Lily Wang

Switch over to full GraphQL

5

Fixes #370, I think. This PR stops using PyGithub entirely and switches over to using GraphQL directly. It's not strictly necessary since the only issue with PyGithub was to do...

Change error to warning on Universe creation

6

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. -...

Deprecate guess_bonds and bond guessing kwargs in Universe

2

Fixes #4756 Changes made in this Pull Request: - Adds deprecation warning to bond keywords PR Checklist ------------ - [x] Tests? - [ ] Docs? - [x] CHANGELOG updated? -...

Switch guessers to catching and raising NoDataErrors

1

Fixes #4749 (maybe?) Changes made in this Pull Request: - Switches errors to NoDataErrors PR Checklist ------------ - [x] Tests? - [ ] Docs? - [ ] CHANGELOG updated? -...

## Expected behavior ## Bond guessing is turned on in two ways in Universe creation: `to_guess("bonds")` or `guess_bonds=True`. The latter should probably be deprecated , as well as the other...

Add deprecation warning for ITPParser

3

Fixes #4698 Changes made in this Pull Request: - Adds deprecation warning for element guessing in ITPParser Please feel free to make any changes desired and push into this branch!...

add default None -> UserWarning

1

Fixes #4746 Changes made in this Pull Request: - This mimics the Python warnings library by setting `category=None` to `UserWarning` by default We don't appear to test our utilities anywhere...

Failing to assign AM1 charges with ambertools on macOS-13

2

**Issue** I'm seeing a weird [issue in NAGL CI](https://github.com/openforcefield/openff-nagl/issues/152) where I can't seem to [assign AM1 charges to methane using AmberTools on macOS-13](https://github.com/openforcefield/openff-nagl/actions/runs/11439639803/job/31823780041?pr=153). This test passes with macOS-latest and a...

## 🐛 Bug ## To Reproduce This is a niche corner case, but hopefully one with an easy-ish solution. If I create a DGL heterograph with no edges, trying to...

There should be either a way to automatically remove outdated dev versions of the user guide, or we should document how to manually do it as this should happen post...