`nb_custom_format` cannot overwrite default `.ipynb` extension

[kai-tub]

Describe the problem

I would like to pre-process my ipynb files and have created a package that does so. The approach is described in Custom notebook formats and Jupytest. However, I am not able to overwrite the default behavior. I would assume that every one that is specifically providing a different entry point for .ipynb files knows what they are doing and expects it to replace the default loader.

Given the documentation, I would expect that the default loader does exactly:

nbformat.reads(ipynb_file_contents, 4

If this is not the case, I am maybe missing something basic and this issue is probably not a bug. :)

Link to your repository or website

No response

Steps to reproduce

Add the following configuration to _conf.yml that is also given in the Custom notebook formats and Jupytest documentation:

sphinx:
  config:
    nb_custom_formats:
      .ipynb:
        - nbformat.reads
        - as_version: 4

An extension error is raised that the source_suffix .ipynb is already registered.

Extension error:
Config Path: <PATH>/_config.yml
source_suffix '.ipynb' is already registered
Output Path: <PATH>/_build/html
Traceback (most recent call last):
Running Sphinx v4.3.2
  File "<PYPATH>/lib/python3.8/site-packages/jupyter_book/sphinx.py", line 114, in build_sphinx
making output directory... done
    app = Sphinx(
ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['jupyter-book', 'build', '<BOOK_NAME>']' command failed.  (See above for error)
error: Recipe `build` failed on line 8 with exit code 1

The version of Python you're using

3.8.12

Your operating system

Linux-amd64

Versions of your packages

Jupyter Book      : 0.12.1
External ToC      : 0.2.3
MyST-Parser       : 0.15.2
MyST-NB           : 0.13.1
Sphinx Book Theme : 0.1.7
Jupyter-Cache     : 0.4.3
NbClient          : 0.5.9

Additional context

No response

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[chrisjsewell]

See: https://github.com/executablebooks/meta/discussions/613#discussioncomment-1913981

[nishikantparmariam]

My use-case is very similar to this - writing a custom preprocessor for notebooks.

I faced the exact issue source_suffix '.ipynb' is already registered when writing nb_custom_format for .ipynb, though it worked for other custom formats like .my_ipynb.

As per this executablebooks/discussions/613#discussioncomment-1913981 answer and my understanding from changelog this feature has been released with MyST-NB v0.14.0. I tried it with MyST-NB v0.15.0 and it works for .ipynb.

The only problem is that JupyterBook gives warnings as it still uses an older version of MyST-NB (ref) . Do we have a timeline to upgrade MyST-NB to v0.14.0 or v0.15.0 in JupyterBook? It would also solve this issue.

Please let me know if I am missing something as I have recently started using JupyterBook. Thank you.