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I've now added the notebooks to the file index.rst, so that they will be recognized by the sphinx build.
The sphinx build was successful, and can now be seen here: https://simpleitk-notebooks--331.org.readthedocs.build/en/331/index.html
I've tried hard to keep the docs/ and the Python/ folder separate following this post:
https://stackoverflow.com/questions/10199233/can-sphinx-link-to-documents-that-are-not-located-in-directories-below-the-root
But I did not manage to accomplish it. Thus, I simply moved the Python folder into the docs/source folder
( e.g. Python/00_Setup.ipynb → docs/source/Python/00_Setup.ipynb )
EDIT: Linked issue: #330