Add information about the settings flag to cli tutorial.

[RiesBen]

No description provided.

[github-actions]

👈 Launch a binder notebook on branch OpenFreeEnergy/ExampleNotebooks/tutorial_add_settings_cli

[dwhswenson]

I think we need a more general refactoring of docs, but for now, could this be moved to a separate file, which is linked in a single-sentence from here? The goal is to make the initial tutorial look absolutely trivial so that new users see that the easiest cases are very easy, but then let users learn layers of complexity over time.

TBH, it probably makes more sense to just put this content in OpenFE docs, as opposed to in this repo (a statement which might also apply to the entire tutorial).

[richardjgowers]

@dwhswenson I think we should be linking to a (currently nonexistant) page in the docs that lists all possibilities from the cli, but I think a quick example that the CLI is extensible via these yaml files isn't making the CLI tutorial overly long

[dwhswenson]

@richardjgowers : This content represents more than 1/5 of the total tutorial. It is a significant increase.

Also, I think we should pay attention to advice from diataxis. (We're far from perfect at that, but we should try to be better.) Specific to this point: https://diataxis.fr/tutorials/#ignore-options-and-alternatives

[RiesBen]

@dwhswenson & @richardjgowers :

Roadmap 🚝 regarding changes 🔧 to this PR will be:

• add additional .ipynb - I suggest under setup/setup_customization/setup_customization.ipynb
• refomulate the text to make it standalone (will take a look at: ttps://diataxis.fr/tutorials/#ignore-options-and-alternatives)
• add reference to Tutorial linking the customization tutorial

could you please give me quick feedback on the .ipynb page location? (that's a bit of work for me and it would be grande if we could agree on one location ☺️)

[dwhswenson]

@RiesBen : Could you give a little more picture of what you're planning for the notebook?

At first guess, it sounds like this is something that belongs in the cookbooks/ directory, and which should also be brought into the core OpenFE documentation.

TBH, notebooks that only exist in this repository without a link in the core docs are probably not what we want. We should be pushing users to https://docs.openfree.energy; the fact that the source is in here is just so we don't bloat the core OpenFE repo.

[RiesBen]

@dwhswenson :
general idea was to give a quick guide on how to customize the setup procedure for RFE approaches (Network algorithm, mapper etc.)

If I extract the block from the current jnb, I either can put it in an minimal example .jnb (in cookbook?) or make some rest text file out of it. depending on how we want to do this. I think best we have a quick chat about this on monday.