marimo notebooks

[tobiasschweizer]

Hi,

Have you considered using marimo notebooks?

• https://marimo.io/
• https://marimo.io/features/vs-jupyter-alternative

Marimo notebooks can also be run as scripts and they can be nicely handled with git and diffed (Jupyter notebooks on the other hand are not very git-friendly ...).

[ljocha]

Hi @tobiasschweizer,

nice idea but it goes a bit beyond the original WP workplan, IMHO. First, have we got some WP7 usecase(s) which would benefit from marimo?

In either case, can you elaborate a bit more on the functionality, please? Do you mean having something like https://github.com/EOSC-Data-Commons/Dispatcher/tree/master/test/alphafind-notebook, but with a marimo notebook instead of ipynb? And what would be the target environment to run it (generic K8s cluster, VM spawned via Infrastructure Manager, ...)?

[tobiasschweizer]

Hi @ljocha,

I am not familiar with the contents you are dealing with, this is more a general statement. I have tried Jupyter notebooks in the past but they were difficult to be tracked with git since the whole output would be there too and another issue was that often when working on such a notebook, you have no linear flow (you do not necessarily execute all cells in a sequential order) which makes it hard to achieve the same results when you re-run the notebook after a while.

I found that marimo addresses these two points very well. If you look at a marimo notebook in Python source, you see that cells are like functions with their own input and output (and some decorators) and marimo keeps track of the dependencies between the cells.

You can also run marimo notebooks as if they were normal Python scripts: https://docs.marimo.io/guides/scripts/ I think all you need is to add marimo as a dependency.

[enolfc]

One thing that I have done in the past for having any other kind of notebooks in jupyter working is to use https://github.com/jupyterhub/jupyter-server-proxy and potentially dedicated extensions to that like https://github.com/jyio/jupyter-marimo-proxy/tree/main.

This would make it really easy to just use binder for building the marimo environment and serve it without the need to create anything special on the dispatcher. If this is proven to be really demanded, the binder config for this can be somehow encoded in the RO-Crate so it's easier to get them running