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

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[codecov]

Codecov Report

Attention: Patch coverage is 97.50000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 92.93%. Comparing base (e45b34e) to head (dbc9d47).

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

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1083      +/-   ##
==========================================
- Coverage   94.62%   92.93%   -1.69%     
==========================================
  Files         136      136              
  Lines       10087    10167      +80     
==========================================
- Hits         9545     9449      -96     
- Misses        542      718     +176     

Flag	Coverage Δ
fast-tests	92.93% <97.50%> (?)
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 ✅