'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:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2024-10-18 21:03:42 UTC