Fix rdkit tests

[IAlibay]

Fixes #4624

Changes made in this Pull Request:

• Update coordinate checks
• Remove numpy >=2 skips (latest release supports numpy 2.0)

PR Checklist

• Tests?
• Docs?
• 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--4640.org.readthedocs.build/en/4640/

[pep8speaks]

Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2024-07-23 22:28:45 UTC

[github-actions]

Linter Bot Results:

Hi @IAlibay! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	✅ Passed
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/10067283837/job/27830432992

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Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.59%. Comparing base (1bf58cc) to head (1378d5c).
Report is 34 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4640      +/-   ##
===========================================
- Coverage    93.61%   93.59%   -0.03%     
===========================================
  Files          171      183      +12     
  Lines        21250    22316    +1066     
  Branches      3936     3936              
===========================================
+ Hits         19893    20886     +993     
- Misses         898      971      +73     
  Partials       459      459              

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[IAlibay]

The test is inherently flawed because we know that even at a fixed seed the conformer generation will differ on different machines (it's caused trouble elsewhere). We should just test against on the fly generated coordinates.

[RMeli]

Mmmh... Not sure why I enabled auto-merge here (I didn't realize)... The few failures in CI are the usual timeouts.