Replace general raise Exception and add missing raise keyword
#3728
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WalkthroughThe recent updates across various components of a widely used library focus primarily on refining error handling mechanisms. By replacing generic exceptions with more specific ones like Changes
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thanks @DanielYang59. it's always nice to reduce code lines but contextlib.suppress is slower than try/except. not sure if it's enough to be noticeable but i think remember reading somewhere it can be quite a lot especially if used in a for loop. perhaps you can find a loop in your code changes and do some before/after run time testing and post the results here?
janosh
added
performance
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Sure I would have a test and let you know (happy to revert these if |
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Could confirm import timeit
common_setup_code = """
import contextlib
test_list = [0, 1, 2]
"""
method1_code = """
try:
test_list[10]
except IndexError:
pass
"""
method2_code = """
with contextlib.suppress(IndexError):
test_list[10]
"""
# Execute method 1 and measure runtime
method1_time = timeit.timeit(stmt=method1_code, setup=common_setup_code, number=100000)
# Execute method 2 and measure runtime
method2_time = timeit.timeit(stmt=method2_code, setup=common_setup_code, number=100000)
print("Method 1 (except block) time:", method1_time)
print("Method 2 (contextlib.suppress) time:", method2_time)Gives: |
probably doesn't matter given we're talking about microseconds here but i'm still a bit ambivalent about this change. also, a slightly cleaner test would be to not include the |
I'm quite unsure about this change too.
I actually included the import block for both intentionally such that import timeit
setup_code = """
test_list = [0, 1, 2]
"""
method1_code = """
try:
test_list[10]
except IndexError:
pass
"""
method2_code = """
import contextlib
with contextlib.suppress(IndexError):
test_list[10]
"""
# Execute method 1 and measure runtime
method1_time = timeit.timeit(stmt=method1_code, setup=setup_code, number=100000)
# Execute method 2 and measure runtime
method2_time = timeit.timeit(stmt=method2_code, setup=setup_code, number=100000)
print("Method 1 (except block) time:", method1_time)
print("Method 2 (contextlib.suppress) time:", method2_time)gives: |
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Well I guess it's better to focus on changes "we really need" at this moment (like type annotation and bug fixes)? I would revert this until we really need it. |
This reverts commit f555334.
DanielYang59
changed the title
Exception with contextlib.suppressraise Exception and add missing raise keyword
|
@coderabbitai review |
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Actionable comments posted: 4
Review Status
Configuration used: CodeRabbit UI
Files selected for processing (9)
- pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py (1 hunks)
- pymatgen/analysis/molecule_matcher.py (1 hunks)
- pymatgen/apps/battery/battery_abc.py (1 hunks)
- pymatgen/core/operations.py (2 hunks)
- pymatgen/electronic_structure/bandstructure.py (1 hunks)
- pymatgen/io/adf.py (1 hunks)
- pymatgen/io/cif.py (2 hunks)
- pymatgen/io/vasp/outputs.py (10 hunks)
- pymatgen/transformations/advanced_transformations.py (2 hunks)
Additional Context Used
Additional comments not posted (26)
pymatgen/apps/battery/battery_abc.py (1)
230-230: The addition of theraisekeyword beforeNotImplementedErroris correct and necessary. This ensures that the exception is properly thrown, indicating that the method must be implemented in subclasses.pymatgen/core/operations.py (2)
487-490: The validation of thetime_reversalparameter in the__init__method is correctly implemented, ensuring that only -1 or 1 are accepted. This is an important step for input validation and prevents potential errors in the use of theMagSymmOpclass.
596-596: Replacing the genericExceptionwith aRuntimeErrorin thefrom_xyzt_strmethod improves error specificity and clarity when the time reversal operator cannot be parsed. This is a good practice in error handling.pymatgen/io/adf.py (1)
379-379: The change from a genericExceptionto a more specificKeyErrorwith a clear error message is a good practice. It makes the error more understandable and debugging easier.pymatgen/electronic_structure/bandstructure.py (1)
217-217: Replacing the genericExceptionwithRuntimeErrorin the conditional check related to projections and structure object presence is a good practice. It provides more specific information about the error, aiding in debugging and maintenance. This change aligns with the PR objectives to enhance error messaging.pymatgen/analysis/molecule_matcher.py (1)
541-541: The change from a generalExceptionto aRuntimeErrorwith a specific error message is a good practice. It enhances the clarity of the error, making it easier for developers to understand the issue without diving deep into the code. This change aligns with the PR's objective to improve error handling by using more specific exceptions.pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py (1)
1192-1192: The use ofRuntimeErrorhere is an improvement over a genericExceptionas it provides more specific information about the type of error that occurred. This change aligns with the PR's objective to enhance error handling by using more descriptive exceptions.pymatgen/io/cif.py (4)
823-823: The deprecation ofget_structuresand the guidance to useparse_structuresinstead are clear and well-documented.
823-823: The implementation ofparse_structuresmethod is comprehensive, correctly handling various aspects of CIF parsing and structure generation.
823-823: In theCifWriterclass, the handling of magnetic moments (write_magmoms) and the option to write site properties (write_site_properties) are well-implemented features that enhance the flexibility of CIF file generation.
823-823: Thestr2floatutility function is robust and handles uncertainties and special cases appropriately.pymatgen/transformations/advanced_transformations.py (15)
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [93-111]
The
ChargeBalanceTransformationclass is well-documented and provides a clear interface for balancing the charge of a structure. Ensure that theapply_transformationmethod correctly handles edge cases, such as whenremoval_fractionis negative or whennum_in_structureis zero.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [113-142]
The
SuperTransformationclass provides a mechanism to apply multiple transformations to a structure. Ensure that theapply_transformationmethod properly handles the case whenreturn_ranked_listis not an integer or False, as this could lead to unexpected behavior.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [144-204]
The
MultipleSubstitutionTransformationclass is designed to perform multiple fractional substitutions on a structure. Ensure that theapply_transformationmethod accurately handles the substitutions and charge balancing, especially in cases wherecharge_balance_speciesis specified.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [206-375]
The
EnumerateStructureTransformationclass aims to order disordered structures using enumlib. Ensure that theapply_transformationmethod correctly handles both ordered and disordered structures, and that it properly manages the enumeration process, especially in terms of performance and accuracy.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [377-423]
The
SubstitutionPredictorTransformationclass uses the structure prediction module to find likely site substitutions. Ensure that theapply_transformationmethod accurately predicts substitutions and applies them to the structure, particularly in terms of maintaining the structure's stability and physical plausibility.
772-778: > 📝 NOTEThis review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [425-774]
The
MagOrderingTransformationclass is designed to generate collinear magnetic orderings from a structure. Ensure that theapply_transformationmethod correctly handles the magnetic ordering process, especially in terms of selecting appropriate magnetic species and managing the enumeration process for different magnetic configurations.
787-793: > 📝 NOTEThis review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [776-802]
The
find_codopantfunction aims to find a suitable codopant based on ionic radius and oxidation state. Ensure that it properly handles cases where no suitable codopant is found or the target species has no defined ionic radius. Consider adding error handling or fallback mechanisms for these scenarios.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [804-918]
The
DopingTransformationclass is designed to perform doping of a structure, with an option for codoping to maintain charge neutrality. Ensure that theapply_transformationmethod accurately handles the doping process, especially in terms of selecting appropriate doping sites and managing charge balancing.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [920-961]
The
SlabTransformationclass provides a mechanism to create a slab from a bulk structure. Ensure that theapply_transformationmethod correctly handles the slab creation process, especially in terms of generating slabs with the specified orientation, vacuum thickness, and centering options.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [963-1001]
The
DisorderOrderedTransformationclass aims to generate a disordered structure from an ordered input structure. Ensure that theapply_transformationmethod accurately generates disordered structures, especially in terms of selecting appropriate sites for disordering and maintaining the physical plausibility of the resulting structure.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1003-1034]
The
GrainBoundaryTransformationclass provides a mechanism to create a grain boundary from a bulk structure. Ensure that theapply_transformationmethod correctly handles the GB creation process, especially in terms of selecting appropriate rotation axes, angles, and managing the expansion of the grain to avoid interaction between GBs in the cell.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1036-1075]
The
CubicSupercellTransformationclass aims to generate a nearly cubic supercell structure. Ensure that theapply_transformationmethod accurately generates cubic supercells, especially in terms of scaling the input structure and handling edge cases where the desired cubic dimensions cannot be achieved.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1077-1105]
The
AddAdsorbateTransformationclass is designed to add an adsorbate to a slab structure. Ensure that theapply_transformationmethod accurately adds the adsorbate to the structure, especially in terms of selecting appropriate adsorption sites and managing the orientation and position of the adsorbate.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1107-1135]
The
SubstituteSurfaceSiteTransformationclass is designed to perform substitution-type doping on the surface of a structure. Ensure that theapply_transformationmethod accurately performs the substitutions, especially in terms of selecting appropriate surface sites for substitution and managing the substitution process on both surfaces if specified.
772-778: > 📝 NOTEThis review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1137-1165]
The
MonteCarloRattleTransformationclass uses a Monte Carlo rattle procedure to randomly perturb the sites in a structure. Ensure that theapply_transformationmethod accurately performs the rattling, especially in terms of managing the minimum interatomic distances and the acceptance probability for each rattle move.
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@janosh Please review. I'm not 100% confident the proper type of |
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thanks @DanielYang59! big fan of more specific error classes. 👍
janosh
removed
performance
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Actionable comments posted: 0
Review Status
Configuration used: CodeRabbit UI
Files selected for processing (7)
- pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py (1 hunks)
- pymatgen/core/operations.py (2 hunks)
- pymatgen/electronic_structure/bandstructure.py (1 hunks)
- pymatgen/io/adf.py (3 hunks)
- pymatgen/io/cif.py (2 hunks)
- pymatgen/io/vasp/outputs.py (10 hunks)
- pymatgen/transformations/advanced_transformations.py (2 hunks)
Files skipped from review as they are similar to previous changes (7)
- pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py
- pymatgen/core/operations.py
- pymatgen/electronic_structure/bandstructure.py
- pymatgen/io/adf.py
- pymatgen/io/cif.py
- pymatgen/io/vasp/outputs.py
- pymatgen/transformations/advanced_transformations.py
Additional Context Used
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Thanks for reviewing. There seems to be quite a lot of "catching general exceptions" as well ( |
Summary
Major changes:
Exceptionis missing theraisekeyword (thought there would be some as I did notice some in previous clean up, but luckily just found one in fae74b0) (triedrepattern:^\s?(?!raise)\s+\w+error\(\w?,^\s?(?!raise)\s+\w?exception\(\w?)raise Exceptionwith specificErrorReverted for now:
Exceptionwithcontextlib.suppressfor simplicity (userepattern:except\s+.*:\n\s+pass)