# Jupyter and Jupytext through IJulia.jl (Jupytext does not really work)

**URL:** <https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330>\
**Category:** Jupyter-Notebook\
**Tags:** jupyter, configuration, conda, conda-forge, jupytext\
**Created:** [June 28, 2024, 1:12am UTC](https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330 "2024-06-28T01:12:11Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Henrique\_Becker](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/henrique_becker/32/15443_2.png) [@Henrique\_Becker](https://discourse.julialang.org/u/Henrique_Becker)\
**Post date:** [June 28, 2024, 1:12am UTC](https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330/1 "2024-06-28T01:12:11Z")

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Is anyone using `IJulia` to provide `jupyter-lab` and employing the `jupytext` extension? I was unable to configure my Arch Linux do to so. I did a fresh install of Julia 1.10.4, then installed the `IJulia` in an environment, and used the `Conda` dependency of `IJulia` (which it uses to install `jupyter`) to then install `jupytext`. It worked to a degree, because the context menu shows the jupytext options but then it errors if I try to use `(right-click on jupytext notebook file) > Open With > Jupytext Notebook`, the error message is:

```julia
UnreadableNotebook: .../file.jl
NotJSONError("Notebook does not appear to be JSON: '# ---\\n# jupyter:\\n# jupytext:\\n# ...")

```

I have tried debugging and the `jupytext` extension is not being really loaded:

```julia
[I 2024-06-27 22:02:03.170 LabApp] JupyterLab extension loaded from /home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyterlab
[I 2024-06-27 22:02:03.170 LabApp] JupyterLab application directory is /home/henrique/.julia/conda/3/x86_64/share/jupyter/lab
[I 2024-06-27 22:02:03.170 LabApp] Extension Manager is 'pypi'.
[I 2024-06-27 22:02:03.180 ServerApp] jupyterlab | extension was successfully loaded.
[W 2024-06-27 22:02:03.181 ServerApp] [Jupytext Server Extension] Async contents managers like AsyncLargeFileManager are not supported at the moment (https://github.com/mwouts/jupytext/issues/1020). We will derive a contents manager from LargeFileManager instead.
[I 2024-06-27 22:02:03.181 ServerApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[W 2024-06-27 22:02:03.181 ServerApp] jupyterlab_jupytext | extension failed loading with message: NameError("name 'build_jupytext_contents_manager_class' is not defined")
    Traceback (most recent call last):
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 360, in load_extension
        extension.load_all_points(self.serverapp)
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 232, in load_all_points
        return [self.load_point(point_name, serverapp) for point_name in self.extension_points]
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 232, in <listcomp>
        return [self.load_point(point_name, serverapp) for point_name in self.extension_points]
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 223, in load_point
        return point.load(serverapp)
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 151, in load
        return loader(serverapp)
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyterlab_jupytext/ __init__.py", line 43, in load_jupyter_server_extension
        app.contents_manager_class = build_jupytext_contents_manager_class(base_class)
    NameError: name 'build_jupytext_contents_manager_class' is not defined. Did you mean: 'build_jupytext_contents_manager'?

```

If I go to that file I see at the start:

```julia
try:
    from jupytext.contentsmanager import build_jupytext_contents_manager_class
except ImportError as err:
    build_jupytext_contents_manager = reraise(err)

[...]

```

So the name should exist, unless it throws an exception. Which it does. If I remove the try-except, I get:

```julia
[W 2024-06-27 22:01:09.027 ServerApp] jupyterlab_jupytext | error adding extension (enabled: True): The module 'jupyterlab_jupytext' could not be found (No module named 'notebook'). Are you sure the extension is installed?
    Traceback (most recent call last):
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 323, in add_extension
        extpkg = ExtensionPackage(name=extension_name, enabled=enabled)
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 187, in __init__
        self._load_metadata()
      File "/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyter_server/extension/manager.py", line 202, in _load_metadata
        raise ExtensionModuleNotFound(msg) from None
    jupyter_server.extension.utils.ExtensionModuleNotFound: The module 'jupyterlab_jupytext' could not be found (No module named 'notebook'). Are you sure the extension is installed?

```

However the files exists in `/home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyterlab_jupytext/` as well as a `jupytext` package and they define the `build_jupytext_contents_manager_class` it is just that it is not being found really.

So I think my question is, really, how I guarantee that this `jupyter` installation inside `.julia/conda` finds the correct Python packages.

---

<div class="post-metadata">

**Author:** ![stevengj](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/stevengj/32/71_2.png) [@stevengj](https://discourse.julialang.org/u/stevengj)\
**Post date:** [June 28, 2024, 3:06am UTC](https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330/2 "2024-06-28T03:06:41Z")

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(Note that you don’t need to use `jupyter` installed via Conda.jl. You can install `jupyter` via Arch Linux’s `pacman`, or in some other way. It will still find the IJulia kernel.)

---

<div class="post-metadata">

**Author:** ![Henrique\_Becker](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/henrique_becker/32/15443_2.png) [@Henrique\_Becker](https://discourse.julialang.org/u/Henrique_Becker)\
**Post date:** [June 28, 2024, 7:30pm UTC](https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330/3 "2024-06-28T19:30:19Z")

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The problem with this alternative is that `jupyter` has an official Arch package but `jupytext` only has one in the AUR (unofficial), and I believe it fails to build. This is the reason I decided to do the things this way.

---

<div class="post-metadata">

**Author:** ![Henrique\_Becker](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/henrique_becker/32/15443_2.png) [@Henrique\_Becker](https://discourse.julialang.org/u/Henrique_Becker)\
**Post date:** [July 3, 2024, 3:07pm UTC](https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330/4 "2024-07-03T15:07:59Z")

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# jupyter / jupyter-lab / jupyter-lab (howto)

Installing `jupyter` by means of `IJulia` seems like a trap. If I do it, I am not able to make `jupytext` work with `jupyter-notebook` or `jupyter-lab`. So what worked for me follows.

- In any folder you can run:
  - `sudo aura -A miniconda3` # aura is my AUR package installer, use yours instead
  - `sudo ln -s /opt/miniconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh`
  - `echo "[-f /opt/miniconda3/etc/profile.d/conda.sh] && source /opt/miniconda3/etc/profile.d/conda.sh" >> ~/.bashrc` # I use bash, if you use zsh adapt

- Reopen the terminal, so it updates the variables, and then run in any folder:
  - `conda create -n myenv jupyter jupytext` # you can give a better name than myenv
  - `conda activate myenv` # not sure if the next steps need conda activated, but we will keep it for the rest of the steps

- The IJulia is still needed to create the Julia Kernel. If you install it locally to an environment (like I do, I never install packages to the global Julia environment), you will need to put the path to the environment in the kernel specification (and basically use one kernel per project).
- So in the folder that you will use as environment for the Julia notebooks do:
  - `julia --project=. -e 'using Pkg: Pkg; Pkg.add("IJulia");'` # will not ask to install jupyter this way, if it asks then refuse
  - `julia --project=. -e 'using IJulia: IJulia; IJulia.installkernel("Julia My Kernel Name", "-O2", "--project=$(pwd())", env=Dict("LD_LIBRARY_PATH" => ""))'` # the LD\_LIBRARY\_PATH=“” comes from an annoying bug of Julia in Arch Linux

- And then finally:
  - `jupyter-lab`

---

<div class="post-metadata">

**Author:** ![tobydriscoll](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tobydriscoll/32/1843_2.png) [@tobydriscoll](https://discourse.julialang.org/u/tobydriscoll)\
**Post date:** [July 3, 2024, 3:51pm UTC](https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330/5 "2024-07-03T15:51:34Z")

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> [@Henrique\_Becker](#):
>
> I did a fresh install of Julia 1.10.4, then installed the `IJulia` in an environment, and used the `Conda` dependency of `IJulia` (which it uses to install `jupyter`) to then install `jupytext`.

I wrote a [book](https://tobydriscoll.net/fnc-julia) using jupytext a couple of years ago, and while it wasn’t all rainbows and kittens, it was pretty easy to use. But I installed and ran jupytext independently outside of Julia from the start. Sometimes I found it easier to copy and edit kernel definition files directly than to install kernels “officially.”