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@salma1601
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try fix #2221

def _list_outputs(self):
outputs = self.output_spec().get()

if not isdefined(self.inputs.out_file):
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@oesteban oesteban Oct 9, 2017

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All of this should not be here:

  1. The out_file input spec can only define one of name_source or genfile (currently it defines both). Since we are trying to deprecate genfile, name_source should be preferred.

  2. In theory, name_source should fix this issue.

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@oesteban - i'm leaving the afni stuff to @Shotgunosine and others to figure out. right now, because of the way afni works with various kinds of extensions, the straight up namesource can run into issues.

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codecov-io commented Oct 10, 2017

Codecov Report

Merging #2222 into master will increase coverage by <.01%.
The diff coverage is 9.09%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2222      +/-   ##
==========================================
+ Coverage   72.31%   72.31%   +<.01%     
==========================================
  Files        1180     1179       -1     
  Lines       58879    58833      -46     
  Branches     8474     8465       -9     
==========================================
- Hits        42579    42546      -33     
+ Misses      14921    14911      -10     
+ Partials     1379     1376       -3
Flag Coverage Δ
#smoketests 72.31% <9.09%> (ø) ⬆️
#unittests 69.88% <9.09%> (ø) ⬆️
Impacted Files Coverage Δ
nipype/interfaces/afni/tests/test_auto_Qwarp.py 85.71% <ø> (ø) ⬆️
nipype/interfaces/afni/preprocess.py 80.32% <9.09%> (-0.31%) ⬇️
nipype/pipeline/plugins/multiproc.py 76.76% <0%> (-1.41%) ⬇️
nipype/interfaces/afni/model.py 84.1% <0%> (-1.35%) ⬇️
...pype/interfaces/afni/tests/test_auto_Deconvolve.py 85.71% <0%> (ø) ⬆️
...terfaces/freesurfer/tests/test_auto_Tkregister2.py 85.71% <0%> (ø) ⬆️
...pype/interfaces/afni/tests/test_auto_Synthesize.py
nipype/interfaces/freesurfer/utils.py 63.54% <0%> (+0.46%) ⬆️
nipype/utils/profiler.py 41.35% <0%> (+1.23%) ⬆️

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@satra satra merged commit 7600dcb into nipy:master Oct 21, 2017
@satra satra added this to the 0.14.0 milestone Oct 28, 2017
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AFNI Qwarp output paths are incorrect

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