So I actually had everything working perfectly with sphinx-codeautolink on my local machine. The problems started as soon as I tried to build the documentation on readthedocs. Unfortunately, I didn't note the versions of all my pip packages before messing with my local machine, and now I can't get sphinx-codeautolink to work on my local machine or readthedocs. I've been messing around with the versions of Sphinx, beautifulsoup, pygments, etc. for hours and I can't seem to get it working again.

Issue

The issue I'm experiencing is that none of the code links are working. I'm using the pydata-sphinx-theme and the jupyter-sphinx extension to run my Python code, and I've set codeautolink_custom_blocks to recognize the jupyter-execute directive provided by jupyter-sphinx.

Since none of the links were working, I set codeautolink_warn_on_missing_inventory and codeautolink_warn_on_failed_resolve to True, and it printed a ton of Inventory missing ... warnings, Could not resolve ... warnings, and Cannot locate modules warnings. Intersphinx is working correctly for all of the normal documentation links.

Steps to reproduce

My conf.py file has the following relevant lines

extensions = [
    'sphinx.ext.napoleon',
    'sphinx.ext.autodoc',
    'sphinx.ext.autosummary',
    'sphinx.ext.intersphinx',
    'sphinx.ext.inheritance_diagram',
    'sphinx.ext.viewcode',
    'sphinxcontrib.bibtex',
    'jupyter_sphinx',
    'sphinx_codeautolink',
]

codeautolink_custom_blocks = {"jupyter-execute": None}
codeautolink_warn_on_missing_inventory = True
codeautolink_warn_on_failed_resolve = True

Here is the log for the readthedocs build with a full description of the installed versions of everything and all the warnings.