Add support for variable position/velocity trajectory writing

[IAlibay]

Depends on: choderalab/openmmtools#767

Also see: OpenFreeEnergy/openfe_analysis#44

TODO:

• Check this works in real life w/ the openfe_analysis patch
• Check that the settings keywords make sense / match other protocols
• Check that the frequency defaults are reasonable / yield sufficiently small trajectories
• Work out the difference in file size compared to current main
• Better document the frequency writing?
• Add pydantic validators (at least positive value checks?)
• Add tests to check that values works (asserting on the reporter's variables) / the right error gets brought up?
• Add news entry

Developers certificate of origin

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

[codecov]

Codecov Report

Attention: Patch coverage is 96.29630% with 3 lines in your changes missing coverage. Please review.

Project coverage is 91.87%. Comparing base (bd95f22) to head (233e90f).
Report is 113 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_utils/omm_settings.py	80.00%	2 Missing ⚠️
openfe/tests/protocols/test_openmm_rfe_slow.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1083      +/-   ##
==========================================
- Coverage   93.49%   91.87%   -1.62%     
==========================================
  Files         142      142              
  Lines       10527    10608      +81     
==========================================
- Hits         9842     9746      -96     
- Misses        685      862     +177     

Flag	Coverage Δ
fast-tests	91.87% <96.29%> (?)
slow-tests	?

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[IAlibay]

Check that the frequency defaults are reasonable / yield sufficiently small trajectories

@hannahbaumann the defaults would now yield 50 frames per replica, down from 5000 frames per replica, which should be a large enough reduction in size, what do you think?

[hannahbaumann]

Yes, that sounds like a good size!

[IAlibay]

I think everything that needs addressing has been addressed, only thing that's blocking is a release of openmmtools and openfe-analysis, but I'll leave it to you to approve @hannahbaumann !

[hannahbaumann]

Thanks @IAlibay , lgtm! We'll just need to change the pin after the openmmtools release.

[IAlibay]

I'm getting the sense the openmmtools release won't be for a few weeks, so we might have to wait until the next OpenFE release to have this merged.

[github-actions]

No API break detected ✅

[IAlibay]

Checked it out locally, should be good to go.