To commit or not commit notebook output...

首先比较 tutorials/rbfe_python_tutorial.html 文档使用的 notebook 与 ExampleNotebooks 中 .github/workflows/CI.yml 的 notebook 列表和执行步骤。查看 OpenFF 如何处理嵌入的 notebook 输出，然后定义并记录一个 workflow，使其完成后的输出在 repository 和渲染后的文档中保持一致。

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