diff --git a/Makefile b/Makefile index 095452210a..48f2c112c2 100644 --- a/Makefile +++ b/Makefile @@ -56,7 +56,7 @@ inplace: $(PYTHON) setup.py build_ext -i test-code: in - py.test --doctest-module nipype + py.test --doctest-modules nipype test-coverage: clean-tests in py.test --doctest-modules --cov-config .coveragerc --cov=nipype nipype diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py index e28c77d467..d216a26a4b 100644 --- a/nipype/algorithms/tests/test_auto_ACompCor.py +++ b/nipype/algorithms/tests/test_auto_ACompCor.py @@ -22,7 +22,10 @@ def test_ACompCor_inputs(): ), num_components=dict(xor=['variance_threshold'], ), pre_filter=dict(usedefault=True, ), - realigned_file=dict(mandatory=True, ), + realigned_file=dict( + extensions=None, + mandatory=True, + ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), save_metadata=dict(usedefault=True, ), @@ -40,9 +43,9 @@ def test_ACompCor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ACompCor_outputs(): output_map = dict( - components_file=dict(), - metadata_file=dict(), - pre_filter_file=dict(), + components_file=dict(extensions=None, ), + metadata_file=dict(extensions=None, ), + pre_filter_file=dict(extensions=None, ), ) outputs = ACompCor.output_spec() diff --git a/nipype/algorithms/tests/test_auto_ActivationCount.py b/nipype/algorithms/tests/test_auto_ActivationCount.py index d6e3ff7165..0925ca1a95 100644 --- a/nipype/algorithms/tests/test_auto_ActivationCount.py +++ b/nipype/algorithms/tests/test_auto_ActivationCount.py @@ -15,9 +15,9 @@ def test_ActivationCount_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ActivationCount_outputs(): output_map = dict( - acm_neg=dict(), - acm_pos=dict(), - out_file=dict(), + acm_neg=dict(extensions=None, ), + acm_pos=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = ActivationCount.output_spec() diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py index feedcf46e8..4acd27380e 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVColumn.py +++ b/nipype/algorithms/tests/test_auto_AddCSVColumn.py @@ -7,8 +7,14 @@ def test_AddCSVColumn_inputs(): input_map = dict( extra_column_heading=dict(), extra_field=dict(), - in_file=dict(mandatory=True, ), - out_file=dict(usedefault=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), + out_file=dict( + extensions=None, + usedefault=True, + ), ) inputs = AddCSVColumn.input_spec() @@ -16,7 +22,7 @@ def test_AddCSVColumn_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVColumn_outputs(): - output_map = dict(csv_file=dict(), ) + output_map = dict(csv_file=dict(extensions=None, ), ) outputs = AddCSVColumn.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index 4666a147d2..3090c8b6a9 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -14,7 +14,7 @@ def test_AddCSVRow_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVRow_outputs(): - output_map = dict(csv_file=dict(), ) + output_map = dict(csv_file=dict(extensions=None, ), ) outputs = AddCSVRow.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_AddNoise.py b/nipype/algorithms/tests/test_auto_AddNoise.py index 6e0655a93e..bc9772d501 100644 --- a/nipype/algorithms/tests/test_auto_AddNoise.py +++ b/nipype/algorithms/tests/test_auto_AddNoise.py @@ -13,9 +13,12 @@ def test_AddNoise_inputs(): mandatory=True, usedefault=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - out_file=dict(), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_mask=dict(extensions=None, ), + out_file=dict(extensions=None, ), snr=dict(usedefault=True, ), ) inputs = AddNoise.input_spec() @@ -24,7 +27,7 @@ def test_AddNoise_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddNoise_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AddNoise.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 85c57b8823..cc09f4feff 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -8,7 +8,7 @@ def test_ArtifactDetect_inputs(): bound_by_brainmask=dict(usedefault=True, ), global_threshold=dict(usedefault=True, ), intersect_mask=dict(usedefault=True, ), - mask_file=dict(), + mask_file=dict(extensions=None, ), mask_threshold=dict(), mask_type=dict(mandatory=True, ), norm_threshold=dict( diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py index 3dbbd772c8..b175f45fa6 100644 --- a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py +++ b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py @@ -6,7 +6,10 @@ def test_CalculateNormalizedMoments_inputs(): input_map = dict( moment=dict(mandatory=True, ), - timeseries_file=dict(mandatory=True, ), + timeseries_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = CalculateNormalizedMoments.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py index ca263c77ac..b6a9b4dfb5 100644 --- a/nipype/algorithms/tests/test_auto_ComputeDVARS.py +++ b/nipype/algorithms/tests/test_auto_ComputeDVARS.py @@ -8,8 +8,14 @@ def test_ComputeDVARS_inputs(): figdpi=dict(usedefault=True, ), figformat=dict(usedefault=True, ), figsize=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_mask=dict( + extensions=None, + mandatory=True, + ), intensity_normalization=dict(usedefault=True, ), remove_zerovariance=dict(usedefault=True, ), save_all=dict(usedefault=True, ), @@ -29,13 +35,13 @@ def test_ComputeDVARS_outputs(): avg_nstd=dict(), avg_std=dict(), avg_vxstd=dict(), - fig_nstd=dict(), - fig_std=dict(), - fig_vxstd=dict(), - out_all=dict(), - out_nstd=dict(), - out_std=dict(), - out_vxstd=dict(), + fig_nstd=dict(extensions=None, ), + fig_std=dict(extensions=None, ), + fig_vxstd=dict(extensions=None, ), + out_all=dict(extensions=None, ), + out_nstd=dict(extensions=None, ), + out_std=dict(extensions=None, ), + out_vxstd=dict(extensions=None, ), ) outputs = ComputeDVARS.output_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index 0308653786..adaebaaa00 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -6,10 +6,22 @@ def test_ComputeMeshWarp_inputs(): input_map = dict( metric=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - out_warp=dict(usedefault=True, ), - surface1=dict(mandatory=True, ), - surface2=dict(mandatory=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), + out_warp=dict( + extensions=None, + usedefault=True, + ), + surface1=dict( + extensions=None, + mandatory=True, + ), + surface2=dict( + extensions=None, + mandatory=True, + ), weighting=dict(usedefault=True, ), ) inputs = ComputeMeshWarp.input_spec() @@ -20,8 +32,8 @@ def test_ComputeMeshWarp_inputs(): def test_ComputeMeshWarp_outputs(): output_map = dict( distance=dict(), - out_file=dict(), - out_warp=dict(), + out_file=dict(extensions=None, ), + out_warp=dict(extensions=None, ), ) outputs = ComputeMeshWarp.output_spec() diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index f8bf8a405f..a40f446d74 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -6,8 +6,14 @@ def test_CreateNifti_inputs(): input_map = dict( affine=dict(), - data_file=dict(mandatory=True, ), - header_file=dict(mandatory=True, ), + data_file=dict( + extensions=None, + mandatory=True, + ), + header_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = CreateNifti.input_spec() @@ -15,7 +21,7 @@ def test_CreateNifti_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateNifti_outputs(): - output_map = dict(nifti_file=dict(), ) + output_map = dict(nifti_file=dict(extensions=None, ), ) outputs = CreateNifti.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 2c5d098d73..5b3a165f56 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -5,10 +5,16 @@ def test_Distance_inputs(): input_map = dict( - mask_volume=dict(), + mask_volume=dict(extensions=None, ), method=dict(usedefault=True, ), - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + extensions=None, + mandatory=True, + ), + volume2=dict( + extensions=None, + mandatory=True, + ), ) inputs = Distance.input_spec() @@ -18,7 +24,7 @@ def test_Distance_inputs(): def test_Distance_outputs(): output_map = dict( distance=dict(), - histogram=dict(), + histogram=dict(extensions=None, ), point1=dict(), point2=dict(), ) diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py index 685dec61e8..47334ab77c 100644 --- a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py +++ b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py @@ -7,10 +7,19 @@ def test_FramewiseDisplacement_inputs(): input_map = dict( figdpi=dict(usedefault=True, ), figsize=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), normalize=dict(usedefault=True, ), - out_figure=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + out_figure=dict( + extensions=None, + usedefault=True, + ), + out_file=dict( + extensions=None, + usedefault=True, + ), parameter_source=dict(mandatory=True, ), radius=dict(usedefault=True, ), save_plot=dict(usedefault=True, ), @@ -24,8 +33,8 @@ def test_FramewiseDisplacement_inputs(): def test_FramewiseDisplacement_outputs(): output_map = dict( fd_average=dict(), - out_figure=dict(), - out_file=dict(), + out_figure=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = FramewiseDisplacement.output_spec() diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index e9e28aaa44..c92c033643 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -5,10 +5,13 @@ def test_FuzzyOverlap_inputs(): input_map = dict( - in_mask=dict(), + in_mask=dict(extensions=None, ), in_ref=dict(mandatory=True, ), in_tst=dict(mandatory=True, ), - out_file=dict(usedefault=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), weighting=dict(usedefault=True, ), ) inputs = FuzzyOverlap.input_spec() diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index f12e1f9b45..e583deaa10 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -4,14 +4,18 @@ def test_Gunzip_inputs(): - input_map = dict(in_file=dict(mandatory=True, ), ) + input_map = dict( + in_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = Gunzip.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_Gunzip_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Gunzip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index 1a4a2b1517..78e600bdd4 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -5,7 +5,10 @@ def test_ICC_inputs(): input_map = dict( - mask=dict(mandatory=True, ), + mask=dict( + extensions=None, + mandatory=True, + ), subjects_sessions=dict(mandatory=True, ), ) inputs = ICC.input_spec() @@ -15,9 +18,9 @@ def test_ICC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ICC_outputs(): output_map = dict( - icc_map=dict(), - session_var_map=dict(), - subject_var_map=dict(), + icc_map=dict(extensions=None, ), + session_var_map=dict(extensions=None, ), + subject_var_map=dict(extensions=None, ), ) outputs = ICC.output_spec() diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py index fcc1648bf9..6bc2a9caba 100644 --- a/nipype/algorithms/tests/test_auto_Matlab2CSV.py +++ b/nipype/algorithms/tests/test_auto_Matlab2CSV.py @@ -5,7 +5,10 @@ def test_Matlab2CSV_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), reshape_matrix=dict(usedefault=True, ), ) inputs = Matlab2CSV.input_spec() diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py index fd882e850a..f109fea025 100644 --- a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py +++ b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py @@ -9,7 +9,10 @@ def test_MergeCSVFiles_inputs(): extra_column_heading=dict(), extra_field=dict(), in_files=dict(mandatory=True, ), - out_file=dict(usedefault=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), row_heading_title=dict(usedefault=True, ), row_headings=dict(), ) @@ -19,7 +22,7 @@ def test_MergeCSVFiles_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeCSVFiles_outputs(): - output_map = dict(csv_file=dict(), ) + output_map = dict(csv_file=dict(extensions=None, ), ) outputs = MergeCSVFiles.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_MergeROIs.py b/nipype/algorithms/tests/test_auto_MergeROIs.py index 01b2b097a8..528f847b22 100644 --- a/nipype/algorithms/tests/test_auto_MergeROIs.py +++ b/nipype/algorithms/tests/test_auto_MergeROIs.py @@ -7,7 +7,7 @@ def test_MergeROIs_inputs(): input_map = dict( in_files=dict(), in_index=dict(), - in_reference=dict(), + in_reference=dict(extensions=None, ), ) inputs = MergeROIs.input_spec() @@ -15,7 +15,7 @@ def test_MergeROIs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeROIs_outputs(): - output_map = dict(merged_file=dict(), ) + output_map = dict(merged_file=dict(extensions=None, ), ) outputs = MergeROIs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index f89b16017b..664e6e2bc3 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -6,14 +6,23 @@ def test_MeshWarpMaths_inputs(): input_map = dict( float_trait=dict(), - in_surf=dict(mandatory=True, ), + in_surf=dict( + extensions=None, + mandatory=True, + ), operation=dict(usedefault=True, ), operator=dict( mandatory=True, usedefault=True, ), - out_file=dict(usedefault=True, ), - out_warp=dict(usedefault=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), + out_warp=dict( + extensions=None, + usedefault=True, + ), ) inputs = MeshWarpMaths.input_spec() @@ -22,8 +31,8 @@ def test_MeshWarpMaths_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MeshWarpMaths_outputs(): output_map = dict( - out_file=dict(), - out_warp=dict(), + out_file=dict(extensions=None, ), + out_warp=dict(extensions=None, ), ) outputs = MeshWarpMaths.output_spec() diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index b86fe3df03..4da9dad47d 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -4,7 +4,11 @@ def test_NonSteadyStateDetector_inputs(): - input_map = dict(in_file=dict(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/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py index 4c9a5584d0..59ffc9d9cb 100644 --- a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py +++ b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py @@ -6,7 +6,7 @@ def test_NormalizeProbabilityMapSet_inputs(): input_map = dict( in_files=dict(), - in_mask=dict(), + in_mask=dict(extensions=None, ), ) inputs = NormalizeProbabilityMapSet.input_spec() diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 9948e3675e..65461ede3c 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -6,10 +6,22 @@ def test_P2PDistance_inputs(): input_map = dict( metric=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - out_warp=dict(usedefault=True, ), - surface1=dict(mandatory=True, ), - surface2=dict(mandatory=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), + out_warp=dict( + extensions=None, + usedefault=True, + ), + surface1=dict( + extensions=None, + mandatory=True, + ), + surface2=dict( + extensions=None, + mandatory=True, + ), weighting=dict(usedefault=True, ), ) inputs = P2PDistance.input_spec() @@ -20,8 +32,8 @@ def test_P2PDistance_inputs(): def test_P2PDistance_outputs(): output_map = dict( distance=dict(), - out_file=dict(), - out_warp=dict(), + out_file=dict(extensions=None, ), + out_warp=dict(extensions=None, ), ) outputs = P2PDistance.output_spec() diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index 3b15c302e5..9787af79dd 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -5,11 +5,14 @@ def test_PickAtlas_inputs(): input_map = dict( - atlas=dict(mandatory=True, ), + atlas=dict( + extensions=None, + mandatory=True, + ), dilation_size=dict(usedefault=True, ), hemi=dict(usedefault=True, ), labels=dict(mandatory=True, ), - output_file=dict(), + output_file=dict(extensions=None, ), ) inputs = PickAtlas.input_spec() @@ -17,7 +20,7 @@ def test_PickAtlas_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PickAtlas_outputs(): - output_map = dict(mask_file=dict(), ) + output_map = dict(mask_file=dict(extensions=None, ), ) outputs = PickAtlas.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index b2ad79b5eb..b74728774c 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -5,11 +5,17 @@ def test_Similarity_inputs(): input_map = dict( - mask1=dict(), - mask2=dict(), + mask1=dict(extensions=None, ), + mask2=dict(extensions=None, ), metric=dict(usedefault=True, ), - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + extensions=None, + mandatory=True, + ), + volume2=dict( + extensions=None, + mandatory=True, + ), ) inputs = Similarity.input_spec() diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index dc12dd3a89..933793f363 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -53,8 +53,8 @@ def test_SpecifySparseModel_inputs(): def test_SpecifySparseModel_outputs(): output_map = dict( session_info=dict(), - sparse_png_file=dict(), - sparse_svg_file=dict(), + sparse_png_file=dict(extensions=None, ), + sparse_svg_file=dict(extensions=None, ), ) outputs = SpecifySparseModel.output_spec() diff --git a/nipype/algorithms/tests/test_auto_SplitROIs.py b/nipype/algorithms/tests/test_auto_SplitROIs.py index 963926666d..23633e98f4 100644 --- a/nipype/algorithms/tests/test_auto_SplitROIs.py +++ b/nipype/algorithms/tests/test_auto_SplitROIs.py @@ -5,8 +5,11 @@ def test_SplitROIs_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), - in_mask=dict(), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_mask=dict(extensions=None, ), roi_size=dict(), ) inputs = SplitROIs.input_spec() diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index 8c7ef276d9..9ed943ce2a 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -8,7 +8,10 @@ def test_StimulusCorrelation_inputs(): concatenated_design=dict(mandatory=True, ), intensity_values=dict(mandatory=True, ), realignment_parameters=dict(mandatory=True, ), - spm_mat_file=dict(mandatory=True, ), + spm_mat_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = StimulusCorrelation.input_spec() diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index c3bdcac192..ba448fd965 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -23,7 +23,10 @@ def test_TCompCor_inputs(): num_components=dict(xor=['variance_threshold'], ), percentile_threshold=dict(usedefault=True, ), pre_filter=dict(usedefault=True, ), - realigned_file=dict(mandatory=True, ), + realigned_file=dict( + extensions=None, + mandatory=True, + ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), save_metadata=dict(usedefault=True, ), @@ -41,10 +44,10 @@ def test_TCompCor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TCompCor_outputs(): output_map = dict( - components_file=dict(), + components_file=dict(extensions=None, ), high_variance_masks=dict(), - metadata_file=dict(), - pre_filter_file=dict(), + metadata_file=dict(extensions=None, ), + pre_filter_file=dict(extensions=None, ), ) outputs = TCompCor.output_spec() diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index b6965065a2..67b101724d 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -10,13 +10,20 @@ def test_WarpPoints_inputs(): usedefault=True, ), out_points=dict( + extensions=None, keep_extension=True, name_source='points', name_template='%s_warped', output_name='out_points', ), - points=dict(mandatory=True, ), - warp=dict(mandatory=True, ), + points=dict( + extensions=None, + mandatory=True, + ), + warp=dict( + extensions=None, + mandatory=True, + ), ) inputs = WarpPoints.input_spec() @@ -24,7 +31,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): - output_map = dict(out_points=dict(), ) + output_map = dict(out_points=dict(extensions=None, ), ) outputs = WarpPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index d4b8e474ff..815f0619c8 100644 --- a/nipype/interfaces/afni/base.py +++ b/nipype/interfaces/afni/base.py @@ -4,7 +4,6 @@ """Provide interface to AFNI commands.""" from __future__ import (print_function, division, unicode_literals, absolute_import) -from builtins import object, str from future.utils import raise_from import os @@ -12,8 +11,7 @@ from distutils import spawn from ... import logging, LooseVersion -from ...utils.filemanip import split_filename, fname_presuffix - +from ...utils.filemanip import split_filename from ..base import (CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec, PackageInfo) from ...external.due import BibTeX @@ -23,14 +21,15 @@ class Info(PackageInfo): - """Handle afni output type and version information. - """ + """Handle afni output type and version information.""" + __outputtype = 'AFNI' ftypes = {'NIFTI': '.nii', 'AFNI': '', 'NIFTI_GZ': '.nii.gz'} version_cmd = 'afni --version' @staticmethod def parse_version(raw_info): + """Check and parse AFNI's version.""" version_stamp = raw_info.split('\n')[0].split('Version ')[1] if version_stamp.startswith('AFNI'): version_stamp = version_stamp.split('AFNI_')[1] @@ -46,7 +45,8 @@ def parse_version(raw_info): @classmethod def output_type_to_ext(cls, outputtype): - """Get the file extension for the given output type. + """ + Get the file extension for the given output type. Parameters ---------- @@ -57,8 +57,8 @@ def output_type_to_ext(cls, outputtype): ------- extension : str The file extension for the output type. - """ + """ try: return cls.ftypes[outputtype] except KeyError as e: @@ -67,24 +67,28 @@ def output_type_to_ext(cls, outputtype): @classmethod def outputtype(cls): - """AFNI has no environment variables, - Output filetypes get set in command line calls - Nipype uses AFNI as default + """ + Set default output filetype. + + AFNI has no environment variables, Output filetypes get set in command line calls + Nipype uses ``AFNI`` as default Returns ------- None + """ - # warn(('AFNI has no environment variable that sets filetype ' - # 'Nipype uses NIFTI_GZ as default')) return 'AFNI' @staticmethod def standard_image(img_name): - '''Grab an image from the standard location. + """ + Grab an image from the standard location. - Could be made more fancy to allow for more relocatability''' + Could be made more fancy to allow for more relocatability + + """ clout = CommandLine( 'which afni', ignore_exception=True, @@ -101,6 +105,7 @@ def standard_image(img_name): class AFNICommandBase(CommandLine): """ A base class to fix a linking problem in OSX and afni. + See http://afni.nimh.nih.gov/afni/community/board/read.php?1,145346,145347#msg-145347 """ @@ -127,7 +132,8 @@ class AFNICommandOutputSpec(TraitedSpec): class AFNICommand(AFNICommandBase): - """Shared options for several AFNI commands """ + """Shared options for several AFNI commands.""" + input_spec = AFNICommandInputSpec _outputtype = None @@ -162,6 +168,7 @@ class AFNICommand(AFNICommandBase): @property def num_threads(self): + """Get number of threads.""" return self.inputs.num_threads @num_threads.setter @@ -170,20 +177,21 @@ def num_threads(self, value): @classmethod def set_default_output_type(cls, outputtype): - """Set the default output type for AFNI classes. + """ + Set the default output type for AFNI classes. This method is used to set the default output type for all afni subclasses. However, setting this will not update the output type for any existing instances. For these, assign the .inputs.outputtype. """ - if outputtype in Info.ftypes: cls._outputtype = outputtype else: raise AttributeError('Invalid AFNI outputtype: %s' % outputtype) def __init__(self, **inputs): + """Instantiate an AFNI command tool wrapper.""" super(AFNICommand, self).__init__(**inputs) self.inputs.on_trait_change(self._output_update, 'outputtype') @@ -199,13 +207,16 @@ def __init__(self, **inputs): self._output_update() def _nthreads_update(self): - """Update environment with new number of threads""" + """Update environment with new number of threads.""" self.inputs.environ['OMP_NUM_THREADS'] = '%d' % self.inputs.num_threads def _output_update(self): - """ i think? updates class private attribute based on instance input - in fsl also updates ENVIRON variable....not valid in afni - as it uses no environment variables + """ + Update the internal property with the provided input. + + i think? updates class private attribute based on instance input + in fsl also updates ENVIRON variable....not valid in afni + as it uses no environment variables """ self._outputtype = self.inputs.outputtype @@ -226,59 +237,9 @@ def _list_outputs(self): outputs[name] = outputs[name] + "+orig.BRIK" return outputs - def _gen_fname(self, - basename, - cwd=None, - suffix=None, - change_ext=True, - ext=None): - """Generate a filename based on the given parameters. - - The filename will take the form: cwd/basename. - If change_ext is True, it will use the extentions specified in - intputs.output_type. - - Parameters - ---------- - basename : str - Filename to base the new filename on. - cwd : str - Path to prefix to the new filename. (default is os.getcwd()) - suffix : str - Suffix to add to the `basename`. (defaults is '' ) - change_ext : bool - Flag to change the filename extension to the FSL output type. - (default True) - - Returns - ------- - fname : str - New filename based on given parameters. - - """ - - if basename == '': - msg = 'Unable to generate filename for command %s. ' % self.cmd - msg += 'basename is not set!' - raise ValueError(msg) - if cwd is None: - cwd = os.getcwd() - if ext is None: - ext = Info.output_type_to_ext(self.inputs.outputtype) - if change_ext: - if suffix: - suffix = ''.join((suffix, ext)) - else: - suffix = ext - if suffix is None: - suffix = '' - fname = fname_presuffix( - basename, suffix=suffix, use_ext=False, newpath=cwd) - return fname - def no_afni(): - """ Checks if AFNI is available """ + """Check whether AFNI is not available.""" if Info.version() is None: return True return False @@ -292,8 +253,11 @@ class AFNIPythonCommandInputSpec(CommandLineInputSpec): class AFNIPythonCommand(AFNICommand): + """A subtype of AFNI command line for Python scripts.""" + @property def cmd(self): + """Revise the command path.""" orig_cmd = super(AFNIPythonCommand, self).cmd found = spawn.find_executable(orig_cmd) return found if found is not None else orig_cmd diff --git a/nipype/interfaces/afni/model.py b/nipype/interfaces/afni/model.py index 2cccdfe869..e091a87c57 100644 --- a/nipype/interfaces/afni/model.py +++ b/nipype/interfaces/afni/model.py @@ -1,11 +1,13 @@ # -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft = python sts = 4 ts = 4 sw = 4 et: -"""AFNI modeling interfaces +""" +AFNI modeling interfaces. Examples -------- See the docstrings of the individual classes for examples. + """ from __future__ import (print_function, division, unicode_literals, absolute_import) @@ -17,7 +19,7 @@ from ...external.due import BibTeX from .base import (AFNICommandBase, AFNICommand, AFNICommandInputSpec, - AFNICommandOutputSpec) + AFNICommandOutputSpec, Info) class DeconvolveInputSpec(AFNICommandInputSpec): @@ -307,6 +309,58 @@ def _list_outputs(self): return outputs + def _gen_fname(self, + basename, + cwd=None, + suffix=None, + change_ext=True, + ext=None): + """Generate a filename based on the given parameters. + + The filename will take the form: cwd/basename. + If change_ext is True, it will use the extentions specified in + intputs.output_type. + + Parameters + ---------- + basename : str + Filename to base the new filename on. + cwd : str + Path to prefix to the new filename. (default is os.getcwd()) + suffix : str + Suffix to add to the `basename`. (defaults is '' ) + change_ext : bool + Flag to change the filename extension to the FSL output type. + (default True) + + Returns + ------- + fname : str + New filename based on given parameters. + + """ + from nipype.utils.filemanip import fname_presuffix + + if basename == '': + msg = 'Unable to generate filename for command %s. ' % self.cmd + msg += 'basename is not set!' + raise ValueError(msg) + if cwd is None: + cwd = os.getcwd() + if ext is None: + ext = Info.output_type_to_ext(self.inputs.outputtype) + if change_ext: + if suffix: + suffix = ''.join((suffix, ext)) + else: + suffix = ext + if suffix is None: + suffix = '' + fname = fname_presuffix( + basename, suffix=suffix, use_ext=False, newpath=cwd) + return fname + + class RemlfitInputSpec(AFNICommandInputSpec): # mandatory files in_files = InputMultiPath( diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index c2ccb1988a..ee81ee7e2f 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -1,8 +1,7 @@ # -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -"""AFNI preprocessing interfaces -""" +"""AFNI preprocessing interfaces.""" from __future__ import (print_function, division, unicode_literals, absolute_import) from builtins import open @@ -757,8 +756,7 @@ class BandpassInputSpec(AFNICommandInputSpec): desc='output file from 3dBandpass', argstr='-prefix %s', position=1, - name_source='in_file', - genfile=True) + name_source='in_file') lowpass = traits.Float( desc='lowpass', argstr='%f', position=-2, mandatory=True) highpass = traits.Float( @@ -3087,43 +3085,42 @@ class QwarpInputSpec(AFNICommandInputSpec): copyfile=False) out_file = File( argstr='-prefix %s', - name_template='%s_QW', + name_template='ppp_%s', name_source=['in_file'], - genfile=True, - desc='out_file ppp' - 'Sets the prefix for the output datasets.' - '* The source dataset is warped to match the base' - 'and gets prefix \'ppp\'. (Except if \'-plusminus\' is used.)' - '* The final interpolation to this output dataset is' - 'done using the \'wsinc5\' method. See the output of' - ' 3dAllineate -HELP' - '(in the "Modifying \'-final wsinc5\'" section) for' - 'the lengthy technical details.' - '* The 3D warp used is saved in a dataset with' - 'prefix \'ppp_WARP\' -- this dataset can be used' - 'with 3dNwarpApply and 3dNwarpCat, for example.' - '* To be clear, this is the warp from source dataset' - ' coordinates to base dataset coordinates, where the' - ' values at each base grid point are the xyz displacments' - ' needed to move that grid point\'s xyz values to the' - ' corresponding xyz values in the source dataset:' - ' base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)' - ' Another way to think of this warp is that it \'pulls\'' - ' values back from source space to base space.' - '* 3dNwarpApply would use \'ppp_WARP\' to transform datasets' - 'aligned with the source dataset to be aligned with the' - 'base dataset.' - '** If you do NOT want this warp saved, use the option \'-nowarp\'.' - '-->> (However, this warp is usually the most valuable possible output!)' - '* If you want to calculate and save the inverse 3D warp,' - 'use the option \'-iwarp\'. This inverse warp will then be' - 'saved in a dataset with prefix \'ppp_WARPINV\'.' - '* This inverse warp could be used to transform data from base' - 'space to source space, if you need to do such an operation.' - '* You can easily compute the inverse later, say by a command like' - ' 3dNwarpCat -prefix Z_WARPINV \'INV(Z_WARP+tlrc)\'' - 'or the inverse can be computed as needed in 3dNwarpApply, like' - ' 3dNwarpApply -nwarp \'INV(Z_WARP+tlrc)\' -source Dataset.nii ...') + desc="""\ +Sets the prefix/suffix for the output datasets. +* The source dataset is warped to match the base +and gets prefix 'ppp'. (Except if '-plusminus' is used +* The final interpolation to this output dataset is +done using the 'wsinc5' method. See the output of + 3dAllineate -HELP +(in the "Modifying '-final wsinc5'" section) for +the lengthy technical details. +* The 3D warp used is saved in a dataset with +prefix 'ppp_WARP' -- this dataset can be used +with 3dNwarpApply and 3dNwarpCat, for example. +* To be clear, this is the warp from source dataset + coordinates to base dataset coordinates, where the + values at each base grid point are the xyz displacments + needed to move that grid point's xyz values to the + corresponding xyz values in the source dataset: + base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z) + Another way to think of this warp is that it 'pulls' + values back from source space to base space. +* 3dNwarpApply would use 'ppp_WARP' to transform datasets +aligned with the source dataset to be aligned with the +base dataset. +** If you do NOT want this warp saved, use the option '-nowarp'. +-->> (However, this warp is usually the most valuable possible output!) +* If you want to calculate and save the inverse 3D warp, +use the option '-iwarp'. This inverse warp will then be +saved in a dataset with prefix 'ppp_WARPINV'. +* This inverse warp could be used to transform data from base +space to source space, if you need to do such an operation. +* You can easily compute the inverse later, say by a command like + 3dNwarpCat -prefix Z_WARPINV 'INV(Z_WARP+tlrc)' +or the inverse can be computed as needed in 3dNwarpApply, like + 3dNwarpApply -nwarp 'INV(Z_WARP+tlrc)' -source Dataset.nii ...""") resample = traits.Bool( desc='This option simply resamples the source dataset to match the' 'base dataset grid. You can use this if the two datasets' @@ -3619,7 +3616,8 @@ class Qwarp(AFNICommand): >>> qwarp.inputs.base_file = 'sub-01_dir-RL_epi.nii.gz' >>> qwarp.inputs.plusminus = True >>> qwarp.cmdline - '3dQwarp -base sub-01_dir-RL_epi.nii.gz -source sub-01_dir-LR_epi.nii.gz -nopadWARP -prefix sub-01_dir-LR_epi_QW -plusminus' + '3dQwarp -base sub-01_dir-RL_epi.nii.gz -source sub-01_dir-LR_epi.nii.gz -nopadWARP \ +-prefix ppp_sub-01_dir-LR_epi -plusminus' >>> res = qwarp.run() # doctest: +SKIP >>> from nipype.interfaces import afni @@ -3628,7 +3626,7 @@ class Qwarp(AFNICommand): >>> qwarp.inputs.base_file = 'mni.nii' >>> qwarp.inputs.resample = True >>> qwarp.cmdline - '3dQwarp -base mni.nii -source structural.nii -prefix structural_QW -resample' + '3dQwarp -base mni.nii -source structural.nii -prefix ppp_structural -resample' >>> res = qwarp.run() # doctest: +SKIP >>> from nipype.interfaces import afni @@ -3642,7 +3640,8 @@ class Qwarp(AFNICommand): >>> qwarp.inputs.iwarp = True >>> qwarp.inputs.blur = [0,3] >>> qwarp.cmdline - '3dQwarp -base epi.nii -blur 0.0 3.0 -source structural.nii -iwarp -prefix anatSSQ.nii.gz -resample -verb -lpc' + '3dQwarp -base epi.nii -blur 0.0 3.0 -source structural.nii -iwarp -prefix anatSSQ.nii.gz \ +-resample -verb -lpc' >>> res = qwarp.run() # doctest: +SKIP >>> from nipype.interfaces import afni @@ -3652,7 +3651,7 @@ class Qwarp(AFNICommand): >>> qwarp.inputs.duplo = True >>> qwarp.inputs.blur = [0,3] >>> qwarp.cmdline - '3dQwarp -base mni.nii -blur 0.0 3.0 -duplo -source structural.nii -prefix structural_QW' + '3dQwarp -base mni.nii -blur 0.0 3.0 -duplo -source structural.nii -prefix ppp_structural' >>> res = qwarp.run() # doctest: +SKIP >>> from nipype.interfaces import afni @@ -3674,7 +3673,8 @@ class Qwarp(AFNICommand): >>> qwarp2.inputs.inilev = 7 >>> qwarp2.inputs.iniwarp = ['Q25_warp+tlrc.HEAD'] >>> qwarp2.cmdline - '3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inilev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11' + '3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inilev 7 -iniwarp Q25_\ +warp+tlrc.HEAD -prefix Q11' >>> res2 = qwarp2.run() # doctest: +SKIP >>> res2 = qwarp2.run() # doctest: +SKIP >>> qwarp3 = afni.Qwarp() @@ -3683,7 +3683,8 @@ class Qwarp(AFNICommand): >>> qwarp3.inputs.allineate = True >>> qwarp3.inputs.allineate_opts = '-cose lpa -verb' >>> qwarp3.cmdline - "3dQwarp -allineate -allineate_opts '-cose lpa -verb' -base mni.nii -source structural.nii -prefix structural_QW" + "3dQwarp -allineate -allineate_opts '-cose lpa -verb' -base mni.nii -source structural.nii \ +-prefix ppp_structural" >>> res3 = qwarp3.run() # doctest: +SKIP """ _cmd = '3dQwarp' input_spec = QwarpInputSpec @@ -3759,8 +3760,8 @@ class QwarpPlusMinusInputSpec(QwarpInputSpec): new_name='in_file', copyfile=False) out_file = File( + 'Qwarp.nii.gz', argstr='-prefix %s', - value='Qwarp.nii.gz', position=0, usedefault=True, desc="Output file") diff --git a/nipype/interfaces/afni/svm.py b/nipype/interfaces/afni/svm.py index d465c1caaa..4a813ddb7e 100644 --- a/nipype/interfaces/afni/svm.py +++ b/nipype/interfaces/afni/svm.py @@ -1,8 +1,7 @@ # -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft = python sts = 4 ts = 4 sw = 4 et: -"""Afni svm interfaces -""" +"""AFNI's svm interfaces.""" from __future__ import (print_function, division, unicode_literals, absolute_import) diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py index 55cb12c27f..db17259c17 100644 --- a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py +++ b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py @@ -13,12 +13,14 @@ def test_ABoverlap_inputs(): in_file_a=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-3, ), in_file_b=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-2, ), @@ -29,6 +31,7 @@ def test_ABoverlap_inputs(): ), out_file=dict( argstr=' |& tee %s', + extensions=None, position=-1, ), outputtype=dict(), @@ -41,7 +44,7 @@ def test_ABoverlap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ABoverlap_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ABoverlap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index 724c98dcb2..f5b7184391 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -16,6 +16,7 @@ def test_AFNICommand_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_afni', ), diff --git a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py index ba2411edfb..e530fc1309 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py @@ -16,6 +16,7 @@ def test_AFNIPythonCommand_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_afni', ), diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index d89519d571..0c8bf19a7a 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -14,6 +14,7 @@ def test_AFNItoNIFTI_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -31,6 +32,7 @@ def test_AFNItoNIFTI_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, hash_files=False, name_source='in_file', name_template='%s.nii', @@ -44,7 +46,7 @@ def test_AFNItoNIFTI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AFNItoNIFTI_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AFNItoNIFTI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py index dfbfc648f7..d177480726 100644 --- a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py +++ b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py @@ -8,6 +8,7 @@ def test_AlignEpiAnatPy_inputs(): anat=dict( argstr='-anat %s', copyfile=False, + extensions=None, mandatory=True, ), anat2epi=dict(argstr='-anat2epi', ), @@ -25,6 +26,7 @@ def test_AlignEpiAnatPy_inputs(): in_file=dict( argstr='-epi %s', copyfile=False, + extensions=None, mandatory=True, ), outputtype=dict(), @@ -50,16 +52,16 @@ def test_AlignEpiAnatPy_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AlignEpiAnatPy_outputs(): output_map = dict( - anat_al_mat=dict(), - anat_al_orig=dict(), - epi_al_mat=dict(), - epi_al_orig=dict(), - epi_al_tlrc_mat=dict(), - epi_reg_al_mat=dict(), - epi_tlrc_al=dict(), - epi_vr_al_mat=dict(), - epi_vr_motion=dict(), - skullstrip=dict(), + anat_al_mat=dict(extensions=None, ), + anat_al_orig=dict(extensions=None, ), + epi_al_mat=dict(extensions=None, ), + epi_al_orig=dict(extensions=None, ), + epi_al_tlrc_mat=dict(extensions=None, ), + epi_reg_al_mat=dict(extensions=None, ), + epi_tlrc_al=dict(extensions=None, ), + epi_vr_al_mat=dict(extensions=None, ), + epi_vr_motion=dict(extensions=None, ), + skullstrip=dict(extensions=None, ), ) outputs = AlignEpiAnatPy.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index be02af14da..0b110e669a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -7,6 +7,7 @@ def test_Allineate_inputs(): input_map = dict( allcostx=dict( argstr='-allcostx |& tee %s', + extensions=None, position=-1, xor=[ 'out_file', 'out_matrix', 'out_param_file', 'out_weight_file' @@ -30,19 +31,25 @@ def test_Allineate_inputs(): in_file=dict( argstr='-source %s', copyfile=False, + extensions=None, mandatory=True, ), in_matrix=dict( argstr='-1Dmatrix_apply %s', + extensions=None, position=-3, xor=['out_matrix'], ), in_param_file=dict( argstr='-1Dparam_apply %s', + extensions=None, xor=['out_param_file'], ), interpolation=dict(argstr='-interp %s', ), - master=dict(argstr='-master %s', ), + master=dict( + argstr='-master %s', + extensions=None, + ), maxrot=dict(argstr='-maxrot %f', ), maxscl=dict(argstr='-maxscl %f', ), maxshf=dict(argstr='-maxshf %f', ), @@ -61,6 +68,7 @@ def test_Allineate_inputs(): one_pass=dict(argstr='-onepass', ), out_file=dict( argstr='-prefix %s', + extensions=None, hash_files=False, name_source='in_file', name_template='%s_allineate', @@ -68,10 +76,12 @@ def test_Allineate_inputs(): ), out_matrix=dict( argstr='-1Dmatrix_save %s', + extensions=None, xor=['in_matrix', 'allcostx'], ), out_param_file=dict( argstr='-1Dparam_save %s', + extensions=None, xor=['in_param_file', 'allcostx'], ), out_weight_file=dict( @@ -81,11 +91,17 @@ def test_Allineate_inputs(): outputtype=dict(), overwrite=dict(argstr='-overwrite', ), quiet=dict(argstr='-quiet', ), - reference=dict(argstr='-base %s', ), + reference=dict( + argstr='-base %s', + extensions=None, + ), replacebase=dict(argstr='-replacebase', ), replacemeth=dict(argstr='-replacemeth %s', ), source_automask=dict(argstr='-source_automask+%d', ), - source_mask=dict(argstr='-source_mask %s', ), + source_mask=dict( + argstr='-source_mask %s', + extensions=None, + ), two_best=dict(argstr='-twobest %d', ), two_blur=dict(argstr='-twoblur %f', ), two_first=dict(argstr='-twofirst', ), @@ -98,6 +114,7 @@ def test_Allineate_inputs(): weight_file=dict( argstr='-weight %s', deprecated='1.0.0', + extensions=None, new_name='weight', ), zclip=dict(argstr='-zclip', ), @@ -109,11 +126,11 @@ def test_Allineate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Allineate_outputs(): output_map = dict( - allcostx=dict(), - out_file=dict(), - out_matrix=dict(), - out_param_file=dict(), - out_weight_file=dict(), + allcostx=dict(extensions=None, ), + out_file=dict(extensions=None, ), + out_matrix=dict(extensions=None, ), + out_param_file=dict(extensions=None, ), + out_weight_file=dict(extensions=None, ), ) outputs = Allineate.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py index bb00b3b585..8d251a9620 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py @@ -17,6 +17,7 @@ def test_AutoTLRC_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, ), no_ss=dict(argstr='-no_ss', ), @@ -28,7 +29,7 @@ def test_AutoTLRC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AutoTLRC_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AutoTLRC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index 424b7d25b1..34c99aa0c0 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -14,16 +14,21 @@ def test_AutoTcorrelate_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), mask_only_targets=dict( argstr='-mask_only_targets', xor=['mask_source'], ), mask_source=dict( argstr='-mask_source %s', + extensions=None, xor=['mask_only_targets'], ), num_threads=dict( @@ -32,6 +37,7 @@ def test_AutoTcorrelate_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_similarity_matrix.1D', ), @@ -44,7 +50,7 @@ def test_AutoTcorrelate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AutoTcorrelate_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AutoTcorrelate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index f158263c54..ab7826469e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -13,6 +13,7 @@ def test_Autobox_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, ), no_clustering=dict(argstr='-noclust', ), @@ -22,6 +23,7 @@ def test_Autobox_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_autobox', ), @@ -35,7 +37,7 @@ def test_Autobox_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Autobox_outputs(): output_map = dict( - out_file=dict(), + out_file=dict(extensions=None, ), x_max=dict(), x_min=dict(), y_max=dict(), diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index efffd19cba..223419ad71 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -8,6 +8,7 @@ def test_Automask_inputs(): args=dict(argstr='%s', ), brain_file=dict( argstr='-apply_prefix %s', + extensions=None, name_source='in_file', name_template='%s_masked', ), @@ -21,6 +22,7 @@ def test_Automask_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -30,6 +32,7 @@ def test_Automask_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_mask', ), @@ -42,8 +45,8 @@ def test_Automask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Automask_outputs(): output_map = dict( - brain_file=dict(), - out_file=dict(), + brain_file=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = Automask.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Axialize.py b/nipype/interfaces/afni/tests/test_auto_Axialize.py index 62b425c932..b89957b6f9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Axialize.py +++ b/nipype/interfaces/afni/tests/test_auto_Axialize.py @@ -21,6 +21,7 @@ def test_Axialize_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-2, ), @@ -31,6 +32,7 @@ def test_Axialize_inputs(): orientation=dict(argstr='-orient %s', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_axialize', ), @@ -47,7 +49,7 @@ def test_Axialize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Axialize_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Axialize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index fb0861a747..c4a3be3022 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -21,6 +21,7 @@ def test_Bandpass_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -32,6 +33,7 @@ def test_Bandpass_inputs(): ), mask=dict( argstr='-mask %s', + extensions=None, position=2, ), nfft=dict(argstr='-nfft %d', ), @@ -42,11 +44,14 @@ def test_Bandpass_inputs(): nohash=True, usedefault=True, ), - orthogonalize_dset=dict(argstr='-dsort %s', ), + orthogonalize_dset=dict( + argstr='-dsort %s', + extensions=None, + ), orthogonalize_file=dict(argstr='-ort %s', ), out_file=dict( argstr='-prefix %s', - genfile=True, + extensions=None, name_source='in_file', name_template='%s_bp', position=1, @@ -60,7 +65,7 @@ def test_Bandpass_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bandpass_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Bandpass.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index 334116d945..bf42a587b7 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -19,11 +19,18 @@ def test_BlurInMask_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=1, ), - mask=dict(argstr='-mask %s', ), - multimask=dict(argstr='-Mmask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), + multimask=dict( + argstr='-Mmask %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, @@ -34,6 +41,7 @@ def test_BlurInMask_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_blur', position=-1, @@ -47,7 +55,7 @@ def test_BlurInMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BlurInMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BlurInMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py index 2f88a1edcb..38864aa09f 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py @@ -7,7 +7,10 @@ def test_BlurToFWHM_inputs(): input_map = dict( args=dict(argstr='%s', ), automask=dict(argstr='-automask', ), - blurmaster=dict(argstr='-blurmaster %s', ), + blurmaster=dict( + argstr='-blurmaster %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -16,15 +19,20 @@ def test_BlurToFWHM_inputs(): fwhmxy=dict(argstr='-FWHMxy %f', ), in_file=dict( argstr='-input %s', + extensions=None, mandatory=True, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_afni', ), @@ -36,7 +44,7 @@ def test_BlurToFWHM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BlurToFWHM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BlurToFWHM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index 0056df5980..d7f36eb79b 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -12,11 +12,13 @@ def test_BrickStat_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), mask=dict( argstr='-mask %s', + extensions=None, position=2, ), max=dict(argstr='-max', ), diff --git a/nipype/interfaces/afni/tests/test_auto_Bucket.py b/nipype/interfaces/afni/tests/test_auto_Bucket.py index c3faf87a09..dfd28d6ccd 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bucket.py +++ b/nipype/interfaces/afni/tests/test_auto_Bucket.py @@ -21,6 +21,7 @@ def test_Bucket_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_template='buck', ), outputtype=dict(), @@ -31,7 +32,7 @@ def test_Bucket_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bucket_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Bucket.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index 28863d5a4b..677cd5dbbf 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -17,24 +17,31 @@ def test_Calc_inputs(): ), in_file_a=dict( argstr='-a %s', + extensions=None, mandatory=True, position=0, ), in_file_b=dict( argstr='-b %s', + extensions=None, position=1, ), in_file_c=dict( argstr='-c %s', + extensions=None, position=2, ), num_threads=dict( nohash=True, usedefault=True, ), - other=dict(argstr='', ), + other=dict( + argstr='', + extensions=None, + ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file_a', name_template='%s_calc', ), @@ -50,7 +57,7 @@ def test_Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index 3da86c66d6..345806f746 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -31,6 +31,7 @@ def test_Cat_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -67,7 +68,7 @@ def test_Cat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Cat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py index b67ab485d4..2250878719 100644 --- a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py +++ b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py @@ -33,6 +33,7 @@ def test_CatMatvec_inputs(): ), out_file=dict( argstr=' > %s', + extensions=None, keep_extension=False, mandatory=True, name_source='in_file', @@ -47,7 +48,7 @@ def test_CatMatvec_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CatMatvec_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = CatMatvec.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_CenterMass.py b/nipype/interfaces/afni/tests/test_auto_CenterMass.py index 322218a50d..41eddd5ed7 100644 --- a/nipype/interfaces/afni/tests/test_auto_CenterMass.py +++ b/nipype/interfaces/afni/tests/test_auto_CenterMass.py @@ -10,6 +10,7 @@ def test_CenterMass_inputs(): automask=dict(argstr='-automask', ), cm_file=dict( argstr='> %s', + extensions=None, hash_files=False, keep_extension=False, name_source='in_file', @@ -23,11 +24,15 @@ def test_CenterMass_inputs(): in_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-2, ), local_ijk=dict(argstr='-local_ijk', ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), roi_vals=dict(argstr='-roi_vals %s', ), set_cm=dict(argstr='-set %f %f %f', ), ) @@ -39,8 +44,8 @@ def test_CenterMass_inputs(): def test_CenterMass_outputs(): output_map = dict( cm=dict(), - cm_file=dict(), - out_file=dict(), + cm_file=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = CenterMass.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index 8b8c61208d..f9b3dbf705 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -22,6 +22,7 @@ def test_ClipLevel_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), diff --git a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py index 06ba3a54f2..39613d7981 100644 --- a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py +++ b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py @@ -12,6 +12,7 @@ def test_ConvertDset_inputs(): ), in_file=dict( argstr='-input %s', + extensions=None, mandatory=True, position=-2, ), @@ -21,6 +22,7 @@ def test_ConvertDset_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, mandatory=True, position=-1, ), @@ -37,7 +39,7 @@ def test_ConvertDset_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertDset_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ConvertDset.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index a8e67d5607..447fcaa24f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -13,6 +13,7 @@ def test_Copy_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-2, ), @@ -22,6 +23,7 @@ def test_Copy_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source='in_file', name_template='%s_copy', position=-1, @@ -35,7 +37,7 @@ def test_Copy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Copy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py index ae42a77019..713589dbc0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py +++ b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py @@ -5,13 +5,19 @@ def test_Deconvolve_inputs(): input_map = dict( - STATmask=dict(argstr='-STATmask %s', ), + STATmask=dict( + argstr='-STATmask %s', + extensions=None, + ), TR_1D=dict(argstr='-TR_1D %f', ), allzero_OK=dict(argstr='-allzero_OK', ), args=dict(argstr='%s', ), automask=dict(argstr='-automask', ), cbucket=dict(argstr='-cbucket %s', ), - censor=dict(argstr='-censor %s', ), + censor=dict( + argstr='-censor %s', + extensions=None, + ), dmbase=dict(argstr='-dmbase', ), dname=dict(argstr='-D%s=%s', ), environ=dict( @@ -43,13 +49,19 @@ def test_Deconvolve_inputs(): position=1, sep=' ', ), - input1D=dict(argstr='-input1D %s', ), + input1D=dict( + argstr='-input1D %s', + extensions=None, + ), legendre=dict(argstr='-legendre', ), local_times=dict( argstr='-local_times', xor=['global_times'], ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), noblock=dict(argstr='-noblock', ), nocond=dict(argstr='-nocond', ), nodmbase=dict(argstr='-nodmbase', ), @@ -69,7 +81,10 @@ def test_Deconvolve_inputs(): nohash=True, ), ortvec=dict(argstr='-ortvec %s %s', ), - out_file=dict(argstr='-bucket %s', ), + out_file=dict( + argstr='-bucket %s', + extensions=None, + ), outputtype=dict(), polort=dict(argstr='-polort %d', ), rmsmin=dict(argstr='-rmsmin %f', ), @@ -96,7 +111,10 @@ def test_Deconvolve_inputs(): xor=['sat'], ), vout=dict(argstr='-vout', ), - x1D=dict(argstr='-x1D %s', ), + x1D=dict( + argstr='-x1D %s', + extensions=None, + ), x1D_stop=dict(argstr='-x1D_stop', ), ) inputs = Deconvolve.input_spec() @@ -106,10 +124,10 @@ def test_Deconvolve_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Deconvolve_outputs(): output_map = dict( - cbucket=dict(), - out_file=dict(), - reml_script=dict(), - x1D=dict(), + cbucket=dict(extensions=None, ), + out_file=dict(extensions=None, ), + reml_script=dict(extensions=None, ), + x1D=dict(extensions=None, ), ) outputs = Deconvolve.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py index 664cca5985..721f161af3 100644 --- a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py +++ b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py @@ -15,10 +15,14 @@ def test_DegreeCentrality_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, @@ -26,6 +30,7 @@ def test_DegreeCentrality_inputs(): oned_file=dict(argstr='-out1D %s', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_afni', ), @@ -41,8 +46,8 @@ def test_DegreeCentrality_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DegreeCentrality_outputs(): output_map = dict( - oned_file=dict(), - out_file=dict(), + oned_file=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = DegreeCentrality.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index ff0b8b532a..cb495e9c5b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -13,6 +13,7 @@ def test_Despike_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -22,6 +23,7 @@ def test_Despike_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_despike', ), @@ -33,7 +35,7 @@ def test_Despike_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Despike_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Despike.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 1938529cf7..6c1bd3cbba 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -13,6 +13,7 @@ def test_Detrend_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -22,6 +23,7 @@ def test_Detrend_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_detrend', ), @@ -33,7 +35,7 @@ def test_Detrend_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Detrend_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Detrend.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Dot.py b/nipype/interfaces/afni/tests/test_auto_Dot.py index 7623e90ca7..66e535dc54 100644 --- a/nipype/interfaces/afni/tests/test_auto_Dot.py +++ b/nipype/interfaces/afni/tests/test_auto_Dot.py @@ -22,7 +22,10 @@ def test_Dot_inputs(): argstr='%s ...', position=-2, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), mrange=dict(argstr='-mrange %s %s', ), num_threads=dict( nohash=True, @@ -30,6 +33,7 @@ def test_Dot_inputs(): ), out_file=dict( argstr=' |& tee %s', + extensions=None, position=-1, ), outputtype=dict(), @@ -42,7 +46,7 @@ def test_Dot_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dot_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Dot.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ECM.py b/nipype/interfaces/afni/tests/test_auto_ECM.py index 8a4793fb7f..9f69ea3c69 100644 --- a/nipype/interfaces/afni/tests/test_auto_ECM.py +++ b/nipype/interfaces/afni/tests/test_auto_ECM.py @@ -18,10 +18,14 @@ def test_ECM_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), max_iter=dict(argstr='-max_iter %d', ), memory=dict(argstr='-memory %f', ), num_threads=dict( @@ -30,6 +34,7 @@ def test_ECM_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_afni', ), @@ -46,7 +51,7 @@ def test_ECM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ECM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ECM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Edge3.py b/nipype/interfaces/afni/tests/test_auto_Edge3.py index 8fc6953c28..722037d2d1 100644 --- a/nipype/interfaces/afni/tests/test_auto_Edge3.py +++ b/nipype/interfaces/afni/tests/test_auto_Edge3.py @@ -22,6 +22,7 @@ def test_Edge3_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=0, ), @@ -35,6 +36,7 @@ def test_Edge3_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, position=-1, ), outputtype=dict(), @@ -50,7 +52,7 @@ def test_Edge3_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Edge3_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Edge3.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 35c1360a6e..9f29aa0b91 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -17,25 +17,32 @@ def test_Eval_inputs(): ), in_file_a=dict( argstr='-a %s', + extensions=None, mandatory=True, position=0, ), in_file_b=dict( argstr='-b %s', + extensions=None, position=1, ), in_file_c=dict( argstr='-c %s', + extensions=None, position=2, ), num_threads=dict( nohash=True, usedefault=True, ), - other=dict(argstr='', ), + other=dict( + argstr='', + extensions=None, + ), out1D=dict(argstr='-1D', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file_a', name_template='%s_calc', ), @@ -50,7 +57,7 @@ def test_Eval_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Eval_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Eval.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_FWHMx.py b/nipype/interfaces/afni/tests/test_auto_FWHMx.py index 14ab26fa4f..ac2fdffbb0 100644 --- a/nipype/interfaces/afni/tests/test_auto_FWHMx.py +++ b/nipype/interfaces/afni/tests/test_auto_FWHMx.py @@ -39,17 +39,23 @@ def test_FWHMx_inputs(): ), in_file=dict( argstr='-input %s', + extensions=None, mandatory=True, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), out_detrend=dict( argstr='-detprefix %s', + extensions=None, keep_extension=False, name_source='in_file', name_template='%s_detrend', ), out_file=dict( argstr='> %s', + extensions=None, keep_extension=False, name_source='in_file', name_template='%s_fwhmx.out', @@ -57,6 +63,7 @@ def test_FWHMx_inputs(): ), out_subbricks=dict( argstr='-out %s', + extensions=None, keep_extension=False, name_source='in_file', name_template='%s_subbricks.out', @@ -72,10 +79,10 @@ def test_FWHMx_outputs(): output_map = dict( acf_param=dict(), fwhm=dict(), - out_acf=dict(), - out_detrend=dict(), - out_file=dict(), - out_subbricks=dict(), + out_acf=dict(extensions=None, ), + out_detrend=dict(extensions=None, ), + out_file=dict(extensions=None, ), + out_subbricks=dict(extensions=None, ), ) outputs = FWHMx.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index 931e5ff244..8550747727 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -16,12 +16,14 @@ def test_Fim_inputs(): ), ideal_file=dict( argstr='-ideal_file %s', + extensions=None, mandatory=True, position=2, ), in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=1, ), @@ -35,6 +37,7 @@ def test_Fim_inputs(): ), out_file=dict( argstr='-bucket %s', + extensions=None, name_source='in_file', name_template='%s_fim', ), @@ -46,7 +49,7 @@ def test_Fim_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Fim_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Fim.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 69cd955cbc..ee3dd6672a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -17,6 +17,7 @@ def test_Fourier_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -30,6 +31,7 @@ def test_Fourier_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_fourier', ), @@ -42,7 +44,7 @@ def test_Fourier_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Fourier_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Fourier.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_GCOR.py b/nipype/interfaces/afni/tests/test_auto_GCOR.py index 9d603dda36..60dfd9f7b3 100644 --- a/nipype/interfaces/afni/tests/test_auto_GCOR.py +++ b/nipype/interfaces/afni/tests/test_auto_GCOR.py @@ -13,12 +13,14 @@ def test_GCOR_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), mask=dict( argstr='-mask %s', copyfile=False, + extensions=None, ), nfirst=dict(argstr='-nfirst %d', ), no_demean=dict(argstr='-no_demean', ), diff --git a/nipype/interfaces/afni/tests/test_auto_Hist.py b/nipype/interfaces/afni/tests/test_auto_Hist.py index 48499a9605..65f4b0566b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Hist.py +++ b/nipype/interfaces/afni/tests/test_auto_Hist.py @@ -14,21 +14,27 @@ def test_Hist_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=1, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), max_value=dict(argstr='-max %f', ), min_value=dict(argstr='-min %f', ), nbin=dict(argstr='-nbin %d', ), out_file=dict( argstr='-prefix %s', + extensions=None, keep_extension=False, name_source=['in_file'], name_template='%s_hist', ), out_show=dict( argstr='> %s', + extensions=None, keep_extension=False, name_source='in_file', name_template='%s_hist.out', @@ -46,8 +52,8 @@ def test_Hist_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Hist_outputs(): output_map = dict( - out_file=dict(), - out_show=dict(), + out_file=dict(extensions=None, ), + out_show=dict(extensions=None, ), ) outputs = Hist.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_LFCD.py b/nipype/interfaces/afni/tests/test_auto_LFCD.py index 9cbde10b56..51a5fffb68 100644 --- a/nipype/interfaces/afni/tests/test_auto_LFCD.py +++ b/nipype/interfaces/afni/tests/test_auto_LFCD.py @@ -15,16 +15,21 @@ def test_LFCD_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_afni', ), @@ -38,7 +43,7 @@ def test_LFCD_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LFCD_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = LFCD.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py index 22f0b717d8..ed3e61d74d 100644 --- a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py +++ b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py @@ -16,11 +16,13 @@ def test_LocalBistat_inputs(): ), in_file1=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), in_file2=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -56,7 +58,7 @@ def test_LocalBistat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LocalBistat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = LocalBistat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Localstat.py b/nipype/interfaces/afni/tests/test_auto_Localstat.py index c2f53c3db0..011ce44da8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Localstat.py +++ b/nipype/interfaces/afni/tests/test_auto_Localstat.py @@ -17,6 +17,7 @@ def test_Localstat_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -63,7 +64,7 @@ def test_Localstat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Localstat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Localstat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index 1644bee878..070686dd8d 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/nipype/interfaces/afni/tests/test_auto_MaskTool.py @@ -36,6 +36,7 @@ def test_MaskTool_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_mask', ), @@ -49,7 +50,7 @@ def test_MaskTool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaskTool_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MaskTool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index a318e685a9..9185f94266 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -13,11 +13,13 @@ def test_Maskave_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-2, ), mask=dict( argstr='-mask %s', + extensions=None, position=1, ), num_threads=dict( @@ -26,6 +28,7 @@ def test_Maskave_inputs(): ), out_file=dict( argstr='> %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_maskave.1D', @@ -43,7 +46,7 @@ def test_Maskave_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Maskave_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Maskave.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index 2e422e68db..9db304bb3d 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -14,11 +14,13 @@ def test_Means_inputs(): ), in_file_a=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), in_file_b=dict( argstr='%s', + extensions=None, position=-1, ), mask_inter=dict(argstr='-mask_inter', ), @@ -30,6 +32,7 @@ def test_Means_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file_a', name_template='%s_mean', ), @@ -45,7 +48,7 @@ def test_Means_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Means_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Means.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index c36ee6f7a1..934bf17b96 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -27,6 +27,7 @@ def test_Merge_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_files', name_template='%s_merge', ), @@ -38,7 +39,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Notes.py b/nipype/interfaces/afni/tests/test_auto_Notes.py index 965bacb000..51084ba3b9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Notes.py +++ b/nipype/interfaces/afni/tests/test_auto_Notes.py @@ -19,6 +19,7 @@ def test_Notes_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -26,7 +27,10 @@ def test_Notes_inputs(): nohash=True, usedefault=True, ), - out_file=dict(argstr='%s', ), + out_file=dict( + argstr='%s', + extensions=None, + ), outputtype=dict(), rep_history=dict( argstr='-HH "%s"', @@ -40,7 +44,7 @@ def test_Notes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Notes_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Notes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py b/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py index 48b59a2968..c4c8dc6804 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py @@ -17,6 +17,7 @@ def test_NwarpAdjust_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, keep_extension=True, name_source='in_files', name_template='%s_NwarpAdjust', @@ -34,7 +35,7 @@ def test_NwarpAdjust_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpAdjust_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = NwarpAdjust.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index 63f6baa044..e00457f4f3 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -23,6 +23,7 @@ def test_NwarpApply_inputs(): master=dict(argstr='-master %s', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_Nwarp', ), @@ -46,7 +47,7 @@ def test_NwarpApply_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpApply_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = NwarpApply.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py index c6b3689c9e..b5724c98dd 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py @@ -27,6 +27,7 @@ def test_NwarpCat_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_files', name_template='%s_NwarpCat', ), @@ -40,7 +41,7 @@ def test_NwarpCat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpCat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = NwarpCat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index fe037851af..f8e664a727 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -16,10 +16,12 @@ def test_OneDToolPy_inputs(): ), in_file=dict( argstr='-infile %s', + extensions=None, mandatory=True, ), out_file=dict( argstr='-write %s', + extensions=None, xor=['show_cormat_warnings'], ), outputtype=dict(), @@ -41,7 +43,7 @@ def test_OneDToolPy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OneDToolPy_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = OneDToolPy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py index a63fbb8bef..2a1eb61af3 100644 --- a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py +++ b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py @@ -26,6 +26,7 @@ def test_OutlierCount_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -39,15 +40,18 @@ def test_OutlierCount_inputs(): ), mask=dict( argstr='-mask %s', + extensions=None, xor=['autoclip', 'automask'], ), out_file=dict( + extensions=None, keep_extension=False, name_source=['in_file'], name_template='%s_outliers', ), outliers_file=dict( argstr='-save %s', + extensions=None, keep_extension=True, name_source=['in_file'], name_template='%s_outliers', @@ -67,8 +71,8 @@ def test_OutlierCount_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_OutlierCount_outputs(): output_map = dict( - out_file=dict(), - out_outliers=dict(), + out_file=dict(extensions=None, ), + out_outliers=dict(extensions=None, ), ) outputs = OutlierCount.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py index 679a3e0393..27fd6727c4 100644 --- a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py +++ b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py @@ -23,6 +23,7 @@ def test_QualityIndex_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -32,10 +33,12 @@ def test_QualityIndex_inputs(): ), mask=dict( argstr='-mask %s', + extensions=None, xor=['autoclip', 'automask'], ), out_file=dict( argstr='> %s', + extensions=None, keep_extension=False, name_source=['in_file'], name_template='%s_tqual', @@ -56,7 +59,7 @@ def test_QualityIndex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_QualityIndex_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = QualityIndex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index f6df3d0ab5..3ef8c2e9b2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -24,6 +24,7 @@ def test_Qwarp_inputs(): base_file=dict( argstr='-base %s', copyfile=False, + extensions=None, mandatory=True, ), baxopt=dict( @@ -41,6 +42,7 @@ def test_Qwarp_inputs(): emask=dict( argstr='-emask %s', copyfile=False, + extensions=None, ), environ=dict( nohash=True, @@ -53,6 +55,7 @@ def test_Qwarp_inputs(): gridlist=dict( argstr='-gridlist %s', copyfile=False, + extensions=None, xor=['duplo', 'plusminus'], ), hel=dict( @@ -62,6 +65,7 @@ def test_Qwarp_inputs(): in_file=dict( argstr='-source %s', copyfile=False, + extensions=None, mandatory=True, ), inilev=dict( @@ -117,9 +121,9 @@ def test_Qwarp_inputs(): ), out_file=dict( argstr='-prefix %s', - genfile=True, + extensions=None, name_source=['in_file'], - name_template='%s_QW', + name_template='ppp_%s', ), out_weight_file=dict(argstr='-wtprefix %s', ), outputtype=dict(), @@ -141,7 +145,10 @@ def test_Qwarp_inputs(): xor=['quiet'], ), wball=dict(argstr='-wball %s', ), - weight=dict(argstr='-weight %s', ), + weight=dict( + argstr='-weight %s', + extensions=None, + ), wmask=dict(argstr='-wpass %s %f', ), workhard=dict( argstr='-workhard', @@ -155,11 +162,11 @@ def test_Qwarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Qwarp_outputs(): output_map = dict( - base_warp=dict(), - source_warp=dict(), - warped_base=dict(), - warped_source=dict(), - weights=dict(), + base_warp=dict(extensions=None, ), + source_warp=dict(extensions=None, ), + warped_base=dict(extensions=None, ), + warped_source=dict(extensions=None, ), + weights=dict(extensions=None, ), ) outputs = Qwarp.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index 340f3a0e4a..ca27a0d682 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -24,6 +24,7 @@ def test_QwarpPlusMinus_inputs(): base_file=dict( argstr='-base %s', copyfile=False, + extensions=None, mandatory=True, ), baxopt=dict( @@ -41,6 +42,7 @@ def test_QwarpPlusMinus_inputs(): emask=dict( argstr='-emask %s', copyfile=False, + extensions=None, ), environ=dict( nohash=True, @@ -53,6 +55,7 @@ def test_QwarpPlusMinus_inputs(): gridlist=dict( argstr='-gridlist %s', copyfile=False, + extensions=None, xor=['duplo', 'plusminus'], ), hel=dict( @@ -62,6 +65,7 @@ def test_QwarpPlusMinus_inputs(): in_file=dict( argstr='-source %s', copyfile=False, + extensions=None, mandatory=True, ), inilev=dict( @@ -117,6 +121,7 @@ def test_QwarpPlusMinus_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, position=0, usedefault=True, ), @@ -141,6 +146,7 @@ def test_QwarpPlusMinus_inputs(): argstr='-source %s', copyfile=False, deprecated='1.1.2', + extensions=None, new_name='in_file', ), verb=dict( @@ -148,7 +154,10 @@ def test_QwarpPlusMinus_inputs(): xor=['quiet'], ), wball=dict(argstr='-wball %s', ), - weight=dict(argstr='-weight %s', ), + weight=dict( + argstr='-weight %s', + extensions=None, + ), wmask=dict(argstr='-wpass %s %f', ), workhard=dict( argstr='-workhard', @@ -162,11 +171,11 @@ def test_QwarpPlusMinus_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_QwarpPlusMinus_outputs(): output_map = dict( - base_warp=dict(), - source_warp=dict(), - warped_base=dict(), - warped_source=dict(), - weights=dict(), + base_warp=dict(extensions=None, ), + source_warp=dict(extensions=None, ), + warped_base=dict(extensions=None, ), + warped_source=dict(extensions=None, ), + weights=dict(extensions=None, ), ) outputs = QwarpPlusMinus.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index fbda92e9a5..d3c956f7c5 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -21,22 +21,28 @@ def test_ROIStats_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), mask=dict( argstr='-mask %s', deprecated='1.1.4', + extensions=None, new_name='mask_file', position=3, ), mask_f2short=dict(argstr='-mask_f2short', ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), nobriklab=dict(argstr='-nobriklab', ), nomeanout=dict(argstr='-nomeanout', ), num_roi=dict(argstr='-numroi %s', ), out_file=dict( argstr='> %s', + extensions=None, keep_extension=False, name_source='in_file', name_template='%s_roistat.1D', @@ -56,7 +62,7 @@ def test_ROIStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ROIStats_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ROIStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ReHo.py b/nipype/interfaces/afni/tests/test_auto_ReHo.py index 1809759485..0edcedcdaf 100644 --- a/nipype/interfaces/afni/tests/test_auto_ReHo.py +++ b/nipype/interfaces/afni/tests/test_auto_ReHo.py @@ -17,10 +17,14 @@ def test_ReHo_inputs(): ), in_file=dict( argstr='-inset %s', + extensions=None, mandatory=True, position=1, ), - label_set=dict(argstr='-in_rois %s', ), + label_set=dict( + argstr='-in_rois %s', + extensions=None, + ), mask_file=dict(argstr='-mask %s', ), neighborhood=dict( argstr='-nneigh %s', @@ -46,8 +50,8 @@ def test_ReHo_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ReHo_outputs(): output_map = dict( - out_file=dict(), - out_vals=dict(), + out_file=dict(extensions=None, ), + out_vals=dict(extensions=None, ), ) outputs = ReHo.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index 4983eafc81..c289f94ce5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -11,7 +11,10 @@ def test_Refit_inputs(): atrint=dict(argstr='-atrint %s %s', ), atrstring=dict(argstr='-atrstring %s %s', ), deoblique=dict(argstr='-deoblique', ), - duporigin_file=dict(argstr='-duporigin %s', ), + duporigin_file=dict( + argstr='-duporigin %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -19,6 +22,7 @@ def test_Refit_inputs(): in_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-1, ), @@ -39,7 +43,7 @@ def test_Refit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Refit_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Refit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index 4cdc8b2ff2..f2e6703bf6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -5,7 +5,10 @@ def test_Remlfit_inputs(): input_map = dict( - STATmask=dict(argstr='-STATmask %s', ), + STATmask=dict( + argstr='-STATmask %s', + extensions=None, + ), addbase=dict( argstr='-addbase %s', copyfile=False, @@ -19,6 +22,7 @@ def test_Remlfit_inputs(): dsort=dict( argstr='-dsort %s', copyfile=False, + extensions=None, ), dsort_nods=dict( argstr='-dsort_nods', @@ -28,10 +32,19 @@ def test_Remlfit_inputs(): nohash=True, usedefault=True, ), - errts_file=dict(argstr='-Rerrts %s', ), - fitts_file=dict(argstr='-Rfitts %s', ), + errts_file=dict( + argstr='-Rerrts %s', + extensions=None, + ), + fitts_file=dict( + argstr='-Rfitts %s', + extensions=None, + ), fout=dict(argstr='-fout', ), - glt_file=dict(argstr='-Rglt %s', ), + glt_file=dict( + argstr='-Rglt %s', + extensions=None, + ), gltsym=dict(argstr='-gltsym "%s" %s...', ), in_files=dict( argstr='-input "%s"', @@ -39,13 +52,17 @@ def test_Remlfit_inputs(): mandatory=True, sep=' ', ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), matim=dict( argstr='-matim %s', xor=['matrix'], ), matrix=dict( argstr='-matrix %s', + extensions=None, mandatory=True, ), nobout=dict(argstr='-nobout', ), @@ -58,28 +75,58 @@ def test_Remlfit_inputs(): nohash=True, usedefault=True, ), - obeta=dict(argstr='-Obeta %s', ), - obuck=dict(argstr='-Obuck %s', ), - oerrts=dict(argstr='-Oerrts %s', ), - ofitts=dict(argstr='-Ofitts %s', ), - oglt=dict(argstr='-Oglt %s', ), - out_file=dict(argstr='-Rbuck %s', ), + obeta=dict( + argstr='-Obeta %s', + extensions=None, + ), + obuck=dict( + argstr='-Obuck %s', + extensions=None, + ), + oerrts=dict( + argstr='-Oerrts %s', + extensions=None, + ), + ofitts=dict( + argstr='-Ofitts %s', + extensions=None, + ), + oglt=dict( + argstr='-Oglt %s', + extensions=None, + ), + out_file=dict( + argstr='-Rbuck %s', + extensions=None, + ), outputtype=dict(), - ovar=dict(argstr='-Ovar %s', ), + ovar=dict( + argstr='-Ovar %s', + extensions=None, + ), polort=dict( argstr='-polort %d', xor=['matrix'], ), quiet=dict(argstr='-quiet', ), - rbeta_file=dict(argstr='-Rbeta %s', ), + rbeta_file=dict( + argstr='-Rbeta %s', + extensions=None, + ), rout=dict(argstr='-rout', ), slibase=dict(argstr='-slibase %s', ), slibase_sm=dict(argstr='-slibase_sm %s', ), tout=dict(argstr='-tout', ), usetemp=dict(argstr='-usetemp', ), - var_file=dict(argstr='-Rvar %s', ), + var_file=dict( + argstr='-Rvar %s', + extensions=None, + ), verb=dict(argstr='-verb', ), - wherr_file=dict(argstr='-Rwherr %s', ), + wherr_file=dict( + argstr='-Rwherr %s', + extensions=None, + ), ) inputs = Remlfit.input_spec() @@ -88,19 +135,19 @@ def test_Remlfit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Remlfit_outputs(): output_map = dict( - errts_file=dict(), - fitts_file=dict(), - glt_file=dict(), - obeta=dict(), - obuck=dict(), - oerrts=dict(), - ofitts=dict(), - oglt=dict(), - out_file=dict(), - ovar=dict(), - rbeta_file=dict(), - var_file=dict(), - wherr_file=dict(), + errts_file=dict(extensions=None, ), + fitts_file=dict(extensions=None, ), + glt_file=dict(extensions=None, ), + obeta=dict(extensions=None, ), + obuck=dict(extensions=None, ), + oerrts=dict(extensions=None, ), + ofitts=dict(extensions=None, ), + oglt=dict(extensions=None, ), + out_file=dict(extensions=None, ), + ovar=dict(extensions=None, ), + rbeta_file=dict(extensions=None, ), + var_file=dict(extensions=None, ), + wherr_file=dict(extensions=None, ), ) outputs = Remlfit.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 9ab2309307..560d883d75 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -13,6 +13,7 @@ def test_Resample_inputs(): in_file=dict( argstr='-inset %s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -24,6 +25,7 @@ def test_Resample_inputs(): orientation=dict(argstr='-orient %s', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_resample', ), @@ -37,7 +39,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 4c2a1c2393..49f3c5ec98 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -8,10 +8,12 @@ def test_Retroicor_inputs(): args=dict(argstr='%s', ), card=dict( argstr='-card %s', + extensions=None, position=-2, ), cardphase=dict( argstr='-cardphase %s', + extensions=None, hash_files=False, position=-6, ), @@ -22,6 +24,7 @@ def test_Retroicor_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -35,6 +38,7 @@ def test_Retroicor_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_retroicor', position=1, @@ -42,10 +46,12 @@ def test_Retroicor_inputs(): outputtype=dict(), resp=dict( argstr='-resp %s', + extensions=None, position=-3, ), respphase=dict( argstr='-respphase %s', + extensions=None, hash_files=False, position=-7, ), @@ -60,7 +66,7 @@ def test_Retroicor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Retroicor_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Retroicor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index 4b31d3a11c..98654e36f3 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -13,6 +13,7 @@ def test_SVMTest_inputs(): ), in_file=dict( argstr='-testvol %s', + extensions=None, mandatory=True, ), model=dict( @@ -29,10 +30,14 @@ def test_SVMTest_inputs(): options=dict(argstr='%s', ), out_file=dict( argstr='-predictions %s', + extensions=None, name_template='%s_predictions', ), outputtype=dict(), - testlabels=dict(argstr='-testlabels %s', ), + testlabels=dict( + argstr='-testlabels %s', + extensions=None, + ), ) inputs = SVMTest.input_spec() @@ -40,7 +45,7 @@ def test_SVMTest_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVMTest_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SVMTest.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index ddb3f8c05f..03e2d95e52 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -7,12 +7,16 @@ def test_SVMTrain_inputs(): input_map = dict( alphas=dict( argstr='-alpha %s', + extensions=None, name_source='in_file', name_template='%s_alphas', suffix='_alphas', ), args=dict(argstr='%s', ), - censor=dict(argstr='-censor %s', ), + censor=dict( + argstr='-censor %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -20,17 +24,20 @@ def test_SVMTrain_inputs(): in_file=dict( argstr='-trainvol %s', copyfile=False, + extensions=None, mandatory=True, ), kernel=dict(argstr='-kernel %s', ), mask=dict( argstr='-mask %s', copyfile=False, + extensions=None, position=-1, ), max_iterations=dict(argstr='-max_iterations %d', ), model=dict( argstr='-model %s', + extensions=None, name_source='in_file', name_template='%s_model', suffix='_model', @@ -43,12 +50,16 @@ def test_SVMTrain_inputs(): options=dict(argstr='%s', ), out_file=dict( argstr='-bucket %s', + extensions=None, name_source='in_file', name_template='%s_vectors', suffix='_bucket', ), outputtype=dict(), - trainlabels=dict(argstr='-trainlabels %s', ), + trainlabels=dict( + argstr='-trainlabels %s', + extensions=None, + ), ttype=dict( argstr='-type %s', mandatory=True, @@ -62,9 +73,9 @@ def test_SVMTrain_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SVMTrain_outputs(): output_map = dict( - alphas=dict(), - model=dict(), - out_file=dict(), + alphas=dict(extensions=None, ), + model=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = SVMTrain.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Seg.py b/nipype/interfaces/afni/tests/test_auto_Seg.py index e93d81a7aa..56720a7e38 100644 --- a/nipype/interfaces/afni/tests/test_auto_Seg.py +++ b/nipype/interfaces/afni/tests/test_auto_Seg.py @@ -18,6 +18,7 @@ def test_Seg_inputs(): in_file=dict( argstr='-anat %s', copyfile=True, + extensions=None, mandatory=True, position=-1, ), @@ -37,7 +38,7 @@ def test_Seg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Seg_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Seg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index e960369787..6fc8d3ad3d 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -13,6 +13,7 @@ def test_SkullStrip_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=1, ), @@ -22,6 +23,7 @@ def test_SkullStrip_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_skullstrip', ), @@ -33,7 +35,7 @@ def test_SkullStrip_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SkullStrip_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SkullStrip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Synthesize.py b/nipype/interfaces/afni/tests/test_auto_Synthesize.py index 87278098fb..8c7ee9afaf 100644 --- a/nipype/interfaces/afni/tests/test_auto_Synthesize.py +++ b/nipype/interfaces/afni/tests/test_auto_Synthesize.py @@ -10,6 +10,7 @@ def test_Synthesize_inputs(): cbucket=dict( argstr='-cbucket %s', copyfile=False, + extensions=None, mandatory=True, ), cenfill=dict(argstr='-cenfill %s', ), @@ -21,6 +22,7 @@ def test_Synthesize_inputs(): matrix=dict( argstr='-matrix %s', copyfile=False, + extensions=None, mandatory=True, ), num_threads=dict( @@ -29,6 +31,7 @@ def test_Synthesize_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_template='syn', ), outputtype=dict(), @@ -43,7 +46,7 @@ def test_Synthesize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Synthesize_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Synthesize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 5c51b02637..042916893e 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -22,6 +22,7 @@ def test_TCat_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_files', name_template='%s_tcat', ), @@ -38,7 +39,7 @@ def test_TCat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TCat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py index 09b21ea408..4f60118e35 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py +++ b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py @@ -22,6 +22,7 @@ def test_TCatSubBrick_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, genfile=True, ), outputtype=dict(), @@ -36,7 +37,7 @@ def test_TCatSubBrick_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCatSubBrick_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TCatSubBrick.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index e1b23a3387..5fe7fffb81 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -21,6 +21,7 @@ def test_TCorr1D_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, keep_extension=True, name_source='xset', name_template='%s_correlation.nii.gz', @@ -44,11 +45,13 @@ def test_TCorr1D_inputs(): xset=dict( argstr=' %s', copyfile=False, + extensions=None, mandatory=True, position=-2, ), y_1d=dict( argstr=' %s', + extensions=None, mandatory=True, position=-1, ), @@ -59,7 +62,7 @@ def test_TCorr1D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCorr1D_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TCorr1D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 32778fcf11..1ea4c0790e 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -7,6 +7,7 @@ def test_TCorrMap_inputs(): input_map = dict( absolute_threshold=dict( argstr='-Thresh %f %s', + extensions=None, name_source='in_file', suffix='_thresh', xor=('absolute_threshold', 'var_absolute_threshold', @@ -16,12 +17,14 @@ def test_TCorrMap_inputs(): automask=dict(argstr='-automask', ), average_expr=dict( argstr='-Aexpr %s %s', + extensions=None, name_source='in_file', suffix='_aexpr', xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), average_expr_nonzero=dict( argstr='-Cexpr %s %s', + extensions=None, name_source='in_file', suffix='_cexpr', xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), @@ -30,10 +33,12 @@ def test_TCorrMap_inputs(): blur_fwhm=dict(argstr='-Gblur %f', ), correlation_maps=dict( argstr='-CorrMap %s', + extensions=None, name_source='in_file', ), correlation_maps_masked=dict( argstr='-CorrMask %s', + extensions=None, name_source='in_file', ), environ=dict( @@ -43,6 +48,7 @@ def test_TCorrMap_inputs(): expr=dict(), histogram=dict( argstr='-Hist %d %s', + extensions=None, name_source='in_file', suffix='_hist', ), @@ -50,11 +56,16 @@ def test_TCorrMap_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), mean_file=dict( argstr='-Mean %s', + extensions=None, name_source='in_file', suffix='_mean', ), @@ -64,24 +75,28 @@ def test_TCorrMap_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_file'], name_template='%s_afni', ), outputtype=dict(), pmean=dict( argstr='-Pmean %s', + extensions=None, name_source='in_file', suffix='_pmean', ), polort=dict(argstr='-polort %d', ), qmean=dict( argstr='-Qmean %s', + extensions=None, name_source='in_file', suffix='_qmean', ), regress_out_timeseries=dict(argstr='-ort %s', ), seeds=dict( argstr='-seed %s', + extensions=None, xor='seeds_width', ), seeds_width=dict( @@ -90,6 +105,7 @@ def test_TCorrMap_inputs(): ), sum_expr=dict( argstr='-Sexpr %s %s', + extensions=None, name_source='in_file', suffix='_sexpr', xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), @@ -97,6 +113,7 @@ def test_TCorrMap_inputs(): thresholds=dict(), var_absolute_threshold=dict( argstr='-VarThresh %f %f %f %s', + extensions=None, name_source='in_file', suffix='_varthresh', xor=('absolute_threshold', 'var_absolute_threshold', @@ -104,6 +121,7 @@ def test_TCorrMap_inputs(): ), var_absolute_threshold_normalize=dict( argstr='-VarThreshN %f %f %f %s', + extensions=None, name_source='in_file', suffix='_varthreshn', xor=('absolute_threshold', 'var_absolute_threshold', @@ -111,6 +129,7 @@ def test_TCorrMap_inputs(): ), zmean=dict( argstr='-Zmean %s', + extensions=None, name_source='in_file', suffix='_zmean', ), @@ -122,19 +141,19 @@ def test_TCorrMap_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TCorrMap_outputs(): output_map = dict( - absolute_threshold=dict(), - average_expr=dict(), - average_expr_nonzero=dict(), - correlation_maps=dict(), - correlation_maps_masked=dict(), - histogram=dict(), - mean_file=dict(), - pmean=dict(), - qmean=dict(), - sum_expr=dict(), - var_absolute_threshold=dict(), - var_absolute_threshold_normalize=dict(), - zmean=dict(), + absolute_threshold=dict(extensions=None, ), + average_expr=dict(extensions=None, ), + average_expr_nonzero=dict(extensions=None, ), + correlation_maps=dict(extensions=None, ), + correlation_maps_masked=dict(extensions=None, ), + histogram=dict(extensions=None, ), + mean_file=dict(extensions=None, ), + pmean=dict(extensions=None, ), + qmean=dict(extensions=None, ), + sum_expr=dict(extensions=None, ), + var_absolute_threshold=dict(extensions=None, ), + var_absolute_threshold_normalize=dict(extensions=None, ), + zmean=dict(extensions=None, ), ) outputs = TCorrMap.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index 8d773f429e..fd3569b0bf 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -16,6 +16,7 @@ def test_TCorrelate_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='xset', name_template='%s_tcorr', ), @@ -25,12 +26,14 @@ def test_TCorrelate_inputs(): xset=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-2, ), yset=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -41,7 +44,7 @@ def test_TCorrelate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCorrelate_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TCorrelate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TNorm.py b/nipype/interfaces/afni/tests/test_auto_TNorm.py index 3fb246684b..a8ba790aa1 100644 --- a/nipype/interfaces/afni/tests/test_auto_TNorm.py +++ b/nipype/interfaces/afni/tests/test_auto_TNorm.py @@ -14,6 +14,7 @@ def test_TNorm_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -27,6 +28,7 @@ def test_TNorm_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_tnorm', ), @@ -39,7 +41,7 @@ def test_TNorm_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TNorm_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TNorm.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TProject.py b/nipype/interfaces/afni/tests/test_auto_TProject.py index ba4efd6189..66f7caadc4 100644 --- a/nipype/interfaces/afni/tests/test_auto_TProject.py +++ b/nipype/interfaces/afni/tests/test_auto_TProject.py @@ -14,9 +14,15 @@ def test_TProject_inputs(): bandpass=dict(argstr='-bandpass %g %g', ), blur=dict(argstr='-blur %g', ), cenmode=dict(argstr='-cenmode %s', ), - censor=dict(argstr='-censor %s', ), + censor=dict( + argstr='-censor %s', + extensions=None, + ), censortr=dict(argstr='-CENSORTR %s', ), - concat=dict(argstr='-concat %s', ), + concat=dict( + argstr='-concat %s', + extensions=None, + ), dsort=dict(argstr='-dsort %s...', ), environ=dict( nohash=True, @@ -25,19 +31,27 @@ def test_TProject_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=1, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), noblock=dict(argstr='-noblock', ), norm=dict(argstr='-norm', ), num_threads=dict( nohash=True, usedefault=True, ), - ort=dict(argstr='-ort %s', ), + ort=dict( + argstr='-ort %s', + extensions=None, + ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_tproject', position=-1, @@ -52,7 +66,7 @@ def test_TProject_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TProject_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TProject.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index b267986952..14d58011a9 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -14,6 +14,7 @@ def test_TShift_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -24,6 +25,7 @@ def test_TShift_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_tshift', ), @@ -56,8 +58,8 @@ def test_TShift_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TShift_outputs(): output_map = dict( - out_file=dict(), - timing_file=dict(), + out_file=dict(extensions=None, ), + timing_file=dict(extensions=None, ), ) outputs = TShift.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index 5a3ebd8a21..8f2da6aeff 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -13,10 +13,14 @@ def test_TStat_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, @@ -24,6 +28,7 @@ def test_TStat_inputs(): options=dict(argstr='%s', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_tstat', ), @@ -35,7 +40,7 @@ def test_TStat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TStat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TStat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 66ccabefcb..90946f4e79 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -25,6 +25,7 @@ def test_To3D_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source=['in_folder'], name_template='%s', ), @@ -37,7 +38,7 @@ def test_To3D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_To3D_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = To3D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Undump.py b/nipype/interfaces/afni/tests/test_auto_Undump.py index 07d0ff8e81..fad4bfc94f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Undump.py +++ b/nipype/interfaces/afni/tests/test_auto_Undump.py @@ -18,10 +18,14 @@ def test_Undump_inputs(): in_file=dict( argstr='-master %s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, @@ -29,6 +33,7 @@ def test_Undump_inputs(): orient=dict(argstr='-orient %s', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', ), outputtype=dict(), @@ -40,7 +45,7 @@ def test_Undump_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Undump_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Undump.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Unifize.py b/nipype/interfaces/afni/tests/test_auto_Unifize.py index 3215d51e64..77b0bed4df 100644 --- a/nipype/interfaces/afni/tests/test_auto_Unifize.py +++ b/nipype/interfaces/afni/tests/test_auto_Unifize.py @@ -20,6 +20,7 @@ def test_Unifize_inputs(): in_file=dict( argstr='-input %s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -30,13 +31,17 @@ def test_Unifize_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_unifized', ), outputtype=dict(), quiet=dict(argstr='-quiet', ), rbt=dict(argstr='-rbt %f %f %f', ), - scale_file=dict(argstr='-ssave %s', ), + scale_file=dict( + argstr='-ssave %s', + extensions=None, + ), t2=dict(argstr='-T2', ), t2_up=dict(argstr='-T2up %f', ), urad=dict(argstr='-Urad %s', ), @@ -48,8 +53,8 @@ def test_Unifize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Unifize_outputs(): output_map = dict( - out_file=dict(), - scale_file=dict(), + out_file=dict(extensions=None, ), + scale_file=dict(extensions=None, ), ) outputs = Unifize.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 293b7613e8..8aba661319 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -8,6 +8,7 @@ def test_Volreg_inputs(): args=dict(argstr='%s', ), basefile=dict( argstr='-base %s', + extensions=None, position=-6, ), copyorigin=dict(argstr='-twodup', ), @@ -18,6 +19,7 @@ def test_Volreg_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -25,6 +27,7 @@ def test_Volreg_inputs(): interp=dict(argstr='-%s', ), md1d_file=dict( argstr='-maxdisp1D %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_md.1D', @@ -36,18 +39,21 @@ def test_Volreg_inputs(): ), oned_file=dict( argstr='-1Dfile %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s.1D', ), oned_matrix_save=dict( argstr='-1Dmatrix_save %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s.aff12.1D', ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_volreg', ), @@ -66,10 +72,10 @@ def test_Volreg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Volreg_outputs(): output_map = dict( - md1d_file=dict(), - oned_file=dict(), - oned_matrix_save=dict(), - out_file=dict(), + md1d_file=dict(extensions=None, ), + oned_file=dict(extensions=None, ), + oned_matrix_save=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = Volreg.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index b85692310a..024d979f41 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -11,24 +11,35 @@ def test_Warp_inputs(): nohash=True, usedefault=True, ), - gridset=dict(argstr='-gridset %s', ), + gridset=dict( + argstr='-gridset %s', + extensions=None, + ), in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), interp=dict(argstr='-%s', ), - matparent=dict(argstr='-matparent %s', ), + matparent=dict( + argstr='-matparent %s', + extensions=None, + ), mni2tta=dict(argstr='-mni2tta', ), newgrid=dict(argstr='-newgrid %f', ), num_threads=dict( nohash=True, usedefault=True, ), - oblique_parent=dict(argstr='-oblique_parent %s', ), + oblique_parent=dict( + argstr='-oblique_parent %s', + extensions=None, + ), out_file=dict( argstr='-prefix %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_warp', @@ -46,8 +57,8 @@ def test_Warp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Warp_outputs(): output_map = dict( - out_file=dict(), - warp_file=dict(), + out_file=dict(extensions=None, ), + warp_file=dict(extensions=None, ), ) outputs = Warp.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index cacb6b1534..2942acad85 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -13,6 +13,7 @@ def test_ZCutUp_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -23,6 +24,7 @@ def test_ZCutUp_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_file', name_template='%s_zcutup', ), @@ -34,7 +36,7 @@ def test_ZCutUp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ZCutUp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ZCutUp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Zcat.py b/nipype/interfaces/afni/tests/test_auto_Zcat.py index 3a2b7ff853..13675f61b9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zcat.py +++ b/nipype/interfaces/afni/tests/test_auto_Zcat.py @@ -31,6 +31,7 @@ def test_Zcat_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_source='in_files', name_template='%s_zcat', ), @@ -43,7 +44,7 @@ def test_Zcat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Zcat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Zcat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index cfba8e2f3c..abeceda432 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -49,6 +49,7 @@ def test_Zeropad_inputs(): in_files=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-1, ), @@ -66,6 +67,7 @@ def test_Zeropad_inputs(): ), out_file=dict( argstr='-prefix %s', + extensions=None, name_template='zeropad', ), outputtype=dict(), @@ -80,7 +82,7 @@ def test_Zeropad_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Zeropad_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Zeropad.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 5fe3e199ec..e16e1bbd79 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -1,11 +1,13 @@ # -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft = python sts = 4 ts = 4 sw = 4 et: -"""AFNI utility interfaces +""" +AFNI utility interfaces. Examples -------- See the docstrings of the individual classes for examples. + """ from __future__ import (print_function, division, unicode_literals, absolute_import) diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 7c7ef6682c..5c6fa2c501 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -84,11 +84,11 @@ def test_ANTS_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ANTS_outputs(): output_map = dict( - affine_transform=dict(), - inverse_warp_transform=dict(), - metaheader=dict(), - metaheader_raw=dict(), - warp_transform=dict(), + affine_transform=dict(extensions=None, ), + inverse_warp_transform=dict(extensions=None, ), + metaheader=dict(extensions=None, ), + metaheader_raw=dict(extensions=None, ), + warp_transform=dict(extensions=None, ), ) outputs = ANTS.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py index fed21cdbef..e2e1d3d53e 100644 --- a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py +++ b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py @@ -17,6 +17,7 @@ def test_AffineInitializer_inputs(): ), fixed_image=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -27,6 +28,7 @@ def test_AffineInitializer_inputs(): ), moving_image=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -36,6 +38,7 @@ def test_AffineInitializer_inputs(): ), out_file=dict( argstr='%s', + extensions=None, position=3, usedefault=True, ), @@ -61,7 +64,7 @@ def test_AffineInitializer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffineInitializer_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AffineInitializer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index 341f250a2c..02ebe6431c 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -36,7 +36,10 @@ def test_AntsJointFusion_inputs(): argstr='-e %s', requires=['exclusion_image'], ), - mask_image=dict(argstr='-x %s', ), + mask_image=dict( + argstr='-x %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, @@ -49,6 +52,7 @@ def test_AntsJointFusion_inputs(): out_intensity_fusion_name_format=dict(argstr='', ), out_label_fusion=dict( argstr='%s', + extensions=None, hash_files=False, ), out_label_post_prob_name_format=dict( @@ -88,7 +92,7 @@ def test_AntsJointFusion_outputs(): output_map = dict( out_atlas_voting_weight_name_format=dict(), out_intensity_fusion_name_format=dict(), - out_label_fusion=dict(), + out_label_fusion=dict(extensions=None, ), out_label_post_prob_name_format=dict(), ) outputs = AntsJointFusion.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index c2bbffa14f..d431323c0b 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -21,6 +21,7 @@ def test_ApplyTransforms_inputs(): ), input_image=dict( argstr='--input %s', + extensions=None, mandatory=True, ), input_image_type=dict(argstr='--input-image-type %d', ), @@ -43,6 +44,7 @@ def test_ApplyTransforms_inputs(): print_out_composite_warp_file=dict(requires=['output_image'], ), reference_image=dict( argstr='--reference-image %s', + extensions=None, mandatory=True, ), transforms=dict( @@ -56,7 +58,7 @@ def test_ApplyTransforms_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransforms_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(extensions=None, ), ) outputs = ApplyTransforms.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index 92c6c21ec1..c0b8f2d8f4 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -13,6 +13,7 @@ def test_ApplyTransformsToPoints_inputs(): ), input_file=dict( argstr='--input %s', + extensions=None, mandatory=True, ), invert_transform_flags=dict(), @@ -37,7 +38,7 @@ def test_ApplyTransformsToPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransformsToPoints_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = ApplyTransformsToPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index 90bc13778a..be1a271f9a 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -28,6 +28,7 @@ def test_Atropos_inputs(): likelihood_model=dict(argstr='--likelihood-model %s', ), mask_image=dict( argstr='--mask-image %s', + extensions=None, mandatory=True, ), maximum_number_of_icm_terations=dict( @@ -42,6 +43,7 @@ def test_Atropos_inputs(): number_of_tissue_classes=dict(mandatory=True, ), out_classified_image_name=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, ), @@ -65,7 +67,7 @@ def test_Atropos_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Atropos_outputs(): output_map = dict( - classified_image=dict(), + classified_image=dict(extensions=None, ), posteriors=dict(), ) outputs = Atropos.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 3fe3abe5cf..a8646c482c 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -21,6 +21,7 @@ def test_AverageAffineTransform_inputs(): ), output_affine_transform=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -36,7 +37,7 @@ def test_AverageAffineTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AverageAffineTransform_outputs(): - output_map = dict(affine_transform=dict(), ) + output_map = dict(affine_transform=dict(extensions=None, ), ) outputs = AverageAffineTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 41e0c99007..fff94b8ec2 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -31,6 +31,7 @@ def test_AverageImages_inputs(): ), output_average_image=dict( argstr='%s', + extensions=None, hash_files=False, position=1, usedefault=True, @@ -42,7 +43,7 @@ def test_AverageImages_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AverageImages_outputs(): - output_map = dict(output_average_image=dict(), ) + output_map = dict(output_average_image=dict(extensions=None, ), ) outputs = AverageImages.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py index 2d48192199..91861ac0b9 100644 --- a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py @@ -7,16 +7,19 @@ def test_BrainExtraction_inputs(): input_map = dict( anatomical_image=dict( argstr='-a %s', + extensions=None, mandatory=True, ), args=dict(argstr='%s', ), brain_probability_mask=dict( argstr='-m %s', copyfile=False, + extensions=None, mandatory=True, ), brain_template=dict( argstr='-e %s', + extensions=None, mandatory=True, ), debug=dict(argstr='-z 1', ), @@ -28,7 +31,10 @@ def test_BrainExtraction_inputs(): nohash=True, usedefault=True, ), - extraction_registration_mask=dict(argstr='-f %s', ), + extraction_registration_mask=dict( + argstr='-f %s', + extensions=None, + ), image_suffix=dict( argstr='-s %s', usedefault=True, @@ -52,24 +58,24 @@ def test_BrainExtraction_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BrainExtraction_outputs(): output_map = dict( - BrainExtractionBrain=dict(), - BrainExtractionCSF=dict(), - BrainExtractionGM=dict(), - BrainExtractionInitialAffine=dict(), - BrainExtractionInitialAffineFixed=dict(), - BrainExtractionInitialAffineMoving=dict(), - BrainExtractionLaplacian=dict(), - BrainExtractionMask=dict(), - BrainExtractionPrior0GenericAffine=dict(), - BrainExtractionPrior1InverseWarp=dict(), - BrainExtractionPrior1Warp=dict(), - BrainExtractionPriorWarped=dict(), - BrainExtractionSegmentation=dict(), - BrainExtractionTemplateLaplacian=dict(), - BrainExtractionTmp=dict(), - BrainExtractionWM=dict(), - N4Corrected0=dict(), - N4Truncated0=dict(), + BrainExtractionBrain=dict(extensions=None, ), + BrainExtractionCSF=dict(extensions=None, ), + BrainExtractionGM=dict(extensions=None, ), + BrainExtractionInitialAffine=dict(extensions=None, ), + BrainExtractionInitialAffineFixed=dict(extensions=None, ), + BrainExtractionInitialAffineMoving=dict(extensions=None, ), + BrainExtractionLaplacian=dict(extensions=None, ), + BrainExtractionMask=dict(extensions=None, ), + BrainExtractionPrior0GenericAffine=dict(extensions=None, ), + BrainExtractionPrior1InverseWarp=dict(extensions=None, ), + BrainExtractionPrior1Warp=dict(extensions=None, ), + BrainExtractionPriorWarped=dict(extensions=None, ), + BrainExtractionSegmentation=dict(extensions=None, ), + BrainExtractionTemplateLaplacian=dict(extensions=None, ), + BrainExtractionTmp=dict(extensions=None, ), + BrainExtractionWM=dict(extensions=None, ), + N4Corrected0=dict(extensions=None, ), + N4Truncated0=dict(extensions=None, ), ) outputs = BrainExtraction.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py index 83fb2ed2aa..1f71fd6c27 100644 --- a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py @@ -21,6 +21,7 @@ def test_ComposeMultiTransform_inputs(): ), output_transform=dict( argstr='%s', + extensions=None, keep_extension=True, name_source=['transforms'], name_template='%s_composed', @@ -28,6 +29,7 @@ def test_ComposeMultiTransform_inputs(): ), reference_image=dict( argstr='%s', + extensions=None, position=2, ), transforms=dict( @@ -42,7 +44,7 @@ def test_ComposeMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeMultiTransform_outputs(): - output_map = dict(output_transform=dict(), ) + output_map = dict(output_transform=dict(extensions=None, ), ) outputs = ComposeMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py b/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py index d2e6f943e2..214ac0d4b5 100644 --- a/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py +++ b/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py @@ -21,6 +21,7 @@ def test_CompositeTransformUtil_inputs(): ), out_file=dict( argstr='%s', + extensions=None, position=2, ), output_prefix=dict( @@ -41,9 +42,9 @@ def test_CompositeTransformUtil_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CompositeTransformUtil_outputs(): output_map = dict( - affine_transform=dict(), - displacement_field=dict(), - out_file=dict(), + affine_transform=dict(extensions=None, ), + displacement_field=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = CompositeTransformUtil.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index ea9a16cbe2..5f44196a51 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -29,11 +29,13 @@ def test_ConvertScalarImageToRGB_inputs(): ), input_image=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), mask_image=dict( argstr='%s', + extensions=None, position=3, usedefault=True, ), @@ -73,7 +75,7 @@ def test_ConvertScalarImageToRGB_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertScalarImageToRGB_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(extensions=None, ), ) outputs = ConvertScalarImageToRGB.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index e2595a710f..005e3c949c 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -7,6 +7,7 @@ def test_CorticalThickness_inputs(): input_map = dict( anatomical_image=dict( argstr='-a %s', + extensions=None, mandatory=True, ), args=dict(argstr='%s', ), @@ -14,13 +15,15 @@ def test_CorticalThickness_inputs(): brain_probability_mask=dict( argstr='-m %s', copyfile=False, + extensions=None, mandatory=True, ), brain_template=dict( argstr='-e %s', + extensions=None, mandatory=True, ), - cortical_label_image=dict(), + cortical_label_image=dict(extensions=None, ), debug=dict(argstr='-z 1', ), dimension=dict( argstr='-d %d', @@ -30,7 +33,10 @@ def test_CorticalThickness_inputs(): nohash=True, usedefault=True, ), - extraction_registration_mask=dict(argstr='-f %s', ), + extraction_registration_mask=dict( + argstr='-f %s', + extensions=None, + ), image_suffix=dict( argstr='-s %s', usedefault=True, @@ -56,6 +62,7 @@ def test_CorticalThickness_inputs(): ), t1_registration_template=dict( argstr='-t %s', + extensions=None, mandatory=True, ), use_floatingpoint_precision=dict(argstr='-j %d', ), @@ -68,19 +75,19 @@ def test_CorticalThickness_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CorticalThickness_outputs(): output_map = dict( - BrainExtractionMask=dict(), - BrainSegmentation=dict(), - BrainSegmentationN4=dict(), + BrainExtractionMask=dict(extensions=None, ), + BrainSegmentation=dict(extensions=None, ), + BrainSegmentationN4=dict(extensions=None, ), BrainSegmentationPosteriors=dict(), - BrainVolumes=dict(), - CorticalThickness=dict(), - CorticalThicknessNormedToTemplate=dict(), - ExtractedBrainN4=dict(), - SubjectToTemplate0GenericAffine=dict(), - SubjectToTemplate1Warp=dict(), - SubjectToTemplateLogJacobian=dict(), - TemplateToSubject0Warp=dict(), - TemplateToSubject1GenericAffine=dict(), + BrainVolumes=dict(extensions=None, ), + CorticalThickness=dict(extensions=None, ), + CorticalThicknessNormedToTemplate=dict(extensions=None, ), + ExtractedBrainN4=dict(extensions=None, ), + SubjectToTemplate0GenericAffine=dict(extensions=None, ), + SubjectToTemplate1Warp=dict(extensions=None, ), + SubjectToTemplateLogJacobian=dict(extensions=None, ), + TemplateToSubject0Warp=dict(extensions=None, ), + TemplateToSubject1GenericAffine=dict(extensions=None, ), ) outputs = CorticalThickness.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py index b32e7b98e0..0734b73c29 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py @@ -8,6 +8,7 @@ def test_CreateJacobianDeterminantImage_inputs(): args=dict(argstr='%s', ), deformationField=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -30,6 +31,7 @@ def test_CreateJacobianDeterminantImage_inputs(): ), outputImage=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -44,7 +46,7 @@ def test_CreateJacobianDeterminantImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateJacobianDeterminantImage_outputs(): - output_map = dict(jacobian_image=dict(), ) + output_map = dict(jacobian_image=dict(extensions=None, ), ) outputs = CreateJacobianDeterminantImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index 74c2b0a7c2..22e160cb10 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -15,9 +15,13 @@ def test_CreateTiledMosaic_inputs(): flip_slice=dict(argstr='-f %s', ), input_image=dict( argstr='-i %s', + extensions=None, mandatory=True, ), - mask_image=dict(argstr='-x %s', ), + mask_image=dict( + argstr='-x %s', + extensions=None, + ), num_threads=dict( nohash=True, usedefault=True, @@ -30,6 +34,7 @@ def test_CreateTiledMosaic_inputs(): permute_axes=dict(argstr='-g', ), rgb_image=dict( argstr='-r %s', + extensions=None, mandatory=True, ), slices=dict(argstr='-s %s', ), @@ -41,7 +46,7 @@ def test_CreateTiledMosaic_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateTiledMosaic_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(extensions=None, ), ) outputs = CreateTiledMosaic.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py index 882cb21854..6b8bebbbe1 100644 --- a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py +++ b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py @@ -13,9 +13,11 @@ def test_DenoiseImage_inputs(): ), input_image=dict( argstr='-i %s', + extensions=None, mandatory=True, ), noise_image=dict( + extensions=None, hash_files=False, keep_extension=True, name_source=['input_image'], @@ -31,6 +33,7 @@ def test_DenoiseImage_inputs(): ), output_image=dict( argstr='-o %s', + extensions=None, hash_files=False, keep_extension=True, name_source=['input_image'], @@ -54,8 +57,8 @@ def test_DenoiseImage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DenoiseImage_outputs(): output_map = dict( - noise_image=dict(), - output_image=dict(), + noise_image=dict(extensions=None, ), + output_image=dict(extensions=None, ), ) outputs = DenoiseImage.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index af91f9a8af..69ed18ff19 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -20,6 +20,7 @@ def test_GenWarpFields_inputs(): input_image=dict( argstr='-i %s', copyfile=False, + extensions=None, mandatory=True, ), inverse_warp_template_labels=dict(argstr='-l', ), @@ -39,6 +40,7 @@ def test_GenWarpFields_inputs(): reference_image=dict( argstr='-r %s', copyfile=True, + extensions=None, mandatory=True, ), similarity_metric=dict(argstr='-s %s', ), @@ -54,11 +56,11 @@ def test_GenWarpFields_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GenWarpFields_outputs(): output_map = dict( - affine_transformation=dict(), - input_file=dict(), - inverse_warp_field=dict(), - output_file=dict(), - warp_field=dict(), + affine_transformation=dict(extensions=None, ), + input_file=dict(extensions=None, ), + inverse_warp_field=dict(extensions=None, ), + output_file=dict(extensions=None, ), + warp_field=dict(extensions=None, ), ) outputs = GenWarpFields.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index 9e82584729..50bb8b1c84 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -26,7 +26,10 @@ def test_JointFusion_inputs(): nohash=True, usedefault=True, ), - exclusion_region=dict(argstr='-x %s', ), + exclusion_region=dict( + argstr='-x %s', + extensions=None, + ), method=dict( argstr='-m %s', usedefault=True, @@ -42,6 +45,7 @@ def test_JointFusion_inputs(): ), output_label_image=dict( argstr='%s', + extensions=None, mandatory=True, name_template='%s', output_name='output_label_image', @@ -76,7 +80,7 @@ def test_JointFusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JointFusion_outputs(): - output_map = dict(output_label_image=dict(), ) + output_map = dict(output_label_image=dict(extensions=None, ), ) outputs = JointFusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py index 6129670d39..aecffa75b7 100644 --- a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py +++ b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py @@ -12,6 +12,7 @@ def test_KellyKapowski_inputs(): ), cortical_thickness=dict( argstr='--output "%s"', + extensions=None, hash_files=False, keep_extension=True, name_source=['segmentation_image'], @@ -31,7 +32,9 @@ def test_KellyKapowski_inputs(): ), gray_matter_label=dict(usedefault=True, ), gray_matter_prob_image=dict( - argstr='--gray-matter-probability-image "%s"', ), + argstr='--gray-matter-probability-image "%s"', + extensions=None, + ), max_invert_displacement_field_iters=dict( argstr= '--maximum-number-of-invert-displacement-field-iterations %d', @@ -47,6 +50,7 @@ def test_KellyKapowski_inputs(): ), segmentation_image=dict( argstr='--segmentation-image "%s"', + extensions=None, mandatory=True, ), smoothing_variance=dict( @@ -61,9 +65,13 @@ def test_KellyKapowski_inputs(): argstr='--thickness-prior-estimate %f', usedefault=True, ), - thickness_prior_image=dict(argstr='--thickness-prior-image "%s"', ), + thickness_prior_image=dict( + argstr='--thickness-prior-image "%s"', + extensions=None, + ), use_bspline_smoothing=dict(argstr='--use-bspline-smoothing 1', ), warped_white_matter=dict( + extensions=None, hash_files=False, keep_extension=True, name_source=['segmentation_image'], @@ -71,7 +79,9 @@ def test_KellyKapowski_inputs(): ), white_matter_label=dict(usedefault=True, ), white_matter_prob_image=dict( - argstr='--white-matter-probability-image "%s"', ), + argstr='--white-matter-probability-image "%s"', + extensions=None, + ), ) inputs = KellyKapowski.input_spec() @@ -80,8 +90,8 @@ def test_KellyKapowski_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_KellyKapowski_outputs(): output_map = dict( - cortical_thickness=dict(), - warped_white_matter=dict(), + cortical_thickness=dict(extensions=None, ), + warped_white_matter=dict(extensions=None, ), ) outputs = KellyKapowski.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py b/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py index a5de244711..cc44d0f059 100644 --- a/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py +++ b/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py @@ -17,12 +17,14 @@ def test_LabelGeometry_inputs(): ), intensity_image=dict( argstr='%s', + extensions=None, mandatory=True, position=2, usedefault=True, ), label_image=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -43,7 +45,7 @@ def test_LabelGeometry_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelGeometry_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = LabelGeometry.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index 608ba10889..d10e154ce6 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -18,12 +18,14 @@ def test_LaplacianThickness_inputs(): input_gm=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=2, ), input_wm=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=1, ), @@ -33,6 +35,7 @@ def test_LaplacianThickness_inputs(): ), output_image=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['input_wm'], @@ -65,7 +68,7 @@ def test_LaplacianThickness_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LaplacianThickness_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(extensions=None, ), ) outputs = LaplacianThickness.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py index 1a5041ae74..88eeaf2360 100644 --- a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py +++ b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py @@ -14,8 +14,14 @@ def test_MeasureImageSimilarity_inputs(): nohash=True, usedefault=True, ), - fixed_image=dict(mandatory=True, ), - fixed_image_mask=dict(argstr='%s', ), + fixed_image=dict( + extensions=None, + mandatory=True, + ), + fixed_image_mask=dict( + argstr='%s', + extensions=None, + ), metric=dict( argstr='%s', mandatory=True, @@ -24,8 +30,14 @@ def test_MeasureImageSimilarity_inputs(): requires=['metric'], usedefault=True, ), - moving_image=dict(mandatory=True, ), - moving_image_mask=dict(requires=['fixed_image_mask'], ), + moving_image=dict( + extensions=None, + mandatory=True, + ), + moving_image_mask=dict( + extensions=None, + requires=['fixed_image_mask'], + ), num_threads=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 1bf787018d..72166bd17d 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -17,6 +17,7 @@ def test_MultiplyImages_inputs(): ), first_input=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -26,6 +27,7 @@ def test_MultiplyImages_inputs(): ), output_product_image=dict( argstr='%s', + extensions=None, mandatory=True, position=3, ), @@ -41,7 +43,7 @@ def test_MultiplyImages_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyImages_outputs(): - output_map = dict(output_product_image=dict(), ) + output_map = dict(output_product_image=dict(extensions=None, ), ) outputs = MultiplyImages.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 66edf0c3d6..c93d847d4b 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -6,7 +6,10 @@ def test_N4BiasFieldCorrection_inputs(): input_map = dict( args=dict(argstr='%s', ), - bias_image=dict(hash_files=False, ), + bias_image=dict( + extensions=None, + hash_files=False, + ), bspline_fitting_distance=dict(argstr='--bspline-fitting %s', ), bspline_order=dict(requires=['bspline_fitting_distance'], ), convergence_threshold=dict(requires=['n_iterations'], ), @@ -24,9 +27,13 @@ def test_N4BiasFieldCorrection_inputs(): ), input_image=dict( argstr='--input-image %s', + extensions=None, mandatory=True, ), - mask_image=dict(argstr='--mask-image %s', ), + mask_image=dict( + argstr='--mask-image %s', + extensions=None, + ), n_iterations=dict(argstr='--convergence %s', ), num_threads=dict( nohash=True, @@ -43,7 +50,10 @@ def test_N4BiasFieldCorrection_inputs(): xor=['bias_image'], ), shrink_factor=dict(argstr='--shrink-factor %d', ), - weight_image=dict(argstr='--weight-image %s', ), + weight_image=dict( + argstr='--weight-image %s', + extensions=None, + ), ) inputs = N4BiasFieldCorrection.input_spec() @@ -52,8 +62,8 @@ def test_N4BiasFieldCorrection_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_N4BiasFieldCorrection_outputs(): output_map = dict( - bias_image=dict(), - output_image=dict(), + bias_image=dict(extensions=None, ), + output_image=dict(extensions=None, ), ) outputs = N4BiasFieldCorrection.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 4bd253c3d0..1b49f44678 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -29,6 +29,7 @@ def test_Registration_inputs(): fixed_image=dict(mandatory=True, ), fixed_image_mask=dict( argstr='%s', + extensions=None, max_ver='2.1.0', xor=['fixed_image_masks'], ), @@ -70,6 +71,7 @@ def test_Registration_inputs(): metric_weight_stage_trait=dict(), moving_image=dict(mandatory=True, ), moving_image_mask=dict( + extensions=None, max_ver='2.1.0', requires=['fixed_image_mask'], xor=['moving_image_masks'], @@ -98,7 +100,10 @@ def test_Registration_inputs(): requires=['metric_weight'], usedefault=True, ), - restore_state=dict(argstr='--restore-state %s', ), + restore_state=dict( + argstr='--restore-state %s', + extensions=None, + ), restrict_deformation=dict(), sampling_percentage=dict(requires=['sampling_strategy'], ), sampling_percentage_item_trait=dict(), @@ -106,7 +111,10 @@ def test_Registration_inputs(): sampling_strategy=dict(requires=['metric_weight'], ), sampling_strategy_item_trait=dict(), sampling_strategy_stage_trait=dict(), - save_state=dict(argstr='--save-state %s', ), + save_state=dict( + argstr='--save-state %s', + extensions=None, + ), shrink_factors=dict(mandatory=True, ), sigma_units=dict(requires=['smoothing_sigmas'], ), smoothing_sigmas=dict(mandatory=True, ), @@ -141,17 +149,17 @@ def test_Registration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Registration_outputs(): output_map = dict( - composite_transform=dict(), + composite_transform=dict(extensions=None, ), elapsed_time=dict(), forward_invert_flags=dict(), forward_transforms=dict(), - inverse_composite_transform=dict(), - inverse_warped_image=dict(), + inverse_composite_transform=dict(extensions=None, ), + inverse_warped_image=dict(extensions=None, ), metric_value=dict(), reverse_invert_flags=dict(), reverse_transforms=dict(), - save_state=dict(), - warped_image=dict(), + save_state=dict(extensions=None, ), + warped_image=dict(extensions=None, ), ) outputs = Registration.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py b/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py index 8bc79392e1..d2b527556b 100644 --- a/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py +++ b/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py @@ -55,11 +55,11 @@ def test_RegistrationSynQuick_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RegistrationSynQuick_outputs(): output_map = dict( - forward_warp_field=dict(), - inverse_warp_field=dict(), - inverse_warped_image=dict(), - out_matrix=dict(), - warped_image=dict(), + forward_warp_field=dict(extensions=None, ), + inverse_warp_field=dict(extensions=None, ), + inverse_warped_image=dict(extensions=None, ), + out_matrix=dict(extensions=None, ), + warped_image=dict(extensions=None, ), ) outputs = RegistrationSynQuick.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index 42020f6db9..8a62b58b42 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -17,6 +17,7 @@ def test_WarpImageMultiTransform_inputs(): ), input_image=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -26,12 +27,14 @@ def test_WarpImageMultiTransform_inputs(): usedefault=True, ), out_postfix=dict( + extensions=None, hash_files=False, usedefault=True, xor=['output_image'], ), output_image=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=3, @@ -39,6 +42,7 @@ def test_WarpImageMultiTransform_inputs(): ), reference_image=dict( argstr='-R %s', + extensions=None, xor=['tightest_box'], ), reslice_by_header=dict(argstr='--reslice-by-header', ), @@ -60,7 +64,7 @@ def test_WarpImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpImageMultiTransform_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(extensions=None, ), ) outputs = WarpImageMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index de3131f056..b9b17585f6 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -18,6 +18,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): input_image=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, ), invert_affine=dict(), @@ -31,6 +32,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): ), reference_image=dict( argstr='-R %s', + extensions=None, xor=['tightest_box'], ), reslice_by_header=dict(argstr='--reslice-by-header', ), @@ -52,7 +54,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpTimeSeriesImageMultiTransform_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(extensions=None, ), ) outputs = WarpTimeSeriesImageMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index fe21858500..d2cdc074a4 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -20,6 +20,7 @@ def test_antsIntroduction_inputs(): input_image=dict( argstr='-i %s', copyfile=False, + extensions=None, mandatory=True, ), inverse_warp_template_labels=dict(argstr='-l', ), @@ -39,6 +40,7 @@ def test_antsIntroduction_inputs(): reference_image=dict( argstr='-r %s', copyfile=True, + extensions=None, mandatory=True, ), similarity_metric=dict(argstr='-s %s', ), @@ -54,11 +56,11 @@ def test_antsIntroduction_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_antsIntroduction_outputs(): output_map = dict( - affine_transformation=dict(), - input_file=dict(), - inverse_warp_field=dict(), - output_file=dict(), - warp_field=dict(), + affine_transformation=dict(extensions=None, ), + input_file=dict(extensions=None, ), + inverse_warp_field=dict(extensions=None, ), + output_file=dict(extensions=None, ), + warp_field=dict(extensions=None, ), ) outputs = antsIntroduction.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index 8513003c29..a1d77b11ac 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -61,7 +61,7 @@ def test_buildtemplateparallel_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_buildtemplateparallel_outputs(): output_map = dict( - final_template_file=dict(), + final_template_file=dict(extensions=None, ), subject_outfiles=dict(), template_files=dict(), ) diff --git a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py index ff705edfeb..a948b7c698 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py @@ -14,6 +14,7 @@ def test_BDP_inputs(): args=dict(argstr='%s', ), bMatrixFile=dict( argstr='--bmat %s', + extensions=None, mandatory=True, position=-1, xor=['BVecBValPair'], @@ -21,17 +22,30 @@ def test_BDP_inputs(): bValRatioThreshold=dict(argstr='--bval-ratio-threshold %f', ), bfcFile=dict( argstr='%s', + extensions=None, mandatory=True, position=0, xor=['noStructuralRegistration'], ), - customDiffusionLabel=dict(argstr='--custom-diffusion-label %s', ), - customLabelXML=dict(argstr='--custom-label-xml %s', ), - customT1Label=dict(argstr='--custom-t1-label %s', ), + customDiffusionLabel=dict( + argstr='--custom-diffusion-label %s', + extensions=None, + ), + customLabelXML=dict( + argstr='--custom-label-xml %s', + extensions=None, + ), + customT1Label=dict( + argstr='--custom-t1-label %s', + extensions=None, + ), dataSinkDelay=dict(argstr='%s', ), dcorrRegMeasure=dict(argstr='--dcorr-reg-method %s', ), dcorrWeight=dict(argstr='--dcorr-regularization-wt %f', ), - dwiMask=dict(argstr='--dwi-mask %s', ), + dwiMask=dict( + argstr='--dwi-mask %s', + extensions=None, + ), echoSpacing=dict(argstr='--echo-spacing=%f', ), environ=dict( nohash=True, @@ -43,6 +57,7 @@ def test_BDP_inputs(): estimateTensors=dict(argstr='--tensors', ), fieldmapCorrection=dict( argstr='--fieldmap-correction %s', + extensions=None, requires=['echoSpacing'], ), fieldmapCorrectionMethod=dict( @@ -50,13 +65,17 @@ def test_BDP_inputs(): xor=['skipIntensityCorr'], ), fieldmapSmooth=dict(argstr='--fieldmap-smooth3=%f', ), - flagConfigFile=dict(argstr='--flag-conf-file %s', ), + flagConfigFile=dict( + argstr='--flag-conf-file %s', + extensions=None, + ), forcePartialROIStats=dict(argstr='--force-partial-roi-stats', ), generateStats=dict(argstr='--generate-stats', ), ignoreFieldmapFOV=dict(argstr='--ignore-fieldmap-fov', ), ignoreMemory=dict(argstr='--ignore-memory', ), inputDiffusionData=dict( argstr='--nii %s', + extensions=None, mandatory=True, position=-2, ), @@ -81,16 +100,29 @@ def test_BDP_inputs(): xor=['fieldmapCorrectionMethod'], ), skipNonuniformityCorr=dict(argstr='--no-nonuniformity-correction', ), - t1Mask=dict(argstr='--t1-mask %s', ), + t1Mask=dict( + argstr='--t1-mask %s', + extensions=None, + ), threads=dict(argstr='--threads=%d', ), transformDataOnly=dict(argstr='--transform-data-only', ), transformDiffusionSurface=dict( - argstr='--transform-diffusion-surface %s', ), + argstr='--transform-diffusion-surface %s', + extensions=None, + ), transformDiffusionVolume=dict( - argstr='--transform-diffusion-volume %s', ), + argstr='--transform-diffusion-volume %s', + extensions=None, + ), transformInterpolation=dict(argstr='--transform-interpolation %s', ), - transformT1Surface=dict(argstr='--transform-t1-surface %s', ), - transformT1Volume=dict(argstr='--transform-t1-volume %s', ), + transformT1Surface=dict( + argstr='--transform-t1-surface %s', + extensions=None, + ), + transformT1Volume=dict( + argstr='--transform-t1-volume %s', + extensions=None, + ), ) inputs = BDP.input_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py index 01200e50fc..a29e1b75cf 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py @@ -14,7 +14,10 @@ def test_Bfc_inputs(): convergenceThreshold=dict(argstr='--eps %f', ), correctWholeVolume=dict(argstr='--extrapolate', ), correctedImagesOutputPrefix=dict(argstr='--prefix %s', ), - correctionScheduleFile=dict(argstr='--schedule %s', ), + correctionScheduleFile=dict( + argstr='--schedule %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -23,10 +26,12 @@ def test_Bfc_inputs(): histogramType=dict(argstr='%s', ), inputMRIFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), inputMaskFile=dict( argstr='-m %s', + extensions=None, hash_files=False, ), intermediate_file_type=dict(argstr='%s', ), @@ -41,15 +46,18 @@ def test_Bfc_inputs(): ), outputBiasField=dict( argstr='--bias %s', + extensions=None, hash_files=False, ), outputMRIVolume=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, ), outputMaskedBiasField=dict( argstr='--maskedbias %s', + extensions=None, hash_files=False, ), splineLambda=dict(argstr='-w %f', ), @@ -63,10 +71,10 @@ def test_Bfc_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Bfc_outputs(): output_map = dict( - correctionScheduleFile=dict(), - outputBiasField=dict(), - outputMRIVolume=dict(), - outputMaskedBiasField=dict(), + correctionScheduleFile=dict(extensions=None, ), + outputBiasField=dict(extensions=None, ), + outputMRIVolume=dict(extensions=None, ), + outputMaskedBiasField=dict(extensions=None, ), ) outputs = Bfc.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py index bbd154bc24..46850631bd 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py @@ -28,32 +28,39 @@ def test_Bse_inputs(): ), inputMRIFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), noRotate=dict(argstr='--norotate', ), outputCortexFile=dict( argstr='--cortex %s', + extensions=None, hash_files=False, ), outputDetailedBrainMask=dict( argstr='--hires %s', + extensions=None, hash_files=False, ), outputDiffusionFilter=dict( argstr='--adf %s', + extensions=None, hash_files=False, ), outputEdgeMap=dict( argstr='--edge %s', + extensions=None, hash_files=False, ), outputMRIVolume=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, ), outputMaskFile=dict( argstr='--mask %s', + extensions=None, genfile=True, hash_files=False, ), @@ -78,12 +85,12 @@ def test_Bse_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Bse_outputs(): output_map = dict( - outputCortexFile=dict(), - outputDetailedBrainMask=dict(), - outputDiffusionFilter=dict(), - outputEdgeMap=dict(), - outputMRIVolume=dict(), - outputMaskFile=dict(), + outputCortexFile=dict(extensions=None, ), + outputDetailedBrainMask=dict(extensions=None, ), + outputDiffusionFilter=dict(extensions=None, ), + outputEdgeMap=dict(extensions=None, ), + outputMRIVolume=dict(extensions=None, ), + outputMaskFile=dict(extensions=None, ), ) outputs = Bse.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py index 808e4347c3..ea0c58c981 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py @@ -16,33 +16,43 @@ def test_Cerebro_inputs(): ), inputAtlasLabelFile=dict( argstr='--atlaslabels %s', + extensions=None, mandatory=True, ), inputAtlasMRIFile=dict( argstr='--atlas %s', + extensions=None, mandatory=True, ), - inputBrainMaskFile=dict(argstr='-m %s', ), + inputBrainMaskFile=dict( + argstr='-m %s', + extensions=None, + ), inputMRIFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), keepTempFiles=dict(argstr='--keep', ), linearConvergence=dict(argstr='--linconv %f', ), outputAffineTransformFile=dict( argstr='--air %s', + extensions=None, genfile=True, ), outputCerebrumMaskFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), outputLabelVolumeFile=dict( argstr='-l %s', + extensions=None, genfile=True, ), outputWarpTransformFile=dict( argstr='--warp %s', + extensions=None, genfile=True, ), tempDirectory=dict(argstr='--tempdir %s', ), @@ -59,10 +69,10 @@ def test_Cerebro_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Cerebro_outputs(): output_map = dict( - outputAffineTransformFile=dict(), - outputCerebrumMaskFile=dict(), - outputLabelVolumeFile=dict(), - outputWarpTransformFile=dict(), + outputAffineTransformFile=dict(extensions=None, ), + outputCerebrumMaskFile=dict(extensions=None, ), + outputLabelVolumeFile=dict(extensions=None, ), + outputWarpTransformFile=dict(extensions=None, ), ) outputs = Cerebro.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py index 536cb158f2..d8099b932c 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py @@ -21,14 +21,17 @@ def test_Cortex_inputs(): ), inputHemisphereLabelFile=dict( argstr='-h %s', + extensions=None, mandatory=True, ), inputTissueFractionFile=dict( argstr='-f %s', + extensions=None, mandatory=True, ), outputCerebrumMask=dict( argstr='-o %s', + extensions=None, genfile=True, ), timer=dict(argstr='--timer', ), @@ -44,7 +47,7 @@ def test_Cortex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cortex_outputs(): - output_map = dict(outputCerebrumMask=dict(), ) + output_map = dict(outputCerebrumMask=dict(extensions=None, ), ) outputs = Cortex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py index ba430fb1fd..276185df1e 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py @@ -12,11 +12,13 @@ def test_Dewisp_inputs(): ), inputMaskFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), maximumIterations=dict(argstr='-n %d', ), outputMaskFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), sizeThreshold=dict(argstr='-t %d', ), @@ -29,7 +31,7 @@ def test_Dewisp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dewisp_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(extensions=None, ), ) outputs = Dewisp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py index c69232fd01..efb216f30d 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py @@ -14,9 +14,13 @@ def test_Dfs_inputs(): nohash=True, usedefault=True, ), - inputShadingVolume=dict(argstr='-c %s', ), + inputShadingVolume=dict( + argstr='-c %s', + extensions=None, + ), inputVolumeFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), noNormalsFlag=dict(argstr='--nonormals', ), @@ -26,6 +30,7 @@ def test_Dfs_inputs(): ), outputSurfaceFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), postSmoothFlag=dict(argstr='--postsmooth', ), @@ -55,7 +60,7 @@ def test_Dfs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dfs_outputs(): - output_map = dict(outputSurfaceFile=dict(), ) + output_map = dict(outputSurfaceFile=dict(extensions=None, ), ) outputs = Dfs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py index 9e3db80dd9..567d3bcdc4 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py @@ -12,29 +12,38 @@ def test_Hemisplit_inputs(): ), inputHemisphereLabelFile=dict( argstr='-l %s', + extensions=None, mandatory=True, ), inputSurfaceFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), outputLeftHemisphere=dict( argstr='--left %s', + extensions=None, genfile=True, ), outputLeftPialHemisphere=dict( argstr='-pl %s', + extensions=None, genfile=True, ), outputRightHemisphere=dict( argstr='--right %s', + extensions=None, genfile=True, ), outputRightPialHemisphere=dict( argstr='-pr %s', + extensions=None, genfile=True, ), - pialSurfaceFile=dict(argstr='-p %s', ), + pialSurfaceFile=dict( + argstr='-p %s', + extensions=None, + ), timer=dict(argstr='--timer', ), verbosity=dict(argstr='-v %d', ), ) @@ -45,10 +54,10 @@ def test_Hemisplit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Hemisplit_outputs(): output_map = dict( - outputLeftHemisphere=dict(), - outputLeftPialHemisphere=dict(), - outputRightHemisphere=dict(), - outputRightPialHemisphere=dict(), + outputLeftHemisphere=dict(extensions=None, ), + outputLeftPialHemisphere=dict(extensions=None, ), + outputRightHemisphere=dict(extensions=None, ), + outputRightPialHemisphere=dict(extensions=None, ), ) outputs = Hemisplit.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py index afc621a56e..125a0504ed 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py @@ -13,14 +13,17 @@ def test_Pialmesh_inputs(): exportPrefix=dict(argstr='--prefix %s', ), inputMaskFile=dict( argstr='-m %s', + extensions=None, mandatory=True, ), inputSurfaceFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), inputTissueFractionFile=dict( argstr='-f %s', + extensions=None, mandatory=True, ), laplacianSmoothing=dict( @@ -45,6 +48,7 @@ def test_Pialmesh_inputs(): ), outputSurfaceFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), recomputeNormals=dict(argstr='--norm', ), @@ -70,7 +74,7 @@ def test_Pialmesh_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Pialmesh_outputs(): - output_map = dict(outputSurfaceFile=dict(), ) + output_map = dict(outputSurfaceFile=dict(extensions=None, ), ) outputs = Pialmesh.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py index d425d4ddac..3f79a0cdf6 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py @@ -12,15 +12,21 @@ def test_Pvc_inputs(): ), inputMRIFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), - inputMaskFile=dict(argstr='-m %s', ), + inputMaskFile=dict( + argstr='-m %s', + extensions=None, + ), outputLabelFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), outputTissueFractionFile=dict( argstr='-f %s', + extensions=None, genfile=True, ), spatialPrior=dict(argstr='-l %f', ), @@ -35,8 +41,8 @@ def test_Pvc_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Pvc_outputs(): output_map = dict( - outputLabelFile=dict(), - outputTissueFractionFile=dict(), + outputLabelFile=dict(extensions=None, ), + outputTissueFractionFile=dict(extensions=None, ), ) outputs = Pvc.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py index eb672d12b7..17ec62fe83 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py @@ -20,11 +20,13 @@ def test_Scrubmask_inputs(): ), inputMaskFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), numberIterations=dict(argstr='-n %d', ), outputMaskFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), timer=dict(argstr='--timer', ), @@ -36,7 +38,7 @@ def test_Scrubmask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Scrubmask_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(extensions=None, ), ) outputs = Scrubmask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py index 2191f7b133..ed921d09b9 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py @@ -14,15 +14,18 @@ def test_Skullfinder_inputs(): ), inputMRIFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), inputMaskFile=dict( argstr='-m %s', + extensions=None, mandatory=True, ), lowerThreshold=dict(argstr='-l %d', ), outputLabelFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), performFinalOpening=dict(argstr='--finalOpening', ), @@ -39,7 +42,7 @@ def test_Skullfinder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Skullfinder_outputs(): - output_map = dict(outputLabelFile=dict(), ) + output_map = dict(outputLabelFile=dict(extensions=None, ), ) outputs = Skullfinder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py index ec2886b42f..94f7868f94 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py @@ -16,6 +16,7 @@ def test_Tca_inputs(): ), inputMaskFile=dict( argstr='-i %s', + extensions=None, mandatory=True, ), maxCorrectionSize=dict(argstr='-n %d', ), @@ -25,6 +26,7 @@ def test_Tca_inputs(): ), outputMaskFile=dict( argstr='-o %s', + extensions=None, genfile=True, ), timer=dict(argstr='--timer', ), @@ -36,7 +38,7 @@ def test_Tca_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tca_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(extensions=None, ), ) outputs = Tca.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index 5d796126cc..28170946ac 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -29,11 +29,13 @@ def test_AnalyzeHeader_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=1, ), initfromheader=dict( argstr='-initfromheader %s', + extensions=None, position=3, ), intelbyteorder=dict(argstr='-intelbyteorder', ), @@ -57,22 +59,27 @@ def test_AnalyzeHeader_inputs(): ), printbigendian=dict( argstr='-printbigendian %s', + extensions=None, position=3, ), printimagedims=dict( argstr='-printimagedims %s', + extensions=None, position=3, ), printintelbyteorder=dict( argstr='-printintelbyteorder %s', + extensions=None, position=3, ), printprogargs=dict( argstr='-printprogargs %s', + extensions=None, position=3, ), readheader=dict( argstr='-readheader %s', + extensions=None, position=3, ), scaleinter=dict( @@ -85,6 +92,7 @@ def test_AnalyzeHeader_inputs(): ), scheme_file=dict( argstr='%s', + extensions=None, position=2, ), voxel_dims=dict( @@ -98,7 +106,7 @@ def test_AnalyzeHeader_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeHeader_outputs(): - output_map = dict(header=dict(), ) + output_map = dict(header=dict(extensions=None, ), ) outputs = AnalyzeHeader.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index caee9e68cf..66ac282175 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -12,6 +12,7 @@ def test_ComputeEigensystem_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=1, ), @@ -37,7 +38,7 @@ def test_ComputeEigensystem_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeEigensystem_outputs(): - output_map = dict(eigen=dict(), ) + output_map = dict(eigen=dict(extensions=None, ), ) outputs = ComputeEigensystem.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 49cfdfd96a..9cfae77b2f 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -12,6 +12,7 @@ def test_ComputeFractionalAnisotropy_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=1, ), @@ -25,6 +26,7 @@ def test_ComputeFractionalAnisotropy_inputs(): outputdatatype=dict(argstr='-outputdatatype %s', ), scheme_file=dict( argstr='%s', + extensions=None, position=2, ), ) @@ -34,7 +36,7 @@ def test_ComputeFractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeFractionalAnisotropy_outputs(): - output_map = dict(fa=dict(), ) + output_map = dict(fa=dict(extensions=None, ), ) outputs = ComputeFractionalAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 212477d149..faff5234c3 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -12,6 +12,7 @@ def test_ComputeMeanDiffusivity_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=1, ), @@ -19,12 +20,14 @@ def test_ComputeMeanDiffusivity_inputs(): inputmodel=dict(argstr='-inputmodel %s', ), out_file=dict( argstr='> %s', + extensions=None, genfile=True, position=-1, ), outputdatatype=dict(argstr='-outputdatatype %s', ), scheme_file=dict( argstr='%s', + extensions=None, position=2, ), ) @@ -34,7 +37,7 @@ def test_ComputeMeanDiffusivity_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMeanDiffusivity_outputs(): - output_map = dict(md=dict(), ) + output_map = dict(md=dict(extensions=None, ), ) outputs = ComputeMeanDiffusivity.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 1112c7c743..1443a253bd 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -12,6 +12,7 @@ def test_ComputeTensorTrace_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=1, ), @@ -25,6 +26,7 @@ def test_ComputeTensorTrace_inputs(): outputdatatype=dict(argstr='-outputdatatype %s', ), scheme_file=dict( argstr='%s', + extensions=None, position=2, ), ) @@ -34,7 +36,7 @@ def test_ComputeTensorTrace_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTensorTrace_outputs(): - output_map = dict(trace=dict(), ) + output_map = dict(trace=dict(extensions=None, ), ) outputs = ComputeTensorTrace.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index 06a76fdf2b..cbcebd61c7 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -12,21 +12,28 @@ def test_Conmat_inputs(): ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, ), output_root=dict( argstr='-outputroot %s', + extensions=None, genfile=True, ), scalar_file=dict( argstr='-scalarfile %s', + extensions=None, requires=['tract_stat'], ), target_file=dict( argstr='-targetfile %s', + extensions=None, mandatory=True, ), - targetname_file=dict(argstr='-targetnamefile %s', ), + targetname_file=dict( + argstr='-targetnamefile %s', + extensions=None, + ), tract_prop=dict( argstr='-tractstat %s', units='NA', @@ -46,8 +53,8 @@ def test_Conmat_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Conmat_outputs(): output_map = dict( - conmat_sc=dict(), - conmat_ts=dict(), + conmat_sc=dict(extensions=None, ), + conmat_ts=dict(extensions=None, ), ) outputs = Conmat.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index b20dcbf3bf..244ef010bd 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -12,16 +12,19 @@ def test_DT2NIfTI_inputs(): ), header_file=dict( argstr='-header %s', + extensions=None, mandatory=True, position=3, ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, position=1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, genfile=True, position=2, ), @@ -33,9 +36,9 @@ def test_DT2NIfTI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DT2NIfTI_outputs(): output_map = dict( - dt=dict(), - exitcode=dict(), - lns0=dict(), + dt=dict(extensions=None, ), + exitcode=dict(extensions=None, ), + lns0=dict(extensions=None, ), ) outputs = DT2NIfTI.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index a23da89552..26d27d57d2 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -6,13 +6,17 @@ def test_DTIFit_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -27,6 +31,7 @@ def test_DTIFit_inputs(): ), scheme_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -37,7 +42,7 @@ def test_DTIFit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): - output_map = dict(tensor_fitted=dict(), ) + output_map = dict(tensor_fitted=dict(extensions=None, ), ) outputs = DTIFit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 95e8e0bea5..f7caf77ef1 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -37,6 +37,7 @@ def test_DTLUTGen_inputs(): ), scheme_file=dict( argstr='-schemefile %s', + extensions=None, mandatory=True, position=2, ), @@ -60,7 +61,7 @@ def test_DTLUTGen_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTLUTGen_outputs(): - output_map = dict(dtLUT=dict(), ) + output_map = dict(dtLUT=dict(extensions=None, ), ) outputs = DTLUTGen.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index 12256a50d8..fd9b6333f4 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -6,9 +6,13 @@ def test_DTMetric_inputs(): input_map = dict( args=dict(argstr='%s', ), - data_header=dict(argstr='-header %s', ), + data_header=dict( + argstr='-header %s', + extensions=None, + ), eigen_data=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, ), environ=dict( @@ -29,6 +33,7 @@ def test_DTMetric_inputs(): ), outputfile=dict( argstr='-outputfile %s', + extensions=None, genfile=True, ), ) @@ -38,7 +43,7 @@ def test_DTMetric_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTMetric_outputs(): - output_map = dict(metric_stats=dict(), ) + output_map = dict(metric_stats=dict(extensions=None, ), ) outputs = DTMetric.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index a2ebfbf0a6..350c604c99 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -12,11 +12,13 @@ def test_FSL2Scheme_inputs(): ), bval_file=dict( argstr='-bvalfile %s', + extensions=None, mandatory=True, position=2, ), bvec_file=dict( argstr='-bvecfile %s', + extensions=None, mandatory=True, position=1, ), @@ -49,7 +51,7 @@ def test_FSL2Scheme_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FSL2Scheme_outputs(): - output_map = dict(scheme=dict(), ) + output_map = dict(scheme=dict(extensions=None, ), ) outputs = FSL2Scheme.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index adae10f0bb..29864bef82 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -12,6 +12,7 @@ def test_Image2Voxel_inputs(): ), in_file=dict( argstr='-4dimage %s', + extensions=None, mandatory=True, position=1, ), @@ -32,7 +33,7 @@ def test_Image2Voxel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Image2Voxel_outputs(): - output_map = dict(voxel_order=dict(), ) + output_map = dict(voxel_order=dict(extensions=None, ), ) outputs = Image2Voxel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index 3813051025..7a16ea7732 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -21,6 +21,7 @@ def test_ImageStats_inputs(): ), output_root=dict( argstr='-outputroot %s', + extensions=None, mandatory=True, ), stat=dict( @@ -35,7 +36,7 @@ def test_ImageStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageStats_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ImageStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 8998f42602..996d8f4b99 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -6,13 +6,17 @@ def test_LinRecon_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -25,11 +29,13 @@ def test_LinRecon_inputs(): ), qball_mat=dict( argstr='%s', + extensions=None, mandatory=True, position=3, ), scheme_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -40,7 +46,7 @@ def test_LinRecon_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LinRecon_outputs(): - output_map = dict(recon_data=dict(), ) + output_map = dict(recon_data=dict(extensions=None, ), ) outputs = LinRecon.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index 73089a3395..57dbbf3b28 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -6,7 +6,10 @@ def test_MESD_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -17,6 +20,7 @@ def test_MESD_inputs(): ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, position=1, ), @@ -43,6 +47,7 @@ def test_MESD_inputs(): ), scheme_file=dict( argstr='-schemefile %s', + extensions=None, mandatory=True, ), ) @@ -52,7 +57,7 @@ def test_MESD_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MESD_outputs(): - output_map = dict(mesd_data=dict(), ) + output_map = dict(mesd_data=dict(extensions=None, ), ) outputs = MESD.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index 04d22bbe59..e5c16ec975 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -6,7 +6,10 @@ def test_ModelFit_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + extensions=None, + ), bgthresh=dict(argstr='-bgthresh %G', ), cfthresh=dict(argstr='-csfthresh %G', ), environ=dict( @@ -17,6 +20,7 @@ def test_ModelFit_inputs(): fixedmodq=dict(argstr='-fixedmod %s', ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -24,17 +28,30 @@ def test_ModelFit_inputs(): argstr='-model %s', mandatory=True, ), - noisemap=dict(argstr='-noisemap %s', ), + noisemap=dict( + argstr='-noisemap %s', + extensions=None, + ), out_file=dict( argstr='> %s', genfile=True, position=-1, ), - outlier=dict(argstr='-outliermap %s', ), - outputfile=dict(argstr='-outputfile %s', ), - residualmap=dict(argstr='-residualmap %s', ), + outlier=dict( + argstr='-outliermap %s', + extensions=None, + ), + outputfile=dict( + argstr='-outputfile %s', + extensions=None, + ), + residualmap=dict( + argstr='-residualmap %s', + extensions=None, + ), scheme_file=dict( argstr='-schemefile %s', + extensions=None, mandatory=True, ), sigma=dict(argstr='-sigma %G', ), @@ -46,7 +63,7 @@ def test_ModelFit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ModelFit_outputs(): - output_map = dict(fitted_data=dict(), ) + output_map = dict(fitted_data=dict(extensions=None, ), ) outputs = ModelFit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 9a4867a73c..0a5583b03e 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -6,23 +6,33 @@ def test_NIfTIDT2Camino_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, position=1, ), - lns0_file=dict(argstr='-lns0 %s', ), + lns0_file=dict( + argstr='-lns0 %s', + extensions=None, + ), out_file=dict( argstr='> %s', genfile=True, position=-1, ), - s0_file=dict(argstr='-s0 %s', ), + s0_file=dict( + argstr='-s0 %s', + extensions=None, + ), scaleinter=dict(argstr='-scaleinter %s', ), scaleslope=dict(argstr='-scaleslope %s', ), uppertriangular=dict(argstr='-uppertriangular %s', ), @@ -33,7 +43,7 @@ def test_NIfTIDT2Camino_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NIfTIDT2Camino_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = NIfTIDT2Camino.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index f2b59666a2..c918a372f1 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -13,6 +13,7 @@ def test_PicoPDFs_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=1, ), @@ -50,7 +51,7 @@ def test_PicoPDFs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PicoPDFs_outputs(): - output_map = dict(pdfs=dict(), ) + output_map = dict(pdfs=dict(extensions=None, ), ) outputs = PicoPDFs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index 8838bb72cf..c30ef08d8c 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -16,15 +16,22 @@ def test_ProcStreamlines_inputs(): units='NA', ), discardloops=dict(argstr='-discardloops', ), - endpointfile=dict(argstr='-endpointfile %s', ), + endpointfile=dict( + argstr='-endpointfile %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), - exclusionfile=dict(argstr='-exclusionfile %s', ), + exclusionfile=dict( + argstr='-exclusionfile %s', + extensions=None, + ), gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, position=1, ), @@ -70,7 +77,10 @@ def test_ProcStreamlines_inputs(): argstr='-outputcp', requires=['outputroot', 'seedfile'], ), - outputroot=dict(argstr='-outputroot %s', ), + outputroot=dict( + argstr='-outputroot %s', + extensions=None, + ), outputsc=dict( argstr='-outputsc', requires=['outputroot', 'seedfile'], @@ -84,7 +94,10 @@ def test_ProcStreamlines_inputs(): argstr='-resamplestepsize %d', units='NA', ), - seedfile=dict(argstr='-seedfile %s', ), + seedfile=dict( + argstr='-seedfile %s', + extensions=None, + ), seedpointmm=dict( argstr='-seedpointmm %s', units='mm', @@ -93,14 +106,20 @@ def test_ProcStreamlines_inputs(): argstr='-seedpointvox %s', units='voxels', ), - targetfile=dict(argstr='-targetfile %s', ), + targetfile=dict( + argstr='-targetfile %s', + extensions=None, + ), truncateinexclusion=dict(argstr='-truncateinexclusion', ), truncateloops=dict(argstr='-truncateloops', ), voxeldims=dict( argstr='-voxeldims %s', units='mm', ), - waypointfile=dict(argstr='-waypointfile %s', ), + waypointfile=dict( + argstr='-waypointfile %s', + extensions=None, + ), ) inputs = ProcStreamlines.input_spec() @@ -110,7 +129,7 @@ def test_ProcStreamlines_inputs(): def test_ProcStreamlines_outputs(): output_map = dict( outputroot_files=dict(), - proc=dict(), + proc=dict(extensions=None, ), ) outputs = ProcStreamlines.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index e965cb606a..7f7d0bc99f 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -33,6 +33,7 @@ def test_QBallMX_inputs(): ), scheme_file=dict( argstr='-schemefile %s', + extensions=None, mandatory=True, ), smoothingsigma=dict( @@ -46,7 +47,7 @@ def test_QBallMX_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_QBallMX_outputs(): - output_map = dict(qmat=dict(), ) + output_map = dict(qmat=dict(extensions=None, ), ) outputs = QBallMX.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index c52ca04929..795138ea89 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -17,10 +17,12 @@ def test_SFLUTGen_inputs(): ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, ), info_file=dict( argstr='-infofile %s', + extensions=None, mandatory=True, ), minvectsperbin=dict( @@ -52,8 +54,8 @@ def test_SFLUTGen_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SFLUTGen_outputs(): output_map = dict( - lut_one_fibre=dict(), - lut_two_fibres=dict(), + lut_one_fibre=dict(extensions=None, ), + lut_two_fibres=dict(extensions=None, ), ) outputs = SFLUTGen.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index e83a01e2c3..80222fce4c 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -12,6 +12,7 @@ def test_SFPICOCalibData_inputs(): ), info_file=dict( argstr='-infooutputfile %s', + extensions=None, genfile=True, hash_files=False, mandatory=True, @@ -31,6 +32,7 @@ def test_SFPICOCalibData_inputs(): ), scheme_file=dict( argstr='-schemefile %s', + extensions=None, mandatory=True, ), seed=dict( @@ -77,8 +79,8 @@ def test_SFPICOCalibData_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SFPICOCalibData_outputs(): output_map = dict( - PICOCalib=dict(), - calib_info=dict(), + PICOCalib=dict(extensions=None, ), + calib_info=dict(extensions=None, ), ) outputs = SFPICOCalibData.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 959545d042..8db250c58c 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -16,6 +16,7 @@ def test_SFPeaks_inputs(): ), in_file=dict( argstr='-inputfile %s', + extensions=None, mandatory=True, ), inputmodel=dict( @@ -52,7 +53,10 @@ def test_SFPeaks_inputs(): argstr='-rbfpointset %d', units='NA', ), - scheme_file=dict(argstr='%s', ), + scheme_file=dict( + argstr='%s', + extensions=None, + ), searchradius=dict( argstr='-searchradius %f', units='NA', @@ -68,7 +72,7 @@ def test_SFPeaks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SFPeaks_outputs(): - output_map = dict(peaks=dict(), ) + output_map = dict(peaks=dict(extensions=None, ), ) outputs = SFPeaks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 1099693874..594b35fc60 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -17,6 +17,7 @@ def test_Shredder_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=-2, ), @@ -42,7 +43,7 @@ def test_Shredder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Shredder_outputs(): - output_map = dict(shredded=dict(), ) + output_map = dict(shredded=dict(extensions=None, ), ) outputs = Shredder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index ad8d3ff2bb..fa03ce29d3 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -5,7 +5,10 @@ def test_Track_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -24,6 +27,7 @@ def test_Track_inputs(): gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -43,16 +47,19 @@ def test_Track_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -74,7 +81,7 @@ def test_Track_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Track_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = Track.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 89515cef55..d6c7d332ac 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -5,7 +5,10 @@ def test_TrackBallStick_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -24,6 +27,7 @@ def test_TrackBallStick_inputs(): gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -43,16 +47,19 @@ def test_TrackBallStick_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -74,7 +81,7 @@ def test_TrackBallStick_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBallStick_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = TrackBallStick.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 2815ef18ee..fe28f030a3 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -5,7 +5,10 @@ def test_TrackBayesDirac_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -25,10 +28,14 @@ def test_TrackBayesDirac_inputs(): usedefault=True, ), extpriordatatype=dict(argstr='-extpriordatatype %s', ), - extpriorfile=dict(argstr='-extpriorfile %s', ), + extpriorfile=dict( + argstr='-extpriorfile %s', + extensions=None, + ), gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -52,11 +59,13 @@ def test_TrackBayesDirac_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), @@ -64,10 +73,12 @@ def test_TrackBayesDirac_inputs(): pointset=dict(argstr='-pointset %s', ), scheme_file=dict( argstr='-schemefile %s', + extensions=None, mandatory=True, ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -89,7 +100,7 @@ def test_TrackBayesDirac_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBayesDirac_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = TrackBayesDirac.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index 827dbb2f27..483e752914 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -5,7 +5,10 @@ def test_TrackBedpostxDeter_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), bedpostxdir=dict( @@ -28,6 +31,7 @@ def test_TrackBedpostxDeter_inputs(): gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -51,16 +55,19 @@ def test_TrackBedpostxDeter_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -82,7 +89,7 @@ def test_TrackBedpostxDeter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxDeter_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = TrackBedpostxDeter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index e250ec9c40..b37cf9e550 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -5,7 +5,10 @@ def test_TrackBedpostxProba_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), bedpostxdir=dict( @@ -28,6 +31,7 @@ def test_TrackBedpostxProba_inputs(): gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -55,16 +59,19 @@ def test_TrackBedpostxProba_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -86,7 +93,7 @@ def test_TrackBedpostxProba_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxProba_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = TrackBedpostxProba.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 90ffd05a2d..dec2509b1f 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -5,10 +5,16 @@ def test_TrackBootstrap_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + extensions=None, + ), bsdatafiles=dict( argstr='-bsdatafile %s', mandatory=True, @@ -29,6 +35,7 @@ def test_TrackBootstrap_inputs(): gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -53,20 +60,24 @@ def test_TrackBootstrap_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), scheme_file=dict( argstr='-schemefile %s', + extensions=None, mandatory=True, ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -88,7 +99,7 @@ def test_TrackBootstrap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBootstrap_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = TrackBootstrap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index 7ab3772468..ace97fc8f7 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -5,7 +5,10 @@ def test_TrackDT_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -24,6 +27,7 @@ def test_TrackDT_inputs(): gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -43,16 +47,19 @@ def test_TrackDT_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -74,7 +81,7 @@ def test_TrackDT_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackDT_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = TrackDT.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index 30ff12db9f..e28e87dc8f 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -5,7 +5,10 @@ def test_TrackPICo_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + extensions=None, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -24,6 +27,7 @@ def test_TrackPICo_inputs(): gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', + extensions=None, position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), @@ -47,17 +51,20 @@ def test_TrackPICo_inputs(): ), out_file=dict( argstr='-outputfile %s', + extensions=None, genfile=True, position=-1, ), output_root=dict( argstr='-outputroot %s', + extensions=None, position=-1, ), outputtracts=dict(argstr='-outputtracts %s', ), pdf=dict(argstr='-pdf %s', ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=2, ), stepsize=dict( @@ -79,7 +86,7 @@ def test_TrackPICo_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackPICo_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = TrackPICo.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index c9cf40e1c3..eeed244533 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -17,6 +17,7 @@ def test_TractShredder_inputs(): ), in_file=dict( argstr='< %s', + extensions=None, mandatory=True, position=-2, ), @@ -42,7 +43,7 @@ def test_TractShredder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TractShredder_outputs(): - output_map = dict(shredded=dict(), ) + output_map = dict(shredded=dict(extensions=None, ), ) outputs = TractShredder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 8dc8bd03e9..72b6f106d8 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -13,6 +13,7 @@ def test_VtkStreamlines_inputs(): ), in_file=dict( argstr=' < %s', + extensions=None, mandatory=True, position=-2, ), @@ -29,14 +30,17 @@ def test_VtkStreamlines_inputs(): ), scalar_file=dict( argstr='-scalarfile %s', + extensions=None, position=3, ), seed_file=dict( argstr='-seedfile %s', + extensions=None, position=1, ), target_file=dict( argstr='-targetfile %s', + extensions=None, position=2, ), voxeldims=dict( @@ -51,7 +55,7 @@ def test_VtkStreamlines_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VtkStreamlines_outputs(): - output_map = dict(vtk=dict(), ) + output_map = dict(vtk=dict(extensions=None, ), ) outputs = VtkStreamlines.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index b4d5092dab..4a88a119fb 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -18,6 +18,7 @@ def test_Camino2Trackvis_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=1, ), @@ -28,10 +29,12 @@ def test_Camino2Trackvis_inputs(): ), nifti_file=dict( argstr='--nifti %s', + extensions=None, position=7, ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, position=2, ), @@ -43,6 +46,7 @@ def test_Camino2Trackvis_inputs(): ), voxel_order=dict( argstr='--voxel-order %s', + extensions=None, mandatory=True, position=6, ), @@ -53,7 +57,7 @@ def test_Camino2Trackvis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Camino2Trackvis_outputs(): - output_map = dict(trackvis=dict(), ) + output_map = dict(trackvis=dict(extensions=None, ), ) outputs = Camino2Trackvis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 978b2439a2..f54284fe50 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -7,6 +7,7 @@ def test_Trackvis2Camino_inputs(): input_map = dict( append_file=dict( argstr='-a %s', + extensions=None, position=2, ), args=dict(argstr='%s', ), @@ -16,11 +17,13 @@ def test_Trackvis2Camino_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=1, ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, position=2, ), @@ -31,7 +34,7 @@ def test_Trackvis2Camino_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Trackvis2Camino_outputs(): - output_map = dict(camino=dict(), ) + output_map = dict(camino=dict(extensions=None, ), ) outputs = Trackvis2Camino.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index a80bbe757a..bf7b1a8553 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -7,9 +7,9 @@ def test_AverageNetworks_inputs(): input_map = dict( group_id=dict(usedefault=True, ), in_files=dict(mandatory=True, ), - out_gexf_groupavg=dict(), - out_gpickled_groupavg=dict(), - resolution_network_file=dict(), + out_gexf_groupavg=dict(extensions=None, ), + out_gpickled_groupavg=dict(extensions=None, ), + resolution_network_file=dict(extensions=None, ), ) inputs = AverageNetworks.input_spec() @@ -18,8 +18,8 @@ def test_AverageNetworks_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AverageNetworks_outputs(): output_map = dict( - gexf_groupavg=dict(), - gpickled_groupavg=dict(), + gexf_groupavg=dict(extensions=None, ), + gpickled_groupavg=dict(extensions=None, ), matlab_groupavgs=dict(), ) outputs = AverageNetworks.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index 00a1acea98..254aa23d6f 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -15,7 +15,10 @@ def test_CFFConverter_inputs(): graphml_networks=dict(), license=dict(), nifti_volumes=dict(), - out_file=dict(usedefault=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), publisher=dict(), references=dict(), relation=dict(), @@ -32,7 +35,7 @@ def test_CFFConverter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CFFConverter_outputs(): - output_map = dict(connectome_file=dict(), ) + output_map = dict(connectome_file=dict(extensions=None, ), ) outputs = CFFConverter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py index 60e8596f5e..282e343c07 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py @@ -6,16 +6,46 @@ def test_CreateMatrix_inputs(): input_map = dict( count_region_intersections=dict(usedefault=True, ), - out_endpoint_array_name=dict(genfile=True, ), - out_fiber_length_std_matrix_mat_file=dict(genfile=True, ), - out_intersection_matrix_mat_file=dict(genfile=True, ), - out_matrix_file=dict(genfile=True, ), - out_matrix_mat_file=dict(usedefault=True, ), - out_mean_fiber_length_matrix_mat_file=dict(genfile=True, ), - out_median_fiber_length_matrix_mat_file=dict(genfile=True, ), - resolution_network_file=dict(mandatory=True, ), - roi_file=dict(mandatory=True, ), - tract_file=dict(mandatory=True, ), + out_endpoint_array_name=dict( + extensions=None, + genfile=True, + ), + out_fiber_length_std_matrix_mat_file=dict( + extensions=None, + genfile=True, + ), + out_intersection_matrix_mat_file=dict( + extensions=None, + genfile=True, + ), + out_matrix_file=dict( + extensions=None, + genfile=True, + ), + out_matrix_mat_file=dict( + extensions=None, + usedefault=True, + ), + out_mean_fiber_length_matrix_mat_file=dict( + extensions=None, + genfile=True, + ), + out_median_fiber_length_matrix_mat_file=dict( + extensions=None, + genfile=True, + ), + resolution_network_file=dict( + extensions=None, + mandatory=True, + ), + roi_file=dict( + extensions=None, + mandatory=True, + ), + tract_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = CreateMatrix.input_spec() @@ -24,24 +54,24 @@ def test_CreateMatrix_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CreateMatrix_outputs(): output_map = dict( - endpoint_file=dict(), - endpoint_file_mm=dict(), - fiber_label_file=dict(), - fiber_labels_noorphans=dict(), - fiber_length_file=dict(), - fiber_length_std_matrix_mat_file=dict(), + endpoint_file=dict(extensions=None, ), + endpoint_file_mm=dict(extensions=None, ), + fiber_label_file=dict(extensions=None, ), + fiber_labels_noorphans=dict(extensions=None, ), + fiber_length_file=dict(extensions=None, ), + fiber_length_std_matrix_mat_file=dict(extensions=None, ), filtered_tractographies=dict(), - filtered_tractography=dict(), - filtered_tractography_by_intersections=dict(), - intersection_matrix_file=dict(), - intersection_matrix_mat_file=dict(), + filtered_tractography=dict(extensions=None, ), + filtered_tractography_by_intersections=dict(extensions=None, ), + intersection_matrix_file=dict(extensions=None, ), + intersection_matrix_mat_file=dict(extensions=None, ), matlab_matrix_files=dict(), - matrix_file=dict(), + matrix_file=dict(extensions=None, ), matrix_files=dict(), - matrix_mat_file=dict(), - mean_fiber_length_matrix_mat_file=dict(), - median_fiber_length_matrix_mat_file=dict(), - stats_file=dict(), + matrix_mat_file=dict(extensions=None, ), + mean_fiber_length_matrix_mat_file=dict(extensions=None, ), + median_fiber_length_matrix_mat_file=dict(extensions=None, ), + stats_file=dict(extensions=None, ), ) outputs = CreateMatrix.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 3635f21e59..ada2fa4b6a 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -5,9 +5,18 @@ def test_CreateNodes_inputs(): input_map = dict( - out_filename=dict(usedefault=True, ), - resolution_network_file=dict(mandatory=True, ), - roi_file=dict(mandatory=True, ), + out_filename=dict( + extensions=None, + usedefault=True, + ), + resolution_network_file=dict( + extensions=None, + mandatory=True, + ), + roi_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = CreateNodes.input_spec() @@ -15,7 +24,7 @@ def test_CreateNodes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateNodes_outputs(): - output_map = dict(node_network=dict(), ) + output_map = dict(node_network=dict(extensions=None, ), ) outputs = CreateNodes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index ceaa6d8dea..770b225e13 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -6,7 +6,10 @@ def test_MergeCNetworks_inputs(): input_map = dict( in_files=dict(mandatory=True, ), - out_file=dict(usedefault=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), ) inputs = MergeCNetworks.input_spec() @@ -14,7 +17,7 @@ def test_MergeCNetworks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeCNetworks_outputs(): - output_map = dict(connectome_file=dict(), ) + output_map = dict(connectome_file=dict(extensions=None, ), ) outputs = MergeCNetworks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index e3220e4790..ac41946548 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -8,10 +8,10 @@ def test_NetworkBasedStatistic_inputs(): edge_key=dict(usedefault=True, ), in_group1=dict(mandatory=True, ), in_group2=dict(mandatory=True, ), - node_position_network=dict(), + node_position_network=dict(extensions=None, ), number_of_permutations=dict(usedefault=True, ), - out_nbs_network=dict(), - out_nbs_pval_network=dict(), + out_nbs_network=dict(extensions=None, ), + out_nbs_pval_network=dict(extensions=None, ), t_tail=dict(usedefault=True, ), threshold=dict(usedefault=True, ), ) @@ -22,8 +22,8 @@ def test_NetworkBasedStatistic_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_NetworkBasedStatistic_outputs(): output_map = dict( - nbs_network=dict(), - nbs_pval_network=dict(), + nbs_network=dict(extensions=None, ), + nbs_pval_network=dict(extensions=None, ), network_files=dict(), ) outputs = NetworkBasedStatistic.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index d9a3f0c740..09b661a3fb 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -6,14 +6,38 @@ def test_NetworkXMetrics_inputs(): input_map = dict( compute_clique_related_measures=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - out_edge_metrics_matlab=dict(genfile=True, ), - out_global_metrics_matlab=dict(genfile=True, ), - out_k_core=dict(usedefault=True, ), - out_k_crust=dict(usedefault=True, ), - out_k_shell=dict(usedefault=True, ), - out_node_metrics_matlab=dict(genfile=True, ), - out_pickled_extra_measures=dict(usedefault=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), + out_edge_metrics_matlab=dict( + extensions=None, + genfile=True, + ), + out_global_metrics_matlab=dict( + extensions=None, + genfile=True, + ), + out_k_core=dict( + extensions=None, + usedefault=True, + ), + out_k_crust=dict( + extensions=None, + usedefault=True, + ), + out_k_shell=dict( + extensions=None, + usedefault=True, + ), + out_node_metrics_matlab=dict( + extensions=None, + genfile=True, + ), + out_pickled_extra_measures=dict( + extensions=None, + usedefault=True, + ), treat_as_weighted_graph=dict(usedefault=True, ), ) inputs = NetworkXMetrics.input_spec() @@ -24,18 +48,18 @@ def test_NetworkXMetrics_inputs(): def test_NetworkXMetrics_outputs(): output_map = dict( edge_measure_networks=dict(), - edge_measures_matlab=dict(), - global_measures_matlab=dict(), + edge_measures_matlab=dict(extensions=None, ), + global_measures_matlab=dict(extensions=None, ), gpickled_network_files=dict(), - k_core=dict(), - k_crust=dict(), + k_core=dict(extensions=None, ), + k_crust=dict(extensions=None, ), k_networks=dict(), - k_shell=dict(), + k_shell=dict(extensions=None, ), matlab_dict_measures=dict(), matlab_matrix_files=dict(), node_measure_networks=dict(), - node_measures_matlab=dict(), - pickled_extra_measures=dict(), + node_measures_matlab=dict(extensions=None, ), + pickled_extra_measures=dict(extensions=None, ), ) outputs = NetworkXMetrics.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index edcdf2e7a1..ca7609298a 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -7,7 +7,10 @@ def test_Parcellate_inputs(): input_map = dict( dilation=dict(usedefault=True, ), freesurfer_dir=dict(), - out_roi_file=dict(genfile=True, ), + out_roi_file=dict( + extensions=None, + genfile=True, + ), parcellation_name=dict(usedefault=True, ), subject_id=dict(mandatory=True, ), subjects_dir=dict(), @@ -19,14 +22,14 @@ def test_Parcellate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Parcellate_outputs(): output_map = dict( - aseg_file=dict(), - cc_unknown_file=dict(), - dilated_roi_file_in_structural_space=dict(), - ribbon_file=dict(), - roi_file=dict(), - roi_file_in_structural_space=dict(), - roiv_file=dict(), - white_matter_mask_file=dict(), + aseg_file=dict(extensions=None, ), + cc_unknown_file=dict(extensions=None, ), + dilated_roi_file_in_structural_space=dict(extensions=None, ), + ribbon_file=dict(extensions=None, ), + roi_file=dict(extensions=None, ), + roi_file_in_structural_space=dict(extensions=None, ), + roiv_file=dict(extensions=None, ), + white_matter_mask_file=dict(extensions=None, ), ) outputs = Parcellate.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index dd2ce50aec..0d6383f391 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -5,11 +5,23 @@ def test_ROIGen_inputs(): input_map = dict( - LUT_file=dict(xor=['use_freesurfer_LUT'], ), - aparc_aseg_file=dict(mandatory=True, ), + LUT_file=dict( + extensions=None, + xor=['use_freesurfer_LUT'], + ), + aparc_aseg_file=dict( + extensions=None, + mandatory=True, + ), freesurfer_dir=dict(requires=['use_freesurfer_LUT'], ), - out_dict_file=dict(genfile=True, ), - out_roi_file=dict(genfile=True, ), + out_dict_file=dict( + extensions=None, + genfile=True, + ), + out_roi_file=dict( + extensions=None, + genfile=True, + ), use_freesurfer_LUT=dict(xor=['LUT_file'], ), ) inputs = ROIGen.input_spec() @@ -19,8 +31,8 @@ def test_ROIGen_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ROIGen_outputs(): output_map = dict( - dict_file=dict(), - roi_file=dict(), + dict_file=dict(extensions=None, ), + roi_file=dict(extensions=None, ), ) outputs = ROIGen.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index a39dbf6c3b..c4faac0a67 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -7,14 +7,19 @@ def test_DTIRecon_inputs(): input_map = dict( DWI=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), args=dict(argstr='%s', ), b0_threshold=dict(argstr='-b0_th', ), - bvals=dict(mandatory=True, ), + bvals=dict( + extensions=None, + mandatory=True, + ), bvecs=dict( argstr='-gm %s', + extensions=None, mandatory=True, ), environ=dict( @@ -41,18 +46,18 @@ def test_DTIRecon_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTIRecon_outputs(): output_map = dict( - ADC=dict(), - B0=dict(), - FA=dict(), - FA_color=dict(), - L1=dict(), - L2=dict(), - L3=dict(), - V1=dict(), - V2=dict(), - V3=dict(), - exp=dict(), - tensor=dict(), + ADC=dict(extensions=None, ), + B0=dict(extensions=None, ), + FA=dict(extensions=None, ), + FA_color=dict(extensions=None, ), + L1=dict(extensions=None, ), + L2=dict(extensions=None, ), + L3=dict(extensions=None, ), + V1=dict(extensions=None, ), + V2=dict(extensions=None, ), + V3=dict(extensions=None, ), + exp=dict(extensions=None, ), + tensor=dict(extensions=None, ), ) outputs = DTIRecon.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index cf483d00d0..3fd69ee6b8 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -23,28 +23,34 @@ def test_DTITracker_inputs(): invert_z=dict(argstr='-iz', ), mask1_file=dict( argstr='-m %s', + extensions=None, mandatory=True, position=2, ), mask1_threshold=dict(position=3, ), mask2_file=dict( argstr='-m2 %s', + extensions=None, position=4, ), mask2_threshold=dict(position=5, ), output_file=dict( argstr='%s', + extensions=None, position=1, usedefault=True, ), - output_mask=dict(argstr='-om %s', ), + output_mask=dict( + argstr='-om %s', + extensions=None, + ), primary_vector=dict(argstr='-%s', ), random_seed=dict(argstr='-rseed %d', ), step_length=dict(argstr='-l %f', ), swap_xy=dict(argstr='-sxy', ), swap_yz=dict(argstr='-syz', ), swap_zx=dict(argstr='-szx', ), - tensor_file=dict(), + tensor_file=dict(extensions=None, ), tracking_method=dict(argstr='-%s', ), ) inputs = DTITracker.input_spec() @@ -54,8 +60,8 @@ def test_DTITracker_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTITracker_outputs(): output_map = dict( - mask_file=dict(), - track_file=dict(), + mask_file=dict(extensions=None, ), + track_file=dict(extensions=None, ), ) outputs = DTITracker.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 59bc8c25a5..5391290021 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -6,9 +6,13 @@ def test_HARDIMat_inputs(): input_map = dict( args=dict(argstr='%s', ), - bvals=dict(mandatory=True, ), + bvals=dict( + extensions=None, + mandatory=True, + ), bvecs=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -16,17 +20,27 @@ def test_HARDIMat_inputs(): nohash=True, usedefault=True, ), - image_info=dict(argstr='-info %s', ), + image_info=dict( + argstr='-info %s', + extensions=None, + ), image_orientation_vectors=dict(argstr='-iop %f', ), oblique_correction=dict(argstr='-oc', ), - odf_file=dict(argstr='-odf %s', ), + odf_file=dict( + argstr='-odf %s', + extensions=None, + ), order=dict(argstr='-order %s', ), out_file=dict( argstr='%s', + extensions=None, position=2, usedefault=True, ), - reference_file=dict(argstr='-ref %s', ), + reference_file=dict( + argstr='-ref %s', + extensions=None, + ), ) inputs = HARDIMat.input_spec() @@ -34,7 +48,7 @@ def test_HARDIMat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HARDIMat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = HARDIMat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index 1e66b93bec..c7a2d30989 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -7,6 +7,7 @@ def test_ODFRecon_inputs(): input_map = dict( DWI=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -20,6 +21,7 @@ def test_ODFRecon_inputs(): image_orientation_vectors=dict(argstr='-iop %f', ), matrix=dict( argstr='-mat %s', + extensions=None, mandatory=True, ), n_b0=dict( @@ -57,11 +59,11 @@ def test_ODFRecon_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ODFRecon_outputs(): output_map = dict( - B0=dict(), - DWI=dict(), - ODF=dict(), - entropy=dict(), - max=dict(), + B0=dict(extensions=None, ), + DWI=dict(extensions=None, ), + ODF=dict(extensions=None, ), + entropy=dict(extensions=None, ), + max=dict(extensions=None, ), ) outputs = ODFRecon.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 41b2d530f6..3973421df8 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -5,7 +5,10 @@ def test_ODFTracker_inputs(): input_map = dict( - ODF=dict(mandatory=True, ), + ODF=dict( + extensions=None, + mandatory=True, + ), angle_threshold=dict(argstr='-at %f', ), args=dict(argstr='%s', ), disc=dict(argstr='-disc', ), @@ -30,18 +33,24 @@ def test_ODFTracker_inputs(): limit=dict(argstr='-limit %d', ), mask1_file=dict( argstr='-m %s', + extensions=None, mandatory=True, position=2, ), mask1_threshold=dict(position=3, ), mask2_file=dict( argstr='-m2 %s', + extensions=None, position=4, ), mask2_threshold=dict(position=5, ), - max=dict(mandatory=True, ), + max=dict( + extensions=None, + mandatory=True, + ), out_file=dict( argstr='%s', + extensions=None, position=1, usedefault=True, ), @@ -60,7 +69,7 @@ def test_ODFTracker_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ODFTracker_outputs(): - output_map = dict(track_file=dict(), ) + output_map = dict(track_file=dict(extensions=None, ), ) outputs = ODFTracker.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index 8648a1f1f9..85c0d08d13 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -12,6 +12,7 @@ def test_SplineFilter_inputs(): ), output_file=dict( argstr='%s', + extensions=None, position=2, usedefault=True, ), @@ -22,6 +23,7 @@ def test_SplineFilter_inputs(): ), track_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -32,7 +34,7 @@ def test_SplineFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SplineFilter_outputs(): - output_map = dict(smoothed_track_file=dict(), ) + output_map = dict(smoothed_track_file=dict(extensions=None, ), ) outputs = SplineFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index b004678175..cf9756887a 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -12,6 +12,7 @@ def test_TrackMerge_inputs(): ), output_file=dict( argstr='%s', + extensions=None, position=-1, usedefault=True, ), @@ -27,7 +28,7 @@ def test_TrackMerge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackMerge_outputs(): - output_map = dict(track_file=dict(), ) + output_map = dict(track_file=dict(extensions=None, ), ) outputs = TrackMerge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_APMQball.py b/nipype/interfaces/dipy/tests/test_auto_APMQball.py index f6f3f2e4c6..b50bd96b58 100644 --- a/nipype/interfaces/dipy/tests/test_auto_APMQball.py +++ b/nipype/interfaces/dipy/tests/test_auto_APMQball.py @@ -6,10 +6,19 @@ def test_APMQball_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - mask_file=dict(), + in_bval=dict( + extensions=None, + mandatory=True, + ), + in_bvec=dict( + extensions=None, + mandatory=True, + ), + in_file=dict( + extensions=None, + mandatory=True, + ), + mask_file=dict(extensions=None, ), out_prefix=dict(), ) inputs = APMQball.input_spec() @@ -18,7 +27,7 @@ def test_APMQball_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_APMQball_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = APMQball.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_CSD.py b/nipype/interfaces/dipy/tests/test_auto_CSD.py index a30efaa3cc..1343c0ddd7 100644 --- a/nipype/interfaces/dipy/tests/test_auto_CSD.py +++ b/nipype/interfaces/dipy/tests/test_auto_CSD.py @@ -6,13 +6,22 @@ def test_CSD_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - out_fods=dict(), + in_bval=dict( + extensions=None, + mandatory=True, + ), + in_bvec=dict( + extensions=None, + mandatory=True, + ), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_mask=dict(extensions=None, ), + out_fods=dict(extensions=None, ), out_prefix=dict(), - response=dict(), + response=dict(extensions=None, ), save_fods=dict(usedefault=True, ), sh_order=dict(usedefault=True, ), ) @@ -23,8 +32,8 @@ def test_CSD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CSD_outputs(): output_map = dict( - model=dict(), - out_fods=dict(), + model=dict(extensions=None, ), + out_fods=dict(extensions=None, ), ) outputs = CSD.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index f543856065..c1c22c6263 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -6,10 +6,19 @@ def test_DTI_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - mask_file=dict(), + in_bval=dict( + extensions=None, + mandatory=True, + ), + in_bvec=dict( + extensions=None, + mandatory=True, + ), + in_file=dict( + extensions=None, + mandatory=True, + ), + mask_file=dict(extensions=None, ), out_prefix=dict(), ) inputs = DTI.input_spec() @@ -19,12 +28,12 @@ def test_DTI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTI_outputs(): output_map = dict( - ad_file=dict(), - color_fa_file=dict(), - fa_file=dict(), - md_file=dict(), - out_file=dict(), - rd_file=dict(), + ad_file=dict(extensions=None, ), + color_fa_file=dict(extensions=None, ), + fa_file=dict(extensions=None, ), + md_file=dict(extensions=None, ), + out_file=dict(extensions=None, ), + rd_file=dict(extensions=None, ), ) outputs = DTI.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_Denoise.py b/nipype/interfaces/dipy/tests/test_auto_Denoise.py index 88a1bc5314..57beb6e06f 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Denoise.py +++ b/nipype/interfaces/dipy/tests/test_auto_Denoise.py @@ -6,15 +6,18 @@ def test_Denoise_inputs(): input_map = dict( block_radius=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - noise_mask=dict(), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_mask=dict(extensions=None, ), + noise_mask=dict(extensions=None, ), noise_model=dict( mandatory=True, usedefault=True, ), patch_radius=dict(usedefault=True, ), - signal_mask=dict(), + signal_mask=dict(extensions=None, ), snr=dict(), ) inputs = Denoise.input_spec() @@ -23,7 +26,7 @@ def test_Denoise_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Denoise_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Denoise.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py index ee9022ca58..99249e3506 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py @@ -6,9 +6,18 @@ def test_DipyDiffusionInterface_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), + in_bval=dict( + extensions=None, + mandatory=True, + ), + in_bvec=dict( + extensions=None, + mandatory=True, + ), + in_file=dict( + extensions=None, + mandatory=True, + ), out_prefix=dict(), ) inputs = DipyDiffusionInterface.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py index 1270d94b13..bf18299fd4 100644 --- a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py +++ b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py @@ -8,15 +8,33 @@ def test_EstimateResponseSH_inputs(): auto=dict(xor=['recursive'], ), b0_thres=dict(usedefault=True, ), fa_thresh=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_evals=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - out_mask=dict(usedefault=True, ), + in_bval=dict( + extensions=None, + mandatory=True, + ), + in_bvec=dict( + extensions=None, + mandatory=True, + ), + in_evals=dict( + extensions=None, + mandatory=True, + ), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_mask=dict(extensions=None, ), + out_mask=dict( + extensions=None, + usedefault=True, + ), out_prefix=dict(), recursive=dict(xor=['auto'], ), - response=dict(usedefault=True, ), + response=dict( + extensions=None, + usedefault=True, + ), roi_radius=dict(usedefault=True, ), ) inputs = EstimateResponseSH.input_spec() @@ -26,8 +44,8 @@ def test_EstimateResponseSH_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseSH_outputs(): output_map = dict( - out_mask=dict(), - response=dict(), + out_mask=dict(extensions=None, ), + response=dict(extensions=None, ), ) outputs = EstimateResponseSH.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py index 9f62d05e0c..9f4e52ee66 100644 --- a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py +++ b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py @@ -6,11 +6,20 @@ def test_RESTORE_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - noise_mask=dict(), + in_bval=dict( + extensions=None, + mandatory=True, + ), + in_bvec=dict( + extensions=None, + mandatory=True, + ), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_mask=dict(extensions=None, ), + noise_mask=dict(extensions=None, ), out_prefix=dict(), ) inputs = RESTORE.input_spec() @@ -20,13 +29,13 @@ def test_RESTORE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RESTORE_outputs(): output_map = dict( - evals=dict(), - evecs=dict(), - fa=dict(), - md=dict(), - mode=dict(), - rd=dict(), - trace=dict(), + evals=dict(extensions=None, ), + evecs=dict(extensions=None, ), + fa=dict(extensions=None, ), + md=dict(extensions=None, ), + mode=dict(extensions=None, ), + rd=dict(extensions=None, ), + trace=dict(extensions=None, ), ) outputs = RESTORE.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_Resample.py b/nipype/interfaces/dipy/tests/test_auto_Resample.py index ff51e0efe4..a3e44c942a 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Resample.py +++ b/nipype/interfaces/dipy/tests/test_auto_Resample.py @@ -5,7 +5,10 @@ def test_Resample_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), interp=dict( mandatory=True, usedefault=True, @@ -18,7 +21,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index db46a3b982..48a12ec076 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -5,23 +5,38 @@ def test_SimulateMultiTensor_inputs(): input_map = dict( - baseline=dict(mandatory=True, ), + baseline=dict( + extensions=None, + mandatory=True, + ), bvalues=dict(usedefault=True, ), diff_iso=dict(usedefault=True, ), diff_sf=dict(usedefault=True, ), - gradients=dict(), - in_bval=dict(), - in_bvec=dict(), + gradients=dict(extensions=None, ), + in_bval=dict(extensions=None, ), + in_bvec=dict(extensions=None, ), in_dirs=dict(mandatory=True, ), in_frac=dict(mandatory=True, ), - in_mask=dict(), + in_mask=dict(extensions=None, ), in_vfms=dict(mandatory=True, ), n_proc=dict(usedefault=True, ), num_dirs=dict(usedefault=True, ), - out_bval=dict(usedefault=True, ), - out_bvec=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - out_mask=dict(usedefault=True, ), + out_bval=dict( + extensions=None, + usedefault=True, + ), + out_bvec=dict( + extensions=None, + usedefault=True, + ), + out_file=dict( + extensions=None, + usedefault=True, + ), + out_mask=dict( + extensions=None, + usedefault=True, + ), snr=dict(usedefault=True, ), ) inputs = SimulateMultiTensor.input_spec() @@ -31,10 +46,10 @@ def test_SimulateMultiTensor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SimulateMultiTensor_outputs(): output_map = dict( - out_bval=dict(), - out_bvec=dict(), - out_file=dict(), - out_mask=dict(), + out_bval=dict(extensions=None, ), + out_bvec=dict(extensions=None, ), + out_file=dict(extensions=None, ), + out_mask=dict(extensions=None, ), ) outputs = SimulateMultiTensor.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py index 1bc1a2ea97..71c20e8ec9 100644 --- a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py +++ b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py @@ -9,9 +9,12 @@ def test_StreamlineTractography_inputs(): mandatory=True, usedefault=True, ), - in_file=dict(mandatory=True, ), - in_model=dict(), - in_peaks=dict(), + in_file=dict( + extensions=None, + mandatory=True, + ), + in_model=dict(extensions=None, ), + in_peaks=dict(extensions=None, ), min_angle=dict( mandatory=True, usedefault=True, @@ -33,9 +36,9 @@ def test_StreamlineTractography_inputs(): mandatory=True, usedefault=True, ), - seed_coord=dict(), - seed_mask=dict(), - tracking_mask=dict(), + seed_coord=dict(extensions=None, ), + seed_mask=dict(extensions=None, ), + tracking_mask=dict(extensions=None, ), ) inputs = StreamlineTractography.input_spec() @@ -44,10 +47,10 @@ def test_StreamlineTractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTractography_outputs(): output_map = dict( - gfa=dict(), - odf_peaks=dict(), - out_seeds=dict(), - tracks=dict(), + gfa=dict(extensions=None, ), + odf_peaks=dict(extensions=None, ), + out_seeds=dict(extensions=None, ), + tracks=dict(extensions=None, ), ) outputs = StreamlineTractography.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index d072af78fc..532b930c80 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -6,10 +6,19 @@ def test_TensorMode_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - mask_file=dict(), + in_bval=dict( + extensions=None, + mandatory=True, + ), + in_bvec=dict( + extensions=None, + mandatory=True, + ), + in_file=dict( + extensions=None, + mandatory=True, + ), + mask_file=dict(extensions=None, ), out_prefix=dict(), ) inputs = TensorMode.input_spec() @@ -18,7 +27,7 @@ def test_TensorMode_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TensorMode_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TensorMode.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 79af3b5940..f1112421f5 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -6,10 +6,16 @@ def test_TrackDensityMap_inputs(): input_map = dict( data_dims=dict(), - in_file=dict(mandatory=True, ), - out_filename=dict(usedefault=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), + out_filename=dict( + extensions=None, + usedefault=True, + ), points_space=dict(usedefault=True, ), - reference=dict(), + reference=dict(extensions=None, ), voxel_dims=dict(), ) inputs = TrackDensityMap.input_spec() @@ -18,7 +24,7 @@ def test_TrackDensityMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackDensityMap_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TrackDensityMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py b/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py index 5f9262d788..f0d6da8d09 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py @@ -20,6 +20,7 @@ def test_AffScalarVol_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -28,16 +29,19 @@ def test_AffScalarVol_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_affxfmd', ), target=dict( argstr='-target %s', + extensions=None, xor=['transform'], ), transform=dict( argstr='-trans %s', + extensions=None, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -51,7 +55,7 @@ def test_AffScalarVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffScalarVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AffScalarVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py b/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py index 6d7abc852a..dd40117ace 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py @@ -20,6 +20,7 @@ def test_AffSymTensor3DVol_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -28,6 +29,7 @@ def test_AffSymTensor3DVol_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_affxfmd', @@ -38,10 +40,12 @@ def test_AffSymTensor3DVol_inputs(): ), target=dict( argstr='-target %s', + extensions=None, xor=['transform'], ), transform=dict( argstr='-trans %s', + extensions=None, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -55,7 +59,7 @@ def test_AffSymTensor3DVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffSymTensor3DVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AffSymTensor3DVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_Affine.py b/nipype/interfaces/dtitk/tests/test_auto_Affine.py index 78d2e6f011..89383c159d 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Affine.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Affine.py @@ -13,6 +13,7 @@ def test_Affine_inputs(): fixed_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=0, ), @@ -25,11 +26,13 @@ def test_Affine_inputs(): initialize_xfm=dict( argstr='%s', copyfile=True, + extensions=None, position=5, ), moving_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=1, ), @@ -53,8 +56,8 @@ def test_Affine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Affine_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(extensions=None, ), + out_file_xfm=dict(extensions=None, ), ) outputs = Affine.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py b/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py index 5f3b43153a..dadba5445f 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py @@ -13,6 +13,7 @@ def test_AffineTask_inputs(): fixed_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=0, ), @@ -25,11 +26,13 @@ def test_AffineTask_inputs(): initialize_xfm=dict( argstr='%s', copyfile=True, + extensions=None, position=5, ), moving_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=1, ), @@ -53,8 +56,8 @@ def test_AffineTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AffineTask_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(extensions=None, ), + out_file_xfm=dict(extensions=None, ), ) outputs = AffineTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py b/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py index cbd4efccb2..9872df1ee3 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py +++ b/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py @@ -12,6 +12,7 @@ def test_BinThresh_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -29,6 +30,7 @@ def test_BinThresh_inputs(): ), out_file=dict( argstr='%s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_thrbin', @@ -53,7 +55,7 @@ def test_BinThresh_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinThresh_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BinThresh.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py b/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py index dcd396abe2..a3cdcb5149 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py @@ -12,6 +12,7 @@ def test_BinThreshTask_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -29,6 +30,7 @@ def test_BinThreshTask_inputs(): ), out_file=dict( argstr='%s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_thrbin', @@ -53,7 +55,7 @@ def test_BinThreshTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinThreshTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BinThreshTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py index 09fcdc186e..a325f68b9f 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py +++ b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py @@ -12,14 +12,17 @@ def test_ComposeXfm_inputs(): ), in_aff=dict( argstr='-aff %s', + extensions=None, mandatory=True, ), in_df=dict( argstr='-df %s', + extensions=None, mandatory=True, ), out_file=dict( argstr='-out %s', + extensions=None, genfile=True, ), ) @@ -29,7 +32,7 @@ def test_ComposeXfm_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeXfm_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ComposeXfm.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py index 99c6f6d340..52bbd5cbcb 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py @@ -12,14 +12,17 @@ def test_ComposeXfmTask_inputs(): ), in_aff=dict( argstr='-aff %s', + extensions=None, mandatory=True, ), in_df=dict( argstr='-df %s', + extensions=None, mandatory=True, ), out_file=dict( argstr='-out %s', + extensions=None, genfile=True, ), ) @@ -29,7 +32,7 @@ def test_ComposeXfmTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeXfmTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ComposeXfmTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py b/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py index ad532bd631..66d28957de 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py @@ -12,6 +12,7 @@ def test_Diffeo_inputs(): ), fixed_file=dict( argstr='%s', + extensions=None, position=0, ), ftol=dict( @@ -28,11 +29,13 @@ def test_Diffeo_inputs(): ), mask_file=dict( argstr='%s', + extensions=None, position=2, ), moving_file=dict( argstr='%s', copyfile=False, + extensions=None, position=1, ), n_iters=dict( @@ -49,8 +52,8 @@ def test_Diffeo_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Diffeo_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(extensions=None, ), + out_file_xfm=dict(extensions=None, ), ) outputs = Diffeo.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py index 7d1305d384..0d459d7a0b 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py @@ -13,6 +13,7 @@ def test_DiffeoScalarVol_inputs(): flip=dict(argstr='-flip %d %d %d', ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -21,6 +22,7 @@ def test_DiffeoScalarVol_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', @@ -28,10 +30,12 @@ def test_DiffeoScalarVol_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + extensions=None, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', + extensions=None, mandatory=True, ), voxel_size=dict( @@ -45,7 +49,7 @@ def test_DiffeoScalarVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoScalarVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = DiffeoScalarVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py index b934c56d2b..a051d9f60f 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py @@ -17,6 +17,7 @@ def test_DiffeoSymTensor3DVol_inputs(): flip=dict(argstr='-flip %d %d %d', ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -25,6 +26,7 @@ def test_DiffeoSymTensor3DVol_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', @@ -36,10 +38,12 @@ def test_DiffeoSymTensor3DVol_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + extensions=None, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', + extensions=None, mandatory=True, ), voxel_size=dict( @@ -53,7 +57,7 @@ def test_DiffeoSymTensor3DVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoSymTensor3DVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = DiffeoSymTensor3DVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py index 5aea665d4c..8d78b37a55 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py @@ -12,6 +12,7 @@ def test_DiffeoTask_inputs(): ), fixed_file=dict( argstr='%s', + extensions=None, position=0, ), ftol=dict( @@ -28,11 +29,13 @@ def test_DiffeoTask_inputs(): ), mask_file=dict( argstr='%s', + extensions=None, position=2, ), moving_file=dict( argstr='%s', copyfile=False, + extensions=None, position=1, ), n_iters=dict( @@ -49,8 +52,8 @@ def test_DiffeoTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoTask_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(extensions=None, ), + out_file_xfm=dict(extensions=None, ), ) outputs = DiffeoTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_Rigid.py b/nipype/interfaces/dtitk/tests/test_auto_Rigid.py index ecb7c2d33b..6e9bf18764 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Rigid.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Rigid.py @@ -13,6 +13,7 @@ def test_Rigid_inputs(): fixed_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=0, ), @@ -25,11 +26,13 @@ def test_Rigid_inputs(): initialize_xfm=dict( argstr='%s', copyfile=True, + extensions=None, position=5, ), moving_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=1, ), @@ -53,8 +56,8 @@ def test_Rigid_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Rigid_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(extensions=None, ), + out_file_xfm=dict(extensions=None, ), ) outputs = Rigid.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py b/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py index c627fda741..987888d80f 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py @@ -13,6 +13,7 @@ def test_RigidTask_inputs(): fixed_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=0, ), @@ -25,11 +26,13 @@ def test_RigidTask_inputs(): initialize_xfm=dict( argstr='%s', copyfile=True, + extensions=None, position=5, ), moving_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=1, ), @@ -53,8 +56,8 @@ def test_RigidTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RigidTask_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(extensions=None, ), + out_file_xfm=dict(extensions=None, ), ) outputs = RigidTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py index 3574906455..51a9bbe4b5 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py @@ -12,6 +12,7 @@ def test_SVAdjustVoxSp_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), origin=dict( @@ -20,12 +21,14 @@ def test_SVAdjustVoxSp_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_avs', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_SVAdjustVoxSp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVAdjustVoxSp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SVAdjustVoxSp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py index 40a7592c19..0c051ef5d2 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py @@ -12,6 +12,7 @@ def test_SVAdjustVoxSpTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), origin=dict( @@ -20,12 +21,14 @@ def test_SVAdjustVoxSpTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_avs', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_SVAdjustVoxSpTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVAdjustVoxSpTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SVAdjustVoxSpTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVResample.py b/nipype/interfaces/dtitk/tests/test_auto_SVResample.py index 91ca638f22..880366e412 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVResample.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVResample.py @@ -17,6 +17,7 @@ def test_SVResample_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), origin=dict( @@ -25,12 +26,14 @@ def test_SVResample_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_resampled', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -44,7 +47,7 @@ def test_SVResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVResample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SVResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py b/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py index 8a7574bfd8..1a8ea16023 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py @@ -17,6 +17,7 @@ def test_SVResampleTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), origin=dict( @@ -25,12 +26,14 @@ def test_SVResampleTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_resampled', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -44,7 +47,7 @@ def test_SVResampleTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVResampleTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SVResampleTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py index bda9128369..3f8f236a6b 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py @@ -12,6 +12,7 @@ def test_TVAdjustOriginTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), origin=dict( @@ -20,12 +21,14 @@ def test_TVAdjustOriginTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_avs', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_TVAdjustOriginTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustOriginTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TVAdjustOriginTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py index b8ce9039d5..9165dce54a 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py @@ -12,6 +12,7 @@ def test_TVAdjustVoxSp_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), origin=dict( @@ -20,12 +21,14 @@ def test_TVAdjustVoxSp_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_avs', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_TVAdjustVoxSp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustVoxSp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TVAdjustVoxSp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py index e9ef8137dc..a04f1078b4 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py @@ -12,6 +12,7 @@ def test_TVAdjustVoxSpTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), origin=dict( @@ -20,12 +21,14 @@ def test_TVAdjustVoxSpTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_avs', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_TVAdjustVoxSpTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustVoxSpTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TVAdjustVoxSpTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVResample.py b/nipype/interfaces/dtitk/tests/test_auto_TVResample.py index aefafc6430..fe7b7bbdbd 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVResample.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVResample.py @@ -17,6 +17,7 @@ def test_TVResample_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict(argstr='-interp %s', ), @@ -26,12 +27,14 @@ def test_TVResample_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_resampled', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -45,7 +48,7 @@ def test_TVResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVResample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TVResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py index b3c70bb729..d2b971fe00 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py @@ -17,6 +17,7 @@ def test_TVResampleTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict(argstr='-interp %s', ), @@ -26,12 +27,14 @@ def test_TVResampleTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_resampled', ), target_file=dict( argstr='-target %s', + extensions=None, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -45,7 +48,7 @@ def test_TVResampleTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVResampleTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TVResampleTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVtool.py b/nipype/interfaces/dtitk/tests/test_auto_TVtool.py index 2267228631..15f06af243 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVtool.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVtool.py @@ -12,11 +12,13 @@ def test_TVtool_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), in_flag=dict(argstr='-%s', ), out_file=dict( argstr='-out %s', + extensions=None, genfile=True, ), ) @@ -26,7 +28,7 @@ def test_TVtool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVtool_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TVtool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py index 252d7c9d0a..eb44949b5d 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py @@ -12,11 +12,13 @@ def test_TVtoolTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), in_flag=dict(argstr='-%s', ), out_file=dict( argstr='-out %s', + extensions=None, genfile=True, ), ) @@ -26,7 +28,7 @@ def test_TVtoolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVtoolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TVtoolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py index 72330737b6..e9aeab1260 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py @@ -20,6 +20,7 @@ def test_affScalarVolTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -28,16 +29,19 @@ def test_affScalarVolTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_affxfmd', ), target=dict( argstr='-target %s', + extensions=None, xor=['transform'], ), transform=dict( argstr='-trans %s', + extensions=None, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -51,7 +55,7 @@ def test_affScalarVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_affScalarVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = affScalarVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py index da8fae25cc..568a83436f 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py @@ -20,6 +20,7 @@ def test_affSymTensor3DVolTask_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -28,6 +29,7 @@ def test_affSymTensor3DVolTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_affxfmd', @@ -38,10 +40,12 @@ def test_affSymTensor3DVolTask_inputs(): ), target=dict( argstr='-target %s', + extensions=None, xor=['transform'], ), transform=dict( argstr='-trans %s', + extensions=None, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -55,7 +59,7 @@ def test_affSymTensor3DVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_affSymTensor3DVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = affSymTensor3DVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py index 10965b7077..b9ed3a7054 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py @@ -13,6 +13,7 @@ def test_diffeoScalarVolTask_inputs(): flip=dict(argstr='-flip %d %d %d', ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -21,6 +22,7 @@ def test_diffeoScalarVolTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', @@ -28,10 +30,12 @@ def test_diffeoScalarVolTask_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + extensions=None, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', + extensions=None, mandatory=True, ), voxel_size=dict( @@ -45,7 +49,7 @@ def test_diffeoScalarVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_diffeoScalarVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = diffeoScalarVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py index 52112735b1..2fc1cd6f6f 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py @@ -17,6 +17,7 @@ def test_diffeoSymTensor3DVolTask_inputs(): flip=dict(argstr='-flip %d %d %d', ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), interpolation=dict( @@ -25,6 +26,7 @@ def test_diffeoSymTensor3DVolTask_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', @@ -36,10 +38,12 @@ def test_diffeoSymTensor3DVolTask_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + extensions=None, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', + extensions=None, mandatory=True, ), voxel_size=dict( @@ -53,7 +57,7 @@ def test_diffeoSymTensor3DVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_diffeoSymTensor3DVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = diffeoSymTensor3DVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index f05821d9c1..d246429304 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -18,7 +18,10 @@ def test_AnalyzeWarp_inputs(): argstr='-jacmat %s', usedefault=True, ), - moving_image=dict(argstr='-in %s', ), + moving_image=dict( + argstr='-in %s', + extensions=None, + ), num_threads=dict( argstr='-threads %01d', nohash=True, @@ -36,6 +39,7 @@ def test_AnalyzeWarp_inputs(): ), transform_file=dict( argstr='-tp %s', + extensions=None, mandatory=True, ), ) @@ -46,9 +50,9 @@ def test_AnalyzeWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeWarp_outputs(): output_map = dict( - disp_field=dict(), - jacdet_map=dict(), - jacmat_map=dict(), + disp_field=dict(extensions=None, ), + jacdet_map=dict(extensions=None, ), + jacmat_map=dict(extensions=None, ), ) outputs = AnalyzeWarp.output_spec() diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index 16f2b54079..f13798790d 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -12,6 +12,7 @@ def test_ApplyWarp_inputs(): ), moving_image=dict( argstr='-in %s', + extensions=None, mandatory=True, ), num_threads=dict( @@ -26,6 +27,7 @@ def test_ApplyWarp_inputs(): ), transform_file=dict( argstr='-tp %s', + extensions=None, mandatory=True, ), ) @@ -35,7 +37,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): - output_map = dict(warped_file=dict(), ) + output_map = dict(warped_file=dict(extensions=None, ), ) outputs = ApplyWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index ef227da7f8..7b67511f43 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -9,11 +9,14 @@ def test_EditTransform_inputs(): argstr='FinalBSplineInterpolationOrder', usedefault=True, ), - output_file=dict(), + output_file=dict(extensions=None, ), output_format=dict(argstr='ResultImageFormat', ), output_type=dict(argstr='ResultImagePixelType', ), - reference_image=dict(), - transform_file=dict(mandatory=True, ), + reference_image=dict(extensions=None, ), + transform_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = EditTransform.input_spec() @@ -21,7 +24,7 @@ def test_EditTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EditTransform_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = EditTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index c93a0526c1..cc6be5c6fb 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -22,10 +22,12 @@ def test_PointsWarp_inputs(): ), points_file=dict( argstr='-def %s', + extensions=None, mandatory=True, ), transform_file=dict( argstr='-tp %s', + extensions=None, mandatory=True, ), ) @@ -35,7 +37,7 @@ def test_PointsWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PointsWarp_outputs(): - output_map = dict(warped_file=dict(), ) + output_map = dict(warped_file=dict(extensions=None, ), ) outputs = PointsWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index 4e774ab036..0c0d45f863 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -12,15 +12,26 @@ def test_Registration_inputs(): ), fixed_image=dict( argstr='-f %s', + extensions=None, mandatory=True, ), - fixed_mask=dict(argstr='-fMask %s', ), - initial_transform=dict(argstr='-t0 %s', ), + fixed_mask=dict( + argstr='-fMask %s', + extensions=None, + ), + initial_transform=dict( + argstr='-t0 %s', + extensions=None, + ), moving_image=dict( argstr='-m %s', + extensions=None, mandatory=True, ), - moving_mask=dict(argstr='-mMask %s', ), + moving_mask=dict( + argstr='-mMask %s', + extensions=None, + ), num_threads=dict( argstr='-threads %01d', nohash=True, @@ -44,7 +55,7 @@ def test_Registration_inputs(): def test_Registration_outputs(): output_map = dict( transform=dict(), - warped_file=dict(), + warped_file=dict(extensions=None, ), warped_files=dict(), warped_files_flags=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py index ed32693df5..03fa095470 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py @@ -13,17 +13,20 @@ def test_AddXFormToHeader_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_file=dict( argstr='%s', + extensions=None, position=-1, usedefault=True, ), subjects_dir=dict(), transform=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -35,7 +38,7 @@ def test_AddXFormToHeader_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddXFormToHeader_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AddXFormToHeader.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index fc5bc39b6f..8a83130a4d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -7,29 +7,63 @@ def test_Aparc2Aseg_inputs(): input_map = dict( a2009s=dict(argstr='--a2009s', ), args=dict(argstr='%s', ), - aseg=dict(argstr='--aseg %s', ), + aseg=dict( + argstr='--aseg %s', + extensions=None, + ), copy_inputs=dict(), - ctxseg=dict(argstr='--ctxseg %s', ), + ctxseg=dict( + argstr='--ctxseg %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), - filled=dict(), + filled=dict(extensions=None, ), hypo_wm=dict(argstr='--hypo-as-wm', ), label_wm=dict(argstr='--labelwm', ), - lh_annotation=dict(mandatory=True, ), - lh_pial=dict(mandatory=True, ), - lh_ribbon=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), + lh_annotation=dict( + extensions=None, + mandatory=True, + ), + lh_pial=dict( + extensions=None, + mandatory=True, + ), + lh_ribbon=dict( + extensions=None, + mandatory=True, + ), + lh_white=dict( + extensions=None, + mandatory=True, + ), out_file=dict( argstr='--o %s', + extensions=None, + mandatory=True, + ), + rh_annotation=dict( + extensions=None, + mandatory=True, + ), + rh_pial=dict( + extensions=None, + mandatory=True, + ), + rh_ribbon=dict( + extensions=None, + mandatory=True, + ), + rh_white=dict( + extensions=None, + mandatory=True, + ), + ribbon=dict( + extensions=None, mandatory=True, ), - rh_annotation=dict(mandatory=True, ), - rh_pial=dict(mandatory=True, ), - rh_ribbon=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), - ribbon=dict(mandatory=True, ), rip_unknown=dict(argstr='--rip-unknown', ), subject_id=dict( argstr='--s %s', @@ -45,7 +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', ), ) + 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 7044fdde2f..fea3617596 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -12,10 +12,12 @@ def test_Apas2Aseg_inputs(): ), in_file=dict( argstr='--i %s', + extensions=None, mandatory=True, ), out_file=dict( argstr='--o %s', + extensions=None, mandatory=True, ), subjects_dir=dict(), @@ -26,7 +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', ), ) + 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_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index 69f56d7dde..c4544feb88 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -12,6 +12,7 @@ def test_ApplyMask_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -19,12 +20,14 @@ def test_ApplyMask_inputs(): keep_mask_deletion_edits=dict(argstr='-keep_mask_deletion_edits', ), mask_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), mask_thresh=dict(argstr='-T %.4f', ), out_file=dict( argstr='%s', + extensions=None, hash_files=True, keep_extension=True, name_source=['in_file'], @@ -34,9 +37,18 @@ def test_ApplyMask_inputs(): subjects_dir=dict(), transfer=dict(argstr='-transfer %d', ), use_abs=dict(argstr='-abs', ), - xfm_file=dict(argstr='-xform %s', ), - xfm_source=dict(argstr='-lta_src %s', ), - xfm_target=dict(argstr='-lta_dst %s', ), + xfm_file=dict( + argstr='-xform %s', + extensions=None, + ), + xfm_source=dict( + argstr='-lta_src %s', + extensions=None, + ), + xfm_target=dict( + argstr='-lta_dst %s', + extensions=None, + ), ) inputs = ApplyMask.input_spec() @@ -44,7 +56,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ApplyMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index c9e8f85904..753be038df 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -18,6 +18,7 @@ def test_ApplyVolTransform_inputs(): ), fsl_reg_file=dict( argstr='--fsl %s', + extensions=None, mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), @@ -30,17 +31,22 @@ def test_ApplyVolTransform_inputs(): ), lta_file=dict( argstr='--lta %s', + extensions=None, mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), lta_inv_file=dict( argstr='--lta-inv %s', + extensions=None, mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), - m3z_file=dict(argstr='--m3z %s', ), + m3z_file=dict( + argstr='--m3z %s', + extensions=None, + ), mni_152_reg=dict( argstr='--regheader', mandatory=True, @@ -54,6 +60,7 @@ def test_ApplyVolTransform_inputs(): no_resample=dict(argstr='--no-resample', ), reg_file=dict( argstr='--reg %s', + extensions=None, mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), @@ -67,6 +74,7 @@ def test_ApplyVolTransform_inputs(): source_file=dict( argstr='--mov %s', copyfile=False, + extensions=None, mandatory=True, ), subject=dict( @@ -84,15 +92,18 @@ def test_ApplyVolTransform_inputs(): tal_resolution=dict(argstr='--talres %.10f', ), target_file=dict( argstr='--targ %s', + extensions=None, mandatory=True, xor=('target_file', 'tal', 'fs_target'), ), transformed_file=dict( argstr='--o %s', + extensions=None, genfile=True, ), xfm_reg_file=dict( argstr='--xfm %s', + extensions=None, mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), @@ -104,7 +115,7 @@ def test_ApplyVolTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyVolTransform_outputs(): - output_map = dict(transformed_file=dict(), ) + output_map = dict(transformed_file=dict(extensions=None, ), ) outputs = ApplyVolTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index 93db55cd30..7dfb9a1815 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -12,6 +12,7 @@ def test_Binarize_inputs(): bin_val_not=dict(argstr='--binvalnot %d', ), binary_file=dict( argstr='--o %s', + extensions=None, genfile=True, ), count_file=dict(argstr='--count %s', ), @@ -26,17 +27,24 @@ def test_Binarize_inputs(): in_file=dict( argstr='--i %s', copyfile=False, + extensions=None, mandatory=True, ), invert=dict(argstr='--inv', ), - mask_file=dict(argstr='--mask maskvol', ), + mask_file=dict( + argstr='--mask maskvol', + extensions=None, + ), mask_thresh=dict(argstr='--mask-thresh %f', ), match=dict(argstr='--match %d...', ), max=dict( argstr='--max %f', xor=['wm_ven_csf'], ), - merge_file=dict(argstr='--merge %s', ), + merge_file=dict( + argstr='--merge %s', + extensions=None, + ), min=dict( argstr='--min %f', xor=['wm_ven_csf'], @@ -61,8 +69,8 @@ def test_Binarize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Binarize_outputs(): output_map = dict( - binary_file=dict(), - count_file=dict(), + binary_file=dict(extensions=None, ), + count_file=dict(extensions=None, ), ) outputs = Binarize.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index 1cf35fcedb..f3bfd5ad62 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -14,16 +14,24 @@ def test_CALabel_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), - in_vol=dict(argstr='-r %s', ), - intensities=dict(argstr='-r %s', ), + in_vol=dict( + argstr='-r %s', + extensions=None, + ), + intensities=dict( + argstr='-r %s', + extensions=None, + ), label=dict(argstr='-l %s', ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -32,11 +40,13 @@ def test_CALabel_inputs(): subjects_dir=dict(), template=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), transform=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -47,7 +57,7 @@ def test_CALabel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CALabel_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = CALabel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index 0e8ec025ec..1f6546ae3a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -8,23 +8,35 @@ def test_CANormalize_inputs(): args=dict(argstr='%s', ), atlas=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), - control_points=dict(argstr='-c %s', ), + control_points=dict( + argstr='-c %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), - long_file=dict(argstr='-long %s', ), - mask=dict(argstr='-mask %s', ), + long_file=dict( + argstr='-long %s', + extensions=None, + ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], @@ -34,6 +46,7 @@ def test_CANormalize_inputs(): subjects_dir=dict(), transform=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -45,7 +58,7 @@ def test_CANormalize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CANormalize_outputs(): output_map = dict( - control_points=dict(), + control_points=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 e3cbf52f10..83f669b218 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -14,6 +14,7 @@ def test_CARegister_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -23,20 +24,28 @@ def test_CARegister_inputs(): ), l_files=dict(argstr='-l %s', ), levels=dict(argstr='-levels %d', ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), subjects_dir=dict(), template=dict( argstr='%s', + extensions=None, position=-2, ), - transform=dict(argstr='-T %s', ), + transform=dict( + argstr='-T %s', + extensions=None, + ), ) inputs = CARegister.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index a7d3ad3bb0..68a5a98e66 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -12,6 +12,7 @@ def test_CheckTalairachAlignment_inputs(): ), in_file=dict( argstr='-xfm %s', + extensions=None, mandatory=True, position=-1, xor=['subject'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index e4e8efb718..72f60e58a8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -10,6 +10,7 @@ def test_Concatenate_inputs(): combine=dict(argstr='--combine', ), concatenated_file=dict( argstr='--o %s', + extensions=None, genfile=True, ), environ=dict( @@ -22,12 +23,18 @@ def test_Concatenate_inputs(): mandatory=True, ), keep_dtype=dict(argstr='--keep-datatype', ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + extensions=None, + ), max_bonfcor=dict(argstr='--max-bonfcor', ), max_index=dict(argstr='--max-index', ), mean_div_n=dict(argstr='--mean-div-n', ), multiply_by=dict(argstr='--mul %f', ), - multiply_matrix_file=dict(argstr='--mtx %s', ), + multiply_matrix_file=dict( + argstr='--mtx %s', + extensions=None, + ), paired_stats=dict(argstr='--paired-%s', ), sign=dict(argstr='--%s', ), sort=dict(argstr='--sort', ), @@ -41,7 +48,7 @@ def test_Concatenate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Concatenate_outputs(): - output_map = dict(concatenated_file=dict(), ) + output_map = dict(concatenated_file=dict(extensions=None, ), ) outputs = Concatenate.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 40a465b249..8acab945c1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -12,6 +12,7 @@ def test_ConcatenateLTA_inputs(): ), in_lta1=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -25,6 +26,7 @@ def test_ConcatenateLTA_inputs(): invert_out=dict(argstr='-invertout', ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_lta1'], @@ -51,7 +53,7 @@ def test_ConcatenateLTA_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConcatenateLTA_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ConcatenateLTA.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index 7999001813..3c4e5aa484 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -17,16 +17,28 @@ def test_Contrast_inputs(): argstr='--%s-only', mandatory=True, ), - orig=dict(mandatory=True, ), - rawavg=dict(mandatory=True, ), + orig=dict( + extensions=None, + mandatory=True, + ), + rawavg=dict( + extensions=None, + mandatory=True, + ), subject_id=dict( argstr='--s %s', mandatory=True, usedefault=True, ), subjects_dir=dict(), - thickness=dict(mandatory=True, ), - white=dict(mandatory=True, ), + thickness=dict( + extensions=None, + mandatory=True, + ), + white=dict( + extensions=None, + mandatory=True, + ), ) inputs = Contrast.input_spec() @@ -35,9 +47,9 @@ def test_Contrast_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Contrast_outputs(): output_map = dict( - out_contrast=dict(), - out_log=dict(), - out_stats=dict(), + out_contrast=dict(extensions=None, ), + out_log=dict(extensions=None, ), + out_stats=dict(extensions=None, ), ) outputs = Contrast.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py index f29b76df29..05bc424830 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py @@ -16,6 +16,7 @@ def test_Curvature_inputs(): in_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-2, ), @@ -31,8 +32,8 @@ def test_Curvature_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Curvature_outputs(): output_map = dict( - out_gauss=dict(), - out_mean=dict(), + out_gauss=dict(extensions=None, ), + out_mean=dict(extensions=None, ), ) outputs = Curvature.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py index 19d6a4772e..f815952eaf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py @@ -9,11 +9,13 @@ def test_CurvatureStats_inputs(): copy_inputs=dict(), curvfile1=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), curvfile2=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -29,6 +31,7 @@ def test_CurvatureStats_inputs(): min_max=dict(argstr='-m', ), out_file=dict( argstr='-o %s', + extensions=None, hash_files=False, name_source=['hemisphere'], name_template='%s.curv.stats', @@ -40,7 +43,10 @@ def test_CurvatureStats_inputs(): usedefault=True, ), subjects_dir=dict(), - surface=dict(argstr='-F %s', ), + surface=dict( + argstr='-F %s', + extensions=None, + ), values=dict(argstr='-G', ), write=dict(argstr='--writeCurvatureFiles', ), ) @@ -50,7 +56,7 @@ def test_CurvatureStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureStats_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = CurvatureStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index efd53fb773..3c0a95c437 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -8,7 +8,7 @@ def test_DICOMConvert_inputs(): args=dict(argstr='%s', ), base_output_dir=dict(mandatory=True, ), dicom_dir=dict(mandatory=True, ), - dicom_info=dict(), + dicom_info=dict(extensions=None, ), environ=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py index e681a03871..2a58c98872 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py @@ -12,14 +12,19 @@ def test_EMRegister_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), nbrspacing=dict(argstr='-uns %d', ), num_threads=dict(), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_file'], @@ -30,10 +35,14 @@ def test_EMRegister_inputs(): subjects_dir=dict(), template=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), - transform=dict(argstr='-t %s', ), + transform=dict( + argstr='-t %s', + extensions=None, + ), ) inputs = EMRegister.input_spec() @@ -41,7 +50,7 @@ def test_EMRegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EMRegister_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = EMRegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py index f971f4fab9..2ca6d59cc2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py @@ -8,6 +8,7 @@ def test_EditWMwithAseg_inputs(): args=dict(argstr='%s', ), brain_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -17,17 +18,20 @@ def test_EditWMwithAseg_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), keep_in=dict(argstr='-keep-in', ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), seg_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -39,7 +43,7 @@ def test_EditWMwithAseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EditWMwithAseg_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = EditWMwithAseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py index 996d079b48..4ab7d9f45c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py @@ -12,6 +12,7 @@ def test_EulerNumber_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -23,7 +24,7 @@ def test_EulerNumber_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EulerNumber_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = EulerNumber.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index f3f4896a75..dba95bb3ba 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -12,11 +12,13 @@ def test_ExtractMainComponent_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), out_file=dict( argstr='%s', + extensions=None, name_source='in_file', name_template='%s.maincmp', position=2, @@ -28,7 +30,7 @@ def test_ExtractMainComponent_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractMainComponent_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ExtractMainComponent.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 9e6b1cbc8b..35dae21d21 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -33,9 +33,9 @@ def test_FitMSParams_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitMSParams_outputs(): output_map = dict( - pd_image=dict(), - t1_image=dict(), - t2star_image=dict(), + pd_image=dict(extensions=None, ), + t1_image=dict(extensions=None, ), + t2star_image=dict(extensions=None, ), ) outputs = FitMSParams.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index 8b61823b42..4ba8442b14 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -17,10 +17,22 @@ def test_FixTopology_inputs(): mandatory=True, position=-1, ), - in_brain=dict(mandatory=True, ), - in_inflated=dict(mandatory=True, ), - in_orig=dict(mandatory=True, ), - in_wm=dict(mandatory=True, ), + in_brain=dict( + extensions=None, + mandatory=True, + ), + in_inflated=dict( + extensions=None, + mandatory=True, + ), + in_orig=dict( + extensions=None, + mandatory=True, + ), + in_wm=dict( + extensions=None, + mandatory=True, + ), mgz=dict(argstr='-mgz', ), seed=dict(argstr='-seed %d', ), sphere=dict(argstr='-sphere %s', ), @@ -38,7 +50,7 @@ def test_FixTopology_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FixTopology_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = FixTopology.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py index 8608444fc8..d2d7467df1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py @@ -23,6 +23,7 @@ def test_FuseSegmentations_inputs(): mandatory=True, ), out_file=dict( + extensions=None, mandatory=True, position=-1, ), @@ -43,7 +44,7 @@ def test_FuseSegmentations_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FuseSegmentations_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = FuseSegmentations.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index 828bbfab03..f2f6a5899f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -19,6 +19,7 @@ def test_GLMFit_inputs(): debug=dict(argstr='--debug', ), design=dict( argstr='--X %s', + extensions=None, xor=('fsgd', 'design', 'one_sample'), ), diag=dict(argstr='--diag %d', ), @@ -33,9 +34,13 @@ def test_GLMFit_inputs(): ), fixed_fx_dof_file=dict( argstr='--ffxdofdat %d', + extensions=None, xor=['fixed_fx_dof'], ), - fixed_fx_var=dict(argstr='--yffxvar %s', ), + fixed_fx_var=dict( + argstr='--yffxvar %s', + extensions=None, + ), force_perm=dict(argstr='--perm-force', ), fsgd=dict( argstr='--fsgd %s %s', @@ -50,14 +55,19 @@ def test_GLMFit_inputs(): in_file=dict( argstr='--y %s', copyfile=False, + extensions=None, mandatory=True, ), invert_mask=dict(argstr='--mask-inv', ), label_file=dict( argstr='--label %s', + extensions=None, xor=['cortex'], ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + extensions=None, + ), no_contrast_ok=dict(argstr='--no-contrasts-ok', ), no_est_fwhm=dict(argstr='--no-est-fwhm', ), no_mask_smooth=dict(argstr='--no-mask-smooth', ), @@ -84,7 +94,10 @@ def test_GLMFit_inputs(): save_residual=dict(argstr='--eres-save', ), seed=dict(argstr='--seed %d', ), self_reg=dict(argstr='--selfreg %d %d %d', ), - sim_done_file=dict(argstr='--sim-done %s', ), + sim_done_file=dict( + argstr='--sim-done %s', + extensions=None, + ), sim_sign=dict(argstr='--sim-sign %s', ), simulation=dict(argstr='--sim %s %d %f %s', ), subject_id=dict(), @@ -98,7 +111,10 @@ def test_GLMFit_inputs(): uniform=dict(argstr='--uniform %f %f', ), var_fwhm=dict(argstr='--var-fwhm %f', ), vox_dump=dict(argstr='--voxdump %d %d %d', ), - weight_file=dict(xor=['weighted_ls'], ), + weight_file=dict( + extensions=None, + xor=['weighted_ls'], + ), weight_inv=dict( argstr='--w-inv', xor=['weighted_ls'], @@ -109,6 +125,7 @@ def test_GLMFit_inputs(): ), weighted_ls=dict( argstr='--wls %s', + extensions=None, xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) @@ -119,23 +136,23 @@ def test_GLMFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GLMFit_outputs(): output_map = dict( - beta_file=dict(), - dof_file=dict(), - error_file=dict(), - error_stddev_file=dict(), - error_var_file=dict(), - estimate_file=dict(), - frame_eigenvectors=dict(), + beta_file=dict(extensions=None, ), + dof_file=dict(extensions=None, ), + error_file=dict(extensions=None, ), + error_stddev_file=dict(extensions=None, ), + error_var_file=dict(extensions=None, ), + estimate_file=dict(extensions=None, ), + frame_eigenvectors=dict(extensions=None, ), ftest_file=dict(), - fwhm_file=dict(), + fwhm_file=dict(extensions=None, ), gamma_file=dict(), gamma_var_file=dict(), glm_dir=dict(), - mask_file=dict(), + mask_file=dict(extensions=None, ), sig_file=dict(), - singular_values=dict(), - spatial_eigenvectors=dict(), - svd_stats_file=dict(), + singular_values=dict(extensions=None, ), + spatial_eigenvectors=dict(extensions=None, ), + svd_stats_file=dict(extensions=None, ), ) outputs = GLMFit.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 2fa225e87e..28be31b456 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -12,6 +12,7 @@ def test_ImageInfo_inputs(): ), in_file=dict( argstr='%s', + extensions=None, position=1, ), subjects_dir=dict(), @@ -31,7 +32,7 @@ def test_ImageInfo_outputs(): file_format=dict(), info=dict(), orientation=dict(), - out_file=dict(), + out_file=dict(extensions=None, ), ph_enc_dir=dict(), vox_sizes=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py index 49f5e6b48f..d3f8f16df3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py @@ -12,16 +12,19 @@ def test_Jacobian_inputs(): ), in_mappedsurf=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), in_origsurf=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_origsurf'], @@ -36,7 +39,7 @@ def test_Jacobian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Jacobian_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Jacobian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py index bcbf971d01..0a2df1b8c4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py @@ -12,12 +12,14 @@ def test_LTAConvert_inputs(): ), in_fsl=dict( argstr='--infsl %s', + extensions=None, mandatory=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_itk=dict( argstr='--initk %s', + extensions=None, mandatory=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), @@ -30,18 +32,21 @@ def test_LTAConvert_inputs(): ), in_mni=dict( argstr='--inmni %s', + extensions=None, mandatory=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_niftyreg=dict( argstr='--inniftyreg %s', + extensions=None, mandatory=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_reg=dict( argstr='--inreg %s', + extensions=None, mandatory=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), @@ -56,9 +61,15 @@ def test_LTAConvert_inputs(): out_lta=dict(argstr='--outlta %s', ), out_mni=dict(argstr='--outmni %s', ), out_reg=dict(argstr='--outreg %s', ), - source_file=dict(argstr='--src %s', ), + source_file=dict( + argstr='--src %s', + extensions=None, + ), target_conform=dict(argstr='--trgconform', ), - target_file=dict(argstr='--trg %s', ), + target_file=dict( + argstr='--trg %s', + extensions=None, + ), ) inputs = LTAConvert.input_spec() @@ -67,11 +78,11 @@ def test_LTAConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_LTAConvert_outputs(): output_map = dict( - out_fsl=dict(), - out_itk=dict(), - out_lta=dict(), - out_mni=dict(), - out_reg=dict(), + out_fsl=dict(extensions=None, ), + out_itk=dict(extensions=None, ), + out_lta=dict(extensions=None, ), + out_mni=dict(extensions=None, ), + out_reg=dict(extensions=None, ), ) outputs = LTAConvert.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index 2d7761006b..b7d594dabd 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -6,7 +6,10 @@ def test_Label2Annot_inputs(): input_map = dict( args=dict(argstr='%s', ), - color_table=dict(argstr='--ctab %s', ), + color_table=dict( + argstr='--ctab %s', + extensions=None, + ), copy_inputs=dict(), environ=dict( nohash=True, @@ -21,7 +24,10 @@ def test_Label2Annot_inputs(): mandatory=True, ), keep_max=dict(argstr='--maxstatwinner', ), - orig=dict(mandatory=True, ), + orig=dict( + extensions=None, + mandatory=True, + ), out_annot=dict( argstr='--a %s', mandatory=True, @@ -40,7 +46,7 @@ def test_Label2Annot_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Annot_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Label2Annot.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index 7511cd0dbb..4cc1b62ec0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -17,6 +17,7 @@ def test_Label2Label_inputs(): ), out_file=dict( argstr='--trglabel %s', + extensions=None, hash_files=False, keep_extension=True, name_source=['source_label'], @@ -28,22 +29,35 @@ def test_Label2Label_inputs(): ), source_label=dict( argstr='--srclabel %s', + extensions=None, + mandatory=True, + ), + source_sphere_reg=dict( + extensions=None, mandatory=True, ), - source_sphere_reg=dict(mandatory=True, ), source_subject=dict( argstr='--srcsubject %s', mandatory=True, ), - source_white=dict(mandatory=True, ), - sphere_reg=dict(mandatory=True, ), + source_white=dict( + extensions=None, + mandatory=True, + ), + sphere_reg=dict( + extensions=None, + mandatory=True, + ), subject_id=dict( argstr='--trgsubject %s', mandatory=True, usedefault=True, ), subjects_dir=dict(), - white=dict(mandatory=True, ), + white=dict( + extensions=None, + mandatory=True, + ), ) inputs = Label2Label.input_spec() @@ -51,7 +65,7 @@ def test_Label2Label_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Label_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Label2Label.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index fb2726635f..fe277288d5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -8,6 +8,7 @@ def test_Label2Vol_inputs(): annot_file=dict( argstr='--annot %s', copyfile=False, + extensions=None, mandatory=True, requires=('subject_id', 'hemi'), xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), @@ -35,9 +36,15 @@ def test_Label2Vol_inputs(): mandatory=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), - label_hit_file=dict(argstr='--hits %s', ), + label_hit_file=dict( + argstr='--hits %s', + extensions=None, + ), label_voxel_volume=dict(argstr='--labvoxvol %f', ), - map_label_stat=dict(argstr='--label-stat %s', ), + map_label_stat=dict( + argstr='--label-stat %s', + extensions=None, + ), native_vox2ras=dict(argstr='--native-vox2ras', ), proj=dict( argstr='--proj %s %f %f %f', @@ -45,15 +52,18 @@ def test_Label2Vol_inputs(): ), reg_file=dict( argstr='--reg %s', + extensions=None, xor=('reg_file', 'reg_header', 'identity'), ), reg_header=dict( argstr='--regheader %s', + extensions=None, xor=('reg_file', 'reg_header', 'identity'), ), seg_file=dict( argstr='--seg %s', copyfile=False, + extensions=None, mandatory=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), @@ -62,10 +72,12 @@ def test_Label2Vol_inputs(): surface=dict(argstr='--surf %s', ), template_file=dict( argstr='--temp %s', + extensions=None, mandatory=True, ), vol_label_file=dict( argstr='--o %s', + extensions=None, genfile=True, ), ) @@ -75,7 +87,7 @@ def test_Label2Vol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Vol_outputs(): - output_map = dict(vol_label_file=dict(), ) + output_map = dict(vol_label_file=dict(extensions=None, ), ) outputs = Label2Vol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py index 7b6ae4a945..da6b2f94ec 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py @@ -13,16 +13,21 @@ def test_MNIBiasCorrection_inputs(): ), in_file=dict( argstr='--i %s', + extensions=None, mandatory=True, ), iterations=dict( argstr='--n %d', usedefault=True, ), - mask=dict(argstr='--mask %s', ), + mask=dict( + argstr='--mask %s', + extensions=None, + ), no_rescale=dict(argstr='--no-rescale', ), out_file=dict( argstr='--o %s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], @@ -32,7 +37,10 @@ def test_MNIBiasCorrection_inputs(): shrink=dict(argstr='--shrink %d', ), stop=dict(argstr='--stop %f', ), subjects_dir=dict(), - transform=dict(argstr='--uchar %s', ), + transform=dict( + argstr='--uchar %s', + extensions=None, + ), ) inputs = MNIBiasCorrection.input_spec() @@ -40,7 +48,7 @@ def test_MNIBiasCorrection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MNIBiasCorrection_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MNIBiasCorrection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py index b4b7436120..44d836fac4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py @@ -12,6 +12,7 @@ def test_MPRtoMNI305_inputs(): ), in_file=dict( argstr='%s', + extensions=None, usedefault=True, ), reference_dir=dict( @@ -31,8 +32,11 @@ def test_MPRtoMNI305_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MPRtoMNI305_outputs(): output_map = dict( - log_file=dict(usedefault=True, ), - out_file=dict(), + log_file=dict( + extensions=None, + usedefault=True, + ), + out_file=dict(extensions=None, ), ) outputs = MPRtoMNI305.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index b44cf7a308..d66ad1a4c4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -5,12 +5,24 @@ def test_MRIConvert_inputs(): input_map = dict( - apply_inv_transform=dict(argstr='--apply_inverse_transform %s', ), - apply_transform=dict(argstr='--apply_transform %s', ), + apply_inv_transform=dict( + argstr='--apply_inverse_transform %s', + extensions=None, + ), + apply_transform=dict( + argstr='--apply_transform %s', + extensions=None, + ), args=dict(argstr='%s', ), ascii=dict(argstr='--ascii', ), - autoalign_matrix=dict(argstr='--autoalign %s', ), - color_file=dict(argstr='--color_file %s', ), + autoalign_matrix=dict( + argstr='--autoalign %s', + extensions=None, + ), + color_file=dict( + argstr='--color_file %s', + extensions=None, + ), conform=dict(argstr='--conform', ), conform_min=dict(argstr='--conform_min', ), conform_size=dict(argstr='--conform_size %s', ), @@ -33,6 +45,7 @@ def test_MRIConvert_inputs(): in_center=dict(argstr='--in_center %s', ), in_file=dict( argstr='--input_volume %s', + extensions=None, mandatory=True, position=-2, ), @@ -43,7 +56,10 @@ def test_MRIConvert_inputs(): in_j_size=dict(argstr='--in_j_size %d', ), in_k_dir=dict(argstr='--in_k_direction %f %f %f', ), in_k_size=dict(argstr='--in_k_size %d', ), - in_like=dict(argstr='--in_like %s', ), + in_like=dict( + argstr='--in_like %s', + extensions=None, + ), in_matrix=dict(argstr='--in_matrix', ), in_orientation=dict(argstr='--in_orientation %s', ), in_scale=dict(argstr='--scale %f', ), @@ -59,6 +75,7 @@ def test_MRIConvert_inputs(): out_datatype=dict(argstr='--out_data_type %s', ), out_file=dict( argstr='--output_volume %s', + extensions=None, genfile=True, position=-1, ), @@ -81,8 +98,14 @@ def test_MRIConvert_inputs(): read_only=dict(argstr='--read_only', ), reorder=dict(argstr='--reorder %d %d %d', ), resample_type=dict(argstr='--resample_type %s', ), - reslice_like=dict(argstr='--reslice_like %s', ), - sdcm_list=dict(argstr='--sdcmlist %s', ), + reslice_like=dict( + argstr='--reslice_like %s', + extensions=None, + ), + sdcm_list=dict( + argstr='--sdcmlist %s', + extensions=None, + ), skip_n=dict(argstr='--nskip %d', ), slice_bias=dict(argstr='--slice-bias %f', ), slice_crop=dict(argstr='--slice-crop %d %d', ), @@ -90,7 +113,10 @@ def test_MRIConvert_inputs(): smooth_parcellation=dict(argstr='--smooth_parcellation', ), sphinx=dict(argstr='--sphinx', ), split=dict(argstr='--split', ), - status_file=dict(argstr='--status %s', ), + status_file=dict( + argstr='--status %s', + extensions=None, + ), subject_name=dict(argstr='--subject_name %s', ), subjects_dir=dict(), te=dict(argstr='-te %d', ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py index 6c12cabdc2..508899d6b0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py @@ -43,6 +43,7 @@ def test_MRICoreg_inputs(): reference_file=dict( argstr='--ref %s', copyfile=False, + extensions=None, mandatory=True, xor=['subject_id'], ), @@ -55,6 +56,7 @@ def test_MRICoreg_inputs(): source_file=dict( argstr='--mov %s', copyfile=False, + extensions=None, mandatory=True, ), source_mask=dict(argstr='--mov-mask', ), @@ -75,9 +77,9 @@ def test_MRICoreg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRICoreg_outputs(): output_map = dict( - out_lta_file=dict(), - out_params_file=dict(), - out_reg_file=dict(), + out_lta_file=dict(extensions=None, ), + out_params_file=dict(extensions=None, ), + out_reg_file=dict(extensions=None, ), ) outputs = MRICoreg.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py index 719986961d..748cc6f5e6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py @@ -12,18 +12,29 @@ def test_MRIFill_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), - log_file=dict(argstr='-a %s', ), + log_file=dict( + argstr='-a %s', + extensions=None, + ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), - segmentation=dict(argstr='-segmentation %s', ), + segmentation=dict( + argstr='-segmentation %s', + extensions=None, + ), subjects_dir=dict(), - transform=dict(argstr='-xform %s', ), + transform=dict( + argstr='-xform %s', + extensions=None, + ), ) inputs = MRIFill.input_spec() @@ -32,8 +43,8 @@ def test_MRIFill_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRIFill_outputs(): output_map = dict( - log_file=dict(), - out_file=dict(), + log_file=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = MRIFill.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index f43d217256..bd22d3f486 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -17,6 +17,7 @@ def test_MRIMarchingCubes_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -27,6 +28,7 @@ def test_MRIMarchingCubes_inputs(): ), out_file=dict( argstr='./%s', + extensions=None, genfile=True, position=-2, ), @@ -38,7 +40,7 @@ def test_MRIMarchingCubes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIMarchingCubes_outputs(): - output_map = dict(surface=dict(), ) + output_map = dict(surface=dict(extensions=None, ), ) outputs = MRIMarchingCubes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 2e7c7d2ea5..ff07c64b42 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -12,11 +12,13 @@ def test_MRIPretess_inputs(): ), in_filled=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), in_norm=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -30,6 +32,7 @@ def test_MRIPretess_inputs(): nocorners=dict(argstr='-nocorners', ), out_file=dict( argstr='%s', + extensions=None, keep_extension=True, name_source=['in_filled'], name_template='%s_pretesswm', @@ -44,7 +47,7 @@ def test_MRIPretess_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIPretess_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRIPretess.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index c92b4fea15..2208760d74 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -12,6 +12,7 @@ def test_MRISPreproc_inputs(): ), fsgd_file=dict( argstr='--fsgd %s', + extensions=None, xor=('subjects', 'fsgd_file', 'subject_file'), ), fwhm=dict( @@ -36,6 +37,7 @@ def test_MRISPreproc_inputs(): ), out_file=dict( argstr='--out %s', + extensions=None, genfile=True, ), proj_frac=dict(argstr='--projfrac %s', ), @@ -43,6 +45,7 @@ def test_MRISPreproc_inputs(): source_format=dict(argstr='--srcfmt %s', ), subject_file=dict( argstr='--f %s', + extensions=None, xor=('subjects', 'fsgd_file', 'subject_file'), ), subjects=dict( @@ -75,7 +78,7 @@ def test_MRISPreproc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreproc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRISPreproc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index e72d8adb9e..3c36fd6a43 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -13,6 +13,7 @@ def test_MRISPreprocReconAll_inputs(): ), fsgd_file=dict( argstr='--fsgd %s', + extensions=None, xor=('subjects', 'fsgd_file', 'subject_file'), ), fwhm=dict( @@ -27,7 +28,10 @@ def test_MRISPreprocReconAll_inputs(): argstr='--hemi %s', mandatory=True, ), - lh_surfreg_target=dict(requires=['surfreg_files'], ), + lh_surfreg_target=dict( + extensions=None, + requires=['surfreg_files'], + ), num_iters=dict( argstr='--niters %d', xor=['fwhm'], @@ -38,14 +42,19 @@ def test_MRISPreprocReconAll_inputs(): ), out_file=dict( argstr='--out %s', + extensions=None, genfile=True, ), proj_frac=dict(argstr='--projfrac %s', ), - rh_surfreg_target=dict(requires=['surfreg_files'], ), + rh_surfreg_target=dict( + extensions=None, + requires=['surfreg_files'], + ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), source_format=dict(argstr='--srcfmt %s', ), subject_file=dict( argstr='--f %s', + extensions=None, xor=('subjects', 'fsgd_file', 'subject_file'), ), subject_id=dict( @@ -69,6 +78,7 @@ def test_MRISPreprocReconAll_inputs(): ), surf_measure_file=dict( argstr='--meas %s', + extensions=None, xor=('surf_measure', 'surf_measure_file', 'surf_area'), ), surfreg_files=dict( @@ -87,7 +97,7 @@ def test_MRISPreprocReconAll_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreprocReconAll_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRISPreprocReconAll.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index a5899cfe70..315cfd7e2f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -12,6 +12,7 @@ def test_MRITessellate_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -22,6 +23,7 @@ def test_MRITessellate_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -35,7 +37,7 @@ def test_MRITessellate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRITessellate_outputs(): - output_map = dict(surface=dict(), ) + output_map = dict(surface=dict(extensions=None, ), ) outputs = MRITessellate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index 441be3e0a4..10c7af6832 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -9,16 +9,21 @@ def test_MRIsCALabel_inputs(): aseg=dict(argstr='-aseg %s', ), canonsurf=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), classifier=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), copy_inputs=dict(), - curv=dict(mandatory=True, ), + curv=dict( + extensions=None, + mandatory=True, + ), environ=dict( nohash=True, usedefault=True, @@ -32,6 +37,7 @@ def test_MRIsCALabel_inputs(): num_threads=dict(), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['hemisphere'], @@ -39,7 +45,10 @@ def test_MRIsCALabel_inputs(): position=-1, ), seed=dict(argstr='-seed %d', ), - smoothwm=dict(mandatory=True, ), + smoothwm=dict( + extensions=None, + mandatory=True, + ), subject_id=dict( argstr='%s', mandatory=True, @@ -47,7 +56,10 @@ def test_MRIsCALabel_inputs(): usedefault=True, ), subjects_dir=dict(), - sulc=dict(mandatory=True, ), + sulc=dict( + extensions=None, + mandatory=True, + ), ) inputs = MRIsCALabel.input_spec() @@ -55,7 +67,7 @@ def test_MRIsCALabel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCALabel_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRIsCALabel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py index cbd68c8457..296b7726a7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py @@ -17,11 +17,13 @@ def test_MRIsCalc_inputs(): ), in_file1=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), in_file2=dict( argstr='%s', + extensions=None, position=-1, xor=['in_float', 'in_int'], ), @@ -37,6 +39,7 @@ def test_MRIsCalc_inputs(): ), out_file=dict( argstr='-o %s', + extensions=None, mandatory=True, ), subjects_dir=dict(), @@ -47,7 +50,7 @@ def test_MRIsCalc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCalc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRIsCalc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py index 657292c5c7..006dd272e1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py @@ -17,6 +17,7 @@ def test_MRIsCombine_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, mandatory=True, position=-1, @@ -29,7 +30,7 @@ def test_MRIsCombine_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCombine_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRIsCombine.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 21622b2449..92c397be96 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -5,21 +5,34 @@ def test_MRIsConvert_inputs(): input_map = dict( - annot_file=dict(argstr='--annot %s', ), + annot_file=dict( + argstr='--annot %s', + extensions=None, + ), args=dict(argstr='%s', ), dataarray_num=dict(argstr='--da_num %d', ), environ=dict( nohash=True, usedefault=True, ), - functional_file=dict(argstr='-f %s', ), + functional_file=dict( + argstr='-f %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), - label_file=dict(argstr='--label %s', ), - labelstats_outfile=dict(argstr='--labelstats %s', ), + label_file=dict( + argstr='--label %s', + extensions=None, + ), + labelstats_outfile=dict( + argstr='--labelstats %s', + extensions=None, + ), normal=dict(argstr='-n', ), origname=dict(argstr='-o %s', ), out_datatype=dict( @@ -28,15 +41,22 @@ def test_MRIsConvert_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, mandatory=True, position=-1, xor=['out_datatype'], ), - parcstats_file=dict(argstr='--parcstats %s', ), + parcstats_file=dict( + argstr='--parcstats %s', + extensions=None, + ), patch=dict(argstr='-p', ), rescale=dict(argstr='-r', ), - scalarcurv_file=dict(argstr='-c %s', ), + scalarcurv_file=dict( + argstr='-c %s', + extensions=None, + ), scale=dict(argstr='-s %.3f', ), subjects_dir=dict(), talairachxfm_subjid=dict(argstr='-t %s', ), @@ -51,7 +71,7 @@ def test_MRIsConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsConvert_outputs(): - output_map = dict(converted=dict(), ) + output_map = dict(converted=dict(extensions=None, ), ) outputs = MRIsConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py index 8639c1e7b6..12f2bfb294 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py @@ -19,6 +19,7 @@ def test_MRIsExpand_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=-3, ), @@ -52,7 +53,7 @@ def test_MRIsExpand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsExpand_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRIsExpand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py index 73e48a2521..147a26275c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py @@ -13,6 +13,7 @@ def test_MRIsInflate_inputs(): in_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-2, ), @@ -22,13 +23,17 @@ def test_MRIsInflate_inputs(): ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], name_template='%s.inflated', position=-1, ), - out_sulc=dict(xor=['no_save_sulc'], ), + out_sulc=dict( + extensions=None, + xor=['no_save_sulc'], + ), subjects_dir=dict(), ) inputs = MRIsInflate.input_spec() @@ -38,8 +43,8 @@ def test_MRIsInflate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsInflate_outputs(): output_map = dict( - out_file=dict(), - out_sulc=dict(), + out_file=dict(extensions=None, ), + out_sulc=dict(extensions=None, ), ) outputs = MRIsInflate.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index f3453818c5..badb3b4f0c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -43,8 +43,8 @@ def test_MS_LDA_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MS_LDA_outputs(): output_map = dict( - vol_synth_file=dict(), - weight_file=dict(), + vol_synth_file=dict(extensions=None, ), + weight_file=dict(extensions=None, ), ) outputs = MS_LDA.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index 5dfb555346..527bc5135b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -12,6 +12,7 @@ def test_MakeAverageSubject_inputs(): ), out_name=dict( argstr='--out %s', + extensions=None, usedefault=True, ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py index 7ff18eeba6..3719b3a8af 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py @@ -17,16 +17,32 @@ def test_MakeSurfaces_inputs(): mandatory=True, position=-1, ), - in_T1=dict(argstr='-T1 %s', ), - in_aseg=dict(argstr='-aseg %s', ), - in_filled=dict(mandatory=True, ), - in_label=dict(xor=['noaparc'], ), + in_T1=dict( + argstr='-T1 %s', + extensions=None, + ), + in_aseg=dict( + argstr='-aseg %s', + extensions=None, + ), + in_filled=dict( + extensions=None, + mandatory=True, + ), + in_label=dict( + extensions=None, + xor=['noaparc'], + ), in_orig=dict( argstr='-orig %s', + extensions=None, + mandatory=True, + ), + in_white=dict(extensions=None, ), + in_wm=dict( + extensions=None, mandatory=True, ), - in_white=dict(), - in_wm=dict(mandatory=True, ), longitudinal=dict(argstr='-long', ), maximum=dict(argstr='-max %.1f', ), mgz=dict(argstr='-mgz', ), @@ -37,9 +53,13 @@ def test_MakeSurfaces_inputs(): ), orig_pial=dict( argstr='-orig_pial %s', + extensions=None, requires=['in_label'], ), - orig_white=dict(argstr='-orig_white %s', ), + orig_white=dict( + argstr='-orig_white %s', + extensions=None, + ), subject_id=dict( argstr='%s', mandatory=True, @@ -57,12 +77,12 @@ def test_MakeSurfaces_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MakeSurfaces_outputs(): output_map = dict( - out_area=dict(), - out_cortex=dict(), - out_curv=dict(), - out_pial=dict(), - out_thickness=dict(), - out_white=dict(), + out_area=dict(extensions=None, ), + out_cortex=dict(extensions=None, ), + out_curv=dict(extensions=None, ), + out_pial=dict(extensions=None, ), + out_thickness=dict(extensions=None, ), + out_white=dict(extensions=None, ), ) outputs = MakeSurfaces.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index 1923b5ceed..2384adbb2b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -13,21 +13,29 @@ def test_Normalize_inputs(): gradient=dict(argstr='-g %d', ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + extensions=None, + ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], name_template='%s_norm', position=-1, ), - segmentation=dict(argstr='-aseg %s', ), + segmentation=dict( + argstr='-aseg %s', + extensions=None, + ), subjects_dir=dict(), - transform=dict(), + transform=dict(extensions=None, ), ) inputs = Normalize.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index 1091bdbdc3..f0d182cb6c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -19,6 +19,7 @@ def test_OneSampleTTest_inputs(): debug=dict(argstr='--debug', ), design=dict( argstr='--X %s', + extensions=None, xor=('fsgd', 'design', 'one_sample'), ), diag=dict(argstr='--diag %d', ), @@ -33,9 +34,13 @@ def test_OneSampleTTest_inputs(): ), fixed_fx_dof_file=dict( argstr='--ffxdofdat %d', + extensions=None, xor=['fixed_fx_dof'], ), - fixed_fx_var=dict(argstr='--yffxvar %s', ), + fixed_fx_var=dict( + argstr='--yffxvar %s', + extensions=None, + ), force_perm=dict(argstr='--perm-force', ), fsgd=dict( argstr='--fsgd %s %s', @@ -50,14 +55,19 @@ def test_OneSampleTTest_inputs(): in_file=dict( argstr='--y %s', copyfile=False, + extensions=None, mandatory=True, ), invert_mask=dict(argstr='--mask-inv', ), label_file=dict( argstr='--label %s', + extensions=None, xor=['cortex'], ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + extensions=None, + ), no_contrast_ok=dict(argstr='--no-contrasts-ok', ), no_est_fwhm=dict(argstr='--no-est-fwhm', ), no_mask_smooth=dict(argstr='--no-mask-smooth', ), @@ -84,7 +94,10 @@ def test_OneSampleTTest_inputs(): save_residual=dict(argstr='--eres-save', ), seed=dict(argstr='--seed %d', ), self_reg=dict(argstr='--selfreg %d %d %d', ), - sim_done_file=dict(argstr='--sim-done %s', ), + sim_done_file=dict( + argstr='--sim-done %s', + extensions=None, + ), sim_sign=dict(argstr='--sim-sign %s', ), simulation=dict(argstr='--sim %s %d %f %s', ), subject_id=dict(), @@ -98,7 +111,10 @@ def test_OneSampleTTest_inputs(): uniform=dict(argstr='--uniform %f %f', ), var_fwhm=dict(argstr='--var-fwhm %f', ), vox_dump=dict(argstr='--voxdump %d %d %d', ), - weight_file=dict(xor=['weighted_ls'], ), + weight_file=dict( + extensions=None, + xor=['weighted_ls'], + ), weight_inv=dict( argstr='--w-inv', xor=['weighted_ls'], @@ -109,6 +125,7 @@ def test_OneSampleTTest_inputs(): ), weighted_ls=dict( argstr='--wls %s', + extensions=None, xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) @@ -119,23 +136,23 @@ def test_OneSampleTTest_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTest_outputs(): output_map = dict( - beta_file=dict(), - dof_file=dict(), - error_file=dict(), - error_stddev_file=dict(), - error_var_file=dict(), - estimate_file=dict(), - frame_eigenvectors=dict(), + beta_file=dict(extensions=None, ), + dof_file=dict(extensions=None, ), + error_file=dict(extensions=None, ), + error_stddev_file=dict(extensions=None, ), + error_var_file=dict(extensions=None, ), + estimate_file=dict(extensions=None, ), + frame_eigenvectors=dict(extensions=None, ), ftest_file=dict(), - fwhm_file=dict(), + fwhm_file=dict(extensions=None, ), gamma_file=dict(), gamma_var_file=dict(), glm_dir=dict(), - mask_file=dict(), + mask_file=dict(extensions=None, ), sig_file=dict(), - singular_values=dict(), - spatial_eigenvectors=dict(), - svd_stats_file=dict(), + singular_values=dict(extensions=None, ), + spatial_eigenvectors=dict(extensions=None, ), + svd_stats_file=dict(extensions=None, ), ) outputs = OneSampleTTest.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py index c452594e55..311af9714b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py @@ -13,11 +13,13 @@ def test_Paint_inputs(): ), in_surf=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_surf'], @@ -27,6 +29,7 @@ def test_Paint_inputs(): subjects_dir=dict(), template=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -38,7 +41,7 @@ def test_Paint_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Paint_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Paint.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 81ac276b2f..be19b2bd37 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -6,10 +6,16 @@ def test_ParcellationStats_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict(mandatory=True, ), - brainmask=dict(mandatory=True, ), + aseg=dict( + extensions=None, + mandatory=True, + ), + brainmask=dict( + extensions=None, + mandatory=True, + ), copy_inputs=dict(), - cortex_label=dict(), + cortex_label=dict(extensions=None, ), environ=dict( nohash=True, usedefault=True, @@ -28,8 +34,14 @@ def test_ParcellationStats_inputs(): argstr='-l %s', xor=['in_annotatoin', 'out_color'], ), - lh_pial=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), + lh_pial=dict( + extensions=None, + mandatory=True, + ), + lh_white=dict( + extensions=None, + mandatory=True, + ), mgz=dict(argstr='-mgz', ), out_color=dict( argstr='-c %s', @@ -41,9 +53,18 @@ def test_ParcellationStats_inputs(): genfile=True, requires=['tabular_output'], ), - rh_pial=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), - ribbon=dict(mandatory=True, ), + rh_pial=dict( + extensions=None, + mandatory=True, + ), + rh_white=dict( + extensions=None, + mandatory=True, + ), + ribbon=dict( + extensions=None, + mandatory=True, + ), subject_id=dict( argstr='%s', mandatory=True, @@ -60,9 +81,18 @@ def test_ParcellationStats_inputs(): argstr='-th3', requires=['cortex_label'], ), - thickness=dict(mandatory=True, ), - transform=dict(mandatory=True, ), - wm=dict(mandatory=True, ), + thickness=dict( + extensions=None, + mandatory=True, + ), + transform=dict( + extensions=None, + mandatory=True, + ), + wm=dict( + extensions=None, + mandatory=True, + ), ) inputs = ParcellationStats.input_spec() @@ -71,8 +101,8 @@ def test_ParcellationStats_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ParcellationStats_outputs(): output_map = dict( - out_color=dict(), - out_table=dict(), + out_color=dict(extensions=None, ), + out_table=dict(extensions=None, ), ) outputs = ParcellationStats.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index 93254ddcb3..148044abd3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -12,6 +12,7 @@ def test_ParseDICOMDir_inputs(): ), dicom_info_file=dict( argstr='--o %s', + extensions=None, usedefault=True, ), environ=dict( @@ -28,7 +29,7 @@ def test_ParseDICOMDir_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ParseDICOMDir_outputs(): - output_map = dict(dicom_info_file=dict(), ) + output_map = dict(dicom_info_file=dict(extensions=None, ), ) outputs = ParseDICOMDir.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 39f6a8c942..18a4dfeb43 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -7,11 +7,13 @@ def test_ReconAll_inputs(): input_map = dict( FLAIR_file=dict( argstr='-FLAIR %s', + extensions=None, min_ver='5.3.0', ), T1_files=dict(argstr='-i %s...', ), T2_file=dict( argstr='-T2 %s', + extensions=None, min_ver='5.3.0', ), args=dict(argstr='%s', ), @@ -26,7 +28,10 @@ def test_ReconAll_inputs(): nohash=True, usedefault=True, ), - expert=dict(argstr='-expert %s', ), + expert=dict( + argstr='-expert %s', + extensions=None, + ), flags=dict(argstr='%s', ), hemi=dict(argstr='-hemi %s', ), hippocampal_subfields_T1=dict( @@ -102,7 +107,10 @@ def test_ReconAll_outputs(): altkey='BA', loc='stats', ), - T1=dict(loc='mri', ), + T1=dict( + extensions=None, + loc='mri', + ), annot=dict( altkey='*annot', loc='label', @@ -123,14 +131,23 @@ def test_ReconAll_outputs(): altkey='area.pial', loc='surf', ), - aseg=dict(loc='mri', ), + aseg=dict( + extensions=None, + loc='mri', + ), aseg_stats=dict( altkey='aseg', loc='stats', ), avg_curv=dict(loc='surf', ), - brain=dict(loc='mri', ), - brainmask=dict(loc='mri', ), + brain=dict( + extensions=None, + loc='mri', + ), + brainmask=dict( + extensions=None, + loc='mri', + ), curv=dict(loc='surf', ), curv_pial=dict( altkey='curv.pial', @@ -144,7 +161,10 @@ def test_ReconAll_outputs(): altkey='entorhinal_exvivo', loc='stats', ), - filled=dict(loc='mri', ), + filled=dict( + extensions=None, + loc='mri', + ), graymid=dict( altkey=['graymid', 'midthickness'], loc='surf', @@ -155,11 +175,23 @@ def test_ReconAll_outputs(): altkey='*label', loc='label', ), - norm=dict(loc='mri', ), - nu=dict(loc='mri', ), - orig=dict(loc='mri', ), + norm=dict( + extensions=None, + loc='mri', + ), + nu=dict( + extensions=None, + loc='mri', + ), + orig=dict( + extensions=None, + loc='mri', + ), pial=dict(loc='surf', ), - rawavg=dict(loc='mri', ), + rawavg=dict( + extensions=None, + loc='mri', + ), ribbon=dict( altkey='*ribbon', loc='mri', @@ -176,8 +208,14 @@ def test_ReconAll_outputs(): thickness=dict(loc='surf', ), volume=dict(loc='surf', ), white=dict(loc='surf', ), - wm=dict(loc='mri', ), - wmparc=dict(loc='mri', ), + wm=dict( + extensions=None, + loc='mri', + ), + wmparc=dict( + extensions=None, + loc='mri', + ), wmparc_stats=dict( altkey='wmparc', loc='stats', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Register.py b/nipype/interfaces/freesurfer/tests/test_auto_Register.py index b4eff5133c..3adccf2139 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Register.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Register.py @@ -14,25 +14,32 @@ def test_Register_inputs(): nohash=True, usedefault=True, ), - in_smoothwm=dict(copyfile=True, ), + in_smoothwm=dict( + copyfile=True, + extensions=None, + ), in_sulc=dict( copyfile=True, + extensions=None, mandatory=True, ), in_surf=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-3, ), out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), subjects_dir=dict(), target=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -43,7 +50,7 @@ def test_Register_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Register_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Register.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index 0bc88bf935..f3406d41fc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -12,22 +12,26 @@ def test_RegisterAVItoTalairach_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), out_file=dict( argstr='%s', + extensions=None, position=3, usedefault=True, ), subjects_dir=dict(), target=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), vox2vox=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -39,7 +43,10 @@ def test_RegisterAVItoTalairach_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RegisterAVItoTalairach_outputs(): output_map = dict( - log_file=dict(usedefault=True, ), + log_file=dict( + extensions=None, + usedefault=True, + ), 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 859aff0820..28ff49d99e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -8,6 +8,7 @@ def test_RelabelHypointensities_inputs(): args=dict(argstr='%s', ), aseg=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -17,10 +18,12 @@ def test_RelabelHypointensities_inputs(): ), lh_white=dict( copyfile=True, + extensions=None, mandatory=True, ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=False, name_source=['aseg'], @@ -29,6 +32,7 @@ def test_RelabelHypointensities_inputs(): ), rh_white=dict( copyfile=True, + extensions=None, mandatory=True, ), subjects_dir=dict(), @@ -44,7 +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', ), ) + 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_RemoveIntersection.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py index 69e1d453a4..38afb704c1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py @@ -13,11 +13,13 @@ def test_RemoveIntersection_inputs(): in_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-2, ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], @@ -32,7 +34,7 @@ def test_RemoveIntersection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RemoveIntersection_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RemoveIntersection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py index 9e095ddba0..f99d1ca785 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py @@ -12,11 +12,13 @@ def test_RemoveNeck_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], @@ -27,11 +29,13 @@ def test_RemoveNeck_inputs(): subjects_dir=dict(), template=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), transform=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -42,7 +46,7 @@ def test_RemoveNeck_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RemoveNeck_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RemoveNeck.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index ecb939d89a..1633369d13 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -12,11 +12,13 @@ def test_Resample_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=-2, ), resampled_file=dict( argstr='-o %s', + extensions=None, genfile=True, position=-1, ), @@ -32,7 +34,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(resampled_file=dict(), ) + output_map = dict(resampled_file=dict(extensions=None, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index af9020c278..0efbe528be 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -24,12 +24,21 @@ def test_RobustRegister_inputs(): half_targ_xfm=dict(argstr='--halfdstlta %s', ), half_weights=dict(argstr='--halfweights %s', ), high_iterations=dict(argstr='--highit %d', ), - in_xfm_file=dict(argstr='--transform', ), + in_xfm_file=dict( + argstr='--transform', + extensions=None, + ), init_orient=dict(argstr='--initorient', ), iteration_thresh=dict(argstr='--epsit %.3f', ), least_squares=dict(argstr='--leastsquares', ), - mask_source=dict(argstr='--maskmov %s', ), - mask_target=dict(argstr='--maskdst %s', ), + mask_source=dict( + argstr='--maskmov %s', + extensions=None, + ), + mask_target=dict( + argstr='--maskdst %s', + extensions=None, + ), max_iterations=dict(argstr='--maxit %d', ), no_init=dict(argstr='--noinit', ), no_multi=dict(argstr='--nomulti', ), @@ -46,12 +55,14 @@ def test_RobustRegister_inputs(): registered_file=dict(argstr='--warp %s', ), source_file=dict( argstr='--mov %s', + extensions=None, mandatory=True, ), subjects_dir=dict(), subsample_thresh=dict(argstr='--subsample %d', ), target_file=dict( argstr='--dst %s', + extensions=None, mandatory=True, ), trans_only=dict(argstr='--transonly', ), @@ -65,14 +76,14 @@ def test_RobustRegister_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustRegister_outputs(): output_map = dict( - half_source=dict(), - half_source_xfm=dict(), - half_targ=dict(), - half_targ_xfm=dict(), - half_weights=dict(), - out_reg_file=dict(), - registered_file=dict(), - weights_file=dict(), + half_source=dict(extensions=None, ), + half_source_xfm=dict(extensions=None, ), + half_targ=dict(extensions=None, ), + half_targ_xfm=dict(extensions=None, ), + half_weights=dict(extensions=None, ), + out_reg_file=dict(extensions=None, ), + registered_file=dict(extensions=None, ), + weights_file=dict(extensions=None, ), ) outputs = RobustRegister.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py index e845a764e4..3b5c635a82 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py @@ -29,6 +29,7 @@ def test_RobustTemplate_inputs(): num_threads=dict(), out_file=dict( argstr='--template %s', + extensions=None, mandatory=True, usedefault=True, ), @@ -49,7 +50,7 @@ def test_RobustTemplate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustTemplate_outputs(): output_map = dict( - out_file=dict(), + out_file=dict(extensions=None, ), scaled_intensity_outputs=dict(), transform_outputs=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index 0926eebba2..f36d84fbfc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -32,6 +32,7 @@ def test_SampleToSurface_inputs(): interp_method=dict(argstr='--interp %s', ), mask_label=dict( argstr='--mask %s', + extensions=None, xor=['cortex_mask'], ), mni152reg=dict( @@ -45,6 +46,7 @@ def test_SampleToSurface_inputs(): ), out_file=dict( argstr='--o %s', + extensions=None, genfile=True, ), out_type=dict(argstr='--out_type %s', ), @@ -56,9 +58,13 @@ def test_SampleToSurface_inputs(): mandatory=True, xor=['sampling_method'], ), - reference_file=dict(argstr='--ref %s', ), + reference_file=dict( + argstr='--ref %s', + extensions=None, + ), reg_file=dict( argstr='--reg %s', + extensions=None, mandatory=True, xor=['reg_file', 'reg_header', 'mni152reg'], ), @@ -86,6 +92,7 @@ def test_SampleToSurface_inputs(): smooth_vol=dict(argstr='--fwhm %.3f', ), source_file=dict( argstr='--mov %s', + extensions=None, mandatory=True, ), subject_id=dict(), @@ -105,9 +112,9 @@ def test_SampleToSurface_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SampleToSurface_outputs(): output_map = dict( - hits_file=dict(), - out_file=dict(), - vox_file=dict(), + hits_file=dict(extensions=None, ), + out_file=dict(extensions=None, ), + vox_file=dict(extensions=None, ), ) outputs = SampleToSurface.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 8feb61d9d8..e9a17b13ea 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -14,11 +14,15 @@ def test_SegStats_inputs(): avgwf_file=dict(argstr='--avgwfvol %s', ), avgwf_txt_file=dict(argstr='--avgwf %s', ), brain_vol=dict(argstr='--%s', ), - brainmask_file=dict(argstr='--brainmask %s', ), + brainmask_file=dict( + argstr='--brainmask %s', + extensions=None, + ), calc_power=dict(argstr='--%s', ), calc_snr=dict(argstr='--snr', ), color_table_file=dict( argstr='--ctab %s', + extensions=None, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), cortex_vol_from_surf=dict(argstr='--surf-ctx-vol', ), @@ -39,26 +43,40 @@ def test_SegStats_inputs(): frame=dict(argstr='--frame %d', ), gca_color_table=dict( argstr='--ctab-gca %s', + extensions=None, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - in_file=dict(argstr='--i %s', ), - in_intensity=dict(argstr='--in %s --in-intensity-name %s', ), + in_file=dict( + argstr='--i %s', + extensions=None, + ), + in_intensity=dict( + argstr='--in %s --in-intensity-name %s', + extensions=None, + ), intensity_units=dict( argstr='--in-intensity-units %s', requires=['in_intensity'], ), mask_erode=dict(argstr='--maskerode %d', ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + extensions=None, + ), mask_frame=dict(requires=['mask_file'], ), mask_invert=dict(argstr='--maskinvert', ), mask_sign=dict(), mask_thresh=dict(argstr='--maskthresh %f', ), multiply=dict(argstr='--mul %f', ), non_empty_only=dict(argstr='--nonempty', ), - partial_volume_file=dict(argstr='--pv %s', ), + partial_volume_file=dict( + argstr='--pv %s', + extensions=None, + ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', + extensions=None, mandatory=True, xor=('segmentation_file', 'annot', 'surf_label'), ), @@ -67,6 +85,7 @@ def test_SegStats_inputs(): subjects_dir=dict(), summary_file=dict( argstr='--sum %s', + extensions=None, genfile=True, position=-1, ), @@ -87,10 +106,10 @@ def test_SegStats_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegStats_outputs(): output_map = dict( - avgwf_file=dict(), - avgwf_txt_file=dict(), - sf_avg_file=dict(), - summary_file=dict(), + avgwf_file=dict(extensions=None, ), + avgwf_txt_file=dict(extensions=None, ), + sf_avg_file=dict(extensions=None, ), + summary_file=dict(extensions=None, ), ) outputs = SegStats.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index e65dc82e3b..3cf47c71ce 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -11,15 +11,19 @@ def test_SegStatsReconAll_inputs(): xor=('segmentation_file', 'annot', 'surf_label'), ), args=dict(argstr='%s', ), - aseg=dict(), + aseg=dict(extensions=None, ), avgwf_file=dict(argstr='--avgwfvol %s', ), avgwf_txt_file=dict(argstr='--avgwf %s', ), brain_vol=dict(argstr='--%s', ), - brainmask_file=dict(argstr='--brainmask %s', ), + brainmask_file=dict( + argstr='--brainmask %s', + extensions=None, + ), calc_power=dict(argstr='--%s', ), calc_snr=dict(argstr='--snr', ), color_table_file=dict( argstr='--ctab %s', + extensions=None, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), copy_inputs=dict(), @@ -41,34 +45,66 @@ def test_SegStatsReconAll_inputs(): frame=dict(argstr='--frame %d', ), gca_color_table=dict( argstr='--ctab-gca %s', + extensions=None, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - in_file=dict(argstr='--i %s', ), - in_intensity=dict(argstr='--in %s --in-intensity-name %s', ), + in_file=dict( + argstr='--i %s', + extensions=None, + ), + in_intensity=dict( + argstr='--in %s --in-intensity-name %s', + extensions=None, + ), intensity_units=dict( argstr='--in-intensity-units %s', requires=['in_intensity'], ), - lh_orig_nofix=dict(mandatory=True, ), - lh_pial=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), + lh_orig_nofix=dict( + extensions=None, + mandatory=True, + ), + lh_pial=dict( + extensions=None, + mandatory=True, + ), + lh_white=dict( + extensions=None, + mandatory=True, + ), mask_erode=dict(argstr='--maskerode %d', ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + extensions=None, + ), mask_frame=dict(requires=['mask_file'], ), mask_invert=dict(argstr='--maskinvert', ), mask_sign=dict(), mask_thresh=dict(argstr='--maskthresh %f', ), multiply=dict(argstr='--mul %f', ), non_empty_only=dict(argstr='--nonempty', ), - partial_volume_file=dict(argstr='--pv %s', ), - presurf_seg=dict(), - rh_orig_nofix=dict(mandatory=True, ), - rh_pial=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), + partial_volume_file=dict( + argstr='--pv %s', + extensions=None, + ), + presurf_seg=dict(extensions=None, ), + rh_orig_nofix=dict( + extensions=None, + mandatory=True, + ), + rh_pial=dict( + extensions=None, + mandatory=True, + ), + rh_white=dict( + extensions=None, + mandatory=True, + ), ribbon=dict(mandatory=True, ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', + extensions=None, mandatory=True, xor=('segmentation_file', 'annot', 'surf_label'), ), @@ -82,6 +118,7 @@ def test_SegStatsReconAll_inputs(): subjects_dir=dict(), summary_file=dict( argstr='--sum %s', + extensions=None, genfile=True, position=-1, ), @@ -92,7 +129,10 @@ def test_SegStatsReconAll_inputs(): xor=('segmentation_file', 'annot', 'surf_label'), ), total_gray=dict(argstr='--totalgray', ), - transform=dict(mandatory=True, ), + transform=dict( + extensions=None, + mandatory=True, + ), vox=dict(argstr='--vox %s', ), wm_vol_from_surf=dict(argstr='--surf-wm-vol', ), ) @@ -103,10 +143,10 @@ def test_SegStatsReconAll_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegStatsReconAll_outputs(): output_map = dict( - avgwf_file=dict(), - avgwf_txt_file=dict(), - sf_avg_file=dict(), - summary_file=dict(), + avgwf_file=dict(extensions=None, ), + avgwf_txt_file=dict(extensions=None, ), + sf_avg_file=dict(extensions=None, ), + summary_file=dict(extensions=None, ), ) outputs = SegStatsReconAll.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py index e6b5fb2679..8cda53a762 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py @@ -13,11 +13,16 @@ def test_SegmentCC_inputs(): ), in_file=dict( argstr='-aseg %s', + extensions=None, + mandatory=True, + ), + in_norm=dict( + extensions=None, mandatory=True, ), - in_norm=dict(mandatory=True, ), out_file=dict( argstr='-o %s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_file'], @@ -25,6 +30,7 @@ def test_SegmentCC_inputs(): ), out_rotation=dict( argstr='-lta %s', + extensions=None, mandatory=True, ), subject_id=dict( @@ -42,8 +48,8 @@ def test_SegmentCC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegmentCC_outputs(): output_map = dict( - out_file=dict(), - out_rotation=dict(), + out_file=dict(extensions=None, ), + out_rotation=dict(extensions=None, ), ) outputs = SegmentCC.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py index aa742e8fea..c86bc926dc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py @@ -12,11 +12,13 @@ def test_SegmentWM_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -28,7 +30,7 @@ def test_SegmentWM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SegmentWM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SegmentWM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index fe4581dee0..3c52c01430 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -12,6 +12,7 @@ def test_Smooth_inputs(): ), in_file=dict( argstr='--i %s', + extensions=None, mandatory=True, ), num_iters=dict( @@ -29,10 +30,12 @@ def test_Smooth_inputs(): ), reg_file=dict( argstr='--reg %s', + extensions=None, mandatory=True, ), smoothed_file=dict( argstr='--o %s', + extensions=None, genfile=True, ), subjects_dir=dict(), @@ -50,7 +53,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): - output_map = dict(smoothed_file=dict(), ) + output_map = dict(smoothed_file=dict(extensions=None, ), ) outputs = Smooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index 8ce4dce075..1f855c5606 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -17,14 +17,22 @@ def test_SmoothTessellation_inputs(): in_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-2, ), normalize_area=dict(argstr='-area', ), - out_area_file=dict(argstr='-b %s', ), - out_curvature_file=dict(argstr='-c %s', ), + out_area_file=dict( + argstr='-b %s', + extensions=None, + ), + out_curvature_file=dict( + argstr='-c %s', + extensions=None, + ), out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -41,7 +49,7 @@ def test_SmoothTessellation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SmoothTessellation_outputs(): - output_map = dict(surface=dict(), ) + output_map = dict(surface=dict(extensions=None, ), ) outputs = SmoothTessellation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py index 461398e6a8..a5795653fc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py @@ -13,14 +13,19 @@ def test_Sphere_inputs(): in_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, position=-2, ), - in_smoothwm=dict(copyfile=True, ), + in_smoothwm=dict( + copyfile=True, + extensions=None, + ), magic=dict(argstr='-q', ), num_threads=dict(), out_file=dict( argstr='%s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s.sphere', @@ -35,7 +40,7 @@ def test_Sphere_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Sphere_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Sphere.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index efdc032787..3a38f8c205 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -26,14 +26,19 @@ def test_SphericalAverage_inputs(): genfile=True, position=-2, ), - in_orig=dict(argstr='-orig %s', ), + in_orig=dict( + argstr='-orig %s', + extensions=None, + ), in_surf=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -55,7 +60,7 @@ def test_SphericalAverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SphericalAverage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SphericalAverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index ca3f96c42b..b291385039 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -21,12 +21,14 @@ def test_Surface2VolTransform_inputs(): projfrac=dict(argstr='--projfrac %s', ), reg_file=dict( argstr='--volreg %s', + extensions=None, mandatory=True, xor=['subject_id'], ), source_file=dict( argstr='--surfval %s', copyfile=False, + extensions=None, mandatory=True, xor=['mkmask'], ), @@ -36,15 +38,20 @@ def test_Surface2VolTransform_inputs(): ), subjects_dir=dict(argstr='--sd %s', ), surf_name=dict(argstr='--surf %s', ), - template_file=dict(argstr='--template %s', ), + template_file=dict( + argstr='--template %s', + extensions=None, + ), transformed_file=dict( argstr='--outvol %s', + extensions=None, hash_files=False, name_source=['source_file'], name_template='%s_asVol.nii', ), vertexvol_file=dict( argstr='--vtxvol %s', + extensions=None, hash_files=False, name_source=['source_file'], name_template='%s_asVol_vertex.nii', @@ -57,8 +64,8 @@ def test_Surface2VolTransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Surface2VolTransform_outputs(): output_map = dict( - transformed_file=dict(), - vertexvol_file=dict(), + transformed_file=dict(extensions=None, ), + vertexvol_file=dict(extensions=None, ), ) outputs = Surface2VolTransform.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index 84bef6ed7a..c845ae50f7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -24,10 +24,12 @@ def test_SurfaceSmooth_inputs(): ), in_file=dict( argstr='--sval %s', + extensions=None, mandatory=True, ), out_file=dict( argstr='--tval %s', + extensions=None, genfile=True, ), reshape=dict(argstr='--reshape', ), @@ -47,7 +49,7 @@ def test_SurfaceSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceSmooth_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SurfaceSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index a413d410b1..26dcbe3458 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -7,6 +7,7 @@ def test_SurfaceSnapshots_inputs(): input_map = dict( annot_file=dict( argstr='-annotation %s', + extensions=None, xor=['annot_name'], ), annot_name=dict( @@ -14,7 +15,10 @@ def test_SurfaceSnapshots_inputs(): xor=['annot_file'], ), args=dict(argstr='%s', ), - colortable=dict(argstr='-colortable %s', ), + colortable=dict( + argstr='-colortable %s', + extensions=None, + ), demean_overlay=dict(argstr='-zm', ), environ=dict( nohash=True, @@ -32,6 +36,7 @@ def test_SurfaceSnapshots_inputs(): invert_overlay=dict(argstr='-invphaseflag 1', ), label_file=dict( argstr='-label %s', + extensions=None, xor=['label_name'], ), label_name=dict( @@ -47,6 +52,7 @@ def test_SurfaceSnapshots_inputs(): orig_suffix=dict(argstr='-orig %s', ), overlay=dict( argstr='-overlay %s', + extensions=None, requires=['overlay_range'], ), overlay_range=dict(argstr='%s', ), @@ -55,7 +61,10 @@ def test_SurfaceSnapshots_inputs(): argstr='-overlay-reg %s', xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), - patch_file=dict(argstr='-patch %s', ), + patch_file=dict( + argstr='-patch %s', + extensions=None, + ), reverse_overlay=dict(argstr='-revphaseflag 1', ), screenshot_stem=dict(), show_color_scale=dict(argstr='-colscalebarflag 1', ), @@ -84,6 +93,7 @@ def test_SurfaceSnapshots_inputs(): ), tcl_script=dict( argstr='%s', + extensions=None, genfile=True, ), truncate_overlay=dict(argstr='-truncphaseflag 1', ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index 0546a275dc..5d0dc75073 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -16,17 +16,20 @@ def test_SurfaceTransform_inputs(): ), out_file=dict( argstr='--tval %s', + extensions=None, genfile=True, ), reshape=dict(argstr='--reshape', ), reshape_factor=dict(argstr='--reshape-factor', ), source_annot_file=dict( argstr='--sval-annot %s', + extensions=None, mandatory=True, xor=['source_file'], ), source_file=dict( argstr='--sval %s', + extensions=None, mandatory=True, xor=['source_annot_file'], ), @@ -52,7 +55,7 @@ def test_SurfaceTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SurfaceTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index ea121d877e..a216d35efa 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -21,16 +21,19 @@ def test_SynthesizeFLASH_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, ), pd_image=dict( argstr='%s', + extensions=None, mandatory=True, position=6, ), subjects_dir=dict(), t1_image=dict( argstr='%s', + extensions=None, mandatory=True, position=5, ), @@ -51,7 +54,7 @@ def test_SynthesizeFLASH_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SynthesizeFLASH_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SynthesizeFLASH.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index 8ce925fcc7..9d248c1a7d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -13,10 +13,12 @@ def test_TalairachAVI_inputs(): ), in_file=dict( argstr='--i %s', + extensions=None, mandatory=True, ), out_file=dict( argstr='--xfm %s', + extensions=None, mandatory=True, ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index d07e572365..053d429c9b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -12,6 +12,7 @@ def test_TalairachQC_inputs(): ), log_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -23,7 +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(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/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index 17f8e53a1f..a1b04aab81 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -10,7 +10,10 @@ def test_Tkregister2_inputs(): nohash=True, usedefault=True, ), - fsl_in_matrix=dict(argstr='--fsl %s', ), + fsl_in_matrix=dict( + argstr='--fsl %s', + extensions=None, + ), fsl_out=dict(argstr='--fslregout %s', ), fstal=dict( argstr='--fstal', @@ -25,10 +28,14 @@ def test_Tkregister2_inputs(): argstr='--ltaout-inv', requires=['lta_in'], ), - lta_in=dict(argstr='--lta %s', ), + lta_in=dict( + argstr='--lta %s', + extensions=None, + ), lta_out=dict(argstr='--ltaout %s', ), moving_image=dict( argstr='--mov %s', + extensions=None, mandatory=True, ), movscale=dict(argstr='--movscale %f', ), @@ -38,6 +45,7 @@ def test_Tkregister2_inputs(): ), reg_file=dict( argstr='--reg %s', + extensions=None, mandatory=True, usedefault=True, ), @@ -46,9 +54,13 @@ def test_Tkregister2_inputs(): subjects_dir=dict(), target_image=dict( argstr='--targ %s', + extensions=None, xor=['fstarg'], ), - xfm=dict(argstr='--xfm %s', ), + xfm=dict( + argstr='--xfm %s', + extensions=None, + ), ) inputs = Tkregister2.input_spec() @@ -57,9 +69,9 @@ def test_Tkregister2_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Tkregister2_outputs(): output_map = dict( - fsl_file=dict(), - lta_file=dict(), - reg_file=dict(), + fsl_file=dict(extensions=None, ), + lta_file=dict(extensions=None, ), + reg_file=dict(extensions=None, ), ) outputs = Tkregister2.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index 9427e60940..11b1d8c2ce 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -8,6 +8,7 @@ def test_UnpackSDICOMDir_inputs(): args=dict(argstr='%s', ), config=dict( argstr='-cfg %s', + extensions=None, mandatory=True, xor=('run_info', 'config', 'seq_config'), ), @@ -16,7 +17,10 @@ def test_UnpackSDICOMDir_inputs(): nohash=True, usedefault=True, ), - log_file=dict(argstr='-log %s', ), + log_file=dict( + argstr='-log %s', + extensions=None, + ), no_info_dump=dict(argstr='-noinfodump', ), no_unpack_err=dict(argstr='-no-unpackerr', ), output_dir=dict(argstr='-targ %s', ), @@ -25,9 +29,13 @@ def test_UnpackSDICOMDir_inputs(): mandatory=True, xor=('run_info', 'config', 'seq_config'), ), - scan_only=dict(argstr='-scanonly %s', ), + scan_only=dict( + argstr='-scanonly %s', + extensions=None, + ), seq_config=dict( argstr='-seqcfg %s', + extensions=None, mandatory=True, xor=('run_info', 'config', 'seq_config'), ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py index 3e898a81f7..bfdf5a457e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py @@ -6,7 +6,10 @@ def test_VolumeMask_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict(xor=['in_aseg'], ), + aseg=dict( + extensions=None, + xor=['in_aseg'], + ), copy_inputs=dict(), environ=dict( nohash=True, @@ -14,6 +17,7 @@ def test_VolumeMask_inputs(): ), in_aseg=dict( argstr='--aseg_name %s', + extensions=None, xor=['aseg'], ), left_ribbonlabel=dict( @@ -24,10 +28,22 @@ def test_VolumeMask_inputs(): argstr='--label_left_white %d', mandatory=True, ), - lh_pial=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), - rh_pial=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), + lh_pial=dict( + extensions=None, + mandatory=True, + ), + lh_white=dict( + extensions=None, + mandatory=True, + ), + rh_pial=dict( + extensions=None, + mandatory=True, + ), + rh_white=dict( + extensions=None, + mandatory=True, + ), right_ribbonlabel=dict( argstr='--label_right_ribbon %d', mandatory=True, @@ -52,9 +68,9 @@ def test_VolumeMask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VolumeMask_outputs(): output_map = dict( - lh_ribbon=dict(), - out_ribbon=dict(), - rh_ribbon=dict(), + lh_ribbon=dict(extensions=None, ), + out_ribbon=dict(extensions=None, ), + rh_ribbon=dict(extensions=None, ), ) outputs = VolumeMask.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py index 3586e7d234..8112a8f52f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py @@ -8,6 +8,7 @@ def test_WatershedSkullStrip_inputs(): args=dict(argstr='%s', ), brain_atlas=dict( argstr='-brain_atlas %s', + extensions=None, position=-4, ), environ=dict( @@ -16,11 +17,13 @@ def test_WatershedSkullStrip_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -29,6 +32,7 @@ def test_WatershedSkullStrip_inputs(): t1=dict(argstr='-T1', ), transform=dict( argstr='%s', + extensions=None, position=-3, ), ) @@ -38,7 +42,7 @@ def test_WatershedSkullStrip_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WatershedSkullStrip_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = WatershedSkullStrip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py index 32efb1826e..260f53b978 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py +++ b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py @@ -17,6 +17,7 @@ def test_AR1Image_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_AR1Image_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_AR1Image_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AR1Image_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = AR1Image.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 062d6367f7..de32f63f5f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -23,6 +23,7 @@ def test_AccuracyTester_inputs(): ), trained_wts_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 8a39956c18..ad8df118b6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -12,6 +12,7 @@ def test_ApplyMask_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -21,6 +22,7 @@ def test_ApplyMask_inputs(): ), mask_file=dict( argstr='-mas %s', + extensions=None, mandatory=True, position=4, ), @@ -30,6 +32,7 @@ def test_ApplyMask_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +49,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ApplyMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 7a803f9695..805884f23c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -9,6 +9,7 @@ def test_ApplyTOPUP_inputs(): datatype=dict(argstr='-d=%s', ), encoding_file=dict( argstr='--datain=%s', + extensions=None, mandatory=True, ), environ=dict( @@ -27,16 +28,19 @@ def test_ApplyTOPUP_inputs(): in_topup_fieldcoef=dict( argstr='--topup=%s', copyfile=False, + extensions=None, requires=['in_topup_movpar'], ), in_topup_movpar=dict( copyfile=False, + extensions=None, requires=['in_topup_fieldcoef'], ), interp=dict(argstr='--interp=%s', ), method=dict(argstr='--method=%s', ), out_corrected=dict( argstr='--out=%s', + extensions=None, name_source=['in_files'], name_template='%s_corrected', ), @@ -48,7 +52,7 @@ def test_ApplyTOPUP_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTOPUP_outputs(): - output_map = dict(out_corrected=dict(), ) + output_map = dict(out_corrected=dict(extensions=None, ), ) outputs = ApplyTOPUP.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index 71977cb873..2af381012b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -15,9 +15,13 @@ def test_ApplyWarp_inputs(): nohash=True, usedefault=True, ), - field_file=dict(argstr='--warp=%s', ), + field_file=dict( + argstr='--warp=%s', + extensions=None, + ), in_file=dict( argstr='--in=%s', + extensions=None, mandatory=True, position=0, ), @@ -25,18 +29,29 @@ def test_ApplyWarp_inputs(): argstr='--interp=%s', position=-2, ), - mask_file=dict(argstr='--mask=%s', ), + mask_file=dict( + argstr='--mask=%s', + extensions=None, + ), out_file=dict( argstr='--out=%s', + extensions=None, genfile=True, hash_files=False, position=2, ), output_type=dict(), - postmat=dict(argstr='--postmat=%s', ), - premat=dict(argstr='--premat=%s', ), + postmat=dict( + argstr='--postmat=%s', + extensions=None, + ), + premat=dict( + argstr='--premat=%s', + extensions=None, + ), ref_file=dict( argstr='--ref=%s', + extensions=None, mandatory=True, position=1, ), @@ -54,7 +69,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ApplyWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py index f515be1f04..38a45ce775 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py @@ -44,10 +44,12 @@ def test_ApplyXFM_inputs(): ), fieldmap=dict( argstr='-fieldmap %s', + extensions=None, min_ver='5.0.0', ), fieldmapmask=dict( argstr='-fieldmapmask %s', + extensions=None, min_ver='5.0.0', ), fine_search=dict( @@ -57,11 +59,18 @@ def test_ApplyXFM_inputs(): force_scaling=dict(argstr='-forcescaling', ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, position=0, ), - in_matrix_file=dict(argstr='-init %s', ), - in_weight=dict(argstr='-inweight %s', ), + in_matrix_file=dict( + argstr='-init %s', + extensions=None, + ), + in_weight=dict( + argstr='-inweight %s', + extensions=None, + ), interp=dict(argstr='-interp %s', ), min_sampling=dict( argstr='-minsampling %f', @@ -73,12 +82,14 @@ def test_ApplyXFM_inputs(): no_search=dict(argstr='-nosearch', ), out_file=dict( argstr='-out %s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_flirt', position=2, ), out_log=dict( + extensions=None, keep_extension=True, name_source=['in_file'], name_template='%s_flirt.log', @@ -86,6 +97,7 @@ def test_ApplyXFM_inputs(): ), out_matrix_file=dict( argstr='-omat %s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], @@ -101,15 +113,22 @@ def test_ApplyXFM_inputs(): argstr='-pedir %d', min_ver='5.0.0', ), - ref_weight=dict(argstr='-refweight %s', ), + ref_weight=dict( + argstr='-refweight %s', + extensions=None, + ), reference=dict( argstr='-ref %s', + extensions=None, mandatory=True, position=1, ), rigid2D=dict(argstr='-2D', ), save_log=dict(), - schedule=dict(argstr='-schedule %s', ), + schedule=dict( + argstr='-schedule %s', + extensions=None, + ), searchr_x=dict( argstr='-searchrx %s', units='degrees', @@ -131,14 +150,17 @@ def test_ApplyXFM_inputs(): verbose=dict(argstr='-verbose %d', ), wm_seg=dict( argstr='-wmseg %s', + extensions=None, min_ver='5.0.0', ), wmcoords=dict( argstr='-wmcoords %s', + extensions=None, min_ver='5.0.0', ), wmnorms=dict( argstr='-wmnorms %s', + extensions=None, min_ver='5.0.0', ), ) @@ -149,9 +171,9 @@ def test_ApplyXFM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyXFM_outputs(): output_map = dict( - out_file=dict(), - out_log=dict(), - out_matrix_file=dict(), + out_file=dict(extensions=None, ), + out_log=dict(extensions=None, ), + out_matrix_file=dict(extensions=None, ), ) outputs = ApplyXFM.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index 762ada916d..a6df228f71 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -13,10 +13,12 @@ def test_AvScale_inputs(): ), mat_file=dict( argstr='%s', + extensions=None, position=-2, ), ref_file=dict( argstr='%s', + extensions=None, position=-1, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py index 96ec6b949c..1127f900d1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py +++ b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py @@ -32,11 +32,13 @@ def test_B0Calc_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=0, ), out_file=dict( argstr='-o %s', + extensions=None, name_source=['in_file'], name_template='%s_b0field', output_name='out_file', @@ -81,7 +83,7 @@ def test_B0Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_B0Calc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = B0Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index 1ac5db111b..e93cf42b9d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -18,13 +18,22 @@ def test_BEDPOSTX5_inputs(): argstr='--burnin_noard=%d', usedefault=True, ), - bvals=dict(mandatory=True, ), - bvecs=dict(mandatory=True, ), + bvals=dict( + extensions=None, + mandatory=True, + ), + bvecs=dict( + extensions=None, + mandatory=True, + ), cnlinear=dict( argstr='--cnonlinear', xor=('no_spat', 'non_linear', 'cnlinear'), ), - dwi=dict(mandatory=True, ), + dwi=dict( + extensions=None, + mandatory=True, + ), environ=dict( nohash=True, usedefault=True, @@ -42,10 +51,13 @@ def test_BEDPOSTX5_inputs(): usedefault=True, ), fudge=dict(argstr='-w %d', ), - grad_dev=dict(), + grad_dev=dict(extensions=None, ), gradnonlin=dict(argstr='-g', ), logdir=dict(argstr='--logdir=%s', ), - mask=dict(mandatory=True, ), + mask=dict( + extensions=None, + mandatory=True, + ), model=dict(argstr='-model %d', ), n_fibres=dict( argstr='-n %d', @@ -96,8 +108,8 @@ def test_BEDPOSTX5_outputs(): output_map = dict( dyads=dict(), dyads_dispersion=dict(), - mean_S0samples=dict(), - mean_dsamples=dict(), + mean_S0samples=dict(extensions=None, ), + mean_dsamples=dict(extensions=None, ), mean_fsamples=dict(), mean_phsamples=dict(), mean_thsamples=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index eccf348b3e..ea155c249b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -22,6 +22,7 @@ def test_BET_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -30,6 +31,7 @@ def test_BET_inputs(): no_output=dict(argstr='-n', ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=1, @@ -68,6 +70,7 @@ def test_BET_inputs(): ), t2_guided=dict( argstr='-A2 %s', + extensions=None, xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), @@ -81,17 +84,17 @@ def test_BET_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BET_outputs(): output_map = dict( - inskull_mask_file=dict(), - inskull_mesh_file=dict(), - mask_file=dict(), - meshfile=dict(), - out_file=dict(), - outline_file=dict(), - outskin_mask_file=dict(), - outskin_mesh_file=dict(), - outskull_mask_file=dict(), - outskull_mesh_file=dict(), - skull_mask_file=dict(), + inskull_mask_file=dict(extensions=None, ), + inskull_mesh_file=dict(extensions=None, ), + mask_file=dict(extensions=None, ), + meshfile=dict(extensions=None, ), + out_file=dict(extensions=None, ), + outline_file=dict(extensions=None, ), + outskin_mask_file=dict(extensions=None, ), + outskin_mesh_file=dict(extensions=None, ), + outskull_mask_file=dict(extensions=None, ), + outskull_mesh_file=dict(extensions=None, ), + skull_mask_file=dict(extensions=None, ), ) outputs = BET.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index 2548ae68e5..8020c49bbc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -12,6 +12,7 @@ def test_BinaryMaths_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -25,6 +26,7 @@ def test_BinaryMaths_inputs(): ), operand_file=dict( argstr='%s', + extensions=None, mandatory=True, position=5, xor=['operand_value'], @@ -42,6 +44,7 @@ def test_BinaryMaths_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -58,7 +61,7 @@ def test_BinaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BinaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index aab508f2bf..665a2cb47d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -12,6 +12,7 @@ def test_ChangeDataType_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -25,6 +26,7 @@ def test_ChangeDataType_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -42,7 +44,7 @@ def test_ChangeDataType_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ChangeDataType_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ChangeDataType.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Classifier.py b/nipype/interfaces/fsl/tests/test_auto_Classifier.py index a8db888acb..b477b38ea4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Classifier.py +++ b/nipype/interfaces/fsl/tests/test_auto_Classifier.py @@ -6,7 +6,7 @@ def test_Classifier_inputs(): input_map = dict( args=dict(argstr='%s', ), - artifacts_list_file=dict(), + artifacts_list_file=dict(extensions=None, ), environ=dict( nohash=True, usedefault=True, @@ -24,6 +24,7 @@ def test_Classifier_inputs(): trained_wts_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=2, ), @@ -34,7 +35,7 @@ def test_Classifier_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Classifier_outputs(): - output_map = dict(artifacts_list_file=dict(), ) + output_map = dict(artifacts_list_file=dict(extensions=None, ), ) outputs = Classifier.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 5fc505a174..a75df99db5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -12,6 +12,7 @@ def test_Cleaner_inputs(): args=dict(argstr='%s', ), artifacts_list_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -47,7 +48,7 @@ def test_Cleaner_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cleaner_outputs(): - output_map = dict(cleaned_functional_file=dict(), ) + output_map = dict(cleaned_functional_file=dict(extensions=None, ), ) outputs = Cleaner.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index f876f85e64..6ed34ab816 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -23,6 +23,7 @@ def test_Cluster_inputs(): ), in_file=dict( argstr='--in=%s', + extensions=None, mandatory=True, ), minclustersize=dict( @@ -72,7 +73,10 @@ def test_Cluster_inputs(): argstr='--pthresh=%.10f', requires=['dlh', 'volume'], ), - std_space_file=dict(argstr='--stdvol=%s', ), + std_space_file=dict( + argstr='--stdvol=%s', + extensions=None, + ), threshold=dict( argstr='--thresh=%.10f', mandatory=True, @@ -82,8 +86,14 @@ def test_Cluster_inputs(): usedefault=True, ), volume=dict(argstr='--volume=%d', ), - warpfield_file=dict(argstr='--warpvol=%s', ), - xfm_file=dict(argstr='--xfm=%s', ), + warpfield_file=dict( + argstr='--warpvol=%s', + extensions=None, + ), + xfm_file=dict( + argstr='--xfm=%s', + extensions=None, + ), ) inputs = Cluster.input_spec() @@ -92,14 +102,14 @@ def test_Cluster_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Cluster_outputs(): output_map = dict( - index_file=dict(), - localmax_txt_file=dict(), - localmax_vol_file=dict(), - max_file=dict(), - mean_file=dict(), - pval_file=dict(), - size_file=dict(), - threshold_file=dict(), + index_file=dict(extensions=None, ), + localmax_txt_file=dict(extensions=None, ), + localmax_vol_file=dict(extensions=None, ), + max_file=dict(extensions=None, ), + mean_file=dict(extensions=None, ), + pval_file=dict(extensions=None, ), + size_file=dict(extensions=None, ), + threshold_file=dict(extensions=None, ), ) outputs = Cluster.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index 7e49bcdfa8..09f2add2bc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -16,10 +16,12 @@ def test_Complex_inputs(): ), complex_in_file=dict( argstr='%s', + extensions=None, position=2, ), complex_in_file2=dict( argstr='%s', + extensions=None, position=3, ), complex_merge=dict( @@ -33,6 +35,7 @@ def test_Complex_inputs(): ), complex_out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-3, xor=[ @@ -67,10 +70,12 @@ def test_Complex_inputs(): ), imaginary_in_file=dict( argstr='%s', + extensions=None, position=3, ), imaginary_out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-3, xor=[ @@ -81,10 +86,12 @@ def test_Complex_inputs(): ), magnitude_in_file=dict( argstr='%s', + extensions=None, position=2, ), magnitude_out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-4, xor=[ @@ -96,10 +103,12 @@ def test_Complex_inputs(): output_type=dict(), phase_in_file=dict( argstr='%s', + extensions=None, position=3, ), phase_out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-3, xor=[ @@ -118,10 +127,12 @@ def test_Complex_inputs(): ), real_in_file=dict( argstr='%s', + extensions=None, position=2, ), real_out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-4, xor=[ @@ -150,11 +161,11 @@ def test_Complex_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Complex_outputs(): output_map = dict( - complex_out_file=dict(), - imaginary_out_file=dict(), - magnitude_out_file=dict(), - phase_out_file=dict(), - real_out_file=dict(), + complex_out_file=dict(extensions=None, ), + imaginary_out_file=dict(extensions=None, ), + magnitude_out_file=dict(extensions=None, ), + phase_out_file=dict(extensions=None, ), + real_out_file=dict(extensions=None, ), ) outputs = Complex.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index a82ea8fe43..7f4c0f5367 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -9,18 +9,23 @@ def test_ContrastMgr_inputs(): contrast_num=dict(argstr='-cope', ), corrections=dict( copyfile=False, + extensions=None, mandatory=True, ), dof_file=dict( argstr='', copyfile=False, + extensions=None, mandatory=True, ), environ=dict( nohash=True, usedefault=True, ), - fcon_file=dict(argstr='-f %s', ), + fcon_file=dict( + argstr='-f %s', + extensions=None, + ), output_type=dict(), param_estimates=dict( argstr='', @@ -30,12 +35,14 @@ def test_ContrastMgr_inputs(): sigmasquareds=dict( argstr='', copyfile=False, + extensions=None, mandatory=True, position=-2, ), suffix=dict(argstr='-suffix %s', ), tcon_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index 2ed14aaad2..602ca86b47 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -17,13 +17,17 @@ def test_ConvertWarp_inputs(): ), jacobian_max=dict(argstr='--jmax=%f', ), jacobian_min=dict(argstr='--jmin=%f', ), - midmat=dict(argstr='--midmat=%s', ), + midmat=dict( + argstr='--midmat=%s', + extensions=None, + ), out_abswarp=dict( argstr='--absout', xor=['out_relwarp'], ), out_file=dict( argstr='--out=%s', + extensions=None, name_source=['reference'], name_template='%s_concatwarp', output_name='out_file', @@ -34,10 +38,17 @@ def test_ConvertWarp_inputs(): xor=['out_abswarp'], ), output_type=dict(), - postmat=dict(argstr='--postmat=%s', ), - premat=dict(argstr='--premat=%s', ), + postmat=dict( + argstr='--postmat=%s', + extensions=None, + ), + premat=dict( + argstr='--premat=%s', + extensions=None, + ), reference=dict( argstr='--ref=%s', + extensions=None, mandatory=True, position=1, ), @@ -49,9 +60,18 @@ def test_ConvertWarp_inputs(): argstr='--shiftdir=%s', requires=['shift_in_file'], ), - shift_in_file=dict(argstr='--shiftmap=%s', ), - warp1=dict(argstr='--warp1=%s', ), - warp2=dict(argstr='--warp2=%s', ), + shift_in_file=dict( + argstr='--shiftmap=%s', + extensions=None, + ), + warp1=dict( + argstr='--warp1=%s', + extensions=None, + ), + warp2=dict( + argstr='--warp2=%s', + extensions=None, + ), ) inputs = ConvertWarp.input_spec() @@ -59,7 +79,7 @@ def test_ConvertWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertWarp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ConvertWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index c017a39a52..a49a846ad9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -24,11 +24,13 @@ def test_ConvertXFM_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), in_file2=dict( argstr='%s', + extensions=None, position=-2, ), invert_xfm=dict( @@ -38,6 +40,7 @@ def test_ConvertXFM_inputs(): ), out_file=dict( argstr='-omat %s', + extensions=None, genfile=True, hash_files=False, position=1, @@ -50,7 +53,7 @@ def test_ConvertXFM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertXFM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ConvertXFM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index c66feff211..2cf330edee 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -9,6 +9,7 @@ def test_CopyGeom_inputs(): dest_file=dict( argstr='%s', copyfile=True, + extensions=None, mandatory=True, name_source='dest_file', name_template='%s', @@ -25,6 +26,7 @@ def test_CopyGeom_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -36,7 +38,7 @@ def test_CopyGeom_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CopyGeom_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = CopyGeom.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index b1d3b4822d..b88fc68c82 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -13,17 +13,23 @@ def test_DTIFit_inputs(): ), bvals=dict( argstr='-b %s', + extensions=None, mandatory=True, position=4, ), bvecs=dict( argstr='-r %s', + extensions=None, mandatory=True, position=3, ), - cni=dict(argstr='--cni=%s', ), + cni=dict( + argstr='--cni=%s', + extensions=None, + ), dwi=dict( argstr='-k %s', + extensions=None, mandatory=True, position=0, ), @@ -31,10 +37,14 @@ def test_DTIFit_inputs(): nohash=True, usedefault=True, ), - gradnonlin=dict(argstr='--gradnonlin=%s', ), + gradnonlin=dict( + argstr='--gradnonlin=%s', + extensions=None, + ), little_bit=dict(argstr='--littlebit', ), mask=dict( argstr='-m %s', + extensions=None, mandatory=True, position=2, ), @@ -55,18 +65,18 @@ def test_DTIFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): output_map = dict( - FA=dict(), - L1=dict(), - L2=dict(), - L3=dict(), - MD=dict(), - MO=dict(), - S0=dict(), - V1=dict(), - V2=dict(), - V3=dict(), - sse=dict(), - tensor=dict(), + FA=dict(extensions=None, ), + L1=dict(extensions=None, ), + L2=dict(extensions=None, ), + L3=dict(extensions=None, ), + MD=dict(extensions=None, ), + MO=dict(extensions=None, ), + S0=dict(extensions=None, ), + V1=dict(extensions=None, ), + V2=dict(extensions=None, ), + V3=dict(extensions=None, ), + sse=dict(extensions=None, ), + tensor=dict(extensions=None, ), ) outputs = DTIFit.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 3ed43fbd22..12df7f13af 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -12,6 +12,7 @@ def test_DilateImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -21,6 +22,7 @@ def test_DilateImage_inputs(): ), kernel_file=dict( argstr='%s', + extensions=None, position=5, xor=['kernel_size'], ), @@ -44,6 +46,7 @@ def test_DilateImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -60,7 +63,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = DilateImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 5f3321de78..88f53ad2eb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -8,6 +8,7 @@ def test_DistanceMap_inputs(): args=dict(argstr='%s', ), distance_map=dict( argstr='--out=%s', + extensions=None, genfile=True, hash_files=False, ), @@ -17,6 +18,7 @@ def test_DistanceMap_inputs(): ), in_file=dict( argstr='--in=%s', + extensions=None, mandatory=True, ), invert_input=dict(argstr='--invert', ), @@ -24,7 +26,10 @@ def test_DistanceMap_inputs(): argstr='--localmax=%s', hash_files=False, ), - mask_file=dict(argstr='--mask=%s', ), + mask_file=dict( + argstr='--mask=%s', + extensions=None, + ), output_type=dict(), ) inputs = DistanceMap.input_spec() @@ -34,8 +39,8 @@ def test_DistanceMap_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMap_outputs(): output_map = dict( - distance_map=dict(), - local_max_file=dict(), + distance_map=dict(extensions=None, ), + local_max_file=dict(extensions=None, ), ) outputs = DistanceMap.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py index 4c2fdd3ceb..99556ae8fa 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py +++ b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py @@ -8,6 +8,7 @@ def test_DualRegression_inputs(): args=dict(argstr='%s', ), con_file=dict( argstr='%s', + extensions=None, position=4, ), des_norm=dict( @@ -17,6 +18,7 @@ def test_DualRegression_inputs(): ), design_file=dict( argstr='%s', + extensions=None, position=3, ), environ=dict( @@ -25,6 +27,7 @@ def test_DualRegression_inputs(): ), group_IC_maps_4D=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index 2a5f0c86b6..fa5fbcf041 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -9,13 +9,17 @@ def test_EPIDeWarp_inputs(): cleanup=dict(argstr='--cleanup', ), dph_file=dict( argstr='--dph %s', + extensions=None, mandatory=True, ), environ=dict( nohash=True, usedefault=True, ), - epi_file=dict(argstr='--epi %s', ), + epi_file=dict( + argstr='--epi %s', + extensions=None, + ), epidw=dict( argstr='--epidw %s', genfile=False, @@ -24,13 +28,17 @@ def test_EPIDeWarp_inputs(): argstr='--esp %s', usedefault=True, ), - exf_file=dict(argstr='--exf %s', ), + exf_file=dict( + argstr='--exf %s', + extensions=None, + ), exfdw=dict( argstr='--exfdw %s', genfile=True, ), mag_file=dict( argstr='--mag %s', + extensions=None, mandatory=True, position=0, ), @@ -63,10 +71,10 @@ def test_EPIDeWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EPIDeWarp_outputs(): output_map = dict( - exf_mask=dict(), - exfdw=dict(), - unwarped_file=dict(), - vsm_file=dict(), + exf_mask=dict(extensions=None, ), + exfdw=dict(extensions=None, ), + unwarped_file=dict(extensions=None, ), + vsm_file=dict(extensions=None, ), ) outputs = EPIDeWarp.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index 55d9409e17..4bd6a3e840 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -18,7 +18,10 @@ def test_Eddy_inputs(): ), fep=dict(argstr='--fep', ), field=dict(argstr='--field=%s', ), - field_mat=dict(argstr='--field_mat=%s', ), + field_mat=dict( + argstr='--field_mat=%s', + extensions=None, + ), flm=dict(argstr='--flm=%s', ), fudge_factor=dict( argstr='--ff=%s', @@ -27,33 +30,43 @@ def test_Eddy_inputs(): fwhm=dict(argstr='--fwhm=%s', ), in_acqp=dict( argstr='--acqp=%s', + extensions=None, mandatory=True, ), in_bval=dict( argstr='--bvals=%s', + extensions=None, mandatory=True, ), in_bvec=dict( argstr='--bvecs=%s', + extensions=None, mandatory=True, ), in_file=dict( argstr='--imain=%s', + extensions=None, mandatory=True, ), in_index=dict( argstr='--index=%s', + extensions=None, mandatory=True, ), in_mask=dict( argstr='--mask=%s', + extensions=None, mandatory=True, ), in_topup_fieldcoef=dict( argstr='--topup=%s', + extensions=None, requires=['in_topup_movpar'], ), - in_topup_movpar=dict(requires=['in_topup_fieldcoef'], ), + in_topup_movpar=dict( + extensions=None, + requires=['in_topup_fieldcoef'], + ), interp=dict(argstr='--interp=%s', ), is_shelled=dict(argstr='--data_is_shelled', ), method=dict(argstr='--resamp=%s', ), @@ -79,7 +92,10 @@ def test_Eddy_inputs(): argstr='--residuals', min_ver='5.0.10', ), - session=dict(argstr='--session=%s', ), + session=dict( + argstr='--session=%s', + extensions=None, + ), slm=dict(argstr='--slm=%s', ), use_cuda=dict(), ) @@ -90,15 +106,15 @@ def test_Eddy_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Eddy_outputs(): output_map = dict( - out_cnr_maps=dict(), - out_corrected=dict(), - out_movement_rms=dict(), - out_outlier_report=dict(), - out_parameter=dict(), - out_residuals=dict(), - out_restricted_movement_rms=dict(), - out_rotated_bvecs=dict(), - out_shell_alignment_parameters=dict(), + out_cnr_maps=dict(extensions=None, ), + out_corrected=dict(extensions=None, ), + out_movement_rms=dict(extensions=None, ), + out_outlier_report=dict(extensions=None, ), + out_parameter=dict(extensions=None, ), + out_residuals=dict(extensions=None, ), + out_restricted_movement_rms=dict(extensions=None, ), + out_rotated_bvecs=dict(extensions=None, ), + out_shell_alignment_parameters=dict(extensions=None, ), ) outputs = Eddy.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index e88219aa04..86134137ac 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -12,11 +12,13 @@ def test_EddyCorrect_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s_edc', output_name='eddy_corrected', @@ -36,7 +38,7 @@ def test_EddyCorrect_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EddyCorrect_outputs(): - output_map = dict(eddy_corrected=dict(), ) + output_map = dict(eddy_corrected=dict(extensions=None, ), ) outputs = EddyCorrect.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py index 3cc6da2027..945b2e54ba 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py @@ -13,20 +13,29 @@ def test_EddyQuad_inputs(): ), bval_file=dict( argstr='--bvals %s', + extensions=None, mandatory=True, ), - bvec_file=dict(argstr='--bvecs %s', ), + bvec_file=dict( + argstr='--bvecs %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), - field=dict(argstr='--field %s', ), + field=dict( + argstr='--field %s', + extensions=None, + ), idx_file=dict( argstr='--eddyIdx %s', + extensions=None, mandatory=True, ), mask_file=dict( argstr='--mask %s', + extensions=None, mandatory=True, ), output_dir=dict( @@ -37,9 +46,13 @@ def test_EddyQuad_inputs(): output_type=dict(), param_file=dict( argstr='--eddyParams %s', + extensions=None, mandatory=True, ), - slice_spec=dict(argstr='--slspec %s', ), + slice_spec=dict( + argstr='--slspec %s', + extensions=None, + ), verbose=dict(argstr='--verbose', ), ) inputs = EddyQuad.input_spec() @@ -51,12 +64,12 @@ def test_EddyQuad_outputs(): output_map = dict( avg_b0_pe_png=dict(), avg_b_png=dict(), - clean_volumes=dict(), + clean_volumes=dict(extensions=None, ), cnr_png=dict(), - qc_json=dict(), - qc_pdf=dict(), - residuals=dict(), - vdm_png=dict(), + qc_json=dict(extensions=None, ), + qc_pdf=dict(extensions=None, ), + residuals=dict(extensions=None, ), + vdm_png=dict(extensions=None, ), ) outputs = EddyQuad.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index 634a75e376..a6b06e0ca7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -13,12 +13,22 @@ def test_EpiReg_inputs(): ), epi=dict( argstr='--epi=%s', + extensions=None, mandatory=True, position=-4, ), - fmap=dict(argstr='--fmap=%s', ), - fmapmag=dict(argstr='--fmapmag=%s', ), - fmapmagbrain=dict(argstr='--fmapmagbrain=%s', ), + fmap=dict( + argstr='--fmap=%s', + extensions=None, + ), + fmapmag=dict( + argstr='--fmapmag=%s', + extensions=None, + ), + fmapmagbrain=dict( + argstr='--fmapmagbrain=%s', + extensions=None, + ), no_clean=dict( argstr='--noclean', usedefault=True, @@ -33,16 +43,24 @@ def test_EpiReg_inputs(): pedir=dict(argstr='--pedir=%s', ), t1_brain=dict( argstr='--t1brain=%s', + extensions=None, mandatory=True, position=-2, ), t1_head=dict( argstr='--t1=%s', + extensions=None, mandatory=True, position=-3, ), - weight_image=dict(argstr='--weight=%s', ), - wmseg=dict(argstr='--wmseg=%s', ), + weight_image=dict( + argstr='--weight=%s', + extensions=None, + ), + wmseg=dict( + argstr='--wmseg=%s', + extensions=None, + ), ) inputs = EpiReg.input_spec() @@ -51,20 +69,20 @@ def test_EpiReg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EpiReg_outputs(): output_map = dict( - epi2str_inv=dict(), - epi2str_mat=dict(), - fmap2epi_mat=dict(), - fmap2str_mat=dict(), - fmap_epi=dict(), - fmap_str=dict(), - fmapmag_str=dict(), - fullwarp=dict(), - out_1vol=dict(), - out_file=dict(), - seg=dict(), - shiftmap=dict(), - wmedge=dict(), - wmseg=dict(), + epi2str_inv=dict(extensions=None, ), + epi2str_mat=dict(extensions=None, ), + fmap2epi_mat=dict(extensions=None, ), + fmap2str_mat=dict(extensions=None, ), + fmap_epi=dict(extensions=None, ), + fmap_str=dict(extensions=None, ), + fmapmag_str=dict(extensions=None, ), + fullwarp=dict(extensions=None, ), + out_1vol=dict(extensions=None, ), + out_file=dict(extensions=None, ), + seg=dict(extensions=None, ), + shiftmap=dict(extensions=None, ), + wmedge=dict(extensions=None, ), + wmseg=dict(extensions=None, ), ) outputs = EpiReg.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index 797a403d45..bd7d6f2b83 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -12,6 +12,7 @@ def test_ErodeImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -21,6 +22,7 @@ def test_ErodeImage_inputs(): ), kernel_file=dict( argstr='%s', + extensions=None, position=5, xor=['kernel_size'], ), @@ -44,6 +46,7 @@ def test_ErodeImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -60,7 +63,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ErodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index df8de64144..414a068177 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -20,12 +20,14 @@ def test_ExtractROI_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), output_type=dict(), roi_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=1, @@ -69,7 +71,7 @@ def test_ExtractROI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractROI_outputs(): - output_map = dict(roi_file=dict(), ) + output_map = dict(roi_file=dict(extensions=None, ), ) outputs = ExtractROI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 0b983181af..b36c941cff 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -24,15 +24,24 @@ def test_FAST_inputs(): position=-1, ), init_seg_smooth=dict(argstr='-f %.3f', ), - init_transform=dict(argstr='-a %s', ), + init_transform=dict( + argstr='-a %s', + extensions=None, + ), iters_afterbias=dict(argstr='-O %d', ), - manual_seg=dict(argstr='-s %s', ), + manual_seg=dict( + argstr='-s %s', + extensions=None, + ), mixel_smooth=dict(argstr='-R %.2f', ), no_bias=dict(argstr='-N', ), no_pve=dict(argstr='--nopve', ), number_classes=dict(argstr='-n %d', ), other_priors=dict(argstr='-A %s', ), - out_basename=dict(argstr='-o %s', ), + out_basename=dict( + argstr='-o %s', + extensions=None, + ), output_biascorrected=dict(argstr='-B', ), output_biasfield=dict(argstr='-b', ), output_type=dict(), @@ -50,13 +59,13 @@ def test_FAST_inputs(): def test_FAST_outputs(): output_map = dict( bias_field=dict(), - mixeltype=dict(), + mixeltype=dict(extensions=None, ), partial_volume_files=dict(), - partial_volume_map=dict(), + partial_volume_map=dict(extensions=None, ), probability_maps=dict(), restored_image=dict(), tissue_class_files=dict(), - tissue_class_map=dict(), + tissue_class_map=dict(extensions=None, ), ) outputs = FAST.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index 01fc72506f..e193a0ae27 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -12,6 +12,7 @@ def test_FEAT_inputs(): ), fsf_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index 34ea37d47f..b1103396d8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -19,6 +19,7 @@ def test_FEATModel_inputs(): fsf_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=0, ), @@ -31,11 +32,11 @@ def test_FEATModel_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FEATModel_outputs(): output_map = dict( - con_file=dict(), - design_cov=dict(), - design_file=dict(), - design_image=dict(), - fcon_file=dict(), + con_file=dict(extensions=None, ), + design_cov=dict(extensions=None, ), + design_file=dict(extensions=None, ), + design_image=dict(extensions=None, ), + fcon_file=dict(extensions=None, ), ) outputs = FEATModel.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index a8f59a0ec3..d0d008956f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -7,7 +7,10 @@ def test_FEATRegister_inputs(): input_map = dict( feat_dirs=dict(mandatory=True, ), reg_dof=dict(usedefault=True, ), - reg_image=dict(mandatory=True, ), + reg_image=dict( + extensions=None, + mandatory=True, + ), ) inputs = FEATRegister.input_spec() @@ -15,7 +18,7 @@ def test_FEATRegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FEATRegister_outputs(): - output_map = dict(fsf_file=dict(), ) + output_map = dict(fsf_file=dict(extensions=None, ), ) outputs = FEATRegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index 964ee4922c..fc7914a828 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -7,6 +7,7 @@ def test_FIRST_inputs(): input_map = dict( affine_file=dict( argstr='-a %s', + extensions=None, position=6, ), args=dict(argstr='%s', ), @@ -21,6 +22,7 @@ def test_FIRST_inputs(): in_file=dict( argstr='-i %s', copyfile=False, + extensions=None, mandatory=True, position=-2, ), @@ -45,6 +47,7 @@ def test_FIRST_inputs(): ), out_file=dict( argstr='-o %s', + extensions=None, hash_files=False, mandatory=True, position=-1, @@ -64,8 +67,8 @@ def test_FIRST_inputs(): def test_FIRST_outputs(): output_map = dict( bvars=dict(), - original_segmentations=dict(), - segmentation_file=dict(), + original_segmentations=dict(extensions=None, ), + segmentation_file=dict(extensions=None, ), vtk_surfaces=dict(), ) outputs = FIRST.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index bd335282e3..5de114a4c3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -9,22 +9,31 @@ def test_FLAMEO_inputs(): burnin=dict(argstr='--burnin=%d', ), cope_file=dict( argstr='--copefile=%s', + extensions=None, mandatory=True, ), cov_split_file=dict( argstr='--covsplitfile=%s', + extensions=None, mandatory=True, ), design_file=dict( argstr='--designfile=%s', + extensions=None, mandatory=True, ), - dof_var_cope_file=dict(argstr='--dofvarcopefile=%s', ), + dof_var_cope_file=dict( + argstr='--dofvarcopefile=%s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), - f_con_file=dict(argstr='--fcontrastsfile=%s', ), + f_con_file=dict( + argstr='--fcontrastsfile=%s', + extensions=None, + ), fix_mean=dict(argstr='--fixmean', ), infer_outliers=dict(argstr='--inferoutliers', ), log_dir=dict( @@ -33,6 +42,7 @@ def test_FLAMEO_inputs(): ), mask_file=dict( argstr='--maskfile=%s', + extensions=None, mandatory=True, ), n_jumps=dict(argstr='--njumps=%d', ), @@ -47,9 +57,13 @@ def test_FLAMEO_inputs(): sigma_dofs=dict(argstr='--sigma_dofs=%d', ), t_con_file=dict( argstr='--tcontrastsfile=%s', + extensions=None, mandatory=True, ), - var_cope_file=dict(argstr='--varcopefile=%s', ), + var_cope_file=dict( + argstr='--varcopefile=%s', + extensions=None, + ), ) inputs = FLAMEO.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index 0b59550e5a..08074ccf94 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -41,10 +41,12 @@ def test_FLIRT_inputs(): ), fieldmap=dict( argstr='-fieldmap %s', + extensions=None, min_ver='5.0.0', ), fieldmapmask=dict( argstr='-fieldmapmask %s', + extensions=None, min_ver='5.0.0', ), fine_search=dict( @@ -54,11 +56,18 @@ def test_FLIRT_inputs(): force_scaling=dict(argstr='-forcescaling', ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, position=0, ), - in_matrix_file=dict(argstr='-init %s', ), - in_weight=dict(argstr='-inweight %s', ), + in_matrix_file=dict( + argstr='-init %s', + extensions=None, + ), + in_weight=dict( + argstr='-inweight %s', + extensions=None, + ), interp=dict(argstr='-interp %s', ), min_sampling=dict( argstr='-minsampling %f', @@ -70,12 +79,14 @@ def test_FLIRT_inputs(): no_search=dict(argstr='-nosearch', ), out_file=dict( argstr='-out %s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_flirt', position=2, ), out_log=dict( + extensions=None, keep_extension=True, name_source=['in_file'], name_template='%s_flirt.log', @@ -83,6 +94,7 @@ def test_FLIRT_inputs(): ), out_matrix_file=dict( argstr='-omat %s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], @@ -98,15 +110,22 @@ def test_FLIRT_inputs(): argstr='-pedir %d', min_ver='5.0.0', ), - ref_weight=dict(argstr='-refweight %s', ), + ref_weight=dict( + argstr='-refweight %s', + extensions=None, + ), reference=dict( argstr='-ref %s', + extensions=None, mandatory=True, position=1, ), rigid2D=dict(argstr='-2D', ), save_log=dict(), - schedule=dict(argstr='-schedule %s', ), + schedule=dict( + argstr='-schedule %s', + extensions=None, + ), searchr_x=dict( argstr='-searchrx %s', units='degrees', @@ -128,14 +147,17 @@ def test_FLIRT_inputs(): verbose=dict(argstr='-verbose %d', ), wm_seg=dict( argstr='-wmseg %s', + extensions=None, min_ver='5.0.0', ), wmcoords=dict( argstr='-wmcoords %s', + extensions=None, min_ver='5.0.0', ), wmnorms=dict( argstr='-wmnorms %s', + extensions=None, min_ver='5.0.0', ), ) @@ -146,9 +168,9 @@ def test_FLIRT_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FLIRT_outputs(): output_map = dict( - out_file=dict(), - out_log=dict(), - out_matrix_file=dict(), + out_file=dict(extensions=None, ), + out_log=dict(extensions=None, ), + out_matrix_file=dict(extensions=None, ), ) outputs = FLIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 2b7d0b1b00..95afc3aa4d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -5,7 +5,10 @@ def test_FNIRT_inputs(): input_map = dict( - affine_file=dict(argstr='--aff=%s', ), + affine_file=dict( + argstr='--aff=%s', + extensions=None, + ), apply_inmask=dict( argstr='--applyinmask=%s', sep=',', @@ -38,6 +41,7 @@ def test_FNIRT_inputs(): hessian_precision=dict(argstr='--numprec=%s', ), in_file=dict( argstr='--in=%s', + extensions=None, mandatory=True, ), in_fwhm=dict( @@ -48,11 +52,17 @@ def test_FNIRT_inputs(): argstr='--intin=%s', copyfile=False, ), - inmask_file=dict(argstr='--inmask=%s', ), + inmask_file=dict( + argstr='--inmask=%s', + extensions=None, + ), inmask_val=dict(argstr='--impinval=%f', ), intensity_mapping_model=dict(argstr='--intmod=%s', ), intensity_mapping_order=dict(argstr='--intorder=%d', ), - inwarp_file=dict(argstr='--inwarp=%s', ), + inwarp_file=dict( + argstr='--inwarp=%s', + extensions=None, + ), jacobian_file=dict( argstr='--jout=%s', hash_files=False, @@ -60,6 +70,7 @@ def test_FNIRT_inputs(): jacobian_range=dict(argstr='--jacrange=%f,%f', ), log_file=dict( argstr='--logout=%s', + extensions=None, genfile=True, hash_files=False, ), @@ -78,13 +89,17 @@ def test_FNIRT_inputs(): output_type=dict(), ref_file=dict( argstr='--ref=%s', + extensions=None, mandatory=True, ), ref_fwhm=dict( argstr='--reffwhm=%s', sep=',', ), - refmask_file=dict(argstr='--refmask=%s', ), + refmask_file=dict( + argstr='--refmask=%s', + extensions=None, + ), refmask_val=dict(argstr='--imprefval=%f', ), regularization_lambda=dict( argstr='--lambda=%s', @@ -114,6 +129,7 @@ def test_FNIRT_inputs(): warp_resolution=dict(argstr='--warpres=%d,%d,%d', ), warped_file=dict( argstr='--iout=%s', + extensions=None, genfile=True, hash_files=False, ), @@ -125,13 +141,13 @@ def test_FNIRT_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FNIRT_outputs(): output_map = dict( - field_file=dict(), - fieldcoeff_file=dict(), - jacobian_file=dict(), - log_file=dict(), - modulatedref_file=dict(), + field_file=dict(extensions=None, ), + fieldcoeff_file=dict(extensions=None, ), + jacobian_file=dict(extensions=None, ), + log_file=dict(extensions=None, ), + modulatedref_file=dict(extensions=None, ), out_intensitymap_file=dict(), - warped_file=dict(), + warped_file=dict(extensions=None, ), ) outputs = FNIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index fd85eee3bf..e0ecf18807 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -20,10 +20,12 @@ def test_FSLXCommand_inputs(): ), bvals=dict( argstr='--bvals=%s', + extensions=None, mandatory=True, ), bvecs=dict( argstr='--bvecs=%s', + extensions=None, mandatory=True, ), cnlinear=dict( @@ -32,6 +34,7 @@ def test_FSLXCommand_inputs(): ), dwi=dict( argstr='--data=%s', + extensions=None, mandatory=True, ), environ=dict( @@ -57,6 +60,7 @@ def test_FSLXCommand_inputs(): ), mask=dict( argstr='--mask=%s', + extensions=None, mandatory=True, ), model=dict(argstr='--model=%d', ), @@ -102,10 +106,10 @@ def test_FSLXCommand_outputs(): output_map = dict( dyads=dict(), fsamples=dict(), - mean_S0samples=dict(), - mean_dsamples=dict(), + mean_S0samples=dict(extensions=None, ), + mean_dsamples=dict(extensions=None, ), mean_fsamples=dict(), - mean_tausamples=dict(), + mean_tausamples=dict(extensions=None, ), phsamples=dict(), thsamples=dict(), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index 0e96f1e867..5862d2e901 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -15,8 +15,14 @@ def test_FUGUE_inputs(): nohash=True, usedefault=True, ), - fmap_in_file=dict(argstr='--loadfmap=%s', ), - fmap_out_file=dict(argstr='--savefmap=%s', ), + fmap_in_file=dict( + argstr='--loadfmap=%s', + extensions=None, + ), + fmap_out_file=dict( + argstr='--savefmap=%s', + extensions=None, + ), forward_warping=dict(usedefault=True, ), fourier_order=dict(argstr='--fourier=%d', ), icorr=dict( @@ -27,8 +33,14 @@ def test_FUGUE_inputs(): argstr='--icorronly', requires=['unwarped_file'], ), - in_file=dict(argstr='--in=%s', ), - mask_file=dict(argstr='--mask=%s', ), + in_file=dict( + argstr='--in=%s', + extensions=None, + ), + mask_file=dict( + argstr='--mask=%s', + extensions=None, + ), median_2dfilter=dict(argstr='--median', ), no_extend=dict(argstr='--noextend', ), no_gap_fill=dict(argstr='--nofill', ), @@ -36,7 +48,10 @@ def test_FUGUE_inputs(): output_type=dict(), pava=dict(argstr='--pava', ), phase_conjugate=dict(argstr='--phaseconj', ), - phasemap_in_file=dict(argstr='--phasemap=%s', ), + phasemap_in_file=dict( + argstr='--phasemap=%s', + extensions=None, + ), poly_order=dict(argstr='--poly=%d', ), save_fmap=dict(xor=['save_unmasked_fmap'], ), save_shift=dict(xor=['save_unmasked_shift'], ), @@ -48,18 +63,26 @@ def test_FUGUE_inputs(): argstr='--unmaskshift', xor=['save_shift'], ), - shift_in_file=dict(argstr='--loadshift=%s', ), - shift_out_file=dict(argstr='--saveshift=%s', ), + shift_in_file=dict( + argstr='--loadshift=%s', + extensions=None, + ), + shift_out_file=dict( + argstr='--saveshift=%s', + extensions=None, + ), smooth2d=dict(argstr='--smooth2=%.2f', ), smooth3d=dict(argstr='--smooth3=%.2f', ), unwarp_direction=dict(argstr='--unwarpdir=%s', ), unwarped_file=dict( argstr='--unwarp=%s', + extensions=None, requires=['in_file'], xor=['warped_file'], ), warped_file=dict( argstr='--warp=%s', + extensions=None, requires=['in_file'], xor=['unwarped_file'], ), @@ -71,10 +94,10 @@ def test_FUGUE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FUGUE_outputs(): output_map = dict( - fmap_out_file=dict(), - shift_out_file=dict(), - unwarped_file=dict(), - warped_file=dict(), + fmap_out_file=dict(extensions=None, ), + shift_out_file=dict(extensions=None, ), + unwarped_file=dict(extensions=None, ), + warped_file=dict(extensions=None, ), ) outputs = FUGUE.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index 36cbb979d7..3e7dcc2c41 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -8,6 +8,7 @@ def test_FilterRegressor_inputs(): args=dict(argstr='%s', ), design_file=dict( argstr='-d %s', + extensions=None, mandatory=True, position=3, ), @@ -29,12 +30,17 @@ def test_FilterRegressor_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=1, ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + extensions=None, + ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, position=2, @@ -49,7 +55,7 @@ def test_FilterRegressor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FilterRegressor_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = FilterRegressor.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 3731c842e7..5c7b717d93 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -17,6 +17,7 @@ def test_FindTheBiggest_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=2, @@ -29,7 +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', ), ) + 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_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index 1dbf7eba19..eb6f49f554 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -6,12 +6,16 @@ def test_GLM_inputs(): input_map = dict( args=dict(argstr='%s', ), - contrasts=dict(argstr='-c %s', ), + contrasts=dict( + argstr='-c %s', + extensions=None, + ), dat_norm=dict(argstr='--dat_norm', ), demean=dict(argstr='--demean', ), des_norm=dict(argstr='--des_norm', ), design=dict( argstr='-d %s', + extensions=None, mandatory=True, position=2, ), @@ -22,28 +26,66 @@ def test_GLM_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=1, ), - mask=dict(argstr='-m %s', ), - out_cope=dict(argstr='--out_cope=%s', ), - out_data_name=dict(argstr='--out_data=%s', ), - out_f_name=dict(argstr='--out_f=%s', ), + mask=dict( + argstr='-m %s', + extensions=None, + ), + out_cope=dict( + argstr='--out_cope=%s', + extensions=None, + ), + out_data_name=dict( + argstr='--out_data=%s', + extensions=None, + ), + out_f_name=dict( + argstr='--out_f=%s', + extensions=None, + ), out_file=dict( argstr='-o %s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_glm', position=3, ), - out_p_name=dict(argstr='--out_p=%s', ), - out_pf_name=dict(argstr='--out_pf=%s', ), - out_res_name=dict(argstr='--out_res=%s', ), - out_sigsq_name=dict(argstr='--out_sigsq=%s', ), - out_t_name=dict(argstr='--out_t=%s', ), - out_varcb_name=dict(argstr='--out_varcb=%s', ), - out_vnscales_name=dict(argstr='--out_vnscales=%s', ), - out_z_name=dict(argstr='--out_z=%s', ), + out_p_name=dict( + argstr='--out_p=%s', + extensions=None, + ), + out_pf_name=dict( + argstr='--out_pf=%s', + extensions=None, + ), + out_res_name=dict( + argstr='--out_res=%s', + extensions=None, + ), + out_sigsq_name=dict( + argstr='--out_sigsq=%s', + extensions=None, + ), + out_t_name=dict( + argstr='--out_t=%s', + extensions=None, + ), + out_varcb_name=dict( + argstr='--out_varcb=%s', + extensions=None, + ), + out_vnscales_name=dict( + argstr='--out_vnscales=%s', + extensions=None, + ), + out_z_name=dict( + argstr='--out_z=%s', + extensions=None, + ), output_type=dict(), var_norm=dict(argstr='--vn', ), ) @@ -57,7 +99,7 @@ def test_GLM_outputs(): out_cope=dict(), out_data=dict(), out_f=dict(), - out_file=dict(), + out_file=dict(extensions=None, ), out_p=dict(), out_pf=dict(), out_res=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py index 05bbb5b106..c3f10c2664 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py +++ b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py @@ -26,24 +26,29 @@ def test_ICA_AROMA_inputs(): ), fnirt_warp_file=dict( argstr='-warp %s', + extensions=None, xor=['feat_dir'], ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, xor=['feat_dir'], ), mask=dict( argstr='-m %s', + extensions=None, xor=['feat_dir'], ), mat_file=dict( argstr='-affmat %s', + extensions=None, xor=['feat_dir'], ), melodic_dir=dict(argstr='-meldir %s', ), motion_parameters=dict( argstr='-mc %s', + extensions=None, mandatory=True, xor=['feat_dir'], ), @@ -60,8 +65,8 @@ def test_ICA_AROMA_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ICA_AROMA_outputs(): output_map = dict( - aggr_denoised_file=dict(), - nonaggr_denoised_file=dict(), + aggr_denoised_file=dict(extensions=None, ), + nonaggr_denoised_file=dict(extensions=None, ), out_dir=dict(), ) outputs = ICA_AROMA.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 6d4e06827e..d25ed8bc77 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -12,14 +12,19 @@ def test_ImageMaths_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), in_file2=dict( argstr='%s', + extensions=None, position=3, ), - mask_file=dict(argstr='-mas %s', ), + mask_file=dict( + argstr='-mas %s', + extensions=None, + ), op_string=dict( argstr='%s', position=2, @@ -30,6 +35,7 @@ def test_ImageMaths_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -43,7 +49,7 @@ def test_ImageMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ImageMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 042f93112b..5c83c40150 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -13,10 +13,14 @@ def test_ImageMeants_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=0, ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + extensions=None, + ), nobin=dict(argstr='--no_bin', ), order=dict( argstr='--order=%d', @@ -24,6 +28,7 @@ def test_ImageMeants_inputs(): ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, ), @@ -39,7 +44,7 @@ def test_ImageMeants_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageMeants_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ImageMeants.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 91a6059798..0230245f2e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -12,10 +12,14 @@ def test_ImageStats_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), - mask_file=dict(argstr='', ), + mask_file=dict( + argstr='', + extensions=None, + ), op_string=dict( argstr='%s', mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index 973f42ea34..fa39ceac7d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -16,6 +16,7 @@ def test_InvWarp_inputs(): ), inverse_warp=dict( argstr='--out=%s', + extensions=None, hash_files=False, name_source=['warp'], name_template='%s_inverse', @@ -27,6 +28,7 @@ def test_InvWarp_inputs(): output_type=dict(), reference=dict( argstr='--ref=%s', + extensions=None, mandatory=True, ), regularise=dict(argstr='--regularise=%f', ), @@ -36,6 +38,7 @@ def test_InvWarp_inputs(): ), warp=dict( argstr='--warp=%s', + extensions=None, mandatory=True, ), ) @@ -45,7 +48,7 @@ def test_InvWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_InvWarp_outputs(): - output_map = dict(inverse_warp=dict(), ) + output_map = dict(inverse_warp=dict(extensions=None, ), ) outputs = InvWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index 4b6192c98d..5c224aeeb6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -18,6 +18,7 @@ def test_IsotropicSmooth_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -31,6 +32,7 @@ def test_IsotropicSmooth_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -53,7 +55,7 @@ def test_IsotropicSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_IsotropicSmooth_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = IsotropicSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 9d3588666f..160fba2fb5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -12,9 +12,9 @@ def test_L2Model_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_L2Model_outputs(): output_map = dict( - design_con=dict(), - design_grp=dict(), - design_mat=dict(), + design_con=dict(extensions=None, ), + design_grp=dict(extensions=None, ), + design_mat=dict(extensions=None, ), ) outputs = L2Model.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index daeca07b10..f9f1868613 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -15,19 +15,27 @@ def test_MCFLIRT_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, position=0, ), - init=dict(argstr='-init %s', ), + init=dict( + argstr='-init %s', + extensions=None, + ), interpolation=dict(argstr='-%s_final', ), mean_vol=dict(argstr='-meanvol', ), out_file=dict( argstr='-out %s', + extensions=None, genfile=True, hash_files=False, ), output_type=dict(), - ref_file=dict(argstr='-reffile %s', ), + ref_file=dict( + argstr='-reffile %s', + extensions=None, + ), ref_vol=dict(argstr='-refvol %d', ), rotation=dict(argstr='-rotation %d', ), save_mats=dict(argstr='-mats', ), @@ -48,12 +56,12 @@ def test_MCFLIRT_inputs(): def test_MCFLIRT_outputs(): output_map = dict( mat_file=dict(), - mean_img=dict(), - out_file=dict(), - par_file=dict(), + mean_img=dict(extensions=None, ), + out_file=dict(extensions=None, ), + par_file=dict(extensions=None, ), rms_files=dict(), - std_img=dict(), - variance_img=dict(), + std_img=dict(extensions=None, ), + variance_img=dict(extensions=None, ), ) outputs = MCFLIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index b22078c450..b024a9f572 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -5,10 +5,16 @@ def test_MELODIC_inputs(): input_map = dict( - ICs=dict(argstr='--ICs=%s', ), + ICs=dict( + argstr='--ICs=%s', + extensions=None, + ), approach=dict(argstr='-a %s', ), args=dict(argstr='%s', ), - bg_image=dict(argstr='--bgimage=%s', ), + bg_image=dict( + argstr='--bgimage=%s', + extensions=None, + ), bg_threshold=dict(argstr='--bgthreshold=%f', ), cov_weight=dict(argstr='--covarweight=%f', ), dim=dict(argstr='-d %d', ), @@ -26,14 +32,20 @@ def test_MELODIC_inputs(): sep=',', ), log_power=dict(argstr='--logPower', ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + extensions=None, + ), max_restart=dict(argstr='--maxrestart=%d', ), maxit=dict(argstr='--maxit=%d', ), migp=dict(argstr='--migp', ), migpN=dict(argstr='--migpN %d', ), migp_factor=dict(argstr='--migp_factor %d', ), migp_shuffle=dict(argstr='--migp_shuffle', ), - mix=dict(argstr='--mix=%s', ), + mix=dict( + argstr='--mix=%s', + extensions=None, + ), mm_thresh=dict(argstr='--mmthresh=%f', ), no_bet=dict(argstr='--nobet', ), no_mask=dict(argstr='--nomask', ), @@ -57,13 +69,28 @@ def test_MELODIC_inputs(): remove_deriv=dict(argstr='--remove_deriv', ), report=dict(argstr='--report', ), report_maps=dict(argstr='--report_maps=%s', ), - s_con=dict(argstr='--Scon=%s', ), - s_des=dict(argstr='--Sdes=%s', ), + s_con=dict( + argstr='--Scon=%s', + extensions=None, + ), + s_des=dict( + argstr='--Sdes=%s', + extensions=None, + ), sep_vn=dict(argstr='--sep_vn', ), sep_whiten=dict(argstr='--sep_whiten', ), - smode=dict(argstr='--smode=%s', ), - t_con=dict(argstr='--Tcon=%s', ), - t_des=dict(argstr='--Tdes=%s', ), + smode=dict( + argstr='--smode=%s', + extensions=None, + ), + t_con=dict( + argstr='--Tcon=%s', + extensions=None, + ), + t_des=dict( + argstr='--Tdes=%s', + extensions=None, + ), tr_sec=dict(argstr='--tr=%f', ), update_mask=dict(argstr='--update_mask', ), var_norm=dict(argstr='--vn', ), diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index c7a5a3e465..832946a499 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -12,10 +12,12 @@ def test_MakeDyadicVectors_inputs(): ), mask=dict( argstr='%s', + extensions=None, position=2, ), output=dict( argstr='%s', + extensions=None, hash_files=False, position=3, usedefault=True, @@ -27,11 +29,13 @@ def test_MakeDyadicVectors_inputs(): ), phi_vol=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), theta_vol=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -43,8 +47,8 @@ def test_MakeDyadicVectors_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MakeDyadicVectors_outputs(): output_map = dict( - dispersion=dict(), - dyads=dict(), + dispersion=dict(extensions=None, ), + dyads=dict(extensions=None, ), ) outputs = MakeDyadicVectors.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index 64b0f8b089..061bb66e99 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -12,6 +12,7 @@ def test_MathsCommand_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -25,6 +26,7 @@ def test_MathsCommand_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -41,7 +43,7 @@ def test_MathsCommand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MathsCommand_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MathsCommand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 9910f9c4e8..608a886199 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -17,6 +17,7 @@ def test_MaxImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_MaxImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_MaxImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaxImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MaxImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py index f49c5f462c..fb6da29ee6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py @@ -17,6 +17,7 @@ def test_MaxnImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_MaxnImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_MaxnImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaxnImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MaxnImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 2172dcfa9e..745be40f92 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -17,6 +17,7 @@ def test_MeanImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_MeanImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_MeanImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MeanImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MeanImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py index c14bf8d839..e777ffbc34 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py @@ -17,6 +17,7 @@ def test_MedianImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_MedianImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_MedianImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MedianImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 826270239e..d6176eb92e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -22,6 +22,7 @@ def test_Merge_inputs(): ), merged_file=dict( argstr='%s', + extensions=None, hash_files=False, name_source='in_files', name_template='%s_merged', @@ -39,7 +40,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(merged_file=dict(), ) + output_map = dict(merged_file=dict(extensions=None, ), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MinImage.py b/nipype/interfaces/fsl/tests/test_auto_MinImage.py index 4e9002c259..88561bbe78 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MinImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MinImage.py @@ -17,6 +17,7 @@ def test_MinImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_MinImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_MinImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MinImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MinImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index 97d2426b53..1c199ca83f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -13,13 +13,18 @@ def test_MotionOutliers_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + extensions=None, + ), metric=dict(argstr='--%s', ), no_motion_correction=dict(argstr='--nomoco', ), out_file=dict( argstr='-o %s', + extensions=None, hash_files=False, keep_extension=True, name_source='in_file', @@ -27,6 +32,7 @@ def test_MotionOutliers_inputs(): ), out_metric_plot=dict( argstr='-p %s', + extensions=None, hash_files=False, keep_extension=True, name_source='in_file', @@ -34,6 +40,7 @@ def test_MotionOutliers_inputs(): ), out_metric_values=dict( argstr='-s %s', + extensions=None, hash_files=False, keep_extension=True, name_source='in_file', @@ -49,9 +56,9 @@ def test_MotionOutliers_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MotionOutliers_outputs(): output_map = dict( - out_file=dict(), - out_metric_plot=dict(), - out_metric_values=dict(), + out_file=dict(extensions=None, ), + out_metric_plot=dict(extensions=None, ), + out_metric_values=dict(extensions=None, ), ) outputs = MotionOutliers.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 50a2977a4c..edeb802c1c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -12,6 +12,7 @@ def test_MultiImageMaths_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -31,6 +32,7 @@ def test_MultiImageMaths_inputs(): operand_files=dict(mandatory=True, ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -47,7 +49,7 @@ def test_MultiImageMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiImageMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MultiImageMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 78bd97ff85..05c67e6d94 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -16,10 +16,10 @@ def test_MultipleRegressDesign_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressDesign_outputs(): output_map = dict( - design_con=dict(), - design_fts=dict(), - design_grp=dict(), - design_mat=dict(), + design_con=dict(extensions=None, ), + design_fts=dict(extensions=None, ), + design_grp=dict(extensions=None, ), + design_mat=dict(extensions=None, ), ) outputs = MultipleRegressDesign.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 9818ae1eda..de4024c36d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -14,6 +14,7 @@ def test_Overlay_inputs(): ), background_image=dict( argstr='%s', + extensions=None, mandatory=True, position=4, ), @@ -35,6 +36,7 @@ def test_Overlay_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-1, @@ -52,11 +54,13 @@ def test_Overlay_inputs(): ), stat_image=dict( argstr='%s', + extensions=None, mandatory=True, position=6, ), stat_image2=dict( argstr='%s', + extensions=None, position=9, xor=['show_negative_stats'], ), @@ -85,7 +89,7 @@ def test_Overlay_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Overlay_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Overlay.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index 328a8e3272..c160745dd5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -8,6 +8,7 @@ def test_PRELUDE_inputs(): args=dict(argstr='%s', ), complex_phase_file=dict( argstr='--complex=%s', + extensions=None, mandatory=True, xor=['magnitude_file', 'phase_file'], ), @@ -18,19 +19,25 @@ def test_PRELUDE_inputs(): ), label_file=dict( argstr='--labels=%s', + extensions=None, hash_files=False, ), labelprocess2d=dict(argstr='--labelslices', ), magnitude_file=dict( argstr='--abs=%s', + extensions=None, mandatory=True, xor=['complex_phase_file'], ), - mask_file=dict(argstr='--mask=%s', ), + mask_file=dict( + argstr='--mask=%s', + extensions=None, + ), num_partitions=dict(argstr='--numphasesplit=%d', ), output_type=dict(), phase_file=dict( argstr='--phase=%s', + extensions=None, mandatory=True, xor=['complex_phase_file'], ), @@ -44,17 +51,20 @@ def test_PRELUDE_inputs(): ), rawphase_file=dict( argstr='--rawphase=%s', + extensions=None, hash_files=False, ), removeramps=dict(argstr='--removeramps', ), savemask_file=dict( argstr='--savemask=%s', + extensions=None, hash_files=False, ), start=dict(argstr='--start=%d', ), threshold=dict(argstr='--thresh=%.10f', ), unwrapped_phase_file=dict( argstr='--unwrap=%s', + extensions=None, genfile=True, hash_files=False, ), @@ -65,7 +75,7 @@ def test_PRELUDE_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PRELUDE_outputs(): - output_map = dict(unwrapped_phase_file=dict(), ) + output_map = dict(unwrapped_phase_file=dict(extensions=None, ), ) outputs = PRELUDE.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py index 4e08c18db0..7a27272e67 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py @@ -17,6 +17,7 @@ def test_PercentileImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_PercentileImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -50,7 +52,7 @@ def test_PercentileImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PercentileImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = PercentileImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 45a5b43945..d88374f105 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -18,6 +18,7 @@ def test_PlotMotionParams_inputs(): in_source=dict(mandatory=True, ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, ), @@ -34,7 +35,7 @@ def test_PlotMotionParams_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PlotMotionParams_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = PlotMotionParams.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 62ced498e1..d923f16b6b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -16,9 +16,13 @@ def test_PlotTimeSeries_inputs(): position=1, ), labels=dict(argstr='%s', ), - legend_file=dict(argstr='--legend=%s', ), + legend_file=dict( + argstr='--legend=%s', + extensions=None, + ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, ), @@ -62,7 +66,7 @@ def test_PlotTimeSeries_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PlotTimeSeries_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = PlotTimeSeries.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 18a812c00b..15e6adc101 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -12,11 +12,13 @@ def test_PowerSpectrum_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=1, @@ -29,7 +31,7 @@ def test_PowerSpectrum_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PowerSpectrum_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = PowerSpectrum.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index 66bfd51fab..d3515701b1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -18,11 +18,13 @@ def test_PrepareFieldmap_inputs(): ), in_magnitude=dict( argstr='%s', + extensions=None, mandatory=True, position=3, ), in_phase=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -33,6 +35,7 @@ def test_PrepareFieldmap_inputs(): ), out_fieldmap=dict( argstr='%s', + extensions=None, position=4, ), output_type=dict(), @@ -48,7 +51,7 @@ def test_PrepareFieldmap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PrepareFieldmap_outputs(): - output_map = dict(out_fieldmap=dict(), ) + output_map = dict(out_fieldmap=dict(extensions=None, ), ) outputs = PrepareFieldmap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index 5368d0dd37..689b8c755d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -6,7 +6,10 @@ def test_ProbTrackX_inputs(): input_map = dict( args=dict(argstr='%s', ), - avoid_mp=dict(argstr='--avoid=%s', ), + avoid_mp=dict( + argstr='--avoid=%s', + extensions=None, + ), c_thresh=dict(argstr='--cthr=%.3f', ), correct_path_distribution=dict(argstr='--pd', ), dist_thresh=dict(argstr='--distthresh=%.3f', ), @@ -20,14 +23,24 @@ def test_ProbTrackX_inputs(): usedefault=True, ), fsamples=dict(mandatory=True, ), - inv_xfm=dict(argstr='--invxfm=%s', ), + inv_xfm=dict( + argstr='--invxfm=%s', + extensions=None, + ), loop_check=dict(argstr='--loopcheck', ), mask=dict( argstr='-m %s', + extensions=None, mandatory=True, ), - mask2=dict(argstr='--mask2=%s', ), - mesh=dict(argstr='--mesh=%s', ), + mask2=dict( + argstr='--mask2=%s', + extensions=None, + ), + mesh=dict( + argstr='--mesh=%s', + extensions=None, + ), mod_euler=dict(argstr='--modeuler', ), mode=dict( argstr='--mode=%s', @@ -62,15 +75,27 @@ def test_ProbTrackX_inputs(): argstr='--seed=%s', mandatory=True, ), - seed_ref=dict(argstr='--seedref=%s', ), + seed_ref=dict( + argstr='--seedref=%s', + extensions=None, + ), step_length=dict(argstr='--steplength=%.3f', ), - stop_mask=dict(argstr='--stop=%s', ), + stop_mask=dict( + argstr='--stop=%s', + extensions=None, + ), target_masks=dict(argstr='--targetmasks=%s', ), thsamples=dict(mandatory=True, ), use_anisotropy=dict(argstr='--usef', ), verbose=dict(argstr='--verbose=%d', ), - waypoints=dict(argstr='--waypoints=%s', ), - xfm=dict(argstr='--xfm=%s', ), + waypoints=dict( + argstr='--waypoints=%s', + extensions=None, + ), + xfm=dict( + argstr='--xfm=%s', + extensions=None, + ), ) inputs = ProbTrackX.input_spec() @@ -80,10 +105,10 @@ def test_ProbTrackX_inputs(): def test_ProbTrackX_outputs(): output_map = dict( fdt_paths=dict(), - log=dict(), + log=dict(extensions=None, ), particle_files=dict(), targets=dict(), - way_total=dict(), + way_total=dict(extensions=None, ), ) outputs = ProbTrackX.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index 8592b5ae1a..8ddf5f3a9a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -6,9 +6,15 @@ def test_ProbTrackX2_inputs(): input_map = dict( args=dict(argstr='%s', ), - avoid_mp=dict(argstr='--avoid=%s', ), + avoid_mp=dict( + argstr='--avoid=%s', + extensions=None, + ), c_thresh=dict(argstr='--cthr=%.3f', ), - colmask4=dict(argstr='--colmask4=%s', ), + colmask4=dict( + argstr='--colmask4=%s', + extensions=None, + ), correct_path_distribution=dict(argstr='--pd', ), dist_thresh=dict(argstr='--distthresh=%.3f', ), distthresh1=dict(argstr='--distthresh1=%.3f', ), @@ -18,17 +24,27 @@ def test_ProbTrackX2_inputs(): usedefault=True, ), fibst=dict(argstr='--fibst=%d', ), - fopd=dict(argstr='--fopd=%s', ), + fopd=dict( + argstr='--fopd=%s', + extensions=None, + ), force_dir=dict( argstr='--forcedir', usedefault=True, ), fsamples=dict(mandatory=True, ), - inv_xfm=dict(argstr='--invxfm=%s', ), + inv_xfm=dict( + argstr='--invxfm=%s', + extensions=None, + ), loop_check=dict(argstr='--loopcheck', ), - lrtarget3=dict(argstr='--lrtarget3=%s', ), + lrtarget3=dict( + argstr='--lrtarget3=%s', + extensions=None, + ), mask=dict( argstr='-m %s', + extensions=None, mandatory=True, ), meshspace=dict(argstr='--meshspace=%s', ), @@ -73,21 +89,42 @@ def test_ProbTrackX2_inputs(): argstr='--seed=%s', mandatory=True, ), - seed_ref=dict(argstr='--seedref=%s', ), + seed_ref=dict( + argstr='--seedref=%s', + extensions=None, + ), simple=dict(argstr='--simple', ), step_length=dict(argstr='--steplength=%.3f', ), - stop_mask=dict(argstr='--stop=%s', ), - target2=dict(argstr='--target2=%s', ), - target3=dict(argstr='--target3=%s', ), - target4=dict(argstr='--target4=%s', ), + stop_mask=dict( + argstr='--stop=%s', + extensions=None, + ), + target2=dict( + argstr='--target2=%s', + extensions=None, + ), + target3=dict( + argstr='--target3=%s', + extensions=None, + ), + target4=dict( + argstr='--target4=%s', + extensions=None, + ), target_masks=dict(argstr='--targetmasks=%s', ), thsamples=dict(mandatory=True, ), use_anisotropy=dict(argstr='--usef', ), verbose=dict(argstr='--verbose=%d', ), waycond=dict(argstr='--waycond=%s', ), wayorder=dict(argstr='--wayorder', ), - waypoints=dict(argstr='--waypoints=%s', ), - xfm=dict(argstr='--xfm=%s', ), + waypoints=dict( + argstr='--waypoints=%s', + extensions=None, + ), + xfm=dict( + argstr='--xfm=%s', + extensions=None, + ), ) inputs = ProbTrackX2.input_spec() @@ -97,15 +134,15 @@ def test_ProbTrackX2_inputs(): def test_ProbTrackX2_outputs(): output_map = dict( fdt_paths=dict(), - log=dict(), - lookup_tractspace=dict(), - matrix1_dot=dict(), - matrix2_dot=dict(), - matrix3_dot=dict(), - network_matrix=dict(), + log=dict(extensions=None, ), + lookup_tractspace=dict(extensions=None, ), + matrix1_dot=dict(extensions=None, ), + matrix2_dot=dict(extensions=None, ), + matrix3_dot=dict(extensions=None, ), + network_matrix=dict(extensions=None, ), particle_files=dict(), targets=dict(), - way_total=dict(), + way_total=dict(extensions=None, ), ) outputs = ProbTrackX2.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 3d52347265..21a9142639 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -16,6 +16,7 @@ def test_Randomise_inputs(): demean=dict(argstr='-D', ), design_mat=dict( argstr='-d %s', + extensions=None, position=2, ), environ=dict( @@ -25,13 +26,20 @@ def test_Randomise_inputs(): f_c_thresh=dict(argstr='-F %.2f', ), f_cm_thresh=dict(argstr='-S %.2f', ), f_only=dict(argstr='--f_only', ), - fcon=dict(argstr='-f %s', ), + fcon=dict( + argstr='-f %s', + extensions=None, + ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=0, ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + extensions=None, + ), num_perm=dict(argstr='-n %d', ), one_sample_group_mean=dict(argstr='-1', ), output_type=dict(), @@ -42,6 +50,7 @@ def test_Randomise_inputs(): show_total_perms=dict(argstr='-q', ), tcon=dict( argstr='-t %s', + extensions=None, position=3, ), tfce=dict(argstr='-T', ), @@ -51,7 +60,10 @@ def test_Randomise_inputs(): tfce_H=dict(argstr='--tfce_H=%.2f', ), var_smooth=dict(argstr='-v %d', ), vox_p_values=dict(argstr='-x', ), - x_block_labels=dict(argstr='-e %s', ), + x_block_labels=dict( + argstr='-e %s', + extensions=None, + ), ) inputs = Randomise.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index 76647d82d8..aeced99424 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -12,10 +12,12 @@ def test_Reorient2Std_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, ), @@ -27,7 +29,7 @@ def test_Reorient2Std_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reorient2Std_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Reorient2Std.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index e1cbac6fc9..d7adfa8ca2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -13,17 +13,20 @@ def test_RobustFOV_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=0, ), out_roi=dict( argstr='-r %s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_ROI', ), out_transform=dict( argstr='-m %s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_to_ROI', @@ -37,8 +40,8 @@ def test_RobustFOV_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustFOV_outputs(): output_map = dict( - out_roi=dict(), - out_transform=dict(), + out_roi=dict(extensions=None, ), + out_transform=dict(extensions=None, ), ) outputs = RobustFOV.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 1e1cc308cc..f42eb5189a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -13,6 +13,7 @@ def test_SMM_inputs(): mask=dict( argstr='--mask="%s"', copyfile=False, + extensions=None, mandatory=True, position=1, ), @@ -24,6 +25,7 @@ def test_SMM_inputs(): spatial_data_file=dict( argstr='--sdf="%s"', copyfile=False, + extensions=None, mandatory=True, position=0, ), @@ -35,9 +37,9 @@ def test_SMM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SMM_outputs(): output_map = dict( - activation_p_map=dict(), - deactivation_p_map=dict(), - null_p_map=dict(), + activation_p_map=dict(extensions=None, ), + deactivation_p_map=dict(extensions=None, ), + null_p_map=dict(extensions=None, ), ) outputs = SMM.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index ebbef0d427..69616b77ac 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -27,11 +27,13 @@ def test_SUSAN_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-1, @@ -54,7 +56,7 @@ def test_SUSAN_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SUSAN_outputs(): - output_map = dict(smoothed_file=dict(), ) + output_map = dict(smoothed_file=dict(extensions=None, ), ) outputs = SUSAN.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index f3be97b350..dc2b91a47f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -13,11 +13,16 @@ def test_SigLoss_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, ), - mask_file=dict(argstr='-m %s', ), + mask_file=dict( + argstr='-m %s', + extensions=None, + ), out_file=dict( argstr='-s %s', + extensions=None, genfile=True, ), output_type=dict(), @@ -29,7 +34,7 @@ def test_SigLoss_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SigLoss_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SigLoss.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Slice.py b/nipype/interfaces/fsl/tests/test_auto_Slice.py index d1e9093e37..d6202b6514 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slice.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slice.py @@ -13,6 +13,7 @@ def test_Slice_inputs(): in_file=dict( argstr='%s', copyfile=False, + extensions=None, mandatory=True, position=0, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index 75b9918ad9..71915c8da9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -6,8 +6,14 @@ def test_SliceTimer_inputs(): input_map = dict( args=dict(argstr='%s', ), - custom_order=dict(argstr='--ocustom=%s', ), - custom_timings=dict(argstr='--tcustom=%s', ), + custom_order=dict( + argstr='--ocustom=%s', + extensions=None, + ), + custom_timings=dict( + argstr='--tcustom=%s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -15,6 +21,7 @@ def test_SliceTimer_inputs(): global_shift=dict(argstr='--tglobal', ), in_file=dict( argstr='--in=%s', + extensions=None, mandatory=True, position=0, ), @@ -22,6 +29,7 @@ def test_SliceTimer_inputs(): interleaved=dict(argstr='--odd', ), out_file=dict( argstr='--out=%s', + extensions=None, genfile=True, hash_files=False, ), @@ -35,7 +43,7 @@ def test_SliceTimer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SliceTimer_outputs(): - output_map = dict(slice_time_corrected_file=dict(), ) + output_map = dict(slice_time_corrected_file=dict(extensions=None, ), ) outputs = SliceTimer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index d313cda474..14ad2d375e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -14,6 +14,7 @@ def test_Slicer_inputs(): args=dict(argstr='%s', ), colour_map=dict( argstr='-l %s', + extensions=None, position=4, ), dither_edges=dict( @@ -26,6 +27,7 @@ def test_Slicer_inputs(): ), image_edges=dict( argstr='%s', + extensions=None, position=2, ), image_width=dict( @@ -34,6 +36,7 @@ def test_Slicer_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -57,6 +60,7 @@ def test_Slicer_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-1, @@ -98,7 +102,7 @@ def test_Slicer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Slicer_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Slicer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index e8d8e06117..a08bd946a0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -18,6 +18,7 @@ def test_Smooth_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -30,6 +31,7 @@ def test_Smooth_inputs(): ), smoothed_file=dict( argstr='%s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_smooth', @@ -42,7 +44,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): - output_map = dict(smoothed_file=dict(), ) + output_map = dict(smoothed_file=dict(extensions=None, ), ) outputs = Smooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index df7544f931..21c1f13b62 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -17,15 +17,18 @@ def test_SmoothEstimate_inputs(): ), mask_file=dict( argstr='--mask=%s', + extensions=None, mandatory=True, ), output_type=dict(), residual_fit_file=dict( argstr='--res=%s', + extensions=None, requires=['dof'], ), zstat_file=dict( argstr='--zstat=%s', + extensions=None, xor=['dof'], ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index d62f904655..3ef493d752 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -12,6 +12,7 @@ def test_SpatialFilter_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -21,6 +22,7 @@ def test_SpatialFilter_inputs(): ), kernel_file=dict( argstr='%s', + extensions=None, position=5, xor=['kernel_size'], ), @@ -44,6 +46,7 @@ def test_SpatialFilter_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -60,7 +63,7 @@ def test_SpatialFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SpatialFilter_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SpatialFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index cec2ab462d..fed820ebbe 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -17,6 +17,7 @@ def test_Split_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_StdImage.py b/nipype/interfaces/fsl/tests/test_auto_StdImage.py index 302ab9c4c2..134d5d0d16 100644 --- a/nipype/interfaces/fsl/tests/test_auto_StdImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_StdImage.py @@ -17,6 +17,7 @@ def test_StdImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_StdImage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_StdImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_StdImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = StdImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 7cbb57491c..78aca77b26 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -12,6 +12,7 @@ def test_SwapDimensions_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position='1', ), @@ -21,6 +22,7 @@ def test_SwapDimensions_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, ), @@ -32,7 +34,7 @@ def test_SwapDimensions_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SwapDimensions_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SwapDimensions.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 3f91b3722a..ef3fed494c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -18,6 +18,7 @@ def test_TOPUP_inputs(): ), encoding_file=dict( argstr='--datain=%s', + extensions=None, mandatory=True, xor=['encoding_direction'], ), @@ -29,6 +30,7 @@ def test_TOPUP_inputs(): fwhm=dict(argstr='--fwhm=%f', ), in_file=dict( argstr='--imain=%s', + extensions=None, mandatory=True, ), interp=dict(argstr='--interp=%s', ), @@ -37,18 +39,21 @@ def test_TOPUP_inputs(): numprec=dict(argstr='--numprec=%s', ), out_base=dict( argstr='--out=%s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_base', ), out_corrected=dict( argstr='--iout=%s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_corrected', ), out_field=dict( argstr='--fout=%s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_field', @@ -60,6 +65,7 @@ def test_TOPUP_inputs(): ), out_logfile=dict( argstr='--logout=%s', + extensions=None, hash_files=False, keep_extension=True, name_source=['in_file'], @@ -97,14 +103,14 @@ def test_TOPUP_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TOPUP_outputs(): output_map = dict( - out_corrected=dict(), - out_enc_file=dict(), - out_field=dict(), - out_fieldcoef=dict(), + out_corrected=dict(extensions=None, ), + out_enc_file=dict(extensions=None, ), + out_field=dict(extensions=None, ), + out_fieldcoef=dict(extensions=None, ), out_jacs=dict(), - out_logfile=dict(), + out_logfile=dict(extensions=None, ), out_mats=dict(), - out_movpar=dict(), + out_movpar=dict(extensions=None, ), out_warps=dict(), ) outputs = TOPUP.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index c762b99d31..61145ebc1a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -17,6 +17,7 @@ def test_TemporalFilter_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -35,6 +36,7 @@ def test_TemporalFilter_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -51,7 +53,7 @@ def test_TemporalFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TemporalFilter_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TemporalFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index 5c2bb46cc8..e09faaa6ea 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -13,6 +13,7 @@ def test_Threshold_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -26,6 +27,7 @@ def test_Threshold_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -49,7 +51,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Threshold.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index 4308ee8153..b46c9d8839 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -5,17 +5,24 @@ def test_TractSkeleton_inputs(): input_map = dict( - alt_data_file=dict(argstr='-a %s', ), - alt_skeleton=dict(argstr='-s %s', ), + alt_data_file=dict( + argstr='-a %s', + extensions=None, + ), + alt_skeleton=dict( + argstr='-s %s', + extensions=None, + ), args=dict(argstr='%s', ), - data_file=dict(), - distance_map=dict(), + data_file=dict(extensions=None, ), + distance_map=dict(extensions=None, ), environ=dict( nohash=True, usedefault=True, ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, ), output_type=dict(), @@ -23,8 +30,11 @@ def test_TractSkeleton_inputs(): argstr='-p %.3f %s %s %s %s', requires=['threshold', 'distance_map', 'data_file'], ), - projected_data=dict(), - search_mask_file=dict(xor=['use_cingulum_mask'], ), + projected_data=dict(extensions=None, ), + search_mask_file=dict( + extensions=None, + xor=['use_cingulum_mask'], + ), skeleton_file=dict(argstr='-o %s', ), threshold=dict(), use_cingulum_mask=dict( @@ -39,8 +49,8 @@ def test_TractSkeleton_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TractSkeleton_outputs(): output_map = dict( - projected_data=dict(), - skeleton_file=dict(), + projected_data=dict(extensions=None, ), + skeleton_file=dict(extensions=None, ), ) outputs = TractSkeleton.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Training.py b/nipype/interfaces/fsl/tests/test_auto_Training.py index 91d48e4c01..1917419503 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Training.py +++ b/nipype/interfaces/fsl/tests/test_auto_Training.py @@ -30,7 +30,7 @@ def test_Training_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Training_outputs(): - output_map = dict(trained_wts_file=dict(), ) + output_map = dict(trained_wts_file=dict(extensions=None, ), ) outputs = Training.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index a0dcf2610d..c92f00eb3b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -12,6 +12,7 @@ def test_UnaryMaths_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -30,6 +31,7 @@ def test_UnaryMaths_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, position=-2, @@ -46,7 +48,7 @@ def test_UnaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = UnaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 61a28f7369..18e7b03dad 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -5,7 +5,10 @@ def test_VecReg_inputs(): input_map = dict( - affine_mat=dict(argstr='-t %s', ), + affine_mat=dict( + argstr='-t %s', + extensions=None, + ), args=dict(argstr='%s', ), environ=dict( nohash=True, @@ -13,24 +16,42 @@ def test_VecReg_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, ), interpolation=dict(argstr='--interp=%s', ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + extensions=None, + ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, ), output_type=dict(), - ref_mask=dict(argstr='--refmask=%s', ), + ref_mask=dict( + argstr='--refmask=%s', + extensions=None, + ), ref_vol=dict( argstr='-r %s', + extensions=None, mandatory=True, ), - rotation_mat=dict(argstr='--rotmat=%s', ), - rotation_warp=dict(argstr='--rotwarp=%s', ), - warp_field=dict(argstr='-w %s', ), + rotation_mat=dict( + argstr='--rotmat=%s', + extensions=None, + ), + rotation_warp=dict( + argstr='--rotwarp=%s', + extensions=None, + ), + warp_field=dict( + argstr='-w %s', + extensions=None, + ), ) inputs = VecReg.input_spec() @@ -38,7 +59,7 @@ def test_VecReg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VecReg_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = VecReg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 30924223cf..d3473c31a5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -16,6 +16,7 @@ def test_WarpPoints_inputs(): ), dest_file=dict( argstr='-dest %s', + extensions=None, mandatory=True, ), environ=dict( @@ -24,24 +25,29 @@ def test_WarpPoints_inputs(): ), in_coords=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), out_file=dict( + extensions=None, name_source='in_coords', name_template='%s_warped', output_name='out_file', ), src_file=dict( argstr='-src %s', + extensions=None, mandatory=True, ), warp_file=dict( argstr='-warp %s', + extensions=None, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', + extensions=None, xor=['warp_file'], ), ) @@ -51,7 +57,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = WarpPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py index 627ef60ad6..e1afc49d9d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py @@ -20,23 +20,28 @@ def test_WarpPointsFromStd_inputs(): ), img_file=dict( argstr='-img %s', + extensions=None, mandatory=True, ), in_coords=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), std_file=dict( argstr='-std %s', + extensions=None, mandatory=True, ), warp_file=dict( argstr='-warp %s', + extensions=None, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', + extensions=None, xor=['warp_file'], ), ) @@ -46,7 +51,7 @@ def test_WarpPointsFromStd_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPointsFromStd_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = WarpPointsFromStd.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index 3d37ad1486..245c587b2e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -20,29 +20,38 @@ def test_WarpPointsToStd_inputs(): ), img_file=dict( argstr='-img %s', + extensions=None, mandatory=True, ), in_coords=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), out_file=dict( + extensions=None, name_source='in_coords', name_template='%s_warped', output_name='out_file', ), - premat_file=dict(argstr='-premat %s', ), + premat_file=dict( + argstr='-premat %s', + extensions=None, + ), std_file=dict( argstr='-std %s', + extensions=None, mandatory=True, ), warp_file=dict( argstr='-warp %s', + extensions=None, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', + extensions=None, xor=['warp_file'], ), ) @@ -52,7 +61,7 @@ def test_WarpPointsToStd_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPointsToStd_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = WarpPointsToStd.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index 04d3a05f14..59f762c2eb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -12,20 +12,26 @@ def test_WarpUtils_inputs(): ), in_file=dict( argstr='--in=%s', + extensions=None, mandatory=True, ), knot_space=dict(argstr='--knotspace=%d,%d,%d', ), out_file=dict( argstr='--out=%s', + extensions=None, name_source=['in_file'], output_name='out_file', position=-1, ), out_format=dict(argstr='--outformat=%s', ), - out_jacobian=dict(argstr='--jac=%s', ), + out_jacobian=dict( + argstr='--jac=%s', + extensions=None, + ), output_type=dict(), reference=dict( argstr='--ref=%s', + extensions=None, mandatory=True, ), warp_resolution=dict(argstr='--warpres=%0.4f,%0.4f,%0.4f', ), @@ -42,8 +48,8 @@ def test_WarpUtils_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_WarpUtils_outputs(): output_map = dict( - out_file=dict(), - out_jacobian=dict(), + out_file=dict(extensions=None, ), + out_jacobian=dict(extensions=None, ), ) outputs = WarpUtils.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index d72bb3bb4b..80ee0fca8f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -20,10 +20,12 @@ def test_XFibres5_inputs(): ), bvals=dict( argstr='--bvals=%s', + extensions=None, mandatory=True, ), bvecs=dict( argstr='--bvecs=%s', + extensions=None, mandatory=True, ), cnlinear=dict( @@ -32,6 +34,7 @@ def test_XFibres5_inputs(): ), dwi=dict( argstr='--data=%s', + extensions=None, mandatory=True, ), environ=dict( @@ -51,13 +54,17 @@ def test_XFibres5_inputs(): usedefault=True, ), fudge=dict(argstr='--fudge=%d', ), - gradnonlin=dict(argstr='--gradnonlin=%s', ), + gradnonlin=dict( + argstr='--gradnonlin=%s', + extensions=None, + ), logdir=dict( argstr='--logdir=%s', usedefault=True, ), mask=dict( argstr='--mask=%s', + extensions=None, mandatory=True, ), model=dict(argstr='--model=%d', ), @@ -103,10 +110,10 @@ def test_XFibres5_outputs(): output_map = dict( dyads=dict(), fsamples=dict(), - mean_S0samples=dict(), - mean_dsamples=dict(), + mean_S0samples=dict(extensions=None, ), + mean_dsamples=dict(extensions=None, ), mean_fsamples=dict(), - mean_tausamples=dict(), + mean_tausamples=dict(extensions=None, ), phsamples=dict(), thsamples=dict(), ) diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 4b9afd1ce1..c409d4e78a 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -1027,9 +1027,9 @@ def s3tolocal(self, s3path, bkt): local_directory = str(self.inputs.local_directory) bucket_path = str(self.inputs.bucket_path) template = str(self.inputs.template) - if not os.path.split(local_directory)[1] == '': + if not os.path.basename(local_directory) == '': local_directory += '/' - if not os.path.split(bucket_path)[1] == '': + if not os.path.basename(bucket_path) == '': bucket_path += '/' if template[0] == '/': template = template[1:] diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 57bdc5ccd2..678ab93a52 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -115,6 +115,7 @@ def test_Average_inputs(): ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_files'], @@ -147,7 +148,7 @@ def test_Average_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Average_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Average.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index a34aeab9b5..c1b3515cea 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -15,6 +15,7 @@ def test_BBox_inputs(): format_mincreshape=dict(argstr='-mincreshape', ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -28,6 +29,7 @@ def test_BBox_inputs(): position=-1, ), output_file=dict( + extensions=None, hash_files=False, keep_extension=False, name_source=['input_file'], @@ -46,7 +48,7 @@ def test_BBox_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BBox_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = BBox.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index 4834cf3c4a..bc4705db2e 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -78,7 +78,7 @@ def test_Beast_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Beast_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Beast.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py index fb9061040a..ef6e5af537 100644 --- a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py +++ b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py @@ -16,6 +16,7 @@ def test_BestLinReg_inputs(): ), output_mnc=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, keep_extension=False, @@ -25,6 +26,7 @@ def test_BestLinReg_inputs(): ), output_xfm=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, keep_extension=False, @@ -34,11 +36,13 @@ def test_BestLinReg_inputs(): ), source=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), target=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -51,8 +55,8 @@ def test_BestLinReg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BestLinReg_outputs(): output_map = dict( - output_mnc=dict(), - output_xfm=dict(), + output_mnc=dict(extensions=None, ), + output_xfm=dict(extensions=None, ), ) outputs = BestLinReg.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_BigAverage.py b/nipype/interfaces/minc/tests/test_auto_BigAverage.py index ce1fb2b91e..b9933c116b 100644 --- a/nipype/interfaces/minc/tests/test_auto_BigAverage.py +++ b/nipype/interfaces/minc/tests/test_auto_BigAverage.py @@ -22,6 +22,7 @@ def test_BigAverage_inputs(): ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_files'], @@ -32,6 +33,7 @@ def test_BigAverage_inputs(): robust=dict(argstr='-robust', ), sd_file=dict( argstr='--sdfile %s', + extensions=None, hash_files=False, name_source=['input_files'], name_template='%s_bigaverage_stdev.mnc', @@ -46,8 +48,8 @@ def test_BigAverage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BigAverage_outputs(): output_map = dict( - output_file=dict(), - sd_file=dict(), + output_file=dict(extensions=None, ), + sd_file=dict(extensions=None, ), ) outputs = BigAverage.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Blob.py b/nipype/interfaces/minc/tests/test_auto_Blob.py index b489ac944a..b83d5b90a5 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blob.py +++ b/nipype/interfaces/minc/tests/test_auto_Blob.py @@ -13,12 +13,14 @@ def test_Blob_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), magnitude=dict(argstr='-magnitude', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -34,7 +36,7 @@ def test_Blob_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Blob_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Blob.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Blur.py b/nipype/interfaces/minc/tests/test_auto_Blur.py index fb6e405012..2342d65974 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blur.py +++ b/nipype/interfaces/minc/tests/test_auto_Blur.py @@ -32,12 +32,14 @@ def test_Blur_inputs(): gradient=dict(argstr='-gradient', ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), no_apodize=dict(argstr='-no_apodize', ), output_file_base=dict( argstr='%s', + extensions=None, position=-1, ), partial=dict(argstr='-partial', ), @@ -58,12 +60,12 @@ def test_Blur_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Blur_outputs(): output_map = dict( - gradient_dxyz=dict(), - output_file=dict(), - partial_dx=dict(), - partial_dxyz=dict(), - partial_dy=dict(), - partial_dz=dict(), + gradient_dxyz=dict(extensions=None, ), + output_file=dict(extensions=None, ), + partial_dx=dict(extensions=None, ), + partial_dxyz=dict(extensions=None, ), + partial_dy=dict(extensions=None, ), + partial_dz=dict(extensions=None, ), ) outputs = Blur.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index 7bec782c1c..e9df677150 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -112,6 +112,7 @@ def test_Calc_inputs(): outfiles=dict(), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_files'], @@ -148,7 +149,7 @@ def test_Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Convert.py b/nipype/interfaces/minc/tests/test_auto_Convert.py index 6df596c682..174efd8a10 100644 --- a/nipype/interfaces/minc/tests/test_auto_Convert.py +++ b/nipype/interfaces/minc/tests/test_auto_Convert.py @@ -18,11 +18,13 @@ def test_Convert_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -38,7 +40,7 @@ def test_Convert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Convert_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Convert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Copy.py b/nipype/interfaces/minc/tests/test_auto_Copy.py index e91470ba6d..d92a63d812 100644 --- a/nipype/interfaces/minc/tests/test_auto_Copy.py +++ b/nipype/interfaces/minc/tests/test_auto_Copy.py @@ -12,11 +12,13 @@ def test_Copy_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -38,7 +40,7 @@ def test_Copy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Copy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index bcca2a4801..19c299dac8 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -28,6 +28,7 @@ def test_Dump_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -39,6 +40,7 @@ def test_Dump_inputs(): position=-1, ), output_file=dict( + extensions=None, hash_files=False, keep_extension=False, name_source=['input_file'], @@ -57,7 +59,7 @@ def test_Dump_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dump_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Dump.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index 77126eac18..35f6162c7f 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -70,6 +70,7 @@ def test_Extract_inputs(): image_range=dict(argstr='-image_range %s %s', ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -87,6 +88,7 @@ def test_Extract_inputs(): position=-1, ), output_file=dict( + extensions=None, hash_files=False, keep_extension=False, name_source=['input_file'], @@ -155,7 +157,7 @@ def test_Extract_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Extract_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Extract.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py index c89dc65de6..0249c861bc 100644 --- a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py +++ b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py @@ -15,9 +15,13 @@ def test_Gennlxfm_inputs(): usedefault=True, ), ident=dict(argstr='-ident', ), - like=dict(argstr='-like %s', ), + like=dict( + argstr='-like %s', + extensions=None, + ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['like'], @@ -34,8 +38,8 @@ def test_Gennlxfm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Gennlxfm_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), + output_file=dict(extensions=None, ), + output_grid=dict(extensions=None, ), ) outputs = Gennlxfm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index 1d011034d2..6bc142b15d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -122,6 +122,7 @@ def test_Math_inputs(): nsegment=dict(argstr='-nsegment -const2 %s %s', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_files'], @@ -161,7 +162,7 @@ def test_Math_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Math_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Math.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_NlpFit.py b/nipype/interfaces/minc/tests/test_auto_NlpFit.py index 1a728a90dd..b0ad4087fa 100644 --- a/nipype/interfaces/minc/tests/test_auto_NlpFit.py +++ b/nipype/interfaces/minc/tests/test_auto_NlpFit.py @@ -12,6 +12,7 @@ def test_NlpFit_inputs(): ), config_file=dict( argstr='-config_file %s', + extensions=None, mandatory=True, ), environ=dict( @@ -20,25 +21,30 @@ def test_NlpFit_inputs(): ), init_xfm=dict( argstr='-init_xfm %s', + extensions=None, mandatory=True, ), input_grid_files=dict(), output_xfm=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), source=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), source_mask=dict( argstr='-source_mask %s', + extensions=None, mandatory=True, ), target=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -51,8 +57,8 @@ def test_NlpFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_NlpFit_outputs(): output_map = dict( - output_grid=dict(), - output_xfm=dict(), + output_grid=dict(extensions=None, ), + output_xfm=dict(extensions=None, ), ) outputs = NlpFit.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index 3a0d28f06d..9fb0d3c5ba 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -21,6 +21,7 @@ def test_Norm_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -30,6 +31,7 @@ def test_Norm_inputs(): out_floor=dict(argstr='-out_floor %s', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -55,8 +57,8 @@ def test_Norm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Norm_outputs(): output_map = dict( - output_file=dict(), - output_threshold_mask=dict(), + output_file=dict(extensions=None, ), + output_threshold_mask=dict(extensions=None, ), ) outputs = Norm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Pik.py b/nipype/interfaces/minc/tests/test_auto_Pik.py index d74d9a86ad..748f21a976 100644 --- a/nipype/interfaces/minc/tests/test_auto_Pik.py +++ b/nipype/interfaces/minc/tests/test_auto_Pik.py @@ -30,6 +30,7 @@ def test_Pik_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -38,6 +39,7 @@ def test_Pik_inputs(): minc_range=dict(argstr='--range %s %s', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, keep_extension=False, @@ -84,7 +86,7 @@ def test_Pik_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Pik_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Pik.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index bd00bd224d..8d4b24ff41 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -84,6 +84,7 @@ def test_Resample_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -118,6 +119,7 @@ def test_Resample_inputs(): origin=dict(argstr='-origin %s %s %s', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -243,7 +245,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index 45e6ddeb4a..669425da95 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -21,6 +21,7 @@ def test_Reshape_inputs(): ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -36,7 +37,7 @@ def test_Reshape_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reshape_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Reshape.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_ToEcat.py b/nipype/interfaces/minc/tests/test_auto_ToEcat.py index 26a3ac0436..b755263566 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToEcat.py +++ b/nipype/interfaces/minc/tests/test_auto_ToEcat.py @@ -21,12 +21,14 @@ def test_ToEcat_inputs(): ignore_study_variable=dict(argstr='-ignore_study_variable', ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), no_decay_corr_fctr=dict(argstr='-no_decay_corr_fctr', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, keep_extension=False, @@ -42,7 +44,7 @@ def test_ToEcat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ToEcat_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = ToEcat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index e010da322d..aeda687c97 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -12,6 +12,7 @@ def test_ToRaw_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -29,6 +30,7 @@ def test_ToRaw_inputs(): position=-1, ), output_file=dict( + extensions=None, hash_files=False, keep_extension=False, name_source=['input_file'], @@ -81,7 +83,7 @@ def test_ToRaw_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ToRaw_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = ToRaw.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index 048ffcde9b..b710d59543 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -10,7 +10,10 @@ def test_VolSymm_inputs(): argstr='-clobber', usedefault=True, ), - config_file=dict(argstr='-config_file %s', ), + config_file=dict( + argstr='-config_file %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -26,6 +29,7 @@ def test_VolSymm_inputs(): nofit=dict(argstr='-nofit', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -53,9 +57,9 @@ def test_VolSymm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VolSymm_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), - trans_file=dict(), + output_file=dict(extensions=None, ), + output_grid=dict(extensions=None, ), + trans_file=dict(extensions=None, ), ) outputs = VolSymm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Volcentre.py b/nipype/interfaces/minc/tests/test_auto_Volcentre.py index b095751a4d..0e54c67583 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volcentre.py +++ b/nipype/interfaces/minc/tests/test_auto_Volcentre.py @@ -18,11 +18,13 @@ def test_Volcentre_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -38,7 +40,7 @@ def test_Volcentre_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Volcentre_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Volcentre.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Voliso.py b/nipype/interfaces/minc/tests/test_auto_Voliso.py index 967642a328..33923046d0 100644 --- a/nipype/interfaces/minc/tests/test_auto_Voliso.py +++ b/nipype/interfaces/minc/tests/test_auto_Voliso.py @@ -17,6 +17,7 @@ def test_Voliso_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -24,6 +25,7 @@ def test_Voliso_inputs(): minstep=dict(argstr='--minstep %s', ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -38,7 +40,7 @@ def test_Voliso_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Voliso_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Voliso.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Volpad.py b/nipype/interfaces/minc/tests/test_auto_Volpad.py index 865bc79e69..c5fe679935 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volpad.py +++ b/nipype/interfaces/minc/tests/test_auto_Volpad.py @@ -19,11 +19,13 @@ def test_Volpad_inputs(): ), input_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_file'], @@ -40,7 +42,7 @@ def test_Volpad_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Volpad_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(extensions=None, ), ) outputs = Volpad.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py index 6d036a0c0e..283ef63e40 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py @@ -27,6 +27,7 @@ def test_XfmAvg_inputs(): input_grid_files=dict(), output_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -39,8 +40,8 @@ def test_XfmAvg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmAvg_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), + output_file=dict(extensions=None, ), + output_grid=dict(extensions=None, ), ) outputs = XfmAvg.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py index eb748953ef..4e42b4ed45 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py @@ -23,6 +23,7 @@ def test_XfmConcat_inputs(): input_grid_files=dict(), output_file=dict( argstr='%s', + extensions=None, genfile=True, hash_files=False, name_source=['input_files'], @@ -38,7 +39,7 @@ def test_XfmConcat_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmConcat_outputs(): output_map = dict( - output_file=dict(), + output_file=dict(extensions=None, ), output_grids=dict(), ) outputs = XfmConcat.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index d729e90639..9e242300da 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -21,6 +21,7 @@ def test_XfmInvert_inputs(): ), output_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -33,8 +34,8 @@ def test_XfmInvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmInvert_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), + output_file=dict(extensions=None, ), + output_grid=dict(extensions=None, ), ) outputs = XfmInvert.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index 16605acbb7..4bc44eaeb5 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -11,18 +11,36 @@ def test_JistBrainMgdmSegmentation_inputs(): usedefault=True, ), inAdjust=dict(argstr='--inAdjust %s', ), - inAtlas=dict(argstr='--inAtlas %s', ), + inAtlas=dict( + argstr='--inAtlas %s', + extensions=None, + ), inCompute=dict(argstr='--inCompute %s', ), inCurvature=dict(argstr='--inCurvature %f', ), inData=dict(argstr='--inData %f', ), - inFLAIR=dict(argstr='--inFLAIR %s', ), - inMP2RAGE=dict(argstr='--inMP2RAGE %s', ), - inMP2RAGE2=dict(argstr='--inMP2RAGE2 %s', ), - inMPRAGE=dict(argstr='--inMPRAGE %s', ), + inFLAIR=dict( + argstr='--inFLAIR %s', + extensions=None, + ), + inMP2RAGE=dict( + argstr='--inMP2RAGE %s', + extensions=None, + ), + inMP2RAGE2=dict( + argstr='--inMP2RAGE2 %s', + extensions=None, + ), + inMPRAGE=dict( + argstr='--inMPRAGE %s', + extensions=None, + ), inMax=dict(argstr='--inMax %d', ), inMin=dict(argstr='--inMin %f', ), inOutput=dict(argstr='--inOutput %s', ), - inPV=dict(argstr='--inPV %s', ), + inPV=dict( + argstr='--inPV %s', + extensions=None, + ), inPosterior=dict(argstr='--inPosterior %f', ), inSteps=dict(argstr='--inSteps %d', ), inTopology=dict(argstr='--inTopology %s', ), @@ -57,10 +75,10 @@ def test_JistBrainMgdmSegmentation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMgdmSegmentation_outputs(): output_map = dict( - outLevelset=dict(), - outPosterior2=dict(), - outPosterior3=dict(), - outSegmented=dict(), + outLevelset=dict(extensions=None, ), + outPosterior2=dict(extensions=None, ), + outPosterior3=dict(extensions=None, ), + outSegmented=dict(extensions=None, ), ) outputs = JistBrainMgdmSegmentation.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index ebb65bb789..9ecec6f789 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -11,8 +11,14 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): usedefault=True, ), inDistance=dict(argstr='--inDistance %f', ), - inSecond=dict(argstr='--inSecond %s', ), - inSkull=dict(argstr='--inSkull %s', ), + inSecond=dict( + argstr='--inSecond %s', + extensions=None, + ), + inSkull=dict( + argstr='--inSkull %s', + extensions=None, + ), inoutput=dict(argstr='--inoutput %s', ), null=dict(argstr='--null %s', ), outDura=dict( @@ -32,7 +38,7 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageDuraEstimation_outputs(): - output_map = dict(outDura=dict(), ) + output_map = dict(outDura=dict(extensions=None, ), ) outputs = JistBrainMp2rageDuraEstimation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index abf794b662..73d02f8c97 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -10,11 +10,23 @@ def test_JistBrainMp2rageSkullStripping_inputs(): nohash=True, usedefault=True, ), - inFilter=dict(argstr='--inFilter %s', ), - inSecond=dict(argstr='--inSecond %s', ), + inFilter=dict( + argstr='--inFilter %s', + extensions=None, + ), + inSecond=dict( + argstr='--inSecond %s', + extensions=None, + ), inSkip=dict(argstr='--inSkip %s', ), - inT1=dict(argstr='--inT1 %s', ), - inT1weighted=dict(argstr='--inT1weighted %s', ), + inT1=dict( + argstr='--inT1 %s', + extensions=None, + ), + inT1weighted=dict( + argstr='--inT1weighted %s', + extensions=None, + ), null=dict(argstr='--null %s', ), outBrain=dict( argstr='--outBrain %s', @@ -46,10 +58,10 @@ def test_JistBrainMp2rageSkullStripping_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageSkullStripping_outputs(): output_map = dict( - outBrain=dict(), - outMasked=dict(), - outMasked2=dict(), - outMasked3=dict(), + outBrain=dict(extensions=None, ), + outMasked=dict(extensions=None, ), + outMasked2=dict(extensions=None, ), + outMasked3=dict(extensions=None, ), ) outputs = JistBrainMp2rageSkullStripping.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index bb86144c20..0ab4cea836 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -10,7 +10,10 @@ def test_JistBrainPartialVolumeFilter_inputs(): nohash=True, usedefault=True, ), - inInput=dict(argstr='--inInput %s', ), + inInput=dict( + argstr='--inInput %s', + extensions=None, + ), inPV=dict(argstr='--inPV %s', ), inoutput=dict(argstr='--inoutput %s', ), null=dict(argstr='--null %s', ), @@ -31,7 +34,7 @@ def test_JistBrainPartialVolumeFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainPartialVolumeFilter_outputs(): - output_map = dict(outPartial=dict(), ) + output_map = dict(outPartial=dict(extensions=None, ), ) outputs = JistBrainPartialVolumeFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index 407b9755ca..5c3a8b1cba 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -10,7 +10,10 @@ def test_JistCortexSurfaceMeshInflation_inputs(): nohash=True, usedefault=True, ), - inLevelset=dict(argstr='--inLevelset %s', ), + inLevelset=dict( + argstr='--inLevelset %s', + extensions=None, + ), inLorentzian=dict(argstr='--inLorentzian %s', ), inMax=dict(argstr='--inMax %d', ), inMean=dict(argstr='--inMean %f', ), @@ -40,8 +43,8 @@ def test_JistCortexSurfaceMeshInflation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistCortexSurfaceMeshInflation_outputs(): output_map = dict( - outInflated=dict(), - outOriginal=dict(), + outInflated=dict(extensions=None, ), + outOriginal=dict(extensions=None, ), ) outputs = JistCortexSurfaceMeshInflation.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index bfdace4944..9b02ce9346 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -12,10 +12,19 @@ def test_JistIntensityMp2rageMasking_inputs(): ), inBackground=dict(argstr='--inBackground %s', ), inMasking=dict(argstr='--inMasking %s', ), - inQuantitative=dict(argstr='--inQuantitative %s', ), - inSecond=dict(argstr='--inSecond %s', ), + inQuantitative=dict( + argstr='--inQuantitative %s', + extensions=None, + ), + inSecond=dict( + argstr='--inSecond %s', + extensions=None, + ), inSkip=dict(argstr='--inSkip %s', ), - inT1weighted=dict(argstr='--inT1weighted %s', ), + inT1weighted=dict( + argstr='--inT1weighted %s', + extensions=None, + ), null=dict(argstr='--null %s', ), outMasked=dict( argstr='--outMasked_T1_Map %s', @@ -47,10 +56,10 @@ def test_JistIntensityMp2rageMasking_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistIntensityMp2rageMasking_outputs(): output_map = dict( - outMasked=dict(), - outMasked2=dict(), - outSignal=dict(), - outSignal2=dict(), + outMasked=dict(extensions=None, ), + outMasked2=dict(extensions=None, ), + outSignal=dict(extensions=None, ), + outSignal2=dict(extensions=None, ), ) outputs = JistIntensityMp2rageMasking.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index 12203a1aa6..e8740dca7f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -10,8 +10,14 @@ def test_JistLaminarProfileCalculator_inputs(): nohash=True, usedefault=True, ), - inIntensity=dict(argstr='--inIntensity %s', ), - inMask=dict(argstr='--inMask %s', ), + inIntensity=dict( + argstr='--inIntensity %s', + extensions=None, + ), + inMask=dict( + argstr='--inMask %s', + extensions=None, + ), incomputed=dict(argstr='--incomputed %s', ), null=dict(argstr='--null %s', ), outResult=dict( @@ -31,7 +37,7 @@ def test_JistLaminarProfileCalculator_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileCalculator_outputs(): - output_map = dict(outResult=dict(), ) + output_map = dict(outResult=dict(extensions=None, ), ) outputs = JistLaminarProfileCalculator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index ddc4d5d922..fd4e496fbf 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -10,7 +10,10 @@ def test_JistLaminarProfileGeometry_inputs(): nohash=True, usedefault=True, ), - inProfile=dict(argstr='--inProfile %s', ), + inProfile=dict( + argstr='--inProfile %s', + extensions=None, + ), incomputed=dict(argstr='--incomputed %s', ), inoutside=dict(argstr='--inoutside %f', ), inregularization=dict(argstr='--inregularization %s', ), @@ -33,7 +36,7 @@ def test_JistLaminarProfileGeometry_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileGeometry_outputs(): - output_map = dict(outResult=dict(), ) + output_map = dict(outResult=dict(extensions=None, ), ) outputs = JistLaminarProfileGeometry.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index 58de472b85..37f4a26212 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -10,9 +10,18 @@ def test_JistLaminarProfileSampling_inputs(): nohash=True, usedefault=True, ), - inCortex=dict(argstr='--inCortex %s', ), - inIntensity=dict(argstr='--inIntensity %s', ), - inProfile=dict(argstr='--inProfile %s', ), + inCortex=dict( + argstr='--inCortex %s', + extensions=None, + ), + inIntensity=dict( + argstr='--inIntensity %s', + extensions=None, + ), + inProfile=dict( + argstr='--inProfile %s', + extensions=None, + ), null=dict(argstr='--null %s', ), outProfile2=dict( argstr='--outProfile2 %s', @@ -36,8 +45,8 @@ def test_JistLaminarProfileSampling_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileSampling_outputs(): output_map = dict( - outProfile2=dict(), - outProfilemapped=dict(), + outProfile2=dict(extensions=None, ), + outProfilemapped=dict(extensions=None, ), ) outputs = JistLaminarProfileSampling.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index bb9577ccee..9ffe1ddb52 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -10,9 +10,18 @@ def test_JistLaminarROIAveraging_inputs(): nohash=True, usedefault=True, ), - inIntensity=dict(argstr='--inIntensity %s', ), - inMask=dict(argstr='--inMask %s', ), - inROI=dict(argstr='--inROI %s', ), + inIntensity=dict( + argstr='--inIntensity %s', + extensions=None, + ), + inMask=dict( + argstr='--inMask %s', + extensions=None, + ), + inROI=dict( + argstr='--inROI %s', + extensions=None, + ), inROI2=dict(argstr='--inROI2 %s', ), null=dict(argstr='--null %s', ), outROI3=dict( @@ -32,7 +41,7 @@ def test_JistLaminarROIAveraging_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarROIAveraging_outputs(): - output_map = dict(outROI3=dict(), ) + output_map = dict(outROI3=dict(extensions=None, ), ) outputs = JistLaminarROIAveraging.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 4aa9f9d77b..1fb5c644cc 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -10,13 +10,19 @@ def test_JistLaminarVolumetricLayering_inputs(): nohash=True, usedefault=True, ), - inInner=dict(argstr='--inInner %s', ), + inInner=dict( + argstr='--inInner %s', + extensions=None, + ), inLayering=dict(argstr='--inLayering %s', ), inLayering2=dict(argstr='--inLayering2 %s', ), inMax=dict(argstr='--inMax %d', ), inMin=dict(argstr='--inMin %f', ), inNumber=dict(argstr='--inNumber %d', ), - inOuter=dict(argstr='--inOuter %s', ), + inOuter=dict( + argstr='--inOuter %s', + extensions=None, + ), inTopology=dict(argstr='--inTopology %s', ), incurvature=dict(argstr='--incurvature %d', ), inpresmooth=dict(argstr='--inpresmooth %s', ), @@ -48,9 +54,9 @@ def test_JistLaminarVolumetricLayering_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarVolumetricLayering_outputs(): output_map = dict( - outContinuous=dict(), - outDiscrete=dict(), - outLayer=dict(), + outContinuous=dict(extensions=None, ), + outDiscrete=dict(extensions=None, ), + outLayer=dict(extensions=None, ), ) outputs = JistLaminarVolumetricLayering.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 016beee263..96dcf57050 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -11,8 +11,14 @@ def test_MedicAlgorithmImageCalculator_inputs(): usedefault=True, ), inOperation=dict(argstr='--inOperation %s', ), - inVolume=dict(argstr='--inVolume %s', ), - inVolume2=dict(argstr='--inVolume2 %s', ), + inVolume=dict( + argstr='--inVolume %s', + extensions=None, + ), + inVolume2=dict( + argstr='--inVolume2 %s', + extensions=None, + ), null=dict(argstr='--null %s', ), outResult=dict( argstr='--outResult %s', @@ -31,7 +37,7 @@ def test_MedicAlgorithmImageCalculator_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmImageCalculator_outputs(): - output_map = dict(outResult=dict(), ) + output_map = dict(outResult=dict(extensions=None, ), ) outputs = MedicAlgorithmImageCalculator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index 87f9ab6a72..c9191fb0e7 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -11,14 +11,26 @@ def test_MedicAlgorithmLesionToads_inputs(): usedefault=True, ), inAtlas=dict(argstr='--inAtlas %s', ), - inAtlas2=dict(argstr='--inAtlas2 %s', ), - inAtlas3=dict(argstr='--inAtlas3 %s', ), - inAtlas4=dict(argstr='--inAtlas4 %s', ), + inAtlas2=dict( + argstr='--inAtlas2 %s', + extensions=None, + ), + inAtlas3=dict( + argstr='--inAtlas3 %s', + extensions=None, + ), + inAtlas4=dict( + argstr='--inAtlas4 %s', + extensions=None, + ), inAtlas5=dict(argstr='--inAtlas5 %f', ), inAtlas6=dict(argstr='--inAtlas6 %s', ), inConnectivity=dict(argstr='--inConnectivity %s', ), inCorrect=dict(argstr='--inCorrect %s', ), - inFLAIR=dict(argstr='--inFLAIR %s', ), + inFLAIR=dict( + argstr='--inFLAIR %s', + extensions=None, + ), inInclude=dict(argstr='--inInclude %s', ), inMaximum=dict(argstr='--inMaximum %d', ), inMaximum2=dict(argstr='--inMaximum2 %d', ), @@ -29,8 +41,14 @@ def test_MedicAlgorithmLesionToads_inputs(): inOutput2=dict(argstr='--inOutput2 %s', ), inOutput3=dict(argstr='--inOutput3 %s', ), inSmooting=dict(argstr='--inSmooting %f', ), - inT1_MPRAGE=dict(argstr='--inT1_MPRAGE %s', ), - inT1_SPGR=dict(argstr='--inT1_SPGR %s', ), + inT1_MPRAGE=dict( + argstr='--inT1_MPRAGE %s', + extensions=None, + ), + inT1_SPGR=dict( + argstr='--inT1_SPGR %s', + extensions=None, + ), null=dict(argstr='--null %s', ), outCortical=dict( argstr='--outCortical %s', @@ -82,15 +100,15 @@ def test_MedicAlgorithmLesionToads_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmLesionToads_outputs(): output_map = dict( - outCortical=dict(), - outFilled=dict(), - outHard=dict(), - outHard2=dict(), - outInhomogeneity=dict(), - outLesion=dict(), - outMembership=dict(), - outSulcal=dict(), - outWM=dict(), + outCortical=dict(extensions=None, ), + outFilled=dict(extensions=None, ), + outHard=dict(extensions=None, ), + outHard2=dict(extensions=None, ), + outInhomogeneity=dict(extensions=None, ), + outLesion=dict(extensions=None, ), + outMembership=dict(extensions=None, ), + outSulcal=dict(extensions=None, ), + outWM=dict(extensions=None, ), ) outputs = MedicAlgorithmLesionToads.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index 7c8c7248ad..4abe453f31 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -17,7 +17,10 @@ def test_MedicAlgorithmMipavReorient_inputs(): argstr='--inSource %s', sep=';', ), - inTemplate=dict(argstr='--inTemplate %s', ), + inTemplate=dict( + argstr='--inTemplate %s', + extensions=None, + ), inUser=dict(argstr='--inUser %s', ), inUser2=dict(argstr='--inUser2 %s', ), inUser3=dict(argstr='--inUser3 %s', ), diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index 9d5a148a24..f06f6f41d8 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -13,7 +13,10 @@ def test_MedicAlgorithmN3_inputs(): inAutomatic=dict(argstr='--inAutomatic %s', ), inEnd=dict(argstr='--inEnd %f', ), inField=dict(argstr='--inField %f', ), - inInput=dict(argstr='--inInput %s', ), + inInput=dict( + argstr='--inInput %s', + extensions=None, + ), inKernel=dict(argstr='--inKernel %f', ), inMaximum=dict(argstr='--inMaximum %d', ), inSignal=dict(argstr='--inSignal %f', ), @@ -42,8 +45,8 @@ def test_MedicAlgorithmN3_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmN3_outputs(): output_map = dict( - outInhomogeneity=dict(), - outInhomogeneity2=dict(), + outInhomogeneity=dict(extensions=None, ), + outInhomogeneity2=dict(extensions=None, ), ) outputs = MedicAlgorithmN3.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index b2d247e9dc..a3cfba10af 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -11,7 +11,10 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): usedefault=True, ), inApply=dict(argstr='--inApply %s', ), - inAtlas=dict(argstr='--inAtlas %s', ), + inAtlas=dict( + argstr='--inAtlas %s', + extensions=None, + ), inBackground=dict(argstr='--inBackground %f', ), inCoarse=dict(argstr='--inCoarse %f', ), inCost=dict(argstr='--inCost %s', ), @@ -22,7 +25,10 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): inInhomogeneity=dict(argstr='--inInhomogeneity %s', ), inInitial=dict(argstr='--inInitial %d', ), inInitial2=dict(argstr='--inInitial2 %f', ), - inInput=dict(argstr='--inInput %s', ), + inInput=dict( + argstr='--inInput %s', + extensions=None, + ), inMMC=dict(argstr='--inMMC %d', ), inMMC2=dict(argstr='--inMMC2 %d', ), inMaximum=dict(argstr='--inMaximum %f', ), @@ -95,15 +101,15 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmSPECTRE2010_outputs(): output_map = dict( - outFANTASM=dict(), - outMask=dict(), - outMidsagittal=dict(), - outOriginal=dict(), - outPrior=dict(), - outSegmentation=dict(), - outSplitHalves=dict(), - outStripped=dict(), - outd0=dict(), + outFANTASM=dict(extensions=None, ), + outMask=dict(extensions=None, ), + outMidsagittal=dict(extensions=None, ), + outOriginal=dict(extensions=None, ), + outPrior=dict(extensions=None, ), + outSegmentation=dict(extensions=None, ), + outSplitHalves=dict(extensions=None, ), + outStripped=dict(extensions=None, ), + outd0=dict(extensions=None, ), ) outputs = MedicAlgorithmSPECTRE2010.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index d3d92142c4..e97aa87285 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -37,7 +37,7 @@ def test_RandomVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RandomVol_outputs(): - output_map = dict(outRand1=dict(), ) + output_map = dict(outRand1=dict(extensions=None, ), ) outputs = RandomVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 4ced8de75a..0fe9f88276 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -35,19 +35,32 @@ def test_WatershedBEM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_WatershedBEM_outputs(): output_map = dict( - brain_surface=dict(loc='bem/watershed', ), + brain_surface=dict( + extensions=None, + loc='bem/watershed', + ), cor_files=dict( altkey='COR', loc='bem/watershed/ws', ), fif_file=dict( altkey='fif', + extensions=None, loc='bem', ), - inner_skull_surface=dict(loc='bem/watershed', ), + inner_skull_surface=dict( + extensions=None, + loc='bem/watershed', + ), mesh_files=dict(), - outer_skin_surface=dict(loc='bem/watershed', ), - outer_skull_surface=dict(loc='bem/watershed', ), + outer_skin_surface=dict( + extensions=None, + loc='bem/watershed', + ), + outer_skull_surface=dict( + extensions=None, + loc='bem/watershed', + ), ) outputs = WatershedBEM.output_spec() diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 78a275f6a7..3b5dd2f5c6 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -9,10 +9,12 @@ def test_ConstrainedSphericalDeconvolution_inputs(): debug=dict(argstr='-debug', ), directions_file=dict( argstr='-directions %s', + extensions=None, position=-2, ), encoding_file=dict( argstr='-grad %s', + extensions=None, position=1, ), environ=dict( @@ -21,10 +23,12 @@ def test_ConstrainedSphericalDeconvolution_inputs(): ), filter_file=dict( argstr='-filter %s', + extensions=None, position=-2, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -32,6 +36,7 @@ def test_ConstrainedSphericalDeconvolution_inputs(): lambda_value=dict(argstr='-lambda %s', ), mask_image=dict( argstr='-mask %s', + extensions=None, position=2, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), @@ -41,11 +46,13 @@ def test_ConstrainedSphericalDeconvolution_inputs(): ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), response_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -57,7 +64,7 @@ def test_ConstrainedSphericalDeconvolution_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConstrainedSphericalDeconvolution_outputs(): - output_map = dict(spherical_harmonics_image=dict(), ) + output_map = dict(spherical_harmonics_image=dict(extensions=None, ), ) outputs = ConstrainedSphericalDeconvolution.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index dc95cff525..6911f153ed 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -8,6 +8,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): args=dict(argstr='%s', ), encoding_file=dict( argstr='-grad %s', + extensions=None, mandatory=True, position=1, ), @@ -17,6 +18,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -27,6 +29,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -37,7 +40,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWI2SphericalHarmonicsImage_outputs(): - output_map = dict(spherical_harmonics_image=dict(), ) + output_map = dict(spherical_harmonics_image=dict(extensions=None, ), ) outputs = DWI2SphericalHarmonicsImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index 86975950bf..0844fb58f2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -12,6 +12,7 @@ def test_DWI2Tensor_inputs(): ), encoding_file=dict( argstr='-grad %s', + extensions=None, position=2, ), environ=dict( @@ -35,6 +36,7 @@ def test_DWI2Tensor_inputs(): ), out_filename=dict( argstr='%s', + extensions=None, name_source='in_file', name_template='%s_tensor.mif', output_name='tensor', @@ -51,7 +53,7 @@ def test_DWI2Tensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWI2Tensor_outputs(): - output_map = dict(tensor=dict(), ) + output_map = dict(tensor=dict(extensions=None, ), ) outputs = DWI2Tensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 2c6417fe3a..4a411a85b2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -18,6 +18,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + extensions=None, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -29,16 +30,19 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), gradient_encoding_file=dict( argstr='-grad %s', + extensions=None, mandatory=True, position=-2, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), include_file=dict( argstr='-include %s', + extensions=None, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -63,6 +67,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + extensions=None, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -88,6 +93,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): no_mask_interpolation=dict(argstr='-nomaskinterp', ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s_tracked.tck', output_name='tracked', @@ -95,6 +101,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), seed_file=dict( argstr='-seed %s', + extensions=None, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -117,7 +124,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorStreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = DiffusionTensorStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index b5474bd18c..a674b2be88 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -14,12 +14,14 @@ def test_Directions2Amplitude_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), num_peaks=dict(argstr='-num %s', ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_file'], @@ -30,7 +32,10 @@ def test_Directions2Amplitude_inputs(): argstr='-direction %s', sep=' ', ), - peaks_image=dict(argstr='-peaks %s', ), + peaks_image=dict( + argstr='-peaks %s', + extensions=None, + ), quiet_display=dict(argstr='-quiet', ), ) inputs = Directions2Amplitude.input_spec() @@ -39,7 +44,7 @@ def test_Directions2Amplitude_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Directions2Amplitude_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Directions2Amplitude.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 6215593ab0..f723a002c1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -20,12 +20,14 @@ def test_Erode_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), number_of_passes=dict(argstr='-npass %s', ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -40,7 +42,7 @@ def test_Erode_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Erode_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Erode.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index 983433104e..25f9718501 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -9,6 +9,7 @@ def test_EstimateResponseForSH_inputs(): debug=dict(argstr='-debug', ), encoding_file=dict( argstr='-grad %s', + extensions=None, mandatory=True, position=1, ), @@ -18,11 +19,13 @@ def test_EstimateResponseForSH_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), mask_image=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -30,6 +33,7 @@ def test_EstimateResponseForSH_inputs(): normalise=dict(argstr='-normalise', ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -41,7 +45,7 @@ def test_EstimateResponseForSH_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseForSH_outputs(): - output_map = dict(response=dict(), ) + output_map = dict(response=dict(extensions=None, ), ) outputs = EstimateResponseForSH.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py index 6261b6b0a5..96ce4a84f4 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py @@ -5,12 +5,21 @@ def test_FSL2MRTrix_inputs(): input_map = dict( - bval_file=dict(mandatory=True, ), - bvec_file=dict(mandatory=True, ), + bval_file=dict( + extensions=None, + mandatory=True, + ), + bvec_file=dict( + extensions=None, + mandatory=True, + ), invert_x=dict(usedefault=True, ), invert_y=dict(usedefault=True, ), invert_z=dict(usedefault=True, ), - out_encoding_file=dict(genfile=True, ), + out_encoding_file=dict( + extensions=None, + genfile=True, + ), ) inputs = FSL2MRTrix.input_spec() @@ -18,7 +27,7 @@ def test_FSL2MRTrix_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FSL2MRTrix_outputs(): - output_map = dict(encoding_file=dict(), ) + output_map = dict(encoding_file=dict(extensions=None, ), ) outputs = FSL2MRTrix.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index 6e0e670d06..182e8f79de 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -16,6 +16,7 @@ def test_FilterTracks_inputs(): ), exclude_file=dict( argstr='-exclude %s', + extensions=None, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -27,11 +28,13 @@ def test_FilterTracks_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), include_file=dict( argstr='-include %s', + extensions=None, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -49,6 +52,7 @@ def test_FilterTracks_inputs(): no_mask_interpolation=dict(argstr='-nomaskinterp', ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, name_source=['in_file'], name_template='%s_filt', @@ -65,7 +69,7 @@ def test_FilterTracks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FilterTracks_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = FilterTracks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 5d9f51739c..7bd9657d66 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -8,6 +8,7 @@ def test_FindShPeaks_inputs(): args=dict(argstr='%s', ), directions_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -19,12 +20,14 @@ def test_FindShPeaks_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), num_peaks=dict(argstr='-num %s', ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_file'], @@ -36,7 +39,10 @@ def test_FindShPeaks_inputs(): sep=' ', ), peak_threshold=dict(argstr='-threshold %s', ), - peaks_image=dict(argstr='-peaks %s', ), + peaks_image=dict( + argstr='-peaks %s', + extensions=None, + ), quiet_display=dict(argstr='-quiet', ), ) inputs = FindShPeaks.input_spec() @@ -45,7 +51,7 @@ def test_FindShPeaks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FindShPeaks_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = FindShPeaks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index 2cfd89bb6f..7449a7fcaa 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -20,6 +20,7 @@ def test_GenerateDirections_inputs(): ), out_file=dict( argstr='%s', + extensions=None, hash_files=False, name_source=['num_dirs'], name_template='directions_%d.txt', @@ -34,7 +35,7 @@ def test_GenerateDirections_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateDirections_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = GenerateDirections.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index 6a0305f9e2..98fa1d6e54 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -8,11 +8,13 @@ def test_GenerateWhiteMatterMask_inputs(): args=dict(argstr='%s', ), binary_mask=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), encoding_file=dict( argstr='-grad %s', + extensions=None, mandatory=True, position=1, ), @@ -22,12 +24,14 @@ def test_GenerateWhiteMatterMask_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), noise_level_margin=dict(argstr='-margin %s', ), out_WMProb_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -38,7 +42,7 @@ def test_GenerateWhiteMatterMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateWhiteMatterMask_outputs(): - output_map = dict(WMprobabilitymap=dict(), ) + output_map = dict(WMprobabilitymap=dict(extensions=None, ), ) outputs = GenerateWhiteMatterMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 5aef0bfd13..2dec516f43 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -25,6 +25,7 @@ def test_MRConvert_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -39,6 +40,7 @@ def test_MRConvert_inputs(): ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -71,7 +73,7 @@ def test_MRConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRConvert_outputs(): - output_map = dict(converted=dict(), ) + output_map = dict(converted=dict(extensions=None, ), ) outputs = MRConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index a5a864289a..c8446664bf 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -21,6 +21,7 @@ def test_MRMultiply_inputs(): ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -35,7 +36,7 @@ def test_MRMultiply_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRMultiply_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRMultiply.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index d6a3db0a1d..31b74cd09d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -29,6 +29,7 @@ def test_MRTransform_inputs(): ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -38,6 +39,7 @@ def test_MRTransform_inputs(): ), reference_image=dict( argstr='-reference %s', + extensions=None, position=1, ), replace_transform=dict( @@ -46,10 +48,12 @@ def test_MRTransform_inputs(): ), template_image=dict( argstr='-template %s', + extensions=None, position=1, ), transformation_file=dict( argstr='-transform %s', + extensions=None, position=1, ), ) @@ -59,7 +63,7 @@ def test_MRTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py index b6fefac9a0..9e663ee818 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py @@ -5,14 +5,18 @@ def test_MRTrix2TrackVis_inputs(): input_map = dict( - image_file=dict(), - in_file=dict(mandatory=True, ), - matrix_file=dict(), + image_file=dict(extensions=None, ), + in_file=dict( + extensions=None, + mandatory=True, + ), + matrix_file=dict(extensions=None, ), out_filename=dict( + extensions=None, genfile=True, usedefault=True, ), - registration_image_file=dict(), + registration_image_file=dict(extensions=None, ), ) inputs = MRTrix2TrackVis.input_spec() @@ -20,7 +24,7 @@ def test_MRTrix2TrackVis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRTrix2TrackVis_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRTrix2TrackVis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 0022de4d7a..05107b81bd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -12,6 +12,7 @@ def test_MRTrixInfo_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 0e7daabcaa..b4c6c2af91 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -16,11 +16,13 @@ def test_MedianFilter3D_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -35,7 +37,7 @@ def test_MedianFilter3D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianFilter3D_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MedianFilter3D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index 6d75b1b9a2..29f0a38e6d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -18,6 +18,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + extensions=None, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -29,11 +30,13 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), include_file=dict( argstr='-include %s', + extensions=None, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -58,6 +61,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + extensions=None, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -84,6 +88,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): no_mask_interpolation=dict(argstr='-nomaskinterp', ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s_tracked.tck', output_name='tracked', @@ -91,6 +96,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), seed_file=dict( argstr='-seed %s', + extensions=None, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -113,7 +119,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = ProbabilisticSphericallyDeconvolutedStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index 9bed95276d..f54aec96a7 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -18,6 +18,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + extensions=None, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -29,11 +30,13 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), include_file=dict( argstr='-include %s', + extensions=None, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -58,6 +61,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + extensions=None, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -83,6 +87,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): no_mask_interpolation=dict(argstr='-nomaskinterp', ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s_tracked.tck', output_name='tracked', @@ -90,6 +95,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), seed_file=dict( argstr='-seed %s', + extensions=None, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -112,7 +118,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SphericallyDeconvolutedStreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = SphericallyDeconvolutedStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index c898a60eb3..69f1ce65c0 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -18,6 +18,7 @@ def test_StreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + extensions=None, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -29,11 +30,13 @@ def test_StreamlineTrack_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), include_file=dict( argstr='-include %s', + extensions=None, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -58,6 +61,7 @@ def test_StreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + extensions=None, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -83,6 +87,7 @@ def test_StreamlineTrack_inputs(): no_mask_interpolation=dict(argstr='-nomaskinterp', ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s_tracked.tck', output_name='tracked', @@ -90,6 +95,7 @@ def test_StreamlineTrack_inputs(): ), seed_file=dict( argstr='-seed %s', + extensions=None, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -112,7 +118,7 @@ def test_StreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(extensions=None, ), ) outputs = StreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index e9546d7e90..dfa7f862e3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -16,11 +16,13 @@ def test_Tensor2ApparentDiffusion_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -35,7 +37,7 @@ def test_Tensor2ApparentDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2ApparentDiffusion_outputs(): - output_map = dict(ADC=dict(), ) + output_map = dict(ADC=dict(extensions=None, ), ) outputs = Tensor2ApparentDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index d16a907f62..eafdba5a7c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -16,11 +16,13 @@ def test_Tensor2FractionalAnisotropy_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -35,7 +37,7 @@ def test_Tensor2FractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2FractionalAnisotropy_outputs(): - output_map = dict(FA=dict(), ) + output_map = dict(FA=dict(extensions=None, ), ) outputs = Tensor2FractionalAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index c07d0a8db4..b982c46bbd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -16,11 +16,13 @@ def test_Tensor2Vector_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -35,7 +37,7 @@ def test_Tensor2Vector_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2Vector_outputs(): - output_map = dict(vector=dict(), ) + output_map = dict(vector=dict(extensions=None, ), ) outputs = Tensor2Vector.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index 39fbf14d2c..f53b8098eb 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -17,6 +17,7 @@ def test_Threshold_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -26,6 +27,7 @@ def test_Threshold_inputs(): ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -45,7 +47,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Threshold.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index f984203ab1..fa9eb184ef 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -20,11 +20,13 @@ def test_Tracks2Prob_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_filename=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), @@ -39,6 +41,7 @@ def test_Tracks2Prob_inputs(): ), template_file=dict( argstr='-template %s', + extensions=None, position=1, ), voxel_dims=dict( @@ -53,7 +56,7 @@ def test_Tracks2Prob_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tracks2Prob_outputs(): - output_map = dict(tract_image=dict(), ) + output_map = dict(tract_image=dict(extensions=None, ), ) outputs = Tracks2Prob.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index abb3ba6831..43f588e075 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -12,11 +12,13 @@ def test_ACTPrepareFSL_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -28,7 +30,7 @@ def test_ACTPrepareFSL_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ACTPrepareFSL_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ACTPrepareFSL.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index c318be0bfd..90c5272ed0 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -11,12 +11,19 @@ def test_BrainMask_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -26,6 +33,7 @@ def test_BrainMask_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -37,7 +45,7 @@ def test_BrainMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BrainMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BrainMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index 95e5797d06..dba96f097e 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -12,15 +12,23 @@ def test_BuildConnectome_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), in_parc=dict( argstr='%s', + extensions=None, position=-2, ), - in_scalar=dict(argstr='-image %s', ), - in_weights=dict(argstr='-tck_weights_in %s', ), + in_scalar=dict( + argstr='-image %s', + extensions=None, + ), + in_weights=dict( + argstr='-tck_weights_in %s', + extensions=None, + ), keep_unassigned=dict(argstr='-keep_unassigned', ), metric=dict(argstr='-metric %s', ), nthreads=dict( @@ -29,6 +37,7 @@ def test_BuildConnectome_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -45,7 +54,7 @@ def test_BuildConnectome_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BuildConnectome_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BuildConnectome.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index 38369e8fe5..b4eb5de3a0 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -8,7 +8,10 @@ def test_ComputeTDI_inputs(): args=dict(argstr='%s', ), contrast=dict(argstr='-constrast %s', ), data_type=dict(argstr='-datatype %s', ), - dixel=dict(argstr='-dixel %s', ), + dixel=dict( + argstr='-dixel %s', + extensions=None, + ), ends_only=dict(argstr='-ends_only', ), environ=dict( nohash=True, @@ -17,10 +20,14 @@ def test_ComputeTDI_inputs(): fwhm_tck=dict(argstr='-fwhm_tck %f', ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), - in_map=dict(argstr='-image %s', ), + in_map=dict( + argstr='-image %s', + extensions=None, + ), map_zero=dict(argstr='-map_zero', ), max_tod=dict(argstr='-tod %d', ), nthreads=dict( @@ -29,14 +36,21 @@ def test_ComputeTDI_inputs(): ), out_file=dict( argstr='%s', + extensions=None, position=-1, usedefault=True, ), precise=dict(argstr='-precise', ), - reference=dict(argstr='-template %s', ), + reference=dict( + argstr='-template %s', + extensions=None, + ), stat_tck=dict(argstr='-stat_tck %s', ), stat_vox=dict(argstr='-stat_vox %s', ), - tck_weights=dict(argstr='-tck_weights_in %s', ), + tck_weights=dict( + argstr='-tck_weights_in %s', + extensions=None, + ), upsample=dict(argstr='-upsample %d', ), use_dec=dict(argstr='-dec', ), vox_size=dict( @@ -50,7 +64,7 @@ def test_ComputeTDI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTDI_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ComputeTDI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py index ea4d3f05d8..d70545be88 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py @@ -6,7 +6,10 @@ def test_DWIBiasCorrect_inputs(): input_map = dict( args=dict(argstr='%s', ), - bias=dict(argstr='-bias %s', ), + bias=dict( + argstr='-bias %s', + extensions=None, + ), bval_scale=dict(argstr='-bvalue_scaling %s', ), environ=dict( nohash=True, @@ -14,20 +17,32 @@ def test_DWIBiasCorrect_inputs(): ), fsl_grad=dict( argstr='-fslgrad %s %s', + extensions=None, xor=('mrtrix_grad', 'fsl_grad'), ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), - in_mask=dict(argstr='-mask %s', ), + in_mask=dict( + argstr='-mask %s', + extensions=None, + ), mrtrix_grad=dict( argstr='-grad %s', + extensions=None, xor=('mrtrix_grad', 'fsl_grad'), ), nthreads=dict( @@ -36,6 +51,7 @@ def test_DWIBiasCorrect_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, keep_extension=True, name_source='in_file', @@ -60,8 +76,8 @@ def test_DWIBiasCorrect_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIBiasCorrect_outputs(): output_map = dict( - bias=dict(), - out_file=dict(), + bias=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = DWIBiasCorrect.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py index 7b6930ee82..97acf7f526 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py @@ -12,26 +12,38 @@ def test_DWIDenoise_inputs(): usedefault=True, ), extent=dict(argstr='-extent %d,%d,%d', ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), mask=dict( argstr='-mask %s', + extensions=None, position=1, ), - noise=dict(argstr='-noise %s', ), + noise=dict( + argstr='-noise %s', + extensions=None, + ), nthreads=dict( argstr='-nthreads %d', nohash=True, ), out_file=dict( argstr='%s', + extensions=None, genfile=True, keep_extension=True, name_source='in_file', @@ -46,8 +58,8 @@ def test_DWIDenoise_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIDenoise_outputs(): output_map = dict( - noise=dict(), - out_file=dict(), + noise=dict(extensions=None, ), + out_file=dict(extensions=None, ), ) outputs = DWIDenoise.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py index 0114c5efe0..7658201223 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py @@ -12,12 +12,19 @@ def test_DWIExtract_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -28,6 +35,7 @@ def test_DWIExtract_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -43,7 +51,7 @@ def test_DWIExtract_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIExtract_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = DWIExtract.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index a5c152e928..c64efa2ca4 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -14,11 +14,13 @@ def test_EstimateFOD_inputs(): bval_scale=dict(argstr='-bvalue_scaling %s', ), csf_odf=dict( argstr='%s', + extensions=None, position=-1, usedefault=True, ), csf_txt=dict( argstr='%s', + extensions=None, position=-2, ), environ=dict( @@ -27,24 +29,39 @@ def test_EstimateFOD_inputs(): ), gm_odf=dict( argstr='%s', + extensions=None, position=-3, usedefault=True, ), gm_txt=dict( argstr='%s', + extensions=None, position=-4, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), - in_dirs=dict(argstr='-directions %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), + in_dirs=dict( + argstr='-directions %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-7, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), max_sh=dict( argstr='-lmax %d', usedefault=True, @@ -59,12 +76,14 @@ def test_EstimateFOD_inputs(): ), wm_odf=dict( argstr='%s', + extensions=None, mandatory=True, position=-5, usedefault=True, ), wm_txt=dict( argstr='%s', + extensions=None, mandatory=True, position=-6, ), @@ -76,9 +95,18 @@ def test_EstimateFOD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateFOD_outputs(): output_map = dict( - csf_odf=dict(argstr='%s', ), - gm_odf=dict(argstr='%s', ), - wm_odf=dict(argstr='%s', ), + csf_odf=dict( + argstr='%s', + extensions=None, + ), + gm_odf=dict( + argstr='%s', + extensions=None, + ), + wm_odf=dict( + argstr='%s', + extensions=None, + ), ) outputs = EstimateFOD.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 85c103cc10..84404fdde6 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -11,16 +11,26 @@ def test_FitTensor_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), - in_mask=dict(argstr='-mask %s', ), + in_mask=dict( + argstr='-mask %s', + extensions=None, + ), method=dict(argstr='-method %s', ), nthreads=dict( argstr='-nthreads %d', @@ -28,6 +38,7 @@ def test_FitTensor_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -43,7 +54,7 @@ def test_FitTensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FitTensor_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = FitTensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index dcfbe1fc6f..92594da593 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -16,12 +16,19 @@ def test_Generate5tt_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -31,6 +38,7 @@ def test_Generate5tt_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -41,7 +49,7 @@ def test_Generate5tt_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Generate5tt_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Generate5tt.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index 2de0e6c115..1dc8d6e0b1 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -12,28 +12,46 @@ def test_LabelConfig_inputs(): ), in_config=dict( argstr='%s', + extensions=None, position=-2, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), - lut_aal=dict(argstr='-lut_aal %s', ), - lut_basic=dict(argstr='-lut_basic %s', ), - lut_fs=dict(argstr='-lut_freesurfer %s', ), - lut_itksnap=dict(argstr='-lut_itksnap %s', ), + lut_aal=dict( + argstr='-lut_aal %s', + extensions=None, + ), + lut_basic=dict( + argstr='-lut_basic %s', + extensions=None, + ), + lut_fs=dict( + argstr='-lut_freesurfer %s', + extensions=None, + ), + lut_itksnap=dict( + argstr='-lut_itksnap %s', + extensions=None, + ), nthreads=dict( argstr='-nthreads %d', nohash=True, ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, ), - spine=dict(argstr='-spine %s', ), + spine=dict( + argstr='-spine %s', + extensions=None, + ), ) inputs = LabelConfig.input_spec() @@ -41,7 +59,7 @@ def test_LabelConfig_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelConfig_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = LabelConfig.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py index 1e93ae82d8..82cebd8bbc 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py @@ -12,15 +12,18 @@ def test_LabelConvert_inputs(): ), in_config=dict( argstr='%s', + extensions=None, position=-2, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), in_lut=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -30,11 +33,15 @@ def test_LabelConvert_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, ), - spine=dict(argstr='-spine %s', ), + spine=dict( + argstr='-spine %s', + extensions=None, + ), ) inputs = LabelConvert.input_spec() @@ -42,7 +49,7 @@ def test_LabelConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelConvert_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = LabelConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py index ece24e1d47..9271d07517 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py @@ -19,12 +19,19 @@ def test_MRConvert_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -34,6 +41,7 @@ def test_MRConvert_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -53,7 +61,7 @@ def test_MRConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRConvert_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py index c9290b562b..e6bdd21243 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py @@ -18,12 +18,19 @@ def test_MRDeGibbs_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -45,6 +52,7 @@ def test_MRDeGibbs_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, keep_extension=True, name_source='in_file', @@ -58,7 +66,7 @@ def test_MRDeGibbs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRDeGibbs_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRDeGibbs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py index eec06b6276..ae494bb932 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py @@ -12,12 +12,19 @@ def test_MRMath_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), @@ -32,6 +39,7 @@ def test_MRMath_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), @@ -42,7 +50,7 @@ def test_MRMath_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRMath_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MRMath.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 9aa29acbe8..f2605532e6 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -12,18 +12,24 @@ def test_Mesh2PVE_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), - in_first=dict(argstr='-first %s', ), + in_first=dict( + argstr='-first %s', + extensions=None, + ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, ), reference=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -34,7 +40,7 @@ def test_Mesh2PVE_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Mesh2PVE_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Mesh2PVE.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index 502a0f7fb1..561a1a9538 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -12,20 +12,24 @@ def test_ReplaceFSwithFIRST_inputs(): ), in_config=dict( argstr='%s', + extensions=None, position=-2, ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-4, ), in_t1w=dict( argstr='%s', + extensions=None, mandatory=True, position=-3, ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, @@ -37,7 +41,7 @@ def test_ReplaceFSwithFIRST_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ReplaceFSwithFIRST_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ReplaceFSwithFIRST.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index f4b4660d78..dd326bad5b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -14,6 +14,7 @@ def test_ResponseSD_inputs(): bval_scale=dict(argstr='-bvalue_scaling %s', ), csf_file=dict( argstr='%s', + extensions=None, position=-1, ), environ=dict( @@ -22,24 +23,36 @@ def test_ResponseSD_inputs(): ), gm_file=dict( argstr='%s', + extensions=None, position=-2, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-5, ), - in_mask=dict(argstr='-mask %s', ), + in_mask=dict( + argstr='-mask %s', + extensions=None, + ), max_sh=dict( argstr='-lmax %s', sep=',', ), mtt_file=dict( argstr='%s', + extensions=None, position=-4, ), nthreads=dict( @@ -48,6 +61,7 @@ def test_ResponseSD_inputs(): ), wm_file=dict( argstr='%s', + extensions=None, position=-3, usedefault=True, ), @@ -59,9 +73,18 @@ def test_ResponseSD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ResponseSD_outputs(): output_map = dict( - csf_file=dict(argstr='%s', ), - gm_file=dict(argstr='%s', ), - wm_file=dict(argstr='%s', ), + csf_file=dict( + argstr='%s', + extensions=None, + ), + gm_file=dict( + argstr='%s', + extensions=None, + ), + wm_file=dict( + argstr='%s', + extensions=None, + ), ) outputs = ResponseSD.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index 93a39484f8..064e15288e 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -12,6 +12,7 @@ def test_TCK2VTK_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -21,11 +22,18 @@ def test_TCK2VTK_inputs(): ), out_file=dict( argstr='%s', + extensions=None, position=-1, usedefault=True, ), - reference=dict(argstr='-image %s', ), - voxel=dict(argstr='-image %s', ), + reference=dict( + argstr='-image %s', + extensions=None, + ), + voxel=dict( + argstr='-image %s', + extensions=None, + ), ) inputs = TCK2VTK.input_spec() @@ -33,7 +41,7 @@ def test_TCK2VTK_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCK2VTK_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TCK2VTK.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index ae532c9910..b6bc738109 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -17,15 +17,31 @@ def test_TensorMetrics_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, ), - in_mask=dict(argstr='-mask %s', ), + in_mask=dict( + argstr='-mask %s', + extensions=None, + ), modulate=dict(argstr='-modulate %s', ), - out_adc=dict(argstr='-adc %s', ), - out_eval=dict(argstr='-value %s', ), - out_evec=dict(argstr='-vector %s', ), - out_fa=dict(argstr='-fa %s', ), + out_adc=dict( + argstr='-adc %s', + extensions=None, + ), + out_eval=dict( + argstr='-value %s', + extensions=None, + ), + out_evec=dict( + argstr='-vector %s', + extensions=None, + ), + out_fa=dict( + argstr='-fa %s', + extensions=None, + ), ) inputs = TensorMetrics.input_spec() @@ -34,10 +50,10 @@ def test_TensorMetrics_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TensorMetrics_outputs(): output_map = dict( - out_adc=dict(), - out_eval=dict(), - out_evec=dict(), - out_fa=dict(), + out_adc=dict(extensions=None, ), + out_eval=dict(extensions=None, ), + out_evec=dict(extensions=None, ), + out_fa=dict(extensions=None, ), ) outputs = TensorMetrics.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index c79fce8867..39f239b81d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -5,7 +5,10 @@ def test_Tractography_inputs(): input_map = dict( - act_file=dict(argstr='-act %s', ), + act_file=dict( + argstr='-act %s', + extensions=None, + ), algorithm=dict( argstr='-algorithm %s', usedefault=True, @@ -22,12 +25,19 @@ def test_Tractography_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + extensions=None, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(extensions=None, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + extensions=None, + ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-2, ), @@ -52,29 +62,41 @@ def test_Tractography_inputs(): ), out_file=dict( argstr='%s', + extensions=None, mandatory=True, position=-1, usedefault=True, ), out_seeds=dict( argstr='-output_seeds %s', + extensions=None, usedefault=True, ), power=dict(argstr='-power %d', ), roi_excl=dict(argstr='-exclude %s', ), roi_incl=dict(argstr='-include %s', ), roi_mask=dict(argstr='-mask %s', ), - seed_dynamic=dict(argstr='-seed_dynamic %s', ), + seed_dynamic=dict( + argstr='-seed_dynamic %s', + extensions=None, + ), seed_gmwmi=dict( argstr='-seed_gmwmi %s', + extensions=None, requires=['act_file'], ), seed_grid_voxel=dict( argstr='-seed_grid_per_voxel %s %d', xor=['seed_image', 'seed_rnd_voxel'], ), - seed_image=dict(argstr='-seed_image %s', ), - seed_rejection=dict(argstr='-seed_rejection %s', ), + seed_image=dict( + argstr='-seed_image %s', + extensions=None, + ), + seed_rejection=dict( + argstr='-seed_rejection %s', + extensions=None, + ), seed_rnd_voxel=dict( argstr='-seed_random_per_voxel %s %d', xor=['seed_image', 'seed_grid_voxel'], @@ -97,8 +119,8 @@ def test_Tractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Tractography_outputs(): output_map = dict( - out_file=dict(), - out_seeds=dict(), + out_file=dict(extensions=None, ), + out_seeds=dict(extensions=None, ), ) outputs = Tractography.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index 0505ee514c..392654fd5c 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -10,6 +10,7 @@ def test_FitQt1_inputs(): b1map=dict(argstr='-b1map %s', ), comp_file=dict( argstr='-comp %s', + extensions=None, name_source=['source_file'], name_template='%s_comp.nii.gz', ), @@ -19,6 +20,7 @@ def test_FitQt1_inputs(): ), error_file=dict( argstr='-error %s', + extensions=None, name_source=['source_file'], name_template='%s_error.nii.gz', ), @@ -41,11 +43,13 @@ def test_FitQt1_inputs(): ), m0map_file=dict( argstr='-m0map %s', + extensions=None, name_source=['source_file'], name_template='%s_m0map.nii.gz', ), mask=dict( argstr='-mask %s', + extensions=None, position=2, ), maxit=dict( @@ -54,6 +58,7 @@ def test_FitQt1_inputs(): ), mcmap_file=dict( argstr='-mcmap %s', + extensions=None, name_source=['source_file'], name_template='%s_mcmap.nii.gz', ), @@ -66,10 +71,12 @@ def test_FitQt1_inputs(): ), prior=dict( argstr='-prior %s', + extensions=None, position=3, ), res_file=dict( argstr='-res %s', + extensions=None, name_source=['source_file'], name_template='%s_res.nii.gz', ), @@ -79,6 +86,7 @@ def test_FitQt1_inputs(): ), source_file=dict( argstr='-source %s', + extensions=None, mandatory=True, position=1, ), @@ -89,12 +97,14 @@ def test_FitQt1_inputs(): ), syn_file=dict( argstr='-syn %s', + extensions=None, name_source=['source_file'], name_template='%s_syn.nii.gz', ), t1_list=dict(argstr='-T1list %s', ), t1map_file=dict( argstr='-t1map %s', + extensions=None, name_source=['source_file'], name_template='%s_t1map.nii.gz', ), @@ -126,13 +136,13 @@ def test_FitQt1_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitQt1_outputs(): output_map = dict( - comp_file=dict(), - error_file=dict(), - m0map_file=dict(), - mcmap_file=dict(), - res_file=dict(), - syn_file=dict(), - t1map_file=dict(), + comp_file=dict(extensions=None, ), + error_file=dict(extensions=None, ), + m0map_file=dict(extensions=None, ), + mcmap_file=dict(extensions=None, ), + res_file=dict(extensions=None, ), + syn_file=dict(extensions=None, ), + t1map_file=dict(extensions=None, ), ) outputs = FitQt1.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py index 9507f53fa9..436fbb9b29 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py @@ -8,6 +8,7 @@ def test_RegAladin_inputs(): aff_direct_flag=dict(argstr='-affDirect', ), aff_file=dict( argstr='-aff %s', + extensions=None, name_source=['flo_file'], name_template='%s_aff.txt', ), @@ -19,14 +20,21 @@ def test_RegAladin_inputs(): ), flo_file=dict( argstr='-flo %s', + extensions=None, mandatory=True, ), flo_low_val=dict(argstr='-floLowThr %f', ), flo_up_val=dict(argstr='-floUpThr %f', ), - fmask_file=dict(argstr='-fmask %s', ), + fmask_file=dict( + argstr='-fmask %s', + extensions=None, + ), gpuid_val=dict(argstr='-gpuid %i', ), i_val=dict(argstr='-pi %d', ), - in_aff_file=dict(argstr='-inaff %s', ), + in_aff_file=dict( + argstr='-inaff %s', + extensions=None, + ), ln_val=dict(argstr='-ln %d', ), lp_val=dict(argstr='-lp %d', ), maxit_val=dict(argstr='-maxit %d', ), @@ -39,17 +47,22 @@ def test_RegAladin_inputs(): platform_val=dict(argstr='-platf %i', ), ref_file=dict( argstr='-ref %s', + extensions=None, mandatory=True, ), ref_low_val=dict(argstr='-refLowThr %f', ), ref_up_val=dict(argstr='-refUpThr %f', ), res_file=dict( argstr='-res %s', + extensions=None, name_source=['flo_file'], name_template='%s_res.nii.gz', ), rig_only_flag=dict(argstr='-rigOnly', ), - rmask_file=dict(argstr='-rmask %s', ), + rmask_file=dict( + argstr='-rmask %s', + extensions=None, + ), smoo_f_val=dict(argstr='-smooF %f', ), smoo_r_val=dict(argstr='-smooR %f', ), v_val=dict(argstr='-pv %d', ), @@ -62,9 +75,9 @@ def test_RegAladin_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RegAladin_outputs(): output_map = dict( - aff_file=dict(), + aff_file=dict(extensions=None, ), avg_output=dict(), - res_file=dict(), + res_file=dict(extensions=None, ), ) outputs = RegAladin.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py index 2510a46eb8..b0a39752cf 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py @@ -26,6 +26,7 @@ def test_RegAverage_inputs(): ), avg_ref_file=dict( argstr='-avg_tran %s', + extensions=None, position=1, requires=['warp_files'], xor=[ @@ -35,6 +36,7 @@ def test_RegAverage_inputs(): ), demean1_ref_file=dict( argstr='-demean1 %s', + extensions=None, position=1, requires=['warp_files'], xor=[ @@ -44,6 +46,7 @@ def test_RegAverage_inputs(): ), demean2_ref_file=dict( argstr='-demean2 %s', + extensions=None, position=1, requires=['warp_files'], xor=[ @@ -53,6 +56,7 @@ def test_RegAverage_inputs(): ), demean3_ref_file=dict( argstr='-demean3 %s', + extensions=None, position=1, requires=['warp_files'], xor=[ @@ -70,6 +74,7 @@ def test_RegAverage_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, position=0, ), @@ -86,7 +91,7 @@ def test_RegAverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegAverage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RegAverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py index e9bdab82c0..7d1fb8d27c 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py @@ -5,12 +5,16 @@ def test_RegF3D_inputs(): input_map = dict( - aff_file=dict(argstr='-aff %s', ), + aff_file=dict( + argstr='-aff %s', + extensions=None, + ), amc_flag=dict(argstr='-amc', ), args=dict(argstr='%s', ), be_val=dict(argstr='-be %f', ), cpp_file=dict( argstr='-cpp %s', + extensions=None, name_source=['flo_file'], name_template='%s_cpp.nii.gz', ), @@ -22,15 +26,22 @@ def test_RegF3D_inputs(): fbn_val=dict(argstr='--fbn %d', ), flo_file=dict( argstr='-flo %s', + extensions=None, mandatory=True, ), flo_smooth_val=dict(argstr='-smooF %f', ), flwth2_thr_val=dict(argstr='-fLwTh %d %f', ), flwth_thr_val=dict(argstr='--fLwTh %f', ), - fmask_file=dict(argstr='-fmask %s', ), + fmask_file=dict( + argstr='-fmask %s', + extensions=None, + ), fupth2_thr_val=dict(argstr='-fUpTh %d %f', ), fupth_thr_val=dict(argstr='--fUpTh %f', ), - incpp_file=dict(argstr='-incpp %s', ), + incpp_file=dict( + argstr='-incpp %s', + extensions=None, + ), jl_val=dict(argstr='-jl %f', ), kld2_flag=dict(argstr='-kld %d', ), kld_flag=dict(argstr='--kld', ), @@ -57,17 +68,22 @@ def test_RegF3D_inputs(): rbn_val=dict(argstr='--rbn %d', ), ref_file=dict( argstr='-ref %s', + extensions=None, mandatory=True, ), ref_smooth_val=dict(argstr='-smooR %f', ), res_file=dict( argstr='-res %s', + extensions=None, name_source=['flo_file'], name_template='%s_res.nii.gz', ), rlwth2_thr_val=dict(argstr='-rLwTh %d %f', ), rlwth_thr_val=dict(argstr='--rLwTh %f', ), - rmask_file=dict(argstr='-rmask %s', ), + rmask_file=dict( + argstr='-rmask %s', + extensions=None, + ), rupth2_thr_val=dict(argstr='-rUpTh %d %f', ), rupth_thr_val=dict(argstr='--rUpTh %f', ), smooth_grad_val=dict(argstr='-smoothGrad %f', ), @@ -87,10 +103,10 @@ def test_RegF3D_inputs(): def test_RegF3D_outputs(): output_map = dict( avg_output=dict(), - cpp_file=dict(), - invcpp_file=dict(), - invres_file=dict(), - res_file=dict(), + cpp_file=dict(extensions=None, ), + invcpp_file=dict(extensions=None, ), + invres_file=dict(extensions=None, ), + res_file=dict(extensions=None, ), ) outputs = RegF3D.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py index 63f917c683..38615d8edd 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py @@ -16,13 +16,18 @@ def test_RegJacobian_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source=['trans_file'], name_template='%s', position=-1, ), - ref_file=dict(argstr='-ref %s', ), + ref_file=dict( + argstr='-ref %s', + extensions=None, + ), trans_file=dict( argstr='-trans %s', + extensions=None, mandatory=True, ), type=dict( @@ -37,7 +42,7 @@ def test_RegJacobian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegJacobian_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RegJacobian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py index 3321d87afc..4f30029e2f 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py @@ -12,6 +12,7 @@ def test_RegMeasure_inputs(): ), flo_file=dict( argstr='-flo %s', + extensions=None, mandatory=True, ), measure_type=dict( @@ -24,11 +25,13 @@ def test_RegMeasure_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, name_source=['flo_file'], name_template='%s', ), ref_file=dict( argstr='-ref %s', + extensions=None, mandatory=True, ), ) @@ -38,7 +41,7 @@ def test_RegMeasure_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegMeasure_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RegMeasure.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py index 06b2b48401..80e4241ec7 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py @@ -12,6 +12,7 @@ def test_RegResample_inputs(): ), flo_file=dict( argstr='-flo %s', + extensions=None, mandatory=True, ), inter_val=dict(argstr='-inter %d', ), @@ -21,6 +22,7 @@ def test_RegResample_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source=['flo_file'], name_template='%s', position=-1, @@ -30,10 +32,14 @@ def test_RegResample_inputs(): psf_flag=dict(argstr='-psf', ), ref_file=dict( argstr='-ref %s', + extensions=None, mandatory=True, ), tensor_flag=dict(argstr='-tensor ', ), - trans_file=dict(argstr='-trans %s', ), + trans_file=dict( + argstr='-trans %s', + extensions=None, + ), type=dict( argstr='-%s', position=-2, @@ -47,7 +53,7 @@ def test_RegResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegResample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RegResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py index 5deb4206e6..c1d1f65542 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py @@ -17,11 +17,15 @@ def test_RegTools_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, ), inter_val=dict(argstr='-interp %d', ), iso_flag=dict(argstr='-iso', ), - mask_file=dict(argstr='-nan %s', ), + mask_file=dict( + argstr='-nan %s', + extensions=None, + ), mul_val=dict(argstr='-mul %s', ), noscl_flag=dict(argstr='-noscl', ), omp_core_val=dict( @@ -30,10 +34,14 @@ def test_RegTools_inputs(): ), out_file=dict( argstr='-out %s', + extensions=None, name_source=['in_file'], name_template='%s_tools.nii.gz', ), - rms_val=dict(argstr='-rms %s', ), + rms_val=dict( + argstr='-rms %s', + extensions=None, + ), smo_g_val=dict(argstr='-smoG %f %f %f', ), smo_s_val=dict(argstr='-smoS %f %f %f', ), sub_val=dict(argstr='-sub %s', ), @@ -45,7 +53,7 @@ def test_RegTools_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegTools_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RegTools.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py index 57c1b0ad86..50f666a1df 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py @@ -7,6 +7,7 @@ def test_RegTransform_inputs(): input_map = dict( aff_2_rig_input=dict( argstr='-aff2rig %s', + extensions=None, position=-2, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', @@ -17,6 +18,7 @@ def test_RegTransform_inputs(): args=dict(argstr='%s', ), comp_input=dict( argstr='-comp %s', + extensions=None, position=-3, requires=['comp_input2'], xor=[ @@ -27,10 +29,12 @@ def test_RegTransform_inputs(): ), comp_input2=dict( argstr='%s', + extensions=None, position=-2, ), def_input=dict( argstr='-def %s', + extensions=None, position=-2, xor=[ 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', @@ -40,6 +44,7 @@ def test_RegTransform_inputs(): ), disp_input=dict( argstr='-disp %s', + extensions=None, position=-2, xor=[ 'def_input', 'flow_input', 'comp_input', 'upd_s_form_input', @@ -62,6 +67,7 @@ def test_RegTransform_inputs(): ), flow_input=dict( argstr='-flow %s', + extensions=None, position=-2, xor=[ 'def_input', 'disp_input', 'comp_input', 'upd_s_form_input', @@ -71,6 +77,7 @@ def test_RegTransform_inputs(): ), half_input=dict( argstr='-half %s', + extensions=None, position=-2, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', @@ -80,6 +87,7 @@ def test_RegTransform_inputs(): ), inv_aff_input=dict( argstr='-invAff %s', + extensions=None, position=-2, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', @@ -111,20 +119,24 @@ def test_RegTransform_inputs(): ), out_file=dict( argstr='%s', + extensions=None, genfile=True, position=-1, ), ref1_file=dict( argstr='-ref %s', + extensions=None, position=0, ), ref2_file=dict( argstr='-ref2 %s', + extensions=None, position=1, requires=['ref1_file'], ), upd_s_form_input=dict( argstr='-updSform %s', + extensions=None, position=-3, requires=['upd_s_form_input2'], xor=[ @@ -135,6 +147,7 @@ def test_RegTransform_inputs(): ), upd_s_form_input2=dict( argstr='%s', + extensions=None, position=-2, requires=['upd_s_form_input'], ), @@ -145,7 +158,7 @@ def test_RegTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = RegTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py index cc7bc896c6..657ceddf4d 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py @@ -12,11 +12,13 @@ def test_BinaryMaths_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), operand_file=dict( argstr='%s', + extensions=None, mandatory=True, position=5, xor=['operand_value', 'operand_str'], @@ -40,6 +42,7 @@ def test_BinaryMaths_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s', position=-2, @@ -55,7 +58,7 @@ def test_BinaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BinaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py index 464ed6f6c4..94ad3be1a4 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py @@ -12,6 +12,7 @@ def test_BinaryMathsInteger_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -27,6 +28,7 @@ def test_BinaryMathsInteger_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s', position=-2, @@ -42,7 +44,7 @@ def test_BinaryMathsInteger_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMathsInteger_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = BinaryMathsInteger.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py index 0771d72f5c..092ccce73a 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py @@ -12,6 +12,7 @@ def test_BinaryStats_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -21,10 +22,12 @@ def test_BinaryStats_inputs(): ), mask_file=dict( argstr='-m %s', + extensions=None, position=-2, ), operand_file=dict( argstr='%s', + extensions=None, mandatory=True, position=5, xor=['operand_value'], diff --git a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py index dceea837c0..d9dd712482 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py @@ -12,6 +12,7 @@ def test_CalcTopNCC_inputs(): ), in_file=dict( argstr='-target %s', + extensions=None, mandatory=True, position=1, ), @@ -20,7 +21,10 @@ def test_CalcTopNCC_inputs(): mandatory=True, position=3, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), num_templates=dict( argstr='-templates %s', mandatory=True, diff --git a/nipype/interfaces/niftyseg/tests/test_auto_EM.py b/nipype/interfaces/niftyseg/tests/test_auto_EM.py index fc270ed22f..1fc798c2ec 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_EM.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_EM.py @@ -20,10 +20,14 @@ def test_EM_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, position=4, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), max_iter=dict( argstr='-max_iter %s', usedefault=True, @@ -40,22 +44,26 @@ def test_EM_inputs(): ), out_bc_file=dict( argstr='-bc_out %s', + extensions=None, name_source=['in_file'], name_template='%s_bc_em.nii.gz', ), out_file=dict( argstr='-out %s', + extensions=None, name_source=['in_file'], name_template='%s_em.nii.gz', ), out_outlier_file=dict( argstr='-out_outlier %s', + extensions=None, name_source=['in_file'], name_template='%s_outlier_em.nii.gz', ), outlier_val=dict(argstr='-outlier %s %s', ), prior_4D=dict( argstr='-prior4D %s', + extensions=None, mandatory=True, xor=['no_prior', 'priors'], ), @@ -74,9 +82,9 @@ def test_EM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EM_outputs(): output_map = dict( - out_bc_file=dict(), - out_file=dict(), - out_outlier_file=dict(), + out_bc_file=dict(extensions=None, ), + out_file=dict(extensions=None, ), + out_outlier_file=dict(extensions=None, ), ) outputs = EM.output_spec() diff --git a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py index 7cbfe58c6c..d798046995 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py @@ -6,7 +6,10 @@ def test_FillLesions_inputs(): input_map = dict( args=dict(argstr='%s', ), - bin_mask=dict(argstr='-mask %s', ), + bin_mask=dict( + argstr='-mask %s', + extensions=None, + ), cwf=dict(argstr='-cwf %f', ), debug=dict(argstr='-debug', ), environ=dict( @@ -16,11 +19,13 @@ def test_FillLesions_inputs(): in_dilation=dict(argstr='-dil %d', ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=1, ), lesion_mask=dict( argstr='-l %s', + extensions=None, mandatory=True, position=2, ), @@ -29,6 +34,7 @@ def test_FillLesions_inputs(): out_datatype=dict(argstr='-odt %s', ), out_file=dict( argstr='-o %s', + extensions=None, name_source=['in_file'], name_template='%s_lesions_filled.nii.gz', position=3, @@ -45,7 +51,7 @@ def test_FillLesions_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FillLesions_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = FillLesions.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py index eea345e1df..f3613f6130 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py @@ -17,18 +17,26 @@ def test_LabelFusion_inputs(): nohash=True, usedefault=True, ), - file_to_seg=dict(mandatory=True, ), + file_to_seg=dict( + extensions=None, + mandatory=True, + ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, position=1, ), kernel_size=dict(), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + extensions=None, + ), max_iter=dict(argstr='-max_iter %d', ), mrf_value=dict(argstr='-MRF_beta %f', ), out_file=dict( argstr='-out %s', + extensions=None, name_source=['in_file'], name_template='%s', ), @@ -41,7 +49,7 @@ def test_LabelFusion_inputs(): position=3, usedefault=True, ), - template_file=dict(), + template_file=dict(extensions=None, ), template_num=dict(), unc=dict(argstr='-unc', ), unc_thresh=dict(argstr='-uncthres %f', ), @@ -53,7 +61,7 @@ def test_LabelFusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelFusion_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = LabelFusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py index 247dc9773e..f93739d102 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py @@ -12,11 +12,13 @@ def test_MathsCommand_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s', position=-2, @@ -32,7 +34,7 @@ def test_MathsCommand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MathsCommand_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MathsCommand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py index c53e4edf40..714a8f87b4 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py @@ -13,6 +13,7 @@ def test_Merge_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -23,6 +24,7 @@ def test_Merge_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s', position=-2, @@ -38,7 +40,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py index bfeded6eef..e88270d650 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py @@ -9,6 +9,7 @@ def test_PatchMatch_inputs(): cs_size=dict(argstr='-cs %i', ), database_file=dict( argstr='-db %s', + extensions=None, mandatory=True, position=3, ), @@ -18,18 +19,21 @@ def test_PatchMatch_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, position=1, ), it_num=dict(argstr='-it %i', ), mask_file=dict( argstr='-m %s', + extensions=None, mandatory=True, position=2, ), match_num=dict(argstr='-match %i', ), out_file=dict( argstr='-o %s', + extensions=None, name_source=['in_file'], name_template='%s_pm.nii.gz', position=4, @@ -43,7 +47,7 @@ def test_PatchMatch_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PatchMatch_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = PatchMatch.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py index e845e18952..9ce93ab93a 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py @@ -12,6 +12,7 @@ def test_StatsCommand_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -21,6 +22,7 @@ def test_StatsCommand_inputs(): ), mask_file=dict( argstr='-m %s', + extensions=None, position=-2, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py index 7241264eee..75177ab0e0 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py @@ -12,17 +12,20 @@ def test_TupleMaths_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), operand_file1=dict( argstr='%s', + extensions=None, mandatory=True, position=5, xor=['operand_value1'], ), operand_file2=dict( argstr='%s', + extensions=None, mandatory=True, position=6, xor=['operand_value2'], @@ -46,6 +49,7 @@ def test_TupleMaths_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s', position=-2, @@ -61,7 +65,7 @@ def test_TupleMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TupleMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = TupleMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py index 9b1cd7d194..0cd68ca4ee 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py @@ -12,6 +12,7 @@ def test_UnaryMaths_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -22,6 +23,7 @@ def test_UnaryMaths_inputs(): ), out_file=dict( argstr='%s', + extensions=None, name_source=['in_file'], name_template='%s', position=-2, @@ -37,7 +39,7 @@ def test_UnaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = UnaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py index 34edf1a190..3f158fac20 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py @@ -12,6 +12,7 @@ def test_UnaryStats_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), @@ -21,6 +22,7 @@ def test_UnaryStats_inputs(): ), mask_file=dict( argstr='-m %s', + extensions=None, position=-2, ), operation=dict( diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index f0f2453274..84e74e969c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -8,8 +8,11 @@ def test_ComputeMask_inputs(): M=dict(), cc=dict(), m=dict(), - mean_volume=dict(mandatory=True, ), - reference_volume=dict(), + mean_volume=dict( + extensions=None, + mandatory=True, + ), + reference_volume=dict(extensions=None, ), ) inputs = ComputeMask.input_spec() @@ -17,7 +20,7 @@ def test_ComputeMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMask_outputs(): - output_map = dict(brain_mask=dict(), ) + output_map = dict(brain_mask=dict(extensions=None, ), ) outputs = ComputeMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 383d1cbea3..3fe17160db 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -6,14 +6,20 @@ def test_EstimateContrast_inputs(): input_map = dict( axis=dict(mandatory=True, ), - beta=dict(mandatory=True, ), + beta=dict( + extensions=None, + mandatory=True, + ), constants=dict(mandatory=True, ), contrasts=dict(mandatory=True, ), dof=dict(mandatory=True, ), mask=dict(), nvbeta=dict(mandatory=True, ), reg_names=dict(mandatory=True, ), - s2=dict(mandatory=True, ), + s2=dict( + extensions=None, + mandatory=True, + ), ) inputs = EstimateContrast.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 4ac3aa720e..a700c18d43 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -23,15 +23,15 @@ def test_FitGLM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitGLM_outputs(): output_map = dict( - a=dict(), + a=dict(extensions=None, ), axis=dict(), - beta=dict(), + beta=dict(extensions=None, ), constants=dict(), dof=dict(), nvbeta=dict(), reg_names=dict(), residuals=dict(), - s2=dict(), + s2=dict(extensions=None, ), ) outputs = FitGLM.output_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index fbdb6fffa6..09a466b8a3 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -5,11 +5,17 @@ def test_Similarity_inputs(): input_map = dict( - mask1=dict(), - mask2=dict(), + mask1=dict(extensions=None, ), + mask2=dict(extensions=None, ), metric=dict(usedefault=True, ), - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + extensions=None, + mandatory=True, + ), + volume2=dict( + extensions=None, + mandatory=True, + ), ) inputs = Similarity.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index 6073c9082b..1e013f2063 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -7,8 +7,11 @@ def test_Trim_inputs(): input_map = dict( begin_index=dict(usedefault=True, ), end_index=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - out_file=dict(), + in_file=dict( + extensions=None, + mandatory=True, + ), + out_file=dict(extensions=None, ), suffix=dict(usedefault=True, ), ) inputs = Trim.input_spec() @@ -17,7 +20,7 @@ def test_Trim_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Trim_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Trim.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 4a641ebb50..a9f1ca8769 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -10,10 +10,13 @@ def test_CoherenceAnalyzer_inputs(): figure_type=dict(usedefault=True, ), frequency_range=dict(usedefault=True, ), in_TS=dict(), - in_file=dict(requires=('TR', ), ), + in_file=dict( + extensions=None, + requires=('TR', ), + ), n_overlap=dict(usedefault=True, ), - output_csv_file=dict(), - output_figure_file=dict(), + output_csv_file=dict(extensions=None, ), + output_figure_file=dict(extensions=None, ), ) inputs = CoherenceAnalyzer.input_spec() @@ -23,11 +26,11 @@ def test_CoherenceAnalyzer_inputs(): def test_CoherenceAnalyzer_outputs(): output_map = dict( coherence_array=dict(), - coherence_csv=dict(), - coherence_fig=dict(), + coherence_csv=dict(extensions=None, ), + coherence_fig=dict(extensions=None, ), timedelay_array=dict(), - timedelay_csv=dict(), - timedelay_fig=dict(), + timedelay_csv=dict(extensions=None, ), + timedelay_fig=dict(extensions=None, ), ) outputs = CoherenceAnalyzer.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 81a22bfe38..88efbd6ed2 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -10,13 +10,34 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): nohash=True, usedefault=True, ), - inputBasalGmVolume=dict(argstr='--inputBasalGmVolume %s', ), - inputCrblGmVolume=dict(argstr='--inputCrblGmVolume %s', ), - inputCrblWmVolume=dict(argstr='--inputCrblWmVolume %s', ), - inputCsfVolume=dict(argstr='--inputCsfVolume %s', ), - inputSurfaceGmVolume=dict(argstr='--inputSurfaceGmVolume %s', ), - inputVbVolume=dict(argstr='--inputVbVolume %s', ), - inputWhiteVolume=dict(argstr='--inputWhiteVolume %s', ), + inputBasalGmVolume=dict( + argstr='--inputBasalGmVolume %s', + extensions=None, + ), + inputCrblGmVolume=dict( + argstr='--inputCrblGmVolume %s', + extensions=None, + ), + inputCrblWmVolume=dict( + argstr='--inputCrblWmVolume %s', + extensions=None, + ), + inputCsfVolume=dict( + argstr='--inputCsfVolume %s', + extensions=None, + ), + inputSurfaceGmVolume=dict( + argstr='--inputSurfaceGmVolume %s', + extensions=None, + ), + inputVbVolume=dict( + argstr='--inputVbVolume %s', + extensions=None, + ), + inputWhiteVolume=dict( + argstr='--inputWhiteVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -28,7 +49,7 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSPosteriorToContinuousClass_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSPosteriorToContinuousClass.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index ac589ad6dc..8161cd4fad 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -30,7 +30,10 @@ def test_BRAINSTalairach_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputBox=dict( argstr='--outputBox %s', hash_files=False, @@ -47,8 +50,8 @@ def test_BRAINSTalairach_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairach_outputs(): output_map = dict( - outputBox=dict(), - outputGrid=dict(), + outputBox=dict(extensions=None, ), + outputGrid=dict(extensions=None, ), ) outputs = BRAINSTalairach.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index 5ada1576e7..19fd531a7e 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -12,13 +12,22 @@ def test_BRAINSTalairachMask_inputs(): ), expand=dict(argstr='--expand ', ), hemisphereMode=dict(argstr='--hemisphereMode %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, ), - talairachBox=dict(argstr='--talairachBox %s', ), - talairachParameters=dict(argstr='--talairachParameters %s', ), + talairachBox=dict( + argstr='--talairachBox %s', + extensions=None, + ), + talairachParameters=dict( + argstr='--talairachParameters %s', + extensions=None, + ), ) inputs = BRAINSTalairachMask.input_spec() @@ -26,7 +35,7 @@ def test_BRAINSTalairachMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairachMask_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSTalairachMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py index eb4bdcffae..a9e12c5584 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py @@ -11,7 +11,10 @@ def test_GenerateEdgeMapImage_inputs(): usedefault=True, ), inputMRVolumes=dict(argstr='--inputMRVolumes %s...', ), - inputMask=dict(argstr='--inputMask %s', ), + inputMask=dict( + argstr='--inputMask %s', + extensions=None, + ), lowerPercentileMatching=dict(argstr='--lowerPercentileMatching %f', ), maximumOutputRange=dict(argstr='--maximumOutputRange %d', ), minimumOutputRange=dict(argstr='--minimumOutputRange %d', ), @@ -33,8 +36,8 @@ def test_GenerateEdgeMapImage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateEdgeMapImage_outputs(): output_map = dict( - outputEdgeMap=dict(), - outputMaximumGradientImage=dict(), + outputEdgeMap=dict(extensions=None, ), + outputMaximumGradientImage=dict(extensions=None, ), ) outputs = GenerateEdgeMapImage.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py index ae16bc8fab..5728b575a3 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py @@ -27,7 +27,7 @@ def test_GeneratePurePlugMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GeneratePurePlugMask_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(extensions=None, ), ) outputs = GeneratePurePlugMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index 1377072149..0f4fbd5a18 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -11,16 +11,28 @@ def test_HistogramMatchingFilter_inputs(): usedefault=True, ), histogramAlgorithm=dict(argstr='--histogramAlgorithm %s', ), - inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputBinaryVolume=dict( + argstr='--inputBinaryVolume %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, ), - referenceBinaryVolume=dict(argstr='--referenceBinaryVolume %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), + referenceBinaryVolume=dict( + argstr='--referenceBinaryVolume %s', + extensions=None, + ), + referenceVolume=dict( + argstr='--referenceVolume %s', + extensions=None, + ), verbose=dict(argstr='--verbose ', ), writeHistogram=dict(argstr='--writeHistogram %s', ), ) @@ -30,7 +42,7 @@ def test_HistogramMatchingFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatchingFilter_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = HistogramMatchingFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index 534488ad10..f66caff4f6 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -5,14 +5,23 @@ def test_SimilarityIndex_inputs(): input_map = dict( - ANNContinuousVolume=dict(argstr='--ANNContinuousVolume %s', ), + ANNContinuousVolume=dict( + argstr='--ANNContinuousVolume %s', + extensions=None, + ), args=dict(argstr='%s', ), environ=dict( nohash=True, usedefault=True, ), - inputManualVolume=dict(argstr='--inputManualVolume %s', ), - outputCSVFilename=dict(argstr='--outputCSVFilename %s', ), + inputManualVolume=dict( + argstr='--inputManualVolume %s', + extensions=None, + ), + outputCSVFilename=dict( + argstr='--outputCSVFilename %s', + extensions=None, + ), thresholdInterval=dict(argstr='--thresholdInterval %f', ), ) inputs = SimilarityIndex.input_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index 05593527fb..734363402a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -13,15 +13,27 @@ def test_DWIConvert_inputs(): usedefault=True, ), fMRI=dict(argstr='--fMRI ', ), - fslNIFTIFile=dict(argstr='--fslNIFTIFile %s', ), + fslNIFTIFile=dict( + argstr='--fslNIFTIFile %s', + extensions=None, + ), gradientVectorFile=dict( argstr='--gradientVectorFile %s', hash_files=False, ), - inputBValues=dict(argstr='--inputBValues %s', ), - inputBVectors=dict(argstr='--inputBVectors %s', ), + inputBValues=dict( + argstr='--inputBValues %s', + extensions=None, + ), + inputBVectors=dict( + argstr='--inputBVectors %s', + extensions=None, + ), inputDicomDirectory=dict(argstr='--inputDicomDirectory %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputBValues=dict( argstr='--outputBValues %s', hash_files=False, @@ -54,11 +66,11 @@ def test_DWIConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIConvert_outputs(): output_map = dict( - gradientVectorFile=dict(), - outputBValues=dict(), - outputBVectors=dict(), + gradientVectorFile=dict(extensions=None, ), + outputBValues=dict(extensions=None, ), + outputBVectors=dict(extensions=None, ), outputDirectory=dict(), - outputVolume=dict(), + outputVolume=dict(extensions=None, ), ) outputs = DWIConvert.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index eb9d8c6184..3ab83055bb 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -13,8 +13,14 @@ def test_compareTractInclusion_inputs(): ), numberOfPoints=dict(argstr='--numberOfPoints %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), - standardFiber=dict(argstr='--standardFiber %s', ), - testFiber=dict(argstr='--testFiber %s', ), + standardFiber=dict( + argstr='--standardFiber %s', + extensions=None, + ), + testFiber=dict( + argstr='--testFiber %s', + extensions=None, + ), testForBijection=dict(argstr='--testForBijection ', ), testForFiberCardinality=dict(argstr='--testForFiberCardinality ', ), writeXMLPolyDataFile=dict(argstr='--writeXMLPolyDataFile ', ), diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index 92c00853f4..6b21e7a648 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -24,7 +24,7 @@ def test_dtiaverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_dtiaverage_outputs(): - output_map = dict(tensor_output=dict(), ) + output_map = dict(tensor_output=dict(extensions=None, ), ) outputs = dtiaverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 440fd4df07..acc0fb30f9 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -15,14 +15,23 @@ def test_dtiestim_inputs(): ), DTI_double=dict(argstr='--DTI_double ', ), args=dict(argstr='%s', ), - bad_region_mask=dict(argstr='--bad_region_mask %s', ), - brain_mask=dict(argstr='--brain_mask %s', ), + bad_region_mask=dict( + argstr='--bad_region_mask %s', + extensions=None, + ), + brain_mask=dict( + argstr='--brain_mask %s', + extensions=None, + ), correction=dict(argstr='--correction %s', ), defaultTensor=dict( argstr='--defaultTensor %s', sep=',', ), - dwi_image=dict(argstr='--dwi_image %s', ), + dwi_image=dict( + argstr='--dwi_image %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -51,10 +60,10 @@ def test_dtiestim_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_dtiestim_outputs(): output_map = dict( - B0=dict(), - B0_mask_output=dict(), - idwi=dict(), - tensor_output=dict(), + B0=dict(extensions=None, ), + B0_mask_output=dict(extensions=None, ), + idwi=dict(extensions=None, ), + tensor_output=dict(extensions=None, ), ) outputs = dtiestim.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index 3148d1edb5..cb06505959 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -10,7 +10,10 @@ def test_dtiprocess_inputs(): argstr='--RD_output %s', hash_files=False, ), - affineitk_file=dict(argstr='--affineitk_file %s', ), + affineitk_file=dict( + argstr='--affineitk_file %s', + extensions=None, + ), args=dict(argstr='%s', ), color_fa_output=dict( argstr='--color_fa_output %s', @@ -21,8 +24,14 @@ def test_dtiprocess_inputs(): argstr='--deformation_output %s', hash_files=False, ), - dof_file=dict(argstr='--dof_file %s', ), - dti_image=dict(argstr='--dti_image %s', ), + dof_file=dict( + argstr='--dof_file %s', + extensions=None, + ), + dti_image=dict( + argstr='--dti_image %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -39,7 +48,10 @@ def test_dtiprocess_inputs(): argstr='--fa_output %s', hash_files=False, ), - forward=dict(argstr='--forward %s', ), + forward=dict( + argstr='--forward %s', + extensions=None, + ), frobenius_norm_output=dict( argstr='--frobenius_norm_output %s', hash_files=False, @@ -58,7 +70,10 @@ def test_dtiprocess_inputs(): argstr='--lambda3_output %s', hash_files=False, ), - mask=dict(argstr='--mask %s', ), + mask=dict( + argstr='--mask %s', + extensions=None, + ), md_output=dict( argstr='--md_output %s', hash_files=False, @@ -67,7 +82,10 @@ def test_dtiprocess_inputs(): argstr='--negative_eigenvector_output %s', hash_files=False, ), - newdof_file=dict(argstr='--newdof_file %s', ), + newdof_file=dict( + argstr='--newdof_file %s', + extensions=None, + ), outmask=dict( argstr='--outmask %s', hash_files=False, @@ -92,21 +110,21 @@ def test_dtiprocess_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_dtiprocess_outputs(): output_map = dict( - RD_output=dict(), - color_fa_output=dict(), - deformation_output=dict(), - fa_gradient_output=dict(), - fa_gradmag_output=dict(), - fa_output=dict(), - frobenius_norm_output=dict(), - lambda1_output=dict(), - lambda2_output=dict(), - lambda3_output=dict(), - md_output=dict(), - negative_eigenvector_output=dict(), - outmask=dict(), - principal_eigenvector_output=dict(), - rot_output=dict(), + RD_output=dict(extensions=None, ), + color_fa_output=dict(extensions=None, ), + deformation_output=dict(extensions=None, ), + fa_gradient_output=dict(extensions=None, ), + fa_gradmag_output=dict(extensions=None, ), + fa_output=dict(extensions=None, ), + frobenius_norm_output=dict(extensions=None, ), + lambda1_output=dict(extensions=None, ), + lambda2_output=dict(extensions=None, ), + lambda3_output=dict(extensions=None, ), + md_output=dict(extensions=None, ), + negative_eigenvector_output=dict(extensions=None, ), + outmask=dict(extensions=None, ), + principal_eigenvector_output=dict(extensions=None, ), + rot_output=dict(extensions=None, ), ) outputs = dtiprocess.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index ac5784f1c7..d39aaec246 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -10,7 +10,10 @@ def test_extractNrrdVectorIndex_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_extractNrrdVectorIndex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_extractNrrdVectorIndex_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = extractNrrdVectorIndex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index 195d7dc3e1..e0d804827c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -11,7 +11,10 @@ def test_gtractAnisotropyMap_inputs(): nohash=True, usedefault=True, ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +27,7 @@ def test_gtractAnisotropyMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractAnisotropyMap_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractAnisotropyMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index fbb5bd6a55..44bd558800 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -12,7 +12,10 @@ def test_gtractAverageBvalues_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_gtractAverageBvalues_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractAverageBvalues_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractAverageBvalues.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index fed980c463..0b3a0505ef 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -12,7 +12,10 @@ def test_gtractClipAnisotropy_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_gtractClipAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractClipAnisotropy_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractClipAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 456e1e79fa..e6c241d053 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -17,9 +17,18 @@ def test_gtractCoRegAnatomy_inputs(): argstr='--gridSize %s', sep=',', ), - inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), - inputRigidTransform=dict(argstr='--inputRigidTransform %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputAnatomicalVolume=dict( + argstr='--inputAnatomicalVolume %s', + extensions=None, + ), + inputRigidTransform=dict( + argstr='--inputRigidTransform %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), maxBSplineDisplacement=dict(argstr='--maxBSplineDisplacement %f', ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), @@ -47,7 +56,7 @@ def test_gtractCoRegAnatomy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoRegAnatomy_outputs(): - output_map = dict(outputTransformName=dict(), ) + output_map = dict(outputTransformName=dict(extensions=None, ), ) outputs = gtractCoRegAnatomy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 7b75858eff..5099ba1bac 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -24,7 +24,7 @@ def test_gtractConcatDwi_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractConcatDwi_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractConcatDwi.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index d9e0b725c8..a464fcd7a1 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -10,8 +10,14 @@ def test_gtractCopyImageOrientation_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +30,7 @@ def test_gtractCopyImageOrientation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCopyImageOrientation_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractCopyImageOrientation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index 3143b16dfb..f99c27aa68 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -12,11 +12,17 @@ def test_gtractCoregBvalues_inputs(): nohash=True, usedefault=True, ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedVolume=dict( + argstr='--fixedVolume %s', + extensions=None, + ), fixedVolumeIndex=dict(argstr='--fixedVolumeIndex %d', ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingVolume=dict( + argstr='--movingVolume %s', + extensions=None, + ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), numberOfSpatialSamples=dict(argstr='--numberOfSpatialSamples %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -40,8 +46,8 @@ def test_gtractCoregBvalues_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoregBvalues_outputs(): output_map = dict( - outputTransform=dict(), - outputVolume=dict(), + outputTransform=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = gtractCoregBvalues.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 32d1e68898..75d5d13e4e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -11,10 +11,18 @@ def test_gtractCostFastMarching_inputs(): nohash=True, usedefault=True, ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + extensions=None, + ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), + argstr='--inputStartingSeedsLabelMapVolume %s', + extensions=None, + ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputCostVolume=dict( argstr='--outputCostVolume %s', @@ -35,8 +43,8 @@ def test_gtractCostFastMarching_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCostFastMarching_outputs(): output_map = dict( - outputCostVolume=dict(), - outputSpeedVolume=dict(), + outputCostVolume=dict(extensions=None, ), + outputSpeedVolume=dict(extensions=None, ), ) outputs = gtractCostFastMarching.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index bbe375bbb9..e2dff9e309 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -10,7 +10,10 @@ def test_gtractCreateGuideFiber_inputs(): nohash=True, usedefault=True, ), - inputFiber=dict(argstr='--inputFiber %s', ), + inputFiber=dict( + argstr='--inputFiber %s', + extensions=None, + ), numberOfPoints=dict(argstr='--numberOfPoints %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFiber=dict( @@ -25,7 +28,7 @@ def test_gtractCreateGuideFiber_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCreateGuideFiber_outputs(): - output_map = dict(outputFiber=dict(), ) + output_map = dict(outputFiber=dict(extensions=None, ), ) outputs = gtractCreateGuideFiber.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index ec3a99b91e..2342a73cb1 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -11,11 +11,22 @@ def test_gtractFastMarchingTracking_inputs(): nohash=True, usedefault=True, ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), - inputCostVolume=dict(argstr='--inputCostVolume %s', ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + extensions=None, + ), + inputCostVolume=dict( + argstr='--inputCostVolume %s', + extensions=None, + ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), + argstr='--inputStartingSeedsLabelMapVolume %s', + extensions=None, + ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + extensions=None, + ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), @@ -35,7 +46,7 @@ def test_gtractFastMarchingTracking_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractFastMarchingTracking_outputs(): - output_map = dict(outputTract=dict(), ) + output_map = dict(outputTract=dict(extensions=None, ), ) outputs = gtractFastMarchingTracking.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index 96c93b8b64..233f7358f5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -16,13 +16,26 @@ def test_gtractFiberTracking_inputs(): ), guidedCurvatureThreshold=dict( argstr='--guidedCurvatureThreshold %f', ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + extensions=None, + ), inputEndingSeedsLabelMapVolume=dict( - argstr='--inputEndingSeedsLabelMapVolume %s', ), + argstr='--inputEndingSeedsLabelMapVolume %s', + extensions=None, + ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), - inputTract=dict(argstr='--inputTract %s', ), + argstr='--inputStartingSeedsLabelMapVolume %s', + extensions=None, + ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + extensions=None, + ), + inputTract=dict( + argstr='--inputTract %s', + extensions=None, + ), maximumBranchPoints=dict(argstr='--maximumBranchPoints %d', ), maximumGuideDistance=dict(argstr='--maximumGuideDistance %f', ), maximumLength=dict(argstr='--maximumLength %f', ), @@ -51,7 +64,7 @@ def test_gtractFiberTracking_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractFiberTracking_outputs(): - output_map = dict(outputTract=dict(), ) + output_map = dict(outputTract=dict(extensions=None, ), ) outputs = gtractFiberTracking.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index 9ddde832b2..e811627909 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -10,8 +10,14 @@ def test_gtractImageConformity_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +30,7 @@ def test_gtractImageConformity_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractImageConformity_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractImageConformity.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index ca642ceb66..9ffcb11e11 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -10,8 +10,14 @@ def test_gtractInvertBSplineTransform_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + extensions=None, + ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), landmarkDensity=dict( argstr='--landmarkDensity %s', sep=',', @@ -28,7 +34,7 @@ def test_gtractInvertBSplineTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertBSplineTransform_outputs(): - output_map = dict(outputTransform=dict(), ) + output_map = dict(outputTransform=dict(extensions=None, ), ) outputs = gtractInvertBSplineTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index e4fd213d39..7d1468dba6 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -6,8 +6,14 @@ def test_gtractInvertDisplacementField_inputs(): input_map = dict( args=dict(argstr='%s', ), - baseImage=dict(argstr='--baseImage %s', ), - deformationImage=dict(argstr='--deformationImage %s', ), + baseImage=dict( + argstr='--baseImage %s', + extensions=None, + ), + deformationImage=dict( + argstr='--deformationImage %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -25,7 +31,7 @@ def test_gtractInvertDisplacementField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertDisplacementField_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractInvertDisplacementField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index c035862663..0d67bb2669 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -10,7 +10,10 @@ def test_gtractInvertRigidTransform_inputs(): nohash=True, usedefault=True, ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputTransform=dict( argstr='--outputTransform %s', @@ -23,7 +26,7 @@ def test_gtractInvertRigidTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertRigidTransform_outputs(): - output_map = dict(outputTransform=dict(), ) + output_map = dict(outputTransform=dict(extensions=None, ), ) outputs = gtractInvertRigidTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index 43f428b233..5e95276c83 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -10,9 +10,18 @@ def test_gtractResampleAnisotropy_inputs(): nohash=True, usedefault=True, ), - inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputAnatomicalVolume=dict( + argstr='--inputAnatomicalVolume %s', + extensions=None, + ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + extensions=None, + ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -26,7 +35,7 @@ def test_gtractResampleAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleAnisotropy_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractResampleAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index 812afca5c0..c9bde14e9a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -10,9 +10,18 @@ def test_gtractResampleB0_inputs(): nohash=True, usedefault=True, ), - inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputAnatomicalVolume=dict( + argstr='--inputAnatomicalVolume %s', + extensions=None, + ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -27,7 +36,7 @@ def test_gtractResampleB0_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleB0_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractResampleB0.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index decc017c60..27ad9e5e7d 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -10,9 +10,18 @@ def test_gtractResampleCodeImage_inputs(): nohash=True, usedefault=True, ), - inputCodeVolume=dict(argstr='--inputCodeVolume %s', ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputCodeVolume=dict( + argstr='--inputCodeVolume %s', + extensions=None, + ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + extensions=None, + ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -26,7 +35,7 @@ def test_gtractResampleCodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleCodeImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractResampleCodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index b815d3d3d6..be98d4a3e3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -15,8 +15,14 @@ def test_gtractResampleDWIInPlace_inputs(): argstr='--imageOutputSize %s', sep=',', ), - inputTransform=dict(argstr='--inputTransform %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputResampledB0=dict( argstr='--outputResampledB0 %s', @@ -26,8 +32,14 @@ def test_gtractResampleDWIInPlace_inputs(): argstr='--outputVolume %s', hash_files=False, ), - referenceVolume=dict(argstr='--referenceVolume %s', ), - warpDWITransform=dict(argstr='--warpDWITransform %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + extensions=None, + ), + warpDWITransform=dict( + argstr='--warpDWITransform %s', + extensions=None, + ), ) inputs = gtractResampleDWIInPlace.input_spec() @@ -36,8 +48,8 @@ def test_gtractResampleDWIInPlace_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleDWIInPlace_outputs(): output_map = dict( - outputResampledB0=dict(), - outputVolume=dict(), + outputResampledB0=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = gtractResampleDWIInPlace.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index d0d2cd5664..ea9612996c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -11,10 +11,17 @@ def test_gtractResampleFibers_inputs(): usedefault=True, ), inputForwardDeformationFieldVolume=dict( - argstr='--inputForwardDeformationFieldVolume %s', ), + argstr='--inputForwardDeformationFieldVolume %s', + extensions=None, + ), inputReverseDeformationFieldVolume=dict( - argstr='--inputReverseDeformationFieldVolume %s', ), - inputTract=dict(argstr='--inputTract %s', ), + argstr='--inputReverseDeformationFieldVolume %s', + extensions=None, + ), + inputTract=dict( + argstr='--inputTract %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputTract=dict( argstr='--outputTract %s', @@ -28,7 +35,7 @@ def test_gtractResampleFibers_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleFibers_outputs(): - output_map = dict(outputTract=dict(), ) + output_map = dict(outputTract=dict(extensions=None, ), ) outputs = gtractResampleFibers.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index ead96d1c71..9887f0e224 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -18,9 +18,15 @@ def test_gtractTensor_inputs(): argstr='--ignoreIndex %s', sep=',', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), maskProcessingMode=dict(argstr='--maskProcessingMode %s', ), - maskVolume=dict(argstr='--maskVolume %s', ), + maskVolume=dict( + argstr='--maskVolume %s', + extensions=None, + ), medianFilterSize=dict( argstr='--medianFilterSize %s', sep=',', @@ -39,7 +45,7 @@ def test_gtractTensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractTensor_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = gtractTensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 2dfde189e2..17731d6648 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -10,8 +10,14 @@ def test_gtractTransformToDisplacementField_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + extensions=None, + ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputDeformationFieldVolume=dict( argstr='--outputDeformationFieldVolume %s', @@ -24,7 +30,7 @@ def test_gtractTransformToDisplacementField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractTransformToDisplacementField_outputs(): - output_map = dict(outputDeformationFieldVolume=dict(), ) + output_map = dict(outputDeformationFieldVolume=dict(extensions=None, ), ) outputs = gtractTransformToDisplacementField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index cc06c5ede5..511e6c8844 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -10,7 +10,10 @@ def test_maxcurvature_inputs(): nohash=True, usedefault=True, ), - image=dict(argstr='--image %s', ), + image=dict( + argstr='--image %s', + extensions=None, + ), output=dict( argstr='--output %s', hash_files=False, @@ -24,7 +27,7 @@ def test_maxcurvature_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_maxcurvature_outputs(): - output_map = dict(output=dict(), ) + output_map = dict(output=dict(extensions=None, ), ) outputs = maxcurvature.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index 7c61974ef3..b713d0b053 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -10,7 +10,10 @@ def test_UKFTractography_inputs(): Qw=dict(argstr='--Qw %f', ), Rs=dict(argstr='--Rs %f', ), args=dict(argstr='%s', ), - dwiFile=dict(argstr='--dwiFile %s', ), + dwiFile=dict( + argstr='--dwiFile %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -21,7 +24,10 @@ def test_UKFTractography_inputs(): argstr='--labels %s', sep=',', ), - maskFile=dict(argstr='--maskFile %s', ), + maskFile=dict( + argstr='--maskFile %s', + extensions=None, + ), maxBranchingAngle=dict(argstr='--maxBranchingAngle %f', ), maxHalfFiberLength=dict(argstr='--maxHalfFiberLength %f', ), minBranchingAngle=dict(argstr='--minBranchingAngle %f', ), @@ -38,7 +44,10 @@ def test_UKFTractography_inputs(): recordTensors=dict(argstr='--recordTensors ', ), recordTrace=dict(argstr='--recordTrace ', ), seedFALimit=dict(argstr='--seedFALimit %f', ), - seedsFile=dict(argstr='--seedsFile %s', ), + seedsFile=dict( + argstr='--seedsFile %s', + extensions=None, + ), seedsPerVoxel=dict(argstr='--seedsPerVoxel %d', ), stepLength=dict(argstr='--stepLength %f', ), storeGlyphs=dict(argstr='--storeGlyphs ', ), @@ -60,8 +69,8 @@ def test_UKFTractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_UKFTractography_outputs(): output_map = dict( - tracts=dict(), - tractsWithSecondTensor=dict(), + tracts=dict(extensions=None, ), + tractsWithSecondTensor=dict(extensions=None, ), ) outputs = UKFTractography.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index b4756a9406..3cd4ad6135 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -6,23 +6,35 @@ def test_fiberprocess_inputs(): input_map = dict( args=dict(argstr='%s', ), - displacement_field=dict(argstr='--displacement_field %s', ), + displacement_field=dict( + argstr='--displacement_field %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), - fiber_file=dict(argstr='--fiber_file %s', ), + fiber_file=dict( + argstr='--fiber_file %s', + extensions=None, + ), fiber_output=dict( argstr='--fiber_output %s', hash_files=False, ), fiber_radius=dict(argstr='--fiber_radius %f', ), - h_field=dict(argstr='--h_field %s', ), + h_field=dict( + argstr='--h_field %s', + extensions=None, + ), index_space=dict(argstr='--index_space ', ), noDataChange=dict(argstr='--noDataChange ', ), no_warp=dict(argstr='--no_warp ', ), saveProperties=dict(argstr='--saveProperties ', ), - tensor_volume=dict(argstr='--tensor_volume %s', ), + tensor_volume=dict( + argstr='--tensor_volume %s', + extensions=None, + ), verbose=dict(argstr='--verbose ', ), voxel_label=dict(argstr='--voxel_label %d', ), voxelize=dict( @@ -38,8 +50,8 @@ def test_fiberprocess_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_fiberprocess_outputs(): output_map = dict( - fiber_output=dict(), - voxelize=dict(), + fiber_output=dict(extensions=None, ), + voxelize=dict(extensions=None, ), ) outputs = fiberprocess.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index d6f3a5cd50..e02ddc54a7 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -10,7 +10,10 @@ def test_fiberstats_inputs(): nohash=True, usedefault=True, ), - fiber_file=dict(argstr='--fiber_file %s', ), + fiber_file=dict( + argstr='--fiber_file %s', + extensions=None, + ), verbose=dict(argstr='--verbose ', ), ) inputs = fiberstats.input_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index 33e57c0ca3..397f7ebd2d 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -12,8 +12,14 @@ def test_fibertrack_inputs(): ), forbidden_label=dict(argstr='--forbidden_label %d', ), force=dict(argstr='--force ', ), - input_roi_file=dict(argstr='--input_roi_file %s', ), - input_tensor_file=dict(argstr='--input_tensor_file %s', ), + input_roi_file=dict( + argstr='--input_roi_file %s', + extensions=None, + ), + input_tensor_file=dict( + argstr='--input_tensor_file %s', + extensions=None, + ), max_angle=dict(argstr='--max_angle %f', ), min_fa=dict(argstr='--min_fa %f', ), output_fiber_file=dict( @@ -33,7 +39,7 @@ def test_fibertrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_fibertrack_outputs(): - output_map = dict(output_fiber_file=dict(), ) + output_map = dict(output_fiber_file=dict(extensions=None, ), ) outputs = fibertrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index cfbee7449c..fbaf4dc841 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -10,7 +10,10 @@ def test_CannyEdge_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), lowerThreshold=dict(argstr='--lowerThreshold %f', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_CannyEdge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CannyEdge_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = CannyEdge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index b4196db823..19bd6122ee 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -13,9 +13,15 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): nohash=True, usedefault=True, ), - initialModel=dict(argstr='--initialModel %s', ), + initialModel=dict( + argstr='--initialModel %s', + extensions=None, + ), initialModelIsovalue=dict(argstr='--initialModelIsovalue %f', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), maxIterations=dict(argstr='--maxIterations %d', ), outputSpeedVolume=dict( argstr='--outputSpeedVolume %s', @@ -33,8 +39,8 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CannySegmentationLevelSetImageFilter_outputs(): output_map = dict( - outputSpeedVolume=dict(), - outputVolume=dict(), + outputSpeedVolume=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = CannySegmentationLevelSetImageFilter.output_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index 7945ec8ade..a054c2cf06 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -10,9 +10,15 @@ def test_DilateImage_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = DilateImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 6bd6235e80..bd1ce09b18 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -10,8 +10,14 @@ def test_DilateMask_inputs(): nohash=True, usedefault=True, ), - inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputBinaryVolume=dict( + argstr='--inputBinaryVolume %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), lowerThreshold=dict(argstr='--lowerThreshold %f', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +31,7 @@ def test_DilateMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateMask_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = DilateMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index f7aaf722c4..d956ea2ac1 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -10,8 +10,14 @@ def test_DistanceMaps_inputs(): nohash=True, usedefault=True, ), - inputLabelVolume=dict(argstr='--inputLabelVolume %s', ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputLabelVolume=dict( + argstr='--inputLabelVolume %s', + extensions=None, + ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), inputTissueLabel=dict(argstr='--inputTissueLabel %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +30,7 @@ def test_DistanceMaps_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMaps_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = DistanceMaps.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index 320bb76b77..9e453b2f86 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -10,8 +10,14 @@ def test_DumpBinaryTrainingVectors_inputs(): nohash=True, usedefault=True, ), - inputHeaderFilename=dict(argstr='--inputHeaderFilename %s', ), - inputVectorFilename=dict(argstr='--inputVectorFilename %s', ), + inputHeaderFilename=dict( + argstr='--inputHeaderFilename %s', + extensions=None, + ), + inputVectorFilename=dict( + argstr='--inputVectorFilename %s', + extensions=None, + ), ) inputs = DumpBinaryTrainingVectors.input_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index 9e096b0062..1180f25bd5 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -10,9 +10,15 @@ def test_ErodeImage_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = ErodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 539660f73b..e0de87a033 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -10,8 +10,14 @@ def test_FlippedDifference_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -23,7 +29,7 @@ def test_FlippedDifference_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FlippedDifference_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = FlippedDifference.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index 0a211f23d2..e987e60e73 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -10,8 +10,14 @@ def test_GenerateBrainClippedImage_inputs(): nohash=True, usedefault=True, ), - inputImg=dict(argstr='--inputImg %s', ), - inputMsk=dict(argstr='--inputMsk %s', ), + inputImg=dict( + argstr='--inputImg %s', + extensions=None, + ), + inputMsk=dict( + argstr='--inputMsk %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFileName=dict( argstr='--outputFileName %s', @@ -24,7 +30,7 @@ def test_GenerateBrainClippedImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateBrainClippedImage_outputs(): - output_map = dict(outputFileName=dict(), ) + output_map = dict(outputFileName=dict(extensions=None, ), ) outputs = GenerateBrainClippedImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index 58d3f35c5a..a538ea0933 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -11,8 +11,14 @@ def test_GenerateSummedGradientImage_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + extensions=None, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFileName=dict( argstr='--outputFileName %s', @@ -25,7 +31,7 @@ def test_GenerateSummedGradientImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateSummedGradientImage_outputs(): - output_map = dict(outputFileName=dict(), ) + output_map = dict(outputFileName=dict(extensions=None, ), ) outputs = GenerateSummedGradientImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index 1348e61d4b..38ff43b5d1 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -10,7 +10,10 @@ def test_GenerateTestImage_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), lowerBoundOfOutputVolume=dict( argstr='--lowerBoundOfOutputVolume %f', ), outputVolume=dict( @@ -27,7 +30,7 @@ def test_GenerateTestImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateTestImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = GenerateTestImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index 27ebb18d29..23e035478e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -11,7 +11,10 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusionImageFilter_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = GradientAnisotropicDiffusionImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 9ad82598bb..0ca8acdee7 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -12,9 +12,18 @@ def test_HammerAttributeCreator_inputs(): nohash=True, usedefault=True, ), - inputCSFVolume=dict(argstr='--inputCSFVolume %s', ), - inputGMVolume=dict(argstr='--inputGMVolume %s', ), - inputWMVolume=dict(argstr='--inputWMVolume %s', ), + inputCSFVolume=dict( + argstr='--inputCSFVolume %s', + extensions=None, + ), + inputGMVolume=dict( + argstr='--inputGMVolume %s', + extensions=None, + ), + inputWMVolume=dict( + argstr='--inputWMVolume %s', + extensions=None, + ), outputVolumeBase=dict(argstr='--outputVolumeBase %s', ), ) inputs = HammerAttributeCreator.input_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index c6b1ef20a9..661b2ba0ae 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -10,9 +10,15 @@ def test_NeighborhoodMean_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_NeighborhoodMean_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMean_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = NeighborhoodMean.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 2c2b2d585f..c3b9895edd 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -10,9 +10,15 @@ def test_NeighborhoodMedian_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_NeighborhoodMedian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMedian_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = NeighborhoodMedian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 75bb83315f..7b68d3d05e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -23,7 +23,7 @@ def test_STAPLEAnalysis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_STAPLEAnalysis_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = STAPLEAnalysis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index cd4b4a1af2..e76b825ca6 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -11,7 +11,10 @@ def test_TextureFromNoiseImageFilter_inputs(): usedefault=True, ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -23,7 +26,7 @@ def test_TextureFromNoiseImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TextureFromNoiseImageFilter_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = TextureFromNoiseImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index 0ad523c7d0..9981d7b8ac 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -11,8 +11,14 @@ def test_TextureMeasureFilter_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), insideROIValue=dict(argstr='--insideROIValue %f', ), outputFilename=dict( argstr='--outputFilename %s', @@ -25,7 +31,7 @@ def test_TextureMeasureFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TextureMeasureFilter_outputs(): - output_map = dict(outputFilename=dict(), ) + output_map = dict(outputFilename=dict(extensions=None, ), ) outputs = TextureMeasureFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index b84cda1fc3..866af46740 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -13,6 +13,7 @@ def test_UnbiasedNonLocalMeans_inputs(): hp=dict(argstr='--hp %f', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), outputVolume=dict( @@ -37,7 +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(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/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index f9ff60cfd9..7be4644031 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -6,13 +6,19 @@ def test_scalartransform_inputs(): input_map = dict( args=dict(argstr='%s', ), - deformation=dict(argstr='--deformation %s', ), + deformation=dict( + argstr='--deformation %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, ), h_field=dict(argstr='--h_field ', ), - input_image=dict(argstr='--input_image %s', ), + input_image=dict( + argstr='--input_image %s', + extensions=None, + ), interpolation=dict(argstr='--interpolation %s', ), invert=dict(argstr='--invert ', ), output_image=dict( @@ -31,8 +37,8 @@ def test_scalartransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_scalartransform_outputs(): output_map = dict( - output_image=dict(), - transformation=dict(), + output_image=dict(extensions=None, ), + transformation=dict(extensions=None, ), ) outputs = scalartransform.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index c631f9b96e..18cd4c63ff 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -19,14 +19,25 @@ def test_BRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + extensions=None, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + extensions=None, + ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + extensions=None, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + extensions=None, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,8 +55,14 @@ def test_BRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + extensions=None, + ), + movingVolume=dict( + argstr='--movingVolume %s', + extensions=None, + ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', sep=',', @@ -92,9 +109,9 @@ def test_BRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(extensions=None, ), + outputDisplacementFieldVolume=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = BRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 18059c4f57..2e949b33fb 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -22,13 +22,25 @@ def test_BRAINSFit_inputs(): usedefault=True, ), failureExitCode=dict(argstr='--failureExitCode %d', ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), - fixedVolume2=dict(argstr='--fixedVolume2 %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + extensions=None, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + extensions=None, + ), + fixedVolume2=dict( + argstr='--fixedVolume2 %s', + extensions=None, + ), fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), - initialTransform=dict(argstr='--initialTransform %s', ), + initialTransform=dict( + argstr='--initialTransform %s', + extensions=None, + ), initializeRegistrationByCurrentGenericTransform=dict( argstr='--initializeRegistrationByCurrentGenericTransform ', ), initializeTransformMode=dict(argstr='--initializeTransformMode %s', ), @@ -59,9 +71,18 @@ def test_BRAINSFit_inputs(): argstr='--minimumStepLength %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), - movingVolume2=dict(argstr='--movingVolume2 %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + extensions=None, + ), + movingVolume=dict( + argstr='--movingVolume %s', + extensions=None, + ), + movingVolume2=dict( + argstr='--movingVolume2 %s', + extensions=None, + ), movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfIterations=dict( @@ -129,14 +150,14 @@ def test_BRAINSFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): output_map = dict( - bsplineTransform=dict(), - linearTransform=dict(), - logFileReport=dict(), - outputFixedVolumeROI=dict(), - outputMovingVolumeROI=dict(), - outputTransform=dict(), - outputVolume=dict(), - strippedOutputTransform=dict(), + bsplineTransform=dict(extensions=None, ), + linearTransform=dict(extensions=None, ), + logFileReport=dict(extensions=None, ), + outputFixedVolumeROI=dict(extensions=None, ), + outputMovingVolumeROI=dict(extensions=None, ), + outputTransform=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), + strippedOutputTransform=dict(extensions=None, ), ) outputs = BRAINSFit.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index 98ec5f4ff3..e8d4c187b0 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -7,7 +7,10 @@ def test_BRAINSResample_inputs(): input_map = dict( args=dict(argstr='%s', ), defaultValue=dict(argstr='--defaultValue %f', ), - deformationVolume=dict(argstr='--deformationVolume %s', ), + deformationVolume=dict( + argstr='--deformationVolume %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -16,7 +19,10 @@ def test_BRAINSResample_inputs(): argstr='--gridSpacing %s', sep=',', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), inverseTransform=dict(argstr='--inverseTransform ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -25,8 +31,14 @@ def test_BRAINSResample_inputs(): hash_files=False, ), pixelType=dict(argstr='--pixelType %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), - warpTransform=dict(argstr='--warpTransform %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + extensions=None, + ), + warpTransform=dict( + argstr='--warpTransform %s', + extensions=None, + ), ) inputs = BRAINSResample.input_spec() @@ -34,7 +46,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 4ce0d7159c..188bb31d49 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -10,7 +10,10 @@ def test_BRAINSResize_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +27,7 @@ def test_BRAINSResize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResize_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSResize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index 2a700eaac7..258a0fcc83 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -11,9 +11,15 @@ def test_BRAINSTransformFromFiducials_inputs(): usedefault=True, ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), - fixedLandmarksFile=dict(argstr='--fixedLandmarksFile %s', ), + fixedLandmarksFile=dict( + argstr='--fixedLandmarksFile %s', + extensions=None, + ), movingLandmarks=dict(argstr='--movingLandmarks %s...', ), - movingLandmarksFile=dict(argstr='--movingLandmarksFile %s', ), + movingLandmarksFile=dict( + argstr='--movingLandmarksFile %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), saveTransform=dict( argstr='--saveTransform %s', @@ -27,7 +33,7 @@ def test_BRAINSTransformFromFiducials_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformFromFiducials_outputs(): - output_map = dict(saveTransform=dict(), ) + output_map = dict(saveTransform=dict(extensions=None, ), ) outputs = BRAINSTransformFromFiducials.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index b3255da1d3..b196d318d4 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -19,14 +19,22 @@ def test_VBRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + extensions=None, + ), fixedVolume=dict(argstr='--fixedVolume %s...', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + extensions=None, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + extensions=None, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,7 +52,10 @@ def test_VBRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + extensions=None, + ), movingVolume=dict(argstr='--movingVolume %s...', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', @@ -96,9 +107,9 @@ def test_VBRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(extensions=None, ), + outputDisplacementFieldVolume=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = VBRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 2d66884522..6efd92d499 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -6,7 +6,10 @@ def test_BRAINSABC_inputs(): input_map = dict( args=dict(argstr='%s', ), - atlasDefinition=dict(argstr='--atlasDefinition %s', ), + atlasDefinition=dict( + argstr='--atlasDefinition %s', + extensions=None, + ), atlasToSubjectInitialTransform=dict( argstr='--atlasToSubjectInitialTransform %s', hash_files=False, @@ -71,7 +74,10 @@ def test_BRAINSABC_inputs(): ), posteriorTemplate=dict(argstr='--posteriorTemplate %s', ), purePlugsThreshold=dict(argstr='--purePlugsThreshold %f', ), - restoreState=dict(argstr='--restoreState %s', ), + restoreState=dict( + argstr='--restoreState %s', + extensions=None, + ), saveState=dict( argstr='--saveState %s', hash_files=False, @@ -88,14 +94,14 @@ def test_BRAINSABC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSABC_outputs(): output_map = dict( - atlasToSubjectInitialTransform=dict(), - atlasToSubjectTransform=dict(), + atlasToSubjectInitialTransform=dict(extensions=None, ), + atlasToSubjectTransform=dict(extensions=None, ), implicitOutputs=dict(), outputDir=dict(), - outputDirtyLabels=dict(), - outputLabels=dict(), + outputDirtyLabels=dict(extensions=None, ), + outputLabels=dict(extensions=None, ), outputVolumes=dict(), - saveState=dict(), + saveState=dict(extensions=None, ), ) outputs = BRAINSABC.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index 9b2d10061c..6f6ceaf53e 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -6,12 +6,24 @@ def test_BRAINSConstellationDetector_inputs(): input_map = dict( BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), - LLSModel=dict(argstr='--LLSModel %s', ), + LLSModel=dict( + argstr='--LLSModel %s', + extensions=None, + ), acLowerBound=dict(argstr='--acLowerBound %f', ), args=dict(argstr='%s', ), - atlasLandmarkWeights=dict(argstr='--atlasLandmarkWeights %s', ), - atlasLandmarks=dict(argstr='--atlasLandmarks %s', ), - atlasVolume=dict(argstr='--atlasVolume %s', ), + atlasLandmarkWeights=dict( + argstr='--atlasLandmarkWeights %s', + extensions=None, + ), + atlasLandmarks=dict( + argstr='--atlasLandmarks %s', + extensions=None, + ), + atlasVolume=dict( + argstr='--atlasVolume %s', + extensions=None, + ), cutOutHeadInOutputVolume=dict(argstr='--cutOutHeadInOutputVolume ', ), debug=dict(argstr='--debug ', ), environ=dict( @@ -37,9 +49,18 @@ def test_BRAINSConstellationDetector_inputs(): sep=',', ), houghEyeDetectorMode=dict(argstr='--houghEyeDetectorMode %d', ), - inputLandmarksEMSP=dict(argstr='--inputLandmarksEMSP %s', ), - inputTemplateModel=dict(argstr='--inputTemplateModel %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputLandmarksEMSP=dict( + argstr='--inputLandmarksEMSP %s', + extensions=None, + ), + inputTemplateModel=dict( + argstr='--inputTemplateModel %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -105,16 +126,16 @@ def test_BRAINSConstellationDetector_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationDetector_outputs(): output_map = dict( - outputLandmarksInACPCAlignedSpace=dict(), - outputLandmarksInInputSpace=dict(), - outputMRML=dict(), - outputResampledVolume=dict(), - outputTransform=dict(), - outputUntransformedClippedVolume=dict(), - outputVerificationScript=dict(), - outputVolume=dict(), + outputLandmarksInACPCAlignedSpace=dict(extensions=None, ), + outputLandmarksInInputSpace=dict(extensions=None, ), + outputMRML=dict(extensions=None, ), + outputResampledVolume=dict(extensions=None, ), + outputTransform=dict(extensions=None, ), + outputUntransformedClippedVolume=dict(extensions=None, ), + outputVerificationScript=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), resultsDir=dict(), - writeBranded2DImage=dict(), + writeBranded2DImage=dict(extensions=None, ), ) outputs = BRAINSConstellationDetector.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index 9f2b00c311..8280bddf37 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -24,7 +24,10 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): ), inclusionThreshold=dict(argstr='--inclusionThreshold %f', ), inputProbabilityVolume=dict(argstr='--inputProbabilityVolume %s...', ), - nonAirRegionMask=dict(argstr='--nonAirRegionMask %s', ), + nonAirRegionMask=dict( + argstr='--nonAirRegionMask %s', + extensions=None, + ), priorLabelCodes=dict( argstr='--priorLabelCodes %s', sep=',', @@ -37,8 +40,8 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): output_map = dict( - cleanLabelVolume=dict(), - dirtyLabelVolume=dict(), + cleanLabelVolume=dict(extensions=None, ), + dirtyLabelVolume=dict(extensions=None, ), ) outputs = BRAINSCreateLabelMapFromProbabilityMaps.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index 9d66d4a463..4f4c336670 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -19,10 +19,15 @@ def test_BRAINSCut_inputs(): histogramEqualization=dict(argstr='--histogramEqualization ', ), method=dict(argstr='--method %s', ), modelConfigurationFilename=dict( - argstr='--modelConfigurationFilename %s', ), + argstr='--modelConfigurationFilename %s', + extensions=None, + ), modelFilename=dict(argstr='--modelFilename %s', ), multiStructureThreshold=dict(argstr='--multiStructureThreshold ', ), - netConfiguration=dict(argstr='--netConfiguration %s', ), + netConfiguration=dict( + argstr='--netConfiguration %s', + extensions=None, + ), numberOfTrees=dict(argstr='--numberOfTrees %d', ), randomTreeDepth=dict(argstr='--randomTreeDepth %d', ), trainModel=dict(argstr='--trainModel ', ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index 826ec19f0e..5b1ba96146 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -10,7 +10,10 @@ def test_BRAINSMultiSTAPLE_inputs(): nohash=True, usedefault=True, ), - inputCompositeT1Volume=dict(argstr='--inputCompositeT1Volume %s', ), + inputCompositeT1Volume=dict( + argstr='--inputCompositeT1Volume %s', + extensions=None, + ), inputLabelVolume=dict(argstr='--inputLabelVolume %s...', ), inputTransform=dict(argstr='--inputTransform %s...', ), labelForUndecidedPixels=dict(argstr='--labelForUndecidedPixels %d', ), @@ -32,8 +35,8 @@ def test_BRAINSMultiSTAPLE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMultiSTAPLE_outputs(): output_map = dict( - outputConfusionMatrix=dict(), - outputMultiSTAPLE=dict(), + outputConfusionMatrix=dict(extensions=None, ), + outputMultiSTAPLE=dict(extensions=None, ), ) outputs = BRAINSMultiSTAPLE.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index 3e70b75883..469387ff3d 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -13,7 +13,10 @@ def test_BRAINSROIAuto_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), maskOutput=dict(argstr='--maskOutput ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), @@ -36,8 +39,8 @@ def test_BRAINSROIAuto_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): output_map = dict( - outputROIMaskVolume=dict(), - outputVolume=dict(), + outputROIMaskVolume=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = BRAINSROIAuto.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index d71e7003ff..126db9eddb 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -10,7 +10,10 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): nohash=True, usedefault=True, ), - inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), + inputBinaryVolume=dict( + argstr='--inputBinaryVolume %s', + extensions=None, + ), inputLandmarkNames=dict( argstr='--inputLandmarkNames %s', sep=',', @@ -19,7 +22,10 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): argstr='--inputLandmarkNamesForObliquePlane %s', sep=',', ), - inputLandmarksFilename=dict(argstr='--inputLandmarksFilename %s', ), + inputLandmarksFilename=dict( + argstr='--inputLandmarksFilename %s', + extensions=None, + ), outputBinaryVolume=dict( argstr='--outputBinaryVolume %s', hash_files=False, @@ -39,7 +45,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaskEditorBasedOnLandmarks_outputs(): - output_map = dict(outputBinaryVolume=dict(), ) + output_map = dict(outputBinaryVolume=dict(extensions=None, ), ) outputs = BinaryMaskEditorBasedOnLandmarks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index 2e099b4f56..f8848a6efb 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -12,7 +12,10 @@ def test_ESLR_inputs(): usedefault=True, ), high=dict(argstr='--high %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), low=dict(argstr='--low %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), openingSize=dict(argstr='--openingSize %d', ), @@ -29,7 +32,7 @@ def test_ESLR_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ESLR_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = ESLR.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index c00b0cc36f..1d9b9f4f71 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -10,8 +10,14 @@ def test_DWICompare_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + extensions=None, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + extensions=None, + ), ) inputs = DWICompare.input_spec() diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index e515bc613c..b76979129f 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -11,8 +11,14 @@ def test_DWISimpleCompare_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + extensions=None, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + extensions=None, + ), ) inputs = DWISimpleCompare.input_spec() diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index 63f45831af..ac8ae0efeb 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -10,7 +10,10 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): nohash=True, usedefault=True, ), - inputCassifiedVolume=dict(argstr='--inputCassifiedVolume %s', ), + inputCassifiedVolume=dict( + argstr='--inputCassifiedVolume %s', + extensions=None, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -22,7 +25,7 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateCsfClippedFromClassifiedImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = GenerateCsfClippedFromClassifiedImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index 27b65a4eba..5db3d12da1 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -15,7 +15,10 @@ def test_BRAINSAlignMSP_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -40,7 +43,7 @@ def test_BRAINSAlignMSP_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSAlignMSP_outputs(): output_map = dict( - OutputresampleMSP=dict(), + OutputresampleMSP=dict(extensions=None, ), resultsDir=dict(), ) outputs = BRAINSAlignMSP.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index 7a0528f201..1585e4152d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -12,7 +12,10 @@ def test_BRAINSClipInferior_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_BRAINSClipInferior_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSClipInferior_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSClipInferior.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index a124ad60d9..38eba27d7e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -11,7 +11,10 @@ def test_BRAINSConstellationModeler_inputs(): nohash=True, usedefault=True, ), - inputTrainingList=dict(argstr='--inputTrainingList %s', ), + inputTrainingList=dict( + argstr='--inputTrainingList %s', + extensions=None, + ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), optimizedLandmarksFilenameExtender=dict( @@ -42,7 +45,7 @@ def test_BRAINSConstellationModeler_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationModeler_outputs(): output_map = dict( - outputModel=dict(), + outputModel=dict(extensions=None, ), resultsDir=dict(), ) outputs = BRAINSConstellationModeler.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index 9df3c8b8d6..0d9179f13f 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -11,7 +11,10 @@ def test_BRAINSEyeDetector_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +27,7 @@ def test_BRAINSEyeDetector_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSEyeDetector_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSEyeDetector.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index bc3807f9f8..46aac4e578 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -10,7 +10,10 @@ def test_BRAINSInitializedControlPoints_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputLandmarksFile=dict(argstr='--outputLandmarksFile %s', ), outputVolume=dict( @@ -32,7 +35,7 @@ def test_BRAINSInitializedControlPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSInitializedControlPoints_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSInitializedControlPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index 2456b8fb4d..172e076e6e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -11,10 +11,17 @@ def test_BRAINSLandmarkInitializer_inputs(): usedefault=True, ), inputFixedLandmarkFilename=dict( - argstr='--inputFixedLandmarkFilename %s', ), + argstr='--inputFixedLandmarkFilename %s', + extensions=None, + ), inputMovingLandmarkFilename=dict( - argstr='--inputMovingLandmarkFilename %s', ), - inputWeightFilename=dict(argstr='--inputWeightFilename %s', ), + argstr='--inputMovingLandmarkFilename %s', + extensions=None, + ), + inputWeightFilename=dict( + argstr='--inputWeightFilename %s', + extensions=None, + ), outputTransformFilename=dict( argstr='--outputTransformFilename %s', hash_files=False, @@ -26,7 +33,7 @@ def test_BRAINSLandmarkInitializer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLandmarkInitializer_outputs(): - output_map = dict(outputTransformFilename=dict(), ) + output_map = dict(outputTransformFilename=dict(extensions=None, ), ) outputs = BRAINSLandmarkInitializer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index b6b83baa12..1dc026f988 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -10,7 +10,10 @@ def test_BRAINSLinearModelerEPCA_inputs(): nohash=True, usedefault=True, ), - inputTrainingList=dict(argstr='--inputTrainingList %s', ), + inputTrainingList=dict( + argstr='--inputTrainingList %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), ) inputs = BRAINSLinearModelerEPCA.input_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 262d948029..876ab830c5 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -10,10 +10,22 @@ def test_BRAINSLmkTransform_inputs(): nohash=True, usedefault=True, ), - inputFixedLandmarks=dict(argstr='--inputFixedLandmarks %s', ), - inputMovingLandmarks=dict(argstr='--inputMovingLandmarks %s', ), - inputMovingVolume=dict(argstr='--inputMovingVolume %s', ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), + inputFixedLandmarks=dict( + argstr='--inputFixedLandmarks %s', + extensions=None, + ), + inputMovingLandmarks=dict( + argstr='--inputMovingLandmarks %s', + extensions=None, + ), + inputMovingVolume=dict( + argstr='--inputMovingVolume %s', + extensions=None, + ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputAffineTransform=dict( argstr='--outputAffineTransform %s', @@ -31,8 +43,8 @@ def test_BRAINSLmkTransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLmkTransform_outputs(): output_map = dict( - outputAffineTransform=dict(), - outputResampledVolume=dict(), + outputAffineTransform=dict(extensions=None, ), + outputResampledVolume=dict(extensions=None, ), ) outputs = BRAINSLmkTransform.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 9627258bcf..cb612ee8f2 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -20,9 +20,18 @@ def test_BRAINSMush_inputs(): nohash=True, usedefault=True, ), - inputFirstVolume=dict(argstr='--inputFirstVolume %s', ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), - inputSecondVolume=dict(argstr='--inputSecondVolume %s', ), + inputFirstVolume=dict( + argstr='--inputFirstVolume %s', + extensions=None, + ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + extensions=None, + ), + inputSecondVolume=dict( + argstr='--inputSecondVolume %s', + extensions=None, + ), lowerThresholdFactor=dict(argstr='--lowerThresholdFactor %f', ), lowerThresholdFactorPre=dict(argstr='--lowerThresholdFactorPre %f', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -52,9 +61,9 @@ def test_BRAINSMush_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMush_outputs(): output_map = dict( - outputMask=dict(), - outputVolume=dict(), - outputWeightsFile=dict(), + outputMask=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), + outputWeightsFile=dict(extensions=None, ), ) outputs = BRAINSMush.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index 1b803956e7..573252e1fc 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -39,7 +39,7 @@ def test_BRAINSSnapShotWriter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSSnapShotWriter_outputs(): - output_map = dict(outputFilename=dict(), ) + output_map = dict(outputFilename=dict(extensions=None, ), ) outputs = BRAINSSnapShotWriter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index c6d10736d7..29309f53b0 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -14,14 +14,20 @@ def test_BRAINSTransformConvert_inputs(): nohash=True, usedefault=True, ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputTransform=dict( + argstr='--inputTransform %s', + extensions=None, + ), outputPrecisionType=dict(argstr='--outputPrecisionType %s', ), outputTransform=dict( argstr='--outputTransform %s', hash_files=False, ), outputTransformType=dict(argstr='--outputTransformType %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + extensions=None, + ), ) inputs = BRAINSTransformConvert.input_spec() @@ -30,8 +36,8 @@ def test_BRAINSTransformConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformConvert_outputs(): output_map = dict( - displacementVolume=dict(), - outputTransform=dict(), + displacementVolume=dict(extensions=None, ), + outputTransform=dict(extensions=None, ), ) outputs = BRAINSTransformConvert.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index d2f3b74140..0bb8f0a13b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -14,7 +14,10 @@ def test_BRAINSTrimForegroundInDirection_inputs(): usedefault=True, ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), outputVolume=dict( @@ -28,7 +31,7 @@ def test_BRAINSTrimForegroundInDirection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTrimForegroundInDirection_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSTrimForegroundInDirection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index 46924bf180..339f9a19ba 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -40,8 +40,14 @@ def test_FindCenterOfBrain_inputs(): generateDebugImages=dict(argstr='--generateDebugImages ', ), headSizeEstimate=dict(argstr='--headSizeEstimate %f', ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - imageMask=dict(argstr='--imageMask %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + imageMask=dict( + argstr='--imageMask %s', + extensions=None, + ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), maximize=dict(argstr='--maximize ', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), ) @@ -52,12 +58,12 @@ def test_FindCenterOfBrain_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FindCenterOfBrain_outputs(): output_map = dict( - clippedImageMask=dict(), - debugAfterGridComputationsForegroundImage=dict(), - debugClippedImageMask=dict(), - debugDistanceImage=dict(), - debugGridImage=dict(), - debugTrimmedImage=dict(), + clippedImageMask=dict(extensions=None, ), + debugAfterGridComputationsForegroundImage=dict(extensions=None, ), + debugClippedImageMask=dict(extensions=None, ), + debugDistanceImage=dict(extensions=None, ), + debugGridImage=dict(extensions=None, ), + debugTrimmedImage=dict(extensions=None, ), ) outputs = FindCenterOfBrain.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index 9087d6667b..caf6323e68 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -23,7 +23,7 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateLabelMapFromProbabilityMap_outputs(): - output_map = dict(outputLabelVolume=dict(), ) + output_map = dict(outputLabelVolume=dict(extensions=None, ), ) outputs = GenerateLabelMapFromProbabilityMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index f5372a240e..3cc1740778 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -10,10 +10,22 @@ def test_ImageRegionPlotter_inputs(): nohash=True, usedefault=True, ), - inputBinaryROIVolume=dict(argstr='--inputBinaryROIVolume %s', ), - inputLabelVolume=dict(argstr='--inputLabelVolume %s', ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputBinaryROIVolume=dict( + argstr='--inputBinaryROIVolume %s', + extensions=None, + ), + inputLabelVolume=dict( + argstr='--inputLabelVolume %s', + extensions=None, + ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + extensions=None, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + extensions=None, + ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), outputJointHistogramData=dict( argstr='--outputJointHistogramData %s', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index daf6d5634f..c686badea2 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -10,10 +10,22 @@ def test_JointHistogram_inputs(): nohash=True, usedefault=True, ), - inputMaskVolumeInXAxis=dict(argstr='--inputMaskVolumeInXAxis %s', ), - inputMaskVolumeInYAxis=dict(argstr='--inputMaskVolumeInYAxis %s', ), - inputVolumeInXAxis=dict(argstr='--inputVolumeInXAxis %s', ), - inputVolumeInYAxis=dict(argstr='--inputVolumeInYAxis %s', ), + inputMaskVolumeInXAxis=dict( + argstr='--inputMaskVolumeInXAxis %s', + extensions=None, + ), + inputMaskVolumeInYAxis=dict( + argstr='--inputMaskVolumeInYAxis %s', + extensions=None, + ), + inputVolumeInXAxis=dict( + argstr='--inputVolumeInXAxis %s', + extensions=None, + ), + inputVolumeInYAxis=dict( + argstr='--inputVolumeInYAxis %s', + extensions=None, + ), outputJointHistogramImage=dict( argstr='--outputJointHistogramImage %s', ), verbose=dict(argstr='--verbose ', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index 7bea38e2f1..1f50a296ab 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -10,7 +10,10 @@ def test_ShuffleVectorsModule_inputs(): nohash=True, usedefault=True, ), - inputVectorFileBaseName=dict(argstr='--inputVectorFileBaseName %s', ), + inputVectorFileBaseName=dict( + argstr='--inputVectorFileBaseName %s', + extensions=None, + ), outputVectorFileBaseName=dict( argstr='--outputVectorFileBaseName %s', hash_files=False, @@ -23,7 +26,7 @@ def test_ShuffleVectorsModule_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ShuffleVectorsModule_outputs(): - output_map = dict(outputVectorFileBaseName=dict(), ) + output_map = dict(outputVectorFileBaseName=dict(extensions=None, ), ) outputs = ShuffleVectorsModule.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index 32e6ce65cd..2134ec42f0 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -11,7 +11,10 @@ def test_fcsv_to_hdf5_inputs(): usedefault=True, ), landmarkGlobPattern=dict(argstr='--landmarkGlobPattern %s', ), - landmarkTypesList=dict(argstr='--landmarkTypesList %s', ), + landmarkTypesList=dict( + argstr='--landmarkTypesList %s', + extensions=None, + ), landmarksInformationFile=dict( argstr='--landmarksInformationFile %s', hash_files=False, @@ -30,8 +33,8 @@ def test_fcsv_to_hdf5_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_fcsv_to_hdf5_outputs(): output_map = dict( - landmarksInformationFile=dict(), - modelFile=dict(), + landmarksInformationFile=dict(extensions=None, ), + modelFile=dict(extensions=None, ), ) outputs = fcsv_to_hdf5.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index 196b09b304..042194c5ea 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -10,7 +10,10 @@ def test_insertMidACPCpoint_inputs(): nohash=True, usedefault=True, ), - inputLandmarkFile=dict(argstr='--inputLandmarkFile %s', ), + inputLandmarkFile=dict( + argstr='--inputLandmarkFile %s', + extensions=None, + ), outputLandmarkFile=dict( argstr='--outputLandmarkFile %s', hash_files=False, @@ -22,7 +25,7 @@ def test_insertMidACPCpoint_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_insertMidACPCpoint_outputs(): - output_map = dict(outputLandmarkFile=dict(), ) + output_map = dict(outputLandmarkFile=dict(extensions=None, ), ) outputs = insertMidACPCpoint.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index 151a2c7b3a..860a0a972e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -10,7 +10,10 @@ def test_landmarksConstellationAligner_inputs(): nohash=True, usedefault=True, ), - inputLandmarksPaired=dict(argstr='--inputLandmarksPaired %s', ), + inputLandmarksPaired=dict( + argstr='--inputLandmarksPaired %s', + extensions=None, + ), outputLandmarksPaired=dict( argstr='--outputLandmarksPaired %s', hash_files=False, @@ -22,7 +25,7 @@ def test_landmarksConstellationAligner_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationAligner_outputs(): - output_map = dict(outputLandmarksPaired=dict(), ) + output_map = dict(outputLandmarksPaired=dict(extensions=None, ), ) outputs = landmarksConstellationAligner.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index 0bcd747d36..689c78de76 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -5,14 +5,23 @@ def test_landmarksConstellationWeights_inputs(): input_map = dict( - LLSModel=dict(argstr='--LLSModel %s', ), + LLSModel=dict( + argstr='--LLSModel %s', + extensions=None, + ), args=dict(argstr='%s', ), environ=dict( nohash=True, usedefault=True, ), - inputTemplateModel=dict(argstr='--inputTemplateModel %s', ), - inputTrainingList=dict(argstr='--inputTrainingList %s', ), + inputTemplateModel=dict( + argstr='--inputTemplateModel %s', + extensions=None, + ), + inputTrainingList=dict( + argstr='--inputTrainingList %s', + extensions=None, + ), outputWeightsList=dict( argstr='--outputWeightsList %s', hash_files=False, @@ -24,7 +33,7 @@ def test_landmarksConstellationWeights_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationWeights_outputs(): - output_map = dict(outputWeightsList=dict(), ) + output_map = dict(outputWeightsList=dict(extensions=None, ), ) outputs = landmarksConstellationWeights.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 c8d5df2ba2..1ca79a6e96 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -12,6 +12,7 @@ def test_DTIexport_inputs(): ), inputTensor=dict( argstr='%s', + extensions=None, position=-2, ), outputFile=dict( @@ -26,7 +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(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 ec1d66bc0b..58ae495f3f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -12,6 +12,7 @@ def test_DTIimport_inputs(): ), inputFile=dict( argstr='%s', + extensions=None, position=-2, ), outputTensor=dict( @@ -27,7 +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(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 a2caa2f633..f8000c49b1 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -13,6 +13,7 @@ def test_DWIJointRicianLMMSEFilter_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), ng=dict(argstr='--ng %d', ), @@ -36,7 +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(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 7eff851562..29b5e0b7e1 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -14,6 +14,7 @@ def test_DWIRicianLMMSEFilter_inputs(): hrf=dict(argstr='--hrf %f', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), iter=dict(argstr='--iter %d', ), @@ -42,7 +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(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_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index 217f91edf0..4f9702bb32 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -13,9 +13,13 @@ def test_DWIToDTIEstimation_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-3, ), - mask=dict(argstr='--mask %s', ), + mask=dict( + argstr='--mask %s', + extensions=None, + ), outputBaseline=dict( argstr='%s', hash_files=False, @@ -35,8 +39,14 @@ def test_DWIToDTIEstimation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIToDTIEstimation_outputs(): output_map = dict( - outputBaseline=dict(position=-1, ), - outputTensor=dict(position=-2, ), + outputBaseline=dict( + extensions=None, + position=-1, + ), + outputTensor=dict( + extensions=None, + position=-2, + ), ) outputs = DWIToDTIEstimation.output_spec() diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index b75989c349..5dcdbd7e2e 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -13,6 +13,7 @@ def test_DiffusionTensorScalarMeasurements_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-3, ), outputScalar=dict( @@ -27,7 +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(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_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index 5e8c39a4ac..e023e6293c 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -12,6 +12,7 @@ def test_DiffusionWeightedVolumeMasking_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-4, ), otsuomegathreshold=dict(argstr='--otsuomegathreshold %f', ), @@ -34,8 +35,14 @@ def test_DiffusionWeightedVolumeMasking_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionWeightedVolumeMasking_outputs(): output_map = dict( - outputBaseline=dict(position=-2, ), - thresholdMask=dict(position=-1, ), + outputBaseline=dict( + extensions=None, + position=-2, + ), + thresholdMask=dict( + extensions=None, + position=-1, + ), ) outputs = DiffusionWeightedVolumeMasking.output_spec() diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 30860d9da0..bd35268bdb 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -7,11 +7,17 @@ def test_ResampleDTIVolume_inputs(): input_map = dict( Inverse_ITK_Transformation=dict( argstr='--Inverse_ITK_Transformation ', ), - Reference=dict(argstr='--Reference %s', ), + Reference=dict( + argstr='--Reference %s', + extensions=None, + ), args=dict(argstr='%s', ), centered_transform=dict(argstr='--centered_transform ', ), correction=dict(argstr='--correction %s', ), - defField=dict(argstr='--defField %s', ), + defField=dict( + argstr='--defField %s', + extensions=None, + ), default_pixel_value=dict(argstr='--default_pixel_value %f', ), direction_matrix=dict( argstr='--direction_matrix %s', @@ -25,6 +31,7 @@ def test_ResampleDTIVolume_inputs(): image_center=dict(argstr='--image_center %s', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), interpolation=dict(argstr='--interpolation %s', ), @@ -54,7 +61,10 @@ def test_ResampleDTIVolume_inputs(): ), transform_order=dict(argstr='--transform_order %s', ), transform_tensor_method=dict(argstr='--transform_tensor_method %s', ), - transformationFile=dict(argstr='--transformationFile %s', ), + transformationFile=dict( + argstr='--transformationFile %s', + extensions=None, + ), window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleDTIVolume.input_spec() @@ -63,7 +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(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/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index 31fb7d5c0d..09fef7d133 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -7,6 +7,7 @@ def test_TractographyLabelMapSeeding_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-2, ), OutputFibers=dict( @@ -20,7 +21,10 @@ def test_TractographyLabelMapSeeding_inputs(): nohash=True, usedefault=True, ), - inputroi=dict(argstr='--inputroi %s', ), + inputroi=dict( + argstr='--inputroi %s', + extensions=None, + ), integrationsteplength=dict(argstr='--integrationsteplength %f', ), label=dict(argstr='--label %d', ), maximumlength=dict(argstr='--maximumlength %f', ), @@ -45,7 +49,10 @@ def test_TractographyLabelMapSeeding_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TractographyLabelMapSeeding_outputs(): output_map = dict( - OutputFibers=dict(position=-1, ), + OutputFibers=dict( + extensions=None, + position=-1, + ), outputdirectory=dict(), ) outputs = TractographyLabelMapSeeding.output_spec() diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 9f2209c1eb..d2b17c562a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -12,10 +12,12 @@ def test_AddScalarVolumes_inputs(): ), inputVolume1=dict( argstr='%s', + extensions=None, position=-3, ), inputVolume2=dict( argstr='%s', + extensions=None, position=-2, ), order=dict(argstr='--order %s', ), @@ -31,7 +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(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 a659aa47f7..bbcb2f077c 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -7,6 +7,7 @@ def test_CastScalarVolume_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-2, ), OutputVolume=dict( @@ -27,7 +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(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 ae662cf2ba..24f5b74307 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -16,10 +16,12 @@ def test_CheckerBoardFilter_inputs(): ), inputVolume1=dict( argstr='%s', + extensions=None, position=-3, ), inputVolume2=dict( argstr='%s', + extensions=None, position=-2, ), outputVolume=dict( @@ -34,7 +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(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 5613eb0c4c..0240ad676a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -13,6 +13,7 @@ def test_CurvatureAnisotropicDiffusion_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), iterations=dict(argstr='--iterations %d', ), @@ -29,7 +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(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 5db6c65c7e..c47382aef5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -7,6 +7,7 @@ def test_ExtractSkeleton_inputs(): input_map = dict( InputImageFileName=dict( argstr='%s', + extensions=None, position=-2, ), OutputImageFileName=dict( @@ -30,7 +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(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 ff46d6d308..2bdb73c4d5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -12,6 +12,7 @@ def test_GaussianBlurImageFilter_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), outputVolume=dict( @@ -27,7 +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(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 8ec7dbb156..6d3e40c8de 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -13,6 +13,7 @@ def test_GradientAnisotropicDiffusion_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), iterations=dict(argstr='--iterations %d', ), @@ -29,7 +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(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 062a23c293..f1ff2c3809 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -12,6 +12,7 @@ def test_GrayscaleFillHoleImageFilter_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), outputVolume=dict( @@ -26,7 +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(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 edb6081ed3..6aee86282a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -12,6 +12,7 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), outputVolume=dict( @@ -26,7 +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(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 f73690586d..c839c50abf 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -12,6 +12,7 @@ def test_HistogramMatching_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-3, ), numberOfHistogramLevels=dict(argstr='--numberOfHistogramLevels %d', ), @@ -23,6 +24,7 @@ def test_HistogramMatching_inputs(): ), referenceVolume=dict( argstr='%s', + extensions=None, position=-2, ), threshold=dict(argstr='--threshold ', ), @@ -33,7 +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(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 0bae22c342..7fd2c31db3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -7,10 +7,12 @@ def test_ImageLabelCombine_inputs(): input_map = dict( InputLabelMap_A=dict( argstr='%s', + extensions=None, position=-3, ), InputLabelMap_B=dict( argstr='%s', + extensions=None, position=-2, ), OutputLabelMap=dict( @@ -31,7 +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(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 cd04072890..56d68199af 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -7,10 +7,12 @@ def test_MaskScalarVolume_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-3, ), MaskVolume=dict( argstr='%s', + extensions=None, position=-2, ), OutputVolume=dict( @@ -32,7 +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(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 35bb9496c9..c0bf97e152 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -12,6 +12,7 @@ def test_MedianImageFilter_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), neighborhood=dict( @@ -30,7 +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(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 6590c4b133..cc39d5b7b1 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -12,10 +12,12 @@ def test_MultiplyScalarVolumes_inputs(): ), inputVolume1=dict( argstr='%s', + extensions=None, position=-3, ), inputVolume2=dict( argstr='%s', + extensions=None, position=-2, ), order=dict(argstr='--order %s', ), @@ -31,7 +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(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_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index c6ad0bf24d..b2ce50a0fa 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -16,12 +16,18 @@ def test_N4ITKBiasFieldCorrection_inputs(): argstr='--histogramsharpening %s', sep=',', ), - inputimage=dict(argstr='--inputimage %s', ), + inputimage=dict( + argstr='--inputimage %s', + extensions=None, + ), iterations=dict( argstr='--iterations %s', sep=',', ), - maskimage=dict(argstr='--maskimage %s', ), + maskimage=dict( + argstr='--maskimage %s', + extensions=None, + ), meshresolution=dict( argstr='--meshresolution %s', sep=',', @@ -36,7 +42,10 @@ def test_N4ITKBiasFieldCorrection_inputs(): ), shrinkfactor=dict(argstr='--shrinkfactor %d', ), splinedistance=dict(argstr='--splinedistance %f', ), - weightimage=dict(argstr='--weightimage %s', ), + weightimage=dict( + argstr='--weightimage %s', + extensions=None, + ), ) inputs = N4ITKBiasFieldCorrection.input_spec() @@ -45,8 +54,8 @@ def test_N4ITKBiasFieldCorrection_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_N4ITKBiasFieldCorrection_outputs(): output_map = dict( - outputbiasfield=dict(), - outputimage=dict(), + outputbiasfield=dict(extensions=None, ), + outputimage=dict(extensions=None, ), ) outputs = N4ITKBiasFieldCorrection.output_spec() diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index ebe34fd9b3..12d7af77c4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -7,10 +7,16 @@ def test_ResampleScalarVectorDWIVolume_inputs(): input_map = dict( Inverse_ITK_Transformation=dict( argstr='--Inverse_ITK_Transformation ', ), - Reference=dict(argstr='--Reference %s', ), + Reference=dict( + argstr='--Reference %s', + extensions=None, + ), args=dict(argstr='%s', ), centered_transform=dict(argstr='--centered_transform ', ), - defField=dict(argstr='--defField %s', ), + defField=dict( + argstr='--defField %s', + extensions=None, + ), default_pixel_value=dict(argstr='--default_pixel_value %f', ), direction_matrix=dict( argstr='--direction_matrix %s', @@ -24,6 +30,7 @@ def test_ResampleScalarVectorDWIVolume_inputs(): image_center=dict(argstr='--image_center %s', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), interpolation=dict(argstr='--interpolation %s', ), @@ -52,7 +59,10 @@ def test_ResampleScalarVectorDWIVolume_inputs(): sep=',', ), transform_order=dict(argstr='--transform_order %s', ), - transformationFile=dict(argstr='--transformationFile %s', ), + transformationFile=dict( + argstr='--transformationFile %s', + extensions=None, + ), window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleScalarVectorDWIVolume.input_spec() @@ -61,7 +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(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 d62589881f..106cd843a4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -12,10 +12,12 @@ def test_SubtractScalarVolumes_inputs(): ), inputVolume1=dict( argstr='%s', + extensions=None, position=-3, ), inputVolume2=dict( argstr='%s', + extensions=None, position=-2, ), order=dict(argstr='--order %s', ), @@ -31,7 +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(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 34de317104..e63ed5923f 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -7,6 +7,7 @@ def test_ThresholdScalarVolume_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-2, ), OutputVolume=dict( @@ -31,7 +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(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 8e7890de85..89832bf9ba 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -14,6 +14,7 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): foreground=dict(argstr='--foreground %d', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), majorityThreshold=dict(argstr='--majorityThreshold %d', ), @@ -33,7 +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(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 0e25ffad9a..f3c1ec6ff0 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -13,6 +13,7 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): hp=dict(argstr='--hp %f', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), ng=dict(argstr='--ng %d', ), @@ -40,7 +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(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_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index 949cdc7f61..059e7ee694 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -7,10 +7,12 @@ def test_AffineRegistration_inputs(): input_map = dict( FixedImageFileName=dict( argstr='%s', + extensions=None, position=-2, ), MovingImageFileName=dict( argstr='%s', + extensions=None, position=-1, ), args=dict(argstr='%s', ), @@ -20,7 +22,10 @@ def test_AffineRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + extensions=None, + ), iterations=dict(argstr='--iterations %d', ), movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', ), outputtransform=dict( @@ -41,8 +46,8 @@ def test_AffineRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AffineRegistration_outputs(): output_map = dict( - outputtransform=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(extensions=None, ), + resampledmovingfilename=dict(extensions=None, ), ) outputs = AffineRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 17339f8859..bee2d60af6 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -7,10 +7,12 @@ def test_BSplineDeformableRegistration_inputs(): input_map = dict( FixedImageFileName=dict( argstr='%s', + extensions=None, position=-2, ), MovingImageFileName=dict( argstr='%s', + extensions=None, position=-1, ), args=dict(argstr='%s', ), @@ -22,7 +24,10 @@ def test_BSplineDeformableRegistration_inputs(): ), gridSize=dict(argstr='--gridSize %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + extensions=None, + ), iterations=dict(argstr='--iterations %d', ), maximumDeformation=dict(argstr='--maximumDeformation %f', ), outputtransform=dict( @@ -46,9 +51,9 @@ def test_BSplineDeformableRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BSplineDeformableRegistration_outputs(): output_map = dict( - outputtransform=dict(), - outputwarp=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(extensions=None, ), + outputwarp=dict(extensions=None, ), + resampledmovingfilename=dict(extensions=None, ), ) outputs = BSplineDeformableRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 8335515c13..cba80ed391 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -14,8 +14,14 @@ def test_BSplineToDeformationField_inputs(): nohash=True, usedefault=True, ), - refImage=dict(argstr='--refImage %s', ), - tfm=dict(argstr='--tfm %s', ), + refImage=dict( + argstr='--refImage %s', + extensions=None, + ), + tfm=dict( + argstr='--tfm %s', + extensions=None, + ), ) inputs = BSplineToDeformationField.input_spec() @@ -23,7 +29,7 @@ def test_BSplineToDeformationField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BSplineToDeformationField_outputs(): - output_map = dict(defImage=dict(), ) + output_map = dict(defImage=dict(extensions=None, ), ) outputs = BSplineToDeformationField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 7fa8b77d63..8cf4622906 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -21,17 +21,25 @@ def test_ExpertAutomatedRegistration_inputs(): expectedSkew=dict(argstr='--expectedSkew %f', ), fixedImage=dict( argstr='%s', + extensions=None, position=-2, ), - fixedImageMask=dict(argstr='--fixedImageMask %s', ), + fixedImageMask=dict( + argstr='--fixedImageMask %s', + extensions=None, + ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), initialization=dict(argstr='--initialization %s', ), interpolation=dict(argstr='--interpolation %s', ), - loadTransform=dict(argstr='--loadTransform %s', ), + loadTransform=dict( + argstr='--loadTransform %s', + extensions=None, + ), metric=dict(argstr='--metric %s', ), minimizeMemory=dict(argstr='--minimizeMemory ', ), movingImage=dict( argstr='%s', + extensions=None, position=-1, ), movingLandmarks=dict(argstr='--movingLandmarks %s...', ), @@ -58,8 +66,8 @@ def test_ExpertAutomatedRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ExpertAutomatedRegistration_outputs(): output_map = dict( - resampledImage=dict(), - saveTransform=dict(), + resampledImage=dict(extensions=None, ), + saveTransform=dict(extensions=None, ), ) outputs = ExpertAutomatedRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index a55432f9b0..50a9f2b292 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -7,10 +7,12 @@ def test_LinearRegistration_inputs(): input_map = dict( FixedImageFileName=dict( argstr='%s', + extensions=None, position=-2, ), MovingImageFileName=dict( argstr='%s', + extensions=None, position=-1, ), args=dict(argstr='%s', ), @@ -20,7 +22,10 @@ def test_LinearRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + extensions=None, + ), iterations=dict( argstr='--iterations %s', sep=',', @@ -48,8 +53,8 @@ def test_LinearRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_LinearRegistration_outputs(): output_map = dict( - outputtransform=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(extensions=None, ), + resampledmovingfilename=dict(extensions=None, ), ) outputs = LinearRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index 7903fd1d5c..f6cfc49710 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -12,13 +12,18 @@ def test_MultiResolutionAffineRegistration_inputs(): ), fixedImage=dict( argstr='%s', + extensions=None, position=-2, ), - fixedImageMask=dict(argstr='--fixedImageMask %s', ), + fixedImageMask=dict( + argstr='--fixedImageMask %s', + extensions=None, + ), fixedImageROI=dict(argstr='--fixedImageROI %s', ), metricTolerance=dict(argstr='--metricTolerance %f', ), movingImage=dict( argstr='%s', + extensions=None, position=-1, ), numIterations=dict(argstr='--numIterations %d', ), @@ -41,8 +46,8 @@ def test_MultiResolutionAffineRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MultiResolutionAffineRegistration_outputs(): output_map = dict( - resampledImage=dict(), - saveTransform=dict(), + resampledImage=dict(extensions=None, ), + saveTransform=dict(extensions=None, ), ) outputs = MultiResolutionAffineRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index a1af6c71b3..19b41f7127 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -12,6 +12,7 @@ def test_OtsuThresholdImageFilter_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), insideValue=dict(argstr='--insideValue %d', ), @@ -29,7 +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(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 02beeee464..b9fa12f2aa 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -14,6 +14,7 @@ def test_OtsuThresholdSegmentation_inputs(): faceConnected=dict(argstr='--faceConnected ', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), minimumObjectSize=dict(argstr='--minimumObjectSize %d', ), @@ -30,7 +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(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 baa698246c..7f1c259cd6 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -7,6 +7,7 @@ def test_ResampleScalarVolume_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-2, ), OutputVolume=dict( @@ -31,7 +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(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/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index 6c2a0eb072..1c29d1295a 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -7,10 +7,12 @@ def test_RigidRegistration_inputs(): input_map = dict( FixedImageFileName=dict( argstr='%s', + extensions=None, position=-2, ), MovingImageFileName=dict( argstr='%s', + extensions=None, position=-1, ), args=dict(argstr='%s', ), @@ -20,7 +22,10 @@ def test_RigidRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + extensions=None, + ), iterations=dict( argstr='--iterations %s', sep=',', @@ -49,8 +54,8 @@ def test_RigidRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RigidRegistration_outputs(): output_map = dict( - outputtransform=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(extensions=None, ), + resampledmovingfilename=dict(extensions=None, ), ) outputs = RigidRegistration.output_spec() diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index e46f046add..386e368de7 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -8,10 +8,12 @@ def test_IntensityDifferenceMetric_inputs(): args=dict(argstr='%s', ), baselineSegmentationVolume=dict( argstr='%s', + extensions=None, position=-3, ), baselineVolume=dict( argstr='%s', + extensions=None, position=-4, ), changingBandSize=dict(argstr='--changingBandSize %d', ), @@ -21,6 +23,7 @@ def test_IntensityDifferenceMetric_inputs(): ), followupVolume=dict( argstr='%s', + extensions=None, position=-2, ), outputVolume=dict( @@ -41,8 +44,11 @@ def test_IntensityDifferenceMetric_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_IntensityDifferenceMetric_outputs(): output_map = dict( - outputVolume=dict(position=-1, ), - reportFileName=dict(), + outputVolume=dict( + extensions=None, + position=-1, + ), + reportFileName=dict(extensions=None, ), ) outputs = IntensityDifferenceMetric.output_spec() diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 61141f65db..51ae985574 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -11,7 +11,10 @@ def test_PETStandardUptakeValueComputation_inputs(): SUVMean=dict(argstr='--SUVMean %s', ), SUVMin=dict(argstr='--SUVMin %s', ), args=dict(argstr='%s', ), - color=dict(argstr='--color %s', ), + color=dict( + argstr='--color %s', + extensions=None, + ), csvFile=dict( argstr='--csvFile %s', hash_files=False, @@ -20,9 +23,15 @@ def test_PETStandardUptakeValueComputation_inputs(): nohash=True, usedefault=True, ), - labelMap=dict(argstr='--labelMap %s', ), + labelMap=dict( + argstr='--labelMap %s', + extensions=None, + ), petDICOMPath=dict(argstr='--petDICOMPath %s', ), - petVolume=dict(argstr='--petVolume %s', ), + petVolume=dict( + argstr='--petVolume %s', + extensions=None, + ), ) inputs = PETStandardUptakeValueComputation.input_spec() @@ -30,7 +39,7 @@ def test_PETStandardUptakeValueComputation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PETStandardUptakeValueComputation_outputs(): - output_map = dict(csvFile=dict(), ) + output_map = dict(csvFile=dict(extensions=None, ), ) outputs = PETStandardUptakeValueComputation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index 454e290102..c8969b06b7 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -24,7 +24,7 @@ def test_ACPCTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ACPCTransform_outputs(): - output_map = dict(outputTransform=dict(), ) + output_map = dict(outputTransform=dict(extensions=None, ), ) outputs = ACPCTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index c631f9b96e..18cd4c63ff 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -19,14 +19,25 @@ def test_BRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + extensions=None, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + extensions=None, + ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + extensions=None, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + extensions=None, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,8 +55,14 @@ def test_BRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + extensions=None, + ), + movingVolume=dict( + argstr='--movingVolume %s', + extensions=None, + ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', sep=',', @@ -92,9 +109,9 @@ def test_BRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(extensions=None, ), + outputDisplacementFieldVolume=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = BRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index bb62633d94..450dc2ed9b 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -28,13 +28,22 @@ def test_BRAINSFit_inputs(): usedefault=True, ), failureExitCode=dict(argstr='--failureExitCode %d', ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + extensions=None, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + extensions=None, + ), fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', ), forceMINumberOfThreads=dict(argstr='--forceMINumberOfThreads %d', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), - initialTransform=dict(argstr='--initialTransform %s', ), + initialTransform=dict( + argstr='--initialTransform %s', + extensions=None, + ), initializeTransformMode=dict(argstr='--initializeTransformMode %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), linearTransform=dict( @@ -54,8 +63,14 @@ def test_BRAINSFit_inputs(): argstr='--minimumStepLength %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + extensions=None, + ), + movingVolume=dict( + argstr='--movingVolume %s', + extensions=None, + ), movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfIterations=dict( @@ -127,13 +142,13 @@ def test_BRAINSFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): output_map = dict( - bsplineTransform=dict(), - linearTransform=dict(), - outputFixedVolumeROI=dict(), - outputMovingVolumeROI=dict(), - outputTransform=dict(), - outputVolume=dict(), - strippedOutputTransform=dict(), + bsplineTransform=dict(extensions=None, ), + linearTransform=dict(extensions=None, ), + outputFixedVolumeROI=dict(extensions=None, ), + outputMovingVolumeROI=dict(extensions=None, ), + outputTransform=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), + strippedOutputTransform=dict(extensions=None, ), ) outputs = BRAINSFit.output_spec() diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index 98ec5f4ff3..e8d4c187b0 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -7,7 +7,10 @@ def test_BRAINSResample_inputs(): input_map = dict( args=dict(argstr='%s', ), defaultValue=dict(argstr='--defaultValue %f', ), - deformationVolume=dict(argstr='--deformationVolume %s', ), + deformationVolume=dict( + argstr='--deformationVolume %s', + extensions=None, + ), environ=dict( nohash=True, usedefault=True, @@ -16,7 +19,10 @@ def test_BRAINSResample_inputs(): argstr='--gridSpacing %s', sep=',', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), inverseTransform=dict(argstr='--inverseTransform ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -25,8 +31,14 @@ def test_BRAINSResample_inputs(): hash_files=False, ), pixelType=dict(argstr='--pixelType %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), - warpTransform=dict(argstr='--warpTransform %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + extensions=None, + ), + warpTransform=dict( + argstr='--warpTransform %s', + extensions=None, + ), ) inputs = BRAINSResample.input_spec() @@ -34,7 +46,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(extensions=None, ), ) outputs = BRAINSResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index 36d42fe8df..d190957049 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -26,7 +26,7 @@ def test_FiducialRegistration_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FiducialRegistration_outputs(): - output_map = dict(saveTransform=dict(), ) + output_map = dict(saveTransform=dict(extensions=None, ), ) outputs = FiducialRegistration.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index b3255da1d3..b196d318d4 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -19,14 +19,22 @@ def test_VBRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + extensions=None, + ), fixedVolume=dict(argstr='--fixedVolume %s...', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + extensions=None, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + extensions=None, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,7 +52,10 @@ def test_VBRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + extensions=None, + ), movingVolume=dict(argstr='--movingVolume %s...', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', @@ -96,9 +107,9 @@ def test_VBRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(extensions=None, ), + outputDisplacementFieldVolume=dict(extensions=None, ), + outputVolume=dict(extensions=None, ), ) outputs = VBRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 89863fb730..8d56bade08 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -12,7 +12,10 @@ def test_BRAINSROIAuto_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + extensions=None, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), outputClippedVolumeROI=dict( @@ -34,8 +37,8 @@ def test_BRAINSROIAuto_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): output_map = dict( - outputClippedVolumeROI=dict(), - outputROIMaskVolume=dict(), + outputClippedVolumeROI=dict(extensions=None, ), + outputROIMaskVolume=dict(extensions=None, ), ) outputs = BRAINSROIAuto.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 09b0b1300f..f5b7a28b99 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -25,7 +25,10 @@ def test_EMSegmentCommandLine_inputs(): keepTempFiles=dict(argstr='--keepTempFiles ', ), loadAtlasNonCentered=dict(argstr='--loadAtlasNonCentered ', ), loadTargetCentered=dict(argstr='--loadTargetCentered ', ), - mrmlSceneFileName=dict(argstr='--mrmlSceneFileName %s', ), + mrmlSceneFileName=dict( + argstr='--mrmlSceneFileName %s', + extensions=None, + ), parametersMRMLNodeName=dict(argstr='--parametersMRMLNodeName %s', ), registrationAffineType=dict(argstr='--registrationAffineType %d', ), registrationDeformableType=dict( @@ -36,7 +39,9 @@ def test_EMSegmentCommandLine_inputs(): hash_files=False, ), resultStandardVolumeFileName=dict( - argstr='--resultStandardVolumeFileName %s', ), + argstr='--resultStandardVolumeFileName %s', + extensions=None, + ), resultVolumeFileName=dict( argstr='--resultVolumeFileName %s', hash_files=False, @@ -53,9 +58,9 @@ def test_EMSegmentCommandLine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentCommandLine_outputs(): output_map = dict( - generateEmptyMRMLSceneAndQuit=dict(), - resultMRMLSceneFileName=dict(), - resultVolumeFileName=dict(), + generateEmptyMRMLSceneAndQuit=dict(extensions=None, ), + resultMRMLSceneFileName=dict(extensions=None, ), + resultVolumeFileName=dict(extensions=None, ), ) outputs = EMSegmentCommandLine.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index ed46177df0..6befb36860 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -15,12 +15,14 @@ def test_RobustStatisticsSegmenter_inputs(): intensityHomogeneity=dict(argstr='--intensityHomogeneity %f', ), labelImageFileName=dict( argstr='%s', + extensions=None, position=-2, ), labelValue=dict(argstr='--labelValue %d', ), maxRunningTime=dict(argstr='--maxRunningTime %f', ), originalImageFileName=dict( argstr='%s', + extensions=None, position=-3, ), segmentedImageFileName=dict( @@ -35,7 +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(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 3c5e2124d0..5f880c08cb 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -12,6 +12,7 @@ def test_SimpleRegionGrowingSegmentation_inputs(): ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), iterations=dict(argstr='--iterations %d', ), @@ -33,7 +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(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_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index 279d68e0ab..8494a85837 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -10,7 +10,10 @@ def test_EMSegmentTransformToNewFormat_inputs(): nohash=True, usedefault=True, ), - inputMRMLFileName=dict(argstr='--inputMRMLFileName %s', ), + inputMRMLFileName=dict( + argstr='--inputMRMLFileName %s', + extensions=None, + ), outputMRMLFileName=dict( argstr='--outputMRMLFileName %s', hash_files=False, @@ -23,7 +26,7 @@ def test_EMSegmentTransformToNewFormat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentTransformToNewFormat_outputs(): - output_map = dict(outputMRMLFileName=dict(), ) + output_map = dict(outputMRMLFileName=dict(extensions=None, ), ) outputs = EMSegmentTransformToNewFormat.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 7ad8cac8e9..3669a21fc3 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -7,6 +7,7 @@ def test_GrayscaleModelMaker_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-2, ), OutputGeometry=dict( @@ -32,7 +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(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 bb3780495b..faf982a342 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -13,6 +13,7 @@ def test_LabelMapSmoothing_inputs(): gaussianSigma=dict(argstr='--gaussianSigma %f', ), inputVolume=dict( argstr='%s', + extensions=None, position=-2, ), labelToSmooth=dict(argstr='--labelToSmooth %d', ), @@ -30,7 +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(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 6453957a79..c25d4ebcf3 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -7,10 +7,12 @@ def test_MergeModels_inputs(): input_map = dict( Model1=dict( argstr='%s', + extensions=None, position=-3, ), Model2=dict( argstr='%s', + extensions=None, position=-2, ), ModelOutput=dict( @@ -30,7 +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(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_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index ed182137cf..164034a4e7 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -7,10 +7,14 @@ def test_ModelMaker_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-1, ), args=dict(argstr='%s', ), - color=dict(argstr='--color %s', ), + color=dict( + argstr='--color %s', + extensions=None, + ), debug=dict(argstr='--debug ', ), decimate=dict(argstr='--decimate %f', ), end=dict(argstr='--end %d', ), diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index efd11f1040..d39ae392bd 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -7,6 +7,7 @@ def test_ModelToLabelMap_inputs(): input_map = dict( InputVolume=dict( argstr='%s', + extensions=None, position=-3, ), OutputVolume=dict( @@ -22,6 +23,7 @@ def test_ModelToLabelMap_inputs(): ), surface=dict( argstr='%s', + extensions=None, position=-2, ), ) @@ -31,7 +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(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 f3d1908cd0..d0d437915b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -12,6 +12,7 @@ def test_OrientScalarVolume_inputs(): ), inputVolume1=dict( argstr='%s', + extensions=None, position=-2, ), orientation=dict(argstr='--orientation %s', ), @@ -27,7 +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(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 32a2fc2139..528ba47e1b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -7,10 +7,12 @@ def test_ProbeVolumeWithModel_inputs(): input_map = dict( InputModel=dict( argstr='%s', + extensions=None, position=-2, ), InputVolume=dict( argstr='%s', + extensions=None, position=-3, ), OutputModel=dict( @@ -30,7 +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(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/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index 1b1aa6edcd..25b577ff96 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -5,7 +5,10 @@ def test_Analyze2nii_inputs(): input_map = dict( - analyze_file=dict(mandatory=True, ), + analyze_file=dict( + extensions=None, + mandatory=True, + ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), @@ -24,7 +27,7 @@ def test_Analyze2nii_outputs(): output_map = dict( matlab_cmd=dict(), mfile=dict(usedefault=True, ), - nifti_file=dict(), + nifti_file=dict(extensions=None, ), paths=dict(), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index bbc925ec9e..a9f652ba6d 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -6,6 +6,7 @@ def test_ApplyDeformations_inputs(): input_map = dict( deformation_field=dict( + extensions=None, field='comp{1}.def', mandatory=True, ), @@ -18,6 +19,7 @@ def test_ApplyDeformations_inputs(): mfile=dict(usedefault=True, ), paths=dict(), reference_volume=dict( + extensions=['.hdr', '.img', '.img.gz', '.nii'], field='comp{2}.id.space', mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index d1c35dbcd2..b2be189f03 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -7,10 +7,12 @@ def test_ApplyInverseDeformation_inputs(): input_map = dict( bounding_box=dict(field='comp{1}.inv.comp{1}.sn2def.bb', ), deformation=dict( + extensions=None, field='comp{1}.inv.comp{1}.sn2def.matname', xor=['deformation_field'], ), deformation_field=dict( + extensions=None, field='comp{1}.inv.comp{1}.def', xor=['deformation'], ), @@ -22,7 +24,10 @@ def test_ApplyInverseDeformation_inputs(): matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), - target=dict(field='comp{1}.inv.space', ), + target=dict( + extensions=None, + field='comp{1}.inv.space', + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index a686e95485..cfef023fa7 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -7,12 +7,19 @@ def test_ApplyTransform_inputs(): input_map = dict( in_file=dict( copyfile=True, + extensions=None, + mandatory=True, + ), + mat=dict( + extensions=None, mandatory=True, ), - mat=dict(mandatory=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - out_file=dict(genfile=True, ), + out_file=dict( + extensions=None, + genfile=True, + ), paths=dict(), use_mcr=dict(), use_v8struct=dict( @@ -26,7 +33,7 @@ def test_ApplyTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = ApplyTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 69695ca7b5..2da4a64024 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -5,16 +5,20 @@ def test_CalcCoregAffine_inputs(): input_map = dict( - invmat=dict(), - mat=dict(), + invmat=dict(extensions=None, ), + mat=dict(extensions=None, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), moving=dict( copyfile=False, + extensions=None, mandatory=True, ), paths=dict(), - target=dict(mandatory=True, ), + target=dict( + extensions=None, + mandatory=True, + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', @@ -28,8 +32,8 @@ def test_CalcCoregAffine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CalcCoregAffine_outputs(): output_map = dict( - invmat=dict(), - mat=dict(), + invmat=dict(extensions=None, ), + mat=dict(extensions=None, ), ) outputs = CalcCoregAffine.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 957a2c84a9..260c3afc03 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -27,6 +27,7 @@ def test_Coregister_inputs(): ), target=dict( copyfile=False, + extensions=['.hdr', '.img', '.img.gz', '.nii'], field='ref', mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index cc1b9eee1b..2cc2485f49 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -34,7 +34,7 @@ def test_DARTEL_inputs(): def test_DARTEL_outputs(): output_map = dict( dartel_flow_fields=dict(), - final_template_file=dict(), + final_template_file=dict(extensions=None, ), template_files=dict(), ) outputs = DARTEL.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index d25bde2e5d..e4818e8b58 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -22,6 +22,7 @@ def test_DARTELNorm2MNI_inputs(): paths=dict(), template_file=dict( copyfile=False, + extensions=['.hdr', '.img', '.img.gz', '.nii'], field='mni_norm.template', mandatory=True, ), @@ -39,7 +40,7 @@ def test_DARTELNorm2MNI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DARTELNorm2MNI_outputs(): output_map = dict( - normalization_parameter_file=dict(), + normalization_parameter_file=dict(extensions=None, ), normalized_files=dict(), ) outputs = DARTELNorm2MNI.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index bc9bb9006e..1b2d20bd04 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -16,10 +16,12 @@ def test_EstimateContrast_inputs(): paths=dict(), residual_image=dict( copyfile=False, + extensions=None, mandatory=True, ), spm_mat_file=dict( copyfile=True, + extensions=None, field='spmmat', mandatory=True, ), @@ -41,7 +43,7 @@ def test_EstimateContrast_outputs(): ess_images=dict(), spmF_images=dict(), spmT_images=dict(), - spm_mat_file=dict(), + spm_mat_file=dict(extensions=None, ), ) outputs = EstimateContrast.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index 05f511a0bd..a143366d8f 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -15,6 +15,7 @@ def test_EstimateModel_inputs(): paths=dict(), spm_mat_file=dict( copyfile=True, + extensions=None, field='spmmat', mandatory=True, ), @@ -34,15 +35,15 @@ def test_EstimateModel_outputs(): output_map = dict( ARcoef=dict(), Cbetas=dict(), - RPVimage=dict(), + RPVimage=dict(extensions=['.hdr', '.img', '.img.gz', '.nii'], ), SDbetas=dict(), SDerror=dict(), beta_images=dict(), - labels=dict(), - mask_image=dict(), - residual_image=dict(), + labels=dict(extensions=['.hdr', '.img', '.img.gz', '.nii'], ), + mask_image=dict(extensions=['.hdr', '.img', '.img.gz', '.nii'], ), + residual_image=dict(extensions=['.hdr', '.img', '.img.gz', '.nii'], ), residual_images=dict(), - spm_mat_file=dict(), + spm_mat_file=dict(extensions=None, ), ) outputs = EstimateModel.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index 38d2b1c6fb..892e1d2694 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -6,7 +6,10 @@ def test_FactorialDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + extensions=None, + field='masking.em', + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -50,7 +53,7 @@ def test_FactorialDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FactorialDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(extensions=None, ), ) outputs = FactorialDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_FieldMap.py b/nipype/interfaces/spm/tests/test_auto_FieldMap.py index 43fbbcb8f4..a680fbd54e 100644 --- a/nipype/interfaces/spm/tests/test_auto_FieldMap.py +++ b/nipype/interfaces/spm/tests/test_auto_FieldMap.py @@ -7,6 +7,7 @@ def test_FieldMap_inputs(): input_map = dict( anat_file=dict( copyfile=False, + extensions=None, field='subj.anat', ), blip_direction=dict( @@ -19,6 +20,7 @@ def test_FieldMap_inputs(): ), epi_file=dict( copyfile=False, + extensions=None, field='subj.session.epi', mandatory=True, ), @@ -33,6 +35,7 @@ def test_FieldMap_inputs(): jobtype=dict(usedefault=True, ), magnitude_file=dict( copyfile=False, + extensions=None, field='subj.data.presubphasemag.magnitude', mandatory=True, ), @@ -73,6 +76,7 @@ def test_FieldMap_inputs(): paths=dict(), phase_file=dict( copyfile=False, + extensions=None, field='subj.data.presubphasemag.phase', mandatory=True, ), @@ -86,6 +90,7 @@ def test_FieldMap_inputs(): ), template=dict( copyfile=False, + extensions=None, field='subj.defaults.defaultsval.mflags.template', ), thresh=dict( @@ -120,7 +125,7 @@ def test_FieldMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FieldMap_outputs(): - output_map = dict(vdm=dict(), ) + output_map = dict(vdm=dict(extensions=None, ), ) outputs = FieldMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 7dce3dda2a..10c74f72b8 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -16,7 +16,10 @@ def test_Level1Design_inputs(): field='timing.RT', mandatory=True, ), - mask_image=dict(field='mask', ), + mask_image=dict( + extensions=None, + field='mask', + ), mask_threshold=dict(usedefault=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), @@ -46,7 +49,7 @@ def test_Level1Design_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Level1Design_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(extensions=None, ), ) outputs = Level1Design.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 26957f2fbb..435c288811 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -6,7 +6,10 @@ def test_MultipleRegressionDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + extensions=None, + field='masking.em', + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -59,7 +62,7 @@ def test_MultipleRegressionDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressionDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(extensions=None, ), ) outputs = MultipleRegressionDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index fde0bf7fff..fbf5e278b0 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -22,6 +22,7 @@ def test_Normalize_inputs(): ), parameter_file=dict( copyfile=False, + extensions=None, field='subj.matname', mandatory=True, xor=['source', 'template'], @@ -36,10 +37,12 @@ def test_Normalize_inputs(): source_image_smoothing=dict(field='eoptions.smosrc', ), source_weight=dict( copyfile=False, + extensions=None, field='subj.wtsrc', ), template=dict( copyfile=False, + extensions=None, field='eoptions.template', mandatory=True, xor=['parameter_file'], @@ -47,6 +50,7 @@ def test_Normalize_inputs(): template_image_smoothing=dict(field='eoptions.smoref', ), template_weight=dict( copyfile=False, + extensions=None, field='eoptions.weight', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index bf8da2dba1..25f77519e0 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -14,12 +14,14 @@ def test_Normalize12_inputs(): bias_regularization=dict(field='eoptions.biasreg', ), deformation_file=dict( copyfile=False, + extensions=['.hdr', '.img', '.img.gz', '.nii'], field='subj.def', mandatory=True, xor=['image_to_align', 'tpm'], ), image_to_align=dict( copyfile=True, + extensions=['.hdr', '.img', '.img.gz', '.nii'], field='subj.vol', mandatory=True, xor=['deformation_file'], @@ -36,6 +38,7 @@ def test_Normalize12_inputs(): smoothness=dict(field='eoptions.fwhm', ), tpm=dict( copyfile=False, + extensions=None, field='eoptions.tpm', xor=['deformation_file'], ), diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index dbb02a6275..d45165957b 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -6,7 +6,10 @@ def test_OneSampleTTestDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + extensions=None, + field='masking.em', + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -54,7 +57,7 @@ def test_OneSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(extensions=None, ), ) outputs = OneSampleTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index 3e1662268a..0ad104820e 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -7,7 +7,10 @@ def test_PairedTTestDesign_inputs(): input_map = dict( ancova=dict(field='des.pt.ancova', ), covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + extensions=None, + field='masking.em', + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -56,7 +59,7 @@ def test_PairedTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PairedTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(extensions=None, ), ) outputs = PairedTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index ac2f5bbd92..4812665c78 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -28,7 +28,10 @@ def test_Realign_inputs(): min_ver='8', usedefault=True, ), - weight_img=dict(field='eoptions.weight', ), + weight_img=dict( + extensions=None, + field='eoptions.weight', + ), wrap=dict(field='eoptions.wrap', ), write_interp=dict(field='roptions.interp', ), write_mask=dict(field='roptions.mask', ), @@ -47,7 +50,7 @@ def test_Realign_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Realign_outputs(): output_map = dict( - mean_image=dict(), + mean_image=dict(extensions=None, ), modified_in_files=dict(), realigned_files=dict(), realignment_parameters=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py index 5c7c36f80b..9517e060d5 100644 --- a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py +++ b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py @@ -44,6 +44,7 @@ def test_RealignUnwarp_inputs(): paths=dict(), phase_map=dict( copyfile=False, + extensions=None, field='data.pmscan', ), quality=dict(field='eoptions.quality', ), @@ -63,7 +64,10 @@ def test_RealignUnwarp_inputs(): min_ver='8', usedefault=True, ), - weight_img=dict(field='eoptions.weight', ), + weight_img=dict( + extensions=None, + field='eoptions.weight', + ), wrap=dict(field='eoptions.ewrap', ), ) inputs = RealignUnwarp.input_spec() @@ -73,7 +77,7 @@ def test_RealignUnwarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RealignUnwarp_outputs(): output_map = dict( - mean_image=dict(), + mean_image=dict(extensions=None, ), modified_in_files=dict(), realigned_unwarped_files=dict(), realignment_parameters=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 81299fc748..08a29b0bd7 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -5,13 +5,19 @@ def test_Reslice_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), interp=dict(usedefault=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - out_file=dict(), + out_file=dict(extensions=None, ), paths=dict(), - space_defining=dict(mandatory=True, ), + space_defining=dict( + extensions=None, + mandatory=True, + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', @@ -24,7 +30,7 @@ def test_Reslice_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reslice_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Reslice.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 3e39ade181..3d5ac6847c 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -14,7 +14,10 @@ def test_ResliceToReference_inputs(): matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), - target=dict(field='comp{1}.id.space', ), + target=dict( + extensions=None, + field='comp{1}.id.space', + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index f6df46e1de..257e7c12ff 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -17,7 +17,10 @@ def test_Segment_inputs(): ), gaussians_per_class=dict(field='opts.ngaus', ), gm_output_type=dict(field='output.GM', ), - mask_image=dict(field='opts.msk', ), + mask_image=dict( + extensions=None, + field='opts.msk', + ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), @@ -40,22 +43,23 @@ def test_Segment_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Segment_outputs(): output_map = dict( - bias_corrected_image=dict(), - inverse_transformation_mat=dict(), - modulated_csf_image=dict(), - modulated_gm_image=dict(), + bias_corrected_image=dict(extensions=None, ), + inverse_transformation_mat=dict(extensions=None, ), + modulated_csf_image=dict(extensions=None, ), + modulated_gm_image=dict(extensions=None, ), modulated_input_image=dict( deprecated='0.10', + extensions=None, new_name='bias_corrected_image', ), - modulated_wm_image=dict(), - native_csf_image=dict(), - native_gm_image=dict(), - native_wm_image=dict(), - normalized_csf_image=dict(), - normalized_gm_image=dict(), - normalized_wm_image=dict(), - transformation_mat=dict(), + modulated_wm_image=dict(extensions=None, ), + native_csf_image=dict(extensions=None, ), + native_gm_image=dict(extensions=None, ), + native_wm_image=dict(extensions=None, ), + normalized_csf_image=dict(extensions=None, ), + normalized_gm_image=dict(extensions=None, ), + normalized_wm_image=dict(extensions=None, ), + transformation_mat=dict(extensions=None, ), ) outputs = Segment.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index 078adb3a1b..ab23139515 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -16,10 +16,12 @@ def test_Threshold_inputs(): paths=dict(), spm_mat_file=dict( copyfile=True, + extensions=None, mandatory=True, ), stat_image=dict( copyfile=False, + extensions=None, mandatory=True, ), use_fwe_correction=dict(usedefault=True, ), @@ -40,9 +42,9 @@ def test_Threshold_outputs(): activation_forced=dict(), cluster_forming_thr=dict(), n_clusters=dict(), - pre_topo_fdr_map=dict(), + pre_topo_fdr_map=dict(extensions=None, ), pre_topo_n_clusters=dict(), - thresholded_map=dict(), + thresholded_map=dict(extensions=None, ), ) outputs = Threshold.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index ccdc441e04..c025f5f4d0 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -13,10 +13,12 @@ def test_ThresholdStatistics_inputs(): paths=dict(), spm_mat_file=dict( copyfile=True, + extensions=None, mandatory=True, ), stat_image=dict( copyfile=False, + extensions=None, mandatory=True, ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index 4dfbc12570..faab30cd06 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -7,7 +7,10 @@ def test_TwoSampleTTestDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), dependent=dict(field='des.t2.dept', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + extensions=None, + field='masking.em', + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -60,7 +63,7 @@ def test_TwoSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TwoSampleTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(extensions=None, ), ) outputs = TwoSampleTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index 6aaac2b489..561c0e6082 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -46,7 +46,9 @@ def test_VBMSegment_inputs(): usedefault=True, ), dartel_template=dict( - field='estwrite.extopts.dartelwarp.normhigh.darteltpm', ), + extensions=['.hdr', '.img', '.img.gz', '.nii'], + field='estwrite.extopts.dartelwarp.normhigh.darteltpm', + ), deformation_field=dict( field='estwrite.output.warps', usedefault=True, @@ -105,7 +107,10 @@ def test_VBMSegment_inputs(): usedefault=True, ), spatial_normalization=dict(usedefault=True, ), - tissues=dict(field='estwrite.tpm', ), + tissues=dict( + extensions=['.hdr', '.img', '.img.gz', '.nii'], + field='estwrite.tpm', + ), use_mcr=dict(), use_sanlm_denoising_filter=dict( field='estwrite.extopts.sanlm', diff --git a/nipype/interfaces/tests/test_auto_Bru2.py b/nipype/interfaces/tests/test_auto_Bru2.py index ce436ac03e..07fda82064 100644 --- a/nipype/interfaces/tests/test_auto_Bru2.py +++ b/nipype/interfaces/tests/test_auto_Bru2.py @@ -30,7 +30,7 @@ def test_Bru2_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bru2_outputs(): - output_map = dict(nii_file=dict(), ) + output_map = dict(nii_file=dict(extensions=None, ), ) outputs = Bru2.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_C3d.py b/nipype/interfaces/tests/test_auto_C3d.py index 9e74e82e2a..1e741f5a09 100644 --- a/nipype/interfaces/tests/test_auto_C3d.py +++ b/nipype/interfaces/tests/test_auto_C3d.py @@ -24,6 +24,7 @@ def test_C3d_inputs(): ), out_file=dict( argstr='-o %s', + extensions=None, position=-1, xor=['out_files'], ), diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 510ea2f02a..1326213e05 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -21,14 +21,17 @@ def test_C3dAffineTool_inputs(): ), reference_file=dict( argstr='-ref %s', + extensions=None, position=1, ), source_file=dict( argstr='-src %s', + extensions=None, position=2, ), transform_file=dict( argstr='%s', + extensions=None, position=3, ), ) @@ -38,7 +41,7 @@ def test_C3dAffineTool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_C3dAffineTool_outputs(): - output_map = dict(itk_transform=dict(), ) + output_map = dict(itk_transform=dict(extensions=None, ), ) outputs = C3dAffineTool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_CopyMeta.py b/nipype/interfaces/tests/test_auto_CopyMeta.py index 012edfa886..afe30789d7 100644 --- a/nipype/interfaces/tests/test_auto_CopyMeta.py +++ b/nipype/interfaces/tests/test_auto_CopyMeta.py @@ -5,10 +5,16 @@ def test_CopyMeta_inputs(): input_map = dict( - dest_file=dict(mandatory=True, ), + dest_file=dict( + extensions=None, + mandatory=True, + ), exclude_classes=dict(), include_classes=dict(), - src_file=dict(mandatory=True, ), + src_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = CopyMeta.input_spec() @@ -16,7 +22,7 @@ def test_CopyMeta_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CopyMeta_outputs(): - output_map = dict(dest_file=dict(), ) + output_map = dict(dest_file=dict(extensions=None, ), ) outputs = CopyMeta.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index 0caa45a1f1..cff1205261 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -16,6 +16,7 @@ def test_Dcm2nii_inputs(): ), config_file=dict( argstr='-b %s', + extensions=None, genfile=True, ), convert_all_pars=dict( diff --git a/nipype/interfaces/tests/test_auto_DcmStack.py b/nipype/interfaces/tests/test_auto_DcmStack.py index 53a5259af5..e9a671b919 100644 --- a/nipype/interfaces/tests/test_auto_DcmStack.py +++ b/nipype/interfaces/tests/test_auto_DcmStack.py @@ -20,7 +20,7 @@ def test_DcmStack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DcmStack_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = DcmStack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index 15ea9c66cd..8942b8d5e1 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -20,7 +20,10 @@ def test_FreeSurferSource_outputs(): altkey='BA', loc='stats', ), - T1=dict(loc='mri', ), + T1=dict( + extensions=None, + loc='mri', + ), annot=dict( altkey='*annot', loc='label', @@ -41,14 +44,23 @@ def test_FreeSurferSource_outputs(): altkey='area.pial', loc='surf', ), - aseg=dict(loc='mri', ), + aseg=dict( + extensions=None, + loc='mri', + ), aseg_stats=dict( altkey='aseg', loc='stats', ), avg_curv=dict(loc='surf', ), - brain=dict(loc='mri', ), - brainmask=dict(loc='mri', ), + brain=dict( + extensions=None, + loc='mri', + ), + brainmask=dict( + extensions=None, + loc='mri', + ), curv=dict(loc='surf', ), curv_pial=dict( altkey='curv.pial', @@ -62,7 +74,10 @@ def test_FreeSurferSource_outputs(): altkey='entorhinal_exvivo', loc='stats', ), - filled=dict(loc='mri', ), + filled=dict( + extensions=None, + loc='mri', + ), graymid=dict( altkey=['graymid', 'midthickness'], loc='surf', @@ -73,11 +88,23 @@ def test_FreeSurferSource_outputs(): altkey='*label', loc='label', ), - norm=dict(loc='mri', ), - nu=dict(loc='mri', ), - orig=dict(loc='mri', ), + norm=dict( + extensions=None, + loc='mri', + ), + nu=dict( + extensions=None, + loc='mri', + ), + orig=dict( + extensions=None, + loc='mri', + ), pial=dict(loc='surf', ), - rawavg=dict(loc='mri', ), + rawavg=dict( + extensions=None, + loc='mri', + ), ribbon=dict( altkey='*ribbon', loc='mri', @@ -92,8 +119,14 @@ def test_FreeSurferSource_outputs(): thickness=dict(loc='surf', ), volume=dict(loc='surf', ), white=dict(loc='surf', ), - wm=dict(loc='mri', ), - wmparc=dict(loc='mri', ), + wm=dict( + extensions=None, + loc='mri', + ), + wmparc=dict( + extensions=None, + loc='mri', + ), wmparc_stats=dict( altkey='wmparc', loc='stats', diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index 03a65cf6c2..7666a5c53f 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -6,7 +6,7 @@ def test_JSONFileGrabber_inputs(): input_map = dict( defaults=dict(), - in_file=dict(), + in_file=dict(extensions=None, ), ) inputs = JSONFileGrabber.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 002997912b..4346a67252 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -7,7 +7,7 @@ def test_JSONFileSink_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), in_dict=dict(usedefault=True, ), - out_file=dict(), + out_file=dict(extensions=None, ), ) inputs = JSONFileSink.input_spec() @@ -15,7 +15,7 @@ def test_JSONFileSink_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JSONFileSink_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = JSONFileSink.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_LookupMeta.py b/nipype/interfaces/tests/test_auto_LookupMeta.py index 29100aaef7..b63b96576a 100644 --- a/nipype/interfaces/tests/test_auto_LookupMeta.py +++ b/nipype/interfaces/tests/test_auto_LookupMeta.py @@ -5,7 +5,10 @@ def test_LookupMeta_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), meta_keys=dict(mandatory=True, ), ) inputs = LookupMeta.input_spec() diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index c1b971d25d..0ab56c426e 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -10,7 +10,10 @@ def test_MatlabCommand_inputs(): nohash=True, usedefault=True, ), - logfile=dict(argstr='-logfile %s', ), + logfile=dict( + argstr='-logfile %s', + extensions=None, + ), mfile=dict(usedefault=True, ), nodesktop=dict( argstr='-nodesktop', @@ -30,7 +33,10 @@ def test_MatlabCommand_inputs(): mandatory=True, position=-1, ), - script_file=dict(usedefault=True, ), + script_file=dict( + extensions=None, + usedefault=True, + ), single_comp_thread=dict( argstr='-singleCompThread', nohash=True, diff --git a/nipype/interfaces/tests/test_auto_MergeNifti.py b/nipype/interfaces/tests/test_auto_MergeNifti.py index 9e0a017c60..9cfde35a9a 100644 --- a/nipype/interfaces/tests/test_auto_MergeNifti.py +++ b/nipype/interfaces/tests/test_auto_MergeNifti.py @@ -18,7 +18,7 @@ def test_MergeNifti_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeNifti_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = MergeNifti.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index f306f4abed..39a8ff5ccf 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -41,11 +41,13 @@ def test_MeshFix_inputs(): ), in_file1=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), in_file2=dict( argstr='%s', + extensions=None, position=2, ), join_closest_components=dict( @@ -60,6 +62,7 @@ def test_MeshFix_inputs(): number_of_biggest_shells=dict(argstr='--shells %d', ), out_filename=dict( argstr='-o %s', + extensions=None, genfile=True, ), output_type=dict(usedefault=True, ), @@ -94,7 +97,7 @@ def test_MeshFix_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MeshFix_outputs(): - output_map = dict(mesh_file=dict(), ) + output_map = dict(mesh_file=dict(extensions=None, ), ) outputs = MeshFix.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 048699659a..d534608fac 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -6,6 +6,7 @@ def test_MySQLSink_inputs(): input_map = dict( config=dict( + extensions=None, mandatory=True, xor=['host'], ), diff --git a/nipype/interfaces/tests/test_auto_PETPVC.py b/nipype/interfaces/tests/test_auto_PETPVC.py index c5283435d5..60f5b29826 100644 --- a/nipype/interfaces/tests/test_auto_PETPVC.py +++ b/nipype/interfaces/tests/test_auto_PETPVC.py @@ -32,10 +32,12 @@ def test_PETPVC_inputs(): ), in_file=dict( argstr='-i %s', + extensions=None, mandatory=True, ), mask_file=dict( argstr='-m %s', + extensions=None, mandatory=True, ), n_deconv=dict( @@ -48,6 +50,7 @@ def test_PETPVC_inputs(): ), out_file=dict( argstr='-o %s', + extensions=None, genfile=True, hash_files=False, ), @@ -66,7 +69,7 @@ def test_PETPVC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PETPVC_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = PETPVC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_Quickshear.py b/nipype/interfaces/tests/test_auto_Quickshear.py index 7f39a6bc96..d08985a639 100644 --- a/nipype/interfaces/tests/test_auto_Quickshear.py +++ b/nipype/interfaces/tests/test_auto_Quickshear.py @@ -16,16 +16,19 @@ def test_Quickshear_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), mask_file=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), out_file=dict( argstr='%s', + extensions=None, keep_extension=True, name_source='in_file', name_template='%s_defaced', @@ -38,7 +41,7 @@ def test_Quickshear_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Quickshear_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Quickshear.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_Reorient.py b/nipype/interfaces/tests/test_auto_Reorient.py index 2e45a1ca7f..76d393e0df 100644 --- a/nipype/interfaces/tests/test_auto_Reorient.py +++ b/nipype/interfaces/tests/test_auto_Reorient.py @@ -5,7 +5,10 @@ def test_Reorient_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), orientation=dict(usedefault=True, ), ) inputs = Reorient.input_spec() @@ -15,8 +18,8 @@ def test_Reorient_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Reorient_outputs(): output_map = dict( - out_file=dict(), - transform=dict(), + out_file=dict(extensions=None, ), + transform=dict(extensions=None, ), ) outputs = Reorient.output_spec() diff --git a/nipype/interfaces/tests/test_auto_Rescale.py b/nipype/interfaces/tests/test_auto_Rescale.py index e180c82988..2bdc274d81 100644 --- a/nipype/interfaces/tests/test_auto_Rescale.py +++ b/nipype/interfaces/tests/test_auto_Rescale.py @@ -5,10 +5,16 @@ def test_Rescale_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), invert=dict(), percentile=dict(usedefault=True, ), - ref_file=dict(mandatory=True, ), + ref_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = Rescale.input_spec() @@ -16,7 +22,7 @@ def test_Rescale_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Rescale_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Rescale.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index ea03663c4c..190e8aeee4 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -5,7 +5,10 @@ def test_SQLiteSink_inputs(): input_map = dict( - database_file=dict(mandatory=True, ), + database_file=dict( + extensions=None, + mandatory=True, + ), table_name=dict(mandatory=True, ), ) inputs = SQLiteSink.input_spec() diff --git a/nipype/interfaces/tests/test_auto_SignalExtraction.py b/nipype/interfaces/tests/test_auto_SignalExtraction.py index bc76f5261a..b102048118 100644 --- a/nipype/interfaces/tests/test_auto_SignalExtraction.py +++ b/nipype/interfaces/tests/test_auto_SignalExtraction.py @@ -7,11 +7,17 @@ def test_SignalExtraction_inputs(): input_map = dict( class_labels=dict(mandatory=True, ), detrend=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), incl_shared_variance=dict(usedefault=True, ), include_global=dict(usedefault=True, ), label_files=dict(mandatory=True, ), - out_file=dict(usedefault=True, ), + out_file=dict( + extensions=None, + usedefault=True, + ), ) inputs = SignalExtraction.input_spec() @@ -19,7 +25,7 @@ def test_SignalExtraction_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SignalExtraction_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = SignalExtraction.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_SplitNifti.py b/nipype/interfaces/tests/test_auto_SplitNifti.py index e1f6539fab..18e8ee9798 100644 --- a/nipype/interfaces/tests/test_auto_SplitNifti.py +++ b/nipype/interfaces/tests/test_auto_SplitNifti.py @@ -5,7 +5,10 @@ def test_SplitNifti_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), out_ext=dict(usedefault=True, ), out_format=dict(), out_path=dict(), diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index b4db5ec8d3..b3e800e4e4 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -9,6 +9,7 @@ def test_XNATSink_inputs(): assessor_id=dict(xor=['reconstruction_id'], ), cache_dir=dict(), config=dict( + extensions=None, mandatory=True, xor=['server'], ), diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index 8faa79af81..adb5d8657a 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -7,6 +7,7 @@ def test_XNATSource_inputs(): input_map = dict( cache_dir=dict(), config=dict( + extensions=None, mandatory=True, xor=['server'], ), diff --git a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py index 284e0f4d62..d0af3a5ed9 100644 --- a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py @@ -5,8 +5,14 @@ def test_AssertEqual_inputs(): input_map = dict( - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + extensions=None, + mandatory=True, + ), + volume2=dict( + extensions=None, + mandatory=True, + ), ) inputs = AssertEqual.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_CSVReader.py b/nipype/interfaces/utility/tests/test_auto_CSVReader.py index 8a51ca4170..b0ce577808 100644 --- a/nipype/interfaces/utility/tests/test_auto_CSVReader.py +++ b/nipype/interfaces/utility/tests/test_auto_CSVReader.py @@ -6,7 +6,10 @@ def test_CSVReader_inputs(): input_map = dict( header=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), ) inputs = CSVReader.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Rename.py b/nipype/interfaces/utility/tests/test_auto_Rename.py index 1e6e1cab34..6b56badd6f 100644 --- a/nipype/interfaces/utility/tests/test_auto_Rename.py +++ b/nipype/interfaces/utility/tests/test_auto_Rename.py @@ -6,7 +6,10 @@ def test_Rename_inputs(): input_map = dict( format_string=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + extensions=None, + mandatory=True, + ), keep_ext=dict(), parse_string=dict(), use_fullpath=dict(usedefault=True, ), diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 785e87e8b1..d5e5958ef4 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -8,6 +8,7 @@ def test_Vnifti2Image_inputs(): args=dict(argstr='%s', ), attributes=dict( argstr='-attr %s', + extensions=None, position=2, ), environ=dict( @@ -16,11 +17,13 @@ def test_Vnifti2Image_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, position=1, ), out_file=dict( argstr='-out %s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_file'], @@ -34,7 +37,7 @@ def test_Vnifti2Image_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Vnifti2Image_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = Vnifti2Image.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index ee16266402..c789175132 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -12,11 +12,13 @@ def test_VtoMat_inputs(): ), in_file=dict( argstr='-in %s', + extensions=None, mandatory=True, position=1, ), out_file=dict( argstr='-out %s', + extensions=None, hash_files=False, keep_extension=False, name_source=['in_file'], @@ -30,7 +32,7 @@ def test_VtoMat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VtoMat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = VtoMat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py b/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py index b510a3b34e..b77a318deb 100644 --- a/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py +++ b/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py @@ -8,15 +8,18 @@ def test_CiftiSmooth_inputs(): args=dict(argstr='%s', ), cerebellum_corrected_areas=dict( argstr='cerebellum-corrected-areas %s', + extensions=None, position=10, requires=['cerebellum_surf'], ), cerebellum_surf=dict( argstr='-cerebellum-surface %s', + extensions=None, position=9, ), cifti_roi=dict( argstr='-cifti-roi %s', + extensions=None, position=11, ), direction=dict( @@ -38,15 +41,18 @@ def test_CiftiSmooth_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), left_corrected_areas=dict( argstr='-left-corrected-areas %s', + extensions=None, position=6, ), left_surf=dict( argstr='-left-surface %s', + extensions=None, mandatory=True, position=5, ), @@ -56,6 +62,7 @@ def test_CiftiSmooth_inputs(): ), out_file=dict( argstr='%s', + extensions=None, keep_extension=True, name_source=['in_file'], name_template='smoothed_%s.nii', @@ -63,10 +70,12 @@ def test_CiftiSmooth_inputs(): ), right_corrected_areas=dict( argstr='-right-corrected-areas %s', + extensions=None, position=8, ), right_surf=dict( argstr='-right-surface %s', + extensions=None, mandatory=True, position=7, ), @@ -87,7 +96,7 @@ def test_CiftiSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CiftiSmooth_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(extensions=None, ), ) outputs = CiftiSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/workbench/tests/test_auto_MetricResample.py b/nipype/interfaces/workbench/tests/test_auto_MetricResample.py index 46a66aa728..ad6494bc09 100644 --- a/nipype/interfaces/workbench/tests/test_auto_MetricResample.py +++ b/nipype/interfaces/workbench/tests/test_auto_MetricResample.py @@ -18,10 +18,12 @@ def test_MetricResample_inputs(): args=dict(argstr='%s', ), current_area=dict( argstr='%s', + extensions=None, position=6, ), current_sphere=dict( argstr='%s', + extensions=None, mandatory=True, position=1, ), @@ -31,6 +33,7 @@ def test_MetricResample_inputs(): ), in_file=dict( argstr='%s', + extensions=None, mandatory=True, position=0, ), @@ -45,15 +48,18 @@ def test_MetricResample_inputs(): ), new_area=dict( argstr='%s', + extensions=None, position=7, ), new_sphere=dict( argstr='%s', + extensions=None, mandatory=True, position=2, ), out_file=dict( argstr='%s', + extensions=None, keep_extension=True, name_source=['new_sphere'], name_template='%s.out', @@ -61,6 +67,7 @@ def test_MetricResample_inputs(): ), roi_metric=dict( argstr='-current-roi %s', + extensions=None, position=8, ), valid_roi_out=dict( @@ -75,8 +82,8 @@ def test_MetricResample_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MetricResample_outputs(): output_map = dict( - out_file=dict(), - roi_file=dict(), + out_file=dict(extensions=None, ), + roi_file=dict(extensions=None, ), ) outputs = MetricResample.output_spec()