bugfix: chargemol runtime directory and `os.path.exists` fix by chiang-yuan · Pull Request #3778 · materialsproject/pymatgen

chiang-yuan · 2024-04-21T21:38:46Z

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

add test
Download chargemol and run real chargemol analysis. This should close Chargemol autodownloads #3474

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.

coderabbitai · 2024-04-21T21:38:53Z

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. |

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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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…pply)

janosh

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

janosh · 2024-04-21T22:51:28Z

+
+            response = subprocess.run(CHARGEMOL_EXE, capture_output=True, check=False)
+            _stdout = response.stdout.decode("utf-8")
+            response.stderr.decode("utf-8")


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

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

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.

chiang-yuan · 2024-05-04T07:29:48Z

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

…into fix-chargemol-path

shyuep · 2026-03-10T02:09:13Z

Thanks. We have refactored pymatgen to move core packages to a separate pymatgen-core repo. If you don't mind, please submit a new PR in that repo. This will also ensure you are properly credited for the contribution. Sorry about the inconvenience.

chiang-yuan added 2 commits April 16, 2024 13:38

bugfix: allow custom chgcar path

fb3dce4

atomic_densities is a direcotry, not file

637501a

chiang-yuan requested review from janosh, mkhorton and shyuep as code owners April 21, 2024 21:38

janosh added 6 commits April 21, 2024 15:41

refactor TestChargemolAnalysis

ba0f1a9

prefer os.path over pathlib

7a29026

fix default atomic_densities_path (set to None, so if == "" doesn't a…

76324b3

…pply)

fix possibly unbound var in get_charge_transfer

1832070

refactor _from_data_dir

a05635e

test_missing_exe_error

01f0283

janosh suggested changes Apr 21, 2024

View reviewed changes

janosh added fix Bug fix PRs analysis Concerning pymatgen.analysis charge Electric charge analysis, partitioning, integrations, etc. labels Apr 21, 2024

remove response

3f3a438

janosh added the needs testing PRs that are not ready to merge due to lacking tests label Apr 25, 2024

janosh added 2 commits April 25, 2024 11:54

Merge branch 'master' into pr/chiang-yuan/3778

e4ccad6

Merge branch 'master' into fix-chargemol-path

8be153a

chiang-yuan added 3 commits May 15, 2024 12:26

Merge branch 'master' of https://github.com/materialsproject/pymatgen …

2d9ffbc

…into fix-chargemol-path

add missing command_line

43b2385

try to use chargemol precompiled binary

6973b7a

chiang-yuan mentioned this pull request Jun 14, 2024

Chargemol autodownloads #3474

Closed

4 tasks

janosh force-pushed the master branch 2 times, most recently from e3fbc67 to 41e6d99 Compare August 3, 2024 19:01

shyuep closed this Mar 10, 2026

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

bugfix: chargemol runtime directory and `os.path.exists` fix#3778
chiang-yuan wants to merge 14 commits intomaterialsproject:masterfrom
chiang-yuan:fix-chargemol-path

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