Jupytext suddenly stopped working with JupyterLab

[yoavxyoav]

Hi, I am using jupytext both in my base conda and a couple of other environments, and suddenly pairing has stopped working to Rmd unless I explicitly pair the notebooks (before it would pair automatically and create an Rmd with any ipynb file I edited or created). It works fine with jupyter-notebook.

I have tried following similar threads here and run jupyter serverextension enable jupytext, and I am getting this:

Config option `kernel_spec_manager_class` not recognized by `EnableServerExtensionApp`.
Enabling: jupytext
- Writing config: /Users/yoav/.jupyter
    - Validating...
      jupytext 1.9.1 OK

My jupyter-lab version s 3.0.7

I will be extremely thankful for any advice!

[mwouts]

Hi @yoavxyoav , thanks for the report.

Given that the creation of the paired file works when you pair it explicitly (do we agree that you're doing that through the "pair notebook with..." commands?), you issue seems to differ from #713 or #721 (still it would be useful if you can confirm that the Jupytext server extension is loaded when you run jupyter lab)

So I think the problem you report might relate to a configuration issue. You seem to expect that all .Rmd and .ipynb files are paired - how did you configure that? Are you using a jupytext.toml file? That is now the recommended way to set a default pairing (and we've seen a few issues recently with the former approach of setting the config on a custom contents manager). See https://jupytext.readthedocs.io/en/latest/config.html#jupytext-configuration-file for more details on the jupytext.toml file.

[yoavxyoav]

@mwouts Thank you for getting back to me about this. The problem was eventually solved after doing several updates. I assume that having poetry installed inside a conda environment created some dependency mess (unfortunately I am compelled to work in such configuration). Anyway, now everything works, but thanks again for the guidance!