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We are observing an INTERNALERROR with pytest 5.3.4. This error is not produced with pytest 5.3.3.
Travis output for 5.3.4 is here, and for 5.3.3 is here. The only difference between the builds is the version of pytest used.
Host information for the Travis instances is available in the linked output -- please let me know if that would be useful to summarize inline and I'll edit this issue accordingly.
After some prodding at the failing test class, I was able to reduce it down to what appears to be a bad interaction with numpy.testing.skipif. A minimal example to produce the INTERNALERROR is below, as is pip list, conda list and host details when exercising the minimal example.
a detailed description of the bug or suggestion
output of pip list from the virtual environment you are using
pytest and operating system versions
minimal example if possible
$ cat minimal.py
import numpy.testing as npt
import unittest
class InternalErrorExample(unittest.TestCase):
@npt.dec.skipif(False, msg='foo')
def test_example(self):
print("asd")
$ pytest minimal.py
===================================================================================================================== test session starts ======================================================================================================================
platform darwin -- Python 3.7.6, pytest-5.3.4, py-1.8.1, pluggy-0.13.1
rootdir: /Users/dtmcdonald/ResearchWork/software/biom-format, inifile: pytest.ini
plugins: cov-2.8.1
collected 1 item
Coverage.py warning: No data was collected. (no-data-collected)
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/main.py", line 197, in wrap_session
INTERNALERROR> session.exitstatus = doit(config, session) or 0
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/main.py", line 247, in _main
INTERNALERROR> config.hook.pytest_runtestloop(session=session)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__
INTERNALERROR>return self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec
INTERNALERROR>return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 87, in<lambda>
INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 203, in _multicall
INTERNALERROR> gen.send(outcome)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
INTERNALERROR> res = hook_impl.function(*args)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/main.py", line 271, in pytest_runtestloop
INTERNALERROR> item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__
INTERNALERROR>return self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec
INTERNALERROR>return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 87, in<lambda>
INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall
INTERNALERROR>returnoutcome.get_result()
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
INTERNALERROR> res = hook_impl.function(*args)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/runner.py", line 83, in pytest_runtest_protocol
INTERNALERROR> item.ihook.pytest_runtest_logstart(nodeid=item.nodeid, location=item.location)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/compat.py", line 420, in __get__
INTERNALERROR> value = instance.__dict__[self.func.__name__] = self.func(instance)
INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/nodes.py", line 465, in location
INTERNALERROR> assert isinstance(location[0], py.path.local), location[0]
INTERNALERROR> AssertionError: /Users/dtmcdonald/ResearchWork/software/biom-format/minimal.py
====================================================================================================================== 1 warning in 0.58s ======================================================================================================================
$ uname -a
Darwin here.local 17.7.0 Darwin Kernel Version 17.7.0: Sun Dec 1 19:19:56 PST 2019; root:xnu-4570.71.63~1/RELEASE_X86_64 x86_64
$ pip list
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
Package Version
------------------ -------------------
attrs 19.3.0
bleach 3.1.0
certifi 2019.11.28
chardet 3.0.4
coverage 5.0.3
Cython 0.29.14
future 0.18.2
h5py 2.9.0
idna 2.8
importlib-metadata 1.3.0
keyring 21.0.0
mkl-fft 1.0.15
mkl-random 1.1.0
mkl-service 2.3.0
more-itertools 8.0.2
nose 1.3.7
numpy 1.18.1
packaging 20.1
pandas 0.25.3
pip 20.0.2
pkginfo 1.5.0.1
pluggy 0.13.1
py 1.8.1
Pygments 2.5.2
pyparsing 2.4.6
pytest 5.3.4
pytest-cov 2.8.1
python-dateutil 2.8.1
pytz 2019.3
readme-renderer 24.0
requests 2.22.0
requests-toolbelt 0.9.1
scipy 1.3.1
setuptools 45.1.0.post20200127
six 1.14.0
tqdm 4.41.1
twine 3.1.1
urllib3 1.25.7
wcwidth 0.1.8
webencodings 0.5.1
wheel 0.33.6
zipp 0.6.0
$ conda list
# packages in environment at /Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest:## Name Version Build Channel
attrs 19.3.0 pypi_0 pypi
blas 1.0 mkl
ca-certificates 2019.11.27 0
certifi 2019.11.28 py37_0
coverage 5.0.3 pypi_0 pypi
cython 0.29.14 py37h0a44026_0
future 0.18.2 pypi_0 pypi
h5py 2.9.0 py37h3134771_0
hdf5 1.10.4 hfa1e0ec_0
intel-openmp 2019.4 233
libcxx 4.0.1 hcfea43d_1
libcxxabi 4.0.1 hcfea43d_1
libedit 3.1.20181209 hb402a30_0
libffi 3.2.1 h475c297_4
libgfortran 3.0.1 h93005f0_2
mkl 2019.4 233
mkl-service 2.3.0 py37hfbe908c_0
mkl_fft 1.0.15 py37h5e564d8_0
mkl_random 1.1.0 py37ha771720_0
ncurses 6.1 h0a44026_1
nose 1.3.7 pypi_0 pypi
numpy 1.18.1 py37h7241aed_0
numpy-base 1.18.1 py37h6575580_1
openssl 1.1.1d h1de35cc_3
packaging 20.1 pypi_0 pypi
pandas 0.25.3 py37h0a44026_0
pip 20.0.2 py37_0
pluggy 0.13.1 pypi_0 pypi
py 1.8.1 pypi_0 pypi
pyparsing 2.4.6 pypi_0 pypi
pytest 5.3.4 pypi_0 pypi
pytest-cov 2.8.1 pypi_0 pypi
python 3.7.6 h359304d_2
python-dateutil 2.8.1 py_0
pytz 2019.3 py_0
readline 7.0 h1de35cc_5
scipy 1.3.1 py37h1410ff5_0
setuptools 45.1.0 py37_0
six 1.14.0 py37_0
sqlite 3.30.1 ha441bb4_0
tk 8.6.8 ha441bb4_0
wcwidth 0.1.8 pypi_0 pypi
wheel 0.33.6 py37_0
xz 5.2.4 h1de35cc_4
zlib 1.2.11 h1de35cc_3
The text was updated successfully, but these errors were encountered:
We are observing an INTERNALERROR with pytest 5.3.4. This error is not produced with pytest 5.3.3.
Travis output for 5.3.4 is here, and for 5.3.3 is here. The only difference between the builds is the version of pytest used.
Host information for the Travis instances is available in the linked output -- please let me know if that would be useful to summarize inline and I'll edit this issue accordingly.
After some prodding at the failing test class, I was able to reduce it down to what appears to be a bad interaction with
numpy.testing.skipif. A minimal example to produce the INTERNALERROR is below, as ispip list,conda listand host details when exercising the minimal example.pip listfrom the virtual environment you are using$ cat minimal.py import numpy.testing as npt import unittest class InternalErrorExample(unittest.TestCase): @npt.dec.skipif(False, msg='foo') def test_example(self): print("asd") $ pytest minimal.py ===================================================================================================================== test session starts ====================================================================================================================== platform darwin -- Python 3.7.6, pytest-5.3.4, py-1.8.1, pluggy-0.13.1 rootdir: /Users/dtmcdonald/ResearchWork/software/biom-format, inifile: pytest.ini plugins: cov-2.8.1 collected 1 item Coverage.py warning: No data was collected. (no-data-collected) INTERNALERROR> Traceback (most recent call last): INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/main.py", line 197, in wrap_session INTERNALERROR> session.exitstatus = doit(config, session) or 0 INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/main.py", line 247, in _main INTERNALERROR> config.hook.pytest_runtestloop(session=session) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__ INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 87, in <lambda> INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 203, in _multicall INTERNALERROR> gen.send(outcome) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result INTERNALERROR> raise ex[1].with_traceback(ex[2]) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall INTERNALERROR> res = hook_impl.function(*args) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/main.py", line 271, in pytest_runtestloop INTERNALERROR> item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__ INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/manager.py", line 87, in <lambda> INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall INTERNALERROR> return outcome.get_result() INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result INTERNALERROR> raise ex[1].with_traceback(ex[2]) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall INTERNALERROR> res = hook_impl.function(*args) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/runner.py", line 83, in pytest_runtest_protocol INTERNALERROR> item.ihook.pytest_runtest_logstart(nodeid=item.nodeid, location=item.location) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/compat.py", line 420, in __get__ INTERNALERROR> value = instance.__dict__[self.func.__name__] = self.func(instance) INTERNALERROR> File "/Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest/lib/python3.7/site-packages/_pytest/nodes.py", line 465, in location INTERNALERROR> assert isinstance(location[0], py.path.local), location[0] INTERNALERROR> AssertionError: /Users/dtmcdonald/ResearchWork/software/biom-format/minimal.py ====================================================================================================================== 1 warning in 0.58s ====================================================================================================================== $ uname -a Darwin here.local 17.7.0 Darwin Kernel Version 17.7.0: Sun Dec 1 19:19:56 PST 2019; root:xnu-4570.71.63~1/RELEASE_X86_64 x86_64 $ pip list WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip. Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue. To avoid this problem you can invoke Python with '-m pip' instead of running pip directly. Package Version ------------------ ------------------- attrs 19.3.0 bleach 3.1.0 certifi 2019.11.28 chardet 3.0.4 coverage 5.0.3 Cython 0.29.14 future 0.18.2 h5py 2.9.0 idna 2.8 importlib-metadata 1.3.0 keyring 21.0.0 mkl-fft 1.0.15 mkl-random 1.1.0 mkl-service 2.3.0 more-itertools 8.0.2 nose 1.3.7 numpy 1.18.1 packaging 20.1 pandas 0.25.3 pip 20.0.2 pkginfo 1.5.0.1 pluggy 0.13.1 py 1.8.1 Pygments 2.5.2 pyparsing 2.4.6 pytest 5.3.4 pytest-cov 2.8.1 python-dateutil 2.8.1 pytz 2019.3 readme-renderer 24.0 requests 2.22.0 requests-toolbelt 0.9.1 scipy 1.3.1 setuptools 45.1.0.post20200127 six 1.14.0 tqdm 4.41.1 twine 3.1.1 urllib3 1.25.7 wcwidth 0.1.8 webencodings 0.5.1 wheel 0.33.6 zipp 0.6.0 $ conda list # packages in environment at /Users/dtmcdonald/miniconda3/envs/biom2.1.8-pytesttest: # # Name Version Build Channel attrs 19.3.0 pypi_0 pypi blas 1.0 mkl ca-certificates 2019.11.27 0 certifi 2019.11.28 py37_0 coverage 5.0.3 pypi_0 pypi cython 0.29.14 py37h0a44026_0 future 0.18.2 pypi_0 pypi h5py 2.9.0 py37h3134771_0 hdf5 1.10.4 hfa1e0ec_0 intel-openmp 2019.4 233 libcxx 4.0.1 hcfea43d_1 libcxxabi 4.0.1 hcfea43d_1 libedit 3.1.20181209 hb402a30_0 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 h93005f0_2 mkl 2019.4 233 mkl-service 2.3.0 py37hfbe908c_0 mkl_fft 1.0.15 py37h5e564d8_0 mkl_random 1.1.0 py37ha771720_0 ncurses 6.1 h0a44026_1 nose 1.3.7 pypi_0 pypi numpy 1.18.1 py37h7241aed_0 numpy-base 1.18.1 py37h6575580_1 openssl 1.1.1d h1de35cc_3 packaging 20.1 pypi_0 pypi pandas 0.25.3 py37h0a44026_0 pip 20.0.2 py37_0 pluggy 0.13.1 pypi_0 pypi py 1.8.1 pypi_0 pypi pyparsing 2.4.6 pypi_0 pypi pytest 5.3.4 pypi_0 pypi pytest-cov 2.8.1 pypi_0 pypi python 3.7.6 h359304d_2 python-dateutil 2.8.1 py_0 pytz 2019.3 py_0 readline 7.0 h1de35cc_5 scipy 1.3.1 py37h1410ff5_0 setuptools 45.1.0 py37_0 six 1.14.0 py37_0 sqlite 3.30.1 ha441bb4_0 tk 8.6.8 ha441bb4_0 wcwidth 0.1.8 pypi_0 pypi wheel 0.33.6 py37_0 xz 5.2.4 h1de35cc_4 zlib 1.2.11 h1de35cc_3The text was updated successfully, but these errors were encountered: