[WIP] Adding tutorial for building AlchemicalNetworks for consumption with fah-alchemy

[dotsdl]

This PR adds the sphinx doc skeleton, along with our first tutorial. The
scope of this tutorial should be AlchemicalNetwork creation, up to
submission using the FahAlchemyClient.

[dotsdl]

Would like to use a real Protocol for this, which includes creating Settings. Need to establish pattern for users for creating Settings.

[codecov-commenter]

Codecov Report

Base: 81.24% // Head: 79.08% // Decreases project coverage by -2.16% ⚠️

Coverage data is based on head (83c9795) compared to base (12961db).
Patch coverage: 51.19% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #46      +/-   ##
==========================================
- Coverage   81.24%   79.08%   -2.17%     
==========================================
  Files          19       19              
  Lines         965     1023      +58     
==========================================
+ Hits          784      809      +25     
- Misses        181      214      +33     

Impacted Files	Coverage Δ
fah_alchemy/base/api.py	74.19% <0.00%> (ø)
fah_alchemy/storage/statestore.py	84.80% <24.13%> (-4.32%)	⬇️
fah_alchemy/compute/api.py	76.00% <44.44%> (-9.00%)	⬇️
fah_alchemy/interface/client.py	72.22% <60.00%> (-6.35%)	⬇️
fah_alchemy/compute/service.py	57.29% <63.63%> (-0.32%)	⬇️
fah_alchemy/base/client.py	92.95% <66.66%> (+0.20%)	⬆️
fah_alchemy/compute/client.py	87.50% <72.72%> (-8.34%)	⬇️
fah_alchemy/interface/api.py	77.77% <83.33%> (-0.28%)	⬇️
... and 1 more

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[JenkeScheen]

I did a run-through of this draft, some quick comments. They are mostly gufe-related, the AlchemicalNetwork operations LGTM!

1. From a ProteinComponent, what is the recommended way of returning the number of atoms in the molecule? This is super helpful for debugging in these kinds of workflows. len(list(protein.to_openmm_positions())) seems convoluted.
2. For Settings(.., forcefield_file="foobar.xml", ..), will this file live on lilac or F@H? Would it be worth absorbing some default ones into fah-alchemy?
3. Are there plans to implement some sort of atom-mapping visualiser and make it requestable from e.g. a Transformation()? This is currently implemented in Perses: https://github.com/choderalab/perses/blob/main/examples/atom-mapping/Atom-mapping.ipynb
4. Between complexed_transformations and solvated_transformations there should be some check in place that makes sure all atom-mappings are the same for all edges between the two phases, or at least give a warning if they are not.
5. Finally a more infrastructural Q: at least when we're deploying this on lilac, where would this notebook be run? Would it work just fine on an interactive node or is the intention to run locally, then send it off to lilac?

[IAlibay]

Are there plans to implement some sort of atom-mapping visualiser

Just a point on this, these are current available under openfe (including an upcoming py3dmol based one), and I think we came to the conclusion that we didn't think pulling the necessary dependencies should be in gufe. I'm not sure if moving them makes sense, probably worth discussing.

[dotsdl]

Per discussion with @IAlibay, may make sense to migrate this tutorial to gufe.

[dotsdl]

@richardjgowers will take over this PR, migrate to gufe.

[hmacdope]

Would people be okay if I split the sphinx docs setup for FAH off this PR? I might do that now so I can work on some of the docs?

[dotsdl]

@hmacdope yes please! Go for it!

[dotsdl]

I'll create a PR into gufe with this notebook, link to the discussion here so @JenkeScheen's comments aren't lost.

[dotsdl]

Will instead make a PR into openfreeenergy/ExampleNotebooks.

[dotsdl]

Superseded by OpenFreeEnergy/ExampleNotebooks#36