Preserve Full Trajectory Information in AnalysisBase

[yuxuanzhuang]

Fixes #4891

Changes made in this Pull Request:
Add self._run_slicer to retrieve global details such as the total number of frames.
Add self._run_frame_index for _single_frame to track the frame index for each frame for the full sliced trajectory that is being analyzed

• create RunConfig to preserve information of run parameters
• create RunState to track information for the whole trajectory slice that is being analyzed.

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4892.org.readthedocs.build/en/4892/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.73%. Comparing base (9cbc8ea) to head (36403f9).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4892   +/-   ##
========================================
  Coverage    92.72%   92.73%           
========================================
  Files          180      180           
  Lines        22475    22505   +30     
  Branches      3190     3191    +1     
========================================
+ Hits         20841    20871   +30     
  Misses        1177     1177           
  Partials       457      457           

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[pep8speaks]

Hello @yuxuanzhuang! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2025-01-14 18:49:12 UTC

[yuxuanzhuang]

I’m not certain that _global_xxx is the most suitable naming convention for these attributes. I’d appreciate any alternative suggestions you might have.

[yuxuanzhuang]

I will work on the documentation if the current implementation seems more logical to you :)

[marinegor]

hey @yuxuanzhuang sorry for delaying response on this one -- I'm slowly getting back to it, and wonder if you indeed need a detailed review here?

I skimmed through the changes and seem to like them (I'm generally a fan of smol specialized classes), but I can look more closely if you need an opinion on the design. And the documentation might come after it.

[yuxuanzhuang]

hey @yuxuanzhuang sorry for delaying response on this one -- I'm slowly getting back to it, and wonder if you indeed need a detailed review here?

I skimmed through the changes and seem to like them (I'm generally a fan of smol specialized classes), but I can look more closely if you need an opinion on the design. And the documentation might come after it.

No worries. I will work on the documentation and pin you when it's done. I might also be slow on it.

[yuxuanzhuang]

@marinegor

I think it’s ready for review now.