Fix numpy boolean frame masks

[sici17]

Fixes #5472

Changes made in this Pull Request:

• Updated AnalysisBase._setup_computation_groups() to recognize both Python bool and NumPy np.bool_ values. NumPy boolean masks are now converted to frame indices correctly.
• Added regression cases in test_base.py for NumPy boolean masks both in serial and multiprocessing scenarios.
• Added a CHANGELOG entry for the fix.
• Documentation changes: clarified boolean frame masks in AnalysisBase.run() and added a 2.11.0 versionchanged note.

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS? (If it is not, add it!)
• I have read and understand the current AI Policy
• LLM/AI disclosure was updated.

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

[read-the-docs-community]

Documentation build overview

📚 MDAnalysis | 🛠️ Build #34811996 | 📁 Comparing 99d4270 against latest (8b8875c)

  🔍 Preview build  

14 files changed · ± 14 modified

± Modified

• index.html
• documentation_pages/analysis/base.html
• documentation_pages/analysis/bat.html
• documentation_pages/analysis/density.html
• documentation_pages/analysis/dihedrals.html
• documentation_pages/analysis/dssp.html
• documentation_pages/analysis/hydrogenbonds.html
• documentation_pages/analysis/msd.html
• documentation_pages/analysis/nucleicacids.html
• documentation_pages/analysis/pca.html
• and 4 more...

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.87%. Comparing base (8b8875c) to head (99d4270).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5476   +/-   ##
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  Coverage    93.87%   93.87%           
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  Files          182      182           
  Lines        22522    22522           
  Branches      3206     3206           
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  Hits         21143    21143           
  Misses         917      917           
  Partials       462      462           

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[orbeckst]

Can you describe in your own words how you've been using AI tools here?

[orbeckst]

Please also update the docs for frame to state explicitly that boolean fancy indexing is supported; add a versionchanged. Check if there are other places in the docs that may need to be updated.

Check the User Guide https://github.com/MDAnalysis/UserGuide/, too, and either make changes via PR or at least raise an issue. The User Guide needs to be kept update with important user-facing updates.

Please also describe briefly in your own words how AI tools were used and what tools you used.

Thank you!

[sici17]

Can you describe in your own words how you've been using AI tools here?

I use ai like a personal mentor, I ask questions to understand the problem, locate the parts of code that matter, discuss possible solutions and documentation changes. I reviewed the changes, asked questions until I understood them, and made the final decisions myself. Since English is not my native language, I also used it to help express what is happening much better than I could ever do. My main goal is understanding how the code works and how to move inside such a big codebase.

[orbeckst]

@sici17 , please have any issues/PRs in the User Guide mention this PR (MDAnalysis/mdanalysis#5476) so that it gets linked automatically and we're seeing that you're also addressing the other parts of #5476 (review)