membrane CLI support

[atravitz]

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
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[codecov]

Codecov Report

❌ Patch coverage is 98.40000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.96%. Comparing base (fc6689e) to head (f3d155d).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/openfecli/commands/plan_rbfe_network.py	81.81%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1896      +/-   ##
==========================================
- Coverage   94.28%   89.96%   -4.33%     
==========================================
  Files         214      215       +1     
  Lines       19000    19327     +327     
==========================================
- Hits        17915    17388     -527     
- Misses       1085     1939     +854     

Flag	Coverage Δ
fast-tests	89.96% <98.40%> (?)
slow-tests	?

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[hannahbaumann]

Thanks @atravitz ! I added some comments regarding validation and error handling.
One thing that's currently missing is that the network planner always adds a SolventComponent to the ChemicalSystem, however the membrane case does not support a SolventComponent in the complex.
Once you add the protocol.validate to the network planner, this would also raise an Error.

[hannahbaumann]

Thanks @atravitz , this looks great! Left some small comments, the only important one is the catching of the actual error which would be very helpful to users I think.

[hannahbaumann]

Would it make sense to directly test for the ComponentValidationError here?

[hannahbaumann]

I think here I would catch and print the actual error. E.g. in the protein membrane case where no box vector is provided, the user wouldn't know why it was unable to load the file. The error would have said:
Error: Could not determine box_vectors. Please provide them explicitly via the ``box_vectors`` argument or enable ``infer_box_vectors``
So maybe something like this?

except ValueError as e:
    click.secho(
        f"Unable to load a {protein_class.__name__} from {input_file}.\nError: {e}",
        err=True
    )

[hannahbaumann]

Would it be safer to check for the file ending? Though of course it could also be gziped, so I'm not sure. I was just thinking in case .pdb could just be part of the file name, without it being a pdb file?

[hannahbaumann]

If you add the actual Error to this, I would here also check for the box vector thing in the error.

[github-actions]

No API break detected ✅