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--4834.org.readthedocs.build/en/4834/

[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 8 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (f4e0f0b) to head (f6f7a4b).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/analysis/encore/similarity.py	75.00%	0 Missing and 3 partials ⚠️
package/MDAnalysis/analysis/base.py	0.00%	1 Missing and 1 partial ⚠️
package/MDAnalysis/topology/ITPParser.py	33.33%	1 Missing and 1 partial ⚠️
package/MDAnalysis/analysis/align.py	66.66%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4834      +/-   ##
===========================================
- Coverage    93.68%   93.63%   -0.06%     
===========================================
  Files          177      189      +12     
  Lines        21743    22829    +1086     
  Branches      3055     3065      +10     
===========================================
+ Hits         20370    21375    +1005     
- Misses         927     1002      +75     
- Partials       446      452       +6     

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[RMeli]

Thank you @tanishy7777, LGTM!

[RMeli]

Can you please fix the conflict on the CHANGELOG?

[tanishy7777]

Can you please fix the conflict on the CHANGELOG?

Yes, I have fixed it

[RMeli]

Thanks @tanishy7777, much appreciated!