'MDAnalysis.analysis.density' parallelization

[talagayev]

Fixes #4677 attempt

Changes made in this Pull Request:

• added backends and aggregators to DensityAnalysis in analysis.density
• added client_DensityAnalysis in conftest.py
• added client_DensityAnalysis to the tests in test_density.py

Here again I am not sure for this case, since the Error message:

AttributeError: 'DensityAnalysis' object has no attribute '_grid' appears in the tests and I am not sure if moving _grid and all the code necessary for it from _prepare to __init__ will fix the case like it was the case in #4718

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--4729.org.readthedocs.build/en/4729/

[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/density.py:

Line 402:1: W293 blank line contains whitespace
Line 406:1: W293 blank line contains whitespace
Line 495:9: E122 continuation line missing indentation or outdented
Line 495:42: E231 missing whitespace after ','
Line 497:1: W293 blank line contains whitespace

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

Line 148:1: W293 blank line contains whitespace

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

Line 384:80: E501 line too long (83 > 79 characters)
Line 396:80: E501 line too long (87 > 79 characters)

Comment last updated at 2024-10-10 00:35:03 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	⚠️ Possible failure
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/11265261686/job/31326801780

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.53%. Comparing base (740e74e) to head (d335131).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4729      +/-   ##
===========================================
- Coverage    93.55%   93.53%   -0.02%     
===========================================
  Files          173      185      +12     
  Lines        21463    22534    +1071     
  Branches      3987     3988       +1     
===========================================
+ Hits         20080    21078     +998     
- Misses         929     1002      +73     
  Partials       454      454              

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[yuxuanzhuang]

Three aspects in my fix.

• Attributes (private or not) that will be used later in _conclude should be defined in __init__, not in _prepare. @marinegor, I think it would be helpful to explicitly mention this in the documentation. Additionally, while the illustrative figure (https://docs.mdanalysis.org/dev/documentation_pages/analysis/parallelization.html#split-apply-combine) suggests that _prepare occurs before splitting, this is not the case.

• The _edges and similar attributes must be defined in __init__ by nature because they need to be consistent across all workers and are determined based on the current positions of the atomgroup (https://github.com/MDAnalysis/mdanalysis/pull/4729/files#diff-28b7c110c6231f9f2ea864bbdecb9cb485edbed494d7e266d37896bde7b50b0dR421) .

• The results being aggregated are actually _grid, not Density—Density serves more as a postprocessing step that summarizes the information.

[orbeckst]

@yuxuanzhuang could you please raise issues for the updates to the parallelization documentation (#4729 (comment)) — I think that's very important to make clear, given that we are now repeatedly running in these issues. Thank you!

[marinegor]

@yuxuanzhuang thanks, the illustration is indeed wrong, as well as the accompanying text. I fixed them in #4760