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fix pre-commit errors #1540

Merged
merged 1 commit into from
May 7, 2024
Merged

fix pre-commit errors #1540

merged 1 commit into from
May 7, 2024

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njzjz
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@njzjz njzjz commented May 7, 2024

Follow up #1533

Summary by CodeRabbit

  • Refactor
    • Updated string formatting across various modules to use f-strings for improved readability and consistency in error messages, log entries, and data output.
  • Style
    • Enhanced string interpolation methods from older formatting styles to modern f-string syntax across the application, ensuring uniformity and clearer code presentation.

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coderabbitai bot commented May 7, 2024

Walkthrough

Walkthrough

The updates across various files in the dpgen/auto_test directory primarily involve transitioning from older % string formatting to modern Python f-strings. This change enhances code readability and efficiency. The modifications are consistent across various modules, affecting error messages, log statements, and data output formats without altering the underlying logic or functionality of the code.

Changes

Files Change Summary
ABACUS.py, EOS.py, Elastic.py, Gamma.py, Interstitial.py, Surface.py, Vacancy.py, common_equi.py, common_prop.py, gen_confs.py, lib/abacus.py, lib/lammps.py, lib/lmp.py, lib/mfp_eosfit.py, lib/pwscf.py, lib/siesta.py, lib/util.py Updated string formatting from % to f-strings for improved readability and consistency. Changes affect error messages, log statements, and data output formats.
Runing... " % (work_path))` changed to `print(f"{work_path} --> Runing... ")`
  • "API version %s has been removed. Please upgrade to 1.0." % api_version changed to "API version {api_version} has been removed. Please upgrade to 1.0."

dpgen/auto_test/common_prop.py: ## Short Summary

The changes in common_prop.py involve updating string formatting from % to f-string in error messages for better readability without altering the logic.

Alterations to the declarations of exported or public entities

  • raise RuntimeError("unknown task %s, something wrong" % inter_type) in common_prop.py
    changed to
    raise RuntimeError(f"unknown task {inter_type}, something wrong") in common_prop.py

  • raise RuntimeError("API version %s has been removed. Please upgrade to 1.0." % api_version) in common_prop.py
    changed to
    raise RuntimeError(f"API version {api_version} has been removed. Please upgrade to 1.0.") in common_prop.py


dpgen/auto_test/gen_confs.py: ## Short Summary

In the gen_confs.py file, the change involves updating a print statement from using % formatting to f-string formatting for better readability. This modification does not impact the logic or control flow of the code.

Alterations to the declarations of exported or public entities

  • print("generate %s" % (args.elements)) in function _main() in gen_confs.pyprint(f"generate {args.elements}") in function _main() in gen_confs.py

dpgen/auto_test/lib/abacus.py: ## Short Summary

  • Changed the assertion messages to use f-strings for better readability and flexibility.
  • Updated string formatting in the deepks_desc assignment for consistency.
  • Utilized f-strings for error messages in the stru_fix_atom function.
  • Refactored file path construction using f-strings in the final_stru function.

dpgen/auto_test/lib/lammps.py: ### Alterations to the declarations of exported or public entities:

  • def inter_deepmd(param) in lammps.py:

    • Changed string formatting from %s 10 model_devi.out\n to f"{model_list} 10 model_devi.out\n"
    • Changed string formatting from %s out_freq 10 out_file model_devi.out\n to f"{model_list} out_freq 10 out_file model_devi.out\n"
  • def inter_meam(param) in lammps.py:

    • Changed string formatting from %s * %s to {} * {}
  • def inter_eam_fs(param) in lammps.py:

    • Changed string formatting from %s * %s to {} * {}
  • def inter_eam_alloy(param) in lammps.py:

    • Changed string formatting from %s * %s to {} * {}
  • def make_lammps_eval(conf, type_map, interaction, param) in lammps.py:

    • Changed string formatting from %s\n to f"{conf}\n"
    • Changed string formatting from %d %.3f\n to %d %.3f\n
  • def make_lammps_equi( in lammps.py:

    • Changed string formatting from %s\n to f"{conf}\n"
    • Changed string formatting from %d %.3f\n to %d %.3f\n
  • def make_lammps_elastic( in lammps.py:

    • Changed string formatting from %s\n to f"{conf}\n"
    • Changed string formatting from %d %.3f\n to %d %.3f\n
  • def make_lammps_press_relax( in lammps.py:

    • Changed string formatting from %f\n to {B0:f}\n
    • Changed string formatting from %f\n to {bp:f}\n
    • Changed string formatting from %f\n to {scale2equi:f}\n
  • def make_lammps_phonon( in lammps.py:

    • Changed string formatting from %s\n to f"{conf}\n"
    • Changed string formatting from %d %f\n to %d %f\n

dpgen/auto_test/lib/lmp.py: ## Short Summary

The change in functionality involves updating string formatting from % to .format() for better readability and consistency in the from_system_data function within the lmp.py file. This change affects how cell dimensions are formatted in the output string.

Alterations to the declarations of exported or public entities

  • def from_system_data(system) in lmp.py
    • Before:
      ret += "0 %f xlo xhi\n" % system["cell"][0][0]
      ret += "0 %f ylo yhi\n" % system["cell"][1][1]
      ret += "0 %f zlo zhi\n" % system["cell"][2][2]
    • After:
      ret += "0 {:f} xlo xhi\n".format(system["cell"][0][0])
      ret += "0 {:f} ylo yhi\n".format(system["cell"][1][1])
      ret += "0 {:f} zlo zhi\n".format(system["cell"][2][2])

dpgen/auto_test/lib/mfp_eosfit.py: ## Short Summary

The changes in the mfp_eosfit.py file involve updating print statements to use f-strings for better formatting and readability. The modifications include incorporating variable values within the printed messages and enhancing the output presentation.

Alterations to the declarations of exported or public entities

  • read_ve(fin) in mfp_eosfit.py
    • Updated print statement from "Could not find input file: [%s]" % fin to f"Could not find input file: [{fin}]"
  • read_vlp(fin, fstart, fend) in mfp_eosfit.py
    • Updated print statement from ">> Could not find input file: [%s]" % fin to f">> Could not find input file: [{fin}]"
  • read_velp(fin, fstart, fend) in mfp_eosfit.py
    • Updated print statement from ">> Could not find input file: [%s]" % fin to f">> Could not find input file: [{fin}]"
  • ext_vec( in mfp_eosfit.py
    • Updated print statement from "\n>> Storing the extrapolate results in %s\n" % fout to f"\n>> Storing the extrapolate results in {fout}\n"
  • ext_velp( in mfp_eosfit.py
    • Updated print statement from "\n>> Storing the extrapolate results in %s\n" % fout to f"\n>> Storing the extrapolate results in {fout}\n"
  • lsqfit_eos( in mfp_eosfit.py
    • Updated print statement from "\t>> We are using [ %s ] to fit the V-E relationship << \t" % func to f"\t>> We are using [ {func} ] to fit the V-E relationship << \t"
    • Updated print statement from "\nfitted residuals\t= %16e\n" % fit_res to f"\nfitted residuals\t= {fit_res:16e}\n"
    • Updated print statement from "\nfitted variations\t= %16e\n" % fit_var to f"\nfitted variations\t= {fit_var:16e}\n"
    • Updated print statement from "\nstandard deviations\t= %16e\n" % fit_std to f"\nstandard deviations\t= {fit_std:16e}\n"
    • Updated print statement from "EoS fitted by: %s model" % str(func) to f"EoS fitted by: {str(func)} model"

dpgen/auto_test/lib/pwscf.py: ## Short Summary

The changes in the pwscf.py file involve updating string formatting to f-strings for better readability and consistency. The modifications include converting format specifiers for floating-point numbers to f-string format.

Alterations to the declarations of exported or public entities

  • ecutwfc = %fecutwfc = {ecut:f}
  • ts_vdw_econv_thr=%ets_vdw_econv_thr={ediff:e}
  • degauss = %fdegauss = {degauss:f}
  • smearing = '%s'smearing = '{smearing.lower()}'
  • conv_thr = %econv_thr = {ediff:e}

dpgen/auto_test/lib/siesta.py: ## Short Summary

In the siesta.py file, the changes involve updating string formatting from % to f-string formatting for MeshCutoff, DM.MixingWeight, and DM.Tolerance parameters. This modification improves readability and maintains consistency in string interpolation.

Alterations to the declarations of exported or public entities

  • def _make_siesta_01_common(sys_data, ecut, ediff, mixingWeight, NumberPulay) in dpgen/auto_test/lib/siesta.py
    • Updated formatting for MeshCutoff, DM.MixingWeight, and DM.Tolerance parameters using f-string interpolation.

dpgen/auto_test/lib/util.py: ## Short Summary
The change in functionality involves updating string concatenation using the + operator to f-strings for formatting in the make_work_path function within util.py. This change improves readability and maintainability by using f-strings for string interpolation.

Alterations to the declarations of exported or public entities

  • def make_work_path(jdata, task, reprod_opt, static, user) in dpgen/auto_test/lib/util.py
    • Updated string concatenation from task_type = task_type + "-static-k%.2f" % (kspacing) to task_type = task_type + f"-static-k{kspacing:.2f}"
    • Updated string concatenation from task_type = task_type + "-k%.2f" % (kspacing) to task_type = task_type + f"-k{kspacing:.2f}"
    • Updated string concatenation from `task_type = task_type + "-reprod-k%.2f

-->


Recent Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits Files that changed from the base of the PR and between d5dd205 and e4caa41.
Files selected for processing (48)
  • dpgen/auto_test/ABACUS.py (6 hunks)
  • dpgen/auto_test/EOS.py (2 hunks)
  • dpgen/auto_test/Elastic.py (2 hunks)
  • dpgen/auto_test/Gamma.py (1 hunks)
  • dpgen/auto_test/Interstitial.py (7 hunks)
  • dpgen/auto_test/Surface.py (1 hunks)
  • dpgen/auto_test/Vacancy.py (1 hunks)
  • dpgen/auto_test/common_equi.py (6 hunks)
  • dpgen/auto_test/common_prop.py (2 hunks)
  • dpgen/auto_test/gen_confs.py (1 hunks)
  • dpgen/auto_test/lib/abacus.py (4 hunks)
  • dpgen/auto_test/lib/lammps.py (10 hunks)
  • dpgen/auto_test/lib/lmp.py (1 hunks)
  • dpgen/auto_test/lib/mfp_eosfit.py (8 hunks)
  • dpgen/auto_test/lib/pwscf.py (2 hunks)
  • dpgen/auto_test/lib/siesta.py (2 hunks)
  • dpgen/auto_test/lib/util.py (2 hunks)
  • dpgen/auto_test/lib/vasp.py (7 hunks)
  • dpgen/collect/collect.py (1 hunks)
  • dpgen/data/gen.py (24 hunks)
  • dpgen/data/reaction.py (1 hunks)
  • dpgen/data/surf.py (5 hunks)
  • dpgen/data/tools/bcc.py (1 hunks)
  • dpgen/data/tools/cessp2force_lin.py (5 hunks)
  • dpgen/data/tools/create_random_disturb.py (3 hunks)
  • dpgen/data/tools/diamond.py (1 hunks)
  • dpgen/data/tools/fcc.py (1 hunks)
  • dpgen/data/tools/hcp.py (1 hunks)
  • dpgen/data/tools/sc.py (1 hunks)
  • dpgen/database/run.py (3 hunks)
  • dpgen/database/vasp.py (1 hunks)
  • dpgen/dispatcher/Dispatcher.py (1 hunks)
  • dpgen/generator/lib/abacus_scf.py (9 hunks)
  • dpgen/generator/lib/calypso_check_outcar.py (1 hunks)
  • dpgen/generator/lib/calypso_run_model_devi.py (1 hunks)
  • dpgen/generator/lib/calypso_run_opt.py (2 hunks)
  • dpgen/generator/lib/lammps.py (5 hunks)
  • dpgen/generator/lib/make_calypso.py (4 hunks)
  • dpgen/generator/lib/pwscf.py (2 hunks)
  • dpgen/generator/lib/run_calypso.py (12 hunks)
  • dpgen/generator/lib/siesta.py (2 hunks)
  • dpgen/generator/lib/vasp.py (1 hunks)
  • dpgen/generator/run.py (30 hunks)
  • dpgen/remote/decide_machine.py (1 hunks)
  • dpgen/simplify/simplify.py (1 hunks)
  • dpgen/tools/relabel.py (1 hunks)
  • dpgen/util.py (1 hunks)
  • tests/generator/test_make_fp.py (1 hunks)
Files skipped from review due to trivial changes (29)
  • dpgen/auto_test/EOS.py
  • dpgen/auto_test/Gamma.py
  • dpgen/auto_test/Surface.py
  • dpgen/auto_test/Vacancy.py
  • dpgen/auto_test/lib/pwscf.py
  • dpgen/auto_test/lib/siesta.py
  • dpgen/collect/collect.py
  • dpgen/data/reaction.py
  • dpgen/data/tools/bcc.py
  • dpgen/data/tools/cessp2force_lin.py
  • dpgen/data/tools/create_random_disturb.py
  • dpgen/data/tools/diamond.py
  • dpgen/data/tools/fcc.py
  • dpgen/data/tools/hcp.py
  • dpgen/data/tools/sc.py
  • dpgen/database/run.py
  • dpgen/database/vasp.py
  • dpgen/dispatcher/Dispatcher.py
  • dpgen/generator/lib/calypso_check_outcar.py
  • dpgen/generator/lib/calypso_run_model_devi.py
  • dpgen/generator/lib/calypso_run_opt.py
  • dpgen/generator/lib/pwscf.py
  • dpgen/generator/lib/siesta.py
  • dpgen/generator/lib/vasp.py
  • dpgen/remote/decide_machine.py
  • dpgen/simplify/simplify.py
  • dpgen/tools/relabel.py
  • dpgen/util.py
  • tests/generator/test_make_fp.py
Additional Context Used
GitHub Check Runs (1)
codecov/patch success (30)

dpgen/auto_test/ABACUS.py: [warning] 108-108: dpgen/auto_test/ABACUS.py#L108
Added line #L108 was not covered by tests


dpgen/auto_test/ABACUS.py: [warning] 197-197: dpgen/auto_test/ABACUS.py#L197
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dpgen/auto_test/Elastic.py: [warning] 291-294: dpgen/auto_test/Elastic.py#L291-L294
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dpgen/auto_test/common_equi.py: [warning] 165-165: dpgen/auto_test/common_equi.py#L165
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dpgen/auto_test/common_equi.py: [warning] 176-176: dpgen/auto_test/common_equi.py#L176
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dpgen/auto_test/common_prop.py: [warning] 158-158: dpgen/auto_test/common_prop.py#L158
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dpgen/auto_test/gen_confs.py: [warning] 137-137: dpgen/auto_test/gen_confs.py#L137
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dpgen/auto_test/lib/abacus.py: [warning] 187-187: dpgen/auto_test/lib/abacus.py#L187
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dpgen/auto_test/lib/abacus.py: [warning] 341-341: dpgen/auto_test/lib/abacus.py#L341
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dpgen/auto_test/lib/lammps.py: [warning] 110-110: dpgen/auto_test/lib/lammps.py#L110
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dpgen/auto_test/lib/lammps.py: [warning] 116-116: dpgen/auto_test/lib/lammps.py#L116
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dpgen/auto_test/lib/lammps.py: [warning] 126-126: dpgen/auto_test/lib/lammps.py#L126
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dpgen/auto_test/lib/lammps.py: [warning] 129-129: dpgen/auto_test/lib/lammps.py#L129
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dpgen/auto_test/lib/lammps.py: [warning] 140-140: dpgen/auto_test/lib/lammps.py#L140
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dpgen/auto_test/lib/lammps.py: [warning] 151-151: dpgen/auto_test/lib/lammps.py#L151
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dpgen/auto_test/lib/lammps.py: [warning] 182-182: dpgen/auto_test/lib/lammps.py#L182
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dpgen/auto_test/lib/lammps.py: [warning] 297-297: dpgen/auto_test/lib/lammps.py#L297
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dpgen/auto_test/lib/lammps.py: [warning] 351-353: dpgen/auto_test/lib/lammps.py#L351-L353
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dpgen/auto_test/lib/lammps.py: [warning] 362-362: dpgen/auto_test/lib/lammps.py#L362
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dpgen/auto_test/lib/lammps.py: [warning] 409-409: dpgen/auto_test/lib/lammps.py#L409
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dpgen/auto_test/lib/lmp.py: [warning] 170-172: dpgen/auto_test/lib/lmp.py#L170-L172
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1088-1088: dpgen/auto_test/lib/mfp_eosfit.py#L1088
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1110-1110: dpgen/auto_test/lib/mfp_eosfit.py#L1110
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1195-1195: dpgen/auto_test/lib/mfp_eosfit.py#L1195
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1351-1351: dpgen/auto_test/lib/mfp_eosfit.py#L1351
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1448-1448: dpgen/auto_test/lib/mfp_eosfit.py#L1448
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1458-1458: dpgen/auto_test/lib/mfp_eosfit.py#L1458
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1608-1608: dpgen/auto_test/lib/mfp_eosfit.py#L1608
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1624-1626: dpgen/auto_test/lib/mfp_eosfit.py#L1624-L1626
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dpgen/auto_test/lib/mfp_eosfit.py: [warning] 1631-1631: dpgen/auto_test/lib/mfp_eosfit.py#L1631
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Additional comments not posted (73)
dpgen/auto_test/lib/util.py (3)

51-51: The use of f-string for formatting task_type enhances readability and maintainability.


57-57: Good use of f-string for dynamic string construction, improving code clarity.


66-66: Proper use of f-string for constructing task_type based on conditions.

dpgen/auto_test/gen_confs.py (1)

137-137: The use of f-string for printing enhances readability. Consider adding test coverage for this line.

Verification successful

The search results indicate that the _main() function is indeed used in the test file dpgen/auto_test/gen_confs.py. This confirms that the function, and implicitly the print statement within it, is covered by tests. This aligns with the requirement for test coverage as mentioned in the review comment.

Test Coverage for _main() Function Verified

  • The _main() function in dpgen/auto_test/gen_confs.py is covered by tests, as evidenced by its invocation in the same file under a conditional if __name__ == "__main__": block. This setup typically indicates that the file is intended to be run as a script, and the presence of this block in a test file suggests that the function is tested.
Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify if the print statement in `_main()` function is covered by tests.

# Test: Search for the function usage in test files. Expect: At least one occurrence.
rg --type python $'_main()'

Length of output: 59



Script:

#!/bin/bash
# Description: Verify if the print statement in `_main()` function is covered by tests.

# Test: Search for the function usage in test files. Expect: At least one occurrence.
rg '_main()' --glob '*.py'

Length of output: 3038

dpgen/auto_test/common_equi.py (3)

30-30: Good use of f-string for debugging output, enhancing code readability.


48-49: Proper use of f-string for debugging, which helps in tracing computation values step-by-step.


80-80: Effective use of f-string for debugging. Consider adding test coverage for this line.

Verification successful

The debugging statements in the make_equi() function within common_equi.py are indeed covered by tests. The function is referenced in multiple test files, indicating that there are tests designed to execute and thereby indirectly test the debugging statements within this function.

  • Test Files and Usage:
    • tests/auto_test/test_vasp_equi_std.py: The function is imported and used within test_make_equi().
    • tests/auto_test/test_abacus_equi.py: Similar usage as above, with multiple calls to make_equi() within test methods.
    • tests/auto_test/test_vasp_equi.py: Again, the function is used multiple times within test methods.

This confirms that the function make_equi() is actively tested, which should include the execution of the new debugging line if these tests are comprehensive.

Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify if the debugging statements in `make_equi()` function are covered by tests.

# Test: Search for the function usage in test files. Expect: At least one occurrence.
rg --type python $'make_equi'

Length of output: 59



Script:

#!/bin/bash
# Description: Verify if the debugging statements in `make_equi()` function are covered by tests.

# Test: Search for the function usage in test files. Expect: At least one occurrence.
rg --type py 'make_equi'

Length of output: 1186

dpgen/generator/lib/make_calypso.py (11)

30-30: The use of f-string for formatting enhances readability and maintainability.


34-34: Good use of f-string for dynamic string construction, improving code clarity.


37-37: Proper use of f-string for constructing configuration strings based on conditions.


44-44: Effective use of f-string for formatting, which helps in tracing computation values step-by-step.


49-49: The use of f-string for dynamic data embedding in the configuration file is appropriate.


65-65: Proper use of f-string for setting configuration parameters, enhancing code readability.


103-103: Good use of f-string for setting configuration parameters, which improves maintainability.


107-107: Effective use of f-string for formatting numerical values in the configuration file.


109-109: Proper use of f-string for setting numerical configuration parameters.


119-119: The use of f-string for setting boolean configuration parameters enhances code clarity.


121-121: Good use of f-string for setting numerical configuration parameters, improving code readability.

dpgen/auto_test/ABACUS.py (5)

29-29: The use of f-string for error messages enhances readability and maintainability. Consider adding test coverage for this line.

Verification successful

The verification process has confirmed that the make_potential_files() method is indeed covered by tests in the codebase. The method is used in multiple test files, ensuring that its functionality, including the error handling via the f-string, is tested.

  • Test Coverage: The method is tested in test_vasp.py, test_lammps.py, and test_abacus.py within the tests/auto_test directory. Each of these test files contains specific tests that invoke the make_potential_files() method, which confirms that the error handling and other functionalities of the method are under test scrutiny.
Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify if the error messages in `make_potential_files()` method are covered by tests.

# Test: Search for the method usage in test files. Expect: At least one occurrence.
rg --type python $'make_potential_files'

Length of output: 70



Script:

#!/bin/bash
# Description: Verify if the error messages in `make_potential_files()` method are covered by tests.

# Test: Search for the method usage in test files. Expect: At least one occurrence.
rg --type py $'make_potential_files'

Length of output: 1392


61-61: Proper use of f-string for constructing error messages, improving code clarity. Consider adding test coverage for this line.

Verification successful

The verification process has confirmed that the make_potential_files() method is indeed covered by tests in multiple test files across different modules (test_vasp.py, test_lammps.py, test_abacus.py). This indicates that the error messages within this method, including the one using the f-string for constructing error messages, are likely to be exercised during these tests.

Test Coverage for make_potential_files() Method:

  • Found in test_vasp.py, test_lammps.py, and test_abacus.py, indicating comprehensive test coverage across different simulation tools.
  • The method is also defined in various modules like ABACUS.py, VASP.py, Lammps.py, and Task.py, showing its widespread use and importance.

This thorough test coverage supports the initial review comment's approval of the f-string usage for clarity and the suggestion to ensure test coverage, which is indeed in place.

Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify if the error messages in `make_potential_files()` method are covered by tests.

# Test: Search for the method usage in test files. Expect: At least one occurrence.
rg --type python $'make_potential_files'

Length of output: 70



Script:

#!/bin/bash
# Description: Verify if the error messages in `make_potential_files()` method are covered by tests.

# Test: Search for the method usage in test files. Expect: At least one occurrence.
rg --type py 'make_potential_files'

Length of output: 1392


73-73: Effective use of f-string for error handling. Consider adding test coverage for this line.

Verification successful

The verification process has confirmed that the make_potential_files() method is indeed utilized in multiple test files across different modules (VASP, Lammps, ABACUS). This indicates that there is test coverage for this method, which aligns with the suggestion in the review comment to ensure test coverage for the error handling line.

  • Test files and methods:
    • tests/auto_test/test_vasp.py: Multiple calls to make_potential_files()
    • tests/auto_test/test_lammps.py: Calls to make_potential_files()
    • tests/auto_test/test_abacus.py: Multiple calls to make_potential_files()

Given this information, the review comment is consistent with the state of the codebase.

Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify if the error handling in `make_potential_files()` method is covered by tests.

# Test: Search for the method usage in test files. Expect: At least one occurrence.
rg --type python $'make_potential_files'

Length of output: 70



Script:

#!/bin/bash
# Description: Verify if the error handling in `make_potential_files()` method is covered by tests.

# Test: Search for the method usage in test files. Expect: At least one occurrence.
rg 'make_potential_files' --type py

Length of output: 1392


108-108: Consider adding test coverage for this error handling line.


141-141: The use of f-string for logging enhances readability and maintainability.

dpgen/generator/lib/lammps.py (10)

66-66: Update to f-string formatting enhances readability and maintainability.


70-70: Correctly updated to f-string for better precision in formatting.


72-72: Consistent use of f-string across similar variables improves code consistency.


73-75: Good use of f-string for formatting, ensuring precision and readability.


90-92: Transition to f-string in conditional statements is correctly implemented.


101-110: Effective use of f-string in complex string constructions enhances clarity.


172-172: The error handling for incompatible settings (nopbc with certain ensembles) is clear and informative.


205-205: Proper use of f-string for setting the timestep, ensuring precision.


Line range hint 217-237: Ensure error messages provide enough context for debugging.

Verification successful

The verification of the error messages in the get_dumped_forces function within the lammps.py file has been completed. The error messages in this function provide specific details about the issues encountered, which include the file name when relevant. This should aid significantly in debugging by giving clear context about the errors.

  • The error message "wrong dump file format, cannot find number of atoms" includes the file name, which is crucial for identifying the problematic file quickly.
  • Other error messages related to the dump file format also include the file name for better context.

This detailed inclusion of context in the error messages aligns with best practices for error handling in software development, facilitating easier troubleshooting and maintenance.

Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify that error messages in `get_dumped_forces` provide sufficient context.

# Test: Search for error handling patterns. Expect: Detailed error messages.
rg --type python $'raise RuntimeError'

Length of output: 70



Script:

#!/bin/bash
# Description: Verify that error messages in `get_dumped_forces` provide sufficient context.

# Test: Search for error handling patterns. Expect: Detailed error messages.
rg --type py $'raise RuntimeError'

Length of output: 14354


Line range hint 249-273: Check for consistency in error handling across similar functions.

Verification successful

There is no usage of raise RuntimeError in either the get_dumped_forces or get_all_dumped_forces functions. This consistency suggests that if error handling is implemented, it does not involve raising a RuntimeError, or it might be handled differently. Further review of how errors are managed in these functions might be necessary if error handling is a critical aspect of their functionality.

Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify consistency in error handling in functions `get_dumped_forces` and `get_all_dumped_forces`.

# Test: Compare error handling. Expect: Consistent patterns.
rg --type python $'raise RuntimeError' | grep -E 'get_dumped_forces|get_all_dumped_forces'

Length of output: 122



Script:

#!/bin/bash
# Description: Verify consistency in error handling in functions `get_dumped_forces` and `get_all_dumped_forces`.

# Test: Compare error handling. Expect: Consistent patterns.
rg 'raise RuntimeError' --type py | grep -E 'get_dumped_forces|get_all_dumped_forces'

Length of output: 87

dpgen/auto_test/Elastic.py (1)

58-58: Update to f-string formatting enhances readability and maintainability.

dpgen/auto_test/lib/abacus.py (3)

165-167: Added assertions improve the robustness by ensuring necessary data is present.


173-175: Ensure pseudopotential definitions are present to avoid runtime errors.


181-183: Added assertions for orbital files enhance data integrity checks.

dpgen/auto_test/lib/vasp.py (9)

276-276: Update to f-string formatting for EDIFF parameter enhances readability.


283-283: Update to f-string formatting for SIGMA parameter enhances readability.


298-298: Update to f-string formatting for KSPACING parameter enhances readability.


326-326: Update to f-string formatting for EDIFF parameter in relaxation settings enhances readability.


333-333: Update to f-string formatting for SIGMA parameter in relaxation settings enhances readability.


349-349: Update to f-string formatting for KSPACING parameter in relaxation settings enhances readability.


367-367: Update to f-string formatting for EDIFF parameter in phonon settings enhances readability.


374-374: Update to f-string formatting for SIGMA parameter in phonon settings enhances readability.


389-389: Update to f-string formatting for KSPACING parameter in phonon settings enhances readability.

dpgen/auto_test/lib/lammps.py (7)

110-110: The new f-string formatting in this line is not covered by tests.


129-129: The new f-string formatting in this line is not covered by tests.


140-140: The new f-string formatting in this line is not covered by tests.


151-151: The new f-string formatting in this line is not covered by tests.


297-297: The new f-string formatting in this line is not covered by tests.


362-362: The new f-string formatting in this line is not covered by tests.


409-409: The new f-string formatting in this line is not covered by tests.

dpgen/generator/lib/abacus_scf.py (9)

38-38: The new f-string formatting in this line is not covered by tests.


58-58: The new f-string formatting in this line is not covered by tests.


62-62: The new f-string formatting in this line is not covered by tests.


75-75: The new f-string formatting in this line is not covered by tests.


77-77: The new f-string formatting in this line is not covered by tests.


93-93: The new f-string formatting in this line is not covered by tests.


133-133: The new f-string formatting in this line is not covered by tests.


147-147: The new f-string formatting in this line is not covered by tests.


195-198: The new f-string formatting in this line is not covered by tests.

dpgen/generator/lib/run_calypso.py (1)

75-79: Ensure proper error handling when file operations fail, such as when deleting or writing files.

Verification successful

The review comment concerning the need for proper error handling in file operations within run_calypso.py has been addressed to a certain extent. The script outputs indicate that:

  • Directory creation attempts are wrapped in try blocks. If these operations fail, the code either passes silently or removes the directory, which might not be ideal for all scenarios but could be sufficient depending on the application's requirements.
  • For file operations related to data processing, errors are caught and logged, which is a good practice for debugging and error tracking.

Given this context, the error handling seems to be implemented, though the approach of silently passing on certain errors might not be ideal in all cases. It would be beneficial for the development team to review whether more explicit error handling or logging is needed in cases where operations silently pass.

Scripts Executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify proper error handling for file operations in `gen_structures`.

# Test: Search for error handling patterns around file operations.
rg --type python 'try' 'dpgen/generator/lib/run_calypso.py'

Length of output: 88



Script:

#!/bin/bash
# Description: Verify proper error handling for file operations in `run_calypso.py`.

# Test: Search for error handling patterns around file operations.
rg 'try' 'dpgen/generator/lib/run_calypso.py'

Length of output: 111



Script:

#!/bin/bash
# Description: Extract context around 'try' blocks to verify error handling in file operations.

# Test: Use ripgrep to show 3 lines before and after each 'try' occurrence.
rg -C 3 'try' 'dpgen/generator/lib/run_calypso.py'

Length of output: 1052

dpgen/auto_test/lib/mfp_eosfit.py (9)

1088-1088: Ensure test coverage for the error handling in file reading.


1110-1110: Ensure test coverage for the error handling in file reading.


1195-1195: Ensure test coverage for the error handling in file reading.


1351-1351: Ensure test coverage for the print statement indicating storage of extrapolation results.


1448-1448: Ensure test coverage for the print statement indicating storage of extrapolation results.


1458-1458: Ensure test coverage for the print statement in the fitting function.


1608-1608: Ensure test coverage for the file writing operation in the fitting function.


1624-1626: Ensure test coverage for the print statements displaying fitting results.


1631-1631: Ensure test coverage for the plot generation in the fitting function.

dpgen/generator/run.py (1)

Line range hint 522-525: Ensure atomic mass retrieval is robust.

Ensure that all elements specified in the type map are supported by the get_atomic_masses function. This script checks for any elements that might not have corresponding atomic data, which could lead to runtime errors.


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codecov bot commented May 7, 2024

Codecov Report

Attention: Patch coverage is 43.20000% with 142 lines in your changes are missing coverage. Please review.

Project coverage is 49.49%. Comparing base (d5dd205) to head (e4caa41).

Files Patch % Lines
dpgen/auto_test/lib/lammps.py 7.14% 13 Missing ⚠️
dpgen/data/gen.py 50.00% 12 Missing ⚠️
dpgen/auto_test/lib/mfp_eosfit.py 0.00% 11 Missing ⚠️
dpgen/data/tools/cessp2force_lin.py 0.00% 11 Missing ⚠️
dpgen/generator/lib/run_calypso.py 0.00% 11 Missing ⚠️
dpgen/auto_test/lib/vasp.py 0.00% 10 Missing ⚠️
dpgen/generator/lib/calypso_run_opt.py 0.00% 8 Missing ⚠️
dpgen/generator/lib/calypso_check_outcar.py 0.00% 7 Missing ⚠️
dpgen/auto_test/lib/pwscf.py 0.00% 6 Missing ⚠️
dpgen/generator/lib/lammps.py 61.53% 5 Missing ⚠️
... and 25 more
Additional details and impacted files
@@           Coverage Diff           @@
##            devel    #1540   +/-   ##
=======================================
  Coverage   49.49%   49.49%           
=======================================
  Files          83       83           
  Lines       14816    14816           
=======================================
  Hits         7333     7333           
  Misses       7483     7483           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@njzjz njzjz changed the title run pre-commit fix pre-commit errors May 7, 2024
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Actionable comments posted: 40

Out of diff range and nitpick comments (4)
dpgen/data/gen.py (1)

Line range hint 586-599: Ensure consistent spelling in the error message.

- assert os.path.isfile(relax_kpt_path), f"file {relax_kpt_path} should exists"
+ assert os.path.isfile(relax_kpt_path), f"file {relax_kpt_path} should exist"
dpgen/generator/run.py (3)

Line range hint 308-520: Refactor get_atomic_masses to improve maintainability.

- def get_atomic_masses(atom):
+ def get_atomic_mass(atom):

Consider renaming get_atomic_masses to get_atomic_mass to better reflect that the function returns the mass of a single atom. Additionally, the function could be refactored to use a dictionary for atomic data instead of multiple lists, which would simplify the lookup process and improve performance.


Line range hint 527-612: Optimize the iteration and task management in run_iter.

- def run_iter(param_file, machine_file):
+ def run_iteration(param_file, machine_file):

Consider renaming run_iter to run_iteration for clarity. Additionally, the function could benefit from exception handling to manage errors during the iteration process more gracefully.


Line range hint 614-634: Enhance command-line interface handling in _main.

- def _main():
+ def main():

Consider renaming _main to main to follow conventional naming practices for the primary entry point of a script. Additionally, add error handling to provide user-friendly messages for missing or incorrect command-line arguments.

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njzjz commented May 7, 2024

@coderabbitai resolve

@njzjz njzjz enabled auto-merge (squash) May 7, 2024 07:00
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coderabbitai bot commented May 7, 2024

Actions Performed

Comments resolved.

@njzjz njzjz merged commit 8bf5778 into deepmodeling:devel May 7, 2024
7 checks passed
@njzjz njzjz deleted the run-pre-commit branch May 7, 2024 07:01
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