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Jupytext failed to open *.py file as notebook in sagemaker studio aws #1162

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ihgumilar opened this issue Nov 18, 2023 · 13 comments
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@ihgumilar
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ihgumilar commented Nov 18, 2023

Hi Team,

I have installed already jupytext, but when I try to open *.py file with jupyter notebook, it throws me an error ( I am using jupyterlab 4 :

image

image

I have installed it in sagemaker studio and also put this code in life cycle configuration as suggested by this forum, but I changed it slightly

#!/bin/bash

set -e

# Install the appropriate version of the Jupytext extension for JupyterLab 3
jupyter labextension install jupyterlab-jupytext@1.3.9 

# Allow Jupyter to open and save notebooks as text files
echo c.NotebookApp.contents_manager_class="jupytext.TextFileContentsManager" >> /home/sagemaker-user/.jupyter/jupyter_notebook_config.py

Note, even though, I remove the configuration file, it still gives me the above error.

I would really appreciate for your help. Thanks a lot for your help :)

@mwouts
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mwouts commented Nov 18, 2023

Hi @ihgumilar , have you installed the Python package? I mean, pip install jupytext<1.16?

Also

  • You don't need the npm extension (jupyterlab-jupytext@1.3.9), it's already in the pip package
  • You don't need to modify your Jupyter configuration (you can remove the line about contents_manager_class)

@ihgumilar
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Hi @mwouts thanks for the reply.
Yes, I installed the package in docker with jupytext 1.15.2

For the last two points, when I excluded them. It still shows the same problem. In fact, I tried to add both of them a bit later after encountering such issue.

Any help ?

@ihgumilar ihgumilar changed the title Jupytext failed to open *.py file as notebook Jupytext failed to open *.py file as notebook in sagemaker studio aws Nov 18, 2023
@henriquebecker91
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I have the same problem, I cannot open jl files as Julia Jupytext Notebooks (even if I used jupytext to convert them in a jl file from a ipynb file). It does not work in Jupyter Notebook or Labs. Pairing a ipynb to a percent format and saving the ipynb also does not generate the percent format file. I am using jupytext-1.16.2.

@mwouts
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mwouts commented Jun 27, 2024

Hi @henriquebecker91 , the problem that you describe is consistent with no having the Jupytext contents manager.

In most cases it's not necessary to install manually the npm extension (the one called jupyterlab-jupytext) since it's provided by the pip package. Installing it manually provides the Jupytext menu and leads you to think that Jupytext is installed, but it's only the menu and hence you don't get the pairing functionality.

You don't need to tweak the configuration file neither.

But you do need to install Jupytext's pip or conda package before launching the Jupyter server.

One way to check that Jupytext's contents manager is installed is to check the icon for .py or .md documents. If you get a notebook icon then the contents manager is active, otherwise it's not.

It might help too to see the logs of the Jupyter server too.

@henriquebecker91
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I have jupyter installed by means of the package IJulia of the Julia language. It provides jupyter by means of the Conda.jl package which creates a conda repository just for Julia separate from the rest of the system. I have installed jupytext using this conda installation. I will try to get the Jupyter server logs.

@henriquebecker91
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The full output if I run Jupyter directly.

pandoc: error while loading shared libraries: libHSfast-logger-3.1.2-FNZAUVo6d0d4dB71mp2JZD-ghc9.2.8.so: cannot open shared object file: No such file or directory
[I 2024-06-27 19:44:12.225 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2024-06-27 19:44:12.228 ServerApp] jupyter_server_terminals | extension was successfully linked.
[I 2024-06-27 19:44:12.231 ServerApp] jupyterlab | extension was successfully linked.
[I 2024-06-27 19:44:12.231 ServerApp] jupyterlab_jupytext | extension was successfully linked.
[I 2024-06-27 19:44:12.231 ServerApp] jupytext | extension was successfully linked.
[I 2024-06-27 19:44:12.234 ServerApp] notebook | extension was successfully linked.
[I 2024-06-27 19:44:12.386 ServerApp] notebook_shim | extension was successfully linked.
[I 2024-06-27 19:44:12.398 ServerApp] notebook_shim | extension was successfully loaded.
[I 2024-06-27 19:44:12.399 ServerApp] jupyter_lsp | extension was successfully loaded.
[I 2024-06-27 19:44:12.400 ServerApp] jupyter_server_terminals | extension was successfully loaded.
[I 2024-06-27 19:44:12.401 LabApp] JupyterLab extension loaded from /home/henrique/.julia/conda/3/x86_64/lib/python3.10/site-packages/jupyterlab
[I 2024-06-27 19:44:12.401 LabApp] JupyterLab application directory is /home/henrique/.julia/conda/3/x86_64/share/jupyter/lab
[I 2024-06-27 19:44:12.401 LabApp] Extension Manager is 'pypi'.
[I 2024-06-27 19:44:12.412 ServerApp] jupyterlab | extension was successfully loaded.
[W 2024-06-27 19:44:12.412 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 19:44:12.412 ServerApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[W 2024-06-27 19:44:12.412 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 44, 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'?
[I 2024-06-27 19:44:12.413 ServerApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from AsyncLargeFileManager
[W 2024-06-27 19:44:12.413 ServerApp] 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/.local/lib/python3.10/site-packages/jupytext/__init__.py", line 40, in load_jupyter_server_extension
        app.contents_manager_class = build_jupytext_contents_manager_class(
    NameError: name 'build_jupytext_contents_manager_class' is not defined. Did you mean: 'build_jupytext_contents_manager'?
[I 2024-06-27 19:44:12.416 ServerApp] notebook | extension was successfully loaded.
[I 2024-06-27 19:44:12.416 ServerApp] Serving notebooks from local directory: /home/henrique/backup_Academia_2024-03-18/colaboracoes/AllReposCollabBeckerLucenaResende2023/BeckerLucenaResende2023/notebooks/old_notebook
[I 2024-06-27 19:44:12.416 ServerApp] Jupyter Server 2.14.1 is running at:
[I 2024-06-27 19:44:12.416 ServerApp] http://localhost:8888/lab?token=7c47ae24564ab0a2daee003e08a66286af931ee01d747b01
[I 2024-06-27 19:44:12.416 ServerApp]     http://127.0.0.1:8888/lab?token=7c47ae24564ab0a2daee003e08a66286af931ee01d747b01
[I 2024-06-27 19:44:12.417 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 2024-06-27 19:44:12.447 ServerApp] 
    
    To access the server, open this file in a browser:
        file:///home/henrique/.local/share/jupyter/runtime/jpserver-58566-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/lab?token=7c47ae24564ab0a2daee003e08a66286af931ee01d747b01
        http://127.0.0.1:8888/lab?token=7c47ae24564ab0a2daee003e08a66286af931ee01d747b01
[I 2024-06-27 19:44:12.801 ServerApp] Skipped non-installed server(s): bash-language-server, dockerfile-language-server-nodejs, javascript-typescript-langserver, jedi-language-server, julia-language-server, pyright, python-language-server, python-lsp-server, r-languageserver, sql-language-server, texlab, typescript-language-server, unified-language-server, vscode-css-languageserver-bin, vscode-html-languageserver-bin, vscode-json-languageserver-bin, yaml-language-server
^C[I 2024-06-27 19:44:14.694 ServerApp] interrupted
[I 2024-06-27 19:44:14.694 ServerApp] Serving notebooks from local directory: /home/henrique/backup_Academia_2024-03-18/colaboracoes/AllReposCollabBeckerLucenaResende2023/BeckerLucenaResende2023/notebooks/old_notebook
    0 active kernels
    Jupyter Server 2.14.1 is running at:
    http://localhost:8888/lab?token=7c47ae24564ab0a2daee003e08a66286af931ee01d747b01
        http://127.0.0.1:8888/lab?token=7c47ae24564ab0a2daee003e08a66286af931ee01d747b01
Shut down this Jupyter server (y/[n])? [I 2024-06-27 19:44:15.389 LabApp] Build is up to date
y
[C 2024-06-27 19:44:15.725 ServerApp] Shutdown confirmed
[I 2024-06-27 19:44:15.726 ServerApp] Shutting down 7 extensions

@henriquebecker91
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@mwouts
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mwouts commented Jun 30, 2024

Hi @henriquebecker91 , thank you for the logs, that's very helpful. I see that there is a typo in the try/except of the import - I'll fix that, but the import should not fail in the first place.

Could you provide some instructions on how to install IJulia locally? And then share the details of how you are installing Jupytext? Thanks!

@mwouts mwouts mentioned this issue Jun 30, 2024
@henriquebecker91
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Sure! Thank your for looking into that.

I downloaded the last stable version of Julia (1.10.4) from here: https://julialang.org/downloads/
After installing (i.e., unzipping and putting the path to julia-1.10.4/bin/ folder in my PATH environment variable), you can create a folder for the Julia project (just we do not install things globally) and inside this folder execute:

julia --project=. -e 'using Pkg: Pkg; Pkg.add("IJulia");'

This should give you a prompt asking if you want to install Jupyter by means a conda installation internal to Julia and only used by Julia, I said yes to that.
Then I installed jupytext using the Julia package that wraps the inner conda installation:

julia --project=. -e 'using Conda: Conda; Conda.add("jupytext");'

We can run Jupyter Lab by means of julia --project=. -e 'using IJulia: IJulia; IJulia.jupyterlab(; dir = pwd())' (this will use the current folder as root for jupyter). However, this does not give a debug output for Jupyter (only print a bunch of env variables set when calling jupyter-lab). I have run /home/henrique/.julia/conda/3/x86_64/bin/jupyter-lab to get the error messages.

@mwouts
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mwouts commented Jul 2, 2024

Hi @henriquebecker91 , thanks for the detailed instructions! I did it a quick try, and I realize that it did not went exactly as the above.

julia --project=. -e 'using Pkg: Pkg; Pkg.add("IJulia");'

That worked

This should give you a prompt asking if you want to install Jupyter by means a conda installation internal to Julia and only used by Julia, I said yes to that.

That did not happen on my end

julia --project=. -e 'using Conda: Conda; Conda.add("jupytext");'

I got that error:

ERROR: ArgumentError: Package Conda not found in current path.
- Run `import Pkg; Pkg.add("Conda")` to install the Conda package.

So I installed conda as instructed, and then installed Jupytext

conda activate /home/marc/.julia/conda/3/x86_64

That worked, but Jupyter Lab was not installed, so I ran julia --project=. -e 'using Conda: Conda; Conda.add("jupyterlab");'

After that I was able to launch jupyter lab and I could create a paired Julia notebook.

julia --project=. -e 'using IJulia: IJulia; IJulia.jupyterlab(; dir = pwd())'

That also seemed to work on my end

@mwouts
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mwouts commented Jul 2, 2024

So I guess the difference between my environment and yours is how Jupyter was installed. Possibly there are additional packages on your end. Maybe we can compare our conda list?

My conda list
# packages in environment at /home/marc/.julia/conda/3/x86_64:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
archspec                  0.2.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h2372a71_4    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
boltons                   24.0.0             pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.28.1               hd590300_0    conda-forge
ca-certificates           2024.6.2             hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2024.6.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py310h2fee648_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
conda                     24.3.0          py310hff52083_0    conda-forge
conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
debugpy                   1.8.2           py310h76e45a6_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distro                    1.9.0              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fmt                       10.2.1               h00ab1b0_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
importlib-metadata        8.0.0              pyha770c72_0    conda-forge
importlib_metadata        8.0.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.26.0             pyh707e725_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py310hff52083_3    conda-forge
jsonschema                4.22.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.22.0             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py310hff52083_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.1             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.2             pyhd8ed1ab_0    conda-forge
jupytext                  1.16.2             pyhd8ed1ab_1    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libarchive                3.7.2                h2aa1ff5_1    conda-forge
libcurl                   8.7.1                hca28451_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libmamba                  1.5.8                had39da4_0    conda-forge
libmambapy                1.5.8           py310h39ff949_0    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.28               hfc55251_2    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.6               h232c23b_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.5.8           py310h51d5547_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.5           py310h2372a71_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mdit-py-plugins           0.4.1              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
menuinst                  2.0.2           py310hff52083_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.4.20240210         h59595ed_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
openssl                   3.3.1                h4ab18f5_1    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.4.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
psutil                    6.0.0           py310hc51659f_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py310h2372a71_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.14         hd12c33a_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    4_cp310    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py310h2372a71_1    conda-forge
pyzmq                     26.0.3          py310h6883aea_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
reproc                    14.2.4.post0         hd590300_1    conda-forge
reproc-cpp                14.2.4.post0         h59595ed_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.18.1          py310he421c4c_0    conda-forge
ruamel.yaml               0.18.6          py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.8           py310h2372a71_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                69.5.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1           py310hc51659f_0    conda-forge
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.6.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.8.0                h59595ed_0    conda-forge
zeromq                    4.3.5                h75354e8_4    conda-forge
zipp                      3.19.2             pyhd8ed1ab_0    conda-forge
zstandard                 0.22.0          py310h1275a96_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

@henriquebecker91
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I executed a diff, and our lists are exactly equal except by the header (because of the home folder name).

So I installed conda as instructed, and then installed Jupytext

conda activate /home/marc/.julia/conda/3/x86_64

I repeated the steps without the above and have the same problem. The step above should not be necessary, as julia manages conda to use the right environment. In my case, I cannot even do it, because I do not have a conda installation outside Julia (I do not have the Arch Linux conda package installed, as there is no official package for conda). I will try to install the unofficial package for miniconda (that seems up to date) and try to install jupyter and jupytext using an external miniconda to activate the conda installation internal to julia.

@henriquebecker91
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I posted my step-by-step to be able to make jupytext work with jupyter in Arch Linux with Julia/IJulia here: https://discourse.julialang.org/t/jupyter-and-jupytext-through-ijulia-jl-jupytext-does-not-really-work/116330/4?u=henrique_becker

It seems like trying to use the jupyter installation provided by julia/IJulia by means of their internal miniconda installation is a trap.

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