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Extension not loading in jupyterlab 3 #713

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gstorer opened this issue Jan 13, 2021 · 28 comments
Closed

Extension not loading in jupyterlab 3 #713

gstorer opened this issue Jan 13, 2021 · 28 comments

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@gstorer
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gstorer commented Jan 13, 2021

In Jupyterlab 3.0.4 with Jupytext 1.9.1 on Ubuntu 20.04.1 LTS the filemanager does not appear to be loading. Specifically the log line that says the jupytext file manager loads in not showing up. I can use the console commands to pair a notebook but no additional files are saved. The GUI also does not show previously paired files as notebooks either.

I can use the most recent version of jupytext with jupyter notebook just fine. I can also downgrade to lab 2.2 and the old plugin and it works fine as well.

I have tried all variations of enabling and configuration files listed in the install documentation and nothing has worked. I am fairly sure there is a bug here but there's no error message so it is a bit hard to say.

Let me know if there's any more information I can provide.

Here's a little bit of additional debug info:

g@g-ThinkPad-P51:~$ jupyter labextension list
JupyterLab v3.0.4
/home/g/.local/share/jupyter/labextensions
        jupyterlab-jupytext v1.3.0 enabled OK (python, jupytext)
        @jupyter-widgets/jupyterlab-manager v3.0.0 enabled OK (python, jupyterlab_widgets)

Other labextensions (built into JupyterLab)
   app dir: /home/g/.local/share/jupyter/lab

Contents of .jupyter/jupyter_notebook_config.json:

{
  "NotebookApp": {
    "nbserver_extensions": {
      "jupytext": true
    }
  }
}
@mwouts
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mwouts commented Jan 13, 2021

Oh, sorry to hear that! And thanks for reporting it.

Well maybe a good starting point will be a comparison with Binder:lab

There we do have the notebook icon for text notebooks - which reveals that the Jupytext contents manager is active. Can you confirm that you don't have notebook icons any more for those files? Also, what is the output of

!jupyter serverextension list

On Binder I get this:

config dir: /srv/conda/envs/notebook/etc/jupyter
    jupyterlab  enabled 
    - Validating...
      jupyterlab 3.0.3 OK
    jupytext  enabled 
    - Validating...
      jupytext 1.9.1+dev OK
    nteract_on_jupyter  enabled 
    - Validating...
      nteract_on_jupyter 2.1.3 OK
    jupyter_offlinenotebook  enabled 
    - Validating...
      jupyter_offlinenotebook  OK
    nbresuse  enabled 
    - Validating...
      nbresuse  OK

Regarding the lab extension, it comes with the pip or conda package, so you're not expected to install it (unless you are using JupyterLab 2.x). My output for

!jupyter labextension list

on Binder, is a bit different from yours, a possible indication that you installed the labextension manually (unnecessary, still I don't think it should break the extension... do you have the 'pair notebook' commands in the commands window?)

JupyterLab v3.0.3
/srv/conda/envs/notebook/share/jupyter/labextensions
        jupyterlab-jupytext v1.3.0 enabled OK (python, jupytext)

Other labextensions (built into JupyterLab)
   app dir: /srv/conda/envs/notebook/share/jupyter/lab
        jupyter-offlinenotebook v0.1.0 enabled  X

   The following extension are outdated:
        jupyter-offlinenotebook
        
   Consider running "jupyter labextension update --all" to check for updates.

@gstorer
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gstorer commented Jan 14, 2021

I had done the manual labextension install. I was jumping backwards and forwards between 2.2 and 3.0 trying to figure out what wasn't working. I figured I needed to explicitly upgrade the labextension from 1.2.2 at the same time as upgrading jupyterlab.

I have just tried removing jupyter, jupyterlab and jupytext and starting again. Behavior is the same. I also installed jupyter_offlinenotebook and explicitly enabled the jupyterlab server extension to make my * list output more similar. It is still not loading. I am assuming nbreuse and nteract won't be having any impact.

Yes the jupytext pair commands show up.

g@g-ThinkPad-P51:~$ jupyter serverextension list
config dir: /home/g/.jupyter
    jupytext  enabled 
    - Validating...
      jupytext 1.9.1 OK
    jupyterlab  enabled 
    - Validating...
      jupyterlab 3.0.4 OK
    jupyter_offlinenotebook  enabled 
    - Validating...
      jupyter_offlinenotebook  OK
g@g-ThinkPad-P51:~$ jupyter labextension list
JupyterLab v3.0.4
/home/g/.local/share/jupyter/labextensions
        jupyterlab-jupytext v1.3.0 enabled OK (python, jupytext)
        jupyter-offlinenotebook v0.2.0 enabled OK

@mwouts
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mwouts commented Jan 14, 2021

Thanks for the update. So the problem is with the server extension, which only role is to replace the contents manager with Jupytext's one. Can you confirm that you don't see any log like

[I 2021-01-14 07:22:27.327 ServerApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager

when you run jupyter lab --log-level INFO? Or any other log that could be issued by the load_jupyter_server_extension function?

Note that, in case we don't find out immediately how to solve this issue with the server extension, you still have the possibility to set the contents manager in your Jupyter config, see https://jupytext.readthedocs.io/en/latest/install.html#jupytext-s-contents-manager

@gstorer
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gstorer commented Jan 14, 2021

This is what I get on startup. The relevant line is missing.

g@g-ThinkPad-P51:~$ jupyter lab --log-level INFO
[I 2021-01-14 17:35:26.596 ServerApp] jupyterlab | extension was successfully linked.
[I 2021-01-14 17:35:26.619 LabApp] JupyterLab extension loaded from /home/g/.local/lib/python3.8/site-packages/jupyterlab
[I 2021-01-14 17:35:26.620 LabApp] JupyterLab application directory is /home/g/.local/share/jupyter/lab
[I 2021-01-14 17:35:26.622 ServerApp] jupyterlab | extension was successfully loaded.
[I 2021-01-14 17:35:26.622 ServerApp] Serving notebooks from local directory: /home/g
[I 2021-01-14 17:35:26.622 ServerApp] Jupyter Server 1.2.1 is running at:
[I 2021-01-14 17:35:26.622 ServerApp] http://localhost:8888/lab?token=8d078599d75be94acf1195ddcccb06a6f6d4ffd687309c41
[I 2021-01-14 17:35:26.622 ServerApp]  or http://127.0.0.1:8888/lab?token=8d078599d75be94acf1195ddcccb06a6f6d4ffd687309c41
[I 2021-01-14 17:35:26.622 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2021-01-14 17:35:26.659 ServerApp] 
    
    To access the server, open this file in a browser:
        file:///home/g/.local/share/jupyter/runtime/jpserver-103756-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/lab?token=8d078599d75be94acf1195ddcccb06a6f6d4ffd687309c41
     or http://127.0.0.1:8888/lab?token=8d078599d75be94acf1195ddcccb06a6f6d4ffd687309c41
[I 2021-01-14 17:35:30.694 LabApp] Build is up to date

Unfortunately adding the below line to .jupyter/jupyter_notebook_config.py is one of the things I have already tried. It seems to have no effect.

c.NotebookApp.contents_manager_class = "jupytext.TextFileContentsManager"

@gstorer
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gstorer commented Jan 14, 2021

It occurred to me that perhaps I should be putting the above line in .jupyter/jupyter_lab_config.py since I am running jupyter lab This finally made something happen:

g@g-ThinkPad-P51:~$ jupyter lab
[W 2021-01-14 17:51:51.883 LabApp] 'contents_manager_class' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-01-14 17:51:51.938 ServerApp] The 'contents_manager_class' trait of a ServerApp instance expected a subclass of 'jupyter_server.services.contents.manager.ContentsManager', not the JupytextContentsManager JupytextContentsManager.
[I 2021-01-14 17:51:51.959 ServerApp] The port 8888 is already in use, trying another port.
[I 2021-01-14 17:51:51.962 LabApp] JupyterLab extension loaded from /home/g/.local/lib/python3.8/site-packages/jupyterlab
[I 2021-01-14 17:51:51.962 LabApp] JupyterLab application directory is /home/g/.local/share/jupyter/lab
[I 2021-01-14 17:51:51.965 ServerApp] jupyterlab | extension was successfully loaded.
[I 2021-01-14 17:51:51.965 ServerApp] Serving notebooks from local directory: /home/g
[I 2021-01-14 17:51:51.965 ServerApp] Jupyter Server 1.2.1 is running at:
[I 2021-01-14 17:51:51.965 ServerApp] http://localhost:8889/lab?token=10bebb1d65dbf85bcdebf776e151ff0fb4ed425d9837229b
[I 2021-01-14 17:51:51.965 ServerApp]  or http://127.0.0.1:8889/lab?token=10bebb1d65dbf85bcdebf776e151ff0fb4ed425d9837229b
[I 2021-01-14 17:51:51.965 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2021-01-14 17:51:52.003 ServerApp] 
    
    To access the server, open this file in a browser:
        file:///home/g/.local/share/jupyter/runtime/jpserver-105819-open.html
    Or copy and paste one of these URLs:
        http://localhost:8889/lab?token=10bebb1d65dbf85bcdebf776e151ff0fb4ed425d9837229b
     or http://127.0.0.1:8889/lab?token=10bebb1d65dbf85bcdebf776e151ff0fb4ed425d9837229b
[I 2021-01-14 17:51:55.656 LabApp] Build is up to date

@mwouts
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mwouts commented Jan 14, 2021

Arg this is becoming very technical... do you notice this?

'contents_manager_class' has moved from NotebookApp to ServerApp
... enpected a subclass of 'jupyter_server.services.contents.manager.ContentsManager'

This is something that is taken care of by the Jupytext server extension:
https://github.com/mwouts/jupytext/blob/master/jupytext/__init__.py#L40-L42

Of course we could reproduce that in your config file - something like

from jupytext.contentsmanager import build_jupytext_contents_manager_class
from jupyter_server.services.contents.largefilemanager import LargeFileManager

c.NotebookApp.contents_manager_class = build_jupytext_contents_manager_class(LargeFileManager)

But I think that a better advice would be to get the server extension working. Would you mind to create a new environment / jupyter config from scratch? Personally I like very much conda/mamba for this, I'd create an environment.yml file with this content (at least):

name: jupytext-env
channels:
  - defaults
  - conda-forge
dependencies:
  - jupyterlab >=3
  - jupytext

and run

mamba env create -n environment.yml

(or conda env ... if you don't have mamba)

@gstorer
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gstorer commented Jan 15, 2021

Ok, I am making some progress. Both the conda environment and your suggested hack in the config file worked. So it looks like its something in my environment that is breaking things.

This is the output from the conda environment.

(environment.yml) g@g-ThinkPad-P51:~$ jupyter lab
[I 2021-01-15 11:55:32.379 ServerApp] jupyterlab | extension was successfully linked.
[I 2021-01-15 11:55:32.379 ServerApp] jupytext | extension was successfully linked.
[I 2021-01-15 11:55:32.521 ServerApp] nbclassic | extension was successfully linked.
[I 2021-01-15 11:55:32.558 LabApp] JupyterLab extension loaded from /home/g/.local/lib/python3.8/site-packages/jupyterlab
[I 2021-01-15 11:55:32.558 LabApp] JupyterLab application directory is /home/g/.local/share/jupyter/lab
[I 2021-01-15 11:55:32.560 ServerApp] jupyterlab | extension was successfully loaded.
[I 2021-01-15 11:55:32.561 ServerApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[I 2021-01-15 11:55:32.561 ServerApp] jupytext | extension was successfully loaded.
[I 2021-01-15 11:55:32.564 ServerApp] nbclassic | extension was successfully loaded.
[I 2021-01-15 11:55:32.564 ServerApp] Serving notebooks from local directory: /home/g
[I 2021-01-15 11:55:32.564 ServerApp] Jupyter Server 1.2.1 is running at:
[I 2021-01-15 11:55:32.564 ServerApp] http://localhost:8888/lab?token=48fae4620011ae30889c74ccf2d851ecff750c6b6c4d3c26
[I 2021-01-15 11:55:32.564 ServerApp]  or http://127.0.0.1:8888/lab?token=48fae4620011ae30889c74ccf2d851ecff750c6b6c4d3c26
[I 2021-01-15 11:55:32.564 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2021-01-15 11:55:32.604 ServerApp] 
    
    To access the server, open this file in a browser:
        file:///home/g/.local/share/jupyter/runtime/jpserver-152979-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/lab?token=48fae4620011ae30889c74ccf2d851ecff750c6b6c4d3c26
     or http://127.0.0.1:8888/lab?token=48fae4620011ae30889c74ccf2d851ecff750c6b6c4d3c26
[I 2021-01-15 11:55:37.075 LabApp] Build is up to date

I typically use pipenv for my virtual python environments, for what its worth, a fresh pipenv environment also works fine. I then tried dumping as many packages as I can easily get from my user environment into the virtual environment (i.e. without ubuntu python packages and packages not on pypi). Jupytext works like this too. So there is something subtle wrong with my user environment.

I will see if a colleague can replicate my problem next week.

@mwouts
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mwouts commented Jan 15, 2021

Good news!

So there is something subtle wrong with my user environment

I agree. I think the point to investigate is why the Jupytext Server Extension is not loaded when you start Jupyter Lab - this is not consistent with what you have in jupyter serverextension list.

@gstorer
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gstorer commented Jan 18, 2021

My colleague can replicate it, although we have similar dev environments. I will try and see if it happens on a fresh Ubuntu 20 install but this may take a bit longer to find time for. It does work I am inclined to leave this issue since I have a couple of work-arounds. If it is broken on a new install I'll keep trying to find the root cause.

@mwouts
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mwouts commented Jan 18, 2021

Hi @gstorer , well I'll be happy to learn more about this - no hurry though. Sure we can keep this open, it can help other users if they face a similar issue.

@Zsailer
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Zsailer commented Jan 19, 2021

This appears to be an issue in the new jupyter_server and nbclassic (a layer to automatically shim extensions/managers from notebook to jupyter_server). An issue was just posted on nbclassic to handle custom manager classes working with jupyter_server and classic notebook's server.

jupyter/nbclassic#41

@mwouts
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mwouts commented Jan 19, 2021

Thanks @Zsailer for the link. It is correct that the inheritance issue appeared above when we tried to set the contents manager manually (as seen above, a workaround is to use the build_jupytext_contents_manager_class function). And I'll be glad to learn of better approaches!

However I am afraid that this is not the main issue in @gstorer's report here. I'd say that the main issue is this: according to jupytext serverextension list, the Jupytext server extension is active, but it is not loaded by Jupyter.

@alusiani
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Hi,

I had the same problem reported by @gstorer and I have solved it. I have jupyterlab < 3 and jupytext and all was fine. When I upgraded to jupyterlab 3.0 jupytext was not enabled any more.

No improvement with enabling / disabling jupytext in the various extensions (labextension, nbextension, serverextension), no improvement with reinstalling from scratch. I removed all user-installed extensions and installed from scratch, in my Linux Fedora 32 and even that did not work.

I started a new environment using pipenv, and that worked. I checked what was different and found that:

  • in the working installation there is a directory in the user config dir, ~/.jupyter/jupyter_notebook_config.d, containing 2 files, jupyterlab.json and jupytext.json;

  • in the non-working installation the config dir has instead a file, ~/.jupyter/jupyter_notebook_config.json, with content that seems appropriate but does not work:

{
  "NotebookApp": {
    "nbserver_extensions": {
      "jupytext": true
    }
  }
}

The problem apparenly is due to the configuration not being updated to a new format. I guess that all the trouble just comes from me having the file ~/.jupyter/jupyter_notebook_config.json in my user config folder. Probably, deleting it and reinstalling would also work, but I did not double check. What is working for me is having deleted ~/.jupyter/jupyter_notebook_config.json and added the folder ~/.jupyter/jupyter_notebook_config.d from the pipenv config folder.

I hope that this could help fixing personal installations and give a hint on what goes wrong in the installation procedure.

@mwouts
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mwouts commented Jan 21, 2021

Thank you @alusiani for the detailed information, that is very helpful! Yes apparently in the new config we don't need to mention jupytext in the jupyter_*_config.json files any more, but instead we need a few jupytext.json files.

In my local JupyterLab 3 install what I have is this:

/home/marc/miniconda3/envs/jupytext-dev/etc/jupyter
├── jupyter_nbconvert_config.json
├── jupyter_notebook_config.d
│   ├── jupyterlab.json
│   └── jupytext.json
├── jupyter_notebook_config.json
├── jupyter_server_config.d
│   ├── jupyterlab.json
│   ├── jupytext.json
│   └── nbclassic.json
└── nbconfig
    ├── notebook.d
    │   ├── jupytext.json
    │   └── widgetsnbextension.json
    ├── notebook.json
    └── tree.json

and my jupyter_notebook_config.json makes no mention of Jupytext.

@martinRenou , are you aware of such a change in the Jupyter configuration system? Do you know how to properly address the configuration update / and why the previous configuration seems to be left behind? Thanks!

@gstorer
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gstorer commented Jan 22, 2021

Thanks @alusiani. This also solved my problem.

Removing the ~/.jupyter directory and re-installing does not solve the problem for me. This was one of the first things I tried and I re-confirmed it this morning.

After an uninstall/reinstall my .jupyter directory is almost empty. Ominously there is a ~/.jupyter/migrated file that contains the install date. Running the command jupyter serverextension enable jupytext after an uninstall/reinstall also incorrectly creates a ~/.jupyter/jupyter_notebook_config.json rather than the correct *.d structure.

@gstorer
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gstorer commented Jan 22, 2021

Small update: the ~/.jupyter/migrated file was because of a old ~/.ipython directory I had from some time ago. I removed the old directory and reinstalled jupyter/ipython and the migrated file no longer appears. The configuration for jupytext and jupyter is still not correct or working without manual intervention.

@martinRenou
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@martinRenou , are you aware of such a change in the Jupyter configuration system?

I am not aware of that no

@0xc1c4da
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Just wanted to register that I am affected by this bug as well, tried the various options and config hacks, pipenv too. I also had the migrated file and ~/.ipython and removed them and reinstalled.

I can get the jupytext menu to appear in notebook but not in lab, and it doesn't appear to be functioning correctly and menu items create new ipynb's

@mwouts
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mwouts commented Feb 19, 2021

Hi @jarradh , thanks for reporting this issue. Could you please tell us what kind of icons you get for .md and .py files? (if you get a notebook icon then it means that Jupytext's contents manager is working OK, if not indeed you have the same issue as the one reported here).

Also it is expected that you get the Jupytext sub menu in Jupyter Notebook only. In JupyterLab all that is available are the Jupyter Commands, under View / Activate Command Palette.

Note that you can compare what you get locally with the screenshot in the documentation, and also compare with Binder:lab

@sbrunk
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sbrunk commented Oct 1, 2021

I just ran into this issue as well after installing jupytext along with jupyterlab outside of a virtual env via pip as a non-root Linux user (which implicitly sets the --user option on a pip install.

This results in the modern directory based config to be put into $HOME/.local/etc/jupyter, like this:

tree ~/.local/etc/jupyter 
.local/etc/jupyter
├── jupyter_notebook_config.d
│   ├── jupyterlab.json
│   ├── jupyter-server-proxy-notebookserverextension.json
│   └── jupytext.json
├── jupyter_server_config.d
│   ├── jupyterlab.json
│   ├── jupyter-server-proxy-jupyterserverextension.json
│   ├── jupytext.json
│   └── nbclassic.json

But jupyter only looks for config in $HOME/.jupyter and system paths, NOT in $HOME/.local/etc/jupyter (you can check with jupyter --paths). This is different in a conda env (and probably virtualenv) where jupyter also looks in /path-to-env/etc/jupyter.

So in my case the workaround was just a cp -r $HOME/.local/etc/jupyter/* $HOME/.jupyter/.

@alusiani
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alusiani commented Oct 1, 2021

I just ran into this issue as well after installing jupytext along with jupyterlab outside of a virtual env via pip as a non-root Linux user (which implicitly sets the --user option on a pip install.
...
So in my case the workaround was just a cp -r $HOME/.local/etc/jupyter/* $HOME/.jupyter/.

I think that you finally understood what happened. I do have $HOME/.local/etc/jupyter/ but I had not realized until now.
Thanks for the message.

@mwouts
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mwouts commented Oct 2, 2021

Well done @sbrunk! Thank you for your help in solving this long standing issue.

Next week I will make sure I can now reproduce the issue (I guess a simple pip install jupytext on a recent Ubuntu should do it?), and then I'll add a mention of the fix (copy the config files at the right place) to the documentation.

@sbrunk
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sbrunk commented Oct 3, 2021

Next week I will make sure I can now reproduce the issue (I guess a simple pip install jupytext on a recent Ubuntu should do it?), and then I'll add a mention of the fix (copy the config files at the right place) to the documentation.

Yes, I ran this on a Ubuntu 21.04 machine with regular Python 3.9 installed via APT.

@mwouts
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mwouts commented Oct 5, 2021

@sbrunk , I confirm that I am able to reproduce the issue and your resolution.

On Ubuntu 20.04, I have run

sudo apt-get install pip
pip install jupytext
pip install jupyter
export PATH=$PATH:~/.local/bin

With the above I do get the configuration files for Jupytext in ~/.local/etc/jupyter

$ tree ~/.local/etc/jupyter/
/home/marc/.local/etc/jupyter/
├── jupyter_notebook_config.d
│   ├── jupyterlab.json
│   └── jupytext.json
├── jupyter_server_config.d
│   ├── jupyterlab.json
│   ├── jupytext.json
│   └── nbclassic.json
└── nbconfig
    └── notebook.d
        └── jupytext.json

4 directories, 6 files

but as you said, they are not effective because that path is not listed in jupyter --paths:

$ jupyter --paths
config:
    /home/marc/.jupyter
    /usr/etc/jupyter
    /usr/local/etc/jupyter
    /etc/jupyter
data:
    /home/marc/.local/share/jupyter
    /usr/local/share/jupyter
    /usr/share/jupyter
runtime:
    /home/marc/.local/share/jupyter/runtime

The workaround cp -r $HOME/.local/etc/jupyter/* $HOME/.jupyter/ does work.

Another possibility seems to be

export JUPYTER_CONFIG_PATH="${HOME}/.local/etc/jupyter"

I think I'll open an issue on the Jupyter project to see what they recommend (I'll also ask if ${HOME}/.local/etc/jupyter is a standard config location, or not)

@mwouts
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mwouts commented Oct 13, 2021

Hi everyone, I wanted to let you know that the issue should be solved in jupyter_core==4.9.0.

At the moment a RC candidate for jupyter_core is available (thanks to @jasongrout)

pip install jupyter_core==4.9.0rc0

Could you please give it a try and confirm that it does solve the issue?

@alusiani
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Hi everyone, I wanted to let you know that the issue should be solved in jupyter_core==4.9.0.

At the moment a RC candidate for jupyter_core is available (thanks to @jasongrout)

pip install jupyter_core==4.9.0rc0

Could you please give it a try and confirm that it does solve the issue?

I will try but I have to find the time...

@gstorer
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gstorer commented Dec 2, 2021

The issue is solved for me with jupyter_core==4.9.1

@mwouts mwouts closed this as completed Dec 10, 2021
@davidbacter01
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Just ran into this issue with jupyterlab 3.6 while developing an extension. Front end part was working but the server part did not although it appeared as enabled.
This was my fix:
copy
C:\Users\<user>\Anaconda3\envs\<extension_env>\etc\jupyter\jupyter_server_config.d\<server_extension>.json
to
C:\Users\<user>\Anaconda3\etc\jupyter\jupyter_server_config.d

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