Irfan Alibay

We're using SMCs from the mappings intead of the Components, which can be rather dangerous. We need to: 1. Make sure the mapping SMCs match the ChemicalSystem Components 2. Use...

The return for `compare_energies` is a bit confusing and likely will be hard to remember what's going on in the future. It needs a) more in-line comments, b) moving to...

Move XML serialize & deserialize methods to openmm utils from septop utils and remove unused file types.

1

These originate from feflow, so they will eventually get moved to a utils repo. That being said, we also have no need for supporting gz, bz2 AND standard XML. We...

These CLI tests are some of the slowest ones in our regular CI runs. These probably don't need to be run on the regular unless we change the CLI functionality,...

Partial charge assignment fails to limit the thread number to 1.

4

I'm bulk assigning partial charges using the CLI with plan-rbfe-network and finding that the thread usage is more than 1 more core during sqm calls. It seems like for some...

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Task creation is noisy with lots of deprecation warnings

2

Generally I would expect task creation to be a tqdm-style progress bar with little output. Instead now every time a task is created I get what's show below. I ended...

Consider removing usage of openfe-benchmarks for docs

1

openfe-benchmarks is used to pull ligands through in the example notebooks. However the openfe-benchmarks API is currently deprecated. It would probably be easier to just pull down the relevant ligands...

The `display_mappings_3d` imports from openfe, which causes an odd type of cyclic import. If needed, we should move that functionality out of kartograf into gufe or somewhere similar.