Add ruff for linter and formatting

[BradyAJohnston]

• cleanup code with ruff
• add ruff GHA
• some cleanup
• fix some problems
• fix lint problems

[codecov]

Codecov Report

Attention: Patch coverage is 64.39716% with 251 lines in your changes missing coverage. Please review.

Project coverage is 74.99%. Comparing base (e18b144) to head (a5853c2).
Report is 35 commits behind head on main.

❗ Current head a5853c2 differs from pull request most recent head 3f2ade8

Please upload reports for the commit 3f2ade8 to get more accurate results.

Files	Patch %	Lines
molecularnodes/utils.py	30.00%	28 Missing ⚠️
molecularnodes/pkg.py	34.28%	23 Missing ⚠️
molecularnodes/ui/node_menu.py	47.72%	23 Missing ⚠️
molecularnodes/io/md.py	16.00%	21 Missing ⚠️
molecularnodes/ui/panel.py	34.48%	19 Missing ⚠️
molecularnodes/io/parse/cif.py	36.00%	16 Missing ⚠️
molecularnodes/io/wwpdb.py	38.09%	13 Missing ⚠️
molecularnodes/io/local.py	20.00%	12 Missing ⚠️
molecularnodes/ui/func.py	14.28%	12 Missing ⚠️
molecularnodes/blender/bones.py	33.33%	10 Missing ⚠️
... and 16 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #508      +/-   ##
==========================================
- Coverage   75.70%   74.99%   -0.72%     
==========================================
  Files          41       41              
  Lines        3742     3783      +41     
==========================================
+ Hits         2833     2837       +4     
- Misses        909      946      +37     

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[BradyAJohnston]

Ruff already implemented, will formalise in a newer cleaner PR.