VEC function integration into smact.properties with a test file to serve as an example for its use. #305
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Actionable comments posted: 3
Outside diff range, codebase verification and nitpick comments (1)
VECexample.py (1)
1-11: Enhance error handling and validation.The example script lacks error handling for file operations and validation for the input compound. Consider adding try-except blocks to handle potential exceptions from the
valence_electron_countfunction, such asFileNotFoundErrorandValueError.try: vec = valence_electron_count(compound, valence_file) print(f"The Valence Electron Count (VEC) for {compound} is: {vec:.2f}") except FileNotFoundError: print(f"Error: The file {valence_file} was not found.") except ValueError as e: print(f"Error: {e}")
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elements_valence_modified.csvis excluded by!**/*.csv
Files selected for processing (2)
- VECexample.py (1 hunks)
- smact/properties.py (2 hunks)
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smact/properties.py
204-204: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
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Thank you for submitting this PR @ryannduma . A few things before I can accept this PR.
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Files selected for processing (3)
- VECexample.py (1 hunks)
- smact/properties.py (2 hunks)
- smact/tests/test_core.py (2 hunks)
Files skipped from review as they are similar to previous changes (1)
- VECexample.py
Additional context used
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smact/properties.py
1-1:
csvimported but unusedRemove unused import:
csv(F401)
197-197: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
Additional comments not posted (3)
smact/properties.py (2)
184-191: Consider refactoringparse_formulafor reusability.The
parse_formulafunction is useful for extracting elements and stoichiometries from chemical formulas. Consider refactoring it into a standalone utility function for broader use within the module.
193-197: Consider refactoringget_element_valencefor reusability.The
get_element_valencefunction is useful for retrieving valence data from CSV rows. Consider refactoring it into a standalone utility function for broader use within the module.Tools
Ruff
197-197: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
smact/tests/test_core.py (1)
94-98: Test functiontest_valence_electron_countis well-structured.The test function effectively validates the
valence_electron_countfunction, covering both correct calculations and error handling for invalid inputs.
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| import csv | |||
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Remove unused import csv.
The csv module is imported but not used in the file. Removing it will clean up the code.
-import csvCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| import csv |
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1-1:
csvimported but unusedRemove unused import:
csv(F401)
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Hey Anthony, I have resolved all conflicts and the code now passes the qa stage of the CI except its failing all the other tests of the CI, how can I resolve that? |
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Files selected for processing (3)
- examples/vec_example.py (1 hunks)
- smact/properties.py (2 hunks)
- smact/tests/test_core.py (2 hunks)
Files skipped from review due to trivial changes (1)
- examples/vec_example.py
Files skipped from review as they are similar to previous changes (1)
- smact/tests/test_core.py
Additional context used
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smact/properties.py
1-1:
csvimported but unusedRemove unused import:
csv(F401)
Additional comments not posted (1)
smact/properties.py (1)
1-1: Remove unused importcsv.The
csvmodule is imported but not used in the file. Removing it will clean up the code.Apply this diff to remove the unused import:
-import csvLikely invalid or redundant comment.
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1-1:
csvimported but unusedRemove unused import:
csv(F401)
properties.py
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Outside diff range, codebase verification and nitpick comments (1)
.pre-commit-config.yaml (1)
7-7: Ensure consistent formatting forisortarguments.The formatting of the
argsfor theisorthook has been adjusted. Ensure that this change aligns with the project's style guidelines.
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Files selected for processing (4)
- .pre-commit-config.yaml (2 hunks)
- examples/Crystal_Space/1_reduction.ipynb (1 hunks)
- smact/properties.py (2 hunks)
- smact/tests/test_core.py (2 hunks)
Files skipped from review due to trivial changes (1)
- examples/Crystal_Space/1_reduction.ipynb
Files skipped from review as they are similar to previous changes (1)
- smact/tests/test_core.py
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smact/properties.py
1-1:
csvimported but unusedRemove unused import:
csv(F401)
Additional comments not posted (4)
.pre-commit-config.yaml (1)
19-23: Update nbQA version and compatibility.The
nbQAversion has been updated to1.8.7, and the Python compatibility fornbqa-pyupgradehas been changed to--py39-plus. Ensure that these changes are compatible with the project's requirements and do not introduce any issues.smact/properties.py (3)
1-1: Remove unused importcsv.The
csvmodule is imported but not used in the file. Removing it will clean up the code.Tools
Ruff
1-1:
csvimported but unusedRemove unused import:
csv(F401)
165-219: Consider refactoring helper functions for reusability.The
valence_electron_countfunction is well-implemented with appropriate error handling. However, consider refactoring theparse_formulaandget_element_valencehelper functions into standalone utility functions for broader use within the module.
193-199: Improve exception handling inget_element_valence.Use
raise ... from Noneto distinguish it from errors in exception handling.
invalid elements ie Lr0
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- smact/tests/test_core.py (2 hunks)
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- smact/tests/test_core.py
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #305 +/- ##
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+ Coverage 75.47% 75.67% +0.19%
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Files 24 24
Lines 2361 2183 -178
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- Hits 1782 1652 -130
+ Misses 579 531 -48 ☔ View full report in Codecov by Sentry. |
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Merged! |
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Hey @AntObi , the code passed the tests after a bunch of minor tweaks here and there to the types of errors raised, I noticed the Lr0 element check passed as a ValueError when passed to the function instead of a TypeError as presumed so I edited that part of the test to match, and it passed, though I dont know if thats exactly right, same to the Xx which isnt a valid element but I guess when parsed over is accepted because of the following codeblock, which ofc down the line, is found to not have a Valence number and then returns a ValueError instead of a NameError - please let me know what your thoughts are on this and whether additional tweaks need to be made. Thank you and have a good evening
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VEC function Pull Request
Description
Hey, I hope this PR finds you well, I have now completed the integration of the VEC function succintly into the smact.properties.py module and attached a relevant example of it's use. I would also like to indicate that the function takes two arguments - the compound in question and a valence file - allowing for the user to select any file say magpie, or any existing valence file that they would like to use, in this case the example uses the modified file you shared.
I would like to highlight that this is a New feature (non-breaking change which adds functionality)
How Has This Been Tested?
Test Configuration: VECexample.py
Reviewers
@AntObi - Admin and Maintainer
Checklist:
Summary by CodeRabbit
New Features
Bug Fixes
Tests