cannot open a jupytext notebook in nb7

[parmentelat]

Describe the bug

The jupytext extension does not work as expected in nb7

To Reproduce
Steps to reproduce the behavior:

1. install jlab4 as released in pip
2. install nb7 with pip install -U --pre notebook
3. install jupytext with pip install jupytext
4. install the jupytext labextension with
   pip install git+https://github.com/mwouts/jupyterlab-jupytext.git@jupyterlab4
5. create a simple jupytext notebook named for instance foo-nb.md
6. under jlab, check that you can open the notebook: right click → "Jupytext Notebook"
7. perform the same operation from the regular notebook tree browser: the "Jupytext Notebook" option is present but does not open the file as a notebook, it shows a text editor instead

Expected behavior

1. we should be able to open a jupytext notebook from the regular notebook file browser;
2. (also when opening a URL like localhost:8888/notebooks/path/file.md we need this to open a notebook and not a text editor, but for that to work the former behaviour 1. must first work)

Screenshots

Desktop (please complete the following information):

• OS: [e.g. iOS] MacOS & linux
• Browser [e.g. chrome, safari] - chrome
• Version [e.g. 22]

• jlab 4.0.2
• notebook 7.0.0b4
• as of this writing, https://github.com/mwouts/jupyterlab-jupytext.git@jupyterlab4 is on commit d451f5c

Additional context

Please see also https://discourse.jupyter.org/t/generic-question-about-jlab4-and-nb7/19846

[jtpio]

Thanks @parmentelat for reporting.

Steps to reproduce the behavior:

Looks like we also need to install jupytext with pip install jupytext? Not sure jupyterlab-jupytext installs jupytext automatically?

After following the instructions above and the additional pip install jupytext it seems like it's possible to open the markdown file with the notebook factory via the context menu:

jupytext-factory.mp4

But the behavior seems to be similar in JupyterLab right? By default double-clicking on the markdown file or opening it with the default "Open" context menu shows the markdown source:

jupytext-jupyterlab.mp4

[jtpio]

Also this might be related to #6324.

[parmentelat]

Looks like we also need to install jupytext with pip install jupytext? Not sure jupyterlab-jupytext installs jupytext automatically?

that is correct, I should have mentioned the pip install jupytext in the steps to reproduce, let me edit them accordingly

[parmentelat]

so, I confirm the I had tried the 'Open with' menu when reporting this

however I must admit that I am juggling between many environments, switching between stable and unstable versions of many different components, this is a bit overwhelming and my envs are in shambles...
so I guess I must have screwed up somehow somewhere; plus, the branches may have changed meanwhile

I will restart from scratch when I have a chance, most likely since all worked well for you, I should be able to report that as a red herring

[jtpio]

ok no problem, thank you so much for trying Notebook 7!

[parmentelat]

all right, so I tried again with the bare minimum set of extensions

and I can still see almost the same behaviour:

• using the Open button, or the Open with → Jupytext Notebook menu
  • I am getting an editor with the raw content
• however, using the Open with → Notebook menu
  • this time it does open a notebook

just to be sure it's not because of the input file, here's the notebook I am trying to open
https://raw.githubusercontent.com/parmentelat/jupyterlab-tpt/main/examples/test-nb.py

same behaviour with a .md here
https://raw.githubusercontent.com/parmentelat/jupyterlab-tpt/main/examples/sandbox-nb.md

here's console screenshots when using the "Jupytext Notebook" path

• the notebook tab
  

• the spawned tab
  

---

this recording ends a little early but the last attempt works fine

[parmentelat]

also, probably relevant to this discussion, I must say that my environment includes the following, which is needed in the context of jlab to get the default action (e.g. double click) to open as a notebook

I might redo the experiment without that in place, if that sounds a useful test (although it should only help, in theory, no ?)

cat ~/.jupyter/labconfig/default_setting_overrides.json
{
  "@jupyterlab/docmanager-extension:plugin": {
      "defaultViewers": {
          "python": "Jupytext Notebook",
          "markdown": "Jupytext Notebook"
    }
  }
}

[jtpio]

Just checked and it seems like the default viewers are not respected in Notebook 7 while they are in JupyterLab:

default-viewers-jupytext.mp4

[jtpio]

Closing as fixed by #6923

While investigating #6923, we noticed something that could also be an issue in JupyterLab (toolbar not rendering), which has been reported in mwouts/jupyterlab-jupytext#3 (comment).

Please feel free to re-open if you are still seeing issues, thanks!

[parmentelat]

Hiya lads

I am currently struggling with a bug on our deployment when trying to use nb7
and it might be related to this issue

in a nutshell, I run something like this

jupyter lab  --NotebookApp.base_url=/some-container-dep-prefix/

and apparently when trying to open a jupytext notebook the app answers with a redirect to
/edit/the-path/to-the-notebook
while I really need it to redirect to
/some-container-dep-prefix/edit/the-path/to-the-notebook

I just came across this and don't yet have an easily reproducible sandbox,
but is it possible that a hasty change has just forgotten to take this base_url setting into account ?

---

admittedly the relationship with this issue is just a hunch on my side,
so please let me know if you'd rather deal with this in a separate issue instead

[jtpio]

Thanks @parmentelat.

Yes it looks like an issue with the base URL.

FYI I submitted a fix for #6940 in #6941 which might be related.

This is available in 7.0.0rc1 if you would like to try it: https://github.com/jupyter/notebook/releases/tag/v7.0.0rc1

Otherwise yes a new issue to track this would be great, thanks!