Error when testing nipype installation

[Michael]

Testing the nipype installation on Ubuntu resulted in the following error

File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/dcm2nii.py", line 52, in nipype.interfaces.dcm2nii.Dcm2nii

Failed example:

    converter.cmdline #doctest: +ELLIPSIS

Exception raised:

    Traceback (most recent call last):

      File "/usr/lib/python2.7/doctest.py", line 1315, in __run

        compileflags, 1) in test.globs

      File "<doctest nipype.interfaces.dcm2nii.Dcm2nii[5]>", line 1, in <module>

        converter.cmdline #doctest: +ELLIPSIS

      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1310, in cmdline

        allargs = self._parse_inputs()

      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1528, in _parse_inputs

        value = self._gen_filename(name)

      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/dcm2nii.py", line 150, in _gen_filename

        f = open(config_file, "w")

    IOError: [Errno 13] Permission denied: 'config.ini'

Any idea how i could solve this issue?

[Michael]

The end of the report is as follows:

...................

======================================================================

ERROR: Failure: KeyError ('in_topup')

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 251, in generate

    for test in g():

  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/fsl/tests/test_auto_Eddy.py", line 57, in test_Eddy_inputs

    yield assert_equal, getattr(inputs.traits()[key], metakey), value

KeyError: 'in_topup'

======================================================================

FAIL: Doctest: nipype.interfaces.dcm2nii.Dcm2nii

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/usr/lib/python2.7/doctest.py", line 2226, in runTest

    raise self.failureException(self.format_failure(new.getvalue()))

AssertionError: Failed doctest test for nipype.interfaces.dcm2nii.Dcm2nii

  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/dcm2nii.py", line 41, in Dcm2nii

----------------------------------------------------------------------

File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/dcm2nii.py", line 52, in nipype.interfaces.dcm2nii.Dcm2nii

Failed example:

    converter.cmdline #doctest: +ELLIPSIS

Exception raised:

    Traceback (most recent call last):

      File "/usr/lib/python2.7/doctest.py", line 1315, in __run

        compileflags, 1) in test.globs

      File "<doctest nipype.interfaces.dcm2nii.Dcm2nii[5]>", line 1, in <module>

        converter.cmdline #doctest: +ELLIPSIS

      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1310, in cmdline

        allargs = self._parse_inputs()

      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1528, in _parse_inputs

        value = self._gen_filename(name)

      File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/dcm2nii.py", line 150, in _gen_filename

        f = open(config_file, "w")

    IOError: [Errno 13] Permission denied: 'config.ini'

======================================================================

FAIL: test_auto_DTIFit.test_DTIFit_inputs('--cni=%s', '-cni %s')

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest

    self.test(*self.arg)

  File "/usr/lib/python2.7/dist-packages/numpy/testing/utils.py", line 317, in assert_equal

    raise AssertionError(msg)

AssertionError: 

Items are not equal:

 ACTUAL: '--cni=%s'

 DESIRED: '-cni %s'

----------------------------------------------------------------------

Ran 7445 tests in 84.909s

FAILED (SKIP=8, errors=1, failures=2)

[Satrajit Ghosh]

hi mike,

the simplest is to remove that line from the doctest and add a unit-test that checks this in a temporary directory.  

however, it would be good to check if there is anything in the config file that cannot be handled by command line arguments to dcm2nii. in which case we should be writing the command line arguments instead of the config file. but i suspect there are a few things that need config file.

also, is thus current master? the other tests that are failing don't fail on travis.

cheers,

satra

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[Michael]

Hi Satra,

Many thanks for your feedback. I just updated to the last master and you are right, now only the dcm2nii failure comes up (not the others).

[thomas.nickson]

I also get this error but I'm not sure what you mean as when I look in dcm2nii there are no doctests? Which file is this in?

Thanks,

Tom

[Satrajit Ghosh]

in current master there is a doctest.

https://github.com/nipy/nipype/blob/master/nipype/interfaces/dcm2nii.py#L47

cheers,

satra