ImportMismatchError from conftest.py confusion

With a recent release of scikit-learn, we have started to see the following error when building packages for Debian using pytest 4.6.9 with Python 3.8 on Debian unstable:

/usr/lib/python3/dist-packages/_pytest/config/__init__.py:440: in _importconftest
    return self._conftestpath2mod[conftestpath]
E   KeyError: local('/build/scikit-learn-0.23.0/sklearn/conftest.py')

The package build happens roughly as follows:

1. python3.8 setup.py config
2. python3.8 setup.py build with a target directory .pybuild/cpython3_3.8/build/sklearn, which is a subdirectory within the source directory
3. cd .pybuild/cpython3_3.8/build/sklearn && python3.8 -m pytest

After step (2.), find . -name conftest.py in the source directory produces the following output (sklearn being the source directory, .pybuild the build directory:

./doc/conftest.py
./.pybuild/cpython3_3.8/build/sklearn/conftest.py
./.pybuild/cpython3_3.8/build/sklearn/externals/conftest.py
./.pybuild/cpython3_3.8/build/sklearn/utils/tests/conftest.py
./.pybuild/cpython3_3.8/build/sklearn/datasets/tests/conftest.py
./sklearn/conftest.py
./sklearn/externals/conftest.py
./sklearn/utils/tests/conftest.py
./sklearn/datasets/tests/conftest.py

Running step (3.) produces the following output:

===================================================== test session starts =====================================================
platform linux -- Python 3.8.3, pytest-4.6.9, py-1.8.1, pluggy-0.13.0 -- /usr/bin/python3.8
cachedir: .pytest_cache
rootdir: /build/scikit-learn-0.23.0, inifile: setup.cfg
collected 0 items / 1 errors                                                                                                  

=========================================================== ERRORS ============================================================
________________________________________________ ERROR collecting test session ________________________________________________
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:440: in _importconftest
    return self._conftestpath2mod[conftestpath]
E   KeyError: local('/build/scikit-learn-0.23.0/sklearn/conftest.py')

During handling of the above exception, another exception occurred:
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:446: in _importconftest
    mod = conftestpath.pyimport()
/usr/lib/python3/dist-packages/py/_path/local.py:721: in pyimport
    raise self.ImportMismatchError(modname, modfile, self)
E   py._path.local.LocalPath.ImportMismatchError: ('sklearn.conftest', '/build/scikit-learn-0.23.0/.pybuild/cpython3_3.8/build/sklearn/conftest.py', local('/build/scikit-learn-0.23.0/sklearn/conftest.py'))

During handling of the above exception, another exception occurred:
/usr/lib/python3/dist-packages/py/_path/common.py:383: in visit
    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
/usr/lib/python3/dist-packages/py/_path/common.py:435: in gen
    for p in self.gen(subdir):
/usr/lib/python3/dist-packages/py/_path/common.py:435: in gen
    for p in self.gen(subdir):
/usr/lib/python3/dist-packages/py/_path/common.py:424: in gen
    dirs = self.optsort([p for p in entries
/usr/lib/python3/dist-packages/py/_path/common.py:425: in <listcomp>
    if p.check(dir=1) and (rec is None or rec(p))])
/usr/lib/python3/dist-packages/_pytest/main.py:667: in _recurse
    ihook = self.gethookproxy(dirpath)
/usr/lib/python3/dist-packages/_pytest/main.py:482: in gethookproxy
    my_conftestmodules = pm._getconftestmodules(fspath)
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:424: in _getconftestmodules
    mod = self._importconftest(conftestpath.realpath())
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:463: in _importconftest
    raise ConftestImportFailure(conftestpath, sys.exc_info())
E   _pytest.config.ConftestImportFailure: (local('/build/scikit-learn-0.23.0/sklearn/conftest.py'), (<class 'py._path.local.LocalPath.ImportMismatchError'>, ImportMismatchError('sklearn.conftest', '/build/scikit-learn-0.23.0/.pybuild/cpython3_3.8/build/sklearn/conftest.py', local('/build/scikit-learn-0.23.0/sklearn/conftest.py')), <traceback object at 0x7f989924cc00>))

I saw that rootdir pointed to the source directory, and not the build directory (the cwd at this time). I assumed this was because the only copy of setup.cfg resided there. I copied that file to the build directory and ran pytest with --rootdir=$PWD, but that didn’t change the outcome.

Oddly enough, removing the following two files from the source directory (not the build directory) resolves the issue.

./sklearn/conftest.py
./sklearn/datasets/tests/conftest.py

The other two conftest.py files in the source directory did not affect the outcome.

What could be going on here?

[RonnyPfannschmidt]

if you create a temporary copy of the package in a folder that is traversed by pytest for test finding, then its going to try and import the folders,

pytest auto-adds package roots of python files it finds to sys.path to import them

as far as i can tell, ./.pybuild/cpython3_3.8/build is discovered as import root and shares structure with . - in turn causing the confusion

[ckastner]

as far as i can tell, ./.pybuild/cpython3_3.8/build is discovered as import root and shares structure with . - in turn causing the confusion

That confusion on behalf of pytest I would understand and expect.

However, in this particular instance, ./.pybuild/cpython3_3.8/build is the current working directory (there was a cd into it). So the confusion comes from ./sklearn and ../../../sklearn.

It’s the latter that I don’t understand. Is it not possible (via an option) to cut off discovery at some base dir? I looked at rootdir (which didn’t work) and confcutdir (which worked for just one of the two conflicting files – the other still raises ImportMismatchError.