Sphinx autosummary “toctree contains reference to nonexisting document” warnings

Question

I am trying to automatically create api docs for a large python codebase using Sphinx.

I have tried using build_modules.py and sphinx-apidoc. With either one, I can

Answer 1

I just encountered this issue too and spend hours on this, The following worked for me:

Sphinx can be fussy, and sometimes about things you weren’t expecting. 
For example, you well encounter something like:

WARNING: toctree contains reference to nonexisting document u'all-about-me'
...
checking consistency...
/my-first-docs/docs/all-about-me.rst::
WARNING: document isn't included in any toctree'

Quite likely, what has happened here is that you indented all-about-me
in your .. toctree:: with four spaces, when Sphinx is expecting three.

Source: docs!