readthedocs.org: Unexpected issue with package import, using cython and numpy

Details

• Read the Docs project URL: https://freud.readthedocs.io/
• Build URL (if applicable): https://readthedocs.org/projects/freud/builds/8431508/ and https://readthedocs.org/projects/freud/builds/8452348/
• Read the Docs username (if applicable): bdice

Expected Result

Build passes, documentation shows module info.

Actual Result

Build passes but doesn’t actually contain module documentation. Builds should show as failing.

Expected result is on stable: https://freud.readthedocs.io/en/stable/box.html Failing result is on latest: https://freud.readthedocs.io/en/latest/box.html

The package appears to build correctly, but we think there is something going wrong with Cython or NumPy and we can’t get enough info to debug it ourselves. When RTD installs on top of our environment.yml file, it changes some package versions, specifically numpy from the openblas to mkl variants. I don’t think that openblas/mkl is the problem, but changing numpy versions may very well invalidate something we rely on. We’ve seen two different error messages but it’s not clear what causes either one.

This failure began appearing about simultaneously with our switch from Bitbucket (https://bitbucket.org/glotzer/freud.git) to GitHub (https://github.com/glotzerlab/freud.git) so we’re not sure what to blame. However, I think I ruled out the repo URL change as a cause. I tried changing the URL back to Bitbucket and the issue can be reproduced. Also I created a fresh RTD project with the GitHub URL and it fails in the same way.

Most recent error (https://readthedocs.org/projects/freud/builds/8452348/):

/home/docs/checkouts/readthedocs.org/user_builds/freud/checkouts/awesome-readme/doc/source/box.rst:7: WARNING: failed to import freud.box.Box
/home/docs/checkouts/readthedocs.org/user_builds/freud/checkouts/awesome-readme/doc/source/box.rst:7: WARNING: failed to import freud.box.ParticleBuffer
WARNING: autodoc: failed to import module 'box' from module 'freud'; the following exception was raised:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/awesome-readme/lib/python3.7/site-packages/sphinx/ext/autodoc/importer.py", line 154, in import_module
    __import__(modname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/awesome-readme/lib/python3.7/site-packages/freud/__init__.py", line 5, in <module>
    from . import box
  File "freud/box.pyx", line 37, in init freud.box
AttributeError: type object 'freud.box.Box' has no attribute '__reduce_cython__'

Previous error from earlier in the month (https://readthedocs.org/projects/freud/builds/8431508/):

/home/docs/checkouts/readthedocs.org/user_builds/freud/checkouts/latest/doc/source/box.rst:7: WARNING: failed to import freud.box.Box
/home/docs/checkouts/readthedocs.org/user_builds/freud/checkouts/latest/doc/source/box.rst:7: WARNING: failed to import freud.box.ParticleBuffer
WARNING: autodoc: failed to import module 'box' from module 'freud'; the following exception was raised:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/sphinx/ext/autodoc/importer.py", line 154, in import_module
    __import__(modname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/freud/__init__.py", line 7, in <module>
    from . import common
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/freud/common.py", line 7, in <module>
    import numpy as np
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/numpy/core/__init__.py", line 59, in <module>
    from . import numeric
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/numpy/core/numeric.py", line 3093, in <module>
    from . import fromnumeric
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 17, in <module>
    from . import _methods
  File "/home/docs/checkouts/readthedocs.org/user_builds/freud/conda/latest/lib/python3.6/site-packages/numpy/core/_methods.py", line 158, in <module>
    _NDARRAY_ARRAY_FUNCTION = mu.ndarray.__array_function__
AttributeError: type object 'numpy.ndarray' has no attribute '__array_function__'