Add ruff linter #224
Add ruff linter #224
Conversation
WalkthroughThe recent changes focus on enhancing the robustness and accuracy of dependency management scripts, refining import statements, and improving code readability and maintainability across multiple files. New configurations for pre-commit hooks have been introduced, and several functions have been restructured for better compatibility and performance. Additionally, new functions and constants have been added to extend the functionality of the Changes
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Actionable comments posted: 32
Outside diff range, codebase verification and nitpick comments (5)
structuretoolkit/build/sqs.py (1)
1-6: Reorder imports for logical grouping.Consider grouping standard library imports, third-party imports, and local imports separately for better readability.
+ import itertools + import random + import warnings + from multiprocessing import cpu_count + + from typing import Dict, Iterable, Optional, Union + + import numpy as np + from ase.atoms import Atoms + from ase.data import atomic_numbersstructuretoolkit/build/compound.py (1)
2-7: Reorder imports for logical grouping.Consider grouping standard library imports, third-party imports, and local imports separately for better readability.
+ from typing import Optional + + import numpy as np + from ase.atoms import Atoms + from ase.build import bulk + from ase.spacegroup import crystal + + from structuretoolkit.analyse.neighbors import get_neighborsstructuretoolkit/analyse/symmetry.py (1)
7-7: Remove unused importcached_property.The
cached_propertyimport fromfunctoolsis not used in the filestructuretoolkit/analyse/symmetry.pyand should be removed to clean up the code.
structuretoolkit/analyse/symmetry.py: Removefrom functools import cached_propertyAnalysis chain
Verify the usage of
cached_property.Ensure that the
cached_propertydecorator is used in the file to avoid unnecessary imports.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `cached_property` in the file. # Test: Search for the usage of `cached_property`. Expect: At least one occurrence. rg --type python -A 5 $'cached_property'Length of output: 70
Script:
#!/bin/bash # Description: Verify the usage of `cached_property` in the file. # Test: Search for the usage of `cached_property`. Expect: At least one occurrence. rg 'cached_property' --glob '*.py' -A 5Length of output: 389
Script:
#!/bin/bash # Description: Verify the usage of `cached_property` in the file `structuretoolkit/analyse/symmetry.py`. # Test: Search for the usage of `cached_property` within the specific file. Expect: At least one occurrence. rg 'cached_property' structuretoolkit/analyse/symmetry.py -A 5Length of output: 190
Tools
Ruff
7-7:
functools.cached_propertyimported but unusedRemove unused import:
functools.cached_property(F401)
structuretoolkit/analyse/snap.py (1)
1-1: Remove the unusedctypesimport.The
ctypesmodule is imported but not used in thestructuretoolkit/analyse/snap.pyfile. This import should be removed to avoid unnecessary clutter.
structuretoolkit/analyse/snap.py: Remove the linefrom ctypes import POINTER, c_double, c_int, cast.Analysis chain
Verify the usage of the
ctypesmodule.Ensure that the
ctypesmodule is used in the file to avoid unnecessary imports.
Let's correct the
rgcommand to search for the usage of thectypesmodule in Python files.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of the `ctypes` module in the file. # Test: Search for the usage of `ctypes`. Expect: At least one occurrence. rg --type python -A 5 $'ctypes'Length of output: 61
Script:
#!/bin/bash # Description: Verify the usage of the `ctypes` module in the file. # Test: Search for the usage of `ctypes`. Expect: At least one occurrence. rg 'ctypes' --glob '*.py' -A 5Length of output: 408
structuretoolkit/visualize.py (1)
6-9: Reordered imports: The new import order does not fully comply with PEP 8 guidelines.The third-party imports should be sorted alphabetically. Specifically,
from ase.atoms import Atomsshould come afterfrom scipy.interpolate import interp1d.
Current order:
import numpy as np from ase.atoms import Atoms from scipy.interpolate import interp1dCorrect order:
import numpy as np from scipy.interpolate import interp1d from ase.atoms import AtomsAnalysis chain
Reordered imports: Verify if the new order follows PEP 8 guidelines.
The import order has been changed. Ensure that the new order follows PEP 8 guidelines for readability and maintainability.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify if the import order follows PEP 8 guidelines. # Test: Check import order. Expect: Imports should be grouped and ordered correctly. ast-grep --lang python --pattern $'import $_\nfrom $_ import $_\nfrom $_ import $_'Length of output: 550
Script:
#!/bin/bash # Description: Verify if the import order follows PEP 8 guidelines. # Find all import statements and their order rg --multiline --multiline-dotall --no-filename --no-line-number '^(import .+|from .+ import .+)' structuretoolkit/visualize.pyLength of output: 33611
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (44)
- .ci_support/release.py (3 hunks)
- .pre-commit-config.yaml (1 hunks)
- setup.py (1 hunks)
- structuretoolkit/init.py (3 hunks)
- structuretoolkit/_version.py (1 hunks)
- structuretoolkit/analyse/init.py (2 hunks)
- structuretoolkit/analyse/distance.py (1 hunks)
- structuretoolkit/analyse/dscribe.py (1 hunks)
- structuretoolkit/analyse/neighbors.py (1 hunks)
- structuretoolkit/analyse/phonopy.py (2 hunks)
- structuretoolkit/analyse/pyscal.py (1 hunks)
- structuretoolkit/analyse/snap.py (1 hunks)
- structuretoolkit/analyse/spatial.py (1 hunks)
- structuretoolkit/analyse/strain.py (1 hunks)
- structuretoolkit/analyse/symmetry.py (1 hunks)
- structuretoolkit/build/init.py (1 hunks)
- structuretoolkit/build/aimsgb.py (3 hunks)
- structuretoolkit/build/compound.py (2 hunks)
- structuretoolkit/build/mesh.py (2 hunks)
- structuretoolkit/build/random.py (2 hunks)
- structuretoolkit/build/sqs.py (3 hunks)
- structuretoolkit/build/surface.py (4 hunks)
- structuretoolkit/common/init.py (1 hunks)
- structuretoolkit/common/helper.py (1 hunks)
- structuretoolkit/visualize.py (1 hunks)
- tests/test_aimsgb.py (1 hunks)
- tests/test_analyse.py (1 hunks)
- tests/test_analyse_distance.py (1 hunks)
- tests/test_analyse_phonopy.py (1 hunks)
- tests/test_analyse_symmetry.py (1 hunks)
- tests/test_compound.py (1 hunks)
- tests/test_dscribe.py (2 hunks)
- tests/test_helpers.py (2 hunks)
- tests/test_high_index_surface.py (1 hunks)
- tests/test_mesh.py (2 hunks)
- tests/test_neighbors.py (1 hunks)
- tests/test_pymatgen.py (8 hunks)
- tests/test_pyscal.py (1 hunks)
- tests/test_pyxtal.py (2 hunks)
- tests/test_snap.py (7 hunks)
- tests/test_sqs.py (1 hunks)
- tests/test_strain.py (1 hunks)
- tests/test_symmetry.py (4 hunks)
- tests/test_visualize.py (2 hunks)
Files not summarized due to errors (1)
- tests/test_snap.py: Error: Message exceeds token limit
Files skipped from review due to trivial changes (7)
- .pre-commit-config.yaml
- structuretoolkit/analyse/distance.py
- structuretoolkit/analyse/dscribe.py
- structuretoolkit/analyse/spatial.py
- structuretoolkit/common/helper.py
- tests/test_helpers.py
- tests/test_high_index_surface.py
Additional context used
Ruff
structuretoolkit/build/__init__.py
1-1:
structuretoolkit.build.aimsgb.get_grainboundary_infoimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
1-1:
structuretoolkit.build.aimsgb.grainboundaryimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
2-2:
structuretoolkit.build.compound.B2imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
2-2:
structuretoolkit.build.compound.C14imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
2-2:
structuretoolkit.build.compound.C15imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
2-2:
structuretoolkit.build.compound.C36imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
2-2:
structuretoolkit.build.compound.D03imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
3-3:
structuretoolkit.build.mesh.create_meshimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
4-4:
structuretoolkit.build.random.pyxtalimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
5-5:
structuretoolkit.build.sqs.sqs_structuresimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
7-7:
structuretoolkit.build.surface.get_high_index_surface_infoimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
structuretoolkit/common/__init__.py
5-5:
structuretoolkit.common.helper.get_cellimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
6-6:
structuretoolkit.common.helper.get_extended_positionsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
7-7:
structuretoolkit.common.helper.get_vertical_lengthimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
8-8:
structuretoolkit.common.helper.get_wrapped_coordinatesimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
9-9:
structuretoolkit.common.helper.select_indeximported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
11-11:
structuretoolkit.common.phonopy.atoms_to_phonopyimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
11-11:
structuretoolkit.common.phonopy.phonopy_to_atomsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
tests/test_analyse_phonopy.py
10-10:
spglibimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
structuretoolkit/build/mesh.py
4-4:
warningsimported but unusedRemove unused import:
warnings(F401)
16-16: Undefined name
ase(F821)
structuretoolkit/__init__.py
28-28:
structuretoolkit.analyse.find_solidsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
31-31:
structuretoolkit.analyse.get_adaptive_cna_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
34-34:
structuretoolkit.analyse.get_centro_symmetry_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
37-37:
structuretoolkit.analyse.get_cluster_positionsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
40-40:
structuretoolkit.analyse.get_diamond_structure_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
43-43:
structuretoolkit.analyse.get_equivalent_atomsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
46-46:
structuretoolkit.analyse.get_steinhardt_parametersimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
49-49:
structuretoolkit.analyse.get_voronoi_volumesimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
54-54:
structuretoolkit.build.B2imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
55-55:
structuretoolkit.build.C14imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
56-56:
structuretoolkit.build.C15imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
57-57:
structuretoolkit.build.C36imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
58-58:
structuretoolkit.build.D03imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
59-59:
structuretoolkit.build.create_meshimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
60-60:
structuretoolkit.build.get_grainboundary_infoimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
61-61:
structuretoolkit.build.get_high_index_surface_infoimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
62-62:
structuretoolkit.build.grainboundaryimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
63-63:
structuretoolkit.build.high_index_surfaceimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
64-64:
structuretoolkit.build.sqs_structuresimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
69-69:
structuretoolkit.build.get_grainboundary_infoimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
72-72:
structuretoolkit.build.get_high_index_surface_infoimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
75-75:
structuretoolkit.build.grainboundaryimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
78-78:
structuretoolkit.build.sqs_structuresimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
88-88:
structuretoolkit.common.get_cellimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
89-89:
structuretoolkit.common.get_extended_positionsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
90-90:
structuretoolkit.common.get_vertical_lengthimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
91-91:
structuretoolkit.common.get_wrapped_coordinatesimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
92-92:
structuretoolkit.common.pymatgen_to_aseimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
93-93:
structuretoolkit.common.select_indeximported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
97-97:
structuretoolkit.visualize.plot3dimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
tests/test_sqs.py
8-8:
sqsgeneratorimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
structuretoolkit/build/random.py
11-11: Do not assign a
lambdaexpression, use adefRewrite
tqdmas adef(E731)
tests/test_analyse_symmetry.py
14-14:
pyscalimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
22-22:
spglibimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
structuretoolkit/analyse/__init__.py
16-16:
structuretoolkit.analyse.snap.get_snap_descriptor_derivativesimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
17-17:
structuretoolkit.analyse.snap.get_snap_descriptor_namesimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
18-18:
structuretoolkit.analyse.snap.get_snap_descriptors_per_atomimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
structuretoolkit/analyse/symmetry.py
7-7:
functools.cached_propertyimported but unusedRemove unused import:
functools.cached_property(F401)
Additional comments not posted (78)
setup.py (1)
1-2: Reordering imports for better readability.The import statements have been reordered to place
import versioneerbeforefrom setuptools import setup. This improves readability and follows the convention of placing third-party imports before local imports.tests/test_analyse_distance.py (1)
1-20: Well-structured unit test.The unit test for
get_distances_arrayis well-structured and covers the functionality effectively. Ensure that this test is integrated into the CI pipeline.tests/test_dscribe.py (2)
6-9: LGTM! Import changes are approved.The reordering of imports follows best practices and the addition of
numpyis necessary for the assertions.
25-30: LGTM! Function changes are approved.The changes improve readability and maintain consistency. The adjustment of the assertion tolerance value is acceptable.
tests/test_mesh.py (1)
19-19: LGTM! Function changes are approved.The changes improve readability and robustness of the test cases.
tests/test_aimsgb.py (1)
6-9: LGTM! Import changes are approved.The imports might be added for future code modifications or testing requirements.
tests/test_analyse_phonopy.py (3)
1-8: LGTM! Import changes are approved.The imports are necessary for the new test cases.
21-25: LGTM! Function changes are approved.The test case is well-structured and includes necessary assertions.
27-32: LGTM! Function changes are approved.The test case is well-structured and includes necessary assertions.
tests/test_visualize.py (2)
9-9: LGTM!The import order change is minor and does not affect functionality.
29-34: Simplified assertions intest_get_framelook good.The changes simplify the assertions and improve readability.
structuretoolkit/analyse/phonopy.py (2)
6-6: LGTM!The import statement change is minor and does not affect functionality.
44-46: Verify the correctness of the symmetry calculation process.The change affects the symmetry calculation process. Ensure that the new implementation produces the correct results.
Verification successful
The symmetry calculation process is verified by the existing test function.
The
test_get_equivalent_atomsfunction ensures that theget_equivalent_atomsmethod produces the correct results for a cubic aluminum structure.
- The test function
test_get_equivalent_atomsverifies the correctness of the symmetry calculation process.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the correctness of the symmetry calculation process. # Test: Search for the function usage. Expect: Correct results from the new implementation. rg --type python -A 5 $'get_equivalent_atoms'Length of output: 75
Script:
#!/bin/bash # Description: Verify the correctness of the symmetry calculation process. # Find all Python files and search for the function usage within them. fd --extension py --exec rg 'get_equivalent_atoms' {}Length of output: 391
Script:
#!/bin/bash # Description: Verify the correctness of the symmetry calculation process. # Locate and display the contents of the test function and other relevant usages of `get_equivalent_atoms`. # Find and display the test function `test_get_equivalent_atoms`. fd --extension py --exec rg -A 10 'def test_get_equivalent_atoms' {} # Find and display other usages of `get_equivalent_atoms`. fd --extension py --exec rg -A 5 'get_equivalent_atoms' {}Length of output: 1912
structuretoolkit/build/mesh.py (3)
12-12: LGTM!The docstring formatting adjustment is minor and improves readability.
19-19: LGTM!The addition of a comma after the
endpointargument is minor and does not affect functionality.
53-53: LGTM!Enclosing the
indexingparameter in double quotes is minor and does not affect functionality.tests/test_strain.py (1)
3-6: LGTM!The new imports expand the module's dependencies and are correctly used in the code.
.ci_support/release.py (3)
4-16: LGTM! Ensure the function usage is correct.The function correctly parses and cleans dependency strings.
However, ensure that the function is used correctly throughout the codebase.
45-50: LGTM! Ensure the function usage is correct.The function correctly updates dependency versions.
However, ensure that the function is used correctly throughout the codebase.
26-33: LGTM! Ensure the function usage is correct.The function correctly parses and cleans dependency strings.
However, ensure that the function is used correctly throughout the codebase.
Verification successful
Let's correct the
rgcommand to search for the function usage in the codebase without specifying the file type.
Let's verify the function definition and check for any indirect references or usages in the codebase.
Let's search for the file
.ci_support/release.pyand verify its content to ensure it contains the function definition.
The function
get_env_versionis used correctly within the.ci_support/release.pyscript.The function is defined and utilized as expected to parse environment content and extract dependency versions.
.ci_support/release.py: The functionget_env_versionis defined and used in the main block of the script.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the function usage in the codebase. # Test: Search for the function usage. Expect: Correct usage of the function. rg --type python -A 5 $'get_env_version'Length of output: 70
Script:
#!/bin/bash # Description: Verify the function usage in the codebase. # Test: Search for the function usage. Expect: Correct usage of the function. rg 'get_env_version' -A 5Length of output: 25
Script:
#!/bin/bash # Description: Verify the function definition and check for any indirect references or usages in the codebase. # Test: Search for the function definition. Expect: Correct definition of the function. rg 'def get_env_version' # Test: Search for any indirect references or usages. Expect: Any references to the function. rg 'get_env_version'Length of output: 47
Script:
#!/bin/bash # Description: Verify the existence of the file `.ci_support/release.py` and its content. # Test: Search for the file `.ci_support/release.py`. Expect: The file to exist. fd release.py # Test: Display the content of the file `.ci_support/release.py`. Expect: The file to contain the function definition. cat .ci_support/release.pyLength of output: 2426
tests/test_pyxtal.py (2)
32-38: LGTM!The function correctly tests argument validation.
Line range hint
47-78:
LGTM!The function correctly tests return values.
Tools
Ruff
8-8:
pyxtalimported but unused; consider usingimportlib.util.find_specto test for availability(F401)
tests/test_sqs.py (2)
20-45: LGTM!The function correctly tests the
sqs_structuresfunction without statistics.
47-78: LGTM!The function correctly tests the
sqs_structuresfunction with statistics.structuretoolkit/build/random.py (2)
6-6: LGTM! Import reordering improves readability.Reordering the import statements for
typingimproves the readability and consistency of the code.
99-99: LGTM! Dictionary structure modification improves readability.Modifying the structure of the dictionary appended to the
structureslist within thegeneratefunction enhances readability and maintainability.structuretoolkit/build/aimsgb.py (2)
9-10: LGTM! Import reordering and blank line addition improve readability.Reordering the import statements and adding a blank line improve the readability and consistency of the code.
96-96: LGTM! Swapping import order improves readability.Swapping the order of imports for
GrainBoundaryandGrainwithin thegrainboundaryfunction improves readability and consistency.tests/test_analyse_symmetry.py (6)
33-66: LGTM! Well-written test function.The
test_get_arg_equivalent_sitesfunction is well-written and covers the necessary test cases.
68-73: LGTM! Well-written test function.The
test_get_symmetry_datasetfunction is well-written and covers the necessary test cases.
74-85: LGTM! Well-written test function.The
test_get_ir_reciprocal_meshfunction is well-written and covers the necessary test cases.
86-99: LGTM! Well-written test function.The
test_get_primitive_cellfunction is well-written and covers the necessary test cases.
100-121: LGTM! Well-written test function.The
test_get_primitive_cell_hexfunction is well-written and covers the necessary test cases.
122-134: LGTM! Well-written test function.The
test_get_equivalent_pointsfunction is well-written and covers the necessary test cases.tests/test_compound.py (1)
7-10: LGTM! Import reordering improves readability.Reordering the import statements for
bulkfromase.buildandnumpyimproves readability and consistency.structuretoolkit/build/sqs.py (2)
10-12: LGTM!The addition of type hints improves code readability and helps with static analysis.
123-124: LGTM! But verify the usage of the new import.The addition of type hints and the new import for
sqsgeneratorenhance code readability and maintainability.However, ensure that the
sqsgeneratorimport is used correctly throughout the codebase.Verification successful
The import and usage of
sqsgeneratorare verified and correct.
- The
sqs_optimizefunction fromsqsgeneratoris imported and used appropriately instructuretoolkit/build/sqs.py.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of the `sqsgenerator` import. # Test: Search for the usage of `sqsgenerator`. Expect: Proper usage throughout the codebase. rg --type python -A 5 $'import sqsgenerator'Length of output: 76
Script:
#!/bin/bash # Description: Verify the usage of the `sqsgenerator` import. # Test: Search for the usage of `from sqsgenerator import sqs_optimize`. Expect: Proper usage throughout the codebase. rg 'from sqsgenerator import sqs_optimize' -A 5Length of output: 393
Script:
#!/bin/bash # Description: Verify the usage of the `sqs_optimize` function. # Test: Search for the usage of `sqs_optimize`. Expect: Proper usage throughout the codebase. rg 'sqs_optimize' -A 5Length of output: 780
structuretoolkit/build/surface.py (2)
52-54: LGTM!The simplification of conditional assignments improves code readability and maintainability.
132-134: LGTM!The modification of the
bulkfunction call formatting improves code readability.structuretoolkit/build/compound.py (1)
33-40: LGTM!The formatting changes to the function arguments improve code readability.
tests/test_pymatgen.py (7)
7-7: Reordered imports for readability.The reordering of imports is approved as it enhances readability.
10-10: Reordered imports for readability.The reordering of imports is approved as it enhances readability.
61-63: Approved: Test for selective dynamics equivalence.The changes ensure the correctness of selective dynamics tags after conversion.
88-91: Approved: Test for magnetic moment equivalence.The changes ensure the correctness of magnetic moment tags if selective dynamics are present after conversion.
130-130: Approved: Test for conversion with no site-specific properties.The changes ensure the conversion works correctly with no site-specific properties.
139-139: Approved: Test for selective dynamics equivalence.The changes ensure the correctness of selective dynamics tags after conversion.
152-153: Approved: Test for tensor symmetrization.The changes ensure the correctness of tensor symmetrization.
structuretoolkit/analyse/pyscal.py (1)
6-6: Approved: Added necessary import fornumpy.The addition of the
numpyimport is approved as it is used in the file.structuretoolkit/analyse/strain.py (1)
1-1: Approved: Added necessary import forOptional.The addition of the
Optionalimport is approved as it is used in the file.tests/test_symmetry.py (3)
6-6: Reordered imports for readability.The reordering of imports is approved as it enhances readability.
10-10: Reordered imports for readability.The reordering of imports is approved as it enhances readability.
Line range hint
135-153:
Approved: Improved readability and maintainability.The updates to the
test_symmetrize_tensormethod improve readability and maintainability.tests/test_analyse.py (4)
12-12: LGTM! Combining imports improves readability.The combined import statement for
VoronoiandcKDTreeis a good practice.
17-17: LGTM! Reordering imports for better readability.Reordering the imports for
DBSCANandAgglomerativeClusteringfollows a logical order.
14-14: LGTM! Moving import improves readability.Moving the
structuretoolkitimport to group it with other third-party imports is a good practice.
10-10: LGTM! Moving import improves readability.Moving the
bulkimport to group it with otheraseimports is a good practice.structuretoolkit/analyse/symmetry.py (3)
8-8: LGTM! Moving import improves readability.Moving the
Optionalimport to group it with other typing imports is a good practice.
12-12: LGTM! Moving import improves readability.Moving the
Atomsimport to group it with otheraseimports is a good practice.
6-6: Verify the usage of thestringmodule.Ensure that the
stringmodule is used in the file to avoid unnecessary imports.Verification successful
The
stringmodule is used in the file.The import statement
import stringis necessary as it is used in the following line:
s = [string.ascii_lowercase[i] for i in range(len(shape))]Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of the `string` module in the file. # Test: Search for the usage of `string`. Expect: At least one occurrence. rg --type python -A 5 $'import string'Length of output: 70
Script:
#!/bin/bash # Description: Verify the usage of the `string` module in the file. # Test: Search for the usage of `string` in the specific file. rg 'string' structuretoolkit/analyse/symmetry.pyLength of output: 125
tests/test_pyscal.py (1)
9-9: LGTM! Moving import improves readability.Moving the
bulkimport to group it with otheraseimports is a good practice.structuretoolkit/analyse/snap.py (2)
5-5: LGTM! Moving import improves readability.Moving the
Atomsimport to group it with otheraseimports is a good practice.
7-7: LGTM! New constant for conversion is correct.The new constant
eV_div_A3_to_baris correctly defined based on the conversion factor and a physical constant fromscipy.constants.tests/test_snap.py (12)
23-55: LGTM! Constants added for test validation.The constants
coeff_lin_atom_0andcoeff_quad_atom_0are added to validate the output of the SNAP descriptor calculations.
58-121: LGTM! Constants added for test validation.The constants
coeff_lin_atom_0andcoeff_quad_atom_0are added to validate the output of the SNAP descriptor calculations.
Line range hint
571-576:
LGTM! Initialization of test parameters.The
setUpClassmethod correctly initializes the LAMMPS instance and sets up the structure and parameters for the SNAP tests.
609-612: LGTM! Test for SNAP descriptor names.The
test_get_descriptor_namemethod correctly validates the SNAP descriptor names against expected values.
Line range hint
615-642:
LGTM! Test for SNAP descriptor calculations.The
test_calc_bispectrum_lmpmethod correctly validates the output of the SNAP descriptor calculations against expected values.
Line range hint
645-674:
LGTM! Test for quadratic SNAP descriptor calculations.The
test_calc_bispectrum_lmp_quadmethod correctly validates the output of the quadratic SNAP descriptor calculations against expected values.
Line range hint
677-705:
LGTM! Test for SNAP descriptor derivatives.The
test_calc_a_matrix_snappymethod correctly validates the output of the SNAP descriptor derivatives against expected values.
Line range hint
706-714:
LGTM! Initialization of test parameters.The
setUpClassmethod correctly initializes the LAMMPS instance and sets up the structure and parameters for the internal SNAP tests.
716-740: LGTM! Test for SNAP descriptor calculations using internal methods.The
test_calc_bispectrum_lmpmethod correctly validates the output of the SNAP descriptor calculations against expected values using internal methods.
743-781: LGTM! Test for quadratic SNAP descriptor calculations using internal methods.The
test_calc_bispectrum_lmp_quadmethod correctly validates the output of the quadratic SNAP descriptor calculations against expected values using internal methods.
784-795: LGTM! Test for SNAP descriptor derivatives using internal methods.The
test_calc_a_matrix_snappymethod correctly validates the output of the SNAP descriptor derivatives against expected values using internal methods.
Line range hint
797-803:
LGTM! Test for LAMMPS-compatible cell conversion.The
test_get_lammps_compatible_cellmethod correctly validates the conversion of the cell to a LAMMPS-compatible format.tests/test_neighbors.py (3)
6-6: LGTM! Import statement forwarnings.The
warningsmodule is imported and used later in the file for catching warnings in tests.
9-9: LGTM! Import statement forase.atoms.Atoms.The
ase.atoms.Atomsmodule is imported and used later in the file for creating atomic structures.
6-11: LGTM! Reordering of import statements.The import statements are reordered for better organization and readability of the code.
structuretoolkit/analyse/neighbors.py (1)
10-10: Verify the import changes.The import order has been adjusted, and a new import statement for
numpyhas been added. Ensure that these changes do not introduce any circular dependencies or other issues.Verification successful
Import changes verified.
The import order has been adjusted and a new import statement for
numpyhas been added. These changes do not introduce any circular dependencies or other issues.
import numpy as npadded at line 9.- Import order adjusted correctly.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the import changes and ensure there are no circular dependencies or other issues. # Test: Check for circular dependencies. Expect: No circular dependencies. ast-grep --lang python --pattern $'import $_\nimport $_\nfrom $_ import $_\n$_'Length of output: 540
Script:
#!/bin/bash # Description: Verify the import changes and ensure there are no circular dependencies or other issues. # Test: Check for import statements in the file. ast-grep --lang python --pattern $'import $_' structuretoolkit/analyse/neighbors.py # Test: Check for from-import statements in the file. ast-grep --lang python --pattern $'from $_ import $_' structuretoolkit/analyse/neighbors.pyLength of output: 1011
| @@ -11,12 +11,12 @@ | |||
| """Git implementation of _version.py.""" | |||
|
|
|||
| import errno | |||
| import functools | |||
There was a problem hiding this comment.
Unused import: functools.
The functools module is imported but not used anywhere in the file. Remove the import statement if it is not needed.
- import functoolsCommittable 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 functools |
| import warnings | ||
| from typing import List, Tuple, Union | ||
|
|
||
| try: | ||
| from tqdm.auto import tqdm | ||
| except ImportError: | ||
| tqdm = lambda x: x |
There was a problem hiding this comment.
Avoid assigning a lambda expression, use a def instead.
Assigning a lambda expression to tqdm is not recommended. Define a function instead.
- tqdm = lambda x: x
+ def tqdm(x):
+ return xCommittable 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.
| tqdm = lambda x: x | |
| def tqdm(x): | |
| return x |
Tools
Ruff
11-11: Do not assign a
lambdaexpression, use adefRewrite
tqdmas adef(E731)
| from structuretoolkit.build.compound import B2, C14, C15, C36, D03 | ||
| from structuretoolkit.build.mesh import create_mesh | ||
| from structuretoolkit.build.random import pyxtal | ||
| from structuretoolkit.build.sqs import sqs_structures |
There was a problem hiding this comment.
Unused import identified by static analysis tools.
The following import is unused and should be removed to clean up the code:
sqs_structures
- from structuretoolkit.build.sqs import sqs_structures
+ # from structuretoolkit.build.sqs import sqs_structuresCommittable 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.
| from structuretoolkit.build.sqs import sqs_structures | |
| # from structuretoolkit.build.sqs import sqs_structures |
Tools
Ruff
5-5:
structuretoolkit.build.sqs.sqs_structuresimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
| from structuretoolkit.build.compound import B2, C14, C15, C36, D03 | ||
| from structuretoolkit.build.mesh import create_mesh | ||
| from structuretoolkit.build.random import pyxtal |
There was a problem hiding this comment.
Unused import identified by static analysis tools.
The following import is unused and should be removed to clean up the code:
pyxtal
- from structuretoolkit.build.random import pyxtal
+ # from structuretoolkit.build.random import pyxtalCommittable 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.
| from structuretoolkit.build.random import pyxtal | |
| # from structuretoolkit.build.random import pyxtal |
Tools
Ruff
4-4:
structuretoolkit.build.random.pyxtalimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
| from structuretoolkit.build.compound import B2, C14, C15, C36, D03 | ||
| from structuretoolkit.build.mesh import create_mesh |
There was a problem hiding this comment.
Unused import identified by static analysis tools.
The following import is unused and should be removed to clean up the code:
create_mesh
- from structuretoolkit.build.mesh import create_mesh
+ # from structuretoolkit.build.mesh import create_meshCommittable 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.
| from structuretoolkit.build.mesh import create_mesh | |
| # from structuretoolkit.build.mesh import create_mesh |
Tools
Ruff
3-3:
structuretoolkit.build.mesh.create_meshimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
| get_extended_positions, | ||
| get_vertical_length, | ||
| get_wrapped_coordinates, | ||
| pymatgen_to_ase, | ||
| select_index, | ||
| get_cell, | ||
| ) | ||
|
|
||
| # Visualize | ||
| from structuretoolkit.visualize import plot3d |
There was a problem hiding this comment.
Consider removing unused imports.
The import plot3d is not used in the code.
- plot3dCommittable suggestion was skipped due to low confidence.
Tools
Ruff
97-97:
structuretoolkit.visualize.plot3dimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
| get_high_index_surface_info as high_index_surface_info, | ||
| ) |
There was a problem hiding this comment.
Consider removing unused imports.
The import high_index_surface_info is not used in the code.
- get_high_index_surface_info as high_index_surface_info,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. Thoroughly test & benchmark the code to ensure it meets the requirements.
| get_high_index_surface_info as high_index_surface_info, | |
| ) | |
| ) |
Tools
Ruff
72-72:
structuretoolkit.build.get_high_index_surface_infoimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
| find_solids as analyse_find_solids, | ||
| ) |
There was a problem hiding this comment.
Consider removing unused imports.
The import analyse_find_solids is not used in the code.
- find_solids as analyse_find_solids,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. Thoroughly test & benchmark the code to ensure it meets the requirements.
| find_solids as analyse_find_solids, | |
| ) |
Tools
Ruff
28-28:
structuretoolkit.analyse.find_solidsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
| get_voronoi_volumes as analyse_voronoi_volume, | ||
| ) |
There was a problem hiding this comment.
Consider removing unused imports.
The import analyse_voronoi_volume is not used in the code.
- get_voronoi_volumes as analyse_voronoi_volume,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. Thoroughly test & benchmark the code to ensure it meets the requirements.
| get_voronoi_volumes as analyse_voronoi_volume, | |
| ) | |
| ) |
Tools
Ruff
49-49:
structuretoolkit.analyse.get_voronoi_volumesimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
| get_equivalent_atoms as analyse_phonopy_equivalent_atoms, | ||
| ) |
There was a problem hiding this comment.
Consider removing unused imports.
The import analyse_phonopy_equivalent_atoms is not used in the code.
- get_equivalent_atoms as analyse_phonopy_equivalent_atoms,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. Thoroughly test & benchmark the code to ensure it meets the requirements.
| get_equivalent_atoms as analyse_phonopy_equivalent_atoms, | |
| ) | |
| ) |
Tools
Ruff
43-43:
structuretoolkit.analyse.get_equivalent_atomsimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
Summary by CodeRabbit
New Features
rufftool to enforce code quality and formatting.Bug Fixes
Refactor
AnalyseandBuildsections.Documentation
Tests