Open
Description
Summary
Merged #3038 and released 1.2.3 this morning, and new errors have popped up.
- Python 3.5 on Travis now exhibits:
[gw0] [ 96%] PASSED utils/tests/test_misc.py::test_rgetcwd INTERNALERROR> Traceback (most recent call last):
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/main.py", line 191, in wrap_session
INTERNALERROR> session.exitstatus = doit(config, session) or 0
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/main.py", line 235, in _main
INTERNALERROR> config.hook.pytest_runtestloop(session=session)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/hooks.py", line 286, in __call__
INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/manager.py", line 92, in _hookexec
INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/manager.py", line 86, in <lambda>
INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 208, in _multicall
INTERNALERROR> return outcome.get_result()
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 80, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 187, in _multicall
INTERNALERROR> res = hook_impl.function(*args)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/xdist/remote.py", line 68, in pytest_runtestloop
INTERNALERROR> self.run_one_test(torun)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/xdist/remote.py", line 85, in run_one_test
INTERNALERROR> self.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/hooks.py", line 286, in __call__
INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/manager.py", line 92, in _hookexec
INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/manager.py", line 86, in <lambda>
INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 208, in _multicall
INTERNALERROR> return outcome.get_result()
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 80, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 182, in _multicall
INTERNALERROR> next(gen) # first yield
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/warnings.py", line 112, in pytest_runtest_protocol
INTERNALERROR> config=item.config, ihook=item.ihook, when="runtest", item=item
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/nodes.py", line 100, in ihook
INTERNALERROR> return self.session.gethookproxy(self.fspath)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/main.py", line 424, in gethookproxy
INTERNALERROR> my_conftestmodules = pm._getconftestmodules(fspath)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/config/__init__.py", line 417, in _getconftestmodules
INTERNALERROR> mod = self._importconftest(conftestpath)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/config/__init__.py", line 437, in _importconftest
INTERNALERROR> key = Path(str(conftestpath)).resolve()
INTERNALERROR> File "/home/travis/build/nipy/nipype/nipype/utils/filemanip.py", line 67, in _patch_resolve
INTERNALERROR> resolved = Path().old_resolve() / self
INTERNALERROR> File "/opt/python/3.5.6/lib/python3.5/pathlib.py", line 1109, in resolve
INTERNALERROR> s = self._flavour.resolve(self)
INTERNALERROR> File "/opt/python/3.5.6/lib/python3.5/pathlib.py", line 329, in resolve
INTERNALERROR> base = '' if path.is_absolute() else os.getcwd()
INTERNALERROR> FileNotFoundError: [Errno 2] No such file or directory
[gw1] [ 96%] PASSED pipeline/engine/tests/test_workflows.py::test_outputs_removal_wf[MultiProc-True-False]
pipeline/engine/tests/test_workflows.py::test_config_setting
[gw1] [ 96%] PASSED pipeline/engine/tests/test_workflows.py::test_config_setting
pipeline/plugins/sge.py::nipype.pipeline.plugins.sge.qsub_sanitize_job_name
[gw1] [ 96%] PASSED pipeline/plugins/sge.py::nipype.pipeline.plugins.sge.qsub_sanitize_job_name
pipeline/plugins/tests/test_base.py::test_scipy_sparse
[gw1] [ 96%] PASSED pipeline/plugins/tests/test_base.py::test_scipy_sparse
pipeline/plugins/tests/test_callback.py::test_callback_normal[Linear]
[gw1] [ 97%] PASSED pipeline/plugins/tests/test_callback.py::test_callback_normal[Linear]
pipeline/plugins/tests/test_callback.py::test_callback_normal[MultiProc] 190923-15:20:56,313 nipype.utils INFO:
Running nipype version 1.2.3 (latest: 1.2.2)
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/main.py", line 191, in wrap_session
INTERNALERROR> session.exitstatus = doit(config, session) or 0
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/_pytest/main.py", line 235, in _main
INTERNALERROR> config.hook.pytest_runtestloop(session=session)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/hooks.py", line 286, in __call__
INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/manager.py", line 92, in _hookexec
INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/manager.py", line 86, in <lambda>
INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 203, in _multicall
INTERNALERROR> gen.send(outcome)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 80, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/pluggy/callers.py", line 187, in _multicall
INTERNALERROR> res = hook_impl.function(*args)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/xdist/dsession.py", line 115, in pytest_runtestloop
INTERNALERROR> self.loop_once()
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/xdist/dsession.py", line 138, in loop_once
INTERNALERROR> call(**kwargs)
INTERNALERROR> File "/home/travis/virtualenv/python3.5.6/lib/python3.5/site-packages/xdist/dsession.py", line 180, in worker_workerfinished
INTERNALERROR> assert not crashitem, (crashitem, node)
INTERNALERROR> AssertionError: ('utils/tests/test_nipype2boutiques.py::test_generate', <WorkerController gw0>)
INTERNALERROR> assert not 'utils/tests/test_nipype2boutiques.py::test_generate'
This seems likely to be related to the Pytest 5.1.3 release this weekend.
Additionally, the newly active dcm2niix tests from #2936 seem to be failing on CircleCI, but only for the tag build, not the master build:
assert <undefined> + where <undefined> = \nbids = <undefined>\nbvals = <undefined>\nbvecs = <undefined>\nconverted_files = <undefined>\n.converted_files + where \nbids = <undefined>\nbvals = <undefined>\nbvecs = <undefined>\nconverted_files = <undefined>\n = <nipype.interfaces.base.support.InterfaceResult object at 0x7fa215e7b588>.outputs
tmpdir = local('/tmp/pytest-of-neuro/pytest-0/popen-gw1/test_dcm2niix_dwi0')
@pytest.mark.skipif(no_datalad, reason="Datalad required")
@pytest.mark.skipif(no_dcm2niix, reason="Dcm2niix required")
def test_dcm2niix_dwi(tmpdir):
tmpdir.chdir()
try:
datadir = fetch_data(tmpdir.strpath, 'Siemens_Sag_DTI_20160825_145811')
except IncompleteResultsError as exc:
pytest.skip("Failed to fetch test data: %s" % str(exc))
def assert_dwi(eg, bids):
"Some assertions we will make"
assert eg.outputs.converted_files
assert eg.outputs.bvals
assert eg.outputs.bvecs
outputs = [y for x,y in eg.outputs.get().items()]
if bids:
# ensure all outputs are of equal lengths
assert len(set(map(len, outputs))) == 1
else:
assert not eg.outputs.bids
dcm = Dcm2niix()
dcm.inputs.source_dir = datadir
dcm.inputs.out_filename = '%u%z'
> assert_dwi(dcm.run(), True)
/src/nipype/nipype/interfaces/tests/test_extra_dcm2nii.py:49:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
eg = <nipype.interfaces.base.support.InterfaceResult object at 0x7fa215e7b588>
bids = True
def assert_dwi(eg, bids):
"Some assertions we will make"
> assert eg.outputs.converted_files
E assert <undefined>
E + where <undefined> = \nbids = <undefined>\nbvals = <undefined>\nbvecs = <undefined>\nconverted_files = <undefined>\n.converted_files
E + where \nbids = <undefined>\nbvals = <undefined>\nbvecs = <undefined>\nconverted_files = <undefined>\n = <nipype.interfaces.base.support.InterfaceResult object at 0x7fa215e7b588>.outputs
/src/nipype/nipype/interfaces/tests/test_extra_dcm2nii.py:36: AssertionError
The reason for this is unclear. In both cases we appear to be building the docker image from scratch, so they should be ostensibly equivalent environments.
I'll plan on building the packages and pushing to PyPI for the sake of the archive (probably tonight), but we should probably figure out what's going on and try to do a quick 1.2.4 fixup release.