MAINT: ensure interface _cmd only includes executable #2674
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effigies reviewed Aug 6, 2018
nipype/interfaces/afni/preprocess.py Outdated
| outputs['warped_source'] = os.path.abspath("Qwarp_PLUS.nii.gz") | ||
| outputs['warped_base'] = os.path.abspath("Qwarp_MINUS.nii.gz") | ||
| outputs['source_warp'] = os.path.abspath("Qwarp_PLUS_WARP.nii.gz") | ||
| outputs['base_warp'] = os.path.abspath("Qwarp_MINUS_WARP.nii.gz") |
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I would drop _list_outputs. This should be handled by Qwarp._list_outputs() and correctly handle non-default out_file selections.
Codecov Report
@@ Coverage Diff @@ ## master #2674 +/- ## ========================================== + Coverage 67.61% 67.64% +0.02% ========================================== Files 340 340 Lines 43076 43060 -16 Branches 5333 5333 ========================================== - Hits 29127 29126 -1 + Misses 13246 13232 -14 + Partials 703 702 -1
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effigies approved these changes Aug 6, 2018
nipype/interfaces/afni/preprocess.py Outdated
| argstr='-source %s', | ||
| mandatory=True, | ||
| exists=True, | ||
| copyfile=False) |
This was referenced Sep 18, 2018
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Summary
Fixes nipreps/fmriprep#1236 .
List of changes proposed in this PR (pull-request)
As discussed in nipreps/fmriprep#1235 (comment), this PR strips down "helper interfaces"
_cmdto only the executable, and adds the necessary arguments as defaults in the inputspec.Acknowledgment