Bump pymatgen from 2025.2.18 to 2025.3.10

[dependabot]

Bumps pymatgen from 2025.2.18 to 2025.3.10.

Release notes

Sourced from pymatgen's releases.

v2025.3.10

1. PR #3680 - Add support for vaspout.h5, improvements to POTCAR handling by @​esoteric-ephemera

   • Added support for parsing vaspout.h5 and improvements in POTCAR handling.
   • Major additions include methods for processing vaspout.h5 and ensuring compatibility with existing VASP I/O infrastructure.

2. PR #4319 - Update abitimer in io.abinit by @​gpetretto

   • Fixes parsing issues for newer versions of Abinit.
   • Updates compatibility with pandas > 2 and includes test files for validation.

3. PR #4315 - Patch to allow pyzeo integration by @​daniel-sintef

   • Provides a patch to swap out zeo++ with pyzeo, which is a more actively maintained version.

4. PR #4281 - Add method to get the Pearson symbol to SpaceGroupAnalyzer by @​CompRhys

   • Introduced a new method to retrieve the Pearson Symbol in SpaceGroupAnalyzer.

5. PR #4295 - Pass kwargs to IStructure.to method in JSON format by @​DanielYang59

   • Provides finer control over json.dumps behavior during format conversion.

6. PR #4306 - IStructure.to defaults to JSON when filename is unspecified by @​DanielYang59

   • Adjusts default file output behavior to JSON.

7. PR #4297 - Bugfix for Structure/ase.Atoms interconversion by @​wolearyc

   • Ensures deep copying to avoid shared memory issues between Atoms.info and Structure.properties.

8. PR #4304 - MagneticStructureEnumerator: Expose max_orderings argument by @​mkhorton

   • Makes max_orderings configurable via keyword argument.

9. PR #4299 - Update inequality in get_linear_interpolated_value by @​kavanase

   • Fixes interpolation logic to handle edge cases more robustly.

Changelog

Sourced from pymatgen's changelog.

v2025.3.10

1. PR #3680 - Add support for vaspout.h5, improvements to POTCAR handling by @​esoteric-ephemera

   • Added support for parsing vaspout.h5 and improvements in POTCAR handling.
   • Major additions include methods for processing vaspout.h5 and ensuring compatibility with existing VASP I/O infrastructure.

2. PR #4319 - Update abitimer in io.abinit by @​gpetretto

   • Fixes parsing issues for newer versions of Abinit.
   • Updates compatibility with pandas > 2 and includes test files for validation.

3. PR #4315 - Patch to allow pyzeo integration by @​daniel-sintef

   • Provides a patch to swap out zeo++ with pyzeo, which is a more actively maintained version.

4. PR #4281 - Add method to get the Pearson symbol to SpaceGroupAnalyzer by @​CompRhys

   • Introduced a new method to retrieve the Pearson Symbol in SpaceGroupAnalyzer.

5. PR #4295 - Pass kwargs to IStructure.to method in JSON format by @​DanielYang59

   • Provides finer control over json.dumps behavior during format conversion.

6. PR #4306 - IStructure.to defaults to JSON when filename is unspecified by @​DanielYang59

   • Adjusts default file output behavior to JSON.

7. PR #4297 - Bugfix for Structure/ase.Atoms interconversion by @​wolearyc

   • Ensures deep copying to avoid shared memory issues between Atoms.info and Structure.properties.

8. PR #4304 - MagneticStructureEnumerator: Expose max_orderings argument by @​mkhorton

   • Makes max_orderings configurable via keyword argument.

9. PR #4299 - Update inequality in get_linear_interpolated_value by @​kavanase

   • Fixes interpolation logic to handle edge cases more robustly.

Commits

• 55d0934 Update docs
• 80d1045 Updated changelog.
• f91f8d5 Add support for vaspout.h5, improvements to potcar handling (#3680)
• 4e2cb01 update abitimer (#4319)
• afa6652 Fix mypy for zeo.
• 4d9e503 patch to allow pyzeo to work (#4315)
• 9523e3c Add method to get the Pearson symbol to SpaceGroupAnalyzer (#4281)
• 4ca6092 Bump nokogiri from 1.16.5 to 1.18.3 in /docs (#4294)
• 0cd9684 Pass kwargs to IStructure.to method in JSON format (#4295)
• 82a4336 IStructure.to default to JSON when filename not specified (#4306)
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[coderabbitai]

Important

Review skipped

Bot user detected.

To trigger a single review, invoke the @coderabbitai review command.

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ 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>, please review it.
  • 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 gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @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.
  • @coderabbitai help me debug CodeRabbit configuration file.

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 using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai generate docstrings to generate docstrings for this PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration 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.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.10%. Comparing base (b3f0e39) to head (867411e).
Report is 11 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #333   +/-   ##
=======================================
  Coverage   83.10%   83.10%           
=======================================
  Files          25       25           
  Lines        1859     1859           
=======================================
  Hits         1545     1545           
  Misses        314      314           

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

🚀 New features to boost your workflow:

• ❄ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.