Clean up tests 2 #3716
Clean up tests 2 #3716
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janosh
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WalkthroughThe recent updates focused on enhancing the clarity and consistency of variable names across various test cases. This comprehensive effort involved renaming variables to more descriptive terms, improving readability and understanding. Changes were made in tests for elasticity, magnetism, structure prediction, adsorption, energy models, phase diagrams, and more, reflecting a systematic refinement of the codebase. Changes
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Actionable comments generated: 5
Configuration used: CodeRabbit UI
Files ignored due to path filters (5)
tests/files/surfaces/CONTCAR.relax1.gzis excluded by:!**/*.gztests/files/surfaces/LOCPOT.gzis excluded by:!**/*.gztests/files/surfaces/OUTCAR.relax1.gzis excluded by:!**/*.gztests/files/surfaces/cs_entries_o_ads.jsonis excluded by:!**/*.jsontests/files/surfaces/cs_entries_slabs.jsonis excluded by:!**/*.json
Files selected for processing (33)
- tests/analysis/elasticity/test_stress.py (1 hunks)
- tests/analysis/magnetism/test_jahnteller.py (1 hunks)
- tests/analysis/structure_prediction/test_volume_predictor.py (1 hunks)
- tests/analysis/test_adsorption.py (1 hunks)
- tests/analysis/test_energy_models.py (1 hunks)
- tests/analysis/test_phase_diagram.py (1 hunks)
- tests/analysis/test_piezo_sensitivity.py (4 hunks)
- tests/analysis/test_quasirrho.py (1 hunks)
- tests/analysis/test_surface_analysis.py (2 hunks)
- tests/apps/battery/test_conversion_battery.py (3 hunks)
- tests/core/test_ion.py (1 hunks)
- tests/core/test_lattice.py (1 hunks)
- tests/core/test_operations.py (1 hunks)
- tests/core/test_periodic_table.py (1 hunks)
- tests/core/test_structure.py (1 hunks)
- tests/core/test_surface.py (19 hunks)
- tests/core/test_tensors.py (1 hunks)
- tests/core/test_trajectory.py (2 hunks)
- tests/core/test_units.py (3 hunks)
- tests/electronic_structure/test_boltztrap.py (1 hunks)
- tests/entries/test_mixing_scheme.py (1 hunks)
- tests/ext/test_matproj.py (1 hunks)
- tests/files/.pytest-split-durations (1 hunks)
- tests/io/cp2k/test_inputs.py (1 hunks)
- tests/io/feff/test_inputs.py (1 hunks)
- tests/io/lammps/test_data.py (9 hunks)
- tests/io/test_adf.py (3 hunks)
- tests/io/test_cif.py (3 hunks)
- tests/io/vasp/test_inputs.py (4 hunks)
- tests/io/vasp/test_outputs.py (2 hunks)
- tests/io/vasp/test_sets.py (2 hunks)
- tests/symmetry/test_groups.py (1 hunks)
- tests/transformations/test_standard_transformations.py (1 hunks)
Files not reviewed due to errors (1)
- test_structure.py (no review received)
Files skipped from review due to trivial changes (11)
- tests/analysis/test_adsorption.py
- tests/analysis/test_energy_models.py
- tests/analysis/test_phase_diagram.py
- tests/analysis/test_piezo_sensitivity.py
- tests/core/test_ion.py
- tests/core/test_operations.py
- tests/core/test_periodic_table.py
- tests/ext/test_matproj.py
- tests/io/lammps/test_data.py
- tests/io/test_adf.py
- tests/transformations/test_standard_transformations.py
Additional comments: 64
tests/analysis/elasticity/test_stress.py (1)
- 39-45: The change from
ftodeformenhances code readability by making the variable name more descriptive. Good job on improving code clarity.tests/analysis/test_quasirrho.py (1)
- 51-57: Renaming
etoe_finalin thetest_rrho_manualmethod improves clarity by making the variable name more descriptive. This is a positive change towards enhancing code readability.tests/analysis/magnetism/test_jahnteller.py (1)
- 19-82: The renaming of
mtomagnitudeacross various test cases significantly enhances the readability and descriptiveness of the code. This change effectively communicates the purpose of the variable, aligning well with the PR's objectives.tests/analysis/structure_prediction/test_volume_predictor.py (1)
- 21-46: Renaming
ptopredictorin thetest_predictmethod improves code readability by making the variable name more descriptive and clearly indicating its role as an instance ofRLSVolumePredictor. This is a positive step towards enhancing code clarity.tests/apps/battery/test_conversion_battery.py (1)
- 121-142: > 📝 NOTE
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Renaming variables to more descriptive names (
ptoprops) and updating loop variables to iterate overprops.items()enhance code readability and clarity. These changes make the code more understandable and maintainable, aligning well with the PR's objectives.tests/io/cp2k/test_inputs.py (1)
- 88-96: Renaming
ptopot_infoin thetest_potential_infomethod improves the descriptiveness and clarity of the variable name, making it clear that it represents potential information. This change aligns well with the PR's objectives of enhancing code readability.tests/core/test_units.py (1)
- 262-277: > 📝 NOTE
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The renaming of variables throughout the file enhances code readability by making the variable names more descriptive and the code more understandable. These changes align well with the PR's objectives of improving code clarity and maintainability.
tests/symmetry/test_groups.py (3)
- 126-127: The renaming of
ptorand_percentand the updated assertion intest_get_orbitenhance code readability and maintain the logical correctness of the test. Good job on making the variable name more descriptive.- 131-137: Renaming
ptorand_percentand updating assertions intest_get_orbit_and_generatorsare excellent improvements. Usingapproxfor floating-point comparisons is a best practice, enhancing the test's reliability.- 126-137: Overall, the changes in
tests/symmetry/test_groups.pyalign well with the PR's objective of improving code readability and maintainability. The consistent application of a more descriptive naming convention and the careful update of assertions contribute positively to the codebase. Keep up the good work!tests/electronic_structure/test_boltztrap.py (1)
- 166-168: Renaming
eigstoeig_valsandref_eigstoref_eig_valsenhances clarity by making it explicit that these variables represent eigenvalues. Good improvement for code readability.tests/io/feff/test_inputs.py (1)
- 46-48: The modification in the
test_get_strmethod to directly compare a specific part of the header string is a good practice for making tests more precise and focused.tests/core/test_trajectory.py (3)
- 32-32: Changing from
appendto+=for adding molecules to the list is a stylistic choice and both are functionally equivalent. This change is acceptable.- 53-57: Simplifying the definition of
coordsby directly assigning them as lists instead of converting to NumPy arrays is a good practice when NumPy functionalities are not required. This makes the code cleaner and potentially more efficient.- 62-66: Directly assigning
coordsas lists instead of usingnp.asarrayis a cleaner approach when the specific functionalities of NumPy are not needed. This change enhances code readability and efficiency.tests/analysis/test_surface_analysis.py (2)
- 21-21: Renaming
TEST_DIRfrom"surface_tests"to"surfaces"improves clarity and aligns with the directory structure, making it easier to locate related test files.- 288-288: Renaming
TestWorkfunctionAnalyzertoTestWorkFunctionAnalyzercorrects the naming convention to follow CamelCase properly, enhancing readability and consistency across the codebase.tests/core/test_tensors.py (1)
- 546-548: Renaming variables
uandptou_matandp_matin thetest_polar_decompositionmethod enhances clarity by making the variable names more descriptive. This change improves code readability and makes it easier to understand the purpose of these variables within the context of the method.tests/core/test_lattice.py (3)
- 484-488: The variable renaming from
mtocubicenhances clarity by using a more descriptive name. This change aligns with the PR's objective of improving code readability.- 500-503: The renaming of
cubic_from_flatto itself does not introduce any changes. If the intention was to improve clarity or consistency, it appears this renaming might have been mistakenly included without actual changes. Please verify if this was intentional or if a different renaming was intended.- 509-509: The use of
cubic_from_flatin this context is consistent with the previous comment. It's important to ensure that the naming across the file remains consistent and clear, especially ifcubic_from_flatwas intended to be renamed.tests/core/test_surface.py (17)
- 33-33: Renaming
zno1to a more descriptive variable name enhances readability and clarity.- 52-54: Renaming
latticeandfrac_coordsimproves the clarity of what these variables represent.- 61-62: Renaming variables to
hydrogenandli_bccmakes the test setup more understandable by clearly indicating the elements and structures being tested.- 74-75: The renaming of
mtomatrixin the context of calculating the surface area is a good practice for clarity.- 118-119: Repeating the renaming of
mtomatrixin another test method maintains consistency across the test class.- 151-157: > 📝 NOTE
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The renaming of variables and the use of
self.ag_fccin generating slabs and calculating surface sites enhance the readability of the test method.
- 194-194: Using
self.ag_fccfor generating all slabs in the symmetry test method is consistent with the rest of the changes and improves clarity.- 269-270: Renaming
mtomatrixin the context of calculating surface area in another test method is consistent and improves readability.- 378-379: Using
np.random.randintto generate random space group numbers for testing slab generation with various lattice systems is a good approach for covering a wide range of cases.- 392-392: Creating structures from space group numbers and testing slab generation ensures coverage across different crystal systems.
- 401-403: Asserting that the dot product of lattice vectors with the normal vector approximates zero is a valid way to verify the orthogonality of the slab's surface to its normal.
- 433-434: Repeating the orthogonality check in another test method ensures consistency in verifying slab generation logic.
- 457-462: Updating file paths and using
self.ag_fccfor generating slabs in the context of bond constraints tests the functionality effectively.- 688-688: Loading a structure from a file for comparison in reconstruction tests ensures that the test is based on a known correct structure.
- 699-700: Updating file paths for loading structures in the setup method of
MillerIndexFinderTestsensures that the tests are run with the correct input data.- 835-839: The test for calculating Miller indices from sites in a cubic lattice system is a good example of ensuring the functionality works as expected across different lattice systems.
- 842-847: Testing the calculation of Miller indices from sites with a custom lattice matrix ensures the functionality's flexibility and correctness.
tests/io/test_cif.py (3)
- 502-502: Renaming
ntonitrogenimproves clarity by using a more descriptive name for the element.- 510-510: Renaming
ntodummy_specin the context of creating structures with dummy species is a good practice for readability and understanding the role of the variable in the test.- 557-557: The renaming of
ntodummy_spechere is consistent with the previous change and enhances the readability by clearly indicating the use of a dummy species in the structure.tests/io/vasp/test_sets.py (8)
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To avoid pollution of the test environment, consider adding a cleanup step to remove the directories and files created during the test execution.
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Looks good, correctly tests the INCAR settings for bulk mode.
- 274-281: > 📝 NOTE
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Correctly tests the INCAR settings for slab mode.
- 274-281: > 📝 NOTE
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Properly tests the KPOINTS settings for slab calculations.
- 274-281: > 📝 NOTE
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Correctly tests the INCAR settings for relaxation calculations.
- 274-281: > 📝 NOTE
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The tests correctly verify the POTCAR functional behavior in
MVLRelax52Set. Consider adding a cleanup step to remove any files or directories created during the test to avoid pollution of the test environment.
- 274-281: > 📝 NOTE
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Comprehensively tests the INCAR settings for Lobster calculations, ensuring the necessary parameters are set correctly for different configurations.
- 274-281: > 📝 NOTE
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Properly tests the KPOINTS settings for Lobster calculations, verifying the grid density.
tests/io/vasp/test_outputs.py (14)
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LGTM!
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LGTM!
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LGTM!
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LGTM!
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LGTM!
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LGTM!
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LGTM!
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LGTM!
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tests/files/.pytest-split-durations (1)
- 654-655: The renaming of
TestWorkfunctionAnalyzertoTestWorkFunctionAnalyzerimproves readability by adhering to the camel case naming convention.Ensure all references to this class in the codebase have been updated to reflect the new name.
Verification successful
The renaming of
TestWorkfunctionAnalyzertoTestWorkFunctionAnalyzerhas been correctly implemented across the codebase, with all references updated to reflect the new name.Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for old class name to ensure it's no longer used. Expecting no results. rg --type py "TestWorkfunctionAnalyzer" # Search for new class name to validate usage. Expecting list of locations where the new name is used. rg --type py "TestWorkFunctionAnalyzer"Length of output: 165
| entry = next(ent for ent in ms_complete.gga_entries if ent.entry_id == "gga-4") | ||
| d_compat = DummyCompatibility() | ||
| d_compat.process_entries(e) | ||
| d_compat.process_entries(entry) | ||
|
|
||
| with pytest.raises(CompatibilityError, match="energy has been modified"): | ||
| mixing_scheme_no_compat.get_adjustments(e, state_data) | ||
| mixing_scheme_no_compat.get_adjustments(entry, state_data) |
There was a problem hiding this comment.
The attempt to modify the energy of an entry directly through the DummyCompatibility class and then check for a CompatibilityError due to energy modification does not actually modify the entry's energy. The DummyCompatibility class's process_entries method expects a list of entries but is given a single entry, which would likely result in an error or no operation. To correctly modify the entry's energy for this test, you should directly adjust the entry's energy attribute.
- d_compat.process_entries(entry)
+ entry.energy -= 1 # Directly modify the entry's energy for the testCommittable 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.
| entry = next(ent for ent in ms_complete.gga_entries if ent.entry_id == "gga-4") | |
| d_compat = DummyCompatibility() | |
| d_compat.process_entries(e) | |
| d_compat.process_entries(entry) | |
| with pytest.raises(CompatibilityError, match="energy has been modified"): | |
| mixing_scheme_no_compat.get_adjustments(e, state_data) | |
| mixing_scheme_no_compat.get_adjustments(entry, state_data) | |
| entry = next(ent for ent in ms_complete.gga_entries if ent.entry_id == "gga-4") | |
| d_compat = DummyCompatibility() | |
| entry.energy -= 1 # Directly modify the entry's energy for the test | |
| with pytest.raises(CompatibilityError, match="energy has been modified"): | |
| mixing_scheme_no_compat.get_adjustments(entry, state_data) |
| hexagonal = Lattice([[2.319, -4.01662582, 0.0], [2.319, 4.01662582, 0.0], [0.0, 0.0, 7.252]]) | ||
|
|
||
| s1 = np.array([2.319, 1.33887527, 6.3455]) | ||
| s2 = np.array([1.1595, 0.66943764, 4.5325]) | ||
| s3 = np.array([1.1595, 0.66943764, 0.9065]) | ||
| hkl = m.get_miller_index_from_coords([s1, s2, s3]) | ||
| hkl = hexagonal.get_miller_index_from_coords([s1, s2, s3]) |
There was a problem hiding this comment.
Renaming hexagonal to Lattice might introduce confusion since Lattice is also the name of the imported class. Consider using a more descriptive name that does not conflict with class names, such as hex_lattice for clarity and to avoid potential confusion.
- hexagonal = Lattice([[2.319, -4.01662582, 0.0], [2.319, 4.01662582, 0.0], [0.0, 0.0, 7.252]])
+ hex_lattice = Lattice([[2.319, -4.01662582, 0.0], [2.319, 4.01662582, 0.0], [0.0, 0.0, 7.252]])Committable 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.
| hexagonal = Lattice([[2.319, -4.01662582, 0.0], [2.319, 4.01662582, 0.0], [0.0, 0.0, 7.252]]) | |
| s1 = np.array([2.319, 1.33887527, 6.3455]) | |
| s2 = np.array([1.1595, 0.66943764, 4.5325]) | |
| s3 = np.array([1.1595, 0.66943764, 0.9065]) | |
| hkl = m.get_miller_index_from_coords([s1, s2, s3]) | |
| hkl = hexagonal.get_miller_index_from_coords([s1, s2, s3]) | |
| hex_lattice = Lattice([[2.319, -4.01662582, 0.0], [2.319, 4.01662582, 0.0], [0.0, 0.0, 7.252]]) | |
| s1 = np.array([2.319, 1.33887527, 6.3455]) | |
| s2 = np.array([1.1595, 0.66943764, 4.5325]) | |
| s3 = np.array([1.1595, 0.66943764, 0.9065]) | |
| hkl = hex_lattice.get_miller_index_from_coords([s1, s2, s3]) |
| incar = Incar.from_str(incar_str) | ||
| assert isinstance(incar["EINT"], list) | ||
| assert incar["EINT"][0] == -0.85 |
There was a problem hiding this comment.
The test method test_types seems to be missing its implementation. It's crucial to ensure that the types of values parsed from the POTCAR files are correctly handled and tested.
Consider implementing this test to verify the correct handling of various types in the Incar class, especially for complex types like lists or specific value conversions.
| incar = Incar.from_str(incar_str) | ||
| assert incar["LHFCALC"] | ||
| assert incar["HFSCREEN"] == 0.2 | ||
| assert incar["ALGO"] == "All" |
There was a problem hiding this comment.
Similar to the previous comment, the test_types method is incomplete and lacks assertions or any form of verification.
This part of the test should verify the correct parsing and handling of boolean values and other special formats in the Incar class. Implementing this test is essential for ensuring robustness in type handling.
| # potcar = Potcar(["Fe", "P"]) | ||
| # assert potcar[0].functional_class == "GGA" | ||
| # assert potcar[1].functional_class == "GGA" | ||
| # SETTINGS["PMG_DEFAULT_FUNCTIONAL"] = "LDA" | ||
| # p = Potcar(["Fe", "P"]) | ||
| # assert p[0].functional_class == "LDA" | ||
| # assert p[1].functional_class == "LDA" | ||
| # potcar = Potcar(["Fe", "P"]) | ||
| # assert potcar[0].functional_class == "LDA" | ||
| # assert potcar[1].functional_class == "LDA" |
There was a problem hiding this comment.
The commented-out test method test_default_functional is not implemented. This test seems intended to verify the handling of the default functional setting for Potcar objects.
It's important to test the behavior of Potcar objects with respect to the default functional setting, as this affects the selection of POTCAR files. Consider implementing this test to ensure that Potcar objects correctly interpret and apply the PMG_DEFAULT_FUNCTIONAL setting.
There was a problem hiding this comment.
Review Status
Actionable comments generated: 0
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Files selected for processing (16)
- tests/analysis/elasticity/test_elastic.py (1 hunks)
- tests/analysis/structure_prediction/test_substitutor.py (1 hunks)
- tests/analysis/test_dimensionality.py (1 hunks)
- tests/analysis/test_ewald.py (1 hunks)
- tests/analysis/test_structure_analyzer.py (1 hunks)
- tests/analysis/test_structure_matcher.py (1 hunks)
- tests/analysis/test_surface_analysis.py (4 hunks)
- tests/command_line/test_enumlib_caller.py (3 hunks)
- tests/core/test_periodic_table.py (2 hunks)
- tests/core/test_units.py (3 hunks)
- tests/io/cp2k/test_inputs.py (3 hunks)
- tests/io/feff/test_sets.py (1 hunks)
- tests/io/vasp/test_inputs.py (6 hunks)
- tests/transformations/test_advanced_transformations.py (4 hunks)
- tests/transformations/test_standard_transformations.py (5 hunks)
- tests/util/test_coord.py (2 hunks)
Files skipped from review due to trivial changes (3)
- tests/analysis/elasticity/test_elastic.py
- tests/analysis/test_dimensionality.py
- tests/command_line/test_enumlib_caller.py
Files skipped from review as they are similar to previous changes (6)
- tests/analysis/test_surface_analysis.py
- tests/core/test_periodic_table.py
- tests/core/test_units.py
- tests/io/cp2k/test_inputs.py
- tests/io/vasp/test_inputs.py
- tests/transformations/test_standard_transformations.py
Additional comments: 24
tests/analysis/structure_prediction/test_substitutor.py (1)
- 23-23: Renaming the variable from
stosubstitutorenhances readability and clarity. Good job on making the code more understandable.tests/analysis/test_ewald.py (1)
- 112-113: Renaming the variable from
stostructimproves readability and clarity. This is a positive change towards making the code more understandable.tests/analysis/test_structure_analyzer.py (1)
- 26-27: Renaming variables from
stostructandsstostructsenhances readability and clarity. Good job on making the code more understandable.tests/io/feff/test_sets.py (1)
- 48-48: Simplifying the logic in the
test_get_headermethod by removing the intermediate variable and directly asserting the condition is a positive change. It makes the code more concise and readable.tests/util/test_coord.py (3)
- 276-278: Renaming the variable from
stosimplexin thetest_bary_coordsmethod enhances readability and clarity. This is a positive change towards making the code more understandable.- 285-288: Renaming the variable from
stosimplexin thetest_intersectionmethod improves readability and clarity. Good job on making the code more understandable.- 324-331: Renaming the variable from
stosimplexin thetest_intersectionmethod for coplanar cases enhances readability and clarity. This is a positive change towards making the code more understandable.tests/analysis/test_structure_matcher.py (9)
- 119-122: The variable names
d,ft, andswere changed todistances,trac_trans_vec, andsolutionrespectively. This improves readability and makes the code more understandable. Good job on enhancing clarity with descriptive variable names.- 125-128: The changes in variable names are consistently applied across different assertions within the
test_cart_distsmethod. This maintains consistency and readability throughout the method.- 131-134: Continuing with the theme of improved variable naming for clarity, the changes here are also consistent and enhance the readability of the test assertions.
- 137-139: The variable naming improvements are consistently applied in this segment as well, contributing to the overall readability and maintainability of the test code.
- 116-142: > 📝 NOTE
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The use of
from __future__ import annotationsis a good practice for forward compatibility with future Python versions, ensuring that type annotations are interpreted as string literals. This can help avoid circular import issues in more complex projects.
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Importing specific classes and functions directly from their modules enhances readability and can improve import efficiency. This practice is well-followed throughout the file.
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The
setUpmethod is used here, which is a pattern fromunittest. Since this file usespytest, consider using fixture functions with the@pytest.fixturedecorator for setup tasks. This approach is more idiomatic topytestand can offer more flexibility and reusability across tests.
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This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [17-17]
The use of
json.loadwithcls=MontyDecoderfor deserializing JSON data into pymatgen objects is a good practice for ensuring that complex objects are correctly instantiated. This demonstrates an effective use of custom deserializers for complex object hierarchies.
- 119-139: The refactoring of variable names in the
test_cart_distsmethod significantly improves the readability and understandability of the test code. This change aligns with the PR's objective of enhancing code readability and maintainability through systematic renaming.tests/transformations/test_advanced_transformations.py (8)
- 96-98: The renaming of
stostruct_trafoimproves readability by making the variable name more descriptive.- 104-109: Renaming
disordtodisorderedenhances clarity and consistency in variable naming.- 116-118: The use of
assert len(...)directly after applying transformations and expecting specific lengths helps ensure the transformations behave as expected. This is a good practice for testing expected outcomes.- 155-157: The renaming of
stostruct_trafohere as well is consistent with earlier changes and improves readability.- 169-171: The renaming of variables and the use of
struct_trafofor transformed structures are consistent with the PR's objectives. It's good to see consistency in naming conventions across different tests.- 185-190: Using
struct_trafofor the transformed structure variable name consistently across different test cases is a good practice. It helps in maintaining readability and understanding of the test's intent.- 198-201: The consistent use of
struct_trafofor naming transformed structures in tests is observed here as well. This consistency is beneficial for readability and maintainability.- 225-228: Again, the use of
struct_trafofor the transformed structure variable name is consistent with the PR's objectives and improves readability.
follow-up to #3713
Summary by CodeRabbit