'MDAnalysis.analysis.align' parallelization

[talagayev]

Fixes #4659 attempt

Changes made in this Pull Request:

• added backends and aggregators to AlignTraj and AverageStructure in analysis.align.
• added the client_AlignTraj and client_AverageStructure in conftest.py
• added client_AlignTraj and client_AverageStructure in run() in test_align.py

Currently for AlignTraj it only accepts serial and dask with multiprocessing leading to the pytests taking forever. An additional error that appears is the following:

OSError: File opened in mode: self.mode. Reading only allow in mode "r"

For AverageStructure the Failure that appears is the following:

AttributeError: 'numpy.ndarray' object has no attribute 'load_new'

Which leads me to believe that AverageStructure can not be parallelized, but I would need additional opinions on it and on AlignTraj :)

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--4738.org.readthedocs.build/en/4738/

[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/test_align.py:

Line 310:80: E501 line too long (86 > 79 characters)
Line 327:80: E501 line too long (87 > 79 characters)
Line 333:80: E501 line too long (97 > 79 characters)
Line 357:80: E501 line too long (85 > 79 characters)
Line 377:80: E501 line too long (91 > 79 characters)

Comment last updated at 2025-01-11 21:40:18 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 93.33333% with 1 line in your changes missing coverage. Please review.

Project coverage is 86.40%. Comparing base (bdfb2c9) to head (c37add2).

Files with missing lines	Patch %	Lines
package/MDAnalysis/analysis/align.py	93.33%	0 Missing and 1 partial ⚠️

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HEAD has 2 uploads less than BASE

Flag	BASE (bdfb2c9)	HEAD (c37add2)
	7	5

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4738      +/-   ##
===========================================
- Coverage    93.66%   86.40%   -7.26%     
===========================================
  Files          177      189      +12     
  Lines        21795    22874    +1079     
  Branches      3067     3068       +1     
===========================================
- Hits         20414    19765     -649     
- Misses         929     2670    +1741     
+ Partials       452      439      -13     

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