'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

• 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--4727.org.readthedocs.build/en/4727/

[github-actions]

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 2024-10-23 00:47:12 UTC

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.62%. Comparing base (740e74e) to head (c68cb84).
Report is 7 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4727      +/-   ##
===========================================
+ Coverage    93.55%   93.62%   +0.07%     
===========================================
  Files          173      187      +14     
  Lines        21463    22634    +1171     
  Branches      3987     3023     -964     
===========================================
+ Hits         20080    21192    +1112     
- Misses         929      998      +69     
+ Partials       454      444      -10     

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[yuxuanzhuang]

Looking good! Could you also help fix the pep8?

[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 :)

[yuxuanzhuang]

lgtm!

[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.)