See for example
which does not show up.
When generating the html locally they all work
Good point - however, all of this is happening in master and I could see other changes taking place. The problem is with some of the sections where docstrings are harvested. Very weird.
Just to update this (since the project name was refactored), an example URL is here:
My local copy shows the full api docs. Note that I have carefully gone through sphinx warnings/errors and fixed them so I don't think it can be attributed to something broken in the docs. My best bet would be that RTD is not able to parse the source files for some reason.
Closing this - all docs are showing nicely for me on InaSAFE.org