Septop pydantic v2

[atravitz]

NOTE: this targets the to_pydantic_v2 branch so that I can get @hannahbaumann's review on just the septop pydanticv2 updates.

[atravitz]

@hannahbaumann I'd like your feedback here - I see you use openmm units in a few places here, and I'm wondering if we can convert these all to openff units?

[hannahbaumann]

Thanks @atravitz !
Regarding the switch of openmm to openff units, for the tests that are using openmm (sampler, forces,..) I think I would stick to openmm units, otherwise you'd need a to_openmm for many things. I think other protocols are also sticking to openmm units for these.

[atravitz]

CI running at: https://github.com/OpenFreeEnergy/openfe/actions/workflows/ci.yaml?query=branch%3Aseptop_pydantic_v2 (not automatic because this isn't merging into main)

merge blocked by OpenFreeEnergy/gufe#637 no longer blocked

ready for review @hannahbaumann!

[hannahbaumann]

Thanks @atravitz , lgtm!

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
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Additional details and impacted files

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##             to_pydantic_v2    #1536   +/-   ##
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  Coverage                  ?   95.30%           
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  Files                     ?      172           
  Lines                     ?    14461           
  Branches                  ?        0           
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  Hits                      ?    13782           
  Misses                    ?      679           
  Partials                  ?        0           

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slow-tests	95.30% <100.00%> (?)

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