Convert all notebooks to .py files with Jupytext

[Nicholaswogan]

Normal notebook files (.ipynb) do not work well with version control. The Jupytext is designed to fix this. Instead, notebooks can be saved in a special format as a .py file. This .py file is what should be tracked by git.

[Nicholaswogan]

@natashabatalha, Jaden (@jajadl) and I are working toward the tutorial that makes a Modern Earth spectrum. I have two questions, one related to this issue:

1. Do you want this new "Modern Earth Spectra" notebook to be in .ipynb format like all the other tutorials? Or should we create a PR with a notebook in .py format (Jupytext)
2. What folder in the docs/notebooks/ would be ideal for a "Modern Earth Spectra" notebook?

[natashabatalha]

This looks promising. Quick question -- so if I understand correctly the to-dos for this would roughly be:

• we install jupytext
• we convert all our ipynb to py
• we do a gitignore on all our ipynb, and start tracking on py
• for readthedocs, does it still track the ipynb??
• for the download links rendered on readthedocs, do those still return ipynb or py??

Do you know off hand how the last two operate??

[natashabatalha]

For new notebooks -- can I punt back to you:

1. do you want new notebook to go in v4 release (upcoming) -- then stick to ipynb.
2. in terms of where.. I think it would be good to start a new folder called "Modeling Benchmark Systems" (or open to other names). We could also have a folder called "Reproduce the Solar System". Open to suggestions/your preference. Earth can be the first one there and we can start dumping the rest of the tour of the SS in there as well with any other good standards.

[Nicholaswogan]

Ya the first 3 bullet points make sense. Re the last two bullet points:

for readthedocs, does it still track the ipynb??

What is your workflow for generating the readthedocs website exactly? Do you build the doc HTML locally then upload that to github pages?

This is how I imagine it all working out. I'm imagining you build the docs locally on your machine:

1. As a part of the doc build process, we can use Jupytext to generate ipynb files for all notebooks from the .py files
2. Next, most all of the same doc workflow applies, which builds based on .ipynb files

for the download links rendered on readthedocs, do those still return ipynb or py??

The github pages cite I think already directly contains .ipynb versions of the notebook: https://natashabatalha.github.io/picaso/_sources/notebooks/1_GetStarted.ipynb.txt, so I think we can just adjust those download links to point to that source? Or the docs could explicitly ship .ipynb files and link to them.

[natashabatalha]

Done in 88dd43b