correct existing linting errors

[mgiulini]

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Closes #647

[codecov-commenter]

Codecov Report

Patch coverage: 85.71% and project coverage change: -0.32 ⚠️

Comparison is base (33b5155) 74.58% compared to head (cd3793c) 74.26%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #649      +/-   ##
==========================================
- Coverage   74.58%   74.26%   -0.32%     
==========================================
  Files         111      111              
  Lines        7565     7565              
==========================================
- Hits         5642     5618      -24     
- Misses       1923     1947      +24     

Impacted Files	Coverage Δ
src/haddock/clis/cli_analyse.py	73.75% <ø> (ø)
src/haddock/libs/libalign.py	67.85% <0.00%> (ø)
src/haddock/libs/libplots.py	96.17% <ø> (ø)
src/haddock/modules/analysis/caprieval/capri.py	82.39% <ø> (ø)
src/haddock/modules/analysis/clustrmsd/__init__.py	90.99% <ø> (ø)
tests/test_module_clustrmsd.py	100.00% <ø> (ø)
src/haddock/__init__.py	96.29% <100.00%> (ø)
tests/test_cli_analyse.py	97.77% <100.00%> (ø)
tests/test_libalign.py	100.00% <100.00%> (ø)
tests/test_module_flexref.py	100.00% <100.00%> (ø)

... and 3 files with indirect coverage changes

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[rvhonorato]

I've fixed all the versions in the ci pipeline, I don't know if there was a reson for them to not be fixed or if it was just a mistake 🔮

there were also some linting issues that I've added FIXME or noqa, imo we should not be waisting time doing this manually when there are ways to automate this code formating.