Pytest 3.9.1 does not respect filterwarnings in setup.cfg

[dionhaefner]

Today, I noticed that my CI tests were failing with a lot of these errors:

tests/drivers/test_staticmethods.py:5: in <module>
    from shapely.geometry import shape, MultiPolygon
../../../virtualenv/python3.6.3/lib/python3.6/site-packages/shapely/geometry/__init__.py:23: in <module>
    import shapely.speedups
../../../virtualenv/python3.6.3/lib/python3.6/site-packages/shapely/speedups/__init__.py:11: in <module>
    from shapely.speedups import _speedups
shapely/speedups/_speedups.pyx:8: in init shapely.speedups._speedups
    ???
E   ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__

In my setup.cfg, I have configured pytest like this:

[tool:pytest]
addopts =
  -W error
  -v
filterwarnings =
  error
  # ignored by default
  ignore::ImportWarning
  ignore::PendingDeprecationWarning
  # raised by Cython, usually harmless
  ignore:numpy.dtype size changed:RuntimeWarning
  ignore:numpy.ufunc size changed:RuntimeWarning
  # raised by Werkzeug
  ignore:Request.is_xhr is deprecated:DeprecationWarning
  # raised by Moto
  ignore:Flags not at the start of the expression:DeprecationWarning

So the ImportWarning should be ignored due to the filterwarnings specification, but for some reason it is not. The -W error however is read and applied correctly, so the file is found and being parsed.

Downgrading to pytest<3.9 fixed the problem.

[vbarbaresi]

This is due to this change: #3947
-W error command line option takes precedence over the filters

You can get the old behavior back by removing -W error from the command line, it's duplicated in the filterwarnings

[nicoddemus]

I think @vbarbaresi nailed it. 👍

I'm closing this for now, feel free to follow up with more questions @dionhaefner.