Membrane support

[hannahbaumann]

[Note from @atravitz: we are making an experimental release from this branch, and so this branch should not be merged into main just yet]

This PR addresses the following issues:

• Membrane support: Protocol updates #1502
• Membrane support: Ensuring that no further solvation is attempted in the protocols #1639
• Add support for a MonteCarloMembraneBarostat in the RBFE protocol #1599
• Changes to the HTF to allow for the MonteCarloMembraneBarostat #1600
• Add barostat settings to integrator settings class #1783
• Membrane: Add warning/validation for barostat usage #1790
• Expand MD Protocol to deal with other kinds of barostats #671

Checklist

• Added a 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

❌ Patch coverage is 62.90984% with 181 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.05%. Comparing base (031e13c) to head (a72e135).

Files with missing lines	Patch %	Lines
...ts/protocols/openmm_septop/test_septop_protocol.py	35.75%	115 Missing ⚠️
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	8.57%	32 Missing ⚠️
.../tests/protocols/openmm_abfe/test_abfe_protocol.py	68.65%	21 Missing ⚠️
src/openfe/protocols/openmm_md/plain_md_methods.py	81.81%	2 Missing ⚠️
...openfe/protocols/openmm_rfe/_rfe_utils/relative.py	66.66%	2 Missing ⚠️
...openfe/protocols/openmm_rfe/hybridtop_protocols.py	60.00%	2 Missing ⚠️
...nfe/protocols/openmm_septop/equil_septop_method.py	90.90%	2 Missing ⚠️
src/openfe/protocols/openmm_utils/omm_settings.py	84.61%	2 Missing ⚠️
src/openfe/protocols/openmm_afe/abfe_units.py	80.00%	1 Missing ⚠️
src/openfe/protocols/openmm_rfe/hybridtop_units.py	50.00%	1 Missing ⚠️
... and 1 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1561      +/-   ##
==========================================
- Coverage   94.79%   91.05%   -3.74%     
==========================================
  Files         205      205              
  Lines       17957    18342     +385     
==========================================
- Hits        17022    16702     -320     
- Misses        935     1640     +705     

Flag	Coverage Δ
fast-tests	91.05% <62.90%> (?)
slow-tests	?

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[hannahbaumann]

pre-commit.ci autofix

[hannahbaumann]

@IAlibay @atravitz this is not very pretty, but since we're not loading the actual components, we cannot check the base types directly. Not sure if there's a better way.

[IAlibay]

Might make sense to spin this off into a separate PR?

[atravitz]

pre-commit.ci autofix

[github-actions]

No API break detected ✅