Fix mypy linter check

[PardhavMaradani]

Fixes #5177, Fixes #4581

Changes made in this Pull Request:

• Fix the mypy error in lib/util.py
• Unpin rdkit
  • The original openfe issue #844 that required this pinning is since fixed
• Unpin numpy
  • This seems to be a carry forward from the past as mypy (for the currently enabled files) seems to work with current version

The root cause of this issue seems to be the rdkit pinning. We use full-deps: true at other places in our tests and they all take a few seconds, where as the one for mypy, which has the rdkit pinned takes over 10 mins, leading to the timeout. Here is a run with the pinned version that times out and an unpinned run that takes only a few seconds (that is the only diff between these two runs). From earlier testing, it seems like mypy doesn't require full-deps to be true, but didn't change it for now as the install issue is now resolved.

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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📚 Documentation preview 📚: https://mdanalysis--5185.org.readthedocs.build/en/5185/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.73%. Comparing base (9fb8b0a) to head (9556a85).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #5185   +/-   ##
========================================
  Coverage    92.72%   92.73%           
========================================
  Files          180      180           
  Lines        22472    22472           
  Branches      3188     3188           
========================================
+ Hits         20838    20839    +1     
  Misses        1176     1176           
+ Partials       458      457    -1     

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