switch kcal/mol to kilocalorie_per_mole for roundtrip consistency

[atravitz]

gufe added new tests to GufeTokenizableTestsMixin for json and msgpack roundtripping, and it caught that roundtripping RelativeHybridTopologyProtocol and AbsoluteSolvationProtocol does not reproduce the same gufe key.

This is because the original object's early_termination_target_error's units are kilocalorie_per_mole, but when it's loaded back in, it's in units of kilocalorie / mole

We think this is because of pydantic casting, and changing the pydantic class to expect kilocalorie_per_mole solves this.

Checklist

• Added a news entry

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• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[atravitz]

@hannahbaumann you made this edit here:573f271#diff-24e303f93e84a4ff799a85a45f35209e516f389c3fa823a2f20106a89843bb25L462

so I'd like to know if there's any reason we should be keeping this as kcal/mol as opposed to kilocalorie_per_mole

my understanding is that this is an openmm vs. openff convention difference: https://github.com/openforcefield/openff-units?tab=readme-ov-file#openmm-interoperability

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.57%. Comparing base (429138a) to head (b17714b).
Report is 101 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1210      +/-   ##
==========================================
- Coverage   93.09%   92.57%   -0.53%     
==========================================
  Files         141      141              
  Lines       10651    10667      +16     
==========================================
- Hits         9916     9875      -41     
- Misses        735      792      +57     

Flag	Coverage Δ
fast-tests	92.57% <100.00%> (?)
slow-tests	?

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[hannahbaumann]

Thanks @atravitz , lgtm!

[ianmkenney]

Under the assumption that this is reasonable for the other reviewers, as they are more familiar with downstream effects, this looks good to me.

It might also be good to check to see what happens if a user provides a quantity in kcal/mol, rather than relying on the default, and if this comes up again.

[mikemhenry]

It might also be good to check to see what happens if a user provides a quantity in kcal/mol, rather than relying on the default, and if this comes up again.

That exact point was raised during our meeting so we will add a test to make sure it works

[mikemhenry]

Just need a test to make sure if a user sets something with 'kcal/mol' style it works -- it absolutely should since that is how this works BUT we will want that test since if we ever change the way our models work, we could introduce a regression

[github-actions]

No API break detected ✅

[mikemhenry]

LGTM!

[mikemhenry]

Also, no need for a news entry since this really does not affect users at all

[IAlibay]

I was looking at the tests earlier today and stumbled upon this - the name is really confusing. Can we maybe consider switching it out to something else? (especially having it in tokenization just threw me off).