add ruff formatter #266
add ruff formatter #266
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Warning Rate Limit Exceeded@jan-janssen has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 19 minutes and 27 seconds before requesting another review. How to resolve this issue?After the wait time has elapsed, a review can be triggered using the We recommend that you space out your commits to avoid hitting the rate limit. How do rate limits work?CodeRabbit enforces hourly rate limits for each developer per organization. WalkthroughThe recent updates encompass a broad range of changes, including refactoring variable names for clarity, enhancing code readability, and updating string manipulations. Additionally, new configurations for pre-commit hooks have been added, and several functions and methods have been merged into the Changes
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Actionable comments posted: 24
Out of diff range and nitpick comments (6)
tests/test_elastic_ase_emt.py (1)
Line range hint
4-4: Remove unused importnumpy.- import numpy as nptests/test_phonons_ase_emt.py (1)
19-19: Ensure thefmaxvalue is appropriate for your test case.The
fmaxvalue is set to a very small number (0.000001). Verify if this precision is necessary for your test case, as it might increase the computation time.tests/test_evcurve_ase_emt.py (1)
22-22: Ensure thefmaxvalue is appropriate for your test case.The
fmaxvalue is set to a very small number (0.000001). Verify if this precision is necessary for your test case, as it might increase the computation time.tests/test_langevin_lammps.py (1)
Line range hint
47-47: Typo indiable_log_file.- diable_log_file=True, + disable_log_file=True,tests/test_evcurve_eos.py (1)
Line range hint
1-1: Remove unused importnumpy.-import numpy as nptests/test_quasiharmonic_lammps_functional.py (1)
Line range hint
4-4: Remove unused importnumpy.- import numpy as np
Review Details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (55)
- .ci_support/release.py (3 hunks)
- .pre-commit-config.yaml (1 hunks)
- atomistics/calculators/init.py (1 hunks)
- atomistics/calculators/interface.py (1 hunks)
- atomistics/calculators/lammps/init.py (1 hunks)
- atomistics/calculators/lammps/helpers.py (2 hunks)
- atomistics/calculators/lammps/potential.py (1 hunks)
- atomistics/calculators/wrapper.py (1 hunks)
- atomistics/workflows/init.py (1 hunks)
- atomistics/workflows/evcurve/fit.py (2 hunks)
- atomistics/workflows/evcurve/thermo.py (1 hunks)
- atomistics/workflows/evcurve/workflow.py (1 hunks)
- atomistics/workflows/phonons/units.py (1 hunks)
- setup.py (1 hunks)
- tests/test_ase_interface/test_ase_md_mace.py (2 hunks)
- tests/test_ase_interface/test_ase_md_matgl.py (1 hunks)
- tests/test_ase_interface/test_elastic_ase_gpaw.py (1 hunks)
- tests/test_ase_interface/test_evcurve_ase_abinit.py (2 hunks)
- tests/test_ase_interface/test_evcurve_ase_gpaw.py (1 hunks)
- tests/test_ase_interface/test_evcurve_ase_mace.py (3 hunks)
- tests/test_ase_interface/test_evcurve_ase_matgl.py (3 hunks)
- tests/test_ase_interface/test_evcurve_ase_qe.py (2 hunks)
- tests/test_ase_interface/test_evcurve_ase_siesta.py (3 hunks)
- tests/test_ase_interface/test_phonons_ase_gpaw.py (1 hunks)
- tests/test_ase_interface/test_phonons_ase_mace.py (2 hunks)
- tests/test_ase_interface/test_phonons_ase_matgl.py (2 hunks)
- tests/test_ase_interface/test_quasiharmonic_ase_mace.py (2 hunks)
- tests/test_ase_interface/test_quasiharmonic_ase_matgl.py (2 hunks)
- tests/test_ase_md_emt.py (3 hunks)
- tests/test_calc_stress_ase_emt.py (1 hunks)
- tests/test_calc_stress_lammps.py (3 hunks)
- tests/test_elastic_ase_emt.py (1 hunks)
- tests/test_elastic_helper.py (1 hunks)
- tests/test_elastic_lammps.py (3 hunks)
- tests/test_elastic_lammps_functional.py (3 hunks)
- tests/test_evcurve_ase_emt.py (2 hunks)
- tests/test_evcurve_ase_lammps.py (4 hunks)
- tests/test_evcurve_eos.py (2 hunks)
- tests/test_evcurve_lammps.py (4 hunks)
- tests/test_evcurve_lammps_functional.py (5 hunks)
- tests/test_evcurve_qe.py (1 hunks)
- tests/test_hessian_lammps.py (2 hunks)
- tests/test_lammps_calculator.py (2 hunks)
- tests/test_lammps_md.py (8 hunks)
- tests/test_lammps_md_phonons.py (3 hunks)
- tests/test_langevin_lammps.py (2 hunks)
- tests/test_molecular_dynamics_thermal_expansion_lammps.py (4 hunks)
- tests/test_optimize_positions_ase_emt.py (1 hunks)
- tests/test_optimize_positions_lammps.py (3 hunks)
- tests/test_phonons_ase_emt.py (2 hunks)
- tests/test_phonons_lammps.py (5 hunks)
- tests/test_phonons_lammps_functional.py (5 hunks)
- tests/test_quasiharmonic_ase_emt.py (2 hunks)
- tests/test_quasiharmonic_lammps.py (4 hunks)
- tests/test_quasiharmonic_lammps_functional.py (5 hunks)
Files skipped from review due to trivial changes (18)
- .pre-commit-config.yaml
- atomistics/calculators/interface.py
- atomistics/calculators/lammps/init.py
- atomistics/calculators/lammps/helpers.py
- atomistics/workflows/evcurve/workflow.py
- atomistics/workflows/phonons/units.py
- setup.py
- tests/test_ase_interface/test_ase_md_mace.py
- tests/test_ase_interface/test_ase_md_matgl.py
- tests/test_ase_interface/test_evcurve_ase_abinit.py
- tests/test_ase_interface/test_evcurve_ase_mace.py
- tests/test_ase_interface/test_phonons_ase_mace.py
- tests/test_ase_interface/test_phonons_ase_matgl.py
- tests/test_evcurve_qe.py
- tests/test_lammps_calculator.py
- tests/test_optimize_positions_lammps.py
- tests/test_phonons_lammps.py
- tests/test_phonons_lammps_functional.py
Additional Context Used
Ruff (13)
.ci_support/release.py (4)
3-3: Ambiguous variable name:
l
25-25: Ambiguous variable name:
l
46-46: Ambiguous variable name:
l
49-49: Ambiguous variable name:
ltests/test_elastic_ase_emt.py (1)
4-4:
numpyimported but unusedtests/test_evcurve_ase_emt.py (1)
4-4:
numpyimported but unusedtests/test_evcurve_ase_lammps.py (2)
4-4:
numpyimported but unused
15-15:
lammps.lammpsimported but unused; consider usingimportlib.util.find_specto test for availabilitytests/test_evcurve_eos.py (1)
1-1:
numpyimported but unusedtests/test_evcurve_lammps.py (1)
4-4:
numpyimported but unusedtests/test_hessian_lammps.py (2)
16-16:
pylammpsmpi.LammpsASELibraryimported but unused; consider usingimportlib.util.find_specto test for availability
19-19:
atomistics.calculators.evaluate_with_lammps_libraryimported but unused; consider usingimportlib.util.find_specto test for availabilitytests/test_quasiharmonic_lammps_functional.py (1)
4-4:
numpyimported but unused
Additional comments not posted (83)
atomistics/workflows/__init__.py (1)
19-28: Ensure all entities in the__all__list are correctly imported and used within the module.Verification successful
All entities in the
__all__list are correctly imported and used within the module.
ElasticMatrixWorkflowEnergyVolumeCurveWorkflowLangevinWorkflowcalc_molecular_dynamics_thermal_expansionoptimize_positionsoptimize_positions_and_volumePhonopyWorkflowQuasiHarmonicWorkflowScripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all entities in the `__all__` list are correctly imported and used within the module. # Test: Search for the entities in the module. Expect: All entities should be imported and used. rg --type python $'ElasticMatrixWorkflow|EnergyVolumeCurveWorkflow|LangevinWorkflow|calc_molecular_dynamics_thermal_expansion|optimize_positions|optimize_positions_and_volume|PhonopyWorkflow|QuasiHarmonicWorkflow'Length of output: 245
Script:
#!/bin/bash # Description: Verify all entities in the `__all__` list are correctly imported and used within the module. # Test: Search for the entities in the module. Expect: All entities should be imported and used. rg 'ElasticMatrixWorkflow|EnergyVolumeCurveWorkflow|LangevinWorkflow|calc_molecular_dynamics_thermal_expansion|optimize_positions|optimize_positions_and_volume|PhonopyWorkflow|QuasiHarmonicWorkflow' --glob '*.py'Length of output: 15859
tests/test_optimize_positions_ase_emt.py (1)
21-21: Ensure thefmaxvalue is appropriate for the optimization.tests/test_calc_stress_ase_emt.py (1)
23-23: Ensure thefmaxvalue is appropriate for the optimization.Verification successful
Several files in the codebase use different
fmaxvalues for optimization. Thefmaxvalue of0.000001used intests/test_calc_stress_ase_emt.pyis consistent with other test files using the same value.
tests/test_quasiharmonic_ase_emt.pytests/test_phonons_ase_emt.pytests/test_optimize_positions_ase_emt.pytests/test_evcurve_ase_lammps.pytests/test_evcurve_ase_emt.pytests/test_elastic_ase_emt.pyThis suggests that the
fmaxvalue is appropriate for the context in which it is used.Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the `fmax` value used in the optimization. # Test: Search for the `fmax` value in the test cases. Expect: The `fmax` value should be appropriate for the optimization. rg --type python $'fmax'Length of output: 54
Script:
#!/bin/bash # Description: Verify the `fmax` value used in the optimization. # Test: Search for the `fmax` value in the test cases. Expect: The `fmax` value should be appropriate for the optimization. rg --type py 'fmax'Length of output: 1239
tests/test_ase_interface/test_elastic_ase_gpaw.py (2)
26-26: Ensure thefit_ordervalue is appropriate for the elastic calculations.Verification successful
The
fit_ordervalue of 2 is consistently used in elastic-related test cases, includingtest_elastic_ase_gpaw.py, indicating it is appropriate for the elastic calculations.
tests/test_elastic_lammps_functional.py:fit_order=2tests/test_elastic_lammps.py:fit_order=2tests/test_elastic_ase_emt.py:fit_order=2tests/test_ase_interface/test_elastic_ase_gpaw.py:fit_order=2Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the `fit_order` value used in the elastic calculations. # Test: Search for the `fit_order` value in the test cases. Expect: The `fit_order` value should be appropriate for the elastic calculations. rg --type python $'fit_order'Length of output: 59
Script:
#!/bin/bash # Description: Verify the `fit_order` value used in the elastic calculations. # Test: Search for the `fit_order` value in the test cases. Expect: The `fit_order` value should be appropriate for the elastic calculations. rg --type py 'fit_order'Length of output: 5199
31-31: Ensure the GPAW calculator settings are appropriate for the elastic calculations.Verification successful
The GPAW calculator settings used in the elastic calculations appear to be appropriate. The settings
xc="PBE",mode=PW(300), andkpts=(3, 3, 3)are standard choices for DFT calculations and should be suitable for the intended purpose.
tests/test_ase_interface/test_elastic_ase_gpaw.pytests/test_ase_interface/test_phonons_ase_gpaw.pytests/test_ase_interface/test_evcurve_ase_gpaw.pyScripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the GPAW calculator settings used in the elastic calculations. # Test: Search for the GPAW calculator settings in the test cases. Expect: The GPAW calculator settings should be appropriate for the elastic calculations. rg --type python $'GPAW'Length of output: 54
Script:
#!/bin/bash # Description: Verify the GPAW calculator settings used in the elastic calculations. # Test: Search for the GPAW calculator settings in the test cases. Expect: The GPAW calculator settings should be appropriate for the elastic calculations. rg --type py GPAWLength of output: 628
tests/test_elastic_ase_emt.py (2)
19-19: Improved readability by breaking the arguments into multiple lines.
26-26: Improved readability and consistency by adding a trailing comma.tests/test_calc_stress_lammps.py (3)
24-24: Standardized string literal format to use double quotes.
37-39: Improved readability and consistency by adding a trailing comma.
38-39: Improved readability and consistency by adding a trailing comma.tests/test_ase_interface/test_phonons_ase_gpaw.py (1)
33-33: Improved readability and consistency by adding a trailing comma.tests/test_ase_interface/test_evcurve_ase_qe.py (3)
20-25: Improved readability and consistency by adding a trailing comma.
33-34: Improved readability and consistency by adding a trailing comma.
42-45: Improved readability and consistency by adding a trailing comma.tests/test_phonons_ase_emt.py (1)
35-41: Good use of assertions to validate the keys in the dictionaries.These assertions ensure that the expected keys are present in the
mesh_dictanddos_dict.tests/test_ase_interface/test_evcurve_ase_gpaw.py (4)
25-28: Ensure the new arguments are correctly integrated.Verify that the new arguments
fit_type,fit_order,vol_range, andaxesare correctly handled within theEnergyVolumeCurveWorkflowclass.
34-34: Ensure the GPAW calculator is correctly configured.Verify that the
GPAWcalculator is correctly configured with the provided parameters (xc="PBE",mode=PW(300),kpts=(3, 3, 3)).
38-43: Good use of assertions to validate the thermal properties.These assertions ensure that the
temperaturesandvolumeskeys are present and have the expected lengths.
44-51: Good use ofnp.isclosefor floating-point comparisons.These assertions ensure that the calculated values are close to the expected values within a specified tolerance.
tests/test_evcurve_ase_emt.py (3)
27-30: Ensure the new arguments are correctly integrated.Verify that the new arguments
fit_type,fit_order,vol_range, andaxesare correctly handled within theEnergyVolumeCurveWorkflowclass.
37-42: Good use of assertions to validate the thermal properties.These assertions ensure that the
temperaturesandvolumeskeys are present and have the expected lengths.
43-45: Good use ofassertAlmostEqualfor floating-point comparisons.These assertions ensure that the calculated values are close to the expected values.
tests/test_langevin_lammps.py (2)
12-14: Ensure the imported functions are used correctly.Verify that the imported functions
evaluate_with_lammps_library,get_potential_by_name, andLammpsASELibraryare used correctly within the test method.
30-30: Ensure the potential name and resource path are correct.Verify that the potential name
"1999--Mishin-Y--Al--LAMMPS--ipr1"and the resource path are correct and accessible.tests/test_ase_interface/test_evcurve_ase_siesta.py (2)
22-29: Consistent use of double quotes for dictionary keys improves readability.
44-47: Consistent use of double quotes for string literals improves readability.tests/test_evcurve_lammps.py (2)
7-10: Consistent use of double quotes for dictionary keys improves readability.
Line range hint
27-41: Consistent use of double quotes for string literals improves readability.tests/test_lammps_md_phonons.py (2)
12-14: Consistent use of double quotes for dictionary keys improves readability.
Line range hint
29-65: Consistent use of double quotes for string literals improves readability.atomistics/calculators/__init__.py (1)
47-72: Properly exporting new functions in the__all__list ensures they are accessible as intended.tests/test_ase_interface/test_evcurve_ase_matgl.py (5)
7-10: Import statements are correctly formatted and necessary for the test.
34-34: The addition ofase_optimizer_kwargsimproves the configurability of the optimizer.
39-42: The additions offit_type,fit_order,vol_range, andaxesenhance the flexibility and specificity of the workflow configuration.
52-57: The new arguments forget_thermal_propertiesimprove the specificity of the thermal properties calculation.
58-65: The assertions enhance the robustness of the test by verifying the expected outcomes..ci_support/release.py (1)
55-69: The code is correctly structured and functional.tests/test_evcurve_ase_lammps.py (6)
8-11: Import statements are correctly formatted and necessary for the test.
27-27: The addition ofcmdsis necessary for configuring the LAMMPS calculator.
38-38: The addition ofase_optimizer_kwargsimproves the configurability of the optimizer.
43-46: The additions offit_type,fit_order,vol_range, andaxesenhance the flexibility and specificity of the workflow configuration.
60-64: The new arguments forget_thermal_propertiesimprove the specificity of the thermal properties calculation.
66-68: The assertions enhance the robustness of the test by verifying the expected outcomes.tests/test_evcurve_lammps_functional.py (4)
14-14: Import statements are correctly formatted and necessary for the test.
Line range hint
28-40: The new arguments forget_potential_by_nameandevaluate_with_lammpsimprove the specificity and configurability of the functions.
50-50: The addition offit_orderimproves the configurability of the function.
62-65: The assertions enhance the robustness of the test by verifying the expected outcomes.tests/test_ase_interface/test_quasiharmonic_ase_mace.py (6)
25-25: Reformatted function arguments for better readability. LGTM!
32-32: Reformatted function arguments for better readability. LGTM!
50-52: Reformatted function arguments for better readability. LGTM!
54-55: Reformatted function arguments for better readability. LGTM!
59-60: Reformatted function arguments for better readability. LGTM!
68-69: Reformatted function arguments for better readability. LGTM!tests/test_evcurve_eos.py (5)
38-40: Reformatted function arguments for better readability. LGTM!
46-48: Reformatted function arguments for better readability. LGTM!
54-56: Reformatted function arguments for better readability. LGTM!
62-66: Reformatted function arguments for better readability. LGTM!
72-74: Reformatted function arguments for better readability. LGTM!atomistics/calculators/wrapper.py (1)
8-8: AddedTYPE_CHECKINGimport for better type checking. LGTM!tests/test_molecular_dynamics_thermal_expansion_lammps.py (5)
32-32: Reformatted function arguments for better readability. LGTM!
43-43: Reformatted function arguments for better readability. LGTM!
54-54: Reformatted function arguments for better readability. LGTM!
80-80: Reformatted function arguments for better readability. LGTM!
95-95: Reformatted function arguments for better readability. LGTM!tests/test_elastic_helper.py (1)
96-96: Ensure theget_symmetry_family_from_SGNfunction raises aValueErrorforSGN=231.Please verify that
get_symmetry_family_from_SGNcorrectly raises aValueErrorforSGN=231. If this is not the intended behavior, update the test accordingly.tests/test_quasiharmonic_lammps.py (3)
24-26: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
48-53: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
83-84: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
tests/test_quasiharmonic_lammps_functional.py (5)
29-31: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
36-46: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
73-79: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
110-113: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
125-128: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
tests/test_elastic_lammps.py (5)
24-26: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
37-37: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
45-59: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
83-87: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
110-121: Reformatting function arguments for better readability.The reformatting of function arguments improves readability. Ensure that the functionality remains unchanged.
tests/test_elastic_lammps_functional.py (1)
13-13: Ensure the imported functionsevaluate_with_lammpsandget_potential_by_nameare used in the test cases.Verification successful
The imported functions
evaluate_with_lammpsandget_potential_by_nameare used in the test cases.
get_potential_by_nameis used at least once.evaluate_with_lammpsis used at least twice.Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `evaluate_with_lammps` and `get_potential_by_name` in the test file. # Test: Search for the function usage. Expect: Occurrences of the functions in the test cases. rg --type python 'evaluate_with_lammps|get_potential_by_name' tests/test_elastic_lammps_functional.pyLength of output: 134
Script:
#!/bin/bash # Description: Verify the usage of `evaluate_with_lammps` and `get_potential_by_name` in the test file. # Test: Search for the function usage. Expect: Occurrences of the functions in the test cases. rg --type py 'evaluate_with_lammps|get_potential_by_name' tests/test_elastic_lammps_functional.pyLength of output: 319
tests/test_lammps_md.py (1)
14-14: Ensure the imported functionget_potential_by_nameis used in the test cases.Verification successful
The function
get_potential_by_nameis used in the test cases withintests/test_lammps_md.py, confirming that the import statement is necessary and correctly used.Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `get_potential_by_name` in the test file. # Test: Search for the function usage. Expect: Occurrences of the function in the test cases. rg --type python 'get_potential_by_name' tests/test_lammps_md.pyLength of output: 95
Script:
#!/bin/bash # Description: Verify the usage of `get_potential_by_name` in the test file. # Test: Search for the function usage. Expect: Occurrences of the function in the test cases. rg 'get_potential_by_name' tests/test_lammps_md.pyLength of output: 326
atomistics/calculators/lammps/potential.py (2)
293-297: Renaming the variableltolineimproves readability. Ensure the change is consistent throughout the function.
304-304: Adding a default argumentenv_variablesimproves the function's usability. Ensure the default values are appropriate for the intended use cases.atomistics/workflows/evcurve/thermo.py (1)
272-272: Changing the exception fromNotImplementedtoNotImplementedErroris appropriate and follows best practices for indicating unimplemented methods.
| def errfunc(p, x, y, fittype): | ||
| return fitfunction(p, x, fittype) - y |
There was a problem hiding this comment.
Add a docstring and type hints to the errfunc function for better readability and maintainability.
def errfunc(p: tuple[float], x: np.ndarray, y: np.ndarray, fittype: str) -> np.ndarray:
"""
Calculate the error between the fitted function and the actual data.
Args:
p (tuple[float]): Fit parameters.
x (np.ndarray): Volumes.
y (np.ndarray): Energies.
fittype (str): Type of fit.
Returns:
np.ndarray: Error between the fitted function and the actual data.
"""
return fitfunction(p, x, fittype) - y| try: | ||
| error.append(np.absolute(pcov[i][i]) ** 0.5) | ||
| except: | ||
| except TypeError: |
There was a problem hiding this comment.
Improve the error handling for the pcov calculation by specifying the exception type.
except TypeError:
error.append(0.00)| @@ -4,12 +4,13 @@ | |||
| import numpy as np | |||
There was a problem hiding this comment.
Remove unused import numpy.
- import numpy as npCommittable 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.
| import numpy as np |
| from atomistics.workflows import ( | ||
| EnergyVolumeCurveWorkflow, | ||
| optimize_positions_and_volume, | ||
| ) |
There was a problem hiding this comment.
Remove unused import numpy.
- import numpy as npCommittable 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.
| from atomistics.workflows import ( | |
| EnergyVolumeCurveWorkflow, | |
| optimize_positions_and_volume, | |
| ) | |
| from atomistics.workflows import ( | |
| EnergyVolumeCurveWorkflow, | |
| optimize_positions_and_volume, | |
| ) |
| @@ -16,7 +16,7 @@ def test_calc_phonons(self): | |||
| task_dict=task_dict, | |||
| ase_calculator=EMT(), | |||
| ase_optimizer=LBFGS, | |||
| ase_optimizer_kwargs={"fmax": 0.000001} | |||
| ase_optimizer_kwargs={"fmax": 0.000001}, | |||
There was a problem hiding this comment.
Ensure consistency in floating-point precision for fmax value.
To maintain consistency, consider using a more readable floating-point precision for fmax value, such as 1e-6 instead of 0.000001.
- ase_optimizer_kwargs={"fmax": 0.000001},
+ ase_optimizer_kwargs={"fmax": 1e-6},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.
| ase_optimizer_kwargs={"fmax": 0.000001}, | |
| ase_optimizer_kwargs={"fmax": 1e-6}, |
| task_dict = { | ||
| "calc_stress": result_dict["structure_with_optimized_positions_and_volume"] | ||
| } |
There was a problem hiding this comment.
Consider adding more assertions to verify the correctness of the stress calculations.
task_dict = {
"calc_stress": result_dict["structure_with_optimized_positions_and_volume"]
}
# Additional assertions
self.assertTrue(
np.allclose(
stress_pre_dict["stress"],
stress_post_dict["stress"],
atol=1e-5
)
)| for l in setup_content: | ||
| if '==' in l: | ||
| lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',') | ||
| if "==" in l: | ||
| lst = ( | ||
| l.split("[")[-1] | ||
| .split("]")[0] | ||
| .replace(" ", "") | ||
| .replace('"', "") | ||
| .replace("'", "") | ||
| .split(",") | ||
| ) | ||
| for dep in lst: | ||
| if dep != '\n': | ||
| version_lst.append(dep.split('==')[1]) | ||
| depend_lst.append(dep.split('==')[0]) | ||
| if dep != "\n": | ||
| version_lst.append(dep.split("==")[1]) | ||
| depend_lst.append(dep.split("==")[0]) |
There was a problem hiding this comment.
Replace the ambiguous variable name l with a more descriptive name like line.
- for l in setup_content:
- if "==" in l:
- lst = (
- l.split("[")[-1]
- .split("]")[0]
- .replace(" ", "")
- .replace('"', "")
- .replace("'", "")
- .split(",")
- )
+ for line in setup_content:
+ if "==" in line:
+ lst = (
+ line.split("[")[-1]
+ .split("]")[0]
+ .replace(" ", "")
+ .replace('"', "")
+ .replace("'", "")
+ .split(",")
+ )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.
| for l in setup_content: | |
| if '==' in l: | |
| lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',') | |
| if "==" in l: | |
| lst = ( | |
| l.split("[")[-1] | |
| .split("]")[0] | |
| .replace(" ", "") | |
| .replace('"', "") | |
| .replace("'", "") | |
| .split(",") | |
| ) | |
| for dep in lst: | |
| if dep != '\n': | |
| version_lst.append(dep.split('==')[1]) | |
| depend_lst.append(dep.split('==')[0]) | |
| if dep != "\n": | |
| version_lst.append(dep.split("==")[1]) | |
| depend_lst.append(dep.split("==")[0]) | |
| for line in setup_content: | |
| if "==" in line: | |
| lst = ( | |
| line.split("[")[-1] | |
| .split("]")[0] | |
| .replace(" ", "") | |
| .replace('"', "") | |
| .replace("'", "") | |
| .split(",") | |
| ) | |
| for dep in lst: | |
| if dep != "\n": | |
| version_lst.append(dep.split("==")[1]) | |
| depend_lst.append(dep.split("==")[0]) |
| if "dependencies:" in l: | ||
| read_flag = True | ||
| elif read_flag: | ||
| lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=") | ||
| lst = l.replace("-", "").replace(" ", "").replace("\n", "").split("=") | ||
| if len(lst) == 2: | ||
| depend_lst.append(lst[0]) | ||
| version_lst.append(lst[1]) | ||
| return {d:v for d, v in zip(depend_lst, version_lst)} | ||
| return {d: v for d, v in zip(depend_lst, version_lst)} |
There was a problem hiding this comment.
Replace the ambiguous variable name l with a more descriptive name like line.
- for l in env_content:
- if "dependencies:" in l:
+ for line in env_content:
+ if "dependencies:" in line:
- lst = l.replace("-", "").replace(" ", "").replace("\n", "").split("=")
+ lst = line.replace("-", "").replace(" ", "").replace("\n", "").split("=")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.
| if "dependencies:" in l: | |
| read_flag = True | |
| elif read_flag: | |
| lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=") | |
| lst = l.replace("-", "").replace(" ", "").replace("\n", "").split("=") | |
| if len(lst) == 2: | |
| depend_lst.append(lst[0]) | |
| version_lst.append(lst[1]) | |
| return {d:v for d, v in zip(depend_lst, version_lst)} | |
| return {d: v for d, v in zip(depend_lst, version_lst)} | |
| for line in env_content: | |
| if "dependencies:" in line: | |
| read_flag = True | |
| elif read_flag: | |
| lst = line.replace("-", "").replace(" ", "").replace("\n", "").split("=") | |
| if len(lst) == 2: | |
| depend_lst.append(lst[0]) | |
| version_lst.append(lst[1]) | |
| return {d: v for d, v in zip(depend_lst, version_lst)} |
| pattern_dict = {d: d + "==" + v for d, v in version_high_dict.items()} | ||
| for l in setup_content: | ||
| for k, v in pattern_dict.items(): | ||
| if v in l: | ||
| l = l.replace(v, version_combo_dict[k]) | ||
| setup_content_new +=l | ||
| setup_content_new += l |
There was a problem hiding this comment.
Replace the ambiguous variable name l with a more descriptive name like line.
- for l in setup_content:
+ for line in setup_content:
- if v in l:
- l = l.replace(v, version_combo_dict[k])
- setup_content_new += l
+ if v in line:
+ line = line.replace(v, version_combo_dict[k])
+ setup_content_new += lineCommittable 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.
| pattern_dict = {d: d + "==" + v for d, v in version_high_dict.items()} | |
| for l in setup_content: | |
| for k, v in pattern_dict.items(): | |
| if v in l: | |
| l = l.replace(v, version_combo_dict[k]) | |
| setup_content_new +=l | |
| setup_content_new += l | |
| pattern_dict = {d: d + "==" + v for d, v in version_high_dict.items()} | |
| for line in setup_content: | |
| for k, v in pattern_dict.items(): | |
| if v in line: | |
| line = line.replace(v, version_combo_dict[k]) | |
| setup_content_new += line |
| self.assertTrue( | ||
| np.isclose(elastic_dict["elastic_matrix"][0, 0], 125.66807354, atol=1e-04) | ||
| ) | ||
| self.assertTrue( | ||
| np.isclose(elastic_dict["elastic_matrix"][0, 1], 68.41418321, atol=1e-04) | ||
| ) | ||
| self.assertTrue( | ||
| np.isclose(elastic_dict["elastic_matrix"][3, 3], 99.29916329, atol=1e-04) | ||
| ) |
There was a problem hiding this comment.
Consider adding more assertions to verify the correctness of the elastic matrix calculations.
self.assertTrue(
np.isclose(elastic_dict["elastic_matrix"][0, 0], 125.66807354, atol=1e-04)
)
self.assertTrue(
np.isclose(elastic_dict["elastic_matrix"][0, 1], 68.41418321, atol=1e-04)
)
self.assertTrue(
np.isclose(elastic_dict["elastic_matrix"][3, 3], 99.29916329, atol=1e-04)
)
# Additional assertions
self.assertTrue(
np.allclose(
elastic_dict["elastic_matrix"],
np.array([[125.66807354, 68.41418321, 0, 0, 0, 0],
[68.41418321, 125.66807354, 0, 0, 0, 0],
[0, 0, 99.29916329, 0, 0, 0],
[0, 0, 0, 99.29916329, 0, 0],
[0, 0, 0, 0, 99.29916329, 0],
[0, 0, 0, 0, 0, 99.29916329]]),
atol=1e-4
)
)
Summary by CodeRabbit
Chores
.pre-commit-config.yamlfor linting and formatting configurations.Refactor
Bug Fixes
get_minimum_energy_pathmethod.Tests