AlchemicalArchive example

[jthorton]

Adds an example script generating alchemical archives from results stored on alchemiscale.

Questions

• should we add a function to the openfe-benchmarks API to generate an archive from a network key for now?
• what metadata if any should be added to the archives?

TODOs

• add a script to combine results from many archives into a results.json

[jaclark5]

I can't fully run this. I made some suggested changes that need to be made to start running it, but I'm hitting a roadblock at RelativeHybridTopologyProtocolUnit not being found. Although listed in docstrings in openfe it's not in the codebase.

I couldn't find a PR that had RelativeHybridTopologyProtocolUnit so let me know how to get it so I can continue running. (see OpenFreeEnergy/gufe#774)

I was able to over come this by making the standard alchemiscale env and then altering it with:

micromamba remove -n alchemiscale-client openfe gufe --force -y
pip install git+https://github.com/OpenFreeEnergy/gufe.git@v1.9.0
pip install git+https://github.com/OpenFreeEnergy/openfe.git@v1.8.1

[jaclark5]

change this file _example*.py to something else, maybe _tmp*.py to avoid triggering CI on it. We don't want to go through providing alchemiscale API keys for this temporary example.

[jthorton]

Tested the new network-key option locally and its working!

[jaclark5]

This works great for me! I tried it with network-key only and with org, campaign, and project. They yielded the same result without issue, except that the gufe keys were different.