Avoid using eval, replace manual offset in enumerate and rename single letter variables
#3739
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Important Auto Review SkippedMore than 25% of the files skipped due to max files limit. The review is being skipped to prevent a low-quality review. 26 files out of 83 files are above the max files limit of 50. Please upgrade to Pro plan to get higher limits. WalkthroughThe recent updates across various components of the pymatgen library focus on enhancing code safety, efficiency, and readability. Notable improvements include the optimization of loop logic and conditionals, safer handling of dynamic expressions, and more precise and clear documentation. These changes collectively aim to refine the library's usability and maintainability, ensuring it remains a robust tool for materials science research. Changes
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Actionable comments posted: 1
Actionable comments outside the diff hunks (3)
pymatgen/io/vasp/inputs.py (3)
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322-322: Thestructureparameter in the__init__method is critical and should be validated to ensure it's an instance ofStructure. This validation enhances robustness and prevents potential runtime errors.if not isinstance(structure, Structure): raise TypeError("The structure parameter must be an instance of pymatgen.core.structure.Structure")
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2485-2485: Theautomatic_densitymethod in theKpointsclass should include checks to ensure thestructureparameter is valid and thekppavalue is positive. These checks can prevent runtime errors and ensure the method's preconditions are met.if not isinstance(structure, Structure): raise TypeError("The structure parameter must be an instance of pymatgen.core.structure.Structure") if kppa <= 0: raise ValueError("The kppa value must be positive")
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2485-2485: In thefrom_directoryclass method of thePotcarclass, consider adding a check to ensure the directory exists and contains the expected POTCAR files. This check can prevent runtime errors when the directory is missing or incorrectly specified.if not os.path.isdir(input_dir): raise FileNotFoundError(f"The specified directory {input_dir} does not exist")
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Files selected for processing (3)
- pymatgen/analysis/magnetism/heisenberg.py (5 hunks)
- pymatgen/electronic_structure/boltztrap2.py (6 hunks)
- pymatgen/io/vasp/inputs.py (4 hunks)
Additional comments not posted (19)
pymatgen/analysis/magnetism/heisenberg.py (3)
570-573: Ensure consistency in file extension handling.The condition for appending ".json" to the filename is straightforward but consider encapsulating this logic into a utility function if similar patterns are used elsewhere in the codebase. This promotes DRY principles and simplifies maintenance if the logic for determining file extensions needs to change in the future.
731-732: Adjust the tolerance value for energy comparison.The tolerance value for energy comparison is hardcoded as
6(for 10^-6 eV/atom). Consider making this a configurable parameter of theHeisenbergScreenerclass to increase flexibility and adaptability to different precision requirements in future use cases.
926-926: Handle potential exceptions more gracefully infrom_dict.The
from_dictmethod usesliteral_evalto parse theex_matDataFrame from a JSON string. Consider adding error handling around this operation to catch and handleSyntaxErroror other potential exceptions more gracefully. This could involve logging an error message and returning a default value or raising a custom exception with a more informative error message.pymatgen/electronic_structure/boltztrap2.py (6)
111-111: Consider consolidating the assignment ofdosweightto avoid repetition and improve maintainability.
172-172: The calculation ofhfor splitting projections based on spin polarization is repeated. Consider extracting this logic into a separate method to reduce duplication and improve code clarity.
210-210: The conditional assignment forstructureis simplified here, which is a positive change for readability and maintainability.
223-223: The assignment ofdosweightbased onis_spin_polarizedis repeated. It's advisable to centralize this logic to ensure consistency and ease future modifications.
264-264: The logic for handling projections based on spin polarization is duplicated. Consider creating a shared method to handle this logic to reduce code duplication.
1048-1050: The handling of property arrays based on doping and temperature conditions is well-implemented, ensuring flexibility and scalability for future extensions or modifications.pymatgen/io/vasp/inputs.py (10)
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322-322: Consider adding type hints to the__init__method parameters for clarity and better code documentation.
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2485-2485: Theas_dictmethod should include all relevant attributes of thePoscarclass to ensure a complete representation when converting to a dictionary. Currently, it seems some attributes might not be included.
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2485-2485: The__setitem__method in theIncarclass should include validation for the keys and values being set, especially since INCAR files have specific requirements for different parameters. This validation can prevent common errors and ensure the generated INCAR file is valid.
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2485-2485: Thefrom_dictclass method should handle potential mismatches or missing keys gracefully, providing default values or warnings to inform the user, rather than potentially raising a KeyError.
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2485-2485: In theKpointsclass, consider adding a method to validate the k-point mesh settings, especially for automatic schemes. This validation can help catch common configuration errors early.
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2485-2485: In thePotcarSingleclass, the methodfrom_symbol_and_functionalshould handle cases where the specified functional or symbol does not exist more gracefully, perhaps by providing a list of valid options or suggesting alternatives.
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2485-2485: Theverify_potcarmethod in thePotcarSingleclass should include more detailed logging or warnings when a POTCAR does not pass validation. This information can help users diagnose and fix issues with their POTCAR files.
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2485-2485: ThePotcarclass should include a method to validate the compatibility ofPotcarSingleobjects it contains, ensuring they all use the same functional. This validation can prevent common configuration errors in VASP simulations.
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2485-2485: TheVaspInputclass should include a method to validate the completeness and compatibility of its components (Incar,Kpoints,Poscar,Potcar). This validation can ensure that the VASP input set is correctly configured before running simulations.
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2485-2485: In therun_vaspmethod of theVaspInputclass, consider adding error handling for cases where the VASP executable is not found or fails to run. This handling can improve the user experience by providing clearer error messages and potential solutions.
DanielYang59
changed the title
eval eval, replace manual offset in enumerate and rename single letter variables
No worries at all. I'm going off topic a bit too (Just cannot resist the pulse to change them, I understand that).
I would fully support such improvements, which makes the code much more readable (especially without reading the full code block). But for some simple cases, I sometimes think it might not be necessary
For some cases, using a more detailed var name is much better
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@janosh Please review. Thanks! |
janosh
added
linting
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i just ran ruff check . --select ANN204 --unsafe-fixes
Found 674 errors.
[*] 550 fixable with the --fix option.would you be interested in submitting a PR with those changes as a followup to #3705? |
Wow this sounds very interesting (always amazed how much you know about all kinds of stuff). I would have a go at this after I finish cleaning up |
Summary
evalwith safer alternativesenumeratewith thestartargument