From 862f9d6e98fd765ad27b815fa9fbafc3eb428632 Mon Sep 17 00:00:00 2001 From: Victor Ferat Date: Tue, 20 Aug 2019 11:10:33 +0200 Subject: [PATCH 1/6] Fix #2995 --- nipype/interfaces/mne/base.py | 110 +++++++++++++++++++--------------- 1 file changed, 62 insertions(+), 48 deletions(-) diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py index 7f53071372..c0aec045f2 100644 --- a/nipype/interfaces/mne/base.py +++ b/nipype/interfaces/mne/base.py @@ -1,6 +1,5 @@ # -*- coding: utf-8 -*- -from __future__ import (print_function, division, unicode_literals, - absolute_import) +from __future__ import print_function, division, unicode_literals, absolute_import from builtins import str, bytes import os.path as op @@ -8,74 +7,86 @@ from ... import logging from ...utils.filemanip import simplify_list -from ..base import (traits, File, Directory, TraitedSpec, OutputMultiPath) +from ..base import traits, File, Directory, TraitedSpec, OutputMultiPath from ..freesurfer.base import FSCommand, FSTraitedSpec -iflogger = logging.getLogger('nipype.interface') +iflogger = logging.getLogger("nipype.interface") class WatershedBEMInputSpec(FSTraitedSpec): subject_id = traits.Str( - argstr='--subject %s', + argstr="--subject %s", mandatory=True, - desc='Subject ID (must have a complete Freesurfer directory)') + desc="Subject ID (must have a complete Freesurfer directory)", + ) subjects_dir = Directory( exists=True, mandatory=True, usedefault=True, - desc='Path to Freesurfer subjects directory') + desc="Path to Freesurfer subjects directory", + ) volume = traits.Enum( - 'T1', - 'aparc+aseg', - 'aseg', - 'brain', - 'orig', - 'brainmask', - 'ribbon', - argstr='--volume %s', + "T1", + "aparc+aseg", + "aseg", + "brain", + "orig", + "brainmask", + "ribbon", + argstr="--volume %s", usedefault=True, - desc='The volume from the "mri" directory to use (defaults to T1)') + desc='The volume from the "mri" directory to use (defaults to T1)', + ) overwrite = traits.Bool( True, usedefault=True, - argstr='--overwrite', - desc='Overwrites the existing files') + argstr="--overwrite", + desc="Overwrites the existing files", + ) atlas_mode = traits.Bool( - argstr='--atlas', - desc='Use atlas mode for registration (default: no rigid alignment)') + argstr="--atlas", + desc="Use atlas mode for registration (default: no rigid alignment)", + ) class WatershedBEMOutputSpec(TraitedSpec): mesh_files = OutputMultiPath( File(exists=True), - desc=('Paths to the output meshes (brain, inner ' - 'skull, outer skull, outer skin)')) + desc=( + "Paths to the output meshes (brain, inner " + "skull, outer skull, outer skin)" + ), + ) brain_surface = File( - exists=True, - loc='bem/watershed', - desc='Brain surface (in Freesurfer format)') + exists=True, loc="bem/watershed", desc="Brain surface (in Freesurfer format)" + ) inner_skull_surface = File( exists=True, - loc='bem/watershed', - desc='Inner skull surface (in Freesurfer format)') + loc="bem/watershed", + desc="Inner skull surface (in Freesurfer format)", + ) outer_skull_surface = File( exists=True, - loc='bem/watershed', - desc='Outer skull surface (in Freesurfer format)') + loc="bem/watershed", + desc="Outer skull surface (in Freesurfer format)", + ) outer_skin_surface = File( exists=True, - loc='bem/watershed', - desc='Outer skin surface (in Freesurfer format)') + loc="bem/watershed", + desc="Outer skin surface (in Freesurfer format)", + ) fif_file = File( exists=True, - loc='bem', - altkey='fif', - desc='"fif" format file for EEG processing in MNE') + loc="bem", + altkey="fif", + desc='"fif" format file for EEG processing in MNE', + ) cor_files = OutputMultiPath( File(exists=True), - loc='bem/watershed/ws', - altkey='COR', - desc='"COR" format files') + loc="bem/watershed/ws", + altkey="COR", + desc='"COR" format files', + ) class WatershedBEM(FSCommand): @@ -94,18 +105,18 @@ class WatershedBEM(FSCommand): """ - _cmd = 'mne_watershed_bem' + _cmd = "mne watershed_bem" input_spec = WatershedBEMInputSpec output_spec = WatershedBEMOutputSpec - _additional_metadata = ['loc', 'altkey'] + _additional_metadata = ["loc", "altkey"] def _get_files(self, path, key, dirval, altkey=None): - globsuffix = '*' - globprefix = '*' + globsuffix = "*" + globprefix = "*" keydir = op.join(path, dirval) if altkey: key = altkey - globpattern = op.join(keydir, ''.join((globprefix, key, globsuffix))) + globpattern = op.join(keydir, "".join((globprefix, key, globsuffix))) return glob.glob(globpattern) def _list_outputs(self): @@ -115,10 +126,13 @@ def _list_outputs(self): output_traits = self._outputs() mesh_paths = [] for k in list(outputs.keys()): - if k != 'mesh_files': - val = self._get_files(subject_path, k, - output_traits.traits()[k].loc, - output_traits.traits()[k].altkey) + if k != "mesh_files": + val = self._get_files( + subject_path, + k, + output_traits.traits()[k].loc, + output_traits.traits()[k].altkey, + ) if val: value_list = simplify_list(val) if isinstance(value_list, list): @@ -130,7 +144,7 @@ def _list_outputs(self): else: raise TypeError outputs[k] = out_files - if not k.rfind('surface') == -1: + if not k.rfind("surface") == -1: mesh_paths.append(out_files) - outputs['mesh_files'] = mesh_paths + outputs["mesh_files"] = mesh_paths return outputs From 6f716542929a77bb61865e2d4c7a0aa67f40ce2e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Victor=20F=C3=A9rat?= Date: Tue, 20 Aug 2019 11:43:10 +0200 Subject: [PATCH 2/6] Fix documentation --- nipype/interfaces/mne/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py index c0aec045f2..7a4f186496 100644 --- a/nipype/interfaces/mne/base.py +++ b/nipype/interfaces/mne/base.py @@ -100,7 +100,7 @@ class WatershedBEM(FSCommand): >>> bem.inputs.subject_id = 'subj1' >>> bem.inputs.subjects_dir = '.' >>> bem.cmdline - 'mne_watershed_bem --overwrite --subject subj1 --volume T1' + 'mne watershed_bem --overwrite --subject subj1 --volume T1' >>> bem.run() # doctest: +SKIP """ From 8129ff4e004fdfcd6ce9b0730ee62d58586ff647 Mon Sep 17 00:00:00 2001 From: Victor Date: Fri, 23 Aug 2019 15:11:54 +0200 Subject: [PATCH 3/6] run make check-before-commit without error --- .../algorithms/tests/test_auto_AddCSVRow.py | 5 +- nipype/algorithms/tests/test_auto_Gunzip.py | 9 ++- .../tests/test_auto_NonSteadyStateDetector.py | 9 ++- .../afni/tests/test_auto_Allineate.py | 1 + nipype/interfaces/afni/tests/test_auto_Cat.py | 7 +-- .../afni/tests/test_auto_ClipLevel.py | 1 + .../afni/tests/test_auto_LocalBistat.py | 7 ++- .../afni/tests/test_auto_Localstat.py | 6 +- .../afni/tests/test_auto_NwarpApply.py | 5 +- .../afni/tests/test_auto_OneDToolPy.py | 1 + .../interfaces/afni/tests/test_auto_Qwarp.py | 5 +- .../afni/tests/test_auto_QwarpPlusMinus.py | 5 +- .../afni/tests/test_auto_ROIStats.py | 5 +- .../interfaces/afni/tests/test_auto_ReHo.py | 6 +- .../afni/tests/test_auto_Remlfit.py | 1 + .../afni/tests/test_auto_Resample.py | 5 +- .../afni/tests/test_auto_TCorrMap.py | 5 +- .../afni/tests/test_auto_Zeropad.py | 1 + .../interfaces/ants/tests/test_auto_ANTS.py | 4 +- .../ants/tests/test_auto_AntsJointFusion.py | 9 ++- .../ants/tests/test_auto_Atropos.py | 4 +- .../base/tests/test_auto_StdOutCommandLine.py | 1 + .../camino/tests/test_auto_AnalyzeHeader.py | 1 + .../tests/test_auto_ComputeEigensystem.py | 1 + .../test_auto_ComputeFractionalAnisotropy.py | 1 + .../tests/test_auto_ComputeTensorTrace.py | 1 + .../camino/tests/test_auto_DTIFit.py | 1 + .../camino/tests/test_auto_DTLUTGen.py | 1 + .../camino/tests/test_auto_FSL2Scheme.py | 1 + .../camino/tests/test_auto_Image2Voxel.py | 1 + .../camino/tests/test_auto_LinRecon.py | 1 + .../interfaces/camino/tests/test_auto_MESD.py | 1 + .../camino/tests/test_auto_ModelFit.py | 1 + .../camino/tests/test_auto_NIfTIDT2Camino.py | 1 + .../camino/tests/test_auto_PicoPDFs.py | 1 + .../camino/tests/test_auto_ProcStreamlines.py | 1 + .../camino/tests/test_auto_QBallMX.py | 1 + .../camino/tests/test_auto_SFLUTGen.py | 1 + .../camino/tests/test_auto_SFPICOCalibData.py | 1 + .../camino/tests/test_auto_SFPeaks.py | 1 + .../camino/tests/test_auto_Shredder.py | 1 + .../camino/tests/test_auto_TractShredder.py | 1 + .../camino/tests/test_auto_VtkStreamlines.py | 1 + .../freesurfer/tests/test_auto_Aparc2Aseg.py | 9 ++- .../freesurfer/tests/test_auto_Apas2Aseg.py | 9 ++- .../freesurfer/tests/test_auto_CALabel.py | 10 +++- .../freesurfer/tests/test_auto_CANormalize.py | 2 +- .../freesurfer/tests/test_auto_CARegister.py | 2 +- .../test_auto_CheckTalairachAlignment.py | 2 +- .../tests/test_auto_ConcatenateLTA.py | 2 + .../freesurfer/tests/test_auto_Contrast.py | 10 +++- .../freesurfer/tests/test_auto_FixTopology.py | 5 +- .../freesurfer/tests/test_auto_MRIsCALabel.py | 10 +++- .../freesurfer/tests/test_auto_MS_LDA.py | 12 +++- .../freesurfer/tests/test_auto_Normalize.py | 2 +- .../tests/test_auto_ParcellationStats.py | 9 ++- .../tests/test_auto_RegisterAVItoTalairach.py | 2 +- .../tests/test_auto_RelabelHypointensities.py | 9 ++- .../tests/test_auto_SegStatsReconAll.py | 5 +- .../tests/test_auto_SurfaceSnapshots.py | 1 + .../tests/test_auto_TalairachAVI.py | 6 +- .../freesurfer/tests/test_auto_TalairachQC.py | 9 ++- .../fsl/tests/test_auto_AccuracyTester.py | 9 ++- .../interfaces/fsl/tests/test_auto_Cleaner.py | 3 + .../interfaces/fsl/tests/test_auto_Cluster.py | 5 +- .../fsl/tests/test_auto_FeatureExtractor.py | 11 ++-- .../fsl/tests/test_auto_FindTheBiggest.py | 9 ++- .../fsl/tests/test_auto_TrainingSetCreator.py | 22 ++++---- .../minc/tests/test_auto_Average.py | 6 +- .../interfaces/minc/tests/test_auto_BBox.py | 1 + .../interfaces/minc/tests/test_auto_Beast.py | 7 ++- .../interfaces/minc/tests/test_auto_Calc.py | 2 + .../interfaces/minc/tests/test_auto_Dump.py | 1 + .../minc/tests/test_auto_Extract.py | 1 + .../interfaces/minc/tests/test_auto_Math.py | 1 + .../interfaces/minc/tests/test_auto_Norm.py | 6 +- .../minc/tests/test_auto_Resample.py | 10 +++- .../minc/tests/test_auto_Reshape.py | 1 + .../interfaces/minc/tests/test_auto_ToRaw.py | 1 + .../minc/tests/test_auto_VolSymm.py | 2 + .../minc/tests/test_auto_XfmInvert.py | 1 + .../mrtrix3/tests/test_auto_BrainMask.py | 6 +- .../mrtrix3/tests/test_auto_DWIExtract.py | 6 +- .../mrtrix3/tests/test_auto_EstimateFOD.py | 6 +- .../mrtrix3/tests/test_auto_FitTensor.py | 6 +- .../mrtrix3/tests/test_auto_Generate5tt.py | 6 +- .../mrtrix3/tests/test_auto_MRConvert.py | 6 +- .../mrtrix3/tests/test_auto_MRMath.py | 6 +- .../mrtrix3/tests/test_auto_ResponseSD.py | 6 +- .../mrtrix3/tests/test_auto_Tractography.py | 6 +- .../niftyfit/tests/test_auto_DwiTool.py | 26 ++++++--- .../niftyfit/tests/test_auto_FitAsl.py | 41 +++++++++++--- .../niftyfit/tests/test_auto_FitDwi.py | 56 ++++++++++++++----- .../niftyfit/tests/test_auto_FitQt1.py | 25 +++++++-- .../nipy/tests/test_auto_EstimateContrast.py | 2 +- .../interfaces/nipy/tests/test_auto_FitGLM.py | 4 +- .../tests/test_auto_UnbiasedNonLocalMeans.py | 9 ++- .../diffusion/tests/test_auto_DTIexport.py | 9 ++- .../diffusion/tests/test_auto_DTIimport.py | 9 ++- .../test_auto_DWIJointRicianLMMSEFilter.py | 9 ++- .../tests/test_auto_DWIRicianLMMSEFilter.py | 9 ++- ..._auto_DiffusionTensorScalarMeasurements.py | 9 ++- .../tests/test_auto_ResampleDTIVolume.py | 9 ++- .../tests/test_auto_AddScalarVolumes.py | 9 ++- .../tests/test_auto_CastScalarVolume.py | 9 ++- .../tests/test_auto_CheckerBoardFilter.py | 9 ++- ...test_auto_CurvatureAnisotropicDiffusion.py | 9 ++- .../tests/test_auto_ExtractSkeleton.py | 9 ++- .../test_auto_GaussianBlurImageFilter.py | 9 ++- .../test_auto_GradientAnisotropicDiffusion.py | 9 ++- .../test_auto_GrayscaleFillHoleImageFilter.py | 9 ++- ...test_auto_GrayscaleGrindPeakImageFilter.py | 9 ++- .../tests/test_auto_HistogramMatching.py | 9 ++- .../tests/test_auto_ImageLabelCombine.py | 9 ++- .../tests/test_auto_MaskScalarVolume.py | 9 ++- .../tests/test_auto_MedianImageFilter.py | 9 ++- .../tests/test_auto_MultiplyScalarVolumes.py | 9 ++- ...test_auto_ResampleScalarVectorDWIVolume.py | 9 ++- .../tests/test_auto_SubtractScalarVolumes.py | 9 ++- .../tests/test_auto_ThresholdScalarVolume.py | 9 ++- ...auto_VotingBinaryHoleFillingImageFilter.py | 9 ++- ...est_auto_DWIUnbiasedNonLocalMeansFilter.py | 9 ++- .../test_auto_OtsuThresholdImageFilter.py | 9 ++- .../test_auto_OtsuThresholdSegmentation.py | 9 ++- .../tests/test_auto_ResampleScalarVolume.py | 9 ++- .../test_auto_RobustStatisticsSegmenter.py | 9 ++- ...st_auto_SimpleRegionGrowingSegmentation.py | 9 ++- .../tests/test_auto_GrayscaleModelMaker.py | 9 ++- .../tests/test_auto_LabelMapSmoothing.py | 9 ++- .../slicer/tests/test_auto_MergeModels.py | 9 ++- .../slicer/tests/test_auto_ModelToLabelMap.py | 9 ++- .../tests/test_auto_OrientScalarVolume.py | 9 ++- .../tests/test_auto_ProbeVolumeWithModel.py | 9 ++- .../utility/tests/test_auto_Rename.py | 2 +- 134 files changed, 541 insertions(+), 340 deletions(-) diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index 3090c8b6a9..a8c4467cbf 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -6,7 +6,10 @@ def test_AddCSVRow_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = AddCSVRow.input_spec() diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index e583deaa10..d84e84ad61 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -4,11 +4,10 @@ def test_Gunzip_inputs(): - input_map = dict( - in_file=dict( - extensions=None, - mandatory=True, - ), ) + input_map = dict(in_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = Gunzip.input_spec() for key, metadata in list(input_map.items()): diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index 4da9dad47d..10eb41190b 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -4,11 +4,10 @@ def test_NonSteadyStateDetector_inputs(): - input_map = dict( - in_file=dict( - extensions=None, - mandatory=True, - ), ) + input_map = dict(in_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = NonSteadyStateDetector.input_spec() for key, metadata in list(input_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 0b110e669a..e1565376bd 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -86,6 +86,7 @@ def test_Allineate_inputs(): ), out_weight_file=dict( argstr='-wtprefix %s', + extensions=None, xor=['allcostx'], ), outputtype=dict(), diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index 345806f746..50806add01 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -21,10 +21,9 @@ def test_Cat_inputs(): usedefault=True, ), omitconst=dict(argstr='-nonconst', ), - out_cint=dict( - xor=[ - 'out_format', 'out_nice', 'out_double', 'out_fint', 'out_int' - ], ), + out_cint=dict(xor=[ + 'out_format', 'out_nice', 'out_double', 'out_fint', 'out_int' + ], ), out_double=dict( argstr='-d', xor=['out_format', 'out_nice', 'out_int', 'out_fint', 'out_cint'], diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index f9b3dbf705..96f928a809 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -17,6 +17,7 @@ def test_ClipLevel_inputs(): ), grad=dict( argstr='-grad %s', + extensions=None, position=3, xor='doall', ), diff --git a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py index ed3e61d74d..4632e4cf7d 100644 --- a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py +++ b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py @@ -26,7 +26,10 @@ def test_LocalBistat_inputs(): mandatory=True, position=-1, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), neighborhood=dict( argstr="-nbhd '%s(%s)'", mandatory=True, @@ -37,6 +40,7 @@ def test_LocalBistat_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, keep_extension=True, name_source='in_file1', name_template='%s_bistat', @@ -49,6 +53,7 @@ def test_LocalBistat_inputs(): ), weight_file=dict( argstr='-weight %s', + extensions=None, xor=['automask'], ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Localstat.py b/nipype/interfaces/afni/tests/test_auto_Localstat.py index 011ce44da8..62dc800941 100644 --- a/nipype/interfaces/afni/tests/test_auto_Localstat.py +++ b/nipype/interfaces/afni/tests/test_auto_Localstat.py @@ -21,7 +21,10 @@ def test_Localstat_inputs(): mandatory=True, position=-1, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), neighborhood=dict( argstr="-nbhd '%s(%s)'", mandatory=True, @@ -33,6 +36,7 @@ def test_Localstat_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_localstat', diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index e00457f4f3..87388c65ec 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -20,7 +20,10 @@ def test_NwarpApply_inputs(): usedefault=True, ), inv_warp=dict(argstr='-iwarp', ), - master=dict(argstr='-master %s', ), + master=dict( + argstr='-master %s', + extensions=None, + ), out_file=dict( argstr='-prefix %s', extensions=None, diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index f8e664a727..114fe53fba 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -30,6 +30,7 @@ def test_OneDToolPy_inputs(): show_censor_count=dict(argstr='-show_censor_count', ), show_cormat_warnings=dict( argstr='-show_cormat_warnings |& tee %s', + extensions=None, position=-1, xor=['out_file'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index 3ef8c2e9b2..0b8a9e38ec 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -125,7 +125,10 @@ def test_Qwarp_inputs(): name_source=['in_file'], name_template='ppp_%s', ), - out_weight_file=dict(argstr='-wtprefix %s', ), + out_weight_file=dict( + argstr='-wtprefix %s', + extensions=None, + ), outputtype=dict(), overwrite=dict(argstr='-overwrite', ), pblur=dict(argstr='-pblur %s', ), diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index ca27a0d682..e282d0d0a5 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -125,7 +125,10 @@ def test_QwarpPlusMinus_inputs(): position=0, usedefault=True, ), - out_weight_file=dict(argstr='-wtprefix %s', ), + out_weight_file=dict( + argstr='-wtprefix %s', + extensions=None, + ), outputtype=dict(), overwrite=dict(argstr='-overwrite', ), pblur=dict(argstr='-pblur %s', ), diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index d3c956f7c5..c7fc517ccc 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -49,7 +49,10 @@ def test_ROIStats_inputs(): position=-1, ), quiet=dict(argstr='-quiet', ), - roisel=dict(argstr='-roisel %s', ), + roisel=dict( + argstr='-roisel %s', + extensions=None, + ), stat=dict(argstr='%s...', ), zerofill=dict( argstr='-zerofill %s', diff --git a/nipype/interfaces/afni/tests/test_auto_ReHo.py b/nipype/interfaces/afni/tests/test_auto_ReHo.py index 0edcedcdaf..cf3e468159 100644 --- a/nipype/interfaces/afni/tests/test_auto_ReHo.py +++ b/nipype/interfaces/afni/tests/test_auto_ReHo.py @@ -25,13 +25,17 @@ def test_ReHo_inputs(): argstr='-in_rois %s', extensions=None, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), neighborhood=dict( argstr='-nneigh %s', xor=['sphere', 'ellipsoid'], ), out_file=dict( argstr='-prefix %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_reho', diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index f2e6703bf6..05ee75210e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -58,6 +58,7 @@ def test_Remlfit_inputs(): ), matim=dict( argstr='-matim %s', + extensions=None, xor=['matrix'], ), matrix=dict( diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 560d883d75..f63e1347f5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -17,7 +17,10 @@ def test_Resample_inputs(): mandatory=True, position=-1, ), - master=dict(argstr='-master %s', ), + master=dict( + argstr='-master %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 1ea4c0790e..209473fe6f 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -93,7 +93,10 @@ def test_TCorrMap_inputs(): name_source='in_file', suffix='_qmean', ), - regress_out_timeseries=dict(argstr='-ort %s', ), + regress_out_timeseries=dict( + argstr='-ort %s', + extensions=None, + ), seeds=dict( argstr='-seed %s', extensions=None, diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index abeceda432..1bd80cfad8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -55,6 +55,7 @@ def test_Zeropad_inputs(): ), master=dict( argstr='-master %s', + extensions=None, xor=['I', 'S', 'A', 'P', 'L', 'R', 'z', 'RL', 'AP', 'IS', 'mm'], ), mm=dict( diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 5c6fa2c501..1ee5cabe21 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -57,8 +57,8 @@ def test_ANTS_inputs(): regularization=dict(argstr='%s', ), regularization_deformation_field_sigma=dict( requires=['regularization'], ), - regularization_gradient_field_sigma=dict( - requires=['regularization'], ), + regularization_gradient_field_sigma=dict(requires=['regularization' + ], ), smoothing_sigmas=dict( argstr='--gaussian-smoothing-sigmas %s', sep='x', diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index 02ebe6431c..a2829be3fa 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -44,11 +44,10 @@ def test_AntsJointFusion_inputs(): nohash=True, usedefault=True, ), - out_atlas_voting_weight_name_format=dict( - requires=[ - 'out_label_fusion', 'out_intensity_fusion_name_format', - 'out_label_post_prob_name_format' - ], ), + out_atlas_voting_weight_name_format=dict(requires=[ + 'out_label_fusion', 'out_intensity_fusion_name_format', + 'out_label_post_prob_name_format' + ], ), out_intensity_fusion_name_format=dict(argstr='', ), out_label_fusion=dict( argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index be1a271f9a..73d7f6813a 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -53,8 +53,8 @@ def test_Atropos_inputs(): prior_probability_threshold=dict(requires=['prior_weighting'], ), prior_weighting=dict(), save_posteriors=dict(), - use_mixture_model_proportions=dict( - requires=['posterior_formulation'], ), + use_mixture_model_proportions=dict(requires=['posterior_formulation' + ], ), use_random_seed=dict( argstr='--use-random-seed %d', usedefault=True, diff --git a/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py index e39dc3acaa..95afcd3216 100644 --- a/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py @@ -12,6 +12,7 @@ def test_StdOutCommandLine_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index 28170946ac..c40082d836 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -50,6 +50,7 @@ def test_AnalyzeHeader_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index 66ac282175..edf38864fa 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -24,6 +24,7 @@ def test_ComputeEigensystem_inputs(): maxcomponents=dict(argstr='-maxcomponents %d', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 9cfae77b2f..75604df01b 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -20,6 +20,7 @@ def test_ComputeFractionalAnisotropy_inputs(): inputmodel=dict(argstr='-inputmodel %s', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 1443a253bd..4d31fa884c 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -20,6 +20,7 @@ def test_ComputeTensorTrace_inputs(): inputmodel=dict(argstr='-inputmodel %s', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index 26d27d57d2..0870a77752 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -26,6 +26,7 @@ def test_DTIFit_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index f7caf77ef1..3242163c3a 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -28,6 +28,7 @@ def test_DTLUTGen_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index 350c604c99..9b8a74be6a 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -40,6 +40,7 @@ def test_FSL2Scheme_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 29864bef82..2c013cf216 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -18,6 +18,7 @@ def test_Image2Voxel_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 996d8f4b99..147cfaab5e 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -24,6 +24,7 @@ def test_LinRecon_inputs(): normalize=dict(argstr='-normalize', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index 57dbbf3b28..f7dfecfdb9 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -42,6 +42,7 @@ def test_MESD_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index e5c16ec975..6d49969eb6 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -34,6 +34,7 @@ def test_ModelFit_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 0a5583b03e..65e0210268 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -26,6 +26,7 @@ def test_NIfTIDT2Camino_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index c918a372f1..e5cdea5cae 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -36,6 +36,7 @@ def test_PicoPDFs_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index c30ef08d8c..0386e0d54f 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -62,6 +62,7 @@ def test_ProcStreamlines_inputs(): noresample=dict(argstr='-noresample', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index 7f7d0bc99f..f452f26350 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -20,6 +20,7 @@ def test_QBallMX_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index 795138ea89..220e116255 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -35,6 +35,7 @@ def test_SFLUTGen_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index 80222fce4c..1b71553676 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -27,6 +27,7 @@ def test_SFPICOCalibData_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 8db250c58c..49ac58aa06 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -38,6 +38,7 @@ def test_SFPeaks_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 594b35fc60..2d8ec43589 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -28,6 +28,7 @@ def test_Shredder_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index eeed244533..e4df010c60 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -28,6 +28,7 @@ def test_TractShredder_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 72b6f106d8..bd8d295572 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -25,6 +25,7 @@ def test_VtkStreamlines_inputs(): interpolatescalars=dict(argstr='-interpolatescalars', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index 8a83130a4d..494ce981c5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -79,11 +79,10 @@ def test_Aparc2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Aparc2Aseg_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict(out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = Aparc2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index fea3617596..03385da2ad 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -28,11 +28,10 @@ def test_Apas2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Apas2Aseg_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict(out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = Apas2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index f3bfd5ad62..4d56d217c7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -7,7 +7,10 @@ def test_CALabel_inputs(): input_map = dict( align=dict(argstr='-align', ), args=dict(argstr='%s', ), - aseg=dict(argstr='-aseg %s', ), + aseg=dict( + argstr='-aseg %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -26,7 +29,10 @@ def test_CALabel_inputs(): argstr='-r %s', extensions=None, ), - label=dict(argstr='-l %s', ), + label=dict( + argstr='-l %s', + extensions=None, + ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), out_file=dict( diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index 1f6546ae3a..5700103e84 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -59,7 +59,7 @@ def test_CANormalize_inputs(): def test_CANormalize_outputs(): output_map = dict( control_points=dict(extensions=None, ), - out_file=dict(), + out_file=dict(extensions=None, ), ) outputs = CANormalize.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index 83f669b218..dcf5aa84a8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -53,7 +53,7 @@ def test_CARegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CARegister_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = CARegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index 68a5a98e66..fe9c1a3121 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -35,7 +35,7 @@ def test_CheckTalairachAlignment_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CheckTalairachAlignment_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = CheckTalairachAlignment.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index 8acab945c1..ee1d3ae7f3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -38,11 +38,13 @@ def test_ConcatenateLTA_inputs(): subjects_dir=dict(), tal_source_file=dict( argstr='-tal %s', + extensions=None, position=-5, requires=['tal_template_file'], ), tal_template_file=dict( argstr='%s', + extensions=None, position=-4, requires=['tal_source_file'], ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index 3c4e5aa484..3cd62e8ee7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -5,10 +5,16 @@ def test_Contrast_inputs(): input_map = dict( - annotation=dict(mandatory=True, ), + annotation=dict( + extensions=None, + mandatory=True, + ), args=dict(argstr='%s', ), copy_inputs=dict(), - cortex=dict(mandatory=True, ), + cortex=dict( + extensions=None, + mandatory=True, + ), environ=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index 4ba8442b14..83427dcd20 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -35,7 +35,10 @@ def test_FixTopology_inputs(): ), mgz=dict(argstr='-mgz', ), seed=dict(argstr='-seed %d', ), - sphere=dict(argstr='-sphere %s', ), + sphere=dict( + argstr='-sphere %s', + extensions=None, + ), subject_id=dict( argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index 10c7af6832..eaf91bc1e8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -6,7 +6,10 @@ def test_MRIsCALabel_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict(argstr='-aseg %s', ), + aseg=dict( + argstr='-aseg %s', + extensions=None, + ), canonsurf=dict( argstr='%s', extensions=None, @@ -33,7 +36,10 @@ def test_MRIsCALabel_inputs(): mandatory=True, position=-4, ), - label=dict(argstr='-l %s', ), + label=dict( + argstr='-l %s', + extensions=None, + ), num_threads=dict(), out_file=dict( argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index badb3b4f0c..3d3f5cde11 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -17,22 +17,30 @@ def test_MS_LDA_inputs(): mandatory=True, position=-1, ), - label_file=dict(argstr='-label %s', ), + label_file=dict( + argstr='-label %s', + extensions=None, + ), lda_labels=dict( argstr='-lda %s', mandatory=True, sep=' ', ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), shift=dict(argstr='-shift %d', ), subjects_dir=dict(), use_weights=dict(argstr='-W', ), vol_synth_file=dict( argstr='-synth %s', + extensions=None, mandatory=True, ), weight_file=dict( argstr='-weight %s', + extensions=None, mandatory=True, ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index 2384adbb2b..baf03f026c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -43,7 +43,7 @@ def test_Normalize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Normalize_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Normalize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index be19b2bd37..8b4ae45d67 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -27,11 +27,16 @@ def test_ParcellationStats_inputs(): ), in_annotation=dict( argstr='-a %s', + extensions=None, xor=['in_label'], ), - in_cortex=dict(argstr='-cortex %s', ), + in_cortex=dict( + argstr='-cortex %s', + extensions=None, + ), in_label=dict( argstr='-l %s', + extensions=None, xor=['in_annotatoin', 'out_color'], ), lh_pial=dict( @@ -45,11 +50,13 @@ def test_ParcellationStats_inputs(): mgz=dict(argstr='-mgz', ), out_color=dict( argstr='-c %s', + extensions=None, genfile=True, xor=['in_label'], ), out_table=dict( argstr='-f %s', + extensions=None, genfile=True, requires=['tabular_output'], ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index f3406d41fc..5a609f586e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -47,7 +47,7 @@ def test_RegisterAVItoTalairach_outputs(): extensions=None, usedefault=True, ), - out_file=dict(), + out_file=dict(extensions=None, ), ) outputs = RegisterAVItoTalairach.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index 28ff49d99e..f99acec899 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -48,11 +48,10 @@ def test_RelabelHypointensities_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RelabelHypointensities_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict(out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = RelabelHypointensities.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index 3cf47c71ce..09da0d001d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -100,7 +100,10 @@ def test_SegStatsReconAll_inputs(): extensions=None, mandatory=True, ), - ribbon=dict(mandatory=True, ), + ribbon=dict( + extensions=None, + mandatory=True, + ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index 26dcbe3458..968041ff67 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -59,6 +59,7 @@ def test_SurfaceSnapshots_inputs(): overlay_range_offset=dict(argstr='-foffset %.3f', ), overlay_reg=dict( argstr='-overlay-reg %s', + extensions=None, xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), patch_file=dict( diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index 9d248c1a7d..2a28765d67 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -30,9 +30,9 @@ def test_TalairachAVI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TalairachAVI_outputs(): output_map = dict( - out_file=dict(), - out_log=dict(), - out_txt=dict(), + out_file=dict(extensions=None, ), + out_log=dict(extensions=None, ), + out_txt=dict(extensions=None, ), ) outputs = TalairachAVI.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index 053d429c9b..1961e3ded6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -24,11 +24,10 @@ def test_TalairachQC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TalairachQC_outputs(): - output_map = dict( - log_file=dict( - extensions=None, - usedefault=True, - ), ) + output_map = dict(log_file=dict( + extensions=None, + usedefault=True, + ), ) outputs = TalairachQC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py index de32f63f5f..ffd5b42bd1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -34,11 +34,10 @@ def test_AccuracyTester_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AccuracyTester_outputs(): - output_map = dict( - output_directory=dict( - argstr='%s', - position=1, - ), ) + output_map = dict(output_directory=dict( + argstr='%s', + position=1, + ), ) outputs = AccuracyTester.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py index a75df99db5..597dc88d5e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -22,14 +22,17 @@ def test_Cleaner_inputs(): ), confound_file=dict( argstr='-x %s', + extensions=None, position=4, ), confound_file_1=dict( argstr='-x %s', + extensions=None, position=5, ), confound_file_2=dict( argstr='-x %s', + extensions=None, position=6, ), environ=dict( diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index 6ed34ab816..19340b9383 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -7,7 +7,10 @@ def test_Cluster_inputs(): input_map = dict( args=dict(argstr='%s', ), connectivity=dict(argstr='--connectivity=%d', ), - cope_file=dict(argstr='--cope=%s', ), + cope_file=dict( + argstr='--cope=%s', + extensions=None, + ), dlh=dict(argstr='--dlh=%.10f', ), environ=dict( nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py index 3945c40a87..eaeeb34ce8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py @@ -22,12 +22,11 @@ def test_FeatureExtractor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FeatureExtractor_outputs(): - output_map = dict( - mel_ica=dict( - argstr='%s', - copyfile=False, - position=-1, - ), ) + output_map = dict(mel_ica=dict( + argstr='%s', + copyfile=False, + position=-1, + ), ) outputs = FeatureExtractor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index 5c7b717d93..a8262c9be1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -30,11 +30,10 @@ def test_FindTheBiggest_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FindTheBiggest_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict(out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = FindTheBiggest.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py index 18ef078a79..638bcdd156 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py +++ b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py @@ -4,24 +4,22 @@ def test_TrainingSetCreator_inputs(): - input_map = dict( - mel_icas_in=dict( - argstr='%s', - copyfile=False, - position=-1, - ), ) + input_map = dict(mel_icas_in=dict( + argstr='%s', + copyfile=False, + position=-1, + ), ) inputs = TrainingSetCreator.input_spec() for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrainingSetCreator_outputs(): - output_map = dict( - mel_icas_out=dict( - argstr='%s', - copyfile=False, - position=-1, - ), ) + output_map = dict(mel_icas_out=dict( + argstr='%s', + copyfile=False, + position=-1, + ), ) outputs = TrainingSetCreator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 678ab93a52..6f0e84d144 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -29,6 +29,7 @@ def test_Average_inputs(): ), filelist=dict( argstr='-filelist %s', + extensions=None, mandatory=True, xor=('input_files', 'filelist'), ), @@ -126,7 +127,10 @@ def test_Average_inputs(): argstr='-quiet', xor=('verbose', 'quiet'), ), - sdfile=dict(argstr='-sdfile %s', ), + sdfile=dict( + argstr='-sdfile %s', + extensions=None, + ), two=dict(argstr='-2', ), verbose=dict( argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index c1b3515cea..7bdf35f03d 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -25,6 +25,7 @@ def test_BBox_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index bc4705db2e..3a44b436b0 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -18,7 +18,10 @@ def test_Beast_inputs(): argstr='-alpha %s', usedefault=True, ), - configuration_file=dict(argstr='-configuration %s', ), + configuration_file=dict( + argstr='-configuration %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -27,6 +30,7 @@ def test_Beast_inputs(): flip_images=dict(argstr='-flip', ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -44,6 +48,7 @@ def test_Beast_inputs(): ), output_file=dict( argstr='%s', + extensions=None, hash_files=False, name_source=['input_file'], name_template='%s_beast_mask.mnc', diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index e9df677150..d5fb316e39 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -26,6 +26,7 @@ def test_Calc_inputs(): eval_width=dict(argstr='-eval_width %s', ), expfile=dict( argstr='-expfile %s', + extensions=None, mandatory=True, xor=('expression', 'expfile'), ), @@ -36,6 +37,7 @@ def test_Calc_inputs(): ), filelist=dict( argstr='-filelist %s', + extensions=None, mandatory=True, xor=('input_files', 'filelist'), ), diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index 19c299dac8..fbd33f5a46 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -36,6 +36,7 @@ def test_Dump_inputs(): netcdf_name=dict(argstr='-n %s', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index 35f6162c7f..fbd0a84729 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -84,6 +84,7 @@ def test_Extract_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index 6bc142b15d..41d75379d4 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -36,6 +36,7 @@ def test_Math_inputs(): exp=dict(argstr='-exp -const2 %s %s', ), filelist=dict( argstr='-filelist %s', + extensions=None, mandatory=True, xor=('input_files', 'filelist'), ), diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index 9fb0d3c5ba..cdd4a3db7c 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -26,7 +26,10 @@ def test_Norm_inputs(): position=-2, ), lower=dict(argstr='-lower %s', ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), out_ceil=dict(argstr='-out_ceil %s', ), out_floor=dict(argstr='-out_floor %s', ), output_file=dict( @@ -40,6 +43,7 @@ def test_Norm_inputs(): ), output_threshold_mask=dict( argstr='-threshold_mask %s', + extensions=None, hash_files=False, name_source=['input_file'], name_template='%s_norm_threshold_mask.mnc', diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index 8d4b24ff41..da512d9f62 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -94,7 +94,10 @@ def test_Resample_inputs(): argstr='-keep_real_range', xor=('keep_real_range', 'nokeep_real_range'), ), - like=dict(argstr='-like %s', ), + like=dict( + argstr='-like %s', + extensions=None, + ), nearest_neighbour_interpolation=dict( argstr='-nearest_neighbour', xor=('trilinear_interpolation', 'tricubic_interpolation', @@ -157,7 +160,10 @@ def test_Resample_inputs(): xor=('nelements', 'nelements_x_y_or_z'), ), talairach=dict(argstr='-talairach', ), - transformation=dict(argstr='-transformation %s', ), + transformation=dict( + argstr='-transformation %s', + extensions=None, + ), transverse_slices=dict( argstr='-transverse', xor=('transverse', 'sagittal', 'coronal'), diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index 669425da95..d80f9a377b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -16,6 +16,7 @@ def test_Reshape_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index aeda687c97..42ba72f145 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -26,6 +26,7 @@ def test_ToRaw_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index b710d59543..ae3332b7f2 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -22,6 +22,7 @@ def test_VolSymm_inputs(): fit_nonlinear=dict(argstr='-nonlinear', ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -38,6 +39,7 @@ def test_VolSymm_inputs(): ), trans_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, keep_extension=False, diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index 9e242300da..69c455f875 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -16,6 +16,7 @@ def test_XfmInvert_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 90c5272ed0..5ee1e8cb00 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -14,8 +14,12 @@ def test_BrainMask_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py index 7658201223..59617b30ab 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py @@ -15,8 +15,12 @@ def test_DWIExtract_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index c64efa2ca4..c2816f2646 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -41,8 +41,12 @@ def test_EstimateFOD_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 84404fdde6..8f8142746a 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -14,8 +14,12 @@ def test_FitTensor_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index 92594da593..f7032cb624 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -19,8 +19,12 @@ def test_Generate5tt_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py index 9271d07517..f11b615cc8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py @@ -22,8 +22,12 @@ def test_MRConvert_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py index ae494bb932..fe934c45b1 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py @@ -15,8 +15,12 @@ def test_MRMath_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index dd326bad5b..9415cae211 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -29,8 +29,12 @@ def test_ResponseSD_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index 39f239b81d..cf685a50d8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -28,8 +28,12 @@ def test_Tractography_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, + xor=['grad_fsl'], + ), + grad_fsl=dict( + argstr='-fslgrad %s %s', + xor=['grad_file'], ), - grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py index 20995e806e..2a58b39d57 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py @@ -8,6 +8,7 @@ def test_DwiTool_inputs(): args=dict(argstr='%s', ), b0_file=dict( argstr='-b0 %s', + extensions=None, position=4, ), ball_flag=dict( @@ -28,11 +29,13 @@ def test_DwiTool_inputs(): ), bval_file=dict( argstr='-bval %s', + extensions=None, mandatory=True, position=2, ), bvec_file=dict( argstr='-bvec %s', + extensions=None, position=3, ), diso_val=dict(argstr='-diso %f', ), @@ -59,6 +62,7 @@ def test_DwiTool_inputs(): ), famap_file=dict( argstr='-famap %s', + extensions=None, name_source=['source_file'], name_template='%s_famap.nii.gz', ), @@ -72,20 +76,24 @@ def test_DwiTool_inputs(): ), logdti_file=dict( argstr='-logdti2 %s', + extensions=None, name_source=['source_file'], name_template='%s_logdti2.nii.gz', ), mask_file=dict( argstr='-mask %s', + extensions=None, position=5, ), mcmap_file=dict( argstr='-mcmap %s', + extensions=None, name_source=['source_file'], name_template='%s_mcmap.nii.gz', ), mdmap_file=dict( argstr='-mdmap %s', + extensions=None, name_source=['source_file'], name_template='%s_mdmap.nii.gz', ), @@ -115,22 +123,26 @@ def test_DwiTool_inputs(): ), rgbmap_file=dict( argstr='-rgbmap %s', + extensions=None, name_source=['source_file'], name_template='%s_rgbmap.nii.gz', ), source_file=dict( argstr='-source %s', + extensions=None, mandatory=True, position=1, ), syn_file=dict( argstr='-syn %s', + extensions=None, name_source=['source_file'], name_template='%s_syn.nii.gz', requires=['bvec_file', 'b0_file'], ), v1map_file=dict( argstr='-v1map %s', + extensions=None, name_source=['source_file'], name_template='%s_v1map.nii.gz', ), @@ -142,13 +154,13 @@ def test_DwiTool_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DwiTool_outputs(): output_map = dict( - famap_file=dict(), - logdti_file=dict(), - mcmap_file=dict(), - mdmap_file=dict(), - rgbmap_file=dict(), - syn_file=dict(), - v1map_file=dict(), + famap_file=dict(extensions=None, ), + logdti_file=dict(extensions=None, ), + mcmap_file=dict(extensions=None, ), + mdmap_file=dict(extensions=None, ), + rgbmap_file=dict(extensions=None, ), + syn_file=dict(extensions=None, ), + v1map_file=dict(extensions=None, ), ) outputs = DwiTool.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py index b2e1bef961..94a489a4ad 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py @@ -8,6 +8,7 @@ def test_FitAsl_inputs(): args=dict(argstr='%s', ), cbf_file=dict( argstr='-cbf %s', + extensions=None, name_source=['source_file'], name_template='%s_cbf.nii.gz', ), @@ -20,19 +21,33 @@ def test_FitAsl_inputs(): ), error_file=dict( argstr='-error %s', + extensions=None, name_source=['source_file'], name_template='%s_error.nii.gz', ), gm_plasma=dict(argstr='-gmL %f', ), gm_t1=dict(argstr='-gmT1 %f', ), gm_ttt=dict(argstr='-gmTTT %f', ), - ir_output=dict(argstr='-IRoutput %s', ), - ir_volume=dict(argstr='-IRvolume %s', ), + ir_output=dict( + argstr='-IRoutput %s', + extensions=None, + ), + ir_volume=dict( + argstr='-IRvolume %s', + extensions=None, + ), ldd=dict(argstr='-LDD %f', ), - m0map=dict(argstr='-m0map %s', ), - m0mape=dict(argstr='-m0mape %s', ), + m0map=dict( + argstr='-m0map %s', + extensions=None, + ), + m0mape=dict( + argstr='-m0mape %s', + extensions=None, + ), mask=dict( argstr='-mask %s', + extensions=None, position=2, ), mul=dict(argstr='-mul %f', ), @@ -46,21 +61,29 @@ def test_FitAsl_inputs(): pv2=dict(argstr='-pv2 %d', ), pv3=dict(argstr='-pv3 %d %d %d', ), pv_threshold=dict(argstr='-pvthreshold', ), - seg=dict(argstr='-seg %s', ), + seg=dict( + argstr='-seg %s', + extensions=None, + ), segstyle=dict(argstr='-segstyle', ), sig=dict(argstr='-sig', ), source_file=dict( argstr='-source %s', + extensions=None, mandatory=True, position=1, ), syn_file=dict( argstr='-syn %s', + extensions=None, name_source=['source_file'], name_template='%s_syn.nii.gz', ), t1_art_cmp=dict(argstr='-T1a %f', ), - t1map=dict(argstr='-t1map %s', ), + t1map=dict( + argstr='-t1map %s', + extensions=None, + ), t_inv1=dict(argstr='-Tinv1 %f', ), t_inv2=dict(argstr='-Tinv2 %f', ), wm_plasma=dict(argstr='-wmL %f', ), @@ -74,9 +97,9 @@ def test_FitAsl_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitAsl_outputs(): output_map = dict( - cbf_file=dict(), - error_file=dict(), - syn_file=dict(), + cbf_file=dict(extensions=None, ), + error_file=dict(extensions=None, ), + syn_file=dict(extensions=None, ), ) outputs = FitAsl.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py index 700d9a31c4..2086d12a2b 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py @@ -25,15 +25,20 @@ def test_FitDwi_inputs(): ), bval_file=dict( argstr='-bval %s', + extensions=None, mandatory=True, position=2, ), bvec_file=dict( argstr='-bvec %s', + extensions=None, mandatory=True, position=3, ), - cov_file=dict(argstr='-cov %s', ), + cov_file=dict( + argstr='-cov %s', + extensions=None, + ), csf_t2_val=dict(argstr='-csfT2 %f', ), diso_val=dict(argstr='-diso %f', ), dpr_val=dict(argstr='-dpr %f', ), @@ -51,11 +56,13 @@ def test_FitDwi_inputs(): ), error_file=dict( argstr='-error %s', + extensions=None, name_source=['source_file'], name_template='%s_error.nii.gz', ), famap_file=dict( argstr='-famap %s', + extensions=None, name_source=['source_file'], name_template='%s_famap.nii.gz', ), @@ -75,13 +82,17 @@ def test_FitDwi_inputs(): argstr='-lm %f %f', requires=['gn_flag'], ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), maxit_val=dict( argstr='-maxit %d', requires=['gn_flag'], ), mcmap_file=dict( argstr='-mcmap %s', + extensions=None, name_source=['source_file'], name_template='%s_mcmap.nii.gz', requires=['nodv_flag'], @@ -89,12 +100,14 @@ def test_FitDwi_inputs(): mcmaxit=dict(argstr='-mcmaxit %d', ), mcout=dict( argstr='-mcout %s', + extensions=None, name_source=['source_file'], name_template='%s_mcout.txt', ), mcsamples=dict(argstr='-mcsamples %d', ), mdmap_file=dict( argstr='-mdmap %s', + extensions=None, name_source=['source_file'], name_template='%s_mdmap.nii.gz', ), @@ -116,6 +129,7 @@ def test_FitDwi_inputs(): ), nodiff_file=dict( argstr='-nodiff %s', + extensions=None, name_source=['source_file'], name_template='%s_no_diff.nii.gz', ), @@ -128,14 +142,19 @@ def test_FitDwi_inputs(): ], ), perf_thr=dict(argstr='-perfthreshold %f', ), - prior_file=dict(argstr='-prior %s', ), + prior_file=dict( + argstr='-prior %s', + extensions=None, + ), res_file=dict( argstr='-res %s', + extensions=None, name_source=['source_file'], name_template='%s_resmap.nii.gz', ), rgbmap_file=dict( argstr='-rgbmap %s', + extensions=None, name_source=['source_file'], name_template='%s_rgbmap.nii.gz', requires=['dti_flag'], @@ -144,38 +163,45 @@ def test_FitDwi_inputs(): slice_no=dict(argstr='-slice %d', ), source_file=dict( argstr='-source %s', + extensions=None, mandatory=True, position=1, ), swls_val=dict(argstr='-swls %f', ), syn_file=dict( argstr='-syn %s', + extensions=None, name_source=['source_file'], name_template='%s_syn.nii.gz', ), te_file=dict( argstr='-TE %s', + extensions=None, xor=['te_file'], ), te_value=dict( argstr='-TE %s', + extensions=None, xor=['te_file'], ), ten_type=dict(usedefault=True, ), tenmap2_file=dict( argstr='-tenmap2 %s', + extensions=None, name_source=['source_file'], name_template='%s_tenmap2.nii.gz', requires=['dti_flag'], ), tenmap_file=dict( argstr='-tenmap %s', + extensions=None, name_source=['source_file'], name_template='%s_tenmap.nii.gz', requires=['dti_flag'], ), v1map_file=dict( argstr='-v1map %s', + extensions=None, name_source=['source_file'], name_template='%s_v1map.nii.gz', ), @@ -194,18 +220,18 @@ def test_FitDwi_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitDwi_outputs(): output_map = dict( - error_file=dict(), - famap_file=dict(), - mcmap_file=dict(), - mcout=dict(), - mdmap_file=dict(), - nodiff_file=dict(), - res_file=dict(), - rgbmap_file=dict(), - syn_file=dict(), - tenmap2_file=dict(), - tenmap_file=dict(), - v1map_file=dict(), + error_file=dict(extensions=None, ), + famap_file=dict(extensions=None, ), + mcmap_file=dict(extensions=None, ), + mcout=dict(extensions=None, ), + mdmap_file=dict(extensions=None, ), + nodiff_file=dict(extensions=None, ), + res_file=dict(extensions=None, ), + rgbmap_file=dict(extensions=None, ), + syn_file=dict(extensions=None, ), + tenmap2_file=dict(extensions=None, ), + tenmap_file=dict(extensions=None, ), + v1map_file=dict(extensions=None, ), ) outputs = FitDwi.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index 392654fd5c..b184e448cd 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -7,7 +7,10 @@ def test_FitQt1_inputs(): input_map = dict( acceptance=dict(argstr='-acceptance %f', ), args=dict(argstr='%s', ), - b1map=dict(argstr='-b1map %s', ), + b1map=dict( + argstr='-b1map %s', + extensions=None, + ), comp_file=dict( argstr='-comp %s', extensions=None, @@ -28,7 +31,10 @@ def test_FitQt1_inputs(): argstr='-flips %s', sep=' ', ), - flips_list=dict(argstr='-fliplist %s', ), + flips_list=dict( + argstr='-fliplist %s', + extensions=None, + ), gn_flag=dict( argstr='-gn', position=8, @@ -63,7 +69,10 @@ def test_FitQt1_inputs(): name_template='%s_mcmap.nii.gz', ), mcmaxit=dict(argstr='-mcmaxit %d', ), - mcout=dict(argstr='-mcout %s', ), + mcout=dict( + argstr='-mcout %s', + extensions=None, + ), mcsamples=dict(argstr='-mcsamples %d', ), nb_comp=dict( argstr='-nc %d', @@ -101,7 +110,10 @@ def test_FitQt1_inputs(): name_source=['source_file'], name_template='%s_syn.nii.gz', ), - t1_list=dict(argstr='-T1list %s', ), + t1_list=dict( + argstr='-T1list %s', + extensions=None, + ), t1map_file=dict( argstr='-t1map %s', extensions=None, @@ -119,7 +131,10 @@ def test_FitQt1_inputs(): position=14, sep=' ', ), - tis_list=dict(argstr='-TIlist %s', ), + tis_list=dict( + argstr='-TIlist %s', + extensions=None, + ), tr_value=dict( argstr='-TR %f', position=5, diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 3fe17160db..9a9b5c421c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -13,7 +13,7 @@ def test_EstimateContrast_inputs(): constants=dict(mandatory=True, ), contrasts=dict(mandatory=True, ), dof=dict(mandatory=True, ), - mask=dict(), + mask=dict(extensions=None, ), nvbeta=dict(mandatory=True, ), reg_names=dict(mandatory=True, ), s2=dict( diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index a700c18d43..71ca221efc 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -8,7 +8,7 @@ def test_FitGLM_inputs(): TR=dict(mandatory=True, ), drift_model=dict(usedefault=True, ), hrf_model=dict(usedefault=True, ), - mask=dict(), + mask=dict(extensions=None, ), method=dict(usedefault=True, ), model=dict(usedefault=True, ), normalize_design_matrix=dict(usedefault=True, ), @@ -30,7 +30,7 @@ def test_FitGLM_outputs(): dof=dict(), nvbeta=dict(), reg_names=dict(), - residuals=dict(), + residuals=dict(extensions=None, ), s2=dict(extensions=None, ), ) outputs = FitGLM.output_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index 866af46740..2eaeb1acef 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -38,11 +38,10 @@ def test_UnbiasedNonLocalMeans_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnbiasedNonLocalMeans_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = UnbiasedNonLocalMeans.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 1ca79a6e96..33e52ed707 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -27,11 +27,10 @@ def test_DTIexport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIexport_outputs(): - output_map = dict( - outputFile=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputFile=dict( + extensions=None, + position=-1, + ), ) outputs = DTIexport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index 58ae495f3f..ddb07c9428 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -28,11 +28,10 @@ def test_DTIimport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIimport_outputs(): - output_map = dict( - outputTensor=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputTensor=dict( + extensions=None, + position=-1, + ), ) outputs = DTIimport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index f8000c49b1..aa0b6f97b5 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -37,11 +37,10 @@ def test_DWIJointRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIJointRicianLMMSEFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = DWIJointRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index 29b5e0b7e1..69509fcf28 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -43,11 +43,10 @@ def test_DWIRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIRicianLMMSEFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = DWIRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index 5dcdbd7e2e..060c47ecc2 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -28,11 +28,10 @@ def test_DiffusionTensorScalarMeasurements_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorScalarMeasurements_outputs(): - output_map = dict( - outputScalar=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputScalar=dict( + extensions=None, + position=-1, + ), ) outputs = DiffusionTensorScalarMeasurements.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index bd35268bdb..9cfcdb14fb 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -73,11 +73,10 @@ def test_ResampleDTIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleDTIVolume_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ResampleDTIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index d2b17c562a..42a7b17a19 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -33,11 +33,10 @@ def test_AddScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddScalarVolumes_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = AddScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index bbcb2f077c..0c05002ff8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -28,11 +28,10 @@ def test_CastScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CastScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = CastScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index 24f5b74307..b602012d0c 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -36,11 +36,10 @@ def test_CheckerBoardFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CheckerBoardFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = CheckerBoardFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index 0240ad676a..7389aa0cee 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -30,11 +30,10 @@ def test_CurvatureAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureAnisotropicDiffusion_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = CurvatureAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index c47382aef5..d6f93cb41d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -31,11 +31,10 @@ def test_ExtractSkeleton_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractSkeleton_outputs(): - output_map = dict( - OutputImageFileName=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputImageFileName=dict( + extensions=None, + position=-1, + ), ) outputs = ExtractSkeleton.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index 2bdb73c4d5..9511f9ce1d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -28,11 +28,10 @@ def test_GaussianBlurImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GaussianBlurImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GaussianBlurImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index 6d3e40c8de..02c9d7fb20 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -30,11 +30,10 @@ def test_GradientAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusion_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GradientAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index f1ff2c3809..45b2b4b8dc 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -27,11 +27,10 @@ def test_GrayscaleFillHoleImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleFillHoleImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GrayscaleFillHoleImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 6aee86282a..77536e147d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -27,11 +27,10 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleGrindPeakImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GrayscaleGrindPeakImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index c839c50abf..9541702731 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -35,11 +35,10 @@ def test_HistogramMatching_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatching_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = HistogramMatching.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 7fd2c31db3..c3373f80ec 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -33,11 +33,10 @@ def test_ImageLabelCombine_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageLabelCombine_outputs(): - output_map = dict( - OutputLabelMap=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputLabelMap=dict( + extensions=None, + position=-1, + ), ) outputs = ImageLabelCombine.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index 56d68199af..11999f2001 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -34,11 +34,10 @@ def test_MaskScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaskScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = MaskScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index c0bf97e152..4c890aa30f 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -31,11 +31,10 @@ def test_MedianImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = MedianImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index cc39d5b7b1..99772b41db 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -33,11 +33,10 @@ def test_MultiplyScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyScalarVolumes_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = MultiplyScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index 12d7af77c4..28a9876943 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -71,11 +71,10 @@ def test_ResampleScalarVectorDWIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVectorDWIVolume_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ResampleScalarVectorDWIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 106cd843a4..62bf214bf4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -33,11 +33,10 @@ def test_SubtractScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SubtractScalarVolumes_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = SubtractScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index e63ed5923f..ce7f97ec58 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -32,11 +32,10 @@ def test_ThresholdScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ThresholdScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ThresholdScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 89832bf9ba..c8100fd74b 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -34,11 +34,10 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VotingBinaryHoleFillingImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = VotingBinaryHoleFillingImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index f3c1ec6ff0..a121f85614 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -41,11 +41,10 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIUnbiasedNonLocalMeansFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = DWIUnbiasedNonLocalMeansFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index 19b41f7127..6af3c1d54c 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -30,11 +30,10 @@ def test_OtsuThresholdImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = OtsuThresholdImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index b9fa12f2aa..c73313751e 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -31,11 +31,10 @@ def test_OtsuThresholdSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdSegmentation_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = OtsuThresholdSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 7f1c259cd6..66207fb604 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -32,11 +32,10 @@ def test_ResampleScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ResampleScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index 6befb36860..c956ae34ec 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -37,11 +37,10 @@ def test_RobustStatisticsSegmenter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RobustStatisticsSegmenter_outputs(): - output_map = dict( - segmentedImageFileName=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(segmentedImageFileName=dict( + extensions=None, + position=-1, + ), ) outputs = RobustStatisticsSegmenter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 5f880c08cb..8ffdd04355 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -34,11 +34,10 @@ def test_SimpleRegionGrowingSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SimpleRegionGrowingSegmentation_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = SimpleRegionGrowingSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index 3669a21fc3..e18c0f0d5d 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -33,11 +33,10 @@ def test_GrayscaleModelMaker_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleModelMaker_outputs(): - output_map = dict( - OutputGeometry=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputGeometry=dict( + extensions=None, + position=-1, + ), ) outputs = GrayscaleModelMaker.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index faf982a342..d196dbf5d8 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -31,11 +31,10 @@ def test_LabelMapSmoothing_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelMapSmoothing_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = LabelMapSmoothing.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index c25d4ebcf3..2e09b69bd1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -32,11 +32,10 @@ def test_MergeModels_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeModels_outputs(): - output_map = dict( - ModelOutput=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(ModelOutput=dict( + extensions=None, + position=-1, + ), ) outputs = MergeModels.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index d39ae392bd..2e684e3e65 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -33,11 +33,10 @@ def test_ModelToLabelMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ModelToLabelMap_outputs(): - output_map = dict( - OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ModelToLabelMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index d0d437915b..479bb842bb 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -28,11 +28,10 @@ def test_OrientScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OrientScalarVolume_outputs(): - output_map = dict( - outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = OrientScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index 528ba47e1b..b4bbdbe283 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -32,11 +32,10 @@ def test_ProbeVolumeWithModel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ProbeVolumeWithModel_outputs(): - output_map = dict( - OutputModel=dict( - extensions=None, - position=-1, - ), ) + output_map = dict(OutputModel=dict( + extensions=None, + position=-1, + ), ) outputs = ProbeVolumeWithModel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/utility/tests/test_auto_Rename.py b/nipype/interfaces/utility/tests/test_auto_Rename.py index 6b56badd6f..70ced0ecdd 100644 --- a/nipype/interfaces/utility/tests/test_auto_Rename.py +++ b/nipype/interfaces/utility/tests/test_auto_Rename.py @@ -20,7 +20,7 @@ def test_Rename_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Rename_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Rename.output_spec() for key, metadata in list(output_map.items()): From 834df60d1b03c82028a894d0fe27825cca04cb0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Victor=20F=C3=A9rat?= Date: Fri, 30 Aug 2019 12:07:50 +0200 Subject: [PATCH 4/6] Revert "Merge pull request #1 from vferat/fix/mne_watershed_bem" This reverts commit 1f92bd569e5d92ee1e3233e093a4a77242759f03, reversing changes made to 8129ff4e004fdfcd6ce9b0730ee62d58586ff647. --- nipype/interfaces/mne/base.py | 112 +++++++++++++++------------------- 1 file changed, 49 insertions(+), 63 deletions(-) diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py index 7a4f186496..7f53071372 100644 --- a/nipype/interfaces/mne/base.py +++ b/nipype/interfaces/mne/base.py @@ -1,5 +1,6 @@ # -*- coding: utf-8 -*- -from __future__ import print_function, division, unicode_literals, absolute_import +from __future__ import (print_function, division, unicode_literals, + absolute_import) from builtins import str, bytes import os.path as op @@ -7,86 +8,74 @@ from ... import logging from ...utils.filemanip import simplify_list -from ..base import traits, File, Directory, TraitedSpec, OutputMultiPath +from ..base import (traits, File, Directory, TraitedSpec, OutputMultiPath) from ..freesurfer.base import FSCommand, FSTraitedSpec -iflogger = logging.getLogger("nipype.interface") +iflogger = logging.getLogger('nipype.interface') class WatershedBEMInputSpec(FSTraitedSpec): subject_id = traits.Str( - argstr="--subject %s", + argstr='--subject %s', mandatory=True, - desc="Subject ID (must have a complete Freesurfer directory)", - ) + desc='Subject ID (must have a complete Freesurfer directory)') subjects_dir = Directory( exists=True, mandatory=True, usedefault=True, - desc="Path to Freesurfer subjects directory", - ) + desc='Path to Freesurfer subjects directory') volume = traits.Enum( - "T1", - "aparc+aseg", - "aseg", - "brain", - "orig", - "brainmask", - "ribbon", - argstr="--volume %s", + 'T1', + 'aparc+aseg', + 'aseg', + 'brain', + 'orig', + 'brainmask', + 'ribbon', + argstr='--volume %s', usedefault=True, - desc='The volume from the "mri" directory to use (defaults to T1)', - ) + desc='The volume from the "mri" directory to use (defaults to T1)') overwrite = traits.Bool( True, usedefault=True, - argstr="--overwrite", - desc="Overwrites the existing files", - ) + argstr='--overwrite', + desc='Overwrites the existing files') atlas_mode = traits.Bool( - argstr="--atlas", - desc="Use atlas mode for registration (default: no rigid alignment)", - ) + argstr='--atlas', + desc='Use atlas mode for registration (default: no rigid alignment)') class WatershedBEMOutputSpec(TraitedSpec): mesh_files = OutputMultiPath( File(exists=True), - desc=( - "Paths to the output meshes (brain, inner " - "skull, outer skull, outer skin)" - ), - ) + desc=('Paths to the output meshes (brain, inner ' + 'skull, outer skull, outer skin)')) brain_surface = File( - exists=True, loc="bem/watershed", desc="Brain surface (in Freesurfer format)" - ) + exists=True, + loc='bem/watershed', + desc='Brain surface (in Freesurfer format)') inner_skull_surface = File( exists=True, - loc="bem/watershed", - desc="Inner skull surface (in Freesurfer format)", - ) + loc='bem/watershed', + desc='Inner skull surface (in Freesurfer format)') outer_skull_surface = File( exists=True, - loc="bem/watershed", - desc="Outer skull surface (in Freesurfer format)", - ) + loc='bem/watershed', + desc='Outer skull surface (in Freesurfer format)') outer_skin_surface = File( exists=True, - loc="bem/watershed", - desc="Outer skin surface (in Freesurfer format)", - ) + loc='bem/watershed', + desc='Outer skin surface (in Freesurfer format)') fif_file = File( exists=True, - loc="bem", - altkey="fif", - desc='"fif" format file for EEG processing in MNE', - ) + loc='bem', + altkey='fif', + desc='"fif" format file for EEG processing in MNE') cor_files = OutputMultiPath( File(exists=True), - loc="bem/watershed/ws", - altkey="COR", - desc='"COR" format files', - ) + loc='bem/watershed/ws', + altkey='COR', + desc='"COR" format files') class WatershedBEM(FSCommand): @@ -100,23 +89,23 @@ class WatershedBEM(FSCommand): >>> bem.inputs.subject_id = 'subj1' >>> bem.inputs.subjects_dir = '.' >>> bem.cmdline - 'mne watershed_bem --overwrite --subject subj1 --volume T1' + 'mne_watershed_bem --overwrite --subject subj1 --volume T1' >>> bem.run() # doctest: +SKIP """ - _cmd = "mne watershed_bem" + _cmd = 'mne_watershed_bem' input_spec = WatershedBEMInputSpec output_spec = WatershedBEMOutputSpec - _additional_metadata = ["loc", "altkey"] + _additional_metadata = ['loc', 'altkey'] def _get_files(self, path, key, dirval, altkey=None): - globsuffix = "*" - globprefix = "*" + globsuffix = '*' + globprefix = '*' keydir = op.join(path, dirval) if altkey: key = altkey - globpattern = op.join(keydir, "".join((globprefix, key, globsuffix))) + globpattern = op.join(keydir, ''.join((globprefix, key, globsuffix))) return glob.glob(globpattern) def _list_outputs(self): @@ -126,13 +115,10 @@ def _list_outputs(self): output_traits = self._outputs() mesh_paths = [] for k in list(outputs.keys()): - if k != "mesh_files": - val = self._get_files( - subject_path, - k, - output_traits.traits()[k].loc, - output_traits.traits()[k].altkey, - ) + if k != 'mesh_files': + val = self._get_files(subject_path, k, + output_traits.traits()[k].loc, + output_traits.traits()[k].altkey) if val: value_list = simplify_list(val) if isinstance(value_list, list): @@ -144,7 +130,7 @@ def _list_outputs(self): else: raise TypeError outputs[k] = out_files - if not k.rfind("surface") == -1: + if not k.rfind('surface') == -1: mesh_paths.append(out_files) - outputs["mesh_files"] = mesh_paths + outputs['mesh_files'] = mesh_paths return outputs From 183ab8823da99abb1b908f9e2a4394484c789dd1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Victor=20F=C3=A9rat?= Date: Fri, 30 Aug 2019 12:08:03 +0200 Subject: [PATCH 5/6] Revert "run make check-before-commit without error" This reverts commit 8129ff4e004fdfcd6ce9b0730ee62d58586ff647. --- .../algorithms/tests/test_auto_AddCSVRow.py | 5 +- nipype/algorithms/tests/test_auto_Gunzip.py | 9 +-- .../tests/test_auto_NonSteadyStateDetector.py | 9 +-- .../afni/tests/test_auto_Allineate.py | 1 - nipype/interfaces/afni/tests/test_auto_Cat.py | 7 ++- .../afni/tests/test_auto_ClipLevel.py | 1 - .../afni/tests/test_auto_LocalBistat.py | 7 +-- .../afni/tests/test_auto_Localstat.py | 6 +- .../afni/tests/test_auto_NwarpApply.py | 5 +- .../afni/tests/test_auto_OneDToolPy.py | 1 - .../interfaces/afni/tests/test_auto_Qwarp.py | 5 +- .../afni/tests/test_auto_QwarpPlusMinus.py | 5 +- .../afni/tests/test_auto_ROIStats.py | 5 +- .../interfaces/afni/tests/test_auto_ReHo.py | 6 +- .../afni/tests/test_auto_Remlfit.py | 1 - .../afni/tests/test_auto_Resample.py | 5 +- .../afni/tests/test_auto_TCorrMap.py | 5 +- .../afni/tests/test_auto_Zeropad.py | 1 - .../interfaces/ants/tests/test_auto_ANTS.py | 4 +- .../ants/tests/test_auto_AntsJointFusion.py | 9 +-- .../ants/tests/test_auto_Atropos.py | 4 +- .../base/tests/test_auto_StdOutCommandLine.py | 1 - .../camino/tests/test_auto_AnalyzeHeader.py | 1 - .../tests/test_auto_ComputeEigensystem.py | 1 - .../test_auto_ComputeFractionalAnisotropy.py | 1 - .../tests/test_auto_ComputeTensorTrace.py | 1 - .../camino/tests/test_auto_DTIFit.py | 1 - .../camino/tests/test_auto_DTLUTGen.py | 1 - .../camino/tests/test_auto_FSL2Scheme.py | 1 - .../camino/tests/test_auto_Image2Voxel.py | 1 - .../camino/tests/test_auto_LinRecon.py | 1 - .../interfaces/camino/tests/test_auto_MESD.py | 1 - .../camino/tests/test_auto_ModelFit.py | 1 - .../camino/tests/test_auto_NIfTIDT2Camino.py | 1 - .../camino/tests/test_auto_PicoPDFs.py | 1 - .../camino/tests/test_auto_ProcStreamlines.py | 1 - .../camino/tests/test_auto_QBallMX.py | 1 - .../camino/tests/test_auto_SFLUTGen.py | 1 - .../camino/tests/test_auto_SFPICOCalibData.py | 1 - .../camino/tests/test_auto_SFPeaks.py | 1 - .../camino/tests/test_auto_Shredder.py | 1 - .../camino/tests/test_auto_TractShredder.py | 1 - .../camino/tests/test_auto_VtkStreamlines.py | 1 - .../freesurfer/tests/test_auto_Aparc2Aseg.py | 9 +-- .../freesurfer/tests/test_auto_Apas2Aseg.py | 9 +-- .../freesurfer/tests/test_auto_CALabel.py | 10 +--- .../freesurfer/tests/test_auto_CANormalize.py | 2 +- .../freesurfer/tests/test_auto_CARegister.py | 2 +- .../test_auto_CheckTalairachAlignment.py | 2 +- .../tests/test_auto_ConcatenateLTA.py | 2 - .../freesurfer/tests/test_auto_Contrast.py | 10 +--- .../freesurfer/tests/test_auto_FixTopology.py | 5 +- .../freesurfer/tests/test_auto_MRIsCALabel.py | 10 +--- .../freesurfer/tests/test_auto_MS_LDA.py | 12 +--- .../freesurfer/tests/test_auto_Normalize.py | 2 +- .../tests/test_auto_ParcellationStats.py | 9 +-- .../tests/test_auto_RegisterAVItoTalairach.py | 2 +- .../tests/test_auto_RelabelHypointensities.py | 9 +-- .../tests/test_auto_SegStatsReconAll.py | 5 +- .../tests/test_auto_SurfaceSnapshots.py | 1 - .../tests/test_auto_TalairachAVI.py | 6 +- .../freesurfer/tests/test_auto_TalairachQC.py | 9 +-- .../fsl/tests/test_auto_AccuracyTester.py | 9 +-- .../interfaces/fsl/tests/test_auto_Cleaner.py | 3 - .../interfaces/fsl/tests/test_auto_Cluster.py | 5 +- .../fsl/tests/test_auto_FeatureExtractor.py | 11 ++-- .../fsl/tests/test_auto_FindTheBiggest.py | 9 +-- .../fsl/tests/test_auto_TrainingSetCreator.py | 22 ++++---- .../minc/tests/test_auto_Average.py | 6 +- .../interfaces/minc/tests/test_auto_BBox.py | 1 - .../interfaces/minc/tests/test_auto_Beast.py | 7 +-- .../interfaces/minc/tests/test_auto_Calc.py | 2 - .../interfaces/minc/tests/test_auto_Dump.py | 1 - .../minc/tests/test_auto_Extract.py | 1 - .../interfaces/minc/tests/test_auto_Math.py | 1 - .../interfaces/minc/tests/test_auto_Norm.py | 6 +- .../minc/tests/test_auto_Resample.py | 10 +--- .../minc/tests/test_auto_Reshape.py | 1 - .../interfaces/minc/tests/test_auto_ToRaw.py | 1 - .../minc/tests/test_auto_VolSymm.py | 2 - .../minc/tests/test_auto_XfmInvert.py | 1 - .../mrtrix3/tests/test_auto_BrainMask.py | 6 +- .../mrtrix3/tests/test_auto_DWIExtract.py | 6 +- .../mrtrix3/tests/test_auto_EstimateFOD.py | 6 +- .../mrtrix3/tests/test_auto_FitTensor.py | 6 +- .../mrtrix3/tests/test_auto_Generate5tt.py | 6 +- .../mrtrix3/tests/test_auto_MRConvert.py | 6 +- .../mrtrix3/tests/test_auto_MRMath.py | 6 +- .../mrtrix3/tests/test_auto_ResponseSD.py | 6 +- .../mrtrix3/tests/test_auto_Tractography.py | 6 +- .../niftyfit/tests/test_auto_DwiTool.py | 26 +++------ .../niftyfit/tests/test_auto_FitAsl.py | 41 +++----------- .../niftyfit/tests/test_auto_FitDwi.py | 56 +++++-------------- .../niftyfit/tests/test_auto_FitQt1.py | 25 ++------- .../nipy/tests/test_auto_EstimateContrast.py | 2 +- .../interfaces/nipy/tests/test_auto_FitGLM.py | 4 +- .../tests/test_auto_UnbiasedNonLocalMeans.py | 9 +-- .../diffusion/tests/test_auto_DTIexport.py | 9 +-- .../diffusion/tests/test_auto_DTIimport.py | 9 +-- .../test_auto_DWIJointRicianLMMSEFilter.py | 9 +-- .../tests/test_auto_DWIRicianLMMSEFilter.py | 9 +-- ..._auto_DiffusionTensorScalarMeasurements.py | 9 +-- .../tests/test_auto_ResampleDTIVolume.py | 9 +-- .../tests/test_auto_AddScalarVolumes.py | 9 +-- .../tests/test_auto_CastScalarVolume.py | 9 +-- .../tests/test_auto_CheckerBoardFilter.py | 9 +-- ...test_auto_CurvatureAnisotropicDiffusion.py | 9 +-- .../tests/test_auto_ExtractSkeleton.py | 9 +-- .../test_auto_GaussianBlurImageFilter.py | 9 +-- .../test_auto_GradientAnisotropicDiffusion.py | 9 +-- .../test_auto_GrayscaleFillHoleImageFilter.py | 9 +-- ...test_auto_GrayscaleGrindPeakImageFilter.py | 9 +-- .../tests/test_auto_HistogramMatching.py | 9 +-- .../tests/test_auto_ImageLabelCombine.py | 9 +-- .../tests/test_auto_MaskScalarVolume.py | 9 +-- .../tests/test_auto_MedianImageFilter.py | 9 +-- .../tests/test_auto_MultiplyScalarVolumes.py | 9 +-- ...test_auto_ResampleScalarVectorDWIVolume.py | 9 +-- .../tests/test_auto_SubtractScalarVolumes.py | 9 +-- .../tests/test_auto_ThresholdScalarVolume.py | 9 +-- ...auto_VotingBinaryHoleFillingImageFilter.py | 9 +-- ...est_auto_DWIUnbiasedNonLocalMeansFilter.py | 9 +-- .../test_auto_OtsuThresholdImageFilter.py | 9 +-- .../test_auto_OtsuThresholdSegmentation.py | 9 +-- .../tests/test_auto_ResampleScalarVolume.py | 9 +-- .../test_auto_RobustStatisticsSegmenter.py | 9 +-- ...st_auto_SimpleRegionGrowingSegmentation.py | 9 +-- .../tests/test_auto_GrayscaleModelMaker.py | 9 +-- .../tests/test_auto_LabelMapSmoothing.py | 9 +-- .../slicer/tests/test_auto_MergeModels.py | 9 +-- .../slicer/tests/test_auto_ModelToLabelMap.py | 9 +-- .../tests/test_auto_OrientScalarVolume.py | 9 +-- .../tests/test_auto_ProbeVolumeWithModel.py | 9 +-- .../utility/tests/test_auto_Rename.py | 2 +- 134 files changed, 340 insertions(+), 541 deletions(-) diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index a8c4467cbf..3090c8b6a9 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -6,10 +6,7 @@ def test_AddCSVRow_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), - in_file=dict( - extensions=None, - mandatory=True, - ), + in_file=dict(mandatory=True, ), ) inputs = AddCSVRow.input_spec() diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index d84e84ad61..e583deaa10 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -4,10 +4,11 @@ def test_Gunzip_inputs(): - input_map = dict(in_file=dict( - extensions=None, - mandatory=True, - ), ) + input_map = dict( + in_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = Gunzip.input_spec() for key, metadata in list(input_map.items()): diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index 10eb41190b..4da9dad47d 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -4,10 +4,11 @@ def test_NonSteadyStateDetector_inputs(): - input_map = dict(in_file=dict( - extensions=None, - mandatory=True, - ), ) + input_map = dict( + in_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = NonSteadyStateDetector.input_spec() for key, metadata in list(input_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index e1565376bd..0b110e669a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -86,7 +86,6 @@ def test_Allineate_inputs(): ), out_weight_file=dict( argstr='-wtprefix %s', - extensions=None, xor=['allcostx'], ), outputtype=dict(), diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index 50806add01..345806f746 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -21,9 +21,10 @@ def test_Cat_inputs(): usedefault=True, ), omitconst=dict(argstr='-nonconst', ), - out_cint=dict(xor=[ - 'out_format', 'out_nice', 'out_double', 'out_fint', 'out_int' - ], ), + out_cint=dict( + xor=[ + 'out_format', 'out_nice', 'out_double', 'out_fint', 'out_int' + ], ), out_double=dict( argstr='-d', xor=['out_format', 'out_nice', 'out_int', 'out_fint', 'out_cint'], diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index 96f928a809..f9b3dbf705 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -17,7 +17,6 @@ def test_ClipLevel_inputs(): ), grad=dict( argstr='-grad %s', - extensions=None, position=3, xor='doall', ), diff --git a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py index 4632e4cf7d..ed3e61d74d 100644 --- a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py +++ b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py @@ -26,10 +26,7 @@ def test_LocalBistat_inputs(): mandatory=True, position=-1, ), - mask_file=dict( - argstr='-mask %s', - extensions=None, - ), + mask_file=dict(argstr='-mask %s', ), neighborhood=dict( argstr="-nbhd '%s(%s)'", mandatory=True, @@ -40,7 +37,6 @@ def test_LocalBistat_inputs(): ), out_file=dict( argstr='-prefix %s', - extensions=None, keep_extension=True, name_source='in_file1', name_template='%s_bistat', @@ -53,7 +49,6 @@ def test_LocalBistat_inputs(): ), weight_file=dict( argstr='-weight %s', - extensions=None, xor=['automask'], ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Localstat.py b/nipype/interfaces/afni/tests/test_auto_Localstat.py index 62dc800941..011ce44da8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Localstat.py +++ b/nipype/interfaces/afni/tests/test_auto_Localstat.py @@ -21,10 +21,7 @@ def test_Localstat_inputs(): mandatory=True, position=-1, ), - mask_file=dict( - argstr='-mask %s', - extensions=None, - ), + mask_file=dict(argstr='-mask %s', ), neighborhood=dict( argstr="-nbhd '%s(%s)'", mandatory=True, @@ -36,7 +33,6 @@ def test_Localstat_inputs(): ), out_file=dict( argstr='-prefix %s', - extensions=None, keep_extension=True, name_source='in_file', name_template='%s_localstat', diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index 87388c65ec..e00457f4f3 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -20,10 +20,7 @@ def test_NwarpApply_inputs(): usedefault=True, ), inv_warp=dict(argstr='-iwarp', ), - master=dict( - argstr='-master %s', - extensions=None, - ), + master=dict(argstr='-master %s', ), out_file=dict( argstr='-prefix %s', extensions=None, diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index 114fe53fba..f8e664a727 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -30,7 +30,6 @@ def test_OneDToolPy_inputs(): show_censor_count=dict(argstr='-show_censor_count', ), show_cormat_warnings=dict( argstr='-show_cormat_warnings |& tee %s', - extensions=None, position=-1, xor=['out_file'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index 0b8a9e38ec..3ef8c2e9b2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -125,10 +125,7 @@ def test_Qwarp_inputs(): name_source=['in_file'], name_template='ppp_%s', ), - out_weight_file=dict( - argstr='-wtprefix %s', - extensions=None, - ), + out_weight_file=dict(argstr='-wtprefix %s', ), outputtype=dict(), overwrite=dict(argstr='-overwrite', ), pblur=dict(argstr='-pblur %s', ), diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index e282d0d0a5..ca27a0d682 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -125,10 +125,7 @@ def test_QwarpPlusMinus_inputs(): position=0, usedefault=True, ), - out_weight_file=dict( - argstr='-wtprefix %s', - extensions=None, - ), + out_weight_file=dict(argstr='-wtprefix %s', ), outputtype=dict(), overwrite=dict(argstr='-overwrite', ), pblur=dict(argstr='-pblur %s', ), diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index c7fc517ccc..d3c956f7c5 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -49,10 +49,7 @@ def test_ROIStats_inputs(): position=-1, ), quiet=dict(argstr='-quiet', ), - roisel=dict( - argstr='-roisel %s', - extensions=None, - ), + roisel=dict(argstr='-roisel %s', ), stat=dict(argstr='%s...', ), zerofill=dict( argstr='-zerofill %s', diff --git a/nipype/interfaces/afni/tests/test_auto_ReHo.py b/nipype/interfaces/afni/tests/test_auto_ReHo.py index cf3e468159..0edcedcdaf 100644 --- a/nipype/interfaces/afni/tests/test_auto_ReHo.py +++ b/nipype/interfaces/afni/tests/test_auto_ReHo.py @@ -25,17 +25,13 @@ def test_ReHo_inputs(): argstr='-in_rois %s', extensions=None, ), - mask_file=dict( - argstr='-mask %s', - extensions=None, - ), + mask_file=dict(argstr='-mask %s', ), neighborhood=dict( argstr='-nneigh %s', xor=['sphere', 'ellipsoid'], ), out_file=dict( argstr='-prefix %s', - extensions=None, keep_extension=True, name_source='in_file', name_template='%s_reho', diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index 05ee75210e..f2e6703bf6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -58,7 +58,6 @@ def test_Remlfit_inputs(): ), matim=dict( argstr='-matim %s', - extensions=None, xor=['matrix'], ), matrix=dict( diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index f63e1347f5..560d883d75 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -17,10 +17,7 @@ def test_Resample_inputs(): mandatory=True, position=-1, ), - master=dict( - argstr='-master %s', - extensions=None, - ), + master=dict(argstr='-master %s', ), num_threads=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 209473fe6f..1ea4c0790e 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -93,10 +93,7 @@ def test_TCorrMap_inputs(): name_source='in_file', suffix='_qmean', ), - regress_out_timeseries=dict( - argstr='-ort %s', - extensions=None, - ), + regress_out_timeseries=dict(argstr='-ort %s', ), seeds=dict( argstr='-seed %s', extensions=None, diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index 1bd80cfad8..abeceda432 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -55,7 +55,6 @@ def test_Zeropad_inputs(): ), master=dict( argstr='-master %s', - extensions=None, xor=['I', 'S', 'A', 'P', 'L', 'R', 'z', 'RL', 'AP', 'IS', 'mm'], ), mm=dict( diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 1ee5cabe21..5c6fa2c501 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -57,8 +57,8 @@ def test_ANTS_inputs(): regularization=dict(argstr='%s', ), regularization_deformation_field_sigma=dict( requires=['regularization'], ), - regularization_gradient_field_sigma=dict(requires=['regularization' - ], ), + regularization_gradient_field_sigma=dict( + requires=['regularization'], ), smoothing_sigmas=dict( argstr='--gaussian-smoothing-sigmas %s', sep='x', diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index a2829be3fa..02ebe6431c 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -44,10 +44,11 @@ def test_AntsJointFusion_inputs(): nohash=True, usedefault=True, ), - out_atlas_voting_weight_name_format=dict(requires=[ - 'out_label_fusion', 'out_intensity_fusion_name_format', - 'out_label_post_prob_name_format' - ], ), + out_atlas_voting_weight_name_format=dict( + requires=[ + 'out_label_fusion', 'out_intensity_fusion_name_format', + 'out_label_post_prob_name_format' + ], ), out_intensity_fusion_name_format=dict(argstr='', ), out_label_fusion=dict( argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index 73d7f6813a..be1a271f9a 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -53,8 +53,8 @@ def test_Atropos_inputs(): prior_probability_threshold=dict(requires=['prior_weighting'], ), prior_weighting=dict(), save_posteriors=dict(), - use_mixture_model_proportions=dict(requires=['posterior_formulation' - ], ), + use_mixture_model_proportions=dict( + requires=['posterior_formulation'], ), use_random_seed=dict( argstr='--use-random-seed %d', usedefault=True, diff --git a/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py index 95afcd3216..e39dc3acaa 100644 --- a/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py @@ -12,7 +12,6 @@ def test_StdOutCommandLine_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index c40082d836..28170946ac 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -50,7 +50,6 @@ def test_AnalyzeHeader_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index edf38864fa..66ac282175 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -24,7 +24,6 @@ def test_ComputeEigensystem_inputs(): maxcomponents=dict(argstr='-maxcomponents %d', ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 75604df01b..9cfae77b2f 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -20,7 +20,6 @@ def test_ComputeFractionalAnisotropy_inputs(): inputmodel=dict(argstr='-inputmodel %s', ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 4d31fa884c..1443a253bd 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -20,7 +20,6 @@ def test_ComputeTensorTrace_inputs(): inputmodel=dict(argstr='-inputmodel %s', ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index 0870a77752..26d27d57d2 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -26,7 +26,6 @@ def test_DTIFit_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 3242163c3a..f7caf77ef1 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -28,7 +28,6 @@ def test_DTLUTGen_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index 9b8a74be6a..350c604c99 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -40,7 +40,6 @@ def test_FSL2Scheme_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 2c013cf216..29864bef82 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -18,7 +18,6 @@ def test_Image2Voxel_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 147cfaab5e..996d8f4b99 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -24,7 +24,6 @@ def test_LinRecon_inputs(): normalize=dict(argstr='-normalize', ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index f7dfecfdb9..57dbbf3b28 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -42,7 +42,6 @@ def test_MESD_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index 6d49969eb6..e5c16ec975 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -34,7 +34,6 @@ def test_ModelFit_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 65e0210268..0a5583b03e 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -26,7 +26,6 @@ def test_NIfTIDT2Camino_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index e5cdea5cae..c918a372f1 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -36,7 +36,6 @@ def test_PicoPDFs_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index 0386e0d54f..c30ef08d8c 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -62,7 +62,6 @@ def test_ProcStreamlines_inputs(): noresample=dict(argstr='-noresample', ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index f452f26350..7f7d0bc99f 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -20,7 +20,6 @@ def test_QBallMX_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index 220e116255..795138ea89 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -35,7 +35,6 @@ def test_SFLUTGen_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index 1b71553676..80222fce4c 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -27,7 +27,6 @@ def test_SFPICOCalibData_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 49ac58aa06..8db250c58c 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -38,7 +38,6 @@ def test_SFPeaks_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 2d8ec43589..594b35fc60 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -28,7 +28,6 @@ def test_Shredder_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index e4df010c60..eeed244533 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -28,7 +28,6 @@ def test_TractShredder_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index bd8d295572..72b6f106d8 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -25,7 +25,6 @@ def test_VtkStreamlines_inputs(): interpolatescalars=dict(argstr='-interpolatescalars', ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index 494ce981c5..8a83130a4d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -79,10 +79,11 @@ def test_Aparc2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Aparc2Aseg_outputs(): - output_map = dict(out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict( + out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = Aparc2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index 03385da2ad..fea3617596 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -28,10 +28,11 @@ def test_Apas2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Apas2Aseg_outputs(): - output_map = dict(out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict( + out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = Apas2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index 4d56d217c7..f3bfd5ad62 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -7,10 +7,7 @@ def test_CALabel_inputs(): input_map = dict( align=dict(argstr='-align', ), args=dict(argstr='%s', ), - aseg=dict( - argstr='-aseg %s', - extensions=None, - ), + aseg=dict(argstr='-aseg %s', ), environ=dict( nohash=True, usedefault=True, @@ -29,10 +26,7 @@ def test_CALabel_inputs(): argstr='-r %s', extensions=None, ), - label=dict( - argstr='-l %s', - extensions=None, - ), + label=dict(argstr='-l %s', ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), out_file=dict( diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index 5700103e84..1f6546ae3a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -59,7 +59,7 @@ def test_CANormalize_inputs(): def test_CANormalize_outputs(): output_map = dict( control_points=dict(extensions=None, ), - out_file=dict(extensions=None, ), + out_file=dict(), ) outputs = CANormalize.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index dcf5aa84a8..83f669b218 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -53,7 +53,7 @@ def test_CARegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CARegister_outputs(): - output_map = dict(out_file=dict(extensions=None, ), ) + output_map = dict(out_file=dict(), ) outputs = CARegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index fe9c1a3121..68a5a98e66 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -35,7 +35,7 @@ def test_CheckTalairachAlignment_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CheckTalairachAlignment_outputs(): - output_map = dict(out_file=dict(extensions=None, ), ) + output_map = dict(out_file=dict(), ) outputs = CheckTalairachAlignment.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index ee1d3ae7f3..8acab945c1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -38,13 +38,11 @@ def test_ConcatenateLTA_inputs(): subjects_dir=dict(), tal_source_file=dict( argstr='-tal %s', - extensions=None, position=-5, requires=['tal_template_file'], ), tal_template_file=dict( argstr='%s', - extensions=None, position=-4, requires=['tal_source_file'], ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index 3cd62e8ee7..3c4e5aa484 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -5,16 +5,10 @@ def test_Contrast_inputs(): input_map = dict( - annotation=dict( - extensions=None, - mandatory=True, - ), + annotation=dict(mandatory=True, ), args=dict(argstr='%s', ), copy_inputs=dict(), - cortex=dict( - extensions=None, - mandatory=True, - ), + cortex=dict(mandatory=True, ), environ=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index 83427dcd20..4ba8442b14 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -35,10 +35,7 @@ def test_FixTopology_inputs(): ), mgz=dict(argstr='-mgz', ), seed=dict(argstr='-seed %d', ), - sphere=dict( - argstr='-sphere %s', - extensions=None, - ), + sphere=dict(argstr='-sphere %s', ), subject_id=dict( argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index eaf91bc1e8..10c7af6832 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -6,10 +6,7 @@ def test_MRIsCALabel_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict( - argstr='-aseg %s', - extensions=None, - ), + aseg=dict(argstr='-aseg %s', ), canonsurf=dict( argstr='%s', extensions=None, @@ -36,10 +33,7 @@ def test_MRIsCALabel_inputs(): mandatory=True, position=-4, ), - label=dict( - argstr='-l %s', - extensions=None, - ), + label=dict(argstr='-l %s', ), num_threads=dict(), out_file=dict( argstr='%s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index 3d3f5cde11..badb3b4f0c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -17,30 +17,22 @@ def test_MS_LDA_inputs(): mandatory=True, position=-1, ), - label_file=dict( - argstr='-label %s', - extensions=None, - ), + label_file=dict(argstr='-label %s', ), lda_labels=dict( argstr='-lda %s', mandatory=True, sep=' ', ), - mask_file=dict( - argstr='-mask %s', - extensions=None, - ), + mask_file=dict(argstr='-mask %s', ), shift=dict(argstr='-shift %d', ), subjects_dir=dict(), use_weights=dict(argstr='-W', ), vol_synth_file=dict( argstr='-synth %s', - extensions=None, mandatory=True, ), weight_file=dict( argstr='-weight %s', - extensions=None, mandatory=True, ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index baf03f026c..2384adbb2b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -43,7 +43,7 @@ def test_Normalize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Normalize_outputs(): - output_map = dict(out_file=dict(extensions=None, ), ) + output_map = dict(out_file=dict(), ) outputs = Normalize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index 8b4ae45d67..be19b2bd37 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -27,16 +27,11 @@ def test_ParcellationStats_inputs(): ), in_annotation=dict( argstr='-a %s', - extensions=None, xor=['in_label'], ), - in_cortex=dict( - argstr='-cortex %s', - extensions=None, - ), + in_cortex=dict(argstr='-cortex %s', ), in_label=dict( argstr='-l %s', - extensions=None, xor=['in_annotatoin', 'out_color'], ), lh_pial=dict( @@ -50,13 +45,11 @@ def test_ParcellationStats_inputs(): mgz=dict(argstr='-mgz', ), out_color=dict( argstr='-c %s', - extensions=None, genfile=True, xor=['in_label'], ), out_table=dict( argstr='-f %s', - extensions=None, genfile=True, requires=['tabular_output'], ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index 5a609f586e..f3406d41fc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -47,7 +47,7 @@ def test_RegisterAVItoTalairach_outputs(): extensions=None, usedefault=True, ), - out_file=dict(extensions=None, ), + out_file=dict(), ) outputs = RegisterAVItoTalairach.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index f99acec899..28ff49d99e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -48,10 +48,11 @@ def test_RelabelHypointensities_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RelabelHypointensities_outputs(): - output_map = dict(out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict( + out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = RelabelHypointensities.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index 09da0d001d..3cf47c71ce 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -100,10 +100,7 @@ def test_SegStatsReconAll_inputs(): extensions=None, mandatory=True, ), - ribbon=dict( - extensions=None, - mandatory=True, - ), + ribbon=dict(mandatory=True, ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index 968041ff67..26dcbe3458 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -59,7 +59,6 @@ def test_SurfaceSnapshots_inputs(): overlay_range_offset=dict(argstr='-foffset %.3f', ), overlay_reg=dict( argstr='-overlay-reg %s', - extensions=None, xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), patch_file=dict( diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index 2a28765d67..9d248c1a7d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -30,9 +30,9 @@ def test_TalairachAVI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TalairachAVI_outputs(): output_map = dict( - out_file=dict(extensions=None, ), - out_log=dict(extensions=None, ), - out_txt=dict(extensions=None, ), + out_file=dict(), + out_log=dict(), + out_txt=dict(), ) outputs = TalairachAVI.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index 1961e3ded6..053d429c9b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -24,10 +24,11 @@ def test_TalairachQC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TalairachQC_outputs(): - output_map = dict(log_file=dict( - extensions=None, - usedefault=True, - ), ) + output_map = dict( + log_file=dict( + extensions=None, + usedefault=True, + ), ) outputs = TalairachQC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py index ffd5b42bd1..de32f63f5f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -34,10 +34,11 @@ def test_AccuracyTester_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AccuracyTester_outputs(): - output_map = dict(output_directory=dict( - argstr='%s', - position=1, - ), ) + output_map = dict( + output_directory=dict( + argstr='%s', + position=1, + ), ) outputs = AccuracyTester.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py index 597dc88d5e..a75df99db5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -22,17 +22,14 @@ def test_Cleaner_inputs(): ), confound_file=dict( argstr='-x %s', - extensions=None, position=4, ), confound_file_1=dict( argstr='-x %s', - extensions=None, position=5, ), confound_file_2=dict( argstr='-x %s', - extensions=None, position=6, ), environ=dict( diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index 19340b9383..6ed34ab816 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -7,10 +7,7 @@ def test_Cluster_inputs(): input_map = dict( args=dict(argstr='%s', ), connectivity=dict(argstr='--connectivity=%d', ), - cope_file=dict( - argstr='--cope=%s', - extensions=None, - ), + cope_file=dict(argstr='--cope=%s', ), dlh=dict(argstr='--dlh=%.10f', ), environ=dict( nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py index eaeeb34ce8..3945c40a87 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py @@ -22,11 +22,12 @@ def test_FeatureExtractor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FeatureExtractor_outputs(): - output_map = dict(mel_ica=dict( - argstr='%s', - copyfile=False, - position=-1, - ), ) + output_map = dict( + mel_ica=dict( + argstr='%s', + copyfile=False, + position=-1, + ), ) outputs = FeatureExtractor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index a8262c9be1..5c7b717d93 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -30,10 +30,11 @@ def test_FindTheBiggest_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FindTheBiggest_outputs(): - output_map = dict(out_file=dict( - argstr='%s', - extensions=None, - ), ) + output_map = dict( + out_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = FindTheBiggest.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py index 638bcdd156..18ef078a79 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py +++ b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py @@ -4,22 +4,24 @@ def test_TrainingSetCreator_inputs(): - input_map = dict(mel_icas_in=dict( - argstr='%s', - copyfile=False, - position=-1, - ), ) + input_map = dict( + mel_icas_in=dict( + argstr='%s', + copyfile=False, + position=-1, + ), ) inputs = TrainingSetCreator.input_spec() for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrainingSetCreator_outputs(): - output_map = dict(mel_icas_out=dict( - argstr='%s', - copyfile=False, - position=-1, - ), ) + output_map = dict( + mel_icas_out=dict( + argstr='%s', + copyfile=False, + position=-1, + ), ) outputs = TrainingSetCreator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 6f0e84d144..678ab93a52 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -29,7 +29,6 @@ def test_Average_inputs(): ), filelist=dict( argstr='-filelist %s', - extensions=None, mandatory=True, xor=('input_files', 'filelist'), ), @@ -127,10 +126,7 @@ def test_Average_inputs(): argstr='-quiet', xor=('verbose', 'quiet'), ), - sdfile=dict( - argstr='-sdfile %s', - extensions=None, - ), + sdfile=dict(argstr='-sdfile %s', ), two=dict(argstr='-2', ), verbose=dict( argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index 7bdf35f03d..c1b3515cea 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -25,7 +25,6 @@ def test_BBox_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index 3a44b436b0..bc4705db2e 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -18,10 +18,7 @@ def test_Beast_inputs(): argstr='-alpha %s', usedefault=True, ), - configuration_file=dict( - argstr='-configuration %s', - extensions=None, - ), + configuration_file=dict(argstr='-configuration %s', ), environ=dict( nohash=True, usedefault=True, @@ -30,7 +27,6 @@ def test_Beast_inputs(): flip_images=dict(argstr='-flip', ), input_file=dict( argstr='%s', - extensions=None, mandatory=True, position=-2, ), @@ -48,7 +44,6 @@ def test_Beast_inputs(): ), output_file=dict( argstr='%s', - extensions=None, hash_files=False, name_source=['input_file'], name_template='%s_beast_mask.mnc', diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index d5fb316e39..e9df677150 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -26,7 +26,6 @@ def test_Calc_inputs(): eval_width=dict(argstr='-eval_width %s', ), expfile=dict( argstr='-expfile %s', - extensions=None, mandatory=True, xor=('expression', 'expfile'), ), @@ -37,7 +36,6 @@ def test_Calc_inputs(): ), filelist=dict( argstr='-filelist %s', - extensions=None, mandatory=True, xor=('input_files', 'filelist'), ), diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index fbd33f5a46..19c299dac8 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -36,7 +36,6 @@ def test_Dump_inputs(): netcdf_name=dict(argstr='-n %s', ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index fbd0a84729..35f6162c7f 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -84,7 +84,6 @@ def test_Extract_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index 41d75379d4..6bc142b15d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -36,7 +36,6 @@ def test_Math_inputs(): exp=dict(argstr='-exp -const2 %s %s', ), filelist=dict( argstr='-filelist %s', - extensions=None, mandatory=True, xor=('input_files', 'filelist'), ), diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index cdd4a3db7c..9fb0d3c5ba 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -26,10 +26,7 @@ def test_Norm_inputs(): position=-2, ), lower=dict(argstr='-lower %s', ), - mask=dict( - argstr='-mask %s', - extensions=None, - ), + mask=dict(argstr='-mask %s', ), out_ceil=dict(argstr='-out_ceil %s', ), out_floor=dict(argstr='-out_floor %s', ), output_file=dict( @@ -43,7 +40,6 @@ def test_Norm_inputs(): ), output_threshold_mask=dict( argstr='-threshold_mask %s', - extensions=None, hash_files=False, name_source=['input_file'], name_template='%s_norm_threshold_mask.mnc', diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index da512d9f62..8d4b24ff41 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -94,10 +94,7 @@ def test_Resample_inputs(): argstr='-keep_real_range', xor=('keep_real_range', 'nokeep_real_range'), ), - like=dict( - argstr='-like %s', - extensions=None, - ), + like=dict(argstr='-like %s', ), nearest_neighbour_interpolation=dict( argstr='-nearest_neighbour', xor=('trilinear_interpolation', 'tricubic_interpolation', @@ -160,10 +157,7 @@ def test_Resample_inputs(): xor=('nelements', 'nelements_x_y_or_z'), ), talairach=dict(argstr='-talairach', ), - transformation=dict( - argstr='-transformation %s', - extensions=None, - ), + transformation=dict(argstr='-transformation %s', ), transverse_slices=dict( argstr='-transverse', xor=('transverse', 'sagittal', 'coronal'), diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index d80f9a377b..669425da95 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -16,7 +16,6 @@ def test_Reshape_inputs(): ), input_file=dict( argstr='%s', - extensions=None, mandatory=True, position=-2, ), diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index 42ba72f145..aeda687c97 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -26,7 +26,6 @@ def test_ToRaw_inputs(): ), out_file=dict( argstr='> %s', - extensions=None, genfile=True, position=-1, ), diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index ae3332b7f2..b710d59543 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -22,7 +22,6 @@ def test_VolSymm_inputs(): fit_nonlinear=dict(argstr='-nonlinear', ), input_file=dict( argstr='%s', - extensions=None, mandatory=True, position=-3, ), @@ -39,7 +38,6 @@ def test_VolSymm_inputs(): ), trans_file=dict( argstr='%s', - extensions=None, genfile=True, hash_files=False, keep_extension=False, diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index 69c455f875..9e242300da 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -16,7 +16,6 @@ def test_XfmInvert_inputs(): ), input_file=dict( argstr='%s', - extensions=None, mandatory=True, position=-2, ), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 5ee1e8cb00..90c5272ed0 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -14,12 +14,8 @@ def test_BrainMask_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py index 59617b30ab..7658201223 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py @@ -15,12 +15,8 @@ def test_DWIExtract_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index c2816f2646..c64efa2ca4 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -41,12 +41,8 @@ def test_EstimateFOD_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 8f8142746a..84404fdde6 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -14,12 +14,8 @@ def test_FitTensor_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index f7032cb624..92594da593 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -19,12 +19,8 @@ def test_Generate5tt_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py index f11b615cc8..9271d07517 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py @@ -22,12 +22,8 @@ def test_MRConvert_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py index fe934c45b1..ae494bb932 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py @@ -15,12 +15,8 @@ def test_MRMath_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index 9415cae211..dd326bad5b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -29,12 +29,8 @@ def test_ResponseSD_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index cf685a50d8..39f239b81d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -28,12 +28,8 @@ def test_Tractography_inputs(): grad_file=dict( argstr='-grad %s', extensions=None, - xor=['grad_fsl'], - ), - grad_fsl=dict( - argstr='-fslgrad %s %s', - xor=['grad_file'], ), + grad_fsl=dict(argstr='-fslgrad %s %s', ), in_bval=dict(extensions=None, ), in_bvec=dict( argstr='-fslgrad %s %s', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py index 2a58b39d57..20995e806e 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py @@ -8,7 +8,6 @@ def test_DwiTool_inputs(): args=dict(argstr='%s', ), b0_file=dict( argstr='-b0 %s', - extensions=None, position=4, ), ball_flag=dict( @@ -29,13 +28,11 @@ def test_DwiTool_inputs(): ), bval_file=dict( argstr='-bval %s', - extensions=None, mandatory=True, position=2, ), bvec_file=dict( argstr='-bvec %s', - extensions=None, position=3, ), diso_val=dict(argstr='-diso %f', ), @@ -62,7 +59,6 @@ def test_DwiTool_inputs(): ), famap_file=dict( argstr='-famap %s', - extensions=None, name_source=['source_file'], name_template='%s_famap.nii.gz', ), @@ -76,24 +72,20 @@ def test_DwiTool_inputs(): ), logdti_file=dict( argstr='-logdti2 %s', - extensions=None, name_source=['source_file'], name_template='%s_logdti2.nii.gz', ), mask_file=dict( argstr='-mask %s', - extensions=None, position=5, ), mcmap_file=dict( argstr='-mcmap %s', - extensions=None, name_source=['source_file'], name_template='%s_mcmap.nii.gz', ), mdmap_file=dict( argstr='-mdmap %s', - extensions=None, name_source=['source_file'], name_template='%s_mdmap.nii.gz', ), @@ -123,26 +115,22 @@ def test_DwiTool_inputs(): ), rgbmap_file=dict( argstr='-rgbmap %s', - extensions=None, name_source=['source_file'], name_template='%s_rgbmap.nii.gz', ), source_file=dict( argstr='-source %s', - extensions=None, mandatory=True, position=1, ), syn_file=dict( argstr='-syn %s', - extensions=None, name_source=['source_file'], name_template='%s_syn.nii.gz', requires=['bvec_file', 'b0_file'], ), v1map_file=dict( argstr='-v1map %s', - extensions=None, name_source=['source_file'], name_template='%s_v1map.nii.gz', ), @@ -154,13 +142,13 @@ def test_DwiTool_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DwiTool_outputs(): output_map = dict( - famap_file=dict(extensions=None, ), - logdti_file=dict(extensions=None, ), - mcmap_file=dict(extensions=None, ), - mdmap_file=dict(extensions=None, ), - rgbmap_file=dict(extensions=None, ), - syn_file=dict(extensions=None, ), - v1map_file=dict(extensions=None, ), + famap_file=dict(), + logdti_file=dict(), + mcmap_file=dict(), + mdmap_file=dict(), + rgbmap_file=dict(), + syn_file=dict(), + v1map_file=dict(), ) outputs = DwiTool.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py index 94a489a4ad..b2e1bef961 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py @@ -8,7 +8,6 @@ def test_FitAsl_inputs(): args=dict(argstr='%s', ), cbf_file=dict( argstr='-cbf %s', - extensions=None, name_source=['source_file'], name_template='%s_cbf.nii.gz', ), @@ -21,33 +20,19 @@ def test_FitAsl_inputs(): ), error_file=dict( argstr='-error %s', - extensions=None, name_source=['source_file'], name_template='%s_error.nii.gz', ), gm_plasma=dict(argstr='-gmL %f', ), gm_t1=dict(argstr='-gmT1 %f', ), gm_ttt=dict(argstr='-gmTTT %f', ), - ir_output=dict( - argstr='-IRoutput %s', - extensions=None, - ), - ir_volume=dict( - argstr='-IRvolume %s', - extensions=None, - ), + ir_output=dict(argstr='-IRoutput %s', ), + ir_volume=dict(argstr='-IRvolume %s', ), ldd=dict(argstr='-LDD %f', ), - m0map=dict( - argstr='-m0map %s', - extensions=None, - ), - m0mape=dict( - argstr='-m0mape %s', - extensions=None, - ), + m0map=dict(argstr='-m0map %s', ), + m0mape=dict(argstr='-m0mape %s', ), mask=dict( argstr='-mask %s', - extensions=None, position=2, ), mul=dict(argstr='-mul %f', ), @@ -61,29 +46,21 @@ def test_FitAsl_inputs(): pv2=dict(argstr='-pv2 %d', ), pv3=dict(argstr='-pv3 %d %d %d', ), pv_threshold=dict(argstr='-pvthreshold', ), - seg=dict( - argstr='-seg %s', - extensions=None, - ), + seg=dict(argstr='-seg %s', ), segstyle=dict(argstr='-segstyle', ), sig=dict(argstr='-sig', ), source_file=dict( argstr='-source %s', - extensions=None, mandatory=True, position=1, ), syn_file=dict( argstr='-syn %s', - extensions=None, name_source=['source_file'], name_template='%s_syn.nii.gz', ), t1_art_cmp=dict(argstr='-T1a %f', ), - t1map=dict( - argstr='-t1map %s', - extensions=None, - ), + t1map=dict(argstr='-t1map %s', ), t_inv1=dict(argstr='-Tinv1 %f', ), t_inv2=dict(argstr='-Tinv2 %f', ), wm_plasma=dict(argstr='-wmL %f', ), @@ -97,9 +74,9 @@ def test_FitAsl_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitAsl_outputs(): output_map = dict( - cbf_file=dict(extensions=None, ), - error_file=dict(extensions=None, ), - syn_file=dict(extensions=None, ), + cbf_file=dict(), + error_file=dict(), + syn_file=dict(), ) outputs = FitAsl.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py index 2086d12a2b..700d9a31c4 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py @@ -25,20 +25,15 @@ def test_FitDwi_inputs(): ), bval_file=dict( argstr='-bval %s', - extensions=None, mandatory=True, position=2, ), bvec_file=dict( argstr='-bvec %s', - extensions=None, mandatory=True, position=3, ), - cov_file=dict( - argstr='-cov %s', - extensions=None, - ), + cov_file=dict(argstr='-cov %s', ), csf_t2_val=dict(argstr='-csfT2 %f', ), diso_val=dict(argstr='-diso %f', ), dpr_val=dict(argstr='-dpr %f', ), @@ -56,13 +51,11 @@ def test_FitDwi_inputs(): ), error_file=dict( argstr='-error %s', - extensions=None, name_source=['source_file'], name_template='%s_error.nii.gz', ), famap_file=dict( argstr='-famap %s', - extensions=None, name_source=['source_file'], name_template='%s_famap.nii.gz', ), @@ -82,17 +75,13 @@ def test_FitDwi_inputs(): argstr='-lm %f %f', requires=['gn_flag'], ), - mask_file=dict( - argstr='-mask %s', - extensions=None, - ), + mask_file=dict(argstr='-mask %s', ), maxit_val=dict( argstr='-maxit %d', requires=['gn_flag'], ), mcmap_file=dict( argstr='-mcmap %s', - extensions=None, name_source=['source_file'], name_template='%s_mcmap.nii.gz', requires=['nodv_flag'], @@ -100,14 +89,12 @@ def test_FitDwi_inputs(): mcmaxit=dict(argstr='-mcmaxit %d', ), mcout=dict( argstr='-mcout %s', - extensions=None, name_source=['source_file'], name_template='%s_mcout.txt', ), mcsamples=dict(argstr='-mcsamples %d', ), mdmap_file=dict( argstr='-mdmap %s', - extensions=None, name_source=['source_file'], name_template='%s_mdmap.nii.gz', ), @@ -129,7 +116,6 @@ def test_FitDwi_inputs(): ), nodiff_file=dict( argstr='-nodiff %s', - extensions=None, name_source=['source_file'], name_template='%s_no_diff.nii.gz', ), @@ -142,19 +128,14 @@ def test_FitDwi_inputs(): ], ), perf_thr=dict(argstr='-perfthreshold %f', ), - prior_file=dict( - argstr='-prior %s', - extensions=None, - ), + prior_file=dict(argstr='-prior %s', ), res_file=dict( argstr='-res %s', - extensions=None, name_source=['source_file'], name_template='%s_resmap.nii.gz', ), rgbmap_file=dict( argstr='-rgbmap %s', - extensions=None, name_source=['source_file'], name_template='%s_rgbmap.nii.gz', requires=['dti_flag'], @@ -163,45 +144,38 @@ def test_FitDwi_inputs(): slice_no=dict(argstr='-slice %d', ), source_file=dict( argstr='-source %s', - extensions=None, mandatory=True, position=1, ), swls_val=dict(argstr='-swls %f', ), syn_file=dict( argstr='-syn %s', - extensions=None, name_source=['source_file'], name_template='%s_syn.nii.gz', ), te_file=dict( argstr='-TE %s', - extensions=None, xor=['te_file'], ), te_value=dict( argstr='-TE %s', - extensions=None, xor=['te_file'], ), ten_type=dict(usedefault=True, ), tenmap2_file=dict( argstr='-tenmap2 %s', - extensions=None, name_source=['source_file'], name_template='%s_tenmap2.nii.gz', requires=['dti_flag'], ), tenmap_file=dict( argstr='-tenmap %s', - extensions=None, name_source=['source_file'], name_template='%s_tenmap.nii.gz', requires=['dti_flag'], ), v1map_file=dict( argstr='-v1map %s', - extensions=None, name_source=['source_file'], name_template='%s_v1map.nii.gz', ), @@ -220,18 +194,18 @@ def test_FitDwi_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitDwi_outputs(): output_map = dict( - error_file=dict(extensions=None, ), - famap_file=dict(extensions=None, ), - mcmap_file=dict(extensions=None, ), - mcout=dict(extensions=None, ), - mdmap_file=dict(extensions=None, ), - nodiff_file=dict(extensions=None, ), - res_file=dict(extensions=None, ), - rgbmap_file=dict(extensions=None, ), - syn_file=dict(extensions=None, ), - tenmap2_file=dict(extensions=None, ), - tenmap_file=dict(extensions=None, ), - v1map_file=dict(extensions=None, ), + error_file=dict(), + famap_file=dict(), + mcmap_file=dict(), + mcout=dict(), + mdmap_file=dict(), + nodiff_file=dict(), + res_file=dict(), + rgbmap_file=dict(), + syn_file=dict(), + tenmap2_file=dict(), + tenmap_file=dict(), + v1map_file=dict(), ) outputs = FitDwi.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index b184e448cd..392654fd5c 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -7,10 +7,7 @@ def test_FitQt1_inputs(): input_map = dict( acceptance=dict(argstr='-acceptance %f', ), args=dict(argstr='%s', ), - b1map=dict( - argstr='-b1map %s', - extensions=None, - ), + b1map=dict(argstr='-b1map %s', ), comp_file=dict( argstr='-comp %s', extensions=None, @@ -31,10 +28,7 @@ def test_FitQt1_inputs(): argstr='-flips %s', sep=' ', ), - flips_list=dict( - argstr='-fliplist %s', - extensions=None, - ), + flips_list=dict(argstr='-fliplist %s', ), gn_flag=dict( argstr='-gn', position=8, @@ -69,10 +63,7 @@ def test_FitQt1_inputs(): name_template='%s_mcmap.nii.gz', ), mcmaxit=dict(argstr='-mcmaxit %d', ), - mcout=dict( - argstr='-mcout %s', - extensions=None, - ), + mcout=dict(argstr='-mcout %s', ), mcsamples=dict(argstr='-mcsamples %d', ), nb_comp=dict( argstr='-nc %d', @@ -110,10 +101,7 @@ def test_FitQt1_inputs(): name_source=['source_file'], name_template='%s_syn.nii.gz', ), - t1_list=dict( - argstr='-T1list %s', - extensions=None, - ), + t1_list=dict(argstr='-T1list %s', ), t1map_file=dict( argstr='-t1map %s', extensions=None, @@ -131,10 +119,7 @@ def test_FitQt1_inputs(): position=14, sep=' ', ), - tis_list=dict( - argstr='-TIlist %s', - extensions=None, - ), + tis_list=dict(argstr='-TIlist %s', ), tr_value=dict( argstr='-TR %f', position=5, diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 9a9b5c421c..3fe17160db 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -13,7 +13,7 @@ def test_EstimateContrast_inputs(): constants=dict(mandatory=True, ), contrasts=dict(mandatory=True, ), dof=dict(mandatory=True, ), - mask=dict(extensions=None, ), + mask=dict(), nvbeta=dict(mandatory=True, ), reg_names=dict(mandatory=True, ), s2=dict( diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 71ca221efc..a700c18d43 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -8,7 +8,7 @@ def test_FitGLM_inputs(): TR=dict(mandatory=True, ), drift_model=dict(usedefault=True, ), hrf_model=dict(usedefault=True, ), - mask=dict(extensions=None, ), + mask=dict(), method=dict(usedefault=True, ), model=dict(usedefault=True, ), normalize_design_matrix=dict(usedefault=True, ), @@ -30,7 +30,7 @@ def test_FitGLM_outputs(): dof=dict(), nvbeta=dict(), reg_names=dict(), - residuals=dict(extensions=None, ), + residuals=dict(), s2=dict(extensions=None, ), ) outputs = FitGLM.output_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index 2eaeb1acef..866af46740 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -38,10 +38,11 @@ def test_UnbiasedNonLocalMeans_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnbiasedNonLocalMeans_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = UnbiasedNonLocalMeans.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 33e52ed707..1ca79a6e96 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -27,10 +27,11 @@ def test_DTIexport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIexport_outputs(): - output_map = dict(outputFile=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputFile=dict( + extensions=None, + position=-1, + ), ) outputs = DTIexport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index ddb07c9428..58ae495f3f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -28,10 +28,11 @@ def test_DTIimport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIimport_outputs(): - output_map = dict(outputTensor=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputTensor=dict( + extensions=None, + position=-1, + ), ) outputs = DTIimport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index aa0b6f97b5..f8000c49b1 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -37,10 +37,11 @@ def test_DWIJointRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIJointRicianLMMSEFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = DWIJointRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index 69509fcf28..29b5e0b7e1 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -43,10 +43,11 @@ def test_DWIRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIRicianLMMSEFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = DWIRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index 060c47ecc2..5dcdbd7e2e 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -28,10 +28,11 @@ def test_DiffusionTensorScalarMeasurements_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorScalarMeasurements_outputs(): - output_map = dict(outputScalar=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputScalar=dict( + extensions=None, + position=-1, + ), ) outputs = DiffusionTensorScalarMeasurements.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 9cfcdb14fb..bd35268bdb 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -73,10 +73,11 @@ def test_ResampleDTIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleDTIVolume_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ResampleDTIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 42a7b17a19..d2b17c562a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -33,10 +33,11 @@ def test_AddScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddScalarVolumes_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = AddScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index 0c05002ff8..bbcb2f077c 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -28,10 +28,11 @@ def test_CastScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CastScalarVolume_outputs(): - output_map = dict(OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = CastScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index b602012d0c..24f5b74307 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -36,10 +36,11 @@ def test_CheckerBoardFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CheckerBoardFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = CheckerBoardFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index 7389aa0cee..0240ad676a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -30,10 +30,11 @@ def test_CurvatureAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureAnisotropicDiffusion_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = CurvatureAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index d6f93cb41d..c47382aef5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -31,10 +31,11 @@ def test_ExtractSkeleton_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractSkeleton_outputs(): - output_map = dict(OutputImageFileName=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputImageFileName=dict( + extensions=None, + position=-1, + ), ) outputs = ExtractSkeleton.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index 9511f9ce1d..2bdb73c4d5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -28,10 +28,11 @@ def test_GaussianBlurImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GaussianBlurImageFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GaussianBlurImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index 02c9d7fb20..6d3e40c8de 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -30,10 +30,11 @@ def test_GradientAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusion_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GradientAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 45b2b4b8dc..f1ff2c3809 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -27,10 +27,11 @@ def test_GrayscaleFillHoleImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleFillHoleImageFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GrayscaleFillHoleImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 77536e147d..6aee86282a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -27,10 +27,11 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleGrindPeakImageFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = GrayscaleGrindPeakImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index 9541702731..c839c50abf 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -35,10 +35,11 @@ def test_HistogramMatching_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatching_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = HistogramMatching.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index c3373f80ec..7fd2c31db3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -33,10 +33,11 @@ def test_ImageLabelCombine_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageLabelCombine_outputs(): - output_map = dict(OutputLabelMap=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputLabelMap=dict( + extensions=None, + position=-1, + ), ) outputs = ImageLabelCombine.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index 11999f2001..56d68199af 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -34,10 +34,11 @@ def test_MaskScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaskScalarVolume_outputs(): - output_map = dict(OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = MaskScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index 4c890aa30f..c0bf97e152 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -31,10 +31,11 @@ def test_MedianImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianImageFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = MedianImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index 99772b41db..cc39d5b7b1 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -33,10 +33,11 @@ def test_MultiplyScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyScalarVolumes_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = MultiplyScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index 28a9876943..12d7af77c4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -71,10 +71,11 @@ def test_ResampleScalarVectorDWIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVectorDWIVolume_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ResampleScalarVectorDWIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 62bf214bf4..106cd843a4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -33,10 +33,11 @@ def test_SubtractScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SubtractScalarVolumes_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = SubtractScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index ce7f97ec58..e63ed5923f 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -32,10 +32,11 @@ def test_ThresholdScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ThresholdScalarVolume_outputs(): - output_map = dict(OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ThresholdScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index c8100fd74b..89832bf9ba 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -34,10 +34,11 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VotingBinaryHoleFillingImageFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = VotingBinaryHoleFillingImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index a121f85614..f3c1ec6ff0 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -41,10 +41,11 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIUnbiasedNonLocalMeansFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = DWIUnbiasedNonLocalMeansFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index 6af3c1d54c..19b41f7127 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -30,10 +30,11 @@ def test_OtsuThresholdImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdImageFilter_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = OtsuThresholdImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index c73313751e..b9fa12f2aa 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -31,10 +31,11 @@ def test_OtsuThresholdSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdSegmentation_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = OtsuThresholdSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 66207fb604..7f1c259cd6 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -32,10 +32,11 @@ def test_ResampleScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVolume_outputs(): - output_map = dict(OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ResampleScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index c956ae34ec..6befb36860 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -37,10 +37,11 @@ def test_RobustStatisticsSegmenter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RobustStatisticsSegmenter_outputs(): - output_map = dict(segmentedImageFileName=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + segmentedImageFileName=dict( + extensions=None, + position=-1, + ), ) outputs = RobustStatisticsSegmenter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 8ffdd04355..5f880c08cb 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -34,10 +34,11 @@ def test_SimpleRegionGrowingSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SimpleRegionGrowingSegmentation_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = SimpleRegionGrowingSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index e18c0f0d5d..3669a21fc3 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -33,10 +33,11 @@ def test_GrayscaleModelMaker_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleModelMaker_outputs(): - output_map = dict(OutputGeometry=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputGeometry=dict( + extensions=None, + position=-1, + ), ) outputs = GrayscaleModelMaker.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index d196dbf5d8..faf982a342 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -31,10 +31,11 @@ def test_LabelMapSmoothing_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelMapSmoothing_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = LabelMapSmoothing.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 2e09b69bd1..c25d4ebcf3 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -32,10 +32,11 @@ def test_MergeModels_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeModels_outputs(): - output_map = dict(ModelOutput=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + ModelOutput=dict( + extensions=None, + position=-1, + ), ) outputs = MergeModels.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 2e684e3e65..d39ae392bd 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -33,10 +33,11 @@ def test_ModelToLabelMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ModelToLabelMap_outputs(): - output_map = dict(OutputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = ModelToLabelMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index 479bb842bb..d0d437915b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -28,10 +28,11 @@ def test_OrientScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OrientScalarVolume_outputs(): - output_map = dict(outputVolume=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + outputVolume=dict( + extensions=None, + position=-1, + ), ) outputs = OrientScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index b4bbdbe283..528ba47e1b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -32,10 +32,11 @@ def test_ProbeVolumeWithModel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ProbeVolumeWithModel_outputs(): - output_map = dict(OutputModel=dict( - extensions=None, - position=-1, - ), ) + output_map = dict( + OutputModel=dict( + extensions=None, + position=-1, + ), ) outputs = ProbeVolumeWithModel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/utility/tests/test_auto_Rename.py b/nipype/interfaces/utility/tests/test_auto_Rename.py index 70ced0ecdd..6b56badd6f 100644 --- a/nipype/interfaces/utility/tests/test_auto_Rename.py +++ b/nipype/interfaces/utility/tests/test_auto_Rename.py @@ -20,7 +20,7 @@ def test_Rename_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Rename_outputs(): - output_map = dict(out_file=dict(extensions=None, ), ) + output_map = dict(out_file=dict(), ) outputs = Rename.output_spec() for key, metadata in list(output_map.items()): From fc221f8dc3275c6e1b8f3baca6bcaab9fb265859 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Victor=20F=C3=A9rat?= Date: Fri, 30 Aug 2019 12:25:50 +0200 Subject: [PATCH 6/6] FIX command --- nipype/interfaces/mne/base.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py index 7f53071372..b6c8320e7a 100644 --- a/nipype/interfaces/mne/base.py +++ b/nipype/interfaces/mne/base.py @@ -89,12 +89,12 @@ class WatershedBEM(FSCommand): >>> bem.inputs.subject_id = 'subj1' >>> bem.inputs.subjects_dir = '.' >>> bem.cmdline - 'mne_watershed_bem --overwrite --subject subj1 --volume T1' + 'mne watershed_bem --overwrite --subject subj1 --volume T1' >>> bem.run() # doctest: +SKIP """ - _cmd = 'mne_watershed_bem' + _cmd = 'mne watershed_bem' input_spec = WatershedBEMInputSpec output_spec = WatershedBEMOutputSpec _additional_metadata = ['loc', 'altkey']