added parallelization in analysis.dihedrals

[orbeckst]

Fixes #4673

Changes made in this Pull Request:

• parallelized Dihedral, Ramachandran, Janin
• added tests (including fixtures in analysis/conftest.py)
• update 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--4682.org.readthedocs.build/en/4682/

[pep8speaks]

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

• In the file package/MDAnalysis/analysis/rms.py:

Line 430:80: E501 line too long (80 > 79 characters)

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

Line 114:1: W293 blank line contains whitespace

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

Line 46:5: E303 too many blank lines (2)
Line 61:80: E501 line too long (80 > 79 characters)
Line 106:80: E501 line too long (92 > 79 characters)
Line 114:80: E501 line too long (82 > 79 characters)

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

Line 270:80: E501 line too long (105 > 79 characters)
Line 284:80: E501 line too long (105 > 79 characters)

Comment last updated at 2024-09-26 01:12:30 UTC

[github-actions]

Linter Bot Results:

Hi @orbeckst! 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/11043710893/job/30678437633

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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 93.52%. Comparing base (8939b3e) to head (8fa8d5f).
Report is 2 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4682      +/-   ##
===========================================
- Coverage    93.54%   93.52%   -0.03%     
===========================================
  Files          173      185      +12     
  Lines        21439    22517    +1078     
  Branches      3983     3985       +2     
===========================================
+ Hits         20056    21058    +1002     
- Misses         929     1004      +75     
- Partials       454      455       +1     

Flag	Coverage Δ
	93.15% <ø> (?)

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[orbeckst]

@yuxuanzhuang could you please shepherd the PR to completion? Thanks!

(When you squash-merge, please write a nice log message such as

* Fixes #4673
* Changes made in this Pull Request:
    - parallelized Dihedral, Ramachandran, Janin
    - added tests (including fixtures in analysis/conftest.py)
    - update CHANGELOG

Co-authored: ...

and keep the co-author line(s), in particular @talagayev ! Thanks!)

[yuxuanzhuang]

lgtm! Thank @talagayev for your help as well!

[talagayev]

Nice, happy to help :)