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

[chiang-yuan]

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 #3474

Checklist

• [x] Google format doc strings added. Check with ruff.
• [x] 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[bot]]

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 e4ccad6223403e92e17e8038cb5c502dbc185e01 and 8be153adcd4b25029d84cba12593ebc97a064916.

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

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share

• X
• Mastodon
• Reddit
• LinkedIn

Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai generate interesting stats about this repository and render them as a table.
  • @coderabbitai show all the console.log statements in this repository.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (invoked as PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger a review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai help to get help.

Additionally, you can add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.

CodeRabbit Configration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.

[chiang-yuan]

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