[fmt] lib

[RMeli]

Format MDAnalysis/lib and MDAnalysisTests/lib.

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--4804.org.readthedocs.build/en/4804/

[pep8speaks]

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

• In the file package/MDAnalysis/lib/correlations.py:

Line 166:56: E203 whitespace before ':'

• In the file package/MDAnalysis/lib/distances.py:

Line 183:1: E402 module level import not at top of file

• In the file package/MDAnalysis/lib/util.py:

Line 399:80: E501 line too long (80 > 79 characters)
Line 434:16: E713 test for membership should be 'not in'
Line 448:80: E501 line too long (80 > 79 characters)
Line 1180:50: E203 whitespace before ':'
Line 1598:80: E501 line too long (102 > 79 characters)
Line 2285:50: E203 whitespace before ':'

• In the file testsuite/MDAnalysisTests/lib/test_distances.py:

Line 934:37: E203 whitespace before ':'
Line 960:37: E203 whitespace before ':'

• In the file testsuite/MDAnalysisTests/lib/test_util.py:

Line 1013:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-11-30 22:14:39 UTC

[IAlibay]

Some quick comments.

[RMeli]

Thanks @IAlibay for the comments. In this one we indeed have a few oddities that should be discussed. Some are probably OK but I wanted a second opinion, others should stay as they were, and a few ugly things are likely caused by inconsistent use of trailing commas in multi-dimensional arrays (so should be fixable by removing the trailing comma).

[codecov]

Codecov Report

Attention: Patch coverage is 90.06211% with 32 lines in your changes missing coverage. Please review.

Project coverage is 86.41%. Comparing base (557f27d) to head (c264f8e).
Report is 2 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/lib/util.py	88.99%	7 Missing and 5 partials ⚠️
package/MDAnalysis/lib/distances.py	92.45%	4 Missing and 4 partials ⚠️
package/MDAnalysis/lib/pkdtree.py	79.16%	4 Missing and 1 partial ⚠️
package/MDAnalysis/lib/transformations.py	86.20%	3 Missing and 1 partial ⚠️
package/MDAnalysis/lib/_distopia.py	50.00%	2 Missing ⚠️
package/MDAnalysis/lib/picklable_file_io.py	96.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4804      +/-   ##
===========================================
+ Coverage    86.08%   86.41%   +0.33%     
===========================================
  Files          177      189      +12     
  Lines        21742    22808    +1066     
  Branches      3055     3055              
===========================================
+ Hits         18717    19710     +993     
- Misses        2593     2666      +73     
  Partials       432      432              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[marinegor]

I've added suggestions removing/adding trailing commas when necessary -- it seems that all the "old is better than new" can be resolved with them (plus some extra newlines where necessary), except for one case in tests with the 3x3 matrix formatting with concrete numbers.

[RMeli]

CI failures are likely un-related to this PR since they showed up also on #4812.

[RMeli]

Merging because the issues with RDKit are known and un-related to this PR.

#4813 #4824