To commit or not commit notebook output...

I do think that it is best practice to not keep the output BUT we need the output so that our docs render the output:
https://docs.openfree.energy/en/stable/tutorials/rbfe_python_tutorial.html

I think what we should do is maybe have CI do the rendering (it already does the running (at least on these notebooks https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/.github/workflows/CI.yml#L68 we will want to make sure those are a 1-1 match of the notebooks we have in our docs))
We could have the result of running the notebooks committed on merge into main? That way it won't clutter up the PR (with each CI run you would need to pull changes) BUT I don't think that would actually help since the output would still be saved...

We could have RTD keep the output which would fix the issue of the docs not having the output BUT that means that if you clone the repo or view the repo with a web browser there still would be no output.

I am not really sure what we should do here, maybe see what OpenFF does? They have the same-ish setup for embedding notebooks in their docs.

This will probably be a bigger issue to work out BUT I think the typo fixes you have here are great 🎉 so could you include the output for now? I will turn this comment into an issue that we can use to discuss what we want to do RE: notebook output being committed.

Originally posted by @mikemhenry in https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/163#issuecomment-2402982475

Inizia confrontando i notebook utilizzati dalla documentazione in tutorials/rbfe_python_tutorial.html con l’elenco dei notebook e i passaggi di esecuzione in .github/workflows/CI.yml di ExampleNotebooks. Esamina come OpenFF gestisce l’output incorporato dei notebook, quindi definisci e documenta un workflow il cui output completato sia coerente nel repository e nella documentazione renderizzata.