TEST: Mock terminal output before testing changing default value

[effigies]

Summary

Closes #3185.

Without pytest-xdist, this reliably fails:

pytest --pdb --doctest-modules nipype/interfaces/base/tests/test_core.py nipype/interfaces/freesurfer/tests/test_utils.py

I assume the intermittent CI failures are for when the two tests were run on the same worker.

List of changes proposed in this PR (pull-request)

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[mgxd]

ah! i wonder if this is somewhat related to failures we saw in #3046 given that that interface also parses stdout

[codecov]

Codecov Report

Merging #3193 into master will increase coverage by 0.08%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #3193      +/-   ##
==========================================
+ Coverage   65.07%   65.16%   +0.08%     
==========================================
  Files         301      301              
  Lines       39624    39652      +28     
  Branches     5247     5263      +16     
==========================================
+ Hits        25786    25839      +53     
+ Misses      12771    12739      -32     
- Partials     1067     1074       +7     

Flag	Coverage Δ
#unittests	65.16% <ø> (+0.08%)	⬆️

Impacted Files	Coverage Δ
nipype/pipeline/plugins/legacymultiproc.py	65.34% <0.00%> (-3.47%)	⬇️
nipype/pipeline/plugins/base.py	62.46% <0.00%> (-1.65%)	⬇️
nipype/interfaces/dcm2nii.py	64.78% <0.00%> (+15.02%)	⬆️
nipype/interfaces/niftyreg/base.py	69.44% <0.00%> (+18.19%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update c37fcfb...5c69cd1. Read the comment docs.

[effigies]

Yes. That error can also be reliably reproduced in the same way, and is resolved by this commit. I will remove the xfail.

We should probably find a less brittle way to extract information from output streams, however...

[effigies]

@mgxd can you look at the failure? I don't get this locally.

[mgxd]

hmm, it looks like the dataset is no longer with us
http://datasets-tests.datalad.org/dicoms/dcm2niix-tests/Siemens_Sag_DTI_20160825_145811/

[effigies]

Now I'm curious why it doesn't fail for me locally...

[effigies]

@mgxd If I run datalad install http://datasets-tests.datalad.org/dicoms/dcm2niix-tests, I still see the dataset correctly.

@yarikoptic Does this error mean anything to you?

fetch_data = <function fetch_data.<locals>._fetch_data at 0x7fc0c80abd08>
tmpdir = local('/tmp/pytest-of-neuro/pytest-1/test_dcm2niix_dti0')

    @pytest.mark.skipif(no_datalad, reason="Datalad required")
    @pytest.mark.skipif(no_dcm2niix, reason="Dcm2niix required")
    def test_dcm2niix_dti(fetch_data, tmpdir):
        tmpdir.chdir()
        datadir = tmpdir.mkdir("data").strpath
>       dicoms = fetch_data(datadir, "Siemens_Sag_DTI_20160825_145811")

/src/nipype/nipype/interfaces/tests/test_extra_dcm2nii.py:38: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/src/nipype/nipype/interfaces/tests/test_extra_dcm2nii.py:25: in _fetch_data
    api.get(path=data)
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/datalad/interface/utils.py:492: in eval_func
    return return_func(generator_func)(*args, **kwargs)
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/datalad/interface/utils.py:480: in return_func
    results = list(results)
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/datalad/interface/utils.py:411: in generator_func
    allkwargs):
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/datalad/interface/utils.py:527: in _process_results
    for res in results:
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/datalad/distribution/get.py:669: in __call__
    dataset, check_installed=True, purpose='get content')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

dataset = None, check_installed = True, purpose = 'get content'

    def require_dataset(dataset, check_installed=True, purpose=None):
        """Helper function to resolve a dataset.
    
        This function tries to resolve a dataset given an input argument,
        or based on the process' working directory, if `None` is given.
    
        Parameters
        ----------
        dataset : None or path or Dataset
          Some value identifying a dataset or `None`. In the latter case
          a dataset will be searched based on the process working directory.
        check_installed : bool, optional
          If True, an optional check whether the resolved dataset is
          properly installed will be performed.
        purpose : str, optional
          This string will be inserted in error messages to make them more
          informative. The pattern is "... dataset for <STRING>".
    
        Returns
        -------
        Dataset
          Or raises an exception (InsufficientArgumentsError).
        """
        if dataset is not None and not isinstance(dataset, Dataset):
            dataset = Dataset(dataset)
    
        if dataset is None:  # possible scenario of cmdline calls
            dspath = get_dataset_root(getpwd())
            if not dspath:
                raise NoDatasetFound(
                    "No dataset found at '{}'.  Specify a dataset to work with "
                    "by providing its path via the `dataset` option, "
                    "or change the current working directory to be in a "
>                   "dataset.".format(getpwd()))
E               datalad.support.exceptions.NoDatasetFound: No dataset found at '/tmp/pytest-of-neuro/pytest-1/test_dcm2niix_dti0'.  Specify a dataset to work with by providing its path via the `dataset` option, or change the current working directory to be in a dataset.

/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/datalad/distribution/dataset.py:570: NoDatasetFound

I've installed the Debian versions of datalad/git-annex to simulate the test conditions, but can't reproduce the issue.

[effigies]

Fiddled with it by SSHing in. It's the datalad change where you need to specify the dataset manually. 5c69cd1 should resolve it.

Still not sure why I couldn't reproduce locally.