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 66.78201% with 192 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.66%. Comparing base (c60db06) to head (5f3e876).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
...ts/protocols/openmm_septop/test_septop_protocol.py	31.54%	115 Missing ⚠️
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	8.57%	32 Missing ⚠️
.../tests/protocols/openmm_abfe/test_abfe_protocol.py	70.29%	30 Missing ⚠️
src/openfe/protocols/openmm_md/plain_md_methods.py	81.25%	3 Missing ⚠️
...openfe/protocols/openmm_rfe/_rfe_utils/relative.py	66.66%	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_afe/base_afe_units.py	66.66%	1 Missing ⚠️
...openfe/protocols/openmm_rfe/hybridtop_protocols.py	90.00%	1 Missing ⚠️
... and 3 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1561      +/-   ##
==========================================
- Coverage   94.62%   90.66%   -3.97%     
==========================================
  Files         206      206              
  Lines       18285    18758     +473     
==========================================
- Hits        17303    17007     -296     
- Misses        982     1751     +769     

Flag	Coverage Δ
fast-tests	90.66% <66.78%> (?)
slow-tests	?

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[jthorton]

Great job, everyone. This is finally ready pending the highlighted changes.

[hannahbaumann]

pre-commit.ci autofix

[IAlibay]

Couple of small things left.

[IAlibay]

Running long CPU tests here: https://github.com/OpenFreeEnergy/openfe/actions/runs/24508465814

[IAlibay]

Running GPU tests here: https://github.com/OpenFreeEnergy/openfe/actions/runs/24508496073

[IAlibay]

Pending test passing, LGTM!

[github-actions]

No API break detected ✅

[IAlibay]

Only failing CPU long test is the one related to #1941 - so we should be good to go.
I'll merge once conventional CI turns green.