Fix for issue #4655 Removing mutable data structures and function calls as default arguments in the entire codebase

[tanishy7777]

Fixes #4655

Changes made in this Pull Request:

• Removing mutable data structures and function calls as default arguments in the entire codebase and initializing/calling them inside the function instead
• There were 12 issues found using the ruff module(select = B006, B008 and ignore=E501) which were all fixed

PR Checklist

• Tests
• 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--4810.org.readthedocs.build/en/4810/

[github-actions]

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[tanishy7777]

Before and after the changes were made (results below are from pytest tests in the testsuite)
Before

After the changes

[codecov]

Codecov Report

Attention: Patch coverage is 57.14286% with 12 lines in your changes missing coverage. Please review.

Project coverage is 86.37%. Comparing base (905f197) to head (dc712ac).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/analysis/encore/similarity.py	62.50%	0 Missing and 3 partials ⚠️
package/MDAnalysis/analysis/base.py	0.00%	1 Missing and 1 partial ⚠️
package/MDAnalysis/analysis/helix_analysis.py	66.66%	1 Missing and 1 partial ⚠️
package/MDAnalysis/core/universe.py	0.00%	2 Missing ⚠️
package/MDAnalysis/topology/ITPParser.py	33.33%	1 Missing and 1 partial ⚠️
package/MDAnalysis/analysis/align.py	66.66%	0 Missing and 1 partial ⚠️

❗ There is a different number of reports uploaded between BASE (905f197) and HEAD (dc712ac). Click for more details.

HEAD has 2 uploads less than BASE

Flag	BASE (905f197)	HEAD (dc712ac)
	7	5

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4810      +/-   ##
===========================================
- Coverage    93.68%   86.37%   -7.31%     
===========================================
  Files          177      189      +12     
  Lines        21742    22832    +1090     
  Branches      3055     3067      +12     
===========================================
- Hits         20369    19722     -647     
- Misses         927     2671    +1744     
+ Partials       446      439       -7     

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[RMeli]

Can you please detail how the error raised in #4810 (comment) is related to the changes?

[tanishy7777]

Can you please detail how the error raised in #4810 (comment) is related to the changes?

I am not sure why the error got resolved, but after making the changes it got solved.

According to the file test_encore from which the error was generated from, the function can result in failure sometimes because the function involves generating random numbers.

[tanishy7777]

I have added the changes that you have mentioned @RMeli