nbconvert is running import code from examples

[eeholmes]

Reference this line in GitHub Action:

coastal_topobathy/.github/workflows/docs_pages.yml

Line 40 in f027c49

jupyter nbconvert --to markdown docs/source/examples/*.ipynb

jupyter nbconvert is not supposed to execute the notebook and it doesn't seem to execute any code blocks except the first code block with imports. The other code blocks are not being run. See for example where you see the 'module not found error showing up'
https://eeholmes.github.io/coastal_topobathy/examples/OpenAltimetry_example.html

Brainstorm of possible problems. Not that any of these really make sense but for the life of me I can't figure out why nbconvert is executing any of the code blocks!

• The notebook state actually has that error. No, it is fine on the JupyterLab notebook that I saved.
• It always runs the first code block; No, problem persists when I put a code block with just # at top
• It always runs the import blocks? Need to test more but there is a lower code with an import that is ok.
• Has something to do with copying the notebooks into docs/source

  coastal_topobathy/.github/workflows/docs_pages.yml

  Line 39 in f027c49

  cp -R examples docs/source

  How would that possibly cause this problem?
• Something else

[iled]

I don't know what is causing this issue, but an alternative would be doing the conversion to markdown through Jupytext

Use the MyST Markdown format, a markdown flavor that “implements the best parts of reStructuredText”, if you wish to render your notebooks using Sphinx or Jupyter Book.

[eeholmes]

Thanks I'll try jupytext conversion to markdown.
https://jupytext.readthedocs.io/en/latest/using-cli.html