Errors building PyMC3 documentation

[rpgoldman]

Description of your problem

Please provide a minimal, self-contained, and reproducible example.

cd docs/source
make clean
make html

Please provide the full traceback.

WARNING: autodoc: failed to import function 't_stick_breaking' from module 'pymc3.distributions.transforms'; the following exception was raised:
Traceback (most recent call last):
  File "/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/sphinx/util/inspect.py", line 334, in safe_getattr
    return getattr(obj, name, *defargs)
AttributeError: module 'pymc3.distributions.transforms' has no attribute 't_stick_breaking'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/sphinx/ext/autodoc/importer.py", line 106, in import_object
    obj = attrgetter(obj, mangled_name)
  File "/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/sphinx/ext/autodoc/__init__.py", line 292, in get_attr
    return autodoc_attrgetter(self.env.app, obj, name, *defargs)
  File "/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/sphinx/ext/autodoc/__init__.py", line 2242, in autodoc_attrgetter
    return safe_getattr(obj, name, *defargs)
  File "/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/sphinx/util/inspect.py", line 350, in safe_getattr
    raise AttributeError(name) from exc
AttributeError: t_stick_breaking

/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/pymc3/distributions/transforms.py:docstring of pymc3.distributions.transforms.StickBreaking:4: WARNING: Unexpected indentation.
/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/pymc3/sampling.py:docstring of pymc3.sampling.init_nuts:31: WARNING: Inline literal start-string without end-string.
/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/pymc3/sampling.py:docstring of pymc3.sampling.sample:127: WARNING: Inline literal start-string without end-string.
/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/pymc3/sampling.py:docstring of pymc3.sampling.sample:155: WARNING: Inline literal start-string without end-string.
/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/pymc3/sampling.py:docstring of pymc3.sampling.sample:149: WARNING: Unexpected indentation.
/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/pymc3/sampling.py:docstring of pymc3.sampling.sample:161: WARNING: Unexpected indentation.
/Users/rpg/.virtualenvs/pymc3/lib/python3.7/site-packages/pymc3/backends/base.py:docstring of pymc3.backends.base.MultiTrace:56: WARNING: Block quote ends without a blank line; unexpected unindent.

Extension error:
Handler <function mangle_signature at 0x13d3d4200> for event 'autodoc-process-signature' threw an exception (exception: The section Notes appears twice in the docstring of Elemwise{clip,no_inplace} in None.)

Versions and main components

• PyMC3 Version: 2669afd (update-theano-doc-pointer)
• Theano Version: Theano-PyMC==1.0.11
• Python Version: 3.7.7
• Operating system: MacOS 10.15.7
• How did you install PyMC3: pip install -e .
• Sphinx version: sphinx-build 3.3.1

[MarcoGorelli]

Is this how the docs here https://docs.pymc.io/ are built?

[rpgoldman]

To the best of my knowledge, yes. I think @ColCarroll is really the expert on the documentation.

It's long been an issue that the build process spews a large number of warnings, making it hard to tell if the build is actually working or not.

Getting the documentation to build cleanly would be a great thing.

[MarcoGorelli]

t_stick_breaking was removed from pymc3/distributions/transforms.py in #4129

[MarcoGorelli]

Including clip in docs/source/api/math.rst causes the docs to fail with

Extension error:
Handler <function mangle_signature at 0x7f176a60c0d0> for event 'autodoc-process-signature' threw an exception (exception: The section Notes appears twice in the docstring of Elemwise{clip,no_inplace} in None.)
Makefile:56: recipe for target 'html' failed
make: *** [html] Error 2

but removing it, the build works

[MarcoGorelli]

If you install the master branch of Theano-PyMC

pip uninstall theano-pymc
pip install git+git://github.com/PyMC-devs/theano-pymc

then this works now.

There are still some warnings (e.g. the one about t_stick_breaking not existing), but they don't prevent the docs from being built.

@rpgoldman if you could confirm it works for you now? If so, can we close?

[michaelosthege]

closed by #4283