Georg,
thanks for taking a look at this, and forwarding to the author of
numpydoc (offline for those following).  I subsequently discovered a
good discussion on this list here:
http://groups.google.com/group/sphinx-dev/browse_thread/thread/300153957f2902f9?pli=1

On Apr 5, 5:36 am, Georg Brandl <[email protected]> wrote:
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> Am 23.03.2010 00:45, schrieb phil_stephens:
>
>
>
>
>
> > Hello,
>
> > Thank you for developing Sphinx. It has enhanced our software
> > documentation so much!
>
> > I am having what appears to be a very uncommon problem, based on
> > searching this group for a standard Sphinx error message "WARNING:
> > toctree contains reference to nonexisting document". That search
> > returns only my previous post! This seems unlikely that I would have
> > 700 WARNINGS and other users would never get this?  Simply, we are
> > looking for a clean build process. These warnings appear to tell us to
> > fix something, do they not?  Each of them refers to a (~) + a method
> > call for a class in our library. I don't know why Sphinx would want to
> > create a document for each method, maybe I am missing something.
>
> > Does anyone else get these warnings? If so, do you simply ignore them?
> > Or, are they indicating to me that something is wrong with the
> > structure of my Sphinx sources?
>
> > Please, please help. I will be glad to share the code with you if you
> > need more information. It sits athttp://code.google.com/p/pysal
>
> > Example stdout:
>
> > /Users/*****/code/pysal/doc/source/library/weights/weights.txt::
> > WARNING: toctree contains reference to nonexisting document 'library/
> > weights/~W.id_order'
>
> First, sorry for the delayed answer.
>
> I see that your conf.py references a "numpydoc" extension.  I assumed that
> this is the one that can be found on PyPI?  With that, I could reproduce
> your problem, and I'll investigate later today when it's more quiet around
> here.
>
> cheers,
> Georg
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