opening jupytext notebooks in jlab

[parmentelat]

Hiya

trying to migrate from classic to something more modern, I'm facing an issue that has to do with the awkward path that seems to be the only way to open a jupytext notebook under jlab

• from the UI, clicking say foo.md in the file browser results in a markdown editor; I need to do right-click → open with → Notebook to get it to open as a notebook
• from the outside, I'd need a way to do the same from a regular URL; opening lab/tree/path/foo.md has the same result as from the UI, so I can't seem to find any way to open it as a notebook from a URL

the first issue is an impediment but of course something I can live with; the second is more of a showstopper for me at this point

I'd love to find a way around this

ps
for reference, I've be stirring this in a couple other threads already
https://discourse.jupyter.org/c/jupyterlab/17
and more marginally in
jupyterlab/retrolab#162

in the latter @jtpio suggested that an extension could come in handy, but I must honestly admit that the whole jlab extension ecosystem has scared the hell out of me a bit, so I am unsure what this would actually involve..

[mwouts]

Hi @parmentelat , well these two issues have been there for a while, cf #271 for instance. But sure I'll be happy to give another try to get them fixed.

For the first point, i.e. the default viewer for .md files, could you give a try at the Jupyter Lab user settings as documented here? Please let us know if that works for you.

I understand that the second item is a bigger problem. I remember discussing with @jasongrout how to change the default viewer for the .md links. That involved overriding some "open" function, but that was a while ago and I can't remember which function that was exactly, and I am not sure I know how to do that in the Jupytext extension neither... help is welcome!

[joelostblom]

For me, changing the document user settings does not seem to change the default viewer for .md files, so I opened jupyterlab/jupyterlab#11195

[alwaysmpe]

Was wanting to set the notebook viewer as the default for python also. Having poked around in the jupyterlab code, looks like there are a few ways forward.

The problem is that jupytext isn't registering as a widget factory and the notebook viewer doesn't explicitly support python/markdown/whatever files (my understanding of jupyter/jupytext internals is pretty rough, but I am a software engineer).

Looks like when a viewer is configured in the setting, it's then trying to map that to the viewer.

This is the CR that added the ability to specify a widget to viewer mapping:
jupyterlab/jupyterlab#6813

Using this registry of viewer factories:
https://github.com/jupyterlab/jupyterlab/tree/997f3af68396539136ab0cb8512c73c07e021e4a/packages/docregistry

The Notebook viewer registers a limited number of file extensions (and I think mime types). It's not possible to add a new type to an existing viewer (ie add python to the notebook viewer) according to this issue:
jupyterlab/jupyterlab#7099

That issue proposes mapping mime types to viewers, also not currently done.

The way I see it, there are a few options to enable the desired behavior.

1. Implement the changes proposed in the above issue (there's a partial PR, I haven't looked at what progress was made), then in jupytext make the necessary changes to add the notebook mime type to python files
2. Wrap the notebook viewer, register jupytext as a distinct viewer, explicitly support whichever file formats desired, perform whatever internal changes are needed.

Option 2 would probably be quickest, but a bit of a hack. Option 1 would likely be preferable long term.

The code for the notebook viewer (as an extension) is this I believe: https://github.com/jupyterlab/jupyterlab/tree/997f3af68396539136ab0cb8512c73c07e021e4a/packages/notebook-extension

And I think it's the widget factory stuff that would need modifying, ie use a different factory name.

That's as far as I got. I'll probably look a bit more at some point, but I'm a little busy. Any pointers welcome.

[alwaysmpe]

This is confusing, so I figured I'd gather a few links to other discussions in one place.

Looks like there's a difference between how links are handled and opening from a file browser (I think, need to read a bit more of this)
jupyterlab/jupyterlab#7776

A fairly equivalent discussion for markdown
#271

This is a bit of a bodge that adds the option to the 'open with' menu, a similar hack could probably also be added when setting defaults (not ideal): https://github.com/jupyterlab/jupyterlab/pull/5247/files

[mwouts]

Thanks to @fcollonval 's contribution #877 we can now:

• open text notebooks with a single click in Jupyter Lab when "Jupytext Notebook" is configured as the default viewer for these notebooks, see the documentation
• open text notebooks with the Notebook view on Binder (requires a default_setting_overrides.json file), like e.g. this one: https://mybinder.org/v2/gh/mwouts/jupytext/main?urlpath=lab/tree/README.md

This new option will be made available with Jupytext 1.13.2 (soon on pip), so I will close this issue (comments are welcome and a confirmation that this also works for people here would be great!)

Note: the question of opening links to .md files as notebooks is still open at the moment, and will be treated separately at #271 .

[astrojuanlu]

Trying to reproduce this for some MyST notebooks, but I can't seem to be able to make it work poliastro/poliastro#1410

I changed "jupytext-md": "Jupytext Notebook" by "jupytext-myst": "Jupytext Notebook", neither option worked. At least I checked that the settings are being properly imported to the Document Manager. Any help welcome 🙏🏽

[fcollonval]

@mwouts from the comment of @astrojuanlu I realize that Jupytext is handling on the server side lots of file extensions than the one appearing for now in the labextension (for instance the one of MyST notebooks). To support them with the one-click feature, they need to be listed as supported extension by the new file type jupytext-md at

jupytext/packages/labextension/src/index.ts

Line 431 in 6fee30c

extensions: [".rmd", ".qmd"],

I let you (or someone with a better knowledge of the supported format) update that list as needed to match the supported extensions.

[mwouts]

I see! Sure I'll do that, I will try to find some time to fix that tonight... Thanks for the pointers!

[mwouts]

Well... @astrojuanlu , which extension do you use for the MyST format?

If you use the .md extension then this user settings should do the trick:

{
  "@jupyterlab/docmanager-extension:plugin": {
    "defaultViewers": {
      "markdown": "Jupytext Notebook"
    }
  }
}

At least it works on Binder with the current version, see this example: https://mybinder.org/v2/gh/mwouts/jupytext/main?urlpath=lab/tree/demo/World population.myst.md

Of course I can add the .myst, .mystnb, and .mnb extensions to the "jupytext-md" file type, but before that maybe I'd prefer to get a confirmation that someone really use them 😄 ?