How do people deal with Markdown syntax compatibility between JupyterBook and live notebook environments?

[fmaussion]

Hi all,

I maintain several tutorials and courses built with JupyterBook, where the typical student workflow looks like this:

1. Students browse the rendered JupyterBook online for guidance.
2. They download the notebooks or open them on a JupyterHub or they own JupyterLab to run and interact with them.

This hybrid workflow is common, but it leads to a frustrating issue: Markdown syntax that works in one environment often breaks or renders poorly in the other.

For example:

• Internal links like [text](#header) work fine in JupyterLab but not in JupyterBook (due to different anchor handling). (https://github.com/orgs/executablebooks/discussions/1261)
• MyST-specific blocks like :::{warning} or {ref} are great for JupyterBook but render weirdly or not at all in standard notebook environments.

This makes writing portable, clean Markdown really difficult. In many cases, I’m forced to abandon MyST features entirely, which defeats the purpose of using JupyterBook in the first place.

So I’m wondering:

• How are others handling this? Are there workflows or syntax patterns that work well in both environments?
• Is there any initiative to make JupyterLab better at rendering MyST-compatible syntax? (see https://github.com/orgs/executablebooks/discussions/1129)
• Are there best practices, linters, or pre-processing tools to help bridge the gap?

I’d love to hear how others are navigating this. Right now (for me), the lack of a consistent rendering experience is one of the biggest friction points in using JupyterBook for reproducible and executable teaching materials.

Thanks!

[fmaussion]

It seems that https://github.com/jupyter-book/jupyterlab-myst is the one answer to all of my queries above - I forgot about it! I will consider what it means to add this dependency to all my projects...

[choldgraf]

That's definitely what I was going to recommend! The project needs more attention than it gets but I think that's the right place to solve this problem. Maybe one day jupyter UIs will natively support MyST syntax but who knows! Right now our biggest challenge is to grow our teams capacity to maintain and build

[bsipocz]

FWIW, I also run into this dilemma a while back, so what we need, I think, is a more prominent mention of the jupyterlab extension in the myst-nb docs, e.g. right at the top, rather than hidden in a "See also" section.

[choldgraf]

@bsipocz happy to review and merge a PR w/ that!

[bsipocz]

OK, I'm adding it to the list. The other documentation part, that I would love to link to from everywhere is a "My Why MyST Markdown and not ipynb" -- directed to end user scientists. This is a recurring question, or actually even an argument, and I would love to have one central and super nice docs rather than bits and pieces here and there.
Also, I would love to have a cleaned up and nicer version of this howto, that includes screenshots etc: https://github.com/NASA-NAVO/navo-workshop/blob/main/00_SETUP.md#8-handling-notebooks-in-myst-markdown-format

[choldgraf]

Do you mean "why" not "my" by any chance? And you mostly want this as a resource for "how to choose when to use each format"?

[bsipocz]

Of course, you need to read between the typos with my comments 😅 (half of my "is" should be "if", etc.)

And I want it as a resource to reassure end users to not panic when they see an .md format file in a repo and believe it's just as good as a notebook an ipynb is and they don't need to convert anything just install 1-2 packages all all will be seamless and good. (And for the love of god, they should not open a PR with an ipynb file including all the outputs into a notebook repo; but that's a neighbouring hill to die on)

[choldgraf]

ok @bsipocz you nerd sniped me. Want to iterate over here:

• Add a brief guide to choosing between .md and .ipynb jupyter-book/mystmd#1969

?