NonEquilibrium switching protocol implementation

[ijpulidos]

These sets of changes are aimed towards a minimally functional implementation of a NonEquilibrium switching protocol, based on the objects and lessons learned from the NonEquilibrium cycling protocol.

Still a WORK IN PROGRESS, but this should be useful as a good first skeleton on what the protocol should look like.

[ijpulidos]

Comments from a meeting with John:

I still like the idea of including [ eq + neq switch ] within a single block, since you can easily chain these together as much as you want or run as many in parallel as you want.
You end up with the same result.

[ijpulidos]

The current status has a NES protocol which is comprised of a SetupUnit (the same setup unit as NE cycling), and parallel forward and reverse switches. The idea is eventually to run all these switches in parallel depending on the availability of resources. It mimics a lot of what the cycling protocol does, except that it uses the base alchemical langevin integrator instead of the periodic one.

One new feature is that it can get snapshots from a predefined trajectory (using MDAnalysis), the idea here is that we can get creative with how we feed in snapshots. Without losing the capability of generating/running an equilibration trajectory itself.

[codecov]

Codecov Report

❌ Patch coverage is 80.55556% with 70 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.22%. Comparing base (639b258) to head (7a07ae6).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
feflow/settings/nonequilibrium_switching.py	52.94%	40 Missing ⚠️
feflow/protocols/nonequilibrium_switching.py	88.10%	27 Missing ⚠️
feflow/settings/integrators.py	93.02%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #70      +/-   ##
==========================================
- Coverage   86.86%   86.22%   -0.64%     
==========================================
  Files          11       16       +5     
  Lines        1439     1895     +456     
==========================================
+ Hits         1250     1634     +384     
- Misses        189      261      +72     

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