Do not use deprecated OpenFF Toolkit iterator

mosdef-hub / foyer

A package for atom-typing as well as applying and disseminating forcefields

https://foyer.mosdef.org

MIT License

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Do not use deprecated OpenFF Toolkit iterator #541

Closed mattwthompson closed 1 year ago

mattwthompson commented 1 year ago

PR Summary:

Topology.topology_atoms was deprecated in 0.11.0 and will be removed in the forthcoming 0.14.0 release.

PR Checklist

[ ] Includes appropriate unit test(s)
[ ] Appropriate docstring(s) are added/updated
[ ] Code is (approximately) PEP8 compliant
[ ] Issue(s) raised/addressed?

codecov[bot] commented 1 year ago

Codecov Report

Merging #541 (03ef4cb) into main (e102f79) will not change coverage. The diff coverage is 0.00%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #541 +/- ## ======================================= Coverage 69.21% 69.21% ======================================= Files 16 16 Lines 1673 1673 ======================================= Hits 1158 1158 Misses 515 515 ```

daico007 commented 1 year ago

Failing test is due to the new pydantic release which impact gmso (https://github.com/mosdef-hub/gmso/issues/742). I have made a new gmso built on its feedstock with pydantic pinned. Rerunning failed tests now and hopefully they will grab the correct build.

mattwthompson commented 1 year ago

Thanks @daico007!