not working if jupyter_contrib_nbextensions are installed

[hoba87]

I tried to convert a Jupyter notebook to python script with jupyter nbconvert --to python ...

This gave me an error if outdated? jupyter_contrib_nbextension is installed:

Traceback (most recent call last):
  File "/opt/python/python-3.10.10/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/opt/python/python-3.10.10/lib/python3.10/site-packages/nbconvert/nbconvertapp.py", line 193, in <module>
    class NbConvertApp(JupyterApp):
  File "/opt/python/python-3.10.10/lib/python3.10/site-packages/nbconvert/nbconvertapp.py", line 252, in NbConvertApp
    Options include {get_export_names()}.
  File "/opt/python/python-3.10.10/lib/python3.10/site-packages/nbconvert/exporters/base.py", line 145, in get_export_names
    e = get_exporter(exporter_name)(config=config)
  File "/opt/python/python-3.10.10/lib/python3.10/site-packages/nbconvert/exporters/base.py", line 106, in get_exporter
    exporter = items[0].load()
  File "/opt/python/python-3.10.10/lib/python3.10/importlib/metadata/__init__.py", line 171, in load
    module = import_module(match.group('module'))
  File "/opt/python/python-3.10.10/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/opt/python/python-3.10.10/lib/python3.10/site-packages/jupyter_contrib_nbextensions/nbconvert_support/__init__.py", line 5, in <module>
    from .collapsible_headings import ExporterCollapsibleHeadings
  File "/opt/python/python-3.10.10/lib/python3.10/site-packages/jupyter_contrib_nbextensions/nbconvert_support/collapsible_headings.py", line 6, in <module>
    from notebook.services.config import ConfigManager
ModuleNotFoundError: No module named 'notebook.services'

However, when I uninstall it, it works.
So probably, the priority to use it should be downgraded or completely removed.

[krassowski]

This issue is in jupyter_contrib_nbextensions and should be reported over there.

[blaiseli]

I have a similar problem, and I would like to point out that I was somehow "forced" to install jupyter_contrib_nbextensions.

I start from a fresh virtual env:

$ /home/bli/python3.11/bin/python3 -m venv .venv
$ source .venv/bin/activate
$ pip install --upgrade pip
$ pip install nbconvert

I check that jupyter nbconvert --help works:

$ jupyter nbconvert --help

Output looks OK.

Then I try the following command:

$ jupyter nbconvert --to notebook --ClearOutputPreprocessor.enabled=True Make_vsRNA_graphs.ipynb --output tmp.ipynb

This ends up with the following error:

ModuleNotFoundError: No module named 'jupyter_contrib_nbextensions'

Is this error due to the particular type of conversion I'm asking jupyter nbconvert to perform? Or can this be related to the content of my notebook?

Anyway, I proceed to install jupyter_contrib_nbextensions:

$ pip install jupyter_contrib_nbextensions

But then jupyter nbconvert --help fails as follows:

    from notebook.services.config import ConfigManager
ModuleNotFoundError: No module named 'notebook.services'

(Same error with jupyter nbconvert --to notebook --ClearOutputPreprocessor.enabled=True Make_vsRNA_graphs.ipynb --output tmp.ipynb)

Some of the latest issues regarding jupyter_contrib_nbextensions suggest me that it will be hard to get a fix on their side:

ipython-contrib/jupyter_contrib_nbextensions#1661

ipython-contrib/jupyter_contrib_nbextensions#1666

ipython-contrib/jupyter_contrib_nbextensions#1667

Pull requests seem to be pending since quite some time:
https://github.com/ipython-contrib/jupyter_contrib_nbextensions/pulls

[blaiseli]

Fixes discussed here work for me:
ipython-contrib/jupyter_contrib_nbextensions#1663 (comment)

I forked the fork on which the above pull request is based and added the extra modification to src/jupyter_contrib_nbextensions/nbconvert_support/execute_time.py:

https://github.com/blaiseli/jupyter_contrib_nbextensions

Then:

pip uninstall jupyter_contrib_nbextensions
pip install git+https://github.com/blaiseli/jupyter_contrib_nbextensions

Now jupyter nbconvert --to notebook --ClearOutputPreprocessor.enabled=True Make_vsRNA_graphs.ipynb --output tmp.ipynb doesn't crash any more.