subclassing xarray.DataArray with autodoc flag :inherited-members: raises opaque error in sphinx 1.6+

[hazbottles]

Subject: subclassing xarray.DataArray with autodoc flag :inherited-members: raises opaque error in sphinx 1.6+

Problem

using :inherited-members: as an autodoc flag raises an opaque error when subclassing xarray.DataArray (http://xarray.pydata.org/en/stable/generated/xarray.DataArray.html) in Sphinx 1.6. This did not occur in Sphinx 1.5.

Procedure to reproduce the problem

see: https://github.com/hazbottles/sphinx_bug_with_xarray_subclass

Error logs / results

# Sphinx version: 1.6.2
# Python version: 3.6.1 (CPython)
# Docutils version: 0.13.1 release
# Jinja2 version: 2.9.6
# Last messages:
#   building [html]: targets for 2 source files that are out of date
#
#   updating environment:
#
#   2 added, 0 changed, 0 removed
#
#   reading sources... [ 50%] index
#
#   reading sources... [100%] my_module
#
# Loaded extensions:
#   alabaster (0.7.10) from /home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/alabaster/__init__.py
#   sphinx.ext.autodoc (1.6.2) from /home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/ext/autodoc.py
Traceback (most recent call last):
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/cmdline.py", line 306, in main
    app.build(opts.force_all, filenames)
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/application.py", line 339, in build
    self.builder.build_update()
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/builders/__init__.py", line 328, in build_update
    'out of date' % len(to_build))
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/builders/__init__.py", line 341, in build
    updated_docnames = set(self.env.update(self.config, self.srcdir, self.doctreedir))
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/environment/__init__.py", line 584, in update
    self._read_serial(docnames, self.app)
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/environment/__init__.py", line 603, in _read_serial
    self.read_doc(docname, app)
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/environment/__init__.py", line 724, in read_doc
    pub.publish()
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/docutils/core.py", line 218, in publish
    self.apply_transforms()
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/docutils/core.py", line 199, in apply_transforms
    self.document.transformer.apply_transforms()
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/docutils/transforms/__init__.py", line 171, in apply_transforms
    transform.apply(**kwargs)
  File "/home/accounts/this_user/local/miniconda2/envs/sphinx_test/lib/python3.6/site-packages/Sphinx-1.6.2-py3.6.egg/sphinx/transforms/__init__.py", line 292, in apply
    if node['names'][0] not in self.document.footnote_refs:
IndexError: list index out of range

Expected results

Raise a warning, but render as it did in sphinx 1.5, or even just a more informative error message (took me a long time to chase down it was a problem with :inherited-members: interacting with xarray's documentation)

Reproducible project / your project

https://github.com/hazbottles/sphinx_bug_with_xarray_subclass

Environment info

• OS: Fedora 23
• Python version: 3.6.1
• Sphinx version: 1.6.2

[tk0miya]

I just reproduced with following code:

.. automodule:: example
   :members:

class Foo(object):
    """Foo class! [1]_

    .. [1] foo
    """

    def bar(self, *args, **kwargs):
        """Foo.bar method! [1]_

        .. [1] bar
        """

[tk0miya]

This is minimal reproducible example. This is not related with autodoc.

# index.rst

.. [1] foo
.. [1] foo

Note:

/Users/tkomiya/work/tmp/doc/index.rst:10: WARNING: Duplicate explicit target name: "1".

[tk0miya]

Fixed at 5123dad.
Thank you for reporting!