Fix equivalent atoms and add tests #219
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WalkthroughThese changes introduce modifications to the Changes
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Actionable comments posted: 2
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Files selected for processing (2)
- structuretoolkit/analyse/phonopy.py (1 hunks)
- tests/test_analyse_phonopy.py (1 hunks)
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structuretoolkit/analyse/phonopy.py (1)
44-46: Approve changes but verify impact on other parts of the codebase.The modification to use
unitcell.totuple()in thespg.get_symmetrycall is approved as it likely enhances the accuracy of symmetry calculations.However, ensure that this change does not affect other parts of the codebase where
get_equivalent_atomsmight be used.
tests/test_analyse_phonopy.py
Outdated
| import unittest | ||
| from ase.build import bulk | ||
| from structuretoolkit.analyse.phonopy import get_equivalent_atoms | ||
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| class TestEquivalentAtoms(unittest.TestCase): | ||
| def test_get_equivalent_atoms(self): | ||
| equivalent_atoms = get_equivalent_atoms( | ||
| structure=bulk("Al", cubic=True), symprec=1e-5, angle_tolerance=-1.0 | ||
| ) | ||
| self.assertTrue(all(equivalent_atoms == [0, 0, 0, 0])) |
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Add comprehensive tests and verify expected results.
The test case only checks one scenario with hard-coded expected results. Consider adding more test cases to cover different scenarios and edge cases, such as non-cubic structures or invalid inputs.
Additionally, verify that the expected results [0, 0, 0, 0] are correct for the given structure and parameters.
Would you like me to help create additional test cases or verify the expected results?
| ops = spg.get_symmetry( | ||
| cell=unitcell.totuple(), symprec=symprec, angle_tolerance=angle_tolerance | ||
| ) |
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Consider adding documentation for the use of totuple().
Adding a comment or updating the documentation to explain why totuple() is used instead of the direct unitcell object could help maintain clarity and assist future maintainers or users of the code.
+ # Convert unitcell to tuple to ensure compatibility with spglib API requirements
ops = spg.get_symmetry(
cell=unitcell.totuple(), symprec=symprec, angle_tolerance=angle_tolerance
)Committable suggestion
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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.
| ops = spg.get_symmetry( | |
| cell=unitcell.totuple(), symprec=symprec, angle_tolerance=angle_tolerance | |
| ) | |
| # Convert unitcell to tuple to ensure compatibility with spglib API requirements | |
| ops = spg.get_symmetry( | |
| cell=unitcell.totuple(), symprec=symprec, angle_tolerance=angle_tolerance | |
| ) |
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Actionable comments posted: 1
Outside diff range, codebase verification and nitpick comments (1)
tests/test_analyse_phonopy.py (1)
8-13: Conditional import ofspglibis valid but can be optimized.The import of
spglibis used to check its availability which is a valid use case. However, usingimportlib.util.find_specmight be a cleaner approach to check for the availability of a package without importing it.- import spglib - spglib_not_available = False + from importlib import util + spglib_not_available = util.find_spec("spglib") is NoneTools
Ruff
9-9:
spglibimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
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- tests/test_analyse_phonopy.py (1 hunks)
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Ruff
tests/test_analyse_phonopy.py
9-9:
spglibimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
Additional comments not posted (2)
tests/test_analyse_phonopy.py (2)
16-18: Proper use of theskipIfdecorator.The decorator is correctly applied to skip tests conditionally based on the availability of
spglib. This is a good practice to ensure tests do not fail due to missing optional dependencies.
26-31: Good initial tests for conversion, but consider more scenarios.The tests ensure that the basic properties of the structure remain unchanged after conversion. To enhance the robustness, consider adding tests for different types of structures and checking for edge cases.
| def test_get_equivalent_atoms(self): | ||
| equivalent_atoms = get_equivalent_atoms( | ||
| structure=bulk("Al", cubic=True), symprec=1e-5, angle_tolerance=-1.0 | ||
| ) | ||
| self.assertTrue(all(equivalent_atoms == [0, 0, 0, 0])) |
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Expand test coverage for get_equivalent_atoms.
The current test checks a specific scenario with a hard-coded expected result. Consider adding more test cases to cover different scenarios and edge cases, such as non-cubic structures or invalid inputs.
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Actionable comments posted: 1
Outside diff range, codebase verification and nitpick comments (1)
tests/test_analyse_phonopy.py (1)
8-13: Conditional import ofspglibis valid but can be optimized.The import of
spglibis used to check its availability which is a valid use case. However, usingimportlib.util.find_specmight be a cleaner approach to check for the availability of a package without importing it.- import spglib - spglib_not_available = False + from importlib import util + spglib_not_available = util.find_spec("spglib") is NoneTools
Ruff
9-9:
spglibimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (1)
- tests/test_analyse_phonopy.py (1 hunks)
Additional context used
Ruff
tests/test_analyse_phonopy.py
9-9:
spglibimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
Additional comments not posted (2)
tests/test_analyse_phonopy.py (2)
16-18: Proper use of theskipIfdecorator.The decorator is correctly applied to skip tests conditionally based on the availability of
spglib. This is a good practice to ensure tests do not fail due to missing optional dependencies.
26-31: Good initial tests for conversion, but consider more scenarios.The tests ensure that the basic properties of the structure remain unchanged after conversion. To enhance the robustness, consider adding tests for different types of structures and checking for edge cases.
Comments failed to post (1)
tests/test_analyse_phonopy.py
20-24: Expand test coverage for
get_equivalent_atoms.The current test checks a specific scenario with a hard-coded expected result. Consider adding more test cases to cover different scenarios and edge cases, such as non-cubic structures or invalid inputs.
Summary by CodeRabbit
Bug Fixes
Tests