'MDAnalysis.analysis.nucleicacids' parallelization

[talagayev]

Fixes #4670 attempt

Changes made in this Pull Request:

• added backends and aggregators to NucPairDist in analysis.nucleicacids
• added the client_NucPairDist in conftest.py
• added client_NucPairDist in run() in test_nucleicacids.py

Here the Error:

AttributeError: 'WatsonCrickDist' object has no attribute '_res_array' appears for all of the tests where the client_NucPairDist is used, same goes not only for WatsonCrickDist, but also for MinorPairDist and MajorPairDist.

I am a little bit stuck, since I am not sure if I need to modify the analysis.nucleicacids to fix this error, thus I made this PR as a draft to get more input and ideas how to fix this issue :)

PR Checklist

• [x] Tests?
• [ ] Docs?
• [ ] CHANGELOG updated?
• [x] Issue raised/referenced?

Developers certificate of origin

• [x] 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.

---

📚 Documentation preview 📚: https://mdanalysis--4727.org.readthedocs.build/en/4727/

[github-actions[bot]]

Linter Bot Results:

Hi @talagayev! Thanks for making this PR. We linted your code and found the following:

There are currently no issues detected! 🎉

[pep8speaks]

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

• In the file package/MDAnalysis/analysis/nucleicacids.py:

Line 178:1: W293 blank line contains whitespace

Comment last updated at 2024-12-14 22:05:51 UTC

[codecov[bot]]

Codecov Report

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

Project coverage is 93.63%. Comparing base (c6bfa09) to head (482c6c9). Report is 45 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4727      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          177      189      +12     
  Lines        21763    22833    +1070     
  Branches      3065     3065              
===========================================
+ Hits         20382    21379     +997     
- Misses         929     1002      +73     
  Partials       452      452              

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[talagayev]

Looking good! Could you also help fix the pep8?

Yes, I have now access again to a PC, although with slow internet, so I will adjust it for pep8 and also add the additional stuff that is missing (changelog etc.).

I would also create an additional PR draft for analysis.align, since there I am not sure if it can be parallelized :)

[orbeckst]

@yuxuanzhuang thanks for the review. Could you please shepherd the PR to completion?

(I think we're in feature-freeze for 2.8.0 #4733 but check the issue for updates.)

[talagayev]

@yuxuanzhuang for this one, since it is also approved it can be merged, but now with the new release the CHANGELOG also changes. should I modify it?

If yes would it be then 2.9.0

[talagayev]

Hey @IAlibay, perfect sounds good 😸

[talagayev]

Alright you're good to go @talagayev - just update against develop and it should be ok (I'm approving as "unblock" I didn't actually read the contents of this PR sorry).

Updated it, should be ready :) All good, was mainly the parallelization implementation similar to some other PR request that I did, with @yuxuanzhuang looking at them

[talagayev]

Ah need to move it to 2.9.0 in the CHANGELOG, will do it now

[orbeckst]

@yuxuanzhuang I think this one is good to go but please have a last look over.

[yuxuanzhuang]

@talagayev Thanks for your contribution!

[talagayev]

@talagayev Thanks for your contribution!

Happy to help :) and thanks to you too, for helping with the PR :)