toctree content regression in sphinx 1.3b3

[jschueller]

we're no longer able to build openturns sphinx documentation since 1.3b3:

Running Sphinx v1.4a0+
making output directory...
loading pickled environment... not yet created
[autosummary] generating ...
...
reading sources... [100%]
user_manual/user_manual
...                                                                                                                  
looking for now-outdated files... none found
pickling environment... done
checking consistency... 
Warning, treated as error:
/home/schueller/projects/openturns/schueller/build/python/src/sphinx_build/user_manual/_generated/openturns.ANCOVA.rst:: WARNING: document isn't included in any toctree

using git-bisect I found the regression to be at 21b8384 (for PR #1663):
could it be that this commit somehow stripped a class from toctree ?

[christianbrodbeck]

I think I might be having the same problem. Classes that are defined in package/_module.py (e.g. class package._module.MyClass, imported in package.__init__.py and listed in the doc like

.. currentmodule:: package
  :toctree: generated

   MyClass

just disappeared form the documentation. Commenting lines 273 and 274 in sphinx/ext/autosummary/__init__.py that were added in 21b8384 brought the classes back into my documentation.

[jschueller]

@lsaffre, maybe you could tell us more about this commit ? I hope removing the two lines added from sphinx/ext/autosummary/init.py in 21b8384 like @christianbrodbeck mentioned does not introduce more regressions towards #1061 and #1656.
maybe the comment of @embray in #1061 is useful

[lsaffre]

Looking from the source code (didn't test) I'd say that these two lines were for #1061 while the other changes were for #1656, and it was just an administrative mistake to solve two tickets with one changeset.

[jschueller]

from what I understood this was a backward-incompatible change to strip imported modules.

[lsaffre]

Ha, I finally found my blog entry which describes the problem that was solved by these two lines:
http://luc.lino-framework.org/blog/2014/1219.html
(Summary: my code imports a class from a third-party package, and this class has a docstring which contains invalid reStructuredText markup. This broke my build since I want it to build without warnings. I want autosummary to document all my classes, but not those imported into my package from a third-party package)

[jschueller]

ok, thanks for the explanation, unfortunately your changes broke several documentations. what about @shimizukawa suggestion to have a keyword imported, and the stack overflow patch mentioned in #1061 ?

[lsaffre]

Yes, that would be perfect! TIA for implementing it, and I'll do my best to help.

[shoyer]

This has broken my docs, and unfortunately, it's a pain to revert to earlier versions of sphinx on ReadTheDocs.

Is there a work around for this issue?

[jschueller]

see pr #1828