_struto reflect the newpp_fileanddest_dirparameters.- Add logging statements for important operations, especially around file handling and symbolic link creation.
- Consider breaking down the
make_unlabeled_strufunction into smaller, more focused functions to improve readability and maintainability.
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📒 Files selected for processing (2)
- dpdata/abacus/scf.py (6 hunks)
- tests/test_abacus_stru_dump.py (1 hunks)
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- tests/test_abacus_stru_dump.py
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🔇 Additional comments (2)
dpdata/abacus/scf.py (2)
702-703: LGTM: Improved handling ofpp_fileThe use of
process_file_inputforpp_fileimproves input validation and flexibility. This change allows for both list and dictionary inputs, which is a good enhancement.
726-733: LGTM: Consistent handling ofnumerical_orbitalThe processing of
numerical_orbitalis now consistent withpp_file, using theprocess_file_inputfunction. This change improves code consistency and reduces duplication.
Summary by CodeRabbit
New Features
Improvements
pp_fileandnumerical_orbital.Bug Fixes
Documentation