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[FIX] Bug fixes for afni.model #2398

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Merged
merged 2 commits into from
Jan 26, 2018
Merged

[FIX] Bug fixes for afni.model #2398

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2b33d79
Bug fixes for afni.model
emdupre Jan 23, 2018
dffae4f
Extend extra Deconvolve test
emdupre Jan 23, 2018
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14 changes: 13 additions & 1 deletion nipype/interfaces/afni/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -293,11 +293,14 @@ def _list_outputs(self):
outputs['x1D'] = self._gen_fname(
suffix='.xmat.1D', **_gen_fname_opts)

if isdefined(self.inputs.cbucket):
outputs['cbucket'] = os.path.abspath(self.inputs.cbucket)

outputs['reml_script'] = self._gen_fname(
suffix='.REML_cmd', **_gen_fname_opts)
# remove out_file from outputs if x1d_stop set to True
if self.inputs.x1D_stop:
del outputs['out_file']
del outputs['out_file'], outputs['cbucket']
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if I may, test_extra_Deconvolve.py could be extended to check for the removal of outputs['cbucket']

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Thanks for reviewing this, @mvdoc ! It sounds like a new release is imminent, but if @effigies doesn't mind me using a circle cycle I'll submit a patch to extend the test.

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@emdupre nothing is building right now and won't probably merge anything more. feel free to use circle, we can always cancel.

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Was going to say what @djarecka said. CI is not really the submitter's problem and we can cancel and restart as needed. I just try to give a heads up when doing that.

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Great, thanks for clarifying !

else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)

Expand Down Expand Up @@ -652,3 +655,12 @@ class Synthesize(AFNICommand):
_cmd = '3dSynthesize'
input_spec = SynthesizeInputSpec
output_spec = AFNICommandOutputSpec

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

for key in outputs.keys():
if isdefined(self.inputs.get()[key]):
outputs[key] = os.path.abspath(self.inputs.get()[key])

return outputs
3 changes: 2 additions & 1 deletion nipype/interfaces/afni/tests/test_extra_Deconvolve.py
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Expand Up @@ -7,4 +7,5 @@ def test_x1dstop():
deconv.inputs.out_file = 'file.nii'
assert 'out_file' in deconv._list_outputs()
deconv.inputs.x1D_stop = True
assert not 'out_file' in deconv._list_outputs()
assert 'out_file' not in deconv._list_outputs()
assert 'cbucket' not in deconv._list_outputs()