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This PR is an attempt to fix some of the sphinx rendering issues - namely the issues with the core functions having sections but no functions/methods showing up.
It does NOT fix all the issues we're aware of, particularly the ReadTheDocs broken links for non-function-reference stuff, but those will take some thought and a redesign.
At least with the local rendering, things look good. This can be reproduced with a source tree by:
caibuild
for my compiled caiman environment)mamba install -c conda-forge sphinx numpydoc
sphinx-build -M html source html
For iterating over errors while changing and fixing things, I replace step 4 with:
pushd .. ; pip install . ; popd ; rm -rf html ; clear ; sphinx-build -M html source html 2>&1 | less
and look for the word ERROR (and at any warnings you see, if you like).
The bulk of this is fixing fiddly comment formatting; sphinx has very particular expectations on how docstrings must be formatted for functions for them to be turned into docs, and I only somewhat understand the rules, but this gets rid of all errors I see when running locally and the functions turn up locally too.