Change error to warning on Universe creation

MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

https://mdanalysis.org

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Change error to warning on Universe creation #4754

Closed lilyminium closed 4 weeks ago

lilyminium commented 1 month ago

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

[x] Tests?
[x] Docs?
[x] CHANGELOG updated?
[x] Issue raised/referenced?

Developers certificate of origin

[x] 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 commented 1 month ago

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! :beers:

Comment last updated at 2024-10-25 04:49:48 UTC

IAlibay commented 1 month ago

@lilyminium can you point out to which specific sub-issue you're fixing under https://github.com/MDAnalysis/mdanalysis/issues/4748?

lilyminium commented 1 month ago

I've edited my comment, thanks

IAlibay commented 1 month ago

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

lilyminium commented 1 month ago

There's already a test for numpy arrays but sure

codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

```diff @@ 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 commented 4 weeks ago

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

lilyminium commented 4 weeks ago

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