Convert "Quantity" to raw value for kinetic_energy and potential_energy in OpenMM reader

MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

https://mdanalysis.org

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Convert "Quantity" to raw value for kinetic_energy and potential_energy in OpenMM reader #4548

Closed orionarcher closed 6 months ago

orionarcher commented 6 months ago

Changes made in this Pull Request:

added .value to kinetic_energy and potential_energy

This is breaking the ability of a downstream MDAkit to write H5MD files. Issue here. I suspect it is more generally breaking the ability to take in OpenMM and output H5MD, but it is only in openmm-reporter that I came across it.

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.

📚 Documentation preview 📚: https://mdanalysis--4548.org.readthedocs.build/en/4548/

github-actions[bot] commented 6 months ago

Linter Bot Results:

Hi @orionarcher! 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	⚠️ Possible failure
testsuite	✅ Passed

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/8495207361/job/23271241401

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

codecov[bot] commented 6 months ago

Codecov Report

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

Project coverage is 93.64%. Comparing base (a2a27aa) to head (54e5664).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #4548 +/- ## =========================================== - Coverage 93.66% 93.64% -0.03% =========================================== Files 168 180 +12 Lines 21248 22327 +1079 Branches 3917 3917 =========================================== + Hits 19902 20908 +1006 - Misses 888 961 +73 Partials 458 458 ```

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pep8speaks commented 6 months ago

Hello @orionarcher! 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: