Change error to warning on Universe creation

[lilyminium]

Fixes #4750

Changes made in this Pull Request:

• This changes the error to a warning on Universe creation for types and masses guessing, which is set by default.
• Also fixes something I noticed about kwargs not getting passed into bond guessing.
• And Universe kwargs were getting passed into guessing when they're documented as being for topologies.

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.

[pep8speaks]

Hello @lilyminium! 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 2024-10-25 04:49:48 UTC

[IAlibay]

@lilyminium can you point out to which specific sub-issue you're fixing under #4748?

[lilyminium]

I've edited my comment, thanks

[IAlibay]

Can you please add in the test from #4750 if it's fixing it too?

[lilyminium]

There's already a test for numpy arrays but sure

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.63%. Comparing base (101008b) to head (43a7aee).
Report is 2 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4754      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          175      187      +12     
  Lines        21564    22640    +1076     
  Branches      3023     3024       +1     
===========================================
+ Hits         20195    21198    +1003     
- Misses         925      998      +73     
  Partials       444      444              

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[orbeckst]

@lilyminium I am assigning the PR to you. You'll know best when to merge.

[lilyminium]

Thanks for the review @orbeckst! I've made some markup changes.

[orbeckst]

Lgtm — but other reviews welcome!

[yuxuanzhuang]

lgtm!