Added tutorial for building AlchemicalNetworks

[dotsdl]

This was originally created for alchemiscale, but is being contributed here instead, since it really is a gufe tutorial.

[github-actions]

👈 Launch a binder notebook on branch dotsdl/openfe-ExampleNotebooks/alchemicalnetwork-tutorial

[dotsdl]

This notebook will require openfe-benchmarks be added to the Binder environment to run.

[dotsdl]

Also need perses, in particular content from this branch: choderalab/perses#1066

perses will require the following as well:

• openmmtools
• openmmforcefields
• openmoltools
• cloudpathlib
• dask
• distributed
• openeye-toolkits
• numba

[dotsdl]

For reference, we used the following environment file for building the conda env used to run this notebook:

name: fah-alchemy-client
channels:
  - jaimergp/label/unsupported-cudatoolkit-shim
  - conda-forge
  - openeye
dependencies:
  - python =3.9

  # gufe dependencies
  - numpy
  - networkx
  - rdkit
  - pip
  - pydantic
  - openff-toolkit
  - openff-units
  - typing-extensions

  # perses dependencies
  - tqdm
  - openmm
  
  ## cli
  - click

  # needed for openfe
  - lomap2>=2.1.0
   
  ## needed for perses
  - openmmtools
  - openmmforcefields
  - openmoltools
  - cloudpathlib
  - dask
  - distributed
  - openeye-toolkits

  - pip:
    - git+https://github.com/OpenFreeEnergy/gufe
    - git+https://github.com/OpenFreeEnergy/openfe
    - git+https://github.com/OpenFreeEnergy/openfe-benchmarks
    - git+https://github.com/mikemhenry/openff-models.git@support_nested_models
    - git+https://github.com/choderalab/perses@protocol-neqcyc

[richardjgowers]

thanks @dotsdl . I can fix this up and take it from here

[dotsdl]

Thanks @richardjgowers! I've pushed my latest updates; I'll pass it off to you from here.

I noticed that our Settings object appears to be unhashable, which chokes up creation of AlchemicalNetworks from a list of Transformations, each with a Settings object. You can see this in cell [24] in the notebook.

[dotsdl]

Might consider using the openfe REPEX protocol as the example instead to avoid OpenEye requirement for perses.

[dotsdl]

We need to use pre-baked mappings in this notebook; currently not using any.

[dotsdl]

@richardjgowers do we have a way to add some pre-baked mappings to this choice of network? That's the only blocker (I think) to this being a functional example notebook, and I'm itching to use it for ad-hoc testing in alchemiscale.

[dotsdl]

We can also switch over to the RepEx protocol in openfe as our example protocol.

[richardjgowers]

superseded: #42