Failing conda environment

[oyvfoss]

(Awesome project! Hoping to contribute here in the future).

Creating a conda/mamba environment from environment.yml, I run into an error:

The issue seems to arise when installing jupyter_contrib_nbextensions.

-> Returns a long string of warnings/errors involving "No module named 'notebook.nbextensions", and stops the installation.

It seems that jupyter_contrib_nbextensions is incompatible with the most recent version of Jupyter notebook
(e.g. ipython-contrib/jupyter_contrib_nbextensions#1650).

Two possible solutions occur to me:

1. Remove jupyter_contrib_nbextensions or replace with alternatives.
2. Force an older version of jupyter notebook.

• Installing notebook=6 before jupyter_contrib_nbextensions gets me a bit further, but still returns in an error.

It seems possible that jupyter_contrib_nbextensions is near- or semi-abandoned (ipython-contrib/jupyter_contrib_nbextensions#1640), so my preference is option 1. However, it is not clear to me what jupyter_contrib_nbextensions is used for exactly -perhaps it isn't viable.

Happy to work on a PR if you agree..

Output when installing the environment

 File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
    from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
    from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
    from ._compat.nbextensions import BaseNBExtensionApp
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
    from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'

| Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
    from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
    from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
    from ._compat.nbextensions import BaseNBExtensionApp
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
    from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'

\ Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/bin/jupyter-nbextensions_configurator", line 6, in <module>
    from jupyter_nbextensions_configurator.application import main
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_nbextensions_configurator/__init__.py", line 17, in <module>
    from notebook import version_info as nb_version_info
ImportError: cannot import name 'version_info' from 'notebook' ([userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/notebook/__init__.py)

- Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
    from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
    from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/bin/jupyter-contrib-nbextension", line 6, in <module>
    from jupyter_contrib_nbextensions.application import main
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_nbextensions/application.py", line 7, in <module>
    from jupyter_contrib_core.notebook_compat.nbextensions import ArgumentConflict
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
    from ._compat.nbextensions import BaseNBExtensionApp
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
    from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'

done
ERROR conda.core.link:_execute(740): An error occurred while installing package 'conda-forge::jupyter_highlight_selected_word-0.2.0-py38h578d9bd_1005'.
Rolling back transaction: done
post-link script failed for package conda-forge::jupyter_highlight_selected_word-0.2.0-py38h578d9bd_1005
location of failed script: [userpath]mambaforge/envs/ctdproc/bin/.jupyter_highlight_selected_word-post-link.sh
==> script messages <==
Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
    from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
    from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
    from ._compat.nbextensions import BaseNBExtensionApp
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
    from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'

==> script output <==
stdout: 
stderr: 
return code: 1

()


LinkError: post-link script failed for package conda-forge::jupyter_highlight_selected_word-0.2.0-py38h578d9bd_1005
location of failed script: [userpath]mambaforge/envs/ctdproc/bin/.jupyter_highlight_selected_word-post-link.sh
==> script messages <==
Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
    from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
    from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
    from ._compat.nbextensions import BaseNBExtensionApp
  File "[userpath]mambaforge/envs/ctdproc/lib/python3.8/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
    from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'

==> script output <==
stdout: 
stderr: 
return code: 1

()

[gunnarvoet]

Hi @oyvlun, thanks so much for your interest in this project!

This was my old environment definition when I started working on the package. As you point out, it is outdated and I think that in fact it should be agnostic of how the user wants to edit code and run jupyter notebooks. I went ahead and updated environment.yml in #33. Let me know if you think this fixes your issue and we can close this.

[oyvfoss]

Great! I can now build the environment from the updated environment.yml. Thanks for fixing!