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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.
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.
See for example
http://risk-in-a-box.readthedocs.org/en/latest/api-docs/gui/riab.html
which does not show up.
But
http://risk-in-a-box.readthedocs.org/en/latest/api-docs/gui/riabexceptions.html
does
When generating the html locally they all work
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