Clean up tests #3713
Clean up tests #3713
Conversation
e.g. remove unnecessary for loops when using pytest.approx()
janosh
added
tests
WalkthroughThe recent updates focus on enhancing code readability and efficiency in a scientific computing library. Changes include variable renaming for clarity, matrix manipulation optimization, and test case refinement for improved precision. These updates aim to boost maintainability and performance, making the codebase more developer-friendly. Changes
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (invoked as PR comments)
Additionally, you can add CodeRabbit Configration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Review Status
Actionable comments generated: 1
Configuration used: CodeRabbit UI
Files selected for processing (16)
- pymatgen/io/lmto.py (3 hunks)
- pymatgen/io/nwchem.py (1 hunks)
- tests/analysis/elasticity/test_elastic.py (1 hunks)
- tests/analysis/test_graphs.py (1 hunks)
- tests/analysis/test_local_env.py (2 hunks)
- tests/core/test_interface.py (1 hunks)
- tests/core/test_lattice.py (1 hunks)
- tests/core/test_surface.py (1 hunks)
- tests/core/test_trajectory.py (3 hunks)
- tests/core/test_units.py (1 hunks)
- tests/electronic_structure/test_boltztrap.py (4 hunks)
- tests/ext/test_matproj.py (1 hunks)
- tests/io/lobster/test_inputs.py (1 hunks)
- tests/io/vasp/test_outputs.py (4 hunks)
- tests/symmetry/test_analyzer.py (2 hunks)
- tests/transformations/test_standard_transformations.py (2 hunks)
Files skipped from review due to trivial changes (4)
- tests/analysis/test_graphs.py
- tests/core/test_interface.py
- tests/core/test_surface.py
- tests/ext/test_matproj.py
Additional comments: 33
tests/core/test_units.py (1)
- 96-126: The renaming of functions from
f,g,h,i, andjtofunc1,func2,func3,func4, andfunc5respectively, improves readability and clarity. This change aligns well with the PR's objective of enhancing code maintainability and clarity. Good job on making these names more descriptive.tests/electronic_structure/test_boltztrap.py (8)
- 93-100: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [96-112]
Replacing loops with direct assertions and adjusting tolerance values in the test cases enhances the clarity and efficiency of the tests. This approach makes the tests more straightforward and easier to understand, which is beneficial for maintainability. Good job on these improvements.
- 119-122: Direct assertions in test cases, as seen here, contribute to making the tests more concise and readable. This change aligns with the PR's goal of cleaning up and optimizing the codebase.
- 126-131: The use of direct assertions and the adjustment of tolerance values in these test cases are excellent examples of the PR's objectives to enhance test clarity and efficiency. These changes make the tests more straightforward and maintainable.
- 135-140: Replacing loops with direct assertions in the test cases, as done here, improves the readability and efficiency of the tests. This aligns with the PR's goal of optimizing the codebase for better maintainability and clarity.
- 108-147: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [144-160]
The modifications to use direct assertions and adjust tolerance values in the test cases are in line with the PR's objectives. These changes contribute to making the tests more concise and easier to understand, which is beneficial for future maintenance.
- 168-168: Using direct assertions in test cases, as demonstrated here, aligns with the PR's goal of enhancing test clarity and efficiency. This approach makes the tests more straightforward and maintainable.
- 172-176: The changes to replace loops with direct assertions and adjust tolerance values in these test cases are excellent examples of the PR's objectives to clean up and optimize the codebase. These modifications enhance the readability and efficiency of the tests.
- 188-189: Using direct assertions in test cases, as seen here, contributes to making the tests more concise and readable. This change aligns with the PR's goal of cleaning up and optimizing the codebase.
pymatgen/io/lmto.py (1)
- 184-196: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [187-217]
Renaming variables for clarity and adjusting variable names in the
from_strmethod of theLMTOCtrlclass enhances code readability and maintainability. These changes align with the PR's objective of improving the clarity and efficiency of the codebase. Good job on making these names more descriptive and the logic more understandable.tests/core/test_trajectory.py (3)
- 74-75: The change from
itoidxin the loop variable name enhances clarity and consistency with the rest of the codebase.- 90-90: The change from
itoidxin the loop variable name enhances clarity and consistency with the rest of the codebase.- 424-428: The change from
itoidxin the loop variable name enhances clarity and consistency with the rest of the codebase.tests/analysis/elasticity/test_elastic.py (1)
- 414-415: The change from
itoidxin the loop variable name enhances clarity and consistency with the rest of the codebase.tests/transformations/test_standard_transformations.py (1)
- 128-128: The change from using
randomtonp.random.randintfor generating random integers is a positive one, as it enhances the reliability and consistency of random number generation. This is particularly important in a testing context where reproducibility of results can be crucial.tests/core/test_lattice.py (1)
- 438-439: The changes to use
np.random.randintandnp.random.randfor generatinglengthsandlatticeimprove readability and efficiency. However, consider adding a comment explaining the choice of random values and ensuring that the randomness does not compromise the test's reliability.tests/symmetry/test_analyzer.py (2)
- 362-367: Renaming
satospg_analyzerin thetest_tricky_structurefunction improves readability and clarity by using a more descriptive variable name. This change aligns well with the PR's objective of enhancing code clarity.- 376-381: The use of different indices in the list comprehensions for
sites1andsites2in thetest_are_symmetrically_equivalentfunction is a logical approach to testing symmetry between different sets of sites. This change contributes to the PR's goal of refining tests for better clarity and efficiency.pymatgen/io/nwchem.py (2)
- 923-926: The logic for ensuring the symmetry of the
hessianmatrix by filling in the upper triangular part based on the lower triangular part is correct. However, consider adding a comment explaining this operation for future maintainability. Additionally, for very large matrices, this nested loop approach might impact performance. It could be beneficial to review if there are more efficient numpy operations that can achieve the same result.- 928-931: Identical considerations as for the
hessianmatrix apply here for ensuring the symmetry of theprojected_hessianmatrix. Adding a comment for clarity and reviewing potential performance implications for large matrices would be beneficial.tests/analysis/test_local_env.py (2)
- 537-548: The changes in the
TestMotifIdentificationclass, specifically the use ofidxinstead ofiin loops and the updated assertion messages, improve readability and maintainability. These modifications align well with the PR's objectives of enhancing clarity and efficiency.- 1009-1009: The assignment of specific parameters to
op_paramsfor indices 1, 2, and 33 is clear and aligns with the PR's goal of optimizing logic. However, the syntax error in the previous comment needs to be addressed for this to work correctly.tests/io/vasp/test_outputs.py (2)
- 240-247: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1983-1985]
LGTM!
- 1996-2010: > 📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [1987-2007]
LGTM!
tests/io/lobster/test_inputs.py (9)
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
Please ensure that all test classes and methods have appropriate docstrings that describe their purpose, inputs, and expected outcomes. This will improve code maintainability and readability.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
Consider adding more edge case tests for
TestLobsterinto cover scenarios where input files might be malformed or missing expected data. This will help ensure robust error handling and validation in theLobsterinclass.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
In
TestBandoverlaps, consider testing the behavior when the band overlap file is incomplete or contains unexpected values. Adding such tests can help identify and handle potential parsing errors more gracefully.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
For
TestGrosspop, adding tests that verify the handling of negative or zero population values could enhance the test coverage, ensuring that the gross population parsing logic is robust against various input scenarios.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
In
TestSitePotentials, it would be beneficial to include tests that check the behavior when site potential data is missing for some sites in the structure. This can help ensure that the code gracefully handles incomplete data.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
For
TestMadelungEnergies, consider adding tests that simulate scenarios with extremely high or low Madelung energies, to ensure that the parsing and handling logic can cope with a wide range of energy values.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
In
TestLobsterMatrices, adding tests for scenarios where matrix files are corrupted or have unexpected formats would improve the robustness of the LobsterMatrices class by ensuring it can handle error conditions effectively.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
For
TestWavefunction, consider implementing tests that verify the behavior when wavefunction files are incomplete or contain non-numeric values. This will help ensure that the wavefunction parsing logic is resilient to various file contents.
- 268-274: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [1-1]
In
TestUtils, adding tests for utility functions with edge case inputs (e.g., empty lists, null values) could enhance the test coverage and ensure that these functions behave as expected under all conditions.
tests/analysis/test_local_env.py
Outdated
| op_params = [None] * range(len(op_types)) | ||
| op_params[1] = {"TA": 1, "IGW_TA": 1.0 / 0.0667} | ||
| op_params[2] = {"TA": 45.0 / 180, "IGW_TA": 1.0 / 0.0667} | ||
| op_params[33] = { | ||
| "TA": 0.6081734479693927, | ||
| "IGW_TA": 18.33, | ||
| "fac_AA": 1.5, | ||
| "exp_cos_AA": 2, | ||
| } | ||
| op_params[33] = {"TA": 0.6081734479693927, "IGW_TA": 18.33, "fac_AA": 1.5, "exp_cos_AA": 2} |
There was a problem hiding this comment.
The initialization of op_params using a list comprehension is a significant improvement in terms of readability and efficiency. However, there's a minor issue with the syntax used for defining the size of op_params. The correct way to initialize a list of a specific size with None values in Python is [None] * len(op_types), not [None] * range(len(op_types)).
- op_params = [None] * range(len(op_types))
+ op_params = [None] * len(op_types)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.
| op_params = [None] * range(len(op_types)) | |
| op_params[1] = {"TA": 1, "IGW_TA": 1.0 / 0.0667} | |
| op_params[2] = {"TA": 45.0 / 180, "IGW_TA": 1.0 / 0.0667} | |
| op_params[33] = { | |
| "TA": 0.6081734479693927, | |
| "IGW_TA": 18.33, | |
| "fac_AA": 1.5, | |
| "exp_cos_AA": 2, | |
| } | |
| op_params[33] = {"TA": 0.6081734479693927, "IGW_TA": 18.33, "fac_AA": 1.5, "exp_cos_AA": 2} | |
| op_params = [None] * len(op_types) | |
| op_params[1] = {"TA": 1, "IGW_TA": 1.0 / 0.0667} | |
| op_params[2] = {"TA": 45.0 / 180, "IGW_TA": 1.0 / 0.0667} | |
| op_params[33] = {"TA": 0.6081734479693927, "IGW_TA": 18.33, "fac_AA": 1.5, "exp_cos_AA": 2} |
There was a problem hiding this comment.
Review Status
Actionable comments generated: 0
Configuration used: CodeRabbit UI
Files selected for processing (5)
- tests/analysis/ferroelectricity/test_polarization.py (1 hunks)
- tests/analysis/test_local_env.py (2 hunks)
- tests/electronic_structure/test_plotter.py (1 hunks)
- tests/io/abinit/test_inputs.py (1 hunks)
- tests/io/test_pwscf.py (1 hunks)
Files skipped from review as they are similar to previous changes (1)
- tests/analysis/test_local_env.py
Additional comments: 5
tests/io/abinit/test_inputs.py (1)
- 223-229: > 📝 NOTE
This review was outside the diff hunks, and no overlapping diff hunk was found. Original lines [20-20]
Renaming the loop variable from
itoidximproves readability and does not introduce any issues.tests/io/test_pwscf.py (2)
- 367-367: Renaming
pwintopw_inimproves readability by making the variable name more descriptive.- 370-370: Renaming
pwouttopw_outenhances clarity and consistency in the code.tests/analysis/ferroelectricity/test_polarization.py (1)
- 20-20: Modifying the range in the list comprehension for generating folder names appears to correctly adjust the folder naming logic. Ensure this change aligns with the intended folder structure and naming convention.
tests/electronic_structure/test_plotter.py (1)
- 232-243: The refactoring of loop variables from
i, j, k, mtoii, jj, kk, llimproves readability by avoiding single-letter variable names that are often used as indices in mathematical contexts. This change aligns with best practices for clarity and maintainability. However, there's an opportunity to further enhance the code by explaining the purpose of these loops and the logic behind the random number generation foraandb. Adding a brief comment could help future maintainers understand the intent behind this code segment more quickly.Consider adding a comment above the loop to explain its purpose and the logic behind the random number assignments to
aandb. This will improve code readability and maintainability.
e.g. remove unnecessary for loops when using pytest.approx()
Summary by CodeRabbit