search

Molara-Lab / Molara

Molara is a Python package for the visualization of chemical structures such as molecules or crystals. It provides a graphical user interface for importing structures from output files of popular computational chemistry software as well as for creating custom structures.
GNU General Public License v3.0
11 stars 0 forks source link

Add .log and .trj to xyzimporter for importing trajectories #367

Closed Michel-Heinz closed 2 months ago

Michel-Heinz commented 2 months ago

Added the ability to parse .log and .trj files by using the same code as the xyz importer

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago

Walkthrough

The update introduces support for ".trj" and ".log" file extensions in the XyzImporter class, enhancing the file compatibility of the Molara molecular visualization tool.

Changes

File Path Change Summary
src/.../io/importer.py Added support for ".trj" and ".log" extensions in XyzImporter class.

Possibly related issues

🐰✨ In the code's woven nest, A fix to make Molara best. ".log" and ".trj" now friends, In digital fields where data bends. Hoppity hop, the bugs we chase, With every line, we set the pace! 🌟📚

Recent Review Details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 86ed36768acaa831ed6f2406f266a266e712ce2c and 0251ebe1e4292e19ceb457097a012548d3a0a5ec.
Files selected for processing (1) * src/molara/Structure/io/importer.py (1 hunks)
Additional comments not posted (1)
src/molara/Structure/io/importer.py (1)
`446-447`: Verify the capability of `XyzImporter` to handle ".trj" and ".log" files. It appears that the `XyzImporter` class is now configured to handle ".trj" and ".log" files. However, there are no changes in the `XyzImporter` class itself to specifically support these new file types. Please ensure that `XyzImporter` is fully capable of processing these formats correctly, or consider implementing the necessary adjustments.
--- 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](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)
Tips ### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit .` - `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](https://docs.coderabbit.ai/guides/configure-coderabbit) 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](https://coderabbit.ai/docs) for detailed information on how to use CodeRabbit. - Join our [Discord Community](https://discord.com/invite/GsXnASn26c) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.
codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 71.70%. Comparing base (86ed367) to head (0251ebe).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #367 +/- ## ======================================= Coverage 71.70% 71.70% ======================================= Files 40 40 Lines 3463 3463 ======================================= Hits 2483 2483 Misses 980 980 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.