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bugfix: chargemol runtime directory and os.path.exists fix #3778

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@chiang-yuan chiang-yuan commented Apr 21, 2024

Summary

  • Improve path logic
  • Allow Chargemol to run in different directory (previously the code has implemented but is not working)
  • Fix os.path.isfile bug. Change it into os.path.exists

Todos

Checklist

  • Google format doc strings added. Check with ruff.
  • Type annotations included. Check with mypy.
  • Tests added for new features/fixes.

Summary by CodeRabbit

  • Refactor
    • Improved file handling and error checking in the charge calculation module.
    • Renamed instances for clarity and added new test methods for enhanced error handling.
    • Modified assertions and introduced patches for improved structure handling.

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coderabbitai bot commented Apr 21, 2024

Walkthrough

The recent changes in chargemol_caller.py and related files refine Chargemol script execution, improve error handling for missing files, and enhance overall script robustness. These updates aim to streamline Chargemol analysis and strengthen code reliability.

Changes

File Summary of Changes
.../chargemol_caller.py
.../test_chargemol_caller.py
  • chargemol_caller.py: Added Pathlib import, updated path handling, refined temporary directory management, and enhanced error checks.
  • test_chargemol_caller.py: Renamed instances, added test_missing_exe_error, adjusted assertions, and introduced error handling patch. |

Recent Review Details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits Files that changed from the base of the PR and between e4ccad6 and 8be153a.
Files selected for processing (1)
  • pymatgen/command_line/chargemol_caller.py (11 hunks)
Files skipped from review as they are similar to previous changes (1)
  • pymatgen/command_line/chargemol_caller.py

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thanks @chiang-yuan for the os.path.isfile fix! 👍


response = subprocess.run(CHARGEMOL_EXE, capture_output=True, check=False)
_stdout = response.stdout.decode("utf-8")
response.stderr.decode("utf-8")
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do these two lines serve a purpose? i don't think these raise when response.returncode != 0? i think we need a test for the previously raised RuntimeError

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maybe we can just use check=True? We don't even need to capture response/stdout here as it is not used?

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yes, let's use check=True. it's a different error type CalledProcessError which I think is better than RuntimeError anyway but we should still add a test for this behavior.

@janosh janosh added fix Bug fix PRs analysis Concerning pymatgen.analysis charge Electric charge analysis, partitioning, integrations, etc. labels Apr 21, 2024
@janosh janosh added the needs testing PRs that are not ready to merge due to lacking tests label Apr 25, 2024
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chiang-yuan commented May 4, 2024

Try to fix the missing command_line in the test file paths but pre-commit keeps failing due to the pyright issue.
I will leave it a bit until the problem is solved globally or just drop the usage of pyright #3777

@chiang-yuan chiang-yuan mentioned this pull request Jun 14, 2024
4 tasks
@janosh janosh force-pushed the master branch 2 times, most recently from e3fbc67 to 41e6d99 Compare August 3, 2024 19:01
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