Switch to jupytext MyST markdown

[StFroese]

fixes #2099

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[maxnoe]

Can we use the same as gammapy here? I like that in that format, the notebooks are actually valid python scripts that can also be run normally.

[StFroese]

Sure, I'll take a look at it. Just to be clear: The .md notebooks can be run by Jupyter without converting them again

[maxnoe]

Out of the box? Or with some extension installed?

[StFroese]

Jupytext has to be installed in the environment

[kosack]

fixes: #2099

[kosack]

Can we use the same as gammapy here? I like that in that format, the notebooks are actually valid python scripts that can also be run normally.

Does jupyter itself support the format GammaPy uses, or do they export to that after editing? With Jupytext, you can use jupyter directly to edit/view the files I think, which is nice.

[maxnoe]

The system gammapy uses is sphinx-gallery: https://sphinx-gallery.github.io/

[kosack]

The system gammapy uses is sphinx-gallery: https://sphinx-gallery.github.io/

That is nice as it lets you download the result as a notebook or a script...

[maxnoe]

Loading the script directly with jupytext also seems to work in that format

[maxnoe]

See https://jupytext.readthedocs.io/en/latest/formats.html#sphinx-gallery-scripts

[nbiederbeck]

should we not include those now in setup.cfg under options.extras_require.docs?

[kosack]

yes. The docs are something the user should be able to build on their local install, without using the CI, so it should be a dependency

[maxnoe]

@StFroese Could you make a new attempt here with the same format Gammapy uses and the current main?

Please add the newly needed packages to the correct extras in setup.cfg and to the conda development environment in environment.yml.

[StFroese]

@maxnoe can do. I'll open a new PR for this

[kosack]

@StFroese Could you make a new attempt here with the same format Gammapy uses and the current main?

I have a quick question, not having worked with the sphinx-gallery text format. Can you open notebooks written in this format directly in Jupyter(lab)? Or do you have to convert to notebook first, edit, and convert back? Or is it just a different variant of format supported by the jupytext plugin?

[maxnoe]

@kosack When you have the jupytext extension installed, they open just fine in jupyter {lab,notebook}

[StFroese]

Can you open notebooks written in this format directly in Jupyter(lab)? Or do you have to convert to notebook first, edit, and convert back? Or is it just a different variant of format supported by the jupytext plugin?

I'm a little confused about this too. Seems like you have to use .py script with sphinx-gallery instead of notebooks. Am I right @maxnoe?
This seems to be a kind of alternative maybe https://sphinx-nbexamples.readthedocs.io/en/latest/

[kosack]

Replaced by #2377