Implementation of parallelization to MDAnalysis.analysis.dssp

[talagayev]

Fixes #4674

Changes made in this Pull Request:

• Parallelization of the backend support to the class DSSP in dssp.py
• Addition of versionchanged to mention the addition of the parallelization
• Addition of parallelization tests in test_dssp.py and fixtures in conftest.py
• Updated Changelog

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--4721.org.readthedocs.build/en/4721/

[pep8speaks]

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

• In the file testsuite/MDAnalysisTests/analysis/conftest.py:

Line 138:1: W293 blank line contains whitespace

Comment last updated at 2024-10-07 17:46:24 UTC

[github-actions]

Linter Bot Results:

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

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	✅ Passed
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/11221046796/job/31190523020

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Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.53%. Comparing base (474be5b) to head (3c6cbec).
Report is 55 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4721      +/-   ##
===========================================
- Coverage    93.55%   93.53%   -0.02%     
===========================================
  Files          173      185      +12     
  Lines        21457    22529    +1072     
  Branches      3986     3987       +1     
===========================================
+ Hits         20074    21073     +999     
- Misses         929     1002      +73     
  Partials       454      454              

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[yuxuanzhuang]

lgtm!

[talagayev]

I would have then also have a quick question:
for example when I try to add the parallelization to desnity.py for the DensityAnalysisI get this during the test_density.py pytests as a Failure message for test_userdefn_boxshape:

AttributeError: 'DensityAnalysis' object has no attribute '_grid'

I am not sure how to fix such cases, should I just create a PR so that the reviewers can take a look at it and suggest a fix?

[RMeli]

@talagayev it would help to see the full backtrace for the error, otherwise it's a bit hard to help.

should I just create a PR so that the reviewers can take a look at it and suggest a fix?

This might be useful if you are planning to work on it regardless. You can open a PR as "draft", to make it explicitly it is work in progress but want early feedback/need some help/want to test in CI.

[talagayev]

@talagayev it would help to see the full backtrace for the error, otherwise it's a bit hard to help.

should I just create a PR so that the reviewers can take a look at it and suggest a fix?

This might be useful if you are planning to work on it regardless. You can open a PR as "draft", to make it explicitly it is work in progress but want early feedback/need some help/want to test in CI.

hey @RMeli, perfect that is what i was looking for, thanks :) I will then create the PR as a draft to get some feedback, since there are also some other cases like MDAnalysis.analysis.align where I tried to parallelize them and think that they are not possible to parallelize, but I can then also create a draft PR with the Failure message, so that I get feedback if I am correct that they can not be parallelized and then adjust everything to mark them as unparallelizable :)

[orbeckst]

@talagayev can you please resolve conflicts?

@yuxuanzhuang can you please squash-merge when you're happy (please also write a good log messages — see, for example, PR #4718 )

[talagayev]

@orbeckst @yuxuanzhuang sorry for the late replies, I am on holiday currently till mid of next week and thus have only sometimes access to the laptop 🙈

@yuxuanzhuang should I do anything else or now that you merged the development branch into the PR branch it is ready to be merged? :)

[yuxuanzhuang]

@talagayev I’ll take care of it, no worries! You’ve been incredibly helpful in moving this forward, no need to apologize!

[talagayev]

@yuxuanzhuang Nice, thanks to you too for looking into the PR's and helping with them :)

I would then create the couple of PR's as drafts today for some functions where I am not sure if they can be parallelized so that you and the other core devs can take a look into it and give your opinions, since I have them prepared locally and am at the laptop right now.

Happy to help :)