test_dcm2niix_dwi failing intermittently #3046

effigies · 2019-09-23T18:07:38Z

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.

The text was updated successfully, but these errors were encountered:

effigies · 2019-09-24T17:10:53Z

@mgxd The dcm2niix test is not resolved by using an old pytest. It's unclear to me why this test is now failing.

satra · 2019-09-30T13:08:27Z

this test also fails in circle on 2.7

effigies · 2019-09-30T13:18:37Z

I'm unclear on why it is now working again for Python 3.

effigies · 2019-09-30T14:14:43Z

Updated the title to reflect current state.

@mgxd Do you have any time to look into this? Should we re-mark it XFAIL?

mgxd · 2019-09-30T14:20:38Z

yeah, I'm taking a look right now

effigies · 2019-10-02T23:27:07Z

I pushed 085767c to mark it xfail. We should get back to this at some point.

effigies added the bug label Sep 23, 2019

effigies mentioned this issue Sep 24, 2019

TEST: Pin pytest < 5.1.3 #3048

Closed

1 task

effigies mentioned this issue Sep 24, 2019

RF: Provide functions to augment old Path.mkdir, Path.resolve methods #3050

Merged

1 task

oesteban mentioned this issue Sep 25, 2019

RFC: Python and Numpy version support and release schedule #3036

Open

satra mentioned this issue Sep 30, 2019

ENH: Delay etelemetry for non-interactive sessions, report bad versions #3049

Merged

1 task

effigies changed the title ~~New test failures~~ test_dcm2niix_dwi failing intermittently Sep 30, 2019

mgxd mentioned this issue Sep 30, 2019

TST: dcm2niix test fix #3058

Merged

1 task

effigies closed this as completed in #3058 Sep 30, 2019

mgxd added the watchlist label Sep 30, 2019

effigies reopened this Oct 2, 2019

mgxd mentioned this issue Mar 23, 2020

TEST: Mock terminal output before testing changing default value #3193

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test_dcm2niix_dwi failing intermittently #3046

test_dcm2niix_dwi failing intermittently #3046

effigies commented Sep 23, 2019

effigies commented Sep 24, 2019

satra commented Sep 30, 2019

effigies commented Sep 30, 2019

effigies commented Sep 30, 2019

mgxd commented Sep 30, 2019

effigies commented Oct 2, 2019

test_dcm2niix_dwi failing intermittently #3046

test_dcm2niix_dwi failing intermittently #3046

Comments

effigies commented Sep 23, 2019

Summary

effigies commented Sep 24, 2019

satra commented Sep 30, 2019

effigies commented Sep 30, 2019

effigies commented Sep 30, 2019

mgxd commented Sep 30, 2019

effigies commented Oct 2, 2019